Multiple sequence alignment - TraesCS7A01G235100

Loading Multiple Alignment...

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 TraesCS7A01G235100 chr7A 100.000 3315 0 0 1 3315 206938345 206935031 0.000000e+00 6122.0
1 TraesCS7A01G235100 chr7A 97.059 34 1 0 2538 2571 206935773 206935740 1.280000e-04 58.4
2 TraesCS7A01G235100 chr7A 97.059 34 1 0 2573 2606 206935808 206935775 1.280000e-04 58.4
3 TraesCS7A01G235100 chr7D 93.177 2609 92 35 1 2539 197878741 197876149 0.000000e+00 3753.0
4 TraesCS7A01G235100 chr7D 83.824 272 24 10 2944 3195 197873968 197873697 1.190000e-59 241.0
5 TraesCS7A01G235100 chr7B 94.095 1321 59 9 571 1880 162115228 162113916 0.000000e+00 1989.0
6 TraesCS7A01G235100 chr7B 97.038 574 17 0 1 574 162115879 162115306 0.000000e+00 966.0
7 TraesCS7A01G235100 chr7B 90.691 709 41 11 1877 2566 162113878 162113176 0.000000e+00 920.0
8 TraesCS7A01G235100 chr7B 92.428 449 32 2 2869 3315 162101592 162101144 1.000000e-179 640.0
9 TraesCS7A01G235100 chr7B 94.444 72 3 1 2801 2871 162101714 162101643 3.500000e-20 110.0
10 TraesCS7A01G235100 chr3A 95.455 44 2 0 2679 2722 1747438 1747395 1.650000e-08 71.3
11 TraesCS7A01G235100 chr2B 97.368 38 1 0 2588 2625 373507136 373507099 7.680000e-07 65.8


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 TraesCS7A01G235100 chr7A 206935031 206938345 3314 True 2079.600000 6122 98.039333 1 3315 3 chr7A.!!$R1 3314
1 TraesCS7A01G235100 chr7D 197873697 197878741 5044 True 1997.000000 3753 88.500500 1 3195 2 chr7D.!!$R1 3194
2 TraesCS7A01G235100 chr7B 162113176 162115879 2703 True 1291.666667 1989 93.941333 1 2566 3 chr7B.!!$R2 2565
3 TraesCS7A01G235100 chr7B 162101144 162101714 570 True 375.000000 640 93.436000 2801 3315 2 chr7B.!!$R1 514

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
980 1071 0.17902 CACCTCACAGGCACAGGAAA 60.179 55.0 0.0 0.0 39.63 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2754 4047 0.035343 GAAGAGTGTTACCTGGGCCC 60.035 60.0 17.59 17.59 0.0 5.8 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
76 77 8.010697 TCCCAAGGTGAGAATATCTTGAGTATA 58.989 37.037 0.00 0.00 38.96 1.47
253 255 4.345257 CAGGGCTGTATGATAGGTTAGTGT 59.655 45.833 0.00 0.00 0.00 3.55
269 271 8.095452 AGGTTAGTGTAAATCCTTCATGAGAT 57.905 34.615 0.00 0.00 0.00 2.75
313 315 6.417191 AAAATTCATTTAGCATTGCAGCTG 57.583 33.333 10.11 10.11 46.11 4.24
561 563 3.995199 TGTATGTATAGGCAGCTCAAGC 58.005 45.455 0.00 0.00 42.49 4.01
580 663 7.361713 GCTCAAGCTGTAGAGTAGTAGGATATG 60.362 44.444 11.36 0.00 38.21 1.78
605 688 3.561725 GTCCTTGCTGGCATGTATAGTTC 59.438 47.826 0.00 0.00 35.26 3.01
615 698 7.094162 GCTGGCATGTATAGTTCTACTCATAGA 60.094 40.741 0.00 0.00 35.53 1.98
710 793 5.302059 TCCTAGAGTACCAGAACATGTATGC 59.698 44.000 0.00 0.00 0.00 3.14
744 827 9.893305 GGAATATGACCTTATTAAAAACATCGG 57.107 33.333 0.00 0.00 0.00 4.18
748 831 5.195185 GACCTTATTAAAAACATCGGGGGA 58.805 41.667 0.00 0.00 0.00 4.81
749 832 5.198207 ACCTTATTAAAAACATCGGGGGAG 58.802 41.667 0.00 0.00 0.00 4.30
752 835 6.183360 CCTTATTAAAAACATCGGGGGAGAAC 60.183 42.308 0.00 0.00 0.00 3.01
781 871 6.280643 TGAGCAATCTATATTTACACGTGCT 58.719 36.000 17.22 5.64 42.20 4.40
799 889 8.484799 ACACGTGCTGTTATAATGTAAATATCG 58.515 33.333 17.22 0.00 0.00 2.92
921 1012 3.533606 ACTCGTCAGCAGCAAATATCT 57.466 42.857 0.00 0.00 0.00 1.98
949 1040 4.530161 AGAGTTTATCTCCAGTTGCTCAGT 59.470 41.667 0.00 0.00 43.71 3.41
964 1055 1.203523 CTCAGTAGTCACAGCCTCACC 59.796 57.143 0.00 0.00 0.00 4.02
965 1056 1.203063 TCAGTAGTCACAGCCTCACCT 60.203 52.381 0.00 0.00 0.00 4.00
966 1057 1.203523 CAGTAGTCACAGCCTCACCTC 59.796 57.143 0.00 0.00 0.00 3.85
967 1058 1.203063 AGTAGTCACAGCCTCACCTCA 60.203 52.381 0.00 0.00 0.00 3.86
968 1059 1.067495 GTAGTCACAGCCTCACCTCAC 60.067 57.143 0.00 0.00 0.00 3.51
980 1071 0.179020 CACCTCACAGGCACAGGAAA 60.179 55.000 0.00 0.00 39.63 3.13
981 1072 0.550914 ACCTCACAGGCACAGGAAAA 59.449 50.000 0.00 0.00 39.63 2.29
1302 1393 8.343366 GTTCTTCGATTTACTCTTCTTTTTGGT 58.657 33.333 0.00 0.00 0.00 3.67
1426 1527 3.562141 TCGTGGTAAACTGTGAATTGGTG 59.438 43.478 0.00 0.00 0.00 4.17
1451 1554 0.033796 CTGTTCAGGGCCATGACCAT 60.034 55.000 21.89 0.00 29.21 3.55
1677 1780 3.883830 ACACCAGTGCTTCAGAGATAG 57.116 47.619 0.00 0.00 0.00 2.08
1728 1831 1.538629 TCACCATGCTGGGGAGACA 60.539 57.895 3.32 0.00 46.95 3.41
1961 2105 1.303561 GGTGCTGGAGTTCATGGCA 60.304 57.895 0.00 0.00 0.00 4.92
2046 2190 4.394712 CGGCGGCCAGGAACTTCT 62.395 66.667 20.71 0.00 34.60 2.85
2132 2276 3.994392 GCTGTTCATTCCTACGAACTGAA 59.006 43.478 11.73 0.00 41.15 3.02
2189 2347 2.580322 TGATTTGCAGGGGGTGAAGATA 59.420 45.455 0.00 0.00 0.00 1.98
2299 2457 2.573915 GTTGGGAGACTGGAGGAAATCT 59.426 50.000 0.00 0.00 0.00 2.40
2322 2480 3.257393 GAACAGACAGGTAGATGTGCAG 58.743 50.000 0.00 0.00 32.25 4.41
2324 2482 2.634940 ACAGACAGGTAGATGTGCAGTT 59.365 45.455 0.00 0.00 32.25 3.16
2333 2491 1.273606 AGATGTGCAGTTGCTAGTCGT 59.726 47.619 5.62 0.00 42.66 4.34
2395 2554 4.544651 TGTTGTACGACGTGCTGTAATAA 58.455 39.130 16.98 0.00 0.00 1.40
2462 2634 7.332557 TGTAGAATTCTCGCCCAACTTTATTA 58.667 34.615 12.24 0.00 0.00 0.98
2463 2635 7.825270 TGTAGAATTCTCGCCCAACTTTATTAA 59.175 33.333 12.24 0.00 0.00 1.40
2464 2636 7.881775 AGAATTCTCGCCCAACTTTATTAAT 57.118 32.000 0.88 0.00 0.00 1.40
2504 2676 8.768397 GTCCATAGGTATAATGGTTGGATCATA 58.232 37.037 0.00 0.00 43.72 2.15
2505 2677 9.519488 TCCATAGGTATAATGGTTGGATCATAT 57.481 33.333 0.00 0.00 43.72 1.78
2509 2681 7.865820 AGGTATAATGGTTGGATCATATGAGG 58.134 38.462 11.78 0.00 0.00 3.86
2510 2682 7.056635 GGTATAATGGTTGGATCATATGAGGG 58.943 42.308 11.78 0.00 0.00 4.30
2511 2683 6.725101 ATAATGGTTGGATCATATGAGGGT 57.275 37.500 11.78 0.00 0.00 4.34
2512 2684 5.408079 AATGGTTGGATCATATGAGGGTT 57.592 39.130 11.78 0.00 0.00 4.11
2534 2706 2.682856 CCCAACCAAATATGACGACCTG 59.317 50.000 0.00 0.00 0.00 4.00
2539 2711 2.936498 CCAAATATGACGACCTGTGTCC 59.064 50.000 0.00 0.00 38.32 4.02
2546 2718 2.492088 TGACGACCTGTGTCCAGATTAG 59.508 50.000 0.00 0.00 41.50 1.73
2558 2730 4.081697 TGTCCAGATTAGATGCGAACTTGA 60.082 41.667 0.00 0.00 0.00 3.02
2566 2738 4.371855 AGATGCGAACTTGACGAGATTA 57.628 40.909 0.00 0.00 0.00 1.75
2567 2739 4.938080 AGATGCGAACTTGACGAGATTAT 58.062 39.130 0.00 0.00 0.00 1.28
2570 3863 6.638873 AGATGCGAACTTGACGAGATTATAAG 59.361 38.462 0.00 0.00 0.00 1.73
2574 3867 6.088350 GCGAACTTGACGAGATTATAAGATCC 59.912 42.308 0.00 0.00 0.00 3.36
2576 3869 7.324856 CGAACTTGACGAGATTATAAGATCCAG 59.675 40.741 0.00 0.00 0.00 3.86
2585 3878 9.462174 CGAGATTATAAGATCCAGATTAGATGC 57.538 37.037 0.00 0.00 0.00 3.91
2586 3879 9.462174 GAGATTATAAGATCCAGATTAGATGCG 57.538 37.037 0.00 0.00 0.00 4.73
2590 3883 5.543507 AAGATCCAGATTAGATGCGAACT 57.456 39.130 0.00 0.00 0.00 3.01
2593 3886 4.736126 TCCAGATTAGATGCGAACTTGA 57.264 40.909 0.00 0.00 0.00 3.02
2595 3888 3.243877 CCAGATTAGATGCGAACTTGACG 59.756 47.826 0.00 0.00 0.00 4.35
2602 3895 4.938080 AGATGCGAACTTGACGAGATTAT 58.062 39.130 0.00 0.00 0.00 1.28
2631 3924 3.297830 AAATTAAAGTTCCTGCACCGC 57.702 42.857 0.00 0.00 0.00 5.68
2634 3927 0.107831 TAAAGTTCCTGCACCGCTGT 59.892 50.000 0.00 0.00 0.00 4.40
2646 3939 0.615331 ACCGCTGTGGACATCTTCAT 59.385 50.000 15.34 0.00 42.00 2.57
2647 3940 1.012086 CCGCTGTGGACATCTTCATG 58.988 55.000 0.00 0.00 42.00 3.07
2652 3945 2.161855 TGTGGACATCTTCATGTTGCC 58.838 47.619 0.00 0.00 43.79 4.52
2653 3946 2.224843 TGTGGACATCTTCATGTTGCCT 60.225 45.455 0.00 0.00 43.79 4.75
2655 3948 3.624861 GTGGACATCTTCATGTTGCCTAG 59.375 47.826 0.00 0.00 43.79 3.02
2657 3950 4.469586 TGGACATCTTCATGTTGCCTAGTA 59.530 41.667 0.00 0.00 43.79 1.82
2660 3953 3.165058 TCTTCATGTTGCCTAGTAGCG 57.835 47.619 0.00 0.00 34.65 4.26
2664 3957 2.761767 TCATGTTGCCTAGTAGCGGTAA 59.238 45.455 0.00 0.00 34.65 2.85
2665 3958 3.196039 TCATGTTGCCTAGTAGCGGTAAA 59.804 43.478 0.00 0.00 34.65 2.01
2666 3959 3.681593 TGTTGCCTAGTAGCGGTAAAA 57.318 42.857 0.00 0.00 34.65 1.52
2667 3960 3.592059 TGTTGCCTAGTAGCGGTAAAAG 58.408 45.455 0.00 0.00 34.65 2.27
2668 3961 2.304751 TGCCTAGTAGCGGTAAAAGC 57.695 50.000 0.00 0.00 34.65 3.51
2669 3962 1.551430 TGCCTAGTAGCGGTAAAAGCA 59.449 47.619 0.00 0.73 37.01 3.91
2670 3963 2.202566 GCCTAGTAGCGGTAAAAGCAG 58.797 52.381 0.00 0.00 37.01 4.24
2671 3964 2.418334 GCCTAGTAGCGGTAAAAGCAGT 60.418 50.000 0.00 0.00 37.01 4.40
2672 3965 3.445857 CCTAGTAGCGGTAAAAGCAGTC 58.554 50.000 0.00 0.00 37.01 3.51
2673 3966 3.119245 CCTAGTAGCGGTAAAAGCAGTCA 60.119 47.826 0.00 0.00 37.01 3.41
2674 3967 3.396260 AGTAGCGGTAAAAGCAGTCAA 57.604 42.857 0.00 0.00 37.01 3.18
2675 3968 3.326747 AGTAGCGGTAAAAGCAGTCAAG 58.673 45.455 0.00 0.00 37.01 3.02
2676 3969 2.256117 AGCGGTAAAAGCAGTCAAGT 57.744 45.000 0.00 0.00 37.01 3.16
2677 3970 2.572290 AGCGGTAAAAGCAGTCAAGTT 58.428 42.857 0.00 0.00 37.01 2.66
2678 3971 2.949644 AGCGGTAAAAGCAGTCAAGTTT 59.050 40.909 0.00 0.00 37.01 2.66
2679 3972 3.380320 AGCGGTAAAAGCAGTCAAGTTTT 59.620 39.130 0.00 0.00 37.01 2.43
2680 3973 4.109766 GCGGTAAAAGCAGTCAAGTTTTT 58.890 39.130 0.00 0.00 36.22 1.94
2708 4001 7.994425 TTTGAGTAGTTTGGATTGCTTATCA 57.006 32.000 2.57 0.00 34.77 2.15
2709 4002 8.579850 TTTGAGTAGTTTGGATTGCTTATCAT 57.420 30.769 2.57 0.00 34.77 2.45
2710 4003 9.679661 TTTGAGTAGTTTGGATTGCTTATCATA 57.320 29.630 2.57 0.00 34.77 2.15
2711 4004 9.851686 TTGAGTAGTTTGGATTGCTTATCATAT 57.148 29.630 2.57 0.00 34.77 1.78
2717 4010 9.797642 AGTTTGGATTGCTTATCATATATGTCA 57.202 29.630 12.42 0.00 34.77 3.58
2718 4011 9.831737 GTTTGGATTGCTTATCATATATGTCAC 57.168 33.333 12.42 0.88 34.77 3.67
2719 4012 9.571816 TTTGGATTGCTTATCATATATGTCACA 57.428 29.630 12.42 3.25 34.77 3.58
2720 4013 9.743581 TTGGATTGCTTATCATATATGTCACAT 57.256 29.630 12.42 0.00 34.77 3.21
2721 4014 9.169592 TGGATTGCTTATCATATATGTCACATG 57.830 33.333 12.42 0.00 34.77 3.21
2722 4015 9.387257 GGATTGCTTATCATATATGTCACATGA 57.613 33.333 12.42 0.00 34.77 3.07
2727 4020 7.708322 GCTTATCATATATGTCACATGATCGGT 59.292 37.037 12.42 0.00 39.50 4.69
2731 4024 8.986477 TCATATATGTCACATGATCGGTAAAG 57.014 34.615 12.42 0.00 0.00 1.85
2746 4039 4.035017 CGGTAAAGCAGTCAAGTTTGTTG 58.965 43.478 0.00 0.00 0.00 3.33
2750 4043 2.648059 AGCAGTCAAGTTTGTTGAGCT 58.352 42.857 0.00 0.00 0.00 4.09
2751 4044 2.615912 AGCAGTCAAGTTTGTTGAGCTC 59.384 45.455 6.82 6.82 0.00 4.09
2753 4046 3.065925 GCAGTCAAGTTTGTTGAGCTCTT 59.934 43.478 16.19 0.00 0.00 2.85
2754 4047 4.595116 CAGTCAAGTTTGTTGAGCTCTTG 58.405 43.478 16.19 9.15 37.44 3.02
2755 4048 3.629398 AGTCAAGTTTGTTGAGCTCTTGG 59.371 43.478 16.19 0.00 36.94 3.61
2756 4049 2.951642 TCAAGTTTGTTGAGCTCTTGGG 59.048 45.455 16.19 0.00 36.94 4.12
2757 4050 1.322442 AGTTTGTTGAGCTCTTGGGC 58.678 50.000 16.19 1.19 0.00 5.36
2758 4051 0.315251 GTTTGTTGAGCTCTTGGGCC 59.685 55.000 16.19 0.00 0.00 5.80
2759 4052 0.827507 TTTGTTGAGCTCTTGGGCCC 60.828 55.000 17.59 17.59 0.00 5.80
2761 4054 1.676967 GTTGAGCTCTTGGGCCCAG 60.677 63.158 26.87 19.10 0.00 4.45
2762 4055 2.910737 TTGAGCTCTTGGGCCCAGG 61.911 63.158 27.81 27.81 0.00 4.45
2763 4056 3.334054 GAGCTCTTGGGCCCAGGT 61.334 66.667 31.34 22.75 0.00 4.00
2764 4057 1.995626 GAGCTCTTGGGCCCAGGTA 60.996 63.158 31.34 17.86 0.00 3.08
2765 4058 1.541368 AGCTCTTGGGCCCAGGTAA 60.541 57.895 31.34 13.91 0.00 2.85
2766 4059 1.378646 GCTCTTGGGCCCAGGTAAC 60.379 63.158 31.34 18.65 0.00 2.50
2775 4387 1.351350 GGCCCAGGTAACACTCTTCTT 59.649 52.381 0.00 0.00 41.41 2.52
2777 4389 2.615747 GCCCAGGTAACACTCTTCTTCC 60.616 54.545 0.00 0.00 41.41 3.46
2786 4398 8.491958 AGGTAACACTCTTCTTCCTTTAAAAGA 58.508 33.333 0.00 0.00 41.41 2.52
2787 4399 8.557864 GGTAACACTCTTCTTCCTTTAAAAGAC 58.442 37.037 0.00 0.00 32.64 3.01
2788 4400 6.846325 ACACTCTTCTTCCTTTAAAAGACG 57.154 37.500 0.00 0.00 32.64 4.18
2789 4401 6.579865 ACACTCTTCTTCCTTTAAAAGACGA 58.420 36.000 0.00 0.00 32.64 4.20
2791 4403 7.171678 ACACTCTTCTTCCTTTAAAAGACGATG 59.828 37.037 0.00 0.00 32.58 3.84
2792 4404 6.147985 ACTCTTCTTCCTTTAAAAGACGATGC 59.852 38.462 0.00 0.00 32.58 3.91
2794 4406 6.710744 TCTTCTTCCTTTAAAAGACGATGCTT 59.289 34.615 0.00 0.00 32.64 3.91
2795 4407 6.877611 TCTTCCTTTAAAAGACGATGCTTT 57.122 33.333 0.00 0.00 39.65 3.51
2796 4408 7.972832 TCTTCCTTTAAAAGACGATGCTTTA 57.027 32.000 0.00 0.00 37.12 1.85
2797 4409 8.561738 TCTTCCTTTAAAAGACGATGCTTTAT 57.438 30.769 0.00 0.00 37.12 1.40
2799 4411 9.626045 CTTCCTTTAAAAGACGATGCTTTATTT 57.374 29.630 0.00 0.00 37.12 1.40
2819 4525 5.523438 TTTGGGCAAACGAGAAGTAAAAT 57.477 34.783 0.00 0.00 0.00 1.82
2823 4529 5.531659 TGGGCAAACGAGAAGTAAAATTACA 59.468 36.000 6.13 0.00 36.12 2.41
2824 4530 6.084277 GGGCAAACGAGAAGTAAAATTACAG 58.916 40.000 6.13 0.00 36.12 2.74
2871 4973 9.337714 ACTATTGTTACTAAGGGGGTTTAGTTA 57.662 33.333 4.02 0.00 40.11 2.24
2877 4979 9.035890 GTTACTAAGGGGGTTTAGTTACTAAGA 57.964 37.037 4.94 0.00 40.11 2.10
2891 4993 7.439108 AGTTACTAAGAGGGTTTATGCAGAT 57.561 36.000 0.00 0.00 0.00 2.90
2899 5001 0.381801 GTTTATGCAGATGCCGGGTG 59.618 55.000 2.18 0.00 41.18 4.61
2903 5005 0.464373 ATGCAGATGCCGGGTGTAAG 60.464 55.000 2.18 0.00 41.18 2.34
2904 5006 1.220749 GCAGATGCCGGGTGTAAGA 59.779 57.895 2.18 0.00 34.31 2.10
2915 5017 4.094442 GCCGGGTGTAAGACTTAAATCTTG 59.906 45.833 9.38 0.00 39.33 3.02
2939 5041 6.935771 TGTAAGTAATAAAGCGACCCTTTTCA 59.064 34.615 0.00 0.00 40.85 2.69
3131 5254 7.415086 TCCTAGGTTTTTAATTATCCAGGCAA 58.585 34.615 9.08 0.00 0.00 4.52
3196 5319 1.267121 GGCCTCTCACTACCTTGACA 58.733 55.000 0.00 0.00 0.00 3.58
3204 5327 2.028476 TCACTACCTTGACAATGTCCGG 60.028 50.000 11.24 13.23 0.00 5.14
3214 5337 3.310860 AATGTCCGGTCAGGCGTCC 62.311 63.158 7.60 0.00 40.77 4.79
3258 5381 2.597510 GCCTGTTTTGTCGGCCCT 60.598 61.111 0.00 0.00 37.86 5.19
3260 5383 1.228124 CCTGTTTTGTCGGCCCTCA 60.228 57.895 0.00 0.00 0.00 3.86
3278 5401 5.988561 GCCCTCATAAGATCTTGACACTTAG 59.011 44.000 18.47 5.70 31.25 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
253 255 7.556275 GGTAAACCACATCTCATGAAGGATTTA 59.444 37.037 0.00 0.00 34.62 1.40
285 287 7.906527 GCTGCAATGCTAAATGAATTTTTAAGG 59.093 33.333 6.82 0.00 0.00 2.69
307 309 2.745492 GGCACACTCCTCAGCTGC 60.745 66.667 9.47 0.00 0.00 5.25
313 315 1.202698 ACTGAAACAGGCACACTCCTC 60.203 52.381 0.00 0.00 35.51 3.71
450 452 1.689575 GGTGACCCATAGAGCTCCTCA 60.690 57.143 10.93 0.00 32.06 3.86
561 563 6.655848 GGACCACATATCCTACTACTCTACAG 59.344 46.154 0.00 0.00 33.03 2.74
580 663 0.322456 TACATGCCAGCAAGGACCAC 60.322 55.000 0.00 0.00 41.22 4.16
605 688 6.522233 GATGTGTTGTGCATCTATGAGTAG 57.478 41.667 0.00 0.00 39.53 2.57
615 698 3.811722 CAACGTAGATGTGTTGTGCAT 57.188 42.857 0.00 0.00 40.37 3.96
710 793 9.489084 TTTAATAAGGTCATATTCCTGATCGTG 57.511 33.333 0.00 0.00 35.27 4.35
738 821 0.399075 AAAACGTTCTCCCCCGATGT 59.601 50.000 0.00 0.00 0.00 3.06
744 827 1.314730 TTGCTCAAAACGTTCTCCCC 58.685 50.000 0.00 0.00 0.00 4.81
749 832 9.982291 TGTAAATATAGATTGCTCAAAACGTTC 57.018 29.630 0.00 0.00 0.00 3.95
752 835 8.114290 ACGTGTAAATATAGATTGCTCAAAACG 58.886 33.333 0.00 0.00 0.00 3.60
799 889 2.623416 ACCAAAAAGCAAGCAGACTACC 59.377 45.455 0.00 0.00 0.00 3.18
875 966 6.489361 ACAAGAAGCTGTCATTTTCAGAGAAT 59.511 34.615 0.00 0.00 35.20 2.40
945 1036 1.203063 AGGTGAGGCTGTGACTACTGA 60.203 52.381 0.00 0.00 0.00 3.41
949 1040 1.257743 GTGAGGTGAGGCTGTGACTA 58.742 55.000 0.00 0.00 0.00 2.59
984 1075 3.565307 TGCCATTTCTCACTTCAGGTTT 58.435 40.909 0.00 0.00 0.00 3.27
1347 1439 1.181741 ACAGCTGCTCCTTGTCGAGA 61.182 55.000 15.27 0.00 30.97 4.04
1362 1457 4.864806 TCTGATATCTCACGACAAAACAGC 59.135 41.667 3.98 0.00 0.00 4.40
1426 1527 2.627699 TCATGGCCCTGAACAGAAAAAC 59.372 45.455 8.44 0.00 0.00 2.43
1451 1554 1.579964 CCTCATTCAGCAACAGCGCA 61.580 55.000 11.47 0.00 0.00 6.09
1562 1665 2.092323 GGCCCATTCCAAGAACTGTAC 58.908 52.381 0.00 0.00 0.00 2.90
1728 1831 2.726821 AGAACATCGTCCATGGCAAAT 58.273 42.857 6.96 0.00 36.72 2.32
1803 1906 1.645710 AACTCGGACCATCTGGACTT 58.354 50.000 2.55 0.00 38.94 3.01
1961 2105 2.397413 CTTCCTTGGGCTGTGGACGT 62.397 60.000 0.00 0.00 0.00 4.34
2015 2159 2.431260 GCCGCGAACACGTCCTTA 60.431 61.111 8.23 0.00 0.00 2.69
2046 2190 1.273606 CTGCTTCTCGAGTTTCCTGGA 59.726 52.381 13.13 0.00 0.00 3.86
2050 2194 2.003196 CTCCTGCTTCTCGAGTTTCC 57.997 55.000 13.13 0.48 0.00 3.13
2132 2276 4.818546 CAGTCTCTGAACTTCACATGGTTT 59.181 41.667 0.00 0.00 32.44 3.27
2189 2347 1.377725 CTGCCGTTTCAGCCTCCAT 60.378 57.895 0.00 0.00 0.00 3.41
2245 2403 0.865769 CGAACAAACTCTTCCACCGG 59.134 55.000 0.00 0.00 0.00 5.28
2299 2457 2.028112 GCACATCTACCTGTCTGTTCCA 60.028 50.000 0.00 0.00 0.00 3.53
2322 2480 3.645884 TCACTAACCAACGACTAGCAAC 58.354 45.455 0.00 0.00 0.00 4.17
2324 2482 3.368013 CCATCACTAACCAACGACTAGCA 60.368 47.826 0.00 0.00 0.00 3.49
2333 2491 4.102524 AGTCTTCACACCATCACTAACCAA 59.897 41.667 0.00 0.00 0.00 3.67
2395 2554 5.723887 GTCATCCTCCATCTTATATCCCAGT 59.276 44.000 0.00 0.00 0.00 4.00
2438 2610 6.679327 AATAAAGTTGGGCGAGAATTCTAC 57.321 37.500 8.25 3.61 0.00 2.59
2489 2661 6.467194 GGAACCCTCATATGATCCAACCATTA 60.467 42.308 15.36 0.00 0.00 1.90
2510 2682 3.128068 GGTCGTCATATTTGGTTGGGAAC 59.872 47.826 0.00 0.00 0.00 3.62
2511 2683 3.009695 AGGTCGTCATATTTGGTTGGGAA 59.990 43.478 0.00 0.00 0.00 3.97
2512 2684 2.574369 AGGTCGTCATATTTGGTTGGGA 59.426 45.455 0.00 0.00 0.00 4.37
2534 2706 3.786635 AGTTCGCATCTAATCTGGACAC 58.213 45.455 0.00 0.00 0.00 3.67
2539 2711 4.105486 TCGTCAAGTTCGCATCTAATCTG 58.895 43.478 0.00 0.00 0.00 2.90
2546 2718 6.637254 TCTTATAATCTCGTCAAGTTCGCATC 59.363 38.462 0.00 0.00 0.00 3.91
2566 2738 7.238486 AGTTCGCATCTAATCTGGATCTTAT 57.762 36.000 0.00 0.00 0.00 1.73
2567 2739 6.656632 AGTTCGCATCTAATCTGGATCTTA 57.343 37.500 0.00 0.00 0.00 2.10
2570 3863 5.176590 GTCAAGTTCGCATCTAATCTGGATC 59.823 44.000 0.00 0.00 0.00 3.36
2574 3867 4.105486 TCGTCAAGTTCGCATCTAATCTG 58.895 43.478 0.00 0.00 0.00 2.90
2576 3869 4.352039 TCTCGTCAAGTTCGCATCTAATC 58.648 43.478 0.00 0.00 0.00 1.75
2585 3878 4.355437 AGCTCATAATCTCGTCAAGTTCG 58.645 43.478 0.00 0.00 0.00 3.95
2586 3879 6.654793 AAAGCTCATAATCTCGTCAAGTTC 57.345 37.500 0.00 0.00 0.00 3.01
2627 3920 0.615331 ATGAAGATGTCCACAGCGGT 59.385 50.000 0.00 0.00 37.34 5.68
2631 3924 2.163010 GGCAACATGAAGATGTCCACAG 59.837 50.000 0.00 0.00 42.30 3.66
2634 3927 2.885135 AGGCAACATGAAGATGTCCA 57.115 45.000 0.00 0.00 42.30 4.02
2646 3939 3.592059 CTTTTACCGCTACTAGGCAACA 58.408 45.455 0.00 0.00 41.41 3.33
2647 3940 2.350804 GCTTTTACCGCTACTAGGCAAC 59.649 50.000 0.00 0.00 0.00 4.17
2652 3945 4.106029 TGACTGCTTTTACCGCTACTAG 57.894 45.455 0.00 0.00 0.00 2.57
2653 3946 4.021719 ACTTGACTGCTTTTACCGCTACTA 60.022 41.667 0.00 0.00 0.00 1.82
2655 3948 3.064931 ACTTGACTGCTTTTACCGCTAC 58.935 45.455 0.00 0.00 0.00 3.58
2657 3950 2.256117 ACTTGACTGCTTTTACCGCT 57.744 45.000 0.00 0.00 0.00 5.52
2682 3975 8.855110 TGATAAGCAATCCAAACTACTCAAAAA 58.145 29.630 0.00 0.00 33.22 1.94
2683 3976 8.402798 TGATAAGCAATCCAAACTACTCAAAA 57.597 30.769 0.00 0.00 33.22 2.44
2684 3977 7.994425 TGATAAGCAATCCAAACTACTCAAA 57.006 32.000 0.00 0.00 33.22 2.69
2685 3978 9.851686 ATATGATAAGCAATCCAAACTACTCAA 57.148 29.630 0.00 0.00 33.22 3.02
2691 3984 9.797642 TGACATATATGATAAGCAATCCAAACT 57.202 29.630 19.63 0.00 33.22 2.66
2692 3985 9.831737 GTGACATATATGATAAGCAATCCAAAC 57.168 33.333 19.63 0.00 33.22 2.93
2693 3986 9.571816 TGTGACATATATGATAAGCAATCCAAA 57.428 29.630 19.63 0.00 33.22 3.28
2694 3987 9.743581 ATGTGACATATATGATAAGCAATCCAA 57.256 29.630 19.63 0.00 33.22 3.53
2695 3988 9.169592 CATGTGACATATATGATAAGCAATCCA 57.830 33.333 19.63 4.99 33.22 3.41
2696 3989 9.387257 TCATGTGACATATATGATAAGCAATCC 57.613 33.333 19.63 0.06 32.70 3.01
2699 3992 9.090692 CGATCATGTGACATATATGATAAGCAA 57.909 33.333 19.63 0.81 44.61 3.91
2700 3993 7.707893 CCGATCATGTGACATATATGATAAGCA 59.292 37.037 19.63 10.25 44.61 3.91
2701 3994 7.708322 ACCGATCATGTGACATATATGATAAGC 59.292 37.037 19.63 5.41 44.61 3.09
2705 3998 9.591792 CTTTACCGATCATGTGACATATATGAT 57.408 33.333 19.63 0.00 46.46 2.45
2706 3999 7.545615 GCTTTACCGATCATGTGACATATATGA 59.454 37.037 19.63 0.00 40.56 2.15
2707 4000 7.331687 TGCTTTACCGATCATGTGACATATATG 59.668 37.037 11.29 11.29 0.00 1.78
2708 4001 7.386059 TGCTTTACCGATCATGTGACATATAT 58.614 34.615 0.00 0.00 0.00 0.86
2709 4002 6.754193 TGCTTTACCGATCATGTGACATATA 58.246 36.000 0.00 0.00 0.00 0.86
2710 4003 5.610398 TGCTTTACCGATCATGTGACATAT 58.390 37.500 0.00 0.00 0.00 1.78
2711 4004 5.017294 TGCTTTACCGATCATGTGACATA 57.983 39.130 0.00 0.00 0.00 2.29
2712 4005 3.872696 TGCTTTACCGATCATGTGACAT 58.127 40.909 0.00 0.00 0.00 3.06
2713 4006 3.261580 CTGCTTTACCGATCATGTGACA 58.738 45.455 0.00 0.00 0.00 3.58
2714 4007 3.262420 ACTGCTTTACCGATCATGTGAC 58.738 45.455 0.00 0.00 0.00 3.67
2715 4008 3.056179 TGACTGCTTTACCGATCATGTGA 60.056 43.478 0.00 0.00 0.00 3.58
2716 4009 3.261580 TGACTGCTTTACCGATCATGTG 58.738 45.455 0.00 0.00 0.00 3.21
2717 4010 3.610040 TGACTGCTTTACCGATCATGT 57.390 42.857 0.00 0.00 0.00 3.21
2718 4011 3.935203 ACTTGACTGCTTTACCGATCATG 59.065 43.478 0.00 0.00 0.00 3.07
2719 4012 4.207891 ACTTGACTGCTTTACCGATCAT 57.792 40.909 0.00 0.00 0.00 2.45
2720 4013 3.678056 ACTTGACTGCTTTACCGATCA 57.322 42.857 0.00 0.00 0.00 2.92
2721 4014 4.213482 ACAAACTTGACTGCTTTACCGATC 59.787 41.667 0.00 0.00 0.00 3.69
2722 4015 4.134563 ACAAACTTGACTGCTTTACCGAT 58.865 39.130 0.00 0.00 0.00 4.18
2723 4016 3.537580 ACAAACTTGACTGCTTTACCGA 58.462 40.909 0.00 0.00 0.00 4.69
2724 4017 3.963383 ACAAACTTGACTGCTTTACCG 57.037 42.857 0.00 0.00 0.00 4.02
2727 4020 4.640201 AGCTCAACAAACTTGACTGCTTTA 59.360 37.500 0.00 0.00 0.00 1.85
2731 4024 2.615912 AGAGCTCAACAAACTTGACTGC 59.384 45.455 17.77 0.00 0.00 4.40
2746 4039 1.562672 TTACCTGGGCCCAAGAGCTC 61.563 60.000 27.82 5.27 0.00 4.09
2750 4043 0.770557 AGTGTTACCTGGGCCCAAGA 60.771 55.000 27.82 11.74 0.00 3.02
2751 4044 0.322546 GAGTGTTACCTGGGCCCAAG 60.323 60.000 28.29 23.78 0.00 3.61
2753 4046 0.770557 AAGAGTGTTACCTGGGCCCA 60.771 55.000 26.67 26.67 0.00 5.36
2754 4047 0.035343 GAAGAGTGTTACCTGGGCCC 60.035 60.000 17.59 17.59 0.00 5.80
2755 4048 0.984995 AGAAGAGTGTTACCTGGGCC 59.015 55.000 0.00 0.00 0.00 5.80
2756 4049 2.615747 GGAAGAAGAGTGTTACCTGGGC 60.616 54.545 0.00 0.00 0.00 5.36
2757 4050 2.907042 AGGAAGAAGAGTGTTACCTGGG 59.093 50.000 0.00 0.00 0.00 4.45
2758 4051 4.625607 AAGGAAGAAGAGTGTTACCTGG 57.374 45.455 0.00 0.00 0.00 4.45
2759 4052 8.446599 TTTTAAAGGAAGAAGAGTGTTACCTG 57.553 34.615 0.00 0.00 0.00 4.00
2761 4054 8.557864 GTCTTTTAAAGGAAGAAGAGTGTTACC 58.442 37.037 1.01 0.00 35.11 2.85
2762 4055 8.274248 CGTCTTTTAAAGGAAGAAGAGTGTTAC 58.726 37.037 7.35 0.00 35.51 2.50
2763 4056 8.199449 TCGTCTTTTAAAGGAAGAAGAGTGTTA 58.801 33.333 12.35 0.00 36.94 2.41
2764 4057 7.046033 TCGTCTTTTAAAGGAAGAAGAGTGTT 58.954 34.615 12.35 0.00 36.94 3.32
2765 4058 6.579865 TCGTCTTTTAAAGGAAGAAGAGTGT 58.420 36.000 12.35 0.00 36.94 3.55
2766 4059 7.513968 CATCGTCTTTTAAAGGAAGAAGAGTG 58.486 38.462 17.24 9.22 42.15 3.51
2775 4387 8.026607 CCAAATAAAGCATCGTCTTTTAAAGGA 58.973 33.333 4.77 0.00 37.46 3.36
2777 4389 7.201435 GCCCAAATAAAGCATCGTCTTTTAAAG 60.201 37.037 0.00 0.00 37.46 1.85
2786 4398 3.584834 GTTTGCCCAAATAAAGCATCGT 58.415 40.909 0.00 0.00 36.20 3.73
2787 4399 2.598192 CGTTTGCCCAAATAAAGCATCG 59.402 45.455 0.00 0.00 36.20 3.84
2788 4400 3.843999 TCGTTTGCCCAAATAAAGCATC 58.156 40.909 0.00 0.00 36.20 3.91
2789 4401 3.509575 TCTCGTTTGCCCAAATAAAGCAT 59.490 39.130 0.00 0.00 36.20 3.79
2791 4403 3.569250 TCTCGTTTGCCCAAATAAAGC 57.431 42.857 0.00 0.00 32.36 3.51
2792 4404 5.121221 ACTTCTCGTTTGCCCAAATAAAG 57.879 39.130 0.00 2.56 32.36 1.85
2794 4406 6.636562 TTTACTTCTCGTTTGCCCAAATAA 57.363 33.333 0.00 0.00 32.36 1.40
2795 4407 6.636562 TTTTACTTCTCGTTTGCCCAAATA 57.363 33.333 0.00 0.00 32.36 1.40
2796 4408 5.523438 TTTTACTTCTCGTTTGCCCAAAT 57.477 34.783 0.00 0.00 32.36 2.32
2797 4409 4.985538 TTTTACTTCTCGTTTGCCCAAA 57.014 36.364 0.00 0.00 0.00 3.28
2799 4411 5.531659 TGTAATTTTACTTCTCGTTTGCCCA 59.468 36.000 2.45 0.00 34.77 5.36
2871 4973 4.455606 GCATCTGCATAAACCCTCTTAGT 58.544 43.478 0.00 0.00 41.59 2.24
2877 4979 0.466189 CCGGCATCTGCATAAACCCT 60.466 55.000 4.33 0.00 44.36 4.34
2891 4993 3.262405 AGATTTAAGTCTTACACCCGGCA 59.738 43.478 0.00 0.00 0.00 5.69
2915 5017 7.368480 TGAAAAGGGTCGCTTTATTACTTAC 57.632 36.000 14.62 2.18 0.00 2.34
2930 5032 6.014242 GGAGGAGATTGATTTTTGAAAAGGGT 60.014 38.462 0.00 0.00 0.00 4.34
2932 5034 7.237209 AGGAGGAGATTGATTTTTGAAAAGG 57.763 36.000 0.00 0.00 0.00 3.11
2939 5041 6.855375 AGGGATAGGAGGAGATTGATTTTT 57.145 37.500 0.00 0.00 0.00 1.94
3030 5152 3.157087 ACAAGCCACCAAACAGGATAAG 58.843 45.455 0.00 0.00 41.22 1.73
3077 5199 7.444629 AAGAACTAATAAAAACGGAAGGGAC 57.555 36.000 0.00 0.00 0.00 4.46
3119 5242 2.102420 TCGTCGATGTTGCCTGGATAAT 59.898 45.455 4.21 0.00 0.00 1.28
3122 5245 0.179100 CTCGTCGATGTTGCCTGGAT 60.179 55.000 4.21 0.00 0.00 3.41
3131 5254 2.970639 CCACCACCTCGTCGATGT 59.029 61.111 4.21 0.00 0.00 3.06
3159 5282 3.054065 AGGCCAAAGAGACCTTATTCCAG 60.054 47.826 5.01 0.00 31.15 3.86
3196 5319 2.264794 GACGCCTGACCGGACATT 59.735 61.111 9.46 0.00 33.16 2.71
3214 5337 2.795231 ACCCTCACAGACCATTCATG 57.205 50.000 0.00 0.00 0.00 3.07
3223 5346 0.685097 GCAACACCTACCCTCACAGA 59.315 55.000 0.00 0.00 0.00 3.41
3226 5349 4.716003 GGCAACACCTACCCTCAC 57.284 61.111 0.00 0.00 34.51 3.51
3244 5367 2.039216 TCTTATGAGGGCCGACAAAACA 59.961 45.455 10.11 0.00 0.00 2.83
3258 5381 8.277490 ACGTACTAAGTGTCAAGATCTTATGA 57.723 34.615 7.86 0.00 0.00 2.15
3260 5383 8.277490 TGACGTACTAAGTGTCAAGATCTTAT 57.723 34.615 7.86 0.00 39.50 1.73
3278 5401 1.864711 TGCTTGTCTTGCTTGACGTAC 59.135 47.619 0.00 0.00 39.64 3.67
3287 5410 4.641777 GCCAACTGCTTGTCTTGC 57.358 55.556 0.00 0.00 36.87 4.01


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

AutoCloner maintained by Alex Coulton.