Multiple sequence alignment - TraesCS1B01G217100

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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 TraesCS1B01G217100 chr1B 100.000 4662 0 0 1 4662 393507920 393512581 0.000000e+00 8610.0
1 TraesCS1B01G217100 chr1B 93.151 73 5 0 4406 4478 542573918 542573846 1.770000e-19 108.0
2 TraesCS1B01G217100 chr1D 96.327 3839 122 15 577 4407 292526449 292530276 0.000000e+00 6290.0
3 TraesCS1B01G217100 chr1A 96.769 3745 105 10 625 4366 364631684 364635415 0.000000e+00 6231.0
4 TraesCS1B01G217100 chr1A 86.432 597 58 6 1 578 442461318 442460726 2.370000e-177 632.0
5 TraesCS1B01G217100 chr1A 89.641 251 13 6 4412 4662 44519574 44519811 1.630000e-79 307.0
6 TraesCS1B01G217100 chr1A 85.714 175 12 8 4408 4575 451738367 451738535 6.200000e-39 172.0
7 TraesCS1B01G217100 chr1A 92.857 84 6 0 4579 4662 451738667 451738750 6.330000e-24 122.0
8 TraesCS1B01G217100 chr1A 92.105 76 5 1 4408 4483 389071396 389071322 6.380000e-19 106.0
9 TraesCS1B01G217100 chr1A 100.000 34 0 0 4374 4407 364635404 364635437 3.890000e-06 63.9
10 TraesCS1B01G217100 chr6A 87.124 598 56 6 1 578 40617663 40618259 0.000000e+00 658.0
11 TraesCS1B01G217100 chr6A 87.409 413 51 1 1 413 55038583 55038994 1.520000e-129 473.0
12 TraesCS1B01G217100 chr6A 88.514 148 16 1 430 577 55143132 55143278 1.330000e-40 178.0
13 TraesCS1B01G217100 chr4B 86.644 599 56 12 1 578 282891529 282892124 3.930000e-180 641.0
14 TraesCS1B01G217100 chr5A 85.930 597 64 6 1 578 90617211 90617806 1.840000e-173 619.0
15 TraesCS1B01G217100 chr3D 84.654 593 71 10 1 573 29713274 29713866 1.460000e-159 573.0
16 TraesCS1B01G217100 chr2B 85.561 187 14 8 4408 4584 58102755 58102938 2.870000e-42 183.0
17 TraesCS1B01G217100 chr2B 86.667 105 14 0 4558 4662 258044316 258044420 2.950000e-22 117.0
18 TraesCS1B01G217100 chr5D 80.952 189 21 11 4408 4585 526092662 526092846 8.140000e-28 135.0
19 TraesCS1B01G217100 chr4A 88.776 98 11 0 4558 4655 312674981 312675078 2.280000e-23 121.0
20 TraesCS1B01G217100 chr7A 86.667 105 14 0 4558 4662 132618196 132618092 2.950000e-22 117.0
21 TraesCS1B01G217100 chr7B 85.714 105 15 0 4558 4662 537784821 537784925 1.370000e-20 111.0
22 TraesCS1B01G217100 chr7B 88.312 77 8 1 4407 4483 11875202 11875127 1.790000e-14 91.6
23 TraesCS1B01G217100 chr7B 98.077 52 1 0 4408 4459 537784627 537784678 1.790000e-14 91.6
24 TraesCS1B01G217100 chr3B 90.000 80 6 2 4405 4483 734742403 734742481 8.250000e-18 102.0
25 TraesCS1B01G217100 chr5B 83.750 80 12 1 4404 4483 61392908 61392986 1.800000e-09 75.0


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 TraesCS1B01G217100 chr1B 393507920 393512581 4661 False 8610.00 8610 100.0000 1 4662 1 chr1B.!!$F1 4661
1 TraesCS1B01G217100 chr1D 292526449 292530276 3827 False 6290.00 6290 96.3270 577 4407 1 chr1D.!!$F1 3830
2 TraesCS1B01G217100 chr1A 364631684 364635437 3753 False 3147.45 6231 98.3845 625 4407 2 chr1A.!!$F2 3782
3 TraesCS1B01G217100 chr1A 442460726 442461318 592 True 632.00 632 86.4320 1 578 1 chr1A.!!$R2 577
4 TraesCS1B01G217100 chr6A 40617663 40618259 596 False 658.00 658 87.1240 1 578 1 chr6A.!!$F1 577
5 TraesCS1B01G217100 chr4B 282891529 282892124 595 False 641.00 641 86.6440 1 578 1 chr4B.!!$F1 577
6 TraesCS1B01G217100 chr5A 90617211 90617806 595 False 619.00 619 85.9300 1 578 1 chr5A.!!$F1 577
7 TraesCS1B01G217100 chr3D 29713274 29713866 592 False 573.00 573 84.6540 1 573 1 chr3D.!!$F1 572

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
870 903 0.249868 CACGACCAGCCTGTTTCTCA 60.250 55.000 0.00 0.00 0.00 3.27 F
1728 1764 0.041684 TGGAGATGCAGAGGTCAGGA 59.958 55.000 0.00 0.00 0.00 3.86 F
2031 2067 1.349026 CAGTTCATGACCAGGTCAGGT 59.651 52.381 29.08 11.72 46.04 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 1791 2.197577 GCGCAGGATCTAAAGACACTC 58.802 52.381 0.30 0.00 0.00 3.51 R
2886 2922 1.747709 CTTCTGCTCCTTGACCATGG 58.252 55.000 11.19 11.19 0.00 3.66 R
3829 3867 1.750778 ACCAGCATAAATGGCGGAAAG 59.249 47.619 0.00 0.00 41.87 2.62 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
30 31 1.831106 TCCCACATCACTTCATAGCGT 59.169 47.619 0.00 0.00 0.00 5.07
96 99 4.743955 GCAGAGTAAAAGAGGACAGTGGTT 60.744 45.833 0.00 0.00 0.00 3.67
112 115 0.739561 GGTTAGATCTCGGCGACACT 59.260 55.000 4.99 8.20 0.00 3.55
185 188 2.802057 GCGACTATATCCAACCGCACTT 60.802 50.000 0.00 0.00 41.89 3.16
196 199 3.245048 CCAACCGCACTTGAACATTTTTC 59.755 43.478 0.00 0.00 0.00 2.29
202 205 4.051237 GCACTTGAACATTTTTCTCACCC 58.949 43.478 0.00 0.00 0.00 4.61
227 230 6.916387 CGACTGATTGTTATTATACGTCCAGT 59.084 38.462 0.00 0.00 0.00 4.00
267 270 4.458397 AGGTCATGCAGATTACATTCAGG 58.542 43.478 0.00 0.00 0.00 3.86
292 295 7.096551 GCAAAACATCCCTAAAAGCTTTCATA 58.903 34.615 13.10 1.06 0.00 2.15
293 296 7.063426 GCAAAACATCCCTAAAAGCTTTCATAC 59.937 37.037 13.10 0.00 0.00 2.39
304 307 1.737793 GCTTTCATACGGGGTTCACTG 59.262 52.381 0.00 0.00 0.00 3.66
305 308 2.614481 GCTTTCATACGGGGTTCACTGA 60.614 50.000 0.00 0.00 0.00 3.41
351 355 4.131376 CCACATGGCCTCGCTAAG 57.869 61.111 3.32 0.00 0.00 2.18
379 383 3.003068 CGATCATGAGCCAAGGTTCATTC 59.997 47.826 14.75 10.55 42.04 2.67
404 408 1.234821 TGGTTTGATGCGTCTCAACC 58.765 50.000 23.64 23.64 38.17 3.77
420 424 4.080582 TCTCAACCGATCCCACATACAATT 60.081 41.667 0.00 0.00 0.00 2.32
425 448 3.433598 CCGATCCCACATACAATTCCACT 60.434 47.826 0.00 0.00 0.00 4.00
428 451 3.684908 TCCCACATACAATTCCACTGTG 58.315 45.455 0.00 0.00 37.53 3.66
457 480 8.534496 CAAAGGTTCCTCTCCATTTTATTTCAT 58.466 33.333 0.00 0.00 0.00 2.57
515 538 8.213518 ACTCCGTAGTTTATTAACTCGACATA 57.786 34.615 13.97 0.00 43.45 2.29
517 540 9.114965 CTCCGTAGTTTATTAACTCGACATATG 57.885 37.037 13.97 0.00 43.45 1.78
527 550 3.995199 ACTCGACATATGCGGAATCATT 58.005 40.909 16.01 0.00 0.00 2.57
574 598 4.277515 TCCCTTTCACAGAGACAATGAG 57.722 45.455 0.00 0.00 0.00 2.90
578 602 4.928615 CCTTTCACAGAGACAATGAGACTC 59.071 45.833 0.00 0.00 38.99 3.36
583 607 3.900601 ACAGAGACAATGAGACTCCTTGT 59.099 43.478 21.63 21.63 39.43 3.16
590 614 2.910688 TGAGACTCCTTGTTGGACAC 57.089 50.000 0.00 0.00 40.56 3.67
611 635 1.263217 GTTGGTGTTGTAAGTGCCTCG 59.737 52.381 0.00 0.00 0.00 4.63
615 639 0.753867 TGTTGTAAGTGCCTCGGTCA 59.246 50.000 0.00 0.00 0.00 4.02
617 641 1.798813 GTTGTAAGTGCCTCGGTCAAG 59.201 52.381 0.00 0.00 0.00 3.02
618 642 0.320374 TGTAAGTGCCTCGGTCAAGG 59.680 55.000 0.00 0.00 39.62 3.61
639 663 3.870606 GCAAGCGCCTCGTTTCTA 58.129 55.556 2.29 0.00 0.00 2.10
676 706 2.676342 CCCCGTGATGTACTTACTTTGC 59.324 50.000 0.00 0.00 0.00 3.68
696 726 9.353999 ACTTTGCTAAAATCCGAATATTTTCAC 57.646 29.630 6.42 2.94 39.27 3.18
824 856 1.553704 AGATAAAAGAGCGTTCCGGGT 59.446 47.619 0.00 0.00 0.00 5.28
863 896 3.680786 TCGGACACGACCAGCCTG 61.681 66.667 0.00 0.00 45.59 4.85
870 903 0.249868 CACGACCAGCCTGTTTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
880 913 2.550978 CCTGTTTCTCAGTGTTCGTGT 58.449 47.619 0.00 0.00 42.19 4.49
881 914 2.540101 CCTGTTTCTCAGTGTTCGTGTC 59.460 50.000 0.00 0.00 42.19 3.67
892 925 1.596752 TTCGTGTCAATGGCGCAGT 60.597 52.632 10.83 0.00 0.00 4.40
1289 1325 4.436998 CTCGCACTCCGGGGACAC 62.437 72.222 9.33 0.00 37.59 3.67
1446 1482 3.998672 GCCTCCGACCGGACAACA 61.999 66.667 9.46 0.00 39.76 3.33
1728 1764 0.041684 TGGAGATGCAGAGGTCAGGA 59.958 55.000 0.00 0.00 0.00 3.86
1838 1874 6.694411 GCACATGCCATAAAGAATAACTTCAG 59.306 38.462 0.00 0.00 34.64 3.02
1841 1877 9.632638 ACATGCCATAAAGAATAACTTCAGTAT 57.367 29.630 0.00 0.00 37.93 2.12
2031 2067 1.349026 CAGTTCATGACCAGGTCAGGT 59.651 52.381 29.08 11.72 46.04 4.00
2184 2220 7.558807 AGAAATGCAATTCTTGATCTGTATGGA 59.441 33.333 11.34 0.00 36.23 3.41
2303 2339 2.962253 GCGCTATGAGGACACCGC 60.962 66.667 0.00 0.00 35.52 5.68
2886 2922 0.737367 TGATATGCGGCTATGCGCTC 60.737 55.000 9.73 0.00 39.13 5.03
3084 3120 3.294079 GCACTTTGCTTGCATGGTT 57.706 47.368 1.34 0.00 40.96 3.67
3242 3278 1.715585 CTGCCGGCAATGTTCTACG 59.284 57.895 32.09 11.67 0.00 3.51
3506 3542 4.723789 ACTGTCTGGATATGACCCTGATTT 59.276 41.667 0.00 0.00 34.80 2.17
3829 3867 4.022935 TGACAGACTTGGCAATTGTGATTC 60.023 41.667 19.27 9.32 40.10 2.52
3928 3966 2.035066 CCCTGTTTTCCTTTCTGCACAG 59.965 50.000 0.00 0.00 32.96 3.66
4076 4114 5.705609 TTTGACAAGAAGCTTGGGATTAC 57.294 39.130 2.10 0.00 0.00 1.89
4115 4153 2.496899 TCCAGAAGATGCAAAGGTCC 57.503 50.000 0.00 0.00 0.00 4.46
4116 4154 1.089920 CCAGAAGATGCAAAGGTCCG 58.910 55.000 0.00 0.00 0.00 4.79
4117 4155 1.611673 CCAGAAGATGCAAAGGTCCGT 60.612 52.381 0.00 0.00 0.00 4.69
4118 4156 1.734465 CAGAAGATGCAAAGGTCCGTC 59.266 52.381 0.00 0.00 0.00 4.79
4119 4157 1.625818 AGAAGATGCAAAGGTCCGTCT 59.374 47.619 0.00 0.00 0.00 4.18
4120 4158 2.832129 AGAAGATGCAAAGGTCCGTCTA 59.168 45.455 0.00 0.00 0.00 2.59
4160 4199 7.178628 AGTGCTAAATGTACTGAAGAGAGGTAA 59.821 37.037 0.00 0.00 40.11 2.85
4163 4202 9.036671 GCTAAATGTACTGAAGAGAGGTAATTC 57.963 37.037 0.00 0.00 0.00 2.17
4198 4237 7.976135 AGTGCATCTGTATTTCCTATCATTC 57.024 36.000 0.00 0.00 0.00 2.67
4267 4306 3.788227 TTGGTTCTGGCTGTTCAGTAT 57.212 42.857 1.78 0.00 36.25 2.12
4372 4411 5.353956 TGTCATATCCCAAATTTCGTGTCAG 59.646 40.000 0.00 0.00 0.00 3.51
4383 4422 5.982890 ATTTCGTGTCAGATCCCAAATTT 57.017 34.783 0.00 0.00 0.00 1.82
4384 4423 5.371115 TTTCGTGTCAGATCCCAAATTTC 57.629 39.130 0.00 0.00 0.00 2.17
4412 4451 3.977134 ATCATAGCTCATAGGCAGTGG 57.023 47.619 0.00 0.00 34.17 4.00
4413 4452 1.345741 TCATAGCTCATAGGCAGTGGC 59.654 52.381 9.02 9.02 40.13 5.01
4414 4453 0.319728 ATAGCTCATAGGCAGTGGCG 59.680 55.000 11.51 0.00 42.47 5.69
4415 4454 1.748329 TAGCTCATAGGCAGTGGCGG 61.748 60.000 11.51 5.41 42.47 6.13
4416 4455 3.094062 GCTCATAGGCAGTGGCGGA 62.094 63.158 11.51 9.50 42.47 5.54
4417 4456 1.068753 CTCATAGGCAGTGGCGGAG 59.931 63.158 11.51 14.91 42.47 4.63
4435 4474 3.983344 CGGAGCTTGAAAGAAAATGTTGG 59.017 43.478 0.00 0.00 0.00 3.77
4436 4475 4.309933 GGAGCTTGAAAGAAAATGTTGGG 58.690 43.478 0.00 0.00 0.00 4.12
4437 4476 3.732212 AGCTTGAAAGAAAATGTTGGGC 58.268 40.909 0.00 0.00 0.00 5.36
4438 4477 2.476241 GCTTGAAAGAAAATGTTGGGCG 59.524 45.455 0.00 0.00 0.00 6.13
4439 4478 2.810439 TGAAAGAAAATGTTGGGCGG 57.190 45.000 0.00 0.00 0.00 6.13
4440 4479 1.342819 TGAAAGAAAATGTTGGGCGGG 59.657 47.619 0.00 0.00 0.00 6.13
4441 4480 0.034756 AAAGAAAATGTTGGGCGGGC 59.965 50.000 0.00 0.00 0.00 6.13
4442 4481 1.826340 AAGAAAATGTTGGGCGGGCC 61.826 55.000 14.65 14.65 0.00 5.80
4443 4482 2.525381 AAAATGTTGGGCGGGCCA 60.525 55.556 20.63 20.63 37.98 5.36
4444 4483 2.505635 GAAAATGTTGGGCGGGCCAG 62.506 60.000 23.18 0.00 37.98 4.85
4445 4484 3.521765 AAATGTTGGGCGGGCCAGA 62.522 57.895 23.18 14.44 37.98 3.86
4446 4485 4.740822 ATGTTGGGCGGGCCAGAC 62.741 66.667 23.18 21.76 37.98 3.51
4448 4487 3.712907 GTTGGGCGGGCCAGACTA 61.713 66.667 23.18 0.00 37.98 2.59
4449 4488 2.931105 TTGGGCGGGCCAGACTAA 60.931 61.111 23.18 5.93 37.98 2.24
4450 4489 2.530672 TTGGGCGGGCCAGACTAAA 61.531 57.895 23.18 4.74 37.98 1.85
4451 4490 2.124695 GGGCGGGCCAGACTAAAG 60.125 66.667 16.76 0.00 37.98 1.85
4452 4491 2.666098 GGGCGGGCCAGACTAAAGA 61.666 63.158 16.76 0.00 37.98 2.52
4453 4492 1.298667 GGCGGGCCAGACTAAAGAA 59.701 57.895 7.23 0.00 35.81 2.52
4454 4493 0.744771 GGCGGGCCAGACTAAAGAAG 60.745 60.000 7.23 0.00 35.81 2.85
4455 4494 0.249398 GCGGGCCAGACTAAAGAAGA 59.751 55.000 7.23 0.00 0.00 2.87
4456 4495 1.740718 GCGGGCCAGACTAAAGAAGAG 60.741 57.143 7.23 0.00 0.00 2.85
4457 4496 1.740718 CGGGCCAGACTAAAGAAGAGC 60.741 57.143 4.39 0.00 0.00 4.09
4458 4497 1.279271 GGGCCAGACTAAAGAAGAGCA 59.721 52.381 4.39 0.00 0.00 4.26
4459 4498 2.092699 GGGCCAGACTAAAGAAGAGCAT 60.093 50.000 4.39 0.00 0.00 3.79
4460 4499 2.941720 GGCCAGACTAAAGAAGAGCATG 59.058 50.000 0.00 0.00 0.00 4.06
4461 4500 3.369892 GGCCAGACTAAAGAAGAGCATGA 60.370 47.826 0.00 0.00 0.00 3.07
4462 4501 4.450053 GCCAGACTAAAGAAGAGCATGAT 58.550 43.478 0.00 0.00 0.00 2.45
4463 4502 4.880696 GCCAGACTAAAGAAGAGCATGATT 59.119 41.667 0.00 0.00 0.00 2.57
4464 4503 5.356470 GCCAGACTAAAGAAGAGCATGATTT 59.644 40.000 0.00 0.00 0.00 2.17
4465 4504 6.458070 GCCAGACTAAAGAAGAGCATGATTTC 60.458 42.308 0.00 0.00 0.00 2.17
4466 4505 6.822676 CCAGACTAAAGAAGAGCATGATTTCT 59.177 38.462 0.00 0.00 32.80 2.52
4467 4506 7.336427 CCAGACTAAAGAAGAGCATGATTTCTT 59.664 37.037 12.38 12.38 41.53 2.52
4468 4507 8.728833 CAGACTAAAGAAGAGCATGATTTCTTT 58.271 33.333 23.98 23.98 46.82 2.52
4469 4508 9.294614 AGACTAAAGAAGAGCATGATTTCTTTT 57.705 29.630 24.88 15.62 44.42 2.27
4470 4509 9.905171 GACTAAAGAAGAGCATGATTTCTTTTT 57.095 29.630 24.88 17.68 44.42 1.94
4471 4510 9.688592 ACTAAAGAAGAGCATGATTTCTTTTTG 57.311 29.630 24.88 21.20 44.42 2.44
4472 4511 9.903682 CTAAAGAAGAGCATGATTTCTTTTTGA 57.096 29.630 24.88 14.49 44.42 2.69
4474 4513 9.603921 AAAGAAGAGCATGATTTCTTTTTGAAA 57.396 25.926 19.21 0.00 44.42 2.69
4509 4548 6.956299 ATTTGATGCAAGTTTACAAGATGC 57.044 33.333 0.00 0.00 37.52 3.91
4512 4551 3.287312 TGCAAGTTTACAAGATGCAGC 57.713 42.857 0.00 0.00 41.67 5.25
4513 4552 2.622470 TGCAAGTTTACAAGATGCAGCA 59.378 40.909 4.07 0.00 41.67 4.41
4514 4553 3.067883 TGCAAGTTTACAAGATGCAGCAA 59.932 39.130 4.07 0.00 41.67 3.91
4515 4554 3.671928 GCAAGTTTACAAGATGCAGCAAG 59.328 43.478 4.07 0.00 37.00 4.01
4516 4555 3.565905 AGTTTACAAGATGCAGCAAGC 57.434 42.857 4.07 0.00 45.96 4.01
4532 4571 7.615582 GCAGCAAGCATATATATAAGGAACA 57.384 36.000 0.00 0.00 44.79 3.18
4533 4572 7.467623 GCAGCAAGCATATATATAAGGAACAC 58.532 38.462 0.00 0.00 44.79 3.32
4534 4573 7.119699 GCAGCAAGCATATATATAAGGAACACA 59.880 37.037 0.00 0.00 44.79 3.72
4535 4574 8.446273 CAGCAAGCATATATATAAGGAACACAC 58.554 37.037 0.00 0.00 0.00 3.82
4536 4575 8.156820 AGCAAGCATATATATAAGGAACACACA 58.843 33.333 0.00 0.00 0.00 3.72
4537 4576 8.230486 GCAAGCATATATATAAGGAACACACAC 58.770 37.037 0.00 0.00 0.00 3.82
4538 4577 8.435430 CAAGCATATATATAAGGAACACACACG 58.565 37.037 0.00 0.00 0.00 4.49
4539 4578 6.590292 AGCATATATATAAGGAACACACACGC 59.410 38.462 0.00 0.00 0.00 5.34
4540 4579 6.367695 GCATATATATAAGGAACACACACGCA 59.632 38.462 0.00 0.00 0.00 5.24
4541 4580 7.621426 GCATATATATAAGGAACACACACGCAC 60.621 40.741 0.00 0.00 0.00 5.34
4542 4581 1.519408 ATAAGGAACACACACGCACC 58.481 50.000 0.00 0.00 0.00 5.01
4543 4582 0.533308 TAAGGAACACACACGCACCC 60.533 55.000 0.00 0.00 0.00 4.61
4544 4583 3.284449 GGAACACACACGCACCCC 61.284 66.667 0.00 0.00 0.00 4.95
4545 4584 2.515057 GAACACACACGCACCCCA 60.515 61.111 0.00 0.00 0.00 4.96
4546 4585 2.044848 AACACACACGCACCCCAA 60.045 55.556 0.00 0.00 0.00 4.12
4547 4586 1.658686 GAACACACACGCACCCCAAA 61.659 55.000 0.00 0.00 0.00 3.28
4548 4587 1.251527 AACACACACGCACCCCAAAA 61.252 50.000 0.00 0.00 0.00 2.44
4549 4588 1.040339 ACACACACGCACCCCAAAAT 61.040 50.000 0.00 0.00 0.00 1.82
4550 4589 0.955178 CACACACGCACCCCAAAATA 59.045 50.000 0.00 0.00 0.00 1.40
4551 4590 0.955905 ACACACGCACCCCAAAATAC 59.044 50.000 0.00 0.00 0.00 1.89
4552 4591 0.955178 CACACGCACCCCAAAATACA 59.045 50.000 0.00 0.00 0.00 2.29
4553 4592 1.068610 CACACGCACCCCAAAATACAG 60.069 52.381 0.00 0.00 0.00 2.74
4554 4593 1.243902 CACGCACCCCAAAATACAGT 58.756 50.000 0.00 0.00 0.00 3.55
4555 4594 1.611491 CACGCACCCCAAAATACAGTT 59.389 47.619 0.00 0.00 0.00 3.16
4556 4595 1.883926 ACGCACCCCAAAATACAGTTC 59.116 47.619 0.00 0.00 0.00 3.01
4557 4596 1.883275 CGCACCCCAAAATACAGTTCA 59.117 47.619 0.00 0.00 0.00 3.18
4558 4597 2.294791 CGCACCCCAAAATACAGTTCAA 59.705 45.455 0.00 0.00 0.00 2.69
4559 4598 3.649073 GCACCCCAAAATACAGTTCAAC 58.351 45.455 0.00 0.00 0.00 3.18
4560 4599 3.554129 GCACCCCAAAATACAGTTCAACC 60.554 47.826 0.00 0.00 0.00 3.77
4561 4600 3.639094 CACCCCAAAATACAGTTCAACCA 59.361 43.478 0.00 0.00 0.00 3.67
4562 4601 4.283212 CACCCCAAAATACAGTTCAACCAT 59.717 41.667 0.00 0.00 0.00 3.55
4563 4602 5.478679 CACCCCAAAATACAGTTCAACCATA 59.521 40.000 0.00 0.00 0.00 2.74
4564 4603 6.015010 CACCCCAAAATACAGTTCAACCATAA 60.015 38.462 0.00 0.00 0.00 1.90
4565 4604 6.555360 ACCCCAAAATACAGTTCAACCATAAA 59.445 34.615 0.00 0.00 0.00 1.40
4566 4605 7.096551 CCCCAAAATACAGTTCAACCATAAAG 58.903 38.462 0.00 0.00 0.00 1.85
4567 4606 6.589907 CCCAAAATACAGTTCAACCATAAAGC 59.410 38.462 0.00 0.00 0.00 3.51
4568 4607 7.151308 CCAAAATACAGTTCAACCATAAAGCA 58.849 34.615 0.00 0.00 0.00 3.91
4569 4608 7.116233 CCAAAATACAGTTCAACCATAAAGCAC 59.884 37.037 0.00 0.00 0.00 4.40
4570 4609 5.897377 ATACAGTTCAACCATAAAGCACC 57.103 39.130 0.00 0.00 0.00 5.01
4571 4610 3.561143 ACAGTTCAACCATAAAGCACCA 58.439 40.909 0.00 0.00 0.00 4.17
4572 4611 4.151883 ACAGTTCAACCATAAAGCACCAT 58.848 39.130 0.00 0.00 0.00 3.55
4573 4612 4.588528 ACAGTTCAACCATAAAGCACCATT 59.411 37.500 0.00 0.00 0.00 3.16
4574 4613 5.772672 ACAGTTCAACCATAAAGCACCATTA 59.227 36.000 0.00 0.00 0.00 1.90
4575 4614 6.266558 ACAGTTCAACCATAAAGCACCATTAA 59.733 34.615 0.00 0.00 0.00 1.40
4576 4615 6.808212 CAGTTCAACCATAAAGCACCATTAAG 59.192 38.462 0.00 0.00 0.00 1.85
4577 4616 6.493458 AGTTCAACCATAAAGCACCATTAAGT 59.507 34.615 0.00 0.00 0.00 2.24
4578 4617 6.909550 TCAACCATAAAGCACCATTAAGTT 57.090 33.333 0.00 0.00 0.00 2.66
4579 4618 8.301002 GTTCAACCATAAAGCACCATTAAGTTA 58.699 33.333 0.00 0.00 0.00 2.24
4580 4619 8.050778 TCAACCATAAAGCACCATTAAGTTAG 57.949 34.615 0.00 0.00 0.00 2.34
4581 4620 6.451064 ACCATAAAGCACCATTAAGTTAGC 57.549 37.500 0.00 0.00 0.00 3.09
4582 4621 6.187682 ACCATAAAGCACCATTAAGTTAGCT 58.812 36.000 0.00 0.00 0.00 3.32
4583 4622 7.343357 ACCATAAAGCACCATTAAGTTAGCTA 58.657 34.615 0.00 0.00 0.00 3.32
4584 4623 7.832187 ACCATAAAGCACCATTAAGTTAGCTAA 59.168 33.333 0.86 0.86 0.00 3.09
4585 4624 8.850156 CCATAAAGCACCATTAAGTTAGCTAAT 58.150 33.333 9.88 0.00 0.00 1.73
4588 4627 7.938140 AAGCACCATTAAGTTAGCTAATTCA 57.062 32.000 9.88 0.00 0.00 2.57
4589 4628 7.938140 AGCACCATTAAGTTAGCTAATTCAA 57.062 32.000 9.88 0.00 0.00 2.69
4590 4629 7.989826 AGCACCATTAAGTTAGCTAATTCAAG 58.010 34.615 9.88 0.00 0.00 3.02
4591 4630 6.693113 GCACCATTAAGTTAGCTAATTCAAGC 59.307 38.462 9.88 2.51 43.11 4.01
4592 4631 7.196331 CACCATTAAGTTAGCTAATTCAAGCC 58.804 38.462 9.88 0.00 43.86 4.35
4593 4632 6.889722 ACCATTAAGTTAGCTAATTCAAGCCA 59.110 34.615 9.88 0.00 43.86 4.75
4594 4633 7.067494 ACCATTAAGTTAGCTAATTCAAGCCAG 59.933 37.037 9.88 0.00 43.86 4.85
4595 4634 7.420800 CATTAAGTTAGCTAATTCAAGCCAGG 58.579 38.462 9.88 0.00 43.86 4.45
4596 4635 3.891049 AGTTAGCTAATTCAAGCCAGGG 58.109 45.455 9.88 0.00 43.86 4.45
4597 4636 3.523564 AGTTAGCTAATTCAAGCCAGGGA 59.476 43.478 9.88 0.00 43.86 4.20
4598 4637 4.018415 AGTTAGCTAATTCAAGCCAGGGAA 60.018 41.667 9.88 0.00 43.86 3.97
4599 4638 3.456380 AGCTAATTCAAGCCAGGGAAA 57.544 42.857 0.00 0.00 43.86 3.13
4600 4639 3.986435 AGCTAATTCAAGCCAGGGAAAT 58.014 40.909 0.00 0.00 43.86 2.17
4601 4640 5.129368 AGCTAATTCAAGCCAGGGAAATA 57.871 39.130 0.00 0.00 43.86 1.40
4602 4641 4.889995 AGCTAATTCAAGCCAGGGAAATAC 59.110 41.667 0.00 0.00 43.86 1.89
4603 4642 4.644685 GCTAATTCAAGCCAGGGAAATACA 59.355 41.667 0.00 0.00 36.45 2.29
4604 4643 5.302823 GCTAATTCAAGCCAGGGAAATACAT 59.697 40.000 0.00 0.00 36.45 2.29
4605 4644 5.603170 AATTCAAGCCAGGGAAATACATG 57.397 39.130 0.00 0.00 0.00 3.21
4606 4645 3.017048 TCAAGCCAGGGAAATACATGG 57.983 47.619 0.00 0.00 35.84 3.66
4607 4646 2.311542 TCAAGCCAGGGAAATACATGGT 59.688 45.455 0.00 0.00 35.17 3.55
4608 4647 2.689983 CAAGCCAGGGAAATACATGGTC 59.310 50.000 0.00 0.00 35.17 4.02
4609 4648 2.208872 AGCCAGGGAAATACATGGTCT 58.791 47.619 0.00 0.00 35.17 3.85
4610 4649 2.582636 AGCCAGGGAAATACATGGTCTT 59.417 45.455 0.00 0.00 35.17 3.01
4611 4650 2.952310 GCCAGGGAAATACATGGTCTTC 59.048 50.000 0.00 0.00 35.17 2.87
4612 4651 3.555966 CCAGGGAAATACATGGTCTTCC 58.444 50.000 11.56 11.56 37.25 3.46
4613 4652 3.203040 CCAGGGAAATACATGGTCTTCCT 59.797 47.826 16.80 6.10 37.94 3.36
4614 4653 4.455606 CAGGGAAATACATGGTCTTCCTC 58.544 47.826 16.80 10.11 37.94 3.71
4615 4654 4.080356 CAGGGAAATACATGGTCTTCCTCA 60.080 45.833 16.80 0.00 37.94 3.86
4616 4655 4.540099 AGGGAAATACATGGTCTTCCTCAA 59.460 41.667 16.80 0.00 37.94 3.02
4617 4656 4.640647 GGGAAATACATGGTCTTCCTCAAC 59.359 45.833 16.80 2.75 37.94 3.18
4618 4657 5.501156 GGAAATACATGGTCTTCCTCAACT 58.499 41.667 12.35 0.00 35.46 3.16
4619 4658 5.946377 GGAAATACATGGTCTTCCTCAACTT 59.054 40.000 12.35 0.00 35.46 2.66
4620 4659 6.094186 GGAAATACATGGTCTTCCTCAACTTC 59.906 42.308 12.35 0.00 35.46 3.01
4621 4660 5.762179 ATACATGGTCTTCCTCAACTTCA 57.238 39.130 0.00 0.00 34.23 3.02
4622 4661 3.744660 ACATGGTCTTCCTCAACTTCAC 58.255 45.455 0.00 0.00 34.23 3.18
4623 4662 3.392616 ACATGGTCTTCCTCAACTTCACT 59.607 43.478 0.00 0.00 34.23 3.41
4624 4663 4.141390 ACATGGTCTTCCTCAACTTCACTT 60.141 41.667 0.00 0.00 34.23 3.16
4625 4664 3.808728 TGGTCTTCCTCAACTTCACTTG 58.191 45.455 0.00 0.00 34.23 3.16
4626 4665 3.199946 TGGTCTTCCTCAACTTCACTTGT 59.800 43.478 0.00 0.00 34.23 3.16
4627 4666 3.561725 GGTCTTCCTCAACTTCACTTGTG 59.438 47.826 0.00 0.00 0.00 3.33
4628 4667 4.192317 GTCTTCCTCAACTTCACTTGTGT 58.808 43.478 0.46 0.00 0.00 3.72
4629 4668 4.271291 GTCTTCCTCAACTTCACTTGTGTC 59.729 45.833 0.46 0.00 0.00 3.67
4630 4669 3.904800 TCCTCAACTTCACTTGTGTCA 57.095 42.857 0.46 0.00 0.00 3.58
4631 4670 4.422073 TCCTCAACTTCACTTGTGTCAT 57.578 40.909 0.46 0.00 0.00 3.06
4632 4671 4.380531 TCCTCAACTTCACTTGTGTCATC 58.619 43.478 0.46 0.00 0.00 2.92
4633 4672 4.101585 TCCTCAACTTCACTTGTGTCATCT 59.898 41.667 0.46 0.00 0.00 2.90
4634 4673 4.450419 CCTCAACTTCACTTGTGTCATCTC 59.550 45.833 0.46 0.00 0.00 2.75
4635 4674 5.022282 TCAACTTCACTTGTGTCATCTCA 57.978 39.130 0.46 0.00 0.00 3.27
4636 4675 5.614308 TCAACTTCACTTGTGTCATCTCAT 58.386 37.500 0.46 0.00 0.00 2.90
4637 4676 6.057533 TCAACTTCACTTGTGTCATCTCATT 58.942 36.000 0.46 0.00 0.00 2.57
4638 4677 6.543465 TCAACTTCACTTGTGTCATCTCATTT 59.457 34.615 0.46 0.00 0.00 2.32
4639 4678 6.551385 ACTTCACTTGTGTCATCTCATTTC 57.449 37.500 0.46 0.00 0.00 2.17
4640 4679 5.471456 ACTTCACTTGTGTCATCTCATTTCC 59.529 40.000 0.46 0.00 0.00 3.13
4641 4680 5.233083 TCACTTGTGTCATCTCATTTCCT 57.767 39.130 0.46 0.00 0.00 3.36
4642 4681 5.624159 TCACTTGTGTCATCTCATTTCCTT 58.376 37.500 0.46 0.00 0.00 3.36
4643 4682 6.064060 TCACTTGTGTCATCTCATTTCCTTT 58.936 36.000 0.46 0.00 0.00 3.11
4644 4683 6.547141 TCACTTGTGTCATCTCATTTCCTTTT 59.453 34.615 0.46 0.00 0.00 2.27
4645 4684 7.719193 TCACTTGTGTCATCTCATTTCCTTTTA 59.281 33.333 0.46 0.00 0.00 1.52
4646 4685 8.352201 CACTTGTGTCATCTCATTTCCTTTTAA 58.648 33.333 0.00 0.00 0.00 1.52
4647 4686 8.912988 ACTTGTGTCATCTCATTTCCTTTTAAA 58.087 29.630 0.00 0.00 0.00 1.52
4648 4687 9.918630 CTTGTGTCATCTCATTTCCTTTTAAAT 57.081 29.630 0.00 0.00 0.00 1.40
4651 4690 9.788960 GTGTCATCTCATTTCCTTTTAAATACC 57.211 33.333 0.00 0.00 0.00 2.73
4652 4691 9.527157 TGTCATCTCATTTCCTTTTAAATACCA 57.473 29.630 0.00 0.00 0.00 3.25
4656 4695 9.875691 ATCTCATTTCCTTTTAAATACCAAAGC 57.124 29.630 0.00 0.00 0.00 3.51
4657 4696 8.865090 TCTCATTTCCTTTTAAATACCAAAGCA 58.135 29.630 0.00 0.00 0.00 3.91
4658 4697 9.143631 CTCATTTCCTTTTAAATACCAAAGCAG 57.856 33.333 0.00 0.00 0.00 4.24
4659 4698 8.646900 TCATTTCCTTTTAAATACCAAAGCAGT 58.353 29.630 0.00 0.00 0.00 4.40
4660 4699 9.271828 CATTTCCTTTTAAATACCAAAGCAGTT 57.728 29.630 0.00 0.00 0.00 3.16
4661 4700 8.880878 TTTCCTTTTAAATACCAAAGCAGTTC 57.119 30.769 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 44 9.399403 GAAGTTGCAAATTAGTAGAAGAAAAGG 57.601 33.333 12.76 0.00 0.00 3.11
52 55 5.560724 TGCCTAGAGAAGTTGCAAATTAGT 58.439 37.500 12.76 2.75 0.00 2.24
96 99 2.904697 TCTAGTGTCGCCGAGATCTA 57.095 50.000 0.00 0.00 0.00 1.98
127 130 2.873245 GCAGGACACTTTCTCTGATGCA 60.873 50.000 0.00 0.00 0.00 3.96
164 167 1.137513 GTGCGGTTGGATATAGTCGC 58.862 55.000 0.00 0.00 42.90 5.19
166 169 4.054780 TCAAGTGCGGTTGGATATAGTC 57.945 45.455 0.00 0.00 0.00 2.59
170 173 3.066291 TGTTCAAGTGCGGTTGGATAT 57.934 42.857 0.00 0.00 0.00 1.63
185 188 3.563808 CAGTCGGGTGAGAAAAATGTTCA 59.436 43.478 0.00 0.00 0.00 3.18
196 199 6.362551 CGTATAATAACAATCAGTCGGGTGAG 59.637 42.308 0.00 0.00 0.00 3.51
202 205 6.916387 ACTGGACGTATAATAACAATCAGTCG 59.084 38.462 0.00 0.00 0.00 4.18
227 230 2.787035 ACCTTGGGTTTAAAGGAGTGGA 59.213 45.455 9.13 0.00 46.08 4.02
267 270 5.296748 TGAAAGCTTTTAGGGATGTTTTGC 58.703 37.500 14.05 0.00 0.00 3.68
316 319 3.254411 TGTGGCAAAGCGAACATATTTCA 59.746 39.130 0.00 0.00 0.00 2.69
347 350 2.257894 GCTCATGATCGGCGATCTTAG 58.742 52.381 39.57 32.61 39.56 2.18
351 355 0.601046 TTGGCTCATGATCGGCGATC 60.601 55.000 36.07 36.07 39.31 3.69
404 408 3.561310 CAGTGGAATTGTATGTGGGATCG 59.439 47.826 0.00 0.00 0.00 3.69
472 495 8.134202 TACGGAGTCCATCATATTGATGTAAT 57.866 34.615 10.49 0.44 46.82 1.89
527 550 1.011595 AGGTCTAGCCCTCTTCTGGA 58.988 55.000 0.00 0.00 38.26 3.86
578 602 0.380378 CACCAACGTGTCCAACAAGG 59.620 55.000 0.00 0.00 35.10 3.61
590 614 1.263217 GAGGCACTTACAACACCAACG 59.737 52.381 0.00 0.00 41.55 4.10
622 646 0.515564 TTTAGAAACGAGGCGCTTGC 59.484 50.000 7.64 0.00 38.11 4.01
623 647 2.961522 TTTTAGAAACGAGGCGCTTG 57.038 45.000 7.64 0.00 0.00 4.01
658 688 7.903431 GGATTTTAGCAAAGTAAGTACATCACG 59.097 37.037 0.00 0.00 0.00 4.35
676 706 7.483375 TGCAACGTGAAAATATTCGGATTTTAG 59.517 33.333 0.00 3.24 38.76 1.85
696 726 4.319046 GGAATGTGAGTATATGCTGCAACG 60.319 45.833 6.36 0.00 0.00 4.10
863 896 4.518217 CATTGACACGAACACTGAGAAAC 58.482 43.478 0.00 0.00 0.00 2.78
870 903 1.841663 GCGCCATTGACACGAACACT 61.842 55.000 0.00 0.00 0.00 3.55
1200 1236 1.672356 GAACACCCTGCGAGCACAT 60.672 57.895 0.00 0.00 0.00 3.21
1386 1422 2.391724 GAAACAGGGCCACCGACTCA 62.392 60.000 6.18 0.00 43.47 3.41
1446 1482 4.452455 CACGACTTTAGAAGGACAGCAAAT 59.548 41.667 0.00 0.00 0.00 2.32
1506 1542 1.314534 CCTTCACCGCCAATGCATGA 61.315 55.000 0.00 0.00 37.32 3.07
1728 1764 4.066139 GGCTGGCTCACCCCCATT 62.066 66.667 0.00 0.00 33.59 3.16
1755 1791 2.197577 GCGCAGGATCTAAAGACACTC 58.802 52.381 0.30 0.00 0.00 3.51
1838 1874 4.255301 TGTCCCAACAATACGGTCAATAC 58.745 43.478 0.00 0.00 30.70 1.89
1841 1877 2.773487 CTGTCCCAACAATACGGTCAA 58.227 47.619 0.00 0.00 34.24 3.18
2031 2067 6.403866 AAACTGACTGCATCAAAACCAATA 57.596 33.333 0.00 0.00 36.69 1.90
2184 2220 4.797275 GCTTCTACCAATGCTTTGCACTTT 60.797 41.667 6.81 0.00 43.04 2.66
2303 2339 5.454554 CGCAGCATCTCATTAAAATGAACTG 59.545 40.000 6.82 11.44 44.20 3.16
2886 2922 1.747709 CTTCTGCTCCTTGACCATGG 58.252 55.000 11.19 11.19 0.00 3.66
3084 3120 4.831155 CCCTTTGACCGTCCTAGTATATCA 59.169 45.833 0.00 0.00 0.00 2.15
3242 3278 3.708631 TGAAGAATCCTCAGGATCCAGTC 59.291 47.826 15.82 0.18 42.27 3.51
3506 3542 3.815401 GTCAACCTCAGCAAAAGAAGCTA 59.185 43.478 0.00 0.00 41.14 3.32
3829 3867 1.750778 ACCAGCATAAATGGCGGAAAG 59.249 47.619 0.00 0.00 41.87 2.62
3877 3915 2.351111 GCACTTACTCTTCTGCTGCATC 59.649 50.000 1.31 0.00 0.00 3.91
3928 3966 4.443394 GCATCAGCAGCAGCAAATTATAAC 59.557 41.667 3.17 0.00 45.49 1.89
4076 4114 4.159506 TGGAAAGTTTGACTTCCCTTGTTG 59.840 41.667 0.00 0.00 37.47 3.33
4115 4153 3.492383 CACTGGATAATGCTTGCTAGACG 59.508 47.826 0.00 0.00 0.00 4.18
4116 4154 3.249559 GCACTGGATAATGCTTGCTAGAC 59.750 47.826 0.00 0.00 38.84 2.59
4117 4155 3.470709 GCACTGGATAATGCTTGCTAGA 58.529 45.455 0.00 0.00 38.84 2.43
4118 4156 3.892918 GCACTGGATAATGCTTGCTAG 57.107 47.619 0.00 0.00 38.84 3.42
4160 4199 5.163301 ACAGATGCACTAAACCGGATAGAAT 60.163 40.000 20.74 12.86 0.00 2.40
4163 4202 4.060038 ACAGATGCACTAAACCGGATAG 57.940 45.455 9.46 13.01 0.00 2.08
4198 4237 7.206981 ACTTCAATTTGTATGAACACTCAGG 57.793 36.000 0.00 0.00 34.61 3.86
4319 4358 3.259064 TGCGGCAAGAGTTCACTATAAC 58.741 45.455 0.00 0.00 0.00 1.89
4407 4446 0.603707 TCTTTCAAGCTCCGCCACTG 60.604 55.000 0.00 0.00 0.00 3.66
4408 4447 0.108585 TTCTTTCAAGCTCCGCCACT 59.891 50.000 0.00 0.00 0.00 4.00
4409 4448 0.951558 TTTCTTTCAAGCTCCGCCAC 59.048 50.000 0.00 0.00 0.00 5.01
4410 4449 1.686355 TTTTCTTTCAAGCTCCGCCA 58.314 45.000 0.00 0.00 0.00 5.69
4411 4450 2.029918 ACATTTTCTTTCAAGCTCCGCC 60.030 45.455 0.00 0.00 0.00 6.13
4412 4451 3.288809 ACATTTTCTTTCAAGCTCCGC 57.711 42.857 0.00 0.00 0.00 5.54
4413 4452 3.983344 CCAACATTTTCTTTCAAGCTCCG 59.017 43.478 0.00 0.00 0.00 4.63
4414 4453 4.309933 CCCAACATTTTCTTTCAAGCTCC 58.690 43.478 0.00 0.00 0.00 4.70
4415 4454 3.742882 GCCCAACATTTTCTTTCAAGCTC 59.257 43.478 0.00 0.00 0.00 4.09
4416 4455 3.732212 GCCCAACATTTTCTTTCAAGCT 58.268 40.909 0.00 0.00 0.00 3.74
4417 4456 2.476241 CGCCCAACATTTTCTTTCAAGC 59.524 45.455 0.00 0.00 0.00 4.01
4418 4457 3.059166 CCGCCCAACATTTTCTTTCAAG 58.941 45.455 0.00 0.00 0.00 3.02
4419 4458 2.224161 CCCGCCCAACATTTTCTTTCAA 60.224 45.455 0.00 0.00 0.00 2.69
4420 4459 1.342819 CCCGCCCAACATTTTCTTTCA 59.657 47.619 0.00 0.00 0.00 2.69
4421 4460 1.939381 GCCCGCCCAACATTTTCTTTC 60.939 52.381 0.00 0.00 0.00 2.62
4422 4461 0.034756 GCCCGCCCAACATTTTCTTT 59.965 50.000 0.00 0.00 0.00 2.52
4423 4462 1.671166 GCCCGCCCAACATTTTCTT 59.329 52.632 0.00 0.00 0.00 2.52
4424 4463 2.282783 GGCCCGCCCAACATTTTCT 61.283 57.895 0.00 0.00 0.00 2.52
4425 4464 2.264480 GGCCCGCCCAACATTTTC 59.736 61.111 0.00 0.00 0.00 2.29
4426 4465 2.525381 TGGCCCGCCCAACATTTT 60.525 55.556 0.00 0.00 41.82 1.82
4427 4466 2.996734 CTGGCCCGCCCAACATTT 60.997 61.111 0.00 0.00 44.81 2.32
4428 4467 3.978193 TCTGGCCCGCCCAACATT 61.978 61.111 0.00 0.00 44.81 2.71
4429 4468 4.740822 GTCTGGCCCGCCCAACAT 62.741 66.667 0.00 0.00 44.81 2.71
4431 4470 2.757980 TTTAGTCTGGCCCGCCCAAC 62.758 60.000 0.00 1.39 44.81 3.77
4432 4471 2.478335 CTTTAGTCTGGCCCGCCCAA 62.478 60.000 0.00 0.00 44.81 4.12
4433 4472 2.931105 TTTAGTCTGGCCCGCCCA 60.931 61.111 0.00 0.00 42.79 5.36
4434 4473 2.124695 CTTTAGTCTGGCCCGCCC 60.125 66.667 0.00 0.00 34.56 6.13
4435 4474 0.744771 CTTCTTTAGTCTGGCCCGCC 60.745 60.000 0.00 0.00 0.00 6.13
4436 4475 0.249398 TCTTCTTTAGTCTGGCCCGC 59.751 55.000 0.00 0.00 0.00 6.13
4437 4476 1.740718 GCTCTTCTTTAGTCTGGCCCG 60.741 57.143 0.00 0.00 0.00 6.13
4438 4477 1.279271 TGCTCTTCTTTAGTCTGGCCC 59.721 52.381 0.00 0.00 0.00 5.80
4439 4478 2.770164 TGCTCTTCTTTAGTCTGGCC 57.230 50.000 0.00 0.00 0.00 5.36
4440 4479 3.866651 TCATGCTCTTCTTTAGTCTGGC 58.133 45.455 0.00 0.00 0.00 4.85
4441 4480 6.822676 AGAAATCATGCTCTTCTTTAGTCTGG 59.177 38.462 0.00 0.00 0.00 3.86
4442 4481 7.846644 AGAAATCATGCTCTTCTTTAGTCTG 57.153 36.000 0.00 0.00 0.00 3.51
4443 4482 8.860780 AAAGAAATCATGCTCTTCTTTAGTCT 57.139 30.769 19.30 4.50 43.91 3.24
4444 4483 9.905171 AAAAAGAAATCATGCTCTTCTTTAGTC 57.095 29.630 20.26 0.00 44.59 2.59
4445 4484 9.688592 CAAAAAGAAATCATGCTCTTCTTTAGT 57.311 29.630 20.26 13.28 44.59 2.24
4446 4485 9.903682 TCAAAAAGAAATCATGCTCTTCTTTAG 57.096 29.630 20.26 17.15 44.59 1.85
4448 4487 9.603921 TTTCAAAAAGAAATCATGCTCTTCTTT 57.396 25.926 16.88 16.88 46.32 2.52
4483 4522 7.756722 GCATCTTGTAAACTTGCATCAAATACT 59.243 33.333 0.00 0.00 33.58 2.12
4484 4523 7.541783 TGCATCTTGTAAACTTGCATCAAATAC 59.458 33.333 0.00 0.00 38.32 1.89
4485 4524 7.600960 TGCATCTTGTAAACTTGCATCAAATA 58.399 30.769 0.00 0.00 38.32 1.40
4486 4525 6.457355 TGCATCTTGTAAACTTGCATCAAAT 58.543 32.000 0.00 0.00 38.32 2.32
4487 4526 5.840715 TGCATCTTGTAAACTTGCATCAAA 58.159 33.333 0.00 0.00 38.32 2.69
4488 4527 5.450592 TGCATCTTGTAAACTTGCATCAA 57.549 34.783 0.00 0.00 38.32 2.57
4489 4528 4.616604 GCTGCATCTTGTAAACTTGCATCA 60.617 41.667 0.00 0.00 41.95 3.07
4490 4529 3.855950 GCTGCATCTTGTAAACTTGCATC 59.144 43.478 0.00 0.00 41.95 3.91
4491 4530 3.256383 TGCTGCATCTTGTAAACTTGCAT 59.744 39.130 0.00 0.00 41.95 3.96
4492 4531 2.622470 TGCTGCATCTTGTAAACTTGCA 59.378 40.909 0.00 0.00 40.73 4.08
4493 4532 3.287312 TGCTGCATCTTGTAAACTTGC 57.713 42.857 0.00 0.00 0.00 4.01
4494 4533 3.671928 GCTTGCTGCATCTTGTAAACTTG 59.328 43.478 1.84 0.00 42.31 3.16
4495 4534 3.905784 GCTTGCTGCATCTTGTAAACTT 58.094 40.909 1.84 0.00 42.31 2.66
4496 4535 3.565905 GCTTGCTGCATCTTGTAAACT 57.434 42.857 1.84 0.00 42.31 2.66
4508 4547 7.119699 TGTGTTCCTTATATATATGCTTGCTGC 59.880 37.037 5.44 0.00 43.25 5.25
4509 4548 8.446273 GTGTGTTCCTTATATATATGCTTGCTG 58.554 37.037 5.44 0.00 0.00 4.41
4510 4549 8.156820 TGTGTGTTCCTTATATATATGCTTGCT 58.843 33.333 5.44 0.00 0.00 3.91
4511 4550 8.230486 GTGTGTGTTCCTTATATATATGCTTGC 58.770 37.037 5.44 0.00 0.00 4.01
4512 4551 8.435430 CGTGTGTGTTCCTTATATATATGCTTG 58.565 37.037 5.44 0.00 0.00 4.01
4513 4552 7.117812 GCGTGTGTGTTCCTTATATATATGCTT 59.882 37.037 5.44 0.00 0.00 3.91
4514 4553 6.590292 GCGTGTGTGTTCCTTATATATATGCT 59.410 38.462 5.44 0.00 0.00 3.79
4515 4554 6.367695 TGCGTGTGTGTTCCTTATATATATGC 59.632 38.462 5.44 0.00 0.00 3.14
4516 4555 7.148639 GGTGCGTGTGTGTTCCTTATATATATG 60.149 40.741 5.44 0.00 0.00 1.78
4517 4556 6.872020 GGTGCGTGTGTGTTCCTTATATATAT 59.128 38.462 0.00 0.00 0.00 0.86
4518 4557 6.218019 GGTGCGTGTGTGTTCCTTATATATA 58.782 40.000 0.00 0.00 0.00 0.86
4519 4558 5.054477 GGTGCGTGTGTGTTCCTTATATAT 58.946 41.667 0.00 0.00 0.00 0.86
4520 4559 4.435425 GGTGCGTGTGTGTTCCTTATATA 58.565 43.478 0.00 0.00 0.00 0.86
4521 4560 3.267483 GGTGCGTGTGTGTTCCTTATAT 58.733 45.455 0.00 0.00 0.00 0.86
4522 4561 2.613474 GGGTGCGTGTGTGTTCCTTATA 60.613 50.000 0.00 0.00 0.00 0.98
4523 4562 1.519408 GGTGCGTGTGTGTTCCTTAT 58.481 50.000 0.00 0.00 0.00 1.73
4524 4563 0.533308 GGGTGCGTGTGTGTTCCTTA 60.533 55.000 0.00 0.00 0.00 2.69
4525 4564 1.822186 GGGTGCGTGTGTGTTCCTT 60.822 57.895 0.00 0.00 0.00 3.36
4526 4565 2.203153 GGGTGCGTGTGTGTTCCT 60.203 61.111 0.00 0.00 0.00 3.36
4527 4566 3.284449 GGGGTGCGTGTGTGTTCC 61.284 66.667 0.00 0.00 0.00 3.62
4528 4567 1.658686 TTTGGGGTGCGTGTGTGTTC 61.659 55.000 0.00 0.00 0.00 3.18
4529 4568 1.251527 TTTTGGGGTGCGTGTGTGTT 61.252 50.000 0.00 0.00 0.00 3.32
4530 4569 1.040339 ATTTTGGGGTGCGTGTGTGT 61.040 50.000 0.00 0.00 0.00 3.72
4531 4570 0.955178 TATTTTGGGGTGCGTGTGTG 59.045 50.000 0.00 0.00 0.00 3.82
4532 4571 0.955905 GTATTTTGGGGTGCGTGTGT 59.044 50.000 0.00 0.00 0.00 3.72
4533 4572 0.955178 TGTATTTTGGGGTGCGTGTG 59.045 50.000 0.00 0.00 0.00 3.82
4534 4573 1.243902 CTGTATTTTGGGGTGCGTGT 58.756 50.000 0.00 0.00 0.00 4.49
4535 4574 1.243902 ACTGTATTTTGGGGTGCGTG 58.756 50.000 0.00 0.00 0.00 5.34
4536 4575 1.883926 GAACTGTATTTTGGGGTGCGT 59.116 47.619 0.00 0.00 0.00 5.24
4537 4576 1.883275 TGAACTGTATTTTGGGGTGCG 59.117 47.619 0.00 0.00 0.00 5.34
4538 4577 3.554129 GGTTGAACTGTATTTTGGGGTGC 60.554 47.826 0.00 0.00 0.00 5.01
4539 4578 3.639094 TGGTTGAACTGTATTTTGGGGTG 59.361 43.478 0.00 0.00 0.00 4.61
4540 4579 3.917300 TGGTTGAACTGTATTTTGGGGT 58.083 40.909 0.00 0.00 0.00 4.95
4541 4580 6.597832 TTATGGTTGAACTGTATTTTGGGG 57.402 37.500 0.00 0.00 0.00 4.96
4542 4581 6.589907 GCTTTATGGTTGAACTGTATTTTGGG 59.410 38.462 0.00 0.00 0.00 4.12
4543 4582 7.116233 GTGCTTTATGGTTGAACTGTATTTTGG 59.884 37.037 0.00 0.00 0.00 3.28
4544 4583 7.116233 GGTGCTTTATGGTTGAACTGTATTTTG 59.884 37.037 0.00 0.00 0.00 2.44
4545 4584 7.151976 GGTGCTTTATGGTTGAACTGTATTTT 58.848 34.615 0.00 0.00 0.00 1.82
4546 4585 6.266558 TGGTGCTTTATGGTTGAACTGTATTT 59.733 34.615 0.00 0.00 0.00 1.40
4547 4586 5.772672 TGGTGCTTTATGGTTGAACTGTATT 59.227 36.000 0.00 0.00 0.00 1.89
4548 4587 5.321102 TGGTGCTTTATGGTTGAACTGTAT 58.679 37.500 0.00 0.00 0.00 2.29
4549 4588 4.720046 TGGTGCTTTATGGTTGAACTGTA 58.280 39.130 0.00 0.00 0.00 2.74
4550 4589 3.561143 TGGTGCTTTATGGTTGAACTGT 58.439 40.909 0.00 0.00 0.00 3.55
4551 4590 4.789012 ATGGTGCTTTATGGTTGAACTG 57.211 40.909 0.00 0.00 0.00 3.16
4552 4591 6.493458 ACTTAATGGTGCTTTATGGTTGAACT 59.507 34.615 0.00 0.00 0.00 3.01
4553 4592 6.687604 ACTTAATGGTGCTTTATGGTTGAAC 58.312 36.000 0.00 0.00 0.00 3.18
4554 4593 6.909550 ACTTAATGGTGCTTTATGGTTGAA 57.090 33.333 0.00 0.00 0.00 2.69
4555 4594 6.909550 AACTTAATGGTGCTTTATGGTTGA 57.090 33.333 0.00 0.00 0.00 3.18
4556 4595 6.751888 GCTAACTTAATGGTGCTTTATGGTTG 59.248 38.462 0.00 0.00 0.00 3.77
4557 4596 6.663523 AGCTAACTTAATGGTGCTTTATGGTT 59.336 34.615 0.00 0.00 0.00 3.67
4558 4597 6.187682 AGCTAACTTAATGGTGCTTTATGGT 58.812 36.000 0.00 0.00 0.00 3.55
4559 4598 6.699575 AGCTAACTTAATGGTGCTTTATGG 57.300 37.500 0.00 0.00 0.00 2.74
4562 4601 9.456147 TGAATTAGCTAACTTAATGGTGCTTTA 57.544 29.630 8.70 0.00 32.72 1.85
4563 4602 8.348285 TGAATTAGCTAACTTAATGGTGCTTT 57.652 30.769 8.70 0.00 32.72 3.51
4564 4603 7.938140 TGAATTAGCTAACTTAATGGTGCTT 57.062 32.000 8.70 0.00 32.72 3.91
4565 4604 7.415653 GCTTGAATTAGCTAACTTAATGGTGCT 60.416 37.037 8.70 0.00 38.15 4.40
4566 4605 6.693113 GCTTGAATTAGCTAACTTAATGGTGC 59.307 38.462 8.70 0.00 38.15 5.01
4567 4606 7.148086 TGGCTTGAATTAGCTAACTTAATGGTG 60.148 37.037 8.70 0.00 40.99 4.17
4568 4607 6.889722 TGGCTTGAATTAGCTAACTTAATGGT 59.110 34.615 8.70 0.00 40.99 3.55
4569 4608 7.333528 TGGCTTGAATTAGCTAACTTAATGG 57.666 36.000 8.70 0.00 40.99 3.16
4570 4609 7.420800 CCTGGCTTGAATTAGCTAACTTAATG 58.579 38.462 8.70 2.35 40.99 1.90
4571 4610 6.547510 CCCTGGCTTGAATTAGCTAACTTAAT 59.452 38.462 8.70 0.00 40.99 1.40
4572 4611 5.885912 CCCTGGCTTGAATTAGCTAACTTAA 59.114 40.000 8.70 0.00 40.99 1.85
4573 4612 5.190925 TCCCTGGCTTGAATTAGCTAACTTA 59.809 40.000 8.70 0.00 40.99 2.24
4574 4613 4.018415 TCCCTGGCTTGAATTAGCTAACTT 60.018 41.667 8.70 4.69 40.99 2.66
4575 4614 3.523564 TCCCTGGCTTGAATTAGCTAACT 59.476 43.478 8.70 0.00 40.99 2.24
4576 4615 3.886123 TCCCTGGCTTGAATTAGCTAAC 58.114 45.455 8.70 0.00 40.99 2.34
4577 4616 4.584638 TTCCCTGGCTTGAATTAGCTAA 57.415 40.909 8.99 8.99 40.99 3.09
4578 4617 4.584638 TTTCCCTGGCTTGAATTAGCTA 57.415 40.909 0.44 0.00 40.99 3.32
4579 4618 3.456380 TTTCCCTGGCTTGAATTAGCT 57.544 42.857 0.00 0.00 40.99 3.32
4580 4619 4.644685 TGTATTTCCCTGGCTTGAATTAGC 59.355 41.667 0.00 0.00 40.48 3.09
4581 4620 6.239120 CCATGTATTTCCCTGGCTTGAATTAG 60.239 42.308 0.00 0.00 0.00 1.73
4582 4621 5.598005 CCATGTATTTCCCTGGCTTGAATTA 59.402 40.000 0.00 0.00 0.00 1.40
4583 4622 4.406649 CCATGTATTTCCCTGGCTTGAATT 59.593 41.667 0.00 0.00 0.00 2.17
4584 4623 3.962718 CCATGTATTTCCCTGGCTTGAAT 59.037 43.478 0.00 0.00 0.00 2.57
4585 4624 3.245586 ACCATGTATTTCCCTGGCTTGAA 60.246 43.478 0.00 0.00 31.72 2.69
4586 4625 2.311542 ACCATGTATTTCCCTGGCTTGA 59.688 45.455 0.00 0.00 31.72 3.02
4587 4626 2.689983 GACCATGTATTTCCCTGGCTTG 59.310 50.000 0.00 0.00 31.72 4.01
4588 4627 2.582636 AGACCATGTATTTCCCTGGCTT 59.417 45.455 0.00 0.00 31.72 4.35
4589 4628 2.208872 AGACCATGTATTTCCCTGGCT 58.791 47.619 0.00 0.00 31.72 4.75
4590 4629 2.736670 AGACCATGTATTTCCCTGGC 57.263 50.000 0.00 0.00 31.72 4.85
4591 4630 3.203040 AGGAAGACCATGTATTTCCCTGG 59.797 47.826 12.95 0.00 39.91 4.45
4592 4631 4.080356 TGAGGAAGACCATGTATTTCCCTG 60.080 45.833 12.95 0.00 39.91 4.45
4593 4632 4.111577 TGAGGAAGACCATGTATTTCCCT 58.888 43.478 12.95 3.48 39.91 4.20
4594 4633 4.503714 TGAGGAAGACCATGTATTTCCC 57.496 45.455 12.95 7.69 39.91 3.97
4595 4634 5.501156 AGTTGAGGAAGACCATGTATTTCC 58.499 41.667 9.98 9.98 39.47 3.13
4596 4635 6.655003 TGAAGTTGAGGAAGACCATGTATTTC 59.345 38.462 0.00 0.00 38.94 2.17
4597 4636 6.431234 GTGAAGTTGAGGAAGACCATGTATTT 59.569 38.462 0.00 0.00 38.94 1.40
4598 4637 5.940470 GTGAAGTTGAGGAAGACCATGTATT 59.060 40.000 0.00 0.00 38.94 1.89
4599 4638 5.249393 AGTGAAGTTGAGGAAGACCATGTAT 59.751 40.000 0.00 0.00 38.94 2.29
4600 4639 4.593206 AGTGAAGTTGAGGAAGACCATGTA 59.407 41.667 0.00 0.00 38.94 2.29
4601 4640 3.392616 AGTGAAGTTGAGGAAGACCATGT 59.607 43.478 0.00 0.00 38.94 3.21
4602 4641 4.013267 AGTGAAGTTGAGGAAGACCATG 57.987 45.455 0.00 0.00 38.94 3.66
4603 4642 4.141390 ACAAGTGAAGTTGAGGAAGACCAT 60.141 41.667 4.90 0.00 38.94 3.55
4604 4643 3.199946 ACAAGTGAAGTTGAGGAAGACCA 59.800 43.478 4.90 0.00 38.94 4.02
4605 4644 3.561725 CACAAGTGAAGTTGAGGAAGACC 59.438 47.826 4.90 0.00 0.00 3.85
4606 4645 4.192317 ACACAAGTGAAGTTGAGGAAGAC 58.808 43.478 7.28 0.00 0.00 3.01
4607 4646 4.081142 TGACACAAGTGAAGTTGAGGAAGA 60.081 41.667 7.28 0.00 0.00 2.87
4608 4647 4.191544 TGACACAAGTGAAGTTGAGGAAG 58.808 43.478 7.28 0.00 0.00 3.46
4609 4648 4.214986 TGACACAAGTGAAGTTGAGGAA 57.785 40.909 7.28 0.00 0.00 3.36
4610 4649 3.904800 TGACACAAGTGAAGTTGAGGA 57.095 42.857 7.28 0.00 0.00 3.71
4611 4650 4.384056 AGATGACACAAGTGAAGTTGAGG 58.616 43.478 7.28 0.03 0.00 3.86
4612 4651 5.052481 TGAGATGACACAAGTGAAGTTGAG 58.948 41.667 7.28 0.00 0.00 3.02
4613 4652 5.022282 TGAGATGACACAAGTGAAGTTGA 57.978 39.130 7.28 0.00 0.00 3.18
4614 4653 5.936686 ATGAGATGACACAAGTGAAGTTG 57.063 39.130 7.28 0.00 0.00 3.16
4615 4654 6.016777 GGAAATGAGATGACACAAGTGAAGTT 60.017 38.462 7.28 0.00 0.00 2.66
4616 4655 5.471456 GGAAATGAGATGACACAAGTGAAGT 59.529 40.000 7.28 0.00 0.00 3.01
4617 4656 5.704515 AGGAAATGAGATGACACAAGTGAAG 59.295 40.000 7.28 0.00 0.00 3.02
4618 4657 5.624159 AGGAAATGAGATGACACAAGTGAA 58.376 37.500 7.28 0.00 0.00 3.18
4619 4658 5.233083 AGGAAATGAGATGACACAAGTGA 57.767 39.130 7.28 0.00 0.00 3.41
4620 4659 5.954296 AAGGAAATGAGATGACACAAGTG 57.046 39.130 0.00 0.00 0.00 3.16
4621 4660 6.966534 AAAAGGAAATGAGATGACACAAGT 57.033 33.333 0.00 0.00 0.00 3.16
4622 4661 9.918630 ATTTAAAAGGAAATGAGATGACACAAG 57.081 29.630 0.00 0.00 0.00 3.16
4625 4664 9.788960 GGTATTTAAAAGGAAATGAGATGACAC 57.211 33.333 0.00 0.00 31.51 3.67
4626 4665 9.527157 TGGTATTTAAAAGGAAATGAGATGACA 57.473 29.630 0.00 0.00 31.51 3.58
4630 4669 9.875691 GCTTTGGTATTTAAAAGGAAATGAGAT 57.124 29.630 0.00 0.00 34.60 2.75
4631 4670 8.865090 TGCTTTGGTATTTAAAAGGAAATGAGA 58.135 29.630 0.00 0.00 34.60 3.27
4632 4671 9.143631 CTGCTTTGGTATTTAAAAGGAAATGAG 57.856 33.333 0.00 0.00 33.99 2.90
4633 4672 8.646900 ACTGCTTTGGTATTTAAAAGGAAATGA 58.353 29.630 0.00 0.00 33.99 2.57
4634 4673 8.831715 ACTGCTTTGGTATTTAAAAGGAAATG 57.168 30.769 0.00 0.00 33.99 2.32
4635 4674 9.489084 GAACTGCTTTGGTATTTAAAAGGAAAT 57.511 29.630 0.00 0.00 33.99 2.17
4636 4675 8.880878 GAACTGCTTTGGTATTTAAAAGGAAA 57.119 30.769 0.00 0.00 33.99 3.13


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

AutoCloner maintained by Alex Coulton.