Multiple sequence alignment - TraesCS4D01G280700

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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 TraesCS4D01G280700 chr4D 100.000 3483 0 0 1 3483 451681873 451685355 0.000000e+00 6433.0
1 TraesCS4D01G280700 chr4D 85.270 611 45 21 692 1284 451640233 451640816 3.870000e-164 588.0
2 TraesCS4D01G280700 chr4D 81.432 447 78 4 2623 3068 40567681 40568123 9.190000e-96 361.0
3 TraesCS4D01G280700 chr4D 90.083 121 11 1 25 145 14524724 14524843 4.650000e-34 156.0
4 TraesCS4D01G280700 chr4D 93.878 49 2 1 716 763 451640320 451640368 4.820000e-09 73.1
5 TraesCS4D01G280700 chr4B 93.514 2775 99 29 758 3480 565090409 565093154 0.000000e+00 4052.0
6 TraesCS4D01G280700 chr4B 80.440 455 82 6 2616 3068 59236273 59236722 1.200000e-89 340.0
7 TraesCS4D01G280700 chr4B 80.682 352 62 5 2616 2965 59226828 59227175 5.730000e-68 268.0
8 TraesCS4D01G280700 chr4A 91.213 2242 94 37 1313 3480 15124496 15126708 0.000000e+00 2953.0
9 TraesCS4D01G280700 chr4A 89.753 527 33 3 776 1295 15123682 15124194 0.000000e+00 654.0
10 TraesCS4D01G280700 chr4A 82.781 453 75 2 2616 3068 559067761 559068210 5.410000e-108 401.0
11 TraesCS4D01G280700 chr7D 98.882 626 6 1 1 626 457598059 457598683 0.000000e+00 1116.0
12 TraesCS4D01G280700 chr7D 100.000 29 0 0 627 655 457598709 457598737 2.000000e-03 54.7
13 TraesCS4D01G280700 chr5A 91.228 627 43 5 1 626 118660142 118659527 0.000000e+00 843.0
14 TraesCS4D01G280700 chr5A 96.970 33 1 0 627 659 118659501 118659469 4.860000e-04 56.5
15 TraesCS4D01G280700 chr5D 83.240 358 42 9 271 626 285159081 285158740 2.610000e-81 313.0
16 TraesCS4D01G280700 chr1A 73.712 563 127 18 2646 3196 474428443 474427890 2.120000e-47 200.0
17 TraesCS4D01G280700 chr6D 89.256 121 12 1 25 145 417886848 417886967 2.170000e-32 150.0


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 TraesCS4D01G280700 chr4D 451681873 451685355 3482 False 6433.00 6433 100.000 1 3483 1 chr4D.!!$F3 3482
1 TraesCS4D01G280700 chr4D 451640233 451640816 583 False 330.55 588 89.574 692 1284 2 chr4D.!!$F4 592
2 TraesCS4D01G280700 chr4B 565090409 565093154 2745 False 4052.00 4052 93.514 758 3480 1 chr4B.!!$F3 2722
3 TraesCS4D01G280700 chr4A 15123682 15126708 3026 False 1803.50 2953 90.483 776 3480 2 chr4A.!!$F2 2704
4 TraesCS4D01G280700 chr7D 457598059 457598737 678 False 585.35 1116 99.441 1 655 2 chr7D.!!$F1 654
5 TraesCS4D01G280700 chr5A 118659469 118660142 673 True 449.75 843 94.099 1 659 2 chr5A.!!$R1 658

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
641 642 0.608035 GGGCAATCAGTCGGTTGGAA 60.608 55.0 0.0 0.0 0.00 3.53 F
1009 1034 0.694444 ACCGTATCCAATGGCTCCCT 60.694 55.0 0.0 0.0 37.86 4.20 F
1584 1898 0.393077 CCCGATCTATCCGCCTGTTT 59.607 55.0 0.0 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 1842 0.318360 GGCAAACCCGTCGGAAAAAG 60.318 55.0 14.39 0.0 0.00 2.27 R
2076 2420 1.145803 GACCAAGTGTCCACGCTTAC 58.854 55.0 5.22 0.0 44.06 2.34 R
2574 2955 2.128771 ACGTGATTGCCTATTTGCCT 57.871 45.0 0.00 0.0 0.00 4.75 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
52 53 4.379143 CGTCGCTCACCGTCGTGA 62.379 66.667 0.00 0.00 46.91 4.35
609 610 2.687566 GAGGTGGGTGGGTCCGAT 60.688 66.667 0.00 0.00 37.00 4.18
628 629 4.778143 GGACGCGTGGAGGGCAAT 62.778 66.667 20.70 0.00 36.05 3.56
629 630 3.195698 GACGCGTGGAGGGCAATC 61.196 66.667 20.70 0.00 36.05 2.67
630 631 3.950794 GACGCGTGGAGGGCAATCA 62.951 63.158 20.70 0.00 36.05 2.57
631 632 3.197790 CGCGTGGAGGGCAATCAG 61.198 66.667 0.00 0.00 0.00 2.90
632 633 2.045926 GCGTGGAGGGCAATCAGT 60.046 61.111 0.00 0.00 0.00 3.41
633 634 2.109126 GCGTGGAGGGCAATCAGTC 61.109 63.158 0.00 0.00 0.00 3.51
634 635 1.811266 CGTGGAGGGCAATCAGTCG 60.811 63.158 0.00 0.00 0.00 4.18
635 636 1.450312 GTGGAGGGCAATCAGTCGG 60.450 63.158 0.00 0.00 0.00 4.79
636 637 1.918293 TGGAGGGCAATCAGTCGGT 60.918 57.895 0.00 0.00 0.00 4.69
637 638 1.299976 GGAGGGCAATCAGTCGGTT 59.700 57.895 0.00 0.00 0.00 4.44
638 639 1.026718 GGAGGGCAATCAGTCGGTTG 61.027 60.000 0.00 0.00 0.00 3.77
639 640 1.002134 AGGGCAATCAGTCGGTTGG 60.002 57.895 0.00 0.00 0.00 3.77
640 641 1.002624 GGGCAATCAGTCGGTTGGA 60.003 57.895 0.00 0.00 0.00 3.53
641 642 0.608035 GGGCAATCAGTCGGTTGGAA 60.608 55.000 0.00 0.00 0.00 3.53
642 643 0.804989 GGCAATCAGTCGGTTGGAAG 59.195 55.000 0.00 0.00 0.00 3.46
643 644 0.804989 GCAATCAGTCGGTTGGAAGG 59.195 55.000 0.00 0.00 0.00 3.46
644 645 1.610624 GCAATCAGTCGGTTGGAAGGA 60.611 52.381 0.00 0.00 0.00 3.36
645 646 2.778299 CAATCAGTCGGTTGGAAGGAA 58.222 47.619 0.00 0.00 0.00 3.36
646 647 3.347216 CAATCAGTCGGTTGGAAGGAAT 58.653 45.455 0.00 0.00 0.00 3.01
647 648 4.513442 CAATCAGTCGGTTGGAAGGAATA 58.487 43.478 0.00 0.00 0.00 1.75
648 649 3.604875 TCAGTCGGTTGGAAGGAATAC 57.395 47.619 0.00 0.00 0.00 1.89
649 650 3.170717 TCAGTCGGTTGGAAGGAATACT 58.829 45.455 0.00 0.00 0.00 2.12
650 651 3.581332 TCAGTCGGTTGGAAGGAATACTT 59.419 43.478 0.00 0.00 43.65 2.24
651 652 4.041198 TCAGTCGGTTGGAAGGAATACTTT 59.959 41.667 0.00 0.00 40.21 2.66
652 653 4.760204 CAGTCGGTTGGAAGGAATACTTTT 59.240 41.667 0.00 0.00 40.21 2.27
653 654 5.001874 AGTCGGTTGGAAGGAATACTTTTC 58.998 41.667 0.00 0.00 40.21 2.29
654 655 4.155462 GTCGGTTGGAAGGAATACTTTTCC 59.845 45.833 0.00 0.00 40.21 3.13
655 656 4.076394 CGGTTGGAAGGAATACTTTTCCA 58.924 43.478 7.10 1.27 46.33 3.53
661 662 7.906199 TGGAAGGAATACTTTTCCAAAAAGA 57.094 32.000 16.72 3.83 45.36 2.52
662 663 7.951591 TGGAAGGAATACTTTTCCAAAAAGAG 58.048 34.615 16.72 0.00 45.36 2.85
663 664 7.563556 TGGAAGGAATACTTTTCCAAAAAGAGT 59.436 33.333 16.72 1.56 45.36 3.24
664 665 8.082852 GGAAGGAATACTTTTCCAAAAAGAGTC 58.917 37.037 16.72 10.65 40.21 3.36
665 666 7.526142 AGGAATACTTTTCCAAAAAGAGTCC 57.474 36.000 16.72 16.70 41.00 3.85
666 667 7.066781 AGGAATACTTTTCCAAAAAGAGTCCA 58.933 34.615 16.72 0.56 41.00 4.02
667 668 7.730332 AGGAATACTTTTCCAAAAAGAGTCCAT 59.270 33.333 16.72 8.34 41.00 3.41
668 669 9.020731 GGAATACTTTTCCAAAAAGAGTCCATA 57.979 33.333 16.72 1.23 38.45 2.74
671 672 9.981460 ATACTTTTCCAAAAAGAGTCCATATCT 57.019 29.630 16.72 0.00 0.00 1.98
672 673 8.712228 ACTTTTCCAAAAAGAGTCCATATCTT 57.288 30.769 16.72 0.00 38.65 2.40
673 674 8.797438 ACTTTTCCAAAAAGAGTCCATATCTTC 58.203 33.333 16.72 0.00 35.98 2.87
674 675 7.703058 TTTCCAAAAAGAGTCCATATCTTCC 57.297 36.000 0.00 0.00 35.98 3.46
675 676 6.387192 TCCAAAAAGAGTCCATATCTTCCA 57.613 37.500 0.00 0.00 35.98 3.53
676 677 6.973642 TCCAAAAAGAGTCCATATCTTCCAT 58.026 36.000 0.00 0.00 35.98 3.41
677 678 6.830324 TCCAAAAAGAGTCCATATCTTCCATG 59.170 38.462 0.00 0.00 35.98 3.66
678 679 6.830324 CCAAAAAGAGTCCATATCTTCCATGA 59.170 38.462 0.00 0.00 35.98 3.07
679 680 7.504911 CCAAAAAGAGTCCATATCTTCCATGAT 59.495 37.037 0.00 0.00 35.98 2.45
680 681 8.910944 CAAAAAGAGTCCATATCTTCCATGATT 58.089 33.333 0.00 0.00 35.98 2.57
681 682 9.484806 AAAAAGAGTCCATATCTTCCATGATTT 57.515 29.630 0.00 0.00 35.98 2.17
682 683 9.484806 AAAAGAGTCCATATCTTCCATGATTTT 57.515 29.630 0.00 0.00 35.98 1.82
683 684 8.688747 AAGAGTCCATATCTTCCATGATTTTC 57.311 34.615 0.00 0.00 31.29 2.29
684 685 8.043429 AGAGTCCATATCTTCCATGATTTTCT 57.957 34.615 0.00 0.00 0.00 2.52
685 686 8.501070 AGAGTCCATATCTTCCATGATTTTCTT 58.499 33.333 0.00 0.00 0.00 2.52
686 687 9.784531 GAGTCCATATCTTCCATGATTTTCTTA 57.215 33.333 0.00 0.00 0.00 2.10
687 688 9.790344 AGTCCATATCTTCCATGATTTTCTTAG 57.210 33.333 0.00 0.00 0.00 2.18
688 689 9.007901 GTCCATATCTTCCATGATTTTCTTAGG 57.992 37.037 0.00 0.00 0.00 2.69
689 690 8.166061 TCCATATCTTCCATGATTTTCTTAGGG 58.834 37.037 0.00 0.00 0.00 3.53
690 691 8.166061 CCATATCTTCCATGATTTTCTTAGGGA 58.834 37.037 0.00 0.00 0.00 4.20
720 721 5.480073 TCCCATGATTAACAACCCTGAAAAG 59.520 40.000 0.00 0.00 0.00 2.27
753 754 6.018262 TCCGTGATTAATAAAGCGAATCCTTG 60.018 38.462 0.00 0.00 0.00 3.61
882 907 3.140623 GGGTCCGCGGCTTATTAAAATA 58.859 45.455 23.51 0.00 0.00 1.40
994 1019 3.720193 CGACCGTCTCGTCACCGT 61.720 66.667 0.00 0.00 37.64 4.83
999 1024 1.371337 CCGTCTCGTCACCGTATCCA 61.371 60.000 0.00 0.00 35.01 3.41
1009 1034 0.694444 ACCGTATCCAATGGCTCCCT 60.694 55.000 0.00 0.00 37.86 4.20
1070 1095 2.427245 CGGCCTCCTCATCCTTCGT 61.427 63.158 0.00 0.00 0.00 3.85
1193 1218 4.394712 GCCCGCTAGCACCACAGT 62.395 66.667 16.45 0.00 0.00 3.55
1222 1247 3.117794 GCATACATAACGTCCGTGCTTA 58.882 45.455 0.00 0.00 31.51 3.09
1355 1662 4.439700 CCGTACGTAGACATTCCATCACTT 60.440 45.833 15.21 0.00 0.00 3.16
1526 1833 4.257654 TCGCCTTCCCGCCACAAA 62.258 61.111 0.00 0.00 0.00 2.83
1527 1834 3.061848 CGCCTTCCCGCCACAAAT 61.062 61.111 0.00 0.00 0.00 2.32
1528 1835 2.885113 GCCTTCCCGCCACAAATC 59.115 61.111 0.00 0.00 0.00 2.17
1530 1837 2.406616 CCTTCCCGCCACAAATCCG 61.407 63.158 0.00 0.00 0.00 4.18
1534 1841 2.675075 CCGCCACAAATCCGGGTT 60.675 61.111 0.00 0.00 38.42 4.11
1535 1842 2.696759 CCGCCACAAATCCGGGTTC 61.697 63.158 0.00 0.00 38.42 3.62
1537 1844 1.241315 CGCCACAAATCCGGGTTCTT 61.241 55.000 0.00 0.00 0.00 2.52
1543 1857 2.295070 ACAAATCCGGGTTCTTTTTCCG 59.705 45.455 0.00 0.00 43.05 4.30
1548 1862 1.571215 CGGGTTCTTTTTCCGACGGG 61.571 60.000 15.25 0.00 45.96 5.28
1553 1867 0.664224 TCTTTTTCCGACGGGTTTGC 59.336 50.000 15.25 0.00 33.83 3.68
1559 1873 3.047877 CGACGGGTTTGCCTCACC 61.048 66.667 0.00 0.00 34.45 4.02
1565 1879 1.598701 GGGTTTGCCTCACCATCTGC 61.599 60.000 0.00 0.00 35.80 4.26
1567 1881 1.304381 TTTGCCTCACCATCTGCCC 60.304 57.895 0.00 0.00 0.00 5.36
1568 1882 3.626996 TTGCCTCACCATCTGCCCG 62.627 63.158 0.00 0.00 0.00 6.13
1572 1886 1.406065 CCTCACCATCTGCCCGATCT 61.406 60.000 0.00 0.00 0.00 2.75
1576 1890 1.066573 CACCATCTGCCCGATCTATCC 60.067 57.143 0.00 0.00 0.00 2.59
1580 1894 2.203640 TGCCCGATCTATCCGCCT 60.204 61.111 0.00 0.00 0.00 5.52
1581 1895 2.262915 GCCCGATCTATCCGCCTG 59.737 66.667 0.00 0.00 0.00 4.85
1582 1896 2.574955 GCCCGATCTATCCGCCTGT 61.575 63.158 0.00 0.00 0.00 4.00
1583 1897 2.050269 CCCGATCTATCCGCCTGTT 58.950 57.895 0.00 0.00 0.00 3.16
1584 1898 0.393077 CCCGATCTATCCGCCTGTTT 59.607 55.000 0.00 0.00 0.00 2.83
1585 1899 1.502231 CCGATCTATCCGCCTGTTTG 58.498 55.000 0.00 0.00 0.00 2.93
1586 1900 1.068588 CCGATCTATCCGCCTGTTTGA 59.931 52.381 0.00 0.00 0.00 2.69
1587 1901 2.289072 CCGATCTATCCGCCTGTTTGAT 60.289 50.000 0.00 0.00 0.00 2.57
1588 1902 3.393800 CGATCTATCCGCCTGTTTGATT 58.606 45.455 0.00 0.00 0.00 2.57
1589 1903 3.809832 CGATCTATCCGCCTGTTTGATTT 59.190 43.478 0.00 0.00 0.00 2.17
1590 1904 4.319046 CGATCTATCCGCCTGTTTGATTTG 60.319 45.833 0.00 0.00 0.00 2.32
1595 1909 4.214986 TCCGCCTGTTTGATTTGATCTA 57.785 40.909 0.00 0.00 0.00 1.98
1596 1910 3.938963 TCCGCCTGTTTGATTTGATCTAC 59.061 43.478 0.00 0.00 0.00 2.59
1599 1913 4.034510 CGCCTGTTTGATTTGATCTACTCC 59.965 45.833 0.00 0.00 0.00 3.85
1606 1920 3.384789 TGATTTGATCTACTCCAGGACCG 59.615 47.826 0.00 0.00 0.00 4.79
1697 2013 2.738521 CCCGGTGCACTGAACTCG 60.739 66.667 27.46 15.13 0.00 4.18
1929 2272 0.822164 CTTCCCCAACTCCGACGTAT 59.178 55.000 0.00 0.00 0.00 3.06
2004 2348 7.480542 CCTACGACCTCGAAATTAATTTGTTTG 59.519 37.037 17.98 8.74 43.02 2.93
2094 2438 0.756903 AGTAAGCGTGGACACTTGGT 59.243 50.000 0.56 0.00 0.00 3.67
2111 2458 5.521735 CACTTGGTCATGCAGATAGTCTTAC 59.478 44.000 0.00 0.00 0.00 2.34
2138 2485 2.064573 TGATGTGACGCACTACACTG 57.935 50.000 10.54 0.00 37.81 3.66
2218 2565 1.228245 GTTCTTCAGCCTGCACCCA 60.228 57.895 0.00 0.00 0.00 4.51
2269 2616 3.781770 GAGCTGCCCCGTGATCGAG 62.782 68.421 0.00 0.00 39.71 4.04
2484 2834 2.413112 CGTGCACCAGTTCATTGTAGAG 59.587 50.000 12.15 0.00 0.00 2.43
2491 2841 6.149474 GCACCAGTTCATTGTAGAGTTGTAAT 59.851 38.462 0.00 0.00 0.00 1.89
2492 2842 7.624344 GCACCAGTTCATTGTAGAGTTGTAATC 60.624 40.741 0.00 0.00 0.00 1.75
2493 2843 6.590292 ACCAGTTCATTGTAGAGTTGTAATCG 59.410 38.462 0.00 0.00 0.00 3.34
2494 2844 6.455646 CCAGTTCATTGTAGAGTTGTAATCGC 60.456 42.308 0.00 0.00 0.00 4.58
2495 2845 6.090763 CAGTTCATTGTAGAGTTGTAATCGCA 59.909 38.462 0.00 0.00 0.00 5.10
2496 2846 6.311445 AGTTCATTGTAGAGTTGTAATCGCAG 59.689 38.462 0.00 0.00 0.00 5.18
2497 2847 5.109210 TCATTGTAGAGTTGTAATCGCAGG 58.891 41.667 0.00 0.00 0.00 4.85
2501 2866 1.623811 AGAGTTGTAATCGCAGGTGGT 59.376 47.619 0.00 0.00 0.00 4.16
2571 2952 9.519191 AAATATATCATCAAATCATTGTCCGGA 57.481 29.630 0.00 0.00 37.79 5.14
2580 2961 4.988744 TTGTCCGGACAAGGCAAA 57.011 50.000 39.59 21.79 45.42 3.68
2581 2962 3.430473 TTGTCCGGACAAGGCAAAT 57.570 47.368 39.59 0.00 45.42 2.32
3116 3497 3.663176 GTGACGACGGACACGGGA 61.663 66.667 10.57 0.00 46.48 5.14
3480 3861 1.685765 TACGCCTCCTGCAGTCCAT 60.686 57.895 13.81 0.00 41.33 3.41
3481 3862 0.396556 TACGCCTCCTGCAGTCCATA 60.397 55.000 13.81 0.00 41.33 2.74
3482 3863 1.264749 ACGCCTCCTGCAGTCCATAA 61.265 55.000 13.81 0.00 41.33 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
406 407 3.199946 CCACCTTATCTTCCCAACAGCTA 59.800 47.826 0.00 0.00 0.00 3.32
407 408 2.025887 CCACCTTATCTTCCCAACAGCT 60.026 50.000 0.00 0.00 0.00 4.24
563 564 1.576356 CTTATCTCCTCAACAGCCGC 58.424 55.000 0.00 0.00 0.00 6.53
626 627 3.721087 ATTCCTTCCAACCGACTGATT 57.279 42.857 0.00 0.00 0.00 2.57
627 628 3.775316 AGTATTCCTTCCAACCGACTGAT 59.225 43.478 0.00 0.00 0.00 2.90
628 629 3.170717 AGTATTCCTTCCAACCGACTGA 58.829 45.455 0.00 0.00 0.00 3.41
629 630 3.611766 AGTATTCCTTCCAACCGACTG 57.388 47.619 0.00 0.00 0.00 3.51
630 631 4.635699 AAAGTATTCCTTCCAACCGACT 57.364 40.909 0.00 0.00 31.27 4.18
631 632 4.155462 GGAAAAGTATTCCTTCCAACCGAC 59.845 45.833 0.00 0.00 38.80 4.79
632 633 4.202482 TGGAAAAGTATTCCTTCCAACCGA 60.202 41.667 8.55 0.00 44.35 4.69
633 634 4.076394 TGGAAAAGTATTCCTTCCAACCG 58.924 43.478 8.55 0.00 44.35 4.44
637 638 7.563556 ACTCTTTTTGGAAAAGTATTCCTTCCA 59.436 33.333 11.60 0.00 45.36 3.53
638 639 7.952671 ACTCTTTTTGGAAAAGTATTCCTTCC 58.047 34.615 11.60 0.00 39.31 3.46
639 640 8.082852 GGACTCTTTTTGGAAAAGTATTCCTTC 58.917 37.037 11.60 0.00 39.31 3.46
640 641 7.563556 TGGACTCTTTTTGGAAAAGTATTCCTT 59.436 33.333 19.20 0.00 39.31 3.36
641 642 7.066781 TGGACTCTTTTTGGAAAAGTATTCCT 58.933 34.615 19.20 0.00 39.31 3.36
642 643 7.284919 TGGACTCTTTTTGGAAAAGTATTCC 57.715 36.000 11.60 13.94 39.03 3.01
645 646 9.981460 AGATATGGACTCTTTTTGGAAAAGTAT 57.019 29.630 11.60 3.42 0.00 2.12
646 647 9.807921 AAGATATGGACTCTTTTTGGAAAAGTA 57.192 29.630 11.60 0.00 28.55 2.24
647 648 8.712228 AAGATATGGACTCTTTTTGGAAAAGT 57.288 30.769 11.60 0.00 28.55 2.66
648 649 8.246871 GGAAGATATGGACTCTTTTTGGAAAAG 58.753 37.037 6.79 6.79 33.18 2.27
649 650 7.728083 TGGAAGATATGGACTCTTTTTGGAAAA 59.272 33.333 0.00 0.00 33.18 2.29
650 651 7.237982 TGGAAGATATGGACTCTTTTTGGAAA 58.762 34.615 0.00 0.00 33.18 3.13
651 652 6.789268 TGGAAGATATGGACTCTTTTTGGAA 58.211 36.000 0.00 0.00 33.18 3.53
652 653 6.387192 TGGAAGATATGGACTCTTTTTGGA 57.613 37.500 0.00 0.00 33.18 3.53
653 654 6.830324 TCATGGAAGATATGGACTCTTTTTGG 59.170 38.462 0.00 0.00 33.18 3.28
654 655 7.870509 TCATGGAAGATATGGACTCTTTTTG 57.129 36.000 0.00 0.00 33.18 2.44
655 656 9.484806 AAATCATGGAAGATATGGACTCTTTTT 57.515 29.630 0.00 0.00 33.18 1.94
656 657 9.484806 AAAATCATGGAAGATATGGACTCTTTT 57.515 29.630 0.00 0.00 33.18 2.27
657 658 9.129532 GAAAATCATGGAAGATATGGACTCTTT 57.870 33.333 0.00 0.00 33.18 2.52
658 659 8.501070 AGAAAATCATGGAAGATATGGACTCTT 58.499 33.333 0.00 0.00 35.69 2.85
659 660 8.043429 AGAAAATCATGGAAGATATGGACTCT 57.957 34.615 0.00 0.00 0.00 3.24
660 661 8.688747 AAGAAAATCATGGAAGATATGGACTC 57.311 34.615 0.00 0.00 0.00 3.36
661 662 9.790344 CTAAGAAAATCATGGAAGATATGGACT 57.210 33.333 0.00 0.00 0.00 3.85
662 663 9.007901 CCTAAGAAAATCATGGAAGATATGGAC 57.992 37.037 0.00 0.00 0.00 4.02
663 664 8.166061 CCCTAAGAAAATCATGGAAGATATGGA 58.834 37.037 0.00 0.00 0.00 3.41
664 665 8.166061 TCCCTAAGAAAATCATGGAAGATATGG 58.834 37.037 0.00 0.00 0.00 2.74
665 666 9.578576 TTCCCTAAGAAAATCATGGAAGATATG 57.421 33.333 0.00 0.00 0.00 1.78
669 670 9.799106 GATATTCCCTAAGAAAATCATGGAAGA 57.201 33.333 0.00 0.00 38.21 2.87
670 671 9.804977 AGATATTCCCTAAGAAAATCATGGAAG 57.195 33.333 0.00 0.00 38.21 3.46
671 672 9.799106 GAGATATTCCCTAAGAAAATCATGGAA 57.201 33.333 0.00 0.00 38.21 3.53
672 673 8.386264 GGAGATATTCCCTAAGAAAATCATGGA 58.614 37.037 0.00 0.00 40.37 3.41
673 674 8.572855 GGAGATATTCCCTAAGAAAATCATGG 57.427 38.462 0.00 0.00 40.37 3.66
688 689 6.434340 GGGTTGTTAATCATGGGAGATATTCC 59.566 42.308 0.00 0.00 46.00 3.01
689 690 7.175641 CAGGGTTGTTAATCATGGGAGATATTC 59.824 40.741 0.00 0.00 0.00 1.75
690 691 7.006509 CAGGGTTGTTAATCATGGGAGATATT 58.993 38.462 0.00 0.00 0.00 1.28
708 709 7.282224 TCACGGATATATTTCTTTTCAGGGTTG 59.718 37.037 0.00 0.00 0.00 3.77
710 711 6.895782 TCACGGATATATTTCTTTTCAGGGT 58.104 36.000 0.00 0.00 0.00 4.34
725 726 8.041323 AGGATTCGCTTTATTAATCACGGATAT 58.959 33.333 0.00 0.00 32.42 1.63
753 754 6.731292 ATTGGCCTTATTAATTCCTTGACC 57.269 37.500 3.32 0.00 0.00 4.02
882 907 1.377994 CTCACTGGCTGAAAGGGCT 59.622 57.895 0.00 0.00 0.00 5.19
994 1019 1.143684 GAGCAAGGGAGCCATTGGATA 59.856 52.381 14.83 0.00 34.23 2.59
999 1024 1.305623 CTGGAGCAAGGGAGCCATT 59.694 57.895 0.00 0.00 34.23 3.16
1182 1207 1.583495 CCGACGAGACTGTGGTGCTA 61.583 60.000 0.00 0.00 0.00 3.49
1193 1218 1.672363 ACGTTATGTATGCCGACGAGA 59.328 47.619 0.00 0.00 37.20 4.04
1518 1825 1.241315 AAGAACCCGGATTTGTGGCG 61.241 55.000 0.73 0.00 0.00 5.69
1519 1826 0.966179 AAAGAACCCGGATTTGTGGC 59.034 50.000 0.73 0.00 0.00 5.01
1521 1828 3.649073 GGAAAAAGAACCCGGATTTGTG 58.351 45.455 0.73 0.00 0.00 3.33
1522 1829 2.295070 CGGAAAAAGAACCCGGATTTGT 59.705 45.455 0.73 0.00 39.59 2.83
1523 1830 2.554893 TCGGAAAAAGAACCCGGATTTG 59.445 45.455 0.73 0.00 43.16 2.32
1524 1831 2.555325 GTCGGAAAAAGAACCCGGATTT 59.445 45.455 0.73 0.00 43.16 2.17
1526 1833 1.817357 GTCGGAAAAAGAACCCGGAT 58.183 50.000 0.73 0.00 43.16 4.18
1527 1834 0.600782 CGTCGGAAAAAGAACCCGGA 60.601 55.000 0.73 0.00 43.16 5.14
1528 1835 1.571215 CCGTCGGAAAAAGAACCCGG 61.571 60.000 4.91 0.00 43.16 5.73
1530 1837 0.535780 ACCCGTCGGAAAAAGAACCC 60.536 55.000 14.39 0.00 0.00 4.11
1534 1841 0.664224 GCAAACCCGTCGGAAAAAGA 59.336 50.000 14.39 0.00 0.00 2.52
1535 1842 0.318360 GGCAAACCCGTCGGAAAAAG 60.318 55.000 14.39 0.00 0.00 2.27
1537 1844 1.152922 AGGCAAACCCGTCGGAAAA 60.153 52.632 14.39 0.00 39.21 2.29
1543 1857 1.303317 ATGGTGAGGCAAACCCGTC 60.303 57.895 6.20 0.00 39.21 4.79
1548 1862 1.598701 GGGCAGATGGTGAGGCAAAC 61.599 60.000 0.00 0.00 0.00 2.93
1553 1867 1.070445 GATCGGGCAGATGGTGAGG 59.930 63.158 4.45 0.00 40.26 3.86
1559 1873 0.459237 GCGGATAGATCGGGCAGATG 60.459 60.000 4.45 0.00 40.26 2.90
1565 1879 0.393077 AAACAGGCGGATAGATCGGG 59.607 55.000 0.00 0.00 0.00 5.14
1567 1881 2.509052 TCAAACAGGCGGATAGATCG 57.491 50.000 0.00 0.00 0.00 3.69
1568 1882 4.816385 TCAAATCAAACAGGCGGATAGATC 59.184 41.667 0.00 0.00 0.00 2.75
1572 1886 4.780815 AGATCAAATCAAACAGGCGGATA 58.219 39.130 0.00 0.00 0.00 2.59
1576 1890 4.034510 GGAGTAGATCAAATCAAACAGGCG 59.965 45.833 0.00 0.00 0.00 5.52
1580 1894 6.173339 GTCCTGGAGTAGATCAAATCAAACA 58.827 40.000 0.00 0.00 0.00 2.83
1581 1895 5.586643 GGTCCTGGAGTAGATCAAATCAAAC 59.413 44.000 0.00 0.00 0.00 2.93
1582 1896 5.626809 CGGTCCTGGAGTAGATCAAATCAAA 60.627 44.000 0.00 0.00 0.00 2.69
1583 1897 4.141937 CGGTCCTGGAGTAGATCAAATCAA 60.142 45.833 0.00 0.00 0.00 2.57
1584 1898 3.384789 CGGTCCTGGAGTAGATCAAATCA 59.615 47.826 0.00 0.00 0.00 2.57
1585 1899 3.637229 TCGGTCCTGGAGTAGATCAAATC 59.363 47.826 0.00 0.00 0.00 2.17
1586 1900 3.639094 CTCGGTCCTGGAGTAGATCAAAT 59.361 47.826 0.00 0.00 0.00 2.32
1587 1901 3.024547 CTCGGTCCTGGAGTAGATCAAA 58.975 50.000 0.00 0.00 0.00 2.69
1588 1902 2.025226 ACTCGGTCCTGGAGTAGATCAA 60.025 50.000 0.00 0.00 42.69 2.57
1589 1903 1.564818 ACTCGGTCCTGGAGTAGATCA 59.435 52.381 0.00 0.00 42.69 2.92
1590 1904 2.351706 ACTCGGTCCTGGAGTAGATC 57.648 55.000 0.00 0.00 42.69 2.75
1595 1909 1.472662 CCACAACTCGGTCCTGGAGT 61.473 60.000 0.00 0.00 46.27 3.85
1596 1910 1.293498 CCACAACTCGGTCCTGGAG 59.707 63.158 0.00 0.00 37.54 3.86
1599 1913 2.738521 CGCCACAACTCGGTCCTG 60.739 66.667 0.00 0.00 0.00 3.86
1606 1920 1.534175 CCTCTATCGTCGCCACAACTC 60.534 57.143 0.00 0.00 0.00 3.01
1929 2272 5.050490 GCTAGGAAACAGATCTGCGATTAA 58.950 41.667 22.83 4.09 0.00 1.40
2076 2420 1.145803 GACCAAGTGTCCACGCTTAC 58.854 55.000 5.22 0.00 44.06 2.34
2111 2458 5.576774 TGTAGTGCGTCACATCAAAAGATAG 59.423 40.000 11.58 0.00 36.74 2.08
2117 2464 2.799978 CAGTGTAGTGCGTCACATCAAA 59.200 45.455 11.58 0.00 36.74 2.69
2138 2485 5.948992 AAGAAATCAGTACTCCAAAGTGC 57.051 39.130 0.00 0.00 38.30 4.40
2218 2565 3.994853 GGGTCCGTCGTCCCGTTT 61.995 66.667 6.93 0.00 33.97 3.60
2269 2616 4.097361 GCCGACCACTTCTCCCCC 62.097 72.222 0.00 0.00 0.00 5.40
2272 2619 2.126031 GTCGCCGACCACTTCTCC 60.126 66.667 5.81 0.00 0.00 3.71
2474 2824 5.109210 CCTGCGATTACAACTCTACAATGA 58.891 41.667 0.00 0.00 0.00 2.57
2484 2834 4.493545 CGATTAACCACCTGCGATTACAAC 60.494 45.833 0.00 0.00 0.00 3.32
2491 2841 2.459060 TTTCGATTAACCACCTGCGA 57.541 45.000 0.00 0.00 0.00 5.10
2492 2842 4.868450 TTATTTCGATTAACCACCTGCG 57.132 40.909 0.00 0.00 0.00 5.18
2493 2843 9.394477 GATATTTTATTTCGATTAACCACCTGC 57.606 33.333 0.00 0.00 0.00 4.85
2571 2952 2.164219 CGTGATTGCCTATTTGCCTTGT 59.836 45.455 0.00 0.00 0.00 3.16
2574 2955 2.128771 ACGTGATTGCCTATTTGCCT 57.871 45.000 0.00 0.00 0.00 4.75
2575 2956 2.163412 TGAACGTGATTGCCTATTTGCC 59.837 45.455 0.00 0.00 0.00 4.52
2576 2957 3.171277 GTGAACGTGATTGCCTATTTGC 58.829 45.455 0.00 0.00 0.00 3.68
2577 2958 3.416277 CGTGAACGTGATTGCCTATTTG 58.584 45.455 0.00 0.00 34.11 2.32
2578 2959 3.740044 CGTGAACGTGATTGCCTATTT 57.260 42.857 0.00 0.00 34.11 1.40


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

AutoCloner maintained by Alex Coulton.