Multiple sequence alignment - TraesCS4D01G304900

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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 TraesCS4D01G304900 chr4D 100.000 2243 0 0 1 2243 473762785 473765027 0.000000e+00 4143.0
1 TraesCS4D01G304900 chr4D 86.607 112 7 1 1592 1695 67466322 67466433 1.410000e-22 117.0
2 TraesCS4D01G304900 chr4D 80.734 109 12 5 1591 1690 66516565 66516457 2.390000e-10 76.8
3 TraesCS4D01G304900 chr4D 97.674 43 1 0 1288 1330 477757225 477757183 8.590000e-10 75.0
4 TraesCS4D01G304900 chr4D 97.674 43 0 1 1288 1330 437514751 437514792 3.090000e-09 73.1
5 TraesCS4D01G304900 chr7D 94.966 1331 64 3 1 1330 580108601 580107273 0.000000e+00 2084.0
6 TraesCS4D01G304900 chr7D 93.321 524 17 9 1738 2243 626192252 626191729 0.000000e+00 758.0
7 TraesCS4D01G304900 chr7D 93.478 46 2 1 1592 1636 65601766 65601721 1.440000e-07 67.6
8 TraesCS4D01G304900 chr6B 92.117 1332 101 4 1 1330 346411566 346410237 0.000000e+00 1875.0
9 TraesCS4D01G304900 chr6B 92.453 53 4 0 1642 1694 52205217 52205165 2.390000e-10 76.8
10 TraesCS4D01G304900 chr6B 90.909 55 3 2 1645 1699 703317958 703317906 3.090000e-09 73.1
11 TraesCS4D01G304900 chr2A 92.111 1331 104 1 1 1330 608931835 608930505 0.000000e+00 1875.0
12 TraesCS4D01G304900 chr2A 81.982 111 10 2 1592 1693 748957449 748957558 3.970000e-13 86.1
13 TraesCS4D01G304900 chr2A 81.081 111 11 5 1592 1693 755931419 755931310 1.850000e-11 80.5
14 TraesCS4D01G304900 chr4B 92.036 1331 104 2 1 1330 92555001 92556330 0.000000e+00 1869.0
15 TraesCS4D01G304900 chr4B 88.991 109 4 2 1590 1690 414860854 414860746 6.500000e-26 128.0
16 TraesCS4D01G304900 chr5B 91.892 1332 106 2 1 1331 239320331 239319001 0.000000e+00 1860.0
17 TraesCS4D01G304900 chr5B 87.963 108 5 1 1591 1690 617823368 617823475 1.090000e-23 121.0
18 TraesCS4D01G304900 chr5B 79.464 112 13 6 1588 1690 445493902 445493792 1.110000e-08 71.3
19 TraesCS4D01G304900 chr7B 91.886 1331 106 2 1 1330 516458007 516459336 0.000000e+00 1858.0
20 TraesCS4D01G304900 chr5A 91.886 1331 106 2 1 1330 320274484 320275813 0.000000e+00 1858.0
21 TraesCS4D01G304900 chr1B 91.811 1331 108 1 1 1330 269056611 269055281 0.000000e+00 1853.0
22 TraesCS4D01G304900 chr3A 91.517 1332 110 3 1 1330 115387861 115386531 0.000000e+00 1831.0
23 TraesCS4D01G304900 chr3A 96.614 502 16 1 1742 2243 119485487 119485987 0.000000e+00 832.0
24 TraesCS4D01G304900 chr3A 90.684 526 20 4 1736 2243 600088609 600089123 0.000000e+00 673.0
25 TraesCS4D01G304900 chr3A 86.607 112 6 2 1587 1690 477332152 477332042 5.060000e-22 115.0
26 TraesCS4D01G304900 chr3A 82.883 111 9 2 1591 1692 722506810 722506919 8.530000e-15 91.6
27 TraesCS4D01G304900 chr1D 97.222 504 14 0 1740 2243 467435931 467435428 0.000000e+00 854.0
28 TraesCS4D01G304900 chr1D 87.037 108 6 1 1592 1691 97921462 97921569 5.060000e-22 115.0
29 TraesCS4D01G304900 chr1D 98.039 51 1 0 1591 1641 52572240 52572290 3.070000e-14 89.8
30 TraesCS4D01G304900 chr1D 100.000 30 0 0 1288 1317 466012444 466012415 3.110000e-04 56.5
31 TraesCS4D01G304900 chr3D 97.211 502 14 0 1742 2243 55370870 55370369 0.000000e+00 850.0
32 TraesCS4D01G304900 chr1A 96.040 505 16 4 1741 2243 463970996 463970494 0.000000e+00 819.0
33 TraesCS4D01G304900 chr1A 93.028 502 30 4 1743 2243 16924570 16925067 0.000000e+00 728.0
34 TraesCS4D01G304900 chr2D 96.185 498 19 0 1746 2243 647089492 647089989 0.000000e+00 815.0
35 TraesCS4D01G304900 chr2D 94.800 500 26 0 1744 2243 646861907 646862406 0.000000e+00 780.0
36 TraesCS4D01G304900 chr5D 94.391 517 13 1 1743 2243 353959039 353958523 0.000000e+00 780.0
37 TraesCS4D01G304900 chr5D 87.500 96 8 4 1236 1330 305190789 305190881 8.470000e-20 108.0
38 TraesCS4D01G304900 chr3B 91.731 520 26 3 1741 2243 581035093 581034574 0.000000e+00 706.0
39 TraesCS4D01G304900 chr4A 86.607 112 7 1 1592 1695 516936217 516936328 1.410000e-22 117.0
40 TraesCS4D01G304900 chr6D 86.111 108 7 1 1591 1690 439917033 439917140 2.360000e-20 110.0
41 TraesCS4D01G304900 chr6D 74.704 253 56 5 1084 1330 265883948 265883698 3.050000e-19 106.0
42 TraesCS4D01G304900 chr6A 81.982 111 10 2 1592 1693 8192965 8193074 3.970000e-13 86.1
43 TraesCS4D01G304900 chr6A 82.178 101 11 2 1591 1684 491039210 491039110 1.850000e-11 80.5
44 TraesCS4D01G304900 chr6A 91.837 49 3 1 1589 1636 573210710 573210662 1.440000e-07 67.6
45 TraesCS4D01G304900 chr7A 95.652 46 1 1 1592 1636 82206167 82206212 3.090000e-09 73.1


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 TraesCS4D01G304900 chr4D 473762785 473765027 2242 False 4143 4143 100.000 1 2243 1 chr4D.!!$F3 2242
1 TraesCS4D01G304900 chr7D 580107273 580108601 1328 True 2084 2084 94.966 1 1330 1 chr7D.!!$R2 1329
2 TraesCS4D01G304900 chr7D 626191729 626192252 523 True 758 758 93.321 1738 2243 1 chr7D.!!$R3 505
3 TraesCS4D01G304900 chr6B 346410237 346411566 1329 True 1875 1875 92.117 1 1330 1 chr6B.!!$R2 1329
4 TraesCS4D01G304900 chr2A 608930505 608931835 1330 True 1875 1875 92.111 1 1330 1 chr2A.!!$R1 1329
5 TraesCS4D01G304900 chr4B 92555001 92556330 1329 False 1869 1869 92.036 1 1330 1 chr4B.!!$F1 1329
6 TraesCS4D01G304900 chr5B 239319001 239320331 1330 True 1860 1860 91.892 1 1331 1 chr5B.!!$R1 1330
7 TraesCS4D01G304900 chr7B 516458007 516459336 1329 False 1858 1858 91.886 1 1330 1 chr7B.!!$F1 1329
8 TraesCS4D01G304900 chr5A 320274484 320275813 1329 False 1858 1858 91.886 1 1330 1 chr5A.!!$F1 1329
9 TraesCS4D01G304900 chr1B 269055281 269056611 1330 True 1853 1853 91.811 1 1330 1 chr1B.!!$R1 1329
10 TraesCS4D01G304900 chr3A 115386531 115387861 1330 True 1831 1831 91.517 1 1330 1 chr3A.!!$R1 1329
11 TraesCS4D01G304900 chr3A 119485487 119485987 500 False 832 832 96.614 1742 2243 1 chr3A.!!$F1 501
12 TraesCS4D01G304900 chr3A 600088609 600089123 514 False 673 673 90.684 1736 2243 1 chr3A.!!$F2 507
13 TraesCS4D01G304900 chr1D 467435428 467435931 503 True 854 854 97.222 1740 2243 1 chr1D.!!$R2 503
14 TraesCS4D01G304900 chr3D 55370369 55370870 501 True 850 850 97.211 1742 2243 1 chr3D.!!$R1 501
15 TraesCS4D01G304900 chr1A 463970494 463970996 502 True 819 819 96.040 1741 2243 1 chr1A.!!$R1 502
16 TraesCS4D01G304900 chr5D 353958523 353959039 516 True 780 780 94.391 1743 2243 1 chr5D.!!$R1 500
17 TraesCS4D01G304900 chr3B 581034574 581035093 519 True 706 706 91.731 1741 2243 1 chr3B.!!$R1 502

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
202 203 1.029681 GGGCACGAACAAGGTTTCTT 58.97 50.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 1357 0.098025 ACGTGCGGTCTGTTTTGTTG 59.902 50.0 0.0 0.0 0.0 3.33 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
84 85 3.052036 CCAAACAATTCTTGTCAAGGCG 58.948 45.455 12.66 2.04 44.59 5.52
95 96 1.909781 TCAAGGCGGTCCTAACGGT 60.910 57.895 0.00 0.00 43.40 4.83
163 164 6.545298 GGTCCTTCAGAAAATTGATAGCATCT 59.455 38.462 0.00 0.00 0.00 2.90
202 203 1.029681 GGGCACGAACAAGGTTTCTT 58.970 50.000 0.00 0.00 0.00 2.52
222 223 6.916360 TCTTGAGGGAAATGCAAAGTAAAT 57.084 33.333 0.00 0.00 0.00 1.40
402 404 2.158561 ATTTCTTTGCGGCAGCCACC 62.159 55.000 13.30 1.71 44.33 4.61
430 432 1.546773 CCGTGGGAAATGGAAGGACAA 60.547 52.381 0.00 0.00 37.06 3.18
488 490 1.101635 CCTCGTGACATCGCTCCCTA 61.102 60.000 0.00 0.00 0.00 3.53
500 502 2.011222 CGCTCCCTATCTCTACGATCC 58.989 57.143 0.00 0.00 33.48 3.36
502 504 2.946791 GCTCCCTATCTCTACGATCCCC 60.947 59.091 0.00 0.00 33.48 4.81
541 543 1.387295 GGTTCAGCAAGCTATGGCCC 61.387 60.000 0.00 0.00 39.73 5.80
848 850 3.589654 CTTCGGACCGCTTGAGCCA 62.590 63.158 9.66 0.00 37.91 4.75
903 905 5.186021 TCTTTGTAAGCAAACCCAAGAAACA 59.814 36.000 0.00 0.00 39.43 2.83
927 929 1.346068 GCTCACCTTCTCTTCCAGTGT 59.654 52.381 0.00 0.00 0.00 3.55
1260 1262 1.653151 AGTCCTTTTATTCGCCGCTC 58.347 50.000 0.00 0.00 0.00 5.03
1286 1289 5.005490 GCGGTTTCTATCTAAACTTTCTCCG 59.995 44.000 0.00 0.00 38.98 4.63
1345 1348 2.989422 AAAAGGTGCTAACGTGCATC 57.011 45.000 3.69 3.35 45.23 3.91
1363 1366 3.894920 CATCGTGGTATGCAACAAAACA 58.105 40.909 0.00 0.00 0.00 2.83
1364 1367 3.617540 TCGTGGTATGCAACAAAACAG 57.382 42.857 0.00 0.00 0.00 3.16
1365 1368 3.206964 TCGTGGTATGCAACAAAACAGA 58.793 40.909 0.00 0.00 0.00 3.41
1366 1369 3.002862 TCGTGGTATGCAACAAAACAGAC 59.997 43.478 0.00 0.00 0.00 3.51
1367 1370 3.638484 GTGGTATGCAACAAAACAGACC 58.362 45.455 0.00 0.00 46.13 3.85
1368 1371 2.928694 GGTATGCAACAAAACAGACCG 58.071 47.619 0.00 0.00 38.30 4.79
1369 1372 2.315901 GTATGCAACAAAACAGACCGC 58.684 47.619 0.00 0.00 0.00 5.68
1370 1373 0.743688 ATGCAACAAAACAGACCGCA 59.256 45.000 0.00 0.00 0.00 5.69
1371 1374 0.179150 TGCAACAAAACAGACCGCAC 60.179 50.000 0.00 0.00 0.00 5.34
1372 1375 1.199852 GCAACAAAACAGACCGCACG 61.200 55.000 0.00 0.00 0.00 5.34
1373 1376 0.098025 CAACAAAACAGACCGCACGT 59.902 50.000 0.00 0.00 0.00 4.49
1374 1377 0.375803 AACAAAACAGACCGCACGTC 59.624 50.000 0.00 0.00 42.32 4.34
1375 1378 1.278637 CAAAACAGACCGCACGTCC 59.721 57.895 0.00 0.00 43.08 4.79
1376 1379 1.153329 AAAACAGACCGCACGTCCA 60.153 52.632 0.00 0.00 43.08 4.02
1377 1380 0.534203 AAAACAGACCGCACGTCCAT 60.534 50.000 0.00 0.00 43.08 3.41
1378 1381 0.949105 AAACAGACCGCACGTCCATC 60.949 55.000 0.00 0.00 43.08 3.51
1379 1382 2.094757 AACAGACCGCACGTCCATCA 62.095 55.000 0.00 0.00 43.08 3.07
1380 1383 1.374125 CAGACCGCACGTCCATCAA 60.374 57.895 0.00 0.00 43.08 2.57
1381 1384 1.079819 AGACCGCACGTCCATCAAG 60.080 57.895 0.00 0.00 43.08 3.02
1382 1385 1.080093 GACCGCACGTCCATCAAGA 60.080 57.895 0.00 0.00 35.23 3.02
1383 1386 0.669318 GACCGCACGTCCATCAAGAA 60.669 55.000 0.00 0.00 35.23 2.52
1384 1387 0.670546 ACCGCACGTCCATCAAGAAG 60.671 55.000 0.00 0.00 0.00 2.85
1385 1388 0.670546 CCGCACGTCCATCAAGAAGT 60.671 55.000 0.00 0.00 0.00 3.01
1386 1389 0.439985 CGCACGTCCATCAAGAAGTG 59.560 55.000 3.67 3.67 45.49 3.16
1387 1390 0.798776 GCACGTCCATCAAGAAGTGG 59.201 55.000 9.13 0.00 43.70 4.00
1388 1391 1.608025 GCACGTCCATCAAGAAGTGGA 60.608 52.381 9.13 0.00 43.70 4.02
1389 1392 2.936993 GCACGTCCATCAAGAAGTGGAT 60.937 50.000 9.13 0.00 45.57 3.41
1390 1393 2.932614 CACGTCCATCAAGAAGTGGATC 59.067 50.000 0.00 0.00 45.57 3.36
1391 1394 2.196749 CGTCCATCAAGAAGTGGATCG 58.803 52.381 0.00 0.76 45.57 3.69
1392 1395 2.417379 CGTCCATCAAGAAGTGGATCGT 60.417 50.000 0.00 0.00 45.57 3.73
1393 1396 2.932614 GTCCATCAAGAAGTGGATCGTG 59.067 50.000 0.00 0.00 45.57 4.35
1394 1397 1.667724 CCATCAAGAAGTGGATCGTGC 59.332 52.381 0.00 0.00 37.72 5.34
1395 1398 1.667724 CATCAAGAAGTGGATCGTGCC 59.332 52.381 0.00 0.00 0.00 5.01
1396 1399 0.684535 TCAAGAAGTGGATCGTGCCA 59.315 50.000 0.00 0.00 35.02 4.92
1397 1400 1.081892 CAAGAAGTGGATCGTGCCAG 58.918 55.000 0.00 0.00 38.95 4.85
1398 1401 0.976641 AAGAAGTGGATCGTGCCAGA 59.023 50.000 0.00 0.00 38.95 3.86
1399 1402 0.247736 AGAAGTGGATCGTGCCAGAC 59.752 55.000 0.00 0.00 38.95 3.51
1433 1436 4.828925 GAGAGGCTCTGTGGCGCC 62.829 72.222 24.21 22.73 46.88 6.53
1438 1441 3.127533 GCTCTGTGGCGCCGATTT 61.128 61.111 23.90 0.00 0.00 2.17
1439 1442 2.690778 GCTCTGTGGCGCCGATTTT 61.691 57.895 23.90 0.00 0.00 1.82
1440 1443 1.135315 CTCTGTGGCGCCGATTTTG 59.865 57.895 23.90 8.60 0.00 2.44
1441 1444 1.577328 CTCTGTGGCGCCGATTTTGT 61.577 55.000 23.90 0.00 0.00 2.83
1442 1445 1.442520 CTGTGGCGCCGATTTTGTG 60.443 57.895 23.90 1.70 0.00 3.33
1443 1446 1.851021 CTGTGGCGCCGATTTTGTGA 61.851 55.000 23.90 0.00 0.00 3.58
1444 1447 1.442017 GTGGCGCCGATTTTGTGAC 60.442 57.895 23.90 7.01 0.00 3.67
1445 1448 1.894282 TGGCGCCGATTTTGTGACA 60.894 52.632 23.90 0.00 0.00 3.58
1446 1449 1.284408 GGCGCCGATTTTGTGACAA 59.716 52.632 12.58 0.00 0.00 3.18
1447 1450 0.318275 GGCGCCGATTTTGTGACAAA 60.318 50.000 12.58 6.66 0.00 2.83
1448 1451 0.775861 GCGCCGATTTTGTGACAAAC 59.224 50.000 10.72 0.00 0.00 2.93
1449 1452 1.041726 CGCCGATTTTGTGACAAACG 58.958 50.000 10.72 11.70 0.00 3.60
1450 1453 1.595976 CGCCGATTTTGTGACAAACGT 60.596 47.619 10.72 2.48 0.00 3.99
1451 1454 2.456010 GCCGATTTTGTGACAAACGTT 58.544 42.857 10.72 0.00 0.00 3.99
1452 1455 2.215363 GCCGATTTTGTGACAAACGTTG 59.785 45.455 10.72 6.58 0.00 4.10
1453 1456 2.215363 CCGATTTTGTGACAAACGTTGC 59.785 45.455 10.72 0.00 0.00 4.17
1454 1457 2.098589 CGATTTTGTGACAAACGTTGCG 60.099 45.455 10.72 6.54 0.00 4.85
1455 1458 1.618861 TTTTGTGACAAACGTTGCGG 58.381 45.000 10.72 0.00 0.00 5.69
1456 1459 0.798771 TTTGTGACAAACGTTGCGGC 60.799 50.000 6.66 0.00 0.00 6.53
1457 1460 2.720750 GTGACAAACGTTGCGGCG 60.721 61.111 0.00 0.51 37.94 6.46
1459 1462 2.720750 GACAAACGTTGCGGCGTG 60.721 61.111 9.37 0.00 45.00 5.34
1460 1463 4.897856 ACAAACGTTGCGGCGTGC 62.898 61.111 9.37 0.00 45.00 5.34
1470 1473 4.803426 CGGCGTGCACTCCTCCTC 62.803 72.222 22.83 0.00 0.00 3.71
1471 1474 4.803426 GGCGTGCACTCCTCCTCG 62.803 72.222 18.74 1.35 0.00 4.63
1472 1475 4.803426 GCGTGCACTCCTCCTCGG 62.803 72.222 16.19 0.00 0.00 4.63
1473 1476 4.803426 CGTGCACTCCTCCTCGGC 62.803 72.222 16.19 0.00 0.00 5.54
1474 1477 4.459089 GTGCACTCCTCCTCGGCC 62.459 72.222 10.32 0.00 0.00 6.13
1492 1495 2.580867 GCTCCACGAGCGCAGTAG 60.581 66.667 11.47 5.82 45.85 2.57
1493 1496 2.580867 CTCCACGAGCGCAGTAGC 60.581 66.667 11.47 0.00 37.42 3.58
1494 1497 3.342370 CTCCACGAGCGCAGTAGCA 62.342 63.158 11.47 0.00 42.27 3.49
1495 1498 2.432456 CCACGAGCGCAGTAGCAA 60.432 61.111 11.47 0.00 42.27 3.91
1496 1499 2.447887 CCACGAGCGCAGTAGCAAG 61.448 63.158 11.47 0.00 42.27 4.01
1497 1500 2.811317 ACGAGCGCAGTAGCAAGC 60.811 61.111 11.47 0.00 42.27 4.01
1503 1506 3.854459 GCAGTAGCAAGCGCCGAC 61.854 66.667 2.29 0.00 41.58 4.79
1504 1507 3.188786 CAGTAGCAAGCGCCGACC 61.189 66.667 2.29 0.00 39.83 4.79
1505 1508 3.691342 AGTAGCAAGCGCCGACCA 61.691 61.111 2.29 0.00 39.83 4.02
1506 1509 3.488090 GTAGCAAGCGCCGACCAC 61.488 66.667 2.29 0.00 39.83 4.16
1507 1510 3.691342 TAGCAAGCGCCGACCACT 61.691 61.111 2.29 0.00 39.83 4.00
1508 1511 3.932580 TAGCAAGCGCCGACCACTG 62.933 63.158 2.29 0.00 39.83 3.66
1510 1513 4.988598 CAAGCGCCGACCACTGGT 62.989 66.667 2.29 0.00 39.44 4.00
1511 1514 4.250305 AAGCGCCGACCACTGGTT 62.250 61.111 2.29 0.00 35.25 3.67
1512 1515 3.767630 AAGCGCCGACCACTGGTTT 62.768 57.895 2.29 0.00 35.25 3.27
1513 1516 4.025401 GCGCCGACCACTGGTTTG 62.025 66.667 1.13 0.00 35.25 2.93
1514 1517 2.590575 CGCCGACCACTGGTTTGT 60.591 61.111 1.13 0.00 35.25 2.83
1515 1518 2.892334 CGCCGACCACTGGTTTGTG 61.892 63.158 1.13 0.00 35.25 3.33
1522 1525 3.073086 CACTGGTTTGTGGTCGACA 57.927 52.632 18.91 0.27 34.56 4.35
1523 1526 1.374560 CACTGGTTTGTGGTCGACAA 58.625 50.000 18.91 2.10 43.11 3.18
1529 1532 1.353804 TTGTGGTCGACAAAAGCGC 59.646 52.632 18.91 0.00 41.80 5.92
1530 1533 2.054140 TTGTGGTCGACAAAAGCGCC 62.054 55.000 18.91 0.00 41.80 6.53
1531 1534 2.203084 TGGTCGACAAAAGCGCCA 60.203 55.556 18.91 0.00 34.36 5.69
1532 1535 2.251371 GGTCGACAAAAGCGCCAC 59.749 61.111 18.91 0.00 0.00 5.01
1533 1536 2.127758 GTCGACAAAAGCGCCACG 60.128 61.111 11.55 1.20 0.00 4.94
1591 1594 3.771160 CCCGCGTGGTTCCTAGCT 61.771 66.667 15.14 0.00 0.00 3.32
1592 1595 2.420568 CCCGCGTGGTTCCTAGCTA 61.421 63.158 15.14 0.00 0.00 3.32
1593 1596 1.226888 CCGCGTGGTTCCTAGCTAC 60.227 63.158 6.91 0.00 0.00 3.58
1594 1597 1.664321 CCGCGTGGTTCCTAGCTACT 61.664 60.000 6.91 0.00 0.00 2.57
1595 1598 1.019673 CGCGTGGTTCCTAGCTACTA 58.980 55.000 0.00 0.00 0.00 1.82
1596 1599 1.268437 CGCGTGGTTCCTAGCTACTAC 60.268 57.143 0.00 0.00 0.00 2.73
1597 1600 1.066757 GCGTGGTTCCTAGCTACTACC 59.933 57.143 7.07 7.07 0.00 3.18
1598 1601 2.652590 CGTGGTTCCTAGCTACTACCT 58.347 52.381 12.81 0.00 0.00 3.08
1599 1602 2.617774 CGTGGTTCCTAGCTACTACCTC 59.382 54.545 12.81 9.49 0.00 3.85
1600 1603 3.684981 CGTGGTTCCTAGCTACTACCTCT 60.685 52.174 12.81 0.00 0.00 3.69
1601 1604 3.633065 GTGGTTCCTAGCTACTACCTCTG 59.367 52.174 12.81 0.00 0.00 3.35
1602 1605 3.268856 TGGTTCCTAGCTACTACCTCTGT 59.731 47.826 12.81 0.00 0.00 3.41
1603 1606 4.264262 TGGTTCCTAGCTACTACCTCTGTT 60.264 45.833 12.81 0.00 0.00 3.16
1604 1607 4.338964 GGTTCCTAGCTACTACCTCTGTTC 59.661 50.000 0.00 0.00 0.00 3.18
1605 1608 4.857130 TCCTAGCTACTACCTCTGTTCA 57.143 45.455 0.00 0.00 0.00 3.18
1606 1609 4.525024 TCCTAGCTACTACCTCTGTTCAC 58.475 47.826 0.00 0.00 0.00 3.18
1607 1610 4.227754 TCCTAGCTACTACCTCTGTTCACT 59.772 45.833 0.00 0.00 0.00 3.41
1608 1611 4.951094 CCTAGCTACTACCTCTGTTCACTT 59.049 45.833 0.00 0.00 0.00 3.16
1609 1612 5.419471 CCTAGCTACTACCTCTGTTCACTTT 59.581 44.000 0.00 0.00 0.00 2.66
1610 1613 5.810080 AGCTACTACCTCTGTTCACTTTT 57.190 39.130 0.00 0.00 0.00 2.27
1611 1614 6.912951 AGCTACTACCTCTGTTCACTTTTA 57.087 37.500 0.00 0.00 0.00 1.52
1612 1615 7.483580 AGCTACTACCTCTGTTCACTTTTAT 57.516 36.000 0.00 0.00 0.00 1.40
1613 1616 8.591114 AGCTACTACCTCTGTTCACTTTTATA 57.409 34.615 0.00 0.00 0.00 0.98
1614 1617 9.032624 AGCTACTACCTCTGTTCACTTTTATAA 57.967 33.333 0.00 0.00 0.00 0.98
1615 1618 9.303537 GCTACTACCTCTGTTCACTTTTATAAG 57.696 37.037 0.00 0.00 37.40 1.73
1618 1621 8.867097 ACTACCTCTGTTCACTTTTATAAGACA 58.133 33.333 0.00 0.00 35.30 3.41
1619 1622 9.877178 CTACCTCTGTTCACTTTTATAAGACAT 57.123 33.333 0.00 0.00 35.30 3.06
1621 1624 9.574516 ACCTCTGTTCACTTTTATAAGACATTT 57.425 29.630 0.00 0.00 35.30 2.32
1637 1640 9.950496 ATAAGACATTTTAGACATTCAGACACT 57.050 29.630 0.00 0.00 0.00 3.55
1638 1641 7.664082 AGACATTTTAGACATTCAGACACTG 57.336 36.000 0.00 0.00 0.00 3.66
1639 1642 7.220030 AGACATTTTAGACATTCAGACACTGT 58.780 34.615 0.00 0.00 32.61 3.55
1640 1643 7.716998 AGACATTTTAGACATTCAGACACTGTT 59.283 33.333 0.00 0.00 32.61 3.16
1641 1644 8.225603 ACATTTTAGACATTCAGACACTGTTT 57.774 30.769 0.00 0.00 32.61 2.83
1642 1645 9.337396 ACATTTTAGACATTCAGACACTGTTTA 57.663 29.630 0.00 0.00 32.61 2.01
1643 1646 9.599322 CATTTTAGACATTCAGACACTGTTTAC 57.401 33.333 0.00 0.00 32.61 2.01
1644 1647 8.725405 TTTTAGACATTCAGACACTGTTTACA 57.275 30.769 0.00 0.00 32.61 2.41
1645 1648 8.725405 TTTAGACATTCAGACACTGTTTACAA 57.275 30.769 0.00 0.00 32.61 2.41
1646 1649 8.725405 TTAGACATTCAGACACTGTTTACAAA 57.275 30.769 0.00 0.00 32.61 2.83
1647 1650 7.251704 AGACATTCAGACACTGTTTACAAAG 57.748 36.000 0.00 0.00 32.61 2.77
1648 1651 5.821204 ACATTCAGACACTGTTTACAAAGC 58.179 37.500 0.00 0.00 32.61 3.51
1649 1652 5.356751 ACATTCAGACACTGTTTACAAAGCA 59.643 36.000 0.00 0.00 32.61 3.91
1650 1653 5.484173 TTCAGACACTGTTTACAAAGCAG 57.516 39.130 2.44 2.44 36.41 4.24
1651 1654 3.876914 TCAGACACTGTTTACAAAGCAGG 59.123 43.478 8.13 1.12 34.79 4.85
1652 1655 2.618709 AGACACTGTTTACAAAGCAGGC 59.381 45.455 8.13 0.00 34.79 4.85
1653 1656 2.618709 GACACTGTTTACAAAGCAGGCT 59.381 45.455 8.13 0.00 34.79 4.58
1654 1657 2.358898 ACACTGTTTACAAAGCAGGCTG 59.641 45.455 10.94 10.94 34.79 4.85
1655 1658 2.358898 CACTGTTTACAAAGCAGGCTGT 59.641 45.455 17.16 0.00 34.79 4.40
1656 1659 2.618709 ACTGTTTACAAAGCAGGCTGTC 59.381 45.455 17.16 8.57 34.79 3.51
1657 1660 2.880890 CTGTTTACAAAGCAGGCTGTCT 59.119 45.455 17.16 10.85 0.00 3.41
1658 1661 2.618241 TGTTTACAAAGCAGGCTGTCTG 59.382 45.455 17.16 4.57 46.03 3.51
1659 1662 2.878406 GTTTACAAAGCAGGCTGTCTGA 59.122 45.455 14.48 0.00 46.18 3.27
1660 1663 2.928801 TACAAAGCAGGCTGTCTGAA 57.071 45.000 14.48 0.00 46.18 3.02
1661 1664 2.057137 ACAAAGCAGGCTGTCTGAAA 57.943 45.000 14.48 0.00 46.18 2.69
1662 1665 2.590821 ACAAAGCAGGCTGTCTGAAAT 58.409 42.857 14.48 0.00 46.18 2.17
1663 1666 2.295349 ACAAAGCAGGCTGTCTGAAATG 59.705 45.455 14.48 9.91 46.18 2.32
1664 1667 0.886563 AAGCAGGCTGTCTGAAATGC 59.113 50.000 14.48 0.00 46.18 3.56
1665 1668 0.964358 AGCAGGCTGTCTGAAATGCC 60.964 55.000 14.48 8.25 46.18 4.40
1672 1675 5.835113 GGCTGTCTGAAATGCCTTATAAA 57.165 39.130 8.85 0.00 41.92 1.40
1673 1676 6.207691 GGCTGTCTGAAATGCCTTATAAAA 57.792 37.500 8.85 0.00 41.92 1.52
1674 1677 6.630071 GGCTGTCTGAAATGCCTTATAAAAA 58.370 36.000 8.85 0.00 41.92 1.94
1675 1678 6.531594 GGCTGTCTGAAATGCCTTATAAAAAC 59.468 38.462 8.85 0.00 41.92 2.43
1676 1679 7.090173 GCTGTCTGAAATGCCTTATAAAAACA 58.910 34.615 0.00 0.00 0.00 2.83
1677 1680 7.598493 GCTGTCTGAAATGCCTTATAAAAACAA 59.402 33.333 0.00 0.00 0.00 2.83
1678 1681 9.474920 CTGTCTGAAATGCCTTATAAAAACAAA 57.525 29.630 0.00 0.00 0.00 2.83
1679 1682 9.255304 TGTCTGAAATGCCTTATAAAAACAAAC 57.745 29.630 0.00 0.00 0.00 2.93
1680 1683 8.424731 GTCTGAAATGCCTTATAAAAACAAACG 58.575 33.333 0.00 0.00 0.00 3.60
1681 1684 7.596995 TCTGAAATGCCTTATAAAAACAAACGG 59.403 33.333 0.00 0.00 0.00 4.44
1682 1685 7.434492 TGAAATGCCTTATAAAAACAAACGGA 58.566 30.769 0.00 0.00 0.00 4.69
1683 1686 7.596995 TGAAATGCCTTATAAAAACAAACGGAG 59.403 33.333 0.00 0.00 0.00 4.63
1684 1687 5.379732 TGCCTTATAAAAACAAACGGAGG 57.620 39.130 0.00 0.00 0.00 4.30
1685 1688 4.218852 TGCCTTATAAAAACAAACGGAGGG 59.781 41.667 0.00 0.00 0.00 4.30
1686 1689 4.460034 GCCTTATAAAAACAAACGGAGGGA 59.540 41.667 0.00 0.00 0.00 4.20
1687 1690 5.392703 GCCTTATAAAAACAAACGGAGGGAG 60.393 44.000 0.00 0.00 0.00 4.30
1688 1691 5.708697 CCTTATAAAAACAAACGGAGGGAGT 59.291 40.000 0.00 0.00 0.00 3.85
1689 1692 6.880529 CCTTATAAAAACAAACGGAGGGAGTA 59.119 38.462 0.00 0.00 0.00 2.59
1690 1693 7.148356 CCTTATAAAAACAAACGGAGGGAGTAC 60.148 40.741 0.00 0.00 0.00 2.73
1691 1694 3.564053 AAAACAAACGGAGGGAGTACA 57.436 42.857 0.00 0.00 0.00 2.90
1692 1695 3.782656 AAACAAACGGAGGGAGTACAT 57.217 42.857 0.00 0.00 0.00 2.29
1693 1696 4.895668 AAACAAACGGAGGGAGTACATA 57.104 40.909 0.00 0.00 0.00 2.29
1694 1697 3.881937 ACAAACGGAGGGAGTACATAC 57.118 47.619 0.00 0.00 0.00 2.39
1695 1698 2.165030 ACAAACGGAGGGAGTACATACG 59.835 50.000 0.00 0.00 0.00 3.06
1696 1699 2.134789 AACGGAGGGAGTACATACGT 57.865 50.000 0.00 0.00 34.25 3.57
1697 1700 3.281727 AACGGAGGGAGTACATACGTA 57.718 47.619 0.00 0.00 32.35 3.57
1705 1708 2.114638 GTACATACGTACCGGCCCA 58.885 57.895 0.00 0.00 41.92 5.36
1706 1709 0.675633 GTACATACGTACCGGCCCAT 59.324 55.000 0.00 0.00 41.92 4.00
1707 1710 0.961019 TACATACGTACCGGCCCATC 59.039 55.000 0.00 0.00 0.00 3.51
1708 1711 1.372499 CATACGTACCGGCCCATCG 60.372 63.158 0.00 1.74 0.00 3.84
1709 1712 1.529010 ATACGTACCGGCCCATCGA 60.529 57.895 0.00 0.00 0.00 3.59
1710 1713 1.799258 ATACGTACCGGCCCATCGAC 61.799 60.000 0.00 0.00 0.00 4.20
1711 1714 4.580551 CGTACCGGCCCATCGACC 62.581 72.222 0.00 0.00 0.00 4.79
1712 1715 3.152400 GTACCGGCCCATCGACCT 61.152 66.667 0.00 0.00 0.00 3.85
1713 1716 3.151710 TACCGGCCCATCGACCTG 61.152 66.667 0.00 0.00 0.00 4.00
1714 1717 3.665515 TACCGGCCCATCGACCTGA 62.666 63.158 0.00 0.00 0.00 3.86
1715 1718 3.781307 CCGGCCCATCGACCTGAA 61.781 66.667 0.00 0.00 0.00 3.02
1716 1719 2.511600 CGGCCCATCGACCTGAAC 60.512 66.667 0.00 0.00 0.00 3.18
1717 1720 2.124695 GGCCCATCGACCTGAACC 60.125 66.667 0.00 0.00 0.00 3.62
1718 1721 2.670148 GGCCCATCGACCTGAACCT 61.670 63.158 0.00 0.00 0.00 3.50
1719 1722 1.450312 GCCCATCGACCTGAACCTG 60.450 63.158 0.00 0.00 0.00 4.00
1720 1723 1.450312 CCCATCGACCTGAACCTGC 60.450 63.158 0.00 0.00 0.00 4.85
1721 1724 1.450312 CCATCGACCTGAACCTGCC 60.450 63.158 0.00 0.00 0.00 4.85
1722 1725 1.811266 CATCGACCTGAACCTGCCG 60.811 63.158 0.00 0.00 0.00 5.69
1723 1726 3.019003 ATCGACCTGAACCTGCCGG 62.019 63.158 0.00 0.00 0.00 6.13
1724 1727 4.760047 CGACCTGAACCTGCCGGG 62.760 72.222 2.18 0.00 41.89 5.73
1727 1730 4.659172 CCTGAACCTGCCGGGCAA 62.659 66.667 23.94 6.67 38.41 4.52
1728 1731 3.058160 CTGAACCTGCCGGGCAAG 61.058 66.667 23.94 19.84 38.41 4.01
1729 1732 3.850098 CTGAACCTGCCGGGCAAGT 62.850 63.158 23.94 20.59 38.41 3.16
1730 1733 2.349755 GAACCTGCCGGGCAAGTA 59.650 61.111 22.78 0.00 38.41 2.24
1731 1734 2.033602 AACCTGCCGGGCAAGTAC 59.966 61.111 22.78 0.00 38.41 2.73
1732 1735 2.465055 GAACCTGCCGGGCAAGTACT 62.465 60.000 22.78 9.12 38.41 2.73
1733 1736 2.125106 CCTGCCGGGCAAGTACTC 60.125 66.667 23.94 0.00 38.41 2.59
1734 1737 2.660064 CCTGCCGGGCAAGTACTCT 61.660 63.158 23.94 0.00 38.41 3.24
1735 1738 1.327690 CCTGCCGGGCAAGTACTCTA 61.328 60.000 23.94 0.00 38.41 2.43
1736 1739 0.535335 CTGCCGGGCAAGTACTCTAA 59.465 55.000 23.94 0.00 38.41 2.10
1737 1740 0.978151 TGCCGGGCAAGTACTCTAAA 59.022 50.000 21.55 0.00 34.76 1.85
1738 1741 1.557832 TGCCGGGCAAGTACTCTAAAT 59.442 47.619 21.55 0.00 34.76 1.40
1838 1841 1.180029 GCCTCAAATGCACCATCTGT 58.820 50.000 0.00 0.00 0.00 3.41
1919 1970 1.600023 TAGTGGACAAACCCAAAGCG 58.400 50.000 0.00 0.00 38.06 4.68
1963 2014 2.550208 CCTGGTGTGTGGTAACCTCTTC 60.550 54.545 0.00 0.00 37.36 2.87
2083 2134 5.929992 GCAGTACCACACTTCATAACAGTTA 59.070 40.000 0.00 0.00 34.26 2.24
2141 2192 0.037232 AGTACGCTGGAAAGAGGTGC 60.037 55.000 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.708341 AGAATTGTTTGGCCTGCAGT 58.292 45.000 13.81 0.00 0.00 4.40
84 85 0.108520 TTGCGATGACCGTTAGGACC 60.109 55.000 0.00 0.00 41.02 4.46
95 96 6.379417 AGGAGTGAGATGATATATTGCGATGA 59.621 38.462 0.00 0.00 0.00 2.92
163 164 1.383456 GCCCAAAGATATGCACGGCA 61.383 55.000 0.00 1.01 44.86 5.69
202 203 5.279910 CCCAATTTACTTTGCATTTCCCTCA 60.280 40.000 0.00 0.00 0.00 3.86
222 223 0.741915 GTTTGCAAACGAGGTCCCAA 59.258 50.000 25.35 0.00 0.00 4.12
366 368 3.517901 AGAAATGGTGGTCATCTTCCGTA 59.482 43.478 0.00 0.00 34.44 4.02
380 382 1.290009 GCTGCCGCAAAGAAATGGT 59.710 52.632 0.00 0.00 35.78 3.55
430 432 2.530701 AGATGAAGTCCAGAACCTCGT 58.469 47.619 0.00 0.00 0.00 4.18
502 504 0.881796 GAGGAGTTTTTCTTGCGGGG 59.118 55.000 0.00 0.00 0.00 5.73
541 543 0.950836 TTCGCAATCCACTGGTTGTG 59.049 50.000 13.54 13.54 45.80 3.33
848 850 2.043980 CAATTAGGCCAACCGCGGT 61.044 57.895 28.70 28.70 42.76 5.68
903 905 0.612744 GGAAGAGAAGGTGAGCTGCT 59.387 55.000 0.00 0.00 0.00 4.24
927 929 1.930503 CAAATGCGTATGGTGTAGCGA 59.069 47.619 0.00 0.00 0.00 4.93
1144 1146 0.632835 ATGATGACCATGCAAGGGGT 59.367 50.000 13.45 10.35 46.47 4.95
1260 1262 6.036191 GGAGAAAGTTTAGATAGAAACCGCAG 59.964 42.308 0.00 0.00 39.66 5.18
1271 1273 9.667107 TCATTGATTAACGGAGAAAGTTTAGAT 57.333 29.630 0.00 0.00 33.42 1.98
1286 1289 8.538409 AAAGACTTGCCATTTCATTGATTAAC 57.462 30.769 0.00 0.00 0.00 2.01
1342 1345 3.894920 TGTTTTGTTGCATACCACGATG 58.105 40.909 0.00 0.00 0.00 3.84
1343 1346 3.818210 TCTGTTTTGTTGCATACCACGAT 59.182 39.130 0.00 0.00 0.00 3.73
1344 1347 3.002862 GTCTGTTTTGTTGCATACCACGA 59.997 43.478 0.00 0.00 0.00 4.35
1345 1348 3.296628 GTCTGTTTTGTTGCATACCACG 58.703 45.455 0.00 0.00 0.00 4.94
1346 1349 3.638484 GGTCTGTTTTGTTGCATACCAC 58.362 45.455 0.00 0.00 33.65 4.16
1347 1350 2.292016 CGGTCTGTTTTGTTGCATACCA 59.708 45.455 0.00 0.00 33.21 3.25
1348 1351 2.920647 GCGGTCTGTTTTGTTGCATACC 60.921 50.000 0.00 0.00 0.00 2.73
1349 1352 2.287308 TGCGGTCTGTTTTGTTGCATAC 60.287 45.455 0.00 0.00 0.00 2.39
1350 1353 1.950216 TGCGGTCTGTTTTGTTGCATA 59.050 42.857 0.00 0.00 0.00 3.14
1351 1354 0.743688 TGCGGTCTGTTTTGTTGCAT 59.256 45.000 0.00 0.00 0.00 3.96
1352 1355 0.179150 GTGCGGTCTGTTTTGTTGCA 60.179 50.000 0.00 0.00 0.00 4.08
1353 1356 1.199852 CGTGCGGTCTGTTTTGTTGC 61.200 55.000 0.00 0.00 0.00 4.17
1354 1357 0.098025 ACGTGCGGTCTGTTTTGTTG 59.902 50.000 0.00 0.00 0.00 3.33
1355 1358 0.375803 GACGTGCGGTCTGTTTTGTT 59.624 50.000 0.00 0.00 42.62 2.83
1356 1359 1.433837 GGACGTGCGGTCTGTTTTGT 61.434 55.000 0.00 0.00 45.35 2.83
1357 1360 1.278637 GGACGTGCGGTCTGTTTTG 59.721 57.895 0.00 0.00 45.35 2.44
1358 1361 0.534203 ATGGACGTGCGGTCTGTTTT 60.534 50.000 1.60 0.00 45.35 2.43
1359 1362 0.949105 GATGGACGTGCGGTCTGTTT 60.949 55.000 1.60 0.00 45.35 2.83
1360 1363 1.374252 GATGGACGTGCGGTCTGTT 60.374 57.895 1.60 0.00 45.35 3.16
1361 1364 2.094757 TTGATGGACGTGCGGTCTGT 62.095 55.000 1.60 0.00 45.35 3.41
1362 1365 1.354337 CTTGATGGACGTGCGGTCTG 61.354 60.000 1.60 0.00 45.35 3.51
1363 1366 1.079819 CTTGATGGACGTGCGGTCT 60.080 57.895 1.60 0.00 45.35 3.85
1364 1367 0.669318 TTCTTGATGGACGTGCGGTC 60.669 55.000 1.60 3.91 45.31 4.79
1365 1368 0.670546 CTTCTTGATGGACGTGCGGT 60.671 55.000 1.60 0.00 0.00 5.68
1366 1369 0.670546 ACTTCTTGATGGACGTGCGG 60.671 55.000 1.60 0.00 0.00 5.69
1367 1370 0.439985 CACTTCTTGATGGACGTGCG 59.560 55.000 1.60 0.00 30.89 5.34
1368 1371 0.798776 CCACTTCTTGATGGACGTGC 59.201 55.000 0.00 0.00 38.34 5.34
1369 1372 2.455674 TCCACTTCTTGATGGACGTG 57.544 50.000 0.00 0.00 40.17 4.49
1374 1377 1.667724 GCACGATCCACTTCTTGATGG 59.332 52.381 0.00 0.00 37.32 3.51
1375 1378 1.667724 GGCACGATCCACTTCTTGATG 59.332 52.381 0.00 0.00 0.00 3.07
1376 1379 1.278985 TGGCACGATCCACTTCTTGAT 59.721 47.619 0.00 0.00 0.00 2.57
1377 1380 0.684535 TGGCACGATCCACTTCTTGA 59.315 50.000 0.00 0.00 0.00 3.02
1378 1381 1.081892 CTGGCACGATCCACTTCTTG 58.918 55.000 0.00 0.00 31.74 3.02
1379 1382 0.976641 TCTGGCACGATCCACTTCTT 59.023 50.000 0.00 0.00 31.74 2.52
1380 1383 0.247736 GTCTGGCACGATCCACTTCT 59.752 55.000 0.00 0.00 31.74 2.85
1381 1384 2.755929 GTCTGGCACGATCCACTTC 58.244 57.895 0.00 0.00 31.74 3.01
1409 1412 4.504916 CAGAGCCTCTCGCCGGTG 62.505 72.222 9.28 9.28 38.78 4.94
1411 1414 4.504916 CACAGAGCCTCTCGCCGG 62.505 72.222 0.00 0.00 38.78 6.13
1412 1415 4.504916 CCACAGAGCCTCTCGCCG 62.505 72.222 0.00 0.00 38.78 6.46
1413 1416 4.828925 GCCACAGAGCCTCTCGCC 62.829 72.222 0.00 0.00 38.78 5.54
1421 1424 2.690778 AAAATCGGCGCCACAGAGC 61.691 57.895 28.98 0.00 38.21 4.09
1422 1425 1.135315 CAAAATCGGCGCCACAGAG 59.865 57.895 28.98 9.94 0.00 3.35
1423 1426 1.599518 ACAAAATCGGCGCCACAGA 60.600 52.632 28.98 16.64 0.00 3.41
1424 1427 1.442520 CACAAAATCGGCGCCACAG 60.443 57.895 28.98 10.81 0.00 3.66
1425 1428 1.894282 TCACAAAATCGGCGCCACA 60.894 52.632 28.98 13.13 0.00 4.17
1426 1429 1.442017 GTCACAAAATCGGCGCCAC 60.442 57.895 28.98 9.85 0.00 5.01
1427 1430 1.448119 TTGTCACAAAATCGGCGCCA 61.448 50.000 28.98 14.46 0.00 5.69
1428 1431 0.318275 TTTGTCACAAAATCGGCGCC 60.318 50.000 19.07 19.07 0.00 6.53
1429 1432 0.775861 GTTTGTCACAAAATCGGCGC 59.224 50.000 4.02 0.00 0.00 6.53
1430 1433 1.041726 CGTTTGTCACAAAATCGGCG 58.958 50.000 4.02 0.00 0.00 6.46
1431 1434 2.113910 ACGTTTGTCACAAAATCGGC 57.886 45.000 15.38 0.00 0.00 5.54
1432 1435 2.215363 GCAACGTTTGTCACAAAATCGG 59.785 45.455 15.38 4.78 0.00 4.18
1433 1436 2.098589 CGCAACGTTTGTCACAAAATCG 60.099 45.455 4.02 8.11 0.00 3.34
1434 1437 2.215363 CCGCAACGTTTGTCACAAAATC 59.785 45.455 4.02 0.00 0.00 2.17
1435 1438 2.189342 CCGCAACGTTTGTCACAAAAT 58.811 42.857 4.02 0.00 0.00 1.82
1436 1439 1.618861 CCGCAACGTTTGTCACAAAA 58.381 45.000 4.02 0.00 0.00 2.44
1437 1440 0.798771 GCCGCAACGTTTGTCACAAA 60.799 50.000 0.00 0.00 0.00 2.83
1438 1441 1.226435 GCCGCAACGTTTGTCACAA 60.226 52.632 0.00 0.00 0.00 3.33
1439 1442 2.405594 GCCGCAACGTTTGTCACA 59.594 55.556 0.00 0.00 0.00 3.58
1440 1443 2.720750 CGCCGCAACGTTTGTCAC 60.721 61.111 0.00 0.00 0.00 3.67
1441 1444 3.196394 ACGCCGCAACGTTTGTCA 61.196 55.556 0.00 0.00 45.75 3.58
1442 1445 2.720750 CACGCCGCAACGTTTGTC 60.721 61.111 0.00 0.00 45.75 3.18
1443 1446 4.897856 GCACGCCGCAACGTTTGT 62.898 61.111 0.00 0.00 45.75 2.83
1453 1456 4.803426 GAGGAGGAGTGCACGCCG 62.803 72.222 30.40 0.00 40.98 6.46
1454 1457 4.803426 CGAGGAGGAGTGCACGCC 62.803 72.222 30.06 30.06 35.95 5.68
1455 1458 4.803426 CCGAGGAGGAGTGCACGC 62.803 72.222 12.67 12.67 45.00 5.34
1456 1459 4.803426 GCCGAGGAGGAGTGCACG 62.803 72.222 12.01 0.00 45.00 5.34
1457 1460 4.459089 GGCCGAGGAGGAGTGCAC 62.459 72.222 9.40 9.40 45.00 4.57
1476 1479 2.580867 GCTACTGCGCTCGTGGAG 60.581 66.667 9.73 3.49 0.00 3.86
1477 1480 2.819117 CTTGCTACTGCGCTCGTGGA 62.819 60.000 9.73 0.00 43.34 4.02
1478 1481 2.432456 TTGCTACTGCGCTCGTGG 60.432 61.111 9.73 9.19 43.34 4.94
1479 1482 3.075998 CTTGCTACTGCGCTCGTG 58.924 61.111 9.73 0.00 43.34 4.35
1480 1483 2.811317 GCTTGCTACTGCGCTCGT 60.811 61.111 9.73 8.66 43.34 4.18
1481 1484 3.906649 CGCTTGCTACTGCGCTCG 61.907 66.667 9.73 1.70 45.50 5.03
1486 1489 3.854459 GTCGGCGCTTGCTACTGC 61.854 66.667 7.64 0.00 39.13 4.40
1487 1490 3.188786 GGTCGGCGCTTGCTACTG 61.189 66.667 7.64 0.00 39.13 2.74
1488 1491 3.691342 TGGTCGGCGCTTGCTACT 61.691 61.111 7.64 0.00 39.13 2.57
1489 1492 3.488090 GTGGTCGGCGCTTGCTAC 61.488 66.667 7.64 1.72 39.13 3.58
1490 1493 3.691342 AGTGGTCGGCGCTTGCTA 61.691 61.111 7.64 0.00 39.13 3.49
1493 1496 4.988598 ACCAGTGGTCGGCGCTTG 62.989 66.667 9.70 0.00 0.00 4.01
1494 1497 3.767630 AAACCAGTGGTCGGCGCTT 62.768 57.895 17.06 1.48 33.12 4.68
1495 1498 4.250305 AAACCAGTGGTCGGCGCT 62.250 61.111 17.06 0.00 33.12 5.92
1496 1499 4.025401 CAAACCAGTGGTCGGCGC 62.025 66.667 17.06 0.00 33.12 6.53
1497 1500 2.590575 ACAAACCAGTGGTCGGCG 60.591 61.111 17.06 0.00 33.12 6.46
1498 1501 3.030652 CACAAACCAGTGGTCGGC 58.969 61.111 17.06 0.00 33.12 5.54
1504 1507 1.374560 TTGTCGACCACAAACCAGTG 58.625 50.000 14.12 0.00 42.35 3.66
1505 1508 3.865477 TTGTCGACCACAAACCAGT 57.135 47.368 14.12 0.00 42.35 4.00
1511 1514 1.353804 GCGCTTTTGTCGACCACAA 59.646 52.632 14.12 0.00 43.68 3.33
1512 1515 2.539338 GGCGCTTTTGTCGACCACA 61.539 57.895 14.12 0.00 0.00 4.17
1513 1516 2.251371 GGCGCTTTTGTCGACCAC 59.749 61.111 14.12 0.00 0.00 4.16
1514 1517 2.203084 TGGCGCTTTTGTCGACCA 60.203 55.556 14.12 0.00 33.18 4.02
1515 1518 2.251371 GTGGCGCTTTTGTCGACC 59.749 61.111 14.12 0.00 33.18 4.79
1516 1519 2.127758 CGTGGCGCTTTTGTCGAC 60.128 61.111 9.11 9.11 35.09 4.20
1574 1577 2.420568 TAGCTAGGAACCACGCGGG 61.421 63.158 12.47 6.05 44.81 6.13
1575 1578 1.226888 GTAGCTAGGAACCACGCGG 60.227 63.158 12.47 0.00 38.77 6.46
1576 1579 1.019673 TAGTAGCTAGGAACCACGCG 58.980 55.000 3.53 3.53 0.00 6.01
1577 1580 1.066757 GGTAGTAGCTAGGAACCACGC 59.933 57.143 12.21 0.00 0.00 5.34
1578 1581 2.617774 GAGGTAGTAGCTAGGAACCACG 59.382 54.545 17.18 0.00 32.43 4.94
1579 1582 3.633065 CAGAGGTAGTAGCTAGGAACCAC 59.367 52.174 17.18 12.55 32.43 4.16
1580 1583 3.268856 ACAGAGGTAGTAGCTAGGAACCA 59.731 47.826 17.18 0.00 32.43 3.67
1581 1584 3.900971 ACAGAGGTAGTAGCTAGGAACC 58.099 50.000 0.89 9.96 0.00 3.62
1582 1585 4.948621 TGAACAGAGGTAGTAGCTAGGAAC 59.051 45.833 0.89 0.00 0.00 3.62
1583 1586 4.948621 GTGAACAGAGGTAGTAGCTAGGAA 59.051 45.833 0.89 0.00 0.00 3.36
1584 1587 4.227754 AGTGAACAGAGGTAGTAGCTAGGA 59.772 45.833 0.89 0.00 0.00 2.94
1585 1588 4.528920 AGTGAACAGAGGTAGTAGCTAGG 58.471 47.826 0.89 0.19 0.00 3.02
1586 1589 6.518208 AAAGTGAACAGAGGTAGTAGCTAG 57.482 41.667 0.89 0.96 0.00 3.42
1587 1590 6.912951 AAAAGTGAACAGAGGTAGTAGCTA 57.087 37.500 0.89 0.00 0.00 3.32
1588 1591 5.810080 AAAAGTGAACAGAGGTAGTAGCT 57.190 39.130 0.36 0.36 0.00 3.32
1589 1592 9.303537 CTTATAAAAGTGAACAGAGGTAGTAGC 57.696 37.037 0.00 0.00 0.00 3.58
1592 1595 8.867097 TGTCTTATAAAAGTGAACAGAGGTAGT 58.133 33.333 0.00 0.00 34.13 2.73
1593 1596 9.877178 ATGTCTTATAAAAGTGAACAGAGGTAG 57.123 33.333 0.00 0.00 34.13 3.18
1595 1598 9.574516 AAATGTCTTATAAAAGTGAACAGAGGT 57.425 29.630 0.00 0.00 34.13 3.85
1611 1614 9.950496 AGTGTCTGAATGTCTAAAATGTCTTAT 57.050 29.630 0.00 0.00 0.00 1.73
1612 1615 9.208022 CAGTGTCTGAATGTCTAAAATGTCTTA 57.792 33.333 0.00 0.00 32.44 2.10
1613 1616 7.716998 ACAGTGTCTGAATGTCTAAAATGTCTT 59.283 33.333 3.70 0.00 35.18 3.01
1614 1617 7.220030 ACAGTGTCTGAATGTCTAAAATGTCT 58.780 34.615 3.70 0.00 35.18 3.41
1615 1618 7.426929 ACAGTGTCTGAATGTCTAAAATGTC 57.573 36.000 3.70 0.00 35.18 3.06
1616 1619 7.807977 AACAGTGTCTGAATGTCTAAAATGT 57.192 32.000 0.00 0.00 35.18 2.71
1617 1620 9.599322 GTAAACAGTGTCTGAATGTCTAAAATG 57.401 33.333 0.00 0.00 35.18 2.32
1618 1621 9.337396 TGTAAACAGTGTCTGAATGTCTAAAAT 57.663 29.630 0.00 0.00 35.18 1.82
1619 1622 8.725405 TGTAAACAGTGTCTGAATGTCTAAAA 57.275 30.769 0.00 0.00 35.18 1.52
1620 1623 8.725405 TTGTAAACAGTGTCTGAATGTCTAAA 57.275 30.769 0.00 0.00 35.18 1.85
1621 1624 8.725405 TTTGTAAACAGTGTCTGAATGTCTAA 57.275 30.769 0.00 0.00 35.18 2.10
1622 1625 7.042051 GCTTTGTAAACAGTGTCTGAATGTCTA 60.042 37.037 0.00 0.00 35.18 2.59
1623 1626 6.238484 GCTTTGTAAACAGTGTCTGAATGTCT 60.238 38.462 0.00 0.00 35.18 3.41
1624 1627 5.909610 GCTTTGTAAACAGTGTCTGAATGTC 59.090 40.000 0.00 0.00 35.18 3.06
1625 1628 5.356751 TGCTTTGTAAACAGTGTCTGAATGT 59.643 36.000 0.00 0.00 35.18 2.71
1626 1629 5.820131 TGCTTTGTAAACAGTGTCTGAATG 58.180 37.500 0.00 0.00 35.18 2.67
1627 1630 5.009010 CCTGCTTTGTAAACAGTGTCTGAAT 59.991 40.000 0.00 0.00 35.18 2.57
1628 1631 4.335315 CCTGCTTTGTAAACAGTGTCTGAA 59.665 41.667 0.00 0.00 35.18 3.02
1629 1632 3.876914 CCTGCTTTGTAAACAGTGTCTGA 59.123 43.478 0.00 0.00 35.18 3.27
1630 1633 3.548818 GCCTGCTTTGTAAACAGTGTCTG 60.549 47.826 0.00 0.00 37.52 3.51
1631 1634 2.618709 GCCTGCTTTGTAAACAGTGTCT 59.381 45.455 0.00 0.00 0.00 3.41
1632 1635 2.618709 AGCCTGCTTTGTAAACAGTGTC 59.381 45.455 0.00 0.00 0.00 3.67
1633 1636 2.358898 CAGCCTGCTTTGTAAACAGTGT 59.641 45.455 0.00 0.00 0.00 3.55
1634 1637 2.358898 ACAGCCTGCTTTGTAAACAGTG 59.641 45.455 0.00 0.00 0.00 3.66
1635 1638 2.618709 GACAGCCTGCTTTGTAAACAGT 59.381 45.455 0.00 0.00 0.00 3.55
1636 1639 2.880890 AGACAGCCTGCTTTGTAAACAG 59.119 45.455 0.00 0.00 0.00 3.16
1637 1640 2.618241 CAGACAGCCTGCTTTGTAAACA 59.382 45.455 0.00 0.00 35.89 2.83
1638 1641 2.878406 TCAGACAGCCTGCTTTGTAAAC 59.122 45.455 0.00 0.00 42.62 2.01
1639 1642 3.207265 TCAGACAGCCTGCTTTGTAAA 57.793 42.857 0.00 0.00 42.62 2.01
1640 1643 2.928801 TCAGACAGCCTGCTTTGTAA 57.071 45.000 0.00 0.00 42.62 2.41
1641 1644 2.928801 TTCAGACAGCCTGCTTTGTA 57.071 45.000 0.00 0.00 42.62 2.41
1642 1645 2.057137 TTTCAGACAGCCTGCTTTGT 57.943 45.000 0.00 0.00 42.62 2.83
1643 1646 2.925306 GCATTTCAGACAGCCTGCTTTG 60.925 50.000 0.00 0.00 42.62 2.77
1644 1647 1.271656 GCATTTCAGACAGCCTGCTTT 59.728 47.619 0.00 0.00 42.62 3.51
1645 1648 0.886563 GCATTTCAGACAGCCTGCTT 59.113 50.000 0.00 0.00 42.62 3.91
1646 1649 0.964358 GGCATTTCAGACAGCCTGCT 60.964 55.000 0.00 0.00 43.70 4.24
1647 1650 1.509923 GGCATTTCAGACAGCCTGC 59.490 57.895 0.00 0.00 43.70 4.85
1651 1654 7.090173 TGTTTTTATAAGGCATTTCAGACAGC 58.910 34.615 0.00 0.00 0.00 4.40
1652 1655 9.474920 TTTGTTTTTATAAGGCATTTCAGACAG 57.525 29.630 0.00 0.00 0.00 3.51
1653 1656 9.255304 GTTTGTTTTTATAAGGCATTTCAGACA 57.745 29.630 0.00 0.00 0.00 3.41
1654 1657 8.424731 CGTTTGTTTTTATAAGGCATTTCAGAC 58.575 33.333 0.00 0.00 0.00 3.51
1655 1658 7.596995 CCGTTTGTTTTTATAAGGCATTTCAGA 59.403 33.333 0.00 0.00 0.00 3.27
1656 1659 7.596995 TCCGTTTGTTTTTATAAGGCATTTCAG 59.403 33.333 0.00 0.00 0.00 3.02
1657 1660 7.434492 TCCGTTTGTTTTTATAAGGCATTTCA 58.566 30.769 0.00 0.00 0.00 2.69
1658 1661 7.062956 CCTCCGTTTGTTTTTATAAGGCATTTC 59.937 37.037 0.00 0.00 0.00 2.17
1659 1662 6.871492 CCTCCGTTTGTTTTTATAAGGCATTT 59.129 34.615 0.00 0.00 0.00 2.32
1660 1663 6.394809 CCTCCGTTTGTTTTTATAAGGCATT 58.605 36.000 0.00 0.00 0.00 3.56
1661 1664 5.105513 CCCTCCGTTTGTTTTTATAAGGCAT 60.106 40.000 0.00 0.00 0.00 4.40
1662 1665 4.218852 CCCTCCGTTTGTTTTTATAAGGCA 59.781 41.667 0.00 0.00 0.00 4.75
1663 1666 4.460034 TCCCTCCGTTTGTTTTTATAAGGC 59.540 41.667 0.00 0.00 0.00 4.35
1664 1667 5.708697 ACTCCCTCCGTTTGTTTTTATAAGG 59.291 40.000 0.00 0.00 0.00 2.69
1665 1668 6.812879 ACTCCCTCCGTTTGTTTTTATAAG 57.187 37.500 0.00 0.00 0.00 1.73
1666 1669 7.222872 TGTACTCCCTCCGTTTGTTTTTATAA 58.777 34.615 0.00 0.00 0.00 0.98
1667 1670 6.767456 TGTACTCCCTCCGTTTGTTTTTATA 58.233 36.000 0.00 0.00 0.00 0.98
1668 1671 5.623169 TGTACTCCCTCCGTTTGTTTTTAT 58.377 37.500 0.00 0.00 0.00 1.40
1669 1672 5.033589 TGTACTCCCTCCGTTTGTTTTTA 57.966 39.130 0.00 0.00 0.00 1.52
1670 1673 3.888583 TGTACTCCCTCCGTTTGTTTTT 58.111 40.909 0.00 0.00 0.00 1.94
1671 1674 3.564053 TGTACTCCCTCCGTTTGTTTT 57.436 42.857 0.00 0.00 0.00 2.43
1672 1675 3.782656 ATGTACTCCCTCCGTTTGTTT 57.217 42.857 0.00 0.00 0.00 2.83
1673 1676 3.367703 CGTATGTACTCCCTCCGTTTGTT 60.368 47.826 0.00 0.00 0.00 2.83
1674 1677 2.165030 CGTATGTACTCCCTCCGTTTGT 59.835 50.000 0.00 0.00 0.00 2.83
1675 1678 2.165030 ACGTATGTACTCCCTCCGTTTG 59.835 50.000 0.00 0.00 0.00 2.93
1676 1679 2.450476 ACGTATGTACTCCCTCCGTTT 58.550 47.619 0.00 0.00 0.00 3.60
1677 1680 2.134789 ACGTATGTACTCCCTCCGTT 57.865 50.000 0.00 0.00 0.00 4.44
1678 1681 2.565841 GTACGTATGTACTCCCTCCGT 58.434 52.381 16.51 0.00 46.07 4.69
1695 1698 3.152400 AGGTCGATGGGCCGGTAC 61.152 66.667 1.90 0.00 0.00 3.34
1696 1699 3.151710 CAGGTCGATGGGCCGGTA 61.152 66.667 1.90 0.00 0.00 4.02
1698 1701 3.781307 TTCAGGTCGATGGGCCGG 61.781 66.667 0.00 0.00 0.00 6.13
1699 1702 2.511600 GTTCAGGTCGATGGGCCG 60.512 66.667 0.00 0.00 0.00 6.13
1700 1703 2.124695 GGTTCAGGTCGATGGGCC 60.125 66.667 0.00 0.00 0.00 5.80
1701 1704 1.450312 CAGGTTCAGGTCGATGGGC 60.450 63.158 0.00 0.00 0.00 5.36
1702 1705 1.450312 GCAGGTTCAGGTCGATGGG 60.450 63.158 0.00 0.00 0.00 4.00
1703 1706 1.450312 GGCAGGTTCAGGTCGATGG 60.450 63.158 0.00 0.00 0.00 3.51
1704 1707 1.811266 CGGCAGGTTCAGGTCGATG 60.811 63.158 0.00 0.00 33.12 3.84
1705 1708 2.579201 CGGCAGGTTCAGGTCGAT 59.421 61.111 0.00 0.00 33.12 3.59
1706 1709 3.691342 CCGGCAGGTTCAGGTCGA 61.691 66.667 0.00 0.00 33.12 4.20
1707 1710 4.760047 CCCGGCAGGTTCAGGTCG 62.760 72.222 1.11 0.00 35.12 4.79
1710 1713 4.659172 TTGCCCGGCAGGTTCAGG 62.659 66.667 12.95 0.00 40.61 3.86
1711 1714 2.463589 TACTTGCCCGGCAGGTTCAG 62.464 60.000 29.92 18.10 46.34 3.02
1712 1715 2.521451 TACTTGCCCGGCAGGTTCA 61.521 57.895 29.92 12.45 46.34 3.18
1713 1716 2.038837 GTACTTGCCCGGCAGGTTC 61.039 63.158 29.92 21.83 46.34 3.62
1714 1717 2.033602 GTACTTGCCCGGCAGGTT 59.966 61.111 29.92 15.34 46.34 3.50
1716 1719 1.327690 TAGAGTACTTGCCCGGCAGG 61.328 60.000 19.51 19.51 40.61 4.85
1717 1720 0.535335 TTAGAGTACTTGCCCGGCAG 59.465 55.000 12.95 9.54 40.61 4.85
1718 1721 0.978151 TTTAGAGTACTTGCCCGGCA 59.022 50.000 8.43 8.43 36.47 5.69
1719 1722 2.210961 GATTTAGAGTACTTGCCCGGC 58.789 52.381 1.04 1.04 0.00 6.13
1720 1723 2.434702 AGGATTTAGAGTACTTGCCCGG 59.565 50.000 0.00 0.00 0.00 5.73
1721 1724 3.821421 AGGATTTAGAGTACTTGCCCG 57.179 47.619 0.00 0.00 0.00 6.13
1722 1725 4.040584 CCCTAGGATTTAGAGTACTTGCCC 59.959 50.000 11.48 0.00 0.00 5.36
1723 1726 4.503469 GCCCTAGGATTTAGAGTACTTGCC 60.503 50.000 11.48 0.00 0.00 4.52
1724 1727 4.633175 GCCCTAGGATTTAGAGTACTTGC 58.367 47.826 11.48 0.00 0.00 4.01
1725 1728 4.341520 ACGCCCTAGGATTTAGAGTACTTG 59.658 45.833 11.48 0.00 0.00 3.16
1726 1729 4.341520 CACGCCCTAGGATTTAGAGTACTT 59.658 45.833 11.48 0.00 0.00 2.24
1727 1730 3.890147 CACGCCCTAGGATTTAGAGTACT 59.110 47.826 11.48 0.00 0.00 2.73
1728 1731 3.635836 ACACGCCCTAGGATTTAGAGTAC 59.364 47.826 11.48 0.00 0.00 2.73
1729 1732 3.907221 ACACGCCCTAGGATTTAGAGTA 58.093 45.455 11.48 0.00 0.00 2.59
1730 1733 2.748388 ACACGCCCTAGGATTTAGAGT 58.252 47.619 11.48 0.00 0.00 3.24
1731 1734 3.821421 AACACGCCCTAGGATTTAGAG 57.179 47.619 11.48 0.00 0.00 2.43
1732 1735 3.370103 CCAAACACGCCCTAGGATTTAGA 60.370 47.826 11.48 0.00 0.00 2.10
1733 1736 2.943033 CCAAACACGCCCTAGGATTTAG 59.057 50.000 11.48 0.00 0.00 1.85
1734 1737 2.306512 ACCAAACACGCCCTAGGATTTA 59.693 45.455 11.48 0.00 0.00 1.40
1735 1738 1.074889 ACCAAACACGCCCTAGGATTT 59.925 47.619 11.48 0.00 0.00 2.17
1736 1739 0.696501 ACCAAACACGCCCTAGGATT 59.303 50.000 11.48 0.00 0.00 3.01
1737 1740 0.696501 AACCAAACACGCCCTAGGAT 59.303 50.000 11.48 0.00 0.00 3.24
1738 1741 0.250553 CAACCAAACACGCCCTAGGA 60.251 55.000 11.48 0.00 0.00 2.94
1838 1841 2.034878 TGCAGGCAACCAAACAACATA 58.965 42.857 0.00 0.00 37.17 2.29
1919 1970 3.444703 TTGCATACAACCAAACACCAC 57.555 42.857 0.00 0.00 0.00 4.16
1963 2014 1.405121 GGTAACCTCACCAACTAGCCG 60.405 57.143 0.00 0.00 38.55 5.52
2141 2192 3.480133 CAAGGAGTAGGGCCGGGG 61.480 72.222 2.18 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.