Multiple sequence alignment - TraesCS2B01G270800

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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 TraesCS2B01G270800 chr2B 100.000 2411 0 0 1 2411 369624130 369621720 0.000000e+00 4453.0
1 TraesCS2B01G270800 chrUn 96.344 1723 46 7 1 1707 93415918 93417639 0.000000e+00 2817.0
2 TraesCS2B01G270800 chrUn 97.126 348 3 5 1705 2045 30304820 30305167 4.470000e-162 580.0
3 TraesCS2B01G270800 chrUn 94.737 323 16 1 2090 2411 28473585 28473907 3.580000e-138 501.0
4 TraesCS2B01G270800 chr5D 96.339 1721 48 7 1 1707 560880896 560879177 0.000000e+00 2815.0
5 TraesCS2B01G270800 chr5D 95.892 1631 56 7 1 1626 329124003 329125627 0.000000e+00 2630.0
6 TraesCS2B01G270800 chr3B 96.383 1714 52 7 1 1707 201523094 201521384 0.000000e+00 2813.0
7 TraesCS2B01G270800 chr3B 97.421 349 4 2 1705 2048 201486057 201485709 7.420000e-165 590.0
8 TraesCS2B01G270800 chr3B 96.857 350 5 4 1705 2048 201489331 201488982 4.470000e-162 580.0
9 TraesCS2B01G270800 chr3B 94.737 323 16 1 2090 2411 417803009 417802687 3.580000e-138 501.0
10 TraesCS2B01G270800 chr3A 96.257 1710 57 6 1 1707 672913922 672915627 0.000000e+00 2796.0
11 TraesCS2B01G270800 chr3A 96.552 348 8 4 1705 2048 524024788 524024441 7.480000e-160 573.0
12 TraesCS2B01G270800 chr2D 96.047 1720 52 7 1 1707 272797807 272799523 0.000000e+00 2785.0
13 TraesCS2B01G270800 chr7B 94.829 1721 67 11 1 1707 559141405 559139693 0.000000e+00 2665.0
14 TraesCS2B01G270800 chr7B 97.135 349 5 2 1705 2048 397631540 397631192 3.450000e-163 584.0
15 TraesCS2B01G270800 chr7B 97.135 349 5 2 1705 2048 662741414 662741762 3.450000e-163 584.0
16 TraesCS2B01G270800 chr7B 93.636 330 20 1 2083 2411 221771691 221772020 2.150000e-135 492.0
17 TraesCS2B01G270800 chr4D 94.316 1724 71 10 1 1707 19924882 19923169 0.000000e+00 2615.0
18 TraesCS2B01G270800 chr4D 94.190 327 18 1 2086 2411 331901714 331901388 4.630000e-137 497.0
19 TraesCS2B01G270800 chr1D 96.112 1106 33 4 608 1707 144238516 144237415 0.000000e+00 1796.0
20 TraesCS2B01G270800 chr1D 96.562 349 6 4 1705 2048 206331084 206330737 7.480000e-160 573.0
21 TraesCS2B01G270800 chr1D 94.172 326 19 0 2086 2411 38651772 38651447 4.630000e-137 497.0
22 TraesCS2B01G270800 chr7A 93.988 1131 63 4 1 1131 352185715 352186840 0.000000e+00 1707.0
23 TraesCS2B01G270800 chr7A 96.552 348 8 4 1705 2048 12216274 12216621 7.480000e-160 573.0
24 TraesCS2B01G270800 chr1A 96.857 350 5 4 1705 2048 554451615 554451964 4.470000e-162 580.0
25 TraesCS2B01G270800 chr1B 94.737 323 16 1 2090 2411 266317254 266317576 3.580000e-138 501.0
26 TraesCS2B01G270800 chr1B 94.427 323 17 1 2090 2411 270763732 270764054 1.660000e-136 496.0
27 TraesCS2B01G270800 chr4B 94.427 323 17 1 2090 2411 433899281 433899603 1.660000e-136 496.0
28 TraesCS2B01G270800 chr4B 92.604 338 24 1 2075 2411 513526571 513526234 3.600000e-133 484.0
29 TraesCS2B01G270800 chr5B 97.436 39 1 0 2049 2087 248502749 248502711 1.550000e-07 67.6
30 TraesCS2B01G270800 chr5B 97.297 37 1 0 2052 2088 160593072 160593108 2.000000e-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 TraesCS2B01G270800 chr2B 369621720 369624130 2410 True 4453 4453 100.000 1 2411 1 chr2B.!!$R1 2410
1 TraesCS2B01G270800 chrUn 93415918 93417639 1721 False 2817 2817 96.344 1 1707 1 chrUn.!!$F3 1706
2 TraesCS2B01G270800 chr5D 560879177 560880896 1719 True 2815 2815 96.339 1 1707 1 chr5D.!!$R1 1706
3 TraesCS2B01G270800 chr5D 329124003 329125627 1624 False 2630 2630 95.892 1 1626 1 chr5D.!!$F1 1625
4 TraesCS2B01G270800 chr3B 201521384 201523094 1710 True 2813 2813 96.383 1 1707 1 chr3B.!!$R1 1706
5 TraesCS2B01G270800 chr3B 201485709 201489331 3622 True 585 590 97.139 1705 2048 2 chr3B.!!$R3 343
6 TraesCS2B01G270800 chr3A 672913922 672915627 1705 False 2796 2796 96.257 1 1707 1 chr3A.!!$F1 1706
7 TraesCS2B01G270800 chr2D 272797807 272799523 1716 False 2785 2785 96.047 1 1707 1 chr2D.!!$F1 1706
8 TraesCS2B01G270800 chr7B 559139693 559141405 1712 True 2665 2665 94.829 1 1707 1 chr7B.!!$R2 1706
9 TraesCS2B01G270800 chr4D 19923169 19924882 1713 True 2615 2615 94.316 1 1707 1 chr4D.!!$R1 1706
10 TraesCS2B01G270800 chr1D 144237415 144238516 1101 True 1796 1796 96.112 608 1707 1 chr1D.!!$R2 1099
11 TraesCS2B01G270800 chr7A 352185715 352186840 1125 False 1707 1707 93.988 1 1131 1 chr7A.!!$F2 1130

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
575 600 1.134491 TCGAGTCATAGGAGCTGTCGA 60.134 52.381 0.0 0.0 32.88 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1712 0.033601 TTTTGACCCGATCCCCCATG 60.034 55.0 0.0 0.0 0.0 3.66 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
31 40 9.401058 GATAGAGGAAGAATGAAAGGAAAATCA 57.599 33.333 0.00 0.00 0.00 2.57
119 128 2.295909 GCGAGACAGATAGAAGCAGGAT 59.704 50.000 0.00 0.00 0.00 3.24
142 151 5.359756 TGAAGAGCAATAACACGATATGCT 58.640 37.500 0.00 0.00 0.00 3.79
279 288 7.293018 GTTGTTAAACCTGGTCGTATACTTTG 58.707 38.462 0.00 0.00 0.00 2.77
286 295 5.642063 ACCTGGTCGTATACTTTGTGAAATG 59.358 40.000 0.56 0.00 0.00 2.32
290 299 4.939439 GTCGTATACTTTGTGAAATGGGGT 59.061 41.667 0.56 0.00 0.00 4.95
572 597 4.036971 GTGTATTCGAGTCATAGGAGCTGT 59.963 45.833 0.00 0.00 0.00 4.40
573 598 4.276183 TGTATTCGAGTCATAGGAGCTGTC 59.724 45.833 0.00 0.00 0.00 3.51
575 600 1.134491 TCGAGTCATAGGAGCTGTCGA 60.134 52.381 0.00 0.00 32.88 4.20
621 646 7.225784 TGGTGATGTTATTGTTGCTGTAATT 57.774 32.000 0.00 0.00 0.00 1.40
637 662 3.759086 TGTAATTAAAGACGCATTGCCCA 59.241 39.130 2.41 0.00 0.00 5.36
713 738 3.026630 AGAGTTCAAATGCGAAGACGA 57.973 42.857 0.00 0.00 42.66 4.20
765 790 7.164230 TGCGGTTATAATTGATCAAAAAGGT 57.836 32.000 13.09 0.00 0.00 3.50
1019 1049 2.442236 ATGGGCAAGGACACTATTGG 57.558 50.000 0.00 0.00 0.00 3.16
1052 1082 8.540388 ACTAACCTCTATAAGAAATGCAGACAA 58.460 33.333 0.00 0.00 0.00 3.18
1140 1172 7.235935 TCTACGAGAGGGTTTTATTGAAAGA 57.764 36.000 0.00 0.00 0.00 2.52
1179 1212 6.817140 AGGAACGTAACAGATATTTCTTGGTC 59.183 38.462 0.00 0.00 0.00 4.02
1259 1292 2.953466 TTAAAGCGTATCAGCCGACT 57.047 45.000 0.00 0.00 38.01 4.18
1418 1451 6.569127 ATGTTATATATGGTAATCGCCCCA 57.431 37.500 0.00 0.00 34.66 4.96
1458 1491 5.855045 TCTATCTCGCCCTTCCTATTTTTC 58.145 41.667 0.00 0.00 0.00 2.29
1461 1494 4.855340 TCTCGCCCTTCCTATTTTTCAAT 58.145 39.130 0.00 0.00 0.00 2.57
1543 1595 9.875691 AAAATGAGAGAAGCAAAAGTAACTTTT 57.124 25.926 0.00 0.00 43.36 2.27
1573 1625 0.614812 TTACGGAAGCCCTACCCAAC 59.385 55.000 0.00 0.00 0.00 3.77
1589 1641 1.335496 CCAACGGAATGTTCCACGTTT 59.665 47.619 12.00 0.00 45.97 3.60
1659 1712 7.650834 ACGGTCTAGTTCTATACGAATACTC 57.349 40.000 0.00 0.00 33.45 2.59
1669 1722 5.892119 TCTATACGAATACTCATGGGGGATC 59.108 44.000 0.00 0.00 0.00 3.36
1818 1871 4.822685 TTTCCGTTATGTAAGCCCACTA 57.177 40.909 0.00 0.00 0.00 2.74
1823 1876 3.802685 CGTTATGTAAGCCCACTAAGCTC 59.197 47.826 0.00 0.00 40.49 4.09
2061 5393 1.388547 TTTGGGCTGATATCGTTGGC 58.611 50.000 0.00 3.52 0.00 4.52
2062 5394 0.546122 TTGGGCTGATATCGTTGGCT 59.454 50.000 13.45 0.00 0.00 4.75
2063 5395 0.546122 TGGGCTGATATCGTTGGCTT 59.454 50.000 13.45 0.00 0.00 4.35
2064 5396 1.765904 TGGGCTGATATCGTTGGCTTA 59.234 47.619 13.45 4.50 0.00 3.09
2065 5397 2.371841 TGGGCTGATATCGTTGGCTTAT 59.628 45.455 13.45 0.00 0.00 1.73
2066 5398 2.744202 GGGCTGATATCGTTGGCTTATG 59.256 50.000 13.45 0.00 0.00 1.90
2067 5399 2.160417 GGCTGATATCGTTGGCTTATGC 59.840 50.000 0.00 0.00 38.76 3.14
2080 5412 2.498167 GCTTATGCCGAAGATGATGGT 58.502 47.619 0.00 0.00 0.00 3.55
2081 5413 2.225019 GCTTATGCCGAAGATGATGGTG 59.775 50.000 0.00 0.00 0.00 4.17
2082 5414 2.549064 TATGCCGAAGATGATGGTGG 57.451 50.000 0.00 0.00 0.00 4.61
2083 5415 0.839277 ATGCCGAAGATGATGGTGGA 59.161 50.000 0.00 0.00 0.00 4.02
2084 5416 0.617935 TGCCGAAGATGATGGTGGAA 59.382 50.000 0.00 0.00 0.00 3.53
2085 5417 1.303309 GCCGAAGATGATGGTGGAAG 58.697 55.000 0.00 0.00 0.00 3.46
2086 5418 1.959042 CCGAAGATGATGGTGGAAGG 58.041 55.000 0.00 0.00 0.00 3.46
2087 5419 1.210478 CCGAAGATGATGGTGGAAGGT 59.790 52.381 0.00 0.00 0.00 3.50
2088 5420 2.434336 CCGAAGATGATGGTGGAAGGTA 59.566 50.000 0.00 0.00 0.00 3.08
2089 5421 3.071602 CCGAAGATGATGGTGGAAGGTAT 59.928 47.826 0.00 0.00 0.00 2.73
2090 5422 4.310769 CGAAGATGATGGTGGAAGGTATC 58.689 47.826 0.00 0.00 0.00 2.24
2091 5423 4.310769 GAAGATGATGGTGGAAGGTATCG 58.689 47.826 0.00 0.00 0.00 2.92
2092 5424 2.634940 AGATGATGGTGGAAGGTATCGG 59.365 50.000 0.00 0.00 0.00 4.18
2093 5425 1.874129 TGATGGTGGAAGGTATCGGT 58.126 50.000 0.00 0.00 0.00 4.69
2094 5426 1.484653 TGATGGTGGAAGGTATCGGTG 59.515 52.381 0.00 0.00 0.00 4.94
2095 5427 1.485066 GATGGTGGAAGGTATCGGTGT 59.515 52.381 0.00 0.00 0.00 4.16
2096 5428 0.899720 TGGTGGAAGGTATCGGTGTC 59.100 55.000 0.00 0.00 0.00 3.67
2097 5429 0.899720 GGTGGAAGGTATCGGTGTCA 59.100 55.000 0.00 0.00 0.00 3.58
2098 5430 1.276989 GGTGGAAGGTATCGGTGTCAA 59.723 52.381 0.00 0.00 0.00 3.18
2099 5431 2.289819 GGTGGAAGGTATCGGTGTCAAA 60.290 50.000 0.00 0.00 0.00 2.69
2100 5432 3.404899 GTGGAAGGTATCGGTGTCAAAA 58.595 45.455 0.00 0.00 0.00 2.44
2101 5433 3.187842 GTGGAAGGTATCGGTGTCAAAAC 59.812 47.826 0.00 0.00 0.00 2.43
2102 5434 2.745821 GGAAGGTATCGGTGTCAAAACC 59.254 50.000 0.00 0.00 36.82 3.27
2108 5440 2.592287 GGTGTCAAAACCGGCGGA 60.592 61.111 35.78 6.54 0.00 5.54
2109 5441 1.969589 GGTGTCAAAACCGGCGGAT 60.970 57.895 35.78 20.37 0.00 4.18
2110 5442 1.500396 GTGTCAAAACCGGCGGATC 59.500 57.895 35.78 9.52 0.00 3.36
2111 5443 0.953960 GTGTCAAAACCGGCGGATCT 60.954 55.000 35.78 13.84 0.00 2.75
2112 5444 0.672401 TGTCAAAACCGGCGGATCTC 60.672 55.000 35.78 16.90 0.00 2.75
2113 5445 1.447140 TCAAAACCGGCGGATCTCG 60.447 57.895 35.78 16.34 42.76 4.04
2114 5446 1.447140 CAAAACCGGCGGATCTCGA 60.447 57.895 35.78 0.00 42.43 4.04
2115 5447 1.153628 AAAACCGGCGGATCTCGAG 60.154 57.895 35.78 5.93 42.43 4.04
2116 5448 1.885163 AAAACCGGCGGATCTCGAGT 61.885 55.000 35.78 3.72 42.43 4.18
2117 5449 1.033746 AAACCGGCGGATCTCGAGTA 61.034 55.000 35.78 0.00 42.43 2.59
2118 5450 1.445716 AACCGGCGGATCTCGAGTAG 61.446 60.000 35.78 0.55 42.43 2.57
2119 5451 2.618219 CCGGCGGATCTCGAGTAGG 61.618 68.421 24.41 1.90 42.43 3.18
2120 5452 2.618219 CGGCGGATCTCGAGTAGGG 61.618 68.421 13.13 2.27 42.43 3.53
2121 5453 2.269529 GGCGGATCTCGAGTAGGGG 61.270 68.421 13.13 0.82 42.43 4.79
2122 5454 2.269529 GCGGATCTCGAGTAGGGGG 61.270 68.421 13.13 0.00 42.43 5.40
2123 5455 1.150992 CGGATCTCGAGTAGGGGGT 59.849 63.158 13.13 0.00 42.43 4.95
2124 5456 0.890090 CGGATCTCGAGTAGGGGGTC 60.890 65.000 13.13 0.00 42.43 4.46
2125 5457 0.540133 GGATCTCGAGTAGGGGGTCC 60.540 65.000 13.13 0.00 0.00 4.46
2126 5458 0.540133 GATCTCGAGTAGGGGGTCCC 60.540 65.000 13.13 0.00 45.90 4.46
2135 5467 4.815108 GGGGGTCCCGGATTGTGC 62.815 72.222 0.73 0.00 36.85 4.57
2139 5471 4.778143 GTCCCGGATTGTGCGCCT 62.778 66.667 0.73 0.00 0.00 5.52
2140 5472 3.078196 TCCCGGATTGTGCGCCTA 61.078 61.111 0.73 0.00 0.00 3.93
2141 5473 2.124901 CCCGGATTGTGCGCCTAA 60.125 61.111 0.73 0.00 0.00 2.69
2142 5474 2.180204 CCCGGATTGTGCGCCTAAG 61.180 63.158 0.73 0.00 0.00 2.18
2143 5475 2.180204 CCGGATTGTGCGCCTAAGG 61.180 63.158 4.18 0.00 0.00 2.69
2144 5476 2.823829 CGGATTGTGCGCCTAAGGC 61.824 63.158 4.18 0.00 46.75 4.35
2158 5490 5.757099 GCCTAAGGCTAATGGTAATAGGA 57.243 43.478 8.47 0.00 46.69 2.94
2159 5491 5.735766 GCCTAAGGCTAATGGTAATAGGAG 58.264 45.833 8.47 0.00 46.69 3.69
2160 5492 5.338463 GCCTAAGGCTAATGGTAATAGGAGG 60.338 48.000 8.47 0.00 46.69 4.30
2161 5493 4.642466 AAGGCTAATGGTAATAGGAGGC 57.358 45.455 0.00 0.00 0.00 4.70
2162 5494 2.567615 AGGCTAATGGTAATAGGAGGCG 59.432 50.000 0.00 0.00 34.88 5.52
2163 5495 2.354805 GGCTAATGGTAATAGGAGGCGG 60.355 54.545 0.00 0.00 0.00 6.13
2164 5496 2.354805 GCTAATGGTAATAGGAGGCGGG 60.355 54.545 0.00 0.00 0.00 6.13
2165 5497 1.064825 AATGGTAATAGGAGGCGGGG 58.935 55.000 0.00 0.00 0.00 5.73
2166 5498 0.840722 ATGGTAATAGGAGGCGGGGG 60.841 60.000 0.00 0.00 0.00 5.40
2167 5499 1.152183 GGTAATAGGAGGCGGGGGA 60.152 63.158 0.00 0.00 0.00 4.81
2168 5500 1.478526 GGTAATAGGAGGCGGGGGAC 61.479 65.000 0.00 0.00 0.00 4.46
2169 5501 0.761702 GTAATAGGAGGCGGGGGACA 60.762 60.000 0.00 0.00 0.00 4.02
2170 5502 0.761702 TAATAGGAGGCGGGGGACAC 60.762 60.000 0.00 0.00 0.00 3.67
2171 5503 2.833151 AATAGGAGGCGGGGGACACA 62.833 60.000 0.00 0.00 0.00 3.72
2172 5504 2.833151 ATAGGAGGCGGGGGACACAA 62.833 60.000 0.00 0.00 0.00 3.33
2173 5505 2.833151 TAGGAGGCGGGGGACACAAT 62.833 60.000 0.00 0.00 0.00 2.71
2174 5506 2.438434 GAGGCGGGGGACACAATG 60.438 66.667 0.00 0.00 0.00 2.82
2175 5507 3.256960 AGGCGGGGGACACAATGT 61.257 61.111 0.00 0.00 0.00 2.71
2176 5508 2.282887 GGCGGGGGACACAATGTT 60.283 61.111 0.00 0.00 0.00 2.71
2177 5509 1.906333 GGCGGGGGACACAATGTTT 60.906 57.895 0.00 0.00 0.00 2.83
2178 5510 0.609681 GGCGGGGGACACAATGTTTA 60.610 55.000 0.00 0.00 0.00 2.01
2179 5511 0.524414 GCGGGGGACACAATGTTTAC 59.476 55.000 0.00 0.00 0.00 2.01
2180 5512 1.170442 CGGGGGACACAATGTTTACC 58.830 55.000 0.00 0.00 0.00 2.85
2181 5513 1.552578 GGGGGACACAATGTTTACCC 58.447 55.000 11.42 11.42 37.95 3.69
2182 5514 1.203075 GGGGGACACAATGTTTACCCA 60.203 52.381 20.61 0.00 39.39 4.51
2183 5515 2.167662 GGGGACACAATGTTTACCCAG 58.832 52.381 14.80 0.00 38.30 4.45
2184 5516 2.167662 GGGACACAATGTTTACCCAGG 58.832 52.381 12.30 0.00 37.50 4.45
2185 5517 2.490168 GGGACACAATGTTTACCCAGGT 60.490 50.000 12.30 0.00 37.50 4.00
2186 5518 3.227614 GGACACAATGTTTACCCAGGTT 58.772 45.455 0.00 0.00 0.00 3.50
2187 5519 3.254903 GGACACAATGTTTACCCAGGTTC 59.745 47.826 0.00 0.00 0.00 3.62
2188 5520 2.882137 ACACAATGTTTACCCAGGTTCG 59.118 45.455 0.00 0.00 0.00 3.95
2189 5521 2.227865 CACAATGTTTACCCAGGTTCGG 59.772 50.000 0.00 0.00 0.00 4.30
2197 5529 3.787001 CCAGGTTCGGGCCCTCTC 61.787 72.222 22.43 9.34 0.00 3.20
2198 5530 2.685380 CAGGTTCGGGCCCTCTCT 60.685 66.667 22.43 9.12 0.00 3.10
2199 5531 1.381327 CAGGTTCGGGCCCTCTCTA 60.381 63.158 22.43 0.00 0.00 2.43
2200 5532 0.760945 CAGGTTCGGGCCCTCTCTAT 60.761 60.000 22.43 0.00 0.00 1.98
2201 5533 0.760945 AGGTTCGGGCCCTCTCTATG 60.761 60.000 22.43 1.43 0.00 2.23
2202 5534 1.749033 GTTCGGGCCCTCTCTATGG 59.251 63.158 22.43 0.54 0.00 2.74
2203 5535 0.759436 GTTCGGGCCCTCTCTATGGA 60.759 60.000 22.43 3.53 0.00 3.41
2204 5536 0.470080 TTCGGGCCCTCTCTATGGAG 60.470 60.000 22.43 0.00 40.73 3.86
2214 5546 5.278127 CCTCTCTATGGAGGTAATACCCT 57.722 47.826 5.71 0.00 45.65 4.34
2215 5547 6.404426 CCTCTCTATGGAGGTAATACCCTA 57.596 45.833 5.71 0.00 45.65 3.53
2216 5548 6.189133 CCTCTCTATGGAGGTAATACCCTAC 58.811 48.000 5.71 0.00 45.65 3.18
2217 5549 6.011451 CCTCTCTATGGAGGTAATACCCTACT 60.011 46.154 5.71 0.00 45.65 2.57
2218 5550 7.417811 TCTCTATGGAGGTAATACCCTACTT 57.582 40.000 5.71 0.00 39.75 2.24
2219 5551 7.468496 TCTCTATGGAGGTAATACCCTACTTC 58.532 42.308 5.71 0.00 39.75 3.01
2220 5552 6.559429 TCTATGGAGGTAATACCCTACTTCC 58.441 44.000 5.71 6.77 44.47 3.46
2221 5553 4.913154 TGGAGGTAATACCCTACTTCCT 57.087 45.455 13.63 0.00 44.50 3.36
2222 5554 6.556644 ATGGAGGTAATACCCTACTTCCTA 57.443 41.667 13.63 3.86 44.50 2.94
2223 5555 5.709594 TGGAGGTAATACCCTACTTCCTAC 58.290 45.833 13.63 0.00 44.50 3.18
2224 5556 5.437714 TGGAGGTAATACCCTACTTCCTACT 59.562 44.000 13.63 0.00 44.50 2.57
2225 5557 6.068021 TGGAGGTAATACCCTACTTCCTACTT 60.068 42.308 13.63 0.00 44.50 2.24
2226 5558 6.267242 GGAGGTAATACCCTACTTCCTACTTG 59.733 46.154 5.71 0.00 42.18 3.16
2227 5559 6.989894 AGGTAATACCCTACTTCCTACTTGA 58.010 40.000 5.71 0.00 39.75 3.02
2228 5560 7.602868 AGGTAATACCCTACTTCCTACTTGAT 58.397 38.462 5.71 0.00 39.75 2.57
2229 5561 8.072480 AGGTAATACCCTACTTCCTACTTGATT 58.928 37.037 5.71 0.00 39.75 2.57
2230 5562 8.148999 GGTAATACCCTACTTCCTACTTGATTG 58.851 40.741 0.00 0.00 30.04 2.67
2231 5563 7.989947 AATACCCTACTTCCTACTTGATTGA 57.010 36.000 0.00 0.00 0.00 2.57
2232 5564 8.568617 AATACCCTACTTCCTACTTGATTGAT 57.431 34.615 0.00 0.00 0.00 2.57
2233 5565 6.487299 ACCCTACTTCCTACTTGATTGATC 57.513 41.667 0.00 0.00 0.00 2.92
2234 5566 5.964477 ACCCTACTTCCTACTTGATTGATCA 59.036 40.000 0.00 0.00 34.44 2.92
2235 5567 6.617371 ACCCTACTTCCTACTTGATTGATCAT 59.383 38.462 0.00 0.00 36.56 2.45
2236 5568 6.933521 CCCTACTTCCTACTTGATTGATCATG 59.066 42.308 0.00 5.59 36.56 3.07
2237 5569 7.202038 CCCTACTTCCTACTTGATTGATCATGA 60.202 40.741 12.23 0.00 36.56 3.07
2238 5570 8.373981 CCTACTTCCTACTTGATTGATCATGAT 58.626 37.037 8.25 8.25 36.56 2.45
2239 5571 9.205719 CTACTTCCTACTTGATTGATCATGATG 57.794 37.037 14.30 0.00 36.56 3.07
2240 5572 7.799081 ACTTCCTACTTGATTGATCATGATGA 58.201 34.615 14.30 0.44 36.56 2.92
2241 5573 8.438373 ACTTCCTACTTGATTGATCATGATGAT 58.562 33.333 14.30 7.81 40.34 2.45
2242 5574 9.939802 CTTCCTACTTGATTGATCATGATGATA 57.060 33.333 14.30 0.00 37.20 2.15
2244 5576 9.886132 TCCTACTTGATTGATCATGATGATATG 57.114 33.333 14.30 0.00 37.20 1.78
2245 5577 9.886132 CCTACTTGATTGATCATGATGATATGA 57.114 33.333 14.30 0.00 37.20 2.15
2277 5609 7.726033 AAGAGTTGATCTACCACAAGATAGT 57.274 36.000 3.54 0.00 37.23 2.12
2278 5610 8.824756 AAGAGTTGATCTACCACAAGATAGTA 57.175 34.615 3.54 0.00 37.23 1.82
2279 5611 8.458573 AGAGTTGATCTACCACAAGATAGTAG 57.541 38.462 3.54 0.00 36.33 2.57
2280 5612 8.275758 AGAGTTGATCTACCACAAGATAGTAGA 58.724 37.037 3.54 1.92 44.75 2.59
2281 5613 8.458573 AGTTGATCTACCACAAGATAGTAGAG 57.541 38.462 3.54 0.00 44.10 2.43
2282 5614 7.504238 AGTTGATCTACCACAAGATAGTAGAGG 59.496 40.741 3.54 0.00 44.10 3.69
2283 5615 5.770663 TGATCTACCACAAGATAGTAGAGGC 59.229 44.000 5.47 1.70 44.10 4.70
2284 5616 5.390087 TCTACCACAAGATAGTAGAGGCT 57.610 43.478 0.00 0.00 38.01 4.58
2285 5617 6.511017 TCTACCACAAGATAGTAGAGGCTA 57.489 41.667 0.00 0.00 38.01 3.93
2286 5618 6.907961 TCTACCACAAGATAGTAGAGGCTAA 58.092 40.000 0.00 0.00 38.01 3.09
2287 5619 7.351952 TCTACCACAAGATAGTAGAGGCTAAA 58.648 38.462 0.00 0.00 38.01 1.85
2288 5620 6.223351 ACCACAAGATAGTAGAGGCTAAAC 57.777 41.667 0.00 0.00 0.00 2.01
2289 5621 5.128991 ACCACAAGATAGTAGAGGCTAAACC 59.871 44.000 0.00 0.00 39.61 3.27
2290 5622 5.453480 CCACAAGATAGTAGAGGCTAAACCC 60.453 48.000 0.00 0.00 40.58 4.11
2291 5623 5.364157 CACAAGATAGTAGAGGCTAAACCCT 59.636 44.000 0.00 0.00 40.58 4.34
2292 5624 6.550108 CACAAGATAGTAGAGGCTAAACCCTA 59.450 42.308 0.00 0.00 40.58 3.53
2293 5625 6.778559 ACAAGATAGTAGAGGCTAAACCCTAG 59.221 42.308 0.00 0.00 40.58 3.02
2294 5626 6.783517 AGATAGTAGAGGCTAAACCCTAGA 57.216 41.667 0.00 0.00 40.58 2.43
2295 5627 7.164233 AGATAGTAGAGGCTAAACCCTAGAA 57.836 40.000 0.00 0.00 40.58 2.10
2296 5628 7.235804 AGATAGTAGAGGCTAAACCCTAGAAG 58.764 42.308 0.00 0.00 40.58 2.85
2297 5629 3.962063 AGTAGAGGCTAAACCCTAGAAGC 59.038 47.826 0.00 0.00 40.58 3.86
2298 5630 3.123392 AGAGGCTAAACCCTAGAAGCT 57.877 47.619 0.00 0.00 40.58 3.74
2299 5631 4.267341 AGAGGCTAAACCCTAGAAGCTA 57.733 45.455 0.00 0.00 40.58 3.32
2300 5632 4.219919 AGAGGCTAAACCCTAGAAGCTAG 58.780 47.826 0.00 0.00 40.58 3.42
2301 5633 2.701423 AGGCTAAACCCTAGAAGCTAGC 59.299 50.000 6.62 6.62 40.58 3.42
2302 5634 2.701423 GGCTAAACCCTAGAAGCTAGCT 59.299 50.000 12.68 12.68 35.30 3.32
2303 5635 3.134985 GGCTAAACCCTAGAAGCTAGCTT 59.865 47.826 29.71 29.71 39.23 3.74
2304 5636 6.913917 AGGCTAAACCCTAGAAGCTAGCTTC 61.914 48.000 38.95 38.95 45.34 3.86
2317 5649 7.727331 GAAGCTAGCTTCTGATTATGATTGT 57.273 36.000 38.57 11.69 46.38 2.71
2318 5650 8.152309 GAAGCTAGCTTCTGATTATGATTGTT 57.848 34.615 38.57 11.32 46.38 2.83
2319 5651 7.493743 AGCTAGCTTCTGATTATGATTGTTG 57.506 36.000 12.68 0.00 0.00 3.33
2320 5652 7.052873 AGCTAGCTTCTGATTATGATTGTTGT 58.947 34.615 12.68 0.00 0.00 3.32
2321 5653 7.555554 AGCTAGCTTCTGATTATGATTGTTGTT 59.444 33.333 12.68 0.00 0.00 2.83
2322 5654 7.642978 GCTAGCTTCTGATTATGATTGTTGTTG 59.357 37.037 7.70 0.00 0.00 3.33
2323 5655 7.458409 AGCTTCTGATTATGATTGTTGTTGT 57.542 32.000 0.00 0.00 0.00 3.32
2324 5656 7.533426 AGCTTCTGATTATGATTGTTGTTGTC 58.467 34.615 0.00 0.00 0.00 3.18
2325 5657 6.749118 GCTTCTGATTATGATTGTTGTTGTCC 59.251 38.462 0.00 0.00 0.00 4.02
2326 5658 7.362401 GCTTCTGATTATGATTGTTGTTGTCCT 60.362 37.037 0.00 0.00 0.00 3.85
2327 5659 9.166173 CTTCTGATTATGATTGTTGTTGTCCTA 57.834 33.333 0.00 0.00 0.00 2.94
2328 5660 8.492673 TCTGATTATGATTGTTGTTGTCCTAC 57.507 34.615 0.00 0.00 0.00 3.18
2329 5661 7.277760 TCTGATTATGATTGTTGTTGTCCTACG 59.722 37.037 0.00 0.00 0.00 3.51
2330 5662 6.315144 TGATTATGATTGTTGTTGTCCTACGG 59.685 38.462 0.00 0.00 0.00 4.02
2331 5663 3.755112 TGATTGTTGTTGTCCTACGGA 57.245 42.857 0.00 0.00 0.00 4.69
2342 5674 2.149973 TCCTACGGACTAAACCCTCC 57.850 55.000 0.00 0.00 0.00 4.30
2358 5690 3.899980 ACCCTCCGGTTTATATAGACACC 59.100 47.826 0.00 2.59 40.58 4.16
2375 5707 2.810403 CGGAGGGGCTACGGTTAC 59.190 66.667 0.00 0.00 33.64 2.50
2376 5708 2.053865 CGGAGGGGCTACGGTTACA 61.054 63.158 0.00 0.00 33.64 2.41
2377 5709 1.397390 CGGAGGGGCTACGGTTACAT 61.397 60.000 0.00 0.00 33.64 2.29
2378 5710 1.708341 GGAGGGGCTACGGTTACATA 58.292 55.000 0.00 0.00 0.00 2.29
2379 5711 1.617357 GGAGGGGCTACGGTTACATAG 59.383 57.143 0.00 0.00 0.00 2.23
2380 5712 2.590821 GAGGGGCTACGGTTACATAGA 58.409 52.381 0.00 0.00 0.00 1.98
2381 5713 2.557490 GAGGGGCTACGGTTACATAGAG 59.443 54.545 0.00 0.00 0.00 2.43
2382 5714 2.091444 AGGGGCTACGGTTACATAGAGT 60.091 50.000 0.00 0.00 0.00 3.24
2383 5715 2.295629 GGGGCTACGGTTACATAGAGTC 59.704 54.545 0.00 0.00 0.00 3.36
2384 5716 2.031333 GGGCTACGGTTACATAGAGTCG 60.031 54.545 0.00 0.00 0.00 4.18
2385 5717 2.031333 GGCTACGGTTACATAGAGTCGG 60.031 54.545 0.00 0.00 0.00 4.79
2386 5718 2.615912 GCTACGGTTACATAGAGTCGGT 59.384 50.000 0.00 0.00 0.00 4.69
2387 5719 3.065925 GCTACGGTTACATAGAGTCGGTT 59.934 47.826 0.00 0.00 0.00 4.44
2388 5720 3.498927 ACGGTTACATAGAGTCGGTTG 57.501 47.619 0.00 0.00 0.00 3.77
2389 5721 2.190981 CGGTTACATAGAGTCGGTTGC 58.809 52.381 0.00 0.00 0.00 4.17
2390 5722 2.416296 CGGTTACATAGAGTCGGTTGCA 60.416 50.000 0.00 0.00 0.00 4.08
2391 5723 3.187700 GGTTACATAGAGTCGGTTGCAG 58.812 50.000 0.00 0.00 0.00 4.41
2392 5724 3.119245 GGTTACATAGAGTCGGTTGCAGA 60.119 47.826 0.00 0.00 0.00 4.26
2393 5725 2.949451 ACATAGAGTCGGTTGCAGAG 57.051 50.000 0.00 0.00 0.00 3.35
2394 5726 2.447443 ACATAGAGTCGGTTGCAGAGA 58.553 47.619 0.00 0.00 0.00 3.10
2395 5727 2.826128 ACATAGAGTCGGTTGCAGAGAA 59.174 45.455 0.00 0.00 0.00 2.87
2396 5728 3.119316 ACATAGAGTCGGTTGCAGAGAAG 60.119 47.826 0.00 0.00 0.00 2.85
2397 5729 0.605589 AGAGTCGGTTGCAGAGAAGG 59.394 55.000 0.00 0.00 0.00 3.46
2398 5730 0.603569 GAGTCGGTTGCAGAGAAGGA 59.396 55.000 0.00 0.00 0.00 3.36
2399 5731 1.000955 GAGTCGGTTGCAGAGAAGGAA 59.999 52.381 0.00 0.00 0.00 3.36
2400 5732 1.416401 AGTCGGTTGCAGAGAAGGAAA 59.584 47.619 0.00 0.00 0.00 3.13
2401 5733 2.039084 AGTCGGTTGCAGAGAAGGAAAT 59.961 45.455 0.00 0.00 0.00 2.17
2402 5734 2.416893 GTCGGTTGCAGAGAAGGAAATC 59.583 50.000 0.00 0.00 0.00 2.17
2403 5735 2.303022 TCGGTTGCAGAGAAGGAAATCT 59.697 45.455 0.00 0.00 0.00 2.40
2404 5736 3.513912 TCGGTTGCAGAGAAGGAAATCTA 59.486 43.478 0.00 0.00 0.00 1.98
2405 5737 3.619038 CGGTTGCAGAGAAGGAAATCTAC 59.381 47.826 0.00 0.00 0.00 2.59
2406 5738 4.579869 GGTTGCAGAGAAGGAAATCTACA 58.420 43.478 0.00 0.00 0.00 2.74
2407 5739 5.189180 GGTTGCAGAGAAGGAAATCTACAT 58.811 41.667 0.00 0.00 0.00 2.29
2408 5740 6.349300 GGTTGCAGAGAAGGAAATCTACATA 58.651 40.000 0.00 0.00 0.00 2.29
2409 5741 6.995091 GGTTGCAGAGAAGGAAATCTACATAT 59.005 38.462 0.00 0.00 0.00 1.78
2410 5742 7.172361 GGTTGCAGAGAAGGAAATCTACATATC 59.828 40.741 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.401058 TGATTTTCCTTTCATTCTTCCTCTATC 57.599 33.333 0.00 0.00 0.00 2.08
119 128 5.359756 AGCATATCGTGTTATTGCTCTTCA 58.640 37.500 0.00 0.00 0.00 3.02
142 151 3.004171 CCATATTTTTCCACCACGACGA 58.996 45.455 0.00 0.00 0.00 4.20
279 288 3.199946 TCAGATACTCCACCCCATTTCAC 59.800 47.826 0.00 0.00 0.00 3.18
286 295 2.572104 ACAGTTTCAGATACTCCACCCC 59.428 50.000 0.00 0.00 0.00 4.95
290 299 6.424032 TCTAGCTACAGTTTCAGATACTCCA 58.576 40.000 0.00 0.00 0.00 3.86
621 646 3.583806 CATTTTGGGCAATGCGTCTTTA 58.416 40.909 0.00 0.00 0.00 1.85
637 662 5.359194 TCGGATCTTTCTAGAGGCATTTT 57.641 39.130 0.00 0.00 32.92 1.82
740 765 7.781056 ACCTTTTTGATCAATTATAACCGCAT 58.219 30.769 9.40 0.00 0.00 4.73
871 896 7.953305 TTAATTCTTTGATCTCAATTTCGCG 57.047 32.000 0.00 0.00 35.55 5.87
1140 1172 2.224209 ACGTTCCTGATGTTTCCGAACT 60.224 45.455 0.00 0.00 36.70 3.01
1179 1212 4.847633 TCTTTTGATGTCGCAAAGTTGAG 58.152 39.130 0.00 0.00 38.80 3.02
1259 1292 5.663456 AGTTGGTATAAATTCGTAAGCCGA 58.337 37.500 0.00 0.00 45.66 5.54
1374 1407 5.970640 ACATAAGACTTCTCCCCCAATTCTA 59.029 40.000 0.00 0.00 0.00 2.10
1418 1451 7.598278 CGAGATAGAATTTGAGCACTATAGGT 58.402 38.462 4.43 0.00 0.00 3.08
1543 1595 3.557686 GGGCTTCCGTAACTAAACCTTCA 60.558 47.826 0.00 0.00 0.00 3.02
1584 1636 3.326747 GTGTCATTCTCTAGCCAAACGT 58.673 45.455 0.00 0.00 0.00 3.99
1589 1641 3.106827 TGATGGTGTCATTCTCTAGCCA 58.893 45.455 0.00 0.00 32.98 4.75
1659 1712 0.033601 TTTTGACCCGATCCCCCATG 60.034 55.000 0.00 0.00 0.00 3.66
1669 1722 4.212636 ACGACTTACTTCAATTTTGACCCG 59.787 41.667 0.00 0.00 36.83 5.28
1823 1876 2.522836 ATGCGATGCTCTAACCTCTG 57.477 50.000 0.00 0.00 0.00 3.35
1893 1946 8.188799 AGATTCTTGTTCGTAGAACATCGATAA 58.811 33.333 15.16 7.18 45.90 1.75
2060 5392 2.225019 CACCATCATCTTCGGCATAAGC 59.775 50.000 0.00 0.00 41.10 3.09
2061 5393 2.810274 CCACCATCATCTTCGGCATAAG 59.190 50.000 0.00 0.00 0.00 1.73
2062 5394 2.437651 TCCACCATCATCTTCGGCATAA 59.562 45.455 0.00 0.00 0.00 1.90
2063 5395 2.046292 TCCACCATCATCTTCGGCATA 58.954 47.619 0.00 0.00 0.00 3.14
2064 5396 0.839277 TCCACCATCATCTTCGGCAT 59.161 50.000 0.00 0.00 0.00 4.40
2065 5397 0.617935 TTCCACCATCATCTTCGGCA 59.382 50.000 0.00 0.00 0.00 5.69
2066 5398 1.303309 CTTCCACCATCATCTTCGGC 58.697 55.000 0.00 0.00 0.00 5.54
2067 5399 1.210478 ACCTTCCACCATCATCTTCGG 59.790 52.381 0.00 0.00 0.00 4.30
2068 5400 2.698855 ACCTTCCACCATCATCTTCG 57.301 50.000 0.00 0.00 0.00 3.79
2069 5401 4.310769 CGATACCTTCCACCATCATCTTC 58.689 47.826 0.00 0.00 0.00 2.87
2070 5402 3.071602 CCGATACCTTCCACCATCATCTT 59.928 47.826 0.00 0.00 0.00 2.40
2071 5403 2.634940 CCGATACCTTCCACCATCATCT 59.365 50.000 0.00 0.00 0.00 2.90
2072 5404 2.368875 ACCGATACCTTCCACCATCATC 59.631 50.000 0.00 0.00 0.00 2.92
2073 5405 2.104792 CACCGATACCTTCCACCATCAT 59.895 50.000 0.00 0.00 0.00 2.45
2074 5406 1.484653 CACCGATACCTTCCACCATCA 59.515 52.381 0.00 0.00 0.00 3.07
2075 5407 1.485066 ACACCGATACCTTCCACCATC 59.515 52.381 0.00 0.00 0.00 3.51
2076 5408 1.485066 GACACCGATACCTTCCACCAT 59.515 52.381 0.00 0.00 0.00 3.55
2077 5409 0.899720 GACACCGATACCTTCCACCA 59.100 55.000 0.00 0.00 0.00 4.17
2078 5410 0.899720 TGACACCGATACCTTCCACC 59.100 55.000 0.00 0.00 0.00 4.61
2079 5411 2.754946 TTGACACCGATACCTTCCAC 57.245 50.000 0.00 0.00 0.00 4.02
2080 5412 3.404899 GTTTTGACACCGATACCTTCCA 58.595 45.455 0.00 0.00 0.00 3.53
2081 5413 2.745821 GGTTTTGACACCGATACCTTCC 59.254 50.000 0.00 0.00 0.00 3.46
2091 5423 1.918868 GATCCGCCGGTTTTGACACC 61.919 60.000 1.63 0.00 0.00 4.16
2092 5424 0.953960 AGATCCGCCGGTTTTGACAC 60.954 55.000 1.63 0.00 0.00 3.67
2093 5425 0.672401 GAGATCCGCCGGTTTTGACA 60.672 55.000 1.63 0.00 0.00 3.58
2094 5426 1.693083 CGAGATCCGCCGGTTTTGAC 61.693 60.000 1.63 0.00 0.00 3.18
2095 5427 1.447140 CGAGATCCGCCGGTTTTGA 60.447 57.895 1.63 0.00 0.00 2.69
2096 5428 1.421410 CTCGAGATCCGCCGGTTTTG 61.421 60.000 6.58 0.00 38.37 2.44
2097 5429 1.153628 CTCGAGATCCGCCGGTTTT 60.154 57.895 6.58 0.00 38.37 2.43
2098 5430 1.033746 TACTCGAGATCCGCCGGTTT 61.034 55.000 21.68 0.00 38.37 3.27
2099 5431 1.445716 CTACTCGAGATCCGCCGGTT 61.446 60.000 21.68 0.00 38.37 4.44
2100 5432 1.892862 CTACTCGAGATCCGCCGGT 60.893 63.158 21.68 0.00 38.37 5.28
2101 5433 2.618219 CCTACTCGAGATCCGCCGG 61.618 68.421 21.68 0.00 38.37 6.13
2102 5434 2.618219 CCCTACTCGAGATCCGCCG 61.618 68.421 21.68 0.00 38.37 6.46
2103 5435 2.269529 CCCCTACTCGAGATCCGCC 61.270 68.421 21.68 0.00 38.37 6.13
2104 5436 2.269529 CCCCCTACTCGAGATCCGC 61.270 68.421 21.68 0.00 38.37 5.54
2105 5437 0.890090 GACCCCCTACTCGAGATCCG 60.890 65.000 21.68 3.40 40.25 4.18
2106 5438 0.540133 GGACCCCCTACTCGAGATCC 60.540 65.000 21.68 9.76 0.00 3.36
2107 5439 0.540133 GGGACCCCCTACTCGAGATC 60.540 65.000 21.68 4.55 41.34 2.75
2108 5440 1.542679 GGGACCCCCTACTCGAGAT 59.457 63.158 21.68 6.08 41.34 2.75
2109 5441 3.013631 GGGACCCCCTACTCGAGA 58.986 66.667 21.68 1.61 41.34 4.04
2110 5442 2.518825 CGGGACCCCCTACTCGAG 60.519 72.222 11.84 11.84 42.67 4.04
2111 5443 4.133373 CCGGGACCCCCTACTCGA 62.133 72.222 4.46 0.00 42.67 4.04
2112 5444 2.941563 AATCCGGGACCCCCTACTCG 62.942 65.000 4.46 0.00 42.67 4.18
2113 5445 1.074699 AATCCGGGACCCCCTACTC 60.075 63.158 4.46 0.00 42.67 2.59
2114 5446 1.384082 CAATCCGGGACCCCCTACT 60.384 63.158 4.46 0.00 42.67 2.57
2115 5447 1.691689 ACAATCCGGGACCCCCTAC 60.692 63.158 4.46 0.00 42.67 3.18
2116 5448 1.691337 CACAATCCGGGACCCCCTA 60.691 63.158 4.46 0.00 42.67 3.53
2117 5449 3.015145 CACAATCCGGGACCCCCT 61.015 66.667 4.46 0.00 42.67 4.79
2118 5450 4.815108 GCACAATCCGGGACCCCC 62.815 72.222 4.46 0.00 41.09 5.40
2122 5454 2.862674 TTAGGCGCACAATCCGGGAC 62.863 60.000 10.83 0.00 0.00 4.46
2123 5455 2.587322 CTTAGGCGCACAATCCGGGA 62.587 60.000 10.83 0.00 0.00 5.14
2124 5456 2.124901 TTAGGCGCACAATCCGGG 60.125 61.111 10.83 0.00 0.00 5.73
2125 5457 2.180204 CCTTAGGCGCACAATCCGG 61.180 63.158 10.83 0.00 0.00 5.14
2126 5458 2.823829 GCCTTAGGCGCACAATCCG 61.824 63.158 7.77 0.00 39.62 4.18
2127 5459 3.111038 GCCTTAGGCGCACAATCC 58.889 61.111 7.77 0.00 39.62 3.01
2137 5469 5.338463 GCCTCCTATTACCATTAGCCTTAGG 60.338 48.000 0.00 0.00 0.00 2.69
2138 5470 5.624738 CGCCTCCTATTACCATTAGCCTTAG 60.625 48.000 0.00 0.00 0.00 2.18
2139 5471 4.222145 CGCCTCCTATTACCATTAGCCTTA 59.778 45.833 0.00 0.00 0.00 2.69
2140 5472 3.008049 CGCCTCCTATTACCATTAGCCTT 59.992 47.826 0.00 0.00 0.00 4.35
2141 5473 2.567615 CGCCTCCTATTACCATTAGCCT 59.432 50.000 0.00 0.00 0.00 4.58
2142 5474 2.354805 CCGCCTCCTATTACCATTAGCC 60.355 54.545 0.00 0.00 0.00 3.93
2143 5475 2.354805 CCCGCCTCCTATTACCATTAGC 60.355 54.545 0.00 0.00 0.00 3.09
2144 5476 2.236395 CCCCGCCTCCTATTACCATTAG 59.764 54.545 0.00 0.00 0.00 1.73
2145 5477 2.262637 CCCCGCCTCCTATTACCATTA 58.737 52.381 0.00 0.00 0.00 1.90
2146 5478 1.064825 CCCCGCCTCCTATTACCATT 58.935 55.000 0.00 0.00 0.00 3.16
2147 5479 0.840722 CCCCCGCCTCCTATTACCAT 60.841 60.000 0.00 0.00 0.00 3.55
2148 5480 1.460689 CCCCCGCCTCCTATTACCA 60.461 63.158 0.00 0.00 0.00 3.25
2149 5481 1.152183 TCCCCCGCCTCCTATTACC 60.152 63.158 0.00 0.00 0.00 2.85
2150 5482 0.761702 TGTCCCCCGCCTCCTATTAC 60.762 60.000 0.00 0.00 0.00 1.89
2151 5483 0.761702 GTGTCCCCCGCCTCCTATTA 60.762 60.000 0.00 0.00 0.00 0.98
2152 5484 2.070650 GTGTCCCCCGCCTCCTATT 61.071 63.158 0.00 0.00 0.00 1.73
2153 5485 2.446036 GTGTCCCCCGCCTCCTAT 60.446 66.667 0.00 0.00 0.00 2.57
2154 5486 2.833151 ATTGTGTCCCCCGCCTCCTA 62.833 60.000 0.00 0.00 0.00 2.94
2155 5487 4.974438 TTGTGTCCCCCGCCTCCT 62.974 66.667 0.00 0.00 0.00 3.69
2156 5488 3.728373 ATTGTGTCCCCCGCCTCC 61.728 66.667 0.00 0.00 0.00 4.30
2157 5489 2.438434 CATTGTGTCCCCCGCCTC 60.438 66.667 0.00 0.00 0.00 4.70
2158 5490 2.366153 AAACATTGTGTCCCCCGCCT 62.366 55.000 0.00 0.00 0.00 5.52
2159 5491 0.609681 TAAACATTGTGTCCCCCGCC 60.610 55.000 0.00 0.00 0.00 6.13
2160 5492 0.524414 GTAAACATTGTGTCCCCCGC 59.476 55.000 0.00 0.00 0.00 6.13
2161 5493 1.170442 GGTAAACATTGTGTCCCCCG 58.830 55.000 0.00 0.00 0.00 5.73
2162 5494 1.203075 TGGGTAAACATTGTGTCCCCC 60.203 52.381 5.22 6.45 33.96 5.40
2163 5495 2.167662 CTGGGTAAACATTGTGTCCCC 58.832 52.381 16.40 10.25 34.88 4.81
2164 5496 2.167662 CCTGGGTAAACATTGTGTCCC 58.832 52.381 13.79 13.79 35.85 4.46
2165 5497 2.871453 ACCTGGGTAAACATTGTGTCC 58.129 47.619 0.00 0.00 0.00 4.02
2166 5498 3.058501 CGAACCTGGGTAAACATTGTGTC 60.059 47.826 0.00 0.00 0.00 3.67
2167 5499 2.882137 CGAACCTGGGTAAACATTGTGT 59.118 45.455 0.00 0.00 0.00 3.72
2168 5500 2.227865 CCGAACCTGGGTAAACATTGTG 59.772 50.000 0.00 0.00 0.00 3.33
2169 5501 2.510613 CCGAACCTGGGTAAACATTGT 58.489 47.619 0.00 0.00 0.00 2.71
2170 5502 1.816224 CCCGAACCTGGGTAAACATTG 59.184 52.381 0.00 0.00 44.76 2.82
2171 5503 2.209690 CCCGAACCTGGGTAAACATT 57.790 50.000 0.00 0.00 44.76 2.71
2172 5504 3.970205 CCCGAACCTGGGTAAACAT 57.030 52.632 0.00 0.00 44.76 2.71
2180 5512 2.873557 TAGAGAGGGCCCGAACCTGG 62.874 65.000 18.44 0.00 38.79 4.45
2181 5513 0.760945 ATAGAGAGGGCCCGAACCTG 60.761 60.000 18.44 0.00 38.79 4.00
2182 5514 0.760945 CATAGAGAGGGCCCGAACCT 60.761 60.000 18.44 14.71 42.18 3.50
2183 5515 1.749033 CATAGAGAGGGCCCGAACC 59.251 63.158 18.44 7.31 0.00 3.62
2184 5516 0.759436 TCCATAGAGAGGGCCCGAAC 60.759 60.000 18.44 12.45 0.00 3.95
2185 5517 0.470080 CTCCATAGAGAGGGCCCGAA 60.470 60.000 18.44 0.98 43.39 4.30
2186 5518 1.153989 CTCCATAGAGAGGGCCCGA 59.846 63.158 18.44 3.54 43.39 5.14
2187 5519 3.784573 CTCCATAGAGAGGGCCCG 58.215 66.667 18.44 0.00 43.39 6.13
2193 5525 7.034967 AGTAGGGTATTACCTCCATAGAGAG 57.965 44.000 12.54 0.00 43.39 3.20
2194 5526 7.417811 AAGTAGGGTATTACCTCCATAGAGA 57.582 40.000 12.54 0.00 43.39 3.10
2195 5527 6.664384 GGAAGTAGGGTATTACCTCCATAGAG 59.336 46.154 12.54 0.00 42.09 2.43
2196 5528 6.337472 AGGAAGTAGGGTATTACCTCCATAGA 59.663 42.308 16.39 0.00 42.09 1.98
2197 5529 6.563163 AGGAAGTAGGGTATTACCTCCATAG 58.437 44.000 16.39 0.00 42.09 2.23
2198 5530 6.556644 AGGAAGTAGGGTATTACCTCCATA 57.443 41.667 16.39 3.42 42.09 2.74
2199 5531 5.435545 AGGAAGTAGGGTATTACCTCCAT 57.564 43.478 16.39 4.17 42.09 3.41
2200 5532 4.913154 AGGAAGTAGGGTATTACCTCCA 57.087 45.455 16.39 0.80 42.09 3.86
2201 5533 5.963092 AGTAGGAAGTAGGGTATTACCTCC 58.037 45.833 12.54 10.66 42.09 4.30
2202 5534 7.065504 TCAAGTAGGAAGTAGGGTATTACCTC 58.934 42.308 12.54 2.11 42.09 3.85
2203 5535 6.989894 TCAAGTAGGAAGTAGGGTATTACCT 58.010 40.000 12.54 0.00 44.75 3.08
2204 5536 7.852550 ATCAAGTAGGAAGTAGGGTATTACC 57.147 40.000 4.11 4.11 37.60 2.85
2205 5537 8.921205 TCAATCAAGTAGGAAGTAGGGTATTAC 58.079 37.037 0.00 0.00 0.00 1.89
2206 5538 9.670442 ATCAATCAAGTAGGAAGTAGGGTATTA 57.330 33.333 0.00 0.00 0.00 0.98
2207 5539 7.989947 TCAATCAAGTAGGAAGTAGGGTATT 57.010 36.000 0.00 0.00 0.00 1.89
2208 5540 7.789831 TGATCAATCAAGTAGGAAGTAGGGTAT 59.210 37.037 0.00 0.00 33.08 2.73
2209 5541 7.130099 TGATCAATCAAGTAGGAAGTAGGGTA 58.870 38.462 0.00 0.00 33.08 3.69
2210 5542 5.964477 TGATCAATCAAGTAGGAAGTAGGGT 59.036 40.000 0.00 0.00 33.08 4.34
2211 5543 6.485830 TGATCAATCAAGTAGGAAGTAGGG 57.514 41.667 0.00 0.00 33.08 3.53
2212 5544 7.730084 TCATGATCAATCAAGTAGGAAGTAGG 58.270 38.462 0.00 0.00 40.69 3.18
2213 5545 9.205719 CATCATGATCAATCAAGTAGGAAGTAG 57.794 37.037 4.86 0.00 40.69 2.57
2214 5546 8.927411 TCATCATGATCAATCAAGTAGGAAGTA 58.073 33.333 4.86 0.00 40.69 2.24
2215 5547 7.799081 TCATCATGATCAATCAAGTAGGAAGT 58.201 34.615 4.86 0.00 40.69 3.01
2216 5548 8.850007 ATCATCATGATCAATCAAGTAGGAAG 57.150 34.615 4.86 0.00 40.69 3.46
2218 5550 9.886132 CATATCATCATGATCAATCAAGTAGGA 57.114 33.333 2.48 0.00 40.69 2.94
2219 5551 9.886132 TCATATCATCATGATCAATCAAGTAGG 57.114 33.333 2.48 0.00 40.69 3.18
2251 5583 9.427821 ACTATCTTGTGGTAGATCAACTCTTAT 57.572 33.333 0.00 0.00 36.34 1.73
2252 5584 8.824756 ACTATCTTGTGGTAGATCAACTCTTA 57.175 34.615 0.00 0.00 36.34 2.10
2253 5585 7.726033 ACTATCTTGTGGTAGATCAACTCTT 57.274 36.000 0.00 0.00 36.34 2.85
2254 5586 8.275758 TCTACTATCTTGTGGTAGATCAACTCT 58.724 37.037 0.00 0.00 43.47 3.24
2255 5587 8.453238 TCTACTATCTTGTGGTAGATCAACTC 57.547 38.462 0.00 0.00 43.47 3.01
2256 5588 7.504238 CCTCTACTATCTTGTGGTAGATCAACT 59.496 40.741 0.00 0.00 46.03 3.16
2257 5589 7.653647 CCTCTACTATCTTGTGGTAGATCAAC 58.346 42.308 0.00 0.00 46.03 3.18
2258 5590 6.265649 GCCTCTACTATCTTGTGGTAGATCAA 59.734 42.308 0.00 0.00 46.03 2.57
2259 5591 5.770663 GCCTCTACTATCTTGTGGTAGATCA 59.229 44.000 0.00 0.00 46.03 2.92
2260 5592 6.007703 AGCCTCTACTATCTTGTGGTAGATC 58.992 44.000 0.00 0.00 46.03 2.75
2261 5593 5.959512 AGCCTCTACTATCTTGTGGTAGAT 58.040 41.667 0.00 0.00 46.03 1.98
2262 5594 5.390087 AGCCTCTACTATCTTGTGGTAGA 57.610 43.478 0.00 0.00 45.35 2.59
2263 5595 7.427214 GTTTAGCCTCTACTATCTTGTGGTAG 58.573 42.308 0.00 0.00 41.75 3.18
2264 5596 6.323225 GGTTTAGCCTCTACTATCTTGTGGTA 59.677 42.308 0.00 0.00 0.00 3.25
2265 5597 5.128991 GGTTTAGCCTCTACTATCTTGTGGT 59.871 44.000 0.00 0.00 0.00 4.16
2266 5598 5.453480 GGGTTTAGCCTCTACTATCTTGTGG 60.453 48.000 0.00 0.00 37.43 4.17
2267 5599 5.364157 AGGGTTTAGCCTCTACTATCTTGTG 59.636 44.000 0.00 0.00 37.43 3.33
2268 5600 5.530243 AGGGTTTAGCCTCTACTATCTTGT 58.470 41.667 0.00 0.00 37.43 3.16
2269 5601 7.005296 TCTAGGGTTTAGCCTCTACTATCTTG 58.995 42.308 3.32 0.00 37.43 3.02
2270 5602 7.164233 TCTAGGGTTTAGCCTCTACTATCTT 57.836 40.000 3.32 0.00 37.43 2.40
2271 5603 6.783517 TCTAGGGTTTAGCCTCTACTATCT 57.216 41.667 3.32 0.00 37.43 1.98
2272 5604 6.071784 GCTTCTAGGGTTTAGCCTCTACTATC 60.072 46.154 3.32 0.00 37.43 2.08
2273 5605 5.776208 GCTTCTAGGGTTTAGCCTCTACTAT 59.224 44.000 3.32 0.00 37.43 2.12
2274 5606 5.103601 AGCTTCTAGGGTTTAGCCTCTACTA 60.104 44.000 3.32 0.00 37.43 1.82
2275 5607 3.962063 GCTTCTAGGGTTTAGCCTCTACT 59.038 47.826 3.32 0.00 37.43 2.57
2276 5608 3.962063 AGCTTCTAGGGTTTAGCCTCTAC 59.038 47.826 3.32 0.00 37.43 2.59
2277 5609 4.267341 AGCTTCTAGGGTTTAGCCTCTA 57.733 45.455 3.32 0.00 37.43 2.43
2278 5610 3.123392 AGCTTCTAGGGTTTAGCCTCT 57.877 47.619 3.32 0.00 37.43 3.69
2279 5611 3.243941 GCTAGCTTCTAGGGTTTAGCCTC 60.244 52.174 7.70 0.00 37.43 4.70
2280 5612 2.701423 GCTAGCTTCTAGGGTTTAGCCT 59.299 50.000 7.70 5.72 37.43 4.58
2281 5613 2.701423 AGCTAGCTTCTAGGGTTTAGCC 59.299 50.000 12.68 0.00 35.34 3.93
2282 5614 4.373527 GAAGCTAGCTTCTAGGGTTTAGC 58.626 47.826 38.57 16.96 46.38 3.09
2294 5626 7.555554 ACAACAATCATAATCAGAAGCTAGCTT 59.444 33.333 29.71 29.71 39.23 3.74
2295 5627 7.052873 ACAACAATCATAATCAGAAGCTAGCT 58.947 34.615 12.68 12.68 0.00 3.32
2296 5628 7.256756 ACAACAATCATAATCAGAAGCTAGC 57.743 36.000 6.62 6.62 0.00 3.42
2297 5629 8.671921 ACAACAACAATCATAATCAGAAGCTAG 58.328 33.333 0.00 0.00 0.00 3.42
2298 5630 8.565896 ACAACAACAATCATAATCAGAAGCTA 57.434 30.769 0.00 0.00 0.00 3.32
2299 5631 7.362401 GGACAACAACAATCATAATCAGAAGCT 60.362 37.037 0.00 0.00 0.00 3.74
2300 5632 6.749118 GGACAACAACAATCATAATCAGAAGC 59.251 38.462 0.00 0.00 0.00 3.86
2301 5633 8.048534 AGGACAACAACAATCATAATCAGAAG 57.951 34.615 0.00 0.00 0.00 2.85
2302 5634 8.946085 GTAGGACAACAACAATCATAATCAGAA 58.054 33.333 0.00 0.00 0.00 3.02
2303 5635 7.277760 CGTAGGACAACAACAATCATAATCAGA 59.722 37.037 0.00 0.00 0.00 3.27
2304 5636 7.401860 CGTAGGACAACAACAATCATAATCAG 58.598 38.462 0.00 0.00 0.00 2.90
2305 5637 7.302350 CGTAGGACAACAACAATCATAATCA 57.698 36.000 0.00 0.00 0.00 2.57
2343 5675 3.260128 CCCCTCCGGTGTCTATATAAACC 59.740 52.174 0.00 0.68 0.00 3.27
2344 5676 3.306571 GCCCCTCCGGTGTCTATATAAAC 60.307 52.174 0.00 0.00 0.00 2.01
2345 5677 2.901839 GCCCCTCCGGTGTCTATATAAA 59.098 50.000 0.00 0.00 0.00 1.40
2346 5678 2.111255 AGCCCCTCCGGTGTCTATATAA 59.889 50.000 0.00 0.00 0.00 0.98
2347 5679 1.714787 AGCCCCTCCGGTGTCTATATA 59.285 52.381 0.00 0.00 0.00 0.86
2348 5680 0.487772 AGCCCCTCCGGTGTCTATAT 59.512 55.000 0.00 0.00 0.00 0.86
2349 5681 1.151760 TAGCCCCTCCGGTGTCTATA 58.848 55.000 0.00 0.00 0.00 1.31
2350 5682 0.469518 GTAGCCCCTCCGGTGTCTAT 60.470 60.000 0.00 0.00 0.00 1.98
2351 5683 1.076485 GTAGCCCCTCCGGTGTCTA 60.076 63.158 0.00 0.00 0.00 2.59
2352 5684 2.363925 GTAGCCCCTCCGGTGTCT 60.364 66.667 0.00 0.00 0.00 3.41
2353 5685 3.834799 CGTAGCCCCTCCGGTGTC 61.835 72.222 0.00 0.00 0.00 3.67
2357 5689 2.442643 TAACCGTAGCCCCTCCGG 60.443 66.667 0.00 0.00 46.93 5.14
2358 5690 1.397390 ATGTAACCGTAGCCCCTCCG 61.397 60.000 0.00 0.00 0.00 4.63
2359 5691 1.617357 CTATGTAACCGTAGCCCCTCC 59.383 57.143 0.00 0.00 0.00 4.30
2360 5692 2.557490 CTCTATGTAACCGTAGCCCCTC 59.443 54.545 0.00 0.00 31.36 4.30
2361 5693 2.091444 ACTCTATGTAACCGTAGCCCCT 60.091 50.000 0.00 0.00 31.36 4.79
2362 5694 2.295629 GACTCTATGTAACCGTAGCCCC 59.704 54.545 0.00 0.00 31.36 5.80
2363 5695 2.031333 CGACTCTATGTAACCGTAGCCC 60.031 54.545 0.00 0.00 31.36 5.19
2364 5696 2.031333 CCGACTCTATGTAACCGTAGCC 60.031 54.545 0.00 0.00 31.36 3.93
2365 5697 2.615912 ACCGACTCTATGTAACCGTAGC 59.384 50.000 0.00 0.00 31.36 3.58
2366 5698 4.595116 CAACCGACTCTATGTAACCGTAG 58.405 47.826 0.00 0.00 0.00 3.51
2367 5699 3.181497 GCAACCGACTCTATGTAACCGTA 60.181 47.826 0.00 0.00 0.00 4.02
2368 5700 2.416431 GCAACCGACTCTATGTAACCGT 60.416 50.000 0.00 0.00 0.00 4.83
2369 5701 2.190981 GCAACCGACTCTATGTAACCG 58.809 52.381 0.00 0.00 0.00 4.44
2370 5702 3.119245 TCTGCAACCGACTCTATGTAACC 60.119 47.826 0.00 0.00 0.00 2.85
2371 5703 4.106029 TCTGCAACCGACTCTATGTAAC 57.894 45.455 0.00 0.00 0.00 2.50
2372 5704 4.014406 TCTCTGCAACCGACTCTATGTAA 58.986 43.478 0.00 0.00 0.00 2.41
2373 5705 3.617284 TCTCTGCAACCGACTCTATGTA 58.383 45.455 0.00 0.00 0.00 2.29
2374 5706 2.447443 TCTCTGCAACCGACTCTATGT 58.553 47.619 0.00 0.00 0.00 2.29
2375 5707 3.443037 CTTCTCTGCAACCGACTCTATG 58.557 50.000 0.00 0.00 0.00 2.23
2376 5708 2.428890 CCTTCTCTGCAACCGACTCTAT 59.571 50.000 0.00 0.00 0.00 1.98
2377 5709 1.819288 CCTTCTCTGCAACCGACTCTA 59.181 52.381 0.00 0.00 0.00 2.43
2378 5710 0.605589 CCTTCTCTGCAACCGACTCT 59.394 55.000 0.00 0.00 0.00 3.24
2379 5711 0.603569 TCCTTCTCTGCAACCGACTC 59.396 55.000 0.00 0.00 0.00 3.36
2380 5712 1.048601 TTCCTTCTCTGCAACCGACT 58.951 50.000 0.00 0.00 0.00 4.18
2381 5713 1.878953 TTTCCTTCTCTGCAACCGAC 58.121 50.000 0.00 0.00 0.00 4.79
2382 5714 2.303022 AGATTTCCTTCTCTGCAACCGA 59.697 45.455 0.00 0.00 0.00 4.69
2383 5715 2.704572 AGATTTCCTTCTCTGCAACCG 58.295 47.619 0.00 0.00 0.00 4.44
2384 5716 4.579869 TGTAGATTTCCTTCTCTGCAACC 58.420 43.478 0.00 0.00 32.25 3.77
2385 5717 8.082334 GATATGTAGATTTCCTTCTCTGCAAC 57.918 38.462 0.00 0.00 37.59 4.17


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

AutoCloner maintained by Alex Coulton.