Multiple sequence alignment - TraesCS1B01G425200

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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 TraesCS1B01G425200 chr1B 100.000 2254 0 0 554 2807 649669619 649671872 0.000000e+00 4163
1 TraesCS1B01G425200 chr1B 100.000 184 0 0 1 184 649669066 649669249 9.630000e-90 340
2 TraesCS1B01G425200 chr1D 92.140 2290 101 29 554 2807 469794964 469797210 0.000000e+00 3158
3 TraesCS1B01G425200 chr1D 91.791 134 6 3 55 184 469794807 469794939 6.180000e-42 182
4 TraesCS1B01G425200 chr1A 91.751 2279 105 26 554 2807 562901909 562904129 0.000000e+00 3090
5 TraesCS1B01G425200 chr6D 90.937 982 52 16 1107 2070 17043031 17042069 0.000000e+00 1286
6 TraesCS1B01G425200 chr7B 89.854 1025 54 25 1063 2070 722094274 722095265 0.000000e+00 1271
7 TraesCS1B01G425200 chr5B 90.236 973 58 18 1108 2061 328273745 328274699 0.000000e+00 1236
8 TraesCS1B01G425200 chr3B 90.031 983 58 18 1107 2070 379653675 379654636 0.000000e+00 1236
9 TraesCS1B01G425200 chr3B 89.533 984 64 16 1107 2070 367032529 367031565 0.000000e+00 1210
10 TraesCS1B01G425200 chr6B 89.725 983 62 17 1107 2070 129701046 129702008 0.000000e+00 1219
11 TraesCS1B01G425200 chr6B 94.271 192 4 3 1615 1805 578775366 578775551 1.270000e-73 287
12 TraesCS1B01G425200 chr2A 89.206 982 68 16 1107 2070 276858821 276859782 0.000000e+00 1192
13 TraesCS1B01G425200 chr4A 87.926 1027 76 23 1063 2070 566610394 566609397 0.000000e+00 1166
14 TraesCS1B01G425200 chr5A 87.829 1027 66 23 1063 2070 69536074 69537060 0.000000e+00 1149
15 TraesCS1B01G425200 chr6A 89.813 697 41 13 1385 2070 214075708 214075031 0.000000e+00 867
16 TraesCS1B01G425200 chr7D 95.812 191 4 1 1615 1805 561875902 561876088 3.510000e-79 305


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 TraesCS1B01G425200 chr1B 649669066 649671872 2806 False 2251.5 4163 100.0000 1 2807 2 chr1B.!!$F1 2806
1 TraesCS1B01G425200 chr1D 469794807 469797210 2403 False 1670.0 3158 91.9655 55 2807 2 chr1D.!!$F1 2752
2 TraesCS1B01G425200 chr1A 562901909 562904129 2220 False 3090.0 3090 91.7510 554 2807 1 chr1A.!!$F1 2253
3 TraesCS1B01G425200 chr6D 17042069 17043031 962 True 1286.0 1286 90.9370 1107 2070 1 chr6D.!!$R1 963
4 TraesCS1B01G425200 chr7B 722094274 722095265 991 False 1271.0 1271 89.8540 1063 2070 1 chr7B.!!$F1 1007
5 TraesCS1B01G425200 chr5B 328273745 328274699 954 False 1236.0 1236 90.2360 1108 2061 1 chr5B.!!$F1 953
6 TraesCS1B01G425200 chr3B 379653675 379654636 961 False 1236.0 1236 90.0310 1107 2070 1 chr3B.!!$F1 963
7 TraesCS1B01G425200 chr3B 367031565 367032529 964 True 1210.0 1210 89.5330 1107 2070 1 chr3B.!!$R1 963
8 TraesCS1B01G425200 chr6B 129701046 129702008 962 False 1219.0 1219 89.7250 1107 2070 1 chr6B.!!$F1 963
9 TraesCS1B01G425200 chr2A 276858821 276859782 961 False 1192.0 1192 89.2060 1107 2070 1 chr2A.!!$F1 963
10 TraesCS1B01G425200 chr4A 566609397 566610394 997 True 1166.0 1166 87.9260 1063 2070 1 chr4A.!!$R1 1007
11 TraesCS1B01G425200 chr5A 69536074 69537060 986 False 1149.0 1149 87.8290 1063 2070 1 chr5A.!!$F1 1007
12 TraesCS1B01G425200 chr6A 214075031 214075708 677 True 867.0 867 89.8130 1385 2070 1 chr6A.!!$R1 685

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
31 32 0.111061 ACTTGCTGAGGGTTGATGCA 59.889 50.0 0.0 0.0 0.00 3.96 F
605 609 0.117140 TCCACACCTGATCCCAGTCT 59.883 55.0 0.0 0.0 38.74 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1597 0.028770 TGCGTCTTTGGTTTTGCTCG 59.971 50.0 0.0 0.0 0.0 5.03 R
2537 2603 0.608035 TTCATTCGGGGTGTTCTGGC 60.608 55.0 0.0 0.0 0.0 4.85 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
22 23 4.358851 CTCTCGAGATTTACTTGCTGAGG 58.641 47.826 17.03 0.00 32.34 3.86
23 24 3.131223 TCTCGAGATTTACTTGCTGAGGG 59.869 47.826 12.08 0.00 0.00 4.30
24 25 2.832129 TCGAGATTTACTTGCTGAGGGT 59.168 45.455 0.00 0.00 0.00 4.34
25 26 3.260884 TCGAGATTTACTTGCTGAGGGTT 59.739 43.478 0.00 0.00 0.00 4.11
26 27 3.372206 CGAGATTTACTTGCTGAGGGTTG 59.628 47.826 0.00 0.00 0.00 3.77
27 28 4.579869 GAGATTTACTTGCTGAGGGTTGA 58.420 43.478 0.00 0.00 0.00 3.18
28 29 5.184892 AGATTTACTTGCTGAGGGTTGAT 57.815 39.130 0.00 0.00 0.00 2.57
29 30 4.946157 AGATTTACTTGCTGAGGGTTGATG 59.054 41.667 0.00 0.00 0.00 3.07
30 31 2.113860 TACTTGCTGAGGGTTGATGC 57.886 50.000 0.00 0.00 0.00 3.91
31 32 0.111061 ACTTGCTGAGGGTTGATGCA 59.889 50.000 0.00 0.00 0.00 3.96
32 33 0.809385 CTTGCTGAGGGTTGATGCAG 59.191 55.000 0.00 0.00 35.02 4.41
33 34 0.401356 TTGCTGAGGGTTGATGCAGA 59.599 50.000 0.00 0.00 35.02 4.26
34 35 0.401356 TGCTGAGGGTTGATGCAGAA 59.599 50.000 0.00 0.00 0.00 3.02
35 36 1.093159 GCTGAGGGTTGATGCAGAAG 58.907 55.000 0.00 0.00 0.00 2.85
36 37 1.612726 GCTGAGGGTTGATGCAGAAGT 60.613 52.381 0.00 0.00 0.00 3.01
37 38 2.082231 CTGAGGGTTGATGCAGAAGTG 58.918 52.381 0.00 0.00 0.00 3.16
38 39 1.699083 TGAGGGTTGATGCAGAAGTGA 59.301 47.619 0.00 0.00 0.00 3.41
39 40 2.289882 TGAGGGTTGATGCAGAAGTGAG 60.290 50.000 0.00 0.00 0.00 3.51
40 41 1.980765 AGGGTTGATGCAGAAGTGAGA 59.019 47.619 0.00 0.00 0.00 3.27
41 42 2.373169 AGGGTTGATGCAGAAGTGAGAA 59.627 45.455 0.00 0.00 0.00 2.87
42 43 3.009916 AGGGTTGATGCAGAAGTGAGAAT 59.990 43.478 0.00 0.00 0.00 2.40
43 44 3.128242 GGGTTGATGCAGAAGTGAGAATG 59.872 47.826 0.00 0.00 0.00 2.67
44 45 4.005650 GGTTGATGCAGAAGTGAGAATGA 58.994 43.478 0.00 0.00 0.00 2.57
45 46 4.639310 GGTTGATGCAGAAGTGAGAATGAT 59.361 41.667 0.00 0.00 0.00 2.45
46 47 5.819379 GGTTGATGCAGAAGTGAGAATGATA 59.181 40.000 0.00 0.00 0.00 2.15
47 48 6.485984 GGTTGATGCAGAAGTGAGAATGATAT 59.514 38.462 0.00 0.00 0.00 1.63
48 49 7.307870 GGTTGATGCAGAAGTGAGAATGATATC 60.308 40.741 0.00 0.00 0.00 1.63
49 50 6.823497 TGATGCAGAAGTGAGAATGATATCA 58.177 36.000 8.10 8.10 0.00 2.15
50 51 7.450903 TGATGCAGAAGTGAGAATGATATCAT 58.549 34.615 12.62 12.62 38.41 2.45
51 52 7.387948 TGATGCAGAAGTGAGAATGATATCATG 59.612 37.037 18.85 5.24 36.56 3.07
52 53 6.823497 TGCAGAAGTGAGAATGATATCATGA 58.177 36.000 18.85 0.00 36.56 3.07
53 54 6.704937 TGCAGAAGTGAGAATGATATCATGAC 59.295 38.462 18.85 15.08 36.56 3.06
61 62 7.009083 GTGAGAATGATATCATGACGCTATCAC 59.991 40.741 18.85 18.89 41.24 3.06
103 106 7.696992 AAATACAGGAAAAATACGTCCACAT 57.303 32.000 0.00 0.00 36.28 3.21
107 110 6.811954 ACAGGAAAAATACGTCCACATTTTT 58.188 32.000 15.76 15.76 43.50 1.94
583 587 2.687418 ATCATGCGCCTCATCCCCAC 62.687 60.000 4.18 0.00 31.79 4.61
604 608 0.539051 CTCCACACCTGATCCCAGTC 59.461 60.000 0.00 0.00 38.74 3.51
605 609 0.117140 TCCACACCTGATCCCAGTCT 59.883 55.000 0.00 0.00 38.74 3.24
682 686 2.801631 GGAGAGATCCAGCCACCCG 61.802 68.421 0.00 0.00 0.00 5.28
874 884 3.126225 GTCGCCGTCGTCCTCTCT 61.126 66.667 0.00 0.00 36.96 3.10
1076 1095 2.466846 GGAGGAGGAAGAAGAAGAGCT 58.533 52.381 0.00 0.00 0.00 4.09
1077 1096 2.430694 GGAGGAGGAAGAAGAAGAGCTC 59.569 54.545 5.27 5.27 0.00 4.09
1078 1097 2.099098 GAGGAGGAAGAAGAAGAGCTCG 59.901 54.545 8.37 0.00 0.00 5.03
1079 1098 2.096248 GGAGGAAGAAGAAGAGCTCGA 58.904 52.381 8.37 0.00 0.00 4.04
1577 1613 1.947456 ACTCCGAGCAAAACCAAAGAC 59.053 47.619 0.00 0.00 0.00 3.01
1787 1827 8.695456 GCTTAAATTCTTTTGATTAGGGGATGA 58.305 33.333 0.00 0.00 0.00 2.92
1911 1957 3.189080 TCATGTTCCTTTCATCTTGCACG 59.811 43.478 0.00 0.00 0.00 5.34
1925 1971 4.049186 TCTTGCACGTCAGTTTTCTAGAC 58.951 43.478 0.00 0.00 0.00 2.59
2025 2073 1.180029 AATCCATGACAGGTGCTTGC 58.820 50.000 0.00 0.00 0.00 4.01
2061 2109 7.790027 TGATTTTCCCTCTCTCTTCTTCTATG 58.210 38.462 0.00 0.00 0.00 2.23
2063 2111 3.571590 TCCCTCTCTCTTCTTCTATGGC 58.428 50.000 0.00 0.00 0.00 4.40
2077 2125 7.200434 TCTTCTATGGCACTCCTTCTATTTT 57.800 36.000 0.00 0.00 0.00 1.82
2272 2325 6.074698 AGCCAACCACCAAGTTATTAGTAT 57.925 37.500 0.00 0.00 0.00 2.12
2273 2326 7.202972 AGCCAACCACCAAGTTATTAGTATA 57.797 36.000 0.00 0.00 0.00 1.47
2315 2368 9.807649 ATGCATTTCTTATGAAGGTTGATTAAC 57.192 29.630 0.00 0.00 33.28 2.01
2324 2377 6.817765 TGAAGGTTGATTAACTCATTCCAC 57.182 37.500 0.00 0.00 36.99 4.02
2327 2380 4.292306 AGGTTGATTAACTCATTCCACCCT 59.708 41.667 0.00 0.00 33.27 4.34
2328 2381 4.399303 GGTTGATTAACTCATTCCACCCTG 59.601 45.833 0.00 0.00 36.99 4.45
2329 2382 3.620488 TGATTAACTCATTCCACCCTGC 58.380 45.455 0.00 0.00 0.00 4.85
2387 2447 7.226128 TGCTATGATTTTTCACATCTGCTAGAG 59.774 37.037 0.00 0.00 32.11 2.43
2397 2457 1.519455 CTGCTAGAGGCCGTTTCCG 60.519 63.158 0.00 0.00 40.92 4.30
2400 2460 1.082679 GCTAGAGGCCGTTTCCGTTC 61.083 60.000 0.00 0.00 34.27 3.95
2420 2484 6.639279 CCGTTCTAGGTTTATTTGGTTGTTTG 59.361 38.462 0.00 0.00 0.00 2.93
2422 2486 7.377662 CGTTCTAGGTTTATTTGGTTGTTTGTC 59.622 37.037 0.00 0.00 0.00 3.18
2513 2579 7.343057 CCAGCCTTTTCTCCTTCCTATAATTTT 59.657 37.037 0.00 0.00 0.00 1.82
2536 2602 0.042535 AACAACGATGCAACGACACG 60.043 50.000 23.89 9.97 37.03 4.49
2537 2603 1.154672 CAACGATGCAACGACACGG 60.155 57.895 23.89 3.53 37.03 4.94
2587 2667 8.093927 ACGAATACCCAAATGTCAAAATGAATT 58.906 29.630 0.00 0.00 0.00 2.17
2611 2691 1.399572 GTCGATGATGTGTCGGATCG 58.600 55.000 0.00 0.00 39.45 3.69
2652 2732 4.828072 AGACGATAAGAGCTCCCTTTTT 57.172 40.909 10.93 0.00 0.00 1.94
2653 2733 4.508662 AGACGATAAGAGCTCCCTTTTTG 58.491 43.478 10.93 1.23 0.00 2.44
2654 2734 4.020128 AGACGATAAGAGCTCCCTTTTTGT 60.020 41.667 10.93 4.53 0.00 2.83
2655 2735 4.254492 ACGATAAGAGCTCCCTTTTTGTC 58.746 43.478 10.93 4.79 0.00 3.18
2656 2736 4.253685 CGATAAGAGCTCCCTTTTTGTCA 58.746 43.478 10.93 0.00 0.00 3.58
2657 2737 4.695455 CGATAAGAGCTCCCTTTTTGTCAA 59.305 41.667 10.93 0.00 0.00 3.18
2658 2738 5.355350 CGATAAGAGCTCCCTTTTTGTCAAT 59.645 40.000 10.93 0.00 0.00 2.57
2659 2739 4.861102 AAGAGCTCCCTTTTTGTCAATG 57.139 40.909 10.93 0.00 0.00 2.82
2660 2740 3.837355 AGAGCTCCCTTTTTGTCAATGT 58.163 40.909 10.93 0.00 0.00 2.71
2661 2741 4.985538 AGAGCTCCCTTTTTGTCAATGTA 58.014 39.130 10.93 0.00 0.00 2.29
2662 2742 5.006386 AGAGCTCCCTTTTTGTCAATGTAG 58.994 41.667 10.93 0.00 0.00 2.74
2663 2743 4.985538 AGCTCCCTTTTTGTCAATGTAGA 58.014 39.130 0.00 0.00 0.00 2.59
2664 2744 5.006386 AGCTCCCTTTTTGTCAATGTAGAG 58.994 41.667 0.00 0.00 0.00 2.43
2665 2745 5.003804 GCTCCCTTTTTGTCAATGTAGAGA 58.996 41.667 0.00 0.00 0.00 3.10
2666 2746 5.123027 GCTCCCTTTTTGTCAATGTAGAGAG 59.877 44.000 0.00 0.00 0.00 3.20
2667 2747 5.003804 TCCCTTTTTGTCAATGTAGAGAGC 58.996 41.667 0.00 0.00 0.00 4.09
2668 2748 5.006386 CCCTTTTTGTCAATGTAGAGAGCT 58.994 41.667 0.00 0.00 0.00 4.09
2669 2749 5.123027 CCCTTTTTGTCAATGTAGAGAGCTC 59.877 44.000 5.27 5.27 0.00 4.09
2670 2750 5.123027 CCTTTTTGTCAATGTAGAGAGCTCC 59.877 44.000 10.93 1.70 0.00 4.70
2671 2751 3.895232 TTGTCAATGTAGAGAGCTCCC 57.105 47.619 10.93 0.00 0.00 4.30
2672 2752 3.107402 TGTCAATGTAGAGAGCTCCCT 57.893 47.619 10.93 6.53 0.00 4.20
2673 2753 3.445008 TGTCAATGTAGAGAGCTCCCTT 58.555 45.455 10.93 0.00 0.00 3.95
2674 2754 3.840666 TGTCAATGTAGAGAGCTCCCTTT 59.159 43.478 10.93 0.00 0.00 3.11
2675 2755 4.287067 TGTCAATGTAGAGAGCTCCCTTTT 59.713 41.667 10.93 0.00 0.00 2.27
2735 2815 1.089112 CAGCAAAGTCGCCATGATGA 58.911 50.000 0.00 0.00 32.45 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.131223 CCCTCAGCAAGTAAATCTCGAGA 59.869 47.826 19.19 19.19 0.00 4.04
2 3 3.118956 ACCCTCAGCAAGTAAATCTCGAG 60.119 47.826 5.93 5.93 0.00 4.04
3 4 2.832129 ACCCTCAGCAAGTAAATCTCGA 59.168 45.455 0.00 0.00 0.00 4.04
4 5 3.252974 ACCCTCAGCAAGTAAATCTCG 57.747 47.619 0.00 0.00 0.00 4.04
5 6 4.579869 TCAACCCTCAGCAAGTAAATCTC 58.420 43.478 0.00 0.00 0.00 2.75
6 7 4.640771 TCAACCCTCAGCAAGTAAATCT 57.359 40.909 0.00 0.00 0.00 2.40
7 8 4.439289 GCATCAACCCTCAGCAAGTAAATC 60.439 45.833 0.00 0.00 0.00 2.17
8 9 3.445096 GCATCAACCCTCAGCAAGTAAAT 59.555 43.478 0.00 0.00 0.00 1.40
9 10 2.819608 GCATCAACCCTCAGCAAGTAAA 59.180 45.455 0.00 0.00 0.00 2.01
10 11 2.224744 TGCATCAACCCTCAGCAAGTAA 60.225 45.455 0.00 0.00 31.42 2.24
11 12 1.350684 TGCATCAACCCTCAGCAAGTA 59.649 47.619 0.00 0.00 31.42 2.24
12 13 0.111061 TGCATCAACCCTCAGCAAGT 59.889 50.000 0.00 0.00 31.42 3.16
13 14 0.809385 CTGCATCAACCCTCAGCAAG 59.191 55.000 0.00 0.00 34.45 4.01
14 15 0.401356 TCTGCATCAACCCTCAGCAA 59.599 50.000 0.00 0.00 34.45 3.91
15 16 0.401356 TTCTGCATCAACCCTCAGCA 59.599 50.000 0.00 0.00 0.00 4.41
16 17 1.093159 CTTCTGCATCAACCCTCAGC 58.907 55.000 0.00 0.00 0.00 4.26
17 18 2.082231 CACTTCTGCATCAACCCTCAG 58.918 52.381 0.00 0.00 0.00 3.35
18 19 1.699083 TCACTTCTGCATCAACCCTCA 59.301 47.619 0.00 0.00 0.00 3.86
19 20 2.027745 TCTCACTTCTGCATCAACCCTC 60.028 50.000 0.00 0.00 0.00 4.30
20 21 1.980765 TCTCACTTCTGCATCAACCCT 59.019 47.619 0.00 0.00 0.00 4.34
21 22 2.479566 TCTCACTTCTGCATCAACCC 57.520 50.000 0.00 0.00 0.00 4.11
22 23 4.005650 TCATTCTCACTTCTGCATCAACC 58.994 43.478 0.00 0.00 0.00 3.77
23 24 5.814764 ATCATTCTCACTTCTGCATCAAC 57.185 39.130 0.00 0.00 0.00 3.18
24 25 7.277396 TGATATCATTCTCACTTCTGCATCAA 58.723 34.615 0.00 0.00 0.00 2.57
25 26 6.823497 TGATATCATTCTCACTTCTGCATCA 58.177 36.000 0.00 0.00 0.00 3.07
26 27 7.603024 TCATGATATCATTCTCACTTCTGCATC 59.397 37.037 15.74 0.00 33.61 3.91
27 28 7.388224 GTCATGATATCATTCTCACTTCTGCAT 59.612 37.037 15.74 0.00 33.61 3.96
28 29 6.704937 GTCATGATATCATTCTCACTTCTGCA 59.295 38.462 15.74 0.00 33.61 4.41
29 30 6.128876 CGTCATGATATCATTCTCACTTCTGC 60.129 42.308 15.74 0.00 33.61 4.26
30 31 6.128876 GCGTCATGATATCATTCTCACTTCTG 60.129 42.308 15.74 2.60 33.61 3.02
31 32 5.925397 GCGTCATGATATCATTCTCACTTCT 59.075 40.000 15.74 0.00 33.61 2.85
32 33 5.925397 AGCGTCATGATATCATTCTCACTTC 59.075 40.000 15.74 5.56 33.61 3.01
33 34 5.851720 AGCGTCATGATATCATTCTCACTT 58.148 37.500 15.74 0.00 33.61 3.16
34 35 5.465532 AGCGTCATGATATCATTCTCACT 57.534 39.130 15.74 7.23 33.61 3.41
35 36 7.448588 GATAGCGTCATGATATCATTCTCAC 57.551 40.000 15.74 9.08 43.82 3.51
48 49 0.786581 GCCATCGTGATAGCGTCATG 59.213 55.000 7.73 7.73 43.82 3.07
49 50 0.676184 AGCCATCGTGATAGCGTCAT 59.324 50.000 0.00 0.00 39.48 3.06
50 51 0.459899 AAGCCATCGTGATAGCGTCA 59.540 50.000 0.00 0.00 30.70 4.35
51 52 1.523095 GAAAGCCATCGTGATAGCGTC 59.477 52.381 0.00 0.00 30.70 5.19
52 53 1.571919 GAAAGCCATCGTGATAGCGT 58.428 50.000 0.00 0.00 30.70 5.07
53 54 0.861837 GGAAAGCCATCGTGATAGCG 59.138 55.000 0.00 0.00 30.70 4.26
83 86 6.399639 AAAATGTGGACGTATTTTTCCTGT 57.600 33.333 1.75 0.00 33.91 4.00
571 575 3.493303 GGAGGGTGGGGATGAGGC 61.493 72.222 0.00 0.00 0.00 4.70
583 587 1.616327 TGGGATCAGGTGTGGAGGG 60.616 63.158 0.00 0.00 0.00 4.30
604 608 4.180946 CGAGGACGCCGTGGAGAG 62.181 72.222 0.00 0.00 0.00 3.20
892 902 2.881352 GGCGAGCGTTTCTCTCCG 60.881 66.667 0.00 0.00 37.00 4.63
929 948 3.542742 GAAGCGGCGTACGTCAGC 61.543 66.667 21.20 22.08 46.52 4.26
930 949 2.879462 GGAAGCGGCGTACGTCAG 60.879 66.667 21.20 13.49 46.52 3.51
931 950 4.424566 GGGAAGCGGCGTACGTCA 62.425 66.667 21.20 0.00 46.52 4.35
952 971 1.212616 ATAAAGCGCGATGAGCTCAC 58.787 50.000 20.97 12.13 45.31 3.51
1078 1097 2.685156 CGTACGCACGCGATCGATC 61.685 63.158 21.57 15.68 42.05 3.69
1079 1098 2.721109 CGTACGCACGCGATCGAT 60.721 61.111 21.57 0.00 42.05 3.59
1561 1597 0.028770 TGCGTCTTTGGTTTTGCTCG 59.971 50.000 0.00 0.00 0.00 5.03
1577 1613 3.218470 TACCCCGTCCCGTATGCG 61.218 66.667 0.00 0.00 37.95 4.73
1911 1957 4.451096 TGAATTGGCGTCTAGAAAACTGAC 59.549 41.667 0.00 0.00 0.00 3.51
1945 1991 1.073284 AGCCCGCTAAAGAAACCTTCA 59.927 47.619 0.00 0.00 0.00 3.02
2025 2073 2.298163 AGGGAAAATCAGCTGCAACAAG 59.702 45.455 9.47 0.00 0.00 3.16
2061 2109 9.788960 CTTACATTTTAAAATAGAAGGAGTGCC 57.211 33.333 12.98 0.00 0.00 5.01
2273 2326 9.715121 AAGAAATGCATCATGATTAGTTTGTTT 57.285 25.926 5.16 1.19 0.00 2.83
2291 2344 9.508567 GAGTTAATCAACCTTCATAAGAAATGC 57.491 33.333 0.00 0.00 35.05 3.56
2348 2408 4.808077 ATCATAGCAATTTGAGCACTCG 57.192 40.909 0.00 0.00 0.00 4.18
2397 2457 8.410912 AGACAAACAACCAAATAAACCTAGAAC 58.589 33.333 0.00 0.00 0.00 3.01
2400 2460 6.640907 GCAGACAAACAACCAAATAAACCTAG 59.359 38.462 0.00 0.00 0.00 3.02
2420 2484 1.815003 CAAAAGGGACCATGAGCAGAC 59.185 52.381 0.00 0.00 0.00 3.51
2422 2486 1.542915 CACAAAAGGGACCATGAGCAG 59.457 52.381 0.00 0.00 0.00 4.24
2513 2579 2.096013 TGTCGTTGCATCGTTGTTTCAA 59.904 40.909 16.21 0.00 0.00 2.69
2536 2602 2.046285 CATTCGGGGTGTTCTGGCC 61.046 63.158 0.00 0.00 0.00 5.36
2537 2603 0.608035 TTCATTCGGGGTGTTCTGGC 60.608 55.000 0.00 0.00 0.00 4.85
2587 2667 2.756207 TCCGACACATCATCGACCTAAA 59.244 45.455 0.00 0.00 42.25 1.85
2611 2691 3.005684 TCTTGGTTGTGGATTTGATGTGC 59.994 43.478 0.00 0.00 0.00 4.57
2652 2732 3.107402 AGGGAGCTCTCTACATTGACA 57.893 47.619 16.53 0.00 0.00 3.58
2653 2733 4.479786 AAAGGGAGCTCTCTACATTGAC 57.520 45.455 18.65 0.00 25.81 3.18
2654 2734 5.221925 ACAAAAAGGGAGCTCTCTACATTGA 60.222 40.000 28.74 0.00 25.81 2.57
2655 2735 5.006386 ACAAAAAGGGAGCTCTCTACATTG 58.994 41.667 18.65 22.11 25.81 2.82
2656 2736 5.221925 TGACAAAAAGGGAGCTCTCTACATT 60.222 40.000 18.65 9.92 0.00 2.71
2657 2737 4.287067 TGACAAAAAGGGAGCTCTCTACAT 59.713 41.667 18.65 3.33 0.00 2.29
2658 2738 3.646162 TGACAAAAAGGGAGCTCTCTACA 59.354 43.478 18.65 7.85 0.00 2.74
2659 2739 4.273148 TGACAAAAAGGGAGCTCTCTAC 57.727 45.455 18.65 5.33 0.00 2.59
2660 2740 4.974645 TTGACAAAAAGGGAGCTCTCTA 57.025 40.909 18.65 0.00 0.00 2.43
2661 2741 3.864789 TTGACAAAAAGGGAGCTCTCT 57.135 42.857 11.38 11.38 0.00 3.10
2662 2742 3.823304 ACATTGACAAAAAGGGAGCTCTC 59.177 43.478 14.64 10.30 0.00 3.20
2663 2743 3.837355 ACATTGACAAAAAGGGAGCTCT 58.163 40.909 14.64 0.00 0.00 4.09
2664 2744 5.003804 TCTACATTGACAAAAAGGGAGCTC 58.996 41.667 4.71 4.71 0.00 4.09
2665 2745 4.985538 TCTACATTGACAAAAAGGGAGCT 58.014 39.130 0.00 0.00 0.00 4.09
2666 2746 5.003804 TCTCTACATTGACAAAAAGGGAGC 58.996 41.667 0.00 0.00 0.00 4.70
2667 2747 5.123027 GCTCTCTACATTGACAAAAAGGGAG 59.877 44.000 15.38 15.38 0.00 4.30
2668 2748 5.003804 GCTCTCTACATTGACAAAAAGGGA 58.996 41.667 0.00 0.00 0.00 4.20
2669 2749 5.006386 AGCTCTCTACATTGACAAAAAGGG 58.994 41.667 0.00 0.00 0.00 3.95
2670 2750 5.123027 GGAGCTCTCTACATTGACAAAAAGG 59.877 44.000 14.64 0.00 0.00 3.11
2671 2751 5.123027 GGGAGCTCTCTACATTGACAAAAAG 59.877 44.000 14.64 0.00 0.00 2.27
2672 2752 5.003804 GGGAGCTCTCTACATTGACAAAAA 58.996 41.667 14.64 0.00 0.00 1.94
2673 2753 4.287067 AGGGAGCTCTCTACATTGACAAAA 59.713 41.667 16.53 0.00 0.00 2.44
2674 2754 3.840666 AGGGAGCTCTCTACATTGACAAA 59.159 43.478 16.53 0.00 0.00 2.83
2675 2755 3.445008 AGGGAGCTCTCTACATTGACAA 58.555 45.455 16.53 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.