Multiple sequence alignment - TraesCS5B01G176300

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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 TraesCS5B01G176300 chr5B 100.000 4728 0 0 1 4728 322276724 322281451 0.000000e+00 8732.0
1 TraesCS5B01G176300 chr5B 91.071 168 10 4 4387 4549 531298075 531298242 6.160000e-54 222.0
2 TraesCS5B01G176300 chr5B 91.071 112 7 3 478 588 617137596 617137705 1.060000e-31 148.0
3 TraesCS5B01G176300 chr5B 93.137 102 5 2 485 585 665560022 665559922 1.060000e-31 148.0
4 TraesCS5B01G176300 chr5B 84.615 104 16 0 4611 4714 361014167 361014270 2.330000e-18 104.0
5 TraesCS5B01G176300 chr5D 96.685 2383 61 11 572 2941 284973471 284975848 0.000000e+00 3947.0
6 TraesCS5B01G176300 chr5D 95.798 1428 33 8 2964 4391 284975918 284977318 0.000000e+00 2279.0
7 TraesCS5B01G176300 chr5D 96.074 484 19 0 1 484 284972986 284973469 0.000000e+00 789.0
8 TraesCS5B01G176300 chr5D 100.000 34 0 0 2931 2964 284975849 284975882 3.950000e-06 63.9
9 TraesCS5B01G176300 chr5A 94.672 1389 48 15 1559 2941 376545804 376547172 0.000000e+00 2132.0
10 TraesCS5B01G176300 chr5A 95.827 1222 41 5 2964 4183 376547240 376548453 0.000000e+00 1965.0
11 TraesCS5B01G176300 chr5A 95.415 916 31 10 567 1475 376544889 376545800 0.000000e+00 1448.0
12 TraesCS5B01G176300 chr5A 93.456 489 24 4 1 486 376544406 376544889 0.000000e+00 719.0
13 TraesCS5B01G176300 chr5A 94.558 147 8 0 4245 4391 376548442 376548588 1.320000e-55 228.0
14 TraesCS5B01G176300 chr5A 85.217 115 17 0 4611 4725 284783638 284783752 8.310000e-23 119.0
15 TraesCS5B01G176300 chr7A 88.649 185 15 5 4372 4551 320981156 320981339 2.210000e-53 220.0
16 TraesCS5B01G176300 chr7A 86.441 118 14 2 4612 4728 218030748 218030864 1.380000e-25 128.0
17 TraesCS5B01G176300 chr6A 89.071 183 13 5 4375 4552 60016887 60016707 2.210000e-53 220.0
18 TraesCS5B01G176300 chr2D 86.111 216 16 12 4390 4599 161906852 161907059 2.210000e-53 220.0
19 TraesCS5B01G176300 chr2D 87.129 101 12 1 4611 4711 507861433 507861532 3.870000e-21 113.0
20 TraesCS5B01G176300 chr2D 90.625 64 5 1 4186 4248 514338392 514338329 3.030000e-12 84.2
21 TraesCS5B01G176300 chr1B 90.173 173 12 5 4383 4550 242176190 242176018 2.210000e-53 220.0
22 TraesCS5B01G176300 chr1B 94.175 103 3 3 482 583 615019075 615018975 2.280000e-33 154.0
23 TraesCS5B01G176300 chr1D 88.298 188 14 8 4386 4568 206955534 206955718 7.970000e-53 219.0
24 TraesCS5B01G176300 chr3D 86.500 200 22 3 4361 4555 522773405 522773206 1.030000e-51 215.0
25 TraesCS5B01G176300 chr3D 93.204 103 6 1 485 587 20348845 20348744 2.950000e-32 150.0
26 TraesCS5B01G176300 chr3D 85.484 124 17 1 4605 4727 116330514 116330637 1.380000e-25 128.0
27 TraesCS5B01G176300 chr2B 88.462 182 16 4 4374 4550 719520489 719520670 1.030000e-51 215.0
28 TraesCS5B01G176300 chr2B 87.255 102 13 0 4611 4712 736190876 736190775 2.990000e-22 117.0
29 TraesCS5B01G176300 chr2B 83.486 109 17 1 4611 4719 48181773 48181880 3.010000e-17 100.0
30 TraesCS5B01G176300 chr2B 90.625 64 5 1 4184 4246 606033504 606033441 3.030000e-12 84.2
31 TraesCS5B01G176300 chr7B 87.047 193 16 7 4389 4575 94885639 94885828 4.790000e-50 209.0
32 TraesCS5B01G176300 chr7D 97.802 91 0 2 485 574 459429336 459429425 6.330000e-34 156.0
33 TraesCS5B01G176300 chr7D 94.000 100 3 3 476 574 506141359 506141456 1.060000e-31 148.0
34 TraesCS5B01G176300 chr7D 91.589 107 6 3 478 584 295855515 295855412 1.370000e-30 145.0
35 TraesCS5B01G176300 chr6B 97.778 90 2 0 481 570 147684223 147684312 6.330000e-34 156.0
36 TraesCS5B01G176300 chr2A 93.396 106 5 2 482 587 17927570 17927467 6.330000e-34 156.0
37 TraesCS5B01G176300 chr3B 85.586 111 15 1 4611 4721 146202714 146202605 1.080000e-21 115.0
38 TraesCS5B01G176300 chr3B 81.667 120 20 2 4605 4723 169902928 169903046 1.080000e-16 99.0


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 TraesCS5B01G176300 chr5B 322276724 322281451 4727 False 8732.000 8732 100.00000 1 4728 1 chr5B.!!$F1 4727
1 TraesCS5B01G176300 chr5D 284972986 284977318 4332 False 1769.725 3947 97.13925 1 4391 4 chr5D.!!$F1 4390
2 TraesCS5B01G176300 chr5A 376544406 376548588 4182 False 1298.400 2132 94.78560 1 4391 5 chr5A.!!$F2 4390

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
55 59 0.323087 GCCCCTTTGGTCCATAACGT 60.323 55.000 0.0 0.0 36.04 3.99 F
402 406 0.543749 ATGGCTGTTCCCTCTAGCAC 59.456 55.000 0.0 0.0 39.15 4.40 F
500 504 0.861155 ATCTACTCCCTCCGTCCCAT 59.139 55.000 0.0 0.0 0.00 4.00 F
505 509 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.0 0.0 0.00 2.71 F
1396 1413 1.606668 TGCCGTGGAACTCAAAACATC 59.393 47.619 0.0 0.0 31.75 3.06 F
3068 3137 1.580845 AATGGCTGCGAAGTCTGCAC 61.581 55.000 0.0 0.0 37.44 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1128 1143 1.105759 ACGTACTATCAGGACCGCCC 61.106 60.000 0.00 0.00 33.31 6.13 R
1730 1747 6.915544 ATGCACATAACTGACAGATAAGTG 57.084 37.500 18.48 18.48 29.25 3.16 R
2326 2345 7.038154 AGAGAGTTGACTATGCTAGATGAAC 57.962 40.000 0.00 0.00 0.00 3.18 R
2478 2500 8.761575 TTTCATTTTGCAGAAATTACTCATCC 57.238 30.769 0.00 0.00 0.00 3.51 R
3376 3445 0.595053 CGCTCGACACTGTGACAGTT 60.595 55.000 16.79 7.78 42.59 3.16 R
4691 4761 0.040425 CGTTTGTCCTTTTGCTCCCG 60.040 55.000 0.00 0.00 0.00 5.14 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
55 59 0.323087 GCCCCTTTGGTCCATAACGT 60.323 55.000 0.00 0.00 36.04 3.99
107 111 4.889409 AGATTATTCACAATTGATGGCCGT 59.111 37.500 13.59 0.00 0.00 5.68
186 190 1.604604 TTGTCTTGCTTAGTGGCCAC 58.395 50.000 29.22 29.22 0.00 5.01
300 304 1.123077 TGTGTTGCCTCTGTGACTCT 58.877 50.000 0.00 0.00 0.00 3.24
402 406 0.543749 ATGGCTGTTCCCTCTAGCAC 59.456 55.000 0.00 0.00 39.15 4.40
421 425 5.401750 AGCACTCTGGGTAGAATATGAGAT 58.598 41.667 0.00 0.00 31.21 2.75
427 431 8.207545 ACTCTGGGTAGAATATGAGATTTTGAC 58.792 37.037 0.00 0.00 31.21 3.18
436 440 4.525912 ATGAGATTTTGACCTGTTTGCC 57.474 40.909 0.00 0.00 0.00 4.52
486 490 7.806014 GCTGTTAGTGCTCTCAGTATTATCTAC 59.194 40.741 6.41 0.00 0.00 2.59
488 492 9.058174 TGTTAGTGCTCTCAGTATTATCTACTC 57.942 37.037 0.00 0.00 0.00 2.59
490 494 6.007703 AGTGCTCTCAGTATTATCTACTCCC 58.992 44.000 0.00 0.00 0.00 4.30
491 495 6.007703 GTGCTCTCAGTATTATCTACTCCCT 58.992 44.000 0.00 0.00 0.00 4.20
492 496 6.150474 GTGCTCTCAGTATTATCTACTCCCTC 59.850 46.154 0.00 0.00 0.00 4.30
493 497 5.650703 GCTCTCAGTATTATCTACTCCCTCC 59.349 48.000 0.00 0.00 0.00 4.30
494 498 5.806818 TCTCAGTATTATCTACTCCCTCCG 58.193 45.833 0.00 0.00 0.00 4.63
495 499 5.310068 TCTCAGTATTATCTACTCCCTCCGT 59.690 44.000 0.00 0.00 0.00 4.69
496 500 5.558818 TCAGTATTATCTACTCCCTCCGTC 58.441 45.833 0.00 0.00 0.00 4.79
497 501 4.701171 CAGTATTATCTACTCCCTCCGTCC 59.299 50.000 0.00 0.00 0.00 4.79
498 502 2.671896 TTATCTACTCCCTCCGTCCC 57.328 55.000 0.00 0.00 0.00 4.46
499 503 1.526315 TATCTACTCCCTCCGTCCCA 58.474 55.000 0.00 0.00 0.00 4.37
500 504 0.861155 ATCTACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
501 505 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
502 506 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
503 507 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
504 508 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
505 509 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
506 510 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
507 511 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
508 512 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
509 513 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
510 514 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
512 516 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
513 517 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
514 518 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
515 519 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
516 520 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
668 672 8.078596 GGTTCTGTATGAAAATTGCCATATCTC 58.921 37.037 4.10 0.00 36.30 2.75
679 683 4.970662 TGCCATATCTCACTGCTTTTTC 57.029 40.909 0.00 0.00 0.00 2.29
844 858 2.585330 TGTTGGTGATCACTGCATGTT 58.415 42.857 24.50 0.00 0.00 2.71
850 864 4.466015 TGGTGATCACTGCATGTTAGACTA 59.534 41.667 24.50 0.00 0.00 2.59
854 868 3.441101 TCACTGCATGTTAGACTACCCT 58.559 45.455 6.18 0.00 0.00 4.34
864 878 9.780186 GCATGTTAGACTACCCTTTCTATTAAT 57.220 33.333 0.00 0.00 0.00 1.40
897 911 9.106070 TCGTTCTCTTAAGGAAATAAAATAGCC 57.894 33.333 1.85 0.00 0.00 3.93
971 986 3.701542 CCACCAGCACTAGAGTCTAATCA 59.298 47.826 0.64 0.00 0.00 2.57
976 991 5.336372 CCAGCACTAGAGTCTAATCATAGCC 60.336 48.000 0.64 0.00 0.00 3.93
1060 1075 2.056577 CAAACAGCAAAGCTAGCTTGC 58.943 47.619 29.94 29.46 41.14 4.01
1128 1143 2.224281 TGTGGAGGCTGTTACTCAACTG 60.224 50.000 0.00 0.00 39.22 3.16
1149 1164 1.949525 GGCGGTCCTGATAGTACGTAA 59.050 52.381 0.00 0.00 0.00 3.18
1155 1170 4.340381 GGTCCTGATAGTACGTAACCACAT 59.660 45.833 0.00 0.00 0.00 3.21
1227 1243 7.328737 ACTGTGTAATCACTTTATGGGACTAC 58.671 38.462 0.00 0.00 44.14 2.73
1396 1413 1.606668 TGCCGTGGAACTCAAAACATC 59.393 47.619 0.00 0.00 31.75 3.06
1480 1497 4.861102 ATAAGCTTGGAATAAGCATGGC 57.139 40.909 9.86 0.00 45.30 4.40
2279 2298 1.663379 CTGTGACTGGCATGGCATGG 61.663 60.000 27.48 14.54 0.00 3.66
2326 2345 6.292381 GCCGTATTCTACAATGCACTAAGAAG 60.292 42.308 0.00 0.00 30.30 2.85
2502 2524 7.894708 TGGATGAGTAATTTCTGCAAAATGAA 58.105 30.769 7.36 0.00 0.00 2.57
2624 2646 5.830912 TCAAACCGATCCATATGCATTTTC 58.169 37.500 3.54 0.00 0.00 2.29
2668 2690 8.511321 AGATGTAATATCGTTGCTTTTTGTTGA 58.489 29.630 0.00 0.00 0.00 3.18
2717 2739 4.380550 GGGGCAAGTCTTTTGCTAATGTAC 60.381 45.833 11.18 0.00 44.36 2.90
3068 3137 1.580845 AATGGCTGCGAAGTCTGCAC 61.581 55.000 0.00 0.00 37.44 4.57
3084 3153 4.752101 GTCTGCACTAGAGACATTGTTTGT 59.248 41.667 0.00 0.00 42.79 2.83
3523 3592 2.029623 GCAATCAAGAGCCCATGTCAT 58.970 47.619 0.00 0.00 0.00 3.06
3583 3652 2.618302 CGGTTCTCCTACTCTCAGTCCA 60.618 54.545 0.00 0.00 0.00 4.02
3914 3983 0.321919 TGGCAGATGAGTTGACCAGC 60.322 55.000 0.00 0.00 0.00 4.85
4080 4150 1.963515 GTTTTCATGTCAGTGCCCCTT 59.036 47.619 0.00 0.00 0.00 3.95
4083 4153 3.517296 TTCATGTCAGTGCCCCTTTTA 57.483 42.857 0.00 0.00 0.00 1.52
4250 4320 9.097257 ACAAAATGTGGAATACAAACTTGAAAG 57.903 29.630 0.00 0.00 43.77 2.62
4251 4321 9.311916 CAAAATGTGGAATACAAACTTGAAAGA 57.688 29.630 0.00 0.00 43.77 2.52
4252 4322 9.883142 AAAATGTGGAATACAAACTTGAAAGAA 57.117 25.926 0.00 0.00 43.77 2.52
4253 4323 8.871686 AATGTGGAATACAAACTTGAAAGAAC 57.128 30.769 0.00 0.00 43.77 3.01
4254 4324 7.397892 TGTGGAATACAAACTTGAAAGAACA 57.602 32.000 0.00 0.00 36.06 3.18
4255 4325 8.006298 TGTGGAATACAAACTTGAAAGAACAT 57.994 30.769 0.00 0.00 36.06 2.71
4256 4326 8.134895 TGTGGAATACAAACTTGAAAGAACATC 58.865 33.333 0.00 0.00 36.06 3.06
4257 4327 8.352942 GTGGAATACAAACTTGAAAGAACATCT 58.647 33.333 0.00 0.00 0.00 2.90
4258 4328 9.567776 TGGAATACAAACTTGAAAGAACATCTA 57.432 29.630 0.00 0.00 0.00 1.98
4259 4329 9.827411 GGAATACAAACTTGAAAGAACATCTAC 57.173 33.333 0.00 0.00 0.00 2.59
4263 4333 8.911247 ACAAACTTGAAAGAACATCTACAAAC 57.089 30.769 0.00 0.00 0.00 2.93
4264 4334 8.739972 ACAAACTTGAAAGAACATCTACAAACT 58.260 29.630 0.00 0.00 0.00 2.66
4265 4335 9.573133 CAAACTTGAAAGAACATCTACAAACTT 57.427 29.630 0.00 0.00 0.00 2.66
4266 4336 9.573133 AAACTTGAAAGAACATCTACAAACTTG 57.427 29.630 0.00 0.00 0.00 3.16
4267 4337 8.506168 ACTTGAAAGAACATCTACAAACTTGA 57.494 30.769 0.00 0.00 0.00 3.02
4268 4338 8.956426 ACTTGAAAGAACATCTACAAACTTGAA 58.044 29.630 0.00 0.00 0.00 2.69
4269 4339 9.787532 CTTGAAAGAACATCTACAAACTTGAAA 57.212 29.630 0.00 0.00 0.00 2.69
4400 4470 8.927675 ATATCATTAGAAACTACTCTCTCCGT 57.072 34.615 0.00 0.00 0.00 4.69
4401 4471 7.648039 ATCATTAGAAACTACTCTCTCCGTT 57.352 36.000 0.00 0.00 0.00 4.44
4402 4472 7.086230 TCATTAGAAACTACTCTCTCCGTTC 57.914 40.000 0.00 0.00 0.00 3.95
4403 4473 5.893897 TTAGAAACTACTCTCTCCGTTCC 57.106 43.478 0.00 0.00 0.00 3.62
4404 4474 4.036941 AGAAACTACTCTCTCCGTTCCT 57.963 45.455 0.00 0.00 0.00 3.36
4405 4475 5.176741 AGAAACTACTCTCTCCGTTCCTA 57.823 43.478 0.00 0.00 0.00 2.94
4406 4476 5.568392 AGAAACTACTCTCTCCGTTCCTAA 58.432 41.667 0.00 0.00 0.00 2.69
4407 4477 6.008960 AGAAACTACTCTCTCCGTTCCTAAA 58.991 40.000 0.00 0.00 0.00 1.85
4408 4478 6.664384 AGAAACTACTCTCTCCGTTCCTAAAT 59.336 38.462 0.00 0.00 0.00 1.40
4409 4479 7.833183 AGAAACTACTCTCTCCGTTCCTAAATA 59.167 37.037 0.00 0.00 0.00 1.40
4410 4480 8.536340 AAACTACTCTCTCCGTTCCTAAATAT 57.464 34.615 0.00 0.00 0.00 1.28
4411 4481 8.536340 AACTACTCTCTCCGTTCCTAAATATT 57.464 34.615 0.00 0.00 0.00 1.28
4412 4482 8.536340 ACTACTCTCTCCGTTCCTAAATATTT 57.464 34.615 5.89 5.89 0.00 1.40
4413 4483 8.414778 ACTACTCTCTCCGTTCCTAAATATTTG 58.585 37.037 11.05 1.40 0.00 2.32
4414 4484 7.184067 ACTCTCTCCGTTCCTAAATATTTGT 57.816 36.000 11.05 0.00 0.00 2.83
4415 4485 7.266400 ACTCTCTCCGTTCCTAAATATTTGTC 58.734 38.462 11.05 0.00 0.00 3.18
4416 4486 7.124448 ACTCTCTCCGTTCCTAAATATTTGTCT 59.876 37.037 11.05 0.00 0.00 3.41
4417 4487 7.848128 TCTCTCCGTTCCTAAATATTTGTCTT 58.152 34.615 11.05 0.00 0.00 3.01
4418 4488 8.319146 TCTCTCCGTTCCTAAATATTTGTCTTT 58.681 33.333 11.05 0.00 0.00 2.52
4419 4489 8.857694 TCTCCGTTCCTAAATATTTGTCTTTT 57.142 30.769 11.05 0.00 0.00 2.27
4420 4490 9.292195 TCTCCGTTCCTAAATATTTGTCTTTTT 57.708 29.630 11.05 0.00 0.00 1.94
4444 4514 9.567776 TTTAGAGATTTCAAATTGACTACCACA 57.432 29.630 0.00 0.00 0.00 4.17
4445 4515 9.739276 TTAGAGATTTCAAATTGACTACCACAT 57.261 29.630 0.00 0.00 0.00 3.21
4447 4517 9.167311 AGAGATTTCAAATTGACTACCACATAC 57.833 33.333 0.00 0.00 0.00 2.39
4448 4518 9.167311 GAGATTTCAAATTGACTACCACATACT 57.833 33.333 0.00 0.00 0.00 2.12
4452 4522 9.733556 TTTCAAATTGACTACCACATACTATGT 57.266 29.630 0.00 0.00 46.22 2.29
4495 4565 7.932335 AGTGTAGATTCACTCCTTTCTATACG 58.068 38.462 0.00 0.00 44.07 3.06
4496 4566 7.013464 AGTGTAGATTCACTCCTTTCTATACGG 59.987 40.741 0.00 0.00 44.07 4.02
4497 4567 7.013083 GTGTAGATTCACTCCTTTCTATACGGA 59.987 40.741 0.00 0.00 35.68 4.69
4504 4574 5.838531 CTCCTTTCTATACGGAGTCACTT 57.161 43.478 0.00 0.00 43.93 3.16
4505 4575 5.578005 TCCTTTCTATACGGAGTCACTTG 57.422 43.478 0.00 0.00 43.93 3.16
4506 4576 5.014858 TCCTTTCTATACGGAGTCACTTGT 58.985 41.667 0.00 0.00 43.93 3.16
4507 4577 5.479375 TCCTTTCTATACGGAGTCACTTGTT 59.521 40.000 0.00 0.00 43.93 2.83
4508 4578 5.805994 CCTTTCTATACGGAGTCACTTGTTC 59.194 44.000 0.00 0.00 43.93 3.18
4509 4579 5.970317 TTCTATACGGAGTCACTTGTTCA 57.030 39.130 0.00 0.00 43.93 3.18
4510 4580 5.970317 TCTATACGGAGTCACTTGTTCAA 57.030 39.130 0.00 0.00 43.93 2.69
4511 4581 6.335471 TCTATACGGAGTCACTTGTTCAAA 57.665 37.500 0.00 0.00 43.93 2.69
4512 4582 6.931838 TCTATACGGAGTCACTTGTTCAAAT 58.068 36.000 0.00 0.00 43.93 2.32
4513 4583 7.033791 TCTATACGGAGTCACTTGTTCAAATC 58.966 38.462 0.00 0.00 43.93 2.17
4514 4584 4.073293 ACGGAGTCACTTGTTCAAATCT 57.927 40.909 0.00 0.00 29.74 2.40
4515 4585 4.058817 ACGGAGTCACTTGTTCAAATCTC 58.941 43.478 0.00 0.00 29.74 2.75
4516 4586 4.202264 ACGGAGTCACTTGTTCAAATCTCT 60.202 41.667 0.00 0.00 29.74 3.10
4517 4587 5.010719 ACGGAGTCACTTGTTCAAATCTCTA 59.989 40.000 0.00 0.00 29.74 2.43
4518 4588 5.574830 CGGAGTCACTTGTTCAAATCTCTAG 59.425 44.000 0.00 0.00 0.00 2.43
4519 4589 6.570571 CGGAGTCACTTGTTCAAATCTCTAGA 60.571 42.308 0.00 0.00 0.00 2.43
4520 4590 7.155328 GGAGTCACTTGTTCAAATCTCTAGAA 58.845 38.462 0.00 0.00 0.00 2.10
4521 4591 7.657761 GGAGTCACTTGTTCAAATCTCTAGAAA 59.342 37.037 0.00 0.00 0.00 2.52
4522 4592 8.600449 AGTCACTTGTTCAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 0.00 2.62
4523 4593 8.424918 AGTCACTTGTTCAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 0.00 2.52
4524 4594 8.491950 GTCACTTGTTCAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 0.00 3.01
4525 4595 8.204160 TCACTTGTTCAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
4526 4596 8.830580 CACTTGTTCAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
4527 4597 9.396022 ACTTGTTCAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
4543 4613 9.413734 AGAAAGACAAATATTTAGGAATGGAGG 57.586 33.333 0.00 0.00 0.00 4.30
4544 4614 8.539117 AAAGACAAATATTTAGGAATGGAGGG 57.461 34.615 0.00 0.00 0.00 4.30
4545 4615 7.465900 AGACAAATATTTAGGAATGGAGGGA 57.534 36.000 0.00 0.00 0.00 4.20
4546 4616 7.521669 AGACAAATATTTAGGAATGGAGGGAG 58.478 38.462 0.00 0.00 0.00 4.30
4547 4617 7.129504 AGACAAATATTTAGGAATGGAGGGAGT 59.870 37.037 0.00 0.00 0.00 3.85
4548 4618 8.344939 ACAAATATTTAGGAATGGAGGGAGTA 57.655 34.615 0.00 0.00 0.00 2.59
4549 4619 8.440771 ACAAATATTTAGGAATGGAGGGAGTAG 58.559 37.037 0.00 0.00 0.00 2.57
4550 4620 8.440771 CAAATATTTAGGAATGGAGGGAGTAGT 58.559 37.037 0.00 0.00 0.00 2.73
4551 4621 9.684702 AAATATTTAGGAATGGAGGGAGTAGTA 57.315 33.333 0.00 0.00 0.00 1.82
4552 4622 9.860393 AATATTTAGGAATGGAGGGAGTAGTAT 57.140 33.333 0.00 0.00 0.00 2.12
4553 4623 9.860393 ATATTTAGGAATGGAGGGAGTAGTATT 57.140 33.333 0.00 0.00 0.00 1.89
4554 4624 8.582891 ATTTAGGAATGGAGGGAGTAGTATTT 57.417 34.615 0.00 0.00 0.00 1.40
4555 4625 8.401955 TTTAGGAATGGAGGGAGTAGTATTTT 57.598 34.615 0.00 0.00 0.00 1.82
4556 4626 6.910259 AGGAATGGAGGGAGTAGTATTTTT 57.090 37.500 0.00 0.00 0.00 1.94
4557 4627 6.901300 AGGAATGGAGGGAGTAGTATTTTTC 58.099 40.000 0.00 0.00 0.00 2.29
4558 4628 6.447084 AGGAATGGAGGGAGTAGTATTTTTCA 59.553 38.462 0.00 0.00 0.00 2.69
4559 4629 7.036863 AGGAATGGAGGGAGTAGTATTTTTCAA 60.037 37.037 0.00 0.00 0.00 2.69
4560 4630 7.780271 GGAATGGAGGGAGTAGTATTTTTCAAT 59.220 37.037 0.00 0.00 0.00 2.57
4561 4631 9.847224 GAATGGAGGGAGTAGTATTTTTCAATA 57.153 33.333 0.00 0.00 0.00 1.90
4563 4633 9.799106 ATGGAGGGAGTAGTATTTTTCAATATG 57.201 33.333 0.00 0.00 0.00 1.78
4564 4634 8.998814 TGGAGGGAGTAGTATTTTTCAATATGA 58.001 33.333 0.00 0.00 0.00 2.15
4565 4635 9.847224 GGAGGGAGTAGTATTTTTCAATATGAA 57.153 33.333 0.00 0.00 34.03 2.57
4588 4658 9.202273 TGAATTCAACAATATACTTTTTGTGGC 57.798 29.630 5.45 0.00 36.26 5.01
4589 4659 9.202273 GAATTCAACAATATACTTTTTGTGGCA 57.798 29.630 0.00 0.00 36.26 4.92
4590 4660 9.723601 AATTCAACAATATACTTTTTGTGGCAT 57.276 25.926 0.00 0.00 36.26 4.40
4591 4661 8.755696 TTCAACAATATACTTTTTGTGGCATC 57.244 30.769 0.00 0.00 36.26 3.91
4592 4662 8.121305 TCAACAATATACTTTTTGTGGCATCT 57.879 30.769 0.00 0.00 36.26 2.90
4593 4663 9.237187 TCAACAATATACTTTTTGTGGCATCTA 57.763 29.630 0.00 0.00 36.26 1.98
4605 4675 8.945481 TTTTGTGGCATCTATTAATTCAATGG 57.055 30.769 0.00 0.00 0.00 3.16
4606 4676 7.658525 TTGTGGCATCTATTAATTCAATGGT 57.341 32.000 0.00 0.00 0.00 3.55
4607 4677 8.759481 TTGTGGCATCTATTAATTCAATGGTA 57.241 30.769 0.00 0.00 0.00 3.25
4608 4678 8.938801 TGTGGCATCTATTAATTCAATGGTAT 57.061 30.769 0.00 0.00 0.00 2.73
4609 4679 8.795513 TGTGGCATCTATTAATTCAATGGTATG 58.204 33.333 0.00 0.00 0.00 2.39
4610 4680 9.013229 GTGGCATCTATTAATTCAATGGTATGA 57.987 33.333 0.00 0.00 0.00 2.15
4611 4681 9.234827 TGGCATCTATTAATTCAATGGTATGAG 57.765 33.333 0.00 0.00 0.00 2.90
4612 4682 8.680903 GGCATCTATTAATTCAATGGTATGAGG 58.319 37.037 0.00 0.00 0.00 3.86
4613 4683 8.186821 GCATCTATTAATTCAATGGTATGAGGC 58.813 37.037 0.00 0.00 0.00 4.70
4614 4684 8.680903 CATCTATTAATTCAATGGTATGAGGCC 58.319 37.037 0.00 0.00 0.00 5.19
4615 4685 7.754624 TCTATTAATTCAATGGTATGAGGCCA 58.245 34.615 5.01 0.00 40.68 5.36
4616 4686 8.224025 TCTATTAATTCAATGGTATGAGGCCAA 58.776 33.333 5.01 0.00 39.72 4.52
4617 4687 6.463995 TTAATTCAATGGTATGAGGCCAAC 57.536 37.500 5.01 0.00 39.72 3.77
4618 4688 3.737559 TTCAATGGTATGAGGCCAACT 57.262 42.857 5.01 0.00 39.72 3.16
4619 4689 3.281727 TCAATGGTATGAGGCCAACTC 57.718 47.619 5.01 0.00 46.78 3.01
4620 4690 2.092429 TCAATGGTATGAGGCCAACTCC 60.092 50.000 5.01 0.85 46.01 3.85
4621 4691 1.595311 ATGGTATGAGGCCAACTCCA 58.405 50.000 5.01 7.36 46.01 3.86
4622 4692 1.367346 TGGTATGAGGCCAACTCCAA 58.633 50.000 5.01 0.00 46.01 3.53
4623 4693 1.004277 TGGTATGAGGCCAACTCCAAC 59.996 52.381 5.01 0.00 46.01 3.77
4624 4694 1.369625 GTATGAGGCCAACTCCAACG 58.630 55.000 5.01 0.00 46.01 4.10
4625 4695 0.392461 TATGAGGCCAACTCCAACGC 60.392 55.000 5.01 0.00 46.01 4.84
4626 4696 2.281484 GAGGCCAACTCCAACGCA 60.281 61.111 5.01 0.00 40.49 5.24
4627 4697 2.594592 AGGCCAACTCCAACGCAC 60.595 61.111 5.01 0.00 0.00 5.34
4628 4698 4.025401 GGCCAACTCCAACGCACG 62.025 66.667 0.00 0.00 0.00 5.34
4629 4699 2.970324 GCCAACTCCAACGCACGA 60.970 61.111 0.00 0.00 0.00 4.35
4630 4700 2.935955 CCAACTCCAACGCACGAC 59.064 61.111 0.00 0.00 0.00 4.34
4631 4701 2.604174 CCAACTCCAACGCACGACC 61.604 63.158 0.00 0.00 0.00 4.79
4632 4702 2.280592 AACTCCAACGCACGACCC 60.281 61.111 0.00 0.00 0.00 4.46
4633 4703 3.819877 AACTCCAACGCACGACCCC 62.820 63.158 0.00 0.00 0.00 4.95
4634 4704 4.308458 CTCCAACGCACGACCCCA 62.308 66.667 0.00 0.00 0.00 4.96
4635 4705 3.818121 CTCCAACGCACGACCCCAA 62.818 63.158 0.00 0.00 0.00 4.12
4636 4706 2.902846 CCAACGCACGACCCCAAA 60.903 61.111 0.00 0.00 0.00 3.28
4637 4707 2.265182 CCAACGCACGACCCCAAAT 61.265 57.895 0.00 0.00 0.00 2.32
4638 4708 1.081509 CAACGCACGACCCCAAATG 60.082 57.895 0.00 0.00 0.00 2.32
4639 4709 2.265182 AACGCACGACCCCAAATGG 61.265 57.895 0.00 0.00 0.00 3.16
4640 4710 2.671619 CGCACGACCCCAAATGGT 60.672 61.111 0.00 0.00 42.79 3.55
4647 4717 1.378762 ACCCCAAATGGTCTGACCG 59.621 57.895 21.15 8.07 42.58 4.79
4648 4718 2.046285 CCCCAAATGGTCTGACCGC 61.046 63.158 21.15 0.00 42.58 5.68
4649 4719 2.398554 CCCAAATGGTCTGACCGCG 61.399 63.158 21.15 0.00 42.58 6.46
4650 4720 1.671054 CCAAATGGTCTGACCGCGT 60.671 57.895 21.15 7.76 42.58 6.01
4651 4721 1.635663 CCAAATGGTCTGACCGCGTC 61.636 60.000 21.15 3.35 42.58 5.19
4652 4722 1.375523 AAATGGTCTGACCGCGTCC 60.376 57.895 21.15 0.00 42.58 4.79
4653 4723 3.642778 AATGGTCTGACCGCGTCCG 62.643 63.158 21.15 0.00 42.58 4.79
4655 4725 4.353437 GGTCTGACCGCGTCCGTT 62.353 66.667 11.71 0.00 0.00 4.44
4656 4726 2.355481 GTCTGACCGCGTCCGTTT 60.355 61.111 4.92 0.00 0.00 3.60
4657 4727 2.355363 TCTGACCGCGTCCGTTTG 60.355 61.111 4.92 0.00 0.00 2.93
4658 4728 3.411351 CTGACCGCGTCCGTTTGG 61.411 66.667 4.92 0.00 0.00 3.28
4659 4729 4.973055 TGACCGCGTCCGTTTGGG 62.973 66.667 4.92 0.00 35.24 4.12
4664 4734 3.597728 GCGTCCGTTTGGGGCAAA 61.598 61.111 0.00 0.00 42.07 3.68
4665 4735 3.121019 CGTCCGTTTGGGGCAAAA 58.879 55.556 0.00 0.00 42.07 2.44
4666 4736 1.299544 CGTCCGTTTGGGGCAAAAC 60.300 57.895 5.27 5.27 42.07 2.43
4670 4740 4.742274 GTTTGGGGCAAAACGGAC 57.258 55.556 0.12 0.00 35.03 4.79
4671 4741 1.817209 GTTTGGGGCAAAACGGACA 59.183 52.632 0.12 0.00 35.03 4.02
4672 4742 0.528901 GTTTGGGGCAAAACGGACAC 60.529 55.000 0.12 0.00 35.03 3.67
4673 4743 0.970937 TTTGGGGCAAAACGGACACA 60.971 50.000 0.00 0.00 29.89 3.72
4674 4744 0.970937 TTGGGGCAAAACGGACACAA 60.971 50.000 0.00 0.00 0.00 3.33
4675 4745 0.970937 TGGGGCAAAACGGACACAAA 60.971 50.000 0.00 0.00 0.00 2.83
4676 4746 0.391228 GGGGCAAAACGGACACAAAT 59.609 50.000 0.00 0.00 0.00 2.32
4677 4747 1.604438 GGGGCAAAACGGACACAAATC 60.604 52.381 0.00 0.00 0.00 2.17
4678 4748 1.404477 GGCAAAACGGACACAAATCG 58.596 50.000 0.00 0.00 0.00 3.34
4679 4749 0.775861 GCAAAACGGACACAAATCGC 59.224 50.000 0.00 0.00 0.00 4.58
4680 4750 1.041726 CAAAACGGACACAAATCGCG 58.958 50.000 0.00 0.00 0.00 5.87
4681 4751 0.040781 AAAACGGACACAAATCGCGG 60.041 50.000 6.13 0.00 0.00 6.46
4682 4752 2.452366 AAACGGACACAAATCGCGGC 62.452 55.000 6.13 0.00 0.00 6.53
4683 4753 4.160635 CGGACACAAATCGCGGCC 62.161 66.667 6.13 0.00 0.00 6.13
4684 4754 3.810896 GGACACAAATCGCGGCCC 61.811 66.667 6.13 0.00 0.00 5.80
4685 4755 3.053291 GACACAAATCGCGGCCCA 61.053 61.111 6.13 0.00 0.00 5.36
4686 4756 2.596046 ACACAAATCGCGGCCCAA 60.596 55.556 6.13 0.00 0.00 4.12
4687 4757 2.126502 CACAAATCGCGGCCCAAC 60.127 61.111 6.13 0.00 0.00 3.77
4688 4758 3.732892 ACAAATCGCGGCCCAACG 61.733 61.111 6.13 0.00 0.00 4.10
4689 4759 3.732892 CAAATCGCGGCCCAACGT 61.733 61.111 6.13 0.00 35.98 3.99
4690 4760 3.732892 AAATCGCGGCCCAACGTG 61.733 61.111 6.13 0.00 45.04 4.49
4709 4779 3.865700 CGGGAGCAAAAGGACAAAC 57.134 52.632 0.00 0.00 0.00 2.93
4710 4780 0.040425 CGGGAGCAAAAGGACAAACG 60.040 55.000 0.00 0.00 0.00 3.60
4711 4781 1.029681 GGGAGCAAAAGGACAAACGT 58.970 50.000 0.00 0.00 0.00 3.99
4712 4782 1.001706 GGGAGCAAAAGGACAAACGTC 60.002 52.381 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.402798 TGATATTTTCAAAGAAACCTGTAGCA 57.597 30.769 0.00 0.00 0.00 3.49
15 16 6.101997 GGGCTGATATTTTCAAAGAAACCTG 58.898 40.000 0.00 0.00 32.78 4.00
55 59 5.497464 TCATAATAGAATGATTCCCGCCA 57.503 39.130 0.75 0.00 30.92 5.69
93 97 1.626686 TCCAAACGGCCATCAATTGT 58.373 45.000 2.24 0.00 0.00 2.71
107 111 4.842531 TGAGCCATTCTAGTCATCCAAA 57.157 40.909 0.00 0.00 0.00 3.28
186 190 0.449388 GCTCAGGCAGGTCAATTTCG 59.551 55.000 0.00 0.00 38.54 3.46
264 268 7.342799 AGGCAACACAAACTGATATTGGAATAT 59.657 33.333 0.00 0.00 41.41 1.28
300 304 7.649533 ACAAGGCAGATCAATCAAATCATAA 57.350 32.000 0.00 0.00 0.00 1.90
402 406 7.659390 GGTCAAAATCTCATATTCTACCCAGAG 59.341 40.741 0.00 0.00 30.73 3.35
421 425 1.415659 CCCATGGCAAACAGGTCAAAA 59.584 47.619 6.09 0.00 0.00 2.44
436 440 3.021695 ACAGAGATGTCATTTGCCCATG 58.978 45.455 0.00 0.00 0.00 3.66
486 490 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
488 492 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
490 494 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
491 495 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
537 541 6.938030 TCTGTCCCATAATGTAAGACGTTTTT 59.062 34.615 0.00 0.00 0.00 1.94
538 542 6.469410 TCTGTCCCATAATGTAAGACGTTTT 58.531 36.000 0.00 0.00 0.00 2.43
539 543 6.045072 TCTGTCCCATAATGTAAGACGTTT 57.955 37.500 0.00 0.00 0.00 3.60
540 544 5.395324 CCTCTGTCCCATAATGTAAGACGTT 60.395 44.000 0.00 0.00 0.00 3.99
541 545 4.099573 CCTCTGTCCCATAATGTAAGACGT 59.900 45.833 0.00 0.00 0.00 4.34
542 546 4.501571 CCCTCTGTCCCATAATGTAAGACG 60.502 50.000 0.00 0.00 0.00 4.18
543 547 4.654262 TCCCTCTGTCCCATAATGTAAGAC 59.346 45.833 0.00 0.00 0.00 3.01
544 548 4.890988 TCCCTCTGTCCCATAATGTAAGA 58.109 43.478 0.00 0.00 0.00 2.10
545 549 4.656112 ACTCCCTCTGTCCCATAATGTAAG 59.344 45.833 0.00 0.00 0.00 2.34
546 550 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
547 551 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
548 552 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
549 553 4.594920 ACATACTCCCTCTGTCCCATAATG 59.405 45.833 0.00 0.00 0.00 1.90
550 554 4.832492 ACATACTCCCTCTGTCCCATAAT 58.168 43.478 0.00 0.00 0.00 1.28
551 555 4.280789 ACATACTCCCTCTGTCCCATAA 57.719 45.455 0.00 0.00 0.00 1.90
552 556 3.993658 ACATACTCCCTCTGTCCCATA 57.006 47.619 0.00 0.00 0.00 2.74
553 557 2.877154 ACATACTCCCTCTGTCCCAT 57.123 50.000 0.00 0.00 0.00 4.00
554 558 2.585900 AGTACATACTCCCTCTGTCCCA 59.414 50.000 0.00 0.00 0.00 4.37
555 559 3.315880 AGTACATACTCCCTCTGTCCC 57.684 52.381 0.00 0.00 0.00 4.46
556 560 6.980416 ATTTAGTACATACTCCCTCTGTCC 57.020 41.667 0.00 0.00 37.73 4.02
668 672 3.209410 ACACCTCAGAGAAAAAGCAGTG 58.791 45.455 0.00 0.00 0.00 3.66
679 683 3.706594 TGCCCTATTAAGACACCTCAGAG 59.293 47.826 0.00 0.00 0.00 3.35
850 864 9.654663 GAACGATGCTATATTAATAGAAAGGGT 57.345 33.333 1.02 0.00 37.84 4.34
872 886 9.110502 AGGCTATTTTATTTCCTTAAGAGAACG 57.889 33.333 3.36 0.00 0.00 3.95
971 986 0.457851 GTGAGCGACTGAGTGGCTAT 59.542 55.000 21.92 1.13 46.79 2.97
976 991 1.735920 GCAGGTGAGCGACTGAGTG 60.736 63.158 0.00 0.00 36.86 3.51
1077 1092 1.639298 GCAACTCATCTGTCCACCGC 61.639 60.000 0.00 0.00 0.00 5.68
1128 1143 1.105759 ACGTACTATCAGGACCGCCC 61.106 60.000 0.00 0.00 33.31 6.13
1433 1450 8.975663 ATGATGTTGAGTTGAGATAATGTGAT 57.024 30.769 0.00 0.00 0.00 3.06
1449 1466 8.786898 GCTTATTCCAAGCTTATATGATGTTGA 58.213 33.333 0.00 0.00 40.01 3.18
1714 1731 9.231297 ACAGATAAGTGCAACATAAGTACATTT 57.769 29.630 0.00 0.00 41.43 2.32
1730 1747 6.915544 ATGCACATAACTGACAGATAAGTG 57.084 37.500 18.48 18.48 29.25 3.16
2007 2025 8.801882 TGTATTTCTGAAAACAGTAATAGGGG 57.198 34.615 6.95 0.00 29.34 4.79
2326 2345 7.038154 AGAGAGTTGACTATGCTAGATGAAC 57.962 40.000 0.00 0.00 0.00 3.18
2478 2500 8.761575 TTTCATTTTGCAGAAATTACTCATCC 57.238 30.769 0.00 0.00 0.00 3.51
2668 2690 5.994250 ACGGATAGCATAGCATGGATAAAT 58.006 37.500 0.00 0.00 0.00 1.40
2717 2739 2.224314 GTCTCCAAGAAAAAGGTCGCTG 59.776 50.000 0.00 0.00 0.00 5.18
2990 3059 3.570125 GGACTTGTTTTTGCCTCTAGCTT 59.430 43.478 0.00 0.00 44.23 3.74
3068 3137 5.236478 ACCGAAACACAAACAATGTCTCTAG 59.764 40.000 0.00 0.00 41.46 2.43
3084 3153 6.869315 TGAATGAGATTACAAACCGAAACA 57.131 33.333 0.00 0.00 0.00 2.83
3219 3288 8.449397 GTTATCAGCACATCTTATCATTGATCC 58.551 37.037 1.55 0.00 0.00 3.36
3376 3445 0.595053 CGCTCGACACTGTGACAGTT 60.595 55.000 16.79 7.78 42.59 3.16
3523 3592 1.725641 CTGTTAGCAGCGGTTCATCA 58.274 50.000 0.00 0.00 35.77 3.07
3583 3652 2.359230 GCTGCCCTCTCGTGCTTT 60.359 61.111 0.00 0.00 0.00 3.51
3622 3691 2.272146 GCCTCCGGGAATTCAGCA 59.728 61.111 7.93 0.00 33.58 4.41
3770 3839 7.990886 GTCAACATACAACATATCCCCTTAGAA 59.009 37.037 0.00 0.00 0.00 2.10
3914 3983 4.994756 GTGCCCACCCCACCCAAG 62.995 72.222 0.00 0.00 0.00 3.61
4000 4070 8.543774 CCCTCATAACAAATAGGAGTAGCATAT 58.456 37.037 0.00 0.00 40.11 1.78
4008 4078 7.282585 TCAATCACCCTCATAACAAATAGGAG 58.717 38.462 0.00 0.00 41.13 3.69
4009 4079 7.206789 TCAATCACCCTCATAACAAATAGGA 57.793 36.000 0.00 0.00 0.00 2.94
4010 4080 7.720957 TCATCAATCACCCTCATAACAAATAGG 59.279 37.037 0.00 0.00 0.00 2.57
4011 4081 8.681486 TCATCAATCACCCTCATAACAAATAG 57.319 34.615 0.00 0.00 0.00 1.73
4012 4082 9.288576 GATCATCAATCACCCTCATAACAAATA 57.711 33.333 0.00 0.00 34.26 1.40
4013 4083 7.781219 TGATCATCAATCACCCTCATAACAAAT 59.219 33.333 0.00 0.00 39.52 2.32
4250 4320 7.968405 ACACAAGTTTCAAGTTTGTAGATGTTC 59.032 33.333 0.00 0.00 33.57 3.18
4251 4321 7.826690 ACACAAGTTTCAAGTTTGTAGATGTT 58.173 30.769 0.00 0.00 33.57 2.71
4252 4322 7.391148 ACACAAGTTTCAAGTTTGTAGATGT 57.609 32.000 0.00 0.00 33.57 3.06
4253 4323 8.612619 AGTACACAAGTTTCAAGTTTGTAGATG 58.387 33.333 0.00 0.00 33.57 2.90
4254 4324 8.732746 AGTACACAAGTTTCAAGTTTGTAGAT 57.267 30.769 0.00 0.00 33.57 1.98
4255 4325 7.279313 GGAGTACACAAGTTTCAAGTTTGTAGA 59.721 37.037 0.00 0.00 33.57 2.59
4256 4326 7.407337 GGAGTACACAAGTTTCAAGTTTGTAG 58.593 38.462 0.00 0.00 33.57 2.74
4257 4327 6.316890 GGGAGTACACAAGTTTCAAGTTTGTA 59.683 38.462 0.00 0.00 33.57 2.41
4258 4328 5.124936 GGGAGTACACAAGTTTCAAGTTTGT 59.875 40.000 0.00 0.00 35.56 2.83
4259 4329 5.357032 AGGGAGTACACAAGTTTCAAGTTTG 59.643 40.000 0.00 0.00 0.00 2.93
4260 4330 5.506708 AGGGAGTACACAAGTTTCAAGTTT 58.493 37.500 0.00 0.00 0.00 2.66
4261 4331 5.112129 AGGGAGTACACAAGTTTCAAGTT 57.888 39.130 0.00 0.00 0.00 2.66
4262 4332 4.444449 GGAGGGAGTACACAAGTTTCAAGT 60.444 45.833 0.00 0.00 0.00 3.16
4263 4333 4.065789 GGAGGGAGTACACAAGTTTCAAG 58.934 47.826 0.00 0.00 0.00 3.02
4264 4334 3.456644 TGGAGGGAGTACACAAGTTTCAA 59.543 43.478 0.00 0.00 0.00 2.69
4265 4335 3.042682 TGGAGGGAGTACACAAGTTTCA 58.957 45.455 0.00 0.00 0.00 2.69
4266 4336 3.764237 TGGAGGGAGTACACAAGTTTC 57.236 47.619 0.00 0.00 0.00 2.78
4267 4337 4.724279 AATGGAGGGAGTACACAAGTTT 57.276 40.909 0.00 0.00 0.00 2.66
4268 4338 4.398319 CAAATGGAGGGAGTACACAAGTT 58.602 43.478 0.00 0.00 0.00 2.66
4269 4339 3.244911 CCAAATGGAGGGAGTACACAAGT 60.245 47.826 0.00 0.00 37.39 3.16
4391 4461 7.493367 AGACAAATATTTAGGAACGGAGAGAG 58.507 38.462 0.00 0.00 0.00 3.20
4392 4462 7.419711 AGACAAATATTTAGGAACGGAGAGA 57.580 36.000 0.00 0.00 0.00 3.10
4393 4463 8.494016 AAAGACAAATATTTAGGAACGGAGAG 57.506 34.615 0.00 0.00 0.00 3.20
4394 4464 8.857694 AAAAGACAAATATTTAGGAACGGAGA 57.142 30.769 0.00 0.00 0.00 3.71
4418 4488 9.567776 TGTGGTAGTCAATTTGAAATCTCTAAA 57.432 29.630 0.00 0.00 0.00 1.85
4419 4489 9.739276 ATGTGGTAGTCAATTTGAAATCTCTAA 57.261 29.630 0.00 0.00 0.00 2.10
4421 4491 9.167311 GTATGTGGTAGTCAATTTGAAATCTCT 57.833 33.333 0.00 0.00 0.00 3.10
4422 4492 9.167311 AGTATGTGGTAGTCAATTTGAAATCTC 57.833 33.333 0.00 0.00 0.00 2.75
4426 4496 9.733556 ACATAGTATGTGGTAGTCAATTTGAAA 57.266 29.630 15.07 0.00 43.01 2.69
4471 4541 7.013083 TCCGTATAGAAAGGAGTGAATCTACAC 59.987 40.741 0.00 0.00 40.60 2.90
4472 4542 7.058525 TCCGTATAGAAAGGAGTGAATCTACA 58.941 38.462 0.00 0.00 31.43 2.74
4473 4543 7.507733 TCCGTATAGAAAGGAGTGAATCTAC 57.492 40.000 0.00 0.00 31.43 2.59
4474 4544 7.747155 CTCCGTATAGAAAGGAGTGAATCTA 57.253 40.000 2.77 0.00 45.80 1.98
4475 4545 6.642707 CTCCGTATAGAAAGGAGTGAATCT 57.357 41.667 2.77 0.00 45.80 2.40
4483 4553 5.014858 ACAAGTGACTCCGTATAGAAAGGA 58.985 41.667 0.00 0.00 34.27 3.36
4484 4554 5.326200 ACAAGTGACTCCGTATAGAAAGG 57.674 43.478 0.00 0.00 0.00 3.11
4485 4555 6.387465 TGAACAAGTGACTCCGTATAGAAAG 58.613 40.000 0.00 0.00 0.00 2.62
4486 4556 6.335471 TGAACAAGTGACTCCGTATAGAAA 57.665 37.500 0.00 0.00 0.00 2.52
4487 4557 5.970317 TGAACAAGTGACTCCGTATAGAA 57.030 39.130 0.00 0.00 0.00 2.10
4488 4558 5.970317 TTGAACAAGTGACTCCGTATAGA 57.030 39.130 0.00 0.00 0.00 1.98
4489 4559 7.036220 AGATTTGAACAAGTGACTCCGTATAG 58.964 38.462 0.00 0.00 0.00 1.31
4490 4560 6.931838 AGATTTGAACAAGTGACTCCGTATA 58.068 36.000 0.00 0.00 0.00 1.47
4491 4561 5.794894 AGATTTGAACAAGTGACTCCGTAT 58.205 37.500 0.00 0.00 0.00 3.06
4492 4562 5.010719 AGAGATTTGAACAAGTGACTCCGTA 59.989 40.000 0.00 0.00 0.00 4.02
4493 4563 4.058817 GAGATTTGAACAAGTGACTCCGT 58.941 43.478 0.00 0.00 0.00 4.69
4494 4564 4.310769 AGAGATTTGAACAAGTGACTCCG 58.689 43.478 0.00 0.00 0.00 4.63
4495 4565 6.692486 TCTAGAGATTTGAACAAGTGACTCC 58.308 40.000 0.00 0.00 0.00 3.85
4496 4566 8.594881 TTTCTAGAGATTTGAACAAGTGACTC 57.405 34.615 0.00 0.00 0.00 3.36
4497 4567 8.424918 TCTTTCTAGAGATTTGAACAAGTGACT 58.575 33.333 0.00 0.00 0.00 3.41
4498 4568 8.491950 GTCTTTCTAGAGATTTGAACAAGTGAC 58.508 37.037 0.00 0.00 0.00 3.67
4499 4569 8.204160 TGTCTTTCTAGAGATTTGAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
4500 4570 8.370493 TGTCTTTCTAGAGATTTGAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
4501 4571 8.964476 TTGTCTTTCTAGAGATTTGAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
4517 4587 9.413734 CCTCCATTCCTAAATATTTGTCTTTCT 57.586 33.333 11.05 0.00 0.00 2.52
4518 4588 8.633561 CCCTCCATTCCTAAATATTTGTCTTTC 58.366 37.037 11.05 0.00 0.00 2.62
4519 4589 8.343787 TCCCTCCATTCCTAAATATTTGTCTTT 58.656 33.333 11.05 0.00 0.00 2.52
4520 4590 7.882755 TCCCTCCATTCCTAAATATTTGTCTT 58.117 34.615 11.05 0.00 0.00 3.01
4521 4591 7.129504 ACTCCCTCCATTCCTAAATATTTGTCT 59.870 37.037 11.05 0.00 0.00 3.41
4522 4592 7.290813 ACTCCCTCCATTCCTAAATATTTGTC 58.709 38.462 11.05 0.00 0.00 3.18
4523 4593 7.226059 ACTCCCTCCATTCCTAAATATTTGT 57.774 36.000 11.05 0.00 0.00 2.83
4524 4594 8.440771 ACTACTCCCTCCATTCCTAAATATTTG 58.559 37.037 11.05 1.40 0.00 2.32
4525 4595 8.582891 ACTACTCCCTCCATTCCTAAATATTT 57.417 34.615 5.89 5.89 0.00 1.40
4526 4596 9.860393 ATACTACTCCCTCCATTCCTAAATATT 57.140 33.333 0.00 0.00 0.00 1.28
4527 4597 9.860393 AATACTACTCCCTCCATTCCTAAATAT 57.140 33.333 0.00 0.00 0.00 1.28
4528 4598 9.684702 AAATACTACTCCCTCCATTCCTAAATA 57.315 33.333 0.00 0.00 0.00 1.40
4529 4599 8.582891 AAATACTACTCCCTCCATTCCTAAAT 57.417 34.615 0.00 0.00 0.00 1.40
4530 4600 8.401955 AAAATACTACTCCCTCCATTCCTAAA 57.598 34.615 0.00 0.00 0.00 1.85
4531 4601 8.401955 AAAAATACTACTCCCTCCATTCCTAA 57.598 34.615 0.00 0.00 0.00 2.69
4532 4602 7.626084 TGAAAAATACTACTCCCTCCATTCCTA 59.374 37.037 0.00 0.00 0.00 2.94
4533 4603 6.447084 TGAAAAATACTACTCCCTCCATTCCT 59.553 38.462 0.00 0.00 0.00 3.36
4534 4604 6.659824 TGAAAAATACTACTCCCTCCATTCC 58.340 40.000 0.00 0.00 0.00 3.01
4535 4605 8.753497 ATTGAAAAATACTACTCCCTCCATTC 57.247 34.615 0.00 0.00 0.00 2.67
4537 4607 9.799106 CATATTGAAAAATACTACTCCCTCCAT 57.201 33.333 0.00 0.00 0.00 3.41
4538 4608 8.998814 TCATATTGAAAAATACTACTCCCTCCA 58.001 33.333 0.00 0.00 0.00 3.86
4539 4609 9.847224 TTCATATTGAAAAATACTACTCCCTCC 57.153 33.333 0.00 0.00 32.71 4.30
4562 4632 9.202273 GCCACAAAAAGTATATTGTTGAATTCA 57.798 29.630 3.38 3.38 37.66 2.57
4563 4633 9.202273 TGCCACAAAAAGTATATTGTTGAATTC 57.798 29.630 0.00 0.00 37.66 2.17
4564 4634 9.723601 ATGCCACAAAAAGTATATTGTTGAATT 57.276 25.926 0.00 0.00 37.66 2.17
4565 4635 9.369904 GATGCCACAAAAAGTATATTGTTGAAT 57.630 29.630 0.00 0.00 37.66 2.57
4566 4636 8.584157 AGATGCCACAAAAAGTATATTGTTGAA 58.416 29.630 0.00 0.00 37.66 2.69
4567 4637 8.121305 AGATGCCACAAAAAGTATATTGTTGA 57.879 30.769 0.00 0.00 37.66 3.18
4579 4649 9.381033 CCATTGAATTAATAGATGCCACAAAAA 57.619 29.630 0.00 0.00 0.00 1.94
4580 4650 8.538701 ACCATTGAATTAATAGATGCCACAAAA 58.461 29.630 0.00 0.00 0.00 2.44
4581 4651 8.076910 ACCATTGAATTAATAGATGCCACAAA 57.923 30.769 0.00 0.00 0.00 2.83
4582 4652 7.658525 ACCATTGAATTAATAGATGCCACAA 57.341 32.000 0.00 0.00 0.00 3.33
4583 4653 8.795513 CATACCATTGAATTAATAGATGCCACA 58.204 33.333 0.00 0.00 0.00 4.17
4584 4654 9.013229 TCATACCATTGAATTAATAGATGCCAC 57.987 33.333 0.00 0.00 0.00 5.01
4585 4655 9.234827 CTCATACCATTGAATTAATAGATGCCA 57.765 33.333 0.00 0.00 0.00 4.92
4586 4656 8.680903 CCTCATACCATTGAATTAATAGATGCC 58.319 37.037 0.00 0.00 0.00 4.40
4587 4657 8.186821 GCCTCATACCATTGAATTAATAGATGC 58.813 37.037 0.00 0.00 0.00 3.91
4588 4658 8.680903 GGCCTCATACCATTGAATTAATAGATG 58.319 37.037 0.00 0.00 0.00 2.90
4589 4659 8.393259 TGGCCTCATACCATTGAATTAATAGAT 58.607 33.333 3.32 0.00 30.29 1.98
4590 4660 7.754624 TGGCCTCATACCATTGAATTAATAGA 58.245 34.615 3.32 0.00 30.29 1.98
4591 4661 8.299570 GTTGGCCTCATACCATTGAATTAATAG 58.700 37.037 3.32 0.00 36.96 1.73
4592 4662 8.004215 AGTTGGCCTCATACCATTGAATTAATA 58.996 33.333 3.32 0.00 36.96 0.98
4593 4663 6.840705 AGTTGGCCTCATACCATTGAATTAAT 59.159 34.615 3.32 0.00 36.96 1.40
4594 4664 6.194235 AGTTGGCCTCATACCATTGAATTAA 58.806 36.000 3.32 0.00 36.96 1.40
4595 4665 5.765510 AGTTGGCCTCATACCATTGAATTA 58.234 37.500 3.32 0.00 36.96 1.40
4596 4666 4.613437 AGTTGGCCTCATACCATTGAATT 58.387 39.130 3.32 0.00 36.96 2.17
4597 4667 4.210331 GAGTTGGCCTCATACCATTGAAT 58.790 43.478 3.32 0.00 40.17 2.57
4598 4668 3.620488 GAGTTGGCCTCATACCATTGAA 58.380 45.455 3.32 0.00 40.17 2.69
4599 4669 2.092429 GGAGTTGGCCTCATACCATTGA 60.092 50.000 3.32 0.00 42.40 2.57
4600 4670 2.301346 GGAGTTGGCCTCATACCATTG 58.699 52.381 3.32 0.00 42.40 2.82
4601 4671 1.922447 TGGAGTTGGCCTCATACCATT 59.078 47.619 3.32 0.00 42.40 3.16
4602 4672 1.595311 TGGAGTTGGCCTCATACCAT 58.405 50.000 3.32 0.00 42.40 3.55
4603 4673 1.004277 GTTGGAGTTGGCCTCATACCA 59.996 52.381 3.32 4.68 42.40 3.25
4604 4674 1.751437 GTTGGAGTTGGCCTCATACC 58.249 55.000 3.32 1.79 42.40 2.73
4605 4675 1.369625 CGTTGGAGTTGGCCTCATAC 58.630 55.000 3.32 0.00 42.40 2.39
4606 4676 0.392461 GCGTTGGAGTTGGCCTCATA 60.392 55.000 3.32 0.00 42.40 2.15
4607 4677 1.675641 GCGTTGGAGTTGGCCTCAT 60.676 57.895 3.32 0.00 42.40 2.90
4608 4678 2.281484 GCGTTGGAGTTGGCCTCA 60.281 61.111 3.32 0.00 42.40 3.86
4609 4679 2.281484 TGCGTTGGAGTTGGCCTC 60.281 61.111 3.32 0.00 39.67 4.70
4610 4680 2.594592 GTGCGTTGGAGTTGGCCT 60.595 61.111 3.32 0.00 0.00 5.19
4611 4681 4.025401 CGTGCGTTGGAGTTGGCC 62.025 66.667 0.00 0.00 0.00 5.36
4612 4682 2.970324 TCGTGCGTTGGAGTTGGC 60.970 61.111 0.00 0.00 0.00 4.52
4613 4683 2.604174 GGTCGTGCGTTGGAGTTGG 61.604 63.158 0.00 0.00 0.00 3.77
4614 4684 2.604174 GGGTCGTGCGTTGGAGTTG 61.604 63.158 0.00 0.00 0.00 3.16
4615 4685 2.280592 GGGTCGTGCGTTGGAGTT 60.281 61.111 0.00 0.00 0.00 3.01
4616 4686 4.309950 GGGGTCGTGCGTTGGAGT 62.310 66.667 0.00 0.00 0.00 3.85
4617 4687 3.818121 TTGGGGTCGTGCGTTGGAG 62.818 63.158 0.00 0.00 0.00 3.86
4618 4688 2.684192 ATTTGGGGTCGTGCGTTGGA 62.684 55.000 0.00 0.00 0.00 3.53
4619 4689 2.265182 ATTTGGGGTCGTGCGTTGG 61.265 57.895 0.00 0.00 0.00 3.77
4620 4690 1.081509 CATTTGGGGTCGTGCGTTG 60.082 57.895 0.00 0.00 0.00 4.10
4621 4691 2.265182 CCATTTGGGGTCGTGCGTT 61.265 57.895 0.00 0.00 0.00 4.84
4622 4692 2.671619 CCATTTGGGGTCGTGCGT 60.672 61.111 0.00 0.00 0.00 5.24
4623 4693 2.671619 ACCATTTGGGGTCGTGCG 60.672 61.111 0.96 0.00 42.91 5.34
4629 4699 1.378762 CGGTCAGACCATTTGGGGT 59.621 57.895 20.13 0.00 46.02 4.95
4630 4700 2.046285 GCGGTCAGACCATTTGGGG 61.046 63.158 20.13 2.27 42.91 4.96
4631 4701 2.398554 CGCGGTCAGACCATTTGGG 61.399 63.158 20.13 7.56 38.47 4.12
4632 4702 1.635663 GACGCGGTCAGACCATTTGG 61.636 60.000 20.13 3.75 38.47 3.28
4633 4703 1.635663 GGACGCGGTCAGACCATTTG 61.636 60.000 20.13 7.97 38.47 2.32
4634 4704 1.375523 GGACGCGGTCAGACCATTT 60.376 57.895 20.13 1.83 38.47 2.32
4635 4705 2.264794 GGACGCGGTCAGACCATT 59.735 61.111 20.13 2.22 38.47 3.16
4636 4706 4.129737 CGGACGCGGTCAGACCAT 62.130 66.667 20.13 4.00 38.47 3.55
4638 4708 3.853597 AAACGGACGCGGTCAGACC 62.854 63.158 12.47 9.92 33.68 3.85
4639 4709 2.355481 AAACGGACGCGGTCAGAC 60.355 61.111 12.47 0.00 33.68 3.51
4640 4710 2.355363 CAAACGGACGCGGTCAGA 60.355 61.111 12.47 0.00 33.68 3.27
4641 4711 3.411351 CCAAACGGACGCGGTCAG 61.411 66.667 12.47 9.10 33.68 3.51
4642 4712 4.973055 CCCAAACGGACGCGGTCA 62.973 66.667 12.47 0.00 33.68 4.02
4647 4717 3.140225 TTTTGCCCCAAACGGACGC 62.140 57.895 0.00 0.00 32.79 5.19
4648 4718 1.299544 GTTTTGCCCCAAACGGACG 60.300 57.895 0.00 0.00 32.79 4.79
4649 4719 1.299544 CGTTTTGCCCCAAACGGAC 60.300 57.895 14.60 0.00 32.79 4.79
4650 4720 2.491022 CCGTTTTGCCCCAAACGGA 61.491 57.895 27.99 0.00 43.46 4.69
4651 4721 2.028337 CCGTTTTGCCCCAAACGG 59.972 61.111 22.67 22.67 39.47 4.44
4652 4722 1.299544 GTCCGTTTTGCCCCAAACG 60.300 57.895 15.18 15.18 32.79 3.60
4653 4723 0.528901 GTGTCCGTTTTGCCCCAAAC 60.529 55.000 0.00 0.00 32.79 2.93
4654 4724 0.970937 TGTGTCCGTTTTGCCCCAAA 60.971 50.000 0.00 0.00 0.00 3.28
4655 4725 0.970937 TTGTGTCCGTTTTGCCCCAA 60.971 50.000 0.00 0.00 0.00 4.12
4656 4726 0.970937 TTTGTGTCCGTTTTGCCCCA 60.971 50.000 0.00 0.00 0.00 4.96
4657 4727 0.391228 ATTTGTGTCCGTTTTGCCCC 59.609 50.000 0.00 0.00 0.00 5.80
4658 4728 1.778334 GATTTGTGTCCGTTTTGCCC 58.222 50.000 0.00 0.00 0.00 5.36
4659 4729 1.404477 CGATTTGTGTCCGTTTTGCC 58.596 50.000 0.00 0.00 0.00 4.52
4660 4730 0.775861 GCGATTTGTGTCCGTTTTGC 59.224 50.000 0.00 0.00 0.00 3.68
4661 4731 1.041726 CGCGATTTGTGTCCGTTTTG 58.958 50.000 0.00 0.00 0.00 2.44
4662 4732 0.040781 CCGCGATTTGTGTCCGTTTT 60.041 50.000 8.23 0.00 0.00 2.43
4663 4733 1.572447 CCGCGATTTGTGTCCGTTT 59.428 52.632 8.23 0.00 0.00 3.60
4664 4734 2.961669 GCCGCGATTTGTGTCCGTT 61.962 57.895 8.23 0.00 0.00 4.44
4665 4735 3.419759 GCCGCGATTTGTGTCCGT 61.420 61.111 8.23 0.00 0.00 4.69
4666 4736 4.160635 GGCCGCGATTTGTGTCCG 62.161 66.667 8.23 0.00 0.00 4.79
4667 4737 3.810896 GGGCCGCGATTTGTGTCC 61.811 66.667 8.23 0.00 0.00 4.02
4668 4738 2.622011 TTGGGCCGCGATTTGTGTC 61.622 57.895 8.23 0.00 0.00 3.67
4669 4739 2.596046 TTGGGCCGCGATTTGTGT 60.596 55.556 8.23 0.00 0.00 3.72
4670 4740 2.126502 GTTGGGCCGCGATTTGTG 60.127 61.111 8.23 0.00 0.00 3.33
4671 4741 3.732892 CGTTGGGCCGCGATTTGT 61.733 61.111 8.23 0.00 0.00 2.83
4672 4742 3.732892 ACGTTGGGCCGCGATTTG 61.733 61.111 23.64 0.00 0.00 2.32
4673 4743 3.732892 CACGTTGGGCCGCGATTT 61.733 61.111 23.64 2.21 0.00 2.17
4689 4759 0.753479 TTTGTCCTTTTGCTCCCGCA 60.753 50.000 0.00 0.00 46.24 5.69
4690 4760 0.318699 GTTTGTCCTTTTGCTCCCGC 60.319 55.000 0.00 0.00 0.00 6.13
4691 4761 0.040425 CGTTTGTCCTTTTGCTCCCG 60.040 55.000 0.00 0.00 0.00 5.14
4692 4762 1.001706 GACGTTTGTCCTTTTGCTCCC 60.002 52.381 0.00 0.00 39.30 4.30
4693 4763 2.401017 GACGTTTGTCCTTTTGCTCC 57.599 50.000 0.00 0.00 39.30 4.70


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

AutoCloner maintained by Alex Coulton.