Multiple sequence alignment - TraesCS5A01G197500

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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 TraesCS5A01G197500 chr5A 100.000 4613 0 0 1 4613 401438220 401442832 0.000000e+00 8519
1 TraesCS5A01G197500 chr5B 95.722 2875 87 13 1 2845 337907743 337904875 0.000000e+00 4595
2 TraesCS5A01G197500 chr5B 95.296 1148 40 4 2858 3999 337904890 337903751 0.000000e+00 1808
3 TraesCS5A01G197500 chr5B 84.154 467 32 8 4001 4457 337903666 337903232 9.230000e-112 414
4 TraesCS5A01G197500 chr5B 88.690 168 11 3 4454 4613 337877996 337877829 1.010000e-46 198
5 TraesCS5A01G197500 chr5D 95.673 2866 90 14 1 2845 297581140 297578288 0.000000e+00 4575
6 TraesCS5A01G197500 chr5D 89.461 1727 98 36 2858 4563 297578303 297576640 0.000000e+00 2104
7 TraesCS5A01G197500 chr4B 85.088 912 113 16 1630 2538 513726134 513725243 0.000000e+00 909
8 TraesCS5A01G197500 chr4B 85.748 428 52 6 1064 1488 513726816 513726395 1.180000e-120 444
9 TraesCS5A01G197500 chr4B 87.109 256 33 0 3359 3614 513724202 513723947 1.620000e-74 291
10 TraesCS5A01G197500 chr4B 87.582 153 17 2 2598 2748 513725138 513724986 4.740000e-40 176
11 TraesCS5A01G197500 chr4A 84.967 918 111 20 1627 2538 47390228 47391124 0.000000e+00 905
12 TraesCS5A01G197500 chr4A 87.661 389 43 5 1076 1460 47389670 47390057 9.100000e-122 448
13 TraesCS5A01G197500 chr4A 87.405 262 32 1 3353 3614 47392143 47392403 2.700000e-77 300
14 TraesCS5A01G197500 chr4A 87.179 156 18 2 2595 2748 47391218 47391373 4.740000e-40 176
15 TraesCS5A01G197500 chr4D 84.632 911 127 11 1630 2538 416763171 416762272 0.000000e+00 894
16 TraesCS5A01G197500 chr4D 87.949 390 43 1 1103 1492 416763700 416763315 1.510000e-124 457
17 TraesCS5A01G197500 chr4D 88.281 256 30 0 3359 3614 416760680 416760425 1.610000e-79 307
18 TraesCS5A01G197500 chr4D 88.079 151 17 1 2599 2748 416762165 416762015 1.320000e-40 178
19 TraesCS5A01G197500 chr2A 92.308 156 11 1 243 398 775658241 775658395 2.160000e-53 220


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 TraesCS5A01G197500 chr5A 401438220 401442832 4612 False 8519.000000 8519 100.00000 1 4613 1 chr5A.!!$F1 4612
1 TraesCS5A01G197500 chr5B 337903232 337907743 4511 True 2272.333333 4595 91.72400 1 4457 3 chr5B.!!$R2 4456
2 TraesCS5A01G197500 chr5D 297576640 297581140 4500 True 3339.500000 4575 92.56700 1 4563 2 chr5D.!!$R1 4562
3 TraesCS5A01G197500 chr4B 513723947 513726816 2869 True 455.000000 909 86.38175 1064 3614 4 chr4B.!!$R1 2550
4 TraesCS5A01G197500 chr4A 47389670 47392403 2733 False 457.250000 905 86.80300 1076 3614 4 chr4A.!!$F1 2538
5 TraesCS5A01G197500 chr4D 416760425 416763700 3275 True 459.000000 894 87.23525 1103 3614 4 chr4D.!!$R1 2511

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
593 595 0.670162 CAGGGTTGCACAGTTTCCTG 59.330 55.000 0.00 0.0 44.68 3.86 F
1291 1302 0.770499 TCCATTCAACCACTGGAGCA 59.230 50.000 0.71 0.0 34.17 4.26 F
2384 2550 2.100252 GCATGCATGTTTAGGTGCTGAT 59.900 45.455 26.79 0.0 41.78 2.90 F
2777 2993 2.508867 CATATGCAGTGTTTGTCGTGC 58.491 47.619 0.00 0.0 36.42 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 1761 1.740025 GTGCACCATTCCTGAGTAAGC 59.260 52.381 5.22 0.0 0.00 3.09 R
2891 3111 1.302192 GGACAGCTTGGTACCGCAA 60.302 57.895 13.45 0.0 0.00 4.85 R
3450 4656 0.467844 TGCACACTCCACCAAATGCT 60.468 50.000 0.00 0.0 34.18 3.79 R
4491 5803 0.034283 TTGCCTGCCTATGATGCACA 60.034 50.000 0.00 0.0 34.46 4.57 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
232 233 3.168528 TAATCCCGCTGCCTCCCC 61.169 66.667 0.00 0.00 0.00 4.81
233 234 3.714078 TAATCCCGCTGCCTCCCCT 62.714 63.158 0.00 0.00 0.00 4.79
268 269 3.148279 GAGGCGATCCGGTGGTCT 61.148 66.667 0.00 0.00 37.47 3.85
319 320 1.922903 CAGATCTGCGTCGCATGTC 59.077 57.895 22.03 20.07 38.13 3.06
350 351 1.471676 GCCTGATCCGTGTCGAAATCT 60.472 52.381 0.00 0.00 0.00 2.40
355 356 0.731514 TCCGTGTCGAAATCTGCGTC 60.732 55.000 0.00 0.00 0.00 5.19
381 382 3.002673 CCGTGTGTGTGTGTGTCG 58.997 61.111 0.00 0.00 0.00 4.35
382 383 1.517475 CCGTGTGTGTGTGTGTCGA 60.517 57.895 0.00 0.00 0.00 4.20
384 385 1.636340 GTGTGTGTGTGTGTCGAGC 59.364 57.895 0.00 0.00 0.00 5.03
386 387 2.279186 TGTGTGTGTGTCGAGCCG 60.279 61.111 0.00 0.00 0.00 5.52
387 388 2.279252 GTGTGTGTGTCGAGCCGT 60.279 61.111 0.00 0.00 0.00 5.68
389 390 3.702555 GTGTGTGTCGAGCCGTGC 61.703 66.667 0.00 0.00 0.00 5.34
390 391 3.911698 TGTGTGTCGAGCCGTGCT 61.912 61.111 0.00 0.00 43.88 4.40
392 393 2.661537 TGTGTCGAGCCGTGCTTG 60.662 61.111 6.76 6.76 39.88 4.01
394 395 2.108157 TGTCGAGCCGTGCTTGTT 59.892 55.556 11.44 0.00 39.88 2.83
395 396 1.954146 TGTCGAGCCGTGCTTGTTC 60.954 57.895 11.44 7.91 39.88 3.18
396 397 1.954146 GTCGAGCCGTGCTTGTTCA 60.954 57.895 11.44 0.00 39.88 3.18
516 517 1.513160 CGTTAATTGGCGGCGGTTG 60.513 57.895 9.78 0.00 0.00 3.77
593 595 0.670162 CAGGGTTGCACAGTTTCCTG 59.330 55.000 0.00 0.00 44.68 3.86
667 669 2.505866 GCTTAGTTTTGAATGGACGCG 58.494 47.619 3.53 3.53 0.00 6.01
759 761 8.196103 GTCTAATTCGGTTACTTTCTGGATAGT 58.804 37.037 0.11 0.11 0.00 2.12
761 763 6.793505 ATTCGGTTACTTTCTGGATAGTCT 57.206 37.500 0.00 0.00 0.00 3.24
793 796 7.945033 TTCATTTTTGAACAGAATTGTAGCC 57.055 32.000 0.00 0.00 36.23 3.93
872 875 4.305989 TCTTGTCTGGTTGCAAATTGAC 57.694 40.909 0.00 10.11 0.00 3.18
876 879 1.406898 TCTGGTTGCAAATTGACGCAA 59.593 42.857 0.00 6.19 45.45 4.85
1013 1016 1.000274 GGGGATAATGCACGAAATGGC 60.000 52.381 0.00 0.00 0.00 4.40
1030 1033 2.823984 TGGCAATTGCTGTGAAGTTTG 58.176 42.857 28.42 0.00 41.70 2.93
1041 1044 4.266265 GCTGTGAAGTTTGCTTTGTTCTTC 59.734 41.667 0.00 0.00 34.61 2.87
1138 1149 1.798735 CTTTCGGGTGCTGCATCTG 59.201 57.895 15.60 15.60 0.00 2.90
1291 1302 0.770499 TCCATTCAACCACTGGAGCA 59.230 50.000 0.71 0.00 34.17 4.26
1396 1407 5.324409 TCTGGAATGGTTATGCAACTTCTT 58.676 37.500 0.00 0.00 34.88 2.52
1465 1476 3.436704 GTGCTCTGCTGTAAGTATTTGCA 59.563 43.478 0.00 0.00 35.30 4.08
1569 1695 7.950512 TGTACAGTGAATGACCAATGAAAATT 58.049 30.769 0.00 0.00 35.87 1.82
1577 1705 6.949578 ATGACCAATGAAAATTGTAAAGCG 57.050 33.333 0.00 0.00 0.00 4.68
1582 1710 5.861251 CCAATGAAAATTGTAAAGCGTGCTA 59.139 36.000 0.00 0.00 0.00 3.49
1628 1761 7.062138 GGCAATATTGTGTTGATGTTGTACTTG 59.938 37.037 16.61 0.00 30.93 3.16
2341 2488 5.936956 GGGCTTCAGTTCCAGATCTATAATG 59.063 44.000 0.00 0.00 0.00 1.90
2344 2491 6.648725 GCTTCAGTTCCAGATCTATAATGACC 59.351 42.308 0.00 0.00 0.00 4.02
2384 2550 2.100252 GCATGCATGTTTAGGTGCTGAT 59.900 45.455 26.79 0.00 41.78 2.90
2591 2760 6.990908 ATACTGTTCAGTATACTTACCCCC 57.009 41.667 19.75 0.00 33.64 5.40
2777 2993 2.508867 CATATGCAGTGTTTGTCGTGC 58.491 47.619 0.00 0.00 36.42 5.34
2794 3010 2.737252 CGTGCCTGGTTACTCTTTCTTC 59.263 50.000 0.00 0.00 0.00 2.87
2811 3029 6.975197 TCTTTCTTCTTACATAGCATGTCTCG 59.025 38.462 5.25 0.00 43.67 4.04
2880 3098 9.830294 GCGAATATTGATTTGATTCATATGTGA 57.170 29.630 1.90 0.00 31.25 3.58
2891 3111 7.984422 TGATTCATATGTGACTGTTTTCACT 57.016 32.000 1.90 0.00 45.34 3.41
2916 3136 3.369052 CGGTACCAAGCTGTCCAATTCTA 60.369 47.826 13.54 0.00 0.00 2.10
3117 3666 4.191544 TCAGCAGTCCTTATGTGTAATGC 58.808 43.478 0.00 0.00 0.00 3.56
3125 3674 3.245284 CCTTATGTGTAATGCGACGAAGG 59.755 47.826 0.00 0.00 0.00 3.46
3331 4536 4.950744 GCAAAGACTGTTGCGCAT 57.049 50.000 12.75 0.00 44.05 4.73
3450 4656 0.679505 GATACATCCCTACTGCCGCA 59.320 55.000 0.00 0.00 0.00 5.69
3498 4704 4.986659 GCATTGACTGTTCTTGCTGATTTT 59.013 37.500 0.00 0.00 32.15 1.82
3537 4743 1.092348 GAACCGGTATTCTGTTGGCC 58.908 55.000 8.00 0.00 0.00 5.36
3628 4834 6.017192 CGGGTTTTGATTGATACATGATAGCA 60.017 38.462 0.00 0.00 0.00 3.49
3941 5147 4.159506 TGGTATATGTTTTTCTTGCCTGCC 59.840 41.667 0.00 0.00 0.00 4.85
3999 5205 6.149807 TCGAGTAGGTTTTTCTGTGTTTTGTT 59.850 34.615 0.00 0.00 0.00 2.83
4018 5307 3.450457 TGTTGAACAAAAATGCCTGACCT 59.550 39.130 0.00 0.00 0.00 3.85
4024 5313 5.499004 ACAAAAATGCCTGACCTAGTCTA 57.501 39.130 0.00 0.00 33.15 2.59
4079 5373 7.654520 AGTTTGCTCAGAAGTAATAACGTGTTA 59.345 33.333 0.00 0.00 0.00 2.41
4104 5398 3.438216 TGAGGTGAATGAATTCTGGCA 57.562 42.857 7.05 0.00 37.67 4.92
4143 5437 3.188460 CGTGTGGACGGAAGAAATGAAAT 59.812 43.478 0.00 0.00 42.18 2.17
4152 5446 5.212194 CGGAAGAAATGAAATGTCACGTTT 58.788 37.500 0.00 0.00 36.31 3.60
4167 5469 4.851558 GTCACGTTTTCAAATAGGATGCAC 59.148 41.667 0.00 0.00 0.00 4.57
4239 5541 6.754675 ACCATAAATACATTTAAAACGCAGCC 59.245 34.615 0.00 0.00 36.02 4.85
4247 5549 2.296831 TAAAACGCAGCCGCACTATA 57.703 45.000 0.00 0.00 38.40 1.31
4257 5559 3.059325 CAGCCGCACTATATGAAAGAAGC 60.059 47.826 0.00 0.00 0.00 3.86
4284 5586 2.026301 CCCGATCGAGCGAAGGAC 59.974 66.667 26.68 1.18 0.00 3.85
4285 5587 2.352457 CCGATCGAGCGAAGGACG 60.352 66.667 26.68 1.94 45.66 4.79
4308 5610 1.436195 GATCGCGCTTTGGTGCCATA 61.436 55.000 5.56 0.00 45.20 2.74
4327 5629 8.507249 GTGCCATACTATTTTATTCCATCTCAC 58.493 37.037 0.00 0.00 0.00 3.51
4342 5644 9.771534 ATTCCATCTCACTTATAGAAAAGCTAC 57.228 33.333 0.00 0.00 0.00 3.58
4364 5673 1.407618 ACTTTTGAACCGTCCCTTTGC 59.592 47.619 0.00 0.00 0.00 3.68
4366 5675 1.770294 TTTGAACCGTCCCTTTGCTT 58.230 45.000 0.00 0.00 0.00 3.91
4367 5676 1.028905 TTGAACCGTCCCTTTGCTTG 58.971 50.000 0.00 0.00 0.00 4.01
4457 5769 1.076533 ATGCCTTCTTGCGTCGTACG 61.077 55.000 9.53 9.53 45.88 3.67
4458 5770 1.443194 GCCTTCTTGCGTCGTACGA 60.443 57.895 15.28 15.28 46.05 3.43
4459 5771 0.801067 GCCTTCTTGCGTCGTACGAT 60.801 55.000 22.57 0.00 46.05 3.73
4462 5774 2.247637 CTTCTTGCGTCGTACGATTGA 58.752 47.619 22.57 12.01 46.05 2.57
4477 5789 8.430063 TCGTACGATTGAATTGACTTAACTTTC 58.570 33.333 15.28 0.00 0.00 2.62
4489 5801 9.877178 ATTGACTTAACTTTCACCTATAGTCAG 57.123 33.333 0.00 0.00 40.98 3.51
4490 5802 7.321153 TGACTTAACTTTCACCTATAGTCAGC 58.679 38.462 0.00 0.00 36.71 4.26
4491 5803 7.178628 TGACTTAACTTTCACCTATAGTCAGCT 59.821 37.037 0.00 0.00 36.71 4.24
4492 5804 7.324178 ACTTAACTTTCACCTATAGTCAGCTG 58.676 38.462 7.63 7.63 0.00 4.24
4493 5805 5.746990 AACTTTCACCTATAGTCAGCTGT 57.253 39.130 14.67 0.00 0.00 4.40
4494 5806 5.078411 ACTTTCACCTATAGTCAGCTGTG 57.922 43.478 14.67 1.68 0.00 3.66
4495 5807 3.526931 TTCACCTATAGTCAGCTGTGC 57.473 47.619 14.67 8.24 0.00 4.57
4496 5808 2.456577 TCACCTATAGTCAGCTGTGCA 58.543 47.619 14.67 0.00 0.00 4.57
4497 5809 3.033909 TCACCTATAGTCAGCTGTGCAT 58.966 45.455 14.67 7.67 0.00 3.96
4498 5810 3.068732 TCACCTATAGTCAGCTGTGCATC 59.931 47.826 14.67 0.94 0.00 3.91
4499 5811 3.033909 ACCTATAGTCAGCTGTGCATCA 58.966 45.455 14.67 0.00 0.00 3.07
4500 5812 3.645212 ACCTATAGTCAGCTGTGCATCAT 59.355 43.478 14.67 2.83 0.00 2.45
4501 5813 4.835056 ACCTATAGTCAGCTGTGCATCATA 59.165 41.667 14.67 3.80 0.00 2.15
4502 5814 5.047448 ACCTATAGTCAGCTGTGCATCATAG 60.047 44.000 14.67 12.01 0.00 2.23
4503 5815 2.616634 AGTCAGCTGTGCATCATAGG 57.383 50.000 14.67 0.00 0.00 2.57
4504 5816 0.942962 GTCAGCTGTGCATCATAGGC 59.057 55.000 14.67 0.00 0.00 3.93
4505 5817 0.542805 TCAGCTGTGCATCATAGGCA 59.457 50.000 14.67 0.00 39.32 4.75
4506 5818 0.945099 CAGCTGTGCATCATAGGCAG 59.055 55.000 5.25 0.00 42.85 4.85
4507 5819 0.179026 AGCTGTGCATCATAGGCAGG 60.179 55.000 0.00 0.00 42.85 4.85
4560 5879 7.330946 GGTGCATTGGAGAACCTTAATTTAAAC 59.669 37.037 0.00 0.00 37.04 2.01
4563 5882 8.088365 GCATTGGAGAACCTTAATTTAAACAGT 58.912 33.333 0.00 0.00 37.04 3.55
4564 5883 9.981114 CATTGGAGAACCTTAATTTAAACAGTT 57.019 29.630 0.00 0.00 37.04 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
268 269 1.001393 GAATCGGGGGCAAAGGACA 60.001 57.895 0.00 0.00 0.00 4.02
319 320 1.372087 GGATCAGGCAGGAAACAGCG 61.372 60.000 0.00 0.00 45.05 5.18
366 367 1.636340 GCTCGACACACACACACAC 59.364 57.895 0.00 0.00 0.00 3.82
381 382 1.089920 ATGATGAACAAGCACGGCTC 58.910 50.000 0.00 0.00 38.25 4.70
382 383 0.806868 CATGATGAACAAGCACGGCT 59.193 50.000 0.00 0.00 42.56 5.52
384 385 0.521867 CGCATGATGAACAAGCACGG 60.522 55.000 0.00 0.00 42.39 4.94
386 387 0.799534 GCCGCATGATGAACAAGCAC 60.800 55.000 0.00 0.00 42.39 4.40
387 388 0.961857 AGCCGCATGATGAACAAGCA 60.962 50.000 0.00 0.00 42.39 3.91
389 390 0.099968 CCAGCCGCATGATGAACAAG 59.900 55.000 0.00 0.00 0.00 3.16
390 391 0.608856 ACCAGCCGCATGATGAACAA 60.609 50.000 0.00 0.00 0.00 2.83
392 393 0.527565 AAACCAGCCGCATGATGAAC 59.472 50.000 0.00 0.00 0.00 3.18
394 395 1.378531 GTAAACCAGCCGCATGATGA 58.621 50.000 0.00 0.00 0.00 2.92
395 396 0.027979 CGTAAACCAGCCGCATGATG 59.972 55.000 0.00 0.00 0.00 3.07
396 397 0.392461 ACGTAAACCAGCCGCATGAT 60.392 50.000 0.00 0.00 0.00 2.45
516 517 1.072331 ACATCATTCCCATCGGCCTAC 59.928 52.381 0.00 0.00 0.00 3.18
593 595 5.314923 ACACATATCAAATGCACCAGAAC 57.685 39.130 0.00 0.00 0.00 3.01
759 761 4.161189 TGTTCAAAAATGAAACCAGGCAGA 59.839 37.500 0.00 0.00 0.00 4.26
761 763 4.161189 TCTGTTCAAAAATGAAACCAGGCA 59.839 37.500 8.44 0.00 0.00 4.75
793 796 5.794687 TGTACTTTCATTAATGCCTGACG 57.205 39.130 10.76 0.00 0.00 4.35
872 875 2.225019 ACAGATTTCTTGCTCAGTTGCG 59.775 45.455 0.00 0.00 35.36 4.85
876 879 3.498774 ACCACAGATTTCTTGCTCAGT 57.501 42.857 0.00 0.00 0.00 3.41
1013 1016 4.330620 ACAAAGCAAACTTCACAGCAATTG 59.669 37.500 0.00 0.00 34.05 2.32
1041 1044 8.914328 TGCACATGACAATCTTAAACATTATG 57.086 30.769 0.00 0.00 0.00 1.90
1291 1302 3.034635 ACGCATCCAGTAGAAAGGATCT 58.965 45.455 0.00 0.00 42.61 2.75
1396 1407 6.078456 ACTTCAATAATCTTGGATCCCACA 57.922 37.500 9.90 0.00 30.78 4.17
1465 1476 8.094798 TGTAACAACGAGATTCTGCTATTTTT 57.905 30.769 0.00 0.00 0.00 1.94
1542 1668 5.940192 TCATTGGTCATTCACTGTACAAC 57.060 39.130 0.00 0.00 0.00 3.32
1547 1673 6.819284 ACAATTTTCATTGGTCATTCACTGT 58.181 32.000 0.31 0.00 43.82 3.55
1569 1695 6.918892 ACATATGAATTAGCACGCTTTACA 57.081 33.333 10.38 0.00 0.00 2.41
1577 1705 7.148573 CCGGAGATACAACATATGAATTAGCAC 60.149 40.741 10.38 0.00 0.00 4.40
1582 1710 5.620206 TGCCGGAGATACAACATATGAATT 58.380 37.500 5.05 0.00 0.00 2.17
1628 1761 1.740025 GTGCACCATTCCTGAGTAAGC 59.260 52.381 5.22 0.00 0.00 3.09
2341 2488 4.130118 CAAATGCTCACCCTACTATGGTC 58.870 47.826 0.00 0.00 32.46 4.02
2344 2491 3.544684 TGCAAATGCTCACCCTACTATG 58.455 45.455 6.97 0.00 42.66 2.23
2384 2550 2.797792 GCTGCACCAACAATGAAAACGA 60.798 45.455 0.00 0.00 0.00 3.85
2591 2760 4.676196 GCCATACTGCAGTTTCCATCAAAG 60.676 45.833 27.06 0.58 0.00 2.77
2767 2983 1.529865 GAGTAACCAGGCACGACAAAC 59.470 52.381 0.00 0.00 0.00 2.93
2774 2990 4.009370 AGAAGAAAGAGTAACCAGGCAC 57.991 45.455 0.00 0.00 0.00 5.01
2777 2993 7.492994 GCTATGTAAGAAGAAAGAGTAACCAGG 59.507 40.741 0.00 0.00 0.00 4.45
2794 3010 4.115516 AGTTGCGAGACATGCTATGTAAG 58.884 43.478 0.00 0.10 45.03 2.34
2811 3029 6.928492 TCAATATTTTCCACAAAAGGAGTTGC 59.072 34.615 0.00 0.00 39.25 4.17
2853 3071 9.615295 CACATATGAATCAAATCAATATTCGCA 57.385 29.630 10.38 0.00 33.28 5.10
2854 3072 9.830294 TCACATATGAATCAAATCAATATTCGC 57.170 29.630 10.38 0.00 33.28 4.70
2862 3080 9.844790 GAAAACAGTCACATATGAATCAAATCA 57.155 29.630 10.38 0.00 36.31 2.57
2863 3081 9.844790 TGAAAACAGTCACATATGAATCAAATC 57.155 29.630 10.38 0.00 36.31 2.17
2864 3082 9.630098 GTGAAAACAGTCACATATGAATCAAAT 57.370 29.630 10.38 0.00 46.00 2.32
2877 3095 1.400494 ACCGCAAGTGAAAACAGTCAC 59.600 47.619 0.00 0.00 46.90 3.67
2880 3098 1.944709 GGTACCGCAAGTGAAAACAGT 59.055 47.619 0.00 0.00 0.00 3.55
2891 3111 1.302192 GGACAGCTTGGTACCGCAA 60.302 57.895 13.45 0.00 0.00 4.85
2938 3158 2.036475 TGCATGGCCGTTTGTACAAATT 59.964 40.909 23.11 3.29 32.36 1.82
3030 3250 6.284459 AGACAAACAAGTCCTAGAAACAGAG 58.716 40.000 0.00 0.00 39.34 3.35
3095 3641 4.191544 GCATTACACATAAGGACTGCTGA 58.808 43.478 0.00 0.00 0.00 4.26
3117 3666 3.855689 TCCTAGTTAAACCCTTCGTCG 57.144 47.619 0.00 0.00 0.00 5.12
3125 3674 9.832445 TTTCTGATATGTCATCCTAGTTAAACC 57.168 33.333 0.00 0.00 32.98 3.27
3326 4522 0.931005 GTTACAGTAGGCTCATGCGC 59.069 55.000 0.00 0.00 40.82 6.09
3367 4573 5.358922 CATCACCATTTGTTGTTCCTGTTT 58.641 37.500 0.00 0.00 0.00 2.83
3450 4656 0.467844 TGCACACTCCACCAAATGCT 60.468 50.000 0.00 0.00 34.18 3.79
3498 4704 1.102154 CTGAACCAATTGCGCCCATA 58.898 50.000 4.18 0.00 0.00 2.74
3537 4743 5.707242 AGTACTGGTATATGATGGTGACG 57.293 43.478 0.00 0.00 0.00 4.35
3628 4834 2.761786 AGCCATAACATGCTCCCAAT 57.238 45.000 0.00 0.00 30.33 3.16
3999 5205 4.469657 ACTAGGTCAGGCATTTTTGTTCA 58.530 39.130 0.00 0.00 0.00 3.18
4079 5373 6.608405 TGCCAGAATTCATTCACCTCAATATT 59.392 34.615 8.44 0.00 39.23 1.28
4104 5398 1.864711 CACGTCATCAAACGAACACCT 59.135 47.619 3.16 0.00 45.37 4.00
4143 5437 4.517075 TGCATCCTATTTGAAAACGTGACA 59.483 37.500 0.00 0.00 0.00 3.58
4152 5446 6.183360 ACAAGGTTTTGTGCATCCTATTTGAA 60.183 34.615 0.00 0.00 45.54 2.69
4167 5469 9.537848 GTCTCGTATAAATTACACAAGGTTTTG 57.462 33.333 0.00 0.00 40.24 2.44
4188 5490 9.724839 TCTTTTAAACCTTACAAAAATGTCTCG 57.275 29.630 0.00 0.00 0.00 4.04
4239 5541 3.121194 GCTCGCTTCTTTCATATAGTGCG 60.121 47.826 0.00 0.00 42.89 5.34
4247 5549 0.950555 TGTGCGCTCGCTTCTTTCAT 60.951 50.000 9.73 0.00 42.51 2.57
4285 5587 3.188786 ACCAAAGCGCGATCGAGC 61.189 61.111 32.62 32.62 41.21 5.03
4286 5588 2.697425 CACCAAAGCGCGATCGAG 59.303 61.111 21.57 18.10 38.10 4.04
4287 5589 3.487202 GCACCAAAGCGCGATCGA 61.487 61.111 21.57 0.00 38.10 3.59
4288 5590 4.520846 GGCACCAAAGCGCGATCG 62.521 66.667 12.10 11.69 39.07 3.69
4301 5603 8.507249 GTGAGATGGAATAAAATAGTATGGCAC 58.493 37.037 0.00 0.00 0.00 5.01
4333 5635 5.337554 ACGGTTCAAAAGTTGTAGCTTTTC 58.662 37.500 0.00 0.00 44.13 2.29
4342 5644 3.443976 CAAAGGGACGGTTCAAAAGTTG 58.556 45.455 0.00 0.00 0.00 3.16
4364 5673 8.801715 ATTAAGCAACGGCAAATAATATCAAG 57.198 30.769 0.00 0.00 44.61 3.02
4366 5675 8.841300 TGTATTAAGCAACGGCAAATAATATCA 58.159 29.630 0.00 0.00 44.61 2.15
4367 5676 9.672086 TTGTATTAAGCAACGGCAAATAATATC 57.328 29.630 0.00 0.00 44.61 1.63
4489 5801 1.793134 GCCTGCCTATGATGCACAGC 61.793 60.000 0.00 0.00 34.46 4.40
4490 5802 0.464916 TGCCTGCCTATGATGCACAG 60.465 55.000 0.00 0.00 34.46 3.66
4491 5803 0.034283 TTGCCTGCCTATGATGCACA 60.034 50.000 0.00 0.00 34.46 4.57
4492 5804 1.325355 ATTGCCTGCCTATGATGCAC 58.675 50.000 0.00 0.00 34.46 4.57
4493 5805 2.076207 AATTGCCTGCCTATGATGCA 57.924 45.000 0.00 0.00 37.17 3.96
4494 5806 3.464111 AAAATTGCCTGCCTATGATGC 57.536 42.857 0.00 0.00 0.00 3.91
4495 5807 6.335471 TGATAAAATTGCCTGCCTATGATG 57.665 37.500 0.00 0.00 0.00 3.07
4496 5808 6.722590 TCATGATAAAATTGCCTGCCTATGAT 59.277 34.615 0.00 0.00 0.00 2.45
4497 5809 6.069994 TCATGATAAAATTGCCTGCCTATGA 58.930 36.000 0.00 0.00 0.00 2.15
4498 5810 6.335471 TCATGATAAAATTGCCTGCCTATG 57.665 37.500 0.00 0.00 0.00 2.23
4499 5811 6.982160 TTCATGATAAAATTGCCTGCCTAT 57.018 33.333 0.00 0.00 0.00 2.57
4500 5812 6.982160 ATTCATGATAAAATTGCCTGCCTA 57.018 33.333 0.00 0.00 0.00 3.93
4501 5813 5.881923 ATTCATGATAAAATTGCCTGCCT 57.118 34.783 0.00 0.00 0.00 4.75
4502 5814 6.930667 AAATTCATGATAAAATTGCCTGCC 57.069 33.333 0.00 0.00 0.00 4.85
4503 5815 7.066043 TCCAAAATTCATGATAAAATTGCCTGC 59.934 33.333 0.00 0.00 0.00 4.85
4504 5816 8.495361 TCCAAAATTCATGATAAAATTGCCTG 57.505 30.769 0.00 0.00 0.00 4.85
4505 5817 7.281549 GCTCCAAAATTCATGATAAAATTGCCT 59.718 33.333 0.00 0.00 0.00 4.75
4506 5818 7.066043 TGCTCCAAAATTCATGATAAAATTGCC 59.934 33.333 0.00 0.00 0.00 4.52
4507 5819 7.906527 GTGCTCCAAAATTCATGATAAAATTGC 59.093 33.333 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.