Multiple sequence alignment - TraesCS1B01G282700

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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 TraesCS1B01G282700 chr1B 100.000 2684 0 0 1 2684 491398174 491400857 0.000000e+00 4957
1 TraesCS1B01G282700 chr1B 95.926 1792 52 12 1 1789 491439429 491441202 0.000000e+00 2885
2 TraesCS1B01G282700 chr1D 95.645 1791 55 14 1 1786 367149309 367151081 0.000000e+00 2854
3 TraesCS1B01G282700 chr1D 96.646 1103 36 1 687 1789 366091308 366092409 0.000000e+00 1831
4 TraesCS1B01G282700 chr1D 98.520 608 7 2 1 607 366090652 366091258 0.000000e+00 1072
5 TraesCS1B01G282700 chr1A 95.259 1793 63 13 1 1789 466337301 466339075 0.000000e+00 2820
6 TraesCS1B01G282700 chr1A 95.603 1751 54 13 1 1747 466037682 466039413 0.000000e+00 2785
7 TraesCS1B01G282700 chr6A 95.294 1785 62 14 9 1789 428665878 428664112 0.000000e+00 2811
8 TraesCS1B01G282700 chr3B 90.781 640 48 4 1810 2446 709305817 709305186 0.000000e+00 845
9 TraesCS1B01G282700 chr3B 83.626 171 7 1 2535 2684 709294703 709294533 1.000000e-29 141
10 TraesCS1B01G282700 chr3B 92.647 68 5 0 2459 2526 709305211 709305144 6.120000e-17 99
11 TraesCS1B01G282700 chr6B 81.326 905 130 19 1810 2684 31948483 31949378 0.000000e+00 699
12 TraesCS1B01G282700 chr7A 84.681 235 35 1 2215 2448 724969865 724969631 1.610000e-57 233


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 TraesCS1B01G282700 chr1B 491398174 491400857 2683 False 4957.0 4957 100.000 1 2684 1 chr1B.!!$F1 2683
1 TraesCS1B01G282700 chr1B 491439429 491441202 1773 False 2885.0 2885 95.926 1 1789 1 chr1B.!!$F2 1788
2 TraesCS1B01G282700 chr1D 367149309 367151081 1772 False 2854.0 2854 95.645 1 1786 1 chr1D.!!$F1 1785
3 TraesCS1B01G282700 chr1D 366090652 366092409 1757 False 1451.5 1831 97.583 1 1789 2 chr1D.!!$F2 1788
4 TraesCS1B01G282700 chr1A 466337301 466339075 1774 False 2820.0 2820 95.259 1 1789 1 chr1A.!!$F2 1788
5 TraesCS1B01G282700 chr1A 466037682 466039413 1731 False 2785.0 2785 95.603 1 1747 1 chr1A.!!$F1 1746
6 TraesCS1B01G282700 chr6A 428664112 428665878 1766 True 2811.0 2811 95.294 9 1789 1 chr6A.!!$R1 1780
7 TraesCS1B01G282700 chr3B 709305144 709305817 673 True 472.0 845 91.714 1810 2526 2 chr3B.!!$R2 716
8 TraesCS1B01G282700 chr6B 31948483 31949378 895 False 699.0 699 81.326 1810 2684 1 chr6B.!!$F1 874

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
681 730 0.174389 CAGAGGTGAGGATGGTGACG 59.826 60.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2016 0.033699 GGGCTGCATCCTCTCCTTTT 60.034 55.0 6.53 0.0 0.0 2.27 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
333 334 7.760794 CCTTGTTCTATATGCTCATCTCATCTC 59.239 40.741 0.00 0.00 0.00 2.75
334 335 8.419922 TTGTTCTATATGCTCATCTCATCTCT 57.580 34.615 0.00 0.00 0.00 3.10
335 336 8.419922 TGTTCTATATGCTCATCTCATCTCTT 57.580 34.615 0.00 0.00 0.00 2.85
626 675 1.567649 ACTGCCAATGAGGATGGTGAT 59.432 47.619 0.00 0.00 41.22 3.06
647 696 0.970937 GAGGTGAGGATGGTGACGGA 60.971 60.000 0.00 0.00 0.00 4.69
648 697 0.972983 AGGTGAGGATGGTGACGGAG 60.973 60.000 0.00 0.00 0.00 4.63
649 698 1.517832 GTGAGGATGGTGACGGAGG 59.482 63.158 0.00 0.00 0.00 4.30
650 699 1.078528 TGAGGATGGTGACGGAGGT 59.921 57.895 0.00 0.00 0.00 3.85
651 700 1.257750 TGAGGATGGTGACGGAGGTG 61.258 60.000 0.00 0.00 0.00 4.00
652 701 0.970937 GAGGATGGTGACGGAGGTGA 60.971 60.000 0.00 0.00 0.00 4.02
653 702 0.972983 AGGATGGTGACGGAGGTGAG 60.973 60.000 0.00 0.00 0.00 3.51
654 703 1.517832 GATGGTGACGGAGGTGAGG 59.482 63.158 0.00 0.00 0.00 3.86
655 704 0.970937 GATGGTGACGGAGGTGAGGA 60.971 60.000 0.00 0.00 0.00 3.71
656 705 0.325671 ATGGTGACGGAGGTGAGGAT 60.326 55.000 0.00 0.00 0.00 3.24
657 706 1.257750 TGGTGACGGAGGTGAGGATG 61.258 60.000 0.00 0.00 0.00 3.51
658 707 1.517832 GTGACGGAGGTGAGGATGG 59.482 63.158 0.00 0.00 0.00 3.51
659 708 1.078528 TGACGGAGGTGAGGATGGT 59.921 57.895 0.00 0.00 0.00 3.55
660 709 1.257750 TGACGGAGGTGAGGATGGTG 61.258 60.000 0.00 0.00 0.00 4.17
661 710 0.970937 GACGGAGGTGAGGATGGTGA 60.971 60.000 0.00 0.00 0.00 4.02
662 711 1.258445 ACGGAGGTGAGGATGGTGAC 61.258 60.000 0.00 0.00 0.00 3.67
674 723 3.794786 TGGTGACAGAGGTGAGGAT 57.205 52.632 0.00 0.00 35.01 3.24
675 724 1.269958 TGGTGACAGAGGTGAGGATG 58.730 55.000 0.00 0.00 35.01 3.51
676 725 0.539051 GGTGACAGAGGTGAGGATGG 59.461 60.000 0.00 0.00 0.00 3.51
677 726 1.270907 GTGACAGAGGTGAGGATGGT 58.729 55.000 0.00 0.00 0.00 3.55
678 727 1.066573 GTGACAGAGGTGAGGATGGTG 60.067 57.143 0.00 0.00 0.00 4.17
679 728 1.203174 TGACAGAGGTGAGGATGGTGA 60.203 52.381 0.00 0.00 0.00 4.02
680 729 1.205893 GACAGAGGTGAGGATGGTGAC 59.794 57.143 0.00 0.00 0.00 3.67
681 730 0.174389 CAGAGGTGAGGATGGTGACG 59.826 60.000 0.00 0.00 0.00 4.35
682 731 0.972983 AGAGGTGAGGATGGTGACGG 60.973 60.000 0.00 0.00 0.00 4.79
683 732 0.970937 GAGGTGAGGATGGTGACGGA 60.971 60.000 0.00 0.00 0.00 4.69
684 733 0.972983 AGGTGAGGATGGTGACGGAG 60.973 60.000 0.00 0.00 0.00 4.63
685 734 1.517832 GTGAGGATGGTGACGGAGG 59.482 63.158 0.00 0.00 0.00 4.30
686 735 1.078528 TGAGGATGGTGACGGAGGT 59.921 57.895 0.00 0.00 0.00 3.85
687 736 1.257750 TGAGGATGGTGACGGAGGTG 61.258 60.000 0.00 0.00 0.00 4.00
688 737 0.970937 GAGGATGGTGACGGAGGTGA 60.971 60.000 0.00 0.00 0.00 4.02
689 738 0.972983 AGGATGGTGACGGAGGTGAG 60.973 60.000 0.00 0.00 0.00 3.51
690 739 1.517832 GATGGTGACGGAGGTGAGG 59.482 63.158 0.00 0.00 0.00 3.86
691 740 0.970937 GATGGTGACGGAGGTGAGGA 60.971 60.000 0.00 0.00 0.00 3.71
692 741 0.325671 ATGGTGACGGAGGTGAGGAT 60.326 55.000 0.00 0.00 0.00 3.24
693 742 1.257750 TGGTGACGGAGGTGAGGATG 61.258 60.000 0.00 0.00 0.00 3.51
694 743 1.517832 GTGACGGAGGTGAGGATGG 59.482 63.158 0.00 0.00 0.00 3.51
695 744 1.078528 TGACGGAGGTGAGGATGGT 59.921 57.895 0.00 0.00 0.00 3.55
696 745 1.257750 TGACGGAGGTGAGGATGGTG 61.258 60.000 0.00 0.00 0.00 4.17
697 746 0.970937 GACGGAGGTGAGGATGGTGA 60.971 60.000 0.00 0.00 0.00 4.02
698 747 0.325671 ACGGAGGTGAGGATGGTGAT 60.326 55.000 0.00 0.00 0.00 3.06
699 748 1.063190 ACGGAGGTGAGGATGGTGATA 60.063 52.381 0.00 0.00 0.00 2.15
700 749 1.615883 CGGAGGTGAGGATGGTGATAG 59.384 57.143 0.00 0.00 0.00 2.08
727 794 3.371965 AGGATGATGCTTCATTTGCCTT 58.628 40.909 15.56 0.00 42.73 4.35
774 841 4.236935 GACGGAGGTGTCAATTTTACGTA 58.763 43.478 0.00 0.00 38.75 3.57
807 874 0.598065 GGCCATTCGTGCAAACTTCT 59.402 50.000 0.00 0.00 0.00 2.85
861 928 7.546667 GGTACCAAAGTTTTGTCATCTATACGA 59.453 37.037 7.15 0.00 36.45 3.43
1579 1646 3.293337 TGCAGCCGTAGAATTAGGAGTA 58.707 45.455 0.00 0.00 0.00 2.59
1791 1859 6.881065 TGTTTGCCAGATCATATTATCTAGGC 59.119 38.462 21.42 21.42 43.30 3.93
1792 1860 5.620738 TGCCAGATCATATTATCTAGGCC 57.379 43.478 23.33 0.00 42.87 5.19
1793 1861 5.032170 TGCCAGATCATATTATCTAGGCCA 58.968 41.667 23.33 15.29 42.87 5.36
1794 1862 5.129980 TGCCAGATCATATTATCTAGGCCAG 59.870 44.000 23.33 0.00 42.87 4.85
1795 1863 5.130145 GCCAGATCATATTATCTAGGCCAGT 59.870 44.000 19.42 0.00 40.51 4.00
1796 1864 6.580788 CCAGATCATATTATCTAGGCCAGTG 58.419 44.000 5.01 0.00 34.40 3.66
1797 1865 6.382282 CCAGATCATATTATCTAGGCCAGTGA 59.618 42.308 5.01 0.00 34.40 3.41
1798 1866 7.070946 CCAGATCATATTATCTAGGCCAGTGAT 59.929 40.741 5.01 7.96 34.40 3.06
1799 1867 9.140874 CAGATCATATTATCTAGGCCAGTGATA 57.859 37.037 5.01 6.89 34.40 2.15
1800 1868 9.720874 AGATCATATTATCTAGGCCAGTGATAA 57.279 33.333 19.93 19.93 37.17 1.75
1808 1876 9.720874 TTATCTAGGCCAGTGATAATATGATCT 57.279 33.333 5.01 0.00 30.57 2.75
1815 1883 4.092529 CAGTGATAATATGATCTGGCGCAC 59.907 45.833 10.83 0.00 0.00 5.34
1816 1884 4.020751 AGTGATAATATGATCTGGCGCACT 60.021 41.667 10.83 0.00 0.00 4.40
1887 1955 1.656095 CAACCGTCAGATCGAAAGCTC 59.344 52.381 0.00 0.00 0.00 4.09
1917 1987 1.362768 GCATCTCGCATCTGAACACA 58.637 50.000 0.00 0.00 41.79 3.72
1962 2040 0.035176 GAGAGGATGCAGCCCAGATC 59.965 60.000 19.48 8.80 0.00 2.75
1982 2060 1.356624 CCGAAATCCATTGCCTCGC 59.643 57.895 0.00 0.00 0.00 5.03
1983 2061 1.097547 CCGAAATCCATTGCCTCGCT 61.098 55.000 0.00 0.00 0.00 4.93
1984 2062 0.028505 CGAAATCCATTGCCTCGCTG 59.971 55.000 0.00 0.00 0.00 5.18
1985 2063 1.098050 GAAATCCATTGCCTCGCTGT 58.902 50.000 0.00 0.00 0.00 4.40
2081 2179 2.047274 CCCCGCTTCTCTTCGCAA 60.047 61.111 0.00 0.00 0.00 4.85
2082 2180 2.391389 CCCCGCTTCTCTTCGCAAC 61.391 63.158 0.00 0.00 0.00 4.17
2092 2190 4.848562 TCTCTTCGCAACTTGAAGTAGA 57.151 40.909 0.00 0.00 42.68 2.59
2135 2233 2.641783 CGTCGTCGTTCCAACACCG 61.642 63.158 0.00 0.00 0.00 4.94
2180 2278 5.068460 TGAACAAAAGTCGGTCCATCAAATT 59.932 36.000 0.00 0.00 0.00 1.82
2204 2302 2.421314 CCCATCATAGCACGGCGA 59.579 61.111 16.62 0.00 0.00 5.54
2247 2345 0.250124 CGTTGACCTGCACCACCTAA 60.250 55.000 0.00 0.00 0.00 2.69
2272 2371 2.024414 AGCGAAAACCAAAACTCAGCT 58.976 42.857 0.00 0.00 0.00 4.24
2281 2380 8.962884 AAAACCAAAACTCAGCTCAAAAATAT 57.037 26.923 0.00 0.00 0.00 1.28
2325 2425 4.883006 ACGGTTCCAGCAAAAAGTAACTTA 59.117 37.500 0.00 0.00 0.00 2.24
2345 2446 0.105964 GGTTCCAGCAAAACAACCCC 59.894 55.000 0.00 0.00 33.42 4.95
2370 2471 9.444600 CCAGTGCTAGAAAATTAGGTAAACTAA 57.555 33.333 0.00 0.00 45.24 2.24
2418 2519 4.202141 CCAGCAAAATCAAACTCTGGTTCA 60.202 41.667 0.00 0.00 37.05 3.18
2419 2520 4.980434 CAGCAAAATCAAACTCTGGTTCAG 59.020 41.667 0.00 0.00 34.14 3.02
2420 2521 3.737774 GCAAAATCAAACTCTGGTTCAGC 59.262 43.478 0.00 0.00 34.14 4.26
2421 2522 4.737352 GCAAAATCAAACTCTGGTTCAGCA 60.737 41.667 0.00 0.00 34.14 4.41
2422 2523 5.350633 CAAAATCAAACTCTGGTTCAGCAA 58.649 37.500 0.00 0.00 34.14 3.91
2423 2524 5.596836 AAATCAAACTCTGGTTCAGCAAA 57.403 34.783 0.00 0.00 34.14 3.68
2424 2525 5.596836 AATCAAACTCTGGTTCAGCAAAA 57.403 34.783 0.00 0.00 34.14 2.44
2425 2526 4.370364 TCAAACTCTGGTTCAGCAAAAC 57.630 40.909 0.00 0.00 34.14 2.43
2434 2535 3.855858 GGTTCAGCAAAACCAAAACTGA 58.144 40.909 13.68 0.00 46.62 3.41
2435 2536 3.865164 GGTTCAGCAAAACCAAAACTGAG 59.135 43.478 13.68 0.00 46.62 3.35
2436 2537 3.163630 TCAGCAAAACCAAAACTGAGC 57.836 42.857 0.00 0.00 32.65 4.26
2437 2538 2.495270 TCAGCAAAACCAAAACTGAGCA 59.505 40.909 0.00 0.00 32.65 4.26
2438 2539 3.056250 TCAGCAAAACCAAAACTGAGCAA 60.056 39.130 0.00 0.00 32.65 3.91
2439 2540 3.307782 CAGCAAAACCAAAACTGAGCAAG 59.692 43.478 0.00 0.00 0.00 4.01
2440 2541 3.055891 AGCAAAACCAAAACTGAGCAAGT 60.056 39.130 0.00 0.00 42.60 3.16
2441 2542 4.159506 AGCAAAACCAAAACTGAGCAAGTA 59.840 37.500 0.00 0.00 38.56 2.24
2442 2543 4.504097 GCAAAACCAAAACTGAGCAAGTAG 59.496 41.667 0.00 0.00 38.56 2.57
2443 2544 4.918810 AAACCAAAACTGAGCAAGTAGG 57.081 40.909 0.00 0.00 38.56 3.18
2444 2545 3.857157 ACCAAAACTGAGCAAGTAGGA 57.143 42.857 10.57 0.00 38.56 2.94
2445 2546 4.164843 ACCAAAACTGAGCAAGTAGGAA 57.835 40.909 10.57 0.00 38.56 3.36
2446 2547 4.729868 ACCAAAACTGAGCAAGTAGGAAT 58.270 39.130 10.57 0.00 38.56 3.01
2447 2548 4.762251 ACCAAAACTGAGCAAGTAGGAATC 59.238 41.667 10.57 0.00 38.56 2.52
2448 2549 4.761739 CCAAAACTGAGCAAGTAGGAATCA 59.238 41.667 0.00 0.00 38.56 2.57
2449 2550 5.416952 CCAAAACTGAGCAAGTAGGAATCAT 59.583 40.000 0.00 0.00 38.56 2.45
2450 2551 6.320171 CAAAACTGAGCAAGTAGGAATCATG 58.680 40.000 0.00 0.00 38.56 3.07
2451 2552 4.148128 ACTGAGCAAGTAGGAATCATGG 57.852 45.455 0.00 0.00 37.36 3.66
2452 2553 3.521126 ACTGAGCAAGTAGGAATCATGGT 59.479 43.478 0.00 0.00 37.36 3.55
2453 2554 4.018960 ACTGAGCAAGTAGGAATCATGGTT 60.019 41.667 0.00 0.00 37.36 3.67
2454 2555 4.517285 TGAGCAAGTAGGAATCATGGTTC 58.483 43.478 10.42 10.42 0.00 3.62
2455 2556 4.225942 TGAGCAAGTAGGAATCATGGTTCT 59.774 41.667 17.99 7.19 0.00 3.01
2456 2557 5.184892 AGCAAGTAGGAATCATGGTTCTT 57.815 39.130 17.99 13.36 0.00 2.52
2490 2630 8.567948 CAAAACTGAGCAAGTAGGAAATTTAGA 58.432 33.333 0.00 0.00 38.56 2.10
2529 2669 8.487313 GAAACAAAAATTTACCTGTTTCCAGT 57.513 30.769 25.35 9.82 46.12 4.00
2530 2670 9.589111 GAAACAAAAATTTACCTGTTTCCAGTA 57.411 29.630 25.35 0.00 46.12 2.74
2531 2671 9.945904 AAACAAAAATTTACCTGTTTCCAGTAA 57.054 25.926 15.15 0.00 37.41 2.24
2532 2672 9.945904 AACAAAAATTTACCTGTTTCCAGTAAA 57.054 25.926 7.18 0.00 36.95 2.01
2533 2673 9.945904 ACAAAAATTTACCTGTTTCCAGTAAAA 57.054 25.926 0.00 0.00 36.95 1.52
2565 2705 4.440112 CCTCCGGTTCCAGCAAAAATAATC 60.440 45.833 0.00 0.00 0.00 1.75
2571 2711 5.343249 GTTCCAGCAAAAATAATCGCATCT 58.657 37.500 0.00 0.00 0.00 2.90
2576 2716 5.030295 AGCAAAAATAATCGCATCTCAACG 58.970 37.500 0.00 0.00 0.00 4.10
2578 2718 5.053025 GCAAAAATAATCGCATCTCAACGTC 60.053 40.000 0.00 0.00 0.00 4.34
2600 2740 2.955660 CAACCTTGTAGCTCCACCAAAA 59.044 45.455 0.00 0.00 0.00 2.44
2604 2744 0.605319 TGTAGCTCCACCAAAAGCCG 60.605 55.000 0.00 0.00 39.39 5.52
2611 2751 1.142748 CACCAAAAGCCGGTTGCAA 59.857 52.632 1.90 0.00 44.83 4.08
2614 2754 0.597377 CCAAAAGCCGGTTGCAACTC 60.597 55.000 27.64 16.97 44.83 3.01
2615 2755 0.597377 CAAAAGCCGGTTGCAACTCC 60.597 55.000 27.64 12.58 44.83 3.85
2617 2757 3.767630 AAGCCGGTTGCAACTCCGT 62.768 57.895 27.64 12.25 44.51 4.69
2621 2761 1.278637 CGGTTGCAACTCCGTTGTC 59.721 57.895 27.64 8.66 44.40 3.18
2622 2762 1.278637 GGTTGCAACTCCGTTGTCG 59.721 57.895 27.64 0.00 44.40 4.35
2624 2764 0.232303 GTTGCAACTCCGTTGTCGAG 59.768 55.000 22.36 0.00 44.40 4.04
2677 2838 2.064762 GTATGCAGCTCTTATGCTCCG 58.935 52.381 0.00 0.00 44.17 4.63
2680 2841 1.227089 CAGCTCTTATGCTCCGCGT 60.227 57.895 4.92 0.00 41.98 6.01
2682 2843 0.807667 AGCTCTTATGCTCCGCGTTG 60.808 55.000 4.92 0.00 39.34 4.10
2683 2844 1.638467 CTCTTATGCTCCGCGTTGC 59.362 57.895 4.92 9.65 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
626 675 1.257750 CGTCACCATCCTCACCTCCA 61.258 60.000 0.00 0.00 0.00 3.86
647 696 1.566211 CTCTGTCACCATCCTCACCT 58.434 55.000 0.00 0.00 0.00 4.00
648 697 0.539051 CCTCTGTCACCATCCTCACC 59.461 60.000 0.00 0.00 0.00 4.02
649 698 1.066573 CACCTCTGTCACCATCCTCAC 60.067 57.143 0.00 0.00 0.00 3.51
650 699 1.203174 TCACCTCTGTCACCATCCTCA 60.203 52.381 0.00 0.00 0.00 3.86
651 700 1.480137 CTCACCTCTGTCACCATCCTC 59.520 57.143 0.00 0.00 0.00 3.71
652 701 1.566211 CTCACCTCTGTCACCATCCT 58.434 55.000 0.00 0.00 0.00 3.24
653 702 0.539051 CCTCACCTCTGTCACCATCC 59.461 60.000 0.00 0.00 0.00 3.51
654 703 1.561643 TCCTCACCTCTGTCACCATC 58.438 55.000 0.00 0.00 0.00 3.51
655 704 1.836166 CATCCTCACCTCTGTCACCAT 59.164 52.381 0.00 0.00 0.00 3.55
656 705 1.269958 CATCCTCACCTCTGTCACCA 58.730 55.000 0.00 0.00 0.00 4.17
657 706 0.539051 CCATCCTCACCTCTGTCACC 59.461 60.000 0.00 0.00 0.00 4.02
658 707 1.066573 CACCATCCTCACCTCTGTCAC 60.067 57.143 0.00 0.00 0.00 3.67
659 708 1.203174 TCACCATCCTCACCTCTGTCA 60.203 52.381 0.00 0.00 0.00 3.58
660 709 1.205893 GTCACCATCCTCACCTCTGTC 59.794 57.143 0.00 0.00 0.00 3.51
661 710 1.270907 GTCACCATCCTCACCTCTGT 58.729 55.000 0.00 0.00 0.00 3.41
662 711 0.174389 CGTCACCATCCTCACCTCTG 59.826 60.000 0.00 0.00 0.00 3.35
663 712 0.972983 CCGTCACCATCCTCACCTCT 60.973 60.000 0.00 0.00 0.00 3.69
664 713 0.970937 TCCGTCACCATCCTCACCTC 60.971 60.000 0.00 0.00 0.00 3.85
665 714 0.972983 CTCCGTCACCATCCTCACCT 60.973 60.000 0.00 0.00 0.00 4.00
666 715 1.517832 CTCCGTCACCATCCTCACC 59.482 63.158 0.00 0.00 0.00 4.02
667 716 1.258445 ACCTCCGTCACCATCCTCAC 61.258 60.000 0.00 0.00 0.00 3.51
668 717 1.078528 ACCTCCGTCACCATCCTCA 59.921 57.895 0.00 0.00 0.00 3.86
669 718 0.970937 TCACCTCCGTCACCATCCTC 60.971 60.000 0.00 0.00 0.00 3.71
670 719 0.972983 CTCACCTCCGTCACCATCCT 60.973 60.000 0.00 0.00 0.00 3.24
671 720 1.517832 CTCACCTCCGTCACCATCC 59.482 63.158 0.00 0.00 0.00 3.51
672 721 0.970937 TCCTCACCTCCGTCACCATC 60.971 60.000 0.00 0.00 0.00 3.51
673 722 0.325671 ATCCTCACCTCCGTCACCAT 60.326 55.000 0.00 0.00 0.00 3.55
674 723 1.078528 ATCCTCACCTCCGTCACCA 59.921 57.895 0.00 0.00 0.00 4.17
675 724 1.517832 CATCCTCACCTCCGTCACC 59.482 63.158 0.00 0.00 0.00 4.02
676 725 1.258445 ACCATCCTCACCTCCGTCAC 61.258 60.000 0.00 0.00 0.00 3.67
677 726 1.078528 ACCATCCTCACCTCCGTCA 59.921 57.895 0.00 0.00 0.00 4.35
678 727 0.970937 TCACCATCCTCACCTCCGTC 60.971 60.000 0.00 0.00 0.00 4.79
679 728 0.325671 ATCACCATCCTCACCTCCGT 60.326 55.000 0.00 0.00 0.00 4.69
680 729 1.615883 CTATCACCATCCTCACCTCCG 59.384 57.143 0.00 0.00 0.00 4.63
681 730 2.896685 CTCTATCACCATCCTCACCTCC 59.103 54.545 0.00 0.00 0.00 4.30
682 731 2.896685 CCTCTATCACCATCCTCACCTC 59.103 54.545 0.00 0.00 0.00 3.85
683 732 2.248686 ACCTCTATCACCATCCTCACCT 59.751 50.000 0.00 0.00 0.00 4.00
684 733 2.366916 CACCTCTATCACCATCCTCACC 59.633 54.545 0.00 0.00 0.00 4.02
685 734 3.300388 TCACCTCTATCACCATCCTCAC 58.700 50.000 0.00 0.00 0.00 3.51
686 735 3.570540 CTCACCTCTATCACCATCCTCA 58.429 50.000 0.00 0.00 0.00 3.86
687 736 2.896685 CCTCACCTCTATCACCATCCTC 59.103 54.545 0.00 0.00 0.00 3.71
688 737 2.520120 TCCTCACCTCTATCACCATCCT 59.480 50.000 0.00 0.00 0.00 3.24
689 738 2.964209 TCCTCACCTCTATCACCATCC 58.036 52.381 0.00 0.00 0.00 3.51
690 739 4.155709 TCATCCTCACCTCTATCACCATC 58.844 47.826 0.00 0.00 0.00 3.51
691 740 4.204792 TCATCCTCACCTCTATCACCAT 57.795 45.455 0.00 0.00 0.00 3.55
692 741 3.688049 TCATCCTCACCTCTATCACCA 57.312 47.619 0.00 0.00 0.00 4.17
693 742 3.306641 GCATCATCCTCACCTCTATCACC 60.307 52.174 0.00 0.00 0.00 4.02
694 743 3.577848 AGCATCATCCTCACCTCTATCAC 59.422 47.826 0.00 0.00 0.00 3.06
695 744 3.854437 AGCATCATCCTCACCTCTATCA 58.146 45.455 0.00 0.00 0.00 2.15
696 745 4.282957 TGAAGCATCATCCTCACCTCTATC 59.717 45.833 0.00 0.00 0.00 2.08
697 746 4.229639 TGAAGCATCATCCTCACCTCTAT 58.770 43.478 0.00 0.00 0.00 1.98
698 747 3.646534 TGAAGCATCATCCTCACCTCTA 58.353 45.455 0.00 0.00 0.00 2.43
699 748 2.475155 TGAAGCATCATCCTCACCTCT 58.525 47.619 0.00 0.00 0.00 3.69
700 749 2.996249 TGAAGCATCATCCTCACCTC 57.004 50.000 0.00 0.00 0.00 3.85
727 794 2.435437 TCTTCATCATCGGAATGCTCCA 59.565 45.455 0.00 0.00 42.58 3.86
774 841 3.216292 GGCCAACACTTGCACCGT 61.216 61.111 0.00 0.00 0.00 4.83
861 928 2.050934 GTACTTCCCCCTCGAGCGT 61.051 63.158 6.99 0.00 0.00 5.07
1579 1646 3.192212 CGGGGTAACTCTAGACGTTCTTT 59.808 47.826 9.83 0.00 31.17 2.52
1754 1822 6.265196 TGATCTGGCAAACATAGACAAAGTTT 59.735 34.615 0.00 0.00 36.00 2.66
1791 1859 3.620374 GCGCCAGATCATATTATCACTGG 59.380 47.826 0.00 0.00 45.01 4.00
1792 1860 4.092529 GTGCGCCAGATCATATTATCACTG 59.907 45.833 4.18 0.00 0.00 3.66
1793 1861 4.020751 AGTGCGCCAGATCATATTATCACT 60.021 41.667 4.18 0.00 0.00 3.41
1794 1862 4.092529 CAGTGCGCCAGATCATATTATCAC 59.907 45.833 4.18 0.00 0.00 3.06
1795 1863 4.248058 CAGTGCGCCAGATCATATTATCA 58.752 43.478 4.18 0.00 0.00 2.15
1796 1864 3.620374 CCAGTGCGCCAGATCATATTATC 59.380 47.826 4.18 0.00 0.00 1.75
1797 1865 3.603532 CCAGTGCGCCAGATCATATTAT 58.396 45.455 4.18 0.00 0.00 1.28
1798 1866 2.871637 GCCAGTGCGCCAGATCATATTA 60.872 50.000 4.18 0.00 0.00 0.98
1799 1867 1.888215 CCAGTGCGCCAGATCATATT 58.112 50.000 4.18 0.00 0.00 1.28
1800 1868 0.604780 GCCAGTGCGCCAGATCATAT 60.605 55.000 4.18 0.00 0.00 1.78
1801 1869 1.227645 GCCAGTGCGCCAGATCATA 60.228 57.895 4.18 0.00 0.00 2.15
1802 1870 2.515523 GCCAGTGCGCCAGATCAT 60.516 61.111 4.18 0.00 0.00 2.45
1815 1883 4.596311 GCCCAAATTTTCGGCCAG 57.404 55.556 13.10 0.00 36.63 4.85
1861 1929 0.172578 CGATCTGACGGTTGGCAGTA 59.827 55.000 0.00 0.00 33.90 2.74
1937 2015 1.618074 GGGCTGCATCCTCTCCTTTTT 60.618 52.381 6.53 0.00 0.00 1.94
1938 2016 0.033699 GGGCTGCATCCTCTCCTTTT 60.034 55.000 6.53 0.00 0.00 2.27
1962 2040 1.356624 GAGGCAATGGATTTCGGCG 59.643 57.895 0.00 0.00 0.00 6.46
2081 2179 3.802685 GCACAACGACTTCTACTTCAAGT 59.197 43.478 0.00 0.00 36.77 3.16
2082 2180 4.376450 GCACAACGACTTCTACTTCAAG 57.624 45.455 0.00 0.00 0.00 3.02
2180 2278 0.249868 GTGCTATGATGGGCTGCGTA 60.250 55.000 0.00 0.00 0.00 4.42
2231 2329 2.107378 TGAAATTAGGTGGTGCAGGTCA 59.893 45.455 0.00 0.00 0.00 4.02
2247 2345 5.004922 TGAGTTTTGGTTTTCGCTGAAAT 57.995 34.783 4.91 0.00 31.34 2.17
2303 2402 3.982576 AGTTACTTTTTGCTGGAACCG 57.017 42.857 0.00 0.00 0.00 4.44
2318 2418 5.761165 TGTTTTGCTGGAACCTAAGTTAC 57.239 39.130 0.00 0.00 35.94 2.50
2325 2425 1.119684 GGGTTGTTTTGCTGGAACCT 58.880 50.000 0.00 0.00 38.36 3.50
2370 2471 7.226523 GGAACAGTGGTAAATTTTTGCTTCAAT 59.773 33.333 0.00 0.00 0.00 2.57
2418 2519 3.055891 ACTTGCTCAGTTTTGGTTTTGCT 60.056 39.130 0.00 0.00 27.32 3.91
2419 2520 3.261580 ACTTGCTCAGTTTTGGTTTTGC 58.738 40.909 0.00 0.00 27.32 3.68
2420 2521 5.043248 CCTACTTGCTCAGTTTTGGTTTTG 58.957 41.667 0.00 0.00 36.88 2.44
2421 2522 4.953579 TCCTACTTGCTCAGTTTTGGTTTT 59.046 37.500 0.00 0.00 36.88 2.43
2422 2523 4.532834 TCCTACTTGCTCAGTTTTGGTTT 58.467 39.130 0.00 0.00 36.88 3.27
2423 2524 4.164843 TCCTACTTGCTCAGTTTTGGTT 57.835 40.909 0.00 0.00 36.88 3.67
2424 2525 3.857157 TCCTACTTGCTCAGTTTTGGT 57.143 42.857 0.00 0.00 36.88 3.67
2425 2526 4.761739 TGATTCCTACTTGCTCAGTTTTGG 59.238 41.667 0.00 0.00 36.88 3.28
2426 2527 5.947228 TGATTCCTACTTGCTCAGTTTTG 57.053 39.130 0.00 0.00 36.88 2.44
2427 2528 5.416952 CCATGATTCCTACTTGCTCAGTTTT 59.583 40.000 0.00 0.00 36.88 2.43
2428 2529 4.946157 CCATGATTCCTACTTGCTCAGTTT 59.054 41.667 0.00 0.00 36.88 2.66
2429 2530 4.018960 ACCATGATTCCTACTTGCTCAGTT 60.019 41.667 0.00 0.00 36.88 3.16
2430 2531 3.521126 ACCATGATTCCTACTTGCTCAGT 59.479 43.478 0.00 0.00 39.87 3.41
2431 2532 4.148128 ACCATGATTCCTACTTGCTCAG 57.852 45.455 0.00 0.00 0.00 3.35
2432 2533 4.225942 AGAACCATGATTCCTACTTGCTCA 59.774 41.667 0.00 0.00 0.00 4.26
2433 2534 4.775236 AGAACCATGATTCCTACTTGCTC 58.225 43.478 0.00 0.00 0.00 4.26
2434 2535 4.851639 AGAACCATGATTCCTACTTGCT 57.148 40.909 0.00 0.00 0.00 3.91
2435 2536 4.439289 GCAAGAACCATGATTCCTACTTGC 60.439 45.833 8.31 8.31 46.88 4.01
2436 2537 4.701651 TGCAAGAACCATGATTCCTACTTG 59.298 41.667 0.00 0.00 37.24 3.16
2437 2538 4.922206 TGCAAGAACCATGATTCCTACTT 58.078 39.130 0.00 0.00 0.00 2.24
2438 2539 4.574674 TGCAAGAACCATGATTCCTACT 57.425 40.909 0.00 0.00 0.00 2.57
2439 2540 5.643379 TTTGCAAGAACCATGATTCCTAC 57.357 39.130 0.00 0.00 0.00 3.18
2440 2541 5.047377 GGTTTTGCAAGAACCATGATTCCTA 60.047 40.000 25.67 0.00 44.71 2.94
2441 2542 4.262592 GGTTTTGCAAGAACCATGATTCCT 60.263 41.667 25.67 0.00 44.71 3.36
2442 2543 3.996363 GGTTTTGCAAGAACCATGATTCC 59.004 43.478 25.67 5.53 44.71 3.01
2450 2551 4.249661 TCAGTTTTGGTTTTGCAAGAACC 58.750 39.130 24.68 24.68 45.39 3.62
2451 2552 4.201714 GCTCAGTTTTGGTTTTGCAAGAAC 60.202 41.667 0.00 7.51 0.00 3.01
2452 2553 3.932089 GCTCAGTTTTGGTTTTGCAAGAA 59.068 39.130 0.00 0.00 0.00 2.52
2453 2554 3.056250 TGCTCAGTTTTGGTTTTGCAAGA 60.056 39.130 0.00 0.00 0.00 3.02
2454 2555 3.260740 TGCTCAGTTTTGGTTTTGCAAG 58.739 40.909 0.00 0.00 0.00 4.01
2455 2556 3.325293 TGCTCAGTTTTGGTTTTGCAA 57.675 38.095 0.00 0.00 0.00 4.08
2456 2557 3.260740 CTTGCTCAGTTTTGGTTTTGCA 58.739 40.909 0.00 0.00 0.00 4.08
2543 2683 4.672409 GATTATTTTTGCTGGAACCGGAG 58.328 43.478 9.46 0.00 0.00 4.63
2544 2684 3.127895 CGATTATTTTTGCTGGAACCGGA 59.872 43.478 9.46 0.00 0.00 5.14
2545 2685 3.434637 CGATTATTTTTGCTGGAACCGG 58.565 45.455 0.00 0.00 0.00 5.28
2546 2686 2.851824 GCGATTATTTTTGCTGGAACCG 59.148 45.455 0.00 0.00 0.00 4.44
2547 2687 3.843999 TGCGATTATTTTTGCTGGAACC 58.156 40.909 0.00 0.00 0.00 3.62
2565 2705 0.670546 AGGTTGGACGTTGAGATGCG 60.671 55.000 0.00 0.00 0.00 4.73
2571 2711 1.414919 AGCTACAAGGTTGGACGTTGA 59.585 47.619 17.27 4.01 44.19 3.18
2576 2716 1.610886 GGTGGAGCTACAAGGTTGGAC 60.611 57.143 0.00 0.00 0.00 4.02
2578 2718 0.400213 TGGTGGAGCTACAAGGTTGG 59.600 55.000 0.00 0.00 0.00 3.77
2621 2761 4.845580 AATCAGCTGCGCCCCTCG 62.846 66.667 9.47 0.00 42.12 4.63
2622 2762 3.207669 CAATCAGCTGCGCCCCTC 61.208 66.667 9.47 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.