Multiple sequence alignment - TraesCS5A01G261100

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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 TraesCS5A01G261100 chr5A 100.000 4122 0 0 1 4122 474952314 474948193 0.000000e+00 7613
1 TraesCS5A01G261100 chr5A 94.841 1725 76 8 567 2281 475272465 475270744 0.000000e+00 2680
2 TraesCS5A01G261100 chr5A 96.679 542 18 0 1 542 548354163 548354704 0.000000e+00 902
3 TraesCS5A01G261100 chr5A 97.180 532 15 0 1 532 559668693 559669224 0.000000e+00 900
4 TraesCS5A01G261100 chr5A 92.295 597 29 4 2345 2939 475270753 475270172 0.000000e+00 832
5 TraesCS5A01G261100 chr5A 89.258 391 25 5 2940 3317 475270139 475269753 1.340000e-129 473
6 TraesCS5A01G261100 chr5D 92.582 1793 107 11 577 2352 371854055 371852272 0.000000e+00 2551
7 TraesCS5A01G261100 chr5D 88.101 874 57 15 2350 3181 371852244 371851376 0.000000e+00 994
8 TraesCS5A01G261100 chr5B 92.885 1012 59 8 737 1746 441675919 441674919 0.000000e+00 1458
9 TraesCS5A01G261100 chr5B 92.670 573 35 7 2370 2939 441673193 441672625 0.000000e+00 819
10 TraesCS5A01G261100 chr5B 92.222 450 25 8 1803 2246 441674922 441674477 2.700000e-176 628
11 TraesCS5A01G261100 chr5B 90.289 381 23 3 2940 3307 441672591 441672212 1.720000e-133 486
12 TraesCS5A01G261100 chr7A 97.022 806 22 2 3318 4122 51646659 51645855 0.000000e+00 1354
13 TraesCS5A01G261100 chr7A 96.663 809 25 1 3316 4122 600995924 600995116 0.000000e+00 1343
14 TraesCS5A01G261100 chr7A 96.530 807 23 2 3318 4122 44986898 44987701 0.000000e+00 1330
15 TraesCS5A01G261100 chr7A 96.273 805 30 0 3318 4122 697516966 697517770 0.000000e+00 1321
16 TraesCS5A01G261100 chr7A 96.149 805 31 0 3318 4122 697509869 697510673 0.000000e+00 1315
17 TraesCS5A01G261100 chr4A 96.292 809 25 4 3317 4122 634331091 634330285 0.000000e+00 1323
18 TraesCS5A01G261100 chr4A 96.691 544 18 0 1 544 590860562 590861105 0.000000e+00 905
19 TraesCS5A01G261100 chr4A 97.180 532 15 0 1 532 12748442 12748973 0.000000e+00 900
20 TraesCS5A01G261100 chr1A 96.292 809 22 4 3318 4122 11127629 11128433 0.000000e+00 1321
21 TraesCS5A01G261100 chr6A 96.159 807 26 3 3318 4122 22132153 22132956 0.000000e+00 1314
22 TraesCS5A01G261100 chr2A 96.149 805 28 1 3318 4122 43711510 43712311 0.000000e+00 1312
23 TraesCS5A01G261100 chr2A 97.180 532 15 0 1 532 748493498 748492967 0.000000e+00 900
24 TraesCS5A01G261100 chr3A 97.186 533 15 0 1 533 100811611 100812143 0.000000e+00 902
25 TraesCS5A01G261100 chr3A 97.180 532 15 0 1 532 542501387 542501918 0.000000e+00 900
26 TraesCS5A01G261100 chr3A 97.180 532 15 0 1 532 633085788 633085257 0.000000e+00 900
27 TraesCS5A01G261100 chr3A 96.337 546 18 1 1 546 581862713 581863256 0.000000e+00 896


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 TraesCS5A01G261100 chr5A 474948193 474952314 4121 True 7613.000000 7613 100.000000 1 4122 1 chr5A.!!$R1 4121
1 TraesCS5A01G261100 chr5A 475269753 475272465 2712 True 1328.333333 2680 92.131333 567 3317 3 chr5A.!!$R2 2750
2 TraesCS5A01G261100 chr5A 548354163 548354704 541 False 902.000000 902 96.679000 1 542 1 chr5A.!!$F1 541
3 TraesCS5A01G261100 chr5A 559668693 559669224 531 False 900.000000 900 97.180000 1 532 1 chr5A.!!$F2 531
4 TraesCS5A01G261100 chr5D 371851376 371854055 2679 True 1772.500000 2551 90.341500 577 3181 2 chr5D.!!$R1 2604
5 TraesCS5A01G261100 chr5B 441672212 441675919 3707 True 847.750000 1458 92.016500 737 3307 4 chr5B.!!$R1 2570
6 TraesCS5A01G261100 chr7A 51645855 51646659 804 True 1354.000000 1354 97.022000 3318 4122 1 chr7A.!!$R1 804
7 TraesCS5A01G261100 chr7A 600995116 600995924 808 True 1343.000000 1343 96.663000 3316 4122 1 chr7A.!!$R2 806
8 TraesCS5A01G261100 chr7A 44986898 44987701 803 False 1330.000000 1330 96.530000 3318 4122 1 chr7A.!!$F1 804
9 TraesCS5A01G261100 chr7A 697516966 697517770 804 False 1321.000000 1321 96.273000 3318 4122 1 chr7A.!!$F3 804
10 TraesCS5A01G261100 chr7A 697509869 697510673 804 False 1315.000000 1315 96.149000 3318 4122 1 chr7A.!!$F2 804
11 TraesCS5A01G261100 chr4A 634330285 634331091 806 True 1323.000000 1323 96.292000 3317 4122 1 chr4A.!!$R1 805
12 TraesCS5A01G261100 chr4A 590860562 590861105 543 False 905.000000 905 96.691000 1 544 1 chr4A.!!$F2 543
13 TraesCS5A01G261100 chr4A 12748442 12748973 531 False 900.000000 900 97.180000 1 532 1 chr4A.!!$F1 531
14 TraesCS5A01G261100 chr1A 11127629 11128433 804 False 1321.000000 1321 96.292000 3318 4122 1 chr1A.!!$F1 804
15 TraesCS5A01G261100 chr6A 22132153 22132956 803 False 1314.000000 1314 96.159000 3318 4122 1 chr6A.!!$F1 804
16 TraesCS5A01G261100 chr2A 43711510 43712311 801 False 1312.000000 1312 96.149000 3318 4122 1 chr2A.!!$F1 804
17 TraesCS5A01G261100 chr2A 748492967 748493498 531 True 900.000000 900 97.180000 1 532 1 chr2A.!!$R1 531
18 TraesCS5A01G261100 chr3A 100811611 100812143 532 False 902.000000 902 97.186000 1 533 1 chr3A.!!$F1 532
19 TraesCS5A01G261100 chr3A 542501387 542501918 531 False 900.000000 900 97.180000 1 532 1 chr3A.!!$F2 531
20 TraesCS5A01G261100 chr3A 633085257 633085788 531 True 900.000000 900 97.180000 1 532 1 chr3A.!!$R1 531
21 TraesCS5A01G261100 chr3A 581862713 581863256 543 False 896.000000 896 96.337000 1 546 1 chr3A.!!$F3 545

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
557 558 1.963515 AGCACAATGGGGTTTCTGAAC 59.036 47.619 0.0 0.0 34.96 3.18 F
1018 1030 1.476488 GAATGGATGTTGGGGTTTCCG 59.524 52.381 0.0 0.0 38.76 4.30 F
1611 1623 1.985473 TGGCAGCTCTTCAAACATGT 58.015 45.000 0.0 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1478 1490 1.067495 ACAGAGGAACTACTGAAGCGC 60.067 52.381 0.0 0.0 41.55 5.92 R
2728 3980 1.062587 GACATGAGGTCGCAATTTCCG 59.937 52.381 0.0 0.0 36.65 4.30 R
3164 4462 0.605319 TTTCATGGTGACTGCGGGAC 60.605 55.000 0.0 0.0 0.00 4.46 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
57 58 2.678336 GACAATCGGAGTGACAAATCCC 59.322 50.000 12.93 0.00 31.43 3.85
234 235 6.770746 AGTCATGAAGAAAGCAATAGCAAT 57.229 33.333 0.00 0.00 45.49 3.56
283 284 3.623703 TGGAATGGGTCATGTCAATCAG 58.376 45.455 0.00 0.00 0.00 2.90
291 292 5.128205 GGGTCATGTCAATCAGATCATTCA 58.872 41.667 0.00 0.00 0.00 2.57
292 293 5.591472 GGGTCATGTCAATCAGATCATTCAA 59.409 40.000 0.00 0.00 0.00 2.69
538 539 9.354673 TCTAGGGCATATTTCCTTCAATTTTAG 57.645 33.333 0.00 0.00 34.75 1.85
544 545 9.101655 GCATATTTCCTTCAATTTTAGCACAAT 57.898 29.630 0.00 0.00 0.00 2.71
546 547 7.910441 ATTTCCTTCAATTTTAGCACAATGG 57.090 32.000 0.00 0.00 0.00 3.16
547 548 5.404466 TCCTTCAATTTTAGCACAATGGG 57.596 39.130 0.00 0.00 0.00 4.00
548 549 4.222588 TCCTTCAATTTTAGCACAATGGGG 59.777 41.667 0.00 0.00 0.00 4.96
549 550 4.020307 CCTTCAATTTTAGCACAATGGGGT 60.020 41.667 0.00 0.00 0.00 4.95
550 551 5.512921 CCTTCAATTTTAGCACAATGGGGTT 60.513 40.000 0.00 0.00 0.00 4.11
551 552 5.559148 TCAATTTTAGCACAATGGGGTTT 57.441 34.783 0.00 0.00 0.00 3.27
552 553 5.546526 TCAATTTTAGCACAATGGGGTTTC 58.453 37.500 0.00 0.00 0.00 2.78
553 554 5.306678 TCAATTTTAGCACAATGGGGTTTCT 59.693 36.000 0.00 0.00 0.00 2.52
554 555 4.599047 TTTTAGCACAATGGGGTTTCTG 57.401 40.909 0.00 0.00 0.00 3.02
555 556 3.517296 TTAGCACAATGGGGTTTCTGA 57.483 42.857 0.00 0.00 0.00 3.27
556 557 2.380064 AGCACAATGGGGTTTCTGAA 57.620 45.000 0.00 0.00 0.00 3.02
557 558 1.963515 AGCACAATGGGGTTTCTGAAC 59.036 47.619 0.00 0.00 34.96 3.18
558 559 1.963515 GCACAATGGGGTTTCTGAACT 59.036 47.619 0.00 0.00 36.03 3.01
559 560 2.365293 GCACAATGGGGTTTCTGAACTT 59.635 45.455 0.00 0.00 36.03 2.66
560 561 3.572255 GCACAATGGGGTTTCTGAACTTA 59.428 43.478 0.00 0.00 36.03 2.24
561 562 4.558697 GCACAATGGGGTTTCTGAACTTAC 60.559 45.833 0.00 0.00 36.03 2.34
562 563 3.818773 ACAATGGGGTTTCTGAACTTACG 59.181 43.478 0.00 0.00 36.03 3.18
563 564 4.069304 CAATGGGGTTTCTGAACTTACGA 58.931 43.478 0.00 0.00 36.03 3.43
564 565 4.569719 ATGGGGTTTCTGAACTTACGAT 57.430 40.909 0.00 0.00 36.03 3.73
565 566 3.934068 TGGGGTTTCTGAACTTACGATC 58.066 45.455 0.00 0.00 36.03 3.69
571 572 6.530887 GGGTTTCTGAACTTACGATCTAGAAC 59.469 42.308 0.00 0.00 36.03 3.01
609 610 7.497249 CCTAGATAGAAGCAAGCAACTAAACAT 59.503 37.037 0.00 0.00 0.00 2.71
615 616 7.212274 AGAAGCAAGCAACTAAACATCATTTT 58.788 30.769 0.00 0.00 0.00 1.82
618 619 5.466393 GCAAGCAACTAAACATCATTTTGGT 59.534 36.000 0.00 0.00 32.02 3.67
661 662 6.800408 CCAGATGCGTCATAAATCATTTGATC 59.200 38.462 8.99 0.00 32.75 2.92
697 703 5.104982 AGTTCATTTGGACAAGGCAAAAAGA 60.105 36.000 0.00 0.00 0.00 2.52
698 704 5.350504 TCATTTGGACAAGGCAAAAAGAA 57.649 34.783 0.00 0.00 0.00 2.52
842 850 7.435068 TTTACTTGGAAGTGTTCTTAGCATC 57.565 36.000 2.14 0.00 40.07 3.91
873 882 3.937706 TGCACCTTTGTTTTGTTCATTGG 59.062 39.130 0.00 0.00 0.00 3.16
966 978 6.604171 TGTATATGGAAGAAGGTACGAGGTA 58.396 40.000 0.00 0.00 0.00 3.08
1018 1030 1.476488 GAATGGATGTTGGGGTTTCCG 59.524 52.381 0.00 0.00 38.76 4.30
1045 1057 5.070047 GGGCTGAAGAATGAAAATGGATCAT 59.930 40.000 0.00 0.00 39.15 2.45
1194 1206 2.910977 TCCTTTGAGTAGGGGTTTCTCC 59.089 50.000 0.00 0.00 35.90 3.71
1242 1254 7.159372 TGTATCTGAAGTGAACTAGGGTTTTC 58.841 38.462 0.00 0.00 35.58 2.29
1265 1277 9.640963 TTTCCTTTTTGAACGAATTTTAGTGAA 57.359 25.926 0.00 0.00 0.00 3.18
1366 1378 5.811399 TCATCTTTGGAAAACGCGATTAT 57.189 34.783 15.93 0.00 0.00 1.28
1379 1391 8.736751 AAAACGCGATTATGAACAAAATAGTT 57.263 26.923 15.93 0.00 0.00 2.24
1449 1461 8.421784 AGGAAATTTATGTTGATAGAGTCGCTA 58.578 33.333 0.00 0.00 0.00 4.26
1611 1623 1.985473 TGGCAGCTCTTCAAACATGT 58.015 45.000 0.00 0.00 0.00 3.21
1653 1665 7.134815 CGAAGATGTTTTCAACTCTGTTTCAT 58.865 34.615 0.00 0.00 31.74 2.57
1810 1822 9.661187 CCATGTTTCAACTATACTACTACGTAG 57.339 37.037 20.97 20.97 41.43 3.51
1838 1850 4.626042 AGCCTATTCTGATTGACGTGATC 58.374 43.478 0.00 0.00 0.00 2.92
1845 1857 6.618287 TTCTGATTGACGTGATCACTTTTT 57.382 33.333 22.95 5.16 36.92 1.94
1914 1926 4.985413 TCAGTTTCTTTTGAACACTGCTG 58.015 39.130 12.04 0.00 41.60 4.41
1945 1957 5.163395 GGTTTTTGATTCCAAGGTTGTACCA 60.163 40.000 0.00 0.00 41.95 3.25
2033 2045 4.182693 TGTAGGTAGAATTGACACCACG 57.817 45.455 3.30 0.00 34.62 4.94
2034 2046 3.827876 TGTAGGTAGAATTGACACCACGA 59.172 43.478 0.00 0.00 34.62 4.35
2239 3447 8.742554 AAAGAATACCTTTTTATGTTGCTTCG 57.257 30.769 0.00 0.00 42.13 3.79
2286 3504 7.990917 TCACACAATCAAACTAAACTTTGCTA 58.009 30.769 0.00 0.00 32.10 3.49
2301 3519 7.870509 AACTTTGCTATTTGATATGCTCAGA 57.129 32.000 0.00 0.00 34.68 3.27
2316 3534 5.571784 TGCTCAGAAATCAACATTCCATC 57.428 39.130 0.00 0.00 0.00 3.51
2342 3560 8.225107 CCAATGATTTGCTGTTAACAATCAAAG 58.775 33.333 26.08 19.09 34.36 2.77
2414 3662 9.994432 GAAGTTTGTATCTCCATGAAAACATAG 57.006 33.333 0.00 0.00 31.53 2.23
2436 3684 6.305272 AGGCATCTTTCTCAATCTCTTACA 57.695 37.500 0.00 0.00 0.00 2.41
2548 3797 9.940166 AACGTTGAGTTAAATTATTTCTCGTTT 57.060 25.926 0.00 0.00 42.14 3.60
2566 3815 2.808543 GTTTGACTTGAAGTGGAGCGAT 59.191 45.455 0.90 0.00 0.00 4.58
2595 3844 5.007724 GCAAACTTCATACTGGTATAGTGCC 59.992 44.000 0.00 0.00 40.65 5.01
2606 3855 5.947566 ACTGGTATAGTGCCGGTAAATTTTT 59.052 36.000 1.90 0.00 43.29 1.94
2613 3862 2.288518 TGCCGGTAAATTTTTGCCTCAC 60.289 45.455 1.90 0.00 40.30 3.51
2620 3869 6.017523 CGGTAAATTTTTGCCTCACCATTTTT 60.018 34.615 8.27 0.00 40.30 1.94
2728 3980 1.408340 TGCTAGCACTGAGATGAGCTC 59.592 52.381 14.93 6.82 44.21 4.09
2738 3990 1.260033 GAGATGAGCTCGGAAATTGCG 59.740 52.381 9.64 0.00 33.17 4.85
2967 4252 7.201652 GCTAATCCTGTTAAATTGTCAGAGTCC 60.202 40.741 6.42 0.00 0.00 3.85
2970 4255 4.389077 CCTGTTAAATTGTCAGAGTCCGAC 59.611 45.833 0.00 0.00 0.00 4.79
2977 4262 0.098376 GTCAGAGTCCGACGCGTATT 59.902 55.000 13.97 0.00 0.00 1.89
2988 4273 2.471749 CGACGCGTATTGTCCTGAAAAC 60.472 50.000 13.97 0.00 32.68 2.43
2996 4281 6.491394 CGTATTGTCCTGAAAACTTTGTTCA 58.509 36.000 0.00 0.00 33.97 3.18
3025 4310 2.915463 CGTGAACTCGTATCTTGGACAC 59.085 50.000 0.00 0.00 0.00 3.67
3068 4353 2.114616 AGGGCTTCGTCATCAGAGATT 58.885 47.619 0.00 0.00 0.00 2.40
3097 4382 5.426689 TCCTCACTTCATACTCAAGCATT 57.573 39.130 0.00 0.00 0.00 3.56
3109 4407 5.551760 ACTCAAGCATTATGTTTCCTTCG 57.448 39.130 0.00 0.00 0.00 3.79
3152 4450 4.837860 TGGAATAAAGCAGGTTGTTGGATT 59.162 37.500 0.00 0.00 0.00 3.01
3158 4456 3.412386 AGCAGGTTGTTGGATTAGTCAC 58.588 45.455 0.00 0.00 0.00 3.67
3164 4462 4.022329 GGTTGTTGGATTAGTCACCAAAGG 60.022 45.833 0.00 0.00 45.75 3.11
3168 4466 2.307686 TGGATTAGTCACCAAAGGTCCC 59.692 50.000 0.00 0.00 31.02 4.46
3218 4516 6.701432 AACTAATGTACGTTGTGAAGCTAC 57.299 37.500 10.68 0.00 0.00 3.58
3235 4533 8.654230 TGAAGCTACTTCATTGATTGTATCTC 57.346 34.615 5.94 0.00 44.27 2.75
3331 4629 0.766674 ACCCCCACTAGTGCAGAACA 60.767 55.000 17.86 0.00 0.00 3.18
3455 4760 0.623723 GGTGCTAAAGGGGATCCACA 59.376 55.000 18.46 0.00 34.83 4.17
3499 4804 1.145598 GGAGCCCTTTAGTACCGGC 59.854 63.158 0.00 0.00 41.96 6.13
3755 5063 7.032580 GCTAGCTATCTAATCATCATCAACGT 58.967 38.462 7.70 0.00 0.00 3.99
3916 5224 1.685077 CCTGCTGCTCCCTCTCAGA 60.685 63.158 0.00 0.00 32.26 3.27
3962 5270 5.146298 AGCTCTCCTGATTCATCATACTGA 58.854 41.667 0.00 0.00 36.02 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.334691 GGATTTGTCACTCCGATTGTCA 58.665 45.455 0.00 0.00 0.00 3.58
57 58 2.031683 GGGTTGGCGTATTTCGAGATTG 59.968 50.000 0.00 0.00 42.86 2.67
234 235 6.210784 AGCTTAGCACCCGATCATTTAGTATA 59.789 38.462 7.07 0.00 0.00 1.47
291 292 7.279615 TGATTAACGGGATCACATCATTAGTT 58.720 34.615 0.00 0.00 0.00 2.24
292 293 6.826668 TGATTAACGGGATCACATCATTAGT 58.173 36.000 0.00 0.00 0.00 2.24
353 354 8.485976 ACTTGACTAGCTCATTAATCAAAGAC 57.514 34.615 0.00 0.00 0.00 3.01
502 503 8.682514 AGGAAATATGCCCTAGAGGAAATAATT 58.317 33.333 0.00 0.00 38.24 1.40
509 510 4.566837 TGAAGGAAATATGCCCTAGAGGA 58.433 43.478 0.00 0.00 38.24 3.71
538 539 1.963515 AGTTCAGAAACCCCATTGTGC 59.036 47.619 0.00 0.00 35.92 4.57
544 545 3.581332 AGATCGTAAGTTCAGAAACCCCA 59.419 43.478 0.00 0.00 38.53 4.96
545 546 4.203654 AGATCGTAAGTTCAGAAACCCC 57.796 45.455 0.00 0.00 38.53 4.95
546 547 6.205101 TCTAGATCGTAAGTTCAGAAACCC 57.795 41.667 0.00 0.00 38.53 4.11
547 548 6.530887 GGTTCTAGATCGTAAGTTCAGAAACC 59.469 42.308 0.00 0.00 36.28 3.27
548 549 7.314393 AGGTTCTAGATCGTAAGTTCAGAAAC 58.686 38.462 0.00 0.00 39.03 2.78
549 550 7.463961 AGGTTCTAGATCGTAAGTTCAGAAA 57.536 36.000 0.00 0.00 38.53 2.52
550 551 8.457261 GTTAGGTTCTAGATCGTAAGTTCAGAA 58.543 37.037 13.61 0.00 38.53 3.02
551 552 7.828223 AGTTAGGTTCTAGATCGTAAGTTCAGA 59.172 37.037 13.61 0.00 38.53 3.27
552 553 7.987649 AGTTAGGTTCTAGATCGTAAGTTCAG 58.012 38.462 13.61 0.00 38.53 3.02
553 554 7.934855 AGTTAGGTTCTAGATCGTAAGTTCA 57.065 36.000 13.61 0.00 38.53 3.18
558 559 9.277783 GGTGTATAGTTAGGTTCTAGATCGTAA 57.722 37.037 10.49 10.49 0.00 3.18
559 560 8.654997 AGGTGTATAGTTAGGTTCTAGATCGTA 58.345 37.037 0.00 0.00 0.00 3.43
560 561 7.516452 AGGTGTATAGTTAGGTTCTAGATCGT 58.484 38.462 0.00 0.00 0.00 3.73
561 562 7.982761 AGGTGTATAGTTAGGTTCTAGATCG 57.017 40.000 0.00 0.00 0.00 3.69
571 572 8.865420 TGCTTCTATCTAGGTGTATAGTTAGG 57.135 38.462 0.00 0.00 30.76 2.69
589 590 7.452880 AATGATGTTTAGTTGCTTGCTTCTA 57.547 32.000 0.00 0.00 0.00 2.10
615 616 8.209802 TCTGGAATTTCTAAGTTACCTTACCA 57.790 34.615 0.00 0.00 31.89 3.25
618 619 7.494625 CGCATCTGGAATTTCTAAGTTACCTTA 59.505 37.037 0.00 0.00 31.89 2.69
635 636 5.821995 TCAAATGATTTATGACGCATCTGGA 59.178 36.000 0.00 0.00 0.00 3.86
639 640 7.578852 TCAGATCAAATGATTTATGACGCATC 58.421 34.615 0.00 0.00 34.37 3.91
661 662 6.375174 TGTCCAAATGAACTGGTTATCATCAG 59.625 38.462 0.00 0.00 35.29 2.90
671 673 1.962807 TGCCTTGTCCAAATGAACTGG 59.037 47.619 0.00 0.00 35.05 4.00
673 675 4.751767 TTTTGCCTTGTCCAAATGAACT 57.248 36.364 0.00 0.00 32.76 3.01
739 746 8.947115 GTGAATCTAGGTAATTAGTTGCTTGTT 58.053 33.333 0.00 0.00 0.00 2.83
842 850 3.525268 AACAAAGGTGCAAGGTTTGAG 57.475 42.857 18.60 0.15 35.55 3.02
873 882 3.386768 ACTATCACATATGTCGCACCC 57.613 47.619 5.07 0.00 0.00 4.61
926 938 7.726216 TCCATATACATGTCAAGGTTGTCTAG 58.274 38.462 0.00 0.00 0.00 2.43
933 945 6.158695 ACCTTCTTCCATATACATGTCAAGGT 59.841 38.462 0.00 4.70 33.83 3.50
1018 1030 3.368739 CCATTTTCATTCTTCAGCCCCAC 60.369 47.826 0.00 0.00 0.00 4.61
1045 1057 7.377398 CCACATTCCATGACAAATAGTTTGAA 58.623 34.615 9.21 0.00 43.26 2.69
1101 1113 5.796502 AAAACCAAGAGGATCCTCCATTA 57.203 39.130 33.81 0.00 43.70 1.90
1242 1254 9.848172 CATTTCACTAAAATTCGTTCAAAAAGG 57.152 29.630 0.00 0.00 35.32 3.11
1265 1277 8.472007 TCAACTGAAGTGGGTTAAATAACATT 57.528 30.769 5.74 0.00 37.92 2.71
1282 1294 9.466497 AAAAAGCAAGAGGATATATCAACTGAA 57.534 29.630 14.60 0.00 0.00 3.02
1350 1362 4.750952 TGTTCATAATCGCGTTTTCCAA 57.249 36.364 5.77 0.00 0.00 3.53
1358 1370 6.628856 CCTCAACTATTTTGTTCATAATCGCG 59.371 38.462 0.00 0.00 0.00 5.87
1366 1378 4.211125 TGCACCCTCAACTATTTTGTTCA 58.789 39.130 0.00 0.00 0.00 3.18
1379 1391 1.219124 GAGCTTCGATGCACCCTCA 59.781 57.895 23.42 0.00 34.99 3.86
1478 1490 1.067495 ACAGAGGAACTACTGAAGCGC 60.067 52.381 0.00 0.00 41.55 5.92
1533 1545 5.221722 TGTCACTCTGAGGAGCAGTTTTATT 60.222 40.000 9.85 0.00 45.14 1.40
1611 1623 4.393834 TCTTCGTCCAATGAAATCCACAA 58.606 39.130 0.00 0.00 0.00 3.33
1810 1822 3.559242 GTCAATCAGAATAGGCTCACTGC 59.441 47.826 0.00 0.00 41.94 4.40
1845 1857 5.235850 TGTAGTAAACCAGCCTGAATGAA 57.764 39.130 0.00 0.00 0.00 2.57
1914 1926 2.247358 TGGAATCAAAAACCTCCAGCC 58.753 47.619 0.00 0.00 32.97 4.85
1970 1982 6.893583 AGGTGATATAGCAGAAATGTTCAGT 58.106 36.000 0.00 0.00 0.00 3.41
2015 2027 3.369471 CCATCGTGGTGTCAATTCTACCT 60.369 47.826 0.00 0.00 35.51 3.08
2033 2045 8.516234 ACGATTACTATGACATCTAAGTCCATC 58.484 37.037 0.00 0.00 37.73 3.51
2034 2046 8.410673 ACGATTACTATGACATCTAAGTCCAT 57.589 34.615 0.00 0.00 37.73 3.41
2218 2236 5.623596 GCCCGAAGCAACATAAAAAGGTATT 60.624 40.000 0.00 0.00 42.97 1.89
2239 3447 6.808704 GTGAAAAGTTGAAATATTGAGAGCCC 59.191 38.462 0.00 0.00 0.00 5.19
2286 3504 9.745880 GAATGTTGATTTCTGAGCATATCAAAT 57.254 29.630 0.00 0.00 38.36 2.32
2301 3519 7.066525 GCAAATCATTGGATGGAATGTTGATTT 59.933 33.333 0.00 0.00 40.84 2.17
2316 3534 7.655236 TTGATTGTTAACAGCAAATCATTGG 57.345 32.000 17.26 0.00 37.02 3.16
2414 3662 6.112058 ACTGTAAGAGATTGAGAAAGATGCC 58.888 40.000 0.00 0.00 37.43 4.40
2474 3723 2.571212 TGCACGTCCAGAAACAGAAAT 58.429 42.857 0.00 0.00 0.00 2.17
2477 3726 1.134521 ACTTGCACGTCCAGAAACAGA 60.135 47.619 0.00 0.00 0.00 3.41
2524 3773 9.588774 TCAAACGAGAAATAATTTAACTCAACG 57.411 29.630 0.00 0.00 0.00 4.10
2548 3797 4.183865 CAATATCGCTCCACTTCAAGTCA 58.816 43.478 0.00 0.00 0.00 3.41
2566 3815 8.491134 ACTATACCAGTATGAAGTTTGCCAATA 58.509 33.333 0.45 0.00 39.69 1.90
2595 3844 3.651803 TGGTGAGGCAAAAATTTACCG 57.348 42.857 0.00 0.00 0.00 4.02
2601 3850 8.518430 AAAACTAAAAATGGTGAGGCAAAAAT 57.482 26.923 0.00 0.00 0.00 1.82
2728 3980 1.062587 GACATGAGGTCGCAATTTCCG 59.937 52.381 0.00 0.00 36.65 4.30
2967 4252 1.342555 TTTCAGGACAATACGCGTCG 58.657 50.000 18.63 8.57 34.04 5.12
2970 4255 3.806316 AAGTTTTCAGGACAATACGCG 57.194 42.857 3.53 3.53 0.00 6.01
2977 4262 4.441356 GGCATGAACAAAGTTTTCAGGACA 60.441 41.667 6.22 0.00 41.48 4.02
2988 4273 2.422597 TCACGTAGGGCATGAACAAAG 58.577 47.619 0.00 0.00 0.00 2.77
2996 4281 1.466856 TACGAGTTCACGTAGGGCAT 58.533 50.000 0.00 0.00 44.72 4.40
3068 4353 8.580720 GCTTGAGTATGAAGTGAGGATATAAGA 58.419 37.037 0.00 0.00 29.53 2.10
3097 4382 3.663995 TGGTTCGACGAAGGAAACATA 57.336 42.857 11.25 0.00 36.25 2.29
3109 4407 5.601662 TCCAGATCTATTCATTGGTTCGAC 58.398 41.667 0.00 0.00 0.00 4.20
3152 4450 1.122632 TGCGGGACCTTTGGTGACTA 61.123 55.000 0.00 0.00 35.25 2.59
3158 4456 1.966451 GTGACTGCGGGACCTTTGG 60.966 63.158 0.00 0.00 0.00 3.28
3164 4462 0.605319 TTTCATGGTGACTGCGGGAC 60.605 55.000 0.00 0.00 0.00 4.46
3168 4466 2.995466 ATTGTTTCATGGTGACTGCG 57.005 45.000 0.00 0.00 0.00 5.18
3218 4516 9.814899 AGACTACAAGAGATACAATCAATGAAG 57.185 33.333 0.00 0.00 0.00 3.02
3235 4533 4.500603 ACAACCGACACTAGACTACAAG 57.499 45.455 0.00 0.00 0.00 3.16
3245 4543 9.880157 ATACTAATTGTTTATACAACCGACACT 57.120 29.630 0.54 0.00 46.38 3.55
3293 4591 6.215841 TGGGGGTGATTATTTACAGACTACAA 59.784 38.462 0.00 0.00 0.00 2.41
3331 4629 1.077716 GAACCGGTGCTATTGCCCT 60.078 57.895 8.52 0.00 38.71 5.19
3478 4783 1.145598 GGTACTAAAGGGCTCCCGC 59.854 63.158 0.00 0.00 41.95 6.13
3512 4817 7.572546 AAAACCTACACCCATTTAGTACCTA 57.427 36.000 0.00 0.00 0.00 3.08
3513 4818 6.458630 AAAACCTACACCCATTTAGTACCT 57.541 37.500 0.00 0.00 0.00 3.08
3755 5063 4.980573 TGTTTCCTCTTTAAGCTAGCCAA 58.019 39.130 12.13 2.84 0.00 4.52
4086 5394 5.068234 CACATGAGTGCATTCAGGATTTT 57.932 39.130 27.45 4.98 39.21 1.82


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

AutoCloner maintained by Alex Coulton.