Multiple sequence alignment - TraesCS5B01G460600

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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 TraesCS5B01G460600 chr5B 100.000 3077 0 0 1 3077 636350166 636347090 0.000000e+00 5683
1 TraesCS5B01G460600 chr5B 80.240 1670 245 45 835 2443 635767688 635769333 0.000000e+00 1177
2 TraesCS5B01G460600 chr5B 81.447 1299 196 32 1007 2285 636541519 636540246 0.000000e+00 1022
3 TraesCS5B01G460600 chr5B 81.145 1188 203 12 930 2099 635776752 635777936 0.000000e+00 933
4 TraesCS5B01G460600 chr5B 79.688 1216 211 22 901 2104 645993272 645992081 0.000000e+00 845
5 TraesCS5B01G460600 chr5B 82.735 892 131 12 1071 1959 646627111 646627982 0.000000e+00 773
6 TraesCS5B01G460600 chr5B 79.795 1074 183 22 900 1967 645063098 645062053 0.000000e+00 750
7 TraesCS5B01G460600 chr5B 81.659 856 132 13 1252 2104 645981257 645980424 0.000000e+00 688
8 TraesCS5B01G460600 chr5A 88.082 2383 205 35 715 3077 633636087 633633764 0.000000e+00 2754
9 TraesCS5B01G460600 chr5A 80.645 1395 227 31 1035 2410 633754606 633753236 0.000000e+00 1040
10 TraesCS5B01G460600 chr5A 80.681 1175 207 11 930 2086 633149251 633150423 0.000000e+00 894
11 TraesCS5B01G460600 chr5A 81.163 1083 171 18 884 1959 642905537 642906593 0.000000e+00 839
12 TraesCS5B01G460600 chr5A 80.037 1067 178 19 900 1959 641781679 641780641 0.000000e+00 758
13 TraesCS5B01G460600 chr5A 79.641 167 19 7 2456 2611 633150806 633150968 4.200000e-19 106
14 TraesCS5B01G460600 chr5D 90.398 1937 142 25 704 2610 505935921 505933999 0.000000e+00 2507
15 TraesCS5B01G460600 chr5D 82.298 1175 191 9 928 2086 505779589 505780762 0.000000e+00 1002
16 TraesCS5B01G460600 chr5D 81.902 1083 164 19 884 1959 514515118 514516175 0.000000e+00 885
17 TraesCS5B01G460600 chr5D 92.813 487 22 5 2592 3077 505933555 505933081 0.000000e+00 693
18 TraesCS5B01G460600 chr6B 88.858 709 43 11 1 706 87921856 87922531 0.000000e+00 839
19 TraesCS5B01G460600 chr6B 88.642 405 33 10 298 693 67518581 67518981 5.970000e-132 481
20 TraesCS5B01G460600 chr1B 87.864 618 54 13 1 603 576755547 576754936 0.000000e+00 706
21 TraesCS5B01G460600 chr2D 90.226 399 30 8 315 706 139259280 139259676 2.120000e-141 512
22 TraesCS5B01G460600 chr1D 89.526 401 30 9 315 706 202316993 202317390 5.930000e-137 497
23 TraesCS5B01G460600 chr4D 89.055 402 29 12 315 706 364587153 364586757 4.610000e-133 484
24 TraesCS5B01G460600 chr7B 88.413 397 42 4 315 707 32122340 32122736 2.780000e-130 475
25 TraesCS5B01G460600 chr3D 88.424 406 30 10 315 706 155957591 155957189 9.990000e-130 473
26 TraesCS5B01G460600 chr2A 87.879 396 39 7 315 706 778135235 778134845 1.010000e-124 457


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 TraesCS5B01G460600 chr5B 636347090 636350166 3076 True 5683 5683 100.0000 1 3077 1 chr5B.!!$R1 3076
1 TraesCS5B01G460600 chr5B 635767688 635769333 1645 False 1177 1177 80.2400 835 2443 1 chr5B.!!$F1 1608
2 TraesCS5B01G460600 chr5B 636540246 636541519 1273 True 1022 1022 81.4470 1007 2285 1 chr5B.!!$R2 1278
3 TraesCS5B01G460600 chr5B 635776752 635777936 1184 False 933 933 81.1450 930 2099 1 chr5B.!!$F2 1169
4 TraesCS5B01G460600 chr5B 645992081 645993272 1191 True 845 845 79.6880 901 2104 1 chr5B.!!$R5 1203
5 TraesCS5B01G460600 chr5B 646627111 646627982 871 False 773 773 82.7350 1071 1959 1 chr5B.!!$F3 888
6 TraesCS5B01G460600 chr5B 645062053 645063098 1045 True 750 750 79.7950 900 1967 1 chr5B.!!$R3 1067
7 TraesCS5B01G460600 chr5B 645980424 645981257 833 True 688 688 81.6590 1252 2104 1 chr5B.!!$R4 852
8 TraesCS5B01G460600 chr5A 633633764 633636087 2323 True 2754 2754 88.0820 715 3077 1 chr5A.!!$R1 2362
9 TraesCS5B01G460600 chr5A 633753236 633754606 1370 True 1040 1040 80.6450 1035 2410 1 chr5A.!!$R2 1375
10 TraesCS5B01G460600 chr5A 642905537 642906593 1056 False 839 839 81.1630 884 1959 1 chr5A.!!$F1 1075
11 TraesCS5B01G460600 chr5A 641780641 641781679 1038 True 758 758 80.0370 900 1959 1 chr5A.!!$R3 1059
12 TraesCS5B01G460600 chr5A 633149251 633150968 1717 False 500 894 80.1610 930 2611 2 chr5A.!!$F2 1681
13 TraesCS5B01G460600 chr5D 505933081 505935921 2840 True 1600 2507 91.6055 704 3077 2 chr5D.!!$R1 2373
14 TraesCS5B01G460600 chr5D 505779589 505780762 1173 False 1002 1002 82.2980 928 2086 1 chr5D.!!$F1 1158
15 TraesCS5B01G460600 chr5D 514515118 514516175 1057 False 885 885 81.9020 884 1959 1 chr5D.!!$F2 1075
16 TraesCS5B01G460600 chr6B 87921856 87922531 675 False 839 839 88.8580 1 706 1 chr6B.!!$F2 705
17 TraesCS5B01G460600 chr1B 576754936 576755547 611 True 706 706 87.8640 1 603 1 chr1B.!!$R1 602

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
660 689 0.039617 CTCGATCGATCTCCCTGTGC 60.040 60.0 19.78 0.0 0.0 4.57 F
744 773 0.172352 CTCTGAGGTCTCTTGTCGCC 59.828 60.0 0.00 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1995 0.450482 GTGTCCGCGTTCAAATCGTG 60.450 55.000 4.92 0.0 38.32 4.35 R
2264 2424 1.063174 GCGCTCCAGATAAAACAGCAG 59.937 52.381 0.00 0.0 0.00 4.24 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
164 165 6.696411 ACACAAACAATTTTCTGAAACTCCA 58.304 32.000 1.58 0.00 0.00 3.86
189 191 8.167985 CAGAACAAAATTGAAAACACGAACAAT 58.832 29.630 0.00 0.00 34.99 2.71
318 343 8.803799 ACAATACTTCAAACATTTTTGTCGAAC 58.196 29.630 4.35 0.00 42.51 3.95
586 615 1.578206 GGCTGGGAACAAGCGAGAAC 61.578 60.000 0.00 0.00 42.06 3.01
593 622 1.192534 GAACAAGCGAGAACGTTCCTG 59.807 52.381 24.22 17.47 41.98 3.86
619 648 3.861689 CCGGAATCGTAGAACCACTTTAC 59.138 47.826 0.00 0.00 43.58 2.01
622 651 3.515330 ATCGTAGAACCACTTTACGGG 57.485 47.619 3.82 0.00 43.58 5.28
655 684 0.599060 GAACCCTCGATCGATCTCCC 59.401 60.000 19.78 4.81 0.00 4.30
656 685 0.186386 AACCCTCGATCGATCTCCCT 59.814 55.000 19.78 0.00 0.00 4.20
657 686 0.538516 ACCCTCGATCGATCTCCCTG 60.539 60.000 19.78 4.72 0.00 4.45
658 687 0.538516 CCCTCGATCGATCTCCCTGT 60.539 60.000 19.78 0.00 0.00 4.00
659 688 0.595588 CCTCGATCGATCTCCCTGTG 59.404 60.000 19.78 3.15 0.00 3.66
660 689 0.039617 CTCGATCGATCTCCCTGTGC 60.040 60.000 19.78 0.00 0.00 4.57
661 690 1.371022 CGATCGATCTCCCTGTGCG 60.371 63.158 22.43 3.48 0.00 5.34
662 691 1.736586 GATCGATCTCCCTGTGCGT 59.263 57.895 18.29 0.00 0.00 5.24
663 692 0.318275 GATCGATCTCCCTGTGCGTC 60.318 60.000 18.29 0.00 0.00 5.19
664 693 1.739338 ATCGATCTCCCTGTGCGTCC 61.739 60.000 0.00 0.00 0.00 4.79
665 694 2.105128 GATCTCCCTGTGCGTCCG 59.895 66.667 0.00 0.00 0.00 4.79
666 695 4.148825 ATCTCCCTGTGCGTCCGC 62.149 66.667 4.42 4.42 42.35 5.54
668 697 4.803426 CTCCCTGTGCGTCCGCTC 62.803 72.222 13.31 9.91 42.51 5.03
672 701 4.700365 CTGTGCGTCCGCTCGACA 62.700 66.667 13.31 8.04 42.07 4.35
673 702 4.273257 TGTGCGTCCGCTCGACAA 62.273 61.111 13.31 0.00 42.07 3.18
674 703 3.764049 GTGCGTCCGCTCGACAAC 61.764 66.667 13.31 0.00 42.07 3.32
675 704 3.973516 TGCGTCCGCTCGACAACT 61.974 61.111 13.31 0.00 42.07 3.16
676 705 2.733593 GCGTCCGCTCGACAACTT 60.734 61.111 4.10 0.00 42.07 2.66
677 706 3.000080 GCGTCCGCTCGACAACTTG 62.000 63.158 4.10 0.00 42.07 3.16
678 707 2.853914 GTCCGCTCGACAACTTGC 59.146 61.111 0.00 0.00 41.54 4.01
679 708 2.357034 TCCGCTCGACAACTTGCC 60.357 61.111 0.00 0.00 0.00 4.52
680 709 3.777925 CCGCTCGACAACTTGCCG 61.778 66.667 0.00 0.00 0.00 5.69
681 710 4.430423 CGCTCGACAACTTGCCGC 62.430 66.667 0.00 0.00 0.00 6.53
682 711 3.345808 GCTCGACAACTTGCCGCA 61.346 61.111 0.00 0.00 0.00 5.69
683 712 2.856032 CTCGACAACTTGCCGCAG 59.144 61.111 0.00 0.00 0.00 5.18
684 713 3.300667 CTCGACAACTTGCCGCAGC 62.301 63.158 0.00 0.00 40.48 5.25
685 714 4.724697 CGACAACTTGCCGCAGCG 62.725 66.667 8.18 8.18 44.31 5.18
686 715 3.345808 GACAACTTGCCGCAGCGA 61.346 61.111 18.75 0.00 44.31 4.93
700 729 4.049393 GCGAGCGGCAAATAGGAT 57.951 55.556 1.45 0.00 42.87 3.24
701 730 3.210857 GCGAGCGGCAAATAGGATA 57.789 52.632 1.45 0.00 42.87 2.59
702 731 1.726853 GCGAGCGGCAAATAGGATAT 58.273 50.000 1.45 0.00 42.87 1.63
703 732 2.076863 GCGAGCGGCAAATAGGATATT 58.923 47.619 1.45 0.00 42.87 1.28
704 733 2.094417 GCGAGCGGCAAATAGGATATTC 59.906 50.000 1.45 0.00 42.87 1.75
705 734 2.673368 CGAGCGGCAAATAGGATATTCC 59.327 50.000 1.45 0.00 36.58 3.01
706 735 2.673368 GAGCGGCAAATAGGATATTCCG 59.327 50.000 1.45 5.67 42.75 4.30
707 736 2.301870 AGCGGCAAATAGGATATTCCGA 59.698 45.455 1.45 0.00 42.75 4.55
712 741 5.562113 CGGCAAATAGGATATTCCGAAAACC 60.562 44.000 4.49 0.00 42.75 3.27
713 742 5.535030 GGCAAATAGGATATTCCGAAAACCT 59.465 40.000 0.00 0.00 42.75 3.50
728 757 0.842467 AACCTAGGCCCAGCAACTCT 60.842 55.000 9.30 0.00 0.00 3.24
737 766 1.265236 CCAGCAACTCTGAGGTCTCT 58.735 55.000 9.85 0.00 45.72 3.10
740 769 2.036992 CAGCAACTCTGAGGTCTCTTGT 59.963 50.000 9.85 0.00 45.72 3.16
742 771 2.924454 GCAACTCTGAGGTCTCTTGTCG 60.924 54.545 9.85 0.00 0.00 4.35
743 772 0.885196 ACTCTGAGGTCTCTTGTCGC 59.115 55.000 9.85 0.00 0.00 5.19
744 773 0.172352 CTCTGAGGTCTCTTGTCGCC 59.828 60.000 0.00 0.00 0.00 5.54
745 774 0.251386 TCTGAGGTCTCTTGTCGCCT 60.251 55.000 0.00 0.00 0.00 5.52
749 784 0.543174 AGGTCTCTTGTCGCCTTCCT 60.543 55.000 0.00 0.00 0.00 3.36
753 788 1.902508 TCTCTTGTCGCCTTCCTCATT 59.097 47.619 0.00 0.00 0.00 2.57
767 802 2.092699 TCCTCATTCCACAACACACACA 60.093 45.455 0.00 0.00 0.00 3.72
773 808 2.230660 TCCACAACACACACAAACACA 58.769 42.857 0.00 0.00 0.00 3.72
774 809 2.623416 TCCACAACACACACAAACACAA 59.377 40.909 0.00 0.00 0.00 3.33
778 813 5.430462 CACAACACACACAAACACAAAAAG 58.570 37.500 0.00 0.00 0.00 2.27
785 820 5.401079 ACACACAAACACAAAAAGTCGAAAG 59.599 36.000 0.00 0.00 0.00 2.62
830 865 2.885644 CGTCGCCATCTCCGGTTG 60.886 66.667 0.00 0.00 0.00 3.77
836 879 2.436646 CATCTCCGGTTGCGCCTT 60.437 61.111 4.18 0.00 34.25 4.35
865 912 1.382695 CCACTCCCCCGTATCCTGT 60.383 63.158 0.00 0.00 0.00 4.00
871 918 0.689745 CCCCCGTATCCTGTTCCTCA 60.690 60.000 0.00 0.00 0.00 3.86
875 922 2.159085 CCCGTATCCTGTTCCTCACTTC 60.159 54.545 0.00 0.00 0.00 3.01
878 925 1.290134 ATCCTGTTCCTCACTTCCCC 58.710 55.000 0.00 0.00 0.00 4.81
879 926 0.193574 TCCTGTTCCTCACTTCCCCT 59.806 55.000 0.00 0.00 0.00 4.79
880 927 0.615850 CCTGTTCCTCACTTCCCCTC 59.384 60.000 0.00 0.00 0.00 4.30
881 928 1.650528 CTGTTCCTCACTTCCCCTCT 58.349 55.000 0.00 0.00 0.00 3.69
882 929 1.552792 CTGTTCCTCACTTCCCCTCTC 59.447 57.143 0.00 0.00 0.00 3.20
976 1031 2.494471 TCGATTCTTTCTTCTACGGCCA 59.506 45.455 2.24 0.00 0.00 5.36
994 1050 1.500474 CAGCAATCCTCCTCCCTGTA 58.500 55.000 0.00 0.00 0.00 2.74
1050 1120 3.068691 CCGGACGAGGCTCAAGGA 61.069 66.667 15.95 0.00 0.00 3.36
1058 1128 0.384669 GAGGCTCAAGGAATGCATGC 59.615 55.000 11.82 11.82 0.00 4.06
1248 1318 3.570975 TGAGTAACAGCACTAAAGTCCGA 59.429 43.478 0.00 0.00 0.00 4.55
1363 1433 2.377193 ACTAAGTTTGCCCCACCACATA 59.623 45.455 0.00 0.00 0.00 2.29
1449 1519 6.399354 CGATAGAATGCATCGTCACTGTTATG 60.399 42.308 0.00 0.00 40.26 1.90
1466 1545 5.911752 TGTTATGAAAAAGCCACATGTTGT 58.088 33.333 0.00 0.00 0.00 3.32
1500 1588 1.889105 CCCCAAGATCGACATGCCG 60.889 63.158 0.00 0.00 0.00 5.69
1519 1607 1.434622 GCCATCTGACATGACTGCGG 61.435 60.000 0.00 3.05 0.00 5.69
1592 1681 2.348472 TGGGGAAGAGACCATTGAAGT 58.652 47.619 0.00 0.00 0.00 3.01
1703 1795 2.165167 CATCAAGGACATGCAACCTGT 58.835 47.619 10.44 1.21 36.56 4.00
1986 2124 3.760151 CAGATGACATGGATGTTGTGGTT 59.240 43.478 0.00 0.00 41.95 3.67
2077 2216 7.226720 AGAGAAGAAAGTTTCGTAAAGCATGAA 59.773 33.333 9.91 0.00 34.02 2.57
2086 2225 4.311606 TCGTAAAGCATGAACAGCTACAA 58.688 39.130 0.00 0.00 42.53 2.41
2150 2294 7.667043 TTGATAAATTTCTCGTACACTTGCT 57.333 32.000 0.00 0.00 0.00 3.91
2173 2317 3.567478 AGGGATGGTAAGCTCAATGTC 57.433 47.619 0.00 0.00 0.00 3.06
2257 2417 8.014070 TCGTAGATCAACCCAGATTTGTATTA 57.986 34.615 0.00 0.00 0.00 0.98
2299 2460 3.093278 CGCTTCCCTGCAATCGTC 58.907 61.111 0.00 0.00 0.00 4.20
2335 2496 8.090831 GTCTTAATCTTCTGGCAAAATTTCCTT 58.909 33.333 0.00 0.00 0.00 3.36
2351 2512 2.722094 TCCTTTCTTGTGTGTGCAACT 58.278 42.857 0.00 0.00 38.04 3.16
2370 2535 3.456280 ACTTTTGTTGCGCATTTGTCAT 58.544 36.364 12.75 0.00 0.00 3.06
2406 2571 0.103026 AGCGAGCAATGCTACGATGA 59.897 50.000 23.61 0.00 41.87 2.92
2417 2582 9.865914 AGCAATGCTACGATGACCTCATCTATG 62.866 44.444 5.69 1.57 42.96 2.23
2446 2615 8.905103 ACATAACAAGATTAAAACGGCATAAC 57.095 30.769 0.00 0.00 0.00 1.89
2461 2694 5.244178 ACGGCATAACTGGGTTAAATTTCAA 59.756 36.000 0.00 0.00 31.56 2.69
2484 2717 8.498192 CAATGATATAGCATTGTAAGTTGCAC 57.502 34.615 27.80 0.00 46.22 4.57
2494 2727 7.227116 AGCATTGTAAGTTGCACATTTTGATTT 59.773 29.630 0.00 0.00 41.35 2.17
2495 2728 7.856894 GCATTGTAAGTTGCACATTTTGATTTT 59.143 29.630 0.00 0.00 38.72 1.82
2507 2740 7.507304 CACATTTTGATTTTCTGAAGCATGAC 58.493 34.615 0.00 0.00 0.00 3.06
2525 2758 5.065602 GCATGACAGAATGATCTTGTGCTAA 59.934 40.000 0.00 0.00 39.69 3.09
2539 2783 6.296026 TCTTGTGCTAAATTGTAAGAGTGGT 58.704 36.000 0.00 0.00 0.00 4.16
2551 2795 1.603739 GAGTGGTCAAACAGGGCCC 60.604 63.158 16.46 16.46 0.00 5.80
2616 3323 1.066908 CTCTAGGAAGAGCTGGCTTCG 59.933 57.143 8.59 0.00 42.79 3.79
2674 3381 6.673796 GCATTTGTATCTGCCATTTTCTTTGC 60.674 38.462 0.00 0.00 32.15 3.68
2685 3392 8.065473 TGCCATTTTCTTTGCTTCTAATATCA 57.935 30.769 0.00 0.00 0.00 2.15
2757 3464 1.338020 GGCTGTTGACAAGTTTGAGGG 59.662 52.381 0.00 0.00 0.00 4.30
2759 3466 2.427095 GCTGTTGACAAGTTTGAGGGTT 59.573 45.455 0.00 0.00 0.00 4.11
2860 3567 1.420138 GGGAGGGAGACACAAACAGAA 59.580 52.381 0.00 0.00 0.00 3.02
2894 3601 5.475564 TGGAAGGGTTAAATGTTAGCTTGAC 59.524 40.000 0.00 0.00 0.00 3.18
2914 3621 7.094634 GCTTGACTATTGAGAGTTTTGATGGAA 60.095 37.037 0.00 0.00 0.00 3.53
2922 3629 7.345422 TGAGAGTTTTGATGGAAATGTGAAA 57.655 32.000 0.00 0.00 0.00 2.69
2938 3645 3.181448 TGTGAAAACCTAACCCTGACCTC 60.181 47.826 0.00 0.00 0.00 3.85
2944 3651 1.916181 CCTAACCCTGACCTCCATTGT 59.084 52.381 0.00 0.00 0.00 2.71
2971 3678 1.612676 AAGAAGCATCACAGCAGCAA 58.387 45.000 0.00 0.00 36.85 3.91
2976 3683 1.684983 AGCATCACAGCAGCAAAAAGT 59.315 42.857 0.00 0.00 36.85 2.66
2989 3696 2.135933 CAAAAAGTCGAAGGAGCTCGT 58.864 47.619 7.83 5.12 39.84 4.18
3062 3769 5.297029 AGTTTGTTAACTTCTCAGGTCTTGC 59.703 40.000 7.22 0.00 41.85 4.01
3069 3776 3.327757 ACTTCTCAGGTCTTGCCAATGTA 59.672 43.478 0.00 0.00 40.61 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.916969 TGTTCGCGTTTTGAAATTTTGTTT 58.083 29.167 5.77 0.00 0.00 2.83
164 165 7.644986 TTGTTCGTGTTTTCAATTTTGTTCT 57.355 28.000 0.00 0.00 0.00 3.01
432 458 6.893005 TCCTTTCCTACCTTTTCAAGTTTTCA 59.107 34.615 0.00 0.00 0.00 2.69
490 517 4.031418 TCTTTTTCGTTTTTCGTTCCCC 57.969 40.909 0.00 0.00 40.80 4.81
593 622 2.669924 GTGGTTCTACGATTCCGGTTTC 59.330 50.000 0.00 0.00 40.78 2.78
638 667 0.538516 CAGGGAGATCGATCGAGGGT 60.539 60.000 23.84 10.08 0.00 4.34
644 673 0.318275 GACGCACAGGGAGATCGATC 60.318 60.000 17.91 17.91 0.00 3.69
645 674 1.736586 GACGCACAGGGAGATCGAT 59.263 57.895 0.00 0.00 0.00 3.59
646 675 2.415608 GGACGCACAGGGAGATCGA 61.416 63.158 0.00 0.00 0.00 3.59
647 676 2.105128 GGACGCACAGGGAGATCG 59.895 66.667 0.00 0.00 0.00 3.69
648 677 2.105128 CGGACGCACAGGGAGATC 59.895 66.667 0.00 0.00 0.00 2.75
649 678 4.148825 GCGGACGCACAGGGAGAT 62.149 66.667 12.31 0.00 41.49 2.75
651 680 4.803426 GAGCGGACGCACAGGGAG 62.803 72.222 19.48 0.00 44.88 4.30
661 690 2.668280 GGCAAGTTGTCGAGCGGAC 61.668 63.158 4.48 4.25 46.27 4.79
662 691 2.357034 GGCAAGTTGTCGAGCGGA 60.357 61.111 4.48 0.00 0.00 5.54
669 698 3.300667 CTCGCTGCGGCAAGTTGTC 62.301 63.158 23.03 0.00 38.60 3.18
670 699 3.349006 CTCGCTGCGGCAAGTTGT 61.349 61.111 23.03 0.00 38.60 3.32
671 700 4.748679 GCTCGCTGCGGCAAGTTG 62.749 66.667 23.03 0.00 38.60 3.16
680 709 2.325857 CTATTTGCCGCTCGCTGC 59.674 61.111 0.00 0.00 38.78 5.25
681 710 0.882042 ATCCTATTTGCCGCTCGCTG 60.882 55.000 0.00 0.00 38.78 5.18
682 711 0.679505 TATCCTATTTGCCGCTCGCT 59.320 50.000 0.00 0.00 38.78 4.93
683 712 1.726853 ATATCCTATTTGCCGCTCGC 58.273 50.000 0.00 0.00 38.31 5.03
684 713 2.673368 GGAATATCCTATTTGCCGCTCG 59.327 50.000 0.00 0.00 32.53 5.03
685 714 2.673368 CGGAATATCCTATTTGCCGCTC 59.327 50.000 0.00 0.00 33.30 5.03
686 715 2.301870 TCGGAATATCCTATTTGCCGCT 59.698 45.455 0.00 0.00 37.36 5.52
687 716 2.695359 TCGGAATATCCTATTTGCCGC 58.305 47.619 0.00 0.00 37.36 6.53
688 717 5.449304 GTTTTCGGAATATCCTATTTGCCG 58.551 41.667 0.00 0.00 38.68 5.69
689 718 5.535030 AGGTTTTCGGAATATCCTATTTGCC 59.465 40.000 6.96 0.00 33.30 4.52
690 719 6.635030 AGGTTTTCGGAATATCCTATTTGC 57.365 37.500 6.96 0.00 33.30 3.68
691 720 7.094762 GCCTAGGTTTTCGGAATATCCTATTTG 60.095 40.741 11.31 8.49 33.30 2.32
692 721 6.940867 GCCTAGGTTTTCGGAATATCCTATTT 59.059 38.462 11.31 0.00 33.30 1.40
693 722 6.473758 GCCTAGGTTTTCGGAATATCCTATT 58.526 40.000 11.31 0.00 33.30 1.73
694 723 5.045797 GGCCTAGGTTTTCGGAATATCCTAT 60.046 44.000 11.31 0.00 33.30 2.57
695 724 4.285260 GGCCTAGGTTTTCGGAATATCCTA 59.715 45.833 11.31 12.25 33.30 2.94
696 725 3.072622 GGCCTAGGTTTTCGGAATATCCT 59.927 47.826 11.31 11.53 33.30 3.24
697 726 3.409570 GGCCTAGGTTTTCGGAATATCC 58.590 50.000 11.31 0.00 0.00 2.59
698 727 3.181448 TGGGCCTAGGTTTTCGGAATATC 60.181 47.826 11.31 0.00 0.00 1.63
699 728 2.781174 TGGGCCTAGGTTTTCGGAATAT 59.219 45.455 11.31 0.00 0.00 1.28
700 729 2.171870 CTGGGCCTAGGTTTTCGGAATA 59.828 50.000 8.57 0.00 0.00 1.75
701 730 0.996583 TGGGCCTAGGTTTTCGGAAT 59.003 50.000 11.31 0.00 0.00 3.01
702 731 0.326927 CTGGGCCTAGGTTTTCGGAA 59.673 55.000 8.57 0.00 0.00 4.30
703 732 1.988015 CTGGGCCTAGGTTTTCGGA 59.012 57.895 8.57 0.00 0.00 4.55
704 733 1.749258 GCTGGGCCTAGGTTTTCGG 60.749 63.158 18.96 4.18 0.00 4.30
705 734 0.608035 TTGCTGGGCCTAGGTTTTCG 60.608 55.000 18.96 0.00 0.00 3.46
706 735 0.888619 GTTGCTGGGCCTAGGTTTTC 59.111 55.000 18.96 0.65 0.00 2.29
707 736 0.482887 AGTTGCTGGGCCTAGGTTTT 59.517 50.000 18.96 0.00 0.00 2.43
712 741 0.177604 CTCAGAGTTGCTGGGCCTAG 59.822 60.000 12.68 12.68 44.98 3.02
713 742 1.267574 CCTCAGAGTTGCTGGGCCTA 61.268 60.000 4.53 0.00 44.16 3.93
728 757 0.603569 GAAGGCGACAAGAGACCTCA 59.396 55.000 0.00 0.00 0.00 3.86
737 766 0.690192 TGGAATGAGGAAGGCGACAA 59.310 50.000 0.00 0.00 0.00 3.18
740 769 0.690192 TTGTGGAATGAGGAAGGCGA 59.310 50.000 0.00 0.00 0.00 5.54
742 771 1.541588 GTGTTGTGGAATGAGGAAGGC 59.458 52.381 0.00 0.00 0.00 4.35
743 772 2.554032 GTGTGTTGTGGAATGAGGAAGG 59.446 50.000 0.00 0.00 0.00 3.46
744 773 3.003689 GTGTGTGTTGTGGAATGAGGAAG 59.996 47.826 0.00 0.00 0.00 3.46
745 774 2.948979 GTGTGTGTTGTGGAATGAGGAA 59.051 45.455 0.00 0.00 0.00 3.36
749 784 3.507622 TGTTTGTGTGTGTTGTGGAATGA 59.492 39.130 0.00 0.00 0.00 2.57
753 788 2.230660 TGTGTTTGTGTGTGTTGTGGA 58.769 42.857 0.00 0.00 0.00 4.02
767 802 7.368059 ACTTTCTCTTTCGACTTTTTGTGTTT 58.632 30.769 0.00 0.00 0.00 2.83
773 808 4.272748 CCCGACTTTCTCTTTCGACTTTTT 59.727 41.667 0.00 0.00 34.62 1.94
774 809 3.808174 CCCGACTTTCTCTTTCGACTTTT 59.192 43.478 0.00 0.00 34.62 2.27
778 813 1.069255 GCCCGACTTTCTCTTTCGAC 58.931 55.000 0.00 0.00 34.62 4.20
813 848 2.885644 CAACCGGAGATGGCGACG 60.886 66.667 9.46 0.00 0.00 5.12
814 849 3.195698 GCAACCGGAGATGGCGAC 61.196 66.667 9.46 0.00 0.00 5.19
815 850 4.812476 CGCAACCGGAGATGGCGA 62.812 66.667 9.46 0.00 0.00 5.54
818 853 2.587322 TAAGGCGCAACCGGAGATGG 62.587 60.000 9.46 0.00 46.52 3.51
819 854 0.742990 TTAAGGCGCAACCGGAGATG 60.743 55.000 9.46 5.25 46.52 2.90
830 865 0.461339 TGGATCGAACCTTAAGGCGC 60.461 55.000 21.92 12.35 39.32 6.53
836 879 1.492764 GGGGAGTGGATCGAACCTTA 58.507 55.000 13.40 0.00 0.00 2.69
865 912 0.793617 AGGAGAGGGGAAGTGAGGAA 59.206 55.000 0.00 0.00 0.00 3.36
871 918 0.118144 AAGCAGAGGAGAGGGGAAGT 59.882 55.000 0.00 0.00 0.00 3.01
875 922 2.069430 GGGAAGCAGAGGAGAGGGG 61.069 68.421 0.00 0.00 0.00 4.79
976 1031 1.840635 GTTACAGGGAGGAGGATTGCT 59.159 52.381 0.00 0.00 0.00 3.91
994 1050 1.006813 TTACATGCCCCCATCTGGTT 58.993 50.000 0.00 0.00 0.00 3.67
1050 1120 1.466856 AGACATGGAACGCATGCATT 58.533 45.000 19.57 9.11 38.12 3.56
1248 1318 3.753434 CTCAGGTCGCAGGACGCT 61.753 66.667 0.00 0.00 44.39 5.07
1363 1433 3.064820 TCGCTTCGCTTTTTGAAAGAAGT 59.935 39.130 4.69 0.00 40.10 3.01
1449 1519 3.347958 TCGACAACATGTGGCTTTTTC 57.652 42.857 0.00 0.00 30.19 2.29
1466 1545 1.916874 TGGGGAATGGTTTGGTATCGA 59.083 47.619 0.00 0.00 0.00 3.59
1500 1588 1.434622 CCGCAGTCATGTCAGATGGC 61.435 60.000 0.00 0.00 0.00 4.40
1519 1607 2.707849 CCAGCAGCCTGCCAACATC 61.708 63.158 14.25 0.00 46.52 3.06
1592 1681 0.530744 AGCGAGAACGAACCTATGCA 59.469 50.000 0.00 0.00 42.66 3.96
1703 1795 0.467290 AAGCAGGGCCTTGAAAACGA 60.467 50.000 20.85 0.00 0.00 3.85
1864 1995 0.450482 GTGTCCGCGTTCAAATCGTG 60.450 55.000 4.92 0.00 38.32 4.35
1986 2124 1.114722 CCTTGAAGCCTTGGGTTGCA 61.115 55.000 8.95 4.58 0.00 4.08
2077 2216 4.010349 GGCAATTCTACCTTTGTAGCTGT 58.990 43.478 0.00 0.00 43.51 4.40
2150 2294 3.780294 ACATTGAGCTTACCATCCCTACA 59.220 43.478 0.00 0.00 0.00 2.74
2200 2353 4.993584 ACATCATCCATATCGCTTGAGAAC 59.006 41.667 0.00 0.00 0.00 3.01
2209 2362 6.128982 CGAGAACTTTCACATCATCCATATCG 60.129 42.308 0.00 0.00 0.00 2.92
2257 2417 6.460676 GCTCCAGATAAAACAGCAGCATAATT 60.461 38.462 0.00 0.00 0.00 1.40
2264 2424 1.063174 GCGCTCCAGATAAAACAGCAG 59.937 52.381 0.00 0.00 0.00 4.24
2299 2460 6.092807 GCCAGAAGATTAAGACCAAGTGTTAG 59.907 42.308 0.00 0.00 0.00 2.34
2335 2496 4.250116 ACAAAAGTTGCACACACAAGAA 57.750 36.364 0.00 0.00 0.00 2.52
2351 2512 2.799412 GGATGACAAATGCGCAACAAAA 59.201 40.909 17.11 0.00 0.00 2.44
2367 2532 5.714806 TCGCTAATGTAGACCATATGGATGA 59.285 40.000 28.77 9.29 38.94 2.92
2370 2535 4.082190 GCTCGCTAATGTAGACCATATGGA 60.082 45.833 28.77 5.58 38.94 3.41
2417 2582 7.302524 TGCCGTTTTAATCTTGTTATGTTCTC 58.697 34.615 0.00 0.00 0.00 2.87
2423 2592 8.188139 CCAGTTATGCCGTTTTAATCTTGTTAT 58.812 33.333 0.00 0.00 0.00 1.89
2461 2694 7.806409 TGTGCAACTTACAATGCTATATCAT 57.194 32.000 0.00 0.00 42.97 2.45
2481 2714 5.910637 TGCTTCAGAAAATCAAAATGTGC 57.089 34.783 0.00 0.00 0.00 4.57
2484 2717 7.597369 TCTGTCATGCTTCAGAAAATCAAAATG 59.403 33.333 10.88 0.00 37.69 2.32
2495 2728 5.354842 AGATCATTCTGTCATGCTTCAGA 57.645 39.130 9.74 9.74 38.66 3.27
2507 2740 9.499585 CTTACAATTTAGCACAAGATCATTCTG 57.500 33.333 0.00 0.00 30.72 3.02
2525 2758 4.827284 CCCTGTTTGACCACTCTTACAATT 59.173 41.667 0.00 0.00 0.00 2.32
2539 2783 1.284785 CCTAATCAGGGCCCTGTTTGA 59.715 52.381 40.72 29.48 43.96 2.69
2551 2795 7.714377 AGAGCTCAATGTTGTAATCCTAATCAG 59.286 37.037 17.77 0.00 0.00 2.90
2616 3323 3.872182 GGTTACCTTTAAGAGCTGCTAGC 59.128 47.826 8.10 8.10 42.84 3.42
2674 3381 5.304101 AGGCTCAGACCAGTGATATTAGAAG 59.696 44.000 0.00 0.00 0.00 2.85
2685 3392 1.825281 GACTGCAGGCTCAGACCAGT 61.825 60.000 19.93 9.91 39.27 4.00
2757 3464 6.993079 ACCATGGGAGAAATTTTACAGAAAC 58.007 36.000 18.09 0.00 0.00 2.78
2819 3526 3.007723 CCACACAGATGCCTCTATGCTAT 59.992 47.826 0.00 0.00 28.37 2.97
2860 3567 0.629058 AACCCTTCCAACACACTGGT 59.371 50.000 0.00 0.00 37.74 4.00
2894 3601 8.733458 TCACATTTCCATCAAAACTCTCAATAG 58.267 33.333 0.00 0.00 0.00 1.73
2914 3621 4.141018 AGGTCAGGGTTAGGTTTTCACATT 60.141 41.667 0.00 0.00 0.00 2.71
2922 3629 2.308866 CAATGGAGGTCAGGGTTAGGTT 59.691 50.000 0.00 0.00 0.00 3.50
2938 3645 4.044336 TGCTTCTTTCACAACACAATGG 57.956 40.909 0.00 0.00 0.00 3.16
2971 3678 2.135933 CAACGAGCTCCTTCGACTTTT 58.864 47.619 8.47 0.00 43.03 2.27
2989 3696 2.885135 AATGACCCTCATCACAGCAA 57.115 45.000 0.00 0.00 35.76 3.91
3030 3737 9.892130 CCTGAGAAGTTAACAAACTAAGGATAT 57.108 33.333 17.82 0.00 31.72 1.63
3031 3738 8.877195 ACCTGAGAAGTTAACAAACTAAGGATA 58.123 33.333 24.34 0.00 31.72 2.59
3032 3739 7.746703 ACCTGAGAAGTTAACAAACTAAGGAT 58.253 34.615 24.34 13.24 31.72 3.24
3033 3740 7.070821 AGACCTGAGAAGTTAACAAACTAAGGA 59.929 37.037 24.34 3.79 31.72 3.36
3034 3741 7.217906 AGACCTGAGAAGTTAACAAACTAAGG 58.782 38.462 19.62 19.62 31.72 2.69
3035 3742 8.552034 CAAGACCTGAGAAGTTAACAAACTAAG 58.448 37.037 8.61 6.29 31.72 2.18
3053 3760 5.587388 AATGATTACATTGGCAAGACCTG 57.413 39.130 5.96 1.12 43.90 4.00


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

AutoCloner maintained by Alex Coulton.