Multiple sequence alignment - TraesCS3B01G161300

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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 TraesCS3B01G161300 chr3B 100.000 3944 0 0 1 3944 157918237 157922180 0.000000e+00 7284.0
1 TraesCS3B01G161300 chr3A 93.279 3050 158 28 897 3916 549622578 549619546 0.000000e+00 4453.0
2 TraesCS3B01G161300 chr3A 97.917 48 1 0 609 656 636996089 636996042 2.530000e-12 84.2
3 TraesCS3B01G161300 chr3A 97.872 47 1 0 610 656 24198417 24198463 9.080000e-12 82.4
4 TraesCS3B01G161300 chr3D 92.500 3080 157 35 898 3934 107068922 107071970 0.000000e+00 4340.0
5 TraesCS3B01G161300 chr3D 93.750 144 9 0 656 799 107068687 107068830 2.390000e-52 217.0
6 TraesCS3B01G161300 chr3D 97.778 45 1 0 612 656 129004720 129004676 1.180000e-10 78.7
7 TraesCS3B01G161300 chr6B 97.694 607 12 2 1 606 143771684 143771079 0.000000e+00 1042.0
8 TraesCS3B01G161300 chr6B 97.044 609 14 4 1 606 143780757 143780150 0.000000e+00 1022.0
9 TraesCS3B01G161300 chr6B 94.780 613 27 5 1 610 138080502 138079892 0.000000e+00 950.0
10 TraesCS3B01G161300 chr7B 97.368 608 14 2 1 606 336315534 336314927 0.000000e+00 1033.0
11 TraesCS3B01G161300 chr7B 96.591 616 15 3 1 610 336306474 336305859 0.000000e+00 1016.0
12 TraesCS3B01G161300 chr7B 92.500 40 2 1 611 649 100350483 100350522 5.510000e-04 56.5
13 TraesCS3B01G161300 chr1B 95.738 610 22 4 1 607 449733859 449734467 0.000000e+00 979.0
14 TraesCS3B01G161300 chr1B 95.254 611 23 5 1 606 449723196 449723805 0.000000e+00 963.0
15 TraesCS3B01G161300 chr2B 94.935 612 23 6 1 606 200814163 200813554 0.000000e+00 952.0
16 TraesCS3B01G161300 chr1A 94.910 609 28 3 1 606 236700284 236699676 0.000000e+00 950.0
17 TraesCS3B01G161300 chr4B 97.826 46 1 0 612 657 137711940 137711895 3.270000e-11 80.5
18 TraesCS3B01G161300 chr4D 92.727 55 3 1 611 665 335895787 335895734 1.180000e-10 78.7
19 TraesCS3B01G161300 chr4A 95.556 45 2 0 611 655 305571139 305571095 5.470000e-09 73.1


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 TraesCS3B01G161300 chr3B 157918237 157922180 3943 False 7284.0 7284 100.000 1 3944 1 chr3B.!!$F1 3943
1 TraesCS3B01G161300 chr3A 549619546 549622578 3032 True 4453.0 4453 93.279 897 3916 1 chr3A.!!$R1 3019
2 TraesCS3B01G161300 chr3D 107068687 107071970 3283 False 2278.5 4340 93.125 656 3934 2 chr3D.!!$F1 3278
3 TraesCS3B01G161300 chr6B 143771079 143771684 605 True 1042.0 1042 97.694 1 606 1 chr6B.!!$R2 605
4 TraesCS3B01G161300 chr6B 143780150 143780757 607 True 1022.0 1022 97.044 1 606 1 chr6B.!!$R3 605
5 TraesCS3B01G161300 chr6B 138079892 138080502 610 True 950.0 950 94.780 1 610 1 chr6B.!!$R1 609
6 TraesCS3B01G161300 chr7B 336314927 336315534 607 True 1033.0 1033 97.368 1 606 1 chr7B.!!$R2 605
7 TraesCS3B01G161300 chr7B 336305859 336306474 615 True 1016.0 1016 96.591 1 610 1 chr7B.!!$R1 609
8 TraesCS3B01G161300 chr1B 449733859 449734467 608 False 979.0 979 95.738 1 607 1 chr1B.!!$F2 606
9 TraesCS3B01G161300 chr1B 449723196 449723805 609 False 963.0 963 95.254 1 606 1 chr1B.!!$F1 605
10 TraesCS3B01G161300 chr2B 200813554 200814163 609 True 952.0 952 94.935 1 606 1 chr2B.!!$R1 605
11 TraesCS3B01G161300 chr1A 236699676 236700284 608 True 950.0 950 94.910 1 606 1 chr1A.!!$R1 605

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
809 827 0.109179 TCTGTTGCGCATGAATTGGC 60.109 50.0 12.75 0.0 0.0 4.52 F
2460 2513 0.463833 GGGAGCACAAGATTACCCCG 60.464 60.0 0.00 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2471 2524 0.109458 GTCGACCATGCACGTGTAGA 60.109 55.0 18.38 2.74 0.0 2.59 R
3819 3949 0.642800 GCTGAGTTTGCGATCGAGAC 59.357 55.0 21.57 13.16 0.0 3.36 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
256 266 4.613925 TCACCTTATGCCATTTTTGCAA 57.386 36.364 0.00 0.00 42.92 4.08
363 379 8.531146 CCAGGGCAAATAATTATCGGATTAATT 58.469 33.333 0.00 3.75 36.17 1.40
576 594 3.873361 TGATGCACAAATGACTAGCTAGC 59.127 43.478 20.91 6.62 0.00 3.42
610 628 4.323792 CCAGACTAGGGATGTGACACAATT 60.324 45.833 13.23 0.00 0.00 2.32
611 629 5.248640 CAGACTAGGGATGTGACACAATTT 58.751 41.667 13.23 0.00 0.00 1.82
612 630 5.352569 CAGACTAGGGATGTGACACAATTTC 59.647 44.000 13.23 5.74 0.00 2.17
613 631 5.249393 AGACTAGGGATGTGACACAATTTCT 59.751 40.000 13.23 10.20 0.00 2.52
614 632 5.491982 ACTAGGGATGTGACACAATTTCTC 58.508 41.667 13.23 5.89 0.00 2.87
615 633 4.647564 AGGGATGTGACACAATTTCTCT 57.352 40.909 13.23 8.30 0.00 3.10
616 634 5.762179 AGGGATGTGACACAATTTCTCTA 57.238 39.130 13.23 0.00 0.00 2.43
617 635 6.126863 AGGGATGTGACACAATTTCTCTAA 57.873 37.500 13.23 0.00 0.00 2.10
618 636 6.725364 AGGGATGTGACACAATTTCTCTAAT 58.275 36.000 13.23 0.00 0.00 1.73
619 637 6.600822 AGGGATGTGACACAATTTCTCTAATG 59.399 38.462 13.23 0.00 0.00 1.90
620 638 6.599244 GGGATGTGACACAATTTCTCTAATGA 59.401 38.462 13.23 0.00 0.00 2.57
621 639 7.121168 GGGATGTGACACAATTTCTCTAATGAA 59.879 37.037 13.23 0.00 0.00 2.57
622 640 8.680903 GGATGTGACACAATTTCTCTAATGAAT 58.319 33.333 13.23 0.00 0.00 2.57
623 641 9.499585 GATGTGACACAATTTCTCTAATGAATG 57.500 33.333 13.23 0.00 0.00 2.67
624 642 8.620116 TGTGACACAATTTCTCTAATGAATGA 57.380 30.769 5.62 0.00 0.00 2.57
625 643 9.234827 TGTGACACAATTTCTCTAATGAATGAT 57.765 29.630 5.62 0.00 0.00 2.45
628 646 9.855361 GACACAATTTCTCTAATGAATGATACG 57.145 33.333 0.00 0.00 0.00 3.06
629 647 8.338259 ACACAATTTCTCTAATGAATGATACGC 58.662 33.333 0.00 0.00 0.00 4.42
630 648 8.337532 CACAATTTCTCTAATGAATGATACGCA 58.662 33.333 0.00 0.00 0.00 5.24
631 649 9.060347 ACAATTTCTCTAATGAATGATACGCAT 57.940 29.630 0.00 0.00 39.43 4.73
632 650 9.326339 CAATTTCTCTAATGAATGATACGCATG 57.674 33.333 0.00 0.00 37.28 4.06
633 651 6.471976 TTCTCTAATGAATGATACGCATGC 57.528 37.500 7.91 7.91 37.28 4.06
634 652 5.787380 TCTCTAATGAATGATACGCATGCT 58.213 37.500 17.13 5.50 37.28 3.79
635 653 6.226052 TCTCTAATGAATGATACGCATGCTT 58.774 36.000 17.13 9.37 37.28 3.91
636 654 6.146673 TCTCTAATGAATGATACGCATGCTTG 59.853 38.462 17.13 3.27 37.28 4.01
637 655 4.906065 AATGAATGATACGCATGCTTGT 57.094 36.364 17.13 9.84 37.28 3.16
638 656 3.678915 TGAATGATACGCATGCTTGTG 57.321 42.857 17.13 11.29 37.28 3.33
640 658 3.181508 TGAATGATACGCATGCTTGTGTG 60.182 43.478 24.44 11.60 45.85 3.82
641 659 1.807139 TGATACGCATGCTTGTGTGT 58.193 45.000 24.44 19.45 45.85 3.72
642 660 2.966050 TGATACGCATGCTTGTGTGTA 58.034 42.857 24.44 17.44 45.85 2.90
645 663 2.900122 ACGCATGCTTGTGTGTATTC 57.100 45.000 17.13 0.00 44.69 1.75
646 664 1.128507 ACGCATGCTTGTGTGTATTCG 59.871 47.619 17.13 4.52 44.69 3.34
647 665 1.393196 CGCATGCTTGTGTGTATTCGA 59.607 47.619 17.13 0.00 0.00 3.71
648 666 2.535534 CGCATGCTTGTGTGTATTCGAG 60.536 50.000 17.13 0.00 0.00 4.04
649 667 2.672874 GCATGCTTGTGTGTATTCGAGA 59.327 45.455 11.37 0.00 0.00 4.04
650 668 3.125146 GCATGCTTGTGTGTATTCGAGAA 59.875 43.478 11.37 0.00 0.00 2.87
651 669 4.378356 GCATGCTTGTGTGTATTCGAGAAA 60.378 41.667 11.37 0.00 0.00 2.52
652 670 5.688823 CATGCTTGTGTGTATTCGAGAAAA 58.311 37.500 0.00 0.00 0.00 2.29
653 671 5.743026 TGCTTGTGTGTATTCGAGAAAAA 57.257 34.783 0.00 0.00 0.00 1.94
676 694 4.843220 AAAGTTGAGGCAATTGAGACAG 57.157 40.909 10.34 0.00 0.00 3.51
681 699 3.603532 TGAGGCAATTGAGACAGTGATC 58.396 45.455 10.34 0.00 0.00 2.92
702 720 0.622665 CTGGAGGCAGATCTTTGGGT 59.377 55.000 0.00 0.00 0.00 4.51
734 752 6.038356 CAGCAATCTTCCCACAATTGTTATC 58.962 40.000 8.77 0.00 33.82 1.75
779 797 8.394877 CGCAAACTATCTTGGACATTGTTATAA 58.605 33.333 0.00 0.00 0.00 0.98
791 809 9.638239 TGGACATTGTTATAAAGAAGCAAATTC 57.362 29.630 0.00 0.00 38.28 2.17
803 821 1.700523 GCAAATTCTGTTGCGCATGA 58.299 45.000 12.75 7.62 44.05 3.07
804 822 2.060284 GCAAATTCTGTTGCGCATGAA 58.940 42.857 12.75 16.59 44.05 2.57
805 823 2.669434 GCAAATTCTGTTGCGCATGAAT 59.331 40.909 12.75 18.10 44.05 2.57
806 824 3.123959 GCAAATTCTGTTGCGCATGAATT 59.876 39.130 26.37 26.37 44.05 2.17
807 825 4.634000 CAAATTCTGTTGCGCATGAATTG 58.366 39.130 29.54 22.95 36.28 2.32
808 826 2.350899 TTCTGTTGCGCATGAATTGG 57.649 45.000 12.75 0.00 0.00 3.16
809 827 0.109179 TCTGTTGCGCATGAATTGGC 60.109 50.000 12.75 0.00 0.00 4.52
810 828 1.079875 CTGTTGCGCATGAATTGGCC 61.080 55.000 12.75 0.00 0.00 5.36
811 829 1.079956 GTTGCGCATGAATTGGCCA 60.080 52.632 12.75 0.00 0.00 5.36
812 830 1.079956 TTGCGCATGAATTGGCCAC 60.080 52.632 12.75 0.00 0.00 5.01
813 831 1.813728 TTGCGCATGAATTGGCCACA 61.814 50.000 12.75 0.00 0.00 4.17
814 832 1.079956 GCGCATGAATTGGCCACAA 60.080 52.632 3.88 0.00 41.59 3.33
815 833 0.669932 GCGCATGAATTGGCCACAAA 60.670 50.000 3.88 0.00 40.55 2.83
816 834 2.008045 GCGCATGAATTGGCCACAAAT 61.008 47.619 3.88 0.00 40.55 2.32
817 835 1.661617 CGCATGAATTGGCCACAAATG 59.338 47.619 3.88 8.77 40.55 2.32
828 846 1.755179 CCACAAATGGCTAGGTCTGG 58.245 55.000 0.00 0.00 39.82 3.86
834 852 4.463891 ACAAATGGCTAGGTCTGGATTTTG 59.536 41.667 0.00 0.00 0.00 2.44
843 861 7.427214 GCTAGGTCTGGATTTTGTAGTACTAG 58.573 42.308 1.87 0.00 0.00 2.57
844 862 7.068470 GCTAGGTCTGGATTTTGTAGTACTAGT 59.932 40.741 1.87 0.00 0.00 2.57
845 863 9.624373 CTAGGTCTGGATTTTGTAGTACTAGTA 57.376 37.037 1.87 0.00 0.00 1.82
846 864 8.291191 AGGTCTGGATTTTGTAGTACTAGTAC 57.709 38.462 23.03 23.03 36.35 2.73
860 878 9.108284 GTAGTACTAGTACTAGGTTTGAAGAGG 57.892 40.741 33.38 5.51 45.97 3.69
865 883 5.152934 AGTACTAGGTTTGAAGAGGTTCCA 58.847 41.667 0.00 0.00 0.00 3.53
867 885 4.974399 ACTAGGTTTGAAGAGGTTCCAAG 58.026 43.478 0.00 0.00 0.00 3.61
888 906 5.528043 AGTGAACTGATCGCTCTATTGAT 57.472 39.130 0.00 0.00 45.82 2.57
889 907 5.911752 AGTGAACTGATCGCTCTATTGATT 58.088 37.500 0.00 0.00 45.82 2.57
890 908 5.982516 AGTGAACTGATCGCTCTATTGATTC 59.017 40.000 0.00 0.00 45.82 2.52
892 910 6.256539 GTGAACTGATCGCTCTATTGATTCAA 59.743 38.462 0.75 0.75 35.60 2.69
894 912 6.154203 ACTGATCGCTCTATTGATTCAAGA 57.846 37.500 5.21 0.00 0.00 3.02
895 913 6.577103 ACTGATCGCTCTATTGATTCAAGAA 58.423 36.000 5.21 0.00 0.00 2.52
903 945 8.060679 CGCTCTATTGATTCAAGAATGTAACTG 58.939 37.037 5.21 0.00 0.00 3.16
922 966 8.556194 TGTAACTGTTGTCACAAGCTAATAAAG 58.444 33.333 2.69 0.00 30.36 1.85
926 970 4.650972 TGTCACAAGCTAATAAAGGGGT 57.349 40.909 0.00 0.00 0.00 4.95
927 971 4.331968 TGTCACAAGCTAATAAAGGGGTG 58.668 43.478 0.00 0.00 0.00 4.61
928 972 4.042311 TGTCACAAGCTAATAAAGGGGTGA 59.958 41.667 0.00 0.00 0.00 4.02
929 973 4.395231 GTCACAAGCTAATAAAGGGGTGAC 59.605 45.833 0.00 0.00 44.51 3.67
1003 1053 2.300967 GGGACCCAGTGCCAGATGA 61.301 63.158 5.33 0.00 43.66 2.92
1181 1231 3.303135 TCCAGACCTTGCGCTCGT 61.303 61.111 9.73 0.81 0.00 4.18
1411 1461 3.083600 GACGCAATGCCGTCGAAGG 62.084 63.158 13.59 13.59 46.52 3.46
1489 1539 1.228245 AGTGCAATGGCCACGTTCT 60.228 52.632 8.16 0.00 40.13 3.01
1596 1649 2.021457 CCGGTGGTTCTTGAACTGTTT 58.979 47.619 12.44 0.00 0.00 2.83
1638 1691 2.971452 GAAGGGAACGCCGAGTCT 59.029 61.111 0.00 0.00 33.83 3.24
1701 1754 1.547495 ATTGGGGAAAGGGAGGGCT 60.547 57.895 0.00 0.00 0.00 5.19
1825 1878 1.074248 GAGGTTTTCCGGGAAGCCA 59.926 57.895 28.37 0.00 46.35 4.75
2148 2201 0.465705 ACGCGATCAGATCCATGGTT 59.534 50.000 15.93 2.52 0.00 3.67
2159 2212 1.603455 CCATGGTTGACCGGCACTT 60.603 57.895 0.00 0.00 39.43 3.16
2233 2286 2.957489 CACGCACGGTGTTCGACA 60.957 61.111 13.72 0.00 41.89 4.35
2439 2492 2.289820 CCGGCTGTTTGATCAGATGATG 59.710 50.000 0.00 0.00 37.61 3.07
2441 2494 2.286831 GGCTGTTTGATCAGATGATGCG 60.287 50.000 0.00 0.00 37.61 4.73
2460 2513 0.463833 GGGAGCACAAGATTACCCCG 60.464 60.000 0.00 0.00 0.00 5.73
2471 2524 0.694444 ATTACCCCGTCCATGGAGCT 60.694 55.000 16.81 0.00 0.00 4.09
2568 2621 4.681978 GGAGCCGACCTGTGCGTT 62.682 66.667 0.00 0.00 0.00 4.84
2649 2702 3.793144 GCGAAGGTTCTGCAGGCG 61.793 66.667 15.13 9.38 0.00 5.52
2885 2938 0.294887 CTCGACGATTTGTACAGCGC 59.705 55.000 0.00 0.00 0.00 5.92
2922 2975 1.613925 CGTACCATGGAGGACGATCAT 59.386 52.381 21.47 0.00 40.83 2.45
2938 2991 4.032900 ACGATCATCACATTGTAAGCGTTC 59.967 41.667 0.00 0.00 0.00 3.95
3015 3094 1.803555 GAGCAAGTCTTTCAGAGTGGC 59.196 52.381 0.20 0.20 43.46 5.01
3059 3138 2.060980 GGGTCCTGCAGATCTCGGT 61.061 63.158 17.39 0.00 0.00 4.69
3268 3347 1.367840 GTCAGGAGGTTGTCGCACT 59.632 57.895 0.00 0.00 0.00 4.40
3535 3633 1.546476 GACTCCCTGTCGATGAAGTGT 59.454 52.381 0.00 0.00 35.81 3.55
3813 3943 0.036164 TAATTGCGGCACTCACACCT 59.964 50.000 0.05 0.00 0.00 4.00
3814 3944 1.237285 AATTGCGGCACTCACACCTC 61.237 55.000 0.05 0.00 0.00 3.85
3815 3945 2.116983 ATTGCGGCACTCACACCTCT 62.117 55.000 0.05 0.00 0.00 3.69
3816 3946 2.433318 GCGGCACTCACACCTCTC 60.433 66.667 0.00 0.00 0.00 3.20
3817 3947 2.126307 CGGCACTCACACCTCTCG 60.126 66.667 0.00 0.00 0.00 4.04
3818 3948 2.626780 CGGCACTCACACCTCTCGA 61.627 63.158 0.00 0.00 0.00 4.04
3819 3949 1.214062 GGCACTCACACCTCTCGAG 59.786 63.158 5.93 5.93 0.00 4.04
3823 3953 1.466950 CACTCACACCTCTCGAGTCTC 59.533 57.143 13.13 0.00 37.92 3.36
3841 3971 0.038251 TCGATCGCAAACTCAGCAGT 60.038 50.000 11.09 0.00 0.00 4.40
3930 4060 2.203308 AGCAGCAGCAGCAACAGT 60.203 55.556 12.92 0.00 45.49 3.55
3934 4064 1.895707 AGCAGCAGCAACAGTCACC 60.896 57.895 3.17 0.00 45.49 4.02
3935 4065 2.188829 GCAGCAGCAACAGTCACCA 61.189 57.895 0.00 0.00 41.58 4.17
3936 4066 1.650912 CAGCAGCAACAGTCACCAC 59.349 57.895 0.00 0.00 0.00 4.16
3937 4067 1.526917 AGCAGCAACAGTCACCACC 60.527 57.895 0.00 0.00 0.00 4.61
3938 4068 2.555547 GCAGCAACAGTCACCACCC 61.556 63.158 0.00 0.00 0.00 4.61
3939 4069 1.152984 CAGCAACAGTCACCACCCA 60.153 57.895 0.00 0.00 0.00 4.51
3940 4070 0.751277 CAGCAACAGTCACCACCCAA 60.751 55.000 0.00 0.00 0.00 4.12
3941 4071 0.466189 AGCAACAGTCACCACCCAAG 60.466 55.000 0.00 0.00 0.00 3.61
3942 4072 1.455383 GCAACAGTCACCACCCAAGG 61.455 60.000 0.00 0.00 0.00 3.61
3943 4073 0.182537 CAACAGTCACCACCCAAGGA 59.817 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
256 266 8.893563 AGCTCTGGAATAATATAGTTAGCTCT 57.106 34.615 0.00 0.00 31.24 4.09
340 356 9.921637 TTGAATTAATCCGATAATTATTTGCCC 57.078 29.630 0.00 0.00 36.01 5.36
363 379 9.339850 CATGGATATTTAATTTTGGCCATTTGA 57.660 29.630 6.09 0.00 32.91 2.69
419 435 8.671921 GTTGCTCTCTGAAAATATTGATCAGAA 58.328 33.333 23.81 17.14 46.38 3.02
425 441 7.926674 TCATGTTGCTCTCTGAAAATATTGA 57.073 32.000 0.00 0.00 0.00 2.57
543 561 9.275398 AGTCATTTGTGCATCATGTTTAAATTT 57.725 25.926 0.00 0.00 0.00 1.82
576 594 3.398292 TCCCTAGTCTGGTATGACCTAGG 59.602 52.174 7.41 7.41 39.58 3.02
610 628 6.226052 AGCATGCGTATCATTCATTAGAGAA 58.774 36.000 13.01 0.00 31.79 2.87
611 629 5.787380 AGCATGCGTATCATTCATTAGAGA 58.213 37.500 13.01 0.00 31.79 3.10
612 630 6.073385 ACAAGCATGCGTATCATTCATTAGAG 60.073 38.462 13.01 0.00 31.79 2.43
613 631 5.759763 ACAAGCATGCGTATCATTCATTAGA 59.240 36.000 13.01 0.00 31.79 2.10
614 632 5.849604 CACAAGCATGCGTATCATTCATTAG 59.150 40.000 13.01 0.00 31.79 1.73
615 633 5.296531 ACACAAGCATGCGTATCATTCATTA 59.703 36.000 13.01 0.00 31.79 1.90
616 634 4.096833 ACACAAGCATGCGTATCATTCATT 59.903 37.500 13.01 0.00 31.79 2.57
617 635 3.628942 ACACAAGCATGCGTATCATTCAT 59.371 39.130 13.01 0.00 31.79 2.57
618 636 3.009026 ACACAAGCATGCGTATCATTCA 58.991 40.909 13.01 0.00 31.79 2.57
619 637 3.181507 ACACACAAGCATGCGTATCATTC 60.182 43.478 13.01 0.00 31.79 2.67
620 638 2.749076 ACACACAAGCATGCGTATCATT 59.251 40.909 13.01 0.00 31.79 2.57
621 639 2.358957 ACACACAAGCATGCGTATCAT 58.641 42.857 13.01 0.00 35.31 2.45
622 640 1.807139 ACACACAAGCATGCGTATCA 58.193 45.000 13.01 0.00 0.00 2.15
623 641 4.518217 GAATACACACAAGCATGCGTATC 58.482 43.478 13.01 4.07 0.00 2.24
624 642 3.001228 CGAATACACACAAGCATGCGTAT 59.999 43.478 13.01 9.74 0.00 3.06
625 643 2.347150 CGAATACACACAAGCATGCGTA 59.653 45.455 13.01 7.68 0.00 4.42
626 644 1.128507 CGAATACACACAAGCATGCGT 59.871 47.619 13.01 6.07 0.00 5.24
627 645 1.393196 TCGAATACACACAAGCATGCG 59.607 47.619 13.01 0.84 0.00 4.73
628 646 2.672874 TCTCGAATACACACAAGCATGC 59.327 45.455 10.51 10.51 0.00 4.06
629 647 4.926860 TTCTCGAATACACACAAGCATG 57.073 40.909 0.00 0.00 0.00 4.06
630 648 5.940192 TTTTCTCGAATACACACAAGCAT 57.060 34.783 0.00 0.00 0.00 3.79
631 649 5.743026 TTTTTCTCGAATACACACAAGCA 57.257 34.783 0.00 0.00 0.00 3.91
653 671 5.127682 ACTGTCTCAATTGCCTCAACTTTTT 59.872 36.000 0.00 0.00 0.00 1.94
654 672 4.646492 ACTGTCTCAATTGCCTCAACTTTT 59.354 37.500 0.00 0.00 0.00 2.27
657 675 3.144506 CACTGTCTCAATTGCCTCAACT 58.855 45.455 0.00 0.00 0.00 3.16
663 681 1.063174 GCGATCACTGTCTCAATTGCC 59.937 52.381 0.00 0.00 0.00 4.52
666 684 2.234661 TCCAGCGATCACTGTCTCAATT 59.765 45.455 9.78 0.00 35.83 2.32
702 720 1.679944 GGGAAGATTGCTGCAGCTACA 60.680 52.381 36.61 22.10 42.66 2.74
734 752 1.196808 CGGGAATTCACAAACGAGGTG 59.803 52.381 8.74 0.00 37.60 4.00
791 809 1.079875 GGCCAATTCATGCGCAACAG 61.080 55.000 17.11 7.99 0.00 3.16
809 827 1.281867 TCCAGACCTAGCCATTTGTGG 59.718 52.381 0.00 0.00 0.00 4.17
810 828 2.787473 TCCAGACCTAGCCATTTGTG 57.213 50.000 0.00 0.00 0.00 3.33
811 829 4.322057 AAATCCAGACCTAGCCATTTGT 57.678 40.909 0.00 0.00 0.00 2.83
812 830 4.463891 ACAAAATCCAGACCTAGCCATTTG 59.536 41.667 0.00 0.00 0.00 2.32
813 831 4.677182 ACAAAATCCAGACCTAGCCATTT 58.323 39.130 0.00 0.00 0.00 2.32
814 832 4.322057 ACAAAATCCAGACCTAGCCATT 57.678 40.909 0.00 0.00 0.00 3.16
815 833 4.475016 ACTACAAAATCCAGACCTAGCCAT 59.525 41.667 0.00 0.00 0.00 4.40
816 834 3.844211 ACTACAAAATCCAGACCTAGCCA 59.156 43.478 0.00 0.00 0.00 4.75
817 835 4.489306 ACTACAAAATCCAGACCTAGCC 57.511 45.455 0.00 0.00 0.00 3.93
818 836 6.223351 AGTACTACAAAATCCAGACCTAGC 57.777 41.667 0.00 0.00 0.00 3.42
819 837 8.522542 ACTAGTACTACAAAATCCAGACCTAG 57.477 38.462 0.00 0.00 0.00 3.02
820 838 9.401058 GTACTAGTACTACAAAATCCAGACCTA 57.599 37.037 23.17 0.00 33.45 3.08
821 839 8.114743 AGTACTAGTACTACAAAATCCAGACCT 58.885 37.037 29.96 4.00 43.98 3.85
822 840 8.291191 AGTACTAGTACTACAAAATCCAGACC 57.709 38.462 29.96 0.90 43.98 3.85
824 842 9.624373 CCTAGTACTAGTACTACAAAATCCAGA 57.376 37.037 30.50 13.87 43.98 3.86
825 843 9.406113 ACCTAGTACTAGTACTACAAAATCCAG 57.594 37.037 30.50 21.41 43.98 3.86
826 844 9.759473 AACCTAGTACTAGTACTACAAAATCCA 57.241 33.333 30.50 14.91 43.98 3.41
834 852 9.108284 CCTCTTCAAACCTAGTACTAGTACTAC 57.892 40.741 30.50 11.78 43.98 2.73
843 861 5.479124 TGGAACCTCTTCAAACCTAGTAC 57.521 43.478 0.00 0.00 0.00 2.73
844 862 5.605488 ACTTGGAACCTCTTCAAACCTAGTA 59.395 40.000 0.00 0.00 33.46 1.82
845 863 4.412528 ACTTGGAACCTCTTCAAACCTAGT 59.587 41.667 0.00 0.00 0.00 2.57
846 864 4.757149 CACTTGGAACCTCTTCAAACCTAG 59.243 45.833 0.00 0.00 0.00 3.02
865 883 5.330455 TCAATAGAGCGATCAGTTCACTT 57.670 39.130 2.38 0.00 31.99 3.16
867 885 5.750547 TGAATCAATAGAGCGATCAGTTCAC 59.249 40.000 2.38 0.00 31.99 3.18
873 891 6.988580 ACATTCTTGAATCAATAGAGCGATCA 59.011 34.615 2.38 0.00 0.00 2.92
874 892 7.418840 ACATTCTTGAATCAATAGAGCGATC 57.581 36.000 0.00 0.00 0.00 3.69
875 893 8.768955 GTTACATTCTTGAATCAATAGAGCGAT 58.231 33.333 0.00 0.00 0.00 4.58
878 896 8.887717 ACAGTTACATTCTTGAATCAATAGAGC 58.112 33.333 0.00 0.00 0.00 4.09
883 901 8.849168 TGACAACAGTTACATTCTTGAATCAAT 58.151 29.630 0.00 0.00 0.00 2.57
884 902 8.128582 GTGACAACAGTTACATTCTTGAATCAA 58.871 33.333 0.00 0.00 0.00 2.57
885 903 7.281999 TGTGACAACAGTTACATTCTTGAATCA 59.718 33.333 0.00 0.00 28.23 2.57
886 904 7.639039 TGTGACAACAGTTACATTCTTGAATC 58.361 34.615 0.00 0.00 28.23 2.52
888 906 6.993786 TGTGACAACAGTTACATTCTTGAA 57.006 33.333 0.00 0.00 28.23 2.69
889 907 6.458206 GCTTGTGACAACAGTTACATTCTTGA 60.458 38.462 0.00 0.00 37.67 3.02
890 908 5.682862 GCTTGTGACAACAGTTACATTCTTG 59.317 40.000 0.00 0.00 37.67 3.02
892 910 5.126067 AGCTTGTGACAACAGTTACATTCT 58.874 37.500 0.00 0.00 37.67 2.40
894 912 6.935741 TTAGCTTGTGACAACAGTTACATT 57.064 33.333 0.00 0.00 37.67 2.71
895 913 8.615878 TTATTAGCTTGTGACAACAGTTACAT 57.384 30.769 0.00 0.00 37.67 2.29
903 945 4.765339 ACCCCTTTATTAGCTTGTGACAAC 59.235 41.667 0.00 0.00 0.00 3.32
1003 1053 2.879233 TTGCTCGGAGGAAACGGCT 61.879 57.895 9.67 0.00 0.00 5.52
1120 1170 2.757124 GGAGGCGGTTCCATGGGAT 61.757 63.158 13.02 0.00 37.20 3.85
1575 1628 0.834612 ACAGTTCAAGAACCACCGGA 59.165 50.000 9.46 0.00 42.06 5.14
1596 1649 2.046988 CTGCGGTGCATGTCTCCA 60.047 61.111 0.00 0.00 38.13 3.86
1681 1734 1.874299 GCCCTCCCTTTCCCCAATGA 61.874 60.000 0.00 0.00 0.00 2.57
1701 1754 0.239082 CGACGCCGTAGCCATGTATA 59.761 55.000 0.00 0.00 34.57 1.47
1825 1878 1.155390 TCACGGTGTTCCTCTCCCT 59.845 57.895 8.17 0.00 0.00 4.20
2049 2102 2.289257 GGTAGCTAAGGTCACCACGTTT 60.289 50.000 0.00 0.00 32.79 3.60
2148 2201 3.858868 GACGAGCAAGTGCCGGTCA 62.859 63.158 15.52 0.00 43.38 4.02
2233 2286 2.114616 CAGGTCCCTGCTCTTCATACT 58.885 52.381 0.00 0.00 37.24 2.12
2421 2474 2.286831 CCGCATCATCTGATCAAACAGC 60.287 50.000 0.00 0.00 37.75 4.40
2439 2492 1.095807 GGGTAATCTTGTGCTCCCGC 61.096 60.000 0.00 0.00 0.00 6.13
2441 2494 0.463833 CGGGGTAATCTTGTGCTCCC 60.464 60.000 0.00 0.00 34.68 4.30
2455 2508 2.238319 TAGAGCTCCATGGACGGGGT 62.238 60.000 11.44 7.17 0.00 4.95
2460 2513 0.818296 ACGTGTAGAGCTCCATGGAC 59.182 55.000 11.44 8.29 0.00 4.02
2471 2524 0.109458 GTCGACCATGCACGTGTAGA 60.109 55.000 18.38 2.74 0.00 2.59
2829 2882 2.825836 GCTCTGGGCATTGACGGG 60.826 66.667 0.00 0.00 41.35 5.28
2835 2888 0.619832 TCTCCTCAGCTCTGGGCATT 60.620 55.000 0.74 0.00 44.79 3.56
2885 2938 2.931536 CGTCTCTCGTCGTCCATTG 58.068 57.895 0.00 0.00 34.52 2.82
2904 2957 2.628178 GTGATGATCGTCCTCCATGGTA 59.372 50.000 12.58 0.00 37.07 3.25
2922 2975 4.989044 TCTATCGAACGCTTACAATGTGA 58.011 39.130 0.00 0.00 0.00 3.58
2938 2991 4.201628 CCGCAAACACTTTCTCTTCTATCG 60.202 45.833 0.00 0.00 0.00 2.92
3015 3094 2.734079 GCTCTTCTTCGGTTCACAAGAG 59.266 50.000 0.00 0.00 42.01 2.85
3312 3391 5.277297 CGTTCTGTGCTGTTCTGTTTTGATA 60.277 40.000 0.00 0.00 0.00 2.15
3330 3413 3.716006 CACACCTGCGGCGTTCTG 61.716 66.667 9.37 1.49 0.00 3.02
3331 3414 4.235762 ACACACCTGCGGCGTTCT 62.236 61.111 9.37 0.00 0.00 3.01
3687 3797 3.793144 GAAAGCAGCCGTCGCAGG 61.793 66.667 0.00 0.00 37.52 4.85
3688 3798 4.139420 CGAAAGCAGCCGTCGCAG 62.139 66.667 2.60 0.00 37.52 5.18
3702 3812 4.036804 GTGCAATGGCCACGCGAA 62.037 61.111 15.93 4.93 40.13 4.70
3816 3946 1.184349 GAGTTTGCGATCGAGACTCG 58.816 55.000 21.57 18.91 42.10 4.18
3817 3947 2.181205 CTGAGTTTGCGATCGAGACTC 58.819 52.381 25.82 25.82 37.75 3.36
3818 3948 1.734047 GCTGAGTTTGCGATCGAGACT 60.734 52.381 21.57 17.74 0.00 3.24
3819 3949 0.642800 GCTGAGTTTGCGATCGAGAC 59.357 55.000 21.57 13.16 0.00 3.36
3823 3953 1.585668 CTACTGCTGAGTTTGCGATCG 59.414 52.381 11.69 11.69 33.21 3.69
3841 3971 1.618447 GGCCCTTCTTGTCCCCCTA 60.618 63.158 0.00 0.00 0.00 3.53
3899 4029 3.713205 CTGCTGCGCTCTGGATCGT 62.713 63.158 9.73 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.