Multiple sequence alignment - TraesCS2A01G200200

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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 TraesCS2A01G200200 chr2A 100.000 5516 0 0 1 5516 173121711 173127226 0.000000e+00 10187
1 TraesCS2A01G200200 chr2A 92.000 75 6 0 5207 5281 173126847 173126921 7.560000e-19 106
2 TraesCS2A01G200200 chr2A 92.000 75 6 0 5137 5211 173126917 173126991 7.560000e-19 106
3 TraesCS2A01G200200 chr2D 96.683 5216 155 11 3 5214 162150983 162156184 0.000000e+00 8658
4 TraesCS2A01G200200 chr2D 94.286 245 14 0 5207 5451 162156107 162156351 5.220000e-100 375
5 TraesCS2A01G200200 chr2B 96.532 5219 163 13 3 5214 221479353 221484560 0.000000e+00 8619
6 TraesCS2A01G200200 chr2B 96.183 393 14 1 3469 3860 571193220 571193612 4.660000e-180 641
7 TraesCS2A01G200200 chr2B 95.135 185 6 2 5207 5391 221484485 221484666 6.990000e-74 289
8 TraesCS2A01G200200 chr2B 96.000 100 4 0 3339 3438 571193118 571193217 4.420000e-36 163
9 TraesCS2A01G200200 chr6A 96.183 393 14 1 3469 3860 558773019 558772627 4.660000e-180 641
10 TraesCS2A01G200200 chr6A 96.000 100 4 0 3339 3438 558773121 558773022 4.420000e-36 163
11 TraesCS2A01G200200 chr4A 96.183 393 14 1 3469 3860 560959024 560958632 4.660000e-180 641
12 TraesCS2A01G200200 chr4A 96.000 100 4 0 3339 3438 560959126 560959027 4.420000e-36 163
13 TraesCS2A01G200200 chr3A 96.183 393 14 1 3469 3860 41548611 41548219 4.660000e-180 641
14 TraesCS2A01G200200 chr3A 96.000 100 4 0 3339 3438 41548713 41548614 4.420000e-36 163
15 TraesCS2A01G200200 chr3A 95.062 81 2 2 5438 5516 51447987 51447907 5.800000e-25 126
16 TraesCS2A01G200200 chr6B 95.929 393 15 1 3469 3860 698422792 698422400 2.170000e-178 636
17 TraesCS2A01G200200 chr6B 96.000 100 4 0 3339 3438 698422894 698422795 4.420000e-36 163
18 TraesCS2A01G200200 chr5A 98.571 70 1 0 5447 5516 537119677 537119746 2.090000e-24 124
19 TraesCS2A01G200200 chr5A 93.750 80 2 2 5440 5516 573562500 573562579 3.490000e-22 117
20 TraesCS2A01G200200 chr7B 97.222 72 2 0 5445 5516 458512282 458512353 7.500000e-24 122
21 TraesCS2A01G200200 chr1A 98.551 69 1 0 5448 5516 427816463 427816395 7.500000e-24 122
22 TraesCS2A01G200200 chr1A 97.183 71 2 0 5446 5516 313736217 313736147 2.700000e-23 121
23 TraesCS2A01G200200 chr4B 92.857 84 4 2 5433 5516 315065360 315065441 2.700000e-23 121
24 TraesCS2A01G200200 chr4D 94.805 77 3 1 5441 5516 155576681 155576757 9.710000e-23 119
25 TraesCS2A01G200200 chr3D 93.671 79 5 0 5438 5516 1118860 1118938 9.710000e-23 119


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 TraesCS2A01G200200 chr2A 173121711 173127226 5515 False 3466.333333 10187 94.666667 1 5516 3 chr2A.!!$F1 5515
1 TraesCS2A01G200200 chr2D 162150983 162156351 5368 False 4516.500000 8658 95.484500 3 5451 2 chr2D.!!$F1 5448
2 TraesCS2A01G200200 chr2B 221479353 221484666 5313 False 4454.000000 8619 95.833500 3 5391 2 chr2B.!!$F1 5388

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
679 683 0.472471 TGGTCCTGGTCCAAACTCAC 59.528 55.000 10.35 0.0 31.50 3.51 F
1281 1285 1.955778 TCTTTTGTGTGTGCAGATGGG 59.044 47.619 0.00 0.0 0.00 4.00 F
1750 1754 1.067354 CCAAAATCTGCTGGGCAAGAC 60.067 52.381 0.00 0.0 38.41 3.01 F
3451 3459 1.059098 AGGCAGAGTCAATGGTCACA 58.941 50.000 0.00 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 1743 1.089920 CAGTACATGTCTTGCCCAGC 58.910 55.000 0.00 0.0 0.00 4.85 R
3246 3254 0.388520 TCACACTGACAGAATCGCCG 60.389 55.000 10.08 0.0 0.00 6.46 R
3696 3704 2.669569 GCGTCAGCTTGCTTCCCA 60.670 61.111 0.00 0.0 41.01 4.37 R
5170 5180 0.107410 CCACAATACCCGGCTAAGCA 60.107 55.000 0.00 0.0 0.00 3.91 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 32 4.359434 TCTAGAGCCGTGAGATATCAGT 57.641 45.455 5.32 0.00 0.00 3.41
34 35 3.027412 AGAGCCGTGAGATATCAGTGTT 58.973 45.455 5.32 0.00 0.00 3.32
78 79 3.617288 GCCCATGTTTCCTTGTCCAATTC 60.617 47.826 0.00 0.00 0.00 2.17
85 87 7.181569 TGTTTCCTTGTCCAATTCTTTTTCT 57.818 32.000 0.00 0.00 0.00 2.52
208 210 6.299141 TCCTTCAATTGTAGCTTTCTGAGTT 58.701 36.000 5.13 0.00 0.00 3.01
345 348 5.343249 CAAAACCTTGTGCTAGAATATGGC 58.657 41.667 0.00 0.00 35.58 4.40
468 472 7.880195 ACTCAATTATTTGCTATAGCCTGGTAG 59.120 37.037 21.84 9.79 41.18 3.18
476 480 7.406031 TTGCTATAGCCTGGTAGACATATAC 57.594 40.000 21.84 0.00 41.18 1.47
492 496 1.197055 ATACTCGTACAATGTGCGCG 58.803 50.000 18.59 15.18 41.09 6.86
497 501 0.643310 CGTACAATGTGCGCGTATGT 59.357 50.000 11.31 7.63 34.73 2.29
535 539 7.532682 TTTGGAAATGTACAAGTGCTTTTTC 57.467 32.000 0.00 3.49 0.00 2.29
562 566 3.937814 TGTGAGCATACACACCCTAAAG 58.062 45.455 7.18 0.00 44.29 1.85
621 625 3.482786 GCACTTCGTGTTTTGAGCTATG 58.517 45.455 0.00 0.00 35.75 2.23
657 661 5.866207 ACTAAGTTTTAGTCAGGTCTTGGG 58.134 41.667 0.00 0.00 0.00 4.12
679 683 0.472471 TGGTCCTGGTCCAAACTCAC 59.528 55.000 10.35 0.00 31.50 3.51
754 758 6.465084 TCAAAGTAGTTTTCCTTCTAGGCTC 58.535 40.000 0.00 0.00 34.61 4.70
783 787 9.198475 AGCTAGGTACATAGTTGTTACTGTTAT 57.802 33.333 15.45 0.00 37.28 1.89
810 814 8.555166 TTTATTTGTTTGAACAGCTACTTTCG 57.445 30.769 0.00 0.00 40.50 3.46
814 818 3.602390 TTGAACAGCTACTTTCGTTGC 57.398 42.857 0.00 0.00 41.30 4.17
866 870 9.919348 GTTTCTCGATAGTTCTAGTAGTACTTG 57.081 37.037 13.88 6.78 37.40 3.16
885 889 6.808008 ACTTGATTCACTATGTTCCAACAG 57.192 37.500 0.00 0.00 43.04 3.16
938 942 8.360390 TGTGCAGTATATCTGTGAATACTAAGG 58.640 37.037 0.00 0.00 45.23 2.69
956 960 2.733956 AGGCACAAGTTGTCCTTTGAA 58.266 42.857 16.66 0.00 28.20 2.69
957 961 3.096092 AGGCACAAGTTGTCCTTTGAAA 58.904 40.909 16.66 0.00 28.20 2.69
958 962 3.706086 AGGCACAAGTTGTCCTTTGAAAT 59.294 39.130 16.66 0.20 28.20 2.17
1032 1036 5.767168 AGTATTTCCCTTCTTATCTGCATGC 59.233 40.000 11.82 11.82 0.00 4.06
1107 1111 9.912634 AAAGTTGACAAAACATGGACTAATATG 57.087 29.630 0.00 0.00 0.00 1.78
1112 1116 7.280876 TGACAAAACATGGACTAATATGCTCTC 59.719 37.037 0.00 0.00 0.00 3.20
1136 1140 5.185454 TGTCCTTTGCTATGTTACAGATGG 58.815 41.667 0.00 0.00 0.00 3.51
1241 1245 9.288576 TGTTTACATATCATTGATCCCAATCTC 57.711 33.333 1.55 0.00 40.81 2.75
1256 1260 4.335594 CCCAATCTCATACCTCCGTTTTTC 59.664 45.833 0.00 0.00 0.00 2.29
1272 1276 6.702282 TCCGTTTTTCTTTTTCTTTTGTGTGT 59.298 30.769 0.00 0.00 0.00 3.72
1281 1285 1.955778 TCTTTTGTGTGTGCAGATGGG 59.044 47.619 0.00 0.00 0.00 4.00
1513 1517 4.062293 TGTTCGGTTTTGAGTATCCTGTG 58.938 43.478 0.00 0.00 0.00 3.66
1516 1520 3.833650 TCGGTTTTGAGTATCCTGTGGTA 59.166 43.478 0.00 0.00 0.00 3.25
1576 1580 5.376625 ACAAGCACTCATGTTAAAGGAGAA 58.623 37.500 0.00 0.00 33.00 2.87
1669 1673 4.457466 TCCCAAGAAGTTTACCTCAACAC 58.543 43.478 0.00 0.00 0.00 3.32
1739 1743 5.726980 TGGTGAGAAATTCCCAAAATCTG 57.273 39.130 0.00 0.00 0.00 2.90
1750 1754 1.067354 CCAAAATCTGCTGGGCAAGAC 60.067 52.381 0.00 0.00 38.41 3.01
1804 1808 4.134563 GCTGTTCTTGTGTAAAGAGGGAA 58.865 43.478 0.00 0.00 0.00 3.97
1844 1848 1.565759 TGCCTGGAATGCCAAGATACT 59.434 47.619 0.00 0.00 45.41 2.12
2056 2060 7.817962 AGATGTATACTTGGGTTGCGTATATTC 59.182 37.037 4.17 0.00 31.18 1.75
2068 2072 3.958147 TGCGTATATTCTCTGGTTCCAGA 59.042 43.478 18.81 18.81 40.34 3.86
2268 2273 3.055891 AGCACAGCCACAATATTTTTCCC 60.056 43.478 0.00 0.00 0.00 3.97
2274 2279 5.363580 CAGCCACAATATTTTTCCCTGGTAT 59.636 40.000 0.00 0.00 0.00 2.73
2331 2337 9.626045 GAAAAGTCCTGGAATTTTGTATACTTG 57.374 33.333 32.11 0.00 39.39 3.16
2332 2338 8.706322 AAAGTCCTGGAATTTTGTATACTTGT 57.294 30.769 15.79 0.00 0.00 3.16
2362 2368 9.722056 CCTCTATTTAATTATGTTGCTGTTGTC 57.278 33.333 0.00 0.00 0.00 3.18
2391 2397 7.707035 CGTCTTACTTATTTTCTGTAGGATGCT 59.293 37.037 0.00 0.00 0.00 3.79
2408 2414 1.672363 TGCTCCTGCATTTTCGCATAG 59.328 47.619 0.00 0.00 45.31 2.23
2433 2439 3.890756 TGTCTTTGCATTGATGTTCACCT 59.109 39.130 0.00 0.00 0.00 4.00
2522 2530 3.955471 TCAAGACATTCAATGAGGGGAC 58.045 45.455 3.79 0.00 0.00 4.46
2604 2612 2.699846 AGAAGCAGTTGGAATTGGCAAA 59.300 40.909 3.01 0.00 0.00 3.68
2757 2765 3.002791 TGATTTCAGACTAAGCAAGGCG 58.997 45.455 0.00 0.00 38.81 5.52
2805 2813 1.375908 CTGGCCTCGCTTACTTGCA 60.376 57.895 3.32 0.00 0.00 4.08
2970 2978 4.206375 TGAGAAAAGTTGCATCTGAACCA 58.794 39.130 0.00 0.00 0.00 3.67
2991 2999 2.165998 AGGCTGCTTGATTTTGGAGTC 58.834 47.619 0.00 0.00 0.00 3.36
2992 3000 1.203287 GGCTGCTTGATTTTGGAGTCC 59.797 52.381 0.73 0.73 0.00 3.85
3037 3045 4.406649 AGGTTAAGATTGCAATTGGATGGG 59.593 41.667 14.33 0.00 0.00 4.00
3163 3171 4.075963 GTGGTGGACACTAGTTTTGGTA 57.924 45.455 0.00 0.00 46.72 3.25
3246 3254 3.437049 GCTACAGTTCTTCACCACATTCC 59.563 47.826 0.00 0.00 0.00 3.01
3325 3333 7.210174 TGAAACTTATGAAGATCTGGATACCG 58.790 38.462 0.00 0.00 0.00 4.02
3328 3336 6.929625 ACTTATGAAGATCTGGATACCGATG 58.070 40.000 0.00 0.00 0.00 3.84
3334 3342 3.332187 AGATCTGGATACCGATGAGAGGA 59.668 47.826 0.00 0.00 0.00 3.71
3350 3358 4.256920 GAGAGGAAAACTGATGCAAGCTA 58.743 43.478 0.00 0.00 0.00 3.32
3398 3406 2.509548 CCCCAACTGGTGATAAGATGGA 59.490 50.000 0.00 0.00 39.34 3.41
3407 3415 3.439476 GGTGATAAGATGGATGCTGATGC 59.561 47.826 0.00 0.00 40.20 3.91
3451 3459 1.059098 AGGCAGAGTCAATGGTCACA 58.941 50.000 0.00 0.00 0.00 3.58
3498 3506 6.493116 CACAATGAATAATGTCTGCTCTTCC 58.507 40.000 0.00 0.00 0.00 3.46
3499 3507 6.094464 CACAATGAATAATGTCTGCTCTTCCA 59.906 38.462 0.00 0.00 0.00 3.53
3543 3551 5.246203 TGGTAATCAGAGGATACATGCTACC 59.754 44.000 0.00 0.00 35.99 3.18
3712 3720 1.737838 TTATGGGAAGCAAGCTGACG 58.262 50.000 0.00 0.00 0.00 4.35
3856 3864 0.518636 CGGACAGCTTCACAATGTGG 59.481 55.000 13.95 0.00 33.87 4.17
3949 3957 3.459232 TGCCTTCTGATTATGAGTCGG 57.541 47.619 0.00 0.00 0.00 4.79
3970 3978 5.129815 TCGGCTACAAGTTATATCCAACCTT 59.870 40.000 0.00 0.00 0.00 3.50
3988 3996 6.350361 CCAACCTTCATCTGACAATAATGCAA 60.350 38.462 0.00 0.00 0.00 4.08
3992 4000 8.408601 ACCTTCATCTGACAATAATGCAATAAC 58.591 33.333 0.00 0.00 0.00 1.89
4022 4030 5.132648 ACATACCTATGCATCCCTCAGAAAA 59.867 40.000 0.19 0.00 37.19 2.29
4063 4071 5.012458 TGCCTTCCAGATATCAATACCTCTG 59.988 44.000 5.32 0.00 35.88 3.35
4080 4088 3.055530 CCTCTGGTAGTGCAATCTTGAGT 60.056 47.826 0.00 0.00 0.00 3.41
4167 4175 0.886563 AAGCTCTTGCATGTGGCTTC 59.113 50.000 20.35 1.37 45.15 3.86
4499 4507 4.803098 AAACGAGTAAGGAGCTACATGT 57.197 40.909 2.69 2.69 0.00 3.21
4577 4585 5.824421 AGAGAATTCCATGATCTTGTGGTT 58.176 37.500 0.65 0.00 36.84 3.67
4634 4642 7.508977 TCAAATTTCTGTTTTGGGTTAGGAGAT 59.491 33.333 0.00 0.00 35.31 2.75
4774 4782 4.202202 TGTTTGCCGTCATTCCTTTTGATT 60.202 37.500 0.00 0.00 0.00 2.57
4904 4912 8.772250 TGGAGATTTTTCTGATGAGTTATACCT 58.228 33.333 0.00 0.00 0.00 3.08
4917 4925 9.134055 GATGAGTTATACCTGTACTCTTTACCT 57.866 37.037 0.00 0.00 39.18 3.08
4955 4964 7.736893 ACTATGTGGAGTTTCTAGAAAACTGT 58.263 34.615 19.30 10.98 40.27 3.55
5009 5018 3.282021 AGCTGAACTTTGAAGTCTTGCA 58.718 40.909 13.34 0.00 38.57 4.08
5046 5055 6.435428 TCAAAAAGGAGAACGCAAAATAGAC 58.565 36.000 0.00 0.00 0.00 2.59
5141 5151 6.508563 GCTTTTGCTCTTTTAGTTTGAGTTGC 60.509 38.462 0.00 0.00 43.35 4.17
5162 5172 3.895656 GCAGGTAGTGACAGTATATGGGA 59.104 47.826 0.00 0.00 0.00 4.37
5170 5180 9.080097 GTAGTGACAGTATATGGGACTAGATTT 57.920 37.037 0.00 0.00 31.14 2.17
5171 5181 7.957002 AGTGACAGTATATGGGACTAGATTTG 58.043 38.462 0.00 0.00 0.00 2.32
5172 5182 6.647067 GTGACAGTATATGGGACTAGATTTGC 59.353 42.308 0.00 0.00 0.00 3.68
5173 5183 6.554982 TGACAGTATATGGGACTAGATTTGCT 59.445 38.462 0.00 0.00 0.00 3.91
5174 5184 7.071196 TGACAGTATATGGGACTAGATTTGCTT 59.929 37.037 0.00 0.00 0.00 3.91
5175 5185 8.492415 ACAGTATATGGGACTAGATTTGCTTA 57.508 34.615 0.00 0.00 0.00 3.09
5176 5186 8.589338 ACAGTATATGGGACTAGATTTGCTTAG 58.411 37.037 0.00 0.00 0.00 2.18
5177 5187 7.547370 CAGTATATGGGACTAGATTTGCTTAGC 59.453 40.741 0.00 0.00 0.00 3.09
5178 5188 3.560636 TGGGACTAGATTTGCTTAGCC 57.439 47.619 0.29 0.00 0.00 3.93
5179 5189 2.158957 TGGGACTAGATTTGCTTAGCCG 60.159 50.000 0.29 0.00 0.00 5.52
5180 5190 2.484889 GGACTAGATTTGCTTAGCCGG 58.515 52.381 0.29 0.00 0.00 6.13
5181 5191 2.484889 GACTAGATTTGCTTAGCCGGG 58.515 52.381 2.18 0.00 0.00 5.73
5182 5192 1.838077 ACTAGATTTGCTTAGCCGGGT 59.162 47.619 12.58 12.58 0.00 5.28
5183 5193 3.036091 ACTAGATTTGCTTAGCCGGGTA 58.964 45.455 9.87 9.87 0.00 3.69
5184 5194 3.646637 ACTAGATTTGCTTAGCCGGGTAT 59.353 43.478 15.31 0.00 0.00 2.73
5185 5195 3.577805 AGATTTGCTTAGCCGGGTATT 57.422 42.857 15.31 0.00 0.00 1.89
5186 5196 3.214328 AGATTTGCTTAGCCGGGTATTG 58.786 45.455 15.31 11.60 0.00 1.90
5187 5197 2.500392 TTTGCTTAGCCGGGTATTGT 57.500 45.000 15.31 0.00 0.00 2.71
5188 5198 1.745232 TTGCTTAGCCGGGTATTGTG 58.255 50.000 15.31 6.66 0.00 3.33
5189 5199 0.107410 TGCTTAGCCGGGTATTGTGG 60.107 55.000 15.31 4.25 0.00 4.17
5193 5203 2.590092 GCCGGGTATTGTGGCTCT 59.410 61.111 2.18 0.00 45.40 4.09
5194 5204 1.819632 GCCGGGTATTGTGGCTCTG 60.820 63.158 2.18 0.00 45.40 3.35
5195 5205 1.602237 CCGGGTATTGTGGCTCTGT 59.398 57.895 0.00 0.00 0.00 3.41
5196 5206 0.828022 CCGGGTATTGTGGCTCTGTA 59.172 55.000 0.00 0.00 0.00 2.74
5197 5207 1.208535 CCGGGTATTGTGGCTCTGTAA 59.791 52.381 0.00 0.00 0.00 2.41
5198 5208 2.277084 CGGGTATTGTGGCTCTGTAAC 58.723 52.381 0.00 0.00 0.00 2.50
5199 5209 2.354303 CGGGTATTGTGGCTCTGTAACA 60.354 50.000 0.00 0.00 0.00 2.41
5200 5210 3.681594 CGGGTATTGTGGCTCTGTAACAT 60.682 47.826 0.00 0.00 0.00 2.71
5201 5211 4.270008 GGGTATTGTGGCTCTGTAACATT 58.730 43.478 0.00 0.00 0.00 2.71
5202 5212 4.705023 GGGTATTGTGGCTCTGTAACATTT 59.295 41.667 0.00 0.00 0.00 2.32
5203 5213 5.883673 GGGTATTGTGGCTCTGTAACATTTA 59.116 40.000 0.00 0.00 0.00 1.40
5204 5214 6.183360 GGGTATTGTGGCTCTGTAACATTTAC 60.183 42.308 0.00 0.00 0.00 2.01
5205 5215 6.598064 GGTATTGTGGCTCTGTAACATTTACT 59.402 38.462 0.00 0.00 0.00 2.24
5206 5216 7.767198 GGTATTGTGGCTCTGTAACATTTACTA 59.233 37.037 0.00 0.00 0.00 1.82
5207 5217 7.849804 ATTGTGGCTCTGTAACATTTACTAG 57.150 36.000 0.00 0.00 0.00 2.57
5208 5218 6.354794 TGTGGCTCTGTAACATTTACTAGT 57.645 37.500 0.00 0.00 0.00 2.57
5209 5219 6.765403 TGTGGCTCTGTAACATTTACTAGTT 58.235 36.000 0.00 0.00 0.00 2.24
5210 5220 6.649141 TGTGGCTCTGTAACATTTACTAGTTG 59.351 38.462 0.00 0.00 0.00 3.16
5211 5221 6.649557 GTGGCTCTGTAACATTTACTAGTTGT 59.350 38.462 0.00 0.00 0.00 3.32
5212 5222 6.649141 TGGCTCTGTAACATTTACTAGTTGTG 59.351 38.462 0.00 0.32 0.00 3.33
5213 5223 6.092259 GGCTCTGTAACATTTACTAGTTGTGG 59.908 42.308 0.00 0.00 0.00 4.17
5214 5224 6.092259 GCTCTGTAACATTTACTAGTTGTGGG 59.908 42.308 0.00 0.00 0.00 4.61
5215 5225 7.069877 TCTGTAACATTTACTAGTTGTGGGT 57.930 36.000 0.00 0.00 0.00 4.51
5216 5226 8.192743 TCTGTAACATTTACTAGTTGTGGGTA 57.807 34.615 0.00 0.00 0.00 3.69
5217 5227 8.308931 TCTGTAACATTTACTAGTTGTGGGTAG 58.691 37.037 0.00 0.00 0.00 3.18
5218 5228 7.965718 TGTAACATTTACTAGTTGTGGGTAGT 58.034 34.615 0.00 0.00 33.92 2.73
5219 5229 7.874016 TGTAACATTTACTAGTTGTGGGTAGTG 59.126 37.037 0.00 0.00 31.79 2.74
5220 5230 5.801380 ACATTTACTAGTTGTGGGTAGTGG 58.199 41.667 0.00 0.00 31.79 4.00
5221 5231 3.967332 TTACTAGTTGTGGGTAGTGGC 57.033 47.619 0.00 0.00 31.79 5.01
5222 5232 1.724545 ACTAGTTGTGGGTAGTGGCA 58.275 50.000 0.00 0.00 0.00 4.92
5223 5233 1.623811 ACTAGTTGTGGGTAGTGGCAG 59.376 52.381 0.00 0.00 0.00 4.85
5224 5234 1.623811 CTAGTTGTGGGTAGTGGCAGT 59.376 52.381 0.00 0.00 0.00 4.40
5225 5235 1.724545 AGTTGTGGGTAGTGGCAGTA 58.275 50.000 0.00 0.00 0.00 2.74
5226 5236 2.266279 AGTTGTGGGTAGTGGCAGTAT 58.734 47.619 5.16 0.00 0.00 2.12
5227 5237 2.027192 AGTTGTGGGTAGTGGCAGTATG 60.027 50.000 5.16 0.00 40.87 2.39
5228 5238 1.651737 TGTGGGTAGTGGCAGTATGT 58.348 50.000 5.16 0.00 39.31 2.29
5229 5239 1.277842 TGTGGGTAGTGGCAGTATGTG 59.722 52.381 5.16 0.00 39.31 3.21
5230 5240 0.908910 TGGGTAGTGGCAGTATGTGG 59.091 55.000 5.16 0.00 39.31 4.17
5231 5241 0.180406 GGGTAGTGGCAGTATGTGGG 59.820 60.000 5.16 0.00 39.31 4.61
5232 5242 0.180406 GGTAGTGGCAGTATGTGGGG 59.820 60.000 5.16 0.00 39.31 4.96
5233 5243 0.463833 GTAGTGGCAGTATGTGGGGC 60.464 60.000 5.16 0.00 39.31 5.80
5234 5244 0.620410 TAGTGGCAGTATGTGGGGCT 60.620 55.000 0.00 0.00 39.31 5.19
5235 5245 0.620410 AGTGGCAGTATGTGGGGCTA 60.620 55.000 0.00 0.00 39.31 3.93
5236 5246 0.179045 GTGGCAGTATGTGGGGCTAG 60.179 60.000 0.00 0.00 39.31 3.42
5237 5247 0.326143 TGGCAGTATGTGGGGCTAGA 60.326 55.000 0.00 0.00 39.31 2.43
5238 5248 1.059913 GGCAGTATGTGGGGCTAGAT 58.940 55.000 0.00 0.00 39.31 1.98
5239 5249 1.421646 GGCAGTATGTGGGGCTAGATT 59.578 52.381 0.00 0.00 39.31 2.40
5256 5266 2.880890 AGATTTGCTTAGCCGGCTATTG 59.119 45.455 35.60 29.01 0.00 1.90
5281 5291 5.642063 TGGCTCTGTAACATTTACTAGTTGC 59.358 40.000 0.00 0.00 0.00 4.17
5391 5401 3.084786 AGGAGTATTTTGGCACTGCTTC 58.915 45.455 0.00 0.00 40.10 3.86
5405 5415 2.484264 ACTGCTTCTATGTCGCAAAACC 59.516 45.455 0.00 0.00 32.66 3.27
5414 5424 3.529634 TGTCGCAAAACCTATGTTTCG 57.470 42.857 0.00 0.00 43.80 3.46
5419 5429 4.152759 TCGCAAAACCTATGTTTCGTAAGG 59.847 41.667 0.00 0.00 43.80 2.69
5462 5472 4.635699 AAAAAGTACTCCCTCCGTTCAT 57.364 40.909 0.00 0.00 0.00 2.57
5463 5473 4.635699 AAAAGTACTCCCTCCGTTCATT 57.364 40.909 0.00 0.00 0.00 2.57
5464 5474 4.635699 AAAGTACTCCCTCCGTTCATTT 57.364 40.909 0.00 0.00 0.00 2.32
5465 5475 4.635699 AAGTACTCCCTCCGTTCATTTT 57.364 40.909 0.00 0.00 0.00 1.82
5466 5476 4.635699 AGTACTCCCTCCGTTCATTTTT 57.364 40.909 0.00 0.00 0.00 1.94
5467 5477 4.324267 AGTACTCCCTCCGTTCATTTTTG 58.676 43.478 0.00 0.00 0.00 2.44
5468 5478 3.223674 ACTCCCTCCGTTCATTTTTGT 57.776 42.857 0.00 0.00 0.00 2.83
5469 5479 4.360951 ACTCCCTCCGTTCATTTTTGTA 57.639 40.909 0.00 0.00 0.00 2.41
5470 5480 4.721132 ACTCCCTCCGTTCATTTTTGTAA 58.279 39.130 0.00 0.00 0.00 2.41
5471 5481 4.760204 ACTCCCTCCGTTCATTTTTGTAAG 59.240 41.667 0.00 0.00 0.00 2.34
5472 5482 4.975631 TCCCTCCGTTCATTTTTGTAAGA 58.024 39.130 0.00 0.00 0.00 2.10
5473 5483 4.758165 TCCCTCCGTTCATTTTTGTAAGAC 59.242 41.667 0.00 0.00 0.00 3.01
5474 5484 4.378046 CCCTCCGTTCATTTTTGTAAGACG 60.378 45.833 0.00 0.00 0.00 4.18
5475 5485 4.212636 CCTCCGTTCATTTTTGTAAGACGT 59.787 41.667 0.00 0.00 0.00 4.34
5476 5486 5.277634 CCTCCGTTCATTTTTGTAAGACGTT 60.278 40.000 0.00 0.00 0.00 3.99
5477 5487 6.121613 TCCGTTCATTTTTGTAAGACGTTT 57.878 33.333 0.00 0.00 0.00 3.60
5478 5488 6.553524 TCCGTTCATTTTTGTAAGACGTTTT 58.446 32.000 0.00 0.00 0.00 2.43
5479 5489 7.692088 TCCGTTCATTTTTGTAAGACGTTTTA 58.308 30.769 0.00 0.00 0.00 1.52
5480 5490 7.851963 TCCGTTCATTTTTGTAAGACGTTTTAG 59.148 33.333 0.00 0.00 0.00 1.85
5481 5491 7.851963 CCGTTCATTTTTGTAAGACGTTTTAGA 59.148 33.333 0.00 0.00 0.00 2.10
5482 5492 8.667204 CGTTCATTTTTGTAAGACGTTTTAGAC 58.333 33.333 0.00 0.00 0.00 2.59
5483 5493 9.493206 GTTCATTTTTGTAAGACGTTTTAGACA 57.507 29.630 0.00 0.00 0.00 3.41
5492 5502 9.531942 TGTAAGACGTTTTAGACATTTAAGACA 57.468 29.630 0.00 0.00 0.00 3.41
5494 5504 7.118422 AGACGTTTTAGACATTTAAGACAGC 57.882 36.000 0.00 0.00 0.00 4.40
5495 5505 6.704493 AGACGTTTTAGACATTTAAGACAGCA 59.296 34.615 0.00 0.00 0.00 4.41
5496 5506 6.656003 ACGTTTTAGACATTTAAGACAGCAC 58.344 36.000 0.00 0.00 0.00 4.40
5497 5507 6.077838 CGTTTTAGACATTTAAGACAGCACC 58.922 40.000 0.00 0.00 0.00 5.01
5498 5508 6.073222 CGTTTTAGACATTTAAGACAGCACCT 60.073 38.462 0.00 0.00 0.00 4.00
5499 5509 7.117236 CGTTTTAGACATTTAAGACAGCACCTA 59.883 37.037 0.00 0.00 0.00 3.08
5500 5510 8.780249 GTTTTAGACATTTAAGACAGCACCTAA 58.220 33.333 0.00 0.00 0.00 2.69
5501 5511 8.911918 TTTAGACATTTAAGACAGCACCTAAA 57.088 30.769 0.00 0.00 0.00 1.85
5502 5512 8.911918 TTAGACATTTAAGACAGCACCTAAAA 57.088 30.769 0.00 0.00 0.00 1.52
5503 5513 7.203255 AGACATTTAAGACAGCACCTAAAAC 57.797 36.000 0.00 0.00 0.00 2.43
5504 5514 6.770785 AGACATTTAAGACAGCACCTAAAACA 59.229 34.615 0.00 0.00 0.00 2.83
5505 5515 6.970484 ACATTTAAGACAGCACCTAAAACAG 58.030 36.000 0.00 0.00 0.00 3.16
5506 5516 6.546034 ACATTTAAGACAGCACCTAAAACAGT 59.454 34.615 0.00 0.00 0.00 3.55
5507 5517 7.068226 ACATTTAAGACAGCACCTAAAACAGTT 59.932 33.333 0.00 0.00 0.00 3.16
5508 5518 6.613755 TTAAGACAGCACCTAAAACAGTTC 57.386 37.500 0.00 0.00 0.00 3.01
5509 5519 4.150897 AGACAGCACCTAAAACAGTTCA 57.849 40.909 0.00 0.00 0.00 3.18
5510 5520 4.523083 AGACAGCACCTAAAACAGTTCAA 58.477 39.130 0.00 0.00 0.00 2.69
5511 5521 5.133221 AGACAGCACCTAAAACAGTTCAAT 58.867 37.500 0.00 0.00 0.00 2.57
5512 5522 5.594317 AGACAGCACCTAAAACAGTTCAATT 59.406 36.000 0.00 0.00 0.00 2.32
5513 5523 6.096846 AGACAGCACCTAAAACAGTTCAATTT 59.903 34.615 0.00 0.00 0.00 1.82
5514 5524 6.273071 ACAGCACCTAAAACAGTTCAATTTC 58.727 36.000 0.00 0.00 0.00 2.17
5515 5525 6.127479 ACAGCACCTAAAACAGTTCAATTTCA 60.127 34.615 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.021229 TCACGGCTCTAGAAAATCCTGTA 58.979 43.478 0.00 0.00 0.00 2.74
1 2 2.832129 TCACGGCTCTAGAAAATCCTGT 59.168 45.455 0.00 0.00 0.00 4.00
16 17 6.700081 TGTTTATAACACTGATATCTCACGGC 59.300 38.462 3.98 0.00 36.25 5.68
31 32 7.489757 GCCAAGAACAAACAAGTGTTTATAACA 59.510 33.333 9.01 0.00 45.54 2.41
34 35 6.461788 GGGCCAAGAACAAACAAGTGTTTATA 60.462 38.462 4.39 0.00 45.54 0.98
78 79 9.044150 TCATCCTTTTGCATTTGTAAGAAAAAG 57.956 29.630 0.00 0.00 35.43 2.27
85 87 7.230849 ACAGATCATCCTTTTGCATTTGTAA 57.769 32.000 0.00 0.00 0.00 2.41
121 123 7.459795 TTGTGTAATATGCCAAAGACATTGA 57.540 32.000 0.00 0.00 41.85 2.57
208 210 1.837051 ATGGGCGCCGAAGATCCTA 60.837 57.895 22.54 0.00 0.00 2.94
313 315 2.731217 CACAAGGTTTTGCTAGCACAC 58.269 47.619 19.17 16.80 37.85 3.82
402 405 5.357032 TCTGAGCTGTATGAGAAATGTACGA 59.643 40.000 0.00 0.00 0.00 3.43
468 472 4.143597 GCGCACATTGTACGAGTATATGTC 60.144 45.833 13.45 0.00 0.00 3.06
476 480 1.072154 CATACGCGCACATTGTACGAG 60.072 52.381 13.45 12.15 0.00 4.18
514 518 4.988540 GGGAAAAAGCACTTGTACATTTCC 59.011 41.667 19.75 19.75 42.14 3.13
535 539 2.112380 TGTGTATGCTCACATGTGGG 57.888 50.000 25.16 23.62 42.36 4.61
657 661 0.698818 AGTTTGGACCAGGACCATCC 59.301 55.000 11.84 5.47 37.26 3.51
679 683 3.574396 TCCTGAGATAAATGAGGCGTAGG 59.426 47.826 0.00 0.00 0.00 3.18
754 758 7.284944 ACAGTAACAACTATGTACCTAGCTAGG 59.715 40.741 33.98 33.98 43.60 3.02
783 787 9.730420 GAAAGTAGCTGTTCAAACAAATAAAGA 57.270 29.630 0.00 0.00 38.66 2.52
866 870 5.122396 GGTGTCTGTTGGAACATAGTGAATC 59.878 44.000 0.00 0.00 39.30 2.52
938 942 6.421377 AAAATTTCAAAGGACAACTTGTGC 57.579 33.333 5.31 5.31 39.96 4.57
1009 1013 5.532406 TGCATGCAGATAAGAAGGGAAATAC 59.468 40.000 18.46 0.00 0.00 1.89
1107 1111 3.258971 ACATAGCAAAGGACAGAGAGC 57.741 47.619 0.00 0.00 0.00 4.09
1112 1116 5.295292 CCATCTGTAACATAGCAAAGGACAG 59.705 44.000 0.00 0.00 35.30 3.51
1229 1233 2.899900 CGGAGGTATGAGATTGGGATCA 59.100 50.000 0.00 0.00 34.60 2.92
1233 1237 3.560636 AAACGGAGGTATGAGATTGGG 57.439 47.619 0.00 0.00 0.00 4.12
1241 1245 8.539674 CAAAAGAAAAAGAAAAACGGAGGTATG 58.460 33.333 0.00 0.00 0.00 2.39
1256 1260 5.005971 CCATCTGCACACACAAAAGAAAAAG 59.994 40.000 0.00 0.00 0.00 2.27
1272 1276 4.079844 TGATTTGAATAGGACCCATCTGCA 60.080 41.667 0.00 0.00 0.00 4.41
1281 1285 8.433421 TTCGTTATCCTTGATTTGAATAGGAC 57.567 34.615 0.00 0.00 39.47 3.85
1576 1580 3.075882 TGTGTCCTGAAAATTCCCTCCAT 59.924 43.478 0.00 0.00 0.00 3.41
1608 1612 6.485984 GTGGCTGTTATGATCATCTTCTGAAT 59.514 38.462 12.53 0.00 37.44 2.57
1669 1673 4.554134 CGCAGACAATCTGGATAAATGCTG 60.554 45.833 7.89 0.00 44.43 4.41
1739 1743 1.089920 CAGTACATGTCTTGCCCAGC 58.910 55.000 0.00 0.00 0.00 4.85
1750 1754 2.855180 CTTTTCGGCAAGCAGTACATG 58.145 47.619 0.00 0.00 0.00 3.21
1804 1808 6.713903 CAGGCAATGGAATATAATCACTGACT 59.286 38.462 0.00 0.00 0.00 3.41
1835 1839 5.152623 TCAACAGACCAGAAGTATCTTGG 57.847 43.478 0.00 0.00 32.03 3.61
1844 1848 3.454447 TGTTCCTCTTCAACAGACCAGAA 59.546 43.478 0.00 0.00 30.16 3.02
1987 1991 4.071961 TGCAGACCATCGTTTATATGCT 57.928 40.909 0.00 0.00 33.68 3.79
2113 2117 3.594134 CTCGAGCAAAGGATCTTGAACT 58.406 45.455 0.00 0.00 0.00 3.01
2181 2185 8.295288 GTGCCAATGATTCAAAGGATCTAATAG 58.705 37.037 10.87 0.00 0.00 1.73
2183 2187 6.608405 TGTGCCAATGATTCAAAGGATCTAAT 59.392 34.615 10.87 0.00 0.00 1.73
2274 2279 9.433153 GCAGAAGAGATATGATTGTAATGATCA 57.567 33.333 0.00 0.00 37.86 2.92
2331 2337 9.722056 CAGCAACATAATTAAATAGAGGTGAAC 57.278 33.333 0.00 0.00 0.00 3.18
2332 2338 9.461312 ACAGCAACATAATTAAATAGAGGTGAA 57.539 29.630 0.00 0.00 0.00 3.18
2355 2361 6.686130 AAATAAGTAAGACGACGACAACAG 57.314 37.500 0.00 0.00 0.00 3.16
2362 2368 7.246311 TCCTACAGAAAATAAGTAAGACGACG 58.754 38.462 0.00 0.00 0.00 5.12
2408 2414 4.090930 GTGAACATCAATGCAAAGACATGC 59.909 41.667 0.00 0.00 46.58 4.06
2433 2439 5.839063 ACTAGCAGGAGCATAAACTGGTATA 59.161 40.000 0.00 0.00 42.25 1.47
2463 2469 8.251026 TGGTAATATATAATTGTCAGCCTCTCG 58.749 37.037 0.00 0.00 0.00 4.04
2604 2612 6.380079 AATCCAGTCAAGTCATACTTTCCT 57.620 37.500 0.00 0.00 36.03 3.36
2757 2765 9.905171 GCTTCCCAAAATAGATCATTAGATTTC 57.095 33.333 0.00 0.00 33.72 2.17
2805 2813 2.203788 TCGGAGTGCCACCCTCTT 60.204 61.111 0.00 0.00 0.00 2.85
2970 2978 2.560105 GACTCCAAAATCAAGCAGCCTT 59.440 45.455 0.00 0.00 0.00 4.35
2991 2999 5.940617 TCACCTCCATTATTATCACCTTGG 58.059 41.667 0.00 0.00 0.00 3.61
2992 3000 6.000219 CCTCACCTCCATTATTATCACCTTG 59.000 44.000 0.00 0.00 0.00 3.61
3037 3045 5.437289 TTGTCAGGTTCAACATCATTGAC 57.563 39.130 0.00 0.00 35.31 3.18
3123 3131 6.150976 CCACCACAGTAAATTTCATAAGCTCA 59.849 38.462 0.00 0.00 0.00 4.26
3163 3171 3.401342 ACCTTACATGGTTCTTCCCCTTT 59.599 43.478 0.00 0.00 36.89 3.11
3246 3254 0.388520 TCACACTGACAGAATCGCCG 60.389 55.000 10.08 0.00 0.00 6.46
3304 3312 6.721668 TCATCGGTATCCAGATCTTCATAAGT 59.278 38.462 0.00 0.00 0.00 2.24
3325 3333 4.438472 GCTTGCATCAGTTTTCCTCTCATC 60.438 45.833 0.00 0.00 0.00 2.92
3328 3336 3.080319 AGCTTGCATCAGTTTTCCTCTC 58.920 45.455 0.00 0.00 0.00 3.20
3334 3342 5.464168 GTCAACATAGCTTGCATCAGTTTT 58.536 37.500 0.00 0.00 0.00 2.43
3398 3406 7.068348 AAGAAATCTTATGAAGTGCATCAGCAT 59.932 33.333 0.00 0.00 43.23 3.79
3407 3415 8.340618 TGGAAAGGAAGAAATCTTATGAAGTG 57.659 34.615 0.00 0.00 36.11 3.16
3451 3459 5.221481 TGCCAACACATTGATCAACTGAAAT 60.221 36.000 11.07 0.00 38.15 2.17
3479 3487 5.181009 CAGTGGAAGAGCAGACATTATTCA 58.819 41.667 0.00 0.00 0.00 2.57
3690 3698 3.019564 GTCAGCTTGCTTCCCATAATGT 58.980 45.455 0.00 0.00 0.00 2.71
3696 3704 2.669569 GCGTCAGCTTGCTTCCCA 60.670 61.111 0.00 0.00 41.01 4.37
3712 3720 3.297620 CACAGGTTGCAGTGGGGC 61.298 66.667 0.00 0.00 32.24 5.80
3856 3864 2.215942 ACCACTTCAACATTAGGGGC 57.784 50.000 0.00 0.00 38.58 5.80
3949 3957 7.934120 AGATGAAGGTTGGATATAACTTGTAGC 59.066 37.037 0.00 0.00 0.00 3.58
3970 3978 7.878547 TGGTTATTGCATTATTGTCAGATGA 57.121 32.000 0.00 0.00 0.00 2.92
3988 3996 5.841267 TGCATAGGTATGTCCATGGTTAT 57.159 39.130 12.58 9.94 39.02 1.89
3992 4000 3.614092 GGATGCATAGGTATGTCCATGG 58.386 50.000 4.97 4.97 39.02 3.66
4022 4030 1.599047 CAGTCATCCGCCTCCTTGT 59.401 57.895 0.00 0.00 0.00 3.16
4063 4071 2.675348 GCTCACTCAAGATTGCACTACC 59.325 50.000 0.00 0.00 0.00 3.18
4067 4075 1.135746 GCTGCTCACTCAAGATTGCAC 60.136 52.381 0.00 0.00 0.00 4.57
4080 4088 2.545526 CGAGTTGAAAGAAAGCTGCTCA 59.454 45.455 1.00 0.00 0.00 4.26
4167 4175 1.180029 CACCTTTCTGCTTCCCCATG 58.820 55.000 0.00 0.00 0.00 3.66
4577 4585 5.124457 GGCATCTGTGATCTTTTGCTTTCTA 59.876 40.000 0.00 0.00 0.00 2.10
4634 4642 6.656632 ATCTGTATAAGCTTCCTCGATTCA 57.343 37.500 0.00 0.00 0.00 2.57
4955 4964 5.538849 TCTTATATGGGCACACGATTACA 57.461 39.130 0.00 0.00 0.00 2.41
5009 5018 6.007703 TCTCCTTTTTGAATTACGGGACAAT 58.992 36.000 0.00 0.00 0.00 2.71
5089 5098 6.255453 ACAGAAATTTGAACATTTGGAACACG 59.745 34.615 0.00 0.00 39.29 4.49
5141 5151 5.141182 AGTCCCATATACTGTCACTACCTG 58.859 45.833 0.00 0.00 0.00 4.00
5162 5172 1.838077 ACCCGGCTAAGCAAATCTAGT 59.162 47.619 0.00 0.00 0.00 2.57
5170 5180 0.107410 CCACAATACCCGGCTAAGCA 60.107 55.000 0.00 0.00 0.00 3.91
5171 5181 1.444917 GCCACAATACCCGGCTAAGC 61.445 60.000 0.00 0.00 42.78 3.09
5172 5182 2.702847 GCCACAATACCCGGCTAAG 58.297 57.895 0.00 0.00 42.78 2.18
5173 5183 4.968370 GCCACAATACCCGGCTAA 57.032 55.556 0.00 0.00 42.78 3.09
5176 5186 1.819632 CAGAGCCACAATACCCGGC 60.820 63.158 0.00 0.00 46.62 6.13
5177 5187 0.828022 TACAGAGCCACAATACCCGG 59.172 55.000 0.00 0.00 0.00 5.73
5178 5188 2.277084 GTTACAGAGCCACAATACCCG 58.723 52.381 0.00 0.00 0.00 5.28
5179 5189 3.343941 TGTTACAGAGCCACAATACCC 57.656 47.619 0.00 0.00 0.00 3.69
5180 5190 5.897377 AAATGTTACAGAGCCACAATACC 57.103 39.130 0.00 0.00 0.00 2.73
5181 5191 7.611213 AGTAAATGTTACAGAGCCACAATAC 57.389 36.000 1.33 0.00 0.00 1.89
5182 5192 8.537016 ACTAGTAAATGTTACAGAGCCACAATA 58.463 33.333 0.00 0.00 0.00 1.90
5183 5193 7.394816 ACTAGTAAATGTTACAGAGCCACAAT 58.605 34.615 0.00 0.00 0.00 2.71
5184 5194 6.765403 ACTAGTAAATGTTACAGAGCCACAA 58.235 36.000 0.00 0.00 0.00 3.33
5185 5195 6.354794 ACTAGTAAATGTTACAGAGCCACA 57.645 37.500 0.00 0.00 0.00 4.17
5186 5196 6.649557 ACAACTAGTAAATGTTACAGAGCCAC 59.350 38.462 0.00 0.00 0.00 5.01
5187 5197 6.649141 CACAACTAGTAAATGTTACAGAGCCA 59.351 38.462 0.00 0.00 0.00 4.75
5188 5198 6.092259 CCACAACTAGTAAATGTTACAGAGCC 59.908 42.308 0.00 0.00 0.00 4.70
5189 5199 6.092259 CCCACAACTAGTAAATGTTACAGAGC 59.908 42.308 0.00 0.00 0.00 4.09
5190 5200 7.159372 ACCCACAACTAGTAAATGTTACAGAG 58.841 38.462 0.00 1.08 0.00 3.35
5191 5201 7.069877 ACCCACAACTAGTAAATGTTACAGA 57.930 36.000 0.00 0.00 0.00 3.41
5192 5202 8.092687 ACTACCCACAACTAGTAAATGTTACAG 58.907 37.037 0.00 0.00 0.00 2.74
5193 5203 7.874016 CACTACCCACAACTAGTAAATGTTACA 59.126 37.037 0.00 0.00 0.00 2.41
5194 5204 7.332678 CCACTACCCACAACTAGTAAATGTTAC 59.667 40.741 0.00 0.00 0.00 2.50
5195 5205 7.388437 CCACTACCCACAACTAGTAAATGTTA 58.612 38.462 0.00 0.00 0.00 2.41
5196 5206 6.235664 CCACTACCCACAACTAGTAAATGTT 58.764 40.000 0.00 0.00 0.00 2.71
5197 5207 5.801380 CCACTACCCACAACTAGTAAATGT 58.199 41.667 0.00 0.00 0.00 2.71
5198 5208 4.634443 GCCACTACCCACAACTAGTAAATG 59.366 45.833 0.00 0.00 0.00 2.32
5199 5209 4.287585 TGCCACTACCCACAACTAGTAAAT 59.712 41.667 0.00 0.00 0.00 1.40
5200 5210 3.647113 TGCCACTACCCACAACTAGTAAA 59.353 43.478 0.00 0.00 0.00 2.01
5201 5211 3.241156 TGCCACTACCCACAACTAGTAA 58.759 45.455 0.00 0.00 0.00 2.24
5202 5212 2.829720 CTGCCACTACCCACAACTAGTA 59.170 50.000 0.00 0.00 0.00 1.82
5203 5213 1.623811 CTGCCACTACCCACAACTAGT 59.376 52.381 0.00 0.00 0.00 2.57
5204 5214 1.623811 ACTGCCACTACCCACAACTAG 59.376 52.381 0.00 0.00 0.00 2.57
5205 5215 1.724545 ACTGCCACTACCCACAACTA 58.275 50.000 0.00 0.00 0.00 2.24
5206 5216 1.724545 TACTGCCACTACCCACAACT 58.275 50.000 0.00 0.00 0.00 3.16
5207 5217 2.290071 ACATACTGCCACTACCCACAAC 60.290 50.000 0.00 0.00 0.00 3.32
5208 5218 1.982226 ACATACTGCCACTACCCACAA 59.018 47.619 0.00 0.00 0.00 3.33
5209 5219 1.277842 CACATACTGCCACTACCCACA 59.722 52.381 0.00 0.00 0.00 4.17
5210 5220 1.406887 CCACATACTGCCACTACCCAC 60.407 57.143 0.00 0.00 0.00 4.61
5211 5221 0.908910 CCACATACTGCCACTACCCA 59.091 55.000 0.00 0.00 0.00 4.51
5212 5222 0.180406 CCCACATACTGCCACTACCC 59.820 60.000 0.00 0.00 0.00 3.69
5213 5223 0.180406 CCCCACATACTGCCACTACC 59.820 60.000 0.00 0.00 0.00 3.18
5214 5224 0.463833 GCCCCACATACTGCCACTAC 60.464 60.000 0.00 0.00 0.00 2.73
5215 5225 0.620410 AGCCCCACATACTGCCACTA 60.620 55.000 0.00 0.00 0.00 2.74
5216 5226 0.620410 TAGCCCCACATACTGCCACT 60.620 55.000 0.00 0.00 0.00 4.00
5217 5227 0.179045 CTAGCCCCACATACTGCCAC 60.179 60.000 0.00 0.00 0.00 5.01
5218 5228 0.326143 TCTAGCCCCACATACTGCCA 60.326 55.000 0.00 0.00 0.00 4.92
5219 5229 1.059913 ATCTAGCCCCACATACTGCC 58.940 55.000 0.00 0.00 0.00 4.85
5220 5230 2.880890 CAAATCTAGCCCCACATACTGC 59.119 50.000 0.00 0.00 0.00 4.40
5221 5231 2.880890 GCAAATCTAGCCCCACATACTG 59.119 50.000 0.00 0.00 0.00 2.74
5222 5232 2.780010 AGCAAATCTAGCCCCACATACT 59.220 45.455 0.00 0.00 0.00 2.12
5223 5233 3.214696 AGCAAATCTAGCCCCACATAC 57.785 47.619 0.00 0.00 0.00 2.39
5224 5234 3.951563 AAGCAAATCTAGCCCCACATA 57.048 42.857 0.00 0.00 0.00 2.29
5225 5235 2.834638 AAGCAAATCTAGCCCCACAT 57.165 45.000 0.00 0.00 0.00 3.21
5226 5236 2.683742 GCTAAGCAAATCTAGCCCCACA 60.684 50.000 0.00 0.00 0.00 4.17
5227 5237 1.950216 GCTAAGCAAATCTAGCCCCAC 59.050 52.381 0.00 0.00 0.00 4.61
5228 5238 1.133792 GGCTAAGCAAATCTAGCCCCA 60.134 52.381 8.63 0.00 46.92 4.96
5229 5239 1.610363 GGCTAAGCAAATCTAGCCCC 58.390 55.000 8.63 0.00 46.92 5.80
5232 5242 0.588737 GCCGGCTAAGCAAATCTAGC 59.411 55.000 22.15 0.00 35.01 3.42
5233 5243 2.246719 AGCCGGCTAAGCAAATCTAG 57.753 50.000 31.86 0.00 0.00 2.43
5234 5244 4.065088 CAATAGCCGGCTAAGCAAATCTA 58.935 43.478 38.14 15.72 31.73 1.98
5235 5245 2.880890 CAATAGCCGGCTAAGCAAATCT 59.119 45.455 38.14 17.88 31.73 2.40
5236 5246 2.618709 ACAATAGCCGGCTAAGCAAATC 59.381 45.455 38.14 0.00 31.73 2.17
5237 5247 2.358898 CACAATAGCCGGCTAAGCAAAT 59.641 45.455 38.14 20.53 31.73 2.32
5238 5248 1.742831 CACAATAGCCGGCTAAGCAAA 59.257 47.619 38.14 19.01 31.73 3.68
5239 5249 1.378531 CACAATAGCCGGCTAAGCAA 58.621 50.000 38.14 19.83 31.73 3.91
5256 5266 6.402226 GCAACTAGTAAATGTTACAGAGCCAC 60.402 42.308 0.00 0.00 0.00 5.01
5281 5291 1.511887 CATTCAAAGCGCGGTTCCG 60.512 57.895 25.23 18.07 0.00 4.30
5391 5401 5.255596 CGAAACATAGGTTTTGCGACATAG 58.744 41.667 6.98 0.00 46.84 2.23
5405 5415 6.258160 CAAGAATTGGCCTTACGAAACATAG 58.742 40.000 3.32 0.00 43.94 2.23
5451 5461 4.378046 CGTCTTACAAAAATGAACGGAGGG 60.378 45.833 0.00 0.00 0.00 4.30
5452 5462 4.212636 ACGTCTTACAAAAATGAACGGAGG 59.787 41.667 0.00 0.00 0.00 4.30
5453 5463 5.338614 ACGTCTTACAAAAATGAACGGAG 57.661 39.130 0.00 0.00 0.00 4.63
5454 5464 5.738118 AACGTCTTACAAAAATGAACGGA 57.262 34.783 0.00 0.00 0.00 4.69
5455 5465 6.799786 AAAACGTCTTACAAAAATGAACGG 57.200 33.333 0.00 0.00 0.00 4.44
5456 5466 8.667204 GTCTAAAACGTCTTACAAAAATGAACG 58.333 33.333 0.00 0.00 0.00 3.95
5457 5467 9.493206 TGTCTAAAACGTCTTACAAAAATGAAC 57.507 29.630 0.00 0.00 0.00 3.18
5466 5476 9.531942 TGTCTTAAATGTCTAAAACGTCTTACA 57.468 29.630 0.00 0.00 0.00 2.41
5468 5478 8.706035 GCTGTCTTAAATGTCTAAAACGTCTTA 58.294 33.333 0.00 0.00 0.00 2.10
5469 5479 7.225931 TGCTGTCTTAAATGTCTAAAACGTCTT 59.774 33.333 0.00 0.00 0.00 3.01
5470 5480 6.704493 TGCTGTCTTAAATGTCTAAAACGTCT 59.296 34.615 0.00 0.00 0.00 4.18
5471 5481 6.790825 GTGCTGTCTTAAATGTCTAAAACGTC 59.209 38.462 0.00 0.00 0.00 4.34
5472 5482 6.293244 GGTGCTGTCTTAAATGTCTAAAACGT 60.293 38.462 0.00 0.00 0.00 3.99
5473 5483 6.073222 AGGTGCTGTCTTAAATGTCTAAAACG 60.073 38.462 0.00 0.00 0.00 3.60
5474 5484 7.203255 AGGTGCTGTCTTAAATGTCTAAAAC 57.797 36.000 0.00 0.00 0.00 2.43
5475 5485 8.911918 TTAGGTGCTGTCTTAAATGTCTAAAA 57.088 30.769 0.00 0.00 0.00 1.52
5476 5486 8.911918 TTTAGGTGCTGTCTTAAATGTCTAAA 57.088 30.769 0.00 0.00 0.00 1.85
5477 5487 8.780249 GTTTTAGGTGCTGTCTTAAATGTCTAA 58.220 33.333 0.00 0.00 0.00 2.10
5478 5488 7.934665 TGTTTTAGGTGCTGTCTTAAATGTCTA 59.065 33.333 0.00 0.00 0.00 2.59
5479 5489 6.770785 TGTTTTAGGTGCTGTCTTAAATGTCT 59.229 34.615 0.00 0.00 0.00 3.41
5480 5490 6.966021 TGTTTTAGGTGCTGTCTTAAATGTC 58.034 36.000 0.00 0.00 0.00 3.06
5481 5491 6.546034 ACTGTTTTAGGTGCTGTCTTAAATGT 59.454 34.615 0.00 0.00 0.00 2.71
5482 5492 6.970484 ACTGTTTTAGGTGCTGTCTTAAATG 58.030 36.000 0.00 0.00 0.00 2.32
5483 5493 7.284489 TGAACTGTTTTAGGTGCTGTCTTAAAT 59.716 33.333 0.00 0.00 0.00 1.40
5484 5494 6.600032 TGAACTGTTTTAGGTGCTGTCTTAAA 59.400 34.615 0.00 0.00 0.00 1.52
5485 5495 6.116806 TGAACTGTTTTAGGTGCTGTCTTAA 58.883 36.000 0.00 0.00 0.00 1.85
5486 5496 5.676552 TGAACTGTTTTAGGTGCTGTCTTA 58.323 37.500 0.00 0.00 0.00 2.10
5487 5497 4.523083 TGAACTGTTTTAGGTGCTGTCTT 58.477 39.130 0.00 0.00 0.00 3.01
5488 5498 4.150897 TGAACTGTTTTAGGTGCTGTCT 57.849 40.909 0.00 0.00 0.00 3.41
5489 5499 4.893424 TTGAACTGTTTTAGGTGCTGTC 57.107 40.909 0.00 0.00 0.00 3.51
5490 5500 5.852282 AATTGAACTGTTTTAGGTGCTGT 57.148 34.783 0.00 0.00 0.00 4.40
5491 5501 6.272318 TGAAATTGAACTGTTTTAGGTGCTG 58.728 36.000 0.00 0.00 0.00 4.41
5492 5502 6.463995 TGAAATTGAACTGTTTTAGGTGCT 57.536 33.333 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.