Multiple sequence alignment - TraesCS2D01G194400

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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 TraesCS2D01G194400 chr2D 100.000 3171 0 0 1 3171 139530436 139527266 0.000000e+00 5856
1 TraesCS2D01G194400 chr2A 90.761 3193 137 56 70 3171 161327755 161330880 0.000000e+00 4117
2 TraesCS2D01G194400 chr2B 90.137 2849 162 56 383 3171 198635745 198638534 0.000000e+00 3594
3 TraesCS2D01G194400 chr2B 89.437 142 8 4 246 387 198635395 198635529 4.210000e-39 172
4 TraesCS2D01G194400 chr3B 87.016 1163 84 26 1060 2194 402914850 402913727 0.000000e+00 1249
5 TraesCS2D01G194400 chr6B 83.862 725 54 28 1513 2209 492508887 492508198 1.600000e-177 632
6 TraesCS2D01G194400 chr6B 89.888 445 43 2 1059 1501 492521739 492521295 3.550000e-159 571
7 TraesCS2D01G194400 chr7D 86.635 419 53 2 1202 1619 150762101 150762517 8.010000e-126 460


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 TraesCS2D01G194400 chr2D 139527266 139530436 3170 True 5856 5856 100.000 1 3171 1 chr2D.!!$R1 3170
1 TraesCS2D01G194400 chr2A 161327755 161330880 3125 False 4117 4117 90.761 70 3171 1 chr2A.!!$F1 3101
2 TraesCS2D01G194400 chr2B 198635395 198638534 3139 False 1883 3594 89.787 246 3171 2 chr2B.!!$F1 2925
3 TraesCS2D01G194400 chr3B 402913727 402914850 1123 True 1249 1249 87.016 1060 2194 1 chr3B.!!$R1 1134
4 TraesCS2D01G194400 chr6B 492508198 492508887 689 True 632 632 83.862 1513 2209 1 chr6B.!!$R1 696

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
364 379 0.398664 CACCTACCCGATCCCTTCCT 60.399 60.0 0.0 0.0 0.0 3.36 F
901 1142 0.598065 GCAACGCACCCAATTCTTCT 59.402 50.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2309 0.601558 TATATCGGAAGCTGCGGGTC 59.398 55.0 0.0 0.0 0.0 4.46 R
2471 2789 0.108585 TTTGGTTGCTTCCTCGCTCT 59.891 50.0 0.0 0.0 0.0 4.09 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
23 24 5.215160 CCATCAAGCTTAAAATCCATACGC 58.785 41.667 0.00 0.00 0.00 4.42
24 25 4.893424 TCAAGCTTAAAATCCATACGCC 57.107 40.909 0.00 0.00 0.00 5.68
25 26 4.523083 TCAAGCTTAAAATCCATACGCCT 58.477 39.130 0.00 0.00 0.00 5.52
26 27 4.947388 TCAAGCTTAAAATCCATACGCCTT 59.053 37.500 0.00 0.00 0.00 4.35
27 28 6.116806 TCAAGCTTAAAATCCATACGCCTTA 58.883 36.000 0.00 0.00 0.00 2.69
28 29 6.037830 TCAAGCTTAAAATCCATACGCCTTAC 59.962 38.462 0.00 0.00 0.00 2.34
29 30 5.433526 AGCTTAAAATCCATACGCCTTACA 58.566 37.500 0.00 0.00 0.00 2.41
30 31 5.296035 AGCTTAAAATCCATACGCCTTACAC 59.704 40.000 0.00 0.00 0.00 2.90
31 32 5.065474 GCTTAAAATCCATACGCCTTACACA 59.935 40.000 0.00 0.00 0.00 3.72
32 33 6.403855 GCTTAAAATCCATACGCCTTACACAA 60.404 38.462 0.00 0.00 0.00 3.33
33 34 5.560966 AAAATCCATACGCCTTACACAAG 57.439 39.130 0.00 0.00 0.00 3.16
34 35 2.018542 TCCATACGCCTTACACAAGC 57.981 50.000 0.00 0.00 0.00 4.01
35 36 1.276705 TCCATACGCCTTACACAAGCA 59.723 47.619 0.00 0.00 0.00 3.91
36 37 2.080693 CCATACGCCTTACACAAGCAA 58.919 47.619 0.00 0.00 0.00 3.91
37 38 2.159572 CCATACGCCTTACACAAGCAAC 60.160 50.000 0.00 0.00 0.00 4.17
38 39 2.536761 TACGCCTTACACAAGCAACT 57.463 45.000 0.00 0.00 0.00 3.16
39 40 2.536761 ACGCCTTACACAAGCAACTA 57.463 45.000 0.00 0.00 0.00 2.24
40 41 2.140717 ACGCCTTACACAAGCAACTAC 58.859 47.619 0.00 0.00 0.00 2.73
41 42 2.139917 CGCCTTACACAAGCAACTACA 58.860 47.619 0.00 0.00 0.00 2.74
42 43 2.157668 CGCCTTACACAAGCAACTACAG 59.842 50.000 0.00 0.00 0.00 2.74
43 44 3.139077 GCCTTACACAAGCAACTACAGT 58.861 45.455 0.00 0.00 0.00 3.55
44 45 4.312443 GCCTTACACAAGCAACTACAGTA 58.688 43.478 0.00 0.00 0.00 2.74
45 46 4.753107 GCCTTACACAAGCAACTACAGTAA 59.247 41.667 0.00 0.00 0.00 2.24
46 47 5.107065 GCCTTACACAAGCAACTACAGTAAG 60.107 44.000 0.00 0.00 37.66 2.34
47 48 6.220930 CCTTACACAAGCAACTACAGTAAGA 58.779 40.000 0.00 0.00 39.29 2.10
48 49 6.874134 CCTTACACAAGCAACTACAGTAAGAT 59.126 38.462 0.00 0.00 39.29 2.40
49 50 7.387948 CCTTACACAAGCAACTACAGTAAGATT 59.612 37.037 0.00 0.00 39.29 2.40
50 51 8.671384 TTACACAAGCAACTACAGTAAGATTT 57.329 30.769 0.00 0.00 0.00 2.17
51 52 9.767228 TTACACAAGCAACTACAGTAAGATTTA 57.233 29.630 0.00 0.00 0.00 1.40
52 53 8.848474 ACACAAGCAACTACAGTAAGATTTAT 57.152 30.769 0.00 0.00 0.00 1.40
53 54 9.284968 ACACAAGCAACTACAGTAAGATTTATT 57.715 29.630 0.00 0.00 0.00 1.40
54 55 9.546909 CACAAGCAACTACAGTAAGATTTATTG 57.453 33.333 0.00 0.00 0.00 1.90
55 56 8.237267 ACAAGCAACTACAGTAAGATTTATTGC 58.763 33.333 0.00 0.00 40.09 3.56
57 58 7.978982 AGCAACTACAGTAAGATTTATTGCTG 58.021 34.615 6.83 2.14 46.17 4.41
65 66 8.665175 CAGTAAGATTTATTGCTGTGAGTTTG 57.335 34.615 0.00 0.00 37.90 2.93
66 67 7.272084 CAGTAAGATTTATTGCTGTGAGTTTGC 59.728 37.037 0.00 0.00 37.90 3.68
67 68 5.064441 AGATTTATTGCTGTGAGTTTGCC 57.936 39.130 0.00 0.00 0.00 4.52
68 69 4.523943 AGATTTATTGCTGTGAGTTTGCCA 59.476 37.500 0.00 0.00 0.00 4.92
79 80 5.008980 TGTGAGTTTGCCATGTGATGATAA 58.991 37.500 0.00 0.00 0.00 1.75
80 81 5.476254 TGTGAGTTTGCCATGTGATGATAAA 59.524 36.000 0.00 0.00 0.00 1.40
85 86 3.966979 TGCCATGTGATGATAAACCAGT 58.033 40.909 0.00 0.00 0.00 4.00
86 87 3.695556 TGCCATGTGATGATAAACCAGTG 59.304 43.478 0.00 0.00 0.00 3.66
87 88 3.489738 GCCATGTGATGATAAACCAGTGC 60.490 47.826 0.00 0.00 0.00 4.40
88 89 3.695556 CCATGTGATGATAAACCAGTGCA 59.304 43.478 0.00 0.00 0.00 4.57
89 90 4.340097 CCATGTGATGATAAACCAGTGCAT 59.660 41.667 0.00 0.00 0.00 3.96
158 167 1.081094 GCAAAAATGCTCATGTGGGC 58.919 50.000 0.00 0.00 0.00 5.36
167 176 1.202533 GCTCATGTGGGCACGTACTAT 60.203 52.381 0.00 0.00 0.00 2.12
168 177 2.035449 GCTCATGTGGGCACGTACTATA 59.965 50.000 0.00 0.00 0.00 1.31
169 178 3.639538 CTCATGTGGGCACGTACTATAC 58.360 50.000 0.00 0.00 0.00 1.47
184 197 5.787062 CGTACTATACGTGGTATGATTCGTG 59.213 44.000 0.00 0.00 46.41 4.35
196 211 3.719173 TGATTCGTGGTATATGACGCA 57.281 42.857 0.00 0.00 35.53 5.24
266 281 2.190578 CGGCCATTCCCCTCACTC 59.809 66.667 2.24 0.00 0.00 3.51
361 376 2.070650 GGCACCTACCCGATCCCTT 61.071 63.158 0.00 0.00 0.00 3.95
364 379 0.398664 CACCTACCCGATCCCTTCCT 60.399 60.000 0.00 0.00 0.00 3.36
373 388 4.733725 TCCCTTCCTCCCACCCCG 62.734 72.222 0.00 0.00 0.00 5.73
375 390 2.609610 CCTTCCTCCCACCCCGAA 60.610 66.667 0.00 0.00 0.00 4.30
376 391 2.670148 CCTTCCTCCCACCCCGAAG 61.670 68.421 0.00 0.00 33.11 3.79
645 878 3.861797 GGATGCCCATCGGACGGT 61.862 66.667 2.47 0.00 38.69 4.83
765 998 1.443802 AGAAGCGGCAGAAAAGTAGC 58.556 50.000 1.45 0.00 0.00 3.58
794 1027 4.623863 AGGGCCATTGGTTGATTATCTTT 58.376 39.130 6.18 0.00 0.00 2.52
901 1142 0.598065 GCAACGCACCCAATTCTTCT 59.402 50.000 0.00 0.00 0.00 2.85
932 1180 1.827789 CCAGCCCCTCTCTCTCTCG 60.828 68.421 0.00 0.00 0.00 4.04
933 1181 2.123897 AGCCCCTCTCTCTCTCGC 60.124 66.667 0.00 0.00 0.00 5.03
934 1182 3.591835 GCCCCTCTCTCTCTCGCG 61.592 72.222 0.00 0.00 0.00 5.87
935 1183 3.591835 CCCCTCTCTCTCTCGCGC 61.592 72.222 0.00 0.00 0.00 6.86
936 1184 3.947841 CCCTCTCTCTCTCGCGCG 61.948 72.222 26.76 26.76 0.00 6.86
937 1185 3.947841 CCTCTCTCTCTCGCGCGG 61.948 72.222 31.69 20.60 0.00 6.46
1113 1361 1.863662 GCGACGACCTCTCCTTCACA 61.864 60.000 0.00 0.00 0.00 3.58
1410 1658 1.000394 TCCATCTGCGACGAGAACAAA 60.000 47.619 0.00 0.00 0.00 2.83
1414 1662 2.215478 CTGCGACGAGAACAAAGCCG 62.215 60.000 0.00 0.00 0.00 5.52
1416 1664 1.487231 CGACGAGAACAAAGCCGTG 59.513 57.895 0.00 0.00 35.22 4.94
1722 1970 2.732619 GGACCTCATGTCGGACCCC 61.733 68.421 5.55 5.35 45.46 4.95
1899 2147 1.098129 TCCTCCAGATCTGCGACGAG 61.098 60.000 17.76 16.62 0.00 4.18
1977 2227 3.965026 CTCCCAGTCCTCCTCCGCA 62.965 68.421 0.00 0.00 0.00 5.69
2019 2295 1.063469 GTACCAATCGTTCGGCCATTG 59.937 52.381 2.24 4.52 0.00 2.82
2025 2301 1.583451 CGTTCGGCCATTGCAATCG 60.583 57.895 9.53 10.78 40.13 3.34
2107 2383 2.308769 GGCGCTGATCGAGATGCTG 61.309 63.158 7.64 0.00 41.67 4.41
2423 2722 4.325344 CCTGTAAATTCATTCTCCCCCACT 60.325 45.833 0.00 0.00 0.00 4.00
2424 2723 4.599041 TGTAAATTCATTCTCCCCCACTG 58.401 43.478 0.00 0.00 0.00 3.66
2426 2725 3.833559 AATTCATTCTCCCCCACTGTT 57.166 42.857 0.00 0.00 0.00 3.16
2475 2793 4.102035 CCAATTTGGTTGCTTCTAGAGC 57.898 45.455 7.31 7.10 41.50 4.09
2531 2878 1.065199 GTGCCAAGTCAGGGATCATCA 60.065 52.381 0.00 0.00 0.00 3.07
2533 2880 2.158711 TGCCAAGTCAGGGATCATCATC 60.159 50.000 0.00 0.00 0.00 2.92
2534 2881 2.763933 CCAAGTCAGGGATCATCATCG 58.236 52.381 0.00 0.00 0.00 3.84
2535 2882 2.103771 CCAAGTCAGGGATCATCATCGT 59.896 50.000 0.00 0.00 0.00 3.73
2536 2883 3.388308 CAAGTCAGGGATCATCATCGTC 58.612 50.000 0.00 0.00 0.00 4.20
2537 2884 2.670939 AGTCAGGGATCATCATCGTCA 58.329 47.619 0.00 0.00 0.00 4.35
2538 2885 3.237746 AGTCAGGGATCATCATCGTCAT 58.762 45.455 0.00 0.00 0.00 3.06
2539 2886 3.645212 AGTCAGGGATCATCATCGTCATT 59.355 43.478 0.00 0.00 0.00 2.57
2540 2887 3.993081 GTCAGGGATCATCATCGTCATTC 59.007 47.826 0.00 0.00 0.00 2.67
2541 2888 3.007290 TCAGGGATCATCATCGTCATTCC 59.993 47.826 0.00 0.00 0.00 3.01
2542 2889 2.028658 AGGGATCATCATCGTCATTCCG 60.029 50.000 0.00 0.00 0.00 4.30
2543 2890 2.341257 GGATCATCATCGTCATTCCGG 58.659 52.381 0.00 0.00 0.00 5.14
2544 2891 2.029020 GGATCATCATCGTCATTCCGGA 60.029 50.000 0.00 0.00 0.00 5.14
2545 2892 2.509052 TCATCATCGTCATTCCGGAC 57.491 50.000 1.83 0.00 34.42 4.79
2546 2893 2.031870 TCATCATCGTCATTCCGGACT 58.968 47.619 1.83 0.00 35.63 3.85
2547 2894 2.034685 TCATCATCGTCATTCCGGACTC 59.965 50.000 1.83 0.00 35.63 3.36
2598 2945 6.122277 AGATTGTGTGTTCTCTGGAAGAAAA 58.878 36.000 0.00 0.00 46.34 2.29
2599 2946 5.818136 TTGTGTGTTCTCTGGAAGAAAAG 57.182 39.130 0.00 0.00 46.34 2.27
2647 3000 3.055719 CAATCCACGGCCGTGCTT 61.056 61.111 45.23 35.93 44.16 3.91
2802 3161 1.006571 TTCAACCGAGGACGACAGC 60.007 57.895 0.00 0.00 42.66 4.40
2803 3162 2.430382 TTCAACCGAGGACGACAGCC 62.430 60.000 0.00 0.00 42.66 4.85
2986 3357 3.267483 AGGTTGGTTGATTATTCGTCCG 58.733 45.455 0.00 0.00 0.00 4.79
3071 3442 3.862402 CCCTCCGACGACGACGAG 61.862 72.222 20.63 14.57 42.66 4.18
3072 3443 3.862402 CCTCCGACGACGACGAGG 61.862 72.222 20.63 18.81 39.87 4.63
3073 3444 4.517703 CTCCGACGACGACGAGGC 62.518 72.222 20.63 2.09 42.66 4.70
3075 3446 4.175489 CCGACGACGACGAGGCAT 62.175 66.667 20.63 0.00 42.66 4.40
3076 3447 2.648102 CGACGACGACGAGGCATC 60.648 66.667 15.32 0.00 42.66 3.91
3095 3466 2.821366 CATGGAGCTCGTGCCCAC 60.821 66.667 17.89 5.51 40.50 4.61
3131 3506 3.074412 GTGTGTATCTTCAAGTGTGGGG 58.926 50.000 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.009010 AGGCGTATGGATTTTAAGCTTGATG 59.991 40.000 9.86 0.00 0.00 3.07
2 3 5.133221 AGGCGTATGGATTTTAAGCTTGAT 58.867 37.500 9.86 0.00 0.00 2.57
3 4 4.523083 AGGCGTATGGATTTTAAGCTTGA 58.477 39.130 9.86 0.00 0.00 3.02
4 5 4.900635 AGGCGTATGGATTTTAAGCTTG 57.099 40.909 9.86 0.00 0.00 4.01
5 6 5.883673 TGTAAGGCGTATGGATTTTAAGCTT 59.116 36.000 3.48 3.48 0.00 3.74
6 7 5.296035 GTGTAAGGCGTATGGATTTTAAGCT 59.704 40.000 0.00 0.00 0.00 3.74
7 8 5.065474 TGTGTAAGGCGTATGGATTTTAAGC 59.935 40.000 0.00 0.00 0.00 3.09
8 9 6.671614 TGTGTAAGGCGTATGGATTTTAAG 57.328 37.500 0.00 0.00 0.00 1.85
9 10 6.403855 GCTTGTGTAAGGCGTATGGATTTTAA 60.404 38.462 0.00 0.00 34.40 1.52
10 11 5.065474 GCTTGTGTAAGGCGTATGGATTTTA 59.935 40.000 0.00 0.00 34.40 1.52
11 12 4.142469 GCTTGTGTAAGGCGTATGGATTTT 60.142 41.667 0.00 0.00 34.40 1.82
12 13 3.377172 GCTTGTGTAAGGCGTATGGATTT 59.623 43.478 0.00 0.00 34.40 2.17
13 14 2.943033 GCTTGTGTAAGGCGTATGGATT 59.057 45.455 0.00 0.00 34.40 3.01
14 15 2.093181 TGCTTGTGTAAGGCGTATGGAT 60.093 45.455 0.00 0.00 34.40 3.41
15 16 1.276705 TGCTTGTGTAAGGCGTATGGA 59.723 47.619 0.00 0.00 34.40 3.41
16 17 1.732941 TGCTTGTGTAAGGCGTATGG 58.267 50.000 0.00 0.00 34.40 2.74
17 18 2.742053 AGTTGCTTGTGTAAGGCGTATG 59.258 45.455 0.00 0.00 34.40 2.39
18 19 3.053831 AGTTGCTTGTGTAAGGCGTAT 57.946 42.857 0.00 0.00 34.40 3.06
19 20 2.536761 AGTTGCTTGTGTAAGGCGTA 57.463 45.000 0.00 0.00 34.40 4.42
20 21 2.140717 GTAGTTGCTTGTGTAAGGCGT 58.859 47.619 0.00 0.00 34.40 5.68
21 22 2.139917 TGTAGTTGCTTGTGTAAGGCG 58.860 47.619 0.00 0.00 34.40 5.52
22 23 3.139077 ACTGTAGTTGCTTGTGTAAGGC 58.861 45.455 0.00 0.00 34.40 4.35
23 24 6.220930 TCTTACTGTAGTTGCTTGTGTAAGG 58.779 40.000 0.00 0.00 37.23 2.69
24 25 7.891183 ATCTTACTGTAGTTGCTTGTGTAAG 57.109 36.000 0.00 0.00 37.67 2.34
25 26 8.671384 AAATCTTACTGTAGTTGCTTGTGTAA 57.329 30.769 0.00 0.00 0.00 2.41
26 27 9.938280 ATAAATCTTACTGTAGTTGCTTGTGTA 57.062 29.630 0.00 0.00 0.00 2.90
27 28 8.848474 ATAAATCTTACTGTAGTTGCTTGTGT 57.152 30.769 0.00 0.00 0.00 3.72
28 29 9.546909 CAATAAATCTTACTGTAGTTGCTTGTG 57.453 33.333 0.00 0.00 0.00 3.33
29 30 8.237267 GCAATAAATCTTACTGTAGTTGCTTGT 58.763 33.333 0.00 0.00 37.16 3.16
30 31 8.454106 AGCAATAAATCTTACTGTAGTTGCTTG 58.546 33.333 0.00 0.00 45.02 4.01
31 32 8.454106 CAGCAATAAATCTTACTGTAGTTGCTT 58.546 33.333 6.08 0.00 45.02 3.91
33 34 7.693951 CACAGCAATAAATCTTACTGTAGTTGC 59.306 37.037 0.00 0.00 36.28 4.17
34 35 8.935844 TCACAGCAATAAATCTTACTGTAGTTG 58.064 33.333 0.00 0.00 36.28 3.16
35 36 9.155975 CTCACAGCAATAAATCTTACTGTAGTT 57.844 33.333 0.00 0.00 36.28 2.24
36 37 8.314751 ACTCACAGCAATAAATCTTACTGTAGT 58.685 33.333 0.00 0.00 36.28 2.73
37 38 8.709386 ACTCACAGCAATAAATCTTACTGTAG 57.291 34.615 0.00 0.00 36.28 2.74
38 39 9.502091 AAACTCACAGCAATAAATCTTACTGTA 57.498 29.630 0.00 0.00 36.28 2.74
39 40 7.986085 AACTCACAGCAATAAATCTTACTGT 57.014 32.000 0.00 0.00 38.84 3.55
40 41 7.272084 GCAAACTCACAGCAATAAATCTTACTG 59.728 37.037 0.00 0.00 0.00 2.74
41 42 7.308435 GCAAACTCACAGCAATAAATCTTACT 58.692 34.615 0.00 0.00 0.00 2.24
42 43 6.528072 GGCAAACTCACAGCAATAAATCTTAC 59.472 38.462 0.00 0.00 0.00 2.34
43 44 6.208402 TGGCAAACTCACAGCAATAAATCTTA 59.792 34.615 0.00 0.00 0.00 2.10
44 45 5.010922 TGGCAAACTCACAGCAATAAATCTT 59.989 36.000 0.00 0.00 0.00 2.40
45 46 4.523943 TGGCAAACTCACAGCAATAAATCT 59.476 37.500 0.00 0.00 0.00 2.40
46 47 4.808558 TGGCAAACTCACAGCAATAAATC 58.191 39.130 0.00 0.00 0.00 2.17
47 48 4.870123 TGGCAAACTCACAGCAATAAAT 57.130 36.364 0.00 0.00 0.00 1.40
48 49 4.039004 ACATGGCAAACTCACAGCAATAAA 59.961 37.500 0.00 0.00 0.00 1.40
49 50 3.573538 ACATGGCAAACTCACAGCAATAA 59.426 39.130 0.00 0.00 0.00 1.40
50 51 3.057386 CACATGGCAAACTCACAGCAATA 60.057 43.478 0.00 0.00 0.00 1.90
51 52 1.965643 ACATGGCAAACTCACAGCAAT 59.034 42.857 0.00 0.00 0.00 3.56
52 53 1.067364 CACATGGCAAACTCACAGCAA 59.933 47.619 0.00 0.00 0.00 3.91
53 54 0.669619 CACATGGCAAACTCACAGCA 59.330 50.000 0.00 0.00 0.00 4.41
54 55 0.953727 TCACATGGCAAACTCACAGC 59.046 50.000 0.00 0.00 0.00 4.40
55 56 2.815503 TCATCACATGGCAAACTCACAG 59.184 45.455 0.00 0.00 0.00 3.66
56 57 2.861274 TCATCACATGGCAAACTCACA 58.139 42.857 0.00 0.00 0.00 3.58
57 58 5.565592 TTATCATCACATGGCAAACTCAC 57.434 39.130 0.00 0.00 0.00 3.51
58 59 5.105797 GGTTTATCATCACATGGCAAACTCA 60.106 40.000 0.00 0.00 36.01 3.41
59 60 5.105797 TGGTTTATCATCACATGGCAAACTC 60.106 40.000 0.00 5.51 36.01 3.01
60 61 4.771577 TGGTTTATCATCACATGGCAAACT 59.228 37.500 0.00 0.00 36.01 2.66
61 62 5.070770 TGGTTTATCATCACATGGCAAAC 57.929 39.130 0.00 0.00 35.49 2.93
62 63 4.771577 ACTGGTTTATCATCACATGGCAAA 59.228 37.500 0.00 0.00 0.00 3.68
63 64 4.158209 CACTGGTTTATCATCACATGGCAA 59.842 41.667 0.00 0.00 0.00 4.52
64 65 3.695556 CACTGGTTTATCATCACATGGCA 59.304 43.478 0.00 0.00 0.00 4.92
65 66 3.489738 GCACTGGTTTATCATCACATGGC 60.490 47.826 0.00 0.00 0.00 4.40
66 67 3.695556 TGCACTGGTTTATCATCACATGG 59.304 43.478 0.00 0.00 0.00 3.66
67 68 4.968812 TGCACTGGTTTATCATCACATG 57.031 40.909 0.00 0.00 0.00 3.21
68 69 4.202080 GCATGCACTGGTTTATCATCACAT 60.202 41.667 14.21 0.00 0.00 3.21
79 80 1.401761 TGTTTCTGCATGCACTGGTT 58.598 45.000 18.46 0.00 0.00 3.67
80 81 1.542915 GATGTTTCTGCATGCACTGGT 59.457 47.619 18.46 0.42 0.00 4.00
85 86 1.546923 CCTTGGATGTTTCTGCATGCA 59.453 47.619 21.29 21.29 43.65 3.96
86 87 1.820519 TCCTTGGATGTTTCTGCATGC 59.179 47.619 11.82 11.82 37.65 4.06
87 88 3.087031 AGTCCTTGGATGTTTCTGCATG 58.913 45.455 0.00 0.00 0.00 4.06
88 89 3.350833 GAGTCCTTGGATGTTTCTGCAT 58.649 45.455 0.00 0.00 0.00 3.96
89 90 2.783135 GAGTCCTTGGATGTTTCTGCA 58.217 47.619 0.00 0.00 0.00 4.41
151 160 2.787601 CGTATAGTACGTGCCCACAT 57.212 50.000 0.00 0.00 46.41 3.21
167 176 6.430616 TCATATACCACGAATCATACCACGTA 59.569 38.462 0.00 0.00 37.22 3.57
168 177 5.242171 TCATATACCACGAATCATACCACGT 59.758 40.000 0.00 0.00 39.53 4.49
169 178 5.571741 GTCATATACCACGAATCATACCACG 59.428 44.000 0.00 0.00 0.00 4.94
172 185 4.561606 GCGTCATATACCACGAATCATACC 59.438 45.833 9.03 0.00 38.32 2.73
184 197 3.005472 TGGCTTCTACTGCGTCATATACC 59.995 47.826 0.00 0.00 0.00 2.73
266 281 0.318699 TTGGCTGTCTTCGTCGTGAG 60.319 55.000 0.00 0.00 0.00 3.51
341 356 3.925090 GGATCGGGTAGGTGCCGG 61.925 72.222 0.00 0.00 0.00 6.13
664 897 0.455633 CCGTCGGAAAGGTACGTGAG 60.456 60.000 4.91 0.00 34.90 3.51
732 965 0.796927 GCTTCTTTGGCTGGTACGAC 59.203 55.000 0.00 0.00 0.00 4.34
805 1038 6.142320 GCTGCTTAAATTAATCGCGCTAATTT 59.858 34.615 27.08 27.08 40.40 1.82
901 1142 2.316586 GGCTGGGGGATGGAAGGAA 61.317 63.158 0.00 0.00 0.00 3.36
1371 1619 4.626081 AGGTTGAGCAGCGCCGTT 62.626 61.111 2.29 0.00 0.00 4.44
1410 1658 4.148825 GCCTCGACCATCACGGCT 62.149 66.667 2.55 0.00 39.03 5.52
1695 1943 0.842030 ACATGAGGTCCAGCAAGGGA 60.842 55.000 0.00 0.00 38.24 4.20
1722 1970 3.770040 TCCACCATGCCGGACTCG 61.770 66.667 5.05 0.00 38.63 4.18
1956 2204 1.760480 GGAGGAGGACTGGGAGAGC 60.760 68.421 0.00 0.00 0.00 4.09
2019 2295 1.212751 GGGTCCTGTTTGCGATTGC 59.787 57.895 0.00 0.00 43.20 3.56
2025 2301 4.043200 GCTGCGGGTCCTGTTTGC 62.043 66.667 0.00 0.00 0.00 3.68
2033 2309 0.601558 TATATCGGAAGCTGCGGGTC 59.398 55.000 0.00 0.00 0.00 4.46
2035 2311 0.732880 CGTATATCGGAAGCTGCGGG 60.733 60.000 0.00 0.00 35.71 6.13
2057 2333 5.213675 CGGAACCGCAAAACAAATTAGTAA 58.786 37.500 0.00 0.00 0.00 2.24
2466 2784 2.535331 GTTGCTTCCTCGCTCTAGAAG 58.465 52.381 0.00 0.00 39.99 2.85
2470 2788 0.973632 TTGGTTGCTTCCTCGCTCTA 59.026 50.000 0.00 0.00 0.00 2.43
2471 2789 0.108585 TTTGGTTGCTTCCTCGCTCT 59.891 50.000 0.00 0.00 0.00 4.09
2472 2790 1.168714 ATTTGGTTGCTTCCTCGCTC 58.831 50.000 0.00 0.00 0.00 5.03
2473 2791 1.541588 GAATTTGGTTGCTTCCTCGCT 59.458 47.619 0.00 0.00 0.00 4.93
2475 2793 1.729149 GCGAATTTGGTTGCTTCCTCG 60.729 52.381 0.00 0.00 0.00 4.63
2557 2904 4.630069 ACAATCTTTCTTTCGTATCCACCG 59.370 41.667 0.00 0.00 0.00 4.94
2647 3000 5.302360 ACAACGCTAGAACCTGAATGTAAA 58.698 37.500 0.00 0.00 0.00 2.01
2752 3111 4.218417 ACATTGCTGATTTACCAAGTCACC 59.782 41.667 0.00 0.00 0.00 4.02
2802 3161 2.277084 CGACCACTAGAAAATTCCGGG 58.723 52.381 0.00 0.00 0.00 5.73
2803 3162 1.664151 GCGACCACTAGAAAATTCCGG 59.336 52.381 0.00 0.00 0.00 5.14
2986 3357 0.444260 GCGTCCTTTTCAGCTACAGC 59.556 55.000 0.00 0.00 42.49 4.40
3030 3401 1.596408 GGCCCGAAAACTACCGGTA 59.404 57.895 14.95 14.95 43.93 4.02
3031 3402 2.348620 GGCCCGAAAACTACCGGT 59.651 61.111 13.98 13.98 43.93 5.28
3065 3436 3.333189 CCATGCGATGCCTCGTCG 61.333 66.667 13.00 4.25 46.71 5.12
3066 3437 1.953138 CTCCATGCGATGCCTCGTC 60.953 63.158 13.00 6.13 46.71 4.20
3067 3438 2.107750 CTCCATGCGATGCCTCGT 59.892 61.111 13.00 0.00 46.71 4.18
3107 3478 3.748048 CCACACTTGAAGATACACACAGG 59.252 47.826 0.00 0.00 0.00 4.00
3131 3506 1.588139 CGTGTCCCGCTATCCGTTC 60.588 63.158 0.00 0.00 34.38 3.95


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

AutoCloner maintained by Alex Coulton.