Multiple sequence alignment - TraesCS3A01G339400

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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 TraesCS3A01G339400 chr3A 100.000 3422 0 0 1 3422 586419076 586415655 0.000000e+00 6320.0
1 TraesCS3A01G339400 chr3A 87.500 96 6 6 2602 2693 529072781 529072874 4.670000e-19 106.0
2 TraesCS3A01G339400 chr3D 93.705 2494 124 7 1 2487 445033800 445031333 0.000000e+00 3705.0
3 TraesCS3A01G339400 chr3D 95.286 594 24 2 2832 3422 445030981 445030389 0.000000e+00 939.0
4 TraesCS3A01G339400 chr3D 83.529 170 22 2 2664 2833 445031226 445031063 1.640000e-33 154.0
5 TraesCS3A01G339400 chr3D 85.366 82 7 1 2521 2597 445031327 445031246 2.830000e-11 80.5
6 TraesCS3A01G339400 chr3B 91.494 1881 111 32 747 2606 583388193 583386341 0.000000e+00 2542.0
7 TraesCS3A01G339400 chr3B 94.134 716 33 5 1 716 583388900 583388194 0.000000e+00 1081.0
8 TraesCS3A01G339400 chr3B 91.797 768 52 6 2664 3422 583386334 583385569 0.000000e+00 1059.0
9 TraesCS3A01G339400 chr3B 89.655 87 7 2 2602 2688 244019301 244019217 3.610000e-20 110.0
10 TraesCS3A01G339400 chr5A 91.667 84 4 3 2602 2685 612924258 612924338 2.790000e-21 113.0
11 TraesCS3A01G339400 chr5A 88.764 89 6 4 2602 2689 643362390 643362305 4.670000e-19 106.0
12 TraesCS3A01G339400 chr2A 90.698 86 5 3 2602 2687 594541788 594541706 1.000000e-20 111.0
13 TraesCS3A01G339400 chr2A 87.000 100 8 4 2602 2701 509418889 509418795 1.300000e-19 108.0
14 TraesCS3A01G339400 chr7A 88.421 95 6 5 2602 2693 495455438 495455530 3.610000e-20 110.0
15 TraesCS3A01G339400 chr4B 88.764 89 6 4 2602 2689 191224806 191224721 4.670000e-19 106.0
16 TraesCS3A01G339400 chr1D 91.139 79 5 2 2601 2679 73687909 73687985 4.670000e-19 106.0


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 TraesCS3A01G339400 chr3A 586415655 586419076 3421 True 6320.000000 6320 100.0000 1 3422 1 chr3A.!!$R1 3421
1 TraesCS3A01G339400 chr3D 445030389 445033800 3411 True 1219.625000 3705 89.4715 1 3422 4 chr3D.!!$R1 3421
2 TraesCS3A01G339400 chr3B 583385569 583388900 3331 True 1560.666667 2542 92.4750 1 3422 3 chr3B.!!$R2 3421

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
706 707 0.526524 CAACATCGAGGAGGAGCGAC 60.527 60.0 3.06 0.0 39.56 5.19 F
2138 2158 0.035458 GGGAGGGCTGGACGATTATG 59.965 60.0 0.00 0.0 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 2397 0.038310 AGCCCAGGAACCTTAACAGC 59.962 55.0 0.0 0.0 0.0 4.40 R
3223 3344 0.539986 TTGTCCGGCTCCATACCTTC 59.460 55.0 0.0 0.0 0.0 3.46 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
59 60 2.616458 GGAGGCCATGGAACTGGGT 61.616 63.158 18.40 0.00 36.75 4.51
123 124 1.872234 GATCGCGCTAGCAACGTCA 60.872 57.895 22.11 8.56 45.49 4.35
706 707 0.526524 CAACATCGAGGAGGAGCGAC 60.527 60.000 3.06 0.00 39.56 5.19
760 761 1.290203 ACTGTCAACAGAGCAACGTG 58.710 50.000 16.71 0.00 46.59 4.49
763 764 0.582005 GTCAACAGAGCAACGTGGTC 59.418 55.000 8.52 8.52 44.62 4.02
802 803 4.571984 AGCAAAAGCACATTCTTTTTGTCC 59.428 37.500 9.72 0.00 42.48 4.02
832 833 2.064581 GCGGGAGGGAGAAAGCCTA 61.065 63.158 0.00 0.00 0.00 3.93
848 849 1.597445 GCCTAGGACGATTTCGAGTCG 60.597 57.143 14.75 17.33 43.02 4.18
863 870 1.985116 GTCGAGCCTCCTCCACCTT 60.985 63.158 0.00 0.00 34.49 3.50
864 871 1.682684 TCGAGCCTCCTCCACCTTC 60.683 63.158 0.00 0.00 34.49 3.46
909 918 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
910 919 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
911 920 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
912 921 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
913 922 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
914 923 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
915 924 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
916 925 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
917 926 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
918 927 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
919 928 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
920 929 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
921 930 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
922 931 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
923 932 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
924 933 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
925 934 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
926 935 4.646945 TCTCTCTCTCTCTCTCTCTCTCAC 59.353 50.000 0.00 0.00 0.00 3.51
1027 1044 3.254024 TTCCCGGCTGACCTCTTGC 62.254 63.158 0.00 0.00 0.00 4.01
1164 1184 4.778143 GCCCGCCAGGTGTTCGAT 62.778 66.667 0.00 0.00 38.26 3.59
1398 1418 1.143183 CTACGTGCATACCGCCCTT 59.857 57.895 0.00 0.00 41.33 3.95
1407 1427 2.457743 ATACCGCCCTTGTCAACGCA 62.458 55.000 1.86 0.00 0.00 5.24
1599 1619 2.158827 CGGGATGATTGATGGGTACACA 60.159 50.000 0.00 0.00 0.00 3.72
1611 1631 1.443872 GTACACACGCTCCTGTCGG 60.444 63.158 0.00 0.00 0.00 4.79
1614 1634 2.597805 ACACGCTCCTGTCGGTCT 60.598 61.111 0.00 0.00 0.00 3.85
1617 1637 2.126307 CGCTCCTGTCGGTCTGTG 60.126 66.667 0.00 0.00 0.00 3.66
1680 1700 4.471904 TGATCCAAGCGAGATAACTGTT 57.528 40.909 0.00 0.00 0.00 3.16
1704 1724 0.173935 CGGTTGTACCTGCGGTATCA 59.826 55.000 10.02 7.82 40.54 2.15
1862 1882 4.748277 AGATTTTCCATGAAATGCTGGG 57.252 40.909 0.00 0.00 44.97 4.45
1902 1922 6.321945 TGTCATGGACATCAATAATTTCAGGG 59.678 38.462 0.00 0.00 37.67 4.45
1903 1923 5.302568 TCATGGACATCAATAATTTCAGGGC 59.697 40.000 0.00 0.00 0.00 5.19
2019 2039 0.037139 TCAATGCTTGCAACCATGGC 60.037 50.000 13.04 4.40 0.00 4.40
2061 2081 5.594317 AGTACTGTTTTTCAGAAGCATGGTT 59.406 36.000 10.50 10.50 46.27 3.67
2072 2092 7.936496 TCAGAAGCATGGTTTATGAATACAA 57.064 32.000 18.58 2.00 39.21 2.41
2091 2111 9.823647 GAATACAATCTAACTCCAGAGATCAAA 57.176 33.333 0.70 0.00 31.02 2.69
2100 2120 5.388654 ACTCCAGAGATCAAACATTTTGGT 58.611 37.500 0.70 0.00 0.00 3.67
2133 2153 2.279073 CTAGGGAGGGCTGGACGA 59.721 66.667 0.00 0.00 0.00 4.20
2138 2158 0.035458 GGGAGGGCTGGACGATTATG 59.965 60.000 0.00 0.00 0.00 1.90
2145 2165 1.202580 GCTGGACGATTATGTGAGGCT 60.203 52.381 0.00 0.00 0.00 4.58
2169 2189 3.264450 AGCAAGTAATAAGTGGTCTGCCT 59.736 43.478 0.00 0.00 35.27 4.75
2187 2207 5.191722 TCTGCCTATGGAGGTTAATTCAGTT 59.808 40.000 0.00 0.00 45.78 3.16
2217 2237 3.846180 CTGCTGGGTTGTTGCAGT 58.154 55.556 6.09 0.00 46.23 4.40
2226 2246 3.073209 TGGGTTGTTGCAGTAAGTATGGA 59.927 43.478 0.00 0.00 0.00 3.41
2242 2262 0.417437 TGGAGAAGTGGAGATGGGGA 59.583 55.000 0.00 0.00 0.00 4.81
2259 2279 2.557452 GGGGAAGAGGGCAATGAAGAAA 60.557 50.000 0.00 0.00 0.00 2.52
2271 2291 7.836183 AGGGCAATGAAGAAAATACTAGACATT 59.164 33.333 0.00 0.00 0.00 2.71
2316 2336 4.518278 TGTGGTGGTATCCAATATGCTT 57.482 40.909 0.00 0.00 39.34 3.91
2325 2345 8.480086 GTGGTATCCAATATGCTTACTGAGCTC 61.480 44.444 6.82 6.82 43.33 4.09
2372 2392 4.036262 AGCACGAAAGCTAGTAGATGAGAG 59.964 45.833 0.00 0.00 44.50 3.20
2373 2393 4.035792 GCACGAAAGCTAGTAGATGAGAGA 59.964 45.833 0.00 0.00 0.00 3.10
2377 2397 7.167302 CACGAAAGCTAGTAGATGAGAGAAATG 59.833 40.741 0.00 0.00 0.00 2.32
2408 2428 1.114722 CCTGGGCTTGCTTTGGTTGA 61.115 55.000 0.00 0.00 0.00 3.18
2422 2442 5.645497 GCTTTGGTTGATGAGAGTCAGTAAT 59.355 40.000 0.00 0.00 0.00 1.89
2425 2445 6.358974 TGGTTGATGAGAGTCAGTAATTCA 57.641 37.500 0.00 0.00 0.00 2.57
2435 2455 7.604164 TGAGAGTCAGTAATTCAGAACCAAATC 59.396 37.037 0.00 0.00 0.00 2.17
2452 2473 3.958798 CAAATCATGGGAAGAAGCTCCAT 59.041 43.478 0.00 0.00 41.53 3.41
2454 2475 3.509517 ATGGGAAGAAGCTCCATGC 57.490 52.632 3.18 0.00 39.56 4.06
2510 2531 5.132502 TGTCTCCCTGCATTATACCAAATG 58.867 41.667 0.00 0.00 39.41 2.32
2590 2616 5.845985 TTCGTGCAAAGATAGAAGAACTG 57.154 39.130 0.00 0.00 0.00 3.16
2594 2620 5.288232 CGTGCAAAGATAGAAGAACTGAGAG 59.712 44.000 0.00 0.00 0.00 3.20
2597 2623 7.172361 GTGCAAAGATAGAAGAACTGAGAGTTT 59.828 37.037 0.00 0.00 38.80 2.66
2598 2624 7.716998 TGCAAAGATAGAAGAACTGAGAGTTTT 59.283 33.333 0.00 0.00 38.80 2.43
2599 2625 8.563732 GCAAAGATAGAAGAACTGAGAGTTTTT 58.436 33.333 0.00 0.00 38.80 1.94
2624 2650 8.691661 TTATCTTATGGGTTTCAAATCTAGCC 57.308 34.615 0.00 0.00 0.00 3.93
2625 2651 6.327386 TCTTATGGGTTTCAAATCTAGCCT 57.673 37.500 0.00 0.00 0.00 4.58
2626 2652 7.446106 TCTTATGGGTTTCAAATCTAGCCTA 57.554 36.000 0.00 0.00 0.00 3.93
2627 2653 7.280356 TCTTATGGGTTTCAAATCTAGCCTAC 58.720 38.462 0.00 0.00 0.00 3.18
2628 2654 4.230745 TGGGTTTCAAATCTAGCCTACC 57.769 45.455 0.00 0.00 0.00 3.18
2629 2655 3.053917 TGGGTTTCAAATCTAGCCTACCC 60.054 47.826 0.00 0.00 43.39 3.69
2630 2656 3.552875 GGTTTCAAATCTAGCCTACCCC 58.447 50.000 0.00 0.00 0.00 4.95
2631 2657 3.053917 GGTTTCAAATCTAGCCTACCCCA 60.054 47.826 0.00 0.00 0.00 4.96
2632 2658 4.569015 GGTTTCAAATCTAGCCTACCCCAA 60.569 45.833 0.00 0.00 0.00 4.12
2633 2659 3.926058 TCAAATCTAGCCTACCCCAAC 57.074 47.619 0.00 0.00 0.00 3.77
2634 2660 3.186283 TCAAATCTAGCCTACCCCAACA 58.814 45.455 0.00 0.00 0.00 3.33
2635 2661 3.785887 TCAAATCTAGCCTACCCCAACAT 59.214 43.478 0.00 0.00 0.00 2.71
2636 2662 3.864789 AATCTAGCCTACCCCAACATG 57.135 47.619 0.00 0.00 0.00 3.21
2637 2663 2.263895 TCTAGCCTACCCCAACATGT 57.736 50.000 0.00 0.00 0.00 3.21
2638 2664 2.557869 TCTAGCCTACCCCAACATGTT 58.442 47.619 4.92 4.92 0.00 2.71
2639 2665 2.916934 TCTAGCCTACCCCAACATGTTT 59.083 45.455 8.77 0.00 0.00 2.83
2640 2666 1.923356 AGCCTACCCCAACATGTTTG 58.077 50.000 8.77 5.40 0.00 2.93
2641 2667 0.894835 GCCTACCCCAACATGTTTGG 59.105 55.000 19.50 19.50 39.25 3.28
2650 2676 4.519540 CCAACATGTTTGGGACTAAAGG 57.480 45.455 8.77 0.00 35.96 3.11
2651 2677 3.306019 CCAACATGTTTGGGACTAAAGGC 60.306 47.826 8.77 0.00 35.96 4.35
2652 2678 3.525800 ACATGTTTGGGACTAAAGGCT 57.474 42.857 0.00 0.00 0.00 4.58
2653 2679 3.844640 ACATGTTTGGGACTAAAGGCTT 58.155 40.909 0.00 0.00 0.00 4.35
2654 2680 4.223144 ACATGTTTGGGACTAAAGGCTTT 58.777 39.130 17.76 17.76 0.00 3.51
2655 2681 4.039124 ACATGTTTGGGACTAAAGGCTTTG 59.961 41.667 22.32 13.97 0.00 2.77
2656 2682 3.637769 TGTTTGGGACTAAAGGCTTTGT 58.362 40.909 22.32 16.86 0.00 2.83
2657 2683 4.027437 TGTTTGGGACTAAAGGCTTTGTT 58.973 39.130 22.32 8.73 0.00 2.83
2658 2684 4.142049 TGTTTGGGACTAAAGGCTTTGTTG 60.142 41.667 22.32 13.85 0.00 3.33
2659 2685 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
2660 2686 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
2661 2687 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
2662 2688 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
2730 2765 7.726216 TCACAATCTCATTATCCACTATTCGT 58.274 34.615 0.00 0.00 0.00 3.85
2732 2767 8.830580 CACAATCTCATTATCCACTATTCGTTT 58.169 33.333 0.00 0.00 0.00 3.60
2771 2806 8.341903 TGTTGTTAATAAGCATCGACAATATGG 58.658 33.333 0.00 0.00 30.79 2.74
2778 2813 5.428496 AGCATCGACAATATGGTCATTTG 57.572 39.130 10.87 5.57 37.66 2.32
2784 2819 5.885352 TCGACAATATGGTCATTTGTTCCAT 59.115 36.000 10.87 12.01 43.30 3.41
2814 2849 9.968743 CAAAAAGACTAGTTCACGGTATTATTC 57.031 33.333 0.00 0.00 0.00 1.75
2819 2854 7.491696 AGACTAGTTCACGGTATTATTCTTTGC 59.508 37.037 0.00 0.00 0.00 3.68
2858 2979 8.129211 AGTTCACAGTATTACTTTTTGTTGCTC 58.871 33.333 0.00 0.00 0.00 4.26
2859 2980 7.801716 TCACAGTATTACTTTTTGTTGCTCT 57.198 32.000 0.00 0.00 0.00 4.09
2895 3016 1.904440 ATCCCTTCCAGGAAGCAGAT 58.096 50.000 22.58 21.15 40.04 2.90
2903 3024 2.082231 CCAGGAAGCAGATGTGTTGAG 58.918 52.381 0.00 0.00 0.00 3.02
2915 3036 1.308047 GTGTTGAGTGACATGTGCCA 58.692 50.000 1.15 0.00 0.00 4.92
2942 3063 2.044793 TTTCCCCTCACTGATCCACT 57.955 50.000 0.00 0.00 0.00 4.00
2950 3071 3.055602 CCTCACTGATCCACTGTTCATGA 60.056 47.826 0.00 0.00 0.00 3.07
3027 3148 2.225091 TGGCCATCTCATTGTTTCTGGT 60.225 45.455 0.00 0.00 0.00 4.00
3223 3344 2.370349 TCTACAAGAAGGCTCGAGGAG 58.630 52.381 15.58 0.00 0.00 3.69
3283 3404 2.819608 GTGAAGGCTTGTGCAAGGATTA 59.180 45.455 3.46 0.00 41.91 1.75
3375 3496 5.006649 CGTTTCCAATTCGCTGATTCATCTA 59.993 40.000 0.00 0.00 0.00 1.98
3402 3523 0.038892 CCTGTGGTGATTTGTGCTGC 60.039 55.000 0.00 0.00 0.00 5.25
3418 3539 1.730446 GCTGCGCAAGATCTGTTTTCC 60.730 52.381 13.05 0.00 43.02 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 227 4.100084 CATCCTCGCCAGGCACCA 62.100 66.667 13.30 0.00 40.12 4.17
634 635 4.241555 CGGCCCCGGATTCTCCAG 62.242 72.222 0.73 0.00 35.91 3.86
706 707 4.271816 CCGCCCGATCCTCACTCG 62.272 72.222 0.00 0.00 35.92 4.18
786 787 3.642705 GTCCAGGACAAAAAGAATGTGC 58.357 45.455 15.43 0.00 39.17 4.57
791 792 1.314730 GGCGTCCAGGACAAAAAGAA 58.685 50.000 20.13 0.00 32.09 2.52
832 833 0.099082 GCTCGACTCGAAATCGTCCT 59.901 55.000 15.94 0.00 40.50 3.85
848 849 0.325203 AGAGAAGGTGGAGGAGGCTC 60.325 60.000 5.78 5.78 0.00 4.70
863 870 2.501723 GGCATTACCTTGTCTGGAGAGA 59.498 50.000 0.00 0.00 34.51 3.10
864 871 2.911484 GGCATTACCTTGTCTGGAGAG 58.089 52.381 0.00 0.00 34.51 3.20
909 918 3.449918 TGGAGTGAGAGAGAGAGAGAGA 58.550 50.000 0.00 0.00 0.00 3.10
910 919 3.912496 TGGAGTGAGAGAGAGAGAGAG 57.088 52.381 0.00 0.00 0.00 3.20
911 920 4.525996 CAATGGAGTGAGAGAGAGAGAGA 58.474 47.826 0.00 0.00 0.00 3.10
912 921 3.067180 GCAATGGAGTGAGAGAGAGAGAG 59.933 52.174 0.00 0.00 0.00 3.20
913 922 3.023119 GCAATGGAGTGAGAGAGAGAGA 58.977 50.000 0.00 0.00 0.00 3.10
914 923 2.759535 TGCAATGGAGTGAGAGAGAGAG 59.240 50.000 0.00 0.00 0.00 3.20
915 924 2.495270 GTGCAATGGAGTGAGAGAGAGA 59.505 50.000 0.00 0.00 0.00 3.10
916 925 2.418471 GGTGCAATGGAGTGAGAGAGAG 60.418 54.545 0.00 0.00 0.00 3.20
917 926 1.552337 GGTGCAATGGAGTGAGAGAGA 59.448 52.381 0.00 0.00 0.00 3.10
918 927 1.277273 TGGTGCAATGGAGTGAGAGAG 59.723 52.381 0.00 0.00 0.00 3.20
919 928 1.351076 TGGTGCAATGGAGTGAGAGA 58.649 50.000 0.00 0.00 0.00 3.10
920 929 2.014857 CATGGTGCAATGGAGTGAGAG 58.985 52.381 0.00 0.00 0.00 3.20
921 930 1.629861 TCATGGTGCAATGGAGTGAGA 59.370 47.619 0.00 0.00 0.00 3.27
922 931 1.741706 GTCATGGTGCAATGGAGTGAG 59.258 52.381 0.00 0.00 0.00 3.51
923 932 1.073603 TGTCATGGTGCAATGGAGTGA 59.926 47.619 0.00 0.00 0.00 3.41
924 933 1.536940 TGTCATGGTGCAATGGAGTG 58.463 50.000 0.00 0.00 0.00 3.51
925 934 2.519771 ATGTCATGGTGCAATGGAGT 57.480 45.000 0.00 0.00 0.00 3.85
926 935 4.825634 AGAATATGTCATGGTGCAATGGAG 59.174 41.667 0.00 0.00 0.00 3.86
1389 1409 2.357760 GCGTTGACAAGGGCGGTA 60.358 61.111 9.75 0.00 0.00 4.02
1398 1418 1.724082 CACACGACATATGCGTTGACA 59.276 47.619 18.33 0.00 40.44 3.58
1407 1427 1.813753 GCACCCGCACACGACATAT 60.814 57.895 0.00 0.00 43.93 1.78
1452 1472 1.227674 ATTCTTCGCCGGCATCTCC 60.228 57.895 28.98 0.00 0.00 3.71
1599 1619 2.597805 ACAGACCGACAGGAGCGT 60.598 61.111 0.00 0.00 41.02 5.07
1611 1631 3.050275 GCAACGGCCTCCACAGAC 61.050 66.667 0.00 0.00 0.00 3.51
1614 1634 3.240134 GAGAGCAACGGCCTCCACA 62.240 63.158 0.00 0.00 42.56 4.17
1617 1637 1.003233 AAAGAGAGCAACGGCCTCC 60.003 57.895 0.00 0.00 42.56 4.30
1650 1670 1.298157 CGCTTGGATCAACGCCTTCA 61.298 55.000 0.00 0.00 0.00 3.02
1680 1700 2.830264 CGCAGGTACAACCGCTAAA 58.170 52.632 0.00 0.00 44.90 1.85
1704 1724 6.630188 CGCCCAAAAGAATCCTTCCAATATTT 60.630 38.462 0.00 0.00 0.00 1.40
1816 1836 6.464222 TCAGTGAGTTGTTTATAGACCCAAG 58.536 40.000 0.00 0.00 0.00 3.61
1830 1850 6.564709 TCATGGAAAATCTTCAGTGAGTTG 57.435 37.500 0.00 0.00 32.75 3.16
1862 1882 4.003648 CCATGACACCAAGTTTCTCCTAC 58.996 47.826 0.00 0.00 0.00 3.18
1902 1922 2.023223 CAACCCGTGCATTGCAAGC 61.023 57.895 13.94 9.48 41.47 4.01
1903 1923 0.664166 GACAACCCGTGCATTGCAAG 60.664 55.000 13.94 15.33 41.47 4.01
2072 2092 8.954350 CAAAATGTTTGATCTCTGGAGTTAGAT 58.046 33.333 0.00 0.00 35.15 1.98
2091 2111 7.340232 AGCATGTCTATGATACAACCAAAATGT 59.660 33.333 0.00 0.00 36.36 2.71
2100 2120 5.481824 CCTCCCTAGCATGTCTATGATACAA 59.518 44.000 0.00 0.00 36.36 2.41
2133 2153 3.641434 ACTTGCTCAGCCTCACATAAT 57.359 42.857 0.00 0.00 0.00 1.28
2138 2158 4.331168 CACTTATTACTTGCTCAGCCTCAC 59.669 45.833 0.00 0.00 0.00 3.51
2145 2165 4.253685 GCAGACCACTTATTACTTGCTCA 58.746 43.478 0.00 0.00 0.00 4.26
2169 2189 5.943416 CCACACAACTGAATTAACCTCCATA 59.057 40.000 0.00 0.00 0.00 2.74
2217 2237 4.901849 CCCATCTCCACTTCTCCATACTTA 59.098 45.833 0.00 0.00 0.00 2.24
2226 2246 2.476199 CTCTTCCCCATCTCCACTTCT 58.524 52.381 0.00 0.00 0.00 2.85
2242 2262 7.554476 GTCTAGTATTTTCTTCATTGCCCTCTT 59.446 37.037 0.00 0.00 0.00 2.85
2259 2279 9.829507 CCAGATTCTCTTTCAATGTCTAGTATT 57.170 33.333 0.00 0.00 0.00 1.89
2271 2291 5.768980 AATCACCTCCAGATTCTCTTTCA 57.231 39.130 0.00 0.00 30.16 2.69
2316 2336 3.693085 CACTAAACCTACCGAGCTCAGTA 59.307 47.826 15.40 12.15 0.00 2.74
2325 2345 3.520290 TCAGCATCACTAAACCTACCG 57.480 47.619 0.00 0.00 0.00 4.02
2355 2375 6.985645 CAGCATTTCTCTCATCTACTAGCTTT 59.014 38.462 0.00 0.00 0.00 3.51
2372 2392 3.193479 CCCAGGAACCTTAACAGCATTTC 59.807 47.826 0.00 0.00 0.00 2.17
2373 2393 3.165071 CCCAGGAACCTTAACAGCATTT 58.835 45.455 0.00 0.00 0.00 2.32
2377 2397 0.038310 AGCCCAGGAACCTTAACAGC 59.962 55.000 0.00 0.00 0.00 4.40
2408 2428 6.611613 TGGTTCTGAATTACTGACTCTCAT 57.388 37.500 0.00 0.00 0.00 2.90
2422 2442 4.996793 TCTTCCCATGATTTGGTTCTGAA 58.003 39.130 0.00 0.00 44.83 3.02
2425 2445 3.766051 GCTTCTTCCCATGATTTGGTTCT 59.234 43.478 0.00 0.00 44.83 3.01
2452 2473 6.692486 TGGAACAAAAACTCTTAAAACTGCA 58.308 32.000 0.00 0.00 31.92 4.41
2483 2504 5.132502 TGGTATAATGCAGGGAGACAATTG 58.867 41.667 3.24 3.24 0.00 2.32
2510 2531 7.329717 CACCATAAAGTAGGAAGATCTAATCGC 59.670 40.741 0.00 0.00 0.00 4.58
2511 2532 7.815068 CCACCATAAAGTAGGAAGATCTAATCG 59.185 40.741 0.00 0.00 0.00 3.34
2512 2533 8.097662 CCCACCATAAAGTAGGAAGATCTAATC 58.902 40.741 0.00 0.00 0.00 1.75
2513 2534 7.572861 ACCCACCATAAAGTAGGAAGATCTAAT 59.427 37.037 0.00 0.00 0.00 1.73
2514 2535 6.906901 ACCCACCATAAAGTAGGAAGATCTAA 59.093 38.462 0.00 0.00 0.00 2.10
2515 2536 6.449956 ACCCACCATAAAGTAGGAAGATCTA 58.550 40.000 0.00 0.00 0.00 1.98
2516 2537 5.289510 ACCCACCATAAAGTAGGAAGATCT 58.710 41.667 0.00 0.00 0.00 2.75
2517 2538 5.632034 ACCCACCATAAAGTAGGAAGATC 57.368 43.478 0.00 0.00 0.00 2.75
2518 2539 6.402981 AAACCCACCATAAAGTAGGAAGAT 57.597 37.500 0.00 0.00 0.00 2.40
2519 2540 5.853572 AAACCCACCATAAAGTAGGAAGA 57.146 39.130 0.00 0.00 0.00 2.87
2571 2597 6.162777 ACTCTCAGTTCTTCTATCTTTGCAC 58.837 40.000 0.00 0.00 0.00 4.57
2598 2624 9.131791 GGCTAGATTTGAAACCCATAAGATAAA 57.868 33.333 0.00 0.00 0.00 1.40
2599 2625 8.502738 AGGCTAGATTTGAAACCCATAAGATAA 58.497 33.333 0.00 0.00 0.00 1.75
2601 2627 6.915786 AGGCTAGATTTGAAACCCATAAGAT 58.084 36.000 0.00 0.00 0.00 2.40
2603 2629 6.486993 GGTAGGCTAGATTTGAAACCCATAAG 59.513 42.308 0.00 0.00 0.00 1.73
2606 2632 4.386424 GGGTAGGCTAGATTTGAAACCCAT 60.386 45.833 10.72 0.00 43.95 4.00
2607 2633 3.053917 GGGTAGGCTAGATTTGAAACCCA 60.054 47.826 10.72 0.00 43.95 4.51
2608 2634 3.552875 GGGTAGGCTAGATTTGAAACCC 58.447 50.000 0.00 0.00 38.66 4.11
2609 2635 3.053917 TGGGGTAGGCTAGATTTGAAACC 60.054 47.826 0.00 0.00 0.00 3.27
2610 2636 4.230745 TGGGGTAGGCTAGATTTGAAAC 57.769 45.455 0.00 0.00 0.00 2.78
2613 2639 3.186283 TGTTGGGGTAGGCTAGATTTGA 58.814 45.455 0.00 0.00 0.00 2.69
2614 2640 3.644966 TGTTGGGGTAGGCTAGATTTG 57.355 47.619 0.00 0.00 0.00 2.32
2615 2641 3.527665 ACATGTTGGGGTAGGCTAGATTT 59.472 43.478 0.00 0.00 0.00 2.17
2616 2642 3.123273 ACATGTTGGGGTAGGCTAGATT 58.877 45.455 0.00 0.00 0.00 2.40
2617 2643 2.776665 ACATGTTGGGGTAGGCTAGAT 58.223 47.619 0.00 0.00 0.00 1.98
2618 2644 2.263895 ACATGTTGGGGTAGGCTAGA 57.736 50.000 0.00 0.00 0.00 2.43
2619 2645 3.016736 CAAACATGTTGGGGTAGGCTAG 58.983 50.000 12.82 0.00 0.00 3.42
2620 2646 2.291282 CCAAACATGTTGGGGTAGGCTA 60.291 50.000 22.73 0.00 35.96 3.93
2621 2647 1.549950 CCAAACATGTTGGGGTAGGCT 60.550 52.381 22.73 0.00 35.96 4.58
2622 2648 0.894835 CCAAACATGTTGGGGTAGGC 59.105 55.000 22.73 0.00 35.96 3.93
2629 2655 3.306019 GCCTTTAGTCCCAAACATGTTGG 60.306 47.826 12.82 14.80 39.25 3.77
2630 2656 3.573967 AGCCTTTAGTCCCAAACATGTTG 59.426 43.478 12.82 6.46 0.00 3.33
2631 2657 3.844640 AGCCTTTAGTCCCAAACATGTT 58.155 40.909 4.92 4.92 0.00 2.71
2632 2658 3.525800 AGCCTTTAGTCCCAAACATGT 57.474 42.857 0.00 0.00 0.00 3.21
2633 2659 4.039124 ACAAAGCCTTTAGTCCCAAACATG 59.961 41.667 0.00 0.00 0.00 3.21
2634 2660 4.223144 ACAAAGCCTTTAGTCCCAAACAT 58.777 39.130 0.00 0.00 0.00 2.71
2635 2661 3.637769 ACAAAGCCTTTAGTCCCAAACA 58.362 40.909 0.00 0.00 0.00 2.83
2636 2662 4.142026 ACAACAAAGCCTTTAGTCCCAAAC 60.142 41.667 0.00 0.00 0.00 2.93
2637 2663 4.027437 ACAACAAAGCCTTTAGTCCCAAA 58.973 39.130 0.00 0.00 0.00 3.28
2638 2664 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
2639 2665 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
2640 2666 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
2641 2667 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
2642 2668 4.267690 GCAACAACAACAAAGCCTTTAGTC 59.732 41.667 0.00 0.00 0.00 2.59
2643 2669 4.081697 AGCAACAACAACAAAGCCTTTAGT 60.082 37.500 0.00 0.00 0.00 2.24
2644 2670 4.268405 CAGCAACAACAACAAAGCCTTTAG 59.732 41.667 0.00 0.00 0.00 1.85
2645 2671 4.081972 TCAGCAACAACAACAAAGCCTTTA 60.082 37.500 0.00 0.00 0.00 1.85
2646 2672 3.002102 CAGCAACAACAACAAAGCCTTT 58.998 40.909 0.00 0.00 0.00 3.11
2647 2673 2.233431 TCAGCAACAACAACAAAGCCTT 59.767 40.909 0.00 0.00 0.00 4.35
2648 2674 1.824230 TCAGCAACAACAACAAAGCCT 59.176 42.857 0.00 0.00 0.00 4.58
2649 2675 2.292103 TCAGCAACAACAACAAAGCC 57.708 45.000 0.00 0.00 0.00 4.35
2650 2676 3.864583 TCATTCAGCAACAACAACAAAGC 59.135 39.130 0.00 0.00 0.00 3.51
2651 2677 6.036300 ACAATCATTCAGCAACAACAACAAAG 59.964 34.615 0.00 0.00 0.00 2.77
2652 2678 5.873712 ACAATCATTCAGCAACAACAACAAA 59.126 32.000 0.00 0.00 0.00 2.83
2653 2679 5.417811 ACAATCATTCAGCAACAACAACAA 58.582 33.333 0.00 0.00 0.00 2.83
2654 2680 5.008619 ACAATCATTCAGCAACAACAACA 57.991 34.783 0.00 0.00 0.00 3.33
2655 2681 5.519566 TCAACAATCATTCAGCAACAACAAC 59.480 36.000 0.00 0.00 0.00 3.32
2656 2682 5.658468 TCAACAATCATTCAGCAACAACAA 58.342 33.333 0.00 0.00 0.00 2.83
2657 2683 5.259832 TCAACAATCATTCAGCAACAACA 57.740 34.783 0.00 0.00 0.00 3.33
2658 2684 6.421501 TGATTCAACAATCATTCAGCAACAAC 59.578 34.615 0.00 0.00 42.99 3.32
2659 2685 6.514063 TGATTCAACAATCATTCAGCAACAA 58.486 32.000 0.00 0.00 42.99 2.83
2660 2686 6.086785 TGATTCAACAATCATTCAGCAACA 57.913 33.333 0.00 0.00 42.99 3.33
2703 2738 9.212641 CGAATAGTGGATAATGAGATTGTGATT 57.787 33.333 0.00 0.00 0.00 2.57
2705 2740 7.726216 ACGAATAGTGGATAATGAGATTGTGA 58.274 34.615 0.00 0.00 0.00 3.58
2778 2813 9.020813 GTGAACTAGTCTTTTTGAAAATGGAAC 57.979 33.333 0.00 0.00 0.00 3.62
2784 2819 6.746745 ACCGTGAACTAGTCTTTTTGAAAA 57.253 33.333 0.00 0.00 0.00 2.29
2814 2849 4.024387 TGAACTAGTACAAAAGCGGCAAAG 60.024 41.667 1.45 0.00 0.00 2.77
2819 2854 4.056050 ACTGTGAACTAGTACAAAAGCGG 58.944 43.478 0.00 0.00 0.00 5.52
2883 3004 2.082231 CTCAACACATCTGCTTCCTGG 58.918 52.381 0.00 0.00 0.00 4.45
2895 3016 1.308047 GGCACATGTCACTCAACACA 58.692 50.000 0.00 0.00 30.55 3.72
2915 3036 2.846206 TCAGTGAGGGGAAATGCAGTAT 59.154 45.455 0.00 0.00 0.00 2.12
3095 3216 6.233434 TGCCCATATACTTTATGAGCAAGAG 58.767 40.000 0.09 0.00 36.07 2.85
3223 3344 0.539986 TTGTCCGGCTCCATACCTTC 59.460 55.000 0.00 0.00 0.00 3.46
3283 3404 3.394606 TGTTTCCCTTCCTTAAGAGCACT 59.605 43.478 3.36 0.00 34.37 4.40
3375 3496 2.691526 CAAATCACCACAGGCAGCATAT 59.308 45.455 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.