Multiple sequence alignment - TraesCS1D01G016900

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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 TraesCS1D01G016900 chr1D 100.000 4791 0 0 1 4791 7605244 7610034 0.000000e+00 8848.0
1 TraesCS1D01G016900 chr1D 84.984 3210 442 24 839 4029 7280527 7277339 0.000000e+00 3221.0
2 TraesCS1D01G016900 chr1D 83.708 2799 435 14 971 3754 10663401 10660609 0.000000e+00 2623.0
3 TraesCS1D01G016900 chr1D 82.234 546 85 8 814 1352 7820867 7821407 1.210000e-125 460.0
4 TraesCS1D01G016900 chr1B 94.577 3264 160 6 905 4161 9558667 9555414 0.000000e+00 5031.0
5 TraesCS1D01G016900 chr1B 85.343 3234 443 20 814 4029 9989401 9992621 0.000000e+00 3317.0
6 TraesCS1D01G016900 chr1B 85.126 2259 317 12 1510 3753 15877084 15879338 0.000000e+00 2292.0
7 TraesCS1D01G016900 chr1B 84.742 911 120 16 1 905 9561132 9560235 0.000000e+00 894.0
8 TraesCS1D01G016900 chr1B 97.260 73 2 0 4658 4730 9554602 9554530 1.810000e-24 124.0
9 TraesCS1D01G016900 chr1A 87.492 3302 359 23 907 4161 8718527 8715233 0.000000e+00 3760.0
10 TraesCS1D01G016900 chr1A 84.071 2800 424 12 971 3753 12503859 12506653 0.000000e+00 2680.0
11 TraesCS1D01G016900 chr1A 84.047 2802 420 22 971 3754 12306461 12303669 0.000000e+00 2673.0
12 TraesCS1D01G016900 chr1A 82.250 2800 472 17 971 3753 12210636 12207845 0.000000e+00 2394.0
13 TraesCS1D01G016900 chr1A 87.828 419 50 1 1251 1668 9251945 9252363 1.550000e-134 490.0
14 TraesCS1D01G016900 chr1A 87.791 172 13 3 4432 4596 8714193 8714023 1.360000e-45 195.0
15 TraesCS1D01G016900 chr1A 97.368 38 1 0 4540 4577 34970871 34970834 1.110000e-06 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 TraesCS1D01G016900 chr1D 7605244 7610034 4790 False 8848.000000 8848 100.0000 1 4791 1 chr1D.!!$F1 4790
1 TraesCS1D01G016900 chr1D 7277339 7280527 3188 True 3221.000000 3221 84.9840 839 4029 1 chr1D.!!$R1 3190
2 TraesCS1D01G016900 chr1D 10660609 10663401 2792 True 2623.000000 2623 83.7080 971 3754 1 chr1D.!!$R2 2783
3 TraesCS1D01G016900 chr1D 7820867 7821407 540 False 460.000000 460 82.2340 814 1352 1 chr1D.!!$F2 538
4 TraesCS1D01G016900 chr1B 9989401 9992621 3220 False 3317.000000 3317 85.3430 814 4029 1 chr1B.!!$F1 3215
5 TraesCS1D01G016900 chr1B 15877084 15879338 2254 False 2292.000000 2292 85.1260 1510 3753 1 chr1B.!!$F2 2243
6 TraesCS1D01G016900 chr1B 9554530 9561132 6602 True 2016.333333 5031 92.1930 1 4730 3 chr1B.!!$R1 4729
7 TraesCS1D01G016900 chr1A 12503859 12506653 2794 False 2680.000000 2680 84.0710 971 3753 1 chr1A.!!$F2 2782
8 TraesCS1D01G016900 chr1A 12303669 12306461 2792 True 2673.000000 2673 84.0470 971 3754 1 chr1A.!!$R2 2783
9 TraesCS1D01G016900 chr1A 12207845 12210636 2791 True 2394.000000 2394 82.2500 971 3753 1 chr1A.!!$R1 2782
10 TraesCS1D01G016900 chr1A 8714023 8718527 4504 True 1977.500000 3760 87.6415 907 4596 2 chr1A.!!$R4 3689

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
552 557 0.032017 AGATCTAGTTGAGCCCCCGT 60.032 55.0 0.00 0.0 0.0 5.28 F
700 705 0.179056 CTCCACTTGTGTTCACCCGT 60.179 55.0 0.37 0.0 0.0 5.28 F
1329 2910 0.999406 CCTGCAACGGTACATCTTCG 59.001 55.0 0.00 0.0 0.0 3.79 F
2798 4396 0.829990 TCGAAGTGCCAGCATCCATA 59.170 50.0 0.00 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 3899 0.767375 TCTTCAGGGAACAAGCTGCT 59.233 50.000 0.0 0.0 0.00 4.24 R
2522 4117 1.072173 TCTTTAGCCACAGCAAGAGCA 59.928 47.619 0.0 0.0 45.49 4.26 R
2828 4426 1.072489 TGGACATTGGTACGCCTCAAA 59.928 47.619 0.0 0.0 35.27 2.69 R
4766 7360 0.033228 CTCTCATCATCCGTCCCAGC 59.967 60.000 0.0 0.0 0.00 4.85 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
18 19 3.980583 TTCACAACCACTCTCCGTC 57.019 52.632 0.00 0.00 0.00 4.79
19 20 1.116308 TTCACAACCACTCTCCGTCA 58.884 50.000 0.00 0.00 0.00 4.35
20 21 1.116308 TCACAACCACTCTCCGTCAA 58.884 50.000 0.00 0.00 0.00 3.18
22 23 0.106149 ACAACCACTCTCCGTCAACC 59.894 55.000 0.00 0.00 0.00 3.77
23 24 0.602905 CAACCACTCTCCGTCAACCC 60.603 60.000 0.00 0.00 0.00 4.11
24 25 0.763223 AACCACTCTCCGTCAACCCT 60.763 55.000 0.00 0.00 0.00 4.34
25 26 1.186267 ACCACTCTCCGTCAACCCTC 61.186 60.000 0.00 0.00 0.00 4.30
26 27 1.213013 CACTCTCCGTCAACCCTCG 59.787 63.158 0.00 0.00 0.00 4.63
30 31 2.993264 TCCGTCAACCCTCGGTCC 60.993 66.667 3.64 0.00 45.88 4.46
31 32 3.307906 CCGTCAACCCTCGGTCCA 61.308 66.667 0.00 0.00 41.58 4.02
43 47 2.233922 CCTCGGTCCACAGTTTACATCT 59.766 50.000 0.00 0.00 0.00 2.90
88 92 1.814429 TGGAGAAAGGAACCCTCACA 58.186 50.000 0.00 0.00 30.89 3.58
92 96 2.554462 GAGAAAGGAACCCTCACAAAGC 59.446 50.000 0.00 0.00 30.89 3.51
95 99 1.896660 GGAACCCTCACAAAGCGCA 60.897 57.895 11.47 0.00 0.00 6.09
99 103 1.244019 ACCCTCACAAAGCGCATTCC 61.244 55.000 11.47 0.00 0.00 3.01
123 127 0.945813 CCACTCGTCGGATAGAGTCC 59.054 60.000 13.70 0.00 44.98 3.85
124 128 1.475392 CCACTCGTCGGATAGAGTCCT 60.475 57.143 13.70 0.00 44.98 3.85
135 139 1.960040 TAGAGTCCTGCATGTGCCCG 61.960 60.000 2.07 0.00 41.18 6.13
159 163 1.302431 CCAGCGGTCAACATGGTCA 60.302 57.895 0.00 0.00 0.00 4.02
165 169 2.550606 GCGGTCAACATGGTCAAAACTA 59.449 45.455 0.00 0.00 0.00 2.24
171 175 6.293462 GGTCAACATGGTCAAAACTAGAGAAC 60.293 42.308 0.00 0.00 0.00 3.01
185 189 2.966050 AGAGAACGAAAGGCAGATCAC 58.034 47.619 0.00 0.00 0.00 3.06
190 194 0.933097 CGAAAGGCAGATCACCATCG 59.067 55.000 14.24 14.24 33.75 3.84
197 201 1.671979 CAGATCACCATCGCCAATGT 58.328 50.000 0.00 0.00 33.75 2.71
200 204 0.752743 ATCACCATCGCCAATGTGGG 60.753 55.000 0.00 0.00 38.19 4.61
236 240 2.125147 CCGCTTCCGCTGGATCAA 60.125 61.111 0.00 0.00 33.54 2.57
240 244 1.435408 GCTTCCGCTGGATCAAGAGC 61.435 60.000 0.00 0.00 0.00 4.09
246 250 1.527034 GCTGGATCAAGAGCACACAA 58.473 50.000 0.00 0.00 35.15 3.33
275 279 1.609239 GGCATCACACCTCCCATCA 59.391 57.895 0.00 0.00 0.00 3.07
276 280 0.465097 GGCATCACACCTCCCATCAG 60.465 60.000 0.00 0.00 0.00 2.90
294 299 2.710902 GGAAGCCAAATGGGGACGC 61.711 63.158 0.90 0.00 37.04 5.19
295 300 2.679996 AAGCCAAATGGGGACGCC 60.680 61.111 0.53 0.53 37.04 5.68
320 325 2.515057 TCAAACACGCGCCACCTT 60.515 55.556 5.73 0.00 0.00 3.50
321 326 2.051345 CAAACACGCGCCACCTTC 60.051 61.111 5.73 0.00 0.00 3.46
339 344 1.153539 TCAACCAAGTTGGATCCCCA 58.846 50.000 28.80 3.02 42.99 4.96
348 353 1.645402 TTGGATCCCCAAGCTAGCCC 61.645 60.000 12.13 3.06 46.94 5.19
359 364 2.109799 CTAGCCCATGCCCAGACG 59.890 66.667 0.00 0.00 38.69 4.18
368 373 4.736896 GCCCAGACGTCGTCCACC 62.737 72.222 21.40 4.64 32.18 4.61
377 382 3.552384 TCGTCCACCACCACCACC 61.552 66.667 0.00 0.00 0.00 4.61
389 394 3.621805 ACCACCCGCACGATGACA 61.622 61.111 0.00 0.00 0.00 3.58
394 399 2.512286 CCGCACGATGACATGGCT 60.512 61.111 0.00 0.00 0.00 4.75
410 415 2.593978 CTGAGGGCCTCCACCATG 59.406 66.667 30.03 9.76 34.83 3.66
422 427 1.616091 CCACCATGGCCAAATCACCC 61.616 60.000 10.96 0.00 0.00 4.61
426 431 3.301222 ATGGCCAAATCACCCGGCT 62.301 57.895 10.96 0.00 45.50 5.52
442 447 0.804156 GGCTAAGACTCTGTGCGAGC 60.804 60.000 0.00 0.00 43.85 5.03
471 476 3.148084 CACCCTCCACAACGACCT 58.852 61.111 0.00 0.00 0.00 3.85
473 478 0.884704 CACCCTCCACAACGACCTTG 60.885 60.000 0.00 0.00 35.77 3.61
481 486 0.179032 ACAACGACCTTGATGTGCCA 60.179 50.000 0.00 0.00 33.59 4.92
485 490 1.302511 GACCTTGATGTGCCACCGT 60.303 57.895 0.00 0.00 0.00 4.83
488 493 1.172180 CCTTGATGTGCCACCGTGTT 61.172 55.000 0.00 0.00 0.00 3.32
497 502 0.960364 GCCACCGTGTTCATCCACAT 60.960 55.000 0.00 0.00 34.98 3.21
503 508 1.267682 CGTGTTCATCCACATGCATCG 60.268 52.381 0.00 0.00 34.98 3.84
510 515 2.751036 CACATGCATCGTGCCCCA 60.751 61.111 13.75 0.00 44.23 4.96
512 517 2.122797 ACATGCATCGTGCCCCATG 61.123 57.895 0.00 7.17 44.23 3.66
514 519 3.726558 ATGCATCGTGCCCCATGCT 62.727 57.895 0.15 0.00 44.23 3.79
515 520 3.896133 GCATCGTGCCCCATGCTG 61.896 66.667 0.00 0.00 41.93 4.41
516 521 2.438975 CATCGTGCCCCATGCTGT 60.439 61.111 0.00 0.00 42.00 4.40
528 533 0.386352 CATGCTGTCGTGCCTTTGTG 60.386 55.000 0.00 0.00 0.00 3.33
529 534 2.050985 GCTGTCGTGCCTTTGTGC 60.051 61.111 0.00 0.00 0.00 4.57
537 542 0.807496 GTGCCTTTGTGCTCCAGATC 59.193 55.000 0.00 0.00 0.00 2.75
539 544 1.908619 TGCCTTTGTGCTCCAGATCTA 59.091 47.619 0.00 0.00 0.00 1.98
542 547 3.620966 GCCTTTGTGCTCCAGATCTAGTT 60.621 47.826 0.00 0.00 0.00 2.24
552 557 0.032017 AGATCTAGTTGAGCCCCCGT 60.032 55.000 0.00 0.00 0.00 5.28
554 559 1.972660 ATCTAGTTGAGCCCCCGTGC 61.973 60.000 0.00 0.00 0.00 5.34
603 608 1.150135 ACAGAGAGGGAGGAGAAACCA 59.850 52.381 0.00 0.00 42.04 3.67
608 613 1.002011 GGGAGGAGAAACCACTGCC 60.002 63.158 0.00 0.00 42.04 4.85
609 614 1.376037 GGAGGAGAAACCACTGCCG 60.376 63.158 0.00 0.00 42.04 5.69
611 616 0.250338 GAGGAGAAACCACTGCCGTT 60.250 55.000 0.00 0.00 42.04 4.44
612 617 0.535102 AGGAGAAACCACTGCCGTTG 60.535 55.000 0.00 0.00 42.04 4.10
621 626 3.818787 CTGCCGTTGCCATCAGCC 61.819 66.667 0.00 0.00 42.71 4.85
627 632 3.204119 TTGCCATCAGCCGCATCG 61.204 61.111 0.00 0.00 42.71 3.84
687 692 2.037367 TACGCTGGAGGCTCCACT 59.963 61.111 32.01 18.64 42.67 4.00
688 693 1.608717 CTACGCTGGAGGCTCCACTT 61.609 60.000 32.01 22.07 42.67 3.16
699 704 1.507141 GCTCCACTTGTGTTCACCCG 61.507 60.000 0.37 0.00 0.00 5.28
700 705 0.179056 CTCCACTTGTGTTCACCCGT 60.179 55.000 0.37 0.00 0.00 5.28
740 745 4.044426 GCGATACGGTTCGGTTTTATAGT 58.956 43.478 10.62 0.00 39.49 2.12
786 791 9.959749 TCAGCCTGTTTTACTAATTTGTTTTAG 57.040 29.630 0.00 0.00 35.68 1.85
809 814 9.845740 TTAGCAATATTCCAGTACACACATATT 57.154 29.630 0.00 0.00 0.00 1.28
850 856 7.546778 TTTTTCTTGGCAAAGTTAATGGTTC 57.453 32.000 0.00 0.00 34.78 3.62
859 865 6.918022 GGCAAAGTTAATGGTTCTACATATGC 59.082 38.462 1.58 0.00 0.00 3.14
870 876 5.347907 GGTTCTACATATGCACTATTACCGC 59.652 44.000 1.58 0.00 0.00 5.68
877 883 1.087771 GCACTATTACCGCGCACCTT 61.088 55.000 8.75 0.00 0.00 3.50
920 2497 8.874744 AATCTGCTATGCTATTACAATCCATT 57.125 30.769 0.00 0.00 0.00 3.16
989 2567 7.767261 TGCATTATATAACTTGTTGGGTGTTC 58.233 34.615 0.00 0.00 0.00 3.18
1056 2634 1.672881 CGAAGATTGGGGCAGTCATTC 59.327 52.381 0.00 0.00 0.00 2.67
1098 2679 4.014406 TGTGGTACAGAAGCTATCGAAGA 58.986 43.478 0.00 0.00 41.80 2.87
1329 2910 0.999406 CCTGCAACGGTACATCTTCG 59.001 55.000 0.00 0.00 0.00 3.79
1658 3239 7.194112 TGTGAAGAATGTGTATGATAGGGAA 57.806 36.000 0.00 0.00 0.00 3.97
1892 3482 4.881273 GTGTGGGACAAAGATGCATATACA 59.119 41.667 0.00 0.00 44.16 2.29
2064 3659 1.756538 CTTTCCACAACAGCCCAAACT 59.243 47.619 0.00 0.00 0.00 2.66
2074 3669 1.529244 GCCCAAACTGTGAGTGCCT 60.529 57.895 0.00 0.00 0.00 4.75
2075 3670 1.799258 GCCCAAACTGTGAGTGCCTG 61.799 60.000 0.00 0.00 0.00 4.85
2086 3681 4.385405 GTGCCTGCCAGAGCTCGT 62.385 66.667 8.37 0.00 40.80 4.18
2200 3795 7.665690 ACAGAGTATGTATGGAATCAGATGTC 58.334 38.462 0.00 0.00 41.60 3.06
2274 3869 4.833478 AATCTGAGCTACCATGACTTGT 57.167 40.909 0.00 0.00 0.00 3.16
2522 4117 2.426522 CATGACATTGTCCGTGACCTT 58.573 47.619 14.05 0.00 0.00 3.50
2580 4175 1.328680 CGAGTGATTCAGGCGAAATGG 59.671 52.381 2.81 0.00 34.01 3.16
2630 4225 1.691976 TCGACATCAAGTGGTTGGACT 59.308 47.619 0.00 0.00 34.09 3.85
2672 4270 2.202479 GAATTTCCACGGCTGCGC 60.202 61.111 0.00 0.00 0.00 6.09
2684 4282 3.104766 CTGCGCACCATCATGTCC 58.895 61.111 5.66 0.00 0.00 4.02
2694 4292 1.105167 CATCATGTCCCTTGCGGCAT 61.105 55.000 2.28 0.00 0.00 4.40
2723 4321 2.932614 CTCTACCAACATGCTTTCCTCG 59.067 50.000 0.00 0.00 0.00 4.63
2798 4396 0.829990 TCGAAGTGCCAGCATCCATA 59.170 50.000 0.00 0.00 0.00 2.74
2801 4399 1.141657 GAAGTGCCAGCATCCATAGGA 59.858 52.381 0.00 0.00 35.55 2.94
2849 4447 0.687920 TGAGGCGTACCAATGTCCAA 59.312 50.000 0.00 0.00 39.06 3.53
2870 4468 1.827344 TCACTGCCAGACACCATAGAG 59.173 52.381 0.00 0.00 0.00 2.43
2885 4483 8.431910 ACACCATAGAGAAACTCTTAAACCTA 57.568 34.615 6.60 0.00 41.50 3.08
2922 4520 7.283127 ACATCAAGCAAACAAGAGTAGAAAAGA 59.717 33.333 0.00 0.00 0.00 2.52
2960 4558 2.687700 AGATTGAGAAGCTGCGACAT 57.312 45.000 0.00 0.00 0.00 3.06
2963 4561 2.001812 TTGAGAAGCTGCGACATCTC 57.998 50.000 15.79 15.79 38.98 2.75
2999 4597 1.806542 GCTGATGAGAAGCAAACCGAA 59.193 47.619 0.00 0.00 40.52 4.30
3164 4762 9.869844 GATAACATTAATGCATCTAACTGTGAC 57.130 33.333 15.48 0.00 0.00 3.67
3197 4795 1.061033 ACCCTCTCAGATATGCCCCTT 60.061 52.381 0.00 0.00 0.00 3.95
3203 4801 4.302067 TCTCAGATATGCCCCTTCTTTCT 58.698 43.478 0.00 0.00 0.00 2.52
3250 4848 5.671493 TGAGAACGAGAAACTTTCTTTCCT 58.329 37.500 5.49 2.00 40.87 3.36
3380 4978 3.646637 AGTACTTGGCTCTAAGTTGGTGT 59.353 43.478 4.02 0.00 41.01 4.16
3551 5149 3.019564 GCCTAATGTCAAGCAACTGGAT 58.980 45.455 0.00 0.00 0.00 3.41
3603 5201 2.287069 GGGATCTACATCGTGTCACTCG 60.287 54.545 0.65 0.00 0.00 4.18
3604 5202 2.355132 GGATCTACATCGTGTCACTCGT 59.645 50.000 0.65 0.00 0.00 4.18
3759 5358 2.416893 GAGCTCCGTTCCTAGCAAAAAG 59.583 50.000 0.87 0.00 41.32 2.27
3822 5421 4.598406 TCTTATGCATTGTAAGTGTGCG 57.402 40.909 3.54 0.00 41.61 5.34
3824 5423 0.880441 ATGCATTGTAAGTGTGCGCA 59.120 45.000 5.66 5.66 41.61 6.09
3839 5438 6.624710 GTGTGCGCACATTTAATTATTTGA 57.375 33.333 42.22 14.77 43.97 2.69
3965 5578 0.329261 CCTTCCTTGCCATCAGGACA 59.671 55.000 0.00 0.00 36.89 4.02
4011 5632 9.218440 TCATTATATATGATTTTCGCTGCTTGA 57.782 29.630 0.00 0.00 0.00 3.02
4015 5636 8.961294 ATATATGATTTTCGCTGCTTGAATTC 57.039 30.769 0.00 0.00 0.00 2.17
4066 5699 5.951148 TCTGGGCAAATTCTTTCATGACATA 59.049 36.000 0.00 0.00 0.00 2.29
4146 5780 0.986019 TTCCACCACCAGGGCGATAT 60.986 55.000 0.00 0.00 42.05 1.63
4170 5804 4.365514 TTTTGGCACAGTCCTAATCTCA 57.634 40.909 0.00 0.00 42.39 3.27
4172 5806 1.555075 TGGCACAGTCCTAATCTCACC 59.445 52.381 0.00 0.00 0.00 4.02
4173 5807 1.134371 GGCACAGTCCTAATCTCACCC 60.134 57.143 0.00 0.00 0.00 4.61
4175 5809 3.031736 GCACAGTCCTAATCTCACCCTA 58.968 50.000 0.00 0.00 0.00 3.53
4176 5810 3.068873 GCACAGTCCTAATCTCACCCTAG 59.931 52.174 0.00 0.00 0.00 3.02
4177 5811 3.068873 CACAGTCCTAATCTCACCCTAGC 59.931 52.174 0.00 0.00 0.00 3.42
4178 5812 3.300388 CAGTCCTAATCTCACCCTAGCA 58.700 50.000 0.00 0.00 0.00 3.49
4180 5814 3.205507 AGTCCTAATCTCACCCTAGCAGA 59.794 47.826 0.00 0.00 0.00 4.26
4181 5815 4.140805 AGTCCTAATCTCACCCTAGCAGAT 60.141 45.833 0.00 0.00 0.00 2.90
4182 5816 4.591072 GTCCTAATCTCACCCTAGCAGATT 59.409 45.833 8.59 8.59 39.63 2.40
4183 5817 5.775701 GTCCTAATCTCACCCTAGCAGATTA 59.224 44.000 9.52 9.52 37.85 1.75
4185 5819 6.438741 TCCTAATCTCACCCTAGCAGATTATG 59.561 42.308 10.01 8.59 38.09 1.90
4187 5821 4.944619 TCTCACCCTAGCAGATTATGTG 57.055 45.455 0.00 0.00 0.00 3.21
4189 5823 4.342378 TCTCACCCTAGCAGATTATGTGAC 59.658 45.833 0.00 0.00 0.00 3.67
4213 6299 7.688372 ACATGAAGATCGTTCAATTATGTGAC 58.312 34.615 0.00 0.00 31.55 3.67
4214 6300 7.334171 ACATGAAGATCGTTCAATTATGTGACA 59.666 33.333 0.00 0.00 31.55 3.58
4216 6302 8.267620 TGAAGATCGTTCAATTATGTGACATT 57.732 30.769 2.29 0.00 0.00 2.71
4233 6319 8.350238 TGTGACATTTATGTTTGTGATGTTTG 57.650 30.769 0.00 0.00 41.95 2.93
4234 6320 7.437565 TGTGACATTTATGTTTGTGATGTTTGG 59.562 33.333 0.00 0.00 41.95 3.28
4235 6321 7.651304 GTGACATTTATGTTTGTGATGTTTGGA 59.349 33.333 0.00 0.00 41.95 3.53
4236 6322 8.200120 TGACATTTATGTTTGTGATGTTTGGAA 58.800 29.630 0.00 0.00 41.95 3.53
4237 6323 8.364129 ACATTTATGTTTGTGATGTTTGGAAC 57.636 30.769 0.00 0.00 37.90 3.62
4238 6324 7.984050 ACATTTATGTTTGTGATGTTTGGAACA 59.016 29.630 0.00 0.00 41.34 3.18
4239 6325 7.763172 TTTATGTTTGTGATGTTTGGAACAC 57.237 32.000 0.00 0.00 45.50 3.32
4240 6326 4.116747 TGTTTGTGATGTTTGGAACACC 57.883 40.909 0.00 0.00 45.50 4.16
4241 6327 3.118956 TGTTTGTGATGTTTGGAACACCC 60.119 43.478 0.00 0.00 45.50 4.61
4242 6328 2.746279 TGTGATGTTTGGAACACCCT 57.254 45.000 0.00 0.00 45.50 4.34
4243 6329 3.866703 TGTGATGTTTGGAACACCCTA 57.133 42.857 0.00 0.00 45.50 3.53
4244 6330 3.750371 TGTGATGTTTGGAACACCCTAG 58.250 45.455 0.00 0.00 45.50 3.02
4245 6331 2.488153 GTGATGTTTGGAACACCCTAGC 59.512 50.000 0.00 0.00 45.50 3.42
4246 6332 2.107378 TGATGTTTGGAACACCCTAGCA 59.893 45.455 0.00 0.00 45.50 3.49
4247 6333 2.270352 TGTTTGGAACACCCTAGCAG 57.730 50.000 0.00 0.00 39.29 4.24
4248 6334 1.771854 TGTTTGGAACACCCTAGCAGA 59.228 47.619 0.00 0.00 39.29 4.26
4249 6335 2.375174 TGTTTGGAACACCCTAGCAGAT 59.625 45.455 0.00 0.00 39.29 2.90
4250 6336 3.181434 TGTTTGGAACACCCTAGCAGATT 60.181 43.478 0.00 0.00 39.29 2.40
4251 6337 3.806949 TTGGAACACCCTAGCAGATTT 57.193 42.857 0.00 0.00 39.29 2.17
4252 6338 3.071874 TGGAACACCCTAGCAGATTTG 57.928 47.619 0.00 0.00 35.38 2.32
4253 6339 2.879756 TGGAACACCCTAGCAGATTTGC 60.880 50.000 0.00 0.00 42.56 3.68
4274 6360 5.487433 TGCCAGATTAAAATTCAGAGTCGA 58.513 37.500 0.00 0.00 0.00 4.20
4275 6361 5.582269 TGCCAGATTAAAATTCAGAGTCGAG 59.418 40.000 0.00 0.00 0.00 4.04
4276 6362 5.812642 GCCAGATTAAAATTCAGAGTCGAGA 59.187 40.000 0.00 0.00 0.00 4.04
4289 6375 1.290324 TCGAGAGACAGGCAGCAAC 59.710 57.895 0.00 0.00 33.31 4.17
4293 6379 2.225467 GAGAGACAGGCAGCAACTTTT 58.775 47.619 0.00 0.00 0.00 2.27
4309 6395 5.388944 CAACTTTTTGAGATGCTAGCTCAC 58.611 41.667 17.23 9.96 41.72 3.51
4311 6397 6.042638 ACTTTTTGAGATGCTAGCTCACTA 57.957 37.500 17.23 4.29 41.72 2.74
4312 6398 5.872070 ACTTTTTGAGATGCTAGCTCACTAC 59.128 40.000 17.23 3.55 41.72 2.73
4313 6399 5.667539 TTTTGAGATGCTAGCTCACTACT 57.332 39.130 17.23 6.01 41.72 2.57
4314 6400 6.775594 TTTTGAGATGCTAGCTCACTACTA 57.224 37.500 17.23 0.00 41.72 1.82
4315 6401 5.759506 TTGAGATGCTAGCTCACTACTAC 57.240 43.478 17.23 1.93 41.72 2.73
4318 6404 5.992829 TGAGATGCTAGCTCACTACTACTAC 59.007 44.000 17.23 0.36 37.46 2.73
4319 6405 6.182507 AGATGCTAGCTCACTACTACTACT 57.817 41.667 17.23 0.00 0.00 2.57
4320 6406 7.015389 TGAGATGCTAGCTCACTACTACTACTA 59.985 40.741 17.23 0.00 37.46 1.82
4322 6408 6.482898 TGCTAGCTCACTACTACTACTAGT 57.517 41.667 17.23 0.00 37.04 2.57
4339 6513 8.908172 ACTACTAGTTCTACAGATTTAAACGC 57.092 34.615 0.00 0.00 0.00 4.84
4352 6526 4.555348 TTTAAACGCTGGTGTCGAATTT 57.445 36.364 0.00 0.00 0.00 1.82
4460 7047 2.222678 GCAGTATCATCAACATGAGCGG 59.777 50.000 0.00 0.00 42.53 5.52
4502 7092 2.436542 AGTGGTGTGGTGCAGTAAGTAA 59.563 45.455 0.00 0.00 0.00 2.24
4589 7183 2.959071 GCAGATCGCCGAGACAGC 60.959 66.667 0.00 0.00 32.94 4.40
4596 7190 4.148825 GCCGAGACAGCCACCGAT 62.149 66.667 0.00 0.00 0.00 4.18
4597 7191 2.202797 CCGAGACAGCCACCGATG 60.203 66.667 0.00 0.00 0.00 3.84
4598 7192 2.573869 CGAGACAGCCACCGATGT 59.426 61.111 0.00 0.00 0.00 3.06
4599 7193 1.807165 CGAGACAGCCACCGATGTG 60.807 63.158 0.00 0.00 42.39 3.21
4632 7226 3.474570 GGATCAGCTCCCAGCCGT 61.475 66.667 0.00 0.00 43.77 5.68
4633 7227 2.107953 GATCAGCTCCCAGCCGTC 59.892 66.667 0.00 0.00 43.77 4.79
4634 7228 2.364842 ATCAGCTCCCAGCCGTCT 60.365 61.111 0.00 0.00 43.77 4.18
4635 7229 2.641439 GATCAGCTCCCAGCCGTCTG 62.641 65.000 0.00 0.00 43.77 3.51
4652 7246 3.660111 GCGGTTGCGGTTGCTTCT 61.660 61.111 0.00 0.00 43.34 2.85
4653 7247 2.252260 CGGTTGCGGTTGCTTCTG 59.748 61.111 0.00 0.00 43.34 3.02
4654 7248 2.050077 GGTTGCGGTTGCTTCTGC 60.050 61.111 5.75 5.75 43.34 4.26
4655 7249 2.555547 GGTTGCGGTTGCTTCTGCT 61.556 57.895 12.18 0.00 43.34 4.24
4656 7250 1.370900 GTTGCGGTTGCTTCTGCTG 60.371 57.895 12.18 0.00 43.34 4.41
4677 7271 2.200337 GGTGGTGGAGGTGGTTTGC 61.200 63.158 0.00 0.00 0.00 3.68
4737 7331 4.664677 CATCGTCGGCCGGGGATC 62.665 72.222 27.83 9.97 37.11 3.36
4744 7338 3.797353 GGCCGGGGATCAGCTCAA 61.797 66.667 2.18 0.00 0.00 3.02
4745 7339 2.514824 GCCGGGGATCAGCTCAAC 60.515 66.667 2.18 0.00 0.00 3.18
4746 7340 2.202932 CCGGGGATCAGCTCAACG 60.203 66.667 0.00 0.00 0.00 4.10
4747 7341 2.892425 CGGGGATCAGCTCAACGC 60.892 66.667 0.00 0.00 39.57 4.84
4756 7350 4.821589 GCTCAACGCTAGCGGGCT 62.822 66.667 37.66 20.76 44.69 5.19
4757 7351 2.887568 CTCAACGCTAGCGGGCTG 60.888 66.667 37.66 29.29 44.69 4.85
4758 7352 3.649277 CTCAACGCTAGCGGGCTGT 62.649 63.158 37.66 16.60 44.69 4.40
4759 7353 2.742372 CAACGCTAGCGGGCTGTT 60.742 61.111 37.66 21.47 44.69 3.16
4760 7354 2.742372 AACGCTAGCGGGCTGTTG 60.742 61.111 37.66 11.11 44.69 3.33
4761 7355 3.234630 AACGCTAGCGGGCTGTTGA 62.235 57.895 37.66 0.00 44.69 3.18
4762 7356 2.887568 CGCTAGCGGGCTGTTGAG 60.888 66.667 29.29 0.00 35.56 3.02
4763 7357 2.512515 GCTAGCGGGCTGTTGAGG 60.513 66.667 0.00 0.00 0.00 3.86
4764 7358 2.512515 CTAGCGGGCTGTTGAGGC 60.513 66.667 2.86 0.00 44.21 4.70
4765 7359 4.451150 TAGCGGGCTGTTGAGGCG 62.451 66.667 2.86 0.00 45.92 5.52
4772 7366 4.020617 CTGTTGAGGCGGCTGGGA 62.021 66.667 19.63 0.00 0.00 4.37
4773 7367 4.329545 TGTTGAGGCGGCTGGGAC 62.330 66.667 19.63 12.53 0.00 4.46
4780 7374 4.241555 GCGGCTGGGACGGATGAT 62.242 66.667 0.00 0.00 36.31 2.45
4781 7375 2.280389 CGGCTGGGACGGATGATG 60.280 66.667 0.00 0.00 36.31 3.07
4782 7376 2.796193 CGGCTGGGACGGATGATGA 61.796 63.158 0.00 0.00 36.31 2.92
4783 7377 1.070445 GGCTGGGACGGATGATGAG 59.930 63.158 0.00 0.00 36.31 2.90
4784 7378 1.402896 GGCTGGGACGGATGATGAGA 61.403 60.000 0.00 0.00 36.31 3.27
4785 7379 0.033228 GCTGGGACGGATGATGAGAG 59.967 60.000 0.00 0.00 36.31 3.20
4786 7380 1.407936 CTGGGACGGATGATGAGAGT 58.592 55.000 0.00 0.00 36.31 3.24
4787 7381 1.068281 CTGGGACGGATGATGAGAGTG 59.932 57.143 0.00 0.00 36.31 3.51
4788 7382 0.390860 GGGACGGATGATGAGAGTGG 59.609 60.000 0.00 0.00 0.00 4.00
4789 7383 1.115467 GGACGGATGATGAGAGTGGT 58.885 55.000 0.00 0.00 0.00 4.16
4790 7384 1.202463 GGACGGATGATGAGAGTGGTG 60.202 57.143 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.004918 CTGTGGACCGAGGGTTGAC 60.005 63.158 0.00 0.00 35.25 3.18
17 18 1.052124 AACTGTGGACCGAGGGTTGA 61.052 55.000 0.00 0.00 35.25 3.18
18 19 0.179029 AAACTGTGGACCGAGGGTTG 60.179 55.000 0.00 0.00 35.25 3.77
19 20 1.071228 GTAAACTGTGGACCGAGGGTT 59.929 52.381 0.00 0.00 35.25 4.11
20 21 0.683412 GTAAACTGTGGACCGAGGGT 59.317 55.000 0.00 0.00 39.44 4.34
22 23 2.233922 AGATGTAAACTGTGGACCGAGG 59.766 50.000 0.00 0.00 0.00 4.63
23 24 3.056821 TGAGATGTAAACTGTGGACCGAG 60.057 47.826 0.00 0.00 0.00 4.63
24 25 2.894765 TGAGATGTAAACTGTGGACCGA 59.105 45.455 0.00 0.00 0.00 4.69
25 26 3.313012 TGAGATGTAAACTGTGGACCG 57.687 47.619 0.00 0.00 0.00 4.79
26 27 3.865745 CGATGAGATGTAAACTGTGGACC 59.134 47.826 0.00 0.00 0.00 4.46
30 31 6.146184 ACTTCAACGATGAGATGTAAACTGTG 59.854 38.462 0.00 0.00 36.78 3.66
31 32 6.223852 ACTTCAACGATGAGATGTAAACTGT 58.776 36.000 0.00 0.00 36.78 3.55
66 70 4.111577 TGTGAGGGTTCCTTTCTCCATAT 58.888 43.478 0.00 0.00 31.76 1.78
67 71 3.526899 TGTGAGGGTTCCTTTCTCCATA 58.473 45.455 0.00 0.00 31.76 2.74
68 72 2.348472 TGTGAGGGTTCCTTTCTCCAT 58.652 47.619 0.00 0.00 31.76 3.41
88 92 3.747976 GGCCACGGAATGCGCTTT 61.748 61.111 9.73 9.03 0.00 3.51
92 96 3.499737 GAGTGGCCACGGAATGCG 61.500 66.667 29.68 0.00 36.20 4.73
95 99 2.264794 GACGAGTGGCCACGGAAT 59.735 61.111 29.68 16.78 36.20 3.01
99 103 2.663630 CTATCCGACGAGTGGCCACG 62.664 65.000 29.68 21.57 36.20 4.94
139 143 3.443045 CCATGTTGACCGCTGGGC 61.443 66.667 0.00 0.00 36.48 5.36
149 153 5.465390 TCGTTCTCTAGTTTTGACCATGTTG 59.535 40.000 0.00 0.00 0.00 3.33
151 155 5.209818 TCGTTCTCTAGTTTTGACCATGT 57.790 39.130 0.00 0.00 0.00 3.21
159 163 4.957296 TCTGCCTTTCGTTCTCTAGTTTT 58.043 39.130 0.00 0.00 0.00 2.43
165 169 2.354203 GGTGATCTGCCTTTCGTTCTCT 60.354 50.000 0.00 0.00 0.00 3.10
171 175 0.933097 CGATGGTGATCTGCCTTTCG 59.067 55.000 13.38 13.38 0.00 3.46
225 229 1.078918 TGTGCTCTTGATCCAGCGG 60.079 57.895 4.48 0.00 38.59 5.52
229 233 1.877680 CGGTTGTGTGCTCTTGATCCA 60.878 52.381 0.00 0.00 0.00 3.41
230 234 0.798776 CGGTTGTGTGCTCTTGATCC 59.201 55.000 0.00 0.00 0.00 3.36
236 240 2.116983 ATCTGGCGGTTGTGTGCTCT 62.117 55.000 0.00 0.00 0.00 4.09
240 244 2.390599 CCGATCTGGCGGTTGTGTG 61.391 63.158 0.00 0.00 46.07 3.82
262 266 0.393537 GCTTCCTGATGGGAGGTGTG 60.394 60.000 0.00 0.00 46.01 3.82
263 267 1.566298 GGCTTCCTGATGGGAGGTGT 61.566 60.000 0.00 0.00 46.01 4.16
265 269 0.846427 TTGGCTTCCTGATGGGAGGT 60.846 55.000 0.00 0.00 46.01 3.85
275 279 1.000896 CGTCCCCATTTGGCTTCCT 60.001 57.895 0.00 0.00 0.00 3.36
276 280 2.710902 GCGTCCCCATTTGGCTTCC 61.711 63.158 0.00 0.00 0.00 3.46
294 299 4.409588 CGTGTTTGAGCGACGCGG 62.410 66.667 15.18 0.00 44.64 6.46
306 311 2.515057 TTGAAGGTGGCGCGTGTT 60.515 55.556 8.43 0.00 0.00 3.32
312 317 0.030638 CAACTTGGTTGAAGGTGGCG 59.969 55.000 4.60 0.00 44.63 5.69
320 325 1.153539 TGGGGATCCAACTTGGTTGA 58.846 50.000 15.23 0.00 45.28 3.18
321 326 3.763931 TGGGGATCCAACTTGGTTG 57.236 52.632 15.23 0.00 40.73 3.77
339 344 2.002977 TCTGGGCATGGGCTAGCTT 61.003 57.895 15.72 0.00 40.87 3.74
348 353 2.509336 GGACGACGTCTGGGCATG 60.509 66.667 25.87 0.00 32.47 4.06
359 364 2.280592 GTGGTGGTGGTGGACGAC 60.281 66.667 0.00 0.00 32.68 4.34
362 367 4.636435 CGGGTGGTGGTGGTGGAC 62.636 72.222 0.00 0.00 0.00 4.02
368 373 4.697756 ATCGTGCGGGTGGTGGTG 62.698 66.667 0.00 0.00 0.00 4.17
377 382 2.512286 AGCCATGTCATCGTGCGG 60.512 61.111 0.00 0.00 0.00 5.69
382 387 1.890979 GCCCTCAGCCATGTCATCG 60.891 63.158 0.00 0.00 34.35 3.84
394 399 3.016971 CCATGGTGGAGGCCCTCA 61.017 66.667 13.90 0.00 40.96 3.86
402 407 0.614415 GGTGATTTGGCCATGGTGGA 60.614 55.000 14.67 0.00 40.96 4.02
422 427 0.524392 CTCGCACAGAGTCTTAGCCG 60.524 60.000 7.74 1.53 41.99 5.52
453 458 2.668550 GGTCGTTGTGGAGGGTGC 60.669 66.667 0.00 0.00 0.00 5.01
458 463 1.800586 CACATCAAGGTCGTTGTGGAG 59.199 52.381 5.25 0.00 36.64 3.86
464 469 0.889186 GGTGGCACATCAAGGTCGTT 60.889 55.000 20.82 0.00 44.52 3.85
471 476 0.464554 TGAACACGGTGGCACATCAA 60.465 50.000 20.82 0.00 41.34 2.57
473 478 0.447801 GATGAACACGGTGGCACATC 59.552 55.000 20.82 19.73 44.52 3.06
481 486 0.250684 TGCATGTGGATGAACACGGT 60.251 50.000 0.00 0.00 44.21 4.83
485 490 1.738908 CACGATGCATGTGGATGAACA 59.261 47.619 2.46 0.00 33.69 3.18
488 493 2.396700 GCACGATGCATGTGGATGA 58.603 52.632 22.36 0.00 44.26 2.92
510 515 1.951510 CACAAAGGCACGACAGCAT 59.048 52.632 0.00 0.00 35.83 3.79
512 517 2.050985 GCACAAAGGCACGACAGC 60.051 61.111 0.00 0.00 0.00 4.40
514 519 1.891919 GGAGCACAAAGGCACGACA 60.892 57.895 0.00 0.00 35.83 4.35
515 520 1.845809 CTGGAGCACAAAGGCACGAC 61.846 60.000 0.00 0.00 35.83 4.34
516 521 1.597854 CTGGAGCACAAAGGCACGA 60.598 57.895 0.00 0.00 35.83 4.35
519 524 0.694771 AGATCTGGAGCACAAAGGCA 59.305 50.000 0.00 0.00 35.83 4.75
529 534 1.691434 GGGGCTCAACTAGATCTGGAG 59.309 57.143 13.73 11.29 0.00 3.86
537 542 2.125106 GCACGGGGGCTCAACTAG 60.125 66.667 0.00 0.00 0.00 2.57
575 580 2.125912 CCCTCTCTGTGTTCGCGG 60.126 66.667 6.13 0.00 0.00 6.46
577 582 1.216710 CCTCCCTCTCTGTGTTCGC 59.783 63.158 0.00 0.00 0.00 4.70
584 589 1.552792 GTGGTTTCTCCTCCCTCTCTG 59.447 57.143 0.00 0.00 37.07 3.35
585 590 1.435168 AGTGGTTTCTCCTCCCTCTCT 59.565 52.381 0.00 0.00 37.07 3.10
603 608 3.058160 GCTGATGGCAACGGCAGT 61.058 61.111 21.98 0.00 42.43 4.40
608 613 3.459378 GATGCGGCTGATGGCAACG 62.459 63.158 0.00 0.00 43.26 4.10
609 614 2.410469 GATGCGGCTGATGGCAAC 59.590 61.111 0.00 0.00 43.26 4.17
630 635 0.462581 CTTCATCGCTGCCAGGCTAA 60.463 55.000 14.15 0.00 0.00 3.09
636 641 3.008517 TCCCCTTCATCGCTGCCA 61.009 61.111 0.00 0.00 0.00 4.92
637 642 2.203126 CTCCCCTTCATCGCTGCC 60.203 66.667 0.00 0.00 0.00 4.85
638 643 2.203126 CCTCCCCTTCATCGCTGC 60.203 66.667 0.00 0.00 0.00 5.25
640 645 1.764054 CTCCCTCCCCTTCATCGCT 60.764 63.158 0.00 0.00 0.00 4.93
675 680 0.108585 GAACACAAGTGGAGCCTCCA 59.891 55.000 10.05 10.05 45.98 3.86
676 681 0.108585 TGAACACAAGTGGAGCCTCC 59.891 55.000 2.98 2.98 36.96 4.30
687 692 2.193517 CCCCACGGGTGAACACAA 59.806 61.111 0.41 0.00 38.25 3.33
688 693 2.768769 TCCCCACGGGTGAACACA 60.769 61.111 0.41 0.00 44.74 3.72
714 719 1.963464 AACCGAACCGTATCGCCCAT 61.963 55.000 1.90 0.00 41.40 4.00
715 720 2.169937 AAACCGAACCGTATCGCCCA 62.170 55.000 1.90 0.00 41.40 5.36
719 724 7.678194 TTAACTATAAAACCGAACCGTATCG 57.322 36.000 0.53 0.53 42.37 2.92
722 727 6.257630 GGCATTAACTATAAAACCGAACCGTA 59.742 38.462 0.00 0.00 0.00 4.02
740 745 5.622007 GCTGAGTACATTTTGCAGGCATTAA 60.622 40.000 0.00 0.00 0.00 1.40
786 791 9.801873 AAAAATATGTGTGTACTGGAATATTGC 57.198 29.630 0.00 0.00 0.00 3.56
850 856 3.303495 GCGCGGTAATAGTGCATATGTAG 59.697 47.826 8.83 0.00 43.84 2.74
859 865 0.928229 GAAGGTGCGCGGTAATAGTG 59.072 55.000 8.83 0.00 0.00 2.74
864 870 0.036765 AAGATGAAGGTGCGCGGTAA 60.037 50.000 8.83 0.00 0.00 2.85
870 876 2.936498 ACGGATAAAAGATGAAGGTGCG 59.064 45.455 0.00 0.00 0.00 5.34
877 883 8.506168 AGCAGATTAAAACGGATAAAAGATGA 57.494 30.769 0.00 0.00 0.00 2.92
920 2497 8.617290 TCGAGTACAATAATACTAGCTGATGA 57.383 34.615 0.00 0.00 35.48 2.92
989 2567 3.623060 CCATCTGGTCCTGAAAATACACG 59.377 47.826 2.14 0.00 0.00 4.49
1056 2634 2.084610 TCCGTGACTGCTTGATTCAG 57.915 50.000 0.00 0.00 37.56 3.02
1098 2679 5.018809 TGGCAATTCCTTTAGAGCTTCAAT 58.981 37.500 0.00 0.00 35.26 2.57
1188 2769 5.352293 TGATGACATTGTTACTGAGATGTGC 59.648 40.000 0.00 0.00 33.21 4.57
1329 2910 3.139077 CCTTTATATGGCGTGAACCTCC 58.861 50.000 0.00 0.00 0.00 4.30
1451 3032 9.181805 GTCTTATCAATCTTTGCATGATCATTG 57.818 33.333 5.16 3.21 35.53 2.82
1658 3239 6.187727 TGAGTATCAGGGAAGTTGACTTTT 57.812 37.500 0.00 0.00 42.56 2.27
1677 3258 2.165167 CACCACAATCCAAGCATGAGT 58.835 47.619 0.00 0.00 0.00 3.41
1892 3482 2.230508 CTGGAAAGCATTGCACATCTGT 59.769 45.455 11.91 0.00 32.98 3.41
2064 3659 2.745698 CTCTGGCAGGCACTCACA 59.254 61.111 15.73 0.00 34.60 3.58
2074 3669 2.203082 ACTGTCACGAGCTCTGGCA 61.203 57.895 12.85 14.93 41.70 4.92
2075 3670 1.735920 CACTGTCACGAGCTCTGGC 60.736 63.158 12.85 11.09 39.06 4.85
2086 3681 1.948834 CAACATCAACAGCCACTGTCA 59.051 47.619 0.00 0.00 44.62 3.58
2135 3730 6.070021 ACAATAGGCTGCCAGCAGATATAATA 60.070 38.462 23.40 6.18 44.75 0.98
2145 3740 1.077501 TGGACAATAGGCTGCCAGC 60.078 57.895 22.65 8.55 41.46 4.85
2200 3795 0.865769 CTCGTCCCGAAGTTGTTTGG 59.134 55.000 0.00 0.00 36.99 3.28
2274 3869 1.552337 GCAGTTCCTGAGATCACCTGA 59.448 52.381 0.00 0.00 32.44 3.86
2304 3899 0.767375 TCTTCAGGGAACAAGCTGCT 59.233 50.000 0.00 0.00 0.00 4.24
2522 4117 1.072173 TCTTTAGCCACAGCAAGAGCA 59.928 47.619 0.00 0.00 45.49 4.26
2580 4175 4.092968 ACGAACTTCTTTATCCATGCGAAC 59.907 41.667 0.00 0.00 0.00 3.95
2630 4225 4.202253 ACTCTTGCATCTGTGTTACTGTCA 60.202 41.667 0.00 0.00 0.00 3.58
2669 4267 1.750399 AAGGGACATGATGGTGCGC 60.750 57.895 0.00 0.00 0.00 6.09
2672 4270 2.100846 CGCAAGGGACATGATGGTG 58.899 57.895 0.00 0.00 0.00 4.17
2694 4292 2.094182 GCATGTTGGTAGAGGACGAAGA 60.094 50.000 0.00 0.00 0.00 2.87
2723 4321 4.019231 AGGTAGTTGGATCCAGAGAAAACC 60.019 45.833 15.53 16.33 0.00 3.27
2798 4396 3.054802 AGCGGAGATTGAACAGATTTCCT 60.055 43.478 0.00 0.00 0.00 3.36
2801 4399 4.832248 TGTAGCGGAGATTGAACAGATTT 58.168 39.130 0.00 0.00 0.00 2.17
2828 4426 1.072489 TGGACATTGGTACGCCTCAAA 59.928 47.619 0.00 0.00 35.27 2.69
2849 4447 2.433604 CTCTATGGTGTCTGGCAGTGAT 59.566 50.000 15.27 3.44 0.00 3.06
2870 4468 8.095169 TCCAATGTCTCTAGGTTTAAGAGTTTC 58.905 37.037 0.44 0.00 41.11 2.78
2885 4483 3.708403 TGCTTGATGTCCAATGTCTCT 57.292 42.857 0.00 0.00 33.68 3.10
2922 4520 2.241176 TCTTTACAATTCCTGGCGGGAT 59.759 45.455 17.51 3.32 44.66 3.85
2960 4558 2.634940 AGCAAACCTGTCTGCTAAGAGA 59.365 45.455 0.00 0.00 46.92 3.10
2993 4591 3.615496 CGACAAAGTATCGGAATTCGGTT 59.385 43.478 12.22 7.26 39.77 4.44
3164 4762 3.211045 TGAGAGGGTTTTGAAAAGGTCG 58.789 45.455 0.00 0.00 0.00 4.79
3197 4795 5.712446 TGCAGAGAGAAGTAAGCTAGAAAGA 59.288 40.000 0.00 0.00 0.00 2.52
3203 4801 7.449704 TCATCATATGCAGAGAGAAGTAAGCTA 59.550 37.037 0.00 0.00 0.00 3.32
3250 4848 6.061022 TCTTGGAAATTGGCACTAGTGATA 57.939 37.500 27.08 11.06 0.00 2.15
3380 4978 4.164221 AGCGGATCTTCTTTCCCAAGATTA 59.836 41.667 0.00 0.00 40.11 1.75
3551 5149 2.580322 TGGAATGGCACCCTCTTCAATA 59.420 45.455 8.90 0.00 0.00 1.90
3603 5201 1.771255 AGGGACCATATTCAGCTCCAC 59.229 52.381 0.00 0.00 0.00 4.02
3604 5202 2.050144 GAGGGACCATATTCAGCTCCA 58.950 52.381 0.00 0.00 0.00 3.86
3759 5358 1.337635 CCGAGGGAGATAGATTGCTGC 60.338 57.143 0.00 0.00 0.00 5.25
3770 5369 6.555463 ACATTTCTTAATAACCGAGGGAGA 57.445 37.500 0.00 0.00 0.00 3.71
3822 5421 7.702348 GGACTCCTGTCAAATAATTAAATGTGC 59.298 37.037 0.00 0.00 44.61 4.57
3898 5497 3.456280 ACAACCAACAATGCATGACAAC 58.544 40.909 0.00 0.00 0.00 3.32
4011 5632 6.870965 GGTCTATCTATGACATCAAGCGAATT 59.129 38.462 0.00 0.00 36.26 2.17
4015 5636 4.083271 TCGGTCTATCTATGACATCAAGCG 60.083 45.833 0.00 0.00 36.26 4.68
4066 5699 2.541466 AGGACCGAAGAGTTTCCTGAT 58.459 47.619 0.00 0.00 37.09 2.90
4080 5713 3.568538 CAGAAGCAATTGAAAAGGACCG 58.431 45.455 10.34 0.00 0.00 4.79
4155 5789 3.068873 GCTAGGGTGAGATTAGGACTGTG 59.931 52.174 0.00 0.00 0.00 3.66
4161 5795 6.212388 ACATAATCTGCTAGGGTGAGATTAGG 59.788 42.308 0.00 0.00 42.26 2.69
4162 5796 7.039434 TCACATAATCTGCTAGGGTGAGATTAG 60.039 40.741 0.00 0.00 40.37 1.73
4163 5797 6.782494 TCACATAATCTGCTAGGGTGAGATTA 59.218 38.462 0.00 0.00 40.96 1.75
4164 5798 5.604231 TCACATAATCTGCTAGGGTGAGATT 59.396 40.000 0.00 0.00 39.31 2.40
4165 5799 5.011533 GTCACATAATCTGCTAGGGTGAGAT 59.988 44.000 0.00 0.00 34.81 2.75
4166 5800 4.342378 GTCACATAATCTGCTAGGGTGAGA 59.658 45.833 0.00 0.00 34.81 3.27
4167 5801 4.100035 TGTCACATAATCTGCTAGGGTGAG 59.900 45.833 0.00 0.00 34.81 3.51
4168 5802 4.030216 TGTCACATAATCTGCTAGGGTGA 58.970 43.478 0.00 0.00 0.00 4.02
4169 5803 4.406648 TGTCACATAATCTGCTAGGGTG 57.593 45.455 0.00 0.00 0.00 4.61
4170 5804 4.655649 TCATGTCACATAATCTGCTAGGGT 59.344 41.667 0.00 0.00 0.00 4.34
4172 5806 6.519382 TCTTCATGTCACATAATCTGCTAGG 58.481 40.000 0.00 0.00 0.00 3.02
4173 5807 7.062022 CGATCTTCATGTCACATAATCTGCTAG 59.938 40.741 0.00 0.00 0.00 3.42
4175 5809 5.695363 CGATCTTCATGTCACATAATCTGCT 59.305 40.000 0.00 0.00 0.00 4.24
4176 5810 5.464722 ACGATCTTCATGTCACATAATCTGC 59.535 40.000 0.00 0.00 0.00 4.26
4177 5811 7.223387 TGAACGATCTTCATGTCACATAATCTG 59.777 37.037 0.00 0.00 0.00 2.90
4178 5812 7.267857 TGAACGATCTTCATGTCACATAATCT 58.732 34.615 0.00 0.00 0.00 2.40
4180 5814 7.848223 TTGAACGATCTTCATGTCACATAAT 57.152 32.000 0.00 0.00 0.00 1.28
4181 5815 7.848223 ATTGAACGATCTTCATGTCACATAA 57.152 32.000 0.00 0.00 0.00 1.90
4182 5816 7.848223 AATTGAACGATCTTCATGTCACATA 57.152 32.000 0.00 0.00 0.00 2.29
4183 5817 6.748333 AATTGAACGATCTTCATGTCACAT 57.252 33.333 7.97 0.00 0.00 3.21
4185 5819 7.637519 CACATAATTGAACGATCTTCATGTCAC 59.362 37.037 7.97 0.00 0.00 3.67
4187 5821 7.848051 GTCACATAATTGAACGATCTTCATGTC 59.152 37.037 7.97 0.00 0.00 3.06
4189 5823 7.687445 TGTCACATAATTGAACGATCTTCATG 58.313 34.615 7.97 6.57 0.00 3.07
4213 6299 8.274939 GTGTTCCAAACATCACAAACATAAATG 58.725 33.333 0.00 0.00 44.35 2.32
4214 6300 7.440856 GGTGTTCCAAACATCACAAACATAAAT 59.559 33.333 0.00 0.00 44.35 1.40
4216 6302 6.276847 GGTGTTCCAAACATCACAAACATAA 58.723 36.000 0.00 0.00 44.35 1.90
4218 6304 4.442753 GGGTGTTCCAAACATCACAAACAT 60.443 41.667 5.53 0.00 44.36 2.71
4227 6313 2.375174 TCTGCTAGGGTGTTCCAAACAT 59.625 45.455 0.00 0.00 44.35 2.71
4228 6314 1.771854 TCTGCTAGGGTGTTCCAAACA 59.228 47.619 0.00 0.00 39.52 2.83
4229 6315 2.561478 TCTGCTAGGGTGTTCCAAAC 57.439 50.000 0.00 0.00 38.24 2.93
4230 6316 3.806949 AATCTGCTAGGGTGTTCCAAA 57.193 42.857 0.00 0.00 38.24 3.28
4231 6317 3.420893 CAAATCTGCTAGGGTGTTCCAA 58.579 45.455 0.00 0.00 38.24 3.53
4232 6318 2.879756 GCAAATCTGCTAGGGTGTTCCA 60.880 50.000 0.00 0.00 45.74 3.53
4233 6319 1.745653 GCAAATCTGCTAGGGTGTTCC 59.254 52.381 0.00 0.00 45.74 3.62
4245 6331 8.248945 ACTCTGAATTTTAATCTGGCAAATCTG 58.751 33.333 0.00 0.00 0.00 2.90
4246 6332 8.358582 ACTCTGAATTTTAATCTGGCAAATCT 57.641 30.769 0.00 0.00 0.00 2.40
4247 6333 7.430502 CGACTCTGAATTTTAATCTGGCAAATC 59.569 37.037 0.00 0.00 0.00 2.17
4248 6334 7.121168 TCGACTCTGAATTTTAATCTGGCAAAT 59.879 33.333 0.00 0.00 0.00 2.32
4249 6335 6.429692 TCGACTCTGAATTTTAATCTGGCAAA 59.570 34.615 0.00 0.00 0.00 3.68
4250 6336 5.937540 TCGACTCTGAATTTTAATCTGGCAA 59.062 36.000 0.00 0.00 0.00 4.52
4251 6337 5.487433 TCGACTCTGAATTTTAATCTGGCA 58.513 37.500 0.00 0.00 0.00 4.92
4252 6338 5.812642 TCTCGACTCTGAATTTTAATCTGGC 59.187 40.000 0.00 0.00 0.00 4.85
4253 6339 7.221838 GTCTCTCGACTCTGAATTTTAATCTGG 59.778 40.741 0.00 0.00 37.19 3.86
4254 6340 7.757173 TGTCTCTCGACTCTGAATTTTAATCTG 59.243 37.037 0.00 0.00 40.86 2.90
4255 6341 7.831753 TGTCTCTCGACTCTGAATTTTAATCT 58.168 34.615 0.00 0.00 40.86 2.40
4256 6342 7.221838 CCTGTCTCTCGACTCTGAATTTTAATC 59.778 40.741 0.00 0.00 40.86 1.75
4257 6343 7.038659 CCTGTCTCTCGACTCTGAATTTTAAT 58.961 38.462 0.00 0.00 40.86 1.40
4258 6344 6.390721 CCTGTCTCTCGACTCTGAATTTTAA 58.609 40.000 0.00 0.00 40.86 1.52
4259 6345 5.622460 GCCTGTCTCTCGACTCTGAATTTTA 60.622 44.000 0.00 0.00 40.86 1.52
4260 6346 4.815269 CCTGTCTCTCGACTCTGAATTTT 58.185 43.478 0.00 0.00 40.86 1.82
4264 6350 1.169577 GCCTGTCTCTCGACTCTGAA 58.830 55.000 0.00 0.00 40.86 3.02
4274 6360 2.355010 AAAAGTTGCTGCCTGTCTCT 57.645 45.000 0.00 0.00 0.00 3.10
4275 6361 2.358898 TCAAAAAGTTGCTGCCTGTCTC 59.641 45.455 0.00 0.00 34.50 3.36
4276 6362 2.360165 CTCAAAAAGTTGCTGCCTGTCT 59.640 45.455 0.00 0.00 34.50 3.41
4289 6375 6.105333 AGTAGTGAGCTAGCATCTCAAAAAG 58.895 40.000 18.83 0.00 41.66 2.27
4293 6379 5.441500 AGTAGTAGTGAGCTAGCATCTCAA 58.558 41.667 18.83 0.00 41.66 3.02
4302 6388 9.194972 TGTAGAACTAGTAGTAGTAGTGAGCTA 57.805 37.037 16.72 14.75 38.66 3.32
4303 6389 8.076910 TGTAGAACTAGTAGTAGTAGTGAGCT 57.923 38.462 16.72 15.52 38.66 4.09
4304 6390 8.196771 TCTGTAGAACTAGTAGTAGTAGTGAGC 58.803 40.741 16.72 10.33 38.66 4.26
4313 6399 9.994432 GCGTTTAAATCTGTAGAACTAGTAGTA 57.006 33.333 2.50 0.00 0.00 1.82
4314 6400 8.738106 AGCGTTTAAATCTGTAGAACTAGTAGT 58.262 33.333 0.00 0.00 0.00 2.73
4315 6401 9.011407 CAGCGTTTAAATCTGTAGAACTAGTAG 57.989 37.037 0.00 0.00 0.00 2.57
4318 6404 6.812160 ACCAGCGTTTAAATCTGTAGAACTAG 59.188 38.462 15.03 0.00 0.00 2.57
4319 6405 6.588756 CACCAGCGTTTAAATCTGTAGAACTA 59.411 38.462 15.03 0.00 0.00 2.24
4320 6406 5.408604 CACCAGCGTTTAAATCTGTAGAACT 59.591 40.000 15.03 0.00 0.00 3.01
4322 6408 5.302360 ACACCAGCGTTTAAATCTGTAGAA 58.698 37.500 15.03 0.00 0.00 2.10
4339 6513 4.970003 GTGAAACTTGAAATTCGACACCAG 59.030 41.667 0.00 0.00 0.00 4.00
4401 6971 6.370442 CCATGTCAGTAAGGACGTTGATTTTA 59.630 38.462 0.00 0.00 40.72 1.52
4407 6977 2.346803 CCCATGTCAGTAAGGACGTTG 58.653 52.381 0.00 0.00 40.72 4.10
4408 6978 1.338769 GCCCATGTCAGTAAGGACGTT 60.339 52.381 0.00 0.00 40.72 3.99
4410 6980 0.249120 TGCCCATGTCAGTAAGGACG 59.751 55.000 0.00 0.00 40.72 4.79
4435 7022 4.815308 GCTCATGTTGATGATACTGCTTCT 59.185 41.667 0.00 0.00 37.97 2.85
4436 7023 4.318618 CGCTCATGTTGATGATACTGCTTC 60.319 45.833 0.00 0.00 37.97 3.86
4438 7025 3.129109 CGCTCATGTTGATGATACTGCT 58.871 45.455 0.00 0.00 37.97 4.24
4439 7026 2.222678 CCGCTCATGTTGATGATACTGC 59.777 50.000 0.00 0.00 37.97 4.40
4440 7027 3.721035 TCCGCTCATGTTGATGATACTG 58.279 45.455 0.00 0.00 37.97 2.74
4441 7028 4.562347 GGATCCGCTCATGTTGATGATACT 60.562 45.833 0.00 0.00 37.97 2.12
4442 7029 3.681897 GGATCCGCTCATGTTGATGATAC 59.318 47.826 0.00 0.00 37.97 2.24
4443 7030 3.614870 CGGATCCGCTCATGTTGATGATA 60.615 47.826 23.37 0.00 37.97 2.15
4444 7031 2.775890 GGATCCGCTCATGTTGATGAT 58.224 47.619 0.00 0.00 37.97 2.45
4445 7032 1.538849 CGGATCCGCTCATGTTGATGA 60.539 52.381 23.37 0.00 37.07 2.92
4446 7033 0.863799 CGGATCCGCTCATGTTGATG 59.136 55.000 23.37 0.00 0.00 3.07
4455 7042 2.202566 CTTAGGTTTTCGGATCCGCTC 58.797 52.381 29.62 17.18 39.59 5.03
4460 7047 2.747446 TGCTTGCTTAGGTTTTCGGATC 59.253 45.455 0.00 0.00 0.00 3.36
4630 7224 4.368808 CAACCGCAACCGCAGACG 62.369 66.667 0.00 0.00 38.40 4.18
4631 7225 4.683334 GCAACCGCAACCGCAGAC 62.683 66.667 0.00 0.00 38.40 3.51
4632 7226 4.927782 AGCAACCGCAACCGCAGA 62.928 61.111 0.00 0.00 42.27 4.26
4633 7227 3.879351 GAAGCAACCGCAACCGCAG 62.879 63.158 0.00 0.00 42.27 5.18
4634 7228 3.959975 GAAGCAACCGCAACCGCA 61.960 61.111 0.00 0.00 42.27 5.69
4635 7229 3.660111 AGAAGCAACCGCAACCGC 61.660 61.111 0.00 0.00 42.27 5.68
4636 7230 2.252260 CAGAAGCAACCGCAACCG 59.748 61.111 0.00 0.00 42.27 4.44
4637 7231 2.050077 GCAGAAGCAACCGCAACC 60.050 61.111 0.00 0.00 42.27 3.77
4638 7232 1.370900 CAGCAGAAGCAACCGCAAC 60.371 57.895 0.00 0.00 45.49 4.17
4639 7233 2.554636 CCAGCAGAAGCAACCGCAA 61.555 57.895 0.00 0.00 45.49 4.85
4640 7234 2.979676 CCAGCAGAAGCAACCGCA 60.980 61.111 0.00 0.00 45.49 5.69
4641 7235 2.980233 ACCAGCAGAAGCAACCGC 60.980 61.111 0.00 0.00 45.49 5.68
4642 7236 2.620112 CCACCAGCAGAAGCAACCG 61.620 63.158 0.00 0.00 45.49 4.44
4643 7237 1.529244 ACCACCAGCAGAAGCAACC 60.529 57.895 0.00 0.00 45.49 3.77
4644 7238 1.656441 CACCACCAGCAGAAGCAAC 59.344 57.895 0.00 0.00 45.49 4.17
4645 7239 1.529010 CCACCACCAGCAGAAGCAA 60.529 57.895 0.00 0.00 45.49 3.91
4646 7240 2.113774 CCACCACCAGCAGAAGCA 59.886 61.111 0.00 0.00 45.49 3.91
4647 7241 2.113986 ACCACCACCAGCAGAAGC 59.886 61.111 0.00 0.00 42.56 3.86
4648 7242 1.601759 CCACCACCACCAGCAGAAG 60.602 63.158 0.00 0.00 0.00 2.85
4649 7243 2.055689 CTCCACCACCACCAGCAGAA 62.056 60.000 0.00 0.00 0.00 3.02
4650 7244 2.447572 TCCACCACCACCAGCAGA 60.448 61.111 0.00 0.00 0.00 4.26
4651 7245 2.033141 CTCCACCACCACCAGCAG 59.967 66.667 0.00 0.00 0.00 4.24
4652 7246 3.569210 CCTCCACCACCACCAGCA 61.569 66.667 0.00 0.00 0.00 4.41
4653 7247 3.570212 ACCTCCACCACCACCAGC 61.570 66.667 0.00 0.00 0.00 4.85
4654 7248 2.431683 CACCTCCACCACCACCAG 59.568 66.667 0.00 0.00 0.00 4.00
4655 7249 3.174987 CCACCTCCACCACCACCA 61.175 66.667 0.00 0.00 0.00 4.17
4656 7250 2.292785 AAACCACCTCCACCACCACC 62.293 60.000 0.00 0.00 0.00 4.61
4677 7271 1.376424 AAGCATGTGCAGGTCTCCG 60.376 57.895 7.83 0.00 45.16 4.63
4730 7324 2.892425 GCGTTGAGCTGATCCCCG 60.892 66.667 0.00 0.00 44.04 5.73
4740 7334 2.887568 CAGCCCGCTAGCGTTGAG 60.888 66.667 33.18 18.88 38.01 3.02
4741 7335 3.234630 AACAGCCCGCTAGCGTTGA 62.235 57.895 33.18 0.00 38.01 3.18
4742 7336 2.742372 AACAGCCCGCTAGCGTTG 60.742 61.111 33.18 27.60 38.01 4.10
4743 7337 2.742372 CAACAGCCCGCTAGCGTT 60.742 61.111 33.18 19.02 38.01 4.84
4744 7338 3.649277 CTCAACAGCCCGCTAGCGT 62.649 63.158 33.18 14.65 38.01 5.07
4745 7339 2.887568 CTCAACAGCCCGCTAGCG 60.888 66.667 29.93 29.93 38.01 4.26
4746 7340 2.512515 CCTCAACAGCCCGCTAGC 60.513 66.667 4.06 4.06 0.00 3.42
4747 7341 2.512515 GCCTCAACAGCCCGCTAG 60.513 66.667 0.00 0.00 0.00 3.42
4748 7342 4.451150 CGCCTCAACAGCCCGCTA 62.451 66.667 0.00 0.00 0.00 4.26
4755 7349 4.020617 TCCCAGCCGCCTCAACAG 62.021 66.667 0.00 0.00 0.00 3.16
4756 7350 4.329545 GTCCCAGCCGCCTCAACA 62.330 66.667 0.00 0.00 0.00 3.33
4763 7357 4.241555 ATCATCCGTCCCAGCCGC 62.242 66.667 0.00 0.00 0.00 6.53
4764 7358 2.280389 CATCATCCGTCCCAGCCG 60.280 66.667 0.00 0.00 0.00 5.52
4765 7359 1.070445 CTCATCATCCGTCCCAGCC 59.930 63.158 0.00 0.00 0.00 4.85
4766 7360 0.033228 CTCTCATCATCCGTCCCAGC 59.967 60.000 0.00 0.00 0.00 4.85
4767 7361 1.068281 CACTCTCATCATCCGTCCCAG 59.932 57.143 0.00 0.00 0.00 4.45
4768 7362 1.114627 CACTCTCATCATCCGTCCCA 58.885 55.000 0.00 0.00 0.00 4.37
4769 7363 0.390860 CCACTCTCATCATCCGTCCC 59.609 60.000 0.00 0.00 0.00 4.46
4770 7364 1.115467 ACCACTCTCATCATCCGTCC 58.885 55.000 0.00 0.00 0.00 4.79
4771 7365 2.215907 CACCACTCTCATCATCCGTC 57.784 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.