Multiple sequence alignment - TraesCS5A01G545800

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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 TraesCS5A01G545800 chr5A 100.000 2919 0 0 1 2919 700445530 700442612 0 5391
1 TraesCS5A01G545800 chrUn 89.176 2975 174 57 33 2919 110522900 110519986 0 3574
2 TraesCS5A01G545800 chr4B 86.364 2904 198 84 122 2919 660591066 660588255 0 2987


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 TraesCS5A01G545800 chr5A 700442612 700445530 2918 True 5391 5391 100.000 1 2919 1 chr5A.!!$R1 2918
1 TraesCS5A01G545800 chrUn 110519986 110522900 2914 True 3574 3574 89.176 33 2919 1 chrUn.!!$R1 2886
2 TraesCS5A01G545800 chr4B 660588255 660591066 2811 True 2987 2987 86.364 122 2919 1 chr4B.!!$R1 2797

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
90 99 0.103208 CAAATAGCCCGTCTCTCGCT 59.897 55.0 0.0 0.0 38.35 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 2069 0.394352 CCACCATTGTAGCTCCACCC 60.394 60.0 0.0 0.0 0.0 4.61 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
30 31 3.492353 CCCGTCCATGGCCCATCT 61.492 66.667 6.96 0.00 0.00 2.90
31 32 2.203252 CCGTCCATGGCCCATCTG 60.203 66.667 6.96 0.00 0.00 2.90
41 42 0.473326 GGCCCATCTGATCTGAGCTT 59.527 55.000 8.37 0.00 0.00 3.74
48 49 1.126488 CTGATCTGAGCTTAGGCCCA 58.874 55.000 5.56 1.11 39.73 5.36
52 57 0.902984 TCTGAGCTTAGGCCCACGAA 60.903 55.000 5.56 0.00 39.73 3.85
66 71 3.055719 CGAACAAGCCCACCGCAT 61.056 61.111 0.00 0.00 41.38 4.73
90 99 0.103208 CAAATAGCCCGTCTCTCGCT 59.897 55.000 0.00 0.00 38.35 4.93
116 125 0.806492 GCATCTCGACGGAAGGGAAC 60.806 60.000 0.00 0.00 0.00 3.62
117 126 0.530744 CATCTCGACGGAAGGGAACA 59.469 55.000 0.00 0.00 0.00 3.18
488 507 0.108138 CCTACCTCGGCTCCAACTTG 60.108 60.000 0.00 0.00 0.00 3.16
531 550 1.279271 CCTTCTCCACCATCTTCGGTT 59.721 52.381 0.00 0.00 37.07 4.44
532 551 2.622436 CTTCTCCACCATCTTCGGTTC 58.378 52.381 0.00 0.00 37.07 3.62
533 552 0.530744 TCTCCACCATCTTCGGTTCG 59.469 55.000 0.00 0.00 37.07 3.95
534 553 0.246635 CTCCACCATCTTCGGTTCGT 59.753 55.000 0.00 0.00 37.07 3.85
535 554 0.245539 TCCACCATCTTCGGTTCGTC 59.754 55.000 0.00 0.00 37.07 4.20
536 555 1.076533 CCACCATCTTCGGTTCGTCG 61.077 60.000 0.00 0.00 37.07 5.12
538 557 0.109412 ACCATCTTCGGTTCGTCGTC 60.109 55.000 0.00 0.00 34.91 4.20
540 559 1.399440 CCATCTTCGGTTCGTCGTCTA 59.601 52.381 0.00 0.00 0.00 2.59
541 560 2.438583 CATCTTCGGTTCGTCGTCTAC 58.561 52.381 0.00 0.00 0.00 2.59
543 562 0.518636 CTTCGGTTCGTCGTCTACCA 59.481 55.000 12.14 1.03 32.12 3.25
544 563 0.238289 TTCGGTTCGTCGTCTACCAC 59.762 55.000 12.14 0.00 32.12 4.16
545 564 1.154150 CGGTTCGTCGTCTACCACC 60.154 63.158 12.14 0.00 32.12 4.61
546 565 1.855213 CGGTTCGTCGTCTACCACCA 61.855 60.000 12.14 0.00 30.96 4.17
547 566 0.529378 GGTTCGTCGTCTACCACCAT 59.471 55.000 8.40 0.00 30.96 3.55
548 567 1.468736 GGTTCGTCGTCTACCACCATC 60.469 57.143 8.40 0.00 30.96 3.51
549 568 1.471684 GTTCGTCGTCTACCACCATCT 59.528 52.381 0.00 0.00 0.00 2.90
550 569 1.830279 TCGTCGTCTACCACCATCTT 58.170 50.000 0.00 0.00 0.00 2.40
551 570 1.741706 TCGTCGTCTACCACCATCTTC 59.258 52.381 0.00 0.00 0.00 2.87
552 571 1.471287 CGTCGTCTACCACCATCTTCA 59.529 52.381 0.00 0.00 0.00 3.02
553 572 2.731341 CGTCGTCTACCACCATCTTCAC 60.731 54.545 0.00 0.00 0.00 3.18
554 573 2.492484 GTCGTCTACCACCATCTTCACT 59.508 50.000 0.00 0.00 0.00 3.41
555 574 3.056749 GTCGTCTACCACCATCTTCACTT 60.057 47.826 0.00 0.00 0.00 3.16
556 575 3.192844 TCGTCTACCACCATCTTCACTTC 59.807 47.826 0.00 0.00 0.00 3.01
557 576 3.056821 CGTCTACCACCATCTTCACTTCA 60.057 47.826 0.00 0.00 0.00 3.02
558 577 4.499183 GTCTACCACCATCTTCACTTCAG 58.501 47.826 0.00 0.00 0.00 3.02
559 578 2.191128 ACCACCATCTTCACTTCAGC 57.809 50.000 0.00 0.00 0.00 4.26
560 579 1.421268 ACCACCATCTTCACTTCAGCA 59.579 47.619 0.00 0.00 0.00 4.41
561 580 2.158623 ACCACCATCTTCACTTCAGCAA 60.159 45.455 0.00 0.00 0.00 3.91
562 581 2.227388 CCACCATCTTCACTTCAGCAAC 59.773 50.000 0.00 0.00 0.00 4.17
563 582 2.227388 CACCATCTTCACTTCAGCAACC 59.773 50.000 0.00 0.00 0.00 3.77
564 583 2.158623 ACCATCTTCACTTCAGCAACCA 60.159 45.455 0.00 0.00 0.00 3.67
565 584 2.886523 CCATCTTCACTTCAGCAACCAA 59.113 45.455 0.00 0.00 0.00 3.67
566 585 3.318839 CCATCTTCACTTCAGCAACCAAA 59.681 43.478 0.00 0.00 0.00 3.28
567 586 4.021719 CCATCTTCACTTCAGCAACCAAAT 60.022 41.667 0.00 0.00 0.00 2.32
568 587 5.510179 CCATCTTCACTTCAGCAACCAAATT 60.510 40.000 0.00 0.00 0.00 1.82
569 588 6.294675 CCATCTTCACTTCAGCAACCAAATTA 60.295 38.462 0.00 0.00 0.00 1.40
570 589 6.072112 TCTTCACTTCAGCAACCAAATTAC 57.928 37.500 0.00 0.00 0.00 1.89
571 590 5.827797 TCTTCACTTCAGCAACCAAATTACT 59.172 36.000 0.00 0.00 0.00 2.24
572 591 6.321181 TCTTCACTTCAGCAACCAAATTACTT 59.679 34.615 0.00 0.00 0.00 2.24
573 592 6.072112 TCACTTCAGCAACCAAATTACTTC 57.928 37.500 0.00 0.00 0.00 3.01
574 593 5.827797 TCACTTCAGCAACCAAATTACTTCT 59.172 36.000 0.00 0.00 0.00 2.85
575 594 5.916883 CACTTCAGCAACCAAATTACTTCTG 59.083 40.000 0.00 0.00 0.00 3.02
576 595 4.503741 TCAGCAACCAAATTACTTCTGC 57.496 40.909 0.00 0.00 0.00 4.26
577 596 4.144297 TCAGCAACCAAATTACTTCTGCT 58.856 39.130 0.00 0.00 39.15 4.24
578 597 4.216257 TCAGCAACCAAATTACTTCTGCTC 59.784 41.667 0.00 0.00 36.56 4.26
579 598 4.217118 CAGCAACCAAATTACTTCTGCTCT 59.783 41.667 0.00 0.00 36.56 4.09
580 599 4.457257 AGCAACCAAATTACTTCTGCTCTC 59.543 41.667 0.00 0.00 33.55 3.20
581 600 4.457257 GCAACCAAATTACTTCTGCTCTCT 59.543 41.667 0.00 0.00 0.00 3.10
582 601 5.643777 GCAACCAAATTACTTCTGCTCTCTA 59.356 40.000 0.00 0.00 0.00 2.43
583 602 6.183360 GCAACCAAATTACTTCTGCTCTCTAG 60.183 42.308 0.00 0.00 0.00 2.43
599 618 5.599732 CTCTCTAGCTACAACATTGATGCT 58.400 41.667 15.83 15.83 40.73 3.79
630 680 7.410800 TTGTTGTTGCTCATTTGATCATTTC 57.589 32.000 0.00 0.00 0.00 2.17
638 696 6.099125 TGCTCATTTGATCATTTCCATCCATT 59.901 34.615 0.00 0.00 0.00 3.16
639 697 6.645415 GCTCATTTGATCATTTCCATCCATTC 59.355 38.462 0.00 0.00 0.00 2.67
640 698 7.663043 TCATTTGATCATTTCCATCCATTCA 57.337 32.000 0.00 0.00 0.00 2.57
641 699 8.257602 TCATTTGATCATTTCCATCCATTCAT 57.742 30.769 0.00 0.00 0.00 2.57
642 700 8.364894 TCATTTGATCATTTCCATCCATTCATC 58.635 33.333 0.00 0.00 0.00 2.92
643 701 6.659745 TTGATCATTTCCATCCATTCATCC 57.340 37.500 0.00 0.00 0.00 3.51
644 702 5.707495 TGATCATTTCCATCCATTCATCCA 58.293 37.500 0.00 0.00 0.00 3.41
645 703 6.319715 TGATCATTTCCATCCATTCATCCAT 58.680 36.000 0.00 0.00 0.00 3.41
651 709 3.920841 TCCATCCATTCATCCATCCAGAT 59.079 43.478 0.00 0.00 0.00 2.90
666 724 0.593518 CAGATGAGTACAGCCGCGAG 60.594 60.000 8.23 0.00 32.31 5.03
714 781 2.720758 CGCGACGGCACAAGAAGAG 61.721 63.158 0.00 0.00 39.92 2.85
720 787 0.321671 CGGCACAAGAAGAGGAGGAA 59.678 55.000 0.00 0.00 0.00 3.36
756 823 3.588277 GCCGATCGAGCCTATTTCA 57.412 52.632 18.66 0.00 0.00 2.69
838 927 1.748879 CATTCCCCACCGTTGCGAT 60.749 57.895 0.00 0.00 0.00 4.58
850 939 3.163594 CCGTTGCGATGATTTTTCTGTC 58.836 45.455 0.00 0.00 0.00 3.51
856 948 6.110543 TGCGATGATTTTTCTGTCACTATG 57.889 37.500 0.00 0.00 0.00 2.23
902 997 3.751479 TCTTCTTACAGTGCTTGCTCA 57.249 42.857 0.00 0.00 0.00 4.26
937 1034 9.296400 TGTTAAAGAAATGTTTGTCTTGTAAGC 57.704 29.630 0.00 0.00 34.33 3.09
965 1062 6.532657 ACTGTGATTTTTCAGCAAGAAAGTTG 59.467 34.615 4.82 0.00 46.24 3.16
1018 1118 6.263168 CAGTGGTGGATAAATGAATTAGTCCC 59.737 42.308 0.00 0.00 0.00 4.46
1039 1139 5.138125 CCAAAATGGGGATCGGAATATTG 57.862 43.478 0.00 0.00 32.67 1.90
1089 1195 3.320541 CAGAAGACTCCGATAATGGCTCT 59.679 47.826 0.00 0.00 0.00 4.09
1090 1196 3.964031 AGAAGACTCCGATAATGGCTCTT 59.036 43.478 0.00 0.00 31.86 2.85
1124 1230 2.658285 TGCCAGCCTCATCCTTATTTG 58.342 47.619 0.00 0.00 0.00 2.32
1178 1290 6.908870 ATTTTTGGCAAACAAGAAGACTTC 57.091 33.333 13.10 7.14 40.82 3.01
1179 1291 5.659440 TTTTGGCAAACAAGAAGACTTCT 57.341 34.783 13.10 12.12 40.82 2.85
1218 1330 2.012237 GACGATGACGACGGCTCTA 58.988 57.895 0.65 0.00 42.66 2.43
1219 1331 0.587285 GACGATGACGACGGCTCTAT 59.413 55.000 0.65 0.00 42.66 1.98
1252 1367 4.161295 CGGCGGCCTTGATCCTGA 62.161 66.667 18.34 0.00 0.00 3.86
1341 1456 1.668793 CGTGGAGCTGTGCATGTCA 60.669 57.895 0.00 0.00 0.00 3.58
1542 1657 4.120331 GTGGGCATGTGCTTCGCC 62.120 66.667 4.84 0.00 45.47 5.54
1747 1862 5.222007 ACCAACCTCATCAAGTGATCTCTTT 60.222 40.000 7.30 0.00 35.97 2.52
1758 1874 5.480642 AGTGATCTCTTTCTTCTTCAGCA 57.519 39.130 0.00 0.00 0.00 4.41
1766 1882 6.040955 TCTCTTTCTTCTTCAGCAAGTACAGA 59.959 38.462 0.00 0.00 0.00 3.41
1777 1898 5.105187 TCAGCAAGTACAGATCAGTAGCATT 60.105 40.000 9.60 0.00 0.00 3.56
1901 2040 1.134759 TGATTGGCAAAATGGCGATGG 60.135 47.619 3.01 0.00 45.76 3.51
1918 2057 2.914695 TGGCATCATCATCATCGTCA 57.085 45.000 0.00 0.00 0.00 4.35
1919 2058 3.412237 TGGCATCATCATCATCGTCAT 57.588 42.857 0.00 0.00 0.00 3.06
1920 2059 3.746940 TGGCATCATCATCATCGTCATT 58.253 40.909 0.00 0.00 0.00 2.57
1930 2069 7.653311 TCATCATCATCGTCATTAAACACTAGG 59.347 37.037 0.00 0.00 0.00 3.02
1931 2070 6.280643 TCATCATCGTCATTAAACACTAGGG 58.719 40.000 0.00 0.00 0.00 3.53
1944 2083 2.119495 CACTAGGGGTGGAGCTACAAT 58.881 52.381 0.00 0.00 41.90 2.71
1945 2084 2.119495 ACTAGGGGTGGAGCTACAATG 58.881 52.381 0.00 0.00 0.00 2.82
1946 2085 1.417890 CTAGGGGTGGAGCTACAATGG 59.582 57.143 0.00 0.00 0.00 3.16
1952 2091 2.438021 GGTGGAGCTACAATGGTGGATA 59.562 50.000 0.00 0.00 0.00 2.59
1953 2092 3.495100 GGTGGAGCTACAATGGTGGATAG 60.495 52.174 0.00 0.00 0.00 2.08
1954 2093 2.705658 TGGAGCTACAATGGTGGATAGG 59.294 50.000 0.00 0.00 0.00 2.57
1961 2100 2.042979 ACAATGGTGGATAGGTTGGCTT 59.957 45.455 0.00 0.00 0.00 4.35
1962 2101 2.689983 CAATGGTGGATAGGTTGGCTTC 59.310 50.000 0.00 0.00 0.00 3.86
1963 2102 0.623723 TGGTGGATAGGTTGGCTTCC 59.376 55.000 0.00 0.00 0.00 3.46
1964 2103 0.623723 GGTGGATAGGTTGGCTTCCA 59.376 55.000 0.00 0.00 35.93 3.53
1990 2129 7.809546 TCCATGAAACAAAACTGTGTATGTA 57.190 32.000 0.00 0.00 0.00 2.29
2017 2156 6.453092 CAATGCAAAGAAAGAGGAACAAGAT 58.547 36.000 0.00 0.00 0.00 2.40
2019 2158 4.279169 TGCAAAGAAAGAGGAACAAGATGG 59.721 41.667 0.00 0.00 0.00 3.51
2025 2164 1.064166 AGAGGAACAAGATGGCATGGG 60.064 52.381 3.81 0.00 0.00 4.00
2026 2165 0.685458 AGGAACAAGATGGCATGGGC 60.685 55.000 3.81 0.00 40.13 5.36
2027 2166 1.434696 GAACAAGATGGCATGGGCG 59.565 57.895 3.81 0.00 42.47 6.13
2028 2167 2.008268 GAACAAGATGGCATGGGCGG 62.008 60.000 3.81 0.00 42.47 6.13
2029 2168 2.440796 CAAGATGGCATGGGCGGT 60.441 61.111 3.81 0.00 42.47 5.68
2098 2238 1.081774 GATCTGGTCGATCCTCGCG 60.082 63.158 0.00 0.00 42.24 5.87
2145 2286 1.962807 CCCACCTGCACAAATTTCAGA 59.037 47.619 6.88 0.00 0.00 3.27
2149 2290 4.482386 CACCTGCACAAATTTCAGATCAG 58.518 43.478 6.88 2.50 0.00 2.90
2230 2394 1.206849 GGAGCACAAGAGAGAAGAGGG 59.793 57.143 0.00 0.00 0.00 4.30
2235 2399 4.017808 GCACAAGAGAGAAGAGGGTACTA 58.982 47.826 0.00 0.00 0.00 1.82
2294 2459 4.699522 GGTTGGGCGCCTCGAACT 62.700 66.667 28.56 0.00 0.00 3.01
2465 2630 0.036022 GACCACCTTGAAGAGCAGCT 59.964 55.000 0.00 0.00 0.00 4.24
2680 2845 2.203153 ACCACCTTGCGAACGCTT 60.203 55.556 19.32 0.00 42.51 4.68
2682 2847 1.961277 CCACCTTGCGAACGCTTCT 60.961 57.895 19.32 0.00 42.51 2.85
2683 2848 1.507141 CCACCTTGCGAACGCTTCTT 61.507 55.000 19.32 0.14 42.51 2.52
2684 2849 0.110644 CACCTTGCGAACGCTTCTTC 60.111 55.000 19.32 0.00 42.51 2.87
2685 2850 1.228657 ACCTTGCGAACGCTTCTTCC 61.229 55.000 19.32 0.00 42.51 3.46
2686 2851 1.497722 CTTGCGAACGCTTCTTCCC 59.502 57.895 19.32 0.00 42.51 3.97
2687 2852 0.951040 CTTGCGAACGCTTCTTCCCT 60.951 55.000 19.32 0.00 42.51 4.20
2688 2853 0.534203 TTGCGAACGCTTCTTCCCTT 60.534 50.000 19.32 0.00 42.51 3.95
2693 2870 1.518903 AACGCTTCTTCCCTTGCTGC 61.519 55.000 0.00 0.00 0.00 5.25
2793 2982 2.106683 GCGCCATGGTGTAGTGGAC 61.107 63.158 25.68 4.16 37.72 4.02
2794 2983 1.295101 CGCCATGGTGTAGTGGACA 59.705 57.895 17.59 0.00 37.72 4.02
2795 2984 0.740868 CGCCATGGTGTAGTGGACAG 60.741 60.000 17.59 0.00 39.29 3.51
2796 2985 0.392998 GCCATGGTGTAGTGGACAGG 60.393 60.000 14.67 0.00 39.29 4.00
2797 2986 1.275666 CCATGGTGTAGTGGACAGGA 58.724 55.000 2.57 0.00 39.29 3.86
2798 2987 1.628340 CCATGGTGTAGTGGACAGGAA 59.372 52.381 2.57 0.00 39.29 3.36
2799 2988 2.355108 CCATGGTGTAGTGGACAGGAAG 60.355 54.545 2.57 0.00 39.29 3.46
2800 2989 1.348064 TGGTGTAGTGGACAGGAAGG 58.652 55.000 0.00 0.00 39.29 3.46
2801 2990 1.132977 TGGTGTAGTGGACAGGAAGGA 60.133 52.381 0.00 0.00 39.29 3.36
2802 2991 1.975680 GGTGTAGTGGACAGGAAGGAA 59.024 52.381 0.00 0.00 39.29 3.36
2803 2992 2.028020 GGTGTAGTGGACAGGAAGGAAG 60.028 54.545 0.00 0.00 39.29 3.46
2804 2993 2.028020 GTGTAGTGGACAGGAAGGAAGG 60.028 54.545 0.00 0.00 39.29 3.46
2805 2994 2.158219 TGTAGTGGACAGGAAGGAAGGA 60.158 50.000 0.00 0.00 32.86 3.36
2806 2995 1.650528 AGTGGACAGGAAGGAAGGAG 58.349 55.000 0.00 0.00 0.00 3.69
2807 2996 1.150135 AGTGGACAGGAAGGAAGGAGA 59.850 52.381 0.00 0.00 0.00 3.71
2808 2997 1.552792 GTGGACAGGAAGGAAGGAGAG 59.447 57.143 0.00 0.00 0.00 3.20
2809 2998 1.433199 TGGACAGGAAGGAAGGAGAGA 59.567 52.381 0.00 0.00 0.00 3.10
2810 2999 2.107366 GGACAGGAAGGAAGGAGAGAG 58.893 57.143 0.00 0.00 0.00 3.20
2811 3000 2.107366 GACAGGAAGGAAGGAGAGAGG 58.893 57.143 0.00 0.00 0.00 3.69
2812 3001 1.719378 ACAGGAAGGAAGGAGAGAGGA 59.281 52.381 0.00 0.00 0.00 3.71
2813 3002 2.112691 ACAGGAAGGAAGGAGAGAGGAA 59.887 50.000 0.00 0.00 0.00 3.36
2814 3003 2.499693 CAGGAAGGAAGGAGAGAGGAAC 59.500 54.545 0.00 0.00 0.00 3.62
2815 3004 1.478916 GGAAGGAAGGAGAGAGGAACG 59.521 57.143 0.00 0.00 0.00 3.95
2816 3005 1.478916 GAAGGAAGGAGAGAGGAACGG 59.521 57.143 0.00 0.00 0.00 4.44
2817 3006 0.705253 AGGAAGGAGAGAGGAACGGA 59.295 55.000 0.00 0.00 0.00 4.69
2818 3007 1.289530 AGGAAGGAGAGAGGAACGGAT 59.710 52.381 0.00 0.00 0.00 4.18
2886 3079 0.178068 TGCTTCTTATCTGGCCGTCC 59.822 55.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.492353 AGATGGGCCATGGACGGG 61.492 66.667 26.77 0.00 0.00 5.28
14 15 2.060567 ATCAGATGGGCCATGGACGG 62.061 60.000 26.77 10.67 0.00 4.79
15 16 0.604780 GATCAGATGGGCCATGGACG 60.605 60.000 26.77 9.21 0.00 4.79
16 17 0.769873 AGATCAGATGGGCCATGGAC 59.230 55.000 26.77 14.40 0.00 4.02
17 18 0.769247 CAGATCAGATGGGCCATGGA 59.231 55.000 26.77 20.98 0.00 3.41
18 19 0.769247 TCAGATCAGATGGGCCATGG 59.231 55.000 26.77 16.03 0.00 3.66
19 20 1.882780 GCTCAGATCAGATGGGCCATG 60.883 57.143 26.77 12.92 38.26 3.66
20 21 0.400975 GCTCAGATCAGATGGGCCAT 59.599 55.000 21.39 21.39 38.26 4.40
21 22 0.693430 AGCTCAGATCAGATGGGCCA 60.693 55.000 9.61 9.61 45.69 5.36
22 23 0.473326 AAGCTCAGATCAGATGGGCC 59.527 55.000 0.00 0.00 45.69 5.80
23 24 2.289569 CCTAAGCTCAGATCAGATGGGC 60.290 54.545 0.00 0.00 44.85 5.36
24 25 2.289569 GCCTAAGCTCAGATCAGATGGG 60.290 54.545 0.00 0.00 35.50 4.00
25 26 2.289569 GGCCTAAGCTCAGATCAGATGG 60.290 54.545 0.00 0.00 39.73 3.51
26 27 2.289569 GGGCCTAAGCTCAGATCAGATG 60.290 54.545 0.84 0.00 40.27 2.90
27 28 1.977129 GGGCCTAAGCTCAGATCAGAT 59.023 52.381 0.84 0.00 40.27 2.90
28 29 1.418334 GGGCCTAAGCTCAGATCAGA 58.582 55.000 0.84 0.00 40.27 3.27
41 42 2.349755 GGCTTGTTCGTGGGCCTA 59.650 61.111 4.53 0.00 41.20 3.93
48 49 2.457743 TATGCGGTGGGCTTGTTCGT 62.458 55.000 0.00 0.00 44.05 3.85
52 57 2.438434 GCTATGCGGTGGGCTTGT 60.438 61.111 0.00 0.00 44.05 3.16
66 71 0.756903 GAGACGGGCTATTTGGGCTA 59.243 55.000 0.00 0.00 0.00 3.93
94 103 2.956964 CTTCCGTCGAGATGCGGC 60.957 66.667 7.28 0.00 46.79 6.53
96 105 2.278857 CCCTTCCGTCGAGATGCG 60.279 66.667 0.00 0.00 42.69 4.73
116 125 1.067000 GGATCCATCCGATCTGCTCTG 60.067 57.143 6.95 0.00 45.90 3.35
117 126 1.265236 GGATCCATCCGATCTGCTCT 58.735 55.000 6.95 0.00 45.90 4.09
531 550 1.741706 GAAGATGGTGGTAGACGACGA 59.258 52.381 0.00 0.00 0.00 4.20
532 551 1.471287 TGAAGATGGTGGTAGACGACG 59.529 52.381 0.00 0.00 0.00 5.12
533 552 2.492484 AGTGAAGATGGTGGTAGACGAC 59.508 50.000 0.00 0.00 0.00 4.34
534 553 2.803956 AGTGAAGATGGTGGTAGACGA 58.196 47.619 0.00 0.00 0.00 4.20
535 554 3.056821 TGAAGTGAAGATGGTGGTAGACG 60.057 47.826 0.00 0.00 0.00 4.18
536 555 4.499183 CTGAAGTGAAGATGGTGGTAGAC 58.501 47.826 0.00 0.00 0.00 2.59
538 557 3.265791 GCTGAAGTGAAGATGGTGGTAG 58.734 50.000 0.00 0.00 0.00 3.18
540 559 1.421268 TGCTGAAGTGAAGATGGTGGT 59.579 47.619 0.00 0.00 0.00 4.16
541 560 2.189594 TGCTGAAGTGAAGATGGTGG 57.810 50.000 0.00 0.00 0.00 4.61
543 562 2.158623 TGGTTGCTGAAGTGAAGATGGT 60.159 45.455 0.00 0.00 0.00 3.55
544 563 2.507484 TGGTTGCTGAAGTGAAGATGG 58.493 47.619 0.00 0.00 0.00 3.51
545 564 4.572985 TTTGGTTGCTGAAGTGAAGATG 57.427 40.909 0.00 0.00 0.00 2.90
546 565 5.796424 AATTTGGTTGCTGAAGTGAAGAT 57.204 34.783 0.00 0.00 0.00 2.40
547 566 5.827797 AGTAATTTGGTTGCTGAAGTGAAGA 59.172 36.000 0.00 0.00 31.05 2.87
548 567 6.076981 AGTAATTTGGTTGCTGAAGTGAAG 57.923 37.500 0.00 0.00 31.05 3.02
549 568 6.321181 AGAAGTAATTTGGTTGCTGAAGTGAA 59.679 34.615 0.00 0.00 32.72 3.18
550 569 5.827797 AGAAGTAATTTGGTTGCTGAAGTGA 59.172 36.000 0.00 0.00 32.72 3.41
551 570 5.916883 CAGAAGTAATTTGGTTGCTGAAGTG 59.083 40.000 0.00 0.00 32.72 3.16
552 571 5.507985 GCAGAAGTAATTTGGTTGCTGAAGT 60.508 40.000 0.00 0.00 32.72 3.01
553 572 4.919754 GCAGAAGTAATTTGGTTGCTGAAG 59.080 41.667 0.00 0.00 32.72 3.02
554 573 4.584325 AGCAGAAGTAATTTGGTTGCTGAA 59.416 37.500 0.00 0.00 38.82 3.02
555 574 4.144297 AGCAGAAGTAATTTGGTTGCTGA 58.856 39.130 0.00 0.00 38.82 4.26
556 575 4.217118 AGAGCAGAAGTAATTTGGTTGCTG 59.783 41.667 8.98 0.00 40.19 4.41
557 576 4.401925 AGAGCAGAAGTAATTTGGTTGCT 58.598 39.130 5.32 5.32 42.53 3.91
558 577 4.457257 AGAGAGCAGAAGTAATTTGGTTGC 59.543 41.667 0.00 0.00 0.00 4.17
559 578 7.301068 CTAGAGAGCAGAAGTAATTTGGTTG 57.699 40.000 0.00 0.00 0.00 3.77
574 593 9.969367 GAGCATCAATGTTGTAGCTAGAGAGCA 62.969 44.444 12.16 0.00 43.43 4.26
575 594 7.713916 GAGCATCAATGTTGTAGCTAGAGAGC 61.714 46.154 12.16 0.00 41.99 4.09
576 595 5.599732 AGCATCAATGTTGTAGCTAGAGAG 58.400 41.667 0.00 0.00 37.51 3.20
577 596 5.362143 AGAGCATCAATGTTGTAGCTAGAGA 59.638 40.000 12.16 0.00 38.64 3.10
578 597 5.599732 AGAGCATCAATGTTGTAGCTAGAG 58.400 41.667 12.16 0.00 38.64 2.43
579 598 5.127682 TGAGAGCATCAATGTTGTAGCTAGA 59.872 40.000 12.16 0.00 38.64 2.43
580 599 5.354767 TGAGAGCATCAATGTTGTAGCTAG 58.645 41.667 12.16 0.00 38.64 3.42
581 600 5.343307 TGAGAGCATCAATGTTGTAGCTA 57.657 39.130 12.16 0.00 38.64 3.32
582 601 4.212143 TGAGAGCATCAATGTTGTAGCT 57.788 40.909 12.07 12.07 40.20 3.32
583 602 4.952262 TTGAGAGCATCAATGTTGTAGC 57.048 40.909 0.59 4.75 43.09 3.58
599 618 6.571605 TCAAATGAGCAACAACAAATTGAGA 58.428 32.000 0.00 0.00 39.30 3.27
630 680 3.801307 TCTGGATGGATGAATGGATGG 57.199 47.619 0.00 0.00 0.00 3.51
638 696 3.323115 GCTGTACTCATCTGGATGGATGA 59.677 47.826 10.22 6.92 46.50 2.92
639 697 3.556633 GGCTGTACTCATCTGGATGGATG 60.557 52.174 10.22 0.00 43.01 3.51
640 698 2.636893 GGCTGTACTCATCTGGATGGAT 59.363 50.000 10.22 2.69 39.24 3.41
641 699 2.042464 GGCTGTACTCATCTGGATGGA 58.958 52.381 10.22 0.00 39.24 3.41
642 700 1.269988 CGGCTGTACTCATCTGGATGG 60.270 57.143 10.22 4.65 39.24 3.51
643 701 1.871408 GCGGCTGTACTCATCTGGATG 60.871 57.143 4.36 4.36 40.09 3.51
644 702 0.390860 GCGGCTGTACTCATCTGGAT 59.609 55.000 0.00 0.00 0.00 3.41
645 703 1.816537 GCGGCTGTACTCATCTGGA 59.183 57.895 0.00 0.00 0.00 3.86
651 709 4.476410 CGCTCGCGGCTGTACTCA 62.476 66.667 6.13 0.00 39.13 3.41
705 772 5.151454 TCTTCTTCTTCCTCCTCTTCTTGT 58.849 41.667 0.00 0.00 0.00 3.16
714 781 1.550976 TCCGCTTCTTCTTCTTCCTCC 59.449 52.381 0.00 0.00 0.00 4.30
720 787 0.534873 GCCTCTCCGCTTCTTCTTCT 59.465 55.000 0.00 0.00 0.00 2.85
750 817 5.761726 GTGATGGATGCTGATGTCTGAAATA 59.238 40.000 0.00 0.00 0.00 1.40
756 823 3.135895 TGATGTGATGGATGCTGATGTCT 59.864 43.478 0.00 0.00 0.00 3.41
838 927 6.595326 CAGCTACCATAGTGACAGAAAAATCA 59.405 38.462 0.00 0.00 0.00 2.57
856 948 3.797184 GCACTACTGCACTATCAGCTACC 60.797 52.174 0.00 0.00 43.62 3.18
902 997 9.665719 ACAAACATTTCTTTAACAGAATTTGGT 57.334 25.926 17.51 9.82 40.41 3.67
923 1018 6.539649 TCACAGTATGCTTACAAGACAAAC 57.460 37.500 11.89 0.00 42.53 2.93
937 1034 7.864379 ACTTTCTTGCTGAAAAATCACAGTATG 59.136 33.333 0.00 0.00 43.25 2.39
965 1062 7.381139 GCTATGTATAGACTCAAGAAGCTCAAC 59.619 40.741 3.15 0.00 32.05 3.18
1018 1118 5.769662 TCTCAATATTCCGATCCCCATTTTG 59.230 40.000 0.00 0.00 0.00 2.44
1030 1130 2.816087 CCCATGGCTTCTCAATATTCCG 59.184 50.000 6.09 0.00 0.00 4.30
1073 1179 2.630580 GGAGAAGAGCCATTATCGGAGT 59.369 50.000 0.00 0.00 0.00 3.85
1089 1195 2.124983 GCATGGCAGAGCGGAGAA 60.125 61.111 0.00 0.00 0.00 2.87
1090 1196 4.166888 GGCATGGCAGAGCGGAGA 62.167 66.667 15.47 0.00 0.00 3.71
1124 1230 4.743057 AAATTATGAGGGAAGCAAAGCC 57.257 40.909 0.00 0.00 0.00 4.35
1178 1290 3.241900 CGTCGCTGTCTTCATTGATTCAG 60.242 47.826 8.11 8.11 0.00 3.02
1179 1291 2.667969 CGTCGCTGTCTTCATTGATTCA 59.332 45.455 0.00 0.00 0.00 2.57
1508 1623 0.732880 CACGTCCTTGTAGAGCGTGG 60.733 60.000 7.39 0.00 45.96 4.94
1542 1657 3.071459 GATCTGGTCGTGCGCGTTG 62.071 63.158 20.50 8.39 39.49 4.10
1543 1658 2.809601 GATCTGGTCGTGCGCGTT 60.810 61.111 20.50 0.00 39.49 4.84
1544 1659 3.567478 TTGATCTGGTCGTGCGCGT 62.567 57.895 20.50 0.00 39.49 6.01
1747 1862 5.244851 ACTGATCTGTACTTGCTGAAGAAGA 59.755 40.000 3.02 0.00 32.98 2.87
1810 1946 9.820229 CACGATTACAACAACACTTGTATAATT 57.180 29.630 0.00 0.00 44.59 1.40
1812 1948 7.292292 GCACGATTACAACAACACTTGTATAA 58.708 34.615 0.00 0.00 44.59 0.98
1814 1950 5.334569 GGCACGATTACAACAACACTTGTAT 60.335 40.000 0.00 0.00 44.59 2.29
1815 1951 4.024725 GGCACGATTACAACAACACTTGTA 60.025 41.667 0.00 0.00 44.59 2.41
1817 1953 3.003275 AGGCACGATTACAACAACACTTG 59.997 43.478 0.00 0.00 0.00 3.16
1899 2038 2.914695 TGACGATGATGATGATGCCA 57.085 45.000 0.00 0.00 0.00 4.92
1901 2040 6.576313 GTGTTTAATGACGATGATGATGATGC 59.424 38.462 0.00 0.00 0.00 3.91
1915 2054 4.514401 CTCCACCCCTAGTGTTTAATGAC 58.486 47.826 0.00 0.00 45.74 3.06
1916 2055 3.054655 GCTCCACCCCTAGTGTTTAATGA 60.055 47.826 0.00 0.00 45.74 2.57
1917 2056 3.054361 AGCTCCACCCCTAGTGTTTAATG 60.054 47.826 0.00 0.00 45.74 1.90
1918 2057 3.190439 AGCTCCACCCCTAGTGTTTAAT 58.810 45.455 0.00 0.00 45.74 1.40
1919 2058 2.627933 AGCTCCACCCCTAGTGTTTAA 58.372 47.619 0.00 0.00 45.74 1.52
1920 2059 2.337359 AGCTCCACCCCTAGTGTTTA 57.663 50.000 0.00 0.00 45.74 2.01
1930 2069 0.394352 CCACCATTGTAGCTCCACCC 60.394 60.000 0.00 0.00 0.00 4.61
1931 2070 0.618458 TCCACCATTGTAGCTCCACC 59.382 55.000 0.00 0.00 0.00 4.61
1934 2073 2.706190 ACCTATCCACCATTGTAGCTCC 59.294 50.000 0.00 0.00 0.00 4.70
1944 2083 0.623723 GGAAGCCAACCTATCCACCA 59.376 55.000 0.00 0.00 32.08 4.17
1945 2084 0.623723 TGGAAGCCAACCTATCCACC 59.376 55.000 0.00 0.00 37.05 4.61
1946 2085 2.736670 ATGGAAGCCAACCTATCCAC 57.263 50.000 0.00 0.00 44.25 4.02
1952 2091 1.358787 TCATGGAATGGAAGCCAACCT 59.641 47.619 12.00 0.00 46.73 3.50
1953 2092 1.851304 TCATGGAATGGAAGCCAACC 58.149 50.000 0.00 0.00 46.73 3.77
1954 2093 3.006752 TGTTTCATGGAATGGAAGCCAAC 59.993 43.478 0.00 0.00 43.94 3.77
1961 2100 5.128499 ACACAGTTTTGTTTCATGGAATGGA 59.872 36.000 0.00 0.00 39.38 3.41
1962 2101 5.358922 ACACAGTTTTGTTTCATGGAATGG 58.641 37.500 0.00 0.00 39.38 3.16
1963 2102 7.652909 ACATACACAGTTTTGTTTCATGGAATG 59.347 33.333 0.00 0.00 39.99 2.67
1964 2103 7.725251 ACATACACAGTTTTGTTTCATGGAAT 58.275 30.769 0.00 0.00 34.62 3.01
1990 2129 4.039488 TGTTCCTCTTTCTTTGCATTGCAT 59.961 37.500 12.95 0.00 38.76 3.96
2025 2164 2.633657 CATGCTAATGGCGACCGC 59.366 61.111 5.75 5.75 45.43 5.68
2026 2165 2.633657 GCATGCTAATGGCGACCG 59.366 61.111 11.37 0.00 45.43 4.79
2098 2238 0.652592 CCAACGACTTCATCATCGCC 59.347 55.000 0.00 0.00 42.12 5.54
2145 2286 3.961480 TCATCGGTGAACTGAACTGAT 57.039 42.857 0.00 0.00 43.01 2.90
2149 2290 3.334691 TGGATTCATCGGTGAACTGAAC 58.665 45.455 14.50 3.17 46.43 3.18
2208 2369 2.301296 CCTCTTCTCTCTTGTGCTCCAA 59.699 50.000 0.00 0.00 0.00 3.53
2209 2370 1.898472 CCTCTTCTCTCTTGTGCTCCA 59.102 52.381 0.00 0.00 0.00 3.86
2216 2380 7.776030 TCAGTTATAGTACCCTCTTCTCTCTTG 59.224 40.741 0.00 0.00 0.00 3.02
2329 2494 0.036388 TCGCCAGGATCAACAAGACC 60.036 55.000 0.00 0.00 0.00 3.85
2331 2496 1.554617 TCATCGCCAGGATCAACAAGA 59.445 47.619 0.00 0.00 31.28 3.02
2545 2710 2.117156 GCTGCACCGCATCCTCATT 61.117 57.895 0.00 0.00 38.13 2.57
2632 2797 3.470888 ATCCTGGGCGACTTCGGG 61.471 66.667 0.02 0.00 40.23 5.14
2675 2840 1.968540 GCAGCAAGGGAAGAAGCGT 60.969 57.895 0.00 0.00 0.00 5.07
2676 2841 1.673665 AGCAGCAAGGGAAGAAGCG 60.674 57.895 0.00 0.00 0.00 4.68
2680 2845 1.073722 CACCAGCAGCAAGGGAAGA 59.926 57.895 8.61 0.00 0.00 2.87
2682 2847 2.598394 GCACCAGCAGCAAGGGAA 60.598 61.111 8.61 0.00 41.58 3.97
2683 2848 4.666253 GGCACCAGCAGCAAGGGA 62.666 66.667 8.61 0.00 44.61 4.20
2686 2851 2.974489 CTTCGGCACCAGCAGCAAG 61.974 63.158 0.00 0.00 44.61 4.01
2687 2852 2.979676 CTTCGGCACCAGCAGCAA 60.980 61.111 0.00 0.00 44.61 3.91
2688 2853 3.889134 CTCTTCGGCACCAGCAGCA 62.889 63.158 0.00 0.00 44.61 4.41
2693 2870 1.831652 AACCTCCTCTTCGGCACCAG 61.832 60.000 0.00 0.00 0.00 4.00
2786 2975 2.382305 TCTCCTTCCTTCCTGTCCACTA 59.618 50.000 0.00 0.00 0.00 2.74
2793 2982 2.499693 GTTCCTCTCTCCTTCCTTCCTG 59.500 54.545 0.00 0.00 0.00 3.86
2794 2983 2.827755 GTTCCTCTCTCCTTCCTTCCT 58.172 52.381 0.00 0.00 0.00 3.36
2795 2984 1.478916 CGTTCCTCTCTCCTTCCTTCC 59.521 57.143 0.00 0.00 0.00 3.46
2796 2985 1.478916 CCGTTCCTCTCTCCTTCCTTC 59.521 57.143 0.00 0.00 0.00 3.46
2797 2986 1.077334 TCCGTTCCTCTCTCCTTCCTT 59.923 52.381 0.00 0.00 0.00 3.36
2798 2987 0.705253 TCCGTTCCTCTCTCCTTCCT 59.295 55.000 0.00 0.00 0.00 3.36
2799 2988 1.410882 CATCCGTTCCTCTCTCCTTCC 59.589 57.143 0.00 0.00 0.00 3.46
2800 2989 1.410882 CCATCCGTTCCTCTCTCCTTC 59.589 57.143 0.00 0.00 0.00 3.46
2801 2990 1.007238 TCCATCCGTTCCTCTCTCCTT 59.993 52.381 0.00 0.00 0.00 3.36
2802 2991 0.631753 TCCATCCGTTCCTCTCTCCT 59.368 55.000 0.00 0.00 0.00 3.69
2803 2992 1.342819 CATCCATCCGTTCCTCTCTCC 59.657 57.143 0.00 0.00 0.00 3.71
2804 2993 1.342819 CCATCCATCCGTTCCTCTCTC 59.657 57.143 0.00 0.00 0.00 3.20
2805 2994 1.062886 TCCATCCATCCGTTCCTCTCT 60.063 52.381 0.00 0.00 0.00 3.10
2806 2995 1.414158 TCCATCCATCCGTTCCTCTC 58.586 55.000 0.00 0.00 0.00 3.20
2807 2996 1.696336 CATCCATCCATCCGTTCCTCT 59.304 52.381 0.00 0.00 0.00 3.69
2808 2997 1.271054 CCATCCATCCATCCGTTCCTC 60.271 57.143 0.00 0.00 0.00 3.71
2809 2998 0.767375 CCATCCATCCATCCGTTCCT 59.233 55.000 0.00 0.00 0.00 3.36
2810 2999 0.764890 TCCATCCATCCATCCGTTCC 59.235 55.000 0.00 0.00 0.00 3.62
2811 3000 2.038952 TCATCCATCCATCCATCCGTTC 59.961 50.000 0.00 0.00 0.00 3.95
2812 3001 2.057140 TCATCCATCCATCCATCCGTT 58.943 47.619 0.00 0.00 0.00 4.44
2813 3002 1.733385 TCATCCATCCATCCATCCGT 58.267 50.000 0.00 0.00 0.00 4.69
2814 3003 2.640184 CATCATCCATCCATCCATCCG 58.360 52.381 0.00 0.00 0.00 4.18
2815 3004 2.376109 GCATCATCCATCCATCCATCC 58.624 52.381 0.00 0.00 0.00 3.51
2816 3005 2.014857 CGCATCATCCATCCATCCATC 58.985 52.381 0.00 0.00 0.00 3.51
2817 3006 1.953785 GCGCATCATCCATCCATCCAT 60.954 52.381 0.30 0.00 0.00 3.41
2818 3007 0.607217 GCGCATCATCCATCCATCCA 60.607 55.000 0.30 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.