Multiple sequence alignment - TraesCS3D01G471300

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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 TraesCS3D01G471300 chr3D 100.000 3104 0 0 1 3104 573726684 573729787 0.000000e+00 5733.0
1 TraesCS3D01G471300 chr3D 76.782 870 174 21 1291 2140 562420574 562419713 2.180000e-126 462.0
2 TraesCS3D01G471300 chr3D 74.074 297 61 11 1802 2093 565605079 565605364 1.180000e-19 108.0
3 TraesCS3D01G471300 chr3B 94.674 1333 64 4 1773 3103 763487462 763486135 0.000000e+00 2061.0
4 TraesCS3D01G471300 chr3B 85.677 768 99 7 833 1598 763727494 763726736 0.000000e+00 798.0
5 TraesCS3D01G471300 chr3B 91.925 483 31 4 846 1326 763487963 763487487 0.000000e+00 669.0
6 TraesCS3D01G471300 chr3B 75.441 851 153 34 1330 2142 763636352 763635520 2.280000e-96 363.0
7 TraesCS3D01G471300 chr3B 73.276 580 123 25 1557 2117 754330890 754331456 1.900000e-42 183.0
8 TraesCS3D01G471300 chr3A 84.100 1849 236 34 700 2518 708484972 708486792 0.000000e+00 1733.0
9 TraesCS3D01G471300 chr3A 95.528 738 27 3 1645 2379 708689429 708690163 0.000000e+00 1175.0
10 TraesCS3D01G471300 chr3A 90.295 814 46 7 846 1653 708688407 708689193 0.000000e+00 1035.0
11 TraesCS3D01G471300 chr3A 75.352 852 153 37 1330 2142 708641301 708642134 1.060000e-94 357.0
12 TraesCS3D01G471300 chr3A 74.501 851 162 35 1330 2142 708540547 708539714 5.000000e-83 318.0
13 TraesCS3D01G471300 chr3A 72.510 502 107 20 1630 2117 700351658 700351174 1.940000e-27 134.0
14 TraesCS3D01G471300 chr3A 79.474 190 35 3 1930 2117 700250063 700250250 6.980000e-27 132.0
15 TraesCS3D01G471300 chrUn 99.360 625 2 1 1 623 45412288 45411664 0.000000e+00 1131.0
16 TraesCS3D01G471300 chrUn 99.774 442 0 1 1 441 303996868 303996427 0.000000e+00 809.0
17 TraesCS3D01G471300 chr4D 83.594 512 76 8 2528 3036 93602389 93601883 1.010000e-129 473.0
18 TraesCS3D01G471300 chr4D 86.486 74 7 3 233 304 320187927 320187999 9.230000e-11 78.7
19 TraesCS3D01G471300 chr5B 87.293 181 22 1 2526 2705 255069871 255070051 4.060000e-49 206.0
20 TraesCS3D01G471300 chr1B 75.104 482 77 27 2638 3104 314557166 314557619 5.290000e-43 185.0
21 TraesCS3D01G471300 chr7B 89.333 75 4 3 232 302 684579859 684579785 1.190000e-14 91.6
22 TraesCS3D01G471300 chr6D 84.375 96 12 2 210 303 269116949 269117043 1.190000e-14 91.6
23 TraesCS3D01G471300 chr6D 85.526 76 9 2 228 302 10016471 10016545 9.230000e-11 78.7
24 TraesCS3D01G471300 chr2B 91.803 61 5 0 243 303 19421639 19421699 5.520000e-13 86.1
25 TraesCS3D01G471300 chr7A 87.143 70 7 2 233 301 696335523 696335591 9.230000e-11 78.7
26 TraesCS3D01G471300 chr6A 84.146 82 11 2 222 302 616227457 616227377 9.230000e-11 78.7


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 TraesCS3D01G471300 chr3D 573726684 573729787 3103 False 5733 5733 100.0000 1 3104 1 chr3D.!!$F2 3103
1 TraesCS3D01G471300 chr3D 562419713 562420574 861 True 462 462 76.7820 1291 2140 1 chr3D.!!$R1 849
2 TraesCS3D01G471300 chr3B 763486135 763487963 1828 True 1365 2061 93.2995 846 3103 2 chr3B.!!$R3 2257
3 TraesCS3D01G471300 chr3B 763726736 763727494 758 True 798 798 85.6770 833 1598 1 chr3B.!!$R2 765
4 TraesCS3D01G471300 chr3B 763635520 763636352 832 True 363 363 75.4410 1330 2142 1 chr3B.!!$R1 812
5 TraesCS3D01G471300 chr3A 708484972 708486792 1820 False 1733 1733 84.1000 700 2518 1 chr3A.!!$F2 1818
6 TraesCS3D01G471300 chr3A 708688407 708690163 1756 False 1105 1175 92.9115 846 2379 2 chr3A.!!$F4 1533
7 TraesCS3D01G471300 chr3A 708641301 708642134 833 False 357 357 75.3520 1330 2142 1 chr3A.!!$F3 812
8 TraesCS3D01G471300 chr3A 708539714 708540547 833 True 318 318 74.5010 1330 2142 1 chr3A.!!$R2 812
9 TraesCS3D01G471300 chrUn 45411664 45412288 624 True 1131 1131 99.3600 1 623 1 chrUn.!!$R1 622
10 TraesCS3D01G471300 chr4D 93601883 93602389 506 True 473 473 83.5940 2528 3036 1 chr4D.!!$R1 508

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
630 633 0.035056 AGGGCATTTTGGACTCCTCG 60.035 55.0 0.0 0.0 0.0 4.63 F
631 634 0.035439 GGGCATTTTGGACTCCTCGA 60.035 55.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 1613 0.179048 TCGCATCTGGCCATTCGATT 60.179 50.0 5.51 0.0 40.31 3.34 R
2569 2876 0.464735 TTAAATGGTATGGCCGCGCT 60.465 50.0 5.56 0.0 41.21 5.92 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
441 444 3.349927 GCACCGTAAAATAAAGGAGGGT 58.650 45.455 0.00 0.00 0.00 4.34
623 626 0.391927 CGTCGGTAGGGCATTTTGGA 60.392 55.000 0.00 0.00 0.00 3.53
624 627 1.092348 GTCGGTAGGGCATTTTGGAC 58.908 55.000 0.00 0.00 0.00 4.02
625 628 0.988832 TCGGTAGGGCATTTTGGACT 59.011 50.000 0.00 0.00 0.00 3.85
626 629 1.065709 TCGGTAGGGCATTTTGGACTC 60.066 52.381 0.00 0.00 0.00 3.36
627 630 1.763968 GGTAGGGCATTTTGGACTCC 58.236 55.000 0.00 0.00 0.00 3.85
628 631 1.285078 GGTAGGGCATTTTGGACTCCT 59.715 52.381 0.00 0.00 0.00 3.69
629 632 2.644676 GTAGGGCATTTTGGACTCCTC 58.355 52.381 0.00 0.00 0.00 3.71
630 633 0.035056 AGGGCATTTTGGACTCCTCG 60.035 55.000 0.00 0.00 0.00 4.63
631 634 0.035439 GGGCATTTTGGACTCCTCGA 60.035 55.000 0.00 0.00 0.00 4.04
632 635 1.373570 GGCATTTTGGACTCCTCGAG 58.626 55.000 5.13 5.13 35.52 4.04
633 636 1.373570 GCATTTTGGACTCCTCGAGG 58.626 55.000 26.32 26.32 33.35 4.63
634 637 1.373570 CATTTTGGACTCCTCGAGGC 58.626 55.000 27.39 13.17 36.87 4.70
639 642 3.035727 GACTCCTCGAGGCCGATC 58.964 66.667 27.39 16.09 44.62 3.69
640 643 1.527380 GACTCCTCGAGGCCGATCT 60.527 63.158 27.39 4.36 44.62 2.75
641 644 1.791103 GACTCCTCGAGGCCGATCTG 61.791 65.000 27.39 11.80 44.62 2.90
642 645 3.206211 CTCCTCGAGGCCGATCTGC 62.206 68.421 27.39 0.00 44.62 4.26
643 646 3.531207 CCTCGAGGCCGATCTGCA 61.531 66.667 20.67 0.00 44.62 4.41
644 647 2.279120 CTCGAGGCCGATCTGCAC 60.279 66.667 11.45 3.80 44.62 4.57
645 648 3.781770 CTCGAGGCCGATCTGCACC 62.782 68.421 11.45 1.15 44.62 5.01
650 653 3.567797 GCCGATCTGCACCGCTTC 61.568 66.667 4.00 0.00 0.00 3.86
651 654 2.892425 CCGATCTGCACCGCTTCC 60.892 66.667 0.00 0.00 0.00 3.46
652 655 2.125552 CGATCTGCACCGCTTCCA 60.126 61.111 0.00 0.00 0.00 3.53
653 656 2.456119 CGATCTGCACCGCTTCCAC 61.456 63.158 0.00 0.00 0.00 4.02
654 657 2.434884 ATCTGCACCGCTTCCACG 60.435 61.111 0.00 0.00 0.00 4.94
663 666 4.666532 GCTTCCACGCGTGTGCAC 62.667 66.667 34.81 19.22 45.04 4.57
664 667 4.012895 CTTCCACGCGTGTGCACC 62.013 66.667 34.81 4.74 45.04 5.01
678 681 3.411351 CACCGCAGCCACACGTAC 61.411 66.667 0.00 0.00 0.00 3.67
679 682 3.918977 ACCGCAGCCACACGTACA 61.919 61.111 0.00 0.00 0.00 2.90
680 683 3.411351 CCGCAGCCACACGTACAC 61.411 66.667 0.00 0.00 0.00 2.90
681 684 3.762992 CGCAGCCACACGTACACG 61.763 66.667 0.00 0.00 46.33 4.49
682 685 4.072088 GCAGCCACACGTACACGC 62.072 66.667 0.85 0.00 44.43 5.34
683 686 2.660224 CAGCCACACGTACACGCA 60.660 61.111 0.85 0.00 44.43 5.24
684 687 2.107343 AGCCACACGTACACGCAA 59.893 55.556 0.85 0.00 44.43 4.85
685 688 1.954146 AGCCACACGTACACGCAAG 60.954 57.895 0.85 0.00 44.43 4.01
686 689 2.549282 CCACACGTACACGCAAGC 59.451 61.111 0.85 0.00 44.43 4.01
687 690 2.167684 CACACGTACACGCAAGCG 59.832 61.111 13.50 13.50 44.43 4.68
688 691 3.033764 ACACGTACACGCAAGCGG 61.034 61.111 19.30 10.04 44.43 5.52
689 692 3.033764 CACGTACACGCAAGCGGT 61.034 61.111 19.30 15.06 44.43 5.68
690 693 3.033764 ACGTACACGCAAGCGGTG 61.034 61.111 19.30 15.55 44.43 4.94
691 694 3.773630 CGTACACGCAAGCGGTGG 61.774 66.667 19.30 10.07 44.69 4.61
692 695 4.084888 GTACACGCAAGCGGTGGC 62.085 66.667 19.30 3.20 44.69 5.01
718 721 3.123959 GCGTGTTGTATTAACCACGATGT 59.876 43.478 14.38 0.00 38.16 3.06
784 792 2.502213 TCCGCATAGGATACAACACG 57.498 50.000 0.00 0.00 45.98 4.49
785 793 2.025898 TCCGCATAGGATACAACACGA 58.974 47.619 0.00 0.00 45.98 4.35
786 794 2.124903 CCGCATAGGATACAACACGAC 58.875 52.381 0.00 0.00 45.00 4.34
787 795 2.480587 CCGCATAGGATACAACACGACA 60.481 50.000 0.00 0.00 45.00 4.35
788 796 3.381045 CGCATAGGATACAACACGACAT 58.619 45.455 0.00 0.00 41.41 3.06
789 797 4.542735 CGCATAGGATACAACACGACATA 58.457 43.478 0.00 0.00 41.41 2.29
790 798 5.161358 CGCATAGGATACAACACGACATAT 58.839 41.667 0.00 0.00 41.41 1.78
791 799 5.060940 CGCATAGGATACAACACGACATATG 59.939 44.000 0.00 0.00 41.41 1.78
792 800 5.926542 GCATAGGATACAACACGACATATGT 59.073 40.000 8.43 8.43 41.41 2.29
793 801 7.088272 GCATAGGATACAACACGACATATGTA 58.912 38.462 8.71 0.00 41.41 2.29
794 802 7.759886 GCATAGGATACAACACGACATATGTAT 59.240 37.037 8.71 0.00 40.63 2.29
808 816 7.832685 ACGACATATGTATAGGCTATGGACTAA 59.167 37.037 17.24 1.82 36.54 2.24
810 818 8.307582 ACATATGTATAGGCTATGGACTAACC 57.692 38.462 17.24 0.00 36.54 2.85
819 827 4.202588 GGCTATGGACTAACCCTCTCTAGA 60.203 50.000 0.00 0.00 38.00 2.43
820 828 4.763279 GCTATGGACTAACCCTCTCTAGAC 59.237 50.000 0.00 0.00 38.00 2.59
862 873 2.170607 ACCCTTGTAATCACCCAGATCG 59.829 50.000 0.00 0.00 35.39 3.69
953 965 2.288825 CCGTCACAACTCCTCTTGCTTA 60.289 50.000 0.00 0.00 0.00 3.09
962 975 0.744771 CCTCTTGCTTAGTTCCCGGC 60.745 60.000 0.00 0.00 0.00 6.13
963 976 0.744771 CTCTTGCTTAGTTCCCGGCC 60.745 60.000 0.00 0.00 0.00 6.13
964 977 2.046700 TTGCTTAGTTCCCGGCCG 60.047 61.111 21.04 21.04 0.00 6.13
965 978 3.615509 TTGCTTAGTTCCCGGCCGG 62.616 63.158 37.99 37.99 0.00 6.13
1015 1030 2.268076 ACCATGAACAAGGCCGCAC 61.268 57.895 0.00 0.00 0.00 5.34
1059 1074 3.568578 GGCCTCCCGGATGAGATT 58.431 61.111 0.73 0.00 34.11 2.40
1111 1128 2.900106 AAAGCCCTCCTTCGCTGCT 61.900 57.895 0.00 0.00 34.94 4.24
1161 1178 2.040178 ACCTCCACTCACGACTTTCTT 58.960 47.619 0.00 0.00 0.00 2.52
1356 1373 4.246053 TGCGATGGCATGCTCATT 57.754 50.000 18.92 0.00 46.21 2.57
1380 1397 0.179181 GCATCGACGACACCGACTTA 60.179 55.000 0.00 0.00 38.97 2.24
1397 1414 4.051922 GACTTATTCGTCTGCAATCCGAT 58.948 43.478 3.29 0.00 0.00 4.18
1614 1646 5.542616 CAGATGCGATTAATCTGGAATCC 57.457 43.478 13.45 0.00 44.83 3.01
1654 1945 0.322098 CCTGCATTGGTACCCAACGA 60.322 55.000 10.07 0.00 46.95 3.85
1736 2027 2.027192 AGATGTGTGCTCCGGTTGTTAT 60.027 45.455 0.00 0.00 0.00 1.89
1885 2176 1.086696 ATTGCCGGTTCAACAGATCG 58.913 50.000 1.90 0.00 0.00 3.69
1896 2187 0.615331 AACAGATCGGGATGCAGTGT 59.385 50.000 0.00 0.00 0.00 3.55
1952 2243 2.903855 CGTGCCAGGGGATGATGC 60.904 66.667 0.00 0.00 0.00 3.91
2088 2379 5.299279 ACAAACTCTTGTTCCACATACCTTG 59.701 40.000 0.00 0.00 43.45 3.61
2157 2448 2.629656 GCTCGTGCTTGGTGGCATT 61.630 57.895 1.41 0.00 44.34 3.56
2350 2654 6.533730 TGTATCCTCACAAGAACATGAAAGT 58.466 36.000 0.00 0.00 0.00 2.66
2480 2787 5.476599 AGAATTTGGACGGTTTGAATGATGA 59.523 36.000 0.00 0.00 0.00 2.92
2481 2788 4.497473 TTTGGACGGTTTGAATGATGAC 57.503 40.909 0.00 0.00 0.00 3.06
2482 2789 3.133141 TGGACGGTTTGAATGATGACA 57.867 42.857 0.00 0.00 0.00 3.58
2483 2790 3.684908 TGGACGGTTTGAATGATGACAT 58.315 40.909 0.00 0.00 38.50 3.06
2520 2827 3.100671 TGGTGGGGCATATTTGTTTACC 58.899 45.455 0.00 0.00 0.00 2.85
2540 2847 0.455005 AAAGAGTACTAGGCGTCGGC 59.545 55.000 11.43 11.43 38.90 5.54
2569 2876 3.594134 CCAAAACTTTTTGCTGGTCACA 58.406 40.909 8.65 0.00 44.62 3.58
2582 2889 4.830765 TCACAGCGCGGCCATACC 62.831 66.667 8.83 0.00 0.00 2.73
2626 2933 2.818132 GCATCTCTCCTCCACCCG 59.182 66.667 0.00 0.00 0.00 5.28
2653 2961 2.752903 CGTTCCCCGATCCAATTTCTTT 59.247 45.455 0.00 0.00 39.56 2.52
2734 3042 3.062466 CCGCGACTGTCCTCTCCA 61.062 66.667 8.23 0.00 0.00 3.86
2746 3054 2.997315 TCTCCAGCCACCGTCCAG 60.997 66.667 0.00 0.00 0.00 3.86
2837 3146 5.883685 TGAAGCATCTCTATTGTGGATCT 57.116 39.130 0.00 0.00 0.00 2.75
2855 3164 6.260936 GTGGATCTCTTCAAAACTTCTTCACA 59.739 38.462 0.00 0.00 0.00 3.58
2877 3186 2.884367 GCAGCTCAGAGTCTCGCT 59.116 61.111 7.49 7.49 0.00 4.93
2901 3210 2.163010 TGGTAGGTCGTCGTCTTCATTC 59.837 50.000 0.00 0.00 0.00 2.67
2914 3223 3.076621 TCTTCATTCATTGCAGCTCGTT 58.923 40.909 0.00 0.00 0.00 3.85
2979 3288 7.487484 TCTGCATCGAATAAAATAAATGCCAA 58.513 30.769 0.00 0.00 38.92 4.52
3072 3382 2.029110 CGCAAAATTGGGACATGGTTCT 60.029 45.455 4.34 0.00 43.04 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
441 444 4.947388 ACAAACTCAACCAGCAACTCTTTA 59.053 37.500 0.00 0.00 0.00 1.85
633 636 3.567797 GAAGCGGTGCAGATCGGC 61.568 66.667 11.23 11.23 0.00 5.54
634 637 2.892425 GGAAGCGGTGCAGATCGG 60.892 66.667 0.00 0.00 0.00 4.18
635 638 2.125552 TGGAAGCGGTGCAGATCG 60.126 61.111 0.00 0.00 0.00 3.69
636 639 2.456119 CGTGGAAGCGGTGCAGATC 61.456 63.158 0.00 0.00 0.00 2.75
637 640 2.434884 CGTGGAAGCGGTGCAGAT 60.435 61.111 0.00 0.00 0.00 2.90
646 649 4.666532 GTGCACACGCGTGGAAGC 62.667 66.667 39.21 35.33 45.87 3.86
647 650 4.012895 GGTGCACACGCGTGGAAG 62.013 66.667 39.21 28.77 45.87 3.46
661 664 3.411351 GTACGTGTGGCTGCGGTG 61.411 66.667 0.00 0.00 0.00 4.94
662 665 3.918977 TGTACGTGTGGCTGCGGT 61.919 61.111 0.00 0.00 0.00 5.68
663 666 3.411351 GTGTACGTGTGGCTGCGG 61.411 66.667 0.00 0.00 0.00 5.69
664 667 3.762992 CGTGTACGTGTGGCTGCG 61.763 66.667 0.00 0.00 34.11 5.18
665 668 4.072088 GCGTGTACGTGTGGCTGC 62.072 66.667 0.00 0.00 42.22 5.25
666 669 2.158058 CTTGCGTGTACGTGTGGCTG 62.158 60.000 0.00 0.00 42.22 4.85
667 670 1.954146 CTTGCGTGTACGTGTGGCT 60.954 57.895 0.00 0.00 42.22 4.75
668 671 2.549282 CTTGCGTGTACGTGTGGC 59.451 61.111 0.00 0.00 42.22 5.01
669 672 2.549282 GCTTGCGTGTACGTGTGG 59.451 61.111 0.00 0.00 42.22 4.17
670 673 2.167684 CGCTTGCGTGTACGTGTG 59.832 61.111 6.86 0.81 42.22 3.82
671 674 3.033764 CCGCTTGCGTGTACGTGT 61.034 61.111 13.97 0.00 42.22 4.49
672 675 3.033764 ACCGCTTGCGTGTACGTG 61.034 61.111 13.97 0.00 42.22 4.49
673 676 3.033764 CACCGCTTGCGTGTACGT 61.034 61.111 13.97 0.00 42.22 3.57
674 677 3.773630 CCACCGCTTGCGTGTACG 61.774 66.667 13.97 0.00 43.27 3.67
675 678 4.084888 GCCACCGCTTGCGTGTAC 62.085 66.667 13.97 4.30 0.00 2.90
686 689 4.326766 CAACACGCTTGGCCACCG 62.327 66.667 20.16 20.16 0.00 4.94
687 690 1.241315 ATACAACACGCTTGGCCACC 61.241 55.000 3.88 0.00 0.00 4.61
688 691 0.596082 AATACAACACGCTTGGCCAC 59.404 50.000 3.88 0.00 0.00 5.01
689 692 2.186532 TAATACAACACGCTTGGCCA 57.813 45.000 0.00 0.00 0.00 5.36
690 693 2.414957 GGTTAATACAACACGCTTGGCC 60.415 50.000 0.00 0.00 0.00 5.36
691 694 2.226912 TGGTTAATACAACACGCTTGGC 59.773 45.455 0.00 0.00 0.00 4.52
692 695 3.817238 GTGGTTAATACAACACGCTTGG 58.183 45.455 0.00 0.00 0.00 3.61
698 701 5.379003 CACACATCGTGGTTAATACAACAC 58.621 41.667 0.00 0.00 42.34 3.32
718 721 0.741574 GACACGGACACAACACCACA 60.742 55.000 0.00 0.00 0.00 4.17
780 788 5.949952 TCCATAGCCTATACATATGTCGTGT 59.050 40.000 12.68 0.09 0.00 4.49
781 789 6.095580 AGTCCATAGCCTATACATATGTCGTG 59.904 42.308 12.68 3.43 0.00 4.35
784 792 8.414778 GGTTAGTCCATAGCCTATACATATGTC 58.585 40.741 12.68 0.00 32.18 3.06
785 793 7.344871 GGGTTAGTCCATAGCCTATACATATGT 59.655 40.741 13.93 13.93 35.19 2.29
786 794 7.565398 AGGGTTAGTCCATAGCCTATACATATG 59.435 40.741 0.00 0.00 40.32 1.78
787 795 7.663041 AGGGTTAGTCCATAGCCTATACATAT 58.337 38.462 0.00 0.00 40.32 1.78
788 796 7.036059 AGAGGGTTAGTCCATAGCCTATACATA 60.036 40.741 0.00 0.00 42.06 2.29
789 797 5.916806 AGGGTTAGTCCATAGCCTATACAT 58.083 41.667 0.00 0.00 40.32 2.29
790 798 5.076039 AGAGGGTTAGTCCATAGCCTATACA 59.924 44.000 0.00 0.00 42.06 2.29
791 799 5.581975 AGAGGGTTAGTCCATAGCCTATAC 58.418 45.833 0.00 0.00 42.06 1.47
792 800 5.556339 AGAGAGGGTTAGTCCATAGCCTATA 59.444 44.000 0.00 0.00 42.06 1.31
793 801 4.358614 AGAGAGGGTTAGTCCATAGCCTAT 59.641 45.833 0.00 0.00 42.06 2.57
794 802 3.727923 AGAGAGGGTTAGTCCATAGCCTA 59.272 47.826 0.00 0.00 42.06 3.93
795 803 2.520549 AGAGAGGGTTAGTCCATAGCCT 59.479 50.000 0.00 0.00 44.53 4.58
796 804 2.965562 AGAGAGGGTTAGTCCATAGCC 58.034 52.381 0.00 0.00 38.11 3.93
808 816 8.653191 CACCGATATATATAGTCTAGAGAGGGT 58.347 40.741 0.00 0.00 0.00 4.34
819 827 6.206243 GGGTCGCATACACCGATATATATAGT 59.794 42.308 0.00 0.00 37.04 2.12
820 828 6.430308 AGGGTCGCATACACCGATATATATAG 59.570 42.308 0.00 0.00 37.04 1.31
831 839 2.389962 TTACAAGGGTCGCATACACC 57.610 50.000 0.00 0.00 28.35 4.16
838 849 0.035820 TGGGTGATTACAAGGGTCGC 60.036 55.000 0.00 0.00 0.00 5.19
839 850 1.553248 TCTGGGTGATTACAAGGGTCG 59.447 52.381 0.00 0.00 0.00 4.79
862 873 2.546789 TCCGGCGAGTTTTCTTTCTTTC 59.453 45.455 9.30 0.00 0.00 2.62
963 976 0.966920 AGTTCTATGTATCCGCCCCG 59.033 55.000 0.00 0.00 0.00 5.73
964 977 2.231721 GAGAGTTCTATGTATCCGCCCC 59.768 54.545 0.00 0.00 0.00 5.80
965 978 2.891580 TGAGAGTTCTATGTATCCGCCC 59.108 50.000 0.00 0.00 0.00 6.13
966 979 3.612955 GCTGAGAGTTCTATGTATCCGCC 60.613 52.174 0.00 0.00 0.00 6.13
967 980 3.254657 AGCTGAGAGTTCTATGTATCCGC 59.745 47.826 0.00 0.00 0.00 5.54
974 987 1.406898 TCGCCAGCTGAGAGTTCTATG 59.593 52.381 17.39 0.00 0.00 2.23
1059 1074 4.087182 GGACGAGGATCTCCCATATTACA 58.913 47.826 0.00 0.00 37.41 2.41
1356 1373 2.483745 GTGTCGTCGATGCGGAGA 59.516 61.111 0.00 0.00 0.00 3.71
1380 1397 2.159043 AGTCATCGGATTGCAGACGAAT 60.159 45.455 12.30 0.00 40.27 3.34
1397 1414 1.404181 GGCAAGCATACTGACGAGTCA 60.404 52.381 5.76 5.76 38.06 3.41
1581 1613 0.179048 TCGCATCTGGCCATTCGATT 60.179 50.000 5.51 0.00 40.31 3.34
1586 1618 3.504906 CAGATTAATCGCATCTGGCCATT 59.495 43.478 5.51 0.00 42.77 3.16
1614 1646 2.606272 GCTACCACGGAAATAAGGTTCG 59.394 50.000 0.00 0.00 35.62 3.95
1654 1945 6.664515 TCGTTTTATTTTCGCTCTCAACATT 58.335 32.000 0.00 0.00 0.00 2.71
1736 2027 2.881513 TCAAACAGGTTAGCGCAATCAA 59.118 40.909 11.47 0.00 0.00 2.57
1778 2069 8.221100 CGGTTTTCATATAATCAACTATGACCG 58.779 37.037 0.00 0.00 38.69 4.79
1885 2176 0.957395 CACCTGTCACACTGCATCCC 60.957 60.000 0.00 0.00 0.00 3.85
1896 2187 1.040893 ACCGACTGTCACACCTGTCA 61.041 55.000 8.73 0.00 34.14 3.58
1952 2243 5.425398 CAAATTTGATCAACACAAGCAACG 58.575 37.500 13.08 0.00 0.00 4.10
2088 2379 8.280497 ACAACATAACTCTACGATGTTTGAAAC 58.720 33.333 0.14 0.14 40.85 2.78
2229 2524 6.764308 AATTCCTCATTATATTCCCGCATG 57.236 37.500 0.00 0.00 0.00 4.06
2368 2672 7.494625 TCAAAATTACACTATTCCGGAGATGAC 59.505 37.037 3.34 0.00 0.00 3.06
2439 2746 9.733556 TCCAAATTCTAAGATGCTTGTTAGTTA 57.266 29.630 13.94 6.52 32.09 2.24
2480 2787 4.335315 CACCATTACATGAAAGGCGTATGT 59.665 41.667 0.00 0.00 38.48 2.29
2481 2788 4.261155 CCACCATTACATGAAAGGCGTATG 60.261 45.833 0.00 0.00 0.00 2.39
2482 2789 3.882888 CCACCATTACATGAAAGGCGTAT 59.117 43.478 0.00 0.00 0.00 3.06
2483 2790 3.275143 CCACCATTACATGAAAGGCGTA 58.725 45.455 0.00 0.00 0.00 4.42
2520 2827 1.798079 GCCGACGCCTAGTACTCTTTG 60.798 57.143 0.00 0.00 0.00 2.77
2540 2847 2.097304 GCAAAAAGTTTTGGCTGGTTGG 59.903 45.455 18.72 0.00 45.73 3.77
2546 2853 2.235898 TGACCAGCAAAAAGTTTTGGCT 59.764 40.909 22.19 22.19 45.73 4.75
2569 2876 0.464735 TTAAATGGTATGGCCGCGCT 60.465 50.000 5.56 0.00 41.21 5.92
2582 2889 1.466950 ACGGTGTGTGCGGATTAAATG 59.533 47.619 0.00 0.00 0.00 2.32
2626 2933 2.396157 GGATCGGGGAACGTTGCAC 61.396 63.158 21.74 17.50 44.69 4.57
2653 2961 0.259647 CTGCCATGAGGATTTGGGGA 59.740 55.000 0.00 0.00 36.89 4.81
2695 3003 2.997315 CAGAGACGGGGTCAGCCA 60.997 66.667 0.00 0.00 34.60 4.75
2837 3146 4.570772 CGACCTGTGAAGAAGTTTTGAAGA 59.429 41.667 0.00 0.00 0.00 2.87
2855 3164 1.304052 AGACTCTGAGCTGCGACCT 60.304 57.895 4.19 0.00 0.00 3.85
2877 3186 0.892358 AAGACGACGACCTACCAGCA 60.892 55.000 0.00 0.00 0.00 4.41
2979 3288 1.210967 CATGCCCCAATTTGCTGGAAT 59.789 47.619 7.22 0.40 38.96 3.01
3081 3392 4.354893 TTTTTGGGCTGCATCATTTTCT 57.645 36.364 0.50 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.