Multiple sequence alignment - TraesCS5D01G207900

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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 TraesCS5D01G207900 chr5D 100.000 2782 0 0 1 2782 313842355 313845136 0.000000e+00 5138
1 TraesCS5D01G207900 chr5D 87.768 466 52 4 2319 2782 480716588 480717050 8.770000e-150 540
2 TraesCS5D01G207900 chr5A 94.739 2129 89 13 665 2782 407940417 407942533 0.000000e+00 3290
3 TraesCS5D01G207900 chr5A 98.336 661 8 2 1 659 407939787 407940446 0.000000e+00 1157
4 TraesCS5D01G207900 chr5B 93.711 636 33 2 1 635 361542294 361542923 0.000000e+00 946
5 TraesCS5D01G207900 chr2A 89.474 475 40 3 2317 2782 258343211 258342738 2.390000e-165 592
6 TraesCS5D01G207900 chr6B 88.627 466 49 4 2320 2782 155640415 155639951 5.200000e-157 564
7 TraesCS5D01G207900 chr7B 88.627 466 47 5 2320 2782 662492683 662492221 1.870000e-156 562
8 TraesCS5D01G207900 chr2D 88.397 474 46 5 2317 2782 239965645 239965173 1.870000e-156 562
9 TraesCS5D01G207900 chr2D 88.197 466 49 4 2319 2779 345630021 345630485 4.050000e-153 551
10 TraesCS5D01G207900 chr2D 87.846 469 48 5 2320 2782 608810652 608811117 2.440000e-150 542
11 TraesCS5D01G207900 chr7A 88.248 468 43 9 2319 2780 257120444 257119983 1.460000e-152 549


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 TraesCS5D01G207900 chr5D 313842355 313845136 2781 False 5138.0 5138 100.0000 1 2782 1 chr5D.!!$F1 2781
1 TraesCS5D01G207900 chr5A 407939787 407942533 2746 False 2223.5 3290 96.5375 1 2782 2 chr5A.!!$F1 2781
2 TraesCS5D01G207900 chr5B 361542294 361542923 629 False 946.0 946 93.7110 1 635 1 chr5B.!!$F1 634

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
521 526 0.179111 GTGACGATCGCCAATCCTCA 60.179 55.0 16.6 6.63 30.04 3.86 F
1060 1070 0.321298 TAAGTTGAAGGACCTGCGGC 60.321 55.0 0.0 0.00 0.00 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 1754 0.600057 CTTGTTGGGCAAGCCTTCTC 59.400 55.0 11.40 0.0 46.68 2.87 R
2608 2624 0.037697 ATGGTCTCGCGCAACTGTTA 60.038 50.0 8.75 0.0 0.00 2.41 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
330 332 0.970937 CCAAGCGGGAGAGGTAGTCA 60.971 60.000 0.00 0.00 40.01 3.41
476 481 4.646945 ACCAGTATGAGTTCGATCTGATGT 59.353 41.667 0.00 0.00 39.69 3.06
521 526 0.179111 GTGACGATCGCCAATCCTCA 60.179 55.000 16.60 6.63 30.04 3.86
522 527 0.534873 TGACGATCGCCAATCCTCAA 59.465 50.000 16.60 0.00 29.73 3.02
659 664 3.483587 TGGGTGCCCAAGAGAGTC 58.516 61.111 7.63 0.00 44.12 3.36
660 665 2.224159 TGGGTGCCCAAGAGAGTCC 61.224 63.158 7.63 0.00 44.12 3.85
661 666 2.266055 GGTGCCCAAGAGAGTCCG 59.734 66.667 0.00 0.00 0.00 4.79
662 667 2.584391 GGTGCCCAAGAGAGTCCGT 61.584 63.158 0.00 0.00 0.00 4.69
663 668 1.079750 GTGCCCAAGAGAGTCCGTC 60.080 63.158 0.00 0.00 0.00 4.79
664 669 1.533033 TGCCCAAGAGAGTCCGTCA 60.533 57.895 0.00 0.00 0.00 4.35
665 670 1.079750 GCCCAAGAGAGTCCGTCAC 60.080 63.158 0.00 0.00 0.00 3.67
666 671 1.816863 GCCCAAGAGAGTCCGTCACA 61.817 60.000 0.00 0.00 0.00 3.58
667 672 0.679505 CCCAAGAGAGTCCGTCACAA 59.320 55.000 0.00 0.00 0.00 3.33
668 673 1.605712 CCCAAGAGAGTCCGTCACAAC 60.606 57.143 0.00 0.00 0.00 3.32
669 674 1.341531 CCAAGAGAGTCCGTCACAACT 59.658 52.381 0.00 0.00 0.00 3.16
670 675 2.224066 CCAAGAGAGTCCGTCACAACTT 60.224 50.000 0.00 0.00 0.00 2.66
671 676 2.797156 CAAGAGAGTCCGTCACAACTTG 59.203 50.000 0.00 0.00 0.00 3.16
672 677 1.341531 AGAGAGTCCGTCACAACTTGG 59.658 52.381 0.00 0.00 0.00 3.61
673 678 1.340248 GAGAGTCCGTCACAACTTGGA 59.660 52.381 0.00 0.00 0.00 3.53
674 679 1.341531 AGAGTCCGTCACAACTTGGAG 59.658 52.381 0.00 0.00 0.00 3.86
675 680 0.393077 AGTCCGTCACAACTTGGAGG 59.607 55.000 0.00 0.00 0.00 4.30
676 681 0.602905 GTCCGTCACAACTTGGAGGG 60.603 60.000 10.46 10.46 39.74 4.30
677 682 1.052124 TCCGTCACAACTTGGAGGGT 61.052 55.000 13.91 0.00 39.47 4.34
678 683 0.884704 CCGTCACAACTTGGAGGGTG 60.885 60.000 9.27 0.00 35.03 4.61
679 684 0.884704 CGTCACAACTTGGAGGGTGG 60.885 60.000 0.00 0.00 32.29 4.61
680 685 0.537371 GTCACAACTTGGAGGGTGGG 60.537 60.000 0.00 0.00 32.29 4.61
681 686 0.991355 TCACAACTTGGAGGGTGGGT 60.991 55.000 0.00 0.00 32.29 4.51
682 687 0.823356 CACAACTTGGAGGGTGGGTG 60.823 60.000 0.00 0.00 0.00 4.61
683 688 1.903404 CAACTTGGAGGGTGGGTGC 60.903 63.158 0.00 0.00 0.00 5.01
684 689 3.146828 AACTTGGAGGGTGGGTGCC 62.147 63.158 0.00 0.00 0.00 5.01
694 699 3.483587 TGGGTGCCCAAGAGAGTC 58.516 61.111 7.63 0.00 44.12 3.36
813 823 3.507233 TCCACAAAAGAGTGCATGATTCC 59.493 43.478 0.00 0.00 38.18 3.01
816 826 3.438087 ACAAAAGAGTGCATGATTCCTCG 59.562 43.478 0.00 0.00 0.00 4.63
876 886 2.224018 CCATCCTAGTGCTCTCTCAAGC 60.224 54.545 0.00 0.00 42.82 4.01
881 891 1.336131 AGTGCTCTCTCAAGCTGTGA 58.664 50.000 0.00 0.00 42.94 3.58
910 920 3.781770 GAGAGCGGGATCTGTGGCG 62.782 68.421 0.00 0.00 0.00 5.69
924 934 3.047877 GGCGTGGGAGTTTCGTGG 61.048 66.667 0.00 0.00 0.00 4.94
966 976 1.382833 GGGGGAGGTAGGTGGAGAC 60.383 68.421 0.00 0.00 0.00 3.36
1054 1064 4.095211 AGTAGAGGGTAAGTTGAAGGACC 58.905 47.826 0.00 0.00 0.00 4.46
1058 1068 1.439679 GGTAAGTTGAAGGACCTGCG 58.560 55.000 0.00 0.00 0.00 5.18
1060 1070 0.321298 TAAGTTGAAGGACCTGCGGC 60.321 55.000 0.00 0.00 0.00 6.53
1066 1076 2.731691 GAAGGACCTGCGGCTGTCAA 62.732 60.000 19.63 0.00 33.09 3.18
1081 1091 3.313526 GCTGTCAAAAGCTGAGAAGAACA 59.686 43.478 0.00 0.00 40.20 3.18
1115 1125 0.886563 AAGAAGCAAGCATGTGCCTC 59.113 50.000 4.77 2.18 46.14 4.70
1116 1126 1.136147 GAAGCAAGCATGTGCCTCG 59.864 57.895 4.77 0.00 46.14 4.63
1136 1146 2.965716 AAGGCGAGCAAGCACCAAGT 62.966 55.000 5.80 0.00 39.27 3.16
1157 1167 7.287927 CCAAGTAGTGGGTAAGATTCTCTCATA 59.712 40.741 0.00 0.00 44.64 2.15
1226 1236 2.151202 GTGCCCGTTCTCAGAAATTCA 58.849 47.619 0.00 0.00 0.00 2.57
1248 1258 3.648339 TGCAAAGATCTTGGCAGAAAC 57.352 42.857 29.89 4.83 43.99 2.78
1308 1318 2.978156 AAGCTTTGGAAGATGGACCA 57.022 45.000 0.00 0.00 0.00 4.02
1390 1401 7.329588 ACGAGTATGAATTTAAAACCATCCC 57.670 36.000 8.41 3.34 0.00 3.85
1441 1452 7.295672 TCCTATGGGGATGATGAGTAAAGAAAT 59.704 37.037 0.00 0.00 39.58 2.17
1501 1512 8.355169 CCTTAATGTGGATTTAGATGACAATGG 58.645 37.037 0.00 0.00 0.00 3.16
1537 1548 5.127031 GGGCTTTTATGAGGATTAAAGTGCA 59.873 40.000 0.00 0.00 32.88 4.57
1541 1552 8.624776 GCTTTTATGAGGATTAAAGTGCATACT 58.375 33.333 0.00 0.00 39.32 2.12
1561 1572 7.332182 GCATACTGATATTACAGCTCCCTTAAC 59.668 40.741 0.00 0.00 41.06 2.01
1568 1579 3.528597 ACAGCTCCCTTAACGAGATTC 57.471 47.619 0.00 0.00 0.00 2.52
1569 1580 2.159226 ACAGCTCCCTTAACGAGATTCG 60.159 50.000 0.00 0.00 46.93 3.34
1603 1614 1.066152 TGATGACGATGAGGAAGAGCG 59.934 52.381 0.00 0.00 0.00 5.03
1740 1751 3.459232 ACTGTGGTATCATCGGACATG 57.541 47.619 0.00 0.00 0.00 3.21
1743 1754 2.138320 GTGGTATCATCGGACATGCAG 58.862 52.381 0.00 0.00 0.00 4.41
1835 1848 0.767375 AAGGGCAGCTCAAGTGAAGA 59.233 50.000 0.00 0.00 0.00 2.87
1838 1851 1.956477 GGGCAGCTCAAGTGAAGAAAA 59.044 47.619 0.00 0.00 0.00 2.29
1846 1859 7.308229 GCAGCTCAAGTGAAGAAAAGAATAGAA 60.308 37.037 0.00 0.00 0.00 2.10
1879 1892 1.783071 GGGGGTTTGGAGAAACAACA 58.217 50.000 0.00 0.00 42.95 3.33
1890 1904 3.939592 GGAGAAACAACAGTATGGGTAGC 59.060 47.826 0.00 0.00 43.62 3.58
1912 1926 2.258013 GGCAGCAAACACGGTAGCA 61.258 57.895 0.00 0.00 0.00 3.49
1961 1975 5.546887 TGATGGATAGAGCTGATGGAGAAAT 59.453 40.000 0.00 0.00 0.00 2.17
1977 1991 5.133830 TGGAGAAATATTAAGGGAAGGGGAC 59.866 44.000 0.00 0.00 0.00 4.46
2032 2046 0.037447 AGGAAGAACAAGCTGGCTCC 59.963 55.000 0.00 0.00 0.00 4.70
2134 2149 0.112606 AGTCGACTGTCTTGGAGGGA 59.887 55.000 19.30 0.00 0.00 4.20
2138 2153 0.461961 GACTGTCTTGGAGGGATCCG 59.538 60.000 5.45 0.00 0.00 4.18
2148 2163 1.673033 GGAGGGATCCGCATCAATACG 60.673 57.143 5.45 0.00 0.00 3.06
2149 2164 1.272490 GAGGGATCCGCATCAATACGA 59.728 52.381 5.45 0.00 0.00 3.43
2192 2207 2.926200 CAGACATCCGAAGTTGTAGCTG 59.074 50.000 0.00 0.00 0.00 4.24
2246 2261 6.705381 TGCTGGTTTCAATTCCAATAAAACAG 59.295 34.615 7.21 7.21 45.27 3.16
2248 2263 7.116805 GCTGGTTTCAATTCCAATAAAACAGAG 59.883 37.037 14.13 8.86 45.30 3.35
2278 2293 4.488879 GAGCAGAAATTTGTAAAGGGCAG 58.511 43.478 0.00 0.00 0.00 4.85
2283 2298 5.922544 CAGAAATTTGTAAAGGGCAGTCAAG 59.077 40.000 0.00 0.00 0.00 3.02
2297 2312 2.050144 AGTCAAGTGGAGGAAGAAGCA 58.950 47.619 0.00 0.00 0.00 3.91
2328 2343 5.360144 GGAGTAGTTGCTAAGTGTAGGATCA 59.640 44.000 0.00 0.00 0.00 2.92
2433 2449 5.880054 TTAGCAATTCTACCAAGTCAAGC 57.120 39.130 0.00 0.00 0.00 4.01
2470 2486 3.133691 CAAGTCTAAGAGTTGTGCAGCA 58.866 45.455 0.00 0.00 37.96 4.41
2479 2495 5.323371 AGAGTTGTGCAGCAAAAAGTAAA 57.677 34.783 0.00 0.00 39.03 2.01
2510 2526 5.758296 GCATATGAACGTAAAGGAGGAATCA 59.242 40.000 6.97 0.00 0.00 2.57
2515 2531 5.245301 TGAACGTAAAGGAGGAATCAGAGAA 59.755 40.000 0.00 0.00 0.00 2.87
2523 2539 6.131972 AGGAGGAATCAGAGAAATCAAACA 57.868 37.500 0.00 0.00 0.00 2.83
2545 2561 6.877236 ACACAATGAAGACAAGGTGATTTTT 58.123 32.000 0.00 0.00 37.47 1.94
2546 2562 6.980397 ACACAATGAAGACAAGGTGATTTTTC 59.020 34.615 0.00 0.00 37.47 2.29
2573 2589 3.200483 GTTCCGATGGGTGGTGTTATAC 58.800 50.000 0.00 0.00 33.83 1.47
2617 2633 1.534729 CCAAGGAGGGTAACAGTTGC 58.465 55.000 0.00 0.00 39.74 4.17
2618 2634 1.156736 CAAGGAGGGTAACAGTTGCG 58.843 55.000 0.00 0.00 39.74 4.85
2619 2635 0.605589 AAGGAGGGTAACAGTTGCGC 60.606 55.000 10.05 10.05 39.74 6.09
2620 2636 2.388232 GGAGGGTAACAGTTGCGCG 61.388 63.158 11.89 0.00 39.74 6.86
2662 2678 1.014564 CGAAGGGTCCACGAAGAAGC 61.015 60.000 0.00 0.00 0.00 3.86
2683 2699 3.364964 GCAAACTTGTCTATTCCACCACG 60.365 47.826 0.00 0.00 0.00 4.94
2721 2737 2.500504 GGACTAACCTCACTTGGGGTAG 59.499 54.545 0.00 4.46 46.46 3.18
2735 2751 4.760530 TGGGGTAGATCTTCATGAAGTG 57.239 45.455 29.80 11.36 39.38 3.16
2741 2757 2.437281 AGATCTTCATGAAGTGGGCGAT 59.563 45.455 29.80 17.76 39.38 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.303747 ACAAATTGGATAAACGCATTCGA 57.696 34.783 0.00 0.00 39.41 3.71
476 481 4.331968 CTTGCATAAACCAGAACTACCCA 58.668 43.478 0.00 0.00 0.00 4.51
521 526 1.429463 GATTTCTCGCACTGGACGTT 58.571 50.000 0.00 0.00 0.00 3.99
522 527 0.732880 CGATTTCTCGCACTGGACGT 60.733 55.000 0.00 0.00 38.20 4.34
659 664 0.884704 CACCCTCCAAGTTGTGACGG 60.885 60.000 1.45 5.26 0.00 4.79
660 665 0.884704 CCACCCTCCAAGTTGTGACG 60.885 60.000 1.45 0.00 0.00 4.35
661 666 0.537371 CCCACCCTCCAAGTTGTGAC 60.537 60.000 1.45 0.00 0.00 3.67
662 667 0.991355 ACCCACCCTCCAAGTTGTGA 60.991 55.000 1.45 0.00 0.00 3.58
663 668 0.823356 CACCCACCCTCCAAGTTGTG 60.823 60.000 1.45 0.00 0.00 3.33
664 669 1.536676 CACCCACCCTCCAAGTTGT 59.463 57.895 1.45 0.00 0.00 3.32
665 670 1.903404 GCACCCACCCTCCAAGTTG 60.903 63.158 0.00 0.00 0.00 3.16
666 671 2.520968 GCACCCACCCTCCAAGTT 59.479 61.111 0.00 0.00 0.00 2.66
667 672 3.580319 GGCACCCACCCTCCAAGT 61.580 66.667 0.00 0.00 0.00 3.16
680 685 0.036858 GGACAGACTCTCTTGGGCAC 60.037 60.000 0.00 0.00 0.00 5.01
681 686 0.471780 TGGACAGACTCTCTTGGGCA 60.472 55.000 0.00 0.00 0.00 5.36
682 687 0.036858 GTGGACAGACTCTCTTGGGC 60.037 60.000 0.00 0.00 0.00 5.36
683 688 1.001406 GTGTGGACAGACTCTCTTGGG 59.999 57.143 0.00 0.00 0.00 4.12
684 689 1.688735 TGTGTGGACAGACTCTCTTGG 59.311 52.381 1.25 0.00 0.00 3.61
685 690 3.006217 TCATGTGTGGACAGACTCTCTTG 59.994 47.826 1.25 0.00 34.87 3.02
686 691 3.006323 GTCATGTGTGGACAGACTCTCTT 59.994 47.826 1.25 0.00 34.87 2.85
687 692 2.560542 GTCATGTGTGGACAGACTCTCT 59.439 50.000 1.25 0.00 34.87 3.10
688 693 2.669670 CGTCATGTGTGGACAGACTCTC 60.670 54.545 1.25 0.00 34.87 3.20
689 694 1.270826 CGTCATGTGTGGACAGACTCT 59.729 52.381 1.25 0.00 34.87 3.24
690 695 1.670087 CCGTCATGTGTGGACAGACTC 60.670 57.143 1.25 0.00 34.87 3.36
691 696 0.318441 CCGTCATGTGTGGACAGACT 59.682 55.000 1.25 0.00 34.87 3.24
692 697 0.033504 ACCGTCATGTGTGGACAGAC 59.966 55.000 7.47 0.00 34.87 3.51
693 698 0.756294 AACCGTCATGTGTGGACAGA 59.244 50.000 7.47 0.00 34.87 3.41
694 699 1.531149 GAAACCGTCATGTGTGGACAG 59.469 52.381 7.47 0.00 34.87 3.51
720 725 2.383527 CCACGAAGTCGCCAGAAGC 61.384 63.158 0.00 0.00 41.61 3.86
783 793 8.149647 TCATGCACTCTTTTGTGGATTTAAAAT 58.850 29.630 0.00 0.00 44.56 1.82
787 797 6.839124 ATCATGCACTCTTTTGTGGATTTA 57.161 33.333 0.00 0.00 44.56 1.40
813 823 2.050895 CGCCGCTACCAGATCGAG 60.051 66.667 0.00 0.00 0.00 4.04
816 826 2.659897 CTGCGCCGCTACCAGATC 60.660 66.667 11.67 0.00 0.00 2.75
876 886 1.824230 CTCTCAGGTTCTCCCTCACAG 59.176 57.143 0.00 0.00 43.86 3.66
898 908 3.391665 CTCCCACGCCACAGATCCC 62.392 68.421 0.00 0.00 0.00 3.85
910 920 0.463116 ACACACCACGAAACTCCCAC 60.463 55.000 0.00 0.00 0.00 4.61
924 934 4.566987 CCTCCCTACAAGAACTAACACAC 58.433 47.826 0.00 0.00 0.00 3.82
1054 1064 1.081641 CAGCTTTTGACAGCCGCAG 60.082 57.895 0.00 0.00 41.12 5.18
1058 1068 2.498167 TCTTCTCAGCTTTTGACAGCC 58.502 47.619 0.00 0.00 41.12 4.85
1060 1070 5.490139 TTGTTCTTCTCAGCTTTTGACAG 57.510 39.130 0.00 0.00 0.00 3.51
1066 1076 5.829924 TCCTGATTTTGTTCTTCTCAGCTTT 59.170 36.000 0.00 0.00 33.58 3.51
1081 1091 3.282885 GCTTCTTCCCGATCCTGATTTT 58.717 45.455 0.00 0.00 0.00 1.82
1115 1125 3.793144 GGTGCTTGCTCGCCTTCG 61.793 66.667 0.00 0.00 33.93 3.79
1116 1126 2.192608 CTTGGTGCTTGCTCGCCTTC 62.193 60.000 5.62 0.00 37.51 3.46
1149 1159 4.744867 GCTTTTGCCTGCCTATATGAGAGA 60.745 45.833 0.00 0.00 40.15 3.10
1226 1236 2.574006 TCTGCCAAGATCTTTGCACT 57.426 45.000 25.76 0.00 36.48 4.40
1248 1258 6.924913 TCATGGATATTAGAGAGGAACCTG 57.075 41.667 0.00 0.00 0.00 4.00
1335 1345 2.799126 TTGGTGCGTAATCCTCCATT 57.201 45.000 0.00 0.00 0.00 3.16
1349 1359 9.961265 TCATACTCGTTATAGTCTTATTTGGTG 57.039 33.333 0.00 0.00 0.00 4.17
1390 1401 3.071023 TCCATAGGCTCTTACCCAAATCG 59.929 47.826 0.00 0.00 0.00 3.34
1441 1452 3.073503 TCGATCTCCTACGAAATCCCCTA 59.926 47.826 0.00 0.00 35.62 3.53
1451 1462 1.961394 TCCCCAATTCGATCTCCTACG 59.039 52.381 0.00 0.00 0.00 3.51
1501 1512 4.772678 AAGCCCCCATTGCTTCTC 57.227 55.556 0.00 0.00 45.58 2.87
1537 1548 7.450634 TCGTTAAGGGAGCTGTAATATCAGTAT 59.549 37.037 0.00 0.00 37.70 2.12
1541 1552 5.831525 TCTCGTTAAGGGAGCTGTAATATCA 59.168 40.000 0.00 0.00 0.00 2.15
1551 1562 1.407979 TCCGAATCTCGTTAAGGGAGC 59.592 52.381 0.00 0.00 38.40 4.70
1561 1572 5.291858 TCAGTGATCAAAATTCCGAATCTCG 59.708 40.000 0.00 0.00 40.07 4.04
1568 1579 4.329801 TCGTCATCAGTGATCAAAATTCCG 59.670 41.667 1.56 0.00 36.60 4.30
1569 1580 5.801350 TCGTCATCAGTGATCAAAATTCC 57.199 39.130 1.56 0.00 36.60 3.01
1721 1732 2.138320 GCATGTCCGATGATACCACAG 58.862 52.381 0.00 0.00 0.00 3.66
1740 1751 1.604593 TTGGGCAAGCCTTCTCTGC 60.605 57.895 11.40 0.00 36.10 4.26
1743 1754 0.600057 CTTGTTGGGCAAGCCTTCTC 59.400 55.000 11.40 0.00 46.68 2.87
1835 1848 4.626172 GGTCGCTCGAACTTCTATTCTTTT 59.374 41.667 0.00 0.00 0.00 2.27
1838 1851 2.223294 CGGTCGCTCGAACTTCTATTCT 60.223 50.000 5.76 0.00 0.00 2.40
1868 1881 3.939592 GCTACCCATACTGTTGTTTCTCC 59.060 47.826 0.00 0.00 0.00 3.71
1870 1883 3.596214 CGCTACCCATACTGTTGTTTCT 58.404 45.455 0.00 0.00 0.00 2.52
1871 1884 2.676342 CCGCTACCCATACTGTTGTTTC 59.324 50.000 0.00 0.00 0.00 2.78
1872 1885 2.303600 TCCGCTACCCATACTGTTGTTT 59.696 45.455 0.00 0.00 0.00 2.83
1875 1888 1.202533 CCTCCGCTACCCATACTGTTG 60.203 57.143 0.00 0.00 0.00 3.33
1876 1889 1.120530 CCTCCGCTACCCATACTGTT 58.879 55.000 0.00 0.00 0.00 3.16
1878 1891 1.367840 GCCTCCGCTACCCATACTG 59.632 63.158 0.00 0.00 0.00 2.74
1879 1892 1.075525 TGCCTCCGCTACCCATACT 60.076 57.895 0.00 0.00 35.36 2.12
1890 1904 3.726517 CCGTGTTTGCTGCCTCCG 61.727 66.667 0.00 0.00 0.00 4.63
1912 1926 1.455822 TTCCTCCAGGTTGGTCCATT 58.544 50.000 0.00 0.00 39.03 3.16
1961 1975 4.080186 CCTTTTCGTCCCCTTCCCTTAATA 60.080 45.833 0.00 0.00 0.00 0.98
1977 1991 2.228103 GGGGCTTGTAACTTCCTTTTCG 59.772 50.000 0.00 0.00 0.00 3.46
2000 2014 7.013369 AGCTTGTTCTTCCTTGGTTACTTTTAG 59.987 37.037 0.00 0.00 0.00 1.85
2001 2015 6.831868 AGCTTGTTCTTCCTTGGTTACTTTTA 59.168 34.615 0.00 0.00 0.00 1.52
2006 2020 3.253432 CCAGCTTGTTCTTCCTTGGTTAC 59.747 47.826 0.00 0.00 0.00 2.50
2048 2062 7.236674 CAAGTTGATTGTCTGCAAAATTCAA 57.763 32.000 0.00 0.00 38.21 2.69
2062 2077 8.925161 TTTCCTTTAGAACAACAAGTTGATTG 57.075 30.769 18.90 12.33 42.93 2.67
2134 2149 1.337260 GCCTCTCGTATTGATGCGGAT 60.337 52.381 0.00 0.00 36.53 4.18
2138 2153 1.506493 CCTGCCTCTCGTATTGATGC 58.494 55.000 0.00 0.00 0.00 3.91
2192 2207 0.778083 AGGTTCAGTTCCTTTCCCCC 59.222 55.000 0.00 0.00 30.18 5.40
2246 2261 1.506025 ATTTCTGCTCCTCTCCCCTC 58.494 55.000 0.00 0.00 0.00 4.30
2248 2263 2.291217 ACAAATTTCTGCTCCTCTCCCC 60.291 50.000 0.00 0.00 0.00 4.81
2278 2293 2.037772 TCTGCTTCTTCCTCCACTTGAC 59.962 50.000 0.00 0.00 0.00 3.18
2283 2298 3.254411 CCTTTTTCTGCTTCTTCCTCCAC 59.746 47.826 0.00 0.00 0.00 4.02
2297 2312 6.592870 ACACTTAGCAACTACTCCTTTTTCT 58.407 36.000 0.00 0.00 0.00 2.52
2328 2343 5.538877 TCATCCCCCTCTAGACATACTTTT 58.461 41.667 0.00 0.00 0.00 2.27
2402 2418 7.284489 ACTTGGTAGAATTGCTAAAACTTGTCA 59.716 33.333 0.00 0.00 0.00 3.58
2412 2428 4.905429 TGCTTGACTTGGTAGAATTGCTA 58.095 39.130 0.00 0.00 0.00 3.49
2433 2449 2.744202 GACTTGCATGTGTAGGGTCTTG 59.256 50.000 10.37 0.00 0.00 3.02
2479 2495 6.170506 TCCTTTACGTTCATATGCAAAGTCT 58.829 36.000 0.00 0.00 0.00 3.24
2510 2526 7.572523 TGTCTTCATTGTGTTTGATTTCTCT 57.427 32.000 0.00 0.00 0.00 3.10
2515 2531 6.096705 TCACCTTGTCTTCATTGTGTTTGATT 59.903 34.615 0.00 0.00 31.69 2.57
2523 2539 6.208644 CGAAAAATCACCTTGTCTTCATTGT 58.791 36.000 0.00 0.00 0.00 2.71
2545 2561 4.444838 CCCATCGGAACCACGCGA 62.445 66.667 15.93 0.00 0.00 5.87
2546 2562 4.752879 ACCCATCGGAACCACGCG 62.753 66.667 3.53 3.53 0.00 6.01
2607 2623 0.942410 TGGTCTCGCGCAACTGTTAC 60.942 55.000 8.75 0.00 0.00 2.50
2608 2624 0.037697 ATGGTCTCGCGCAACTGTTA 60.038 50.000 8.75 0.00 0.00 2.41
2609 2625 1.301716 ATGGTCTCGCGCAACTGTT 60.302 52.632 8.75 0.00 0.00 3.16
2610 2626 2.029288 CATGGTCTCGCGCAACTGT 61.029 57.895 8.75 0.00 0.00 3.55
2611 2627 2.743752 CCATGGTCTCGCGCAACTG 61.744 63.158 8.75 0.00 0.00 3.16
2612 2628 2.434884 CCATGGTCTCGCGCAACT 60.435 61.111 8.75 0.00 0.00 3.16
2613 2629 2.434185 TCCATGGTCTCGCGCAAC 60.434 61.111 12.58 0.89 0.00 4.17
2614 2630 2.125552 CTCCATGGTCTCGCGCAA 60.126 61.111 12.58 0.00 0.00 4.85
2615 2631 4.147449 CCTCCATGGTCTCGCGCA 62.147 66.667 12.58 0.00 0.00 6.09
2616 2632 4.899239 CCCTCCATGGTCTCGCGC 62.899 72.222 12.58 0.00 0.00 6.86
2617 2633 4.899239 GCCCTCCATGGTCTCGCG 62.899 72.222 12.58 0.00 0.00 5.87
2618 2634 3.453070 GAGCCCTCCATGGTCTCGC 62.453 68.421 12.58 9.49 0.00 5.03
2619 2635 2.818132 GAGCCCTCCATGGTCTCG 59.182 66.667 12.58 0.00 0.00 4.04
2662 2678 3.188460 CCGTGGTGGAATAGACAAGTTTG 59.812 47.826 0.00 0.00 42.00 2.93
2683 2699 0.038892 TCCTTCGTGTGACGTAAGCC 60.039 55.000 0.00 0.00 43.14 4.35
2721 2737 2.315925 TCGCCCACTTCATGAAGATC 57.684 50.000 36.15 20.97 40.79 2.75
2741 2757 2.039879 GGAGTTTGTAAGGGCAAGGAGA 59.960 50.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.