Multiple sequence alignment - TraesCS7B01G265500

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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 TraesCS7B01G265500 chr7B 100.000 6405 0 0 1 6405 487815793 487809389 0.000000e+00 11828.0
1 TraesCS7B01G265500 chr7B 94.286 105 3 3 3927 4030 715360307 715360409 2.390000e-34 158.0
2 TraesCS7B01G265500 chr7B 95.918 98 1 3 3931 4027 304493245 304493150 8.600000e-34 156.0
3 TraesCS7B01G265500 chr7A 91.774 3635 208 44 340 3936 536521471 536517890 0.000000e+00 4972.0
4 TraesCS7B01G265500 chr7A 92.167 1915 88 31 4017 5893 536517893 536516003 0.000000e+00 2649.0
5 TraesCS7B01G265500 chr7A 88.191 398 14 19 6027 6405 536515904 536515521 1.640000e-120 444.0
6 TraesCS7B01G265500 chr7A 86.111 144 20 0 3325 3468 193560953 193560810 8.600000e-34 156.0
7 TraesCS7B01G265500 chr7D 91.344 3177 170 39 680 3833 463877929 463881023 0.000000e+00 4246.0
8 TraesCS7B01G265500 chr7D 92.933 1882 81 27 4017 5858 463883728 463885597 0.000000e+00 2691.0
9 TraesCS7B01G265500 chr7D 88.555 533 26 15 5895 6405 463885701 463886220 1.180000e-171 614.0
10 TraesCS7B01G265500 chr7D 88.739 444 29 8 182 610 463877204 463877641 2.050000e-144 523.0
11 TraesCS7B01G265500 chr7D 91.860 172 9 1 1 172 463873385 463873551 1.070000e-57 235.0
12 TraesCS7B01G265500 chr7D 96.800 125 4 0 3812 3936 463883607 463883731 6.510000e-50 209.0
13 TraesCS7B01G265500 chr7D 94.545 110 3 2 3926 4033 463109033 463109141 3.970000e-37 167.0
14 TraesCS7B01G265500 chr7D 90.741 54 5 0 5895 5948 299189146 299189199 8.910000e-09 73.1
15 TraesCS7B01G265500 chr2A 84.941 591 68 16 3085 3661 753810623 753811206 4.310000e-161 579.0
16 TraesCS7B01G265500 chr2A 89.908 327 30 2 2755 3079 753798041 753798366 9.930000e-113 418.0
17 TraesCS7B01G265500 chr2A 91.228 57 5 0 5895 5951 28827499 28827443 1.910000e-10 78.7
18 TraesCS7B01G265500 chr6D 89.202 213 23 0 2721 2933 161974034 161974246 3.810000e-67 267.0
19 TraesCS7B01G265500 chr6D 90.698 129 12 0 2452 2580 161973750 161973878 8.540000e-39 172.0
20 TraesCS7B01G265500 chr6D 84.848 165 23 2 3305 3468 161975041 161975204 1.430000e-36 165.0
21 TraesCS7B01G265500 chr6D 92.381 105 8 0 1799 1903 161973117 161973221 4.000000e-32 150.0
22 TraesCS7B01G265500 chr6D 100.000 28 0 0 5950 5977 356601362 356601389 1.200000e-02 52.8
23 TraesCS7B01G265500 chr6B 89.855 207 21 0 2727 2933 300721918 300721712 3.810000e-67 267.0
24 TraesCS7B01G265500 chr6B 90.152 132 13 0 2455 2586 300722204 300722073 8.540000e-39 172.0
25 TraesCS7B01G265500 chr6B 88.112 143 17 0 3326 3468 300720899 300720757 3.070000e-38 171.0
26 TraesCS7B01G265500 chr6B 93.333 105 7 0 1799 1903 300722846 300722742 8.600000e-34 156.0
27 TraesCS7B01G265500 chr6A 88.732 213 24 0 2721 2933 221344755 221344967 1.770000e-65 261.0
28 TraesCS7B01G265500 chr6A 90.698 129 12 0 2452 2580 221344472 221344600 8.540000e-39 172.0
29 TraesCS7B01G265500 chr6A 86.076 158 22 0 3311 3468 221345770 221345927 3.070000e-38 171.0
30 TraesCS7B01G265500 chr6A 93.333 105 7 0 1799 1903 221343839 221343943 8.600000e-34 156.0
31 TraesCS7B01G265500 chr6A 92.982 57 4 0 5895 5951 588060184 588060128 4.120000e-12 84.2
32 TraesCS7B01G265500 chr6A 91.071 56 5 0 5896 5951 588045391 588045336 6.890000e-10 76.8
33 TraesCS7B01G265500 chrUn 90.152 132 13 0 2455 2586 212095079 212094948 8.540000e-39 172.0
34 TraesCS7B01G265500 chrUn 95.000 100 3 2 3935 4033 37006447 37006349 8.600000e-34 156.0
35 TraesCS7B01G265500 chrUn 95.000 100 3 2 3935 4033 38258668 38258570 8.600000e-34 156.0
36 TraesCS7B01G265500 chrUn 95.000 100 3 2 3935 4033 196709562 196709660 8.600000e-34 156.0
37 TraesCS7B01G265500 chrUn 92.381 105 8 0 1799 1903 212095715 212095611 4.000000e-32 150.0
38 TraesCS7B01G265500 chr5A 95.876 97 3 1 3934 4030 706441154 706441059 8.600000e-34 156.0
39 TraesCS7B01G265500 chr5A 91.228 57 5 0 5895 5951 602844039 602843983 1.910000e-10 78.7
40 TraesCS7B01G265500 chr3D 86.111 144 20 0 3325 3468 351126158 351126015 8.600000e-34 156.0
41 TraesCS7B01G265500 chr3D 93.023 43 1 2 5907 5948 590391525 590391566 1.930000e-05 62.1
42 TraesCS7B01G265500 chr3B 86.111 144 20 0 3325 3468 449810889 449810746 8.600000e-34 156.0
43 TraesCS7B01G265500 chr1B 92.035 113 5 4 3934 4044 117282828 117282718 8.600000e-34 156.0
44 TraesCS7B01G265500 chr5B 91.150 113 6 4 3935 4044 591579755 591579866 4.000000e-32 150.0
45 TraesCS7B01G265500 chr1A 91.228 57 5 0 5895 5951 581544474 581544418 1.910000e-10 78.7
46 TraesCS7B01G265500 chr1A 100.000 28 0 0 5950 5977 9639022 9639049 1.200000e-02 52.8
47 TraesCS7B01G265500 chr1A 100.000 28 0 0 5950 5977 558308779 558308806 1.200000e-02 52.8
48 TraesCS7B01G265500 chr2B 89.831 59 4 2 5895 5952 627951703 627951646 2.480000e-09 75.0
49 TraesCS7B01G265500 chr4D 90.741 54 5 0 5895 5948 421896413 421896466 8.910000e-09 73.1
50 TraesCS7B01G265500 chr5D 88.889 54 6 0 5895 5948 483269382 483269435 4.140000e-07 67.6
51 TraesCS7B01G265500 chr5D 93.333 45 2 1 5907 5951 251300419 251300376 1.490000e-06 65.8
52 TraesCS7B01G265500 chr5D 96.774 31 1 0 5950 5980 283112197 283112167 1.200000e-02 52.8
53 TraesCS7B01G265500 chr4B 88.889 54 6 0 5895 5948 249050349 249050296 4.140000e-07 67.6


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 TraesCS7B01G265500 chr7B 487809389 487815793 6404 True 11828.000000 11828 100.000000 1 6405 1 chr7B.!!$R2 6404
1 TraesCS7B01G265500 chr7A 536515521 536521471 5950 True 2688.333333 4972 90.710667 340 6405 3 chr7A.!!$R2 6065
2 TraesCS7B01G265500 chr7D 463873385 463886220 12835 False 1419.666667 4246 91.705167 1 6405 6 chr7D.!!$F3 6404
3 TraesCS7B01G265500 chr2A 753810623 753811206 583 False 579.000000 579 84.941000 3085 3661 1 chr2A.!!$F2 576

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
130 131 0.029567 GAGTAGGCGACGATGACCTG 59.970 60.0 0.00 0.00 34.92 4.00 F
439 4105 0.110823 CTGACACGCAAAAGCGGTAC 60.111 55.0 14.62 5.37 37.53 3.34 F
1851 5760 0.257039 GATTGGGAGATGGCACCACT 59.743 55.0 0.00 0.00 33.20 4.00 F
2433 6350 0.179076 AGCTGCCACTTTTTGTTGCC 60.179 50.0 0.00 0.00 36.60 4.52 F
3948 10488 0.257039 TGTAGTACTCCCTCCGTCCC 59.743 60.0 0.00 0.00 0.00 4.46 F
5096 11666 0.112995 TCCAGGCCATGAAAGCAGTT 59.887 50.0 5.01 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1190 5090 0.618458 TTCCTATCCAAAGCTGGCGT 59.382 50.000 0.00 0.00 43.17 5.68 R
2292 6209 0.605319 CAGTTGCGGTGCCTCCTTAA 60.605 55.000 0.00 0.00 0.00 1.85 R
2969 6887 1.067706 CAAGCAATGATTTGGCCACGA 60.068 47.619 3.88 0.00 33.22 4.35 R
4379 10936 0.028505 GGCGCACATGCTAGATTGTG 59.971 55.000 10.83 16.85 44.75 3.33 R
5344 11925 1.179174 TCGCAGGGATACGATGGAGG 61.179 60.000 0.00 0.00 32.45 4.30 R
6363 13046 0.116342 TAAGTGACTCTGCTCCCCCA 59.884 55.000 0.00 0.00 0.00 4.96 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
85 86 5.223225 GCAGAGAGCATTTTTGGTAGTAC 57.777 43.478 0.00 0.00 44.79 2.73
122 123 3.712091 ATCTTTTAGGAGTAGGCGACG 57.288 47.619 0.00 0.00 0.00 5.12
130 131 0.029567 GAGTAGGCGACGATGACCTG 59.970 60.000 0.00 0.00 34.92 4.00
140 141 3.555518 GACGATGACCTGTTGAAAAAGC 58.444 45.455 0.00 0.00 0.00 3.51
143 144 0.383949 TGACCTGTTGAAAAAGCGGC 59.616 50.000 0.00 0.00 0.00 6.53
144 145 0.383949 GACCTGTTGAAAAAGCGGCA 59.616 50.000 1.45 0.00 0.00 5.69
224 3868 1.518572 ATCGTTCGACCACCGCATC 60.519 57.895 0.00 0.00 38.37 3.91
225 3869 1.945354 ATCGTTCGACCACCGCATCT 61.945 55.000 0.00 0.00 38.37 2.90
228 3872 0.165944 GTTCGACCACCGCATCTTTG 59.834 55.000 0.00 0.00 38.37 2.77
229 3873 1.573829 TTCGACCACCGCATCTTTGC 61.574 55.000 0.00 0.00 45.78 3.68
246 3890 3.351604 GCGAACAGCGAACTCAAAG 57.648 52.632 0.00 0.00 44.57 2.77
258 3918 7.174253 ACAGCGAACTCAAAGGAAAATGTAATA 59.826 33.333 0.00 0.00 0.00 0.98
284 3944 2.101582 CACCCTCCTATTCTTGAGTCCG 59.898 54.545 0.00 0.00 0.00 4.79
322 3982 2.959507 AAAAACAGCCACACAGGAAC 57.040 45.000 0.00 0.00 41.22 3.62
334 3995 5.280945 CCACACAGGAACACAGTATTTTTG 58.719 41.667 0.00 0.00 41.22 2.44
335 3996 5.067153 CCACACAGGAACACAGTATTTTTGA 59.933 40.000 0.00 0.00 41.22 2.69
336 3997 6.405286 CCACACAGGAACACAGTATTTTTGAA 60.405 38.462 0.00 0.00 41.22 2.69
338 3999 6.183360 ACACAGGAACACAGTATTTTTGAAGG 60.183 38.462 0.00 0.00 0.00 3.46
341 4002 5.770162 AGGAACACAGTATTTTTGAAGGAGG 59.230 40.000 0.00 0.00 0.00 4.30
342 4003 5.768164 GGAACACAGTATTTTTGAAGGAGGA 59.232 40.000 0.00 0.00 0.00 3.71
396 4062 0.176219 CCTGTCACGGGGCGTATTTA 59.824 55.000 0.00 0.00 38.32 1.40
419 4085 1.213296 ATTCGGTATTCCTGCAGGGT 58.787 50.000 32.23 22.53 36.25 4.34
438 4104 0.249531 TCTGACACGCAAAAGCGGTA 60.250 50.000 14.62 0.00 37.53 4.02
439 4105 0.110823 CTGACACGCAAAAGCGGTAC 60.111 55.000 14.62 5.37 37.53 3.34
440 4106 1.205820 GACACGCAAAAGCGGTACC 59.794 57.895 14.62 0.16 37.53 3.34
441 4107 2.172419 CACGCAAAAGCGGTACCG 59.828 61.111 30.06 30.06 43.09 4.02
442 4108 2.280321 ACGCAAAAGCGGTACCGT 60.280 55.556 33.34 18.51 42.09 4.83
504 4170 2.837291 CTGCCCCTCCTCTCTCCG 60.837 72.222 0.00 0.00 0.00 4.63
577 4251 4.214327 CCTCCCTCTTCTCGCCGC 62.214 72.222 0.00 0.00 0.00 6.53
615 4289 3.674050 GAGGTACGCTCCCTCCCCA 62.674 68.421 4.66 0.00 42.29 4.96
624 4298 2.364317 CCCTCCCCAGCTCTCGAA 60.364 66.667 0.00 0.00 0.00 3.71
627 4301 1.684049 CTCCCCAGCTCTCGAACCT 60.684 63.158 0.00 0.00 0.00 3.50
628 4302 1.229209 TCCCCAGCTCTCGAACCTT 60.229 57.895 0.00 0.00 0.00 3.50
633 4307 0.318441 CAGCTCTCGAACCTTCCACA 59.682 55.000 0.00 0.00 0.00 4.17
637 4311 0.471211 TCTCGAACCTTCCACACCCT 60.471 55.000 0.00 0.00 0.00 4.34
645 4319 4.567597 TCCACACCCTGGTCCCGT 62.568 66.667 0.00 0.00 41.52 5.28
787 4684 1.072965 CCAATGCCTAGATCTGGGTCC 59.927 57.143 24.55 10.87 33.26 4.46
833 4730 1.154225 GGTTGTCGCGCCTGAATTG 60.154 57.895 0.00 0.00 0.00 2.32
839 4736 2.751436 GCGCCTGAATTGGGAGCA 60.751 61.111 14.70 0.00 46.34 4.26
872 4769 1.229428 GCAGACAGCTTGCTGTGTAA 58.771 50.000 29.60 0.00 41.15 2.41
873 4770 1.808945 GCAGACAGCTTGCTGTGTAAT 59.191 47.619 29.60 12.01 41.15 1.89
924 4821 1.646540 CGCGTTGTTTGGAGAAGCA 59.353 52.632 0.00 0.00 0.00 3.91
932 4832 1.019278 TTTGGAGAAGCACGGATCGC 61.019 55.000 0.00 0.00 0.00 4.58
938 4838 3.876300 AGCACGGATCGCTTTGTC 58.124 55.556 0.00 0.00 35.82 3.18
941 4841 1.421485 CACGGATCGCTTTGTCTGC 59.579 57.895 0.00 0.00 0.00 4.26
1103 5003 6.812160 CGTTTAGTGTCTCCTTATGCTTTAGT 59.188 38.462 0.00 0.00 0.00 2.24
1125 5025 1.228124 GTGTGCCCAGCAGTGGTTA 60.228 57.895 0.00 0.00 43.23 2.85
1190 5090 0.587768 CGTCAGCACTTGCATTGTCA 59.412 50.000 3.62 0.00 45.16 3.58
1228 5133 5.426504 AGGAAGTTTGAGATGCTGACTATG 58.573 41.667 0.00 0.00 0.00 2.23
1430 5336 3.947196 CAGGTCTTGCACTATGCCAATTA 59.053 43.478 0.00 0.00 44.23 1.40
1437 5343 8.405531 GTCTTGCACTATGCCAATTATTTTAGA 58.594 33.333 0.00 0.00 44.23 2.10
1441 5347 9.573166 TGCACTATGCCAATTATTTTAGACTAT 57.427 29.630 0.00 0.00 44.23 2.12
1477 5386 8.472007 TCTTCTAATGTTAGCCTTTTTGGAAA 57.528 30.769 0.00 0.00 38.35 3.13
1485 5394 7.334858 TGTTAGCCTTTTTGGAAACTTCATTT 58.665 30.769 0.00 0.00 38.35 2.32
1537 5446 3.822594 TCATTGTTGTCAACGGCATAC 57.177 42.857 11.03 0.00 36.33 2.39
1538 5447 3.407698 TCATTGTTGTCAACGGCATACT 58.592 40.909 11.03 0.00 36.33 2.12
1559 5468 4.991056 ACTGTCAAAGTGCACATACTAGTG 59.009 41.667 21.04 1.68 37.88 2.74
1617 5526 4.444536 ACAAAGACGGTGCTTACTAAACA 58.555 39.130 0.00 0.00 0.00 2.83
1697 5606 4.517453 TGGACAAAGTAAAGGTGTGTATGC 59.483 41.667 0.00 0.00 0.00 3.14
1710 5619 7.759489 AGGTGTGTATGCTTTTCTAATTTGA 57.241 32.000 0.00 0.00 0.00 2.69
1711 5620 8.177119 AGGTGTGTATGCTTTTCTAATTTGAA 57.823 30.769 0.00 0.00 0.00 2.69
1762 5671 3.071167 ACCGGATTATTCTAGCAGTTCCC 59.929 47.826 9.46 0.00 0.00 3.97
1851 5760 0.257039 GATTGGGAGATGGCACCACT 59.743 55.000 0.00 0.00 33.20 4.00
1917 5828 9.937175 GTTGTGCAGGTTAATTAATATTCTCTC 57.063 33.333 0.31 0.00 0.00 3.20
1965 5876 9.784531 AATGTTCAATCTAGTCTCTTTCTGAAA 57.215 29.630 2.44 2.44 0.00 2.69
2047 5958 5.285607 CGAGTAAACTTTAGACTGCCGTTAG 59.714 44.000 0.00 0.00 0.00 2.34
2072 5987 6.238484 GCTATGTTTATCTGAACGGCTTGATT 60.238 38.462 0.00 0.00 32.18 2.57
2073 5988 5.295431 TGTTTATCTGAACGGCTTGATTG 57.705 39.130 0.00 0.00 32.18 2.67
2074 5989 5.000591 TGTTTATCTGAACGGCTTGATTGA 58.999 37.500 0.00 0.00 32.18 2.57
2075 5990 5.647658 TGTTTATCTGAACGGCTTGATTGAT 59.352 36.000 0.00 0.00 32.18 2.57
2088 6003 6.073548 CGGCTTGATTGATTATACAGGTCTTC 60.074 42.308 0.00 0.00 0.00 2.87
2164 6079 4.895297 AGGTAAATGCCCATTATCCACAAG 59.105 41.667 13.10 0.00 0.00 3.16
2228 6145 1.535462 CTTTCGGTTGGCCACTGTTAG 59.465 52.381 3.88 4.69 32.85 2.34
2229 6146 0.470766 TTCGGTTGGCCACTGTTAGT 59.529 50.000 3.88 0.00 32.85 2.24
2230 6147 1.340088 TCGGTTGGCCACTGTTAGTA 58.660 50.000 3.88 0.00 32.85 1.82
2268 6185 7.949690 TGATGAGGACATTCATTCTTGAAAT 57.050 32.000 0.00 0.00 44.70 2.17
2271 6188 7.528996 TGAGGACATTCATTCTTGAAATTGT 57.471 32.000 0.00 0.00 44.70 2.71
2303 6220 5.125417 TGCTTATTGTTGATTAAGGAGGCAC 59.875 40.000 0.00 0.00 0.00 5.01
2305 6222 2.107950 TGTTGATTAAGGAGGCACCG 57.892 50.000 0.00 0.00 44.74 4.94
2316 6233 1.077501 AGGCACCGCAACTGCATAT 60.078 52.632 2.12 0.00 42.21 1.78
2325 6242 2.223112 CGCAACTGCATATCACTGGAAC 60.223 50.000 2.12 0.00 42.21 3.62
2326 6243 3.012518 GCAACTGCATATCACTGGAACT 58.987 45.455 0.00 0.00 41.59 3.01
2328 6245 4.256110 CAACTGCATATCACTGGAACTGA 58.744 43.478 0.00 0.00 0.00 3.41
2334 6251 6.413892 TGCATATCACTGGAACTGAATAACA 58.586 36.000 0.00 0.00 0.00 2.41
2339 6256 5.491070 TCACTGGAACTGAATAACATGGAG 58.509 41.667 0.00 0.00 0.00 3.86
2407 6324 8.999431 TGTCTTCCTTCTTGTTTGTATATGAAC 58.001 33.333 0.00 0.00 0.00 3.18
2433 6350 0.179076 AGCTGCCACTTTTTGTTGCC 60.179 50.000 0.00 0.00 36.60 4.52
2482 6399 2.368875 GGTCCTGAAAACTCCTGTCTCA 59.631 50.000 0.00 0.00 0.00 3.27
2500 6417 2.279741 TCACTTGATATGCTTGGACGC 58.720 47.619 0.00 0.00 0.00 5.19
2592 6509 2.480419 CCGGTAAGTGCTTTCTCAGTTG 59.520 50.000 0.00 0.00 32.39 3.16
2615 6532 5.938125 TGAAGGACACTGTTATTTAAGAGCC 59.062 40.000 0.00 0.00 30.40 4.70
2637 6554 6.319658 AGCCTCATGGTTAATTGTATGTTCAG 59.680 38.462 0.00 0.00 35.27 3.02
2639 6556 7.282224 GCCTCATGGTTAATTGTATGTTCAGTA 59.718 37.037 0.00 0.00 35.27 2.74
2784 6702 3.626670 CAGAGGAGATGATTCAAACAGGC 59.373 47.826 0.00 0.00 0.00 4.85
2969 6887 8.010733 TCTTTGAAAGAGACCATTTTGTCAAT 57.989 30.769 3.02 0.00 37.73 2.57
3017 6935 9.676861 TGATTGATCTGATTTCTTTGATGTACT 57.323 29.630 0.00 0.00 0.00 2.73
3100 7018 1.000274 ACAGCCCAATTCTTCAAACGC 60.000 47.619 0.00 0.00 0.00 4.84
3323 7253 2.547211 CACTCTGCTCCTGTTTGTCTTG 59.453 50.000 0.00 0.00 0.00 3.02
3512 7442 6.421485 ACTAGAGCATGATTCCATTGAAGTT 58.579 36.000 0.00 0.00 33.05 2.66
3582 7512 4.037446 TGTTTTGCCAGTGACCTGAATAAC 59.963 41.667 0.00 0.00 41.50 1.89
3633 7563 9.855021 GATAAAATTGTATAACCTTTGCACACT 57.145 29.630 0.00 0.00 0.00 3.55
3644 7577 4.832266 ACCTTTGCACACTAAAATCCATCA 59.168 37.500 0.00 0.00 0.00 3.07
3668 7601 9.638239 TCAATCTAATTGCAAAAATTACTGTCC 57.362 29.630 1.71 0.00 40.05 4.02
3746 7681 1.798813 GTTTGGTCGTGATCTGGTGTC 59.201 52.381 0.00 0.00 0.00 3.67
3747 7682 1.044611 TTGGTCGTGATCTGGTGTCA 58.955 50.000 0.00 0.00 0.00 3.58
3752 7687 3.502211 GGTCGTGATCTGGTGTCAAAATT 59.498 43.478 0.00 0.00 0.00 1.82
3758 7693 7.390440 TCGTGATCTGGTGTCAAAATTATCTTT 59.610 33.333 0.00 0.00 0.00 2.52
3890 10430 8.311836 TGTAGTTTTCTCTATCCAGTAAGTTGG 58.688 37.037 0.00 0.00 39.70 3.77
3932 10472 9.850628 GTAGTATTGCATTTCGGAGTATATGTA 57.149 33.333 0.00 0.00 0.00 2.29
3933 10473 8.988064 AGTATTGCATTTCGGAGTATATGTAG 57.012 34.615 0.00 0.00 0.00 2.74
3934 10474 8.585881 AGTATTGCATTTCGGAGTATATGTAGT 58.414 33.333 0.00 0.00 0.00 2.73
3935 10475 9.850628 GTATTGCATTTCGGAGTATATGTAGTA 57.149 33.333 0.00 0.00 0.00 1.82
3936 10476 8.758633 ATTGCATTTCGGAGTATATGTAGTAC 57.241 34.615 0.00 0.00 0.00 2.73
3937 10477 7.520451 TGCATTTCGGAGTATATGTAGTACT 57.480 36.000 0.00 0.00 35.20 2.73
3938 10478 7.591165 TGCATTTCGGAGTATATGTAGTACTC 58.409 38.462 0.00 5.04 44.60 2.59
3945 10485 5.803552 GAGTATATGTAGTACTCCCTCCGT 58.196 45.833 0.00 0.00 41.27 4.69
3946 10486 5.803552 AGTATATGTAGTACTCCCTCCGTC 58.196 45.833 0.00 0.00 0.00 4.79
3947 10487 2.361643 ATGTAGTACTCCCTCCGTCC 57.638 55.000 0.00 0.00 0.00 4.79
3948 10488 0.257039 TGTAGTACTCCCTCCGTCCC 59.743 60.000 0.00 0.00 0.00 4.46
3949 10489 0.257039 GTAGTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.00 0.00 4.37
3950 10490 1.133544 GTAGTACTCCCTCCGTCCCAT 60.134 57.143 0.00 0.00 0.00 4.00
3951 10491 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3952 10492 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3953 10493 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3954 10494 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
3955 10495 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3956 10496 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3957 10497 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3958 10498 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3959 10499 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3960 10500 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
3961 10501 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
3962 10502 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
3963 10503 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
3964 10504 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
3965 10505 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
3966 10506 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
3967 10507 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
3968 10508 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
3969 10509 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
3970 10510 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
3971 10511 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
3972 10512 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
3979 10519 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
3980 10520 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
3981 10521 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
4012 10552 7.989416 AAACGTTCTTATATTTTGGGACAGA 57.011 32.000 0.00 0.00 42.39 3.41
4013 10553 7.611213 AACGTTCTTATATTTTGGGACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
4014 10554 6.113411 ACGTTCTTATATTTTGGGACAGAGG 58.887 40.000 0.00 0.00 42.39 3.69
4015 10555 5.527582 CGTTCTTATATTTTGGGACAGAGGG 59.472 44.000 0.00 0.00 42.39 4.30
4193 10733 2.395360 GCGTGCTGGGCGTATTGAA 61.395 57.895 0.00 0.00 0.00 2.69
4254 10794 6.702329 ACTATGCCTAATGATGGTAAGTAGC 58.298 40.000 0.00 0.00 0.00 3.58
4289 10835 7.091443 GCTCTGTATTTCTTATATAGCACCGT 58.909 38.462 0.00 0.00 0.00 4.83
4300 10846 9.419297 TCTTATATAGCACCGTCAATTATGTTC 57.581 33.333 0.00 0.00 0.00 3.18
4302 10848 9.772973 TTATATAGCACCGTCAATTATGTTCTT 57.227 29.630 0.00 0.00 0.00 2.52
4327 10873 5.601662 ACATGCTAATATACTTGACGTGCT 58.398 37.500 0.00 0.00 0.00 4.40
4346 10892 9.140286 GACGTGCTATAGATTAAAATCAGCATA 57.860 33.333 15.21 5.87 41.19 3.14
4379 10936 0.676184 TGCTGAGTCCTGAGTGTGAC 59.324 55.000 0.00 0.00 0.00 3.67
4408 10965 0.812811 CATGTGCGCCACTCTAGCAT 60.813 55.000 4.18 0.00 43.17 3.79
4426 10988 7.711846 TCTAGCATGAGTATCTCTCTTGTTTC 58.288 38.462 0.00 0.00 44.80 2.78
4428 10990 5.105554 AGCATGAGTATCTCTCTTGTTTCGT 60.106 40.000 0.00 0.00 44.80 3.85
4429 10991 5.231147 GCATGAGTATCTCTCTTGTTTCGTC 59.769 44.000 0.00 0.00 44.80 4.20
4433 10995 2.701073 TCTCTCTTGTTTCGTCGACC 57.299 50.000 10.58 0.00 0.00 4.79
4521 11083 8.530311 ACCATTTTACATAAGAATGCAATGACA 58.470 29.630 2.39 0.00 36.50 3.58
4639 11201 5.013183 AGCTCCATAACAGACAGGTACTTTT 59.987 40.000 0.00 0.00 34.60 2.27
4640 11202 6.212791 AGCTCCATAACAGACAGGTACTTTTA 59.787 38.462 0.00 0.00 34.60 1.52
4670 11232 5.072741 TCTTTTACTTCTGGAATGCAGCTT 58.927 37.500 0.00 0.00 0.00 3.74
4826 11394 3.131396 CCGCTTACCAATCGAGCTTTAT 58.869 45.455 0.00 0.00 34.33 1.40
4835 11403 6.177610 ACCAATCGAGCTTTATAAAACTGGA 58.822 36.000 13.52 13.52 0.00 3.86
4853 11421 9.533831 AAAACTGGATCCATTACTTTAAGATGT 57.466 29.630 16.63 1.41 0.00 3.06
4890 11458 9.449719 TCATCCTGAAATTTAGTTCTAAGAACC 57.550 33.333 0.00 0.00 0.00 3.62
4968 11537 5.185249 TCAGATGTGTCTAACCAGGTACTTC 59.815 44.000 0.00 0.00 30.42 3.01
4996 11565 6.432783 TGAACACTGTATATTTGGTTCCCTTG 59.567 38.462 0.00 0.00 35.09 3.61
5026 11596 7.401860 CAATTGTAACATACAGAGGAATCACG 58.598 38.462 0.00 0.00 40.24 4.35
5030 11600 4.937201 ACATACAGAGGAATCACGCATA 57.063 40.909 0.00 0.00 0.00 3.14
5063 11633 2.951642 TCAGCTTTATGCCAACTATGCC 59.048 45.455 0.00 0.00 44.23 4.40
5096 11666 0.112995 TCCAGGCCATGAAAGCAGTT 59.887 50.000 5.01 0.00 0.00 3.16
5132 11702 4.887071 GCTCTCTCTTCTGAAGATCTGGTA 59.113 45.833 19.61 3.46 36.82 3.25
5133 11703 5.536161 GCTCTCTCTTCTGAAGATCTGGTAT 59.464 44.000 19.61 0.00 36.82 2.73
5135 11705 5.301551 TCTCTCTTCTGAAGATCTGGTATGC 59.698 44.000 19.61 0.00 36.82 3.14
5136 11706 5.207354 TCTCTTCTGAAGATCTGGTATGCT 58.793 41.667 19.61 0.00 36.82 3.79
5145 11715 4.158786 AGATCTGGTATGCTACTGCTCAT 58.841 43.478 0.00 0.00 40.48 2.90
5148 11718 5.869649 TCTGGTATGCTACTGCTCATTAA 57.130 39.130 0.00 0.00 40.48 1.40
5150 11720 4.368315 TGGTATGCTACTGCTCATTAACG 58.632 43.478 0.00 0.00 40.48 3.18
5157 11727 6.338146 TGCTACTGCTCATTAACGAACTAAT 58.662 36.000 0.00 0.00 40.48 1.73
5158 11728 6.255670 TGCTACTGCTCATTAACGAACTAATG 59.744 38.462 0.00 0.00 40.48 1.90
5159 11729 5.470845 ACTGCTCATTAACGAACTAATGC 57.529 39.130 0.00 0.00 38.59 3.56
5161 11731 5.586243 ACTGCTCATTAACGAACTAATGCAT 59.414 36.000 0.00 0.00 38.59 3.96
5162 11732 5.809464 TGCTCATTAACGAACTAATGCATG 58.191 37.500 0.00 0.00 38.59 4.06
5163 11733 5.207768 GCTCATTAACGAACTAATGCATGG 58.792 41.667 0.00 0.00 38.59 3.66
5165 11735 6.358118 TCATTAACGAACTAATGCATGGAC 57.642 37.500 0.00 0.00 38.59 4.02
5166 11736 5.877564 TCATTAACGAACTAATGCATGGACA 59.122 36.000 0.00 0.00 38.59 4.02
5167 11737 6.542005 TCATTAACGAACTAATGCATGGACAT 59.458 34.615 0.00 0.00 38.59 3.06
5168 11738 7.713073 TCATTAACGAACTAATGCATGGACATA 59.287 33.333 0.00 0.00 38.59 2.29
5169 11739 5.734855 AACGAACTAATGCATGGACATAC 57.265 39.130 0.00 0.00 0.00 2.39
5170 11740 4.765273 ACGAACTAATGCATGGACATACA 58.235 39.130 0.00 0.00 0.00 2.29
5173 11754 5.050769 CGAACTAATGCATGGACATACAGTC 60.051 44.000 0.00 0.00 46.83 3.51
5177 11758 6.886459 ACTAATGCATGGACATACAGTCTTTT 59.114 34.615 0.00 0.00 46.72 2.27
5178 11759 8.046708 ACTAATGCATGGACATACAGTCTTTTA 58.953 33.333 0.00 0.00 46.72 1.52
5182 11763 7.592938 TGCATGGACATACAGTCTTTTAAAAG 58.407 34.615 19.91 19.91 46.72 2.27
5183 11764 7.230510 TGCATGGACATACAGTCTTTTAAAAGT 59.769 33.333 23.75 10.89 46.72 2.66
5184 11765 8.082242 GCATGGACATACAGTCTTTTAAAAGTT 58.918 33.333 23.75 13.04 46.72 2.66
5236 11817 5.819379 TGTGCAGCTTTATCTAGAATTCCTG 59.181 40.000 0.65 1.75 0.00 3.86
5275 11856 3.931907 TTTGTAGCACAGGGAGCATAT 57.068 42.857 0.00 0.00 0.00 1.78
5323 11904 2.025981 TGACCTAGCATGGACATTGCTT 60.026 45.455 3.24 0.00 39.79 3.91
5344 11925 1.299773 CATCTTCCCTCGCGAGCTC 60.300 63.158 30.49 2.73 0.00 4.09
5377 11958 0.674581 CTGCGAAGACCTTGGATGCA 60.675 55.000 0.00 0.00 0.00 3.96
5404 11990 1.600638 CAGAGATGCTGCCCACTGA 59.399 57.895 9.66 0.00 37.90 3.41
5405 11991 0.180642 CAGAGATGCTGCCCACTGAT 59.819 55.000 9.66 0.00 37.90 2.90
5406 11992 0.469070 AGAGATGCTGCCCACTGATC 59.531 55.000 0.00 0.00 0.00 2.92
5407 11993 0.469070 GAGATGCTGCCCACTGATCT 59.531 55.000 0.00 0.00 0.00 2.75
5408 11994 0.469070 AGATGCTGCCCACTGATCTC 59.531 55.000 0.00 0.00 0.00 2.75
5477 12063 2.575532 TGAGCAGTTCAAACTTCTGGG 58.424 47.619 0.00 0.00 37.08 4.45
5657 12250 3.208747 TGGTTTCACTTCCTGGAACTC 57.791 47.619 4.68 0.00 38.35 3.01
5761 12354 2.048222 GCTGGACTGCACGTGCTA 60.048 61.111 37.59 23.81 42.66 3.49
5777 12370 2.921754 GTGCTAGTGTACATCGTCAACC 59.078 50.000 0.00 0.00 0.00 3.77
5895 12526 1.915614 CTGCCTTGACCATGTCACGC 61.916 60.000 0.00 2.91 42.60 5.34
5896 12527 2.690778 GCCTTGACCATGTCACGCC 61.691 63.158 0.00 0.00 42.60 5.68
5898 12529 1.021390 CCTTGACCATGTCACGCCTC 61.021 60.000 0.00 0.00 42.60 4.70
5899 12530 0.036952 CTTGACCATGTCACGCCTCT 60.037 55.000 0.00 0.00 42.60 3.69
5900 12531 0.396435 TTGACCATGTCACGCCTCTT 59.604 50.000 0.00 0.00 42.60 2.85
5914 12576 5.831525 TCACGCCTCTTATAGAAATGTAGGA 59.168 40.000 0.00 0.00 0.00 2.94
5918 12580 8.867097 ACGCCTCTTATAGAAATGTAGGAAATA 58.133 33.333 0.00 0.00 0.00 1.40
5936 12598 4.939052 AATAGCTGCGTACAATAGACCT 57.061 40.909 0.00 0.00 0.00 3.85
6149 12812 4.344448 CGAACTAAGCGTAGAGAAAGAGG 58.656 47.826 13.91 0.00 0.00 3.69
6154 12817 3.878160 AGCGTAGAGAAAGAGGAAAGG 57.122 47.619 0.00 0.00 0.00 3.11
6242 12925 5.996644 TGGTTTGGTACTGGGATATACTTG 58.003 41.667 0.00 0.00 0.00 3.16
6272 12955 8.232913 TCATTAGTGCCTTTCTGTTAACTTTT 57.767 30.769 7.22 0.00 0.00 2.27
6341 13024 8.240682 CCGAGTGTTATATGTGGAATTTTGAAA 58.759 33.333 0.00 0.00 0.00 2.69
6361 13044 9.868277 TTTGAAATAGAAAGAAAATGTGTGTGT 57.132 25.926 0.00 0.00 0.00 3.72
6362 13045 8.854979 TGAAATAGAAAGAAAATGTGTGTGTG 57.145 30.769 0.00 0.00 0.00 3.82
6363 13046 8.465999 TGAAATAGAAAGAAAATGTGTGTGTGT 58.534 29.630 0.00 0.00 0.00 3.72
6398 13081 4.682787 TCACTTATGACTGCCTAATGACG 58.317 43.478 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 8.591114 AAGATACACTACCAATGTACTGTACT 57.409 34.615 17.98 1.18 35.43 2.73
82 83 9.649167 AAAAGATACACTACCAATGTACTGTAC 57.351 33.333 10.98 10.98 35.43 2.90
84 85 9.871238 CTAAAAGATACACTACCAATGTACTGT 57.129 33.333 0.00 0.00 35.43 3.55
85 86 9.314321 CCTAAAAGATACACTACCAATGTACTG 57.686 37.037 0.00 0.00 35.43 2.74
100 101 4.274459 TCGTCGCCTACTCCTAAAAGATAC 59.726 45.833 0.00 0.00 0.00 2.24
102 103 3.285484 TCGTCGCCTACTCCTAAAAGAT 58.715 45.455 0.00 0.00 0.00 2.40
105 106 3.018856 TCATCGTCGCCTACTCCTAAAA 58.981 45.455 0.00 0.00 0.00 1.52
122 123 2.922335 GCCGCTTTTTCAACAGGTCATC 60.922 50.000 0.00 0.00 0.00 2.92
130 131 1.548132 CCGCTTGCCGCTTTTTCAAC 61.548 55.000 0.00 0.00 36.13 3.18
143 144 1.283793 CACTTGGTTCAGCCGCTTG 59.716 57.895 0.00 0.00 41.21 4.01
144 145 0.751643 AACACTTGGTTCAGCCGCTT 60.752 50.000 0.00 0.00 41.21 4.68
179 203 9.461312 GGGAATTGAACCTGTGCATATATATAA 57.539 33.333 0.00 0.00 0.00 0.98
183 207 5.704354 TGGGAATTGAACCTGTGCATATAT 58.296 37.500 0.00 0.00 0.00 0.86
194 3838 2.095372 GTCGAACGATGGGAATTGAACC 59.905 50.000 0.00 0.00 0.00 3.62
198 3842 1.396996 GTGGTCGAACGATGGGAATTG 59.603 52.381 0.00 0.00 0.00 2.32
224 3868 0.581529 TGAGTTCGCTGTTCGCAAAG 59.418 50.000 0.00 0.00 39.08 2.77
225 3869 1.010580 TTGAGTTCGCTGTTCGCAAA 58.989 45.000 0.00 0.00 39.08 3.68
228 3872 0.110644 CCTTTGAGTTCGCTGTTCGC 60.111 55.000 0.00 0.00 38.27 4.70
229 3873 1.497991 TCCTTTGAGTTCGCTGTTCG 58.502 50.000 0.00 0.00 40.15 3.95
230 3874 3.963383 TTTCCTTTGAGTTCGCTGTTC 57.037 42.857 0.00 0.00 0.00 3.18
231 3875 4.097892 ACATTTTCCTTTGAGTTCGCTGTT 59.902 37.500 0.00 0.00 0.00 3.16
232 3876 3.632145 ACATTTTCCTTTGAGTTCGCTGT 59.368 39.130 0.00 0.00 0.00 4.40
233 3877 4.228912 ACATTTTCCTTTGAGTTCGCTG 57.771 40.909 0.00 0.00 0.00 5.18
234 3878 6.575162 ATTACATTTTCCTTTGAGTTCGCT 57.425 33.333 0.00 0.00 0.00 4.93
246 3890 7.290813 AGGAGGGTGAGAATATTACATTTTCC 58.709 38.462 0.00 2.01 0.00 3.13
258 3918 5.284582 ACTCAAGAATAGGAGGGTGAGAAT 58.715 41.667 5.54 0.00 36.75 2.40
265 3925 1.689273 CCGGACTCAAGAATAGGAGGG 59.311 57.143 0.00 0.00 35.45 4.30
309 3969 1.128200 TACTGTGTTCCTGTGTGGCT 58.872 50.000 0.00 0.00 35.26 4.75
334 3995 6.017026 CCGCCTCTAAAATTTTATCCTCCTTC 60.017 42.308 10.97 0.00 0.00 3.46
335 3996 5.828328 CCGCCTCTAAAATTTTATCCTCCTT 59.172 40.000 10.97 0.00 0.00 3.36
336 3997 5.377478 CCGCCTCTAAAATTTTATCCTCCT 58.623 41.667 10.97 0.00 0.00 3.69
338 3999 4.023107 GCCCGCCTCTAAAATTTTATCCTC 60.023 45.833 10.97 1.83 0.00 3.71
341 4002 4.578928 TCAGCCCGCCTCTAAAATTTTATC 59.421 41.667 10.97 1.53 0.00 1.75
342 4003 4.532834 TCAGCCCGCCTCTAAAATTTTAT 58.467 39.130 10.97 0.00 0.00 1.40
355 4016 1.153086 AGACATGAATCAGCCCGCC 60.153 57.895 0.00 0.00 0.00 6.13
396 4062 3.545703 CCTGCAGGAATACCGAATTTCT 58.454 45.455 29.88 0.00 41.83 2.52
438 4104 0.690077 GTTGAGGGAGGGGATACGGT 60.690 60.000 0.00 0.00 37.60 4.83
439 4105 1.745320 CGTTGAGGGAGGGGATACGG 61.745 65.000 0.00 0.00 37.60 4.02
440 4106 0.754217 TCGTTGAGGGAGGGGATACG 60.754 60.000 0.00 0.00 37.60 3.06
441 4107 1.718280 ATCGTTGAGGGAGGGGATAC 58.282 55.000 0.00 0.00 0.00 2.24
442 4108 2.047061 CAATCGTTGAGGGAGGGGATA 58.953 52.381 0.00 0.00 0.00 2.59
504 4170 0.107752 CAGCTGGGAGAAGAAGAGGC 60.108 60.000 5.57 0.00 0.00 4.70
577 4251 3.537874 GTCGGGATCGGTGGGAGG 61.538 72.222 0.00 0.00 36.95 4.30
615 4289 0.318762 GTGTGGAAGGTTCGAGAGCT 59.681 55.000 0.00 0.00 37.82 4.09
900 4797 3.943034 CCAAACAACGCGCGGACA 61.943 61.111 35.22 0.00 0.00 4.02
901 4798 3.573489 CTCCAAACAACGCGCGGAC 62.573 63.158 35.22 0.00 0.00 4.79
908 4805 0.041312 CCGTGCTTCTCCAAACAACG 60.041 55.000 0.00 0.00 0.00 4.10
909 4806 1.305201 TCCGTGCTTCTCCAAACAAC 58.695 50.000 0.00 0.00 0.00 3.32
924 4821 1.016130 CAGCAGACAAAGCGATCCGT 61.016 55.000 0.00 0.00 37.01 4.69
932 4832 3.181499 GCCATCAGAATCAGCAGACAAAG 60.181 47.826 0.00 0.00 0.00 2.77
938 4838 1.647629 GCGCCATCAGAATCAGCAG 59.352 57.895 0.00 0.00 0.00 4.24
941 4841 1.091771 AACCGCGCCATCAGAATCAG 61.092 55.000 0.00 0.00 0.00 2.90
1103 5003 1.674764 CCACTGCTGGGCACACAAAA 61.675 55.000 0.00 0.00 33.79 2.44
1125 5025 1.818959 AACAGGCAATGGCGCAACAT 61.819 50.000 10.83 0.46 42.47 2.71
1190 5090 0.618458 TTCCTATCCAAAGCTGGCGT 59.382 50.000 0.00 0.00 43.17 5.68
1441 5347 8.234546 GGCTAACATTAGAAGAAAAATGAACGA 58.765 33.333 2.75 0.00 36.73 3.85
1453 5359 8.360390 AGTTTCCAAAAAGGCTAACATTAGAAG 58.640 33.333 2.75 0.00 35.40 2.85
1465 5374 9.267084 TGTTATAAATGAAGTTTCCAAAAAGGC 57.733 29.630 0.00 0.00 37.29 4.35
1477 5386 9.423061 GAATGCACCTTTTGTTATAAATGAAGT 57.577 29.630 0.00 0.00 0.00 3.01
1485 5394 4.364415 GCGGAATGCACCTTTTGTTATA 57.636 40.909 0.00 0.00 45.45 0.98
1537 5446 5.521516 CACTAGTATGTGCACTTTGACAG 57.478 43.478 19.41 10.38 0.00 3.51
1583 5492 1.137513 GTCTTTGTTCGGTCGTCTGG 58.862 55.000 0.00 0.00 0.00 3.86
1617 5526 7.620880 TGTCCTGTACTCTGCATAAGTAAATT 58.379 34.615 9.89 0.00 31.32 1.82
1710 5619 6.252599 TGTGGGAATATGCTAAGAGATGTT 57.747 37.500 0.00 0.00 0.00 2.71
1711 5620 5.894298 TGTGGGAATATGCTAAGAGATGT 57.106 39.130 0.00 0.00 0.00 3.06
1794 5703 4.044065 TCCTGGTATTTTGGGCCCTATATG 59.956 45.833 25.70 11.45 0.00 1.78
1795 5704 4.256231 TCCTGGTATTTTGGGCCCTATAT 58.744 43.478 25.70 18.51 0.00 0.86
1851 5760 1.300620 CAGAACTTGACCACGCCGA 60.301 57.895 0.00 0.00 0.00 5.54
2047 5958 4.570772 TCAAGCCGTTCAGATAAACATAGC 59.429 41.667 0.00 0.00 0.00 2.97
2072 5987 4.404394 TGCCTTCGAAGACCTGTATAATCA 59.596 41.667 26.61 0.00 34.32 2.57
2073 5988 4.745620 GTGCCTTCGAAGACCTGTATAATC 59.254 45.833 26.61 0.00 34.32 1.75
2074 5989 4.406003 AGTGCCTTCGAAGACCTGTATAAT 59.594 41.667 26.61 0.00 34.32 1.28
2075 5990 3.767673 AGTGCCTTCGAAGACCTGTATAA 59.232 43.478 26.61 0.00 34.32 0.98
2088 6003 3.190874 GTCTATTCCTGAAGTGCCTTCG 58.809 50.000 9.47 5.60 42.78 3.79
2192 6109 4.283722 ACCGAAAGCTTCCTTTTAGAGAGA 59.716 41.667 0.00 0.00 41.22 3.10
2212 6129 2.396590 ATACTAACAGTGGCCAACCG 57.603 50.000 7.24 0.26 39.70 4.44
2228 6145 8.309656 TGTCCTCATCATCAGTTCATCATATAC 58.690 37.037 0.00 0.00 0.00 1.47
2229 6146 8.426569 TGTCCTCATCATCAGTTCATCATATA 57.573 34.615 0.00 0.00 0.00 0.86
2230 6147 7.312415 TGTCCTCATCATCAGTTCATCATAT 57.688 36.000 0.00 0.00 0.00 1.78
2292 6209 0.605319 CAGTTGCGGTGCCTCCTTAA 60.605 55.000 0.00 0.00 0.00 1.85
2303 6220 0.659427 CCAGTGATATGCAGTTGCGG 59.341 55.000 0.00 0.00 45.83 5.69
2305 6222 3.012518 AGTTCCAGTGATATGCAGTTGC 58.987 45.455 0.00 0.00 42.50 4.17
2316 6233 5.248248 TCTCCATGTTATTCAGTTCCAGTGA 59.752 40.000 0.00 0.00 0.00 3.41
2325 6242 3.889815 TGGGCTTCTCCATGTTATTCAG 58.110 45.455 0.00 0.00 36.21 3.02
2326 6243 4.524802 ATGGGCTTCTCCATGTTATTCA 57.475 40.909 0.00 0.00 45.13 2.57
2386 6303 8.946085 GTCATGTTCATATACAAACAAGAAGGA 58.054 33.333 7.97 0.82 38.74 3.36
2407 6324 2.798283 CAAAAAGTGGCAGCTTGTCATG 59.202 45.455 0.00 0.00 33.03 3.07
2433 6350 5.464722 CACAGAAGCAGCATACCATAAGTAG 59.535 44.000 0.00 0.00 33.42 2.57
2482 6399 2.401583 TGCGTCCAAGCATATCAAGT 57.598 45.000 0.00 0.00 42.92 3.16
2500 6417 4.684242 GGTTTTCCAGAGCCGTTAAAAATG 59.316 41.667 0.00 0.00 40.31 2.32
2592 6509 6.174049 AGGCTCTTAAATAACAGTGTCCTTC 58.826 40.000 0.00 0.00 0.00 3.46
2739 6657 2.938956 AGGTTCTCTCACTTGGGTTG 57.061 50.000 0.00 0.00 0.00 3.77
2964 6882 3.181397 CAATGATTTGGCCACGATTGAC 58.819 45.455 3.88 0.00 0.00 3.18
2969 6887 1.067706 CAAGCAATGATTTGGCCACGA 60.068 47.619 3.88 0.00 33.22 4.35
3017 6935 1.906574 GTCATCTTCACCACCACCCTA 59.093 52.381 0.00 0.00 0.00 3.53
3100 7018 6.529125 CCATTGAACCATTCTCTTCAAAATCG 59.471 38.462 0.00 0.00 39.28 3.34
3276 7206 8.900762 GTTAAATTATGTTTTGTTTGGCATTGC 58.099 29.630 0.00 0.00 0.00 3.56
3323 7253 2.325583 TCGTGGGATCATTTGCCTAC 57.674 50.000 0.00 0.00 36.61 3.18
3512 7442 8.109634 AGGAAGAGCTAACTGATTGGAAAATAA 58.890 33.333 0.00 0.00 0.00 1.40
3626 7556 7.936496 TTAGATTGATGGATTTTAGTGTGCA 57.064 32.000 0.00 0.00 0.00 4.57
3627 7557 9.241317 CAATTAGATTGATGGATTTTAGTGTGC 57.759 33.333 0.00 0.00 42.83 4.57
3628 7558 9.241317 GCAATTAGATTGATGGATTTTAGTGTG 57.759 33.333 4.92 0.00 42.83 3.82
3644 7577 8.519526 TCGGACAGTAATTTTTGCAATTAGATT 58.480 29.630 0.00 1.44 0.00 2.40
3772 7707 6.435591 TGGCAGTGGTGTGATGATAATAAAAA 59.564 34.615 0.00 0.00 0.00 1.94
3773 7708 5.948758 TGGCAGTGGTGTGATGATAATAAAA 59.051 36.000 0.00 0.00 0.00 1.52
3774 7709 5.504853 TGGCAGTGGTGTGATGATAATAAA 58.495 37.500 0.00 0.00 0.00 1.40
3775 7710 5.109500 TGGCAGTGGTGTGATGATAATAA 57.891 39.130 0.00 0.00 0.00 1.40
3776 7711 4.769345 TGGCAGTGGTGTGATGATAATA 57.231 40.909 0.00 0.00 0.00 0.98
3777 7712 3.650281 TGGCAGTGGTGTGATGATAAT 57.350 42.857 0.00 0.00 0.00 1.28
3778 7713 3.431673 TTGGCAGTGGTGTGATGATAA 57.568 42.857 0.00 0.00 0.00 1.75
3779 7714 3.081061 GTTTGGCAGTGGTGTGATGATA 58.919 45.455 0.00 0.00 0.00 2.15
3780 7715 1.888512 GTTTGGCAGTGGTGTGATGAT 59.111 47.619 0.00 0.00 0.00 2.45
3890 10430 6.183360 GCAATACTACCAAGGTGGAAATCTTC 60.183 42.308 9.75 0.00 40.96 2.87
3932 10472 1.229131 TATGGGACGGAGGGAGTACT 58.771 55.000 0.00 0.00 0.00 2.73
3933 10473 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
3934 10474 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
3935 10475 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
3936 10476 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
3937 10477 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
3938 10478 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
3939 10479 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
3940 10480 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
3941 10481 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
3942 10482 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
3943 10483 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
3944 10484 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
3945 10485 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
3946 10486 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
3952 10492 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
3953 10493 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
3954 10494 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
3955 10495 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
3956 10496 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
3957 10497 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
3958 10498 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
3986 10526 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
3987 10527 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
3988 10528 7.120726 CCTCTGTCCCAAAATATAAGAACGTTT 59.879 37.037 0.46 0.00 0.00 3.60
3989 10529 6.598064 CCTCTGTCCCAAAATATAAGAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
3990 10530 6.113411 CCTCTGTCCCAAAATATAAGAACGT 58.887 40.000 0.00 0.00 0.00 3.99
3991 10531 5.527582 CCCTCTGTCCCAAAATATAAGAACG 59.472 44.000 0.00 0.00 0.00 3.95
3992 10532 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
3993 10533 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
3994 10534 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
3995 10535 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
3996 10536 7.404980 AGTTACTCCCTCTGTCCCAAAATATAA 59.595 37.037 0.00 0.00 0.00 0.98
3997 10537 6.906901 AGTTACTCCCTCTGTCCCAAAATATA 59.093 38.462 0.00 0.00 0.00 0.86
3998 10538 5.731678 AGTTACTCCCTCTGTCCCAAAATAT 59.268 40.000 0.00 0.00 0.00 1.28
3999 10539 5.098663 AGTTACTCCCTCTGTCCCAAAATA 58.901 41.667 0.00 0.00 0.00 1.40
4000 10540 3.916989 AGTTACTCCCTCTGTCCCAAAAT 59.083 43.478 0.00 0.00 0.00 1.82
4001 10541 3.323775 AGTTACTCCCTCTGTCCCAAAA 58.676 45.455 0.00 0.00 0.00 2.44
4002 10542 2.986050 AGTTACTCCCTCTGTCCCAAA 58.014 47.619 0.00 0.00 0.00 3.28
4003 10543 2.715763 AGTTACTCCCTCTGTCCCAA 57.284 50.000 0.00 0.00 0.00 4.12
4004 10544 2.715763 AAGTTACTCCCTCTGTCCCA 57.284 50.000 0.00 0.00 0.00 4.37
4005 10545 5.429130 CATAAAAGTTACTCCCTCTGTCCC 58.571 45.833 0.00 0.00 0.00 4.46
4006 10546 4.876679 GCATAAAAGTTACTCCCTCTGTCC 59.123 45.833 0.00 0.00 0.00 4.02
4007 10547 5.735766 AGCATAAAAGTTACTCCCTCTGTC 58.264 41.667 0.00 0.00 0.00 3.51
4008 10548 5.248477 TGAGCATAAAAGTTACTCCCTCTGT 59.752 40.000 0.00 0.00 0.00 3.41
4009 10549 5.734720 TGAGCATAAAAGTTACTCCCTCTG 58.265 41.667 0.00 0.00 0.00 3.35
4010 10550 6.013293 AGTTGAGCATAAAAGTTACTCCCTCT 60.013 38.462 0.00 0.00 0.00 3.69
4011 10551 6.092807 CAGTTGAGCATAAAAGTTACTCCCTC 59.907 42.308 0.00 0.00 0.00 4.30
4012 10552 5.940470 CAGTTGAGCATAAAAGTTACTCCCT 59.060 40.000 0.00 0.00 0.00 4.20
4013 10553 5.705905 ACAGTTGAGCATAAAAGTTACTCCC 59.294 40.000 0.00 0.00 0.00 4.30
4014 10554 6.803154 ACAGTTGAGCATAAAAGTTACTCC 57.197 37.500 0.00 0.00 0.00 3.85
4193 10733 2.239907 GGTAATGGAGCCTGTTCTTCCT 59.760 50.000 0.00 0.00 0.00 3.36
4254 10794 3.062639 AGAAATACAGAGCACGCAATTCG 59.937 43.478 0.00 0.00 45.38 3.34
4300 10846 8.004344 GCACGTCAAGTATATTAGCATGTTAAG 58.996 37.037 8.07 0.00 0.00 1.85
4302 10848 7.207383 AGCACGTCAAGTATATTAGCATGTTA 58.793 34.615 0.00 0.00 0.00 2.41
4346 10892 4.217118 GGACTCAGCAAAATGACAGACAAT 59.783 41.667 0.00 0.00 0.00 2.71
4379 10936 0.028505 GGCGCACATGCTAGATTGTG 59.971 55.000 10.83 16.85 44.75 3.33
4400 10957 6.882610 ACAAGAGAGATACTCATGCTAGAG 57.117 41.667 0.00 4.71 44.90 2.43
4426 10988 0.163788 GCAGTTGATGTTGGTCGACG 59.836 55.000 9.92 0.00 37.54 5.12
4428 10990 1.960417 TTGCAGTTGATGTTGGTCGA 58.040 45.000 0.00 0.00 0.00 4.20
4429 10991 2.772568 TTTGCAGTTGATGTTGGTCG 57.227 45.000 0.00 0.00 0.00 4.79
4433 10995 6.389622 CAATCAGATTTGCAGTTGATGTTG 57.610 37.500 0.00 0.53 31.11 3.33
4521 11083 5.843019 TGGAGGGAAAAGAACACTCTATT 57.157 39.130 0.00 0.00 37.84 1.73
4524 11086 4.207955 GTTTGGAGGGAAAAGAACACTCT 58.792 43.478 0.00 0.00 37.84 3.24
4639 11201 8.349983 GCATTCCAGAAGTAAAAGAACAAGTTA 58.650 33.333 0.00 0.00 0.00 2.24
4640 11202 7.147915 TGCATTCCAGAAGTAAAAGAACAAGTT 60.148 33.333 0.00 0.00 0.00 2.66
4664 11226 7.315890 ACAGGTTCTAAATGATAAAAAGCTGC 58.684 34.615 10.89 0.00 42.77 5.25
4868 11436 7.386848 TGACGGTTCTTAGAACTAAATTTCAGG 59.613 37.037 22.26 4.62 0.00 3.86
4870 11438 8.665643 TTGACGGTTCTTAGAACTAAATTTCA 57.334 30.769 22.26 13.22 0.00 2.69
4890 11458 4.093998 AGCACTCTGCAAGAATTATTGACG 59.906 41.667 16.76 6.26 46.34 4.35
4934 11503 1.929836 GACACATCTGAATGGTCTCGC 59.070 52.381 0.00 0.00 37.19 5.03
4968 11537 6.852664 GGAACCAAATATACAGTGTTCAAGG 58.147 40.000 0.00 0.00 35.09 3.61
4996 11565 4.201950 CCTCTGTATGTTACAATTGGCTGC 60.202 45.833 10.83 0.00 38.38 5.25
5030 11600 4.320788 GCATAAAGCTGAACAGAAAGCAGT 60.321 41.667 5.97 0.00 42.06 4.40
5063 11633 1.753073 GCCTGGACATCCTTTCCAATG 59.247 52.381 0.00 0.00 42.76 2.82
5096 11666 3.195438 AGAGCCTCCTCTCCCACA 58.805 61.111 0.00 0.00 45.21 4.17
5132 11702 4.759782 AGTTCGTTAATGAGCAGTAGCAT 58.240 39.130 13.24 0.00 45.49 3.79
5133 11703 4.188247 AGTTCGTTAATGAGCAGTAGCA 57.812 40.909 13.24 0.00 45.49 3.49
5135 11705 6.255670 TGCATTAGTTCGTTAATGAGCAGTAG 59.744 38.462 13.24 2.96 41.44 2.57
5136 11706 6.103330 TGCATTAGTTCGTTAATGAGCAGTA 58.897 36.000 13.24 0.00 41.44 2.74
5145 11715 6.819146 TGTATGTCCATGCATTAGTTCGTTAA 59.181 34.615 0.00 0.00 0.00 2.01
5148 11718 4.765273 TGTATGTCCATGCATTAGTTCGT 58.235 39.130 0.00 0.00 0.00 3.85
5150 11720 6.051717 AGACTGTATGTCCATGCATTAGTTC 58.948 40.000 0.00 0.00 46.46 3.01
5157 11727 7.230510 ACTTTTAAAAGACTGTATGTCCATGCA 59.769 33.333 29.97 0.00 46.46 3.96
5158 11728 7.593825 ACTTTTAAAAGACTGTATGTCCATGC 58.406 34.615 29.97 0.00 46.46 4.06
5196 11777 5.242393 AGCTGCACAAGAGAAACAACAATAT 59.758 36.000 1.02 0.00 0.00 1.28
5208 11789 7.254727 GGAATTCTAGATAAAGCTGCACAAGAG 60.255 40.741 5.23 0.00 0.00 2.85
5209 11790 6.540189 GGAATTCTAGATAAAGCTGCACAAGA 59.460 38.462 5.23 0.00 0.00 3.02
5344 11925 1.179174 TCGCAGGGATACGATGGAGG 61.179 60.000 0.00 0.00 32.45 4.30
5404 11990 4.476113 TGGATCTCCCAACAAAGATGAGAT 59.524 41.667 0.00 0.00 43.29 2.75
5405 11991 3.845992 TGGATCTCCCAACAAAGATGAGA 59.154 43.478 0.00 0.00 43.29 3.27
5406 11992 4.226427 TGGATCTCCCAACAAAGATGAG 57.774 45.455 0.00 0.00 43.29 2.90
5657 12250 3.137533 GGCCTAGAATGCTCTTGCTAAG 58.862 50.000 0.00 0.00 40.48 2.18
5761 12354 2.750948 GTGTGGTTGACGATGTACACT 58.249 47.619 0.00 0.00 36.43 3.55
5777 12370 2.132762 GTTACAGACAGAACCCGTGTG 58.867 52.381 0.00 0.00 34.04 3.82
5898 12529 8.651588 CGCAGCTATTTCCTACATTTCTATAAG 58.348 37.037 0.00 0.00 0.00 1.73
5899 12530 8.148351 ACGCAGCTATTTCCTACATTTCTATAA 58.852 33.333 0.00 0.00 0.00 0.98
5900 12531 7.667557 ACGCAGCTATTTCCTACATTTCTATA 58.332 34.615 0.00 0.00 0.00 1.31
5914 12576 5.277857 AGGTCTATTGTACGCAGCTATTT 57.722 39.130 0.00 0.00 0.00 1.40
5918 12580 4.159879 ACTTTAGGTCTATTGTACGCAGCT 59.840 41.667 0.00 0.00 0.00 4.24
5936 12598 2.349755 GCAGGCCCGACCACTTTA 59.650 61.111 0.00 0.00 43.14 1.85
5980 12643 8.056407 AGTTTCAGAAAAGTAAAGCAAAGACT 57.944 30.769 0.00 0.00 0.00 3.24
6029 12692 7.757624 TGCGTTTCAAGTTTCAGAAAAGTAAAT 59.242 29.630 0.00 0.00 36.20 1.40
6149 12812 7.280205 ACGATCAACATTAATGACTACCCTTTC 59.720 37.037 22.16 5.43 0.00 2.62
6154 12817 7.970384 TGAAACGATCAACATTAATGACTACC 58.030 34.615 22.16 7.06 34.30 3.18
6242 12925 9.129209 GTTAACAGAAAGGCACTAATGAAATTC 57.871 33.333 0.00 0.00 38.49 2.17
6341 13024 6.239008 CCCACACACACACATTTTCTTTCTAT 60.239 38.462 0.00 0.00 0.00 1.98
6355 13038 3.093172 TGCTCCCCCACACACACA 61.093 61.111 0.00 0.00 0.00 3.72
6356 13039 2.281761 CTGCTCCCCCACACACAC 60.282 66.667 0.00 0.00 0.00 3.82
6357 13040 2.447572 TCTGCTCCCCCACACACA 60.448 61.111 0.00 0.00 0.00 3.72
6358 13041 2.348998 CTCTGCTCCCCCACACAC 59.651 66.667 0.00 0.00 0.00 3.82
6359 13042 2.122413 ACTCTGCTCCCCCACACA 60.122 61.111 0.00 0.00 0.00 3.72
6360 13043 2.217038 TGACTCTGCTCCCCCACAC 61.217 63.158 0.00 0.00 0.00 3.82
6361 13044 2.204034 TGACTCTGCTCCCCCACA 59.796 61.111 0.00 0.00 0.00 4.17
6362 13045 1.484444 AAGTGACTCTGCTCCCCCAC 61.484 60.000 0.00 0.00 0.00 4.61
6363 13046 0.116342 TAAGTGACTCTGCTCCCCCA 59.884 55.000 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.