Multiple sequence alignment - TraesCS1D01G141100

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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 TraesCS1D01G141100 chr1D 100.000 3422 0 0 1 3422 194458246 194454825 0 6320
1 TraesCS1D01G141100 chr1B 95.654 2094 55 7 883 2967 271905200 271907266 0 3330
2 TraesCS1D01G141100 chr1B 91.699 783 38 18 3 778 271904384 271905146 0 1061
3 TraesCS1D01G141100 chr1A 98.095 1785 29 3 887 2670 241984781 241983001 0 3103
4 TraesCS1D01G141100 chr1A 90.677 783 38 19 1 777 241993644 241992891 0 1009
5 TraesCS1D01G141100 chr3B 90.263 647 49 11 2780 3421 43823105 43823742 0 833
6 TraesCS1D01G141100 chr5B 89.645 647 52 8 2780 3421 154032575 154031939 0 809
7 TraesCS1D01G141100 chr5B 89.181 647 55 8 2780 3421 154085692 154085056 0 793
8 TraesCS1D01G141100 chr4D 89.335 647 56 7 2780 3421 342538686 342539324 0 800
9 TraesCS1D01G141100 chr2A 89.335 647 56 7 2780 3421 117352991 117353629 0 800
10 TraesCS1D01G141100 chr6D 89.319 646 56 7 2780 3420 368119086 368118449 0 798
11 TraesCS1D01G141100 chr5A 89.181 647 57 7 2780 3421 18778289 18778927 0 795
12 TraesCS1D01G141100 chr5D 89.026 647 58 7 2780 3421 439298000 439298638 0 789
13 TraesCS1D01G141100 chr6B 88.872 647 58 8 2780 3421 44071946 44071309 0 784


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 TraesCS1D01G141100 chr1D 194454825 194458246 3421 True 6320.0 6320 100.0000 1 3422 1 chr1D.!!$R1 3421
1 TraesCS1D01G141100 chr1B 271904384 271907266 2882 False 2195.5 3330 93.6765 3 2967 2 chr1B.!!$F1 2964
2 TraesCS1D01G141100 chr1A 241983001 241984781 1780 True 3103.0 3103 98.0950 887 2670 1 chr1A.!!$R1 1783
3 TraesCS1D01G141100 chr1A 241992891 241993644 753 True 1009.0 1009 90.6770 1 777 1 chr1A.!!$R2 776
4 TraesCS1D01G141100 chr3B 43823105 43823742 637 False 833.0 833 90.2630 2780 3421 1 chr3B.!!$F1 641
5 TraesCS1D01G141100 chr5B 154031939 154032575 636 True 809.0 809 89.6450 2780 3421 1 chr5B.!!$R1 641
6 TraesCS1D01G141100 chr5B 154085056 154085692 636 True 793.0 793 89.1810 2780 3421 1 chr5B.!!$R2 641
7 TraesCS1D01G141100 chr4D 342538686 342539324 638 False 800.0 800 89.3350 2780 3421 1 chr4D.!!$F1 641
8 TraesCS1D01G141100 chr2A 117352991 117353629 638 False 800.0 800 89.3350 2780 3421 1 chr2A.!!$F1 641
9 TraesCS1D01G141100 chr6D 368118449 368119086 637 True 798.0 798 89.3190 2780 3420 1 chr6D.!!$R1 640
10 TraesCS1D01G141100 chr5A 18778289 18778927 638 False 795.0 795 89.1810 2780 3421 1 chr5A.!!$F1 641
11 TraesCS1D01G141100 chr5D 439298000 439298638 638 False 789.0 789 89.0260 2780 3421 1 chr5D.!!$F1 641
12 TraesCS1D01G141100 chr6B 44071309 44071946 637 True 784.0 784 88.8720 2780 3421 1 chr6B.!!$R1 641

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
924 954 0.034476 AACCCCGTTCCTCTTTCGTC 59.966 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 2663 0.037512 CTGACAGCAGTAGCAGCACT 60.038 55.0 0.0 0.0 45.49 4.4 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
73 74 5.163184 TGGTAAACCACACAGAATCTGGTAA 60.163 40.000 15.38 0.00 42.01 2.85
100 101 3.738282 CGAGCATTTAATCTCCGGAGAAG 59.262 47.826 36.58 21.57 41.36 2.85
126 128 3.512033 AACGAAGAAGAGAGGGATTCG 57.488 47.619 4.28 4.28 46.03 3.34
398 403 3.492353 CCGCCATGGGAGTGGGAT 61.492 66.667 15.13 0.00 39.73 3.85
442 449 2.032981 CAAGTCCACAACCACCTGC 58.967 57.895 0.00 0.00 0.00 4.85
447 454 3.286751 CACAACCACCTGCCACCG 61.287 66.667 0.00 0.00 0.00 4.94
530 537 0.184933 AGATCGGGAGACTGGAGGAG 59.815 60.000 0.00 0.00 44.82 3.69
656 664 4.430765 GAAAGCGACGGCGAGGGA 62.431 66.667 18.90 0.00 46.35 4.20
657 665 4.436998 AAAGCGACGGCGAGGGAG 62.437 66.667 18.90 0.29 46.35 4.30
659 667 4.790962 AGCGACGGCGAGGGAGTA 62.791 66.667 18.90 0.00 46.35 2.59
660 668 4.549516 GCGACGGCGAGGGAGTAC 62.550 72.222 18.90 0.00 40.82 2.73
661 669 3.885521 CGACGGCGAGGGAGTACC 61.886 72.222 16.62 0.00 40.82 3.34
662 670 2.753043 GACGGCGAGGGAGTACCA 60.753 66.667 16.62 0.00 43.89 3.25
663 671 3.061260 GACGGCGAGGGAGTACCAC 62.061 68.421 16.62 0.00 43.89 4.16
664 672 2.754658 CGGCGAGGGAGTACCACT 60.755 66.667 0.00 0.00 43.89 4.00
687 695 3.936372 TGGCACACTACACTAAGTCTC 57.064 47.619 0.00 0.00 0.00 3.36
710 718 3.303406 GTCGCGCTAGTTTATACGGATT 58.697 45.455 5.56 0.00 0.00 3.01
734 742 0.106894 CCCTTCCTAGGCGGATGTTC 59.893 60.000 16.15 0.00 42.70 3.18
742 750 2.264794 GCGGATGTTCGTGACCCT 59.735 61.111 0.00 0.00 0.00 4.34
753 763 1.756665 GTGACCCTAAACCCGGTGT 59.243 57.895 0.00 0.00 30.56 4.16
768 778 2.281517 CGGTGTTTATGGCGGTAATCA 58.718 47.619 0.00 0.00 0.00 2.57
778 788 1.152383 GCGGTAATCAGCTCCGTTCC 61.152 60.000 11.89 0.00 45.11 3.62
779 789 0.870307 CGGTAATCAGCTCCGTTCCG 60.870 60.000 2.73 2.66 39.51 4.30
780 790 0.458669 GGTAATCAGCTCCGTTCCGA 59.541 55.000 0.00 0.00 0.00 4.55
781 791 1.068741 GGTAATCAGCTCCGTTCCGAT 59.931 52.381 0.00 0.00 0.00 4.18
782 792 2.295349 GGTAATCAGCTCCGTTCCGATA 59.705 50.000 0.00 0.00 0.00 2.92
783 793 2.802787 AATCAGCTCCGTTCCGATAG 57.197 50.000 0.00 0.00 0.00 2.08
784 794 1.693627 ATCAGCTCCGTTCCGATAGT 58.306 50.000 0.00 0.00 0.00 2.12
785 795 2.336945 TCAGCTCCGTTCCGATAGTA 57.663 50.000 0.00 0.00 0.00 1.82
786 796 2.860009 TCAGCTCCGTTCCGATAGTAT 58.140 47.619 0.00 0.00 0.00 2.12
787 797 3.220110 TCAGCTCCGTTCCGATAGTATT 58.780 45.455 0.00 0.00 0.00 1.89
788 798 3.635373 TCAGCTCCGTTCCGATAGTATTT 59.365 43.478 0.00 0.00 0.00 1.40
789 799 4.098960 TCAGCTCCGTTCCGATAGTATTTT 59.901 41.667 0.00 0.00 0.00 1.82
790 800 4.809426 CAGCTCCGTTCCGATAGTATTTTT 59.191 41.667 0.00 0.00 0.00 1.94
812 822 6.767524 TTTTTCTCTTTGAAGGTAAGCACA 57.232 33.333 0.00 0.00 35.89 4.57
813 823 6.377327 TTTTCTCTTTGAAGGTAAGCACAG 57.623 37.500 0.00 0.00 35.89 3.66
814 824 4.008074 TCTCTTTGAAGGTAAGCACAGG 57.992 45.455 0.00 0.00 0.00 4.00
815 825 2.485814 CTCTTTGAAGGTAAGCACAGGC 59.514 50.000 0.00 0.00 41.61 4.85
816 826 2.158682 TCTTTGAAGGTAAGCACAGGCA 60.159 45.455 0.00 0.00 44.61 4.75
817 827 1.604604 TTGAAGGTAAGCACAGGCAC 58.395 50.000 0.00 0.00 44.61 5.01
818 828 0.602638 TGAAGGTAAGCACAGGCACG 60.603 55.000 0.00 0.00 44.61 5.34
819 829 1.298859 GAAGGTAAGCACAGGCACGG 61.299 60.000 0.00 0.00 44.61 4.94
820 830 2.746277 GGTAAGCACAGGCACGGG 60.746 66.667 0.00 0.00 44.61 5.28
821 831 3.431725 GTAAGCACAGGCACGGGC 61.432 66.667 0.00 0.00 44.61 6.13
822 832 3.636231 TAAGCACAGGCACGGGCT 61.636 61.111 10.74 1.05 44.61 5.19
832 842 4.003788 CACGGGCTGGGAACGAGT 62.004 66.667 0.00 0.00 0.00 4.18
833 843 4.003788 ACGGGCTGGGAACGAGTG 62.004 66.667 0.00 0.00 0.00 3.51
834 844 4.760047 CGGGCTGGGAACGAGTGG 62.760 72.222 0.00 0.00 0.00 4.00
835 845 3.319198 GGGCTGGGAACGAGTGGA 61.319 66.667 0.00 0.00 0.00 4.02
836 846 2.047179 GGCTGGGAACGAGTGGAC 60.047 66.667 0.00 0.00 0.00 4.02
837 847 2.741092 GCTGGGAACGAGTGGACA 59.259 61.111 0.00 0.00 0.00 4.02
838 848 1.296715 GCTGGGAACGAGTGGACAT 59.703 57.895 0.00 0.00 0.00 3.06
839 849 1.021390 GCTGGGAACGAGTGGACATG 61.021 60.000 0.00 0.00 0.00 3.21
840 850 0.391661 CTGGGAACGAGTGGACATGG 60.392 60.000 0.00 0.00 0.00 3.66
841 851 1.745489 GGGAACGAGTGGACATGGC 60.745 63.158 0.00 0.00 0.00 4.40
842 852 2.100631 GGAACGAGTGGACATGGCG 61.101 63.158 0.00 0.00 0.00 5.69
843 853 2.740714 GAACGAGTGGACATGGCGC 61.741 63.158 0.00 0.00 0.00 6.53
844 854 4.760047 ACGAGTGGACATGGCGCC 62.760 66.667 22.73 22.73 0.00 6.53
846 856 4.760047 GAGTGGACATGGCGCCGT 62.760 66.667 23.90 20.88 0.00 5.68
847 857 4.329545 AGTGGACATGGCGCCGTT 62.330 61.111 21.21 10.89 0.00 4.44
848 858 3.799755 GTGGACATGGCGCCGTTC 61.800 66.667 21.21 18.80 0.00 3.95
860 870 0.108329 CGCCGTTCTGGTGGTTAGAT 60.108 55.000 0.00 0.00 44.97 1.98
861 871 1.369625 GCCGTTCTGGTGGTTAGATG 58.630 55.000 0.00 0.00 41.21 2.90
862 872 2.012051 GCCGTTCTGGTGGTTAGATGG 61.012 57.143 0.00 0.00 41.21 3.51
863 873 1.278127 CCGTTCTGGTGGTTAGATGGT 59.722 52.381 0.00 0.00 0.00 3.55
864 874 2.346803 CGTTCTGGTGGTTAGATGGTG 58.653 52.381 0.00 0.00 0.00 4.17
865 875 2.084546 GTTCTGGTGGTTAGATGGTGC 58.915 52.381 0.00 0.00 0.00 5.01
870 893 3.573491 GGTTAGATGGTGCCGCGC 61.573 66.667 0.00 0.00 0.00 6.86
903 933 2.070783 GGCCGAATCAACGACTTAACA 58.929 47.619 0.00 0.00 35.09 2.41
919 949 1.137697 AACAGAACCCCGTTCCTCTT 58.862 50.000 0.98 0.00 42.85 2.85
920 950 1.137697 ACAGAACCCCGTTCCTCTTT 58.862 50.000 0.98 0.00 42.85 2.52
922 952 0.320697 AGAACCCCGTTCCTCTTTCG 59.679 55.000 0.98 0.00 42.85 3.46
924 954 0.034476 AACCCCGTTCCTCTTTCGTC 59.966 55.000 0.00 0.00 0.00 4.20
2298 2328 0.716591 TGGAGAAGGGAGGGAAGCTA 59.283 55.000 0.00 0.00 0.00 3.32
2394 2424 1.279271 CCACCCAAAGACGAGGAAGAT 59.721 52.381 0.00 0.00 0.00 2.40
2517 2553 6.813649 TCTCTTCACAGCAGTACATGAATAAC 59.186 38.462 0.00 0.00 31.00 1.89
2544 2580 7.654923 AGAATGCAATTTTCCTTCTTTGTTCTC 59.345 33.333 0.00 0.00 36.07 2.87
2551 2587 4.771114 TCCTTCTTTGTTCTCCAAGTCA 57.229 40.909 0.00 0.00 33.75 3.41
2581 2641 0.890996 GGCAGGTGCAGTGCTTTAGT 60.891 55.000 17.60 0.00 44.36 2.24
2582 2642 1.610624 GGCAGGTGCAGTGCTTTAGTA 60.611 52.381 17.60 0.00 44.36 1.82
2583 2643 2.359900 GCAGGTGCAGTGCTTTAGTAT 58.640 47.619 17.60 0.00 41.59 2.12
2584 2644 2.749621 GCAGGTGCAGTGCTTTAGTATT 59.250 45.455 17.60 0.00 41.59 1.89
2585 2645 3.938963 GCAGGTGCAGTGCTTTAGTATTA 59.061 43.478 17.60 0.00 41.59 0.98
2586 2646 4.394920 GCAGGTGCAGTGCTTTAGTATTAA 59.605 41.667 17.60 0.00 41.59 1.40
2587 2647 5.106317 GCAGGTGCAGTGCTTTAGTATTAAA 60.106 40.000 17.60 0.00 41.59 1.52
2588 2648 6.314784 CAGGTGCAGTGCTTTAGTATTAAAC 58.685 40.000 17.60 0.80 0.00 2.01
2589 2649 6.001460 AGGTGCAGTGCTTTAGTATTAAACA 58.999 36.000 17.60 0.00 0.00 2.83
2590 2650 6.149474 AGGTGCAGTGCTTTAGTATTAAACAG 59.851 38.462 17.60 0.00 0.00 3.16
2591 2651 6.314784 GTGCAGTGCTTTAGTATTAAACAGG 58.685 40.000 17.60 0.00 0.00 4.00
2592 2652 6.001460 TGCAGTGCTTTAGTATTAAACAGGT 58.999 36.000 17.60 0.00 0.00 4.00
2593 2653 6.072728 TGCAGTGCTTTAGTATTAAACAGGTG 60.073 38.462 17.60 0.00 0.00 4.00
2594 2654 6.314784 CAGTGCTTTAGTATTAAACAGGTGC 58.685 40.000 0.00 0.00 0.00 5.01
2595 2655 6.001460 AGTGCTTTAGTATTAAACAGGTGCA 58.999 36.000 0.00 0.00 0.00 4.57
2596 2656 6.149474 AGTGCTTTAGTATTAAACAGGTGCAG 59.851 38.462 0.00 0.00 30.43 4.41
2597 2657 6.001460 TGCTTTAGTATTAAACAGGTGCAGT 58.999 36.000 0.00 0.00 0.00 4.40
2598 2658 6.072728 TGCTTTAGTATTAAACAGGTGCAGTG 60.073 38.462 0.00 0.00 0.00 3.66
2599 2659 5.873179 TTAGTATTAAACAGGTGCAGTGC 57.127 39.130 8.58 8.58 0.00 4.40
2600 2660 4.021102 AGTATTAAACAGGTGCAGTGCT 57.979 40.909 17.60 0.00 0.00 4.40
2601 2661 4.398319 AGTATTAAACAGGTGCAGTGCTT 58.602 39.130 17.60 3.36 0.00 3.91
2602 2662 4.827284 AGTATTAAACAGGTGCAGTGCTTT 59.173 37.500 17.60 10.37 0.00 3.51
2603 2663 6.001460 AGTATTAAACAGGTGCAGTGCTTTA 58.999 36.000 17.60 9.35 0.00 1.85
2604 2664 4.829064 TTAAACAGGTGCAGTGCTTTAG 57.171 40.909 17.60 6.66 0.00 1.85
2640 2701 6.623549 GCTGTCAGTGCTTATATTTGCTGAAA 60.624 38.462 0.93 0.00 35.20 2.69
2659 2720 5.428253 TGAAATCAGCTGGTTAGATACACC 58.572 41.667 13.78 0.00 34.52 4.16
2693 2756 6.087423 TCACAAAACACGATTTATCAATTGCG 59.913 34.615 0.00 0.00 0.00 4.85
2696 2759 7.060174 ACAAAACACGATTTATCAATTGCGTAC 59.940 33.333 0.00 0.00 0.00 3.67
2697 2760 5.151632 ACACGATTTATCAATTGCGTACC 57.848 39.130 0.00 0.00 0.00 3.34
2763 2826 1.730064 TCAAAGATAAGACGGCGCAAC 59.270 47.619 10.83 0.00 0.00 4.17
2816 2879 0.321653 ATTCAGCGGTTCAGACCCAC 60.322 55.000 0.00 0.00 43.42 4.61
2925 2989 0.597568 CAAACGGCCTTCATGCAAGA 59.402 50.000 0.00 0.00 33.29 3.02
2927 2991 0.883833 AACGGCCTTCATGCAAGAAG 59.116 50.000 21.87 21.87 43.60 2.85
2944 3008 5.877564 GCAAGAAGGGAATATACTAGATGGC 59.122 44.000 0.00 0.00 0.00 4.40
3036 3102 6.545666 TGACTTTGAAAAAGCCTATGACAAGA 59.454 34.615 0.00 0.00 0.00 3.02
3038 3104 7.955918 ACTTTGAAAAAGCCTATGACAAGATT 58.044 30.769 0.00 0.00 0.00 2.40
3040 3106 9.565213 CTTTGAAAAAGCCTATGACAAGATTAG 57.435 33.333 0.00 0.00 0.00 1.73
3075 3141 5.576563 TCAACAGACCCTAAGGATGAAAA 57.423 39.130 0.00 0.00 36.73 2.29
3094 3160 5.475220 TGAAAAGTTTCTCCGATAAATGGCA 59.525 36.000 5.45 0.00 38.02 4.92
3121 3187 6.325919 GTGGATCCACAATTTTGTAACTGA 57.674 37.500 35.21 0.00 45.53 3.41
3132 3198 7.554835 ACAATTTTGTAACTGAAGGTAGTGTGA 59.445 33.333 0.00 0.00 40.16 3.58
3164 3230 6.236409 AGTCAATGATGATGTAGGCCATTAG 58.764 40.000 5.01 0.00 38.01 1.73
3166 3232 6.148480 GTCAATGATGATGTAGGCCATTAGTC 59.852 42.308 5.01 0.00 38.01 2.59
3170 3236 4.672587 TGATGTAGGCCATTAGTCTCAC 57.327 45.455 5.01 0.00 32.56 3.51
3175 3241 3.059352 AGGCCATTAGTCTCACACAAC 57.941 47.619 5.01 0.00 0.00 3.32
3181 3247 5.008613 GCCATTAGTCTCACACAACAAAAGA 59.991 40.000 0.00 0.00 0.00 2.52
3193 3259 2.875933 CAACAAAAGAACTACGGCAGGA 59.124 45.455 0.00 0.00 0.00 3.86
3198 3264 0.824759 AGAACTACGGCAGGATGACC 59.175 55.000 0.00 0.00 46.22 4.02
3206 3272 1.639635 GGCAGGATGACCCCATGTCT 61.640 60.000 0.00 0.00 39.24 3.41
3209 3275 0.695803 AGGATGACCCCATGTCTCCC 60.696 60.000 0.00 0.00 44.75 4.30
3238 3305 2.319136 AACACCGTTGCTGACTGTTA 57.681 45.000 0.00 0.00 28.26 2.41
3241 3308 0.393077 ACCGTTGCTGACTGTTAGCT 59.607 50.000 22.68 2.15 41.66 3.32
3247 3314 5.340803 CGTTGCTGACTGTTAGCTATTCTA 58.659 41.667 22.68 1.46 41.66 2.10
3299 3366 1.899814 CAGGAGTAGTGCCACACCTTA 59.100 52.381 0.00 0.00 37.40 2.69
3304 3371 2.910319 AGTAGTGCCACACCTTATGGAA 59.090 45.455 0.81 0.00 39.87 3.53
3305 3372 2.496899 AGTGCCACACCTTATGGAAG 57.503 50.000 0.81 0.00 39.87 3.46
3306 3373 1.705186 AGTGCCACACCTTATGGAAGT 59.295 47.619 0.81 0.00 39.87 3.01
3307 3374 2.910319 AGTGCCACACCTTATGGAAGTA 59.090 45.455 0.81 0.00 39.87 2.24
3308 3375 3.055094 AGTGCCACACCTTATGGAAGTAG 60.055 47.826 0.81 0.00 39.87 2.57
3309 3376 3.055385 GTGCCACACCTTATGGAAGTAGA 60.055 47.826 0.81 0.00 39.87 2.59
3337 3404 6.712547 GTGGCCTCTCTATTTTACAATATGCT 59.287 38.462 3.32 0.00 0.00 3.79
3386 3454 0.955919 CTGGACAAGGCTCGAAACCC 60.956 60.000 0.56 0.00 0.00 4.11
3421 3489 0.385974 AGCGTTTGAGCAAATGTCGC 60.386 50.000 16.59 16.59 40.94 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 3.374058 CCGGAGATTAAATGCTCGTTTGT 59.626 43.478 0.00 0.00 31.95 2.83
100 101 5.340439 TCCCTCTCTTCTTCGTTTTATCC 57.660 43.478 0.00 0.00 0.00 2.59
126 128 2.579787 CGACCGATCTGTGTCGCC 60.580 66.667 13.76 0.00 46.41 5.54
183 188 7.088272 CCTGCTTGGGTTTAAGTTATTGTTAC 58.912 38.462 0.00 0.00 0.00 2.50
184 189 6.294843 GCCTGCTTGGGTTTAAGTTATTGTTA 60.295 38.462 0.00 0.00 36.00 2.41
185 190 5.510690 GCCTGCTTGGGTTTAAGTTATTGTT 60.511 40.000 0.00 0.00 36.00 2.83
187 192 4.021544 TGCCTGCTTGGGTTTAAGTTATTG 60.022 41.667 0.00 0.00 36.00 1.90
447 454 1.139308 TTGTTGTGCACTGTGCTGC 59.861 52.632 30.43 22.91 45.31 5.25
464 471 0.601841 CGTAGGGTTCACGCCTTGTT 60.602 55.000 0.00 0.00 31.94 2.83
465 472 1.005394 CGTAGGGTTCACGCCTTGT 60.005 57.895 0.00 0.00 31.94 3.16
530 537 3.490348 CTCTCCTCCTCTCATCTCTTCC 58.510 54.545 0.00 0.00 0.00 3.46
583 590 4.657814 AGAAGAATAAAGGCCTTGTGGA 57.342 40.909 21.33 5.37 34.57 4.02
661 669 4.022242 ACTTAGTGTAGTGTGCCACTAGTG 60.022 45.833 16.34 16.34 45.88 2.74
662 670 4.150359 ACTTAGTGTAGTGTGCCACTAGT 58.850 43.478 13.35 7.50 45.88 2.57
663 671 4.459685 AGACTTAGTGTAGTGTGCCACTAG 59.540 45.833 13.35 7.00 45.88 2.57
664 672 4.404640 AGACTTAGTGTAGTGTGCCACTA 58.595 43.478 10.03 10.03 43.46 2.74
675 683 0.723414 CGCGACCGAGACTTAGTGTA 59.277 55.000 0.00 0.00 36.29 2.90
676 684 1.500844 CGCGACCGAGACTTAGTGT 59.499 57.895 0.00 0.00 36.29 3.55
681 689 1.584380 AACTAGCGCGACCGAGACTT 61.584 55.000 12.10 0.00 36.29 3.01
687 695 1.040232 CGTATAAACTAGCGCGACCG 58.960 55.000 12.10 0.00 37.57 4.79
734 742 1.375013 CACCGGGTTTAGGGTCACG 60.375 63.158 6.32 0.00 33.23 4.35
753 763 2.805295 CGGAGCTGATTACCGCCATAAA 60.805 50.000 0.00 0.00 40.19 1.40
789 799 6.183360 CCTGTGCTTACCTTCAAAGAGAAAAA 60.183 38.462 0.00 0.00 35.40 1.94
790 800 5.299279 CCTGTGCTTACCTTCAAAGAGAAAA 59.701 40.000 0.00 0.00 35.40 2.29
791 801 4.821805 CCTGTGCTTACCTTCAAAGAGAAA 59.178 41.667 0.00 0.00 35.40 2.52
792 802 4.389374 CCTGTGCTTACCTTCAAAGAGAA 58.611 43.478 0.00 0.00 34.41 2.87
793 803 3.807209 GCCTGTGCTTACCTTCAAAGAGA 60.807 47.826 0.00 0.00 33.53 3.10
794 804 2.485814 GCCTGTGCTTACCTTCAAAGAG 59.514 50.000 0.00 0.00 33.53 2.85
795 805 2.158682 TGCCTGTGCTTACCTTCAAAGA 60.159 45.455 0.00 0.00 38.71 2.52
796 806 2.030805 GTGCCTGTGCTTACCTTCAAAG 60.031 50.000 0.00 0.00 38.71 2.77
797 807 1.953686 GTGCCTGTGCTTACCTTCAAA 59.046 47.619 0.00 0.00 38.71 2.69
798 808 1.604604 GTGCCTGTGCTTACCTTCAA 58.395 50.000 0.00 0.00 38.71 2.69
799 809 0.602638 CGTGCCTGTGCTTACCTTCA 60.603 55.000 0.00 0.00 38.71 3.02
800 810 1.298859 CCGTGCCTGTGCTTACCTTC 61.299 60.000 0.00 0.00 38.71 3.46
801 811 1.302511 CCGTGCCTGTGCTTACCTT 60.303 57.895 0.00 0.00 38.71 3.50
802 812 2.347490 CCGTGCCTGTGCTTACCT 59.653 61.111 0.00 0.00 38.71 3.08
803 813 2.746277 CCCGTGCCTGTGCTTACC 60.746 66.667 0.00 0.00 38.71 2.85
804 814 3.431725 GCCCGTGCCTGTGCTTAC 61.432 66.667 0.00 0.00 38.71 2.34
805 815 3.636231 AGCCCGTGCCTGTGCTTA 61.636 61.111 0.00 0.00 38.69 3.09
815 825 4.003788 ACTCGTTCCCAGCCCGTG 62.004 66.667 0.00 0.00 0.00 4.94
816 826 4.003788 CACTCGTTCCCAGCCCGT 62.004 66.667 0.00 0.00 0.00 5.28
817 827 4.760047 CCACTCGTTCCCAGCCCG 62.760 72.222 0.00 0.00 0.00 6.13
818 828 3.319198 TCCACTCGTTCCCAGCCC 61.319 66.667 0.00 0.00 0.00 5.19
819 829 2.047179 GTCCACTCGTTCCCAGCC 60.047 66.667 0.00 0.00 0.00 4.85
820 830 1.021390 CATGTCCACTCGTTCCCAGC 61.021 60.000 0.00 0.00 0.00 4.85
821 831 0.391661 CCATGTCCACTCGTTCCCAG 60.392 60.000 0.00 0.00 0.00 4.45
822 832 1.676968 CCATGTCCACTCGTTCCCA 59.323 57.895 0.00 0.00 0.00 4.37
823 833 1.745489 GCCATGTCCACTCGTTCCC 60.745 63.158 0.00 0.00 0.00 3.97
824 834 2.100631 CGCCATGTCCACTCGTTCC 61.101 63.158 0.00 0.00 0.00 3.62
825 835 2.740714 GCGCCATGTCCACTCGTTC 61.741 63.158 0.00 0.00 0.00 3.95
826 836 2.742372 GCGCCATGTCCACTCGTT 60.742 61.111 0.00 0.00 0.00 3.85
827 837 4.760047 GGCGCCATGTCCACTCGT 62.760 66.667 24.80 0.00 0.00 4.18
829 839 4.760047 ACGGCGCCATGTCCACTC 62.760 66.667 28.98 0.00 0.00 3.51
830 840 4.329545 AACGGCGCCATGTCCACT 62.330 61.111 28.98 0.00 0.00 4.00
831 841 3.799755 GAACGGCGCCATGTCCAC 61.800 66.667 28.98 8.62 0.00 4.02
832 842 4.015406 AGAACGGCGCCATGTCCA 62.015 61.111 28.98 0.00 0.00 4.02
833 843 3.499737 CAGAACGGCGCCATGTCC 61.500 66.667 28.98 4.60 0.00 4.02
834 844 3.499737 CCAGAACGGCGCCATGTC 61.500 66.667 28.98 19.47 0.00 3.06
835 845 4.329545 ACCAGAACGGCGCCATGT 62.330 61.111 28.98 14.92 39.03 3.21
836 846 3.803082 CACCAGAACGGCGCCATG 61.803 66.667 28.98 18.24 39.03 3.66
839 849 3.887335 TAACCACCAGAACGGCGCC 62.887 63.158 19.07 19.07 39.03 6.53
840 850 2.357760 TAACCACCAGAACGGCGC 60.358 61.111 6.90 0.00 39.03 6.53
841 851 0.108329 ATCTAACCACCAGAACGGCG 60.108 55.000 4.80 4.80 39.03 6.46
842 852 1.369625 CATCTAACCACCAGAACGGC 58.630 55.000 0.00 0.00 39.03 5.68
843 853 1.278127 ACCATCTAACCACCAGAACGG 59.722 52.381 0.00 0.00 42.50 4.44
844 854 2.346803 CACCATCTAACCACCAGAACG 58.653 52.381 0.00 0.00 0.00 3.95
845 855 2.084546 GCACCATCTAACCACCAGAAC 58.915 52.381 0.00 0.00 0.00 3.01
846 856 1.004277 GGCACCATCTAACCACCAGAA 59.996 52.381 0.00 0.00 0.00 3.02
847 857 0.618458 GGCACCATCTAACCACCAGA 59.382 55.000 0.00 0.00 0.00 3.86
848 858 0.744414 CGGCACCATCTAACCACCAG 60.744 60.000 0.00 0.00 0.00 4.00
860 870 2.560119 AAATTCAAGCGCGGCACCA 61.560 52.632 8.83 0.00 0.00 4.17
861 871 2.088178 CAAATTCAAGCGCGGCACC 61.088 57.895 8.83 0.00 0.00 5.01
862 872 2.088178 CCAAATTCAAGCGCGGCAC 61.088 57.895 8.83 0.00 0.00 5.01
863 873 2.257980 CCAAATTCAAGCGCGGCA 59.742 55.556 8.83 0.00 0.00 5.69
864 874 3.181290 GCCAAATTCAAGCGCGGC 61.181 61.111 8.83 1.55 0.00 6.53
865 875 2.875711 CGCCAAATTCAAGCGCGG 60.876 61.111 8.83 0.00 43.72 6.46
870 893 1.872197 TTCGGCCCGCCAAATTCAAG 61.872 55.000 6.52 0.00 35.37 3.02
883 906 2.070783 TGTTAAGTCGTTGATTCGGCC 58.929 47.619 0.00 0.00 35.98 6.13
903 933 0.320697 CGAAAGAGGAACGGGGTTCT 59.679 55.000 8.25 0.00 41.70 3.01
919 949 3.664888 TCTCGGGGAGGGGACGAA 61.665 66.667 0.00 0.00 36.08 3.85
920 950 4.437587 GTCTCGGGGAGGGGACGA 62.438 72.222 0.00 0.00 35.14 4.20
922 952 4.437587 TCGTCTCGGGGAGGGGAC 62.438 72.222 0.00 0.00 0.00 4.46
924 954 4.124943 TCTCGTCTCGGGGAGGGG 62.125 72.222 0.00 0.00 0.00 4.79
1091 1121 2.577059 CGGCGATGGTGTAGGTGT 59.423 61.111 0.00 0.00 0.00 4.16
1902 1932 2.757917 GCCTCGAGCTCCTCCACT 60.758 66.667 6.99 0.00 38.99 4.00
2298 2328 2.121963 TTGCCCCTCTCCACCACT 60.122 61.111 0.00 0.00 0.00 4.00
2517 2553 7.440255 AGAACAAAGAAGGAAAATTGCATTCTG 59.560 33.333 1.20 0.00 30.90 3.02
2544 2580 4.142093 CCTGCCAATTTTCCTATGACTTGG 60.142 45.833 0.00 0.00 36.94 3.61
2551 2587 2.762327 CTGCACCTGCCAATTTTCCTAT 59.238 45.455 0.00 0.00 41.18 2.57
2581 2641 6.001460 ACTAAAGCACTGCACCTGTTTAATA 58.999 36.000 3.30 0.00 0.00 0.98
2582 2642 4.827284 ACTAAAGCACTGCACCTGTTTAAT 59.173 37.500 3.30 0.00 0.00 1.40
2583 2643 4.036262 CACTAAAGCACTGCACCTGTTTAA 59.964 41.667 3.30 0.00 0.00 1.52
2584 2644 3.563808 CACTAAAGCACTGCACCTGTTTA 59.436 43.478 3.30 0.00 0.00 2.01
2585 2645 2.358898 CACTAAAGCACTGCACCTGTTT 59.641 45.455 3.30 0.00 0.00 2.83
2586 2646 1.949525 CACTAAAGCACTGCACCTGTT 59.050 47.619 3.30 0.00 0.00 3.16
2587 2647 1.597742 CACTAAAGCACTGCACCTGT 58.402 50.000 3.30 0.00 0.00 4.00
2588 2648 0.239347 GCACTAAAGCACTGCACCTG 59.761 55.000 3.30 0.00 0.00 4.00
2589 2649 0.109342 AGCACTAAAGCACTGCACCT 59.891 50.000 3.30 0.00 36.85 4.00
2590 2650 0.239347 CAGCACTAAAGCACTGCACC 59.761 55.000 3.30 0.00 36.85 5.01
2591 2651 3.761481 CAGCACTAAAGCACTGCAC 57.239 52.632 3.30 0.00 36.85 4.57
2594 2654 2.414481 CAGTAGCAGCACTAAAGCACTG 59.586 50.000 0.00 0.00 36.85 3.66
2595 2655 2.693069 CAGTAGCAGCACTAAAGCACT 58.307 47.619 0.00 0.00 36.85 4.40
2596 2656 1.129437 GCAGTAGCAGCACTAAAGCAC 59.871 52.381 0.00 0.00 41.58 4.40
2597 2657 1.002430 AGCAGTAGCAGCACTAAAGCA 59.998 47.619 0.00 0.00 45.49 3.91
2598 2658 1.396301 CAGCAGTAGCAGCACTAAAGC 59.604 52.381 0.00 0.00 45.49 3.51
2599 2659 2.670414 GACAGCAGTAGCAGCACTAAAG 59.330 50.000 0.00 0.00 45.49 1.85
2600 2660 2.037121 TGACAGCAGTAGCAGCACTAAA 59.963 45.455 0.00 0.00 45.49 1.85
2601 2661 1.618343 TGACAGCAGTAGCAGCACTAA 59.382 47.619 0.00 0.00 45.49 2.24
2602 2662 1.203287 CTGACAGCAGTAGCAGCACTA 59.797 52.381 0.00 0.00 45.49 2.74
2603 2663 0.037512 CTGACAGCAGTAGCAGCACT 60.038 55.000 0.00 0.00 45.49 4.40
2604 2664 2.453843 CTGACAGCAGTAGCAGCAC 58.546 57.895 0.00 0.00 45.49 4.40
2640 2701 3.384168 TGGGTGTATCTAACCAGCTGAT 58.616 45.455 17.39 6.23 39.65 2.90
2693 2756 3.257624 CCGGGTACATAAGATGGAGGTAC 59.742 52.174 0.00 0.00 34.20 3.34
2696 2759 2.299297 GTCCGGGTACATAAGATGGAGG 59.701 54.545 0.00 0.00 33.60 4.30
2697 2760 2.030185 CGTCCGGGTACATAAGATGGAG 60.030 54.545 0.00 0.00 33.60 3.86
2790 2853 1.328680 CTGAACCGCTGAATCCATTCG 59.671 52.381 0.00 0.00 39.62 3.34
2816 2879 4.202441 AGCTAACATTAAGGAGTGGCATG 58.798 43.478 0.00 0.00 0.00 4.06
2925 2989 6.254522 ACTACGCCATCTAGTATATTCCCTT 58.745 40.000 0.00 0.00 0.00 3.95
2927 2991 7.636150 TTACTACGCCATCTAGTATATTCCC 57.364 40.000 0.00 0.00 0.00 3.97
2944 3008 3.643763 GGTCTCATGCAGGATTACTACG 58.356 50.000 0.00 0.00 0.00 3.51
3023 3089 4.040755 ACCACCTAATCTTGTCATAGGCT 58.959 43.478 0.00 0.00 39.89 4.58
3026 3092 6.763610 GGAAAGACCACCTAATCTTGTCATAG 59.236 42.308 0.00 0.00 35.34 2.23
3036 3102 5.073144 TCTGTTGAAGGAAAGACCACCTAAT 59.927 40.000 0.00 0.00 42.04 1.73
3038 3104 3.971305 TCTGTTGAAGGAAAGACCACCTA 59.029 43.478 0.00 0.00 42.04 3.08
3040 3106 2.879026 GTCTGTTGAAGGAAAGACCACC 59.121 50.000 0.00 0.00 42.04 4.61
3075 3141 3.279434 GGTGCCATTTATCGGAGAAACT 58.721 45.455 0.00 0.00 43.58 2.66
3094 3160 3.575805 ACAAAATTGTGGATCCACTGGT 58.424 40.909 37.92 22.75 46.30 4.00
3121 3187 4.102524 TGACTTTGATGGTCACACTACCTT 59.897 41.667 0.00 0.00 40.44 3.50
3132 3198 6.544931 CCTACATCATCATTGACTTTGATGGT 59.455 38.462 23.07 15.13 46.75 3.55
3164 3230 5.490213 CGTAGTTCTTTTGTTGTGTGAGAC 58.510 41.667 0.00 0.00 0.00 3.36
3166 3232 4.785341 GCCGTAGTTCTTTTGTTGTGTGAG 60.785 45.833 0.00 0.00 0.00 3.51
3170 3236 3.548014 CCTGCCGTAGTTCTTTTGTTGTG 60.548 47.826 0.00 0.00 0.00 3.33
3175 3241 3.125316 GTCATCCTGCCGTAGTTCTTTTG 59.875 47.826 0.00 0.00 0.00 2.44
3181 3247 1.623542 GGGGTCATCCTGCCGTAGTT 61.624 60.000 0.00 0.00 35.33 2.24
3206 3272 4.082679 GCAACGGTGTTAAATAACATGGGA 60.083 41.667 0.66 0.00 46.56 4.37
3209 3275 5.567534 GTCAGCAACGGTGTTAAATAACATG 59.432 40.000 0.66 7.79 46.56 3.21
3223 3289 2.363788 TAGCTAACAGTCAGCAACGG 57.636 50.000 0.00 0.00 41.66 4.44
3224 3290 4.177026 AGAATAGCTAACAGTCAGCAACG 58.823 43.478 0.00 0.00 41.66 4.10
3238 3305 1.795286 GCGCGCTCAATTAGAATAGCT 59.205 47.619 26.67 0.00 32.73 3.32
3241 3308 2.232756 TGGCGCGCTCAATTAGAATA 57.767 45.000 32.29 0.00 0.00 1.75
3247 3314 3.332493 CTGCTTGGCGCGCTCAATT 62.332 57.895 32.29 0.00 43.27 2.32
3299 3366 1.771255 GAGGCCACCATCTACTTCCAT 59.229 52.381 5.01 0.00 0.00 3.41
3304 3371 3.913370 ATAGAGAGGCCACCATCTACT 57.087 47.619 5.01 1.60 30.60 2.57
3305 3372 4.965200 AAATAGAGAGGCCACCATCTAC 57.035 45.455 5.01 0.00 30.60 2.59
3306 3373 5.903010 TGTAAAATAGAGAGGCCACCATCTA 59.097 40.000 5.01 7.11 31.77 1.98
3307 3374 4.721776 TGTAAAATAGAGAGGCCACCATCT 59.278 41.667 5.01 4.81 0.00 2.90
3308 3375 5.036117 TGTAAAATAGAGAGGCCACCATC 57.964 43.478 5.01 0.00 0.00 3.51
3309 3376 5.450818 TTGTAAAATAGAGAGGCCACCAT 57.549 39.130 5.01 0.00 0.00 3.55
3337 3404 9.941325 ATGTTCATAAAAAGAATTGTGCCATTA 57.059 25.926 0.00 0.00 0.00 1.90
3342 3409 9.362539 AGATCATGTTCATAAAAAGAATTGTGC 57.637 29.630 6.55 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.