Multiple sequence alignment - TraesCS7D01G515900

Loading Multiple Alignment...

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 TraesCS7D01G515900 chr7D 100.000 2317 0 0 1 2317 615912061 615909745 0 4279
1 TraesCS7D01G515900 chr1D 94.337 1342 74 2 1 1341 475891462 475892802 0 2056
2 TraesCS7D01G515900 chr6B 93.890 1342 80 2 1 1341 151387191 151385851 0 2023
3 TraesCS7D01G515900 chr7B 93.239 1346 87 4 1 1344 192798491 192797148 0 1978
4 TraesCS7D01G515900 chr7B 91.437 1343 112 3 1 1341 552700429 552699088 0 1840
5 TraesCS7D01G515900 chr7B 91.327 1326 112 3 1 1324 552747418 552746094 0 1808
6 TraesCS7D01G515900 chr7B 84.278 706 65 18 1582 2272 708961850 708961176 0 647
7 TraesCS7D01G515900 chr5A 93.145 1342 90 2 1 1341 71139706 71141046 0 1967
8 TraesCS7D01G515900 chr5B 90.767 1343 119 4 1 1341 348576109 348574770 0 1788
9 TraesCS7D01G515900 chr4A 87.816 1346 161 3 1 1344 669052073 669050729 0 1574
10 TraesCS7D01G515900 chr4A 87.620 1349 159 6 1 1346 676915478 676914135 0 1559


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 TraesCS7D01G515900 chr7D 615909745 615912061 2316 True 4279 4279 100.000 1 2317 1 chr7D.!!$R1 2316
1 TraesCS7D01G515900 chr1D 475891462 475892802 1340 False 2056 2056 94.337 1 1341 1 chr1D.!!$F1 1340
2 TraesCS7D01G515900 chr6B 151385851 151387191 1340 True 2023 2023 93.890 1 1341 1 chr6B.!!$R1 1340
3 TraesCS7D01G515900 chr7B 192797148 192798491 1343 True 1978 1978 93.239 1 1344 1 chr7B.!!$R1 1343
4 TraesCS7D01G515900 chr7B 552699088 552700429 1341 True 1840 1840 91.437 1 1341 1 chr7B.!!$R2 1340
5 TraesCS7D01G515900 chr7B 552746094 552747418 1324 True 1808 1808 91.327 1 1324 1 chr7B.!!$R3 1323
6 TraesCS7D01G515900 chr7B 708961176 708961850 674 True 647 647 84.278 1582 2272 1 chr7B.!!$R4 690
7 TraesCS7D01G515900 chr5A 71139706 71141046 1340 False 1967 1967 93.145 1 1341 1 chr5A.!!$F1 1340
8 TraesCS7D01G515900 chr5B 348574770 348576109 1339 True 1788 1788 90.767 1 1341 1 chr5B.!!$R1 1340
9 TraesCS7D01G515900 chr4A 669050729 669052073 1344 True 1574 1574 87.816 1 1344 1 chr4A.!!$R1 1343
10 TraesCS7D01G515900 chr4A 676914135 676915478 1343 True 1559 1559 87.620 1 1346 1 chr4A.!!$R2 1345

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
333 334 1.040339 AGGCTGCGGTTCCACAAAAA 61.04 50.0 0.0 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1705 0.031994 GTTGGTGCGTGGCTTTTCAT 59.968 50.0 0.0 0.0 0.0 2.57 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
128 129 2.486191 GGCCTATGGATGTTGACCAGAG 60.486 54.545 0.00 0.00 43.67 3.35
205 206 5.279506 CCTGAGAAGAGTGGTTGCTTTACTA 60.280 44.000 0.00 0.00 0.00 1.82
210 211 5.091261 AGAGTGGTTGCTTTACTATGAGG 57.909 43.478 0.00 0.00 0.00 3.86
221 222 6.183361 TGCTTTACTATGAGGAGTGCATACAT 60.183 38.462 0.00 0.00 0.00 2.29
264 265 3.988525 GCAACGGCCAATGGTGCA 61.989 61.111 13.60 0.00 0.00 4.57
333 334 1.040339 AGGCTGCGGTTCCACAAAAA 61.040 50.000 0.00 0.00 0.00 1.94
426 429 4.866508 ATCGACAAGTTCTACCTGTCAA 57.133 40.909 8.72 0.00 0.00 3.18
636 639 3.091545 GTTGATCTGGAGGATTTGGCAA 58.908 45.455 0.00 0.00 34.33 4.52
761 764 3.263170 TCAACGGAGGAAATCATCAAGGA 59.737 43.478 0.00 0.00 0.00 3.36
788 791 2.301577 CCACTTTCGGCTCTTCCTAG 57.698 55.000 0.00 0.00 0.00 3.02
792 795 1.137282 CTTTCGGCTCTTCCTAGTCCC 59.863 57.143 0.00 0.00 0.00 4.46
936 939 2.959421 ATGAGAAGGGAGAGGTCCTT 57.041 50.000 0.00 0.00 46.37 3.36
1012 1015 0.107263 TGCGATAATGCAGGGCTTGA 60.107 50.000 0.00 0.00 40.62 3.02
1065 1068 1.371558 GGTGCAAACGGACTCCTCT 59.628 57.895 0.00 0.00 0.00 3.69
1091 1094 3.065233 GCGCTATCATGTTTGACCAATGA 59.935 43.478 0.00 0.00 33.85 2.57
1223 1227 6.455647 CCATCAATTGGCTAAGTATAGTCGA 58.544 40.000 5.42 0.00 39.09 4.20
1358 1362 5.948992 AAAAATAAGAGACACCTGAGCAC 57.051 39.130 0.00 0.00 0.00 4.40
1359 1363 3.618690 AATAAGAGACACCTGAGCACC 57.381 47.619 0.00 0.00 0.00 5.01
1360 1364 2.310779 TAAGAGACACCTGAGCACCT 57.689 50.000 0.00 0.00 0.00 4.00
1361 1365 2.310779 AAGAGACACCTGAGCACCTA 57.689 50.000 0.00 0.00 0.00 3.08
1362 1366 1.846007 AGAGACACCTGAGCACCTAG 58.154 55.000 0.00 0.00 0.00 3.02
1363 1367 0.174617 GAGACACCTGAGCACCTAGC 59.825 60.000 0.00 0.00 46.19 3.42
1373 1377 2.772739 GCACCTAGCTCCACACATG 58.227 57.895 0.00 0.00 41.15 3.21
1374 1378 0.036010 GCACCTAGCTCCACACATGT 60.036 55.000 0.00 0.00 41.15 3.21
1375 1379 1.611673 GCACCTAGCTCCACACATGTT 60.612 52.381 0.00 0.00 41.15 2.71
1376 1380 2.350522 CACCTAGCTCCACACATGTTC 58.649 52.381 0.00 0.00 0.00 3.18
1377 1381 1.977854 ACCTAGCTCCACACATGTTCA 59.022 47.619 0.00 0.00 0.00 3.18
1378 1382 2.027745 ACCTAGCTCCACACATGTTCAG 60.028 50.000 0.00 0.00 0.00 3.02
1379 1383 2.027745 CCTAGCTCCACACATGTTCAGT 60.028 50.000 0.00 0.00 0.00 3.41
1380 1384 2.645838 AGCTCCACACATGTTCAGTT 57.354 45.000 0.00 0.00 0.00 3.16
1381 1385 2.498167 AGCTCCACACATGTTCAGTTC 58.502 47.619 0.00 0.00 0.00 3.01
1382 1386 2.105477 AGCTCCACACATGTTCAGTTCT 59.895 45.455 0.00 0.00 0.00 3.01
1383 1387 2.481952 GCTCCACACATGTTCAGTTCTC 59.518 50.000 0.00 0.00 0.00 2.87
1384 1388 3.732212 CTCCACACATGTTCAGTTCTCA 58.268 45.455 0.00 0.00 0.00 3.27
1385 1389 4.129380 CTCCACACATGTTCAGTTCTCAA 58.871 43.478 0.00 0.00 0.00 3.02
1386 1390 3.876914 TCCACACATGTTCAGTTCTCAAC 59.123 43.478 0.00 0.00 0.00 3.18
1387 1391 3.879295 CCACACATGTTCAGTTCTCAACT 59.121 43.478 0.00 0.00 44.06 3.16
1388 1392 4.336433 CCACACATGTTCAGTTCTCAACTT 59.664 41.667 0.00 0.00 40.46 2.66
1389 1393 5.504665 CCACACATGTTCAGTTCTCAACTTC 60.505 44.000 0.00 0.00 40.46 3.01
1390 1394 5.295292 CACACATGTTCAGTTCTCAACTTCT 59.705 40.000 0.00 0.00 40.46 2.85
1391 1395 5.525378 ACACATGTTCAGTTCTCAACTTCTC 59.475 40.000 0.00 0.00 40.46 2.87
1392 1396 4.747108 ACATGTTCAGTTCTCAACTTCTCG 59.253 41.667 0.00 0.00 40.46 4.04
1393 1397 4.386867 TGTTCAGTTCTCAACTTCTCGT 57.613 40.909 0.00 0.00 40.46 4.18
1394 1398 4.755411 TGTTCAGTTCTCAACTTCTCGTT 58.245 39.130 0.00 0.00 40.46 3.85
1395 1399 4.804139 TGTTCAGTTCTCAACTTCTCGTTC 59.196 41.667 0.00 0.00 40.46 3.95
1396 1400 3.978687 TCAGTTCTCAACTTCTCGTTCC 58.021 45.455 0.00 0.00 40.46 3.62
1397 1401 3.383505 TCAGTTCTCAACTTCTCGTTCCA 59.616 43.478 0.00 0.00 40.46 3.53
1398 1402 4.119862 CAGTTCTCAACTTCTCGTTCCAA 58.880 43.478 0.00 0.00 40.46 3.53
1399 1403 4.570772 CAGTTCTCAACTTCTCGTTCCAAA 59.429 41.667 0.00 0.00 40.46 3.28
1400 1404 5.064707 CAGTTCTCAACTTCTCGTTCCAAAA 59.935 40.000 0.00 0.00 40.46 2.44
1401 1405 5.823045 AGTTCTCAACTTCTCGTTCCAAAAT 59.177 36.000 0.00 0.00 39.04 1.82
1402 1406 5.673337 TCTCAACTTCTCGTTCCAAAATG 57.327 39.130 0.00 0.00 32.27 2.32
1403 1407 4.024048 TCTCAACTTCTCGTTCCAAAATGC 60.024 41.667 0.00 0.00 32.27 3.56
1404 1408 3.629855 TCAACTTCTCGTTCCAAAATGCA 59.370 39.130 0.00 0.00 32.27 3.96
1405 1409 4.097135 TCAACTTCTCGTTCCAAAATGCAA 59.903 37.500 0.00 0.00 32.27 4.08
1406 1410 4.647424 ACTTCTCGTTCCAAAATGCAAA 57.353 36.364 0.00 0.00 0.00 3.68
1407 1411 5.004922 ACTTCTCGTTCCAAAATGCAAAA 57.995 34.783 0.00 0.00 0.00 2.44
1408 1412 4.803613 ACTTCTCGTTCCAAAATGCAAAAC 59.196 37.500 0.00 0.00 0.00 2.43
1409 1413 3.712187 TCTCGTTCCAAAATGCAAAACC 58.288 40.909 0.00 0.00 0.00 3.27
1410 1414 2.464865 TCGTTCCAAAATGCAAAACCG 58.535 42.857 0.00 0.00 0.00 4.44
1411 1415 2.099263 TCGTTCCAAAATGCAAAACCGA 59.901 40.909 0.00 0.00 0.00 4.69
1412 1416 2.470999 CGTTCCAAAATGCAAAACCGAG 59.529 45.455 0.00 0.00 0.00 4.63
1413 1417 2.799978 GTTCCAAAATGCAAAACCGAGG 59.200 45.455 0.00 0.00 0.00 4.63
1414 1418 1.342819 TCCAAAATGCAAAACCGAGGG 59.657 47.619 0.00 0.00 0.00 4.30
1415 1419 1.607767 CCAAAATGCAAAACCGAGGGG 60.608 52.381 0.00 0.00 40.11 4.79
1416 1420 0.684535 AAAATGCAAAACCGAGGGGG 59.315 50.000 0.00 0.00 43.62 5.40
1417 1421 1.826340 AAATGCAAAACCGAGGGGGC 61.826 55.000 0.00 0.00 40.62 5.80
1418 1422 4.986708 TGCAAAACCGAGGGGGCC 62.987 66.667 0.00 0.00 40.62 5.80
1453 1457 3.294750 CGGTCCCGGATCACAAGA 58.705 61.111 0.73 0.00 35.56 3.02
1454 1458 1.153628 CGGTCCCGGATCACAAGAC 60.154 63.158 0.73 0.00 35.56 3.01
1455 1459 1.884075 CGGTCCCGGATCACAAGACA 61.884 60.000 0.73 0.00 35.56 3.41
1456 1460 0.391263 GGTCCCGGATCACAAGACAC 60.391 60.000 0.73 0.00 0.00 3.67
1457 1461 0.391263 GTCCCGGATCACAAGACACC 60.391 60.000 0.73 0.00 0.00 4.16
1458 1462 0.544357 TCCCGGATCACAAGACACCT 60.544 55.000 0.73 0.00 0.00 4.00
1459 1463 0.391661 CCCGGATCACAAGACACCTG 60.392 60.000 0.73 0.00 0.00 4.00
1460 1464 0.321671 CCGGATCACAAGACACCTGT 59.678 55.000 0.00 0.00 0.00 4.00
1461 1465 1.548719 CCGGATCACAAGACACCTGTA 59.451 52.381 0.00 0.00 0.00 2.74
1462 1466 2.607187 CGGATCACAAGACACCTGTAC 58.393 52.381 0.00 0.00 0.00 2.90
1463 1467 2.029380 CGGATCACAAGACACCTGTACA 60.029 50.000 0.00 0.00 0.00 2.90
1464 1468 3.554129 CGGATCACAAGACACCTGTACAA 60.554 47.826 0.00 0.00 0.00 2.41
1465 1469 4.385825 GGATCACAAGACACCTGTACAAA 58.614 43.478 0.00 0.00 0.00 2.83
1466 1470 4.213482 GGATCACAAGACACCTGTACAAAC 59.787 45.833 0.00 0.00 0.00 2.93
1467 1471 3.537580 TCACAAGACACCTGTACAAACC 58.462 45.455 0.00 0.00 0.00 3.27
1468 1472 2.286833 CACAAGACACCTGTACAAACCG 59.713 50.000 0.00 0.00 0.00 4.44
1469 1473 2.093341 ACAAGACACCTGTACAAACCGT 60.093 45.455 0.00 0.00 0.00 4.83
1470 1474 2.940410 CAAGACACCTGTACAAACCGTT 59.060 45.455 0.00 0.00 0.00 4.44
1471 1475 2.557317 AGACACCTGTACAAACCGTTG 58.443 47.619 0.00 0.00 40.84 4.10
1473 1477 3.132646 AGACACCTGTACAAACCGTTGTA 59.867 43.478 0.00 0.00 46.33 2.41
1480 1484 2.125773 ACAAACCGTTGTAACCACCA 57.874 45.000 0.00 0.00 46.33 4.17
1481 1485 2.018515 ACAAACCGTTGTAACCACCAG 58.981 47.619 0.00 0.00 46.33 4.00
1482 1486 1.026584 AAACCGTTGTAACCACCAGC 58.973 50.000 0.00 0.00 0.00 4.85
1483 1487 0.181824 AACCGTTGTAACCACCAGCT 59.818 50.000 0.00 0.00 0.00 4.24
1484 1488 1.050204 ACCGTTGTAACCACCAGCTA 58.950 50.000 0.00 0.00 0.00 3.32
1485 1489 1.270465 ACCGTTGTAACCACCAGCTAC 60.270 52.381 0.00 0.00 0.00 3.58
1486 1490 1.435577 CGTTGTAACCACCAGCTACC 58.564 55.000 0.00 0.00 0.00 3.18
1487 1491 1.270412 CGTTGTAACCACCAGCTACCA 60.270 52.381 0.00 0.00 0.00 3.25
1488 1492 2.148768 GTTGTAACCACCAGCTACCAC 58.851 52.381 0.00 0.00 0.00 4.16
1489 1493 1.425694 TGTAACCACCAGCTACCACA 58.574 50.000 0.00 0.00 0.00 4.17
1490 1494 1.769465 TGTAACCACCAGCTACCACAA 59.231 47.619 0.00 0.00 0.00 3.33
1491 1495 2.172930 TGTAACCACCAGCTACCACAAA 59.827 45.455 0.00 0.00 0.00 2.83
1492 1496 2.445682 AACCACCAGCTACCACAAAA 57.554 45.000 0.00 0.00 0.00 2.44
1493 1497 2.445682 ACCACCAGCTACCACAAAAA 57.554 45.000 0.00 0.00 0.00 1.94
1494 1498 2.028876 ACCACCAGCTACCACAAAAAC 58.971 47.619 0.00 0.00 0.00 2.43
1495 1499 1.001815 CCACCAGCTACCACAAAAACG 60.002 52.381 0.00 0.00 0.00 3.60
1496 1500 1.673920 CACCAGCTACCACAAAAACGT 59.326 47.619 0.00 0.00 0.00 3.99
1497 1501 2.098443 CACCAGCTACCACAAAAACGTT 59.902 45.455 0.00 0.00 0.00 3.99
1498 1502 2.098443 ACCAGCTACCACAAAAACGTTG 59.902 45.455 0.00 0.00 0.00 4.10
1499 1503 2.356382 CCAGCTACCACAAAAACGTTGA 59.644 45.455 0.00 0.00 0.00 3.18
1500 1504 3.359654 CAGCTACCACAAAAACGTTGAC 58.640 45.455 0.00 0.00 0.00 3.18
1501 1505 3.011119 AGCTACCACAAAAACGTTGACA 58.989 40.909 0.00 0.00 0.00 3.58
1502 1506 3.440872 AGCTACCACAAAAACGTTGACAA 59.559 39.130 0.00 0.00 0.00 3.18
1503 1507 4.097286 AGCTACCACAAAAACGTTGACAAT 59.903 37.500 0.00 0.00 0.00 2.71
1504 1508 4.801516 GCTACCACAAAAACGTTGACAATT 59.198 37.500 0.00 0.00 0.00 2.32
1505 1509 5.972382 GCTACCACAAAAACGTTGACAATTA 59.028 36.000 0.00 0.00 0.00 1.40
1506 1510 6.472808 GCTACCACAAAAACGTTGACAATTAA 59.527 34.615 0.00 0.00 0.00 1.40
1507 1511 7.168469 GCTACCACAAAAACGTTGACAATTAAT 59.832 33.333 0.00 0.00 0.00 1.40
1508 1512 7.458038 ACCACAAAAACGTTGACAATTAATC 57.542 32.000 0.00 0.00 0.00 1.75
1509 1513 6.197468 ACCACAAAAACGTTGACAATTAATCG 59.803 34.615 0.00 0.00 0.00 3.34
1510 1514 6.197468 CCACAAAAACGTTGACAATTAATCGT 59.803 34.615 0.00 0.00 0.00 3.73
1511 1515 7.048432 CACAAAAACGTTGACAATTAATCGTG 58.952 34.615 0.00 0.00 0.00 4.35
1512 1516 6.748198 ACAAAAACGTTGACAATTAATCGTGT 59.252 30.769 0.00 0.00 0.00 4.49
1513 1517 7.273815 ACAAAAACGTTGACAATTAATCGTGTT 59.726 29.630 0.00 0.70 31.55 3.32
1514 1518 7.743520 AAAACGTTGACAATTAATCGTGTTT 57.256 28.000 0.00 3.45 0.00 2.83
1515 1519 6.726035 AACGTTGACAATTAATCGTGTTTG 57.274 33.333 0.00 0.00 0.00 2.93
1516 1520 5.812652 ACGTTGACAATTAATCGTGTTTGT 58.187 33.333 0.56 0.00 35.14 2.83
1517 1521 6.259638 ACGTTGACAATTAATCGTGTTTGTT 58.740 32.000 0.56 0.00 32.73 2.83
1518 1522 6.412653 ACGTTGACAATTAATCGTGTTTGTTC 59.587 34.615 0.56 0.00 32.73 3.18
1519 1523 6.412362 CGTTGACAATTAATCGTGTTTGTTCA 59.588 34.615 0.00 0.00 32.73 3.18
1520 1524 7.044641 CGTTGACAATTAATCGTGTTTGTTCAA 60.045 33.333 0.00 0.00 32.73 2.69
1521 1525 8.751335 GTTGACAATTAATCGTGTTTGTTCAAT 58.249 29.630 0.00 0.00 32.73 2.57
1522 1526 8.500837 TGACAATTAATCGTGTTTGTTCAATC 57.499 30.769 0.00 0.00 32.73 2.67
1523 1527 8.131731 TGACAATTAATCGTGTTTGTTCAATCA 58.868 29.630 0.00 0.00 32.73 2.57
1524 1528 8.864069 ACAATTAATCGTGTTTGTTCAATCAA 57.136 26.923 0.00 0.00 0.00 2.57
1525 1529 8.751335 ACAATTAATCGTGTTTGTTCAATCAAC 58.249 29.630 0.00 0.00 35.28 3.18
1526 1530 8.967218 CAATTAATCGTGTTTGTTCAATCAACT 58.033 29.630 0.00 0.00 35.79 3.16
1527 1531 7.906611 TTAATCGTGTTTGTTCAATCAACTG 57.093 32.000 0.00 0.00 35.79 3.16
1528 1532 4.285807 TCGTGTTTGTTCAATCAACTGG 57.714 40.909 0.00 0.00 35.79 4.00
1529 1533 3.066064 TCGTGTTTGTTCAATCAACTGGG 59.934 43.478 0.00 0.00 35.79 4.45
1530 1534 3.123050 GTGTTTGTTCAATCAACTGGGC 58.877 45.455 0.00 0.00 35.79 5.36
1531 1535 2.762887 TGTTTGTTCAATCAACTGGGCA 59.237 40.909 0.00 0.00 35.79 5.36
1532 1536 3.196469 TGTTTGTTCAATCAACTGGGCAA 59.804 39.130 0.00 0.00 35.79 4.52
1533 1537 4.141756 TGTTTGTTCAATCAACTGGGCAAT 60.142 37.500 0.00 0.00 35.79 3.56
1534 1538 3.940209 TGTTCAATCAACTGGGCAATC 57.060 42.857 0.00 0.00 35.79 2.67
1535 1539 3.499338 TGTTCAATCAACTGGGCAATCT 58.501 40.909 0.00 0.00 35.79 2.40
1536 1540 3.256383 TGTTCAATCAACTGGGCAATCTG 59.744 43.478 0.00 0.00 35.79 2.90
1537 1541 3.438216 TCAATCAACTGGGCAATCTGA 57.562 42.857 0.00 0.00 0.00 3.27
1538 1542 3.972133 TCAATCAACTGGGCAATCTGAT 58.028 40.909 0.00 0.00 0.00 2.90
1539 1543 4.346730 TCAATCAACTGGGCAATCTGATT 58.653 39.130 0.00 0.00 37.24 2.57
1540 1544 4.773674 TCAATCAACTGGGCAATCTGATTT 59.226 37.500 0.00 0.00 35.15 2.17
1541 1545 5.246656 TCAATCAACTGGGCAATCTGATTTT 59.753 36.000 0.00 0.00 35.15 1.82
1542 1546 4.789012 TCAACTGGGCAATCTGATTTTC 57.211 40.909 0.00 0.00 0.00 2.29
1543 1547 3.191162 TCAACTGGGCAATCTGATTTTCG 59.809 43.478 0.00 0.00 0.00 3.46
1544 1548 2.795329 ACTGGGCAATCTGATTTTCGT 58.205 42.857 0.00 0.00 0.00 3.85
1545 1549 3.157087 ACTGGGCAATCTGATTTTCGTT 58.843 40.909 0.00 0.00 0.00 3.85
1546 1550 4.331968 ACTGGGCAATCTGATTTTCGTTA 58.668 39.130 0.00 0.00 0.00 3.18
1547 1551 4.949856 ACTGGGCAATCTGATTTTCGTTAT 59.050 37.500 0.00 0.00 0.00 1.89
1548 1552 5.418840 ACTGGGCAATCTGATTTTCGTTATT 59.581 36.000 0.00 0.00 0.00 1.40
1549 1553 6.071391 ACTGGGCAATCTGATTTTCGTTATTT 60.071 34.615 0.00 0.00 0.00 1.40
1550 1554 6.696411 TGGGCAATCTGATTTTCGTTATTTT 58.304 32.000 0.00 0.00 0.00 1.82
1551 1555 7.158021 TGGGCAATCTGATTTTCGTTATTTTT 58.842 30.769 0.00 0.00 0.00 1.94
1552 1556 8.307483 TGGGCAATCTGATTTTCGTTATTTTTA 58.693 29.630 0.00 0.00 0.00 1.52
1553 1557 8.807581 GGGCAATCTGATTTTCGTTATTTTTAG 58.192 33.333 0.00 0.00 0.00 1.85
1554 1558 9.353999 GGCAATCTGATTTTCGTTATTTTTAGT 57.646 29.630 0.00 0.00 0.00 2.24
1596 1600 3.057969 TGCAGAAAAGATCGTGTCCAT 57.942 42.857 0.00 0.00 0.00 3.41
1618 1622 9.407380 TCCATAGCTATGTCAAACATAACATTT 57.593 29.630 27.75 0.00 40.23 2.32
1665 1669 0.447801 CCGAAATGCCCAGAAGTTCG 59.552 55.000 0.00 0.00 40.47 3.95
1674 1678 2.807108 GCCCAGAAGTTCGTTCAAGTCT 60.807 50.000 0.00 0.00 37.67 3.24
1698 1702 4.915667 TGACAGAAACTAGTCAAATCGTCG 59.084 41.667 0.00 0.00 41.42 5.12
1701 1705 5.981315 ACAGAAACTAGTCAAATCGTCGAAA 59.019 36.000 0.00 0.00 0.00 3.46
1702 1706 6.645415 ACAGAAACTAGTCAAATCGTCGAAAT 59.355 34.615 0.00 0.00 0.00 2.17
1703 1707 6.950428 CAGAAACTAGTCAAATCGTCGAAATG 59.050 38.462 0.00 1.41 0.00 2.32
1705 1709 7.384115 AGAAACTAGTCAAATCGTCGAAATGAA 59.616 33.333 13.05 1.46 0.00 2.57
1706 1710 7.416154 AACTAGTCAAATCGTCGAAATGAAA 57.584 32.000 13.05 6.06 0.00 2.69
1709 1713 5.147162 AGTCAAATCGTCGAAATGAAAAGC 58.853 37.500 13.05 3.87 0.00 3.51
1712 1716 2.961522 TCGTCGAAATGAAAAGCCAC 57.038 45.000 0.00 0.00 0.00 5.01
1713 1717 1.193650 TCGTCGAAATGAAAAGCCACG 59.806 47.619 0.00 0.00 0.00 4.94
1714 1718 1.327507 GTCGAAATGAAAAGCCACGC 58.672 50.000 0.00 0.00 0.00 5.34
1715 1719 0.947960 TCGAAATGAAAAGCCACGCA 59.052 45.000 0.00 0.00 0.00 5.24
1716 1720 1.052287 CGAAATGAAAAGCCACGCAC 58.948 50.000 0.00 0.00 0.00 5.34
1717 1721 1.418373 GAAATGAAAAGCCACGCACC 58.582 50.000 0.00 0.00 0.00 5.01
1718 1722 0.749649 AAATGAAAAGCCACGCACCA 59.250 45.000 0.00 0.00 0.00 4.17
1719 1723 0.749649 AATGAAAAGCCACGCACCAA 59.250 45.000 0.00 0.00 0.00 3.67
1720 1724 0.031994 ATGAAAAGCCACGCACCAAC 59.968 50.000 0.00 0.00 0.00 3.77
1721 1725 1.657181 GAAAAGCCACGCACCAACG 60.657 57.895 0.00 0.00 39.50 4.10
1722 1726 2.999363 GAAAAGCCACGCACCAACGG 62.999 60.000 0.00 0.00 37.37 4.44
1723 1727 4.555709 AAGCCACGCACCAACGGA 62.556 61.111 0.00 0.00 37.37 4.69
1726 1730 3.345808 CCACGCACCAACGGACTG 61.346 66.667 0.00 0.00 37.37 3.51
1727 1731 3.345808 CACGCACCAACGGACTGG 61.346 66.667 0.00 0.00 42.68 4.00
1737 1741 3.677527 CGGACTGGTGTACGGACT 58.322 61.111 0.00 0.00 46.11 3.85
1738 1742 2.858622 CGGACTGGTGTACGGACTA 58.141 57.895 0.00 0.00 46.11 2.59
1739 1743 1.386533 CGGACTGGTGTACGGACTAT 58.613 55.000 0.00 0.00 46.11 2.12
1751 1755 7.093640 TGGTGTACGGACTATTAAGTTTCAGAT 60.094 37.037 0.00 0.00 35.56 2.90
1759 1763 9.235537 GGACTATTAAGTTTCAGATACGTCTTC 57.764 37.037 0.00 0.00 35.56 2.87
1785 1789 3.751175 TCAAGTTTAGCCGAATGACAAGG 59.249 43.478 0.00 0.00 0.00 3.61
1800 1804 3.164610 AAGGCAGCCCACCAATGGT 62.165 57.895 8.22 0.00 45.66 3.55
1827 1832 0.741326 TGAGTAGCAGGCTTAGAGCG 59.259 55.000 0.00 0.00 43.62 5.03
1838 1843 4.035558 CAGGCTTAGAGCGCATCAAATTTA 59.964 41.667 11.47 0.00 43.62 1.40
1840 1845 5.300286 AGGCTTAGAGCGCATCAAATTTAAT 59.700 36.000 11.47 0.00 43.62 1.40
1842 1847 6.201517 GCTTAGAGCGCATCAAATTTAATGA 58.798 36.000 11.47 0.00 0.00 2.57
1846 1851 5.357878 AGAGCGCATCAAATTTAATGAGGAA 59.642 36.000 11.47 0.00 30.48 3.36
1848 1853 6.038356 AGCGCATCAAATTTAATGAGGAAAG 58.962 36.000 11.47 0.00 30.48 2.62
1857 1862 8.462016 CAAATTTAATGAGGAAAGTCTTCGGAT 58.538 33.333 0.00 0.00 31.77 4.18
1917 1922 1.943340 GCACTTCCTTCATCCGGATTC 59.057 52.381 16.19 0.00 0.00 2.52
1920 1925 3.562973 CACTTCCTTCATCCGGATTCATG 59.437 47.826 16.19 5.12 0.00 3.07
1923 1928 3.041211 TCCTTCATCCGGATTCATGAGT 58.959 45.455 16.19 0.00 30.68 3.41
1941 1946 4.526970 TGAGTCCCCTTCATATTTTCTGC 58.473 43.478 0.00 0.00 0.00 4.26
1943 1948 5.428457 TGAGTCCCCTTCATATTTTCTGCTA 59.572 40.000 0.00 0.00 0.00 3.49
2013 2029 7.687941 TGAAAGAACCTTCCAATGATACTTC 57.312 36.000 0.00 0.00 0.00 3.01
2073 2089 8.918202 AATCTATGGTACTTTGACTCAAAACA 57.082 30.769 5.72 3.75 32.75 2.83
2080 2096 2.012937 TTGACTCAAAACACGACGGT 57.987 45.000 0.00 0.00 0.00 4.83
2124 2140 4.347000 GGGAGTATGTCATTAACCTGGCTA 59.653 45.833 0.00 0.00 0.00 3.93
2146 2162 2.095059 GTGCCATTCTTGCAAGTGTAGG 60.095 50.000 25.19 21.38 41.06 3.18
2153 2169 4.893424 TCTTGCAAGTGTAGGTTGAAAC 57.107 40.909 25.19 0.00 0.00 2.78
2155 2171 4.095782 TCTTGCAAGTGTAGGTTGAAACAC 59.904 41.667 25.19 0.00 45.06 3.32
2157 2173 3.759086 TGCAAGTGTAGGTTGAAACACAA 59.241 39.130 8.18 0.00 46.71 3.33
2160 2176 5.458779 GCAAGTGTAGGTTGAAACACAAATC 59.541 40.000 8.18 0.00 46.71 2.17
2164 2180 6.321181 AGTGTAGGTTGAAACACAAATCATGT 59.679 34.615 8.18 0.00 46.71 3.21
2200 2217 8.477419 TCATGGGATCCTAAATCATTTTTACC 57.523 34.615 12.58 0.00 0.00 2.85
2201 2218 8.288812 TCATGGGATCCTAAATCATTTTTACCT 58.711 33.333 12.58 0.00 0.00 3.08
2215 2232 5.917541 TTTTTACCTGACTTCATCACGAC 57.082 39.130 0.00 0.00 32.37 4.34
2216 2233 3.587797 TTACCTGACTTCATCACGACC 57.412 47.619 0.00 0.00 32.37 4.79
2217 2234 1.338107 ACCTGACTTCATCACGACCA 58.662 50.000 0.00 0.00 32.37 4.02
2234 2251 4.603985 CGACCATCGTGCTAGTAACAATA 58.396 43.478 0.00 0.00 34.72 1.90
2235 2252 5.038683 CGACCATCGTGCTAGTAACAATAA 58.961 41.667 0.00 0.00 34.72 1.40
2257 2274 4.946784 AAAAACGTCAGCATACCATCTC 57.053 40.909 0.00 0.00 0.00 2.75
2263 2280 4.943705 ACGTCAGCATACCATCTCAAAAAT 59.056 37.500 0.00 0.00 0.00 1.82
2264 2281 5.163723 ACGTCAGCATACCATCTCAAAAATG 60.164 40.000 0.00 0.00 0.00 2.32
2265 2282 5.163723 CGTCAGCATACCATCTCAAAAATGT 60.164 40.000 0.00 0.00 0.00 2.71
2266 2283 6.261118 GTCAGCATACCATCTCAAAAATGTC 58.739 40.000 0.00 0.00 0.00 3.06
2267 2284 5.945191 TCAGCATACCATCTCAAAAATGTCA 59.055 36.000 0.00 0.00 0.00 3.58
2268 2285 6.604396 TCAGCATACCATCTCAAAAATGTCAT 59.396 34.615 0.00 0.00 0.00 3.06
2269 2286 6.916387 CAGCATACCATCTCAAAAATGTCATC 59.084 38.462 0.00 0.00 0.00 2.92
2270 2287 6.604396 AGCATACCATCTCAAAAATGTCATCA 59.396 34.615 0.00 0.00 0.00 3.07
2271 2288 7.287005 AGCATACCATCTCAAAAATGTCATCAT 59.713 33.333 0.00 0.00 35.59 2.45
2272 2289 7.924412 GCATACCATCTCAAAAATGTCATCATT 59.076 33.333 0.00 0.00 44.94 2.57
2275 2292 8.812513 ACCATCTCAAAAATGTCATCATTAGA 57.187 30.769 0.00 0.00 42.60 2.10
2276 2293 9.246670 ACCATCTCAAAAATGTCATCATTAGAA 57.753 29.630 0.00 0.00 42.60 2.10
2291 2308 9.558648 TCATCATTAGAATGTGAAAAACATTCG 57.441 29.630 19.87 10.03 44.51 3.34
2292 2309 9.345517 CATCATTAGAATGTGAAAAACATTCGT 57.654 29.630 19.87 13.32 44.51 3.85
2298 2315 8.045750 AGAATGTGAAAAACATTCGTAAAACG 57.954 30.769 19.87 0.00 44.51 3.60
2299 2316 7.911205 AGAATGTGAAAAACATTCGTAAAACGA 59.089 29.630 19.87 0.00 45.63 3.85
2314 2331 6.936374 CGTAAAACGAACAGAAAACTTAGGA 58.064 36.000 0.00 0.00 46.05 2.94
2315 2332 7.401080 CGTAAAACGAACAGAAAACTTAGGAA 58.599 34.615 0.00 0.00 46.05 3.36
2316 2333 7.904461 CGTAAAACGAACAGAAAACTTAGGAAA 59.096 33.333 0.00 0.00 46.05 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.348666 CGAAACCCTATTGAAGCGACAG 59.651 50.000 0.00 0.00 0.00 3.51
33 34 1.551430 TCCGAAACCCTATTGAAGCGA 59.449 47.619 0.00 0.00 0.00 4.93
96 97 4.263905 ACATCCATAGGCCAGAAAAACTCA 60.264 41.667 5.01 0.00 0.00 3.41
128 129 3.003482 AGGCGATGTACGTATCTTCAGTC 59.997 47.826 0.00 0.63 44.60 3.51
205 206 3.244353 GCCAGTATGTATGCACTCCTCAT 60.244 47.826 0.00 0.00 0.00 2.90
210 211 2.213499 GTGGCCAGTATGTATGCACTC 58.787 52.381 5.11 0.00 0.00 3.51
221 222 2.183300 GATCGTGCGTGGCCAGTA 59.817 61.111 5.11 0.00 0.00 2.74
333 334 4.406648 TCTCCATGCGTGTATCTTCATT 57.593 40.909 4.96 0.00 0.00 2.57
426 429 0.838122 CCTCCTCAACCCCACAGAGT 60.838 60.000 0.00 0.00 0.00 3.24
533 536 7.703058 TCCTTCCCATCAAATAAAAGAAGAC 57.297 36.000 0.00 0.00 32.83 3.01
690 693 6.607600 ACTTGTAGTAGCTGTCCAGATATTCA 59.392 38.462 0.00 0.00 31.46 2.57
781 784 1.394618 CTCCGACAGGGACTAGGAAG 58.605 60.000 0.00 0.00 40.94 3.46
936 939 0.753867 TGAAACGATAGGCCGCCATA 59.246 50.000 13.15 1.52 43.77 2.74
1012 1015 2.494870 GAGAATGCTGAATTGCAAGGGT 59.505 45.455 4.94 0.00 46.61 4.34
1065 1068 2.677836 GGTCAAACATGATAGCGCTTCA 59.322 45.455 18.68 19.31 0.00 3.02
1091 1094 2.430921 CCGAGCGAAGAAGTGCGT 60.431 61.111 0.00 0.00 35.87 5.24
1241 1245 0.036294 GAACCGAGCCTAGCCAAACT 60.036 55.000 0.00 0.00 0.00 2.66
1341 1345 2.310779 AGGTGCTCAGGTGTCTCTTA 57.689 50.000 0.00 0.00 0.00 2.10
1344 1348 0.174617 GCTAGGTGCTCAGGTGTCTC 59.825 60.000 0.00 0.00 38.95 3.36
1345 1349 2.281830 GCTAGGTGCTCAGGTGTCT 58.718 57.895 0.00 0.00 38.95 3.41
1346 1350 4.921834 GCTAGGTGCTCAGGTGTC 57.078 61.111 0.00 0.00 38.95 3.67
1355 1359 0.036010 ACATGTGTGGAGCTAGGTGC 60.036 55.000 6.48 6.48 43.29 5.01
1356 1360 2.289631 TGAACATGTGTGGAGCTAGGTG 60.290 50.000 0.00 0.00 0.00 4.00
1357 1361 1.977854 TGAACATGTGTGGAGCTAGGT 59.022 47.619 0.00 0.00 0.00 3.08
1358 1362 2.027745 ACTGAACATGTGTGGAGCTAGG 60.028 50.000 0.00 0.00 0.00 3.02
1359 1363 3.325293 ACTGAACATGTGTGGAGCTAG 57.675 47.619 0.00 0.00 0.00 3.42
1360 1364 3.324846 AGAACTGAACATGTGTGGAGCTA 59.675 43.478 0.00 0.00 0.00 3.32
1361 1365 2.105477 AGAACTGAACATGTGTGGAGCT 59.895 45.455 0.00 0.00 0.00 4.09
1362 1366 2.481952 GAGAACTGAACATGTGTGGAGC 59.518 50.000 0.00 0.00 0.00 4.70
1363 1367 3.732212 TGAGAACTGAACATGTGTGGAG 58.268 45.455 0.00 0.00 0.00 3.86
1364 1368 3.836365 TGAGAACTGAACATGTGTGGA 57.164 42.857 0.00 0.00 0.00 4.02
1365 1369 3.879295 AGTTGAGAACTGAACATGTGTGG 59.121 43.478 0.00 0.00 41.01 4.17
1366 1370 5.295292 AGAAGTTGAGAACTGAACATGTGTG 59.705 40.000 0.00 0.00 41.91 3.82
1367 1371 5.431765 AGAAGTTGAGAACTGAACATGTGT 58.568 37.500 0.00 0.00 41.91 3.72
1368 1372 5.332883 CGAGAAGTTGAGAACTGAACATGTG 60.333 44.000 0.00 0.00 41.91 3.21
1369 1373 4.747108 CGAGAAGTTGAGAACTGAACATGT 59.253 41.667 6.88 0.00 41.91 3.21
1370 1374 4.747108 ACGAGAAGTTGAGAACTGAACATG 59.253 41.667 6.88 0.00 41.91 3.21
1371 1375 4.950050 ACGAGAAGTTGAGAACTGAACAT 58.050 39.130 6.88 0.00 41.91 2.71
1372 1376 4.386867 ACGAGAAGTTGAGAACTGAACA 57.613 40.909 6.88 0.00 41.91 3.18
1373 1377 4.209495 GGAACGAGAAGTTGAGAACTGAAC 59.791 45.833 0.00 0.00 44.35 3.18
1374 1378 4.142026 TGGAACGAGAAGTTGAGAACTGAA 60.142 41.667 0.00 0.00 44.35 3.02
1375 1379 3.383505 TGGAACGAGAAGTTGAGAACTGA 59.616 43.478 0.00 0.00 44.35 3.41
1376 1380 3.717707 TGGAACGAGAAGTTGAGAACTG 58.282 45.455 0.00 0.00 44.35 3.16
1377 1381 4.402056 TTGGAACGAGAAGTTGAGAACT 57.598 40.909 0.00 0.00 44.35 3.01
1378 1382 5.479716 TTTTGGAACGAGAAGTTGAGAAC 57.520 39.130 0.00 0.00 44.35 3.01
1379 1383 5.505654 GCATTTTGGAACGAGAAGTTGAGAA 60.506 40.000 0.00 0.00 44.35 2.87
1380 1384 4.024048 GCATTTTGGAACGAGAAGTTGAGA 60.024 41.667 0.00 0.00 44.35 3.27
1381 1385 4.222114 GCATTTTGGAACGAGAAGTTGAG 58.778 43.478 0.00 0.00 44.35 3.02
1382 1386 3.629855 TGCATTTTGGAACGAGAAGTTGA 59.370 39.130 0.00 0.00 44.35 3.18
1383 1387 3.963665 TGCATTTTGGAACGAGAAGTTG 58.036 40.909 0.00 0.00 44.35 3.16
1385 1389 4.647424 TTTGCATTTTGGAACGAGAAGT 57.353 36.364 0.00 0.00 0.00 3.01
1386 1390 4.209080 GGTTTTGCATTTTGGAACGAGAAG 59.791 41.667 0.00 0.00 0.00 2.85
1387 1391 4.116238 GGTTTTGCATTTTGGAACGAGAA 58.884 39.130 0.00 0.00 0.00 2.87
1388 1392 3.712187 GGTTTTGCATTTTGGAACGAGA 58.288 40.909 0.00 0.00 0.00 4.04
1389 1393 2.470999 CGGTTTTGCATTTTGGAACGAG 59.529 45.455 0.00 0.00 0.00 4.18
1390 1394 2.099263 TCGGTTTTGCATTTTGGAACGA 59.901 40.909 0.00 0.00 0.00 3.85
1391 1395 2.464865 TCGGTTTTGCATTTTGGAACG 58.535 42.857 0.00 0.00 0.00 3.95
1392 1396 2.799978 CCTCGGTTTTGCATTTTGGAAC 59.200 45.455 0.00 0.00 0.00 3.62
1393 1397 2.224161 CCCTCGGTTTTGCATTTTGGAA 60.224 45.455 0.00 0.00 0.00 3.53
1394 1398 1.342819 CCCTCGGTTTTGCATTTTGGA 59.657 47.619 0.00 0.00 0.00 3.53
1395 1399 1.607767 CCCCTCGGTTTTGCATTTTGG 60.608 52.381 0.00 0.00 0.00 3.28
1396 1400 1.607767 CCCCCTCGGTTTTGCATTTTG 60.608 52.381 0.00 0.00 0.00 2.44
1397 1401 0.684535 CCCCCTCGGTTTTGCATTTT 59.315 50.000 0.00 0.00 0.00 1.82
1398 1402 1.826340 GCCCCCTCGGTTTTGCATTT 61.826 55.000 0.00 0.00 0.00 2.32
1399 1403 2.282783 GCCCCCTCGGTTTTGCATT 61.283 57.895 0.00 0.00 0.00 3.56
1400 1404 2.679996 GCCCCCTCGGTTTTGCAT 60.680 61.111 0.00 0.00 0.00 3.96
1401 1405 4.986708 GGCCCCCTCGGTTTTGCA 62.987 66.667 0.00 0.00 0.00 4.08
1436 1440 1.153628 GTCTTGTGATCCGGGACCG 60.154 63.158 0.00 3.25 39.44 4.79
1437 1441 0.391263 GTGTCTTGTGATCCGGGACC 60.391 60.000 0.00 0.00 0.00 4.46
1438 1442 0.391263 GGTGTCTTGTGATCCGGGAC 60.391 60.000 0.00 0.00 0.00 4.46
1439 1443 0.544357 AGGTGTCTTGTGATCCGGGA 60.544 55.000 0.00 0.00 0.00 5.14
1440 1444 0.391661 CAGGTGTCTTGTGATCCGGG 60.392 60.000 0.00 0.00 0.00 5.73
1441 1445 0.321671 ACAGGTGTCTTGTGATCCGG 59.678 55.000 0.00 0.00 0.00 5.14
1442 1446 2.029380 TGTACAGGTGTCTTGTGATCCG 60.029 50.000 0.00 0.00 0.00 4.18
1443 1447 3.678056 TGTACAGGTGTCTTGTGATCC 57.322 47.619 0.00 0.00 0.00 3.36
1444 1448 4.213482 GGTTTGTACAGGTGTCTTGTGATC 59.787 45.833 0.00 0.00 0.00 2.92
1445 1449 4.134563 GGTTTGTACAGGTGTCTTGTGAT 58.865 43.478 0.00 0.00 0.00 3.06
1446 1450 3.537580 GGTTTGTACAGGTGTCTTGTGA 58.462 45.455 0.00 0.00 0.00 3.58
1447 1451 2.286833 CGGTTTGTACAGGTGTCTTGTG 59.713 50.000 0.00 0.00 0.00 3.33
1448 1452 2.093341 ACGGTTTGTACAGGTGTCTTGT 60.093 45.455 0.00 0.00 0.00 3.16
1449 1453 2.557317 ACGGTTTGTACAGGTGTCTTG 58.443 47.619 0.00 0.00 0.00 3.02
1450 1454 2.940410 CAACGGTTTGTACAGGTGTCTT 59.060 45.455 0.00 0.00 33.20 3.01
1451 1455 2.093341 ACAACGGTTTGTACAGGTGTCT 60.093 45.455 0.00 0.00 45.43 3.41
1452 1456 2.282407 ACAACGGTTTGTACAGGTGTC 58.718 47.619 0.00 0.00 45.43 3.67
1453 1457 2.406596 ACAACGGTTTGTACAGGTGT 57.593 45.000 0.00 0.00 44.53 4.16
1454 1458 3.002553 GGTTACAACGGTTTGTACAGGTG 59.997 47.826 0.00 0.00 45.90 4.00
1455 1459 3.205338 GGTTACAACGGTTTGTACAGGT 58.795 45.455 0.00 0.00 45.90 4.00
1456 1460 3.002553 GTGGTTACAACGGTTTGTACAGG 59.997 47.826 0.00 0.00 45.90 4.00
1457 1461 3.002553 GGTGGTTACAACGGTTTGTACAG 59.997 47.826 0.00 0.00 45.90 2.74
1458 1462 2.941720 GGTGGTTACAACGGTTTGTACA 59.058 45.455 0.00 0.00 45.90 2.90
1459 1463 2.941720 TGGTGGTTACAACGGTTTGTAC 59.058 45.455 0.00 0.00 45.90 2.90
1460 1464 3.204526 CTGGTGGTTACAACGGTTTGTA 58.795 45.455 0.00 0.00 44.53 2.41
1462 1466 1.268845 GCTGGTGGTTACAACGGTTTG 60.269 52.381 0.00 0.00 42.86 2.93
1463 1467 1.026584 GCTGGTGGTTACAACGGTTT 58.973 50.000 0.00 0.00 42.86 3.27
1464 1468 0.181824 AGCTGGTGGTTACAACGGTT 59.818 50.000 0.00 0.00 42.86 4.44
1465 1469 1.050204 TAGCTGGTGGTTACAACGGT 58.950 50.000 0.00 0.00 42.86 4.83
1466 1470 1.435577 GTAGCTGGTGGTTACAACGG 58.564 55.000 0.00 0.00 43.79 4.44
1467 1471 1.270412 TGGTAGCTGGTGGTTACAACG 60.270 52.381 0.00 0.00 37.00 4.10
1468 1472 2.148768 GTGGTAGCTGGTGGTTACAAC 58.851 52.381 0.00 0.00 34.02 3.32
1469 1473 1.769465 TGTGGTAGCTGGTGGTTACAA 59.231 47.619 0.00 0.00 34.02 2.41
1470 1474 1.425694 TGTGGTAGCTGGTGGTTACA 58.574 50.000 0.00 0.00 34.02 2.41
1471 1475 2.554370 TTGTGGTAGCTGGTGGTTAC 57.446 50.000 0.00 0.00 0.00 2.50
1472 1476 3.579534 TTTTGTGGTAGCTGGTGGTTA 57.420 42.857 0.00 0.00 0.00 2.85
1473 1477 2.429250 GTTTTTGTGGTAGCTGGTGGTT 59.571 45.455 0.00 0.00 0.00 3.67
1474 1478 2.028876 GTTTTTGTGGTAGCTGGTGGT 58.971 47.619 0.00 0.00 0.00 4.16
1475 1479 1.001815 CGTTTTTGTGGTAGCTGGTGG 60.002 52.381 0.00 0.00 0.00 4.61
1476 1480 1.673920 ACGTTTTTGTGGTAGCTGGTG 59.326 47.619 0.00 0.00 0.00 4.17
1477 1481 2.047002 ACGTTTTTGTGGTAGCTGGT 57.953 45.000 0.00 0.00 0.00 4.00
1478 1482 2.356382 TCAACGTTTTTGTGGTAGCTGG 59.644 45.455 0.00 0.00 0.00 4.85
1479 1483 3.181505 TGTCAACGTTTTTGTGGTAGCTG 60.182 43.478 0.00 0.00 0.00 4.24
1480 1484 3.011119 TGTCAACGTTTTTGTGGTAGCT 58.989 40.909 0.00 0.00 0.00 3.32
1481 1485 3.408288 TGTCAACGTTTTTGTGGTAGC 57.592 42.857 0.00 0.00 0.00 3.58
1482 1486 7.972623 TTAATTGTCAACGTTTTTGTGGTAG 57.027 32.000 0.00 0.00 0.00 3.18
1483 1487 7.376336 CGATTAATTGTCAACGTTTTTGTGGTA 59.624 33.333 0.00 0.00 0.00 3.25
1484 1488 6.197468 CGATTAATTGTCAACGTTTTTGTGGT 59.803 34.615 0.00 0.00 0.00 4.16
1485 1489 6.197468 ACGATTAATTGTCAACGTTTTTGTGG 59.803 34.615 0.00 0.00 0.00 4.17
1486 1490 7.048432 CACGATTAATTGTCAACGTTTTTGTG 58.952 34.615 5.29 0.00 31.82 3.33
1487 1491 6.748198 ACACGATTAATTGTCAACGTTTTTGT 59.252 30.769 5.29 0.00 31.82 2.83
1488 1492 7.144007 ACACGATTAATTGTCAACGTTTTTG 57.856 32.000 5.29 0.00 31.82 2.44
1489 1493 7.743520 AACACGATTAATTGTCAACGTTTTT 57.256 28.000 5.29 0.00 31.82 1.94
1490 1494 7.273815 ACAAACACGATTAATTGTCAACGTTTT 59.726 29.630 14.74 5.45 30.58 2.43
1491 1495 6.748198 ACAAACACGATTAATTGTCAACGTTT 59.252 30.769 5.29 9.96 30.58 3.60
1492 1496 6.259638 ACAAACACGATTAATTGTCAACGTT 58.740 32.000 5.29 0.00 30.58 3.99
1493 1497 5.812652 ACAAACACGATTAATTGTCAACGT 58.187 33.333 5.29 0.00 30.58 3.99
1494 1498 6.412362 TGAACAAACACGATTAATTGTCAACG 59.588 34.615 5.29 0.00 35.09 4.10
1495 1499 7.672351 TGAACAAACACGATTAATTGTCAAC 57.328 32.000 5.29 0.00 35.09 3.18
1496 1500 8.864069 ATTGAACAAACACGATTAATTGTCAA 57.136 26.923 5.29 5.97 35.09 3.18
1497 1501 8.131731 TGATTGAACAAACACGATTAATTGTCA 58.868 29.630 5.29 0.00 35.09 3.58
1498 1502 8.500837 TGATTGAACAAACACGATTAATTGTC 57.499 30.769 5.29 0.00 35.09 3.18
1499 1503 8.751335 GTTGATTGAACAAACACGATTAATTGT 58.249 29.630 2.21 2.21 37.59 2.71
1500 1504 8.967218 AGTTGATTGAACAAACACGATTAATTG 58.033 29.630 0.78 0.78 36.98 2.32
1501 1505 8.967218 CAGTTGATTGAACAAACACGATTAATT 58.033 29.630 0.00 0.00 36.98 1.40
1502 1506 7.594758 CCAGTTGATTGAACAAACACGATTAAT 59.405 33.333 0.00 0.00 36.98 1.40
1503 1507 6.915300 CCAGTTGATTGAACAAACACGATTAA 59.085 34.615 0.00 0.00 36.98 1.40
1504 1508 6.434596 CCAGTTGATTGAACAAACACGATTA 58.565 36.000 0.00 0.00 36.98 1.75
1505 1509 5.280945 CCAGTTGATTGAACAAACACGATT 58.719 37.500 0.00 0.00 36.98 3.34
1506 1510 4.261572 CCCAGTTGATTGAACAAACACGAT 60.262 41.667 0.00 0.00 36.98 3.73
1507 1511 3.066064 CCCAGTTGATTGAACAAACACGA 59.934 43.478 0.00 0.00 36.98 4.35
1508 1512 3.371168 CCCAGTTGATTGAACAAACACG 58.629 45.455 0.00 0.00 36.98 4.49
1509 1513 3.123050 GCCCAGTTGATTGAACAAACAC 58.877 45.455 0.00 0.00 36.98 3.32
1510 1514 2.762887 TGCCCAGTTGATTGAACAAACA 59.237 40.909 0.00 0.00 36.98 2.83
1511 1515 3.451141 TGCCCAGTTGATTGAACAAAC 57.549 42.857 0.00 0.00 36.98 2.93
1512 1516 4.344679 AGATTGCCCAGTTGATTGAACAAA 59.655 37.500 0.00 0.00 36.98 2.83
1513 1517 3.896888 AGATTGCCCAGTTGATTGAACAA 59.103 39.130 0.00 0.00 36.98 2.83
1514 1518 3.256383 CAGATTGCCCAGTTGATTGAACA 59.744 43.478 0.00 0.00 36.98 3.18
1515 1519 3.507233 TCAGATTGCCCAGTTGATTGAAC 59.493 43.478 0.00 0.00 34.40 3.18
1516 1520 3.765381 TCAGATTGCCCAGTTGATTGAA 58.235 40.909 0.00 0.00 0.00 2.69
1517 1521 3.438216 TCAGATTGCCCAGTTGATTGA 57.562 42.857 0.00 0.00 0.00 2.57
1518 1522 4.730949 AATCAGATTGCCCAGTTGATTG 57.269 40.909 0.00 0.00 37.17 2.67
1519 1523 5.622914 CGAAAATCAGATTGCCCAGTTGATT 60.623 40.000 0.00 0.00 39.45 2.57
1520 1524 4.142315 CGAAAATCAGATTGCCCAGTTGAT 60.142 41.667 0.00 0.00 0.00 2.57
1521 1525 3.191162 CGAAAATCAGATTGCCCAGTTGA 59.809 43.478 0.00 0.00 0.00 3.18
1522 1526 3.057315 ACGAAAATCAGATTGCCCAGTTG 60.057 43.478 0.00 0.00 0.00 3.16
1523 1527 3.157087 ACGAAAATCAGATTGCCCAGTT 58.843 40.909 0.00 0.00 0.00 3.16
1524 1528 2.795329 ACGAAAATCAGATTGCCCAGT 58.205 42.857 0.00 0.00 0.00 4.00
1525 1529 3.855689 AACGAAAATCAGATTGCCCAG 57.144 42.857 0.00 0.00 0.00 4.45
1526 1530 5.913137 AATAACGAAAATCAGATTGCCCA 57.087 34.783 0.00 0.00 0.00 5.36
1527 1531 7.595311 AAAAATAACGAAAATCAGATTGCCC 57.405 32.000 0.00 0.00 0.00 5.36
1528 1532 9.353999 ACTAAAAATAACGAAAATCAGATTGCC 57.646 29.630 0.00 0.00 0.00 4.52
1562 1566 9.630098 GATCTTTTCTGCATTCATTAACAAGAA 57.370 29.630 0.00 0.00 0.00 2.52
1563 1567 7.964559 CGATCTTTTCTGCATTCATTAACAAGA 59.035 33.333 0.00 0.00 0.00 3.02
1564 1568 7.752239 ACGATCTTTTCTGCATTCATTAACAAG 59.248 33.333 0.00 0.00 0.00 3.16
1565 1569 7.538334 CACGATCTTTTCTGCATTCATTAACAA 59.462 33.333 0.00 0.00 0.00 2.83
1566 1570 7.022979 CACGATCTTTTCTGCATTCATTAACA 58.977 34.615 0.00 0.00 0.00 2.41
1567 1571 7.023575 ACACGATCTTTTCTGCATTCATTAAC 58.976 34.615 0.00 0.00 0.00 2.01
1568 1572 7.144722 ACACGATCTTTTCTGCATTCATTAA 57.855 32.000 0.00 0.00 0.00 1.40
1569 1573 6.183360 GGACACGATCTTTTCTGCATTCATTA 60.183 38.462 0.00 0.00 0.00 1.90
1570 1574 5.392380 GGACACGATCTTTTCTGCATTCATT 60.392 40.000 0.00 0.00 0.00 2.57
1571 1575 4.095483 GGACACGATCTTTTCTGCATTCAT 59.905 41.667 0.00 0.00 0.00 2.57
1572 1576 3.436704 GGACACGATCTTTTCTGCATTCA 59.563 43.478 0.00 0.00 0.00 2.57
1573 1577 3.436704 TGGACACGATCTTTTCTGCATTC 59.563 43.478 0.00 0.00 0.00 2.67
1574 1578 3.411446 TGGACACGATCTTTTCTGCATT 58.589 40.909 0.00 0.00 0.00 3.56
1575 1579 3.057969 TGGACACGATCTTTTCTGCAT 57.942 42.857 0.00 0.00 0.00 3.96
1576 1580 2.542020 TGGACACGATCTTTTCTGCA 57.458 45.000 0.00 0.00 0.00 4.41
1577 1581 3.001736 GCTATGGACACGATCTTTTCTGC 59.998 47.826 0.00 0.00 0.00 4.26
1578 1582 4.437239 AGCTATGGACACGATCTTTTCTG 58.563 43.478 0.00 0.00 0.00 3.02
1579 1583 4.744795 AGCTATGGACACGATCTTTTCT 57.255 40.909 0.00 0.00 0.00 2.52
1580 1584 5.986135 ACATAGCTATGGACACGATCTTTTC 59.014 40.000 31.87 0.00 38.00 2.29
1586 1590 4.937201 TTGACATAGCTATGGACACGAT 57.063 40.909 31.87 13.52 38.00 3.73
1618 1622 6.993786 TTCGCATGAACTTGGATTACAATA 57.006 33.333 0.00 0.00 38.65 1.90
1620 1624 5.697473 TTTCGCATGAACTTGGATTACAA 57.303 34.783 0.00 0.00 37.55 2.41
1621 1625 5.392919 CCATTTCGCATGAACTTGGATTACA 60.393 40.000 0.00 0.00 38.82 2.41
1665 1669 6.757010 TGACTAGTTTCTGTCAAGACTTGAAC 59.243 38.462 19.32 13.17 42.15 3.18
1694 1698 1.591248 CGTGGCTTTTCATTTCGACG 58.409 50.000 0.00 0.00 0.00 5.12
1698 1702 1.269517 TGGTGCGTGGCTTTTCATTTC 60.270 47.619 0.00 0.00 0.00 2.17
1701 1705 0.031994 GTTGGTGCGTGGCTTTTCAT 59.968 50.000 0.00 0.00 0.00 2.57
1702 1706 1.435515 GTTGGTGCGTGGCTTTTCA 59.564 52.632 0.00 0.00 0.00 2.69
1703 1707 1.657181 CGTTGGTGCGTGGCTTTTC 60.657 57.895 0.00 0.00 0.00 2.29
1705 1709 3.591835 CCGTTGGTGCGTGGCTTT 61.592 61.111 0.00 0.00 0.00 3.51
1706 1710 4.555709 TCCGTTGGTGCGTGGCTT 62.556 61.111 0.00 0.00 0.00 4.35
1709 1713 3.345808 CAGTCCGTTGGTGCGTGG 61.346 66.667 0.00 0.00 0.00 4.94
1716 1720 1.373748 CCGTACACCAGTCCGTTGG 60.374 63.158 0.00 0.00 44.09 3.77
1717 1721 0.665369 GTCCGTACACCAGTCCGTTG 60.665 60.000 0.00 0.00 0.00 4.10
1718 1722 0.825010 AGTCCGTACACCAGTCCGTT 60.825 55.000 0.00 0.00 0.00 4.44
1719 1723 0.036732 TAGTCCGTACACCAGTCCGT 59.963 55.000 0.00 0.00 0.00 4.69
1720 1724 1.386533 ATAGTCCGTACACCAGTCCG 58.613 55.000 0.00 0.00 0.00 4.79
1721 1725 4.400567 ACTTAATAGTCCGTACACCAGTCC 59.599 45.833 0.00 0.00 0.00 3.85
1722 1726 5.573337 ACTTAATAGTCCGTACACCAGTC 57.427 43.478 0.00 0.00 0.00 3.51
1723 1727 5.990120 AACTTAATAGTCCGTACACCAGT 57.010 39.130 0.00 0.00 31.99 4.00
1724 1728 6.392354 TGAAACTTAATAGTCCGTACACCAG 58.608 40.000 0.00 0.00 31.99 4.00
1725 1729 6.209192 TCTGAAACTTAATAGTCCGTACACCA 59.791 38.462 0.00 0.00 31.99 4.17
1726 1730 6.624423 TCTGAAACTTAATAGTCCGTACACC 58.376 40.000 0.00 0.00 31.99 4.16
1727 1731 9.230932 GTATCTGAAACTTAATAGTCCGTACAC 57.769 37.037 0.00 0.00 31.99 2.90
1728 1732 8.124823 CGTATCTGAAACTTAATAGTCCGTACA 58.875 37.037 0.00 0.00 31.99 2.90
1729 1733 8.125448 ACGTATCTGAAACTTAATAGTCCGTAC 58.875 37.037 0.00 0.00 31.99 3.67
1730 1734 8.213518 ACGTATCTGAAACTTAATAGTCCGTA 57.786 34.615 0.00 0.00 31.99 4.02
1731 1735 7.066766 AGACGTATCTGAAACTTAATAGTCCGT 59.933 37.037 0.00 0.00 32.29 4.69
1732 1736 7.416022 AGACGTATCTGAAACTTAATAGTCCG 58.584 38.462 0.00 0.00 32.29 4.79
1733 1737 9.235537 GAAGACGTATCTGAAACTTAATAGTCC 57.764 37.037 0.00 0.00 34.48 3.85
1734 1738 8.945930 CGAAGACGTATCTGAAACTTAATAGTC 58.054 37.037 0.00 0.00 34.48 2.59
1735 1739 7.914346 CCGAAGACGTATCTGAAACTTAATAGT 59.086 37.037 0.00 0.00 34.48 2.12
1736 1740 8.127327 TCCGAAGACGTATCTGAAACTTAATAG 58.873 37.037 0.00 0.00 34.48 1.73
1737 1741 7.988737 TCCGAAGACGTATCTGAAACTTAATA 58.011 34.615 0.00 0.00 34.48 0.98
1738 1742 6.860080 TCCGAAGACGTATCTGAAACTTAAT 58.140 36.000 0.00 0.00 34.48 1.40
1739 1743 6.258230 TCCGAAGACGTATCTGAAACTTAA 57.742 37.500 0.00 0.00 34.48 1.85
1751 1755 4.418392 GCTAAACTTGATCCGAAGACGTA 58.582 43.478 0.00 0.00 37.88 3.57
1759 1763 3.001330 GTCATTCGGCTAAACTTGATCCG 59.999 47.826 0.00 0.00 41.30 4.18
1767 1771 1.810151 TGCCTTGTCATTCGGCTAAAC 59.190 47.619 9.04 0.00 44.09 2.01
1800 1804 6.071320 TCTAAGCCTGCTACTCATCTGAATA 58.929 40.000 0.00 0.00 0.00 1.75
1827 1832 8.992835 AAGACTTTCCTCATTAAATTTGATGC 57.007 30.769 16.08 2.48 0.00 3.91
1838 1843 6.712276 ACTTAATCCGAAGACTTTCCTCATT 58.288 36.000 0.00 0.00 0.00 2.57
1840 1845 5.740290 ACTTAATCCGAAGACTTTCCTCA 57.260 39.130 0.00 0.00 0.00 3.86
1842 1847 6.531021 TGAAACTTAATCCGAAGACTTTCCT 58.469 36.000 0.00 0.00 0.00 3.36
1846 1851 9.503399 AGTATTTGAAACTTAATCCGAAGACTT 57.497 29.630 0.00 0.00 0.00 3.01
1897 1902 1.943340 GAATCCGGATGAAGGAAGTGC 59.057 52.381 19.95 0.00 41.69 4.40
1898 1903 3.266510 TGAATCCGGATGAAGGAAGTG 57.733 47.619 19.95 0.00 41.69 3.16
1903 1908 3.397482 GACTCATGAATCCGGATGAAGG 58.603 50.000 19.95 11.30 0.00 3.46
1908 1913 1.059913 GGGGACTCATGAATCCGGAT 58.940 55.000 16.62 12.38 35.67 4.18
1917 1922 5.009410 GCAGAAAATATGAAGGGGACTCATG 59.991 44.000 0.00 0.00 42.68 3.07
1920 1925 4.786425 AGCAGAAAATATGAAGGGGACTC 58.214 43.478 0.00 0.00 42.68 3.36
1923 1928 6.731467 AGTTTAGCAGAAAATATGAAGGGGA 58.269 36.000 0.00 0.00 0.00 4.81
1984 2000 9.358872 GTATCATTGGAAGGTTCTTTCAAATTC 57.641 33.333 5.59 0.00 30.11 2.17
1986 2002 8.655935 AGTATCATTGGAAGGTTCTTTCAAAT 57.344 30.769 5.59 0.00 32.21 2.32
1997 2013 9.613428 TGTAACAATAGAAGTATCATTGGAAGG 57.387 33.333 0.00 0.00 34.63 3.46
2072 2088 2.925563 GGGTTTATTAGTCACCGTCGTG 59.074 50.000 0.00 0.00 41.72 4.35
2073 2089 2.415893 CGGGTTTATTAGTCACCGTCGT 60.416 50.000 0.00 0.00 36.78 4.34
2080 2096 3.918294 CCCCTTCGGGTTTATTAGTCA 57.082 47.619 0.00 0.00 45.50 3.41
2100 2116 3.747708 GCCAGGTTAATGACATACTCCCC 60.748 52.174 0.00 0.00 0.00 4.81
2101 2117 3.136626 AGCCAGGTTAATGACATACTCCC 59.863 47.826 0.00 0.00 0.00 4.30
2135 2151 3.348119 TGTGTTTCAACCTACACTTGCA 58.652 40.909 0.00 0.00 43.82 4.08
2180 2197 8.753497 AGTCAGGTAAAAATGATTTAGGATCC 57.247 34.615 2.48 2.48 0.00 3.36
2198 2215 1.338107 TGGTCGTGATGAAGTCAGGT 58.662 50.000 0.00 0.00 42.07 4.00
2200 2217 2.188524 CGATGGTCGTGATGAAGTCAG 58.811 52.381 0.00 0.00 37.56 3.51
2201 2218 2.278026 CGATGGTCGTGATGAAGTCA 57.722 50.000 0.00 0.00 34.72 3.41
2212 2229 2.554806 TGTTACTAGCACGATGGTCG 57.445 50.000 0.00 0.00 46.93 4.79
2290 2307 6.936374 TCCTAAGTTTTCTGTTCGTTTTACG 58.064 36.000 0.00 0.00 44.19 3.18


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

AutoCloner maintained by Alex Coulton.