Multiple sequence alignment - TraesCS6B01G245000

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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 TraesCS6B01G245000 chr6B 100.000 3041 0 0 1 3041 437472854 437469814 0.000000e+00 5616.0
1 TraesCS6B01G245000 chr6B 93.642 173 11 0 2795 2967 685981607 685981435 3.010000e-65 259.0
2 TraesCS6B01G245000 chr6D 94.079 2280 83 14 550 2793 275668191 275665928 0.000000e+00 3415.0
3 TraesCS6B01G245000 chr6D 92.377 446 23 6 55 497 275668626 275668189 2.570000e-175 625.0
4 TraesCS6B01G245000 chr6D 96.512 86 3 0 2956 3041 275665926 275665841 3.160000e-30 143.0
5 TraesCS6B01G245000 chr6A 93.473 2283 91 20 554 2793 396292305 396290038 0.000000e+00 3338.0
6 TraesCS6B01G245000 chr6A 92.493 373 23 4 129 497 396292680 396292309 2.080000e-146 529.0
7 TraesCS6B01G245000 chr6A 90.805 87 5 1 2958 3041 396290037 396289951 2.480000e-21 113.0
8 TraesCS6B01G245000 chr6A 94.643 56 3 0 4 59 101339478 101339533 1.500000e-13 87.9
9 TraesCS6B01G245000 chr7B 89.721 1148 95 10 947 2082 479238246 479237110 0.000000e+00 1445.0
10 TraesCS6B01G245000 chr7B 84.935 697 52 17 2077 2731 479234525 479233840 0.000000e+00 656.0
11 TraesCS6B01G245000 chr7B 93.220 59 4 0 1 59 41290974 41291032 1.500000e-13 87.9
12 TraesCS6B01G245000 chr7B 87.097 62 8 0 1 62 509601364 509601303 1.510000e-08 71.3
13 TraesCS6B01G245000 chr7B 100.000 35 0 0 25 59 572946406 572946372 7.040000e-07 65.8
14 TraesCS6B01G245000 chr7D 89.373 1148 105 8 945 2082 457150089 457148949 0.000000e+00 1428.0
15 TraesCS6B01G245000 chr7D 84.648 697 54 19 2077 2731 457148797 457148112 0.000000e+00 645.0
16 TraesCS6B01G245000 chr7D 94.706 170 9 0 2791 2960 202716676 202716845 6.460000e-67 265.0
17 TraesCS6B01G245000 chr7D 93.103 58 4 0 495 552 531176889 531176832 5.400000e-13 86.1
18 TraesCS6B01G245000 chr7A 88.442 1194 88 22 1472 2624 543341168 543342352 0.000000e+00 1395.0
19 TraesCS6B01G245000 chr7A 86.803 538 59 4 938 1468 543340507 543341039 9.390000e-165 590.0
20 TraesCS6B01G245000 chr7A 94.915 59 3 0 1 59 561787558 561787616 3.230000e-15 93.5
21 TraesCS6B01G245000 chr5A 94.737 171 9 0 2795 2965 694983678 694983848 1.800000e-67 267.0
22 TraesCS6B01G245000 chr5A 94.220 173 10 0 2792 2964 382566635 382566807 6.460000e-67 265.0
23 TraesCS6B01G245000 chr2D 95.238 168 8 0 2792 2959 196347495 196347328 1.800000e-67 267.0
24 TraesCS6B01G245000 chr4D 93.785 177 10 1 2786 2962 477898967 477898792 6.460000e-67 265.0
25 TraesCS6B01G245000 chr4D 100.000 47 0 0 491 537 473819487 473819441 1.500000e-13 87.9
26 TraesCS6B01G245000 chr2B 94.675 169 9 0 2792 2960 174794989 174794821 2.330000e-66 263.0
27 TraesCS6B01G245000 chr2B 89.831 59 6 0 1 59 703836253 703836195 3.250000e-10 76.8
28 TraesCS6B01G245000 chr5D 93.220 177 11 1 2790 2965 312116184 312116360 3.010000e-65 259.0
29 TraesCS6B01G245000 chrUn 92.265 181 12 2 2789 2968 74544776 74544597 3.890000e-64 255.0
30 TraesCS6B01G245000 chr1A 79.365 252 38 10 1685 1928 483617919 483618164 6.750000e-37 165.0
31 TraesCS6B01G245000 chr3B 96.491 57 1 1 495 551 763936594 763936649 3.230000e-15 93.5
32 TraesCS6B01G245000 chr3B 93.333 60 4 0 1 60 807678888 807678947 4.180000e-14 89.8
33 TraesCS6B01G245000 chr3B 92.982 57 4 0 495 551 622273191 622273247 1.940000e-12 84.2
34 TraesCS6B01G245000 chr2A 93.443 61 4 0 1 61 767803796 767803736 1.160000e-14 91.6
35 TraesCS6B01G245000 chr2A 96.078 51 0 2 495 545 753520669 753520717 6.990000e-12 82.4
36 TraesCS6B01G245000 chr1D 96.000 50 2 0 491 540 340456248 340456199 6.990000e-12 82.4
37 TraesCS6B01G245000 chr1D 96.000 50 2 0 491 540 369899298 369899347 6.990000e-12 82.4
38 TraesCS6B01G245000 chr1D 96.000 50 2 0 491 540 447863716 447863765 6.990000e-12 82.4
39 TraesCS6B01G245000 chr4B 89.831 59 6 0 493 551 491838502 491838560 3.250000e-10 76.8
40 TraesCS6B01G245000 chr1B 86.441 59 8 0 1 59 41316542 41316600 7.040000e-07 65.8


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 TraesCS6B01G245000 chr6B 437469814 437472854 3040 True 5616.000000 5616 100.000000 1 3041 1 chr6B.!!$R1 3040
1 TraesCS6B01G245000 chr6D 275665841 275668626 2785 True 1394.333333 3415 94.322667 55 3041 3 chr6D.!!$R1 2986
2 TraesCS6B01G245000 chr6A 396289951 396292680 2729 True 1326.666667 3338 92.257000 129 3041 3 chr6A.!!$R1 2912
3 TraesCS6B01G245000 chr7B 479233840 479238246 4406 True 1050.500000 1445 87.328000 947 2731 2 chr7B.!!$R3 1784
4 TraesCS6B01G245000 chr7D 457148112 457150089 1977 True 1036.500000 1428 87.010500 945 2731 2 chr7D.!!$R2 1786
5 TraesCS6B01G245000 chr7A 543340507 543342352 1845 False 992.500000 1395 87.622500 938 2624 2 chr7A.!!$F2 1686

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
29 30 0.179015 TGGCTAAACCTCACGGCAAA 60.179 50.0 0.00 0.0 40.22 3.68 F
423 433 0.394565 ACTGCGGCTGGATAGGATTC 59.605 55.0 11.64 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1586 1740 0.670239 GCAAAATGTCCAAAGCCCGG 60.670 55.0 0.0 0.0 0.0 5.73 R
2180 4930 1.107538 TGGTCTTATCCTCCTCGGCG 61.108 60.0 0.0 0.0 0.0 6.46 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
20 21 3.290948 TTCACACAAGTGGCTAAACCT 57.709 42.857 5.08 0.00 45.91 3.50
21 22 2.846193 TCACACAAGTGGCTAAACCTC 58.154 47.619 5.08 0.00 45.91 3.85
22 23 2.171659 TCACACAAGTGGCTAAACCTCA 59.828 45.455 5.08 0.00 45.91 3.86
23 24 2.290641 CACACAAGTGGCTAAACCTCAC 59.709 50.000 5.08 0.00 42.13 3.51
24 25 1.531149 CACAAGTGGCTAAACCTCACG 59.469 52.381 0.00 0.00 40.22 4.35
25 26 1.156736 CAAGTGGCTAAACCTCACGG 58.843 55.000 0.00 0.00 40.22 4.94
26 27 0.605589 AAGTGGCTAAACCTCACGGC 60.606 55.000 0.00 0.00 40.22 5.68
27 28 1.302192 GTGGCTAAACCTCACGGCA 60.302 57.895 0.00 0.00 40.22 5.69
28 29 0.887387 GTGGCTAAACCTCACGGCAA 60.887 55.000 0.00 0.00 40.22 4.52
29 30 0.179015 TGGCTAAACCTCACGGCAAA 60.179 50.000 0.00 0.00 40.22 3.68
30 31 0.955905 GGCTAAACCTCACGGCAAAA 59.044 50.000 0.00 0.00 34.51 2.44
31 32 1.338655 GGCTAAACCTCACGGCAAAAA 59.661 47.619 0.00 0.00 34.51 1.94
32 33 2.390938 GCTAAACCTCACGGCAAAAAC 58.609 47.619 0.00 0.00 0.00 2.43
33 34 2.034179 GCTAAACCTCACGGCAAAAACT 59.966 45.455 0.00 0.00 0.00 2.66
34 35 3.490249 GCTAAACCTCACGGCAAAAACTT 60.490 43.478 0.00 0.00 0.00 2.66
35 36 2.577449 AACCTCACGGCAAAAACTTG 57.423 45.000 0.00 0.00 0.00 3.16
36 37 0.744281 ACCTCACGGCAAAAACTTGG 59.256 50.000 0.00 0.00 0.00 3.61
37 38 0.597377 CCTCACGGCAAAAACTTGGC 60.597 55.000 1.58 1.58 43.18 4.52
38 39 0.597377 CTCACGGCAAAAACTTGGCC 60.597 55.000 0.00 0.00 43.65 5.36
39 40 1.040339 TCACGGCAAAAACTTGGCCT 61.040 50.000 3.32 0.00 45.53 5.19
40 41 0.875474 CACGGCAAAAACTTGGCCTG 60.875 55.000 3.32 0.00 45.53 4.85
41 42 1.300853 CGGCAAAAACTTGGCCTGG 60.301 57.895 3.32 0.00 45.53 4.45
42 43 1.743321 CGGCAAAAACTTGGCCTGGA 61.743 55.000 3.32 0.00 45.53 3.86
43 44 0.467804 GGCAAAAACTTGGCCTGGAA 59.532 50.000 3.32 0.00 44.32 3.53
44 45 1.072173 GGCAAAAACTTGGCCTGGAAT 59.928 47.619 3.32 0.00 44.32 3.01
45 46 2.301583 GGCAAAAACTTGGCCTGGAATA 59.698 45.455 3.32 0.00 44.32 1.75
46 47 3.588955 GCAAAAACTTGGCCTGGAATAG 58.411 45.455 3.32 0.00 0.00 1.73
47 48 3.258123 GCAAAAACTTGGCCTGGAATAGA 59.742 43.478 3.32 0.00 0.00 1.98
48 49 4.619160 GCAAAAACTTGGCCTGGAATAGAG 60.619 45.833 3.32 0.00 0.00 2.43
49 50 3.372440 AAACTTGGCCTGGAATAGAGG 57.628 47.619 3.32 0.00 0.00 3.69
56 57 1.216990 CCTGGAATAGAGGCTTGGGT 58.783 55.000 0.00 0.00 0.00 4.51
57 58 2.408565 CCTGGAATAGAGGCTTGGGTA 58.591 52.381 0.00 0.00 0.00 3.69
58 59 2.982488 CCTGGAATAGAGGCTTGGGTAT 59.018 50.000 0.00 0.00 0.00 2.73
83 84 2.761767 TGTGATTAGCATGCTGCCAAAT 59.238 40.909 30.42 20.64 46.52 2.32
121 122 3.496507 GCCTCTCTGTTTCAGTTGAACTC 59.503 47.826 0.00 0.00 33.13 3.01
145 147 3.706594 CCACATACTGGAGAAGCCTCTAA 59.293 47.826 0.00 0.00 43.95 2.10
171 178 2.203280 CAGCGTGGGACCAAACCA 60.203 61.111 0.00 0.00 35.14 3.67
172 179 1.826054 CAGCGTGGGACCAAACCAA 60.826 57.895 0.00 0.00 40.24 3.67
173 180 1.076632 AGCGTGGGACCAAACCAAA 60.077 52.632 0.00 0.00 40.24 3.28
174 181 1.066752 GCGTGGGACCAAACCAAAC 59.933 57.895 0.00 0.00 40.24 2.93
175 182 1.668101 GCGTGGGACCAAACCAAACA 61.668 55.000 0.00 0.00 40.24 2.83
240 247 2.245546 TGAGCATCCCCAAATCCATCTT 59.754 45.455 0.00 0.00 0.00 2.40
289 297 1.005394 CCGCCGGTGTGTAGTTTCT 60.005 57.895 15.14 0.00 0.00 2.52
416 426 2.749044 CAAGCACTGCGGCTGGAT 60.749 61.111 11.64 0.00 45.07 3.41
423 433 0.394565 ACTGCGGCTGGATAGGATTC 59.605 55.000 11.64 0.00 0.00 2.52
459 471 7.125391 TGTAGAAATAATGAGGAAAATGCCCT 58.875 34.615 0.00 0.00 36.57 5.19
493 505 5.742562 TTATAGAACCACCCCAATCCAAT 57.257 39.130 0.00 0.00 0.00 3.16
494 506 4.625225 ATAGAACCACCCCAATCCAATT 57.375 40.909 0.00 0.00 0.00 2.32
495 507 5.742562 ATAGAACCACCCCAATCCAATTA 57.257 39.130 0.00 0.00 0.00 1.40
496 508 3.708451 AGAACCACCCCAATCCAATTAC 58.292 45.455 0.00 0.00 0.00 1.89
497 509 3.336694 AGAACCACCCCAATCCAATTACT 59.663 43.478 0.00 0.00 0.00 2.24
498 510 3.382083 ACCACCCCAATCCAATTACTC 57.618 47.619 0.00 0.00 0.00 2.59
499 511 2.024369 ACCACCCCAATCCAATTACTCC 60.024 50.000 0.00 0.00 0.00 3.85
500 512 2.666317 CACCCCAATCCAATTACTCCC 58.334 52.381 0.00 0.00 0.00 4.30
501 513 2.244769 CACCCCAATCCAATTACTCCCT 59.755 50.000 0.00 0.00 0.00 4.20
502 514 2.514160 ACCCCAATCCAATTACTCCCTC 59.486 50.000 0.00 0.00 0.00 4.30
503 515 2.158460 CCCCAATCCAATTACTCCCTCC 60.158 54.545 0.00 0.00 0.00 4.30
504 516 2.487265 CCCAATCCAATTACTCCCTCCG 60.487 54.545 0.00 0.00 0.00 4.63
505 517 2.172717 CCAATCCAATTACTCCCTCCGT 59.827 50.000 0.00 0.00 0.00 4.69
506 518 3.389983 CCAATCCAATTACTCCCTCCGTA 59.610 47.826 0.00 0.00 0.00 4.02
507 519 4.141574 CCAATCCAATTACTCCCTCCGTAA 60.142 45.833 0.00 0.00 0.00 3.18
508 520 5.433526 CAATCCAATTACTCCCTCCGTAAA 58.566 41.667 0.00 0.00 31.36 2.01
509 521 4.476628 TCCAATTACTCCCTCCGTAAAC 57.523 45.455 0.00 0.00 31.36 2.01
510 522 4.098894 TCCAATTACTCCCTCCGTAAACT 58.901 43.478 0.00 0.00 31.36 2.66
511 523 5.271598 TCCAATTACTCCCTCCGTAAACTA 58.728 41.667 0.00 0.00 31.36 2.24
512 524 5.721000 TCCAATTACTCCCTCCGTAAACTAA 59.279 40.000 0.00 0.00 31.36 2.24
513 525 6.384886 TCCAATTACTCCCTCCGTAAACTAAT 59.615 38.462 0.00 0.00 31.36 1.73
514 526 7.564660 TCCAATTACTCCCTCCGTAAACTAATA 59.435 37.037 0.00 0.00 31.36 0.98
515 527 8.373220 CCAATTACTCCCTCCGTAAACTAATAT 58.627 37.037 0.00 0.00 31.36 1.28
521 533 7.930325 ACTCCCTCCGTAAACTAATATAAAAGC 59.070 37.037 0.00 0.00 0.00 3.51
522 534 6.925165 TCCCTCCGTAAACTAATATAAAAGCG 59.075 38.462 0.00 0.00 0.00 4.68
523 535 6.703165 CCCTCCGTAAACTAATATAAAAGCGT 59.297 38.462 0.00 0.00 0.00 5.07
524 536 7.225341 CCCTCCGTAAACTAATATAAAAGCGTT 59.775 37.037 0.00 0.00 0.00 4.84
525 537 8.606602 CCTCCGTAAACTAATATAAAAGCGTTT 58.393 33.333 2.53 2.53 0.00 3.60
540 552 7.592439 AAAAGCGTTTAGATCACTACCTTAC 57.408 36.000 0.00 0.00 0.00 2.34
541 553 5.909621 AGCGTTTAGATCACTACCTTACA 57.090 39.130 0.00 0.00 0.00 2.41
542 554 5.892568 AGCGTTTAGATCACTACCTTACAG 58.107 41.667 0.00 0.00 0.00 2.74
543 555 5.418209 AGCGTTTAGATCACTACCTTACAGT 59.582 40.000 0.00 0.00 0.00 3.55
544 556 5.515626 GCGTTTAGATCACTACCTTACAGTG 59.484 44.000 0.00 0.00 43.92 3.66
545 557 6.034591 CGTTTAGATCACTACCTTACAGTGG 58.965 44.000 0.00 0.00 42.98 4.00
546 558 6.338937 GTTTAGATCACTACCTTACAGTGGG 58.661 44.000 0.00 0.00 42.98 4.61
547 559 4.332683 AGATCACTACCTTACAGTGGGA 57.667 45.455 0.00 0.00 42.98 4.37
548 560 4.282496 AGATCACTACCTTACAGTGGGAG 58.718 47.826 0.00 0.00 42.98 4.30
572 586 1.102809 TGTGTGCAGTTTGCTGGAGG 61.103 55.000 2.48 0.00 43.71 4.30
579 594 2.101415 GCAGTTTGCTGGAGGTTTTTCT 59.899 45.455 0.00 0.00 42.78 2.52
631 651 5.422214 ACCACACTTAGGTTGGAATCTAG 57.578 43.478 8.16 0.00 35.33 2.43
645 665 6.884472 TGGAATCTAGATTGGTGGTAAGAA 57.116 37.500 22.61 0.00 0.00 2.52
663 683 3.843999 AGAAGATGAGACGCTTTCAGAC 58.156 45.455 0.00 0.00 0.00 3.51
688 708 1.659794 CTGGGTTGGGAAAACGCTG 59.340 57.895 6.80 3.06 34.63 5.18
819 840 6.851609 ACATGCTCTCTCGACTGATATTATC 58.148 40.000 0.00 0.00 0.00 1.75
846 867 1.203052 AGGCATTCTGATTTTGTGGCG 59.797 47.619 0.00 0.00 39.93 5.69
849 870 2.598589 CATTCTGATTTTGTGGCGTGG 58.401 47.619 0.00 0.00 0.00 4.94
859 880 2.280797 TGGCGTGGTTCTGACTGC 60.281 61.111 0.00 0.00 0.00 4.40
888 909 2.936993 GCTTCACGTTCATGTCAGGGAT 60.937 50.000 0.00 0.00 0.00 3.85
909 930 5.888161 GGATTCCTGGTACATGATTTCTGTT 59.112 40.000 0.00 0.00 38.20 3.16
1031 1052 2.358737 CGAAGCTGGAAAGCCCGT 60.359 61.111 0.00 0.00 37.93 5.28
1124 1145 1.602377 GGACCGCACCATTAAGTATGC 59.398 52.381 0.00 0.00 32.60 3.14
1160 1188 7.062322 TCTGGTAGATGGTGATATTTGCAATT 58.938 34.615 0.00 0.00 0.00 2.32
1217 1245 9.093970 TGATTTAATTCTCATAGGTGTTACACG 57.906 33.333 9.52 0.00 34.83 4.49
1302 1330 1.814429 TCTTGGGTTTGGACCTGAGA 58.186 50.000 0.00 0.00 45.75 3.27
1373 1401 5.119931 TCGCAATTGTTTCTAATGCAACT 57.880 34.783 7.40 0.00 0.00 3.16
1382 1410 6.215121 TGTTTCTAATGCAACTGGTTTGATG 58.785 36.000 0.00 0.00 37.39 3.07
1428 1456 5.046529 GTGTGTATCTGCCTCAGTGATAAG 58.953 45.833 0.00 0.00 32.61 1.73
1429 1457 4.956075 TGTGTATCTGCCTCAGTGATAAGA 59.044 41.667 0.00 0.00 32.61 2.10
1430 1458 5.600069 TGTGTATCTGCCTCAGTGATAAGAT 59.400 40.000 13.72 13.72 32.61 2.40
1431 1459 6.777580 TGTGTATCTGCCTCAGTGATAAGATA 59.222 38.462 12.28 12.28 32.61 1.98
1432 1460 7.287696 TGTGTATCTGCCTCAGTGATAAGATAA 59.712 37.037 15.70 8.22 30.64 1.75
1456 1485 0.890683 GGCAAACTGATGGGGTCTTG 59.109 55.000 0.00 0.00 0.00 3.02
1535 1689 1.071699 TCCACCTCCTGTTGTGCTAAC 59.928 52.381 0.00 0.00 0.00 2.34
1586 1740 5.334879 GGTGTTGACAAGTATGACATTGGAC 60.335 44.000 0.00 0.00 31.48 4.02
1879 2034 4.022329 TCTCTGTCAAGTTATGCTTCGTGA 60.022 41.667 0.00 0.00 34.69 4.35
1912 2067 4.215613 TGATCGGTCTATCATGTTCTACGG 59.784 45.833 0.00 0.00 30.92 4.02
1988 2147 8.915036 TCCTTTCTGTATATTCTCTAGGACAAC 58.085 37.037 0.00 0.00 0.00 3.32
2051 2211 2.238144 CCCTTGGATGAAGCTTCTGAGA 59.762 50.000 26.09 7.35 0.00 3.27
2141 4891 3.795623 ATTTTGATGGACTGAGCATGC 57.204 42.857 10.51 10.51 0.00 4.06
2248 5014 2.299013 CAAGGGCAATGCATATGCTCAT 59.701 45.455 27.13 16.55 46.90 2.90
2262 5028 4.942761 ATGCTCATGTTTTGACAAGGTT 57.057 36.364 0.00 0.00 0.00 3.50
2263 5029 4.734398 TGCTCATGTTTTGACAAGGTTT 57.266 36.364 0.00 0.00 0.00 3.27
2264 5030 5.083533 TGCTCATGTTTTGACAAGGTTTT 57.916 34.783 0.00 0.00 0.00 2.43
2265 5031 5.486526 TGCTCATGTTTTGACAAGGTTTTT 58.513 33.333 0.00 0.00 0.00 1.94
2298 5067 8.415950 TGCATTATTTCCTCTTTAGGTTTTGA 57.584 30.769 0.00 0.00 44.09 2.69
2409 5184 4.100279 ACCAAAGAACTAGGTGGAAAGG 57.900 45.455 0.00 0.00 33.57 3.11
2468 5243 4.223923 ACGAAGATCACCTCTTTCCTTGAT 59.776 41.667 0.00 0.00 44.42 2.57
2799 5606 7.650834 TTGCTTGTAAATGCAAAAATACTCC 57.349 32.000 3.79 0.00 44.75 3.85
2800 5607 6.162777 TGCTTGTAAATGCAAAAATACTCCC 58.837 36.000 0.00 0.00 36.15 4.30
2801 5608 6.014669 TGCTTGTAAATGCAAAAATACTCCCT 60.015 34.615 0.00 0.00 36.15 4.20
2802 5609 6.531594 GCTTGTAAATGCAAAAATACTCCCTC 59.468 38.462 0.00 0.00 0.00 4.30
2803 5610 6.524101 TGTAAATGCAAAAATACTCCCTCC 57.476 37.500 0.00 0.00 0.00 4.30
2804 5611 6.013379 TGTAAATGCAAAAATACTCCCTCCA 58.987 36.000 0.00 0.00 0.00 3.86
2805 5612 6.667414 TGTAAATGCAAAAATACTCCCTCCAT 59.333 34.615 0.00 0.00 0.00 3.41
2806 5613 6.625532 AAATGCAAAAATACTCCCTCCATT 57.374 33.333 0.00 0.00 0.00 3.16
2807 5614 5.859205 ATGCAAAAATACTCCCTCCATTC 57.141 39.130 0.00 0.00 0.00 2.67
2808 5615 4.023291 TGCAAAAATACTCCCTCCATTCC 58.977 43.478 0.00 0.00 0.00 3.01
2809 5616 4.264352 TGCAAAAATACTCCCTCCATTCCT 60.264 41.667 0.00 0.00 0.00 3.36
2810 5617 5.044476 TGCAAAAATACTCCCTCCATTCCTA 60.044 40.000 0.00 0.00 0.00 2.94
2811 5618 5.891551 GCAAAAATACTCCCTCCATTCCTAA 59.108 40.000 0.00 0.00 0.00 2.69
2812 5619 6.379988 GCAAAAATACTCCCTCCATTCCTAAA 59.620 38.462 0.00 0.00 0.00 1.85
2813 5620 7.069950 GCAAAAATACTCCCTCCATTCCTAAAT 59.930 37.037 0.00 0.00 0.00 1.40
2814 5621 9.640952 CAAAAATACTCCCTCCATTCCTAAATA 57.359 33.333 0.00 0.00 0.00 1.40
2818 5625 9.813826 AATACTCCCTCCATTCCTAAATATTTG 57.186 33.333 11.05 1.40 0.00 2.32
2819 5626 7.226059 ACTCCCTCCATTCCTAAATATTTGT 57.774 36.000 11.05 0.00 0.00 2.83
2820 5627 7.290813 ACTCCCTCCATTCCTAAATATTTGTC 58.709 38.462 11.05 0.00 0.00 3.18
2821 5628 7.129504 ACTCCCTCCATTCCTAAATATTTGTCT 59.870 37.037 11.05 0.00 0.00 3.41
2822 5629 7.882755 TCCCTCCATTCCTAAATATTTGTCTT 58.117 34.615 11.05 0.00 0.00 3.01
2823 5630 8.343787 TCCCTCCATTCCTAAATATTTGTCTTT 58.656 33.333 11.05 0.00 0.00 2.52
2824 5631 8.981659 CCCTCCATTCCTAAATATTTGTCTTTT 58.018 33.333 11.05 0.00 0.00 2.27
2842 5649 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
2843 5650 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
2849 5656 9.958180 TTTAGAGATTTCAAATGGACTATCACA 57.042 29.630 0.00 0.00 0.00 3.58
2852 5659 9.553064 AGAGATTTCAAATGGACTATCACATAC 57.447 33.333 0.00 0.00 0.00 2.39
2853 5660 8.370493 AGATTTCAAATGGACTATCACATACG 57.630 34.615 0.00 0.00 0.00 3.06
2854 5661 5.984233 TTCAAATGGACTATCACATACGC 57.016 39.130 0.00 0.00 0.00 4.42
2855 5662 5.017294 TCAAATGGACTATCACATACGCA 57.983 39.130 0.00 0.00 0.00 5.24
2856 5663 5.610398 TCAAATGGACTATCACATACGCAT 58.390 37.500 0.00 0.00 0.00 4.73
2857 5664 5.466393 TCAAATGGACTATCACATACGCATG 59.534 40.000 0.00 0.00 38.21 4.06
2858 5665 4.607293 ATGGACTATCACATACGCATGT 57.393 40.909 0.00 0.00 46.58 3.21
2859 5666 5.722021 ATGGACTATCACATACGCATGTA 57.278 39.130 0.00 0.00 43.73 2.29
2860 5667 5.722021 TGGACTATCACATACGCATGTAT 57.278 39.130 0.00 0.00 43.73 2.29
2861 5668 6.096673 TGGACTATCACATACGCATGTATT 57.903 37.500 0.00 0.00 43.73 1.89
2862 5669 6.521162 TGGACTATCACATACGCATGTATTT 58.479 36.000 0.00 0.00 43.73 1.40
2863 5670 7.662897 TGGACTATCACATACGCATGTATTTA 58.337 34.615 0.00 0.00 43.73 1.40
2864 5671 7.812669 TGGACTATCACATACGCATGTATTTAG 59.187 37.037 0.00 5.77 43.73 1.85
2865 5672 8.027189 GGACTATCACATACGCATGTATTTAGA 58.973 37.037 0.00 0.00 43.73 2.10
2866 5673 8.744008 ACTATCACATACGCATGTATTTAGAC 57.256 34.615 0.00 0.00 43.73 2.59
2867 5674 8.357402 ACTATCACATACGCATGTATTTAGACA 58.643 33.333 0.00 0.00 43.73 3.41
2868 5675 9.358872 CTATCACATACGCATGTATTTAGACAT 57.641 33.333 0.00 0.00 43.73 3.06
2870 5677 9.875691 ATCACATACGCATGTATTTAGACATAT 57.124 29.630 0.00 0.00 43.73 1.78
2871 5678 9.705290 TCACATACGCATGTATTTAGACATATT 57.295 29.630 0.00 0.00 43.73 1.28
2897 5704 6.259550 AGAGTGTAGGTTCATTCATTTTGC 57.740 37.500 0.00 0.00 0.00 3.68
2898 5705 5.183904 AGAGTGTAGGTTCATTCATTTTGCC 59.816 40.000 0.00 0.00 0.00 4.52
2899 5706 4.220602 AGTGTAGGTTCATTCATTTTGCCC 59.779 41.667 0.00 0.00 0.00 5.36
2900 5707 3.513515 TGTAGGTTCATTCATTTTGCCCC 59.486 43.478 0.00 0.00 0.00 5.80
2901 5708 1.550072 AGGTTCATTCATTTTGCCCCG 59.450 47.619 0.00 0.00 0.00 5.73
2902 5709 1.275010 GGTTCATTCATTTTGCCCCGT 59.725 47.619 0.00 0.00 0.00 5.28
2903 5710 2.494073 GGTTCATTCATTTTGCCCCGTA 59.506 45.455 0.00 0.00 0.00 4.02
2904 5711 3.132111 GGTTCATTCATTTTGCCCCGTAT 59.868 43.478 0.00 0.00 0.00 3.06
2905 5712 4.111916 GTTCATTCATTTTGCCCCGTATG 58.888 43.478 0.00 0.00 0.00 2.39
2906 5713 3.360867 TCATTCATTTTGCCCCGTATGT 58.639 40.909 0.00 0.00 0.00 2.29
2907 5714 4.527944 TCATTCATTTTGCCCCGTATGTA 58.472 39.130 0.00 0.00 0.00 2.29
2908 5715 4.578516 TCATTCATTTTGCCCCGTATGTAG 59.421 41.667 0.00 0.00 0.00 2.74
2909 5716 3.637911 TCATTTTGCCCCGTATGTAGT 57.362 42.857 0.00 0.00 0.00 2.73
2910 5717 3.537580 TCATTTTGCCCCGTATGTAGTC 58.462 45.455 0.00 0.00 0.00 2.59
2911 5718 3.055021 TCATTTTGCCCCGTATGTAGTCA 60.055 43.478 0.00 0.00 0.00 3.41
2912 5719 3.637911 TTTTGCCCCGTATGTAGTCAT 57.362 42.857 0.00 0.00 38.00 3.06
2913 5720 3.637911 TTTGCCCCGTATGTAGTCATT 57.362 42.857 0.00 0.00 35.70 2.57
2914 5721 3.637911 TTGCCCCGTATGTAGTCATTT 57.362 42.857 0.00 0.00 35.70 2.32
2915 5722 2.912771 TGCCCCGTATGTAGTCATTTG 58.087 47.619 0.00 0.00 35.70 2.32
2916 5723 2.237643 TGCCCCGTATGTAGTCATTTGT 59.762 45.455 0.00 0.00 35.70 2.83
2917 5724 3.275999 GCCCCGTATGTAGTCATTTGTT 58.724 45.455 0.00 0.00 35.70 2.83
2918 5725 3.064820 GCCCCGTATGTAGTCATTTGTTG 59.935 47.826 0.00 0.00 35.70 3.33
2919 5726 4.509616 CCCCGTATGTAGTCATTTGTTGA 58.490 43.478 0.00 0.00 35.70 3.18
2920 5727 4.938832 CCCCGTATGTAGTCATTTGTTGAA 59.061 41.667 0.00 0.00 35.70 2.69
2921 5728 5.413213 CCCCGTATGTAGTCATTTGTTGAAA 59.587 40.000 0.00 0.00 35.70 2.69
2922 5729 6.094881 CCCCGTATGTAGTCATTTGTTGAAAT 59.905 38.462 0.00 0.00 35.70 2.17
2923 5730 7.186804 CCCGTATGTAGTCATTTGTTGAAATC 58.813 38.462 0.00 0.00 35.70 2.17
2924 5731 7.065803 CCCGTATGTAGTCATTTGTTGAAATCT 59.934 37.037 0.00 0.00 35.70 2.40
2925 5732 8.116753 CCGTATGTAGTCATTTGTTGAAATCTC 58.883 37.037 0.00 0.00 35.70 2.75
2926 5733 8.873830 CGTATGTAGTCATTTGTTGAAATCTCT 58.126 33.333 0.00 0.00 35.70 3.10
2930 5737 9.996554 TGTAGTCATTTGTTGAAATCTCTAGAA 57.003 29.630 0.00 0.00 35.70 2.10
2933 5740 9.784531 AGTCATTTGTTGAAATCTCTAGAAAGA 57.215 29.630 0.00 0.00 35.70 2.52
2934 5741 9.818796 GTCATTTGTTGAAATCTCTAGAAAGAC 57.181 33.333 0.00 0.00 35.70 3.01
2935 5742 9.559732 TCATTTGTTGAAATCTCTAGAAAGACA 57.440 29.630 0.00 0.00 28.65 3.41
2953 5760 8.947115 AGAAAGACAAATATTTAGAAACGGAGG 58.053 33.333 0.00 0.00 0.00 4.30
2954 5761 7.625828 AAGACAAATATTTAGAAACGGAGGG 57.374 36.000 0.00 0.00 0.00 4.30
2977 5784 7.125053 AGGGAGTAGAAAATTGGAAAACAACAA 59.875 33.333 0.00 0.00 42.94 2.83
3021 5828 4.270325 CCTAGGTGTAGCGAGCAAATTAAC 59.730 45.833 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.211045 GAGGTTTAGCCACTTGTGTGAA 58.789 45.455 0.00 0.00 46.55 3.18
1 2 2.171659 TGAGGTTTAGCCACTTGTGTGA 59.828 45.455 0.00 0.00 46.55 3.58
2 3 2.290641 GTGAGGTTTAGCCACTTGTGTG 59.709 50.000 0.00 0.00 43.45 3.82
3 4 2.572290 GTGAGGTTTAGCCACTTGTGT 58.428 47.619 0.00 0.00 40.61 3.72
4 5 1.531149 CGTGAGGTTTAGCCACTTGTG 59.469 52.381 0.00 0.00 40.61 3.33
5 6 1.878953 CGTGAGGTTTAGCCACTTGT 58.121 50.000 0.00 0.00 40.61 3.16
19 20 0.597377 GGCCAAGTTTTTGCCGTGAG 60.597 55.000 0.00 0.00 32.79 3.51
20 21 1.040339 AGGCCAAGTTTTTGCCGTGA 61.040 50.000 5.01 0.00 36.34 4.35
21 22 0.875474 CAGGCCAAGTTTTTGCCGTG 60.875 55.000 5.01 0.00 36.34 4.94
22 23 1.441311 CAGGCCAAGTTTTTGCCGT 59.559 52.632 5.01 0.00 36.34 5.68
23 24 1.300853 CCAGGCCAAGTTTTTGCCG 60.301 57.895 5.01 0.00 36.34 5.69
24 25 0.467804 TTCCAGGCCAAGTTTTTGCC 59.532 50.000 5.01 0.00 32.79 4.52
25 26 2.549064 ATTCCAGGCCAAGTTTTTGC 57.451 45.000 5.01 0.00 32.79 3.68
26 27 4.082026 CCTCTATTCCAGGCCAAGTTTTTG 60.082 45.833 5.01 0.00 0.00 2.44
27 28 4.089361 CCTCTATTCCAGGCCAAGTTTTT 58.911 43.478 5.01 0.00 0.00 1.94
28 29 3.701664 CCTCTATTCCAGGCCAAGTTTT 58.298 45.455 5.01 0.00 0.00 2.43
29 30 3.372440 CCTCTATTCCAGGCCAAGTTT 57.628 47.619 5.01 0.00 0.00 2.66
37 38 1.216990 ACCCAAGCCTCTATTCCAGG 58.783 55.000 0.00 0.00 0.00 4.45
38 39 3.392616 ACATACCCAAGCCTCTATTCCAG 59.607 47.826 0.00 0.00 0.00 3.86
39 40 3.393687 ACATACCCAAGCCTCTATTCCA 58.606 45.455 0.00 0.00 0.00 3.53
40 41 4.439253 AACATACCCAAGCCTCTATTCC 57.561 45.455 0.00 0.00 0.00 3.01
41 42 5.066505 CACAAACATACCCAAGCCTCTATTC 59.933 44.000 0.00 0.00 0.00 1.75
42 43 4.949856 CACAAACATACCCAAGCCTCTATT 59.050 41.667 0.00 0.00 0.00 1.73
43 44 4.227300 TCACAAACATACCCAAGCCTCTAT 59.773 41.667 0.00 0.00 0.00 1.98
44 45 3.585289 TCACAAACATACCCAAGCCTCTA 59.415 43.478 0.00 0.00 0.00 2.43
45 46 2.375174 TCACAAACATACCCAAGCCTCT 59.625 45.455 0.00 0.00 0.00 3.69
46 47 2.790433 TCACAAACATACCCAAGCCTC 58.210 47.619 0.00 0.00 0.00 4.70
47 48 2.969821 TCACAAACATACCCAAGCCT 57.030 45.000 0.00 0.00 0.00 4.58
48 49 4.440112 GCTAATCACAAACATACCCAAGCC 60.440 45.833 0.00 0.00 0.00 4.35
49 50 4.157656 TGCTAATCACAAACATACCCAAGC 59.842 41.667 0.00 0.00 0.00 4.01
50 51 5.895636 TGCTAATCACAAACATACCCAAG 57.104 39.130 0.00 0.00 0.00 3.61
51 52 5.394005 GCATGCTAATCACAAACATACCCAA 60.394 40.000 11.37 0.00 0.00 4.12
52 53 4.097741 GCATGCTAATCACAAACATACCCA 59.902 41.667 11.37 0.00 0.00 4.51
53 54 4.339247 AGCATGCTAATCACAAACATACCC 59.661 41.667 21.21 0.00 0.00 3.69
54 55 5.276270 CAGCATGCTAATCACAAACATACC 58.724 41.667 22.19 0.00 0.00 2.73
83 84 1.070786 GGCGTCCAGGTTCTGTCAA 59.929 57.895 0.00 0.00 0.00 3.18
145 147 3.710722 CCCACGCTGAGGAGGCTT 61.711 66.667 0.00 0.00 0.00 4.35
171 178 2.359531 TCGGCTTGATTCGGTTTTGTTT 59.640 40.909 0.00 0.00 0.00 2.83
172 179 1.950909 TCGGCTTGATTCGGTTTTGTT 59.049 42.857 0.00 0.00 0.00 2.83
173 180 1.600023 TCGGCTTGATTCGGTTTTGT 58.400 45.000 0.00 0.00 0.00 2.83
174 181 2.919666 ATCGGCTTGATTCGGTTTTG 57.080 45.000 0.00 0.00 31.57 2.44
175 182 4.881850 AGATAATCGGCTTGATTCGGTTTT 59.118 37.500 7.80 0.00 44.01 2.43
255 262 2.751688 GGGTAACGGGAGCAACCA 59.248 61.111 2.58 0.00 39.12 3.67
289 297 2.286365 AAGAAAGGAATGCGGAACCA 57.714 45.000 6.33 0.00 0.00 3.67
443 454 3.303049 GGATCAGGGCATTTTCCTCATT 58.697 45.455 0.00 0.00 31.06 2.57
447 458 0.918983 TCGGATCAGGGCATTTTCCT 59.081 50.000 0.00 0.00 34.39 3.36
455 467 2.640316 ATAAAAGGTCGGATCAGGGC 57.360 50.000 0.00 0.00 0.00 5.19
459 471 5.395990 GGTGGTTCTATAAAAGGTCGGATCA 60.396 44.000 0.00 0.00 0.00 2.92
495 507 7.930325 GCTTTTATATTAGTTTACGGAGGGAGT 59.070 37.037 0.00 0.00 0.00 3.85
496 508 7.115947 CGCTTTTATATTAGTTTACGGAGGGAG 59.884 40.741 0.00 0.00 0.00 4.30
497 509 6.925165 CGCTTTTATATTAGTTTACGGAGGGA 59.075 38.462 0.00 0.00 0.00 4.20
498 510 6.703165 ACGCTTTTATATTAGTTTACGGAGGG 59.297 38.462 0.00 0.00 0.00 4.30
499 511 7.704789 ACGCTTTTATATTAGTTTACGGAGG 57.295 36.000 0.00 0.00 0.00 4.30
514 526 9.310716 GTAAGGTAGTGATCTAAACGCTTTTAT 57.689 33.333 0.00 0.00 0.00 1.40
515 527 8.306038 TGTAAGGTAGTGATCTAAACGCTTTTA 58.694 33.333 0.00 0.00 0.00 1.52
516 528 7.156673 TGTAAGGTAGTGATCTAAACGCTTTT 58.843 34.615 0.00 0.00 0.00 2.27
517 529 6.694447 TGTAAGGTAGTGATCTAAACGCTTT 58.306 36.000 0.00 0.00 0.00 3.51
518 530 6.071503 ACTGTAAGGTAGTGATCTAAACGCTT 60.072 38.462 0.00 0.00 39.30 4.68
519 531 5.418209 ACTGTAAGGTAGTGATCTAAACGCT 59.582 40.000 0.00 0.00 39.30 5.07
520 532 5.515626 CACTGTAAGGTAGTGATCTAAACGC 59.484 44.000 0.00 0.00 46.52 4.84
521 533 6.034591 CCACTGTAAGGTAGTGATCTAAACG 58.965 44.000 6.70 0.00 46.52 3.60
522 534 6.154021 TCCCACTGTAAGGTAGTGATCTAAAC 59.846 42.308 6.70 0.00 46.52 2.01
523 535 6.258354 TCCCACTGTAAGGTAGTGATCTAAA 58.742 40.000 6.70 0.00 46.52 1.85
524 536 5.834460 TCCCACTGTAAGGTAGTGATCTAA 58.166 41.667 6.70 0.00 46.52 2.10
525 537 5.044328 ACTCCCACTGTAAGGTAGTGATCTA 60.044 44.000 6.70 0.00 46.52 1.98
526 538 4.264442 ACTCCCACTGTAAGGTAGTGATCT 60.264 45.833 6.70 0.00 46.52 2.75
527 539 4.024670 ACTCCCACTGTAAGGTAGTGATC 58.975 47.826 6.70 0.00 46.52 2.92
528 540 4.062490 ACTCCCACTGTAAGGTAGTGAT 57.938 45.455 6.70 0.00 46.52 3.06
529 541 3.537795 ACTCCCACTGTAAGGTAGTGA 57.462 47.619 6.70 0.00 46.52 3.41
530 542 4.084287 TGTACTCCCACTGTAAGGTAGTG 58.916 47.826 0.00 0.00 43.94 2.74
531 543 4.393239 TGTACTCCCACTGTAAGGTAGT 57.607 45.455 0.00 0.00 39.30 2.73
532 544 4.710375 ACATGTACTCCCACTGTAAGGTAG 59.290 45.833 0.00 0.00 39.30 3.18
533 545 4.464951 CACATGTACTCCCACTGTAAGGTA 59.535 45.833 0.00 0.00 39.30 3.08
534 546 3.260884 CACATGTACTCCCACTGTAAGGT 59.739 47.826 0.00 0.00 39.30 3.50
535 547 3.260884 ACACATGTACTCCCACTGTAAGG 59.739 47.826 0.00 0.00 39.30 2.69
536 548 4.245660 CACACATGTACTCCCACTGTAAG 58.754 47.826 0.00 0.00 42.29 2.34
537 549 3.556213 GCACACATGTACTCCCACTGTAA 60.556 47.826 0.00 0.00 0.00 2.41
538 550 2.028476 GCACACATGTACTCCCACTGTA 60.028 50.000 0.00 0.00 0.00 2.74
539 551 1.270839 GCACACATGTACTCCCACTGT 60.271 52.381 0.00 0.00 0.00 3.55
540 552 1.270785 TGCACACATGTACTCCCACTG 60.271 52.381 0.00 0.00 0.00 3.66
541 553 1.002430 CTGCACACATGTACTCCCACT 59.998 52.381 0.00 0.00 0.00 4.00
542 554 1.270839 ACTGCACACATGTACTCCCAC 60.271 52.381 0.00 0.00 0.00 4.61
543 555 1.055849 ACTGCACACATGTACTCCCA 58.944 50.000 0.00 0.00 0.00 4.37
544 556 2.185004 AACTGCACACATGTACTCCC 57.815 50.000 0.00 0.00 0.00 4.30
545 557 2.350772 GCAAACTGCACACATGTACTCC 60.351 50.000 0.00 0.00 44.26 3.85
546 558 2.921126 GCAAACTGCACACATGTACTC 58.079 47.619 0.00 0.00 44.26 2.59
585 600 4.663592 TCTCCTCCTAAACCCAAGTTTCTT 59.336 41.667 0.00 0.00 42.67 2.52
587 602 4.635699 TCTCCTCCTAAACCCAAGTTTC 57.364 45.455 0.00 0.00 42.67 2.78
591 606 2.642807 TGGTTCTCCTCCTAAACCCAAG 59.357 50.000 1.37 0.00 41.44 3.61
593 608 1.982958 GTGGTTCTCCTCCTAAACCCA 59.017 52.381 1.37 0.00 41.44 4.51
594 609 1.982958 TGTGGTTCTCCTCCTAAACCC 59.017 52.381 1.37 0.00 41.44 4.11
631 651 4.806247 CGTCTCATCTTCTTACCACCAATC 59.194 45.833 0.00 0.00 0.00 2.67
645 665 2.175202 AGGTCTGAAAGCGTCTCATCT 58.825 47.619 0.00 0.00 0.00 2.90
663 683 0.178964 TTTCCCAACCCAGCTCAAGG 60.179 55.000 0.00 0.00 0.00 3.61
688 708 9.456797 CGTTACTCACTCGTACAAAATAAAATC 57.543 33.333 0.00 0.00 0.00 2.17
819 840 5.407387 CACAAAATCAGAATGCCTCAAAAGG 59.593 40.000 0.00 0.00 46.44 3.11
846 867 0.249489 ACTCACGCAGTCAGAACCAC 60.249 55.000 0.00 0.00 41.61 4.16
849 870 1.068194 AGCTACTCACGCAGTCAGAAC 60.068 52.381 0.00 0.00 41.61 3.01
888 909 4.935205 CGAACAGAAATCATGTACCAGGAA 59.065 41.667 0.00 0.00 0.00 3.36
1031 1052 2.203640 ACTCCAGCACGACCTCCA 60.204 61.111 0.00 0.00 0.00 3.86
1160 1188 8.882736 CATCAGCACAAACATACTAGTAATGAA 58.117 33.333 6.70 0.00 0.00 2.57
1217 1245 2.591571 GCTTCATCCCAAAGCATTCC 57.408 50.000 3.12 0.00 46.63 3.01
1302 1330 5.067674 TCAGCTCAAGTGCAAAATTAGTGTT 59.932 36.000 0.00 0.00 34.99 3.32
1348 1376 3.057666 TGCATTAGAAACAATTGCGAGCA 60.058 39.130 5.05 2.39 0.00 4.26
1373 1401 6.723298 AACATTAACAAGGACATCAAACCA 57.277 33.333 0.00 0.00 0.00 3.67
1382 1410 4.609783 CGTCGACCAAACATTAACAAGGAC 60.610 45.833 10.58 0.00 0.00 3.85
1428 1456 4.520492 CCCCATCAGTTTGCCAGTATTATC 59.480 45.833 0.00 0.00 0.00 1.75
1429 1457 4.079212 ACCCCATCAGTTTGCCAGTATTAT 60.079 41.667 0.00 0.00 0.00 1.28
1430 1458 3.268334 ACCCCATCAGTTTGCCAGTATTA 59.732 43.478 0.00 0.00 0.00 0.98
1431 1459 2.042979 ACCCCATCAGTTTGCCAGTATT 59.957 45.455 0.00 0.00 0.00 1.89
1432 1460 1.640670 ACCCCATCAGTTTGCCAGTAT 59.359 47.619 0.00 0.00 0.00 2.12
1456 1485 4.057432 GGCTCATATGCAGAGAGAAGAAC 58.943 47.826 14.78 0.00 35.09 3.01
1535 1689 4.421058 TCTATCAAACGAGAACGGACATG 58.579 43.478 0.00 0.00 44.46 3.21
1586 1740 0.670239 GCAAAATGTCCAAAGCCCGG 60.670 55.000 0.00 0.00 0.00 5.73
1912 2067 8.173542 TCTCCTTTTACAAAACAATACCTTCC 57.826 34.615 0.00 0.00 0.00 3.46
2051 2211 4.973168 TGTACTGAGGCACATCTTTCTTT 58.027 39.130 0.00 0.00 0.00 2.52
2180 4930 1.107538 TGGTCTTATCCTCCTCGGCG 61.108 60.000 0.00 0.00 0.00 6.46
2298 5067 6.257630 GCAACACAACAACCATTAAGAAATGT 59.742 34.615 0.00 0.00 40.84 2.71
2382 5157 4.412858 TCCACCTAGTTCTTTGGTAACCAA 59.587 41.667 0.00 0.00 42.29 3.67
2409 5184 2.125106 CCCAGGCTGCCGTAGAAC 60.125 66.667 13.96 0.00 0.00 3.01
2468 5243 1.299648 CACTTTCCAGCCATCGGGA 59.700 57.895 0.00 0.00 35.59 5.14
2668 5467 3.119849 AGCAATTATCGGTCACTTTGTGC 60.120 43.478 0.00 0.00 32.98 4.57
2793 5600 8.960064 ACAAATATTTAGGAATGGAGGGAGTAT 58.040 33.333 0.00 0.00 0.00 2.12
2794 5601 8.344939 ACAAATATTTAGGAATGGAGGGAGTA 57.655 34.615 0.00 0.00 0.00 2.59
2795 5602 7.129504 AGACAAATATTTAGGAATGGAGGGAGT 59.870 37.037 0.00 0.00 0.00 3.85
2796 5603 7.521669 AGACAAATATTTAGGAATGGAGGGAG 58.478 38.462 0.00 0.00 0.00 4.30
2797 5604 7.465900 AGACAAATATTTAGGAATGGAGGGA 57.534 36.000 0.00 0.00 0.00 4.20
2798 5605 8.539117 AAAGACAAATATTTAGGAATGGAGGG 57.461 34.615 0.00 0.00 0.00 4.30
2816 5623 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
2817 5624 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
2823 5630 9.958180 TGTGATAGTCCATTTGAAATCTCTAAA 57.042 29.630 0.00 0.00 0.00 1.85
2826 5633 9.553064 GTATGTGATAGTCCATTTGAAATCTCT 57.447 33.333 0.00 0.00 0.00 3.10
2827 5634 8.491152 CGTATGTGATAGTCCATTTGAAATCTC 58.509 37.037 0.00 0.00 0.00 2.75
2828 5635 7.041780 GCGTATGTGATAGTCCATTTGAAATCT 60.042 37.037 0.00 0.00 0.00 2.40
2829 5636 7.072030 GCGTATGTGATAGTCCATTTGAAATC 58.928 38.462 0.00 0.00 0.00 2.17
2830 5637 6.542005 TGCGTATGTGATAGTCCATTTGAAAT 59.458 34.615 0.00 0.00 0.00 2.17
2831 5638 5.877564 TGCGTATGTGATAGTCCATTTGAAA 59.122 36.000 0.00 0.00 0.00 2.69
2832 5639 5.423886 TGCGTATGTGATAGTCCATTTGAA 58.576 37.500 0.00 0.00 0.00 2.69
2833 5640 5.017294 TGCGTATGTGATAGTCCATTTGA 57.983 39.130 0.00 0.00 0.00 2.69
2834 5641 5.237127 ACATGCGTATGTGATAGTCCATTTG 59.763 40.000 18.78 0.00 45.54 2.32
2835 5642 5.368145 ACATGCGTATGTGATAGTCCATTT 58.632 37.500 18.78 0.00 45.54 2.32
2836 5643 4.960938 ACATGCGTATGTGATAGTCCATT 58.039 39.130 18.78 0.00 45.54 3.16
2837 5644 4.607293 ACATGCGTATGTGATAGTCCAT 57.393 40.909 18.78 0.00 45.54 3.41
2838 5645 5.722021 ATACATGCGTATGTGATAGTCCA 57.278 39.130 26.72 6.66 46.63 4.02
2839 5646 8.027189 TCTAAATACATGCGTATGTGATAGTCC 58.973 37.037 26.72 0.00 46.63 3.85
2840 5647 8.851416 GTCTAAATACATGCGTATGTGATAGTC 58.149 37.037 26.72 17.85 46.63 2.59
2841 5648 8.357402 TGTCTAAATACATGCGTATGTGATAGT 58.643 33.333 26.72 5.74 46.63 2.12
2842 5649 8.742554 TGTCTAAATACATGCGTATGTGATAG 57.257 34.615 26.72 22.32 46.63 2.08
2844 5651 9.875691 ATATGTCTAAATACATGCGTATGTGAT 57.124 29.630 26.72 13.64 46.63 3.06
2845 5652 9.705290 AATATGTCTAAATACATGCGTATGTGA 57.295 29.630 26.72 13.43 46.63 3.58
2871 5678 8.296713 GCAAAATGAATGAACCTACACTCTAAA 58.703 33.333 0.00 0.00 0.00 1.85
2872 5679 7.094377 GGCAAAATGAATGAACCTACACTCTAA 60.094 37.037 0.00 0.00 0.00 2.10
2873 5680 6.374333 GGCAAAATGAATGAACCTACACTCTA 59.626 38.462 0.00 0.00 0.00 2.43
2874 5681 5.183904 GGCAAAATGAATGAACCTACACTCT 59.816 40.000 0.00 0.00 0.00 3.24
2875 5682 5.402398 GGCAAAATGAATGAACCTACACTC 58.598 41.667 0.00 0.00 0.00 3.51
2876 5683 4.220602 GGGCAAAATGAATGAACCTACACT 59.779 41.667 0.00 0.00 0.00 3.55
2877 5684 4.494484 GGGCAAAATGAATGAACCTACAC 58.506 43.478 0.00 0.00 0.00 2.90
2878 5685 3.513515 GGGGCAAAATGAATGAACCTACA 59.486 43.478 0.00 0.00 0.00 2.74
2879 5686 3.428862 CGGGGCAAAATGAATGAACCTAC 60.429 47.826 0.00 0.00 0.00 3.18
2880 5687 2.757868 CGGGGCAAAATGAATGAACCTA 59.242 45.455 0.00 0.00 0.00 3.08
2881 5688 1.550072 CGGGGCAAAATGAATGAACCT 59.450 47.619 0.00 0.00 0.00 3.50
2882 5689 1.275010 ACGGGGCAAAATGAATGAACC 59.725 47.619 0.00 0.00 0.00 3.62
2883 5690 2.741759 ACGGGGCAAAATGAATGAAC 57.258 45.000 0.00 0.00 0.00 3.18
2884 5691 3.766591 ACATACGGGGCAAAATGAATGAA 59.233 39.130 0.00 0.00 0.00 2.57
2885 5692 3.360867 ACATACGGGGCAAAATGAATGA 58.639 40.909 0.00 0.00 0.00 2.57
2886 5693 3.799281 ACATACGGGGCAAAATGAATG 57.201 42.857 0.00 0.00 0.00 2.67
2887 5694 4.532834 ACTACATACGGGGCAAAATGAAT 58.467 39.130 0.00 0.00 0.00 2.57
2888 5695 3.942748 GACTACATACGGGGCAAAATGAA 59.057 43.478 0.00 0.00 0.00 2.57
2889 5696 3.055021 TGACTACATACGGGGCAAAATGA 60.055 43.478 0.00 0.00 0.00 2.57
2890 5697 3.275143 TGACTACATACGGGGCAAAATG 58.725 45.455 0.00 0.00 0.00 2.32
2891 5698 3.637911 TGACTACATACGGGGCAAAAT 57.362 42.857 0.00 0.00 0.00 1.82
2892 5699 3.637911 ATGACTACATACGGGGCAAAA 57.362 42.857 0.00 0.00 34.71 2.44
2893 5700 3.637911 AATGACTACATACGGGGCAAA 57.362 42.857 0.00 0.00 35.50 3.68
2894 5701 3.275143 CAAATGACTACATACGGGGCAA 58.725 45.455 0.00 0.00 35.50 4.52
2895 5702 2.237643 ACAAATGACTACATACGGGGCA 59.762 45.455 0.00 0.00 35.50 5.36
2896 5703 2.914059 ACAAATGACTACATACGGGGC 58.086 47.619 0.00 0.00 35.50 5.80
2897 5704 4.509616 TCAACAAATGACTACATACGGGG 58.490 43.478 0.00 0.00 35.50 5.73
2898 5705 6.489127 TTTCAACAAATGACTACATACGGG 57.511 37.500 0.00 0.00 37.92 5.28
2899 5706 7.974675 AGATTTCAACAAATGACTACATACGG 58.025 34.615 0.00 0.00 37.92 4.02
2900 5707 8.873830 AGAGATTTCAACAAATGACTACATACG 58.126 33.333 0.00 0.00 37.92 3.06
2904 5711 9.996554 TTCTAGAGATTTCAACAAATGACTACA 57.003 29.630 0.00 0.00 37.92 2.74
2907 5714 9.784531 TCTTTCTAGAGATTTCAACAAATGACT 57.215 29.630 0.00 0.00 37.92 3.41
2908 5715 9.818796 GTCTTTCTAGAGATTTCAACAAATGAC 57.181 33.333 0.00 0.00 37.92 3.06
2909 5716 9.559732 TGTCTTTCTAGAGATTTCAACAAATGA 57.440 29.630 0.00 0.00 31.94 2.57
2927 5734 8.947115 CCTCCGTTTCTAAATATTTGTCTTTCT 58.053 33.333 11.05 0.00 0.00 2.52
2928 5735 8.182227 CCCTCCGTTTCTAAATATTTGTCTTTC 58.818 37.037 11.05 0.00 0.00 2.62
2929 5736 7.886446 TCCCTCCGTTTCTAAATATTTGTCTTT 59.114 33.333 11.05 0.00 0.00 2.52
2930 5737 7.399634 TCCCTCCGTTTCTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
2931 5738 6.954232 TCCCTCCGTTTCTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
2932 5739 6.822170 ACTCCCTCCGTTTCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
2933 5740 6.718294 ACTCCCTCCGTTTCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
2934 5741 8.202137 TCTACTCCCTCCGTTTCTAAATATTTG 58.798 37.037 11.05 1.65 0.00 2.32
2935 5742 8.315220 TCTACTCCCTCCGTTTCTAAATATTT 57.685 34.615 5.89 5.89 0.00 1.40
2936 5743 7.909485 TCTACTCCCTCCGTTTCTAAATATT 57.091 36.000 0.00 0.00 0.00 1.28
2937 5744 7.909485 TTCTACTCCCTCCGTTTCTAAATAT 57.091 36.000 0.00 0.00 0.00 1.28
2938 5745 7.722949 TTTCTACTCCCTCCGTTTCTAAATA 57.277 36.000 0.00 0.00 0.00 1.40
2939 5746 6.616237 TTTCTACTCCCTCCGTTTCTAAAT 57.384 37.500 0.00 0.00 0.00 1.40
2940 5747 6.423776 TTTTCTACTCCCTCCGTTTCTAAA 57.576 37.500 0.00 0.00 0.00 1.85
2941 5748 6.616237 ATTTTCTACTCCCTCCGTTTCTAA 57.384 37.500 0.00 0.00 0.00 2.10
2942 5749 6.403878 CAATTTTCTACTCCCTCCGTTTCTA 58.596 40.000 0.00 0.00 0.00 2.10
2943 5750 5.246307 CAATTTTCTACTCCCTCCGTTTCT 58.754 41.667 0.00 0.00 0.00 2.52
2944 5751 4.395231 CCAATTTTCTACTCCCTCCGTTTC 59.605 45.833 0.00 0.00 0.00 2.78
2945 5752 4.042435 TCCAATTTTCTACTCCCTCCGTTT 59.958 41.667 0.00 0.00 0.00 3.60
2946 5753 3.585732 TCCAATTTTCTACTCCCTCCGTT 59.414 43.478 0.00 0.00 0.00 4.44
2947 5754 3.178865 TCCAATTTTCTACTCCCTCCGT 58.821 45.455 0.00 0.00 0.00 4.69
2948 5755 3.906720 TCCAATTTTCTACTCCCTCCG 57.093 47.619 0.00 0.00 0.00 4.63
2949 5756 5.773176 TGTTTTCCAATTTTCTACTCCCTCC 59.227 40.000 0.00 0.00 0.00 4.30
2950 5757 6.894339 TGTTTTCCAATTTTCTACTCCCTC 57.106 37.500 0.00 0.00 0.00 4.30
2951 5758 6.609616 TGTTGTTTTCCAATTTTCTACTCCCT 59.390 34.615 0.00 0.00 35.02 4.20
2952 5759 6.811954 TGTTGTTTTCCAATTTTCTACTCCC 58.188 36.000 0.00 0.00 35.02 4.30
2953 5760 7.762159 TGTTGTTGTTTTCCAATTTTCTACTCC 59.238 33.333 0.00 0.00 35.02 3.85
2954 5761 8.696410 TGTTGTTGTTTTCCAATTTTCTACTC 57.304 30.769 0.00 0.00 35.02 2.59
2977 5784 6.067217 AGGATGCCTACTTTCTTACAATGT 57.933 37.500 0.00 0.00 28.47 2.71
3021 5828 0.161446 GCCGCACGCAAAAATTCTTG 59.839 50.000 0.00 0.00 37.47 3.02


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

AutoCloner maintained by Alex Coulton.