Multiple sequence alignment - TraesCS1D01G156700

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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 TraesCS1D01G156700 chr1D 100.000 3201 0 0 1 3201 220890901 220887701 0.000000e+00 5912.0
1 TraesCS1D01G156700 chr1A 96.263 2007 69 5 581 2583 284914148 284912144 0.000000e+00 3286.0
2 TraesCS1D01G156700 chr1A 94.751 381 16 3 120 499 284914524 284914147 9.890000e-165 590.0
3 TraesCS1D01G156700 chr1A 86.649 382 27 16 2662 3020 284912028 284911648 4.970000e-108 401.0
4 TraesCS1D01G156700 chr1A 97.183 71 2 0 1 71 284914933 284914863 1.560000e-23 121.0
5 TraesCS1D01G156700 chr1A 97.619 42 1 0 2622 2663 284912151 284912110 4.430000e-09 73.1
6 TraesCS1D01G156700 chr1B 90.553 2170 124 29 581 2721 317322077 317319960 0.000000e+00 2796.0
7 TraesCS1D01G156700 chr1B 94.318 440 19 4 63 499 317322512 317322076 0.000000e+00 669.0
8 TraesCS1D01G156700 chr1B 83.333 264 25 5 2769 3031 317319892 317319647 3.210000e-55 226.0
9 TraesCS1D01G156700 chr1B 87.273 165 10 7 3046 3201 317319506 317319344 9.120000e-41 178.0
10 TraesCS1D01G156700 chr5D 83.929 392 56 7 48 433 505897014 505897404 5.040000e-98 368.0
11 TraesCS1D01G156700 chr5D 74.545 440 73 20 2776 3201 41539412 41539826 4.280000e-34 156.0
12 TraesCS1D01G156700 chr5D 91.860 86 7 0 498 583 389033682 389033767 1.560000e-23 121.0
13 TraesCS1D01G156700 chr4A 75.395 443 87 15 2772 3201 517581521 517581954 9.060000e-46 195.0
14 TraesCS1D01G156700 chr4A 94.382 89 5 0 496 584 684920397 684920485 1.550000e-28 137.0
15 TraesCS1D01G156700 chr5A 74.773 440 72 22 2776 3201 29885206 29885620 9.190000e-36 161.0
16 TraesCS1D01G156700 chr5A 73.451 452 92 21 2768 3201 666826379 666826820 9.250000e-31 145.0
17 TraesCS1D01G156700 chr7D 77.143 280 51 10 2791 3067 610760886 610760617 1.990000e-32 150.0
18 TraesCS1D01G156700 chr7D 87.143 70 9 0 2632 2701 65010305 65010374 2.650000e-11 80.5
19 TraesCS1D01G156700 chr4B 91.000 100 6 3 484 583 653746012 653746108 7.210000e-27 132.0
20 TraesCS1D01G156700 chr4B 76.562 128 29 1 2870 2997 30834456 30834330 5.730000e-08 69.4
21 TraesCS1D01G156700 chr2D 93.023 86 6 0 497 582 186756030 186755945 3.350000e-25 126.0
22 TraesCS1D01G156700 chr2D 92.045 88 5 1 496 583 27072095 27072180 4.340000e-24 122.0
23 TraesCS1D01G156700 chr2D 88.660 97 10 1 493 589 593132125 593132220 2.020000e-22 117.0
24 TraesCS1D01G156700 chr6D 92.045 88 7 0 496 583 60049529 60049616 1.210000e-24 124.0
25 TraesCS1D01G156700 chr2B 73.051 449 84 28 2768 3192 485901626 485902061 1.210000e-24 124.0
26 TraesCS1D01G156700 chr6A 90.217 92 9 0 498 589 610350314 610350223 1.560000e-23 121.0
27 TraesCS1D01G156700 chr7B 88.660 97 9 2 495 591 625161227 625161321 2.020000e-22 117.0
28 TraesCS1D01G156700 chr3A 88.889 72 8 0 2629 2700 492748800 492748729 4.400000e-14 89.8


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 TraesCS1D01G156700 chr1D 220887701 220890901 3200 True 5912.00 5912 100.00000 1 3201 1 chr1D.!!$R1 3200
1 TraesCS1D01G156700 chr1A 284911648 284914933 3285 True 894.22 3286 94.49300 1 3020 5 chr1A.!!$R1 3019
2 TraesCS1D01G156700 chr1B 317319344 317322512 3168 True 967.25 2796 88.86925 63 3201 4 chr1B.!!$R1 3138

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
38 39 0.411848 CTCCTATCCTCTCCTCCCCC 59.588 65.0 0.0 0.0 0.0 5.40 F
1359 1657 0.033504 AGGCTGTACACAAGACCACG 59.966 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 1705 1.484653 TCGATACCAGGGATGGTGTTG 59.515 52.381 10.17 7.53 43.03 3.33 R
2752 3166 0.101759 TGTATCGCTCGTTGCTACCC 59.898 55.000 0.00 0.00 40.11 3.69 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
38 39 0.411848 CTCCTATCCTCTCCTCCCCC 59.588 65.000 0.00 0.00 0.00 5.40
134 425 3.304559 CGCTAGCGGCAATACAATATCTC 59.695 47.826 29.29 0.00 41.91 2.75
167 458 2.607892 GCGCGGTTCTGTTTGCTCT 61.608 57.895 8.83 0.00 0.00 4.09
323 614 0.599991 TGCGCTGTGTTCTGTGTAGG 60.600 55.000 9.73 0.00 0.00 3.18
341 635 4.949238 TGTAGGACGTATGCTACTTGGTAA 59.051 41.667 7.38 0.00 46.91 2.85
437 731 7.497909 GTGGGCAGAGCTTTATTAGTATGTTTA 59.502 37.037 0.00 0.00 0.00 2.01
468 763 3.879892 GGAGTCTAATCACAGAAATGGGC 59.120 47.826 0.00 0.00 0.00 5.36
506 801 9.790389 CATTCGATGATTATTACTACTACCTCC 57.210 37.037 0.00 0.00 0.00 4.30
507 802 7.606858 TCGATGATTATTACTACTACCTCCG 57.393 40.000 0.00 0.00 0.00 4.63
508 803 7.164122 TCGATGATTATTACTACTACCTCCGT 58.836 38.462 0.00 0.00 0.00 4.69
509 804 7.332926 TCGATGATTATTACTACTACCTCCGTC 59.667 40.741 0.00 0.00 0.00 4.79
510 805 7.413877 CGATGATTATTACTACTACCTCCGTCC 60.414 44.444 0.00 0.00 0.00 4.79
511 806 6.006449 TGATTATTACTACTACCTCCGTCCC 58.994 44.000 0.00 0.00 0.00 4.46
512 807 3.959495 ATTACTACTACCTCCGTCCCA 57.041 47.619 0.00 0.00 0.00 4.37
513 808 3.959495 TTACTACTACCTCCGTCCCAT 57.041 47.619 0.00 0.00 0.00 4.00
514 809 5.589367 ATTACTACTACCTCCGTCCCATA 57.411 43.478 0.00 0.00 0.00 2.74
515 810 3.959495 ACTACTACCTCCGTCCCATAA 57.041 47.619 0.00 0.00 0.00 1.90
516 811 4.466255 ACTACTACCTCCGTCCCATAAT 57.534 45.455 0.00 0.00 0.00 1.28
517 812 5.589367 ACTACTACCTCCGTCCCATAATA 57.411 43.478 0.00 0.00 0.00 0.98
518 813 6.150034 ACTACTACCTCCGTCCCATAATAT 57.850 41.667 0.00 0.00 0.00 1.28
519 814 7.276088 ACTACTACCTCCGTCCCATAATATA 57.724 40.000 0.00 0.00 0.00 0.86
520 815 7.702785 ACTACTACCTCCGTCCCATAATATAA 58.297 38.462 0.00 0.00 0.00 0.98
521 816 7.833183 ACTACTACCTCCGTCCCATAATATAAG 59.167 40.741 0.00 0.00 0.00 1.73
522 817 6.797707 ACTACCTCCGTCCCATAATATAAGA 58.202 40.000 0.00 0.00 0.00 2.10
523 818 6.890814 ACTACCTCCGTCCCATAATATAAGAG 59.109 42.308 0.00 0.00 0.00 2.85
524 819 4.466726 ACCTCCGTCCCATAATATAAGAGC 59.533 45.833 0.00 0.00 0.00 4.09
525 820 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
526 821 3.119245 TCCGTCCCATAATATAAGAGCGC 60.119 47.826 0.00 0.00 0.00 5.92
527 822 3.119101 CCGTCCCATAATATAAGAGCGCT 60.119 47.826 11.27 11.27 0.00 5.92
528 823 4.495422 CGTCCCATAATATAAGAGCGCTT 58.505 43.478 13.26 8.09 38.15 4.68
529 824 4.929808 CGTCCCATAATATAAGAGCGCTTT 59.070 41.667 13.26 1.42 35.56 3.51
530 825 5.408604 CGTCCCATAATATAAGAGCGCTTTT 59.591 40.000 17.98 17.98 35.56 2.27
531 826 6.073222 CGTCCCATAATATAAGAGCGCTTTTT 60.073 38.462 19.12 15.06 35.56 1.94
532 827 7.117236 CGTCCCATAATATAAGAGCGCTTTTTA 59.883 37.037 19.12 16.70 35.56 1.52
533 828 8.228464 GTCCCATAATATAAGAGCGCTTTTTAC 58.772 37.037 19.12 1.07 35.56 2.01
534 829 7.934665 TCCCATAATATAAGAGCGCTTTTTACA 59.065 33.333 19.12 7.25 35.56 2.41
535 830 8.015658 CCCATAATATAAGAGCGCTTTTTACAC 58.984 37.037 19.12 0.00 35.56 2.90
536 831 8.774586 CCATAATATAAGAGCGCTTTTTACACT 58.225 33.333 19.12 2.20 35.56 3.55
539 834 8.712285 AATATAAGAGCGCTTTTTACACTACA 57.288 30.769 19.12 0.00 35.56 2.74
540 835 4.727235 AAGAGCGCTTTTTACACTACAC 57.273 40.909 13.26 0.00 0.00 2.90
541 836 3.991367 AGAGCGCTTTTTACACTACACT 58.009 40.909 13.26 0.00 0.00 3.55
542 837 5.130292 AGAGCGCTTTTTACACTACACTA 57.870 39.130 13.26 0.00 0.00 2.74
543 838 5.162075 AGAGCGCTTTTTACACTACACTAG 58.838 41.667 13.26 0.00 0.00 2.57
544 839 4.879598 AGCGCTTTTTACACTACACTAGT 58.120 39.130 2.64 0.00 40.28 2.57
570 865 8.210946 TGTCAAGAACACTCTTATATTATGGGG 58.789 37.037 0.00 0.00 40.05 4.96
571 866 7.173390 GTCAAGAACACTCTTATATTATGGGGC 59.827 40.741 0.00 0.00 40.05 5.80
572 867 5.794894 AGAACACTCTTATATTATGGGGCG 58.205 41.667 0.00 0.00 0.00 6.13
573 868 4.553330 ACACTCTTATATTATGGGGCGG 57.447 45.455 0.00 0.00 0.00 6.13
574 869 4.164981 ACACTCTTATATTATGGGGCGGA 58.835 43.478 0.00 0.00 0.00 5.54
575 870 4.223032 ACACTCTTATATTATGGGGCGGAG 59.777 45.833 0.00 0.00 0.00 4.63
576 871 3.775316 ACTCTTATATTATGGGGCGGAGG 59.225 47.826 0.00 0.00 0.00 4.30
577 872 3.112263 TCTTATATTATGGGGCGGAGGG 58.888 50.000 0.00 0.00 0.00 4.30
578 873 2.953093 TATATTATGGGGCGGAGGGA 57.047 50.000 0.00 0.00 0.00 4.20
579 874 1.584724 ATATTATGGGGCGGAGGGAG 58.415 55.000 0.00 0.00 0.00 4.30
694 989 7.056844 AGTAGTATCTTTGATTAGTGGCTCC 57.943 40.000 0.00 0.00 0.00 4.70
825 1120 5.075493 GGTCGAGGTTATTCCCTGTCTATA 58.925 45.833 0.00 0.00 34.03 1.31
889 1184 2.832129 TCTGTTCTTATGCGGACCTCTT 59.168 45.455 0.00 0.00 0.00 2.85
897 1192 1.919240 TGCGGACCTCTTCTCTGTTA 58.081 50.000 0.00 0.00 0.00 2.41
1196 1494 5.878116 GGTATGTATGTGGAAACAGTGCTAA 59.122 40.000 0.00 0.00 44.46 3.09
1200 1498 3.222173 TGTGGAAACAGTGCTAACCAT 57.778 42.857 0.00 0.00 44.46 3.55
1320 1618 6.734502 TCGTCATGTTAAATATGGTCCCTA 57.265 37.500 0.00 0.00 0.00 3.53
1359 1657 0.033504 AGGCTGTACACAAGACCACG 59.966 55.000 0.00 0.00 0.00 4.94
1407 1705 5.018149 AGTACCCTGAAAAGAGTAGGAGTC 58.982 45.833 0.00 0.00 33.33 3.36
1678 1989 5.306678 TGCCCTTGGTCATTTTACTTCATTT 59.693 36.000 0.00 0.00 0.00 2.32
2041 2360 2.435059 GACAACCTGCGGAGGCTC 60.435 66.667 24.53 11.40 44.33 4.70
2096 2415 3.094062 GCTGGCATCGAGGCTGGTA 62.094 63.158 22.57 5.44 44.55 3.25
2107 2426 2.592993 GGCTGGTACCAGTGCAGGA 61.593 63.158 36.31 3.95 45.24 3.86
2128 2447 2.505118 GCTCAGGCTGACGACGAC 60.505 66.667 14.43 0.00 35.22 4.34
2182 2501 0.320771 TTGAAGAGGCCGCTGAAGAC 60.321 55.000 10.77 0.48 0.00 3.01
2315 2634 0.535553 GCCAGTGGACCGGTTTTGTA 60.536 55.000 15.20 0.00 0.00 2.41
2415 2735 7.796660 TCTCAAATCGTGTCTTTAAATGTTTCG 59.203 33.333 0.00 0.00 0.00 3.46
2561 2891 6.177610 TGGTTAGACTATTTGGTTCCATGAC 58.822 40.000 0.00 0.00 0.00 3.06
2575 2905 2.159240 TCCATGACTGTGATACACGAGC 60.159 50.000 0.00 0.00 37.14 5.03
2576 2906 1.848608 CATGACTGTGATACACGAGCG 59.151 52.381 0.00 0.00 37.14 5.03
2577 2907 1.161843 TGACTGTGATACACGAGCGA 58.838 50.000 0.00 0.00 37.14 4.93
2578 2908 1.135774 TGACTGTGATACACGAGCGAC 60.136 52.381 0.00 0.00 37.14 5.19
2579 2909 0.879090 ACTGTGATACACGAGCGACA 59.121 50.000 0.00 0.00 37.14 4.35
2580 2910 1.472878 ACTGTGATACACGAGCGACAT 59.527 47.619 0.00 0.00 37.14 3.06
2581 2911 1.848608 CTGTGATACACGAGCGACATG 59.151 52.381 0.00 0.00 37.14 3.21
2582 2912 1.201414 TGTGATACACGAGCGACATGT 59.799 47.619 0.00 0.00 37.14 3.21
2583 2913 1.846782 GTGATACACGAGCGACATGTC 59.153 52.381 16.21 16.21 0.00 3.06
2584 2914 1.743394 TGATACACGAGCGACATGTCT 59.257 47.619 22.95 5.76 0.00 3.41
2585 2915 2.163613 TGATACACGAGCGACATGTCTT 59.836 45.455 22.95 11.48 0.00 3.01
2586 2916 2.717580 TACACGAGCGACATGTCTTT 57.282 45.000 22.95 11.12 0.00 2.52
2587 2917 1.865865 ACACGAGCGACATGTCTTTT 58.134 45.000 22.95 8.62 0.00 2.27
2588 2918 2.210116 ACACGAGCGACATGTCTTTTT 58.790 42.857 22.95 6.17 0.00 1.94
2632 2962 7.851228 ACTTTGATCAACACTGATATGTAGGA 58.149 34.615 7.89 0.00 42.60 2.94
2732 3146 6.558771 CATGGAATGTCTATTATTTGCGGA 57.441 37.500 0.00 0.00 40.20 5.54
2736 3150 7.479980 TGGAATGTCTATTATTTGCGGAAAAG 58.520 34.615 6.08 0.00 0.00 2.27
2737 3151 6.417930 GGAATGTCTATTATTTGCGGAAAAGC 59.582 38.462 6.08 0.00 37.71 3.51
2741 3155 6.374333 TGTCTATTATTTGCGGAAAAGCTCTT 59.626 34.615 6.08 0.00 38.13 2.85
2742 3156 7.094377 TGTCTATTATTTGCGGAAAAGCTCTTT 60.094 33.333 6.08 0.00 38.13 2.52
2743 3157 7.429630 GTCTATTATTTGCGGAAAAGCTCTTTC 59.570 37.037 6.08 10.92 38.13 2.62
2746 3160 0.586319 TGCGGAAAAGCTCTTTCACG 59.414 50.000 17.41 17.35 38.13 4.35
2747 3161 0.865769 GCGGAAAAGCTCTTTCACGA 59.134 50.000 21.36 0.00 35.24 4.35
2748 3162 1.136224 GCGGAAAAGCTCTTTCACGAG 60.136 52.381 21.36 12.91 35.24 4.18
2755 3169 1.587054 CTCTTTCACGAGCGAGGGT 59.413 57.895 0.00 0.00 0.00 4.34
2758 3172 0.802607 CTTTCACGAGCGAGGGTAGC 60.803 60.000 0.00 0.00 0.00 3.58
2761 3175 1.805945 CACGAGCGAGGGTAGCAAC 60.806 63.158 0.00 0.00 37.01 4.17
2763 3177 2.882876 GAGCGAGGGTAGCAACGA 59.117 61.111 12.64 0.00 37.01 3.85
2765 3179 2.886124 GCGAGGGTAGCAACGAGC 60.886 66.667 12.64 0.00 46.19 5.03
2956 3394 8.886719 AGGTAAAACTTAGGAATTAATACGCAC 58.113 33.333 0.00 0.00 0.00 5.34
3099 3672 5.577164 CCGTTTCGAATCTGACTAAACATCT 59.423 40.000 0.00 0.00 31.85 2.90
3101 3674 6.454318 CGTTTCGAATCTGACTAAACATCTGG 60.454 42.308 0.00 0.00 31.85 3.86
3139 3712 2.371179 ACATCTGATCCTCATCCGCATT 59.629 45.455 0.00 0.00 0.00 3.56
3140 3713 2.827800 TCTGATCCTCATCCGCATTC 57.172 50.000 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 425 2.326897 CGCCGATGCTTGATGCTG 59.673 61.111 0.00 0.00 43.37 4.41
148 439 3.595108 GAGCAAACAGAACCGCGCC 62.595 63.158 0.00 0.00 0.00 6.53
167 458 3.833732 AGTACAGATCCAATCGCTCCTA 58.166 45.455 0.00 0.00 0.00 2.94
247 538 3.530910 AACCAGTCCAACCGCTCGG 62.531 63.158 6.79 6.79 42.03 4.63
341 635 7.920682 GCAAATACCTTCCGTAAATGAAATCAT 59.079 33.333 0.00 0.00 38.41 2.45
443 737 5.945784 CCCATTTCTGTGATTAGACTCCAAA 59.054 40.000 0.00 0.00 0.00 3.28
444 738 5.500234 CCCATTTCTGTGATTAGACTCCAA 58.500 41.667 0.00 0.00 0.00 3.53
445 739 4.626287 GCCCATTTCTGTGATTAGACTCCA 60.626 45.833 0.00 0.00 0.00 3.86
446 740 3.879892 GCCCATTTCTGTGATTAGACTCC 59.120 47.826 0.00 0.00 0.00 3.85
447 741 3.557595 CGCCCATTTCTGTGATTAGACTC 59.442 47.826 0.00 0.00 0.00 3.36
455 750 1.140852 CCTATCCGCCCATTTCTGTGA 59.859 52.381 0.00 0.00 0.00 3.58
468 763 8.703604 ATAATCATCGAATGTAAACCTATCCG 57.296 34.615 0.00 0.00 0.00 4.18
497 792 7.932134 TCTTATATTATGGGACGGAGGTAGTA 58.068 38.462 0.00 0.00 0.00 1.82
498 793 6.797707 TCTTATATTATGGGACGGAGGTAGT 58.202 40.000 0.00 0.00 0.00 2.73
499 794 6.183360 GCTCTTATATTATGGGACGGAGGTAG 60.183 46.154 0.00 0.00 0.00 3.18
500 795 5.655532 GCTCTTATATTATGGGACGGAGGTA 59.344 44.000 0.00 0.00 0.00 3.08
501 796 4.466726 GCTCTTATATTATGGGACGGAGGT 59.533 45.833 0.00 0.00 0.00 3.85
502 797 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
503 798 4.673441 CGCTCTTATATTATGGGACGGAG 58.327 47.826 0.00 0.00 0.00 4.63
504 799 3.119245 GCGCTCTTATATTATGGGACGGA 60.119 47.826 0.00 0.00 0.00 4.69
505 800 3.119101 AGCGCTCTTATATTATGGGACGG 60.119 47.826 2.64 0.00 0.00 4.79
506 801 4.111375 AGCGCTCTTATATTATGGGACG 57.889 45.455 2.64 0.00 0.00 4.79
507 802 6.803154 AAAAGCGCTCTTATATTATGGGAC 57.197 37.500 12.06 0.00 31.02 4.46
508 803 7.934665 TGTAAAAAGCGCTCTTATATTATGGGA 59.065 33.333 12.06 0.00 31.02 4.37
509 804 8.015658 GTGTAAAAAGCGCTCTTATATTATGGG 58.984 37.037 12.06 0.00 31.02 4.00
510 805 8.774586 AGTGTAAAAAGCGCTCTTATATTATGG 58.225 33.333 12.06 0.00 31.02 2.74
513 808 9.806203 TGTAGTGTAAAAAGCGCTCTTATATTA 57.194 29.630 12.06 8.51 31.02 0.98
514 809 8.601476 GTGTAGTGTAAAAAGCGCTCTTATATT 58.399 33.333 12.06 9.47 31.02 1.28
515 810 7.980099 AGTGTAGTGTAAAAAGCGCTCTTATAT 59.020 33.333 12.06 4.96 31.02 0.86
516 811 7.318141 AGTGTAGTGTAAAAAGCGCTCTTATA 58.682 34.615 12.06 7.48 31.02 0.98
517 812 6.164176 AGTGTAGTGTAAAAAGCGCTCTTAT 58.836 36.000 12.06 0.00 31.02 1.73
518 813 5.535333 AGTGTAGTGTAAAAAGCGCTCTTA 58.465 37.500 12.06 9.23 31.02 2.10
519 814 4.377897 AGTGTAGTGTAAAAAGCGCTCTT 58.622 39.130 12.06 10.38 0.00 2.85
520 815 3.991367 AGTGTAGTGTAAAAAGCGCTCT 58.009 40.909 12.06 3.67 0.00 4.09
521 816 4.922103 ACTAGTGTAGTGTAAAAAGCGCTC 59.078 41.667 12.06 0.00 37.69 5.03
522 817 4.879598 ACTAGTGTAGTGTAAAAAGCGCT 58.120 39.130 2.64 2.64 37.69 5.92
544 839 8.210946 CCCCATAATATAAGAGTGTTCTTGACA 58.789 37.037 0.26 0.00 43.41 3.58
545 840 7.173390 GCCCCATAATATAAGAGTGTTCTTGAC 59.827 40.741 0.26 0.00 43.41 3.18
546 841 7.224297 GCCCCATAATATAAGAGTGTTCTTGA 58.776 38.462 0.26 0.00 43.41 3.02
547 842 6.147821 CGCCCCATAATATAAGAGTGTTCTTG 59.852 42.308 0.26 0.00 43.41 3.02
548 843 6.231211 CGCCCCATAATATAAGAGTGTTCTT 58.769 40.000 0.00 0.00 45.45 2.52
549 844 5.280011 CCGCCCCATAATATAAGAGTGTTCT 60.280 44.000 0.00 0.00 34.29 3.01
550 845 4.935808 CCGCCCCATAATATAAGAGTGTTC 59.064 45.833 0.00 0.00 0.00 3.18
551 846 4.595781 TCCGCCCCATAATATAAGAGTGTT 59.404 41.667 0.00 0.00 0.00 3.32
552 847 4.164981 TCCGCCCCATAATATAAGAGTGT 58.835 43.478 0.00 0.00 0.00 3.55
553 848 4.383118 CCTCCGCCCCATAATATAAGAGTG 60.383 50.000 0.00 0.00 0.00 3.51
554 849 3.775316 CCTCCGCCCCATAATATAAGAGT 59.225 47.826 0.00 0.00 0.00 3.24
555 850 3.134804 CCCTCCGCCCCATAATATAAGAG 59.865 52.174 0.00 0.00 0.00 2.85
556 851 3.112263 CCCTCCGCCCCATAATATAAGA 58.888 50.000 0.00 0.00 0.00 2.10
557 852 3.112263 TCCCTCCGCCCCATAATATAAG 58.888 50.000 0.00 0.00 0.00 1.73
558 853 3.112263 CTCCCTCCGCCCCATAATATAA 58.888 50.000 0.00 0.00 0.00 0.98
559 854 2.045326 ACTCCCTCCGCCCCATAATATA 59.955 50.000 0.00 0.00 0.00 0.86
560 855 1.203440 ACTCCCTCCGCCCCATAATAT 60.203 52.381 0.00 0.00 0.00 1.28
561 856 0.192566 ACTCCCTCCGCCCCATAATA 59.807 55.000 0.00 0.00 0.00 0.98
562 857 0.192566 TACTCCCTCCGCCCCATAAT 59.807 55.000 0.00 0.00 0.00 1.28
563 858 0.471211 CTACTCCCTCCGCCCCATAA 60.471 60.000 0.00 0.00 0.00 1.90
564 859 1.155390 CTACTCCCTCCGCCCCATA 59.845 63.158 0.00 0.00 0.00 2.74
565 860 2.122813 CTACTCCCTCCGCCCCAT 60.123 66.667 0.00 0.00 0.00 4.00
567 862 4.862823 AGCTACTCCCTCCGCCCC 62.863 72.222 0.00 0.00 0.00 5.80
568 863 1.911702 AAAAGCTACTCCCTCCGCCC 61.912 60.000 0.00 0.00 0.00 6.13
569 864 0.828677 TAAAAGCTACTCCCTCCGCC 59.171 55.000 0.00 0.00 0.00 6.13
570 865 2.912690 ATAAAAGCTACTCCCTCCGC 57.087 50.000 0.00 0.00 0.00 5.54
571 866 4.217983 ACGATATAAAAGCTACTCCCTCCG 59.782 45.833 0.00 0.00 0.00 4.63
572 867 5.725325 ACGATATAAAAGCTACTCCCTCC 57.275 43.478 0.00 0.00 0.00 4.30
573 868 8.521176 TGATAACGATATAAAAGCTACTCCCTC 58.479 37.037 0.00 0.00 0.00 4.30
574 869 8.418597 TGATAACGATATAAAAGCTACTCCCT 57.581 34.615 0.00 0.00 0.00 4.20
575 870 9.088512 CATGATAACGATATAAAAGCTACTCCC 57.911 37.037 0.00 0.00 0.00 4.30
576 871 9.856488 TCATGATAACGATATAAAAGCTACTCC 57.144 33.333 0.00 0.00 0.00 3.85
694 989 1.703438 GCTTCTGGCTCATGTCTGCG 61.703 60.000 0.00 0.00 38.06 5.18
889 1184 9.725019 AGATACATTCACAAACAATAACAGAGA 57.275 29.630 0.00 0.00 0.00 3.10
897 1192 8.017373 CGAAGACAAGATACATTCACAAACAAT 58.983 33.333 0.00 0.00 0.00 2.71
922 1217 3.681417 GGCTAACCTAACAAGTAACACCG 59.319 47.826 0.00 0.00 0.00 4.94
1104 1399 6.582295 ACAGCAAAATAGTTAAAAGTGCATCG 59.418 34.615 0.00 0.00 32.98 3.84
1163 1461 5.574891 TCCACATACATACCAAAATGCAC 57.425 39.130 0.00 0.00 0.00 4.57
1243 1541 5.006068 GGCACAGATATCATACGCATACATG 59.994 44.000 5.32 0.00 0.00 3.21
1320 1618 4.807643 GCCTTCTTCTTCCTACACCAACAT 60.808 45.833 0.00 0.00 0.00 2.71
1359 1657 3.935828 GGAGCCTTTTGTCATCTGTAGTC 59.064 47.826 0.00 0.00 0.00 2.59
1407 1705 1.484653 TCGATACCAGGGATGGTGTTG 59.515 52.381 10.17 7.53 43.03 3.33
1678 1989 4.359434 TGCAAGTGGGTACAAGAACATA 57.641 40.909 0.00 0.00 0.00 2.29
1949 2268 7.360101 GCACCACTCACTAGTTTTGTACTATTG 60.360 40.741 0.00 0.00 39.89 1.90
1995 2314 4.349636 TGTCAGGACCTGAATACAAGGAAA 59.650 41.667 25.93 0.00 42.46 3.13
2004 2323 2.711009 TCCAAGTTGTCAGGACCTGAAT 59.289 45.455 25.93 9.60 42.46 2.57
2041 2360 1.336148 TGCTTTTGGAATTGCTCTGCG 60.336 47.619 0.00 0.00 0.00 5.18
2107 2426 2.993840 TCGTCAGCCTGAGCAGCT 60.994 61.111 0.00 0.00 43.56 4.24
2128 2447 2.606725 GACAAGCTCAGGAACATCATCG 59.393 50.000 0.00 0.00 0.00 3.84
2182 2501 3.904136 AATCACGACTCTGCCTTTTTG 57.096 42.857 0.00 0.00 0.00 2.44
2315 2634 1.983605 CAGACGAAACTCGCGTACATT 59.016 47.619 5.77 0.00 45.12 2.71
2415 2735 0.682292 GAGGTACATAGGCTGGGAGC 59.318 60.000 0.00 0.00 41.46 4.70
2561 2891 1.848608 CATGTCGCTCGTGTATCACAG 59.151 52.381 1.00 0.00 33.40 3.66
2591 2921 9.990360 TTGATCAAAGTATGCCGTAAGATTATA 57.010 29.630 5.45 0.00 43.02 0.98
2592 2922 8.774586 GTTGATCAAAGTATGCCGTAAGATTAT 58.225 33.333 10.35 0.00 43.02 1.28
2593 2923 7.766738 TGTTGATCAAAGTATGCCGTAAGATTA 59.233 33.333 10.35 0.00 43.02 1.75
2594 2924 6.597672 TGTTGATCAAAGTATGCCGTAAGATT 59.402 34.615 10.35 0.00 43.02 2.40
2595 2925 6.037172 GTGTTGATCAAAGTATGCCGTAAGAT 59.963 38.462 10.35 0.00 43.02 2.40
2596 2926 5.350365 GTGTTGATCAAAGTATGCCGTAAGA 59.650 40.000 10.35 0.00 43.02 2.10
2632 2962 1.217057 ATCCCCTGCCATGTTCCACT 61.217 55.000 0.00 0.00 0.00 4.00
2712 3126 6.417930 GCTTTTCCGCAAATAATAGACATTCC 59.582 38.462 0.00 0.00 0.00 3.01
2714 3128 7.067494 AGAGCTTTTCCGCAAATAATAGACATT 59.933 33.333 0.00 0.00 0.00 2.71
2724 3138 3.642705 GTGAAAGAGCTTTTCCGCAAAT 58.357 40.909 14.65 0.00 32.11 2.32
2725 3139 2.540769 CGTGAAAGAGCTTTTCCGCAAA 60.541 45.455 14.65 0.00 32.11 3.68
2726 3140 1.002900 CGTGAAAGAGCTTTTCCGCAA 60.003 47.619 14.65 0.00 32.11 4.85
2728 3142 0.865769 TCGTGAAAGAGCTTTTCCGC 59.134 50.000 14.65 0.00 32.11 5.54
2729 3143 2.863658 CTCGTGAAAGAGCTTTTCCG 57.136 50.000 14.65 15.66 32.11 4.30
2737 3151 0.809385 TACCCTCGCTCGTGAAAGAG 59.191 55.000 0.00 0.00 41.03 2.85
2741 3155 1.529152 TTGCTACCCTCGCTCGTGAA 61.529 55.000 0.00 0.00 0.00 3.18
2742 3156 1.974875 TTGCTACCCTCGCTCGTGA 60.975 57.895 0.00 0.00 0.00 4.35
2743 3157 1.805945 GTTGCTACCCTCGCTCGTG 60.806 63.158 0.00 0.00 0.00 4.35
2746 3160 1.226717 CTCGTTGCTACCCTCGCTC 60.227 63.158 0.00 0.00 0.00 5.03
2747 3161 2.885861 CTCGTTGCTACCCTCGCT 59.114 61.111 0.00 0.00 0.00 4.93
2748 3162 2.886124 GCTCGTTGCTACCCTCGC 60.886 66.667 0.00 0.00 38.95 5.03
2749 3163 2.337749 ATCGCTCGTTGCTACCCTCG 62.338 60.000 0.00 0.00 40.11 4.63
2750 3164 0.666913 TATCGCTCGTTGCTACCCTC 59.333 55.000 0.00 0.00 40.11 4.30
2751 3165 0.384669 GTATCGCTCGTTGCTACCCT 59.615 55.000 0.00 0.00 40.11 4.34
2752 3166 0.101759 TGTATCGCTCGTTGCTACCC 59.898 55.000 0.00 0.00 40.11 3.69
2755 3169 4.674475 TGTATTTGTATCGCTCGTTGCTA 58.326 39.130 2.29 0.00 40.11 3.49
2758 3172 8.272866 TCATATTTGTATTTGTATCGCTCGTTG 58.727 33.333 0.00 0.00 0.00 4.10
2761 3175 7.736017 GTGTCATATTTGTATTTGTATCGCTCG 59.264 37.037 0.00 0.00 0.00 5.03
2763 3177 7.436970 TCGTGTCATATTTGTATTTGTATCGCT 59.563 33.333 0.00 0.00 0.00 4.93
2765 3179 8.964150 TCTCGTGTCATATTTGTATTTGTATCG 58.036 33.333 0.00 0.00 0.00 2.92
2872 3309 9.165035 CTTTTATGTTGGATAATTGGCATGTTT 57.835 29.630 0.00 0.00 0.00 2.83
2956 3394 9.674824 CAGGTTTACGAATAACCACTACTATAG 57.325 37.037 16.29 0.00 46.01 1.31
3065 3629 5.518847 TCAGATTCGAAACGGATTACATCAC 59.481 40.000 0.00 0.00 0.00 3.06
3068 3632 5.661458 AGTCAGATTCGAAACGGATTACAT 58.339 37.500 11.05 0.00 0.00 2.29
3071 3635 7.092079 TGTTTAGTCAGATTCGAAACGGATTA 58.908 34.615 11.05 8.70 34.72 1.75
3072 3636 5.929992 TGTTTAGTCAGATTCGAAACGGATT 59.070 36.000 11.05 9.61 34.72 3.01
3073 3637 5.475719 TGTTTAGTCAGATTCGAAACGGAT 58.524 37.500 11.05 4.32 34.72 4.18
3077 3650 6.369065 ACCAGATGTTTAGTCAGATTCGAAAC 59.631 38.462 0.00 0.00 33.39 2.78
3139 3712 3.737032 TGCGAATATGGATGTTACCGA 57.263 42.857 0.00 0.00 0.00 4.69
3140 3713 4.450757 TGAATGCGAATATGGATGTTACCG 59.549 41.667 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.