Multiple sequence alignment - TraesCS3D01G156000

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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 TraesCS3D01G156000 chr3D 100.000 3483 0 0 1 3483 123567970 123564488 0.000000e+00 6433.0
1 TraesCS3D01G156000 chr3D 90.335 1076 63 16 2442 3483 513667698 513668766 0.000000e+00 1373.0
2 TraesCS3D01G156000 chr3D 92.377 551 33 2 1 542 254775886 254775336 0.000000e+00 776.0
3 TraesCS3D01G156000 chr3D 81.754 855 100 32 1005 1838 123517234 123516415 0.000000e+00 664.0
4 TraesCS3D01G156000 chr3D 72.852 512 114 22 1109 1613 110183017 110182524 6.020000e-33 152.0
5 TraesCS3D01G156000 chr3B 89.754 1786 93 22 710 2442 176860357 176858609 0.000000e+00 2202.0
6 TraesCS3D01G156000 chr3B 89.754 1786 93 22 710 2442 176880108 176878360 0.000000e+00 2202.0
7 TraesCS3D01G156000 chr3B 82.349 1490 173 51 1005 2442 176783580 176782129 0.000000e+00 1212.0
8 TraesCS3D01G156000 chr3B 88.740 968 91 13 2528 3483 804717958 804718919 0.000000e+00 1168.0
9 TraesCS3D01G156000 chr3B 81.354 1507 177 57 1005 2442 176636737 176635266 0.000000e+00 1131.0
10 TraesCS3D01G156000 chr6D 93.352 1053 50 14 2449 3483 461498305 461499355 0.000000e+00 1539.0
11 TraesCS3D01G156000 chr6D 89.991 1069 67 16 2443 3483 49838666 49839722 0.000000e+00 1345.0
12 TraesCS3D01G156000 chr6D 89.013 1074 85 11 2442 3483 102461699 102462771 0.000000e+00 1299.0
13 TraesCS3D01G156000 chr6D 89.266 177 8 3 2442 2607 3197097 3196921 9.790000e-51 211.0
14 TraesCS3D01G156000 chr5D 91.776 1070 53 13 2443 3483 445876245 445875182 0.000000e+00 1456.0
15 TraesCS3D01G156000 chr5D 92.414 1015 53 16 2487 3483 23692041 23693049 0.000000e+00 1426.0
16 TraesCS3D01G156000 chr5D 88.007 567 64 4 1 564 493129456 493128891 0.000000e+00 667.0
17 TraesCS3D01G156000 chr5D 86.425 221 25 4 1400 1618 391854690 391854473 1.620000e-58 237.0
18 TraesCS3D01G156000 chr3A 90.571 1103 73 22 1361 2442 131415717 131416809 0.000000e+00 1432.0
19 TraesCS3D01G156000 chr3A 88.936 714 41 15 1 705 565790647 565791331 0.000000e+00 846.0
20 TraesCS3D01G156000 chr3A 88.702 593 49 12 707 1296 131415108 131415685 0.000000e+00 708.0
21 TraesCS3D01G156000 chr3A 84.211 608 49 17 1005 1611 131084146 131083585 6.570000e-152 547.0
22 TraesCS3D01G156000 chr3A 83.304 569 71 12 1894 2442 131077411 131076847 1.440000e-138 503.0
23 TraesCS3D01G156000 chr3A 90.323 124 12 0 1690 1813 131081113 131080990 2.780000e-36 163.0
24 TraesCS3D01G156000 chr7B 88.458 979 86 15 2526 3483 293067794 293068766 0.000000e+00 1157.0
25 TraesCS3D01G156000 chr7B 92.887 478 24 4 6 473 115543155 115542678 0.000000e+00 686.0
26 TraesCS3D01G156000 chr6A 87.963 972 89 14 2531 3481 11992517 11991553 0.000000e+00 1122.0
27 TraesCS3D01G156000 chr1D 84.158 1010 89 46 2487 3483 118505173 118504222 0.000000e+00 913.0
28 TraesCS3D01G156000 chr1D 82.530 166 13 6 2443 2596 69480620 69480781 7.840000e-27 132.0
29 TraesCS3D01G156000 chr7D 94.655 580 22 2 1 571 64259712 64260291 0.000000e+00 891.0
30 TraesCS3D01G156000 chr7D 94.949 99 5 0 607 705 388132273 388132371 4.650000e-34 156.0
31 TraesCS3D01G156000 chr7D 93.939 99 6 0 607 705 64260296 64260394 2.170000e-32 150.0
32 TraesCS3D01G156000 chr1A 93.588 577 28 4 4 571 566605139 566605715 0.000000e+00 852.0
33 TraesCS3D01G156000 chr1A 93.939 99 6 0 607 705 566605720 566605818 2.170000e-32 150.0
34 TraesCS3D01G156000 chr1A 81.768 181 14 11 2443 2607 113232802 113232625 2.180000e-27 134.0
35 TraesCS3D01G156000 chr1A 84.615 143 10 1 2442 2572 521934727 521934869 7.840000e-27 132.0
36 TraesCS3D01G156000 chr5B 87.456 574 68 4 1 571 608357124 608356552 0.000000e+00 658.0
37 TraesCS3D01G156000 chr5B 86.063 574 74 5 1 571 608211843 608211273 2.300000e-171 612.0
38 TraesCS3D01G156000 chr5B 83.636 220 27 6 1400 1613 472288177 472287961 7.630000e-47 198.0
39 TraesCS3D01G156000 chr5A 84.801 579 79 8 1 571 616151148 616150571 1.080000e-159 573.0
40 TraesCS3D01G156000 chr5A 92.453 106 7 1 607 711 653384750 653384855 2.170000e-32 150.0
41 TraesCS3D01G156000 chr4D 79.545 528 70 18 2442 2947 399607771 399607260 3.330000e-90 342.0
42 TraesCS3D01G156000 chr4D 81.215 181 14 7 2446 2610 399576091 399575915 1.010000e-25 128.0
43 TraesCS3D01G156000 chrUn 82.734 278 25 11 2442 2701 87261043 87260771 3.500000e-55 226.0
44 TraesCS3D01G156000 chrUn 82.734 278 25 11 2442 2701 235076902 235076630 3.500000e-55 226.0
45 TraesCS3D01G156000 chrUn 82.635 167 17 9 2542 2701 346719491 346719652 1.690000e-28 137.0
46 TraesCS3D01G156000 chr7A 94.118 102 4 2 612 712 486872381 486872481 1.670000e-33 154.0
47 TraesCS3D01G156000 chr4A 79.545 176 33 1 1123 1295 697951922 697952097 4.720000e-24 122.0
48 TraesCS3D01G156000 chr6B 77.848 158 32 3 1688 1843 25571630 25571786 1.030000e-15 95.3
49 TraesCS3D01G156000 chr2D 86.585 82 11 0 624 705 15132939 15133020 1.330000e-14 91.6


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 TraesCS3D01G156000 chr3D 123564488 123567970 3482 True 6433.000000 6433 100.0000 1 3483 1 chr3D.!!$R3 3482
1 TraesCS3D01G156000 chr3D 513667698 513668766 1068 False 1373.000000 1373 90.3350 2442 3483 1 chr3D.!!$F1 1041
2 TraesCS3D01G156000 chr3D 254775336 254775886 550 True 776.000000 776 92.3770 1 542 1 chr3D.!!$R4 541
3 TraesCS3D01G156000 chr3D 123516415 123517234 819 True 664.000000 664 81.7540 1005 1838 1 chr3D.!!$R2 833
4 TraesCS3D01G156000 chr3B 176858609 176860357 1748 True 2202.000000 2202 89.7540 710 2442 1 chr3B.!!$R3 1732
5 TraesCS3D01G156000 chr3B 176878360 176880108 1748 True 2202.000000 2202 89.7540 710 2442 1 chr3B.!!$R4 1732
6 TraesCS3D01G156000 chr3B 176782129 176783580 1451 True 1212.000000 1212 82.3490 1005 2442 1 chr3B.!!$R2 1437
7 TraesCS3D01G156000 chr3B 804717958 804718919 961 False 1168.000000 1168 88.7400 2528 3483 1 chr3B.!!$F1 955
8 TraesCS3D01G156000 chr3B 176635266 176636737 1471 True 1131.000000 1131 81.3540 1005 2442 1 chr3B.!!$R1 1437
9 TraesCS3D01G156000 chr6D 461498305 461499355 1050 False 1539.000000 1539 93.3520 2449 3483 1 chr6D.!!$F3 1034
10 TraesCS3D01G156000 chr6D 49838666 49839722 1056 False 1345.000000 1345 89.9910 2443 3483 1 chr6D.!!$F1 1040
11 TraesCS3D01G156000 chr6D 102461699 102462771 1072 False 1299.000000 1299 89.0130 2442 3483 1 chr6D.!!$F2 1041
12 TraesCS3D01G156000 chr5D 445875182 445876245 1063 True 1456.000000 1456 91.7760 2443 3483 1 chr5D.!!$R2 1040
13 TraesCS3D01G156000 chr5D 23692041 23693049 1008 False 1426.000000 1426 92.4140 2487 3483 1 chr5D.!!$F1 996
14 TraesCS3D01G156000 chr5D 493128891 493129456 565 True 667.000000 667 88.0070 1 564 1 chr5D.!!$R3 563
15 TraesCS3D01G156000 chr3A 131415108 131416809 1701 False 1070.000000 1432 89.6365 707 2442 2 chr3A.!!$F2 1735
16 TraesCS3D01G156000 chr3A 565790647 565791331 684 False 846.000000 846 88.9360 1 705 1 chr3A.!!$F1 704
17 TraesCS3D01G156000 chr3A 131076847 131084146 7299 True 404.333333 547 85.9460 1005 2442 3 chr3A.!!$R1 1437
18 TraesCS3D01G156000 chr7B 293067794 293068766 972 False 1157.000000 1157 88.4580 2526 3483 1 chr7B.!!$F1 957
19 TraesCS3D01G156000 chr6A 11991553 11992517 964 True 1122.000000 1122 87.9630 2531 3481 1 chr6A.!!$R1 950
20 TraesCS3D01G156000 chr1D 118504222 118505173 951 True 913.000000 913 84.1580 2487 3483 1 chr1D.!!$R1 996
21 TraesCS3D01G156000 chr7D 64259712 64260394 682 False 520.500000 891 94.2970 1 705 2 chr7D.!!$F2 704
22 TraesCS3D01G156000 chr1A 566605139 566605818 679 False 501.000000 852 93.7635 4 705 2 chr1A.!!$F2 701
23 TraesCS3D01G156000 chr5B 608356552 608357124 572 True 658.000000 658 87.4560 1 571 1 chr5B.!!$R3 570
24 TraesCS3D01G156000 chr5B 608211273 608211843 570 True 612.000000 612 86.0630 1 571 1 chr5B.!!$R2 570
25 TraesCS3D01G156000 chr5A 616150571 616151148 577 True 573.000000 573 84.8010 1 571 1 chr5A.!!$R1 570
26 TraesCS3D01G156000 chr4D 399607260 399607771 511 True 342.000000 342 79.5450 2442 2947 1 chr4D.!!$R2 505

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
76 77 0.764890 CCTATCCAGCCCAAATCCGA 59.235 55.0 0.00 0.0 0.00 4.55 F
571 588 0.824109 TGCTAGAGTGAACGGGGATG 59.176 55.0 0.00 0.0 0.00 3.51 F
2196 8173 0.179234 TGGTTGAGTCACCTCGCAAA 59.821 50.0 11.48 0.0 40.85 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 8044 0.327924 TGTTGTGGTGCATCCCTAGG 59.672 55.000 0.06 0.06 34.77 3.02 R
2249 8245 1.522668 TCAAACCCTGCAGAATGACG 58.477 50.000 17.39 0.00 39.69 4.35 R
3411 9484 1.593750 GCGAGCGGATGATCAAGCT 60.594 57.895 19.26 19.26 43.33 3.74 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
76 77 0.764890 CCTATCCAGCCCAAATCCGA 59.235 55.000 0.00 0.00 0.00 4.55
105 106 2.627699 TGATGTGAAGGGGAAGCAAAAC 59.372 45.455 0.00 0.00 0.00 2.43
191 200 4.929211 CCGCGGATCACATAAAGATCAATA 59.071 41.667 24.07 0.00 42.84 1.90
310 320 1.044790 TGGATGCTCGGATGCAGAGA 61.045 55.000 5.67 0.00 46.71 3.10
517 533 5.163141 TGTTCTGTTTCCAAAGTCCATAGGA 60.163 40.000 0.00 0.00 0.00 2.94
571 588 0.824109 TGCTAGAGTGAACGGGGATG 59.176 55.000 0.00 0.00 0.00 3.51
573 590 2.029623 GCTAGAGTGAACGGGGATGTA 58.970 52.381 0.00 0.00 0.00 2.29
574 591 2.429610 GCTAGAGTGAACGGGGATGTAA 59.570 50.000 0.00 0.00 0.00 2.41
575 592 3.069729 GCTAGAGTGAACGGGGATGTAAT 59.930 47.826 0.00 0.00 0.00 1.89
577 594 3.873910 AGAGTGAACGGGGATGTAATTG 58.126 45.455 0.00 0.00 0.00 2.32
578 595 2.354821 GAGTGAACGGGGATGTAATTGC 59.645 50.000 0.00 0.00 0.00 3.56
579 596 2.026262 AGTGAACGGGGATGTAATTGCT 60.026 45.455 0.00 0.00 0.00 3.91
580 597 2.752903 GTGAACGGGGATGTAATTGCTT 59.247 45.455 0.00 0.00 0.00 3.91
581 598 3.013921 TGAACGGGGATGTAATTGCTTC 58.986 45.455 1.41 1.41 0.00 3.86
582 599 3.279434 GAACGGGGATGTAATTGCTTCT 58.721 45.455 8.87 0.00 0.00 2.85
583 600 2.643551 ACGGGGATGTAATTGCTTCTG 58.356 47.619 8.87 3.50 0.00 3.02
584 601 2.238646 ACGGGGATGTAATTGCTTCTGA 59.761 45.455 8.87 0.00 0.00 3.27
585 602 3.117888 ACGGGGATGTAATTGCTTCTGAT 60.118 43.478 8.87 0.00 0.00 2.90
586 603 3.885297 CGGGGATGTAATTGCTTCTGATT 59.115 43.478 8.87 0.00 0.00 2.57
587 604 4.261322 CGGGGATGTAATTGCTTCTGATTG 60.261 45.833 8.87 0.00 0.00 2.67
588 605 4.646492 GGGGATGTAATTGCTTCTGATTGT 59.354 41.667 8.87 0.00 0.00 2.71
589 606 5.827797 GGGGATGTAATTGCTTCTGATTGTA 59.172 40.000 8.87 0.00 0.00 2.41
590 607 6.491403 GGGGATGTAATTGCTTCTGATTGTAT 59.509 38.462 8.87 0.00 0.00 2.29
591 608 7.014615 GGGGATGTAATTGCTTCTGATTGTATT 59.985 37.037 8.87 0.00 0.00 1.89
592 609 7.864379 GGGATGTAATTGCTTCTGATTGTATTG 59.136 37.037 8.87 0.00 0.00 1.90
593 610 8.408601 GGATGTAATTGCTTCTGATTGTATTGT 58.591 33.333 8.87 0.00 0.00 2.71
599 616 8.638685 ATTGCTTCTGATTGTATTGTATTTGC 57.361 30.769 0.00 0.00 0.00 3.68
600 617 7.395190 TGCTTCTGATTGTATTGTATTTGCT 57.605 32.000 0.00 0.00 0.00 3.91
601 618 7.829725 TGCTTCTGATTGTATTGTATTTGCTT 58.170 30.769 0.00 0.00 0.00 3.91
602 619 7.970061 TGCTTCTGATTGTATTGTATTTGCTTC 59.030 33.333 0.00 0.00 0.00 3.86
603 620 8.186821 GCTTCTGATTGTATTGTATTTGCTTCT 58.813 33.333 0.00 0.00 0.00 2.85
604 621 9.499585 CTTCTGATTGTATTGTATTTGCTTCTG 57.500 33.333 0.00 0.00 0.00 3.02
605 622 8.791327 TCTGATTGTATTGTATTTGCTTCTGA 57.209 30.769 0.00 0.00 0.00 3.27
608 625 9.791820 TGATTGTATTGTATTTGCTTCTGATTG 57.208 29.630 0.00 0.00 0.00 2.67
634 651 1.241165 CTGATGTGCCACAAGCTTCA 58.759 50.000 0.00 0.00 44.23 3.02
651 668 7.925483 ACAAGCTTCAAAACATGTAATTGCTTA 59.075 29.630 15.85 6.48 35.64 3.09
699 716 3.277715 GAATGAAGCTCTCCCTTTCCTG 58.722 50.000 0.00 0.00 0.00 3.86
705 722 3.760738 AGCTCTCCCTTTCCTGAAAAAG 58.239 45.455 0.00 0.00 36.26 2.27
736 754 1.375523 GGTCGGTGGGTGATGTGTC 60.376 63.158 0.00 0.00 0.00 3.67
737 755 1.375523 GTCGGTGGGTGATGTGTCC 60.376 63.158 0.00 0.00 0.00 4.02
760 778 2.235155 TGCTCGGCACCTTTGTATCTTA 59.765 45.455 0.00 0.00 31.71 2.10
763 781 2.492881 TCGGCACCTTTGTATCTTACGA 59.507 45.455 0.00 0.00 0.00 3.43
772 790 3.812156 TGTATCTTACGATGGGTGTGG 57.188 47.619 0.00 0.00 0.00 4.17
774 792 1.580059 ATCTTACGATGGGTGTGGGT 58.420 50.000 0.00 0.00 0.00 4.51
802 820 4.702612 TGTGATGGTACTGTGTGTTTGTTT 59.297 37.500 0.00 0.00 0.00 2.83
811 829 2.029828 TGTGTGTTTGTTTGGCTTTCGT 60.030 40.909 0.00 0.00 0.00 3.85
817 835 4.621886 TGTTTGTTTGGCTTTCGTTTGTAC 59.378 37.500 0.00 0.00 0.00 2.90
828 846 3.646611 TCGTTTGTACTCGATGGTTGA 57.353 42.857 0.00 0.00 0.00 3.18
832 850 5.467399 TCGTTTGTACTCGATGGTTGAAATT 59.533 36.000 0.00 0.00 0.00 1.82
932 957 9.577110 TGCTCTGATTTTGATGTGATAAATTTC 57.423 29.630 0.00 0.00 0.00 2.17
935 960 9.577110 TCTGATTTTGATGTGATAAATTTCAGC 57.423 29.630 0.00 0.00 32.35 4.26
1088 1116 1.895707 CATGGGCGCTGATCCCTTC 60.896 63.158 7.64 0.00 44.23 3.46
1089 1117 2.074948 ATGGGCGCTGATCCCTTCT 61.075 57.895 7.64 0.00 44.23 2.85
1090 1118 2.049627 ATGGGCGCTGATCCCTTCTC 62.050 60.000 7.64 0.00 44.23 2.87
1244 1279 3.068881 CTCCACCTTCTTCGGCCA 58.931 61.111 2.24 0.00 0.00 5.36
1245 1280 1.604378 CTCCACCTTCTTCGGCCAT 59.396 57.895 2.24 0.00 0.00 4.40
1344 1384 3.668447 TCAACAAACTCTCCTGATCTGC 58.332 45.455 0.00 0.00 0.00 4.26
1352 1392 2.027314 CCTGATCTGCGGCGAGAG 59.973 66.667 12.98 5.40 0.00 3.20
1359 1399 3.655810 CTGCGGCGAGAGAGGCTTT 62.656 63.158 12.98 0.00 34.19 3.51
1367 1407 2.376109 CGAGAGAGGCTTTAGGTGGTA 58.624 52.381 0.00 0.00 0.00 3.25
1368 1408 2.758979 CGAGAGAGGCTTTAGGTGGTAA 59.241 50.000 0.00 0.00 0.00 2.85
1369 1409 3.385111 CGAGAGAGGCTTTAGGTGGTAAT 59.615 47.826 0.00 0.00 0.00 1.89
1624 4031 3.496331 AACCCAAGGTTGGTGTATTCAG 58.504 45.455 7.96 0.00 45.07 3.02
1673 4114 1.353804 GAAACTGAAACACGCGCCA 59.646 52.632 5.73 0.00 0.00 5.69
1747 4188 3.131478 GTGGGCGAATTCGGGGTG 61.131 66.667 27.78 1.38 40.23 4.61
1800 4241 1.263776 CTGCAAGAGATCACGTCGTC 58.736 55.000 0.00 0.00 34.07 4.20
1828 7751 2.038295 GGATGTGATCAGGACCATCTCC 59.962 54.545 18.33 6.13 39.81 3.71
1902 7879 5.823209 TGAAACAGAGCATGGTATTGATG 57.177 39.130 13.89 4.52 0.00 3.07
2067 8044 2.156098 TGCCGGGAAGATTACAACAAC 58.844 47.619 2.18 0.00 0.00 3.32
2086 8063 0.327924 CCTAGGGATGCACCACAACA 59.672 55.000 0.00 0.00 41.20 3.33
2196 8173 0.179234 TGGTTGAGTCACCTCGCAAA 59.821 50.000 11.48 0.00 40.85 3.68
2207 8184 2.290641 CACCTCGCAAATATGGTAAGCC 59.709 50.000 0.00 0.00 0.00 4.35
2249 8245 1.168714 GCAGGTCAAGGTTGATGGTC 58.831 55.000 0.00 0.00 39.73 4.02
2297 8293 2.614983 GTTCTTACCAACTGTTGCGGAA 59.385 45.455 14.94 10.05 0.00 4.30
2552 8573 6.243148 TGTACTCAATATATACTCGCCCTCA 58.757 40.000 0.00 0.00 0.00 3.86
2584 8615 7.792374 ATAATACATCCATCATATTCCGCAC 57.208 36.000 0.00 0.00 0.00 5.34
2588 8619 3.289407 TCCATCATATTCCGCACCAAA 57.711 42.857 0.00 0.00 0.00 3.28
2790 8840 1.491668 TTCCGATCCTTTGATCCGGA 58.508 50.000 6.61 6.61 43.82 5.14
3033 9088 4.082523 GCCGTCACTGCCCTGCTA 62.083 66.667 0.00 0.00 0.00 3.49
3054 9109 4.082523 CCGGGACACCTGCATCGT 62.083 66.667 0.00 0.00 33.28 3.73
3093 9148 2.711311 CATGCGACGGCCAATCAG 59.289 61.111 2.24 0.00 38.85 2.90
3194 9257 4.421479 CTCGTCCTCGGCTGCGTT 62.421 66.667 0.00 0.00 37.69 4.84
3254 9317 2.825836 CCGCTGCTCCATTGGTCC 60.826 66.667 1.86 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.772605 TCCTCAAGAAAATCACAGAATCTCA 58.227 36.000 0.00 0.00 0.00 3.27
76 77 5.127682 GCTTCCCCTTCACATCATTTACAAT 59.872 40.000 0.00 0.00 0.00 2.71
110 111 3.263261 GCAGGCTAGAAGTTAACTCCAC 58.737 50.000 8.95 4.12 0.00 4.02
167 176 2.364002 TGATCTTTATGTGATCCGCGGA 59.636 45.455 33.12 33.12 39.48 5.54
191 200 2.076100 TGCAATGAAAGAAGCGTCGAT 58.924 42.857 0.00 0.00 0.00 3.59
310 320 2.034221 GGCCTGGACTTCGGCTTT 59.966 61.111 0.00 0.00 45.57 3.51
517 533 3.271014 CGCAGCCACATTGCTCTT 58.729 55.556 0.00 0.00 40.32 2.85
573 590 9.090692 GCAAATACAATACAATCAGAAGCAATT 57.909 29.630 0.00 0.00 0.00 2.32
574 591 8.472413 AGCAAATACAATACAATCAGAAGCAAT 58.528 29.630 0.00 0.00 0.00 3.56
575 592 7.829725 AGCAAATACAATACAATCAGAAGCAA 58.170 30.769 0.00 0.00 0.00 3.91
577 594 8.186821 AGAAGCAAATACAATACAATCAGAAGC 58.813 33.333 0.00 0.00 0.00 3.86
578 595 9.499585 CAGAAGCAAATACAATACAATCAGAAG 57.500 33.333 0.00 0.00 0.00 2.85
579 596 9.230122 TCAGAAGCAAATACAATACAATCAGAA 57.770 29.630 0.00 0.00 0.00 3.02
580 597 8.791327 TCAGAAGCAAATACAATACAATCAGA 57.209 30.769 0.00 0.00 0.00 3.27
582 599 9.791820 CAATCAGAAGCAAATACAATACAATCA 57.208 29.630 0.00 0.00 0.00 2.57
583 600 9.793252 ACAATCAGAAGCAAATACAATACAATC 57.207 29.630 0.00 0.00 0.00 2.67
589 606 9.956720 GCTAATACAATCAGAAGCAAATACAAT 57.043 29.630 0.00 0.00 0.00 2.71
590 607 9.177608 AGCTAATACAATCAGAAGCAAATACAA 57.822 29.630 0.00 0.00 32.42 2.41
591 608 8.615211 CAGCTAATACAATCAGAAGCAAATACA 58.385 33.333 0.00 0.00 32.42 2.29
592 609 8.830580 TCAGCTAATACAATCAGAAGCAAATAC 58.169 33.333 0.00 0.00 32.42 1.89
593 610 8.962884 TCAGCTAATACAATCAGAAGCAAATA 57.037 30.769 0.00 0.00 32.42 1.40
594 611 7.870509 TCAGCTAATACAATCAGAAGCAAAT 57.129 32.000 0.00 0.00 32.42 2.32
595 612 7.337689 ACATCAGCTAATACAATCAGAAGCAAA 59.662 33.333 0.00 0.00 32.42 3.68
596 613 6.825213 ACATCAGCTAATACAATCAGAAGCAA 59.175 34.615 0.00 0.00 32.42 3.91
597 614 6.259387 CACATCAGCTAATACAATCAGAAGCA 59.741 38.462 0.00 0.00 32.42 3.91
598 615 6.656945 CACATCAGCTAATACAATCAGAAGC 58.343 40.000 0.00 0.00 0.00 3.86
599 616 6.293298 GGCACATCAGCTAATACAATCAGAAG 60.293 42.308 0.00 0.00 34.17 2.85
600 617 5.528690 GGCACATCAGCTAATACAATCAGAA 59.471 40.000 0.00 0.00 34.17 3.02
601 618 5.059161 GGCACATCAGCTAATACAATCAGA 58.941 41.667 0.00 0.00 34.17 3.27
602 619 4.818005 TGGCACATCAGCTAATACAATCAG 59.182 41.667 0.00 0.00 34.17 2.90
603 620 4.576053 GTGGCACATCAGCTAATACAATCA 59.424 41.667 13.86 0.00 44.52 2.57
604 621 4.576053 TGTGGCACATCAGCTAATACAATC 59.424 41.667 17.96 0.00 44.52 2.67
605 622 4.525996 TGTGGCACATCAGCTAATACAAT 58.474 39.130 17.96 0.00 44.52 2.71
608 625 3.242870 GCTTGTGGCACATCAGCTAATAC 60.243 47.826 28.41 6.79 44.52 1.89
699 716 4.265320 CGACCAACAAGCAAACTCTTTTTC 59.735 41.667 0.00 0.00 0.00 2.29
705 722 1.021968 ACCGACCAACAAGCAAACTC 58.978 50.000 0.00 0.00 0.00 3.01
760 778 1.228124 CACAACCCACACCCATCGT 60.228 57.895 0.00 0.00 0.00 3.73
763 781 0.754957 CACACACAACCCACACCCAT 60.755 55.000 0.00 0.00 0.00 4.00
772 790 2.548057 CACAGTACCATCACACACAACC 59.452 50.000 0.00 0.00 0.00 3.77
774 792 3.202097 CACACAGTACCATCACACACAA 58.798 45.455 0.00 0.00 0.00 3.33
802 820 2.512485 TCGAGTACAAACGAAAGCCA 57.488 45.000 7.21 0.00 35.62 4.75
811 829 5.533154 ACCAATTTCAACCATCGAGTACAAA 59.467 36.000 0.00 0.00 0.00 2.83
817 835 4.439153 CCATCACCAATTTCAACCATCGAG 60.439 45.833 0.00 0.00 0.00 4.04
878 903 1.873698 TTGTTGTCGACAAGCTACCC 58.126 50.000 30.38 17.79 43.13 3.69
886 911 2.212869 AGTAAGCGTTGTTGTCGACA 57.787 45.000 15.76 15.76 36.19 4.35
889 914 1.260561 AGCAAGTAAGCGTTGTTGTCG 59.739 47.619 0.00 0.00 40.15 4.35
1027 1052 2.548295 GGAACAGCAAAACGGCGGA 61.548 57.895 13.24 0.00 39.27 5.54
1028 1053 2.050442 GGAACAGCAAAACGGCGG 60.050 61.111 13.24 0.00 39.27 6.13
1065 1090 4.889112 ATCAGCGCCCATGCCCAG 62.889 66.667 2.29 0.00 34.65 4.45
1344 1384 1.066587 CCTAAAGCCTCTCTCGCCG 59.933 63.158 0.00 0.00 0.00 6.46
1352 1392 5.985911 TGAGTTATTACCACCTAAAGCCTC 58.014 41.667 0.00 0.00 0.00 4.70
1359 1399 5.188359 GGACCAGTTGAGTTATTACCACCTA 59.812 44.000 0.00 0.00 0.00 3.08
1367 1407 3.074412 CAAGCGGACCAGTTGAGTTATT 58.926 45.455 0.00 0.00 0.00 1.40
1368 1408 2.699954 CAAGCGGACCAGTTGAGTTAT 58.300 47.619 0.00 0.00 0.00 1.89
1369 1409 1.876416 GCAAGCGGACCAGTTGAGTTA 60.876 52.381 6.94 0.00 0.00 2.24
1641 4082 2.170397 TCAGTTTCCTGTCACTCTGCAA 59.830 45.455 0.00 0.00 39.82 4.08
1667 4108 1.520368 GAAGAAAAACGTATGGCGCG 58.480 50.000 0.00 0.00 46.11 6.86
1673 4114 2.147958 TGCAGCGGAAGAAAAACGTAT 58.852 42.857 0.00 0.00 0.00 3.06
1677 4118 1.604278 ACTCTGCAGCGGAAGAAAAAC 59.396 47.619 9.47 0.00 0.00 2.43
1747 4188 4.236147 GGAAAGAGAAGTGGTAGTCGTTC 58.764 47.826 0.00 0.00 0.00 3.95
1828 7751 2.548067 GGTAGGTACCTCGATTGCCATG 60.548 54.545 20.32 0.00 43.10 3.66
1854 7777 2.037902 TGAAATGCAGGTTGACGAGGTA 59.962 45.455 0.00 0.00 0.00 3.08
1856 7779 1.197721 GTGAAATGCAGGTTGACGAGG 59.802 52.381 0.00 0.00 0.00 4.63
1857 7780 1.197721 GGTGAAATGCAGGTTGACGAG 59.802 52.381 0.00 0.00 0.00 4.18
1888 7848 2.359981 AGCTGCATCAATACCATGCT 57.640 45.000 1.02 0.00 45.90 3.79
1889 7849 3.119602 CCATAGCTGCATCAATACCATGC 60.120 47.826 1.02 0.00 45.92 4.06
1902 7879 0.383231 GTCACCATTGCCATAGCTGC 59.617 55.000 0.00 0.00 40.80 5.25
1997 7974 0.741221 GTCTTTGGCGAGGTAGCTGG 60.741 60.000 0.00 0.00 37.29 4.85
2067 8044 0.327924 TGTTGTGGTGCATCCCTAGG 59.672 55.000 0.06 0.06 34.77 3.02
2207 8184 2.031333 GCAAGACAACAGCTCTGAAAGG 60.031 50.000 3.60 0.00 0.00 3.11
2249 8245 1.522668 TCAAACCCTGCAGAATGACG 58.477 50.000 17.39 0.00 39.69 4.35
2474 8470 9.816787 AGAGATAAGGTAGGAATCCTAAACTAG 57.183 37.037 11.12 0.00 37.91 2.57
2552 8573 9.986157 AATATGATGGATGTATTATTGAGCCTT 57.014 29.630 0.00 0.00 0.00 4.35
2584 8615 5.730296 TGTTAGAAGAGAGAGAGGTTTGG 57.270 43.478 0.00 0.00 0.00 3.28
2588 8619 4.941713 ACCATGTTAGAAGAGAGAGAGGT 58.058 43.478 0.00 0.00 0.00 3.85
2790 8840 1.135333 GACCGGCGAGAGAGAGAAAAT 59.865 52.381 9.30 0.00 0.00 1.82
3247 9310 3.090532 GAGGCCCGAGGGACCAAT 61.091 66.667 11.10 0.00 46.93 3.16
3411 9484 1.593750 GCGAGCGGATGATCAAGCT 60.594 57.895 19.26 19.26 43.33 3.74


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

AutoCloner maintained by Alex Coulton.