Multiple sequence alignment - TraesCS3D01G040100

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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 TraesCS3D01G040100 chr3D 100.000 2939 0 0 1 2939 15330494 15333432 0.000000e+00 5428.0
1 TraesCS3D01G040100 chr3D 79.783 920 161 17 1053 1960 15916606 15917512 0.000000e+00 645.0
2 TraesCS3D01G040100 chr3D 100.000 45 0 0 2701 2745 15333156 15333200 1.880000e-12 84.2
3 TraesCS3D01G040100 chr3D 100.000 45 0 0 2663 2707 15333194 15333238 1.880000e-12 84.2
4 TraesCS3D01G040100 chr3A 90.782 1790 140 19 916 2694 20966383 20964608 0.000000e+00 2368.0
5 TraesCS3D01G040100 chr3A 91.039 1261 84 13 677 1924 21066508 21065264 0.000000e+00 1676.0
6 TraesCS3D01G040100 chr3A 91.505 930 61 13 665 1584 20990160 20989239 0.000000e+00 1264.0
7 TraesCS3D01G040100 chr3A 92.956 653 40 4 3 649 21067487 21066835 0.000000e+00 946.0
8 TraesCS3D01G040100 chr3A 88.660 776 85 3 1922 2696 21065171 21064398 0.000000e+00 942.0
9 TraesCS3D01G040100 chr3A 79.912 911 163 12 1022 1926 20727275 20726379 0.000000e+00 651.0
10 TraesCS3D01G040100 chr3A 88.063 444 34 9 1576 2006 20973501 20973064 2.610000e-140 508.0
11 TraesCS3D01G040100 chr3A 94.142 239 9 2 2701 2939 21064431 21064198 2.790000e-95 359.0
12 TraesCS3D01G040100 chr3A 90.171 234 12 3 660 891 20972393 20972169 7.970000e-76 294.0
13 TraesCS3D01G040100 chr3A 94.624 93 4 1 558 649 21066773 21066681 3.050000e-30 143.0
14 TraesCS3D01G040100 chr3B 89.379 838 66 14 676 1509 22443450 22444268 0.000000e+00 1033.0
15 TraesCS3D01G040100 chr3B 90.013 791 52 14 1505 2269 22449585 22450374 0.000000e+00 998.0
16 TraesCS3D01G040100 chr3B 79.701 936 170 15 1029 1957 22831273 22832195 0.000000e+00 658.0
17 TraesCS3D01G040100 chr3B 84.812 665 63 23 3 649 22205239 22205883 4.130000e-178 634.0
18 TraesCS3D01G040100 chr3B 79.114 948 164 21 1022 1960 22802683 22803605 8.940000e-175 623.0
19 TraesCS3D01G040100 chr3B 78.970 913 166 20 1063 1960 22784747 22785648 1.510000e-167 599.0
20 TraesCS3D01G040100 chr3B 78.168 939 190 10 1027 1960 22674904 22675832 4.220000e-163 584.0
21 TraesCS3D01G040100 chr3B 84.673 398 46 9 2306 2697 22450371 22450759 1.650000e-102 383.0
22 TraesCS3D01G040100 chr3B 93.776 241 8 3 2701 2939 22450725 22450960 3.600000e-94 355.0
23 TraesCS3D01G040100 chr3B 91.875 160 10 2 665 821 22443033 22443192 1.370000e-53 220.0
24 TraesCS3D01G040100 chr5D 98.044 409 4 2 649 1053 398786378 398785970 0.000000e+00 708.0
25 TraesCS3D01G040100 chr6B 84.189 487 75 1 1031 1517 707804075 707804559 3.430000e-129 472.0


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 TraesCS3D01G040100 chr3D 15330494 15333432 2938 False 1865.466667 5428 100.000000 1 2939 3 chr3D.!!$F2 2938
1 TraesCS3D01G040100 chr3D 15916606 15917512 906 False 645.000000 645 79.783000 1053 1960 1 chr3D.!!$F1 907
2 TraesCS3D01G040100 chr3A 20964608 20966383 1775 True 2368.000000 2368 90.782000 916 2694 1 chr3A.!!$R2 1778
3 TraesCS3D01G040100 chr3A 20989239 20990160 921 True 1264.000000 1264 91.505000 665 1584 1 chr3A.!!$R3 919
4 TraesCS3D01G040100 chr3A 21064198 21067487 3289 True 813.200000 1676 92.284200 3 2939 5 chr3A.!!$R5 2936
5 TraesCS3D01G040100 chr3A 20726379 20727275 896 True 651.000000 651 79.912000 1022 1926 1 chr3A.!!$R1 904
6 TraesCS3D01G040100 chr3A 20972169 20973501 1332 True 401.000000 508 89.117000 660 2006 2 chr3A.!!$R4 1346
7 TraesCS3D01G040100 chr3B 22831273 22832195 922 False 658.000000 658 79.701000 1029 1957 1 chr3B.!!$F5 928
8 TraesCS3D01G040100 chr3B 22205239 22205883 644 False 634.000000 634 84.812000 3 649 1 chr3B.!!$F1 646
9 TraesCS3D01G040100 chr3B 22443033 22444268 1235 False 626.500000 1033 90.627000 665 1509 2 chr3B.!!$F6 844
10 TraesCS3D01G040100 chr3B 22802683 22803605 922 False 623.000000 623 79.114000 1022 1960 1 chr3B.!!$F4 938
11 TraesCS3D01G040100 chr3B 22784747 22785648 901 False 599.000000 599 78.970000 1063 1960 1 chr3B.!!$F3 897
12 TraesCS3D01G040100 chr3B 22674904 22675832 928 False 584.000000 584 78.168000 1027 1960 1 chr3B.!!$F2 933
13 TraesCS3D01G040100 chr3B 22449585 22450960 1375 False 578.666667 998 89.487333 1505 2939 3 chr3B.!!$F7 1434

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
817 1143 0.386985 GGAAGTCGTCTCGTGTCACC 60.387 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2710 3693 0.035439 ACAAAGGGGTGGCTATCACG 60.035 55.0 0.0 0.0 46.96 4.35 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
36 37 4.339748 TGTGCTTTCATGTATTAAGCCCA 58.660 39.130 16.16 11.26 42.70 5.36
37 38 4.769488 TGTGCTTTCATGTATTAAGCCCAA 59.231 37.500 16.16 5.33 42.70 4.12
54 55 3.181450 GCCCAAGCTACACATTATCTCCT 60.181 47.826 0.00 0.00 35.50 3.69
72 73 4.584743 TCTCCTGTGGTGTATGCTATACAG 59.415 45.833 8.62 0.00 36.27 2.74
77 78 7.070696 TCCTGTGGTGTATGCTATACAGTATTT 59.929 37.037 0.00 0.00 35.09 1.40
124 126 7.183580 GATGGCTGAACATCTTGTAATCTAC 57.816 40.000 0.00 0.00 43.02 2.59
201 205 4.036518 AGCCTGGAGATGAATCTGTAACT 58.963 43.478 0.00 0.00 37.25 2.24
265 269 3.592059 TGACAAGGGTTATACGCTTCAC 58.408 45.455 6.20 4.96 46.59 3.18
440 444 9.349713 TCTTTTACAGGAATATTGAGTGTTTGT 57.650 29.630 0.00 0.00 0.00 2.83
445 449 8.635765 ACAGGAATATTGAGTGTTTGTGTATT 57.364 30.769 0.00 0.00 0.00 1.89
464 470 1.122632 TCCCTGCCTAACCGTGTCAA 61.123 55.000 0.00 0.00 0.00 3.18
493 499 2.396590 TGTTATTTCCTCCCACGAGC 57.603 50.000 0.00 0.00 34.49 5.03
516 522 4.920927 CCCATGTACAATTTTCGTTTCACC 59.079 41.667 0.00 0.00 0.00 4.02
768 1090 3.511146 GGGAAAATCTGCAAGGATCACAA 59.489 43.478 0.00 0.00 0.00 3.33
811 1137 1.471684 GTATGGTGGAAGTCGTCTCGT 59.528 52.381 0.00 0.00 0.00 4.18
817 1143 0.386985 GGAAGTCGTCTCGTGTCACC 60.387 60.000 0.00 0.00 0.00 4.02
828 1556 3.172106 TGTCACCGGGGGCTTTCA 61.172 61.111 11.04 0.00 0.00 2.69
855 1586 1.067821 TGGCCGATTGTGTTTTTGGAC 59.932 47.619 0.00 0.00 0.00 4.02
905 1636 7.642669 ACTTGAATTGATACAACTTGTGACAG 58.357 34.615 4.57 0.00 0.00 3.51
906 1637 7.498900 ACTTGAATTGATACAACTTGTGACAGA 59.501 33.333 4.57 0.00 0.00 3.41
907 1638 7.425577 TGAATTGATACAACTTGTGACAGAG 57.574 36.000 4.57 0.00 0.00 3.35
1001 1732 2.181954 ACTCCTGCTTGCTTTCTCAG 57.818 50.000 0.00 0.00 0.00 3.35
1051 1786 1.422531 TGGCTTCAATTTGTTGGGCT 58.577 45.000 0.00 0.00 0.00 5.19
1103 1841 2.363975 GCCACCTCCGACACCCATA 61.364 63.158 0.00 0.00 0.00 2.74
1218 1959 1.211212 CCTTGAGTCATGGCAGGATGA 59.789 52.381 11.82 0.00 39.69 2.92
1253 1994 2.991540 GGGAAGGTGTTGGCTGCC 60.992 66.667 12.87 12.87 0.00 4.85
1399 2145 3.197790 CAGTGCAATCTCCCGGCG 61.198 66.667 0.00 0.00 0.00 6.46
1735 2494 2.683867 TCTTCCGAATCTCCGAGTTCTC 59.316 50.000 0.00 0.00 0.00 2.87
1774 2533 1.824852 CTTGTTGGTCCTATTTGCCCC 59.175 52.381 0.00 0.00 0.00 5.80
1915 2691 4.804108 TGGAAAAATATCCAACGCTTGTG 58.196 39.130 0.00 0.00 46.36 3.33
1975 2851 5.394443 CCTTGATTTGTTGGGACATGGTATG 60.394 44.000 0.00 0.00 39.30 2.39
1977 2853 5.083122 TGATTTGTTGGGACATGGTATGTT 58.917 37.500 0.00 0.00 45.03 2.71
1980 2856 5.506730 TTGTTGGGACATGGTATGTTAGA 57.493 39.130 0.00 0.00 45.03 2.10
2072 3029 7.028926 AGGTACTCAGATGTAATACGACTTG 57.971 40.000 0.00 0.00 0.00 3.16
2116 3081 4.688879 TGAAGTTCACATATGTTCCGTGTC 59.311 41.667 5.37 0.85 32.42 3.67
2123 3088 5.041287 CACATATGTTCCGTGTCGTAGAAT 58.959 41.667 5.37 0.00 39.69 2.40
2181 3146 4.378563 CGACGGCTTATCTGTAGGAGTATG 60.379 50.000 0.00 0.00 33.57 2.39
2284 3257 9.474968 CAGGTACTATTGCGACATGAATGCAAA 62.475 40.741 21.19 12.97 45.05 3.68
2303 3276 5.091431 GCAAACAGTCATATTGCAGAGTTC 58.909 41.667 4.96 0.00 46.57 3.01
2322 3295 6.152661 AGAGTTCTTATTCCTCTGTCTGTCAG 59.847 42.308 0.00 0.00 44.85 3.51
2337 3310 7.391275 TCTGTCTGTCAGATCATTGCAAAAATA 59.609 33.333 1.71 0.00 46.77 1.40
2377 3350 4.083164 TGCAGAGTTGTGAATTATGTGCTG 60.083 41.667 0.00 0.00 0.00 4.41
2381 3354 2.212812 TGTGAATTATGTGCTGGCCA 57.787 45.000 4.71 4.71 0.00 5.36
2423 3400 2.030412 TCCGACGCACATGCAGTT 59.970 55.556 4.49 0.00 42.21 3.16
2437 3414 2.162716 CAGTTCGTGCTAGGCCAAC 58.837 57.895 5.01 0.00 0.00 3.77
2451 3428 1.310933 GCCAACAGCCTGTGATCCAG 61.311 60.000 0.00 4.67 41.15 3.86
2470 3447 2.869636 CTGCCTCAGCTTGCTGATT 58.130 52.632 23.20 0.00 40.80 2.57
2481 3458 3.057315 AGCTTGCTGATTTTATTGCGTGT 60.057 39.130 0.00 0.00 0.00 4.49
2523 3500 4.305539 AGATGGTGTGGATGATGAACAA 57.694 40.909 0.00 0.00 0.00 2.83
2538 3515 0.532115 AACAATTGCGCAATCCCTCC 59.468 50.000 33.93 0.00 0.00 4.30
2614 3591 3.880047 ACAGCATGAATCCACATTTGG 57.120 42.857 0.00 0.00 41.56 3.28
2620 3597 0.896923 GAATCCACATTTGGCTGCCA 59.103 50.000 19.30 19.30 43.56 4.92
2631 3614 2.260869 GGCTGCCAAAGACGAAGCA 61.261 57.895 15.17 0.00 35.55 3.91
2685 3668 2.109181 GCTCCGTGATAGCCACCC 59.891 66.667 0.00 0.00 42.76 4.61
2696 3679 0.891904 TAGCCACCCCTTTGTTTCGC 60.892 55.000 0.00 0.00 0.00 4.70
2697 3680 2.200337 GCCACCCCTTTGTTTCGCT 61.200 57.895 0.00 0.00 0.00 4.93
2699 3682 0.313987 CCACCCCTTTGTTTCGCTTC 59.686 55.000 0.00 0.00 0.00 3.86
2700 3683 0.040425 CACCCCTTTGTTTCGCTTCG 60.040 55.000 0.00 0.00 0.00 3.79
2701 3684 1.081442 CCCCTTTGTTTCGCTTCGC 60.081 57.895 0.00 0.00 0.00 4.70
2702 3685 1.652012 CCCTTTGTTTCGCTTCGCA 59.348 52.632 0.00 0.00 0.00 5.10
2703 3686 0.240945 CCCTTTGTTTCGCTTCGCAT 59.759 50.000 0.00 0.00 0.00 4.73
2704 3687 1.330306 CCTTTGTTTCGCTTCGCATG 58.670 50.000 0.00 0.00 0.00 4.06
2705 3688 1.330306 CTTTGTTTCGCTTCGCATGG 58.670 50.000 0.00 0.00 0.00 3.66
2706 3689 0.039617 TTTGTTTCGCTTCGCATGGG 60.040 50.000 2.76 2.76 0.00 4.00
2707 3690 2.202479 GTTTCGCTTCGCATGGGC 60.202 61.111 4.59 0.00 0.00 5.36
2708 3691 2.359850 TTTCGCTTCGCATGGGCT 60.360 55.556 4.59 0.00 38.10 5.19
2709 3692 2.398554 TTTCGCTTCGCATGGGCTC 61.399 57.895 4.59 0.00 38.10 4.70
2710 3693 4.838152 TCGCTTCGCATGGGCTCC 62.838 66.667 4.59 0.00 38.10 4.70
2713 3696 3.197790 CTTCGCATGGGCTCCGTG 61.198 66.667 4.59 8.60 42.95 4.94
2714 3697 3.664025 CTTCGCATGGGCTCCGTGA 62.664 63.158 15.31 0.25 42.73 4.35
2715 3698 2.930385 CTTCGCATGGGCTCCGTGAT 62.930 60.000 15.31 0.00 42.73 3.06
2716 3699 1.681486 TTCGCATGGGCTCCGTGATA 61.681 55.000 15.31 2.12 42.73 2.15
2717 3700 1.665916 CGCATGGGCTCCGTGATAG 60.666 63.158 15.31 4.41 42.73 2.08
2718 3701 1.963338 GCATGGGCTCCGTGATAGC 60.963 63.158 15.31 0.00 42.73 2.97
2723 3706 2.109181 GCTCCGTGATAGCCACCC 59.891 66.667 0.00 0.00 42.76 4.61
2724 3707 2.822399 CTCCGTGATAGCCACCCC 59.178 66.667 0.00 0.00 42.76 4.95
2725 3708 1.762460 CTCCGTGATAGCCACCCCT 60.762 63.158 0.00 0.00 42.76 4.79
2726 3709 1.306654 TCCGTGATAGCCACCCCTT 60.307 57.895 0.00 0.00 42.76 3.95
2727 3710 0.912487 TCCGTGATAGCCACCCCTTT 60.912 55.000 0.00 0.00 42.76 3.11
2728 3711 0.748005 CCGTGATAGCCACCCCTTTG 60.748 60.000 0.00 0.00 42.76 2.77
2729 3712 0.035439 CGTGATAGCCACCCCTTTGT 60.035 55.000 0.00 0.00 42.76 2.83
2730 3713 1.613255 CGTGATAGCCACCCCTTTGTT 60.613 52.381 0.00 0.00 42.76 2.83
2731 3714 2.525368 GTGATAGCCACCCCTTTGTTT 58.475 47.619 0.00 0.00 39.86 2.83
2732 3715 2.492088 GTGATAGCCACCCCTTTGTTTC 59.508 50.000 0.00 0.00 39.86 2.78
2733 3716 1.743394 GATAGCCACCCCTTTGTTTCG 59.257 52.381 0.00 0.00 0.00 3.46
2734 3717 0.891904 TAGCCACCCCTTTGTTTCGC 60.892 55.000 0.00 0.00 0.00 4.70
2735 3718 2.200337 GCCACCCCTTTGTTTCGCT 61.200 57.895 0.00 0.00 0.00 4.93
2736 3719 1.744320 GCCACCCCTTTGTTTCGCTT 61.744 55.000 0.00 0.00 0.00 4.68
2737 3720 0.313987 CCACCCCTTTGTTTCGCTTC 59.686 55.000 0.00 0.00 0.00 3.86
2738 3721 0.040425 CACCCCTTTGTTTCGCTTCG 60.040 55.000 0.00 0.00 0.00 3.79
2870 4171 1.026182 TTGCTGCGATGGTGATGTCC 61.026 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.655733 AAGCACAGCACACAACGTAC 59.344 50.000 0.00 0.00 0.00 3.67
5 6 2.121786 CATGAAAGCACAGCACACAAC 58.878 47.619 0.00 0.00 0.00 3.32
8 9 3.837213 ATACATGAAAGCACAGCACAC 57.163 42.857 0.00 0.00 0.00 3.82
36 37 4.471386 ACCACAGGAGATAATGTGTAGCTT 59.529 41.667 0.00 0.00 44.24 3.74
37 38 4.033709 ACCACAGGAGATAATGTGTAGCT 58.966 43.478 4.78 0.00 44.24 3.32
54 55 8.018537 AGAAATACTGTATAGCATACACCACA 57.981 34.615 0.00 0.00 0.00 4.17
72 73 7.939588 AGCCATCTAATCTAACCCAAGAAATAC 59.060 37.037 0.00 0.00 0.00 1.89
77 78 6.382087 TCTAGCCATCTAATCTAACCCAAGA 58.618 40.000 0.00 0.00 0.00 3.02
397 401 9.628746 CTGTAAAAGAGAGGTAGAGAAACTAAC 57.371 37.037 0.00 0.00 38.94 2.34
440 444 1.208535 CACGGTTAGGCAGGGAATACA 59.791 52.381 0.00 0.00 0.00 2.29
445 449 1.122632 TTGACACGGTTAGGCAGGGA 61.123 55.000 0.00 0.00 0.00 4.20
464 470 7.362920 CGTGGGAGGAAATAACAATGAGAAAAT 60.363 37.037 0.00 0.00 0.00 1.82
493 499 4.920927 GGTGAAACGAAAATTGTACATGGG 59.079 41.667 0.00 0.00 38.12 4.00
593 764 9.283768 TCATGCAGAAGAACAAAATTACTAGAA 57.716 29.630 0.00 0.00 0.00 2.10
649 820 6.071447 AGTGGCACTAGCTAGATTAGATGATG 60.071 42.308 27.45 12.17 41.70 3.07
651 822 5.242615 CAGTGGCACTAGCTAGATTAGATGA 59.757 44.000 27.45 0.00 41.70 2.92
652 823 5.468592 CAGTGGCACTAGCTAGATTAGATG 58.531 45.833 27.45 14.28 41.70 2.90
654 825 3.891977 CCAGTGGCACTAGCTAGATTAGA 59.108 47.826 27.45 4.14 41.70 2.10
656 827 2.965831 CCCAGTGGCACTAGCTAGATTA 59.034 50.000 27.45 7.60 41.70 1.75
657 828 1.765314 CCCAGTGGCACTAGCTAGATT 59.235 52.381 27.45 2.54 41.70 2.40
658 829 1.062886 TCCCAGTGGCACTAGCTAGAT 60.063 52.381 27.45 8.78 41.70 1.98
660 831 0.461961 GTCCCAGTGGCACTAGCTAG 59.538 60.000 21.59 19.44 41.70 3.42
661 832 0.252057 TGTCCCAGTGGCACTAGCTA 60.252 55.000 21.59 3.37 41.70 3.32
663 834 1.078848 CTGTCCCAGTGGCACTAGC 60.079 63.158 21.59 10.93 41.10 3.42
768 1090 1.375523 GAGACGGGTTGCGTGGAAT 60.376 57.895 0.00 0.00 0.00 3.01
811 1137 2.075355 AATGAAAGCCCCCGGTGACA 62.075 55.000 0.00 0.00 0.00 3.58
840 1570 5.356882 TCAGATCGTCCAAAAACACAATC 57.643 39.130 0.00 0.00 0.00 2.67
855 1586 1.298713 CCGGTCTTCGCTCAGATCG 60.299 63.158 7.52 7.52 45.45 3.69
905 1636 5.651530 TCAGAAATTGTAGTGACGGATCTC 58.348 41.667 0.00 0.00 0.00 2.75
906 1637 5.661056 TCAGAAATTGTAGTGACGGATCT 57.339 39.130 0.00 0.00 0.00 2.75
907 1638 5.063564 GGTTCAGAAATTGTAGTGACGGATC 59.936 44.000 0.00 0.00 0.00 3.36
956 1687 8.596781 ACAGTTAGGCTTTATAGAGAGAAGAA 57.403 34.615 0.00 0.00 0.00 2.52
957 1688 9.122779 GTACAGTTAGGCTTTATAGAGAGAAGA 57.877 37.037 0.00 0.00 0.00 2.87
958 1689 9.127277 AGTACAGTTAGGCTTTATAGAGAGAAG 57.873 37.037 0.00 0.00 0.00 2.85
1001 1732 8.980610 GTTCTAAGTAGTTGTTTCTCTTCCTTC 58.019 37.037 0.00 0.00 0.00 3.46
1051 1786 8.677148 AAAACATTGCAAGAAAGAGTAGTAGA 57.323 30.769 4.94 0.00 0.00 2.59
1158 1899 3.895232 AAGAGAAGGATCGCTTTAGCA 57.105 42.857 2.29 0.00 42.17 3.49
1218 1959 1.663695 CCAAAGACAACAGTCGGTGT 58.336 50.000 0.00 0.00 43.24 4.16
1253 1994 1.227263 CATACCCCGAGGAGTTGCG 60.227 63.158 0.00 0.00 36.73 4.85
1267 2008 0.528684 GCTCCAGAGCGGTGACATAC 60.529 60.000 3.49 0.00 45.29 2.39
1288 2029 4.243270 GACTGTACAAGCCACGATTACTT 58.757 43.478 0.00 0.00 0.00 2.24
1292 2033 2.831685 TGACTGTACAAGCCACGATT 57.168 45.000 0.00 0.00 0.00 3.34
1293 2034 2.612972 CCTTGACTGTACAAGCCACGAT 60.613 50.000 0.00 0.00 43.83 3.73
1324 2070 1.734465 GAGGTGAGGTTGAAGATTGCG 59.266 52.381 0.00 0.00 0.00 4.85
1399 2145 1.079057 GAGCCTCTCAAACCCGGTC 60.079 63.158 0.00 0.00 0.00 4.79
1529 2275 6.715718 CCATTAAGAGAATCATCAGAAGCCAT 59.284 38.462 0.00 0.00 37.82 4.40
1531 2277 5.048852 GCCATTAAGAGAATCATCAGAAGCC 60.049 44.000 0.00 0.00 37.82 4.35
1735 2494 8.127327 CCAACAAGATTACAATATCTCAAGCTG 58.873 37.037 0.00 0.00 33.81 4.24
1774 2533 2.997315 TGCAGGGTCGACAGGGAG 60.997 66.667 18.91 3.20 0.00 4.30
1912 2688 3.719871 TGGAAGATTCTACTAGGGCACA 58.280 45.455 0.00 0.00 0.00 4.57
1915 2691 8.747538 TTTTTATTGGAAGATTCTACTAGGGC 57.252 34.615 0.00 0.00 0.00 5.19
1977 2853 9.812347 AGATGGAAAATATTGGCACATAATCTA 57.188 29.630 0.00 0.00 39.30 1.98
2090 3055 5.062683 CACGGAACATATGTGAACTTCAGAG 59.937 44.000 9.63 0.00 0.00 3.35
2181 3146 3.129287 CCATCTAGGCCAAACAACATCAC 59.871 47.826 5.01 0.00 0.00 3.06
2206 3171 6.239176 GCTTATGTTCCAGAGCTAGTACATCT 60.239 42.308 6.45 0.00 32.54 2.90
2284 3257 7.497249 GGAATAAGAACTCTGCAATATGACTGT 59.503 37.037 0.00 0.00 0.00 3.55
2317 3290 7.930325 TGGTTTTATTTTTGCAATGATCTGACA 59.070 29.630 0.00 0.00 0.00 3.58
2318 3291 8.309163 TGGTTTTATTTTTGCAATGATCTGAC 57.691 30.769 0.00 0.00 0.00 3.51
2322 3295 7.131498 TGCTGGTTTTATTTTTGCAATGATC 57.869 32.000 0.00 0.00 0.00 2.92
2381 3354 3.618351 CATTCAGGTTGATCAGCCTTCT 58.382 45.455 26.95 12.50 40.24 2.85
2423 3400 2.047274 GCTGTTGGCCTAGCACGA 60.047 61.111 18.30 0.00 39.67 4.35
2433 3410 2.864114 CTGGATCACAGGCTGTTGG 58.136 57.895 19.43 8.14 43.70 3.77
2470 3447 3.665848 GCAGTTCGCTTACACGCAATAAA 60.666 43.478 0.00 0.00 37.77 1.40
2481 3458 2.434185 CAGCCGGCAGTTCGCTTA 60.434 61.111 31.54 0.00 41.91 3.09
2500 3477 4.665451 TGTTCATCATCCACACCATCTTT 58.335 39.130 0.00 0.00 0.00 2.52
2614 3591 1.081840 GTGCTTCGTCTTTGGCAGC 60.082 57.895 0.00 0.00 35.29 5.25
2640 3623 4.416620 CTGGACACTAGAAACGATCACTC 58.583 47.826 0.00 0.00 0.00 3.51
2700 3683 1.963338 GCTATCACGGAGCCCATGC 60.963 63.158 0.00 0.00 33.60 4.06
2701 3684 4.368391 GCTATCACGGAGCCCATG 57.632 61.111 0.00 0.00 33.60 3.66
2706 3689 2.109181 GGGTGGCTATCACGGAGC 59.891 66.667 0.00 0.00 46.96 4.70
2707 3690 1.338136 AAGGGGTGGCTATCACGGAG 61.338 60.000 0.00 0.00 46.96 4.63
2708 3691 0.912487 AAAGGGGTGGCTATCACGGA 60.912 55.000 0.00 0.00 46.96 4.69
2709 3692 0.748005 CAAAGGGGTGGCTATCACGG 60.748 60.000 0.00 0.00 46.96 4.94
2710 3693 0.035439 ACAAAGGGGTGGCTATCACG 60.035 55.000 0.00 0.00 46.96 4.35
2711 3694 2.215942 AACAAAGGGGTGGCTATCAC 57.784 50.000 0.00 0.00 45.34 3.06
2712 3695 2.802719 GAAACAAAGGGGTGGCTATCA 58.197 47.619 0.00 0.00 0.00 2.15
2713 3696 1.743394 CGAAACAAAGGGGTGGCTATC 59.257 52.381 0.00 0.00 0.00 2.08
2714 3697 1.834188 CGAAACAAAGGGGTGGCTAT 58.166 50.000 0.00 0.00 0.00 2.97
2715 3698 0.891904 GCGAAACAAAGGGGTGGCTA 60.892 55.000 0.00 0.00 0.00 3.93
2716 3699 2.200337 GCGAAACAAAGGGGTGGCT 61.200 57.895 0.00 0.00 0.00 4.75
2717 3700 1.744320 AAGCGAAACAAAGGGGTGGC 61.744 55.000 0.00 0.00 0.00 5.01
2718 3701 0.313987 GAAGCGAAACAAAGGGGTGG 59.686 55.000 0.00 0.00 0.00 4.61
2719 3702 0.040425 CGAAGCGAAACAAAGGGGTG 60.040 55.000 0.00 0.00 0.00 4.61
2720 3703 2.327228 CGAAGCGAAACAAAGGGGT 58.673 52.632 0.00 0.00 0.00 4.95
2870 4171 3.181534 ACAATCATCGCGAACTGTAAACG 60.182 43.478 15.24 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.