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COPYING
View file @ dc5a63cb
tRNAscan-SE -- a program for finding transfer RNAs
Copyright (C) 1996 Todd M.J. Lowe & Sean R. Eddy
Copyright (C) 2017 Patricia P. Chan, Brian Lin, and Todd M. Lowe
This set of programs is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of the
published by the Free Software Foundation; either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but
......@@ -13,8 +13,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program, in the file GNULICENSE; if not, write to the Free
Software Foundation, Inc., 675 Mass. Ave, Cambridge, MA 02139 USA.
along with this program, in the file GNULICENSE; if not, check out
the web site at https://www.gnu.org/licenses/gpl-3.0.en.html.
This distribution includes source code originally derived from other
sources. In particular, modified source code from the program
......
Cove/COPYING deleted 100644 → 0
View file @ ca28b8d2
cove -- programs to apply covariance models to RNA sequence analysis
Copyright (C) 1993,1994 Sean R. Eddy
This set of programs is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program, in the file GNULICENSE; if not, write to the Free
Software Foundation, Inc., 675 Mass. Ave, Cambridge, MA 02139 USA.
This distribution may include source code originally derived from
other sources. In particular, my general sequence library includes
source code that derives from Henry Spencer (regexp() functions), and
Don Gilbert (sequence i/o functions). Borrowed code is annotated and
credited in the source files whenever it appears. The copying policies
of my benefactors are compatible with the GNU Public License under
which this package is distributed.
Cove/DEMO deleted 100644 → 0
View file @ ca28b8d2
Demonstrations of the covariance model programs
-----------------------------------------------
As an introduction to how the software works, this file contains
instructions on how to reproduce the results in our paper. (Note
that this version of the code is newer, somewhat less buggy, and
faster than the version used for our original experiments. There may
be minor differences between the results we report in our paper and
the results you get from these demos.)
For more details, refer to S.R. Eddy and R. Durbin, "RNA Sequence
Analysis Using Covariance Models", NAR 22:2079-2088, 1994.
The directory Demos/ contains the data files:
TRNA2.cm - A very good tRNA model
7SL-euk.cm - A model of 7SL signal recognition particle RNA
7SL-euk.fa - 37 eukaryotic 7SL RNAs (includes some fragments)
trna1415.slx - Steinberg/Sprinzl trusted tRNA alignment
sim65.slx - alignment of 100 dissimilar tRNAs
sim100.slx - alignment of 100 randomly chosen tRNAs
test100.fa - 100 unaligned, randomly chosen independent test tRNAs
sim65.fa - unaligned SIM65 sequences
sim100.fa - unaligned SIM100 sequences
fig5.slx - Trusted alignment of 5 tRNAs, from our figure 5
fig5.fa - unaligned tRNA sequences of fig5.slx
yeast-phe.fa - S. cerevisiae tRNA-Phe sequence
K11H3frag.fa - fragment of C. elegans cosmid K11H3, which contains 2 tRNA genes
## Constructing a model from trusted alignments:
> covet -a sim100.slx A100.cm sim100.fa
> covet -a sim65.slx A65.cm sim65.fa
Produces models A100 and A65. Uses trusted alignments (sim100.slx,
sim65.slx) to construct the initial models; then uses sim100.fa or
sim65.fa as training sequences.
Takes about fifteen minutes per model on an R4000 Indigo.
## Constructing a model from unaligned sequences:
> covet U100.cm sim100.fa
> covet U65.cm sim65.fa
Produces models U100 and U65 from unaligned training sequences in sim100.fa
and sim65.fa.
Takes about an hour per model on an R4000 Indigo.
## Multiple RNA sequence alignment using a trained model:
> covea A100.cm fig5.fa
> covea U100.cm fig5.fa
Produces a multiple sequence alignment of the 5 sequences in fig5.fa
and prints it to the screen. Compare to the trusted alignment
(fig5.slx) or our preprint's Figure 5.
Takes about ten seconds.
## Scoring example sequences using a trained model:
> coves A100.cm fig5.fa
Calculates and prints alignment scores (in bits) for the 5 sequences in
fig5.fa.
Takes about ten seconds.
## Structure prediction of individual sequences using a trained model:
> coves -s A100.cm yeast-phe.fa
> coves -m A100.cm yeast-phe.fa
Aligns the model A100.cm to yeast tRNA-Phe, and prints out the alignment
score. The -s option to coves prints out a secondary structure representation
for the sequence as well. This representation uses ">" and "<" characters
to represent pairwise assignments. The -m option to coves produces a
"mountain" representation of the structure. Both of these representations
are described in a paper by Danielle Konings (Konings and Hogeweg,
J. Mol. Biol. 207:597-614, 1989). Covariance models typically
overpredict pairs; the predicted pairs are a superset of the
secondary structure pairings. [One of the major weaknesses in the package at the
moment is a lack of graphical secondary structure display and a lack of
automatic classification of predicted pairs as secondary structure vs. tertiary
structure or overprediction.]
Takes about ten seconds.
## Searching a database for new tRNAs:
> covels -c A100.cm K11H3frag.fa
Searches a 500 bp fragment of the C. elegans cosmid K11H3 for tRNAs,
on both strands (the -c option asks for both strands to be searched).
This fragment contains two predicted tRNA genes.
Takes about two minutes.
> covels -c -w 150 TRNA2.cm K11H3frag.fa
Same as above, except using a model trained on 1315 different tRNA
sequences. This model is known to recognize all known cytoplasmic
eukaryotic tRNAs with scores > 20 bits. The -w option allows tRNAs
up to 150 nt in length. Using covels with this model is the most
sensitive means I know of for detecting tRNAs in genomic sequence.
Cove/Demos/7SL-euk.cm deleted 100644 → 0
View file @ ca28b8d2
This diff is collapsed.
Cove/Demos/7SL-euk.fa deleted 100644 → 0
View file @ ca28b8d2
> ZEA.M._A
NCCgAGCUCuguagcgaGAGCUuguaaCCCGagCGGGGGCauuaAGGUGG
UGugaaUGCUUugcGAuggcuUUCUGggcccugGGCUCGuugUgacacug
gcCGGCUUGcCcaUCCCAagUUGGuAGuguCUGguGGGGgcucuAGCgaa
aGCUuuggguCUCUgCAGaCcuggaGcGGCAGgaauggCGuaaggCUGgc
uucaCAGagcagCGaucaCUGCCgaCUcCCAAcggUGGGAgGauaaCGaA
GCCGcugcAcuuUGAGCCuaacucaggcuCAGAAccUCacuAAGCAaacC
ACCAUCUuu
> ZEA.M._B
NCCgAGCUCuguagcgaGAGCUuguaaCCCGagCGGGGGCauuaAGGUGG
cGcggaUGCUuugcGAugguuUCUGggccugGGCUCGuugUgacucuagc
CGGCUUGcCcaUCCCAagUUGGuAGuguCUGacGGGGcucuAGCgaaaGC
UuuggguCUCUgCAGaCcuacaGcGGCAGgaauggCGuaaggCUGgcuuc
aCAGagcagCGaucaCUcGCCcaCUuCCAAcggUGGGAgGauaaCAAGCC
GcugcAcuuUGAGCCcaacacagaccCAGAuccUCucuuAGCAaacCaCC
AUCUuu
> ZEA.M._C
NCCgAGCUCuguagcgaGAGCUuguaaCCCGagCGGGGGCauuaAGGUGG
UGuggaUGCUUgguaccguGUCUuugccugGGUUCAuggugUgccuuugu
UGGCCUGcCcgUUCCAagUUGGuAGuggCCGuuGGAAgcuugGGCguagG
CCcugggcUUCCuUGGaCcuauaGuGGCAGgaacggCGugaggCUGucuu
caCAGagcagCGaucaCUGCCggCUaUUAAcggUGGAAgGauaaCAGGCC
AcugcAgcaUGGGCUcgcuuaaggccUAGACuucauacuaAAGCAgacCA
CCAUUUuu
> ZEA.M._D
NCCgAGCUCuguagcgaGAGCUuguaaCCCGagCGGGGGCauuaAGGUGG
UGcggaUuCUUugcGAuggcuUUCUGggcccgGGCUCGcuaugUgccuuu
ggcCGGCCUGcCcgUCCCAagUUGGuAGuggCUGgcGGAGgcuuuAGCgg
aaGCUuugguCUCUcCAGaCcugaaGuGGCAGgaauggCGugaggCUGgc
uucaCAGagcagCGaucaCUcGCCcgCUuCCAAcggUGGGAgGauaaCAG
GCCGcugcAcuuCGAGCCcaacucaggccCAGAGccUCacuAAGcAgacC
ACCAUCUu
> ZEA.M._E
NCCgAGCUCuguagcgaGAGCUuguaaCCCGagCGGGGGCauuaAGGUGG
UGcggaUUCUUugcGAuggcuUUCUGggcccgGGCUCGcuaugUgccuuu
ggcCGGCCUGcCcgUCCCAagUUGGuAGuggCUGgcGGAGgcuuuAGCgg
aaGCUuugguCUCUcCAGaCcugaaGuGGCAGgaauggCGugaggCUGgc
uucaCAGagcagCGaucaCUcGCCggCUuCCAAcggUGGGAgGauaaCGG
GCCGcugcAcuuCGAGCCcaacucaggccCAGAGccUCacuAAGCAgacC
ACCAUCUuu
> ZEA.M._F
NCCgAGCUCuguagcgaGAGCUuguaaCCUaagcGGGGGCauuaAGGUGG
UGuggaUGUUUccuGAcggaUUCUGggccugGGCUUGuaugUgccacugg
cCGGCCUGcCcgUUCCAagUUGGuuGuggCUGguGGGGcucgGGCgaagG
CCugggcCUCUuUAGaCcugaaGcGGCAGgcauggCGugaggCUGgcuuc
aCAGagcagCGaucaCUcGCCcgCuuCCAAcggUGGGAgGauaaCAGGCC
GcugcAuugCAAGCCcaacucggucCAGAGccUCauuAAACAgacCACCA
UCUuu
> ZEA.M._G
NCCgAGCUCuguagcgaGAGCUuguaaCCCGagCGGGGGCauuaAGGUGG
UGcggaUuCUUugcGAuggcuUUCUGggcccgGGCUCGcuaugUgccuuu
ggcCGGCCUGcCcgUCCCAagUUGGuAGuggCUGgcGGAGgcuuuAGCgg
aaGCUuugguCUCUcCAGaCcugaaGuGGCAGgaauggCGugaggCUGgc
uucaCAGagcagCGaucaCUGCCcgCUuCCAAcggUGGGAgGauaaCGGG
CCGcugcAcuuCGAGCCcaacucaggccCAGAGccUCacuAAGcAgacCA
CCAUCUuu
> ZEA.M._H
NCCgAGCuCuguagcgaGuGCUuguaaCCCGagCGGGGGCaauaagguag
uguggaugucaauuguggugcaugugccugGGUCUAgugCuacaaacugU
GGacCAcCcaUUCCAagUUGcGuaGuggGUUucGGAUgccuuGGCgaaaG
CUuugcAUCCcAACaCUaaAGuGGCGGacauugCGugaggCUGgcuucaU
AGagcagCGaguaCCGCCcgCcaCCAGcggUGGAAgGauaaUGagUCGcu
auGcuaUAGGCCcaau
> TRI.A._A
NCCgAGCUCaguugcgaGAGCUuguaaCCCGagUGGGGGCauuaaaguGa
UGugaacGCUGuugUAgcgCUGCGggccugGUCUGGgugUgcuacugcUG
GCCCGcCcgUUCCAagUUGcGuAGuggACCgccUGGGgcuuauGCgaaaG
CuggguCUCAcGGUcCAuaaUGuGGCAGgcacagCGugaggCUGgcuuca
CAGagcagCGacaaCUGCCcgCUuCCAAcggUGGAAgGauaaUGGGCCGc
ugcAcucCUAGGCcaauugggccuCGCAGccUAcucCAGCagacCAcC
> TRI.A._B
NCCgAGCUaguugcgggAGCUugucaCCCAugUGGGGGCauugAGGcGGU
GuggaUGCUuggUGcgguuUGuuggccugGGCUUGugaugUaaccuugcU
GGCCUGcCcgUUCCAagUUGGuAGugggCUgGGuGgcuggGGCgaaaGCU
ucgccUuCUcAGgcCUuaAGuGGCAGgcaccaCGuuaggCUGguuucaCA
GagcagCGacaaCUGCCgCUuCCAAcggUGGAAgGauaaCAGGCCGcugc
AgcaUGGGCCcgcucugggccuccUAcccCGccauAGCAgacCACCaUCU
uu
> TRI.A._C
ggUGGUCUGcCcgUUCCAagUUGaGuAGuggACCgcuUGGGgccuauGCg
aaaGUugggcCUCAcGGUcCAuaaUGuGGCAGgcaccgCGugaggCUGgc
uucaCAGagcagCGacaaCUGCCcgCUuCCAAcggUGGAAgGauaaCGGG
CCGcugcacuccuaggccgcuugggccucguagccuacuccagcgaccac
cauc
> ARA.THA.
GUCgAGCUAaguaacaaUAGCUuguaaCCCAugUGGGGACauuaAGAUGG
UGggaCAcUGgUUcgguUccUCggaucgGUUCUGaugugGgcauguuucU
GAGCUGcCcaGUCCAagCUGUgAGuaAUUaguGUugaguugAGCgaagGC
UuggcucauGCaGGUucUagaGucGGAGGguaaugCGugaggCUGgcuuc
aCAGagcagCGacuaCUUCCcgCUuACAGcagUGGACgGaucaCGGUUUA
gcguCgcuCAGAACcacuauggccuGcuGGuccGAucucaUAUGaacCAC
CAUUUu
> HUM.JAP.
GGCCUaGcaacgUGGGCCuguaaCCCAagUGGGggcauguGGGAGAUGgg
acuuuggGUcagcccauuggaucgGGUCCAguguuAgcugcuugcUGGUC
UGcCcaUUCCAagCCGAgAGuugGGCuguGUGaucugGGCgaagGCUggg
gucgCACaGCUcCUaaAGaGGAGGgcaaugCGugaggCUGguuucaCAGa
gcagCGaccaCCUCCcgCUcUCGGcagUGGAAgGauaaCGGGUCGgugcU
acuUGGGCCaccauggucacugcaugcACucuuaaucagacCAUCUCUUu
u
> HUM.L._A
GCCGGUCUuaGcaacgUGGGCCuguaaCCCAagUGGGGGCauguGGGAAA
UGggacuuuggGUcaacCUAGuggaucgGGUCCAguguuAgcugcuuacU
GGUCUGcCcaUUCCAagCCGGgAGuugggcugaGUGaccugGgCgaagGg
CuggguugCGCacgucCUagAGuGGAGGgcaaugCGugaggCUGgcuuca
CAGagcagCGacuaCCUCCcgCUcUCGGcagUGGAAgGauaaCGGGCCGg
ugcUaccUGGGUCcaccaugcuucaCUAGgcugACucuuaauaggacCAU
UUCUUuu
> HUM.L._B
GGCCUuaGcaacgUGGGCCuguaaCCCAagUGGGggcauguGGGAAAUGg
aacauuggGUcagcCCAGuggaucgGGuCCAguguuAgcugcuuacUGGU
CUGcCcaUUCCAagCCGGgAGuugGGCugaGUGaccugGGCgaagGCCug
gguugCGCaGCUcCUagAGuGGAGGgcaaugCGugaggCUGguuucaCAG
agcagCGacuaCCUCCcgCUcCCGGcagUGGAAgGauaaCGGGCCGgugc
UacuUGGuCCaccauguucaCUGGuccugACucuuaaucggacCAUUUCC
Uuu
> HUM.L._C
GGuCUuaGcaacuUGGuCCuguaaCCCAagUGGGggcauguGGGAAAUGg
aacuuuggGUcaacCCAGugguncgGGncCAgugcuagcugcuuacCcGg
CUGcCcaUUCCAagCCGGgAGgugGGcugaGgGaccugGGCgaagGCUnn
nggngCgCaCUccUagAcuGGAGGgcaaugCGugaggCUGgcuucaCAGa
gcagCGacuaCCUCCcgCUcUCGGcagUGGAAgGauaaCGGgCcGgugcg
ccuUGagCCaacacuguucaaCUGGgcugACucuuaauaggacCAUUUCU
Uuu
> LYC.ESC.
GgCgAGCUUaGuaacgUGGGCUuguaaUCCAagUGGAGaCaucaAaGUGG
UUgaaUAUUGgGCuuuaCCAgaagguugGGCUUGgugGgcuuaguucUGG
CCUGcCcugUCCAagCACAgAGuugGAUCucGAGGCCCAaAUgaaaAUaU
GGGCUUCuuGAuUCCUaaAGuGGGGCggaccgCAugaggCUGgcuucaCA
GagcagUGaacGCUCCcgCUcUGUGcagUGGAagGauaaUGGGUCGgugu
CuuauCAAGUUcaguaacgccuaaUGGguuGCucCAAUAaacAACCACcU
uu
> CIN.HYB.
ACCgGGCUugGuaacgCuAGUCuauaaCUCAagUGAGGGUaucaAAGUGG
GUugaaCUuUgaGCuuggcUUAGcuaguugGGUCUGuagaCaccgcaccU
GGCUUGcCcgUUCCAagUCGAgAGuggGUUCAUGUUuCCUGAGCgaagGC
UCGGGuGAUGUGAGCuuUagaAucGGGGGgcaaugCGuuaggCUGguuuc
aCAGagcugCGaaaaCCUCUacCUcUCGAcugUGGAAgGauuaCAAGCCG
gaguGucuUAGGCUcauauaaccagcCUGGcuaGCccaAcAGgacACCCA
UUU
> PER.AME.
GaUCcGuaacgCGAgCuuauaaCUCGagCGGGggcuauaaagguggugug
gaacgagcugacucgaccugccggguugggccagggacugcggugcuggc
ucgcccguuccaagucggguagugGGCCAuGuGGCUUGGGCgaagGCCUG
GGUUuCuUGGCC
> COL.BLU.
CCgaaCCucAuuaccUuGGccuguuacCCCAaguUGGGGGucuuuaaggu
uauuugaukuukggccuaugcuacckgcckggcucugguccugcuuauuc
uggcccgcccguuccaagccgggaguugGCCcauGuGGUUUAUGCgaagG
UAUAGGCUuCgguGGUucc
> CRY.MOR.
aaagugguuggacuuugucuuggancagnugguuggguncgcccgcgcag
cacccggcccgnncauuncaagccgagaggccggnnang
> GYN.AUR.
ACCgGGCuugGcaacgCuuGCCuauaaCUCAagUGAGGGUaagaaaaagg
guuggaauugaaaggg
> BEN.HIS.
GCCgAGCUCaGcagugUGAGCUugcaaYUCGaaCGGGGGCaucaaggugg
uuggagguuggacagnacacagagcagggcauuucgagacaca
> YAR.L._A
CUUagcuguaaUGGCauuuuGUCGGAGugguaAAUCGUcuucUUGUuguG
cgUUCgagucuUGggcucugCAcuugGCCAUUUGGUUGuCcuUuCCGaaU
UCUGCgguugaUGGGcgUCUCgGuCUGAguaaUCGGcUuuGAGAuuUCCG
uUCuaaGAuUAACUgggaaaCUucaguGGAgcaaUCCagcagAGauccAG
UUGccGUGGGuAuggCGGuGgGaucgCAACCAAGUGGUauaUGuUAugGA
AgaUauuuACGAucACGAUU
> YAR.L._B
agcuguaaUGGCauuuuGUCGgagugguaAaUCGccuucUUGUuguGCgU
UCgaguucUGgacucugCAcuggGCUACUUUGUUGuCcuUuCCGaaUUCU
GCgguugaUGGGcgUCUCgGuCUGAguaaUCGGcUuuGAGAuuUCCGuUC
uaaGAuUAACUgggauaCUucaguGGAgcaaUCCagcagAGauccAGUUG
ccGUGGGuAuggCGGuGgGauagCAACAAAGUGGUauaUGuUAugGAAgG
UauuuGCAAucaCGAcUcuc
> SCH.POM.
cGCuguaaugGCuUGGUCgaaGUGUUUAgUACUcCCAauagUGCAUguuC
gGUGgucucggguucgAGUCUCGcUuUCGauccCUCGAucuGCCAcgUcU
guuCGAAGAguagUCUUCGugGcAacUGGCaGUuaaACcguGUAguaccG
AUggaggUUGgaaaCAAugcacAUCacUACcgggucUUGGGcagugCGAu
AgcgaUGGGAUUcaccuuCGCaGgauGUGCAUGGaAGUAUAAACACaacG
GUCGuu
> TET.THE.
GCCagGGUAgcaaUACCugugucuauauguGGCauaaacAAUguaGGUUg
UGAUAGaUAgGAUaugaGAguuugaugaGACAGUUugcuaaGAGUGUGcC
cgCUCCAaaCAAUGAGuUGCUauGGUGguaaCCUAguaaUAGGacucCAC
CagGGCAUUaaaGAgcUAAGgaaacgCCucaggCUGgcaaCAGaacagGG
aaaaCUUGccgCUUGUUGuggUGGAAgGauaaCAUACUCauuAACUGUCa
aacuaaUCgGUUcUACUAUCAaAGCCagacAUU
> TET.ROS.
GCCagGGUAgcaaUGCCugugaccucguguGGCauaaacAaUguaGGUUa
GAAUAGuCAgAGUaugaGAguuugaugaGACAGUUugcuaaGAGUGUGcC
cgUUCCAaaCAGUGAGuUGCUauGGUGgaaaCCUAguaaUAGGacuuCAC
CagGGCAUUaaaGAgcUGAGgaaccgCCucaggCUGgcaaCAGaacagGG
aaaaCUUGccgCUUAUUGuggUGGAAgGauaaCAUACUCauuAACUGUCa
agcuaaUCgGUUcUGCUAUUCuGAUCagacAcU
> TRY.BRU.
AGCcgGAGCGcauUGCUCuguaaCCUucgGGGGCUgaucCCGCUuaGCGG
gGACGuCUuGGacaaGCGggggUUCUGuUGCguugaCUUGGUGuUcugCu
ugguuGCGUGucGGUGuuGAGGucGCCaCUguagAGaGGCguUCUCgCGC
CgUUaaAGUgGGGggaacGGGucaggCCGgugaCGGagcagCCCacCUUG
cgCACGUucccguucGagAagcaCACCGAGgaGCAucuCAGGAcuuugCG
CcCCaAGUGUCgUCGCgaGGCGG
> XEN.LAE.
GCCgGGCGCuGuggcgUGUGCCuguaaUCCAgcuacuUGGAGGCuuGGGC
UGUcggaUCGCUugaGUcCAGGaguuCUGggcugCACUGaGCUAUgucga
uCGGGUGuCcgCACUAaguUCGGUAuCAAUauGGUGuuCCuGGGggagCC
UcGGauCACCagGUUGcUCuaaGGaGGGGUgaaccGGCccaggUCGgaaa
CGGagcagGUCaaaACCCCcgUGCCGAucagUAGUGgGaucgCGCCUGug
aAUAGCCGGUGcagaaCAGCCUGaACaacacAGCGAgacACAGUUCu
> DRO.MEL.
GACugGAAGgUuggcaGCUUCuguaaCUCAcgcuucugUGAGGUCuGAUU
GUGggaUGGCCugaGGcUGGGaucuaCUGcguagcggacCAGcUCAUguu
gaCGGaACGuCcgCACUAagCUUGCCAuCAAUauGGGUgcCAUGGAggag
UCCGUGgcAUUCagGUUGgCUaaGGaGGGAUgaaccgGGccaggGGUgaa
aACCagcagCCaagaGUUCCcgUGGUAGGcagUAGUGgGauagCGUaCCG
gaGUGGaCUGccguuauCAGCCCAaCCgauauGGUUGgacCACAAUCuuu
> RAT.RAT.
GCCgGGCGcgGuggcgCaCGCCuguagUCCCagcuacucGGGAGGCuGAG
GacaGaggaUCGCUugaGUcCAGGaguuCUGggcugUAGUGcGCUAUgcc
gauCGGGUGuCcgCACUAaguUCGGCAuCAAUauGGUGacCUCCCGggag
CGGGGGacCACCagGUUGCCuaaGGaGGGGUgaaccGGCccaggUCGgaa
aCGGagcagGUCaaaACUCCcgUGCUGAucagUAGUGgGaucgCGCCUGu
gaAUAGCCACUGcacucCAGCCUGgGCaacauAGCGAgacCccgUCUCuu
> MUS.M.B1
gaGCCgGGUGUgGuggcgCACACCuuuaaUCCCagcacucGGGAGGCaGA
GGCAGGcggaUUUCUgaGUucgaggccagccuggucuacaaagugagcuc
caggacagccaggGCuacacAGAGAaacCCUGUCUC
> MUS.MUS.
GCCuguagUUCCagcuacucGGGAGGCugagacaggaggaucgcuugagu
ccaagaguucugggcuguagugcgcuaugccgaucggguguccgcacuaa
guucggcaaCAAUauGGUGacCUCCCGggagCGGGGGacCACCaaGUUGc
> CAN.SPE.
GCCgGGCGCgGuggcgCGCGCCuguagUCCCagcuacucGGGAGGCuGAG
GCaGGaggaUCGCUugaGCcCAGGaguuCUGggcugCAGUGcGCUAUgcc
gauCGGGUGuCcgCACUAaguUCGGCAuCAAUauGGUGacCUCCCGggag
CGGGGGacCACCagGUUGCCuaaGGaGGGGUgaaccGGCccaggUCGgaa
aCGGagcagGUCaaaACUCCcgUGCUGAucagUAGUGgGaucgCGCCUGu
gaAUAGCCACUGcacucCAGCCUGuGCaacauAGCGAgacCCcGUCUCu
> HOM.S._A
GCCgGGCGCgGuggcgCGUGCCuguagUCCCagcuacucGGGAGGCuGAG
GCuGGaggaUCGCUugaGUcCAGGaguuCUGggcugUAGUGcGCUAUgcc
gauCGGGUGuCcgCACUAaguUCGGCAuCAAUauGGUGacCUCCCGggag
CGGGGGacCACCagGUUGCCuaaGGaGGGGUgaaccGGCccaggUCGgaa
aCGGagcagGUCaaaACUCCcgUGCUGAucagUAGUGgGaucgCGCCUGu
gaAUAGCCACUGcacucCAGCCUGuGCaacauAGCGAgacCCcGUCUCuu
> HOM.S._B
GCCgGGCGCgGuggcgCGUGCCuguagUCCCagcuacucGGGAGGCuGAG
GUGGGaggaUCGCUugaGCcCAGGaguuCUGggcugUAGUGcGCUAUgcc
gaugGGGUGuCcgCACUAaguUCGGCAuCAAUauGGUGacCUCCCGggag
CGGGGGacCACCagGUUGCCuaaGGaGGGGUgaaccGGCccaggUCGgaa
aCGGagcagGUCaaaACUCCcgUGCUGAucagUAGUGgGaucgCGCCUgu
gaAUAGCCACUGcacucCAGCCUGaGCaacauAGCGAgacCCCGUCUCu
Cove/Demos/K11H3frag.fa deleted 100644 → 0
View file @ ca28b8d2
>K11H3/930125 : fragment from 29971 to 29472 of original 33000 length, 500 bases, 9599 checksum.
GTGCAGTCATGTCCGAGTGGTTAAGGAGATTGACTAGAAATCAATTGGGC
TTTGCCCGCGTAGGTTCGAATCCTGCTGACTGCGAACGTTTTTGTTCTTT
TTCTATTTTCTATCGATTATTTGTTCAAGATATAATCGAATTTTTTTGAT
ATATAGGCTGTATTATCTTAGGTTCAAAAATGCAAGGCACAATTTTTCTT
TTAATGGTTTTTTAAGTTAGAAAAAGTATTTCGGATTTTGTTTTCTATTT
CTCTTCTACCCATACAGTACTTTGAACTAGATGTAGATTATCGTCAATCA
CTGAGTCTCTAATATACTTCCATTACTGACAATTCTCTATTTTACTTTCC
ATCTTGCAAGCAGGCACATGACCCCGCGTCCGCTTTCTCTATTCCTCTTT
CGTCGAGTATTCGGCACGCAGTCATGTCCGAGTGGTTAAGGAGTTTGACT
CGAAATCAAATGGGCTCTGCCCGCGTAGGTTCGAATCCTGCTGACTGCGA
Cove/Demos/fig5.fa deleted 100644 → 0
View file @ ca28b8d2
> DF6280
GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA
> DF6280G
GCGGATTTAGCTCAGTTGGGAGAGCGCCAGACTGAAGAAATACTTCGGTCAAGTTATCTGGAGGTCCTGTGTTCGATCCACAGAATTCGCA
> DD6280
UCCGUGAUAGUUUAAUGGUCAGAAUGGGCGCUUGUCGCGUGCCAGAUCGGGGUUCAAUUCCCCGUCGCGGAGCCA
> DX1661
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAAUCCGGCCCCCGCAACCA
> DS6280
GGCAACUUGGCCGAGUGGUUAAGGCGAAAGAUUAGAAAUCUUUUGGGCUUUGCCCGCGCAGGUUCGAGUCCUGCAGUUGUCGCCA
Cove/Demos/fig5.slx deleted 100644 → 0
View file @ ca28b8d2
DF6280 GCGGAUUUAGCUCAGUU GGG AGAGCGCCAGACUGAAG AUCUGGAG GUCCUGUGUUCGAUCCACAGAAUUCGCACCA
DF6280G GCGGAUUUAGCUCAGUU GGG AGAGCGCCAGACUGAAGAAAUACUUCGGUCAAGUUAUCUGGAG GUCCUGUGUUCGAUCCACAGAAUUCGCA
DD6280 UCCGUGAUAGUUUAAU GGUCAGAAUGGGCGCUUGUCG CGUGCCAG A UCGGGGUUCAAUUCCCCGUCGCGGAGCCA
DX1661 CGCGGGGUGGAGCAGCCUGGU AGCUCGUCGGGCUCAUA ACCCGAAG GUCGUCGGUUCAAAUCCGGCCCCCGCAACCA
DS6280 GGCAACUUGGCCGAGU GGUUAAGGCGAAAGAUUAGAA AUCUUUU GGGCUUUGCCCG CGCAGGUUCGAGUCCUGCAGUUGUCGCCA
Cove/Demos/sim100.fa deleted 100644 → 0
View file @ ca28b8d2
> DK0660
GGGCCCGUAGCUUAGUCUGGUAGAGCGCCUGACUUUUAAUCAGGCGGUCGAGGGUUCGAAUCCCUUCGGGCCCG
> DE2520
GCCCCCAUCGUCUAGAGGCCUAGGACAUCUCCCUUUCACGGAGGCAACGGGGAUUCGAAUUCCCCUGGGGGUA
> DT5320
GUCUUGAUAGUAUAAACAUUACUCUGGUCUUGUAAACCUGAAAUGAAGAUCUUCUCUUCUCAAGACA
> DR1181
GCCCAUGUAGCUCAGUAGGAUAGAGCACGCGCCUUCUAAGCGUGAGGUCGGAAGUUCGAGCCUUCUCGUGGGCACCA
> DC2720
GGCGGCAUGGCCAAGUGGUAAGGCAGGGGACUGCAAAUCCUUUACCCCCAGUUCAAAUCUGGGUGCCGCCU
> DL5720
ACUUUUAAAGGAUAACAGCCAUCCGUUGGUCUUAGGCCCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUA
> DC2680
GGCGGCAUGGCCAAGCGGUAAGGCAGGGGACUGCAAAUCCUUUAUCCCCAGUUCAAAUCUGGGUGCCGCCU
> DM3920
ACCUGGGUAGUUUAAAGGUAAAACCUUAAUUUCAUACAUUAAAGAUGAGAAUUCGAUUUUCUCCCCAGGUN
> DD4700
UUAAAAGUAGUUAAUAUAUAACUUAGAAUUGUCAGUUCUAGAUUCCUUUUACUAAGGCUUUUUAU
> DY6280
CUCUCGGUAGCCAAGUUGGUUUAAGGCGCAAGACUGUAAAUCUUGAGAUCGGGCGUUCGACUCGCCCCCGGGAGA
> DT5080
GCCUUGAAAGCUCAACAACUAGAGCUUUGGUCUUGUAAACCAGGAGAGAGGGUAAACUCCCUCUCAAGGCU
> DR4000
GCUCUCUUAGCUUAAUGGUUAAAGCAUAAUACUUCUAAUAUUAAUAUUCCAUGUUCAAAUCAUGGAGAGAGUA
> DL2601
GGGGGUAUGGCGAAAUUGGUAGACGCUGCGGACUUAAAAUCCGUUGGCUUUAAAGACCGUGAGGGUUCAAGUCCCUCUACCCCCA
> DV6161
GGUCGGAUGGUGUAGUCGGUUAUCACGGUUGCUUUACACGCAACAGGUCUCGAGUUCGAUCCUCGGUCGGAUCA
> DH4700
AAAAAAGUAGUUUAAUUUAAGAACGAUAGGUUGUGGGGCUAUUAGCGGUGUUAACCCUUUUUUA
> DK4030
GAGAGUAUUGUUUAAUGGUAAAACAUUCUGUCUUUUAAGCAGUCUAUAGUGGUUCGAUUCCACUUAUUCUCA
> DG2601
GCGGGUAUAGUUUAGUGGUAAAACCUUAGCCUUCCAAGCUAACGAUGCGGGUUCGAUUCCCGCUACCCGCU
> DE1140
GGCCUGUUGGUGAAGCGGUUAACACACACGGUUUUCAUCCGUGGACACACGGGUUCGAACCCCGUACAGGCUACCA
> DS3881
GGGAAAGUUUCCAUGGGUAGGGUAAGAUAUUUGCUAAAUAUUGUGCGUUUGCACAUAGAUGUUCGAAUCAUCUCUUUCCCG
> DY5000
GAUUGGGUGGCAGAUAGGGAUGCACUAGAUUGUAAAUCUAGGUAGGAAGGUUCAAGUCCUUUCCUGGUCA
> DI2580
GGGUUAUUAGCUCAGUUGGUUAGAGCACACCCCUGAUAAGGGUGAGGUCCCUGGUUCAAAUCCAGGAUAACCCA
> DX4880
AAAAAGAUAAGCUAAUUAAGCUACUGGGUUCAUACCCCAUUUAUAAAGGUUAUAAUCCUUUUCUUUUUA
> DD6280
UCCGUGAUAGUUUAAUGGUCAGAAUGGGCGCUUGUCGCGUGCCAGAUCGGGGUUCAAUUCCCCGUCGCGGAG
> DS2920
GGAGAGAUGGCUGAGUGGACUAAAGCGGCGGAUUGCUAAUCCGUUGUACGAGUUAAUCGUACCGAGGGUUCGAAUCCCUCUCUUUCCG
> DK7680
GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG
> DI5120
GGAAAUGUGCCCGAAAGUAGGGAUCACUUUGAUAGAGUGAAAUAUAUGGGUUCAAACCCCAUCAUCUCCU
> DI4080
GAAACUAUAAUUCAAUUGGUUAGAAUAGUAUUUUGAUAAGGUACCAAUAUAGGUUCGAUUCCUGUUAGUUUCA
> DV6280
GGUUUCGUGGUCUAGUCGGUUAUGGCAUCUGCUUAACACGCAGAACGUCCCCAGUUCGAUCCUGGGCGAAAUCA
> DA5040
GUGGUUCUAGUUUAGUGAAAAACGUUUGCUUUGCAAGCAGAAAUCCUAAGUUAAAUUCUUAGGAACUACA
> DY6742
CCGACCUUAGCUCUGUUGGUAUAGCGGAGGACUGUAGAUCCUUAGGUCACUGGUUCGAAUUCGGUAGGUCGGA
> DH2600
GGCGGACGUAGCCAAGUGGAUUAAGGCAGUGGAUUGUGGAUCCUCUACGCGCGGGUUCAAUUCCCGUCGUUCGCC
> DH5880
GUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGCUUACGACCCCUUAUUUACC
> DT5220
ACUCUAAUAGUUUAUGAAAAACAUUGGUCUUGUAAACCAAAAACUGAAGACUCCACCCUUCUUAGAGUA
> DI2440
GGGCUAUUAGCUCAGUUGGUUAGAGCGUUGCUUUGAUAAGGCAAAAGUCGAAAGUUCAAAUCUUUCAUAGCCCA
> DS6241
GGCGCGAUGGCAGAGUGGUCUAAUGCGUGAGACUUGAAAUCUCAUUUCUUCGGAAGCGUCGGUUCAAAUCCGGCUCGCGUCG
> DM6160
AGCUUCUUAACUCAGGGGUAGAGUGCGAGGCCCAUAACCUCGAGGUCCUAGGAUCGAAACCUAGAGAAGCUA
> DT5360
GUCUUUGUAGUACAUCUAAUAUACUGGUCUUGUAAACCAGAGAAGGAGAACAACUAACCUCCCUAAGACU
> DA0380
GGGCCCAUAGCUCAGUGGUAGAGUGCCUCCUUUGCAAGGAGGAUGCCCUGGGUUCGAAUCCCAGUGGGUCCA
> DW4980
AGAGAUUUAAGUUAAUAAAACUGAAAACCUUCAAAGUUUUAAAUAAGAGUGGAACUCUCUUAGUCUUUA
> DR2700
GCGUCCAUUGUCUAAUGGAUAGGACAGAGGUCUUCUAAACCUUUGGUAUAGGUUCAAAUCCUAUUGGACGCU
> DH5840
GUAAAUAUAGUUUAACCAAAACAUUAGAUUGUGAAUCUAAUAAUAGGGCCCCACAACCCCUUAUUUACC
> DA4500
GGGGACGUAGCUCAAUUGGUAGAGCGUAUGUUUUGCAAGCAUAAAGCUGUCGGUUCAAAUCCGAUCGUCUCCA
> DQ9991
GUCUCUGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGAUUGGUGGUUCGAGCCCACCCAGGGACG
> DP1140
CGGGAAGUGGCUCAGUUUGGUAGAGCAUUCGGUUUGGGACCGAAGGGUCGCAGGUUCAAAUCCUGUCUUCCCGACCA
> DV0860
GGGCCCGUCGUCUAGCCUGGUUAGGACGCUGCCCUGACGCGGCAGAAAUCCUGGGUUCAAGUCCCAGCGGGCCCA
> DG1500
GCGGAAGUAGUUCAGUGGUAGAACAUCACCUUGCCAUGGUGGGGGUCGCGGGUUCGAAUCCCGUCUUCCGCU
> DG2681
GCGGGUAUAGUUUAGUGGUAAAACCCUAGCCUUCCAAGCUAACGAUGCGGGUUCGAUUCCCGCUACCCGCU
> DP1662
CGGCACGUAGCGCAGCCUGGUAGCGCACCGUCAUGGGGUGUCGGGGGUCGGAGGUUCAAAUCCUCUCGUGCCGACCA
> DF5920
GUUAAUGUAGCUUUAAAAUUAAAGCAAGGCACUGAAAAUGCCUAGAUGAGUGCUCCAACUCCAUAAACA
> DN5000
UGGGUUGUAGCCUAAUGGAAAGGCAAUUGGCCGUUAACCAGGAGAUAACAAGAUCAAUACUUGUCAACUCAG
> DG4501
GCGGAUAUAGAUUAAAGGUAAAUUAUCUGCCUUCCAAGCAGAGGAUAUGGGUUCGAUUCCCGUUAUCCGCA
> DC4840
GGUCUUAUAGUCAAUAAUGAUAUCAAACUGCAAUUUUGAAGGAGUAAGUUUUACUAAGGCUU
> DC5160
GGCCUUGGGGUGUCAACACGUGGGGUUGCAAACCCCAAGAUGCAGUAUAAUACCUGCCGGGGCUU
> DD1180
GGCCCCAUAGCGAACGUUGGUUAUCGCGCCUCCCUGUCACGGAGGAGAUCACGGGUUCGAGUCCCGUUGGGGUCGCCA
> DA2520
GGGGGUAUAGCUCAGUUGGUAGAGCGCUGCCUUUGCAAGGCAGAUGUCAGCGGUUCGAGUCCGCUUAUCUCCA
> DN6060
GCUCGAUUAGCUCAGCUGGUUAGAGCAUGCGGCUGUUAACCGCAAGGUCGUAGGUUCGAUCCCUACAUCGAGCG
> DF5970
GUUCAUGUAGCUUAAAACCAAAGCAAGGCAUUGAAAAUGCCUAGAUGAGUAUAUUAACUCCAUAAACA
> DD1140
GGCCCCAUAGCGAAGUUGGUUAUCGCGCCUCCCUGUCACGGAGGAGAUCACGGGUUCGAGUCCCGUUGGGGUCGCCA
> DF7740
GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCCGGUUCAAUCCCGGGUUUCGGCA
> DW5040
AAGAGCUUAAGUUAAAUAAACUGAAAGCCUUCAAAGCUUUUUAUAAGAAUGGAAACUUCUUAGCUCUUG
> DF4700
GAUACGGUAGCUUAAUUAAAGCGUCUCAUUGAAAAUGAGGAAGAUGGUACUUUAGUACCUUGUGUCA
> DP7560
GGCCGAAUGGUCUAGUGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAUCCCCGGUUCGGCCC
> DW3960
AAGAGUAUAGUUUAAAGGUAAAACAGAAAGCUUCAACCUUUAAUUUCUUAGUUCGAGUCUAAGUGCUCUUG
> DA2540
GGGGGUAUAGCUCAGUUGGUAGAGCGCUGCCUUUGCACGGCAGAUGUCAGGGGUUCGAGUCCCCUUACCUCCA
> DA1540
GGGGCCUUAGCUCAGCUGGGAGAGCGCCUGCUUUGCACGCAGGAGGUCAGCGGUUCGAUCCCGCUAGGCUCCA
> DQ4440
UGGAGUAUAGCCAAGUGGUAAGGCAUCGGUUUUUGGUAUCGGCAUGCAAAGGUUCGAAUCCUUUUACUCCAG
> DL5560
ACUUUUAAAGGAUAACAGCUAUCCAUUGGCCUUAGGAGUCAAAAAUAUUGGUGCAACUCCAAAUAAAAGUA
> DL2180
GGGGAUGUGGUGGAAUUGGUAGACGCAACGGACUUAAAAUCCGUCGAUUGUAUAGAUCGUGAGGGUUCAAGUCCCUCCGUCCCCA
> DX0980
AGCGGGGUAGGCCAGCCAGGUAGGCCGCGGGGCUCAUANCCCCGAGGUCCCGGGUUCAAAUCCCGGCCCCGCUA
> DY4480
GGGAGAGUGGCCGAGCGGUCAAAAGCGACAGACUGUAAAUCUGUUGAAGGUUUUCUACGUAGGUUCGAAUCCUGCCUCUCCCA
> DN1541
UCCGCAGUAGCUCAGUGGUAGAGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAAUCCUACCUGCGGAG
> DR2602
GCGUCCAUCGUCUAAAGGAUAGGACAGAGGUUUUCUAAACCUCCAGUAUAGGUUCGAAUCCUAUUGGACGUA
> DX1660
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAAUCCGGCCCCCGCAACCA
> DS2602
GGAAAGAUGGUUGAGUGGUUUAAGGCGUAGCAUUGGAAAUGCUAUGUAGGCUUUUGGUCUAUCGAGGGUUCGAAUCCCUCUCUUUCCG
> DV2601
AGGGCUAUAGCUCAGCGGUAGAGCGCCUCGUUUACACCGAGAAUGUCUACGGUUCAAAUCCGUAUAGCCCUA
> DQ2920
UGGGGCGUGGCCAAGUGGUAAGGCAACGGGUUUUGGUCCCGCUAUUCGGAGGUUCGAAUCCUUCCGUCCCAG
> DS4362
GGAGGUAUGGCUGAGUGGCUUAAGGCAUUGGUUUGCUAAAUCGACAUACAAUAAGAUUGUAUCAUGGGUUCGAAUCCCAUUUCCUCCG
> DS1520
GGAGAGUUGGCAGAGCGGUAAUGCAGCGGACUCGAAAUCCGCCGAGCCAAUGUUGAAUUGGGUCGCAGGUUCAAAUCCUGUACUCUCCU
> DT3360
GCCCUUUUAACUCAGUGGUAGAGUAACGCCAUGGUAAGGCGUAAGUCAUCGGUUCAAAUCCGAUAAGGGGCU
> DG4080
AUAGAUAUAAGUUAAGUGGUAAACUGAAUGUCUUCCACACAUUGAUUGUGAGUUCGAUUCUCACUAUCUAGA
> DG4700
GCAUAUAUAGUAAACAAUAUUAUAUUUGCCUUCCAAGCAAAAGUCCUAAUAAAAUUAGUGUAUGCU
> DS6744
GUGGACGUGCCGGAGUGGUUAUCGGGCAUAACUAGAAAUCAUGUGGGCUUUGCCCGCGCAGGUUCGAAUCCUGCCGUUCACG
> DN1350
UCCUCGGUAGCUCAAUUGGCAGAGCAGCCGGCUGUUAACCGGCAGGUUACUGGUUCGAGUCCAGUCCGGGGAG
> DQ6050
GGUCCUAUAGUGUAGUGGUUAUCACUUCGGACUUUGAAUCCGAAAACCCAGGUUCGAAUCCUGGUAGGACCA
> DF5400
GUCUACGUAGCUUAACCCCCAAAGCAAGACACUGAAAAUGCCUAGAUGGAUUCACACAUCCCAUAGACA
> DD2600
GGGAUUGUAGUUCAAUUGGUUAGAGUACCGCCCUGUCAAGACGGAAGUUGCGGGUUCGAGCCCCGUCAAUCCCG
> DS1664
GGUGAGGUGUCCGAGUGGCUGAAGGAGCACGCCUGGAAAGUGUGUAUACGGCAACGUAUCGGGGGUUCGAAUCCCCCCCUCACCGCCA
> DS3880
AGAGAGUUGGCUGAGUGGUAAGGCGACUAGCUUGAGUCUAGUUAAGUUAAAACUUUCAUAUGUUCGAAUCAUAUACUCUCUG
> DP5120
CGGGAGAGAAUUUAAAUUAGAAUGUUGGCUUUGGGGGUCAAUAGUGGAGGUUUGAGUCCUUCUUUCUCGA
> DR4800
AAAUAUGAAGCGAUUUAUUGCAAUUAGUUUCGACCUAAUCUUAGGUGAAAUUCACCCCAUAUUUU
> DP5200
CAAGGAAUAGUUUAUGUAGAAUUCCAGCUUUGGGUGUUGGUGGUGAGGUUUAAUGUCUCUUCCUUGA
> DN5160
UAGAAUGAAGCUCGCUGGAUAGAGUGUUUAGCUGUUAACUAAAAUAUUACGGGAUCGAGGCCCGUCAUUCUAG
> DE2500
GCCCCCAUCGUCUAGUGGUUCAGGACAUCUCUCUUUCAAGGAGGCAGCGGGGAUUCGACUUCCCCUGGGGGUA
> DZ7560
GCCCGGAUGAACCAUGGCGGUCUGUGGUGCAGACUUCAAAUCUGUAGGCGGUUAGCGCCGCAGUGGUUCGACUCCACCUUUCGGGUG
> DG5120
ACUUUCUUAGUAUUAACCAGUACACGUGACUUCCAAUCACAAAGUCUUAGUAGAAUCUAAGAGAAAGUA
> DX3720
GCAGCAAGGGUGGUCUCAACCUGGGUUCAUUCCCCAGCUAAUAAAGUUCGAUUCUUUGUAGCGGCU
> DE4980
AUUCCUGUAGUUGAAACAACAAUAACUUUUCAUGUUAUAGGUUUAGGUUGAACCCCUAACAGGAAUC
> DW2720
GCGCUCUUAGUUCAGUUUGGUAGAACGCGGGUCUCCAAAACCCGAUGUCGUAGGUUCAAAUCCUACAGAGCGUG
> DF6280
GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA
> DP8041
GGCUCGUUGGUCUAGGGGUAUGAUUCUCGCUUCGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC
Cove/Demos/sim100.slx deleted 100644 → 0
View file @ ca28b8d2
DK0660 GGGC CC GU A GCUUAGUC UGGU AGAGCG C CUGAC UUUUAAUCAG GCG GU CGAG GGU UCG AA UCC CU U CGGGCCC G
DE2520 GCCC CC AU C GUCUAGA GGCCU AGGACA U CUCCC UUUCACGGAG GCA A CGGG GAU UCG AA UUC CC C UGGGGGU A
DT5320 GUCU UG AU A GUAUAA AC AUUACU C UGGUC UUGUAAACCU GAA A UGAA G A UCU UC U C UU C UCAAGAC A
DR1181 GCCC AU GU A GCUCAGUA GGAU AGAGCA C GCGCC UUCUAAGCGU GAG GU CGGA AGU UCG AG CCU UC U CGUGGGC ACCA
DC2720 GGCG GC AU G GCCAAGU GGU AAGGCA G GGGAC UGCAAAUCCU UUA C CCCC AGU UCA AA UCU GG G UGCCGCC U
DL5720 ACUU UU AA A GGAUAAC AGC CAUCCG U UGGUC UUAGGCCCCA AAA A UUUU GGU GCA AC UCC AA A UAAAAGU A
DC2680 GGCG GC AU G GCCAAGC GGU AAGGCA G GGGAC UGCAAAUCCU UUA U CCCC AGU UCA AA UCU GG G UGCCGCC U
DM3920 ACCU GG GU A GUUUAAA GGU AAAACC U UAAUU UCAUACAUUA AAG A UGAG AAU UCG AU UUU CU C CCCAGGU N
DD4700 UUAA AA GU A GUUAAU AU AUAACU U AGAAU UGUCAGUUCU AGA U UCCU U U UAC U A AG G CUUUUUA U
DY6280 CUCU CG GU A GCCAAGUU GGUUU AAGGCG C AAGAC UGUAAAUCUU GAG AU CGGG CGU UCG AC UCG CC C CCGGGAG A
DT5080 GCCU UG AA A GCUCAAC AACU AGAGCU U UGGUC UUGUAAACCA GGA G AGAG GGU AAA CU CC CU C UCAAGGC U
DR4000 GCUC UC UU A GCUUAAU GGUU AAAGCA U AAUAC UUCUAAUAUU AAU AU UCCA UGU UCA AA UCA UG G AGAGAGU A
DL2601 GGGG GU AU G GCGAAAUU GGUA GACGCU G CGGAC UUAAAAUCCG UU GGC UU UAA AG ACCG UGAG GGU UCA AG UCC CU C UACCCCC A
DV6161 GGUC GG AU G GUGUAGUC GGUU AUCACG G UUGCU UUACACGCAA CAG GU CUCG AGU UCG AU CCU CG G UCGGAUC A
DH4700 AAAA AA GU A GUUUAAUU UA AGAACG A UAGGU UGUGGGGCUA UUA G CGGU GUU A AC C CUUUUUU A
DK4030 GAGA GU AU UGUUUAAU GGUA AAACAU U CUGUC UUUUAAGCAG UCU A UAGU GGU UCG AU UCC AC U UAUUCUC A
DG2601 GCGG GU AU A GUUUAGU GGU AAAACC U UAGCC UUCCAAGCUA ACG A UGCG GGU UCG AU UCC CG C UACCCGC U
DE1140 GGCC UG UU G GUGAAGC GGUU AACACA C ACGGU UUUCAUCCGU GGA CA CACG GGU UCG AA CCC CG U ACAGGCU ACCA
DS3881 GGGA AA GU UUCCAUG GGUA GGGUAA G AUAUU UGCUAAAUAU UG UGC G UUU G C ACA UAGA UGU UCG AA UCA UC U CUUUCCC G
DY5000 GAUU GG GU G GCAGAUA GG GAUGCA C UAGAU UGUAAAUCUA GGU A GGAA GGU UCA AG UCC UU U CCUGGUC A
DI2580 GGGU UA UU A GCUCAGUU GGUU AGAGCA C ACCCC UGAUAAGGGU GAG GU CCCU GGU UCA AA UCC AG G AUAACCC A
DX4880 AAAA AG AU A AGCUAA UU AAGCUA C UGGGU UCAUACCCCA UUU A UAAA GGU UAU AA UCC UU U UCUUUUU A
DD6280 UCCG UG AU A GUUUAAU GGUC AGAAUG G GCGCU UGUCGCGUGC CAG A UCGG GGU UCA AU UCC CC G UCGCGGA G
DS2920 GGAG AG AU G GCUGAGU GGACU AAAGCG G CGGAU UGCUAAUCCG UU GUA CGA GUU AA UCG UAC CGAG GGU UCG AA UCC CU C UCUUUCC G
DK7680 GCCC GG CU A GCUCAGUC GGU AGAGCA U GAGAC UCUUAAUCUC AGG GU CGUG GGU UCG AG CCC CA C GUUGGGC G
DI5120 GGAA AU GU G CCCGAA AG UAGGGA U CACUU UGAUAGAGUG AAA UA UAUG GGU UCA AA CCC CA U CAUCUCC U
DI4080 GAAA CU AU A AUUCAAUU GGUU AGAAUA G UAUUU UGAUAAGGUA CCA A UAUA GGU UCG AU UCC UG U UAGUUUC A
DV6280 GGUU UC GU G GUCUAGUC GGUU AUGGCA U CUGCU UAACACGCAG AAC GU CCCC AGU UCG AU CCU GG G CGAAAUC A
DA5040 GUGG UU CU A GUUUAGU GA AAAACG U UUGCU UUGCAAGCAG AAA U CCUA AGU UAA AU UCU UA G GAACUAC A
DY6742 CCGA CC UU A GCUCUGUU GGU AUAGCG G AGGAC UGUAGAUCCU UAG GU CACU GGU UCG AA UUC GG U AGGUCGG A
DH2600 G GCGG AC GU A GCCAAGU GGAUU AAGGCA G UGGAU UGUGGAUCCU CUA CG CGCG GGU UCA AU UCC CG U CGUUCGC C
DH5880 GUAA AU AU A GUUUAA CC AAAACA U CAGAU UGUGAAUCUG ACA A CAGA GGC UUA CG ACC CC U UAUUUAC C
DT5220 ACUC UA AU A GUUUAU GA AAAACA U UGGUC UUGUAAACCA AAA AC UGAA GAC UCC AC CC UU C UUAGAGU A
DI2440 GGGC UA UU A GCUCAGUU GGUU AGAGCG U UGCUU UGAUAAGGCA AAA GU CGAA AGU UCA AA UCU UU C AUAGCCC A
DS6241 GGCG CG AU G GCAGAGU GGUCU AAUGCG U GAGAC UUGAAAUCUC AU UUC UUC G GAAG CGUC GGU UCA AA UCC GG C UCGCGUC G
DM6160 AGCU UC UU A ACUCAGG GGU AGAGUG C GAGGC CCAUAACCUC GAG GU CCUA GGA UCG AA ACC UA G AGAAGCU A
DT5360 GUCU UU GU A GUACAU CU AAUAUA C UGGUC UUGUAAACCA GAG A AGGA GAA CAA CU AACC UC C CUAAGAC U
DA0380 GGGC CC AU A GCUCAGU GGU AGAGUG C CUCCU UUGCAAGGAG GAU GC CCUG GGU UCG AA UCC CA G UGGGUCC A
DW4980 AGAG AU UU A AGUUAA UA AAACUG A AAACC UUCAAAGUUU UAA A UAAG AGU GGA AC UCU CU U AGUCUUU A
DR2700 GCGU CC AU U GUCUAAU GGAU AGGACA G AGGUC UUCUAAACCU UUG G UAUA GGU UCA AA UCC UA U UGGACGC U
DH5840 GUAA AU AU A GUUUAA CC AAAACA U UAGAU UGUGAAUCUA AUA A UAGG GCC CCA CA ACC CC U UAUUUAC C
DA4500 GGGG AC GU A GCUCAAUU GGU AGAGCG U AUGUU UUGCAAGCAU AAA GC UGUC GGU UCA AA UCC GA U CGUCUCC A
DQ9991 GUCU CU GU G GCGCAAUC GGUU AGCGCG U UCGGC UGUUAACCGA AAG AU UGGU GGU UCG AG CCC AC C CAGGGAC G
DP1140 CGGG AA GU G GCUCAGUU UGGU AGAGCA U UCGGU UUGGGACCGA AGG GU CGCA GGU UCA AA UCC UG U CUUCCCG ACCA
DV0860 GGGC CC GU C GUCUAGCC UGGUU AGGACG C UGCCC UGACGCGGCA GAA AU CCUG GGU UCA AG UCC CA G CGGGCCC A
DG1500 GCGG AA GU A GUUCAGU GGU AGAACA U CACCU UGCCAUGGUG GGG GU CGCG GGU UCG AA UCC CG U CUUCCGC U
DG2681 GCGG GU AU A GUUUAGU GGU AAAACC C UAGCC UUCCAAGCUA ACG A UGCG GGU UCG AU UCC CG C UACCCGC U
DP1662 CGGC AC GU A GCGCAGCC UGGU AGCGCA C CGUCA UGGGGUGUCG GGG GU CGGA GGU UCA AA UCC UC U CGUGCCG ACCA
DF5920 GUUA AU GU A GCUUUAA AAUU AAAGCA A GGCAC UGAAAAUGCC UAG A UGAG U G CUC CA A CU C CAUAAAC A
DN5000 UGGG UU GU A GCCUAAU GGA AAGGCA A UUGGC CGUUAACCAG GAG AU AACA AGA UCA AU ACU UG U CAACUCA G
DG4501 GCGG AU AU A GAUUAAA GGU AAAUUA U CUGCC UUCCAAGCAG AGG A UAUG GGU UCG AU UCC CG U UAUCCGC A
DC4840 GGUC UU AU A GUCAAUA AUGAUA U CAAAC UGCAAUUUUG AAG G AGUA A GUU U UA C UAAGGCU U
DC5160 GGCC UU GG G GUGUC AACACG U GGGGU UGCAAACCCC AAG A UGCA GUA UAA UA CC UG C CGGGGCU U
DD1180 GGCC CC AU A GCGAACGU UGGUU AUCGCG C CUCCC UGUCACGGAG GAG AU CACG GGU UCG AG UCC CG U UGGGGUC GCCA
DA2520 GGGG GU AU A GCUCAGUU GGU AGAGCG C UGCCU UUGCAAGGCA GAU GU CAGC GGU UCG AG UCC GC U UAUCUCC A
DN6060 GCUC GA UU A GCUCAGCU GGUU AGAGCA U GCGGC UGUUAACCGC AAG GU CGUA GGU UCG AU CCC UA C AUCGAGC G
DF5970 GUUC AU GU A GCUUAAA ACC AAAGCA A GGCAU UGAAAAUGCC UAG A UGAG U A UAU UA A CU C CAUAAAC A
DD1140 GGCC CC AU A GCGAAGUU GGUU AUCGCG C CUCCC UGUCACGGAG GAG AU CACG GGU UCG AG UCC CG U UGGGGUC GCCA
DF7740 GCCG AA AU A GCUCAGUU GGG AGAGCG U UAGAC UGAAGAUCUA AAG GU CCCC GGU UCA AU CCC GG G UUUCGGC A
DW5040 AAGA GC UU A AGUUAA AU AAACUG A AAGCC UUCAAAGCUU UUU A UAAG AAU GGA AA CUU CU U AGCUCUU G
DF4700 GAUA CG GU A GCUUAA UU AAAGCG U CUCAU UGAAAAUGAG GAA GA UGGU AC UUU A GU AC C UUGUGUC A
DP7560 GGCC GA AU G GUCUAGU GGU AUGAUU C UCGCU UUGGGUGCGA GAG GU CCCG GGU UCA AU CCC CG G UUCGGCC C
DW3960 AAGA GU AU A GUUUAAA GGU AAAACA G AAAGC UUCAACCUUU AAU U UCUU AGU UCG AG UCU AA G UGCUCUU G
DA2540 GGGG GU AU A GCUCAGUU GGU AGAGCG C UGCCU UUGCACGGCA GAU GU CAGG GGU UCG AG UCC CC U UACCUCC A
DA1540 GGGG CC UU A GCUCAGCU GGG AGAGCG C CUGCU UUGCACGCAG GAG GU CAGC GGU UCG AU CCC GC U AGGCUCC A
DQ4440 UGGA GU AU A GCCAAGU GGU AAGGCA U CGGUU UUUGGUAUCG GCA UG CAAA GGU UCG AA UCC UU U UACUCCA G
DL5560 ACUU UU AA A GGAUAAC AGC UAUCCA U UGGCC UUAGGAGUCA AAA A UAUU GGU GCA AC UCC AA A UAAAAGU A
DL2180 GGGG AU GU G GUGGAAUU GGUA GACGCA A CGGAC UUAAAAUCCG UC GAU U GUA UA G AUCG UGAG GGU UCA AG UCC CU C CGUCCCC A
DX0980 AGCG GG GU A GGCCAGCC AGGU AGGCCG C GGGGC UCAUANCCCC GAG GU CCCG GGU UCA AA UCC CG G CCCCGCU A
DY4480 GGGA GA GU G GCCGAGC GGUCA AAAGCG A CAGAC UGUAAAUCUG UU GAA GGU U UUCUA CGUA GGU UCG AA UCC UG C CUCUCCC A
DN1541 UCCG CA GU A GCUCAGU GGU AGAGCU A UCGGC UGUUAACCGA UCG GU CGUA GGU UCG AA UCC UA C CUGCGGA G
DR2602 GCGU CC AU C GUCUAAA GGAU AGGACA G AGGUU UUCUAAACCU CCA G UAUA GGU UCG AA UCC UA U UGGACGU A
DX1660 CGCG GG GU G GAGCAGCC UGGU AGCUCG U CGGGC UCAUAACCCG AAG AU CGUC GGU UCA AA UCC GG C CCCCGCA ACCA
DS2602 GGAA AG AU G GUUGAGU GGUUU AAGGCG U AGCAU UGGAAAUGCU AU GUA GGCUUUU GGUC UAU CGAG GGU UCG AA UCC CU C UCUUUCC G
DV2601 AGGG CU AU A GCUCAGC GGU AGAGCG C CUCGU UUACACCGAG AAU GU CUAC GGU UCA AA UCC GU A UAGCCCU A
DQ2920 UGGG GC GU G GCCAAGU GGU AAGGCA A CGGGU UUUGGUCCCG CUA UU CGGA GGU UCG AA UCC UU C CGUCCCA G
DS4362 GGAG GU AU G GCUGAGU GGCUU AAGGCA U UGGUU UGCUAAAUCG AC AUA CAAUAAG AUUG UAU CAUG GGU UCG AA UCC CA U UUCCUCC G
DS1520 GGAG AG UU G GCAGAGC GGU AAUGCA G CGGAC UCGAAAUCCG CCG AGC CAAUGUU GAAUUG GGU CGCA GGU UCA AA UCC UG U ACUCUCC U
DT3360 GCCC UU UU A ACUCAGU GGU AGAGUA A CGCCA UGGUAAGGCG UAA GU CAUC GGU UCA AA UCC GA U AAGGGGC U
DG4080 AUAG AU AU A AGUUAAGU GGU AAACUG A AUGUC UUCCACACAU UGA U UGUG AGU UCG AU UCU CA C UAUCUAG A
DG4700 GCAU AU AU A GUAAACA AU AUUAUA U UUGCC UUCCAAGCAA AAG U CCUA AU AAA AU UA G UGUAUGC U
DS6744 GUGG AC GU G CCGGAGU GGUU AUCGGG C AUAAC UAGAAAUCAU GU GGG C UUU G CCCG CGCA GGU UCG AA UCC UG C CGUUCAC G
DN1350 UCCU CG GU A GCUCAAUU GGC AGAGCA G CCGGC UGUUAACCGG CAG GU UACU GGU UCG AG UCC AG U CCGGGGA G
DQ6050 GGUC CU AU A GUGUAGU GGUU AUCACU U CGGAC UUUGAAUCCG AAA A CCCA GGU UCG AA UCC UG G UAGGACC A
DF5400 GUCU AC GU A GCUUAACC CCC AAAGCA A GACAC UGAAAAUGCC UAG A UGGA U U CAC AC A UC C CAUAGAC A
DD2600 GGGA UU GU A GUUCAAUU GGUU AGAGUA C CGCCC UGUCAAGACG GAA GU UGCG GGU UCG AG CCC CG U CAAUCCC G
DS1664 GGUG AG GU G UCCGAGU GGCUG AAGGAG C ACGCC UGGAAAGUGU GU AUA CG GCA A CG UAU CGGG GGU UCG AA UCC CC C CCUCACC GCCA
DS3880 AGAG AG UU G GCUGAGU GGU AAGGCG A CUAGC UUGAGUCUAG UU AAG UU AAA AC UUU CAUA UGU UCG AA UCA UA U ACUCUCU G
DP5120 CGGG AG AG A AUUUAAA UU AGAAUG U UGGCU UUGGGGGUCA AUA G UGGA GGU UUG AG UCC UU C UUUCUCG A
DR4800 AAAU AU GA A GCGAUUU AUUGCA A UUAGU UUCGACCUAA UCU U AGGU G AAA UU C AC CCCAUAUUU U
DP5200 CAAG GA AU A GUUUAU GU AGAAUU C CAGCU UUGGGUGUUG GUG G UGAG GU UUA AU GU CU C UUCCUUG A
DN5160 UAGA AU GA A GCUCGCU GGAU AGAGUG U UUAGC UGUUAACUAA AAU AU UACG GGA UCG AG GCC CG U CAUUCUA G
DE2500 GCCC CC AU C GUCUAGUG GUUC AGGACA U CUCUC UUUCAAGGAG GCA G CGGG GAU UCG AC UUC CC C UGGGGGU A
DZ7560 GCCC GG AUGAACCAUGGC GGUC UGUGGU G CAGAC UUCAAAUCUG UA GGC G GUU AG C GCCG CAGU GGU UCG AC UCC ACCU UUCGGGU G
DG5120 ACUU UC UU A GUAUUAA CC AGUACA C GUGAC UUCCAAUCAC AAA G UCUU AGU AGA AU CU AA G AGAAAGU A
DX3720 GCAG CA AG G GUGGU CUCAAC C UGGGU UCAUUCCCCA GCU A AUAA AGU UCG AU UCU UU G UAGCGGC U
DE4980 AUUC CU GU A GUUGAA ACAACA A UAACU UUUCAUGUUA UAG G UUUA GGU UGA AC CCC UA A CAGGAAU C
DW2720 GCGC UC UU A GUUCAGUU UGGU AGAACG C GGGUC UCCAAAACCC GAU GU CGUA GGU UCA AA UCC UA C AGAGCGU G
DF6280 GCGG AU UU A GCUCAGUU GGG AGAGCG C CAGAC UGAAGAUCUG GAG GU CCUG UGU UCG AU CCA CA G AAUUCGC A
DP8041 GGCU CG UU G GUCUAGG GGU AUGAUU C UCGCU UCGGGUGCGA GAG GU CCCG GGU UCA AA UCC CG G ACGAGCC C
Cove/Demos/sim65.fa deleted 100644 → 0
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DM4080 ACUU GU AU A GUUUAAAU GGUU AAAACA U UUGUC UCAUAAACAA AUA AU GUAA GGU UCA AA UCC UU C UACAAGU A
DD5880 AAGG UA UU A GAAAAA CC AUUUCA U AACUU UGUCAAAGUU AAA U UAUA GGC UAA AU CC UA U AUAUCUU A
DP3880 CAGG UU AG A GCCAGGU GGU UAGGCG U CUUGU UUGGGUCAAG AAA UU GUUA UGU UCG AA UCA UA A UAACCUG A
DR6160 GGGA CU AU A GUUUAGUU GGAU AUAACG A CCGGC UACGAACCGG UAG GU CUCA GGU UCG AC CCC UG A UGGUCUC G
DM0900 AGCG GG GU G GGGUAGUC AGGA AAUCCG A UGGGC UCAUAACCCG UAG AU CGAU GGU UCA AA UCC AU C CCCCGCU A
DC0500 GCCA AG GU G GCAGAGUU CGGCCC AACGCA U CCGCC UGCAGAGCGG AAC CC CCGCC GGU UCA AA UCC GG C CCUUGGC UCCA
DP0260 CUCC GA UU A GCUCAAUU GGCU AGAGUA C ACCGU UUGGGGCGGU GGG GU UGAA GGU UCG AG UCC UU C AUUGGAG ACCA
DP5080 CAGG AG AA A GUUUAAU AA AAAACC G CAGCU UUGGAAGUUG CAA U GUAA GG UAA G CC UU AUUCUCUUG A
DN4700 GGCC AA AU A GUUUAAC UU AAAACG U UGAGC UGUUAAUUCA AAA U UGCA G U AAU U UG C UUUGGCU U
DA4700 AGAA UG GU A CUUUAA AA AAAAGA A UUGGU UUGCAUCUAA UAU UAAG C CUG A G CU U UCAUUCU U
DI4000 GAAA CU AU A AUUCAAUU GGUU AGAAUA G UAUUU UGAUAAGGUA CAA A UAUA GGU UCA AU CCC UG U UAGUUUC A
DG4080 AUAG AU AU A AGUUAAGU GGU AAACUG A AUGUC UUCCACACAU UGA U UGUG AGU UCG AU UCU CA C UAUCUAG A
DY5020 GGCA GG GU G GCAGAAA GUC AAUGCG C UAAAU UGUAAAUUUA UAA A AAAA GGU UUA AU UCC UU U CUUUGCC A
DG2920 GCGG GU AU A GUUUAGU GGU AAAACC C UAGCC UUCCAAGCUA ACG A UGCG GGU UCG AU UCC CG C UACCCGC U
DZ1662 GGAAG AU CG U CGUCUCC GGUG AGGCGG C UGGAC UUCAAAUCCA GU UGG GGCCGCCA GCGGUC CCG GGCA GGU UCG AC UCC UG U GAUCUUCCGCCA
DF5950 GUUA AU GU A GCUUAAA CU AAAGCA A GGCAC UGAAAAUGCC UAG A UGGG U A UUU A A CU C CAUAAAC A
DG5080 GCUU UA UG A AUACAAC AGUAUU U UUGAC UUCCAAUCAG ACA G UCUU GGU GAA AA UUU AA G AUAAAGC A
DC4700 UGCU UA GU A GUUAAUGU UAAU AUAACU A AGAAC UGCAAAUUCU UCA U AGUC U A GUU A GA C CUAAGCU U
DD0260 GCGA CC GG G GCUGGCUU GGUA AUGGUA C UCCCC UGUCACGGGA GAG AA UGUG GGU UCA AA UCC CA U CGGUCGC GCCA
DG4700 GCAU AU AU A GUAAACA AU AUUAUA U UUGCC UUCCAAGCAA AAG U CCUA AU AAA AU UA G UGUAUGC U
DK0740 GGGC CC GU A GCUUAGUC UGGU AGAGCG C CUGGC UUUUAAUCAG GCG GU CGAG GGU UCG AA UCC CU U CGGGCCC G
DX4000 UGCA AU AU G AUGUAAUU GGUU AACAUU U UAGGG UCAUGACCUA AUU A UAUA CGU UCA AA UCG UA U UAUUGCU A
DA0260 GGGC GA AU A GUGUCAGC GGG AGCACA C CAGAC UUGCAAUCUG GUA G GGAG GGU UCG AG UCC CU C UUUGUCC ACCA
DN4000 GUCC UU AU A GCUUAUC GGUU AAAGCA U CUCAC UGUUAAUGAG AAU A GAUG GGU UCA AU UCC UA U UAAGGAC G
DT4980 CCUU AA AG C UACAAA AAGCAG A CAAUC UUGUAAAUUG UAA GA UAAA AGG UUU AA GUC CU U UUUAAGG U
DM3881 AAGA CU AU A GCUUAAUC GGU AAAGCG A ACCAC UCAUGAUGGU UUG AG UAAA UGU UCA AG UCA UU U UAGUCUU A
DH5280 GUAG AU AU A GUUUAC AA AAAACA U UAGAC UGUGAAUCUA ACA A CAGG AAA UCA AA UU CC U UAUUUAC C
DT4081 GUAG AU AU A AUUUAAUC GGU AAAAUGUA UGUUU UUAGGGUACA UAU UA UCUA AGU UCA AA UCU UA G UAUUUAC A
DR5120 GAGU UG UU A GUCUAA AC AAGACA G UUGUU UUCGGCACAA CAA A UUAU GGU UAA AC CCC AU A AUAACUC U
DM3640 AGAC AC GU A GCUUAGU GGU AAAGCA C UGGUC UCAUAAGCCA GCU AU CGCA AGU UCG AA UCU CG C CGUGUCU A
DT4070 GUUG CA UU A GCUCAAUU GGU AGAGCG U UUGUU UUGUAAUCAA AAG GU UUAG AGU UCA AC UCU CU A AUGCANU N
DD4620 UCAU UU CU A GUCUAGU UA AGGAUG U UGCUU UGUCGUGGCG GUG G GGUA U GUU UU G UA C GGGAUGA G
DA0340 GGGC UC GU A GCUCAGC GGG AGAGCG C CGCCU UUGCGAGGCG GAG GC CGCG GGU UCA AA UCC CG C CGAGUCC A
DS0260 GGAA GG UA G GGCGUAGU GGU ACGCAA C UAGUC UUGAAAACUA GC CCGCUGU AGU G AUA CGG UGAU GGU UCG AC UCC AU U ACCUUCC UCCA
DP4060 CAGA UU GU C UCGUAAUU GGUU AUCGAG C CUACA UUGGGUGUAG GAU UU UGAG GGU UCA AG UCC UU C CAAUCUG A
DQ1341 A UGGG CU AU G GUGUAAUU GGC AGCACG A GUGAU UCUGGUUCAU UUA G UCUA GGU UCG AG UCC UG G UAGCCCA G
DI1860 GGGC CU AU A GCUCAGCU GGUU AGAGUG C ACCCC UGAUAAGGGU GAG GU CACA AGU UCA AG UCU UG U UAGGCCC ACCA
DL5221 GCUA GC GU G GCAGAGCU CGGCA AAUGCA A AAGGC UUAAGCCCUU UAU C CAGA GGU UCA AA UCC UC U CCCUAGC U
DW5220 AGAA AC UU A GGAUUAAC UGUCACCAAACCA A AGGCC UUCAAAGCCU UAA A UAAG AGU UAA AC UCU CU U AGUUUCU G
DR4880 GAAU AU GA A GCGAUUA AUUGCA G UUAGU UUCGACCUAA CCU U AGGU A UUA UA U AC C CUUAUUU U
DX4980 GUA AA GU A AGCUAAAU GUU AAGCUU U UGGGU UCAUACCUCA AGA A UAGAAGGA UAA AA ACC UC U CUUUAUC
DT5281 GUCC CG AU A GUAUAA AA AUUACU C UGGUC UUGUAAGCCA AAA A UGAA GAG UCA GC UC UU C UCGGGAC A
DD3280 GGGA UU GU A GUUCAAUU GGUU AGAGCA C CGCCC UGUCAAGGCG GAA GC UGCG GGU UCG AG CCC CG U CAGUCCC G
DW2680 GCGC UC UU A GUUCAGUU CGGU AGAACG C GGGUC UCCAAAACCC GAU GU CGUA GGU UCA AA UCC UA C AGAGCGU G
DW5360 AGGA AU UU A GGUUAA AC AGACCA A GAGCC UUCAAAGCCC UAA G CAAG U A CAA UU U A CU U AAUUCCU G
DG5280 ACUC CC UU A GUAUAA AC AAUACA A CUGAC UUCCAAUCAG UUA A UUCU GAA AAA AC UC AG A AGAGAGU A
DW4620 AGUG AU CU A GGUUAUU UU GGACUG U CUGUU UUCAAAACAG GAG G UGGC UUU G GU C GGUUGCU G
DG1230 GUCG GU GU C GUAUAU GGU U AUUAC A GGCCU UGCCAAGGCU UAG A CGGC AGU UCG AU CCU GC U CACCGGC UCCA
DR1664 GUCC UC UU A GUUAAAU GGAU AUAACG A GCCCC UCCUAAGGGC UAA U UGCA GGU UCG AU UCC UG C AGGGGAC ACCA
DW3880 AAGA GU AU A GUUUAAU GGU AAAACU G UAAGC UUCAACCUUA UAU U UCUU AGU UCA AA UCU AA G UACUCUU G
DM0260 AGUU AG UU G GCAGAGU GGU UAUGCA C CUCCU UCAUACGGAG CG ACUACAGU GGU UCA AA UCC AC U ACUAACU ACCA
DP5000 CAGA AA AU A GUUUAG UG AGAAUG A UAGCU UUGGGAGCUG UUG G UGUA AGU AUA AA GUCU UG C UUUUCUG A
DC5360 AGCC CU GU G GUGAAUU UACACG U UGAAU UGCAAAUUCA GAG A AGCA GCU UCA AU UC UG C CGGGGCU U
DS4701 AUUU GU GA U UUUCAC GC CGAGAG U GUUUC UUGAGGAGGU AAU G CACU A AUG AA G GG U UACAAGG C
DM4701 GGUA AA GU G GUCUAAU AU U AGGAUA U AGGGC UCAUGCCCCU AAG G CGCC A C GCG UA A U GG C CUUUAUC U
DG5020 UCUA UU A A UAUAACA GUAUAU U UAGUU UUCCAAAUUA AAA G GCCU GUU A G AA GUC AG G UAGUAAA A
DW6160 GACU CC UU A GCAUAGU GGUUU AUUGUA A UUGUC UCCAAAGCAG UUG GU CCAG GGU UCA AC UCC CU G AGGGGUC U
DG9160 GCGU UG GU G GUAUAGU GGUG AGCAUA G CUGCC UUCCAAGCAG UUG A CCCG GGU UCG AU UCC CG G CCAACGC A
DA5000 GUGG AC UU A GUUUAAAA GAU AAAACA A UUGAU UUGCAAUCAG UAA C UCCA AGU UUA AC UCU CG G AGUCCAC A
DN2920 UCCU CA GU A GCUCAGU GGU AGAGCG G UCGGC UGUUAACCGA UUG GU CGUA GGU UCG UA ACC UA C UUGGGGA G
DT3200 GCCC UU UU A ACUCAGU GGU AGAGUA A CGCCA UGGUAAGGCG UAA GU CGUC GGU UCA AA UCC GA U AAAGGGC U
DS6240 GUCA GC AU G GCAGAGU GGUCU AAUGCG U UAGAC UUGAAAUCUA AU UCC UUC G GGAG CGUA GGU UCG AA CCC UA C UGCUGAC G
DP4620 CAGUUUA GU A GUUUAAU GA AGAAUG C UAGCU UUGGGGGUUG GGA G UCUC UG GUU UG GA G UUGGCUG G
DR0220 GUCC CG CU G GUGUAAU GGAU AGCAUA C GAUCC UUCUAAGUUU GCG G UCCU GGU UCG AU CCC AG G GCGGGAU ACCA
DW4700 AAGA AA GU A AUUUAAG UU AAAAUA U UUUGU UUCAAACAUA ACU A UAGG UA GUC AU UA CC U CUUUCUU G
DC4080 GGAG GU GU U GUUUAAA GGUU AAGCUA U UAGAU UGCAGAUCUA CUU AU UAAG AGU UCG AU UCU CU U CAUCUCU U
DE4700 GCUU AA GU A GUUUAG GG AAAACA U AAGAU UUUCAUUCUU AAG U CAGA A A GCA G U UC U CUUAAGU U
DK5080 CCUU AA UU A GCUUAU UU AAAGCU U UAGAC UCUUAAUUUA AAG A AAUU AGC UAA UA CCU AU U AUUAAGG A
DA5100 AAGG UC UU A GCUUAA UU AAAGUA U UUGUU UUGCAUACAG AAG A UGUG GGG UAG UG UCC UG C AGAUCUU A
DQ5160 UAAG GA GU A GUAUAAA GGA AGUACA A AGGGU UUUGAUCUCU UAA G UAUA GGU UCA AU UCC UA U CUCUUUA G
DV4700 UGUA AG AU A AUAUAAA CC AGUAUA A UUCAU UUACACUGAA UGU G UCAG AU AA U GU CU G UCUUACU U
DT5060 GCCC UA GU A GCUCAGC GC C AGAGCG C CGGUC UUGUAAUCCG GAA GU CGGA GGU UAA AA CCC UC C CUAGUGC U
DE4240 GUCC CU UU C GUCCAGU GGUUA AGGACA U CGUCU UUUCAUGUCG AAG A CACG GGU UCC AU UCC CG U AAGGGAU A
DI0260 ACUU CG GU A GCUUAGC GAUCU AAAGCA C UCGGC UGAUAACCGA GAG AU CGGG GGU UUA AA UCC CU C CCGGAGU ACCA
DR4080 GCUC UC UU A GCUUAAU GGUU AAAGCA U AAUAC UUCUAAUAUU AAU AU UCCA UGU UCA AA UCA UG G AGAGAGU A
DM4700 GGUA AA GU A GUCUAAU GA AGGACA G AAGAC CUAUGAUUUU CAA G UGUU A UAA U U AA C CUUUACU U
DG0260 GCGG UU AA G CACACG GGUU GUGUCG C AGGCC UUCCAAGCCU CGC UG AGUAG GGU UCG AU UCC CU C UAGCCGC UCCA
DL4701 CACA AG CU G GCAGAC AU AAUGCA U ACGAU UUAAGCUCGU CUU A UAAG A U CAU AU U CU U GUUUGUG U
DI2922 GCAU CC AU G GCUGAAU GGUU AAAGCG C CCAAC UCAUAAUUGG CGA AU UCGUA GGU UCA AU UCC UA C UGGAUGC A
DR5220 AGAA AG UU A GUCUAA CU AAGACA G CUGGU UUCGACCCAG CAA A UUAU AGA CCC AC CU AU A ACUUUCU U
DT0260 GCUC CU AA A GCAUUGUU GGU GAUGCA G UUGCC UUGUAAGCAU CUG A ACCG GGU UCG AU UCC UA G UGGGAGC ACCA
DR2600 GGGU UU GU A GCUCAGA GGAUU AGAGCA C GUGGC UACGAACCAC GGU GU CGGG GGU UCG AA UCC CU C CUUGCCC A
DC3920 GAUU AC GA U GUAAAU GGU UUACCC U UUGAC UGCAAAUCUU AAG GA UUAG G U UCG AU U C CU A CGUAAUC C
DL4840 UCUA AU AU G GCAGAUU AGUGCA A UAGAU UUAAGCUCUA UAU A UAAA GU AUU UU AC UU U UAUUAGA A
DV9990 GUUU CC GU A GUGUAGU GGUU AUCACG U UCGCC UAACACGCGA AAG GU CCCC GGU UCG AA ACC GG G CGGAAAC A
DQ4070 UGAA UU GU A GACUAAUA GGU AAGUCC C CAAAA UUUGAGUUUG GCU U UA GGUG UGU UCG AA UCA CC C CAAUUCA A
DE5220 GUUC CC GU A GUUGAGAA CAACA A UGGCU UUUCAAGCCG UAG U CCUU GGG GUC UA ACC AA G CGGGAAU A
DC3881 AGGA GU UU G AGCAAAU GGUU UUGCGU U UUGAU UGCAAAUUGA AAU A UAGG GAU UCG AUU UCC CC G GACUCCU C
DS5080 GGAG AA GU G GCACGAUA GG AAUGCA U GCGGC UUGAAACCGU UUG A UAGA GGU UUC UU CC UC U CUUCUCU U
DE4080 GAUC UU AU C GUCUAAU GGUU ACGACA U CAACU UUUCAUGUUG AAA A UGUU GGU UCA AU CCC AA C UAAGAUU A
DE0660 GCUC CG GU G GUGUAGUC CGGCCA AUCAUG C UGGCC UUUCGAGCCA GCG A CUCG GGU UCA AA UCC CG G CCGGAGC A
DW4840 AAGG CU UU A AGUUAA UA AAACUA A UAACC UUCAAAGCUA UAA A UAAA G A AAU UU C UU U AAGCCUU A
DI5160 GGAA GC GU G CCUGAA AGU UAAGGA C CUCCU UGAUAGGGAG GCU UA UAGG GGU UCA AA CCC CC U CACUUCC U
DA4620 GACG GU AU A GUUUAA GUU GAGAUG U GUGCU CUGCGAGCAU UCG G UAGA G GUU UC U UGCCGUU G
DH1540 G GCGG UU GU G GCGAAGU GGUU AACGCA C CAGAU UGUGGCUCUG GCA CU CGUG GGU UCG AU UCC CA U CAAUCGC CCCA
DM4501 GUCG GA AU A GUUUAGUA GGGU AGAACA G CGGGA UCAUAAUUCG CAC A CGGG GGU UCA AA UCC CU C UUCCGAU A
DA6281 GGGC GU GU G GCGUAGUC GGU AGCGCG C UCCCU UAGCAUGGGA GAG GU CUCC GGU UCG AU UCC GG A CUCGUCC A
DP4700 CUAG AU AU A GUUUAGA GC AAAAUA U UGGCU UUGGGAGCUA AAG A CACU U UUA U G AG U UUUCUAG A
DD4700 UUAA AA GU A GUUAAU AU AUAACU U AGAAU UGUCAGUUCU AGA U UCCU U U UAC U A AG G CUUUUUA U
DG4980 CUU UA UU AGUAUAAU UA GUAUA U UUGAU UUCCAAUCAA AAG G GCUU UGU UAAGAA UCA AA G AUGGAGU
Cove/Demos/test100.fa deleted 100644 → 0
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Cove/Demos/test100.slx deleted 100644 → 0
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Cove/Demos/trna1415.slx deleted 100644 → 0
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Cove/Demos/yeast-phe.fa deleted 100644 → 0
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> DF6280
GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA
Cove/Guide.tex deleted 100644 → 0
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>DQ6060 TTA TETRAHYMENA THERM. CY SIN
GGUUCCAUAGUAUAGUGGUUAGUACUGGGGACUUUAAAUCCCUUGACCUG
GGUUCGAAUCCCAGUGGGACCU
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CELF22B7 12618 12738 CELF22B7.tRNA1-LeuCAA 742 + 12618 12738 0 2 38,46, 0,74,
CELF22B7 19479 19561 CELF22B7.tRNA2-SerAGA 816 + 19479 19561 0 1 82, 0,
CELF22B7 23693 23765 CELF22B7.tRNA5-ProCGG 715 - 23693 23765 0 1 72, 0,
CELF22B7 26366 26439 CELF22B7.tRNA3-PheGAA 825 + 26366 26439 0 1 73, 0,
CELF22B7 26919 26992 CELF22B7.tRNA4-PheGAA 825 - 26919 26992 0 1 73, 0,