Multiple sequence alignment - TraesCS1A01G170300

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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 TraesCS1A01G170300 chr1A 100.000 7859 0 0 1 7859 304037374 304029516 0.000000e+00 14513.0
1 TraesCS1A01G170300 chr1D 96.173 2613 57 17 1844 4447 240123690 240121112 0.000000e+00 4231.0
2 TraesCS1A01G170300 chr1D 95.833 1104 40 5 6353 7454 240118960 240117861 0.000000e+00 1779.0
3 TraesCS1A01G170300 chr1D 92.393 1078 33 23 780 1855 240125672 240124642 0.000000e+00 1491.0
4 TraesCS1A01G170300 chr1D 95.941 813 22 3 4492 5304 240121121 240120320 0.000000e+00 1308.0
5 TraesCS1A01G170300 chr1D 92.094 721 40 8 20 736 240126379 240125672 0.000000e+00 1000.0
6 TraesCS1A01G170300 chr1D 92.441 635 32 7 5736 6359 240119892 240119263 0.000000e+00 893.0
7 TraesCS1A01G170300 chr1D 92.786 402 11 4 5302 5702 240120280 240119896 4.120000e-157 566.0
8 TraesCS1A01G170300 chr1D 93.443 366 24 0 7494 7859 240117859 240117494 1.930000e-150 544.0
9 TraesCS1A01G170300 chr1B 93.047 1697 77 22 20 1694 334312547 334310870 0.000000e+00 2442.0
10 TraesCS1A01G170300 chr1B 92.806 1251 60 11 1730 2970 334310873 334309643 0.000000e+00 1784.0
11 TraesCS1A01G170300 chr1B 94.291 1016 41 8 3485 4495 334309148 334308145 0.000000e+00 1539.0
12 TraesCS1A01G170300 chr1B 93.293 656 40 3 4651 5304 334307563 334306910 0.000000e+00 965.0
13 TraesCS1A01G170300 chr1B 90.634 662 52 5 6392 7053 334305785 334305134 0.000000e+00 870.0
14 TraesCS1A01G170300 chr1B 95.701 442 12 5 3058 3494 334309605 334309166 0.000000e+00 704.0
15 TraesCS1A01G170300 chr1B 87.643 526 46 10 5824 6341 334306299 334305785 1.890000e-165 593.0
16 TraesCS1A01G170300 chr1B 93.294 343 13 6 5486 5823 334306670 334306333 1.520000e-136 497.0
17 TraesCS1A01G170300 chr1B 96.429 140 5 0 4487 4626 334307698 334307559 1.710000e-56 231.0
18 TraesCS1A01G170300 chr1B 87.200 125 7 5 7041 7165 334304060 334303945 4.950000e-27 134.0
19 TraesCS1A01G170300 chr2A 96.471 85 3 0 5403 5487 608647358 608647274 2.960000e-29 141.0
20 TraesCS1A01G170300 chr2A 95.294 85 4 0 5403 5487 608647274 608647358 1.380000e-27 135.0
21 TraesCS1A01G170300 chr6B 94.318 88 5 0 5400 5487 560192916 560192829 1.380000e-27 135.0
22 TraesCS1A01G170300 chr2B 95.294 85 4 0 5403 5487 546987571 546987487 1.380000e-27 135.0
23 TraesCS1A01G170300 chr2D 95.294 85 3 1 5403 5487 467971426 467971343 4.950000e-27 134.0
24 TraesCS1A01G170300 chr2D 96.970 33 1 0 761 793 234936569 234936601 1.000000e-03 56.5
25 TraesCS1A01G170300 chr6A 93.182 88 6 0 5400 5487 500507918 500508005 6.400000e-26 130.0
26 TraesCS1A01G170300 chr6A 74.000 300 60 16 499 790 22430721 22430432 1.080000e-18 106.0
27 TraesCS1A01G170300 chr4A 92.308 91 7 0 5403 5493 90592984 90592894 6.400000e-26 130.0
28 TraesCS1A01G170300 chr3D 94.118 85 5 0 5403 5487 25130689 25130773 6.400000e-26 130.0
29 TraesCS1A01G170300 chr4D 74.061 293 58 14 506 792 363298561 363298841 3.880000e-18 104.0
30 TraesCS1A01G170300 chr7B 77.778 180 29 10 499 673 97197446 97197619 5.020000e-17 100.0


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 TraesCS1A01G170300 chr1A 304029516 304037374 7858 True 14513.0 14513 100.0000 1 7859 1 chr1A.!!$R1 7858
1 TraesCS1A01G170300 chr1D 240117494 240126379 8885 True 1476.5 4231 93.8880 20 7859 8 chr1D.!!$R1 7839
2 TraesCS1A01G170300 chr1B 334303945 334312547 8602 True 975.9 2442 92.4338 20 7165 10 chr1B.!!$R1 7145

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
567 574 0.026285 GGTCGTTTCGATTCGCATGG 59.974 55.000 0.00 0.0 38.42 3.66 F
1292 1312 0.478072 TTCTTCAAGGCCTGCTCCAA 59.522 50.000 5.69 0.0 0.00 3.53 F
2379 3377 0.038067 ACTTGGCGCACATACGTACA 60.038 50.000 10.83 0.0 34.88 2.90 F
4232 5328 3.071602 GCTTATCCTGCTTCTGGGTATCA 59.928 47.826 0.00 0.0 0.00 2.15 F
5928 7677 0.250684 TGCATGTCATGGTGTCCGTT 60.251 50.000 14.64 0.0 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1733 1.031235 CACACAATTCACACCAGCCA 58.969 50.000 0.00 0.0 0.00 4.75 R
2655 3667 0.321564 CTTGATGGTGCGAACCTGGA 60.322 55.000 15.35 0.0 0.00 3.86 R
4362 5458 3.368739 GGATTCAGACTGGCCCATTTTTG 60.369 47.826 0.00 0.0 0.00 2.44 R
6156 7907 1.721926 GGCTTAATCGCTAGCGTGATC 59.278 52.381 34.10 19.2 39.36 2.92 R
7584 10740 0.458370 GGAAATGTTCCGCACCATGC 60.458 55.000 0.00 0.0 40.59 4.06 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
17 18 4.655527 CGCTGTCTTCCGTGACTT 57.344 55.556 0.00 0.00 37.79 3.01
18 19 2.435741 CGCTGTCTTCCGTGACTTC 58.564 57.895 0.00 0.00 37.79 3.01
19 20 0.039074 CGCTGTCTTCCGTGACTTCT 60.039 55.000 0.00 0.00 37.79 2.85
20 21 1.704070 GCTGTCTTCCGTGACTTCTC 58.296 55.000 0.00 0.00 37.79 2.87
21 22 1.670380 GCTGTCTTCCGTGACTTCTCC 60.670 57.143 0.00 0.00 37.79 3.71
22 23 1.613925 CTGTCTTCCGTGACTTCTCCA 59.386 52.381 0.00 0.00 37.79 3.86
23 24 1.613925 TGTCTTCCGTGACTTCTCCAG 59.386 52.381 0.00 0.00 37.79 3.86
24 25 1.614413 GTCTTCCGTGACTTCTCCAGT 59.386 52.381 0.00 0.00 39.07 4.00
29 30 1.336332 CCGTGACTTCTCCAGTGACTG 60.336 57.143 5.42 5.42 37.47 3.51
47 48 1.063616 CTGCTTCACCATGCTGATTCG 59.936 52.381 0.00 0.00 0.00 3.34
258 260 4.202151 GGGGAGATGGCAATGTTTGTATTC 60.202 45.833 0.00 0.00 0.00 1.75
366 368 2.289506 GCTAGGGGAGTTCGACTGTTTT 60.290 50.000 0.00 0.00 0.00 2.43
496 499 1.121407 GGGCAAACTCTTGGGGCTTT 61.121 55.000 0.00 0.00 32.76 3.51
497 500 0.033920 GGCAAACTCTTGGGGCTTTG 59.966 55.000 0.00 0.00 32.76 2.77
498 501 1.039856 GCAAACTCTTGGGGCTTTGA 58.960 50.000 0.00 0.00 32.76 2.69
500 503 2.037641 GCAAACTCTTGGGGCTTTGATT 59.962 45.455 0.00 0.00 32.76 2.57
501 504 3.494924 GCAAACTCTTGGGGCTTTGATTT 60.495 43.478 0.00 0.00 32.76 2.17
502 505 4.060205 CAAACTCTTGGGGCTTTGATTTG 58.940 43.478 0.00 0.00 0.00 2.32
503 506 3.243359 ACTCTTGGGGCTTTGATTTGA 57.757 42.857 0.00 0.00 0.00 2.69
504 507 3.782992 ACTCTTGGGGCTTTGATTTGAT 58.217 40.909 0.00 0.00 0.00 2.57
517 523 7.173735 GGCTTTGATTTGATGGAATTTTGAAGT 59.826 33.333 0.00 0.00 0.00 3.01
541 548 9.374711 AGTATTGGAAACCTTAGGAATTTTTCA 57.625 29.630 4.77 0.00 0.00 2.69
556 563 6.253512 GGAATTTTTCATATGCTGGTCGTTTC 59.746 38.462 0.00 0.00 0.00 2.78
563 570 1.058903 GCTGGTCGTTTCGATTCGC 59.941 57.895 0.00 1.83 38.42 4.70
567 574 0.026285 GGTCGTTTCGATTCGCATGG 59.974 55.000 0.00 0.00 38.42 3.66
579 586 5.527214 TCGATTCGCATGGTTGAATTCTATT 59.473 36.000 7.05 0.00 35.06 1.73
620 627 9.066892 AGCATTCGTTTGTATTACATTCCATAT 57.933 29.630 0.00 0.00 0.00 1.78
652 659 4.098807 GCACCCACTCAAACCTCTTAAAAA 59.901 41.667 0.00 0.00 0.00 1.94
658 665 7.014230 CCCACTCAAACCTCTTAAAAAGAATCA 59.986 37.037 0.00 0.00 37.02 2.57
695 706 3.383620 TGCAGGCAAACCAAGTTAATG 57.616 42.857 0.00 0.00 39.06 1.90
696 707 2.697751 TGCAGGCAAACCAAGTTAATGT 59.302 40.909 0.00 0.00 39.06 2.71
697 708 3.891977 TGCAGGCAAACCAAGTTAATGTA 59.108 39.130 0.00 0.00 39.06 2.29
698 709 4.526262 TGCAGGCAAACCAAGTTAATGTAT 59.474 37.500 0.00 0.00 39.06 2.29
699 710 5.011533 TGCAGGCAAACCAAGTTAATGTATT 59.988 36.000 0.00 0.00 39.06 1.89
700 711 5.348451 GCAGGCAAACCAAGTTAATGTATTG 59.652 40.000 0.00 0.00 39.06 1.90
735 752 6.040278 TCAAAAGAACATGACATTGCAACCTA 59.960 34.615 0.00 0.00 0.00 3.08
743 760 6.015180 ACATGACATTGCAACCTATGTTTTCT 60.015 34.615 0.00 0.00 37.50 2.52
744 761 6.403866 TGACATTGCAACCTATGTTTTCTT 57.596 33.333 0.00 0.00 37.50 2.52
745 762 6.446318 TGACATTGCAACCTATGTTTTCTTC 58.554 36.000 0.00 0.00 37.50 2.87
747 764 7.054491 ACATTGCAACCTATGTTTTCTTCTT 57.946 32.000 0.00 0.00 34.48 2.52
748 765 7.147976 ACATTGCAACCTATGTTTTCTTCTTC 58.852 34.615 0.00 0.00 34.48 2.87
751 768 7.346751 TGCAACCTATGTTTTCTTCTTCTTT 57.653 32.000 0.00 0.00 30.42 2.52
753 770 8.257306 TGCAACCTATGTTTTCTTCTTCTTTTT 58.743 29.630 0.00 0.00 30.42 1.94
1292 1312 0.478072 TTCTTCAAGGCCTGCTCCAA 59.522 50.000 5.69 0.00 0.00 3.53
1462 1482 2.149578 GAATGTTGTGTGCAGCTCTCT 58.850 47.619 0.00 0.00 0.00 3.10
1616 1636 1.098712 TCCACCGCGCTCTTTTTGTT 61.099 50.000 5.56 0.00 0.00 2.83
1656 1690 8.610248 AGATCATTTCTAGAGAATTGCATCAG 57.390 34.615 17.31 0.00 36.13 2.90
1665 1699 6.395426 AGAGAATTGCATCAGTTTTTGACA 57.605 33.333 0.00 0.00 38.99 3.58
1667 1701 6.263842 AGAGAATTGCATCAGTTTTTGACAGA 59.736 34.615 0.00 0.00 38.99 3.41
1677 1712 4.869297 CAGTTTTTGACAGAAACCATTGCA 59.131 37.500 15.82 0.00 37.64 4.08
1690 1725 2.424601 ACCATTGCATCAATTGGTCGAG 59.575 45.455 5.42 0.00 33.44 4.04
1691 1726 2.424601 CCATTGCATCAATTGGTCGAGT 59.575 45.455 5.42 0.00 31.05 4.18
1692 1727 3.119388 CCATTGCATCAATTGGTCGAGTT 60.119 43.478 5.42 0.00 31.05 3.01
1693 1728 4.096231 CCATTGCATCAATTGGTCGAGTTA 59.904 41.667 5.42 0.00 31.05 2.24
1694 1729 5.221106 CCATTGCATCAATTGGTCGAGTTAT 60.221 40.000 5.42 0.00 31.05 1.89
1695 1730 5.895636 TTGCATCAATTGGTCGAGTTATT 57.104 34.783 5.42 0.00 0.00 1.40
1696 1731 6.993786 TTGCATCAATTGGTCGAGTTATTA 57.006 33.333 5.42 0.00 0.00 0.98
1697 1732 7.566760 TTGCATCAATTGGTCGAGTTATTAT 57.433 32.000 5.42 0.00 0.00 1.28
1698 1733 7.566760 TGCATCAATTGGTCGAGTTATTATT 57.433 32.000 5.42 0.00 0.00 1.40
1699 1734 7.416817 TGCATCAATTGGTCGAGTTATTATTG 58.583 34.615 5.42 0.00 0.00 1.90
1700 1735 6.857964 GCATCAATTGGTCGAGTTATTATTGG 59.142 38.462 5.42 0.00 0.00 3.16
1701 1736 6.371809 TCAATTGGTCGAGTTATTATTGGC 57.628 37.500 5.42 0.00 0.00 4.52
1702 1737 6.119536 TCAATTGGTCGAGTTATTATTGGCT 58.880 36.000 5.42 0.00 0.00 4.75
1703 1738 6.038161 TCAATTGGTCGAGTTATTATTGGCTG 59.962 38.462 5.42 0.00 0.00 4.85
1704 1739 3.804036 TGGTCGAGTTATTATTGGCTGG 58.196 45.455 0.00 0.00 0.00 4.85
1705 1740 3.199071 TGGTCGAGTTATTATTGGCTGGT 59.801 43.478 0.00 0.00 0.00 4.00
1706 1741 3.560068 GGTCGAGTTATTATTGGCTGGTG 59.440 47.826 0.00 0.00 0.00 4.17
1707 1742 4.189231 GTCGAGTTATTATTGGCTGGTGT 58.811 43.478 0.00 0.00 0.00 4.16
1708 1743 4.034048 GTCGAGTTATTATTGGCTGGTGTG 59.966 45.833 0.00 0.00 0.00 3.82
1709 1744 4.081365 TCGAGTTATTATTGGCTGGTGTGA 60.081 41.667 0.00 0.00 0.00 3.58
1710 1745 4.634004 CGAGTTATTATTGGCTGGTGTGAA 59.366 41.667 0.00 0.00 0.00 3.18
1711 1746 5.296780 CGAGTTATTATTGGCTGGTGTGAAT 59.703 40.000 0.00 0.00 0.00 2.57
1712 1747 6.183360 CGAGTTATTATTGGCTGGTGTGAATT 60.183 38.462 0.00 0.00 0.00 2.17
1713 1748 6.866480 AGTTATTATTGGCTGGTGTGAATTG 58.134 36.000 0.00 0.00 0.00 2.32
1714 1749 6.437162 AGTTATTATTGGCTGGTGTGAATTGT 59.563 34.615 0.00 0.00 0.00 2.71
1715 1750 4.517952 TTATTGGCTGGTGTGAATTGTG 57.482 40.909 0.00 0.00 0.00 3.33
1716 1751 1.774110 TTGGCTGGTGTGAATTGTGT 58.226 45.000 0.00 0.00 0.00 3.72
1717 1752 1.031235 TGGCTGGTGTGAATTGTGTG 58.969 50.000 0.00 0.00 0.00 3.82
1718 1753 1.032014 GGCTGGTGTGAATTGTGTGT 58.968 50.000 0.00 0.00 0.00 3.72
1719 1754 1.269206 GGCTGGTGTGAATTGTGTGTG 60.269 52.381 0.00 0.00 0.00 3.82
1720 1755 1.675483 GCTGGTGTGAATTGTGTGTGA 59.325 47.619 0.00 0.00 0.00 3.58
1721 1756 2.541588 GCTGGTGTGAATTGTGTGTGAC 60.542 50.000 0.00 0.00 0.00 3.67
1722 1757 2.682352 CTGGTGTGAATTGTGTGTGACA 59.318 45.455 0.00 0.00 0.00 3.58
1762 1797 8.548877 TGCTAGGTTAATACTTTTGGAATCTCT 58.451 33.333 0.00 0.00 0.00 3.10
1793 1828 1.382522 TGCTGCATGCTTAGCCTTAC 58.617 50.000 22.99 1.14 43.37 2.34
1903 2901 4.641541 TCGTTAAGGTCGATTACTGGATCA 59.358 41.667 0.00 0.00 32.30 2.92
1931 2929 5.409520 TGCTACTGTCATGAATGTTCAGTTC 59.590 40.000 17.89 12.13 41.08 3.01
1940 2938 6.825213 TCATGAATGTTCAGTTCCTGGATTAG 59.175 38.462 0.00 0.00 41.08 1.73
1955 2953 6.374333 TCCTGGATTAGTCAGTTGTAATTTGC 59.626 38.462 0.00 0.00 0.00 3.68
2004 3002 5.708697 TGATCAAGTCGAACTAGAACTGGTA 59.291 40.000 0.00 0.00 0.00 3.25
2097 3095 9.144747 CTTAGCTCTTGTTATGCATATACGATT 57.855 33.333 7.36 0.00 0.00 3.34
2200 3198 4.937620 GGACATTGCTCTCATACAGTTTCA 59.062 41.667 0.00 0.00 0.00 2.69
2379 3377 0.038067 ACTTGGCGCACATACGTACA 60.038 50.000 10.83 0.00 34.88 2.90
2460 3459 7.540400 TGTTATTTGATTTGTGCGGTTATTGAG 59.460 33.333 0.00 0.00 0.00 3.02
2490 3489 7.711339 AGGCTTGTCTGTACTGCTTTATATAAC 59.289 37.037 0.00 0.00 0.00 1.89
2571 3570 4.513692 CCATTGTCTGTTCGAACAAAGGTA 59.486 41.667 29.32 15.28 38.66 3.08
2572 3571 5.440685 CATTGTCTGTTCGAACAAAGGTAC 58.559 41.667 29.32 20.92 38.66 3.34
2573 3572 4.395959 TGTCTGTTCGAACAAAGGTACT 57.604 40.909 29.32 0.00 38.66 2.73
2851 3863 6.872020 TCTGTGCTTAGATTGTAACCTTGTAC 59.128 38.462 0.00 0.00 0.00 2.90
2858 3870 9.886132 CTTAGATTGTAACCTTGTACCAATAGT 57.114 33.333 0.00 0.00 0.00 2.12
3048 4073 4.156556 GGGGACTGTTTATTCCGTTAAACC 59.843 45.833 9.18 0.00 40.00 3.27
3049 4074 5.005740 GGGACTGTTTATTCCGTTAAACCT 58.994 41.667 9.18 0.00 40.00 3.50
3050 4075 6.172630 GGGACTGTTTATTCCGTTAAACCTA 58.827 40.000 9.18 0.00 40.00 3.08
3051 4076 6.825213 GGGACTGTTTATTCCGTTAAACCTAT 59.175 38.462 9.18 0.00 40.00 2.57
3052 4077 7.986889 GGGACTGTTTATTCCGTTAAACCTATA 59.013 37.037 9.18 0.00 40.00 1.31
3053 4078 9.038803 GGACTGTTTATTCCGTTAAACCTATAG 57.961 37.037 9.18 0.00 40.00 1.31
3054 4079 8.429493 ACTGTTTATTCCGTTAAACCTATAGC 57.571 34.615 0.00 0.00 40.00 2.97
3055 4080 8.042515 ACTGTTTATTCCGTTAAACCTATAGCA 58.957 33.333 0.00 0.00 40.00 3.49
3056 4081 8.967664 TGTTTATTCCGTTAAACCTATAGCAT 57.032 30.769 0.00 0.00 40.00 3.79
3057 4082 9.398538 TGTTTATTCCGTTAAACCTATAGCATT 57.601 29.630 0.00 0.00 40.00 3.56
3058 4083 9.659830 GTTTATTCCGTTAAACCTATAGCATTG 57.340 33.333 0.00 0.00 36.50 2.82
3059 4084 8.967664 TTATTCCGTTAAACCTATAGCATTGT 57.032 30.769 0.00 0.00 0.00 2.71
3060 4085 7.875327 ATTCCGTTAAACCTATAGCATTGTT 57.125 32.000 0.00 0.00 0.00 2.83
3061 4086 7.690952 TTCCGTTAAACCTATAGCATTGTTT 57.309 32.000 9.05 9.05 35.32 2.83
3062 4087 8.789825 TTCCGTTAAACCTATAGCATTGTTTA 57.210 30.769 7.55 7.55 33.36 2.01
3063 4088 8.967664 TCCGTTAAACCTATAGCATTGTTTAT 57.032 30.769 10.81 0.00 34.29 1.40
3064 4089 9.398538 TCCGTTAAACCTATAGCATTGTTTATT 57.601 29.630 10.81 0.00 34.29 1.40
3065 4090 9.659830 CCGTTAAACCTATAGCATTGTTTATTC 57.340 33.333 10.81 7.97 34.29 1.75
3066 4091 9.659830 CGTTAAACCTATAGCATTGTTTATTCC 57.340 33.333 10.81 4.75 34.29 3.01
3067 4092 9.659830 GTTAAACCTATAGCATTGTTTATTCCG 57.340 33.333 10.81 0.00 34.29 4.30
3068 4093 7.875327 AAACCTATAGCATTGTTTATTCCGT 57.125 32.000 3.79 0.00 0.00 4.69
3069 4094 7.875327 AACCTATAGCATTGTTTATTCCGTT 57.125 32.000 0.00 0.00 0.00 4.44
3070 4095 8.967664 AACCTATAGCATTGTTTATTCCGTTA 57.032 30.769 0.00 0.00 0.00 3.18
3071 4096 8.967664 ACCTATAGCATTGTTTATTCCGTTAA 57.032 30.769 0.00 0.00 0.00 2.01
3072 4097 9.398538 ACCTATAGCATTGTTTATTCCGTTAAA 57.601 29.630 0.00 0.00 0.00 1.52
3192 4245 8.174422 CCCTTTAAATTGTTTAAATTGATGCGG 58.826 33.333 7.76 4.88 42.36 5.69
3200 4253 5.708230 TGTTTAAATTGATGCGGTTAGTCCT 59.292 36.000 0.00 0.00 0.00 3.85
3519 4603 7.798596 ATAAATGAATGGCTAGTCTGAGTTG 57.201 36.000 0.00 0.00 0.00 3.16
3766 4850 8.834465 CCTGTCCTCTCTTTTGATATTTATGTG 58.166 37.037 0.00 0.00 0.00 3.21
3799 4883 7.710907 TGACTACAATGATATCTAGTTGGTTGC 59.289 37.037 3.98 1.21 0.00 4.17
4096 5183 3.745799 TGTGGAACGGCAAAATCTTAGA 58.254 40.909 0.00 0.00 42.39 2.10
4231 5327 3.326297 AGCTTATCCTGCTTCTGGGTATC 59.674 47.826 0.00 0.00 37.52 2.24
4232 5328 3.071602 GCTTATCCTGCTTCTGGGTATCA 59.928 47.826 0.00 0.00 0.00 2.15
4233 5329 4.444876 GCTTATCCTGCTTCTGGGTATCAA 60.445 45.833 0.00 0.00 0.00 2.57
4234 5330 5.684704 CTTATCCTGCTTCTGGGTATCAAA 58.315 41.667 0.00 0.00 0.00 2.69
4235 5331 4.803329 ATCCTGCTTCTGGGTATCAAAT 57.197 40.909 0.00 0.00 0.00 2.32
4236 5332 4.591321 TCCTGCTTCTGGGTATCAAATT 57.409 40.909 0.00 0.00 0.00 1.82
4362 5458 6.272558 AGGGTTCTTACCTGATATTCCCATAC 59.727 42.308 0.00 0.00 44.38 2.39
4389 5485 1.680249 GGGCCAGTCTGAATCCACTTC 60.680 57.143 4.39 0.00 0.00 3.01
4428 5524 2.430694 TCACGTCCCAGGTGAGATATTG 59.569 50.000 0.00 0.00 37.99 1.90
4442 5538 6.481644 GGTGAGATATTGTCTTTTCCTAGCTG 59.518 42.308 0.00 0.00 37.29 4.24
4460 5556 1.270274 CTGGCTTGTGTAATTGCAGCA 59.730 47.619 0.00 0.00 0.00 4.41
4461 5557 1.894466 TGGCTTGTGTAATTGCAGCAT 59.106 42.857 0.00 0.00 0.00 3.79
4464 5560 2.789208 CTTGTGTAATTGCAGCATCCG 58.211 47.619 0.00 0.00 0.00 4.18
4649 6200 4.447138 TCTCAAGCCTTTCCTTGGTTAA 57.553 40.909 2.49 0.00 41.89 2.01
4668 6219 3.425162 AAATCTGTCACCTGGGAACTC 57.575 47.619 0.00 0.00 0.00 3.01
4819 6370 6.992123 TGCTGAACTAGGATAATAACCACATG 59.008 38.462 0.00 0.00 0.00 3.21
4831 6382 9.872757 GATAATAACCACATGTTTTATGTACGG 57.127 33.333 0.00 0.00 38.42 4.02
4853 6404 3.855689 ATGGTTTGAAGGCTTGAATCG 57.144 42.857 3.46 0.00 0.00 3.34
5135 6686 5.437060 TGATAGGTTGATCTGGTTTTAGCC 58.563 41.667 0.00 0.00 0.00 3.93
5146 6697 7.554118 TGATCTGGTTTTAGCCTTTCATTAGAG 59.446 37.037 0.00 0.00 0.00 2.43
5185 6736 5.291128 CGGTGTTCGACAGCTTCTTAAATAT 59.709 40.000 12.87 0.00 43.87 1.28
5315 6909 5.107530 CGCATGTGGTTCTTTGTATTTTTGG 60.108 40.000 0.00 0.00 0.00 3.28
5444 7155 2.223745 GAGACGTTGGGGCAGTTTAAA 58.776 47.619 0.00 0.00 0.00 1.52
5469 7180 3.926058 ACTGCCCCAACGTCTTATATT 57.074 42.857 0.00 0.00 0.00 1.28
5529 7240 6.323266 TCATCAAACTCGTTACTTCTCTAGC 58.677 40.000 0.00 0.00 0.00 3.42
5592 7304 7.597288 TGAGTAATCTAGGTTGCAGCTAATA 57.403 36.000 6.60 0.00 0.00 0.98
5718 7430 6.721668 CCTGGTGAGGACACTATGAATAGATA 59.278 42.308 4.34 0.00 42.93 1.98
5900 7649 7.201530 GGTGTAAGACATAGGAATTGAAACGAG 60.202 40.741 0.00 0.00 0.00 4.18
5923 7672 1.627329 AGAGTCTGCATGTCATGGTGT 59.373 47.619 14.64 0.00 0.00 4.16
5928 7677 0.250684 TGCATGTCATGGTGTCCGTT 60.251 50.000 14.64 0.00 0.00 4.44
5929 7678 1.002544 TGCATGTCATGGTGTCCGTTA 59.997 47.619 14.64 0.00 0.00 3.18
5930 7679 1.665679 GCATGTCATGGTGTCCGTTAG 59.334 52.381 14.64 0.00 0.00 2.34
5931 7680 2.279741 CATGTCATGGTGTCCGTTAGG 58.720 52.381 4.78 0.00 39.46 2.69
5932 7681 1.634960 TGTCATGGTGTCCGTTAGGA 58.365 50.000 0.00 0.00 46.11 2.94
5944 7693 4.644103 TCCGTTAGGAAAACCGAGATAG 57.356 45.455 0.00 0.00 45.12 2.08
5946 7695 2.787680 CGTTAGGAAAACCGAGATAGCG 59.212 50.000 0.00 0.00 0.00 4.26
5947 7696 3.488047 CGTTAGGAAAACCGAGATAGCGA 60.488 47.826 0.00 0.00 0.00 4.93
5949 7698 5.561532 CGTTAGGAAAACCGAGATAGCGATA 60.562 44.000 0.00 0.00 0.00 2.92
5950 7699 4.931661 AGGAAAACCGAGATAGCGATAA 57.068 40.909 0.00 0.00 0.00 1.75
5951 7700 4.872664 AGGAAAACCGAGATAGCGATAAG 58.127 43.478 0.00 0.00 0.00 1.73
5952 7701 4.341520 AGGAAAACCGAGATAGCGATAAGT 59.658 41.667 0.00 0.00 0.00 2.24
5953 7702 5.048507 GGAAAACCGAGATAGCGATAAGTT 58.951 41.667 0.00 0.00 0.00 2.66
5954 7703 5.522824 GGAAAACCGAGATAGCGATAAGTTT 59.477 40.000 0.00 0.00 0.00 2.66
5955 7704 6.036844 GGAAAACCGAGATAGCGATAAGTTTT 59.963 38.462 0.00 0.00 35.88 2.43
6051 7802 4.844884 AGTGATTAGTTTCTTGGGCTACC 58.155 43.478 0.00 0.00 37.24 3.18
6156 7907 1.135333 GTAAGCCTCCGAACCTCTCTG 59.865 57.143 0.00 0.00 0.00 3.35
6164 7915 0.453793 CGAACCTCTCTGATCACGCT 59.546 55.000 0.00 0.00 0.00 5.07
6178 7929 1.069258 ACGCTAGCGATTAAGCCCC 59.931 57.895 41.33 0.00 42.83 5.80
6210 7961 3.104843 GACAGAGTGTCATATCCCTGC 57.895 52.381 2.12 0.00 46.22 4.85
6253 8012 4.848562 ATTGCACATCATGGATGACATC 57.151 40.909 12.79 6.91 42.09 3.06
6298 8057 3.678056 TCATACAAGCGTCCTTCAAGT 57.322 42.857 0.00 0.00 0.00 3.16
6547 8615 7.743749 AGATCTCTGGAATTACATTGTATGCT 58.256 34.615 0.00 0.00 0.00 3.79
6688 8756 3.670055 CGTTGATCGCTTTGCAGATTTTT 59.330 39.130 0.00 0.00 0.00 1.94
6772 8840 4.860022 CCTTCAGGGTGAACCATATTCTT 58.140 43.478 1.16 0.00 43.89 2.52
6962 9032 0.838608 TAGTGTGTTTTGGGTCGGGT 59.161 50.000 0.00 0.00 0.00 5.28
7031 9101 1.312815 GCTCAGACCCAATATGCCAC 58.687 55.000 0.00 0.00 0.00 5.01
7054 10210 4.070009 GGAGAATGTTCGGGTTTAGTGTT 58.930 43.478 0.00 0.00 0.00 3.32
7102 10258 4.387437 CCATTACCATGGTATCCAAAGGGT 60.387 45.833 25.12 12.52 44.81 4.34
7123 10279 3.260632 GTGCCCCCATTTGTACAAAATCT 59.739 43.478 23.97 6.12 33.56 2.40
7125 10281 4.020662 TGCCCCCATTTGTACAAAATCTTC 60.021 41.667 23.97 12.38 33.56 2.87
7293 10449 3.845781 TCATAGCCTTTCACATCCTCC 57.154 47.619 0.00 0.00 0.00 4.30
7334 10490 2.094894 GTCGGTGCATCTGAAAGTGATG 59.905 50.000 0.00 0.00 42.86 3.07
7345 10501 6.174720 TCTGAAAGTGATGGTGAAAGTAGT 57.825 37.500 0.00 0.00 33.76 2.73
7390 10546 3.926616 TGCAAAGTAGTTCCTGTAGAGC 58.073 45.455 0.00 0.00 0.00 4.09
7414 10570 0.111832 CATGCCCATCTGCCCTATGT 59.888 55.000 0.00 0.00 0.00 2.29
7442 10598 1.272769 GGACCAGATGCTCCGGTATAC 59.727 57.143 0.00 0.00 31.63 1.47
7461 10617 8.732746 GGTATACGATATGATTGGCCTTTTAT 57.267 34.615 3.32 0.00 0.00 1.40
7462 10618 9.174166 GGTATACGATATGATTGGCCTTTTATT 57.826 33.333 3.32 0.00 0.00 1.40
7463 10619 9.988350 GTATACGATATGATTGGCCTTTTATTG 57.012 33.333 3.32 1.32 0.00 1.90
7464 10620 6.331369 ACGATATGATTGGCCTTTTATTGG 57.669 37.500 3.32 0.00 0.00 3.16
7465 10621 5.833131 ACGATATGATTGGCCTTTTATTGGT 59.167 36.000 3.32 0.00 0.00 3.67
7466 10622 6.151691 CGATATGATTGGCCTTTTATTGGTG 58.848 40.000 3.32 0.00 0.00 4.17
7467 10623 6.016360 CGATATGATTGGCCTTTTATTGGTGA 60.016 38.462 3.32 0.00 0.00 4.02
7468 10624 7.309377 CGATATGATTGGCCTTTTATTGGTGAT 60.309 37.037 3.32 0.00 0.00 3.06
7469 10625 5.341872 TGATTGGCCTTTTATTGGTGATG 57.658 39.130 3.32 0.00 0.00 3.07
7470 10626 5.022122 TGATTGGCCTTTTATTGGTGATGA 58.978 37.500 3.32 0.00 0.00 2.92
7471 10627 5.127519 TGATTGGCCTTTTATTGGTGATGAG 59.872 40.000 3.32 0.00 0.00 2.90
7472 10628 2.760092 TGGCCTTTTATTGGTGATGAGC 59.240 45.455 3.32 0.00 0.00 4.26
7473 10629 3.026694 GGCCTTTTATTGGTGATGAGCT 58.973 45.455 0.00 0.00 0.00 4.09
7474 10630 3.067320 GGCCTTTTATTGGTGATGAGCTC 59.933 47.826 6.82 6.82 0.00 4.09
7475 10631 3.242870 GCCTTTTATTGGTGATGAGCTCG 60.243 47.826 9.64 0.00 0.00 5.03
7476 10632 3.941483 CCTTTTATTGGTGATGAGCTCGT 59.059 43.478 8.55 8.55 0.00 4.18
7477 10633 5.116180 CCTTTTATTGGTGATGAGCTCGTA 58.884 41.667 8.83 0.00 0.00 3.43
7478 10634 5.760253 CCTTTTATTGGTGATGAGCTCGTAT 59.240 40.000 8.83 0.67 0.00 3.06
7479 10635 6.293081 CCTTTTATTGGTGATGAGCTCGTATG 60.293 42.308 8.83 0.00 0.00 2.39
7480 10636 5.529581 TTATTGGTGATGAGCTCGTATGA 57.470 39.130 8.83 0.00 0.00 2.15
7481 10637 3.443099 TTGGTGATGAGCTCGTATGAG 57.557 47.619 8.83 7.65 45.49 2.90
7482 10638 1.683385 TGGTGATGAGCTCGTATGAGG 59.317 52.381 8.83 0.00 42.79 3.86
7528 10684 4.940046 AGATAAGCTCTGTTGACAATGTGG 59.060 41.667 0.00 0.00 31.12 4.17
7535 10691 1.269673 TGTTGACAATGTGGCATGCAC 60.270 47.619 21.36 15.73 33.90 4.57
7537 10693 0.599060 TGACAATGTGGCATGCACTG 59.401 50.000 21.36 12.62 24.43 3.66
7584 10740 5.857268 AGTTGGGGTTTTGAATTCAATGAG 58.143 37.500 21.10 0.00 35.55 2.90
7603 10759 0.458370 GCATGGTGCGGAACATTTCC 60.458 55.000 4.03 0.00 46.62 3.13
7629 10785 6.053650 TGAGAGTCATATTCTTGCATTCCAG 58.946 40.000 0.00 0.00 0.00 3.86
7659 10815 6.313905 CCATTTTGATACAGAGTGTAGGTGAC 59.686 42.308 0.00 0.00 36.14 3.67
7676 10832 3.002656 GGTGACAGATAATTCATGCGTGG 59.997 47.826 5.98 0.00 0.00 4.94
7723 10879 9.486123 TTTCCATATTGGTATTCTTGAATTCCA 57.514 29.630 14.81 14.81 39.03 3.53
7727 10883 8.582437 CATATTGGTATTCTTGAATTCCATGCT 58.418 33.333 18.01 11.01 31.13 3.79
7765 10921 7.227314 TCACATGTTTCATGATCACCTTATAGC 59.773 37.037 15.25 0.00 0.00 2.97
7773 10929 7.062322 TCATGATCACCTTATAGCCATTTTGT 58.938 34.615 0.00 0.00 0.00 2.83
7780 10936 5.716703 ACCTTATAGCCATTTTGTGCTCTTT 59.283 36.000 0.00 0.00 39.00 2.52
7817 10973 3.299503 AGCATTGTTGGGTCTTGTCTTT 58.700 40.909 0.00 0.00 0.00 2.52
7841 10997 8.650143 TTATCTTCAAGAAAATAAGCCCAAGT 57.350 30.769 0.00 0.00 0.00 3.16
7844 11000 5.705609 TCAAGAAAATAAGCCCAAGTGAC 57.294 39.130 0.00 0.00 0.00 3.67
7845 11001 5.385198 TCAAGAAAATAAGCCCAAGTGACT 58.615 37.500 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.039074 AGAAGTCACGGAAGACAGCG 60.039 55.000 7.50 0.00 40.98 5.18
1 2 1.670380 GGAGAAGTCACGGAAGACAGC 60.670 57.143 7.50 0.18 40.98 4.40
3 4 1.613925 CTGGAGAAGTCACGGAAGACA 59.386 52.381 7.50 0.00 40.98 3.41
4 5 1.614413 ACTGGAGAAGTCACGGAAGAC 59.386 52.381 0.00 0.00 31.64 3.01
5 6 1.613925 CACTGGAGAAGTCACGGAAGA 59.386 52.381 0.00 0.00 36.83 2.87
6 7 1.613925 TCACTGGAGAAGTCACGGAAG 59.386 52.381 0.00 0.00 36.83 3.46
7 8 1.340248 GTCACTGGAGAAGTCACGGAA 59.660 52.381 0.00 0.00 36.83 4.30
8 9 0.959553 GTCACTGGAGAAGTCACGGA 59.040 55.000 0.00 0.00 36.83 4.69
9 10 0.962489 AGTCACTGGAGAAGTCACGG 59.038 55.000 0.00 0.00 34.53 4.94
10 11 1.932604 GCAGTCACTGGAGAAGTCACG 60.933 57.143 7.00 0.00 34.53 4.35
11 12 1.342819 AGCAGTCACTGGAGAAGTCAC 59.657 52.381 7.00 0.00 36.83 3.67
12 13 1.709578 AGCAGTCACTGGAGAAGTCA 58.290 50.000 7.00 0.00 36.83 3.41
13 14 2.036475 TGAAGCAGTCACTGGAGAAGTC 59.964 50.000 7.00 0.00 36.83 3.01
14 15 2.042464 TGAAGCAGTCACTGGAGAAGT 58.958 47.619 7.00 0.00 40.93 3.01
15 16 2.827800 TGAAGCAGTCACTGGAGAAG 57.172 50.000 7.00 0.00 31.21 2.85
24 25 0.397564 TCAGCATGGTGAAGCAGTCA 59.602 50.000 24.64 0.00 36.16 3.41
29 30 1.063174 GACGAATCAGCATGGTGAAGC 59.937 52.381 29.58 21.91 36.16 3.86
47 48 3.381949 CCAAGCGGCAACTACTATAGAC 58.618 50.000 6.78 0.00 0.00 2.59
415 418 3.739519 GCAGCTTCCGTCTCATCTAACAT 60.740 47.826 0.00 0.00 0.00 2.71
496 499 9.656040 CCAATACTTCAAAATTCCATCAAATCA 57.344 29.630 0.00 0.00 0.00 2.57
497 500 9.874205 TCCAATACTTCAAAATTCCATCAAATC 57.126 29.630 0.00 0.00 0.00 2.17
500 503 9.487790 GTTTCCAATACTTCAAAATTCCATCAA 57.512 29.630 0.00 0.00 0.00 2.57
501 504 8.093927 GGTTTCCAATACTTCAAAATTCCATCA 58.906 33.333 0.00 0.00 0.00 3.07
502 505 8.314021 AGGTTTCCAATACTTCAAAATTCCATC 58.686 33.333 0.00 0.00 0.00 3.51
503 506 8.206126 AGGTTTCCAATACTTCAAAATTCCAT 57.794 30.769 0.00 0.00 0.00 3.41
504 507 7.610580 AGGTTTCCAATACTTCAAAATTCCA 57.389 32.000 0.00 0.00 0.00 3.53
541 548 2.794910 CGAATCGAAACGACCAGCATAT 59.205 45.455 0.00 0.00 39.18 1.78
544 551 1.623081 GCGAATCGAAACGACCAGCA 61.623 55.000 6.91 0.00 39.18 4.41
556 563 3.680642 AGAATTCAACCATGCGAATCG 57.319 42.857 8.44 0.00 30.64 3.34
620 627 4.038642 GGTTTGAGTGGGTGCTAAAATTCA 59.961 41.667 0.00 0.00 0.00 2.57
632 639 6.709018 TTCTTTTTAAGAGGTTTGAGTGGG 57.291 37.500 0.00 0.00 39.03 4.61
652 659 9.558396 TGCAAAATAGGAAAAACAAATGATTCT 57.442 25.926 0.00 0.00 0.00 2.40
658 665 6.060788 TGCCTGCAAAATAGGAAAAACAAAT 58.939 32.000 0.00 0.00 37.52 2.32
673 683 3.895232 TTAACTTGGTTTGCCTGCAAA 57.105 38.095 12.97 12.97 42.77 3.68
674 684 3.133721 ACATTAACTTGGTTTGCCTGCAA 59.866 39.130 0.00 0.00 35.27 4.08
697 708 9.699410 TCATGTTCTTTTGAATCCTATACCAAT 57.301 29.630 0.00 0.00 40.94 3.16
698 709 8.956426 GTCATGTTCTTTTGAATCCTATACCAA 58.044 33.333 0.00 0.00 40.94 3.67
699 710 8.106462 TGTCATGTTCTTTTGAATCCTATACCA 58.894 33.333 0.00 0.00 40.94 3.25
700 711 8.506168 TGTCATGTTCTTTTGAATCCTATACC 57.494 34.615 0.00 0.00 40.94 2.73
753 770 9.519191 TCTTTGATTCATAGGATTTCAGAACAA 57.481 29.630 4.57 0.00 0.00 2.83
765 782 3.872459 AGGGCCTCTTTGATTCATAGG 57.128 47.619 0.00 5.38 0.00 2.57
769 786 3.744940 ATCAAGGGCCTCTTTGATTCA 57.255 42.857 6.46 2.40 32.41 2.57
1616 1636 6.595326 AGAAATGATCTAATGCACTTCGTGAA 59.405 34.615 0.00 0.00 36.32 3.18
1640 1674 7.587629 TGTCAAAAACTGATGCAATTCTCTAG 58.412 34.615 0.00 0.00 36.14 2.43
1656 1690 5.523188 TGATGCAATGGTTTCTGTCAAAAAC 59.477 36.000 0.00 0.00 36.18 2.43
1665 1699 4.618927 CGACCAATTGATGCAATGGTTTCT 60.619 41.667 7.12 0.00 36.32 2.52
1667 1701 3.257873 TCGACCAATTGATGCAATGGTTT 59.742 39.130 7.12 0.00 36.32 3.27
1677 1712 6.772716 AGCCAATAATAACTCGACCAATTGAT 59.227 34.615 7.12 0.00 0.00 2.57
1690 1725 6.531240 CACAATTCACACCAGCCAATAATAAC 59.469 38.462 0.00 0.00 0.00 1.89
1691 1726 6.210385 ACACAATTCACACCAGCCAATAATAA 59.790 34.615 0.00 0.00 0.00 1.40
1692 1727 5.714333 ACACAATTCACACCAGCCAATAATA 59.286 36.000 0.00 0.00 0.00 0.98
1693 1728 4.527816 ACACAATTCACACCAGCCAATAAT 59.472 37.500 0.00 0.00 0.00 1.28
1694 1729 3.894427 ACACAATTCACACCAGCCAATAA 59.106 39.130 0.00 0.00 0.00 1.40
1695 1730 3.255395 CACACAATTCACACCAGCCAATA 59.745 43.478 0.00 0.00 0.00 1.90
1696 1731 2.036217 CACACAATTCACACCAGCCAAT 59.964 45.455 0.00 0.00 0.00 3.16
1697 1732 1.408340 CACACAATTCACACCAGCCAA 59.592 47.619 0.00 0.00 0.00 4.52
1698 1733 1.031235 CACACAATTCACACCAGCCA 58.969 50.000 0.00 0.00 0.00 4.75
1699 1734 1.032014 ACACACAATTCACACCAGCC 58.968 50.000 0.00 0.00 0.00 4.85
1700 1735 1.675483 TCACACACAATTCACACCAGC 59.325 47.619 0.00 0.00 0.00 4.85
1701 1736 2.682352 TGTCACACACAATTCACACCAG 59.318 45.455 0.00 0.00 29.30 4.00
1702 1737 2.716217 TGTCACACACAATTCACACCA 58.284 42.857 0.00 0.00 29.30 4.17
1713 1748 4.092383 AGTTTAACTGAACGTGTCACACAC 59.908 41.667 9.06 2.95 45.26 3.82
1714 1749 4.247258 AGTTTAACTGAACGTGTCACACA 58.753 39.130 9.06 0.00 33.40 3.72
1715 1750 4.852609 AGTTTAACTGAACGTGTCACAC 57.147 40.909 0.00 0.00 34.74 3.82
1793 1828 1.800586 CATGACCACACCGACAAGAAG 59.199 52.381 0.00 0.00 0.00 2.85
1903 2901 4.292186 ACATTCATGACAGTAGCAAGGT 57.708 40.909 0.00 0.00 0.00 3.50
1931 2929 6.150976 TGCAAATTACAACTGACTAATCCAGG 59.849 38.462 0.00 0.00 36.03 4.45
1940 2938 3.179599 GCAACGTGCAAATTACAACTGAC 59.820 43.478 0.00 0.00 44.26 3.51
1955 2953 2.548057 ACCATACTGAAACTGCAACGTG 59.452 45.455 0.00 0.00 0.00 4.49
2004 3002 6.042437 TCTCACATGTGCTGATACCTCATATT 59.958 38.462 21.38 0.00 0.00 1.28
2097 3095 5.316167 ACCTGCAAATCTATGAACAGAACA 58.684 37.500 0.00 0.00 0.00 3.18
2200 3198 8.562892 CAGTCAAACTTTGTGACAGAATAAGAT 58.437 33.333 7.26 0.00 46.44 2.40
2460 3459 1.941668 GCAGTACAGACAAGCCTGGAC 60.942 57.143 0.00 0.00 46.02 4.02
2490 3489 2.677573 TACGCTCCGCATCACCATCG 62.678 60.000 0.00 0.00 0.00 3.84
2655 3667 0.321564 CTTGATGGTGCGAACCTGGA 60.322 55.000 15.35 0.00 0.00 3.86
2858 3870 7.169645 GCAAGCATGAAAAGAAAATGTGAACTA 59.830 33.333 0.00 0.00 0.00 2.24
2902 3926 4.045636 GCAGAAAGCTGAACTGGAAAAA 57.954 40.909 14.04 0.00 45.17 1.94
2903 3927 3.715628 GCAGAAAGCTGAACTGGAAAA 57.284 42.857 14.04 0.00 45.17 2.29
2953 3978 1.284982 CTCGGCGATAAGAATGCGGG 61.285 60.000 11.27 0.00 0.00 6.13
2994 4019 3.081554 CCAGGGGAGAACACTGGG 58.918 66.667 7.75 0.00 46.24 4.45
3050 4075 8.736244 ACAGTTTAACGGAATAAACAATGCTAT 58.264 29.630 17.37 0.05 44.49 2.97
3051 4076 8.101654 ACAGTTTAACGGAATAAACAATGCTA 57.898 30.769 17.37 0.00 44.49 3.49
3052 4077 6.977213 ACAGTTTAACGGAATAAACAATGCT 58.023 32.000 17.37 1.07 44.49 3.79
3053 4078 8.019094 ACTACAGTTTAACGGAATAAACAATGC 58.981 33.333 17.37 0.00 44.49 3.56
3056 4081 9.762933 AGTACTACAGTTTAACGGAATAAACAA 57.237 29.630 17.37 6.80 44.49 2.83
3057 4082 9.195411 CAGTACTACAGTTTAACGGAATAAACA 57.805 33.333 17.37 3.08 44.49 2.83
3058 4083 9.196552 ACAGTACTACAGTTTAACGGAATAAAC 57.803 33.333 1.74 10.83 43.11 2.01
3059 4084 9.762933 AACAGTACTACAGTTTAACGGAATAAA 57.237 29.630 1.74 0.00 0.00 1.40
3060 4085 9.762933 AAACAGTACTACAGTTTAACGGAATAA 57.237 29.630 7.71 0.00 36.30 1.40
3062 4087 9.933723 ATAAACAGTACTACAGTTTAACGGAAT 57.066 29.630 16.48 3.03 41.27 3.01
3063 4088 9.762933 AATAAACAGTACTACAGTTTAACGGAA 57.237 29.630 16.48 1.21 41.27 4.30
3064 4089 9.762933 AAATAAACAGTACTACAGTTTAACGGA 57.237 29.630 16.48 1.76 41.27 4.69
3156 4205 8.312564 TTAAACAATTTAAAGGGAATAACCCCG 58.687 33.333 0.00 0.00 43.36 5.73
3186 4235 6.250344 AGTTTTAAAAGGACTAACCGCATC 57.750 37.500 0.00 0.00 44.74 3.91
3519 4603 6.354130 TGCAGAGGTCCCTGTATAAAAATAC 58.646 40.000 8.59 0.00 36.57 1.89
3766 4850 8.129840 ACTAGATATCATTGTAGTCAACACGTC 58.870 37.037 5.32 0.00 38.00 4.34
3864 4948 5.393027 GCTGACAAAAAGAAAAGAGGTGTGA 60.393 40.000 0.00 0.00 0.00 3.58
3865 4949 4.800471 GCTGACAAAAAGAAAAGAGGTGTG 59.200 41.667 0.00 0.00 0.00 3.82
3866 4950 4.142160 GGCTGACAAAAAGAAAAGAGGTGT 60.142 41.667 0.00 0.00 0.00 4.16
3867 4951 4.098501 AGGCTGACAAAAAGAAAAGAGGTG 59.901 41.667 0.00 0.00 0.00 4.00
3868 4952 4.281657 AGGCTGACAAAAAGAAAAGAGGT 58.718 39.130 0.00 0.00 0.00 3.85
3870 4954 6.293680 GGAGTAGGCTGACAAAAAGAAAAGAG 60.294 42.308 0.00 0.00 0.00 2.85
3872 4956 5.299279 TGGAGTAGGCTGACAAAAAGAAAAG 59.701 40.000 0.00 0.00 0.00 2.27
3873 4957 5.197451 TGGAGTAGGCTGACAAAAAGAAAA 58.803 37.500 0.00 0.00 0.00 2.29
4096 5183 9.353999 GTTTTGTTAAACTTCACAGAACAAGAT 57.646 29.630 5.69 0.00 40.14 2.40
4231 5327 9.853921 GAAAAATTGCAAGACTAACTCAATTTG 57.146 29.630 4.94 0.00 39.68 2.32
4232 5328 9.822185 AGAAAAATTGCAAGACTAACTCAATTT 57.178 25.926 4.94 0.00 40.97 1.82
4233 5329 9.252962 CAGAAAAATTGCAAGACTAACTCAATT 57.747 29.630 4.94 0.00 35.78 2.32
4234 5330 7.383300 GCAGAAAAATTGCAAGACTAACTCAAT 59.617 33.333 4.94 0.00 41.17 2.57
4235 5331 6.697019 GCAGAAAAATTGCAAGACTAACTCAA 59.303 34.615 4.94 0.00 41.17 3.02
4236 5332 6.039717 AGCAGAAAAATTGCAAGACTAACTCA 59.960 34.615 4.94 0.00 43.92 3.41
4362 5458 3.368739 GGATTCAGACTGGCCCATTTTTG 60.369 47.826 0.00 0.00 0.00 2.44
4389 5485 4.131714 CGTGAACGAACAAATACTTGACG 58.868 43.478 0.00 0.00 43.02 4.35
4428 5524 2.485814 CACAAGCCAGCTAGGAAAAGAC 59.514 50.000 6.40 0.00 41.22 3.01
4442 5538 2.533266 GATGCTGCAATTACACAAGCC 58.467 47.619 6.36 0.00 0.00 4.35
4460 5556 0.179073 GACATGTGCTAGCACCGGAT 60.179 55.000 37.90 25.18 45.63 4.18
4461 5557 1.218047 GACATGTGCTAGCACCGGA 59.782 57.895 37.90 24.16 45.63 5.14
4464 5560 1.081892 CTGTGACATGTGCTAGCACC 58.918 55.000 37.90 25.37 45.63 5.01
4469 5565 2.833943 AGATCCACTGTGACATGTGCTA 59.166 45.455 9.86 0.00 33.26 3.49
4474 5570 4.134379 AGCTAAGATCCACTGTGACATG 57.866 45.455 9.86 0.00 0.00 3.21
4649 6200 1.276421 CGAGTTCCCAGGTGACAGATT 59.724 52.381 0.00 0.00 0.00 2.40
4668 6219 5.050490 AGGCACTTTAGCAGATGTAATACG 58.950 41.667 0.00 0.00 27.25 3.06
4773 6324 9.399797 TCAGCAAATATAAACTGTCAGATGAAT 57.600 29.630 6.91 0.00 0.00 2.57
4774 6325 8.791327 TCAGCAAATATAAACTGTCAGATGAA 57.209 30.769 6.91 0.00 0.00 2.57
4775 6326 8.668353 GTTCAGCAAATATAAACTGTCAGATGA 58.332 33.333 6.91 0.00 0.00 2.92
4819 6370 7.245604 CCTTCAAACCATACCGTACATAAAAC 58.754 38.462 0.00 0.00 0.00 2.43
4829 6380 2.432444 TCAAGCCTTCAAACCATACCG 58.568 47.619 0.00 0.00 0.00 4.02
4831 6382 4.438744 CCGATTCAAGCCTTCAAACCATAC 60.439 45.833 0.00 0.00 0.00 2.39
4853 6404 8.154649 TGAGAAGAGTAAAAAGAAATGTGACC 57.845 34.615 0.00 0.00 0.00 4.02
5135 6686 8.598075 GCAACCAAAAATATGCTCTAATGAAAG 58.402 33.333 0.00 0.00 35.93 2.62
5146 6697 2.682836 ACACCGCAACCAAAAATATGC 58.317 42.857 0.00 0.00 35.49 3.14
5290 6842 4.846779 AAATACAAAGAACCACATGCGT 57.153 36.364 0.00 0.00 0.00 5.24
5315 6909 3.181483 CCTGAAGGCCATTAGCATGAAAC 60.181 47.826 5.01 0.00 46.50 2.78
5374 6969 9.842775 ATCACATACATCAGAAATACTCAATGT 57.157 29.630 0.00 0.00 36.57 2.71
5444 7155 2.579410 AGACGTTGGGGCAGTTTAAT 57.421 45.000 0.00 0.00 0.00 1.40
5469 7180 8.108364 GCTATCTACTACTACCTCCATTCCTAA 58.892 40.741 0.00 0.00 0.00 2.69
5491 7202 9.113838 ACGAGTTTGATGATCTAAATTTGCTAT 57.886 29.630 0.00 0.00 0.00 2.97
5592 7304 7.157347 ACTGACACAGCATTATATTCATCGAT 58.843 34.615 0.00 0.00 34.37 3.59
5875 7624 7.331193 ACTCGTTTCAATTCCTATGTCTTACAC 59.669 37.037 0.00 0.00 0.00 2.90
5900 7649 3.620374 CACCATGACATGCAGACTCTAAC 59.380 47.826 10.10 0.00 0.00 2.34
5923 7672 3.181483 GCTATCTCGGTTTTCCTAACGGA 60.181 47.826 0.00 0.00 37.95 4.69
5928 7677 5.533903 ACTTATCGCTATCTCGGTTTTCCTA 59.466 40.000 0.00 0.00 37.95 2.94
5929 7678 4.341520 ACTTATCGCTATCTCGGTTTTCCT 59.658 41.667 0.00 0.00 37.95 3.36
5930 7679 4.618965 ACTTATCGCTATCTCGGTTTTCC 58.381 43.478 0.00 0.00 0.00 3.13
5931 7680 6.585389 AAACTTATCGCTATCTCGGTTTTC 57.415 37.500 0.00 0.00 0.00 2.29
5932 7681 6.980051 AAAACTTATCGCTATCTCGGTTTT 57.020 33.333 0.00 0.00 32.96 2.43
5933 7682 7.763071 ACTTAAAACTTATCGCTATCTCGGTTT 59.237 33.333 0.00 0.00 0.00 3.27
5934 7683 7.263496 ACTTAAAACTTATCGCTATCTCGGTT 58.737 34.615 0.00 0.00 0.00 4.44
5935 7684 6.803642 ACTTAAAACTTATCGCTATCTCGGT 58.196 36.000 0.00 0.00 0.00 4.69
5938 7687 9.303537 ACTGAACTTAAAACTTATCGCTATCTC 57.696 33.333 0.00 0.00 0.00 2.75
5939 7688 9.654663 AACTGAACTTAAAACTTATCGCTATCT 57.345 29.630 0.00 0.00 0.00 1.98
5943 7692 8.092687 TCCTAACTGAACTTAAAACTTATCGCT 58.907 33.333 0.00 0.00 0.00 4.93
5944 7693 8.248117 TCCTAACTGAACTTAAAACTTATCGC 57.752 34.615 0.00 0.00 0.00 4.58
5949 7698 8.186163 CGGTTTTCCTAACTGAACTTAAAACTT 58.814 33.333 0.00 0.00 36.25 2.66
5950 7699 7.553760 TCGGTTTTCCTAACTGAACTTAAAACT 59.446 33.333 0.00 0.00 36.25 2.66
5951 7700 7.696755 TCGGTTTTCCTAACTGAACTTAAAAC 58.303 34.615 0.00 0.00 37.95 2.43
5952 7701 7.769970 TCTCGGTTTTCCTAACTGAACTTAAAA 59.230 33.333 0.00 0.00 35.35 1.52
5953 7702 7.274447 TCTCGGTTTTCCTAACTGAACTTAAA 58.726 34.615 0.00 0.00 35.35 1.52
5954 7703 6.819284 TCTCGGTTTTCCTAACTGAACTTAA 58.181 36.000 0.00 0.00 35.35 1.85
5955 7704 6.409524 TCTCGGTTTTCCTAACTGAACTTA 57.590 37.500 0.00 0.00 35.35 2.24
6130 7881 2.105993 AGGTTCGGAGGCTTACAGTTTT 59.894 45.455 0.00 0.00 0.00 2.43
6156 7907 1.721926 GGCTTAATCGCTAGCGTGATC 59.278 52.381 34.10 19.20 39.36 2.92
6298 8057 4.957327 TTGATGATCAAATGGATGCTTCCA 59.043 37.500 22.42 22.42 42.94 3.53
6345 8104 7.434897 CACAATTGCACACAGTAGTAACAAAAT 59.565 33.333 5.05 0.00 0.00 1.82
6649 8717 7.305763 GCGATCAACGTTCAACAAACTAAAATT 60.306 33.333 0.00 0.00 44.60 1.82
6688 8756 0.522626 TGTTCTATTCCGCGTCGACA 59.477 50.000 17.16 0.00 0.00 4.35
6759 8827 8.862325 AAGTACATCAACAAGAATATGGTTCA 57.138 30.769 0.00 0.00 0.00 3.18
6772 8840 9.772973 AGTACAATAAACAGAAGTACATCAACA 57.227 29.630 0.31 0.00 37.96 3.33
6918 8986 3.423539 AATGCAGAAGGTAACAGAGCA 57.576 42.857 0.00 0.00 41.41 4.26
7031 9101 2.671396 CACTAAACCCGAACATTCTCCG 59.329 50.000 0.00 0.00 0.00 4.63
7054 10210 1.157276 CCCCCATTTGTCCACCCAA 59.843 57.895 0.00 0.00 0.00 4.12
7102 10258 3.515562 AGATTTTGTACAAATGGGGGCA 58.484 40.909 21.17 5.53 0.00 5.36
7217 10373 7.496591 CCGGGCTACTTCAACTGTTTAATAATA 59.503 37.037 0.00 0.00 0.00 0.98
7229 10385 3.574780 GCACCGGGCTACTTCAAC 58.425 61.111 6.32 0.00 40.25 3.18
7293 10449 4.085466 CGACATTTGTTCTTGCACATTGTG 60.085 41.667 12.54 12.54 36.51 3.33
7334 10490 5.412904 CCTTTTCATCCTCACTACTTTCACC 59.587 44.000 0.00 0.00 0.00 4.02
7345 10501 0.984230 AGCCGACCTTTTCATCCTCA 59.016 50.000 0.00 0.00 0.00 3.86
7390 10546 1.826921 GGCAGATGGGCATGTCCTG 60.827 63.158 19.09 8.90 42.77 3.86
7414 10570 3.272574 GAGCATCTGGTCCTCAATTGA 57.727 47.619 8.12 8.12 36.62 2.57
7442 10598 6.016360 TCACCAATAAAAGGCCAATCATATCG 60.016 38.462 5.01 0.00 0.00 2.92
7454 10610 3.941483 ACGAGCTCATCACCAATAAAAGG 59.059 43.478 15.40 0.00 0.00 3.11
7455 10611 6.479990 TCATACGAGCTCATCACCAATAAAAG 59.520 38.462 15.40 0.00 0.00 2.27
7456 10612 6.345298 TCATACGAGCTCATCACCAATAAAA 58.655 36.000 15.40 0.00 0.00 1.52
7457 10613 5.912892 TCATACGAGCTCATCACCAATAAA 58.087 37.500 15.40 0.00 0.00 1.40
7458 10614 5.509670 CCTCATACGAGCTCATCACCAATAA 60.510 44.000 15.40 0.00 38.00 1.40
7459 10615 4.021981 CCTCATACGAGCTCATCACCAATA 60.022 45.833 15.40 0.00 38.00 1.90
7460 10616 3.244009 CCTCATACGAGCTCATCACCAAT 60.244 47.826 15.40 0.00 38.00 3.16
7461 10617 2.101415 CCTCATACGAGCTCATCACCAA 59.899 50.000 15.40 0.00 38.00 3.67
7462 10618 1.683385 CCTCATACGAGCTCATCACCA 59.317 52.381 15.40 0.00 38.00 4.17
7463 10619 1.683917 ACCTCATACGAGCTCATCACC 59.316 52.381 15.40 0.00 38.00 4.02
7464 10620 2.099921 ACACCTCATACGAGCTCATCAC 59.900 50.000 15.40 0.00 38.00 3.06
7465 10621 2.379005 ACACCTCATACGAGCTCATCA 58.621 47.619 15.40 0.00 38.00 3.07
7466 10622 3.444703 AACACCTCATACGAGCTCATC 57.555 47.619 15.40 0.00 38.00 2.92
7467 10623 3.895232 AAACACCTCATACGAGCTCAT 57.105 42.857 15.40 0.00 38.00 2.90
7468 10624 3.678056 AAAACACCTCATACGAGCTCA 57.322 42.857 15.40 0.00 38.00 4.26
7489 10645 9.520515 AGAGCTTATCTTCACAAATTCCTTTAA 57.479 29.630 0.00 0.00 32.99 1.52
7490 10646 8.950210 CAGAGCTTATCTTCACAAATTCCTTTA 58.050 33.333 0.00 0.00 35.47 1.85
7491 10647 7.449704 ACAGAGCTTATCTTCACAAATTCCTTT 59.550 33.333 0.00 0.00 35.47 3.11
7492 10648 6.944862 ACAGAGCTTATCTTCACAAATTCCTT 59.055 34.615 0.00 0.00 35.47 3.36
7501 10657 6.148480 ACATTGTCAACAGAGCTTATCTTCAC 59.852 38.462 0.00 0.00 35.47 3.18
7511 10667 0.953727 TGCCACATTGTCAACAGAGC 59.046 50.000 0.00 0.00 0.00 4.09
7528 10684 2.287728 TGATGTTGTCAACAGTGCATGC 60.288 45.455 22.16 11.82 45.95 4.06
7559 10715 5.365025 TCATTGAATTCAAAACCCCAACTCA 59.635 36.000 23.91 0.00 39.55 3.41
7584 10740 0.458370 GGAAATGTTCCGCACCATGC 60.458 55.000 0.00 0.00 40.59 4.06
7594 10750 8.674263 AGAATATGACTCTCATGGAAATGTTC 57.326 34.615 0.00 0.00 37.70 3.18
7596 10752 7.013083 GCAAGAATATGACTCTCATGGAAATGT 59.987 37.037 0.00 0.00 37.70 2.71
7603 10759 6.485648 TGGAATGCAAGAATATGACTCTCATG 59.514 38.462 0.00 0.00 37.70 3.07
7608 10764 6.541641 AGTTCTGGAATGCAAGAATATGACTC 59.458 38.462 0.00 0.00 35.03 3.36
7613 10769 5.759059 TGGAGTTCTGGAATGCAAGAATAT 58.241 37.500 0.00 0.00 35.03 1.28
7629 10785 7.278868 CCTACACTCTGTATCAAAATGGAGTTC 59.721 40.741 0.00 0.00 31.66 3.01
7659 10815 2.287188 GGCACCACGCATGAATTATCTG 60.287 50.000 0.00 0.00 45.17 2.90
7676 10832 2.890808 TTCCTCGATGAGTATGGCAC 57.109 50.000 0.00 0.00 0.00 5.01
7723 10879 7.944729 AACATGTGAGGAGTAAAAATAGCAT 57.055 32.000 0.00 0.00 0.00 3.79
7727 10883 9.513906 TCATGAAACATGTGAGGAGTAAAAATA 57.486 29.630 0.00 0.00 0.00 1.40
7765 10921 4.044336 TCACACAAAGAGCACAAAATGG 57.956 40.909 0.00 0.00 0.00 3.16
7773 10929 5.833406 TCAAAAGATTCACACAAAGAGCA 57.167 34.783 0.00 0.00 0.00 4.26
7780 10936 5.904941 ACAATGCTTCAAAAGATTCACACA 58.095 33.333 0.00 0.00 0.00 3.72
7817 10973 7.888021 TCACTTGGGCTTATTTTCTTGAAGATA 59.112 33.333 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.