Multiple sequence alignment - TraesCS4A01G097300

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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 TraesCS4A01G097300 chr4A 100.000 2360 0 0 1 2360 107232284 107229925 0.000000e+00 4359.0
1 TraesCS4A01G097300 chr4A 92.582 337 24 1 1393 1728 720024492 720024156 1.270000e-132 483.0
2 TraesCS4A01G097300 chr3D 97.038 1384 41 0 1 1384 69660429 69661812 0.000000e+00 2329.0
3 TraesCS4A01G097300 chr6A 96.532 1384 45 1 1 1384 502339292 502340672 0.000000e+00 2287.0
4 TraesCS4A01G097300 chr6A 96.570 1312 45 0 73 1384 532870195 532871506 0.000000e+00 2174.0
5 TraesCS4A01G097300 chr7B 96.168 1383 52 1 1 1383 84527265 84528646 0.000000e+00 2259.0
6 TraesCS4A01G097300 chr7B 93.571 280 18 0 1446 1725 207772070 207772349 3.630000e-113 418.0
7 TraesCS4A01G097300 chr7B 84.000 225 35 1 1498 1721 637866636 637866860 5.110000e-52 215.0
8 TraesCS4A01G097300 chr3A 95.743 1386 58 1 1 1386 681100867 681099483 0.000000e+00 2231.0
9 TraesCS4A01G097300 chr3A 89.796 49 3 2 2122 2169 21284205 21284158 7.040000e-06 62.1
10 TraesCS4A01G097300 chr2B 96.077 1351 51 1 40 1388 717931261 717929911 0.000000e+00 2200.0
11 TraesCS4A01G097300 chr2B 78.733 221 33 3 1501 1721 108636706 108636500 4.090000e-28 135.0
12 TraesCS4A01G097300 chr2B 95.238 42 2 0 2121 2162 785930575 785930534 1.510000e-07 67.6
13 TraesCS4A01G097300 chr2A 94.801 1385 63 5 1 1384 148651647 148653023 0.000000e+00 2150.0
14 TraesCS4A01G097300 chr2A 84.000 225 35 1 1498 1721 24902230 24902006 5.110000e-52 215.0
15 TraesCS4A01G097300 chr6B 94.436 1384 77 0 1 1384 695056653 695058036 0.000000e+00 2130.0
16 TraesCS4A01G097300 chr5B 94.440 1385 76 1 1 1385 633276927 633278310 0.000000e+00 2130.0
17 TraesCS4A01G097300 chr5B 84.000 225 35 1 1498 1721 443264054 443263830 5.110000e-52 215.0
18 TraesCS4A01G097300 chr4D 90.016 621 46 12 1752 2358 358084430 358085048 0.000000e+00 789.0
19 TraesCS4A01G097300 chr4B 83.465 635 77 15 1741 2357 441327300 441327924 1.220000e-157 566.0
20 TraesCS4A01G097300 chr1A 81.513 238 43 1 1484 1721 390802176 390802412 6.660000e-46 195.0
21 TraesCS4A01G097300 chr7D 85.106 188 23 4 1463 1645 6721298 6721485 1.110000e-43 187.0
22 TraesCS4A01G097300 chr7A 81.609 87 13 3 2087 2171 112968672 112968587 4.210000e-08 69.4
23 TraesCS4A01G097300 chr7A 92.683 41 2 1 2122 2161 635682685 635682725 9.110000e-05 58.4
24 TraesCS4A01G097300 chr1B 88.000 50 6 0 2122 2171 61464050 61464001 2.530000e-05 60.2


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 TraesCS4A01G097300 chr4A 107229925 107232284 2359 True 4359 4359 100.000 1 2360 1 chr4A.!!$R1 2359
1 TraesCS4A01G097300 chr3D 69660429 69661812 1383 False 2329 2329 97.038 1 1384 1 chr3D.!!$F1 1383
2 TraesCS4A01G097300 chr6A 502339292 502340672 1380 False 2287 2287 96.532 1 1384 1 chr6A.!!$F1 1383
3 TraesCS4A01G097300 chr6A 532870195 532871506 1311 False 2174 2174 96.570 73 1384 1 chr6A.!!$F2 1311
4 TraesCS4A01G097300 chr7B 84527265 84528646 1381 False 2259 2259 96.168 1 1383 1 chr7B.!!$F1 1382
5 TraesCS4A01G097300 chr3A 681099483 681100867 1384 True 2231 2231 95.743 1 1386 1 chr3A.!!$R2 1385
6 TraesCS4A01G097300 chr2B 717929911 717931261 1350 True 2200 2200 96.077 40 1388 1 chr2B.!!$R2 1348
7 TraesCS4A01G097300 chr2A 148651647 148653023 1376 False 2150 2150 94.801 1 1384 1 chr2A.!!$F1 1383
8 TraesCS4A01G097300 chr6B 695056653 695058036 1383 False 2130 2130 94.436 1 1384 1 chr6B.!!$F1 1383
9 TraesCS4A01G097300 chr5B 633276927 633278310 1383 False 2130 2130 94.440 1 1385 1 chr5B.!!$F1 1384
10 TraesCS4A01G097300 chr4D 358084430 358085048 618 False 789 789 90.016 1752 2358 1 chr4D.!!$F1 606
11 TraesCS4A01G097300 chr4B 441327300 441327924 624 False 566 566 83.465 1741 2357 1 chr4B.!!$F1 616

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
157 158 1.62834 ACCTCATTGATCCGGTGACAA 59.372 47.619 0.0 7.25 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 1623 0.031449 GATCTGCGCTGGTCTCCTAC 59.969 60.0 19.17 0.0 0.0 3.18 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
157 158 1.628340 ACCTCATTGATCCGGTGACAA 59.372 47.619 0.00 7.25 0.00 3.18
220 221 4.398319 AGTGGATGTTCGAAGGATTTTGT 58.602 39.130 0.00 0.00 0.00 2.83
413 414 2.619074 GGAACTTAGTCTGCCCAGCAAT 60.619 50.000 0.00 0.00 38.41 3.56
438 439 3.428746 AAAATATTTATGTGGCGCGCA 57.571 38.095 34.42 16.55 0.00 6.09
461 462 1.833630 CCAGAGTGCTATTCCCTGTCA 59.166 52.381 0.00 0.00 0.00 3.58
503 504 7.750229 AGCACTTGAAAATGAATCTGAGTTA 57.250 32.000 0.00 0.00 0.00 2.24
636 637 2.664402 AAGTTGACAAGGCAGGTGAT 57.336 45.000 0.00 0.00 0.00 3.06
934 937 4.620567 CGGGATTTGATAGTGACACACTCA 60.621 45.833 8.59 7.15 41.21 3.41
956 959 3.004734 ACAGCAACATTTGGAGCAGTTAC 59.995 43.478 0.00 0.00 0.00 2.50
1025 1029 2.069273 CCTTTGCTTCGACTCGTTCAT 58.931 47.619 0.00 0.00 0.00 2.57
1039 1043 5.419542 ACTCGTTCATAGCAGAAGCAATTA 58.580 37.500 0.00 0.00 45.49 1.40
1063 1067 5.422012 ACAGTGAGGTTTGGTTTGAATCTTT 59.578 36.000 0.00 0.00 0.00 2.52
1122 1126 0.249398 ATAGCGTGGAGGTGGTGAAC 59.751 55.000 0.00 0.00 0.00 3.18
1168 1172 6.816136 TCTTCAGTCGCTTCATCCATTATAA 58.184 36.000 0.00 0.00 0.00 0.98
1198 1202 8.784043 ACTGTTATTTCATGTCACTAGGTTTTC 58.216 33.333 0.00 0.00 0.00 2.29
1279 1283 5.473846 GCAAGGTTAGCTAGGTTTTCTTCTT 59.526 40.000 0.00 0.00 0.00 2.52
1300 1304 4.545208 TCGAGTGTTTGGATGGATAACA 57.455 40.909 0.00 0.00 0.00 2.41
1333 1337 7.747690 TGAGGTTATCCCTTTACTTGTAAACA 58.252 34.615 2.22 0.00 46.51 2.83
1399 1403 1.698506 AAAAAGGTCCGGCAACATCA 58.301 45.000 0.00 0.00 0.00 3.07
1400 1404 1.698506 AAAAGGTCCGGCAACATCAA 58.301 45.000 0.00 0.00 0.00 2.57
1401 1405 1.247567 AAAGGTCCGGCAACATCAAG 58.752 50.000 0.00 0.00 0.00 3.02
1402 1406 0.400213 AAGGTCCGGCAACATCAAGA 59.600 50.000 0.00 0.00 0.00 3.02
1403 1407 0.321653 AGGTCCGGCAACATCAAGAC 60.322 55.000 0.00 0.00 0.00 3.01
1404 1408 0.321653 GGTCCGGCAACATCAAGACT 60.322 55.000 0.00 0.00 0.00 3.24
1405 1409 1.523758 GTCCGGCAACATCAAGACTT 58.476 50.000 0.00 0.00 0.00 3.01
1406 1410 1.880027 GTCCGGCAACATCAAGACTTT 59.120 47.619 0.00 0.00 0.00 2.66
1407 1411 1.879380 TCCGGCAACATCAAGACTTTG 59.121 47.619 0.00 0.00 35.57 2.77
1408 1412 1.666888 CCGGCAACATCAAGACTTTGC 60.667 52.381 8.31 8.31 42.98 3.68
1412 1416 3.826466 GCAACATCAAGACTTTGCCTAC 58.174 45.455 6.30 0.00 38.74 3.18
1413 1417 3.253188 GCAACATCAAGACTTTGCCTACA 59.747 43.478 6.30 0.00 38.74 2.74
1414 1418 4.614535 GCAACATCAAGACTTTGCCTACAG 60.615 45.833 6.30 0.00 38.74 2.74
1415 1419 3.077359 ACATCAAGACTTTGCCTACAGC 58.923 45.455 0.00 0.00 44.14 4.40
1416 1420 3.244700 ACATCAAGACTTTGCCTACAGCT 60.245 43.478 0.00 0.00 44.23 4.24
1417 1421 2.771089 TCAAGACTTTGCCTACAGCTG 58.229 47.619 13.48 13.48 44.23 4.24
1418 1422 2.104792 TCAAGACTTTGCCTACAGCTGT 59.895 45.455 25.12 25.12 44.23 4.40
1419 1423 3.323691 TCAAGACTTTGCCTACAGCTGTA 59.676 43.478 24.63 24.63 44.23 2.74
1420 1424 3.320673 AGACTTTGCCTACAGCTGTAC 57.679 47.619 22.67 14.32 44.23 2.90
1421 1425 2.028020 AGACTTTGCCTACAGCTGTACC 60.028 50.000 22.67 16.02 44.23 3.34
1422 1426 1.697432 ACTTTGCCTACAGCTGTACCA 59.303 47.619 22.67 18.27 44.23 3.25
1423 1427 2.289694 ACTTTGCCTACAGCTGTACCAG 60.290 50.000 22.67 14.85 44.23 4.00
1424 1428 0.613260 TTGCCTACAGCTGTACCAGG 59.387 55.000 24.30 24.30 44.23 4.45
1425 1429 1.153349 GCCTACAGCTGTACCAGGC 60.153 63.158 32.80 32.80 39.32 4.85
1426 1430 1.617947 GCCTACAGCTGTACCAGGCT 61.618 60.000 36.18 12.16 41.67 4.58
1430 1434 2.985456 AGCTGTACCAGGCTGAGC 59.015 61.111 17.94 16.71 37.41 4.26
1431 1435 1.915266 AGCTGTACCAGGCTGAGCA 60.915 57.895 22.96 14.43 37.41 4.26
1432 1436 1.222936 GCTGTACCAGGCTGAGCAT 59.777 57.895 17.94 0.00 31.21 3.79
1433 1437 0.813210 GCTGTACCAGGCTGAGCATC 60.813 60.000 17.94 3.71 31.21 3.91
1434 1438 3.449489 GCTGTACCAGGCTGAGCATCA 62.449 57.143 17.94 6.84 35.56 3.07
1453 1457 3.770625 GCTCCTGTTAGCTCCTTCC 57.229 57.895 0.00 0.00 39.50 3.46
1454 1458 1.199615 GCTCCTGTTAGCTCCTTCCT 58.800 55.000 0.00 0.00 39.50 3.36
1455 1459 1.138069 GCTCCTGTTAGCTCCTTCCTC 59.862 57.143 0.00 0.00 39.50 3.71
1456 1460 1.407258 CTCCTGTTAGCTCCTTCCTCG 59.593 57.143 0.00 0.00 0.00 4.63
1457 1461 0.179097 CCTGTTAGCTCCTTCCTCGC 60.179 60.000 0.00 0.00 0.00 5.03
1458 1462 0.820871 CTGTTAGCTCCTTCCTCGCT 59.179 55.000 0.00 0.00 37.77 4.93
1459 1463 1.205893 CTGTTAGCTCCTTCCTCGCTT 59.794 52.381 0.00 0.00 35.33 4.68
1460 1464 1.066858 TGTTAGCTCCTTCCTCGCTTG 60.067 52.381 0.00 0.00 35.33 4.01
1461 1465 0.537188 TTAGCTCCTTCCTCGCTTGG 59.463 55.000 0.00 0.00 35.33 3.61
1462 1466 1.961180 TAGCTCCTTCCTCGCTTGGC 61.961 60.000 0.00 0.00 35.33 4.52
1463 1467 2.124942 CTCCTTCCTCGCTTGGCC 60.125 66.667 0.00 0.00 0.00 5.36
1464 1468 3.689002 CTCCTTCCTCGCTTGGCCC 62.689 68.421 0.00 0.00 0.00 5.80
1474 1478 4.020617 CTTGGCCCGCTGGACTCA 62.021 66.667 0.18 0.00 42.00 3.41
1475 1479 3.551496 CTTGGCCCGCTGGACTCAA 62.551 63.158 0.18 0.13 42.00 3.02
1476 1480 2.826777 CTTGGCCCGCTGGACTCAAT 62.827 60.000 0.18 0.00 42.00 2.57
1477 1481 2.044946 GGCCCGCTGGACTCAATT 60.045 61.111 0.00 0.00 36.35 2.32
1478 1482 2.115291 GGCCCGCTGGACTCAATTC 61.115 63.158 0.00 0.00 36.35 2.17
1479 1483 1.078143 GCCCGCTGGACTCAATTCT 60.078 57.895 0.00 0.00 0.00 2.40
1480 1484 1.372087 GCCCGCTGGACTCAATTCTG 61.372 60.000 0.00 0.00 0.00 3.02
1481 1485 0.250234 CCCGCTGGACTCAATTCTGA 59.750 55.000 0.00 0.00 0.00 3.27
1482 1486 1.134280 CCCGCTGGACTCAATTCTGAT 60.134 52.381 0.00 0.00 0.00 2.90
1483 1487 1.938577 CCGCTGGACTCAATTCTGATG 59.061 52.381 0.00 0.00 0.00 3.07
1484 1488 1.329906 CGCTGGACTCAATTCTGATGC 59.670 52.381 0.00 0.00 0.00 3.91
1485 1489 2.362736 GCTGGACTCAATTCTGATGCA 58.637 47.619 0.00 0.00 0.00 3.96
1486 1490 2.751259 GCTGGACTCAATTCTGATGCAA 59.249 45.455 0.00 0.00 0.00 4.08
1487 1491 3.380637 GCTGGACTCAATTCTGATGCAAT 59.619 43.478 0.00 0.00 0.00 3.56
1488 1492 4.497674 GCTGGACTCAATTCTGATGCAATC 60.498 45.833 0.00 0.00 45.83 2.67
1501 1505 2.676632 TGCAATCATGGCATCCAAAC 57.323 45.000 0.00 0.00 36.95 2.93
1502 1506 1.900486 TGCAATCATGGCATCCAAACA 59.100 42.857 0.00 0.00 36.95 2.83
1503 1507 2.273557 GCAATCATGGCATCCAAACAC 58.726 47.619 0.00 0.00 36.95 3.32
1504 1508 2.896168 CAATCATGGCATCCAAACACC 58.104 47.619 0.00 0.00 36.95 4.16
1505 1509 2.234168 CAATCATGGCATCCAAACACCA 59.766 45.455 0.00 0.00 36.95 4.17
1506 1510 1.255882 TCATGGCATCCAAACACCAC 58.744 50.000 0.00 0.00 36.95 4.16
1507 1511 0.109179 CATGGCATCCAAACACCACG 60.109 55.000 0.00 0.00 36.95 4.94
1508 1512 0.539438 ATGGCATCCAAACACCACGT 60.539 50.000 0.00 0.00 36.95 4.49
1509 1513 0.108774 TGGCATCCAAACACCACGTA 59.891 50.000 0.00 0.00 0.00 3.57
1510 1514 0.802494 GGCATCCAAACACCACGTAG 59.198 55.000 0.00 0.00 0.00 3.51
1511 1515 0.802494 GCATCCAAACACCACGTAGG 59.198 55.000 0.00 0.00 45.67 3.18
1523 1527 3.900446 ACGTAGGTGAAAACCTCCG 57.100 52.632 8.16 8.16 43.56 4.63
1524 1528 1.331214 ACGTAGGTGAAAACCTCCGA 58.669 50.000 15.57 0.00 40.98 4.55
1525 1529 1.271656 ACGTAGGTGAAAACCTCCGAG 59.728 52.381 15.57 2.95 40.98 4.63
1526 1530 1.403780 CGTAGGTGAAAACCTCCGAGG 60.404 57.143 13.31 13.31 40.98 4.63
1536 1540 2.887790 CCTCCGAGGTGATCTGACA 58.112 57.895 6.24 0.00 0.00 3.58
1537 1541 0.457851 CCTCCGAGGTGATCTGACAC 59.542 60.000 6.24 0.00 39.70 3.67
1538 1542 1.468985 CTCCGAGGTGATCTGACACT 58.531 55.000 0.00 0.00 40.22 3.55
1539 1543 1.133982 CTCCGAGGTGATCTGACACTG 59.866 57.143 0.00 0.00 40.22 3.66
1540 1544 0.459237 CCGAGGTGATCTGACACTGC 60.459 60.000 0.00 0.00 40.22 4.40
1541 1545 0.459237 CGAGGTGATCTGACACTGCC 60.459 60.000 0.00 0.00 40.22 4.85
1542 1546 0.459237 GAGGTGATCTGACACTGCCG 60.459 60.000 0.00 0.00 40.22 5.69
1543 1547 1.188219 AGGTGATCTGACACTGCCGT 61.188 55.000 0.00 0.00 40.22 5.68
1544 1548 0.737715 GGTGATCTGACACTGCCGTC 60.738 60.000 0.00 0.00 40.22 4.79
1545 1549 1.073216 GTGATCTGACACTGCCGTCG 61.073 60.000 0.00 0.00 38.84 5.12
1546 1550 1.213013 GATCTGACACTGCCGTCGT 59.787 57.895 0.00 0.00 38.84 4.34
1547 1551 0.798771 GATCTGACACTGCCGTCGTC 60.799 60.000 0.00 4.66 38.84 4.20
1548 1552 1.244697 ATCTGACACTGCCGTCGTCT 61.245 55.000 10.44 0.00 38.84 4.18
1549 1553 1.442857 CTGACACTGCCGTCGTCTC 60.443 63.158 10.44 0.00 38.84 3.36
1550 1554 2.126424 GACACTGCCGTCGTCTCC 60.126 66.667 0.00 0.00 0.00 3.71
1551 1555 3.948086 GACACTGCCGTCGTCTCCG 62.948 68.421 0.00 0.00 0.00 4.63
1552 1556 4.039357 CACTGCCGTCGTCTCCGT 62.039 66.667 0.00 0.00 35.01 4.69
1553 1557 3.735029 ACTGCCGTCGTCTCCGTC 61.735 66.667 0.00 0.00 35.01 4.79
1554 1558 4.813526 CTGCCGTCGTCTCCGTCG 62.814 72.222 0.00 0.00 43.51 5.12
1556 1560 4.808238 GCCGTCGTCTCCGTCGTC 62.808 72.222 0.00 0.00 42.61 4.20
1557 1561 4.495939 CCGTCGTCTCCGTCGTCG 62.496 72.222 0.00 0.00 42.61 5.12
1559 1563 4.808238 GTCGTCTCCGTCGTCGCC 62.808 72.222 0.00 0.00 35.54 5.54
1561 1565 4.394078 CGTCTCCGTCGTCGCCAA 62.394 66.667 0.00 0.00 35.54 4.52
1562 1566 2.049802 GTCTCCGTCGTCGCCAAA 60.050 61.111 0.00 0.00 35.54 3.28
1563 1567 1.662446 GTCTCCGTCGTCGCCAAAA 60.662 57.895 0.00 0.00 35.54 2.44
1564 1568 1.662446 TCTCCGTCGTCGCCAAAAC 60.662 57.895 0.00 0.00 35.54 2.43
1565 1569 2.662527 TCCGTCGTCGCCAAAACC 60.663 61.111 0.00 0.00 35.54 3.27
1566 1570 3.719144 CCGTCGTCGCCAAAACCC 61.719 66.667 0.00 0.00 35.54 4.11
1567 1571 3.719144 CGTCGTCGCCAAAACCCC 61.719 66.667 0.00 0.00 0.00 4.95
1568 1572 2.592287 GTCGTCGCCAAAACCCCA 60.592 61.111 0.00 0.00 0.00 4.96
1569 1573 2.188161 GTCGTCGCCAAAACCCCAA 61.188 57.895 0.00 0.00 0.00 4.12
1570 1574 1.894756 TCGTCGCCAAAACCCCAAG 60.895 57.895 0.00 0.00 0.00 3.61
1571 1575 2.914908 CGTCGCCAAAACCCCAAGG 61.915 63.158 0.00 0.00 40.04 3.61
1572 1576 2.915137 TCGCCAAAACCCCAAGGC 60.915 61.111 0.00 0.00 43.61 4.35
1573 1577 4.002506 CGCCAAAACCCCAAGGCC 62.003 66.667 0.00 0.00 44.18 5.19
1574 1578 4.002506 GCCAAAACCCCAAGGCCG 62.003 66.667 0.00 0.00 41.25 6.13
1575 1579 3.310307 CCAAAACCCCAAGGCCGG 61.310 66.667 0.00 0.00 36.11 6.13
1576 1580 3.310307 CAAAACCCCAAGGCCGGG 61.310 66.667 12.41 12.41 46.94 5.73
1600 1604 3.161557 GACCAGCTGTCCCCTTGT 58.838 61.111 13.81 0.51 38.09 3.16
1601 1605 1.456287 GACCAGCTGTCCCCTTGTT 59.544 57.895 13.81 0.00 38.09 2.83
1602 1606 0.606673 GACCAGCTGTCCCCTTGTTC 60.607 60.000 13.81 0.00 38.09 3.18
1603 1607 1.352622 ACCAGCTGTCCCCTTGTTCA 61.353 55.000 13.81 0.00 0.00 3.18
1604 1608 0.178992 CCAGCTGTCCCCTTGTTCAA 60.179 55.000 13.81 0.00 0.00 2.69
1605 1609 0.954452 CAGCTGTCCCCTTGTTCAAC 59.046 55.000 5.25 0.00 0.00 3.18
1606 1610 0.178990 AGCTGTCCCCTTGTTCAACC 60.179 55.000 0.00 0.00 0.00 3.77
1607 1611 1.179174 GCTGTCCCCTTGTTCAACCC 61.179 60.000 0.00 0.00 0.00 4.11
1608 1612 0.889186 CTGTCCCCTTGTTCAACCCG 60.889 60.000 0.00 0.00 0.00 5.28
1609 1613 1.346479 TGTCCCCTTGTTCAACCCGA 61.346 55.000 0.00 0.00 0.00 5.14
1610 1614 0.605589 GTCCCCTTGTTCAACCCGAG 60.606 60.000 0.00 0.00 0.00 4.63
1611 1615 1.303317 CCCCTTGTTCAACCCGAGG 60.303 63.158 0.00 0.00 0.00 4.63
1612 1616 1.303317 CCCTTGTTCAACCCGAGGG 60.303 63.158 6.63 6.63 40.99 4.30
1613 1617 1.758592 CCTTGTTCAACCCGAGGGA 59.241 57.895 16.26 0.00 38.96 4.20
1614 1618 0.328258 CCTTGTTCAACCCGAGGGAT 59.672 55.000 16.26 0.00 38.96 3.85
1615 1619 1.453155 CTTGTTCAACCCGAGGGATG 58.547 55.000 16.26 13.77 39.11 3.51
1616 1620 0.037590 TTGTTCAACCCGAGGGATGG 59.962 55.000 16.26 3.78 38.41 3.51
1617 1621 1.749258 GTTCAACCCGAGGGATGGC 60.749 63.158 16.26 6.66 38.41 4.40
1618 1622 3.323758 TTCAACCCGAGGGATGGCG 62.324 63.158 16.26 0.00 38.41 5.69
1619 1623 4.856801 CAACCCGAGGGATGGCGG 62.857 72.222 16.26 0.00 46.80 6.13
1621 1625 3.988050 AACCCGAGGGATGGCGGTA 62.988 63.158 16.26 0.00 45.85 4.02
1622 1626 3.616721 CCCGAGGGATGGCGGTAG 61.617 72.222 0.84 0.00 45.85 3.18
1623 1627 3.616721 CCGAGGGATGGCGGTAGG 61.617 72.222 0.00 0.00 42.49 3.18
1624 1628 2.520982 CGAGGGATGGCGGTAGGA 60.521 66.667 0.00 0.00 0.00 2.94
1625 1629 2.565645 CGAGGGATGGCGGTAGGAG 61.566 68.421 0.00 0.00 0.00 3.69
1626 1630 1.152525 GAGGGATGGCGGTAGGAGA 60.153 63.158 0.00 0.00 0.00 3.71
1627 1631 1.457831 AGGGATGGCGGTAGGAGAC 60.458 63.158 0.00 0.00 0.00 3.36
1628 1632 2.508751 GGGATGGCGGTAGGAGACC 61.509 68.421 0.00 0.00 45.91 3.85
1636 1640 3.604629 GTAGGAGACCAGCGCAGA 58.395 61.111 11.47 0.00 0.00 4.26
1637 1641 2.119886 GTAGGAGACCAGCGCAGAT 58.880 57.895 11.47 0.00 0.00 2.90
1638 1642 0.031449 GTAGGAGACCAGCGCAGATC 59.969 60.000 11.47 0.00 0.00 2.75
1639 1643 0.395724 TAGGAGACCAGCGCAGATCA 60.396 55.000 11.47 0.00 0.00 2.92
1640 1644 1.047596 AGGAGACCAGCGCAGATCAT 61.048 55.000 11.47 0.00 0.00 2.45
1641 1645 0.879400 GGAGACCAGCGCAGATCATG 60.879 60.000 11.47 0.00 0.00 3.07
1642 1646 0.179089 GAGACCAGCGCAGATCATGT 60.179 55.000 11.47 0.00 0.00 3.21
1643 1647 1.067669 GAGACCAGCGCAGATCATGTA 59.932 52.381 11.47 0.00 0.00 2.29
1644 1648 1.202463 AGACCAGCGCAGATCATGTAC 60.202 52.381 11.47 0.00 0.00 2.90
1645 1649 0.179073 ACCAGCGCAGATCATGTACC 60.179 55.000 11.47 0.00 0.00 3.34
1646 1650 1.217585 CCAGCGCAGATCATGTACCG 61.218 60.000 11.47 0.00 0.00 4.02
1647 1651 1.068083 AGCGCAGATCATGTACCGG 59.932 57.895 11.47 0.00 0.00 5.28
1648 1652 1.067416 GCGCAGATCATGTACCGGA 59.933 57.895 9.46 0.00 0.00 5.14
1649 1653 0.319900 GCGCAGATCATGTACCGGAT 60.320 55.000 9.46 0.00 0.00 4.18
1650 1654 1.067846 GCGCAGATCATGTACCGGATA 60.068 52.381 9.46 0.00 0.00 2.59
1651 1655 2.868662 CGCAGATCATGTACCGGATAG 58.131 52.381 9.46 0.00 0.00 2.08
1665 1669 4.069300 CCGGATAGGTAAGGGAAAACTC 57.931 50.000 0.00 0.00 34.51 3.01
1666 1670 3.453353 CCGGATAGGTAAGGGAAAACTCA 59.547 47.826 0.00 0.00 34.51 3.41
1667 1671 4.080751 CCGGATAGGTAAGGGAAAACTCAA 60.081 45.833 0.00 0.00 34.51 3.02
1668 1672 4.874396 CGGATAGGTAAGGGAAAACTCAAC 59.126 45.833 0.00 0.00 0.00 3.18
1669 1673 4.874396 GGATAGGTAAGGGAAAACTCAACG 59.126 45.833 0.00 0.00 0.00 4.10
1670 1674 5.337813 GGATAGGTAAGGGAAAACTCAACGA 60.338 44.000 0.00 0.00 0.00 3.85
1671 1675 4.635699 AGGTAAGGGAAAACTCAACGAT 57.364 40.909 0.00 0.00 0.00 3.73
1672 1676 4.324267 AGGTAAGGGAAAACTCAACGATG 58.676 43.478 0.00 0.00 0.00 3.84
1673 1677 3.439129 GGTAAGGGAAAACTCAACGATGG 59.561 47.826 0.00 0.00 0.00 3.51
1674 1678 1.534729 AGGGAAAACTCAACGATGGC 58.465 50.000 0.00 0.00 0.00 4.40
1675 1679 1.202879 AGGGAAAACTCAACGATGGCA 60.203 47.619 0.00 0.00 0.00 4.92
1676 1680 1.200020 GGGAAAACTCAACGATGGCAG 59.800 52.381 0.00 0.00 0.00 4.85
1677 1681 2.151202 GGAAAACTCAACGATGGCAGA 58.849 47.619 0.00 0.00 0.00 4.26
1678 1682 2.160417 GGAAAACTCAACGATGGCAGAG 59.840 50.000 0.00 0.00 0.00 3.35
1679 1683 1.160137 AAACTCAACGATGGCAGAGC 58.840 50.000 0.00 0.00 0.00 4.09
1689 1693 3.461773 GGCAGAGCCGCTGGAGTA 61.462 66.667 0.00 0.00 45.03 2.59
1690 1694 2.579201 GCAGAGCCGCTGGAGTAA 59.421 61.111 0.00 0.00 45.03 2.24
1691 1695 1.079127 GCAGAGCCGCTGGAGTAAA 60.079 57.895 0.00 0.00 45.03 2.01
1692 1696 1.086634 GCAGAGCCGCTGGAGTAAAG 61.087 60.000 0.00 0.00 45.03 1.85
1693 1697 0.532573 CAGAGCCGCTGGAGTAAAGA 59.467 55.000 0.00 0.00 41.07 2.52
1694 1698 1.066858 CAGAGCCGCTGGAGTAAAGAA 60.067 52.381 0.00 0.00 41.07 2.52
1695 1699 1.623811 AGAGCCGCTGGAGTAAAGAAA 59.376 47.619 0.00 0.00 0.00 2.52
1696 1700 2.038557 AGAGCCGCTGGAGTAAAGAAAA 59.961 45.455 0.00 0.00 0.00 2.29
1697 1701 2.152016 AGCCGCTGGAGTAAAGAAAAC 58.848 47.619 0.00 0.00 0.00 2.43
1698 1702 1.199327 GCCGCTGGAGTAAAGAAAACC 59.801 52.381 0.00 0.00 0.00 3.27
1699 1703 1.810755 CCGCTGGAGTAAAGAAAACCC 59.189 52.381 0.00 0.00 0.00 4.11
1700 1704 2.552373 CCGCTGGAGTAAAGAAAACCCT 60.552 50.000 0.00 0.00 0.00 4.34
1701 1705 3.307199 CCGCTGGAGTAAAGAAAACCCTA 60.307 47.826 0.00 0.00 0.00 3.53
1702 1706 3.933332 CGCTGGAGTAAAGAAAACCCTAG 59.067 47.826 0.00 0.00 0.00 3.02
1703 1707 4.562963 CGCTGGAGTAAAGAAAACCCTAGT 60.563 45.833 0.00 0.00 0.00 2.57
1704 1708 4.936411 GCTGGAGTAAAGAAAACCCTAGTC 59.064 45.833 0.00 0.00 0.00 2.59
1705 1709 5.143376 TGGAGTAAAGAAAACCCTAGTCG 57.857 43.478 0.00 0.00 0.00 4.18
1706 1710 3.931468 GGAGTAAAGAAAACCCTAGTCGC 59.069 47.826 0.00 0.00 0.00 5.19
1707 1711 3.931468 GAGTAAAGAAAACCCTAGTCGCC 59.069 47.826 0.00 0.00 0.00 5.54
1708 1712 2.943036 AAAGAAAACCCTAGTCGCCA 57.057 45.000 0.00 0.00 0.00 5.69
1709 1713 3.434940 AAAGAAAACCCTAGTCGCCAT 57.565 42.857 0.00 0.00 0.00 4.40
1710 1714 2.403252 AGAAAACCCTAGTCGCCATG 57.597 50.000 0.00 0.00 0.00 3.66
1711 1715 1.065418 AGAAAACCCTAGTCGCCATGG 60.065 52.381 7.63 7.63 0.00 3.66
1712 1716 0.679960 AAAACCCTAGTCGCCATGGC 60.680 55.000 27.67 27.67 37.85 4.40
1722 1726 2.972505 GCCATGGCGACGGGTATG 60.973 66.667 23.48 0.00 0.00 2.39
1723 1727 2.504032 CCATGGCGACGGGTATGT 59.496 61.111 0.00 0.00 0.00 2.29
1724 1728 1.153249 CCATGGCGACGGGTATGTT 60.153 57.895 0.00 0.00 0.00 2.71
1725 1729 0.746563 CCATGGCGACGGGTATGTTT 60.747 55.000 0.00 0.00 0.00 2.83
1726 1730 1.473610 CCATGGCGACGGGTATGTTTA 60.474 52.381 0.00 0.00 0.00 2.01
1727 1731 1.864711 CATGGCGACGGGTATGTTTAG 59.135 52.381 0.00 0.00 0.00 1.85
1728 1732 0.176219 TGGCGACGGGTATGTTTAGG 59.824 55.000 0.00 0.00 0.00 2.69
1729 1733 0.461135 GGCGACGGGTATGTTTAGGA 59.539 55.000 0.00 0.00 0.00 2.94
1730 1734 1.069668 GGCGACGGGTATGTTTAGGAT 59.930 52.381 0.00 0.00 0.00 3.24
1731 1735 2.132762 GCGACGGGTATGTTTAGGATG 58.867 52.381 0.00 0.00 0.00 3.51
1732 1736 2.750948 CGACGGGTATGTTTAGGATGG 58.249 52.381 0.00 0.00 0.00 3.51
1733 1737 2.490991 GACGGGTATGTTTAGGATGGC 58.509 52.381 0.00 0.00 0.00 4.40
1734 1738 2.104281 GACGGGTATGTTTAGGATGGCT 59.896 50.000 0.00 0.00 0.00 4.75
1735 1739 2.158813 ACGGGTATGTTTAGGATGGCTG 60.159 50.000 0.00 0.00 0.00 4.85
1736 1740 2.230660 GGGTATGTTTAGGATGGCTGC 58.769 52.381 0.00 0.00 0.00 5.25
1737 1741 2.158608 GGGTATGTTTAGGATGGCTGCT 60.159 50.000 0.00 0.00 0.00 4.24
1738 1742 3.142174 GGTATGTTTAGGATGGCTGCTC 58.858 50.000 0.00 0.00 0.00 4.26
1739 1743 3.181450 GGTATGTTTAGGATGGCTGCTCT 60.181 47.826 0.00 0.00 0.00 4.09
1753 1757 3.137533 GCTGCTCTCACATAGGGAATTC 58.862 50.000 0.00 0.00 0.00 2.17
1764 1768 4.899457 ACATAGGGAATTCGTAGATCCACA 59.101 41.667 0.00 0.00 37.43 4.17
1788 1792 0.102844 CTTGCATTGGTAATGGGCCG 59.897 55.000 0.00 0.00 39.31 6.13
1820 1831 4.142227 TGGCGTAAAAGTTGTTTTTGCCTA 60.142 37.500 19.05 9.35 46.32 3.93
1823 1834 6.018588 GGCGTAAAAGTTGTTTTTGCCTATTT 60.019 34.615 14.49 0.00 44.62 1.40
1835 1846 8.697292 TGTTTTTGCCTATTTGTTTACCTAGTT 58.303 29.630 0.00 0.00 0.00 2.24
2258 2277 9.663904 ATCATCATGTATTAAAAATTCGTTCGG 57.336 29.630 0.00 0.00 0.00 4.30
2261 2280 5.280328 TGTATTAAAAATTCGTTCGGCGT 57.720 34.783 6.85 0.00 42.13 5.68
2338 2363 8.917415 ACAAGAAACAATTCTGAAAAGAACTC 57.083 30.769 0.00 0.00 45.19 3.01
2339 2364 8.522830 ACAAGAAACAATTCTGAAAAGAACTCA 58.477 29.630 0.00 0.00 45.19 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 1.628340 TGTCACCGGATCAATGAGGTT 59.372 47.619 9.46 0.00 34.25 3.50
157 158 0.913451 AGCTGCTCATCCCAACTCCT 60.913 55.000 0.00 0.00 0.00 3.69
220 221 5.665360 TCTCATGTAATGGTAGTGGAATGGA 59.335 40.000 0.00 0.00 46.73 3.41
413 414 5.627367 GCGCGCCACATAAATATTTTTATCA 59.373 36.000 23.24 0.00 36.16 2.15
438 439 2.114616 CAGGGAATAGCACTCTGGAGT 58.885 52.381 0.00 0.00 43.61 3.85
492 493 4.965200 ATAGGCTGGGTAACTCAGATTC 57.035 45.455 0.00 0.00 37.13 2.52
503 504 1.765393 GCCCCTAGTTATAGGCTGGGT 60.765 57.143 0.00 0.00 46.50 4.51
904 907 2.675844 CACTATCAAATCCCGCGTCAAA 59.324 45.455 4.92 0.00 0.00 2.69
934 937 1.696063 ACTGCTCCAAATGTTGCTGT 58.304 45.000 0.00 0.00 33.85 4.40
984 988 3.950395 GGTCCATCTTTTCATTAGCAGCT 59.050 43.478 0.00 0.00 0.00 4.24
1025 1029 4.020218 ACCTCACTGTAATTGCTTCTGCTA 60.020 41.667 0.00 0.00 40.48 3.49
1039 1043 4.536765 AGATTCAAACCAAACCTCACTGT 58.463 39.130 0.00 0.00 0.00 3.55
1063 1067 9.570468 AATCTTACTACATCCGACAGTATTAGA 57.430 33.333 0.00 0.00 0.00 2.10
1122 1126 0.320771 AGTAGCCTTGGCTCAACACG 60.321 55.000 18.28 0.00 0.00 4.49
1168 1172 6.590292 CCTAGTGACATGAAATAACAGTCGTT 59.410 38.462 0.00 0.00 39.24 3.85
1189 1193 6.833416 TCATAAATGACATGGGGAAAACCTAG 59.167 38.462 0.00 0.00 40.03 3.02
1198 1202 6.659745 ACAATGATCATAAATGACATGGGG 57.340 37.500 9.04 0.13 40.03 4.96
1232 1236 6.207614 TGCTAGTTCATGAGCTACTCGATTAT 59.792 38.462 14.61 0.00 39.54 1.28
1279 1283 4.250464 GTGTTATCCATCCAAACACTCGA 58.750 43.478 9.64 0.00 45.98 4.04
1386 1390 1.523758 AAGTCTTGATGTTGCCGGAC 58.476 50.000 5.05 0.00 0.00 4.79
1387 1391 1.879380 CAAAGTCTTGATGTTGCCGGA 59.121 47.619 5.05 0.00 34.14 5.14
1388 1392 1.666888 GCAAAGTCTTGATGTTGCCGG 60.667 52.381 0.00 0.00 40.35 6.13
1389 1393 1.689959 GCAAAGTCTTGATGTTGCCG 58.310 50.000 8.91 0.00 40.35 5.69
1391 1395 3.253188 TGTAGGCAAAGTCTTGATGTTGC 59.747 43.478 10.70 10.70 44.43 4.17
1392 1396 4.614535 GCTGTAGGCAAAGTCTTGATGTTG 60.615 45.833 0.00 0.00 41.35 3.33
1393 1397 3.503748 GCTGTAGGCAAAGTCTTGATGTT 59.496 43.478 0.00 0.00 41.35 2.71
1394 1398 3.077359 GCTGTAGGCAAAGTCTTGATGT 58.923 45.455 0.00 0.00 41.35 3.06
1395 1399 3.126514 CAGCTGTAGGCAAAGTCTTGATG 59.873 47.826 5.25 0.00 44.79 3.07
1396 1400 3.244700 ACAGCTGTAGGCAAAGTCTTGAT 60.245 43.478 20.16 0.00 44.79 2.57
1397 1401 2.104792 ACAGCTGTAGGCAAAGTCTTGA 59.895 45.455 20.16 0.00 44.79 3.02
1398 1402 2.498167 ACAGCTGTAGGCAAAGTCTTG 58.502 47.619 20.16 0.00 44.79 3.02
1399 1403 2.938956 ACAGCTGTAGGCAAAGTCTT 57.061 45.000 20.16 0.00 44.79 3.01
1400 1404 2.028020 GGTACAGCTGTAGGCAAAGTCT 60.028 50.000 26.70 0.00 44.79 3.24
1401 1405 2.289444 TGGTACAGCTGTAGGCAAAGTC 60.289 50.000 26.70 12.03 44.79 3.01
1402 1406 1.697432 TGGTACAGCTGTAGGCAAAGT 59.303 47.619 26.70 0.00 44.79 2.66
1403 1407 2.472695 TGGTACAGCTGTAGGCAAAG 57.527 50.000 26.70 0.00 44.79 2.77
1415 1419 1.472904 CTGATGCTCAGCCTGGTACAG 60.473 57.143 0.00 0.00 45.57 2.74
1416 1420 0.538584 CTGATGCTCAGCCTGGTACA 59.461 55.000 0.00 0.00 37.72 2.90
1417 1421 3.376218 CTGATGCTCAGCCTGGTAC 57.624 57.895 0.00 0.00 37.72 3.34
1435 1439 1.138069 GAGGAAGGAGCTAACAGGAGC 59.862 57.143 0.00 0.00 43.19 4.70
1436 1440 1.407258 CGAGGAAGGAGCTAACAGGAG 59.593 57.143 0.00 0.00 0.00 3.69
1437 1441 1.475403 CGAGGAAGGAGCTAACAGGA 58.525 55.000 0.00 0.00 0.00 3.86
1438 1442 0.179097 GCGAGGAAGGAGCTAACAGG 60.179 60.000 0.00 0.00 0.00 4.00
1439 1443 0.820871 AGCGAGGAAGGAGCTAACAG 59.179 55.000 0.00 0.00 39.74 3.16
1440 1444 1.066858 CAAGCGAGGAAGGAGCTAACA 60.067 52.381 0.00 0.00 40.78 2.41
1441 1445 1.646189 CAAGCGAGGAAGGAGCTAAC 58.354 55.000 0.00 0.00 40.78 2.34
1442 1446 0.537188 CCAAGCGAGGAAGGAGCTAA 59.463 55.000 0.00 0.00 40.78 3.09
1443 1447 1.961180 GCCAAGCGAGGAAGGAGCTA 61.961 60.000 1.32 0.00 40.78 3.32
1444 1448 2.985456 CCAAGCGAGGAAGGAGCT 59.015 61.111 0.00 0.00 43.90 4.09
1445 1449 2.821810 GCCAAGCGAGGAAGGAGC 60.822 66.667 1.32 0.00 0.00 4.70
1446 1450 2.124942 GGCCAAGCGAGGAAGGAG 60.125 66.667 0.00 0.00 0.00 3.69
1447 1451 3.717294 GGGCCAAGCGAGGAAGGA 61.717 66.667 4.39 0.00 0.00 3.36
1457 1461 2.826777 ATTGAGTCCAGCGGGCCAAG 62.827 60.000 4.39 0.00 0.00 3.61
1458 1462 2.424842 AATTGAGTCCAGCGGGCCAA 62.425 55.000 4.39 2.93 0.00 4.52
1459 1463 2.819984 GAATTGAGTCCAGCGGGCCA 62.820 60.000 4.39 0.00 0.00 5.36
1460 1464 2.044946 AATTGAGTCCAGCGGGCC 60.045 61.111 0.00 0.00 0.00 5.80
1461 1465 1.078143 AGAATTGAGTCCAGCGGGC 60.078 57.895 0.00 0.00 0.00 6.13
1462 1466 0.250234 TCAGAATTGAGTCCAGCGGG 59.750 55.000 0.00 0.00 0.00 6.13
1463 1467 1.938577 CATCAGAATTGAGTCCAGCGG 59.061 52.381 0.00 0.00 36.61 5.52
1464 1468 1.329906 GCATCAGAATTGAGTCCAGCG 59.670 52.381 0.00 0.00 36.61 5.18
1465 1469 2.362736 TGCATCAGAATTGAGTCCAGC 58.637 47.619 0.00 0.00 36.61 4.85
1466 1470 4.638865 TGATTGCATCAGAATTGAGTCCAG 59.361 41.667 0.00 0.00 36.61 3.86
1467 1471 4.591929 TGATTGCATCAGAATTGAGTCCA 58.408 39.130 0.00 0.00 36.61 4.02
1468 1472 5.507482 CCATGATTGCATCAGAATTGAGTCC 60.507 44.000 0.00 0.00 43.53 3.85
1469 1473 5.520632 CCATGATTGCATCAGAATTGAGTC 58.479 41.667 0.00 0.00 43.53 3.36
1470 1474 4.202121 GCCATGATTGCATCAGAATTGAGT 60.202 41.667 0.00 0.00 43.53 3.41
1471 1475 4.202111 TGCCATGATTGCATCAGAATTGAG 60.202 41.667 0.00 0.00 43.53 3.02
1472 1476 3.702045 TGCCATGATTGCATCAGAATTGA 59.298 39.130 0.00 0.00 43.53 2.57
1473 1477 4.053469 TGCCATGATTGCATCAGAATTG 57.947 40.909 0.00 0.00 43.53 2.32
1474 1478 4.955811 ATGCCATGATTGCATCAGAATT 57.044 36.364 0.00 0.00 46.04 2.17
1482 1486 1.900486 TGTTTGGATGCCATGATTGCA 59.100 42.857 0.00 0.00 43.97 4.08
1483 1487 2.273557 GTGTTTGGATGCCATGATTGC 58.726 47.619 0.00 0.00 31.53 3.56
1484 1488 2.234168 TGGTGTTTGGATGCCATGATTG 59.766 45.455 0.00 0.00 31.53 2.67
1485 1489 2.234414 GTGGTGTTTGGATGCCATGATT 59.766 45.455 0.00 0.00 31.53 2.57
1486 1490 1.826720 GTGGTGTTTGGATGCCATGAT 59.173 47.619 0.00 0.00 31.53 2.45
1487 1491 1.255882 GTGGTGTTTGGATGCCATGA 58.744 50.000 0.00 0.00 31.53 3.07
1488 1492 0.109179 CGTGGTGTTTGGATGCCATG 60.109 55.000 0.00 0.00 31.53 3.66
1489 1493 0.539438 ACGTGGTGTTTGGATGCCAT 60.539 50.000 0.00 0.00 31.53 4.40
1490 1494 0.108774 TACGTGGTGTTTGGATGCCA 59.891 50.000 0.00 0.00 0.00 4.92
1491 1495 0.802494 CTACGTGGTGTTTGGATGCC 59.198 55.000 0.00 0.00 0.00 4.40
1492 1496 0.802494 CCTACGTGGTGTTTGGATGC 59.198 55.000 0.00 0.00 0.00 3.91
1518 1522 0.457851 GTGTCAGATCACCTCGGAGG 59.542 60.000 22.40 22.40 42.49 4.30
1519 1523 1.133982 CAGTGTCAGATCACCTCGGAG 59.866 57.143 0.00 0.00 38.91 4.63
1520 1524 1.177401 CAGTGTCAGATCACCTCGGA 58.823 55.000 0.00 0.00 38.91 4.55
1521 1525 0.459237 GCAGTGTCAGATCACCTCGG 60.459 60.000 0.00 0.00 38.91 4.63
1522 1526 0.459237 GGCAGTGTCAGATCACCTCG 60.459 60.000 0.00 0.00 38.91 4.63
1523 1527 0.459237 CGGCAGTGTCAGATCACCTC 60.459 60.000 0.00 0.00 38.91 3.85
1524 1528 1.188219 ACGGCAGTGTCAGATCACCT 61.188 55.000 0.00 0.00 38.91 4.00
1525 1529 0.737715 GACGGCAGTGTCAGATCACC 60.738 60.000 0.00 0.00 38.91 4.02
1526 1530 1.073216 CGACGGCAGTGTCAGATCAC 61.073 60.000 0.00 0.00 38.84 3.06
1527 1531 1.212751 CGACGGCAGTGTCAGATCA 59.787 57.895 0.00 0.00 38.84 2.92
1528 1532 0.798771 GACGACGGCAGTGTCAGATC 60.799 60.000 0.00 0.00 38.84 2.75
1529 1533 1.213013 GACGACGGCAGTGTCAGAT 59.787 57.895 0.00 0.00 38.84 2.90
1530 1534 1.853114 GAGACGACGGCAGTGTCAGA 61.853 60.000 2.19 0.00 38.84 3.27
1531 1535 1.442857 GAGACGACGGCAGTGTCAG 60.443 63.158 2.19 7.42 38.84 3.51
1532 1536 2.643272 GAGACGACGGCAGTGTCA 59.357 61.111 2.19 0.00 38.84 3.58
1533 1537 2.126424 GGAGACGACGGCAGTGTC 60.126 66.667 2.19 2.84 35.49 3.67
1545 1549 1.662446 TTTTGGCGACGACGGAGAC 60.662 57.895 9.67 0.00 40.15 3.36
1546 1550 1.662446 GTTTTGGCGACGACGGAGA 60.662 57.895 9.67 0.00 40.15 3.71
1547 1551 2.664436 GGTTTTGGCGACGACGGAG 61.664 63.158 9.67 0.00 40.15 4.63
1548 1552 2.662527 GGTTTTGGCGACGACGGA 60.663 61.111 9.67 0.00 40.15 4.69
1549 1553 3.719144 GGGTTTTGGCGACGACGG 61.719 66.667 9.67 0.00 40.15 4.79
1550 1554 3.719144 GGGGTTTTGGCGACGACG 61.719 66.667 2.12 2.12 42.93 5.12
1551 1555 2.125202 CTTGGGGTTTTGGCGACGAC 62.125 60.000 0.00 0.00 0.00 4.34
1552 1556 1.894756 CTTGGGGTTTTGGCGACGA 60.895 57.895 0.00 0.00 0.00 4.20
1553 1557 2.642700 CTTGGGGTTTTGGCGACG 59.357 61.111 0.00 0.00 0.00 5.12
1554 1558 3.047735 CCTTGGGGTTTTGGCGAC 58.952 61.111 0.00 0.00 0.00 5.19
1555 1559 2.915137 GCCTTGGGGTTTTGGCGA 60.915 61.111 0.00 0.00 35.79 5.54
1556 1560 4.002506 GGCCTTGGGGTTTTGGCG 62.003 66.667 0.00 0.00 45.75 5.69
1557 1561 4.002506 CGGCCTTGGGGTTTTGGC 62.003 66.667 0.00 0.00 44.22 4.52
1558 1562 3.310307 CCGGCCTTGGGGTTTTGG 61.310 66.667 0.00 0.00 34.45 3.28
1559 1563 3.310307 CCCGGCCTTGGGGTTTTG 61.310 66.667 7.83 0.00 46.17 2.44
1583 1587 0.606673 GAACAAGGGGACAGCTGGTC 60.607 60.000 19.93 12.72 46.20 4.02
1584 1588 1.352622 TGAACAAGGGGACAGCTGGT 61.353 55.000 19.93 3.31 0.00 4.00
1585 1589 0.178992 TTGAACAAGGGGACAGCTGG 60.179 55.000 19.93 0.00 0.00 4.85
1586 1590 0.954452 GTTGAACAAGGGGACAGCTG 59.046 55.000 13.48 13.48 0.00 4.24
1587 1591 0.178990 GGTTGAACAAGGGGACAGCT 60.179 55.000 0.00 0.00 0.00 4.24
1588 1592 1.179174 GGGTTGAACAAGGGGACAGC 61.179 60.000 0.00 0.00 0.00 4.40
1589 1593 0.889186 CGGGTTGAACAAGGGGACAG 60.889 60.000 0.00 0.00 0.00 3.51
1590 1594 1.149627 CGGGTTGAACAAGGGGACA 59.850 57.895 0.00 0.00 0.00 4.02
1591 1595 0.605589 CTCGGGTTGAACAAGGGGAC 60.606 60.000 0.00 0.00 0.00 4.46
1592 1596 1.758592 CTCGGGTTGAACAAGGGGA 59.241 57.895 0.00 0.00 0.00 4.81
1593 1597 1.303317 CCTCGGGTTGAACAAGGGG 60.303 63.158 0.00 0.00 0.00 4.79
1594 1598 1.303317 CCCTCGGGTTGAACAAGGG 60.303 63.158 13.12 13.12 40.75 3.95
1595 1599 0.328258 ATCCCTCGGGTTGAACAAGG 59.672 55.000 1.18 0.76 36.47 3.61
1596 1600 1.453155 CATCCCTCGGGTTGAACAAG 58.547 55.000 7.17 0.00 37.20 3.16
1597 1601 0.037590 CCATCCCTCGGGTTGAACAA 59.962 55.000 13.44 0.00 37.20 2.83
1598 1602 1.682849 CCATCCCTCGGGTTGAACA 59.317 57.895 13.44 0.00 37.20 3.18
1599 1603 1.749258 GCCATCCCTCGGGTTGAAC 60.749 63.158 13.44 3.27 37.20 3.18
1600 1604 2.674754 GCCATCCCTCGGGTTGAA 59.325 61.111 13.44 0.00 37.20 2.69
1601 1605 3.781307 CGCCATCCCTCGGGTTGA 61.781 66.667 13.44 0.00 37.20 3.18
1602 1606 4.856801 CCGCCATCCCTCGGGTTG 62.857 72.222 1.18 3.99 41.82 3.77
1607 1611 2.520982 TCCTACCGCCATCCCTCG 60.521 66.667 0.00 0.00 0.00 4.63
1608 1612 1.152525 TCTCCTACCGCCATCCCTC 60.153 63.158 0.00 0.00 0.00 4.30
1609 1613 1.457831 GTCTCCTACCGCCATCCCT 60.458 63.158 0.00 0.00 0.00 4.20
1610 1614 2.508751 GGTCTCCTACCGCCATCCC 61.509 68.421 0.00 0.00 38.88 3.85
1611 1615 3.139565 GGTCTCCTACCGCCATCC 58.860 66.667 0.00 0.00 38.88 3.51
1619 1623 0.031449 GATCTGCGCTGGTCTCCTAC 59.969 60.000 19.17 0.00 0.00 3.18
1620 1624 0.395724 TGATCTGCGCTGGTCTCCTA 60.396 55.000 25.25 5.25 0.00 2.94
1621 1625 1.047596 ATGATCTGCGCTGGTCTCCT 61.048 55.000 25.25 9.87 0.00 3.69
1622 1626 0.879400 CATGATCTGCGCTGGTCTCC 60.879 60.000 25.25 3.63 0.00 3.71
1623 1627 0.179089 ACATGATCTGCGCTGGTCTC 60.179 55.000 25.25 14.80 0.00 3.36
1624 1628 1.114627 TACATGATCTGCGCTGGTCT 58.885 50.000 25.25 10.46 0.00 3.85
1625 1629 1.212616 GTACATGATCTGCGCTGGTC 58.787 55.000 19.57 19.57 0.00 4.02
1626 1630 0.179073 GGTACATGATCTGCGCTGGT 60.179 55.000 14.70 7.19 0.00 4.00
1627 1631 1.217585 CGGTACATGATCTGCGCTGG 61.218 60.000 14.70 4.50 0.00 4.85
1628 1632 1.217585 CCGGTACATGATCTGCGCTG 61.218 60.000 9.73 8.88 0.00 5.18
1629 1633 1.068083 CCGGTACATGATCTGCGCT 59.932 57.895 9.73 0.00 0.00 5.92
1630 1634 0.319900 ATCCGGTACATGATCTGCGC 60.320 55.000 0.00 0.00 0.00 6.09
1631 1635 2.416027 CCTATCCGGTACATGATCTGCG 60.416 54.545 0.00 0.00 0.00 5.18
1632 1636 2.563179 ACCTATCCGGTACATGATCTGC 59.437 50.000 0.00 0.00 46.73 4.26
1642 1646 4.623863 AGTTTTCCCTTACCTATCCGGTA 58.376 43.478 0.00 0.00 46.73 4.02
1644 1648 3.453353 TGAGTTTTCCCTTACCTATCCGG 59.547 47.826 0.00 0.00 39.35 5.14
1645 1649 4.748277 TGAGTTTTCCCTTACCTATCCG 57.252 45.455 0.00 0.00 0.00 4.18
1646 1650 4.874396 CGTTGAGTTTTCCCTTACCTATCC 59.126 45.833 0.00 0.00 0.00 2.59
1647 1651 5.727434 TCGTTGAGTTTTCCCTTACCTATC 58.273 41.667 0.00 0.00 0.00 2.08
1648 1652 5.750352 TCGTTGAGTTTTCCCTTACCTAT 57.250 39.130 0.00 0.00 0.00 2.57
1649 1653 5.484715 CATCGTTGAGTTTTCCCTTACCTA 58.515 41.667 0.00 0.00 0.00 3.08
1650 1654 4.324267 CATCGTTGAGTTTTCCCTTACCT 58.676 43.478 0.00 0.00 0.00 3.08
1651 1655 3.439129 CCATCGTTGAGTTTTCCCTTACC 59.561 47.826 0.00 0.00 0.00 2.85
1652 1656 3.119955 GCCATCGTTGAGTTTTCCCTTAC 60.120 47.826 0.00 0.00 0.00 2.34
1653 1657 3.078837 GCCATCGTTGAGTTTTCCCTTA 58.921 45.455 0.00 0.00 0.00 2.69
1654 1658 1.886542 GCCATCGTTGAGTTTTCCCTT 59.113 47.619 0.00 0.00 0.00 3.95
1655 1659 1.202879 TGCCATCGTTGAGTTTTCCCT 60.203 47.619 0.00 0.00 0.00 4.20
1656 1660 1.200020 CTGCCATCGTTGAGTTTTCCC 59.800 52.381 0.00 0.00 0.00 3.97
1657 1661 2.151202 TCTGCCATCGTTGAGTTTTCC 58.849 47.619 0.00 0.00 0.00 3.13
1658 1662 2.413371 GCTCTGCCATCGTTGAGTTTTC 60.413 50.000 0.00 0.00 0.00 2.29
1659 1663 1.537202 GCTCTGCCATCGTTGAGTTTT 59.463 47.619 0.00 0.00 0.00 2.43
1660 1664 1.160137 GCTCTGCCATCGTTGAGTTT 58.840 50.000 0.00 0.00 0.00 2.66
1661 1665 2.846371 GCTCTGCCATCGTTGAGTT 58.154 52.632 0.00 0.00 0.00 3.01
1662 1666 4.606071 GCTCTGCCATCGTTGAGT 57.394 55.556 0.00 0.00 0.00 3.41
1672 1676 2.521958 TTTACTCCAGCGGCTCTGCC 62.522 60.000 0.00 0.00 46.75 4.85
1673 1677 1.079127 TTTACTCCAGCGGCTCTGC 60.079 57.895 0.00 0.00 41.50 4.26
1674 1678 0.532573 TCTTTACTCCAGCGGCTCTG 59.467 55.000 0.00 0.00 42.49 3.35
1675 1679 1.267121 TTCTTTACTCCAGCGGCTCT 58.733 50.000 0.00 0.00 0.00 4.09
1676 1680 2.094762 TTTCTTTACTCCAGCGGCTC 57.905 50.000 0.00 0.00 0.00 4.70
1677 1681 2.152016 GTTTTCTTTACTCCAGCGGCT 58.848 47.619 0.00 0.00 0.00 5.52
1678 1682 1.199327 GGTTTTCTTTACTCCAGCGGC 59.801 52.381 0.00 0.00 0.00 6.53
1679 1683 1.810755 GGGTTTTCTTTACTCCAGCGG 59.189 52.381 0.00 0.00 0.00 5.52
1680 1684 2.779506 AGGGTTTTCTTTACTCCAGCG 58.220 47.619 0.00 0.00 0.00 5.18
1681 1685 4.907809 ACTAGGGTTTTCTTTACTCCAGC 58.092 43.478 0.00 0.00 0.00 4.85
1682 1686 5.169295 CGACTAGGGTTTTCTTTACTCCAG 58.831 45.833 0.00 0.00 0.00 3.86
1683 1687 4.562143 GCGACTAGGGTTTTCTTTACTCCA 60.562 45.833 0.00 0.00 0.00 3.86
1684 1688 3.931468 GCGACTAGGGTTTTCTTTACTCC 59.069 47.826 0.00 0.00 0.00 3.85
1685 1689 3.931468 GGCGACTAGGGTTTTCTTTACTC 59.069 47.826 0.00 0.00 0.00 2.59
1686 1690 3.325716 TGGCGACTAGGGTTTTCTTTACT 59.674 43.478 0.00 0.00 0.00 2.24
1687 1691 3.667360 TGGCGACTAGGGTTTTCTTTAC 58.333 45.455 0.00 0.00 0.00 2.01
1688 1692 4.258543 CATGGCGACTAGGGTTTTCTTTA 58.741 43.478 0.00 0.00 0.00 1.85
1689 1693 2.943036 TGGCGACTAGGGTTTTCTTT 57.057 45.000 0.00 0.00 0.00 2.52
1690 1694 2.618045 CCATGGCGACTAGGGTTTTCTT 60.618 50.000 0.00 0.00 0.00 2.52
1691 1695 1.065418 CCATGGCGACTAGGGTTTTCT 60.065 52.381 0.00 0.00 0.00 2.52
1692 1696 1.379527 CCATGGCGACTAGGGTTTTC 58.620 55.000 0.00 0.00 0.00 2.29
1693 1697 0.679960 GCCATGGCGACTAGGGTTTT 60.680 55.000 23.48 0.00 0.00 2.43
1694 1698 1.077716 GCCATGGCGACTAGGGTTT 60.078 57.895 23.48 0.00 0.00 3.27
1695 1699 2.590092 GCCATGGCGACTAGGGTT 59.410 61.111 23.48 0.00 0.00 4.11
1705 1709 2.972505 CATACCCGTCGCCATGGC 60.973 66.667 27.67 27.67 37.85 4.40
1706 1710 0.746563 AAACATACCCGTCGCCATGG 60.747 55.000 7.63 7.63 0.00 3.66
1707 1711 1.864711 CTAAACATACCCGTCGCCATG 59.135 52.381 0.00 0.00 0.00 3.66
1708 1712 1.202604 CCTAAACATACCCGTCGCCAT 60.203 52.381 0.00 0.00 0.00 4.40
1709 1713 0.176219 CCTAAACATACCCGTCGCCA 59.824 55.000 0.00 0.00 0.00 5.69
1710 1714 0.461135 TCCTAAACATACCCGTCGCC 59.539 55.000 0.00 0.00 0.00 5.54
1711 1715 2.132762 CATCCTAAACATACCCGTCGC 58.867 52.381 0.00 0.00 0.00 5.19
1712 1716 2.750948 CCATCCTAAACATACCCGTCG 58.249 52.381 0.00 0.00 0.00 5.12
1713 1717 2.104281 AGCCATCCTAAACATACCCGTC 59.896 50.000 0.00 0.00 0.00 4.79
1714 1718 2.124411 AGCCATCCTAAACATACCCGT 58.876 47.619 0.00 0.00 0.00 5.28
1715 1719 2.494059 CAGCCATCCTAAACATACCCG 58.506 52.381 0.00 0.00 0.00 5.28
1716 1720 2.158608 AGCAGCCATCCTAAACATACCC 60.159 50.000 0.00 0.00 0.00 3.69
1717 1721 3.142174 GAGCAGCCATCCTAAACATACC 58.858 50.000 0.00 0.00 0.00 2.73
1718 1722 4.061596 GAGAGCAGCCATCCTAAACATAC 58.938 47.826 0.00 0.00 0.00 2.39
1719 1723 3.711190 TGAGAGCAGCCATCCTAAACATA 59.289 43.478 0.00 0.00 0.00 2.29
1720 1724 2.507058 TGAGAGCAGCCATCCTAAACAT 59.493 45.455 0.00 0.00 0.00 2.71
1721 1725 1.908619 TGAGAGCAGCCATCCTAAACA 59.091 47.619 0.00 0.00 0.00 2.83
1722 1726 2.284190 GTGAGAGCAGCCATCCTAAAC 58.716 52.381 0.00 0.00 0.00 2.01
1723 1727 1.908619 TGTGAGAGCAGCCATCCTAAA 59.091 47.619 0.00 0.00 0.00 1.85
1724 1728 1.571955 TGTGAGAGCAGCCATCCTAA 58.428 50.000 0.00 0.00 0.00 2.69
1725 1729 1.798626 ATGTGAGAGCAGCCATCCTA 58.201 50.000 0.00 0.00 0.00 2.94
1726 1730 1.693062 CTATGTGAGAGCAGCCATCCT 59.307 52.381 0.00 0.00 0.00 3.24
1727 1731 1.270732 CCTATGTGAGAGCAGCCATCC 60.271 57.143 0.00 0.00 0.00 3.51
1728 1732 1.270732 CCCTATGTGAGAGCAGCCATC 60.271 57.143 0.00 0.00 0.00 3.51
1729 1733 0.763652 CCCTATGTGAGAGCAGCCAT 59.236 55.000 0.00 0.00 0.00 4.40
1730 1734 0.325577 TCCCTATGTGAGAGCAGCCA 60.326 55.000 0.00 0.00 0.00 4.75
1731 1735 0.833287 TTCCCTATGTGAGAGCAGCC 59.167 55.000 0.00 0.00 0.00 4.85
1732 1736 2.926778 ATTCCCTATGTGAGAGCAGC 57.073 50.000 0.00 0.00 0.00 5.25
1733 1737 3.181471 ACGAATTCCCTATGTGAGAGCAG 60.181 47.826 0.00 0.00 0.00 4.24
1734 1738 2.766263 ACGAATTCCCTATGTGAGAGCA 59.234 45.455 0.00 0.00 0.00 4.26
1735 1739 3.460857 ACGAATTCCCTATGTGAGAGC 57.539 47.619 0.00 0.00 0.00 4.09
1736 1740 6.349777 GGATCTACGAATTCCCTATGTGAGAG 60.350 46.154 0.00 0.00 0.00 3.20
1737 1741 5.477291 GGATCTACGAATTCCCTATGTGAGA 59.523 44.000 0.00 0.00 0.00 3.27
1738 1742 5.243954 TGGATCTACGAATTCCCTATGTGAG 59.756 44.000 0.00 0.00 0.00 3.51
1739 1743 5.010719 GTGGATCTACGAATTCCCTATGTGA 59.989 44.000 0.00 0.00 0.00 3.58
1753 1757 1.863454 GCAAGCAGATGTGGATCTACG 59.137 52.381 4.63 0.00 36.75 3.51
1764 1768 2.696707 CCCATTACCAATGCAAGCAGAT 59.303 45.455 0.00 0.00 37.57 2.90
2011 2024 7.755822 ACAATAAACTTTCTTTAACACACGCAA 59.244 29.630 0.00 0.00 0.00 4.85
2232 2250 9.663904 CCGAACGAATTTTTAATACATGATGAT 57.336 29.630 0.00 0.00 0.00 2.45
2292 2312 5.181748 TGTTTGCTTGGTTTTGTATGCTTT 58.818 33.333 0.00 0.00 0.00 3.51
2295 2315 4.808364 TCTTGTTTGCTTGGTTTTGTATGC 59.192 37.500 0.00 0.00 0.00 3.14
2296 2316 6.900568 TTCTTGTTTGCTTGGTTTTGTATG 57.099 33.333 0.00 0.00 0.00 2.39
2298 2318 6.223852 TGTTTCTTGTTTGCTTGGTTTTGTA 58.776 32.000 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.