Multiple sequence alignment - TraesCS4D01G054900

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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 TraesCS4D01G054900 chr4D 100.000 3380 0 0 1 3380 30393520 30390141 0.000000e+00 6242
1 TraesCS4D01G054900 chr4D 95.374 562 26 0 2816 3377 470263917 470264478 0.000000e+00 894
2 TraesCS4D01G054900 chr4B 92.322 1654 85 19 993 2629 43595369 43593741 0.000000e+00 2313
3 TraesCS4D01G054900 chr4B 88.119 202 11 8 806 996 43595602 43595403 9.430000e-56 228
4 TraesCS4D01G054900 chr4B 89.423 104 3 3 657 753 43595728 43595626 1.270000e-24 124
5 TraesCS4D01G054900 chr4A 95.551 1371 61 0 995 2365 572641039 572642409 0.000000e+00 2194
6 TraesCS4D01G054900 chr4A 83.287 359 34 15 657 996 572640656 572641007 1.180000e-79 307
7 TraesCS4D01G054900 chr4A 84.615 234 27 4 2577 2808 572642504 572642730 1.220000e-54 224
8 TraesCS4D01G054900 chr4A 81.974 233 40 2 2466 2698 713290330 713290100 2.660000e-46 196
9 TraesCS4D01G054900 chr6A 95.613 661 24 2 1 660 535422447 535423103 0.000000e+00 1055
10 TraesCS4D01G054900 chr6A 90.468 577 34 8 2816 3380 337207426 337207993 0.000000e+00 741
11 TraesCS4D01G054900 chr2D 95.745 658 23 2 1 657 568756780 568756127 0.000000e+00 1055
12 TraesCS4D01G054900 chr2D 91.986 574 36 3 2817 3380 99203851 99203278 0.000000e+00 797
13 TraesCS4D01G054900 chr2D 97.688 346 8 0 1 346 576860689 576860344 2.250000e-166 595
14 TraesCS4D01G054900 chr7D 95.599 659 21 5 1 656 207789711 207790364 0.000000e+00 1050
15 TraesCS4D01G054900 chr7D 95.175 228 10 1 430 656 207736399 207736626 3.210000e-95 359
16 TraesCS4D01G054900 chr5B 95.310 661 26 2 1 660 524222310 524222966 0.000000e+00 1044
17 TraesCS4D01G054900 chr3A 94.872 663 27 3 1 660 434798670 434798012 0.000000e+00 1029
18 TraesCS4D01G054900 chr1B 94.570 663 28 5 1 660 443489451 443490108 0.000000e+00 1018
19 TraesCS4D01G054900 chr7A 93.212 604 32 6 19 620 48767511 48768107 0.000000e+00 880
20 TraesCS4D01G054900 chr2B 94.241 573 22 4 2817 3380 431166292 431166862 0.000000e+00 865
21 TraesCS4D01G054900 chrUn 93.531 572 27 3 2819 3380 284406204 284405633 0.000000e+00 843
22 TraesCS4D01G054900 chrUn 93.531 572 27 3 2819 3380 284412738 284412167 0.000000e+00 843
23 TraesCS4D01G054900 chrUn 93.531 572 27 3 2819 3380 376834083 376833512 0.000000e+00 843
24 TraesCS4D01G054900 chr1D 92.696 575 32 4 2816 3380 1442443 1441869 0.000000e+00 821
25 TraesCS4D01G054900 chr2A 91.826 575 32 5 2816 3380 30855758 30855189 0.000000e+00 787
26 TraesCS4D01G054900 chr6B 92.870 547 29 3 2844 3380 29312712 29312166 0.000000e+00 785
27 TraesCS4D01G054900 chr1A 92.828 488 34 1 170 656 512464928 512464441 0.000000e+00 706
28 TraesCS4D01G054900 chr1A 95.954 173 3 1 1 173 512465176 512465008 9.240000e-71 278


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 TraesCS4D01G054900 chr4D 30390141 30393520 3379 True 6242.000000 6242 100.000000 1 3380 1 chr4D.!!$R1 3379
1 TraesCS4D01G054900 chr4D 470263917 470264478 561 False 894.000000 894 95.374000 2816 3377 1 chr4D.!!$F1 561
2 TraesCS4D01G054900 chr4B 43593741 43595728 1987 True 888.333333 2313 89.954667 657 2629 3 chr4B.!!$R1 1972
3 TraesCS4D01G054900 chr4A 572640656 572642730 2074 False 908.333333 2194 87.817667 657 2808 3 chr4A.!!$F1 2151
4 TraesCS4D01G054900 chr6A 535422447 535423103 656 False 1055.000000 1055 95.613000 1 660 1 chr6A.!!$F2 659
5 TraesCS4D01G054900 chr6A 337207426 337207993 567 False 741.000000 741 90.468000 2816 3380 1 chr6A.!!$F1 564
6 TraesCS4D01G054900 chr2D 568756127 568756780 653 True 1055.000000 1055 95.745000 1 657 1 chr2D.!!$R2 656
7 TraesCS4D01G054900 chr2D 99203278 99203851 573 True 797.000000 797 91.986000 2817 3380 1 chr2D.!!$R1 563
8 TraesCS4D01G054900 chr7D 207789711 207790364 653 False 1050.000000 1050 95.599000 1 656 1 chr7D.!!$F2 655
9 TraesCS4D01G054900 chr5B 524222310 524222966 656 False 1044.000000 1044 95.310000 1 660 1 chr5B.!!$F1 659
10 TraesCS4D01G054900 chr3A 434798012 434798670 658 True 1029.000000 1029 94.872000 1 660 1 chr3A.!!$R1 659
11 TraesCS4D01G054900 chr1B 443489451 443490108 657 False 1018.000000 1018 94.570000 1 660 1 chr1B.!!$F1 659
12 TraesCS4D01G054900 chr7A 48767511 48768107 596 False 880.000000 880 93.212000 19 620 1 chr7A.!!$F1 601
13 TraesCS4D01G054900 chr2B 431166292 431166862 570 False 865.000000 865 94.241000 2817 3380 1 chr2B.!!$F1 563
14 TraesCS4D01G054900 chrUn 284405633 284406204 571 True 843.000000 843 93.531000 2819 3380 1 chrUn.!!$R1 561
15 TraesCS4D01G054900 chrUn 284412167 284412738 571 True 843.000000 843 93.531000 2819 3380 1 chrUn.!!$R2 561
16 TraesCS4D01G054900 chrUn 376833512 376834083 571 True 843.000000 843 93.531000 2819 3380 1 chrUn.!!$R3 561
17 TraesCS4D01G054900 chr1D 1441869 1442443 574 True 821.000000 821 92.696000 2816 3380 1 chr1D.!!$R1 564
18 TraesCS4D01G054900 chr2A 30855189 30855758 569 True 787.000000 787 91.826000 2816 3380 1 chr2A.!!$R1 564
19 TraesCS4D01G054900 chr6B 29312166 29312712 546 True 785.000000 785 92.870000 2844 3380 1 chr6B.!!$R1 536
20 TraesCS4D01G054900 chr1A 512464441 512465176 735 True 492.000000 706 94.391000 1 656 2 chr1A.!!$R1 655

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
839 943 0.250901 GCCCACTTCTTCTGGAGCAA 60.251 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2389 2539 1.152383 GACGGCTCAATAGAACGGGC 61.152 60.0 0.0 0.0 0.0 6.13 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
237 324 0.459899 CTGATAGGCACGCACCTGTA 59.540 55.000 7.07 0.00 41.34 2.74
266 353 5.335897 GCAGGCATTCAGACAAACATTCTAA 60.336 40.000 0.00 0.00 0.00 2.10
332 419 5.233083 TCCTCATCTTGTTCTGTGTGAAT 57.767 39.130 0.00 0.00 36.99 2.57
375 462 1.317431 ACGATCGAACATGGGACCGA 61.317 55.000 24.34 4.38 35.43 4.69
397 484 2.642427 TGAGTTGTTTGCTGAGCTCAA 58.358 42.857 18.85 0.00 31.14 3.02
574 663 0.478072 ACATGAGGTGCAAGTTGGGA 59.522 50.000 4.75 0.00 0.00 4.37
612 701 6.649155 AGTTTTGCAAGTTTGGGACTAAATT 58.351 32.000 0.00 0.00 37.72 1.82
687 777 1.332178 GAGAGTTCACTTCAGACGCG 58.668 55.000 3.53 3.53 0.00 6.01
800 897 0.725784 CAAGCAATGCCGACGTTCAC 60.726 55.000 0.00 0.00 0.00 3.18
801 898 1.852067 AAGCAATGCCGACGTTCACC 61.852 55.000 0.00 0.00 0.00 4.02
804 901 3.229156 AATGCCGACGTTCACCCGA 62.229 57.895 0.00 0.00 0.00 5.14
805 902 2.515996 AATGCCGACGTTCACCCGAT 62.516 55.000 0.00 0.00 0.00 4.18
806 903 3.186047 GCCGACGTTCACCCGATG 61.186 66.667 0.00 0.00 0.00 3.84
807 904 3.186047 CCGACGTTCACCCGATGC 61.186 66.667 0.00 0.00 0.00 3.91
808 905 2.431771 CGACGTTCACCCGATGCA 60.432 61.111 0.00 0.00 0.00 3.96
813 912 1.139520 GTTCACCCGATGCAATGCC 59.860 57.895 1.53 0.00 0.00 4.40
815 914 2.811542 TTCACCCGATGCAATGCCGA 62.812 55.000 1.53 0.00 0.00 5.54
839 943 0.250901 GCCCACTTCTTCTGGAGCAA 60.251 55.000 0.00 0.00 0.00 3.91
886 993 0.321122 CTCCGCCATTAGGATCAGGC 60.321 60.000 0.00 0.00 43.61 4.85
917 1024 7.504926 TTACTTGTGGAATAATCCTACACCT 57.495 36.000 0.00 0.00 46.70 4.00
936 1043 3.521531 ACCTTTCTTCTTCCTCCATCTCC 59.478 47.826 0.00 0.00 0.00 3.71
938 1045 1.115467 TCTTCTTCCTCCATCTCCGC 58.885 55.000 0.00 0.00 0.00 5.54
944 1051 1.112113 TCCTCCATCTCCGCTGTAAC 58.888 55.000 0.00 0.00 0.00 2.50
973 1086 1.371183 CCCCAAGACGAAGAGCACA 59.629 57.895 0.00 0.00 0.00 4.57
1426 1576 3.770040 CCTCCATGGTCGCCGTCA 61.770 66.667 12.58 0.00 0.00 4.35
1548 1698 2.928396 CACCTCCCCCTGTTCCGT 60.928 66.667 0.00 0.00 0.00 4.69
2219 2369 4.451150 GCTGATGGACGGCGGTGA 62.451 66.667 13.24 0.00 41.21 4.02
2302 2452 2.107141 CGGAAGGAGGGTCATCGC 59.893 66.667 0.00 0.00 0.00 4.58
2307 2457 4.899239 GGAGGGTCATCGCGCAGG 62.899 72.222 8.75 0.00 0.00 4.85
2381 2531 4.659088 GATGCACTGATTGACAAGTGATG 58.341 43.478 9.48 0.09 33.09 3.07
2384 2534 3.120060 GCACTGATTGACAAGTGATGGTC 60.120 47.826 9.48 0.00 33.09 4.02
2408 2558 1.152383 GCCCGTTCTATTGAGCCGTC 61.152 60.000 0.00 0.00 0.00 4.79
2433 2583 3.611433 GCATAAGCTGCGGTGAAAG 57.389 52.632 0.00 0.00 41.97 2.62
2434 2584 0.804989 GCATAAGCTGCGGTGAAAGT 59.195 50.000 0.00 0.00 41.97 2.66
2484 2644 8.275040 ACTATAGTGAAAATAAGCCATCCAGTT 58.725 33.333 4.10 0.00 0.00 3.16
2486 2646 4.706962 AGTGAAAATAAGCCATCCAGTTCC 59.293 41.667 0.00 0.00 0.00 3.62
2491 2651 7.453126 TGAAAATAAGCCATCCAGTTCCTTTTA 59.547 33.333 0.00 0.00 0.00 1.52
2528 2688 8.830915 TTTAGTTTATTTTCCTCATATGCCCA 57.169 30.769 0.00 0.00 0.00 5.36
2543 2703 8.394971 TCATATGCCCAATGAATAGTTTGTAG 57.605 34.615 0.00 0.00 30.52 2.74
2544 2704 7.998383 TCATATGCCCAATGAATAGTTTGTAGT 59.002 33.333 0.00 0.00 30.52 2.73
2545 2705 9.283768 CATATGCCCAATGAATAGTTTGTAGTA 57.716 33.333 0.00 0.00 0.00 1.82
2546 2706 6.995511 TGCCCAATGAATAGTTTGTAGTAC 57.004 37.500 0.00 0.00 0.00 2.73
2557 2717 8.619683 AATAGTTTGTAGTACCCTTGGACTAT 57.380 34.615 0.00 0.99 31.10 2.12
2558 2718 9.719433 AATAGTTTGTAGTACCCTTGGACTATA 57.281 33.333 0.00 0.00 31.10 1.31
2559 2719 9.719433 ATAGTTTGTAGTACCCTTGGACTATAA 57.281 33.333 0.00 0.00 31.10 0.98
2560 2720 8.619683 AGTTTGTAGTACCCTTGGACTATAAT 57.380 34.615 0.00 0.00 31.78 1.28
2561 2721 9.054580 AGTTTGTAGTACCCTTGGACTATAATT 57.945 33.333 0.00 0.00 31.78 1.40
2562 2722 9.676861 GTTTGTAGTACCCTTGGACTATAATTT 57.323 33.333 0.00 0.00 31.78 1.82
2563 2723 9.895138 TTTGTAGTACCCTTGGACTATAATTTC 57.105 33.333 0.00 0.00 31.78 2.17
2564 2724 7.719483 TGTAGTACCCTTGGACTATAATTTCG 58.281 38.462 0.00 0.00 31.10 3.46
2565 2725 6.803366 AGTACCCTTGGACTATAATTTCGT 57.197 37.500 0.00 0.00 0.00 3.85
2566 2726 7.191593 AGTACCCTTGGACTATAATTTCGTT 57.808 36.000 0.00 0.00 0.00 3.85
2567 2727 7.270779 AGTACCCTTGGACTATAATTTCGTTC 58.729 38.462 0.00 0.00 0.00 3.95
2568 2728 6.309389 ACCCTTGGACTATAATTTCGTTCT 57.691 37.500 0.00 0.00 0.00 3.01
2569 2729 6.346896 ACCCTTGGACTATAATTTCGTTCTC 58.653 40.000 0.00 0.00 0.00 2.87
2570 2730 5.462398 CCCTTGGACTATAATTTCGTTCTCG 59.538 44.000 0.00 0.00 38.55 4.04
2571 2731 6.040878 CCTTGGACTATAATTTCGTTCTCGT 58.959 40.000 0.00 0.00 38.33 4.18
2631 2796 8.325282 CACACATATGAACATCAAATTGATTGC 58.675 33.333 10.38 0.00 34.28 3.56
2636 2801 9.923143 ATATGAACATCAAATTGATTGCTATGG 57.077 29.630 5.63 0.00 34.28 2.74
2643 2808 9.406828 CATCAAATTGATTGCTATGGTATCTTG 57.593 33.333 5.63 0.00 34.28 3.02
2650 2815 4.330944 TGCTATGGTATCTTGGTTACGG 57.669 45.455 0.00 0.00 0.00 4.02
2654 2819 5.510861 GCTATGGTATCTTGGTTACGGACAT 60.511 44.000 0.00 0.00 0.00 3.06
2655 2820 4.829872 TGGTATCTTGGTTACGGACATT 57.170 40.909 0.00 0.00 0.00 2.71
2660 2825 6.204108 GGTATCTTGGTTACGGACATTATTGG 59.796 42.308 0.00 0.00 0.00 3.16
2672 2837 4.036262 GGACATTATTGGCTTGCATACGAA 59.964 41.667 0.00 0.00 0.00 3.85
2680 2845 4.388485 TGGCTTGCATACGAATATCACAT 58.612 39.130 0.00 0.00 0.00 3.21
2682 2847 5.994668 TGGCTTGCATACGAATATCACATAA 59.005 36.000 0.00 0.00 0.00 1.90
2701 2866 9.168451 TCACATAATGTTAAACACCATTACGAT 57.832 29.630 0.00 0.00 36.62 3.73
2702 2867 9.781834 CACATAATGTTAAACACCATTACGATT 57.218 29.630 0.00 0.00 36.62 3.34
2706 2871 9.970243 TAATGTTAAACACCATTACGATTTACG 57.030 29.630 0.00 0.00 38.79 3.18
2707 2872 7.649370 TGTTAAACACCATTACGATTTACGA 57.351 32.000 0.00 0.00 45.77 3.43
2711 2876 7.830940 AAACACCATTACGATTTACGATACA 57.169 32.000 0.00 0.00 45.77 2.29
2727 2892 6.897259 ACGATACACATGTTTATACCACAC 57.103 37.500 4.51 0.00 0.00 3.82
2728 2893 6.399743 ACGATACACATGTTTATACCACACA 58.600 36.000 4.51 0.00 0.00 3.72
2729 2894 6.311935 ACGATACACATGTTTATACCACACAC 59.688 38.462 4.51 0.00 0.00 3.82
2739 2904 5.548181 TTATACCACACACACCAACAGTA 57.452 39.130 0.00 0.00 0.00 2.74
2744 2909 3.243035 CCACACACACCAACAGTACAATG 60.243 47.826 0.00 0.00 0.00 2.82
2749 2914 6.151312 ACACACACCAACAGTACAATGTTTAA 59.849 34.615 0.00 0.00 41.41 1.52
2842 3010 2.437002 AAAAACGGATCGCCCCCA 59.563 55.556 0.00 0.00 0.00 4.96
2891 3059 3.015332 ATCTCCTCCGCCCTCCACT 62.015 63.158 0.00 0.00 0.00 4.00
2996 3164 3.642778 ATTCTACGTGCAGCGGCGT 62.643 57.895 17.08 17.08 46.52 5.68
3059 3236 1.842007 CCTGGGGTATGAGCTGCAT 59.158 57.895 1.02 0.00 41.08 3.96
3111 3288 2.831526 TCTGGATCAAGTGGTCGATCAA 59.168 45.455 0.00 0.00 39.88 2.57
3164 3341 1.610673 GGTGTCTCCTCCTCTGGCA 60.611 63.158 0.00 0.00 0.00 4.92
3303 3483 0.462581 GATCTTCGTGCATGGAGCCA 60.463 55.000 9.59 0.00 44.83 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 324 1.449246 GTCTGAATGCCTGCGCTCT 60.449 57.895 9.73 0.00 35.36 4.09
266 353 2.915869 ACACCGGCTGTCAAGGTT 59.084 55.556 0.00 0.00 35.85 3.50
375 462 3.216800 TGAGCTCAGCAAACAACTCAAT 58.783 40.909 13.74 0.00 31.60 2.57
397 484 3.139025 CCCAGGTGTTCCCTATCATGATT 59.861 47.826 14.65 0.00 43.86 2.57
574 663 7.951591 ACTTGCAAAACTTTACTTCACCATAT 58.048 30.769 0.00 0.00 0.00 1.78
633 722 2.022330 AGGTAATAGCACCCCAGGTACT 60.022 50.000 0.00 0.00 39.62 2.73
687 777 3.000825 GGTTTGTTTCACGAATTTGTGGC 59.999 43.478 22.88 14.67 40.31 5.01
729 826 1.126113 GATGCGTGTACAAACTCGTGG 59.874 52.381 0.00 0.00 42.90 4.94
757 854 1.529713 TTTTTGGGTCAGACGGCCC 60.530 57.895 0.00 0.00 45.04 5.80
758 855 4.167597 TTTTTGGGTCAGACGGCC 57.832 55.556 0.00 0.00 0.00 6.13
792 889 0.096976 CATTGCATCGGGTGAACGTC 59.903 55.000 0.00 0.00 34.94 4.34
794 891 1.226379 GCATTGCATCGGGTGAACG 60.226 57.895 3.15 0.00 0.00 3.95
795 892 1.139520 GGCATTGCATCGGGTGAAC 59.860 57.895 11.39 0.00 0.00 3.18
796 893 2.405805 CGGCATTGCATCGGGTGAA 61.406 57.895 11.39 0.00 0.00 3.18
797 894 2.823593 CGGCATTGCATCGGGTGA 60.824 61.111 11.39 0.00 0.00 4.02
800 897 3.940640 CGTCGGCATTGCATCGGG 61.941 66.667 11.39 0.00 0.00 5.14
801 898 4.596180 GCGTCGGCATTGCATCGG 62.596 66.667 11.39 0.00 39.62 4.18
815 914 3.626924 AGAAGAAGTGGGCGGCGT 61.627 61.111 9.37 0.00 0.00 5.68
839 943 1.005289 ATGGGGGAGAGCCATGACT 59.995 57.895 0.00 0.00 35.15 3.41
886 993 6.375455 AGGATTATTCCACAAGTAAGCAACAG 59.625 38.462 6.44 0.00 45.30 3.16
917 1024 2.093447 GCGGAGATGGAGGAAGAAGAAA 60.093 50.000 0.00 0.00 0.00 2.52
936 1043 3.252458 GGGGCAATTTATAGGTTACAGCG 59.748 47.826 0.00 0.00 0.00 5.18
938 1045 6.039382 GTCTTGGGGCAATTTATAGGTTACAG 59.961 42.308 0.00 0.00 0.00 2.74
944 1051 3.815809 TCGTCTTGGGGCAATTTATAGG 58.184 45.455 0.00 0.00 0.00 2.57
973 1086 4.024048 CGATCCTTAAAACTGTGTGCACTT 60.024 41.667 19.41 5.16 0.00 3.16
1023 1173 3.119096 GCGAGGAAGGGCACGAAC 61.119 66.667 0.00 0.00 0.00 3.95
1450 1600 4.436998 GACAGCGACGGGGTCCTG 62.437 72.222 0.00 10.62 37.11 3.86
1728 1878 2.304056 CCACTGCAGGATGGGGTCT 61.304 63.158 19.93 0.00 35.86 3.85
1852 2002 4.680237 CCAGAGGAACGGCGTGCA 62.680 66.667 21.39 0.00 0.00 4.57
2307 2457 3.248446 TACAAGCCGTGCCCAGTCC 62.248 63.158 0.00 0.00 0.00 3.85
2369 2519 2.622942 GCCTTTGACCATCACTTGTCAA 59.377 45.455 1.23 1.23 46.60 3.18
2381 2531 1.743394 CAATAGAACGGGCCTTTGACC 59.257 52.381 0.84 0.00 0.00 4.02
2384 2534 1.401905 GCTCAATAGAACGGGCCTTTG 59.598 52.381 0.84 0.00 0.00 2.77
2388 2538 1.887707 CGGCTCAATAGAACGGGCC 60.888 63.158 0.00 0.00 36.60 5.80
2389 2539 1.152383 GACGGCTCAATAGAACGGGC 61.152 60.000 0.00 0.00 0.00 6.13
2428 2578 6.068010 TCTCCAAGGCTTATTTTCACTTTCA 58.932 36.000 0.00 0.00 0.00 2.69
2429 2579 6.575162 TCTCCAAGGCTTATTTTCACTTTC 57.425 37.500 0.00 0.00 0.00 2.62
2430 2580 6.015095 CCTTCTCCAAGGCTTATTTTCACTTT 60.015 38.462 0.00 0.00 43.14 2.66
2431 2581 5.478332 CCTTCTCCAAGGCTTATTTTCACTT 59.522 40.000 0.00 0.00 43.14 3.16
2432 2582 5.012893 CCTTCTCCAAGGCTTATTTTCACT 58.987 41.667 0.00 0.00 43.14 3.41
2433 2583 5.316327 CCTTCTCCAAGGCTTATTTTCAC 57.684 43.478 0.00 0.00 43.14 3.18
2455 2605 7.715249 TGGATGGCTTATTTTCACTATAGTGTC 59.285 37.037 27.83 15.29 45.76 3.67
2456 2606 7.573710 TGGATGGCTTATTTTCACTATAGTGT 58.426 34.615 27.83 14.29 45.76 3.55
2457 2607 7.716998 ACTGGATGGCTTATTTTCACTATAGTG 59.283 37.037 24.37 24.37 46.91 2.74
2458 2608 7.806180 ACTGGATGGCTTATTTTCACTATAGT 58.194 34.615 0.00 0.00 0.00 2.12
2459 2609 8.682936 AACTGGATGGCTTATTTTCACTATAG 57.317 34.615 0.00 0.00 0.00 1.31
2460 2610 7.719633 GGAACTGGATGGCTTATTTTCACTATA 59.280 37.037 0.00 0.00 0.00 1.31
2461 2611 6.547510 GGAACTGGATGGCTTATTTTCACTAT 59.452 38.462 0.00 0.00 0.00 2.12
2462 2612 5.885912 GGAACTGGATGGCTTATTTTCACTA 59.114 40.000 0.00 0.00 0.00 2.74
2463 2613 4.706962 GGAACTGGATGGCTTATTTTCACT 59.293 41.667 0.00 0.00 0.00 3.41
2464 2614 4.706962 AGGAACTGGATGGCTTATTTTCAC 59.293 41.667 0.00 0.00 37.18 3.18
2518 2678 7.998383 ACTACAAACTATTCATTGGGCATATGA 59.002 33.333 6.97 0.00 0.00 2.15
2525 2685 6.659824 AGGGTACTACAAACTATTCATTGGG 58.340 40.000 0.00 0.00 0.00 4.12
2527 2687 7.827236 TCCAAGGGTACTACAAACTATTCATTG 59.173 37.037 0.00 0.00 0.00 2.82
2528 2688 7.827729 GTCCAAGGGTACTACAAACTATTCATT 59.172 37.037 0.00 0.00 0.00 2.57
2543 2703 7.270779 AGAACGAAATTATAGTCCAAGGGTAC 58.729 38.462 0.00 0.00 0.00 3.34
2544 2704 7.427989 AGAACGAAATTATAGTCCAAGGGTA 57.572 36.000 0.00 0.00 0.00 3.69
2545 2705 6.309389 AGAACGAAATTATAGTCCAAGGGT 57.691 37.500 0.00 0.00 0.00 4.34
2546 2706 5.462398 CGAGAACGAAATTATAGTCCAAGGG 59.538 44.000 0.00 0.00 42.66 3.95
2558 2718 9.104965 TCCATATCATTTAACGAGAACGAAATT 57.895 29.630 0.00 0.00 42.66 1.82
2559 2719 8.657074 TCCATATCATTTAACGAGAACGAAAT 57.343 30.769 0.00 0.00 42.66 2.17
2560 2720 7.762615 ACTCCATATCATTTAACGAGAACGAAA 59.237 33.333 0.00 0.00 42.66 3.46
2561 2721 7.262772 ACTCCATATCATTTAACGAGAACGAA 58.737 34.615 0.00 0.00 42.66 3.85
2562 2722 6.802608 ACTCCATATCATTTAACGAGAACGA 58.197 36.000 0.00 0.00 42.66 3.85
2563 2723 7.464830 AACTCCATATCATTTAACGAGAACG 57.535 36.000 0.00 0.00 45.75 3.95
2631 2796 5.524971 TGTCCGTAACCAAGATACCATAG 57.475 43.478 0.00 0.00 0.00 2.23
2636 2801 6.293244 GCCAATAATGTCCGTAACCAAGATAC 60.293 42.308 0.00 0.00 0.00 2.24
2643 2808 3.488553 GCAAGCCAATAATGTCCGTAACC 60.489 47.826 0.00 0.00 0.00 2.85
2650 2815 4.811555 TCGTATGCAAGCCAATAATGTC 57.188 40.909 0.00 0.00 0.00 3.06
2654 2819 6.484977 TGTGATATTCGTATGCAAGCCAATAA 59.515 34.615 0.00 0.00 0.00 1.40
2655 2820 5.994668 TGTGATATTCGTATGCAAGCCAATA 59.005 36.000 0.00 0.00 0.00 1.90
2660 2825 7.521529 ACATTATGTGATATTCGTATGCAAGC 58.478 34.615 0.00 0.00 0.00 4.01
2680 2845 9.970243 CGTAAATCGTAATGGTGTTTAACATTA 57.030 29.630 0.00 0.00 38.24 1.90
2682 2847 8.254178 TCGTAAATCGTAATGGTGTTTAACAT 57.746 30.769 0.00 0.00 40.80 2.71
2690 2855 6.815672 TGTGTATCGTAAATCGTAATGGTG 57.184 37.500 0.00 0.00 40.80 4.17
2701 2866 8.871862 GTGTGGTATAAACATGTGTATCGTAAA 58.128 33.333 11.96 0.00 0.00 2.01
2702 2867 8.033626 TGTGTGGTATAAACATGTGTATCGTAA 58.966 33.333 11.96 0.00 0.00 3.18
2703 2868 7.488792 GTGTGTGGTATAAACATGTGTATCGTA 59.511 37.037 11.96 0.00 0.00 3.43
2704 2869 6.311935 GTGTGTGGTATAAACATGTGTATCGT 59.688 38.462 11.96 0.00 0.00 3.73
2705 2870 6.311690 TGTGTGTGGTATAAACATGTGTATCG 59.688 38.462 11.96 0.00 0.00 2.92
2706 2871 7.413657 GGTGTGTGTGGTATAAACATGTGTATC 60.414 40.741 11.96 4.71 0.00 2.24
2707 2872 6.373216 GGTGTGTGTGGTATAAACATGTGTAT 59.627 38.462 13.13 13.13 0.00 2.29
2711 2876 4.720046 TGGTGTGTGTGGTATAAACATGT 58.280 39.130 0.00 0.00 0.00 3.21
2727 2892 8.641499 AAATTAAACATTGTACTGTTGGTGTG 57.359 30.769 1.61 0.00 39.25 3.82
2728 2893 9.308318 GAAAATTAAACATTGTACTGTTGGTGT 57.692 29.630 1.61 0.00 39.25 4.16
2729 2894 9.528018 AGAAAATTAAACATTGTACTGTTGGTG 57.472 29.630 1.61 0.00 39.25 4.17
2940 3108 2.282745 GGCTGCAGGGACTTTGCT 60.283 61.111 17.12 0.00 42.02 3.91
2975 3143 1.999051 CCGCTGCACGTAGAATGAC 59.001 57.895 0.00 0.00 41.42 3.06
2996 3164 1.227234 CTGCCACATACGCATCCGA 60.227 57.895 0.00 0.00 35.25 4.55
3043 3220 1.533219 CCATGCAGCTCATACCCCA 59.467 57.895 0.00 0.00 33.19 4.96
3059 3236 2.046023 CAAGATCACAGGCCGCCA 60.046 61.111 13.15 0.00 0.00 5.69
3111 3288 2.357517 CCTGCGACTTGAAGCCGT 60.358 61.111 2.39 0.00 0.00 5.68
3164 3341 0.392729 CTGGAGTCCCTACGTCGTCT 60.393 60.000 6.74 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.