Multiple sequence alignment - TraesCS2B01G629900

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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 TraesCS2B01G629900 chr2B 100.000 2351 0 0 1 2351 800989025 800986675 0.000000e+00 4342.0
1 TraesCS2B01G629900 chr2D 90.057 1227 71 13 1 1200 640978847 640977645 0.000000e+00 1543.0
2 TraesCS2B01G629900 chr2D 88.046 778 47 12 695 1446 640425394 640426151 0.000000e+00 880.0
3 TraesCS2B01G629900 chr5B 91.552 509 35 4 1841 2349 598997610 598998110 0.000000e+00 695.0
4 TraesCS2B01G629900 chr2A 83.526 777 68 21 765 1506 765867534 765868285 0.000000e+00 671.0
5 TraesCS2B01G629900 chr2A 83.946 517 71 9 1840 2351 143673263 143672754 3.510000e-133 484.0
6 TraesCS2B01G629900 chr2A 81.574 521 75 19 1841 2351 759588095 759587586 6.050000e-111 411.0
7 TraesCS2B01G629900 chr2A 97.143 35 1 0 1528 1562 22615050 22615084 2.520000e-05 60.2
8 TraesCS2B01G629900 chrUn 83.946 517 71 9 1840 2351 310890238 310889729 3.510000e-133 484.0
9 TraesCS2B01G629900 chrUn 83.946 517 71 9 1840 2351 358229339 358229848 3.510000e-133 484.0
10 TraesCS2B01G629900 chrUn 84.487 419 23 11 769 1161 478417758 478417356 2.210000e-100 375.0
11 TraesCS2B01G629900 chrUn 97.143 35 1 0 1528 1562 462337601 462337635 2.520000e-05 60.2
12 TraesCS2B01G629900 chr7A 83.721 516 69 13 1841 2351 690578716 690579221 7.600000e-130 473.0
13 TraesCS2B01G629900 chr7A 96.875 32 0 1 1533 1564 724631345 724631375 4.000000e-03 52.8
14 TraesCS2B01G629900 chr3B 83.430 519 71 11 1838 2351 378143122 378143630 3.540000e-128 468.0
15 TraesCS2B01G629900 chr3B 74.277 311 51 23 64 361 182390582 182390288 1.150000e-18 104.0
16 TraesCS2B01G629900 chr1A 82.558 516 77 11 1840 2350 257095946 257095439 2.140000e-120 442.0
17 TraesCS2B01G629900 chr1A 76.833 600 116 21 99 686 316952962 316952374 1.360000e-82 316.0
18 TraesCS2B01G629900 chr4B 81.625 517 74 16 1843 2351 323660732 323661235 2.170000e-110 409.0
19 TraesCS2B01G629900 chr4B 82.418 91 11 3 1509 1598 510849134 510849220 9.010000e-10 75.0
20 TraesCS2B01G629900 chr5D 79.287 589 104 17 90 672 299838680 299838104 1.690000e-106 396.0
21 TraesCS2B01G629900 chr5D 100.000 31 0 0 1536 1566 441395980 441396010 9.080000e-05 58.4
22 TraesCS2B01G629900 chr4D 78.752 593 108 17 95 681 315087265 315087845 4.740000e-102 381.0
23 TraesCS2B01G629900 chr4A 78.595 612 104 21 91 686 160247889 160247289 1.710000e-101 379.0
24 TraesCS2B01G629900 chr4A 76.701 588 117 17 91 670 616622191 616621616 2.270000e-80 309.0
25 TraesCS2B01G629900 chr4A 84.444 90 8 4 1506 1593 558226378 558226463 1.500000e-12 84.2
26 TraesCS2B01G629900 chr1B 78.037 601 109 22 98 686 366876796 366876207 7.990000e-95 357.0
27 TraesCS2B01G629900 chr3D 77.647 595 106 19 105 685 497898666 497898085 1.040000e-88 337.0
28 TraesCS2B01G629900 chr7B 76.059 614 118 24 81 682 633043518 633044114 2.290000e-75 292.0
29 TraesCS2B01G629900 chr7B 79.012 162 32 2 110 271 613988380 613988539 2.470000e-20 110.0
30 TraesCS2B01G629900 chr3A 76.316 228 41 11 61 284 696615945 696616163 2.470000e-20 110.0
31 TraesCS2B01G629900 chr6A 87.324 71 5 2 1528 1598 27188992 27188926 6.970000e-11 78.7
32 TraesCS2B01G629900 chr1D 90.566 53 4 1 1509 1560 109944729 109944781 4.190000e-08 69.4
33 TraesCS2B01G629900 chr1D 100.000 35 0 0 1528 1562 422057521 422057487 5.420000e-07 65.8


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 TraesCS2B01G629900 chr2B 800986675 800989025 2350 True 4342 4342 100.000 1 2351 1 chr2B.!!$R1 2350
1 TraesCS2B01G629900 chr2D 640977645 640978847 1202 True 1543 1543 90.057 1 1200 1 chr2D.!!$R1 1199
2 TraesCS2B01G629900 chr2D 640425394 640426151 757 False 880 880 88.046 695 1446 1 chr2D.!!$F1 751
3 TraesCS2B01G629900 chr5B 598997610 598998110 500 False 695 695 91.552 1841 2349 1 chr5B.!!$F1 508
4 TraesCS2B01G629900 chr2A 765867534 765868285 751 False 671 671 83.526 765 1506 1 chr2A.!!$F2 741
5 TraesCS2B01G629900 chr2A 143672754 143673263 509 True 484 484 83.946 1840 2351 1 chr2A.!!$R1 511
6 TraesCS2B01G629900 chr2A 759587586 759588095 509 True 411 411 81.574 1841 2351 1 chr2A.!!$R2 510
7 TraesCS2B01G629900 chrUn 310889729 310890238 509 True 484 484 83.946 1840 2351 1 chrUn.!!$R1 511
8 TraesCS2B01G629900 chrUn 358229339 358229848 509 False 484 484 83.946 1840 2351 1 chrUn.!!$F1 511
9 TraesCS2B01G629900 chr7A 690578716 690579221 505 False 473 473 83.721 1841 2351 1 chr7A.!!$F1 510
10 TraesCS2B01G629900 chr3B 378143122 378143630 508 False 468 468 83.430 1838 2351 1 chr3B.!!$F1 513
11 TraesCS2B01G629900 chr1A 257095439 257095946 507 True 442 442 82.558 1840 2350 1 chr1A.!!$R1 510
12 TraesCS2B01G629900 chr1A 316952374 316952962 588 True 316 316 76.833 99 686 1 chr1A.!!$R2 587
13 TraesCS2B01G629900 chr4B 323660732 323661235 503 False 409 409 81.625 1843 2351 1 chr4B.!!$F1 508
14 TraesCS2B01G629900 chr5D 299838104 299838680 576 True 396 396 79.287 90 672 1 chr5D.!!$R1 582
15 TraesCS2B01G629900 chr4D 315087265 315087845 580 False 381 381 78.752 95 681 1 chr4D.!!$F1 586
16 TraesCS2B01G629900 chr4A 160247289 160247889 600 True 379 379 78.595 91 686 1 chr4A.!!$R1 595
17 TraesCS2B01G629900 chr4A 616621616 616622191 575 True 309 309 76.701 91 670 1 chr4A.!!$R2 579
18 TraesCS2B01G629900 chr1B 366876207 366876796 589 True 357 357 78.037 98 686 1 chr1B.!!$R1 588
19 TraesCS2B01G629900 chr3D 497898085 497898666 581 True 337 337 77.647 105 685 1 chr3D.!!$R1 580
20 TraesCS2B01G629900 chr7B 633043518 633044114 596 False 292 292 76.059 81 682 1 chr7B.!!$F2 601

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
992 1039 0.179059 CCAGCATATACACGGTGGCA 60.179 55.0 13.48 0.0 43.26 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1857 0.031917 TCCAATGACTACGGCCCCTA 60.032 55.0 0.0 0.0 0.0 3.53 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
24 25 2.236766 TCTGCTAGCGTAAGATACCCC 58.763 52.381 10.77 0.00 43.02 4.95
75 76 1.078143 ATGGCTTTCCGCTGACTCC 60.078 57.895 0.00 0.00 39.13 3.85
79 80 0.603975 GCTTTCCGCTGACTCCTGTT 60.604 55.000 0.00 0.00 35.14 3.16
243 254 1.795286 GGACTGCAACGACTTTCTGAG 59.205 52.381 0.00 0.00 0.00 3.35
323 334 0.744281 GGGTGTGTGGAGGTTTGTTG 59.256 55.000 0.00 0.00 0.00 3.33
496 513 3.334691 CTTAGCATGACAACTTCCCGAA 58.665 45.455 0.00 0.00 0.00 4.30
507 524 4.771054 ACAACTTCCCGAATGTCTACTACT 59.229 41.667 0.00 0.00 0.00 2.57
567 588 1.267261 CACGTGTCTTCGGTTCTCTCT 59.733 52.381 7.58 0.00 34.94 3.10
574 595 3.940221 GTCTTCGGTTCTCTCTAGTGCTA 59.060 47.826 0.00 0.00 0.00 3.49
756 777 8.672815 GTTGAAACGTAGTATCTCTAGTAGGTT 58.327 37.037 0.00 0.00 45.00 3.50
832 870 2.002586 CGTCGATGCTCAAATGGAACT 58.997 47.619 0.00 0.00 0.00 3.01
875 922 5.583457 GCGTAAGTAGGTGGATGTGTTATTT 59.417 40.000 0.00 0.00 41.68 1.40
893 940 1.810959 TTTGGTTGGTTATCCGGTCG 58.189 50.000 0.00 0.00 36.30 4.79
923 970 0.663688 GCGCACTAGCTAGCTACTCA 59.336 55.000 20.67 2.24 39.10 3.41
940 987 7.679783 AGCTACTCAAACCATGCATATATACA 58.320 34.615 0.00 0.00 0.00 2.29
958 1005 2.397597 ACAACCTTGGGCAACAAAGAT 58.602 42.857 0.00 0.00 38.91 2.40
989 1036 1.487482 CGACCAGCATATACACGGTG 58.513 55.000 6.58 6.58 0.00 4.94
991 1038 2.616969 CCAGCATATACACGGTGGC 58.383 57.895 13.48 5.66 43.26 5.01
992 1039 0.179059 CCAGCATATACACGGTGGCA 60.179 55.000 13.48 0.00 43.26 4.92
993 1040 0.937304 CAGCATATACACGGTGGCAC 59.063 55.000 9.70 9.70 0.00 5.01
1205 1260 2.281484 GCTGAGTTGGGCGGACAA 60.281 61.111 0.00 0.00 0.00 3.18
1225 1280 4.338710 TCCTTGGGGGAAACGGCG 62.339 66.667 4.80 4.80 41.91 6.46
1228 1283 3.835790 CTTGGGGGAAACGGCGTCA 62.836 63.158 15.17 2.15 0.00 4.35
1339 1397 4.298332 GTGCAACTACAGGGAAAAATGTG 58.702 43.478 0.00 0.00 0.00 3.21
1391 1449 2.489329 GCCAGCCGAAATATATGCATGT 59.511 45.455 10.16 5.06 0.00 3.21
1410 1468 0.750249 TATCGGCGCCAGAAATCAGA 59.250 50.000 28.98 13.33 0.00 3.27
1495 1553 4.019681 TCCAAGATTACACACTACCCCTTG 60.020 45.833 0.00 0.00 0.00 3.61
1506 1564 0.470766 TACCCCTTGCGTTCACTGTT 59.529 50.000 0.00 0.00 0.00 3.16
1507 1565 0.818040 ACCCCTTGCGTTCACTGTTC 60.818 55.000 0.00 0.00 0.00 3.18
1508 1566 0.535102 CCCCTTGCGTTCACTGTTCT 60.535 55.000 0.00 0.00 0.00 3.01
1509 1567 1.308998 CCCTTGCGTTCACTGTTCTT 58.691 50.000 0.00 0.00 0.00 2.52
1510 1568 1.676006 CCCTTGCGTTCACTGTTCTTT 59.324 47.619 0.00 0.00 0.00 2.52
1511 1569 2.099098 CCCTTGCGTTCACTGTTCTTTT 59.901 45.455 0.00 0.00 0.00 2.27
1512 1570 3.428862 CCCTTGCGTTCACTGTTCTTTTT 60.429 43.478 0.00 0.00 0.00 1.94
1533 1591 7.887996 TTTTTAATTGGACGTACGTAGACAT 57.112 32.000 22.87 10.55 0.00 3.06
1534 1592 6.874297 TTTAATTGGACGTACGTAGACATG 57.126 37.500 22.87 0.00 0.00 3.21
1535 1593 4.445452 AATTGGACGTACGTAGACATGT 57.555 40.909 22.87 0.00 0.00 3.21
1536 1594 3.921119 TTGGACGTACGTAGACATGTT 57.079 42.857 22.87 0.00 0.00 2.71
1537 1595 3.921119 TGGACGTACGTAGACATGTTT 57.079 42.857 22.87 0.00 0.00 2.83
1538 1596 4.241590 TGGACGTACGTAGACATGTTTT 57.758 40.909 22.87 0.00 0.00 2.43
1539 1597 5.369685 TGGACGTACGTAGACATGTTTTA 57.630 39.130 22.87 0.00 0.00 1.52
1540 1598 5.153513 TGGACGTACGTAGACATGTTTTAC 58.846 41.667 22.87 3.53 0.00 2.01
1541 1599 5.048782 TGGACGTACGTAGACATGTTTTACT 60.049 40.000 22.87 0.00 0.00 2.24
1542 1600 5.284660 GGACGTACGTAGACATGTTTTACTG 59.715 44.000 22.87 5.94 0.00 2.74
1543 1601 5.762045 ACGTACGTAGACATGTTTTACTGT 58.238 37.500 21.41 10.69 0.00 3.55
1544 1602 5.626543 ACGTACGTAGACATGTTTTACTGTG 59.373 40.000 21.41 0.00 0.00 3.66
1545 1603 5.626543 CGTACGTAGACATGTTTTACTGTGT 59.373 40.000 7.22 3.38 0.00 3.72
1546 1604 6.142798 CGTACGTAGACATGTTTTACTGTGTT 59.857 38.462 7.22 0.00 0.00 3.32
1547 1605 6.913873 ACGTAGACATGTTTTACTGTGTTT 57.086 33.333 0.00 0.00 0.00 2.83
1548 1606 6.711579 ACGTAGACATGTTTTACTGTGTTTG 58.288 36.000 0.00 0.00 0.00 2.93
1549 1607 6.314400 ACGTAGACATGTTTTACTGTGTTTGT 59.686 34.615 0.00 0.00 0.00 2.83
1550 1608 7.148373 ACGTAGACATGTTTTACTGTGTTTGTT 60.148 33.333 0.00 0.00 0.00 2.83
1551 1609 7.372396 CGTAGACATGTTTTACTGTGTTTGTTC 59.628 37.037 0.00 0.00 0.00 3.18
1552 1610 7.151999 AGACATGTTTTACTGTGTTTGTTCA 57.848 32.000 0.00 0.00 0.00 3.18
1553 1611 7.027161 AGACATGTTTTACTGTGTTTGTTCAC 58.973 34.615 0.00 0.00 38.63 3.18
1554 1612 6.919721 ACATGTTTTACTGTGTTTGTTCACT 58.080 32.000 0.00 0.00 38.90 3.41
1555 1613 7.027161 ACATGTTTTACTGTGTTTGTTCACTC 58.973 34.615 0.00 0.00 38.90 3.51
1556 1614 6.561737 TGTTTTACTGTGTTTGTTCACTCA 57.438 33.333 0.00 0.00 38.90 3.41
1557 1615 7.151999 TGTTTTACTGTGTTTGTTCACTCAT 57.848 32.000 0.00 0.00 38.90 2.90
1558 1616 7.598278 TGTTTTACTGTGTTTGTTCACTCATT 58.402 30.769 0.00 0.00 38.90 2.57
1559 1617 8.085296 TGTTTTACTGTGTTTGTTCACTCATTT 58.915 29.630 0.00 0.00 38.90 2.32
1560 1618 8.921670 GTTTTACTGTGTTTGTTCACTCATTTT 58.078 29.630 0.00 0.00 38.90 1.82
1564 1622 8.856490 ACTGTGTTTGTTCACTCATTTTAATC 57.144 30.769 0.00 0.00 38.90 1.75
1565 1623 7.920682 ACTGTGTTTGTTCACTCATTTTAATCC 59.079 33.333 0.00 0.00 38.90 3.01
1566 1624 8.006298 TGTGTTTGTTCACTCATTTTAATCCT 57.994 30.769 0.00 0.00 38.90 3.24
1567 1625 8.474025 TGTGTTTGTTCACTCATTTTAATCCTT 58.526 29.630 0.00 0.00 38.90 3.36
1568 1626 9.313118 GTGTTTGTTCACTCATTTTAATCCTTT 57.687 29.630 0.00 0.00 35.68 3.11
1612 1670 8.876275 AAATATCCAAATTGTATCACACATGC 57.124 30.769 0.00 0.00 36.90 4.06
1613 1671 5.918426 ATCCAAATTGTATCACACATGCA 57.082 34.783 0.00 0.00 36.90 3.96
1614 1672 5.718724 TCCAAATTGTATCACACATGCAA 57.281 34.783 0.00 0.00 36.90 4.08
1615 1673 6.094193 TCCAAATTGTATCACACATGCAAA 57.906 33.333 0.00 0.00 36.90 3.68
1616 1674 6.519382 TCCAAATTGTATCACACATGCAAAA 58.481 32.000 0.00 0.00 36.90 2.44
1617 1675 6.988580 TCCAAATTGTATCACACATGCAAAAA 59.011 30.769 0.00 0.00 36.90 1.94
1641 1699 2.901042 GGAGTACCCGCCTCCTTG 59.099 66.667 0.00 0.00 44.29 3.61
1642 1700 2.187163 GAGTACCCGCCTCCTTGC 59.813 66.667 0.00 0.00 0.00 4.01
1650 1708 3.191539 GCCTCCTTGCGCTTCTCG 61.192 66.667 9.73 0.00 42.12 4.04
1665 1723 4.779966 TCGCGGGCGAGAGAGTCT 62.780 66.667 12.26 0.00 44.01 3.24
1666 1724 4.244802 CGCGGGCGAGAGAGTCTC 62.245 72.222 12.54 12.54 42.83 3.36
1667 1725 2.826738 GCGGGCGAGAGAGTCTCT 60.827 66.667 22.85 22.85 44.28 3.10
1668 1726 2.411504 GCGGGCGAGAGAGTCTCTT 61.412 63.158 23.44 7.89 41.35 2.85
1669 1727 1.431440 CGGGCGAGAGAGTCTCTTG 59.569 63.158 27.20 27.20 41.35 3.02
1673 1731 2.572733 CGAGAGAGTCTCTTGCCCA 58.427 57.895 23.44 0.00 41.35 5.36
1674 1732 1.110442 CGAGAGAGTCTCTTGCCCAT 58.890 55.000 23.44 0.00 41.35 4.00
1675 1733 1.066908 CGAGAGAGTCTCTTGCCCATC 59.933 57.143 23.44 8.48 41.35 3.51
1676 1734 1.412343 GAGAGAGTCTCTTGCCCATCC 59.588 57.143 23.44 4.89 41.35 3.51
1677 1735 1.198713 GAGAGTCTCTTGCCCATCCA 58.801 55.000 13.17 0.00 0.00 3.41
1678 1736 1.767681 GAGAGTCTCTTGCCCATCCAT 59.232 52.381 13.17 0.00 0.00 3.41
1679 1737 2.172293 GAGAGTCTCTTGCCCATCCATT 59.828 50.000 13.17 0.00 0.00 3.16
1680 1738 2.092538 AGAGTCTCTTGCCCATCCATTG 60.093 50.000 0.00 0.00 0.00 2.82
1681 1739 1.637553 AGTCTCTTGCCCATCCATTGT 59.362 47.619 0.00 0.00 0.00 2.71
1682 1740 2.019984 GTCTCTTGCCCATCCATTGTC 58.980 52.381 0.00 0.00 0.00 3.18
1683 1741 1.064463 TCTCTTGCCCATCCATTGTCC 60.064 52.381 0.00 0.00 0.00 4.02
1684 1742 0.394216 TCTTGCCCATCCATTGTCCG 60.394 55.000 0.00 0.00 0.00 4.79
1685 1743 1.379710 TTGCCCATCCATTGTCCGG 60.380 57.895 0.00 0.00 0.00 5.14
1686 1744 2.148723 TTGCCCATCCATTGTCCGGT 62.149 55.000 0.00 0.00 0.00 5.28
1687 1745 2.120909 GCCCATCCATTGTCCGGTG 61.121 63.158 0.00 0.00 0.00 4.94
1688 1746 1.453745 CCCATCCATTGTCCGGTGG 60.454 63.158 0.00 0.89 36.82 4.61
1689 1747 2.120909 CCATCCATTGTCCGGTGGC 61.121 63.158 0.00 0.00 35.43 5.01
1690 1748 1.077501 CATCCATTGTCCGGTGGCT 60.078 57.895 0.00 0.00 35.43 4.75
1691 1749 0.680921 CATCCATTGTCCGGTGGCTT 60.681 55.000 0.00 0.00 35.43 4.35
1692 1750 0.394352 ATCCATTGTCCGGTGGCTTC 60.394 55.000 0.00 0.00 35.43 3.86
1693 1751 1.002134 CCATTGTCCGGTGGCTTCT 60.002 57.895 0.00 0.00 0.00 2.85
1694 1752 1.308069 CCATTGTCCGGTGGCTTCTG 61.308 60.000 0.00 0.00 0.00 3.02
1695 1753 0.606401 CATTGTCCGGTGGCTTCTGT 60.606 55.000 0.00 0.00 0.00 3.41
1696 1754 0.321653 ATTGTCCGGTGGCTTCTGTC 60.322 55.000 0.00 0.00 0.00 3.51
1697 1755 2.432628 GTCCGGTGGCTTCTGTCG 60.433 66.667 0.00 0.00 0.00 4.35
1698 1756 3.691342 TCCGGTGGCTTCTGTCGG 61.691 66.667 0.00 0.00 41.80 4.79
1699 1757 4.760047 CCGGTGGCTTCTGTCGGG 62.760 72.222 0.00 0.00 37.35 5.14
1700 1758 3.691342 CGGTGGCTTCTGTCGGGA 61.691 66.667 0.00 0.00 0.00 5.14
1701 1759 2.266055 GGTGGCTTCTGTCGGGAG 59.734 66.667 0.00 0.00 0.00 4.30
1702 1760 2.435059 GTGGCTTCTGTCGGGAGC 60.435 66.667 2.94 2.94 0.00 4.70
1703 1761 3.706373 TGGCTTCTGTCGGGAGCC 61.706 66.667 22.84 22.84 45.19 4.70
1704 1762 3.394836 GGCTTCTGTCGGGAGCCT 61.395 66.667 22.41 0.00 41.99 4.58
1705 1763 2.185608 GCTTCTGTCGGGAGCCTC 59.814 66.667 0.00 0.00 0.00 4.70
1706 1764 2.355193 GCTTCTGTCGGGAGCCTCT 61.355 63.158 0.00 0.00 0.00 3.69
1707 1765 1.813192 CTTCTGTCGGGAGCCTCTC 59.187 63.158 0.00 0.00 0.00 3.20
1708 1766 0.682855 CTTCTGTCGGGAGCCTCTCT 60.683 60.000 0.00 0.00 0.00 3.10
1709 1767 0.681564 TTCTGTCGGGAGCCTCTCTC 60.682 60.000 0.00 0.00 41.15 3.20
1720 1778 3.898509 CTCTCTCGGCCGCTCCTG 61.899 72.222 23.51 8.69 0.00 3.86
1723 1781 4.841617 TCTCGGCCGCTCCTGGAT 62.842 66.667 23.51 0.00 0.00 3.41
1724 1782 4.598894 CTCGGCCGCTCCTGGATG 62.599 72.222 23.51 0.00 0.00 3.51
1726 1784 4.899239 CGGCCGCTCCTGGATGTC 62.899 72.222 14.67 0.00 0.00 3.06
1727 1785 3.474570 GGCCGCTCCTGGATGTCT 61.475 66.667 0.00 0.00 0.00 3.41
1728 1786 2.586792 GCCGCTCCTGGATGTCTT 59.413 61.111 0.00 0.00 0.00 3.01
1729 1787 1.686325 GGCCGCTCCTGGATGTCTTA 61.686 60.000 0.00 0.00 0.00 2.10
1730 1788 0.394565 GCCGCTCCTGGATGTCTTAT 59.605 55.000 0.00 0.00 0.00 1.73
1731 1789 1.606737 GCCGCTCCTGGATGTCTTATC 60.607 57.143 0.00 0.00 0.00 1.75
1732 1790 1.967066 CCGCTCCTGGATGTCTTATCT 59.033 52.381 0.00 0.00 0.00 1.98
1733 1791 2.288702 CCGCTCCTGGATGTCTTATCTG 60.289 54.545 0.00 0.00 0.00 2.90
1734 1792 2.765122 GCTCCTGGATGTCTTATCTGC 58.235 52.381 0.00 0.00 0.00 4.26
1735 1793 2.549778 GCTCCTGGATGTCTTATCTGCC 60.550 54.545 0.00 0.00 0.00 4.85
1736 1794 2.038295 CTCCTGGATGTCTTATCTGCCC 59.962 54.545 0.00 0.00 0.00 5.36
1737 1795 1.770658 CCTGGATGTCTTATCTGCCCA 59.229 52.381 0.00 0.00 0.00 5.36
1738 1796 2.224475 CCTGGATGTCTTATCTGCCCAG 60.224 54.545 0.00 0.00 39.38 4.45
1739 1797 2.702478 CTGGATGTCTTATCTGCCCAGA 59.298 50.000 0.00 0.00 41.49 3.86
1740 1798 2.435805 TGGATGTCTTATCTGCCCAGAC 59.564 50.000 0.00 0.00 40.75 3.51
1743 1801 1.208052 TGTCTTATCTGCCCAGACAGC 59.792 52.381 0.00 0.00 41.60 4.40
1744 1802 1.484240 GTCTTATCTGCCCAGACAGCT 59.516 52.381 0.00 0.00 40.75 4.24
1745 1803 1.759445 TCTTATCTGCCCAGACAGCTC 59.241 52.381 0.00 0.00 40.75 4.09
1746 1804 1.483827 CTTATCTGCCCAGACAGCTCA 59.516 52.381 0.00 0.00 40.75 4.26
1747 1805 1.117994 TATCTGCCCAGACAGCTCAG 58.882 55.000 0.00 0.00 40.75 3.35
1748 1806 0.616964 ATCTGCCCAGACAGCTCAGA 60.617 55.000 0.00 1.94 40.75 3.27
1749 1807 1.079266 CTGCCCAGACAGCTCAGAC 60.079 63.158 0.00 0.00 0.00 3.51
1750 1808 2.267324 GCCCAGACAGCTCAGACC 59.733 66.667 0.00 0.00 0.00 3.85
1751 1809 2.985456 CCCAGACAGCTCAGACCC 59.015 66.667 0.00 0.00 0.00 4.46
1752 1810 2.575993 CCAGACAGCTCAGACCCG 59.424 66.667 0.00 0.00 0.00 5.28
1753 1811 2.575993 CAGACAGCTCAGACCCGG 59.424 66.667 0.00 0.00 0.00 5.73
1754 1812 2.681778 AGACAGCTCAGACCCGGG 60.682 66.667 22.25 22.25 0.00 5.73
1755 1813 4.459089 GACAGCTCAGACCCGGGC 62.459 72.222 24.08 14.21 0.00 6.13
1757 1815 4.020617 CAGCTCAGACCCGGGCAA 62.021 66.667 24.08 1.86 0.00 4.52
1758 1816 4.021925 AGCTCAGACCCGGGCAAC 62.022 66.667 24.08 12.96 0.00 4.17
1782 1840 3.180449 TGGAGGGTCCATGACAAGT 57.820 52.632 0.00 0.00 42.67 3.16
1783 1841 1.444933 TGGAGGGTCCATGACAAGTT 58.555 50.000 0.00 0.00 42.67 2.66
1784 1842 1.073763 TGGAGGGTCCATGACAAGTTG 59.926 52.381 0.00 0.00 42.67 3.16
1785 1843 1.351017 GGAGGGTCCATGACAAGTTGA 59.649 52.381 10.54 0.00 36.28 3.18
1786 1844 2.427506 GAGGGTCCATGACAAGTTGAC 58.572 52.381 10.54 3.81 33.68 3.18
1787 1845 1.073923 AGGGTCCATGACAAGTTGACC 59.926 52.381 10.54 5.23 43.78 4.02
1788 1846 1.202879 GGGTCCATGACAAGTTGACCA 60.203 52.381 10.54 7.48 45.81 4.02
1789 1847 1.880027 GGTCCATGACAAGTTGACCAC 59.120 52.381 10.54 0.00 43.92 4.16
1790 1848 1.880027 GTCCATGACAAGTTGACCACC 59.120 52.381 10.54 0.00 32.09 4.61
1791 1849 0.874390 CCATGACAAGTTGACCACCG 59.126 55.000 10.54 2.81 0.00 4.94
1792 1850 0.874390 CATGACAAGTTGACCACCGG 59.126 55.000 10.54 0.00 0.00 5.28
1793 1851 0.250727 ATGACAAGTTGACCACCGGG 60.251 55.000 10.54 0.00 41.29 5.73
1803 1861 2.045340 CCACCGGGTTTGCTAGGG 60.045 66.667 6.32 0.00 0.00 3.53
1804 1862 2.045340 CACCGGGTTTGCTAGGGG 60.045 66.667 6.32 0.00 0.00 4.79
1805 1863 4.043100 ACCGGGTTTGCTAGGGGC 62.043 66.667 6.32 0.00 42.22 5.80
1806 1864 4.815108 CCGGGTTTGCTAGGGGCC 62.815 72.222 0.00 0.00 40.92 5.80
1808 1866 4.043100 GGGTTTGCTAGGGGCCGT 62.043 66.667 3.37 3.37 40.92 5.68
1809 1867 2.672181 GGGTTTGCTAGGGGCCGTA 61.672 63.158 5.73 5.73 40.92 4.02
1810 1868 1.153229 GGTTTGCTAGGGGCCGTAG 60.153 63.158 25.30 25.30 40.92 3.51
1811 1869 1.600638 GTTTGCTAGGGGCCGTAGT 59.399 57.895 28.49 3.56 40.92 2.73
1812 1870 0.461516 GTTTGCTAGGGGCCGTAGTC 60.462 60.000 28.49 21.76 40.92 2.59
1813 1871 0.905809 TTTGCTAGGGGCCGTAGTCA 60.906 55.000 28.49 23.59 40.92 3.41
1814 1872 0.689745 TTGCTAGGGGCCGTAGTCAT 60.690 55.000 28.49 0.00 40.92 3.06
1815 1873 0.689745 TGCTAGGGGCCGTAGTCATT 60.690 55.000 28.49 0.00 40.92 2.57
1816 1874 0.249911 GCTAGGGGCCGTAGTCATTG 60.250 60.000 28.49 8.93 34.27 2.82
1817 1875 0.393077 CTAGGGGCCGTAGTCATTGG 59.607 60.000 22.22 0.00 0.00 3.16
1818 1876 0.031917 TAGGGGCCGTAGTCATTGGA 60.032 55.000 0.89 0.00 0.00 3.53
1819 1877 1.153229 GGGGCCGTAGTCATTGGAC 60.153 63.158 0.00 0.00 44.66 4.02
1827 1885 3.186047 GTCATTGGACGGCGTCGG 61.186 66.667 31.02 20.48 41.39 4.79
1828 1886 4.444838 TCATTGGACGGCGTCGGG 62.445 66.667 31.02 20.15 41.39 5.14
1869 1927 0.179084 CGTACCACCAAGGCGATCAT 60.179 55.000 0.00 0.00 43.14 2.45
1925 1983 2.045926 GGATCGTGCAGCCCAACT 60.046 61.111 0.00 0.00 0.00 3.16
2044 2106 2.507324 GACAGACGGCGGCTTCTC 60.507 66.667 15.41 7.05 0.00 2.87
2061 2129 0.340208 CTCTCCCTTCCCCACCTACT 59.660 60.000 0.00 0.00 0.00 2.57
2071 2139 1.670059 CCCACCTACTTCCCTTCCTT 58.330 55.000 0.00 0.00 0.00 3.36
2189 2262 2.289532 GCCCAGCACCACTCTCTCT 61.290 63.158 0.00 0.00 0.00 3.10
2190 2263 1.896694 CCCAGCACCACTCTCTCTC 59.103 63.158 0.00 0.00 0.00 3.20
2191 2264 0.614415 CCCAGCACCACTCTCTCTCT 60.614 60.000 0.00 0.00 0.00 3.10
2192 2265 0.817013 CCAGCACCACTCTCTCTCTC 59.183 60.000 0.00 0.00 0.00 3.20
2217 2292 4.323477 CGGCGACCTGGAAACCCA 62.323 66.667 0.00 0.00 0.00 4.51
2260 2335 3.083600 CTTCGTCGCCGCCATTGAC 62.084 63.158 0.00 0.00 0.00 3.18
2264 2339 4.108299 TCGCCGCCATTGACCCAT 62.108 61.111 0.00 0.00 0.00 4.00
2340 2415 0.392729 GTCCTCAAGCAGCTGCAGAT 60.393 55.000 38.24 22.12 45.16 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.351544 GCGAAGGGGTATCTTACGCTAG 60.352 54.545 0.00 0.00 40.97 3.42
14 15 2.769602 AGGAGCGAAGGGGTATCTTA 57.230 50.000 0.00 0.00 0.00 2.10
24 25 3.248171 GCGTGCGTAGGAGCGAAG 61.248 66.667 0.00 0.00 40.67 3.79
61 62 1.151668 CAACAGGAGTCAGCGGAAAG 58.848 55.000 0.00 0.00 0.00 2.62
150 151 1.614241 ATACGAAAGCCTCCTGCCGT 61.614 55.000 0.00 0.00 42.71 5.68
243 254 2.975489 TGGAGAGAGCCTTATTCCATCC 59.025 50.000 0.00 0.00 33.21 3.51
496 513 6.239232 CCGGCAAACCTTATAGTAGTAGACAT 60.239 42.308 0.00 0.00 0.00 3.06
507 524 0.179067 CGGAGCCGGCAAACCTTATA 60.179 55.000 31.54 0.00 35.56 0.98
567 588 4.202336 ACCTAGCGATGACTACTAGCACTA 60.202 45.833 0.00 0.00 33.53 2.74
574 595 2.092321 AGACCACCTAGCGATGACTACT 60.092 50.000 0.00 0.00 0.00 2.57
689 710 6.169800 GCTACCAGATCTTTCTCTTCTGTTT 58.830 40.000 0.00 0.00 36.06 2.83
690 711 5.247110 TGCTACCAGATCTTTCTCTTCTGTT 59.753 40.000 0.00 0.00 36.06 3.16
691 712 4.774726 TGCTACCAGATCTTTCTCTTCTGT 59.225 41.667 0.00 0.00 36.06 3.41
692 713 5.336150 TGCTACCAGATCTTTCTCTTCTG 57.664 43.478 0.00 0.00 37.27 3.02
693 714 5.483583 ACTTGCTACCAGATCTTTCTCTTCT 59.516 40.000 0.00 0.00 0.00 2.85
756 777 7.359681 GCCGTTCAAGAAAAGAAAAGAAAAACA 60.360 33.333 0.00 0.00 0.00 2.83
832 870 1.285280 CATTGTGGGAGTCCCTACCA 58.715 55.000 28.73 18.79 43.15 3.25
864 908 6.750039 CGGATAACCAACCAAAATAACACATC 59.250 38.462 0.00 0.00 35.59 3.06
875 922 0.975135 TCGACCGGATAACCAACCAA 59.025 50.000 9.46 0.00 35.59 3.67
893 940 2.611292 AGCTAGTGCGCTCAATGATTTC 59.389 45.455 9.73 0.00 45.42 2.17
916 963 7.905604 TGTATATATGCATGGTTTGAGTAGC 57.094 36.000 10.16 0.00 0.00 3.58
917 964 8.721478 GGTTGTATATATGCATGGTTTGAGTAG 58.279 37.037 10.16 0.00 0.00 2.57
918 965 8.436778 AGGTTGTATATATGCATGGTTTGAGTA 58.563 33.333 10.16 0.00 0.00 2.59
919 966 7.290061 AGGTTGTATATATGCATGGTTTGAGT 58.710 34.615 10.16 0.00 0.00 3.41
923 970 6.267471 CCCAAGGTTGTATATATGCATGGTTT 59.733 38.462 10.16 0.00 0.00 3.27
940 987 2.485302 GCAATCTTTGTTGCCCAAGGTT 60.485 45.455 0.33 0.00 46.69 3.50
989 1036 2.429571 CGTGCATTGTGCTGTGCC 60.430 61.111 3.41 0.00 45.31 5.01
990 1037 2.429571 CCGTGCATTGTGCTGTGC 60.430 61.111 3.41 0.00 45.31 4.57
991 1038 1.794151 TTCCCGTGCATTGTGCTGTG 61.794 55.000 3.41 0.00 45.31 3.66
992 1039 1.106351 TTTCCCGTGCATTGTGCTGT 61.106 50.000 3.41 0.00 45.31 4.40
993 1040 0.664166 GTTTCCCGTGCATTGTGCTG 60.664 55.000 3.41 0.00 45.31 4.41
1072 1127 3.188786 CTTGCCGCTGTACGCTCC 61.189 66.667 7.82 0.79 41.76 4.70
1073 1128 3.188786 CCTTGCCGCTGTACGCTC 61.189 66.667 7.82 1.71 41.76 5.03
1074 1129 4.760047 CCCTTGCCGCTGTACGCT 62.760 66.667 7.82 0.00 41.76 5.07
1225 1280 0.601558 TCCAAGGTGTCGTAGCTGAC 59.398 55.000 0.00 0.00 37.17 3.51
1228 1283 1.874345 CGGTCCAAGGTGTCGTAGCT 61.874 60.000 0.00 0.00 39.21 3.32
1301 1356 3.712907 ACGGGCGGGTGTATGCTT 61.713 61.111 0.00 0.00 0.00 3.91
1379 1437 2.872245 GGCGCCGATACATGCATATATT 59.128 45.455 12.58 0.00 0.00 1.28
1391 1449 0.750249 TCTGATTTCTGGCGCCGATA 59.250 50.000 23.90 16.78 0.00 2.92
1410 1468 3.344904 GCATGTTGCGCTTATTGAGAT 57.655 42.857 9.73 0.00 31.71 2.75
1453 1511 3.064682 TGGATTGCATTCCAACGATTACG 59.935 43.478 24.51 0.00 42.82 3.18
1462 1520 5.015515 TGTGTAATCTTGGATTGCATTCCA 58.984 37.500 23.27 23.27 44.08 3.53
1472 1530 3.798515 AGGGGTAGTGTGTAATCTTGGA 58.201 45.455 0.00 0.00 0.00 3.53
1473 1531 4.261801 CAAGGGGTAGTGTGTAATCTTGG 58.738 47.826 0.00 0.00 0.00 3.61
1483 1541 0.250166 GTGAACGCAAGGGGTAGTGT 60.250 55.000 0.00 0.00 46.39 3.55
1509 1567 7.384660 ACATGTCTACGTACGTCCAATTAAAAA 59.615 33.333 26.53 1.70 0.00 1.94
1510 1568 6.867816 ACATGTCTACGTACGTCCAATTAAAA 59.132 34.615 26.53 2.52 0.00 1.52
1511 1569 6.389091 ACATGTCTACGTACGTCCAATTAAA 58.611 36.000 26.53 3.34 0.00 1.52
1512 1570 5.953183 ACATGTCTACGTACGTCCAATTAA 58.047 37.500 26.53 4.18 0.00 1.40
1513 1571 5.565592 ACATGTCTACGTACGTCCAATTA 57.434 39.130 26.53 5.01 0.00 1.40
1514 1572 4.445452 ACATGTCTACGTACGTCCAATT 57.555 40.909 26.53 5.71 0.00 2.32
1515 1573 4.445452 AACATGTCTACGTACGTCCAAT 57.555 40.909 26.53 11.72 0.00 3.16
1516 1574 3.921119 AACATGTCTACGTACGTCCAA 57.079 42.857 26.53 6.69 0.00 3.53
1517 1575 3.921119 AAACATGTCTACGTACGTCCA 57.079 42.857 26.53 19.55 0.00 4.02
1518 1576 5.284660 CAGTAAAACATGTCTACGTACGTCC 59.715 44.000 26.53 14.41 0.00 4.79
1519 1577 5.853282 ACAGTAAAACATGTCTACGTACGTC 59.147 40.000 26.53 11.59 0.00 4.34
1520 1578 5.626543 CACAGTAAAACATGTCTACGTACGT 59.373 40.000 25.98 25.98 0.00 3.57
1521 1579 5.626543 ACACAGTAAAACATGTCTACGTACG 59.373 40.000 15.01 15.01 0.00 3.67
1522 1580 6.998258 ACACAGTAAAACATGTCTACGTAC 57.002 37.500 0.00 0.00 0.00 3.67
1523 1581 7.492020 ACAAACACAGTAAAACATGTCTACGTA 59.508 33.333 0.00 0.00 0.00 3.57
1524 1582 6.314400 ACAAACACAGTAAAACATGTCTACGT 59.686 34.615 0.00 0.00 0.00 3.57
1525 1583 6.711579 ACAAACACAGTAAAACATGTCTACG 58.288 36.000 0.00 4.08 0.00 3.51
1526 1584 8.178964 TGAACAAACACAGTAAAACATGTCTAC 58.821 33.333 0.00 4.36 0.00 2.59
1527 1585 8.178964 GTGAACAAACACAGTAAAACATGTCTA 58.821 33.333 0.00 0.00 40.11 2.59
1528 1586 7.027161 GTGAACAAACACAGTAAAACATGTCT 58.973 34.615 0.00 0.00 40.11 3.41
1529 1587 7.027161 AGTGAACAAACACAGTAAAACATGTC 58.973 34.615 0.00 0.00 42.45 3.06
1530 1588 6.919721 AGTGAACAAACACAGTAAAACATGT 58.080 32.000 0.00 0.00 42.45 3.21
1531 1589 7.026562 TGAGTGAACAAACACAGTAAAACATG 58.973 34.615 0.00 0.00 42.45 3.21
1532 1590 7.151999 TGAGTGAACAAACACAGTAAAACAT 57.848 32.000 0.00 0.00 42.45 2.71
1533 1591 6.561737 TGAGTGAACAAACACAGTAAAACA 57.438 33.333 0.00 0.00 42.45 2.83
1534 1592 8.460831 AAATGAGTGAACAAACACAGTAAAAC 57.539 30.769 0.00 0.00 42.45 2.43
1538 1596 9.944663 GATTAAAATGAGTGAACAAACACAGTA 57.055 29.630 0.00 0.00 42.45 2.74
1539 1597 7.920682 GGATTAAAATGAGTGAACAAACACAGT 59.079 33.333 0.00 0.00 42.45 3.55
1540 1598 8.137437 AGGATTAAAATGAGTGAACAAACACAG 58.863 33.333 0.00 0.00 42.45 3.66
1541 1599 8.006298 AGGATTAAAATGAGTGAACAAACACA 57.994 30.769 0.00 0.00 42.45 3.72
1542 1600 8.871686 AAGGATTAAAATGAGTGAACAAACAC 57.128 30.769 0.00 0.00 40.60 3.32
1586 1644 9.316730 GCATGTGTGATACAATTTGGATATTTT 57.683 29.630 0.78 0.00 43.77 1.82
1587 1645 8.476447 TGCATGTGTGATACAATTTGGATATTT 58.524 29.630 0.78 0.00 43.77 1.40
1588 1646 8.009622 TGCATGTGTGATACAATTTGGATATT 57.990 30.769 0.78 0.00 43.77 1.28
1589 1647 7.585579 TGCATGTGTGATACAATTTGGATAT 57.414 32.000 0.78 0.00 43.77 1.63
1590 1648 7.401955 TTGCATGTGTGATACAATTTGGATA 57.598 32.000 0.78 0.00 43.77 2.59
1591 1649 5.918426 TGCATGTGTGATACAATTTGGAT 57.082 34.783 0.00 0.00 43.77 3.41
1592 1650 5.718724 TTGCATGTGTGATACAATTTGGA 57.281 34.783 0.78 0.00 43.77 3.53
1593 1651 6.782298 TTTTGCATGTGTGATACAATTTGG 57.218 33.333 0.78 0.00 43.77 3.28
1625 1683 2.187163 GCAAGGAGGCGGGTACTC 59.813 66.667 0.00 0.00 0.00 2.59
1633 1691 3.191539 CGAGAAGCGCAAGGAGGC 61.192 66.667 11.47 0.00 38.28 4.70
1648 1706 4.779966 AGACTCTCTCGCCCGCGA 62.780 66.667 8.23 11.79 46.87 5.87
1649 1707 4.244802 GAGACTCTCTCGCCCGCG 62.245 72.222 0.00 0.00 33.35 6.46
1656 1714 1.412343 GGATGGGCAAGAGACTCTCTC 59.588 57.143 9.10 0.47 40.28 3.20
1657 1715 1.273495 TGGATGGGCAAGAGACTCTCT 60.273 52.381 5.20 2.39 43.37 3.10
1658 1716 1.198713 TGGATGGGCAAGAGACTCTC 58.801 55.000 5.20 0.00 0.00 3.20
1659 1717 1.890552 ATGGATGGGCAAGAGACTCT 58.109 50.000 0.00 0.00 0.00 3.24
1660 1718 2.295885 CAATGGATGGGCAAGAGACTC 58.704 52.381 0.00 0.00 0.00 3.36
1661 1719 1.637553 ACAATGGATGGGCAAGAGACT 59.362 47.619 0.00 0.00 0.00 3.24
1662 1720 2.019984 GACAATGGATGGGCAAGAGAC 58.980 52.381 0.00 0.00 0.00 3.36
1663 1721 1.064463 GGACAATGGATGGGCAAGAGA 60.064 52.381 0.00 0.00 0.00 3.10
1664 1722 1.396653 GGACAATGGATGGGCAAGAG 58.603 55.000 0.00 0.00 0.00 2.85
1665 1723 0.394216 CGGACAATGGATGGGCAAGA 60.394 55.000 0.00 0.00 0.00 3.02
1666 1724 1.386525 CCGGACAATGGATGGGCAAG 61.387 60.000 0.00 0.00 0.00 4.01
1667 1725 1.379710 CCGGACAATGGATGGGCAA 60.380 57.895 0.00 0.00 0.00 4.52
1668 1726 2.275089 CCGGACAATGGATGGGCA 59.725 61.111 0.00 0.00 0.00 5.36
1669 1727 2.120909 CACCGGACAATGGATGGGC 61.121 63.158 9.46 0.00 0.00 5.36
1670 1728 1.453745 CCACCGGACAATGGATGGG 60.454 63.158 9.46 0.00 38.34 4.00
1671 1729 2.120909 GCCACCGGACAATGGATGG 61.121 63.158 9.46 3.20 38.34 3.51
1672 1730 0.680921 AAGCCACCGGACAATGGATG 60.681 55.000 9.46 0.00 38.34 3.51
1673 1731 0.394352 GAAGCCACCGGACAATGGAT 60.394 55.000 9.46 0.00 38.34 3.41
1674 1732 1.002624 GAAGCCACCGGACAATGGA 60.003 57.895 9.46 0.00 38.34 3.41
1675 1733 1.002134 AGAAGCCACCGGACAATGG 60.002 57.895 9.46 6.42 39.16 3.16
1676 1734 0.606401 ACAGAAGCCACCGGACAATG 60.606 55.000 9.46 0.00 0.00 2.82
1677 1735 0.321653 GACAGAAGCCACCGGACAAT 60.322 55.000 9.46 0.00 0.00 2.71
1678 1736 1.070786 GACAGAAGCCACCGGACAA 59.929 57.895 9.46 0.00 0.00 3.18
1679 1737 2.741092 GACAGAAGCCACCGGACA 59.259 61.111 9.46 0.00 0.00 4.02
1680 1738 2.432628 CGACAGAAGCCACCGGAC 60.433 66.667 9.46 0.00 0.00 4.79
1681 1739 3.691342 CCGACAGAAGCCACCGGA 61.691 66.667 9.46 0.00 42.49 5.14
1682 1740 4.760047 CCCGACAGAAGCCACCGG 62.760 72.222 0.00 0.00 39.85 5.28
1683 1741 3.649277 CTCCCGACAGAAGCCACCG 62.649 68.421 0.00 0.00 0.00 4.94
1684 1742 2.266055 CTCCCGACAGAAGCCACC 59.734 66.667 0.00 0.00 0.00 4.61
1685 1743 2.435059 GCTCCCGACAGAAGCCAC 60.435 66.667 0.00 0.00 0.00 5.01
1686 1744 3.706373 GGCTCCCGACAGAAGCCA 61.706 66.667 7.71 0.00 44.42 4.75
1687 1745 3.378399 GAGGCTCCCGACAGAAGCC 62.378 68.421 2.15 4.46 45.30 4.35
1688 1746 2.185608 GAGGCTCCCGACAGAAGC 59.814 66.667 2.15 0.00 0.00 3.86
1689 1747 0.682855 AGAGAGGCTCCCGACAGAAG 60.683 60.000 11.71 0.00 0.00 2.85
1690 1748 0.681564 GAGAGAGGCTCCCGACAGAA 60.682 60.000 11.71 0.00 37.69 3.02
1691 1749 1.077357 GAGAGAGGCTCCCGACAGA 60.077 63.158 11.71 0.00 37.69 3.41
1692 1750 2.477176 CGAGAGAGGCTCCCGACAG 61.477 68.421 11.71 0.00 40.70 3.51
1693 1751 2.438614 CGAGAGAGGCTCCCGACA 60.439 66.667 11.71 0.00 40.70 4.35
1694 1752 3.213402 CCGAGAGAGGCTCCCGAC 61.213 72.222 18.80 6.77 40.70 4.79
1703 1761 3.898509 CAGGAGCGGCCGAGAGAG 61.899 72.222 33.48 11.47 43.43 3.20
1706 1764 4.841617 ATCCAGGAGCGGCCGAGA 62.842 66.667 33.48 14.87 43.43 4.04
1707 1765 4.598894 CATCCAGGAGCGGCCGAG 62.599 72.222 33.48 12.19 43.43 4.63
1709 1767 4.899239 GACATCCAGGAGCGGCCG 62.899 72.222 24.05 24.05 43.43 6.13
1710 1768 1.686325 TAAGACATCCAGGAGCGGCC 61.686 60.000 0.00 0.00 0.00 6.13
1711 1769 0.394565 ATAAGACATCCAGGAGCGGC 59.605 55.000 0.00 0.00 0.00 6.53
1712 1770 1.967066 AGATAAGACATCCAGGAGCGG 59.033 52.381 0.00 0.00 0.00 5.52
1713 1771 2.865670 GCAGATAAGACATCCAGGAGCG 60.866 54.545 0.00 0.00 0.00 5.03
1714 1772 2.549778 GGCAGATAAGACATCCAGGAGC 60.550 54.545 0.00 0.00 0.00 4.70
1715 1773 2.038295 GGGCAGATAAGACATCCAGGAG 59.962 54.545 0.00 0.00 0.00 3.69
1716 1774 2.050144 GGGCAGATAAGACATCCAGGA 58.950 52.381 0.00 0.00 0.00 3.86
1717 1775 1.770658 TGGGCAGATAAGACATCCAGG 59.229 52.381 0.00 0.00 0.00 4.45
1718 1776 2.702478 TCTGGGCAGATAAGACATCCAG 59.298 50.000 0.00 0.00 40.99 3.86
1719 1777 2.435805 GTCTGGGCAGATAAGACATCCA 59.564 50.000 0.00 0.00 40.08 3.41
1720 1778 2.435805 TGTCTGGGCAGATAAGACATCC 59.564 50.000 0.76 0.00 44.01 3.51
1721 1779 3.726607 CTGTCTGGGCAGATAAGACATC 58.273 50.000 5.29 0.00 46.74 3.06
1722 1780 2.158842 GCTGTCTGGGCAGATAAGACAT 60.159 50.000 6.37 0.00 46.74 3.06
1723 1781 1.208052 GCTGTCTGGGCAGATAAGACA 59.792 52.381 6.37 4.80 46.05 3.41
1724 1782 1.484240 AGCTGTCTGGGCAGATAAGAC 59.516 52.381 6.37 0.00 39.97 3.01
1725 1783 1.759445 GAGCTGTCTGGGCAGATAAGA 59.241 52.381 6.37 0.00 39.97 2.10
1726 1784 1.483827 TGAGCTGTCTGGGCAGATAAG 59.516 52.381 6.37 0.00 39.97 1.73
1727 1785 1.483827 CTGAGCTGTCTGGGCAGATAA 59.516 52.381 6.37 0.00 39.97 1.75
1728 1786 1.117994 CTGAGCTGTCTGGGCAGATA 58.882 55.000 6.37 0.00 39.97 1.98
1729 1787 0.616964 TCTGAGCTGTCTGGGCAGAT 60.617 55.000 6.37 0.00 39.97 2.90
1730 1788 1.228988 TCTGAGCTGTCTGGGCAGA 60.229 57.895 6.37 0.00 38.70 4.26
1731 1789 1.079266 GTCTGAGCTGTCTGGGCAG 60.079 63.158 0.00 0.00 39.37 4.85
1732 1790 2.587247 GGTCTGAGCTGTCTGGGCA 61.587 63.158 0.00 0.00 0.00 5.36
1733 1791 2.267324 GGTCTGAGCTGTCTGGGC 59.733 66.667 0.00 0.00 0.00 5.36
1734 1792 2.985456 GGGTCTGAGCTGTCTGGG 59.015 66.667 6.83 0.00 0.00 4.45
1735 1793 2.575993 CGGGTCTGAGCTGTCTGG 59.424 66.667 7.51 0.00 0.00 3.86
1736 1794 2.575993 CCGGGTCTGAGCTGTCTG 59.424 66.667 14.06 0.00 0.00 3.51
1737 1795 2.681778 CCCGGGTCTGAGCTGTCT 60.682 66.667 14.18 0.00 0.00 3.41
1738 1796 4.459089 GCCCGGGTCTGAGCTGTC 62.459 72.222 24.63 0.00 0.00 3.51
1740 1798 4.020617 TTGCCCGGGTCTGAGCTG 62.021 66.667 24.63 8.69 0.00 4.24
1741 1799 4.021925 GTTGCCCGGGTCTGAGCT 62.022 66.667 24.63 0.00 0.00 4.09
1743 1801 4.410400 GGGTTGCCCGGGTCTGAG 62.410 72.222 24.63 0.00 32.13 3.35
1752 1810 4.748144 CCTCCAGCTGGGTTGCCC 62.748 72.222 32.23 0.00 45.71 5.36
1753 1811 4.748144 CCCTCCAGCTGGGTTGCC 62.748 72.222 32.23 0.00 39.82 4.52
1765 1823 1.351017 TCAACTTGTCATGGACCCTCC 59.649 52.381 0.00 0.00 36.96 4.30
1766 1824 2.427506 GTCAACTTGTCATGGACCCTC 58.572 52.381 0.00 0.00 0.00 4.30
1767 1825 1.073923 GGTCAACTTGTCATGGACCCT 59.926 52.381 0.00 0.00 41.67 4.34
1768 1826 1.202879 TGGTCAACTTGTCATGGACCC 60.203 52.381 11.16 0.00 45.81 4.46
1769 1827 1.880027 GTGGTCAACTTGTCATGGACC 59.120 52.381 7.80 7.80 46.40 4.46
1770 1828 1.880027 GGTGGTCAACTTGTCATGGAC 59.120 52.381 0.00 0.00 0.00 4.02
1771 1829 1.542328 CGGTGGTCAACTTGTCATGGA 60.542 52.381 0.00 0.00 0.00 3.41
1772 1830 0.874390 CGGTGGTCAACTTGTCATGG 59.126 55.000 0.00 0.00 0.00 3.66
1773 1831 0.874390 CCGGTGGTCAACTTGTCATG 59.126 55.000 0.00 0.00 0.00 3.07
1774 1832 0.250727 CCCGGTGGTCAACTTGTCAT 60.251 55.000 0.00 0.00 0.00 3.06
1775 1833 1.147376 CCCGGTGGTCAACTTGTCA 59.853 57.895 0.00 0.00 0.00 3.58
1776 1834 1.147600 ACCCGGTGGTCAACTTGTC 59.852 57.895 0.00 0.00 43.06 3.18
1777 1835 3.326900 ACCCGGTGGTCAACTTGT 58.673 55.556 0.00 0.00 43.06 3.16
1786 1844 2.045340 CCCTAGCAAACCCGGTGG 60.045 66.667 0.00 0.00 37.80 4.61
1787 1845 2.045340 CCCCTAGCAAACCCGGTG 60.045 66.667 0.00 0.00 0.00 4.94
1788 1846 4.043100 GCCCCTAGCAAACCCGGT 62.043 66.667 0.00 0.00 42.97 5.28
1789 1847 4.815108 GGCCCCTAGCAAACCCGG 62.815 72.222 0.00 0.00 46.50 5.73
1791 1849 2.604299 CTACGGCCCCTAGCAAACCC 62.604 65.000 0.00 0.00 46.50 4.11
1792 1850 1.153229 CTACGGCCCCTAGCAAACC 60.153 63.158 0.00 0.00 46.50 3.27
1793 1851 0.461516 GACTACGGCCCCTAGCAAAC 60.462 60.000 0.00 0.00 46.50 2.93
1794 1852 0.905809 TGACTACGGCCCCTAGCAAA 60.906 55.000 0.00 0.00 46.50 3.68
1795 1853 0.689745 ATGACTACGGCCCCTAGCAA 60.690 55.000 0.00 0.00 46.50 3.91
1796 1854 0.689745 AATGACTACGGCCCCTAGCA 60.690 55.000 0.00 0.00 46.50 3.49
1797 1855 0.249911 CAATGACTACGGCCCCTAGC 60.250 60.000 0.00 0.00 42.60 3.42
1798 1856 0.393077 CCAATGACTACGGCCCCTAG 59.607 60.000 0.00 0.00 0.00 3.02
1799 1857 0.031917 TCCAATGACTACGGCCCCTA 60.032 55.000 0.00 0.00 0.00 3.53
1800 1858 1.306654 TCCAATGACTACGGCCCCT 60.307 57.895 0.00 0.00 0.00 4.79
1801 1859 1.153229 GTCCAATGACTACGGCCCC 60.153 63.158 0.00 0.00 38.53 5.80
1802 1860 1.520787 CGTCCAATGACTACGGCCC 60.521 63.158 0.00 0.00 39.47 5.80
1803 1861 4.104143 CGTCCAATGACTACGGCC 57.896 61.111 0.00 0.00 39.47 6.13
1806 1864 1.138047 GACGCCGTCCAATGACTACG 61.138 60.000 5.81 0.00 40.88 3.51
1807 1865 1.138047 CGACGCCGTCCAATGACTAC 61.138 60.000 12.26 0.00 39.47 2.73
1808 1866 1.138036 CGACGCCGTCCAATGACTA 59.862 57.895 12.26 0.00 39.47 2.59
1809 1867 2.126071 CGACGCCGTCCAATGACT 60.126 61.111 12.26 0.00 39.47 3.41
1810 1868 3.186047 CCGACGCCGTCCAATGAC 61.186 66.667 12.26 0.00 38.18 3.06
1811 1869 4.444838 CCCGACGCCGTCCAATGA 62.445 66.667 12.26 0.00 0.00 2.57
1836 1894 2.355363 TACGTGCGCTGACACCAC 60.355 61.111 9.73 0.00 37.25 4.16
1925 1983 0.970640 TCCGACCCAACGAATCTTCA 59.029 50.000 0.00 0.00 35.09 3.02
2044 2106 1.205055 GAAGTAGGTGGGGAAGGGAG 58.795 60.000 0.00 0.00 0.00 4.30
2061 2129 1.073098 GTGGGGAAGAAGGAAGGGAA 58.927 55.000 0.00 0.00 0.00 3.97
2071 2139 2.883888 GCCTTGCTATTTGTGGGGAAGA 60.884 50.000 0.00 0.00 31.62 2.87
2202 2275 2.671963 GGTGGGTTTCCAGGTCGC 60.672 66.667 0.00 0.00 45.05 5.19
2217 2292 2.125106 GCGCTTGGATTCTCCGGT 60.125 61.111 0.00 0.00 40.17 5.28
2260 2335 0.105039 GGTACTCCTTGAGCGATGGG 59.895 60.000 0.00 0.00 32.04 4.00


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

AutoCloner maintained by Alex Coulton.