Multiple sequence alignment - TraesCS1B01G098100

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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 TraesCS1B01G098100 chr1B 100.000 3005 0 0 1 3005 104765639 104768643 0.000000e+00 5550.0
1 TraesCS1B01G098100 chr1D 93.184 2054 73 28 706 2736 63944386 63946395 0.000000e+00 2955.0
2 TraesCS1B01G098100 chr1D 90.942 276 11 6 2735 3005 63946427 63946693 2.850000e-95 359.0
3 TraesCS1B01G098100 chr1A 92.541 2078 81 30 706 2736 63045817 63047867 0.000000e+00 2911.0
4 TraesCS1B01G098100 chr1A 86.131 274 15 6 2735 3005 63047899 63048152 1.060000e-69 274.0
5 TraesCS1B01G098100 chr3B 98.884 627 7 0 3 629 51965497 51966123 0.000000e+00 1120.0
6 TraesCS1B01G098100 chr3B 98.649 74 1 0 629 702 51980084 51980157 6.760000e-27 132.0
7 TraesCS1B01G098100 chr5B 88.649 185 19 2 1 183 508272472 508272656 1.080000e-54 224.0
8 TraesCS1B01G098100 chr5B 97.143 35 1 0 2766 2800 326609365 326609331 3.240000e-05 60.2
9 TraesCS1B01G098100 chr3A 100.000 28 0 0 2782 2809 128548317 128548344 5.000000e-03 52.8


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 TraesCS1B01G098100 chr1B 104765639 104768643 3004 False 5550.0 5550 100.000 1 3005 1 chr1B.!!$F1 3004
1 TraesCS1B01G098100 chr1D 63944386 63946693 2307 False 1657.0 2955 92.063 706 3005 2 chr1D.!!$F1 2299
2 TraesCS1B01G098100 chr1A 63045817 63048152 2335 False 1592.5 2911 89.336 706 3005 2 chr1A.!!$F1 2299
3 TraesCS1B01G098100 chr3B 51965497 51966123 626 False 1120.0 1120 98.884 3 629 1 chr3B.!!$F1 626

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
657 658 0.036388 ATCAACGATGTTCGGCTGGT 60.036 50.000 1.69 0.0 45.59 4.00 F
960 988 0.399233 AATCTTCCCCTCTCCTCCCG 60.399 60.000 0.00 0.0 0.00 5.14 F
1315 1349 1.215382 CTCTTCGTCGCCCATGTCA 59.785 57.895 0.00 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1833 0.459585 CAATGGTGGCATTGAGCTGC 60.460 55.0 0.0 0.0 43.26 5.25 R
1811 1845 0.468958 TGGTGGGGTTGACAATGGTG 60.469 55.0 0.0 0.0 0.00 4.17 R
2250 2304 0.531200 ACTCGCTTAGGTTTCCTCGG 59.469 55.0 0.0 0.0 34.61 4.63 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
127 128 9.581099 CAACCAATTAGTCAAGTAACACTTTTT 57.419 29.630 0.00 0.00 36.03 1.94
228 229 1.895051 TTAGTCGCGTTAGTTACCGC 58.105 50.000 5.77 0.00 46.10 5.68
330 331 1.835267 TGTACCTGTCACCCGCACT 60.835 57.895 0.00 0.00 0.00 4.40
459 460 2.825264 GGAGATGGCCGGAGAAGG 59.175 66.667 5.05 0.00 0.00 3.46
629 630 1.025812 CTACTCCCGAGCGTCAGATT 58.974 55.000 0.00 0.00 0.00 2.40
630 631 1.405821 CTACTCCCGAGCGTCAGATTT 59.594 52.381 0.00 0.00 0.00 2.17
631 632 0.108615 ACTCCCGAGCGTCAGATTTG 60.109 55.000 0.00 0.00 0.00 2.32
632 633 0.807667 CTCCCGAGCGTCAGATTTGG 60.808 60.000 0.00 0.00 0.00 3.28
633 634 1.218047 CCCGAGCGTCAGATTTGGA 59.782 57.895 0.00 0.00 0.00 3.53
634 635 0.807667 CCCGAGCGTCAGATTTGGAG 60.808 60.000 0.00 0.00 0.00 3.86
635 636 0.108615 CCGAGCGTCAGATTTGGAGT 60.109 55.000 0.00 0.00 0.00 3.85
636 637 1.134367 CCGAGCGTCAGATTTGGAGTA 59.866 52.381 0.00 0.00 0.00 2.59
637 638 2.416836 CCGAGCGTCAGATTTGGAGTAA 60.417 50.000 0.00 0.00 0.00 2.24
638 639 3.250744 CGAGCGTCAGATTTGGAGTAAA 58.749 45.455 0.00 0.00 0.00 2.01
639 640 3.865745 CGAGCGTCAGATTTGGAGTAAAT 59.134 43.478 0.00 0.00 41.59 1.40
651 652 5.524511 TTGGAGTAAATCAACGATGTTCG 57.475 39.130 0.00 0.00 46.93 3.95
652 653 3.930229 TGGAGTAAATCAACGATGTTCGG 59.070 43.478 1.69 0.00 45.59 4.30
653 654 3.242316 GGAGTAAATCAACGATGTTCGGC 60.242 47.826 1.69 0.00 45.59 5.54
654 655 3.596214 AGTAAATCAACGATGTTCGGCT 58.404 40.909 1.69 0.00 45.59 5.52
655 656 2.900122 AAATCAACGATGTTCGGCTG 57.100 45.000 1.69 0.00 45.59 4.85
656 657 1.086696 AATCAACGATGTTCGGCTGG 58.913 50.000 1.69 0.00 45.59 4.85
657 658 0.036388 ATCAACGATGTTCGGCTGGT 60.036 50.000 1.69 0.00 45.59 4.00
658 659 0.669318 TCAACGATGTTCGGCTGGTC 60.669 55.000 1.69 0.00 45.59 4.02
659 660 0.670546 CAACGATGTTCGGCTGGTCT 60.671 55.000 1.69 0.00 45.59 3.85
660 661 0.670546 AACGATGTTCGGCTGGTCTG 60.671 55.000 1.69 0.00 45.59 3.51
661 662 1.811266 CGATGTTCGGCTGGTCTGG 60.811 63.158 0.00 0.00 36.00 3.86
662 663 2.045926 ATGTTCGGCTGGTCTGGC 60.046 61.111 0.00 0.00 0.00 4.85
668 669 3.785859 GGCTGGTCTGGCGATGGA 61.786 66.667 0.00 0.00 0.00 3.41
669 670 2.202987 GCTGGTCTGGCGATGGAG 60.203 66.667 0.00 0.00 0.00 3.86
670 671 3.023949 GCTGGTCTGGCGATGGAGT 62.024 63.158 0.00 0.00 0.00 3.85
671 672 1.142748 CTGGTCTGGCGATGGAGTC 59.857 63.158 0.00 0.00 0.00 3.36
672 673 1.305297 TGGTCTGGCGATGGAGTCT 60.305 57.895 0.00 0.00 0.00 3.24
673 674 0.904865 TGGTCTGGCGATGGAGTCTT 60.905 55.000 0.00 0.00 0.00 3.01
674 675 1.112113 GGTCTGGCGATGGAGTCTTA 58.888 55.000 0.00 0.00 0.00 2.10
675 676 1.689273 GGTCTGGCGATGGAGTCTTAT 59.311 52.381 0.00 0.00 0.00 1.73
676 677 2.288518 GGTCTGGCGATGGAGTCTTATC 60.289 54.545 0.00 0.00 0.00 1.75
677 678 2.362397 GTCTGGCGATGGAGTCTTATCA 59.638 50.000 0.00 0.00 0.00 2.15
678 679 2.625314 TCTGGCGATGGAGTCTTATCAG 59.375 50.000 0.00 0.00 0.00 2.90
679 680 2.625314 CTGGCGATGGAGTCTTATCAGA 59.375 50.000 0.00 0.00 0.00 3.27
694 695 8.568732 GTCTTATCAGACTATAGACACAAAGC 57.431 38.462 6.78 0.00 45.54 3.51
695 696 7.377397 GTCTTATCAGACTATAGACACAAAGCG 59.623 40.741 6.78 0.00 45.54 4.68
696 697 5.584253 ATCAGACTATAGACACAAAGCGT 57.416 39.130 6.78 0.00 0.00 5.07
697 698 5.386958 TCAGACTATAGACACAAAGCGTT 57.613 39.130 6.78 0.00 0.00 4.84
698 699 5.779922 TCAGACTATAGACACAAAGCGTTT 58.220 37.500 6.78 0.00 0.00 3.60
699 700 5.862323 TCAGACTATAGACACAAAGCGTTTC 59.138 40.000 6.78 0.00 0.00 2.78
700 701 5.062308 CAGACTATAGACACAAAGCGTTTCC 59.938 44.000 6.78 0.00 0.00 3.13
701 702 4.251268 ACTATAGACACAAAGCGTTTCCC 58.749 43.478 6.78 0.00 0.00 3.97
702 703 2.922740 TAGACACAAAGCGTTTCCCT 57.077 45.000 0.00 0.00 0.00 4.20
703 704 2.922740 AGACACAAAGCGTTTCCCTA 57.077 45.000 0.00 0.00 0.00 3.53
704 705 3.418684 AGACACAAAGCGTTTCCCTAT 57.581 42.857 0.00 0.00 0.00 2.57
742 743 1.595466 AAGCGAGTCGATCTACCGAT 58.405 50.000 18.61 3.67 40.91 4.18
743 744 2.452295 AGCGAGTCGATCTACCGATA 57.548 50.000 18.61 0.00 40.91 2.92
747 748 3.315418 CGAGTCGATCTACCGATACTGA 58.685 50.000 6.73 0.00 40.91 3.41
750 751 3.499157 AGTCGATCTACCGATACTGAAGC 59.501 47.826 0.00 0.00 40.91 3.86
764 765 1.138247 GAAGCTTTCATGCAGCCCG 59.862 57.895 0.00 0.00 38.09 6.13
765 766 1.589716 GAAGCTTTCATGCAGCCCGT 61.590 55.000 0.00 0.47 38.09 5.28
767 768 1.153958 GCTTTCATGCAGCCCGTTC 60.154 57.895 5.60 0.00 0.00 3.95
769 770 1.228398 TTTCATGCAGCCCGTTCCA 60.228 52.632 0.00 0.00 0.00 3.53
773 779 3.628646 ATGCAGCCCGTTCCACTCC 62.629 63.158 0.00 0.00 0.00 3.85
827 844 0.608640 CTACCTCCTTTGCTCGTGGT 59.391 55.000 0.00 0.00 0.00 4.16
835 852 2.438951 TTTGCTCGTGGTACCCCGTC 62.439 60.000 16.58 10.18 0.00 4.79
836 853 3.066814 GCTCGTGGTACCCCGTCT 61.067 66.667 16.58 0.00 0.00 4.18
837 854 2.882876 CTCGTGGTACCCCGTCTG 59.117 66.667 16.58 4.95 0.00 3.51
838 855 1.676635 CTCGTGGTACCCCGTCTGA 60.677 63.158 16.58 0.00 0.00 3.27
839 856 1.000521 TCGTGGTACCCCGTCTGAT 60.001 57.895 16.58 0.00 0.00 2.90
840 857 0.612732 TCGTGGTACCCCGTCTGATT 60.613 55.000 16.58 0.00 0.00 2.57
849 866 1.676014 CCCCGTCTGATTCTGAACACC 60.676 57.143 0.00 0.00 0.00 4.16
858 875 3.831911 TGATTCTGAACACCAAATTCCCC 59.168 43.478 0.00 0.00 0.00 4.81
893 911 5.948992 AAAGGAAGAAAAATCTCTCACCG 57.051 39.130 0.00 0.00 31.32 4.94
945 963 3.014110 TCCTCCCTCAGAAACCCTAATCT 59.986 47.826 0.00 0.00 0.00 2.40
954 982 4.041464 AGAAACCCTAATCTTCCCCTCTC 58.959 47.826 0.00 0.00 0.00 3.20
955 983 2.498473 ACCCTAATCTTCCCCTCTCC 57.502 55.000 0.00 0.00 0.00 3.71
956 984 1.948243 ACCCTAATCTTCCCCTCTCCT 59.052 52.381 0.00 0.00 0.00 3.69
957 985 2.090437 ACCCTAATCTTCCCCTCTCCTC 60.090 54.545 0.00 0.00 0.00 3.71
958 986 2.615391 CCTAATCTTCCCCTCTCCTCC 58.385 57.143 0.00 0.00 0.00 4.30
959 987 2.615391 CTAATCTTCCCCTCTCCTCCC 58.385 57.143 0.00 0.00 0.00 4.30
960 988 0.399233 AATCTTCCCCTCTCCTCCCG 60.399 60.000 0.00 0.00 0.00 5.14
961 989 1.595058 ATCTTCCCCTCTCCTCCCGT 61.595 60.000 0.00 0.00 0.00 5.28
962 990 1.758906 CTTCCCCTCTCCTCCCGTC 60.759 68.421 0.00 0.00 0.00 4.79
963 991 2.231540 CTTCCCCTCTCCTCCCGTCT 62.232 65.000 0.00 0.00 0.00 4.18
964 992 2.123640 CCCCTCTCCTCCCGTCTC 60.124 72.222 0.00 0.00 0.00 3.36
965 993 2.695970 CCCCTCTCCTCCCGTCTCT 61.696 68.421 0.00 0.00 0.00 3.10
1179 1207 4.521062 CCCGCCTCCTTCTGCTCG 62.521 72.222 0.00 0.00 0.00 5.03
1209 1237 3.374402 CTCCTCCACACGGACGCT 61.374 66.667 0.00 0.00 35.91 5.07
1315 1349 1.215382 CTCTTCGTCGCCCATGTCA 59.785 57.895 0.00 0.00 0.00 3.58
1563 1597 2.436646 CGGGAAATGCTGGACGCT 60.437 61.111 0.00 0.00 40.11 5.07
1808 1842 2.478890 GCTCATGCGGCAGCTCAAT 61.479 57.895 10.92 0.00 45.42 2.57
1810 1844 2.278596 CATGCGGCAGCTCAATGC 60.279 61.111 10.92 0.00 45.42 3.56
1828 1874 1.815817 GCCACCATTGTCAACCCCAC 61.816 60.000 0.00 0.00 0.00 4.61
1851 1897 0.674895 CCAAGGAGGACAAGAAGCCG 60.675 60.000 0.00 0.00 41.22 5.52
1864 1913 1.065854 AGAAGCCGATGAAACAGGAGG 60.066 52.381 0.00 0.00 0.00 4.30
1926 1976 7.318141 CAGCCAATTGTTCTGTTCAATAATCT 58.682 34.615 13.71 0.00 34.92 2.40
1968 2020 1.893137 ACGGACACAGTAGCAGATGAA 59.107 47.619 0.00 0.00 0.00 2.57
2042 2095 0.743097 GCCCATCTGTTTGATCTGCC 59.257 55.000 0.00 0.00 32.05 4.85
2073 2126 2.907634 TGTTGTTGCTAAGTGAACCGA 58.092 42.857 0.00 0.00 0.00 4.69
2108 2161 9.305925 CTTTGCTTGAATTTAATGAATCCCTAC 57.694 33.333 0.00 0.00 0.00 3.18
2118 2171 0.693430 GAATCCCTACCCCGGAACCT 60.693 60.000 0.73 0.00 31.75 3.50
2183 2236 7.338710 TCTTATTTATGTAGCTGCTTCACCTT 58.661 34.615 7.79 0.00 0.00 3.50
2271 2325 1.794437 CGAGGAAACCTAAGCGAGTCG 60.794 57.143 8.54 8.54 31.76 4.18
2350 2405 3.988379 TGTTGAATGTGCAAGTTCCTC 57.012 42.857 9.18 4.33 0.00 3.71
2354 2409 1.881973 GAATGTGCAAGTTCCTCTGCA 59.118 47.619 0.00 0.00 34.67 4.41
2355 2410 1.985473 ATGTGCAAGTTCCTCTGCAA 58.015 45.000 0.00 0.00 39.10 4.08
2356 2411 1.985473 TGTGCAAGTTCCTCTGCAAT 58.015 45.000 0.00 0.00 39.10 3.56
2378 2433 8.327429 GCAATAATATTGTGTAAATGCACCAAC 58.673 33.333 13.77 0.00 38.52 3.77
2411 2469 5.989477 TCTTTATCCCCATTCAGTACACAG 58.011 41.667 0.00 0.00 0.00 3.66
2437 2495 6.775142 TGGAAAATCAAAGAAGTGGTGTGATA 59.225 34.615 0.00 0.00 0.00 2.15
2457 2515 7.395772 TGTGATAGCAGATTGAAAATTACCCAA 59.604 33.333 0.00 0.00 0.00 4.12
2495 2553 8.877864 TTTCCTGAACATGACTTGGTATAATT 57.122 30.769 0.00 0.00 0.00 1.40
2600 2661 3.253188 TGCAAACTCTGTATTTGAGCACC 59.747 43.478 9.51 0.00 39.01 5.01
2750 2851 4.192317 GTTACTCTTATGGGTGGCTTCTG 58.808 47.826 0.00 0.00 0.00 3.02
2803 2904 3.641436 CCAAAAGAACTGGCCCTTACTTT 59.359 43.478 0.00 4.78 0.00 2.66
2850 2951 0.916086 AATCGTATTGAGGCCCCACA 59.084 50.000 0.00 0.00 0.00 4.17
2851 2952 0.916086 ATCGTATTGAGGCCCCACAA 59.084 50.000 0.00 4.41 0.00 3.33
2852 2953 0.916086 TCGTATTGAGGCCCCACAAT 59.084 50.000 19.30 19.30 39.71 2.71
2853 2954 1.134220 TCGTATTGAGGCCCCACAATC 60.134 52.381 19.03 12.21 38.05 2.67
2854 2955 1.408127 CGTATTGAGGCCCCACAATCA 60.408 52.381 19.03 5.02 38.05 2.57
2855 2956 2.749466 CGTATTGAGGCCCCACAATCAT 60.749 50.000 19.03 0.00 38.05 2.45
2856 2957 3.495983 CGTATTGAGGCCCCACAATCATA 60.496 47.826 19.03 0.00 38.05 2.15
2857 2958 3.909427 ATTGAGGCCCCACAATCATAT 57.091 42.857 12.61 0.00 33.21 1.78
2872 2973 2.990195 TCATATATCCTGGTGCCACCT 58.010 47.619 16.23 0.00 39.58 4.00
2873 2974 3.326521 TCATATATCCTGGTGCCACCTT 58.673 45.455 16.23 0.05 39.58 3.50
2900 3001 1.297664 CAGCTTCACCTATGCTGCTC 58.702 55.000 0.00 0.00 45.90 4.26
2906 3007 2.136878 ACCTATGCTGCTCCCTCGG 61.137 63.158 0.00 0.00 0.00 4.63
2913 3014 1.142748 CTGCTCCCTCGGTAAGCTG 59.857 63.158 0.00 5.15 36.96 4.24
2929 3030 1.252904 GCTGACCATTGGTGTGGCAT 61.253 55.000 14.44 0.00 43.27 4.40
2935 3036 1.259609 CATTGGTGTGGCATTGTCCT 58.740 50.000 0.00 0.00 0.00 3.85
2978 3080 1.202734 GCAAGAGGCATGCCATAGAGA 60.203 52.381 37.18 0.00 43.97 3.10
2981 3083 1.549620 AGAGGCATGCCATAGAGATCG 59.450 52.381 37.18 0.00 38.92 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 128 6.039717 CCTCAGGTTGTTTTTCATTCTTCTGA 59.960 38.462 0.00 0.00 0.00 3.27
411 412 0.967887 CCTCCTTCTCTCCTCGTGCA 60.968 60.000 0.00 0.00 0.00 4.57
603 604 1.142097 GCTCGGGAGTAGTCTTGCC 59.858 63.158 0.00 0.00 0.00 4.52
629 630 4.390603 CCGAACATCGTTGATTTACTCCAA 59.609 41.667 0.00 0.00 38.40 3.53
630 631 3.930229 CCGAACATCGTTGATTTACTCCA 59.070 43.478 0.00 0.00 38.40 3.86
631 632 3.242316 GCCGAACATCGTTGATTTACTCC 60.242 47.826 0.00 0.00 38.40 3.85
632 633 3.617263 AGCCGAACATCGTTGATTTACTC 59.383 43.478 0.00 0.00 38.40 2.59
633 634 3.370978 CAGCCGAACATCGTTGATTTACT 59.629 43.478 0.00 0.00 38.40 2.24
634 635 3.485216 CCAGCCGAACATCGTTGATTTAC 60.485 47.826 0.00 0.00 38.40 2.01
635 636 2.675844 CCAGCCGAACATCGTTGATTTA 59.324 45.455 0.00 0.00 38.40 1.40
636 637 1.468520 CCAGCCGAACATCGTTGATTT 59.531 47.619 0.00 0.00 38.40 2.17
637 638 1.086696 CCAGCCGAACATCGTTGATT 58.913 50.000 0.00 0.00 38.40 2.57
638 639 0.036388 ACCAGCCGAACATCGTTGAT 60.036 50.000 0.00 0.00 38.40 2.57
639 640 0.669318 GACCAGCCGAACATCGTTGA 60.669 55.000 0.00 0.00 38.40 3.18
640 641 0.670546 AGACCAGCCGAACATCGTTG 60.671 55.000 0.00 0.00 38.40 4.10
641 642 0.670546 CAGACCAGCCGAACATCGTT 60.671 55.000 0.00 0.00 38.40 3.85
642 643 1.079819 CAGACCAGCCGAACATCGT 60.080 57.895 0.00 0.00 38.40 3.73
643 644 1.811266 CCAGACCAGCCGAACATCG 60.811 63.158 0.00 0.00 40.07 3.84
644 645 2.109126 GCCAGACCAGCCGAACATC 61.109 63.158 0.00 0.00 0.00 3.06
645 646 2.045926 GCCAGACCAGCCGAACAT 60.046 61.111 0.00 0.00 0.00 2.71
646 647 4.680237 CGCCAGACCAGCCGAACA 62.680 66.667 0.00 0.00 0.00 3.18
647 648 3.665675 ATCGCCAGACCAGCCGAAC 62.666 63.158 0.00 0.00 33.10 3.95
648 649 3.390521 ATCGCCAGACCAGCCGAA 61.391 61.111 0.00 0.00 33.10 4.30
649 650 4.147449 CATCGCCAGACCAGCCGA 62.147 66.667 0.00 0.00 0.00 5.54
651 652 3.746949 CTCCATCGCCAGACCAGCC 62.747 68.421 0.00 0.00 0.00 4.85
652 653 2.202987 CTCCATCGCCAGACCAGC 60.203 66.667 0.00 0.00 0.00 4.85
653 654 1.142748 GACTCCATCGCCAGACCAG 59.857 63.158 0.00 0.00 0.00 4.00
654 655 0.904865 AAGACTCCATCGCCAGACCA 60.905 55.000 0.00 0.00 0.00 4.02
655 656 1.112113 TAAGACTCCATCGCCAGACC 58.888 55.000 0.00 0.00 0.00 3.85
656 657 2.362397 TGATAAGACTCCATCGCCAGAC 59.638 50.000 0.00 0.00 0.00 3.51
657 658 2.625314 CTGATAAGACTCCATCGCCAGA 59.375 50.000 0.00 0.00 0.00 3.86
658 659 2.625314 TCTGATAAGACTCCATCGCCAG 59.375 50.000 0.00 0.00 0.00 4.85
659 660 2.362397 GTCTGATAAGACTCCATCGCCA 59.638 50.000 2.58 0.00 36.01 5.69
660 661 2.625790 AGTCTGATAAGACTCCATCGCC 59.374 50.000 6.95 0.00 45.09 5.54
661 662 5.637006 ATAGTCTGATAAGACTCCATCGC 57.363 43.478 16.56 0.00 45.09 4.58
662 663 7.604545 TGTCTATAGTCTGATAAGACTCCATCG 59.395 40.741 16.56 2.49 45.09 3.84
663 664 8.726988 GTGTCTATAGTCTGATAAGACTCCATC 58.273 40.741 16.56 5.86 45.09 3.51
664 665 8.221251 TGTGTCTATAGTCTGATAAGACTCCAT 58.779 37.037 16.56 8.24 45.09 3.41
665 666 7.574607 TGTGTCTATAGTCTGATAAGACTCCA 58.425 38.462 16.56 0.19 45.09 3.86
666 667 8.453238 TTGTGTCTATAGTCTGATAAGACTCC 57.547 38.462 16.56 2.09 45.09 3.85
667 668 9.944663 CTTTGTGTCTATAGTCTGATAAGACTC 57.055 37.037 16.56 2.58 45.09 3.36
669 670 7.377397 CGCTTTGTGTCTATAGTCTGATAAGAC 59.623 40.741 1.38 1.38 39.00 3.01
670 671 7.067129 ACGCTTTGTGTCTATAGTCTGATAAGA 59.933 37.037 0.00 0.00 0.00 2.10
671 672 7.197017 ACGCTTTGTGTCTATAGTCTGATAAG 58.803 38.462 0.00 0.44 0.00 1.73
672 673 7.096884 ACGCTTTGTGTCTATAGTCTGATAA 57.903 36.000 0.00 0.00 0.00 1.75
673 674 6.694877 ACGCTTTGTGTCTATAGTCTGATA 57.305 37.500 0.00 0.00 0.00 2.15
674 675 5.584253 ACGCTTTGTGTCTATAGTCTGAT 57.416 39.130 0.00 0.00 0.00 2.90
675 676 5.386958 AACGCTTTGTGTCTATAGTCTGA 57.613 39.130 0.00 0.00 0.00 3.27
676 677 5.062308 GGAAACGCTTTGTGTCTATAGTCTG 59.938 44.000 0.00 0.00 34.98 3.51
677 678 5.169295 GGAAACGCTTTGTGTCTATAGTCT 58.831 41.667 0.00 0.00 34.98 3.24
678 679 4.329256 GGGAAACGCTTTGTGTCTATAGTC 59.671 45.833 0.00 0.00 34.98 2.59
679 680 4.020485 AGGGAAACGCTTTGTGTCTATAGT 60.020 41.667 0.00 0.00 34.98 2.12
680 681 4.504858 AGGGAAACGCTTTGTGTCTATAG 58.495 43.478 0.00 0.00 34.98 1.31
681 682 4.546829 AGGGAAACGCTTTGTGTCTATA 57.453 40.909 0.00 0.00 34.98 1.31
682 683 3.418684 AGGGAAACGCTTTGTGTCTAT 57.581 42.857 0.00 0.00 34.98 1.98
683 684 2.922740 AGGGAAACGCTTTGTGTCTA 57.077 45.000 0.00 0.00 34.98 2.59
684 685 2.922740 TAGGGAAACGCTTTGTGTCT 57.077 45.000 0.00 0.00 34.98 3.41
685 686 4.694037 ACTTATAGGGAAACGCTTTGTGTC 59.306 41.667 0.00 0.00 33.70 3.67
686 687 4.648651 ACTTATAGGGAAACGCTTTGTGT 58.351 39.130 0.00 0.00 0.00 3.72
687 688 5.622770 AACTTATAGGGAAACGCTTTGTG 57.377 39.130 0.00 0.00 0.00 3.33
688 689 5.766174 TGAAACTTATAGGGAAACGCTTTGT 59.234 36.000 0.00 0.00 0.00 2.83
689 690 6.249035 TGAAACTTATAGGGAAACGCTTTG 57.751 37.500 0.00 0.00 0.00 2.77
690 691 6.657541 TCATGAAACTTATAGGGAAACGCTTT 59.342 34.615 0.00 0.00 0.00 3.51
691 692 6.177610 TCATGAAACTTATAGGGAAACGCTT 58.822 36.000 0.00 0.00 0.00 4.68
692 693 5.741011 TCATGAAACTTATAGGGAAACGCT 58.259 37.500 0.00 0.00 0.00 5.07
693 694 6.619801 ATCATGAAACTTATAGGGAAACGC 57.380 37.500 0.00 0.00 0.00 4.84
703 704 9.994432 CTCGCTTTCTTTTATCATGAAACTTAT 57.006 29.630 0.00 0.00 0.00 1.73
704 705 8.999431 ACTCGCTTTCTTTTATCATGAAACTTA 58.001 29.630 0.00 0.00 0.00 2.24
721 722 1.329906 TCGGTAGATCGACTCGCTTTC 59.670 52.381 5.91 0.00 33.92 2.62
742 743 2.086869 GGCTGCATGAAAGCTTCAGTA 58.913 47.619 17.31 0.00 43.98 2.74
743 744 0.886563 GGCTGCATGAAAGCTTCAGT 59.113 50.000 17.31 0.00 43.98 3.41
747 748 1.181098 AACGGGCTGCATGAAAGCTT 61.181 50.000 17.31 0.00 40.64 3.74
750 751 1.243342 TGGAACGGGCTGCATGAAAG 61.243 55.000 0.50 0.00 0.00 2.62
764 765 0.836400 TGGAGTGGGAGGAGTGGAAC 60.836 60.000 0.00 0.00 0.00 3.62
765 766 0.836400 GTGGAGTGGGAGGAGTGGAA 60.836 60.000 0.00 0.00 0.00 3.53
767 768 2.294078 GGTGGAGTGGGAGGAGTGG 61.294 68.421 0.00 0.00 0.00 4.00
769 770 2.283966 CGGTGGAGTGGGAGGAGT 60.284 66.667 0.00 0.00 0.00 3.85
773 779 2.876368 GATTGCCGGTGGAGTGGGAG 62.876 65.000 1.90 0.00 0.00 4.30
827 844 2.232941 GTGTTCAGAATCAGACGGGGTA 59.767 50.000 0.00 0.00 0.00 3.69
835 852 4.082026 GGGGAATTTGGTGTTCAGAATCAG 60.082 45.833 0.00 0.00 0.00 2.90
836 853 3.831911 GGGGAATTTGGTGTTCAGAATCA 59.168 43.478 0.00 0.00 0.00 2.57
837 854 4.089361 AGGGGAATTTGGTGTTCAGAATC 58.911 43.478 0.00 0.00 0.00 2.52
838 855 4.132122 AGGGGAATTTGGTGTTCAGAAT 57.868 40.909 0.00 0.00 0.00 2.40
839 856 3.611025 AGGGGAATTTGGTGTTCAGAA 57.389 42.857 0.00 0.00 0.00 3.02
840 857 4.508405 CCTTAGGGGAATTTGGTGTTCAGA 60.508 45.833 0.00 0.00 37.23 3.27
893 911 3.660732 GAACCCCGAACGGCTCCTC 62.661 68.421 7.80 0.00 0.00 3.71
913 931 3.393149 GAGGGAGGAAAGGCTCGGC 62.393 68.421 0.00 0.00 0.00 5.54
945 963 2.226149 GAGACGGGAGGAGAGGGGAA 62.226 65.000 0.00 0.00 0.00 3.97
954 982 2.123640 GGGAGGAGAGACGGGAGG 60.124 72.222 0.00 0.00 0.00 4.30
955 983 0.753848 GAAGGGAGGAGAGACGGGAG 60.754 65.000 0.00 0.00 0.00 4.30
956 984 1.306970 GAAGGGAGGAGAGACGGGA 59.693 63.158 0.00 0.00 0.00 5.14
957 985 1.758906 GGAAGGGAGGAGAGACGGG 60.759 68.421 0.00 0.00 0.00 5.28
958 986 1.758906 GGGAAGGGAGGAGAGACGG 60.759 68.421 0.00 0.00 0.00 4.79
959 987 1.758906 GGGGAAGGGAGGAGAGACG 60.759 68.421 0.00 0.00 0.00 4.18
960 988 0.689412 CAGGGGAAGGGAGGAGAGAC 60.689 65.000 0.00 0.00 0.00 3.36
961 989 1.156322 ACAGGGGAAGGGAGGAGAGA 61.156 60.000 0.00 0.00 0.00 3.10
962 990 0.637195 TACAGGGGAAGGGAGGAGAG 59.363 60.000 0.00 0.00 0.00 3.20
963 991 1.098589 TTACAGGGGAAGGGAGGAGA 58.901 55.000 0.00 0.00 0.00 3.71
964 992 1.840635 CTTTACAGGGGAAGGGAGGAG 59.159 57.143 0.00 0.00 0.00 3.69
965 993 1.966845 CTTTACAGGGGAAGGGAGGA 58.033 55.000 0.00 0.00 0.00 3.71
1179 1207 4.814041 AGGAGGAGGAGGCAGGCC 62.814 72.222 0.97 0.97 0.00 5.19
1799 1833 0.459585 CAATGGTGGCATTGAGCTGC 60.460 55.000 0.00 0.00 43.26 5.25
1800 1834 0.892755 ACAATGGTGGCATTGAGCTG 59.107 50.000 2.69 0.00 43.26 4.24
1801 1835 1.180029 GACAATGGTGGCATTGAGCT 58.820 50.000 2.69 0.00 43.26 4.09
1802 1836 0.889994 TGACAATGGTGGCATTGAGC 59.110 50.000 2.69 0.00 38.09 4.26
1803 1837 2.353011 GGTTGACAATGGTGGCATTGAG 60.353 50.000 2.69 0.00 44.33 3.02
1808 1842 1.532794 GGGGTTGACAATGGTGGCA 60.533 57.895 0.00 0.00 42.77 4.92
1810 1844 1.184970 GGTGGGGTTGACAATGGTGG 61.185 60.000 0.00 0.00 0.00 4.61
1811 1845 0.468958 TGGTGGGGTTGACAATGGTG 60.469 55.000 0.00 0.00 0.00 4.17
1812 1846 0.469144 GTGGTGGGGTTGACAATGGT 60.469 55.000 0.00 0.00 0.00 3.55
1828 1874 0.771127 TTCTTGTCCTCCTTGGGTGG 59.229 55.000 0.00 0.00 37.67 4.61
1851 1897 2.290577 ACCTTGCTCCTCCTGTTTCATC 60.291 50.000 0.00 0.00 0.00 2.92
1864 1913 5.086104 TCCAGTAGTTATTCACCTTGCTC 57.914 43.478 0.00 0.00 0.00 4.26
1926 1976 5.334802 CGTTGAACCTGCAAGAATGATTACA 60.335 40.000 0.00 0.00 34.07 2.41
1968 2020 2.597455 CCAAACAACCCCTTCACATCT 58.403 47.619 0.00 0.00 0.00 2.90
2042 2095 6.019640 CACTTAGCAACAACAAACAAATGGAG 60.020 38.462 0.00 0.00 0.00 3.86
2073 2126 2.071778 TTCAAGCAAAGCCTCCTTGT 57.928 45.000 0.00 0.00 37.72 3.16
2108 2161 3.400054 GGTGAGGAGGTTCCGGGG 61.400 72.222 0.00 0.00 42.75 5.73
2118 2171 4.401519 CAGGACTAGAATTTACGGTGAGGA 59.598 45.833 0.00 0.00 0.00 3.71
2183 2236 7.325660 AGAGTATAATAACGAAAGGACACGA 57.674 36.000 0.00 0.00 0.00 4.35
2250 2304 0.531200 ACTCGCTTAGGTTTCCTCGG 59.469 55.000 0.00 0.00 34.61 4.63
2350 2405 7.705752 TGGTGCATTTACACAATATTATTGCAG 59.294 33.333 14.88 10.84 42.55 4.41
2354 2409 9.585099 CAGTTGGTGCATTTACACAATATTATT 57.415 29.630 0.00 0.00 42.55 1.40
2355 2410 8.196771 CCAGTTGGTGCATTTACACAATATTAT 58.803 33.333 0.00 0.00 42.55 1.28
2356 2411 7.542890 CCAGTTGGTGCATTTACACAATATTA 58.457 34.615 0.00 0.00 42.55 0.98
2378 2433 4.682778 TGGGGATAAAGATTACGACCAG 57.317 45.455 0.00 0.00 0.00 4.00
2411 2469 5.043248 CACACCACTTCTTTGATTTTCCAC 58.957 41.667 0.00 0.00 0.00 4.02
2437 2495 5.011943 TGCTTTGGGTAATTTTCAATCTGCT 59.988 36.000 0.00 0.00 0.00 4.24
2457 2515 5.815581 TGTTCAGGAAATGGTACTATGCTT 58.184 37.500 0.00 0.00 0.00 3.91
2600 2661 4.389687 GCAAAATTTAGCACATGTGGAAGG 59.610 41.667 26.55 1.58 0.00 3.46
2698 2766 7.615403 TCATTTATGAGCATATCAGGTAGGAC 58.385 38.462 0.00 0.00 42.53 3.85
2750 2851 6.405538 TGGATGACTGCCAAAATTTTATTCC 58.594 36.000 2.44 2.78 31.13 3.01
2803 2904 4.819630 CCTCACCAACAGTTTAGTTAAGCA 59.180 41.667 0.00 0.00 0.00 3.91
2850 2951 3.918912 AGGTGGCACCAGGATATATGATT 59.081 43.478 36.28 9.92 41.95 2.57
2851 2952 3.535239 AGGTGGCACCAGGATATATGAT 58.465 45.455 36.28 10.13 41.95 2.45
2852 2953 2.990195 AGGTGGCACCAGGATATATGA 58.010 47.619 36.28 0.00 41.95 2.15
2853 2954 3.795688 AAGGTGGCACCAGGATATATG 57.204 47.619 36.28 0.00 41.95 1.78
2854 2955 3.074538 GGAAAGGTGGCACCAGGATATAT 59.925 47.826 36.28 12.25 41.95 0.86
2855 2956 2.441750 GGAAAGGTGGCACCAGGATATA 59.558 50.000 36.28 0.00 41.95 0.86
2856 2957 1.215423 GGAAAGGTGGCACCAGGATAT 59.785 52.381 36.28 13.83 41.95 1.63
2857 2958 0.623723 GGAAAGGTGGCACCAGGATA 59.376 55.000 36.28 0.00 41.95 2.59
2872 2973 2.260869 GGTGAAGCTGCTGCGGAAA 61.261 57.895 13.72 0.00 45.42 3.13
2873 2974 1.826340 TAGGTGAAGCTGCTGCGGAA 61.826 55.000 13.72 0.00 45.42 4.30
2900 3001 0.541863 AATGGTCAGCTTACCGAGGG 59.458 55.000 12.39 0.00 42.91 4.30
2906 3007 1.812571 CCACACCAATGGTCAGCTTAC 59.187 52.381 0.00 0.00 34.77 2.34
2913 3014 0.968405 ACAATGCCACACCAATGGTC 59.032 50.000 0.00 0.00 42.28 4.02


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

AutoCloner maintained by Alex Coulton.