Multiple sequence alignment - TraesCS2B01G292700

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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 TraesCS2B01G292700 chr2B 100.000 3827 0 0 1 3827 407885883 407889709 0.000000e+00 7068
1 TraesCS2B01G292700 chr2B 97.403 924 24 0 1 924 371367128 371366205 0.000000e+00 1574
2 TraesCS2B01G292700 chr2B 92.259 1098 41 9 2343 3400 51455682 51454589 0.000000e+00 1517
3 TraesCS2B01G292700 chr2B 84.127 378 48 10 3456 3827 669356090 669356461 4.700000e-94 355
4 TraesCS2B01G292700 chr2B 84.169 379 44 14 3456 3827 430819693 430819324 1.690000e-93 353
5 TraesCS2B01G292700 chr2B 83.989 356 47 9 3478 3827 435755727 435755376 2.200000e-87 333
6 TraesCS2B01G292700 chr2B 84.091 352 46 9 3482 3827 602888264 602887917 7.920000e-87 331
7 TraesCS2B01G292700 chr6D 91.109 2182 146 26 1673 3827 77329886 77332046 0.000000e+00 2911
8 TraesCS2B01G292700 chr6D 92.508 921 55 3 758 1668 77327964 77328880 0.000000e+00 1306
9 TraesCS2B01G292700 chr6D 83.380 355 48 9 3478 3827 338130698 338130350 6.170000e-83 318
10 TraesCS2B01G292700 chr6B 96.465 1669 57 2 1 1668 570078900 570080567 0.000000e+00 2754
11 TraesCS2B01G292700 chr6B 96.108 1670 60 2 1 1669 308976448 308978113 0.000000e+00 2719
12 TraesCS2B01G292700 chr6B 96.046 1669 65 1 1 1668 361272642 361270974 0.000000e+00 2715
13 TraesCS2B01G292700 chr6B 93.300 1791 55 18 1673 3413 361269954 361268179 0.000000e+00 2582
14 TraesCS2B01G292700 chr6B 93.183 1775 63 14 1669 3394 570081568 570083333 0.000000e+00 2555
15 TraesCS2B01G292700 chr6B 96.092 870 26 4 1673 2534 308979133 308980002 0.000000e+00 1411
16 TraesCS2B01G292700 chr5B 94.200 1776 50 12 1673 3400 176791772 176790002 0.000000e+00 2660
17 TraesCS2B01G292700 chr5B 92.736 1776 70 15 1673 3400 204613872 204612108 0.000000e+00 2510
18 TraesCS2B01G292700 chr5B 97.170 1449 40 1 221 1668 176794241 176792793 0.000000e+00 2447
19 TraesCS2B01G292700 chr5B 95.859 1449 58 2 221 1668 204616339 204614892 0.000000e+00 2342
20 TraesCS2B01G292700 chr1B 93.789 1771 56 12 1673 3394 192675879 192677644 0.000000e+00 2612
21 TraesCS2B01G292700 chr1B 92.772 1771 65 27 1673 3394 177160595 177162351 0.000000e+00 2503
22 TraesCS2B01G292700 chr1B 96.549 1449 49 1 221 1668 177158127 177159575 0.000000e+00 2398
23 TraesCS2B01G292700 chr1B 95.652 1449 50 4 221 1668 192673422 192674858 0.000000e+00 2314
24 TraesCS2B01G292700 chr1B 96.429 924 33 0 1 924 411019221 411018298 0.000000e+00 1524
25 TraesCS2B01G292700 chr7B 92.943 1672 62 31 1780 3405 131515161 131513500 0.000000e+00 2383
26 TraesCS2B01G292700 chr7B 96.355 823 28 2 1 822 131515987 131515166 0.000000e+00 1352
27 TraesCS2B01G292700 chr2D 93.722 1099 49 11 1675 2764 244756273 244757360 0.000000e+00 1629
28 TraesCS2B01G292700 chr2D 93.377 921 47 4 758 1668 244754335 244755251 0.000000e+00 1351
29 TraesCS2B01G292700 chr2D 83.754 357 47 8 3478 3827 161648627 161648275 1.030000e-85 327
30 TraesCS2B01G292700 chr1D 90.723 733 55 8 758 1479 348124535 348125265 0.000000e+00 965
31 TraesCS2B01G292700 chr6A 92.908 423 28 2 1 423 370481719 370482139 7.030000e-172 614
32 TraesCS2B01G292700 chr3A 84.551 356 45 9 3478 3827 217015353 217015704 1.020000e-90 344
33 TraesCS2B01G292700 chr3A 83.989 356 47 9 3478 3827 216939689 216940040 2.200000e-87 333


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 TraesCS2B01G292700 chr2B 407885883 407889709 3826 False 7068.0 7068 100.0000 1 3827 1 chr2B.!!$F1 3826
1 TraesCS2B01G292700 chr2B 371366205 371367128 923 True 1574.0 1574 97.4030 1 924 1 chr2B.!!$R2 923
2 TraesCS2B01G292700 chr2B 51454589 51455682 1093 True 1517.0 1517 92.2590 2343 3400 1 chr2B.!!$R1 1057
3 TraesCS2B01G292700 chr6D 77327964 77332046 4082 False 2108.5 2911 91.8085 758 3827 2 chr6D.!!$F1 3069
4 TraesCS2B01G292700 chr6B 570078900 570083333 4433 False 2654.5 2754 94.8240 1 3394 2 chr6B.!!$F2 3393
5 TraesCS2B01G292700 chr6B 361268179 361272642 4463 True 2648.5 2715 94.6730 1 3413 2 chr6B.!!$R1 3412
6 TraesCS2B01G292700 chr6B 308976448 308980002 3554 False 2065.0 2719 96.1000 1 2534 2 chr6B.!!$F1 2533
7 TraesCS2B01G292700 chr5B 176790002 176794241 4239 True 2553.5 2660 95.6850 221 3400 2 chr5B.!!$R1 3179
8 TraesCS2B01G292700 chr5B 204612108 204616339 4231 True 2426.0 2510 94.2975 221 3400 2 chr5B.!!$R2 3179
9 TraesCS2B01G292700 chr1B 192673422 192677644 4222 False 2463.0 2612 94.7205 221 3394 2 chr1B.!!$F2 3173
10 TraesCS2B01G292700 chr1B 177158127 177162351 4224 False 2450.5 2503 94.6605 221 3394 2 chr1B.!!$F1 3173
11 TraesCS2B01G292700 chr1B 411018298 411019221 923 True 1524.0 1524 96.4290 1 924 1 chr1B.!!$R1 923
12 TraesCS2B01G292700 chr7B 131513500 131515987 2487 True 1867.5 2383 94.6490 1 3405 2 chr7B.!!$R1 3404
13 TraesCS2B01G292700 chr2D 244754335 244757360 3025 False 1490.0 1629 93.5495 758 2764 2 chr2D.!!$F1 2006
14 TraesCS2B01G292700 chr1D 348124535 348125265 730 False 965.0 965 90.7230 758 1479 1 chr1D.!!$F1 721

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
198 200 0.320771 AGCGGCTACTGAACTTGTGG 60.321 55.0 0.0 0.0 0.0 4.17 F
1285 1309 0.924090 CTTATTGTCGGTCGCTCAGC 59.076 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 1559 1.340114 GGGAAGAAGCCGTTTGATCCT 60.340 52.381 0.0 0.0 0.0 3.24 R
2861 3960 5.545063 TTATCCTCATTGCCTTCATCGTA 57.455 39.130 0.0 0.0 0.0 3.43 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
88 90 6.843069 AACATGCATTTTAGTTCAAACACC 57.157 33.333 0.00 0.00 0.00 4.16
198 200 0.320771 AGCGGCTACTGAACTTGTGG 60.321 55.000 0.00 0.00 0.00 4.17
368 370 2.887568 CAACTGCGCCGCCTCTAG 60.888 66.667 6.63 0.00 0.00 2.43
824 826 4.885907 AGCCCATTCAAAGTAGTCATGATG 59.114 41.667 0.00 0.00 0.00 3.07
1111 1133 4.989279 AAGGTTCGTAATCGGCTACTTA 57.011 40.909 0.00 0.00 37.69 2.24
1113 1135 5.526506 AGGTTCGTAATCGGCTACTTAAT 57.473 39.130 0.00 0.00 37.69 1.40
1227 1249 7.279313 GTCTTATACTTTGCCCTTCAAATACGA 59.721 37.037 0.00 0.00 43.14 3.43
1285 1309 0.924090 CTTATTGTCGGTCGCTCAGC 59.076 55.000 0.00 0.00 0.00 4.26
1534 1559 6.899393 AATCTGCAGTTTTCAGGATAAACA 57.101 33.333 14.67 0.00 37.83 2.83
1617 1642 0.540365 CTCCCAGGCACAACCACAAT 60.540 55.000 0.00 0.00 43.14 2.71
1668 1693 3.030291 TGTGGTCCAAGTTCAGCAAATT 58.970 40.909 0.00 0.00 0.00 1.82
1669 1694 3.181477 TGTGGTCCAAGTTCAGCAAATTG 60.181 43.478 0.00 0.00 37.34 2.32
1671 1696 3.068024 TGGTCCAAGTTCAGCAAATTGAC 59.932 43.478 0.00 0.00 39.48 3.18
1778 2837 8.575589 CACTTGGCCTAGATAGCTCATATATAG 58.424 40.741 21.63 0.00 36.04 1.31
1826 2885 6.547141 TCAAGTCACAAGTTTGGAGATGATTT 59.453 34.615 0.00 0.00 0.00 2.17
2081 3143 8.328758 TGTTCCTTGTATTGATAGAGGATTGTT 58.671 33.333 0.00 0.00 0.00 2.83
2142 3204 2.092968 TCACATATGAGTTGGTGCTCCC 60.093 50.000 10.38 0.00 34.74 4.30
2318 3381 9.905713 TTTCTCTGGTGCTATAGTTCAATTTAT 57.094 29.630 0.84 0.00 0.00 1.40
2861 3960 4.445448 CCAAGCAGGCTAAGGATGAAGTAT 60.445 45.833 6.81 0.00 0.00 2.12
2881 3980 4.630644 ATACGATGAAGGCAATGAGGAT 57.369 40.909 0.00 0.00 0.00 3.24
3002 4102 8.519799 AGTTTGATGTTTCTACAAGAAAGGAA 57.480 30.769 2.42 0.00 44.07 3.36
3191 4303 9.354673 TCTATGGAATTTGAGAAAGTTTGTCTT 57.645 29.630 13.36 0.54 38.10 3.01
3337 4451 6.452494 TCAACCCAAAACATTTTCGAACTA 57.548 33.333 0.00 0.00 0.00 2.24
3340 4454 6.642707 ACCCAAAACATTTTCGAACTATGA 57.357 33.333 20.50 0.00 0.00 2.15
3341 4455 7.045126 ACCCAAAACATTTTCGAACTATGAA 57.955 32.000 20.50 4.39 0.00 2.57
3342 4456 7.493367 ACCCAAAACATTTTCGAACTATGAAA 58.507 30.769 20.50 3.73 33.73 2.69
3343 4457 7.982354 ACCCAAAACATTTTCGAACTATGAAAA 59.018 29.630 20.50 3.67 46.04 2.29
3344 4458 8.821894 CCCAAAACATTTTCGAACTATGAAAAA 58.178 29.630 20.50 2.42 45.38 1.94
3353 4467 8.842358 TTTCGAACTATGAAAAATACCTCAGT 57.158 30.769 0.00 0.00 32.70 3.41
3354 4468 9.932207 TTTCGAACTATGAAAAATACCTCAGTA 57.068 29.630 0.00 0.00 32.70 2.74
3355 4469 8.922058 TCGAACTATGAAAAATACCTCAGTAC 57.078 34.615 0.00 0.00 0.00 2.73
3356 4470 8.525316 TCGAACTATGAAAAATACCTCAGTACA 58.475 33.333 0.00 0.00 0.00 2.90
3357 4471 9.146984 CGAACTATGAAAAATACCTCAGTACAA 57.853 33.333 0.00 0.00 0.00 2.41
3360 4474 9.787435 ACTATGAAAAATACCTCAGTACAAACA 57.213 29.630 0.00 0.00 0.00 2.83
3400 4514 5.982324 CAAGTACTTTGTTTTCCGGACTAC 58.018 41.667 1.83 5.84 31.92 2.73
3401 4515 5.280654 AGTACTTTGTTTTCCGGACTACA 57.719 39.130 1.83 8.91 0.00 2.74
3402 4516 5.295152 AGTACTTTGTTTTCCGGACTACAG 58.705 41.667 1.83 3.31 0.00 2.74
3403 4517 4.411256 ACTTTGTTTTCCGGACTACAGA 57.589 40.909 1.83 5.91 0.00 3.41
3404 4518 4.969484 ACTTTGTTTTCCGGACTACAGAT 58.031 39.130 1.83 0.00 0.00 2.90
3405 4519 6.105397 ACTTTGTTTTCCGGACTACAGATA 57.895 37.500 1.83 0.65 0.00 1.98
3406 4520 6.708285 ACTTTGTTTTCCGGACTACAGATAT 58.292 36.000 1.83 0.00 0.00 1.63
3407 4521 7.844009 ACTTTGTTTTCCGGACTACAGATATA 58.156 34.615 1.83 0.00 0.00 0.86
3408 4522 8.483758 ACTTTGTTTTCCGGACTACAGATATAT 58.516 33.333 1.83 0.00 0.00 0.86
3409 4523 9.326413 CTTTGTTTTCCGGACTACAGATATATT 57.674 33.333 1.83 0.00 0.00 1.28
3411 4525 9.976511 TTGTTTTCCGGACTACAGATATATTAG 57.023 33.333 1.83 0.00 0.00 1.73
3412 4526 9.139734 TGTTTTCCGGACTACAGATATATTAGT 57.860 33.333 1.83 0.00 0.00 2.24
3434 4548 7.895975 AGTATAACTACTTTGTTTTCGGGAC 57.104 36.000 0.00 0.00 34.42 4.46
3435 4549 6.587608 AGTATAACTACTTTGTTTTCGGGACG 59.412 38.462 0.00 0.00 44.74 4.79
3436 4550 8.266841 AGTATAACTACTTTGTTTTCGGGACGG 61.267 40.741 0.00 0.00 43.91 4.79
3490 4604 9.986833 CAAAATATATCATTCAGTTCAACGACA 57.013 29.630 0.00 0.00 0.00 4.35
3495 4609 5.856126 TCATTCAGTTCAACGACATAACC 57.144 39.130 0.00 0.00 0.00 2.85
3496 4610 5.547465 TCATTCAGTTCAACGACATAACCT 58.453 37.500 0.00 0.00 0.00 3.50
3497 4611 6.693466 TCATTCAGTTCAACGACATAACCTA 58.307 36.000 0.00 0.00 0.00 3.08
3498 4612 7.327975 TCATTCAGTTCAACGACATAACCTAT 58.672 34.615 0.00 0.00 0.00 2.57
3499 4613 6.961359 TTCAGTTCAACGACATAACCTATG 57.039 37.500 0.00 0.00 41.88 2.23
3500 4614 4.868171 TCAGTTCAACGACATAACCTATGC 59.132 41.667 0.00 0.00 39.79 3.14
3501 4615 4.629634 CAGTTCAACGACATAACCTATGCA 59.370 41.667 0.00 0.00 39.79 3.96
3502 4616 5.121611 CAGTTCAACGACATAACCTATGCAA 59.878 40.000 0.00 0.00 39.79 4.08
3503 4617 5.351465 AGTTCAACGACATAACCTATGCAAG 59.649 40.000 0.00 0.00 39.79 4.01
3504 4618 4.827692 TCAACGACATAACCTATGCAAGT 58.172 39.130 0.00 0.00 39.79 3.16
3505 4619 5.242434 TCAACGACATAACCTATGCAAGTT 58.758 37.500 0.00 0.00 39.79 2.66
3506 4620 5.703592 TCAACGACATAACCTATGCAAGTTT 59.296 36.000 5.58 0.00 39.79 2.66
3507 4621 5.545658 ACGACATAACCTATGCAAGTTTG 57.454 39.130 5.58 6.78 39.79 2.93
3508 4622 5.242434 ACGACATAACCTATGCAAGTTTGA 58.758 37.500 5.58 0.00 39.79 2.69
3509 4623 5.703592 ACGACATAACCTATGCAAGTTTGAA 59.296 36.000 5.58 0.00 39.79 2.69
3510 4624 6.128282 ACGACATAACCTATGCAAGTTTGAAG 60.128 38.462 5.58 6.60 39.79 3.02
3511 4625 6.092122 CGACATAACCTATGCAAGTTTGAAGA 59.908 38.462 5.58 0.00 39.79 2.87
3512 4626 7.145932 ACATAACCTATGCAAGTTTGAAGAC 57.854 36.000 5.58 0.00 39.79 3.01
3513 4627 6.942576 ACATAACCTATGCAAGTTTGAAGACT 59.057 34.615 5.58 0.00 39.79 3.24
3514 4628 8.100791 ACATAACCTATGCAAGTTTGAAGACTA 58.899 33.333 5.58 0.00 39.79 2.59
3515 4629 9.113838 CATAACCTATGCAAGTTTGAAGACTAT 57.886 33.333 5.58 0.00 0.00 2.12
3516 4630 6.992063 ACCTATGCAAGTTTGAAGACTATG 57.008 37.500 0.00 0.00 0.00 2.23
3517 4631 6.711277 ACCTATGCAAGTTTGAAGACTATGA 58.289 36.000 0.00 0.00 0.00 2.15
3518 4632 7.341805 ACCTATGCAAGTTTGAAGACTATGAT 58.658 34.615 0.00 0.00 0.00 2.45
3519 4633 8.486210 ACCTATGCAAGTTTGAAGACTATGATA 58.514 33.333 0.00 0.00 0.00 2.15
3520 4634 9.499479 CCTATGCAAGTTTGAAGACTATGATAT 57.501 33.333 0.00 0.00 0.00 1.63
3522 4636 7.468922 TGCAAGTTTGAAGACTATGATATCG 57.531 36.000 0.00 0.00 0.00 2.92
3523 4637 7.041721 TGCAAGTTTGAAGACTATGATATCGT 58.958 34.615 2.37 2.37 0.00 3.73
3524 4638 8.194769 TGCAAGTTTGAAGACTATGATATCGTA 58.805 33.333 4.59 4.59 0.00 3.43
3525 4639 9.031360 GCAAGTTTGAAGACTATGATATCGTAA 57.969 33.333 6.14 0.00 0.00 3.18
3532 4646 9.516314 TGAAGACTATGATATCGTAAACAGTTG 57.484 33.333 6.14 0.00 0.00 3.16
3533 4647 9.731819 GAAGACTATGATATCGTAAACAGTTGA 57.268 33.333 6.14 0.00 0.00 3.18
3545 4659 9.931210 ATCGTAAACAGTTGAAAAAGTTAAGAG 57.069 29.630 0.00 0.00 0.00 2.85
3546 4660 9.153721 TCGTAAACAGTTGAAAAAGTTAAGAGA 57.846 29.630 0.00 0.00 0.00 3.10
3547 4661 9.763465 CGTAAACAGTTGAAAAAGTTAAGAGAA 57.237 29.630 0.00 0.00 0.00 2.87
3551 4665 9.974980 AACAGTTGAAAAAGTTAAGAGAAAACA 57.025 25.926 0.00 0.00 0.00 2.83
3552 4666 9.626045 ACAGTTGAAAAAGTTAAGAGAAAACAG 57.374 29.630 0.00 0.00 0.00 3.16
3553 4667 9.626045 CAGTTGAAAAAGTTAAGAGAAAACAGT 57.374 29.630 0.00 0.00 0.00 3.55
3629 4989 5.511386 AATGGAGATCAGTTTGAGTCCTT 57.489 39.130 0.00 3.65 35.52 3.36
3636 4996 5.823045 AGATCAGTTTGAGTCCTTCGTTTTT 59.177 36.000 0.00 0.00 0.00 1.94
3684 5044 1.078759 ATAGCTCAGCGCGAACACAC 61.079 55.000 12.10 0.00 45.59 3.82
3686 5046 2.546321 CTCAGCGCGAACACACAC 59.454 61.111 12.10 0.00 0.00 3.82
3687 5047 3.268446 CTCAGCGCGAACACACACG 62.268 63.158 12.10 0.00 0.00 4.49
3697 5057 3.668757 GCGAACACACACGTAGATCAGTA 60.669 47.826 0.00 0.00 0.00 2.74
3715 5075 4.807304 TCAGTACGACAACTCTGTTTTTCC 59.193 41.667 0.00 0.00 35.30 3.13
3716 5076 4.809426 CAGTACGACAACTCTGTTTTTCCT 59.191 41.667 0.00 0.00 35.30 3.36
3717 5077 5.981315 CAGTACGACAACTCTGTTTTTCCTA 59.019 40.000 0.00 0.00 35.30 2.94
3718 5078 6.477688 CAGTACGACAACTCTGTTTTTCCTAA 59.522 38.462 0.00 0.00 35.30 2.69
3719 5079 5.986004 ACGACAACTCTGTTTTTCCTAAG 57.014 39.130 0.00 0.00 35.30 2.18
3720 5080 4.814771 ACGACAACTCTGTTTTTCCTAAGG 59.185 41.667 0.00 0.00 35.30 2.69
3751 5111 4.868067 ACACGATGGATCTTACCGTATTC 58.132 43.478 0.00 0.00 31.83 1.75
3753 5113 5.163488 ACACGATGGATCTTACCGTATTCAA 60.163 40.000 0.00 0.00 31.83 2.69
3770 5130 6.464834 CGTATTCAAAATTACTCTTCAACGGC 59.535 38.462 0.00 0.00 0.00 5.68
3772 5132 7.681939 ATTCAAAATTACTCTTCAACGGCTA 57.318 32.000 0.00 0.00 0.00 3.93
3773 5133 7.499321 TTCAAAATTACTCTTCAACGGCTAA 57.501 32.000 0.00 0.00 0.00 3.09
3777 5137 7.923414 AAATTACTCTTCAACGGCTAAGAAT 57.077 32.000 0.00 0.00 31.61 2.40
3787 5147 6.435428 TCAACGGCTAAGAATTTGAGAAAAC 58.565 36.000 0.00 0.00 0.00 2.43
3788 5148 5.030874 ACGGCTAAGAATTTGAGAAAACG 57.969 39.130 0.00 0.00 0.00 3.60
3789 5149 4.514066 ACGGCTAAGAATTTGAGAAAACGT 59.486 37.500 0.00 0.00 0.00 3.99
3790 5150 5.080068 CGGCTAAGAATTTGAGAAAACGTC 58.920 41.667 0.00 0.00 0.00 4.34
3807 5170 6.445357 AAACGTCCAACATGACTAAGTTTT 57.555 33.333 0.00 0.00 32.97 2.43
3815 5178 7.768120 TCCAACATGACTAAGTTTTGCATTTTT 59.232 29.630 0.00 0.00 0.00 1.94
3823 5186 9.840427 GACTAAGTTTTGCATTTTTGATAGCTA 57.160 29.630 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 90 3.694072 TGAACTCTGTGGTCCAAAACTTG 59.306 43.478 0.00 0.00 0.00 3.16
198 200 0.318445 CAGTCCAAAAGCAGCAGCAC 60.318 55.000 3.17 0.00 45.49 4.40
313 315 6.482308 GTGTAAGTTTCAACTATCAGGTGTGT 59.518 38.462 0.00 0.00 38.57 3.72
368 370 2.751806 CAAGTCATTCCCAAGGAGCTTC 59.248 50.000 0.00 0.00 31.21 3.86
667 669 8.362464 ACTGAGATGGTCAACTAATTGTACTA 57.638 34.615 0.00 0.00 37.11 1.82
824 826 5.869888 CGATAAAACATAGCATCCTAGTCCC 59.130 44.000 0.00 0.00 0.00 4.46
970 981 6.230472 TGCAGCAGTTTCTGTAGAAATTCTA 58.770 36.000 9.98 0.00 44.69 2.10
1119 1141 5.198207 ACCTTTACCCACATAATAGCAACC 58.802 41.667 0.00 0.00 0.00 3.77
1129 1151 4.675063 AAATGAGGACCTTTACCCACAT 57.325 40.909 0.00 0.00 0.00 3.21
1534 1559 1.340114 GGGAAGAAGCCGTTTGATCCT 60.340 52.381 0.00 0.00 0.00 3.24
1617 1642 5.414454 CGGTCAATTTGGACTGAAAAGGATA 59.586 40.000 0.00 0.00 45.13 2.59
1668 1693 3.079578 ACGAACTTATCTGAGACGGTCA 58.920 45.455 11.27 0.00 0.00 4.02
1669 1694 3.126514 TCACGAACTTATCTGAGACGGTC 59.873 47.826 0.00 0.00 0.00 4.79
1671 1696 3.759527 TCACGAACTTATCTGAGACGG 57.240 47.619 0.00 0.00 0.00 4.79
1971 3031 3.484806 AGGGCACACGAACCACCA 61.485 61.111 0.00 0.00 0.00 4.17
2081 3143 2.086869 GTGCAGCTGGCTTTAGATTCA 58.913 47.619 17.12 0.00 45.15 2.57
2142 3204 6.403333 TTTGCTAATTAGAACACTACTGCG 57.597 37.500 16.85 0.00 0.00 5.18
2179 3241 8.893563 AATATTTAACCACCATCTTCTTTCCA 57.106 30.769 0.00 0.00 0.00 3.53
2861 3960 5.545063 TTATCCTCATTGCCTTCATCGTA 57.455 39.130 0.00 0.00 0.00 3.43
2881 3980 9.887629 ATGTTTATGGATTGCATGTTTTCATTA 57.112 25.926 0.28 0.00 38.64 1.90
3154 4266 6.414732 TCAAATTCCATAGAAGAACCGACAT 58.585 36.000 0.00 0.00 34.86 3.06
3186 4298 6.767902 GCATATATTCCTCAGGTTCAAAGACA 59.232 38.462 0.00 0.00 0.00 3.41
3191 4303 6.499106 TGAGCATATATTCCTCAGGTTCAA 57.501 37.500 8.19 0.00 32.30 2.69
3377 4491 5.524646 TGTAGTCCGGAAAACAAAGTACTTG 59.475 40.000 15.80 6.22 41.19 3.16
3378 4492 5.673514 TGTAGTCCGGAAAACAAAGTACTT 58.326 37.500 15.80 1.12 0.00 2.24
3379 4493 5.069516 TCTGTAGTCCGGAAAACAAAGTACT 59.930 40.000 18.02 6.06 0.00 2.73
3380 4494 5.291971 TCTGTAGTCCGGAAAACAAAGTAC 58.708 41.667 18.02 8.00 0.00 2.73
3381 4495 5.534207 TCTGTAGTCCGGAAAACAAAGTA 57.466 39.130 18.02 5.04 0.00 2.24
3382 4496 4.411256 TCTGTAGTCCGGAAAACAAAGT 57.589 40.909 18.02 0.00 0.00 2.66
3383 4497 8.888579 ATATATCTGTAGTCCGGAAAACAAAG 57.111 34.615 18.02 9.86 30.50 2.77
3385 4499 9.976511 CTAATATATCTGTAGTCCGGAAAACAA 57.023 33.333 18.02 11.18 30.50 2.83
3386 4500 9.139734 ACTAATATATCTGTAGTCCGGAAAACA 57.860 33.333 5.23 13.02 30.50 2.83
3408 4522 9.423061 GTCCCGAAAACAAAGTAGTTATACTAA 57.577 33.333 0.00 0.00 41.54 2.24
3409 4523 7.754924 CGTCCCGAAAACAAAGTAGTTATACTA 59.245 37.037 0.00 0.00 41.54 1.82
3410 4524 6.587608 CGTCCCGAAAACAAAGTAGTTATACT 59.412 38.462 0.00 0.00 44.37 2.12
3411 4525 6.183360 CCGTCCCGAAAACAAAGTAGTTATAC 60.183 42.308 0.00 0.00 0.00 1.47
3412 4526 5.868801 CCGTCCCGAAAACAAAGTAGTTATA 59.131 40.000 0.00 0.00 0.00 0.98
3413 4527 4.692155 CCGTCCCGAAAACAAAGTAGTTAT 59.308 41.667 0.00 0.00 0.00 1.89
3414 4528 4.057432 CCGTCCCGAAAACAAAGTAGTTA 58.943 43.478 0.00 0.00 0.00 2.24
3415 4529 2.874086 CCGTCCCGAAAACAAAGTAGTT 59.126 45.455 0.00 0.00 0.00 2.24
3416 4530 2.486918 CCGTCCCGAAAACAAAGTAGT 58.513 47.619 0.00 0.00 0.00 2.73
3417 4531 1.802365 CCCGTCCCGAAAACAAAGTAG 59.198 52.381 0.00 0.00 0.00 2.57
3418 4532 1.415659 TCCCGTCCCGAAAACAAAGTA 59.584 47.619 0.00 0.00 0.00 2.24
3419 4533 0.180878 TCCCGTCCCGAAAACAAAGT 59.819 50.000 0.00 0.00 0.00 2.66
3420 4534 0.872388 CTCCCGTCCCGAAAACAAAG 59.128 55.000 0.00 0.00 0.00 2.77
3421 4535 0.469070 TCTCCCGTCCCGAAAACAAA 59.531 50.000 0.00 0.00 0.00 2.83
3422 4536 0.469070 TTCTCCCGTCCCGAAAACAA 59.531 50.000 0.00 0.00 0.00 2.83
3423 4537 0.469070 TTTCTCCCGTCCCGAAAACA 59.531 50.000 0.00 0.00 0.00 2.83
3424 4538 0.870393 GTTTCTCCCGTCCCGAAAAC 59.130 55.000 0.00 0.00 0.00 2.43
3425 4539 0.760572 AGTTTCTCCCGTCCCGAAAA 59.239 50.000 0.00 0.00 0.00 2.29
3426 4540 0.319405 GAGTTTCTCCCGTCCCGAAA 59.681 55.000 0.00 0.00 0.00 3.46
3427 4541 0.828762 TGAGTTTCTCCCGTCCCGAA 60.829 55.000 0.00 0.00 0.00 4.30
3428 4542 1.228644 TGAGTTTCTCCCGTCCCGA 60.229 57.895 0.00 0.00 0.00 5.14
3429 4543 1.080025 GTGAGTTTCTCCCGTCCCG 60.080 63.158 0.00 0.00 0.00 5.14
3430 4544 1.080025 CGTGAGTTTCTCCCGTCCC 60.080 63.158 0.00 0.00 0.00 4.46
3431 4545 0.316204 TTCGTGAGTTTCTCCCGTCC 59.684 55.000 2.25 0.00 33.45 4.79
3432 4546 2.144482 TTTCGTGAGTTTCTCCCGTC 57.856 50.000 2.25 0.00 33.45 4.79
3433 4547 2.833631 ATTTCGTGAGTTTCTCCCGT 57.166 45.000 2.25 0.00 33.45 5.28
3434 4548 5.796350 AATAATTTCGTGAGTTTCTCCCG 57.204 39.130 0.00 0.00 33.01 5.14
3464 4578 9.986833 TGTCGTTGAACTGAATGATATATTTTG 57.013 29.630 0.00 0.00 0.00 2.44
3469 4583 9.256477 GGTTATGTCGTTGAACTGAATGATATA 57.744 33.333 0.00 0.00 0.00 0.86
3470 4584 7.987458 AGGTTATGTCGTTGAACTGAATGATAT 59.013 33.333 0.00 0.00 0.00 1.63
3471 4585 7.327975 AGGTTATGTCGTTGAACTGAATGATA 58.672 34.615 0.00 0.00 0.00 2.15
3472 4586 6.173339 AGGTTATGTCGTTGAACTGAATGAT 58.827 36.000 0.00 0.00 0.00 2.45
3473 4587 5.547465 AGGTTATGTCGTTGAACTGAATGA 58.453 37.500 0.00 0.00 0.00 2.57
3474 4588 5.862924 AGGTTATGTCGTTGAACTGAATG 57.137 39.130 0.00 0.00 0.00 2.67
3475 4589 6.037172 GCATAGGTTATGTCGTTGAACTGAAT 59.963 38.462 0.00 0.00 38.43 2.57
3476 4590 5.350365 GCATAGGTTATGTCGTTGAACTGAA 59.650 40.000 0.00 0.00 38.43 3.02
3477 4591 4.868171 GCATAGGTTATGTCGTTGAACTGA 59.132 41.667 0.00 0.00 38.43 3.41
3478 4592 4.629634 TGCATAGGTTATGTCGTTGAACTG 59.370 41.667 0.00 0.00 38.43 3.16
3479 4593 4.827692 TGCATAGGTTATGTCGTTGAACT 58.172 39.130 0.00 0.00 38.43 3.01
3480 4594 5.121768 ACTTGCATAGGTTATGTCGTTGAAC 59.878 40.000 0.00 0.00 38.43 3.18
3481 4595 5.242434 ACTTGCATAGGTTATGTCGTTGAA 58.758 37.500 0.00 0.00 38.43 2.69
3482 4596 4.827692 ACTTGCATAGGTTATGTCGTTGA 58.172 39.130 0.00 0.00 38.43 3.18
3483 4597 5.545658 AACTTGCATAGGTTATGTCGTTG 57.454 39.130 0.00 0.00 38.43 4.10
3484 4598 5.703592 TCAAACTTGCATAGGTTATGTCGTT 59.296 36.000 0.00 0.00 38.43 3.85
3485 4599 5.242434 TCAAACTTGCATAGGTTATGTCGT 58.758 37.500 0.00 0.00 38.43 4.34
3486 4600 5.794687 TCAAACTTGCATAGGTTATGTCG 57.205 39.130 0.00 0.00 38.43 4.35
3487 4601 7.119846 AGTCTTCAAACTTGCATAGGTTATGTC 59.880 37.037 0.00 0.00 38.43 3.06
3488 4602 6.942576 AGTCTTCAAACTTGCATAGGTTATGT 59.057 34.615 0.00 0.00 38.43 2.29
3489 4603 7.383102 AGTCTTCAAACTTGCATAGGTTATG 57.617 36.000 0.00 0.00 39.18 1.90
3490 4604 9.113838 CATAGTCTTCAAACTTGCATAGGTTAT 57.886 33.333 0.00 0.00 29.95 1.89
3491 4605 8.318412 TCATAGTCTTCAAACTTGCATAGGTTA 58.682 33.333 0.00 0.00 29.95 2.85
3492 4606 7.168219 TCATAGTCTTCAAACTTGCATAGGTT 58.832 34.615 0.00 0.00 32.68 3.50
3493 4607 6.711277 TCATAGTCTTCAAACTTGCATAGGT 58.289 36.000 0.00 0.00 0.00 3.08
3494 4608 7.798596 ATCATAGTCTTCAAACTTGCATAGG 57.201 36.000 0.00 0.00 0.00 2.57
3496 4610 9.196552 CGATATCATAGTCTTCAAACTTGCATA 57.803 33.333 3.12 0.00 0.00 3.14
3497 4611 7.712639 ACGATATCATAGTCTTCAAACTTGCAT 59.287 33.333 3.12 0.00 0.00 3.96
3498 4612 7.041721 ACGATATCATAGTCTTCAAACTTGCA 58.958 34.615 3.12 0.00 0.00 4.08
3499 4613 7.470289 ACGATATCATAGTCTTCAAACTTGC 57.530 36.000 3.12 0.00 0.00 4.01
3506 4620 9.516314 CAACTGTTTACGATATCATAGTCTTCA 57.484 33.333 3.12 0.00 0.00 3.02
3507 4621 9.731819 TCAACTGTTTACGATATCATAGTCTTC 57.268 33.333 3.12 0.00 0.00 2.87
3519 4633 9.931210 CTCTTAACTTTTTCAACTGTTTACGAT 57.069 29.630 0.00 0.00 0.00 3.73
3520 4634 9.153721 TCTCTTAACTTTTTCAACTGTTTACGA 57.846 29.630 0.00 0.00 0.00 3.43
3521 4635 9.763465 TTCTCTTAACTTTTTCAACTGTTTACG 57.237 29.630 0.00 0.00 0.00 3.18
3525 4639 9.974980 TGTTTTCTCTTAACTTTTTCAACTGTT 57.025 25.926 0.00 0.00 0.00 3.16
3526 4640 9.626045 CTGTTTTCTCTTAACTTTTTCAACTGT 57.374 29.630 0.00 0.00 0.00 3.55
3527 4641 9.626045 ACTGTTTTCTCTTAACTTTTTCAACTG 57.374 29.630 0.00 0.00 0.00 3.16
3563 4677 9.844257 GTGTTTTATAGACTAGACCCTACTCTA 57.156 37.037 0.00 0.00 0.00 2.43
3564 4678 7.498570 CGTGTTTTATAGACTAGACCCTACTCT 59.501 40.741 0.00 0.00 0.00 3.24
3565 4679 7.638134 CGTGTTTTATAGACTAGACCCTACTC 58.362 42.308 0.00 0.00 0.00 2.59
3566 4680 6.039159 GCGTGTTTTATAGACTAGACCCTACT 59.961 42.308 0.00 0.00 0.00 2.57
3567 4681 6.039159 AGCGTGTTTTATAGACTAGACCCTAC 59.961 42.308 0.00 0.00 0.00 3.18
3568 4682 6.125029 AGCGTGTTTTATAGACTAGACCCTA 58.875 40.000 0.00 0.00 0.00 3.53
3569 4683 4.954826 AGCGTGTTTTATAGACTAGACCCT 59.045 41.667 0.00 0.00 0.00 4.34
3570 4684 5.163581 TGAGCGTGTTTTATAGACTAGACCC 60.164 44.000 0.00 0.00 0.00 4.46
3571 4685 5.888105 TGAGCGTGTTTTATAGACTAGACC 58.112 41.667 0.00 0.00 0.00 3.85
3572 4686 6.553524 ACTGAGCGTGTTTTATAGACTAGAC 58.446 40.000 0.00 0.00 0.00 2.59
3573 4687 6.754702 ACTGAGCGTGTTTTATAGACTAGA 57.245 37.500 0.00 0.00 0.00 2.43
3574 4688 7.470079 TGTACTGAGCGTGTTTTATAGACTAG 58.530 38.462 0.00 0.00 0.00 2.57
3575 4689 7.381766 TGTACTGAGCGTGTTTTATAGACTA 57.618 36.000 0.00 0.00 0.00 2.59
3576 4690 6.263516 TGTACTGAGCGTGTTTTATAGACT 57.736 37.500 0.00 0.00 0.00 3.24
3577 4691 6.939551 TTGTACTGAGCGTGTTTTATAGAC 57.060 37.500 0.00 0.00 0.00 2.59
3578 4692 6.366877 GGTTTGTACTGAGCGTGTTTTATAGA 59.633 38.462 0.00 0.00 0.00 1.98
3579 4693 6.401796 GGGTTTGTACTGAGCGTGTTTTATAG 60.402 42.308 0.00 0.00 0.00 1.31
3580 4694 5.409214 GGGTTTGTACTGAGCGTGTTTTATA 59.591 40.000 0.00 0.00 0.00 0.98
3581 4695 4.214758 GGGTTTGTACTGAGCGTGTTTTAT 59.785 41.667 0.00 0.00 0.00 1.40
3582 4696 3.560896 GGGTTTGTACTGAGCGTGTTTTA 59.439 43.478 0.00 0.00 0.00 1.52
3625 4985 9.511144 GTTTTGAATTCTTCTAAAAACGAAGGA 57.489 29.630 7.05 0.00 38.66 3.36
3668 5028 3.337889 TGTGTGTTCGCGCTGAGC 61.338 61.111 5.56 7.49 43.95 4.26
3673 5033 1.342082 ATCTACGTGTGTGTTCGCGC 61.342 55.000 0.00 0.00 43.75 6.86
3674 5034 0.633733 GATCTACGTGTGTGTTCGCG 59.366 55.000 0.00 0.00 45.12 5.87
3675 5035 1.649171 CTGATCTACGTGTGTGTTCGC 59.351 52.381 0.00 0.00 0.00 4.70
3677 5037 3.844657 CGTACTGATCTACGTGTGTGTTC 59.155 47.826 0.00 0.00 35.74 3.18
3684 5044 4.093115 AGAGTTGTCGTACTGATCTACGTG 59.907 45.833 12.58 0.00 40.38 4.49
3686 5046 4.093115 ACAGAGTTGTCGTACTGATCTACG 59.907 45.833 7.93 7.93 40.77 3.51
3687 5047 5.548706 ACAGAGTTGTCGTACTGATCTAC 57.451 43.478 0.00 0.00 34.88 2.59
3697 5057 4.814771 CCTTAGGAAAAACAGAGTTGTCGT 59.185 41.667 0.00 0.00 36.23 4.34
3731 5091 5.524971 TTGAATACGGTAAGATCCATCGT 57.475 39.130 8.16 8.16 37.78 3.73
3742 5102 8.649841 CGTTGAAGAGTAATTTTGAATACGGTA 58.350 33.333 0.00 0.00 0.00 4.02
3743 5103 7.360607 CCGTTGAAGAGTAATTTTGAATACGGT 60.361 37.037 0.00 0.00 37.93 4.83
3744 5104 6.959311 CCGTTGAAGAGTAATTTTGAATACGG 59.041 38.462 0.00 0.00 36.72 4.02
3751 5111 7.129109 TCTTAGCCGTTGAAGAGTAATTTTG 57.871 36.000 0.00 0.00 0.00 2.44
3753 5113 7.923414 ATTCTTAGCCGTTGAAGAGTAATTT 57.077 32.000 0.00 0.00 33.38 1.82
3770 5130 7.414436 TGTTGGACGTTTTCTCAAATTCTTAG 58.586 34.615 0.00 0.00 0.00 2.18
3772 5132 6.202516 TGTTGGACGTTTTCTCAAATTCTT 57.797 33.333 0.00 0.00 0.00 2.52
3773 5133 5.828299 TGTTGGACGTTTTCTCAAATTCT 57.172 34.783 0.00 0.00 0.00 2.40
3777 5137 4.638421 AGTCATGTTGGACGTTTTCTCAAA 59.362 37.500 0.00 0.00 42.62 2.69
3787 5147 4.219033 GCAAAACTTAGTCATGTTGGACG 58.781 43.478 0.00 0.00 42.62 4.79
3788 5148 5.181690 TGCAAAACTTAGTCATGTTGGAC 57.818 39.130 0.00 0.00 38.08 4.02
3789 5149 6.403866 AATGCAAAACTTAGTCATGTTGGA 57.596 33.333 0.00 0.00 0.00 3.53
3790 5150 7.481275 AAAATGCAAAACTTAGTCATGTTGG 57.519 32.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.