Multiple sequence alignment - TraesCS3A01G303100

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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 TraesCS3A01G303100 chr3A 100.000 3900 0 0 1 3900 537497276 537501175 0.000000e+00 7203.0
1 TraesCS3A01G303100 chr3A 100.000 1569 0 0 4187 5755 537501462 537503030 0.000000e+00 2898.0
2 TraesCS3A01G303100 chr3D 94.659 2902 113 18 979 3865 412827807 412824933 0.000000e+00 4462.0
3 TraesCS3A01G303100 chr3D 95.258 970 37 6 1 962 412828826 412827858 0.000000e+00 1528.0
4 TraesCS3A01G303100 chr3D 94.839 620 26 4 4187 4806 412824525 412823912 0.000000e+00 963.0
5 TraesCS3A01G303100 chr3D 91.089 707 34 16 5063 5755 412822919 412822228 0.000000e+00 929.0
6 TraesCS3A01G303100 chr3D 97.297 37 1 0 3864 3900 412824905 412824869 4.810000e-06 63.9
7 TraesCS3A01G303100 chr3B 90.551 1905 132 31 848 2726 539598902 539597020 0.000000e+00 2477.0
8 TraesCS3A01G303100 chr3B 94.391 838 33 5 1 829 539661370 539660538 0.000000e+00 1275.0
9 TraesCS3A01G303100 chr3B 87.344 964 92 17 2786 3729 539597002 539596049 0.000000e+00 1077.0
10 TraesCS3A01G303100 chr3B 90.620 629 44 9 4187 4806 539595714 539595092 0.000000e+00 821.0
11 TraesCS3A01G303100 chr3B 89.385 537 28 19 5227 5755 539594729 539594214 0.000000e+00 649.0
12 TraesCS3A01G303100 chr3B 89.163 203 19 3 2937 3138 71883399 71883599 3.440000e-62 250.0
13 TraesCS3A01G303100 chr3B 89.163 203 19 3 2937 3138 328604432 328604632 3.440000e-62 250.0
14 TraesCS3A01G303100 chr3B 88.591 149 6 9 5104 5243 539594889 539594743 2.760000e-38 171.0
15 TraesCS3A01G303100 chr1A 87.922 563 50 10 2942 3490 77161627 77162185 0.000000e+00 647.0
16 TraesCS3A01G303100 chr1A 90.299 134 12 1 3680 3812 77162481 77162614 2.130000e-39 174.0
17 TraesCS3A01G303100 chr6B 87.211 563 54 10 2942 3490 80463111 80462553 4.900000e-175 625.0
18 TraesCS3A01G303100 chr2A 87.246 541 51 10 2942 3468 23546625 23546089 8.250000e-168 601.0
19 TraesCS3A01G303100 chr2A 89.091 220 19 2 3276 3490 379360730 379360511 9.510000e-68 268.0
20 TraesCS3A01G303100 chr2A 88.670 203 20 3 2937 3138 74111706 74111906 1.600000e-60 244.0
21 TraesCS3A01G303100 chr2A 86.697 218 26 2 3529 3743 379360510 379360293 7.450000e-59 239.0
22 TraesCS3A01G303100 chr6D 89.041 219 19 2 3277 3490 225837305 225837087 3.420000e-67 267.0
23 TraesCS3A01G303100 chr6D 89.163 203 16 6 2937 3138 374767726 374767529 1.240000e-61 248.0
24 TraesCS3A01G303100 chr7A 89.163 203 19 3 2937 3138 679416397 679416597 3.440000e-62 250.0
25 TraesCS3A01G303100 chr7A 90.909 99 5 2 3333 3427 680718511 680718609 4.680000e-26 130.0
26 TraesCS3A01G303100 chr2B 89.163 203 19 3 2937 3138 118095643 118095443 3.440000e-62 250.0
27 TraesCS3A01G303100 chr7B 88.670 203 20 3 2937 3138 394824064 394823864 1.600000e-60 244.0


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 TraesCS3A01G303100 chr3A 537497276 537503030 5754 False 5050.50 7203 100.0000 1 5755 2 chr3A.!!$F1 5754
1 TraesCS3A01G303100 chr3D 412822228 412828826 6598 True 1589.18 4462 94.6284 1 5755 5 chr3D.!!$R1 5754
2 TraesCS3A01G303100 chr3B 539660538 539661370 832 True 1275.00 1275 94.3910 1 829 1 chr3B.!!$R1 828
3 TraesCS3A01G303100 chr3B 539594214 539598902 4688 True 1039.00 2477 89.2982 848 5755 5 chr3B.!!$R2 4907
4 TraesCS3A01G303100 chr1A 77161627 77162614 987 False 410.50 647 89.1105 2942 3812 2 chr1A.!!$F1 870
5 TraesCS3A01G303100 chr6B 80462553 80463111 558 True 625.00 625 87.2110 2942 3490 1 chr6B.!!$R1 548
6 TraesCS3A01G303100 chr2A 23546089 23546625 536 True 601.00 601 87.2460 2942 3468 1 chr2A.!!$R1 526

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
846 860 1.961394 GTCCACCGGCAGTCTATATCA 59.039 52.381 0.0 0.0 0.00 2.15 F
1626 1695 0.169009 GCACAGGTGAATTTCGGCTC 59.831 55.000 3.1 0.0 0.00 4.70 F
1648 1717 0.319211 CGGCGGTGTCTCTTGTTACA 60.319 55.000 0.0 0.0 0.00 2.41 F
1758 1827 1.271543 TGCTGCACCTCTGTTAAGCAT 60.272 47.619 0.0 0.0 36.12 3.79 F
2150 2219 2.417933 GTGTATGCTCTCCTTGTTGCTG 59.582 50.000 0.0 0.0 0.00 4.41 F
3714 3945 2.785357 TTGTTCCTGGGGTCCATTTT 57.215 45.000 0.0 0.0 30.82 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1726 1.333619 GTGACAATCAAACGGCACACT 59.666 47.619 0.0 0.0 0.00 3.55 R
2796 2868 1.760613 CGACCAGGCACCTATTCCTAA 59.239 52.381 0.0 0.0 0.00 2.69 R
3079 3152 3.144506 CCAAGCTCATGTCACAAGTTCT 58.855 45.455 0.0 0.0 0.00 3.01 R
3714 3945 1.626321 TCAGCGAATGGAACCTTACCA 59.374 47.619 0.0 0.0 41.83 3.25 R
3778 4109 4.916983 TGCTAGAATGCACAAAAGTTGT 57.083 36.364 0.0 0.0 46.75 3.32 R
4845 6152 0.034337 CAACGGTCCCTCGGAAAAGA 59.966 55.000 0.0 0.0 31.38 2.52 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
270 271 4.426313 GTAGCCAGCGCCCCCTTT 62.426 66.667 2.29 0.00 34.57 3.11
313 317 2.498078 GACCAAACAACCCAAAACTCCA 59.502 45.455 0.00 0.00 0.00 3.86
324 328 7.507616 ACAACCCAAAACTCCATGTAATTAAGA 59.492 33.333 0.00 0.00 0.00 2.10
515 519 4.803426 CTCACCGGCAGGAGCGTC 62.803 72.222 10.86 0.00 43.41 5.19
738 752 4.954970 CACGGGTTGGCTGCCTGT 62.955 66.667 21.03 7.67 45.80 4.00
846 860 1.961394 GTCCACCGGCAGTCTATATCA 59.039 52.381 0.00 0.00 0.00 2.15
870 884 2.261361 GGAACAAATGGGCCGTGC 59.739 61.111 0.00 0.00 0.00 5.34
914 929 2.084546 AGCCCAAGTGCGAGTTTAATC 58.915 47.619 0.00 0.00 36.02 1.75
972 991 3.924114 TGTTGGATCCCACACGATTAT 57.076 42.857 14.51 0.00 30.78 1.28
974 993 4.699637 TGTTGGATCCCACACGATTATAC 58.300 43.478 14.51 0.00 30.78 1.47
976 995 4.600692 TGGATCCCACACGATTATACAG 57.399 45.455 9.90 0.00 0.00 2.74
1029 1087 1.648504 CGAGGTTTTAGGGGTAAGCG 58.351 55.000 0.00 0.00 0.00 4.68
1034 1092 2.419713 GGTTTTAGGGGTAAGCGGAGAG 60.420 54.545 0.00 0.00 0.00 3.20
1477 1545 3.244976 CAAAATGGTAGCTTTCTTGCCG 58.755 45.455 0.00 0.00 0.00 5.69
1485 1553 1.578206 GCTTTCTTGCCGGACTGGTC 61.578 60.000 5.05 0.00 41.21 4.02
1522 1590 2.767960 GGAACGGTTGTAAGAGGGGATA 59.232 50.000 0.00 0.00 0.00 2.59
1524 1592 1.761198 ACGGTTGTAAGAGGGGATAGC 59.239 52.381 0.00 0.00 0.00 2.97
1525 1593 1.760613 CGGTTGTAAGAGGGGATAGCA 59.239 52.381 0.00 0.00 0.00 3.49
1550 1619 5.792741 TGGATGCTTATGGTTTCCTTTTTG 58.207 37.500 0.00 0.00 0.00 2.44
1626 1695 0.169009 GCACAGGTGAATTTCGGCTC 59.831 55.000 3.10 0.00 0.00 4.70
1648 1717 0.319211 CGGCGGTGTCTCTTGTTACA 60.319 55.000 0.00 0.00 0.00 2.41
1657 1726 3.639561 TGTCTCTTGTTACAGTGGTGCTA 59.360 43.478 0.00 0.00 0.00 3.49
1758 1827 1.271543 TGCTGCACCTCTGTTAAGCAT 60.272 47.619 0.00 0.00 36.12 3.79
1840 1909 5.767816 ACACTGTAACTGGAATTTGAACC 57.232 39.130 0.00 0.00 0.00 3.62
1841 1910 5.445964 ACACTGTAACTGGAATTTGAACCT 58.554 37.500 0.00 0.00 0.00 3.50
2013 2082 4.203226 TGTGCTGACCAGTGAATTGTTTA 58.797 39.130 0.00 0.00 0.00 2.01
2150 2219 2.417933 GTGTATGCTCTCCTTGTTGCTG 59.582 50.000 0.00 0.00 0.00 4.41
2271 2340 8.610035 GGTATAAAACAGACTTTCCTTAATCCG 58.390 37.037 0.00 0.00 0.00 4.18
2293 2362 3.490419 GCCTCGCGAACTAAATAGAAGGA 60.490 47.826 11.33 0.00 0.00 3.36
2364 2433 8.411991 AATTTTCCTTTTCCATGCAAATGAAT 57.588 26.923 0.00 0.00 0.00 2.57
2369 2438 5.810587 CCTTTTCCATGCAAATGAATGAGAG 59.189 40.000 2.80 0.00 32.66 3.20
2386 2455 5.113446 TGAGAGTCCTAGTACTAACCCTG 57.887 47.826 3.76 0.00 0.00 4.45
2388 2457 5.728253 TGAGAGTCCTAGTACTAACCCTGTA 59.272 44.000 3.76 0.00 0.00 2.74
2434 2503 9.813080 GTGCTTAACATAACTAGTTCTTTCTTG 57.187 33.333 12.39 4.53 0.00 3.02
2645 2717 5.865552 CCCTATTGCACAGAAATCAAAACAG 59.134 40.000 0.00 0.00 0.00 3.16
2758 2830 7.094032 CCCTTCTATATCTTTTTGGGATGCATC 60.094 40.741 18.81 18.81 35.64 3.91
2784 2856 6.258727 GTGATATTGGTCAGGTGACATTAGTG 59.741 42.308 12.09 0.00 46.47 2.74
2857 2929 6.581712 ACTAAATGAAAATGCACACCTTGTT 58.418 32.000 0.00 0.00 0.00 2.83
2929 3001 3.850273 GCATGAGAACTTGAAATGAAGCG 59.150 43.478 0.00 0.00 0.00 4.68
3120 3193 4.355549 TGGCCTCATGGAAAAATCATTCT 58.644 39.130 3.32 0.00 34.57 2.40
3416 3501 7.710907 TGACCGGAAATTATCTGTTAGAAGATG 59.289 37.037 9.46 0.00 37.48 2.90
3590 3679 7.453393 TCAATCTTCAGTATTCCTGTTGTCTT 58.547 34.615 0.00 0.00 42.19 3.01
3607 3696 4.265893 TGTCTTGGTTTTGCACAGTTCTA 58.734 39.130 0.00 0.00 0.00 2.10
3608 3697 4.702612 TGTCTTGGTTTTGCACAGTTCTAA 59.297 37.500 0.00 0.00 0.00 2.10
3609 3698 5.184096 TGTCTTGGTTTTGCACAGTTCTAAA 59.816 36.000 0.00 0.00 0.00 1.85
3610 3699 6.127479 TGTCTTGGTTTTGCACAGTTCTAAAT 60.127 34.615 0.00 0.00 0.00 1.40
3611 3700 6.417930 GTCTTGGTTTTGCACAGTTCTAAATC 59.582 38.462 0.00 0.00 0.00 2.17
3616 3706 3.788227 TGCACAGTTCTAAATCCACCT 57.212 42.857 0.00 0.00 0.00 4.00
3637 3727 4.798387 CCTTTTTGTGTAAAGTGACTGCAC 59.202 41.667 7.84 7.84 45.49 4.57
3714 3945 2.785357 TTGTTCCTGGGGTCCATTTT 57.215 45.000 0.00 0.00 30.82 1.82
3855 4186 4.679373 CAGAGTGCCTGTATGGATAACT 57.321 45.455 0.00 0.00 38.10 2.24
3865 4196 6.595682 CCTGTATGGATAACTGTGGATTCTT 58.404 40.000 0.00 0.00 38.35 2.52
3866 4197 6.484643 CCTGTATGGATAACTGTGGATTCTTG 59.515 42.308 0.00 0.00 38.35 3.02
3867 4198 7.194112 TGTATGGATAACTGTGGATTCTTGA 57.806 36.000 0.00 0.00 0.00 3.02
4335 4755 7.389607 TGAGTAACTGGGTTAAATCTTTACAGC 59.610 37.037 0.00 0.00 29.42 4.40
4401 4821 4.681744 TGCAGATGAACAAAAACAAGGAC 58.318 39.130 0.00 0.00 0.00 3.85
4413 4833 3.453679 AAGGACGAGGAGAGCGGC 61.454 66.667 0.00 0.00 35.64 6.53
4414 4834 4.742649 AGGACGAGGAGAGCGGCA 62.743 66.667 1.45 0.00 38.88 5.69
4425 4845 4.457496 AGCGGCACATCAGTCCCG 62.457 66.667 1.45 0.00 43.38 5.14
4431 4851 1.576356 GCACATCAGTCCCGAAGATC 58.424 55.000 0.00 0.00 0.00 2.75
4595 5015 8.958175 TGTAAAAGGATATTTAGTTTTGTGCG 57.042 30.769 0.00 0.00 0.00 5.34
4625 5045 2.353803 CCTTCGGGGTGTTCTAACTCAG 60.354 54.545 0.00 0.00 0.00 3.35
4640 5060 0.449388 CTCAGCGGAGAAATGCCAAC 59.551 55.000 8.31 0.00 44.26 3.77
4706 5126 1.324383 TGACCAGTGAGCTTACGACA 58.676 50.000 2.59 0.23 0.00 4.35
4761 5181 6.552445 AAGTGTAGGATTCTGAAGCTGTAT 57.448 37.500 5.56 0.00 0.00 2.29
4762 5182 6.552445 AGTGTAGGATTCTGAAGCTGTATT 57.448 37.500 5.56 0.00 0.00 1.89
4763 5183 7.661536 AGTGTAGGATTCTGAAGCTGTATTA 57.338 36.000 5.56 0.00 0.00 0.98
4807 6114 1.817740 GCTGTTGCTGGTTTACCTCCA 60.818 52.381 0.00 0.00 36.82 3.86
4818 6125 3.323979 GGTTTACCTCCAGAGACAAGTCA 59.676 47.826 2.72 0.00 0.00 3.41
4829 6136 1.420138 AGACAAGTCAACATTCCCCGT 59.580 47.619 2.72 0.00 0.00 5.28
4830 6137 2.158667 AGACAAGTCAACATTCCCCGTT 60.159 45.455 2.72 0.00 0.00 4.44
4831 6138 1.953686 ACAAGTCAACATTCCCCGTTG 59.046 47.619 0.00 0.00 44.11 4.10
4838 6145 4.616181 CAACATTCCCCGTTGAACTATC 57.384 45.455 0.00 0.00 45.30 2.08
4839 6146 4.261801 CAACATTCCCCGTTGAACTATCT 58.738 43.478 0.00 0.00 45.30 1.98
4840 6147 3.873910 ACATTCCCCGTTGAACTATCTG 58.126 45.455 0.00 0.00 0.00 2.90
4841 6148 3.263425 ACATTCCCCGTTGAACTATCTGT 59.737 43.478 0.00 0.00 0.00 3.41
4842 6149 4.261801 CATTCCCCGTTGAACTATCTGTT 58.738 43.478 0.00 0.00 42.38 3.16
4843 6150 4.360951 TTCCCCGTTGAACTATCTGTTT 57.639 40.909 0.00 0.00 39.30 2.83
4844 6151 4.360951 TCCCCGTTGAACTATCTGTTTT 57.639 40.909 0.00 0.00 39.30 2.43
4845 6152 4.721132 TCCCCGTTGAACTATCTGTTTTT 58.279 39.130 0.00 0.00 39.30 1.94
4846 6153 4.758165 TCCCCGTTGAACTATCTGTTTTTC 59.242 41.667 0.00 0.00 39.30 2.29
4847 6154 4.760204 CCCCGTTGAACTATCTGTTTTTCT 59.240 41.667 0.00 0.00 39.30 2.52
4848 6155 5.240844 CCCCGTTGAACTATCTGTTTTTCTT 59.759 40.000 0.00 0.00 39.30 2.52
4849 6156 6.238925 CCCCGTTGAACTATCTGTTTTTCTTT 60.239 38.462 0.00 0.00 39.30 2.52
4850 6157 7.200455 CCCGTTGAACTATCTGTTTTTCTTTT 58.800 34.615 0.00 0.00 39.30 2.27
4851 6158 7.378728 CCCGTTGAACTATCTGTTTTTCTTTTC 59.621 37.037 0.00 0.00 39.30 2.29
4852 6159 7.378728 CCGTTGAACTATCTGTTTTTCTTTTCC 59.621 37.037 0.00 0.00 39.30 3.13
4853 6160 7.111593 CGTTGAACTATCTGTTTTTCTTTTCCG 59.888 37.037 0.00 0.00 39.30 4.30
4854 6161 7.795482 TGAACTATCTGTTTTTCTTTTCCGA 57.205 32.000 0.00 0.00 39.30 4.55
4855 6162 7.861630 TGAACTATCTGTTTTTCTTTTCCGAG 58.138 34.615 0.00 0.00 39.30 4.63
4856 6163 6.803154 ACTATCTGTTTTTCTTTTCCGAGG 57.197 37.500 0.00 0.00 0.00 4.63
4857 6164 5.705905 ACTATCTGTTTTTCTTTTCCGAGGG 59.294 40.000 0.00 0.00 0.00 4.30
4858 6165 4.159244 TCTGTTTTTCTTTTCCGAGGGA 57.841 40.909 0.00 0.00 0.00 4.20
4859 6166 3.881089 TCTGTTTTTCTTTTCCGAGGGAC 59.119 43.478 0.00 0.00 0.00 4.46
4860 6167 2.953648 TGTTTTTCTTTTCCGAGGGACC 59.046 45.455 0.00 0.00 0.00 4.46
4861 6168 1.886886 TTTTCTTTTCCGAGGGACCG 58.113 50.000 0.00 0.00 0.00 4.79
4862 6169 0.760572 TTTCTTTTCCGAGGGACCGT 59.239 50.000 0.00 0.00 0.00 4.83
4863 6170 0.760572 TTCTTTTCCGAGGGACCGTT 59.239 50.000 0.00 0.00 0.00 4.44
4864 6171 0.034337 TCTTTTCCGAGGGACCGTTG 59.966 55.000 0.00 0.00 0.00 4.10
4865 6172 0.034337 CTTTTCCGAGGGACCGTTGA 59.966 55.000 2.78 0.00 0.00 3.18
4866 6173 0.469070 TTTTCCGAGGGACCGTTGAA 59.531 50.000 2.78 0.08 0.00 2.69
4867 6174 0.249996 TTTCCGAGGGACCGTTGAAC 60.250 55.000 2.78 0.00 0.00 3.18
4868 6175 1.117142 TTCCGAGGGACCGTTGAACT 61.117 55.000 2.78 0.00 0.00 3.01
4869 6176 0.251297 TCCGAGGGACCGTTGAACTA 60.251 55.000 2.78 0.00 0.00 2.24
4870 6177 0.822164 CCGAGGGACCGTTGAACTAT 59.178 55.000 2.78 0.00 0.00 2.12
4871 6178 1.202382 CCGAGGGACCGTTGAACTATC 60.202 57.143 2.78 0.00 0.00 2.08
4872 6179 1.749634 CGAGGGACCGTTGAACTATCT 59.250 52.381 0.00 0.00 0.00 1.98
4873 6180 2.479730 CGAGGGACCGTTGAACTATCTG 60.480 54.545 0.00 0.00 0.00 2.90
4874 6181 2.496470 GAGGGACCGTTGAACTATCTGT 59.504 50.000 0.00 0.00 0.00 3.41
4875 6182 2.904434 AGGGACCGTTGAACTATCTGTT 59.096 45.455 0.00 0.00 42.38 3.16
4876 6183 3.326880 AGGGACCGTTGAACTATCTGTTT 59.673 43.478 0.00 0.00 39.30 2.83
4877 6184 4.529377 AGGGACCGTTGAACTATCTGTTTA 59.471 41.667 0.00 0.00 39.30 2.01
4878 6185 5.012354 AGGGACCGTTGAACTATCTGTTTAA 59.988 40.000 0.00 0.00 39.30 1.52
4879 6186 5.878669 GGGACCGTTGAACTATCTGTTTAAT 59.121 40.000 0.00 0.00 39.30 1.40
4880 6187 6.373495 GGGACCGTTGAACTATCTGTTTAATT 59.627 38.462 0.00 0.00 39.30 1.40
4881 6188 7.094506 GGGACCGTTGAACTATCTGTTTAATTT 60.095 37.037 0.00 0.00 39.30 1.82
4882 6189 8.294577 GGACCGTTGAACTATCTGTTTAATTTT 58.705 33.333 0.00 0.00 39.30 1.82
4883 6190 9.113876 GACCGTTGAACTATCTGTTTAATTTTG 57.886 33.333 0.00 0.00 39.30 2.44
4884 6191 8.842280 ACCGTTGAACTATCTGTTTAATTTTGA 58.158 29.630 0.00 0.00 39.30 2.69
4885 6192 9.329913 CCGTTGAACTATCTGTTTAATTTTGAG 57.670 33.333 0.00 0.00 39.30 3.02
4886 6193 8.840867 CGTTGAACTATCTGTTTAATTTTGAGC 58.159 33.333 0.00 0.00 39.30 4.26
4887 6194 9.129209 GTTGAACTATCTGTTTAATTTTGAGCC 57.871 33.333 0.00 0.00 39.30 4.70
4888 6195 7.826690 TGAACTATCTGTTTAATTTTGAGCCC 58.173 34.615 0.00 0.00 39.30 5.19
4889 6196 7.669722 TGAACTATCTGTTTAATTTTGAGCCCT 59.330 33.333 0.00 0.00 39.30 5.19
4890 6197 7.631717 ACTATCTGTTTAATTTTGAGCCCTC 57.368 36.000 0.00 0.00 0.00 4.30
4891 6198 5.567138 ATCTGTTTAATTTTGAGCCCTCG 57.433 39.130 0.00 0.00 0.00 4.63
4892 6199 4.647611 TCTGTTTAATTTTGAGCCCTCGA 58.352 39.130 0.00 0.00 0.00 4.04
4893 6200 4.454504 TCTGTTTAATTTTGAGCCCTCGAC 59.545 41.667 0.00 0.00 0.00 4.20
4894 6201 4.138290 TGTTTAATTTTGAGCCCTCGACA 58.862 39.130 0.00 0.00 0.00 4.35
4895 6202 4.023536 TGTTTAATTTTGAGCCCTCGACAC 60.024 41.667 0.00 0.00 0.00 3.67
4896 6203 1.534729 AATTTTGAGCCCTCGACACC 58.465 50.000 0.00 0.00 0.00 4.16
4897 6204 0.322546 ATTTTGAGCCCTCGACACCC 60.323 55.000 0.00 0.00 0.00 4.61
4898 6205 1.701031 TTTTGAGCCCTCGACACCCA 61.701 55.000 0.00 0.00 0.00 4.51
4899 6206 1.701031 TTTGAGCCCTCGACACCCAA 61.701 55.000 0.00 0.00 0.00 4.12
4900 6207 1.701031 TTGAGCCCTCGACACCCAAA 61.701 55.000 0.00 0.00 0.00 3.28
4901 6208 1.671379 GAGCCCTCGACACCCAAAC 60.671 63.158 0.00 0.00 0.00 2.93
4902 6209 2.112297 GCCCTCGACACCCAAACA 59.888 61.111 0.00 0.00 0.00 2.83
4903 6210 1.966451 GCCCTCGACACCCAAACAG 60.966 63.158 0.00 0.00 0.00 3.16
4904 6211 1.752198 CCCTCGACACCCAAACAGA 59.248 57.895 0.00 0.00 0.00 3.41
4905 6212 0.320771 CCCTCGACACCCAAACAGAG 60.321 60.000 0.00 0.00 0.00 3.35
4906 6213 0.393077 CCTCGACACCCAAACAGAGT 59.607 55.000 0.00 0.00 0.00 3.24
4907 6214 1.616865 CCTCGACACCCAAACAGAGTA 59.383 52.381 0.00 0.00 0.00 2.59
4908 6215 2.609737 CCTCGACACCCAAACAGAGTAC 60.610 54.545 0.00 0.00 0.00 2.73
4909 6216 2.296471 CTCGACACCCAAACAGAGTACT 59.704 50.000 0.00 0.00 0.00 2.73
4910 6217 2.696707 TCGACACCCAAACAGAGTACTT 59.303 45.455 0.00 0.00 0.00 2.24
4911 6218 3.133362 TCGACACCCAAACAGAGTACTTT 59.867 43.478 0.00 0.00 0.00 2.66
4912 6219 3.875134 CGACACCCAAACAGAGTACTTTT 59.125 43.478 0.00 0.00 0.00 2.27
4913 6220 5.051816 CGACACCCAAACAGAGTACTTTTA 58.948 41.667 0.00 0.00 0.00 1.52
4914 6221 5.699458 CGACACCCAAACAGAGTACTTTTAT 59.301 40.000 0.00 0.00 0.00 1.40
4915 6222 6.128634 CGACACCCAAACAGAGTACTTTTATC 60.129 42.308 0.00 0.00 0.00 1.75
4916 6223 6.838382 ACACCCAAACAGAGTACTTTTATCT 58.162 36.000 0.00 0.00 0.00 1.98
4917 6224 6.935208 ACACCCAAACAGAGTACTTTTATCTC 59.065 38.462 0.00 0.00 0.00 2.75
4918 6225 6.934645 CACCCAAACAGAGTACTTTTATCTCA 59.065 38.462 0.00 0.00 0.00 3.27
4919 6226 6.935208 ACCCAAACAGAGTACTTTTATCTCAC 59.065 38.462 0.00 0.00 0.00 3.51
4920 6227 6.371825 CCCAAACAGAGTACTTTTATCTCACC 59.628 42.308 0.00 0.00 0.00 4.02
4921 6228 6.371825 CCAAACAGAGTACTTTTATCTCACCC 59.628 42.308 0.00 0.00 0.00 4.61
4922 6229 6.681729 AACAGAGTACTTTTATCTCACCCA 57.318 37.500 0.00 0.00 0.00 4.51
4923 6230 6.681729 ACAGAGTACTTTTATCTCACCCAA 57.318 37.500 0.00 0.00 0.00 4.12
4924 6231 6.465084 ACAGAGTACTTTTATCTCACCCAAC 58.535 40.000 0.00 0.00 0.00 3.77
4925 6232 6.270231 ACAGAGTACTTTTATCTCACCCAACT 59.730 38.462 0.00 0.00 0.00 3.16
4926 6233 6.591834 CAGAGTACTTTTATCTCACCCAACTG 59.408 42.308 0.00 0.00 0.00 3.16
4927 6234 6.270231 AGAGTACTTTTATCTCACCCAACTGT 59.730 38.462 0.00 0.00 0.00 3.55
4936 6243 4.957296 TCTCACCCAACTGTTAGAACTTC 58.043 43.478 0.00 0.00 0.00 3.01
4947 6254 7.404139 ACTGTTAGAACTTCATTTCGTGTAC 57.596 36.000 0.00 0.00 0.00 2.90
4949 6256 5.403166 TGTTAGAACTTCATTTCGTGTACCG 59.597 40.000 0.00 0.00 38.13 4.02
4971 6291 1.144057 GTACCGAGGTGGCATCCTG 59.856 63.158 12.43 3.44 43.94 3.86
4978 6298 2.352422 GTGGCATCCTGGTCAGCA 59.648 61.111 0.00 0.00 0.00 4.41
4986 6306 4.217118 GGCATCCTGGTCAGCATAAATAAG 59.783 45.833 9.25 0.00 0.00 1.73
5015 6342 2.224378 CGGTCCCACATCTCATGCTAAT 60.224 50.000 0.00 0.00 0.00 1.73
5016 6343 3.006859 CGGTCCCACATCTCATGCTAATA 59.993 47.826 0.00 0.00 0.00 0.98
5018 6345 5.376625 GGTCCCACATCTCATGCTAATAAA 58.623 41.667 0.00 0.00 0.00 1.40
5020 6347 5.822519 GTCCCACATCTCATGCTAATAAACA 59.177 40.000 0.00 0.00 0.00 2.83
5022 6349 5.009010 CCCACATCTCATGCTAATAAACACC 59.991 44.000 0.00 0.00 0.00 4.16
5047 6374 5.845391 TTTTTCTCCTTCGTCATTTTGGT 57.155 34.783 0.00 0.00 0.00 3.67
5048 6375 5.845391 TTTTCTCCTTCGTCATTTTGGTT 57.155 34.783 0.00 0.00 0.00 3.67
5049 6376 5.845391 TTTCTCCTTCGTCATTTTGGTTT 57.155 34.783 0.00 0.00 0.00 3.27
5050 6377 5.845391 TTCTCCTTCGTCATTTTGGTTTT 57.155 34.783 0.00 0.00 0.00 2.43
5051 6378 5.845391 TCTCCTTCGTCATTTTGGTTTTT 57.155 34.783 0.00 0.00 0.00 1.94
5089 6416 4.314522 TCATTTTGGTTATCTCTGGCCA 57.685 40.909 4.71 4.71 0.00 5.36
5098 6429 0.844660 ATCTCTGGCCACATCTGCAT 59.155 50.000 0.00 0.00 0.00 3.96
5102 6433 0.107361 CTGGCCACATCTGCATCTCA 60.107 55.000 0.00 0.00 0.00 3.27
5160 6492 1.680522 ATAGGCCCTGCTGTCGACAG 61.681 60.000 35.80 35.80 46.40 3.51
5161 6493 4.008933 GGCCCTGCTGTCGACAGT 62.009 66.667 38.11 0.00 45.45 3.55
5189 6521 1.268625 CACCGCCTAAACCAAAAGGAC 59.731 52.381 0.00 0.00 34.58 3.85
5190 6522 1.144298 ACCGCCTAAACCAAAAGGACT 59.856 47.619 0.00 0.00 34.58 3.85
5270 6638 4.619852 GGCTCCTCCCGTTTCTTC 57.380 61.111 0.00 0.00 0.00 2.87
5314 6682 1.656095 GCAAACGAGTCGATGAAGAGG 59.344 52.381 21.50 0.82 0.00 3.69
5325 6693 3.254411 TCGATGAAGAGGATCGGATCAAG 59.746 47.826 18.99 0.00 42.43 3.02
5328 6696 5.605534 GATGAAGAGGATCGGATCAAGAAA 58.394 41.667 18.99 1.36 42.67 2.52
5415 6788 0.329931 TGTCACCTTGTGGTTGTGGT 59.670 50.000 0.00 0.00 46.05 4.16
5423 6796 3.819652 TGGTTGTGGTGGCCAGCT 61.820 61.111 33.29 0.00 32.34 4.24
5424 6797 3.297620 GGTTGTGGTGGCCAGCTG 61.298 66.667 33.29 6.78 32.34 4.24
5484 6857 1.347050 CGCTGGATGGAGATGGAGATT 59.653 52.381 0.00 0.00 0.00 2.40
5488 6861 3.902467 CTGGATGGAGATGGAGATTCAGA 59.098 47.826 0.00 0.00 0.00 3.27
5489 6862 4.301205 TGGATGGAGATGGAGATTCAGAA 58.699 43.478 0.00 0.00 0.00 3.02
5491 6864 4.347583 GGATGGAGATGGAGATTCAGAACT 59.652 45.833 0.00 0.00 0.00 3.01
5510 6883 2.192861 CGCAGGTGCCAAGTCCAAA 61.193 57.895 0.00 0.00 37.91 3.28
5529 6902 1.293498 CTGGTCCTGGTCGGTTCAG 59.707 63.158 0.00 0.00 0.00 3.02
5552 6925 2.073716 AACCGAGTTCCCACCCACA 61.074 57.895 0.00 0.00 0.00 4.17
5568 6943 5.221048 CCACCCACACTTGTTTTAAGAAGAG 60.221 44.000 6.40 1.59 33.83 2.85
5569 6944 4.887655 ACCCACACTTGTTTTAAGAAGAGG 59.112 41.667 6.40 5.30 33.83 3.69
5571 6946 5.592688 CCCACACTTGTTTTAAGAAGAGGAA 59.407 40.000 6.40 0.00 33.83 3.36
5572 6947 6.096282 CCCACACTTGTTTTAAGAAGAGGAAA 59.904 38.462 6.40 0.00 33.83 3.13
5573 6948 7.363443 CCCACACTTGTTTTAAGAAGAGGAAAA 60.363 37.037 6.40 0.00 33.83 2.29
5574 6949 8.032451 CCACACTTGTTTTAAGAAGAGGAAAAA 58.968 33.333 6.40 0.00 33.83 1.94
5575 6950 9.076596 CACACTTGTTTTAAGAAGAGGAAAAAG 57.923 33.333 6.40 0.00 33.83 2.27
5576 6951 9.020731 ACACTTGTTTTAAGAAGAGGAAAAAGA 57.979 29.630 6.40 0.00 33.83 2.52
5577 6952 9.508567 CACTTGTTTTAAGAAGAGGAAAAAGAG 57.491 33.333 6.40 0.00 33.83 2.85
5628 7004 4.098914 ACAAGGGTGAAACAGCAAGATA 57.901 40.909 0.00 0.00 39.98 1.98
5631 7007 6.426587 ACAAGGGTGAAACAGCAAGATATAT 58.573 36.000 0.00 0.00 39.98 0.86
5632 7008 6.543831 ACAAGGGTGAAACAGCAAGATATATC 59.456 38.462 4.42 4.42 39.98 1.63
5633 7009 6.252599 AGGGTGAAACAGCAAGATATATCA 57.747 37.500 15.08 0.00 39.98 2.15
5634 7010 6.662755 AGGGTGAAACAGCAAGATATATCAA 58.337 36.000 15.08 0.00 39.98 2.57
5635 7011 6.769822 AGGGTGAAACAGCAAGATATATCAAG 59.230 38.462 15.08 7.64 39.98 3.02
5636 7012 6.767902 GGGTGAAACAGCAAGATATATCAAGA 59.232 38.462 15.08 0.00 39.98 3.02
5637 7013 7.041508 GGGTGAAACAGCAAGATATATCAAGAG 60.042 40.741 15.08 3.60 39.98 2.85
5638 7014 7.041508 GGTGAAACAGCAAGATATATCAAGAGG 60.042 40.741 15.08 4.23 39.98 3.69
5699 7075 3.851098 GAGCTACAGGTCGATCTTTGTT 58.149 45.455 0.00 0.00 32.58 2.83
5751 7129 8.450964 TGCATCAAGTAGCTGAAATACTTAAAC 58.549 33.333 0.00 0.00 40.61 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
270 271 5.237779 GTCATTTTGGTTTTCGTGTCTCCTA 59.762 40.000 0.00 0.00 0.00 2.94
313 317 5.114081 GCTGGTGGTACGTCTTAATTACAT 58.886 41.667 0.00 0.00 0.00 2.29
324 328 0.820482 GGTTTTGGCTGGTGGTACGT 60.820 55.000 0.00 0.00 0.00 3.57
826 840 1.961394 TGATATAGACTGCCGGTGGAC 59.039 52.381 1.90 0.00 0.00 4.02
827 841 1.961394 GTGATATAGACTGCCGGTGGA 59.039 52.381 1.90 0.00 0.00 4.02
829 843 2.623416 TCAGTGATATAGACTGCCGGTG 59.377 50.000 1.90 0.00 40.64 4.94
846 860 1.620822 GCCCATTTGTTCCAGTCAGT 58.379 50.000 0.00 0.00 0.00 3.41
870 884 2.099098 GGAAAACATGGCCCAATAGTCG 59.901 50.000 0.00 0.00 0.00 4.18
972 991 2.674420 GTATCCCTGTGGCTACCTGTA 58.326 52.381 0.00 0.00 28.74 2.74
974 993 0.389391 CGTATCCCTGTGGCTACCTG 59.611 60.000 0.00 0.00 30.87 4.00
976 995 1.069258 GCGTATCCCTGTGGCTACC 59.931 63.158 0.00 0.00 30.87 3.18
1067 1125 1.002900 CTCGCTTCGACATCTCTCTCC 60.003 57.143 0.00 0.00 0.00 3.71
1183 1249 4.811557 CACAAGAACGGAAAAGAGAAGACT 59.188 41.667 0.00 0.00 0.00 3.24
1477 1545 1.108776 TACTATGCGGTGACCAGTCC 58.891 55.000 1.11 0.00 0.00 3.85
1485 1553 2.286833 CGTTCCCAAATACTATGCGGTG 59.713 50.000 0.00 0.00 0.00 4.94
1524 1592 5.603170 AAGGAAACCATAAGCATCCATTG 57.397 39.130 0.00 0.00 32.47 2.82
1525 1593 6.625532 AAAAGGAAACCATAAGCATCCATT 57.374 33.333 0.00 0.00 32.47 3.16
1543 1611 3.269178 TCTGGCTGCAAAAACAAAAAGG 58.731 40.909 0.50 0.00 0.00 3.11
1550 1619 1.211743 GCACTTCTGGCTGCAAAAAC 58.788 50.000 0.50 0.00 33.31 2.43
1634 1703 2.544267 GCACCACTGTAACAAGAGACAC 59.456 50.000 0.00 0.00 0.00 3.67
1648 1717 2.040009 AACGGCACACTAGCACCACT 62.040 55.000 0.00 0.00 35.83 4.00
1657 1726 1.333619 GTGACAATCAAACGGCACACT 59.666 47.619 0.00 0.00 0.00 3.55
1758 1827 1.354368 GGGGATCACCTTCCAACAAGA 59.646 52.381 6.79 0.00 40.03 3.02
1822 1891 6.783708 AACAAGGTTCAAATTCCAGTTACA 57.216 33.333 0.00 0.00 0.00 2.41
1825 1894 9.679661 AAATAAAACAAGGTTCAAATTCCAGTT 57.320 25.926 0.00 0.00 0.00 3.16
1826 1895 9.679661 AAAATAAAACAAGGTTCAAATTCCAGT 57.320 25.926 0.00 0.00 0.00 4.00
1859 1928 6.542005 AGACAACACTGAATCATTACAACACA 59.458 34.615 0.00 0.00 0.00 3.72
1869 1938 4.346709 TCCCTACAAGACAACACTGAATCA 59.653 41.667 0.00 0.00 0.00 2.57
2013 2082 4.411540 CCCTAGCATATCTGATGGCCTATT 59.588 45.833 3.32 0.00 0.00 1.73
2150 2219 3.690139 GCTTCTTAGGCCAGTTTAGAACC 59.310 47.826 5.01 0.00 0.00 3.62
2271 2340 2.795470 CCTTCTATTTAGTTCGCGAGGC 59.205 50.000 9.59 6.79 0.00 4.70
2351 2420 3.952323 AGGACTCTCATTCATTTGCATGG 59.048 43.478 0.00 0.00 0.00 3.66
2364 2433 4.539293 ACAGGGTTAGTACTAGGACTCTCA 59.461 45.833 12.02 0.00 0.00 3.27
2369 2438 7.894753 AAGATTACAGGGTTAGTACTAGGAC 57.105 40.000 2.23 0.00 0.00 3.85
2386 2455 4.811557 ACGCTCATCCAAGCTAAAGATTAC 59.188 41.667 0.00 0.00 40.23 1.89
2388 2457 3.624861 CACGCTCATCCAAGCTAAAGATT 59.375 43.478 0.00 0.00 40.23 2.40
2434 2503 8.286996 GAAGCCATTCTTCTTTTAAAGACAAC 57.713 34.615 6.93 0.00 45.99 3.32
2677 2749 3.270027 TGAGGTTTTGCTCATATGACGG 58.730 45.455 0.00 0.00 0.00 4.79
2758 2830 3.245518 TGTCACCTGACCAATATCACG 57.754 47.619 2.98 0.00 44.15 4.35
2784 2856 6.372937 GCACCTATTCCTAATCTAAGAATGCC 59.627 42.308 0.00 0.00 32.64 4.40
2796 2868 1.760613 CGACCAGGCACCTATTCCTAA 59.239 52.381 0.00 0.00 0.00 2.69
2857 2929 7.809546 TGTACATAACATTGTGAACCAGAAA 57.190 32.000 0.00 0.00 31.43 2.52
3079 3152 3.144506 CCAAGCTCATGTCACAAGTTCT 58.855 45.455 0.00 0.00 0.00 3.01
3120 3193 7.615403 AGTTTGAATAGAGATGTCTGCAGTAA 58.385 34.615 14.67 3.38 33.84 2.24
3295 3379 7.217200 TGAATTGCACAGTAAAGAACTCTAGT 58.783 34.615 0.00 0.00 35.76 2.57
3416 3501 3.481453 GAATGCTTATTCCTCCAGGACC 58.519 50.000 0.00 0.00 45.39 4.46
3577 3666 3.450457 TGCAAAACCAAGACAACAGGAAT 59.550 39.130 0.00 0.00 0.00 3.01
3590 3679 4.646945 TGGATTTAGAACTGTGCAAAACCA 59.353 37.500 0.00 7.89 32.43 3.67
3607 3696 7.039270 GTCACTTTACACAAAAAGGTGGATTT 58.961 34.615 0.00 0.00 43.08 2.17
3608 3697 6.379988 AGTCACTTTACACAAAAAGGTGGATT 59.620 34.615 0.00 0.00 43.08 3.01
3609 3698 5.891551 AGTCACTTTACACAAAAAGGTGGAT 59.108 36.000 0.00 0.00 43.08 3.41
3610 3699 5.124776 CAGTCACTTTACACAAAAAGGTGGA 59.875 40.000 0.00 0.00 43.08 4.02
3611 3700 5.339990 CAGTCACTTTACACAAAAAGGTGG 58.660 41.667 0.00 0.00 43.08 4.61
3616 3706 5.378292 TGTGCAGTCACTTTACACAAAAA 57.622 34.783 3.13 0.00 43.49 1.94
3714 3945 1.626321 TCAGCGAATGGAACCTTACCA 59.374 47.619 0.00 0.00 41.83 3.25
3778 4109 4.916983 TGCTAGAATGCACAAAAGTTGT 57.083 36.364 0.00 0.00 46.75 3.32
3779 4110 7.086376 ACTAATGCTAGAATGCACAAAAGTTG 58.914 34.615 0.00 0.00 46.33 3.16
3855 4186 9.527157 TTTCCTGTATATTTTCAAGAATCCACA 57.473 29.630 0.00 0.00 0.00 4.17
4273 4690 4.396166 CACACTGAACCAGAGTTTCAGTTT 59.604 41.667 13.69 6.55 39.86 2.66
4401 4821 2.279120 GATGTGCCGCTCTCCTCG 60.279 66.667 0.00 0.00 0.00 4.63
4413 4833 1.845266 CGATCTTCGGGACTGATGTG 58.155 55.000 0.00 0.00 36.00 3.21
4414 4834 0.103208 GCGATCTTCGGGACTGATGT 59.897 55.000 0.00 0.00 40.84 3.06
4425 4845 1.661743 CGATCTCGGTCTGCGATCTTC 60.662 57.143 9.43 0.00 33.20 2.87
4449 4869 1.228459 AACAGGGAAAAGGTCGCCC 60.228 57.895 0.00 0.00 40.05 6.13
4605 5025 2.931320 GCTGAGTTAGAACACCCCGAAG 60.931 54.545 0.00 0.00 0.00 3.79
4609 5029 0.391263 CCGCTGAGTTAGAACACCCC 60.391 60.000 0.00 0.00 0.00 4.95
4625 5045 0.598065 AAGTGTTGGCATTTCTCCGC 59.402 50.000 0.00 0.00 0.00 5.54
4706 5126 4.862641 AGCATAACATAACTGGGAAGGT 57.137 40.909 0.00 0.00 0.00 3.50
4807 6114 2.289694 CGGGGAATGTTGACTTGTCTCT 60.290 50.000 2.35 0.00 0.00 3.10
4818 6125 4.261801 CAGATAGTTCAACGGGGAATGTT 58.738 43.478 0.00 0.00 0.00 2.71
4829 6136 8.215926 TCGGAAAAGAAAAACAGATAGTTCAA 57.784 30.769 0.00 0.00 40.26 2.69
4830 6137 7.041372 CCTCGGAAAAGAAAAACAGATAGTTCA 60.041 37.037 0.00 0.00 40.26 3.18
4831 6138 7.298854 CCTCGGAAAAGAAAAACAGATAGTTC 58.701 38.462 0.00 0.00 40.26 3.01
4832 6139 6.206829 CCCTCGGAAAAGAAAAACAGATAGTT 59.793 38.462 0.00 0.00 43.89 2.24
4833 6140 5.705905 CCCTCGGAAAAGAAAAACAGATAGT 59.294 40.000 0.00 0.00 0.00 2.12
4834 6141 5.938125 TCCCTCGGAAAAGAAAAACAGATAG 59.062 40.000 0.00 0.00 0.00 2.08
4835 6142 5.704053 GTCCCTCGGAAAAGAAAAACAGATA 59.296 40.000 0.00 0.00 31.38 1.98
4836 6143 4.519350 GTCCCTCGGAAAAGAAAAACAGAT 59.481 41.667 0.00 0.00 31.38 2.90
4837 6144 3.881089 GTCCCTCGGAAAAGAAAAACAGA 59.119 43.478 0.00 0.00 31.38 3.41
4838 6145 3.004419 GGTCCCTCGGAAAAGAAAAACAG 59.996 47.826 0.00 0.00 31.38 3.16
4839 6146 2.953648 GGTCCCTCGGAAAAGAAAAACA 59.046 45.455 0.00 0.00 31.38 2.83
4840 6147 2.031420 CGGTCCCTCGGAAAAGAAAAAC 60.031 50.000 0.00 0.00 31.38 2.43
4841 6148 2.223745 CGGTCCCTCGGAAAAGAAAAA 58.776 47.619 0.00 0.00 31.38 1.94
4842 6149 1.141455 ACGGTCCCTCGGAAAAGAAAA 59.859 47.619 0.00 0.00 31.38 2.29
4843 6150 0.760572 ACGGTCCCTCGGAAAAGAAA 59.239 50.000 0.00 0.00 31.38 2.52
4844 6151 0.760572 AACGGTCCCTCGGAAAAGAA 59.239 50.000 0.00 0.00 31.38 2.52
4845 6152 0.034337 CAACGGTCCCTCGGAAAAGA 59.966 55.000 0.00 0.00 31.38 2.52
4846 6153 0.034337 TCAACGGTCCCTCGGAAAAG 59.966 55.000 0.00 0.00 31.38 2.27
4847 6154 0.469070 TTCAACGGTCCCTCGGAAAA 59.531 50.000 0.00 0.00 31.38 2.29
4848 6155 0.249996 GTTCAACGGTCCCTCGGAAA 60.250 55.000 0.00 0.00 31.38 3.13
4849 6156 1.117142 AGTTCAACGGTCCCTCGGAA 61.117 55.000 0.00 0.00 31.38 4.30
4850 6157 0.251297 TAGTTCAACGGTCCCTCGGA 60.251 55.000 0.00 0.00 0.00 4.55
4851 6158 0.822164 ATAGTTCAACGGTCCCTCGG 59.178 55.000 0.00 0.00 0.00 4.63
4852 6159 1.749634 AGATAGTTCAACGGTCCCTCG 59.250 52.381 0.00 0.00 0.00 4.63
4853 6160 2.496470 ACAGATAGTTCAACGGTCCCTC 59.504 50.000 0.00 0.00 0.00 4.30
4854 6161 2.537143 ACAGATAGTTCAACGGTCCCT 58.463 47.619 0.00 0.00 0.00 4.20
4855 6162 3.329929 AACAGATAGTTCAACGGTCCC 57.670 47.619 0.00 0.00 34.74 4.46
4856 6163 6.980051 ATTAAACAGATAGTTCAACGGTCC 57.020 37.500 0.00 0.00 40.26 4.46
4857 6164 9.113876 CAAAATTAAACAGATAGTTCAACGGTC 57.886 33.333 0.00 0.00 40.26 4.79
4858 6165 8.842280 TCAAAATTAAACAGATAGTTCAACGGT 58.158 29.630 0.00 0.00 40.26 4.83
4859 6166 9.329913 CTCAAAATTAAACAGATAGTTCAACGG 57.670 33.333 0.00 0.00 40.26 4.44
4860 6167 8.840867 GCTCAAAATTAAACAGATAGTTCAACG 58.159 33.333 0.00 0.00 40.26 4.10
4861 6168 9.129209 GGCTCAAAATTAAACAGATAGTTCAAC 57.871 33.333 0.00 0.00 40.26 3.18
4862 6169 8.303876 GGGCTCAAAATTAAACAGATAGTTCAA 58.696 33.333 0.00 0.00 40.26 2.69
4863 6170 7.669722 AGGGCTCAAAATTAAACAGATAGTTCA 59.330 33.333 0.00 0.00 40.26 3.18
4864 6171 8.056407 AGGGCTCAAAATTAAACAGATAGTTC 57.944 34.615 0.00 0.00 40.26 3.01
4865 6172 7.148239 CGAGGGCTCAAAATTAAACAGATAGTT 60.148 37.037 0.00 0.00 43.89 2.24
4866 6173 6.316390 CGAGGGCTCAAAATTAAACAGATAGT 59.684 38.462 0.00 0.00 0.00 2.12
4867 6174 6.538742 TCGAGGGCTCAAAATTAAACAGATAG 59.461 38.462 0.00 0.00 0.00 2.08
4868 6175 6.315393 GTCGAGGGCTCAAAATTAAACAGATA 59.685 38.462 0.00 0.00 0.00 1.98
4869 6176 5.123979 GTCGAGGGCTCAAAATTAAACAGAT 59.876 40.000 0.00 0.00 0.00 2.90
4870 6177 4.454504 GTCGAGGGCTCAAAATTAAACAGA 59.545 41.667 0.00 0.00 0.00 3.41
4871 6178 4.215399 TGTCGAGGGCTCAAAATTAAACAG 59.785 41.667 0.00 0.00 0.00 3.16
4872 6179 4.023536 GTGTCGAGGGCTCAAAATTAAACA 60.024 41.667 0.00 0.00 0.00 2.83
4873 6180 4.473199 GTGTCGAGGGCTCAAAATTAAAC 58.527 43.478 0.00 0.00 0.00 2.01
4874 6181 3.504520 GGTGTCGAGGGCTCAAAATTAAA 59.495 43.478 0.00 0.00 0.00 1.52
4875 6182 3.078837 GGTGTCGAGGGCTCAAAATTAA 58.921 45.455 0.00 0.00 0.00 1.40
4876 6183 2.617021 GGGTGTCGAGGGCTCAAAATTA 60.617 50.000 0.00 0.00 0.00 1.40
4877 6184 1.534729 GGTGTCGAGGGCTCAAAATT 58.465 50.000 0.00 0.00 0.00 1.82
4878 6185 0.322546 GGGTGTCGAGGGCTCAAAAT 60.323 55.000 0.00 0.00 0.00 1.82
4879 6186 1.072505 GGGTGTCGAGGGCTCAAAA 59.927 57.895 0.00 0.00 0.00 2.44
4880 6187 1.701031 TTGGGTGTCGAGGGCTCAAA 61.701 55.000 0.00 0.00 0.00 2.69
4881 6188 1.701031 TTTGGGTGTCGAGGGCTCAA 61.701 55.000 0.00 0.00 0.00 3.02
4882 6189 2.144078 TTTGGGTGTCGAGGGCTCA 61.144 57.895 0.00 0.00 0.00 4.26
4883 6190 1.671379 GTTTGGGTGTCGAGGGCTC 60.671 63.158 0.00 0.00 0.00 4.70
4884 6191 2.397413 CTGTTTGGGTGTCGAGGGCT 62.397 60.000 0.00 0.00 0.00 5.19
4885 6192 1.966451 CTGTTTGGGTGTCGAGGGC 60.966 63.158 0.00 0.00 0.00 5.19
4886 6193 0.320771 CTCTGTTTGGGTGTCGAGGG 60.321 60.000 0.00 0.00 0.00 4.30
4887 6194 0.393077 ACTCTGTTTGGGTGTCGAGG 59.607 55.000 0.00 0.00 0.00 4.63
4888 6195 2.296471 AGTACTCTGTTTGGGTGTCGAG 59.704 50.000 0.00 0.00 0.00 4.04
4889 6196 2.313317 AGTACTCTGTTTGGGTGTCGA 58.687 47.619 0.00 0.00 0.00 4.20
4890 6197 2.814280 AGTACTCTGTTTGGGTGTCG 57.186 50.000 0.00 0.00 0.00 4.35
4891 6198 6.935208 AGATAAAAGTACTCTGTTTGGGTGTC 59.065 38.462 0.00 0.00 0.00 3.67
4892 6199 6.838382 AGATAAAAGTACTCTGTTTGGGTGT 58.162 36.000 0.00 0.00 0.00 4.16
4893 6200 6.934645 TGAGATAAAAGTACTCTGTTTGGGTG 59.065 38.462 0.00 0.00 0.00 4.61
4894 6201 6.935208 GTGAGATAAAAGTACTCTGTTTGGGT 59.065 38.462 0.00 0.00 0.00 4.51
4895 6202 6.371825 GGTGAGATAAAAGTACTCTGTTTGGG 59.628 42.308 0.00 0.00 0.00 4.12
4896 6203 6.371825 GGGTGAGATAAAAGTACTCTGTTTGG 59.628 42.308 0.00 0.00 0.00 3.28
4897 6204 6.934645 TGGGTGAGATAAAAGTACTCTGTTTG 59.065 38.462 0.00 0.00 0.00 2.93
4898 6205 7.074653 TGGGTGAGATAAAAGTACTCTGTTT 57.925 36.000 0.00 0.00 0.00 2.83
4899 6206 6.681729 TGGGTGAGATAAAAGTACTCTGTT 57.318 37.500 0.00 0.00 0.00 3.16
4900 6207 6.270231 AGTTGGGTGAGATAAAAGTACTCTGT 59.730 38.462 0.00 0.00 0.00 3.41
4901 6208 6.591834 CAGTTGGGTGAGATAAAAGTACTCTG 59.408 42.308 0.00 0.00 0.00 3.35
4902 6209 6.270231 ACAGTTGGGTGAGATAAAAGTACTCT 59.730 38.462 0.00 0.00 0.00 3.24
4903 6210 6.465084 ACAGTTGGGTGAGATAAAAGTACTC 58.535 40.000 0.00 0.00 0.00 2.59
4904 6211 6.435292 ACAGTTGGGTGAGATAAAAGTACT 57.565 37.500 0.00 0.00 0.00 2.73
4905 6212 8.092687 TCTAACAGTTGGGTGAGATAAAAGTAC 58.907 37.037 0.00 0.00 0.00 2.73
4906 6213 8.197592 TCTAACAGTTGGGTGAGATAAAAGTA 57.802 34.615 0.00 0.00 0.00 2.24
4907 6214 7.074653 TCTAACAGTTGGGTGAGATAAAAGT 57.925 36.000 0.00 0.00 0.00 2.66
4908 6215 7.661847 AGTTCTAACAGTTGGGTGAGATAAAAG 59.338 37.037 0.00 0.00 28.36 2.27
4909 6216 7.514721 AGTTCTAACAGTTGGGTGAGATAAAA 58.485 34.615 0.00 0.00 28.36 1.52
4910 6217 7.074653 AGTTCTAACAGTTGGGTGAGATAAA 57.925 36.000 0.00 0.00 28.36 1.40
4911 6218 6.681729 AGTTCTAACAGTTGGGTGAGATAA 57.318 37.500 0.00 0.00 28.36 1.75
4912 6219 6.269077 TGAAGTTCTAACAGTTGGGTGAGATA 59.731 38.462 4.17 0.00 28.36 1.98
4913 6220 5.071788 TGAAGTTCTAACAGTTGGGTGAGAT 59.928 40.000 4.17 0.00 28.36 2.75
4914 6221 4.407621 TGAAGTTCTAACAGTTGGGTGAGA 59.592 41.667 4.17 0.00 0.00 3.27
4915 6222 4.703897 TGAAGTTCTAACAGTTGGGTGAG 58.296 43.478 4.17 0.00 0.00 3.51
4916 6223 4.764050 TGAAGTTCTAACAGTTGGGTGA 57.236 40.909 4.17 0.00 0.00 4.02
4917 6224 6.391227 AAATGAAGTTCTAACAGTTGGGTG 57.609 37.500 4.17 0.00 0.00 4.61
4918 6225 5.238650 CGAAATGAAGTTCTAACAGTTGGGT 59.761 40.000 4.17 0.00 0.00 4.51
4919 6226 5.238650 ACGAAATGAAGTTCTAACAGTTGGG 59.761 40.000 4.17 0.00 0.00 4.12
4920 6227 6.136071 CACGAAATGAAGTTCTAACAGTTGG 58.864 40.000 4.17 0.00 0.00 3.77
4921 6228 6.715464 ACACGAAATGAAGTTCTAACAGTTG 58.285 36.000 4.17 0.00 0.00 3.16
4922 6229 6.920569 ACACGAAATGAAGTTCTAACAGTT 57.079 33.333 4.17 0.00 0.00 3.16
4923 6230 6.423001 GGTACACGAAATGAAGTTCTAACAGT 59.577 38.462 4.17 0.00 0.00 3.55
4924 6231 6.818416 GGTACACGAAATGAAGTTCTAACAG 58.182 40.000 4.17 0.00 0.00 3.16
4925 6232 6.774354 GGTACACGAAATGAAGTTCTAACA 57.226 37.500 4.17 0.00 0.00 2.41
4947 6254 1.105167 TGCCACCTCGGTACTATCGG 61.105 60.000 0.00 0.00 36.97 4.18
4949 6256 1.272769 GGATGCCACCTCGGTACTATC 59.727 57.143 0.00 0.00 36.97 2.08
4971 6291 6.037172 CCGCCATATACTTATTTATGCTGACC 59.963 42.308 0.00 0.00 0.00 4.02
4978 6298 6.013206 TGTGGGACCGCCATATACTTATTTAT 60.013 38.462 0.00 0.00 35.15 1.40
4986 6306 1.623811 AGATGTGGGACCGCCATATAC 59.376 52.381 0.00 0.00 35.15 1.47
5051 6378 8.875168 ACCAAAATGATCAAGGTACCATAAAAA 58.125 29.630 15.94 0.00 0.00 1.94
5052 6379 8.429237 ACCAAAATGATCAAGGTACCATAAAA 57.571 30.769 15.94 0.00 0.00 1.52
5053 6380 8.429237 AACCAAAATGATCAAGGTACCATAAA 57.571 30.769 15.94 0.00 31.10 1.40
5054 6381 9.707957 ATAACCAAAATGATCAAGGTACCATAA 57.292 29.630 15.94 0.00 31.10 1.90
5055 6382 9.349713 GATAACCAAAATGATCAAGGTACCATA 57.650 33.333 15.94 0.00 31.10 2.74
5056 6383 8.061304 AGATAACCAAAATGATCAAGGTACCAT 58.939 33.333 15.94 0.00 31.10 3.55
5057 6384 7.410174 AGATAACCAAAATGATCAAGGTACCA 58.590 34.615 15.94 0.00 31.10 3.25
5058 6385 7.775561 AGAGATAACCAAAATGATCAAGGTACC 59.224 37.037 2.73 2.73 31.10 3.34
5059 6386 8.616076 CAGAGATAACCAAAATGATCAAGGTAC 58.384 37.037 0.00 2.49 31.10 3.34
5060 6387 7.775093 CCAGAGATAACCAAAATGATCAAGGTA 59.225 37.037 0.00 0.00 31.10 3.08
5061 6388 6.604795 CCAGAGATAACCAAAATGATCAAGGT 59.395 38.462 0.00 2.98 0.00 3.50
5089 6416 2.027745 ACGGAAAGTGAGATGCAGATGT 60.028 45.455 0.00 0.00 0.00 3.06
5098 6429 0.319555 CTTGCGGACGGAAAGTGAGA 60.320 55.000 0.00 0.00 0.00 3.27
5102 6433 1.961277 CAGCTTGCGGACGGAAAGT 60.961 57.895 0.00 0.00 0.00 2.66
5160 6492 1.070376 GTTTAGGCGGTGTTCGTTCAC 60.070 52.381 4.66 4.66 41.72 3.18
5161 6493 1.219646 GTTTAGGCGGTGTTCGTTCA 58.780 50.000 0.00 0.00 41.72 3.18
5217 6556 9.327628 GGGAATAACTTTACTCCTGTAAATCTC 57.672 37.037 2.46 0.00 44.57 2.75
5223 6562 5.104652 GGCTGGGAATAACTTTACTCCTGTA 60.105 44.000 0.00 0.00 30.14 2.74
5224 6563 4.324331 GGCTGGGAATAACTTTACTCCTGT 60.324 45.833 0.00 0.00 30.14 4.00
5225 6564 4.200092 GGCTGGGAATAACTTTACTCCTG 58.800 47.826 0.00 0.00 30.14 3.86
5266 6634 3.964688 TGGTGTTACTCAGAGGTTGAAGA 59.035 43.478 1.53 0.00 34.81 2.87
5270 6638 2.800544 CGTTGGTGTTACTCAGAGGTTG 59.199 50.000 1.53 0.00 0.00 3.77
5314 6682 0.938008 GCGGGTTTCTTGATCCGATC 59.062 55.000 4.71 1.01 44.69 3.69
5325 6693 0.108329 TTCTCCATCTCGCGGGTTTC 60.108 55.000 5.57 0.00 0.00 2.78
5328 6696 0.757188 ATCTTCTCCATCTCGCGGGT 60.757 55.000 5.57 0.00 0.00 5.28
5423 6796 2.046988 CGAGTCATGCCTGGCACA 60.047 61.111 25.99 11.11 43.04 4.57
5424 6797 3.503363 GCGAGTCATGCCTGGCAC 61.503 66.667 25.99 11.89 43.04 5.01
5442 6815 4.090057 GTTCTTCCACAGCGCCGC 62.090 66.667 2.29 0.00 0.00 6.53
5484 6857 2.038814 TTGGCACCTGCGAGTTCTGA 62.039 55.000 0.00 0.00 43.26 3.27
5488 6861 1.598130 GACTTGGCACCTGCGAGTT 60.598 57.895 6.44 0.00 43.26 3.01
5489 6862 2.031163 GACTTGGCACCTGCGAGT 59.969 61.111 5.03 5.03 43.26 4.18
5491 6864 2.616797 TTTGGACTTGGCACCTGCGA 62.617 55.000 0.00 0.00 43.26 5.10
5510 6883 1.458777 TGAACCGACCAGGACCAGT 60.459 57.895 0.00 0.00 45.00 4.00
5529 6902 1.235281 GGTGGGAACTCGGTTGAAGC 61.235 60.000 0.00 0.00 0.00 3.86
5552 6925 9.462606 TCTCTTTTTCCTCTTCTTAAAACAAGT 57.537 29.630 0.00 0.00 0.00 3.16
5568 6943 4.284746 TGGGAACTCTCTCTCTCTTTTTCC 59.715 45.833 0.00 0.00 0.00 3.13
5569 6944 5.234752 GTGGGAACTCTCTCTCTCTTTTTC 58.765 45.833 0.00 0.00 0.00 2.29
5571 6946 3.580895 GGTGGGAACTCTCTCTCTCTTTT 59.419 47.826 0.00 0.00 0.00 2.27
5572 6947 3.169908 GGTGGGAACTCTCTCTCTCTTT 58.830 50.000 0.00 0.00 0.00 2.52
5573 6948 2.558800 GGGTGGGAACTCTCTCTCTCTT 60.559 54.545 0.00 0.00 0.00 2.85
5574 6949 1.006639 GGGTGGGAACTCTCTCTCTCT 59.993 57.143 0.00 0.00 0.00 3.10
5575 6950 1.272760 TGGGTGGGAACTCTCTCTCTC 60.273 57.143 0.00 0.00 0.00 3.20
5576 6951 0.787084 TGGGTGGGAACTCTCTCTCT 59.213 55.000 0.00 0.00 0.00 3.10
5577 6952 0.899019 GTGGGTGGGAACTCTCTCTC 59.101 60.000 0.00 0.00 0.00 3.20
5699 7075 3.576118 GGCACAGATCTCTAGGCTAATGA 59.424 47.826 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.