debian/changelog

-circos-tools (0.22-3) UNRELEASED; urgency=medium
+circos-tools (0.23-1) unstable; urgency=medium
 
+  [ Jelmer Vernooij ]
   * Use secure copyright file specification URI.
   * Trim trailing whitespace.
 
- -- Jelmer Vernooij <jelmer@debian.org>  Sat, 20 Oct 2018 13:40:16 +0000
+  [ Andreas Tille ]
+  * New upstream version
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Remove trailing whitespace in debian/rules
+  * Fix Perl interpreter path
+
+ -- Andreas Tille <tille@debian.org>  Sun, 28 Oct 2018 07:28:13 +0100
 
 circos-tools (0.22-2) unstable; urgency=medium
 

debian/compat

-10
+11

debian/control

@@ -4,10 +4,10 @@ Uploaders: Olivier Sallou <osallou@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10)
-Standards-Version: 4.0.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/circos-tools.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/circos-tools.git
+Build-Depends: debhelper (>= 11~)
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/circos-tools
+Vcs-Git: https://salsa.debian.org/med-team/circos-tools.git
 Homepage: http://circos.ca/
 
 Package: circos-tools

debian/rules

@@ -14,3 +14,6 @@ override_dh_install:
 	-e 's,include data,include /var/lib/circos/data,g' \
 	-e 's,home/martink/bin/perl,usr/bin/perl,g' \
 	-e 's,!/bin/env,!/usr/bin/env,g'
+	for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
+	    sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
+	done

tools/clustal2link/1/#README#

+One of the Circos tools is clustal2link, which parses clustal alignments and generates Circos input files to draw the alignments and coverage.
+
+You'll find this tool in the Circos installation directory under 
+
+# tools/clustal2link
+
+Let's quickly run it on the data and see what the image looks like.
+
+# #parse the alignment files
+# > ./run.sh
+# 
+# > cd circos
+# > circos
\ No newline at end of file

tools/clustal2link/1/README

+One of the Circos tools is clustal2link, which parses clustal alignments and generates Circos input files to draw the alignments and coverage.
+
+You'll find this tool in the Circos installation directory under 
+
+# tools/clustal2link
+
+Let's quickly run it on the data and see what the image looks like.
+
+# > ./run.sh
+# > cd circos
+# > circos
\ No newline at end of file

tools/clustal2link/1/circos/highlight.celA.txt

+hsa8K 581 589
+hsa8K 603 609
+hsa8K 659 663
+hsa8K 781 787
+hsa8K 811 813
+hsa8K 1239 1242
+hsa8K 1257 1258
+hsa8K 1642 1644
+hsa8K 1661 1663
+hsa8K 1812 1813
+hsa8K 1862 1871
+hsa8K 1957 1960
+hsa8K 2068 2071
+hsa8K 2104 2105
+hsa8K 2162 2165
+hsa8K 2184 2193
+hsa8K 2385 2387
+hsa8K 2407 2411
+hsa8K 2417 2421
+hsa8K 2467 2472
+hsa8K 2474 2477
+hsa8K 2545 2551
+hsa8K 2579 2583
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+hsa8K 2623 2627
+hsa8K 2746 2749
+hsa8K 2829 2833
+hsa8K 2841 2841
+hsa8K 2845 2848
+hsa8K 2865 2884
+hsa8K 2885 2891
+hsa8K 2904 2913
+hsa8K 2999 3000
+hsa8K 3018 3025
+hsa8K 3074 3076
+hsa8K 3078 3078
+hsa8K 3166 3176
+hsa8K 3205 3207
+hsa8K 3216 3219
+hsa8K 3222 3223
+hsa8K 3259 3261
+hsa8K 3264 3267
+hsa8K 3284 3294
+hsa8K 3372 3375
+hsa8K 3379 3382
+hsa8K 3388 3392

tools/clustal2link/1/circos/highlight.dmeA.txt

+hsa8K 566 597
+hsa8K 603 643
+hsa8K 651 687
+hsa8K 717 724
+hsa8K 774 787
+hsa8K 811 815
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+hsa8K 2068 2071
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+hsa8K 2211 2222
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+hsa8K 2904 2913
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+hsa8K 3259 3261
+hsa8K 3264 3270
+hsa8K 3278 3307
+hsa8K 3372 3382
+hsa8K 3388 3438

tools/clustal2link/1/circos/highlight.dreA.txt

+hsa8K 717 724
+hsa8K 776 779
+hsa8K 782 784
+hsa8K 811 814
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+hsa8K 3286 3290
+hsa8K 3375 3381
+hsa8K 3388 3389

tools/clustal2link/1/circos/highlight.dreB.txt

+hsa8K 292 628
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+hsa8K 717 724
+hsa8K 769 787
+hsa8K 811 815
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+hsa8K 2712 2794
+hsa8K 2828 2835
+hsa8K 2836 3025
+hsa8K 3026 3215
+hsa8K 3216 4099

tools/clustal2link/1/circos/highlight.ggaA.txt

+hsa8K 980 983
+hsa8K 1053 1055
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+hsa8K 1188 1191
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+hsa8K 2615 2618
+hsa8K 2620 2620
+hsa8K 2626 2629
+hsa8K 2829 2832
+hsa8K 2836 2841

tools/clustal2link/1/circos/highlight.ggaB.txt

+hsa8K 604 612
+hsa8K 656 662
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+hsa8K 717 724
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+hsa8K 2887 2889
+hsa8K 2891 2897
+hsa8K 2964 2967
+hsa8K 2997 3000
+hsa8K 3014 3025

tools/clustal2link/1/circos/highlight.hsaA.txt

+hsa8K 363 381
+hsa8K 385 446
+hsa8K 468 666
+hsa8K 668 726
+hsa8K 769 779
+hsa8K 782 794
+hsa8K 811 862
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+hsa8K 3040 3095
+hsa8K 3166 3178
+hsa8K 3180 3182
+hsa8K 3187 3325
+hsa8K 3361 3557

tools/clustal2link/1/circos/highlight.hsaD.txt

+hsa8K 605 610
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+hsa8K 769 769
+hsa8K 782 787
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+hsa8K 2828 2834
+hsa8K 2836 2839

tools/clustal2link/1/circos/highlight.rnoA.txt

+hsa8K 363 426
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+hsa8K 717 724
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+hsa8K 3166 3178
+hsa8K 3180 3182
+hsa8K 3187 3232
+hsa8K 3234 3325
+hsa8K 3361 3550

tools/clustal2link/1/circos/highlight.rnoB.txt

+hsa8K 597 628
+hsa8K 655 670
+hsa8K 675 681
+hsa8K 717 724
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+hsa8K 811 815
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+hsa8K 1328 1330
+hsa8K 1341 1345
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+hsa8K 1864 1876
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+hsa8K 2219 2221
+hsa8K 2307 2310
+hsa8K 2311 2313
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+hsa8K 2383 2383
+hsa8K 2384 2388
+hsa8K 2405 2409
+hsa8K 2417 2427
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+hsa8K 3026 3095
+hsa8K 3146 3215
+hsa8K 3216 3243
+hsa8K 3257 3325
+hsa8K 3353 3435
+hsa8K 3479 3512
+hsa8K 3550 3624
+hsa8K 3663 3752

tools/clustal2link/1/circos/karyotype.txt

+chr - celA cela 0 263 cela
+chr - dmeA dmea 0 979 dmea
+chr - dreA drea 0 421 drea
+chr - dreB dreb 0 3247 dreb
+chr - ggaA ggaa 0 312 ggaa
+chr - ggaB ggab 0 466 ggab
+chr - hsa8K hsa8k 0 8268 hsa8k
+chr - hsaA hsaa 0 2384 hsaa
+chr - hsaD hsad 0 426 hsad
+chr - rnoA rnoa 0 2352 rnoa
+chr - rnoB rnob 0 1221 rnob

tools/clustal2link/1/circos/links.txt

+celA 1 9 hsa8K 581 589
+celA 10 16 hsa8K 603 609
+celA 17 21 hsa8K 659 663
+celA 22 28 hsa8K 781 787
+celA 29 31 hsa8K 811 813
+celA 32 35 hsa8K 1239 1242
+celA 36 37 hsa8K 1257 1258
+celA 38 40 hsa8K 1642 1644
+celA 41 43 hsa8K 1661 1663
+celA 50 51 hsa8K 1812 1813
+celA 52 61 hsa8K 1862 1871
+celA 62 65 hsa8K 1957 1960
+celA 69 72 hsa8K 2068 2071
+celA 73 74 hsa8K 2104 2105
+celA 75 78 hsa8K 2162 2165
+celA 84 93 hsa8K 2184 2193
+celA 94 96 hsa8K 2385 2387
+celA 97 101 hsa8K 2407 2411
+celA 103 107 hsa8K 2417 2421
+celA 108 115 hsa8K 2467 2472
+celA 116 119 hsa8K 2474 2477
+celA 120 126 hsa8K 2545 2551
+celA 127 131 hsa8K 2579 2583
+celA 132 135 hsa8K 2598 2601
+celA 136 140 hsa8K 2615 2619
+celA 142 146 hsa8K 2623 2627
+celA 147 150 hsa8K 2746 2749
+celA 151 155 hsa8K 2829 2833
+celA 156 156 hsa8K 2841 2841
+celA 158 161 hsa8K 2845 2848
+celA 162 181 hsa8K 2865 2884
+celA 182 188 hsa8K 2885 2891
+celA 189 198 hsa8K 2904 2913
+celA 199 200 hsa8K 2999 3000
+celA 201 208 hsa8K 3018 3025
+celA 209 211 hsa8K 3074 3076
+celA 212 212 hsa8K 3078 3078
+celA 213 223 hsa8K 3166 3176
+celA 224 226 hsa8K 3205 3207
+celA 227 230 hsa8K 3216 3219
+celA 231 232 hsa8K 3222 3223
+celA 233 235 hsa8K 3259 3261
+celA 236 239 hsa8K 3264 3267
+celA 240 250 hsa8K 3284 3294
+celA 251 254 hsa8K 3372 3375
+celA 255 258 hsa8K 3379 3382
+celA 259 263 hsa8K 3388 3392
+dmeA 1 32 hsa8K 566 597
+dmeA 33 73 hsa8K 603 643
+dmeA 75 111 hsa8K 651 687
+dmeA 117 124 hsa8K 717 724
+dmeA 125 138 hsa8K 774 787
+dmeA 139 143 hsa8K 811 815
+dmeA 144 161 hsa8K 977 994
+dmeA 162 166 hsa8K 997 1001
+dmeA 167 177 hsa8K 1009 1019
+dmeA 178 202 hsa8K 1034 1058
+dmeA 203 205 hsa8K 1184 1186
+dmeA 206 210 hsa8K 1188 1192
+dmeA 211 230 hsa8K 1200 1219
+dmeA 231 237 hsa8K 1221 1227
+dmeA 238 241 hsa8K 1239 1242
+dmeA 242 250 hsa8K 1257 1265
+dmeA 251 255 hsa8K 1296 1300
+dmeA 256 261 hsa8K 1327 1332
+dmeA 264 268 hsa8K 1341 1345
+dmeA 269 273 hsa8K 1439 1443
+dmeA 274 282 hsa8K 1523 1531
+dmeA 283 289 hsa8K 1566 1572
+dmeA 292 300 hsa8K 1573 1581
+dmeA 301 307 hsa8K 1608 1614
+dmeA 308 312 hsa8K 1641 1645
+dmeA 313 323 hsa8K 1661 1671
+dmeA 339 342 hsa8K 1718 1721
+dmeA 343 358 hsa8K 1727 1742
+dmeA 359 426 hsa8K 1752 1784
+dmeA 427 430 hsa8K 1810 1813
+dmeA 431 447 hsa8K 1862 1878
+dmeA 448 456 hsa8K 1952 1960
+dmeA 460 466 hsa8K 1961 1967
+dmeA 467 470 hsa8K 1973 1976
+dmeA 471 474 hsa8K 2068 2071
+dmeA 475 480 hsa8K 2104 2109
+dmeA 482 503 hsa8K 2162 2183
+dmeA 510 520 hsa8K 2184 2194
+dmeA 521 532 hsa8K 2211 2222
+dmeA 533 537 hsa8K 2306 2310
+dmeA 544 557 hsa8K 2311 2324
+dmeA 558 573 hsa8K 2368 2383
+dmeA 574 577 hsa8K 2384 2387
+dmeA 578 582 hsa8K 2407 2411
+dmeA 584 597 hsa8K 2417 2430
+dmeA 599 615 hsa8K 2432 2448
+dmeA 616 623 hsa8K 2456 2463
+dmeA 624 632 hsa8K 2466 2472
+dmeA 633 637 hsa8K 2474 2478
+dmeA 638 644 hsa8K 2495 2501
+dmeA 647 685 hsa8K 2537 2575
+dmeA 686 695 hsa8K 2576 2585
+dmeA 696 699 hsa8K 2598 2601
+dmeA 700 705 hsa8K 2615 2620
+dmeA 707 715 hsa8K 2623 2631
+dmeA 716 718 hsa8K 2717 2719
+dmeA 719 728 hsa8K 2740 2749
+dmeA 729 734 hsa8K 2829 2834
+dmeA 736 741 hsa8K 2836 2841
+dmeA 743 751 hsa8K 2845 2853
+dmeA 752 785 hsa8K 2861 2891
+dmeA 786 795 hsa8K 2904 2913
+dmeA 796 822 hsa8K 2999 3025
+dmeA 823 827 hsa8K 3074 3078
+dmeA 828 869 hsa8K 3166 3207
+dmeA 870 877 hsa8K 3216 3223
+dmeA 878 880 hsa8K 3259 3261
+dmeA 881 887 hsa8K 3264 3270
+dmeA 888 917 hsa8K 3278 3307
+dmeA 918 928 hsa8K 3372 3382
+dmeA 929 979 hsa8K 3388 3438
+dreA 1 8 hsa8K 717 724
+dreA 9 12 hsa8K 776 779
+dreA 13 15 hsa8K 782 784
+dreA 16 19 hsa8K 811 814
+dreA 20 22 hsa8K 977 979
+dreA 23 26 hsa8K 981 984
+dreA 27 36 hsa8K 1009 1018
+dreA 37 39 hsa8K 1052 1054
+dreA 40 41 hsa8K 1185 1186
+dreA 42 43 hsa8K 1188 1189
+dreA 44 44 hsa8K 1191 1191
+dreA 45 49 hsa8K 1200 1204
+dreA 50 53 hsa8K 1216 1219
+dreA 54 58 hsa8K 1221 1225
+dreA 59 59 hsa8K 1227 1227
+dreA 60 63 hsa8K 1239 1242
+dreA 64 69 hsa8K 1257 1262
+dreA 70 74 hsa8K 1296 1300
+dreA 75 78 hsa8K 1327 1330
+dreA 80 83 hsa8K 1341 1344
+dreA 84 85 hsa8K 1439 1440
+dreA 86 91 hsa8K 1526 1531
+dreA 92 98 hsa8K 1566 1572
+dreA 101 102 hsa8K 1573 1574
+dreA 103 106 hsa8K 1610 1613
+dreA 107 110 hsa8K 1641 1644
+dreA 111 119 hsa8K 1661 1669
+dreA 130 133 hsa8K 1718 1721
+dreA 134 135 hsa8K 1764 1765
+dreA 136 138 hsa8K 1767 1769
+dreA 140 147 hsa8K 1774 1781
+dreA 148 150 hsa8K 1810 1812
+dreA 151 156 hsa8K 1866 1871
+dreA 157 165 hsa8K 1952 1960
+dreA 167 173 hsa8K 1961 1967
+dreA 174 175 hsa8K 1975 1976
+dreA 176 179 hsa8K 2068 2071
+dreA 180 181 hsa8K 2104 2105
+dreA 182 184 hsa8K 2162 2164
+dreA 187 196 hsa8K 2184 2193
+dreA 197 200 hsa8K 2306 2309
+dreA 203 205 hsa8K 2311 2313
+dreA 206 219 hsa8K 2370 2383
+dreA 220 222 hsa8K 2385 2387
+dreA 223 228 hsa8K 2406 2411
+dreA 230 238 hsa8K 2417 2425
+dreA 239 244 hsa8K 2458 2463
+dreA 245 251 hsa8K 2465 2469
+dreA 252 256 hsa8K 2474 2478
+dreA 257 257 hsa8K 2495 2495
+dreA 258 270 hsa8K 2546 2558
+dreA 271 271 hsa8K 2573 2573
+dreA 272 275 hsa8K 2580 2583
+dreA 281 282 hsa8K 2600 2601
+dreA 283 287 hsa8K 2615 2619
+dreA 288 293 hsa8K 2624 2629
+dreA 294 294 hsa8K 2712 2712
+dreA 295 303 hsa8K 2741 2749
+dreA 304 307 hsa8K 2829 2832
+dreA 308 312 hsa8K 2837 2841
+dreA 313 319 hsa8K 2845 2851
+dreA 320 321 hsa8K 2862 2863
+dreA 322 328 hsa8K 2872 2878
+dreA 329 333 hsa8K 2885 2889
+dreA 334 340 hsa8K 2904 2910
+dreA 341 349 hsa8K 3016 3024
+dreA 350 356 hsa8K 3073 3079
+dreA 357 369 hsa8K 3166 3178
+dreA 370 372 hsa8K 3180 3182
+dreA 373 374 hsa8K 3187 3188
+dreA 375 382 hsa8K 3200 3207
+dreA 383 388 hsa8K 3216 3221
+dreA 389 392 hsa8K 3258 3261
+dreA 393 400 hsa8K 3264 3271
+dreA 401 407 hsa8K 3277 3283
+dreA 408 412 hsa8K 3286 3290
+dreA 413 419 hsa8K 3375 3381
+dreA 420 421 hsa8K 3388 3389
+dreB 1 337 hsa8K 292 628
+dreB 338 391 hsa8K 655 708
+dreB 392 399 hsa8K 717 724
+dreB 400 418 hsa8K 769 787
+dreB 419 423 hsa8K 811 815
+dreB 424 431 hsa8K 928 935
+dreB 432 438 hsa8K 978 984
+dreB 439 451 hsa8K 986 998
+dreB 452 460 hsa8K 1011 1019
+dreB 461 489 hsa8K 1048 1076
+dreB 490 498 hsa8K 1178 1186
+dreB 499 584 hsa8K 1188 1238
+dreB 601 652 hsa8K 1239 1290
+dreB 653 657 hsa8K 1296 1300
+dreB 658 675 hsa8K 1306 1323
+dreB 676 678 hsa8K 1328 1330
+dreB 679 683 hsa8K 1341 1345
+dreB 684 693 hsa8K 1437 1446
+dreB 694 717 hsa8K 1524 1547
+dreB 718 777 hsa8K 1564 1603
+dreB 787 857 hsa8K 1604 1645
+dreB 858 973 hsa8K 1660 1731
+dreB 974 992 hsa8K 1756 1773
+dreB 998 1005 hsa8K 1774 1781
+dreB 1006 1010 hsa8K 1808 1812
+dreB 1011 1034 hsa8K 1864 1887
+dreB 1035 1067 hsa8K 1951 1967
+dreB 1068 1097 hsa8K 1973 2002
+dreB 1098 1103 hsa8K 2066 2071
+dreB 1104 1289 hsa8K 2103 2196
+dreB 1290 1330 hsa8K 2219 2259
+dreB 1331 1399 hsa8K 2307 2324
+dreB 1400 1400 hsa8K 2325 2325
+dreB 1401 1415 hsa8K 2366 2380
+dreB 1416 1416 hsa8K 2383 2383
+dreB 1417 1421 hsa8K 2384 2388
+dreB 1422 1450 hsa8K 2405 2431
+dreB 1451 1467 hsa8K 2432 2448
+dreB 1468 1478 hsa8K 2458 2468
+dreB 1479 1482 hsa8K 2470 2473
+dreB 1483 1486 hsa8K 2474 2477
+dreB 1487 1631 hsa8K 2495 2588
+dreB 1632 1636 hsa8K 2597 2601
+dreB 1637 1689 hsa8K 2615 2641
+dreB 1690 1772 hsa8K 2712 2794
+dreB 1773 1780 hsa8K 2828 2835
+dreB 1870 2173 hsa8K 2836 3025
+dreB 2174 2363 hsa8K 3026 3215
+dreB 2364 3247 hsa8K 3216 4099
+ggaA 1 4 hsa8K 980 983
+ggaA 5 7 hsa8K 1053 1055
+ggaA 8 13 hsa8K 1181 1186
+ggaA 14 17 hsa8K 1188 1191
+ggaA 18 24 hsa8K 1213 1219
+ggaA 25 31 hsa8K 1221 1227
+ggaA 32 36 hsa8K 1239 1243
+ggaA 37 42 hsa8K 1257 1262
+ggaA 43 46 hsa8K 1297 1300
+ggaA 47 49 hsa8K 1306 1308
+ggaA 50 52 hsa8K 1328 1330
+ggaA 53 57 hsa8K 1341 1345
+ggaA 58 59 hsa8K 1437 1438
+ggaA 60 62 hsa8K 1440 1442
+ggaA 63 70 hsa8K 1524 1531
+ggaA 71 78 hsa8K 1565 1572
+ggaA 80 82 hsa8K 1573 1575
+ggaA 83 91 hsa8K 1608 1616
+ggaA 92 96 hsa8K 1641 1645
+ggaA 97 104 hsa8K 1660 1667
+ggaA 105 107 hsa8K 1718 1720
+ggaA 108 111 hsa8K 1759 1762
+ggaA 112 121 hsa8K 1763 1772
+ggaA 124 131 hsa8K 1774 1781
+ggaA 132 132 hsa8K 1808 1808
+ggaA 133 135 hsa8K 1810 1812
+ggaA 136 150 hsa8K 1864 1878
+ggaA 151 156 hsa8K 1952 1957
+ggaA 157 157 hsa8K 1960 1960
+ggaA 161 168 hsa8K 1961 1968
+ggaA 169 172 hsa8K 1973 1976
+ggaA 173 182 hsa8K 2067 2076
+ggaA 183 185 hsa8K 2103 2105
+ggaA 186 194 hsa8K 2162 2170
+ggaA 195 203 hsa8K 2184 2192
+ggaA 204 206 hsa8K 2219 2221
+ggaA 207 210 hsa8K 2307 2310
+ggaA 212 216 hsa8K 2311 2315
+ggaA 217 228 hsa8K 2369 2380
+ggaA 229 229 hsa8K 2383 2383
+ggaA 230 234 hsa8K 2384 2388
+ggaA 235 239 hsa8K 2405 2409
+ggaA 241 251 hsa8K 2417 2427
+ggaA 252 256 hsa8K 2436 2440
+ggaA 257 265 hsa8K 2460 2468
+ggaA 267 271 hsa8K 2469 2473
+ggaA 272 275 hsa8K 2474 2477
+ggaA 276 278 hsa8K 2495 2497
+ggaA 279 287 hsa8K 2546 2554
+ggaA 288 288 hsa8K 2583 2583
+ggaA 289 290 hsa8K 2600 2601
+ggaA 291 294 hsa8K 2615 2618
+ggaA 295 295 hsa8K 2620 2620
+ggaA 296 299 hsa8K 2626 2629
+ggaA 300 303 hsa8K 2829 2832
+ggaA 304 309 hsa8K 2836 2841
+ggaB 1 9 hsa8K 604 612
+ggaB 10 16 hsa8K 656 662
+ggaB 17 19 hsa8K 664 666
+ggaB 20 26 hsa8K 676 682
+ggaB 27 34 hsa8K 717 724
+ggaB 35 39 hsa8K 769 773
+ggaB 40 42 hsa8K 784 786
+ggaB 43 45 hsa8K 813 815
+ggaB 46 49 hsa8K 928 931
+ggaB 50 71 hsa8K 978 999
+ggaB 72 79 hsa8K 1011 1018
+ggaB 80 91 hsa8K 1047 1058
+ggaB 92 98 hsa8K 1185 1191
+ggaB 99 108 hsa8K 1211 1220
+ggaB 109 110 hsa8K 1221 1222
+ggaB 111 112 hsa8K 1225 1226
+ggaB 113 118 hsa8K 1239 1244
+ggaB 119 122 hsa8K 1260 1263
+ggaB 123 127 hsa8K 1296 1300
+ggaB 128 132 hsa8K 1304 1308
+ggaB 133 135 hsa8K 1328 1330
+ggaB 136 140 hsa8K 1341 1345
+ggaB 141 146 hsa8K 1437 1442
+ggaB 147 155 hsa8K 1525 1533
+ggaB 156 162 hsa8K 1566 1572
+ggaB 163 165 hsa8K 1573 1575
+ggaB 166 169 hsa8K 1609 1612
+ggaB 170 175 hsa8K 1640 1645
+ggaB 176 182 hsa8K 1659 1665
+ggaB 183 187 hsa8K 1718 1722
+ggaB 188 189 hsa8K 1761 1762
+ggaB 190 190 hsa8K 1763 1763
+ggaB 191 195 hsa8K 1768 1772
+ggaB 196 200 hsa8K 1776 1780
+ggaB 201 205 hsa8K 1808 1812
+ggaB 206 211 hsa8K 1864 1869
+ggaB 212 221 hsa8K 1951 1960
+ggaB 222 227 hsa8K 1961 1966
+ggaB 228 232 hsa8K 1972 1976
+ggaB 233 239 hsa8K 2066 2072
+ggaB 240 242 hsa8K 2103 2105
+ggaB 243 248 hsa8K 2163 2168
+ggaB 249 254 hsa8K 2187 2192
+ggaB 255 257 hsa8K 2219 2221
+ggaB 258 260 hsa8K 2308 2310
+ggaB 261 263 hsa8K 2311 2313
+ggaB 264 277 hsa8K 2366 2379
+ggaB 278 278 hsa8K 2383 2383
+ggaB 279 282 hsa8K 2384 2387
+ggaB 283 284 hsa8K 2406 2407
+ggaB 285 292 hsa8K 2417 2424
+ggaB 293 296 hsa8K 2435 2438
+ggaB 297 304 hsa8K 2458 2465
+ggaB 305 305 hsa8K 2468 2468
+ggaB 306 310 hsa8K 2469 2473
+ggaB 311 314 hsa8K 2474 2477
+ggaB 315 317 hsa8K 2484 2486
+ggaB 318 322 hsa8K 2495 2499
+ggaB 323 331 hsa8K 2502 2510
+ggaB 332 341 hsa8K 2547 2556
+ggaB 342 346 hsa8K 2579 2583
+ggaB 347 351 hsa8K 2597 2601
+ggaB 352 359 hsa8K 2615 2622
+ggaB 360 372 hsa8K 2623 2635
+ggaB 373 380 hsa8K 2712 2719
+ggaB 381 389 hsa8K 2743 2751
+ggaB 390 394 hsa8K 2785 2789
+ggaB 395 402 hsa8K 2828 2835
+ggaB 403 408 hsa8K 2836 2841
+ggaB 409 420 hsa8K 2842 2853
+ggaB 421 425 hsa8K 2863 2867
+ggaB 426 436 hsa8K 2873 2883
+ggaB 437 439 hsa8K 2887 2889
+ggaB 440 446 hsa8K 2891 2897
+ggaB 447 450 hsa8K 2964 2967
+ggaB 451 454 hsa8K 2997 3000
+ggaB 455 466 hsa8K 3014 3025
+hsaA 1 19 hsa8K 363 381
+hsaA 20 81 hsa8K 385 446
+hsaA 82 282 hsa8K 468 666
+hsaA 283 362 hsa8K 668 726
+hsaA 363 373 hsa8K 769 779
+hsaA 374 386 hsa8K 782 794
+hsaA 387 438 hsa8K 811 862
+hsaA 439 477 hsa8K 941 979
+hsaA 478 498 hsa8K 981 1001
+hsaA 499 595 hsa8K 1009 1059
+hsaA 596 601 hsa8K 1181 1186
+hsaA 602 605 hsa8K 1188 1191
+hsaA 606 626 hsa8K 1200 1220
+hsaA 632 636 hsa8K 1221 1225
+hsaA 637 676 hsa8K 1227 1242
+hsaA 677 685 hsa8K 1257 1265
+hsaA 686 691 hsa8K 1296 1301
+hsaA 692 720 hsa8K 1322 1344
+hsaA 721 736 hsa8K 1439 1454
+hsaA 737 745 hsa8K 1523 1531
+hsaA 746 752 hsa8K 1566 1572
+hsaA 755 803 hsa8K 1573 1605
+hsaA 804 815 hsa8K 1607 1618
+hsaA 816 819 hsa8K 1641 1644
+hsaA 820 830 hsa8K 1661 1671
+hsaA 848 872 hsa8K 1718 1742
+hsaA 873 887 hsa8K 1752 1765
+hsaA 888 970 hsa8K 1767 1815
+hsaA 971 988 hsa8K 1862 1879
+hsaA 989 1026 hsa8K 1946 1967
+hsaA 1027 1030 hsa8K 1973 1976
+hsaA 1031 1034 hsa8K 2068 2071
+hsaA 1035 1036 hsa8K 2104 2105
+hsaA 1037 1058 hsa8K 2162 2183
+hsaA 1065 1085 hsa8K 2184 2204
+hsaA 1086 1097 hsa8K 2211 2222
+hsaA 1098 1101 hsa8K 2306 2309
+hsaA 1104 1117 hsa8K 2311 2324
+hsaA 1134 1206 hsa8K 2325 2389
+hsaA 1207 1226 hsa8K 2392 2411
+hsaA 1228 1314 hsa8K 2417 2463
+hsaA 1315 1342 hsa8K 2465 2478
+hsaA 1343 1383 hsa8K 2495 2530
+hsaA 1396 1432 hsa8K 2537 2573
+hsaA 1433 1449 hsa8K 2580 2596
+hsaA 1614 1618 hsa8K 2597 2601
+hsaA 1619 1625 hsa8K 2615 2621
+hsaA 1627 1633 hsa8K 2623 2629
+hsaA 1634 1641 hsa8K 2712 2719
+hsaA 1642 1651 hsa8K 2740 2749
+hsaA 1652 1658 hsa8K 2829 2835
+hsaA 1769 1774 hsa8K 2836 2841
+hsaA 1775 1781 hsa8K 2845 2851
+hsaA 1782 1804 hsa8K 2862 2884
+hsaA 1806 1876 hsa8K 2885 2955
+hsaA 1888 1941 hsa8K 2956 3009
+hsaA 1942 1971 hsa8K 3012 3038
+hsaA 1972 2027 hsa8K 3040 3095
+hsaA 2028 2040 hsa8K 3166 3178
+hsaA 2041 2043 hsa8K 3180 3182
+hsaA 2044 2187 hsa8K 3187 3325
+hsaA 2188 2384 hsa8K 3361 3557
+hsaD 1 6 hsa8K 605 610
+hsaD 7 13 hsa8K 655 661
+hsaD 14 20 hsa8K 675 681
+hsaD 21 28 hsa8K 717 724
+hsaD 29 29 hsa8K 769 769
+hsaD 30 35 hsa8K 782 787
+hsaD 36 40 hsa8K 811 815
+hsaD 41 41 hsa8K 928 928
+hsaD 42 46 hsa8K 980 984
+hsaD 47 59 hsa8K 986 998
+hsaD 60 67 hsa8K 1011 1018
+hsaD 68 75 hsa8K 1048 1055
+hsaD 76 80 hsa8K 1182 1186
+hsaD 81 83 hsa8K 1188 1190
+hsaD 84 90 hsa8K 1212 1218
+hsaD 93 99 hsa8K 1221 1227
+hsaD 109 113 hsa8K 1239 1243
+hsaD 114 119 hsa8K 1257 1262
+hsaD 120 124 hsa8K 1296 1300
+hsaD 125 125 hsa8K 1306 1306
+hsaD 126 127 hsa8K 1329 1330
+hsaD 128 132 hsa8K 1341 1345
+hsaD 133 138 hsa8K 1437 1442
+hsaD 139 146 hsa8K 1524 1531
+hsaD 147 155 hsa8K 1564 1572
+hsaD 157 159 hsa8K 1573 1575
+hsaD 160 165 hsa8K 1609 1614
+hsaD 166 171 hsa8K 1640 1645
+hsaD 172 179 hsa8K 1660 1667
+hsaD 189 191 hsa8K 1718 1720
+hsaD 192 196 hsa8K 1756 1760
+hsaD 197 206 hsa8K 1763 1772
+hsaD 208 215 hsa8K 1774 1781
+hsaD 216 220 hsa8K 1808 1812
+hsaD 221 230 hsa8K 1866 1875
+hsaD 231 239 hsa8K 1952 1960
+hsaD 243 249 hsa8K 1961 1967
+hsaD 250 252 hsa8K 1973 1975
+hsaD 253 255 hsa8K 2069 2071
+hsaD 256 258 hsa8K 2103 2105
+hsaD 261 268 hsa8K 2162 2169
+hsaD 271 279 hsa8K 2184 2192
+hsaD 280 282 hsa8K 2219 2221
+hsaD 283 286 hsa8K 2307 2310
+hsaD 292 296 hsa8K 2311 2315
+hsaD 297 308 hsa8K 2369 2380
+hsaD 309 309 hsa8K 2383 2383
+hsaD 310 312 hsa8K 2384 2386
+hsaD 313 317 hsa8K 2405 2409
+hsaD 318 325 hsa8K 2417 2424
+hsaD 326 328 hsa8K 2436 2438
+hsaD 329 337 hsa8K 2460 2468
+hsaD 338 340 hsa8K 2470 2472
+hsaD 341 342 hsa8K 2476 2477
+hsaD 343 345 hsa8K 2495 2497
+hsaD 346 352 hsa8K 2504 2510
+hsaD 353 360 hsa8K 2547 2554
+hsaD 361 362 hsa8K 2560 2561
+hsaD 363 370 hsa8K 2577 2584
+hsaD 371 372 hsa8K 2600 2601
+hsaD 373 379 hsa8K 2615 2621
+hsaD 380 384 hsa8K 2625 2629
+hsaD 385 389 hsa8K 2715 2719
+hsaD 390 404 hsa8K 2737 2751
+hsaD 405 411 hsa8K 2828 2834
+hsaD 423 426 hsa8K 2836 2839
+rnoA 1 64 hsa8K 363 426
+rnoA 65 142 hsa8K 428 505
+rnoA 143 304 hsa8K 507 666
+rnoA 305 339 hsa8K 668 702
+rnoA 346 353 hsa8K 717 724
+rnoA 354 364 hsa8K 769 779
+rnoA 365 377 hsa8K 782 794
+rnoA 378 430 hsa8K 811 863
+rnoA 431 482 hsa8K 928 979
+rnoA 483 496 hsa8K 981 994
+rnoA 497 502 hsa8K 996 1001
+rnoA 503 524 hsa8K 1009 1030
+rnoA 570 597 hsa8K 1032 1059
+rnoA 598 603 hsa8K 1181 1186
+rnoA 604 607 hsa8K 1188 1191
+rnoA 608 628 hsa8K 1200 1220
+rnoA 635 652 hsa8K 1221 1238
+rnoA 675 680 hsa8K 1239 1244
+rnoA 681 689 hsa8K 1257 1265
+rnoA 690 695 hsa8K 1296 1301
+rnoA 696 725 hsa8K 1322 1345
+rnoA 726 741 hsa8K 1439 1454
+rnoA 742 750 hsa8K 1523 1531
+rnoA 751 757 hsa8K 1566 1572
+rnoA 760 821 hsa8K 1573 1618
+rnoA 822 826 hsa8K 1641 1645
+rnoA 827 835 hsa8K 1661 1669
+rnoA 853 877 hsa8K 1718 1742
+rnoA 878 892 hsa8K 1752 1765
+rnoA 893 975 hsa8K 1767 1815
+rnoA 976 992 hsa8K 1862 1878
+rnoA 993 1030 hsa8K 1946 1967
+rnoA 1031 1034 hsa8K 1973 1976
+rnoA 1035 1038 hsa8K 2068 2071
+rnoA 1039 1040 hsa8K 2104 2105
+rnoA 1041 1062 hsa8K 2162 2183
+rnoA 1068 1088 hsa8K 2184 2204
+rnoA 1089 1100 hsa8K 2211 2222
+rnoA 1101 1104 hsa8K 2306 2309
+rnoA 1107 1163 hsa8K 2311 2350
+rnoA 1164 1203 hsa8K 2359 2390
+rnoA 1204 1223 hsa8K 2392 2411
+rnoA 1225 1227 hsa8K 2417 2419
+rnoA 1228 1338 hsa8K 2422 2478
+rnoA 1339 1345 hsa8K 2495 2501
+rnoA 1348 1375 hsa8K 2503 2530
+rnoA 1385 1422 hsa8K 2538 2575
+rnoA 1423 1443 hsa8K 2576 2596
+rnoA 1597 1601 hsa8K 2597 2601
+rnoA 1602 1606 hsa8K 2615 2619
+rnoA 1607 1618 hsa8K 2623 2634
+rnoA 1619 1626 hsa8K 2712 2719
+rnoA 1627 1636 hsa8K 2740 2749
+rnoA 1637 1643 hsa8K 2829 2835
+rnoA 1757 1762 hsa8K 2836 2841
+rnoA 1763 1768 hsa8K 2845 2850
+rnoA 1769 1865 hsa8K 2862 2955
+rnoA 1876 1986 hsa8K 2956 3063
+rnoA 1987 2003 hsa8K 3073 3089
+rnoA 2004 2016 hsa8K 3166 3178
+rnoA 2017 2019 hsa8K 3180 3182
+rnoA 2020 2070 hsa8K 3187 3232
+rnoA 2071 2162 hsa8K 3234 3325
+rnoA 2163 2352 hsa8K 3361 3550
+rnoB 1 32 hsa8K 597 628
+rnoB 33 48 hsa8K 655 670
+rnoB 49 55 hsa8K 675 681
+rnoB 56 63 hsa8K 717 724
+rnoB 64 83 hsa8K 769 788
+rnoB 84 88 hsa8K 811 815
+rnoB 89 96 hsa8K 928 935
+rnoB 97 117 hsa8K 978 998
+rnoB 118 125 hsa8K 1011 1018
+rnoB 126 134 hsa8K 1048 1056
+rnoB 135 143 hsa8K 1178 1186
+rnoB 144 147 hsa8K 1188 1191
+rnoB 148 154 hsa8K 1213 1219
+rnoB 155 161 hsa8K 1221 1227
+rnoB 162 166 hsa8K 1239 1243
+rnoB 167 172 hsa8K 1257 1262
+rnoB 173 176 hsa8K 1297 1300
+rnoB 177 179 hsa8K 1306 1308
+rnoB 180 182 hsa8K 1328 1330
+rnoB 183 187 hsa8K 1341 1345
+rnoB 188 189 hsa8K 1437 1438
+rnoB 190 192 hsa8K 1440 1442
+rnoB 193 200 hsa8K 1524 1531
+rnoB 201 208 hsa8K 1565 1572
+rnoB 210 212 hsa8K 1573 1575
+rnoB 213 221 hsa8K 1608 1616
+rnoB 222 226 hsa8K 1641 1645
+rnoB 227 234 hsa8K 1660 1667
+rnoB 235 237 hsa8K 1718 1720
+rnoB 238 241 hsa8K 1759 1762
+rnoB 242 251 hsa8K 1763 1772
+rnoB 254 261 hsa8K 1774 1781
+rnoB 262 266 hsa8K 1808 1812
+rnoB 267 279 hsa8K 1864 1876
+rnoB 280 285 hsa8K 1952 1957
+rnoB 286 286 hsa8K 1960 1960
+rnoB 290 297 hsa8K 1961 1968
+rnoB 298 301 hsa8K 1973 1976
+rnoB 302 311 hsa8K 2067 2076
+rnoB 312 318 hsa8K 2103 2109
+rnoB 321 329 hsa8K 2162 2170
+rnoB 330 338 hsa8K 2184 2192
+rnoB 339 341 hsa8K 2219 2221
+rnoB 342 345 hsa8K 2307 2310
+rnoB 347 349 hsa8K 2311 2313
+rnoB 350 361 hsa8K 2369 2380
+rnoB 362 362 hsa8K 2383 2383
+rnoB 363 367 hsa8K 2384 2388
+rnoB 368 372 hsa8K 2405 2409
+rnoB 374 384 hsa8K 2417 2427
+rnoB 385 389 hsa8K 2436 2440
+rnoB 390 405 hsa8K 2460 2473
+rnoB 406 409 hsa8K 2474 2477
+rnoB 410 412 hsa8K 2495 2497
+rnoB 413 428 hsa8K 2546 2561
+rnoB 429 435 hsa8K 2577 2583
+rnoB 436 437 hsa8K 2600 2601
+rnoB 438 443 hsa8K 2615 2620
+rnoB 444 449 hsa8K 2626 2631
+rnoB 450 454 hsa8K 2715 2719
+rnoB 455 468 hsa8K 2738 2751
+rnoB 469 475 hsa8K 2829 2835
+rnoB 507 632 hsa8K 2836 2912
+rnoB 633 702 hsa8K 2956 3025
+rnoB 703 772 hsa8K 3026 3095
+rnoB 773 842 hsa8K 3146 3215
+rnoB 843 870 hsa8K 3216 3243
+rnoB 871 939 hsa8K 3257 3325
+rnoB 940 1022 hsa8K 3353 3435
+rnoB 1023 1056 hsa8K 3479 3512
+rnoB 1057 1131 hsa8K 3550 3624
+rnoB 1132 1221 hsa8K 3663 3752

tools/clustal2link/1/data/highlight.celA.txt

+hsa8K 581 589
+hsa8K 603 609
+hsa8K 659 663
+hsa8K 781 787
+hsa8K 811 813
+hsa8K 1239 1242
+hsa8K 1257 1258
+hsa8K 1642 1644
+hsa8K 1661 1663
+hsa8K 1812 1813
+hsa8K 1862 1871
+hsa8K 1957 1960
+hsa8K 2068 2071
+hsa8K 2104 2105
+hsa8K 2162 2165
+hsa8K 2184 2193
+hsa8K 2385 2387
+hsa8K 2407 2411
+hsa8K 2417 2421
+hsa8K 2467 2472
+hsa8K 2474 2477
+hsa8K 2545 2551
+hsa8K 2579 2583
+hsa8K 2598 2601
+hsa8K 2615 2619
+hsa8K 2623 2627
+hsa8K 2746 2749
+hsa8K 2829 2833
+hsa8K 2841 2841
+hsa8K 2845 2848
+hsa8K 2865 2884
+hsa8K 2885 2891
+hsa8K 2904 2913
+hsa8K 2999 3000
+hsa8K 3018 3025
+hsa8K 3074 3076
+hsa8K 3078 3078
+hsa8K 3166 3176
+hsa8K 3205 3207
+hsa8K 3216 3219
+hsa8K 3222 3223
+hsa8K 3259 3261
+hsa8K 3264 3267
+hsa8K 3284 3294
+hsa8K 3372 3375
+hsa8K 3379 3382
+hsa8K 3388 3392

tools/clustal2link/1/data/highlight.dmeA.txt

+hsa8K 566 597
+hsa8K 603 643
+hsa8K 651 687
+hsa8K 717 724
+hsa8K 774 787
+hsa8K 811 815
+hsa8K 977 994
+hsa8K 997 1001
+hsa8K 1009 1019
+hsa8K 1034 1058
+hsa8K 1184 1186
+hsa8K 1188 1192
+hsa8K 1200 1219
+hsa8K 1221 1227
+hsa8K 1239 1242
+hsa8K 1257 1265
+hsa8K 1296 1300
+hsa8K 1327 1332
+hsa8K 1341 1345
+hsa8K 1439 1443
+hsa8K 1523 1531
+hsa8K 1566 1572
+hsa8K 1573 1581
+hsa8K 1608 1614
+hsa8K 1641 1645
+hsa8K 1661 1671
+hsa8K 1718 1721
+hsa8K 1727 1742
+hsa8K 1752 1784
+hsa8K 1810 1813
+hsa8K 1862 1878
+hsa8K 1952 1960
+hsa8K 1961 1967
+hsa8K 1973 1976
+hsa8K 2068 2071
+hsa8K 2104 2109
+hsa8K 2162 2183
+hsa8K 2184 2194
+hsa8K 2211 2222
+hsa8K 2306 2310
+hsa8K 2311 2324
+hsa8K 2368 2383
+hsa8K 2384 2387
+hsa8K 2407 2411
+hsa8K 2417 2430
+hsa8K 2432 2448
+hsa8K 2456 2463
+hsa8K 2466 2472
+hsa8K 2474 2478
+hsa8K 2495 2501
+hsa8K 2537 2575
+hsa8K 2576 2585
+hsa8K 2598 2601
+hsa8K 2615 2620
+hsa8K 2623 2631
+hsa8K 2717 2719
+hsa8K 2740 2749
+hsa8K 2829 2834
+hsa8K 2836 2841
+hsa8K 2845 2853
+hsa8K 2861 2891
+hsa8K 2904 2913
+hsa8K 2999 3025
+hsa8K 3074 3078
+hsa8K 3166 3207
+hsa8K 3216 3223
+hsa8K 3259 3261
+hsa8K 3264 3270
+hsa8K 3278 3307
+hsa8K 3372 3382
+hsa8K 3388 3438