Multiple sequence alignment - TraesCS1D01G418200

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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 TraesCS1D01G418200 chr1D 100.000 2318 0 0 1 2318 475891461 475893778 0.000000e+00 4281
1 TraesCS1D01G418200 chr1D 82.927 656 96 11 1673 2318 24544624 24543975 5.550000e-161 577
2 TraesCS1D01G418200 chr1D 93.200 250 13 4 1418 1666 84708877 84709123 4.710000e-97 364
3 TraesCS1D01G418200 chr7D 94.341 1343 74 2 1 1342 615912062 615910721 0.000000e+00 2058
4 TraesCS1D01G418200 chr6B 94.118 1343 77 2 1 1342 151387192 151385851 0.000000e+00 2041
5 TraesCS1D01G418200 chr6B 83.562 657 87 15 1673 2318 184546005 184546651 1.530000e-166 595
6 TraesCS1D01G418200 chr6B 94.828 232 11 1 1436 1666 22894003 22894234 6.090000e-96 361
7 TraesCS1D01G418200 chr6B 94.397 232 12 1 1436 1666 560641942 560642173 2.830000e-94 355
8 TraesCS1D01G418200 chr7B 93.452 1344 84 4 1 1342 192798492 192797151 0.000000e+00 1991
9 TraesCS1D01G418200 chr7B 92.279 1347 102 2 1 1346 552700430 552699085 0.000000e+00 1910
10 TraesCS1D01G418200 chr7B 92.296 1324 101 1 1 1323 552747419 552746096 0.000000e+00 1879
11 TraesCS1D01G418200 chr7B 83.920 653 92 9 1673 2318 229837642 229836996 1.520000e-171 612
12 TraesCS1D01G418200 chr5A 93.155 1344 90 2 1 1343 71139705 71141047 0.000000e+00 1971
13 TraesCS1D01G418200 chr5A 94.397 232 12 1 1436 1666 519849557 519849788 2.830000e-94 355
14 TraesCS1D01G418200 chr5B 91.301 1345 112 4 1 1343 348576110 348574769 0.000000e+00 1831
15 TraesCS1D01G418200 chr5B 83.896 652 89 11 1673 2318 405708082 405708723 1.970000e-170 608
16 TraesCS1D01G418200 chr4A 88.476 1345 150 5 1 1342 669052074 669050732 0.000000e+00 1620
17 TraesCS1D01G418200 chr4A 88.170 1344 153 4 1 1342 676915479 676914140 0.000000e+00 1596
18 TraesCS1D01G418200 chr4A 96.104 231 9 0 1436 1666 693284307 693284077 6.050000e-101 377
19 TraesCS1D01G418200 chr4D 85.758 653 81 8 1673 2318 150967432 150966785 0.000000e+00 680
20 TraesCS1D01G418200 chr2B 85.015 654 84 10 1673 2318 412769686 412770333 0.000000e+00 652
21 TraesCS1D01G418200 chr1B 84.663 652 89 7 1673 2318 403125542 403124896 6.980000e-180 640
22 TraesCS1D01G418200 chr1B 85.814 571 80 1 1749 2318 661996746 661997316 2.550000e-169 604
23 TraesCS1D01G418200 chr1B 90.717 237 17 4 1432 1666 174985169 174985402 6.220000e-81 311
24 TraesCS1D01G418200 chr3B 82.901 655 94 12 1673 2318 473739848 473739203 7.180000e-160 573
25 TraesCS1D01G418200 chr5D 96.537 231 8 0 1436 1666 45668009 45667779 1.300000e-102 383
26 TraesCS1D01G418200 chr2A 94.215 242 11 3 1436 1676 424511745 424511506 1.310000e-97 366
27 TraesCS1D01G418200 chr1A 91.949 236 19 0 1436 1671 529672067 529671832 4.770000e-87 331


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 TraesCS1D01G418200 chr1D 475891461 475893778 2317 False 4281 4281 100.000 1 2318 1 chr1D.!!$F2 2317
1 TraesCS1D01G418200 chr1D 24543975 24544624 649 True 577 577 82.927 1673 2318 1 chr1D.!!$R1 645
2 TraesCS1D01G418200 chr7D 615910721 615912062 1341 True 2058 2058 94.341 1 1342 1 chr7D.!!$R1 1341
3 TraesCS1D01G418200 chr6B 151385851 151387192 1341 True 2041 2041 94.118 1 1342 1 chr6B.!!$R1 1341
4 TraesCS1D01G418200 chr6B 184546005 184546651 646 False 595 595 83.562 1673 2318 1 chr6B.!!$F2 645
5 TraesCS1D01G418200 chr7B 192797151 192798492 1341 True 1991 1991 93.452 1 1342 1 chr7B.!!$R1 1341
6 TraesCS1D01G418200 chr7B 552699085 552700430 1345 True 1910 1910 92.279 1 1346 1 chr7B.!!$R3 1345
7 TraesCS1D01G418200 chr7B 552746096 552747419 1323 True 1879 1879 92.296 1 1323 1 chr7B.!!$R4 1322
8 TraesCS1D01G418200 chr7B 229836996 229837642 646 True 612 612 83.920 1673 2318 1 chr7B.!!$R2 645
9 TraesCS1D01G418200 chr5A 71139705 71141047 1342 False 1971 1971 93.155 1 1343 1 chr5A.!!$F1 1342
10 TraesCS1D01G418200 chr5B 348574769 348576110 1341 True 1831 1831 91.301 1 1343 1 chr5B.!!$R1 1342
11 TraesCS1D01G418200 chr5B 405708082 405708723 641 False 608 608 83.896 1673 2318 1 chr5B.!!$F1 645
12 TraesCS1D01G418200 chr4A 669050732 669052074 1342 True 1620 1620 88.476 1 1342 1 chr4A.!!$R1 1341
13 TraesCS1D01G418200 chr4A 676914140 676915479 1339 True 1596 1596 88.170 1 1342 1 chr4A.!!$R2 1341
14 TraesCS1D01G418200 chr4D 150966785 150967432 647 True 680 680 85.758 1673 2318 1 chr4D.!!$R1 645
15 TraesCS1D01G418200 chr2B 412769686 412770333 647 False 652 652 85.015 1673 2318 1 chr2B.!!$F1 645
16 TraesCS1D01G418200 chr1B 403124896 403125542 646 True 640 640 84.663 1673 2318 1 chr1B.!!$R1 645
17 TraesCS1D01G418200 chr1B 661996746 661997316 570 False 604 604 85.814 1749 2318 1 chr1B.!!$F2 569
18 TraesCS1D01G418200 chr3B 473739203 473739848 645 True 573 573 82.901 1673 2318 1 chr3B.!!$R1 645

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
798 801 0.318441 CTGTTCCTGCTCCTTGTCGA 59.682 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 1637 0.040499 TTTATGCCCCCAACTCACCC 59.96 55.0 0.0 0.0 0.0 4.61 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
48 49 0.746659 AATTGCCGCTTCAATAGGGC 59.253 50.000 1.52 0.00 39.38 5.19
122 123 4.016444 GTTTTTCTGGCCTATGGATGTCA 58.984 43.478 3.32 0.00 0.00 3.58
231 232 2.220653 AGTGCATACAAACTGGCCAT 57.779 45.000 5.51 0.00 0.00 4.40
253 254 2.798499 GCATGATCAGAATGTTGCAGCC 60.798 50.000 11.00 0.00 37.40 4.85
409 412 8.948631 ATGCAAGGTTTATAGACATATATCGG 57.051 34.615 0.00 0.00 0.00 4.18
424 427 4.755266 ATATCGGCAAGTTCTACCTGTT 57.245 40.909 0.00 0.00 0.00 3.16
681 684 3.740115 GAAAGAAGTTCCACTAGTGCCA 58.260 45.455 17.86 2.90 0.00 4.92
788 791 1.576421 CACTTTCGGCTGTTCCTGC 59.424 57.895 0.00 0.00 0.00 4.85
798 801 0.318441 CTGTTCCTGCTCCTTGTCGA 59.682 55.000 0.00 0.00 0.00 4.20
884 887 1.446272 GCTCGTTCCTCAAGGACGG 60.446 63.158 15.91 5.56 45.39 4.79
927 930 3.055094 TGGTACTCAGAAATGAGAAGGGC 60.055 47.826 12.00 0.00 39.14 5.19
950 953 1.152247 TCCTCATGGCGGCCTATCT 60.152 57.895 21.46 0.00 0.00 1.98
965 968 6.516860 GCGGCCTATCTTTTCATCTTCTACTA 60.517 42.308 0.00 0.00 0.00 1.82
1038 1041 6.238925 CCATTGCAATTCAGCATTCTCATCTA 60.239 38.462 9.83 0.00 45.19 1.98
1114 1117 0.601558 ACTTCTTCGCTCGGCTTACA 59.398 50.000 0.00 0.00 0.00 2.41
1323 1326 5.575157 TCTTTACCCATGCAATAAACTCCA 58.425 37.500 0.00 0.00 0.00 3.86
1361 1364 7.914427 AAAAAGACTACAAATTCCTTCCCTT 57.086 32.000 0.00 0.00 0.00 3.95
1362 1365 7.914427 AAAAGACTACAAATTCCTTCCCTTT 57.086 32.000 0.00 0.00 0.00 3.11
1363 1366 9.429109 AAAAAGACTACAAATTCCTTCCCTTTA 57.571 29.630 0.00 0.00 0.00 1.85
1364 1367 7.997773 AAGACTACAAATTCCTTCCCTTTAC 57.002 36.000 0.00 0.00 0.00 2.01
1365 1368 7.331089 AGACTACAAATTCCTTCCCTTTACT 57.669 36.000 0.00 0.00 0.00 2.24
1366 1369 8.445361 AGACTACAAATTCCTTCCCTTTACTA 57.555 34.615 0.00 0.00 0.00 1.82
1367 1370 9.059023 AGACTACAAATTCCTTCCCTTTACTAT 57.941 33.333 0.00 0.00 0.00 2.12
1372 1375 8.495260 ACAAATTCCTTCCCTTTACTATAGAGG 58.505 37.037 6.78 2.77 0.00 3.69
1394 1397 9.571816 AGAGGGAATAAAAGATGAGATCAATTC 57.428 33.333 0.00 0.00 0.00 2.17
1395 1398 8.703378 AGGGAATAAAAGATGAGATCAATTCC 57.297 34.615 11.01 11.01 40.14 3.01
1396 1399 8.284435 AGGGAATAAAAGATGAGATCAATTCCA 58.716 33.333 17.32 0.00 41.80 3.53
1397 1400 8.355913 GGGAATAAAAGATGAGATCAATTCCAC 58.644 37.037 17.32 8.20 41.80 4.02
1398 1401 8.072567 GGAATAAAAGATGAGATCAATTCCACG 58.927 37.037 13.27 0.00 40.43 4.94
1399 1402 4.889832 AAAGATGAGATCAATTCCACGC 57.110 40.909 0.00 0.00 0.00 5.34
1400 1403 3.548745 AGATGAGATCAATTCCACGCA 57.451 42.857 0.00 0.00 0.00 5.24
1401 1404 3.201290 AGATGAGATCAATTCCACGCAC 58.799 45.455 0.00 0.00 0.00 5.34
1402 1405 2.470983 TGAGATCAATTCCACGCACA 57.529 45.000 0.00 0.00 0.00 4.57
1403 1406 2.777094 TGAGATCAATTCCACGCACAA 58.223 42.857 0.00 0.00 0.00 3.33
1404 1407 3.346315 TGAGATCAATTCCACGCACAAT 58.654 40.909 0.00 0.00 0.00 2.71
1405 1408 3.127376 TGAGATCAATTCCACGCACAATG 59.873 43.478 0.00 0.00 0.00 2.82
1406 1409 3.346315 AGATCAATTCCACGCACAATGA 58.654 40.909 0.00 0.00 0.00 2.57
1407 1410 3.376234 AGATCAATTCCACGCACAATGAG 59.624 43.478 0.00 0.00 0.00 2.90
1408 1411 2.777094 TCAATTCCACGCACAATGAGA 58.223 42.857 0.00 0.00 0.00 3.27
1409 1412 3.145286 TCAATTCCACGCACAATGAGAA 58.855 40.909 0.00 0.00 0.00 2.87
1410 1413 3.567585 TCAATTCCACGCACAATGAGAAA 59.432 39.130 0.00 0.00 0.00 2.52
1411 1414 3.837213 ATTCCACGCACAATGAGAAAG 57.163 42.857 0.00 0.00 0.00 2.62
1412 1415 0.874390 TCCACGCACAATGAGAAAGC 59.126 50.000 0.00 0.00 0.00 3.51
1413 1416 0.877071 CCACGCACAATGAGAAAGCT 59.123 50.000 0.00 0.00 0.00 3.74
1414 1417 1.135859 CCACGCACAATGAGAAAGCTC 60.136 52.381 0.00 0.00 41.67 4.09
1415 1418 1.802960 CACGCACAATGAGAAAGCTCT 59.197 47.619 0.00 0.00 41.84 4.09
1416 1419 2.225019 CACGCACAATGAGAAAGCTCTT 59.775 45.455 0.00 0.00 41.84 2.85
1417 1420 2.225019 ACGCACAATGAGAAAGCTCTTG 59.775 45.455 0.00 0.00 41.84 3.02
1418 1421 2.413765 CGCACAATGAGAAAGCTCTTGG 60.414 50.000 0.00 0.00 41.84 3.61
1419 1422 2.094854 GCACAATGAGAAAGCTCTTGGG 60.095 50.000 0.00 0.00 41.84 4.12
1420 1423 2.094854 CACAATGAGAAAGCTCTTGGGC 60.095 50.000 0.00 0.00 41.84 5.36
1421 1424 1.475682 CAATGAGAAAGCTCTTGGGCC 59.524 52.381 0.00 0.00 41.84 5.80
1422 1425 0.998145 ATGAGAAAGCTCTTGGGCCT 59.002 50.000 4.53 0.00 41.84 5.19
1423 1426 0.037303 TGAGAAAGCTCTTGGGCCTG 59.963 55.000 4.53 0.00 41.84 4.85
1424 1427 0.679321 GAGAAAGCTCTTGGGCCTGG 60.679 60.000 4.53 0.00 38.16 4.45
1425 1428 1.075659 GAAAGCTCTTGGGCCTGGT 59.924 57.895 4.53 0.00 0.00 4.00
1426 1429 1.228675 AAAGCTCTTGGGCCTGGTG 60.229 57.895 4.53 0.00 0.00 4.17
1427 1430 2.720144 AAAGCTCTTGGGCCTGGTGG 62.720 60.000 4.53 0.00 0.00 4.61
1428 1431 4.748144 GCTCTTGGGCCTGGTGGG 62.748 72.222 4.53 0.00 38.36 4.61
1437 1440 4.684623 CCTGGTGGGCTTAATGGG 57.315 61.111 0.00 0.00 0.00 4.00
1438 1441 1.697297 CCTGGTGGGCTTAATGGGT 59.303 57.895 0.00 0.00 0.00 4.51
1439 1442 0.923358 CCTGGTGGGCTTAATGGGTA 59.077 55.000 0.00 0.00 0.00 3.69
1440 1443 1.499007 CCTGGTGGGCTTAATGGGTAT 59.501 52.381 0.00 0.00 0.00 2.73
1441 1444 2.586425 CTGGTGGGCTTAATGGGTATG 58.414 52.381 0.00 0.00 0.00 2.39
1442 1445 1.926665 TGGTGGGCTTAATGGGTATGT 59.073 47.619 0.00 0.00 0.00 2.29
1443 1446 2.313342 TGGTGGGCTTAATGGGTATGTT 59.687 45.455 0.00 0.00 0.00 2.71
1444 1447 3.245803 TGGTGGGCTTAATGGGTATGTTT 60.246 43.478 0.00 0.00 0.00 2.83
1445 1448 3.132111 GGTGGGCTTAATGGGTATGTTTG 59.868 47.826 0.00 0.00 0.00 2.93
1446 1449 3.132111 GTGGGCTTAATGGGTATGTTTGG 59.868 47.826 0.00 0.00 0.00 3.28
1447 1450 3.245803 TGGGCTTAATGGGTATGTTTGGT 60.246 43.478 0.00 0.00 0.00 3.67
1448 1451 3.772572 GGGCTTAATGGGTATGTTTGGTT 59.227 43.478 0.00 0.00 0.00 3.67
1449 1452 4.142026 GGGCTTAATGGGTATGTTTGGTTC 60.142 45.833 0.00 0.00 0.00 3.62
1450 1453 4.709886 GGCTTAATGGGTATGTTTGGTTCT 59.290 41.667 0.00 0.00 0.00 3.01
1451 1454 5.186992 GGCTTAATGGGTATGTTTGGTTCTT 59.813 40.000 0.00 0.00 0.00 2.52
1452 1455 6.099341 GCTTAATGGGTATGTTTGGTTCTTG 58.901 40.000 0.00 0.00 0.00 3.02
1453 1456 4.535526 AATGGGTATGTTTGGTTCTTGC 57.464 40.909 0.00 0.00 0.00 4.01
1454 1457 2.243810 TGGGTATGTTTGGTTCTTGCC 58.756 47.619 0.00 0.00 0.00 4.52
1455 1458 2.158385 TGGGTATGTTTGGTTCTTGCCT 60.158 45.455 0.00 0.00 0.00 4.75
1456 1459 3.074687 TGGGTATGTTTGGTTCTTGCCTA 59.925 43.478 0.00 0.00 0.00 3.93
1457 1460 4.264172 TGGGTATGTTTGGTTCTTGCCTAT 60.264 41.667 0.00 0.00 0.00 2.57
1458 1461 5.044772 TGGGTATGTTTGGTTCTTGCCTATA 60.045 40.000 0.00 0.00 0.00 1.31
1459 1462 5.531287 GGGTATGTTTGGTTCTTGCCTATAG 59.469 44.000 0.00 0.00 0.00 1.31
1460 1463 5.008712 GGTATGTTTGGTTCTTGCCTATAGC 59.991 44.000 0.00 0.00 44.14 2.97
1461 1464 4.301072 TGTTTGGTTCTTGCCTATAGCT 57.699 40.909 0.00 0.00 44.23 3.32
1462 1465 4.009675 TGTTTGGTTCTTGCCTATAGCTG 58.990 43.478 0.00 0.00 44.23 4.24
1463 1466 2.332063 TGGTTCTTGCCTATAGCTGC 57.668 50.000 0.00 0.00 44.23 5.25
1464 1467 1.134098 TGGTTCTTGCCTATAGCTGCC 60.134 52.381 0.00 0.00 44.23 4.85
1465 1468 1.598882 GTTCTTGCCTATAGCTGCCC 58.401 55.000 0.00 0.00 44.23 5.36
1466 1469 1.141858 GTTCTTGCCTATAGCTGCCCT 59.858 52.381 0.00 0.00 44.23 5.19
1467 1470 2.368875 GTTCTTGCCTATAGCTGCCCTA 59.631 50.000 0.00 0.00 44.23 3.53
1468 1471 1.971357 TCTTGCCTATAGCTGCCCTAC 59.029 52.381 0.00 0.00 44.23 3.18
1469 1472 1.002544 CTTGCCTATAGCTGCCCTACC 59.997 57.143 0.00 0.00 44.23 3.18
1470 1473 0.105194 TGCCTATAGCTGCCCTACCA 60.105 55.000 0.00 0.00 44.23 3.25
1471 1474 1.056660 GCCTATAGCTGCCCTACCAA 58.943 55.000 0.00 0.00 38.99 3.67
1472 1475 1.630878 GCCTATAGCTGCCCTACCAAT 59.369 52.381 0.00 0.00 38.99 3.16
1473 1476 2.838202 GCCTATAGCTGCCCTACCAATA 59.162 50.000 0.00 0.00 38.99 1.90
1474 1477 3.456277 GCCTATAGCTGCCCTACCAATAT 59.544 47.826 0.00 0.00 38.99 1.28
1475 1478 4.080299 GCCTATAGCTGCCCTACCAATATT 60.080 45.833 0.00 0.00 38.99 1.28
1476 1479 5.431765 CCTATAGCTGCCCTACCAATATTG 58.568 45.833 8.58 8.58 0.00 1.90
1492 1495 6.961576 CCAATATTGGCTTGCCAATTATTTG 58.038 36.000 35.14 30.62 42.21 2.32
1504 1507 4.644498 CCAATTATTTGGCATGGGATTCC 58.356 43.478 3.53 0.00 45.71 3.01
1505 1508 4.102838 CCAATTATTTGGCATGGGATTCCA 59.897 41.667 4.80 0.00 45.71 3.53
1506 1509 5.397672 CCAATTATTTGGCATGGGATTCCAA 60.398 40.000 0.00 0.00 45.24 3.53
1507 1510 7.408236 CCAATTATTTGGCATGGGATTCCAAC 61.408 42.308 0.00 0.00 45.24 3.77
1513 1516 2.354729 TGGGATTCCAACGCCCAG 59.645 61.111 4.80 0.00 46.57 4.45
1514 1517 2.440247 GGGATTCCAACGCCCAGG 60.440 66.667 4.80 0.00 41.64 4.45
1515 1518 2.440247 GGATTCCAACGCCCAGGG 60.440 66.667 0.00 0.00 0.00 4.45
1516 1519 2.355115 GATTCCAACGCCCAGGGT 59.645 61.111 7.55 0.00 0.00 4.34
1517 1520 1.304134 GATTCCAACGCCCAGGGTT 60.304 57.895 7.55 0.00 39.22 4.11
1525 1528 3.313524 GCCCAGGGTTGGCCAAAG 61.314 66.667 22.47 10.52 43.58 2.77
1526 1529 2.525592 CCCAGGGTTGGCCAAAGA 59.474 61.111 22.47 0.00 43.58 2.52
1527 1530 1.079073 CCCAGGGTTGGCCAAAGAT 59.921 57.895 22.47 5.67 43.58 2.40
1528 1531 0.545071 CCCAGGGTTGGCCAAAGATT 60.545 55.000 22.47 3.26 43.58 2.40
1529 1532 1.351076 CCAGGGTTGGCCAAAGATTT 58.649 50.000 22.47 1.26 37.73 2.17
1530 1533 1.002315 CCAGGGTTGGCCAAAGATTTG 59.998 52.381 22.47 13.85 37.73 2.32
1544 1547 5.775686 CAAAGATTTGGCAAGAATCTGTGA 58.224 37.500 20.41 0.00 45.49 3.58
1545 1548 6.218019 CAAAGATTTGGCAAGAATCTGTGAA 58.782 36.000 20.41 0.00 45.49 3.18
1546 1549 5.640189 AGATTTGGCAAGAATCTGTGAAG 57.360 39.130 12.45 0.00 41.13 3.02
1547 1550 4.461781 AGATTTGGCAAGAATCTGTGAAGG 59.538 41.667 12.45 0.00 41.13 3.46
1548 1551 3.507162 TTGGCAAGAATCTGTGAAGGA 57.493 42.857 0.00 0.00 0.00 3.36
1549 1552 3.507162 TGGCAAGAATCTGTGAAGGAA 57.493 42.857 0.00 0.00 0.00 3.36
1550 1553 3.415212 TGGCAAGAATCTGTGAAGGAAG 58.585 45.455 0.00 0.00 0.00 3.46
1551 1554 2.163211 GGCAAGAATCTGTGAAGGAAGC 59.837 50.000 0.00 0.00 0.00 3.86
1552 1555 2.816087 GCAAGAATCTGTGAAGGAAGCA 59.184 45.455 0.00 0.00 0.00 3.91
1553 1556 3.254166 GCAAGAATCTGTGAAGGAAGCAA 59.746 43.478 0.00 0.00 0.00 3.91
1554 1557 4.791974 CAAGAATCTGTGAAGGAAGCAAC 58.208 43.478 0.00 0.00 0.00 4.17
1555 1558 4.090761 AGAATCTGTGAAGGAAGCAACA 57.909 40.909 0.00 0.00 0.00 3.33
1556 1559 4.464008 AGAATCTGTGAAGGAAGCAACAA 58.536 39.130 0.00 0.00 0.00 2.83
1557 1560 5.075493 AGAATCTGTGAAGGAAGCAACAAT 58.925 37.500 0.00 0.00 0.00 2.71
1558 1561 4.778534 ATCTGTGAAGGAAGCAACAATG 57.221 40.909 0.00 0.00 0.00 2.82
1559 1562 3.819368 TCTGTGAAGGAAGCAACAATGA 58.181 40.909 0.00 0.00 0.00 2.57
1560 1563 4.206375 TCTGTGAAGGAAGCAACAATGAA 58.794 39.130 0.00 0.00 0.00 2.57
1561 1564 4.036734 TCTGTGAAGGAAGCAACAATGAAC 59.963 41.667 0.00 0.00 0.00 3.18
1562 1565 3.953612 TGTGAAGGAAGCAACAATGAACT 59.046 39.130 0.00 0.00 0.00 3.01
1563 1566 4.036734 TGTGAAGGAAGCAACAATGAACTC 59.963 41.667 0.00 0.00 0.00 3.01
1564 1567 3.250762 TGAAGGAAGCAACAATGAACTCG 59.749 43.478 0.00 0.00 0.00 4.18
1565 1568 2.851195 AGGAAGCAACAATGAACTCGT 58.149 42.857 0.00 0.00 0.00 4.18
1566 1569 3.214328 AGGAAGCAACAATGAACTCGTT 58.786 40.909 0.00 0.00 0.00 3.85
1567 1570 3.003689 AGGAAGCAACAATGAACTCGTTG 59.996 43.478 9.61 9.61 45.70 4.10
1568 1571 3.300009 GAAGCAACAATGAACTCGTTGG 58.700 45.455 14.53 1.37 44.80 3.77
1569 1572 1.001378 AGCAACAATGAACTCGTTGGC 60.001 47.619 14.53 9.68 44.80 4.52
1570 1573 1.268999 GCAACAATGAACTCGTTGGCA 60.269 47.619 14.53 0.00 44.80 4.92
1571 1574 2.653890 CAACAATGAACTCGTTGGCAG 58.346 47.619 14.53 2.47 44.80 4.85
1572 1575 0.593128 ACAATGAACTCGTTGGCAGC 59.407 50.000 14.53 0.00 44.80 5.25
1573 1576 0.109597 CAATGAACTCGTTGGCAGCC 60.110 55.000 3.66 3.66 38.77 4.85
1574 1577 0.537143 AATGAACTCGTTGGCAGCCA 60.537 50.000 11.22 11.22 0.00 4.75
1575 1578 0.537143 ATGAACTCGTTGGCAGCCAA 60.537 50.000 23.88 23.88 41.69 4.52
1576 1579 0.749818 TGAACTCGTTGGCAGCCAAA 60.750 50.000 29.04 13.46 45.73 3.28
1577 1580 0.598065 GAACTCGTTGGCAGCCAAAT 59.402 50.000 29.04 11.75 45.73 2.32
1578 1581 1.810151 GAACTCGTTGGCAGCCAAATA 59.190 47.619 29.04 17.79 45.73 1.40
1579 1582 2.128771 ACTCGTTGGCAGCCAAATAT 57.871 45.000 29.04 11.75 45.73 1.28
1580 1583 2.446435 ACTCGTTGGCAGCCAAATATT 58.554 42.857 29.04 10.90 45.73 1.28
1581 1584 2.825532 ACTCGTTGGCAGCCAAATATTT 59.174 40.909 29.04 9.43 45.73 1.40
1582 1585 3.181397 CTCGTTGGCAGCCAAATATTTG 58.819 45.455 29.04 19.40 45.73 2.32
1601 1604 2.577225 GCGACAAGCCAAACAACAC 58.423 52.632 0.00 0.00 40.81 3.32
1602 1605 0.179150 GCGACAAGCCAAACAACACA 60.179 50.000 0.00 0.00 40.81 3.72
1603 1606 1.535860 GCGACAAGCCAAACAACACAT 60.536 47.619 0.00 0.00 40.81 3.21
1604 1607 2.287308 GCGACAAGCCAAACAACACATA 60.287 45.455 0.00 0.00 40.81 2.29
1605 1608 3.793801 GCGACAAGCCAAACAACACATAA 60.794 43.478 0.00 0.00 40.81 1.90
1606 1609 3.974401 CGACAAGCCAAACAACACATAAG 59.026 43.478 0.00 0.00 0.00 1.73
1607 1610 4.298332 GACAAGCCAAACAACACATAAGG 58.702 43.478 0.00 0.00 0.00 2.69
1608 1611 3.957497 ACAAGCCAAACAACACATAAGGA 59.043 39.130 0.00 0.00 0.00 3.36
1609 1612 4.404073 ACAAGCCAAACAACACATAAGGAA 59.596 37.500 0.00 0.00 0.00 3.36
1610 1613 5.070313 ACAAGCCAAACAACACATAAGGAAT 59.930 36.000 0.00 0.00 0.00 3.01
1611 1614 5.806654 AGCCAAACAACACATAAGGAATT 57.193 34.783 0.00 0.00 0.00 2.17
1612 1615 6.173427 AGCCAAACAACACATAAGGAATTT 57.827 33.333 0.00 0.00 0.00 1.82
1613 1616 5.990996 AGCCAAACAACACATAAGGAATTTG 59.009 36.000 0.00 0.00 0.00 2.32
1614 1617 5.179182 GCCAAACAACACATAAGGAATTTGG 59.821 40.000 7.83 7.83 44.94 3.28
1615 1618 5.179182 CCAAACAACACATAAGGAATTTGGC 59.821 40.000 0.00 0.00 38.66 4.52
1616 1619 5.543507 AACAACACATAAGGAATTTGGCA 57.456 34.783 0.00 0.00 0.00 4.92
1617 1620 5.743636 ACAACACATAAGGAATTTGGCAT 57.256 34.783 0.00 0.00 0.00 4.40
1618 1621 5.481105 ACAACACATAAGGAATTTGGCATG 58.519 37.500 0.00 0.00 0.00 4.06
1619 1622 5.245751 ACAACACATAAGGAATTTGGCATGA 59.754 36.000 0.00 0.00 0.00 3.07
1620 1623 5.329035 ACACATAAGGAATTTGGCATGAC 57.671 39.130 0.00 0.00 0.00 3.06
1621 1624 4.160252 ACACATAAGGAATTTGGCATGACC 59.840 41.667 0.00 0.00 39.84 4.02
1643 1646 6.207691 CCAATATTTTGGTAGGGTGAGTTG 57.792 41.667 6.76 0.00 46.27 3.16
1644 1647 5.127031 CCAATATTTTGGTAGGGTGAGTTGG 59.873 44.000 6.76 0.00 46.27 3.77
1645 1648 2.668144 TTTTGGTAGGGTGAGTTGGG 57.332 50.000 0.00 0.00 0.00 4.12
1646 1649 0.774908 TTTGGTAGGGTGAGTTGGGG 59.225 55.000 0.00 0.00 0.00 4.96
1647 1650 1.137594 TTGGTAGGGTGAGTTGGGGG 61.138 60.000 0.00 0.00 0.00 5.40
1648 1651 2.675371 GTAGGGTGAGTTGGGGGC 59.325 66.667 0.00 0.00 0.00 5.80
1649 1652 2.208640 TAGGGTGAGTTGGGGGCA 59.791 61.111 0.00 0.00 0.00 5.36
1650 1653 1.230149 TAGGGTGAGTTGGGGGCAT 60.230 57.895 0.00 0.00 0.00 4.40
1651 1654 0.045008 TAGGGTGAGTTGGGGGCATA 59.955 55.000 0.00 0.00 0.00 3.14
1652 1655 0.849094 AGGGTGAGTTGGGGGCATAA 60.849 55.000 0.00 0.00 0.00 1.90
1653 1656 0.040499 GGGTGAGTTGGGGGCATAAA 59.960 55.000 0.00 0.00 0.00 1.40
1654 1657 1.182667 GGTGAGTTGGGGGCATAAAC 58.817 55.000 0.00 0.00 0.00 2.01
1655 1658 1.182667 GTGAGTTGGGGGCATAAACC 58.817 55.000 0.00 0.00 0.00 3.27
1656 1659 0.780637 TGAGTTGGGGGCATAAACCA 59.219 50.000 0.00 0.00 0.00 3.67
1657 1660 1.148027 TGAGTTGGGGGCATAAACCAA 59.852 47.619 0.00 0.00 41.66 3.67
1658 1661 2.252714 GAGTTGGGGGCATAAACCAAA 58.747 47.619 0.00 0.00 45.04 3.28
1659 1662 1.974957 AGTTGGGGGCATAAACCAAAC 59.025 47.619 0.00 0.00 45.04 2.93
1660 1663 1.694696 GTTGGGGGCATAAACCAAACA 59.305 47.619 0.00 0.00 45.04 2.83
1661 1664 1.638529 TGGGGGCATAAACCAAACAG 58.361 50.000 0.00 0.00 0.00 3.16
1662 1665 0.901827 GGGGGCATAAACCAAACAGG 59.098 55.000 0.00 0.00 45.67 4.00
1663 1666 0.249120 GGGGCATAAACCAAACAGGC 59.751 55.000 0.00 0.00 43.14 4.85
1664 1667 0.249120 GGGCATAAACCAAACAGGCC 59.751 55.000 0.00 0.00 43.14 5.19
1665 1668 0.249120 GGCATAAACCAAACAGGCCC 59.751 55.000 0.00 0.00 43.14 5.80
1666 1669 0.972883 GCATAAACCAAACAGGCCCA 59.027 50.000 0.00 0.00 43.14 5.36
1667 1670 1.346068 GCATAAACCAAACAGGCCCAA 59.654 47.619 0.00 0.00 43.14 4.12
1668 1671 2.027285 GCATAAACCAAACAGGCCCAAT 60.027 45.455 0.00 0.00 43.14 3.16
1669 1672 3.196685 GCATAAACCAAACAGGCCCAATA 59.803 43.478 0.00 0.00 43.14 1.90
1670 1673 4.754322 CATAAACCAAACAGGCCCAATAC 58.246 43.478 0.00 0.00 43.14 1.89
1671 1674 1.639722 AACCAAACAGGCCCAATACC 58.360 50.000 0.00 0.00 43.14 2.73
1706 1709 7.538334 GCAAGGCAAAATATTTTCCATTTTCAC 59.462 33.333 21.37 3.79 34.22 3.18
1739 1746 7.979537 AGAAAGAAGGTTTTAAATGGTCACAAC 59.020 33.333 0.00 0.00 0.00 3.32
1745 1752 0.035036 TAAATGGTCACAACGCCGGA 59.965 50.000 5.05 0.00 0.00 5.14
1747 1754 1.512156 AATGGTCACAACGCCGGAAC 61.512 55.000 5.05 0.00 0.00 3.62
1751 1758 0.309612 GTCACAACGCCGGAACAAAT 59.690 50.000 5.05 0.00 0.00 2.32
1769 1776 4.397417 ACAAATAACTACTACTCTCGCGGT 59.603 41.667 6.13 0.00 0.00 5.68
1817 1824 3.415457 GCTATAGCCCAAAGATGAGCT 57.585 47.619 14.13 0.00 39.37 4.09
1876 1883 1.966451 CGGTGCTGTGAAAGACCCC 60.966 63.158 0.00 0.00 0.00 4.95
1913 1920 7.728083 TCTTTCCAAATCTCCCAAGACATAAAA 59.272 33.333 0.00 0.00 33.32 1.52
1927 1934 7.432869 CAAGACATAAAAATGAACAAGGTGGA 58.567 34.615 0.00 0.00 0.00 4.02
1998 2007 2.494471 TCTCGAACCGAAGCCTCAAATA 59.506 45.455 0.00 0.00 34.74 1.40
1999 2008 2.603560 CTCGAACCGAAGCCTCAAATAC 59.396 50.000 0.00 0.00 34.74 1.89
2001 2010 2.706890 GAACCGAAGCCTCAAATACCA 58.293 47.619 0.00 0.00 0.00 3.25
2002 2011 3.279434 GAACCGAAGCCTCAAATACCAT 58.721 45.455 0.00 0.00 0.00 3.55
2018 2028 1.925255 ACCATCCCTTCACCACATCAT 59.075 47.619 0.00 0.00 0.00 2.45
2046 2056 1.176527 CCAATCCACGATGCAACCTT 58.823 50.000 0.00 0.00 0.00 3.50
2061 2071 3.742640 GCAACCTTGGCCAAAACACATTA 60.743 43.478 20.91 0.00 0.00 1.90
2093 2103 1.980765 ACTGGAAGAGAAGATGTGCCA 59.019 47.619 0.00 0.00 37.43 4.92
2094 2104 2.575279 ACTGGAAGAGAAGATGTGCCAT 59.425 45.455 0.00 0.00 37.43 4.40
2109 2119 1.133199 TGCCATGGTTTCCTGGACTTT 60.133 47.619 14.67 0.00 34.24 2.66
2113 2123 4.662278 CCATGGTTTCCTGGACTTTCTTA 58.338 43.478 2.57 0.00 34.24 2.10
2119 2129 5.593095 GGTTTCCTGGACTTTCTTACAAAGT 59.407 40.000 0.00 0.00 42.62 2.66
2150 2160 0.745845 GCAGTTCGGTCAGCCATGAT 60.746 55.000 0.00 0.00 37.87 2.45
2153 2163 1.097547 GTTCGGTCAGCCATGATGGG 61.098 60.000 14.26 0.00 38.19 4.00
2177 2187 2.250646 CGATCGGTCGGCCATACTA 58.749 57.895 11.03 0.00 44.00 1.82
2183 2193 2.957680 TCGGTCGGCCATACTATGTTTA 59.042 45.455 6.96 0.00 34.09 2.01
2188 2198 7.122501 TCGGTCGGCCATACTATGTTTATAATA 59.877 37.037 6.96 0.00 34.09 0.98
2225 2238 3.955543 TTGCATTTCGGAGGGGCCC 62.956 63.158 17.12 17.12 0.00 5.80
2234 2247 2.531326 GAGGGGCCCCAAACCTTT 59.469 61.111 42.48 21.04 38.92 3.11
2265 2278 2.803133 GCAGGCATGATGCTAGTTCGTA 60.803 50.000 17.84 0.00 44.28 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.312815 GCCATCCAGGAAATCCGAAG 58.687 55.000 0.00 0.00 41.22 3.79
122 123 7.520131 CGATGTACGTATCTTCAGTATCTGGTT 60.520 40.741 0.00 0.00 37.22 3.67
231 232 2.159296 GCTGCAACATTCTGATCATGCA 60.159 45.455 16.30 16.30 41.08 3.96
294 295 0.895530 CCAGACGAGGTTCCAAGCTA 59.104 55.000 0.00 0.00 36.78 3.32
374 377 7.334421 GTCTATAAACCTTGCATCTTTGAGTCA 59.666 37.037 0.00 0.00 0.00 3.41
409 412 3.929610 CAGAGCTAACAGGTAGAACTTGC 59.070 47.826 0.00 0.00 30.50 4.01
424 427 0.116342 TCCTCAACCCCACAGAGCTA 59.884 55.000 0.00 0.00 0.00 3.32
464 467 0.662374 CGCGTGAGTACAAACGACCT 60.662 55.000 20.47 0.00 42.32 3.85
681 684 0.389391 CCAGATATTCGACCGTGGCT 59.611 55.000 0.00 0.00 0.00 4.75
798 801 0.535102 CTTCGGGTGGCTTGTCACTT 60.535 55.000 5.33 0.00 37.75 3.16
842 845 2.357517 CGGACAGCGCCAGTCTTT 60.358 61.111 24.22 0.00 36.29 2.52
884 887 3.034923 CGATAGCAGCTGAGCCGC 61.035 66.667 20.43 4.09 34.23 6.53
927 930 4.899239 GCCGCCATGAGGACCTCG 62.899 72.222 16.81 4.81 36.89 4.63
950 953 6.161381 GGGTCGTTGTAGTAGAAGATGAAAA 58.839 40.000 0.00 0.00 0.00 2.29
965 968 2.030562 CCTCAAGCGGGTCGTTGT 59.969 61.111 0.00 0.00 0.00 3.32
1015 1018 5.854010 AGATGAGAATGCTGAATTGCAAT 57.146 34.783 5.99 5.99 46.61 3.56
1038 1041 2.831284 GTTTGCACCACCACCGGT 60.831 61.111 0.00 0.00 41.07 5.28
1139 1142 3.029483 ACTCCCTACTACCTAACAGGC 57.971 52.381 0.00 0.00 39.63 4.85
1346 1349 8.495260 CCTCTATAGTAAAGGGAAGGAATTTGT 58.505 37.037 0.00 0.00 0.00 2.83
1347 1350 8.910351 CCTCTATAGTAAAGGGAAGGAATTTG 57.090 38.462 0.00 0.00 0.00 2.32
1368 1371 9.571816 GAATTGATCTCATCTTTTATTCCCTCT 57.428 33.333 0.00 0.00 0.00 3.69
1369 1372 8.791675 GGAATTGATCTCATCTTTTATTCCCTC 58.208 37.037 0.00 0.00 35.75 4.30
1370 1373 8.284435 TGGAATTGATCTCATCTTTTATTCCCT 58.716 33.333 12.94 0.00 39.19 4.20
1371 1374 8.355913 GTGGAATTGATCTCATCTTTTATTCCC 58.644 37.037 12.94 5.13 39.19 3.97
1372 1375 8.072567 CGTGGAATTGATCTCATCTTTTATTCC 58.927 37.037 10.24 10.24 39.95 3.01
1373 1376 7.589221 GCGTGGAATTGATCTCATCTTTTATTC 59.411 37.037 0.00 0.00 0.00 1.75
1374 1377 7.067372 TGCGTGGAATTGATCTCATCTTTTATT 59.933 33.333 0.00 0.00 0.00 1.40
1375 1378 6.543465 TGCGTGGAATTGATCTCATCTTTTAT 59.457 34.615 0.00 0.00 0.00 1.40
1376 1379 5.879777 TGCGTGGAATTGATCTCATCTTTTA 59.120 36.000 0.00 0.00 0.00 1.52
1377 1380 4.701651 TGCGTGGAATTGATCTCATCTTTT 59.298 37.500 0.00 0.00 0.00 2.27
1378 1381 4.095483 GTGCGTGGAATTGATCTCATCTTT 59.905 41.667 0.00 0.00 0.00 2.52
1379 1382 3.624861 GTGCGTGGAATTGATCTCATCTT 59.375 43.478 0.00 0.00 0.00 2.40
1380 1383 3.201290 GTGCGTGGAATTGATCTCATCT 58.799 45.455 0.00 0.00 0.00 2.90
1381 1384 2.938451 TGTGCGTGGAATTGATCTCATC 59.062 45.455 0.00 0.00 0.00 2.92
1382 1385 2.989909 TGTGCGTGGAATTGATCTCAT 58.010 42.857 0.00 0.00 0.00 2.90
1383 1386 2.470983 TGTGCGTGGAATTGATCTCA 57.529 45.000 0.00 0.00 0.00 3.27
1384 1387 3.374988 TCATTGTGCGTGGAATTGATCTC 59.625 43.478 0.00 0.00 0.00 2.75
1385 1388 3.346315 TCATTGTGCGTGGAATTGATCT 58.654 40.909 0.00 0.00 0.00 2.75
1386 1389 3.374988 TCTCATTGTGCGTGGAATTGATC 59.625 43.478 0.00 0.00 0.00 2.92
1387 1390 3.346315 TCTCATTGTGCGTGGAATTGAT 58.654 40.909 0.00 0.00 0.00 2.57
1388 1391 2.777094 TCTCATTGTGCGTGGAATTGA 58.223 42.857 0.00 0.00 0.00 2.57
1389 1392 3.557577 TTCTCATTGTGCGTGGAATTG 57.442 42.857 0.00 0.00 0.00 2.32
1390 1393 3.612479 GCTTTCTCATTGTGCGTGGAATT 60.612 43.478 0.00 0.00 0.00 2.17
1391 1394 2.095059 GCTTTCTCATTGTGCGTGGAAT 60.095 45.455 0.00 0.00 0.00 3.01
1392 1395 1.266718 GCTTTCTCATTGTGCGTGGAA 59.733 47.619 0.00 0.00 0.00 3.53
1393 1396 0.874390 GCTTTCTCATTGTGCGTGGA 59.126 50.000 0.00 0.00 0.00 4.02
1394 1397 0.877071 AGCTTTCTCATTGTGCGTGG 59.123 50.000 0.00 0.00 0.00 4.94
1395 1398 1.802960 AGAGCTTTCTCATTGTGCGTG 59.197 47.619 0.00 0.00 41.81 5.34
1396 1399 2.175878 AGAGCTTTCTCATTGTGCGT 57.824 45.000 0.00 0.00 41.81 5.24
1397 1400 2.413765 CCAAGAGCTTTCTCATTGTGCG 60.414 50.000 0.00 0.00 41.81 5.34
1398 1401 2.094854 CCCAAGAGCTTTCTCATTGTGC 60.095 50.000 0.00 0.00 41.81 4.57
1399 1402 2.094854 GCCCAAGAGCTTTCTCATTGTG 60.095 50.000 0.00 0.00 41.81 3.33
1400 1403 2.165998 GCCCAAGAGCTTTCTCATTGT 58.834 47.619 0.00 0.00 41.81 2.71
1401 1404 1.475682 GGCCCAAGAGCTTTCTCATTG 59.524 52.381 0.00 0.00 41.81 2.82
1402 1405 1.357079 AGGCCCAAGAGCTTTCTCATT 59.643 47.619 0.00 0.00 41.81 2.57
1403 1406 0.998145 AGGCCCAAGAGCTTTCTCAT 59.002 50.000 0.00 0.00 41.81 2.90
1404 1407 0.037303 CAGGCCCAAGAGCTTTCTCA 59.963 55.000 0.00 0.00 41.81 3.27
1405 1408 0.679321 CCAGGCCCAAGAGCTTTCTC 60.679 60.000 0.00 0.00 39.65 2.87
1406 1409 1.381851 CCAGGCCCAAGAGCTTTCT 59.618 57.895 0.00 0.00 0.00 2.52
1407 1410 1.075659 ACCAGGCCCAAGAGCTTTC 59.924 57.895 0.00 0.00 0.00 2.62
1408 1411 1.228675 CACCAGGCCCAAGAGCTTT 60.229 57.895 0.00 0.00 0.00 3.51
1409 1412 2.437897 CACCAGGCCCAAGAGCTT 59.562 61.111 0.00 0.00 0.00 3.74
1410 1413 3.655211 CCACCAGGCCCAAGAGCT 61.655 66.667 0.00 0.00 0.00 4.09
1411 1414 4.748144 CCCACCAGGCCCAAGAGC 62.748 72.222 0.00 0.00 0.00 4.09
1420 1423 0.923358 TACCCATTAAGCCCACCAGG 59.077 55.000 0.00 0.00 39.47 4.45
1421 1424 2.091885 ACATACCCATTAAGCCCACCAG 60.092 50.000 0.00 0.00 0.00 4.00
1422 1425 1.926665 ACATACCCATTAAGCCCACCA 59.073 47.619 0.00 0.00 0.00 4.17
1423 1426 2.748209 ACATACCCATTAAGCCCACC 57.252 50.000 0.00 0.00 0.00 4.61
1424 1427 3.132111 CCAAACATACCCATTAAGCCCAC 59.868 47.826 0.00 0.00 0.00 4.61
1425 1428 3.245803 ACCAAACATACCCATTAAGCCCA 60.246 43.478 0.00 0.00 0.00 5.36
1426 1429 3.371034 ACCAAACATACCCATTAAGCCC 58.629 45.455 0.00 0.00 0.00 5.19
1427 1430 4.709886 AGAACCAAACATACCCATTAAGCC 59.290 41.667 0.00 0.00 0.00 4.35
1428 1431 5.914898 AGAACCAAACATACCCATTAAGC 57.085 39.130 0.00 0.00 0.00 3.09
1429 1432 6.099341 GCAAGAACCAAACATACCCATTAAG 58.901 40.000 0.00 0.00 0.00 1.85
1430 1433 5.046950 GGCAAGAACCAAACATACCCATTAA 60.047 40.000 0.00 0.00 0.00 1.40
1431 1434 4.464597 GGCAAGAACCAAACATACCCATTA 59.535 41.667 0.00 0.00 0.00 1.90
1432 1435 3.260632 GGCAAGAACCAAACATACCCATT 59.739 43.478 0.00 0.00 0.00 3.16
1433 1436 2.831526 GGCAAGAACCAAACATACCCAT 59.168 45.455 0.00 0.00 0.00 4.00
1434 1437 2.158385 AGGCAAGAACCAAACATACCCA 60.158 45.455 0.00 0.00 0.00 4.51
1435 1438 2.525368 AGGCAAGAACCAAACATACCC 58.475 47.619 0.00 0.00 0.00 3.69
1436 1439 5.008712 GCTATAGGCAAGAACCAAACATACC 59.991 44.000 1.04 0.00 41.35 2.73
1437 1440 5.823045 AGCTATAGGCAAGAACCAAACATAC 59.177 40.000 1.04 0.00 44.79 2.39
1438 1441 5.822519 CAGCTATAGGCAAGAACCAAACATA 59.177 40.000 1.04 0.00 44.79 2.29
1439 1442 4.641989 CAGCTATAGGCAAGAACCAAACAT 59.358 41.667 1.04 0.00 44.79 2.71
1440 1443 4.009675 CAGCTATAGGCAAGAACCAAACA 58.990 43.478 1.04 0.00 44.79 2.83
1441 1444 3.181496 GCAGCTATAGGCAAGAACCAAAC 60.181 47.826 1.04 0.00 44.79 2.93
1442 1445 3.016736 GCAGCTATAGGCAAGAACCAAA 58.983 45.455 1.04 0.00 44.79 3.28
1443 1446 2.643551 GCAGCTATAGGCAAGAACCAA 58.356 47.619 1.04 0.00 44.79 3.67
1444 1447 1.134098 GGCAGCTATAGGCAAGAACCA 60.134 52.381 1.04 0.00 44.79 3.67
1445 1448 1.598882 GGCAGCTATAGGCAAGAACC 58.401 55.000 1.04 0.00 44.79 3.62
1446 1449 1.141858 AGGGCAGCTATAGGCAAGAAC 59.858 52.381 1.04 0.00 44.79 3.01
1447 1450 1.511613 AGGGCAGCTATAGGCAAGAA 58.488 50.000 1.04 0.00 44.79 2.52
1448 1451 1.971357 GTAGGGCAGCTATAGGCAAGA 59.029 52.381 1.04 0.00 44.79 3.02
1449 1452 1.002544 GGTAGGGCAGCTATAGGCAAG 59.997 57.143 1.04 0.00 44.79 4.01
1450 1453 1.056660 GGTAGGGCAGCTATAGGCAA 58.943 55.000 1.04 0.00 44.79 4.52
1451 1454 0.105194 TGGTAGGGCAGCTATAGGCA 60.105 55.000 1.04 0.00 44.79 4.75
1452 1455 1.056660 TTGGTAGGGCAGCTATAGGC 58.943 55.000 1.04 0.00 42.19 3.93
1453 1456 5.431765 CAATATTGGTAGGGCAGCTATAGG 58.568 45.833 7.62 0.00 0.00 2.57
1454 1457 5.431765 CCAATATTGGTAGGGCAGCTATAG 58.568 45.833 24.12 0.00 43.43 1.31
1455 1458 5.435686 CCAATATTGGTAGGGCAGCTATA 57.564 43.478 24.12 0.00 43.43 1.31
1456 1459 4.307032 CCAATATTGGTAGGGCAGCTAT 57.693 45.455 24.12 0.00 43.43 2.97
1457 1460 3.788227 CCAATATTGGTAGGGCAGCTA 57.212 47.619 24.12 0.00 43.43 3.32
1458 1461 2.664402 CCAATATTGGTAGGGCAGCT 57.336 50.000 24.12 0.00 43.43 4.24
1483 1486 5.293319 TGGAATCCCATGCCAAATAATTG 57.707 39.130 0.00 0.00 37.58 2.32
1484 1487 5.683681 GTTGGAATCCCATGCCAAATAATT 58.316 37.500 0.00 0.00 42.77 1.40
1485 1488 4.202243 CGTTGGAATCCCATGCCAAATAAT 60.202 41.667 0.00 0.00 42.77 1.28
1486 1489 3.131933 CGTTGGAATCCCATGCCAAATAA 59.868 43.478 0.00 0.00 42.77 1.40
1487 1490 2.692557 CGTTGGAATCCCATGCCAAATA 59.307 45.455 0.00 0.00 42.77 1.40
1488 1491 1.481772 CGTTGGAATCCCATGCCAAAT 59.518 47.619 0.00 0.00 42.77 2.32
1489 1492 0.894141 CGTTGGAATCCCATGCCAAA 59.106 50.000 0.00 0.00 42.77 3.28
1490 1493 1.603236 GCGTTGGAATCCCATGCCAA 61.603 55.000 6.30 0.00 43.12 4.52
1491 1494 2.051518 GCGTTGGAATCCCATGCCA 61.052 57.895 6.30 0.00 43.12 4.92
1492 1495 2.807622 GCGTTGGAATCCCATGCC 59.192 61.111 6.30 0.00 43.12 4.40
1493 1496 2.785425 GGGCGTTGGAATCCCATGC 61.785 63.158 8.90 8.90 43.12 4.06
1494 1497 1.379710 TGGGCGTTGGAATCCCATG 60.380 57.895 0.00 0.00 44.62 3.66
1495 1498 3.095421 TGGGCGTTGGAATCCCAT 58.905 55.556 0.00 0.00 44.62 4.00
1497 1500 2.440247 CCTGGGCGTTGGAATCCC 60.440 66.667 0.00 0.00 40.47 3.85
1498 1501 2.440247 CCCTGGGCGTTGGAATCC 60.440 66.667 0.00 0.00 0.00 3.01
1499 1502 1.304134 AACCCTGGGCGTTGGAATC 60.304 57.895 14.08 0.00 0.00 2.52
1500 1503 1.606313 CAACCCTGGGCGTTGGAAT 60.606 57.895 14.08 0.00 37.53 3.01
1501 1504 2.203422 CAACCCTGGGCGTTGGAA 60.203 61.111 14.08 0.00 37.53 3.53
1509 1512 0.545071 AATCTTTGGCCAACCCTGGG 60.545 55.000 20.35 12.28 43.74 4.45
1510 1513 1.002315 CAAATCTTTGGCCAACCCTGG 59.998 52.381 20.35 6.47 46.65 4.45
1511 1514 2.460757 CAAATCTTTGGCCAACCCTG 57.539 50.000 20.35 9.10 34.59 4.45
1521 1524 5.775686 TCACAGATTCTTGCCAAATCTTTG 58.224 37.500 10.44 10.44 40.61 2.77
1522 1525 6.409524 TTCACAGATTCTTGCCAAATCTTT 57.590 33.333 3.35 0.00 40.61 2.52
1523 1526 5.047519 CCTTCACAGATTCTTGCCAAATCTT 60.048 40.000 3.35 0.00 40.61 2.40
1524 1527 4.461781 CCTTCACAGATTCTTGCCAAATCT 59.538 41.667 0.80 0.80 42.74 2.40
1525 1528 4.460382 TCCTTCACAGATTCTTGCCAAATC 59.540 41.667 0.00 0.00 34.08 2.17
1526 1529 4.410099 TCCTTCACAGATTCTTGCCAAAT 58.590 39.130 0.00 0.00 0.00 2.32
1527 1530 3.831323 TCCTTCACAGATTCTTGCCAAA 58.169 40.909 0.00 0.00 0.00 3.28
1528 1531 3.507162 TCCTTCACAGATTCTTGCCAA 57.493 42.857 0.00 0.00 0.00 4.52
1529 1532 3.415212 CTTCCTTCACAGATTCTTGCCA 58.585 45.455 0.00 0.00 0.00 4.92
1530 1533 2.163211 GCTTCCTTCACAGATTCTTGCC 59.837 50.000 0.00 0.00 0.00 4.52
1531 1534 2.816087 TGCTTCCTTCACAGATTCTTGC 59.184 45.455 0.00 0.00 0.00 4.01
1532 1535 4.276678 TGTTGCTTCCTTCACAGATTCTTG 59.723 41.667 0.00 0.00 0.00 3.02
1533 1536 4.464008 TGTTGCTTCCTTCACAGATTCTT 58.536 39.130 0.00 0.00 0.00 2.52
1534 1537 4.090761 TGTTGCTTCCTTCACAGATTCT 57.909 40.909 0.00 0.00 0.00 2.40
1535 1538 4.836125 TTGTTGCTTCCTTCACAGATTC 57.164 40.909 0.00 0.00 0.00 2.52
1536 1539 4.828939 TCATTGTTGCTTCCTTCACAGATT 59.171 37.500 0.00 0.00 0.00 2.40
1537 1540 4.401022 TCATTGTTGCTTCCTTCACAGAT 58.599 39.130 0.00 0.00 0.00 2.90
1538 1541 3.819368 TCATTGTTGCTTCCTTCACAGA 58.181 40.909 0.00 0.00 0.00 3.41
1539 1542 4.037208 AGTTCATTGTTGCTTCCTTCACAG 59.963 41.667 0.00 0.00 0.00 3.66
1540 1543 3.953612 AGTTCATTGTTGCTTCCTTCACA 59.046 39.130 0.00 0.00 0.00 3.58
1541 1544 4.540824 GAGTTCATTGTTGCTTCCTTCAC 58.459 43.478 0.00 0.00 0.00 3.18
1542 1545 3.250762 CGAGTTCATTGTTGCTTCCTTCA 59.749 43.478 0.00 0.00 0.00 3.02
1543 1546 3.251004 ACGAGTTCATTGTTGCTTCCTTC 59.749 43.478 0.00 0.00 0.00 3.46
1544 1547 3.214328 ACGAGTTCATTGTTGCTTCCTT 58.786 40.909 0.00 0.00 0.00 3.36
1545 1548 2.851195 ACGAGTTCATTGTTGCTTCCT 58.149 42.857 0.00 0.00 0.00 3.36
1546 1549 3.300009 CAACGAGTTCATTGTTGCTTCC 58.700 45.455 0.00 0.00 44.41 3.46
1552 1555 1.001378 GCTGCCAACGAGTTCATTGTT 60.001 47.619 0.00 0.00 35.78 2.83
1553 1556 0.593128 GCTGCCAACGAGTTCATTGT 59.407 50.000 0.00 0.00 0.00 2.71
1554 1557 0.109597 GGCTGCCAACGAGTTCATTG 60.110 55.000 15.17 0.00 0.00 2.82
1555 1558 0.537143 TGGCTGCCAACGAGTTCATT 60.537 50.000 21.08 0.00 0.00 2.57
1556 1559 0.537143 TTGGCTGCCAACGAGTTCAT 60.537 50.000 29.24 0.00 38.75 2.57
1557 1560 0.749818 TTTGGCTGCCAACGAGTTCA 60.750 50.000 32.36 14.33 43.82 3.18
1558 1561 0.598065 ATTTGGCTGCCAACGAGTTC 59.402 50.000 32.36 0.00 43.82 3.01
1559 1562 1.904287 TATTTGGCTGCCAACGAGTT 58.096 45.000 32.36 16.94 43.82 3.01
1560 1563 2.128771 ATATTTGGCTGCCAACGAGT 57.871 45.000 32.36 20.05 43.82 4.18
1561 1564 3.181397 CAAATATTTGGCTGCCAACGAG 58.819 45.455 32.36 15.52 43.82 4.18
1562 1565 3.229276 CAAATATTTGGCTGCCAACGA 57.771 42.857 32.36 22.79 43.82 3.85
1583 1586 0.179150 TGTGTTGTTTGGCTTGTCGC 60.179 50.000 0.00 0.00 38.13 5.19
1584 1587 2.490328 ATGTGTTGTTTGGCTTGTCG 57.510 45.000 0.00 0.00 0.00 4.35
1585 1588 4.037446 TCCTTATGTGTTGTTTGGCTTGTC 59.963 41.667 0.00 0.00 0.00 3.18
1586 1589 3.957497 TCCTTATGTGTTGTTTGGCTTGT 59.043 39.130 0.00 0.00 0.00 3.16
1587 1590 4.582701 TCCTTATGTGTTGTTTGGCTTG 57.417 40.909 0.00 0.00 0.00 4.01
1588 1591 5.806654 ATTCCTTATGTGTTGTTTGGCTT 57.193 34.783 0.00 0.00 0.00 4.35
1589 1592 5.806654 AATTCCTTATGTGTTGTTTGGCT 57.193 34.783 0.00 0.00 0.00 4.75
1590 1593 5.179182 CCAAATTCCTTATGTGTTGTTTGGC 59.821 40.000 0.00 0.00 38.26 4.52
1591 1594 5.179182 GCCAAATTCCTTATGTGTTGTTTGG 59.821 40.000 8.70 8.70 44.31 3.28
1592 1595 5.757320 TGCCAAATTCCTTATGTGTTGTTTG 59.243 36.000 0.00 0.00 0.00 2.93
1593 1596 5.923204 TGCCAAATTCCTTATGTGTTGTTT 58.077 33.333 0.00 0.00 0.00 2.83
1594 1597 5.543507 TGCCAAATTCCTTATGTGTTGTT 57.456 34.783 0.00 0.00 0.00 2.83
1595 1598 5.245751 TCATGCCAAATTCCTTATGTGTTGT 59.754 36.000 0.00 0.00 0.00 3.32
1596 1599 5.577945 GTCATGCCAAATTCCTTATGTGTTG 59.422 40.000 0.00 0.00 0.00 3.33
1597 1600 5.337491 GGTCATGCCAAATTCCTTATGTGTT 60.337 40.000 1.78 0.00 37.17 3.32
1598 1601 4.160252 GGTCATGCCAAATTCCTTATGTGT 59.840 41.667 1.78 0.00 37.17 3.72
1599 1602 4.160065 TGGTCATGCCAAATTCCTTATGTG 59.840 41.667 6.42 0.00 45.94 3.21
1600 1603 4.352009 TGGTCATGCCAAATTCCTTATGT 58.648 39.130 6.42 0.00 45.94 2.29
1621 1624 5.127031 CCCAACTCACCCTACCAAAATATTG 59.873 44.000 0.00 0.00 36.25 1.90
1622 1625 5.269189 CCCAACTCACCCTACCAAAATATT 58.731 41.667 0.00 0.00 0.00 1.28
1623 1626 4.325816 CCCCAACTCACCCTACCAAAATAT 60.326 45.833 0.00 0.00 0.00 1.28
1624 1627 3.010808 CCCCAACTCACCCTACCAAAATA 59.989 47.826 0.00 0.00 0.00 1.40
1625 1628 2.225267 CCCCAACTCACCCTACCAAAAT 60.225 50.000 0.00 0.00 0.00 1.82
1626 1629 1.146152 CCCCAACTCACCCTACCAAAA 59.854 52.381 0.00 0.00 0.00 2.44
1627 1630 0.774908 CCCCAACTCACCCTACCAAA 59.225 55.000 0.00 0.00 0.00 3.28
1628 1631 1.137594 CCCCCAACTCACCCTACCAA 61.138 60.000 0.00 0.00 0.00 3.67
1629 1632 1.540367 CCCCCAACTCACCCTACCA 60.540 63.158 0.00 0.00 0.00 3.25
1630 1633 2.980177 GCCCCCAACTCACCCTACC 61.980 68.421 0.00 0.00 0.00 3.18
1631 1634 1.571773 ATGCCCCCAACTCACCCTAC 61.572 60.000 0.00 0.00 0.00 3.18
1632 1635 0.045008 TATGCCCCCAACTCACCCTA 59.955 55.000 0.00 0.00 0.00 3.53
1633 1636 0.849094 TTATGCCCCCAACTCACCCT 60.849 55.000 0.00 0.00 0.00 4.34
1634 1637 0.040499 TTTATGCCCCCAACTCACCC 59.960 55.000 0.00 0.00 0.00 4.61
1635 1638 1.182667 GTTTATGCCCCCAACTCACC 58.817 55.000 0.00 0.00 0.00 4.02
1636 1639 1.182667 GGTTTATGCCCCCAACTCAC 58.817 55.000 0.00 0.00 0.00 3.51
1637 1640 0.780637 TGGTTTATGCCCCCAACTCA 59.219 50.000 0.00 0.00 0.00 3.41
1638 1641 1.931635 TTGGTTTATGCCCCCAACTC 58.068 50.000 0.00 0.00 33.43 3.01
1639 1642 1.974957 GTTTGGTTTATGCCCCCAACT 59.025 47.619 0.00 0.00 37.95 3.16
1640 1643 1.694696 TGTTTGGTTTATGCCCCCAAC 59.305 47.619 0.00 0.00 37.95 3.77
1641 1644 1.974236 CTGTTTGGTTTATGCCCCCAA 59.026 47.619 0.00 0.00 36.49 4.12
1642 1645 1.638529 CTGTTTGGTTTATGCCCCCA 58.361 50.000 0.00 0.00 0.00 4.96
1643 1646 0.901827 CCTGTTTGGTTTATGCCCCC 59.098 55.000 0.00 0.00 0.00 5.40
1644 1647 0.249120 GCCTGTTTGGTTTATGCCCC 59.751 55.000 0.00 0.00 38.35 5.80
1645 1648 0.249120 GGCCTGTTTGGTTTATGCCC 59.751 55.000 0.00 0.00 38.35 5.36
1646 1649 0.249120 GGGCCTGTTTGGTTTATGCC 59.751 55.000 0.84 0.00 38.35 4.40
1647 1650 0.972883 TGGGCCTGTTTGGTTTATGC 59.027 50.000 4.53 0.00 38.35 3.14
1648 1651 3.979101 ATTGGGCCTGTTTGGTTTATG 57.021 42.857 4.53 0.00 38.35 1.90
1649 1652 3.772572 GGTATTGGGCCTGTTTGGTTTAT 59.227 43.478 4.53 0.00 38.35 1.40
1650 1653 3.166679 GGTATTGGGCCTGTTTGGTTTA 58.833 45.455 4.53 0.00 38.35 2.01
1651 1654 1.974957 GGTATTGGGCCTGTTTGGTTT 59.025 47.619 4.53 0.00 38.35 3.27
1652 1655 1.149077 AGGTATTGGGCCTGTTTGGTT 59.851 47.619 4.53 0.00 38.35 3.67
1653 1656 0.783850 AGGTATTGGGCCTGTTTGGT 59.216 50.000 4.53 0.00 38.35 3.67
1654 1657 1.937191 AAGGTATTGGGCCTGTTTGG 58.063 50.000 4.53 0.00 36.30 3.28
1655 1658 4.350368 AAAAAGGTATTGGGCCTGTTTG 57.650 40.909 4.53 0.00 40.86 2.93
1696 1699 8.796475 CCTTCTTTCTTAATCAGTGAAAATGGA 58.204 33.333 0.00 0.00 29.44 3.41
1715 1718 6.754675 CGTTGTGACCATTTAAAACCTTCTTT 59.245 34.615 0.00 0.00 0.00 2.52
1731 1738 1.716826 TTTGTTCCGGCGTTGTGACC 61.717 55.000 6.01 0.00 0.00 4.02
1733 1740 1.880271 TATTTGTTCCGGCGTTGTGA 58.120 45.000 6.01 0.00 0.00 3.58
1739 1746 4.427312 AGTAGTAGTTATTTGTTCCGGCG 58.573 43.478 0.00 0.00 0.00 6.46
1745 1752 5.105997 ACCGCGAGAGTAGTAGTTATTTGTT 60.106 40.000 8.23 0.00 0.00 2.83
1747 1754 4.918037 ACCGCGAGAGTAGTAGTTATTTG 58.082 43.478 8.23 0.00 0.00 2.32
1751 1758 6.280643 TGTAATACCGCGAGAGTAGTAGTTA 58.719 40.000 8.23 0.00 0.00 2.24
1769 1776 6.320164 GTGCCACCCACTTGAATATTGTAATA 59.680 38.462 0.00 0.00 41.35 0.98
1817 1824 2.607187 GTCGCGAAGATCAAAGAGGAA 58.393 47.619 12.06 0.00 0.00 3.36
1866 1873 1.527380 GCAACACGGGGGTCTTTCA 60.527 57.895 0.00 0.00 0.00 2.69
1876 1883 1.781025 TTGGAAAGAGCGCAACACGG 61.781 55.000 11.47 0.00 43.93 4.94
1913 1920 3.010584 AGGCTATGTCCACCTTGTTCATT 59.989 43.478 0.00 0.00 0.00 2.57
1927 1934 5.624738 CGTGGAAACTAGAGAAAGGCTATGT 60.625 44.000 0.00 0.00 0.00 2.29
1998 2007 1.371467 TGATGTGGTGAAGGGATGGT 58.629 50.000 0.00 0.00 0.00 3.55
1999 2008 2.092267 TGATGATGTGGTGAAGGGATGG 60.092 50.000 0.00 0.00 0.00 3.51
2001 2010 3.203710 ACATGATGATGTGGTGAAGGGAT 59.796 43.478 0.00 0.00 41.52 3.85
2002 2011 2.577563 ACATGATGATGTGGTGAAGGGA 59.422 45.455 0.00 0.00 41.52 4.20
2018 2028 1.199615 TCGTGGATTGGCCTACATGA 58.800 50.000 3.32 0.00 37.63 3.07
2046 2056 3.517296 TCTCCTAATGTGTTTTGGCCA 57.483 42.857 0.00 0.00 31.08 5.36
2061 2071 0.689623 CTTCCAGTGCAGGTTCTCCT 59.310 55.000 0.00 0.00 46.37 3.69
2093 2103 5.319043 TGTAAGAAAGTCCAGGAAACCAT 57.681 39.130 0.00 0.00 0.00 3.55
2094 2104 4.781775 TGTAAGAAAGTCCAGGAAACCA 57.218 40.909 0.00 0.00 0.00 3.67
2109 2119 5.499139 CAACCTTTGCTCACTTTGTAAGA 57.501 39.130 0.00 0.00 0.00 2.10
2150 2160 2.504032 GACCGATCGATTGCCCCA 59.496 61.111 18.66 0.00 0.00 4.96
2183 2193 9.643693 CAAGTCTTTTGCTTGGTTGATTATTAT 57.356 29.630 0.00 0.00 39.53 1.28
2188 2198 4.122046 GCAAGTCTTTTGCTTGGTTGATT 58.878 39.130 4.73 0.00 42.44 2.57
2225 2238 3.594134 TGCTGTTGTTTGAAAGGTTTGG 58.406 40.909 0.00 0.00 0.00 3.28
2234 2247 1.689984 TCATGCCTGCTGTTGTTTGA 58.310 45.000 0.00 0.00 0.00 2.69
2265 2278 0.398696 TGGTGTAGTTTGCGGGACAT 59.601 50.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.