Multiple sequence alignment - TraesCS5A01G434500

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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 TraesCS5A01G434500 chr5A 100.000 4166 0 0 970 5135 617358253 617362418 0.000000e+00 7694.0
1 TraesCS5A01G434500 chr5A 100.000 623 0 0 1 623 617357284 617357906 0.000000e+00 1151.0
2 TraesCS5A01G434500 chr5A 77.949 390 48 20 4020 4393 618433647 618434014 5.210000e-50 209.0
3 TraesCS5A01G434500 chr5A 95.876 97 2 2 4591 4686 580273571 580273666 6.880000e-34 156.0
4 TraesCS5A01G434500 chr5A 95.699 93 2 2 4601 4693 332947291 332947201 1.150000e-31 148.0
5 TraesCS5A01G434500 chr5A 95.699 93 3 1 4598 4690 612226749 612226840 1.150000e-31 148.0
6 TraesCS5A01G434500 chr5A 87.838 74 9 0 1314 1387 122377447 122377520 2.550000e-13 87.9
7 TraesCS5A01G434500 chr5B 92.371 1809 75 29 1004 2776 610689669 610691450 0.000000e+00 2518.0
8 TraesCS5A01G434500 chr5B 93.253 1082 43 9 3335 4403 610692030 610693094 0.000000e+00 1567.0
9 TraesCS5A01G434500 chr5B 93.204 515 29 5 2822 3336 610691467 610691975 0.000000e+00 752.0
10 TraesCS5A01G434500 chr5B 86.090 647 40 25 1 623 610688567 610689187 0.000000e+00 651.0
11 TraesCS5A01G434500 chr5B 80.319 188 24 7 4064 4251 610924191 610924365 4.170000e-26 130.0
12 TraesCS5A01G434500 chr5D 95.095 1101 29 8 1011 2101 494469726 494470811 0.000000e+00 1711.0
13 TraesCS5A01G434500 chr5D 91.997 1237 42 18 2127 3335 494471044 494472251 0.000000e+00 1683.0
14 TraesCS5A01G434500 chr5D 94.958 1071 38 6 3334 4403 494472311 494473366 0.000000e+00 1664.0
15 TraesCS5A01G434500 chr5D 88.287 572 30 21 1 554 494468712 494469264 0.000000e+00 651.0
16 TraesCS5A01G434500 chr5D 89.790 333 12 12 4684 5008 494473719 494474037 1.720000e-109 407.0
17 TraesCS5A01G434500 chr5D 88.021 192 9 5 4410 4600 494473543 494473721 1.120000e-51 215.0
18 TraesCS5A01G434500 chr5D 93.243 74 0 3 555 623 494469288 494469361 2.530000e-18 104.0
19 TraesCS5A01G434500 chr7A 97.778 90 2 0 4597 4686 301100420 301100509 6.880000e-34 156.0
20 TraesCS5A01G434500 chr7A 90.826 109 7 3 4586 4692 420669809 420669916 5.360000e-30 143.0
21 TraesCS5A01G434500 chr3B 97.727 88 2 0 4598 4685 820469691 820469778 8.910000e-33 152.0
22 TraesCS5A01G434500 chr3B 95.506 89 4 0 4598 4686 622768714 622768802 5.360000e-30 143.0
23 TraesCS5A01G434500 chr2A 95.604 91 4 0 4596 4686 127212228 127212318 4.140000e-31 147.0
24 TraesCS5A01G434500 chr7D 91.346 104 7 2 4594 4697 94261221 94261322 1.930000e-29 141.0


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 TraesCS5A01G434500 chr5A 617357284 617362418 5134 False 4422.500000 7694 100.000000 1 5135 2 chr5A.!!$F5 5134
1 TraesCS5A01G434500 chr5B 610688567 610693094 4527 False 1372.000000 2518 91.229500 1 4403 4 chr5B.!!$F2 4402
2 TraesCS5A01G434500 chr5D 494468712 494474037 5325 False 919.285714 1711 91.627286 1 5008 7 chr5D.!!$F1 5007

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
147 153 0.037697 CAGTGCGCTGGTTAGTGGTA 60.038 55.000 19.78 0.0 39.01 3.25 F
148 154 0.246635 AGTGCGCTGGTTAGTGGTAG 59.753 55.000 9.73 0.0 34.97 3.18 F
308 337 0.555769 AGGTTGGTGGGCAGAAAGAA 59.444 50.000 0.00 0.0 0.00 2.52 F
472 505 1.069535 TTTCCTCCCCCGGAAAACCT 61.070 55.000 0.73 0.0 46.92 3.50 F
2397 3117 1.001641 GGTGCCTCAGTGATTGCCT 60.002 57.895 11.12 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 2598 1.313812 CCTCCTGAGCGAACCGTAGT 61.314 60.000 0.0 0.00 0.00 2.73 R
2103 2599 1.433879 CCTCCTGAGCGAACCGTAG 59.566 63.158 0.0 0.00 0.00 3.51 R
2196 2907 1.870402 CAAACATCGCTACACCACACA 59.130 47.619 0.0 0.00 0.00 3.72 R
2401 3121 1.688811 GTACTTGGTGGCCCATCCA 59.311 57.895 0.0 3.45 41.49 3.41 R
4354 5168 0.033208 AATGACCAACGCCCCATCAT 60.033 50.000 0.0 0.00 0.00 2.45 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
22 24 2.833604 AATCTGCCTCCTGCTGGTGC 62.834 60.000 9.73 13.55 42.00 5.01
120 126 2.260743 GGACGTCGGTGGGACTTC 59.739 66.667 9.92 0.00 43.79 3.01
121 127 2.260743 GACGTCGGTGGGACTTCC 59.739 66.667 0.00 0.00 43.79 3.46
146 152 1.301716 CAGTGCGCTGGTTAGTGGT 60.302 57.895 19.78 0.00 39.01 4.16
147 153 0.037697 CAGTGCGCTGGTTAGTGGTA 60.038 55.000 19.78 0.00 39.01 3.25
148 154 0.246635 AGTGCGCTGGTTAGTGGTAG 59.753 55.000 9.73 0.00 34.97 3.18
149 155 0.739813 GTGCGCTGGTTAGTGGTAGG 60.740 60.000 9.73 0.00 34.97 3.18
163 172 1.202964 TGGTAGGAGTCGTCAGTGGAA 60.203 52.381 0.00 0.00 0.00 3.53
216 225 8.900781 AGTACTACAGCGAAATCAGAATTAGTA 58.099 33.333 0.00 0.00 0.00 1.82
217 226 7.988904 ACTACAGCGAAATCAGAATTAGTAC 57.011 36.000 0.00 0.00 0.00 2.73
218 227 6.979238 ACTACAGCGAAATCAGAATTAGTACC 59.021 38.462 0.00 0.00 0.00 3.34
219 228 5.730550 ACAGCGAAATCAGAATTAGTACCA 58.269 37.500 0.00 0.00 0.00 3.25
220 229 5.812642 ACAGCGAAATCAGAATTAGTACCAG 59.187 40.000 0.00 0.00 0.00 4.00
221 230 5.812642 CAGCGAAATCAGAATTAGTACCAGT 59.187 40.000 0.00 0.00 0.00 4.00
222 231 6.313905 CAGCGAAATCAGAATTAGTACCAGTT 59.686 38.462 0.00 0.00 0.00 3.16
236 247 8.726870 TTAGTACCAGTTTTAGCATATCCAAC 57.273 34.615 0.00 0.00 0.00 3.77
264 285 7.127339 ACAAGTTCAAGGGATTATTAGGCTAGA 59.873 37.037 0.00 0.00 0.00 2.43
305 334 1.707989 TGATAGGTTGGTGGGCAGAAA 59.292 47.619 0.00 0.00 0.00 2.52
306 335 2.290896 TGATAGGTTGGTGGGCAGAAAG 60.291 50.000 0.00 0.00 0.00 2.62
307 336 1.440618 TAGGTTGGTGGGCAGAAAGA 58.559 50.000 0.00 0.00 0.00 2.52
308 337 0.555769 AGGTTGGTGGGCAGAAAGAA 59.444 50.000 0.00 0.00 0.00 2.52
321 350 4.467735 GCAGAAAGAAAGCCTAGAAAACG 58.532 43.478 0.00 0.00 0.00 3.60
404 437 3.435186 GTGCTCCTCCGCAAAGGC 61.435 66.667 0.00 0.00 42.32 4.35
472 505 1.069535 TTTCCTCCCCCGGAAAACCT 61.070 55.000 0.73 0.00 46.92 3.50
998 1067 2.440247 CCCCATCGCAAACTCCCC 60.440 66.667 0.00 0.00 0.00 4.81
999 1068 2.440247 CCCATCGCAAACTCCCCC 60.440 66.667 0.00 0.00 0.00 5.40
1039 1514 3.631046 GATCCCCGCCCAGCTAGG 61.631 72.222 0.00 0.00 37.03 3.02
1781 2266 3.382832 CGCCGAGTGGAAGGAGGT 61.383 66.667 0.00 0.00 37.49 3.85
1982 2467 6.441222 AGGATGACATGGAAGGTAGTACTTA 58.559 40.000 0.00 0.00 0.00 2.24
2101 2597 3.887621 TCCAGCGTTTAGATGCTACTT 57.112 42.857 0.00 0.00 46.23 2.24
2102 2598 4.994907 TCCAGCGTTTAGATGCTACTTA 57.005 40.909 0.00 0.00 46.23 2.24
2103 2599 4.679662 TCCAGCGTTTAGATGCTACTTAC 58.320 43.478 0.00 0.00 46.23 2.34
2111 2611 6.413235 CGTTTAGATGCTACTTACTACGGTTC 59.587 42.308 0.00 0.00 0.00 3.62
2119 2619 1.741706 CTTACTACGGTTCGCTCAGGA 59.258 52.381 0.00 0.00 0.00 3.86
2121 2621 1.313812 ACTACGGTTCGCTCAGGAGG 61.314 60.000 0.00 0.00 0.00 4.30
2185 2896 6.535508 AGCAAGTCTTATCGAACTGGTAATTC 59.464 38.462 0.00 0.00 0.00 2.17
2196 2907 5.296780 CGAACTGGTAATTCATAAGCCACAT 59.703 40.000 0.00 0.00 0.00 3.21
2303 3022 1.407618 TGTCACTGTCGTAGCAAGTGT 59.592 47.619 2.31 0.00 32.84 3.55
2397 3117 1.001641 GGTGCCTCAGTGATTGCCT 60.002 57.895 11.12 0.00 0.00 4.75
2401 3121 0.610232 GCCTCAGTGATTGCCTTGGT 60.610 55.000 0.00 0.00 0.00 3.67
2587 3311 1.971695 GGGTTGCTGTGGTGTAGCC 60.972 63.158 0.00 0.00 40.42 3.93
2777 3508 6.655078 AAAAATACATCAAGAGTGGTGCTT 57.345 33.333 0.00 0.00 39.73 3.91
2778 3509 6.655078 AAAATACATCAAGAGTGGTGCTTT 57.345 33.333 0.00 0.00 39.73 3.51
2779 3510 6.655078 AAATACATCAAGAGTGGTGCTTTT 57.345 33.333 0.00 0.00 39.73 2.27
2807 3538 8.050778 TCCGATAAAGTGTGATGCTTTTTATT 57.949 30.769 0.00 0.00 37.37 1.40
2808 3539 7.967854 TCCGATAAAGTGTGATGCTTTTTATTG 59.032 33.333 0.00 0.00 37.37 1.90
2816 3547 7.011189 GTGTGATGCTTTTTATTGAAACATGC 58.989 34.615 0.00 0.00 0.00 4.06
2851 3582 8.486210 TGTAATCTCAGTTATCCAGTAAATGCT 58.514 33.333 0.00 0.00 38.06 3.79
2852 3583 9.331282 GTAATCTCAGTTATCCAGTAAATGCTT 57.669 33.333 0.00 0.00 38.06 3.91
2919 3650 2.292569 CAGTTGGCCTGATCATGTATGC 59.707 50.000 3.32 0.00 44.49 3.14
2920 3651 1.265095 GTTGGCCTGATCATGTATGCG 59.735 52.381 3.32 0.00 0.00 4.73
2941 3672 1.926511 GCTGCTGGCGCTTTGTACAT 61.927 55.000 7.64 0.00 36.97 2.29
3081 3812 0.313672 TTGATGCCGTGAACTTTGCC 59.686 50.000 0.00 0.00 0.00 4.52
3138 3869 6.030082 AGTCCCTCTTTTGAAATCCTACCTA 58.970 40.000 0.00 0.00 0.00 3.08
3289 4029 6.352516 ACAGGGCTTTCTGAAAGATATACAG 58.647 40.000 29.14 15.13 46.36 2.74
3304 4044 6.789262 AGATATACAGATGTTTGCTTGTTGC 58.211 36.000 0.00 0.00 43.25 4.17
3382 4183 0.960364 TTGTGGCTTTGGCGAGGATC 60.960 55.000 0.00 0.00 39.81 3.36
3450 4251 4.377431 CGTCTCTTGTAGGTCAATGCAAAC 60.377 45.833 0.00 0.00 35.35 2.93
3637 4438 1.303561 AAGCGCATCAAAGGGAGCA 60.304 52.632 11.47 0.00 0.00 4.26
3639 4440 3.056313 GCGCATCAAAGGGAGCACC 62.056 63.158 0.30 0.00 40.67 5.01
3702 4503 2.040544 CACCGGTGCACCATCTTCC 61.041 63.158 34.16 6.96 35.14 3.46
3873 4674 1.159285 CATATGCATACCCACCTGCG 58.841 55.000 8.99 0.00 41.32 5.18
3940 4741 1.978580 CCATGACCTACCCCATCTACC 59.021 57.143 0.00 0.00 0.00 3.18
3942 4743 1.326055 TGACCTACCCCATCTACCCT 58.674 55.000 0.00 0.00 0.00 4.34
4051 4862 1.402968 CCAAATGACAAGAGCCGATGG 59.597 52.381 0.00 0.00 0.00 3.51
4140 4954 7.507733 ACGTCCTTAATACATCACTACTAGG 57.492 40.000 0.00 0.00 0.00 3.02
4189 5003 7.148306 CCGGTTATTAGCACTCATGTTTACTTT 60.148 37.037 0.00 0.00 0.00 2.66
4198 5012 4.449068 ACTCATGTTTACTTTCGCACTGAG 59.551 41.667 0.00 0.00 35.04 3.35
4219 5033 8.956426 ACTGAGAACTGAAAAACTGAATGTAAA 58.044 29.630 0.00 0.00 0.00 2.01
4220 5034 9.956720 CTGAGAACTGAAAAACTGAATGTAAAT 57.043 29.630 0.00 0.00 0.00 1.40
4262 5076 3.886505 TGTGGACCTTGTGTTGTAATTCC 59.113 43.478 0.00 0.00 0.00 3.01
4334 5148 7.664082 AATCCTCGAGCATTGACTATTAATG 57.336 36.000 6.99 0.00 38.30 1.90
4403 5217 3.628942 TCTGATTATTGCATCTGTGTGCC 59.371 43.478 0.00 0.00 44.43 5.01
4406 5220 1.753930 TATTGCATCTGTGTGCCTGG 58.246 50.000 0.00 0.00 44.43 4.45
4407 5221 1.601419 ATTGCATCTGTGTGCCTGGC 61.601 55.000 12.87 12.87 44.43 4.85
4408 5222 3.807538 GCATCTGTGTGCCTGGCG 61.808 66.667 14.98 0.00 39.18 5.69
4410 5224 1.968017 CATCTGTGTGCCTGGCGTT 60.968 57.895 14.98 0.00 0.00 4.84
4411 5225 0.673333 CATCTGTGTGCCTGGCGTTA 60.673 55.000 14.98 0.00 0.00 3.18
4412 5226 0.391661 ATCTGTGTGCCTGGCGTTAG 60.392 55.000 14.98 9.67 0.00 2.34
4413 5227 1.301716 CTGTGTGCCTGGCGTTAGT 60.302 57.895 14.98 0.00 0.00 2.24
4414 5228 1.568612 CTGTGTGCCTGGCGTTAGTG 61.569 60.000 14.98 0.00 0.00 2.74
4426 5410 3.570550 TGGCGTTAGTGGTTATGCTTTTT 59.429 39.130 0.00 0.00 0.00 1.94
4427 5411 4.163552 GGCGTTAGTGGTTATGCTTTTTC 58.836 43.478 0.00 0.00 0.00 2.29
4469 5453 7.919690 TGCTATTTATTCAAAGACATCGGAAG 58.080 34.615 0.00 0.00 0.00 3.46
4478 5462 2.950781 AGACATCGGAAGCCTCTGATA 58.049 47.619 6.32 0.00 44.49 2.15
4493 5477 5.528690 GCCTCTGATACAATAATGTGCAGAA 59.471 40.000 15.04 4.79 44.43 3.02
4496 5480 8.715998 CCTCTGATACAATAATGTGCAGAATAC 58.284 37.037 15.04 0.00 44.43 1.89
4497 5481 9.264719 CTCTGATACAATAATGTGCAGAATACA 57.735 33.333 15.04 0.00 44.43 2.29
4498 5482 9.612066 TCTGATACAATAATGTGCAGAATACAA 57.388 29.630 12.98 0.00 43.32 2.41
4501 5485 9.831737 GATACAATAATGTGCAGAATACAATCC 57.168 33.333 0.00 0.00 40.84 3.01
4502 5486 6.728200 ACAATAATGTGCAGAATACAATCCG 58.272 36.000 0.00 0.00 38.69 4.18
4503 5487 5.947228 ATAATGTGCAGAATACAATCCGG 57.053 39.130 0.00 0.00 0.00 5.14
4504 5488 2.779755 TGTGCAGAATACAATCCGGT 57.220 45.000 0.00 0.00 0.00 5.28
4505 5489 2.355197 TGTGCAGAATACAATCCGGTG 58.645 47.619 0.00 0.00 0.00 4.94
4506 5490 1.670811 GTGCAGAATACAATCCGGTGG 59.329 52.381 0.00 0.00 0.00 4.61
4507 5491 1.557371 TGCAGAATACAATCCGGTGGA 59.443 47.619 0.00 0.00 35.55 4.02
4508 5492 1.940613 GCAGAATACAATCCGGTGGAC 59.059 52.381 0.00 0.00 32.98 4.02
4573 5558 2.292569 AGTCAAAACATGAGCAGCACTG 59.707 45.455 0.00 0.00 39.19 3.66
4574 5559 2.033801 GTCAAAACATGAGCAGCACTGT 59.966 45.455 0.00 0.00 39.19 3.55
4576 5561 2.787601 AAACATGAGCAGCACTGTTG 57.212 45.000 0.00 0.00 32.44 3.33
4597 5582 0.392193 CTGTTCGATGAGCCCAGCTT 60.392 55.000 0.00 0.00 39.88 3.74
4598 5583 0.901827 TGTTCGATGAGCCCAGCTTA 59.098 50.000 0.00 0.00 39.88 3.09
4599 5584 1.291132 GTTCGATGAGCCCAGCTTAC 58.709 55.000 0.00 0.00 39.88 2.34
4600 5585 1.134670 GTTCGATGAGCCCAGCTTACT 60.135 52.381 0.00 0.00 39.88 2.24
4601 5586 2.067365 TCGATGAGCCCAGCTTACTA 57.933 50.000 0.00 0.00 39.88 1.82
4602 5587 1.681793 TCGATGAGCCCAGCTTACTAC 59.318 52.381 0.00 0.00 39.88 2.73
4603 5588 1.683917 CGATGAGCCCAGCTTACTACT 59.316 52.381 0.00 0.00 39.88 2.57
4604 5589 2.287909 CGATGAGCCCAGCTTACTACTC 60.288 54.545 0.00 0.00 39.88 2.59
4605 5590 1.486211 TGAGCCCAGCTTACTACTCC 58.514 55.000 0.00 0.00 39.88 3.85
4606 5591 0.753867 GAGCCCAGCTTACTACTCCC 59.246 60.000 0.00 0.00 39.88 4.30
4607 5592 0.340208 AGCCCAGCTTACTACTCCCT 59.660 55.000 0.00 0.00 33.89 4.20
4608 5593 1.205055 GCCCAGCTTACTACTCCCTT 58.795 55.000 0.00 0.00 0.00 3.95
4609 5594 1.560146 GCCCAGCTTACTACTCCCTTT 59.440 52.381 0.00 0.00 0.00 3.11
4610 5595 2.681097 GCCCAGCTTACTACTCCCTTTG 60.681 54.545 0.00 0.00 0.00 2.77
4611 5596 2.572104 CCCAGCTTACTACTCCCTTTGT 59.428 50.000 0.00 0.00 0.00 2.83
4612 5597 3.773119 CCCAGCTTACTACTCCCTTTGTA 59.227 47.826 0.00 0.00 0.00 2.41
4613 5598 4.224370 CCCAGCTTACTACTCCCTTTGTAA 59.776 45.833 0.00 0.00 0.00 2.41
4614 5599 5.280317 CCCAGCTTACTACTCCCTTTGTAAA 60.280 44.000 0.00 0.00 0.00 2.01
4615 5600 5.642491 CCAGCTTACTACTCCCTTTGTAAAC 59.358 44.000 0.00 0.00 0.00 2.01
4616 5601 6.465084 CAGCTTACTACTCCCTTTGTAAACT 58.535 40.000 0.00 0.00 0.00 2.66
4617 5602 7.310237 CCAGCTTACTACTCCCTTTGTAAACTA 60.310 40.741 0.00 0.00 0.00 2.24
4618 5603 8.092687 CAGCTTACTACTCCCTTTGTAAACTAA 58.907 37.037 0.00 0.00 0.00 2.24
4619 5604 8.823794 AGCTTACTACTCCCTTTGTAAACTAAT 58.176 33.333 0.00 0.00 0.00 1.73
4679 5664 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
4680 5665 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
4681 5666 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
4682 5667 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
4744 5729 2.637382 TGATTAGTGTCCCAACAGCTGA 59.363 45.455 23.35 0.00 35.64 4.26
4754 5739 3.055094 TCCCAACAGCTGATAGGTTCTTC 60.055 47.826 23.35 0.00 0.00 2.87
4767 5752 0.799393 GTTCTTCCTCCTTGCTTCGC 59.201 55.000 0.00 0.00 0.00 4.70
4768 5753 0.396435 TTCTTCCTCCTTGCTTCGCA 59.604 50.000 0.00 0.00 36.47 5.10
4769 5754 0.036952 TCTTCCTCCTTGCTTCGCAG 60.037 55.000 0.00 0.00 40.61 5.18
4777 5762 2.867333 CTTGCTTCGCAGCCAGCATG 62.867 60.000 13.56 12.14 46.74 4.06
4803 5788 3.137728 ACCACCACCTTACAGTAAGCTTT 59.862 43.478 14.18 0.00 34.46 3.51
4816 5801 1.238439 AAGCTTTGACATGACCACCG 58.762 50.000 0.00 0.00 0.00 4.94
4821 5806 0.687920 TTGACATGACCACCGCCTTA 59.312 50.000 0.00 0.00 0.00 2.69
4825 5810 0.249120 CATGACCACCGCCTTACAGA 59.751 55.000 0.00 0.00 0.00 3.41
4828 5813 0.249398 GACCACCGCCTTACAGACAT 59.751 55.000 0.00 0.00 0.00 3.06
4830 5815 0.249120 CCACCGCCTTACAGACATGA 59.751 55.000 0.00 0.00 0.00 3.07
4831 5816 1.338674 CCACCGCCTTACAGACATGAA 60.339 52.381 0.00 0.00 0.00 2.57
4832 5817 2.002586 CACCGCCTTACAGACATGAAG 58.997 52.381 0.00 0.00 0.00 3.02
4833 5818 1.623811 ACCGCCTTACAGACATGAAGT 59.376 47.619 0.00 0.00 0.00 3.01
4896 5881 0.787787 CACGCCAGAATTTCGACGAA 59.212 50.000 6.10 6.10 0.00 3.85
4907 5892 3.653539 TTTCGACGAACTCCAGATTCA 57.346 42.857 10.38 0.00 0.00 2.57
4935 5920 2.225727 CCGGAAAGAAGTAACAAGCACC 59.774 50.000 0.00 0.00 0.00 5.01
4949 5934 2.657237 CACCTCCTCGGAAAGCGT 59.343 61.111 0.00 0.00 36.31 5.07
4965 5958 1.210413 CGTCGGTGTGGTCTCTGAG 59.790 63.158 0.00 0.00 0.00 3.35
5002 5995 4.704540 TCTCCTTTGTCAGCAAGTTTCAAA 59.295 37.500 0.00 0.00 35.82 2.69
5003 5996 4.997565 TCCTTTGTCAGCAAGTTTCAAAG 58.002 39.130 0.00 0.00 42.25 2.77
5004 5997 4.704540 TCCTTTGTCAGCAAGTTTCAAAGA 59.295 37.500 14.68 2.44 44.04 2.52
5005 5998 4.800471 CCTTTGTCAGCAAGTTTCAAAGAC 59.200 41.667 14.68 0.00 44.04 3.01
5006 5999 5.384063 TTTGTCAGCAAGTTTCAAAGACA 57.616 34.783 0.00 0.00 35.82 3.41
5007 6000 4.621068 TGTCAGCAAGTTTCAAAGACAG 57.379 40.909 0.00 0.00 31.63 3.51
5008 6001 4.009675 TGTCAGCAAGTTTCAAAGACAGT 58.990 39.130 0.00 0.00 31.63 3.55
5009 6002 4.094887 TGTCAGCAAGTTTCAAAGACAGTC 59.905 41.667 0.00 0.00 31.63 3.51
5010 6003 4.333926 GTCAGCAAGTTTCAAAGACAGTCT 59.666 41.667 0.00 0.00 0.00 3.24
5011 6004 4.572389 TCAGCAAGTTTCAAAGACAGTCTC 59.428 41.667 2.72 0.00 0.00 3.36
5012 6005 4.574013 CAGCAAGTTTCAAAGACAGTCTCT 59.426 41.667 2.72 0.00 0.00 3.10
5013 6006 4.813697 AGCAAGTTTCAAAGACAGTCTCTC 59.186 41.667 2.72 0.00 0.00 3.20
5014 6007 4.813697 GCAAGTTTCAAAGACAGTCTCTCT 59.186 41.667 2.72 0.00 0.00 3.10
5015 6008 5.050431 GCAAGTTTCAAAGACAGTCTCTCTC 60.050 44.000 2.72 0.00 0.00 3.20
5016 6009 6.279882 CAAGTTTCAAAGACAGTCTCTCTCT 58.720 40.000 2.72 0.00 0.00 3.10
5017 6010 6.084326 AGTTTCAAAGACAGTCTCTCTCTC 57.916 41.667 2.72 0.00 0.00 3.20
5018 6011 5.833131 AGTTTCAAAGACAGTCTCTCTCTCT 59.167 40.000 2.72 0.00 0.00 3.10
5019 6012 5.957842 TTCAAAGACAGTCTCTCTCTCTC 57.042 43.478 2.72 0.00 0.00 3.20
5020 6013 4.979335 TCAAAGACAGTCTCTCTCTCTCA 58.021 43.478 2.72 0.00 0.00 3.27
5021 6014 5.380900 TCAAAGACAGTCTCTCTCTCTCAA 58.619 41.667 2.72 0.00 0.00 3.02
5022 6015 5.830457 TCAAAGACAGTCTCTCTCTCTCAAA 59.170 40.000 2.72 0.00 0.00 2.69
5023 6016 6.322456 TCAAAGACAGTCTCTCTCTCTCAAAA 59.678 38.462 2.72 0.00 0.00 2.44
5024 6017 6.723298 AAGACAGTCTCTCTCTCTCAAAAA 57.277 37.500 2.72 0.00 0.00 1.94
5046 6039 3.978718 AGAGCAAGTTTCAAAGACAGC 57.021 42.857 0.00 0.00 0.00 4.40
5047 6040 2.620585 AGAGCAAGTTTCAAAGACAGCC 59.379 45.455 0.00 0.00 0.00 4.85
5048 6041 1.683385 AGCAAGTTTCAAAGACAGCCC 59.317 47.619 0.00 0.00 0.00 5.19
5049 6042 1.683385 GCAAGTTTCAAAGACAGCCCT 59.317 47.619 0.00 0.00 0.00 5.19
5050 6043 2.884639 GCAAGTTTCAAAGACAGCCCTA 59.115 45.455 0.00 0.00 0.00 3.53
5051 6044 3.507622 GCAAGTTTCAAAGACAGCCCTAT 59.492 43.478 0.00 0.00 0.00 2.57
5052 6045 4.379918 GCAAGTTTCAAAGACAGCCCTATC 60.380 45.833 0.00 0.00 0.00 2.08
5053 6046 4.640771 AGTTTCAAAGACAGCCCTATCA 57.359 40.909 0.00 0.00 0.00 2.15
5054 6047 4.985538 AGTTTCAAAGACAGCCCTATCAA 58.014 39.130 0.00 0.00 0.00 2.57
5055 6048 4.762251 AGTTTCAAAGACAGCCCTATCAAC 59.238 41.667 0.00 0.00 0.00 3.18
5056 6049 2.972625 TCAAAGACAGCCCTATCAACG 58.027 47.619 0.00 0.00 0.00 4.10
5057 6050 1.398390 CAAAGACAGCCCTATCAACGC 59.602 52.381 0.00 0.00 0.00 4.84
5058 6051 0.905357 AAGACAGCCCTATCAACGCT 59.095 50.000 0.00 0.00 0.00 5.07
5059 6052 0.905357 AGACAGCCCTATCAACGCTT 59.095 50.000 0.00 0.00 0.00 4.68
5060 6053 1.279271 AGACAGCCCTATCAACGCTTT 59.721 47.619 0.00 0.00 0.00 3.51
5061 6054 1.666189 GACAGCCCTATCAACGCTTTC 59.334 52.381 0.00 0.00 0.00 2.62
5062 6055 1.017387 CAGCCCTATCAACGCTTTCC 58.983 55.000 0.00 0.00 0.00 3.13
5063 6056 0.912486 AGCCCTATCAACGCTTTCCT 59.088 50.000 0.00 0.00 0.00 3.36
5064 6057 1.282157 AGCCCTATCAACGCTTTCCTT 59.718 47.619 0.00 0.00 0.00 3.36
5065 6058 2.504175 AGCCCTATCAACGCTTTCCTTA 59.496 45.455 0.00 0.00 0.00 2.69
5066 6059 3.136626 AGCCCTATCAACGCTTTCCTTAT 59.863 43.478 0.00 0.00 0.00 1.73
5067 6060 3.498777 GCCCTATCAACGCTTTCCTTATC 59.501 47.826 0.00 0.00 0.00 1.75
5068 6061 4.743955 GCCCTATCAACGCTTTCCTTATCT 60.744 45.833 0.00 0.00 0.00 1.98
5069 6062 5.368989 CCCTATCAACGCTTTCCTTATCTT 58.631 41.667 0.00 0.00 0.00 2.40
5070 6063 5.467063 CCCTATCAACGCTTTCCTTATCTTC 59.533 44.000 0.00 0.00 0.00 2.87
5071 6064 6.049149 CCTATCAACGCTTTCCTTATCTTCA 58.951 40.000 0.00 0.00 0.00 3.02
5072 6065 6.201806 CCTATCAACGCTTTCCTTATCTTCAG 59.798 42.308 0.00 0.00 0.00 3.02
5073 6066 3.684788 TCAACGCTTTCCTTATCTTCAGC 59.315 43.478 0.00 0.00 0.00 4.26
5074 6067 2.633488 ACGCTTTCCTTATCTTCAGCC 58.367 47.619 0.00 0.00 0.00 4.85
5075 6068 2.027192 ACGCTTTCCTTATCTTCAGCCA 60.027 45.455 0.00 0.00 0.00 4.75
5076 6069 3.009723 CGCTTTCCTTATCTTCAGCCAA 58.990 45.455 0.00 0.00 0.00 4.52
5077 6070 3.181506 CGCTTTCCTTATCTTCAGCCAAC 60.182 47.826 0.00 0.00 0.00 3.77
5078 6071 3.129462 GCTTTCCTTATCTTCAGCCAACC 59.871 47.826 0.00 0.00 0.00 3.77
5079 6072 4.335416 CTTTCCTTATCTTCAGCCAACCA 58.665 43.478 0.00 0.00 0.00 3.67
5080 6073 4.591321 TTCCTTATCTTCAGCCAACCAT 57.409 40.909 0.00 0.00 0.00 3.55
5081 6074 4.156455 TCCTTATCTTCAGCCAACCATC 57.844 45.455 0.00 0.00 0.00 3.51
5082 6075 3.117888 TCCTTATCTTCAGCCAACCATCC 60.118 47.826 0.00 0.00 0.00 3.51
5083 6076 3.117738 CCTTATCTTCAGCCAACCATCCT 60.118 47.826 0.00 0.00 0.00 3.24
5084 6077 2.725221 ATCTTCAGCCAACCATCCTC 57.275 50.000 0.00 0.00 0.00 3.71
5085 6078 1.661463 TCTTCAGCCAACCATCCTCT 58.339 50.000 0.00 0.00 0.00 3.69
5086 6079 1.280133 TCTTCAGCCAACCATCCTCTG 59.720 52.381 0.00 0.00 0.00 3.35
5087 6080 1.280133 CTTCAGCCAACCATCCTCTGA 59.720 52.381 0.00 0.00 32.58 3.27
5088 6081 0.615331 TCAGCCAACCATCCTCTGAC 59.385 55.000 0.00 0.00 0.00 3.51
5089 6082 0.742281 CAGCCAACCATCCTCTGACG 60.742 60.000 0.00 0.00 0.00 4.35
5090 6083 1.450312 GCCAACCATCCTCTGACGG 60.450 63.158 0.00 0.00 0.00 4.79
5091 6084 1.983224 CCAACCATCCTCTGACGGT 59.017 57.895 0.00 0.00 39.15 4.83
5093 6086 1.271379 CCAACCATCCTCTGACGGTTT 60.271 52.381 0.00 0.00 44.32 3.27
5094 6087 2.076863 CAACCATCCTCTGACGGTTTC 58.923 52.381 0.00 0.00 44.32 2.78
5095 6088 0.613777 ACCATCCTCTGACGGTTTCC 59.386 55.000 0.00 0.00 31.71 3.13
5096 6089 0.613260 CCATCCTCTGACGGTTTCCA 59.387 55.000 0.00 0.00 0.00 3.53
5097 6090 1.003118 CCATCCTCTGACGGTTTCCAA 59.997 52.381 0.00 0.00 0.00 3.53
5098 6091 2.076863 CATCCTCTGACGGTTTCCAAC 58.923 52.381 0.00 0.00 0.00 3.77
5108 6101 0.170339 GGTTTCCAACCGTATGCTGC 59.830 55.000 0.00 0.00 42.62 5.25
5109 6102 0.878416 GTTTCCAACCGTATGCTGCA 59.122 50.000 4.13 4.13 0.00 4.41
5110 6103 0.878416 TTTCCAACCGTATGCTGCAC 59.122 50.000 3.57 0.00 0.00 4.57
5111 6104 0.036164 TTCCAACCGTATGCTGCACT 59.964 50.000 3.57 0.00 0.00 4.40
5112 6105 0.673333 TCCAACCGTATGCTGCACTG 60.673 55.000 3.57 0.00 0.00 3.66
5113 6106 0.955428 CCAACCGTATGCTGCACTGT 60.955 55.000 3.57 0.00 0.00 3.55
5114 6107 0.443869 CAACCGTATGCTGCACTGTC 59.556 55.000 3.57 0.00 0.00 3.51
5115 6108 0.321671 AACCGTATGCTGCACTGTCT 59.678 50.000 3.57 0.00 0.00 3.41
5116 6109 0.108615 ACCGTATGCTGCACTGTCTC 60.109 55.000 3.57 0.00 0.00 3.36
5117 6110 0.807667 CCGTATGCTGCACTGTCTCC 60.808 60.000 3.57 0.00 0.00 3.71
5118 6111 0.807667 CGTATGCTGCACTGTCTCCC 60.808 60.000 3.57 0.00 0.00 4.30
5119 6112 0.807667 GTATGCTGCACTGTCTCCCG 60.808 60.000 3.57 0.00 0.00 5.14
5120 6113 2.578163 TATGCTGCACTGTCTCCCGC 62.578 60.000 3.57 0.00 0.00 6.13
5121 6114 4.687215 GCTGCACTGTCTCCCGCA 62.687 66.667 0.00 0.00 0.00 5.69
5122 6115 2.740055 CTGCACTGTCTCCCGCAC 60.740 66.667 0.00 0.00 0.00 5.34
5123 6116 3.231889 CTGCACTGTCTCCCGCACT 62.232 63.158 0.00 0.00 0.00 4.40
5124 6117 2.433318 GCACTGTCTCCCGCACTC 60.433 66.667 0.00 0.00 0.00 3.51
5125 6118 2.936912 GCACTGTCTCCCGCACTCT 61.937 63.158 0.00 0.00 0.00 3.24
5126 6119 1.595993 GCACTGTCTCCCGCACTCTA 61.596 60.000 0.00 0.00 0.00 2.43
5127 6120 0.453793 CACTGTCTCCCGCACTCTAG 59.546 60.000 0.00 0.00 0.00 2.43
5128 6121 0.038455 ACTGTCTCCCGCACTCTAGT 59.962 55.000 0.00 0.00 0.00 2.57
5129 6122 1.281287 ACTGTCTCCCGCACTCTAGTA 59.719 52.381 0.00 0.00 0.00 1.82
5130 6123 1.944024 CTGTCTCCCGCACTCTAGTAG 59.056 57.143 0.00 0.00 0.00 2.57
5131 6124 1.558294 TGTCTCCCGCACTCTAGTAGA 59.442 52.381 0.00 0.00 0.00 2.59
5132 6125 1.941975 GTCTCCCGCACTCTAGTAGAC 59.058 57.143 0.00 0.00 0.00 2.59
5133 6126 1.838715 TCTCCCGCACTCTAGTAGACT 59.161 52.381 0.00 0.00 0.00 3.24
5134 6127 2.239150 TCTCCCGCACTCTAGTAGACTT 59.761 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 64 0.667792 GGTCCTCTCGTGTGAACTGC 60.668 60.000 0.00 0.00 0.00 4.40
73 75 4.154347 CGCTGGCCTGGTCCTCTC 62.154 72.222 12.06 0.00 0.00 3.20
146 152 3.150458 TCTTTCCACTGACGACTCCTA 57.850 47.619 0.00 0.00 0.00 2.94
147 153 1.996798 TCTTTCCACTGACGACTCCT 58.003 50.000 0.00 0.00 0.00 3.69
148 154 2.405172 GTTCTTTCCACTGACGACTCC 58.595 52.381 0.00 0.00 0.00 3.85
149 155 2.052157 CGTTCTTTCCACTGACGACTC 58.948 52.381 0.00 0.00 0.00 3.36
176 185 4.823157 TGTAGTACTTTGTGTGTGTGTGT 58.177 39.130 0.00 0.00 0.00 3.72
177 186 4.260212 GCTGTAGTACTTTGTGTGTGTGTG 60.260 45.833 0.00 0.00 0.00 3.82
187 196 6.706055 TTCTGATTTCGCTGTAGTACTTTG 57.294 37.500 0.00 0.00 0.00 2.77
189 198 8.251721 ACTAATTCTGATTTCGCTGTAGTACTT 58.748 33.333 0.00 0.00 0.00 2.24
190 199 7.773149 ACTAATTCTGATTTCGCTGTAGTACT 58.227 34.615 0.00 0.00 0.00 2.73
191 200 7.988904 ACTAATTCTGATTTCGCTGTAGTAC 57.011 36.000 0.00 0.00 0.00 2.73
192 201 8.133627 GGTACTAATTCTGATTTCGCTGTAGTA 58.866 37.037 0.00 0.00 0.00 1.82
193 202 6.979238 GGTACTAATTCTGATTTCGCTGTAGT 59.021 38.462 0.00 0.00 0.00 2.73
194 203 6.978659 TGGTACTAATTCTGATTTCGCTGTAG 59.021 38.462 0.00 0.00 0.00 2.74
216 225 5.772672 TGTTGTTGGATATGCTAAAACTGGT 59.227 36.000 11.72 0.00 0.00 4.00
217 226 6.266168 TGTTGTTGGATATGCTAAAACTGG 57.734 37.500 11.72 0.00 0.00 4.00
218 227 7.370383 ACTTGTTGTTGGATATGCTAAAACTG 58.630 34.615 11.72 7.92 0.00 3.16
219 228 7.524717 ACTTGTTGTTGGATATGCTAAAACT 57.475 32.000 11.72 0.00 0.00 2.66
220 229 7.865385 TGAACTTGTTGTTGGATATGCTAAAAC 59.135 33.333 5.05 5.05 39.30 2.43
221 230 7.946207 TGAACTTGTTGTTGGATATGCTAAAA 58.054 30.769 0.00 0.00 39.30 1.52
222 231 7.517614 TGAACTTGTTGTTGGATATGCTAAA 57.482 32.000 0.00 0.00 39.30 1.85
236 247 6.378280 AGCCTAATAATCCCTTGAACTTGTTG 59.622 38.462 0.00 0.00 0.00 3.33
305 334 3.263261 GCTAGCGTTTTCTAGGCTTTCT 58.737 45.455 0.00 0.00 45.24 2.52
306 335 3.660054 GCTAGCGTTTTCTAGGCTTTC 57.340 47.619 0.00 0.00 45.24 2.62
321 350 1.515521 AATTATTGCGCGGGGCTAGC 61.516 55.000 18.19 6.04 44.05 3.42
969 1038 0.395724 CGATGGGGAAAGGGAAAGGG 60.396 60.000 0.00 0.00 0.00 3.95
970 1039 1.037579 GCGATGGGGAAAGGGAAAGG 61.038 60.000 0.00 0.00 0.00 3.11
971 1040 0.323360 TGCGATGGGGAAAGGGAAAG 60.323 55.000 0.00 0.00 0.00 2.62
974 1043 0.610785 GTTTGCGATGGGGAAAGGGA 60.611 55.000 0.00 0.00 36.57 4.20
1001 1070 4.858680 GGAACCCTAGCTGCGGGC 62.859 72.222 19.68 7.25 46.04 6.13
1830 2315 4.254709 ACGTGCTGCAGGAAGGCA 62.255 61.111 26.94 9.76 42.53 4.75
1982 2467 5.568392 AGAGCTGAAATGTGGAGAGAAATT 58.432 37.500 0.00 0.00 0.00 1.82
2101 2597 1.376543 CTCCTGAGCGAACCGTAGTA 58.623 55.000 0.00 0.00 0.00 1.82
2102 2598 1.313812 CCTCCTGAGCGAACCGTAGT 61.314 60.000 0.00 0.00 0.00 2.73
2103 2599 1.433879 CCTCCTGAGCGAACCGTAG 59.566 63.158 0.00 0.00 0.00 3.51
2111 2611 1.903877 AATCCACACCCTCCTGAGCG 61.904 60.000 0.00 0.00 0.00 5.03
2119 2619 5.216665 TCTACTAACCTAATCCACACCCT 57.783 43.478 0.00 0.00 0.00 4.34
2121 2621 8.474710 TCTTATCTACTAACCTAATCCACACC 57.525 38.462 0.00 0.00 0.00 4.16
2159 2870 3.589988 ACCAGTTCGATAAGACTTGCTG 58.410 45.455 0.00 0.00 0.00 4.41
2196 2907 1.870402 CAAACATCGCTACACCACACA 59.130 47.619 0.00 0.00 0.00 3.72
2303 3022 4.515361 TGAAAGACTGTAACGTTTCCCAA 58.485 39.130 5.91 0.00 0.00 4.12
2401 3121 1.688811 GTACTTGGTGGCCCATCCA 59.311 57.895 0.00 3.45 41.49 3.41
2544 3268 5.304101 ACTTGTGGCTTATCAATTGAAACCA 59.696 36.000 13.09 14.00 0.00 3.67
2587 3311 4.881019 TCCCAACAATAACCCAAACATG 57.119 40.909 0.00 0.00 0.00 3.21
2686 3417 0.599558 TGGAAGACTGTACCGTTCCG 59.400 55.000 4.34 0.00 41.29 4.30
2778 3509 5.957842 AGCATCACACTTTATCGGAAAAA 57.042 34.783 0.00 0.00 0.00 1.94
2779 3510 5.957842 AAGCATCACACTTTATCGGAAAA 57.042 34.783 0.00 0.00 0.00 2.29
2781 3512 5.957842 AAAAGCATCACACTTTATCGGAA 57.042 34.783 0.00 0.00 36.35 4.30
2782 3513 5.957842 AAAAAGCATCACACTTTATCGGA 57.042 34.783 0.00 0.00 36.35 4.55
2783 3514 7.967854 TCAATAAAAAGCATCACACTTTATCGG 59.032 33.333 0.00 0.00 36.35 4.18
2784 3515 8.894409 TCAATAAAAAGCATCACACTTTATCG 57.106 30.769 0.00 0.00 36.35 2.92
2787 3518 9.809096 TGTTTCAATAAAAAGCATCACACTTTA 57.191 25.926 0.00 0.00 36.35 1.85
2788 3519 8.715191 TGTTTCAATAAAAAGCATCACACTTT 57.285 26.923 0.00 0.00 38.98 2.66
2789 3520 8.767085 CATGTTTCAATAAAAAGCATCACACTT 58.233 29.630 0.00 0.00 0.00 3.16
2790 3521 7.095523 GCATGTTTCAATAAAAAGCATCACACT 60.096 33.333 0.00 0.00 0.00 3.55
2791 3522 7.011189 GCATGTTTCAATAAAAAGCATCACAC 58.989 34.615 0.00 0.00 0.00 3.82
2792 3523 6.704937 TGCATGTTTCAATAAAAAGCATCACA 59.295 30.769 0.00 0.00 30.87 3.58
2793 3524 7.119605 TGCATGTTTCAATAAAAAGCATCAC 57.880 32.000 0.00 0.00 30.87 3.06
2794 3525 7.226128 TGTTGCATGTTTCAATAAAAAGCATCA 59.774 29.630 0.00 0.00 33.88 3.07
2795 3526 7.531534 GTGTTGCATGTTTCAATAAAAAGCATC 59.468 33.333 0.00 0.00 33.88 3.91
2796 3527 7.227116 AGTGTTGCATGTTTCAATAAAAAGCAT 59.773 29.630 0.00 0.00 33.88 3.79
2797 3528 6.538021 AGTGTTGCATGTTTCAATAAAAAGCA 59.462 30.769 0.00 0.00 32.74 3.91
2798 3529 6.947258 AGTGTTGCATGTTTCAATAAAAAGC 58.053 32.000 0.00 0.00 0.00 3.51
2799 3530 8.389603 ACAAGTGTTGCATGTTTCAATAAAAAG 58.610 29.630 0.00 0.00 0.00 2.27
2807 3538 3.865011 ACACAAGTGTTGCATGTTTCA 57.135 38.095 0.00 0.00 41.83 2.69
2808 3539 6.208644 AGATTACACAAGTGTTGCATGTTTC 58.791 36.000 11.50 0.00 41.83 2.78
2816 3547 7.387673 TGGATAACTGAGATTACACAAGTGTTG 59.612 37.037 11.50 0.00 41.83 3.33
2862 3593 1.542915 CCCAACAAGGCAAGTCTCATG 59.457 52.381 0.00 0.00 35.39 3.07
2886 3617 1.686052 GGCCAACTGAAATGGTCACAA 59.314 47.619 0.00 0.00 42.25 3.33
2913 3644 3.126879 GCCAGCAGCACGCATACA 61.127 61.111 0.00 0.00 46.13 2.29
2991 3722 6.460261 CGATTCAGGTCAGATAAGACAGCTTA 60.460 42.308 0.00 0.00 40.29 3.09
3081 3812 2.392662 TCCAGAAGACCAGCCTCATAG 58.607 52.381 0.00 0.00 0.00 2.23
3174 3905 2.111669 CCACTGCTGGTGCTCACA 59.888 61.111 2.21 0.00 44.08 3.58
3304 4044 6.821388 ACAGAGGTAAACTGGAATATAGCTG 58.179 40.000 0.00 0.00 39.38 4.24
3312 4052 4.164843 AGCAAACAGAGGTAAACTGGAA 57.835 40.909 0.00 0.00 39.38 3.53
3313 4053 3.857157 AGCAAACAGAGGTAAACTGGA 57.143 42.857 0.00 0.00 39.38 3.86
3382 4183 2.075338 GAGAAACAGAGCAGGCAGAAG 58.925 52.381 0.00 0.00 0.00 2.85
3450 4251 1.633852 GCGCAGACTGCTCCTTCTTG 61.634 60.000 24.36 7.99 42.25 3.02
3552 4353 3.072915 TCTCAGTCTTTGCCATCTCCAAA 59.927 43.478 0.00 0.00 0.00 3.28
3637 4438 3.728373 GGACATTGCTCCCCCGGT 61.728 66.667 0.00 0.00 0.00 5.28
3873 4674 1.677633 AACATTAGGCACCGGCACC 60.678 57.895 0.00 2.39 43.71 5.01
3940 4741 1.819632 GGCCGCTGTTGTATCCAGG 60.820 63.158 0.00 0.00 0.00 4.45
3942 4743 1.078497 CAGGCCGCTGTTGTATCCA 60.078 57.895 0.00 0.00 0.00 3.41
4057 4868 4.675029 CCGTTGACGAAGCCCCGT 62.675 66.667 4.91 0.33 46.43 5.28
4103 4914 0.895100 AGGACGTACGCAACCTACCA 60.895 55.000 21.73 0.00 0.00 3.25
4140 4954 5.163982 GGACAGAACGAAGTAACATAAGCAC 60.164 44.000 0.00 0.00 45.00 4.40
4189 5003 3.309682 CAGTTTTTCAGTTCTCAGTGCGA 59.690 43.478 0.00 0.00 0.00 5.10
4219 5033 5.700832 CACATACACGGCATCCATACTAAAT 59.299 40.000 0.00 0.00 0.00 1.40
4220 5034 5.053811 CACATACACGGCATCCATACTAAA 58.946 41.667 0.00 0.00 0.00 1.85
4221 5035 4.502431 CCACATACACGGCATCCATACTAA 60.502 45.833 0.00 0.00 0.00 2.24
4222 5036 3.006430 CCACATACACGGCATCCATACTA 59.994 47.826 0.00 0.00 0.00 1.82
4262 5076 3.799137 TTTCGCCTAGTGCTTTAAACG 57.201 42.857 2.39 0.00 38.05 3.60
4334 5148 9.632807 CCATCATAAGTATAGCTAACAGAAGAC 57.367 37.037 0.00 0.00 0.00 3.01
4351 5165 1.308998 GACCAACGCCCCATCATAAG 58.691 55.000 0.00 0.00 0.00 1.73
4354 5168 0.033208 AATGACCAACGCCCCATCAT 60.033 50.000 0.00 0.00 0.00 2.45
4355 5169 0.621082 TAATGACCAACGCCCCATCA 59.379 50.000 0.00 0.00 0.00 3.07
4403 5217 2.024176 AGCATAACCACTAACGCCAG 57.976 50.000 0.00 0.00 0.00 4.85
4406 5220 5.043189 AGAAAAAGCATAACCACTAACGC 57.957 39.130 0.00 0.00 0.00 4.84
4407 5221 6.092259 AGCTAGAAAAAGCATAACCACTAACG 59.908 38.462 0.00 0.00 45.30 3.18
4408 5222 7.379098 AGCTAGAAAAAGCATAACCACTAAC 57.621 36.000 0.00 0.00 45.30 2.34
4410 5224 8.943002 GTTAAGCTAGAAAAAGCATAACCACTA 58.057 33.333 11.08 0.00 44.75 2.74
4411 5225 7.817641 GTTAAGCTAGAAAAAGCATAACCACT 58.182 34.615 11.08 0.00 44.75 4.00
4469 5453 5.059161 TCTGCACATTATTGTATCAGAGGC 58.941 41.667 13.45 3.68 38.57 4.70
4478 5462 6.238731 CCGGATTGTATTCTGCACATTATTGT 60.239 38.462 0.00 0.00 36.15 2.71
4493 5477 6.271391 TGGAATTATAGTCCACCGGATTGTAT 59.729 38.462 9.46 0.75 40.33 2.29
4496 5480 4.968259 TGGAATTATAGTCCACCGGATTG 58.032 43.478 9.46 0.00 40.33 2.67
4504 5488 6.212589 TCTGTCAAGTGTGGAATTATAGTCCA 59.787 38.462 3.65 3.65 43.03 4.02
4505 5489 6.640518 TCTGTCAAGTGTGGAATTATAGTCC 58.359 40.000 0.00 0.00 35.55 3.85
4506 5490 7.324178 ACTCTGTCAAGTGTGGAATTATAGTC 58.676 38.462 0.00 0.00 0.00 2.59
4507 5491 7.246171 ACTCTGTCAAGTGTGGAATTATAGT 57.754 36.000 0.00 0.00 0.00 2.12
4508 5492 8.037758 AGAACTCTGTCAAGTGTGGAATTATAG 58.962 37.037 0.00 0.00 30.67 1.31
4653 5638 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
4654 5639 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
4655 5640 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
4656 5641 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
4657 5642 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
4666 5651 9.413734 GTATAAGGTACTCCCTCTGTAAACTAA 57.586 37.037 0.00 0.00 45.47 2.24
4667 5652 7.716998 CGTATAAGGTACTCCCTCTGTAAACTA 59.283 40.741 0.00 0.00 45.47 2.24
4668 5653 6.545298 CGTATAAGGTACTCCCTCTGTAAACT 59.455 42.308 0.00 0.00 45.47 2.66
4669 5654 6.733145 CGTATAAGGTACTCCCTCTGTAAAC 58.267 44.000 0.00 0.00 45.47 2.01
4670 5655 5.300286 GCGTATAAGGTACTCCCTCTGTAAA 59.700 44.000 0.00 0.00 45.47 2.01
4671 5656 4.823989 GCGTATAAGGTACTCCCTCTGTAA 59.176 45.833 0.00 0.00 45.47 2.41
4672 5657 4.103785 AGCGTATAAGGTACTCCCTCTGTA 59.896 45.833 0.00 0.00 45.47 2.74
4673 5658 3.117587 AGCGTATAAGGTACTCCCTCTGT 60.118 47.826 0.00 0.00 45.47 3.41
4674 5659 3.253677 CAGCGTATAAGGTACTCCCTCTG 59.746 52.174 0.00 0.00 45.47 3.35
4675 5660 3.488363 CAGCGTATAAGGTACTCCCTCT 58.512 50.000 0.00 0.00 45.47 3.69
4676 5661 2.030096 GCAGCGTATAAGGTACTCCCTC 60.030 54.545 0.00 0.00 45.47 4.30
4678 5663 1.335689 CGCAGCGTATAAGGTACTCCC 60.336 57.143 6.65 0.00 38.49 4.30
4679 5664 2.047679 CGCAGCGTATAAGGTACTCC 57.952 55.000 6.65 0.00 38.49 3.85
4712 5697 4.508662 GGACACTAATCAAGGACCTCAAG 58.491 47.826 0.00 0.00 0.00 3.02
4767 5752 2.046988 TGGTCGACATGCTGGCTG 60.047 61.111 18.91 0.00 0.00 4.85
4768 5753 2.046892 GTGGTCGACATGCTGGCT 60.047 61.111 18.91 0.00 0.00 4.75
4769 5754 3.127533 GGTGGTCGACATGCTGGC 61.128 66.667 18.91 0.00 0.00 4.85
4770 5755 2.034879 GTGGTGGTCGACATGCTGG 61.035 63.158 18.91 0.00 0.00 4.85
4777 5762 0.677842 ACTGTAAGGTGGTGGTCGAC 59.322 55.000 7.13 7.13 39.30 4.20
4803 5788 0.036765 GTAAGGCGGTGGTCATGTCA 60.037 55.000 0.00 0.00 0.00 3.58
4825 5810 4.139786 AGAATGTGCAACTGACTTCATGT 58.860 39.130 0.00 0.00 38.04 3.21
4828 5813 5.450412 GGAAAAGAATGTGCAACTGACTTCA 60.450 40.000 0.00 0.00 38.04 3.02
4830 5815 4.646492 AGGAAAAGAATGTGCAACTGACTT 59.354 37.500 0.00 0.00 38.04 3.01
4831 5816 4.210331 AGGAAAAGAATGTGCAACTGACT 58.790 39.130 0.00 0.00 38.04 3.41
4832 5817 4.036734 TGAGGAAAAGAATGTGCAACTGAC 59.963 41.667 0.00 0.00 38.04 3.51
4833 5818 4.206375 TGAGGAAAAGAATGTGCAACTGA 58.794 39.130 0.00 0.00 38.04 3.41
4834 5819 4.543692 CTGAGGAAAAGAATGTGCAACTG 58.456 43.478 0.00 0.00 38.04 3.16
4835 5820 3.005155 GCTGAGGAAAAGAATGTGCAACT 59.995 43.478 0.00 0.00 38.04 3.16
4836 5821 3.243501 TGCTGAGGAAAAGAATGTGCAAC 60.244 43.478 0.00 0.00 37.35 4.17
4837 5822 2.957680 TGCTGAGGAAAAGAATGTGCAA 59.042 40.909 0.00 0.00 0.00 4.08
4838 5823 2.585330 TGCTGAGGAAAAGAATGTGCA 58.415 42.857 0.00 0.00 0.00 4.57
4839 5824 3.572584 CTTGCTGAGGAAAAGAATGTGC 58.427 45.455 0.00 0.00 0.00 4.57
4840 5825 3.255149 AGCTTGCTGAGGAAAAGAATGTG 59.745 43.478 0.00 0.00 0.00 3.21
4841 5826 3.255149 CAGCTTGCTGAGGAAAAGAATGT 59.745 43.478 16.78 0.00 0.00 2.71
4896 5881 0.250513 GGAGGCGTTGAATCTGGAGT 59.749 55.000 0.00 0.00 0.00 3.85
4935 5920 2.202623 CCGACGCTTTCCGAGGAG 60.203 66.667 0.00 0.00 39.36 3.69
4949 5934 1.112916 TTGCTCAGAGACCACACCGA 61.113 55.000 0.00 0.00 0.00 4.69
4965 5958 0.178990 AGGAGAGGGTGGTGTTTTGC 60.179 55.000 0.00 0.00 0.00 3.68
5022 6015 5.578336 GCTGTCTTTGAAACTTGCTCTTTTT 59.422 36.000 0.00 0.00 0.00 1.94
5023 6016 5.105063 GCTGTCTTTGAAACTTGCTCTTTT 58.895 37.500 0.00 0.00 0.00 2.27
5024 6017 4.440663 GGCTGTCTTTGAAACTTGCTCTTT 60.441 41.667 0.00 0.00 0.00 2.52
5025 6018 3.067320 GGCTGTCTTTGAAACTTGCTCTT 59.933 43.478 0.00 0.00 0.00 2.85
5026 6019 2.620585 GGCTGTCTTTGAAACTTGCTCT 59.379 45.455 0.00 0.00 0.00 4.09
5027 6020 2.287849 GGGCTGTCTTTGAAACTTGCTC 60.288 50.000 0.00 0.00 0.00 4.26
5028 6021 1.683385 GGGCTGTCTTTGAAACTTGCT 59.317 47.619 0.00 0.00 0.00 3.91
5029 6022 1.683385 AGGGCTGTCTTTGAAACTTGC 59.317 47.619 0.00 0.00 0.00 4.01
5030 6023 4.761739 TGATAGGGCTGTCTTTGAAACTTG 59.238 41.667 0.00 0.00 0.00 3.16
5031 6024 4.985538 TGATAGGGCTGTCTTTGAAACTT 58.014 39.130 0.00 0.00 0.00 2.66
5032 6025 4.640771 TGATAGGGCTGTCTTTGAAACT 57.359 40.909 0.00 0.00 0.00 2.66
5033 6026 4.378459 CGTTGATAGGGCTGTCTTTGAAAC 60.378 45.833 0.00 0.00 0.00 2.78
5034 6027 3.751175 CGTTGATAGGGCTGTCTTTGAAA 59.249 43.478 0.00 0.00 0.00 2.69
5035 6028 3.334691 CGTTGATAGGGCTGTCTTTGAA 58.665 45.455 0.00 0.00 0.00 2.69
5036 6029 2.935238 GCGTTGATAGGGCTGTCTTTGA 60.935 50.000 0.00 0.00 0.00 2.69
5037 6030 1.398390 GCGTTGATAGGGCTGTCTTTG 59.602 52.381 0.00 0.00 0.00 2.77
5038 6031 1.279271 AGCGTTGATAGGGCTGTCTTT 59.721 47.619 0.00 0.00 35.31 2.52
5039 6032 0.905357 AGCGTTGATAGGGCTGTCTT 59.095 50.000 0.00 0.00 35.31 3.01
5040 6033 0.905357 AAGCGTTGATAGGGCTGTCT 59.095 50.000 0.00 0.00 37.06 3.41
5041 6034 1.666189 GAAAGCGTTGATAGGGCTGTC 59.334 52.381 0.00 0.00 37.06 3.51
5042 6035 1.679032 GGAAAGCGTTGATAGGGCTGT 60.679 52.381 0.00 0.00 37.06 4.40
5043 6036 1.017387 GGAAAGCGTTGATAGGGCTG 58.983 55.000 0.00 0.00 37.06 4.85
5044 6037 0.912486 AGGAAAGCGTTGATAGGGCT 59.088 50.000 0.00 0.00 39.01 5.19
5045 6038 1.751437 AAGGAAAGCGTTGATAGGGC 58.249 50.000 0.00 0.00 0.00 5.19
5046 6039 4.962155 AGATAAGGAAAGCGTTGATAGGG 58.038 43.478 0.00 0.00 0.00 3.53
5047 6040 6.049149 TGAAGATAAGGAAAGCGTTGATAGG 58.951 40.000 0.00 0.00 0.00 2.57
5048 6041 6.292596 GCTGAAGATAAGGAAAGCGTTGATAG 60.293 42.308 0.00 0.00 0.00 2.08
5049 6042 5.523916 GCTGAAGATAAGGAAAGCGTTGATA 59.476 40.000 0.00 0.00 0.00 2.15
5050 6043 4.333926 GCTGAAGATAAGGAAAGCGTTGAT 59.666 41.667 0.00 0.00 0.00 2.57
5051 6044 3.684788 GCTGAAGATAAGGAAAGCGTTGA 59.315 43.478 0.00 0.00 0.00 3.18
5052 6045 3.181506 GGCTGAAGATAAGGAAAGCGTTG 60.182 47.826 0.00 0.00 0.00 4.10
5053 6046 3.010420 GGCTGAAGATAAGGAAAGCGTT 58.990 45.455 0.00 0.00 0.00 4.84
5054 6047 2.027192 TGGCTGAAGATAAGGAAAGCGT 60.027 45.455 0.00 0.00 0.00 5.07
5055 6048 2.632377 TGGCTGAAGATAAGGAAAGCG 58.368 47.619 0.00 0.00 0.00 4.68
5056 6049 3.129462 GGTTGGCTGAAGATAAGGAAAGC 59.871 47.826 0.00 0.00 0.00 3.51
5057 6050 4.335416 TGGTTGGCTGAAGATAAGGAAAG 58.665 43.478 0.00 0.00 0.00 2.62
5058 6051 4.380843 TGGTTGGCTGAAGATAAGGAAA 57.619 40.909 0.00 0.00 0.00 3.13
5059 6052 4.526970 GATGGTTGGCTGAAGATAAGGAA 58.473 43.478 0.00 0.00 0.00 3.36
5060 6053 3.117888 GGATGGTTGGCTGAAGATAAGGA 60.118 47.826 0.00 0.00 0.00 3.36
5061 6054 3.117738 AGGATGGTTGGCTGAAGATAAGG 60.118 47.826 0.00 0.00 0.00 2.69
5062 6055 4.133078 GAGGATGGTTGGCTGAAGATAAG 58.867 47.826 0.00 0.00 0.00 1.73
5063 6056 3.782523 AGAGGATGGTTGGCTGAAGATAA 59.217 43.478 0.00 0.00 0.00 1.75
5064 6057 3.135348 CAGAGGATGGTTGGCTGAAGATA 59.865 47.826 0.00 0.00 0.00 1.98
5065 6058 2.092538 CAGAGGATGGTTGGCTGAAGAT 60.093 50.000 0.00 0.00 0.00 2.40
5066 6059 1.280133 CAGAGGATGGTTGGCTGAAGA 59.720 52.381 0.00 0.00 0.00 2.87
5067 6060 1.280133 TCAGAGGATGGTTGGCTGAAG 59.720 52.381 0.00 0.00 33.11 3.02
5068 6061 1.003580 GTCAGAGGATGGTTGGCTGAA 59.996 52.381 0.00 0.00 37.35 3.02
5069 6062 0.615331 GTCAGAGGATGGTTGGCTGA 59.385 55.000 0.00 0.00 33.58 4.26
5070 6063 0.742281 CGTCAGAGGATGGTTGGCTG 60.742 60.000 0.00 0.00 0.00 4.85
5071 6064 1.599047 CGTCAGAGGATGGTTGGCT 59.401 57.895 0.00 0.00 0.00 4.75
5072 6065 1.450312 CCGTCAGAGGATGGTTGGC 60.450 63.158 0.00 0.00 43.95 4.52
5073 6066 4.941609 CCGTCAGAGGATGGTTGG 57.058 61.111 0.00 0.00 43.95 3.77
5078 6071 2.076863 GTTGGAAACCGTCAGAGGATG 58.923 52.381 0.00 0.00 42.21 3.51
5079 6072 2.474410 GTTGGAAACCGTCAGAGGAT 57.526 50.000 0.00 0.00 42.21 3.24
5091 6084 0.878416 GTGCAGCATACGGTTGGAAA 59.122 50.000 0.00 0.00 28.20 3.13
5092 6085 0.036164 AGTGCAGCATACGGTTGGAA 59.964 50.000 0.00 0.00 28.20 3.53
5093 6086 0.673333 CAGTGCAGCATACGGTTGGA 60.673 55.000 0.00 0.00 0.00 3.53
5094 6087 0.955428 ACAGTGCAGCATACGGTTGG 60.955 55.000 0.00 0.00 0.00 3.77
5095 6088 0.443869 GACAGTGCAGCATACGGTTG 59.556 55.000 0.00 0.00 0.00 3.77
5096 6089 0.321671 AGACAGTGCAGCATACGGTT 59.678 50.000 0.00 0.00 0.00 4.44
5097 6090 0.108615 GAGACAGTGCAGCATACGGT 60.109 55.000 0.00 0.00 0.00 4.83
5098 6091 0.807667 GGAGACAGTGCAGCATACGG 60.808 60.000 0.00 0.00 0.00 4.02
5099 6092 0.807667 GGGAGACAGTGCAGCATACG 60.808 60.000 0.00 0.00 0.00 3.06
5100 6093 0.807667 CGGGAGACAGTGCAGCATAC 60.808 60.000 0.00 0.00 0.00 2.39
5101 6094 1.517361 CGGGAGACAGTGCAGCATA 59.483 57.895 0.00 0.00 0.00 3.14
5102 6095 2.267006 CGGGAGACAGTGCAGCAT 59.733 61.111 0.00 0.00 0.00 3.79
5103 6096 4.687215 GCGGGAGACAGTGCAGCA 62.687 66.667 0.00 0.00 37.64 4.41
5104 6097 4.687215 TGCGGGAGACAGTGCAGC 62.687 66.667 0.00 0.00 38.21 5.25
5105 6098 2.740055 GTGCGGGAGACAGTGCAG 60.740 66.667 0.00 0.00 38.14 4.41
5106 6099 3.226429 GAGTGCGGGAGACAGTGCA 62.226 63.158 0.00 0.00 34.44 4.57
5107 6100 1.595993 TAGAGTGCGGGAGACAGTGC 61.596 60.000 0.00 0.00 0.00 4.40
5108 6101 0.453793 CTAGAGTGCGGGAGACAGTG 59.546 60.000 0.00 0.00 0.00 3.66
5109 6102 0.038455 ACTAGAGTGCGGGAGACAGT 59.962 55.000 0.00 0.00 0.00 3.55
5110 6103 1.944024 CTACTAGAGTGCGGGAGACAG 59.056 57.143 0.00 0.00 0.00 3.51
5111 6104 1.558294 TCTACTAGAGTGCGGGAGACA 59.442 52.381 0.00 0.00 0.00 3.41
5112 6105 1.941975 GTCTACTAGAGTGCGGGAGAC 59.058 57.143 0.00 0.00 0.00 3.36
5113 6106 1.838715 AGTCTACTAGAGTGCGGGAGA 59.161 52.381 0.00 0.00 0.00 3.71
5114 6107 2.335316 AGTCTACTAGAGTGCGGGAG 57.665 55.000 0.00 0.00 0.00 4.30
5115 6108 2.803030 AAGTCTACTAGAGTGCGGGA 57.197 50.000 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.