Multiple sequence alignment - TraesCS1A01G303000

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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 TraesCS1A01G303000 chr1A 100.000 4196 0 0 1 4196 496483334 496479139 0.000000e+00 7749.0
1 TraesCS1A01G303000 chr1A 89.157 83 9 0 1234 1316 496481993 496481911 2.060000e-18 104.0
2 TraesCS1A01G303000 chr1D 92.636 2716 108 36 771 3456 400066933 400064280 0.000000e+00 3823.0
3 TraesCS1A01G303000 chr1D 92.776 263 9 3 3494 3748 400064283 400064023 5.120000e-99 372.0
4 TraesCS1A01G303000 chr1D 88.000 225 17 6 3976 4196 400063729 400063511 1.500000e-64 257.0
5 TraesCS1A01G303000 chr1D 94.012 167 8 1 3777 3943 400064024 400063860 6.960000e-63 252.0
6 TraesCS1A01G303000 chr1D 83.648 159 20 2 4041 4193 190781253 190781411 1.220000e-30 145.0
7 TraesCS1A01G303000 chr1D 85.926 135 14 1 3972 4106 400063859 400063730 5.660000e-29 139.0
8 TraesCS1A01G303000 chr1D 98.361 61 1 0 771 831 400070207 400070147 1.600000e-19 108.0
9 TraesCS1A01G303000 chr1D 91.892 74 6 0 1234 1307 400066368 400066295 2.060000e-18 104.0
10 TraesCS1A01G303000 chr1B 92.888 2278 107 18 771 3044 536776279 536774053 0.000000e+00 3258.0
11 TraesCS1A01G303000 chr1B 86.631 561 45 9 2828 3373 536774225 536773680 1.000000e-165 593.0
12 TraesCS1A01G303000 chr1B 84.746 177 21 5 3772 3947 536773537 536773366 5.580000e-39 172.0
13 TraesCS1A01G303000 chr5B 86.802 788 78 16 1 772 558560842 558561619 0.000000e+00 856.0
14 TraesCS1A01G303000 chr5B 92.000 50 4 0 4041 4090 618275953 618275904 2.090000e-08 71.3
15 TraesCS1A01G303000 chrUn 87.287 763 72 17 1 746 38163639 38164393 0.000000e+00 848.0
16 TraesCS1A01G303000 chr7B 86.504 778 77 16 7 770 725189508 725188745 0.000000e+00 830.0
17 TraesCS1A01G303000 chr2B 85.841 791 75 21 7 770 140228822 140228042 0.000000e+00 806.0
18 TraesCS1A01G303000 chr2B 81.959 776 89 22 1 767 713921320 713922053 9.970000e-171 610.0
19 TraesCS1A01G303000 chr3B 85.090 778 89 17 9 772 42722349 42723113 0.000000e+00 769.0
20 TraesCS1A01G303000 chr2D 84.557 790 87 26 5 768 643180731 643181511 0.000000e+00 750.0
21 TraesCS1A01G303000 chr5D 84.015 782 98 20 1 772 553419845 553420609 0.000000e+00 726.0
22 TraesCS1A01G303000 chr7A 84.131 731 87 20 55 770 668778296 668779012 0.000000e+00 680.0
23 TraesCS1A01G303000 chr3D 84.795 684 74 21 105 770 188867802 188868473 0.000000e+00 660.0
24 TraesCS1A01G303000 chr7D 84.034 595 70 16 1 578 555535992 555536578 2.210000e-152 549.0
25 TraesCS1A01G303000 chr4D 84.390 410 51 7 3384 3781 40456560 40456152 1.410000e-104 390.0
26 TraesCS1A01G303000 chr4D 80.380 158 25 4 4042 4193 443728431 443728274 9.530000e-22 115.0
27 TraesCS1A01G303000 chr4B 84.406 404 52 5 3388 3781 58975864 58975462 1.830000e-103 387.0
28 TraesCS1A01G303000 chr5A 85.616 146 16 1 4052 4192 387924113 387923968 9.400000e-32 148.0
29 TraesCS1A01G303000 chr4A 81.013 158 24 4 4042 4193 24207446 24207603 2.050000e-23 121.0


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 TraesCS1A01G303000 chr1A 496479139 496483334 4195 True 3926.500000 7749 94.578500 1 4196 2 chr1A.!!$R1 4195
1 TraesCS1A01G303000 chr1D 400063511 400070207 6696 True 722.142857 3823 91.943286 771 4196 7 chr1D.!!$R1 3425
2 TraesCS1A01G303000 chr1B 536773366 536776279 2913 True 1341.000000 3258 88.088333 771 3947 3 chr1B.!!$R1 3176
3 TraesCS1A01G303000 chr5B 558560842 558561619 777 False 856.000000 856 86.802000 1 772 1 chr5B.!!$F1 771
4 TraesCS1A01G303000 chrUn 38163639 38164393 754 False 848.000000 848 87.287000 1 746 1 chrUn.!!$F1 745
5 TraesCS1A01G303000 chr7B 725188745 725189508 763 True 830.000000 830 86.504000 7 770 1 chr7B.!!$R1 763
6 TraesCS1A01G303000 chr2B 140228042 140228822 780 True 806.000000 806 85.841000 7 770 1 chr2B.!!$R1 763
7 TraesCS1A01G303000 chr2B 713921320 713922053 733 False 610.000000 610 81.959000 1 767 1 chr2B.!!$F1 766
8 TraesCS1A01G303000 chr3B 42722349 42723113 764 False 769.000000 769 85.090000 9 772 1 chr3B.!!$F1 763
9 TraesCS1A01G303000 chr2D 643180731 643181511 780 False 750.000000 750 84.557000 5 768 1 chr2D.!!$F1 763
10 TraesCS1A01G303000 chr5D 553419845 553420609 764 False 726.000000 726 84.015000 1 772 1 chr5D.!!$F1 771
11 TraesCS1A01G303000 chr7A 668778296 668779012 716 False 680.000000 680 84.131000 55 770 1 chr7A.!!$F1 715
12 TraesCS1A01G303000 chr3D 188867802 188868473 671 False 660.000000 660 84.795000 105 770 1 chr3D.!!$F1 665
13 TraesCS1A01G303000 chr7D 555535992 555536578 586 False 549.000000 549 84.034000 1 578 1 chr7D.!!$F1 577

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
648 710 0.108329 AGTATTCCCGGTGTGCGAAG 60.108 55.0 0.00 0.0 0.00 3.79 F
845 4184 0.179233 CTAAAAACGCGGGCGAGTTC 60.179 55.0 20.98 0.0 42.83 3.01 F
955 4294 0.331278 CCACCACCTATGCTTGGGAA 59.669 55.0 9.11 0.0 37.18 3.97 F
1054 4393 0.391597 GAACACCTTCGTGGAGGACA 59.608 55.0 0.00 0.0 44.86 4.02 F
2285 5641 0.040067 GCTGGCGTTGGAGTTTCTTG 60.040 55.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 5342 0.179187 AAGTCGACGATCGCTGTCTG 60.179 55.0 16.60 2.76 40.21 3.51 R
1991 5343 0.179187 CAAGTCGACGATCGCTGTCT 60.179 55.0 16.60 8.04 40.21 3.41 R
1992 5344 0.454620 ACAAGTCGACGATCGCTGTC 60.455 55.0 16.60 4.44 40.21 3.51 R
3003 6404 0.402861 GAGATGGGGGATTGGGGGTA 60.403 60.0 0.00 0.00 0.00 3.69 R
3753 7309 0.028110 GCCAAACGGATGCGATCTTC 59.972 55.0 15.49 0.00 0.00 2.87 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
82 83 3.670625 TGTTGTAGTGGCTAGCGAAATT 58.329 40.909 9.00 0.00 0.00 1.82
86 87 1.954927 AGTGGCTAGCGAAATTAGGC 58.045 50.000 9.00 0.00 42.30 3.93
123 124 2.422597 CAAGTTTGACTCCACGGCATA 58.577 47.619 0.00 0.00 0.00 3.14
186 188 8.710835 AAAAGAAAGAAAGAATTTTTACGGCA 57.289 26.923 0.00 0.00 39.27 5.69
259 268 5.003804 AGTCTGCAACTAACAATCCGAAAT 58.996 37.500 0.00 0.00 36.07 2.17
364 400 4.311816 AGCATGTGAAAAACTGTTGGAG 57.688 40.909 0.00 0.00 0.00 3.86
375 411 5.505173 AAACTGTTGGAGTTCTGAACATG 57.495 39.130 21.50 0.00 44.68 3.21
486 546 9.092876 GGATTGAATTCGTGCCAAAATATAAAA 57.907 29.630 0.04 0.00 0.00 1.52
562 624 4.908736 ACTTCACGAATTCTTGTTGTGTG 58.091 39.130 11.31 6.47 32.55 3.82
588 650 2.578664 CCGGCCCAAATTCTTGCC 59.421 61.111 0.00 2.77 40.54 4.52
589 651 2.578664 CGGCCCAAATTCTTGCCC 59.421 61.111 0.00 0.00 40.87 5.36
590 652 2.578664 GGCCCAAATTCTTGCCCG 59.421 61.111 0.00 0.00 37.94 6.13
591 653 2.282783 GGCCCAAATTCTTGCCCGT 61.283 57.895 0.00 0.00 37.94 5.28
592 654 1.079888 GCCCAAATTCTTGCCCGTG 60.080 57.895 0.00 0.00 0.00 4.94
593 655 1.531739 GCCCAAATTCTTGCCCGTGA 61.532 55.000 0.00 0.00 0.00 4.35
608 670 1.366679 CGTGACCGTGAGAGTAGCTA 58.633 55.000 0.00 0.00 0.00 3.32
645 707 2.012937 TTTAGTATTCCCGGTGTGCG 57.987 50.000 0.00 0.00 0.00 5.34
648 710 0.108329 AGTATTCCCGGTGTGCGAAG 60.108 55.000 0.00 0.00 0.00 3.79
662 724 3.927555 CGAAGCAGGTTTAGGGTCA 57.072 52.632 0.00 0.00 0.00 4.02
711 776 6.209391 AGAGTGTCAATTTTCGGGATTCAAAT 59.791 34.615 0.00 0.00 0.00 2.32
728 793 8.935844 GGATTCAAATTTCAGGGTTTGATTTAC 58.064 33.333 1.89 0.00 42.12 2.01
729 794 9.710900 GATTCAAATTTCAGGGTTTGATTTACT 57.289 29.630 1.89 0.00 42.12 2.24
759 824 8.149647 TGTCTACAACTTCCGAGGTTTATTTTA 58.850 33.333 0.00 0.00 0.00 1.52
845 4184 0.179233 CTAAAAACGCGGGCGAGTTC 60.179 55.000 20.98 0.00 42.83 3.01
935 4274 3.184683 GAAGAGAGCACCGCAGCG 61.185 66.667 8.18 8.18 40.15 5.18
953 4292 1.754234 GCCACCACCTATGCTTGGG 60.754 63.158 0.00 0.00 37.18 4.12
954 4293 1.998530 CCACCACCTATGCTTGGGA 59.001 57.895 9.11 0.00 37.18 4.37
955 4294 0.331278 CCACCACCTATGCTTGGGAA 59.669 55.000 9.11 0.00 37.18 3.97
980 4319 1.101635 TAGGACTGCGACTCCATCCG 61.102 60.000 0.00 0.00 34.46 4.18
1054 4393 0.391597 GAACACCTTCGTGGAGGACA 59.608 55.000 0.00 0.00 44.86 4.02
1059 4398 1.374252 CTTCGTGGAGGACAACCGG 60.374 63.158 0.00 0.00 41.83 5.28
1223 4562 3.554692 CGACCGCTTCACCGCATC 61.555 66.667 0.00 0.00 0.00 3.91
1224 4563 3.195698 GACCGCTTCACCGCATCC 61.196 66.667 0.00 0.00 0.00 3.51
1464 4804 2.041922 TCCCCCATCTCCTCCGTG 60.042 66.667 0.00 0.00 0.00 4.94
1521 4861 1.743321 CTGAGACCTCGCAGGATCCC 61.743 65.000 8.55 0.00 39.61 3.85
1578 4918 0.663568 ACGACGACTCCAAGCTTTCG 60.664 55.000 14.96 14.96 37.50 3.46
1581 4921 2.730672 CGACTCCAAGCTTTCGCCG 61.731 63.158 5.42 0.00 36.60 6.46
1590 4930 0.951040 AGCTTTCGCCGGTGAAGAAG 60.951 55.000 27.92 23.85 36.60 2.85
1653 4993 2.169789 CAAGGCCATGCTCGACGAG 61.170 63.158 20.56 20.56 0.00 4.18
1697 5037 3.150949 CCAGCCTCTGGTCACACA 58.849 61.111 4.74 0.00 45.82 3.72
1732 5072 1.645710 AAGGATCGGTCACCTGTTCT 58.354 50.000 0.00 0.00 36.56 3.01
1733 5073 1.645710 AGGATCGGTCACCTGTTCTT 58.354 50.000 0.00 0.00 34.99 2.52
1734 5074 1.978580 AGGATCGGTCACCTGTTCTTT 59.021 47.619 0.00 0.00 34.99 2.52
1735 5075 2.028020 AGGATCGGTCACCTGTTCTTTC 60.028 50.000 0.00 0.00 34.99 2.62
1753 5093 5.603596 TCTTTCCATGGAAATATGCAATGC 58.396 37.500 34.40 0.00 42.34 3.56
1812 5152 6.161381 CACTCCATTTAAGCTTTGATTTGCT 58.839 36.000 3.20 0.00 41.82 3.91
1815 5155 6.757237 TCCATTTAAGCTTTGATTTGCTTCA 58.243 32.000 3.20 0.00 45.09 3.02
1832 5183 3.364366 GCTTCACAACATTTCTCACCTCG 60.364 47.826 0.00 0.00 0.00 4.63
1845 5196 1.013005 CACCTCGTCAGCAAGCTCAG 61.013 60.000 0.00 0.00 0.00 3.35
1985 5337 1.027792 GGCTAATTCCGGCGTCCAAA 61.028 55.000 6.01 0.00 0.00 3.28
1997 5349 1.279840 GTCCAAACGCACAGACAGC 59.720 57.895 0.00 0.00 0.00 4.40
2285 5641 0.040067 GCTGGCGTTGGAGTTTCTTG 60.040 55.000 0.00 0.00 0.00 3.02
2287 5643 0.106918 TGGCGTTGGAGTTTCTTGGT 60.107 50.000 0.00 0.00 0.00 3.67
2289 5645 2.223745 GGCGTTGGAGTTTCTTGGTTA 58.776 47.619 0.00 0.00 0.00 2.85
2486 5842 0.462047 GCCAACGAGGACCTGGTATG 60.462 60.000 9.85 9.97 41.22 2.39
2490 5846 0.465705 ACGAGGACCTGGTATGCATG 59.534 55.000 10.16 0.00 0.00 4.06
2537 5893 3.451894 CCTTGCACCGGCCATTCC 61.452 66.667 0.00 0.00 40.13 3.01
2545 5901 1.049289 ACCGGCCATTCCTACTCCTC 61.049 60.000 0.00 0.00 0.00 3.71
2567 5923 1.443194 GACATGGTTGCTTGCTGCG 60.443 57.895 0.00 0.00 46.63 5.18
2568 5924 2.807895 CATGGTTGCTTGCTGCGC 60.808 61.111 0.00 0.00 46.63 6.09
2569 5925 3.296836 ATGGTTGCTTGCTGCGCA 61.297 55.556 10.98 10.98 46.63 6.09
2570 5926 2.642254 ATGGTTGCTTGCTGCGCAT 61.642 52.632 12.24 0.00 46.63 4.73
2727 6083 1.885887 GAGGACATCATCGAGGAGGAG 59.114 57.143 19.38 7.06 0.00 3.69
2746 6102 6.215495 AGGAGGAAGAAGAAGAAGAATACG 57.785 41.667 0.00 0.00 0.00 3.06
2747 6103 5.952947 AGGAGGAAGAAGAAGAAGAATACGA 59.047 40.000 0.00 0.00 0.00 3.43
2748 6104 6.096282 AGGAGGAAGAAGAAGAAGAATACGAG 59.904 42.308 0.00 0.00 0.00 4.18
2784 6140 2.514582 AGAATACGAGGAGGAGGAGGAA 59.485 50.000 0.00 0.00 0.00 3.36
2785 6141 2.668144 ATACGAGGAGGAGGAGGAAG 57.332 55.000 0.00 0.00 0.00 3.46
2786 6142 1.592948 TACGAGGAGGAGGAGGAAGA 58.407 55.000 0.00 0.00 0.00 2.87
2808 6164 4.664677 GAGCACGACACACCGGCT 62.665 66.667 0.00 0.00 38.24 5.52
2810 6166 3.110178 GCACGACACACCGGCTAC 61.110 66.667 0.00 0.00 0.00 3.58
2812 6168 2.913578 ACGACACACCGGCTACCA 60.914 61.111 0.00 0.00 0.00 3.25
2813 6169 2.340809 CGACACACCGGCTACCAA 59.659 61.111 0.00 0.00 0.00 3.67
2814 6170 1.736645 CGACACACCGGCTACCAAG 60.737 63.158 0.00 0.00 0.00 3.61
2861 6217 1.340889 ACATCACACCAACAATGTGCC 59.659 47.619 0.20 0.00 45.82 5.01
2974 6375 3.569210 CTGCCCCACAGTCACCCA 61.569 66.667 0.00 0.00 41.86 4.51
3003 6404 2.616330 CGACAATGTGCCGGTTGCT 61.616 57.895 1.90 0.00 42.00 3.91
3023 6424 1.387926 CCCCCAATCCCCCATCTCT 60.388 63.158 0.00 0.00 0.00 3.10
3039 6440 0.390866 CTCTCTGCACCGACAATGCT 60.391 55.000 0.00 0.00 43.77 3.79
3150 6560 4.332819 CAGACAAACCCCATTCGAGATAAC 59.667 45.833 0.00 0.00 0.00 1.89
3196 6609 0.815734 GCAGCAATGCCAAGACTGAT 59.184 50.000 0.00 0.00 0.00 2.90
3199 6612 2.490509 CAGCAATGCCAAGACTGATGAA 59.509 45.455 0.00 0.00 0.00 2.57
3314 6732 2.163818 TTACCAGTTCGCCTGTTCAG 57.836 50.000 1.99 0.00 39.74 3.02
3353 6771 2.299013 GCATCATATCCGTGGGTCTGTA 59.701 50.000 0.00 0.00 0.00 2.74
3425 6973 6.502136 TGTTGCATACCGTTTCATTGATAA 57.498 33.333 0.00 0.00 0.00 1.75
3427 6975 6.150307 TGTTGCATACCGTTTCATTGATAAGT 59.850 34.615 0.00 0.00 0.00 2.24
3442 6990 5.562506 TGATAAGTGGAGAGAACGTACAG 57.437 43.478 0.00 0.00 0.00 2.74
3448 6996 1.272769 GGAGAGAACGTACAGGTTGCT 59.727 52.381 0.00 0.00 0.00 3.91
3453 7001 1.654105 GAACGTACAGGTTGCTGATCG 59.346 52.381 0.00 0.00 0.00 3.69
3454 7002 0.885879 ACGTACAGGTTGCTGATCGA 59.114 50.000 1.14 0.00 0.00 3.59
3455 7003 1.135373 ACGTACAGGTTGCTGATCGAG 60.135 52.381 1.14 0.00 0.00 4.04
3456 7004 1.799181 CGTACAGGTTGCTGATCGAGG 60.799 57.143 0.00 0.00 0.00 4.63
3457 7005 0.824109 TACAGGTTGCTGATCGAGGG 59.176 55.000 0.00 0.00 0.00 4.30
3458 7006 1.153289 CAGGTTGCTGATCGAGGGG 60.153 63.158 0.00 0.00 0.00 4.79
3459 7007 2.190578 GGTTGCTGATCGAGGGGG 59.809 66.667 0.00 0.00 0.00 5.40
3460 7008 2.514824 GTTGCTGATCGAGGGGGC 60.515 66.667 0.00 0.00 0.00 5.80
3461 7009 3.008517 TTGCTGATCGAGGGGGCA 61.009 61.111 0.00 0.00 0.00 5.36
3462 7010 2.377810 TTGCTGATCGAGGGGGCAT 61.378 57.895 6.10 0.00 32.87 4.40
3463 7011 1.053835 TTGCTGATCGAGGGGGCATA 61.054 55.000 6.10 0.00 32.87 3.14
3464 7012 1.004440 GCTGATCGAGGGGGCATAC 60.004 63.158 0.00 0.00 0.00 2.39
3465 7013 1.758440 GCTGATCGAGGGGGCATACA 61.758 60.000 0.00 0.00 0.00 2.29
3466 7014 0.034059 CTGATCGAGGGGGCATACAC 59.966 60.000 0.00 0.00 0.00 2.90
3467 7015 1.006102 GATCGAGGGGGCATACACG 60.006 63.158 0.00 0.00 0.00 4.49
3468 7016 1.745320 GATCGAGGGGGCATACACGT 61.745 60.000 0.00 0.00 0.00 4.49
3469 7017 0.468585 ATCGAGGGGGCATACACGTA 60.469 55.000 0.00 0.00 0.00 3.57
3470 7018 0.468585 TCGAGGGGGCATACACGTAT 60.469 55.000 0.00 0.00 0.00 3.06
3471 7019 0.038526 CGAGGGGGCATACACGTATC 60.039 60.000 0.00 0.00 0.00 2.24
3472 7020 1.045407 GAGGGGGCATACACGTATCA 58.955 55.000 0.00 0.00 0.00 2.15
3473 7021 1.000955 GAGGGGGCATACACGTATCAG 59.999 57.143 0.00 0.00 0.00 2.90
3474 7022 0.602905 GGGGGCATACACGTATCAGC 60.603 60.000 0.00 0.00 0.00 4.26
3475 7023 0.105964 GGGGCATACACGTATCAGCA 59.894 55.000 0.00 0.00 0.00 4.41
3476 7024 1.270839 GGGGCATACACGTATCAGCAT 60.271 52.381 0.00 0.00 0.00 3.79
3477 7025 2.069273 GGGCATACACGTATCAGCATC 58.931 52.381 0.00 0.00 0.00 3.91
3478 7026 2.069273 GGCATACACGTATCAGCATCC 58.931 52.381 0.00 0.00 0.00 3.51
3479 7027 2.069273 GCATACACGTATCAGCATCCC 58.931 52.381 0.00 0.00 0.00 3.85
3480 7028 2.688507 CATACACGTATCAGCATCCCC 58.311 52.381 0.00 0.00 0.00 4.81
3481 7029 1.783071 TACACGTATCAGCATCCCCA 58.217 50.000 0.00 0.00 0.00 4.96
3482 7030 0.465705 ACACGTATCAGCATCCCCAG 59.534 55.000 0.00 0.00 0.00 4.45
3483 7031 0.250038 CACGTATCAGCATCCCCAGG 60.250 60.000 0.00 0.00 0.00 4.45
3484 7032 0.398522 ACGTATCAGCATCCCCAGGA 60.399 55.000 0.00 0.00 35.55 3.86
3485 7033 0.319728 CGTATCAGCATCCCCAGGAG 59.680 60.000 0.00 0.00 34.05 3.69
3486 7034 0.036022 GTATCAGCATCCCCAGGAGC 59.964 60.000 0.00 0.00 34.05 4.70
3487 7035 0.400381 TATCAGCATCCCCAGGAGCA 60.400 55.000 0.00 0.00 34.05 4.26
3488 7036 1.992519 ATCAGCATCCCCAGGAGCAC 61.993 60.000 0.00 0.00 34.05 4.40
3489 7037 2.611800 AGCATCCCCAGGAGCACA 60.612 61.111 0.00 0.00 34.05 4.57
3490 7038 2.124403 GCATCCCCAGGAGCACAG 60.124 66.667 0.00 0.00 34.05 3.66
3491 7039 2.124403 CATCCCCAGGAGCACAGC 60.124 66.667 0.00 0.00 34.05 4.40
3492 7040 2.611800 ATCCCCAGGAGCACAGCA 60.612 61.111 0.00 0.00 34.05 4.41
3533 7081 0.108329 AGCCTCGGTACATTCGGTTG 60.108 55.000 0.00 0.00 0.00 3.77
3534 7082 1.087771 GCCTCGGTACATTCGGTTGG 61.088 60.000 0.00 0.00 0.00 3.77
3535 7083 0.533491 CCTCGGTACATTCGGTTGGA 59.467 55.000 0.00 0.00 0.00 3.53
3550 7106 3.126831 GGTTGGAGATCACTAATGCGAG 58.873 50.000 0.00 0.00 0.00 5.03
3598 7154 1.117749 CCGAGCCTCCTCCATGATGA 61.118 60.000 0.00 0.00 34.49 2.92
3612 7168 0.248784 TGATGATGCAGACGAGCTCG 60.249 55.000 33.45 33.45 46.33 5.03
3636 7192 1.305297 AGATGGCTGGAGGTCGTCA 60.305 57.895 0.00 0.00 37.98 4.35
3662 7218 2.823829 CGGCGTTGCTATGCTTCCC 61.824 63.158 12.07 0.00 36.50 3.97
3675 7231 0.106708 GCTTCCCGATACTCCATGCA 59.893 55.000 0.00 0.00 0.00 3.96
3698 7254 7.149307 GCAGTTAGGGCTATAAGAGAGTTAAG 58.851 42.308 0.00 0.00 0.00 1.85
3749 7305 2.352805 GGAGGCAGACCACCAAGG 59.647 66.667 0.00 0.00 45.56 3.61
3750 7306 2.352805 GAGGCAGACCACCAAGGG 59.647 66.667 0.00 0.00 43.89 3.95
3751 7307 2.121963 AGGCAGACCACCAAGGGA 60.122 61.111 0.00 0.00 43.89 4.20
3752 7308 1.774217 AGGCAGACCACCAAGGGAA 60.774 57.895 0.00 0.00 43.89 3.97
3753 7309 1.303643 GGCAGACCACCAAGGGAAG 60.304 63.158 0.00 0.00 43.89 3.46
3754 7310 1.761174 GCAGACCACCAAGGGAAGA 59.239 57.895 0.00 0.00 43.89 2.87
3755 7311 0.110486 GCAGACCACCAAGGGAAGAA 59.890 55.000 0.00 0.00 43.89 2.52
3756 7312 1.884067 GCAGACCACCAAGGGAAGAAG 60.884 57.143 0.00 0.00 43.89 2.85
3757 7313 1.699634 CAGACCACCAAGGGAAGAAGA 59.300 52.381 0.00 0.00 43.89 2.87
3758 7314 2.307098 CAGACCACCAAGGGAAGAAGAT 59.693 50.000 0.00 0.00 43.89 2.40
3759 7315 2.573915 AGACCACCAAGGGAAGAAGATC 59.426 50.000 0.00 0.00 43.89 2.75
3760 7316 1.279271 ACCACCAAGGGAAGAAGATCG 59.721 52.381 0.00 0.00 43.89 3.69
3761 7317 1.373570 CACCAAGGGAAGAAGATCGC 58.626 55.000 0.00 0.00 0.00 4.58
3762 7318 0.984230 ACCAAGGGAAGAAGATCGCA 59.016 50.000 0.00 0.00 34.91 5.10
3763 7319 1.561542 ACCAAGGGAAGAAGATCGCAT 59.438 47.619 0.00 0.00 34.91 4.73
3764 7320 2.216898 CCAAGGGAAGAAGATCGCATC 58.783 52.381 0.00 0.00 34.91 3.91
3765 7321 2.216898 CAAGGGAAGAAGATCGCATCC 58.783 52.381 4.83 4.83 34.91 3.51
3766 7322 0.390860 AGGGAAGAAGATCGCATCCG 59.609 55.000 6.75 0.00 34.91 4.18
3767 7323 0.105039 GGGAAGAAGATCGCATCCGT 59.895 55.000 6.75 0.00 35.54 4.69
3768 7324 1.473434 GGGAAGAAGATCGCATCCGTT 60.473 52.381 6.75 0.00 35.54 4.44
3769 7325 2.280628 GGAAGAAGATCGCATCCGTTT 58.719 47.619 0.00 0.00 35.54 3.60
3770 7326 2.030946 GGAAGAAGATCGCATCCGTTTG 59.969 50.000 0.00 0.00 35.54 2.93
3771 7327 1.656652 AGAAGATCGCATCCGTTTGG 58.343 50.000 0.00 0.00 35.54 3.28
3772 7328 0.028110 GAAGATCGCATCCGTTTGGC 59.972 55.000 0.00 0.00 35.54 4.52
3773 7329 0.676466 AAGATCGCATCCGTTTGGCA 60.676 50.000 0.00 0.00 35.54 4.92
3774 7330 0.676466 AGATCGCATCCGTTTGGCAA 60.676 50.000 0.00 0.00 35.54 4.52
3868 7424 2.159037 GCCACACTTAAGGCGAGTTTAC 59.841 50.000 7.53 0.00 41.70 2.01
3870 7426 3.054878 CACACTTAAGGCGAGTTTACGT 58.945 45.455 7.53 0.00 35.59 3.57
3880 7436 1.497991 GAGTTTACGTCAGCTGTGCA 58.502 50.000 14.67 0.00 0.00 4.57
3902 7458 5.567915 GCAAACTGCGGAATTCTAGTAAAAC 59.432 40.000 5.23 0.00 31.71 2.43
3903 7459 6.567891 GCAAACTGCGGAATTCTAGTAAAACT 60.568 38.462 5.23 0.00 31.71 2.66
3954 7510 8.731275 ATGATTCTAATTAACGTTCACATCCA 57.269 30.769 2.82 0.00 0.00 3.41
3955 7511 8.731275 TGATTCTAATTAACGTTCACATCCAT 57.269 30.769 2.82 0.00 0.00 3.41
3956 7512 9.825109 TGATTCTAATTAACGTTCACATCCATA 57.175 29.630 2.82 0.00 0.00 2.74
3960 7516 9.878667 TCTAATTAACGTTCACATCCATAAAGA 57.121 29.630 2.82 0.00 0.00 2.52
3966 7522 8.519492 AACGTTCACATCCATAAAGAAAAATG 57.481 30.769 0.00 0.00 0.00 2.32
3967 7523 7.881142 ACGTTCACATCCATAAAGAAAAATGA 58.119 30.769 0.00 0.00 0.00 2.57
3968 7524 7.807907 ACGTTCACATCCATAAAGAAAAATGAC 59.192 33.333 0.00 0.00 0.00 3.06
3969 7525 8.023128 CGTTCACATCCATAAAGAAAAATGACT 58.977 33.333 0.00 0.00 0.00 3.41
3970 7526 9.132521 GTTCACATCCATAAAGAAAAATGACTG 57.867 33.333 0.00 0.00 0.00 3.51
4022 7641 4.233521 TGAGGTCTAGGGAAGGGTTATACA 59.766 45.833 0.00 0.00 0.00 2.29
4023 7642 4.817286 AGGTCTAGGGAAGGGTTATACAG 58.183 47.826 0.00 0.00 0.00 2.74
4056 7733 3.328505 CCTTGCCCAATGTTAAAAGCTG 58.671 45.455 0.00 0.00 0.00 4.24
4059 7736 1.276138 GCCCAATGTTAAAAGCTGCCT 59.724 47.619 0.00 0.00 0.00 4.75
4062 7739 3.578688 CCAATGTTAAAAGCTGCCTCAC 58.421 45.455 0.00 0.00 0.00 3.51
4075 7752 3.072476 CTCACCAGGTGGGGTCTG 58.928 66.667 20.14 0.15 39.79 3.51
4090 7767 3.583526 GGGGTCTGGAGAAGGATTATACC 59.416 52.174 0.00 0.00 0.00 2.73
4091 7768 4.232091 GGGTCTGGAGAAGGATTATACCA 58.768 47.826 0.00 0.00 0.00 3.25
4092 7769 4.284746 GGGTCTGGAGAAGGATTATACCAG 59.715 50.000 0.00 0.00 41.08 4.00
4093 7770 5.148502 GGTCTGGAGAAGGATTATACCAGA 58.851 45.833 0.00 0.00 43.80 3.86
4096 7773 6.202331 TCTGGAGAAGGATTATACCAGACAA 58.798 40.000 0.00 0.00 42.40 3.18
4099 7776 5.297569 AGAAGGATTATACCAGACAAGCC 57.702 43.478 0.00 0.00 0.00 4.35
4100 7777 4.971924 AGAAGGATTATACCAGACAAGCCT 59.028 41.667 0.00 0.00 39.68 4.58
4101 7778 5.717119 AAGGATTATACCAGACAAGCCTT 57.283 39.130 0.00 0.00 41.85 4.35
4102 7779 6.615726 AGAAGGATTATACCAGACAAGCCTTA 59.384 38.462 3.30 0.00 45.46 2.69
4122 7802 1.637553 ACCCCAGTGCAATTCAGAGAT 59.362 47.619 0.00 0.00 0.00 2.75
4127 7807 2.089980 AGTGCAATTCAGAGATGCCAC 58.910 47.619 6.96 5.85 39.31 5.01
4128 7808 1.814394 GTGCAATTCAGAGATGCCACA 59.186 47.619 6.96 0.00 39.31 4.17
4144 7824 1.888512 CCACATCAAACCCAAGACCTG 59.111 52.381 0.00 0.00 0.00 4.00
4154 7834 0.751277 CCAAGACCTGTTGGCACACA 60.751 55.000 0.00 0.00 40.70 3.72
4161 7841 1.228521 TGTTGGCACACATGGGGAG 60.229 57.895 0.00 0.00 39.29 4.30
4177 7857 1.608283 GGGAGTACTTCACCACTGTGC 60.608 57.143 2.92 0.00 42.46 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.720090 ACAACAGACGACTATGACTTACG 58.280 43.478 6.82 0.00 0.00 3.18
63 64 4.439057 CCTAATTTCGCTAGCCACTACAA 58.561 43.478 9.66 0.00 0.00 2.41
92 93 0.260230 TCAAACTTGGGACCTGGCAA 59.740 50.000 0.00 0.00 0.00 4.52
208 217 0.322187 ACGGCCCACCAGACATAAAC 60.322 55.000 0.00 0.00 34.57 2.01
364 400 7.275341 TCACATTTGTCAAAACATGTTCAGAAC 59.725 33.333 12.39 6.32 34.73 3.01
588 650 1.136984 GCTACTCTCACGGTCACGG 59.863 63.158 0.00 0.00 46.48 4.94
590 652 2.358015 ACTAGCTACTCTCACGGTCAC 58.642 52.381 0.00 0.00 0.00 3.67
591 653 2.783609 ACTAGCTACTCTCACGGTCA 57.216 50.000 0.00 0.00 0.00 4.02
592 654 4.213906 GGATAACTAGCTACTCTCACGGTC 59.786 50.000 0.00 0.00 0.00 4.79
593 655 4.136051 GGATAACTAGCTACTCTCACGGT 58.864 47.826 0.00 0.00 0.00 4.83
627 689 1.184431 TCGCACACCGGGAATACTAA 58.816 50.000 6.32 0.00 37.59 2.24
645 707 4.929819 TTTTTGACCCTAAACCTGCTTC 57.070 40.909 0.00 0.00 0.00 3.86
648 710 4.556233 GTCATTTTTGACCCTAAACCTGC 58.444 43.478 0.00 0.00 32.97 4.85
662 724 5.536916 TGAACTTGTAATCCCGGTCATTTTT 59.463 36.000 0.00 0.00 0.00 1.94
711 776 8.536175 AGACAAAAAGTAAATCAAACCCTGAAA 58.464 29.630 0.00 0.00 37.67 2.69
728 793 4.814771 ACCTCGGAAGTTGTAGACAAAAAG 59.185 41.667 0.00 0.00 37.63 2.27
729 794 4.773013 ACCTCGGAAGTTGTAGACAAAAA 58.227 39.130 0.00 0.00 37.63 1.94
935 4274 1.754234 CCCAAGCATAGGTGGTGGC 60.754 63.158 0.00 0.00 35.94 5.01
953 4292 0.731855 GTCGCAGTCCTACCGTGTTC 60.732 60.000 0.00 0.00 0.00 3.18
954 4293 1.177256 AGTCGCAGTCCTACCGTGTT 61.177 55.000 0.00 0.00 0.00 3.32
955 4294 1.584380 GAGTCGCAGTCCTACCGTGT 61.584 60.000 0.00 0.00 0.00 4.49
1209 4548 2.892425 GAGGATGCGGTGAAGCGG 60.892 66.667 3.89 0.00 40.67 5.52
1256 4595 3.606065 GACGACGTGACGGGGTCAG 62.606 68.421 20.41 5.48 43.57 3.51
1444 4784 1.532794 CGGAGGAGATGGGGGAGAG 60.533 68.421 0.00 0.00 0.00 3.20
1446 4786 2.136878 CACGGAGGAGATGGGGGAG 61.137 68.421 0.00 0.00 0.00 4.30
1447 4787 2.041922 CACGGAGGAGATGGGGGA 60.042 66.667 0.00 0.00 0.00 4.81
1448 4788 3.164269 CCACGGAGGAGATGGGGG 61.164 72.222 0.00 0.00 41.22 5.40
1449 4789 3.866582 GCCACGGAGGAGATGGGG 61.867 72.222 0.00 0.00 41.22 4.96
1495 4835 1.138671 GCGAGGTCTCAGAGCAGAC 59.861 63.158 6.64 0.00 41.99 3.51
1578 4918 1.446272 CTCGTCCTTCTTCACCGGC 60.446 63.158 0.00 0.00 0.00 6.13
1581 4921 0.879765 TCGTCTCGTCCTTCTTCACC 59.120 55.000 0.00 0.00 0.00 4.02
1590 4930 1.446272 CCCTTGCTTCGTCTCGTCC 60.446 63.158 0.00 0.00 0.00 4.79
1732 5072 4.706035 GGCATTGCATATTTCCATGGAAA 58.294 39.130 35.78 35.78 46.37 3.13
1733 5073 3.243805 CGGCATTGCATATTTCCATGGAA 60.244 43.478 23.63 23.63 40.02 3.53
1734 5074 2.296752 CGGCATTGCATATTTCCATGGA 59.703 45.455 11.44 11.44 0.00 3.41
1735 5075 2.679450 CGGCATTGCATATTTCCATGG 58.321 47.619 11.39 4.97 0.00 3.66
1753 5093 1.541147 TGAAGCAAAATCTGAAGGCGG 59.459 47.619 0.00 0.00 0.00 6.13
1812 5152 3.804036 ACGAGGTGAGAAATGTTGTGAA 58.196 40.909 0.00 0.00 0.00 3.18
1815 5155 3.393800 CTGACGAGGTGAGAAATGTTGT 58.606 45.455 0.00 0.00 0.00 3.32
1832 5183 1.287730 CCGTGACTGAGCTTGCTGAC 61.288 60.000 0.00 0.00 0.00 3.51
1845 5196 1.211190 GTCGTAGGACCACCGTGAC 59.789 63.158 4.15 0.00 41.83 3.67
1902 5253 1.574702 CGAACTTTGGCCCTTCCGAC 61.575 60.000 0.00 0.00 37.80 4.79
1914 5265 0.322546 GCCCTCCCATGTCGAACTTT 60.323 55.000 0.00 0.00 0.00 2.66
1988 5340 1.128724 GTCGACGATCGCTGTCTGTG 61.129 60.000 16.60 0.00 40.21 3.66
1989 5341 1.134901 GTCGACGATCGCTGTCTGT 59.865 57.895 16.60 0.00 40.21 3.41
1990 5342 0.179187 AAGTCGACGATCGCTGTCTG 60.179 55.000 16.60 2.76 40.21 3.51
1991 5343 0.179187 CAAGTCGACGATCGCTGTCT 60.179 55.000 16.60 8.04 40.21 3.41
1992 5344 0.454620 ACAAGTCGACGATCGCTGTC 60.455 55.000 16.60 4.44 40.21 3.51
1993 5345 0.454620 GACAAGTCGACGATCGCTGT 60.455 55.000 16.60 8.96 40.21 4.40
1997 5349 0.523546 CCCTGACAAGTCGACGATCG 60.524 60.000 14.88 14.88 42.10 3.69
2101 5457 1.227497 GATCTGCAGCTTCCTCCCG 60.227 63.158 9.47 0.00 0.00 5.14
2155 5511 2.985847 GTGCCCAGGTTCAGGTGC 60.986 66.667 0.00 0.00 0.00 5.01
2179 5535 0.746659 TCATCATCGGCGACATGAGT 59.253 50.000 22.79 8.68 33.48 3.41
2267 5623 0.593128 CCAAGAAACTCCAACGCCAG 59.407 55.000 0.00 0.00 0.00 4.85
2271 5627 5.878116 TCCATATAACCAAGAAACTCCAACG 59.122 40.000 0.00 0.00 0.00 4.10
2277 5633 7.500559 GCTCTCATTCCATATAACCAAGAAACT 59.499 37.037 0.00 0.00 0.00 2.66
2285 5641 4.904241 AGCTGCTCTCATTCCATATAACC 58.096 43.478 0.00 0.00 0.00 2.85
2287 5643 5.555017 GGAAGCTGCTCTCATTCCATATAA 58.445 41.667 11.49 0.00 40.78 0.98
2289 5645 3.556633 CGGAAGCTGCTCTCATTCCATAT 60.557 47.826 15.49 0.00 41.08 1.78
2319 5675 2.047274 ATCACGTTCGCCACCTGG 60.047 61.111 0.00 0.00 38.53 4.45
2486 5842 1.293267 GCCAACCACAACATGCATGC 61.293 55.000 26.53 11.82 0.00 4.06
2490 5846 3.136750 TGGCCAACCACAACATGC 58.863 55.556 0.61 0.00 42.67 4.06
2537 5893 3.686726 GCAACCATGTCTTTGAGGAGTAG 59.313 47.826 3.73 0.00 0.00 2.57
2545 5901 2.400399 CAGCAAGCAACCATGTCTTTG 58.600 47.619 0.00 0.00 0.00 2.77
2567 5923 1.709147 CTGCTTCCGTACCTGCATGC 61.709 60.000 11.82 11.82 34.79 4.06
2568 5924 1.709147 GCTGCTTCCGTACCTGCATG 61.709 60.000 0.00 0.00 34.79 4.06
2569 5925 1.450312 GCTGCTTCCGTACCTGCAT 60.450 57.895 0.00 0.00 34.79 3.96
2570 5926 2.047274 GCTGCTTCCGTACCTGCA 60.047 61.111 0.00 0.00 0.00 4.41
2727 6083 6.210287 TCCTCGTATTCTTCTTCTTCTTCC 57.790 41.667 0.00 0.00 0.00 3.46
2746 6102 5.221165 CGTATTCTTCTTCTTCCTCCTCCTC 60.221 48.000 0.00 0.00 0.00 3.71
2747 6103 4.647399 CGTATTCTTCTTCTTCCTCCTCCT 59.353 45.833 0.00 0.00 0.00 3.69
2748 6104 4.645588 TCGTATTCTTCTTCTTCCTCCTCC 59.354 45.833 0.00 0.00 0.00 4.30
2784 6140 4.057428 GTGTCGTGCTCGGCCTCT 62.057 66.667 10.59 0.00 41.33 3.69
2785 6141 4.357947 TGTGTCGTGCTCGGCCTC 62.358 66.667 10.59 4.38 41.33 4.70
2786 6142 4.664677 GTGTGTCGTGCTCGGCCT 62.665 66.667 10.59 0.00 41.33 5.19
2897 6253 2.180017 CAGGAACAGCGGCATTGC 59.820 61.111 1.45 0.00 0.00 3.56
2922 6278 2.122167 GGTGCGACGAGAGGGAGAT 61.122 63.158 0.00 0.00 0.00 2.75
3003 6404 0.402861 GAGATGGGGGATTGGGGGTA 60.403 60.000 0.00 0.00 0.00 3.69
3010 6411 0.842635 GTGCAGAGAGATGGGGGATT 59.157 55.000 0.00 0.00 0.00 3.01
3023 6424 1.375908 GGAGCATTGTCGGTGCAGA 60.376 57.895 0.00 0.00 44.87 4.26
3039 6440 2.750637 GTGCTCCTCGACTCCGGA 60.751 66.667 2.93 2.93 36.24 5.14
3196 6609 0.457851 CAAACACCAAAGGCCGTTCA 59.542 50.000 0.00 0.00 0.00 3.18
3199 6612 1.756561 AGCAAACACCAAAGGCCGT 60.757 52.632 0.00 0.00 0.00 5.68
3230 6643 0.995728 TACATGCGTGCGTGTACATG 59.004 50.000 19.96 10.89 43.52 3.21
3314 6732 6.291648 TGATGCTCATATTAGATCTCACCC 57.708 41.667 0.00 0.00 0.00 4.61
3411 6959 5.419542 TCTCTCCACTTATCAATGAAACGG 58.580 41.667 0.00 0.00 0.00 4.44
3425 6973 2.289592 ACCTGTACGTTCTCTCCACT 57.710 50.000 0.00 0.00 0.00 4.00
3427 6975 1.000506 GCAACCTGTACGTTCTCTCCA 59.999 52.381 0.00 0.00 0.00 3.86
3442 6990 2.190578 CCCCCTCGATCAGCAACC 59.809 66.667 0.00 0.00 0.00 3.77
3448 6996 1.744320 CGTGTATGCCCCCTCGATCA 61.744 60.000 0.00 0.00 0.00 2.92
3453 7001 1.000955 CTGATACGTGTATGCCCCCTC 59.999 57.143 0.00 0.00 0.00 4.30
3454 7002 1.048601 CTGATACGTGTATGCCCCCT 58.951 55.000 0.00 0.00 0.00 4.79
3455 7003 0.602905 GCTGATACGTGTATGCCCCC 60.603 60.000 0.00 0.00 0.00 5.40
3456 7004 0.105964 TGCTGATACGTGTATGCCCC 59.894 55.000 0.00 0.00 0.00 5.80
3457 7005 2.069273 GATGCTGATACGTGTATGCCC 58.931 52.381 0.00 0.00 0.00 5.36
3458 7006 2.069273 GGATGCTGATACGTGTATGCC 58.931 52.381 0.00 0.00 0.00 4.40
3459 7007 2.069273 GGGATGCTGATACGTGTATGC 58.931 52.381 0.00 0.00 0.00 3.14
3460 7008 2.037121 TGGGGATGCTGATACGTGTATG 59.963 50.000 0.00 0.00 0.00 2.39
3461 7009 2.300152 CTGGGGATGCTGATACGTGTAT 59.700 50.000 0.00 0.00 0.00 2.29
3462 7010 1.686587 CTGGGGATGCTGATACGTGTA 59.313 52.381 0.00 0.00 0.00 2.90
3463 7011 0.465705 CTGGGGATGCTGATACGTGT 59.534 55.000 0.00 0.00 0.00 4.49
3464 7012 0.250038 CCTGGGGATGCTGATACGTG 60.250 60.000 0.00 0.00 0.00 4.49
3465 7013 0.398522 TCCTGGGGATGCTGATACGT 60.399 55.000 0.00 0.00 0.00 3.57
3466 7014 0.319728 CTCCTGGGGATGCTGATACG 59.680 60.000 0.00 0.00 0.00 3.06
3467 7015 0.036022 GCTCCTGGGGATGCTGATAC 59.964 60.000 0.00 0.00 0.00 2.24
3468 7016 0.400381 TGCTCCTGGGGATGCTGATA 60.400 55.000 0.00 0.00 30.89 2.15
3469 7017 1.695239 TGCTCCTGGGGATGCTGAT 60.695 57.895 0.00 0.00 30.89 2.90
3470 7018 2.285592 TGCTCCTGGGGATGCTGA 60.286 61.111 0.00 0.00 30.89 4.26
3471 7019 2.124403 GTGCTCCTGGGGATGCTG 60.124 66.667 0.00 0.00 30.89 4.41
3472 7020 2.611800 TGTGCTCCTGGGGATGCT 60.612 61.111 0.00 0.00 30.89 3.79
3473 7021 2.124403 CTGTGCTCCTGGGGATGC 60.124 66.667 0.00 0.00 0.00 3.91
3474 7022 2.124403 GCTGTGCTCCTGGGGATG 60.124 66.667 0.00 0.00 0.00 3.51
3475 7023 2.005266 ATGCTGTGCTCCTGGGGAT 61.005 57.895 0.00 0.00 0.00 3.85
3476 7024 2.611800 ATGCTGTGCTCCTGGGGA 60.612 61.111 0.00 0.00 0.00 4.81
3477 7025 2.439701 CATGCTGTGCTCCTGGGG 60.440 66.667 0.00 0.00 0.00 4.96
3478 7026 1.451567 CTCATGCTGTGCTCCTGGG 60.452 63.158 0.00 0.00 0.00 4.45
3479 7027 2.113433 GCTCATGCTGTGCTCCTGG 61.113 63.158 0.00 0.00 34.37 4.45
3480 7028 0.748367 ATGCTCATGCTGTGCTCCTG 60.748 55.000 10.19 0.00 37.71 3.86
3481 7029 0.748367 CATGCTCATGCTGTGCTCCT 60.748 55.000 10.19 0.00 37.71 3.69
3482 7030 0.746923 TCATGCTCATGCTGTGCTCC 60.747 55.000 5.04 0.00 37.71 4.70
3483 7031 1.002359 CATCATGCTCATGCTGTGCTC 60.002 52.381 5.04 0.00 37.71 4.26
3484 7032 1.025041 CATCATGCTCATGCTGTGCT 58.975 50.000 5.04 0.00 37.71 4.40
3485 7033 0.030773 CCATCATGCTCATGCTGTGC 59.969 55.000 11.32 4.06 38.65 4.57
3486 7034 1.604278 CTCCATCATGCTCATGCTGTG 59.396 52.381 11.32 7.47 38.65 3.66
3487 7035 1.477014 CCTCCATCATGCTCATGCTGT 60.477 52.381 11.32 0.00 38.65 4.40
3488 7036 1.239347 CCTCCATCATGCTCATGCTG 58.761 55.000 5.04 5.94 38.65 4.41
3489 7037 0.844660 ACCTCCATCATGCTCATGCT 59.155 50.000 5.04 0.00 38.65 3.79
3490 7038 1.337071 CAACCTCCATCATGCTCATGC 59.663 52.381 5.04 0.00 38.65 4.06
3491 7039 1.337071 GCAACCTCCATCATGCTCATG 59.663 52.381 3.55 3.55 40.09 3.07
3492 7040 1.214673 AGCAACCTCCATCATGCTCAT 59.785 47.619 0.00 0.00 45.49 2.90
3533 7081 2.625790 AGGACTCGCATTAGTGATCTCC 59.374 50.000 0.00 0.00 33.90 3.71
3534 7082 4.314740 AAGGACTCGCATTAGTGATCTC 57.685 45.455 0.00 0.00 33.04 2.75
3535 7083 4.437239 CAAAGGACTCGCATTAGTGATCT 58.563 43.478 0.00 0.00 33.04 2.75
3567 7123 3.741476 GCTCGGCTTTGGGCACTG 61.741 66.667 0.00 0.00 44.01 3.66
3612 7168 2.202987 CTCCAGCCATCTGCCGAC 60.203 66.667 0.00 0.00 42.71 4.79
3617 7173 1.142748 GACGACCTCCAGCCATCTG 59.857 63.158 0.00 0.00 40.02 2.90
3636 7192 1.732259 CATAGCAACGCCGTTCTCTTT 59.268 47.619 0.00 0.00 0.00 2.52
3662 7218 2.868044 GCCCTAACTGCATGGAGTATCG 60.868 54.545 21.06 11.26 34.37 2.92
3675 7231 6.268158 GCCTTAACTCTCTTATAGCCCTAACT 59.732 42.308 0.00 0.00 0.00 2.24
3698 7254 1.367471 GCAAGTTTGTGGAAGGGCC 59.633 57.895 0.00 0.00 37.10 5.80
3748 7304 0.105039 ACGGATGCGATCTTCTTCCC 59.895 55.000 15.49 0.00 0.00 3.97
3749 7305 1.941325 AACGGATGCGATCTTCTTCC 58.059 50.000 15.49 0.00 0.00 3.46
3750 7306 2.030946 CCAAACGGATGCGATCTTCTTC 59.969 50.000 15.49 0.00 0.00 2.87
3751 7307 2.009774 CCAAACGGATGCGATCTTCTT 58.990 47.619 15.49 0.00 0.00 2.52
3752 7308 1.656652 CCAAACGGATGCGATCTTCT 58.343 50.000 15.49 0.00 0.00 2.85
3753 7309 0.028110 GCCAAACGGATGCGATCTTC 59.972 55.000 15.49 0.00 0.00 2.87
3754 7310 0.676466 TGCCAAACGGATGCGATCTT 60.676 50.000 15.49 0.20 0.00 2.40
3755 7311 0.676466 TTGCCAAACGGATGCGATCT 60.676 50.000 15.49 0.00 0.00 2.75
3756 7312 0.170116 TTTGCCAAACGGATGCGATC 59.830 50.000 15.49 0.00 0.00 3.69
3757 7313 0.600557 TTTTGCCAAACGGATGCGAT 59.399 45.000 15.49 0.00 0.00 4.58
3758 7314 0.385751 TTTTTGCCAAACGGATGCGA 59.614 45.000 15.49 0.00 0.00 5.10
3759 7315 0.506506 GTTTTTGCCAAACGGATGCG 59.493 50.000 4.58 4.58 0.00 4.73
3760 7316 1.260297 GTGTTTTTGCCAAACGGATGC 59.740 47.619 0.00 0.00 33.05 3.91
3761 7317 2.544685 TGTGTTTTTGCCAAACGGATG 58.455 42.857 0.00 0.00 33.05 3.51
3762 7318 2.969628 TGTGTTTTTGCCAAACGGAT 57.030 40.000 0.00 0.00 33.05 4.18
3763 7319 2.969628 ATGTGTTTTTGCCAAACGGA 57.030 40.000 0.00 0.00 33.05 4.69
3764 7320 5.064071 AGTTTTATGTGTTTTTGCCAAACGG 59.936 36.000 0.00 0.00 33.05 4.44
3765 7321 6.100792 AGTTTTATGTGTTTTTGCCAAACG 57.899 33.333 0.00 0.00 33.05 3.60
3766 7322 7.522374 TGAAGTTTTATGTGTTTTTGCCAAAC 58.478 30.769 0.00 2.35 0.00 2.93
3767 7323 7.672983 TGAAGTTTTATGTGTTTTTGCCAAA 57.327 28.000 0.00 0.00 0.00 3.28
3768 7324 7.389053 AGTTGAAGTTTTATGTGTTTTTGCCAA 59.611 29.630 0.00 0.00 0.00 4.52
3769 7325 6.876257 AGTTGAAGTTTTATGTGTTTTTGCCA 59.124 30.769 0.00 0.00 0.00 4.92
3770 7326 7.302350 AGTTGAAGTTTTATGTGTTTTTGCC 57.698 32.000 0.00 0.00 0.00 4.52
3771 7327 8.865001 TGTAGTTGAAGTTTTATGTGTTTTTGC 58.135 29.630 0.00 0.00 0.00 3.68
3868 7424 1.369689 GCAGTTTGCACAGCTGACG 60.370 57.895 23.35 12.22 44.26 4.35
3870 7426 2.545596 CCGCAGTTTGCACAGCTGA 61.546 57.895 23.35 0.00 45.36 4.26
3880 7436 6.128634 CGAGTTTTACTAGAATTCCGCAGTTT 60.129 38.462 0.65 0.00 0.00 2.66
3902 7458 2.169769 TCCTAATTGTAGGGGCAACGAG 59.830 50.000 0.00 0.00 46.34 4.18
3903 7459 2.189676 TCCTAATTGTAGGGGCAACGA 58.810 47.619 0.00 0.00 46.34 3.85
3943 7499 8.023128 AGTCATTTTTCTTTATGGATGTGAACG 58.977 33.333 0.00 0.00 0.00 3.95
3944 7500 9.132521 CAGTCATTTTTCTTTATGGATGTGAAC 57.867 33.333 0.00 0.00 0.00 3.18
3946 7502 8.514594 GTCAGTCATTTTTCTTTATGGATGTGA 58.485 33.333 0.00 0.00 0.00 3.58
3947 7503 7.756722 GGTCAGTCATTTTTCTTTATGGATGTG 59.243 37.037 0.00 0.00 0.00 3.21
3948 7504 7.362056 CGGTCAGTCATTTTTCTTTATGGATGT 60.362 37.037 0.00 0.00 0.00 3.06
3949 7505 6.968904 CGGTCAGTCATTTTTCTTTATGGATG 59.031 38.462 0.00 0.00 0.00 3.51
3950 7506 6.884295 TCGGTCAGTCATTTTTCTTTATGGAT 59.116 34.615 0.00 0.00 0.00 3.41
3951 7507 6.234920 TCGGTCAGTCATTTTTCTTTATGGA 58.765 36.000 0.00 0.00 0.00 3.41
3952 7508 6.494893 TCGGTCAGTCATTTTTCTTTATGG 57.505 37.500 0.00 0.00 0.00 2.74
3953 7509 8.023128 ACATTCGGTCAGTCATTTTTCTTTATG 58.977 33.333 0.00 0.00 0.00 1.90
3954 7510 8.110860 ACATTCGGTCAGTCATTTTTCTTTAT 57.889 30.769 0.00 0.00 0.00 1.40
3955 7511 7.504924 ACATTCGGTCAGTCATTTTTCTTTA 57.495 32.000 0.00 0.00 0.00 1.85
3956 7512 6.391227 ACATTCGGTCAGTCATTTTTCTTT 57.609 33.333 0.00 0.00 0.00 2.52
3957 7513 6.391227 AACATTCGGTCAGTCATTTTTCTT 57.609 33.333 0.00 0.00 0.00 2.52
3958 7514 6.934645 TCTAACATTCGGTCAGTCATTTTTCT 59.065 34.615 0.00 0.00 0.00 2.52
3959 7515 7.129109 TCTAACATTCGGTCAGTCATTTTTC 57.871 36.000 0.00 0.00 0.00 2.29
3960 7516 7.504924 TTCTAACATTCGGTCAGTCATTTTT 57.495 32.000 0.00 0.00 0.00 1.94
3961 7517 6.348540 GCTTCTAACATTCGGTCAGTCATTTT 60.349 38.462 0.00 0.00 0.00 1.82
3962 7518 5.122396 GCTTCTAACATTCGGTCAGTCATTT 59.878 40.000 0.00 0.00 0.00 2.32
3963 7519 4.631813 GCTTCTAACATTCGGTCAGTCATT 59.368 41.667 0.00 0.00 0.00 2.57
3964 7520 4.081420 AGCTTCTAACATTCGGTCAGTCAT 60.081 41.667 0.00 0.00 0.00 3.06
3965 7521 3.258372 AGCTTCTAACATTCGGTCAGTCA 59.742 43.478 0.00 0.00 0.00 3.41
3966 7522 3.851098 AGCTTCTAACATTCGGTCAGTC 58.149 45.455 0.00 0.00 0.00 3.51
3967 7523 3.368531 GGAGCTTCTAACATTCGGTCAGT 60.369 47.826 0.00 0.00 0.00 3.41
3968 7524 3.190874 GGAGCTTCTAACATTCGGTCAG 58.809 50.000 0.00 0.00 0.00 3.51
3969 7525 2.093658 GGGAGCTTCTAACATTCGGTCA 60.094 50.000 0.00 0.00 0.00 4.02
3970 7526 2.093658 TGGGAGCTTCTAACATTCGGTC 60.094 50.000 0.00 0.00 0.00 4.79
4056 7733 4.035102 GACCCCACCTGGTGAGGC 62.035 72.222 25.55 16.03 44.33 4.70
4059 7736 2.529136 CCAGACCCCACCTGGTGA 60.529 66.667 27.94 0.00 44.66 4.02
4075 7752 5.301555 GCTTGTCTGGTATAATCCTTCTCC 58.698 45.833 0.00 0.00 0.00 3.71
4090 7767 0.693049 ACTGGGGTAAGGCTTGTCTG 59.307 55.000 10.69 3.61 0.00 3.51
4091 7768 0.693049 CACTGGGGTAAGGCTTGTCT 59.307 55.000 10.69 0.00 0.00 3.41
4092 7769 0.960861 GCACTGGGGTAAGGCTTGTC 60.961 60.000 10.69 2.83 0.00 3.18
4093 7770 1.074951 GCACTGGGGTAAGGCTTGT 59.925 57.895 10.69 0.00 0.00 3.16
4094 7771 0.539438 TTGCACTGGGGTAAGGCTTG 60.539 55.000 10.69 0.00 0.00 4.01
4096 7773 0.409484 AATTGCACTGGGGTAAGGCT 59.591 50.000 0.00 0.00 0.00 4.58
4099 7776 3.012518 CTCTGAATTGCACTGGGGTAAG 58.987 50.000 0.00 0.00 0.00 2.34
4100 7777 2.642311 TCTCTGAATTGCACTGGGGTAA 59.358 45.455 0.00 0.00 0.00 2.85
4101 7778 2.265367 TCTCTGAATTGCACTGGGGTA 58.735 47.619 0.00 0.00 0.00 3.69
4102 7779 1.067295 TCTCTGAATTGCACTGGGGT 58.933 50.000 0.00 0.00 0.00 4.95
4122 7802 1.327303 GTCTTGGGTTTGATGTGGCA 58.673 50.000 0.00 0.00 0.00 4.92
4127 7807 2.297033 CCAACAGGTCTTGGGTTTGATG 59.703 50.000 0.00 0.00 37.62 3.07
4128 7808 2.597455 CCAACAGGTCTTGGGTTTGAT 58.403 47.619 0.00 0.00 37.62 2.57
4144 7824 0.037590 TACTCCCCATGTGTGCCAAC 59.962 55.000 0.00 0.00 0.00 3.77
4154 7834 1.909302 CAGTGGTGAAGTACTCCCCAT 59.091 52.381 10.32 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.