Multiple sequence alignment - TraesCS6A01G220400

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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 TraesCS6A01G220400 chr6A 100.000 4784 0 0 1 4784 409410574 409415357 0.000000e+00 8835.0
1 TraesCS6A01G220400 chr6D 89.487 4889 289 91 6 4782 305183028 305178253 0.000000e+00 5973.0
2 TraesCS6A01G220400 chr6B 91.537 3096 143 38 757 3800 471628051 471631079 0.000000e+00 4156.0
3 TraesCS6A01G220400 chr6B 88.584 657 66 8 4032 4683 471638071 471638723 0.000000e+00 789.0
4 TraesCS6A01G220400 chr6B 88.957 326 28 5 3 326 471552700 471553019 3.470000e-106 396.0
5 TraesCS6A01G220400 chr6B 84.615 286 38 4 332 614 471553299 471553581 3.650000e-71 279.0
6 TraesCS6A01G220400 chr4B 80.919 849 136 21 3945 4781 273678484 273679318 0.000000e+00 647.0
7 TraesCS6A01G220400 chr4B 80.445 854 137 19 3945 4784 260059124 260058287 4.070000e-175 625.0
8 TraesCS6A01G220400 chrUn 80.796 854 134 19 3945 4784 332209508 332208671 4.040000e-180 641.0
9 TraesCS6A01G220400 chr4D 80.494 851 136 20 3945 4781 277414244 277415078 4.070000e-175 625.0
10 TraesCS6A01G220400 chr1A 80.491 856 133 21 3945 4784 235657362 235656525 4.070000e-175 625.0
11 TraesCS6A01G220400 chr1B 80.328 854 138 19 3945 4784 476337828 476336991 1.890000e-173 619.0
12 TraesCS6A01G220400 chr1B 96.875 32 0 1 127 158 57236638 57236608 9.000000e-03 52.8
13 TraesCS6A01G220400 chr2B 80.118 850 139 19 3945 4781 173474476 173475308 1.470000e-169 606.0
14 TraesCS6A01G220400 chr5B 79.953 853 136 23 3945 4781 315621548 315622381 3.190000e-166 595.0
15 TraesCS6A01G220400 chr7D 82.550 149 24 2 3258 3405 241883129 241883276 3.890000e-26 130.0
16 TraesCS6A01G220400 chr7B 82.550 149 24 2 3258 3405 217625990 217626137 3.890000e-26 130.0
17 TraesCS6A01G220400 chr7A 81.013 158 28 2 3258 3414 256213519 256213363 1.810000e-24 124.0


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 TraesCS6A01G220400 chr6A 409410574 409415357 4783 False 8835.0 8835 100.000 1 4784 1 chr6A.!!$F1 4783
1 TraesCS6A01G220400 chr6D 305178253 305183028 4775 True 5973.0 5973 89.487 6 4782 1 chr6D.!!$R1 4776
2 TraesCS6A01G220400 chr6B 471628051 471631079 3028 False 4156.0 4156 91.537 757 3800 1 chr6B.!!$F1 3043
3 TraesCS6A01G220400 chr6B 471638071 471638723 652 False 789.0 789 88.584 4032 4683 1 chr6B.!!$F2 651
4 TraesCS6A01G220400 chr6B 471552700 471553581 881 False 337.5 396 86.786 3 614 2 chr6B.!!$F3 611
5 TraesCS6A01G220400 chr4B 273678484 273679318 834 False 647.0 647 80.919 3945 4781 1 chr4B.!!$F1 836
6 TraesCS6A01G220400 chr4B 260058287 260059124 837 True 625.0 625 80.445 3945 4784 1 chr4B.!!$R1 839
7 TraesCS6A01G220400 chrUn 332208671 332209508 837 True 641.0 641 80.796 3945 4784 1 chrUn.!!$R1 839
8 TraesCS6A01G220400 chr4D 277414244 277415078 834 False 625.0 625 80.494 3945 4781 1 chr4D.!!$F1 836
9 TraesCS6A01G220400 chr1A 235656525 235657362 837 True 625.0 625 80.491 3945 4784 1 chr1A.!!$R1 839
10 TraesCS6A01G220400 chr1B 476336991 476337828 837 True 619.0 619 80.328 3945 4784 1 chr1B.!!$R2 839
11 TraesCS6A01G220400 chr2B 173474476 173475308 832 False 606.0 606 80.118 3945 4781 1 chr2B.!!$F1 836
12 TraesCS6A01G220400 chr5B 315621548 315622381 833 False 595.0 595 79.953 3945 4781 1 chr5B.!!$F1 836

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
539 817 0.179086 TGCACGTGCTCTTGAGAACA 60.179 50.0 37.59 13.75 42.66 3.18 F
1065 1368 0.179215 CGCCGTTCTGCTGAATTGTC 60.179 55.0 9.40 0.00 34.40 3.18 F
1769 2115 0.464036 TTCTGCTCTTGACACGGTGT 59.536 50.0 14.66 14.66 0.00 4.16 F
3155 3531 0.030101 CGGCGATCTCCAGAAGAGTC 59.970 60.0 0.00 0.00 43.71 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 2523 0.387622 CTCAATTGCAAGGCCGTGTG 60.388 55.000 20.23 10.34 0.00 3.82 R
2454 2830 2.100991 CGAATTGCTGCCCTTCGC 59.899 61.111 16.89 0.00 35.85 4.70 R
3638 4016 0.391661 ACACCAAGAGCTGCCATACG 60.392 55.000 0.00 0.00 0.00 3.06 R
4244 4678 0.390472 GGTCTGCTTCTCCTTCCACG 60.390 60.000 0.00 0.00 0.00 4.94 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
71 72 2.754552 GCATAGCCCTCAAATGTCACAA 59.245 45.455 0.00 0.00 0.00 3.33
123 124 4.387256 GTCTCTCACAAGAACATCGAAAGG 59.613 45.833 0.00 0.00 0.00 3.11
205 207 6.775939 ATGCAACATGACTTATGAGATACG 57.224 37.500 0.00 0.00 39.21 3.06
217 219 1.132453 TGAGATACGCACGGTCAGAAG 59.868 52.381 0.00 0.00 0.00 2.85
319 322 4.830600 TGTTTTTCCTATTGAGTCAACCCC 59.169 41.667 7.96 0.00 0.00 4.95
384 660 4.947388 AGAAGTACAAAGCACCTCAAAACA 59.053 37.500 0.00 0.00 0.00 2.83
389 665 8.630054 AGTACAAAGCACCTCAAAACATAATA 57.370 30.769 0.00 0.00 0.00 0.98
424 700 1.290130 AGGTCCCTATACCACGGAACT 59.710 52.381 0.00 0.00 42.40 3.01
426 702 2.889678 GGTCCCTATACCACGGAACTAG 59.110 54.545 0.00 0.00 39.50 2.57
427 703 3.560105 GTCCCTATACCACGGAACTAGT 58.440 50.000 0.00 0.00 0.00 2.57
431 709 4.441079 CCCTATACCACGGAACTAGTTGTG 60.441 50.000 14.14 15.13 0.00 3.33
442 720 5.491982 GGAACTAGTTGTGGTCATCAGAAT 58.508 41.667 14.14 0.00 31.11 2.40
460 738 4.189580 GAGCCGCCAATGCCCCTA 62.190 66.667 0.00 0.00 0.00 3.53
468 746 1.762708 CCAATGCCCCTATGTCGTTT 58.237 50.000 0.00 0.00 0.00 3.60
475 753 1.134491 CCCCTATGTCGTTTCTCCCAC 60.134 57.143 0.00 0.00 0.00 4.61
477 755 2.418746 CCCTATGTCGTTTCTCCCACAG 60.419 54.545 0.00 0.00 0.00 3.66
478 756 2.496070 CCTATGTCGTTTCTCCCACAGA 59.504 50.000 0.00 0.00 0.00 3.41
496 774 1.819903 AGAGGAGACGTCTAACCTTGC 59.180 52.381 22.79 13.41 32.53 4.01
497 775 0.526662 AGGAGACGTCTAACCTTGCG 59.473 55.000 20.09 0.00 0.00 4.85
505 783 2.695359 GTCTAACCTTGCGGATGACAA 58.305 47.619 0.00 0.00 32.27 3.18
506 784 2.673368 GTCTAACCTTGCGGATGACAAG 59.327 50.000 0.00 0.00 43.36 3.16
529 807 1.001378 GGAAGTTTTCATGCACGTGCT 60.001 47.619 37.59 22.19 42.66 4.40
539 817 0.179086 TGCACGTGCTCTTGAGAACA 60.179 50.000 37.59 13.75 42.66 3.18
578 856 5.696724 ACAGTCTTCGTTGTTGAATCCTTAG 59.303 40.000 0.00 0.00 0.00 2.18
585 863 6.338146 TCGTTGTTGAATCCTTAGATCGATT 58.662 36.000 0.00 0.00 0.00 3.34
623 901 6.612247 TCAAAGTTTGTCATTGTGTACGAT 57.388 33.333 15.08 0.00 0.00 3.73
633 911 3.755112 TTGTGTACGATGAGAAACCCA 57.245 42.857 0.00 0.00 0.00 4.51
634 912 3.034721 TGTGTACGATGAGAAACCCAC 57.965 47.619 0.00 0.00 0.00 4.61
636 914 3.007506 TGTGTACGATGAGAAACCCACAT 59.992 43.478 0.00 0.00 0.00 3.21
637 915 3.617263 GTGTACGATGAGAAACCCACATC 59.383 47.826 0.00 0.00 37.59 3.06
638 916 3.259625 TGTACGATGAGAAACCCACATCA 59.740 43.478 0.00 0.00 39.93 3.07
639 917 2.699954 ACGATGAGAAACCCACATCAC 58.300 47.619 0.00 0.00 39.93 3.06
640 918 2.009774 CGATGAGAAACCCACATCACC 58.990 52.381 0.00 0.00 39.93 4.02
641 919 2.615240 CGATGAGAAACCCACATCACCA 60.615 50.000 0.00 0.00 39.93 4.17
643 921 1.774254 TGAGAAACCCACATCACCACT 59.226 47.619 0.00 0.00 0.00 4.00
644 922 2.224523 TGAGAAACCCACATCACCACTC 60.225 50.000 0.00 0.00 0.00 3.51
646 924 0.850100 AAACCCACATCACCACTCCA 59.150 50.000 0.00 0.00 0.00 3.86
653 933 2.038952 CACATCACCACTCCAAGGAAGA 59.961 50.000 0.00 0.00 0.00 2.87
656 936 1.694150 TCACCACTCCAAGGAAGACAG 59.306 52.381 0.00 0.00 0.00 3.51
657 937 1.059913 ACCACTCCAAGGAAGACAGG 58.940 55.000 0.00 0.00 0.00 4.00
660 940 2.307098 CCACTCCAAGGAAGACAGGAAT 59.693 50.000 0.00 0.00 0.00 3.01
673 953 1.089920 CAGGAATTTGCGCAGTAGCT 58.910 50.000 11.31 0.00 39.10 3.32
690 970 3.644966 AGCTCATTTTAATCCGTCCCA 57.355 42.857 0.00 0.00 0.00 4.37
692 972 3.694566 AGCTCATTTTAATCCGTCCCAAC 59.305 43.478 0.00 0.00 0.00 3.77
693 973 3.442273 GCTCATTTTAATCCGTCCCAACA 59.558 43.478 0.00 0.00 0.00 3.33
696 976 5.774630 TCATTTTAATCCGTCCCAACAAAC 58.225 37.500 0.00 0.00 0.00 2.93
697 977 5.302059 TCATTTTAATCCGTCCCAACAAACA 59.698 36.000 0.00 0.00 0.00 2.83
698 978 5.593679 TTTTAATCCGTCCCAACAAACAA 57.406 34.783 0.00 0.00 0.00 2.83
699 979 5.593679 TTTAATCCGTCCCAACAAACAAA 57.406 34.783 0.00 0.00 0.00 2.83
700 980 3.446310 AATCCGTCCCAACAAACAAAC 57.554 42.857 0.00 0.00 0.00 2.93
711 991 4.210955 CCAACAAACAAACCAAATGATCGG 59.789 41.667 0.00 0.00 0.00 4.18
715 995 2.795329 ACAAACCAAATGATCGGAGCT 58.205 42.857 0.00 0.00 0.00 4.09
724 1004 3.616956 ATGATCGGAGCTCAAAAGACA 57.383 42.857 17.19 7.92 0.00 3.41
736 1016 6.030228 AGCTCAAAAGACAAACTCGAAAAAG 58.970 36.000 0.00 0.00 0.00 2.27
753 1035 1.422161 AAGAAGCAGAGCACCACCCT 61.422 55.000 0.00 0.00 0.00 4.34
754 1036 1.673665 GAAGCAGAGCACCACCCTG 60.674 63.158 0.00 0.00 0.00 4.45
764 1046 1.140852 GCACCACCCTGCACATATCTA 59.859 52.381 0.00 0.00 37.11 1.98
796 1094 0.462759 GAGGCACCAAGATTCCCTCG 60.463 60.000 0.00 0.00 33.49 4.63
850 1151 0.971386 CTTTGTCCAATTGCCTGGCT 59.029 50.000 21.03 0.00 36.32 4.75
879 1180 2.170012 AGAAAGGCGTGGTCCCTATA 57.830 50.000 0.00 0.00 30.93 1.31
880 1181 2.040178 AGAAAGGCGTGGTCCCTATAG 58.960 52.381 0.00 0.00 30.93 1.31
1027 1330 3.561725 GCCATCAGGAGCACATAAAGTAC 59.438 47.826 0.00 0.00 36.89 2.73
1065 1368 0.179215 CGCCGTTCTGCTGAATTGTC 60.179 55.000 9.40 0.00 34.40 3.18
1128 1431 2.198287 TCTACGCCCCTACGATGGC 61.198 63.158 0.00 0.00 44.41 4.40
1166 1469 2.414029 CCGTCCATGGTTGTTGATTTCG 60.414 50.000 12.58 2.89 0.00 3.46
1204 1507 1.618837 GAAAAGGAAAGAACCAGCCCC 59.381 52.381 0.00 0.00 0.00 5.80
1240 1546 3.821421 TCTTTCTTTATCCTCGCCTCC 57.179 47.619 0.00 0.00 0.00 4.30
1254 1560 1.800655 CGCCTCCGTCTCTGAATTCAG 60.801 57.143 26.56 26.56 45.08 3.02
1275 1581 7.667575 TCAGGAGATTTCTAAGCAAGTATCT 57.332 36.000 0.00 0.00 33.38 1.98
1276 1582 8.083828 TCAGGAGATTTCTAAGCAAGTATCTT 57.916 34.615 0.00 0.00 31.93 2.40
1277 1583 8.200792 TCAGGAGATTTCTAAGCAAGTATCTTC 58.799 37.037 0.00 0.00 31.93 2.87
1278 1584 7.440856 CAGGAGATTTCTAAGCAAGTATCTTCC 59.559 40.741 0.00 0.00 31.93 3.46
1279 1585 6.422400 GGAGATTTCTAAGCAAGTATCTTCCG 59.578 42.308 0.00 0.00 31.93 4.30
1280 1586 6.879400 AGATTTCTAAGCAAGTATCTTCCGT 58.121 36.000 0.00 0.00 29.30 4.69
1281 1587 7.331791 AGATTTCTAAGCAAGTATCTTCCGTT 58.668 34.615 0.00 0.00 29.30 4.44
1282 1588 7.824779 AGATTTCTAAGCAAGTATCTTCCGTTT 59.175 33.333 0.00 0.00 29.30 3.60
1283 1589 6.963049 TTCTAAGCAAGTATCTTCCGTTTC 57.037 37.500 0.00 0.00 0.00 2.78
1284 1590 6.032956 TCTAAGCAAGTATCTTCCGTTTCA 57.967 37.500 0.00 0.00 0.00 2.69
1285 1591 6.640518 TCTAAGCAAGTATCTTCCGTTTCAT 58.359 36.000 0.00 0.00 0.00 2.57
1286 1592 5.551760 AAGCAAGTATCTTCCGTTTCATG 57.448 39.130 0.00 0.00 0.00 3.07
1287 1593 4.832248 AGCAAGTATCTTCCGTTTCATGA 58.168 39.130 0.00 0.00 0.00 3.07
1288 1594 4.872691 AGCAAGTATCTTCCGTTTCATGAG 59.127 41.667 0.00 0.00 0.00 2.90
1289 1595 4.034510 GCAAGTATCTTCCGTTTCATGAGG 59.965 45.833 0.00 0.00 0.00 3.86
1290 1596 5.178797 CAAGTATCTTCCGTTTCATGAGGT 58.821 41.667 0.00 0.00 0.00 3.85
1291 1597 4.759782 AGTATCTTCCGTTTCATGAGGTG 58.240 43.478 0.00 0.00 0.00 4.00
1292 1598 2.472695 TCTTCCGTTTCATGAGGTGG 57.527 50.000 0.00 0.00 0.00 4.61
1293 1599 1.003118 TCTTCCGTTTCATGAGGTGGG 59.997 52.381 0.00 0.00 0.00 4.61
1294 1600 0.768622 TTCCGTTTCATGAGGTGGGT 59.231 50.000 0.00 0.00 0.00 4.51
1295 1601 1.646912 TCCGTTTCATGAGGTGGGTA 58.353 50.000 0.00 0.00 0.00 3.69
1296 1602 2.193127 TCCGTTTCATGAGGTGGGTAT 58.807 47.619 0.00 0.00 0.00 2.73
1297 1603 2.169769 TCCGTTTCATGAGGTGGGTATC 59.830 50.000 0.00 0.00 0.00 2.24
1322 1628 7.647715 TCCTTGTTTCTGAAATTGATTCGAAAC 59.352 33.333 19.54 19.54 46.79 2.78
1323 1629 7.096065 CCTTGTTTCTGAAATTGATTCGAAACC 60.096 37.037 21.38 0.00 46.51 3.27
1424 1739 1.682451 TACCCTGGCGGAAGAATCGG 61.682 60.000 0.00 0.00 34.64 4.18
1434 1749 2.010497 GGAAGAATCGGCTGAAAGGTC 58.990 52.381 0.00 0.00 0.00 3.85
1449 1764 5.183228 TGAAAGGTCGGTCTATTCCATTTC 58.817 41.667 0.00 0.00 0.00 2.17
1502 1817 7.377766 TCTTCTCCTTTGTTAATTTGGATCG 57.622 36.000 0.00 0.00 0.00 3.69
1504 1819 6.985188 TCTCCTTTGTTAATTTGGATCGAG 57.015 37.500 0.00 0.00 0.00 4.04
1566 1881 1.937223 CACACTGGTAACGTTTGCTCA 59.063 47.619 5.91 0.00 42.51 4.26
1668 1983 4.437239 AGTATGAGAACTTCAATCAGCGG 58.563 43.478 0.00 0.00 39.77 5.52
1718 2064 3.855689 AGCTTTTCATCATCCGGTTTG 57.144 42.857 0.00 0.36 0.00 2.93
1735 2081 4.629634 CGGTTTGTATGTCATCACTTGCTA 59.370 41.667 0.00 0.00 0.00 3.49
1769 2115 0.464036 TTCTGCTCTTGACACGGTGT 59.536 50.000 14.66 14.66 0.00 4.16
1770 2116 0.464036 TCTGCTCTTGACACGGTGTT 59.536 50.000 15.94 0.00 0.00 3.32
1855 2201 5.472820 GGATCATCTGAATTCATCCTGTTCC 59.527 44.000 8.96 14.78 0.00 3.62
1870 2216 0.603569 GTTCCGAGGCAAGAGACAGA 59.396 55.000 0.00 0.00 0.00 3.41
1875 2221 1.402194 CGAGGCAAGAGACAGACAGAC 60.402 57.143 0.00 0.00 0.00 3.51
1878 2224 2.435805 AGGCAAGAGACAGACAGACAAA 59.564 45.455 0.00 0.00 0.00 2.83
1888 2234 6.352516 AGACAGACAGACAAAATTTCACTCT 58.647 36.000 0.00 0.00 0.00 3.24
1889 2235 6.259608 AGACAGACAGACAAAATTTCACTCTG 59.740 38.462 14.01 14.01 35.48 3.35
1890 2236 6.115446 ACAGACAGACAAAATTTCACTCTGA 58.885 36.000 19.22 0.00 33.86 3.27
1892 2238 6.259608 CAGACAGACAAAATTTCACTCTGAGT 59.740 38.462 19.22 4.06 33.86 3.41
1927 2273 1.522258 CCAAATTTGTGCACGCAACTC 59.478 47.619 16.73 0.00 0.00 3.01
1938 2312 2.738643 GCACGCAACTCTATCTGCCTTA 60.739 50.000 0.00 0.00 35.01 2.69
1943 2317 4.624882 CGCAACTCTATCTGCCTTATGATC 59.375 45.833 0.00 0.00 35.01 2.92
1944 2318 5.545588 GCAACTCTATCTGCCTTATGATCA 58.454 41.667 0.00 0.00 32.18 2.92
1945 2319 5.638657 GCAACTCTATCTGCCTTATGATCAG 59.361 44.000 0.09 0.00 32.18 2.90
1946 2320 6.740960 GCAACTCTATCTGCCTTATGATCAGT 60.741 42.308 0.09 0.00 32.18 3.41
1947 2321 6.992664 ACTCTATCTGCCTTATGATCAGTT 57.007 37.500 0.09 0.00 0.00 3.16
1948 2322 8.363390 CAACTCTATCTGCCTTATGATCAGTTA 58.637 37.037 0.09 0.00 30.90 2.24
1949 2323 8.484214 ACTCTATCTGCCTTATGATCAGTTAA 57.516 34.615 0.09 0.00 0.00 2.01
1950 2324 9.099071 ACTCTATCTGCCTTATGATCAGTTAAT 57.901 33.333 0.09 0.00 0.00 1.40
1951 2325 9.941325 CTCTATCTGCCTTATGATCAGTTAATT 57.059 33.333 0.09 0.00 0.00 1.40
1955 2329 8.668510 TCTGCCTTATGATCAGTTAATTTCTC 57.331 34.615 0.09 0.00 0.00 2.87
1956 2330 8.489489 TCTGCCTTATGATCAGTTAATTTCTCT 58.511 33.333 0.09 0.00 0.00 3.10
1972 2346 1.070758 TCTCTGTTTCAGGTGGACAGC 59.929 52.381 8.62 0.00 40.36 4.40
2036 2410 1.808133 GCGATCTTGACCTCACCATCC 60.808 57.143 0.00 0.00 0.00 3.51
2077 2451 0.479815 ATGGCGGATGGTTCATGGAT 59.520 50.000 0.00 0.00 0.00 3.41
2085 2459 4.505566 CGGATGGTTCATGGATGGTAAGAT 60.506 45.833 0.00 0.00 0.00 2.40
2149 2523 8.462016 AGCATCATTACTCCAACTTAAATTGTC 58.538 33.333 0.00 0.00 0.00 3.18
2162 2536 1.106351 AATTGTCACACGGCCTTGCA 61.106 50.000 9.57 0.00 0.00 4.08
2183 2558 4.260743 GCAATTGAGCTGTATATTGCGACA 60.261 41.667 10.34 0.00 42.12 4.35
2251 2626 2.834549 ACCGATGAGAAGACCATTCAGT 59.165 45.455 0.00 0.00 0.00 3.41
2256 2631 6.239036 CCGATGAGAAGACCATTCAGTACATA 60.239 42.308 0.00 0.00 0.00 2.29
2450 2826 2.270850 GGCAGCAACATACCGGGA 59.729 61.111 6.32 0.00 0.00 5.14
2454 2830 2.895372 GCAACATACCGGGAGCGG 60.895 66.667 6.32 0.00 0.00 5.52
2847 3223 3.315142 ATGCACGCCGACATGGACT 62.315 57.895 0.00 0.00 42.00 3.85
2949 3325 1.007038 TACTCGGTGGTGAACGTGC 60.007 57.895 0.00 0.00 0.00 5.34
2960 3336 4.329545 AACGTGCGGTGCAGGGAT 62.330 61.111 14.92 2.08 46.80 3.85
3074 3450 0.175760 TCCAGGAGCTGTACATTCGC 59.824 55.000 0.00 0.00 0.00 4.70
3110 3486 2.507992 CTGCTGAAGGACGAGGCG 60.508 66.667 0.00 0.00 0.00 5.52
3155 3531 0.030101 CGGCGATCTCCAGAAGAGTC 59.970 60.000 0.00 0.00 43.71 3.36
3170 3546 4.083862 GTCTCCGAGGTGGGTGGC 62.084 72.222 0.00 0.00 38.76 5.01
3187 3564 1.082496 GCACAGCAACAGAACTCGC 60.082 57.895 0.00 0.00 0.00 5.03
3226 3603 1.151668 GCGTGCTGTTTCTGACTGAT 58.848 50.000 0.00 0.00 0.00 2.90
3487 3865 2.742372 CGTCAAGAAGGTGCCCGG 60.742 66.667 0.00 0.00 0.00 5.73
3577 3955 1.670811 CGCCAAACTCGGAGCATAATT 59.329 47.619 4.58 0.00 0.00 1.40
3586 3964 1.583054 GGAGCATAATTTCCGTCGCT 58.417 50.000 0.00 0.00 0.00 4.93
3587 3965 1.261619 GGAGCATAATTTCCGTCGCTG 59.738 52.381 0.00 0.00 0.00 5.18
3588 3966 2.201732 GAGCATAATTTCCGTCGCTGA 58.798 47.619 0.00 0.00 0.00 4.26
3589 3967 2.802816 GAGCATAATTTCCGTCGCTGAT 59.197 45.455 0.00 0.00 0.00 2.90
3590 3968 2.802816 AGCATAATTTCCGTCGCTGATC 59.197 45.455 0.00 0.00 0.00 2.92
3591 3969 2.096218 GCATAATTTCCGTCGCTGATCC 60.096 50.000 0.00 0.00 0.00 3.36
3592 3970 3.393800 CATAATTTCCGTCGCTGATCCT 58.606 45.455 0.00 0.00 0.00 3.24
3593 3971 2.403252 AATTTCCGTCGCTGATCCTT 57.597 45.000 0.00 0.00 0.00 3.36
3594 3972 3.536956 AATTTCCGTCGCTGATCCTTA 57.463 42.857 0.00 0.00 0.00 2.69
3595 3973 2.288961 TTTCCGTCGCTGATCCTTAC 57.711 50.000 0.00 0.00 0.00 2.34
3596 3974 0.458669 TTCCGTCGCTGATCCTTACC 59.541 55.000 0.00 0.00 0.00 2.85
3597 3975 1.299165 CCGTCGCTGATCCTTACCG 60.299 63.158 0.00 0.00 0.00 4.02
3598 3976 1.432251 CGTCGCTGATCCTTACCGT 59.568 57.895 0.00 0.00 0.00 4.83
3599 3977 0.591741 CGTCGCTGATCCTTACCGTC 60.592 60.000 0.00 0.00 0.00 4.79
3600 3978 0.591741 GTCGCTGATCCTTACCGTCG 60.592 60.000 0.00 0.00 0.00 5.12
3603 3981 0.454600 GCTGATCCTTACCGTCGTGA 59.545 55.000 0.00 0.00 0.00 4.35
3623 4001 5.235186 CGTGAAAATTGTTGTAAAATGGCCA 59.765 36.000 8.56 8.56 0.00 5.36
3626 4004 6.259608 TGAAAATTGTTGTAAAATGGCCACAG 59.740 34.615 8.16 0.00 0.00 3.66
3638 4016 0.747852 GGCCACAGCTAGAGTAGTCC 59.252 60.000 0.00 0.00 39.73 3.85
3660 4041 0.987294 ATGGCAGCTCTTGGTGTACT 59.013 50.000 0.00 0.00 43.05 2.73
3664 4045 2.226674 GGCAGCTCTTGGTGTACTTTTC 59.773 50.000 0.00 0.00 43.05 2.29
3667 4048 4.636249 CAGCTCTTGGTGTACTTTTCTCT 58.364 43.478 0.00 0.00 36.97 3.10
3737 4120 6.642707 TTCGAAGAGAGAGATAAAGGATCC 57.357 41.667 2.48 2.48 38.43 3.36
3740 4123 6.836527 TCGAAGAGAGAGATAAAGGATCCTTT 59.163 38.462 35.75 35.75 46.56 3.11
3788 4175 6.959639 TGATGCCTATATTTTTCTCAACCC 57.040 37.500 0.00 0.00 0.00 4.11
3840 4254 9.284968 CACTTTCTACCTTTTCTTATTTCCTCA 57.715 33.333 0.00 0.00 0.00 3.86
3874 4288 4.290459 TGGAATATAAGGGCATCTGAGCAT 59.710 41.667 0.00 0.00 35.83 3.79
3911 4325 8.625786 TTAGGGGACATTTAGTAAGTTTTCAC 57.374 34.615 0.00 0.00 0.00 3.18
3912 4326 5.704053 AGGGGACATTTAGTAAGTTTTCACG 59.296 40.000 0.00 0.00 0.00 4.35
3916 4330 6.203338 GGACATTTAGTAAGTTTTCACGGTCA 59.797 38.462 0.00 0.00 0.00 4.02
3932 4346 0.319641 GTCACGGTGGACCTTCTCAC 60.320 60.000 8.50 0.00 0.00 3.51
3935 4349 2.571216 CGGTGGACCTTCTCACGGT 61.571 63.158 0.00 0.00 37.50 4.83
3936 4350 1.752833 GGTGGACCTTCTCACGGTT 59.247 57.895 0.00 0.00 34.19 4.44
3937 4351 0.971386 GGTGGACCTTCTCACGGTTA 59.029 55.000 0.00 0.00 34.19 2.85
3938 4352 1.553704 GGTGGACCTTCTCACGGTTAT 59.446 52.381 0.00 0.00 34.19 1.89
3939 4353 2.027469 GGTGGACCTTCTCACGGTTATT 60.027 50.000 0.00 0.00 34.19 1.40
3940 4354 3.558533 GGTGGACCTTCTCACGGTTATTT 60.559 47.826 0.00 0.00 34.19 1.40
3941 4355 4.070009 GTGGACCTTCTCACGGTTATTTT 58.930 43.478 0.00 0.00 34.19 1.82
3942 4356 4.069304 TGGACCTTCTCACGGTTATTTTG 58.931 43.478 0.00 0.00 34.19 2.44
3943 4357 4.202377 TGGACCTTCTCACGGTTATTTTGA 60.202 41.667 0.00 0.00 34.19 2.69
3954 4368 3.056891 CGGTTATTTTGACAACCTGCCAT 60.057 43.478 2.34 0.00 41.75 4.40
4020 4434 3.023119 GTTGACATGGATGTTGGCCATA 58.977 45.455 6.09 0.00 44.08 2.74
4023 4437 4.288398 TGACATGGATGTTGGCCATATTT 58.712 39.130 6.09 0.00 44.08 1.40
4036 4450 5.083122 TGGCCATATTTTTCTTGGAAGACA 58.917 37.500 0.00 0.00 34.13 3.41
4056 4470 3.118186 ACATTGGCAATTTGATGGGGATG 60.118 43.478 10.65 0.00 0.00 3.51
4058 4474 0.831966 GGCAATTTGATGGGGATGCA 59.168 50.000 0.00 0.00 35.57 3.96
4146 4574 9.474920 TCATTATTCAACCAAACAAAACTGATC 57.525 29.630 0.00 0.00 0.00 2.92
4149 4580 4.915704 TCAACCAAACAAAACTGATCGTC 58.084 39.130 0.00 0.00 0.00 4.20
4244 4678 8.135529 GGAGGTAAATTTGTGTATTGGCTTATC 58.864 37.037 0.00 0.00 0.00 1.75
4248 4682 4.955925 TTTGTGTATTGGCTTATCGTGG 57.044 40.909 0.00 0.00 0.00 4.94
4260 4694 3.452474 CTTATCGTGGAAGGAGAAGCAG 58.548 50.000 0.00 0.00 42.08 4.24
4266 4700 0.035915 GGAAGGAGAAGCAGACCCAC 60.036 60.000 0.00 0.00 0.00 4.61
4282 4716 4.223032 AGACCCACATGTCGAAATTCTAGT 59.777 41.667 0.00 0.00 40.26 2.57
4331 4765 2.853731 AGAACATACTTCGAGAGCCG 57.146 50.000 0.00 0.00 40.25 5.52
4389 4825 5.362556 TTGACTTAACTTCATGAGCAAGC 57.637 39.130 0.00 0.00 0.00 4.01
4412 4848 5.680151 GCGCTTTCTAATCTTCCTCACTACT 60.680 44.000 0.00 0.00 0.00 2.57
4447 4883 8.579006 ACAAAAGAGCATGATGTATTGAAAGAA 58.421 29.630 0.00 0.00 0.00 2.52
4467 4907 6.908870 AGAAAAACTGAAGGATTTTGTTGC 57.091 33.333 2.13 0.00 0.00 4.17
4485 4925 4.035324 TGTTGCAAAAATGCACATTTGAGG 59.965 37.500 23.23 8.71 45.32 3.86
4505 4945 6.905736 TGAGGAAATATTAGCCCATGTGTTA 58.094 36.000 4.17 0.00 0.00 2.41
4514 4954 1.409521 GCCCATGTGTTATACCAGCCA 60.410 52.381 0.00 0.00 0.00 4.75
4545 4985 4.897140 CCAAAGAAAGATGGATTTTGGCA 58.103 39.130 1.82 0.00 40.69 4.92
4587 5027 5.452255 AGCCATCAACAAGATCACCATAAT 58.548 37.500 0.00 0.00 33.72 1.28
4619 5059 0.692476 TATTCCCCGCCTGGATGATG 59.308 55.000 0.00 0.00 37.49 3.07
4658 5099 0.954452 GGCAAGAGTGTTCACCAAGG 59.046 55.000 0.00 0.00 0.00 3.61
4717 5158 4.086706 ACCTGGAGATGAACGAAAAACT 57.913 40.909 0.00 0.00 0.00 2.66
4721 5162 4.320870 TGGAGATGAACGAAAAACTACCC 58.679 43.478 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.819632 CTACCGTCCCCAATGCAGC 60.820 63.158 0.00 0.00 0.00 5.25
1 2 1.819632 GCTACCGTCCCCAATGCAG 60.820 63.158 0.00 0.00 0.00 4.41
51 52 5.389859 TTTTGTGACATTTGAGGGCTATG 57.610 39.130 0.00 0.00 0.00 2.23
57 58 8.592105 ACACATTATTTTTGTGACATTTGAGG 57.408 30.769 10.51 0.00 45.83 3.86
188 190 3.670523 CCGTGCGTATCTCATAAGTCATG 59.329 47.826 0.00 0.00 35.81 3.07
205 207 5.120830 CCTATTATATTGCTTCTGACCGTGC 59.879 44.000 0.00 0.00 0.00 5.34
424 700 4.507710 GCTCATTCTGATGACCACAACTA 58.492 43.478 0.00 0.00 37.37 2.24
426 702 2.421424 GGCTCATTCTGATGACCACAAC 59.579 50.000 0.00 0.00 37.37 3.32
427 703 2.715046 GGCTCATTCTGATGACCACAA 58.285 47.619 0.00 0.00 37.37 3.33
431 709 1.162800 GGCGGCTCATTCTGATGACC 61.163 60.000 0.00 0.00 37.37 4.02
433 711 0.252761 TTGGCGGCTCATTCTGATGA 59.747 50.000 11.43 0.00 39.92 2.92
453 731 0.539986 GGAGAAACGACATAGGGGCA 59.460 55.000 0.00 0.00 0.00 5.36
460 738 1.276421 CCTCTGTGGGAGAAACGACAT 59.724 52.381 0.00 0.00 44.45 3.06
475 753 2.416162 GCAAGGTTAGACGTCTCCTCTG 60.416 54.545 23.89 21.01 0.00 3.35
477 755 1.467713 CGCAAGGTTAGACGTCTCCTC 60.468 57.143 23.89 13.13 0.00 3.71
478 756 0.526662 CGCAAGGTTAGACGTCTCCT 59.473 55.000 23.89 20.35 0.00 3.69
496 774 0.673644 AACTTCCCGCTTGTCATCCG 60.674 55.000 0.00 0.00 0.00 4.18
497 775 1.534729 AAACTTCCCGCTTGTCATCC 58.465 50.000 0.00 0.00 0.00 3.51
505 783 0.598065 GTGCATGAAAACTTCCCGCT 59.402 50.000 0.00 0.00 0.00 5.52
506 784 0.729140 CGTGCATGAAAACTTCCCGC 60.729 55.000 0.00 0.00 0.00 6.13
529 807 1.961793 CGGGGTGTTTGTTCTCAAGA 58.038 50.000 0.00 0.00 34.88 3.02
539 817 4.514585 TGTGGCTGCGGGGTGTTT 62.515 61.111 0.00 0.00 0.00 2.83
578 856 7.474398 TGATGTGAGATTCTTGAAATCGATC 57.526 36.000 0.00 0.00 0.00 3.69
585 863 7.999679 ACAAACTTTGATGTGAGATTCTTGAA 58.000 30.769 8.55 0.00 0.00 2.69
623 901 1.774254 AGTGGTGATGTGGGTTTCTCA 59.226 47.619 0.00 0.00 0.00 3.27
633 911 2.039084 GTCTTCCTTGGAGTGGTGATGT 59.961 50.000 0.00 0.00 0.00 3.06
634 912 2.038952 TGTCTTCCTTGGAGTGGTGATG 59.961 50.000 0.00 0.00 0.00 3.07
636 914 1.694150 CTGTCTTCCTTGGAGTGGTGA 59.306 52.381 0.00 0.00 0.00 4.02
637 915 1.271054 CCTGTCTTCCTTGGAGTGGTG 60.271 57.143 0.00 0.00 0.00 4.17
638 916 1.059913 CCTGTCTTCCTTGGAGTGGT 58.940 55.000 0.00 0.00 0.00 4.16
639 917 1.352083 TCCTGTCTTCCTTGGAGTGG 58.648 55.000 0.00 0.00 0.00 4.00
640 918 3.710209 ATTCCTGTCTTCCTTGGAGTG 57.290 47.619 0.00 0.00 0.00 3.51
641 919 4.401925 CAAATTCCTGTCTTCCTTGGAGT 58.598 43.478 0.00 0.00 0.00 3.85
643 921 3.157087 GCAAATTCCTGTCTTCCTTGGA 58.843 45.455 0.00 0.00 0.00 3.53
644 922 2.095059 CGCAAATTCCTGTCTTCCTTGG 60.095 50.000 0.00 0.00 0.00 3.61
646 924 1.541588 GCGCAAATTCCTGTCTTCCTT 59.458 47.619 0.30 0.00 0.00 3.36
653 933 0.804989 GCTACTGCGCAAATTCCTGT 59.195 50.000 13.05 6.48 0.00 4.00
656 936 1.086696 TGAGCTACTGCGCAAATTCC 58.913 50.000 13.05 0.00 45.49 3.01
673 953 5.302059 TGTTTGTTGGGACGGATTAAAATGA 59.698 36.000 0.00 0.00 0.00 2.57
690 970 5.269505 TCCGATCATTTGGTTTGTTTGTT 57.730 34.783 0.00 0.00 0.00 2.83
692 972 3.674753 GCTCCGATCATTTGGTTTGTTTG 59.325 43.478 0.00 0.00 0.00 2.93
693 973 3.573967 AGCTCCGATCATTTGGTTTGTTT 59.426 39.130 0.00 0.00 0.00 2.83
696 976 2.749076 TGAGCTCCGATCATTTGGTTTG 59.251 45.455 12.15 0.00 0.00 2.93
697 977 3.071874 TGAGCTCCGATCATTTGGTTT 57.928 42.857 12.15 0.00 0.00 3.27
698 978 2.787473 TGAGCTCCGATCATTTGGTT 57.213 45.000 12.15 0.00 0.00 3.67
699 979 2.787473 TTGAGCTCCGATCATTTGGT 57.213 45.000 12.15 0.00 0.00 3.67
700 980 3.691118 TCTTTTGAGCTCCGATCATTTGG 59.309 43.478 12.15 0.00 0.00 3.28
711 991 4.795970 TTCGAGTTTGTCTTTTGAGCTC 57.204 40.909 6.82 6.82 0.00 4.09
715 995 6.526674 GCTTCTTTTTCGAGTTTGTCTTTTGA 59.473 34.615 0.00 0.00 0.00 2.69
724 1004 3.627577 TGCTCTGCTTCTTTTTCGAGTTT 59.372 39.130 0.00 0.00 0.00 2.66
736 1016 1.673665 CAGGGTGGTGCTCTGCTTC 60.674 63.158 0.00 0.00 39.10 3.86
753 1035 4.515567 CACTCCGACTAGTAGATATGTGCA 59.484 45.833 3.59 0.00 0.00 4.57
754 1036 4.083217 CCACTCCGACTAGTAGATATGTGC 60.083 50.000 3.59 0.00 0.00 4.57
755 1037 5.306394 TCCACTCCGACTAGTAGATATGTG 58.694 45.833 3.59 5.65 0.00 3.21
764 1046 0.966370 GTGCCTCCACTCCGACTAGT 60.966 60.000 0.00 0.00 38.93 2.57
850 1151 1.061546 ACGCCTTTCTTTCCCCACTA 58.938 50.000 0.00 0.00 0.00 2.74
879 1180 2.167693 TCAAGAACACGTCAGGTTCACT 59.832 45.455 16.69 3.86 45.45 3.41
880 1181 2.546778 TCAAGAACACGTCAGGTTCAC 58.453 47.619 16.69 0.00 45.45 3.18
1027 1330 0.890683 GAGTGGCTGTGGAAAATGGG 59.109 55.000 0.00 0.00 0.00 4.00
1128 1431 2.618709 GACGGGCAATATTTCCTTGAGG 59.381 50.000 4.07 0.00 0.00 3.86
1166 1469 2.871096 TCCAGGGAACAATGGTGTAC 57.129 50.000 0.00 0.00 36.80 2.90
1204 1507 3.871594 AGAAAGAAATACCTGGAATCGCG 59.128 43.478 0.00 0.00 0.00 5.87
1240 1546 5.659463 AGAAATCTCCTGAATTCAGAGACG 58.341 41.667 32.49 17.84 46.59 4.18
1254 1560 6.422400 CGGAAGATACTTGCTTAGAAATCTCC 59.578 42.308 0.00 0.00 32.61 3.71
1275 1581 0.768622 ACCCACCTCATGAAACGGAA 59.231 50.000 6.49 0.00 0.00 4.30
1276 1582 1.646912 TACCCACCTCATGAAACGGA 58.353 50.000 6.49 0.00 0.00 4.69
1277 1583 2.561569 GATACCCACCTCATGAAACGG 58.438 52.381 0.00 0.00 0.00 4.44
1278 1584 2.170607 AGGATACCCACCTCATGAAACG 59.829 50.000 0.00 0.00 31.43 3.60
1279 1585 3.933861 AGGATACCCACCTCATGAAAC 57.066 47.619 0.00 0.00 31.43 2.78
1280 1586 3.591527 ACAAGGATACCCACCTCATGAAA 59.408 43.478 0.00 0.00 36.67 2.69
1281 1587 3.189606 ACAAGGATACCCACCTCATGAA 58.810 45.455 0.00 0.00 36.67 2.57
1282 1588 2.845659 ACAAGGATACCCACCTCATGA 58.154 47.619 0.00 0.00 36.67 3.07
1283 1589 3.652057 AACAAGGATACCCACCTCATG 57.348 47.619 0.00 0.00 36.67 3.07
1284 1590 3.852578 AGAAACAAGGATACCCACCTCAT 59.147 43.478 0.00 0.00 36.67 2.90
1285 1591 3.009033 CAGAAACAAGGATACCCACCTCA 59.991 47.826 0.00 0.00 36.67 3.86
1286 1592 3.263425 TCAGAAACAAGGATACCCACCTC 59.737 47.826 0.00 0.00 36.67 3.85
1287 1593 3.256704 TCAGAAACAAGGATACCCACCT 58.743 45.455 0.00 0.00 39.69 4.00
1288 1594 3.713826 TCAGAAACAAGGATACCCACC 57.286 47.619 0.00 0.00 33.88 4.61
1289 1595 6.208599 TCAATTTCAGAAACAAGGATACCCAC 59.791 38.462 0.00 0.00 33.88 4.61
1290 1596 6.310941 TCAATTTCAGAAACAAGGATACCCA 58.689 36.000 0.00 0.00 33.88 4.51
1291 1597 6.834168 TCAATTTCAGAAACAAGGATACCC 57.166 37.500 0.00 0.00 37.17 3.69
1292 1598 7.698130 CGAATCAATTTCAGAAACAAGGATACC 59.302 37.037 0.00 0.00 33.66 2.73
1293 1599 8.450964 TCGAATCAATTTCAGAAACAAGGATAC 58.549 33.333 0.00 0.00 33.66 2.24
1294 1600 8.560355 TCGAATCAATTTCAGAAACAAGGATA 57.440 30.769 0.00 0.00 33.66 2.59
1295 1601 7.452880 TCGAATCAATTTCAGAAACAAGGAT 57.547 32.000 0.00 0.00 33.66 3.24
1296 1602 6.875948 TCGAATCAATTTCAGAAACAAGGA 57.124 33.333 0.00 0.00 33.66 3.36
1297 1603 7.096065 GGTTTCGAATCAATTTCAGAAACAAGG 60.096 37.037 22.03 0.00 46.05 3.61
1322 1628 3.550437 ATCCTGAAAAGTCATCGGAGG 57.450 47.619 0.00 0.00 31.85 4.30
1323 1629 4.141937 TGGTATCCTGAAAAGTCATCGGAG 60.142 45.833 0.00 0.00 31.85 4.63
1424 1739 2.093658 TGGAATAGACCGACCTTTCAGC 60.094 50.000 0.00 0.00 0.00 4.26
1434 1749 1.493022 TGGGGGAAATGGAATAGACCG 59.507 52.381 0.00 0.00 0.00 4.79
1449 1764 2.356135 CAGACGTAATCACTTTGGGGG 58.644 52.381 0.00 0.00 0.00 5.40
1502 1817 0.842635 AATCATGGGAGCAGGACCTC 59.157 55.000 0.00 0.00 0.00 3.85
1504 1819 0.466922 CCAATCATGGGAGCAGGACC 60.467 60.000 0.00 0.00 43.51 4.46
1527 1842 3.002791 GTGATCCATGTATGTATGGCGG 58.997 50.000 5.43 0.00 45.83 6.13
1553 1868 6.142817 AGAATCAATTGTGAGCAAACGTTAC 58.857 36.000 0.00 0.00 37.14 2.50
1566 1881 2.557924 TGCCGCTGAAAGAATCAATTGT 59.442 40.909 5.13 0.00 37.67 2.71
1607 1922 1.923395 ATCTTTCCCCGGCAGTGGA 60.923 57.895 0.00 0.00 0.00 4.02
1608 1923 1.750399 CATCTTTCCCCGGCAGTGG 60.750 63.158 0.00 0.00 0.00 4.00
1609 1924 2.409870 GCATCTTTCCCCGGCAGTG 61.410 63.158 0.00 0.00 0.00 3.66
1610 1925 2.044946 GCATCTTTCCCCGGCAGT 60.045 61.111 0.00 0.00 0.00 4.40
1611 1926 3.204827 CGCATCTTTCCCCGGCAG 61.205 66.667 0.00 0.00 0.00 4.85
1668 1983 1.437986 CGACCGAGGAGGGTTGATC 59.562 63.158 0.00 0.00 46.96 2.92
1718 2064 6.989169 AGGATTTCTAGCAAGTGATGACATAC 59.011 38.462 0.00 0.00 0.00 2.39
1820 2166 5.359194 TTCAGATGATCCTTACCTTCACC 57.641 43.478 0.00 0.00 0.00 4.02
1855 2201 0.884514 TCTGTCTGTCTCTTGCCTCG 59.115 55.000 0.00 0.00 0.00 4.63
1888 2234 9.781633 AAATTTGGATTTTGAAATGATCACTCA 57.218 25.926 0.00 0.78 37.92 3.41
1890 2236 9.563748 ACAAATTTGGATTTTGAAATGATCACT 57.436 25.926 21.74 0.00 37.92 3.41
1892 2238 8.291032 GCACAAATTTGGATTTTGAAATGATCA 58.709 29.630 21.74 0.00 33.25 2.92
1938 2312 8.954350 CCTGAAACAGAGAAATTAACTGATCAT 58.046 33.333 0.00 0.00 34.08 2.45
1943 2317 6.486657 TCCACCTGAAACAGAGAAATTAACTG 59.513 38.462 0.00 0.00 37.62 3.16
1944 2318 6.486993 GTCCACCTGAAACAGAGAAATTAACT 59.513 38.462 0.00 0.00 32.44 2.24
1945 2319 6.262273 TGTCCACCTGAAACAGAGAAATTAAC 59.738 38.462 0.00 0.00 32.44 2.01
1946 2320 6.361433 TGTCCACCTGAAACAGAGAAATTAA 58.639 36.000 0.00 0.00 32.44 1.40
1947 2321 5.935945 TGTCCACCTGAAACAGAGAAATTA 58.064 37.500 0.00 0.00 32.44 1.40
1948 2322 4.792068 TGTCCACCTGAAACAGAGAAATT 58.208 39.130 0.00 0.00 32.44 1.82
1949 2323 4.392940 CTGTCCACCTGAAACAGAGAAAT 58.607 43.478 0.00 0.00 42.37 2.17
1950 2324 3.808728 CTGTCCACCTGAAACAGAGAAA 58.191 45.455 0.00 0.00 42.37 2.52
1951 2325 2.485479 GCTGTCCACCTGAAACAGAGAA 60.485 50.000 5.95 0.00 42.37 2.87
1952 2326 1.070758 GCTGTCCACCTGAAACAGAGA 59.929 52.381 5.95 0.00 42.37 3.10
1953 2327 1.202687 TGCTGTCCACCTGAAACAGAG 60.203 52.381 5.95 0.00 42.37 3.35
1954 2328 0.836606 TGCTGTCCACCTGAAACAGA 59.163 50.000 5.95 0.00 42.37 3.41
1955 2329 1.538512 CATGCTGTCCACCTGAAACAG 59.461 52.381 0.00 0.00 42.59 3.16
1956 2330 1.142667 TCATGCTGTCCACCTGAAACA 59.857 47.619 0.00 0.00 0.00 2.83
1961 2335 1.538512 CTTGTTCATGCTGTCCACCTG 59.461 52.381 0.00 0.00 0.00 4.00
2036 2410 1.920574 CGAGGTGATGTACGCTTTCAG 59.079 52.381 0.00 0.00 0.00 3.02
2114 2488 8.609483 AGTTGGAGTAATGATGCTATATGGAAT 58.391 33.333 0.00 0.00 0.00 3.01
2122 2496 9.461312 ACAATTTAAGTTGGAGTAATGATGCTA 57.539 29.630 14.38 0.00 33.40 3.49
2145 2519 1.106351 ATTGCAAGGCCGTGTGACAA 61.106 50.000 20.23 15.29 0.00 3.18
2149 2523 0.387622 CTCAATTGCAAGGCCGTGTG 60.388 55.000 20.23 10.34 0.00 3.82
2162 2536 6.435430 TTTGTCGCAATATACAGCTCAATT 57.565 33.333 0.00 0.00 0.00 2.32
2223 2598 2.611518 GTCTTCTCATCGGTCACCTTG 58.388 52.381 0.00 0.00 0.00 3.61
2251 2626 6.945435 TGGAATTTGCAAACCTTCTCTATGTA 59.055 34.615 15.41 0.00 0.00 2.29
2256 2631 5.305128 TGATTGGAATTTGCAAACCTTCTCT 59.695 36.000 15.41 4.72 29.75 3.10
2454 2830 2.100991 CGAATTGCTGCCCTTCGC 59.899 61.111 16.89 0.00 35.85 4.70
2960 3336 4.269523 AACAGCAGCTTGGGCCGA 62.270 61.111 0.00 0.00 39.73 5.54
3041 3417 3.792053 CTGGACGCCGTAGATGCCC 62.792 68.421 0.00 0.00 0.00 5.36
3110 3486 0.606673 GGCACTTGGTCACCTTCTCC 60.607 60.000 0.00 0.00 0.00 3.71
3155 3531 4.394712 GTGCCACCCACCTCGGAG 62.395 72.222 0.00 0.00 38.55 4.63
3170 3546 0.940126 AAGCGAGTTCTGTTGCTGTG 59.060 50.000 0.00 0.00 37.25 3.66
3187 3564 1.401670 CCGTCGACCAGAGAACTGAAG 60.402 57.143 10.58 0.00 46.03 3.02
3577 3955 0.458669 GGTAAGGATCAGCGACGGAA 59.541 55.000 0.00 0.00 0.00 4.30
3585 3963 2.933495 TTCACGACGGTAAGGATCAG 57.067 50.000 0.00 0.00 0.00 2.90
3586 3964 3.663995 TTTTCACGACGGTAAGGATCA 57.336 42.857 0.00 0.00 0.00 2.92
3587 3965 4.390909 ACAATTTTCACGACGGTAAGGATC 59.609 41.667 0.00 0.00 0.00 3.36
3588 3966 4.320870 ACAATTTTCACGACGGTAAGGAT 58.679 39.130 0.00 0.00 0.00 3.24
3589 3967 3.731089 ACAATTTTCACGACGGTAAGGA 58.269 40.909 0.00 0.00 0.00 3.36
3590 3968 4.215965 CAACAATTTTCACGACGGTAAGG 58.784 43.478 0.00 0.00 0.00 2.69
3591 3969 4.839796 ACAACAATTTTCACGACGGTAAG 58.160 39.130 0.00 0.00 0.00 2.34
3592 3970 4.879104 ACAACAATTTTCACGACGGTAA 57.121 36.364 0.00 0.00 0.00 2.85
3593 3971 5.980698 TTACAACAATTTTCACGACGGTA 57.019 34.783 0.00 0.00 0.00 4.02
3594 3972 4.879104 TTACAACAATTTTCACGACGGT 57.121 36.364 0.00 0.00 0.00 4.83
3595 3973 6.345408 CCATTTTACAACAATTTTCACGACGG 60.345 38.462 0.00 0.00 0.00 4.79
3596 3974 6.568057 CCATTTTACAACAATTTTCACGACG 58.432 36.000 0.00 0.00 0.00 5.12
3597 3975 6.351749 GCCATTTTACAACAATTTTCACGAC 58.648 36.000 0.00 0.00 0.00 4.34
3598 3976 5.463724 GGCCATTTTACAACAATTTTCACGA 59.536 36.000 0.00 0.00 0.00 4.35
3599 3977 5.235186 TGGCCATTTTACAACAATTTTCACG 59.765 36.000 0.00 0.00 0.00 4.35
3600 3978 6.037610 TGTGGCCATTTTACAACAATTTTCAC 59.962 34.615 9.72 0.00 0.00 3.18
3603 3981 5.008514 GCTGTGGCCATTTTACAACAATTTT 59.991 36.000 9.72 0.00 0.00 1.82
3623 4001 3.478509 CCATACGGACTACTCTAGCTGT 58.521 50.000 0.00 0.00 0.00 4.40
3626 4004 2.226912 CTGCCATACGGACTACTCTAGC 59.773 54.545 0.00 0.00 0.00 3.42
3638 4016 0.391661 ACACCAAGAGCTGCCATACG 60.392 55.000 0.00 0.00 0.00 3.06
3660 4041 7.201965 GGAAATGGGGAAACTTGTTAGAGAAAA 60.202 37.037 0.00 0.00 0.00 2.29
3664 4045 5.325239 AGGAAATGGGGAAACTTGTTAGAG 58.675 41.667 0.00 0.00 0.00 2.43
3667 4048 4.076394 CGAGGAAATGGGGAAACTTGTTA 58.924 43.478 0.00 0.00 0.00 2.41
3703 4085 6.056236 TCTCTCTCTTCGAAAGATTATCGGA 58.944 40.000 0.00 0.00 41.60 4.55
3709 4091 8.299990 TCCTTTATCTCTCTCTTCGAAAGATT 57.700 34.615 13.06 1.81 41.60 2.40
3811 4224 7.039993 GGAAATAAGAAAAGGTAGAAAGTGCCA 60.040 37.037 0.00 0.00 31.94 4.92
3814 4227 9.284968 TGAGGAAATAAGAAAAGGTAGAAAGTG 57.715 33.333 0.00 0.00 0.00 3.16
3842 4256 9.692325 AGATGCCCTTATATTCCATAGAAAATC 57.308 33.333 0.00 0.00 35.09 2.17
3847 4261 6.126940 GCTCAGATGCCCTTATATTCCATAGA 60.127 42.308 0.00 0.00 0.00 1.98
3848 4262 6.054295 GCTCAGATGCCCTTATATTCCATAG 58.946 44.000 0.00 0.00 0.00 2.23
3850 4264 4.290459 TGCTCAGATGCCCTTATATTCCAT 59.710 41.667 0.00 0.00 0.00 3.41
3893 4307 6.292488 CGTGACCGTGAAAACTTACTAAATGT 60.292 38.462 0.00 0.00 0.00 2.71
3899 4313 2.159057 ACCGTGACCGTGAAAACTTACT 60.159 45.455 0.00 0.00 0.00 2.24
3916 4330 2.571216 CCGTGAGAAGGTCCACCGT 61.571 63.158 0.00 0.00 42.08 4.83
3918 4332 0.971386 TAACCGTGAGAAGGTCCACC 59.029 55.000 0.00 0.00 41.95 4.61
4012 4426 5.541868 TGTCTTCCAAGAAAAATATGGCCAA 59.458 36.000 10.96 0.00 36.68 4.52
4014 4428 5.659440 TGTCTTCCAAGAAAAATATGGCC 57.341 39.130 0.00 0.00 36.68 5.36
4020 4434 5.549742 TGCCAATGTCTTCCAAGAAAAAT 57.450 34.783 0.00 0.00 36.68 1.82
4023 4437 5.549742 AATTGCCAATGTCTTCCAAGAAA 57.450 34.783 0.00 0.00 36.68 2.52
4036 4450 2.158726 GCATCCCCATCAAATTGCCAAT 60.159 45.455 0.00 0.00 0.00 3.16
4056 4470 2.307934 TTTTCTTGGCCTTGTGTTGC 57.692 45.000 3.32 0.00 0.00 4.17
4058 4474 6.670695 AGATATTTTTCTTGGCCTTGTGTT 57.329 33.333 3.32 0.00 0.00 3.32
4108 4536 8.761575 TGGTTGAATAATGATTTTTCTCTTGC 57.238 30.769 9.23 0.00 0.00 4.01
4158 4590 4.341487 AGTTAACATACTTTTCCCTGCCC 58.659 43.478 8.61 0.00 0.00 5.36
4161 4593 8.683615 GGGAAATAGTTAACATACTTTTCCCTG 58.316 37.037 27.89 0.00 46.23 4.45
4244 4678 0.390472 GGTCTGCTTCTCCTTCCACG 60.390 60.000 0.00 0.00 0.00 4.94
4248 4682 0.687354 TGTGGGTCTGCTTCTCCTTC 59.313 55.000 0.00 0.00 0.00 3.46
4260 4694 4.504858 ACTAGAATTTCGACATGTGGGTC 58.495 43.478 1.15 0.00 34.42 4.46
4266 4700 7.463544 TGTGCATTTACTAGAATTTCGACATG 58.536 34.615 0.00 0.00 0.00 3.21
4303 4737 8.874816 GCTCTCGAAGTATGTTCTAAAATTCTT 58.125 33.333 0.00 0.00 0.00 2.52
4331 4765 0.810648 TTTCATCGGTGGCATCTTGC 59.189 50.000 0.00 0.00 44.08 4.01
4361 4797 8.256611 TGCTCATGAAGTTAAGTCAATTCTAC 57.743 34.615 0.00 0.00 0.00 2.59
4389 4825 5.746245 CAGTAGTGAGGAAGATTAGAAAGCG 59.254 44.000 0.00 0.00 0.00 4.68
4412 4848 6.656270 ACATCATGCTCTTTTGTACTCATTCA 59.344 34.615 0.00 0.00 0.00 2.57
4447 4883 7.446001 TTTTGCAACAAAATCCTTCAGTTTT 57.554 28.000 0.00 0.00 0.00 2.43
4485 4925 8.630054 TGGTATAACACATGGGCTAATATTTC 57.370 34.615 0.00 0.00 0.00 2.17
4505 4945 4.863707 CGTGAGCATGGCTGGTAT 57.136 55.556 0.00 0.00 39.88 2.73
4545 4985 2.614057 GCTCTACTTTGCACACACAAGT 59.386 45.455 6.04 6.04 34.09 3.16
4558 4998 5.181748 GTGATCTTGTTGATGGCTCTACTT 58.818 41.667 0.00 0.00 35.14 2.24
4587 5027 3.055385 GCGGGGAATAGGCAATCTATACA 60.055 47.826 0.00 0.00 37.69 2.29
4597 5037 2.529744 ATCCAGGCGGGGAATAGGC 61.530 63.158 3.19 0.00 41.12 3.93
4619 5059 3.057526 GCCCCACTAAGTTGATTCAACAC 60.058 47.826 26.73 6.37 45.66 3.32
4717 5158 2.642807 CCCTTCCTTTGTCTTGAGGGTA 59.357 50.000 0.00 0.00 33.73 3.69
4721 5162 3.555966 ACAACCCTTCCTTTGTCTTGAG 58.444 45.455 0.00 0.00 29.75 3.02


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

AutoCloner maintained by Alex Coulton.