Multiple sequence alignment - TraesCS7A01G053700

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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 TraesCS7A01G053700 chr7A 100.000 5189 0 0 1 5189 26029204 26034392 0.000000e+00 9583.0
1 TraesCS7A01G053700 chr7A 85.685 1935 231 24 2290 4200 26043909 26045821 0.000000e+00 1997.0
2 TraesCS7A01G053700 chr7A 83.455 1910 273 29 2297 4182 25752563 25750673 0.000000e+00 1736.0
3 TraesCS7A01G053700 chr7A 83.150 1911 276 28 2297 4182 37720383 37722272 0.000000e+00 1703.0
4 TraesCS7A01G053700 chr7A 92.965 597 31 7 865 1459 25754873 25754286 0.000000e+00 859.0
5 TraesCS7A01G053700 chr7A 91.444 561 43 4 922 1480 26039580 26040137 0.000000e+00 765.0
6 TraesCS7A01G053700 chr7D 89.868 3109 202 46 1718 4763 25190126 25193184 0.000000e+00 3892.0
7 TraesCS7A01G053700 chr7D 85.018 1929 234 34 2290 4187 25271664 25273568 0.000000e+00 1910.0
8 TraesCS7A01G053700 chr7D 88.953 1557 94 26 3 1537 25188438 25189938 0.000000e+00 1851.0
9 TraesCS7A01G053700 chr7D 83.394 1927 281 25 2297 4201 24947602 24945693 0.000000e+00 1749.0
10 TraesCS7A01G053700 chr7D 94.424 538 30 0 922 1459 24949545 24949008 0.000000e+00 828.0
11 TraesCS7A01G053700 chr7D 91.979 561 41 3 922 1480 25270337 25270895 0.000000e+00 784.0
12 TraesCS7A01G053700 chr7D 85.870 368 37 8 4798 5154 25193188 25193551 1.360000e-100 377.0
13 TraesCS7A01G053700 chr4A 83.552 1909 276 24 2297 4182 708612430 708614323 0.000000e+00 1751.0
14 TraesCS7A01G053700 chr4A 92.217 591 39 6 865 1453 708610386 708610971 0.000000e+00 830.0
15 TraesCS7A01G053700 chrUn 91.070 1019 73 11 2013 3022 332282626 332283635 0.000000e+00 1362.0
16 TraesCS7A01G053700 chrUn 89.017 1038 51 20 439 1453 332281248 332282245 0.000000e+00 1227.0
17 TraesCS7A01G053700 chrUn 90.676 740 40 15 3023 3746 468581920 468582646 0.000000e+00 957.0
18 TraesCS7A01G053700 chrUn 87.982 649 75 3 3541 4187 50424715 50425362 0.000000e+00 763.0
19 TraesCS7A01G053700 chrUn 88.419 544 52 8 2943 3485 50424044 50424577 0.000000e+00 645.0
20 TraesCS7A01G053700 chrUn 82.459 553 49 24 4627 5134 334883405 334883954 1.720000e-119 440.0
21 TraesCS7A01G053700 chrUn 91.481 270 14 4 4301 4564 334883028 334883294 3.820000e-96 363.0
22 TraesCS7A01G053700 chrUn 88.793 232 26 0 184 415 332280962 332281193 8.500000e-73 285.0
23 TraesCS7A01G053700 chrUn 90.741 162 13 2 1778 1938 332282468 332282628 1.130000e-51 215.0
24 TraesCS7A01G053700 chrUn 89.916 119 11 1 3 120 326028681 326028799 9.000000e-33 152.0
25 TraesCS7A01G053700 chrUn 89.916 119 11 1 3 120 327955896 327956014 9.000000e-33 152.0
26 TraesCS7A01G053700 chrUn 89.916 119 11 1 3 120 339889374 339889492 9.000000e-33 152.0
27 TraesCS7A01G053700 chrUn 89.916 119 11 1 3 120 349957804 349957922 9.000000e-33 152.0
28 TraesCS7A01G053700 chrUn 89.916 119 11 1 3 120 387893438 387893320 9.000000e-33 152.0
29 TraesCS7A01G053700 chrUn 89.831 59 1 3 1701 1757 332282413 332282468 2.590000e-08 71.3
30 TraesCS7A01G053700 chr6B 80.851 1222 188 30 2297 3483 125727640 125728850 0.000000e+00 918.0
31 TraesCS7A01G053700 chr6B 90.244 615 60 0 3564 4178 125728987 125729601 0.000000e+00 804.0
32 TraesCS7A01G053700 chr6B 93.246 533 36 0 922 1454 125725326 125725858 0.000000e+00 785.0
33 TraesCS7A01G053700 chr6D 93.246 533 36 0 922 1454 55882281 55882813 0.000000e+00 785.0
34 TraesCS7A01G053700 chr6D 83.574 554 68 12 2944 3483 55894498 55895042 1.000000e-136 497.0
35 TraesCS7A01G053700 chr5A 97.778 45 1 0 1650 1694 490326108 490326152 1.550000e-10 78.7
36 TraesCS7A01G053700 chr5A 97.778 45 1 0 1650 1694 490416138 490416182 1.550000e-10 78.7
37 TraesCS7A01G053700 chr3D 92.593 54 2 1 1645 1696 437475397 437475344 5.570000e-10 76.8
38 TraesCS7A01G053700 chr1D 94.000 50 3 0 1651 1700 141706018 141705969 5.570000e-10 76.8
39 TraesCS7A01G053700 chr1D 97.727 44 1 0 1651 1694 350947647 350947604 5.570000e-10 76.8
40 TraesCS7A01G053700 chr1B 94.000 50 3 0 1651 1700 195591242 195591193 5.570000e-10 76.8
41 TraesCS7A01G053700 chr1B 95.745 47 1 1 1650 1696 308288370 308288325 2.000000e-09 75.0
42 TraesCS7A01G053700 chr2A 95.745 47 1 1 1650 1696 153533751 153533796 2.000000e-09 75.0
43 TraesCS7A01G053700 chr6A 92.157 51 4 0 1651 1701 605337391 605337441 7.210000e-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 TraesCS7A01G053700 chr7A 26029204 26034392 5188 False 9583.000000 9583 100.000000 1 5189 1 chr7A.!!$F1 5188
1 TraesCS7A01G053700 chr7A 37720383 37722272 1889 False 1703.000000 1703 83.150000 2297 4182 1 chr7A.!!$F2 1885
2 TraesCS7A01G053700 chr7A 26039580 26045821 6241 False 1381.000000 1997 88.564500 922 4200 2 chr7A.!!$F3 3278
3 TraesCS7A01G053700 chr7A 25750673 25754873 4200 True 1297.500000 1736 88.210000 865 4182 2 chr7A.!!$R1 3317
4 TraesCS7A01G053700 chr7D 25188438 25193551 5113 False 2040.000000 3892 88.230333 3 5154 3 chr7D.!!$F1 5151
5 TraesCS7A01G053700 chr7D 25270337 25273568 3231 False 1347.000000 1910 88.498500 922 4187 2 chr7D.!!$F2 3265
6 TraesCS7A01G053700 chr7D 24945693 24949545 3852 True 1288.500000 1749 88.909000 922 4201 2 chr7D.!!$R1 3279
7 TraesCS7A01G053700 chr4A 708610386 708614323 3937 False 1290.500000 1751 87.884500 865 4182 2 chr4A.!!$F1 3317
8 TraesCS7A01G053700 chrUn 468581920 468582646 726 False 957.000000 957 90.676000 3023 3746 1 chrUn.!!$F5 723
9 TraesCS7A01G053700 chrUn 50424044 50425362 1318 False 704.000000 763 88.200500 2943 4187 2 chrUn.!!$F6 1244
10 TraesCS7A01G053700 chrUn 332280962 332283635 2673 False 632.060000 1362 89.890400 184 3022 5 chrUn.!!$F7 2838
11 TraesCS7A01G053700 chrUn 334883028 334883954 926 False 401.500000 440 86.970000 4301 5134 2 chrUn.!!$F8 833
12 TraesCS7A01G053700 chr6B 125725326 125729601 4275 False 835.666667 918 88.113667 922 4178 3 chr6B.!!$F1 3256
13 TraesCS7A01G053700 chr6D 55882281 55882813 532 False 785.000000 785 93.246000 922 1454 1 chr6D.!!$F1 532
14 TraesCS7A01G053700 chr6D 55894498 55895042 544 False 497.000000 497 83.574000 2944 3483 1 chr6D.!!$F2 539

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
721 783 0.107945 AAGAAGAGGACGAGCATGGC 60.108 55.0 0.00 0.00 0.00 4.40 F
1544 1671 0.246086 TTGGCCGGTCAAAATGATGC 59.754 50.0 21.49 0.00 0.00 3.91 F
1961 2996 0.539438 TGTGAGTTGTTGGGGCCATC 60.539 55.0 4.39 0.00 0.00 3.51 F
2550 6920 0.990374 GGGCATCCATCTCCAGCTAT 59.010 55.0 0.00 0.00 0.00 2.97 F
3248 7662 0.879839 TCATCACGGCATGCCATACG 60.880 55.0 34.93 23.04 35.37 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 2803 0.106519 AACTCACAGGGGCCATATGC 60.107 55.000 4.39 0.00 40.16 3.14 R
2550 6920 0.624254 TGACGAGAGGGCTTCCTAGA 59.376 55.000 0.00 0.00 41.93 2.43 R
3234 7639 0.679505 AGATACGTATGGCATGCCGT 59.320 50.000 33.05 33.05 39.42 5.68 R
3862 8430 1.665679 CACGGGCATGTTGATGAGTAC 59.334 52.381 0.00 0.00 0.00 2.73 R
5166 9884 0.178970 TATACCAGTCCCTCGGCCTC 60.179 60.000 0.00 0.00 0.00 4.70 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
30 31 0.596082 GCTGAGATAGGACCTCGCTC 59.404 60.000 13.91 13.91 33.51 5.03
44 45 1.797933 CGCTCGAGACAGGACAACG 60.798 63.158 18.75 2.45 0.00 4.10
48 49 1.199327 CTCGAGACAGGACAACGCTAA 59.801 52.381 6.58 0.00 0.00 3.09
110 111 4.308458 TTGACGGGTGCGGGTCAG 62.308 66.667 0.00 0.00 43.40 3.51
117 118 3.775654 GTGCGGGTCAGGGAGGAG 61.776 72.222 0.00 0.00 0.00 3.69
163 164 4.664677 GGTGTCGTCGGCACTGCT 62.665 66.667 27.39 0.00 37.07 4.24
164 165 2.257371 GTGTCGTCGGCACTGCTA 59.743 61.111 22.26 0.00 34.30 3.49
165 166 2.087009 GTGTCGTCGGCACTGCTAC 61.087 63.158 22.26 0.00 34.30 3.58
166 167 2.874780 GTCGTCGGCACTGCTACG 60.875 66.667 17.88 17.88 38.48 3.51
210 212 2.343758 GCGGTGGAGACAAGCAGA 59.656 61.111 0.00 0.00 46.06 4.26
226 239 2.184631 AGAAGGGGTGAGGGGAGGA 61.185 63.158 0.00 0.00 0.00 3.71
363 377 1.152589 TTGTGGCTGTTGGATGGCA 60.153 52.632 0.00 0.00 36.39 4.92
416 430 2.816087 TGGTGTTGGTAGAGTCGTACTC 59.184 50.000 6.85 6.85 45.38 2.59
471 516 1.603802 TCGTTGAGAAACGGACGTACT 59.396 47.619 10.72 0.97 45.45 2.73
492 537 2.129146 TCGACCCAGACCACGTTGT 61.129 57.895 0.00 0.00 0.00 3.32
493 538 1.227438 CGACCCAGACCACGTTGTT 60.227 57.895 0.00 0.00 0.00 2.83
494 539 1.495584 CGACCCAGACCACGTTGTTG 61.496 60.000 0.00 0.00 0.00 3.33
495 540 1.782028 GACCCAGACCACGTTGTTGC 61.782 60.000 0.00 0.00 0.00 4.17
595 640 3.708451 AGTCCAAACCTTCCAAAACAGT 58.292 40.909 0.00 0.00 0.00 3.55
596 641 4.862371 AGTCCAAACCTTCCAAAACAGTA 58.138 39.130 0.00 0.00 0.00 2.74
597 642 4.643334 AGTCCAAACCTTCCAAAACAGTAC 59.357 41.667 0.00 0.00 0.00 2.73
632 677 2.730715 CGACAGCTGAAGCAGTAGAGAC 60.731 54.545 23.35 0.00 40.94 3.36
633 678 2.491693 GACAGCTGAAGCAGTAGAGACT 59.508 50.000 23.35 0.00 40.94 3.24
673 735 3.083997 ATGGCGTCCTCCTCCCAC 61.084 66.667 0.00 0.00 0.00 4.61
674 736 3.625632 ATGGCGTCCTCCTCCCACT 62.626 63.158 0.00 0.00 0.00 4.00
675 737 3.003763 GGCGTCCTCCTCCCACTT 61.004 66.667 0.00 0.00 0.00 3.16
676 738 2.579738 GCGTCCTCCTCCCACTTC 59.420 66.667 0.00 0.00 0.00 3.01
677 739 3.020237 GCGTCCTCCTCCCACTTCC 62.020 68.421 0.00 0.00 0.00 3.46
678 740 1.609501 CGTCCTCCTCCCACTTCCA 60.610 63.158 0.00 0.00 0.00 3.53
679 741 1.889530 CGTCCTCCTCCCACTTCCAC 61.890 65.000 0.00 0.00 0.00 4.02
685 747 1.557269 CCTCCCACTTCCACTCCCAG 61.557 65.000 0.00 0.00 0.00 4.45
700 762 0.326264 CCCAGTCCCACCAAGAAGAG 59.674 60.000 0.00 0.00 0.00 2.85
706 768 2.372172 GTCCCACCAAGAAGAGGAAGAA 59.628 50.000 0.00 0.00 0.00 2.52
707 769 2.639839 TCCCACCAAGAAGAGGAAGAAG 59.360 50.000 0.00 0.00 0.00 2.85
708 770 2.639839 CCCACCAAGAAGAGGAAGAAGA 59.360 50.000 0.00 0.00 0.00 2.87
709 771 3.307339 CCCACCAAGAAGAGGAAGAAGAG 60.307 52.174 0.00 0.00 0.00 2.85
710 772 3.307339 CCACCAAGAAGAGGAAGAAGAGG 60.307 52.174 0.00 0.00 0.00 3.69
711 773 3.580458 CACCAAGAAGAGGAAGAAGAGGA 59.420 47.826 0.00 0.00 0.00 3.71
712 774 3.580895 ACCAAGAAGAGGAAGAAGAGGAC 59.419 47.826 0.00 0.00 0.00 3.85
721 783 0.107945 AAGAAGAGGACGAGCATGGC 60.108 55.000 0.00 0.00 0.00 4.40
725 787 4.457496 AGGACGAGCATGGCCACG 62.457 66.667 8.16 10.31 35.71 4.94
782 847 3.071206 GTGAGCCGCCTCCTCTCA 61.071 66.667 0.00 0.00 37.29 3.27
815 880 4.697756 GTGCACGCACCCCTGCTA 62.698 66.667 11.13 0.00 41.77 3.49
834 899 0.957395 ACGCCAGCTGACCATTTCTG 60.957 55.000 17.39 0.00 0.00 3.02
875 940 2.968697 GAACCGGCCGTCAACGTT 60.969 61.111 26.12 20.11 37.74 3.99
881 946 2.539338 GGCCGTCAACGTTGCAGAA 61.539 57.895 23.47 3.11 37.74 3.02
947 1015 4.148825 GCCGATCGAGCAGGTGGT 62.149 66.667 18.66 0.00 0.00 4.16
1105 1173 2.418777 CCATCTCCGCGCAGATCA 59.581 61.111 10.22 0.00 30.07 2.92
1283 1351 2.342279 CATCCACGTGGTCACCGT 59.658 61.111 32.74 11.30 39.52 4.83
1503 1622 7.575365 ACTTCATTTTCGAATTTTTCATTGCC 58.425 30.769 0.00 0.00 0.00 4.52
1506 1625 7.574496 TCATTTTCGAATTTTTCATTGCCTTG 58.426 30.769 0.00 0.00 0.00 3.61
1537 1664 4.319177 CCAAATTTAATTGGCCGGTCAAA 58.681 39.130 27.72 9.85 43.11 2.69
1544 1671 0.246086 TTGGCCGGTCAAAATGATGC 59.754 50.000 21.49 0.00 0.00 3.91
1548 1675 1.468054 GCCGGTCAAAATGATGCACTC 60.468 52.381 1.90 0.00 0.00 3.51
1549 1676 1.811965 CCGGTCAAAATGATGCACTCA 59.188 47.619 0.00 0.00 38.53 3.41
1550 1677 2.159476 CCGGTCAAAATGATGCACTCAG 60.159 50.000 0.00 0.00 37.28 3.35
1551 1678 2.743664 CGGTCAAAATGATGCACTCAGA 59.256 45.455 0.00 0.00 37.28 3.27
1556 1683 6.441274 GTCAAAATGATGCACTCAGAAAGAA 58.559 36.000 0.00 0.00 37.28 2.52
1557 1684 6.919662 GTCAAAATGATGCACTCAGAAAGAAA 59.080 34.615 0.00 0.00 37.28 2.52
1558 1685 6.919662 TCAAAATGATGCACTCAGAAAGAAAC 59.080 34.615 0.00 0.00 37.28 2.78
1560 1687 7.750229 AAATGATGCACTCAGAAAGAAACTA 57.250 32.000 0.00 0.00 37.28 2.24
1561 1688 6.981762 ATGATGCACTCAGAAAGAAACTAG 57.018 37.500 0.00 0.00 37.28 2.57
1562 1689 5.240891 TGATGCACTCAGAAAGAAACTAGG 58.759 41.667 0.00 0.00 0.00 3.02
1643 1994 5.033326 TGCGTGCAAGCAATGTATATATG 57.967 39.130 25.22 0.00 45.06 1.78
1645 1996 4.406069 CGTGCAAGCAATGTATATATGCC 58.594 43.478 0.00 0.00 40.93 4.40
1650 2001 5.413833 GCAAGCAATGTATATATGCCTCTGT 59.586 40.000 3.67 0.00 40.93 3.41
1651 2002 6.072286 GCAAGCAATGTATATATGCCTCTGTT 60.072 38.462 3.67 0.00 40.93 3.16
1652 2003 7.522725 GCAAGCAATGTATATATGCCTCTGTTT 60.523 37.037 3.67 0.00 40.93 2.83
1653 2004 9.002600 CAAGCAATGTATATATGCCTCTGTTTA 57.997 33.333 3.67 0.00 40.93 2.01
1654 2005 9.573166 AAGCAATGTATATATGCCTCTGTTTAA 57.427 29.630 3.67 0.00 40.93 1.52
1655 2006 9.573166 AGCAATGTATATATGCCTCTGTTTAAA 57.427 29.630 3.67 0.00 40.93 1.52
1656 2007 9.612620 GCAATGTATATATGCCTCTGTTTAAAC 57.387 33.333 11.54 11.54 34.03 2.01
1659 2010 8.378172 TGTATATATGCCTCTGTTTAAACTGC 57.622 34.615 18.72 15.15 0.00 4.40
1660 2011 6.884280 ATATATGCCTCTGTTTAAACTGCC 57.116 37.500 18.72 10.40 0.00 4.85
1661 2012 2.356665 TGCCTCTGTTTAAACTGCCA 57.643 45.000 18.72 12.43 0.00 4.92
1662 2013 2.660572 TGCCTCTGTTTAAACTGCCAA 58.339 42.857 18.72 2.97 0.00 4.52
1663 2014 3.027412 TGCCTCTGTTTAAACTGCCAAA 58.973 40.909 18.72 2.65 0.00 3.28
1664 2015 3.449018 TGCCTCTGTTTAAACTGCCAAAA 59.551 39.130 18.72 2.31 0.00 2.44
1665 2016 3.802139 GCCTCTGTTTAAACTGCCAAAAC 59.198 43.478 18.72 3.26 34.45 2.43
1666 2017 4.041723 CCTCTGTTTAAACTGCCAAAACG 58.958 43.478 18.72 0.00 36.19 3.60
1667 2018 4.439563 CCTCTGTTTAAACTGCCAAAACGT 60.440 41.667 18.72 0.00 36.19 3.99
1668 2019 4.664188 TCTGTTTAAACTGCCAAAACGTC 58.336 39.130 18.72 0.00 36.19 4.34
1669 2020 4.396790 TCTGTTTAAACTGCCAAAACGTCT 59.603 37.500 18.72 0.00 36.19 4.18
1670 2021 5.061920 TGTTTAAACTGCCAAAACGTCTT 57.938 34.783 18.72 0.00 36.19 3.01
1671 2022 6.093771 TCTGTTTAAACTGCCAAAACGTCTTA 59.906 34.615 18.72 0.00 36.19 2.10
1672 2023 6.797454 TGTTTAAACTGCCAAAACGTCTTAT 58.203 32.000 18.72 0.00 36.19 1.73
1673 2024 7.928103 TGTTTAAACTGCCAAAACGTCTTATA 58.072 30.769 18.72 0.00 36.19 0.98
1674 2025 8.569641 TGTTTAAACTGCCAAAACGTCTTATAT 58.430 29.630 18.72 0.00 36.19 0.86
1675 2026 9.401873 GTTTAAACTGCCAAAACGTCTTATATT 57.598 29.630 11.18 0.00 0.00 1.28
1676 2027 9.968870 TTTAAACTGCCAAAACGTCTTATATTT 57.031 25.926 0.00 0.00 0.00 1.40
1679 2030 9.567848 AAACTGCCAAAACGTCTTATATTTATG 57.432 29.630 0.00 0.00 0.00 1.90
1680 2031 8.500753 ACTGCCAAAACGTCTTATATTTATGA 57.499 30.769 0.00 0.00 0.00 2.15
1681 2032 8.952278 ACTGCCAAAACGTCTTATATTTATGAA 58.048 29.630 0.00 0.00 0.00 2.57
1682 2033 9.221775 CTGCCAAAACGTCTTATATTTATGAAC 57.778 33.333 0.00 0.00 0.00 3.18
1683 2034 8.731605 TGCCAAAACGTCTTATATTTATGAACA 58.268 29.630 0.00 0.00 0.00 3.18
1684 2035 9.221775 GCCAAAACGTCTTATATTTATGAACAG 57.778 33.333 0.00 0.00 0.00 3.16
1688 2039 8.888579 AACGTCTTATATTTATGAACAGAGGG 57.111 34.615 0.00 0.00 0.00 4.30
1689 2040 8.019656 ACGTCTTATATTTATGAACAGAGGGT 57.980 34.615 0.00 0.00 0.00 4.34
1690 2041 7.926555 ACGTCTTATATTTATGAACAGAGGGTG 59.073 37.037 0.00 0.00 0.00 4.61
1691 2042 7.926555 CGTCTTATATTTATGAACAGAGGGTGT 59.073 37.037 0.00 0.00 43.24 4.16
1696 2047 8.964476 ATATTTATGAACAGAGGGTGTACTTG 57.036 34.615 0.00 0.00 39.03 3.16
1697 2048 2.543777 TGAACAGAGGGTGTACTTGC 57.456 50.000 0.00 0.00 39.03 4.01
1698 2049 2.047061 TGAACAGAGGGTGTACTTGCT 58.953 47.619 0.00 0.00 39.03 3.91
1715 2066 6.240549 ACTTGCTATATGCTTCCAAGTAGT 57.759 37.500 2.81 0.00 42.87 2.73
1779 2161 2.891580 GTGTGGAGAAGTAGACACCTCA 59.108 50.000 0.00 0.00 33.97 3.86
1848 2709 7.166691 AGAAAATTAGATGATTGCAACAGCT 57.833 32.000 18.84 18.84 37.71 4.24
1857 2718 1.178534 TTGCAACAGCTTAGCCACCC 61.179 55.000 0.00 0.00 0.00 4.61
1867 2728 2.424956 GCTTAGCCACCCAAAGATTCTG 59.575 50.000 0.00 0.00 0.00 3.02
1886 2759 7.502226 AGATTCTGAACACAACCATAAAACTCA 59.498 33.333 0.00 0.00 0.00 3.41
1900 2773 8.826765 ACCATAAAACTCAGGATTAAGAGAGAA 58.173 33.333 0.00 0.00 35.83 2.87
1930 2803 7.948278 AAACTCCGATCGAGGATTAAATTAG 57.052 36.000 18.66 0.00 43.57 1.73
1961 2996 0.539438 TGTGAGTTGTTGGGGCCATC 60.539 55.000 4.39 0.00 0.00 3.51
2020 3055 5.839621 TCAGTTAACACCACTTGAGAGTAC 58.160 41.667 8.61 0.00 33.90 2.73
2029 3064 7.291566 ACACCACTTGAGAGTACTATATAGCT 58.708 38.462 9.78 0.00 33.90 3.32
2068 3994 5.647589 TGACAACGACTACTGAATGGTATC 58.352 41.667 0.00 0.00 0.00 2.24
2072 4010 4.621991 ACGACTACTGAATGGTATCATGC 58.378 43.478 0.00 0.00 33.18 4.06
2078 4675 5.045012 ACTGAATGGTATCATGCTGACAT 57.955 39.130 7.80 0.00 36.79 3.06
2103 4708 5.726397 CTCATGCCTTCCATTCATTGAAAA 58.274 37.500 2.68 0.00 29.71 2.29
2128 6047 9.725019 AAAACATGGAGAAAATAAAGAAATCCC 57.275 29.630 0.00 0.00 0.00 3.85
2155 6075 4.162320 TCCATCTCAGGGAAATACAGTGAC 59.838 45.833 0.00 0.00 0.00 3.67
2169 6089 9.099454 GAAATACAGTGACCTAATTAAGACAGG 57.901 37.037 0.00 0.00 35.45 4.00
2184 6104 8.614469 ATTAAGACAGGCAGAATAAGATTAGC 57.386 34.615 0.00 0.00 0.00 3.09
2206 6189 6.947258 AGCACAAACATTTATTTGCTTTGAC 58.053 32.000 0.00 0.00 42.29 3.18
2282 6421 3.784178 TCCCTGAGAAGTGAGAACTCAT 58.216 45.455 7.77 0.00 42.18 2.90
2287 6426 4.564041 TGAGAAGTGAGAACTCATGCTTC 58.436 43.478 18.81 18.81 42.18 3.86
2493 6863 4.079850 CAGCAGCTCGGCTCAGGT 62.080 66.667 0.00 0.00 43.68 4.00
2550 6920 0.990374 GGGCATCCATCTCCAGCTAT 59.010 55.000 0.00 0.00 0.00 2.97
2553 6923 3.102972 GGCATCCATCTCCAGCTATCTA 58.897 50.000 0.00 0.00 0.00 1.98
2556 6926 4.608269 CATCCATCTCCAGCTATCTAGGA 58.392 47.826 0.00 0.00 0.00 2.94
2694 7064 1.834263 CCCATCTTCTCTTCCGGTCTT 59.166 52.381 0.00 0.00 0.00 3.01
2703 7073 1.346722 TCTTCCGGTCTTTTCACCTCC 59.653 52.381 0.00 0.00 33.77 4.30
2705 7075 4.278956 CGGTCTTTTCACCTCCGG 57.721 61.111 0.00 0.00 37.92 5.14
2754 7124 3.193903 TCGTGGACGACAATTTCCATCTA 59.806 43.478 0.00 0.00 43.85 1.98
3067 7468 3.609853 GTGGTTCATCTGCATCCTTGTA 58.390 45.455 0.00 0.00 0.00 2.41
3079 7480 4.157656 TGCATCCTTGTAGTTAACATTGCC 59.842 41.667 8.61 0.00 38.10 4.52
3229 7634 7.272144 ACCAGGTAAGGATTCTATCAACTTT 57.728 36.000 0.00 0.00 0.00 2.66
3233 7638 9.050601 CAGGTAAGGATTCTATCAACTTTCATC 57.949 37.037 0.00 0.00 0.00 2.92
3234 7639 8.772250 AGGTAAGGATTCTATCAACTTTCATCA 58.228 33.333 0.00 0.00 0.00 3.07
3235 7640 8.831550 GGTAAGGATTCTATCAACTTTCATCAC 58.168 37.037 0.00 0.00 0.00 3.06
3248 7662 0.879839 TCATCACGGCATGCCATACG 60.880 55.000 34.93 23.04 35.37 3.06
3249 7663 1.146041 ATCACGGCATGCCATACGT 59.854 52.632 34.93 23.71 40.60 3.57
3255 7669 1.336795 CGGCATGCCATACGTATCTGA 60.337 52.381 34.93 0.00 35.37 3.27
3263 7677 3.792401 CCATACGTATCTGAAGCACCAA 58.208 45.455 4.74 0.00 0.00 3.67
3299 7721 2.540383 TCTTCCACTGTATGCAGACCT 58.460 47.619 18.40 0.00 45.28 3.85
3488 7914 3.827008 TTATGGCTCAGGTAAGCTCTG 57.173 47.619 0.00 0.00 42.13 3.35
3504 7996 2.357009 GCTCTGTTTGGCCATCATAGTG 59.643 50.000 6.09 6.59 0.00 2.74
3547 8046 1.815003 AGTGCACAGAAGGCATTAAGC 59.185 47.619 21.04 0.00 44.11 3.09
3660 8228 2.931969 CAACATCTGCGACATTGAGCTA 59.068 45.455 9.45 0.87 0.00 3.32
3828 8396 1.111116 CCCCGCTCCTCGTATGGTTA 61.111 60.000 0.00 0.00 36.19 2.85
3888 8456 1.138036 CAACATGCCCGTGATGCTG 59.862 57.895 0.00 0.00 0.00 4.41
3957 8525 6.356556 CACATGGATACTGATTGGGTTTCTA 58.643 40.000 0.00 0.00 37.61 2.10
3972 8540 5.727279 TGGGTTTCTATCAGGTTATGTGGTA 59.273 40.000 0.00 0.00 0.00 3.25
4129 8697 1.971149 TGACTTGGATGGATGTCCCT 58.029 50.000 0.00 0.00 37.48 4.20
4242 8811 5.334337 GGAAAAATTGGAATTGTGAGCAAGC 60.334 40.000 0.00 0.00 38.10 4.01
4243 8812 4.339872 AAATTGGAATTGTGAGCAAGCA 57.660 36.364 0.00 0.00 38.10 3.91
4273 8842 7.523219 TCGATGTAAATAGCGAATGTTTGTTT 58.477 30.769 0.00 0.00 0.00 2.83
4296 8865 9.196552 GTTTGGACCTTTTAAAGATGAGAAATG 57.803 33.333 6.24 0.00 0.00 2.32
4299 8868 6.437477 GGACCTTTTAAAGATGAGAAATGGGT 59.563 38.462 6.24 0.00 33.71 4.51
4343 8939 4.549458 CAAAGTACCACAAAGATTGCCTG 58.451 43.478 0.00 0.00 0.00 4.85
4392 8988 6.981559 GGTTTTCACTGCCAAATTAACTGTTA 59.018 34.615 0.00 0.00 0.00 2.41
4402 8998 6.459710 GCCAAATTAACTGTTATCCCAGCTAC 60.460 42.308 0.37 0.00 35.83 3.58
4404 9000 7.990886 CCAAATTAACTGTTATCCCAGCTACTA 59.009 37.037 0.37 0.00 35.83 1.82
4405 9001 9.046296 CAAATTAACTGTTATCCCAGCTACTAG 57.954 37.037 0.37 0.00 35.83 2.57
4406 9002 7.916077 ATTAACTGTTATCCCAGCTACTAGT 57.084 36.000 0.00 0.00 35.83 2.57
4413 9009 9.694137 CTGTTATCCCAGCTACTAGTAAATAAC 57.306 37.037 3.76 10.74 0.00 1.89
4487 9087 6.826612 GCAAGTTGCAAGTTTTTAACTGAAA 58.173 32.000 22.90 0.00 44.26 2.69
4526 9126 6.649141 CACACACAATGTACCACAACTAGTAT 59.351 38.462 0.00 0.00 40.64 2.12
4558 9158 7.591057 TGACTGCAAATTCTTATTCTTTGTTCG 59.409 33.333 0.00 0.00 33.46 3.95
4559 9159 7.648142 ACTGCAAATTCTTATTCTTTGTTCGA 58.352 30.769 0.00 0.00 33.46 3.71
4600 9209 2.238521 TCACCAGAATGAAACCCTTGC 58.761 47.619 0.00 0.00 39.69 4.01
4621 9251 0.817634 AGGTGCAAAAGCAGTACGCA 60.818 50.000 11.30 0.00 46.13 5.24
4663 9316 7.493320 CAGTTGCCATTATATGACTGCAATTTT 59.507 33.333 8.22 0.00 37.32 1.82
4698 9357 5.478679 ACAGAGATAATGATAGAGGGAACGG 59.521 44.000 0.00 0.00 0.00 4.44
4708 9367 2.169330 AGAGGGAACGGTCAACTACTC 58.831 52.381 1.31 1.53 0.00 2.59
4744 9411 2.308866 GTCCAGATTTCTCCCCTCCAAA 59.691 50.000 0.00 0.00 0.00 3.28
4747 9414 3.511540 CCAGATTTCTCCCCTCCAAAAAC 59.488 47.826 0.00 0.00 0.00 2.43
4754 9421 4.151883 TCTCCCCTCCAAAAACTGAAATG 58.848 43.478 0.00 0.00 0.00 2.32
4760 9427 4.100808 CCTCCAAAAACTGAAATGGAACCA 59.899 41.667 0.00 0.00 41.20 3.67
4761 9428 5.221702 CCTCCAAAAACTGAAATGGAACCAT 60.222 40.000 0.00 0.00 41.20 3.55
4762 9429 5.609423 TCCAAAAACTGAAATGGAACCATG 58.391 37.500 7.12 0.00 38.95 3.66
4765 9438 6.238429 CCAAAAACTGAAATGGAACCATGTTG 60.238 38.462 7.12 2.51 36.68 3.33
4772 9445 7.450014 ACTGAAATGGAACCATGTTGTATTACA 59.550 33.333 7.12 0.00 36.68 2.41
4773 9446 8.359875 TGAAATGGAACCATGTTGTATTACAT 57.640 30.769 7.12 0.00 39.27 2.29
4795 9468 7.918076 ACATCAATATATGGAAGGAATACGGT 58.082 34.615 0.00 0.00 0.00 4.83
4796 9469 9.042450 ACATCAATATATGGAAGGAATACGGTA 57.958 33.333 0.00 0.00 0.00 4.02
4852 9542 6.420008 CAGTGCCAAGAATTTTCTTCAGAAAG 59.580 38.462 2.59 0.00 45.23 2.62
4865 9555 7.715265 TTCTTCAGAAAGTACTCATGACAAC 57.285 36.000 0.00 0.00 33.95 3.32
4902 9597 0.323629 TTTAGGCTTGCAGGCGTAGT 59.676 50.000 20.33 6.15 46.58 2.73
4922 9617 6.356452 CGTAGTCTACACATCGCATTACTAAC 59.644 42.308 10.59 0.00 0.00 2.34
4935 9637 7.423199 TCGCATTACTAACTATTCACAGTAGG 58.577 38.462 0.00 0.00 0.00 3.18
4947 9649 6.681729 ATTCACAGTAGGGTTTACTCTGAA 57.318 37.500 7.25 7.25 37.06 3.02
5125 9843 3.743017 GGATTGGAGGGCTGGCCA 61.743 66.667 23.25 4.71 37.98 5.36
5154 9872 3.818787 GCAAGGCATGGCTCGGTG 61.819 66.667 23.56 17.90 0.00 4.94
5155 9873 3.818787 CAAGGCATGGCTCGGTGC 61.819 66.667 23.56 0.00 40.55 5.01
5156 9874 4.039092 AAGGCATGGCTCGGTGCT 62.039 61.111 23.56 2.14 41.04 4.40
5157 9875 4.790962 AGGCATGGCTCGGTGCTG 62.791 66.667 17.44 0.00 41.04 4.41
5159 9877 4.783621 GCATGGCTCGGTGCTGGA 62.784 66.667 1.77 0.00 42.39 3.86
5160 9878 2.513204 CATGGCTCGGTGCTGGAG 60.513 66.667 1.77 0.00 42.39 3.86
5161 9879 2.685017 ATGGCTCGGTGCTGGAGA 60.685 61.111 1.77 0.00 42.39 3.71
5162 9880 3.023949 ATGGCTCGGTGCTGGAGAC 62.024 63.158 1.77 1.47 40.09 3.36
5163 9881 4.803426 GGCTCGGTGCTGGAGACG 62.803 72.222 1.77 0.00 42.39 4.18
5164 9882 3.749064 GCTCGGTGCTGGAGACGA 61.749 66.667 0.00 0.00 38.95 4.20
5165 9883 2.179517 CTCGGTGCTGGAGACGAC 59.820 66.667 0.00 0.00 33.27 4.34
5166 9884 3.669036 CTCGGTGCTGGAGACGACG 62.669 68.421 0.00 0.00 33.27 5.12
5167 9885 3.733960 CGGTGCTGGAGACGACGA 61.734 66.667 0.00 0.00 0.00 4.20
5168 9886 2.179517 GGTGCTGGAGACGACGAG 59.820 66.667 0.00 0.00 0.00 4.18
5169 9887 2.179517 GTGCTGGAGACGACGAGG 59.820 66.667 0.00 0.00 0.00 4.63
5170 9888 3.749064 TGCTGGAGACGACGAGGC 61.749 66.667 0.00 0.00 0.00 4.70
5171 9889 4.500116 GCTGGAGACGACGAGGCC 62.500 72.222 0.00 0.00 0.00 5.19
5172 9890 4.180946 CTGGAGACGACGAGGCCG 62.181 72.222 0.00 0.00 42.50 6.13
5173 9891 4.710167 TGGAGACGACGAGGCCGA 62.710 66.667 0.00 0.00 39.50 5.54
5174 9892 3.878519 GGAGACGACGAGGCCGAG 61.879 72.222 0.00 0.00 39.50 4.63
5175 9893 3.878519 GAGACGACGAGGCCGAGG 61.879 72.222 0.00 0.00 39.50 4.63
5180 9898 3.827898 GACGAGGCCGAGGGACTG 61.828 72.222 0.00 0.00 43.92 3.51
5183 9901 2.043248 GAGGCCGAGGGACTGGTA 60.043 66.667 0.00 0.00 43.92 3.25
5184 9902 1.457831 GAGGCCGAGGGACTGGTAT 60.458 63.158 0.00 0.00 43.92 2.73
5185 9903 0.178970 GAGGCCGAGGGACTGGTATA 60.179 60.000 0.00 0.00 43.92 1.47
5186 9904 0.487772 AGGCCGAGGGACTGGTATAT 59.512 55.000 0.00 0.00 41.17 0.86
5187 9905 1.132817 AGGCCGAGGGACTGGTATATT 60.133 52.381 0.00 0.00 41.17 1.28
5188 9906 1.275573 GGCCGAGGGACTGGTATATTC 59.724 57.143 0.00 0.00 41.55 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.698506 CGAGGTCCTATCTCAGCCTT 58.301 55.000 0.00 0.00 0.00 4.35
13 14 0.468648 TCGAGCGAGGTCCTATCTCA 59.531 55.000 16.08 5.05 0.00 3.27
17 18 0.180642 TGTCTCGAGCGAGGTCCTAT 59.819 55.000 18.57 0.00 42.20 2.57
30 31 1.199327 TCTTAGCGTTGTCCTGTCTCG 59.801 52.381 0.00 0.00 0.00 4.04
44 45 1.077858 AGCTTGCTGCCCTCTTAGC 60.078 57.895 0.00 0.00 44.23 3.09
48 49 2.033757 CACAGCTTGCTGCCCTCT 59.966 61.111 20.92 0.00 44.23 3.69
153 154 2.004808 CTGATCCGTAGCAGTGCCGA 62.005 60.000 12.58 2.73 0.00 5.54
154 155 1.589993 CTGATCCGTAGCAGTGCCG 60.590 63.158 12.58 9.25 0.00 5.69
155 156 1.884926 GCTGATCCGTAGCAGTGCC 60.885 63.158 12.58 0.00 40.81 5.01
156 157 1.142748 AGCTGATCCGTAGCAGTGC 59.857 57.895 7.13 7.13 43.53 4.40
157 158 0.529337 CCAGCTGATCCGTAGCAGTG 60.529 60.000 17.39 0.00 43.53 3.66
158 159 1.680522 CCCAGCTGATCCGTAGCAGT 61.681 60.000 17.39 0.00 43.53 4.40
159 160 1.068753 CCCAGCTGATCCGTAGCAG 59.931 63.158 17.39 0.00 43.53 4.24
160 161 3.094062 GCCCAGCTGATCCGTAGCA 62.094 63.158 17.39 0.00 43.53 3.49
161 162 2.280457 GCCCAGCTGATCCGTAGC 60.280 66.667 17.39 2.34 41.43 3.58
162 163 1.040646 TAAGCCCAGCTGATCCGTAG 58.959 55.000 17.39 0.00 39.62 3.51
163 164 0.750850 GTAAGCCCAGCTGATCCGTA 59.249 55.000 17.39 2.66 39.62 4.02
164 165 1.264749 TGTAAGCCCAGCTGATCCGT 61.265 55.000 17.39 3.66 39.62 4.69
165 166 0.531532 CTGTAAGCCCAGCTGATCCG 60.532 60.000 17.39 0.00 39.62 4.18
166 167 0.179034 CCTGTAAGCCCAGCTGATCC 60.179 60.000 17.39 2.46 39.62 3.36
200 202 0.689623 CTCACCCCTTCTGCTTGTCT 59.310 55.000 0.00 0.00 0.00 3.41
210 212 1.308216 CATCCTCCCCTCACCCCTT 60.308 63.158 0.00 0.00 0.00 3.95
300 314 3.702048 CTTCCTCCCGCCGAACCA 61.702 66.667 0.00 0.00 0.00 3.67
346 360 0.542467 ATTGCCATCCAACAGCCACA 60.542 50.000 0.00 0.00 35.99 4.17
416 430 1.404391 ACTACGACTTGGGTATCAGCG 59.596 52.381 0.00 0.00 0.00 5.18
471 516 3.359523 CGTGGTCTGGGTCGACGA 61.360 66.667 9.92 0.00 38.81 4.20
478 523 0.250124 TAGCAACAACGTGGTCTGGG 60.250 55.000 0.00 0.00 0.00 4.45
495 540 0.247736 GGGCATCCATAGGAGCGTAG 59.752 60.000 0.00 0.00 34.05 3.51
542 587 5.010112 GTCGAGATCTAGGAAACATCCATCA 59.990 44.000 0.00 0.00 0.00 3.07
595 640 2.608090 CTGTCGTCTCTGCATCGTAGTA 59.392 50.000 0.00 0.00 0.00 1.82
596 641 1.398739 CTGTCGTCTCTGCATCGTAGT 59.601 52.381 0.00 0.00 0.00 2.73
597 642 1.858000 GCTGTCGTCTCTGCATCGTAG 60.858 57.143 0.00 0.00 33.55 3.51
632 677 4.367450 GTTATCTGTCTCAAGCTGGCTAG 58.633 47.826 0.00 0.00 0.00 3.42
633 678 3.133003 GGTTATCTGTCTCAAGCTGGCTA 59.867 47.826 0.00 0.00 0.00 3.93
673 735 1.679898 GTGGGACTGGGAGTGGAAG 59.320 63.158 0.00 0.00 0.00 3.46
674 736 1.846124 GGTGGGACTGGGAGTGGAA 60.846 63.158 0.00 0.00 0.00 3.53
675 737 2.203938 GGTGGGACTGGGAGTGGA 60.204 66.667 0.00 0.00 0.00 4.02
676 738 2.129555 CTTGGTGGGACTGGGAGTGG 62.130 65.000 0.00 0.00 0.00 4.00
677 739 1.127567 TCTTGGTGGGACTGGGAGTG 61.128 60.000 0.00 0.00 0.00 3.51
678 740 0.401395 TTCTTGGTGGGACTGGGAGT 60.401 55.000 0.00 0.00 0.00 3.85
679 741 0.326264 CTTCTTGGTGGGACTGGGAG 59.674 60.000 0.00 0.00 0.00 4.30
685 747 1.978580 TCTTCCTCTTCTTGGTGGGAC 59.021 52.381 0.00 0.00 0.00 4.46
700 762 1.472376 CCATGCTCGTCCTCTTCTTCC 60.472 57.143 0.00 0.00 0.00 3.46
706 768 2.685017 TGGCCATGCTCGTCCTCT 60.685 61.111 0.00 0.00 0.00 3.69
707 769 2.512515 GTGGCCATGCTCGTCCTC 60.513 66.667 9.72 0.00 0.00 3.71
708 770 4.457496 CGTGGCCATGCTCGTCCT 62.457 66.667 13.11 0.00 0.00 3.85
767 832 2.420890 CATGAGAGGAGGCGGCTC 59.579 66.667 29.56 29.56 0.00 4.70
782 847 1.141881 CACGGACGGAGCTAAGCAT 59.858 57.895 0.00 0.00 0.00 3.79
815 880 0.957395 CAGAAATGGTCAGCTGGCGT 60.957 55.000 15.13 0.68 0.00 5.68
834 899 1.152989 CGCCATGAGAAGAGCAGAGC 61.153 60.000 0.00 0.00 0.00 4.09
875 940 4.742201 GCTCCGGCGAGTTCTGCA 62.742 66.667 9.30 0.00 38.49 4.41
914 982 1.298488 GGCGAGTTCTCCGACGATC 60.298 63.158 0.00 0.00 0.00 3.69
1283 1351 2.780643 CGTAGAAGACGCGGACGA 59.219 61.111 12.47 0.00 46.27 4.20
1305 1373 2.037381 GGAGACGAAGAAGGTGAGGTTT 59.963 50.000 0.00 0.00 0.00 3.27
1490 1573 6.072563 GCCATGTAACAAGGCAATGAAAAATT 60.073 34.615 10.18 0.00 46.03 1.82
1492 1575 4.754114 GCCATGTAACAAGGCAATGAAAAA 59.246 37.500 10.18 0.00 46.03 1.94
1503 1622 7.750769 CCAATTAAATTTGGCCATGTAACAAG 58.249 34.615 6.09 0.00 39.76 3.16
1528 1647 0.527565 AGTGCATCATTTTGACCGGC 59.472 50.000 0.00 0.00 0.00 6.13
1537 1664 6.373774 CCTAGTTTCTTTCTGAGTGCATCATT 59.626 38.462 0.00 0.00 37.28 2.57
1544 1671 8.433421 TTGTTAACCTAGTTTCTTTCTGAGTG 57.567 34.615 2.48 0.00 0.00 3.51
1589 1902 9.445786 CACCAGTAATTGTACACAAGTTTTAAG 57.554 33.333 0.00 0.00 39.47 1.85
1592 1905 7.399245 ACACCAGTAATTGTACACAAGTTTT 57.601 32.000 0.00 0.00 39.47 2.43
1593 1906 7.399245 AACACCAGTAATTGTACACAAGTTT 57.601 32.000 0.00 0.00 39.47 2.66
1596 1909 7.022055 TCAAACACCAGTAATTGTACACAAG 57.978 36.000 0.00 0.00 39.47 3.16
1599 1912 5.856455 GCATCAAACACCAGTAATTGTACAC 59.144 40.000 0.00 0.00 32.12 2.90
1605 1956 3.611530 GCACGCATCAAACACCAGTAATT 60.612 43.478 0.00 0.00 0.00 1.40
1606 1957 2.095263 GCACGCATCAAACACCAGTAAT 60.095 45.455 0.00 0.00 0.00 1.89
1609 1960 1.100463 TGCACGCATCAAACACCAGT 61.100 50.000 0.00 0.00 0.00 4.00
1639 1990 4.599041 TGGCAGTTTAAACAGAGGCATAT 58.401 39.130 20.06 0.00 31.74 1.78
1640 1991 4.027674 TGGCAGTTTAAACAGAGGCATA 57.972 40.909 20.06 8.22 31.74 3.14
1641 1992 2.875296 TGGCAGTTTAAACAGAGGCAT 58.125 42.857 20.06 0.00 31.74 4.40
1643 1994 3.726291 TTTGGCAGTTTAAACAGAGGC 57.274 42.857 20.06 19.17 0.00 4.70
1645 1996 4.668289 ACGTTTTGGCAGTTTAAACAGAG 58.332 39.130 20.06 10.43 32.67 3.35
1650 2001 9.968870 AAATATAAGACGTTTTGGCAGTTTAAA 57.031 25.926 0.83 0.00 0.00 1.52
1653 2004 9.567848 CATAAATATAAGACGTTTTGGCAGTTT 57.432 29.630 0.83 0.00 0.00 2.66
1654 2005 8.952278 TCATAAATATAAGACGTTTTGGCAGTT 58.048 29.630 0.83 0.00 0.00 3.16
1655 2006 8.500753 TCATAAATATAAGACGTTTTGGCAGT 57.499 30.769 0.83 0.00 0.00 4.40
1656 2007 9.221775 GTTCATAAATATAAGACGTTTTGGCAG 57.778 33.333 0.83 0.00 0.00 4.85
1657 2008 8.731605 TGTTCATAAATATAAGACGTTTTGGCA 58.268 29.630 0.83 0.00 0.00 4.92
1658 2009 9.221775 CTGTTCATAAATATAAGACGTTTTGGC 57.778 33.333 0.83 0.00 0.00 4.52
1662 2013 9.326413 CCCTCTGTTCATAAATATAAGACGTTT 57.674 33.333 0.00 0.00 0.00 3.60
1663 2014 8.483758 ACCCTCTGTTCATAAATATAAGACGTT 58.516 33.333 0.00 0.00 0.00 3.99
1664 2015 7.926555 CACCCTCTGTTCATAAATATAAGACGT 59.073 37.037 0.00 0.00 0.00 4.34
1665 2016 7.926555 ACACCCTCTGTTCATAAATATAAGACG 59.073 37.037 0.00 0.00 0.00 4.18
1671 2022 7.499232 GCAAGTACACCCTCTGTTCATAAATAT 59.501 37.037 0.00 0.00 33.91 1.28
1672 2023 6.821665 GCAAGTACACCCTCTGTTCATAAATA 59.178 38.462 0.00 0.00 33.91 1.40
1673 2024 5.648092 GCAAGTACACCCTCTGTTCATAAAT 59.352 40.000 0.00 0.00 33.91 1.40
1674 2025 5.001232 GCAAGTACACCCTCTGTTCATAAA 58.999 41.667 0.00 0.00 33.91 1.40
1675 2026 4.286032 AGCAAGTACACCCTCTGTTCATAA 59.714 41.667 0.00 0.00 33.91 1.90
1676 2027 3.838317 AGCAAGTACACCCTCTGTTCATA 59.162 43.478 0.00 0.00 33.91 2.15
1677 2028 2.639839 AGCAAGTACACCCTCTGTTCAT 59.360 45.455 0.00 0.00 33.91 2.57
1678 2029 2.047061 AGCAAGTACACCCTCTGTTCA 58.953 47.619 0.00 0.00 33.91 3.18
1679 2030 2.841442 AGCAAGTACACCCTCTGTTC 57.159 50.000 0.00 0.00 33.91 3.18
1680 2031 5.685075 GCATATAGCAAGTACACCCTCTGTT 60.685 44.000 0.00 0.00 44.79 3.16
1681 2032 4.202264 GCATATAGCAAGTACACCCTCTGT 60.202 45.833 0.00 0.00 44.79 3.41
1682 2033 4.310769 GCATATAGCAAGTACACCCTCTG 58.689 47.826 0.00 0.00 44.79 3.35
1683 2034 4.608948 GCATATAGCAAGTACACCCTCT 57.391 45.455 0.00 0.00 44.79 3.69
1696 2047 6.434652 TCTCCTACTACTTGGAAGCATATAGC 59.565 42.308 0.00 0.00 46.19 2.97
1697 2048 8.588290 ATCTCCTACTACTTGGAAGCATATAG 57.412 38.462 0.00 0.00 31.23 1.31
1698 2049 8.958060 AATCTCCTACTACTTGGAAGCATATA 57.042 34.615 0.00 0.00 31.23 0.86
1715 2066 9.426837 CAATTTGCTCAAAATTCAAATCTCCTA 57.573 29.630 0.00 0.00 44.88 2.94
1779 2161 0.684535 TGACGTGTCATGACCCACAT 59.315 50.000 22.85 3.95 40.17 3.21
1848 2709 4.079253 GTTCAGAATCTTTGGGTGGCTAA 58.921 43.478 0.00 0.00 0.00 3.09
1857 2718 8.755018 GTTTTATGGTTGTGTTCAGAATCTTTG 58.245 33.333 0.00 0.00 0.00 2.77
1867 2728 6.575162 ATCCTGAGTTTTATGGTTGTGTTC 57.425 37.500 0.00 0.00 0.00 3.18
1930 2803 0.106519 AACTCACAGGGGCCATATGC 60.107 55.000 4.39 0.00 40.16 3.14
1998 3033 5.844004 AGTACTCTCAAGTGGTGTTAACTG 58.156 41.667 7.22 0.00 36.92 3.16
2003 3038 7.780745 AGCTATATAGTACTCTCAAGTGGTGTT 59.219 37.037 11.38 0.00 36.92 3.32
2004 3039 7.291566 AGCTATATAGTACTCTCAAGTGGTGT 58.708 38.462 11.38 0.00 36.92 4.16
2020 3055 8.091449 CAGAACCAGGAACCTTAAGCTATATAG 58.909 40.741 5.30 5.30 0.00 1.31
2029 3064 4.457466 GTTGTCAGAACCAGGAACCTTAA 58.543 43.478 0.00 0.00 0.00 1.85
2072 4010 1.022735 GGAAGGCATGAGCATGTCAG 58.977 55.000 16.42 0.00 45.39 3.51
2078 4675 2.429250 CAATGAATGGAAGGCATGAGCA 59.571 45.455 0.00 0.00 44.61 4.26
2103 4708 8.034804 CGGGATTTCTTTATTTTCTCCATGTTT 58.965 33.333 0.00 0.00 0.00 2.83
2112 4717 6.262193 TGGACACGGGATTTCTTTATTTTC 57.738 37.500 0.00 0.00 0.00 2.29
2128 6047 2.698855 ATTTCCCTGAGATGGACACG 57.301 50.000 0.00 0.00 0.00 4.49
2155 6075 9.566432 AATCTTATTCTGCCTGTCTTAATTAGG 57.434 33.333 0.00 0.00 34.67 2.69
2169 6089 8.693542 AAATGTTTGTGCTAATCTTATTCTGC 57.306 30.769 0.00 0.00 0.00 4.26
2184 6104 7.159437 TCGTCAAAGCAAATAAATGTTTGTG 57.841 32.000 4.85 0.00 40.38 3.33
2201 6184 5.939883 ACCATTGATTTCTCTGATCGTCAAA 59.060 36.000 0.00 0.00 0.00 2.69
2206 6189 6.426980 TCAAACCATTGATTTCTCTGATCG 57.573 37.500 0.00 0.00 40.59 3.69
2245 6384 4.724399 TCAGGGAAAACTGCTCAAACATA 58.276 39.130 0.00 0.00 38.36 2.29
2287 6426 1.965643 CCTGGTGGGAATATGCATTGG 59.034 52.381 3.54 0.00 37.23 3.16
2310 6680 0.250513 GCCTTTCATCCTCGTGGAGT 59.749 55.000 12.42 0.00 46.91 3.85
2550 6920 0.624254 TGACGAGAGGGCTTCCTAGA 59.376 55.000 0.00 0.00 41.93 2.43
2553 6923 2.355193 GCTGACGAGAGGGCTTCCT 61.355 63.158 0.00 0.00 45.23 3.36
2556 6926 3.394836 GGGCTGACGAGAGGGCTT 61.395 66.667 0.00 0.00 0.00 4.35
2703 7073 2.047655 TTGTACTTCTGCCCGCCG 60.048 61.111 0.00 0.00 0.00 6.46
2705 7075 0.727398 GATGTTGTACTTCTGCCCGC 59.273 55.000 0.00 0.00 0.00 6.13
2754 7124 6.703607 CGTTTTTCTCATATGCCTCTGTATCT 59.296 38.462 0.00 0.00 0.00 1.98
3079 7480 1.059692 CGCAAGCGAATACAGTGACAG 59.940 52.381 9.11 0.00 42.83 3.51
3229 7634 0.879839 CGTATGGCATGCCGTGATGA 60.880 55.000 36.66 17.75 39.42 2.92
3233 7638 0.790207 GATACGTATGGCATGCCGTG 59.210 55.000 36.66 24.88 39.42 4.94
3234 7639 0.679505 AGATACGTATGGCATGCCGT 59.320 50.000 33.05 33.05 39.42 5.68
3235 7640 1.070821 CAGATACGTATGGCATGCCG 58.929 55.000 30.87 20.90 39.42 5.69
3248 7662 4.009675 TGTGGATTTGGTGCTTCAGATAC 58.990 43.478 0.00 0.00 0.00 2.24
3249 7663 4.299586 TGTGGATTTGGTGCTTCAGATA 57.700 40.909 0.00 0.00 0.00 1.98
3255 7669 2.362077 GTGAGTTGTGGATTTGGTGCTT 59.638 45.455 0.00 0.00 0.00 3.91
3263 7677 4.520492 GTGGAAGAATGTGAGTTGTGGATT 59.480 41.667 0.00 0.00 0.00 3.01
3299 7721 3.834231 TCTGTGATGATGTTCAGTCCTGA 59.166 43.478 0.00 0.00 37.91 3.86
3488 7914 7.767261 TGTTAAATACACTATGATGGCCAAAC 58.233 34.615 10.96 8.09 0.00 2.93
3547 8046 5.756347 CCTGCCATGTTCCAAAATATTGATG 59.244 40.000 0.00 0.00 38.94 3.07
3548 8047 5.426185 ACCTGCCATGTTCCAAAATATTGAT 59.574 36.000 0.00 0.00 38.94 2.57
3549 8048 4.776837 ACCTGCCATGTTCCAAAATATTGA 59.223 37.500 0.00 0.00 38.94 2.57
3552 8051 3.451902 CCACCTGCCATGTTCCAAAATAT 59.548 43.478 0.00 0.00 0.00 1.28
3553 8052 2.830923 CCACCTGCCATGTTCCAAAATA 59.169 45.455 0.00 0.00 0.00 1.40
3862 8430 1.665679 CACGGGCATGTTGATGAGTAC 59.334 52.381 0.00 0.00 0.00 2.73
3972 8540 5.354513 CCACCAGTCACGTCGATATCTATAT 59.645 44.000 0.00 0.00 0.00 0.86
4213 8782 4.057432 CACAATTCCAATTTTTCCAGCGT 58.943 39.130 0.00 0.00 0.00 5.07
4215 8784 4.152938 GCTCACAATTCCAATTTTTCCAGC 59.847 41.667 0.00 0.00 0.00 4.85
4220 8789 5.124645 TGCTTGCTCACAATTCCAATTTTT 58.875 33.333 0.00 0.00 34.61 1.94
4242 8811 6.584184 ACATTCGCTATTTACATCGATCTCTG 59.416 38.462 0.00 0.00 0.00 3.35
4243 8812 6.682746 ACATTCGCTATTTACATCGATCTCT 58.317 36.000 0.00 0.00 0.00 3.10
4273 8842 6.437162 CCCATTTCTCATCTTTAAAAGGTCCA 59.563 38.462 0.00 0.00 0.00 4.02
4307 8876 9.674068 TTGTGGTACTTTGCACAATAGAATATA 57.326 29.630 10.27 0.00 33.30 0.86
4308 8877 8.574251 TTGTGGTACTTTGCACAATAGAATAT 57.426 30.769 10.27 0.00 33.30 1.28
4343 8939 6.072112 TGTTGCCACTAAAGATTGTTCTTC 57.928 37.500 0.00 0.00 41.42 2.87
4392 8988 8.728596 ATCAGTTATTTACTAGTAGCTGGGAT 57.271 34.615 2.23 0.35 34.56 3.85
4413 9009 6.016024 TGGACTTCAAACAATCAAGGAATCAG 60.016 38.462 0.00 0.00 0.00 2.90
4487 9087 7.719483 ACATTGTGTGTGAGAAATTCAGAAAT 58.281 30.769 0.00 0.00 40.28 2.17
4565 9165 1.334160 GGTGAATGGAACCGGGTTTT 58.666 50.000 14.69 4.33 0.00 2.43
4581 9190 1.962807 TGCAAGGGTTTCATTCTGGTG 59.037 47.619 0.00 0.00 0.00 4.17
4621 9251 3.251004 GCAACTGACAAGTCGAGGAATTT 59.749 43.478 0.00 0.00 34.77 1.82
4698 9357 5.105716 TGCTAATGTCAGAGGAGTAGTTGAC 60.106 44.000 0.00 0.00 40.17 3.18
4708 9367 2.762887 TCTGGACTGCTAATGTCAGAGG 59.237 50.000 0.00 0.00 36.26 3.69
4744 9411 5.612725 ACAACATGGTTCCATTTCAGTTT 57.387 34.783 1.11 0.00 0.00 2.66
4747 9414 7.825681 TGTAATACAACATGGTTCCATTTCAG 58.174 34.615 1.11 0.00 0.00 3.02
4793 9466 9.321562 TCACCGTGAAATAAGAAGATTATTACC 57.678 33.333 0.00 0.00 0.00 2.85
4795 9468 9.878667 TGTCACCGTGAAATAAGAAGATTATTA 57.121 29.630 1.88 0.00 0.00 0.98
4796 9469 8.786826 TGTCACCGTGAAATAAGAAGATTATT 57.213 30.769 1.88 0.00 0.00 1.40
4852 9542 8.534333 TTATTCTGTCAAGTTGTCATGAGTAC 57.466 34.615 0.00 0.00 0.00 2.73
4865 9555 8.329203 AGCCTAAAACTTCTTATTCTGTCAAG 57.671 34.615 0.00 0.00 0.00 3.02
4902 9597 8.626526 TGAATAGTTAGTAATGCGATGTGTAGA 58.373 33.333 0.00 0.00 0.00 2.59
4922 9617 7.406031 TCAGAGTAAACCCTACTGTGAATAG 57.594 40.000 8.76 0.00 42.41 1.73
4935 9637 5.245526 TCTGGTAAGAGGTTCAGAGTAAACC 59.754 44.000 0.00 0.00 45.41 3.27
5003 9709 1.745489 GGGACAGGTTCGGTCATGC 60.745 63.158 0.00 0.00 37.00 4.06
5012 9720 1.007359 GGAGAGGAGTAGGGACAGGTT 59.993 57.143 0.00 0.00 0.00 3.50
5082 9790 0.768622 ATTTTGTCAGTCCCCGACCA 59.231 50.000 0.00 0.00 32.18 4.02
5150 9868 3.669036 CTCGTCGTCTCCAGCACCG 62.669 68.421 0.00 0.00 0.00 4.94
5151 9869 2.179517 CTCGTCGTCTCCAGCACC 59.820 66.667 0.00 0.00 0.00 5.01
5153 9871 3.749064 GCCTCGTCGTCTCCAGCA 61.749 66.667 0.00 0.00 0.00 4.41
5154 9872 4.500116 GGCCTCGTCGTCTCCAGC 62.500 72.222 0.00 0.00 0.00 4.85
5155 9873 4.180946 CGGCCTCGTCGTCTCCAG 62.181 72.222 0.00 0.00 0.00 3.86
5156 9874 4.710167 TCGGCCTCGTCGTCTCCA 62.710 66.667 0.00 0.00 37.69 3.86
5157 9875 3.878519 CTCGGCCTCGTCGTCTCC 61.879 72.222 0.00 0.00 37.69 3.71
5158 9876 3.878519 CCTCGGCCTCGTCGTCTC 61.879 72.222 0.00 0.00 37.69 3.36
5163 9881 3.827898 CAGTCCCTCGGCCTCGTC 61.828 72.222 0.00 0.00 37.69 4.20
5165 9883 3.874501 TATACCAGTCCCTCGGCCTCG 62.875 61.905 0.00 0.00 37.82 4.63
5166 9884 0.178970 TATACCAGTCCCTCGGCCTC 60.179 60.000 0.00 0.00 0.00 4.70
5167 9885 0.487772 ATATACCAGTCCCTCGGCCT 59.512 55.000 0.00 0.00 0.00 5.19
5168 9886 1.275573 GAATATACCAGTCCCTCGGCC 59.724 57.143 0.00 0.00 0.00 6.13
5169 9887 2.745515 GAATATACCAGTCCCTCGGC 57.254 55.000 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.