Multiple sequence alignment - TraesCS5D01G470300

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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 TraesCS5D01G470300 chr5D 100.000 3300 0 0 1 3300 510976792 510973493 0.000000e+00 6095.0
1 TraesCS5D01G470300 chr5D 80.974 431 48 21 786 1196 482006018 482006434 8.890000e-81 311.0
2 TraesCS5D01G470300 chr5D 96.429 56 2 0 2767 2822 510973962 510973907 3.510000e-15 93.5
3 TraesCS5D01G470300 chr5D 96.429 56 2 0 2831 2886 510974026 510973971 3.510000e-15 93.5
4 TraesCS5D01G470300 chr5B 91.991 2647 103 40 60 2649 642274186 642276780 0.000000e+00 3613.0
5 TraesCS5D01G470300 chr5B 78.588 439 38 29 786 1206 591446613 591447013 4.260000e-59 239.0
6 TraesCS5D01G470300 chr5A 93.044 2099 70 29 754 2822 639308000 639305948 0.000000e+00 2998.0
7 TraesCS5D01G470300 chr5A 90.707 721 36 13 2 705 639308706 639308000 0.000000e+00 931.0
8 TraesCS5D01G470300 chr5A 88.983 472 40 7 2831 3300 639306003 639305542 1.030000e-159 573.0


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 TraesCS5D01G470300 chr5D 510973493 510976792 3299 True 2094.000000 6095 97.619333 1 3300 3 chr5D.!!$R1 3299
1 TraesCS5D01G470300 chr5B 642274186 642276780 2594 False 3613.000000 3613 91.991000 60 2649 1 chr5B.!!$F2 2589
2 TraesCS5D01G470300 chr5A 639305542 639308706 3164 True 1500.666667 2998 90.911333 2 3300 3 chr5A.!!$R1 3298

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
990 1064 0.174389 ATCACTAGCTGCTCACGGTG 59.826 55.0 4.91 11.45 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2925 3054 0.386731 GCGAATGGTGTGGTTTTCCG 60.387 55.0 0.0 0.0 44.36 4.3 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
17 18 4.745751 CGGCGGACAACGGGCTAA 62.746 66.667 0.00 0.00 44.51 3.09
23 24 0.886043 GGACAACGGGCTAAAACGGT 60.886 55.000 0.00 0.00 0.00 4.83
26 27 2.609759 AACGGGCTAAAACGGTGCG 61.610 57.895 0.00 0.00 0.00 5.34
33 34 1.613270 CTAAAACGGTGCGGCAATTC 58.387 50.000 3.23 0.00 0.00 2.17
46 47 1.741401 CAATTCTGCCGTCCGAGCA 60.741 57.895 0.00 3.53 38.82 4.26
118 121 4.022416 GTGATTTGGTGCATCACTAAACCA 60.022 41.667 0.00 4.96 44.80 3.67
119 122 4.771577 TGATTTGGTGCATCACTAAACCAT 59.228 37.500 0.00 0.00 44.80 3.55
374 392 5.401674 CACTCTGTAGACCAGTAAACGAAAC 59.598 44.000 0.00 0.00 42.19 2.78
404 422 7.676004 TGAGAAACATCAAACATGGTACTCTA 58.324 34.615 0.00 0.00 0.00 2.43
405 423 7.819415 TGAGAAACATCAAACATGGTACTCTAG 59.181 37.037 0.00 0.00 0.00 2.43
406 424 6.595716 AGAAACATCAAACATGGTACTCTAGC 59.404 38.462 0.00 0.00 0.00 3.42
407 425 5.683876 ACATCAAACATGGTACTCTAGCT 57.316 39.130 0.00 0.00 0.00 3.32
408 426 6.791867 ACATCAAACATGGTACTCTAGCTA 57.208 37.500 0.00 0.00 0.00 3.32
612 635 1.573932 CGGTCCACACACGTACGTA 59.426 57.895 22.34 0.52 0.00 3.57
613 636 0.725784 CGGTCCACACACGTACGTAC 60.726 60.000 22.34 15.90 0.00 3.67
664 687 7.805071 GTCACACGAGAATTTCATTTTCTGAAT 59.195 33.333 0.00 0.00 43.30 2.57
665 688 8.017373 TCACACGAGAATTTCATTTTCTGAATC 58.983 33.333 0.00 0.00 43.30 2.52
705 777 3.065925 CCCGGAATTCTTGAATCTTCAGC 59.934 47.826 0.73 0.00 38.61 4.26
706 778 3.944015 CCGGAATTCTTGAATCTTCAGCT 59.056 43.478 5.23 0.00 38.61 4.24
707 779 4.034975 CCGGAATTCTTGAATCTTCAGCTC 59.965 45.833 5.23 0.00 38.61 4.09
708 780 4.034975 CGGAATTCTTGAATCTTCAGCTCC 59.965 45.833 5.23 0.00 38.61 4.70
709 781 4.034975 GGAATTCTTGAATCTTCAGCTCCG 59.965 45.833 5.23 0.00 38.61 4.63
710 782 3.685139 TTCTTGAATCTTCAGCTCCGT 57.315 42.857 0.00 0.00 38.61 4.69
711 783 2.964740 TCTTGAATCTTCAGCTCCGTG 58.035 47.619 0.00 0.00 38.61 4.94
712 784 2.005451 CTTGAATCTTCAGCTCCGTGG 58.995 52.381 0.00 0.00 38.61 4.94
713 785 0.391661 TGAATCTTCAGCTCCGTGGC 60.392 55.000 0.00 0.00 32.50 5.01
714 786 1.078143 AATCTTCAGCTCCGTGGCC 60.078 57.895 0.00 0.00 0.00 5.36
715 787 1.841302 AATCTTCAGCTCCGTGGCCA 61.841 55.000 0.00 0.00 0.00 5.36
716 788 2.249413 ATCTTCAGCTCCGTGGCCAG 62.249 60.000 5.11 0.00 0.00 4.85
717 789 3.241530 TTCAGCTCCGTGGCCAGT 61.242 61.111 5.11 0.00 0.00 4.00
718 790 1.888436 CTTCAGCTCCGTGGCCAGTA 61.888 60.000 5.11 0.00 0.00 2.74
719 791 1.888436 TTCAGCTCCGTGGCCAGTAG 61.888 60.000 5.11 4.92 0.00 2.57
720 792 3.775654 AGCTCCGTGGCCAGTAGC 61.776 66.667 21.02 21.02 42.60 3.58
721 793 4.082523 GCTCCGTGGCCAGTAGCA 62.083 66.667 22.78 0.00 46.50 3.49
722 794 2.125512 CTCCGTGGCCAGTAGCAC 60.126 66.667 5.11 0.00 46.50 4.40
723 795 3.665675 CTCCGTGGCCAGTAGCACC 62.666 68.421 5.11 0.00 46.50 5.01
724 796 4.015406 CCGTGGCCAGTAGCACCA 62.015 66.667 5.11 0.00 46.50 4.17
725 797 2.031919 CGTGGCCAGTAGCACCAA 59.968 61.111 5.11 0.00 46.50 3.67
726 798 2.325082 CGTGGCCAGTAGCACCAAC 61.325 63.158 5.11 0.00 46.50 3.77
727 799 1.971695 GTGGCCAGTAGCACCAACC 60.972 63.158 5.11 0.00 46.50 3.77
728 800 2.746277 GGCCAGTAGCACCAACCG 60.746 66.667 0.00 0.00 46.50 4.44
729 801 2.746277 GCCAGTAGCACCAACCGG 60.746 66.667 0.00 0.00 42.97 5.28
731 803 1.375523 CCAGTAGCACCAACCGGTC 60.376 63.158 8.04 0.00 44.71 4.79
732 804 1.736645 CAGTAGCACCAACCGGTCG 60.737 63.158 8.04 3.29 44.71 4.79
733 805 3.116531 GTAGCACCAACCGGTCGC 61.117 66.667 8.04 9.00 44.71 5.19
734 806 4.728102 TAGCACCAACCGGTCGCG 62.728 66.667 8.04 0.00 44.71 5.87
988 1062 1.929836 GAAATCACTAGCTGCTCACGG 59.070 52.381 4.91 0.00 0.00 4.94
989 1063 0.898320 AATCACTAGCTGCTCACGGT 59.102 50.000 4.91 0.00 0.00 4.83
990 1064 0.174389 ATCACTAGCTGCTCACGGTG 59.826 55.000 4.91 11.45 0.00 4.94
991 1065 0.893727 TCACTAGCTGCTCACGGTGA 60.894 55.000 4.91 10.88 0.00 4.02
992 1066 0.734253 CACTAGCTGCTCACGGTGAC 60.734 60.000 4.91 5.35 0.00 3.67
1299 1379 2.285220 CGACTTGGTAATTCATCAGCCG 59.715 50.000 0.00 0.00 0.00 5.52
1302 1382 3.118408 ACTTGGTAATTCATCAGCCGCTA 60.118 43.478 0.00 0.00 0.00 4.26
1308 1388 1.195115 TTCATCAGCCGCTACTCCTT 58.805 50.000 0.00 0.00 0.00 3.36
1310 1390 0.596083 CATCAGCCGCTACTCCTTCG 60.596 60.000 0.00 0.00 0.00 3.79
1420 1500 3.674997 TGGAACATCTCTTACCAACAGC 58.325 45.455 0.00 0.00 0.00 4.40
1426 1506 2.889512 TCTCTTACCAACAGCTCCTCA 58.110 47.619 0.00 0.00 0.00 3.86
1493 1577 9.533831 ACATGGTCAAGAATAGGTTTTATTTCT 57.466 29.630 0.00 0.00 0.00 2.52
1544 1631 8.597167 TGAGGGGAATGAATATGTGAATAGTAG 58.403 37.037 0.00 0.00 0.00 2.57
1545 1632 8.511748 AGGGGAATGAATATGTGAATAGTAGT 57.488 34.615 0.00 0.00 0.00 2.73
1546 1633 9.615660 AGGGGAATGAATATGTGAATAGTAGTA 57.384 33.333 0.00 0.00 0.00 1.82
1684 1771 2.528378 AACCCACCCAGCTACCGT 60.528 61.111 0.00 0.00 0.00 4.83
1865 1953 6.627087 TCTTGGAAAGGTATGAACAGATCT 57.373 37.500 0.00 0.00 46.24 2.75
1866 1954 6.409704 TCTTGGAAAGGTATGAACAGATCTG 58.590 40.000 21.37 21.37 46.24 2.90
2051 2152 3.091545 ACCCAATCAACATGCCACTAAG 58.908 45.455 0.00 0.00 0.00 2.18
2068 2169 3.564225 ACTAAGTTTCACCGCAAAAGGAG 59.436 43.478 0.00 0.00 34.73 3.69
2105 2206 1.942712 CGCACGACCTGCCGTATAC 60.943 63.158 0.00 0.00 43.84 1.47
2109 2210 1.924524 CACGACCTGCCGTATACTTTG 59.075 52.381 0.56 0.00 41.29 2.77
2162 2264 2.795175 GCATCTGATTTGCTCATGGG 57.205 50.000 0.00 0.00 37.14 4.00
2236 2338 1.219124 GAACCTGGAGCTGATGCGA 59.781 57.895 0.00 0.00 45.42 5.10
2266 2368 2.501610 GAGACGGTCATCTGGCCC 59.498 66.667 11.27 0.00 36.14 5.80
2284 2386 1.519676 CACCGACGACACCAACACA 60.520 57.895 0.00 0.00 0.00 3.72
2350 2454 8.345565 CCGCTGAAGTTCATTAATTAATTAGCT 58.654 33.333 5.91 5.55 0.00 3.32
2351 2455 9.374960 CGCTGAAGTTCATTAATTAATTAGCTC 57.625 33.333 5.91 3.34 0.00 4.09
2451 2561 6.150396 ACTAGCACAGAGTGTATATGGTTC 57.850 41.667 0.00 0.00 35.75 3.62
2453 2563 3.699538 AGCACAGAGTGTATATGGTTCGA 59.300 43.478 0.00 0.00 35.75 3.71
2464 2574 6.537301 GTGTATATGGTTCGATCTTTTGGTGA 59.463 38.462 0.00 0.00 0.00 4.02
2472 2582 7.039882 GGTTCGATCTTTTGGTGAAGATACTA 58.960 38.462 0.50 0.00 44.27 1.82
2511 2630 0.944386 GTATAATGTGCCGCCTGTGG 59.056 55.000 0.00 0.00 0.00 4.17
2512 2631 0.544223 TATAATGTGCCGCCTGTGGT 59.456 50.000 0.00 0.00 0.00 4.16
2513 2632 1.031571 ATAATGTGCCGCCTGTGGTG 61.032 55.000 0.00 0.00 0.00 4.17
2603 2726 5.104859 TGTGTTTGAGCCCGGAGTTATATAA 60.105 40.000 0.73 0.00 0.00 0.98
2636 2759 2.435805 TGTTATGTGCCTCTCCATCTCC 59.564 50.000 0.00 0.00 0.00 3.71
2715 2838 4.230964 ACCACCCCTTATGTAAAAGCCATA 59.769 41.667 0.00 0.00 0.00 2.74
2735 2858 5.299279 CCATAAGTTGTGGCCGATCTAAAAT 59.701 40.000 5.64 0.00 0.00 1.82
2740 2863 1.597663 GTGGCCGATCTAAAATGTCCG 59.402 52.381 0.00 0.00 0.00 4.79
2745 2868 3.527533 CCGATCTAAAATGTCCGAACCA 58.472 45.455 0.00 0.00 0.00 3.67
2751 2880 4.925054 TCTAAAATGTCCGAACCACTTACG 59.075 41.667 0.00 0.00 0.00 3.18
2804 2933 9.332502 TCTATGTTTAACACAACACAATACACT 57.667 29.630 0.00 0.00 39.48 3.55
2807 2936 8.454293 TGTTTAACACAACACAATACACTTTG 57.546 30.769 0.00 0.00 31.48 2.77
2819 2948 7.338449 ACACAATACACTTTGTACCTTTGAACT 59.662 33.333 5.55 0.00 37.73 3.01
2820 2949 8.188139 CACAATACACTTTGTACCTTTGAACTT 58.812 33.333 5.55 0.00 37.73 2.66
2821 2950 9.398538 ACAATACACTTTGTACCTTTGAACTTA 57.601 29.630 5.55 0.00 38.04 2.24
2824 2953 9.841295 ATACACTTTGTACCTTTGAACTTAAGA 57.159 29.630 10.09 0.00 35.42 2.10
2825 2954 8.747538 ACACTTTGTACCTTTGAACTTAAGAT 57.252 30.769 10.09 0.00 0.00 2.40
2826 2955 8.621286 ACACTTTGTACCTTTGAACTTAAGATG 58.379 33.333 10.09 0.00 0.00 2.90
2827 2956 7.591426 CACTTTGTACCTTTGAACTTAAGATGC 59.409 37.037 10.09 0.00 0.00 3.91
2828 2957 7.284489 ACTTTGTACCTTTGAACTTAAGATGCA 59.716 33.333 10.09 0.00 0.00 3.96
2829 2958 7.575414 TTGTACCTTTGAACTTAAGATGCAA 57.425 32.000 10.09 7.32 0.00 4.08
2830 2959 7.759489 TGTACCTTTGAACTTAAGATGCAAT 57.241 32.000 10.09 0.00 0.00 3.56
2831 2960 7.816640 TGTACCTTTGAACTTAAGATGCAATC 58.183 34.615 10.09 0.00 46.04 2.67
2848 2977 8.789825 GATGCAATCCTAGATTGATTCTATGT 57.210 34.615 18.95 0.00 37.38 2.29
2849 2978 9.228949 GATGCAATCCTAGATTGATTCTATGTT 57.771 33.333 18.95 0.00 37.38 2.71
2850 2979 8.985315 TGCAATCCTAGATTGATTCTATGTTT 57.015 30.769 18.95 0.00 36.35 2.83
2868 2997 9.426837 TCTATGTTTAACACAACACTATACACC 57.573 33.333 0.00 0.00 39.48 4.16
2869 2998 9.431887 CTATGTTTAACACAACACTATACACCT 57.568 33.333 0.00 0.00 39.48 4.00
2870 2999 8.685838 ATGTTTAACACAACACTATACACCTT 57.314 30.769 0.00 0.00 39.48 3.50
2871 3000 7.921787 TGTTTAACACAACACTATACACCTTG 58.078 34.615 0.00 0.00 31.48 3.61
2872 3001 7.553402 TGTTTAACACAACACTATACACCTTGT 59.447 33.333 0.00 0.00 31.48 3.16
2873 3002 9.044150 GTTTAACACAACACTATACACCTTGTA 57.956 33.333 0.00 0.00 37.24 2.41
2874 3003 8.592105 TTAACACAACACTATACACCTTGTAC 57.408 34.615 0.00 0.00 35.42 2.90
2875 3004 5.544650 ACACAACACTATACACCTTGTACC 58.455 41.667 0.00 0.00 35.42 3.34
2876 3005 5.306160 ACACAACACTATACACCTTGTACCT 59.694 40.000 0.00 0.00 35.42 3.08
2877 3006 6.183361 ACACAACACTATACACCTTGTACCTT 60.183 38.462 0.00 0.00 35.42 3.50
2878 3007 6.708949 CACAACACTATACACCTTGTACCTTT 59.291 38.462 0.00 0.00 35.42 3.11
2879 3008 6.708949 ACAACACTATACACCTTGTACCTTTG 59.291 38.462 0.00 0.00 35.42 2.77
2880 3009 6.675413 ACACTATACACCTTGTACCTTTGA 57.325 37.500 0.00 0.00 35.42 2.69
2881 3010 7.069877 ACACTATACACCTTGTACCTTTGAA 57.930 36.000 0.00 0.00 35.42 2.69
2882 3011 6.932960 ACACTATACACCTTGTACCTTTGAAC 59.067 38.462 0.00 0.00 35.42 3.18
2883 3012 7.159372 CACTATACACCTTGTACCTTTGAACT 58.841 38.462 0.00 0.00 35.42 3.01
2888 3017 6.181908 ACACCTTGTACCTTTGAACTTACAA 58.818 36.000 0.00 0.00 34.20 2.41
2899 3028 7.608761 ACCTTTGAACTTACAACAAAGTACTCA 59.391 33.333 0.65 0.00 44.78 3.41
2901 3030 9.438291 CTTTGAACTTACAACAAAGTACTCATG 57.562 33.333 0.00 1.10 42.76 3.07
2912 3041 7.468141 ACAAAGTACTCATGAGTCATGACTA 57.532 36.000 31.09 20.83 44.60 2.59
2921 3050 7.067615 ACTCATGAGTCATGACTATCGTTACTT 59.932 37.037 28.18 9.32 44.60 2.24
2922 3051 8.446599 TCATGAGTCATGACTATCGTTACTTA 57.553 34.615 28.18 4.70 44.60 2.24
2928 3057 7.658982 AGTCATGACTATCGTTACTTATACGGA 59.341 37.037 26.87 0.00 40.43 4.69
2930 3059 8.839343 TCATGACTATCGTTACTTATACGGAAA 58.161 33.333 0.00 0.00 39.38 3.13
2931 3060 9.454585 CATGACTATCGTTACTTATACGGAAAA 57.545 33.333 0.00 0.00 39.38 2.29
2934 3063 7.771183 ACTATCGTTACTTATACGGAAAACCA 58.229 34.615 0.00 0.00 39.38 3.67
2938 3067 5.163963 CGTTACTTATACGGAAAACCACACC 60.164 44.000 0.00 0.00 35.47 4.16
2948 3077 3.427503 GGAAAACCACACCATTCGCTATG 60.428 47.826 0.00 0.00 0.00 2.23
2961 3090 5.745294 CCATTCGCTATGAGAAATTTGTTGG 59.255 40.000 0.00 0.00 36.26 3.77
2967 3096 9.990360 TCGCTATGAGAAATTTGTTGGTATATA 57.010 29.630 0.00 0.00 0.00 0.86
2981 3110 8.480133 TGTTGGTATATAACAGGTTTTTGGTT 57.520 30.769 0.00 0.00 33.43 3.67
3017 3146 9.247861 GGAAACATCATATAATGGCCTAAATCT 57.752 33.333 3.32 0.00 0.00 2.40
3026 3155 7.732222 ATAATGGCCTAAATCTGGTTTCAAA 57.268 32.000 3.32 0.00 0.00 2.69
3173 3302 4.080356 TGTTCATGCTTTAGATGCTACCCT 60.080 41.667 0.00 0.00 0.00 4.34
3174 3303 4.778213 TCATGCTTTAGATGCTACCCTT 57.222 40.909 0.00 0.00 0.00 3.95
3181 3310 5.524281 GCTTTAGATGCTACCCTTACTCAAC 59.476 44.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.745751 TTAGCCCGTTGTCCGCCG 62.746 66.667 0.00 0.00 34.38 6.46
2 3 1.208358 GTTTTAGCCCGTTGTCCGC 59.792 57.895 0.00 0.00 34.38 5.54
3 4 1.494189 CGTTTTAGCCCGTTGTCCG 59.506 57.895 0.00 0.00 0.00 4.79
4 5 0.886043 ACCGTTTTAGCCCGTTGTCC 60.886 55.000 0.00 0.00 0.00 4.02
8 9 2.609759 CGCACCGTTTTAGCCCGTT 61.610 57.895 0.00 0.00 0.00 4.44
11 12 4.111016 GCCGCACCGTTTTAGCCC 62.111 66.667 0.00 0.00 0.00 5.19
17 18 1.285641 CAGAATTGCCGCACCGTTT 59.714 52.632 0.00 0.00 0.00 3.60
54 55 1.080025 CTTTCGTCCCACGTCCTCC 60.080 63.158 0.00 0.00 43.14 4.30
56 57 0.317479 CTTCTTTCGTCCCACGTCCT 59.683 55.000 0.00 0.00 43.14 3.85
57 58 0.033090 ACTTCTTTCGTCCCACGTCC 59.967 55.000 0.00 0.00 43.14 4.79
58 59 1.137513 CACTTCTTTCGTCCCACGTC 58.862 55.000 0.00 0.00 43.14 4.34
59 60 0.748450 TCACTTCTTTCGTCCCACGT 59.252 50.000 0.00 0.00 43.14 4.49
60 61 1.137513 GTCACTTCTTTCGTCCCACG 58.862 55.000 0.00 0.00 44.19 4.94
61 62 2.135933 CAGTCACTTCTTTCGTCCCAC 58.864 52.381 0.00 0.00 0.00 4.61
62 63 2.036387 TCAGTCACTTCTTTCGTCCCA 58.964 47.619 0.00 0.00 0.00 4.37
63 64 2.814280 TCAGTCACTTCTTTCGTCCC 57.186 50.000 0.00 0.00 0.00 4.46
106 109 7.630242 AATGTCACCTTATGGTTTAGTGATG 57.370 36.000 0.00 0.00 46.05 3.07
174 183 9.924650 GCTCGGATTTTTCTAAGAATACCTATA 57.075 33.333 0.00 0.00 0.00 1.31
176 185 7.788026 TGCTCGGATTTTTCTAAGAATACCTA 58.212 34.615 0.00 0.00 0.00 3.08
177 186 6.650120 TGCTCGGATTTTTCTAAGAATACCT 58.350 36.000 0.00 0.00 0.00 3.08
178 187 6.920569 TGCTCGGATTTTTCTAAGAATACC 57.079 37.500 0.00 0.00 0.00 2.73
179 188 8.279103 CAGATGCTCGGATTTTTCTAAGAATAC 58.721 37.037 0.00 0.00 0.00 1.89
181 190 6.238593 GCAGATGCTCGGATTTTTCTAAGAAT 60.239 38.462 0.00 0.00 38.21 2.40
182 191 5.065218 GCAGATGCTCGGATTTTTCTAAGAA 59.935 40.000 0.00 0.00 38.21 2.52
183 192 4.572389 GCAGATGCTCGGATTTTTCTAAGA 59.428 41.667 0.00 0.00 38.21 2.10
184 193 4.842029 GCAGATGCTCGGATTTTTCTAAG 58.158 43.478 0.00 0.00 38.21 2.18
185 194 4.882671 GCAGATGCTCGGATTTTTCTAA 57.117 40.909 0.00 0.00 38.21 2.10
212 221 4.479158 TCCAAGGAGTACAAGGCAAAAAT 58.521 39.130 0.00 0.00 0.00 1.82
374 392 4.400845 CATGTTTGATGTTTCTCAGCTCG 58.599 43.478 0.00 0.00 33.14 5.03
404 422 0.041238 TCCAGCCAGGTACAGTAGCT 59.959 55.000 6.46 6.46 39.02 3.32
405 423 0.902531 TTCCAGCCAGGTACAGTAGC 59.097 55.000 1.13 1.13 39.02 3.58
406 424 1.482593 CCTTCCAGCCAGGTACAGTAG 59.517 57.143 0.00 0.00 39.02 2.57
407 425 1.078159 TCCTTCCAGCCAGGTACAGTA 59.922 52.381 0.00 0.00 39.02 2.74
408 426 0.178903 TCCTTCCAGCCAGGTACAGT 60.179 55.000 0.00 0.00 39.02 3.55
460 483 2.046988 TGCATGCTGGTCTCGGTG 60.047 61.111 20.33 0.00 0.00 4.94
612 635 1.574428 GTCATTTGACAAGGCGCGT 59.426 52.632 8.43 0.00 44.18 6.01
613 636 4.440214 GTCATTTGACAAGGCGCG 57.560 55.556 0.00 0.00 44.18 6.86
664 687 3.697166 GGGTAAATTTGGCAGGAAGAGA 58.303 45.455 0.00 0.00 0.00 3.10
665 688 2.423538 CGGGTAAATTTGGCAGGAAGAG 59.576 50.000 0.00 0.00 0.00 2.85
705 777 2.125512 GTGCTACTGGCCACGGAG 60.126 66.667 0.00 5.61 40.92 4.63
706 778 3.702048 GGTGCTACTGGCCACGGA 61.702 66.667 0.00 0.00 40.92 4.69
707 779 3.545124 TTGGTGCTACTGGCCACGG 62.545 63.158 0.00 0.00 40.92 4.94
708 780 2.031919 TTGGTGCTACTGGCCACG 59.968 61.111 0.00 0.00 40.92 4.94
709 781 1.971695 GGTTGGTGCTACTGGCCAC 60.972 63.158 0.00 0.00 40.92 5.01
710 782 2.434331 GGTTGGTGCTACTGGCCA 59.566 61.111 4.71 4.71 40.92 5.36
711 783 2.746277 CGGTTGGTGCTACTGGCC 60.746 66.667 0.00 0.00 40.92 5.36
712 784 2.746277 CCGGTTGGTGCTACTGGC 60.746 66.667 0.00 0.00 35.39 4.85
756 828 1.754380 GCACCACCAGGGGAAAAACC 61.754 60.000 0.00 0.00 42.79 3.27
757 829 0.759060 AGCACCACCAGGGGAAAAAC 60.759 55.000 0.00 0.00 42.79 2.43
758 830 0.854218 TAGCACCACCAGGGGAAAAA 59.146 50.000 0.00 0.00 42.79 1.94
988 1062 4.913126 GGTCATCCTCACCGTCAC 57.087 61.111 0.00 0.00 0.00 3.67
993 1067 0.175989 GAACTCCGGTCATCCTCACC 59.824 60.000 0.00 0.00 0.00 4.02
1119 1199 1.963338 AGCAAACAGGCTCGTGCTC 60.963 57.895 9.61 0.00 43.76 4.26
1299 1379 4.167268 CAACAAGTAGACGAAGGAGTAGC 58.833 47.826 0.00 0.00 0.00 3.58
1302 1382 3.228453 TCCAACAAGTAGACGAAGGAGT 58.772 45.455 0.00 0.00 0.00 3.85
1379 1459 2.634453 CAAGAAATTCCCCAAGGTGCTT 59.366 45.455 0.00 0.00 0.00 3.91
1459 1539 8.235359 ACCTATTCTTGACCATGTACTAGTAC 57.765 38.462 23.58 23.58 36.63 2.73
1488 1572 8.546597 ACAAAGCTGTAACAACAAAAAGAAAT 57.453 26.923 0.00 0.00 32.54 2.17
1492 1576 6.014898 GCAACAAAGCTGTAACAACAAAAAG 58.985 36.000 0.00 0.00 33.45 2.27
1493 1577 5.698545 AGCAACAAAGCTGTAACAACAAAAA 59.301 32.000 0.00 0.00 44.66 1.94
1496 1580 4.448537 AGCAACAAAGCTGTAACAACAA 57.551 36.364 0.00 0.00 44.66 2.83
1498 1582 4.420168 TCAAGCAACAAAGCTGTAACAAC 58.580 39.130 0.00 0.00 45.89 3.32
1499 1583 4.439974 CCTCAAGCAACAAAGCTGTAACAA 60.440 41.667 0.00 0.00 45.89 2.83
1500 1584 3.066621 CCTCAAGCAACAAAGCTGTAACA 59.933 43.478 0.00 0.00 45.89 2.41
1504 1588 1.035139 CCCTCAAGCAACAAAGCTGT 58.965 50.000 0.00 0.00 45.89 4.40
1546 1633 9.942850 TTTTCTTTTCTTGGAGAAACTTGAAAT 57.057 25.926 16.72 0.00 43.25 2.17
1684 1771 8.630054 AAATATGTTGTTACTTGTAGAGCCAA 57.370 30.769 0.00 0.00 0.00 4.52
1865 1953 2.158827 TGTAGCAGTGCAAGAAGAACCA 60.159 45.455 19.20 0.00 0.00 3.67
1866 1954 2.494059 TGTAGCAGTGCAAGAAGAACC 58.506 47.619 19.20 0.00 0.00 3.62
2028 2129 3.168035 AGTGGCATGTTGATTGGGTAA 57.832 42.857 0.00 0.00 0.00 2.85
2029 2130 2.897271 AGTGGCATGTTGATTGGGTA 57.103 45.000 0.00 0.00 0.00 3.69
2031 2132 3.091545 ACTTAGTGGCATGTTGATTGGG 58.908 45.455 0.00 0.00 0.00 4.12
2051 2152 3.430333 TTTCTCCTTTTGCGGTGAAAC 57.570 42.857 0.00 0.00 39.98 2.78
2068 2169 5.506832 CGTGCGTAAAATTAGTGGATGTTTC 59.493 40.000 0.00 0.00 0.00 2.78
2161 2263 4.449743 TCACATTTCTGCACGTTAAGTACC 59.550 41.667 0.00 0.00 0.00 3.34
2162 2264 5.371629 GTCACATTTCTGCACGTTAAGTAC 58.628 41.667 0.00 0.00 0.00 2.73
2236 2338 0.754957 CCGTCTCCATGAGCCTCTCT 60.755 60.000 0.00 0.00 0.00 3.10
2266 2368 1.487452 CTGTGTTGGTGTCGTCGGTG 61.487 60.000 0.00 0.00 0.00 4.94
2284 2386 1.117994 TGCATCAGCCGATCTTCTCT 58.882 50.000 0.00 0.00 41.13 3.10
2350 2454 6.569801 CGCTCTACCTAATTAACCGATGATGA 60.570 42.308 0.00 0.00 0.00 2.92
2351 2455 5.573282 CGCTCTACCTAATTAACCGATGATG 59.427 44.000 0.00 0.00 0.00 3.07
2352 2456 5.475909 TCGCTCTACCTAATTAACCGATGAT 59.524 40.000 0.00 0.00 0.00 2.45
2428 2538 5.221067 CGAACCATATACACTCTGTGCTAGT 60.221 44.000 0.00 0.00 36.98 2.57
2429 2539 5.008712 TCGAACCATATACACTCTGTGCTAG 59.991 44.000 0.00 0.00 36.98 3.42
2430 2540 4.885325 TCGAACCATATACACTCTGTGCTA 59.115 41.667 0.00 0.00 36.98 3.49
2441 2551 7.494625 TCTTCACCAAAAGATCGAACCATATAC 59.505 37.037 0.00 0.00 30.38 1.47
2451 2561 8.425577 AACATAGTATCTTCACCAAAAGATCG 57.574 34.615 2.59 0.00 43.32 3.69
2453 2563 9.520515 ACAAACATAGTATCTTCACCAAAAGAT 57.479 29.630 4.70 4.70 45.59 2.40
2464 2574 6.147164 CGACACCAACACAAACATAGTATCTT 59.853 38.462 0.00 0.00 0.00 2.40
2472 2582 1.403679 CACCGACACCAACACAAACAT 59.596 47.619 0.00 0.00 0.00 2.71
2511 2630 4.034510 GCTAGTCAATGTGCCTATCAACAC 59.965 45.833 0.00 0.00 37.31 3.32
2512 2631 4.080919 AGCTAGTCAATGTGCCTATCAACA 60.081 41.667 0.00 0.00 0.00 3.33
2513 2632 4.272018 CAGCTAGTCAATGTGCCTATCAAC 59.728 45.833 0.00 0.00 0.00 3.18
2603 2726 3.564511 GCACATAACACGTGAGCATTTT 58.435 40.909 25.01 7.35 36.43 1.82
2636 2759 7.010460 TGACAGTATTGAGAGATGCATAAAACG 59.990 37.037 0.00 0.00 0.00 3.60
2715 2838 4.079253 ACATTTTAGATCGGCCACAACTT 58.921 39.130 2.24 0.00 0.00 2.66
2735 2858 2.679450 CAATCGTAAGTGGTTCGGACA 58.321 47.619 0.00 0.00 39.48 4.02
2740 2863 4.851558 GTCAAATGCAATCGTAAGTGGTTC 59.148 41.667 0.00 0.00 39.48 3.62
2745 2868 3.071479 ACCGTCAAATGCAATCGTAAGT 58.929 40.909 0.00 0.00 39.48 2.24
2751 2880 3.531538 TCTAGGACCGTCAAATGCAATC 58.468 45.455 0.00 0.00 0.00 2.67
2804 2933 7.575414 TGCATCTTAAGTTCAAAGGTACAAA 57.425 32.000 1.63 0.00 0.00 2.83
2807 2936 7.121315 AGGATTGCATCTTAAGTTCAAAGGTAC 59.879 37.037 1.63 0.00 0.00 3.34
2821 2950 9.451002 CATAGAATCAATCTAGGATTGCATCTT 57.549 33.333 20.87 11.41 43.53 2.40
2822 2951 8.604184 ACATAGAATCAATCTAGGATTGCATCT 58.396 33.333 20.18 20.18 43.53 2.90
2823 2952 8.789825 ACATAGAATCAATCTAGGATTGCATC 57.210 34.615 13.48 13.00 43.53 3.91
2824 2953 9.584008 AAACATAGAATCAATCTAGGATTGCAT 57.416 29.630 13.48 6.42 43.53 3.96
2825 2954 8.985315 AAACATAGAATCAATCTAGGATTGCA 57.015 30.769 13.48 5.53 43.53 4.08
2842 2971 9.426837 GGTGTATAGTGTTGTGTTAAACATAGA 57.573 33.333 0.00 0.00 41.81 1.98
2843 2972 9.431887 AGGTGTATAGTGTTGTGTTAAACATAG 57.568 33.333 0.00 0.00 41.81 2.23
2844 2973 9.781633 AAGGTGTATAGTGTTGTGTTAAACATA 57.218 29.630 0.00 0.00 41.81 2.29
2845 2974 8.564574 CAAGGTGTATAGTGTTGTGTTAAACAT 58.435 33.333 0.00 0.00 41.81 2.71
2846 2975 7.553402 ACAAGGTGTATAGTGTTGTGTTAAACA 59.447 33.333 0.00 0.00 37.71 2.83
2847 2976 7.922837 ACAAGGTGTATAGTGTTGTGTTAAAC 58.077 34.615 0.00 0.00 30.25 2.01
2848 2977 9.044150 GTACAAGGTGTATAGTGTTGTGTTAAA 57.956 33.333 0.00 0.00 35.05 1.52
2849 2978 7.656948 GGTACAAGGTGTATAGTGTTGTGTTAA 59.343 37.037 0.00 0.00 35.05 2.01
2850 2979 7.015487 AGGTACAAGGTGTATAGTGTTGTGTTA 59.985 37.037 0.00 0.00 35.05 2.41
2851 2980 5.993441 GGTACAAGGTGTATAGTGTTGTGTT 59.007 40.000 0.00 0.00 35.05 3.32
2852 2981 5.306160 AGGTACAAGGTGTATAGTGTTGTGT 59.694 40.000 0.00 0.00 35.05 3.72
2853 2982 5.790593 AGGTACAAGGTGTATAGTGTTGTG 58.209 41.667 0.00 0.00 35.05 3.33
2854 2983 6.429521 AAGGTACAAGGTGTATAGTGTTGT 57.570 37.500 0.00 0.00 35.05 3.32
2855 2984 6.932400 TCAAAGGTACAAGGTGTATAGTGTTG 59.068 38.462 0.00 0.00 35.05 3.33
2856 2985 7.069877 TCAAAGGTACAAGGTGTATAGTGTT 57.930 36.000 0.00 0.00 35.05 3.32
2857 2986 6.675413 TCAAAGGTACAAGGTGTATAGTGT 57.325 37.500 0.00 0.00 35.05 3.55
2858 2987 7.159372 AGTTCAAAGGTACAAGGTGTATAGTG 58.841 38.462 0.00 0.00 35.05 2.74
2859 2988 7.312415 AGTTCAAAGGTACAAGGTGTATAGT 57.688 36.000 0.00 0.00 35.05 2.12
2860 2989 9.148104 GTAAGTTCAAAGGTACAAGGTGTATAG 57.852 37.037 0.00 0.00 35.05 1.31
2861 2990 8.649591 TGTAAGTTCAAAGGTACAAGGTGTATA 58.350 33.333 0.00 0.00 35.05 1.47
2862 2991 7.511268 TGTAAGTTCAAAGGTACAAGGTGTAT 58.489 34.615 0.00 0.00 35.05 2.29
2863 2992 6.887013 TGTAAGTTCAAAGGTACAAGGTGTA 58.113 36.000 0.00 0.00 0.00 2.90
2864 2993 5.747342 TGTAAGTTCAAAGGTACAAGGTGT 58.253 37.500 0.00 0.00 0.00 4.16
2865 2994 6.094325 TGTTGTAAGTTCAAAGGTACAAGGTG 59.906 38.462 0.00 0.00 37.18 4.00
2866 2995 6.181908 TGTTGTAAGTTCAAAGGTACAAGGT 58.818 36.000 0.00 0.00 37.18 3.50
2867 2996 6.687081 TGTTGTAAGTTCAAAGGTACAAGG 57.313 37.500 0.00 0.00 37.18 3.61
2868 2997 8.241367 ACTTTGTTGTAAGTTCAAAGGTACAAG 58.759 33.333 17.12 0.00 46.73 3.16
2869 2998 8.113173 ACTTTGTTGTAAGTTCAAAGGTACAA 57.887 30.769 17.12 1.56 46.73 2.41
2870 2999 7.690952 ACTTTGTTGTAAGTTCAAAGGTACA 57.309 32.000 17.12 0.00 46.73 2.90
2871 3000 8.886719 AGTACTTTGTTGTAAGTTCAAAGGTAC 58.113 33.333 17.12 15.40 46.73 3.34
2872 3001 9.101655 GAGTACTTTGTTGTAAGTTCAAAGGTA 57.898 33.333 17.12 7.80 46.73 3.08
2873 3002 7.608761 TGAGTACTTTGTTGTAAGTTCAAAGGT 59.391 33.333 17.12 8.50 46.73 3.50
2874 3003 7.981142 TGAGTACTTTGTTGTAAGTTCAAAGG 58.019 34.615 17.12 4.33 46.73 3.11
2876 3005 9.168451 TCATGAGTACTTTGTTGTAAGTTCAAA 57.832 29.630 0.00 0.00 39.08 2.69
2877 3006 8.725405 TCATGAGTACTTTGTTGTAAGTTCAA 57.275 30.769 0.00 0.00 39.08 2.69
2878 3007 7.985184 ACTCATGAGTACTTTGTTGTAAGTTCA 59.015 33.333 26.87 0.00 40.43 3.18
2879 3008 8.366671 ACTCATGAGTACTTTGTTGTAAGTTC 57.633 34.615 26.87 0.00 40.43 3.01
2880 3009 7.985184 TGACTCATGAGTACTTTGTTGTAAGTT 59.015 33.333 27.95 0.00 42.66 2.66
2881 3010 7.497595 TGACTCATGAGTACTTTGTTGTAAGT 58.502 34.615 27.95 0.28 42.66 2.24
2882 3011 7.946655 TGACTCATGAGTACTTTGTTGTAAG 57.053 36.000 27.95 0.00 42.66 2.34
2883 3012 8.147704 TCATGACTCATGAGTACTTTGTTGTAA 58.852 33.333 27.95 5.06 44.60 2.41
2912 3041 6.311200 GTGTGGTTTTCCGTATAAGTAACGAT 59.689 38.462 0.00 0.00 42.90 3.73
2921 3050 3.933955 CGAATGGTGTGGTTTTCCGTATA 59.066 43.478 0.00 0.00 44.36 1.47
2922 3051 2.745281 CGAATGGTGTGGTTTTCCGTAT 59.255 45.455 0.00 0.00 44.36 3.06
2925 3054 0.386731 GCGAATGGTGTGGTTTTCCG 60.387 55.000 0.00 0.00 44.36 4.30
2928 3057 3.417101 TCATAGCGAATGGTGTGGTTTT 58.583 40.909 2.76 0.00 35.66 2.43
2930 3059 2.236146 TCTCATAGCGAATGGTGTGGTT 59.764 45.455 2.76 0.00 35.66 3.67
2931 3060 1.831106 TCTCATAGCGAATGGTGTGGT 59.169 47.619 2.76 0.00 35.66 4.16
2934 3063 5.415701 ACAAATTTCTCATAGCGAATGGTGT 59.584 36.000 2.76 0.00 36.15 4.16
2938 3067 6.324819 ACCAACAAATTTCTCATAGCGAATG 58.675 36.000 0.00 0.00 36.88 2.67
2967 3096 6.372937 CCAACAAACATAACCAAAAACCTGTT 59.627 34.615 0.00 0.00 0.00 3.16
2987 3116 6.135454 AGGCCATTATATGATGTTTCCAACA 58.865 36.000 5.01 0.00 46.94 3.33
2988 3117 6.655078 AGGCCATTATATGATGTTTCCAAC 57.345 37.500 5.01 0.00 0.00 3.77
3017 3146 6.323482 TGATCACTGAAGGAAATTTGAAACCA 59.677 34.615 0.00 0.00 0.00 3.67
3026 3155 4.082571 CCGCTTTTGATCACTGAAGGAAAT 60.083 41.667 0.00 0.00 0.00 2.17
3066 3195 4.062293 TCAACATAAAGAAGTGTCACCCG 58.938 43.478 0.00 0.00 0.00 5.28
3148 3277 5.300286 GGGTAGCATCTAAAGCATGAACATT 59.700 40.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.