Multiple sequence alignment - TraesCS5D01G400900

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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 TraesCS5D01G400900 chr5D 100.000 3033 0 0 1 3033 465905047 465908079 0.000000e+00 5602
1 TraesCS5D01G400900 chr5B 90.882 2720 130 47 3 2638 573141455 573144140 0.000000e+00 3541
2 TraesCS5D01G400900 chr5B 85.903 227 8 6 2807 3033 573145563 573145765 1.420000e-53 220
3 TraesCS5D01G400900 chr5B 84.393 173 8 4 2659 2813 573144237 573144408 5.240000e-33 152
4 TraesCS5D01G400900 chr5A 88.776 3047 125 80 118 3033 586306807 586309767 0.000000e+00 3531
5 TraesCS5D01G400900 chr5A 96.203 79 3 0 1 79 586306720 586306798 2.450000e-26 130


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 TraesCS5D01G400900 chr5D 465905047 465908079 3032 False 5602.000000 5602 100.000000 1 3033 1 chr5D.!!$F1 3032
1 TraesCS5D01G400900 chr5B 573141455 573145765 4310 False 1304.333333 3541 87.059333 3 3033 3 chr5B.!!$F1 3030
2 TraesCS5D01G400900 chr5A 586306720 586309767 3047 False 1830.500000 3531 92.489500 1 3033 2 chr5A.!!$F1 3032

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
79 80 0.400594 ACCACCCAGAGTTAAGCACC 59.599 55.0 0.0 0.0 0.0 5.01 F
559 588 0.630673 CCTCCCACATCCAATTCCCA 59.369 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1021 1085 0.745845 ATGGTCGGCATCTGCACTTC 60.746 55.0 4.33 0.0 44.36 3.01 R
2539 2690 0.037975 GTTTGCTTGGCCTCCACATG 60.038 55.0 3.32 0.0 30.78 3.21 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
69 70 1.425066 AGCAAAAGATGACCACCCAGA 59.575 47.619 0.00 0.00 0.00 3.86
79 80 0.400594 ACCACCCAGAGTTAAGCACC 59.599 55.000 0.00 0.00 0.00 5.01
81 82 1.523758 CACCCAGAGTTAAGCACCAC 58.476 55.000 0.00 0.00 0.00 4.16
82 83 1.072331 CACCCAGAGTTAAGCACCACT 59.928 52.381 0.00 0.00 0.00 4.00
83 84 1.072331 ACCCAGAGTTAAGCACCACTG 59.928 52.381 0.00 0.00 32.94 3.66
84 85 1.072331 CCCAGAGTTAAGCACCACTGT 59.928 52.381 0.00 0.00 31.89 3.55
85 86 2.301870 CCCAGAGTTAAGCACCACTGTA 59.698 50.000 0.00 0.00 31.89 2.74
86 87 3.244422 CCCAGAGTTAAGCACCACTGTAA 60.244 47.826 0.00 0.00 31.89 2.41
87 88 4.565652 CCCAGAGTTAAGCACCACTGTAAT 60.566 45.833 0.00 0.00 31.89 1.89
88 89 5.003804 CCAGAGTTAAGCACCACTGTAATT 58.996 41.667 0.00 0.00 31.89 1.40
110 111 3.706373 CCCTCCCACAGTCACCGG 61.706 72.222 0.00 0.00 0.00 5.28
143 144 3.790437 CCATGGGCTCTGGCTCGT 61.790 66.667 2.85 0.00 43.00 4.18
144 145 2.434843 CCATGGGCTCTGGCTCGTA 61.435 63.158 2.85 0.00 43.00 3.43
145 146 1.068753 CATGGGCTCTGGCTCGTAG 59.931 63.158 0.00 0.00 43.00 3.51
146 147 2.136878 ATGGGCTCTGGCTCGTAGG 61.137 63.158 0.00 0.00 43.00 3.18
147 148 4.228567 GGGCTCTGGCTCGTAGGC 62.229 72.222 2.24 2.24 41.77 3.93
182 183 1.856265 CGCCACTTGCCTTTCTCACC 61.856 60.000 0.00 0.00 36.24 4.02
184 185 1.576421 CACTTGCCTTTCTCACCGC 59.424 57.895 0.00 0.00 0.00 5.68
192 193 1.078759 CTTTCTCACCGCGCGAGAAT 61.079 55.000 34.63 11.00 46.15 2.40
226 227 1.023513 GCTCAGTGTCACATCCAGCC 61.024 60.000 5.62 0.00 0.00 4.85
531 559 1.299541 GTATTCATCCACACCGCCTG 58.700 55.000 0.00 0.00 0.00 4.85
559 588 0.630673 CCTCCCACATCCAATTCCCA 59.369 55.000 0.00 0.00 0.00 4.37
567 598 1.285962 CATCCAATTCCCACTCCACCT 59.714 52.381 0.00 0.00 0.00 4.00
589 620 1.687493 CTCCTTCTCGGCCCTTCCT 60.687 63.158 0.00 0.00 0.00 3.36
592 623 3.075005 TTCTCGGCCCTTCCTCGG 61.075 66.667 0.00 0.00 0.00 4.63
651 694 1.929836 GATGCACATCGTTGTCTCTCC 59.070 52.381 0.00 0.00 32.34 3.71
690 741 8.461222 CAGAAACATGCATTTGATTTAGGACTA 58.539 33.333 0.00 0.00 0.00 2.59
704 755 6.778834 TTTAGGACTACGTGTGGATGATTA 57.221 37.500 0.00 0.00 0.00 1.75
817 872 3.001414 GCTTCGAACTACCCTTTCTTCC 58.999 50.000 0.00 0.00 0.00 3.46
818 873 3.306849 GCTTCGAACTACCCTTTCTTCCT 60.307 47.826 0.00 0.00 0.00 3.36
826 881 8.202137 CGAACTACCCTTTCTTCCTATCAATTA 58.798 37.037 0.00 0.00 0.00 1.40
872 930 1.945522 CGTGAACCGGTTGCAATCA 59.054 52.632 27.87 13.84 0.00 2.57
910 969 2.451490 TCGATCTCCTCTTTGCTCTGT 58.549 47.619 0.00 0.00 0.00 3.41
917 976 1.668919 CCTCTTTGCTCTGTTCGCGTA 60.669 52.381 5.77 0.00 0.00 4.42
959 1020 6.560253 TTCATTTTCTAACTCTGTTCTGCC 57.440 37.500 0.00 0.00 0.00 4.85
981 1042 4.101741 CCAAGGAAGAGACTATAAGGTGGG 59.898 50.000 0.00 0.00 0.00 4.61
1005 1066 6.761714 GGAAATTTCGGCTAGAATTCTGACTA 59.238 38.462 18.47 0.00 38.86 2.59
1019 1083 1.546476 CTGACTAGGGAGGTGTGTGTC 59.454 57.143 0.00 0.00 0.00 3.67
1020 1084 1.147191 TGACTAGGGAGGTGTGTGTCT 59.853 52.381 0.00 0.00 0.00 3.41
1021 1085 1.546476 GACTAGGGAGGTGTGTGTCTG 59.454 57.143 0.00 0.00 0.00 3.51
1022 1086 1.147191 ACTAGGGAGGTGTGTGTCTGA 59.853 52.381 0.00 0.00 0.00 3.27
1185 1250 2.096013 GGCGTTAGTTTTGAGCCTGATC 59.904 50.000 0.00 0.00 44.06 2.92
1188 1253 3.181530 CGTTAGTTTTGAGCCTGATCGTG 60.182 47.826 0.00 0.00 0.00 4.35
1194 1259 2.084610 TGAGCCTGATCGTGTTCTTG 57.915 50.000 0.00 0.00 0.00 3.02
1207 1277 0.944386 GTTCTTGGCGTGCAGAGAAA 59.056 50.000 9.68 0.00 30.67 2.52
1783 1880 2.230940 CGGCGGCTACAAGATCGTG 61.231 63.158 7.61 7.13 0.00 4.35
1829 1926 0.712222 CGCCATCATGTGATCGATCG 59.288 55.000 20.03 9.36 31.21 3.69
1830 1927 1.666888 CGCCATCATGTGATCGATCGA 60.667 52.381 21.86 21.86 31.21 3.59
1831 1928 2.614779 GCCATCATGTGATCGATCGAT 58.385 47.619 29.76 29.76 37.59 3.59
1843 1940 4.750952 ATCGATCGATCAATCAGTACGT 57.249 40.909 24.60 0.00 0.00 3.57
1875 1984 2.926242 TTCCCACCACCTCCGTCC 60.926 66.667 0.00 0.00 0.00 4.79
1993 2107 2.171027 ACACCTACTCTCTACTCCCTCG 59.829 54.545 0.00 0.00 0.00 4.63
2044 2162 7.721399 AGAAGCCAGAATAAAATACATACCCAG 59.279 37.037 0.00 0.00 0.00 4.45
2186 2304 1.516161 TGTGCTGCTGTGACATCTTC 58.484 50.000 0.00 0.00 0.00 2.87
2245 2365 0.679002 CTGATGGAGTTGTGCTGGGG 60.679 60.000 0.00 0.00 0.00 4.96
2349 2469 9.767684 TGCTTTCTCGTGTATTATTTATTGTTG 57.232 29.630 0.00 0.00 0.00 3.33
2427 2547 0.753479 GAGGAGCGTCATCAGGAGGA 60.753 60.000 0.00 0.00 33.18 3.71
2428 2548 0.754957 AGGAGCGTCATCAGGAGGAG 60.755 60.000 0.00 0.00 33.18 3.69
2449 2569 0.528901 TGATTAGGCGCGCACGTAAT 60.529 50.000 34.42 28.22 42.83 1.89
2528 2679 1.375908 CGGTGGTGGGTGACATGAG 60.376 63.158 0.00 0.00 0.00 2.90
2529 2680 1.002134 GGTGGTGGGTGACATGAGG 60.002 63.158 0.00 0.00 0.00 3.86
2530 2681 1.002134 GTGGTGGGTGACATGAGGG 60.002 63.158 0.00 0.00 0.00 4.30
2531 2682 1.463214 TGGTGGGTGACATGAGGGT 60.463 57.895 0.00 0.00 0.00 4.34
2532 2683 1.002134 GGTGGGTGACATGAGGGTG 60.002 63.158 0.00 0.00 0.00 4.61
2533 2684 1.675641 GTGGGTGACATGAGGGTGC 60.676 63.158 0.00 0.00 0.00 5.01
2534 2685 2.152729 TGGGTGACATGAGGGTGCA 61.153 57.895 0.00 0.00 0.00 4.57
2535 2686 1.304282 GGGTGACATGAGGGTGCAT 59.696 57.895 0.00 0.00 0.00 3.96
2537 2688 0.035152 GGTGACATGAGGGTGCATGA 60.035 55.000 10.93 0.00 46.64 3.07
2538 2689 1.614051 GGTGACATGAGGGTGCATGAA 60.614 52.381 10.93 0.00 46.64 2.57
2539 2690 1.470098 GTGACATGAGGGTGCATGAAC 59.530 52.381 10.93 0.00 46.64 3.18
2540 2691 1.073603 TGACATGAGGGTGCATGAACA 59.926 47.619 6.08 7.76 46.64 3.18
2541 2692 2.291089 TGACATGAGGGTGCATGAACAT 60.291 45.455 6.08 0.00 46.64 2.71
2542 2693 2.097036 ACATGAGGGTGCATGAACATG 58.903 47.619 6.08 18.27 46.64 3.21
2604 2755 2.096417 GTCGAATTCACACGGAAACAGG 60.096 50.000 6.22 0.00 39.39 4.00
2623 2833 1.069427 GGCCATGCAAACACAAGCA 59.931 52.632 0.00 0.00 45.92 3.91
2624 2834 0.947180 GGCCATGCAAACACAAGCAG 60.947 55.000 0.00 0.00 44.94 4.24
2625 2835 0.032403 GCCATGCAAACACAAGCAGA 59.968 50.000 0.00 0.00 44.94 4.26
2626 2836 1.933500 GCCATGCAAACACAAGCAGAG 60.934 52.381 0.00 0.00 44.94 3.35
2628 2838 2.553602 CCATGCAAACACAAGCAGAGTA 59.446 45.455 0.00 0.00 44.94 2.59
2629 2839 3.192001 CCATGCAAACACAAGCAGAGTAT 59.808 43.478 0.00 0.00 44.94 2.12
2631 2841 3.213506 TGCAAACACAAGCAGAGTATGT 58.786 40.909 0.00 0.00 35.51 2.29
2638 2848 5.709011 CACAAGCAGAGTATGTGTGTATC 57.291 43.478 1.41 0.00 39.60 2.24
2642 2852 4.926244 AGCAGAGTATGTGTGTATCTTCG 58.074 43.478 0.00 0.00 0.00 3.79
2644 2854 5.103000 GCAGAGTATGTGTGTATCTTCGTT 58.897 41.667 0.00 0.00 0.00 3.85
2648 2880 5.103000 AGTATGTGTGTATCTTCGTTCAGC 58.897 41.667 0.00 0.00 0.00 4.26
2649 2881 3.660501 TGTGTGTATCTTCGTTCAGCT 57.339 42.857 0.00 0.00 0.00 4.24
2652 2884 4.217767 TGTGTGTATCTTCGTTCAGCTAGT 59.782 41.667 0.00 0.00 0.00 2.57
2656 2888 6.037098 GTGTATCTTCGTTCAGCTAGTTCAT 58.963 40.000 0.00 0.00 0.00 2.57
2657 2889 6.531948 GTGTATCTTCGTTCAGCTAGTTCATT 59.468 38.462 0.00 0.00 0.00 2.57
2660 2892 5.538118 TCTTCGTTCAGCTAGTTCATTTCA 58.462 37.500 0.00 0.00 0.00 2.69
2674 2906 2.542178 TCATTTCACGAGTTCACCGTTG 59.458 45.455 0.00 0.00 38.29 4.10
2702 2937 2.095461 TCGTGAGGTGGAGAATCAGAG 58.905 52.381 0.00 0.00 36.25 3.35
2714 2949 0.179100 AATCAGAGGTCGCATCCACG 60.179 55.000 0.00 0.00 0.00 4.94
2723 2972 0.522626 TCGCATCCACGTCGTTCTTA 59.477 50.000 0.00 0.00 0.00 2.10
2732 2985 2.538449 CACGTCGTTCTTATGGTATGGC 59.462 50.000 0.00 0.00 0.00 4.40
2864 4278 2.306384 GGGTGGGGTTGGTCCTAGG 61.306 68.421 0.82 0.82 36.25 3.02
2865 4279 2.675371 GTGGGGTTGGTCCTAGGC 59.325 66.667 2.96 0.00 36.25 3.93
2866 4280 1.923909 GTGGGGTTGGTCCTAGGCT 60.924 63.158 2.96 0.00 36.25 4.58
2867 4281 1.615424 TGGGGTTGGTCCTAGGCTC 60.615 63.158 2.96 0.00 36.25 4.70
2868 4282 2.732619 GGGGTTGGTCCTAGGCTCG 61.733 68.421 2.96 0.00 36.25 5.03
2869 4283 1.988406 GGGTTGGTCCTAGGCTCGT 60.988 63.158 2.96 0.00 36.25 4.18
2870 4284 0.685458 GGGTTGGTCCTAGGCTCGTA 60.685 60.000 2.96 0.00 36.25 3.43
2871 4285 0.459078 GGTTGGTCCTAGGCTCGTAC 59.541 60.000 2.96 0.00 0.00 3.67
2872 4286 0.459078 GTTGGTCCTAGGCTCGTACC 59.541 60.000 2.96 6.78 0.00 3.34
2873 4287 0.333993 TTGGTCCTAGGCTCGTACCT 59.666 55.000 15.63 4.46 44.31 3.08
2874 4288 0.106819 TGGTCCTAGGCTCGTACCTC 60.107 60.000 15.63 0.00 41.50 3.85
2875 4289 1.165284 GGTCCTAGGCTCGTACCTCG 61.165 65.000 2.96 0.00 41.50 4.63
2876 4290 0.463474 GTCCTAGGCTCGTACCTCGT 60.463 60.000 2.96 0.00 41.50 4.18
2877 4291 1.123077 TCCTAGGCTCGTACCTCGTA 58.877 55.000 2.96 0.00 41.50 3.43
2878 4292 1.069823 TCCTAGGCTCGTACCTCGTAG 59.930 57.143 2.96 0.00 41.50 3.51
2879 4293 1.202627 CCTAGGCTCGTACCTCGTAGT 60.203 57.143 0.00 0.00 41.50 2.73
2961 4375 2.363172 GGTCCTGTCCTCCTCAGCC 61.363 68.421 0.00 0.00 0.00 4.85
2963 4377 2.040278 CCTGTCCTCCTCAGCCCT 59.960 66.667 0.00 0.00 0.00 5.19
2971 4385 4.154347 CCTCAGCCCTGCCTCGAC 62.154 72.222 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.612972 GCTCAGACAAGAAATGGACCGA 60.613 50.000 0.00 0.00 0.00 4.69
69 70 4.689345 GTCGAATTACAGTGGTGCTTAACT 59.311 41.667 0.00 0.00 0.00 2.24
79 80 1.134491 GGGAGGGGTCGAATTACAGTG 60.134 57.143 0.00 0.00 0.00 3.66
81 82 1.134491 GTGGGAGGGGTCGAATTACAG 60.134 57.143 0.00 0.00 0.00 2.74
82 83 0.906775 GTGGGAGGGGTCGAATTACA 59.093 55.000 0.00 0.00 0.00 2.41
83 84 0.906775 TGTGGGAGGGGTCGAATTAC 59.093 55.000 0.00 0.00 0.00 1.89
84 85 1.200519 CTGTGGGAGGGGTCGAATTA 58.799 55.000 0.00 0.00 0.00 1.40
85 86 0.840722 ACTGTGGGAGGGGTCGAATT 60.841 55.000 0.00 0.00 0.00 2.17
86 87 1.229529 ACTGTGGGAGGGGTCGAAT 60.230 57.895 0.00 0.00 0.00 3.34
87 88 1.911766 GACTGTGGGAGGGGTCGAA 60.912 63.158 0.00 0.00 0.00 3.71
88 89 2.283676 GACTGTGGGAGGGGTCGA 60.284 66.667 0.00 0.00 0.00 4.20
110 111 4.832608 GGTGCCACCCGACCGATC 62.833 72.222 1.17 0.00 30.04 3.69
124 125 2.124403 GAGCCAGAGCCCATGGTG 60.124 66.667 11.73 1.64 41.25 4.17
125 126 3.790437 CGAGCCAGAGCCCATGGT 61.790 66.667 11.73 0.00 41.25 3.55
176 177 1.063649 GTATTCTCGCGCGGTGAGA 59.936 57.895 31.69 22.57 45.72 3.27
182 183 2.035674 CAGTTTGTAGTATTCTCGCGCG 60.036 50.000 26.76 26.76 0.00 6.86
184 185 4.144902 CGATCAGTTTGTAGTATTCTCGCG 59.855 45.833 0.00 0.00 0.00 5.87
226 227 1.478510 CTACTGGTGGTGGTAGAGCAG 59.521 57.143 0.00 0.00 42.26 4.24
546 574 1.005924 GGTGGAGTGGGAATTGGATGT 59.994 52.381 0.00 0.00 0.00 3.06
559 588 1.985116 GAAGGAGCGGAGGTGGAGT 60.985 63.158 0.00 0.00 39.88 3.85
651 694 2.964740 TGTTTCTGATTGCGAGAGAGG 58.035 47.619 0.00 0.00 0.00 3.69
690 741 5.937540 TCAAATCAACTAATCATCCACACGT 59.062 36.000 0.00 0.00 0.00 4.49
817 872 7.922811 GGCACAAAAGAGGGAAATAATTGATAG 59.077 37.037 0.00 0.00 0.00 2.08
818 873 7.619302 AGGCACAAAAGAGGGAAATAATTGATA 59.381 33.333 0.00 0.00 0.00 2.15
826 881 3.092301 GCTAGGCACAAAAGAGGGAAAT 58.908 45.455 0.00 0.00 0.00 2.17
868 926 1.608590 CGACCAAACCAACTGCTGATT 59.391 47.619 0.00 0.00 0.00 2.57
872 930 1.523758 GATCGACCAAACCAACTGCT 58.476 50.000 0.00 0.00 0.00 4.24
917 976 3.005684 TGAAACAGAGGCGCATCAATTTT 59.994 39.130 25.38 18.36 0.00 1.82
959 1020 4.962995 TCCCACCTTATAGTCTCTTCCTTG 59.037 45.833 0.00 0.00 0.00 3.61
981 1042 6.670077 AGTCAGAATTCTAGCCGAAATTTC 57.330 37.500 7.86 8.20 34.79 2.17
1005 1066 1.051812 CTTCAGACACACACCTCCCT 58.948 55.000 0.00 0.00 0.00 4.20
1019 1083 1.364626 GGTCGGCATCTGCACTTCAG 61.365 60.000 4.33 0.00 44.36 3.02
1020 1084 1.375908 GGTCGGCATCTGCACTTCA 60.376 57.895 4.33 0.00 44.36 3.02
1021 1085 0.745845 ATGGTCGGCATCTGCACTTC 60.746 55.000 4.33 0.00 44.36 3.01
1022 1086 0.745845 GATGGTCGGCATCTGCACTT 60.746 55.000 4.33 0.00 44.36 3.16
1185 1250 2.162921 CTCTGCACGCCAAGAACACG 62.163 60.000 0.00 0.00 0.00 4.49
1188 1253 0.944386 TTTCTCTGCACGCCAAGAAC 59.056 50.000 3.47 0.00 0.00 3.01
1194 1259 3.793144 CGCCTTTCTCTGCACGCC 61.793 66.667 0.00 0.00 0.00 5.68
1207 1277 3.587095 TCGATCACGAACTCGCCT 58.413 55.556 0.00 0.00 45.74 5.52
1555 1634 3.000819 TCCACGATCTTGGGCGGT 61.001 61.111 17.57 0.00 37.24 5.68
1565 1644 2.718073 GGTACGGCACCTCCACGAT 61.718 63.158 0.00 0.00 44.79 3.73
1783 1880 3.462678 GAGGGGTCCTCCTCGCAC 61.463 72.222 9.81 0.00 44.36 5.34
1829 1926 4.906423 ACTGTACGACGTACTGATTGATC 58.094 43.478 36.35 13.71 39.29 2.92
1830 1927 4.959596 ACTGTACGACGTACTGATTGAT 57.040 40.909 36.35 19.95 39.29 2.57
1831 1928 4.931601 AGTACTGTACGACGTACTGATTGA 59.068 41.667 36.35 21.79 43.29 2.57
1832 1929 5.213913 AGTACTGTACGACGTACTGATTG 57.786 43.478 36.35 23.19 43.29 2.67
1843 1940 1.271325 TGGGAACGGAGTACTGTACGA 60.271 52.381 15.52 0.00 45.00 3.43
1993 2107 5.652452 ACTAATCACAGGGGAAATAAACAGC 59.348 40.000 0.00 0.00 0.00 4.40
2044 2162 3.623060 ACGAAGTACCACATGAATGCATC 59.377 43.478 0.00 0.00 41.94 3.91
2082 2200 5.131784 TCTCGGATCCTCCTTAGTTTCTAC 58.868 45.833 10.75 0.00 33.30 2.59
2109 2227 0.039437 ACGACAGACACACCGATGAC 60.039 55.000 0.00 0.00 0.00 3.06
2115 2233 2.061773 CAATGAGACGACAGACACACC 58.938 52.381 0.00 0.00 0.00 4.16
2202 2320 6.827251 AGATCAGAGTGCAACATACATGAATT 59.173 34.615 0.00 0.00 41.43 2.17
2245 2365 5.819901 AGTAAAGCTGCTGAGGATAATGAAC 59.180 40.000 1.35 0.00 0.00 3.18
2259 2379 2.399396 TCGCAACAAAGTAAAGCTGC 57.601 45.000 0.00 0.00 0.00 5.25
2349 2469 2.612212 CGCCCCATCTTTACATGTACAC 59.388 50.000 4.68 0.00 0.00 2.90
2353 2473 2.799126 TTCGCCCCATCTTTACATGT 57.201 45.000 2.69 2.69 0.00 3.21
2427 2547 2.511600 GTGCGCGCCTAATCACCT 60.512 61.111 30.77 0.00 0.00 4.00
2428 2548 3.925238 CGTGCGCGCCTAATCACC 61.925 66.667 30.77 4.90 0.00 4.02
2449 2569 0.672889 GATCAGAGATCGCCTCAGCA 59.327 55.000 7.27 0.00 44.40 4.41
2480 2600 2.186644 CGGGCGACACATCATCCA 59.813 61.111 0.00 0.00 0.00 3.41
2528 2679 0.813184 CTCCACATGTTCATGCACCC 59.187 55.000 12.00 0.00 0.00 4.61
2529 2680 0.813184 CCTCCACATGTTCATGCACC 59.187 55.000 12.00 0.00 0.00 5.01
2530 2681 0.171903 GCCTCCACATGTTCATGCAC 59.828 55.000 12.00 0.00 0.00 4.57
2531 2682 0.966875 GGCCTCCACATGTTCATGCA 60.967 55.000 12.00 0.00 0.00 3.96
2532 2683 0.966875 TGGCCTCCACATGTTCATGC 60.967 55.000 3.32 0.00 0.00 4.06
2533 2684 1.475280 CTTGGCCTCCACATGTTCATG 59.525 52.381 3.32 10.72 30.78 3.07
2534 2685 1.843368 CTTGGCCTCCACATGTTCAT 58.157 50.000 3.32 0.00 30.78 2.57
2535 2686 0.895100 GCTTGGCCTCCACATGTTCA 60.895 55.000 3.32 0.00 30.78 3.18
2536 2687 0.895100 TGCTTGGCCTCCACATGTTC 60.895 55.000 3.32 0.00 30.78 3.18
2537 2688 0.469705 TTGCTTGGCCTCCACATGTT 60.470 50.000 3.32 0.00 30.78 2.71
2538 2689 0.469705 TTTGCTTGGCCTCCACATGT 60.470 50.000 3.32 0.00 30.78 3.21
2539 2690 0.037975 GTTTGCTTGGCCTCCACATG 60.038 55.000 3.32 0.00 30.78 3.21
2540 2691 1.187567 GGTTTGCTTGGCCTCCACAT 61.188 55.000 3.32 0.00 30.78 3.21
2541 2692 1.832167 GGTTTGCTTGGCCTCCACA 60.832 57.895 3.32 0.00 30.78 4.17
2542 2693 1.832167 TGGTTTGCTTGGCCTCCAC 60.832 57.895 3.32 0.00 30.78 4.02
2597 2748 0.320683 GTTTGCATGGCCCCTGTTTC 60.321 55.000 0.00 0.00 0.00 2.78
2604 2755 1.668793 GCTTGTGTTTGCATGGCCC 60.669 57.895 0.00 0.00 0.00 5.80
2623 2833 6.510879 TGAACGAAGATACACACATACTCT 57.489 37.500 0.00 0.00 0.00 3.24
2624 2834 5.230306 GCTGAACGAAGATACACACATACTC 59.770 44.000 0.00 0.00 0.00 2.59
2625 2835 5.103000 GCTGAACGAAGATACACACATACT 58.897 41.667 0.00 0.00 0.00 2.12
2626 2836 5.103000 AGCTGAACGAAGATACACACATAC 58.897 41.667 0.00 0.00 0.00 2.39
2628 2838 4.193826 AGCTGAACGAAGATACACACAT 57.806 40.909 0.00 0.00 0.00 3.21
2629 2839 3.660501 AGCTGAACGAAGATACACACA 57.339 42.857 0.00 0.00 0.00 3.72
2631 2841 5.048294 TGAACTAGCTGAACGAAGATACACA 60.048 40.000 0.00 0.00 0.00 3.72
2633 2843 5.638596 TGAACTAGCTGAACGAAGATACA 57.361 39.130 0.00 0.00 0.00 2.29
2634 2844 7.275779 TGAAATGAACTAGCTGAACGAAGATAC 59.724 37.037 0.00 0.00 0.00 2.24
2635 2845 7.275779 GTGAAATGAACTAGCTGAACGAAGATA 59.724 37.037 0.00 0.00 0.00 1.98
2636 2846 6.091441 GTGAAATGAACTAGCTGAACGAAGAT 59.909 38.462 0.00 0.00 0.00 2.40
2638 2848 5.612865 GTGAAATGAACTAGCTGAACGAAG 58.387 41.667 0.00 0.00 0.00 3.79
2642 2852 4.686554 ACTCGTGAAATGAACTAGCTGAAC 59.313 41.667 0.00 0.00 0.00 3.18
2644 2854 4.521130 ACTCGTGAAATGAACTAGCTGA 57.479 40.909 0.00 0.00 0.00 4.26
2648 2880 4.090066 CGGTGAACTCGTGAAATGAACTAG 59.910 45.833 0.00 0.00 0.00 2.57
2649 2881 3.985279 CGGTGAACTCGTGAAATGAACTA 59.015 43.478 0.00 0.00 0.00 2.24
2652 2884 2.828877 ACGGTGAACTCGTGAAATGAA 58.171 42.857 0.00 0.00 39.55 2.57
2656 2888 1.292061 CCAACGGTGAACTCGTGAAA 58.708 50.000 0.00 0.00 40.96 2.69
2657 2889 0.176219 ACCAACGGTGAACTCGTGAA 59.824 50.000 0.00 0.00 40.96 3.18
2660 2892 1.011333 CAAACCAACGGTGAACTCGT 58.989 50.000 0.00 0.00 43.14 4.18
2674 2906 1.602377 CTCCACCTCACGAAACAAACC 59.398 52.381 0.00 0.00 0.00 3.27
2702 2937 2.431942 AACGACGTGGATGCGACC 60.432 61.111 3.97 0.00 35.59 4.79
2732 2985 1.889170 GGCAAGGAAGAAGAAAGGGTG 59.111 52.381 0.00 0.00 0.00 4.61
2845 4259 2.608368 TAGGACCAACCCCACCCG 60.608 66.667 0.00 0.00 40.05 5.28
2857 4271 0.463474 ACGAGGTACGAGCCTAGGAC 60.463 60.000 14.75 3.76 45.77 3.85
2860 4274 1.865970 CACTACGAGGTACGAGCCTAG 59.134 57.143 2.77 5.74 45.77 3.02
2864 4278 1.726265 CCCACTACGAGGTACGAGC 59.274 63.158 0.00 0.00 45.77 5.03
2865 4279 1.726265 GCCCACTACGAGGTACGAG 59.274 63.158 0.00 0.00 45.77 4.18
2866 4280 2.108514 CGCCCACTACGAGGTACGA 61.109 63.158 0.00 0.00 45.77 3.43
2868 4282 2.048603 ACCGCCCACTACGAGGTAC 61.049 63.158 0.00 0.00 32.76 3.34
2869 4283 2.048023 CACCGCCCACTACGAGGTA 61.048 63.158 0.00 0.00 33.30 3.08
2870 4284 3.379445 CACCGCCCACTACGAGGT 61.379 66.667 0.00 0.00 35.24 3.85
2871 4285 4.143333 CCACCGCCCACTACGAGG 62.143 72.222 0.00 0.00 0.00 4.63
2872 4286 4.143333 CCCACCGCCCACTACGAG 62.143 72.222 0.00 0.00 0.00 4.18
2874 4288 2.567564 CTAACCCACCGCCCACTACG 62.568 65.000 0.00 0.00 0.00 3.51
2875 4289 1.219935 CTAACCCACCGCCCACTAC 59.780 63.158 0.00 0.00 0.00 2.73
2876 4290 1.078891 TCTAACCCACCGCCCACTA 59.921 57.895 0.00 0.00 0.00 2.74
2877 4291 2.203877 TCTAACCCACCGCCCACT 60.204 61.111 0.00 0.00 0.00 4.00
2878 4292 2.046604 GTCTAACCCACCGCCCAC 60.047 66.667 0.00 0.00 0.00 4.61
2879 4293 2.203877 AGTCTAACCCACCGCCCA 60.204 61.111 0.00 0.00 0.00 5.36
2961 4375 2.351244 TAGGCACAGTCGAGGCAGG 61.351 63.158 0.00 0.00 0.00 4.85
2963 4377 2.646175 GGTAGGCACAGTCGAGGCA 61.646 63.158 0.00 0.00 0.00 4.75
2971 4385 2.893398 GTCCTCCGGTAGGCACAG 59.107 66.667 13.41 0.00 46.10 3.66


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

AutoCloner maintained by Alex Coulton.