Multiple sequence alignment - TraesCS5A01G112000

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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 TraesCS5A01G112000 chr5A 100.000 2653 0 0 1 2653 216962496 216959844 0.000000e+00 4900
1 TraesCS5A01G112000 chr5B 91.660 1295 37 20 948 2195 210168186 210166916 0.000000e+00 1727
2 TraesCS5A01G112000 chr5B 91.975 810 57 7 1 807 682405237 682404433 0.000000e+00 1129
3 TraesCS5A01G112000 chr5B 91.985 811 56 8 1 807 682432571 682431766 0.000000e+00 1129
4 TraesCS5A01G112000 chr5B 91.826 367 14 6 2194 2546 210166887 210166523 5.100000e-137 497
5 TraesCS5A01G112000 chr5D 88.187 1219 36 22 948 2088 199723790 199722602 0.000000e+00 1354
6 TraesCS5A01G112000 chr5D 94.633 708 34 4 1 706 11462519 11463224 0.000000e+00 1094
7 TraesCS5A01G112000 chr5D 91.690 361 13 4 2194 2546 199722130 199721779 3.970000e-133 484
8 TraesCS5A01G112000 chr5D 94.828 116 6 0 2080 2195 199722274 199722159 5.830000e-42 182
9 TraesCS5A01G112000 chr5D 90.476 105 9 1 847 951 11463272 11463375 1.280000e-28 137
10 TraesCS5A01G112000 chr5D 96.970 66 2 0 738 803 11463212 11463277 7.760000e-21 111
11 TraesCS5A01G112000 chr7D 84.496 258 26 13 497 745 5278251 5277999 2.640000e-60 243
12 TraesCS5A01G112000 chr2A 90.291 103 10 0 314 416 612308781 612308679 4.610000e-28 135
13 TraesCS5A01G112000 chr6B 81.325 166 24 7 489 650 234684342 234684180 7.710000e-26 128
14 TraesCS5A01G112000 chr2D 85.859 99 11 2 318 414 35555335 35555238 4.670000e-18 102


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 TraesCS5A01G112000 chr5A 216959844 216962496 2652 True 4900.000000 4900 100.000000 1 2653 1 chr5A.!!$R1 2652
1 TraesCS5A01G112000 chr5B 682404433 682405237 804 True 1129.000000 1129 91.975000 1 807 1 chr5B.!!$R1 806
2 TraesCS5A01G112000 chr5B 682431766 682432571 805 True 1129.000000 1129 91.985000 1 807 1 chr5B.!!$R2 806
3 TraesCS5A01G112000 chr5B 210166523 210168186 1663 True 1112.000000 1727 91.743000 948 2546 2 chr5B.!!$R3 1598
4 TraesCS5A01G112000 chr5D 199721779 199723790 2011 True 673.333333 1354 91.568333 948 2546 3 chr5D.!!$R1 1598
5 TraesCS5A01G112000 chr5D 11462519 11463375 856 False 447.333333 1094 94.026333 1 951 3 chr5D.!!$F1 950

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
809 818 0.107945 ACGAAGAGGAAGCATGAGGC 60.108 55.0 0.0 0.0 45.3 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 2097 0.318441 CCTCGTGAGCTGTTTCAGGA 59.682 55.0 0.0 0.0 39.04 3.86 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
153 156 5.851720 TGGAAGCATCAATTTGTTTTGCTA 58.148 33.333 17.85 6.62 42.50 3.49
165 168 2.884639 TGTTTTGCTAGAACCAGCTTCC 59.115 45.455 0.00 0.00 42.30 3.46
197 200 2.996621 GAGGATCGACCAACAGACTTTG 59.003 50.000 6.78 0.00 42.04 2.77
383 386 4.735369 TGAGGAAAAAGCTTCCACCATAA 58.265 39.130 0.00 0.00 41.00 1.90
556 561 0.521291 CGGCGAGGCATTTCTTTGAA 59.479 50.000 0.00 0.00 0.00 2.69
573 579 6.717413 TCTTTGAATTTTTGCTGCATTTGTC 58.283 32.000 1.84 0.00 0.00 3.18
575 581 5.910637 TGAATTTTTGCTGCATTTGTCTC 57.089 34.783 1.84 0.00 0.00 3.36
584 592 3.551454 GCTGCATTTGTCTCTTTTGCTGA 60.551 43.478 0.00 0.00 35.16 4.26
589 597 5.594926 CATTTGTCTCTTTTGCTGAAACCT 58.405 37.500 0.00 0.00 0.00 3.50
596 604 7.554835 TGTCTCTTTTGCTGAAACCTTTAACTA 59.445 33.333 0.00 0.00 0.00 2.24
625 633 6.514947 TGCTACAATGAGCTTTTGATTTTGT 58.485 32.000 15.02 7.76 43.27 2.83
657 665 1.205893 GAAGCGGAACTGAGACCAGAT 59.794 52.381 0.00 0.00 43.02 2.90
694 702 8.843885 TTGATTTTATTGCAACAATCCAATCA 57.156 26.923 18.46 14.79 33.93 2.57
727 735 2.182030 GAGTAGCAACGCGAGCCT 59.818 61.111 15.93 9.89 0.00 4.58
807 816 1.480137 AGGACGAAGAGGAAGCATGAG 59.520 52.381 0.00 0.00 0.00 2.90
808 817 1.472376 GGACGAAGAGGAAGCATGAGG 60.472 57.143 0.00 0.00 0.00 3.86
809 818 0.107945 ACGAAGAGGAAGCATGAGGC 60.108 55.000 0.00 0.00 45.30 4.70
820 829 2.926778 GCATGAGGCATAGAGGAACT 57.073 50.000 0.00 0.00 43.22 3.01
821 830 2.492012 GCATGAGGCATAGAGGAACTG 58.508 52.381 0.00 0.00 40.89 3.16
822 831 2.158842 GCATGAGGCATAGAGGAACTGT 60.159 50.000 0.00 0.00 40.89 3.55
823 832 3.683847 GCATGAGGCATAGAGGAACTGTT 60.684 47.826 0.00 0.00 40.89 3.16
824 833 3.616956 TGAGGCATAGAGGAACTGTTG 57.383 47.619 0.00 0.00 41.55 3.33
825 834 2.906389 TGAGGCATAGAGGAACTGTTGT 59.094 45.455 0.00 0.00 41.55 3.32
826 835 3.265791 GAGGCATAGAGGAACTGTTGTG 58.734 50.000 0.00 0.00 41.55 3.33
827 836 2.639839 AGGCATAGAGGAACTGTTGTGT 59.360 45.455 0.00 0.00 41.55 3.72
828 837 2.744202 GGCATAGAGGAACTGTTGTGTG 59.256 50.000 0.00 0.00 41.55 3.82
829 838 2.744202 GCATAGAGGAACTGTTGTGTGG 59.256 50.000 0.00 0.00 41.55 4.17
830 839 3.557054 GCATAGAGGAACTGTTGTGTGGA 60.557 47.826 0.00 0.00 41.55 4.02
831 840 4.641396 CATAGAGGAACTGTTGTGTGGAA 58.359 43.478 0.00 0.00 41.55 3.53
832 841 3.199880 AGAGGAACTGTTGTGTGGAAG 57.800 47.619 0.00 0.00 41.55 3.46
833 842 2.158755 AGAGGAACTGTTGTGTGGAAGG 60.159 50.000 0.00 0.00 41.55 3.46
834 843 1.843851 AGGAACTGTTGTGTGGAAGGA 59.156 47.619 0.00 0.00 37.18 3.36
835 844 2.158755 AGGAACTGTTGTGTGGAAGGAG 60.159 50.000 0.00 0.00 37.18 3.69
836 845 2.158813 GGAACTGTTGTGTGGAAGGAGA 60.159 50.000 0.00 0.00 0.00 3.71
837 846 2.622064 ACTGTTGTGTGGAAGGAGAC 57.378 50.000 0.00 0.00 0.00 3.36
838 847 1.837439 ACTGTTGTGTGGAAGGAGACA 59.163 47.619 0.00 0.00 0.00 3.41
839 848 2.213499 CTGTTGTGTGGAAGGAGACAC 58.787 52.381 0.00 0.00 42.40 3.67
840 849 1.217882 GTTGTGTGGAAGGAGACACG 58.782 55.000 0.00 0.00 44.55 4.49
841 850 0.531974 TTGTGTGGAAGGAGACACGC 60.532 55.000 0.00 0.00 44.55 5.34
842 851 2.022129 GTGTGGAAGGAGACACGCG 61.022 63.158 3.53 3.53 40.39 6.01
843 852 3.112709 GTGGAAGGAGACACGCGC 61.113 66.667 5.73 0.00 0.00 6.86
844 853 3.611674 TGGAAGGAGACACGCGCA 61.612 61.111 5.73 0.00 0.00 6.09
845 854 2.125512 GGAAGGAGACACGCGCAT 60.126 61.111 5.73 0.00 0.00 4.73
846 855 2.456119 GGAAGGAGACACGCGCATG 61.456 63.158 5.73 4.48 0.00 4.06
847 856 2.434884 AAGGAGACACGCGCATGG 60.435 61.111 8.88 0.00 0.00 3.66
848 857 2.835701 GAAGGAGACACGCGCATGGA 62.836 60.000 8.88 0.00 0.00 3.41
849 858 2.842394 AAGGAGACACGCGCATGGAG 62.842 60.000 8.88 0.00 0.00 3.86
850 859 2.887568 GAGACACGCGCATGGAGG 60.888 66.667 8.88 0.00 0.00 4.30
851 860 4.457496 AGACACGCGCATGGAGGG 62.457 66.667 8.88 0.00 0.00 4.30
860 869 3.170672 CATGGAGGGCGGGATGGA 61.171 66.667 0.00 0.00 0.00 3.41
918 927 2.036006 CCGACCGGCCGAAATTTCA 61.036 57.895 30.73 0.00 0.00 2.69
923 932 3.585856 GGCCGAAATTTCAGCCGA 58.414 55.556 25.61 0.00 40.58 5.54
994 1006 1.982660 AGGCGATCGATGACTCCTAA 58.017 50.000 21.57 0.00 0.00 2.69
1117 1150 1.397672 TGCTCTCATCTTCTCCTCCG 58.602 55.000 0.00 0.00 0.00 4.63
1542 1580 2.125912 CCGCGACCTCAGACAAGG 60.126 66.667 8.23 0.00 42.55 3.61
1543 1581 2.125912 CGCGACCTCAGACAAGGG 60.126 66.667 0.00 0.00 41.04 3.95
1647 1700 3.305398 TTTGGTCGTGTTTTGTGCTTT 57.695 38.095 0.00 0.00 0.00 3.51
1724 1786 5.768164 AGAGGAATTAGAGACTACTGCTAGC 59.232 44.000 8.10 8.10 0.00 3.42
1801 1888 9.822185 AAACTTATGTTCTTTCTTTTGCTGAAT 57.178 25.926 0.00 0.00 34.96 2.57
1816 1903 3.056678 TGCTGAATTTTGGGTATGCTGTG 60.057 43.478 0.00 0.00 0.00 3.66
1817 1904 3.056607 GCTGAATTTTGGGTATGCTGTGT 60.057 43.478 0.00 0.00 0.00 3.72
1818 1905 4.561326 GCTGAATTTTGGGTATGCTGTGTT 60.561 41.667 0.00 0.00 0.00 3.32
1819 1906 5.132897 TGAATTTTGGGTATGCTGTGTTC 57.867 39.130 0.00 0.00 0.00 3.18
1949 2047 4.997395 TCTTTTGTAACAGCTGATCCAGAC 59.003 41.667 23.35 4.03 32.44 3.51
2052 2152 1.425412 GCTTCTTGGCACATTGCTTG 58.575 50.000 0.00 0.00 44.28 4.01
2119 2555 0.742990 TCCGGATAACGCAAGCCTTG 60.743 55.000 0.00 0.00 42.52 3.61
2153 2589 2.835027 CTGGGTTTAGATTCTACCGGC 58.165 52.381 0.00 0.00 32.61 6.13
2182 2623 2.846652 ATCATCTCCCCGACGACGC 61.847 63.158 0.64 0.00 38.29 5.19
2389 2861 8.064222 ACGAATCTAAAATATCACAAAGATGCG 58.936 33.333 8.57 8.57 44.43 4.73
2458 2930 8.298729 TCTCTACATCATGTCAAAGTCATACT 57.701 34.615 0.00 0.00 0.00 2.12
2459 2931 9.408648 TCTCTACATCATGTCAAAGTCATACTA 57.591 33.333 0.00 0.00 0.00 1.82
2526 3010 2.032377 TCTTGTTTCTAAAACAGGCGCG 60.032 45.455 0.00 0.00 0.00 6.86
2546 3031 5.751680 CGCGAAATATGTCCATCTGATTTT 58.248 37.500 0.00 0.00 0.00 1.82
2547 3032 5.622448 CGCGAAATATGTCCATCTGATTTTG 59.378 40.000 0.00 0.00 0.00 2.44
2548 3033 6.498304 GCGAAATATGTCCATCTGATTTTGT 58.502 36.000 0.00 0.00 0.00 2.83
2549 3034 7.518211 CGCGAAATATGTCCATCTGATTTTGTA 60.518 37.037 0.00 0.00 0.00 2.41
2550 3035 8.128582 GCGAAATATGTCCATCTGATTTTGTAA 58.871 33.333 0.00 0.00 0.00 2.41
2551 3036 9.655769 CGAAATATGTCCATCTGATTTTGTAAG 57.344 33.333 0.00 0.00 0.00 2.34
2552 3037 9.455847 GAAATATGTCCATCTGATTTTGTAAGC 57.544 33.333 0.00 0.00 0.00 3.09
2553 3038 8.523915 AATATGTCCATCTGATTTTGTAAGCA 57.476 30.769 0.00 0.00 0.00 3.91
2554 3039 5.627499 TGTCCATCTGATTTTGTAAGCAC 57.373 39.130 0.00 0.00 0.00 4.40
2555 3040 4.458989 TGTCCATCTGATTTTGTAAGCACC 59.541 41.667 0.00 0.00 0.00 5.01
2556 3041 4.458989 GTCCATCTGATTTTGTAAGCACCA 59.541 41.667 0.00 0.00 0.00 4.17
2557 3042 5.048083 GTCCATCTGATTTTGTAAGCACCAA 60.048 40.000 0.00 0.00 0.00 3.67
2558 3043 5.716228 TCCATCTGATTTTGTAAGCACCAAT 59.284 36.000 0.00 0.00 0.00 3.16
2559 3044 6.211184 TCCATCTGATTTTGTAAGCACCAATT 59.789 34.615 0.00 0.00 0.00 2.32
2560 3045 6.311935 CCATCTGATTTTGTAAGCACCAATTG 59.688 38.462 0.00 0.00 0.00 2.32
2573 3058 4.943142 CACCAATTGCTTTCTCTCTCTC 57.057 45.455 0.00 0.00 0.00 3.20
2574 3059 4.577875 CACCAATTGCTTTCTCTCTCTCT 58.422 43.478 0.00 0.00 0.00 3.10
2575 3060 4.630940 CACCAATTGCTTTCTCTCTCTCTC 59.369 45.833 0.00 0.00 0.00 3.20
2576 3061 4.531732 ACCAATTGCTTTCTCTCTCTCTCT 59.468 41.667 0.00 0.00 0.00 3.10
2577 3062 5.111293 CCAATTGCTTTCTCTCTCTCTCTC 58.889 45.833 0.00 0.00 0.00 3.20
2578 3063 5.105228 CCAATTGCTTTCTCTCTCTCTCTCT 60.105 44.000 0.00 0.00 0.00 3.10
2579 3064 5.841957 ATTGCTTTCTCTCTCTCTCTCTC 57.158 43.478 0.00 0.00 0.00 3.20
2580 3065 4.574674 TGCTTTCTCTCTCTCTCTCTCT 57.425 45.455 0.00 0.00 0.00 3.10
2581 3066 4.517285 TGCTTTCTCTCTCTCTCTCTCTC 58.483 47.826 0.00 0.00 0.00 3.20
2582 3067 4.019411 TGCTTTCTCTCTCTCTCTCTCTCA 60.019 45.833 0.00 0.00 0.00 3.27
2583 3068 4.943705 GCTTTCTCTCTCTCTCTCTCTCAA 59.056 45.833 0.00 0.00 0.00 3.02
2584 3069 5.591877 GCTTTCTCTCTCTCTCTCTCTCAAT 59.408 44.000 0.00 0.00 0.00 2.57
2585 3070 6.096001 GCTTTCTCTCTCTCTCTCTCTCAATT 59.904 42.308 0.00 0.00 0.00 2.32
2586 3071 7.363268 GCTTTCTCTCTCTCTCTCTCTCAATTT 60.363 40.741 0.00 0.00 0.00 1.82
2587 3072 9.177608 CTTTCTCTCTCTCTCTCTCTCAATTTA 57.822 37.037 0.00 0.00 0.00 1.40
2588 3073 8.737168 TTCTCTCTCTCTCTCTCTCAATTTAG 57.263 38.462 0.00 0.00 0.00 1.85
2589 3074 7.861629 TCTCTCTCTCTCTCTCTCAATTTAGT 58.138 38.462 0.00 0.00 0.00 2.24
2590 3075 7.770433 TCTCTCTCTCTCTCTCTCAATTTAGTG 59.230 40.741 0.00 0.00 0.00 2.74
2591 3076 7.402054 TCTCTCTCTCTCTCTCAATTTAGTGT 58.598 38.462 0.00 0.00 0.00 3.55
2592 3077 7.552687 TCTCTCTCTCTCTCTCAATTTAGTGTC 59.447 40.741 0.00 0.00 0.00 3.67
2593 3078 7.402054 TCTCTCTCTCTCTCAATTTAGTGTCT 58.598 38.462 0.00 0.00 0.00 3.41
2594 3079 8.544622 TCTCTCTCTCTCTCAATTTAGTGTCTA 58.455 37.037 0.00 0.00 0.00 2.59
2595 3080 8.731275 TCTCTCTCTCTCAATTTAGTGTCTAG 57.269 38.462 0.00 0.00 0.00 2.43
2596 3081 8.325787 TCTCTCTCTCTCAATTTAGTGTCTAGT 58.674 37.037 0.00 0.00 0.00 2.57
2597 3082 8.871629 TCTCTCTCTCAATTTAGTGTCTAGTT 57.128 34.615 0.00 0.00 0.00 2.24
2598 3083 8.735315 TCTCTCTCTCAATTTAGTGTCTAGTTG 58.265 37.037 0.00 0.00 0.00 3.16
2599 3084 8.637196 TCTCTCTCAATTTAGTGTCTAGTTGA 57.363 34.615 0.00 0.00 0.00 3.18
2600 3085 9.249053 TCTCTCTCAATTTAGTGTCTAGTTGAT 57.751 33.333 0.00 0.00 0.00 2.57
2601 3086 9.868277 CTCTCTCAATTTAGTGTCTAGTTGATT 57.132 33.333 0.00 0.00 0.00 2.57
2613 3098 9.950496 AGTGTCTAGTTGATTACAGATTTGAAT 57.050 29.630 0.00 0.00 0.00 2.57
2621 3106 9.859427 GTTGATTACAGATTTGAATTCAATCCA 57.141 29.630 21.10 7.58 35.55 3.41
2624 3109 9.525409 GATTACAGATTTGAATTCAATCCAAGG 57.475 33.333 21.10 11.37 35.55 3.61
2625 3110 8.648698 TTACAGATTTGAATTCAATCCAAGGA 57.351 30.769 21.10 5.37 35.55 3.36
2626 3111 6.928520 ACAGATTTGAATTCAATCCAAGGAC 58.071 36.000 21.10 7.31 35.55 3.85
2627 3112 6.032094 CAGATTTGAATTCAATCCAAGGACG 58.968 40.000 21.10 1.09 35.55 4.79
2628 3113 5.945784 AGATTTGAATTCAATCCAAGGACGA 59.054 36.000 21.10 3.19 35.55 4.20
2629 3114 5.627499 TTTGAATTCAATCCAAGGACGAG 57.373 39.130 21.10 0.00 35.55 4.18
2630 3115 3.609853 TGAATTCAATCCAAGGACGAGG 58.390 45.455 5.45 0.00 0.00 4.63
2631 3116 3.263170 TGAATTCAATCCAAGGACGAGGA 59.737 43.478 5.45 0.00 38.50 3.71
2632 3117 4.261801 GAATTCAATCCAAGGACGAGGAA 58.738 43.478 0.00 0.00 37.48 3.36
2633 3118 3.334583 TTCAATCCAAGGACGAGGAAG 57.665 47.619 0.00 0.00 37.48 3.46
2634 3119 1.555075 TCAATCCAAGGACGAGGAAGG 59.445 52.381 0.00 0.00 37.48 3.46
2635 3120 1.555075 CAATCCAAGGACGAGGAAGGA 59.445 52.381 0.00 0.00 37.48 3.36
2636 3121 1.952621 ATCCAAGGACGAGGAAGGAA 58.047 50.000 0.00 0.00 37.48 3.36
2637 3122 1.267121 TCCAAGGACGAGGAAGGAAG 58.733 55.000 0.00 0.00 0.00 3.46
2638 3123 1.203137 TCCAAGGACGAGGAAGGAAGA 60.203 52.381 0.00 0.00 0.00 2.87
2639 3124 1.623811 CCAAGGACGAGGAAGGAAGAA 59.376 52.381 0.00 0.00 0.00 2.52
2640 3125 2.613223 CCAAGGACGAGGAAGGAAGAAC 60.613 54.545 0.00 0.00 0.00 3.01
2641 3126 2.011122 AGGACGAGGAAGGAAGAACA 57.989 50.000 0.00 0.00 0.00 3.18
2642 3127 1.896465 AGGACGAGGAAGGAAGAACAG 59.104 52.381 0.00 0.00 0.00 3.16
2643 3128 1.893801 GGACGAGGAAGGAAGAACAGA 59.106 52.381 0.00 0.00 0.00 3.41
2644 3129 2.094442 GGACGAGGAAGGAAGAACAGAG 60.094 54.545 0.00 0.00 0.00 3.35
2645 3130 2.820787 GACGAGGAAGGAAGAACAGAGA 59.179 50.000 0.00 0.00 0.00 3.10
2646 3131 3.231818 ACGAGGAAGGAAGAACAGAGAA 58.768 45.455 0.00 0.00 0.00 2.87
2647 3132 3.641906 ACGAGGAAGGAAGAACAGAGAAA 59.358 43.478 0.00 0.00 0.00 2.52
2648 3133 3.991121 CGAGGAAGGAAGAACAGAGAAAC 59.009 47.826 0.00 0.00 0.00 2.78
2649 3134 4.501571 CGAGGAAGGAAGAACAGAGAAACA 60.502 45.833 0.00 0.00 0.00 2.83
2650 3135 5.368989 GAGGAAGGAAGAACAGAGAAACAA 58.631 41.667 0.00 0.00 0.00 2.83
2651 3136 5.126779 AGGAAGGAAGAACAGAGAAACAAC 58.873 41.667 0.00 0.00 0.00 3.32
2652 3137 4.881850 GGAAGGAAGAACAGAGAAACAACA 59.118 41.667 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 156 0.612744 GCTCTGAGGAAGCTGGTTCT 59.387 55.000 17.95 5.57 35.25 3.01
165 168 1.008652 CGATCCTCGCAGCTCTGAG 60.009 63.158 0.00 0.00 31.14 3.35
197 200 4.494484 AGAAACACTGCTTCCAACAAAAC 58.506 39.130 0.00 0.00 0.00 2.43
203 206 3.932089 GCAAAAAGAAACACTGCTTCCAA 59.068 39.130 0.00 0.00 0.00 3.53
400 403 3.325716 ACAGCCATTGAAGCTTTTTCCAT 59.674 39.130 0.00 0.00 38.95 3.41
547 552 7.536855 ACAAATGCAGCAAAAATTCAAAGAAA 58.463 26.923 0.00 0.00 0.00 2.52
556 561 6.721321 CAAAAGAGACAAATGCAGCAAAAAT 58.279 32.000 0.00 0.00 0.00 1.82
573 579 9.750125 AATTAGTTAAAGGTTTCAGCAAAAGAG 57.250 29.630 0.00 0.00 0.00 2.85
596 604 8.611654 AATCAAAAGCTCATTGTAGCAAAATT 57.388 26.923 10.87 1.53 45.30 1.82
709 717 3.248171 GGCTCGCGTTGCTACTCG 61.248 66.667 21.30 4.27 33.94 4.18
775 783 1.497309 TTCGTCCTCCCATGGCCTTT 61.497 55.000 6.09 0.00 0.00 3.11
776 784 1.915078 CTTCGTCCTCCCATGGCCTT 61.915 60.000 6.09 0.00 0.00 4.35
807 816 2.744202 CACACAACAGTTCCTCTATGCC 59.256 50.000 0.00 0.00 0.00 4.40
808 817 2.744202 CCACACAACAGTTCCTCTATGC 59.256 50.000 0.00 0.00 0.00 3.14
809 818 4.271696 TCCACACAACAGTTCCTCTATG 57.728 45.455 0.00 0.00 0.00 2.23
810 819 4.263068 CCTTCCACACAACAGTTCCTCTAT 60.263 45.833 0.00 0.00 0.00 1.98
811 820 3.071023 CCTTCCACACAACAGTTCCTCTA 59.929 47.826 0.00 0.00 0.00 2.43
812 821 2.158755 CCTTCCACACAACAGTTCCTCT 60.159 50.000 0.00 0.00 0.00 3.69
813 822 2.158813 TCCTTCCACACAACAGTTCCTC 60.159 50.000 0.00 0.00 0.00 3.71
814 823 1.843851 TCCTTCCACACAACAGTTCCT 59.156 47.619 0.00 0.00 0.00 3.36
815 824 2.158813 TCTCCTTCCACACAACAGTTCC 60.159 50.000 0.00 0.00 0.00 3.62
816 825 2.872858 GTCTCCTTCCACACAACAGTTC 59.127 50.000 0.00 0.00 0.00 3.01
817 826 2.238646 TGTCTCCTTCCACACAACAGTT 59.761 45.455 0.00 0.00 0.00 3.16
818 827 1.837439 TGTCTCCTTCCACACAACAGT 59.163 47.619 0.00 0.00 0.00 3.55
819 828 2.213499 GTGTCTCCTTCCACACAACAG 58.787 52.381 0.00 0.00 42.20 3.16
820 829 1.472552 CGTGTCTCCTTCCACACAACA 60.473 52.381 3.33 0.00 42.67 3.33
821 830 1.217882 CGTGTCTCCTTCCACACAAC 58.782 55.000 3.33 0.00 42.67 3.32
822 831 0.531974 GCGTGTCTCCTTCCACACAA 60.532 55.000 3.33 0.00 42.67 3.33
823 832 1.069090 GCGTGTCTCCTTCCACACA 59.931 57.895 3.33 0.00 42.67 3.72
824 833 2.022129 CGCGTGTCTCCTTCCACAC 61.022 63.158 0.00 0.00 39.70 3.82
825 834 2.338620 CGCGTGTCTCCTTCCACA 59.661 61.111 0.00 0.00 0.00 4.17
826 835 3.112709 GCGCGTGTCTCCTTCCAC 61.113 66.667 8.43 0.00 0.00 4.02
827 836 2.942796 ATGCGCGTGTCTCCTTCCA 61.943 57.895 8.43 0.00 0.00 3.53
828 837 2.125512 ATGCGCGTGTCTCCTTCC 60.126 61.111 8.43 0.00 0.00 3.46
829 838 2.456119 CCATGCGCGTGTCTCCTTC 61.456 63.158 26.86 0.00 0.00 3.46
830 839 2.434884 CCATGCGCGTGTCTCCTT 60.435 61.111 26.86 0.00 0.00 3.36
831 840 3.362399 CTCCATGCGCGTGTCTCCT 62.362 63.158 26.86 0.00 0.00 3.69
832 841 2.887568 CTCCATGCGCGTGTCTCC 60.888 66.667 26.86 0.00 0.00 3.71
833 842 2.887568 CCTCCATGCGCGTGTCTC 60.888 66.667 26.86 0.00 0.00 3.36
834 843 4.457496 CCCTCCATGCGCGTGTCT 62.457 66.667 26.86 0.00 0.00 3.41
842 851 4.962836 CCATCCCGCCCTCCATGC 62.963 72.222 0.00 0.00 0.00 4.06
843 852 2.072874 ATTCCATCCCGCCCTCCATG 62.073 60.000 0.00 0.00 0.00 3.66
844 853 1.775877 ATTCCATCCCGCCCTCCAT 60.776 57.895 0.00 0.00 0.00 3.41
845 854 2.368192 ATTCCATCCCGCCCTCCA 60.368 61.111 0.00 0.00 0.00 3.86
846 855 2.432123 GATTCCATCCCGCCCTCC 59.568 66.667 0.00 0.00 0.00 4.30
847 856 2.031163 CGATTCCATCCCGCCCTC 59.969 66.667 0.00 0.00 0.00 4.30
848 857 2.768344 ACGATTCCATCCCGCCCT 60.768 61.111 0.00 0.00 0.00 5.19
849 858 2.591715 CACGATTCCATCCCGCCC 60.592 66.667 0.00 0.00 0.00 6.13
850 859 2.180204 CACACGATTCCATCCCGCC 61.180 63.158 0.00 0.00 0.00 6.13
851 860 2.180204 CCACACGATTCCATCCCGC 61.180 63.158 0.00 0.00 0.00 6.13
852 861 0.810031 GACCACACGATTCCATCCCG 60.810 60.000 0.00 0.00 0.00 5.14
853 862 0.541863 AGACCACACGATTCCATCCC 59.458 55.000 0.00 0.00 0.00 3.85
856 865 0.253044 CCCAGACCACACGATTCCAT 59.747 55.000 0.00 0.00 0.00 3.41
860 869 1.292223 CGTCCCAGACCACACGATT 59.708 57.895 0.00 0.00 34.06 3.34
901 910 1.423845 CTGAAATTTCGGCCGGTCG 59.576 57.895 25.52 25.52 0.00 4.79
938 947 1.682684 AGGATCGGAAGGCGACTGT 60.683 57.895 0.00 0.00 42.68 3.55
994 1006 4.079787 TCTCCCACCTTTTTATGCTGCTAT 60.080 41.667 0.00 0.00 0.00 2.97
1106 1127 3.134804 GGAATTTGGATCGGAGGAGAAGA 59.865 47.826 0.00 0.00 0.00 2.87
1117 1150 6.616774 TTTTGCTTGTTTGGAATTTGGATC 57.383 33.333 0.00 0.00 0.00 3.36
1542 1580 2.946762 GTCAACCGCTGCACTTCC 59.053 61.111 0.00 0.00 0.00 3.46
1543 1581 2.551270 CGTCAACCGCTGCACTTC 59.449 61.111 0.00 0.00 0.00 3.01
1647 1700 8.998377 TCTAATTTCTCGATGTTTCATTTCACA 58.002 29.630 0.00 0.00 0.00 3.58
1686 1748 9.495754 CTCTAATTCCTCTAATTTCGCAAAAAG 57.504 33.333 0.00 0.00 38.71 2.27
1724 1786 5.996219 TGTTAATCACGGTGACAAGAAATG 58.004 37.500 13.92 0.00 0.00 2.32
1801 1888 3.561143 AGTGAACACAGCATACCCAAAA 58.439 40.909 7.68 0.00 0.00 2.44
1816 1903 6.793492 AGCAAGTCAGATTAGAAAGTGAAC 57.207 37.500 0.00 0.00 0.00 3.18
1817 1904 7.283127 ACAAAGCAAGTCAGATTAGAAAGTGAA 59.717 33.333 0.00 0.00 0.00 3.18
1818 1905 6.767902 ACAAAGCAAGTCAGATTAGAAAGTGA 59.232 34.615 0.00 0.00 0.00 3.41
1819 1906 6.963796 ACAAAGCAAGTCAGATTAGAAAGTG 58.036 36.000 0.00 0.00 0.00 3.16
1847 1943 3.367743 ACAACGAGCGAGCGGGTA 61.368 61.111 0.00 0.00 35.12 3.69
1949 2047 8.601243 ATTTCAAGATAATTCACTTTAACGCG 57.399 30.769 3.53 3.53 0.00 6.01
1996 2096 1.270305 CCTCGTGAGCTGTTTCAGGAA 60.270 52.381 0.00 0.00 40.31 3.36
1997 2097 0.318441 CCTCGTGAGCTGTTTCAGGA 59.682 55.000 0.00 0.00 39.04 3.86
2012 2112 2.782192 CGTATGTTTAAGCTCGTCCTCG 59.218 50.000 0.00 0.00 38.55 4.63
2052 2152 2.248487 CGATTTGCTTGCTCTTGCTTC 58.752 47.619 0.00 0.00 40.48 3.86
2153 2589 1.303309 GGAGATGATGAAACCTGGCG 58.697 55.000 0.00 0.00 0.00 5.69
2389 2861 1.465187 GGAGCAACCGAAAATGTACGC 60.465 52.381 0.00 0.00 0.00 4.42
2459 2931 8.830580 CCTGATTTGTCGTCTTTGTGATATAAT 58.169 33.333 0.00 0.00 0.00 1.28
2522 3006 2.135139 TCAGATGGACATATTTCGCGC 58.865 47.619 0.00 0.00 0.00 6.86
2526 3010 9.455847 GCTTACAAAATCAGATGGACATATTTC 57.544 33.333 0.00 0.00 0.00 2.17
2552 3037 4.577875 AGAGAGAGAGAAAGCAATTGGTG 58.422 43.478 11.56 0.00 0.00 4.17
2553 3038 4.531732 AGAGAGAGAGAGAAAGCAATTGGT 59.468 41.667 3.82 3.82 0.00 3.67
2554 3039 5.088680 AGAGAGAGAGAGAAAGCAATTGG 57.911 43.478 7.72 0.00 0.00 3.16
2555 3040 5.969423 AGAGAGAGAGAGAGAAAGCAATTG 58.031 41.667 0.00 0.00 0.00 2.32
2556 3041 5.954150 AGAGAGAGAGAGAGAGAAAGCAATT 59.046 40.000 0.00 0.00 0.00 2.32
2557 3042 5.513233 AGAGAGAGAGAGAGAGAAAGCAAT 58.487 41.667 0.00 0.00 0.00 3.56
2558 3043 4.922206 AGAGAGAGAGAGAGAGAAAGCAA 58.078 43.478 0.00 0.00 0.00 3.91
2559 3044 4.019411 TGAGAGAGAGAGAGAGAGAAAGCA 60.019 45.833 0.00 0.00 0.00 3.91
2560 3045 4.517285 TGAGAGAGAGAGAGAGAGAAAGC 58.483 47.826 0.00 0.00 0.00 3.51
2561 3046 7.636150 AATTGAGAGAGAGAGAGAGAGAAAG 57.364 40.000 0.00 0.00 0.00 2.62
2562 3047 9.177608 CTAAATTGAGAGAGAGAGAGAGAGAAA 57.822 37.037 0.00 0.00 0.00 2.52
2563 3048 8.328758 ACTAAATTGAGAGAGAGAGAGAGAGAA 58.671 37.037 0.00 0.00 0.00 2.87
2564 3049 7.770433 CACTAAATTGAGAGAGAGAGAGAGAGA 59.230 40.741 0.00 0.00 0.00 3.10
2565 3050 7.554118 ACACTAAATTGAGAGAGAGAGAGAGAG 59.446 40.741 0.00 0.00 0.00 3.20
2566 3051 7.402054 ACACTAAATTGAGAGAGAGAGAGAGA 58.598 38.462 0.00 0.00 0.00 3.10
2567 3052 7.554118 AGACACTAAATTGAGAGAGAGAGAGAG 59.446 40.741 0.00 0.00 0.00 3.20
2568 3053 7.402054 AGACACTAAATTGAGAGAGAGAGAGA 58.598 38.462 0.00 0.00 0.00 3.10
2569 3054 7.630242 AGACACTAAATTGAGAGAGAGAGAG 57.370 40.000 0.00 0.00 0.00 3.20
2570 3055 8.325787 ACTAGACACTAAATTGAGAGAGAGAGA 58.674 37.037 0.00 0.00 0.00 3.10
2571 3056 8.506168 ACTAGACACTAAATTGAGAGAGAGAG 57.494 38.462 0.00 0.00 0.00 3.20
2572 3057 8.735315 CAACTAGACACTAAATTGAGAGAGAGA 58.265 37.037 0.00 0.00 0.00 3.10
2573 3058 8.735315 TCAACTAGACACTAAATTGAGAGAGAG 58.265 37.037 0.00 0.00 0.00 3.20
2574 3059 8.637196 TCAACTAGACACTAAATTGAGAGAGA 57.363 34.615 0.00 0.00 0.00 3.10
2575 3060 9.868277 AATCAACTAGACACTAAATTGAGAGAG 57.132 33.333 0.00 0.00 30.20 3.20
2587 3072 9.950496 ATTCAAATCTGTAATCAACTAGACACT 57.050 29.630 0.00 0.00 0.00 3.55
2595 3080 9.859427 TGGATTGAATTCAAATCTGTAATCAAC 57.141 29.630 23.91 4.69 39.55 3.18
2598 3083 9.525409 CCTTGGATTGAATTCAAATCTGTAATC 57.475 33.333 23.91 13.88 39.55 1.75
2599 3084 9.258629 TCCTTGGATTGAATTCAAATCTGTAAT 57.741 29.630 23.91 5.69 39.55 1.89
2600 3085 8.522830 GTCCTTGGATTGAATTCAAATCTGTAA 58.477 33.333 23.91 12.31 39.55 2.41
2601 3086 7.148255 CGTCCTTGGATTGAATTCAAATCTGTA 60.148 37.037 23.91 0.30 39.55 2.74
2602 3087 6.349611 CGTCCTTGGATTGAATTCAAATCTGT 60.350 38.462 23.91 7.93 39.55 3.41
2603 3088 6.032094 CGTCCTTGGATTGAATTCAAATCTG 58.968 40.000 23.91 12.96 39.55 2.90
2604 3089 5.945784 TCGTCCTTGGATTGAATTCAAATCT 59.054 36.000 23.91 8.69 39.55 2.40
2605 3090 6.194796 TCGTCCTTGGATTGAATTCAAATC 57.805 37.500 23.91 19.23 39.55 2.17
2606 3091 5.126061 CCTCGTCCTTGGATTGAATTCAAAT 59.874 40.000 23.91 12.81 39.55 2.32
2607 3092 4.458989 CCTCGTCCTTGGATTGAATTCAAA 59.541 41.667 23.91 5.97 39.55 2.69
2608 3093 4.009675 CCTCGTCCTTGGATTGAATTCAA 58.990 43.478 22.52 22.52 40.51 2.69
2609 3094 3.263170 TCCTCGTCCTTGGATTGAATTCA 59.737 43.478 3.38 3.38 0.00 2.57
2610 3095 3.873910 TCCTCGTCCTTGGATTGAATTC 58.126 45.455 0.00 0.00 0.00 2.17
2611 3096 4.265073 CTTCCTCGTCCTTGGATTGAATT 58.735 43.478 0.00 0.00 31.76 2.17
2612 3097 3.370953 CCTTCCTCGTCCTTGGATTGAAT 60.371 47.826 0.00 0.00 31.76 2.57
2613 3098 2.027192 CCTTCCTCGTCCTTGGATTGAA 60.027 50.000 0.00 0.00 31.76 2.69
2614 3099 1.555075 CCTTCCTCGTCCTTGGATTGA 59.445 52.381 0.00 0.00 31.76 2.57
2615 3100 1.555075 TCCTTCCTCGTCCTTGGATTG 59.445 52.381 0.00 0.00 31.76 2.67
2616 3101 1.952621 TCCTTCCTCGTCCTTGGATT 58.047 50.000 0.00 0.00 31.76 3.01
2617 3102 1.834263 CTTCCTTCCTCGTCCTTGGAT 59.166 52.381 0.00 0.00 31.76 3.41
2618 3103 1.203137 TCTTCCTTCCTCGTCCTTGGA 60.203 52.381 0.00 0.00 0.00 3.53
2619 3104 1.267121 TCTTCCTTCCTCGTCCTTGG 58.733 55.000 0.00 0.00 0.00 3.61
2620 3105 2.037251 TGTTCTTCCTTCCTCGTCCTTG 59.963 50.000 0.00 0.00 0.00 3.61
2621 3106 2.300437 CTGTTCTTCCTTCCTCGTCCTT 59.700 50.000 0.00 0.00 0.00 3.36
2622 3107 1.896465 CTGTTCTTCCTTCCTCGTCCT 59.104 52.381 0.00 0.00 0.00 3.85
2623 3108 1.893801 TCTGTTCTTCCTTCCTCGTCC 59.106 52.381 0.00 0.00 0.00 4.79
2624 3109 2.820787 TCTCTGTTCTTCCTTCCTCGTC 59.179 50.000 0.00 0.00 0.00 4.20
2625 3110 2.877866 TCTCTGTTCTTCCTTCCTCGT 58.122 47.619 0.00 0.00 0.00 4.18
2626 3111 3.944055 TTCTCTGTTCTTCCTTCCTCG 57.056 47.619 0.00 0.00 0.00 4.63
2627 3112 4.962155 TGTTTCTCTGTTCTTCCTTCCTC 58.038 43.478 0.00 0.00 0.00 3.71
2628 3113 5.126779 GTTGTTTCTCTGTTCTTCCTTCCT 58.873 41.667 0.00 0.00 0.00 3.36
2629 3114 4.881850 TGTTGTTTCTCTGTTCTTCCTTCC 59.118 41.667 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.