Multiple sequence alignment - TraesCS4A01G173600

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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 TraesCS4A01G173600 chr4A 100.000 2576 0 0 1 2576 441779142 441776567 0.000000e+00 4758
1 TraesCS4A01G173600 chr4A 96.126 826 31 1 4 828 621416229 621415404 0.000000e+00 1347
2 TraesCS4A01G173600 chr4A 89.567 393 30 7 1931 2322 565845623 565846005 2.980000e-134 488
3 TraesCS4A01G173600 chr4D 94.180 1134 48 7 816 1943 127155060 127156181 0.000000e+00 1712
4 TraesCS4A01G173600 chr4B 97.030 808 23 1 1137 1943 191220425 191221232 0.000000e+00 1358
5 TraesCS4A01G173600 chr4B 95.307 831 36 3 1 830 671686032 671686860 0.000000e+00 1315
6 TraesCS4A01G173600 chr4B 93.617 141 7 1 899 1037 191219954 191220094 2.600000e-50 209
7 TraesCS4A01G173600 chr1A 95.657 829 35 1 1 828 504402809 504403637 0.000000e+00 1330
8 TraesCS4A01G173600 chr1A 95.657 829 34 2 1 828 534887788 534886961 0.000000e+00 1330
9 TraesCS4A01G173600 chr1A 95.296 829 37 2 1 828 534906785 534905958 0.000000e+00 1314
10 TraesCS4A01G173600 chr1A 87.462 654 43 25 1933 2576 16799009 16799633 0.000000e+00 717
11 TraesCS4A01G173600 chr6A 95.427 831 36 2 1 830 584974123 584973294 0.000000e+00 1323
12 TraesCS4A01G173600 chr6A 87.154 1121 109 15 827 1926 47104869 47105975 0.000000e+00 1240
13 TraesCS4A01G173600 chr6A 95.426 634 20 6 1944 2576 103896244 103896869 0.000000e+00 1002
14 TraesCS4A01G173600 chr6A 92.558 645 23 7 1932 2576 144202262 144202881 0.000000e+00 902
15 TraesCS4A01G173600 chr6A 90.256 390 29 6 1928 2314 6485352 6484969 3.830000e-138 501
16 TraesCS4A01G173600 chr2A 95.427 831 37 1 1 830 717255936 717256766 0.000000e+00 1323
17 TraesCS4A01G173600 chr2A 91.049 391 27 5 1932 2322 768029142 768028760 2.940000e-144 521
18 TraesCS4A01G173600 chr3A 95.416 829 36 2 1 828 10475723 10474896 0.000000e+00 1319
19 TraesCS4A01G173600 chr3A 94.945 633 20 6 1944 2576 731170662 731171282 0.000000e+00 981
20 TraesCS4A01G173600 chr3A 94.637 634 23 8 1944 2576 589903909 589903286 0.000000e+00 972
21 TraesCS4A01G173600 chr3A 94.087 389 19 3 1932 2319 126662844 126663229 2.860000e-164 588
22 TraesCS4A01G173600 chr7A 95.296 829 38 1 1 828 627154387 627153559 0.000000e+00 1314
23 TraesCS4A01G173600 chr7A 94.811 636 22 4 1943 2576 673655430 673656056 0.000000e+00 981
24 TraesCS4A01G173600 chr7A 94.375 640 23 6 1940 2576 81847559 81848188 0.000000e+00 970
25 TraesCS4A01G173600 chr7A 94.349 637 27 3 1944 2576 685620523 685619892 0.000000e+00 968
26 TraesCS4A01G173600 chr7A 90.951 652 29 12 1943 2576 167969381 167968742 0.000000e+00 850
27 TraesCS4A01G173600 chrUn 87.566 1134 109 16 826 1943 26921706 26920589 0.000000e+00 1284
28 TraesCS4A01G173600 chrUn 87.128 1142 108 17 827 1943 26996835 26997962 0.000000e+00 1258
29 TraesCS4A01G173600 chr6B 86.649 1116 106 17 827 1926 82326340 82327428 0.000000e+00 1195
30 TraesCS4A01G173600 chr6B 90.922 727 62 3 1204 1926 82527192 82527918 0.000000e+00 974
31 TraesCS4A01G173600 chr6B 87.675 357 41 2 1553 1906 82399765 82400121 1.840000e-111 412
32 TraesCS4A01G173600 chr5A 94.704 642 18 6 1943 2576 12497171 12497804 0.000000e+00 983
33 TraesCS4A01G173600 chr5A 94.357 638 29 5 1944 2576 32114202 32114837 0.000000e+00 972
34 TraesCS4A01G173600 chr5A 94.497 636 19 5 1943 2576 682355529 682354908 0.000000e+00 966
35 TraesCS4A01G173600 chr5A 91.358 648 30 12 1943 2576 576768951 576768316 0.000000e+00 863
36 TraesCS4A01G173600 chr5A 91.163 645 29 9 1933 2576 506416145 506416762 0.000000e+00 850
37 TraesCS4A01G173600 chr5A 75.505 841 161 28 1108 1931 531019325 531020137 1.130000e-98 370
38 TraesCS4A01G173600 chr5B 78.230 565 108 9 1108 1670 504775454 504776005 5.280000e-92 348


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 TraesCS4A01G173600 chr4A 441776567 441779142 2575 True 4758.0 4758 100.0000 1 2576 1 chr4A.!!$R1 2575
1 TraesCS4A01G173600 chr4A 621415404 621416229 825 True 1347.0 1347 96.1260 4 828 1 chr4A.!!$R2 824
2 TraesCS4A01G173600 chr4D 127155060 127156181 1121 False 1712.0 1712 94.1800 816 1943 1 chr4D.!!$F1 1127
3 TraesCS4A01G173600 chr4B 671686032 671686860 828 False 1315.0 1315 95.3070 1 830 1 chr4B.!!$F1 829
4 TraesCS4A01G173600 chr4B 191219954 191221232 1278 False 783.5 1358 95.3235 899 1943 2 chr4B.!!$F2 1044
5 TraesCS4A01G173600 chr1A 504402809 504403637 828 False 1330.0 1330 95.6570 1 828 1 chr1A.!!$F2 827
6 TraesCS4A01G173600 chr1A 534886961 534887788 827 True 1330.0 1330 95.6570 1 828 1 chr1A.!!$R1 827
7 TraesCS4A01G173600 chr1A 534905958 534906785 827 True 1314.0 1314 95.2960 1 828 1 chr1A.!!$R2 827
8 TraesCS4A01G173600 chr1A 16799009 16799633 624 False 717.0 717 87.4620 1933 2576 1 chr1A.!!$F1 643
9 TraesCS4A01G173600 chr6A 584973294 584974123 829 True 1323.0 1323 95.4270 1 830 1 chr6A.!!$R2 829
10 TraesCS4A01G173600 chr6A 47104869 47105975 1106 False 1240.0 1240 87.1540 827 1926 1 chr6A.!!$F1 1099
11 TraesCS4A01G173600 chr6A 103896244 103896869 625 False 1002.0 1002 95.4260 1944 2576 1 chr6A.!!$F2 632
12 TraesCS4A01G173600 chr6A 144202262 144202881 619 False 902.0 902 92.5580 1932 2576 1 chr6A.!!$F3 644
13 TraesCS4A01G173600 chr2A 717255936 717256766 830 False 1323.0 1323 95.4270 1 830 1 chr2A.!!$F1 829
14 TraesCS4A01G173600 chr3A 10474896 10475723 827 True 1319.0 1319 95.4160 1 828 1 chr3A.!!$R1 827
15 TraesCS4A01G173600 chr3A 731170662 731171282 620 False 981.0 981 94.9450 1944 2576 1 chr3A.!!$F2 632
16 TraesCS4A01G173600 chr3A 589903286 589903909 623 True 972.0 972 94.6370 1944 2576 1 chr3A.!!$R2 632
17 TraesCS4A01G173600 chr7A 627153559 627154387 828 True 1314.0 1314 95.2960 1 828 1 chr7A.!!$R2 827
18 TraesCS4A01G173600 chr7A 673655430 673656056 626 False 981.0 981 94.8110 1943 2576 1 chr7A.!!$F2 633
19 TraesCS4A01G173600 chr7A 81847559 81848188 629 False 970.0 970 94.3750 1940 2576 1 chr7A.!!$F1 636
20 TraesCS4A01G173600 chr7A 685619892 685620523 631 True 968.0 968 94.3490 1944 2576 1 chr7A.!!$R3 632
21 TraesCS4A01G173600 chr7A 167968742 167969381 639 True 850.0 850 90.9510 1943 2576 1 chr7A.!!$R1 633
22 TraesCS4A01G173600 chrUn 26920589 26921706 1117 True 1284.0 1284 87.5660 826 1943 1 chrUn.!!$R1 1117
23 TraesCS4A01G173600 chrUn 26996835 26997962 1127 False 1258.0 1258 87.1280 827 1943 1 chrUn.!!$F1 1116
24 TraesCS4A01G173600 chr6B 82326340 82327428 1088 False 1195.0 1195 86.6490 827 1926 1 chr6B.!!$F1 1099
25 TraesCS4A01G173600 chr6B 82527192 82527918 726 False 974.0 974 90.9220 1204 1926 1 chr6B.!!$F3 722
26 TraesCS4A01G173600 chr5A 12497171 12497804 633 False 983.0 983 94.7040 1943 2576 1 chr5A.!!$F1 633
27 TraesCS4A01G173600 chr5A 32114202 32114837 635 False 972.0 972 94.3570 1944 2576 1 chr5A.!!$F2 632
28 TraesCS4A01G173600 chr5A 682354908 682355529 621 True 966.0 966 94.4970 1943 2576 1 chr5A.!!$R2 633
29 TraesCS4A01G173600 chr5A 576768316 576768951 635 True 863.0 863 91.3580 1943 2576 1 chr5A.!!$R1 633
30 TraesCS4A01G173600 chr5A 506416145 506416762 617 False 850.0 850 91.1630 1933 2576 1 chr5A.!!$F3 643
31 TraesCS4A01G173600 chr5A 531019325 531020137 812 False 370.0 370 75.5050 1108 1931 1 chr5A.!!$F4 823
32 TraesCS4A01G173600 chr5B 504775454 504776005 551 False 348.0 348 78.2300 1108 1670 1 chr5B.!!$F1 562

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
380 381 0.10212 GAGTCCATCGCTGAGTCAGG 59.898 60.0 21.54 11.62 33.32 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 2120 1.025113 CGCTCTCGTAGGTCCTCACA 61.025 60.0 0.0 0.0 0.0 3.58 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
32 33 1.026182 CCAAGAGCGCCAGTGCAATA 61.026 55.000 2.29 0.00 37.32 1.90
54 55 8.935844 CAATACATCTTGCACTTGAAGTAGTTA 58.064 33.333 0.00 0.00 0.00 2.24
185 186 2.503356 AGTAGAGCATGCAGTAGCCTTT 59.497 45.455 21.98 0.00 41.13 3.11
380 381 0.102120 GAGTCCATCGCTGAGTCAGG 59.898 60.000 21.54 11.62 33.32 3.86
463 464 1.529244 GGAAACACCCAGCTGCTGT 60.529 57.895 26.41 8.86 0.00 4.40
562 563 2.803956 CCGGGATATAGCTAGTGGTGA 58.196 52.381 0.00 0.00 0.00 4.02
608 609 2.303890 GAGTCGGGGGAAGAAAACCTTA 59.696 50.000 0.00 0.00 34.68 2.69
610 611 3.138839 AGTCGGGGGAAGAAAACCTTAAA 59.861 43.478 0.00 0.00 34.68 1.52
611 612 3.254166 GTCGGGGGAAGAAAACCTTAAAC 59.746 47.826 0.00 0.00 34.68 2.01
612 613 3.138839 TCGGGGGAAGAAAACCTTAAACT 59.861 43.478 0.00 0.00 34.68 2.66
613 614 3.893200 CGGGGGAAGAAAACCTTAAACTT 59.107 43.478 0.00 0.00 34.68 2.66
614 615 4.342951 CGGGGGAAGAAAACCTTAAACTTT 59.657 41.667 0.00 0.00 34.68 2.66
615 616 5.508489 CGGGGGAAGAAAACCTTAAACTTTC 60.508 44.000 0.00 0.00 34.68 2.62
616 617 5.221581 GGGGGAAGAAAACCTTAAACTTTCC 60.222 44.000 0.00 0.00 35.99 3.13
617 618 5.221581 GGGGAAGAAAACCTTAAACTTTCCC 60.222 44.000 9.86 9.86 45.39 3.97
618 619 5.221581 GGGAAGAAAACCTTAAACTTTCCCC 60.222 44.000 7.56 0.00 34.68 4.81
619 620 5.601313 GGAAGAAAACCTTAAACTTTCCCCT 59.399 40.000 0.00 0.00 34.68 4.79
620 621 6.462487 GGAAGAAAACCTTAAACTTTCCCCTG 60.462 42.308 0.00 0.00 34.68 4.45
621 622 5.525484 AGAAAACCTTAAACTTTCCCCTGT 58.475 37.500 0.00 0.00 30.83 4.00
622 623 5.597182 AGAAAACCTTAAACTTTCCCCTGTC 59.403 40.000 0.00 0.00 30.83 3.51
623 624 3.136009 ACCTTAAACTTTCCCCTGTCG 57.864 47.619 0.00 0.00 0.00 4.35
624 625 2.224695 ACCTTAAACTTTCCCCTGTCGG 60.225 50.000 0.00 0.00 0.00 4.79
625 626 2.224695 CCTTAAACTTTCCCCTGTCGGT 60.225 50.000 0.00 0.00 0.00 4.69
626 627 2.554370 TAAACTTTCCCCTGTCGGTG 57.446 50.000 0.00 0.00 0.00 4.94
627 628 0.549469 AAACTTTCCCCTGTCGGTGT 59.451 50.000 0.00 0.00 0.00 4.16
628 629 0.179029 AACTTTCCCCTGTCGGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
629 630 1.302511 CTTTCCCCTGTCGGTGTGG 60.303 63.158 0.00 0.00 0.00 4.17
630 631 2.748058 CTTTCCCCTGTCGGTGTGGG 62.748 65.000 0.00 0.00 40.59 4.61
634 635 4.704833 CCTGTCGGTGTGGGCCAG 62.705 72.222 6.40 0.00 0.00 4.85
635 636 4.704833 CTGTCGGTGTGGGCCAGG 62.705 72.222 6.40 0.00 0.00 4.45
644 645 4.912395 TGGGCCAGGCGTGCTTTT 62.912 61.111 0.00 0.00 0.00 2.27
645 646 4.056125 GGGCCAGGCGTGCTTTTC 62.056 66.667 4.39 0.00 0.00 2.29
646 647 4.056125 GGCCAGGCGTGCTTTTCC 62.056 66.667 5.00 0.00 0.00 3.13
647 648 4.056125 GCCAGGCGTGCTTTTCCC 62.056 66.667 0.00 0.00 0.00 3.97
648 649 2.282462 CCAGGCGTGCTTTTCCCT 60.282 61.111 0.00 0.00 0.00 4.20
649 650 1.002624 CCAGGCGTGCTTTTCCCTA 60.003 57.895 0.00 0.00 0.00 3.53
650 651 1.026718 CCAGGCGTGCTTTTCCCTAG 61.027 60.000 0.00 0.00 0.00 3.02
651 652 1.377333 AGGCGTGCTTTTCCCTAGC 60.377 57.895 0.00 0.00 39.10 3.42
652 653 2.750888 GGCGTGCTTTTCCCTAGCG 61.751 63.158 0.00 0.00 41.54 4.26
653 654 2.785258 CGTGCTTTTCCCTAGCGC 59.215 61.111 0.00 0.00 43.78 5.92
654 655 2.750888 CGTGCTTTTCCCTAGCGCC 61.751 63.158 2.29 0.00 44.22 6.53
655 656 2.435938 TGCTTTTCCCTAGCGCCG 60.436 61.111 2.29 0.00 41.54 6.46
656 657 3.202706 GCTTTTCCCTAGCGCCGG 61.203 66.667 2.29 4.78 0.00 6.13
657 658 2.582436 CTTTTCCCTAGCGCCGGA 59.418 61.111 5.05 9.50 0.00 5.14
658 659 1.521681 CTTTTCCCTAGCGCCGGAG 60.522 63.158 5.05 1.55 0.00 4.63
659 660 3.675619 TTTTCCCTAGCGCCGGAGC 62.676 63.158 23.92 23.92 37.41 4.70
673 674 4.432741 GAGCCCCCAACTGCTCCC 62.433 72.222 0.08 0.00 46.50 4.30
677 678 4.748144 CCCCAACTGCTCCCCAGC 62.748 72.222 0.00 0.00 45.78 4.85
735 736 2.398036 CCGAACCGGCGATTTTCG 59.602 61.111 22.71 22.71 41.17 3.46
744 745 2.393557 GCGATTTTCGGCATCCTGA 58.606 52.632 0.00 0.00 40.84 3.86
745 746 0.305922 GCGATTTTCGGCATCCTGAG 59.694 55.000 0.00 0.00 40.84 3.35
746 747 0.940126 CGATTTTCGGCATCCTGAGG 59.060 55.000 0.00 0.00 36.00 3.86
747 748 1.312815 GATTTTCGGCATCCTGAGGG 58.687 55.000 0.00 0.00 0.00 4.30
748 749 0.753111 ATTTTCGGCATCCTGAGGGC 60.753 55.000 0.00 0.00 0.00 5.19
754 755 3.842923 CATCCTGAGGGCGCGACT 61.843 66.667 13.91 7.89 0.00 4.18
755 756 3.842923 ATCCTGAGGGCGCGACTG 61.843 66.667 13.91 0.00 0.00 3.51
765 766 3.656045 CGCGACTGGGCCGTTTTT 61.656 61.111 0.00 0.00 0.00 1.94
766 767 2.254350 GCGACTGGGCCGTTTTTC 59.746 61.111 0.00 0.00 0.00 2.29
767 768 2.554272 CGACTGGGCCGTTTTTCG 59.446 61.111 0.00 0.00 39.52 3.46
793 794 2.650778 GCCGAAAAAGTGGCCTGG 59.349 61.111 3.32 0.00 45.73 4.45
794 795 2.931068 GCCGAAAAAGTGGCCTGGG 61.931 63.158 3.32 0.00 45.73 4.45
795 796 2.275380 CCGAAAAAGTGGCCTGGGG 61.275 63.158 3.32 0.00 0.00 4.96
796 797 2.275380 CGAAAAAGTGGCCTGGGGG 61.275 63.158 3.32 0.00 0.00 5.40
832 833 0.839946 GGCTGGAGATGCCCTAAAGA 59.160 55.000 0.00 0.00 44.32 2.52
849 850 1.079266 GAGGTGCTCCAGTCAGCTG 60.079 63.158 7.63 7.63 41.72 4.24
851 852 1.670406 GGTGCTCCAGTCAGCTGTG 60.670 63.158 14.67 5.40 41.02 3.66
852 853 2.031616 TGCTCCAGTCAGCTGTGC 59.968 61.111 14.67 8.24 41.02 4.57
855 856 1.892819 GCTCCAGTCAGCTGTGCCTA 61.893 60.000 14.67 0.00 41.02 3.93
856 857 0.175302 CTCCAGTCAGCTGTGCCTAG 59.825 60.000 14.67 3.80 41.02 3.02
857 858 1.449246 CCAGTCAGCTGTGCCTAGC 60.449 63.158 14.67 1.32 44.01 3.42
878 886 0.528017 CTAGCGAGCTCAGTTCCACA 59.472 55.000 15.40 0.00 0.00 4.17
879 887 0.243907 TAGCGAGCTCAGTTCCACAC 59.756 55.000 15.40 0.00 0.00 3.82
902 915 7.100409 CACCTCGATATGTCTCTCTGTATCTA 58.900 42.308 0.00 0.00 0.00 1.98
974 995 4.036734 TCCAAACAAGCAAAGACAAGCTAG 59.963 41.667 0.00 0.00 40.90 3.42
1037 1078 2.442272 GAGCCGGAGACCAGCCTA 60.442 66.667 5.05 0.00 0.00 3.93
1142 1414 1.762858 TGACGGTGTTCTGGGGACA 60.763 57.895 0.00 0.00 39.59 4.02
1296 1568 3.204827 GGCGCCGACATCAAGCAT 61.205 61.111 12.58 0.00 0.00 3.79
1655 2120 1.299468 GATCTTCGAGCGCGTCCAT 60.299 57.895 10.30 0.00 38.98 3.41
1726 2198 1.296715 GCTCGTGGGACAAGTGGAT 59.703 57.895 0.00 0.00 44.16 3.41
1757 2229 2.633099 GCCACGCGGTTTTACGTT 59.367 55.556 12.47 0.00 41.32 3.99
1768 2240 0.179051 TTTTACGTTGGGCTCACGGT 60.179 50.000 12.14 4.01 0.00 4.83
2158 2654 7.140048 GTCACCAACCGTTATTAAAATGTTGA 58.860 34.615 12.16 0.00 36.15 3.18
2163 2659 5.326900 ACCGTTATTAAAATGTTGAGGGGT 58.673 37.500 0.00 0.00 0.00 4.95
2259 2757 5.345702 ACGATACTACATATTGTGCACGTT 58.654 37.500 13.13 4.36 36.64 3.99
2260 2758 6.497437 ACGATACTACATATTGTGCACGTTA 58.503 36.000 13.13 6.69 36.64 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 6.311445 CGATAACTACTTCAAGTGCAAGATGT 59.689 38.462 0.00 0.00 0.00 3.06
54 55 4.699192 TCCATCCGGGAGTTCGAT 57.301 55.556 0.00 0.00 42.15 3.59
185 186 0.320374 AAAGAACCGGCATCGTCTCA 59.680 50.000 0.00 0.00 33.95 3.27
380 381 0.649993 CAAGGTGTTTGGCGTTTTGC 59.350 50.000 0.00 0.00 45.38 3.68
424 425 3.186047 CACGGAGGCGCGGTTTAG 61.186 66.667 8.83 0.00 0.00 1.85
481 482 0.726827 CGGAAAATAGCAGCGCTTCA 59.273 50.000 7.50 0.00 40.44 3.02
595 596 5.601313 AGGGGAAAGTTTAAGGTTTTCTTCC 59.399 40.000 0.00 0.00 36.93 3.46
608 609 0.549469 ACACCGACAGGGGAAAGTTT 59.451 50.000 0.00 0.00 46.39 2.66
610 611 1.450211 CACACCGACAGGGGAAAGT 59.550 57.895 0.00 0.00 46.39 2.66
611 612 1.302511 CCACACCGACAGGGGAAAG 60.303 63.158 0.00 0.00 46.39 2.62
612 613 2.824880 CCCACACCGACAGGGGAAA 61.825 63.158 0.00 0.00 46.39 3.13
613 614 3.246112 CCCACACCGACAGGGGAA 61.246 66.667 0.00 0.00 46.39 3.97
617 618 4.704833 CTGGCCCACACCGACAGG 62.705 72.222 0.00 0.00 45.13 4.00
618 619 4.704833 CCTGGCCCACACCGACAG 62.705 72.222 0.00 0.00 0.00 3.51
627 628 4.912395 AAAAGCACGCCTGGCCCA 62.912 61.111 14.12 0.00 0.00 5.36
628 629 4.056125 GAAAAGCACGCCTGGCCC 62.056 66.667 14.12 1.57 0.00 5.80
629 630 4.056125 GGAAAAGCACGCCTGGCC 62.056 66.667 14.12 0.00 0.00 5.36
630 631 4.056125 GGGAAAAGCACGCCTGGC 62.056 66.667 9.11 9.11 0.00 4.85
631 632 1.002624 TAGGGAAAAGCACGCCTGG 60.003 57.895 0.00 0.00 0.00 4.45
632 633 1.648467 GCTAGGGAAAAGCACGCCTG 61.648 60.000 0.00 0.00 39.83 4.85
633 634 1.377333 GCTAGGGAAAAGCACGCCT 60.377 57.895 0.00 0.00 39.83 5.52
634 635 2.750888 CGCTAGGGAAAAGCACGCC 61.751 63.158 0.00 0.00 40.08 5.68
635 636 2.785258 CGCTAGGGAAAAGCACGC 59.215 61.111 0.00 0.00 40.08 5.34
636 637 2.750888 GGCGCTAGGGAAAAGCACG 61.751 63.158 11.61 0.00 40.08 5.34
637 638 2.750888 CGGCGCTAGGGAAAAGCAC 61.751 63.158 11.61 0.00 40.08 4.40
638 639 2.435938 CGGCGCTAGGGAAAAGCA 60.436 61.111 11.61 0.00 40.08 3.91
639 640 3.202706 CCGGCGCTAGGGAAAAGC 61.203 66.667 11.61 0.00 36.60 3.51
640 641 1.521681 CTCCGGCGCTAGGGAAAAG 60.522 63.158 19.31 8.14 0.00 2.27
641 642 2.582436 CTCCGGCGCTAGGGAAAA 59.418 61.111 19.31 2.81 0.00 2.29
642 643 4.157120 GCTCCGGCGCTAGGGAAA 62.157 66.667 19.31 3.12 0.00 3.13
659 660 4.052518 CTGGGGAGCAGTTGGGGG 62.053 72.222 0.00 0.00 0.00 5.40
660 661 4.748144 GCTGGGGAGCAGTTGGGG 62.748 72.222 0.00 0.00 34.41 4.96
694 695 4.629523 TTTCCACCCGGCGGTCAC 62.630 66.667 26.32 0.00 42.04 3.67
695 696 3.417167 TTTTTCCACCCGGCGGTCA 62.417 57.895 26.32 1.81 42.04 4.02
696 697 2.595172 TTTTTCCACCCGGCGGTC 60.595 61.111 26.32 0.00 42.04 4.79
719 720 2.398036 CCGAAAATCGCCGGTTCG 59.602 61.111 15.14 15.14 42.85 3.95
720 721 1.988834 ATGCCGAAAATCGCCGGTTC 61.989 55.000 1.90 0.00 46.84 3.62
721 722 1.988834 GATGCCGAAAATCGCCGGTT 61.989 55.000 1.90 0.00 46.84 4.44
722 723 2.437716 ATGCCGAAAATCGCCGGT 60.438 55.556 1.90 0.00 46.84 5.28
724 725 2.180204 AGGATGCCGAAAATCGCCG 61.180 57.895 0.00 0.00 38.82 6.46
725 726 1.095228 TCAGGATGCCGAAAATCGCC 61.095 55.000 0.00 0.00 34.40 5.54
726 727 0.305922 CTCAGGATGCCGAAAATCGC 59.694 55.000 0.00 0.00 34.40 4.58
727 728 0.940126 CCTCAGGATGCCGAAAATCG 59.060 55.000 0.00 0.00 35.25 3.34
728 729 1.312815 CCCTCAGGATGCCGAAAATC 58.687 55.000 0.00 0.00 34.76 2.17
729 730 0.753111 GCCCTCAGGATGCCGAAAAT 60.753 55.000 0.00 0.00 34.76 1.82
730 731 1.378514 GCCCTCAGGATGCCGAAAA 60.379 57.895 0.00 0.00 34.76 2.29
731 732 2.272146 GCCCTCAGGATGCCGAAA 59.728 61.111 0.00 0.00 34.76 3.46
732 733 4.161295 CGCCCTCAGGATGCCGAA 62.161 66.667 0.00 0.00 34.76 4.30
737 738 3.842923 AGTCGCGCCCTCAGGATG 61.843 66.667 0.00 0.00 33.47 3.51
738 739 3.842923 CAGTCGCGCCCTCAGGAT 61.843 66.667 0.00 0.00 33.47 3.24
748 749 3.588891 GAAAAACGGCCCAGTCGCG 62.589 63.158 0.00 0.00 32.11 5.87
749 750 2.254350 GAAAAACGGCCCAGTCGC 59.746 61.111 0.00 0.00 32.11 5.19
750 751 2.554272 CGAAAAACGGCCCAGTCG 59.446 61.111 0.00 0.00 38.46 4.18
771 772 4.398598 CCACTTTTTCGGCGCCGG 62.399 66.667 44.95 31.46 40.25 6.13
777 778 2.275380 CCCCAGGCCACTTTTTCGG 61.275 63.158 5.01 0.00 0.00 4.30
778 779 2.275380 CCCCCAGGCCACTTTTTCG 61.275 63.158 5.01 0.00 0.00 3.46
779 780 3.791640 CCCCCAGGCCACTTTTTC 58.208 61.111 5.01 0.00 0.00 2.29
814 815 1.202746 CCTCTTTAGGGCATCTCCAGC 60.203 57.143 0.00 0.00 39.48 4.85
832 833 3.067091 CAGCTGACTGGAGCACCT 58.933 61.111 8.42 0.00 41.83 4.00
849 850 2.731374 CTCGCTAGGGCTAGGCAC 59.269 66.667 19.14 7.62 36.09 5.01
856 857 1.227118 GAACTGAGCTCGCTAGGGC 60.227 63.158 9.64 0.00 46.47 5.19
857 858 1.323271 TGGAACTGAGCTCGCTAGGG 61.323 60.000 9.64 0.00 0.00 3.53
878 886 6.121776 AGATACAGAGAGACATATCGAGGT 57.878 41.667 0.00 0.00 0.00 3.85
879 887 6.537301 GGTAGATACAGAGAGACATATCGAGG 59.463 46.154 0.00 0.00 0.00 4.63
902 915 7.184022 GGGGTATATATAGTGGATTTTGGAGGT 59.816 40.741 0.00 0.00 0.00 3.85
974 995 1.807142 GTTTCTCCAAGTACTGGCTGC 59.193 52.381 0.00 0.00 45.98 5.25
1037 1078 1.661004 GGAGAGGAGGGCTAGGAGGT 61.661 65.000 0.00 0.00 0.00 3.85
1142 1414 2.529389 ACCCCTCCGCCTTGTTCT 60.529 61.111 0.00 0.00 0.00 3.01
1228 1500 1.228033 GGTGGTACTTGCCGTTGGT 60.228 57.895 0.00 0.00 0.00 3.67
1655 2120 1.025113 CGCTCTCGTAGGTCCTCACA 61.025 60.000 0.00 0.00 0.00 3.58
1745 2217 1.208358 GAGCCCAACGTAAAACCGC 59.792 57.895 0.00 0.00 0.00 5.68
1751 2223 1.301087 CACCGTGAGCCCAACGTAA 60.301 57.895 0.00 0.00 0.00 3.18
1797 2269 2.260481 GCTGTAGTAGACGTTCTTGGC 58.740 52.381 0.00 0.00 0.00 4.52
2144 2635 7.072581 ACCCAAAACCCCTCAACATTTTAATAA 59.927 33.333 0.00 0.00 0.00 1.40
2158 2654 5.411493 AGAAATCATAAACCCAAAACCCCT 58.589 37.500 0.00 0.00 0.00 4.79
2441 2999 2.158957 CCGAAGGCACCAATTAGCTAGA 60.159 50.000 0.00 0.00 46.14 2.43


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

AutoCloner maintained by Alex Coulton.