Multiple sequence alignment - TraesCS7A01G298500

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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 TraesCS7A01G298500 chr7A 100.000 2276 0 0 1 2276 403989206 403986931 0.000000e+00 4204.0
1 TraesCS7A01G298500 chr7A 98.507 67 1 0 1391 1457 403987751 403987685 3.970000e-23 119.0
2 TraesCS7A01G298500 chr7A 98.507 67 1 0 1456 1522 403987816 403987750 3.970000e-23 119.0
3 TraesCS7A01G298500 chr5A 90.853 1454 116 10 6 1448 669851392 669849945 0.000000e+00 1932.0
4 TraesCS7A01G298500 chr5A 87.500 80 8 2 106 183 126262666 126262587 8.660000e-15 91.6
5 TraesCS7A01G298500 chr5A 89.286 56 1 5 1461 1513 633109319 633109372 5.250000e-07 65.8
6 TraesCS7A01G298500 chr2A 90.840 1452 105 13 1 1449 15725025 15723599 0.000000e+00 1919.0
7 TraesCS7A01G298500 chr2A 95.404 544 25 0 1733 2276 18066078 18065535 0.000000e+00 867.0
8 TraesCS7A01G298500 chr2A 94.455 541 28 2 1737 2276 772012434 772012973 0.000000e+00 832.0
9 TraesCS7A01G298500 chr2A 74.388 695 101 47 786 1453 713870913 713871557 2.270000e-55 226.0
10 TraesCS7A01G298500 chr2A 96.078 51 1 1 1468 1518 713871508 713871557 5.210000e-12 82.4
11 TraesCS7A01G298500 chr2A 91.228 57 5 0 1458 1514 15723655 15723599 6.740000e-11 78.7
12 TraesCS7A01G298500 chr3B 82.025 1452 198 32 35 1449 760388801 760390226 0.000000e+00 1177.0
13 TraesCS7A01G298500 chr3B 74.201 814 130 52 685 1449 808631405 808630623 1.340000e-67 267.0
14 TraesCS7A01G298500 chr3B 97.872 47 1 0 1468 1514 808630669 808630623 5.210000e-12 82.4
15 TraesCS7A01G298500 chr1B 81.561 1486 202 36 10 1459 198416978 198415529 0.000000e+00 1160.0
16 TraesCS7A01G298500 chr1B 81.325 1494 210 37 1 1449 647473887 647475356 0.000000e+00 1149.0
17 TraesCS7A01G298500 chr1B 84.211 133 9 9 1328 1453 18357010 18357137 3.970000e-23 119.0
18 TraesCS7A01G298500 chr1B 96.078 51 1 1 1468 1518 18357088 18357137 5.210000e-12 82.4
19 TraesCS7A01G298500 chr1B 97.297 37 1 0 1686 1722 336645749 336645785 1.890000e-06 63.9
20 TraesCS7A01G298500 chr7B 81.343 1474 207 32 10 1449 615892056 615890617 0.000000e+00 1136.0
21 TraesCS7A01G298500 chr7B 81.208 1474 207 33 10 1449 615924423 615922986 0.000000e+00 1123.0
22 TraesCS7A01G298500 chr2B 79.350 1385 214 34 104 1449 67890982 67892333 0.000000e+00 907.0
23 TraesCS7A01G298500 chr2B 93.103 58 1 3 1468 1523 67892287 67892343 5.210000e-12 82.4
24 TraesCS7A01G298500 chr2D 84.934 677 82 13 651 1320 162492514 162491851 0.000000e+00 667.0
25 TraesCS7A01G298500 chr2D 82.474 97 12 5 1355 1449 81735943 81736036 1.870000e-11 80.5
26 TraesCS7A01G298500 chr2D 95.652 46 2 0 1469 1514 81735991 81736036 8.720000e-10 75.0
27 TraesCS7A01G298500 chr4B 81.878 607 77 12 345 927 666729742 666730339 4.400000e-132 481.0
28 TraesCS7A01G298500 chr7D 96.154 182 6 1 1513 1693 365930906 365930725 1.710000e-76 296.0
29 TraesCS7A01G298500 chr5B 82.731 249 35 7 483 725 528776393 528776639 4.920000e-52 215.0
30 TraesCS7A01G298500 chr6B 72.907 454 67 38 1014 1440 11750946 11751370 3.090000e-19 106.0
31 TraesCS7A01G298500 chr6B 95.745 47 2 0 1468 1514 11751333 11751379 2.420000e-10 76.8
32 TraesCS7A01G298500 chr1A 100.000 37 0 0 1686 1722 301200802 301200766 4.060000e-08 69.4


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 TraesCS7A01G298500 chr7A 403986931 403989206 2275 True 1480.666667 4204 99.004667 1 2276 3 chr7A.!!$R1 2275
1 TraesCS7A01G298500 chr5A 669849945 669851392 1447 True 1932.000000 1932 90.853000 6 1448 1 chr5A.!!$R2 1442
2 TraesCS7A01G298500 chr2A 15723599 15725025 1426 True 998.850000 1919 91.034000 1 1514 2 chr2A.!!$R2 1513
3 TraesCS7A01G298500 chr2A 18065535 18066078 543 True 867.000000 867 95.404000 1733 2276 1 chr2A.!!$R1 543
4 TraesCS7A01G298500 chr2A 772012434 772012973 539 False 832.000000 832 94.455000 1737 2276 1 chr2A.!!$F1 539
5 TraesCS7A01G298500 chr3B 760388801 760390226 1425 False 1177.000000 1177 82.025000 35 1449 1 chr3B.!!$F1 1414
6 TraesCS7A01G298500 chr1B 198415529 198416978 1449 True 1160.000000 1160 81.561000 10 1459 1 chr1B.!!$R1 1449
7 TraesCS7A01G298500 chr1B 647473887 647475356 1469 False 1149.000000 1149 81.325000 1 1449 1 chr1B.!!$F2 1448
8 TraesCS7A01G298500 chr7B 615890617 615892056 1439 True 1136.000000 1136 81.343000 10 1449 1 chr7B.!!$R1 1439
9 TraesCS7A01G298500 chr7B 615922986 615924423 1437 True 1123.000000 1123 81.208000 10 1449 1 chr7B.!!$R2 1439
10 TraesCS7A01G298500 chr2B 67890982 67892343 1361 False 494.700000 907 86.226500 104 1523 2 chr2B.!!$F1 1419
11 TraesCS7A01G298500 chr2D 162491851 162492514 663 True 667.000000 667 84.934000 651 1320 1 chr2D.!!$R1 669
12 TraesCS7A01G298500 chr4B 666729742 666730339 597 False 481.000000 481 81.878000 345 927 1 chr4B.!!$F1 582

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
185 192 0.032130 TTCACGAGGACACTGACTGC 59.968 55.0 0.00 0.00 0.00 4.40 F
190 197 0.250038 GAGGACACTGACTGCAGCAA 60.250 55.0 15.27 0.39 46.26 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1178 1311 0.033796 CATGAATGCCCTGTCCACCT 60.034 55.0 0.00 0.0 0.0 4.00 R
1504 1641 0.105964 TTATGTAATCGGGCGCTGCT 59.894 50.0 7.64 0.0 0.0 4.24 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
100 106 1.389555 TCGAGACATATGACGGCTGT 58.610 50.000 10.38 0.00 0.00 4.40
103 109 2.735444 CGAGACATATGACGGCTGTGTT 60.735 50.000 10.38 0.00 0.00 3.32
104 110 2.604914 GAGACATATGACGGCTGTGTTG 59.395 50.000 10.38 0.00 0.00 3.33
179 186 1.416401 ACAACCATTCACGAGGACACT 59.584 47.619 0.00 0.00 0.00 3.55
183 190 1.273606 CCATTCACGAGGACACTGACT 59.726 52.381 0.00 0.00 0.00 3.41
184 191 2.332104 CATTCACGAGGACACTGACTG 58.668 52.381 0.00 0.00 0.00 3.51
185 192 0.032130 TTCACGAGGACACTGACTGC 59.968 55.000 0.00 0.00 0.00 4.40
186 193 1.106944 TCACGAGGACACTGACTGCA 61.107 55.000 0.00 0.00 0.00 4.41
188 195 1.735920 CGAGGACACTGACTGCAGC 60.736 63.158 15.27 7.45 46.26 5.25
189 196 1.368950 GAGGACACTGACTGCAGCA 59.631 57.895 15.27 12.02 46.26 4.41
190 197 0.250038 GAGGACACTGACTGCAGCAA 60.250 55.000 15.27 0.39 46.26 3.91
191 198 0.399454 AGGACACTGACTGCAGCAAT 59.601 50.000 15.27 0.00 46.26 3.56
202 218 2.147958 CTGCAGCAATGCCATTTTTGT 58.852 42.857 0.00 0.00 0.00 2.83
211 227 2.983229 TGCCATTTTTGTTGCAAGTGT 58.017 38.095 0.00 0.00 0.00 3.55
255 271 6.745450 CCGATGTTGATATTTGTTACAACCAC 59.255 38.462 0.00 0.00 40.91 4.16
258 274 8.635765 ATGTTGATATTTGTTACAACCACTCT 57.364 30.769 0.00 0.00 40.91 3.24
296 341 1.413767 CGACGGCGAAGATGTCCTTG 61.414 60.000 16.62 0.00 40.82 3.61
311 356 8.389354 AAGATGTCCTTGTTTTTGCTACTAGCA 61.389 37.037 6.66 6.66 40.87 3.49
393 457 3.219281 ACCGGTGTGAATTTTTGCTACT 58.781 40.909 6.12 0.00 0.00 2.57
400 464 7.064134 CGGTGTGAATTTTTGCTACTATCTGTA 59.936 37.037 0.00 0.00 0.00 2.74
409 473 4.278310 TGCTACTATCTGTAACAGCAGGA 58.722 43.478 0.00 0.00 37.12 3.86
440 504 2.981400 CAACCGGCGAGTTGTTTTAT 57.019 45.000 23.89 0.00 41.80 1.40
464 528 4.469657 AGGACCAGTGTGAATTTTTGCTA 58.530 39.130 0.00 0.00 0.00 3.49
472 536 4.209080 GTGTGAATTTTTGCTACAACCTGC 59.791 41.667 0.00 0.00 0.00 4.85
498 562 2.547642 GCAGGGCATTTTTGCTACAACA 60.548 45.455 0.00 0.00 35.05 3.33
499 563 3.319755 CAGGGCATTTTTGCTACAACAG 58.680 45.455 0.00 0.00 34.73 3.16
501 565 3.059166 GGGCATTTTTGCTACAACAGTG 58.941 45.455 0.00 0.00 34.73 3.66
502 566 3.243704 GGGCATTTTTGCTACAACAGTGA 60.244 43.478 0.00 0.00 34.73 3.41
503 567 3.983344 GGCATTTTTGCTACAACAGTGAG 59.017 43.478 0.00 0.00 34.73 3.51
504 568 4.499696 GGCATTTTTGCTACAACAGTGAGT 60.500 41.667 0.00 0.00 34.73 3.41
505 569 5.278266 GGCATTTTTGCTACAACAGTGAGTA 60.278 40.000 0.00 0.00 34.73 2.59
506 570 5.853282 GCATTTTTGCTACAACAGTGAGTAG 59.147 40.000 17.45 17.45 40.45 2.57
682 752 2.096713 CCAGCGAGAATATTTGCTACGC 60.097 50.000 9.56 0.00 43.84 4.42
701 771 1.811266 CGCTGGAACCGGTGATCAG 60.811 63.158 20.95 20.95 34.98 2.90
727 797 1.161843 TGGAACCGGCGAGAATTTTC 58.838 50.000 9.30 0.00 0.00 2.29
736 806 3.163594 GGCGAGAATTTTCATTGTGACG 58.836 45.455 0.00 0.00 0.00 4.35
1210 1343 2.173519 CATTCATGGAAGCTGGGTGTT 58.826 47.619 0.00 0.00 0.00 3.32
1277 1410 3.512516 GTTCCATGCGGGCTGAGC 61.513 66.667 0.00 0.00 36.21 4.26
1320 1453 2.614983 GTGTTCAGCGGGTTCAGTTTTA 59.385 45.455 0.00 0.00 0.00 1.52
1323 1456 4.453136 TGTTCAGCGGGTTCAGTTTTATAC 59.547 41.667 0.00 0.00 0.00 1.47
1324 1457 4.274602 TCAGCGGGTTCAGTTTTATACA 57.725 40.909 0.00 0.00 0.00 2.29
1352 1485 2.730928 GTGGGTTCAATTTTGCATGACG 59.269 45.455 0.00 0.00 0.00 4.35
1353 1486 2.625314 TGGGTTCAATTTTGCATGACGA 59.375 40.909 0.00 0.00 0.00 4.20
1396 1533 4.635769 GGACGCATCCAATGGACA 57.364 55.556 3.09 0.00 45.47 4.02
1400 1537 0.327924 ACGCATCCAATGGACAAGGA 59.672 50.000 3.09 0.30 32.98 3.36
1451 1588 4.218578 CGCAGAGCAGCTCCCGAT 62.219 66.667 22.27 1.88 30.85 4.18
1453 1590 1.443407 GCAGAGCAGCTCCCGATTA 59.557 57.895 19.40 0.00 0.00 1.75
1454 1591 0.878086 GCAGAGCAGCTCCCGATTAC 60.878 60.000 19.40 0.00 0.00 1.89
1455 1592 0.461548 CAGAGCAGCTCCCGATTACA 59.538 55.000 19.40 0.00 0.00 2.41
1456 1593 1.069823 CAGAGCAGCTCCCGATTACAT 59.930 52.381 19.40 0.00 0.00 2.29
1457 1594 1.069823 AGAGCAGCTCCCGATTACATG 59.930 52.381 19.40 0.00 0.00 3.21
1458 1595 0.107456 AGCAGCTCCCGATTACATGG 59.893 55.000 0.00 0.00 0.00 3.66
1459 1596 0.106708 GCAGCTCCCGATTACATGGA 59.893 55.000 0.00 0.00 0.00 3.41
1460 1597 1.871080 CAGCTCCCGATTACATGGAC 58.129 55.000 0.00 0.00 0.00 4.02
1461 1598 1.138859 CAGCTCCCGATTACATGGACA 59.861 52.381 0.00 0.00 0.00 4.02
1462 1599 1.837439 AGCTCCCGATTACATGGACAA 59.163 47.619 0.00 0.00 0.00 3.18
1463 1600 2.158900 AGCTCCCGATTACATGGACAAG 60.159 50.000 0.00 0.00 0.00 3.16
1464 1601 2.838736 CTCCCGATTACATGGACAAGG 58.161 52.381 0.00 0.00 0.00 3.61
1465 1602 2.434336 CTCCCGATTACATGGACAAGGA 59.566 50.000 0.00 0.00 0.00 3.36
1466 1603 2.841266 TCCCGATTACATGGACAAGGAA 59.159 45.455 0.00 0.00 0.00 3.36
1467 1604 3.118408 TCCCGATTACATGGACAAGGAAG 60.118 47.826 0.00 0.00 0.00 3.46
1468 1605 3.206150 CCGATTACATGGACAAGGAAGG 58.794 50.000 0.00 0.00 0.00 3.46
1469 1606 3.118408 CCGATTACATGGACAAGGAAGGA 60.118 47.826 0.00 0.00 0.00 3.36
1470 1607 3.871594 CGATTACATGGACAAGGAAGGAC 59.128 47.826 0.00 0.00 0.00 3.85
1471 1608 3.713826 TTACATGGACAAGGAAGGACC 57.286 47.619 0.00 0.00 39.35 4.46
1472 1609 0.324943 ACATGGACAAGGAAGGACCG 59.675 55.000 0.00 0.00 44.74 4.79
1473 1610 0.392998 CATGGACAAGGAAGGACCGG 60.393 60.000 0.00 0.00 44.74 5.28
1474 1611 2.046217 GGACAAGGAAGGACCGGC 60.046 66.667 0.00 0.00 44.74 6.13
1475 1612 2.434359 GACAAGGAAGGACCGGCG 60.434 66.667 0.00 0.00 44.74 6.46
1476 1613 3.952628 GACAAGGAAGGACCGGCGG 62.953 68.421 27.06 27.06 44.74 6.13
1477 1614 3.702048 CAAGGAAGGACCGGCGGA 61.702 66.667 35.78 0.00 44.74 5.54
1478 1615 3.391382 AAGGAAGGACCGGCGGAG 61.391 66.667 35.78 7.40 44.74 4.63
1518 1655 2.106938 CAGAGCAGCGCCCGATTA 59.893 61.111 2.29 0.00 0.00 1.75
1519 1656 2.107141 AGAGCAGCGCCCGATTAC 59.893 61.111 2.29 0.00 0.00 1.89
1520 1657 2.202878 GAGCAGCGCCCGATTACA 60.203 61.111 2.29 0.00 0.00 2.41
1521 1658 1.595382 GAGCAGCGCCCGATTACAT 60.595 57.895 2.29 0.00 0.00 2.29
1522 1659 0.319555 GAGCAGCGCCCGATTACATA 60.320 55.000 2.29 0.00 0.00 2.29
1523 1660 0.105964 AGCAGCGCCCGATTACATAA 59.894 50.000 2.29 0.00 0.00 1.90
1524 1661 0.512952 GCAGCGCCCGATTACATAAG 59.487 55.000 2.29 0.00 0.00 1.73
1525 1662 1.872237 GCAGCGCCCGATTACATAAGA 60.872 52.381 2.29 0.00 0.00 2.10
1526 1663 1.792949 CAGCGCCCGATTACATAAGAC 59.207 52.381 2.29 0.00 0.00 3.01
1527 1664 1.687123 AGCGCCCGATTACATAAGACT 59.313 47.619 2.29 0.00 0.00 3.24
1528 1665 1.792949 GCGCCCGATTACATAAGACTG 59.207 52.381 0.00 0.00 0.00 3.51
1529 1666 2.545113 GCGCCCGATTACATAAGACTGA 60.545 50.000 0.00 0.00 0.00 3.41
1530 1667 3.861131 GCGCCCGATTACATAAGACTGAT 60.861 47.826 0.00 0.00 0.00 2.90
1531 1668 3.675225 CGCCCGATTACATAAGACTGATG 59.325 47.826 0.00 0.00 0.00 3.07
1532 1669 4.632153 GCCCGATTACATAAGACTGATGT 58.368 43.478 10.43 10.43 40.59 3.06
1533 1670 5.057149 GCCCGATTACATAAGACTGATGTT 58.943 41.667 10.85 0.00 38.47 2.71
1534 1671 5.050091 GCCCGATTACATAAGACTGATGTTG 60.050 44.000 10.85 0.06 38.47 3.33
1535 1672 6.280643 CCCGATTACATAAGACTGATGTTGA 58.719 40.000 10.85 1.47 38.47 3.18
1536 1673 6.931281 CCCGATTACATAAGACTGATGTTGAT 59.069 38.462 10.85 6.07 38.47 2.57
1537 1674 8.088365 CCCGATTACATAAGACTGATGTTGATA 58.912 37.037 10.85 0.00 38.47 2.15
1538 1675 9.133627 CCGATTACATAAGACTGATGTTGATAG 57.866 37.037 10.85 6.48 38.47 2.08
1539 1676 9.684448 CGATTACATAAGACTGATGTTGATAGT 57.316 33.333 10.85 0.00 38.47 2.12
1548 1685 9.809096 AAGACTGATGTTGATAGTTATGTGTAG 57.191 33.333 0.00 0.00 0.00 2.74
1549 1686 9.190317 AGACTGATGTTGATAGTTATGTGTAGA 57.810 33.333 0.00 0.00 0.00 2.59
1550 1687 9.239002 GACTGATGTTGATAGTTATGTGTAGAC 57.761 37.037 0.00 0.00 0.00 2.59
1551 1688 8.972127 ACTGATGTTGATAGTTATGTGTAGACT 58.028 33.333 0.00 0.00 0.00 3.24
1552 1689 9.457110 CTGATGTTGATAGTTATGTGTAGACTC 57.543 37.037 0.00 0.00 0.00 3.36
1553 1690 8.414003 TGATGTTGATAGTTATGTGTAGACTCC 58.586 37.037 0.00 0.00 0.00 3.85
1554 1691 7.956328 TGTTGATAGTTATGTGTAGACTCCT 57.044 36.000 0.00 0.00 0.00 3.69
1555 1692 9.642343 ATGTTGATAGTTATGTGTAGACTCCTA 57.358 33.333 0.00 0.00 0.00 2.94
1556 1693 9.470399 TGTTGATAGTTATGTGTAGACTCCTAA 57.530 33.333 0.00 0.00 0.00 2.69
1557 1694 9.733219 GTTGATAGTTATGTGTAGACTCCTAAC 57.267 37.037 0.00 0.00 0.00 2.34
1558 1695 9.470399 TTGATAGTTATGTGTAGACTCCTAACA 57.530 33.333 10.47 0.00 0.00 2.41
1559 1696 9.121658 TGATAGTTATGTGTAGACTCCTAACAG 57.878 37.037 10.47 0.00 0.00 3.16
1560 1697 9.339850 GATAGTTATGTGTAGACTCCTAACAGA 57.660 37.037 10.47 0.00 0.00 3.41
1561 1698 7.633193 AGTTATGTGTAGACTCCTAACAGAG 57.367 40.000 10.47 0.00 39.91 3.35
1616 1753 9.987272 AAATAAAAGAAACTCCAGGATTGAAAG 57.013 29.630 0.00 0.00 0.00 2.62
1617 1754 6.410942 AAAAGAAACTCCAGGATTGAAAGG 57.589 37.500 0.00 0.00 0.00 3.11
1618 1755 3.425659 AGAAACTCCAGGATTGAAAGGC 58.574 45.455 0.00 0.00 0.00 4.35
1619 1756 3.075134 AGAAACTCCAGGATTGAAAGGCT 59.925 43.478 0.00 0.00 0.00 4.58
1620 1757 3.532641 AACTCCAGGATTGAAAGGCTT 57.467 42.857 0.00 0.00 0.00 4.35
1621 1758 3.532641 ACTCCAGGATTGAAAGGCTTT 57.467 42.857 13.25 13.25 0.00 3.51
1622 1759 3.160269 ACTCCAGGATTGAAAGGCTTTG 58.840 45.455 18.79 1.14 0.00 2.77
1623 1760 2.494870 CTCCAGGATTGAAAGGCTTTGG 59.505 50.000 18.79 11.34 0.00 3.28
1624 1761 1.551883 CCAGGATTGAAAGGCTTTGGG 59.448 52.381 18.79 3.54 0.00 4.12
1625 1762 1.551883 CAGGATTGAAAGGCTTTGGGG 59.448 52.381 18.79 0.00 0.00 4.96
1626 1763 1.432807 AGGATTGAAAGGCTTTGGGGA 59.567 47.619 18.79 0.46 0.00 4.81
1627 1764 1.827344 GGATTGAAAGGCTTTGGGGAG 59.173 52.381 18.79 0.00 0.00 4.30
1628 1765 2.557452 GGATTGAAAGGCTTTGGGGAGA 60.557 50.000 18.79 0.00 0.00 3.71
1629 1766 2.999185 TTGAAAGGCTTTGGGGAGAT 57.001 45.000 18.79 0.00 0.00 2.75
1630 1767 2.220653 TGAAAGGCTTTGGGGAGATG 57.779 50.000 18.79 0.00 0.00 2.90
1631 1768 0.820226 GAAAGGCTTTGGGGAGATGC 59.180 55.000 18.79 0.00 0.00 3.91
1632 1769 0.615827 AAAGGCTTTGGGGAGATGCC 60.616 55.000 12.53 0.00 43.52 4.40
1633 1770 1.803453 AAGGCTTTGGGGAGATGCCA 61.803 55.000 0.00 0.00 45.42 4.92
1634 1771 2.054453 GGCTTTGGGGAGATGCCAC 61.054 63.158 0.00 0.00 42.79 5.01
1635 1772 2.054453 GCTTTGGGGAGATGCCACC 61.054 63.158 0.00 0.00 40.40 4.61
1636 1773 1.383799 CTTTGGGGAGATGCCACCA 59.616 57.895 0.00 0.00 40.40 4.17
1637 1774 0.967380 CTTTGGGGAGATGCCACCAC 60.967 60.000 0.00 0.00 40.40 4.16
1638 1775 2.439553 TTTGGGGAGATGCCACCACC 62.440 60.000 0.00 0.00 40.40 4.61
1639 1776 4.489771 GGGGAGATGCCACCACCG 62.490 72.222 0.00 0.00 38.95 4.94
1640 1777 3.399181 GGGAGATGCCACCACCGA 61.399 66.667 0.00 0.00 38.95 4.69
1641 1778 2.125106 GGAGATGCCACCACCGAC 60.125 66.667 0.00 0.00 36.34 4.79
1642 1779 2.662596 GAGATGCCACCACCGACA 59.337 61.111 0.00 0.00 0.00 4.35
1643 1780 1.448540 GAGATGCCACCACCGACAG 60.449 63.158 0.00 0.00 0.00 3.51
1644 1781 2.172483 GAGATGCCACCACCGACAGT 62.172 60.000 0.00 0.00 0.00 3.55
1645 1782 1.302511 GATGCCACCACCGACAGTT 60.303 57.895 0.00 0.00 0.00 3.16
1646 1783 0.889186 GATGCCACCACCGACAGTTT 60.889 55.000 0.00 0.00 0.00 2.66
1647 1784 1.172180 ATGCCACCACCGACAGTTTG 61.172 55.000 0.00 0.00 0.00 2.93
1648 1785 2.551912 GCCACCACCGACAGTTTGG 61.552 63.158 0.00 0.00 33.61 3.28
1649 1786 1.153046 CCACCACCGACAGTTTGGT 60.153 57.895 0.00 0.00 44.83 3.67
1653 1790 4.870190 ACCGACAGTTTGGTGGAC 57.130 55.556 0.00 0.00 38.22 4.02
1654 1791 1.147600 ACCGACAGTTTGGTGGACC 59.852 57.895 0.00 0.00 38.22 4.46
1655 1792 1.342672 ACCGACAGTTTGGTGGACCT 61.343 55.000 0.00 0.00 38.22 3.85
1656 1793 0.682852 CCGACAGTTTGGTGGACCTA 59.317 55.000 0.00 0.00 36.82 3.08
1657 1794 1.607251 CCGACAGTTTGGTGGACCTAC 60.607 57.143 0.00 0.00 36.82 3.18
1658 1795 1.343465 CGACAGTTTGGTGGACCTACT 59.657 52.381 0.00 0.00 36.82 2.57
1659 1796 2.767505 GACAGTTTGGTGGACCTACTG 58.232 52.381 20.74 20.74 45.85 2.74
1660 1797 2.930826 CAGTTTGGTGGACCTACTGT 57.069 50.000 16.97 0.00 40.84 3.55
1661 1798 2.494059 CAGTTTGGTGGACCTACTGTG 58.506 52.381 16.97 2.19 40.84 3.66
1662 1799 1.420138 AGTTTGGTGGACCTACTGTGG 59.580 52.381 0.00 0.00 36.82 4.17
1663 1800 1.142262 GTTTGGTGGACCTACTGTGGT 59.858 52.381 0.00 2.24 44.10 4.16
1664 1801 2.369532 GTTTGGTGGACCTACTGTGGTA 59.630 50.000 0.00 0.00 41.00 3.25
1665 1802 1.933021 TGGTGGACCTACTGTGGTAG 58.067 55.000 0.00 0.00 43.58 3.18
1666 1803 0.535797 GGTGGACCTACTGTGGTAGC 59.464 60.000 0.00 0.00 42.85 3.58
1667 1804 1.263356 GTGGACCTACTGTGGTAGCA 58.737 55.000 0.00 0.00 42.85 3.49
1668 1805 1.621814 GTGGACCTACTGTGGTAGCAA 59.378 52.381 0.00 0.00 42.85 3.91
1669 1806 2.038033 GTGGACCTACTGTGGTAGCAAA 59.962 50.000 0.00 0.00 42.85 3.68
1670 1807 2.706723 TGGACCTACTGTGGTAGCAAAA 59.293 45.455 0.00 0.00 42.85 2.44
1671 1808 3.136809 TGGACCTACTGTGGTAGCAAAAA 59.863 43.478 0.00 0.00 42.85 1.94
1672 1809 3.751698 GGACCTACTGTGGTAGCAAAAAG 59.248 47.826 0.00 0.00 42.85 2.27
1673 1810 3.751518 ACCTACTGTGGTAGCAAAAAGG 58.248 45.455 10.34 10.34 42.85 3.11
1674 1811 3.393278 ACCTACTGTGGTAGCAAAAAGGA 59.607 43.478 16.46 3.47 42.85 3.36
1675 1812 4.003648 CCTACTGTGGTAGCAAAAAGGAG 58.996 47.826 7.18 6.56 42.85 3.69
1676 1813 2.863809 ACTGTGGTAGCAAAAAGGAGG 58.136 47.619 0.00 0.00 0.00 4.30
1677 1814 2.441750 ACTGTGGTAGCAAAAAGGAGGA 59.558 45.455 0.00 0.00 0.00 3.71
1678 1815 3.117663 ACTGTGGTAGCAAAAAGGAGGAA 60.118 43.478 0.00 0.00 0.00 3.36
1679 1816 3.888930 CTGTGGTAGCAAAAAGGAGGAAA 59.111 43.478 0.00 0.00 0.00 3.13
1680 1817 4.479158 TGTGGTAGCAAAAAGGAGGAAAT 58.521 39.130 0.00 0.00 0.00 2.17
1681 1818 5.636123 TGTGGTAGCAAAAAGGAGGAAATA 58.364 37.500 0.00 0.00 0.00 1.40
1682 1819 6.252995 TGTGGTAGCAAAAAGGAGGAAATAT 58.747 36.000 0.00 0.00 0.00 1.28
1683 1820 6.723977 TGTGGTAGCAAAAAGGAGGAAATATT 59.276 34.615 0.00 0.00 0.00 1.28
1684 1821 7.234577 TGTGGTAGCAAAAAGGAGGAAATATTT 59.765 33.333 0.00 0.00 0.00 1.40
1685 1822 8.745590 GTGGTAGCAAAAAGGAGGAAATATTTA 58.254 33.333 0.00 0.00 0.00 1.40
1686 1823 9.315363 TGGTAGCAAAAAGGAGGAAATATTTAA 57.685 29.630 0.00 0.00 0.00 1.52
1687 1824 9.803315 GGTAGCAAAAAGGAGGAAATATTTAAG 57.197 33.333 0.00 0.00 0.00 1.85
1690 1827 8.314021 AGCAAAAAGGAGGAAATATTTAAGTGG 58.686 33.333 0.00 0.00 0.00 4.00
1691 1828 8.094548 GCAAAAAGGAGGAAATATTTAAGTGGT 58.905 33.333 0.00 0.00 0.00 4.16
1692 1829 9.996554 CAAAAAGGAGGAAATATTTAAGTGGTT 57.003 29.630 0.00 0.00 0.00 3.67
1693 1830 9.996554 AAAAAGGAGGAAATATTTAAGTGGTTG 57.003 29.630 0.00 0.00 0.00 3.77
1694 1831 8.950007 AAAGGAGGAAATATTTAAGTGGTTGA 57.050 30.769 0.00 0.00 0.00 3.18
1695 1832 7.939784 AGGAGGAAATATTTAAGTGGTTGAC 57.060 36.000 0.00 0.00 0.00 3.18
1696 1833 6.598064 AGGAGGAAATATTTAAGTGGTTGACG 59.402 38.462 0.00 0.00 0.00 4.35
1697 1834 6.596497 GGAGGAAATATTTAAGTGGTTGACGA 59.404 38.462 0.00 0.00 0.00 4.20
1698 1835 7.373778 AGGAAATATTTAAGTGGTTGACGAC 57.626 36.000 0.00 0.00 0.00 4.34
1699 1836 6.938030 AGGAAATATTTAAGTGGTTGACGACA 59.062 34.615 0.00 0.00 0.00 4.35
1700 1837 7.610305 AGGAAATATTTAAGTGGTTGACGACAT 59.390 33.333 0.00 0.00 0.00 3.06
1701 1838 8.241367 GGAAATATTTAAGTGGTTGACGACATT 58.759 33.333 0.00 0.00 0.00 2.71
1702 1839 8.964420 AAATATTTAAGTGGTTGACGACATTG 57.036 30.769 0.00 0.00 0.00 2.82
1703 1840 7.915293 ATATTTAAGTGGTTGACGACATTGA 57.085 32.000 0.00 0.00 0.00 2.57
1704 1841 6.627395 ATTTAAGTGGTTGACGACATTGAA 57.373 33.333 0.00 0.00 0.00 2.69
1705 1842 5.666969 TTAAGTGGTTGACGACATTGAAG 57.333 39.130 0.00 0.00 0.00 3.02
1706 1843 3.469008 AGTGGTTGACGACATTGAAGA 57.531 42.857 0.00 0.00 0.00 2.87
1707 1844 3.804036 AGTGGTTGACGACATTGAAGAA 58.196 40.909 0.00 0.00 0.00 2.52
1708 1845 4.196193 AGTGGTTGACGACATTGAAGAAA 58.804 39.130 0.00 0.00 0.00 2.52
1709 1846 4.638421 AGTGGTTGACGACATTGAAGAAAA 59.362 37.500 0.00 0.00 0.00 2.29
1710 1847 5.124776 AGTGGTTGACGACATTGAAGAAAAA 59.875 36.000 0.00 0.00 0.00 1.94
1849 1986 2.348472 TCAGTGAAGGGGAGTGGATTT 58.652 47.619 0.00 0.00 0.00 2.17
1986 2123 2.395988 AATCGGCAGTGTGGCACAGA 62.396 55.000 22.75 14.74 43.94 3.41
2043 2180 8.046107 AGTAAGAATCAAAGAGAAGATTGGGAG 58.954 37.037 0.00 0.00 34.79 4.30
2056 2193 0.608035 TTGGGAGGATGCGTTTGGAC 60.608 55.000 0.00 0.00 0.00 4.02
2109 2246 1.286880 CAGCGGCAAAAGGTTCAGG 59.713 57.895 1.45 0.00 0.00 3.86
2119 2256 0.606401 AAGGTTCAGGTGTGCGGATG 60.606 55.000 0.00 0.00 0.00 3.51
2123 2260 0.541392 TTCAGGTGTGCGGATGCTAT 59.459 50.000 0.00 0.00 43.34 2.97
2142 2279 4.502950 GCTATCTGATCCTCCAGACAAAGG 60.503 50.000 0.00 0.00 44.93 3.11
2170 2307 4.042560 GGATGGGATCCATTCTCTGATTCA 59.957 45.833 15.23 0.00 45.26 2.57
2239 2376 3.282885 GGAGGAAATTCCATGTCCTGAC 58.717 50.000 15.21 0.00 41.98 3.51
2245 2382 0.612744 TTCCATGTCCTGACGATGCA 59.387 50.000 0.00 0.00 0.00 3.96
2246 2383 0.832626 TCCATGTCCTGACGATGCAT 59.167 50.000 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 58 4.683501 TCAATGGTTGTCACAATCATCG 57.316 40.909 16.81 6.03 0.00 3.84
53 59 6.032094 GTCATCAATGGTTGTCACAATCATC 58.968 40.000 16.81 0.00 0.00 2.92
54 60 5.392272 CGTCATCAATGGTTGTCACAATCAT 60.392 40.000 10.73 10.73 0.00 2.45
55 61 4.083377 CGTCATCAATGGTTGTCACAATCA 60.083 41.667 5.80 5.80 0.00 2.57
100 106 1.620739 TTGCAGCAAAAGGCCCAACA 61.621 50.000 4.99 0.00 46.50 3.33
103 109 1.761667 AGTTGCAGCAAAAGGCCCA 60.762 52.632 10.11 0.00 46.50 5.36
104 110 1.301165 CAGTTGCAGCAAAAGGCCC 60.301 57.895 10.11 0.00 46.50 5.80
138 144 3.855689 AGCAATTGTCAACATGGTAGC 57.144 42.857 7.40 0.00 0.00 3.58
184 191 5.390218 TGCAACAAAAATGGCATTGCTGC 62.390 43.478 14.47 15.83 44.66 5.25
185 192 2.290916 TGCAACAAAAATGGCATTGCTG 59.709 40.909 14.47 15.58 44.69 4.41
186 193 2.573369 TGCAACAAAAATGGCATTGCT 58.427 38.095 14.47 1.05 44.69 3.91
187 194 3.243134 ACTTGCAACAAAAATGGCATTGC 60.243 39.130 14.47 13.57 44.66 3.56
188 195 4.201930 ACACTTGCAACAAAAATGGCATTG 60.202 37.500 14.47 5.57 35.98 2.82
189 196 3.946558 ACACTTGCAACAAAAATGGCATT 59.053 34.783 6.96 6.96 35.98 3.56
190 197 3.543665 ACACTTGCAACAAAAATGGCAT 58.456 36.364 0.00 0.00 35.98 4.40
191 198 2.983229 ACACTTGCAACAAAAATGGCA 58.017 38.095 0.00 0.00 0.00 4.92
202 218 2.983136 CAAAACACGACAACACTTGCAA 59.017 40.909 0.00 0.00 0.00 4.08
211 227 2.796031 CGGTAGTAGCAAAACACGACAA 59.204 45.455 0.00 0.00 0.00 3.18
255 271 0.389166 GCCGTCTGTGTCCTTGAGAG 60.389 60.000 0.00 0.00 0.00 3.20
258 274 2.338620 CGCCGTCTGTGTCCTTGA 59.661 61.111 0.00 0.00 0.00 3.02
286 331 5.412904 GCTAGTAGCAAAAACAAGGACATCT 59.587 40.000 17.47 0.00 41.89 2.90
311 356 0.944386 GGATGCAACACGTCAACACT 59.056 50.000 0.00 0.00 35.86 3.55
338 383 0.818938 TTGCCGGTTGTAGCTCGATA 59.181 50.000 1.90 0.00 0.00 2.92
393 457 6.349280 GCAAAAATGTCCTGCTGTTACAGATA 60.349 38.462 17.40 3.11 40.25 1.98
400 464 3.636300 TGTAGCAAAAATGTCCTGCTGTT 59.364 39.130 6.07 0.00 45.73 3.16
409 473 1.335506 CGCCGGTTGTAGCAAAAATGT 60.336 47.619 1.90 0.00 0.00 2.71
440 504 4.892934 AGCAAAAATTCACACTGGTCCTAA 59.107 37.500 0.00 0.00 0.00 2.69
472 536 1.085501 GCAAAAATGCCCTGCCATCG 61.086 55.000 0.00 0.00 0.00 3.84
498 562 2.224548 GGTCCCAGCAAAACTACTCACT 60.225 50.000 0.00 0.00 0.00 3.41
499 563 2.152016 GGTCCCAGCAAAACTACTCAC 58.848 52.381 0.00 0.00 0.00 3.51
501 565 2.224548 ACAGGTCCCAGCAAAACTACTC 60.225 50.000 0.00 0.00 0.00 2.59
502 566 1.774856 ACAGGTCCCAGCAAAACTACT 59.225 47.619 0.00 0.00 0.00 2.57
503 567 1.880027 CACAGGTCCCAGCAAAACTAC 59.120 52.381 0.00 0.00 0.00 2.73
504 568 1.493022 ACACAGGTCCCAGCAAAACTA 59.507 47.619 0.00 0.00 0.00 2.24
505 569 0.258774 ACACAGGTCCCAGCAAAACT 59.741 50.000 0.00 0.00 0.00 2.66
506 570 0.385390 CACACAGGTCCCAGCAAAAC 59.615 55.000 0.00 0.00 0.00 2.43
701 771 0.317519 CTCGCCGGTTCCAACAAAAC 60.318 55.000 1.90 0.00 0.00 2.43
736 806 0.958876 AAAAATCTCACCGGTCGCCC 60.959 55.000 2.59 0.00 0.00 6.13
798 887 0.110867 TCGCAGCAAAAATGTCGTCG 60.111 50.000 0.00 0.00 0.00 5.12
829 939 3.251004 ACCAGAAATTCTCAGCGACAAAC 59.749 43.478 0.00 0.00 0.00 2.93
1089 1210 2.407210 CGGCAAACACGCTGTTGT 59.593 55.556 4.51 0.00 40.14 3.32
1092 1213 2.281484 ATCCGGCAAACACGCTGT 60.281 55.556 0.00 0.00 36.48 4.40
1178 1311 0.033796 CATGAATGCCCTGTCCACCT 60.034 55.000 0.00 0.00 0.00 4.00
1210 1343 1.831389 GCTTTGCTCGTTGACTCGCA 61.831 55.000 0.00 0.00 0.00 5.10
1277 1410 3.229276 TGCAAAAACTGAACCTGTGTG 57.771 42.857 0.00 0.00 0.00 3.82
1280 1413 3.195396 ACACATGCAAAAACTGAACCTGT 59.805 39.130 0.00 0.00 0.00 4.00
1320 1453 3.478857 TTGAACCCACTGAACGTGTAT 57.521 42.857 0.00 0.00 42.20 2.29
1323 1456 3.708563 AAATTGAACCCACTGAACGTG 57.291 42.857 0.00 0.00 43.41 4.49
1324 1457 3.736740 GCAAAATTGAACCCACTGAACGT 60.737 43.478 0.00 0.00 0.00 3.99
1340 1473 4.380867 GGATCTGGTTTCGTCATGCAAAAT 60.381 41.667 0.00 0.00 0.00 1.82
1352 1485 4.698304 TCCGTAAACATTGGATCTGGTTTC 59.302 41.667 0.00 0.00 35.33 2.78
1353 1486 4.658063 TCCGTAAACATTGGATCTGGTTT 58.342 39.130 0.00 0.00 37.28 3.27
1391 1528 2.890766 GCCGGTCCTTCCTTGTCCA 61.891 63.158 1.90 0.00 0.00 4.02
1396 1533 3.391382 CTCCGCCGGTCCTTCCTT 61.391 66.667 1.63 0.00 0.00 3.36
1441 1578 1.138859 TGTCCATGTAATCGGGAGCTG 59.861 52.381 0.00 0.00 0.00 4.24
1445 1582 2.473070 TCCTTGTCCATGTAATCGGGA 58.527 47.619 0.00 0.00 0.00 5.14
1449 1586 4.200092 GGTCCTTCCTTGTCCATGTAATC 58.800 47.826 0.00 0.00 0.00 1.75
1450 1587 3.370527 CGGTCCTTCCTTGTCCATGTAAT 60.371 47.826 0.00 0.00 0.00 1.89
1451 1588 2.027561 CGGTCCTTCCTTGTCCATGTAA 60.028 50.000 0.00 0.00 0.00 2.41
1453 1590 0.324943 CGGTCCTTCCTTGTCCATGT 59.675 55.000 0.00 0.00 0.00 3.21
1454 1591 0.392998 CCGGTCCTTCCTTGTCCATG 60.393 60.000 0.00 0.00 0.00 3.66
1455 1592 1.991230 CCGGTCCTTCCTTGTCCAT 59.009 57.895 0.00 0.00 0.00 3.41
1456 1593 2.890766 GCCGGTCCTTCCTTGTCCA 61.891 63.158 1.90 0.00 0.00 4.02
1457 1594 2.046217 GCCGGTCCTTCCTTGTCC 60.046 66.667 1.90 0.00 0.00 4.02
1458 1595 2.434359 CGCCGGTCCTTCCTTGTC 60.434 66.667 1.90 0.00 0.00 3.18
1459 1596 4.016706 CCGCCGGTCCTTCCTTGT 62.017 66.667 1.90 0.00 0.00 3.16
1460 1597 3.665675 CTCCGCCGGTCCTTCCTTG 62.666 68.421 1.63 0.00 0.00 3.61
1461 1598 3.391382 CTCCGCCGGTCCTTCCTT 61.391 66.667 1.63 0.00 0.00 3.36
1501 1638 2.106938 TAATCGGGCGCTGCTCTG 59.893 61.111 7.64 0.00 0.00 3.35
1502 1639 2.032860 ATGTAATCGGGCGCTGCTCT 62.033 55.000 7.64 0.00 0.00 4.09
1503 1640 0.319555 TATGTAATCGGGCGCTGCTC 60.320 55.000 7.64 0.00 0.00 4.26
1504 1641 0.105964 TTATGTAATCGGGCGCTGCT 59.894 50.000 7.64 0.00 0.00 4.24
1505 1642 0.512952 CTTATGTAATCGGGCGCTGC 59.487 55.000 7.64 0.00 0.00 5.25
1506 1643 1.792949 GTCTTATGTAATCGGGCGCTG 59.207 52.381 7.64 0.00 0.00 5.18
1507 1644 1.687123 AGTCTTATGTAATCGGGCGCT 59.313 47.619 7.64 0.00 0.00 5.92
1508 1645 1.792949 CAGTCTTATGTAATCGGGCGC 59.207 52.381 0.00 0.00 0.00 6.53
1509 1646 3.364889 TCAGTCTTATGTAATCGGGCG 57.635 47.619 0.00 0.00 0.00 6.13
1510 1647 4.632153 ACATCAGTCTTATGTAATCGGGC 58.368 43.478 0.00 0.00 35.82 6.13
1511 1648 6.280643 TCAACATCAGTCTTATGTAATCGGG 58.719 40.000 0.06 0.00 36.56 5.14
1512 1649 7.953158 ATCAACATCAGTCTTATGTAATCGG 57.047 36.000 0.06 0.00 36.56 4.18
1513 1650 9.684448 ACTATCAACATCAGTCTTATGTAATCG 57.316 33.333 0.06 0.00 36.56 3.34
1522 1659 9.809096 CTACACATAACTATCAACATCAGTCTT 57.191 33.333 0.00 0.00 0.00 3.01
1523 1660 9.190317 TCTACACATAACTATCAACATCAGTCT 57.810 33.333 0.00 0.00 0.00 3.24
1524 1661 9.239002 GTCTACACATAACTATCAACATCAGTC 57.761 37.037 0.00 0.00 0.00 3.51
1525 1662 8.972127 AGTCTACACATAACTATCAACATCAGT 58.028 33.333 0.00 0.00 0.00 3.41
1526 1663 9.457110 GAGTCTACACATAACTATCAACATCAG 57.543 37.037 0.00 0.00 0.00 2.90
1527 1664 8.414003 GGAGTCTACACATAACTATCAACATCA 58.586 37.037 0.00 0.00 0.00 3.07
1528 1665 8.634444 AGGAGTCTACACATAACTATCAACATC 58.366 37.037 0.00 0.00 0.00 3.06
1529 1666 8.540507 AGGAGTCTACACATAACTATCAACAT 57.459 34.615 0.00 0.00 0.00 2.71
1530 1667 7.956328 AGGAGTCTACACATAACTATCAACA 57.044 36.000 0.00 0.00 0.00 3.33
1531 1668 9.733219 GTTAGGAGTCTACACATAACTATCAAC 57.267 37.037 7.53 0.00 0.00 3.18
1532 1669 9.470399 TGTTAGGAGTCTACACATAACTATCAA 57.530 33.333 13.46 0.00 0.00 2.57
1533 1670 9.121658 CTGTTAGGAGTCTACACATAACTATCA 57.878 37.037 13.46 0.00 0.00 2.15
1534 1671 9.339850 TCTGTTAGGAGTCTACACATAACTATC 57.660 37.037 13.46 0.00 0.00 2.08
1535 1672 9.344772 CTCTGTTAGGAGTCTACACATAACTAT 57.655 37.037 13.46 0.00 0.00 2.12
1536 1673 8.327271 ACTCTGTTAGGAGTCTACACATAACTA 58.673 37.037 13.46 4.63 42.15 2.24
1537 1674 7.121463 CACTCTGTTAGGAGTCTACACATAACT 59.879 40.741 13.46 0.00 43.75 2.24
1538 1675 7.120873 TCACTCTGTTAGGAGTCTACACATAAC 59.879 40.741 7.76 7.76 43.75 1.89
1539 1676 7.173032 TCACTCTGTTAGGAGTCTACACATAA 58.827 38.462 0.00 0.00 43.75 1.90
1540 1677 6.718294 TCACTCTGTTAGGAGTCTACACATA 58.282 40.000 0.00 0.00 43.75 2.29
1541 1678 5.571285 TCACTCTGTTAGGAGTCTACACAT 58.429 41.667 0.00 0.00 43.75 3.21
1542 1679 4.981812 TCACTCTGTTAGGAGTCTACACA 58.018 43.478 0.00 0.00 43.75 3.72
1543 1680 5.961396 TTCACTCTGTTAGGAGTCTACAC 57.039 43.478 0.00 0.00 43.75 2.90
1544 1681 6.971726 TTTTCACTCTGTTAGGAGTCTACA 57.028 37.500 0.00 0.00 43.75 2.74
1565 1702 7.637631 TTTGCCTTTAGATTTTTGGCTTTTT 57.362 28.000 0.00 0.00 43.57 1.94
1566 1703 7.637631 TTTTGCCTTTAGATTTTTGGCTTTT 57.362 28.000 0.00 0.00 43.57 2.27
1567 1704 7.637631 TTTTTGCCTTTAGATTTTTGGCTTT 57.362 28.000 0.00 0.00 43.57 3.51
1590 1727 9.987272 CTTTCAATCCTGGAGTTTCTTTTATTT 57.013 29.630 1.52 0.00 0.00 1.40
1591 1728 8.588472 CCTTTCAATCCTGGAGTTTCTTTTATT 58.412 33.333 1.52 0.00 0.00 1.40
1592 1729 7.310052 GCCTTTCAATCCTGGAGTTTCTTTTAT 60.310 37.037 1.52 0.00 0.00 1.40
1593 1730 6.015434 GCCTTTCAATCCTGGAGTTTCTTTTA 60.015 38.462 1.52 0.00 0.00 1.52
1594 1731 5.221521 GCCTTTCAATCCTGGAGTTTCTTTT 60.222 40.000 1.52 0.00 0.00 2.27
1595 1732 4.281941 GCCTTTCAATCCTGGAGTTTCTTT 59.718 41.667 1.52 0.00 0.00 2.52
1596 1733 3.829026 GCCTTTCAATCCTGGAGTTTCTT 59.171 43.478 1.52 0.00 0.00 2.52
1597 1734 3.075134 AGCCTTTCAATCCTGGAGTTTCT 59.925 43.478 1.52 0.00 0.00 2.52
1598 1735 3.425659 AGCCTTTCAATCCTGGAGTTTC 58.574 45.455 1.52 0.00 0.00 2.78
1599 1736 3.532641 AGCCTTTCAATCCTGGAGTTT 57.467 42.857 1.52 0.00 0.00 2.66
1600 1737 3.532641 AAGCCTTTCAATCCTGGAGTT 57.467 42.857 1.52 0.00 0.00 3.01
1601 1738 3.160269 CAAAGCCTTTCAATCCTGGAGT 58.840 45.455 1.52 0.00 0.00 3.85
1602 1739 2.494870 CCAAAGCCTTTCAATCCTGGAG 59.505 50.000 1.52 0.00 0.00 3.86
1603 1740 2.528564 CCAAAGCCTTTCAATCCTGGA 58.471 47.619 0.00 0.00 0.00 3.86
1604 1741 1.551883 CCCAAAGCCTTTCAATCCTGG 59.448 52.381 0.00 0.00 0.00 4.45
1605 1742 1.551883 CCCCAAAGCCTTTCAATCCTG 59.448 52.381 0.00 0.00 0.00 3.86
1606 1743 1.432807 TCCCCAAAGCCTTTCAATCCT 59.567 47.619 0.00 0.00 0.00 3.24
1607 1744 1.827344 CTCCCCAAAGCCTTTCAATCC 59.173 52.381 0.00 0.00 0.00 3.01
1608 1745 2.807676 TCTCCCCAAAGCCTTTCAATC 58.192 47.619 0.00 0.00 0.00 2.67
1609 1746 2.999185 TCTCCCCAAAGCCTTTCAAT 57.001 45.000 0.00 0.00 0.00 2.57
1610 1747 2.528564 CATCTCCCCAAAGCCTTTCAA 58.471 47.619 0.00 0.00 0.00 2.69
1611 1748 1.892329 GCATCTCCCCAAAGCCTTTCA 60.892 52.381 0.00 0.00 0.00 2.69
1612 1749 0.820226 GCATCTCCCCAAAGCCTTTC 59.180 55.000 0.00 0.00 0.00 2.62
1613 1750 0.615827 GGCATCTCCCCAAAGCCTTT 60.616 55.000 0.00 0.00 42.01 3.11
1614 1751 1.000866 GGCATCTCCCCAAAGCCTT 59.999 57.895 0.00 0.00 42.01 4.35
1615 1752 2.240918 TGGCATCTCCCCAAAGCCT 61.241 57.895 0.00 0.00 45.42 4.58
1616 1753 2.054453 GTGGCATCTCCCCAAAGCC 61.054 63.158 0.00 0.00 45.41 4.35
1617 1754 2.054453 GGTGGCATCTCCCCAAAGC 61.054 63.158 0.00 0.00 33.39 3.51
1618 1755 0.967380 GTGGTGGCATCTCCCCAAAG 60.967 60.000 0.00 0.00 37.07 2.77
1619 1756 1.076549 GTGGTGGCATCTCCCCAAA 59.923 57.895 0.00 0.00 37.07 3.28
1620 1757 2.763215 GTGGTGGCATCTCCCCAA 59.237 61.111 0.00 0.00 37.07 4.12
1621 1758 3.338250 GGTGGTGGCATCTCCCCA 61.338 66.667 7.64 0.00 34.20 4.96
1622 1759 4.489771 CGGTGGTGGCATCTCCCC 62.490 72.222 12.96 2.74 0.00 4.81
1623 1760 3.399181 TCGGTGGTGGCATCTCCC 61.399 66.667 12.96 5.21 0.00 4.30
1624 1761 2.125106 GTCGGTGGTGGCATCTCC 60.125 66.667 8.81 8.81 0.00 3.71
1625 1762 1.448540 CTGTCGGTGGTGGCATCTC 60.449 63.158 0.00 0.00 0.00 2.75
1626 1763 1.768684 AACTGTCGGTGGTGGCATCT 61.769 55.000 0.00 0.00 0.00 2.90
1627 1764 0.889186 AAACTGTCGGTGGTGGCATC 60.889 55.000 0.00 0.00 0.00 3.91
1628 1765 1.150536 AAACTGTCGGTGGTGGCAT 59.849 52.632 0.00 0.00 0.00 4.40
1629 1766 1.821759 CAAACTGTCGGTGGTGGCA 60.822 57.895 0.00 0.00 0.00 4.92
1630 1767 2.551912 CCAAACTGTCGGTGGTGGC 61.552 63.158 2.57 0.00 30.44 5.01
1631 1768 1.153046 ACCAAACTGTCGGTGGTGG 60.153 57.895 11.61 11.61 44.05 4.61
1632 1769 4.551729 ACCAAACTGTCGGTGGTG 57.448 55.556 9.26 0.00 44.05 4.17
1636 1773 1.147600 GGTCCACCAAACTGTCGGT 59.852 57.895 0.00 0.00 35.27 4.69
1637 1774 0.682852 TAGGTCCACCAAACTGTCGG 59.317 55.000 0.00 0.00 38.89 4.79
1638 1775 1.343465 AGTAGGTCCACCAAACTGTCG 59.657 52.381 0.00 0.00 38.89 4.35
1639 1776 2.767505 CAGTAGGTCCACCAAACTGTC 58.232 52.381 17.29 0.00 42.50 3.51
1640 1777 2.930826 CAGTAGGTCCACCAAACTGT 57.069 50.000 17.29 0.00 42.50 3.55
1642 1779 1.420138 CCACAGTAGGTCCACCAAACT 59.580 52.381 0.00 0.00 38.89 2.66
1643 1780 1.142262 ACCACAGTAGGTCCACCAAAC 59.858 52.381 0.00 0.00 37.28 2.93
1644 1781 1.513858 ACCACAGTAGGTCCACCAAA 58.486 50.000 0.00 0.00 37.28 3.28
1645 1782 2.253610 CTACCACAGTAGGTCCACCAA 58.746 52.381 0.00 0.00 42.05 3.67
1646 1783 1.933021 CTACCACAGTAGGTCCACCA 58.067 55.000 0.00 0.00 42.05 4.17
1647 1784 0.535797 GCTACCACAGTAGGTCCACC 59.464 60.000 2.67 0.00 45.29 4.61
1648 1785 1.263356 TGCTACCACAGTAGGTCCAC 58.737 55.000 2.67 0.00 45.29 4.02
1649 1786 2.018355 TTGCTACCACAGTAGGTCCA 57.982 50.000 2.67 0.00 45.29 4.02
1650 1787 3.412237 TTTTGCTACCACAGTAGGTCC 57.588 47.619 2.67 0.00 45.29 4.46
1651 1788 3.751698 CCTTTTTGCTACCACAGTAGGTC 59.248 47.826 2.67 0.00 45.29 3.85
1652 1789 3.393278 TCCTTTTTGCTACCACAGTAGGT 59.607 43.478 2.67 0.00 45.29 3.08
1653 1790 4.003648 CTCCTTTTTGCTACCACAGTAGG 58.996 47.826 2.67 0.00 45.29 3.18
1655 1792 3.649023 TCCTCCTTTTTGCTACCACAGTA 59.351 43.478 0.00 0.00 0.00 2.74
1656 1793 2.441750 TCCTCCTTTTTGCTACCACAGT 59.558 45.455 0.00 0.00 0.00 3.55
1657 1794 3.140325 TCCTCCTTTTTGCTACCACAG 57.860 47.619 0.00 0.00 0.00 3.66
1658 1795 3.586470 TTCCTCCTTTTTGCTACCACA 57.414 42.857 0.00 0.00 0.00 4.17
1659 1796 6.775594 ATATTTCCTCCTTTTTGCTACCAC 57.224 37.500 0.00 0.00 0.00 4.16
1660 1797 7.790782 AAATATTTCCTCCTTTTTGCTACCA 57.209 32.000 0.00 0.00 0.00 3.25
1661 1798 9.803315 CTTAAATATTTCCTCCTTTTTGCTACC 57.197 33.333 3.39 0.00 0.00 3.18
1664 1801 8.314021 CCACTTAAATATTTCCTCCTTTTTGCT 58.686 33.333 3.39 0.00 0.00 3.91
1665 1802 8.094548 ACCACTTAAATATTTCCTCCTTTTTGC 58.905 33.333 3.39 0.00 0.00 3.68
1666 1803 9.996554 AACCACTTAAATATTTCCTCCTTTTTG 57.003 29.630 3.39 0.00 0.00 2.44
1667 1804 9.996554 CAACCACTTAAATATTTCCTCCTTTTT 57.003 29.630 3.39 0.00 0.00 1.94
1668 1805 9.374711 TCAACCACTTAAATATTTCCTCCTTTT 57.625 29.630 3.39 0.00 0.00 2.27
1669 1806 8.803235 GTCAACCACTTAAATATTTCCTCCTTT 58.197 33.333 3.39 0.00 0.00 3.11
1670 1807 7.120726 CGTCAACCACTTAAATATTTCCTCCTT 59.879 37.037 3.39 0.00 0.00 3.36
1671 1808 6.598064 CGTCAACCACTTAAATATTTCCTCCT 59.402 38.462 3.39 0.00 0.00 3.69
1672 1809 6.596497 TCGTCAACCACTTAAATATTTCCTCC 59.404 38.462 3.39 0.00 0.00 4.30
1673 1810 7.118680 TGTCGTCAACCACTTAAATATTTCCTC 59.881 37.037 3.39 0.00 0.00 3.71
1674 1811 6.938030 TGTCGTCAACCACTTAAATATTTCCT 59.062 34.615 3.39 0.00 0.00 3.36
1675 1812 7.136289 TGTCGTCAACCACTTAAATATTTCC 57.864 36.000 3.39 0.00 0.00 3.13
1676 1813 9.061610 CAATGTCGTCAACCACTTAAATATTTC 57.938 33.333 3.39 0.00 0.00 2.17
1677 1814 8.788806 TCAATGTCGTCAACCACTTAAATATTT 58.211 29.630 5.89 5.89 0.00 1.40
1678 1815 8.330466 TCAATGTCGTCAACCACTTAAATATT 57.670 30.769 0.00 0.00 0.00 1.28
1679 1816 7.915293 TCAATGTCGTCAACCACTTAAATAT 57.085 32.000 0.00 0.00 0.00 1.28
1680 1817 7.658167 TCTTCAATGTCGTCAACCACTTAAATA 59.342 33.333 0.00 0.00 0.00 1.40
1681 1818 6.485313 TCTTCAATGTCGTCAACCACTTAAAT 59.515 34.615 0.00 0.00 0.00 1.40
1682 1819 5.818336 TCTTCAATGTCGTCAACCACTTAAA 59.182 36.000 0.00 0.00 0.00 1.52
1683 1820 5.361427 TCTTCAATGTCGTCAACCACTTAA 58.639 37.500 0.00 0.00 0.00 1.85
1684 1821 4.951254 TCTTCAATGTCGTCAACCACTTA 58.049 39.130 0.00 0.00 0.00 2.24
1685 1822 3.804036 TCTTCAATGTCGTCAACCACTT 58.196 40.909 0.00 0.00 0.00 3.16
1686 1823 3.469008 TCTTCAATGTCGTCAACCACT 57.531 42.857 0.00 0.00 0.00 4.00
1687 1824 4.545823 TTTCTTCAATGTCGTCAACCAC 57.454 40.909 0.00 0.00 0.00 4.16
1688 1825 5.568685 TTTTTCTTCAATGTCGTCAACCA 57.431 34.783 0.00 0.00 0.00 3.67
1712 1849 9.410556 GCTCATCTTCTAGAGATTATCAAACTC 57.589 37.037 0.00 0.00 42.55 3.01
1713 1850 8.081633 CGCTCATCTTCTAGAGATTATCAAACT 58.918 37.037 0.00 0.00 42.55 2.66
1714 1851 7.148820 GCGCTCATCTTCTAGAGATTATCAAAC 60.149 40.741 0.00 0.00 42.55 2.93
1715 1852 6.865726 GCGCTCATCTTCTAGAGATTATCAAA 59.134 38.462 0.00 0.00 42.55 2.69
1716 1853 6.015940 TGCGCTCATCTTCTAGAGATTATCAA 60.016 38.462 9.73 0.00 42.55 2.57
1717 1854 5.474876 TGCGCTCATCTTCTAGAGATTATCA 59.525 40.000 9.73 0.00 42.55 2.15
1718 1855 5.948588 TGCGCTCATCTTCTAGAGATTATC 58.051 41.667 9.73 0.00 42.55 1.75
1719 1856 5.973899 TGCGCTCATCTTCTAGAGATTAT 57.026 39.130 9.73 0.00 42.55 1.28
1720 1857 5.774498 TTGCGCTCATCTTCTAGAGATTA 57.226 39.130 9.73 0.00 42.55 1.75
1721 1858 4.662468 TTGCGCTCATCTTCTAGAGATT 57.338 40.909 9.73 0.00 42.55 2.40
1722 1859 4.870123 ATTGCGCTCATCTTCTAGAGAT 57.130 40.909 9.73 0.00 46.12 2.75
1723 1860 4.662468 AATTGCGCTCATCTTCTAGAGA 57.338 40.909 9.73 0.00 39.13 3.10
1724 1861 4.385447 GCTAATTGCGCTCATCTTCTAGAG 59.615 45.833 9.73 0.00 35.01 2.43
1725 1862 4.302455 GCTAATTGCGCTCATCTTCTAGA 58.698 43.478 9.73 0.00 0.00 2.43
1726 1863 4.644044 GCTAATTGCGCTCATCTTCTAG 57.356 45.455 9.73 1.03 0.00 2.43
1849 1986 0.970937 GTCCCTCCACACGATCCTCA 60.971 60.000 0.00 0.00 0.00 3.86
1986 2123 7.559170 CCTCTTCAGATGTTAATCCCTGATTTT 59.441 37.037 0.00 0.00 35.82 1.82
2043 2180 1.595093 CCCAAGGTCCAAACGCATCC 61.595 60.000 0.00 0.00 0.00 3.51
2056 2193 3.439857 TCCAGAAATCTGTTCCCAAGG 57.560 47.619 9.43 0.00 42.27 3.61
2109 2246 2.064762 GATCAGATAGCATCCGCACAC 58.935 52.381 0.00 0.00 42.27 3.82
2119 2256 4.502950 CCTTTGTCTGGAGGATCAGATAGC 60.503 50.000 0.00 0.00 44.43 2.97
2123 2260 1.556911 GCCTTTGTCTGGAGGATCAGA 59.443 52.381 0.00 0.00 41.03 3.27
2170 2307 3.713826 TCTTTACCTGGCCTCGAATTT 57.286 42.857 3.32 0.00 0.00 1.82
2245 2382 4.097418 CCAGATCCTTTATACTCCCCGAT 58.903 47.826 0.00 0.00 0.00 4.18
2246 2383 3.507411 CCAGATCCTTTATACTCCCCGA 58.493 50.000 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.