Multiple sequence alignment - TraesCS3B01G204300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G204300 chr3B 100.000 2183 0 0 1 2183 238497344 238495162 0.000000e+00 4032
1 TraesCS3B01G204300 chr3A 88.404 1009 63 19 372 1372 191838122 191837160 0.000000e+00 1166
2 TraesCS3B01G204300 chr3A 89.982 549 34 12 1650 2183 191836861 191836319 0.000000e+00 689
3 TraesCS3B01G204300 chr3A 87.885 454 24 6 10 433 191838575 191838123 2.500000e-139 505
4 TraesCS3B01G204300 chr3D 90.467 535 36 8 1658 2183 161928191 161927663 0.000000e+00 691
5 TraesCS3B01G204300 chr3D 92.517 441 23 3 873 1313 161929104 161928674 6.620000e-175 623
6 TraesCS3B01G204300 chr3D 79.464 672 74 34 9 647 161929968 161929328 3.350000e-113 418
7 TraesCS3B01G204300 chr5D 95.500 200 9 0 1453 1652 495422930 495422731 9.720000e-84 320
8 TraesCS3B01G204300 chr1B 94.686 207 10 1 1452 1658 14825759 14825554 9.720000e-84 320
9 TraesCS3B01G204300 chr1B 92.417 211 16 0 1450 1660 161543701 161543491 3.520000e-78 302
10 TraesCS3B01G204300 chr7D 94.231 208 10 2 1454 1660 396856160 396855954 1.260000e-82 316
11 TraesCS3B01G204300 chr2D 95.025 201 10 0 1452 1652 374124374 374124174 1.260000e-82 316
12 TraesCS3B01G204300 chr4A 94.527 201 11 0 1452 1652 729882761 729882961 5.850000e-81 311
13 TraesCS3B01G204300 chr2B 94.118 204 12 0 1449 1652 171459765 171459968 5.850000e-81 311
14 TraesCS3B01G204300 chr6B 94.527 201 10 1 1452 1652 571739929 571740128 2.100000e-80 309
15 TraesCS3B01G204300 chr6D 93.659 205 12 1 1454 1658 269564369 269564572 2.720000e-79 305


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G204300 chr3B 238495162 238497344 2182 True 4032.000000 4032 100.000000 1 2183 1 chr3B.!!$R1 2182
1 TraesCS3B01G204300 chr3A 191836319 191838575 2256 True 786.666667 1166 88.757000 10 2183 3 chr3A.!!$R1 2173
2 TraesCS3B01G204300 chr3D 161927663 161929968 2305 True 577.333333 691 87.482667 9 2183 3 chr3D.!!$R1 2174

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
370 405 0.035317 GATGGCACCTGCGATGGATA 59.965 55.0 0.0 0.0 39.59 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 2313 0.032813 CCCCAAGCATCTCCCATTGT 60.033 55.0 0.0 0.0 0.0 2.71 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 0.108804 GAACCGTGGATCTTGAGCGA 60.109 55.000 0.00 0.00 0.00 4.93
63 64 1.212616 CCGTGGATCTTGAGCGAATC 58.787 55.000 0.00 0.00 0.00 2.52
122 123 1.302192 CCCCGCTTTTCCGTTCAGA 60.302 57.895 0.00 0.00 0.00 3.27
140 141 3.118454 GCGCAGTGGCTTCGCTTA 61.118 61.111 0.30 0.00 44.79 3.09
148 149 2.017049 GTGGCTTCGCTTATGTGGATT 58.983 47.619 0.00 0.00 0.00 3.01
163 164 2.484264 GTGGATTGCTCAGTGTTGTACC 59.516 50.000 0.00 0.00 0.00 3.34
254 258 3.844943 GCGCCAGTATTTTTACGATCTGC 60.845 47.826 0.00 0.00 0.00 4.26
278 282 1.675714 CCTCGAGTGCAACAGCCATAA 60.676 52.381 12.31 0.00 41.43 1.90
307 315 6.808212 CCATTTGGTCATGTTGTAATGAACTC 59.192 38.462 4.06 0.00 43.45 3.01
370 405 0.035317 GATGGCACCTGCGATGGATA 59.965 55.000 0.00 0.00 39.59 2.59
431 528 6.465439 TCGTTCCATGTATCTTATGTCACT 57.535 37.500 0.00 0.00 0.00 3.41
432 529 6.504398 TCGTTCCATGTATCTTATGTCACTC 58.496 40.000 0.00 0.00 0.00 3.51
433 530 6.096282 TCGTTCCATGTATCTTATGTCACTCA 59.904 38.462 0.00 0.00 0.00 3.41
434 531 6.199154 CGTTCCATGTATCTTATGTCACTCAC 59.801 42.308 0.00 0.00 0.00 3.51
440 541 8.624776 CATGTATCTTATGTCACTCACTCACTA 58.375 37.037 0.00 0.00 0.00 2.74
455 556 2.681848 CTCACTAGGCATGCCTCTTTTG 59.318 50.000 41.83 30.00 44.43 2.44
478 579 5.365605 TGTGAGGTCCCTACATAATAACCAG 59.634 44.000 0.00 0.00 0.00 4.00
576 695 6.045318 TCGCTTCTTCAATTATCTCTGAAGG 58.955 40.000 10.91 0.00 45.67 3.46
603 723 4.164822 AGTACATTGCTTTGACACATGC 57.835 40.909 0.00 0.00 0.00 4.06
653 773 4.682778 TTATTTCTACATCCCACCGAGG 57.317 45.455 0.00 0.00 37.03 4.63
722 1011 4.953940 AAACCATGTACAATGCAAGGTT 57.046 36.364 0.00 5.15 45.99 3.50
738 1027 6.827727 TGCAAGGTTCTTAGAGAAGTACTTT 58.172 36.000 10.02 0.00 34.42 2.66
866 1158 0.871722 GCACCTTGCATTGTACGTGA 59.128 50.000 0.00 0.00 44.26 4.35
871 1163 2.671396 CCTTGCATTGTACGTGACCTAC 59.329 50.000 0.00 0.00 0.00 3.18
904 1196 6.428083 TCAGTTAATGGTCTTCTTGTGGTA 57.572 37.500 0.00 0.00 0.00 3.25
906 1198 6.878923 TCAGTTAATGGTCTTCTTGTGGTATG 59.121 38.462 0.00 0.00 0.00 2.39
907 1199 5.648092 AGTTAATGGTCTTCTTGTGGTATGC 59.352 40.000 0.00 0.00 0.00 3.14
921 1213 4.218200 TGTGGTATGCAATGGTTCAGAAAG 59.782 41.667 0.00 0.00 0.00 2.62
922 1214 4.458989 GTGGTATGCAATGGTTCAGAAAGA 59.541 41.667 0.00 0.00 0.00 2.52
923 1215 5.048083 GTGGTATGCAATGGTTCAGAAAGAA 60.048 40.000 0.00 0.00 0.00 2.52
972 1264 4.225942 ACTTCCTTATGCTGATTCCAGTCA 59.774 41.667 0.00 0.00 42.35 3.41
1095 1387 1.588674 TGTTTGCCTTCATCGTCGTT 58.411 45.000 0.00 0.00 0.00 3.85
1130 1422 2.683362 TGTCCTCACTCTACGCATACAG 59.317 50.000 0.00 0.00 0.00 2.74
1246 1538 8.757982 ATGTATCATCTTGTTGGCTAATTTCT 57.242 30.769 0.00 0.00 0.00 2.52
1283 1575 7.039882 CCAGTAAATGGTACGTAGACAGATTT 58.960 38.462 0.00 0.37 44.91 2.17
1284 1576 8.192774 CCAGTAAATGGTACGTAGACAGATTTA 58.807 37.037 0.00 0.00 44.91 1.40
1285 1577 9.745880 CAGTAAATGGTACGTAGACAGATTTAT 57.254 33.333 0.00 0.00 0.00 1.40
1316 1608 4.566907 GCCATGTTTAGTTCCTCTTACCCA 60.567 45.833 0.00 0.00 0.00 4.51
1318 1610 4.628963 TGTTTAGTTCCTCTTACCCACC 57.371 45.455 0.00 0.00 0.00 4.61
1337 1964 7.739498 CCCACCTGGTACATTGTATTAATAC 57.261 40.000 17.18 17.18 38.20 1.89
1338 1965 7.514721 CCCACCTGGTACATTGTATTAATACT 58.485 38.462 22.82 8.37 38.20 2.12
1339 1966 7.996644 CCCACCTGGTACATTGTATTAATACTT 59.003 37.037 22.82 10.47 38.20 2.24
1340 1967 8.836413 CCACCTGGTACATTGTATTAATACTTG 58.164 37.037 22.82 20.76 38.20 3.16
1342 1969 9.969001 ACCTGGTACATTGTATTAATACTTGTT 57.031 29.630 25.85 16.49 38.20 2.83
1380 2230 8.728088 TTTCTTTGACTTGATATTTTTCTCGC 57.272 30.769 0.00 0.00 0.00 5.03
1401 2251 3.418995 CCTGGGATGATATTGCTGGAAG 58.581 50.000 0.00 0.00 0.00 3.46
1407 2257 4.461781 GGATGATATTGCTGGAAGGATTGG 59.538 45.833 0.00 0.00 30.66 3.16
1412 2262 2.620251 TGCTGGAAGGATTGGTATCG 57.380 50.000 0.00 0.00 0.00 2.92
1420 2270 1.160137 GGATTGGTATCGATGGCAGC 58.840 55.000 8.54 0.00 0.00 5.25
1424 2275 0.541392 TGGTATCGATGGCAGCTGTT 59.459 50.000 16.64 0.05 0.00 3.16
1458 2309 8.430573 AACTGTTTTTATGGTTTATTAGGCCT 57.569 30.769 11.78 11.78 0.00 5.19
1459 2310 8.430573 ACTGTTTTTATGGTTTATTAGGCCTT 57.569 30.769 12.58 0.00 0.00 4.35
1460 2311 8.311109 ACTGTTTTTATGGTTTATTAGGCCTTG 58.689 33.333 12.58 0.00 0.00 3.61
1461 2312 8.196378 TGTTTTTATGGTTTATTAGGCCTTGT 57.804 30.769 12.58 1.94 0.00 3.16
1462 2313 9.310449 TGTTTTTATGGTTTATTAGGCCTTGTA 57.690 29.630 12.58 0.73 0.00 2.41
1463 2314 9.577110 GTTTTTATGGTTTATTAGGCCTTGTAC 57.423 33.333 12.58 2.39 0.00 2.90
1464 2315 8.880991 TTTTATGGTTTATTAGGCCTTGTACA 57.119 30.769 12.58 1.72 0.00 2.90
1465 2316 8.880991 TTTATGGTTTATTAGGCCTTGTACAA 57.119 30.769 12.58 8.28 0.00 2.41
1466 2317 9.482175 TTTATGGTTTATTAGGCCTTGTACAAT 57.518 29.630 12.58 6.77 0.00 2.71
1467 2318 6.767524 TGGTTTATTAGGCCTTGTACAATG 57.232 37.500 12.58 7.68 0.00 2.82
1468 2319 5.654650 TGGTTTATTAGGCCTTGTACAATGG 59.345 40.000 12.58 13.26 0.00 3.16
1469 2320 5.068591 GGTTTATTAGGCCTTGTACAATGGG 59.931 44.000 12.58 14.91 0.00 4.00
1470 2321 5.718801 TTATTAGGCCTTGTACAATGGGA 57.281 39.130 12.58 0.00 0.00 4.37
1471 2322 3.644966 TTAGGCCTTGTACAATGGGAG 57.355 47.619 12.58 1.65 0.00 4.30
1472 2323 1.668826 AGGCCTTGTACAATGGGAGA 58.331 50.000 16.08 0.00 0.00 3.71
1473 2324 2.208872 AGGCCTTGTACAATGGGAGAT 58.791 47.619 16.08 0.53 0.00 2.75
1474 2325 2.092212 AGGCCTTGTACAATGGGAGATG 60.092 50.000 16.08 0.00 0.00 2.90
1475 2326 1.678101 GCCTTGTACAATGGGAGATGC 59.322 52.381 16.08 3.76 0.00 3.91
1476 2327 2.684927 GCCTTGTACAATGGGAGATGCT 60.685 50.000 16.08 0.00 0.00 3.79
1477 2328 3.624777 CCTTGTACAATGGGAGATGCTT 58.375 45.455 9.13 0.00 0.00 3.91
1478 2329 3.379372 CCTTGTACAATGGGAGATGCTTG 59.621 47.826 9.13 0.00 0.00 4.01
1479 2330 3.003394 TGTACAATGGGAGATGCTTGG 57.997 47.619 0.00 0.00 0.00 3.61
1480 2331 2.301346 GTACAATGGGAGATGCTTGGG 58.699 52.381 0.00 0.00 0.00 4.12
1481 2332 0.032813 ACAATGGGAGATGCTTGGGG 60.033 55.000 0.00 0.00 0.00 4.96
1482 2333 0.259647 CAATGGGAGATGCTTGGGGA 59.740 55.000 0.00 0.00 0.00 4.81
1483 2334 0.554792 AATGGGAGATGCTTGGGGAG 59.445 55.000 0.00 0.00 0.00 4.30
1484 2335 1.358830 ATGGGAGATGCTTGGGGAGG 61.359 60.000 0.00 0.00 0.00 4.30
1485 2336 2.003548 GGGAGATGCTTGGGGAGGT 61.004 63.158 0.00 0.00 0.00 3.85
1486 2337 1.225704 GGAGATGCTTGGGGAGGTG 59.774 63.158 0.00 0.00 0.00 4.00
1487 2338 1.452833 GAGATGCTTGGGGAGGTGC 60.453 63.158 0.00 0.00 0.00 5.01
1488 2339 1.919600 GAGATGCTTGGGGAGGTGCT 61.920 60.000 0.00 0.00 0.00 4.40
1489 2340 1.000396 GATGCTTGGGGAGGTGCTT 60.000 57.895 0.00 0.00 0.00 3.91
1490 2341 0.255890 GATGCTTGGGGAGGTGCTTA 59.744 55.000 0.00 0.00 0.00 3.09
1491 2342 0.257039 ATGCTTGGGGAGGTGCTTAG 59.743 55.000 0.00 0.00 0.00 2.18
1492 2343 0.840288 TGCTTGGGGAGGTGCTTAGA 60.840 55.000 0.00 0.00 0.00 2.10
1493 2344 0.328258 GCTTGGGGAGGTGCTTAGAA 59.672 55.000 0.00 0.00 0.00 2.10
1494 2345 1.271926 GCTTGGGGAGGTGCTTAGAAA 60.272 52.381 0.00 0.00 0.00 2.52
1495 2346 2.817839 GCTTGGGGAGGTGCTTAGAAAA 60.818 50.000 0.00 0.00 0.00 2.29
1496 2347 3.496331 CTTGGGGAGGTGCTTAGAAAAA 58.504 45.455 0.00 0.00 0.00 1.94
1497 2348 3.825908 TGGGGAGGTGCTTAGAAAAAT 57.174 42.857 0.00 0.00 0.00 1.82
1498 2349 4.938575 TGGGGAGGTGCTTAGAAAAATA 57.061 40.909 0.00 0.00 0.00 1.40
1499 2350 5.263872 TGGGGAGGTGCTTAGAAAAATAA 57.736 39.130 0.00 0.00 0.00 1.40
1500 2351 5.646215 TGGGGAGGTGCTTAGAAAAATAAA 58.354 37.500 0.00 0.00 0.00 1.40
1501 2352 6.260663 TGGGGAGGTGCTTAGAAAAATAAAT 58.739 36.000 0.00 0.00 0.00 1.40
1502 2353 6.379988 TGGGGAGGTGCTTAGAAAAATAAATC 59.620 38.462 0.00 0.00 0.00 2.17
1503 2354 6.459710 GGGGAGGTGCTTAGAAAAATAAATCG 60.460 42.308 0.00 0.00 0.00 3.34
1504 2355 6.317893 GGGAGGTGCTTAGAAAAATAAATCGA 59.682 38.462 0.00 0.00 0.00 3.59
1505 2356 7.410485 GGAGGTGCTTAGAAAAATAAATCGAG 58.590 38.462 0.00 0.00 0.00 4.04
1506 2357 7.065923 GGAGGTGCTTAGAAAAATAAATCGAGT 59.934 37.037 0.00 0.00 0.00 4.18
1507 2358 8.336801 AGGTGCTTAGAAAAATAAATCGAGTT 57.663 30.769 2.72 2.72 0.00 3.01
1508 2359 8.793592 AGGTGCTTAGAAAAATAAATCGAGTTT 58.206 29.630 2.37 0.82 0.00 2.66
1509 2360 9.406828 GGTGCTTAGAAAAATAAATCGAGTTTT 57.593 29.630 2.37 0.00 29.82 2.43
1517 2368 9.995379 GAAAAATAAATCGAGTTTTTCTGAAGC 57.005 29.630 21.16 6.49 43.37 3.86
1518 2369 9.528018 AAAAATAAATCGAGTTTTTCTGAAGCA 57.472 25.926 2.37 0.00 31.46 3.91
1519 2370 8.507470 AAATAAATCGAGTTTTTCTGAAGCAC 57.493 30.769 2.37 0.00 0.00 4.40
1520 2371 4.489679 AATCGAGTTTTTCTGAAGCACC 57.510 40.909 0.00 0.00 0.00 5.01
1521 2372 1.864711 TCGAGTTTTTCTGAAGCACCG 59.135 47.619 0.00 0.00 0.00 4.94
1522 2373 1.069906 CGAGTTTTTCTGAAGCACCGG 60.070 52.381 0.00 0.00 0.00 5.28
1523 2374 1.947456 GAGTTTTTCTGAAGCACCGGT 59.053 47.619 0.00 0.00 0.00 5.28
1524 2375 1.676006 AGTTTTTCTGAAGCACCGGTG 59.324 47.619 30.66 30.66 0.00 4.94
1536 2387 2.684001 CACCGGTGCCTATTTCTACA 57.316 50.000 24.02 0.00 0.00 2.74
1537 2388 2.550978 CACCGGTGCCTATTTCTACAG 58.449 52.381 24.02 0.00 0.00 2.74
1538 2389 1.485066 ACCGGTGCCTATTTCTACAGG 59.515 52.381 6.12 0.00 35.04 4.00
1539 2390 1.760613 CCGGTGCCTATTTCTACAGGA 59.239 52.381 0.00 0.00 33.42 3.86
1540 2391 2.224066 CCGGTGCCTATTTCTACAGGAG 60.224 54.545 0.00 0.00 33.42 3.69
1541 2392 2.693591 CGGTGCCTATTTCTACAGGAGA 59.306 50.000 0.00 0.00 33.42 3.71
1542 2393 3.243569 CGGTGCCTATTTCTACAGGAGAG 60.244 52.174 0.00 0.00 34.93 3.20
1543 2394 3.961408 GGTGCCTATTTCTACAGGAGAGA 59.039 47.826 0.00 0.00 34.93 3.10
1544 2395 4.202172 GGTGCCTATTTCTACAGGAGAGAC 60.202 50.000 0.00 0.00 34.93 3.36
1545 2396 3.632604 TGCCTATTTCTACAGGAGAGACG 59.367 47.826 0.00 0.00 34.93 4.18
1546 2397 3.551250 GCCTATTTCTACAGGAGAGACGC 60.551 52.174 0.00 0.00 34.93 5.19
1547 2398 3.886505 CCTATTTCTACAGGAGAGACGCT 59.113 47.826 0.00 0.00 34.93 5.07
1548 2399 4.339814 CCTATTTCTACAGGAGAGACGCTT 59.660 45.833 0.00 0.00 34.93 4.68
1549 2400 5.531659 CCTATTTCTACAGGAGAGACGCTTA 59.468 44.000 0.00 0.00 34.93 3.09
1550 2401 4.966965 TTTCTACAGGAGAGACGCTTAG 57.033 45.455 0.00 0.00 34.93 2.18
1551 2402 3.630892 TCTACAGGAGAGACGCTTAGT 57.369 47.619 0.00 0.00 0.00 2.24
1552 2403 3.952931 TCTACAGGAGAGACGCTTAGTT 58.047 45.455 0.00 0.00 0.00 2.24
1553 2404 5.095145 TCTACAGGAGAGACGCTTAGTTA 57.905 43.478 0.00 0.00 0.00 2.24
1554 2405 5.494724 TCTACAGGAGAGACGCTTAGTTAA 58.505 41.667 0.00 0.00 0.00 2.01
1555 2406 4.705337 ACAGGAGAGACGCTTAGTTAAG 57.295 45.455 0.00 0.00 36.40 1.85
1556 2407 9.223557 TTCTACAGGAGAGACGCTTAGTTAAGC 62.224 44.444 12.72 12.72 44.08 3.09
1570 2421 7.024340 CTTAGTTAAGCGTCTATCCTGTACA 57.976 40.000 0.00 0.00 0.00 2.90
1571 2422 5.909621 AGTTAAGCGTCTATCCTGTACAA 57.090 39.130 0.00 0.00 0.00 2.41
1572 2423 6.276832 AGTTAAGCGTCTATCCTGTACAAA 57.723 37.500 0.00 0.00 0.00 2.83
1573 2424 6.875076 AGTTAAGCGTCTATCCTGTACAAAT 58.125 36.000 0.00 0.00 0.00 2.32
1574 2425 8.004087 AGTTAAGCGTCTATCCTGTACAAATA 57.996 34.615 0.00 0.00 0.00 1.40
1575 2426 8.472413 AGTTAAGCGTCTATCCTGTACAAATAA 58.528 33.333 0.00 0.00 0.00 1.40
1576 2427 8.753175 GTTAAGCGTCTATCCTGTACAAATAAG 58.247 37.037 0.00 0.00 0.00 1.73
1577 2428 5.290386 AGCGTCTATCCTGTACAAATAAGC 58.710 41.667 0.00 4.79 0.00 3.09
1578 2429 5.047847 GCGTCTATCCTGTACAAATAAGCA 58.952 41.667 0.00 0.00 0.00 3.91
1579 2430 5.050972 GCGTCTATCCTGTACAAATAAGCAC 60.051 44.000 0.00 0.00 0.00 4.40
1580 2431 5.173312 CGTCTATCCTGTACAAATAAGCACG 59.827 44.000 0.00 3.91 0.00 5.34
1581 2432 5.462398 GTCTATCCTGTACAAATAAGCACGG 59.538 44.000 0.00 0.00 0.00 4.94
1582 2433 2.980568 TCCTGTACAAATAAGCACGGG 58.019 47.619 0.00 0.00 38.56 5.28
1583 2434 2.303600 TCCTGTACAAATAAGCACGGGT 59.696 45.455 0.00 0.00 38.39 5.28
1584 2435 2.418628 CCTGTACAAATAAGCACGGGTG 59.581 50.000 0.00 0.00 33.51 4.61
1597 2448 3.537793 CACGGGTGCTTAAGAAAAGTC 57.462 47.619 6.67 0.00 0.00 3.01
1598 2449 3.139077 CACGGGTGCTTAAGAAAAGTCT 58.861 45.455 6.67 0.00 34.72 3.24
1599 2450 3.058914 CACGGGTGCTTAAGAAAAGTCTG 60.059 47.826 6.67 0.00 33.05 3.51
1600 2451 2.484264 CGGGTGCTTAAGAAAAGTCTGG 59.516 50.000 6.67 0.00 33.05 3.86
1601 2452 3.487372 GGGTGCTTAAGAAAAGTCTGGT 58.513 45.455 6.67 0.00 33.05 4.00
1602 2453 3.889538 GGGTGCTTAAGAAAAGTCTGGTT 59.110 43.478 6.67 0.00 33.05 3.67
1603 2454 4.341235 GGGTGCTTAAGAAAAGTCTGGTTT 59.659 41.667 6.67 0.00 33.05 3.27
1604 2455 5.533528 GGGTGCTTAAGAAAAGTCTGGTTTA 59.466 40.000 6.67 0.00 33.05 2.01
1605 2456 6.208797 GGGTGCTTAAGAAAAGTCTGGTTTAT 59.791 38.462 6.67 0.00 33.05 1.40
1606 2457 7.255836 GGGTGCTTAAGAAAAGTCTGGTTTATT 60.256 37.037 6.67 0.00 33.05 1.40
1607 2458 8.141909 GGTGCTTAAGAAAAGTCTGGTTTATTT 58.858 33.333 6.67 0.00 33.05 1.40
1608 2459 9.181805 GTGCTTAAGAAAAGTCTGGTTTATTTC 57.818 33.333 6.67 0.00 33.05 2.17
1609 2460 9.131791 TGCTTAAGAAAAGTCTGGTTTATTTCT 57.868 29.630 6.67 0.00 40.90 2.52
1610 2461 9.613957 GCTTAAGAAAAGTCTGGTTTATTTCTC 57.386 33.333 6.67 0.00 38.89 2.87
1615 2466 9.004717 AGAAAAGTCTGGTTTATTTCTCTAAGC 57.995 33.333 0.00 0.00 35.96 3.09
1616 2467 8.691661 AAAAGTCTGGTTTATTTCTCTAAGCA 57.308 30.769 0.00 0.00 0.00 3.91
1617 2468 7.674471 AAGTCTGGTTTATTTCTCTAAGCAC 57.326 36.000 0.00 0.00 0.00 4.40
1618 2469 6.174049 AGTCTGGTTTATTTCTCTAAGCACC 58.826 40.000 0.00 0.00 0.00 5.01
1619 2470 6.013293 AGTCTGGTTTATTTCTCTAAGCACCT 60.013 38.462 0.00 0.00 0.00 4.00
1620 2471 6.314152 GTCTGGTTTATTTCTCTAAGCACCTC 59.686 42.308 0.00 0.00 0.00 3.85
1621 2472 6.213600 TCTGGTTTATTTCTCTAAGCACCTCT 59.786 38.462 0.00 0.00 0.00 3.69
1622 2473 6.407202 TGGTTTATTTCTCTAAGCACCTCTC 58.593 40.000 0.00 0.00 0.00 3.20
1623 2474 5.818336 GGTTTATTTCTCTAAGCACCTCTCC 59.182 44.000 0.00 0.00 0.00 3.71
1624 2475 6.352308 GGTTTATTTCTCTAAGCACCTCTCCT 60.352 42.308 0.00 0.00 0.00 3.69
1625 2476 7.147707 GGTTTATTTCTCTAAGCACCTCTCCTA 60.148 40.741 0.00 0.00 0.00 2.94
1626 2477 7.973048 TTATTTCTCTAAGCACCTCTCCTAA 57.027 36.000 0.00 0.00 0.00 2.69
1627 2478 5.923733 TTTCTCTAAGCACCTCTCCTAAG 57.076 43.478 0.00 0.00 0.00 2.18
1628 2479 3.292460 TCTCTAAGCACCTCTCCTAAGC 58.708 50.000 0.00 0.00 0.00 3.09
1629 2480 3.027412 CTCTAAGCACCTCTCCTAAGCA 58.973 50.000 0.00 0.00 0.00 3.91
1630 2481 3.640967 CTCTAAGCACCTCTCCTAAGCAT 59.359 47.826 0.00 0.00 0.00 3.79
1631 2482 2.998316 AAGCACCTCTCCTAAGCATC 57.002 50.000 0.00 0.00 0.00 3.91
1632 2483 2.173126 AGCACCTCTCCTAAGCATCT 57.827 50.000 0.00 0.00 0.00 2.90
1633 2484 2.476199 AGCACCTCTCCTAAGCATCTT 58.524 47.619 0.00 0.00 0.00 2.40
1634 2485 2.170187 AGCACCTCTCCTAAGCATCTTG 59.830 50.000 0.00 0.00 0.00 3.02
1635 2486 2.559440 CACCTCTCCTAAGCATCTTGC 58.441 52.381 0.00 0.00 45.46 4.01
1647 2498 2.533266 GCATCTTGCATTGTACAAGGC 58.467 47.619 32.34 32.34 46.98 4.35
1648 2499 2.736400 GCATCTTGCATTGTACAAGGCC 60.736 50.000 34.56 20.76 46.35 5.19
1649 2500 2.584835 TCTTGCATTGTACAAGGCCT 57.415 45.000 34.56 0.00 46.35 5.19
1650 2501 2.875296 TCTTGCATTGTACAAGGCCTT 58.125 42.857 34.56 13.78 46.35 4.35
1651 2502 4.027674 TCTTGCATTGTACAAGGCCTTA 57.972 40.909 34.56 21.73 46.35 2.69
1652 2503 3.756434 TCTTGCATTGTACAAGGCCTTAC 59.244 43.478 34.56 14.80 46.35 2.34
1653 2504 3.433306 TGCATTGTACAAGGCCTTACT 57.567 42.857 34.56 8.97 46.35 2.24
1654 2505 3.081061 TGCATTGTACAAGGCCTTACTG 58.919 45.455 34.56 17.47 46.35 2.74
1655 2506 2.423538 GCATTGTACAAGGCCTTACTGG 59.576 50.000 29.85 8.49 41.71 4.00
1699 2550 2.286025 GCTCAAGCAAAGCAAAAGTTGG 59.714 45.455 0.00 0.00 41.59 3.77
1746 2597 4.801147 TCTGCTAATTATTCTGCTTGCG 57.199 40.909 4.94 0.00 0.00 4.85
1881 2735 4.595538 TCGGTCGGTTGTTGCGCT 62.596 61.111 9.73 0.00 0.00 5.92
1924 2778 3.872182 CAGCAGATGAATGTCTCCTTCTG 59.128 47.826 0.00 0.00 36.81 3.02
1933 2787 2.042464 TGTCTCCTTCTGTGCTCTGTT 58.958 47.619 0.00 0.00 0.00 3.16
1937 2791 1.072806 TCCTTCTGTGCTCTGTTGCAT 59.927 47.619 0.00 0.00 45.23 3.96
2025 2879 7.327214 ACAGTTCTTGTTGCCTTTAAAAATCA 58.673 30.769 0.00 0.00 36.31 2.57
2026 2880 7.986889 ACAGTTCTTGTTGCCTTTAAAAATCAT 59.013 29.630 0.00 0.00 36.31 2.45
2027 2881 8.277713 CAGTTCTTGTTGCCTTTAAAAATCATG 58.722 33.333 0.00 0.00 0.00 3.07
2029 2883 9.255304 GTTCTTGTTGCCTTTAAAAATCATGTA 57.745 29.630 0.00 0.00 0.00 2.29
2098 2955 7.646548 AATAAGAGGGGAAAAGTAAGCATTC 57.353 36.000 0.00 0.00 0.00 2.67
2121 2978 7.786178 TCCTTCGTTATCCTTTTGTATCATG 57.214 36.000 0.00 0.00 0.00 3.07
2124 2981 8.765219 CCTTCGTTATCCTTTTGTATCATGTAG 58.235 37.037 0.00 0.00 0.00 2.74
2125 2982 7.709269 TCGTTATCCTTTTGTATCATGTAGC 57.291 36.000 0.00 0.00 0.00 3.58
2126 2983 7.497595 TCGTTATCCTTTTGTATCATGTAGCT 58.502 34.615 0.00 0.00 0.00 3.32
2128 2985 8.276325 CGTTATCCTTTTGTATCATGTAGCTTC 58.724 37.037 0.00 0.00 0.00 3.86
2129 2986 6.851222 ATCCTTTTGTATCATGTAGCTTCG 57.149 37.500 0.00 0.00 0.00 3.79
2131 2988 4.572389 CCTTTTGTATCATGTAGCTTCGCT 59.428 41.667 0.00 0.00 43.41 4.93
2132 2989 5.753438 CCTTTTGTATCATGTAGCTTCGCTA 59.247 40.000 0.00 0.00 40.44 4.26
2133 2990 6.425114 CCTTTTGTATCATGTAGCTTCGCTAT 59.575 38.462 0.00 0.00 43.30 2.97
2134 2991 7.041780 CCTTTTGTATCATGTAGCTTCGCTATT 60.042 37.037 0.00 0.00 43.30 1.73
2135 2992 6.769608 TTGTATCATGTAGCTTCGCTATTG 57.230 37.500 0.00 1.58 43.30 1.90
2136 2993 5.842907 TGTATCATGTAGCTTCGCTATTGT 58.157 37.500 0.00 0.00 43.30 2.71
2137 2994 5.920840 TGTATCATGTAGCTTCGCTATTGTC 59.079 40.000 0.00 0.00 43.30 3.18
2139 2996 3.132111 TCATGTAGCTTCGCTATTGTCCA 59.868 43.478 0.00 0.00 43.30 4.02
2140 2997 2.888594 TGTAGCTTCGCTATTGTCCAC 58.111 47.619 0.00 0.00 43.30 4.02
2141 2998 1.852895 GTAGCTTCGCTATTGTCCACG 59.147 52.381 0.00 0.00 43.30 4.94
2145 3010 0.170784 TTCGCTATTGTCCACGCGTA 59.829 50.000 13.44 0.00 45.25 4.42
2147 3012 0.776451 CGCTATTGTCCACGCGTATC 59.224 55.000 13.44 5.96 40.64 2.24
2180 3045 0.842613 CGCGTTGATGAGATGAGACG 59.157 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.285977 GAAATTAATCACCCGACGGCT 58.714 47.619 8.86 0.00 0.00 5.52
1 2 1.004292 CGAAATTAATCACCCGACGGC 60.004 52.381 8.86 0.00 0.00 5.68
2 3 1.595794 CCGAAATTAATCACCCGACGG 59.404 52.381 6.99 6.99 0.00 4.79
3 4 2.273557 ACCGAAATTAATCACCCGACG 58.726 47.619 0.00 0.00 0.00 5.12
4 5 3.437741 ACAACCGAAATTAATCACCCGAC 59.562 43.478 0.00 0.00 0.00 4.79
5 6 3.437395 CACAACCGAAATTAATCACCCGA 59.563 43.478 0.00 0.00 0.00 5.14
6 7 3.426963 CCACAACCGAAATTAATCACCCG 60.427 47.826 0.00 0.00 0.00 5.28
7 8 3.119280 CCCACAACCGAAATTAATCACCC 60.119 47.826 0.00 0.00 0.00 4.61
92 93 1.345715 AAGCGGGGATCTACCAAGGG 61.346 60.000 7.57 0.00 41.20 3.95
140 141 2.867624 ACAACACTGAGCAATCCACAT 58.132 42.857 0.00 0.00 0.00 3.21
148 149 1.577468 CAACGGTACAACACTGAGCA 58.423 50.000 0.00 0.00 36.95 4.26
254 258 1.734477 CTGTTGCACTCGAGGGACG 60.734 63.158 21.51 3.82 44.09 4.79
278 282 3.243359 ACAACATGACCAAATGGAGGT 57.757 42.857 6.42 0.00 43.46 3.85
307 315 0.609151 TGCAAATCAAGGGCCATGTG 59.391 50.000 6.18 0.00 0.00 3.21
370 405 6.656902 TGCAGGAAATGATGTTCTAAGATCT 58.343 36.000 0.00 0.00 30.61 2.75
431 528 2.996985 AGGCATGCCTAGTGAGTGA 58.003 52.632 37.99 0.00 46.14 3.41
455 556 5.365895 ACTGGTTATTATGTAGGGACCTCAC 59.634 44.000 0.00 0.00 0.00 3.51
478 579 5.245531 TGTTAACTCATGAATCCAGTCCAC 58.754 41.667 7.22 0.00 0.00 4.02
576 695 5.008217 TGTGTCAAAGCAATGTACTACCAAC 59.992 40.000 0.00 0.00 0.00 3.77
603 723 4.668576 ATTACGGCGATATTGCATCTTG 57.331 40.909 16.62 3.53 36.28 3.02
647 767 3.199071 TCACAGTAATAAATGCCCTCGGT 59.801 43.478 0.00 0.00 0.00 4.69
648 768 3.804036 TCACAGTAATAAATGCCCTCGG 58.196 45.455 0.00 0.00 0.00 4.63
649 769 5.300752 AGATCACAGTAATAAATGCCCTCG 58.699 41.667 0.00 0.00 0.00 4.63
712 1000 7.010339 AGTACTTCTCTAAGAACCTTGCATT 57.990 36.000 0.00 0.00 36.50 3.56
714 1002 6.420913 AAGTACTTCTCTAAGAACCTTGCA 57.579 37.500 1.12 0.00 36.50 4.08
715 1003 6.706716 ACAAAGTACTTCTCTAAGAACCTTGC 59.293 38.462 8.95 0.00 36.50 4.01
767 1056 6.493458 ACCCTGTTATAGAAACAAGCAACAAT 59.507 34.615 0.00 0.00 0.00 2.71
768 1057 5.830991 ACCCTGTTATAGAAACAAGCAACAA 59.169 36.000 0.00 0.00 0.00 2.83
769 1058 5.240623 CACCCTGTTATAGAAACAAGCAACA 59.759 40.000 0.00 0.00 0.00 3.33
781 1070 2.418368 TGCTTGGCACCCTGTTATAG 57.582 50.000 0.00 0.00 31.71 1.31
817 1107 3.181494 GGTGCTTGTAAAACGAACAGGTT 60.181 43.478 0.00 0.00 0.00 3.50
819 1109 2.616842 AGGTGCTTGTAAAACGAACAGG 59.383 45.455 0.00 0.00 0.00 4.00
821 1111 3.537580 AGAGGTGCTTGTAAAACGAACA 58.462 40.909 0.00 0.00 0.00 3.18
822 1112 3.808174 AGAGAGGTGCTTGTAAAACGAAC 59.192 43.478 0.00 0.00 0.00 3.95
823 1113 4.067972 AGAGAGGTGCTTGTAAAACGAA 57.932 40.909 0.00 0.00 0.00 3.85
825 1115 3.927142 CCTAGAGAGGTGCTTGTAAAACG 59.073 47.826 0.00 0.00 38.16 3.60
826 1116 3.685272 GCCTAGAGAGGTGCTTGTAAAAC 59.315 47.826 0.00 0.00 45.78 2.43
849 1141 1.071699 AGGTCACGTACAATGCAAGGT 59.928 47.619 0.00 0.00 0.00 3.50
859 1151 2.719426 AACTGCAGTAGGTCACGTAC 57.281 50.000 22.01 0.00 0.00 3.67
863 1155 4.822026 ACTGATTAACTGCAGTAGGTCAC 58.178 43.478 22.01 10.33 43.10 3.67
866 1158 6.823689 CCATTAACTGATTAACTGCAGTAGGT 59.176 38.462 22.01 14.62 44.06 3.08
871 1163 6.992063 AGACCATTAACTGATTAACTGCAG 57.008 37.500 13.48 13.48 33.09 4.41
936 1228 5.705905 GCATAAGGAAGTTGTGTAAGGAACT 59.294 40.000 0.00 0.00 31.92 3.01
941 1233 6.992063 ATCAGCATAAGGAAGTTGTGTAAG 57.008 37.500 0.00 0.00 30.10 2.34
972 1264 4.458295 CACTTCTGACAATGCCAAGAGAAT 59.542 41.667 0.00 0.00 0.00 2.40
1130 1422 2.633488 GTCCTTTGCTCATCCAGTACC 58.367 52.381 0.00 0.00 0.00 3.34
1284 1576 8.815912 AGAGGAACTAAACATGGCAAAATAAAT 58.184 29.630 0.00 0.00 41.55 1.40
1285 1577 8.189119 AGAGGAACTAAACATGGCAAAATAAA 57.811 30.769 0.00 0.00 41.55 1.40
1286 1578 7.775053 AGAGGAACTAAACATGGCAAAATAA 57.225 32.000 0.00 0.00 41.55 1.40
1287 1579 7.775053 AAGAGGAACTAAACATGGCAAAATA 57.225 32.000 0.00 0.00 41.55 1.40
1288 1580 6.670695 AAGAGGAACTAAACATGGCAAAAT 57.329 33.333 0.00 0.00 41.55 1.82
1316 1608 9.969001 AACAAGTATTAATACAATGTACCAGGT 57.031 29.630 25.10 13.53 35.75 4.00
1337 1964 9.405587 TCAAAGAAAAGAGTGTAACAAAACAAG 57.594 29.630 0.00 0.00 41.43 3.16
1338 1965 9.187455 GTCAAAGAAAAGAGTGTAACAAAACAA 57.813 29.630 0.00 0.00 41.43 2.83
1339 1966 8.573035 AGTCAAAGAAAAGAGTGTAACAAAACA 58.427 29.630 0.00 0.00 41.43 2.83
1340 1967 8.965986 AGTCAAAGAAAAGAGTGTAACAAAAC 57.034 30.769 0.00 0.00 41.43 2.43
1342 1969 8.788806 TCAAGTCAAAGAAAAGAGTGTAACAAA 58.211 29.630 0.00 0.00 41.43 2.83
1343 1970 8.330466 TCAAGTCAAAGAAAAGAGTGTAACAA 57.670 30.769 0.00 0.00 41.43 2.83
1379 2229 1.074405 TCCAGCAATATCATCCCAGGC 59.926 52.381 0.00 0.00 0.00 4.85
1380 2230 3.418995 CTTCCAGCAATATCATCCCAGG 58.581 50.000 0.00 0.00 0.00 4.45
1401 2251 1.160137 GCTGCCATCGATACCAATCC 58.840 55.000 0.00 0.00 0.00 3.01
1407 2257 1.656652 ACAACAGCTGCCATCGATAC 58.343 50.000 15.27 0.00 0.00 2.24
1412 2262 0.316204 AAGCAACAACAGCTGCCATC 59.684 50.000 15.27 0.00 42.53 3.51
1420 2270 8.327429 CCATAAAAACAGTTAAAGCAACAACAG 58.673 33.333 0.00 0.00 39.81 3.16
1424 2275 8.779354 AAACCATAAAAACAGTTAAAGCAACA 57.221 26.923 0.00 0.00 39.81 3.33
1451 2302 3.186283 TCTCCCATTGTACAAGGCCTAA 58.814 45.455 14.66 0.00 0.00 2.69
1453 2304 1.668826 TCTCCCATTGTACAAGGCCT 58.331 50.000 14.66 0.00 0.00 5.19
1455 2306 1.678101 GCATCTCCCATTGTACAAGGC 59.322 52.381 14.66 0.00 0.00 4.35
1456 2307 3.287867 AGCATCTCCCATTGTACAAGG 57.712 47.619 14.65 13.92 0.00 3.61
1457 2308 3.379372 CCAAGCATCTCCCATTGTACAAG 59.621 47.826 14.65 6.30 0.00 3.16
1458 2309 3.355378 CCAAGCATCTCCCATTGTACAA 58.645 45.455 11.41 11.41 0.00 2.41
1459 2310 2.357050 CCCAAGCATCTCCCATTGTACA 60.357 50.000 0.00 0.00 0.00 2.90
1460 2311 2.301346 CCCAAGCATCTCCCATTGTAC 58.699 52.381 0.00 0.00 0.00 2.90
1461 2312 1.215173 CCCCAAGCATCTCCCATTGTA 59.785 52.381 0.00 0.00 0.00 2.41
1462 2313 0.032813 CCCCAAGCATCTCCCATTGT 60.033 55.000 0.00 0.00 0.00 2.71
1463 2314 0.259647 TCCCCAAGCATCTCCCATTG 59.740 55.000 0.00 0.00 0.00 2.82
1464 2315 0.554792 CTCCCCAAGCATCTCCCATT 59.445 55.000 0.00 0.00 0.00 3.16
1465 2316 1.358830 CCTCCCCAAGCATCTCCCAT 61.359 60.000 0.00 0.00 0.00 4.00
1466 2317 2.002977 CCTCCCCAAGCATCTCCCA 61.003 63.158 0.00 0.00 0.00 4.37
1467 2318 2.003548 ACCTCCCCAAGCATCTCCC 61.004 63.158 0.00 0.00 0.00 4.30
1468 2319 1.225704 CACCTCCCCAAGCATCTCC 59.774 63.158 0.00 0.00 0.00 3.71
1469 2320 1.452833 GCACCTCCCCAAGCATCTC 60.453 63.158 0.00 0.00 0.00 2.75
1470 2321 1.504275 AAGCACCTCCCCAAGCATCT 61.504 55.000 0.00 0.00 0.00 2.90
1471 2322 0.255890 TAAGCACCTCCCCAAGCATC 59.744 55.000 0.00 0.00 0.00 3.91
1472 2323 0.257039 CTAAGCACCTCCCCAAGCAT 59.743 55.000 0.00 0.00 0.00 3.79
1473 2324 0.840288 TCTAAGCACCTCCCCAAGCA 60.840 55.000 0.00 0.00 0.00 3.91
1474 2325 0.328258 TTCTAAGCACCTCCCCAAGC 59.672 55.000 0.00 0.00 0.00 4.01
1475 2326 2.879103 TTTCTAAGCACCTCCCCAAG 57.121 50.000 0.00 0.00 0.00 3.61
1476 2327 3.603965 TTTTTCTAAGCACCTCCCCAA 57.396 42.857 0.00 0.00 0.00 4.12
1477 2328 3.825908 ATTTTTCTAAGCACCTCCCCA 57.174 42.857 0.00 0.00 0.00 4.96
1478 2329 6.459710 CGATTTATTTTTCTAAGCACCTCCCC 60.460 42.308 0.00 0.00 0.00 4.81
1479 2330 6.317893 TCGATTTATTTTTCTAAGCACCTCCC 59.682 38.462 0.00 0.00 0.00 4.30
1480 2331 7.065923 ACTCGATTTATTTTTCTAAGCACCTCC 59.934 37.037 0.00 0.00 0.00 4.30
1481 2332 7.975750 ACTCGATTTATTTTTCTAAGCACCTC 58.024 34.615 0.00 0.00 0.00 3.85
1482 2333 7.923414 ACTCGATTTATTTTTCTAAGCACCT 57.077 32.000 0.00 0.00 0.00 4.00
1483 2334 8.965986 AAACTCGATTTATTTTTCTAAGCACC 57.034 30.769 0.00 0.00 0.00 5.01
1491 2342 9.995379 GCTTCAGAAAAACTCGATTTATTTTTC 57.005 29.630 19.25 19.25 45.95 2.29
1492 2343 9.528018 TGCTTCAGAAAAACTCGATTTATTTTT 57.472 25.926 8.46 8.46 38.03 1.94
1493 2344 8.968242 GTGCTTCAGAAAAACTCGATTTATTTT 58.032 29.630 0.00 0.00 0.00 1.82
1494 2345 7.595130 GGTGCTTCAGAAAAACTCGATTTATTT 59.405 33.333 0.00 0.00 0.00 1.40
1495 2346 7.084486 GGTGCTTCAGAAAAACTCGATTTATT 58.916 34.615 0.00 0.00 0.00 1.40
1496 2347 6.612306 GGTGCTTCAGAAAAACTCGATTTAT 58.388 36.000 0.00 0.00 0.00 1.40
1497 2348 5.333798 CGGTGCTTCAGAAAAACTCGATTTA 60.334 40.000 0.00 0.00 0.00 1.40
1498 2349 4.554723 CGGTGCTTCAGAAAAACTCGATTT 60.555 41.667 0.00 0.00 0.00 2.17
1499 2350 3.058914 CGGTGCTTCAGAAAAACTCGATT 60.059 43.478 0.00 0.00 0.00 3.34
1500 2351 2.480419 CGGTGCTTCAGAAAAACTCGAT 59.520 45.455 0.00 0.00 0.00 3.59
1501 2352 1.864711 CGGTGCTTCAGAAAAACTCGA 59.135 47.619 0.00 0.00 0.00 4.04
1502 2353 1.069906 CCGGTGCTTCAGAAAAACTCG 60.070 52.381 0.00 0.00 0.00 4.18
1503 2354 1.947456 ACCGGTGCTTCAGAAAAACTC 59.053 47.619 6.12 0.00 0.00 3.01
1504 2355 1.676006 CACCGGTGCTTCAGAAAAACT 59.324 47.619 24.02 0.00 0.00 2.66
1505 2356 2.119671 CACCGGTGCTTCAGAAAAAC 57.880 50.000 24.02 0.00 0.00 2.43
1517 2368 2.550978 CTGTAGAAATAGGCACCGGTG 58.449 52.381 30.66 30.66 0.00 4.94
1518 2369 1.485066 CCTGTAGAAATAGGCACCGGT 59.515 52.381 0.00 0.00 0.00 5.28
1519 2370 1.760613 TCCTGTAGAAATAGGCACCGG 59.239 52.381 0.00 0.00 34.08 5.28
1520 2371 2.693591 TCTCCTGTAGAAATAGGCACCG 59.306 50.000 0.00 0.00 34.08 4.94
1521 2372 3.961408 TCTCTCCTGTAGAAATAGGCACC 59.039 47.826 0.00 0.00 34.08 5.01
1522 2373 4.498345 CGTCTCTCCTGTAGAAATAGGCAC 60.498 50.000 0.00 0.00 34.08 5.01
1523 2374 3.632604 CGTCTCTCCTGTAGAAATAGGCA 59.367 47.826 0.00 0.00 34.08 4.75
1524 2375 3.551250 GCGTCTCTCCTGTAGAAATAGGC 60.551 52.174 0.00 0.00 34.08 3.93
1525 2376 3.886505 AGCGTCTCTCCTGTAGAAATAGG 59.113 47.826 0.00 0.00 35.36 2.57
1526 2377 5.508200 AAGCGTCTCTCCTGTAGAAATAG 57.492 43.478 0.00 0.00 32.46 1.73
1527 2378 6.120905 ACTAAGCGTCTCTCCTGTAGAAATA 58.879 40.000 0.00 0.00 32.46 1.40
1528 2379 4.951094 ACTAAGCGTCTCTCCTGTAGAAAT 59.049 41.667 0.00 0.00 32.46 2.17
1529 2380 4.333690 ACTAAGCGTCTCTCCTGTAGAAA 58.666 43.478 0.00 0.00 32.46 2.52
1530 2381 3.952931 ACTAAGCGTCTCTCCTGTAGAA 58.047 45.455 0.00 0.00 32.46 2.10
1531 2382 3.630892 ACTAAGCGTCTCTCCTGTAGA 57.369 47.619 0.00 0.00 0.00 2.59
1532 2383 5.812652 CTTAACTAAGCGTCTCTCCTGTAG 58.187 45.833 0.00 0.00 0.00 2.74
1533 2384 5.814764 CTTAACTAAGCGTCTCTCCTGTA 57.185 43.478 0.00 0.00 0.00 2.74
1534 2385 4.705337 CTTAACTAAGCGTCTCTCCTGT 57.295 45.455 0.00 0.00 0.00 4.00
1546 2397 7.024340 TGTACAGGATAGACGCTTAACTAAG 57.976 40.000 0.00 0.00 36.40 2.18
1547 2398 7.395190 TTGTACAGGATAGACGCTTAACTAA 57.605 36.000 0.00 0.00 0.00 2.24
1548 2399 7.395190 TTTGTACAGGATAGACGCTTAACTA 57.605 36.000 0.00 0.00 0.00 2.24
1549 2400 5.909621 TTGTACAGGATAGACGCTTAACT 57.090 39.130 0.00 0.00 0.00 2.24
1550 2401 8.638685 TTATTTGTACAGGATAGACGCTTAAC 57.361 34.615 0.00 0.00 0.00 2.01
1551 2402 7.437267 GCTTATTTGTACAGGATAGACGCTTAA 59.563 37.037 0.00 0.00 0.00 1.85
1552 2403 6.921857 GCTTATTTGTACAGGATAGACGCTTA 59.078 38.462 0.00 0.00 0.00 3.09
1553 2404 5.753921 GCTTATTTGTACAGGATAGACGCTT 59.246 40.000 0.00 0.00 0.00 4.68
1554 2405 5.163447 TGCTTATTTGTACAGGATAGACGCT 60.163 40.000 0.00 0.00 0.00 5.07
1555 2406 5.047847 TGCTTATTTGTACAGGATAGACGC 58.952 41.667 0.00 4.64 0.00 5.19
1556 2407 5.173312 CGTGCTTATTTGTACAGGATAGACG 59.827 44.000 0.00 5.73 0.00 4.18
1557 2408 5.462398 CCGTGCTTATTTGTACAGGATAGAC 59.538 44.000 0.00 0.00 0.00 2.59
1558 2409 5.452776 CCCGTGCTTATTTGTACAGGATAGA 60.453 44.000 0.00 0.00 0.00 1.98
1559 2410 4.750098 CCCGTGCTTATTTGTACAGGATAG 59.250 45.833 0.00 0.00 0.00 2.08
1560 2411 4.162698 ACCCGTGCTTATTTGTACAGGATA 59.837 41.667 0.00 0.00 0.00 2.59
1561 2412 3.054655 ACCCGTGCTTATTTGTACAGGAT 60.055 43.478 0.00 0.00 0.00 3.24
1562 2413 2.303600 ACCCGTGCTTATTTGTACAGGA 59.696 45.455 0.00 0.00 0.00 3.86
1563 2414 2.418628 CACCCGTGCTTATTTGTACAGG 59.581 50.000 0.00 0.00 0.00 4.00
1564 2415 3.740044 CACCCGTGCTTATTTGTACAG 57.260 47.619 0.00 0.00 0.00 2.74
1577 2428 3.058914 CAGACTTTTCTTAAGCACCCGTG 60.059 47.826 0.00 0.00 0.00 4.94
1578 2429 3.139077 CAGACTTTTCTTAAGCACCCGT 58.861 45.455 0.00 0.00 0.00 5.28
1579 2430 2.484264 CCAGACTTTTCTTAAGCACCCG 59.516 50.000 0.00 0.00 0.00 5.28
1580 2431 3.487372 ACCAGACTTTTCTTAAGCACCC 58.513 45.455 0.00 0.00 0.00 4.61
1581 2432 5.515797 AAACCAGACTTTTCTTAAGCACC 57.484 39.130 0.00 0.00 0.00 5.01
1582 2433 9.181805 GAAATAAACCAGACTTTTCTTAAGCAC 57.818 33.333 0.00 0.00 0.00 4.40
1583 2434 9.131791 AGAAATAAACCAGACTTTTCTTAAGCA 57.868 29.630 0.00 0.00 33.97 3.91
1584 2435 9.613957 GAGAAATAAACCAGACTTTTCTTAAGC 57.386 33.333 0.00 0.00 36.91 3.09
1589 2440 9.004717 GCTTAGAGAAATAAACCAGACTTTTCT 57.995 33.333 0.00 0.00 38.86 2.52
1590 2441 8.784043 TGCTTAGAGAAATAAACCAGACTTTTC 58.216 33.333 0.00 0.00 0.00 2.29
1591 2442 8.568794 GTGCTTAGAGAAATAAACCAGACTTTT 58.431 33.333 0.00 0.00 0.00 2.27
1592 2443 7.175119 GGTGCTTAGAGAAATAAACCAGACTTT 59.825 37.037 0.00 0.00 0.00 2.66
1593 2444 6.655425 GGTGCTTAGAGAAATAAACCAGACTT 59.345 38.462 0.00 0.00 0.00 3.01
1594 2445 6.013293 AGGTGCTTAGAGAAATAAACCAGACT 60.013 38.462 0.00 0.00 0.00 3.24
1595 2446 6.174049 AGGTGCTTAGAGAAATAAACCAGAC 58.826 40.000 0.00 0.00 0.00 3.51
1596 2447 6.213600 AGAGGTGCTTAGAGAAATAAACCAGA 59.786 38.462 0.00 0.00 0.00 3.86
1597 2448 6.410540 AGAGGTGCTTAGAGAAATAAACCAG 58.589 40.000 0.00 0.00 0.00 4.00
1598 2449 6.374417 AGAGGTGCTTAGAGAAATAAACCA 57.626 37.500 0.00 0.00 0.00 3.67
1599 2450 5.818336 GGAGAGGTGCTTAGAGAAATAAACC 59.182 44.000 0.00 0.00 0.00 3.27
1600 2451 6.645306 AGGAGAGGTGCTTAGAGAAATAAAC 58.355 40.000 0.00 0.00 0.00 2.01
1601 2452 6.875972 AGGAGAGGTGCTTAGAGAAATAAA 57.124 37.500 0.00 0.00 0.00 1.40
1602 2453 7.418025 GCTTAGGAGAGGTGCTTAGAGAAATAA 60.418 40.741 0.00 0.00 0.00 1.40
1603 2454 6.041069 GCTTAGGAGAGGTGCTTAGAGAAATA 59.959 42.308 0.00 0.00 0.00 1.40
1604 2455 5.163353 GCTTAGGAGAGGTGCTTAGAGAAAT 60.163 44.000 0.00 0.00 0.00 2.17
1605 2456 4.160626 GCTTAGGAGAGGTGCTTAGAGAAA 59.839 45.833 0.00 0.00 0.00 2.52
1606 2457 3.702045 GCTTAGGAGAGGTGCTTAGAGAA 59.298 47.826 0.00 0.00 0.00 2.87
1607 2458 3.292460 GCTTAGGAGAGGTGCTTAGAGA 58.708 50.000 0.00 0.00 0.00 3.10
1608 2459 3.027412 TGCTTAGGAGAGGTGCTTAGAG 58.973 50.000 0.00 0.00 0.00 2.43
1609 2460 3.101643 TGCTTAGGAGAGGTGCTTAGA 57.898 47.619 0.00 0.00 0.00 2.10
1610 2461 3.640967 AGATGCTTAGGAGAGGTGCTTAG 59.359 47.826 0.00 0.00 0.00 2.18
1611 2462 3.647636 AGATGCTTAGGAGAGGTGCTTA 58.352 45.455 0.00 0.00 0.00 3.09
1612 2463 2.476199 AGATGCTTAGGAGAGGTGCTT 58.524 47.619 0.00 0.00 0.00 3.91
1613 2464 2.170187 CAAGATGCTTAGGAGAGGTGCT 59.830 50.000 0.00 0.00 0.00 4.40
1614 2465 2.559440 CAAGATGCTTAGGAGAGGTGC 58.441 52.381 0.00 0.00 0.00 5.01
1615 2466 2.093288 TGCAAGATGCTTAGGAGAGGTG 60.093 50.000 3.78 0.00 45.31 4.00
1616 2467 2.191400 TGCAAGATGCTTAGGAGAGGT 58.809 47.619 3.78 0.00 45.31 3.85
1617 2468 2.996249 TGCAAGATGCTTAGGAGAGG 57.004 50.000 3.78 0.00 45.31 3.69
1618 2469 4.197750 ACAATGCAAGATGCTTAGGAGAG 58.802 43.478 3.78 0.00 45.31 3.20
1619 2470 4.226427 ACAATGCAAGATGCTTAGGAGA 57.774 40.909 3.78 0.00 45.31 3.71
1620 2471 4.877823 TGTACAATGCAAGATGCTTAGGAG 59.122 41.667 3.78 0.00 45.31 3.69
1621 2472 4.842574 TGTACAATGCAAGATGCTTAGGA 58.157 39.130 3.78 0.00 45.31 2.94
1622 2473 5.449588 CCTTGTACAATGCAAGATGCTTAGG 60.450 44.000 9.13 0.00 45.31 2.69
1623 2474 5.575957 CCTTGTACAATGCAAGATGCTTAG 58.424 41.667 9.13 0.00 45.31 2.18
1624 2475 4.142403 GCCTTGTACAATGCAAGATGCTTA 60.142 41.667 25.28 0.00 45.31 3.09
1625 2476 3.367703 GCCTTGTACAATGCAAGATGCTT 60.368 43.478 25.28 0.00 45.31 3.91
1626 2477 2.165030 GCCTTGTACAATGCAAGATGCT 59.835 45.455 25.28 0.00 45.31 3.79
1627 2478 2.533266 GCCTTGTACAATGCAAGATGC 58.467 47.619 25.28 8.66 44.29 3.91
1628 2479 2.756760 AGGCCTTGTACAATGCAAGATG 59.243 45.455 29.20 8.77 44.29 2.90
1629 2480 3.091633 AGGCCTTGTACAATGCAAGAT 57.908 42.857 29.20 14.27 44.29 2.40
1630 2481 2.584835 AGGCCTTGTACAATGCAAGA 57.415 45.000 29.20 0.00 44.29 3.02
1631 2482 3.758554 AGTAAGGCCTTGTACAATGCAAG 59.241 43.478 29.20 10.69 42.00 4.01
1632 2483 3.505680 CAGTAAGGCCTTGTACAATGCAA 59.494 43.478 29.20 15.91 34.30 4.08
1633 2484 3.081061 CAGTAAGGCCTTGTACAATGCA 58.919 45.455 29.20 12.62 34.30 3.96
1634 2485 2.423538 CCAGTAAGGCCTTGTACAATGC 59.576 50.000 28.77 23.06 0.00 3.56
1647 2498 3.244770 TGGTTAGTTCCAAGCCAGTAAGG 60.245 47.826 0.00 0.00 35.92 2.69
1648 2499 3.751698 GTGGTTAGTTCCAAGCCAGTAAG 59.248 47.826 0.00 0.00 39.34 2.34
1649 2500 3.393278 AGTGGTTAGTTCCAAGCCAGTAA 59.607 43.478 0.00 0.00 39.34 2.24
1650 2501 2.976882 AGTGGTTAGTTCCAAGCCAGTA 59.023 45.455 0.00 0.00 39.34 2.74
1651 2502 1.774856 AGTGGTTAGTTCCAAGCCAGT 59.225 47.619 0.00 0.00 39.34 4.00
1652 2503 2.154462 CAGTGGTTAGTTCCAAGCCAG 58.846 52.381 0.00 0.00 39.34 4.85
1653 2504 1.493022 ACAGTGGTTAGTTCCAAGCCA 59.507 47.619 0.00 0.00 39.34 4.75
1654 2505 2.271944 ACAGTGGTTAGTTCCAAGCC 57.728 50.000 0.00 0.00 39.34 4.35
1655 2506 2.287608 GCAACAGTGGTTAGTTCCAAGC 60.288 50.000 0.00 0.00 39.34 4.01
1656 2507 3.003689 CAGCAACAGTGGTTAGTTCCAAG 59.996 47.826 0.00 0.00 39.34 3.61
1665 2516 1.027357 CTTGAGCAGCAACAGTGGTT 58.973 50.000 0.00 0.00 37.87 3.67
1699 2550 5.970023 GCAGAATCATGAAGCAACTCATAAC 59.030 40.000 0.00 0.00 34.20 1.89
1772 2626 2.350522 ACAGCGACATGGTTGAGAATC 58.649 47.619 0.00 0.00 0.00 2.52
1811 2665 7.994425 TCCATTATGTGTGTACTTTCATGTT 57.006 32.000 0.00 0.00 0.00 2.71
1933 2787 4.524802 AAGGTCCCAATAAGATGATGCA 57.475 40.909 0.00 0.00 0.00 3.96
1937 2791 6.318648 CGATTGAAAAGGTCCCAATAAGATGA 59.681 38.462 0.00 0.00 31.40 2.92
1974 2828 5.109210 TGAACGTTTCGATATTCATCTGCT 58.891 37.500 0.46 0.00 0.00 4.24
1975 2829 5.389642 TGAACGTTTCGATATTCATCTGC 57.610 39.130 0.46 0.00 0.00 4.26
1976 2830 7.059817 GTCATGAACGTTTCGATATTCATCTG 58.940 38.462 0.46 4.44 39.25 2.90
1977 2831 6.756542 TGTCATGAACGTTTCGATATTCATCT 59.243 34.615 0.46 0.00 39.25 2.90
1978 2832 6.933130 TGTCATGAACGTTTCGATATTCATC 58.067 36.000 0.46 3.66 39.25 2.92
1979 2833 6.535150 ACTGTCATGAACGTTTCGATATTCAT 59.465 34.615 0.46 0.00 41.37 2.57
1980 2834 5.867174 ACTGTCATGAACGTTTCGATATTCA 59.133 36.000 0.46 0.00 35.64 2.57
2025 2879 7.646548 TTCAGCTCAGTCAGTAATACTACAT 57.353 36.000 0.00 0.00 0.00 2.29
2026 2880 7.462571 TTTCAGCTCAGTCAGTAATACTACA 57.537 36.000 0.00 0.00 0.00 2.74
2027 2881 8.410141 AGATTTCAGCTCAGTCAGTAATACTAC 58.590 37.037 0.00 0.00 0.00 2.73
2029 2883 7.416964 AGATTTCAGCTCAGTCAGTAATACT 57.583 36.000 0.00 0.00 0.00 2.12
2044 2898 4.929808 TCGAAACTTCAGGTAGATTTCAGC 59.070 41.667 0.00 0.00 31.11 4.26
2089 2946 6.679327 AAAGGATAACGAAGGAATGCTTAC 57.321 37.500 0.00 0.00 31.93 2.34
2093 2950 5.310720 ACAAAAGGATAACGAAGGAATGC 57.689 39.130 0.00 0.00 0.00 3.56
2098 2955 7.553881 ACATGATACAAAAGGATAACGAAGG 57.446 36.000 0.00 0.00 0.00 3.46
2129 2986 1.137513 GGATACGCGTGGACAATAGC 58.862 55.000 24.59 1.53 0.00 2.97


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.