Multiple sequence alignment - TraesCS3D01G367500

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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 TraesCS3D01G367500 chr3D 100.000 3470 0 0 1 3470 481517831 481514362 0.000000e+00 6408.0
1 TraesCS3D01G367500 chr3D 94.380 605 24 7 2873 3470 141467385 141467986 0.000000e+00 920.0
2 TraesCS3D01G367500 chr3D 91.770 243 16 3 2576 2816 10339525 10339285 5.550000e-88 335.0
3 TraesCS3D01G367500 chr3B 95.559 1824 65 8 736 2554 642487149 642485337 0.000000e+00 2905.0
4 TraesCS3D01G367500 chr3B 85.770 766 77 13 2 740 39592786 39593546 0.000000e+00 782.0
5 TraesCS3D01G367500 chr3B 85.176 398 32 11 2886 3260 703891015 703891408 1.950000e-102 383.0
6 TraesCS3D01G367500 chr3B 93.074 231 16 0 2576 2806 168523584 168523814 4.290000e-89 339.0
7 TraesCS3D01G367500 chr3B 93.023 86 5 1 2803 2887 642483218 642483133 1.310000e-24 124.0
8 TraesCS3D01G367500 chr3A 94.812 1831 72 13 735 2556 624530300 624528484 0.000000e+00 2833.0
9 TraesCS3D01G367500 chr3A 88.322 745 67 11 1 729 724638710 724639450 0.000000e+00 876.0
10 TraesCS3D01G367500 chr2A 92.108 1812 115 16 759 2561 393339342 393341134 0.000000e+00 2529.0
11 TraesCS3D01G367500 chr2A 91.949 236 19 0 2576 2811 192092509 192092744 7.180000e-87 331.0
12 TraesCS3D01G367500 chr2D 91.653 1821 123 15 748 2556 324863219 324861416 0.000000e+00 2494.0
13 TraesCS3D01G367500 chr2D 92.735 234 16 1 2576 2809 64978261 64978493 1.540000e-88 337.0
14 TraesCS3D01G367500 chr2B 91.357 1805 116 19 748 2542 393861069 393859295 0.000000e+00 2433.0
15 TraesCS3D01G367500 chr7D 91.712 736 47 11 1 731 580169966 580170692 0.000000e+00 1009.0
16 TraesCS3D01G367500 chr5D 90.970 742 54 8 1 731 550983250 550983989 0.000000e+00 987.0
17 TraesCS3D01G367500 chr5D 88.313 753 63 10 1 729 440967421 440968172 0.000000e+00 880.0
18 TraesCS3D01G367500 chr5D 93.392 227 14 1 2576 2802 299883624 299883849 5.550000e-88 335.0
19 TraesCS3D01G367500 chr4D 94.907 589 24 3 2888 3470 402943417 402944005 0.000000e+00 917.0
20 TraesCS3D01G367500 chr4D 92.517 588 34 9 2885 3466 19675437 19674854 0.000000e+00 833.0
21 TraesCS3D01G367500 chr5B 88.874 737 69 8 9 734 488828436 488827702 0.000000e+00 894.0
22 TraesCS3D01G367500 chr5B 87.433 748 71 18 1 735 470182295 470181558 0.000000e+00 839.0
23 TraesCS3D01G367500 chr5B 85.831 367 29 8 2887 3233 495222610 495222973 5.470000e-98 368.0
24 TraesCS3D01G367500 chr4B 90.970 598 38 7 2888 3470 619436136 619435540 0.000000e+00 791.0
25 TraesCS3D01G367500 chr4B 90.445 607 38 7 2884 3470 91120899 91121505 0.000000e+00 782.0
26 TraesCS3D01G367500 chr4B 89.552 603 41 8 2888 3470 88095322 88094722 0.000000e+00 745.0
27 TraesCS3D01G367500 chr4B 89.386 603 42 9 2888 3470 538839986 538840586 0.000000e+00 739.0
28 TraesCS3D01G367500 chr7B 90.713 603 35 8 2888 3470 658129497 658128896 0.000000e+00 784.0
29 TraesCS3D01G367500 chr7B 84.532 737 74 24 9 734 59080928 59080221 0.000000e+00 693.0
30 TraesCS3D01G367500 chr7B 92.672 232 16 1 2576 2807 464539919 464539689 2.000000e-87 333.0
31 TraesCS3D01G367500 chr6A 84.966 745 84 17 1 731 606621796 606622526 0.000000e+00 730.0
32 TraesCS3D01G367500 chr1B 90.175 570 35 8 2921 3470 593012819 593012251 0.000000e+00 723.0
33 TraesCS3D01G367500 chr1B 84.615 65 3 4 2815 2873 623837532 623837595 1.350000e-04 58.4
34 TraesCS3D01G367500 chr6B 93.421 228 15 0 2576 2803 550778149 550777922 4.290000e-89 339.0
35 TraesCS3D01G367500 chr6D 92.373 236 18 0 2576 2811 151317246 151317481 1.540000e-88 337.0
36 TraesCS3D01G367500 chr4A 93.043 230 16 0 2576 2805 494702556 494702785 1.540000e-88 337.0


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 TraesCS3D01G367500 chr3D 481514362 481517831 3469 True 6408.0 6408 100.000 1 3470 1 chr3D.!!$R2 3469
1 TraesCS3D01G367500 chr3D 141467385 141467986 601 False 920.0 920 94.380 2873 3470 1 chr3D.!!$F1 597
2 TraesCS3D01G367500 chr3B 642483133 642487149 4016 True 1514.5 2905 94.291 736 2887 2 chr3B.!!$R1 2151
3 TraesCS3D01G367500 chr3B 39592786 39593546 760 False 782.0 782 85.770 2 740 1 chr3B.!!$F1 738
4 TraesCS3D01G367500 chr3A 624528484 624530300 1816 True 2833.0 2833 94.812 735 2556 1 chr3A.!!$R1 1821
5 TraesCS3D01G367500 chr3A 724638710 724639450 740 False 876.0 876 88.322 1 729 1 chr3A.!!$F1 728
6 TraesCS3D01G367500 chr2A 393339342 393341134 1792 False 2529.0 2529 92.108 759 2561 1 chr2A.!!$F2 1802
7 TraesCS3D01G367500 chr2D 324861416 324863219 1803 True 2494.0 2494 91.653 748 2556 1 chr2D.!!$R1 1808
8 TraesCS3D01G367500 chr2B 393859295 393861069 1774 True 2433.0 2433 91.357 748 2542 1 chr2B.!!$R1 1794
9 TraesCS3D01G367500 chr7D 580169966 580170692 726 False 1009.0 1009 91.712 1 731 1 chr7D.!!$F1 730
10 TraesCS3D01G367500 chr5D 550983250 550983989 739 False 987.0 987 90.970 1 731 1 chr5D.!!$F3 730
11 TraesCS3D01G367500 chr5D 440967421 440968172 751 False 880.0 880 88.313 1 729 1 chr5D.!!$F2 728
12 TraesCS3D01G367500 chr4D 402943417 402944005 588 False 917.0 917 94.907 2888 3470 1 chr4D.!!$F1 582
13 TraesCS3D01G367500 chr4D 19674854 19675437 583 True 833.0 833 92.517 2885 3466 1 chr4D.!!$R1 581
14 TraesCS3D01G367500 chr5B 488827702 488828436 734 True 894.0 894 88.874 9 734 1 chr5B.!!$R2 725
15 TraesCS3D01G367500 chr5B 470181558 470182295 737 True 839.0 839 87.433 1 735 1 chr5B.!!$R1 734
16 TraesCS3D01G367500 chr4B 619435540 619436136 596 True 791.0 791 90.970 2888 3470 1 chr4B.!!$R2 582
17 TraesCS3D01G367500 chr4B 91120899 91121505 606 False 782.0 782 90.445 2884 3470 1 chr4B.!!$F1 586
18 TraesCS3D01G367500 chr4B 88094722 88095322 600 True 745.0 745 89.552 2888 3470 1 chr4B.!!$R1 582
19 TraesCS3D01G367500 chr4B 538839986 538840586 600 False 739.0 739 89.386 2888 3470 1 chr4B.!!$F2 582
20 TraesCS3D01G367500 chr7B 658128896 658129497 601 True 784.0 784 90.713 2888 3470 1 chr7B.!!$R3 582
21 TraesCS3D01G367500 chr7B 59080221 59080928 707 True 693.0 693 84.532 9 734 1 chr7B.!!$R1 725
22 TraesCS3D01G367500 chr6A 606621796 606622526 730 False 730.0 730 84.966 1 731 1 chr6A.!!$F1 730
23 TraesCS3D01G367500 chr1B 593012251 593012819 568 True 723.0 723 90.175 2921 3470 1 chr1B.!!$R1 549

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
804 854 0.464036 CCCGAGGAATCCATCGTGAA 59.536 55.0 15.96 0.0 37.23 3.18 F
1086 1145 0.106769 TGCCACACCTGAGAAAGCAA 60.107 50.0 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1889 1.816224 TGACGTTGTCGATGATCTCCA 59.184 47.619 0.0 0.0 40.62 3.86 R
2913 4880 0.974010 TTCCGCCGGACCTCTACAAT 60.974 55.000 4.7 0.0 0.00 2.71 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
228 233 9.193133 GTATAGTTCTTTCGTGCATACATACAT 57.807 33.333 0.00 0.00 0.00 2.29
230 235 7.464830 AGTTCTTTCGTGCATACATACATAC 57.535 36.000 0.00 0.00 0.00 2.39
404 426 6.608610 AGTTTCCGTGCTGTAATGTAATTTC 58.391 36.000 0.00 0.00 37.87 2.17
421 443 8.402326 TGTAATTTCTACATGTAGTACTTGCG 57.598 34.615 27.83 5.58 34.84 4.85
532 569 5.937187 ACAAAAGCAAACACATGGAAAAAC 58.063 33.333 0.00 0.00 0.00 2.43
546 584 1.208009 AAAAACAGCATGCACGCACG 61.208 50.000 21.98 0.00 42.53 5.34
559 598 0.960364 ACGCACGAAATTCAGCCCAT 60.960 50.000 0.00 0.00 0.00 4.00
573 613 1.083489 GCCCATGAACGAAATCGACA 58.917 50.000 10.16 9.43 43.02 4.35
582 622 2.413837 ACGAAATCGACAGACCCAAAG 58.586 47.619 10.16 0.00 43.02 2.77
614 655 6.013898 TCAATCAAATCCAAACAGCCCAATAA 60.014 34.615 0.00 0.00 0.00 1.40
632 673 5.509501 CCAATAACACCAGCAAAACATGACT 60.510 40.000 0.00 0.00 0.00 3.41
804 854 0.464036 CCCGAGGAATCCATCGTGAA 59.536 55.000 15.96 0.00 37.23 3.18
805 855 1.134521 CCCGAGGAATCCATCGTGAAA 60.135 52.381 15.96 0.00 37.23 2.69
806 856 2.485479 CCCGAGGAATCCATCGTGAAAT 60.485 50.000 15.96 0.00 37.23 2.17
807 857 3.244078 CCCGAGGAATCCATCGTGAAATA 60.244 47.826 15.96 0.00 37.23 1.40
808 858 4.377021 CCGAGGAATCCATCGTGAAATAA 58.623 43.478 15.96 0.00 37.23 1.40
809 859 4.997395 CCGAGGAATCCATCGTGAAATAAT 59.003 41.667 15.96 0.00 37.23 1.28
810 860 5.470098 CCGAGGAATCCATCGTGAAATAATT 59.530 40.000 15.96 0.00 37.23 1.40
811 861 6.347725 CCGAGGAATCCATCGTGAAATAATTC 60.348 42.308 15.96 0.00 37.23 2.17
812 862 6.347725 CGAGGAATCCATCGTGAAATAATTCC 60.348 42.308 0.61 0.00 40.50 3.01
813 863 6.364701 AGGAATCCATCGTGAAATAATTCCA 58.635 36.000 0.61 0.00 41.91 3.53
814 864 7.006509 AGGAATCCATCGTGAAATAATTCCAT 58.993 34.615 0.61 0.00 41.91 3.41
815 865 7.175641 AGGAATCCATCGTGAAATAATTCCATC 59.824 37.037 0.61 0.00 41.91 3.51
970 1029 4.692625 AGTGTCCATCTGATCAGAAAAACG 59.307 41.667 28.40 14.21 41.36 3.60
971 1030 4.002982 TGTCCATCTGATCAGAAAAACGG 58.997 43.478 28.40 21.24 41.36 4.44
977 1036 3.191162 TCTGATCAGAAAAACGGCCATTG 59.809 43.478 23.17 0.00 33.91 2.82
978 1037 2.230992 TGATCAGAAAAACGGCCATTGG 59.769 45.455 2.24 0.00 0.00 3.16
1007 1066 5.184671 AGCTTGGATCAAGAAAGATGGAAAC 59.815 40.000 11.35 0.00 43.42 2.78
1086 1145 0.106769 TGCCACACCTGAGAAAGCAA 60.107 50.000 0.00 0.00 0.00 3.91
1417 1476 2.896801 CGCGTAAGGGCCATGATGC 61.897 63.158 9.06 9.06 45.71 3.91
1675 1735 2.876368 GATCCCGGTGAACCTGCCTG 62.876 65.000 0.00 0.00 0.00 4.85
1696 1756 2.348998 CCTCCTTCGGCAAGTGCT 59.651 61.111 2.85 0.00 41.70 4.40
2185 2245 4.547367 GGGACCCGGCCATCTTCG 62.547 72.222 2.24 0.00 0.00 3.79
2208 2268 2.032528 CCAAGCAGGTTCGAGCCA 59.967 61.111 21.22 0.00 0.00 4.75
2440 2502 2.360350 AGCCAATGGACACAGCCG 60.360 61.111 2.05 0.00 0.00 5.52
2558 2626 7.381678 GTGAAATGTACGATTACAGATACTCCC 59.618 40.741 0.00 0.00 41.62 4.30
2559 2627 7.287005 TGAAATGTACGATTACAGATACTCCCT 59.713 37.037 0.00 0.00 41.62 4.20
2560 2628 6.821031 ATGTACGATTACAGATACTCCCTC 57.179 41.667 0.00 0.00 41.62 4.30
2562 2630 5.763698 TGTACGATTACAGATACTCCCTCTG 59.236 44.000 0.00 0.00 44.60 3.35
2571 2639 6.083098 CAGATACTCCCTCTGTTCATGTAG 57.917 45.833 0.00 0.00 36.26 2.74
2572 2640 5.596361 CAGATACTCCCTCTGTTCATGTAGT 59.404 44.000 0.00 0.00 36.26 2.73
2573 2641 5.596361 AGATACTCCCTCTGTTCATGTAGTG 59.404 44.000 0.00 0.00 0.00 2.74
2574 2642 2.234908 ACTCCCTCTGTTCATGTAGTGC 59.765 50.000 0.00 0.00 0.00 4.40
2575 2643 2.234661 CTCCCTCTGTTCATGTAGTGCA 59.765 50.000 0.00 0.00 0.00 4.57
2576 2644 2.840038 TCCCTCTGTTCATGTAGTGCAT 59.160 45.455 0.00 0.00 38.60 3.96
2577 2645 3.264193 TCCCTCTGTTCATGTAGTGCATT 59.736 43.478 0.00 0.00 35.19 3.56
2578 2646 4.012374 CCCTCTGTTCATGTAGTGCATTT 58.988 43.478 0.00 0.00 35.19 2.32
2580 2648 5.047802 CCCTCTGTTCATGTAGTGCATTTTT 60.048 40.000 0.00 0.00 35.19 1.94
2581 2649 5.860182 CCTCTGTTCATGTAGTGCATTTTTG 59.140 40.000 0.00 0.00 35.19 2.44
2582 2650 5.221880 TCTGTTCATGTAGTGCATTTTTGC 58.778 37.500 0.00 0.00 35.19 3.68
2583 2651 4.941657 TGTTCATGTAGTGCATTTTTGCA 58.058 34.783 0.00 0.00 43.22 4.08
2626 4589 8.567285 ACTTTAACCATATCCACAGAGAAAAG 57.433 34.615 0.00 0.00 0.00 2.27
2627 4590 8.164070 ACTTTAACCATATCCACAGAGAAAAGT 58.836 33.333 0.00 0.00 0.00 2.66
2628 4591 9.667107 CTTTAACCATATCCACAGAGAAAAGTA 57.333 33.333 0.00 0.00 0.00 2.24
2629 4592 9.667107 TTTAACCATATCCACAGAGAAAAGTAG 57.333 33.333 0.00 0.00 0.00 2.57
2630 4593 6.240549 ACCATATCCACAGAGAAAAGTAGG 57.759 41.667 0.00 0.00 0.00 3.18
2631 4594 5.726793 ACCATATCCACAGAGAAAAGTAGGT 59.273 40.000 0.00 0.00 0.00 3.08
2632 4595 6.901300 ACCATATCCACAGAGAAAAGTAGGTA 59.099 38.462 0.00 0.00 0.00 3.08
2633 4596 7.147707 ACCATATCCACAGAGAAAAGTAGGTAC 60.148 40.741 0.00 0.00 0.00 3.34
2634 4597 7.147724 CCATATCCACAGAGAAAAGTAGGTACA 60.148 40.741 0.00 0.00 0.00 2.90
2636 4599 6.282199 TCCACAGAGAAAAGTAGGTACATC 57.718 41.667 0.00 0.00 0.00 3.06
2637 4600 6.017192 TCCACAGAGAAAAGTAGGTACATCT 58.983 40.000 0.00 0.00 0.00 2.90
2638 4601 7.179966 TCCACAGAGAAAAGTAGGTACATCTA 58.820 38.462 0.00 0.00 0.00 1.98
2639 4602 7.339721 TCCACAGAGAAAAGTAGGTACATCTAG 59.660 40.741 0.00 0.00 0.00 2.43
2644 4607 9.617523 AGAGAAAAGTAGGTACATCTAGACTAC 57.382 37.037 8.67 8.67 35.45 2.73
2645 4608 9.393512 GAGAAAAGTAGGTACATCTAGACTACA 57.606 37.037 15.85 0.00 37.17 2.74
2653 4616 7.042335 AGGTACATCTAGACTACAAAATGCAC 58.958 38.462 0.00 0.00 0.00 4.57
2659 4622 8.618677 CATCTAGACTACAAAATGCACATCATT 58.381 33.333 0.00 0.00 46.82 2.57
2660 4623 7.977904 TCTAGACTACAAAATGCACATCATTG 58.022 34.615 0.00 7.28 44.23 2.82
2661 4624 5.957798 AGACTACAAAATGCACATCATTGG 58.042 37.500 11.50 0.00 44.23 3.16
2711 4674 9.935682 GAATGTACATGTTTGGTATTGTAGATG 57.064 33.333 9.63 0.00 31.34 2.90
2714 4677 9.594478 TGTACATGTTTGGTATTGTAGATGTAG 57.406 33.333 2.30 0.00 0.00 2.74
2716 4679 8.718102 ACATGTTTGGTATTGTAGATGTAGAC 57.282 34.615 0.00 0.00 0.00 2.59
2718 4681 8.820933 CATGTTTGGTATTGTAGATGTAGACAG 58.179 37.037 0.00 0.00 0.00 3.51
2719 4682 7.903145 TGTTTGGTATTGTAGATGTAGACAGT 58.097 34.615 0.00 0.00 0.00 3.55
2721 4684 9.216117 GTTTGGTATTGTAGATGTAGACAGTTT 57.784 33.333 0.00 0.00 0.00 2.66
2763 4726 7.637709 AAAGTTGACAAAGTTTGACTTTCAC 57.362 32.000 22.23 11.03 44.47 3.18
2768 4731 8.331742 GTTGACAAAGTTTGACTTTCACAAAAA 58.668 29.630 22.23 0.79 44.47 1.94
2769 4732 8.600449 TGACAAAGTTTGACTTTCACAAAAAT 57.400 26.923 22.23 0.00 44.47 1.82
2778 4741 7.994425 TGACTTTCACAAAAATCTATAGGCA 57.006 32.000 0.00 0.00 0.00 4.75
2779 4742 7.816640 TGACTTTCACAAAAATCTATAGGCAC 58.183 34.615 0.00 0.00 0.00 5.01
2780 4743 7.665559 TGACTTTCACAAAAATCTATAGGCACT 59.334 33.333 0.00 0.00 46.37 4.40
2795 4758 4.032960 AGGCACTACATTGTGAAATGGA 57.967 40.909 0.00 0.00 40.12 3.41
2796 4759 4.012374 AGGCACTACATTGTGAAATGGAG 58.988 43.478 8.77 8.77 44.77 3.86
2797 4760 3.129287 GGCACTACATTGTGAAATGGAGG 59.871 47.826 13.76 5.57 43.78 4.30
2798 4761 4.009675 GCACTACATTGTGAAATGGAGGA 58.990 43.478 13.76 0.00 43.78 3.71
2799 4762 4.458989 GCACTACATTGTGAAATGGAGGAA 59.541 41.667 13.76 0.00 43.78 3.36
2800 4763 5.392380 GCACTACATTGTGAAATGGAGGAAG 60.392 44.000 13.76 5.90 43.78 3.46
2801 4764 5.707298 CACTACATTGTGAAATGGAGGAAGT 59.293 40.000 13.76 2.71 43.78 3.01
2806 4769 7.458397 ACATTGTGAAATGGAGGAAGTACTAA 58.542 34.615 0.00 0.00 34.56 2.24
2853 4816 2.879826 TGTGTGCATCACTCGATACAG 58.120 47.619 16.70 0.00 46.27 2.74
2913 4880 9.168451 GGAAAAAGTCCATTTTAAACCTTGAAA 57.832 29.630 0.00 0.00 46.97 2.69
2974 4942 1.403647 CGGTCGATTGCACCTGAACTA 60.404 52.381 0.00 0.00 0.00 2.24
2982 4950 3.354948 TGCACCTGAACTATGCAATCT 57.645 42.857 0.00 0.00 45.96 2.40
3046 5014 2.605295 ACGTGGACCGGGATTGGA 60.605 61.111 6.32 0.00 42.24 3.53
3129 5106 8.202745 TGCTTCCATTTTTCGTTTGTTATTTT 57.797 26.923 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 214 9.535878 TTATTGTATGTATGTATGCACGAAAGA 57.464 29.630 0.00 0.00 0.00 2.52
421 443 5.524511 TGAGTGCGTGAAAATGTATACAC 57.475 39.130 7.96 0.00 0.00 2.90
532 569 0.730155 AATTTCGTGCGTGCATGCTG 60.730 50.000 29.83 21.90 35.36 4.41
546 584 3.848272 TTCGTTCATGGGCTGAATTTC 57.152 42.857 0.00 0.00 45.36 2.17
559 598 1.341852 TGGGTCTGTCGATTTCGTTCA 59.658 47.619 0.00 1.09 40.80 3.18
565 604 3.326880 ACCTACTTTGGGTCTGTCGATTT 59.673 43.478 0.00 0.00 30.15 2.17
573 613 3.650942 TGATTGACACCTACTTTGGGTCT 59.349 43.478 0.00 0.00 34.44 3.85
582 622 6.325919 TGTTTGGATTTGATTGACACCTAC 57.674 37.500 0.00 0.00 0.00 3.18
614 655 2.653726 TCAGTCATGTTTTGCTGGTGT 58.346 42.857 0.00 0.00 33.18 4.16
722 769 8.854614 AGCGAGGATTAATTCAATTTAGCTAT 57.145 30.769 0.00 0.00 0.00 2.97
767 814 5.080969 TCGGGAGTACAGACAAAATTAGG 57.919 43.478 0.00 0.00 0.00 2.69
804 854 5.060427 TGGTGGGAATCGATGGAATTATT 57.940 39.130 0.00 0.00 0.00 1.40
805 855 4.722526 TGGTGGGAATCGATGGAATTAT 57.277 40.909 0.00 0.00 0.00 1.28
806 856 4.511786 TTGGTGGGAATCGATGGAATTA 57.488 40.909 0.00 0.00 0.00 1.40
807 857 3.380471 TTGGTGGGAATCGATGGAATT 57.620 42.857 0.00 0.00 0.00 2.17
808 858 3.600448 ATTGGTGGGAATCGATGGAAT 57.400 42.857 0.00 0.00 0.00 3.01
809 859 4.511786 TTATTGGTGGGAATCGATGGAA 57.488 40.909 0.00 0.00 0.00 3.53
810 860 4.722526 ATTATTGGTGGGAATCGATGGA 57.277 40.909 0.00 0.00 0.00 3.41
811 861 4.218417 GGAATTATTGGTGGGAATCGATGG 59.782 45.833 0.00 0.00 0.00 3.51
812 862 4.083324 CGGAATTATTGGTGGGAATCGATG 60.083 45.833 0.00 0.00 0.00 3.84
813 863 4.072131 CGGAATTATTGGTGGGAATCGAT 58.928 43.478 0.00 0.00 0.00 3.59
814 864 3.134985 TCGGAATTATTGGTGGGAATCGA 59.865 43.478 0.00 0.00 0.00 3.59
815 865 3.250040 GTCGGAATTATTGGTGGGAATCG 59.750 47.826 0.00 0.00 0.00 3.34
970 1029 1.755783 CAAGCTCTCCCCAATGGCC 60.756 63.158 0.00 0.00 0.00 5.36
971 1030 1.755783 CCAAGCTCTCCCCAATGGC 60.756 63.158 0.00 0.00 0.00 4.40
977 1036 1.207791 TCTTGATCCAAGCTCTCCCC 58.792 55.000 2.04 0.00 40.84 4.81
978 1037 3.054802 TCTTTCTTGATCCAAGCTCTCCC 60.055 47.826 2.04 0.00 40.84 4.30
1039 1098 6.128172 ACCAAGAAGATGAAAGCAACGATTAG 60.128 38.462 0.00 0.00 0.00 1.73
1086 1145 1.336440 CGATCGTCCTGAGATGAGCTT 59.664 52.381 7.03 0.00 41.38 3.74
1829 1889 1.816224 TGACGTTGTCGATGATCTCCA 59.184 47.619 0.00 0.00 40.62 3.86
2185 2245 3.435186 GAACCTGCTTGGCTCCGC 61.435 66.667 0.00 0.00 40.22 5.54
2208 2268 3.453679 GGGCTCTCGAACCTCGCT 61.454 66.667 0.00 0.00 40.21 4.93
2558 2626 5.344128 GCAAAAATGCACTACATGAACAGAG 59.656 40.000 0.00 0.00 39.60 3.35
2559 2627 5.221204 TGCAAAAATGCACTACATGAACAGA 60.221 36.000 0.00 0.00 39.60 3.41
2560 2628 4.983538 TGCAAAAATGCACTACATGAACAG 59.016 37.500 0.00 0.00 39.60 3.16
2562 2630 5.903764 TTGCAAAAATGCACTACATGAAC 57.096 34.783 0.00 0.00 45.32 3.18
2564 2632 6.047870 ACTTTTGCAAAAATGCACTACATGA 58.952 32.000 23.92 0.00 45.32 3.07
2565 2633 6.289745 ACTTTTGCAAAAATGCACTACATG 57.710 33.333 23.92 11.06 45.32 3.21
2567 2635 7.834068 TTAACTTTTGCAAAAATGCACTACA 57.166 28.000 23.92 0.00 45.32 2.74
2594 4557 9.747898 TCTGTGGATATGGTTAAAGTTTGTAAT 57.252 29.630 0.00 0.00 0.00 1.89
2597 4560 7.458397 TCTCTGTGGATATGGTTAAAGTTTGT 58.542 34.615 0.00 0.00 0.00 2.83
2606 4569 6.215636 ACCTACTTTTCTCTGTGGATATGGTT 59.784 38.462 0.00 0.00 0.00 3.67
2612 4575 6.670027 AGATGTACCTACTTTTCTCTGTGGAT 59.330 38.462 0.00 0.00 0.00 3.41
2614 4577 6.287589 AGATGTACCTACTTTTCTCTGTGG 57.712 41.667 0.00 0.00 0.00 4.17
2615 4578 8.185505 GTCTAGATGTACCTACTTTTCTCTGTG 58.814 40.741 0.00 0.00 0.00 3.66
2617 4580 8.514330 AGTCTAGATGTACCTACTTTTCTCTG 57.486 38.462 0.00 0.00 0.00 3.35
2626 4589 8.195436 TGCATTTTGTAGTCTAGATGTACCTAC 58.805 37.037 9.47 9.47 0.00 3.18
2627 4590 8.195436 GTGCATTTTGTAGTCTAGATGTACCTA 58.805 37.037 0.00 0.00 0.00 3.08
2628 4591 7.042335 GTGCATTTTGTAGTCTAGATGTACCT 58.958 38.462 0.00 0.00 0.00 3.08
2629 4592 6.816640 TGTGCATTTTGTAGTCTAGATGTACC 59.183 38.462 0.00 0.00 31.81 3.34
2630 4593 7.827819 TGTGCATTTTGTAGTCTAGATGTAC 57.172 36.000 0.00 2.03 32.91 2.90
2631 4594 8.257306 TGATGTGCATTTTGTAGTCTAGATGTA 58.743 33.333 0.00 0.00 0.00 2.29
2632 4595 7.105588 TGATGTGCATTTTGTAGTCTAGATGT 58.894 34.615 0.00 0.00 0.00 3.06
2633 4596 7.543947 TGATGTGCATTTTGTAGTCTAGATG 57.456 36.000 0.00 0.00 0.00 2.90
2634 4597 8.618677 CAATGATGTGCATTTTGTAGTCTAGAT 58.381 33.333 0.00 0.00 44.68 1.98
2636 4599 7.066163 TCCAATGATGTGCATTTTGTAGTCTAG 59.934 37.037 0.00 0.00 44.68 2.43
2637 4600 6.883756 TCCAATGATGTGCATTTTGTAGTCTA 59.116 34.615 0.00 0.00 44.68 2.59
2638 4601 5.711506 TCCAATGATGTGCATTTTGTAGTCT 59.288 36.000 0.00 0.00 44.68 3.24
2639 4602 5.953183 TCCAATGATGTGCATTTTGTAGTC 58.047 37.500 0.00 0.00 44.68 2.59
2644 4607 6.981559 TGATGTATCCAATGATGTGCATTTTG 59.018 34.615 0.00 0.00 44.68 2.44
2645 4608 7.114866 TGATGTATCCAATGATGTGCATTTT 57.885 32.000 0.00 0.00 44.68 1.82
2685 4648 9.935682 CATCTACAATACCAAACATGTACATTC 57.064 33.333 5.37 0.00 0.00 2.67
2692 4655 8.716646 TGTCTACATCTACAATACCAAACATG 57.283 34.615 0.00 0.00 0.00 3.21
2695 4658 8.773404 AACTGTCTACATCTACAATACCAAAC 57.227 34.615 0.00 0.00 0.00 2.93
2711 4674 8.305317 ACCAAGTGTATAGAGAAAACTGTCTAC 58.695 37.037 0.00 0.00 0.00 2.59
2714 4677 7.152645 TGACCAAGTGTATAGAGAAAACTGTC 58.847 38.462 0.00 0.00 0.00 3.51
2716 4679 7.962964 TTGACCAAGTGTATAGAGAAAACTG 57.037 36.000 0.00 0.00 0.00 3.16
2718 4681 8.379457 ACTTTGACCAAGTGTATAGAGAAAAC 57.621 34.615 0.00 0.00 44.70 2.43
2719 4682 8.836413 CAACTTTGACCAAGTGTATAGAGAAAA 58.164 33.333 0.00 0.00 45.77 2.29
2721 4684 7.732025 TCAACTTTGACCAAGTGTATAGAGAA 58.268 34.615 0.00 0.00 45.77 2.87
2755 4718 8.045176 AGTGCCTATAGATTTTTGTGAAAGTC 57.955 34.615 0.00 0.00 33.17 3.01
2758 4721 8.856153 TGTAGTGCCTATAGATTTTTGTGAAA 57.144 30.769 0.00 0.00 0.00 2.69
2759 4722 9.461312 AATGTAGTGCCTATAGATTTTTGTGAA 57.539 29.630 0.00 0.00 0.00 3.18
2760 4723 8.892723 CAATGTAGTGCCTATAGATTTTTGTGA 58.107 33.333 0.00 0.00 0.00 3.58
2761 4724 8.677300 ACAATGTAGTGCCTATAGATTTTTGTG 58.323 33.333 0.00 0.00 0.00 3.33
2762 4725 8.677300 CACAATGTAGTGCCTATAGATTTTTGT 58.323 33.333 0.00 0.00 32.04 2.83
2763 4726 8.892723 TCACAATGTAGTGCCTATAGATTTTTG 58.107 33.333 0.00 0.00 39.35 2.44
2768 4731 7.663081 CCATTTCACAATGTAGTGCCTATAGAT 59.337 37.037 0.00 0.00 38.58 1.98
2769 4732 6.992123 CCATTTCACAATGTAGTGCCTATAGA 59.008 38.462 0.00 0.00 38.58 1.98
2773 4736 5.172687 TCCATTTCACAATGTAGTGCCTA 57.827 39.130 0.00 0.00 38.58 3.93
2775 4738 3.129287 CCTCCATTTCACAATGTAGTGCC 59.871 47.826 0.00 0.00 38.58 5.01
2778 4741 5.880901 ACTTCCTCCATTTCACAATGTAGT 58.119 37.500 0.00 0.00 38.58 2.73
2779 4742 7.106239 AGTACTTCCTCCATTTCACAATGTAG 58.894 38.462 0.00 0.00 38.58 2.74
2780 4743 7.016153 AGTACTTCCTCCATTTCACAATGTA 57.984 36.000 0.00 0.00 38.58 2.29
2781 4744 5.880901 AGTACTTCCTCCATTTCACAATGT 58.119 37.500 0.00 0.00 38.58 2.71
2782 4745 7.921786 TTAGTACTTCCTCCATTTCACAATG 57.078 36.000 0.00 0.00 39.79 2.82
2783 4746 9.533831 AATTTAGTACTTCCTCCATTTCACAAT 57.466 29.630 0.00 0.00 0.00 2.71
2784 4747 8.934023 AATTTAGTACTTCCTCCATTTCACAA 57.066 30.769 0.00 0.00 0.00 3.33
2792 4755 9.603921 CCGTTTTATAATTTAGTACTTCCTCCA 57.396 33.333 0.00 0.00 0.00 3.86
2793 4756 9.822185 TCCGTTTTATAATTTAGTACTTCCTCC 57.178 33.333 0.00 0.00 0.00 4.30
2795 4758 9.828039 CCTCCGTTTTATAATTTAGTACTTCCT 57.172 33.333 0.00 0.00 0.00 3.36
2796 4759 9.049523 CCCTCCGTTTTATAATTTAGTACTTCC 57.950 37.037 0.00 0.00 0.00 3.46
2797 4760 9.822185 TCCCTCCGTTTTATAATTTAGTACTTC 57.178 33.333 0.00 0.00 0.00 3.01
2798 4761 9.828039 CTCCCTCCGTTTTATAATTTAGTACTT 57.172 33.333 0.00 0.00 0.00 2.24
2799 4762 8.985922 ACTCCCTCCGTTTTATAATTTAGTACT 58.014 33.333 0.00 0.00 0.00 2.73
2806 4769 8.887393 ACCATATACTCCCTCCGTTTTATAATT 58.113 33.333 0.00 0.00 0.00 1.40
2817 4780 3.744530 GCACACAACCATATACTCCCTCC 60.745 52.174 0.00 0.00 0.00 4.30
2913 4880 0.974010 TTCCGCCGGACCTCTACAAT 60.974 55.000 4.70 0.00 0.00 2.71
2974 4942 4.322080 TCGATTTAGACCGAGATTGCAT 57.678 40.909 0.00 0.00 0.00 3.96
3026 4994 1.004320 CAATCCCGGTCCACGTCAA 60.004 57.895 0.00 0.00 42.24 3.18
3046 5014 2.433318 GCTGCGAGCGTTTCCTCT 60.433 61.111 0.00 0.00 0.00 3.69
3129 5106 7.875554 AGCAAAACCAGTAAAGAGAAACAAAAA 59.124 29.630 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.