Multiple sequence alignment - TraesCS5B01G192800

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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 TraesCS5B01G192800 chr5B 100.000 4821 0 0 1 4821 347982620 347987440 0.000000e+00 8903
1 TraesCS5B01G192800 chr5A 93.520 2886 141 25 1561 4423 394758761 394755899 0.000000e+00 4252
2 TraesCS5B01G192800 chr5A 93.921 839 37 6 781 1607 394759586 394758750 0.000000e+00 1254
3 TraesCS5B01G192800 chr5A 93.425 365 15 6 4463 4821 394755900 394755539 2.550000e-147 532
4 TraesCS5B01G192800 chr5A 93.103 116 6 2 571 686 308040830 308040717 8.300000e-38 169
5 TraesCS5B01G192800 chr5A 93.458 107 6 1 571 676 308041035 308040929 1.800000e-34 158
6 TraesCS5B01G192800 chr5D 94.842 2346 92 14 781 3102 302967580 302969920 0.000000e+00 3635
7 TraesCS5B01G192800 chr5D 95.771 1726 63 6 3099 4821 302970006 302971724 0.000000e+00 2774
8 TraesCS5B01G192800 chr3B 95.716 677 28 1 1 676 513674300 513673624 0.000000e+00 1088
9 TraesCS5B01G192800 chr2B 95.716 677 28 1 1 676 99540694 99540018 0.000000e+00 1088
10 TraesCS5B01G192800 chr7A 95.549 674 28 2 1 673 49226220 49226892 0.000000e+00 1077
11 TraesCS5B01G192800 chr6B 95.301 681 23 6 1 676 648278542 648279218 0.000000e+00 1072
12 TraesCS5B01G192800 chr4B 95.353 538 22 3 1 537 128949787 128949252 0.000000e+00 852
13 TraesCS5B01G192800 chrUn 95.429 525 16 3 32 549 90487042 90486519 0.000000e+00 830
14 TraesCS5B01G192800 chrUn 93.346 541 30 4 1 537 248890697 248890159 0.000000e+00 795
15 TraesCS5B01G192800 chrUn 93.161 541 31 4 1 537 269800468 269799930 0.000000e+00 789
16 TraesCS5B01G192800 chr1D 94.646 523 20 5 34 549 462983224 462983745 0.000000e+00 804
17 TraesCS5B01G192800 chr1A 91.667 108 8 1 570 677 187143707 187143601 1.080000e-31 148
18 TraesCS5B01G192800 chr1A 90.909 110 9 1 570 678 10998916 10999025 3.890000e-31 147
19 TraesCS5B01G192800 chr7B 90.826 109 10 0 570 678 676796314 676796206 3.890000e-31 147


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 TraesCS5B01G192800 chr5B 347982620 347987440 4820 False 8903.000000 8903 100.0000 1 4821 1 chr5B.!!$F1 4820
1 TraesCS5B01G192800 chr5A 394755539 394759586 4047 True 2012.666667 4252 93.6220 781 4821 3 chr5A.!!$R2 4040
2 TraesCS5B01G192800 chr5D 302967580 302971724 4144 False 3204.500000 3635 95.3065 781 4821 2 chr5D.!!$F1 4040
3 TraesCS5B01G192800 chr3B 513673624 513674300 676 True 1088.000000 1088 95.7160 1 676 1 chr3B.!!$R1 675
4 TraesCS5B01G192800 chr2B 99540018 99540694 676 True 1088.000000 1088 95.7160 1 676 1 chr2B.!!$R1 675
5 TraesCS5B01G192800 chr7A 49226220 49226892 672 False 1077.000000 1077 95.5490 1 673 1 chr7A.!!$F1 672
6 TraesCS5B01G192800 chr6B 648278542 648279218 676 False 1072.000000 1072 95.3010 1 676 1 chr6B.!!$F1 675
7 TraesCS5B01G192800 chr4B 128949252 128949787 535 True 852.000000 852 95.3530 1 537 1 chr4B.!!$R1 536
8 TraesCS5B01G192800 chrUn 90486519 90487042 523 True 830.000000 830 95.4290 32 549 1 chrUn.!!$R1 517
9 TraesCS5B01G192800 chrUn 248890159 248890697 538 True 795.000000 795 93.3460 1 537 1 chrUn.!!$R2 536
10 TraesCS5B01G192800 chrUn 269799930 269800468 538 True 789.000000 789 93.1610 1 537 1 chrUn.!!$R3 536
11 TraesCS5B01G192800 chr1D 462983224 462983745 521 False 804.000000 804 94.6460 34 549 1 chr1D.!!$F1 515

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
164 169 0.037326 GAGGATGCGTTGACCTGTGA 60.037 55.000 0.00 0.0 33.89 3.58 F
1238 1260 1.566018 CCTCGTTTCGGTTGCTGGTC 61.566 60.000 0.00 0.0 0.00 4.02 F
1319 1343 0.179054 GGAGGATTCGGGCCTGTAAC 60.179 60.000 12.43 0.0 35.44 2.50 F
1321 1345 0.252197 AGGATTCGGGCCTGTAACAC 59.748 55.000 12.43 0.0 33.59 3.32 F
1444 1468 0.467384 ATGCCTCGCTATGCAGTCTT 59.533 50.000 0.00 0.0 41.46 3.01 F
2779 2845 2.438434 CCAGATGTGGGGCCGAAC 60.438 66.667 0.00 0.0 40.67 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 1323 0.619255 TTACAGGCCCGAATCCTCCA 60.619 55.0 0.00 0.00 0.00 3.86 R
2460 2522 1.436600 AACTGCATCTCACAGAAGCG 58.563 50.0 0.00 0.00 41.44 4.68 R
2852 2922 2.119801 ATGCGAAAAGATGAGGTGCT 57.880 45.0 0.00 0.00 0.00 4.40 R
3199 3365 4.022416 TGCGGATTGTCAGCAATTTTAAGT 60.022 37.5 2.36 0.00 44.13 2.24 R
3414 3580 5.126061 GGTTCCAATGACATAGAACAAGCAT 59.874 40.0 22.87 0.00 40.27 3.79 R
4631 4810 0.675083 CATTGCCAAACTGCAGGTGA 59.325 50.0 19.93 0.46 43.21 4.02 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
164 169 0.037326 GAGGATGCGTTGACCTGTGA 60.037 55.000 0.00 0.00 33.89 3.58
181 186 4.514577 AAGCTCGCCGTCGGATGG 62.515 66.667 17.49 12.04 36.13 3.51
274 282 2.561569 CGTGAGTTGTGGGAAAAGACT 58.438 47.619 0.00 0.00 0.00 3.24
575 586 1.618143 TGGGGAATCGGTGGGATGT 60.618 57.895 0.00 0.00 34.93 3.06
676 688 7.721842 CCAACTGAGACATTAGGAGTAGAGATA 59.278 40.741 0.00 0.00 0.00 1.98
677 689 8.783093 CAACTGAGACATTAGGAGTAGAGATAG 58.217 40.741 0.00 0.00 0.00 2.08
678 690 6.940298 ACTGAGACATTAGGAGTAGAGATAGC 59.060 42.308 0.00 0.00 0.00 2.97
679 691 6.842676 TGAGACATTAGGAGTAGAGATAGCA 58.157 40.000 0.00 0.00 0.00 3.49
680 692 6.712998 TGAGACATTAGGAGTAGAGATAGCAC 59.287 42.308 0.00 0.00 0.00 4.40
681 693 5.703592 AGACATTAGGAGTAGAGATAGCACG 59.296 44.000 0.00 0.00 0.00 5.34
682 694 5.622180 ACATTAGGAGTAGAGATAGCACGA 58.378 41.667 0.00 0.00 0.00 4.35
683 695 6.062749 ACATTAGGAGTAGAGATAGCACGAA 58.937 40.000 0.00 0.00 0.00 3.85
684 696 6.016943 ACATTAGGAGTAGAGATAGCACGAAC 60.017 42.308 0.00 0.00 0.00 3.95
685 697 3.887352 AGGAGTAGAGATAGCACGAACA 58.113 45.455 0.00 0.00 0.00 3.18
686 698 3.628487 AGGAGTAGAGATAGCACGAACAC 59.372 47.826 0.00 0.00 0.00 3.32
687 699 3.546417 GGAGTAGAGATAGCACGAACACG 60.546 52.174 0.00 0.00 0.00 4.49
688 700 3.268330 AGTAGAGATAGCACGAACACGA 58.732 45.455 0.00 0.00 0.00 4.35
689 701 3.688185 AGTAGAGATAGCACGAACACGAA 59.312 43.478 0.00 0.00 0.00 3.85
690 702 3.138205 AGAGATAGCACGAACACGAAG 57.862 47.619 0.00 0.00 0.00 3.79
691 703 2.747989 AGAGATAGCACGAACACGAAGA 59.252 45.455 0.00 0.00 0.00 2.87
692 704 3.378742 AGAGATAGCACGAACACGAAGAT 59.621 43.478 0.00 0.00 0.00 2.40
693 705 4.575236 AGAGATAGCACGAACACGAAGATA 59.425 41.667 0.00 0.00 0.00 1.98
694 706 4.599047 AGATAGCACGAACACGAAGATAC 58.401 43.478 0.00 0.00 0.00 2.24
695 707 4.335874 AGATAGCACGAACACGAAGATACT 59.664 41.667 0.00 0.00 0.00 2.12
696 708 2.864968 AGCACGAACACGAAGATACTC 58.135 47.619 0.00 0.00 0.00 2.59
697 709 1.578023 GCACGAACACGAAGATACTCG 59.422 52.381 0.00 0.00 44.50 4.18
727 739 9.803315 AATTTACTTCTCAGAAAAAGTGAAACC 57.197 29.630 7.75 0.00 35.47 3.27
728 740 8.575649 TTTACTTCTCAGAAAAAGTGAAACCT 57.424 30.769 7.75 0.00 37.80 3.50
729 741 9.675464 TTTACTTCTCAGAAAAAGTGAAACCTA 57.325 29.630 7.75 0.00 37.80 3.08
730 742 9.675464 TTACTTCTCAGAAAAAGTGAAACCTAA 57.325 29.630 7.75 0.00 37.80 2.69
731 743 7.986562 ACTTCTCAGAAAAAGTGAAACCTAAC 58.013 34.615 0.00 0.00 37.80 2.34
732 744 7.829706 ACTTCTCAGAAAAAGTGAAACCTAACT 59.170 33.333 0.00 0.00 37.80 2.24
733 745 8.575649 TTCTCAGAAAAAGTGAAACCTAACTT 57.424 30.769 0.00 0.00 37.80 2.66
734 746 7.985476 TCTCAGAAAAAGTGAAACCTAACTTG 58.015 34.615 0.00 0.00 37.80 3.16
735 747 7.827236 TCTCAGAAAAAGTGAAACCTAACTTGA 59.173 33.333 0.00 0.00 37.80 3.02
736 748 8.343168 TCAGAAAAAGTGAAACCTAACTTGAA 57.657 30.769 0.00 0.00 37.80 2.69
737 749 8.798402 TCAGAAAAAGTGAAACCTAACTTGAAA 58.202 29.630 0.00 0.00 37.80 2.69
738 750 9.418045 CAGAAAAAGTGAAACCTAACTTGAAAA 57.582 29.630 0.00 0.00 37.80 2.29
739 751 9.990360 AGAAAAAGTGAAACCTAACTTGAAAAA 57.010 25.926 0.00 0.00 37.80 1.94
765 777 7.980742 AAAAGTGAAACGTTCTATGTTTTCC 57.019 32.000 0.00 0.00 45.86 3.13
766 778 6.937436 AAGTGAAACGTTCTATGTTTTCCT 57.063 33.333 0.00 0.00 45.86 3.36
767 779 6.937436 AGTGAAACGTTCTATGTTTTCCTT 57.063 33.333 0.00 0.00 45.86 3.36
768 780 8.441312 AAGTGAAACGTTCTATGTTTTCCTTA 57.559 30.769 0.00 0.00 45.86 2.69
769 781 8.441312 AGTGAAACGTTCTATGTTTTCCTTAA 57.559 30.769 0.00 0.00 45.86 1.85
770 782 8.895737 AGTGAAACGTTCTATGTTTTCCTTAAA 58.104 29.630 0.00 0.00 45.86 1.52
771 783 9.166126 GTGAAACGTTCTATGTTTTCCTTAAAG 57.834 33.333 0.00 0.00 37.43 1.85
772 784 9.111613 TGAAACGTTCTATGTTTTCCTTAAAGA 57.888 29.630 0.00 0.00 37.43 2.52
933 955 2.226170 ACCTCCAAAATACTCCCCTCCT 60.226 50.000 0.00 0.00 0.00 3.69
953 975 1.747444 ACAGTTCCACTCCATCCCTT 58.253 50.000 0.00 0.00 0.00 3.95
957 979 2.124570 CCACTCCATCCCTTGCCG 60.125 66.667 0.00 0.00 0.00 5.69
958 980 2.669133 CCACTCCATCCCTTGCCGA 61.669 63.158 0.00 0.00 0.00 5.54
1166 1188 2.317609 CGCGCTACCTGTTTGTGCT 61.318 57.895 5.56 0.00 35.36 4.40
1238 1260 1.566018 CCTCGTTTCGGTTGCTGGTC 61.566 60.000 0.00 0.00 0.00 4.02
1299 1323 0.386476 TCTGTGCGTTGTAGGAACGT 59.614 50.000 8.57 0.00 44.69 3.99
1316 1340 2.285368 TGGAGGATTCGGGCCTGT 60.285 61.111 12.43 0.00 35.44 4.00
1317 1341 1.002403 TGGAGGATTCGGGCCTGTA 59.998 57.895 12.43 1.22 35.44 2.74
1319 1343 0.179054 GGAGGATTCGGGCCTGTAAC 60.179 60.000 12.43 0.00 35.44 2.50
1320 1344 0.539986 GAGGATTCGGGCCTGTAACA 59.460 55.000 12.43 0.00 35.44 2.41
1321 1345 0.252197 AGGATTCGGGCCTGTAACAC 59.748 55.000 12.43 0.00 33.59 3.32
1358 1382 4.633126 GGTCGGAGTTGGGAGTAAATTAAC 59.367 45.833 0.00 0.00 0.00 2.01
1360 1384 5.350640 GTCGGAGTTGGGAGTAAATTAACTG 59.649 44.000 0.00 0.00 32.23 3.16
1362 1386 5.570034 CGGAGTTGGGAGTAAATTAACTGGA 60.570 44.000 0.00 0.00 32.23 3.86
1367 1391 3.784202 GGGAGTAAATTAACTGGAGGGGA 59.216 47.826 0.00 0.00 0.00 4.81
1374 1398 8.177456 AGTAAATTAACTGGAGGGGAAATTTCT 58.823 33.333 17.42 0.00 31.21 2.52
1377 1401 3.441500 ACTGGAGGGGAAATTTCTGTC 57.558 47.619 17.42 11.15 0.00 3.51
1428 1452 2.102946 GCCCTGCACGCTTTATGC 59.897 61.111 0.00 0.00 43.68 3.14
1432 1456 1.349627 CTGCACGCTTTATGCCTCG 59.650 57.895 0.00 0.00 42.69 4.63
1444 1468 0.467384 ATGCCTCGCTATGCAGTCTT 59.533 50.000 0.00 0.00 41.46 3.01
1457 1481 4.472691 TGCAGTCTTTGTTCTTCATTCG 57.527 40.909 0.00 0.00 0.00 3.34
1477 1501 2.613691 GGATTCAGGTGCTGCATTTTG 58.386 47.619 5.27 5.16 0.00 2.44
1708 1768 6.494491 TGATAATCATTTTCTGCCCCTTATGG 59.506 38.462 0.00 0.00 0.00 2.74
1712 1772 4.079269 TCATTTTCTGCCCCTTATGGATGA 60.079 41.667 0.00 0.00 35.39 2.92
1722 1782 4.018960 CCCCTTATGGATGATAGACCTTGG 60.019 50.000 0.00 0.00 35.39 3.61
1733 1793 5.359756 TGATAGACCTTGGATTGAATGTCG 58.640 41.667 0.00 0.00 0.00 4.35
1824 1884 5.563867 GCTTCCTACCTGTCGATATTCTCAG 60.564 48.000 0.00 0.00 0.00 3.35
1862 1922 5.414454 TGTATGTTGTTCAACCTAGGCATTC 59.586 40.000 9.30 0.36 0.00 2.67
1866 1926 4.207891 TGTTCAACCTAGGCATTCTCTC 57.792 45.455 9.30 0.00 0.00 3.20
2161 2221 4.661222 TCATGGCTTATTGGTGAACTTCA 58.339 39.130 0.00 0.00 0.00 3.02
2353 2414 7.251704 TCTTCAGAAGTGATGTTTCTTGTTC 57.748 36.000 10.09 0.00 32.75 3.18
2399 2461 9.023962 TGATGTATTAATCTTTTCAGCCAGTTT 57.976 29.630 0.00 0.00 0.00 2.66
2537 2599 3.719352 GCTTGAACGAAAAACAGTTCTCG 59.281 43.478 13.59 13.59 44.95 4.04
2779 2845 2.438434 CCAGATGTGGGGCCGAAC 60.438 66.667 0.00 0.00 40.67 3.95
2825 2891 4.519213 TGTTAAGCTGTTAGGTGTGTTGT 58.481 39.130 0.00 0.00 0.00 3.32
2852 2922 4.949238 CACATCCTGAATACACCATTGGAA 59.051 41.667 10.37 0.00 0.00 3.53
2867 2937 4.381292 CCATTGGAAGCACCTCATCTTTTC 60.381 45.833 0.00 0.00 39.86 2.29
3199 3365 6.872020 GCCTGAACTACTAATTGTCTGTTGTA 59.128 38.462 0.00 0.00 0.00 2.41
3220 3386 6.607689 TGTACTTAAAATTGCTGACAATCCG 58.392 36.000 0.00 0.00 45.90 4.18
3237 3403 6.265577 ACAATCCGCAATTTAAAGCATCTAC 58.734 36.000 0.00 0.00 0.00 2.59
3290 3456 9.383519 GGTTTGTTATCTTCATGATCTCTTACA 57.616 33.333 0.00 0.00 36.65 2.41
3414 3580 5.480772 GGCATATCTTAGTGGTAAGCCTCTA 59.519 44.000 0.00 0.00 39.18 2.43
3439 3605 4.437390 GCTTGTTCTATGTCATTGGAACCG 60.437 45.833 19.53 14.58 37.74 4.44
3460 3626 4.436852 CCGTCAGTTTTGCGCTATATTTGT 60.437 41.667 9.73 0.00 0.00 2.83
3814 3980 3.311871 AGAAAGCATCTAATTCAGCAGCG 59.688 43.478 0.00 0.00 36.32 5.18
4121 4292 2.959465 AAGTTTTAGACCCTGCTGCT 57.041 45.000 0.00 0.00 0.00 4.24
4312 4486 9.462606 TTTCTACTGTTCTGTAGATAGATCACA 57.537 33.333 16.20 0.00 45.46 3.58
4362 4536 4.678287 GTGTGCATGAAAGAGTTTGATGTG 59.322 41.667 0.00 0.00 36.74 3.21
4363 4537 3.671928 GTGCATGAAAGAGTTTGATGTGC 59.328 43.478 0.00 0.00 36.74 4.57
4406 4580 6.645700 AACACAGTTTTGCTACAACAATTG 57.354 33.333 3.24 3.24 0.00 2.32
4426 4600 1.401905 GTTGCAGGGCCTAATTCTTCG 59.598 52.381 5.28 0.00 0.00 3.79
4502 4678 2.047274 CCGGTGACATGGCGAACT 60.047 61.111 0.00 0.00 0.00 3.01
4543 4719 7.690301 GCCTTCAAGTGATTCAGGATCCTATTA 60.690 40.741 15.67 2.80 33.60 0.98
4544 4720 8.381636 CCTTCAAGTGATTCAGGATCCTATTAT 58.618 37.037 15.67 8.04 33.60 1.28
4545 4721 9.434420 CTTCAAGTGATTCAGGATCCTATTATC 57.566 37.037 15.67 16.63 33.60 1.75
4552 4728 8.354486 TGATTCAGGATCCTATTATCCCTATCA 58.646 37.037 15.67 9.65 45.74 2.15
4578 4754 5.457148 CGCTCTTTGCTGTATAACTAGACTG 59.543 44.000 0.00 0.00 40.11 3.51
4623 4802 4.377445 CACGCAACGAATGTTTTTACGAAT 59.623 37.500 0.00 0.00 35.72 3.34
4629 4808 7.937294 GCAACGAATGTTTTTACGAATTTACAG 59.063 33.333 0.00 0.00 35.72 2.74
4631 4810 9.887406 AACGAATGTTTTTACGAATTTACAGAT 57.113 25.926 0.00 0.00 33.53 2.90
4707 4886 2.094700 TCTAACTCGATGCGCTGAAACT 60.095 45.455 9.73 0.00 0.00 2.66
4720 4900 5.353956 TGCGCTGAAACTAATGTAATCATGT 59.646 36.000 9.73 0.00 34.19 3.21
4770 4950 3.517296 TGCCTTTTGGATGAACAGGTA 57.483 42.857 0.00 0.00 44.07 3.08
4808 4988 2.357009 GCCCATGTTCTGTCATGTGATC 59.643 50.000 11.86 0.00 42.29 2.92
4812 4992 6.002082 CCCATGTTCTGTCATGTGATCATAT 58.998 40.000 0.00 0.00 42.29 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.285215 GCGTCGCTATCGGAGGGA 61.285 66.667 10.68 1.70 44.44 4.20
39 40 3.319198 ACGCCTTCCCACCATCGT 61.319 61.111 0.00 0.00 0.00 3.73
164 169 4.514577 CCATCCGACGGCGAGCTT 62.515 66.667 15.16 0.00 40.82 3.74
575 586 0.914417 GTCCTCAATCCCACCTCCCA 60.914 60.000 0.00 0.00 0.00 4.37
676 688 2.728225 CGAGTATCTTCGTGTTCGTGCT 60.728 50.000 0.00 0.00 38.33 4.40
677 689 1.578023 CGAGTATCTTCGTGTTCGTGC 59.422 52.381 0.00 0.00 38.33 5.34
701 713 9.803315 GGTTTCACTTTTTCTGAGAAGTAAATT 57.197 29.630 0.00 0.00 34.52 1.82
702 714 9.190317 AGGTTTCACTTTTTCTGAGAAGTAAAT 57.810 29.630 0.00 0.00 34.52 1.40
703 715 8.575649 AGGTTTCACTTTTTCTGAGAAGTAAA 57.424 30.769 0.00 0.00 34.52 2.01
704 716 9.675464 TTAGGTTTCACTTTTTCTGAGAAGTAA 57.325 29.630 0.00 0.00 34.52 2.24
705 717 9.106070 GTTAGGTTTCACTTTTTCTGAGAAGTA 57.894 33.333 0.00 0.00 34.52 2.24
706 718 7.829706 AGTTAGGTTTCACTTTTTCTGAGAAGT 59.170 33.333 0.00 3.54 36.58 3.01
707 719 8.214721 AGTTAGGTTTCACTTTTTCTGAGAAG 57.785 34.615 0.00 2.50 0.00 2.85
708 720 8.458843 CAAGTTAGGTTTCACTTTTTCTGAGAA 58.541 33.333 0.00 0.00 30.48 2.87
709 721 7.827236 TCAAGTTAGGTTTCACTTTTTCTGAGA 59.173 33.333 0.00 0.00 30.48 3.27
710 722 7.985476 TCAAGTTAGGTTTCACTTTTTCTGAG 58.015 34.615 0.00 0.00 30.48 3.35
711 723 7.931578 TCAAGTTAGGTTTCACTTTTTCTGA 57.068 32.000 0.00 0.00 30.48 3.27
712 724 8.980143 TTTCAAGTTAGGTTTCACTTTTTCTG 57.020 30.769 0.00 0.00 30.48 3.02
713 725 9.990360 TTTTTCAAGTTAGGTTTCACTTTTTCT 57.010 25.926 0.00 0.00 30.48 2.52
740 752 8.248253 AGGAAAACATAGAACGTTTCACTTTTT 58.752 29.630 0.46 6.43 35.57 1.94
741 753 7.768240 AGGAAAACATAGAACGTTTCACTTTT 58.232 30.769 0.46 3.55 35.57 2.27
742 754 7.329588 AGGAAAACATAGAACGTTTCACTTT 57.670 32.000 0.46 0.00 35.57 2.66
743 755 6.937436 AGGAAAACATAGAACGTTTCACTT 57.063 33.333 0.46 0.00 35.57 3.16
744 756 6.937436 AAGGAAAACATAGAACGTTTCACT 57.063 33.333 0.46 0.00 35.57 3.41
745 757 9.166126 CTTTAAGGAAAACATAGAACGTTTCAC 57.834 33.333 0.46 0.00 35.57 3.18
746 758 9.111613 TCTTTAAGGAAAACATAGAACGTTTCA 57.888 29.630 0.46 0.00 35.57 2.69
790 802 1.880027 GCCGGTTCATTTTCACAGTCT 59.120 47.619 1.90 0.00 0.00 3.24
1092 1114 1.889530 GACACGAGGTAAGCCAGCCT 61.890 60.000 0.00 0.00 37.91 4.58
1192 1214 1.588082 GGACGAACTAAGGACGCCA 59.412 57.895 0.00 0.00 0.00 5.69
1196 1218 1.153686 GGCCGGACGAACTAAGGAC 60.154 63.158 5.05 0.00 0.00 3.85
1285 1309 1.012486 CCTCCACGTTCCTACAACGC 61.012 60.000 6.79 0.00 46.58 4.84
1299 1323 0.619255 TTACAGGCCCGAATCCTCCA 60.619 55.000 0.00 0.00 0.00 3.86
1320 1344 1.863662 CGACCAGTCTACACAGCGGT 61.864 60.000 0.00 0.00 0.00 5.68
1321 1345 1.154016 CGACCAGTCTACACAGCGG 60.154 63.158 0.00 0.00 0.00 5.52
1335 1359 3.345508 AATTTACTCCCAACTCCGACC 57.654 47.619 0.00 0.00 0.00 4.79
1358 1382 3.439857 TGACAGAAATTTCCCCTCCAG 57.560 47.619 14.61 0.00 0.00 3.86
1360 1384 3.767711 ACTTGACAGAAATTTCCCCTCC 58.232 45.455 14.61 1.38 0.00 4.30
1362 1386 5.222337 ACCATACTTGACAGAAATTTCCCCT 60.222 40.000 14.61 0.00 0.00 4.79
1367 1391 8.918202 TCACTAACCATACTTGACAGAAATTT 57.082 30.769 0.00 0.00 0.00 1.82
1374 1398 4.868171 GCGATTCACTAACCATACTTGACA 59.132 41.667 0.00 0.00 0.00 3.58
1377 1401 3.245284 CGGCGATTCACTAACCATACTTG 59.755 47.826 0.00 0.00 0.00 3.16
1428 1452 2.015736 ACAAAGACTGCATAGCGAGG 57.984 50.000 0.00 0.00 0.00 4.63
1432 1456 5.557891 ATGAAGAACAAAGACTGCATAGC 57.442 39.130 0.00 0.00 31.41 2.97
1444 1468 4.455533 CACCTGAATCCGAATGAAGAACAA 59.544 41.667 0.00 0.00 0.00 2.83
1457 1481 2.028748 ACAAAATGCAGCACCTGAATCC 60.029 45.455 0.00 0.00 26.32 3.01
1477 1501 6.092670 AGCAATCACTAATCACATACACACAC 59.907 38.462 0.00 0.00 0.00 3.82
1632 1691 9.070179 TCAATAATTCATTCCTACCATGATGTG 57.930 33.333 0.00 0.00 30.63 3.21
1697 1756 2.912956 GGTCTATCATCCATAAGGGGCA 59.087 50.000 0.00 0.00 37.22 5.36
1708 1768 6.146837 CGACATTCAATCCAAGGTCTATCATC 59.853 42.308 0.00 0.00 35.39 2.92
1712 1772 5.359194 ACGACATTCAATCCAAGGTCTAT 57.641 39.130 0.00 0.00 35.39 1.98
1722 1782 8.407457 TGAGTAATGACTAACGACATTCAATC 57.593 34.615 0.00 0.00 36.95 2.67
1824 1884 3.855689 ACATACATGCAAACAGGCTTC 57.144 42.857 0.00 0.00 34.04 3.86
1862 1922 6.481644 AGAACTGCAGAGTTAAACAAAGAGAG 59.518 38.462 23.35 0.00 42.80 3.20
1866 1926 6.555315 ACAAGAACTGCAGAGTTAAACAAAG 58.445 36.000 23.35 0.57 42.80 2.77
2129 2189 7.040478 TCACCAATAAGCCATGATAATAGTTGC 60.040 37.037 0.00 0.00 0.00 4.17
2161 2221 9.520515 AGTCCACATGTCAAATAAGAAACTATT 57.479 29.630 0.00 0.00 0.00 1.73
2399 2461 2.357637 GCAACACTGACTGCCAAAGTTA 59.642 45.455 0.00 0.00 40.07 2.24
2436 2498 9.262358 GCGAAGAAACTCTGGTATTCTAATATT 57.738 33.333 0.00 0.00 33.26 1.28
2460 2522 1.436600 AACTGCATCTCACAGAAGCG 58.563 50.000 0.00 0.00 41.44 4.68
2779 2845 2.868662 TCAGCGATCTTCTCAACTTCG 58.131 47.619 0.00 0.00 0.00 3.79
2825 2891 5.708736 ATGGTGTATTCAGGATGTGGTAA 57.291 39.130 0.00 0.00 37.40 2.85
2852 2922 2.119801 ATGCGAAAAGATGAGGTGCT 57.880 45.000 0.00 0.00 0.00 4.40
3020 3097 6.558488 AATTGGATGCTTTTAGCCCAAATA 57.442 33.333 11.60 0.00 42.79 1.40
3199 3365 4.022416 TGCGGATTGTCAGCAATTTTAAGT 60.022 37.500 2.36 0.00 44.13 2.24
3220 3386 7.809806 ACACAGAAAGTAGATGCTTTAAATTGC 59.190 33.333 0.00 0.00 38.64 3.56
3237 3403 6.674694 AAGCAGAATATAGCACACAGAAAG 57.325 37.500 0.00 0.00 0.00 2.62
3414 3580 5.126061 GGTTCCAATGACATAGAACAAGCAT 59.874 40.000 22.87 0.00 40.27 3.79
3439 3605 7.216317 CACTTACAAATATAGCGCAAAACTGAC 59.784 37.037 11.47 0.00 0.00 3.51
3472 3638 5.106791 CGAATTCTGCAGTTCAAATGAGACT 60.107 40.000 14.67 0.00 0.00 3.24
3814 3980 6.460399 CCACAGGCAATCTACTAGACTACTTC 60.460 46.154 0.00 0.00 0.00 3.01
3928 4095 5.814705 CAGATACTTGCTACTTCCAGAAAGG 59.185 44.000 0.00 0.00 39.47 3.11
3941 4108 6.879276 TCTATTAGTACGCAGATACTTGCT 57.121 37.500 0.00 0.00 41.90 3.91
3969 4136 5.256806 AGCCACCTAAGGTAAGAAATGTT 57.743 39.130 0.00 0.00 32.11 2.71
3971 4138 5.622233 GCAAAGCCACCTAAGGTAAGAAATG 60.622 44.000 0.00 0.00 32.11 2.32
3972 4139 4.462834 GCAAAGCCACCTAAGGTAAGAAAT 59.537 41.667 0.00 0.00 32.11 2.17
3980 4148 1.747355 CATCTGCAAAGCCACCTAAGG 59.253 52.381 0.00 0.00 0.00 2.69
3988 4156 1.135199 CACCATCACATCTGCAAAGCC 60.135 52.381 0.00 0.00 0.00 4.35
4103 4274 2.355209 GCTAGCAGCAGGGTCTAAAACT 60.355 50.000 10.63 0.00 41.89 2.66
4312 4486 6.446318 ACAAAAATTGTGCAGAATACGATGT 58.554 32.000 9.82 9.80 43.48 3.06
4362 4536 6.581166 GTGTTAGCACCATTACTTAAACTTGC 59.419 38.462 0.00 0.00 39.61 4.01
4363 4537 7.644490 TGTGTTAGCACCATTACTTAAACTTG 58.356 34.615 7.29 0.00 44.65 3.16
4406 4580 1.401905 CGAAGAATTAGGCCCTGCAAC 59.598 52.381 0.00 0.00 0.00 4.17
4426 4600 4.809426 CAGACATTGGAAACTACCGATACC 59.191 45.833 0.00 0.00 33.19 2.73
4502 4678 1.895131 GAAGGCAGGGCAAAATGAAGA 59.105 47.619 0.00 0.00 0.00 2.87
4543 4719 3.051081 GCAAAGAGCGATGATAGGGAT 57.949 47.619 0.00 0.00 0.00 3.85
4544 4720 2.533266 GCAAAGAGCGATGATAGGGA 57.467 50.000 0.00 0.00 0.00 4.20
4578 4754 1.404851 GGCACTCTACACTTCTGCTCC 60.405 57.143 0.00 0.00 0.00 4.70
4605 4784 9.887406 ATCTGTAAATTCGTAAAAACATTCGTT 57.113 25.926 0.00 0.00 36.73 3.85
4623 4802 3.820467 CCAAACTGCAGGTGATCTGTAAA 59.180 43.478 19.93 0.00 45.08 2.01
4629 4808 0.961019 TTGCCAAACTGCAGGTGATC 59.039 50.000 19.93 10.84 43.21 2.92
4631 4810 0.675083 CATTGCCAAACTGCAGGTGA 59.325 50.000 19.93 0.46 43.21 4.02
4707 4886 5.460748 CGTGCTACGGAACATGATTACATTA 59.539 40.000 0.00 0.00 38.08 1.90
4770 4950 3.295973 TGGGCTGTAAAGCTTCTTGTTT 58.704 40.909 4.54 0.00 34.73 2.83


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

AutoCloner maintained by Alex Coulton.