Multiple sequence alignment - TraesCS6D01G334500

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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 TraesCS6D01G334500 chr6D 100.000 2674 0 0 1 2674 436475358 436472685 0.000000e+00 4939.0
1 TraesCS6D01G334500 chr6D 95.282 869 23 2 1810 2674 271014034 271014888 0.000000e+00 1362.0
2 TraesCS6D01G334500 chr6D 88.481 599 48 15 892 1479 436638045 436638633 0.000000e+00 704.0
3 TraesCS6D01G334500 chr6D 84.854 581 47 19 922 1482 436420921 436421480 5.030000e-152 547.0
4 TraesCS6D01G334500 chr6D 81.410 312 32 12 1478 1776 436639422 436639720 5.760000e-57 231.0
5 TraesCS6D01G334500 chr6D 80.814 172 9 2 823 970 436552762 436552591 2.180000e-21 113.0
6 TraesCS6D01G334500 chr6D 100.000 28 0 0 377 404 436474955 436474982 5.000000e-03 52.8
7 TraesCS6D01G334500 chr5D 93.511 863 55 1 1812 2674 381159308 381158447 0.000000e+00 1282.0
8 TraesCS6D01G334500 chr6B 92.477 864 64 1 1811 2674 16537602 16536740 0.000000e+00 1234.0
9 TraesCS6D01G334500 chr6B 90.698 688 24 8 823 1482 659808620 659809295 0.000000e+00 880.0
10 TraesCS6D01G334500 chr6B 94.366 71 4 0 683 753 659808257 659808327 2.810000e-20 110.0
11 TraesCS6D01G334500 chr3B 92.902 789 56 0 1810 2598 187837211 187836423 0.000000e+00 1147.0
12 TraesCS6D01G334500 chr3B 89.003 582 36 16 915 1482 663573491 663574058 0.000000e+00 695.0
13 TraesCS6D01G334500 chr7D 95.971 695 22 5 1 692 17853011 17853702 0.000000e+00 1123.0
14 TraesCS6D01G334500 chr7A 94.391 731 41 0 1944 2674 448117456 448118186 0.000000e+00 1123.0
15 TraesCS6D01G334500 chr7A 92.836 684 46 3 1 683 479845414 479846095 0.000000e+00 989.0
16 TraesCS6D01G334500 chr7A 100.000 35 0 0 1810 1844 448117188 448117222 6.180000e-07 65.8
17 TraesCS6D01G334500 chr2A 93.245 681 41 4 1 680 310057151 310057827 0.000000e+00 998.0
18 TraesCS6D01G334500 chr4A 92.836 684 33 4 1 683 275749098 275749766 0.000000e+00 977.0
19 TraesCS6D01G334500 chr4A 91.860 688 39 5 1 687 346533547 346532876 0.000000e+00 944.0
20 TraesCS6D01G334500 chr4A 91.520 684 41 5 1 683 225978670 225979337 0.000000e+00 926.0
21 TraesCS6D01G334500 chr4A 91.815 672 37 5 1 671 345660222 345660876 0.000000e+00 920.0
22 TraesCS6D01G334500 chr5A 92.453 689 36 4 1 688 575089296 575089969 0.000000e+00 970.0
23 TraesCS6D01G334500 chr5A 92.555 685 35 4 1 684 519569445 519570114 0.000000e+00 968.0
24 TraesCS6D01G334500 chr5A 83.953 860 138 0 1812 2671 156223046 156223905 0.000000e+00 824.0
25 TraesCS6D01G334500 chr5A 89.238 669 53 1 2006 2674 175841025 175840376 0.000000e+00 819.0
26 TraesCS6D01G334500 chr5A 96.328 463 17 0 1 463 145745246 145745708 0.000000e+00 761.0
27 TraesCS6D01G334500 chr5A 93.814 194 11 1 1810 2003 175849977 175849785 9.360000e-75 291.0
28 TraesCS6D01G334500 chr6A 88.016 751 53 20 743 1482 584757793 584758517 0.000000e+00 854.0
29 TraesCS6D01G334500 chr6A 91.869 578 31 11 922 1490 584695519 584694949 0.000000e+00 793.0
30 TraesCS6D01G334500 chr6A 92.449 543 20 8 892 1425 584717895 584717365 0.000000e+00 756.0
31 TraesCS6D01G334500 chr6A 85.464 571 51 10 922 1475 584593395 584593950 1.390000e-157 566.0
32 TraesCS6D01G334500 chr6A 88.704 301 27 4 1478 1776 584716658 584716363 7.040000e-96 361.0
33 TraesCS6D01G334500 chr6A 88.704 301 27 4 1478 1776 584759302 584759597 7.040000e-96 361.0
34 TraesCS6D01G334500 chr6A 95.620 137 6 0 683 819 584757445 584757581 1.250000e-53 220.0
35 TraesCS6D01G334500 chr6A 75.478 314 33 19 1478 1776 584761245 584761529 2.180000e-21 113.0
36 TraesCS6D01G334500 chr1A 84.473 863 134 0 1812 2674 290414003 290413141 0.000000e+00 852.0
37 TraesCS6D01G334500 chr1A 85.827 127 16 2 1580 1705 511606947 511607072 1.670000e-27 134.0
38 TraesCS6D01G334500 chr3D 89.842 571 31 16 922 1482 502158164 502158717 0.000000e+00 708.0
39 TraesCS6D01G334500 chr3D 94.631 447 21 2 238 683 141342531 141342975 0.000000e+00 689.0
40 TraesCS6D01G334500 chr2D 94.407 447 21 3 238 683 245320875 245321318 0.000000e+00 684.0
41 TraesCS6D01G334500 chr4B 84.211 209 33 0 1812 2020 180999865 180999657 1.260000e-48 204.0
42 TraesCS6D01G334500 chr7B 72.018 436 96 20 1950 2372 571584239 571584661 3.640000e-19 106.0


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 TraesCS6D01G334500 chr6D 436472685 436475358 2673 True 4939.0 4939 100.0000 1 2674 1 chr6D.!!$R1 2673
1 TraesCS6D01G334500 chr6D 271014034 271014888 854 False 1362.0 1362 95.2820 1810 2674 1 chr6D.!!$F1 864
2 TraesCS6D01G334500 chr6D 436420921 436421480 559 False 547.0 547 84.8540 922 1482 1 chr6D.!!$F2 560
3 TraesCS6D01G334500 chr6D 436638045 436639720 1675 False 467.5 704 84.9455 892 1776 2 chr6D.!!$F4 884
4 TraesCS6D01G334500 chr5D 381158447 381159308 861 True 1282.0 1282 93.5110 1812 2674 1 chr5D.!!$R1 862
5 TraesCS6D01G334500 chr6B 16536740 16537602 862 True 1234.0 1234 92.4770 1811 2674 1 chr6B.!!$R1 863
6 TraesCS6D01G334500 chr6B 659808257 659809295 1038 False 495.0 880 92.5320 683 1482 2 chr6B.!!$F1 799
7 TraesCS6D01G334500 chr3B 187836423 187837211 788 True 1147.0 1147 92.9020 1810 2598 1 chr3B.!!$R1 788
8 TraesCS6D01G334500 chr3B 663573491 663574058 567 False 695.0 695 89.0030 915 1482 1 chr3B.!!$F1 567
9 TraesCS6D01G334500 chr7D 17853011 17853702 691 False 1123.0 1123 95.9710 1 692 1 chr7D.!!$F1 691
10 TraesCS6D01G334500 chr7A 479845414 479846095 681 False 989.0 989 92.8360 1 683 1 chr7A.!!$F1 682
11 TraesCS6D01G334500 chr7A 448117188 448118186 998 False 594.4 1123 97.1955 1810 2674 2 chr7A.!!$F2 864
12 TraesCS6D01G334500 chr2A 310057151 310057827 676 False 998.0 998 93.2450 1 680 1 chr2A.!!$F1 679
13 TraesCS6D01G334500 chr4A 275749098 275749766 668 False 977.0 977 92.8360 1 683 1 chr4A.!!$F2 682
14 TraesCS6D01G334500 chr4A 346532876 346533547 671 True 944.0 944 91.8600 1 687 1 chr4A.!!$R1 686
15 TraesCS6D01G334500 chr4A 225978670 225979337 667 False 926.0 926 91.5200 1 683 1 chr4A.!!$F1 682
16 TraesCS6D01G334500 chr4A 345660222 345660876 654 False 920.0 920 91.8150 1 671 1 chr4A.!!$F3 670
17 TraesCS6D01G334500 chr5A 575089296 575089969 673 False 970.0 970 92.4530 1 688 1 chr5A.!!$F4 687
18 TraesCS6D01G334500 chr5A 519569445 519570114 669 False 968.0 968 92.5550 1 684 1 chr5A.!!$F3 683
19 TraesCS6D01G334500 chr5A 156223046 156223905 859 False 824.0 824 83.9530 1812 2671 1 chr5A.!!$F2 859
20 TraesCS6D01G334500 chr5A 175840376 175841025 649 True 819.0 819 89.2380 2006 2674 1 chr5A.!!$R1 668
21 TraesCS6D01G334500 chr6A 584694949 584695519 570 True 793.0 793 91.8690 922 1490 1 chr6A.!!$R1 568
22 TraesCS6D01G334500 chr6A 584593395 584593950 555 False 566.0 566 85.4640 922 1475 1 chr6A.!!$F1 553
23 TraesCS6D01G334500 chr6A 584716363 584717895 1532 True 558.5 756 90.5765 892 1776 2 chr6A.!!$R2 884
24 TraesCS6D01G334500 chr6A 584757445 584761529 4084 False 387.0 854 86.9545 683 1776 4 chr6A.!!$F2 1093
25 TraesCS6D01G334500 chr1A 290413141 290414003 862 True 852.0 852 84.4730 1812 2674 1 chr1A.!!$R1 862
26 TraesCS6D01G334500 chr3D 502158164 502158717 553 False 708.0 708 89.8420 922 1482 1 chr3D.!!$F2 560

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
532 534 0.179067 AACAAGCCGACGAACTTCCA 60.179 50.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 5098 0.179045 GGTGAGACTGCCACAACACT 60.179 55.0 0.0 0.0 36.31 3.55 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
62 63 9.234827 TCAATGTTGATGATCTCAAACAACTAT 57.765 29.630 21.94 15.48 45.27 2.12
111 112 2.224597 TGGATGTGTGCACAATGAGAGT 60.225 45.455 23.59 2.28 45.41 3.24
262 264 1.645710 AGGTCAAGACGAGGTGGATT 58.354 50.000 0.00 0.00 0.00 3.01
359 361 4.390909 GCCTTCAAAAATCAAGCCATGAAG 59.609 41.667 0.00 6.39 42.54 3.02
432 434 5.565509 TCTTTGTGGCACATATTTACCTCA 58.434 37.500 22.73 0.00 44.52 3.86
481 483 5.238650 GGACCCCATTAAAGATTACATCACG 59.761 44.000 0.00 0.00 0.00 4.35
532 534 0.179067 AACAAGCCGACGAACTTCCA 60.179 50.000 0.00 0.00 0.00 3.53
537 539 0.878961 GCCGACGAACTTCCACACTT 60.879 55.000 0.00 0.00 0.00 3.16
547 549 5.007626 CGAACTTCCACACTTGAGAATTCAA 59.992 40.000 8.44 0.00 40.92 2.69
588 594 0.594602 CCACACTGCACAACCTGATG 59.405 55.000 0.00 0.00 0.00 3.07
597 603 2.045926 AACCTGATGCTCGTGCCC 60.046 61.111 7.05 0.00 38.71 5.36
635 641 7.631717 ACTTTAGTTGAAGGAAGGATAATGC 57.368 36.000 0.00 0.00 0.00 3.56
658 664 4.081322 GGGATGCTATTTTCTCCCGTTA 57.919 45.455 0.00 0.00 38.15 3.18
772 1022 5.186409 ACGGACTTGTAGTAGAGGCAAATTA 59.814 40.000 0.00 0.00 0.00 1.40
773 1023 6.127140 ACGGACTTGTAGTAGAGGCAAATTAT 60.127 38.462 0.00 0.00 0.00 1.28
823 1073 6.998968 AAGAAGAGAAATTGCTATGGACAG 57.001 37.500 0.00 0.00 0.00 3.51
824 1074 6.305272 AGAAGAGAAATTGCTATGGACAGA 57.695 37.500 0.00 0.00 0.00 3.41
825 1075 6.715280 AGAAGAGAAATTGCTATGGACAGAA 58.285 36.000 0.00 0.00 0.00 3.02
826 1076 7.170965 AGAAGAGAAATTGCTATGGACAGAAA 58.829 34.615 0.00 0.00 0.00 2.52
827 1077 7.667219 AGAAGAGAAATTGCTATGGACAGAAAA 59.333 33.333 0.00 0.00 0.00 2.29
828 1078 7.388460 AGAGAAATTGCTATGGACAGAAAAG 57.612 36.000 0.00 0.00 0.00 2.27
835 1311 5.713025 TGCTATGGACAGAAAAGAAATTGC 58.287 37.500 0.00 0.00 0.00 3.56
836 1312 5.243507 TGCTATGGACAGAAAAGAAATTGCA 59.756 36.000 0.00 0.00 0.00 4.08
1019 1563 1.464608 CATTGATCCAACACGTTCGCT 59.535 47.619 0.00 0.00 0.00 4.93
1020 1564 1.144969 TTGATCCAACACGTTCGCTC 58.855 50.000 0.00 0.00 0.00 5.03
1021 1565 0.669318 TGATCCAACACGTTCGCTCC 60.669 55.000 0.00 0.00 0.00 4.70
1022 1566 1.683790 GATCCAACACGTTCGCTCCG 61.684 60.000 0.00 0.00 0.00 4.63
1023 1567 3.411351 CCAACACGTTCGCTCCGG 61.411 66.667 0.00 0.00 0.00 5.14
1024 1568 4.072088 CAACACGTTCGCTCCGGC 62.072 66.667 0.00 0.00 0.00 6.13
1462 2030 2.885861 GAGCACGTCCAGATCGGT 59.114 61.111 0.00 0.00 35.57 4.69
1491 2849 1.227674 CCTTGGGATAGCAGCGGTC 60.228 63.158 0.00 0.00 0.00 4.79
1524 2882 1.675552 TGCCTGATCTCGACGACATA 58.324 50.000 0.00 0.00 0.00 2.29
1540 2898 7.119846 TCGACGACATAGAGATGTGATGATAAT 59.880 37.037 0.00 0.00 46.64 1.28
1542 2900 8.754230 ACGACATAGAGATGTGATGATAATTG 57.246 34.615 0.00 0.00 46.64 2.32
1631 2998 7.545965 ACTTGAACTATGGTTTTAGATGTCTCG 59.454 37.037 10.01 0.00 35.58 4.04
1641 3008 7.822334 TGGTTTTAGATGTCTCGAATACACAAT 59.178 33.333 2.59 0.00 0.00 2.71
1647 3014 7.743104 AGATGTCTCGAATACACAATTTTGAC 58.257 34.615 0.00 0.00 0.00 3.18
1659 3026 9.912634 ATACACAATTTTGACCACTTATTTCTG 57.087 29.630 0.00 0.00 0.00 3.02
1666 3033 6.509418 TTGACCACTTATTTCTGTTATGCC 57.491 37.500 0.00 0.00 0.00 4.40
1669 3036 7.342581 TGACCACTTATTTCTGTTATGCCATA 58.657 34.615 0.00 0.00 0.00 2.74
1671 3038 9.502091 GACCACTTATTTCTGTTATGCCATATA 57.498 33.333 0.00 0.00 0.00 0.86
1672 3039 9.860650 ACCACTTATTTCTGTTATGCCATATAA 57.139 29.630 0.00 0.00 0.00 0.98
1756 5057 7.615582 TCAATGCAGAAATCTACCAAGTTAG 57.384 36.000 0.00 0.00 0.00 2.34
1766 5067 4.680407 TCTACCAAGTTAGTAAGCTCCCA 58.320 43.478 0.00 0.00 0.00 4.37
1785 5086 3.146618 CAAGAATTGCTGACTCATGGC 57.853 47.619 0.00 0.00 40.39 4.40
1786 5087 2.753452 CAAGAATTGCTGACTCATGGCT 59.247 45.455 0.00 0.00 40.39 4.75
1787 5088 3.083122 AGAATTGCTGACTCATGGCTT 57.917 42.857 0.00 0.00 0.00 4.35
1788 5089 2.753452 AGAATTGCTGACTCATGGCTTG 59.247 45.455 0.00 0.00 0.00 4.01
1789 5090 1.471119 ATTGCTGACTCATGGCTTGG 58.529 50.000 0.09 0.00 0.00 3.61
1790 5091 0.111061 TTGCTGACTCATGGCTTGGT 59.889 50.000 0.09 0.00 0.00 3.67
1791 5092 0.983467 TGCTGACTCATGGCTTGGTA 59.017 50.000 0.09 0.00 0.00 3.25
1792 5093 1.350684 TGCTGACTCATGGCTTGGTAA 59.649 47.619 0.09 0.00 0.00 2.85
1793 5094 2.224744 TGCTGACTCATGGCTTGGTAAA 60.225 45.455 0.09 0.00 0.00 2.01
1794 5095 2.162408 GCTGACTCATGGCTTGGTAAAC 59.838 50.000 0.09 0.00 0.00 2.01
1795 5096 2.749621 CTGACTCATGGCTTGGTAAACC 59.250 50.000 0.09 0.00 0.00 3.27
1796 5097 2.375174 TGACTCATGGCTTGGTAAACCT 59.625 45.455 0.02 0.00 36.82 3.50
1797 5098 3.585289 TGACTCATGGCTTGGTAAACCTA 59.415 43.478 0.02 0.00 36.82 3.08
1798 5099 4.192317 GACTCATGGCTTGGTAAACCTAG 58.808 47.826 6.27 6.27 40.99 3.02
1799 5100 3.587506 ACTCATGGCTTGGTAAACCTAGT 59.412 43.478 11.42 0.00 40.32 2.57
1800 5101 3.941483 CTCATGGCTTGGTAAACCTAGTG 59.059 47.826 11.42 3.68 40.32 2.74
1801 5102 3.329520 TCATGGCTTGGTAAACCTAGTGT 59.670 43.478 11.42 0.00 40.32 3.55
1802 5103 3.868619 TGGCTTGGTAAACCTAGTGTT 57.131 42.857 11.42 0.00 40.32 3.32
1803 5104 3.482436 TGGCTTGGTAAACCTAGTGTTG 58.518 45.455 11.42 0.00 40.32 3.33
1804 5105 3.117813 TGGCTTGGTAAACCTAGTGTTGT 60.118 43.478 11.42 0.00 40.32 3.32
1805 5106 3.252458 GGCTTGGTAAACCTAGTGTTGTG 59.748 47.826 11.42 0.00 40.32 3.33
1806 5107 3.252458 GCTTGGTAAACCTAGTGTTGTGG 59.748 47.826 11.42 0.00 40.32 4.17
1807 5108 2.853705 TGGTAAACCTAGTGTTGTGGC 58.146 47.619 0.02 0.00 37.23 5.01
1808 5109 2.172930 TGGTAAACCTAGTGTTGTGGCA 59.827 45.455 0.02 0.00 37.23 4.92
2004 5439 1.330655 GGGGAAGAGGAGATCGCACA 61.331 60.000 0.00 0.00 0.00 4.57
2064 5499 1.898472 CATCATCTACCTCGGCATCCT 59.102 52.381 0.00 0.00 0.00 3.24
2159 5594 2.705821 CGCGCAACTCTCCTCTCCT 61.706 63.158 8.75 0.00 0.00 3.69
2374 5832 2.435938 GACGGCCTCGGCATCAAA 60.436 61.111 10.51 0.00 45.37 2.69
2398 5856 0.106967 TATACCGCCAAGGCATTGCA 60.107 50.000 11.39 0.00 46.52 4.08
2431 5889 2.186826 GTTGTGGCTCCAACGCACT 61.187 57.895 5.16 0.00 35.78 4.40
2438 5896 2.847234 TCCAACGCACTGACCCCT 60.847 61.111 0.00 0.00 0.00 4.79
2439 5897 2.113139 CCAACGCACTGACCCCTT 59.887 61.111 0.00 0.00 0.00 3.95
2586 6044 0.304705 CAGACTGTGTTTGACGTGGC 59.695 55.000 0.00 0.00 0.00 5.01
2587 6045 0.814010 AGACTGTGTTTGACGTGGCC 60.814 55.000 0.00 0.00 0.00 5.36
2588 6046 1.782028 GACTGTGTTTGACGTGGCCC 61.782 60.000 0.00 0.00 0.00 5.80
2589 6047 2.517402 TGTGTTTGACGTGGCCCC 60.517 61.111 0.00 0.00 0.00 5.80
2590 6048 2.203294 GTGTTTGACGTGGCCCCT 60.203 61.111 0.00 0.00 0.00 4.79
2591 6049 1.826487 GTGTTTGACGTGGCCCCTT 60.826 57.895 0.00 0.00 0.00 3.95
2592 6050 1.527380 TGTTTGACGTGGCCCCTTC 60.527 57.895 0.00 0.00 0.00 3.46
2593 6051 2.114411 TTTGACGTGGCCCCTTCC 59.886 61.111 0.00 0.00 0.00 3.46
2594 6052 3.501040 TTTGACGTGGCCCCTTCCC 62.501 63.158 0.00 0.00 0.00 3.97
2595 6053 4.974438 TGACGTGGCCCCTTCCCT 62.974 66.667 0.00 0.00 0.00 4.20
2596 6054 4.097361 GACGTGGCCCCTTCCCTC 62.097 72.222 0.00 0.00 0.00 4.30
2599 6057 2.042261 GTGGCCCCTTCCCTCCTA 59.958 66.667 0.00 0.00 0.00 2.94
2620 6092 4.351938 CTTGTCCCACGACGCCGA 62.352 66.667 0.00 0.00 42.37 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 8.783093 CCTGTAACATCAACAATCAGAACTAAA 58.217 33.333 0.00 0.00 0.00 1.85
111 112 4.132336 GTTTCTGCTATCTCCATGATGCA 58.868 43.478 0.00 0.00 37.09 3.96
262 264 5.071788 CCTACCCAACTTAGGCAGATGAATA 59.928 44.000 0.00 0.00 29.85 1.75
401 403 7.886629 AATATGTGCCACAAAGAGATAATGT 57.113 32.000 0.00 0.00 0.00 2.71
402 404 9.669353 GTAAATATGTGCCACAAAGAGATAATG 57.331 33.333 0.00 0.00 0.00 1.90
432 434 5.768164 AGTTAACATGGAAACCGTTGAAGAT 59.232 36.000 8.61 0.00 0.00 2.40
481 483 2.802816 CTCATATTGAGTTGGCGCCTAC 59.197 50.000 30.21 30.21 39.58 3.18
556 561 3.181455 TGCAGTGTGGTAGACATGAAACT 60.181 43.478 0.00 0.00 36.78 2.66
588 594 3.958147 TAGCTTGCAGGGCACGAGC 62.958 63.158 14.52 6.76 41.16 5.03
597 603 7.364522 TCAACTAAAGTAACATAGCTTGCAG 57.635 36.000 0.00 0.00 0.00 4.41
658 664 0.596341 GAAAATTGCCCGTGCGTTGT 60.596 50.000 0.00 0.00 41.78 3.32
805 1055 7.383102 TCTTTTCTGTCCATAGCAATTTCTC 57.617 36.000 0.00 0.00 0.00 2.87
823 1073 5.055812 TGGTGTCCATTGCAATTTCTTTTC 58.944 37.500 9.83 0.00 0.00 2.29
824 1074 5.033589 TGGTGTCCATTGCAATTTCTTTT 57.966 34.783 9.83 0.00 0.00 2.27
825 1075 4.503643 CCTGGTGTCCATTGCAATTTCTTT 60.504 41.667 9.83 0.00 30.82 2.52
826 1076 3.007182 CCTGGTGTCCATTGCAATTTCTT 59.993 43.478 9.83 0.00 30.82 2.52
827 1077 2.564062 CCTGGTGTCCATTGCAATTTCT 59.436 45.455 9.83 0.00 30.82 2.52
828 1078 2.932187 GCCTGGTGTCCATTGCAATTTC 60.932 50.000 9.83 3.88 33.30 2.17
835 1311 0.606401 AACGAGCCTGGTGTCCATTG 60.606 55.000 0.00 0.00 30.82 2.82
836 1312 0.606401 CAACGAGCCTGGTGTCCATT 60.606 55.000 0.00 0.00 30.82 3.16
887 1387 3.421919 TGTTTCCCTAACCCTAAACGG 57.578 47.619 0.00 0.00 35.81 4.44
1024 1568 3.175240 CGTGAGTTGCGAGCGGAG 61.175 66.667 0.00 0.00 0.00 4.63
1485 2843 1.302271 GGGAAAACGAAGGACCGCT 60.302 57.895 0.00 0.00 0.00 5.52
1491 2849 0.527565 CAGGCATGGGAAAACGAAGG 59.472 55.000 0.00 0.00 0.00 3.46
1524 2882 5.310068 AGCCCTCAATTATCATCACATCTCT 59.690 40.000 0.00 0.00 0.00 3.10
1540 2898 6.891908 AGAAGAAAAATAAGCATAGCCCTCAA 59.108 34.615 0.00 0.00 0.00 3.02
1542 2900 6.951062 AGAAGAAAAATAAGCATAGCCCTC 57.049 37.500 0.00 0.00 0.00 4.30
1641 3008 7.014711 TGGCATAACAGAAATAAGTGGTCAAAA 59.985 33.333 0.00 0.00 0.00 2.44
1724 3096 8.632679 TGGTAGATTTCTGCATTGATATTTTCC 58.367 33.333 0.00 0.00 0.00 3.13
1739 3111 7.364851 GGGAGCTTACTAACTTGGTAGATTTCT 60.365 40.741 0.00 0.00 0.00 2.52
1740 3112 6.762187 GGGAGCTTACTAACTTGGTAGATTTC 59.238 42.308 0.00 0.00 0.00 2.17
1756 5057 3.127721 GTCAGCAATTCTTGGGAGCTTAC 59.872 47.826 0.00 0.00 32.35 2.34
1766 5067 3.083122 AGCCATGAGTCAGCAATTCTT 57.917 42.857 7.08 0.00 0.00 2.52
1776 5077 3.073274 AGGTTTACCAAGCCATGAGTC 57.927 47.619 1.13 0.00 38.89 3.36
1777 5078 3.587506 ACTAGGTTTACCAAGCCATGAGT 59.412 43.478 1.13 0.00 38.89 3.41
1778 5079 3.941483 CACTAGGTTTACCAAGCCATGAG 59.059 47.826 1.13 0.00 38.89 2.90
1779 5080 3.329520 ACACTAGGTTTACCAAGCCATGA 59.670 43.478 1.13 0.00 38.89 3.07
1780 5081 3.686016 ACACTAGGTTTACCAAGCCATG 58.314 45.455 1.13 0.00 38.89 3.66
1781 5082 4.079253 CAACACTAGGTTTACCAAGCCAT 58.921 43.478 1.13 0.00 37.72 4.40
1782 5083 3.117813 ACAACACTAGGTTTACCAAGCCA 60.118 43.478 1.13 0.00 37.72 4.75
1783 5084 3.252458 CACAACACTAGGTTTACCAAGCC 59.748 47.826 1.13 0.00 37.72 4.35
1784 5085 3.252458 CCACAACACTAGGTTTACCAAGC 59.748 47.826 1.13 0.00 37.72 4.01
1785 5086 3.252458 GCCACAACACTAGGTTTACCAAG 59.748 47.826 1.13 0.00 37.72 3.61
1786 5087 3.215975 GCCACAACACTAGGTTTACCAA 58.784 45.455 1.13 0.00 37.72 3.67
1787 5088 2.172930 TGCCACAACACTAGGTTTACCA 59.827 45.455 1.13 0.00 37.72 3.25
1788 5089 2.812011 CTGCCACAACACTAGGTTTACC 59.188 50.000 0.00 0.00 37.72 2.85
1789 5090 3.473625 ACTGCCACAACACTAGGTTTAC 58.526 45.455 0.00 0.00 37.72 2.01
1790 5091 3.389983 AGACTGCCACAACACTAGGTTTA 59.610 43.478 0.00 0.00 37.72 2.01
1791 5092 2.172717 AGACTGCCACAACACTAGGTTT 59.827 45.455 0.00 0.00 37.72 3.27
1792 5093 1.768870 AGACTGCCACAACACTAGGTT 59.231 47.619 0.00 0.00 41.47 3.50
1793 5094 1.344763 GAGACTGCCACAACACTAGGT 59.655 52.381 0.00 0.00 0.00 3.08
1794 5095 1.344438 TGAGACTGCCACAACACTAGG 59.656 52.381 0.00 0.00 0.00 3.02
1795 5096 2.408050 GTGAGACTGCCACAACACTAG 58.592 52.381 0.00 0.00 34.81 2.57
1796 5097 1.070134 GGTGAGACTGCCACAACACTA 59.930 52.381 0.00 0.00 36.31 2.74
1797 5098 0.179045 GGTGAGACTGCCACAACACT 60.179 55.000 0.00 0.00 36.31 3.55
1798 5099 1.498865 CGGTGAGACTGCCACAACAC 61.499 60.000 0.00 0.00 36.31 3.32
1799 5100 1.227527 CGGTGAGACTGCCACAACA 60.228 57.895 0.00 0.00 36.31 3.33
1800 5101 2.607892 GCGGTGAGACTGCCACAAC 61.608 63.158 0.00 0.00 44.50 3.32
1801 5102 2.280797 GCGGTGAGACTGCCACAA 60.281 61.111 0.00 0.00 44.50 3.33
2004 5439 1.515020 GTCAGCTCGCTCTGGATGT 59.485 57.895 4.35 0.00 34.91 3.06
2131 5566 2.050533 GTTGCGCGCCATGTTGAA 60.051 55.556 30.77 11.58 0.00 2.69
2159 5594 2.904866 GGCAAGGCGTTCACCACA 60.905 61.111 3.42 0.00 0.00 4.17
2358 5816 2.436646 CTTTGATGCCGAGGCCGT 60.437 61.111 12.05 0.00 41.09 5.68
2374 5832 0.689745 TGCCTTGGCGGTATAGGTCT 60.690 55.000 7.18 0.00 34.25 3.85
2431 5889 1.133809 CCCAAGGTCTGAAGGGGTCA 61.134 60.000 0.00 0.00 37.66 4.02
2438 5896 1.067295 AGATGTGCCCAAGGTCTGAA 58.933 50.000 0.00 0.00 0.00 3.02
2439 5897 1.003580 GAAGATGTGCCCAAGGTCTGA 59.996 52.381 0.00 0.00 0.00 3.27
2586 6044 2.039724 GGGGTAGGAGGGAAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
2587 6045 0.988678 CAAGGGGTAGGAGGGAAGGG 60.989 65.000 0.00 0.00 0.00 3.95
2588 6046 0.253207 ACAAGGGGTAGGAGGGAAGG 60.253 60.000 0.00 0.00 0.00 3.46
2589 6047 1.205055 GACAAGGGGTAGGAGGGAAG 58.795 60.000 0.00 0.00 0.00 3.46
2590 6048 0.253020 GGACAAGGGGTAGGAGGGAA 60.253 60.000 0.00 0.00 0.00 3.97
2591 6049 1.394963 GGACAAGGGGTAGGAGGGA 59.605 63.158 0.00 0.00 0.00 4.20
2592 6050 1.693103 GGGACAAGGGGTAGGAGGG 60.693 68.421 0.00 0.00 0.00 4.30
2593 6051 1.082206 TGGGACAAGGGGTAGGAGG 59.918 63.158 0.00 0.00 31.92 4.30
2594 6052 1.614241 CGTGGGACAAGGGGTAGGAG 61.614 65.000 0.00 0.00 44.16 3.69
2595 6053 1.611261 CGTGGGACAAGGGGTAGGA 60.611 63.158 0.00 0.00 44.16 2.94
2596 6054 1.611261 TCGTGGGACAAGGGGTAGG 60.611 63.158 0.00 0.00 44.16 3.18
2597 6055 1.595357 GTCGTGGGACAAGGGGTAG 59.405 63.158 0.00 0.00 44.16 3.18
2598 6056 2.277591 CGTCGTGGGACAAGGGGTA 61.278 63.158 0.00 0.00 44.16 3.69
2599 6057 3.622826 CGTCGTGGGACAAGGGGT 61.623 66.667 0.00 0.00 44.16 4.95


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

AutoCloner maintained by Alex Coulton.