Multiple sequence alignment - TraesCS5B01G170600

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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 TraesCS5B01G170600 chr5B 100.000 5466 0 0 1 5466 315609123 315614588 0.000000e+00 10094.0
1 TraesCS5B01G170600 chr5B 84.524 84 11 2 1739 1821 388482863 388482781 1.260000e-11 82.4
2 TraesCS5B01G170600 chr5B 100.000 34 0 0 377 410 166816772 166816805 4.570000e-06 63.9
3 TraesCS5B01G170600 chr5D 92.920 5551 250 57 4 5466 277554968 277560463 0.000000e+00 7941.0
4 TraesCS5B01G170600 chr5D 100.000 33 0 0 378 410 169967279 169967247 1.640000e-05 62.1
5 TraesCS5B01G170600 chr5A 94.611 3637 127 15 1881 5466 366630720 366634338 0.000000e+00 5566.0
6 TraesCS5B01G170600 chr5A 85.258 1472 118 43 343 1798 366629292 366630680 0.000000e+00 1424.0
7 TraesCS5B01G170600 chr5A 87.576 330 27 9 3 320 366628974 366629301 2.400000e-98 370.0
8 TraesCS5B01G170600 chr4A 75.908 303 52 15 1525 1815 546074284 546074577 9.550000e-28 135.0
9 TraesCS5B01G170600 chr1B 84.545 110 12 5 1706 1814 302234805 302234910 2.690000e-18 104.0
10 TraesCS5B01G170600 chr2A 89.610 77 6 2 1739 1814 193724642 193724567 4.510000e-16 97.1
11 TraesCS5B01G170600 chr2A 73.585 318 52 25 1509 1813 402859557 402859855 5.830000e-15 93.5
12 TraesCS5B01G170600 chr2A 86.765 68 9 0 1754 1821 203459566 203459499 5.870000e-10 76.8
13 TraesCS5B01G170600 chr2A 91.111 45 2 2 3555 3597 138531310 138531354 5.910000e-05 60.2
14 TraesCS5B01G170600 chr7A 85.897 78 9 2 1739 1815 230594950 230595026 1.260000e-11 82.4
15 TraesCS5B01G170600 chr7B 89.062 64 7 0 210 273 198964205 198964142 4.540000e-11 80.5
16 TraesCS5B01G170600 chr7D 90.000 60 6 0 207 266 227287431 227287372 1.630000e-10 78.7


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 TraesCS5B01G170600 chr5B 315609123 315614588 5465 False 10094.000000 10094 100.000000 1 5466 1 chr5B.!!$F2 5465
1 TraesCS5B01G170600 chr5D 277554968 277560463 5495 False 7941.000000 7941 92.920000 4 5466 1 chr5D.!!$F1 5462
2 TraesCS5B01G170600 chr5A 366628974 366634338 5364 False 2453.333333 5566 89.148333 3 5466 3 chr5A.!!$F1 5463

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
428 472 0.185175 GACACCCACAAAGTCCCCTT 59.815 55.0 0.00 0.0 0.00 3.95 F
566 611 0.898320 AAGGGTCAGTGTCGGAGATG 59.102 55.0 0.00 0.0 40.67 2.90 F
1541 1606 0.178961 AGGCCTCCTTTGGTTTGGAC 60.179 55.0 0.00 0.0 0.00 4.02 F
2742 2823 0.036483 TGCGAACTTGCAGCAGGATA 60.036 50.0 12.26 0.0 40.62 2.59 F
3839 3960 1.839424 CCCTGAAACCAAGGACATCC 58.161 55.0 0.00 0.0 36.91 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1239 1295 0.745468 CGCCAGTTAGAGGGTCCTAC 59.255 60.000 0.00 0.00 0.00 3.18 R
1642 1713 0.763652 CCTGAGATGTGGAGGATGGG 59.236 60.000 0.00 0.00 0.00 4.00 R
3493 3588 0.097674 CTTCCTACGCACTTGCATGC 59.902 55.000 11.82 11.82 42.21 4.06 R
4417 4538 3.380320 TGCAAGCATGAGAATCCATCTTG 59.620 43.478 0.00 0.00 38.96 3.02 R
4813 4948 0.247460 GAGCAAAATGAGCCCAACCC 59.753 55.000 0.00 0.00 0.00 4.11 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
61 62 2.698803 TGGTGACAACATCAAGATCCG 58.301 47.619 0.00 0.00 39.72 4.18
74 75 1.337118 AGATCCGAGGAAGATCCAGC 58.663 55.000 0.00 0.00 40.92 4.85
79 80 3.798954 GAGGAAGATCCAGCGCCGG 62.799 68.421 2.25 2.25 39.61 6.13
140 151 1.478916 GGGAGAAGAAGAGGAGTTCGG 59.521 57.143 0.00 0.00 0.00 4.30
203 214 6.994421 TGGAGAACAGATTATATAGGCACA 57.006 37.500 0.00 0.00 0.00 4.57
267 279 4.023707 CACAATGGTCAGAGTTGGTTTCTC 60.024 45.833 0.00 0.00 0.00 2.87
278 290 0.542333 TGGTTTCTCGGGACAACACA 59.458 50.000 10.95 5.57 0.00 3.72
281 293 2.550208 GGTTTCTCGGGACAACACATCT 60.550 50.000 10.95 0.00 0.00 2.90
317 361 3.583054 CCTGTCTGGTGGCATCAAT 57.417 52.632 0.41 0.00 0.00 2.57
318 362 1.100510 CCTGTCTGGTGGCATCAATG 58.899 55.000 0.41 0.00 0.00 2.82
328 372 4.798288 CATCAATGCCGGTTGCTG 57.202 55.556 1.90 0.00 42.00 4.41
329 373 1.885157 CATCAATGCCGGTTGCTGT 59.115 52.632 1.90 0.00 42.00 4.40
330 374 0.457166 CATCAATGCCGGTTGCTGTG 60.457 55.000 1.90 0.00 42.00 3.66
331 375 1.597797 ATCAATGCCGGTTGCTGTGG 61.598 55.000 1.90 0.00 42.00 4.17
336 380 3.052082 CCGGTTGCTGTGGCTCTG 61.052 66.667 0.00 0.00 39.59 3.35
337 381 3.052082 CGGTTGCTGTGGCTCTGG 61.052 66.667 0.00 0.00 39.59 3.86
338 382 2.674380 GGTTGCTGTGGCTCTGGG 60.674 66.667 0.00 0.00 39.59 4.45
339 383 3.368571 GTTGCTGTGGCTCTGGGC 61.369 66.667 0.00 0.00 39.59 5.36
371 415 2.331809 GGTGCATCCGTTGAAGAAAC 57.668 50.000 0.00 0.00 35.25 2.78
412 456 3.936203 GGCCAGGTGTGTCGGACA 61.936 66.667 6.76 6.76 0.00 4.02
422 466 0.463116 GTGTCGGACACCCACAAAGT 60.463 55.000 26.86 0.00 43.05 2.66
428 472 0.185175 GACACCCACAAAGTCCCCTT 59.815 55.000 0.00 0.00 0.00 3.95
440 484 3.520691 AGTCCCCTTTGGTTTACTTCC 57.479 47.619 0.00 0.00 34.77 3.46
441 485 2.156917 GTCCCCTTTGGTTTACTTCCG 58.843 52.381 0.00 0.00 34.77 4.30
442 486 1.074244 TCCCCTTTGGTTTACTTCCGG 59.926 52.381 0.00 0.00 34.77 5.14
471 515 1.673808 AACAGACGCCCGGACCTATC 61.674 60.000 0.73 0.00 0.00 2.08
479 523 3.929002 CGGACCTATCCACGGACA 58.071 61.111 0.00 0.00 46.67 4.02
481 525 1.735376 CGGACCTATCCACGGACAGG 61.735 65.000 8.94 8.94 46.67 4.00
482 526 1.442148 GACCTATCCACGGACAGGC 59.558 63.158 10.45 0.05 42.28 4.85
483 527 1.305802 ACCTATCCACGGACAGGCA 60.306 57.895 10.45 0.00 42.28 4.75
489 533 4.308458 CACGGACAGGCACGGGAA 62.308 66.667 0.00 0.00 35.00 3.97
496 540 2.158871 GGACAGGCACGGGAATATGTTA 60.159 50.000 0.00 0.00 0.00 2.41
502 546 3.496160 GGCACGGGAATATGTTAGATGGT 60.496 47.826 0.00 0.00 0.00 3.55
507 552 7.040686 GCACGGGAATATGTTAGATGGTAAAAT 60.041 37.037 0.00 0.00 0.00 1.82
520 565 3.324993 TGGTAAAATACGTCCGAACCAC 58.675 45.455 0.00 0.00 30.84 4.16
521 566 3.244009 TGGTAAAATACGTCCGAACCACA 60.244 43.478 0.00 0.00 30.84 4.17
523 568 2.529780 AAATACGTCCGAACCACACA 57.470 45.000 0.00 0.00 0.00 3.72
524 569 2.074547 AATACGTCCGAACCACACAG 57.925 50.000 0.00 0.00 0.00 3.66
526 571 1.603456 TACGTCCGAACCACACAGTA 58.397 50.000 0.00 0.00 0.00 2.74
529 574 1.001048 CGTCCGAACCACACAGTAGAA 60.001 52.381 0.00 0.00 0.00 2.10
531 576 3.660865 GTCCGAACCACACAGTAGAAAT 58.339 45.455 0.00 0.00 0.00 2.17
536 581 4.695455 CGAACCACACAGTAGAAATGGATT 59.305 41.667 0.00 0.00 34.38 3.01
538 583 6.293955 CGAACCACACAGTAGAAATGGATTTT 60.294 38.462 0.00 0.00 34.38 1.82
540 585 5.163513 CCACACAGTAGAAATGGATTTTGC 58.836 41.667 0.00 0.00 31.69 3.68
555 600 4.321974 GGATTTTGCTGGTTTAAGGGTCAG 60.322 45.833 0.00 0.00 0.00 3.51
559 604 2.152016 GCTGGTTTAAGGGTCAGTGTC 58.848 52.381 0.00 0.00 0.00 3.67
566 611 0.898320 AAGGGTCAGTGTCGGAGATG 59.102 55.000 0.00 0.00 40.67 2.90
582 627 7.771361 TGTCGGAGATGCCTAATGTATTTTAAA 59.229 33.333 0.00 0.00 40.67 1.52
694 741 1.134965 CCGTCTCTCCGCATTTCTCTT 60.135 52.381 0.00 0.00 0.00 2.85
762 809 2.740055 GCTCACCCACAGCAGTCG 60.740 66.667 0.00 0.00 36.82 4.18
880 927 3.076092 CCAGGCTCTGGTCTTGCT 58.924 61.111 11.85 0.00 45.82 3.91
954 1001 1.285950 TCGCAAGACCGAGTCACAG 59.714 57.895 6.78 0.00 45.01 3.66
965 1012 1.759994 GAGTCACAGTCACACTCACG 58.240 55.000 0.00 0.00 37.17 4.35
1009 1056 1.284111 ATCCTCTGCCATGGCCAGAA 61.284 55.000 33.44 20.02 41.09 3.02
1044 1091 2.237643 GTTCCCCTTCTTCTTCCTCCTC 59.762 54.545 0.00 0.00 0.00 3.71
1050 1097 3.169099 CTTCTTCTTCCTCCTCCTGTCA 58.831 50.000 0.00 0.00 0.00 3.58
1122 1169 4.047166 AGATGGGGTAATGGATCTGTCAA 58.953 43.478 0.00 0.00 0.00 3.18
1131 1178 7.015292 GGGTAATGGATCTGTCAACTCTGTATA 59.985 40.741 0.00 0.00 0.00 1.47
1239 1295 5.120208 CCGTGTGGTTAAGTACTGATTTGAG 59.880 44.000 0.00 0.00 0.00 3.02
1265 1325 1.347320 CCTCTAACTGGCGAACGTTC 58.653 55.000 18.47 18.47 0.00 3.95
1274 1334 2.433491 CGAACGTTCGCCATGGGA 60.433 61.111 34.54 6.34 44.26 4.37
1275 1335 2.736682 CGAACGTTCGCCATGGGAC 61.737 63.158 34.54 1.91 44.26 4.46
1300 1360 0.709467 CGGCACATGCAAACAATTCG 59.291 50.000 6.15 0.00 44.36 3.34
1357 1417 6.753744 GTGGCATTTTCTTCACAAGATATTCC 59.246 38.462 0.00 0.00 37.38 3.01
1382 1444 7.222654 CCGTTTTACAACTAAAACTACTAGCG 58.777 38.462 12.10 0.00 45.21 4.26
1470 1535 4.973168 TCTTCCTGCAGTAGTCACAAAAT 58.027 39.130 13.81 0.00 0.00 1.82
1541 1606 0.178961 AGGCCTCCTTTGGTTTGGAC 60.179 55.000 0.00 0.00 0.00 4.02
1545 1610 2.035961 GCCTCCTTTGGTTTGGACTTTC 59.964 50.000 0.00 0.00 0.00 2.62
1616 1681 9.856162 TCTTTTTATAGTCCTTTGGTTTGTAGT 57.144 29.630 0.00 0.00 0.00 2.73
1683 1755 8.548877 TCAGGAAAATAACATTAGCCTAGACTT 58.451 33.333 0.00 0.00 0.00 3.01
1712 1787 9.787532 AAAATAATCCTATGATGTGAACAAACG 57.212 29.630 0.00 0.00 0.00 3.60
1824 1901 2.543777 TGAACCAAAGAAGACCCGAG 57.456 50.000 0.00 0.00 0.00 4.63
1999 2076 7.444487 AGGTGATAATCCGAAAAATAGGTAAGC 59.556 37.037 0.00 0.00 0.00 3.09
2130 2207 0.392461 TGCGAAACTGGGGTATGAGC 60.392 55.000 0.00 0.00 0.00 4.26
2156 2233 2.927477 CAACTTAGGTAATCGCTTCGCA 59.073 45.455 0.00 0.00 0.00 5.10
2235 2312 5.106396 GCCTGCAATATTCACAGTGGATATC 60.106 44.000 13.96 4.58 0.00 1.63
2352 2433 9.015577 CGTGTAAATAGAAAGAGCAAAACAAAA 57.984 29.630 0.00 0.00 0.00 2.44
2650 2731 2.309528 TGATATGACTGGGAACACGC 57.690 50.000 0.00 0.00 35.60 5.34
2701 2782 4.061596 GGATCTCTCCCTTGCTTAAATCG 58.938 47.826 0.00 0.00 35.28 3.34
2740 2821 2.110835 TGCGAACTTGCAGCAGGA 59.889 55.556 12.26 0.00 40.62 3.86
2742 2823 0.036483 TGCGAACTTGCAGCAGGATA 60.036 50.000 12.26 0.00 40.62 2.59
2867 2953 4.479156 AAAATGGTTTTCCTGGTAGGGA 57.521 40.909 0.00 0.00 41.38 4.20
2978 3064 3.270877 CATCAGCCCACTAACAAGGTAC 58.729 50.000 0.00 0.00 0.00 3.34
2991 3077 9.457436 CACTAACAAGGTACCCTTTACAATTAT 57.543 33.333 8.74 0.00 41.69 1.28
2992 3078 9.457436 ACTAACAAGGTACCCTTTACAATTATG 57.543 33.333 8.74 0.00 41.69 1.90
3012 3098 3.390135 TGGAACTTAGAAGCTTGTCACG 58.610 45.455 2.10 0.00 0.00 4.35
3345 3440 3.491447 CCCTTCCAAACTTCTGCAAAGTG 60.491 47.826 12.87 4.53 0.00 3.16
3478 3573 1.861982 TGGTTAGTCTCTGTAGGCCC 58.138 55.000 0.00 0.00 0.00 5.80
3481 3576 3.052414 TGGTTAGTCTCTGTAGGCCCATA 60.052 47.826 0.00 0.00 0.00 2.74
3493 3588 8.463930 TCTGTAGGCCCATAATAAAATTTGAG 57.536 34.615 0.00 0.00 0.00 3.02
3504 3601 5.789710 ATAAAATTTGAGCATGCAAGTGC 57.210 34.783 21.98 4.04 45.38 4.40
3514 3611 2.283298 CATGCAAGTGCGTAGGAAGAT 58.717 47.619 0.00 0.00 45.83 2.40
3658 3759 5.292101 GGATGACAATAGAAGAGAACCGTTG 59.708 44.000 0.00 0.00 0.00 4.10
3760 3881 8.071177 AGGGAAGAATTTTCACAAGATTATGG 57.929 34.615 5.72 0.00 0.00 2.74
3794 3915 5.305644 GGATTCAACTAGGCTCCTCTGATAA 59.694 44.000 0.00 0.00 0.00 1.75
3839 3960 1.839424 CCCTGAAACCAAGGACATCC 58.161 55.000 0.00 0.00 36.91 3.51
3856 3977 4.597004 ACATCCTCAGCAATCAGAATGTT 58.403 39.130 0.00 0.00 37.40 2.71
3882 4003 5.479306 TGCAGTTAATCAAGGTAGAGTCAC 58.521 41.667 0.00 0.00 0.00 3.67
3907 4028 6.477053 TCTCCAAAATGGTCATGTGAAAAA 57.523 33.333 0.00 0.00 39.03 1.94
4271 4392 3.386768 TCTGTGGACAGTAAGCACTTC 57.613 47.619 6.68 0.00 44.12 3.01
4417 4538 1.002792 GTGCAAGGAAACCTGACGAAC 60.003 52.381 0.00 0.00 32.13 3.95
4451 4572 2.925578 TGCTTGCAAGATGTATGTGC 57.074 45.000 30.39 12.39 38.78 4.57
4478 4599 7.027874 ACCCCAAAATAGAACAGTATTCTCA 57.972 36.000 0.00 0.00 0.00 3.27
4586 4707 5.009010 CCAAACATTGATAGTGCTACATCCC 59.991 44.000 0.00 0.00 0.00 3.85
4587 4708 5.636903 AACATTGATAGTGCTACATCCCT 57.363 39.130 0.00 0.00 0.00 4.20
4588 4709 5.636903 ACATTGATAGTGCTACATCCCTT 57.363 39.130 0.00 0.00 0.00 3.95
4589 4710 5.371526 ACATTGATAGTGCTACATCCCTTG 58.628 41.667 0.00 0.00 0.00 3.61
4590 4711 5.130975 ACATTGATAGTGCTACATCCCTTGA 59.869 40.000 0.00 0.00 0.00 3.02
4591 4712 5.692115 TTGATAGTGCTACATCCCTTGAA 57.308 39.130 0.00 0.00 0.00 2.69
4592 4713 5.282055 TGATAGTGCTACATCCCTTGAAG 57.718 43.478 0.00 0.00 0.00 3.02
4593 4714 4.962362 TGATAGTGCTACATCCCTTGAAGA 59.038 41.667 0.00 0.00 0.00 2.87
4594 4715 5.604231 TGATAGTGCTACATCCCTTGAAGAT 59.396 40.000 0.00 0.00 0.00 2.40
4595 4716 6.782494 TGATAGTGCTACATCCCTTGAAGATA 59.218 38.462 0.00 0.00 0.00 1.98
4609 4730 6.813649 CCCTTGAAGATATATACCATGTCACG 59.186 42.308 0.00 0.00 0.00 4.35
4758 4893 6.149308 TGCATGTCACTAAATTTCAGTACCAG 59.851 38.462 0.00 0.00 0.00 4.00
4813 4948 1.081892 CGTCAATTCTGGCACTCCTG 58.918 55.000 0.00 0.00 0.00 3.86
4847 4982 0.764369 TGCTCCCTCTCAACACCACT 60.764 55.000 0.00 0.00 0.00 4.00
5005 5140 4.836825 CATCTTTCTCCACTTCAGCCTTA 58.163 43.478 0.00 0.00 0.00 2.69
5135 5270 5.679638 GCACCAGAGTTTGTTTTTGACTGAT 60.680 40.000 0.00 0.00 0.00 2.90
5233 5368 3.896479 GCTTTCGGCTCTTCAGGG 58.104 61.111 0.00 0.00 38.06 4.45
5265 5400 2.421399 GCTTGGGATCTGGGCTTGC 61.421 63.158 0.00 0.00 0.00 4.01
5381 5516 3.942829 TCAGCTAAGGGTTCAGATTGTG 58.057 45.455 0.00 0.00 0.00 3.33
5393 5528 2.749076 TCAGATTGTGTGCAGTAATGGC 59.251 45.455 0.00 0.00 0.00 4.40
5442 5578 7.554118 CACCGGGCTAGATCATTAATTCATTAT 59.446 37.037 6.32 0.00 0.00 1.28
5444 5580 9.784531 CCGGGCTAGATCATTAATTCATTATAT 57.215 33.333 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.838271 CTCGGCCGCTAGCTCCAA 61.838 66.667 23.51 0.00 43.05 3.53
1 2 4.815108 TCTCGGCCGCTAGCTCCA 62.815 66.667 23.51 0.00 43.05 3.86
44 45 2.831526 TCCTCGGATCTTGATGTTGTCA 59.168 45.455 0.00 0.00 34.25 3.58
48 49 4.202305 GGATCTTCCTCGGATCTTGATGTT 60.202 45.833 0.00 0.00 39.41 2.71
49 50 3.323403 GGATCTTCCTCGGATCTTGATGT 59.677 47.826 0.00 0.00 39.41 3.06
61 62 2.279784 CGGCGCTGGATCTTCCTC 60.280 66.667 8.83 0.00 37.46 3.71
267 279 1.135603 CAATGCAGATGTGTTGTCCCG 60.136 52.381 0.00 0.00 0.00 5.14
278 290 0.171903 GTTGCCGCTTCAATGCAGAT 59.828 50.000 0.00 0.00 36.21 2.90
281 293 2.254951 CGTTGCCGCTTCAATGCA 59.745 55.556 0.00 0.00 0.00 3.96
319 363 3.052082 CAGAGCCACAGCAACCGG 61.052 66.667 0.00 0.00 43.56 5.28
320 364 3.052082 CCAGAGCCACAGCAACCG 61.052 66.667 0.00 0.00 43.56 4.44
321 365 2.674380 CCCAGAGCCACAGCAACC 60.674 66.667 0.00 0.00 43.56 3.77
322 366 3.368571 GCCCAGAGCCACAGCAAC 61.369 66.667 0.00 0.00 43.56 4.17
331 375 1.455217 ATTCATGCTGGCCCAGAGC 60.455 57.895 16.85 6.61 42.60 4.09
332 376 2.415825 CATTCATGCTGGCCCAGAG 58.584 57.895 16.85 3.22 32.44 3.35
333 377 4.670199 CATTCATGCTGGCCCAGA 57.330 55.556 16.85 0.00 32.44 3.86
354 398 3.347958 GTTGTTTCTTCAACGGATGCA 57.652 42.857 0.00 0.00 38.36 3.96
371 415 0.951558 CAAAACCCTCTCCCACGTTG 59.048 55.000 0.00 0.00 0.00 4.10
375 419 0.539669 CACCCAAAACCCTCTCCCAC 60.540 60.000 0.00 0.00 0.00 4.61
408 452 1.228459 GGGGACTTTGTGGGTGTCC 60.228 63.158 0.00 0.00 46.83 4.02
410 454 4.099940 AGGGGACTTTGTGGGTGT 57.900 55.556 0.00 0.00 37.44 4.16
422 466 1.074244 CCGGAAGTAAACCAAAGGGGA 59.926 52.381 0.00 0.00 41.15 4.81
428 472 0.945813 CGCAACCGGAAGTAAACCAA 59.054 50.000 9.46 0.00 0.00 3.67
440 484 1.281656 GTCTGTTTTCCCGCAACCG 59.718 57.895 0.00 0.00 0.00 4.44
441 485 1.281656 CGTCTGTTTTCCCGCAACC 59.718 57.895 0.00 0.00 0.00 3.77
442 486 1.370051 GCGTCTGTTTTCCCGCAAC 60.370 57.895 0.00 0.00 45.12 4.17
479 523 3.244561 CCATCTAACATATTCCCGTGCCT 60.245 47.826 0.00 0.00 0.00 4.75
481 525 3.740115 ACCATCTAACATATTCCCGTGC 58.260 45.455 0.00 0.00 0.00 5.34
482 526 7.795482 TTTTACCATCTAACATATTCCCGTG 57.205 36.000 0.00 0.00 0.00 4.94
483 527 9.498176 GTATTTTACCATCTAACATATTCCCGT 57.502 33.333 0.00 0.00 0.00 5.28
488 532 9.199982 CGGACGTATTTTACCATCTAACATATT 57.800 33.333 0.00 0.00 0.00 1.28
489 533 8.579006 TCGGACGTATTTTACCATCTAACATAT 58.421 33.333 0.00 0.00 0.00 1.78
496 540 4.081531 TGGTTCGGACGTATTTTACCATCT 60.082 41.667 0.00 0.00 29.78 2.90
502 546 3.987547 TGTGTGGTTCGGACGTATTTTA 58.012 40.909 0.00 0.00 0.00 1.52
507 552 1.536766 CTACTGTGTGGTTCGGACGTA 59.463 52.381 0.00 0.00 0.00 3.57
520 565 5.047802 ACCAGCAAAATCCATTTCTACTGTG 60.048 40.000 0.00 0.00 0.00 3.66
521 566 5.079643 ACCAGCAAAATCCATTTCTACTGT 58.920 37.500 0.00 0.00 0.00 3.55
523 568 6.670695 AAACCAGCAAAATCCATTTCTACT 57.329 33.333 0.00 0.00 0.00 2.57
524 569 7.545615 CCTTAAACCAGCAAAATCCATTTCTAC 59.454 37.037 0.00 0.00 0.00 2.59
526 571 6.466812 CCTTAAACCAGCAAAATCCATTTCT 58.533 36.000 0.00 0.00 0.00 2.52
529 574 4.597075 ACCCTTAAACCAGCAAAATCCATT 59.403 37.500 0.00 0.00 0.00 3.16
531 576 3.576550 GACCCTTAAACCAGCAAAATCCA 59.423 43.478 0.00 0.00 0.00 3.41
536 581 2.955660 CACTGACCCTTAAACCAGCAAA 59.044 45.455 0.00 0.00 0.00 3.68
538 583 1.493022 ACACTGACCCTTAAACCAGCA 59.507 47.619 0.00 0.00 0.00 4.41
540 585 2.413837 CGACACTGACCCTTAAACCAG 58.586 52.381 0.00 0.00 0.00 4.00
555 600 2.604046 ACATTAGGCATCTCCGACAC 57.396 50.000 0.00 0.00 40.77 3.67
559 604 7.925993 TGTTTAAAATACATTAGGCATCTCCG 58.074 34.615 0.00 0.00 40.77 4.63
566 611 8.232913 TGGGAGATGTTTAAAATACATTAGGC 57.767 34.615 0.00 0.00 36.41 3.93
582 627 0.836400 ACCACCGACTTGGGAGATGT 60.836 55.000 3.18 0.00 44.64 3.06
694 741 0.888619 CACGCCTCTACTTCACTCCA 59.111 55.000 0.00 0.00 0.00 3.86
762 809 5.947228 TGGTCATCTGAGAAACATGTTTC 57.053 39.130 34.21 34.21 46.85 2.78
806 853 2.857186 TTCCTTCATGCAGCTGTGTA 57.143 45.000 16.64 2.57 0.00 2.90
879 926 1.069513 TGGGTGAGGTCGTTGTAACAG 59.930 52.381 0.00 0.00 0.00 3.16
880 927 1.069513 CTGGGTGAGGTCGTTGTAACA 59.930 52.381 0.00 0.00 0.00 2.41
1024 1071 2.552367 GAGGAGGAAGAAGAAGGGGAA 58.448 52.381 0.00 0.00 0.00 3.97
1044 1091 1.946156 CGGCGATGTCGATGACAGG 60.946 63.158 0.00 1.77 46.04 4.00
1122 1169 9.862371 CAAAACTGACTGAATAGTATACAGAGT 57.138 33.333 5.50 0.00 37.25 3.24
1131 1178 7.773690 AGTTACAACCAAAACTGACTGAATAGT 59.226 33.333 0.00 0.00 40.66 2.12
1183 1231 5.129320 TCCGAAAAAGAGAGGATCATCATCA 59.871 40.000 10.44 0.00 37.82 3.07
1184 1232 5.605534 TCCGAAAAAGAGAGGATCATCATC 58.394 41.667 10.44 4.62 37.82 2.92
1185 1233 5.620738 TCCGAAAAAGAGAGGATCATCAT 57.379 39.130 10.44 0.00 37.82 2.45
1186 1234 5.420725 TTCCGAAAAAGAGAGGATCATCA 57.579 39.130 10.44 0.00 37.82 3.07
1187 1235 6.202570 CAGATTCCGAAAAAGAGAGGATCATC 59.797 42.308 0.00 0.00 37.82 2.92
1188 1236 6.054295 CAGATTCCGAAAAAGAGAGGATCAT 58.946 40.000 0.00 0.00 37.82 2.45
1189 1237 5.423015 CAGATTCCGAAAAAGAGAGGATCA 58.577 41.667 0.00 0.00 37.82 2.92
1190 1238 4.813697 CCAGATTCCGAAAAAGAGAGGATC 59.186 45.833 0.00 0.00 32.19 3.36
1191 1239 4.226168 ACCAGATTCCGAAAAAGAGAGGAT 59.774 41.667 0.00 0.00 32.19 3.24
1192 1240 3.583086 ACCAGATTCCGAAAAAGAGAGGA 59.417 43.478 0.00 0.00 0.00 3.71
1193 1241 3.935828 GACCAGATTCCGAAAAAGAGAGG 59.064 47.826 0.00 0.00 0.00 3.69
1194 1242 3.935828 GGACCAGATTCCGAAAAAGAGAG 59.064 47.826 0.00 0.00 0.00 3.20
1195 1243 3.939066 GGACCAGATTCCGAAAAAGAGA 58.061 45.455 0.00 0.00 0.00 3.10
1239 1295 0.745468 CGCCAGTTAGAGGGTCCTAC 59.255 60.000 0.00 0.00 0.00 3.18
1300 1360 6.532657 CCACTTCATCAACTAAAAATGCCATC 59.467 38.462 0.00 0.00 0.00 3.51
1376 1436 2.993899 CAAACGAACCATCTTCGCTAGT 59.006 45.455 2.47 0.00 44.98 2.57
1382 1444 1.068541 GGTGGCAAACGAACCATCTTC 60.069 52.381 0.00 0.00 38.46 2.87
1425 1487 6.263168 AGAGACAATCAAACGAAAATGTTCCT 59.737 34.615 0.00 0.00 0.00 3.36
1470 1535 2.224233 GGCAAGAGCAGAGCAGATCATA 60.224 50.000 0.00 0.00 44.61 2.15
1590 1655 9.856162 ACTACAAACCAAAGGACTATAAAAAGA 57.144 29.630 0.00 0.00 0.00 2.52
1642 1713 0.763652 CCTGAGATGTGGAGGATGGG 59.236 60.000 0.00 0.00 0.00 4.00
1650 1721 7.420800 GCTAATGTTATTTTCCTGAGATGTGG 58.579 38.462 0.00 0.00 0.00 4.17
1690 1765 6.537301 GTCCGTTTGTTCACATCATAGGATTA 59.463 38.462 0.00 0.00 0.00 1.75
1748 1825 8.893219 TGTAGGAATTGAGATGTCATGTATTC 57.107 34.615 7.05 7.05 30.97 1.75
1798 1875 5.163343 CGGGTCTTCTTTGGTTCATAGGATA 60.163 44.000 0.00 0.00 0.00 2.59
1800 1877 3.055385 CGGGTCTTCTTTGGTTCATAGGA 60.055 47.826 0.00 0.00 0.00 2.94
1818 1895 1.545706 GGCTTGAAGAGGACTCGGGT 61.546 60.000 0.00 0.00 34.09 5.28
1824 1901 1.867363 TAGAGGGGCTTGAAGAGGAC 58.133 55.000 0.00 0.00 0.00 3.85
1999 2076 1.004044 AGAGAACAAGGGAGCACCATG 59.996 52.381 1.58 3.07 43.89 3.66
2014 2091 5.762179 TGATTTTCCTGGCTAAGAGAGAA 57.238 39.130 0.00 0.00 0.00 2.87
2130 2207 5.276395 CGAAGCGATTACCTAAGTTGACATG 60.276 44.000 0.00 0.00 0.00 3.21
2156 2233 4.083802 CGAAAACCAAAGAGAGCGAGAAAT 60.084 41.667 0.00 0.00 0.00 2.17
2235 2312 6.021468 CAGTCGTCTGCAGTTTTAAAACAAAG 60.021 38.462 28.03 21.30 36.83 2.77
2244 2321 1.670811 CCAACAGTCGTCTGCAGTTTT 59.329 47.619 14.67 0.00 44.77 2.43
2268 2345 1.136695 CTGGGAGTCTCTGTCATGAGC 59.863 57.143 0.00 0.00 34.29 4.26
2315 2396 9.196552 TCTTTCTATTTACACGCATATCATCTG 57.803 33.333 0.00 0.00 0.00 2.90
2326 2407 8.555166 TTTGTTTTGCTCTTTCTATTTACACG 57.445 30.769 0.00 0.00 0.00 4.49
2378 2459 3.155093 GCTTATGCTGGTTTCACATGG 57.845 47.619 0.00 0.00 36.03 3.66
2617 2698 8.137437 CCCAGTCATATCATAAACATTTTGACC 58.863 37.037 0.00 0.00 34.27 4.02
2630 2711 2.803133 CGCGTGTTCCCAGTCATATCAT 60.803 50.000 0.00 0.00 0.00 2.45
2650 2731 0.109412 GGGGTACTTGTCACGTCTCG 60.109 60.000 0.00 0.00 0.00 4.04
2661 2742 0.991920 CCATGTGGACTGGGGTACTT 59.008 55.000 0.00 0.00 37.39 2.24
2701 2782 3.063485 GTCTGAAAAGAGAGAGTGGTGC 58.937 50.000 0.00 0.00 0.00 5.01
2740 2821 1.740285 CTAGCGAACCGGGCTGTAT 59.260 57.895 13.30 0.00 41.69 2.29
2742 2823 3.771160 CCTAGCGAACCGGGCTGT 61.771 66.667 13.30 0.00 41.69 4.40
2830 2911 9.877178 AAAACCATTTTTGACATGTGTAAGTTA 57.123 25.926 1.15 0.00 33.45 2.24
2867 2953 5.705400 TCAGTTTTTCTCCTCCTTTGGAAT 58.295 37.500 0.00 0.00 35.43 3.01
2978 3064 8.406297 GCTTCTAAGTTCCATAATTGTAAAGGG 58.594 37.037 0.00 0.00 0.00 3.95
2991 3077 3.181469 ACGTGACAAGCTTCTAAGTTCCA 60.181 43.478 0.00 0.00 0.00 3.53
2992 3078 3.391049 ACGTGACAAGCTTCTAAGTTCC 58.609 45.455 0.00 0.00 0.00 3.62
3345 3440 9.487442 AGGATAGGAATTAGAATCTCCATCTAC 57.513 37.037 0.00 0.00 0.00 2.59
3478 3573 7.849026 GCACTTGCATGCTCAAATTTTATTATG 59.151 33.333 20.33 0.00 42.62 1.90
3481 3576 5.163933 CGCACTTGCATGCTCAAATTTTATT 60.164 36.000 20.33 0.00 43.80 1.40
3493 3588 0.097674 CTTCCTACGCACTTGCATGC 59.902 55.000 11.82 11.82 42.21 4.06
3504 3601 5.013547 AGATCCTACATCCATCTTCCTACG 58.986 45.833 0.00 0.00 0.00 3.51
3514 3611 2.509548 CAAACCCCAGATCCTACATCCA 59.490 50.000 0.00 0.00 0.00 3.41
3651 3752 4.142403 CCATATGCTGAAATGACAACGGTT 60.142 41.667 0.00 0.00 0.00 4.44
3658 3759 3.484407 AGAGCCCATATGCTGAAATGAC 58.516 45.455 0.00 0.00 42.95 3.06
3729 3830 9.807921 ATCTTGTGAAAATTCTTCCCTAGTTTA 57.192 29.630 0.00 0.00 0.00 2.01
3731 3832 8.712228 AATCTTGTGAAAATTCTTCCCTAGTT 57.288 30.769 0.00 0.00 0.00 2.24
3732 3833 9.981460 ATAATCTTGTGAAAATTCTTCCCTAGT 57.019 29.630 0.00 0.00 0.00 2.57
3738 3859 9.696917 AACACCATAATCTTGTGAAAATTCTTC 57.303 29.630 0.00 0.00 34.18 2.87
3856 3977 7.764443 GTGACTCTACCTTGATTAACTGCAATA 59.236 37.037 0.00 0.00 0.00 1.90
3882 4003 5.710513 TTCACATGACCATTTTGGAGAAG 57.289 39.130 0.00 0.00 40.96 2.85
3907 4028 8.480501 TCGGTAAAGCTTAGTACCATCTTTAAT 58.519 33.333 21.72 0.00 39.92 1.40
4271 4392 4.381398 CCAGGAGGCTCATATGATTAGACG 60.381 50.000 17.69 0.00 0.00 4.18
4417 4538 3.380320 TGCAAGCATGAGAATCCATCTTG 59.620 43.478 0.00 0.00 38.96 3.02
4451 4572 7.112779 AGAATACTGTTCTATTTTGGGGTCAG 58.887 38.462 0.00 0.00 0.00 3.51
4526 4647 7.859325 ACACATACCAAGGTAATACATTGTC 57.141 36.000 15.30 0.00 38.12 3.18
4586 4707 7.867909 ACACGTGACATGGTATATATCTTCAAG 59.132 37.037 25.01 0.70 0.00 3.02
4587 4708 7.651704 CACACGTGACATGGTATATATCTTCAA 59.348 37.037 25.01 0.00 0.00 2.69
4588 4709 7.145323 CACACGTGACATGGTATATATCTTCA 58.855 38.462 25.01 0.00 0.00 3.02
4589 4710 7.145985 ACACACGTGACATGGTATATATCTTC 58.854 38.462 25.01 0.00 0.00 2.87
4590 4711 7.050970 ACACACGTGACATGGTATATATCTT 57.949 36.000 25.01 0.00 0.00 2.40
4591 4712 6.294564 GGACACACGTGACATGGTATATATCT 60.295 42.308 25.01 0.00 0.00 1.98
4592 4713 5.862323 GGACACACGTGACATGGTATATATC 59.138 44.000 25.01 1.87 0.00 1.63
4593 4714 5.303333 TGGACACACGTGACATGGTATATAT 59.697 40.000 25.01 0.00 0.00 0.86
4594 4715 4.645588 TGGACACACGTGACATGGTATATA 59.354 41.667 25.01 0.00 0.00 0.86
4595 4716 3.449377 TGGACACACGTGACATGGTATAT 59.551 43.478 25.01 0.00 0.00 0.86
4758 4893 6.251376 CGCCAATGCTTTTGTATAAGTTTCTC 59.749 38.462 0.00 0.00 34.43 2.87
4787 4922 3.451178 AGTGCCAGAATTGACGTAGGTAT 59.549 43.478 0.00 0.00 0.00 2.73
4813 4948 0.247460 GAGCAAAATGAGCCCAACCC 59.753 55.000 0.00 0.00 0.00 4.11
5005 5140 2.964209 TCTCAGTCCCTCAACACTCTT 58.036 47.619 0.00 0.00 0.00 2.85
5192 5327 0.673437 GCAGCTGTAAAAAGTGCCCA 59.327 50.000 16.64 0.00 0.00 5.36
5233 5368 1.508088 CAAGCCATGGTCCGCTTTC 59.492 57.895 14.67 0.00 42.61 2.62
5265 5400 3.981071 TTACATCAAGTCCAGGGACAG 57.019 47.619 19.92 11.98 46.76 3.51
5393 5528 9.736023 GGTGTTTCCAATTTCATAGCTAATTAG 57.264 33.333 8.20 8.20 35.97 1.73
5406 5542 2.167662 CTAGCCCGGTGTTTCCAATTT 58.832 47.619 0.00 0.00 35.57 1.82


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

AutoCloner maintained by Alex Coulton.