Multiple sequence alignment - TraesCS6D01G337100

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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 TraesCS6D01G337100 chr6D 100.000 4939 0 0 1 4939 437802180 437807118 0.000000e+00 9121.0
1 TraesCS6D01G337100 chr6D 80.454 573 88 18 1285 1850 437803325 437803880 2.750000e-112 416.0
2 TraesCS6D01G337100 chr6D 80.385 571 92 14 1146 1701 437803464 437804029 2.750000e-112 416.0
3 TraesCS6D01G337100 chr6D 97.959 49 1 0 2255 2303 437804404 437804452 8.810000e-13 86.1
4 TraesCS6D01G337100 chr6D 97.959 49 1 0 2225 2273 437804434 437804482 8.810000e-13 86.1
5 TraesCS6D01G337100 chr6B 92.686 2885 134 29 1285 4153 662510823 662513646 0.000000e+00 4087.0
6 TraesCS6D01G337100 chr6B 85.930 1194 94 30 548 1701 662510212 662511371 0.000000e+00 1206.0
7 TraesCS6D01G337100 chr6B 92.664 518 20 2 4440 4939 662513699 662514216 0.000000e+00 730.0
8 TraesCS6D01G337100 chr6B 86.120 598 50 14 1 565 662509665 662510262 9.090000e-172 614.0
9 TraesCS6D01G337100 chr6A 92.996 2113 85 27 2255 4341 586098527 586100602 0.000000e+00 3024.0
10 TraesCS6D01G337100 chr6A 86.833 2005 157 45 1 1922 586096110 586098090 0.000000e+00 2141.0
11 TraesCS6D01G337100 chr6A 93.233 532 19 9 4424 4939 586100700 586101230 0.000000e+00 767.0
12 TraesCS6D01G337100 chr6A 95.115 348 17 0 1922 2269 586098224 586098571 2.600000e-152 549.0
13 TraesCS6D01G337100 chr6A 80.887 586 75 22 1285 1858 586097320 586097880 1.270000e-115 427.0
14 TraesCS6D01G337100 chr6A 79.418 447 57 14 1426 1860 586097317 586097740 2.910000e-72 283.0
15 TraesCS6D01G337100 chr6A 100.000 31 0 0 4390 4420 586100632 586100662 1.920000e-04 58.4


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 TraesCS6D01G337100 chr6D 437802180 437807118 4938 False 2025.040000 9121 91.351400 1 4939 5 chr6D.!!$F1 4938
1 TraesCS6D01G337100 chr6B 662509665 662514216 4551 False 1659.250000 4087 89.350000 1 4939 4 chr6B.!!$F1 4938
2 TraesCS6D01G337100 chr6A 586096110 586101230 5120 False 1035.628571 3024 89.783143 1 4939 7 chr6A.!!$F1 4938

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
477 517 0.038744 CTCCTGCCCATTGGACACTT 59.961 55.0 3.62 0.0 0.00 3.16 F
1463 1559 0.037326 CCGCTTCTGCTTCCACTGTA 60.037 55.0 0.00 0.0 36.97 2.74 F
1482 1578 0.178813 AGGTAGATGGGGTTTGGGGT 60.179 55.0 0.00 0.0 0.00 4.95 F
1768 2005 0.391661 CGCTGCAGGTAGATGTGGTT 60.392 55.0 17.12 0.0 0.00 3.67 F
2769 3149 0.941542 TTGCCTCAAACGAGTTTCCG 59.058 50.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2292 2669 0.108138 CAGAACGGCCCTTGGTAGAG 60.108 60.000 0.00 0.00 0.00 2.43 R
3330 3717 1.077005 CTTCACCCCATCCCTTTGGAA 59.923 52.381 0.00 0.00 45.98 3.53 R
3398 3788 2.034687 GCCTGCCAGCCTCAAGAA 59.965 61.111 0.00 0.00 0.00 2.52 R
3719 4109 1.805254 GCCTGCAGCAATGGTGTAG 59.195 57.895 20.78 20.78 41.88 2.74 R
4384 4788 0.179084 AACGGTCCATATCACGGCAG 60.179 55.000 0.00 0.00 0.00 4.85 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
27 28 1.518572 CGTCGGTATTGCGCTTCCT 60.519 57.895 9.73 0.00 0.00 3.36
65 66 2.282816 CGGATGTTGTTGCCCCCA 60.283 61.111 0.00 0.00 0.00 4.96
66 67 1.682005 CGGATGTTGTTGCCCCCAT 60.682 57.895 0.00 0.00 0.00 4.00
83 84 1.203758 CCATACGCCGCATCCACTATA 59.796 52.381 0.00 0.00 0.00 1.31
293 317 2.028778 GCACAATGGCGGCAACAA 59.971 55.556 18.31 0.00 0.00 2.83
294 318 1.374505 GCACAATGGCGGCAACAAT 60.375 52.632 18.31 0.00 0.00 2.71
337 361 4.368543 GACGGGGAAGACGGCGTT 62.369 66.667 16.19 0.00 35.23 4.84
376 400 2.884207 CTTCGAGGGCGCGGTAAC 60.884 66.667 8.83 0.00 37.46 2.50
477 517 0.038744 CTCCTGCCCATTGGACACTT 59.961 55.000 3.62 0.00 0.00 3.16
529 569 4.400251 ACGTACGTCCAGAGAAATATGGAA 59.600 41.667 16.72 0.00 46.87 3.53
693 765 0.179078 AACAAGGGACGTACGTGCAA 60.179 50.000 35.38 0.00 38.24 4.08
696 768 1.216941 AAGGGACGTACGTGCAAACG 61.217 55.000 35.38 13.97 44.47 3.60
703 775 3.223186 CGTACGTGCAAACGTTAAGTT 57.777 42.857 7.22 0.00 44.63 2.66
818 899 4.100084 CACGAGCCCCATCAGCCA 62.100 66.667 0.00 0.00 0.00 4.75
860 941 2.143925 GCGTCCCAGATTATAACCAGC 58.856 52.381 0.00 0.00 0.00 4.85
953 1039 1.277557 CTTCCATCTGATCCGATCCCC 59.722 57.143 5.91 0.00 0.00 4.81
1103 1196 2.041405 CCTGGAGGAGGAGGGGTC 60.041 72.222 0.00 0.00 46.33 4.46
1142 1238 0.171455 ACTCAGAAGCGCGTTAGGAG 59.829 55.000 8.43 12.03 0.00 3.69
1143 1239 0.171455 CTCAGAAGCGCGTTAGGAGT 59.829 55.000 8.43 0.00 0.00 3.85
1144 1240 0.601558 TCAGAAGCGCGTTAGGAGTT 59.398 50.000 8.43 0.00 0.00 3.01
1145 1241 0.716108 CAGAAGCGCGTTAGGAGTTG 59.284 55.000 8.43 0.00 0.00 3.16
1146 1242 0.389948 AGAAGCGCGTTAGGAGTTGG 60.390 55.000 8.43 0.00 0.00 3.77
1147 1243 0.389426 GAAGCGCGTTAGGAGTTGGA 60.389 55.000 8.43 0.00 0.00 3.53
1189 1285 1.661341 GCTTCCACTGCAGGTAGATG 58.339 55.000 19.93 13.69 0.00 2.90
1190 1286 1.745141 GCTTCCACTGCAGGTAGATGG 60.745 57.143 19.93 15.98 0.00 3.51
1192 1288 0.252696 TCCACTGCAGGTAGATGGGT 60.253 55.000 19.93 0.00 0.00 4.51
1193 1289 0.620556 CCACTGCAGGTAGATGGGTT 59.379 55.000 19.93 0.00 0.00 4.11
1194 1290 1.004745 CCACTGCAGGTAGATGGGTTT 59.995 52.381 19.93 0.00 0.00 3.27
1196 1292 3.308117 CCACTGCAGGTAGATGGGTTTTA 60.308 47.826 19.93 0.00 0.00 1.52
1197 1293 3.689649 CACTGCAGGTAGATGGGTTTTAC 59.310 47.826 19.93 0.00 0.00 2.01
1198 1294 3.587506 ACTGCAGGTAGATGGGTTTTACT 59.412 43.478 19.93 0.00 0.00 2.24
1199 1295 3.941483 CTGCAGGTAGATGGGTTTTACTG 59.059 47.826 5.57 0.00 0.00 2.74
1220 1316 5.163581 ACTGTAGTAGTTTACTATGGTGGCG 60.164 44.000 0.00 0.00 42.68 5.69
1222 1318 2.498481 AGTAGTTTACTATGGTGGCGCA 59.502 45.455 10.83 0.00 37.23 6.09
1229 1325 1.745087 ACTATGGTGGCGCAAAGATTG 59.255 47.619 10.83 0.00 0.00 2.67
1234 1330 1.742831 GGTGGCGCAAAGATTGTATCA 59.257 47.619 10.83 0.00 0.00 2.15
1246 1342 6.851222 AAGATTGTATCATTGGCGTAGAAG 57.149 37.500 0.00 0.00 0.00 2.85
1321 1417 1.285023 GCTTGTGCTTCCACTGCAG 59.715 57.895 13.48 13.48 42.54 4.41
1366 1462 8.645730 TTAGTATTTTTAATATGGTGACGCGA 57.354 30.769 15.93 0.00 0.00 5.87
1367 1463 7.542534 AGTATTTTTAATATGGTGACGCGAA 57.457 32.000 15.93 0.00 0.00 4.70
1368 1464 7.627340 AGTATTTTTAATATGGTGACGCGAAG 58.373 34.615 15.93 0.00 0.00 3.79
1369 1465 6.671614 ATTTTTAATATGGTGACGCGAAGA 57.328 33.333 15.93 0.00 0.00 2.87
1370 1466 6.671614 TTTTTAATATGGTGACGCGAAGAT 57.328 33.333 15.93 0.00 0.00 2.40
1371 1467 6.671614 TTTTAATATGGTGACGCGAAGATT 57.328 33.333 15.93 4.48 0.00 2.40
1372 1468 6.671614 TTTAATATGGTGACGCGAAGATTT 57.328 33.333 15.93 0.00 0.00 2.17
1373 1469 6.671614 TTAATATGGTGACGCGAAGATTTT 57.328 33.333 15.93 1.64 0.00 1.82
1374 1470 2.900122 ATGGTGACGCGAAGATTTTG 57.100 45.000 15.93 0.00 0.00 2.44
1375 1471 1.588674 TGGTGACGCGAAGATTTTGT 58.411 45.000 15.93 0.00 0.00 2.83
1376 1472 1.529438 TGGTGACGCGAAGATTTTGTC 59.471 47.619 15.93 0.00 0.00 3.18
1377 1473 1.461888 GGTGACGCGAAGATTTTGTCG 60.462 52.381 15.93 0.00 40.24 4.35
1378 1474 1.191647 GTGACGCGAAGATTTTGTCGT 59.808 47.619 15.93 0.00 39.46 4.34
1379 1475 1.862201 TGACGCGAAGATTTTGTCGTT 59.138 42.857 15.93 0.00 39.46 3.85
1380 1476 2.222624 GACGCGAAGATTTTGTCGTTG 58.777 47.619 15.93 0.00 39.46 4.10
1381 1477 1.070175 ACGCGAAGATTTTGTCGTTGG 60.070 47.619 15.93 0.00 39.46 3.77
1382 1478 1.193650 CGCGAAGATTTTGTCGTTGGA 59.806 47.619 0.00 0.00 39.46 3.53
1383 1479 2.721797 CGCGAAGATTTTGTCGTTGGAG 60.722 50.000 0.00 0.00 39.46 3.86
1384 1480 2.223377 GCGAAGATTTTGTCGTTGGAGT 59.777 45.455 0.00 0.00 39.46 3.85
1385 1481 3.430895 GCGAAGATTTTGTCGTTGGAGTA 59.569 43.478 0.00 0.00 39.46 2.59
1386 1482 4.665897 GCGAAGATTTTGTCGTTGGAGTAC 60.666 45.833 0.00 0.00 39.46 2.73
1387 1483 4.446385 CGAAGATTTTGTCGTTGGAGTACA 59.554 41.667 0.00 0.00 32.61 2.90
1388 1484 5.050634 CGAAGATTTTGTCGTTGGAGTACAA 60.051 40.000 0.00 0.00 36.54 2.41
1389 1485 6.347402 CGAAGATTTTGTCGTTGGAGTACAAT 60.347 38.462 0.00 0.00 41.95 2.71
1390 1486 6.877611 AGATTTTGTCGTTGGAGTACAATT 57.122 33.333 0.00 0.00 41.95 2.32
1391 1487 7.272037 AGATTTTGTCGTTGGAGTACAATTT 57.728 32.000 0.00 0.00 41.95 1.82
1392 1488 8.385898 AGATTTTGTCGTTGGAGTACAATTTA 57.614 30.769 0.00 0.00 41.95 1.40
1393 1489 8.842280 AGATTTTGTCGTTGGAGTACAATTTAA 58.158 29.630 0.00 0.00 41.95 1.52
1394 1490 9.453325 GATTTTGTCGTTGGAGTACAATTTAAA 57.547 29.630 0.00 0.00 41.95 1.52
1395 1491 9.974980 ATTTTGTCGTTGGAGTACAATTTAAAT 57.025 25.926 0.00 0.00 41.95 1.40
1396 1492 9.804758 TTTTGTCGTTGGAGTACAATTTAAATT 57.195 25.926 7.64 7.64 41.95 1.82
1402 1498 9.940166 CGTTGGAGTACAATTTAAATTATACCC 57.060 33.333 20.54 19.99 41.95 3.69
1403 1499 9.940166 GTTGGAGTACAATTTAAATTATACCCG 57.060 33.333 20.54 8.41 41.95 5.28
1404 1500 9.683870 TTGGAGTACAATTTAAATTATACCCGT 57.316 29.630 20.54 12.82 30.51 5.28
1405 1501 9.683870 TGGAGTACAATTTAAATTATACCCGTT 57.316 29.630 20.54 7.03 30.51 4.44
1421 1517 9.991906 TTATACCCGTTATTATTTCTCTTGAGG 57.008 33.333 0.00 0.00 0.00 3.86
1422 1518 6.555463 ACCCGTTATTATTTCTCTTGAGGA 57.445 37.500 0.00 0.00 0.00 3.71
1423 1519 6.954232 ACCCGTTATTATTTCTCTTGAGGAA 58.046 36.000 0.00 0.00 0.00 3.36
1424 1520 7.574607 ACCCGTTATTATTTCTCTTGAGGAAT 58.425 34.615 8.94 8.94 0.00 3.01
1425 1521 8.053355 ACCCGTTATTATTTCTCTTGAGGAATT 58.947 33.333 9.19 0.00 0.00 2.17
1426 1522 8.903820 CCCGTTATTATTTCTCTTGAGGAATTT 58.096 33.333 9.19 1.98 0.00 1.82
1427 1523 9.722056 CCGTTATTATTTCTCTTGAGGAATTTG 57.278 33.333 9.19 0.00 0.00 2.32
1428 1524 9.722056 CGTTATTATTTCTCTTGAGGAATTTGG 57.278 33.333 9.19 0.00 0.00 3.28
1430 1526 9.989296 TTATTATTTCTCTTGAGGAATTTGGGA 57.011 29.630 9.19 0.00 0.00 4.37
1432 1528 6.786967 ATTTCTCTTGAGGAATTTGGGATG 57.213 37.500 0.00 0.00 0.00 3.51
1433 1529 4.240881 TCTCTTGAGGAATTTGGGATGG 57.759 45.455 0.00 0.00 0.00 3.51
1434 1530 2.692041 CTCTTGAGGAATTTGGGATGGC 59.308 50.000 0.00 0.00 0.00 4.40
1435 1531 1.406539 CTTGAGGAATTTGGGATGGCG 59.593 52.381 0.00 0.00 0.00 5.69
1436 1532 1.037030 TGAGGAATTTGGGATGGCGC 61.037 55.000 0.00 0.00 0.00 6.53
1437 1533 1.000233 AGGAATTTGGGATGGCGCA 60.000 52.632 10.83 0.00 34.89 6.09
1438 1534 1.039233 AGGAATTTGGGATGGCGCAG 61.039 55.000 10.83 0.00 38.28 5.18
1456 1552 2.747855 CCACCCCGCTTCTGCTTC 60.748 66.667 0.00 0.00 36.97 3.86
1457 1553 2.747855 CACCCCGCTTCTGCTTCC 60.748 66.667 0.00 0.00 36.97 3.46
1458 1554 3.249189 ACCCCGCTTCTGCTTCCA 61.249 61.111 0.00 0.00 36.97 3.53
1459 1555 2.747855 CCCCGCTTCTGCTTCCAC 60.748 66.667 0.00 0.00 36.97 4.02
1460 1556 2.348998 CCCGCTTCTGCTTCCACT 59.651 61.111 0.00 0.00 36.97 4.00
1461 1557 2.037136 CCCGCTTCTGCTTCCACTG 61.037 63.158 0.00 0.00 36.97 3.66
1462 1558 1.302033 CCGCTTCTGCTTCCACTGT 60.302 57.895 0.00 0.00 36.97 3.55
1463 1559 0.037326 CCGCTTCTGCTTCCACTGTA 60.037 55.000 0.00 0.00 36.97 2.74
1464 1560 1.354040 CGCTTCTGCTTCCACTGTAG 58.646 55.000 0.00 0.00 36.97 2.74
1465 1561 1.731720 GCTTCTGCTTCCACTGTAGG 58.268 55.000 0.00 0.00 36.03 3.18
1466 1562 1.002544 GCTTCTGCTTCCACTGTAGGT 59.997 52.381 0.00 0.00 36.03 3.08
1467 1563 2.233922 GCTTCTGCTTCCACTGTAGGTA 59.766 50.000 0.00 0.00 36.03 3.08
1468 1564 3.677424 GCTTCTGCTTCCACTGTAGGTAG 60.677 52.174 0.00 0.00 36.03 3.18
1469 1565 3.451402 TCTGCTTCCACTGTAGGTAGA 57.549 47.619 6.95 0.00 0.00 2.59
1470 1566 3.982516 TCTGCTTCCACTGTAGGTAGAT 58.017 45.455 6.95 0.00 0.00 1.98
1471 1567 3.701542 TCTGCTTCCACTGTAGGTAGATG 59.298 47.826 6.95 0.00 0.00 2.90
1472 1568 2.766263 TGCTTCCACTGTAGGTAGATGG 59.234 50.000 6.95 0.00 0.00 3.51
1473 1569 2.103263 GCTTCCACTGTAGGTAGATGGG 59.897 54.545 6.95 0.00 0.00 4.00
1474 1570 2.471815 TCCACTGTAGGTAGATGGGG 57.528 55.000 0.00 0.00 0.00 4.96
1475 1571 1.649633 TCCACTGTAGGTAGATGGGGT 59.350 52.381 0.00 0.00 0.00 4.95
1476 1572 2.045326 TCCACTGTAGGTAGATGGGGTT 59.955 50.000 0.00 0.00 0.00 4.11
1477 1573 2.844348 CCACTGTAGGTAGATGGGGTTT 59.156 50.000 0.00 0.00 0.00 3.27
1478 1574 3.370527 CCACTGTAGGTAGATGGGGTTTG 60.371 52.174 0.00 0.00 0.00 2.93
1479 1575 2.844348 ACTGTAGGTAGATGGGGTTTGG 59.156 50.000 0.00 0.00 0.00 3.28
1480 1576 2.172717 CTGTAGGTAGATGGGGTTTGGG 59.827 54.545 0.00 0.00 0.00 4.12
1481 1577 1.493446 GTAGGTAGATGGGGTTTGGGG 59.507 57.143 0.00 0.00 0.00 4.96
1482 1578 0.178813 AGGTAGATGGGGTTTGGGGT 60.179 55.000 0.00 0.00 0.00 4.95
1483 1579 0.708209 GGTAGATGGGGTTTGGGGTT 59.292 55.000 0.00 0.00 0.00 4.11
1484 1580 1.078159 GGTAGATGGGGTTTGGGGTTT 59.922 52.381 0.00 0.00 0.00 3.27
1485 1581 2.493875 GGTAGATGGGGTTTGGGGTTTT 60.494 50.000 0.00 0.00 0.00 2.43
1486 1582 3.245694 GGTAGATGGGGTTTGGGGTTTTA 60.246 47.826 0.00 0.00 0.00 1.52
1487 1583 3.184382 AGATGGGGTTTGGGGTTTTAG 57.816 47.619 0.00 0.00 0.00 1.85
1488 1584 2.453212 AGATGGGGTTTGGGGTTTTAGT 59.547 45.455 0.00 0.00 0.00 2.24
1489 1585 3.663632 AGATGGGGTTTGGGGTTTTAGTA 59.336 43.478 0.00 0.00 0.00 1.82
1490 1586 4.296583 AGATGGGGTTTGGGGTTTTAGTAT 59.703 41.667 0.00 0.00 0.00 2.12
1491 1587 4.488914 TGGGGTTTGGGGTTTTAGTATT 57.511 40.909 0.00 0.00 0.00 1.89
1492 1588 4.828963 TGGGGTTTGGGGTTTTAGTATTT 58.171 39.130 0.00 0.00 0.00 1.40
1493 1589 5.225227 TGGGGTTTGGGGTTTTAGTATTTT 58.775 37.500 0.00 0.00 0.00 1.82
1571 1805 8.668353 CATTATTTTCTCTGTTGAGGAATTCGA 58.332 33.333 0.00 0.00 37.62 3.71
1595 1831 2.044946 GCATCCACCCCGCTTCTT 60.045 61.111 0.00 0.00 0.00 2.52
1617 1854 3.271225 TCTTCCACTGTAGGTAGATGGGA 59.729 47.826 0.00 0.00 31.12 4.37
1658 1895 1.745232 ATGGTGGCGCGAAGATTTTA 58.255 45.000 12.10 0.00 0.00 1.52
1762 1999 2.801631 GCCTCCGCTGCAGGTAGAT 61.802 63.158 17.12 0.00 32.98 1.98
1766 2003 1.522355 CCGCTGCAGGTAGATGTGG 60.522 63.158 17.12 0.00 0.00 4.17
1767 2004 1.219124 CGCTGCAGGTAGATGTGGT 59.781 57.895 17.12 0.00 0.00 4.16
1768 2005 0.391661 CGCTGCAGGTAGATGTGGTT 60.392 55.000 17.12 0.00 0.00 3.67
1769 2006 1.373570 GCTGCAGGTAGATGTGGTTC 58.626 55.000 17.12 0.00 0.00 3.62
1881 2121 6.778821 TCAAATAGGAAGTTCAACTCATCCA 58.221 36.000 10.38 0.00 29.49 3.41
1933 2310 4.630111 TGTTTTGCCTTGATTGATTGACC 58.370 39.130 0.00 0.00 0.00 4.02
2166 2543 2.871096 TTAATGAACCGCTCCCACTT 57.129 45.000 0.00 0.00 0.00 3.16
2276 2653 6.010219 CCAAGGAAATCTCTACCAAGGAAAA 58.990 40.000 0.00 0.00 0.00 2.29
2277 2654 6.071896 CCAAGGAAATCTCTACCAAGGAAAAC 60.072 42.308 0.00 0.00 0.00 2.43
2278 2655 6.455690 AGGAAATCTCTACCAAGGAAAACT 57.544 37.500 0.00 0.00 0.00 2.66
2279 2656 6.477253 AGGAAATCTCTACCAAGGAAAACTC 58.523 40.000 0.00 0.00 0.00 3.01
2280 2657 6.273495 AGGAAATCTCTACCAAGGAAAACTCT 59.727 38.462 0.00 0.00 0.00 3.24
2281 2658 7.458170 AGGAAATCTCTACCAAGGAAAACTCTA 59.542 37.037 0.00 0.00 0.00 2.43
2282 2659 7.549842 GGAAATCTCTACCAAGGAAAACTCTAC 59.450 40.741 0.00 0.00 0.00 2.59
2283 2660 5.997384 TCTCTACCAAGGAAAACTCTACC 57.003 43.478 0.00 0.00 0.00 3.18
2284 2661 5.399991 TCTCTACCAAGGAAAACTCTACCA 58.600 41.667 0.00 0.00 0.00 3.25
2285 2662 5.842328 TCTCTACCAAGGAAAACTCTACCAA 59.158 40.000 0.00 0.00 0.00 3.67
2286 2663 6.014499 TCTCTACCAAGGAAAACTCTACCAAG 60.014 42.308 0.00 0.00 0.00 3.61
2287 2664 4.100279 ACCAAGGAAAACTCTACCAAGG 57.900 45.455 0.00 0.00 0.00 3.61
2288 2665 3.720002 ACCAAGGAAAACTCTACCAAGGA 59.280 43.478 0.00 0.00 0.00 3.36
2289 2666 4.167307 ACCAAGGAAAACTCTACCAAGGAA 59.833 41.667 0.00 0.00 0.00 3.36
2290 2667 5.137551 CCAAGGAAAACTCTACCAAGGAAA 58.862 41.667 0.00 0.00 0.00 3.13
2291 2668 5.775195 CCAAGGAAAACTCTACCAAGGAAAT 59.225 40.000 0.00 0.00 0.00 2.17
2292 2669 6.071896 CCAAGGAAAACTCTACCAAGGAAATC 60.072 42.308 0.00 0.00 0.00 2.17
2769 3149 0.941542 TTGCCTCAAACGAGTTTCCG 59.058 50.000 0.00 0.00 0.00 4.30
2998 3378 6.435430 TGATTTATGGTGTAGATGTGTTGC 57.565 37.500 0.00 0.00 0.00 4.17
3131 3515 1.080974 GCATGTTTTGCGCTGCTCT 60.081 52.632 9.73 0.00 42.54 4.09
3236 3620 6.774170 TCATGTCAGATTCTCCATTTATTGGG 59.226 38.462 0.00 0.00 46.45 4.12
3238 3622 6.730447 TGTCAGATTCTCCATTTATTGGGAA 58.270 36.000 0.00 0.00 46.45 3.97
3318 3702 6.923928 CACATCATGTGTTACCATGTGATA 57.076 37.500 9.87 0.00 44.76 2.15
3324 3711 7.041721 TCATGTGTTACCATGTGATACTTCTC 58.958 38.462 11.51 0.00 42.29 2.87
3330 3717 3.840666 ACCATGTGATACTTCTCCAGTGT 59.159 43.478 0.00 0.00 35.97 3.55
3398 3788 6.394345 AAGTATCCCCTTCTTCAGACAAAT 57.606 37.500 0.00 0.00 0.00 2.32
3401 3791 5.527026 ATCCCCTTCTTCAGACAAATTCT 57.473 39.130 0.00 0.00 33.33 2.40
3442 3832 6.765989 TCCATGCCACACTTATAATCTTGTAC 59.234 38.462 0.00 0.00 0.00 2.90
3443 3833 6.767902 CCATGCCACACTTATAATCTTGTACT 59.232 38.462 0.00 0.00 0.00 2.73
3444 3834 7.931407 CCATGCCACACTTATAATCTTGTACTA 59.069 37.037 0.00 0.00 0.00 1.82
3719 4109 1.661112 GTATCTGTTCCTGAGCGCAAC 59.339 52.381 11.47 5.24 0.00 4.17
3720 4110 0.322975 ATCTGTTCCTGAGCGCAACT 59.677 50.000 11.47 0.00 0.00 3.16
3885 4278 0.534203 GGCGGGTCTGTTTGAGAACA 60.534 55.000 0.00 0.00 40.67 3.18
4016 4418 4.822350 GCCTTCTTAGACTTGTTTTGGTCT 59.178 41.667 0.00 0.00 43.93 3.85
4087 4489 1.247567 ACCCCATTTCGCTGTTCTTG 58.752 50.000 0.00 0.00 0.00 3.02
4101 4503 4.201666 GCTGTTCTTGCTACATTTCTCTCG 60.202 45.833 0.00 0.00 0.00 4.04
4112 4514 5.074584 ACATTTCTCTCGGTACTTTCTCC 57.925 43.478 0.00 0.00 0.00 3.71
4125 4527 0.181587 TTTCTCCGTTGGCCTGTGAA 59.818 50.000 3.32 0.09 0.00 3.18
4214 4616 8.299570 CAAAGTATCCACAAATTAACAGCTTCT 58.700 33.333 0.00 0.00 0.00 2.85
4230 4632 3.381908 AGCTTCTCCGGTAGAGTGTTATG 59.618 47.826 0.00 0.00 43.71 1.90
4268 4670 4.864806 TCATTCAACTACTGCATCTCGTTC 59.135 41.667 0.00 0.00 0.00 3.95
4330 4734 2.887152 GTGTTTGGATTGTTCTCCTGCT 59.113 45.455 0.00 0.00 36.20 4.24
4341 4745 4.144297 TGTTCTCCTGCTAGCAAATGTTT 58.856 39.130 19.86 0.00 0.00 2.83
4342 4746 4.216257 TGTTCTCCTGCTAGCAAATGTTTC 59.784 41.667 19.86 7.51 0.00 2.78
4343 4747 4.019792 TCTCCTGCTAGCAAATGTTTCA 57.980 40.909 19.86 0.00 0.00 2.69
4345 4749 3.485394 TCCTGCTAGCAAATGTTTCACA 58.515 40.909 19.86 0.00 0.00 3.58
4347 4751 4.523943 TCCTGCTAGCAAATGTTTCACAAT 59.476 37.500 19.86 0.00 0.00 2.71
4348 4752 4.860907 CCTGCTAGCAAATGTTTCACAATC 59.139 41.667 19.86 0.00 0.00 2.67
4349 4753 5.336213 CCTGCTAGCAAATGTTTCACAATCT 60.336 40.000 19.86 0.00 0.00 2.40
4350 4754 6.088016 TGCTAGCAAATGTTTCACAATCTT 57.912 33.333 16.84 0.00 0.00 2.40
4352 4756 7.656412 TGCTAGCAAATGTTTCACAATCTTTA 58.344 30.769 16.84 0.00 0.00 1.85
4353 4757 7.594758 TGCTAGCAAATGTTTCACAATCTTTAC 59.405 33.333 16.84 0.00 0.00 2.01
4354 4758 7.809806 GCTAGCAAATGTTTCACAATCTTTACT 59.190 33.333 10.63 0.00 0.00 2.24
4355 4759 9.334693 CTAGCAAATGTTTCACAATCTTTACTC 57.665 33.333 0.00 0.00 0.00 2.59
4357 4761 9.066892 AGCAAATGTTTCACAATCTTTACTCTA 57.933 29.630 0.00 0.00 0.00 2.43
4364 4768 9.841880 GTTTCACAATCTTTACTCTATTTTCCC 57.158 33.333 0.00 0.00 0.00 3.97
4365 4769 8.575649 TTCACAATCTTTACTCTATTTTCCCC 57.424 34.615 0.00 0.00 0.00 4.81
4366 4770 7.928873 TCACAATCTTTACTCTATTTTCCCCT 58.071 34.615 0.00 0.00 0.00 4.79
4367 4771 7.829211 TCACAATCTTTACTCTATTTTCCCCTG 59.171 37.037 0.00 0.00 0.00 4.45
4368 4772 7.829211 CACAATCTTTACTCTATTTTCCCCTGA 59.171 37.037 0.00 0.00 0.00 3.86
4369 4773 7.829706 ACAATCTTTACTCTATTTTCCCCTGAC 59.170 37.037 0.00 0.00 0.00 3.51
4370 4774 6.945636 TCTTTACTCTATTTTCCCCTGACA 57.054 37.500 0.00 0.00 0.00 3.58
4371 4775 7.510675 TCTTTACTCTATTTTCCCCTGACAT 57.489 36.000 0.00 0.00 0.00 3.06
4372 4776 7.338710 TCTTTACTCTATTTTCCCCTGACATG 58.661 38.462 0.00 0.00 0.00 3.21
4373 4777 3.891049 ACTCTATTTTCCCCTGACATGC 58.109 45.455 0.00 0.00 0.00 4.06
4374 4778 3.217626 CTCTATTTTCCCCTGACATGCC 58.782 50.000 0.00 0.00 0.00 4.40
4375 4779 2.580322 TCTATTTTCCCCTGACATGCCA 59.420 45.455 0.00 0.00 0.00 4.92
4376 4780 2.555732 ATTTTCCCCTGACATGCCAT 57.444 45.000 0.00 0.00 0.00 4.40
4377 4781 2.323999 TTTTCCCCTGACATGCCATT 57.676 45.000 0.00 0.00 0.00 3.16
4378 4782 1.851304 TTTCCCCTGACATGCCATTC 58.149 50.000 0.00 0.00 0.00 2.67
4379 4783 0.703488 TTCCCCTGACATGCCATTCA 59.297 50.000 0.00 0.00 0.00 2.57
4380 4784 0.928505 TCCCCTGACATGCCATTCAT 59.071 50.000 0.00 0.00 35.31 2.57
4381 4785 1.288633 TCCCCTGACATGCCATTCATT 59.711 47.619 0.00 0.00 31.79 2.57
4382 4786 2.112998 CCCCTGACATGCCATTCATTT 58.887 47.619 0.00 0.00 31.79 2.32
4383 4787 2.159014 CCCCTGACATGCCATTCATTTG 60.159 50.000 0.00 0.00 31.79 2.32
4384 4788 2.546778 CCTGACATGCCATTCATTTGC 58.453 47.619 0.00 0.00 31.79 3.68
4385 4789 2.167693 CCTGACATGCCATTCATTTGCT 59.832 45.455 0.00 0.00 31.79 3.91
4386 4790 3.186909 CTGACATGCCATTCATTTGCTG 58.813 45.455 0.00 0.00 31.79 4.41
4387 4791 1.931172 GACATGCCATTCATTTGCTGC 59.069 47.619 0.00 0.00 31.79 5.25
4388 4792 1.295792 CATGCCATTCATTTGCTGCC 58.704 50.000 0.00 0.00 31.79 4.85
4420 4824 1.802880 CGTTGGAGAAGCCCTGATACG 60.803 57.143 0.00 0.00 34.97 3.06
4421 4825 1.207329 GTTGGAGAAGCCCTGATACGT 59.793 52.381 0.00 0.00 34.97 3.57
4422 4826 1.112113 TGGAGAAGCCCTGATACGTC 58.888 55.000 0.00 0.00 34.97 4.34
4436 4874 2.537639 TACGTCATGACACTAGTGCG 57.462 50.000 24.93 17.95 0.00 5.34
4461 4899 7.010830 CGTCACATTTGTAGATCAGATGTCATT 59.989 37.037 0.00 0.00 44.87 2.57
4463 4901 7.825761 TCACATTTGTAGATCAGATGTCATTGT 59.174 33.333 0.00 0.00 44.87 2.71
4492 4932 9.839589 CTTCGAAATATGAAATAAAAATGCAGC 57.160 29.630 0.00 0.00 29.06 5.25
4493 4933 8.923609 TCGAAATATGAAATAAAAATGCAGCA 57.076 26.923 0.00 0.00 29.06 4.41
4691 5148 3.112263 TCCGGGATACTCTCAAATTGGT 58.888 45.455 0.00 0.00 0.00 3.67
4803 5260 1.840737 CCTCTTCTCCTTCCTCGTCA 58.159 55.000 0.00 0.00 0.00 4.35
4818 5275 1.259507 TCGTCAAAGGCTTCGTTTTCG 59.740 47.619 0.00 0.87 45.64 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 3.194755 TCAATATAGTGGATGCGGCGTAT 59.805 43.478 11.03 11.03 0.00 3.06
66 67 2.559231 TCAATATAGTGGATGCGGCGTA 59.441 45.455 9.37 3.65 0.00 4.42
123 124 0.933791 AGAGGAGAGGAGGGGATGGT 60.934 60.000 0.00 0.00 0.00 3.55
234 250 0.532640 ATGTTGACACTCGCACAGCA 60.533 50.000 0.00 0.00 0.00 4.41
237 253 1.799994 CATGATGTTGACACTCGCACA 59.200 47.619 0.00 0.00 0.00 4.57
289 313 1.004745 ACATCTTCCCCGAGCATTGTT 59.995 47.619 0.00 0.00 0.00 2.83
293 317 1.832912 GGACATCTTCCCCGAGCAT 59.167 57.895 0.00 0.00 38.70 3.79
294 318 3.309582 GGACATCTTCCCCGAGCA 58.690 61.111 0.00 0.00 38.70 4.26
316 340 4.143333 CCGTCTTCCCCGTCGCAT 62.143 66.667 0.00 0.00 0.00 4.73
392 416 2.761195 CGGAGTCGAGACCATGCGA 61.761 63.158 8.26 0.00 39.00 5.10
477 517 1.177895 TGCCTCTTCGCCATTTTGCA 61.178 50.000 0.00 0.00 0.00 4.08
512 552 7.454260 AAGTTTGTTCCATATTTCTCTGGAC 57.546 36.000 0.00 0.00 41.20 4.02
573 613 4.752101 CGTTTGTCCACATTTCTCTCTTCT 59.248 41.667 0.00 0.00 0.00 2.85
693 765 2.855660 GTTGCCACCAACTTAACGTT 57.144 45.000 5.88 5.88 46.13 3.99
703 775 4.308458 CTCGGTCGGTTGCCACCA 62.308 66.667 7.86 0.00 44.53 4.17
929 1012 3.262915 GGATCGGATCAGATGGAAGGAAT 59.737 47.826 18.99 0.00 0.00 3.01
953 1039 2.498726 GAGAGGAAGGAGCAGGCG 59.501 66.667 0.00 0.00 0.00 5.52
1050 1140 2.125912 CGAGGGGCAACAGTCTCG 60.126 66.667 0.00 0.00 43.00 4.04
1103 1196 2.202932 CCTCATTCCCGTCGCCTG 60.203 66.667 0.00 0.00 0.00 4.85
1189 1285 9.591792 CCATAGTAAACTACTACAGTAAAACCC 57.408 37.037 0.00 0.00 43.46 4.11
1193 1289 8.253113 GCCACCATAGTAAACTACTACAGTAAA 58.747 37.037 0.00 0.00 43.46 2.01
1194 1290 7.415541 CGCCACCATAGTAAACTACTACAGTAA 60.416 40.741 0.00 0.00 43.46 2.24
1196 1292 5.163581 CGCCACCATAGTAAACTACTACAGT 60.164 44.000 0.00 0.00 43.46 3.55
1197 1293 5.279384 CGCCACCATAGTAAACTACTACAG 58.721 45.833 0.00 0.00 43.46 2.74
1198 1294 4.440525 GCGCCACCATAGTAAACTACTACA 60.441 45.833 0.00 0.00 43.46 2.74
1199 1295 4.047142 GCGCCACCATAGTAAACTACTAC 58.953 47.826 0.00 0.00 43.46 2.73
1220 1316 4.032703 ACGCCAATGATACAATCTTTGC 57.967 40.909 9.04 5.54 40.87 3.68
1222 1318 6.823689 ACTTCTACGCCAATGATACAATCTTT 59.176 34.615 0.00 0.00 0.00 2.52
1234 1330 7.994334 TGGGTATAATTTAACTTCTACGCCAAT 59.006 33.333 12.30 0.00 0.00 3.16
1291 1387 1.149174 CACAAGCGGGGATGGCTAT 59.851 57.895 0.00 0.00 40.53 2.97
1321 1417 0.708209 AACCCCAAACCCCATCTACC 59.292 55.000 0.00 0.00 0.00 3.18
1358 1454 1.191647 ACGACAAAATCTTCGCGTCAC 59.808 47.619 5.77 0.00 38.88 3.67
1366 1462 6.877611 ATTGTACTCCAACGACAAAATCTT 57.122 33.333 0.00 0.00 36.70 2.40
1367 1463 6.877611 AATTGTACTCCAACGACAAAATCT 57.122 33.333 0.00 0.00 36.70 2.40
1368 1464 9.453325 TTTAAATTGTACTCCAACGACAAAATC 57.547 29.630 0.00 0.00 36.70 2.17
1369 1465 9.974980 ATTTAAATTGTACTCCAACGACAAAAT 57.025 25.926 0.00 0.00 36.70 1.82
1370 1466 9.804758 AATTTAAATTGTACTCCAACGACAAAA 57.195 25.926 12.62 0.00 36.70 2.44
1376 1472 9.940166 GGGTATAATTTAAATTGTACTCCAACG 57.060 33.333 30.53 0.00 40.60 4.10
1377 1473 9.940166 CGGGTATAATTTAAATTGTACTCCAAC 57.060 33.333 30.53 20.40 39.12 3.77
1378 1474 9.683870 ACGGGTATAATTTAAATTGTACTCCAA 57.316 29.630 30.53 11.26 39.12 3.53
1379 1475 9.683870 AACGGGTATAATTTAAATTGTACTCCA 57.316 29.630 30.53 11.83 39.12 3.86
1395 1491 9.991906 CCTCAAGAGAAATAATAACGGGTATAA 57.008 33.333 0.00 0.00 0.00 0.98
1396 1492 9.370930 TCCTCAAGAGAAATAATAACGGGTATA 57.629 33.333 0.00 0.00 0.00 1.47
1397 1493 8.258850 TCCTCAAGAGAAATAATAACGGGTAT 57.741 34.615 0.00 0.00 0.00 2.73
1398 1494 7.664552 TCCTCAAGAGAAATAATAACGGGTA 57.335 36.000 0.00 0.00 0.00 3.69
1399 1495 6.555463 TCCTCAAGAGAAATAATAACGGGT 57.445 37.500 0.00 0.00 0.00 5.28
1400 1496 8.451908 AATTCCTCAAGAGAAATAATAACGGG 57.548 34.615 0.00 0.00 0.00 5.28
1401 1497 9.722056 CAAATTCCTCAAGAGAAATAATAACGG 57.278 33.333 0.00 0.00 0.00 4.44
1402 1498 9.722056 CCAAATTCCTCAAGAGAAATAATAACG 57.278 33.333 0.00 0.00 0.00 3.18
1404 1500 9.989296 TCCCAAATTCCTCAAGAGAAATAATAA 57.011 29.630 0.00 0.00 0.00 1.40
1406 1502 8.921205 CATCCCAAATTCCTCAAGAGAAATAAT 58.079 33.333 0.00 0.00 0.00 1.28
1407 1503 7.342799 CCATCCCAAATTCCTCAAGAGAAATAA 59.657 37.037 0.00 0.00 0.00 1.40
1408 1504 6.835488 CCATCCCAAATTCCTCAAGAGAAATA 59.165 38.462 0.00 0.00 0.00 1.40
1409 1505 5.659971 CCATCCCAAATTCCTCAAGAGAAAT 59.340 40.000 0.00 0.00 0.00 2.17
1410 1506 5.018809 CCATCCCAAATTCCTCAAGAGAAA 58.981 41.667 0.00 0.00 0.00 2.52
1411 1507 4.603131 CCATCCCAAATTCCTCAAGAGAA 58.397 43.478 0.00 0.00 0.00 2.87
1412 1508 3.625716 GCCATCCCAAATTCCTCAAGAGA 60.626 47.826 0.00 0.00 0.00 3.10
1413 1509 2.692041 GCCATCCCAAATTCCTCAAGAG 59.308 50.000 0.00 0.00 0.00 2.85
1414 1510 2.738743 GCCATCCCAAATTCCTCAAGA 58.261 47.619 0.00 0.00 0.00 3.02
1415 1511 1.406539 CGCCATCCCAAATTCCTCAAG 59.593 52.381 0.00 0.00 0.00 3.02
1416 1512 1.473258 CGCCATCCCAAATTCCTCAA 58.527 50.000 0.00 0.00 0.00 3.02
1417 1513 1.037030 GCGCCATCCCAAATTCCTCA 61.037 55.000 0.00 0.00 0.00 3.86
1418 1514 1.037030 TGCGCCATCCCAAATTCCTC 61.037 55.000 4.18 0.00 0.00 3.71
1419 1515 1.000233 TGCGCCATCCCAAATTCCT 60.000 52.632 4.18 0.00 0.00 3.36
1420 1516 1.438814 CTGCGCCATCCCAAATTCC 59.561 57.895 4.18 0.00 0.00 3.01
1421 1517 1.227060 GCTGCGCCATCCCAAATTC 60.227 57.895 4.18 0.00 0.00 2.17
1422 1518 2.894919 GCTGCGCCATCCCAAATT 59.105 55.556 4.18 0.00 0.00 1.82
1446 1542 1.002544 ACCTACAGTGGAAGCAGAAGC 59.997 52.381 0.00 0.00 42.56 3.86
1447 1543 3.764434 TCTACCTACAGTGGAAGCAGAAG 59.236 47.826 0.00 0.00 32.20 2.85
1448 1544 3.774734 TCTACCTACAGTGGAAGCAGAA 58.225 45.455 0.00 0.00 32.20 3.02
1449 1545 3.451402 TCTACCTACAGTGGAAGCAGA 57.549 47.619 0.00 0.00 32.20 4.26
1450 1546 3.181471 CCATCTACCTACAGTGGAAGCAG 60.181 52.174 0.00 0.00 39.70 4.24
1451 1547 2.766263 CCATCTACCTACAGTGGAAGCA 59.234 50.000 0.00 0.00 39.70 3.91
1452 1548 2.103263 CCCATCTACCTACAGTGGAAGC 59.897 54.545 0.00 0.00 39.70 3.86
1453 1549 2.700897 CCCCATCTACCTACAGTGGAAG 59.299 54.545 0.00 0.00 39.70 3.46
1454 1550 2.045326 ACCCCATCTACCTACAGTGGAA 59.955 50.000 0.00 0.00 39.70 3.53
1455 1551 1.649633 ACCCCATCTACCTACAGTGGA 59.350 52.381 0.00 0.00 40.67 4.02
1456 1552 2.176247 ACCCCATCTACCTACAGTGG 57.824 55.000 0.00 0.00 0.00 4.00
1457 1553 3.370527 CCAAACCCCATCTACCTACAGTG 60.371 52.174 0.00 0.00 0.00 3.66
1458 1554 2.844348 CCAAACCCCATCTACCTACAGT 59.156 50.000 0.00 0.00 0.00 3.55
1459 1555 2.172717 CCCAAACCCCATCTACCTACAG 59.827 54.545 0.00 0.00 0.00 2.74
1460 1556 2.201830 CCCAAACCCCATCTACCTACA 58.798 52.381 0.00 0.00 0.00 2.74
1461 1557 1.493446 CCCCAAACCCCATCTACCTAC 59.507 57.143 0.00 0.00 0.00 3.18
1462 1558 1.083222 ACCCCAAACCCCATCTACCTA 59.917 52.381 0.00 0.00 0.00 3.08
1463 1559 0.178813 ACCCCAAACCCCATCTACCT 60.179 55.000 0.00 0.00 0.00 3.08
1464 1560 0.708209 AACCCCAAACCCCATCTACC 59.292 55.000 0.00 0.00 0.00 3.18
1465 1561 2.615986 AAACCCCAAACCCCATCTAC 57.384 50.000 0.00 0.00 0.00 2.59
1466 1562 3.663632 ACTAAAACCCCAAACCCCATCTA 59.336 43.478 0.00 0.00 0.00 1.98
1467 1563 2.453212 ACTAAAACCCCAAACCCCATCT 59.547 45.455 0.00 0.00 0.00 2.90
1468 1564 2.897350 ACTAAAACCCCAAACCCCATC 58.103 47.619 0.00 0.00 0.00 3.51
1469 1565 4.703101 ATACTAAAACCCCAAACCCCAT 57.297 40.909 0.00 0.00 0.00 4.00
1470 1566 4.488914 AATACTAAAACCCCAAACCCCA 57.511 40.909 0.00 0.00 0.00 4.96
1471 1567 5.829062 AAAATACTAAAACCCCAAACCCC 57.171 39.130 0.00 0.00 0.00 4.95
1478 1574 9.955208 CGACCATATTAAAAATACTAAAACCCC 57.045 33.333 0.00 0.00 0.00 4.95
1479 1575 9.454585 GCGACCATATTAAAAATACTAAAACCC 57.545 33.333 0.00 0.00 0.00 4.11
1480 1576 9.161684 CGCGACCATATTAAAAATACTAAAACC 57.838 33.333 0.00 0.00 0.00 3.27
1481 1577 9.706846 ACGCGACCATATTAAAAATACTAAAAC 57.293 29.630 15.93 0.00 0.00 2.43
1482 1578 9.705471 CACGCGACCATATTAAAAATACTAAAA 57.295 29.630 15.93 0.00 0.00 1.52
1483 1579 9.096160 TCACGCGACCATATTAAAAATACTAAA 57.904 29.630 15.93 0.00 0.00 1.85
1484 1580 8.645730 TCACGCGACCATATTAAAAATACTAA 57.354 30.769 15.93 0.00 0.00 2.24
1485 1581 8.645730 TTCACGCGACCATATTAAAAATACTA 57.354 30.769 15.93 0.00 0.00 1.82
1486 1582 7.493320 TCTTCACGCGACCATATTAAAAATACT 59.507 33.333 15.93 0.00 0.00 2.12
1487 1583 7.623770 TCTTCACGCGACCATATTAAAAATAC 58.376 34.615 15.93 0.00 0.00 1.89
1488 1584 7.773864 TCTTCACGCGACCATATTAAAAATA 57.226 32.000 15.93 0.00 0.00 1.40
1489 1585 6.671614 TCTTCACGCGACCATATTAAAAAT 57.328 33.333 15.93 0.00 0.00 1.82
1490 1586 6.671614 ATCTTCACGCGACCATATTAAAAA 57.328 33.333 15.93 0.00 0.00 1.94
1491 1587 6.671614 AATCTTCACGCGACCATATTAAAA 57.328 33.333 15.93 0.00 0.00 1.52
1492 1588 6.671614 AAATCTTCACGCGACCATATTAAA 57.328 33.333 15.93 0.00 0.00 1.52
1493 1589 6.092944 ACAAAATCTTCACGCGACCATATTAA 59.907 34.615 15.93 0.00 0.00 1.40
1503 1599 3.177643 GTCAACAACAAAATCTTCACGCG 59.822 43.478 3.53 3.53 0.00 6.01
1558 1792 1.000145 GCCGTCTCGAATTCCTCAAC 59.000 55.000 0.00 0.00 0.00 3.18
1595 1831 3.271225 TCCCATCTACCTACAGTGGAAGA 59.729 47.826 0.00 0.00 39.70 2.87
1625 1862 6.073657 TCGCGCCACCATATAAAATACTAAAC 60.074 38.462 0.00 0.00 0.00 2.01
1701 1938 4.927425 TCGTCGTCCTGAATTCCTAAAAAG 59.073 41.667 2.27 0.00 0.00 2.27
1702 1939 4.885413 TCGTCGTCCTGAATTCCTAAAAA 58.115 39.130 2.27 0.00 0.00 1.94
1706 1943 2.159282 GCTTCGTCGTCCTGAATTCCTA 60.159 50.000 2.27 0.00 0.00 2.94
1801 2041 4.759516 ATTCTACGCCAACGACAAAATT 57.240 36.364 0.00 0.00 43.93 1.82
1900 2143 8.610896 CAATCAAGGCAAAACATTAACTTCAAA 58.389 29.630 0.00 0.00 0.00 2.69
2106 2483 7.568349 TGTCCTGCAAAACATAATCTCTCTAT 58.432 34.615 0.00 0.00 0.00 1.98
2166 2543 3.135994 GCTCTTTTTCAACCGTAGACCA 58.864 45.455 0.00 0.00 0.00 4.02
2213 2590 6.317893 GGTAGAGTTTTCCTTTGAAAGACACA 59.682 38.462 6.49 0.00 41.31 3.72
2276 2653 5.590818 TGGTAGAGATTTCCTTGGTAGAGT 58.409 41.667 0.00 0.00 0.00 3.24
2277 2654 6.407525 CCTTGGTAGAGATTTCCTTGGTAGAG 60.408 46.154 0.00 0.00 0.00 2.43
2278 2655 5.425539 CCTTGGTAGAGATTTCCTTGGTAGA 59.574 44.000 0.00 0.00 0.00 2.59
2279 2656 5.396884 CCCTTGGTAGAGATTTCCTTGGTAG 60.397 48.000 0.00 0.00 0.00 3.18
2280 2657 4.473559 CCCTTGGTAGAGATTTCCTTGGTA 59.526 45.833 0.00 0.00 0.00 3.25
2281 2658 3.267031 CCCTTGGTAGAGATTTCCTTGGT 59.733 47.826 0.00 0.00 0.00 3.67
2282 2659 3.891049 CCCTTGGTAGAGATTTCCTTGG 58.109 50.000 0.00 0.00 0.00 3.61
2283 2660 3.282885 GCCCTTGGTAGAGATTTCCTTG 58.717 50.000 0.00 0.00 0.00 3.61
2284 2661 2.242452 GGCCCTTGGTAGAGATTTCCTT 59.758 50.000 0.00 0.00 0.00 3.36
2285 2662 1.847088 GGCCCTTGGTAGAGATTTCCT 59.153 52.381 0.00 0.00 0.00 3.36
2286 2663 1.475213 CGGCCCTTGGTAGAGATTTCC 60.475 57.143 0.00 0.00 0.00 3.13
2287 2664 1.209747 ACGGCCCTTGGTAGAGATTTC 59.790 52.381 0.00 0.00 0.00 2.17
2288 2665 1.286248 ACGGCCCTTGGTAGAGATTT 58.714 50.000 0.00 0.00 0.00 2.17
2289 2666 1.209747 GAACGGCCCTTGGTAGAGATT 59.790 52.381 0.00 0.00 0.00 2.40
2290 2667 0.831307 GAACGGCCCTTGGTAGAGAT 59.169 55.000 0.00 0.00 0.00 2.75
2291 2668 0.252103 AGAACGGCCCTTGGTAGAGA 60.252 55.000 0.00 0.00 0.00 3.10
2292 2669 0.108138 CAGAACGGCCCTTGGTAGAG 60.108 60.000 0.00 0.00 0.00 2.43
2468 2846 5.646692 AGGCAGTATTTATGGGAAGCTTA 57.353 39.130 0.00 0.00 0.00 3.09
2475 2853 6.153680 TGTTTTGGTTAGGCAGTATTTATGGG 59.846 38.462 0.00 0.00 0.00 4.00
2769 3149 4.467735 GCCGAGACAACTTCAAAAAGATC 58.532 43.478 0.00 0.00 36.30 2.75
2965 3345 8.978874 TCTACACCATAAATCATAGCAACAAT 57.021 30.769 0.00 0.00 0.00 2.71
2970 3350 7.508687 ACACATCTACACCATAAATCATAGCA 58.491 34.615 0.00 0.00 0.00 3.49
2974 3354 6.238456 CGCAACACATCTACACCATAAATCAT 60.238 38.462 0.00 0.00 0.00 2.45
3131 3515 2.595124 TTCTGCTCAACACACTCGAA 57.405 45.000 0.00 0.00 0.00 3.71
3273 3657 1.570857 AACATGGATGAAGGGCCGGA 61.571 55.000 5.05 0.00 0.00 5.14
3307 3691 5.023452 ACACTGGAGAAGTATCACATGGTA 58.977 41.667 0.00 0.00 36.83 3.25
3313 3697 4.537135 TGGAACACTGGAGAAGTATCAC 57.463 45.455 0.00 0.00 36.83 3.06
3318 3702 2.158608 CCCTTTGGAACACTGGAGAAGT 60.159 50.000 0.00 0.00 39.29 3.01
3324 3711 1.549203 CCATCCCTTTGGAACACTGG 58.451 55.000 0.00 0.00 45.98 4.00
3330 3717 1.077005 CTTCACCCCATCCCTTTGGAA 59.923 52.381 0.00 0.00 45.98 3.53
3398 3788 2.034687 GCCTGCCAGCCTCAAGAA 59.965 61.111 0.00 0.00 0.00 2.52
3401 3791 2.034687 GAAGCCTGCCAGCCTCAA 59.965 61.111 0.00 0.00 0.00 3.02
3451 3841 7.231467 TGAGAAAGGCTTACTGTTAAAGGAAT 58.769 34.615 0.00 0.00 0.00 3.01
3719 4109 1.805254 GCCTGCAGCAATGGTGTAG 59.195 57.895 20.78 20.78 41.88 2.74
3720 4110 2.039974 CGCCTGCAGCAATGGTGTA 61.040 57.895 14.21 8.71 44.04 2.90
3885 4278 2.048222 CGGTATGCGGCGATGGAT 60.048 61.111 12.98 0.00 0.00 3.41
4016 4418 4.737578 AGTCAGGTAAGTTACAGACAGGA 58.262 43.478 26.36 10.19 37.57 3.86
4087 4489 5.652518 AGAAAGTACCGAGAGAAATGTAGC 58.347 41.667 0.00 0.00 0.00 3.58
4101 4503 0.323957 AGGCCAACGGAGAAAGTACC 59.676 55.000 5.01 0.00 0.00 3.34
4125 4527 1.377725 CGGCTTGTTGGAGATGCCT 60.378 57.895 0.00 0.00 41.25 4.75
4214 4616 1.855295 TGGCATAACACTCTACCGGA 58.145 50.000 9.46 0.00 0.00 5.14
4230 4632 2.027385 GAATGATCTTGGAGGGTTGGC 58.973 52.381 0.00 0.00 0.00 4.52
4341 4745 7.829211 CAGGGGAAAATAGAGTAAAGATTGTGA 59.171 37.037 0.00 0.00 0.00 3.58
4342 4746 7.829211 TCAGGGGAAAATAGAGTAAAGATTGTG 59.171 37.037 0.00 0.00 0.00 3.33
4343 4747 7.829706 GTCAGGGGAAAATAGAGTAAAGATTGT 59.170 37.037 0.00 0.00 0.00 2.71
4345 4749 7.928873 TGTCAGGGGAAAATAGAGTAAAGATT 58.071 34.615 0.00 0.00 0.00 2.40
4347 4751 6.945636 TGTCAGGGGAAAATAGAGTAAAGA 57.054 37.500 0.00 0.00 0.00 2.52
4348 4752 6.038714 GCATGTCAGGGGAAAATAGAGTAAAG 59.961 42.308 0.00 0.00 0.00 1.85
4349 4753 5.885912 GCATGTCAGGGGAAAATAGAGTAAA 59.114 40.000 0.00 0.00 0.00 2.01
4350 4754 5.437060 GCATGTCAGGGGAAAATAGAGTAA 58.563 41.667 0.00 0.00 0.00 2.24
4352 4756 3.372025 GGCATGTCAGGGGAAAATAGAGT 60.372 47.826 0.00 0.00 0.00 3.24
4353 4757 3.217626 GGCATGTCAGGGGAAAATAGAG 58.782 50.000 0.00 0.00 0.00 2.43
4354 4758 2.580322 TGGCATGTCAGGGGAAAATAGA 59.420 45.455 0.00 0.00 0.00 1.98
4355 4759 3.017048 TGGCATGTCAGGGGAAAATAG 57.983 47.619 0.00 0.00 0.00 1.73
4357 4761 2.555732 ATGGCATGTCAGGGGAAAAT 57.444 45.000 6.04 0.00 0.00 1.82
4360 4764 0.703488 TGAATGGCATGTCAGGGGAA 59.297 50.000 6.04 0.00 0.00 3.97
4362 4766 1.784358 AATGAATGGCATGTCAGGGG 58.216 50.000 6.04 0.00 37.28 4.79
4363 4767 2.740580 GCAAATGAATGGCATGTCAGGG 60.741 50.000 6.04 2.99 37.28 4.45
4364 4768 2.167693 AGCAAATGAATGGCATGTCAGG 59.832 45.455 6.04 3.30 37.28 3.86
4365 4769 3.186909 CAGCAAATGAATGGCATGTCAG 58.813 45.455 6.04 0.00 37.28 3.51
4366 4770 2.675603 GCAGCAAATGAATGGCATGTCA 60.676 45.455 0.60 0.60 37.28 3.58
4367 4771 1.931172 GCAGCAAATGAATGGCATGTC 59.069 47.619 0.00 1.70 37.28 3.06
4368 4772 1.406341 GGCAGCAAATGAATGGCATGT 60.406 47.619 0.00 0.00 37.28 3.21
4369 4773 1.295792 GGCAGCAAATGAATGGCATG 58.704 50.000 0.00 0.00 37.28 4.06
4370 4774 0.179094 CGGCAGCAAATGAATGGCAT 60.179 50.000 0.00 0.00 39.31 4.40
4371 4775 1.215912 CGGCAGCAAATGAATGGCA 59.784 52.632 0.00 0.00 39.31 4.92
4372 4776 1.079875 CACGGCAGCAAATGAATGGC 61.080 55.000 0.00 3.51 36.25 4.40
4373 4777 0.527113 TCACGGCAGCAAATGAATGG 59.473 50.000 0.00 0.00 0.00 3.16
4374 4778 2.572191 ATCACGGCAGCAAATGAATG 57.428 45.000 0.00 0.00 0.00 2.67
4375 4779 3.005050 CCATATCACGGCAGCAAATGAAT 59.995 43.478 0.00 0.00 0.00 2.57
4376 4780 2.358582 CCATATCACGGCAGCAAATGAA 59.641 45.455 0.00 0.00 0.00 2.57
4377 4781 1.948834 CCATATCACGGCAGCAAATGA 59.051 47.619 0.00 0.00 0.00 2.57
4378 4782 1.948834 TCCATATCACGGCAGCAAATG 59.051 47.619 0.00 0.00 0.00 2.32
4379 4783 1.949525 GTCCATATCACGGCAGCAAAT 59.050 47.619 0.00 0.00 0.00 2.32
4380 4784 1.378531 GTCCATATCACGGCAGCAAA 58.621 50.000 0.00 0.00 0.00 3.68
4381 4785 0.463654 GGTCCATATCACGGCAGCAA 60.464 55.000 0.00 0.00 0.00 3.91
4382 4786 1.146041 GGTCCATATCACGGCAGCA 59.854 57.895 0.00 0.00 0.00 4.41
4383 4787 1.956170 CGGTCCATATCACGGCAGC 60.956 63.158 0.00 0.00 0.00 5.25
4384 4788 0.179084 AACGGTCCATATCACGGCAG 60.179 55.000 0.00 0.00 0.00 4.85
4385 4789 0.461163 CAACGGTCCATATCACGGCA 60.461 55.000 0.00 0.00 0.00 5.69
4386 4790 1.157870 CCAACGGTCCATATCACGGC 61.158 60.000 0.00 0.00 0.00 5.68
4387 4791 0.462375 TCCAACGGTCCATATCACGG 59.538 55.000 0.00 0.00 0.00 4.94
4388 4792 1.407618 TCTCCAACGGTCCATATCACG 59.592 52.381 0.00 0.00 0.00 4.35
4436 4874 7.783090 ATGACATCTGATCTACAAATGTGAC 57.217 36.000 0.00 0.00 39.85 3.67
4481 4919 0.967662 TGCCAGCTGCTGCATTTTTA 59.032 45.000 23.86 1.88 42.74 1.52
4492 4932 7.660112 TGGTATTATGATTATTTTGCCAGCTG 58.340 34.615 6.78 6.78 0.00 4.24
4493 4933 7.838079 TGGTATTATGATTATTTTGCCAGCT 57.162 32.000 0.00 0.00 0.00 4.24
4509 4949 9.573166 AATGCAAGTGTGTGTATATGGTATTAT 57.427 29.630 0.00 0.00 0.00 1.28
4691 5148 2.945440 GCAGCATGTCCATCTTTGGGTA 60.945 50.000 0.00 0.00 39.29 3.69
4706 5163 0.682209 AGAAAAGGCATCCGCAGCAT 60.682 50.000 0.00 0.00 41.24 3.79
4803 5260 2.540973 GCTTGACGAAAACGAAGCCTTT 60.541 45.455 0.00 0.00 35.76 3.11
4818 5275 3.920144 GCTGATGAGCATGCTTGAC 57.080 52.632 23.61 15.65 45.46 3.18


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

AutoCloner maintained by Alex Coulton.