Multiple sequence alignment - TraesCS3B01G040800

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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 TraesCS3B01G040800 chr3B 100.000 2482 0 0 1 2482 20318983 20321464 0.000000e+00 4584.0
1 TraesCS3B01G040800 chr3B 81.747 641 49 31 1084 1708 20430806 20430218 8.030000e-130 473.0
2 TraesCS3B01G040800 chr3D 87.208 1243 46 54 628 1804 13964331 13965526 0.000000e+00 1310.0
3 TraesCS3B01G040800 chr3D 88.308 402 26 8 1077 1472 13989175 13988789 1.740000e-126 462.0
4 TraesCS3B01G040800 chr3D 83.158 285 24 17 1976 2256 13965951 13966215 3.190000e-59 239.0
5 TraesCS3B01G040800 chr3D 87.791 172 15 3 1811 1977 13965720 13965890 1.950000e-46 196.0
6 TraesCS3B01G040800 chr3D 92.683 123 4 2 441 558 13964161 13964283 3.280000e-39 172.0
7 TraesCS3B01G040800 chr3D 90.667 75 7 0 2250 2324 13966428 13966502 1.570000e-17 100.0
8 TraesCS3B01G040800 chr3A 82.160 1278 112 59 473 1681 22832210 22830980 0.000000e+00 990.0
9 TraesCS3B01G040800 chr3A 87.661 389 27 14 1090 1472 22786866 22787239 1.360000e-117 433.0
10 TraesCS3B01G040800 chr3A 87.778 270 25 7 1 268 22832654 22832391 2.400000e-80 309.0
11 TraesCS3B01G040800 chr2B 85.246 61 9 0 5 65 23730276 23730336 2.060000e-06 63.9


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 TraesCS3B01G040800 chr3B 20318983 20321464 2481 False 4584.0 4584 100.0000 1 2482 1 chr3B.!!$F1 2481
1 TraesCS3B01G040800 chr3B 20430218 20430806 588 True 473.0 473 81.7470 1084 1708 1 chr3B.!!$R1 624
2 TraesCS3B01G040800 chr3D 13964161 13966502 2341 False 403.4 1310 88.3014 441 2324 5 chr3D.!!$F1 1883
3 TraesCS3B01G040800 chr3A 22830980 22832654 1674 True 649.5 990 84.9690 1 1681 2 chr3A.!!$R1 1680

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
362 365 0.034059 AAGTGTCTGAAGAGTGCCGG 59.966 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 1926 0.398696 TAACCCTTCCATGTGCACGT 59.601 50.0 13.13 9.52 0.0 4.49 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
52 53 9.311916 CCTCATGAACAGTAAAAATCAAACAAA 57.688 29.630 0.00 0.00 0.00 2.83
167 170 2.693074 TGCTCTGGGAAAGGAACAAAAC 59.307 45.455 0.00 0.00 0.00 2.43
172 175 4.076394 CTGGGAAAGGAACAAAACCGATA 58.924 43.478 0.00 0.00 0.00 2.92
184 187 7.539710 GGAACAAAACCGATACTCCAAAAATAC 59.460 37.037 0.00 0.00 0.00 1.89
213 216 5.276440 TGAAGGTATGTTGGGGCATTATTT 58.724 37.500 0.00 0.00 0.00 1.40
215 218 5.612725 AGGTATGTTGGGGCATTATTTTG 57.387 39.130 0.00 0.00 0.00 2.44
218 221 6.670027 AGGTATGTTGGGGCATTATTTTGTTA 59.330 34.615 0.00 0.00 0.00 2.41
225 228 5.099575 GGGGCATTATTTTGTTACAGAACG 58.900 41.667 0.00 0.00 38.51 3.95
236 239 4.624015 TGTTACAGAACGTTAGGAAGGTG 58.376 43.478 0.00 0.00 38.51 4.00
264 267 8.676454 TTTTACGGAAATTTGCACATATGTAC 57.324 30.769 8.32 3.18 0.00 2.90
265 268 5.888691 ACGGAAATTTGCACATATGTACA 57.111 34.783 8.32 6.32 0.00 2.90
266 269 6.260870 ACGGAAATTTGCACATATGTACAA 57.739 33.333 16.03 16.03 30.07 2.41
267 270 6.682746 ACGGAAATTTGCACATATGTACAAA 58.317 32.000 28.04 28.04 43.11 2.83
268 271 7.148641 ACGGAAATTTGCACATATGTACAAAA 58.851 30.769 29.06 19.61 42.48 2.44
269 272 7.816995 ACGGAAATTTGCACATATGTACAAAAT 59.183 29.630 29.06 21.78 42.48 1.82
270 273 8.655092 CGGAAATTTGCACATATGTACAAAATT 58.345 29.630 29.06 26.93 42.48 1.82
275 278 7.559835 TTGCACATATGTACAAAATTTGTCG 57.440 32.000 17.37 1.47 44.12 4.35
276 279 6.903419 TGCACATATGTACAAAATTTGTCGA 58.097 32.000 15.22 3.51 44.12 4.20
277 280 7.534282 TGCACATATGTACAAAATTTGTCGAT 58.466 30.769 15.22 10.52 44.12 3.59
278 281 7.484324 TGCACATATGTACAAAATTTGTCGATG 59.516 33.333 15.22 14.99 44.12 3.84
279 282 7.484641 GCACATATGTACAAAATTTGTCGATGT 59.515 33.333 15.22 15.53 44.12 3.06
280 283 9.340695 CACATATGTACAAAATTTGTCGATGTT 57.659 29.630 15.22 4.01 44.12 2.71
281 284 9.906660 ACATATGTACAAAATTTGTCGATGTTT 57.093 25.926 15.22 0.00 44.12 2.83
283 286 9.906660 ATATGTACAAAATTTGTCGATGTTTGT 57.093 25.926 15.22 14.78 44.12 2.83
284 287 8.641499 ATGTACAAAATTTGTCGATGTTTGTT 57.359 26.923 15.22 0.00 44.12 2.83
285 288 7.889745 TGTACAAAATTTGTCGATGTTTGTTG 58.110 30.769 15.22 8.09 44.12 3.33
286 289 5.794720 ACAAAATTTGTCGATGTTTGTTGC 58.205 33.333 5.41 0.00 40.56 4.17
287 290 5.196825 CAAAATTTGTCGATGTTTGTTGCC 58.803 37.500 0.00 0.00 0.00 4.52
288 291 3.724508 ATTTGTCGATGTTTGTTGCCA 57.275 38.095 0.00 0.00 0.00 4.92
359 362 5.931441 AATTACAAGTGTCTGAAGAGTGC 57.069 39.130 0.00 0.00 0.00 4.40
360 363 2.246719 ACAAGTGTCTGAAGAGTGCC 57.753 50.000 0.00 0.00 0.00 5.01
362 365 0.034059 AAGTGTCTGAAGAGTGCCGG 59.966 55.000 0.00 0.00 0.00 6.13
363 366 1.374758 GTGTCTGAAGAGTGCCGGG 60.375 63.158 2.18 0.00 0.00 5.73
364 367 1.837051 TGTCTGAAGAGTGCCGGGT 60.837 57.895 2.18 0.00 0.00 5.28
367 370 0.251653 TCTGAAGAGTGCCGGGTACT 60.252 55.000 18.15 18.15 0.00 2.73
368 371 0.173708 CTGAAGAGTGCCGGGTACTC 59.826 60.000 30.75 30.75 43.73 2.59
369 372 1.255667 TGAAGAGTGCCGGGTACTCC 61.256 60.000 32.99 22.47 44.30 3.85
370 373 1.957765 GAAGAGTGCCGGGTACTCCC 61.958 65.000 32.99 23.87 44.30 4.30
391 394 3.981211 CATTTTCTGGAGTGGTTGGTTG 58.019 45.455 0.00 0.00 0.00 3.77
392 395 2.065899 TTTCTGGAGTGGTTGGTTGG 57.934 50.000 0.00 0.00 0.00 3.77
393 396 0.184933 TTCTGGAGTGGTTGGTTGGG 59.815 55.000 0.00 0.00 0.00 4.12
398 401 1.173913 GAGTGGTTGGTTGGGTATGC 58.826 55.000 0.00 0.00 0.00 3.14
407 410 3.687125 TGGTTGGGTATGCATTTTACGA 58.313 40.909 3.54 0.00 0.00 3.43
424 427 0.803768 CGATGTCTGAAGAGTGCCGG 60.804 60.000 0.00 0.00 0.00 6.13
434 437 0.395448 AGAGTGCCGGGTACTCCTAC 60.395 60.000 32.99 15.65 44.30 3.18
436 439 1.683365 GTGCCGGGTACTCCTACCA 60.683 63.158 8.11 0.00 44.18 3.25
458 496 7.945134 ACCATTTTGTATGATTAAGGAGATGC 58.055 34.615 0.00 0.00 0.00 3.91
520 563 0.748005 AAACTGCAGACGGTTGTGCT 60.748 50.000 23.35 0.00 44.83 4.40
558 601 3.512680 CGAAGTTGGAGAGCTATTCGTT 58.487 45.455 0.00 0.00 35.91 3.85
564 607 2.771943 TGGAGAGCTATTCGTTGGGAAT 59.228 45.455 0.00 0.00 46.86 3.01
580 623 1.298859 GAATCACTGGTGGGCACGAC 61.299 60.000 0.00 0.00 35.92 4.34
586 629 3.343421 GGTGGGCACGACGAACAC 61.343 66.667 0.00 4.73 38.18 3.32
592 635 4.679690 CACGACGAACACGCGTGC 62.680 66.667 37.35 21.78 45.72 5.34
611 659 1.289109 CGCGGTCGACCATGAAGTTT 61.289 55.000 32.80 0.00 38.10 2.66
614 662 2.139917 CGGTCGACCATGAAGTTTTGA 58.860 47.619 32.80 0.00 35.14 2.69
615 663 2.742053 CGGTCGACCATGAAGTTTTGAT 59.258 45.455 32.80 0.00 35.14 2.57
616 664 3.188460 CGGTCGACCATGAAGTTTTGATT 59.812 43.478 32.80 0.00 35.14 2.57
617 665 4.669197 CGGTCGACCATGAAGTTTTGATTC 60.669 45.833 32.80 0.99 35.14 2.52
619 667 5.106157 GGTCGACCATGAAGTTTTGATTCAT 60.106 40.000 29.75 0.00 45.88 2.57
626 674 4.801891 TGAAGTTTTGATTCATGCAGAGC 58.198 39.130 0.00 0.00 31.86 4.09
632 693 1.003928 TGATTCATGCAGAGCACCACT 59.996 47.619 0.00 0.00 43.04 4.00
649 710 2.506865 CACTCGACTACACGATGACAC 58.493 52.381 0.00 0.00 41.39 3.67
665 726 3.123050 TGACACACACTGACAATTCTCG 58.877 45.455 0.00 0.00 0.00 4.04
666 727 3.181480 TGACACACACTGACAATTCTCGA 60.181 43.478 0.00 0.00 0.00 4.04
701 762 0.096976 CGTGTGATGTTTCGGGCATC 59.903 55.000 7.49 7.49 42.10 3.91
702 763 0.451783 GTGTGATGTTTCGGGCATCC 59.548 55.000 10.57 5.13 41.32 3.51
713 776 0.811281 CGGGCATCCTTGAAAGTTCC 59.189 55.000 0.00 0.00 0.00 3.62
717 780 2.827921 GGCATCCTTGAAAGTTCCACAT 59.172 45.455 0.00 0.00 0.00 3.21
727 790 6.618287 TGAAAGTTCCACATCTACAAACAG 57.382 37.500 0.00 0.00 0.00 3.16
768 851 1.794222 CGCAATTCTCGTTGGGTCC 59.206 57.895 0.00 0.00 37.29 4.46
796 879 2.355837 CACCTGCAGTGCGTACGT 60.356 61.111 17.90 0.00 40.28 3.57
797 880 1.081041 CACCTGCAGTGCGTACGTA 60.081 57.895 17.90 10.06 40.28 3.57
798 881 1.071019 CACCTGCAGTGCGTACGTAG 61.071 60.000 17.90 2.49 40.28 3.51
799 882 2.158959 CCTGCAGTGCGTACGTAGC 61.159 63.158 17.90 13.50 0.00 3.58
800 883 2.126228 TGCAGTGCGTACGTAGCC 60.126 61.111 17.90 1.14 0.00 3.93
801 884 2.126228 GCAGTGCGTACGTAGCCA 60.126 61.111 17.90 2.92 0.00 4.75
802 885 2.158959 GCAGTGCGTACGTAGCCAG 61.159 63.158 17.90 3.70 0.00 4.85
803 886 1.211969 CAGTGCGTACGTAGCCAGT 59.788 57.895 17.90 6.14 0.00 4.00
804 887 1.071019 CAGTGCGTACGTAGCCAGTG 61.071 60.000 17.90 14.45 0.00 3.66
805 888 2.126228 TGCGTACGTAGCCAGTGC 60.126 61.111 17.90 0.00 37.95 4.40
807 890 3.245315 CGTACGTAGCCAGTGCGC 61.245 66.667 7.22 0.00 44.33 6.09
808 891 3.245315 GTACGTAGCCAGTGCGCG 61.245 66.667 0.00 0.00 44.33 6.86
810 893 2.397754 TACGTAGCCAGTGCGCGTA 61.398 57.895 8.43 0.00 46.32 4.42
811 894 2.582202 TACGTAGCCAGTGCGCGTAC 62.582 60.000 20.26 20.26 46.32 3.67
812 895 3.245315 GTAGCCAGTGCGCGTACG 61.245 66.667 21.51 11.84 44.33 3.67
813 896 3.740397 TAGCCAGTGCGCGTACGT 61.740 61.111 21.51 10.27 44.33 3.57
936 1020 5.607119 TTTCACCGCTCTCTAAATTGTTC 57.393 39.130 0.00 0.00 0.00 3.18
1055 1146 1.809567 GCTCACCCACCAAGCAAAGG 61.810 60.000 0.00 0.00 36.06 3.11
1494 1639 1.104577 AGCCTAGAGTAGAGCCGCAC 61.105 60.000 0.00 0.00 0.00 5.34
1495 1640 1.649815 CCTAGAGTAGAGCCGCACG 59.350 63.158 0.00 0.00 0.00 5.34
1497 1642 0.814410 CTAGAGTAGAGCCGCACGGA 60.814 60.000 14.43 0.00 37.50 4.69
1498 1643 0.179026 TAGAGTAGAGCCGCACGGAT 60.179 55.000 14.43 6.35 37.50 4.18
1594 1747 4.148825 GGCGGCGACACTCTCCAT 62.149 66.667 12.98 0.00 0.00 3.41
1595 1748 2.887568 GCGGCGACACTCTCCATG 60.888 66.667 12.98 0.00 0.00 3.66
1596 1749 2.887568 CGGCGACACTCTCCATGC 60.888 66.667 0.00 0.00 0.00 4.06
1699 1867 7.447853 AGTGGTAATTCGGTATGTTTAAACCAA 59.552 33.333 15.59 0.90 35.24 3.67
1705 1873 9.849166 AATTCGGTATGTTTAAACCAACATTAG 57.151 29.630 15.59 6.79 43.54 1.73
1793 1970 4.142708 TGCTGTACCGTTGCTTCATTATTG 60.143 41.667 0.00 0.00 0.00 1.90
1804 1981 3.777478 CTTCATTATTGGTGCCTGCTTG 58.223 45.455 0.00 0.00 0.00 4.01
1805 1982 3.084536 TCATTATTGGTGCCTGCTTGA 57.915 42.857 0.00 0.00 0.00 3.02
1806 1983 2.754552 TCATTATTGGTGCCTGCTTGAC 59.245 45.455 0.00 0.00 0.00 3.18
1807 1984 2.584835 TTATTGGTGCCTGCTTGACT 57.415 45.000 0.00 0.00 0.00 3.41
1808 1985 2.113860 TATTGGTGCCTGCTTGACTC 57.886 50.000 0.00 0.00 0.00 3.36
1809 1986 0.111061 ATTGGTGCCTGCTTGACTCA 59.889 50.000 0.00 0.00 0.00 3.41
1846 2210 5.335976 GCTTAATCACAGCCCTATTATTGCC 60.336 44.000 0.00 0.00 0.00 4.52
1849 2213 4.183223 TCACAGCCCTATTATTGCCAAT 57.817 40.909 0.00 0.00 0.00 3.16
1894 2258 5.957842 TTTTTGGACGCTTGTATCTGAAT 57.042 34.783 0.00 0.00 0.00 2.57
1896 2260 5.957842 TTTGGACGCTTGTATCTGAATTT 57.042 34.783 0.00 0.00 0.00 1.82
1897 2261 5.957842 TTGGACGCTTGTATCTGAATTTT 57.042 34.783 0.00 0.00 0.00 1.82
1903 2272 5.123979 ACGCTTGTATCTGAATTTTCCTTCC 59.876 40.000 0.00 0.00 0.00 3.46
1908 2277 8.491045 TTGTATCTGAATTTTCCTTCCCTTTT 57.509 30.769 0.00 0.00 0.00 2.27
1916 2285 3.849563 TTCCTTCCCTTTTGAGACGAA 57.150 42.857 0.00 0.00 0.00 3.85
1925 2294 5.718130 TCCCTTTTGAGACGAATTAGTAGGA 59.282 40.000 4.93 0.00 0.00 2.94
1991 2379 8.287439 ACTCTCTAGGACAATAATATGGATCG 57.713 38.462 0.00 0.00 0.00 3.69
2009 2443 4.504514 GGATCGGGGGAGTAGTTTTTATCC 60.505 50.000 0.00 0.00 0.00 2.59
2022 2456 4.081476 AGTTTTTATCCCAAGGCTCAATGC 60.081 41.667 0.00 0.00 41.94 3.56
2025 2459 2.242882 ATCCCAAGGCTCAATGCTTT 57.757 45.000 0.00 0.00 41.89 3.51
2026 2460 2.897271 TCCCAAGGCTCAATGCTTTA 57.103 45.000 0.00 0.00 39.02 1.85
2060 2494 6.729690 AATTTGTGGTCCAATCTTTCTGAA 57.270 33.333 0.00 0.00 31.81 3.02
2063 2497 7.831691 TTTGTGGTCCAATCTTTCTGAATAA 57.168 32.000 0.00 0.00 31.81 1.40
2064 2498 6.817765 TGTGGTCCAATCTTTCTGAATAAC 57.182 37.500 0.00 0.00 0.00 1.89
2074 2508 3.306917 TTCTGAATAACCGACAGCGAA 57.693 42.857 0.00 0.00 40.82 4.70
2075 2509 2.876091 TCTGAATAACCGACAGCGAAG 58.124 47.619 0.00 0.00 40.82 3.79
2081 2515 2.228138 AACCGACAGCGAAGTAAACA 57.772 45.000 0.00 0.00 40.82 2.83
2084 2518 3.916761 ACCGACAGCGAAGTAAACAATA 58.083 40.909 0.00 0.00 40.82 1.90
2085 2519 4.501071 ACCGACAGCGAAGTAAACAATAT 58.499 39.130 0.00 0.00 40.82 1.28
2087 2521 4.025979 CCGACAGCGAAGTAAACAATATCC 60.026 45.833 0.00 0.00 40.82 2.59
2088 2522 4.804139 CGACAGCGAAGTAAACAATATCCT 59.196 41.667 0.00 0.00 40.82 3.24
2089 2523 5.975344 CGACAGCGAAGTAAACAATATCCTA 59.025 40.000 0.00 0.00 40.82 2.94
2090 2524 6.074994 CGACAGCGAAGTAAACAATATCCTAC 60.075 42.308 0.00 0.00 40.82 3.18
2091 2525 6.636705 ACAGCGAAGTAAACAATATCCTACA 58.363 36.000 0.00 0.00 0.00 2.74
2092 2526 7.101054 ACAGCGAAGTAAACAATATCCTACAA 58.899 34.615 0.00 0.00 0.00 2.41
2095 2529 7.822822 AGCGAAGTAAACAATATCCTACAAACT 59.177 33.333 0.00 0.00 0.00 2.66
2097 2531 9.755064 CGAAGTAAACAATATCCTACAAACTTG 57.245 33.333 0.00 0.00 0.00 3.16
2098 2532 9.556030 GAAGTAAACAATATCCTACAAACTTGC 57.444 33.333 0.00 0.00 0.00 4.01
2099 2533 8.863872 AGTAAACAATATCCTACAAACTTGCT 57.136 30.769 0.00 0.00 0.00 3.91
2100 2534 8.947115 AGTAAACAATATCCTACAAACTTGCTC 58.053 33.333 0.00 0.00 0.00 4.26
2101 2535 8.947115 GTAAACAATATCCTACAAACTTGCTCT 58.053 33.333 0.00 0.00 0.00 4.09
2102 2536 8.409358 AAACAATATCCTACAAACTTGCTCTT 57.591 30.769 0.00 0.00 0.00 2.85
2103 2537 7.617041 ACAATATCCTACAAACTTGCTCTTC 57.383 36.000 0.00 0.00 0.00 2.87
2104 2538 7.398024 ACAATATCCTACAAACTTGCTCTTCT 58.602 34.615 0.00 0.00 0.00 2.85
2105 2539 8.540388 ACAATATCCTACAAACTTGCTCTTCTA 58.460 33.333 0.00 0.00 0.00 2.10
2106 2540 8.821894 CAATATCCTACAAACTTGCTCTTCTAC 58.178 37.037 0.00 0.00 0.00 2.59
2107 2541 4.806330 TCCTACAAACTTGCTCTTCTACG 58.194 43.478 0.00 0.00 0.00 3.51
2108 2542 4.280174 TCCTACAAACTTGCTCTTCTACGT 59.720 41.667 0.00 0.00 0.00 3.57
2109 2543 5.474532 TCCTACAAACTTGCTCTTCTACGTA 59.525 40.000 0.00 0.00 0.00 3.57
2110 2544 5.572126 CCTACAAACTTGCTCTTCTACGTAC 59.428 44.000 0.00 0.00 0.00 3.67
2111 2545 4.304939 ACAAACTTGCTCTTCTACGTACC 58.695 43.478 0.00 0.00 0.00 3.34
2115 2549 5.211174 ACTTGCTCTTCTACGTACCTTTT 57.789 39.130 0.00 0.00 0.00 2.27
2117 2551 6.388278 ACTTGCTCTTCTACGTACCTTTTAG 58.612 40.000 0.00 0.00 0.00 1.85
2119 2553 6.579666 TGCTCTTCTACGTACCTTTTAGAA 57.420 37.500 0.00 0.00 32.26 2.10
2122 2556 7.597743 TGCTCTTCTACGTACCTTTTAGAAAAG 59.402 37.037 7.63 7.63 43.82 2.27
2137 2571 9.899226 CTTTTAGAAAAGGAAATAGAACACCAG 57.101 33.333 6.82 0.00 41.23 4.00
2141 2575 8.712228 AGAAAAGGAAATAGAACACCAGAATT 57.288 30.769 0.00 0.00 0.00 2.17
2142 2576 9.807921 AGAAAAGGAAATAGAACACCAGAATTA 57.192 29.630 0.00 0.00 0.00 1.40
2151 2585 6.727824 AGAACACCAGAATTAATTGACGAG 57.272 37.500 5.17 0.00 0.00 4.18
2158 2592 5.447818 CCAGAATTAATTGACGAGGACAAGC 60.448 44.000 5.17 0.00 0.00 4.01
2178 2612 5.649782 AGCTTGGTGGTCATCTTTATTTG 57.350 39.130 0.00 0.00 0.00 2.32
2200 2634 8.934023 TTTGTTGATATGTCCCTACTTTTTCT 57.066 30.769 0.00 0.00 0.00 2.52
2256 2690 2.437359 CCACAGCCCTGCTACTGC 60.437 66.667 0.00 0.00 36.40 4.40
2257 2691 2.437359 CACAGCCCTGCTACTGCC 60.437 66.667 0.00 0.00 36.40 4.85
2271 2924 1.649321 ACTGCCAGGTCTGAGATTGA 58.351 50.000 0.00 0.00 0.00 2.57
2279 2932 4.440880 CAGGTCTGAGATTGATGTCTTCC 58.559 47.826 0.00 0.00 0.00 3.46
2284 2937 4.405036 TCTGAGATTGATGTCTTCCTCCTG 59.595 45.833 0.00 0.00 0.00 3.86
2285 2938 4.356436 TGAGATTGATGTCTTCCTCCTGA 58.644 43.478 0.00 0.00 0.00 3.86
2316 2969 2.067414 ACGCGTTCTCCTTCTCTTTC 57.933 50.000 5.58 0.00 0.00 2.62
2324 2977 5.932303 CGTTCTCCTTCTCTTTCCACAATAA 59.068 40.000 0.00 0.00 0.00 1.40
2325 2978 6.595716 CGTTCTCCTTCTCTTTCCACAATAAT 59.404 38.462 0.00 0.00 0.00 1.28
2326 2979 7.764443 CGTTCTCCTTCTCTTTCCACAATAATA 59.236 37.037 0.00 0.00 0.00 0.98
2327 2980 9.449719 GTTCTCCTTCTCTTTCCACAATAATAA 57.550 33.333 0.00 0.00 0.00 1.40
2363 3016 8.826710 TCTGCTGAATTAAATAACCAATACTCG 58.173 33.333 0.00 0.00 0.00 4.18
2364 3017 7.925993 TGCTGAATTAAATAACCAATACTCGG 58.074 34.615 0.00 0.00 0.00 4.63
2365 3018 7.554835 TGCTGAATTAAATAACCAATACTCGGT 59.445 33.333 0.00 0.00 38.85 4.69
2366 3019 9.048446 GCTGAATTAAATAACCAATACTCGGTA 57.952 33.333 0.00 0.00 34.99 4.02
2385 3038 7.642586 ACTCGGTATAAAATTTTGAATTAGCGC 59.357 33.333 13.76 0.00 0.00 5.92
2386 3039 7.473366 TCGGTATAAAATTTTGAATTAGCGCA 58.527 30.769 11.47 0.00 0.00 6.09
2387 3040 7.642194 TCGGTATAAAATTTTGAATTAGCGCAG 59.358 33.333 11.47 0.00 0.00 5.18
2388 3041 7.431084 CGGTATAAAATTTTGAATTAGCGCAGT 59.569 33.333 11.47 0.00 0.00 4.40
2389 3042 8.531530 GGTATAAAATTTTGAATTAGCGCAGTG 58.468 33.333 11.47 0.00 0.00 3.66
2390 3043 9.072294 GTATAAAATTTTGAATTAGCGCAGTGT 57.928 29.630 11.47 0.00 0.00 3.55
2391 3044 6.843069 AAAATTTTGAATTAGCGCAGTGTT 57.157 29.167 11.47 0.00 0.00 3.32
2392 3045 6.843069 AAATTTTGAATTAGCGCAGTGTTT 57.157 29.167 11.47 0.00 0.00 2.83
2393 3046 6.843069 AATTTTGAATTAGCGCAGTGTTTT 57.157 29.167 11.47 0.00 0.00 2.43
2394 3047 5.633996 TTTTGAATTAGCGCAGTGTTTTG 57.366 34.783 11.47 0.00 0.00 2.44
2395 3048 3.980646 TGAATTAGCGCAGTGTTTTGT 57.019 38.095 11.47 0.00 0.00 2.83
2396 3049 3.884169 TGAATTAGCGCAGTGTTTTGTC 58.116 40.909 11.47 0.00 0.00 3.18
2397 3050 2.594529 ATTAGCGCAGTGTTTTGTCG 57.405 45.000 11.47 0.00 0.00 4.35
2398 3051 0.041663 TTAGCGCAGTGTTTTGTCGC 60.042 50.000 11.47 2.81 40.95 5.19
2399 3052 1.837538 TAGCGCAGTGTTTTGTCGCC 61.838 55.000 11.47 0.00 41.28 5.54
2400 3053 2.712539 CGCAGTGTTTTGTCGCCA 59.287 55.556 0.00 0.00 0.00 5.69
2401 3054 1.063327 CGCAGTGTTTTGTCGCCAA 59.937 52.632 0.00 0.00 0.00 4.52
2402 3055 0.524392 CGCAGTGTTTTGTCGCCAAA 60.524 50.000 0.00 0.00 38.77 3.28
2403 3056 1.634702 GCAGTGTTTTGTCGCCAAAA 58.365 45.000 0.00 0.00 45.76 2.44
2412 3065 4.653806 TTTGTCGCCAAAACAAAAACTG 57.346 36.364 0.00 0.00 42.09 3.16
2413 3066 2.611518 TGTCGCCAAAACAAAAACTGG 58.388 42.857 0.00 0.00 0.00 4.00
2414 3067 2.028930 TGTCGCCAAAACAAAAACTGGT 60.029 40.909 0.00 0.00 0.00 4.00
2415 3068 2.997303 GTCGCCAAAACAAAAACTGGTT 59.003 40.909 0.00 0.00 36.08 3.67
2416 3069 4.174762 GTCGCCAAAACAAAAACTGGTTA 58.825 39.130 0.00 0.00 32.08 2.85
2417 3070 4.626172 GTCGCCAAAACAAAAACTGGTTAA 59.374 37.500 0.00 0.00 32.08 2.01
2418 3071 5.292345 GTCGCCAAAACAAAAACTGGTTAAT 59.708 36.000 0.00 0.00 32.08 1.40
2419 3072 5.875359 TCGCCAAAACAAAAACTGGTTAATT 59.125 32.000 0.00 0.00 32.08 1.40
2420 3073 6.371825 TCGCCAAAACAAAAACTGGTTAATTT 59.628 30.769 0.00 0.00 32.08 1.82
2421 3074 6.467364 CGCCAAAACAAAAACTGGTTAATTTG 59.533 34.615 8.28 8.28 32.08 2.32
2422 3075 7.309177 GCCAAAACAAAAACTGGTTAATTTGT 58.691 30.769 9.23 9.23 45.17 2.83
2423 3076 7.272299 GCCAAAACAAAAACTGGTTAATTTGTG 59.728 33.333 13.48 0.00 43.16 3.33
2424 3077 7.752686 CCAAAACAAAAACTGGTTAATTTGTGG 59.247 33.333 13.48 9.13 43.16 4.17
2425 3078 7.987750 AAACAAAAACTGGTTAATTTGTGGT 57.012 28.000 13.48 6.05 43.16 4.16
2426 3079 7.987750 AACAAAAACTGGTTAATTTGTGGTT 57.012 28.000 13.48 1.35 43.16 3.67
2427 3080 7.987750 ACAAAAACTGGTTAATTTGTGGTTT 57.012 28.000 12.53 0.00 42.57 3.27
2428 3081 7.811653 ACAAAAACTGGTTAATTTGTGGTTTG 58.188 30.769 12.53 7.34 42.57 2.93
2429 3082 7.661847 ACAAAAACTGGTTAATTTGTGGTTTGA 59.338 29.630 12.53 0.00 42.57 2.69
2430 3083 8.507249 CAAAAACTGGTTAATTTGTGGTTTGAA 58.493 29.630 0.00 0.00 0.00 2.69
2431 3084 7.841915 AAACTGGTTAATTTGTGGTTTGAAG 57.158 32.000 0.00 0.00 0.00 3.02
2432 3085 6.783708 ACTGGTTAATTTGTGGTTTGAAGA 57.216 33.333 0.00 0.00 0.00 2.87
2433 3086 6.805713 ACTGGTTAATTTGTGGTTTGAAGAG 58.194 36.000 0.00 0.00 0.00 2.85
2434 3087 5.596845 TGGTTAATTTGTGGTTTGAAGAGC 58.403 37.500 0.00 0.00 0.00 4.09
2435 3088 4.679654 GGTTAATTTGTGGTTTGAAGAGCG 59.320 41.667 0.00 0.00 0.00 5.03
2436 3089 2.422276 ATTTGTGGTTTGAAGAGCGC 57.578 45.000 0.00 0.00 0.00 5.92
2437 3090 0.028770 TTTGTGGTTTGAAGAGCGCG 59.971 50.000 0.00 0.00 0.00 6.86
2438 3091 1.781025 TTGTGGTTTGAAGAGCGCGG 61.781 55.000 8.83 0.00 0.00 6.46
2439 3092 2.110213 TGGTTTGAAGAGCGCGGT 59.890 55.556 12.23 12.23 0.00 5.68
2440 3093 2.250939 TGGTTTGAAGAGCGCGGTG 61.251 57.895 18.92 0.00 0.00 4.94
2441 3094 1.959226 GGTTTGAAGAGCGCGGTGA 60.959 57.895 18.92 0.00 0.00 4.02
2442 3095 1.503818 GGTTTGAAGAGCGCGGTGAA 61.504 55.000 18.92 0.00 0.00 3.18
2443 3096 0.517316 GTTTGAAGAGCGCGGTGAAT 59.483 50.000 18.92 0.00 0.00 2.57
2444 3097 0.796312 TTTGAAGAGCGCGGTGAATC 59.204 50.000 18.92 11.62 0.00 2.52
2445 3098 1.351430 TTGAAGAGCGCGGTGAATCG 61.351 55.000 18.92 0.00 0.00 3.34
2446 3099 2.509336 AAGAGCGCGGTGAATCGG 60.509 61.111 18.92 0.00 0.00 4.18
2452 3105 2.559330 GCGGTGAATCGGCGTTTT 59.441 55.556 6.85 1.64 33.07 2.43
2453 3106 1.789116 GCGGTGAATCGGCGTTTTA 59.211 52.632 6.85 0.00 33.07 1.52
2454 3107 0.166379 GCGGTGAATCGGCGTTTTAA 59.834 50.000 6.85 0.00 33.07 1.52
2455 3108 1.399984 GCGGTGAATCGGCGTTTTAAA 60.400 47.619 6.85 0.00 33.07 1.52
2456 3109 2.917296 GCGGTGAATCGGCGTTTTAAAA 60.917 45.455 6.85 0.00 33.07 1.52
2457 3110 3.298317 CGGTGAATCGGCGTTTTAAAAA 58.702 40.909 6.85 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.457598 TGAGGGAGTATTTGAGCTCGT 58.542 47.619 9.64 0.00 32.83 4.18
22 23 6.542821 TGATTTTTACTGTTCATGAGGGAGT 58.457 36.000 0.00 2.23 0.00 3.85
130 133 6.071391 TCCCAGAGCATTTAGGAATGTTTTTC 60.071 38.462 1.63 0.00 43.67 2.29
137 140 4.230502 TCCTTTCCCAGAGCATTTAGGAAT 59.769 41.667 0.00 0.00 36.53 3.01
151 154 2.438800 TCGGTTTTGTTCCTTTCCCA 57.561 45.000 0.00 0.00 0.00 4.37
184 187 4.709397 TGCCCCAACATACCTTCAAAATAG 59.291 41.667 0.00 0.00 0.00 1.73
201 204 5.336055 CGTTCTGTAACAAAATAATGCCCCA 60.336 40.000 0.00 0.00 35.16 4.96
204 207 7.483691 CCTAACGTTCTGTAACAAAATAATGCC 59.516 37.037 2.82 0.00 35.16 4.40
213 216 5.051816 CACCTTCCTAACGTTCTGTAACAA 58.948 41.667 2.82 0.00 35.16 2.83
215 218 4.625028 ACACCTTCCTAACGTTCTGTAAC 58.375 43.478 2.82 0.00 0.00 2.50
218 221 3.832615 AACACCTTCCTAACGTTCTGT 57.167 42.857 2.82 0.00 0.00 3.41
242 245 6.986904 TGTACATATGTGCAAATTTCCGTA 57.013 33.333 22.35 0.00 37.70 4.02
252 255 6.903419 TCGACAAATTTTGTACATATGTGCA 58.097 32.000 21.01 21.01 45.52 4.57
261 264 6.838806 GCAACAAACATCGACAAATTTTGTAC 59.161 34.615 14.49 7.89 45.52 2.90
262 265 6.019479 GGCAACAAACATCGACAAATTTTGTA 60.019 34.615 14.49 1.15 45.52 2.41
264 267 5.196825 GGCAACAAACATCGACAAATTTTG 58.803 37.500 7.59 7.59 34.10 2.44
265 268 5.402464 GGCAACAAACATCGACAAATTTT 57.598 34.783 0.00 0.00 0.00 1.82
335 338 6.426937 GGCACTCTTCAGACACTTGTAATTTA 59.573 38.462 0.00 0.00 0.00 1.40
337 340 4.757149 GGCACTCTTCAGACACTTGTAATT 59.243 41.667 0.00 0.00 0.00 1.40
349 352 0.173708 GAGTACCCGGCACTCTTCAG 59.826 60.000 21.20 0.00 39.48 3.02
350 353 1.255667 GGAGTACCCGGCACTCTTCA 61.256 60.000 25.10 0.00 41.78 3.02
351 354 1.516423 GGAGTACCCGGCACTCTTC 59.484 63.158 25.10 12.22 41.78 2.87
352 355 3.709567 GGAGTACCCGGCACTCTT 58.290 61.111 25.10 0.58 41.78 2.85
370 373 3.243839 CCAACCAACCACTCCAGAAAATG 60.244 47.826 0.00 0.00 0.00 2.32
371 374 2.965147 CCAACCAACCACTCCAGAAAAT 59.035 45.455 0.00 0.00 0.00 1.82
375 378 0.991355 ACCCAACCAACCACTCCAGA 60.991 55.000 0.00 0.00 0.00 3.86
376 379 0.768622 TACCCAACCAACCACTCCAG 59.231 55.000 0.00 0.00 0.00 3.86
378 381 1.834188 CATACCCAACCAACCACTCC 58.166 55.000 0.00 0.00 0.00 3.85
379 382 1.173913 GCATACCCAACCAACCACTC 58.826 55.000 0.00 0.00 0.00 3.51
380 383 0.480690 TGCATACCCAACCAACCACT 59.519 50.000 0.00 0.00 0.00 4.00
381 384 1.555967 ATGCATACCCAACCAACCAC 58.444 50.000 0.00 0.00 0.00 4.16
383 386 3.694043 AAAATGCATACCCAACCAACC 57.306 42.857 0.00 0.00 0.00 3.77
384 387 4.082679 TCGTAAAATGCATACCCAACCAAC 60.083 41.667 0.00 0.00 0.00 3.77
385 388 4.079970 TCGTAAAATGCATACCCAACCAA 58.920 39.130 0.00 0.00 0.00 3.67
386 389 3.687125 TCGTAAAATGCATACCCAACCA 58.313 40.909 0.00 0.00 0.00 3.67
387 390 4.097286 ACATCGTAAAATGCATACCCAACC 59.903 41.667 0.00 0.00 0.00 3.77
388 391 5.065988 AGACATCGTAAAATGCATACCCAAC 59.934 40.000 0.00 0.00 0.00 3.77
389 392 5.065859 CAGACATCGTAAAATGCATACCCAA 59.934 40.000 0.00 0.00 0.00 4.12
390 393 4.574421 CAGACATCGTAAAATGCATACCCA 59.426 41.667 0.00 0.00 0.00 4.51
391 394 4.814234 TCAGACATCGTAAAATGCATACCC 59.186 41.667 0.00 0.00 0.00 3.69
392 395 5.984233 TCAGACATCGTAAAATGCATACC 57.016 39.130 0.00 0.00 0.00 2.73
393 396 7.010552 ACTCTTCAGACATCGTAAAATGCATAC 59.989 37.037 0.00 0.00 0.00 2.39
398 401 5.446473 GGCACTCTTCAGACATCGTAAAATG 60.446 44.000 0.00 0.00 0.00 2.32
407 410 1.194781 ACCCGGCACTCTTCAGACAT 61.195 55.000 0.00 0.00 0.00 3.06
434 437 7.944061 TGCATCTCCTTAATCATACAAAATGG 58.056 34.615 0.00 0.00 0.00 3.16
436 439 7.286087 TGCTGCATCTCCTTAATCATACAAAAT 59.714 33.333 0.00 0.00 0.00 1.82
486 529 0.600255 AGTTTCGACACGGGAAGCAG 60.600 55.000 0.00 0.00 0.00 4.24
495 538 0.874607 ACCGTCTGCAGTTTCGACAC 60.875 55.000 22.18 9.16 0.00 3.67
520 563 1.214325 CGTCATGGTGCCTACGTCA 59.786 57.895 0.00 0.00 0.00 4.35
558 601 2.159490 TGCCCACCAGTGATTCCCA 61.159 57.895 0.00 0.00 0.00 4.37
564 607 4.293648 CGTCGTGCCCACCAGTGA 62.294 66.667 0.00 0.00 0.00 3.41
592 635 1.289109 AAACTTCATGGTCGACCGCG 61.289 55.000 28.70 21.58 39.43 6.46
594 637 2.139917 TCAAAACTTCATGGTCGACCG 58.860 47.619 28.70 16.15 39.43 4.79
595 638 4.215399 TGAATCAAAACTTCATGGTCGACC 59.785 41.667 28.17 28.17 0.00 4.79
611 659 1.814394 GTGGTGCTCTGCATGAATCAA 59.186 47.619 0.00 0.00 41.91 2.57
614 662 1.747709 GAGTGGTGCTCTGCATGAAT 58.252 50.000 0.00 0.00 41.91 2.57
615 663 0.671472 CGAGTGGTGCTCTGCATGAA 60.671 55.000 0.00 0.00 41.91 2.57
616 664 1.079612 CGAGTGGTGCTCTGCATGA 60.080 57.895 0.00 0.00 41.91 3.07
617 665 1.079612 TCGAGTGGTGCTCTGCATG 60.080 57.895 0.00 0.00 41.91 4.06
619 667 0.893727 TAGTCGAGTGGTGCTCTGCA 60.894 55.000 2.10 0.00 41.98 4.41
620 668 0.456995 GTAGTCGAGTGGTGCTCTGC 60.457 60.000 2.10 0.00 41.98 4.26
622 670 0.882474 GTGTAGTCGAGTGGTGCTCT 59.118 55.000 2.10 0.00 41.98 4.09
624 672 0.887836 TCGTGTAGTCGAGTGGTGCT 60.888 55.000 2.10 0.00 34.85 4.40
625 673 0.170561 ATCGTGTAGTCGAGTGGTGC 59.829 55.000 2.10 0.00 43.00 5.01
626 674 1.467342 TCATCGTGTAGTCGAGTGGTG 59.533 52.381 2.10 0.00 43.00 4.17
632 693 1.874872 TGTGTGTCATCGTGTAGTCGA 59.125 47.619 0.00 0.00 43.86 4.20
634 695 2.980476 CAGTGTGTGTCATCGTGTAGTC 59.020 50.000 0.00 0.00 0.00 2.59
649 710 2.738314 TGCATCGAGAATTGTCAGTGTG 59.262 45.455 3.24 0.00 0.00 3.82
665 726 0.597637 ACGGTCGATTCGGATGCATC 60.598 55.000 18.81 18.81 0.00 3.91
666 727 0.875908 CACGGTCGATTCGGATGCAT 60.876 55.000 0.00 0.00 0.00 3.96
701 762 6.039270 TGTTTGTAGATGTGGAACTTTCAAGG 59.961 38.462 0.00 0.00 38.04 3.61
702 763 7.012327 TCTGTTTGTAGATGTGGAACTTTCAAG 59.988 37.037 0.00 0.00 38.04 3.02
713 776 4.169508 CTCCTCGTCTGTTTGTAGATGTG 58.830 47.826 0.00 0.00 35.63 3.21
717 780 2.229062 CTGCTCCTCGTCTGTTTGTAGA 59.771 50.000 0.00 0.00 0.00 2.59
727 790 2.125753 CTGGCACTGCTCCTCGTC 60.126 66.667 0.00 0.00 0.00 4.20
789 872 3.245315 CGCACTGGCTACGTACGC 61.245 66.667 16.72 0.00 38.10 4.42
790 873 3.245315 GCGCACTGGCTACGTACG 61.245 66.667 15.01 15.01 38.10 3.67
791 874 2.582202 TACGCGCACTGGCTACGTAC 62.582 60.000 5.73 0.00 44.90 3.67
792 875 2.397754 TACGCGCACTGGCTACGTA 61.398 57.895 5.73 0.00 44.90 3.57
794 877 3.245315 GTACGCGCACTGGCTACG 61.245 66.667 5.73 0.00 41.31 3.51
795 878 2.582202 TACGTACGCGCACTGGCTAC 62.582 60.000 16.72 0.00 42.83 3.58
796 879 2.397754 TACGTACGCGCACTGGCTA 61.398 57.895 16.72 0.00 42.83 3.93
797 880 3.740397 TACGTACGCGCACTGGCT 61.740 61.111 16.72 0.00 42.83 4.75
798 881 3.539107 GTACGTACGCGCACTGGC 61.539 66.667 16.72 0.00 42.83 4.85
799 882 3.235437 CGTACGTACGCGCACTGG 61.235 66.667 32.36 6.87 43.14 4.00
813 896 3.376347 GTACCGTTGTACGCACGTA 57.624 52.632 14.32 0.00 40.91 3.57
841 924 1.039785 TCCCATCCTGCTCACGAGAG 61.040 60.000 5.40 5.40 44.96 3.20
1055 1146 2.423039 GTCGTTGCGCGTGTGTTC 60.423 61.111 8.43 0.00 42.13 3.18
1466 1611 1.066303 CTACTCTAGGCTTGCACCTCG 59.934 57.143 0.00 0.00 41.50 4.63
1494 1639 2.408022 GGTCGTCCTCGTCATCCG 59.592 66.667 0.00 0.00 38.33 4.18
1495 1640 2.783288 GGGGTCGTCCTCGTCATCC 61.783 68.421 0.00 0.00 38.33 3.51
1497 1642 2.052690 CAGGGGTCGTCCTCGTCAT 61.053 63.158 0.00 0.00 39.67 3.06
1498 1643 2.675423 CAGGGGTCGTCCTCGTCA 60.675 66.667 0.00 0.00 39.67 4.35
1593 1746 1.961180 GCGGTGGTACAGAGGAGCAT 61.961 60.000 0.00 0.00 41.80 3.79
1594 1747 2.646175 GCGGTGGTACAGAGGAGCA 61.646 63.158 0.00 0.00 41.80 4.26
1595 1748 2.184579 GCGGTGGTACAGAGGAGC 59.815 66.667 0.00 0.00 41.80 4.70
1596 1749 2.722201 GGGCGGTGGTACAGAGGAG 61.722 68.421 0.00 0.00 41.80 3.69
1728 1905 6.581542 CACGTACGTCTCTGAAGAAATTAAGT 59.418 38.462 19.94 0.00 31.93 2.24
1729 1906 6.452611 GCACGTACGTCTCTGAAGAAATTAAG 60.453 42.308 19.94 1.87 31.93 1.85
1744 1921 0.713883 CTTCCATGTGCACGTACGTC 59.286 55.000 19.94 13.82 0.00 4.34
1749 1926 0.398696 TAACCCTTCCATGTGCACGT 59.601 50.000 13.13 9.52 0.00 4.49
1793 1970 1.068055 CATTTGAGTCAAGCAGGCACC 60.068 52.381 5.56 0.00 0.00 5.01
1808 1985 9.017669 GCTGTGATTAAGCTAGAAAATCATTTG 57.982 33.333 14.22 10.22 40.61 2.32
1809 1986 8.193438 GGCTGTGATTAAGCTAGAAAATCATTT 58.807 33.333 14.22 0.00 40.61 2.32
1846 2210 4.183865 TGAAACTACCGATCTCAGCATTG 58.816 43.478 0.00 0.00 0.00 2.82
1849 2213 2.826128 ACTGAAACTACCGATCTCAGCA 59.174 45.455 5.94 0.00 37.60 4.41
1879 2243 5.123979 GGAAGGAAAATTCAGATACAAGCGT 59.876 40.000 0.00 0.00 0.00 5.07
1880 2244 5.449177 GGGAAGGAAAATTCAGATACAAGCG 60.449 44.000 0.00 0.00 0.00 4.68
1883 2247 8.367156 CAAAAGGGAAGGAAAATTCAGATACAA 58.633 33.333 0.00 0.00 0.00 2.41
1887 2251 7.012607 TCTCAAAAGGGAAGGAAAATTCAGAT 58.987 34.615 0.00 0.00 0.00 2.90
1889 2253 6.450545 GTCTCAAAAGGGAAGGAAAATTCAG 58.549 40.000 0.00 0.00 0.00 3.02
1890 2254 5.009610 CGTCTCAAAAGGGAAGGAAAATTCA 59.990 40.000 0.00 0.00 0.00 2.57
1892 2256 5.137551 TCGTCTCAAAAGGGAAGGAAAATT 58.862 37.500 0.00 0.00 0.00 1.82
1893 2257 4.725490 TCGTCTCAAAAGGGAAGGAAAAT 58.275 39.130 0.00 0.00 0.00 1.82
1894 2258 4.159244 TCGTCTCAAAAGGGAAGGAAAA 57.841 40.909 0.00 0.00 0.00 2.29
1896 2260 3.849563 TTCGTCTCAAAAGGGAAGGAA 57.150 42.857 0.00 0.00 0.00 3.36
1897 2261 4.367039 AATTCGTCTCAAAAGGGAAGGA 57.633 40.909 0.00 0.00 0.00 3.36
1903 2272 6.631962 ACTCCTACTAATTCGTCTCAAAAGG 58.368 40.000 0.00 0.00 0.00 3.11
1970 2339 5.661312 CCCCGATCCATATTATTGTCCTAGA 59.339 44.000 0.00 0.00 0.00 2.43
1973 2342 3.523564 CCCCCGATCCATATTATTGTCCT 59.476 47.826 0.00 0.00 0.00 3.85
1991 2379 4.533815 CTTGGGATAAAAACTACTCCCCC 58.466 47.826 4.10 0.00 45.77 5.40
2022 2456 7.116233 GGACCACAAATTAACTTGCACATAAAG 59.884 37.037 0.00 0.00 0.00 1.85
2025 2459 5.536538 TGGACCACAAATTAACTTGCACATA 59.463 36.000 0.00 0.00 0.00 2.29
2026 2460 4.343526 TGGACCACAAATTAACTTGCACAT 59.656 37.500 0.00 0.00 0.00 3.21
2060 2494 3.916761 TGTTTACTTCGCTGTCGGTTAT 58.083 40.909 0.00 0.00 36.13 1.89
2063 2497 2.228138 TTGTTTACTTCGCTGTCGGT 57.772 45.000 0.00 0.00 36.13 4.69
2064 2498 4.025979 GGATATTGTTTACTTCGCTGTCGG 60.026 45.833 0.00 0.00 36.13 4.79
2074 2508 8.863872 AGCAAGTTTGTAGGATATTGTTTACT 57.136 30.769 0.00 0.00 0.00 2.24
2075 2509 8.947115 AGAGCAAGTTTGTAGGATATTGTTTAC 58.053 33.333 0.00 0.00 0.00 2.01
2081 2515 7.707035 CGTAGAAGAGCAAGTTTGTAGGATATT 59.293 37.037 0.00 0.00 0.00 1.28
2084 2518 5.047235 ACGTAGAAGAGCAAGTTTGTAGGAT 60.047 40.000 0.00 0.00 0.00 3.24
2085 2519 4.280174 ACGTAGAAGAGCAAGTTTGTAGGA 59.720 41.667 0.00 0.00 0.00 2.94
2087 2521 5.572126 GGTACGTAGAAGAGCAAGTTTGTAG 59.428 44.000 0.00 0.00 0.00 2.74
2088 2522 5.242393 AGGTACGTAGAAGAGCAAGTTTGTA 59.758 40.000 0.00 0.00 0.00 2.41
2089 2523 4.038883 AGGTACGTAGAAGAGCAAGTTTGT 59.961 41.667 0.00 0.00 0.00 2.83
2090 2524 4.557205 AGGTACGTAGAAGAGCAAGTTTG 58.443 43.478 0.00 0.00 0.00 2.93
2091 2525 4.868314 AGGTACGTAGAAGAGCAAGTTT 57.132 40.909 0.00 0.00 0.00 2.66
2092 2526 4.868314 AAGGTACGTAGAAGAGCAAGTT 57.132 40.909 0.00 0.00 0.00 2.66
2095 2529 6.579666 TCTAAAAGGTACGTAGAAGAGCAA 57.420 37.500 0.00 0.00 0.00 3.91
2097 2531 7.880059 TTTTCTAAAAGGTACGTAGAAGAGC 57.120 36.000 0.00 0.00 35.77 4.09
2111 2545 9.899226 CTGGTGTTCTATTTCCTTTTCTAAAAG 57.101 33.333 8.00 8.00 43.82 2.27
2115 2549 9.807921 AATTCTGGTGTTCTATTTCCTTTTCTA 57.192 29.630 0.00 0.00 0.00 2.10
2122 2556 9.788960 GTCAATTAATTCTGGTGTTCTATTTCC 57.211 33.333 0.00 0.00 0.00 3.13
2123 2557 9.490663 CGTCAATTAATTCTGGTGTTCTATTTC 57.509 33.333 0.00 0.00 0.00 2.17
2124 2558 9.226606 TCGTCAATTAATTCTGGTGTTCTATTT 57.773 29.630 0.00 0.00 0.00 1.40
2127 2561 6.816640 CCTCGTCAATTAATTCTGGTGTTCTA 59.183 38.462 0.00 0.00 0.00 2.10
2135 2569 5.352569 AGCTTGTCCTCGTCAATTAATTCTG 59.647 40.000 0.00 0.00 0.00 3.02
2137 2571 5.803020 AGCTTGTCCTCGTCAATTAATTC 57.197 39.130 0.00 0.00 0.00 2.17
2141 2575 3.244422 ACCAAGCTTGTCCTCGTCAATTA 60.244 43.478 24.35 0.00 0.00 1.40
2142 2576 2.154462 CCAAGCTTGTCCTCGTCAATT 58.846 47.619 24.35 0.00 0.00 2.32
2151 2585 1.168714 GATGACCACCAAGCTTGTCC 58.831 55.000 24.35 9.25 0.00 4.02
2158 2592 6.980593 TCAACAAATAAAGATGACCACCAAG 58.019 36.000 0.00 0.00 0.00 3.61
2222 2656 2.101582 TGTGGTTAAAGCCGTGCAAATT 59.898 40.909 0.00 0.00 0.00 1.82
2256 2690 4.440880 GAAGACATCAATCTCAGACCTGG 58.559 47.826 0.00 0.00 0.00 4.45
2257 2691 4.161942 AGGAAGACATCAATCTCAGACCTG 59.838 45.833 0.00 0.00 0.00 4.00
2279 2932 4.809426 ACGCGTAAATAATTCCTTCAGGAG 59.191 41.667 11.67 0.00 46.36 3.69
2284 2937 5.522824 AGGAGAACGCGTAAATAATTCCTTC 59.477 40.000 14.46 0.78 0.00 3.46
2285 2938 5.425630 AGGAGAACGCGTAAATAATTCCTT 58.574 37.500 14.46 0.00 0.00 3.36
2337 2990 8.826710 CGAGTATTGGTTATTTAATTCAGCAGA 58.173 33.333 0.00 0.00 0.00 4.26
2338 2991 8.070171 CCGAGTATTGGTTATTTAATTCAGCAG 58.930 37.037 0.00 0.00 33.79 4.24
2339 2992 7.925993 CCGAGTATTGGTTATTTAATTCAGCA 58.074 34.615 0.00 0.00 33.79 4.41
2359 3012 7.642586 GCGCTAATTCAAAATTTTATACCGAGT 59.357 33.333 2.44 0.00 0.00 4.18
2360 3013 7.642194 TGCGCTAATTCAAAATTTTATACCGAG 59.358 33.333 9.73 0.00 0.00 4.63
2361 3014 7.473366 TGCGCTAATTCAAAATTTTATACCGA 58.527 30.769 9.73 0.00 0.00 4.69
2362 3015 7.431084 ACTGCGCTAATTCAAAATTTTATACCG 59.569 33.333 9.73 2.35 0.00 4.02
2363 3016 8.531530 CACTGCGCTAATTCAAAATTTTATACC 58.468 33.333 9.73 0.00 0.00 2.73
2364 3017 9.072294 ACACTGCGCTAATTCAAAATTTTATAC 57.928 29.630 9.73 0.00 0.00 1.47
2365 3018 9.632807 AACACTGCGCTAATTCAAAATTTTATA 57.367 25.926 9.73 0.00 0.00 0.98
2366 3019 8.532977 AACACTGCGCTAATTCAAAATTTTAT 57.467 26.923 9.73 0.00 0.00 1.40
2367 3020 7.938563 AACACTGCGCTAATTCAAAATTTTA 57.061 28.000 9.73 0.00 0.00 1.52
2368 3021 6.843069 AACACTGCGCTAATTCAAAATTTT 57.157 29.167 9.73 0.00 0.00 1.82
2369 3022 6.843069 AAACACTGCGCTAATTCAAAATTT 57.157 29.167 9.73 0.00 0.00 1.82
2370 3023 6.257630 ACAAAACACTGCGCTAATTCAAAATT 59.742 30.769 9.73 0.00 0.00 1.82
2371 3024 5.752955 ACAAAACACTGCGCTAATTCAAAAT 59.247 32.000 9.73 0.00 0.00 1.82
2372 3025 5.105752 ACAAAACACTGCGCTAATTCAAAA 58.894 33.333 9.73 0.00 0.00 2.44
2373 3026 4.677584 ACAAAACACTGCGCTAATTCAAA 58.322 34.783 9.73 0.00 0.00 2.69
2374 3027 4.286910 GACAAAACACTGCGCTAATTCAA 58.713 39.130 9.73 0.00 0.00 2.69
2375 3028 3.605922 CGACAAAACACTGCGCTAATTCA 60.606 43.478 9.73 0.00 0.00 2.57
2376 3029 2.902484 CGACAAAACACTGCGCTAATTC 59.098 45.455 9.73 0.00 0.00 2.17
2377 3030 2.916111 CGACAAAACACTGCGCTAATT 58.084 42.857 9.73 0.00 0.00 1.40
2378 3031 1.399727 GCGACAAAACACTGCGCTAAT 60.400 47.619 9.73 0.00 43.85 1.73
2379 3032 0.041663 GCGACAAAACACTGCGCTAA 60.042 50.000 9.73 0.00 43.85 3.09
2380 3033 1.567537 GCGACAAAACACTGCGCTA 59.432 52.632 9.73 0.00 43.85 4.26
2381 3034 2.327940 GCGACAAAACACTGCGCT 59.672 55.556 9.73 0.00 43.85 5.92
2382 3035 2.725815 GGCGACAAAACACTGCGC 60.726 61.111 0.00 0.00 46.20 6.09
2383 3036 2.712539 TGGCGACAAAACACTGCG 59.287 55.556 0.00 0.00 37.44 5.18
2393 3046 2.028930 ACCAGTTTTTGTTTTGGCGACA 60.029 40.909 0.00 0.00 39.83 4.35
2394 3047 2.612604 ACCAGTTTTTGTTTTGGCGAC 58.387 42.857 0.00 0.00 33.98 5.19
2395 3048 3.320673 AACCAGTTTTTGTTTTGGCGA 57.679 38.095 0.00 0.00 33.98 5.54
2396 3049 5.726729 ATTAACCAGTTTTTGTTTTGGCG 57.273 34.783 0.00 0.00 33.98 5.69
2397 3050 7.272299 CACAAATTAACCAGTTTTTGTTTTGGC 59.728 33.333 9.52 0.00 39.55 4.52
2398 3051 7.752686 CCACAAATTAACCAGTTTTTGTTTTGG 59.247 33.333 9.52 6.21 39.55 3.28
2399 3052 8.293157 ACCACAAATTAACCAGTTTTTGTTTTG 58.707 29.630 9.52 6.34 39.55 2.44
2400 3053 8.397575 ACCACAAATTAACCAGTTTTTGTTTT 57.602 26.923 9.52 0.48 39.55 2.43
2401 3054 7.987750 ACCACAAATTAACCAGTTTTTGTTT 57.012 28.000 9.52 0.75 39.55 2.83
2402 3055 7.987750 AACCACAAATTAACCAGTTTTTGTT 57.012 28.000 9.52 0.00 39.55 2.83
2403 3056 7.661847 TCAAACCACAAATTAACCAGTTTTTGT 59.338 29.630 7.27 7.27 41.58 2.83
2404 3057 8.034058 TCAAACCACAAATTAACCAGTTTTTG 57.966 30.769 6.27 6.27 35.66 2.44
2405 3058 8.622948 TTCAAACCACAAATTAACCAGTTTTT 57.377 26.923 0.00 0.00 0.00 1.94
2406 3059 8.097662 TCTTCAAACCACAAATTAACCAGTTTT 58.902 29.630 0.00 0.00 0.00 2.43
2407 3060 7.616313 TCTTCAAACCACAAATTAACCAGTTT 58.384 30.769 0.00 0.00 0.00 2.66
2408 3061 7.176589 TCTTCAAACCACAAATTAACCAGTT 57.823 32.000 0.00 0.00 0.00 3.16
2409 3062 6.682861 GCTCTTCAAACCACAAATTAACCAGT 60.683 38.462 0.00 0.00 0.00 4.00
2410 3063 5.691754 GCTCTTCAAACCACAAATTAACCAG 59.308 40.000 0.00 0.00 0.00 4.00
2411 3064 5.596845 GCTCTTCAAACCACAAATTAACCA 58.403 37.500 0.00 0.00 0.00 3.67
2412 3065 4.679654 CGCTCTTCAAACCACAAATTAACC 59.320 41.667 0.00 0.00 0.00 2.85
2413 3066 4.148174 GCGCTCTTCAAACCACAAATTAAC 59.852 41.667 0.00 0.00 0.00 2.01
2414 3067 4.295051 GCGCTCTTCAAACCACAAATTAA 58.705 39.130 0.00 0.00 0.00 1.40
2415 3068 3.608241 CGCGCTCTTCAAACCACAAATTA 60.608 43.478 5.56 0.00 0.00 1.40
2416 3069 2.742774 GCGCTCTTCAAACCACAAATT 58.257 42.857 0.00 0.00 0.00 1.82
2417 3070 1.334960 CGCGCTCTTCAAACCACAAAT 60.335 47.619 5.56 0.00 0.00 2.32
2418 3071 0.028770 CGCGCTCTTCAAACCACAAA 59.971 50.000 5.56 0.00 0.00 2.83
2419 3072 1.646540 CGCGCTCTTCAAACCACAA 59.353 52.632 5.56 0.00 0.00 3.33
2420 3073 2.250939 CCGCGCTCTTCAAACCACA 61.251 57.895 5.56 0.00 0.00 4.17
2421 3074 2.251642 ACCGCGCTCTTCAAACCAC 61.252 57.895 5.56 0.00 0.00 4.16
2422 3075 2.110213 ACCGCGCTCTTCAAACCA 59.890 55.556 5.56 0.00 0.00 3.67
2423 3076 1.503818 TTCACCGCGCTCTTCAAACC 61.504 55.000 5.56 0.00 0.00 3.27
2424 3077 0.517316 ATTCACCGCGCTCTTCAAAC 59.483 50.000 5.56 0.00 0.00 2.93
2425 3078 0.796312 GATTCACCGCGCTCTTCAAA 59.204 50.000 5.56 0.00 0.00 2.69
2426 3079 1.351430 CGATTCACCGCGCTCTTCAA 61.351 55.000 5.56 0.00 0.00 2.69
2427 3080 1.805539 CGATTCACCGCGCTCTTCA 60.806 57.895 5.56 0.00 0.00 3.02
2428 3081 2.517450 CCGATTCACCGCGCTCTTC 61.517 63.158 5.56 0.00 0.00 2.87
2429 3082 2.509336 CCGATTCACCGCGCTCTT 60.509 61.111 5.56 0.00 0.00 2.85
2434 3087 1.957711 TAAAACGCCGATTCACCGCG 61.958 55.000 0.00 0.00 36.03 6.46
2435 3088 0.166379 TTAAAACGCCGATTCACCGC 59.834 50.000 0.00 0.00 0.00 5.68
2436 3089 2.598000 TTTAAAACGCCGATTCACCG 57.402 45.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.