Multiple sequence alignment - TraesCS2D01G552600

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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 TraesCS2D01G552600 chr2D 100.000 2363 0 0 1 2363 627824867 627822505 0.000000e+00 4364.0
1 TraesCS2D01G552600 chr2D 88.726 683 33 15 1 642 469245600 469246279 0.000000e+00 795.0
2 TraesCS2D01G552600 chr2D 100.000 31 0 0 1672 1702 627822923 627822893 9.120000e-05 58.4
3 TraesCS2D01G552600 chr2D 100.000 31 0 0 1945 1975 627823196 627823166 9.120000e-05 58.4
4 TraesCS2D01G552600 chr2B 86.989 807 66 23 696 1491 770072066 770071288 0.000000e+00 872.0
5 TraesCS2D01G552600 chr2B 86.865 571 44 16 1806 2363 770071245 770070693 5.580000e-171 610.0
6 TraesCS2D01G552600 chr6D 89.774 665 32 15 1 630 419656352 419657015 0.000000e+00 819.0
7 TraesCS2D01G552600 chr2A 87.280 739 50 21 664 1397 758280946 758280247 0.000000e+00 804.0
8 TraesCS2D01G552600 chr2A 93.103 348 17 3 1796 2138 758280097 758279752 9.750000e-139 503.0
9 TraesCS2D01G552600 chr2A 88.333 180 11 5 2191 2363 758279757 758279581 8.560000e-50 207.0
10 TraesCS2D01G552600 chr2A 85.380 171 4 8 1674 1844 758280245 758280096 8.740000e-35 158.0
11 TraesCS2D01G552600 chr2A 100.000 29 0 0 1947 1975 758280245 758280217 1.000000e-03 54.7
12 TraesCS2D01G552600 chr5A 89.140 663 38 11 1 633 592399995 592399337 0.000000e+00 795.0
13 TraesCS2D01G552600 chr5A 87.667 673 43 18 1 637 611820036 611819368 0.000000e+00 747.0
14 TraesCS2D01G552600 chr7A 88.806 670 38 18 1 636 54940964 54940298 0.000000e+00 787.0
15 TraesCS2D01G552600 chr7A 88.182 660 43 16 1 628 639278071 639277415 0.000000e+00 754.0
16 TraesCS2D01G552600 chr7A 86.165 665 37 24 1 629 5758388 5757743 0.000000e+00 667.0
17 TraesCS2D01G552600 chr7A 87.464 351 30 10 1058 1397 271723909 271723562 2.200000e-105 392.0
18 TraesCS2D01G552600 chr7A 87.402 127 13 1 1042 1165 271724012 271723886 2.450000e-30 143.0
19 TraesCS2D01G552600 chr7A 87.755 49 2 3 1586 1634 294921694 294921738 1.000000e-03 54.7
20 TraesCS2D01G552600 chr1D 89.259 661 28 12 1 629 464829812 464830461 0.000000e+00 787.0
21 TraesCS2D01G552600 chr1D 87.685 674 32 14 1 638 474061745 474061087 0.000000e+00 737.0
22 TraesCS2D01G552600 chr6A 88.805 661 41 11 1 631 146439666 146440323 0.000000e+00 780.0
23 TraesCS2D01G552600 chr6A 100.000 28 0 0 1603 1630 508457957 508457984 4.000000e-03 52.8
24 TraesCS2D01G552600 chr4A 88.705 664 41 12 1 631 530826262 530826924 0.000000e+00 780.0
25 TraesCS2D01G552600 chr4A 83.871 62 6 3 1573 1634 83119577 83119634 3.280000e-04 56.5
26 TraesCS2D01G552600 chr7B 85.427 398 46 7 1058 1448 226441477 226441869 1.020000e-108 403.0
27 TraesCS2D01G552600 chr7B 87.500 128 11 5 1042 1165 226441374 226441500 2.450000e-30 143.0
28 TraesCS2D01G552600 chr7D 84.634 410 37 14 1058 1453 249485517 249485914 3.680000e-103 385.0
29 TraesCS2D01G552600 chr7D 85.938 128 13 3 1042 1165 249485414 249485540 5.300000e-27 132.0
30 TraesCS2D01G552600 chr7D 100.000 28 0 0 1607 1634 374806976 374806949 4.000000e-03 52.8
31 TraesCS2D01G552600 chr3A 77.901 629 91 24 46 629 11589358 11588733 4.830000e-92 348.0
32 TraesCS2D01G552600 chr3A 93.182 44 2 1 2177 2220 27592273 27592231 1.960000e-06 63.9
33 TraesCS2D01G552600 chr3A 85.455 55 4 3 1580 1634 387105324 387105374 1.000000e-03 54.7
34 TraesCS2D01G552600 chr4B 84.810 237 35 1 1703 1938 605389741 605389977 1.090000e-58 237.0
35 TraesCS2D01G552600 chr4B 87.755 49 2 3 1586 1634 366119942 366119898 1.000000e-03 54.7
36 TraesCS2D01G552600 chr6B 81.183 186 29 5 2160 2341 600787982 600788165 6.810000e-31 145.0
37 TraesCS2D01G552600 chr3B 78.947 133 21 6 1510 1640 824012979 824013106 1.500000e-12 84.2
38 TraesCS2D01G552600 chr3B 93.617 47 3 0 2176 2222 32292965 32292919 1.170000e-08 71.3
39 TraesCS2D01G552600 chr3B 93.617 47 3 0 2176 2222 32340837 32340791 1.170000e-08 71.3
40 TraesCS2D01G552600 chr3D 93.617 47 3 0 2176 2222 19962976 19962930 1.170000e-08 71.3
41 TraesCS2D01G552600 chr1B 85.455 55 4 3 1580 1634 308160984 308161034 1.000000e-03 54.7


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 TraesCS2D01G552600 chr2D 627822505 627824867 2362 True 1493.60 4364 100.0000 1 2363 3 chr2D.!!$R1 2362
1 TraesCS2D01G552600 chr2D 469245600 469246279 679 False 795.00 795 88.7260 1 642 1 chr2D.!!$F1 641
2 TraesCS2D01G552600 chr2B 770070693 770072066 1373 True 741.00 872 86.9270 696 2363 2 chr2B.!!$R1 1667
3 TraesCS2D01G552600 chr6D 419656352 419657015 663 False 819.00 819 89.7740 1 630 1 chr6D.!!$F1 629
4 TraesCS2D01G552600 chr2A 758279581 758280946 1365 True 345.34 804 90.8192 664 2363 5 chr2A.!!$R1 1699
5 TraesCS2D01G552600 chr5A 592399337 592399995 658 True 795.00 795 89.1400 1 633 1 chr5A.!!$R1 632
6 TraesCS2D01G552600 chr5A 611819368 611820036 668 True 747.00 747 87.6670 1 637 1 chr5A.!!$R2 636
7 TraesCS2D01G552600 chr7A 54940298 54940964 666 True 787.00 787 88.8060 1 636 1 chr7A.!!$R2 635
8 TraesCS2D01G552600 chr7A 639277415 639278071 656 True 754.00 754 88.1820 1 628 1 chr7A.!!$R3 627
9 TraesCS2D01G552600 chr7A 5757743 5758388 645 True 667.00 667 86.1650 1 629 1 chr7A.!!$R1 628
10 TraesCS2D01G552600 chr1D 464829812 464830461 649 False 787.00 787 89.2590 1 629 1 chr1D.!!$F1 628
11 TraesCS2D01G552600 chr1D 474061087 474061745 658 True 737.00 737 87.6850 1 638 1 chr1D.!!$R1 637
12 TraesCS2D01G552600 chr6A 146439666 146440323 657 False 780.00 780 88.8050 1 631 1 chr6A.!!$F1 630
13 TraesCS2D01G552600 chr4A 530826262 530826924 662 False 780.00 780 88.7050 1 631 1 chr4A.!!$F2 630
14 TraesCS2D01G552600 chr7D 249485414 249485914 500 False 258.50 385 85.2860 1042 1453 2 chr7D.!!$F1 411
15 TraesCS2D01G552600 chr3A 11588733 11589358 625 True 348.00 348 77.9010 46 629 1 chr3A.!!$R1 583

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
888 944 0.250124 TGGGACGCACAAACACCTAG 60.25 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 2536 0.166814 GTTGCATGACCGAACAGCTC 59.833 55.0 0.0 0.0 0.0 4.09 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
281 295 4.778904 GCACAACGCAATACTAAAGTTGA 58.221 39.130 12.67 0.00 43.24 3.18
295 309 9.726438 ATACTAAAGTTGAACCATATAGCATCC 57.274 33.333 0.00 0.00 0.00 3.51
306 321 5.222109 ACCATATAGCATCCAAGTTGGCATA 60.222 40.000 17.68 9.15 37.47 3.14
351 391 2.029964 GTCGCGAGGGTTCCAACA 59.970 61.111 10.24 0.00 0.00 3.33
443 496 6.363065 AGCTAAATCAGTCACATGAATGGAT 58.637 36.000 9.26 0.24 40.22 3.41
485 538 9.182642 TCCTTCTAATTATATTCCTTGGTCCAT 57.817 33.333 0.00 0.00 0.00 3.41
540 595 3.616956 ACGATTCAGACCATGTGACAT 57.383 42.857 0.00 0.00 0.00 3.06
543 598 3.554731 CGATTCAGACCATGTGACATCTG 59.445 47.826 8.07 8.07 39.99 2.90
660 716 7.713734 ATATAGGCACATACCTACGTTATGT 57.286 36.000 5.70 5.70 45.03 2.29
661 717 8.812513 ATATAGGCACATACCTACGTTATGTA 57.187 34.615 10.27 3.14 45.03 2.29
662 718 7.154435 ATAGGCACATACCTACGTTATGTAG 57.846 40.000 10.27 4.70 45.03 2.74
715 771 2.858344 CGACCGACCTAGCTTGTTAATG 59.142 50.000 0.00 0.00 0.00 1.90
716 772 3.428452 CGACCGACCTAGCTTGTTAATGA 60.428 47.826 0.00 0.00 0.00 2.57
789 845 2.235402 GGAACCCCGACTACATTTCAGA 59.765 50.000 0.00 0.00 0.00 3.27
792 848 5.221661 GGAACCCCGACTACATTTCAGATAT 60.222 44.000 0.00 0.00 0.00 1.63
800 856 6.563567 CGACTACATTTCAGATATGCTGCTTG 60.564 42.308 0.00 0.00 44.52 4.01
869 925 4.645136 TCGGCCGCTCTATATAATCTCAAT 59.355 41.667 23.51 0.00 0.00 2.57
875 931 5.974158 CGCTCTATATAATCTCAATGGGACG 59.026 44.000 0.00 0.00 0.00 4.79
878 934 6.631016 TCTATATAATCTCAATGGGACGCAC 58.369 40.000 0.00 0.00 0.00 5.34
879 935 3.558931 ATAATCTCAATGGGACGCACA 57.441 42.857 0.00 0.00 0.00 4.57
880 936 2.198827 AATCTCAATGGGACGCACAA 57.801 45.000 0.00 0.00 0.00 3.33
881 937 2.198827 ATCTCAATGGGACGCACAAA 57.801 45.000 0.00 0.00 0.00 2.83
883 939 0.950836 CTCAATGGGACGCACAAACA 59.049 50.000 0.00 0.00 0.00 2.83
885 941 0.318614 CAATGGGACGCACAAACACC 60.319 55.000 0.00 0.00 0.00 4.16
886 942 0.467290 AATGGGACGCACAAACACCT 60.467 50.000 0.00 0.00 0.00 4.00
887 943 0.398696 ATGGGACGCACAAACACCTA 59.601 50.000 0.00 0.00 0.00 3.08
888 944 0.250124 TGGGACGCACAAACACCTAG 60.250 55.000 0.00 0.00 0.00 3.02
906 962 7.501844 ACACCTAGCTTAATTCTGTATTCTCC 58.498 38.462 0.00 0.00 0.00 3.71
915 971 0.735978 CTGTATTCTCCACGCACGCA 60.736 55.000 0.00 0.00 0.00 5.24
965 1021 2.026522 GGGAGACGATCAGACGAGG 58.973 63.158 0.00 0.00 37.03 4.63
966 1022 1.448922 GGGAGACGATCAGACGAGGG 61.449 65.000 0.00 0.00 37.03 4.30
967 1023 1.448922 GGAGACGATCAGACGAGGGG 61.449 65.000 0.00 0.00 37.03 4.79
968 1024 0.748729 GAGACGATCAGACGAGGGGT 60.749 60.000 0.00 0.00 37.03 4.95
1098 1241 1.471119 CCGAGTACCTGCAGTTCCTA 58.529 55.000 13.81 0.00 0.00 2.94
1109 1252 1.758906 AGTTCCTAGAGGAGGCGGC 60.759 63.158 0.00 0.00 46.25 6.53
1182 1331 2.101415 GGCCAACTTTCTGCAGTTTCTT 59.899 45.455 14.67 0.00 34.60 2.52
1197 1346 0.603569 TTCTTGGAGAGGACGAGCAC 59.396 55.000 0.00 0.00 0.00 4.40
1220 1369 3.733236 TGCACTACGATAGCACCAC 57.267 52.632 0.00 0.00 42.67 4.16
1285 1440 0.179043 CGACGAGGAGGAGGAGATGA 60.179 60.000 0.00 0.00 0.00 2.92
1361 1519 1.926511 GCCACCTCGGTGCAAGATTG 61.927 60.000 10.59 0.00 44.16 2.67
1367 1525 0.534873 TCGGTGCAAGATTGATCGGA 59.465 50.000 0.00 0.00 0.00 4.55
1368 1530 0.933097 CGGTGCAAGATTGATCGGAG 59.067 55.000 0.00 0.00 0.00 4.63
1376 1538 2.369257 GATTGATCGGAGCGGCCTGA 62.369 60.000 0.00 0.00 0.00 3.86
1392 1554 3.937706 GGCCTGATTCGGATCAAGATATG 59.062 47.826 8.00 0.00 41.55 1.78
1393 1555 3.373439 GCCTGATTCGGATCAAGATATGC 59.627 47.826 8.00 0.64 41.55 3.14
1394 1556 4.829968 CCTGATTCGGATCAAGATATGCT 58.170 43.478 8.00 0.00 41.55 3.79
1395 1557 5.625426 GCCTGATTCGGATCAAGATATGCTA 60.625 44.000 8.00 0.00 41.55 3.49
1397 1559 6.350864 CCTGATTCGGATCAAGATATGCTAGT 60.351 42.308 8.00 0.00 41.55 2.57
1398 1560 7.148000 CCTGATTCGGATCAAGATATGCTAGTA 60.148 40.741 8.00 0.00 41.55 1.82
1399 1561 7.766283 TGATTCGGATCAAGATATGCTAGTAG 58.234 38.462 3.16 0.00 39.29 2.57
1400 1562 5.568685 TCGGATCAAGATATGCTAGTAGC 57.431 43.478 15.56 15.56 42.82 3.58
1401 1563 5.257262 TCGGATCAAGATATGCTAGTAGCT 58.743 41.667 22.34 10.82 42.97 3.32
1402 1564 5.124617 TCGGATCAAGATATGCTAGTAGCTG 59.875 44.000 22.34 11.46 42.97 4.24
1403 1565 5.108517 GGATCAAGATATGCTAGTAGCTGC 58.891 45.833 22.34 9.33 42.97 5.25
1416 1578 2.352805 GCTGCCTAGCTGGTTGGT 59.647 61.111 8.99 0.00 46.57 3.67
1480 1644 6.404734 GCCTTTGAAGATGAAAACGGATGTAT 60.405 38.462 0.00 0.00 0.00 2.29
1488 1652 8.964476 AGATGAAAACGGATGTATTGTTATCT 57.036 30.769 0.00 0.00 0.00 1.98
1491 1655 8.196802 TGAAAACGGATGTATTGTTATCTCTG 57.803 34.615 0.00 0.00 0.00 3.35
1492 1656 8.038351 TGAAAACGGATGTATTGTTATCTCTGA 58.962 33.333 0.00 0.00 0.00 3.27
1493 1657 7.772332 AAACGGATGTATTGTTATCTCTGAC 57.228 36.000 0.00 0.00 0.00 3.51
1496 1660 5.853810 CGGATGTATTGTTATCTCTGACGAG 59.146 44.000 0.00 0.00 38.67 4.18
1506 1670 1.474478 TCTCTGACGAGATTCCACTGC 59.526 52.381 0.00 0.00 41.26 4.40
1508 1672 0.171231 CTGACGAGATTCCACTGCGA 59.829 55.000 0.00 0.00 0.00 5.10
1509 1673 0.601057 TGACGAGATTCCACTGCGAA 59.399 50.000 0.00 0.00 0.00 4.70
1510 1674 0.992802 GACGAGATTCCACTGCGAAC 59.007 55.000 0.00 0.00 0.00 3.95
1512 1676 1.816835 ACGAGATTCCACTGCGAACTA 59.183 47.619 0.00 0.00 0.00 2.24
1513 1677 2.186076 CGAGATTCCACTGCGAACTAC 58.814 52.381 0.00 0.00 0.00 2.73
1514 1678 2.186076 GAGATTCCACTGCGAACTACG 58.814 52.381 0.00 0.00 45.66 3.51
1516 1680 2.751259 AGATTCCACTGCGAACTACGTA 59.249 45.455 0.00 0.00 44.60 3.57
1517 1681 2.336554 TTCCACTGCGAACTACGTAC 57.663 50.000 0.00 0.00 44.60 3.67
1518 1682 0.166597 TCCACTGCGAACTACGTACG 59.833 55.000 15.01 15.01 44.60 3.67
1519 1683 0.795735 CCACTGCGAACTACGTACGG 60.796 60.000 21.06 5.00 44.60 4.02
1520 1684 0.795735 CACTGCGAACTACGTACGGG 60.796 60.000 21.06 14.05 44.60 5.28
1521 1685 1.237285 ACTGCGAACTACGTACGGGT 61.237 55.000 21.06 14.72 44.60 5.28
1522 1686 0.795735 CTGCGAACTACGTACGGGTG 60.796 60.000 21.06 11.20 44.60 4.61
1523 1687 1.210155 GCGAACTACGTACGGGTGT 59.790 57.895 21.06 11.85 44.60 4.16
1524 1688 0.446222 GCGAACTACGTACGGGTGTA 59.554 55.000 21.06 1.47 44.60 2.90
1525 1689 1.064060 GCGAACTACGTACGGGTGTAT 59.936 52.381 21.06 3.33 44.60 2.29
1526 1690 2.286833 GCGAACTACGTACGGGTGTATA 59.713 50.000 21.06 0.30 44.60 1.47
1527 1691 3.058914 GCGAACTACGTACGGGTGTATAT 60.059 47.826 21.06 2.61 44.60 0.86
1528 1692 4.151689 GCGAACTACGTACGGGTGTATATA 59.848 45.833 21.06 0.00 44.60 0.86
1529 1693 5.668866 GCGAACTACGTACGGGTGTATATAG 60.669 48.000 21.06 11.46 44.60 1.31
1530 1694 5.633601 CGAACTACGTACGGGTGTATATAGA 59.366 44.000 21.06 0.00 37.22 1.98
1531 1695 6.311445 CGAACTACGTACGGGTGTATATAGAT 59.689 42.308 21.06 4.11 37.22 1.98
1532 1696 7.488150 CGAACTACGTACGGGTGTATATAGATA 59.512 40.741 21.06 0.00 37.22 1.98
1533 1697 9.319143 GAACTACGTACGGGTGTATATAGATAT 57.681 37.037 21.06 2.31 32.11 1.63
1534 1698 8.654230 ACTACGTACGGGTGTATATAGATATG 57.346 38.462 21.06 0.00 32.11 1.78
1535 1699 8.260818 ACTACGTACGGGTGTATATAGATATGT 58.739 37.037 21.06 0.00 32.11 2.29
1536 1700 7.928307 ACGTACGGGTGTATATAGATATGTT 57.072 36.000 21.06 0.00 32.11 2.71
1537 1701 8.340618 ACGTACGGGTGTATATAGATATGTTT 57.659 34.615 21.06 0.00 32.11 2.83
1538 1702 8.796475 ACGTACGGGTGTATATAGATATGTTTT 58.204 33.333 21.06 0.00 32.11 2.43
1570 1734 7.829378 AGATTCACTCATTTTTACTCCGTAC 57.171 36.000 0.00 0.00 0.00 3.67
1571 1735 7.383687 AGATTCACTCATTTTTACTCCGTACA 58.616 34.615 0.00 0.00 0.00 2.90
1572 1736 8.041323 AGATTCACTCATTTTTACTCCGTACAT 58.959 33.333 0.00 0.00 0.00 2.29
1573 1737 6.961359 TCACTCATTTTTACTCCGTACATG 57.039 37.500 0.00 0.00 0.00 3.21
1574 1738 5.872617 TCACTCATTTTTACTCCGTACATGG 59.127 40.000 0.00 0.00 0.00 3.66
1575 1739 5.642063 CACTCATTTTTACTCCGTACATGGT 59.358 40.000 0.00 0.00 0.00 3.55
1576 1740 6.148811 CACTCATTTTTACTCCGTACATGGTT 59.851 38.462 0.00 0.00 0.00 3.67
1577 1741 7.332430 CACTCATTTTTACTCCGTACATGGTTA 59.668 37.037 0.00 0.00 0.00 2.85
1578 1742 7.548075 ACTCATTTTTACTCCGTACATGGTTAG 59.452 37.037 0.00 0.00 0.00 2.34
1579 1743 7.388437 TCATTTTTACTCCGTACATGGTTAGT 58.612 34.615 0.00 0.00 0.00 2.24
1580 1744 8.530311 TCATTTTTACTCCGTACATGGTTAGTA 58.470 33.333 0.00 0.00 0.00 1.82
1581 1745 9.153721 CATTTTTACTCCGTACATGGTTAGTAA 57.846 33.333 0.00 1.43 0.00 2.24
1582 1746 9.895138 ATTTTTACTCCGTACATGGTTAGTAAT 57.105 29.630 0.00 0.00 31.56 1.89
1583 1747 8.706492 TTTTACTCCGTACATGGTTAGTAATG 57.294 34.615 0.00 0.00 31.56 1.90
1584 1748 7.643569 TTACTCCGTACATGGTTAGTAATGA 57.356 36.000 0.00 0.00 0.00 2.57
1585 1749 6.534475 ACTCCGTACATGGTTAGTAATGAA 57.466 37.500 0.00 0.00 0.00 2.57
1586 1750 6.938507 ACTCCGTACATGGTTAGTAATGAAA 58.061 36.000 0.00 0.00 0.00 2.69
1587 1751 7.562135 ACTCCGTACATGGTTAGTAATGAAAT 58.438 34.615 0.00 0.00 0.00 2.17
1588 1752 7.709613 ACTCCGTACATGGTTAGTAATGAAATC 59.290 37.037 0.00 0.00 0.00 2.17
1589 1753 7.788026 TCCGTACATGGTTAGTAATGAAATCT 58.212 34.615 0.00 0.00 0.00 2.40
1590 1754 7.924412 TCCGTACATGGTTAGTAATGAAATCTC 59.076 37.037 0.00 0.00 0.00 2.75
1591 1755 7.926555 CCGTACATGGTTAGTAATGAAATCTCT 59.073 37.037 0.00 0.00 0.00 3.10
1592 1756 9.961265 CGTACATGGTTAGTAATGAAATCTCTA 57.039 33.333 0.00 0.00 0.00 2.43
1629 1793 7.902920 AATATTTAGGAACGGAGGTAGTACA 57.097 36.000 2.06 0.00 0.00 2.90
1630 1794 8.488308 AATATTTAGGAACGGAGGTAGTACAT 57.512 34.615 2.06 0.00 0.00 2.29
1631 1795 6.803366 ATTTAGGAACGGAGGTAGTACATT 57.197 37.500 2.06 0.00 0.00 2.71
1632 1796 7.902920 ATTTAGGAACGGAGGTAGTACATTA 57.097 36.000 2.06 0.00 0.00 1.90
1633 1797 6.699575 TTAGGAACGGAGGTAGTACATTAC 57.300 41.667 2.06 0.00 0.00 1.89
1634 1798 4.864726 AGGAACGGAGGTAGTACATTACT 58.135 43.478 2.06 0.00 42.68 2.24
1635 1799 4.643784 AGGAACGGAGGTAGTACATTACTG 59.356 45.833 2.06 0.00 39.81 2.74
1636 1800 4.357996 GAACGGAGGTAGTACATTACTGC 58.642 47.826 2.06 0.00 39.81 4.40
1637 1801 3.359033 ACGGAGGTAGTACATTACTGCA 58.641 45.455 2.06 0.00 42.29 4.41
1638 1802 3.958798 ACGGAGGTAGTACATTACTGCAT 59.041 43.478 2.06 0.00 42.29 3.96
1639 1803 4.202121 ACGGAGGTAGTACATTACTGCATG 60.202 45.833 2.06 0.00 42.29 4.06
1640 1804 4.037565 CGGAGGTAGTACATTACTGCATGA 59.962 45.833 0.00 0.00 42.29 3.07
1641 1805 5.533482 GGAGGTAGTACATTACTGCATGAG 58.467 45.833 0.00 0.00 42.29 2.90
1642 1806 4.950050 AGGTAGTACATTACTGCATGAGC 58.050 43.478 0.00 0.00 42.29 4.26
1643 1807 4.651503 AGGTAGTACATTACTGCATGAGCT 59.348 41.667 0.00 0.00 42.29 4.09
1644 1808 4.985409 GGTAGTACATTACTGCATGAGCTC 59.015 45.833 6.82 6.82 42.29 4.09
1656 1820 2.419713 GCATGAGCTCTGTTGGATCAGA 60.420 50.000 16.19 0.00 41.40 3.27
1666 1830 5.993055 TCTGTTGGATCAGAGAATAATGCA 58.007 37.500 0.00 0.00 39.20 3.96
1667 1831 6.598503 TCTGTTGGATCAGAGAATAATGCAT 58.401 36.000 0.00 0.00 39.20 3.96
1668 1832 7.058525 TCTGTTGGATCAGAGAATAATGCATT 58.941 34.615 17.56 17.56 39.20 3.56
1669 1833 7.558807 TCTGTTGGATCAGAGAATAATGCATTT 59.441 33.333 18.75 0.00 39.20 2.32
1670 1834 8.070034 TGTTGGATCAGAGAATAATGCATTTT 57.930 30.769 18.75 6.94 0.00 1.82
1671 1835 9.187996 TGTTGGATCAGAGAATAATGCATTTTA 57.812 29.630 18.75 0.00 0.00 1.52
1721 1885 1.720781 AAGGGTTGCAATGGAAGCTT 58.279 45.000 15.68 6.07 0.00 3.74
1738 1902 5.590259 GGAAGCTTTGGTCAGATTATAAGCA 59.410 40.000 0.00 0.00 40.19 3.91
1741 1905 7.466746 AGCTTTGGTCAGATTATAAGCAAAA 57.533 32.000 3.17 0.00 39.18 2.44
1743 1907 8.193438 AGCTTTGGTCAGATTATAAGCAAAATC 58.807 33.333 3.17 0.00 39.18 2.17
1746 1910 9.859427 TTTGGTCAGATTATAAGCAAAATCAAG 57.141 29.630 3.17 0.00 37.42 3.02
1756 1920 4.698583 AGCAAAATCAAGCTTAGAGCAG 57.301 40.909 0.00 0.00 45.56 4.24
1757 1921 4.330250 AGCAAAATCAAGCTTAGAGCAGA 58.670 39.130 0.00 0.00 45.56 4.26
1758 1922 4.763793 AGCAAAATCAAGCTTAGAGCAGAA 59.236 37.500 0.00 0.00 45.56 3.02
1759 1923 5.242393 AGCAAAATCAAGCTTAGAGCAGAAA 59.758 36.000 0.00 0.00 45.56 2.52
1760 1924 5.922544 GCAAAATCAAGCTTAGAGCAGAAAA 59.077 36.000 0.00 0.00 45.56 2.29
1761 1925 6.128982 GCAAAATCAAGCTTAGAGCAGAAAAC 60.129 38.462 0.00 0.00 45.56 2.43
1762 1926 6.890979 AAATCAAGCTTAGAGCAGAAAACT 57.109 33.333 0.00 0.00 45.56 2.66
1763 1927 6.890979 AATCAAGCTTAGAGCAGAAAACTT 57.109 33.333 0.00 0.00 45.56 2.66
1764 1928 6.890979 ATCAAGCTTAGAGCAGAAAACTTT 57.109 33.333 0.00 0.00 45.56 2.66
1765 1929 6.064846 TCAAGCTTAGAGCAGAAAACTTTG 57.935 37.500 0.00 0.00 45.56 2.77
1766 1930 5.822519 TCAAGCTTAGAGCAGAAAACTTTGA 59.177 36.000 0.00 0.00 45.56 2.69
1767 1931 5.681337 AGCTTAGAGCAGAAAACTTTGAC 57.319 39.130 2.47 0.00 45.56 3.18
1768 1932 5.372373 AGCTTAGAGCAGAAAACTTTGACT 58.628 37.500 2.47 0.00 45.56 3.41
1769 1933 5.238214 AGCTTAGAGCAGAAAACTTTGACTG 59.762 40.000 2.47 0.00 45.56 3.51
1770 1934 5.008118 GCTTAGAGCAGAAAACTTTGACTGT 59.992 40.000 0.00 0.00 41.89 3.55
1771 1935 6.202954 GCTTAGAGCAGAAAACTTTGACTGTA 59.797 38.462 0.00 0.00 41.89 2.74
1772 1936 5.993106 AGAGCAGAAAACTTTGACTGTAC 57.007 39.130 0.00 0.00 33.57 2.90
1803 1967 6.481954 TTTGAAGGTCGAGCTTCTAATTTC 57.518 37.500 40.93 24.63 0.00 2.17
1844 2055 7.124901 AGCCAAGTACTCTCAATCTTTAGATCA 59.875 37.037 0.00 0.00 32.75 2.92
1910 2121 7.874940 TGTATTTCAAACTCTGTGATCTTTGG 58.125 34.615 0.00 0.00 0.00 3.28
2025 2241 3.212538 GCTATACGCTGCGTCACG 58.787 61.111 32.44 20.11 41.54 4.35
2095 2315 4.870123 AATTTGCCACATTTCACAGCTA 57.130 36.364 0.00 0.00 0.00 3.32
2134 2354 7.669089 TGGTACATGTGGTATCTAGATGAAA 57.331 36.000 15.79 0.00 34.02 2.69
2135 2355 7.726216 TGGTACATGTGGTATCTAGATGAAAG 58.274 38.462 15.79 1.82 34.02 2.62
2136 2356 7.344612 TGGTACATGTGGTATCTAGATGAAAGT 59.655 37.037 15.79 7.21 34.02 2.66
2137 2357 8.204836 GGTACATGTGGTATCTAGATGAAAGTT 58.795 37.037 15.79 0.00 33.76 2.66
2138 2358 9.601217 GTACATGTGGTATCTAGATGAAAGTTT 57.399 33.333 15.79 0.00 33.76 2.66
2139 2359 8.723942 ACATGTGGTATCTAGATGAAAGTTTC 57.276 34.615 15.79 8.75 0.00 2.78
2140 2360 8.321353 ACATGTGGTATCTAGATGAAAGTTTCA 58.679 33.333 20.14 20.14 45.01 2.69
2141 2361 9.166173 CATGTGGTATCTAGATGAAAGTTTCAA 57.834 33.333 21.57 5.92 43.95 2.69
2142 2362 8.547967 TGTGGTATCTAGATGAAAGTTTCAAC 57.452 34.615 21.57 18.56 43.95 3.18
2143 2363 8.375506 TGTGGTATCTAGATGAAAGTTTCAACT 58.624 33.333 25.78 25.78 43.95 3.16
2158 2378 7.138692 AGTTTCAACTTGATAGAGTTCATGC 57.861 36.000 0.00 0.00 37.76 4.06
2159 2379 6.939163 AGTTTCAACTTGATAGAGTTCATGCT 59.061 34.615 0.00 0.00 37.76 3.79
2160 2380 7.446625 AGTTTCAACTTGATAGAGTTCATGCTT 59.553 33.333 0.00 0.00 37.76 3.91
2161 2381 7.750229 TTCAACTTGATAGAGTTCATGCTTT 57.250 32.000 0.00 0.00 37.76 3.51
2162 2382 7.750229 TCAACTTGATAGAGTTCATGCTTTT 57.250 32.000 0.00 0.00 37.76 2.27
2163 2383 8.169977 TCAACTTGATAGAGTTCATGCTTTTT 57.830 30.769 0.00 0.00 37.76 1.94
2183 2403 5.528043 TTTTGGCAGAACTAATTCTTGCA 57.472 34.783 9.45 0.00 42.91 4.08
2184 2404 5.726980 TTTGGCAGAACTAATTCTTGCAT 57.273 34.783 9.45 0.00 42.91 3.96
2185 2405 5.726980 TTGGCAGAACTAATTCTTGCATT 57.273 34.783 9.45 0.00 42.91 3.56
2186 2406 6.832520 TTGGCAGAACTAATTCTTGCATTA 57.167 33.333 9.45 0.00 42.91 1.90
2187 2407 6.194796 TGGCAGAACTAATTCTTGCATTAC 57.805 37.500 9.45 0.00 42.91 1.89
2188 2408 5.945784 TGGCAGAACTAATTCTTGCATTACT 59.054 36.000 9.45 0.00 42.91 2.24
2189 2409 6.094048 TGGCAGAACTAATTCTTGCATTACTC 59.906 38.462 9.45 0.00 42.91 2.59
2254 2536 3.746900 GGCCAAAGCATAGCCAAAG 57.253 52.632 0.00 0.00 46.34 2.77
2291 2575 3.306641 GCAACCTACCAAAATTGCCATGA 60.307 43.478 0.00 0.00 41.25 3.07
2316 2605 2.700897 GACTAGCCCTATTTCTGCTCCA 59.299 50.000 0.00 0.00 36.57 3.86
2319 2608 1.064389 AGCCCTATTTCTGCTCCAACC 60.064 52.381 0.00 0.00 0.00 3.77
2350 2639 0.749091 TGCAAGAATCGCATCCCCAG 60.749 55.000 0.00 0.00 33.55 4.45
2352 2641 1.816961 GCAAGAATCGCATCCCCAGAT 60.817 52.381 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 214 5.766174 ACAAAATTTTGGAGCTGCATGATTT 59.234 32.000 29.37 14.90 42.34 2.17
281 295 3.891366 GCCAACTTGGATGCTATATGGTT 59.109 43.478 12.37 0.00 40.96 3.67
312 327 6.747739 CGACGAGATCTTCAAAACTAGATGAA 59.252 38.462 0.00 3.62 34.57 2.57
313 328 6.258899 CGACGAGATCTTCAAAACTAGATGA 58.741 40.000 0.00 0.00 0.00 2.92
314 329 5.052040 GCGACGAGATCTTCAAAACTAGATG 60.052 44.000 0.00 0.00 0.00 2.90
443 496 2.170012 AGGAAAGGTAGCCCGTGATA 57.830 50.000 0.00 0.00 35.12 2.15
485 538 3.132111 TGGACTGTTGCGCTCTCATATAA 59.868 43.478 9.73 0.00 0.00 0.98
540 595 0.736636 CGTGCATACGTAGTCCCAGA 59.263 55.000 0.08 0.00 43.93 3.86
650 706 2.349249 CGCGTCTCCCTACATAACGTAG 60.349 54.545 0.00 0.00 46.27 3.51
651 707 1.599071 CGCGTCTCCCTACATAACGTA 59.401 52.381 0.00 0.00 35.85 3.57
652 708 0.379669 CGCGTCTCCCTACATAACGT 59.620 55.000 0.00 0.00 35.85 3.99
653 709 0.933509 GCGCGTCTCCCTACATAACG 60.934 60.000 8.43 0.00 36.48 3.18
654 710 0.933509 CGCGCGTCTCCCTACATAAC 60.934 60.000 24.19 0.00 0.00 1.89
655 711 1.357690 CGCGCGTCTCCCTACATAA 59.642 57.895 24.19 0.00 0.00 1.90
656 712 2.549198 CCGCGCGTCTCCCTACATA 61.549 63.158 29.95 0.00 0.00 2.29
657 713 3.900892 CCGCGCGTCTCCCTACAT 61.901 66.667 29.95 0.00 0.00 2.29
715 771 7.433680 GGAGAGATCAAGATTTTCCTAGTCTC 58.566 42.308 0.00 0.00 0.00 3.36
716 772 6.326323 GGGAGAGATCAAGATTTTCCTAGTCT 59.674 42.308 0.00 0.00 0.00 3.24
789 845 1.745087 CCAAACCGTCAAGCAGCATAT 59.255 47.619 0.00 0.00 0.00 1.78
792 848 1.453015 ACCAAACCGTCAAGCAGCA 60.453 52.632 0.00 0.00 0.00 4.41
828 884 4.736896 AACGCGACTTCCTCCGGC 62.737 66.667 15.93 0.00 0.00 6.13
829 885 2.048503 AAACGCGACTTCCTCCGG 60.049 61.111 15.93 0.00 0.00 5.14
869 925 0.250124 CTAGGTGTTTGTGCGTCCCA 60.250 55.000 0.00 0.00 0.00 4.37
875 931 5.048713 ACAGAATTAAGCTAGGTGTTTGTGC 60.049 40.000 0.00 0.00 0.00 4.57
878 934 9.167311 AGAATACAGAATTAAGCTAGGTGTTTG 57.833 33.333 0.00 0.00 0.00 2.93
879 935 9.384764 GAGAATACAGAATTAAGCTAGGTGTTT 57.615 33.333 0.00 0.00 0.00 2.83
880 936 7.988028 GGAGAATACAGAATTAAGCTAGGTGTT 59.012 37.037 0.00 0.00 0.00 3.32
881 937 7.125811 TGGAGAATACAGAATTAAGCTAGGTGT 59.874 37.037 0.00 0.00 0.00 4.16
883 939 7.501844 GTGGAGAATACAGAATTAAGCTAGGT 58.498 38.462 0.00 0.00 0.00 3.08
885 941 6.144724 GCGTGGAGAATACAGAATTAAGCTAG 59.855 42.308 0.00 0.00 0.00 3.42
886 942 5.983720 GCGTGGAGAATACAGAATTAAGCTA 59.016 40.000 0.00 0.00 0.00 3.32
887 943 4.811557 GCGTGGAGAATACAGAATTAAGCT 59.188 41.667 0.00 0.00 0.00 3.74
888 944 4.570772 TGCGTGGAGAATACAGAATTAAGC 59.429 41.667 0.00 0.00 0.00 3.09
906 962 1.767127 TAGGTGTTTGTGCGTGCGTG 61.767 55.000 0.00 0.00 0.00 5.34
915 971 2.303311 GGAGGAGAAGCTAGGTGTTTGT 59.697 50.000 0.00 0.00 0.00 2.83
956 1012 1.379977 CTGGCTACCCCTCGTCTGA 60.380 63.158 0.00 0.00 0.00 3.27
957 1013 3.082579 GCTGGCTACCCCTCGTCTG 62.083 68.421 0.00 0.00 0.00 3.51
960 1016 4.753662 TCGCTGGCTACCCCTCGT 62.754 66.667 0.00 0.00 33.87 4.18
961 1017 3.905678 CTCGCTGGCTACCCCTCG 61.906 72.222 0.00 0.00 0.00 4.63
962 1018 2.022240 CTTCTCGCTGGCTACCCCTC 62.022 65.000 0.00 0.00 0.00 4.30
963 1019 2.038975 TTCTCGCTGGCTACCCCT 59.961 61.111 0.00 0.00 0.00 4.79
964 1020 2.022240 CTCTTCTCGCTGGCTACCCC 62.022 65.000 0.00 0.00 0.00 4.95
965 1021 1.439644 CTCTTCTCGCTGGCTACCC 59.560 63.158 0.00 0.00 0.00 3.69
966 1022 1.227118 GCTCTTCTCGCTGGCTACC 60.227 63.158 0.00 0.00 0.00 3.18
967 1023 1.227118 GGCTCTTCTCGCTGGCTAC 60.227 63.158 0.00 0.00 0.00 3.58
968 1024 1.670949 CTGGCTCTTCTCGCTGGCTA 61.671 60.000 0.00 0.00 0.00 3.93
1004 1060 1.772308 TGGACGTACTCCAGGGTCT 59.228 57.895 0.00 0.00 44.99 3.85
1211 1360 1.077930 CTGCTGCTGGTGGTGCTAT 60.078 57.895 0.00 0.00 0.00 2.97
1361 1519 1.666234 GAATCAGGCCGCTCCGATC 60.666 63.158 0.00 0.00 40.77 3.69
1367 1525 1.971505 TTGATCCGAATCAGGCCGCT 61.972 55.000 0.00 0.00 42.72 5.52
1368 1530 1.502163 CTTGATCCGAATCAGGCCGC 61.502 60.000 0.00 0.00 42.72 6.53
1376 1538 6.379703 AGCTACTAGCATATCTTGATCCGAAT 59.620 38.462 10.73 0.00 45.56 3.34
1400 1562 1.279271 AGTAACCAACCAGCTAGGCAG 59.721 52.381 2.50 0.00 43.14 4.85
1401 1563 1.358152 AGTAACCAACCAGCTAGGCA 58.642 50.000 2.50 0.00 43.14 4.75
1402 1564 2.084546 CAAGTAACCAACCAGCTAGGC 58.915 52.381 2.50 0.00 43.14 3.93
1403 1565 2.039879 ACCAAGTAACCAACCAGCTAGG 59.960 50.000 0.00 0.00 45.67 3.02
1411 1573 2.956333 AGCAGGAAACCAAGTAACCAAC 59.044 45.455 0.00 0.00 0.00 3.77
1416 1578 4.892934 ACATGAAAGCAGGAAACCAAGTAA 59.107 37.500 0.00 0.00 0.00 2.24
1456 1620 5.376854 ACATCCGTTTTCATCTTCAAAGG 57.623 39.130 0.00 0.00 0.00 3.11
1488 1652 0.171231 CGCAGTGGAATCTCGTCAGA 59.829 55.000 0.00 0.00 0.00 3.27
1491 1655 0.992802 GTTCGCAGTGGAATCTCGTC 59.007 55.000 0.00 0.00 0.00 4.20
1492 1656 0.603569 AGTTCGCAGTGGAATCTCGT 59.396 50.000 0.00 0.00 0.00 4.18
1493 1657 2.186076 GTAGTTCGCAGTGGAATCTCG 58.814 52.381 0.00 0.00 0.00 4.04
1496 1660 1.992170 ACGTAGTTCGCAGTGGAATC 58.008 50.000 0.00 0.00 37.78 2.52
1497 1661 2.730090 CGTACGTAGTTCGCAGTGGAAT 60.730 50.000 7.22 0.00 45.19 3.01
1498 1662 1.400113 CGTACGTAGTTCGCAGTGGAA 60.400 52.381 7.22 0.00 45.19 3.53
1500 1664 2.633639 CGTACGTAGTTCGCAGTGG 58.366 57.895 7.22 0.00 45.19 4.00
1508 1672 9.102757 CATATCTATATACACCCGTACGTAGTT 57.897 37.037 15.21 4.62 37.78 2.24
1510 1674 8.654230 ACATATCTATATACACCCGTACGTAG 57.346 38.462 15.21 7.77 0.00 3.51
1512 1676 7.928307 AACATATCTATATACACCCGTACGT 57.072 36.000 15.21 0.00 0.00 3.57
1561 1725 7.643569 TTCATTACTAACCATGTACGGAGTA 57.356 36.000 0.00 0.00 45.11 2.59
1563 1727 7.926555 AGATTTCATTACTAACCATGTACGGAG 59.073 37.037 0.00 0.00 0.00 4.63
1564 1728 7.788026 AGATTTCATTACTAACCATGTACGGA 58.212 34.615 0.00 0.00 0.00 4.69
1565 1729 7.926555 AGAGATTTCATTACTAACCATGTACGG 59.073 37.037 0.00 0.00 0.00 4.02
1566 1730 8.873215 AGAGATTTCATTACTAACCATGTACG 57.127 34.615 0.00 0.00 0.00 3.67
1603 1767 9.592196 TGTACTACCTCCGTTCCTAAATATTAT 57.408 33.333 0.00 0.00 0.00 1.28
1604 1768 8.995027 TGTACTACCTCCGTTCCTAAATATTA 57.005 34.615 0.00 0.00 0.00 0.98
1605 1769 7.902920 TGTACTACCTCCGTTCCTAAATATT 57.097 36.000 0.00 0.00 0.00 1.28
1606 1770 8.488308 AATGTACTACCTCCGTTCCTAAATAT 57.512 34.615 0.00 0.00 0.00 1.28
1607 1771 7.902920 AATGTACTACCTCCGTTCCTAAATA 57.097 36.000 0.00 0.00 0.00 1.40
1608 1772 6.803366 AATGTACTACCTCCGTTCCTAAAT 57.197 37.500 0.00 0.00 0.00 1.40
1609 1773 6.891908 AGTAATGTACTACCTCCGTTCCTAAA 59.108 38.462 0.00 0.00 37.23 1.85
1610 1774 6.319658 CAGTAATGTACTACCTCCGTTCCTAA 59.680 42.308 0.00 0.00 37.23 2.69
1611 1775 5.824624 CAGTAATGTACTACCTCCGTTCCTA 59.175 44.000 0.00 0.00 37.23 2.94
1612 1776 4.643784 CAGTAATGTACTACCTCCGTTCCT 59.356 45.833 0.00 0.00 37.23 3.36
1613 1777 4.735873 GCAGTAATGTACTACCTCCGTTCC 60.736 50.000 0.00 0.00 37.23 3.62
1614 1778 4.142315 TGCAGTAATGTACTACCTCCGTTC 60.142 45.833 0.00 0.00 37.23 3.95
1615 1779 3.765511 TGCAGTAATGTACTACCTCCGTT 59.234 43.478 0.00 0.00 37.23 4.44
1616 1780 3.359033 TGCAGTAATGTACTACCTCCGT 58.641 45.455 0.00 0.00 37.23 4.69
1617 1781 4.037565 TCATGCAGTAATGTACTACCTCCG 59.962 45.833 0.00 0.00 37.23 4.63
1618 1782 5.531122 TCATGCAGTAATGTACTACCTCC 57.469 43.478 0.00 0.00 37.23 4.30
1619 1783 4.985409 GCTCATGCAGTAATGTACTACCTC 59.015 45.833 0.00 0.00 37.23 3.85
1620 1784 4.651503 AGCTCATGCAGTAATGTACTACCT 59.348 41.667 0.00 0.00 42.74 3.08
1621 1785 4.950050 AGCTCATGCAGTAATGTACTACC 58.050 43.478 0.00 0.00 42.74 3.18
1622 1786 5.689514 CAGAGCTCATGCAGTAATGTACTAC 59.310 44.000 17.77 0.00 42.74 2.73
1623 1787 5.360999 ACAGAGCTCATGCAGTAATGTACTA 59.639 40.000 17.77 0.00 42.74 1.82
1624 1788 4.161189 ACAGAGCTCATGCAGTAATGTACT 59.839 41.667 17.77 0.00 42.74 2.73
1625 1789 4.437239 ACAGAGCTCATGCAGTAATGTAC 58.563 43.478 17.77 0.00 42.74 2.90
1626 1790 4.743057 ACAGAGCTCATGCAGTAATGTA 57.257 40.909 17.77 0.00 42.74 2.29
1627 1791 3.623906 ACAGAGCTCATGCAGTAATGT 57.376 42.857 17.77 5.02 42.74 2.71
1628 1792 3.064958 CCAACAGAGCTCATGCAGTAATG 59.935 47.826 17.77 4.32 42.74 1.90
1629 1793 3.054875 TCCAACAGAGCTCATGCAGTAAT 60.055 43.478 17.77 0.00 42.74 1.89
1630 1794 2.302733 TCCAACAGAGCTCATGCAGTAA 59.697 45.455 17.77 0.00 42.74 2.24
1631 1795 1.901833 TCCAACAGAGCTCATGCAGTA 59.098 47.619 17.77 0.00 42.74 2.74
1632 1796 0.689055 TCCAACAGAGCTCATGCAGT 59.311 50.000 17.77 3.27 42.74 4.40
1633 1797 1.941294 GATCCAACAGAGCTCATGCAG 59.059 52.381 17.77 7.34 42.74 4.41
1634 1798 1.279846 TGATCCAACAGAGCTCATGCA 59.720 47.619 17.77 0.00 42.74 3.96
1635 1799 1.941294 CTGATCCAACAGAGCTCATGC 59.059 52.381 17.77 0.60 39.94 4.06
1636 1800 3.538634 TCTGATCCAACAGAGCTCATG 57.461 47.619 17.77 13.44 41.21 3.07
1643 1807 5.993055 TGCATTATTCTCTGATCCAACAGA 58.007 37.500 0.00 0.00 43.39 3.41
1644 1808 6.879276 ATGCATTATTCTCTGATCCAACAG 57.121 37.500 0.00 0.00 39.02 3.16
1656 1820 8.576442 CCCCGAATAGTTAAAATGCATTATTCT 58.424 33.333 13.39 11.13 0.00 2.40
1658 1822 8.245195 ACCCCGAATAGTTAAAATGCATTATT 57.755 30.769 13.39 7.46 0.00 1.40
1659 1823 7.833285 ACCCCGAATAGTTAAAATGCATTAT 57.167 32.000 13.39 0.00 0.00 1.28
1660 1824 7.484975 CAACCCCGAATAGTTAAAATGCATTA 58.515 34.615 13.39 0.00 0.00 1.90
1662 1826 5.681179 GCAACCCCGAATAGTTAAAATGCAT 60.681 40.000 0.00 0.00 0.00 3.96
1664 1828 4.109766 GCAACCCCGAATAGTTAAAATGC 58.890 43.478 0.00 0.00 0.00 3.56
1665 1829 5.576447 AGCAACCCCGAATAGTTAAAATG 57.424 39.130 0.00 0.00 0.00 2.32
1666 1830 5.949952 AGAAGCAACCCCGAATAGTTAAAAT 59.050 36.000 0.00 0.00 0.00 1.82
1667 1831 5.318630 AGAAGCAACCCCGAATAGTTAAAA 58.681 37.500 0.00 0.00 0.00 1.52
1668 1832 4.913784 AGAAGCAACCCCGAATAGTTAAA 58.086 39.130 0.00 0.00 0.00 1.52
1669 1833 4.563140 AGAAGCAACCCCGAATAGTTAA 57.437 40.909 0.00 0.00 0.00 2.01
1670 1834 4.563140 AAGAAGCAACCCCGAATAGTTA 57.437 40.909 0.00 0.00 0.00 2.24
1671 1835 3.434940 AAGAAGCAACCCCGAATAGTT 57.565 42.857 0.00 0.00 0.00 2.24
1672 1836 3.081804 CAAAGAAGCAACCCCGAATAGT 58.918 45.455 0.00 0.00 0.00 2.12
1721 1885 7.975616 GCTTGATTTTGCTTATAATCTGACCAA 59.024 33.333 0.00 0.00 33.08 3.67
1738 1902 7.282332 AGTTTTCTGCTCTAAGCTTGATTTT 57.718 32.000 9.86 0.00 42.97 1.82
1741 1905 6.488006 TCAAAGTTTTCTGCTCTAAGCTTGAT 59.512 34.615 9.86 0.00 42.97 2.57
1743 1907 5.911838 GTCAAAGTTTTCTGCTCTAAGCTTG 59.088 40.000 9.86 0.00 42.97 4.01
1746 1910 5.008118 ACAGTCAAAGTTTTCTGCTCTAAGC 59.992 40.000 14.02 0.00 42.82 3.09
1749 1913 5.989777 GGTACAGTCAAAGTTTTCTGCTCTA 59.010 40.000 14.02 2.04 0.00 2.43
1750 1914 4.816925 GGTACAGTCAAAGTTTTCTGCTCT 59.183 41.667 14.02 2.74 0.00 4.09
1751 1915 4.816925 AGGTACAGTCAAAGTTTTCTGCTC 59.183 41.667 14.02 9.18 0.00 4.26
1752 1916 4.781934 AGGTACAGTCAAAGTTTTCTGCT 58.218 39.130 14.02 4.82 0.00 4.24
1753 1917 4.816925 AGAGGTACAGTCAAAGTTTTCTGC 59.183 41.667 14.02 3.54 0.00 4.26
1754 1918 8.608844 AATAGAGGTACAGTCAAAGTTTTCTG 57.391 34.615 13.03 13.03 0.00 3.02
1755 1919 9.628500 AAAATAGAGGTACAGTCAAAGTTTTCT 57.372 29.630 0.00 0.00 0.00 2.52
1758 1922 9.403583 TCAAAAATAGAGGTACAGTCAAAGTTT 57.596 29.630 0.00 0.00 0.00 2.66
1759 1923 8.974060 TCAAAAATAGAGGTACAGTCAAAGTT 57.026 30.769 0.00 0.00 0.00 2.66
1760 1924 8.974060 TTCAAAAATAGAGGTACAGTCAAAGT 57.026 30.769 0.00 0.00 0.00 2.66
1761 1925 8.507249 CCTTCAAAAATAGAGGTACAGTCAAAG 58.493 37.037 0.00 0.00 0.00 2.77
1762 1926 7.996644 ACCTTCAAAAATAGAGGTACAGTCAAA 59.003 33.333 0.00 0.00 0.00 2.69
1763 1927 7.514721 ACCTTCAAAAATAGAGGTACAGTCAA 58.485 34.615 0.00 0.00 0.00 3.18
1764 1928 7.074653 ACCTTCAAAAATAGAGGTACAGTCA 57.925 36.000 0.00 0.00 0.00 3.41
1765 1929 6.310711 CGACCTTCAAAAATAGAGGTACAGTC 59.689 42.308 0.00 0.00 0.00 3.51
1766 1930 6.014840 TCGACCTTCAAAAATAGAGGTACAGT 60.015 38.462 0.00 0.00 0.00 3.55
1767 1931 6.395629 TCGACCTTCAAAAATAGAGGTACAG 58.604 40.000 0.00 0.00 0.00 2.74
1768 1932 6.349243 TCGACCTTCAAAAATAGAGGTACA 57.651 37.500 0.00 0.00 0.00 2.90
1769 1933 5.291371 GCTCGACCTTCAAAAATAGAGGTAC 59.709 44.000 0.00 0.00 0.00 3.34
1770 1934 5.187186 AGCTCGACCTTCAAAAATAGAGGTA 59.813 40.000 0.00 0.00 34.10 3.08
1771 1935 4.020128 AGCTCGACCTTCAAAAATAGAGGT 60.020 41.667 0.00 0.00 0.00 3.85
1772 1936 4.508662 AGCTCGACCTTCAAAAATAGAGG 58.491 43.478 0.00 0.00 0.00 3.69
1803 1967 3.189287 ACTTGGCTAACGAATGAGCTTTG 59.811 43.478 0.00 0.00 38.79 2.77
1955 2171 4.725556 TGTCGTCATACAAAGAAGCAAC 57.274 40.909 0.00 0.00 0.00 4.17
2110 2330 7.344612 ACTTTCATCTAGATACCACATGTACCA 59.655 37.037 4.54 0.00 30.62 3.25
2117 2337 8.375506 AGTTGAAACTTTCATCTAGATACCACA 58.624 33.333 4.54 0.00 39.84 4.17
2132 2352 8.078596 GCATGAACTCTATCAAGTTGAAACTTT 58.921 33.333 10.14 0.01 46.52 2.66
2134 2354 6.939163 AGCATGAACTCTATCAAGTTGAAACT 59.061 34.615 10.14 0.00 39.55 2.66
2135 2355 7.138692 AGCATGAACTCTATCAAGTTGAAAC 57.861 36.000 10.14 0.00 39.55 2.78
2136 2356 7.750229 AAGCATGAACTCTATCAAGTTGAAA 57.250 32.000 10.14 0.00 39.55 2.69
2137 2357 7.750229 AAAGCATGAACTCTATCAAGTTGAA 57.250 32.000 10.14 0.00 39.55 2.69
2138 2358 7.750229 AAAAGCATGAACTCTATCAAGTTGA 57.250 32.000 8.27 8.27 39.55 3.18
2160 2380 5.911752 TGCAAGAATTAGTTCTGCCAAAAA 58.088 33.333 14.90 0.65 43.80 1.94
2161 2381 5.528043 TGCAAGAATTAGTTCTGCCAAAA 57.472 34.783 14.90 0.90 43.80 2.44
2162 2382 5.726980 ATGCAAGAATTAGTTCTGCCAAA 57.273 34.783 14.90 3.39 43.80 3.28
2163 2383 5.726980 AATGCAAGAATTAGTTCTGCCAA 57.273 34.783 14.90 3.88 43.80 4.52
2164 2384 5.945784 AGTAATGCAAGAATTAGTTCTGCCA 59.054 36.000 14.90 9.99 43.80 4.92
2165 2385 6.094048 TGAGTAATGCAAGAATTAGTTCTGCC 59.906 38.462 14.90 5.89 43.80 4.85
2166 2386 7.076842 TGAGTAATGCAAGAATTAGTTCTGC 57.923 36.000 0.66 8.04 43.80 4.26
2167 2387 9.897744 TTTTGAGTAATGCAAGAATTAGTTCTG 57.102 29.630 0.66 0.00 43.80 3.02
2186 2406 9.052759 ACGAGATTGTAACACTTAATTTTGAGT 57.947 29.630 0.00 0.00 0.00 3.41
2187 2407 9.530129 GACGAGATTGTAACACTTAATTTTGAG 57.470 33.333 0.00 0.00 0.00 3.02
2188 2408 8.500773 GGACGAGATTGTAACACTTAATTTTGA 58.499 33.333 0.00 0.00 0.00 2.69
2189 2409 8.286800 TGGACGAGATTGTAACACTTAATTTTG 58.713 33.333 0.00 0.00 0.00 2.44
2254 2536 0.166814 GTTGCATGACCGAACAGCTC 59.833 55.000 0.00 0.00 0.00 4.09
2291 2575 5.372373 GAGCAGAAATAGGGCTAGTCATTT 58.628 41.667 0.00 0.00 38.15 2.32
2316 2605 6.238103 CGATTCTTGCATTACTCGTATTGGTT 60.238 38.462 0.00 0.00 0.00 3.67
2319 2608 5.133264 GCGATTCTTGCATTACTCGTATTG 58.867 41.667 9.32 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.