Multiple sequence alignment - TraesCS2D01G456600

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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 TraesCS2D01G456600 chr2D 100.000 4349 0 0 1 4349 564382868 564387216 0.000000e+00 8032.0
1 TraesCS2D01G456600 chr2D 93.860 114 7 0 1401 1514 326217471 326217584 5.780000e-39 172.0
2 TraesCS2D01G456600 chr2B 93.029 2539 116 30 1860 4349 675514964 675517490 0.000000e+00 3651.0
3 TraesCS2D01G456600 chr2B 95.195 1311 43 9 72 1368 675513471 675514775 0.000000e+00 2054.0
4 TraesCS2D01G456600 chr2B 93.966 116 7 0 1403 1518 672018321 672018436 4.470000e-40 176.0
5 TraesCS2D01G456600 chr2A 91.482 2442 162 26 1931 4349 705069159 705071577 0.000000e+00 3315.0
6 TraesCS2D01G456600 chr2A 95.394 1346 45 13 72 1408 705067412 705068749 0.000000e+00 2126.0
7 TraesCS2D01G456600 chr2A 91.200 125 8 3 1396 1517 646728388 646728264 2.690000e-37 167.0
8 TraesCS2D01G456600 chr2A 96.104 77 2 1 1609 1685 705068972 705069047 1.640000e-24 124.0
9 TraesCS2D01G456600 chr2A 96.552 58 2 0 1 58 705067313 705067370 3.580000e-16 97.1
10 TraesCS2D01G456600 chr7B 96.296 108 4 0 1407 1514 233285521 233285628 1.240000e-40 178.0
11 TraesCS2D01G456600 chr6A 95.495 111 5 0 1406 1516 579148320 579148210 1.240000e-40 178.0
12 TraesCS2D01G456600 chr3A 93.277 119 6 2 1406 1524 552620481 552620365 1.610000e-39 174.0
13 TraesCS2D01G456600 chr3A 94.643 112 6 0 1403 1514 697472452 697472341 1.610000e-39 174.0
14 TraesCS2D01G456600 chr3A 93.162 117 8 0 1407 1523 588942226 588942342 5.780000e-39 172.0
15 TraesCS2D01G456600 chr3A 85.542 83 10 2 1234 1315 749469853 749469934 7.750000e-13 86.1
16 TraesCS2D01G456600 chr4A 93.103 116 8 0 1406 1521 274959062 274958947 2.080000e-38 171.0
17 TraesCS2D01G456600 chr4A 83.607 122 16 4 1169 1288 40860275 40860394 1.280000e-20 111.0
18 TraesCS2D01G456600 chr4D 83.200 125 17 4 1169 1291 423429801 423429679 1.280000e-20 111.0
19 TraesCS2D01G456600 chr4B 83.200 125 17 4 1169 1291 519824565 519824443 1.280000e-20 111.0
20 TraesCS2D01G456600 chr5B 79.720 143 25 4 1151 1291 580366671 580366531 2.770000e-17 100.0
21 TraesCS2D01G456600 chr5A 79.720 143 25 4 1151 1291 592638835 592638695 2.770000e-17 100.0
22 TraesCS2D01G456600 chr3B 86.747 83 9 2 1234 1315 823029116 823029197 1.670000e-14 91.6


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 TraesCS2D01G456600 chr2D 564382868 564387216 4348 False 8032.000 8032 100.000 1 4349 1 chr2D.!!$F2 4348
1 TraesCS2D01G456600 chr2B 675513471 675517490 4019 False 2852.500 3651 94.112 72 4349 2 chr2B.!!$F2 4277
2 TraesCS2D01G456600 chr2A 705067313 705071577 4264 False 1415.525 3315 94.883 1 4349 4 chr2A.!!$F1 4348

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
58 59 0.106918 TCTCTCCTCTTCTCTCGGCC 60.107 60.0 0.0 0.0 0.00 6.13 F
1422 1502 0.113776 TGGTACTCCCTCCGTTCACT 59.886 55.0 0.0 0.0 0.00 3.41 F
1703 1914 0.033090 TCATAGGCATCTGCGAGCAG 59.967 55.0 18.2 18.2 44.86 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 1896 0.033090 TCTGCTCGCAGATGCCTATG 59.967 55.000 17.01 0.0 46.80 2.23 R
2823 3071 0.531200 AGGGCTCGGAAGTTAGAACG 59.469 55.000 0.00 0.0 0.00 3.95 R
3665 3922 1.618837 AGCCAAGCTTCAACTCTCGTA 59.381 47.619 0.00 0.0 33.89 3.43 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
58 59 0.106918 TCTCTCCTCTTCTCTCGGCC 60.107 60.000 0.00 0.00 0.00 6.13
62 63 3.509757 CTCTTCTCTCGGCCGCGA 61.510 66.667 23.51 20.65 0.00 5.87
63 64 2.829003 TCTTCTCTCGGCCGCGAT 60.829 61.111 23.51 0.00 0.00 4.58
64 65 1.507974 CTCTTCTCTCGGCCGCGATA 61.508 60.000 23.51 10.23 0.00 2.92
65 66 1.370657 CTTCTCTCGGCCGCGATAC 60.371 63.158 23.51 0.00 0.00 2.24
66 67 3.177272 TTCTCTCGGCCGCGATACG 62.177 63.158 23.51 8.56 43.15 3.06
335 372 1.332552 CGTGCTTTCGTTTGCTTACGT 60.333 47.619 10.20 0.00 42.01 3.57
336 373 2.097299 CGTGCTTTCGTTTGCTTACGTA 60.097 45.455 10.20 0.00 42.01 3.57
337 374 3.212887 GTGCTTTCGTTTGCTTACGTAC 58.787 45.455 0.00 0.00 42.01 3.67
361 398 5.796935 CGTACTTATAACAGTACAGTGCGTT 59.203 40.000 12.89 4.79 46.66 4.84
496 533 2.203153 CCGGCGACCCCTTTATGG 60.203 66.667 9.30 0.00 0.00 2.74
558 595 3.498777 CACTGCATGCATTATCTGGAGAG 59.501 47.826 22.97 7.24 33.18 3.20
672 709 3.057526 GCAAGTACCTGAAAACCATCACC 60.058 47.826 0.00 0.00 0.00 4.02
877 914 2.094675 GGTACGTAGGCACAAGGAGTA 58.905 52.381 0.00 0.00 0.00 2.59
953 999 1.084290 CAACTGCGTCGACGTGTTG 60.084 57.895 37.30 37.30 43.16 3.33
1012 1058 4.344865 GTGGGATGTGGCCGTGGT 62.345 66.667 0.00 0.00 0.00 4.16
1182 1228 0.942884 ACTTTTCCTTCGCCGTCGTC 60.943 55.000 0.00 0.00 36.96 4.20
1200 1246 2.743928 CAGGCCAACGAGGTGCTC 60.744 66.667 5.01 0.00 40.61 4.26
1366 1446 7.330262 ACCCCATTTATTTCAGCTATGTTTTG 58.670 34.615 0.00 0.00 0.00 2.44
1367 1447 7.038373 ACCCCATTTATTTCAGCTATGTTTTGT 60.038 33.333 0.00 0.00 0.00 2.83
1374 1454 7.744087 ATTTCAGCTATGTTTTGTGTCACTA 57.256 32.000 4.27 0.00 0.00 2.74
1378 1458 6.816640 TCAGCTATGTTTTGTGTCACTATACC 59.183 38.462 4.27 0.00 0.00 2.73
1408 1488 5.121142 TGTTCGCTAGCTTACAAATTGGTAC 59.879 40.000 13.93 0.00 0.00 3.34
1409 1489 5.080969 TCGCTAGCTTACAAATTGGTACT 57.919 39.130 13.93 0.00 0.00 2.73
1410 1490 5.107133 TCGCTAGCTTACAAATTGGTACTC 58.893 41.667 13.93 0.00 0.00 2.59
1411 1491 4.270325 CGCTAGCTTACAAATTGGTACTCC 59.730 45.833 13.93 0.00 0.00 3.85
1412 1492 4.575236 GCTAGCTTACAAATTGGTACTCCC 59.425 45.833 7.70 0.00 0.00 4.30
1414 1494 4.844884 AGCTTACAAATTGGTACTCCCTC 58.155 43.478 0.00 0.00 0.00 4.30
1415 1495 3.945921 GCTTACAAATTGGTACTCCCTCC 59.054 47.826 0.00 0.00 0.00 4.30
1416 1496 2.781681 ACAAATTGGTACTCCCTCCG 57.218 50.000 0.00 0.00 0.00 4.63
1417 1497 1.982958 ACAAATTGGTACTCCCTCCGT 59.017 47.619 0.00 0.00 0.00 4.69
1418 1498 2.374170 ACAAATTGGTACTCCCTCCGTT 59.626 45.455 0.00 0.00 0.00 4.44
1419 1499 3.007635 CAAATTGGTACTCCCTCCGTTC 58.992 50.000 0.00 0.00 0.00 3.95
1420 1500 1.946984 ATTGGTACTCCCTCCGTTCA 58.053 50.000 0.00 0.00 0.00 3.18
1421 1501 0.971386 TTGGTACTCCCTCCGTTCAC 59.029 55.000 0.00 0.00 0.00 3.18
1422 1502 0.113776 TGGTACTCCCTCCGTTCACT 59.886 55.000 0.00 0.00 0.00 3.41
1423 1503 1.264295 GGTACTCCCTCCGTTCACTT 58.736 55.000 0.00 0.00 0.00 3.16
1424 1504 1.622312 GGTACTCCCTCCGTTCACTTT 59.378 52.381 0.00 0.00 0.00 2.66
1425 1505 2.038164 GGTACTCCCTCCGTTCACTTTT 59.962 50.000 0.00 0.00 0.00 2.27
1426 1506 2.256117 ACTCCCTCCGTTCACTTTTG 57.744 50.000 0.00 0.00 0.00 2.44
1427 1507 1.489230 ACTCCCTCCGTTCACTTTTGT 59.511 47.619 0.00 0.00 0.00 2.83
1428 1508 2.701951 ACTCCCTCCGTTCACTTTTGTA 59.298 45.455 0.00 0.00 0.00 2.41
1429 1509 3.135167 ACTCCCTCCGTTCACTTTTGTAA 59.865 43.478 0.00 0.00 0.00 2.41
1430 1510 3.735591 TCCCTCCGTTCACTTTTGTAAG 58.264 45.455 0.00 0.00 37.40 2.34
1431 1511 3.135167 TCCCTCCGTTCACTTTTGTAAGT 59.865 43.478 0.00 0.00 45.40 2.24
1432 1512 3.497262 CCCTCCGTTCACTTTTGTAAGTC 59.503 47.826 0.00 0.00 42.67 3.01
1433 1513 4.124238 CCTCCGTTCACTTTTGTAAGTCA 58.876 43.478 0.00 0.00 42.67 3.41
1434 1514 4.755123 CCTCCGTTCACTTTTGTAAGTCAT 59.245 41.667 0.00 0.00 42.67 3.06
1435 1515 5.238650 CCTCCGTTCACTTTTGTAAGTCATT 59.761 40.000 0.00 0.00 42.67 2.57
1436 1516 6.238648 CCTCCGTTCACTTTTGTAAGTCATTT 60.239 38.462 0.00 0.00 42.67 2.32
1437 1517 6.721321 TCCGTTCACTTTTGTAAGTCATTTC 58.279 36.000 0.00 0.00 42.67 2.17
1438 1518 6.316640 TCCGTTCACTTTTGTAAGTCATTTCA 59.683 34.615 0.00 0.00 42.67 2.69
1439 1519 6.632834 CCGTTCACTTTTGTAAGTCATTTCAG 59.367 38.462 0.00 0.00 42.67 3.02
1440 1520 7.406553 CGTTCACTTTTGTAAGTCATTTCAGA 58.593 34.615 0.00 0.00 42.67 3.27
1441 1521 7.373441 CGTTCACTTTTGTAAGTCATTTCAGAC 59.627 37.037 0.00 0.00 42.67 3.51
1442 1522 7.857734 TCACTTTTGTAAGTCATTTCAGACA 57.142 32.000 0.00 0.00 42.67 3.41
1443 1523 8.275015 TCACTTTTGTAAGTCATTTCAGACAA 57.725 30.769 0.00 0.00 42.67 3.18
1444 1524 8.181573 TCACTTTTGTAAGTCATTTCAGACAAC 58.818 33.333 0.00 0.00 42.67 3.32
1445 1525 8.184192 CACTTTTGTAAGTCATTTCAGACAACT 58.816 33.333 0.00 0.00 42.67 3.16
1446 1526 8.739972 ACTTTTGTAAGTCATTTCAGACAACTT 58.260 29.630 0.00 0.00 40.60 2.66
1454 1534 8.463930 AGTCATTTCAGACAACTTAAAATGGA 57.536 30.769 0.00 0.00 40.98 3.41
1455 1535 8.352942 AGTCATTTCAGACAACTTAAAATGGAC 58.647 33.333 0.00 0.00 40.98 4.02
1456 1536 8.352942 GTCATTTCAGACAACTTAAAATGGACT 58.647 33.333 0.00 0.00 38.40 3.85
1457 1537 8.352201 TCATTTCAGACAACTTAAAATGGACTG 58.648 33.333 0.00 0.00 0.00 3.51
1458 1538 7.639113 TTTCAGACAACTTAAAATGGACTGT 57.361 32.000 0.00 0.00 31.75 3.55
1459 1539 7.639113 TTCAGACAACTTAAAATGGACTGTT 57.361 32.000 0.00 0.00 31.75 3.16
1460 1540 7.639113 TCAGACAACTTAAAATGGACTGTTT 57.361 32.000 0.00 0.00 31.75 2.83
1461 1541 8.062065 TCAGACAACTTAAAATGGACTGTTTT 57.938 30.769 0.00 0.00 33.67 2.43
1462 1542 7.973388 TCAGACAACTTAAAATGGACTGTTTTG 59.027 33.333 0.00 0.00 31.71 2.44
1463 1543 7.759433 CAGACAACTTAAAATGGACTGTTTTGT 59.241 33.333 0.00 0.00 31.71 2.83
1464 1544 8.962679 AGACAACTTAAAATGGACTGTTTTGTA 58.037 29.630 0.00 0.00 31.71 2.41
1465 1545 8.920509 ACAACTTAAAATGGACTGTTTTGTAC 57.079 30.769 0.00 0.00 31.71 2.90
1466 1546 8.524487 ACAACTTAAAATGGACTGTTTTGTACA 58.476 29.630 0.00 0.00 34.98 2.90
1467 1547 9.528018 CAACTTAAAATGGACTGTTTTGTACAT 57.472 29.630 0.00 0.00 42.81 2.29
1472 1552 6.959639 AATGGACTGTTTTGTACATTGTCT 57.040 33.333 0.00 0.00 46.34 3.41
1473 1553 5.749596 TGGACTGTTTTGTACATTGTCTG 57.250 39.130 0.00 0.00 35.85 3.51
1474 1554 5.432645 TGGACTGTTTTGTACATTGTCTGA 58.567 37.500 0.00 0.00 35.85 3.27
1475 1555 5.883115 TGGACTGTTTTGTACATTGTCTGAA 59.117 36.000 0.00 0.00 35.85 3.02
1476 1556 6.375736 TGGACTGTTTTGTACATTGTCTGAAA 59.624 34.615 0.00 0.00 35.85 2.69
1477 1557 7.068103 TGGACTGTTTTGTACATTGTCTGAAAT 59.932 33.333 0.00 0.00 35.85 2.17
1478 1558 7.379529 GGACTGTTTTGTACATTGTCTGAAATG 59.620 37.037 0.00 9.50 42.21 2.32
1480 1560 7.915397 ACTGTTTTGTACATTGTCTGAAATGTC 59.085 33.333 16.13 11.24 45.47 3.06
1481 1561 7.995289 TGTTTTGTACATTGTCTGAAATGTCT 58.005 30.769 16.13 3.09 45.47 3.41
1482 1562 8.465999 TGTTTTGTACATTGTCTGAAATGTCTT 58.534 29.630 16.13 2.61 45.47 3.01
1483 1563 8.958043 GTTTTGTACATTGTCTGAAATGTCTTC 58.042 33.333 16.13 11.26 45.47 2.87
1484 1564 7.800155 TTGTACATTGTCTGAAATGTCTTCA 57.200 32.000 16.13 12.76 45.47 3.02
1485 1565 7.800155 TGTACATTGTCTGAAATGTCTTCAA 57.200 32.000 16.13 0.18 45.47 2.69
1486 1566 8.219546 TGTACATTGTCTGAAATGTCTTCAAA 57.780 30.769 16.13 2.61 45.47 2.69
1487 1567 8.128582 TGTACATTGTCTGAAATGTCTTCAAAC 58.871 33.333 16.13 11.08 45.47 2.93
1488 1568 7.338800 ACATTGTCTGAAATGTCTTCAAACT 57.661 32.000 10.41 0.00 45.47 2.66
1489 1569 7.420800 ACATTGTCTGAAATGTCTTCAAACTC 58.579 34.615 10.41 0.00 45.47 3.01
1490 1570 7.284034 ACATTGTCTGAAATGTCTTCAAACTCT 59.716 33.333 10.41 0.00 45.47 3.24
1491 1571 7.630242 TTGTCTGAAATGTCTTCAAACTCTT 57.370 32.000 0.00 0.00 0.00 2.85
1492 1572 8.731275 TTGTCTGAAATGTCTTCAAACTCTTA 57.269 30.769 0.00 0.00 0.00 2.10
1493 1573 8.908786 TGTCTGAAATGTCTTCAAACTCTTAT 57.091 30.769 0.00 0.00 0.00 1.73
1494 1574 9.996554 TGTCTGAAATGTCTTCAAACTCTTATA 57.003 29.630 0.00 0.00 0.00 0.98
1509 1589 9.884465 CAAACTCTTATAAAAGTGAACAGAAGG 57.116 33.333 0.00 0.00 34.13 3.46
1510 1590 9.847224 AAACTCTTATAAAAGTGAACAGAAGGA 57.153 29.630 0.00 0.00 34.13 3.36
1511 1591 9.495572 AACTCTTATAAAAGTGAACAGAAGGAG 57.504 33.333 0.00 0.00 34.13 3.69
1512 1592 8.652290 ACTCTTATAAAAGTGAACAGAAGGAGT 58.348 33.333 0.00 0.00 34.13 3.85
1515 1595 8.773404 TTATAAAAGTGAACAGAAGGAGTAGC 57.227 34.615 0.00 0.00 0.00 3.58
1516 1596 4.689612 AAAGTGAACAGAAGGAGTAGCA 57.310 40.909 0.00 0.00 0.00 3.49
1572 1653 5.039984 GCACTATGACTATGAGTGACACAG 58.960 45.833 8.59 0.00 42.65 3.66
1623 1834 8.764558 TCCTTGATTTATACTAGTTGCCAGTAA 58.235 33.333 0.00 0.00 32.47 2.24
1685 1896 2.803451 CGAGAGCCTCAGTACAACATC 58.197 52.381 0.00 0.00 0.00 3.06
1686 1897 2.164422 CGAGAGCCTCAGTACAACATCA 59.836 50.000 0.00 0.00 0.00 3.07
1687 1898 3.181482 CGAGAGCCTCAGTACAACATCAT 60.181 47.826 0.00 0.00 0.00 2.45
1688 1899 4.036852 CGAGAGCCTCAGTACAACATCATA 59.963 45.833 0.00 0.00 0.00 2.15
1689 1900 5.527951 GAGAGCCTCAGTACAACATCATAG 58.472 45.833 0.00 0.00 0.00 2.23
1690 1901 4.343526 AGAGCCTCAGTACAACATCATAGG 59.656 45.833 0.00 0.00 0.00 2.57
1691 1902 3.134458 GCCTCAGTACAACATCATAGGC 58.866 50.000 0.00 0.00 41.27 3.93
1692 1903 3.432186 GCCTCAGTACAACATCATAGGCA 60.432 47.826 0.00 0.00 45.99 4.75
1693 1904 4.744867 GCCTCAGTACAACATCATAGGCAT 60.745 45.833 0.00 0.00 45.99 4.40
1694 1905 4.993584 CCTCAGTACAACATCATAGGCATC 59.006 45.833 0.00 0.00 0.00 3.91
1695 1906 5.221601 CCTCAGTACAACATCATAGGCATCT 60.222 44.000 0.00 0.00 0.00 2.90
1696 1907 5.604565 TCAGTACAACATCATAGGCATCTG 58.395 41.667 0.00 0.00 0.00 2.90
1697 1908 4.212847 CAGTACAACATCATAGGCATCTGC 59.787 45.833 0.00 0.00 41.14 4.26
1698 1909 2.216046 ACAACATCATAGGCATCTGCG 58.784 47.619 0.00 0.00 43.26 5.18
1699 1910 2.158914 ACAACATCATAGGCATCTGCGA 60.159 45.455 0.00 0.00 43.26 5.10
1700 1911 2.452295 ACATCATAGGCATCTGCGAG 57.548 50.000 0.00 0.00 43.26 5.03
1701 1912 1.077123 CATCATAGGCATCTGCGAGC 58.923 55.000 0.00 0.00 43.26 5.03
1702 1913 0.683412 ATCATAGGCATCTGCGAGCA 59.317 50.000 0.00 0.00 43.26 4.26
1703 1914 0.033090 TCATAGGCATCTGCGAGCAG 59.967 55.000 18.20 18.20 44.86 4.24
1711 1922 1.588597 TCTGCGAGCAGAGTTGAGG 59.411 57.895 22.28 0.00 46.80 3.86
1712 1923 0.895559 TCTGCGAGCAGAGTTGAGGA 60.896 55.000 22.28 0.00 46.80 3.71
1713 1924 0.175302 CTGCGAGCAGAGTTGAGGAT 59.825 55.000 19.40 0.00 46.30 3.24
1714 1925 0.108472 TGCGAGCAGAGTTGAGGATG 60.108 55.000 0.00 0.00 0.00 3.51
1715 1926 1.427592 GCGAGCAGAGTTGAGGATGC 61.428 60.000 0.00 0.00 38.97 3.91
1716 1927 0.809241 CGAGCAGAGTTGAGGATGCC 60.809 60.000 0.00 0.00 39.51 4.40
1717 1928 0.540923 GAGCAGAGTTGAGGATGCCT 59.459 55.000 0.00 0.00 39.51 4.75
1718 1929 1.759445 GAGCAGAGTTGAGGATGCCTA 59.241 52.381 0.00 0.00 39.51 3.93
1719 1930 2.169352 GAGCAGAGTTGAGGATGCCTAA 59.831 50.000 0.00 0.00 39.51 2.69
1720 1931 2.776536 AGCAGAGTTGAGGATGCCTAAT 59.223 45.455 0.00 0.00 39.51 1.73
1721 1932 3.969976 AGCAGAGTTGAGGATGCCTAATA 59.030 43.478 0.00 0.00 39.51 0.98
1722 1933 4.061596 GCAGAGTTGAGGATGCCTAATAC 58.938 47.826 0.00 0.00 31.76 1.89
1723 1934 4.636249 CAGAGTTGAGGATGCCTAATACC 58.364 47.826 0.00 0.00 31.76 2.73
1724 1935 4.101585 CAGAGTTGAGGATGCCTAATACCA 59.898 45.833 0.00 0.00 31.76 3.25
1725 1936 4.910304 AGAGTTGAGGATGCCTAATACCAT 59.090 41.667 0.00 0.00 31.76 3.55
1726 1937 5.370880 AGAGTTGAGGATGCCTAATACCATT 59.629 40.000 0.00 0.00 31.76 3.16
1727 1938 6.018433 AGTTGAGGATGCCTAATACCATTT 57.982 37.500 0.00 0.00 31.76 2.32
1728 1939 6.064717 AGTTGAGGATGCCTAATACCATTTC 58.935 40.000 0.00 0.00 31.76 2.17
1729 1940 5.645056 TGAGGATGCCTAATACCATTTCA 57.355 39.130 0.00 0.00 31.76 2.69
1730 1941 5.376625 TGAGGATGCCTAATACCATTTCAC 58.623 41.667 0.00 0.00 31.76 3.18
1731 1942 5.132648 TGAGGATGCCTAATACCATTTCACT 59.867 40.000 0.00 0.00 31.76 3.41
1732 1943 5.625150 AGGATGCCTAATACCATTTCACTC 58.375 41.667 0.00 0.00 28.47 3.51
1733 1944 5.132648 AGGATGCCTAATACCATTTCACTCA 59.867 40.000 0.00 0.00 28.47 3.41
1734 1945 5.239525 GGATGCCTAATACCATTTCACTCAC 59.760 44.000 0.00 0.00 0.00 3.51
1735 1946 4.188462 TGCCTAATACCATTTCACTCACG 58.812 43.478 0.00 0.00 0.00 4.35
1736 1947 4.189231 GCCTAATACCATTTCACTCACGT 58.811 43.478 0.00 0.00 0.00 4.49
1737 1948 4.634443 GCCTAATACCATTTCACTCACGTT 59.366 41.667 0.00 0.00 0.00 3.99
1738 1949 5.123344 GCCTAATACCATTTCACTCACGTTT 59.877 40.000 0.00 0.00 0.00 3.60
1739 1950 6.349033 GCCTAATACCATTTCACTCACGTTTT 60.349 38.462 0.00 0.00 0.00 2.43
1740 1951 7.021196 CCTAATACCATTTCACTCACGTTTTG 58.979 38.462 0.00 0.00 0.00 2.44
1741 1952 6.385649 AATACCATTTCACTCACGTTTTGT 57.614 33.333 0.00 0.00 0.00 2.83
1742 1953 7.499321 AATACCATTTCACTCACGTTTTGTA 57.501 32.000 0.00 0.00 0.00 2.41
1743 1954 5.164606 ACCATTTCACTCACGTTTTGTAC 57.835 39.130 0.00 0.00 0.00 2.90
1744 1955 4.636648 ACCATTTCACTCACGTTTTGTACA 59.363 37.500 0.00 0.00 0.00 2.90
1745 1956 5.124138 ACCATTTCACTCACGTTTTGTACAA 59.876 36.000 3.59 3.59 0.00 2.41
1746 1957 6.030849 CCATTTCACTCACGTTTTGTACAAA 58.969 36.000 17.01 17.01 0.00 2.83
1747 1958 6.528423 CCATTTCACTCACGTTTTGTACAAAA 59.472 34.615 26.05 26.05 37.90 2.44
1748 1959 7.221838 CCATTTCACTCACGTTTTGTACAAAAT 59.778 33.333 30.65 17.01 41.64 1.82
1749 1960 8.591312 CATTTCACTCACGTTTTGTACAAAATT 58.409 29.630 30.65 20.26 41.64 1.82
1750 1961 7.728580 TTCACTCACGTTTTGTACAAAATTC 57.271 32.000 30.65 20.04 41.64 2.17
1751 1962 7.079182 TCACTCACGTTTTGTACAAAATTCT 57.921 32.000 30.65 16.43 41.64 2.40
1752 1963 8.199176 TCACTCACGTTTTGTACAAAATTCTA 57.801 30.769 30.65 18.19 41.64 2.10
1753 1964 8.666573 TCACTCACGTTTTGTACAAAATTCTAA 58.333 29.630 30.65 17.06 41.64 2.10
1754 1965 9.279904 CACTCACGTTTTGTACAAAATTCTAAA 57.720 29.630 30.65 16.23 41.64 1.85
1755 1966 9.281075 ACTCACGTTTTGTACAAAATTCTAAAC 57.719 29.630 30.65 18.45 41.64 2.01
1756 1967 9.279904 CTCACGTTTTGTACAAAATTCTAAACA 57.720 29.630 30.65 8.07 41.64 2.83
1757 1968 9.790389 TCACGTTTTGTACAAAATTCTAAACAT 57.210 25.926 30.65 8.20 41.64 2.71
1811 2022 3.000041 GTGCCACTGTAATGACGAATGA 59.000 45.455 0.00 0.00 0.00 2.57
1814 2025 4.517075 TGCCACTGTAATGACGAATGAAAA 59.483 37.500 0.00 0.00 0.00 2.29
1815 2026 4.851558 GCCACTGTAATGACGAATGAAAAC 59.148 41.667 0.00 0.00 0.00 2.43
1823 2034 9.743057 TGTAATGACGAATGAAAACTTGAAATT 57.257 25.926 0.00 0.00 0.00 1.82
1827 2038 8.114359 TGACGAATGAAAACTTGAAATTTCAC 57.886 30.769 20.35 8.62 45.34 3.18
1828 2039 7.221838 TGACGAATGAAAACTTGAAATTTCACC 59.778 33.333 20.35 6.64 45.34 4.02
1829 2040 7.038659 ACGAATGAAAACTTGAAATTTCACCA 58.961 30.769 20.35 6.39 45.34 4.17
1830 2041 7.710475 ACGAATGAAAACTTGAAATTTCACCAT 59.290 29.630 20.35 12.87 45.34 3.55
1831 2042 8.550376 CGAATGAAAACTTGAAATTTCACCATT 58.450 29.630 20.35 18.77 45.34 3.16
1834 2045 8.558973 TGAAAACTTGAAATTTCACCATTTGT 57.441 26.923 20.35 9.58 39.81 2.83
1835 2046 9.007901 TGAAAACTTGAAATTTCACCATTTGTT 57.992 25.926 20.35 14.07 39.81 2.83
1836 2047 9.489393 GAAAACTTGAAATTTCACCATTTGTTC 57.511 29.630 20.35 12.83 36.83 3.18
1837 2048 8.791327 AAACTTGAAATTTCACCATTTGTTCT 57.209 26.923 20.35 7.40 36.83 3.01
1838 2049 8.424274 AACTTGAAATTTCACCATTTGTTCTC 57.576 30.769 20.35 0.00 36.83 2.87
1839 2050 7.555087 ACTTGAAATTTCACCATTTGTTCTCA 58.445 30.769 20.35 0.62 36.83 3.27
1840 2051 8.206189 ACTTGAAATTTCACCATTTGTTCTCAT 58.794 29.630 20.35 0.00 36.83 2.90
1841 2052 8.592105 TTGAAATTTCACCATTTGTTCTCATC 57.408 30.769 20.35 0.00 36.83 2.92
1842 2053 7.153985 TGAAATTTCACCATTTGTTCTCATCC 58.846 34.615 16.91 0.00 31.01 3.51
1843 2054 6.669125 AATTTCACCATTTGTTCTCATCCA 57.331 33.333 0.00 0.00 0.00 3.41
1844 2055 5.452078 TTTCACCATTTGTTCTCATCCAC 57.548 39.130 0.00 0.00 0.00 4.02
1845 2056 4.097551 TCACCATTTGTTCTCATCCACA 57.902 40.909 0.00 0.00 0.00 4.17
1846 2057 4.074259 TCACCATTTGTTCTCATCCACAG 58.926 43.478 0.00 0.00 0.00 3.66
1847 2058 2.821969 ACCATTTGTTCTCATCCACAGC 59.178 45.455 0.00 0.00 0.00 4.40
1848 2059 2.821378 CCATTTGTTCTCATCCACAGCA 59.179 45.455 0.00 0.00 0.00 4.41
1849 2060 3.446161 CCATTTGTTCTCATCCACAGCAT 59.554 43.478 0.00 0.00 0.00 3.79
1850 2061 4.081862 CCATTTGTTCTCATCCACAGCATT 60.082 41.667 0.00 0.00 0.00 3.56
1851 2062 4.508461 TTTGTTCTCATCCACAGCATTG 57.492 40.909 0.00 0.00 0.00 2.82
1852 2063 2.439409 TGTTCTCATCCACAGCATTGG 58.561 47.619 0.00 0.00 38.10 3.16
1853 2064 2.224843 TGTTCTCATCCACAGCATTGGT 60.225 45.455 3.70 0.00 37.93 3.67
1854 2065 2.821969 GTTCTCATCCACAGCATTGGTT 59.178 45.455 3.70 0.00 37.93 3.67
1855 2066 3.998913 TCTCATCCACAGCATTGGTTA 57.001 42.857 3.70 0.00 37.93 2.85
1856 2067 3.877559 TCTCATCCACAGCATTGGTTAG 58.122 45.455 3.70 1.37 37.93 2.34
1857 2068 3.519107 TCTCATCCACAGCATTGGTTAGA 59.481 43.478 3.70 3.35 37.93 2.10
1858 2069 4.164796 TCTCATCCACAGCATTGGTTAGAT 59.835 41.667 3.70 0.00 37.93 1.98
1875 2086 6.072175 TGGTTAGATTGCAACATAGTTCAACC 60.072 38.462 0.00 11.00 0.00 3.77
1902 2113 7.350467 CGTTTAACTGTTCCTTTACTTCCTTC 58.650 38.462 0.00 0.00 0.00 3.46
1920 2131 4.047822 CCTTCGATGACTGCTACAGATTC 58.952 47.826 0.78 0.00 35.18 2.52
1965 2176 5.678583 TCTGATTCATCTCCCTGACAATTC 58.321 41.667 0.00 0.00 0.00 2.17
1975 2186 4.836825 TCCCTGACAATTCTTCTTGCTAG 58.163 43.478 0.00 0.00 0.00 3.42
1983 2194 8.585881 TGACAATTCTTCTTGCTAGTTAGTAGT 58.414 33.333 0.00 0.00 0.00 2.73
2170 2408 8.164070 AGGACACACTTGATAAAACCTTCTATT 58.836 33.333 0.00 0.00 0.00 1.73
2285 2523 9.313118 GTTGTTTAGTTGGATCAAACAAGATTT 57.687 29.630 15.42 0.00 46.84 2.17
2365 2603 5.295540 GCTTAAATCTCTTCACCCTGATGAC 59.704 44.000 0.00 0.00 0.00 3.06
2392 2630 5.754890 ACAGATTGTTGTTCTGAAAAATGGC 59.245 36.000 7.63 0.00 42.63 4.40
2442 2680 9.832445 ACAGGTATACAATACAGACCTTTTATG 57.168 33.333 5.01 0.00 38.49 1.90
2455 2693 5.940470 AGACCTTTTATGACAAGCCTTGTAG 59.060 40.000 10.65 2.96 45.52 2.74
2458 2696 6.653740 ACCTTTTATGACAAGCCTTGTAGTAC 59.346 38.462 10.65 0.00 45.52 2.73
2474 2712 5.730550 TGTAGTACTTATGAAGCTTGGGTG 58.269 41.667 2.10 0.00 0.00 4.61
2484 2730 4.832248 TGAAGCTTGGGTGAACATACTAG 58.168 43.478 2.10 0.00 0.00 2.57
2485 2731 3.914426 AGCTTGGGTGAACATACTAGG 57.086 47.619 0.00 0.00 0.00 3.02
2666 2914 9.573166 TTGGAAAATATGTTATGTCATCTAGGG 57.427 33.333 0.00 0.00 0.00 3.53
2668 2916 7.121315 GGAAAATATGTTATGTCATCTAGGGCC 59.879 40.741 0.00 0.00 0.00 5.80
2705 2953 7.596749 TCTGAATTATTCTTCTTCGGAACAC 57.403 36.000 6.50 0.00 32.73 3.32
2752 3000 7.175347 TCAAGGTCTATAGGTGATGCATATC 57.825 40.000 0.00 0.00 0.00 1.63
2775 3023 3.820777 AAGAAGCAAGAATTCGCTGTC 57.179 42.857 8.39 8.30 38.82 3.51
2781 3029 2.270923 CAAGAATTCGCTGTCGATCCA 58.729 47.619 0.00 0.00 45.04 3.41
2841 3089 0.459759 CCGTTCTAACTTCCGAGCCC 60.460 60.000 0.00 0.00 0.00 5.19
2856 3104 0.179000 AGCCCTCAATAAGCACGAGG 59.821 55.000 0.00 0.00 45.02 4.63
2968 3216 5.407084 CACAACAATCCACGTGAAGTATGTA 59.593 40.000 19.30 0.00 0.00 2.29
3012 3260 4.520492 TCTTTGCTTTTCTGGATGAACCTC 59.480 41.667 0.00 0.00 39.86 3.85
3189 3443 8.218338 ACGATATTACGAAACTAGAGAAAGGA 57.782 34.615 0.00 0.00 37.03 3.36
3307 3561 2.404923 TCGTGGGTTTGTTGAGTCAA 57.595 45.000 0.08 0.08 0.00 3.18
3528 3784 1.185618 TCCGGCTACAGTGCTTGTCT 61.186 55.000 0.00 0.00 41.29 3.41
3529 3785 0.530744 CCGGCTACAGTGCTTGTCTA 59.469 55.000 0.00 0.00 41.29 2.59
3543 3799 8.580720 CAGTGCTTGTCTATACTGTCCTATAAT 58.419 37.037 0.00 0.00 36.63 1.28
3561 3817 9.101325 TCCTATAATAATAAGCACTGTTAGCCT 57.899 33.333 0.00 0.00 0.00 4.58
3565 3821 3.981071 ATAAGCACTGTTAGCCTGACA 57.019 42.857 0.00 0.00 0.00 3.58
3623 3880 9.965902 AAGATATGGTATTTGTGAACTCTTCTT 57.034 29.630 0.00 0.00 0.00 2.52
3634 3891 5.163416 TGTGAACTCTTCTTGTGAGATGTGA 60.163 40.000 0.00 0.00 35.66 3.58
3638 3895 6.357579 ACTCTTCTTGTGAGATGTGATCTT 57.642 37.500 0.00 0.00 40.38 2.40
3665 3922 6.951198 TGGAATTGGTGGTTTATCTAATGTGT 59.049 34.615 0.00 0.00 0.00 3.72
3690 3947 2.234908 AGAGTTGAAGCTTGGCTCGTAT 59.765 45.455 2.10 0.00 38.25 3.06
3695 3952 3.407698 TGAAGCTTGGCTCGTATTTTCA 58.592 40.909 2.10 0.00 38.25 2.69
3725 3982 1.945394 CTGAAAATCTGAGATGGGCCG 59.055 52.381 0.00 0.00 0.00 6.13
3750 4007 5.532406 TGATAAAACTTTGCAGCTCTTGTCT 59.468 36.000 0.00 0.00 0.00 3.41
3763 4020 4.041444 AGCTCTTGTCTCTCCTTTGTTCAT 59.959 41.667 0.00 0.00 0.00 2.57
3771 4028 6.038603 TGTCTCTCCTTTGTTCATTCAGTTTG 59.961 38.462 0.00 0.00 0.00 2.93
3874 4131 3.081061 TGTTGATATGCACTTGGTGACC 58.919 45.455 0.00 0.00 35.23 4.02
3881 4138 1.680735 TGCACTTGGTGACCAATTGTC 59.319 47.619 28.08 21.79 43.25 3.18
3938 4197 0.776810 TGTGGAATTCTGGCCTCCAA 59.223 50.000 12.02 0.00 40.87 3.53
3950 4209 2.441750 TGGCCTCCAACAAGTAGAAAGT 59.558 45.455 3.32 0.00 0.00 2.66
3957 4216 6.486657 CCTCCAACAAGTAGAAAGTTGATCAA 59.513 38.462 3.38 3.38 43.93 2.57
3999 4258 2.880890 AGAACTGACATGGCAAACAGAC 59.119 45.455 19.93 14.36 34.88 3.51
4014 4273 6.094048 GGCAAACAGACAAATGAGATTAGCTA 59.906 38.462 0.00 0.00 0.00 3.32
4054 4316 1.137086 GTGCACGACTATGGATCCACT 59.863 52.381 18.99 9.21 0.00 4.00
4220 4484 6.723131 ATGATATCTCGACGATAAAGACGA 57.277 37.500 3.98 0.00 38.08 4.20
4245 4510 2.280628 GTCTGGAATAAAGGCTCCACG 58.719 52.381 0.00 0.00 36.79 4.94
4279 4545 0.106469 TGGTGTGGCTTTTGTGGCTA 60.106 50.000 0.00 0.00 0.00 3.93
4315 4581 4.211125 TGCAAAGGATGTGGTGTTTTAGA 58.789 39.130 0.00 0.00 0.00 2.10
4319 4585 2.714250 AGGATGTGGTGTTTTAGACCCA 59.286 45.455 0.00 0.00 31.84 4.51
4335 4601 5.373812 AGACCCACGGATTAATGATTCTT 57.626 39.130 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.154798 GACCGTACTGCAGGCACAGA 62.155 60.000 19.93 0.00 40.25 3.41
23 24 0.029567 GAGATCGGACCGTACTGCAG 59.970 60.000 13.48 13.48 0.00 4.41
62 63 1.372997 GGCGATCGGTGATGCGTAT 60.373 57.895 18.30 0.00 0.00 3.06
63 64 2.027024 GGCGATCGGTGATGCGTA 59.973 61.111 18.30 0.00 0.00 4.42
67 68 4.923710 TCGCGGCGATCGGTGATG 62.924 66.667 22.69 0.00 39.69 3.07
69 70 4.923710 CATCGCGGCGATCGGTGA 62.924 66.667 32.73 13.33 45.19 4.02
234 268 3.503363 GTGGGCGCTGACAGATGC 61.503 66.667 7.64 9.09 0.00 3.91
321 358 3.884169 AGTACGTACGTAAGCAAACGAA 58.116 40.909 28.34 2.71 45.68 3.85
361 398 1.177895 ATGACCAAATGCACGCACCA 61.178 50.000 0.00 0.00 0.00 4.17
558 595 0.183731 GGGAAGGGGTCATGTGATCC 59.816 60.000 3.63 3.63 44.64 3.36
692 729 1.025812 TGGAAAAAGCGCGAAAAGGA 58.974 45.000 12.10 0.00 0.00 3.36
877 914 1.004044 CAGATCACAAGGCCAGGTCTT 59.996 52.381 5.01 0.00 0.00 3.01
953 999 0.105709 AGAGAAGAGAGCTAGCCCCC 60.106 60.000 12.13 0.75 0.00 5.40
1012 1058 1.019278 GCGGACGCAATCTTCTCCAA 61.019 55.000 12.31 0.00 41.49 3.53
1167 1213 3.277211 CTGGACGACGGCGAAGGAA 62.277 63.158 22.49 0.00 41.64 3.36
1182 1228 4.335647 AGCACCTCGTTGGCCTGG 62.336 66.667 3.32 0.81 40.22 4.45
1200 1246 3.302347 GACCTGGCTGTGGTCCTCG 62.302 68.421 11.83 0.00 46.01 4.63
1366 1446 3.594603 ACAGCACAGGTATAGTGACAC 57.405 47.619 0.00 0.00 39.30 3.67
1367 1447 3.366985 CGAACAGCACAGGTATAGTGACA 60.367 47.826 0.00 0.00 39.30 3.58
1408 1488 2.256117 ACAAAAGTGAACGGAGGGAG 57.744 50.000 0.00 0.00 0.00 4.30
1409 1489 3.135167 ACTTACAAAAGTGAACGGAGGGA 59.865 43.478 0.00 0.00 44.40 4.20
1410 1490 3.473625 ACTTACAAAAGTGAACGGAGGG 58.526 45.455 0.00 0.00 44.40 4.30
1411 1491 4.124238 TGACTTACAAAAGTGAACGGAGG 58.876 43.478 0.00 0.00 46.09 4.30
1412 1492 5.924475 ATGACTTACAAAAGTGAACGGAG 57.076 39.130 0.00 0.00 46.09 4.63
1414 1494 6.491394 TGAAATGACTTACAAAAGTGAACGG 58.509 36.000 0.00 0.00 46.09 4.44
1415 1495 7.373441 GTCTGAAATGACTTACAAAAGTGAACG 59.627 37.037 0.00 0.00 46.09 3.95
1416 1496 8.181573 TGTCTGAAATGACTTACAAAAGTGAAC 58.818 33.333 0.00 0.00 46.09 3.18
1417 1497 8.275015 TGTCTGAAATGACTTACAAAAGTGAA 57.725 30.769 0.00 0.00 46.09 3.18
1418 1498 7.857734 TGTCTGAAATGACTTACAAAAGTGA 57.142 32.000 0.00 0.00 46.09 3.41
1419 1499 8.184192 AGTTGTCTGAAATGACTTACAAAAGTG 58.816 33.333 0.00 0.00 46.09 3.16
1428 1508 8.912988 TCCATTTTAAGTTGTCTGAAATGACTT 58.087 29.630 8.27 0.00 38.65 3.01
1429 1509 8.352942 GTCCATTTTAAGTTGTCTGAAATGACT 58.647 33.333 8.27 0.00 38.65 3.41
1430 1510 8.352942 AGTCCATTTTAAGTTGTCTGAAATGAC 58.647 33.333 8.27 0.00 38.65 3.06
1431 1511 8.352201 CAGTCCATTTTAAGTTGTCTGAAATGA 58.648 33.333 8.27 0.00 38.65 2.57
1432 1512 8.137437 ACAGTCCATTTTAAGTTGTCTGAAATG 58.863 33.333 0.00 0.00 37.54 2.32
1433 1513 8.237811 ACAGTCCATTTTAAGTTGTCTGAAAT 57.762 30.769 0.00 0.00 0.00 2.17
1434 1514 7.639113 ACAGTCCATTTTAAGTTGTCTGAAA 57.361 32.000 0.00 0.00 0.00 2.69
1435 1515 7.639113 AACAGTCCATTTTAAGTTGTCTGAA 57.361 32.000 0.00 0.00 0.00 3.02
1436 1516 7.639113 AAACAGTCCATTTTAAGTTGTCTGA 57.361 32.000 0.00 0.00 0.00 3.27
1437 1517 7.759433 ACAAAACAGTCCATTTTAAGTTGTCTG 59.241 33.333 0.00 0.00 0.00 3.51
1438 1518 7.836842 ACAAAACAGTCCATTTTAAGTTGTCT 58.163 30.769 0.00 0.00 0.00 3.41
1439 1519 9.016623 GTACAAAACAGTCCATTTTAAGTTGTC 57.983 33.333 0.00 0.00 0.00 3.18
1440 1520 8.524487 TGTACAAAACAGTCCATTTTAAGTTGT 58.476 29.630 0.00 0.00 33.01 3.32
1441 1521 8.918961 TGTACAAAACAGTCCATTTTAAGTTG 57.081 30.769 0.00 0.00 33.01 3.16
1443 1523 9.528018 CAATGTACAAAACAGTCCATTTTAAGT 57.472 29.630 0.00 0.00 42.70 2.24
1444 1524 9.528018 ACAATGTACAAAACAGTCCATTTTAAG 57.472 29.630 0.00 0.00 42.70 1.85
1445 1525 9.522804 GACAATGTACAAAACAGTCCATTTTAA 57.477 29.630 0.00 0.00 42.70 1.52
1446 1526 8.908903 AGACAATGTACAAAACAGTCCATTTTA 58.091 29.630 0.00 0.00 42.70 1.52
1447 1527 7.706179 CAGACAATGTACAAAACAGTCCATTTT 59.294 33.333 0.00 0.00 42.70 1.82
1448 1528 7.068103 TCAGACAATGTACAAAACAGTCCATTT 59.932 33.333 0.00 0.00 42.70 2.32
1449 1529 6.545666 TCAGACAATGTACAAAACAGTCCATT 59.454 34.615 0.00 0.00 42.70 3.16
1450 1530 6.061441 TCAGACAATGTACAAAACAGTCCAT 58.939 36.000 0.00 0.00 42.70 3.41
1451 1531 5.432645 TCAGACAATGTACAAAACAGTCCA 58.567 37.500 0.00 0.00 42.70 4.02
1452 1532 6.371809 TTCAGACAATGTACAAAACAGTCC 57.628 37.500 0.00 0.00 42.70 3.85
1453 1533 7.915397 ACATTTCAGACAATGTACAAAACAGTC 59.085 33.333 0.00 4.19 44.08 3.51
1454 1534 7.771183 ACATTTCAGACAATGTACAAAACAGT 58.229 30.769 0.00 0.00 44.08 3.55
1455 1535 8.131100 AGACATTTCAGACAATGTACAAAACAG 58.869 33.333 0.00 0.00 45.55 3.16
1456 1536 7.995289 AGACATTTCAGACAATGTACAAAACA 58.005 30.769 0.00 0.00 45.55 2.83
1457 1537 8.856490 AAGACATTTCAGACAATGTACAAAAC 57.144 30.769 0.00 0.00 45.55 2.43
1458 1538 8.681806 TGAAGACATTTCAGACAATGTACAAAA 58.318 29.630 0.00 0.00 45.55 2.44
1459 1539 8.219546 TGAAGACATTTCAGACAATGTACAAA 57.780 30.769 0.00 0.00 45.55 2.83
1460 1540 7.800155 TGAAGACATTTCAGACAATGTACAA 57.200 32.000 0.00 0.00 45.55 2.41
1461 1541 7.800155 TTGAAGACATTTCAGACAATGTACA 57.200 32.000 0.00 0.00 45.55 2.90
1462 1542 8.345565 AGTTTGAAGACATTTCAGACAATGTAC 58.654 33.333 11.53 0.00 45.55 2.90
1463 1543 8.450578 AGTTTGAAGACATTTCAGACAATGTA 57.549 30.769 11.53 0.00 45.55 2.29
1465 1545 7.646314 AGAGTTTGAAGACATTTCAGACAATG 58.354 34.615 11.53 0.00 39.67 2.82
1466 1546 7.814264 AGAGTTTGAAGACATTTCAGACAAT 57.186 32.000 11.53 0.00 36.39 2.71
1467 1547 7.630242 AAGAGTTTGAAGACATTTCAGACAA 57.370 32.000 11.53 0.00 36.39 3.18
1468 1548 8.908786 ATAAGAGTTTGAAGACATTTCAGACA 57.091 30.769 11.53 0.00 36.39 3.41
1483 1563 9.884465 CCTTCTGTTCACTTTTATAAGAGTTTG 57.116 33.333 5.94 0.00 35.30 2.93
1484 1564 9.847224 TCCTTCTGTTCACTTTTATAAGAGTTT 57.153 29.630 5.94 0.00 35.30 2.66
1485 1565 9.495572 CTCCTTCTGTTCACTTTTATAAGAGTT 57.504 33.333 5.94 0.00 35.30 3.01
1486 1566 8.652290 ACTCCTTCTGTTCACTTTTATAAGAGT 58.348 33.333 2.87 2.87 35.30 3.24
1489 1569 8.874816 GCTACTCCTTCTGTTCACTTTTATAAG 58.125 37.037 0.00 0.00 37.40 1.73
1490 1570 8.372459 TGCTACTCCTTCTGTTCACTTTTATAA 58.628 33.333 0.00 0.00 0.00 0.98
1491 1571 7.903145 TGCTACTCCTTCTGTTCACTTTTATA 58.097 34.615 0.00 0.00 0.00 0.98
1492 1572 6.769512 TGCTACTCCTTCTGTTCACTTTTAT 58.230 36.000 0.00 0.00 0.00 1.40
1493 1573 6.169557 TGCTACTCCTTCTGTTCACTTTTA 57.830 37.500 0.00 0.00 0.00 1.52
1494 1574 5.036117 TGCTACTCCTTCTGTTCACTTTT 57.964 39.130 0.00 0.00 0.00 2.27
1495 1575 4.101741 ACTGCTACTCCTTCTGTTCACTTT 59.898 41.667 0.00 0.00 0.00 2.66
1496 1576 3.643792 ACTGCTACTCCTTCTGTTCACTT 59.356 43.478 0.00 0.00 0.00 3.16
1497 1577 3.235200 ACTGCTACTCCTTCTGTTCACT 58.765 45.455 0.00 0.00 0.00 3.41
1498 1578 3.669251 ACTGCTACTCCTTCTGTTCAC 57.331 47.619 0.00 0.00 0.00 3.18
1499 1579 4.689612 AAACTGCTACTCCTTCTGTTCA 57.310 40.909 0.00 0.00 0.00 3.18
1500 1580 4.452795 GGAAAACTGCTACTCCTTCTGTTC 59.547 45.833 0.00 0.00 0.00 3.18
1501 1581 4.390264 GGAAAACTGCTACTCCTTCTGTT 58.610 43.478 0.00 0.00 0.00 3.16
1502 1582 3.244596 GGGAAAACTGCTACTCCTTCTGT 60.245 47.826 0.00 0.00 0.00 3.41
1503 1583 3.339141 GGGAAAACTGCTACTCCTTCTG 58.661 50.000 0.00 0.00 0.00 3.02
1504 1584 2.306219 GGGGAAAACTGCTACTCCTTCT 59.694 50.000 0.00 0.00 0.00 2.85
1505 1585 2.618302 GGGGGAAAACTGCTACTCCTTC 60.618 54.545 0.00 0.00 0.00 3.46
1506 1586 1.354705 GGGGGAAAACTGCTACTCCTT 59.645 52.381 0.00 0.00 0.00 3.36
1507 1587 0.992695 GGGGGAAAACTGCTACTCCT 59.007 55.000 0.00 0.00 0.00 3.69
1508 1588 3.571748 GGGGGAAAACTGCTACTCC 57.428 57.895 0.00 0.00 0.00 3.85
1557 1638 5.667539 ATACAAGCTGTGTCACTCATAGT 57.332 39.130 4.27 0.96 41.98 2.12
1558 1639 6.974932 AAATACAAGCTGTGTCACTCATAG 57.025 37.500 4.27 0.00 41.98 2.23
1559 1640 7.744087 AAAAATACAAGCTGTGTCACTCATA 57.256 32.000 4.27 0.00 41.98 2.15
1560 1641 6.639632 AAAAATACAAGCTGTGTCACTCAT 57.360 33.333 4.27 0.00 41.98 2.90
1614 1825 4.083537 CGCAGACAAAATAGTTACTGGCAA 60.084 41.667 0.00 0.00 0.00 4.52
1623 1834 3.257393 CTCTGCTCGCAGACAAAATAGT 58.743 45.455 17.01 0.00 46.80 2.12
1685 1896 0.033090 TCTGCTCGCAGATGCCTATG 59.967 55.000 17.01 0.00 46.80 2.23
1686 1897 2.434317 TCTGCTCGCAGATGCCTAT 58.566 52.632 17.01 0.00 46.80 2.57
1687 1898 3.939564 TCTGCTCGCAGATGCCTA 58.060 55.556 17.01 0.00 46.80 3.93
1694 1905 0.175302 ATCCTCAACTCTGCTCGCAG 59.825 55.000 12.54 12.54 44.86 5.18
1695 1906 0.108472 CATCCTCAACTCTGCTCGCA 60.108 55.000 0.00 0.00 0.00 5.10
1696 1907 1.427592 GCATCCTCAACTCTGCTCGC 61.428 60.000 0.00 0.00 0.00 5.03
1697 1908 0.809241 GGCATCCTCAACTCTGCTCG 60.809 60.000 0.00 0.00 35.03 5.03
1698 1909 0.540923 AGGCATCCTCAACTCTGCTC 59.459 55.000 0.00 0.00 35.03 4.26
1699 1910 1.871418 TAGGCATCCTCAACTCTGCT 58.129 50.000 0.00 0.00 34.61 4.24
1700 1911 2.698855 TTAGGCATCCTCAACTCTGC 57.301 50.000 0.00 0.00 34.61 4.26
1701 1912 4.101585 TGGTATTAGGCATCCTCAACTCTG 59.898 45.833 0.00 0.00 34.61 3.35
1702 1913 4.298626 TGGTATTAGGCATCCTCAACTCT 58.701 43.478 0.00 0.00 34.61 3.24
1703 1914 4.689612 TGGTATTAGGCATCCTCAACTC 57.310 45.455 0.00 0.00 34.61 3.01
1704 1915 5.653255 AATGGTATTAGGCATCCTCAACT 57.347 39.130 0.00 0.00 34.61 3.16
1705 1916 5.827797 TGAAATGGTATTAGGCATCCTCAAC 59.172 40.000 0.00 0.00 34.61 3.18
1706 1917 5.827797 GTGAAATGGTATTAGGCATCCTCAA 59.172 40.000 0.00 0.00 34.61 3.02
1707 1918 5.132648 AGTGAAATGGTATTAGGCATCCTCA 59.867 40.000 0.00 0.00 34.61 3.86
1708 1919 5.625150 AGTGAAATGGTATTAGGCATCCTC 58.375 41.667 0.00 0.00 34.61 3.71
1709 1920 5.132648 TGAGTGAAATGGTATTAGGCATCCT 59.867 40.000 0.00 0.00 37.71 3.24
1710 1921 5.239525 GTGAGTGAAATGGTATTAGGCATCC 59.760 44.000 0.00 0.00 0.00 3.51
1711 1922 5.050091 CGTGAGTGAAATGGTATTAGGCATC 60.050 44.000 0.00 0.00 0.00 3.91
1712 1923 4.816385 CGTGAGTGAAATGGTATTAGGCAT 59.184 41.667 0.00 0.00 0.00 4.40
1713 1924 4.188462 CGTGAGTGAAATGGTATTAGGCA 58.812 43.478 0.00 0.00 0.00 4.75
1714 1925 4.189231 ACGTGAGTGAAATGGTATTAGGC 58.811 43.478 0.00 0.00 46.97 3.93
1730 1941 9.279904 TGTTTAGAATTTTGTACAAAACGTGAG 57.720 29.630 30.66 0.00 42.32 3.51
1731 1942 9.790389 ATGTTTAGAATTTTGTACAAAACGTGA 57.210 25.926 30.66 16.62 42.32 4.35
1732 1943 9.828220 CATGTTTAGAATTTTGTACAAAACGTG 57.172 29.630 30.66 23.43 42.32 4.49
1733 1944 9.790389 TCATGTTTAGAATTTTGTACAAAACGT 57.210 25.926 30.66 22.64 42.32 3.99
1742 1953 9.965902 ACTCCTAGATCATGTTTAGAATTTTGT 57.034 29.630 0.00 0.00 0.00 2.83
1745 1956 9.771534 GCTACTCCTAGATCATGTTTAGAATTT 57.228 33.333 0.00 0.00 0.00 1.82
1746 1957 9.153479 AGCTACTCCTAGATCATGTTTAGAATT 57.847 33.333 0.00 0.00 0.00 2.17
1747 1958 8.719645 AGCTACTCCTAGATCATGTTTAGAAT 57.280 34.615 0.00 0.00 0.00 2.40
1748 1959 9.815306 ATAGCTACTCCTAGATCATGTTTAGAA 57.185 33.333 0.00 0.00 0.00 2.10
1749 1960 9.815306 AATAGCTACTCCTAGATCATGTTTAGA 57.185 33.333 0.00 0.00 0.00 2.10
1779 1990 9.801873 GTCATTACAGTGGCACATATAAAAATT 57.198 29.630 21.41 0.00 44.52 1.82
1780 1991 8.128582 CGTCATTACAGTGGCACATATAAAAAT 58.871 33.333 21.41 6.49 44.52 1.82
1781 1992 7.334671 TCGTCATTACAGTGGCACATATAAAAA 59.665 33.333 21.41 4.39 44.52 1.94
1782 1993 6.819146 TCGTCATTACAGTGGCACATATAAAA 59.181 34.615 21.41 5.45 44.52 1.52
1783 1994 6.342111 TCGTCATTACAGTGGCACATATAAA 58.658 36.000 21.41 6.87 44.52 1.40
1784 1995 5.908341 TCGTCATTACAGTGGCACATATAA 58.092 37.500 21.41 14.49 44.52 0.98
1788 1999 2.760634 TCGTCATTACAGTGGCACAT 57.239 45.000 21.41 10.07 44.52 3.21
1802 2013 7.221838 GGTGAAATTTCAAGTTTTCATTCGTCA 59.778 33.333 22.07 0.00 42.12 4.35
1811 2022 9.230122 AGAACAAATGGTGAAATTTCAAGTTTT 57.770 25.926 22.07 16.88 39.21 2.43
1814 2025 7.555087 TGAGAACAAATGGTGAAATTTCAAGT 58.445 30.769 22.07 11.02 39.21 3.16
1815 2026 8.597662 ATGAGAACAAATGGTGAAATTTCAAG 57.402 30.769 22.07 10.46 39.21 3.02
1823 2034 4.468713 TGTGGATGAGAACAAATGGTGAA 58.531 39.130 0.00 0.00 0.00 3.18
1824 2035 4.074259 CTGTGGATGAGAACAAATGGTGA 58.926 43.478 0.00 0.00 0.00 4.02
1827 2038 2.821378 TGCTGTGGATGAGAACAAATGG 59.179 45.455 0.00 0.00 0.00 3.16
1828 2039 4.713824 ATGCTGTGGATGAGAACAAATG 57.286 40.909 0.00 0.00 0.00 2.32
1829 2040 4.081862 CCAATGCTGTGGATGAGAACAAAT 60.082 41.667 0.22 0.00 41.65 2.32
1830 2041 3.256383 CCAATGCTGTGGATGAGAACAAA 59.744 43.478 0.22 0.00 41.65 2.83
1831 2042 2.821378 CCAATGCTGTGGATGAGAACAA 59.179 45.455 0.22 0.00 41.65 2.83
1832 2043 2.224843 ACCAATGCTGTGGATGAGAACA 60.225 45.455 12.54 0.00 41.65 3.18
1833 2044 2.440409 ACCAATGCTGTGGATGAGAAC 58.560 47.619 12.54 0.00 41.65 3.01
1834 2045 2.885135 ACCAATGCTGTGGATGAGAA 57.115 45.000 12.54 0.00 41.65 2.87
1835 2046 2.885135 AACCAATGCTGTGGATGAGA 57.115 45.000 12.54 0.00 41.65 3.27
1836 2047 3.877559 TCTAACCAATGCTGTGGATGAG 58.122 45.455 12.54 6.79 41.65 2.90
1837 2048 3.998913 TCTAACCAATGCTGTGGATGA 57.001 42.857 12.54 5.29 41.65 2.92
1838 2049 4.735578 GCAATCTAACCAATGCTGTGGATG 60.736 45.833 12.54 3.38 41.65 3.51
1839 2050 3.382546 GCAATCTAACCAATGCTGTGGAT 59.617 43.478 12.54 4.05 41.65 3.41
1840 2051 2.754552 GCAATCTAACCAATGCTGTGGA 59.245 45.455 12.54 0.00 41.65 4.02
1841 2052 2.492881 TGCAATCTAACCAATGCTGTGG 59.507 45.455 4.84 4.84 44.92 4.17
1842 2053 3.853831 TGCAATCTAACCAATGCTGTG 57.146 42.857 0.00 0.00 39.49 3.66
1843 2054 3.573538 TGTTGCAATCTAACCAATGCTGT 59.426 39.130 0.59 0.00 39.49 4.40
1844 2055 4.177165 TGTTGCAATCTAACCAATGCTG 57.823 40.909 0.59 0.00 39.49 4.41
1845 2056 5.653769 ACTATGTTGCAATCTAACCAATGCT 59.346 36.000 0.59 0.00 39.49 3.79
1846 2057 5.894807 ACTATGTTGCAATCTAACCAATGC 58.105 37.500 0.59 0.00 39.22 3.56
1847 2058 7.537715 TGAACTATGTTGCAATCTAACCAATG 58.462 34.615 0.59 0.00 0.00 2.82
1848 2059 7.701539 TGAACTATGTTGCAATCTAACCAAT 57.298 32.000 0.59 0.00 0.00 3.16
1849 2060 7.367285 GTTGAACTATGTTGCAATCTAACCAA 58.633 34.615 0.59 0.00 0.00 3.67
1850 2061 6.072175 GGTTGAACTATGTTGCAATCTAACCA 60.072 38.462 0.59 0.00 34.40 3.67
1851 2062 6.322491 GGTTGAACTATGTTGCAATCTAACC 58.678 40.000 0.59 7.96 0.00 2.85
1852 2063 6.021596 CGGTTGAACTATGTTGCAATCTAAC 58.978 40.000 0.59 2.95 0.00 2.34
1853 2064 5.391523 GCGGTTGAACTATGTTGCAATCTAA 60.392 40.000 0.59 0.00 0.00 2.10
1854 2065 4.094294 GCGGTTGAACTATGTTGCAATCTA 59.906 41.667 0.59 0.00 0.00 1.98
1855 2066 3.119849 GCGGTTGAACTATGTTGCAATCT 60.120 43.478 0.59 0.00 0.00 2.40
1856 2067 3.171277 GCGGTTGAACTATGTTGCAATC 58.829 45.455 0.59 0.00 0.00 2.67
1857 2068 2.414029 CGCGGTTGAACTATGTTGCAAT 60.414 45.455 0.59 0.00 0.00 3.56
1858 2069 1.069568 CGCGGTTGAACTATGTTGCAA 60.070 47.619 0.00 0.00 0.00 4.08
1875 2086 4.720530 AGTAAAGGAACAGTTAAACGCG 57.279 40.909 3.53 3.53 0.00 6.01
1902 2113 4.289342 CTCAGAATCTGTAGCAGTCATCG 58.711 47.826 10.36 0.00 32.61 3.84
2071 2309 4.223700 ACAACATTCTCAGATACTGCTCCA 59.776 41.667 0.00 0.00 0.00 3.86
2170 2408 1.820906 GCAAGATCCGATGGCAGCA 60.821 57.895 2.73 0.00 0.00 4.41
2285 2523 1.005512 TCGTTAGCTGCTCGGCAAA 60.006 52.632 4.91 0.00 38.41 3.68
2365 2603 7.168637 CCATTTTTCAGAACAACAATCTGTGAG 59.831 37.037 3.72 0.00 43.77 3.51
2442 2680 6.036191 GCTTCATAAGTACTACAAGGCTTGTC 59.964 42.308 34.23 20.52 44.12 3.18
2455 2693 5.001232 TGTTCACCCAAGCTTCATAAGTAC 58.999 41.667 0.00 0.00 0.00 2.73
2458 2696 5.882557 AGTATGTTCACCCAAGCTTCATAAG 59.117 40.000 0.00 0.00 0.00 1.73
2484 2730 8.626526 TCTTCTTCCACAACAAAAGTATAAACC 58.373 33.333 0.00 0.00 0.00 3.27
2581 2829 1.063469 GTGACCACCTGTTTGTTGTCG 59.937 52.381 0.00 0.00 34.53 4.35
2705 2953 2.356382 ACCTAAGAGCGAATCAGACGAG 59.644 50.000 0.00 0.00 0.00 4.18
2752 3000 5.288543 ACAGCGAATTCTTGCTTCTTTAG 57.711 39.130 5.23 0.00 40.03 1.85
2775 3023 4.177026 GGAATCGAGTTATGGATGGATCG 58.823 47.826 0.00 0.00 0.00 3.69
2823 3071 0.531200 AGGGCTCGGAAGTTAGAACG 59.469 55.000 0.00 0.00 0.00 3.95
2856 3104 6.663944 AAACTATCTTGTGGACGAATAAGC 57.336 37.500 0.00 0.00 0.00 3.09
2968 3216 5.824421 AGACAGAGGGTGAAATGATGAAAT 58.176 37.500 0.00 0.00 0.00 2.17
3189 3443 2.100197 TCATGGAAGAATCGACGGACT 58.900 47.619 0.00 0.00 0.00 3.85
3394 3648 8.387354 CAAAAGACGGCTTCAAAGTTTAAATTT 58.613 29.630 2.63 0.00 31.82 1.82
3401 3655 2.758423 ACCAAAAGACGGCTTCAAAGTT 59.242 40.909 2.63 0.00 31.82 2.66
3413 3667 6.528072 GCTATGCAATAACAGAACCAAAAGAC 59.472 38.462 0.00 0.00 0.00 3.01
3543 3799 5.414789 TGTCAGGCTAACAGTGCTTATTA 57.585 39.130 0.00 0.00 0.00 0.98
3561 3817 5.908916 TTATTGTTCGATGAACGTTGTCA 57.091 34.783 5.00 0.00 44.55 3.58
3565 3821 5.938322 AGCAATTATTGTTCGATGAACGTT 58.062 33.333 0.00 0.00 44.55 3.99
3623 3880 5.688814 ATTCCAGAAGATCACATCTCACA 57.311 39.130 0.00 0.00 39.08 3.58
3634 3891 6.735556 AGATAAACCACCAATTCCAGAAGAT 58.264 36.000 0.00 0.00 0.00 2.40
3638 3895 7.339212 CACATTAGATAAACCACCAATTCCAGA 59.661 37.037 0.00 0.00 0.00 3.86
3665 3922 1.618837 AGCCAAGCTTCAACTCTCGTA 59.381 47.619 0.00 0.00 33.89 3.43
3695 3952 9.401058 CCATCTCAGATTTTCAGGTAATAAACT 57.599 33.333 0.00 0.00 0.00 2.66
3725 3982 5.523369 ACAAGAGCTGCAAAGTTTTATCAC 58.477 37.500 1.02 0.00 0.00 3.06
3750 4007 4.037923 GCCAAACTGAATGAACAAAGGAGA 59.962 41.667 0.00 0.00 0.00 3.71
3763 4020 6.581712 AGCAAGAAAATTAAGCCAAACTGAA 58.418 32.000 0.00 0.00 0.00 3.02
3771 4028 7.386025 ACTCAATTGAAGCAAGAAAATTAAGCC 59.614 33.333 9.88 0.00 0.00 4.35
3832 4089 8.595421 TCAACAGTTTAAGTACCACCACATATA 58.405 33.333 0.00 0.00 0.00 0.86
3833 4090 7.455058 TCAACAGTTTAAGTACCACCACATAT 58.545 34.615 0.00 0.00 0.00 1.78
3874 4131 5.864418 ATCTCAATCCCAATGGACAATTG 57.136 39.130 0.00 3.24 45.58 2.32
3909 4168 3.828451 CCAGAATTCCACACATCCAAGTT 59.172 43.478 0.65 0.00 0.00 2.66
3938 4197 6.150140 GCATCCTTGATCAACTTTCTACTTGT 59.850 38.462 3.38 0.00 0.00 3.16
3950 4209 5.635278 TCCTGAATAGCATCCTTGATCAA 57.365 39.130 8.12 8.12 0.00 2.57
3957 4216 4.723789 TCTCCTTTTCCTGAATAGCATCCT 59.276 41.667 0.00 0.00 0.00 3.24
3999 4258 9.064706 ACCAAGATTCATAGCTAATCTCATTTG 57.935 33.333 10.03 5.71 41.68 2.32
4014 4273 6.040842 GTGCACCCAAATATACCAAGATTCAT 59.959 38.462 5.22 0.00 0.00 2.57
4054 4316 7.217200 GGTTGAGAGCTACCATCATAATGTTA 58.783 38.462 0.00 0.00 39.36 2.41
4133 4397 3.833559 ACTTGATCATTGGTTCCCCTT 57.166 42.857 0.00 0.00 0.00 3.95
4201 4465 5.919272 ACATCGTCTTTATCGTCGAGATA 57.081 39.130 0.00 0.00 40.66 1.98
4220 4484 4.263905 TGGAGCCTTTATTCCAGACAACAT 60.264 41.667 0.00 0.00 38.53 2.71
4245 4510 4.404691 CCAGAACTGGGCAGAACC 57.595 61.111 12.54 0.00 46.81 3.62
4279 4545 2.228822 CCTTTGCAGTATCGGCTTTGTT 59.771 45.455 0.00 0.00 0.00 2.83
4293 4559 4.037446 GTCTAAAACACCACATCCTTTGCA 59.963 41.667 0.00 0.00 0.00 4.08
4315 4581 5.110814 TGAAGAATCATTAATCCGTGGGT 57.889 39.130 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.