Multiple sequence alignment - TraesCS3B01G165300

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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 TraesCS3B01G165300 chr3B 100.000 3695 0 0 1 3695 163657631 163661325 0.000000e+00 6824
1 TraesCS3B01G165300 chr3B 99.180 122 1 0 1 122 241708486 241708365 1.730000e-53 220
2 TraesCS3B01G165300 chr3B 99.187 123 0 1 1 123 256781426 256781305 1.730000e-53 220
3 TraesCS3B01G165300 chr3B 98.387 124 2 0 1 124 783212826 783212703 6.210000e-53 219
4 TraesCS3B01G165300 chr3A 88.077 3011 204 76 275 3167 108372984 108375957 0.000000e+00 3428
5 TraesCS3B01G165300 chr3A 93.424 441 23 5 3256 3695 108376293 108376728 0.000000e+00 649
6 TraesCS3B01G165300 chr3D 92.528 2021 67 34 106 2073 112690998 112692987 0.000000e+00 2819
7 TraesCS3B01G165300 chr3D 93.746 1487 55 13 2234 3695 112693183 112694656 0.000000e+00 2196
8 TraesCS3B01G165300 chr5B 99.180 122 1 0 1 122 709856519 709856640 1.730000e-53 220
9 TraesCS3B01G165300 chr2A 99.187 123 0 1 1 123 113822411 113822290 1.730000e-53 220
10 TraesCS3B01G165300 chr5A 99.174 121 1 0 1 121 675526935 675527055 6.210000e-53 219
11 TraesCS3B01G165300 chr2B 96.269 134 3 2 1 133 425356421 425356289 6.210000e-53 219
12 TraesCS3B01G165300 chr2B 96.923 130 2 2 1 128 344866682 344866553 2.230000e-52 217
13 TraesCS3B01G165300 chr1B 96.850 127 4 0 1 127 310923602 310923728 2.890000e-51 213


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 TraesCS3B01G165300 chr3B 163657631 163661325 3694 False 6824.0 6824 100.0000 1 3695 1 chr3B.!!$F1 3694
1 TraesCS3B01G165300 chr3A 108372984 108376728 3744 False 2038.5 3428 90.7505 275 3695 2 chr3A.!!$F1 3420
2 TraesCS3B01G165300 chr3D 112690998 112694656 3658 False 2507.5 2819 93.1370 106 3695 2 chr3D.!!$F1 3589

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
926 970 0.179140 CCATACATTTGGCGGTGTGC 60.179 55.0 0.29 0.0 45.38 4.57 F
1678 1773 0.097674 GTACGTATGTCTCACGCCGT 59.902 55.0 0.00 0.0 43.10 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2682 2880 1.179174 GGTTTGGTCAGCCCTTCCAC 61.179 60.0 0.0 0.0 0.0 4.02 R
3094 3328 0.589479 CATGTGTGTGTGTGTGTGCG 60.589 55.0 0.0 0.0 0.0 5.34 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
55 56 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
56 57 5.536554 AGTGTAGATTCACTCATTTTGCG 57.463 39.130 0.00 0.00 44.07 4.85
57 58 4.091424 GTGTAGATTCACTCATTTTGCGC 58.909 43.478 0.00 0.00 35.68 6.09
58 59 2.927553 AGATTCACTCATTTTGCGCC 57.072 45.000 4.18 0.00 0.00 6.53
59 60 1.131126 AGATTCACTCATTTTGCGCCG 59.869 47.619 4.18 0.00 0.00 6.46
60 61 0.881118 ATTCACTCATTTTGCGCCGT 59.119 45.000 4.18 0.00 0.00 5.68
61 62 1.514003 TTCACTCATTTTGCGCCGTA 58.486 45.000 4.18 0.00 0.00 4.02
62 63 1.732941 TCACTCATTTTGCGCCGTAT 58.267 45.000 4.18 0.00 0.00 3.06
63 64 1.396648 TCACTCATTTTGCGCCGTATG 59.603 47.619 4.18 5.63 0.00 2.39
64 65 1.130373 CACTCATTTTGCGCCGTATGT 59.870 47.619 4.18 0.00 0.00 2.29
65 66 2.350192 CACTCATTTTGCGCCGTATGTA 59.650 45.455 4.18 0.00 0.00 2.29
66 67 2.607635 ACTCATTTTGCGCCGTATGTAG 59.392 45.455 4.18 7.56 0.00 2.74
67 68 2.607635 CTCATTTTGCGCCGTATGTAGT 59.392 45.455 4.18 0.00 0.00 2.73
68 69 2.605818 TCATTTTGCGCCGTATGTAGTC 59.394 45.455 4.18 0.00 0.00 2.59
69 70 2.081725 TTTTGCGCCGTATGTAGTCA 57.918 45.000 4.18 0.00 0.00 3.41
70 71 1.352114 TTTGCGCCGTATGTAGTCAC 58.648 50.000 4.18 0.00 0.00 3.67
71 72 0.528924 TTGCGCCGTATGTAGTCACT 59.471 50.000 4.18 0.00 0.00 3.41
72 73 0.528924 TGCGCCGTATGTAGTCACTT 59.471 50.000 4.18 0.00 0.00 3.16
73 74 0.921347 GCGCCGTATGTAGTCACTTG 59.079 55.000 0.00 0.00 0.00 3.16
74 75 1.734707 GCGCCGTATGTAGTCACTTGT 60.735 52.381 0.00 0.00 0.00 3.16
75 76 2.602878 CGCCGTATGTAGTCACTTGTT 58.397 47.619 0.00 0.00 0.00 2.83
76 77 2.344441 CGCCGTATGTAGTCACTTGTTG 59.656 50.000 0.00 0.00 0.00 3.33
77 78 3.581755 GCCGTATGTAGTCACTTGTTGA 58.418 45.455 0.00 0.00 0.00 3.18
78 79 3.991773 GCCGTATGTAGTCACTTGTTGAA 59.008 43.478 0.00 0.00 35.39 2.69
79 80 4.449743 GCCGTATGTAGTCACTTGTTGAAA 59.550 41.667 0.00 0.00 35.39 2.69
80 81 5.121768 GCCGTATGTAGTCACTTGTTGAAAT 59.878 40.000 0.00 0.00 35.39 2.17
81 82 6.672357 GCCGTATGTAGTCACTTGTTGAAATC 60.672 42.308 0.00 0.00 35.39 2.17
82 83 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
83 84 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
84 85 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
85 86 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
86 87 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
87 88 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
88 89 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
89 90 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
90 91 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
91 92 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
92 93 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
93 94 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
94 95 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
95 96 9.050601 ACTTGTTGAAATCTCTAGAAAGACAAG 57.949 33.333 17.75 17.75 33.18 3.16
96 97 8.964476 TTGTTGAAATCTCTAGAAAGACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
118 119 6.141790 AGTATTTAGGAACGGAGGGAGTAAT 58.858 40.000 0.00 0.00 0.00 1.89
122 123 7.441903 TTTAGGAACGGAGGGAGTAATTAAT 57.558 36.000 0.00 0.00 0.00 1.40
152 159 4.280461 CTGATATAGACGTCGGTGTTGAC 58.720 47.826 10.46 0.00 35.49 3.18
155 162 0.311790 TAGACGTCGGTGTTGACCAC 59.688 55.000 10.46 0.00 43.33 4.16
168 186 7.170151 TCGGTGTTGACCACATAATTAATATCG 59.830 37.037 0.00 0.00 46.44 2.92
172 190 9.819267 TGTTGACCACATAATTAATATCGTACA 57.181 29.630 0.00 0.00 0.00 2.90
203 221 8.752766 TCAACGGACGATTAATATCCTATTTC 57.247 34.615 13.73 0.00 0.00 2.17
204 222 8.582437 TCAACGGACGATTAATATCCTATTTCT 58.418 33.333 13.73 0.00 0.00 2.52
205 223 9.850628 CAACGGACGATTAATATCCTATTTCTA 57.149 33.333 13.73 0.00 0.00 2.10
246 264 7.544622 TCTAAGACAAACTTGCATAGTACGAT 58.455 34.615 0.00 0.00 39.38 3.73
442 460 1.488812 TCGGAGAAGGAGAGAGAGAGG 59.511 57.143 0.00 0.00 0.00 3.69
540 568 4.082517 ACAAGATACGATCCCATCATCTCG 60.083 45.833 0.00 0.00 37.17 4.04
562 590 2.161855 CTCATCTCATCTCCCTCCTCG 58.838 57.143 0.00 0.00 0.00 4.63
866 910 1.893808 CGTTGCACCTCTGTTGGCT 60.894 57.895 0.00 0.00 0.00 4.75
919 963 0.238289 CGCGATCCCATACATTTGGC 59.762 55.000 0.00 0.00 35.29 4.52
926 970 0.179140 CCATACATTTGGCGGTGTGC 60.179 55.000 0.29 0.00 45.38 4.57
928 972 2.013400 CATACATTTGGCGGTGTGCTA 58.987 47.619 0.29 0.00 45.43 3.49
942 986 1.000607 TGTGCTAACTTCTCGCGTTCT 60.001 47.619 5.77 0.00 0.00 3.01
952 996 3.470567 CGCGTTCTGTGAGGCGTC 61.471 66.667 0.00 0.00 45.63 5.19
953 997 3.470567 GCGTTCTGTGAGGCGTCG 61.471 66.667 1.39 0.00 0.00 5.12
954 998 3.470567 CGTTCTGTGAGGCGTCGC 61.471 66.667 9.22 9.22 0.00 5.19
1298 1351 3.434319 CACGCTGCACCATCACCC 61.434 66.667 0.00 0.00 0.00 4.61
1415 1468 2.762745 GAAGCACCCGTACAAGAGAAA 58.237 47.619 0.00 0.00 0.00 2.52
1460 1513 3.391382 GGTACGTGCCTGCCCTCT 61.391 66.667 16.23 0.00 0.00 3.69
1473 1547 3.374402 CCTCTCCACGTCACCGCT 61.374 66.667 0.00 0.00 37.70 5.52
1475 1549 2.596338 TCTCCACGTCACCGCTCA 60.596 61.111 0.00 0.00 37.70 4.26
1506 1587 3.337358 TGTCTATACACGAACGAGGTCA 58.663 45.455 0.14 0.00 0.00 4.02
1514 1595 1.931172 ACGAACGAGGTCACAAACTTG 59.069 47.619 0.14 0.00 0.00 3.16
1609 1691 4.298332 CCTTCAAACCAAATGTACAGCAC 58.702 43.478 0.33 0.00 0.00 4.40
1613 1704 1.909700 ACCAAATGTACAGCACCAGG 58.090 50.000 0.33 0.08 0.00 4.45
1678 1773 0.097674 GTACGTATGTCTCACGCCGT 59.902 55.000 0.00 0.00 43.10 5.68
1683 1778 1.252215 TATGTCTCACGCCGTTCCCA 61.252 55.000 0.00 0.00 0.00 4.37
1699 1800 0.458669 CCCATGATGAACTTGCCTGC 59.541 55.000 0.00 0.00 0.00 4.85
1700 1801 0.458669 CCATGATGAACTTGCCTGCC 59.541 55.000 0.00 0.00 0.00 4.85
1742 1843 4.847512 TGGATTTGGGTAGAGTGTAGGAAA 59.152 41.667 0.00 0.00 0.00 3.13
1936 2037 6.377327 ACCAATTATTTCAGGTAGATTGCG 57.623 37.500 0.00 0.00 31.32 4.85
1964 2066 3.997021 AGCTCACCGTTTCAGTTTATCAG 59.003 43.478 0.00 0.00 0.00 2.90
1983 2085 6.765915 ATCAGAGTTTAAATTCTTGCCTCC 57.234 37.500 10.29 0.00 0.00 4.30
2024 2126 3.928375 GGGCAAGTAATTTCACTGCATTG 59.072 43.478 0.00 0.00 0.00 2.82
2025 2127 4.559153 GGCAAGTAATTTCACTGCATTGT 58.441 39.130 3.77 0.00 0.00 2.71
2026 2128 4.990426 GGCAAGTAATTTCACTGCATTGTT 59.010 37.500 3.77 0.00 0.00 2.83
2041 2143 7.385752 CACTGCATTGTTGTTATTTCCAGAATT 59.614 33.333 0.00 0.00 0.00 2.17
2052 2154 8.726988 TGTTATTTCCAGAATTGTAGTAACTGC 58.273 33.333 0.00 0.00 0.00 4.40
2065 2224 5.715279 TGTAGTAACTGCTCTTGTATCCAGT 59.285 40.000 0.00 0.00 40.02 4.00
2083 2242 6.532119 TCCAGTAGTTACTCCTATCCATCT 57.468 41.667 0.00 0.00 33.46 2.90
2096 2256 9.253832 ACTCCTATCCATCTCAATATCACTAAG 57.746 37.037 0.00 0.00 0.00 2.18
2113 2273 5.248477 TCACTAAGATTTACAGCTTCACCCT 59.752 40.000 0.00 0.00 0.00 4.34
2126 2287 3.751698 GCTTCACCCTCGTTGAATTTACT 59.248 43.478 0.00 0.00 0.00 2.24
2136 2297 9.855021 CCCTCGTTGAATTTACTTGATAAAAAT 57.145 29.630 0.00 0.00 36.35 1.82
2186 2373 6.790285 AAAAGTATTGCATTTTGGCAGAAG 57.210 33.333 0.00 0.00 45.88 2.85
2199 2386 8.776470 CATTTTGGCAGAAGTTTGTTTTGATAT 58.224 29.630 0.00 0.00 0.00 1.63
2205 2392 6.922957 GCAGAAGTTTGTTTTGATATCAACCA 59.077 34.615 17.76 14.00 35.28 3.67
2206 2393 7.115378 GCAGAAGTTTGTTTTGATATCAACCAG 59.885 37.037 17.76 5.65 35.28 4.00
2223 2410 5.308497 TCAACCAGGTGTTCTTGGAGTATAA 59.692 40.000 0.00 0.00 42.48 0.98
2229 2416 6.758886 CAGGTGTTCTTGGAGTATAATCTGTC 59.241 42.308 0.00 0.00 0.00 3.51
2251 2439 6.826231 TGTCTTGTTTTTCACCTTCATCTGTA 59.174 34.615 0.00 0.00 0.00 2.74
2320 2511 0.249911 AGTTCGGTCACTGCAAGGAC 60.250 55.000 8.52 8.52 39.30 3.85
2474 2671 1.734117 GCAAGTGAAACGCCATGCC 60.734 57.895 0.00 0.00 45.86 4.40
2490 2687 0.984230 TGCCCTTCTGAACCCTGTAG 59.016 55.000 0.00 0.00 0.00 2.74
2526 2724 4.991056 TGCTCTGACTGTAACTGATGAAAC 59.009 41.667 0.00 0.00 0.00 2.78
2700 2898 0.467290 TGTGGAAGGGCTGACCAAAC 60.467 55.000 0.47 0.00 43.89 2.93
2761 2960 4.815269 AGAGACAGATGTGTTCAAGTAGC 58.185 43.478 0.00 0.00 36.88 3.58
2951 3182 6.017440 TGCCAAATGTAGTAGAAACTCAACAC 60.017 38.462 0.00 0.00 37.15 3.32
3068 3302 2.005451 CTCCTGTGCACATCTAGCAAC 58.995 52.381 22.00 0.00 44.64 4.17
3071 3305 1.736126 CTGTGCACATCTAGCAACTGG 59.264 52.381 22.00 0.00 44.64 4.00
3093 3327 5.056894 GCACAATGCAATTTTCTCTCTCT 57.943 39.130 0.00 0.00 44.26 3.10
3094 3328 5.094134 GCACAATGCAATTTTCTCTCTCTC 58.906 41.667 0.00 0.00 44.26 3.20
3095 3329 5.322310 CACAATGCAATTTTCTCTCTCTCG 58.678 41.667 0.00 0.00 31.22 4.04
3096 3330 4.142730 ACAATGCAATTTTCTCTCTCTCGC 60.143 41.667 0.00 0.00 31.22 5.03
3097 3331 3.044235 TGCAATTTTCTCTCTCTCGCA 57.956 42.857 0.00 0.00 0.00 5.10
3098 3332 2.738846 TGCAATTTTCTCTCTCTCGCAC 59.261 45.455 0.00 0.00 0.00 5.34
3099 3333 2.738846 GCAATTTTCTCTCTCTCGCACA 59.261 45.455 0.00 0.00 0.00 4.57
3100 3334 3.424170 GCAATTTTCTCTCTCTCGCACAC 60.424 47.826 0.00 0.00 0.00 3.82
3146 3389 5.841957 AAATGCCACTCCATAATCTTCAC 57.158 39.130 0.00 0.00 0.00 3.18
3149 3392 3.264193 TGCCACTCCATAATCTTCACACT 59.736 43.478 0.00 0.00 0.00 3.55
3150 3393 3.624861 GCCACTCCATAATCTTCACACTG 59.375 47.826 0.00 0.00 0.00 3.66
3171 3694 7.025963 CACTGAGAGCAAAATCCAGATAAAAC 58.974 38.462 0.00 0.00 0.00 2.43
3181 3704 9.289303 CAAAATCCAGATAAAACAGGTTAATCG 57.711 33.333 0.00 0.00 0.00 3.34
3228 3754 3.861276 CGGTATCCTCCGCATTATGTA 57.139 47.619 0.00 0.00 43.96 2.29
3234 3760 8.304596 CGGTATCCTCCGCATTATGTATAATAT 58.695 37.037 0.00 0.00 43.96 1.28
3239 3765 8.638873 TCCTCCGCATTATGTATAATATACCAG 58.361 37.037 7.85 0.00 32.05 4.00
3263 3789 3.053455 CCGAAGAGAAGAGAACACACAC 58.947 50.000 0.00 0.00 0.00 3.82
3422 3949 1.540267 GCGTGTGTCCAGACTAGAAGA 59.460 52.381 0.00 0.00 0.00 2.87
3426 3953 4.499183 GTGTGTCCAGACTAGAAGAATGG 58.501 47.826 0.00 0.00 0.00 3.16
3495 4022 1.751924 GTCAGAGGGTACAGCAGGTAG 59.248 57.143 0.00 0.00 31.13 3.18
3546 4073 1.048601 TCCGGAAGCTTGTGAAGAGT 58.951 50.000 2.10 0.00 0.00 3.24
3666 4193 1.939934 AGTGTGTTGTTCATGGTCACG 59.060 47.619 0.00 0.00 32.55 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.091424 GCGCAAAATGAGTGAATCTACAC 58.909 43.478 0.30 0.00 40.60 2.90
36 37 3.126858 GGCGCAAAATGAGTGAATCTACA 59.873 43.478 10.83 0.00 0.00 2.74
37 38 3.685058 GGCGCAAAATGAGTGAATCTAC 58.315 45.455 10.83 0.00 0.00 2.59
38 39 2.351418 CGGCGCAAAATGAGTGAATCTA 59.649 45.455 10.83 0.00 0.00 1.98
39 40 1.131126 CGGCGCAAAATGAGTGAATCT 59.869 47.619 10.83 0.00 0.00 2.40
40 41 1.135689 ACGGCGCAAAATGAGTGAATC 60.136 47.619 10.83 0.00 0.00 2.52
41 42 0.881118 ACGGCGCAAAATGAGTGAAT 59.119 45.000 10.83 0.00 0.00 2.57
42 43 1.514003 TACGGCGCAAAATGAGTGAA 58.486 45.000 10.83 0.00 0.00 3.18
43 44 1.396648 CATACGGCGCAAAATGAGTGA 59.603 47.619 10.83 0.00 0.00 3.41
44 45 1.130373 ACATACGGCGCAAAATGAGTG 59.870 47.619 10.83 0.00 0.00 3.51
45 46 1.448985 ACATACGGCGCAAAATGAGT 58.551 45.000 10.83 0.00 0.00 3.41
46 47 2.607635 ACTACATACGGCGCAAAATGAG 59.392 45.455 10.83 10.39 0.00 2.90
47 48 2.605818 GACTACATACGGCGCAAAATGA 59.394 45.455 10.83 0.00 0.00 2.57
48 49 2.350192 TGACTACATACGGCGCAAAATG 59.650 45.455 10.83 11.57 0.00 2.32
49 50 2.350498 GTGACTACATACGGCGCAAAAT 59.650 45.455 10.83 0.00 0.00 1.82
50 51 1.727880 GTGACTACATACGGCGCAAAA 59.272 47.619 10.83 0.00 0.00 2.44
51 52 1.067425 AGTGACTACATACGGCGCAAA 60.067 47.619 10.83 0.00 0.00 3.68
52 53 0.528924 AGTGACTACATACGGCGCAA 59.471 50.000 10.83 0.00 0.00 4.85
53 54 0.528924 AAGTGACTACATACGGCGCA 59.471 50.000 10.83 0.00 0.00 6.09
54 55 0.921347 CAAGTGACTACATACGGCGC 59.079 55.000 6.90 0.00 0.00 6.53
55 56 2.273370 ACAAGTGACTACATACGGCG 57.727 50.000 4.80 4.80 0.00 6.46
56 57 3.581755 TCAACAAGTGACTACATACGGC 58.418 45.455 0.00 0.00 0.00 5.68
57 58 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
58 59 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
59 60 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
61 62 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
62 63 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
63 64 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
64 65 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
65 66 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
66 67 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
67 68 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
68 69 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
69 70 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
70 71 9.050601 ACTTGTCTTTCTAGAGATTTCAACAAG 57.949 33.333 18.42 18.42 32.73 3.16
71 72 8.964476 ACTTGTCTTTCTAGAGATTTCAACAA 57.036 30.769 0.00 0.00 0.00 2.83
81 82 9.291664 CGTTCCTAAATACTTGTCTTTCTAGAG 57.708 37.037 0.00 0.00 0.00 2.43
82 83 8.248945 CCGTTCCTAAATACTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
83 84 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
84 85 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
85 86 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
86 87 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
87 88 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
88 89 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
89 90 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
90 91 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
91 92 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
92 93 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
93 94 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
94 95 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
95 96 5.859205 TTACTCCCTCCGTTCCTAAATAC 57.141 43.478 0.00 0.00 0.00 1.89
96 97 8.551682 TTAATTACTCCCTCCGTTCCTAAATA 57.448 34.615 0.00 0.00 0.00 1.40
97 98 5.970501 AATTACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
98 99 6.872585 TTAATTACTCCCTCCGTTCCTAAA 57.127 37.500 0.00 0.00 0.00 1.85
99 100 8.731591 ATATTAATTACTCCCTCCGTTCCTAA 57.268 34.615 0.00 0.00 0.00 2.69
100 101 7.951806 TGATATTAATTACTCCCTCCGTTCCTA 59.048 37.037 0.00 0.00 0.00 2.94
101 102 6.785963 TGATATTAATTACTCCCTCCGTTCCT 59.214 38.462 0.00 0.00 0.00 3.36
102 103 7.001099 TGATATTAATTACTCCCTCCGTTCC 57.999 40.000 0.00 0.00 0.00 3.62
103 104 9.583765 GTATGATATTAATTACTCCCTCCGTTC 57.416 37.037 0.00 0.00 0.00 3.95
104 105 8.537858 GGTATGATATTAATTACTCCCTCCGTT 58.462 37.037 0.00 0.00 0.00 4.44
227 245 6.017440 ACAACAATCGTACTATGCAAGTTTGT 60.017 34.615 6.82 8.23 37.14 2.83
246 264 2.103432 TCCGCTTAACTCTCCACAACAA 59.897 45.455 0.00 0.00 0.00 2.83
301 319 4.761975 TCAGTTTTCGTCACCAACTAAGT 58.238 39.130 0.00 0.00 0.00 2.24
302 320 4.318831 GCTCAGTTTTCGTCACCAACTAAG 60.319 45.833 0.00 0.00 0.00 2.18
303 321 3.558418 GCTCAGTTTTCGTCACCAACTAA 59.442 43.478 0.00 0.00 0.00 2.24
304 322 3.128349 GCTCAGTTTTCGTCACCAACTA 58.872 45.455 0.00 0.00 0.00 2.24
310 328 0.599204 TCGGGCTCAGTTTTCGTCAC 60.599 55.000 0.00 0.00 0.00 3.67
442 460 1.203523 ACACAAGCTCGATGTCTCTCC 59.796 52.381 0.00 0.00 0.00 3.71
540 568 3.157087 GAGGAGGGAGATGAGATGAGAC 58.843 54.545 0.00 0.00 0.00 3.36
562 590 3.255969 AGACTAGACACGGAGAGAGAC 57.744 52.381 0.00 0.00 0.00 3.36
844 888 0.588252 CAACAGAGGTGCAACGGAAG 59.412 55.000 0.00 0.00 38.12 3.46
900 944 0.238289 GCCAAATGTATGGGATCGCG 59.762 55.000 0.00 0.00 41.01 5.87
919 963 1.674611 CGCGAGAAGTTAGCACACCG 61.675 60.000 0.00 0.00 0.00 4.94
926 970 2.911723 CTCACAGAACGCGAGAAGTTAG 59.088 50.000 15.93 3.23 31.14 2.34
928 972 1.603172 CCTCACAGAACGCGAGAAGTT 60.603 52.381 15.93 0.00 34.07 2.66
975 1022 2.673114 GCGCCGAATCAACCGAACA 61.673 57.895 0.00 0.00 0.00 3.18
985 1032 2.655364 CATCTCGTCGCGCCGAAT 60.655 61.111 14.89 7.52 37.72 3.34
1019 1066 3.982241 GGTGGTGGTTGCTGCTGC 61.982 66.667 8.89 8.89 40.20 5.25
1415 1468 4.021925 GAGGTTGCGGGCAGAGGT 62.022 66.667 0.00 0.00 0.00 3.85
1473 1547 4.546570 GTGTATAGACATGCATACGCTGA 58.453 43.478 0.00 0.00 38.04 4.26
1475 1549 3.252458 TCGTGTATAGACATGCATACGCT 59.748 43.478 17.30 0.00 41.62 5.07
1506 1587 2.788786 CGAAAGATTTGCGCAAGTTTGT 59.211 40.909 23.68 11.00 41.68 2.83
1609 1691 3.847602 CGCTGCTCCTCCTCCTGG 61.848 72.222 0.00 0.00 0.00 4.45
1678 1773 2.449464 CAGGCAAGTTCATCATGGGAA 58.551 47.619 0.00 0.00 0.00 3.97
1683 1778 1.754803 CATGGCAGGCAAGTTCATCAT 59.245 47.619 0.00 0.00 0.00 2.45
1699 1800 9.472940 AAATCCACATTTAGCAACCATCCATGG 62.473 40.741 4.97 4.97 40.94 3.66
1700 1801 3.700539 TCCACATTTAGCAACCATCCATG 59.299 43.478 0.00 0.00 0.00 3.66
1710 1811 5.186256 TCTACCCAAATCCACATTTAGCA 57.814 39.130 0.00 0.00 30.51 3.49
1936 2037 2.876550 ACTGAAACGGTGAGCTAAAACC 59.123 45.455 3.15 3.15 0.00 3.27
1964 2066 5.372547 AACGGAGGCAAGAATTTAAACTC 57.627 39.130 0.00 0.00 0.00 3.01
2026 2128 8.726988 GCAGTTACTACAATTCTGGAAATAACA 58.273 33.333 0.00 0.00 0.00 2.41
2096 2256 2.973945 ACGAGGGTGAAGCTGTAAATC 58.026 47.619 0.00 0.00 0.00 2.17
2110 2270 9.855021 ATTTTTATCAAGTAAATTCAACGAGGG 57.145 29.630 0.00 0.00 32.56 4.30
2147 2308 9.855021 GCAATACTTTTTCATGGTAAATACAGT 57.145 29.630 0.00 0.00 0.00 3.55
2148 2309 9.853555 TGCAATACTTTTTCATGGTAAATACAG 57.146 29.630 0.00 0.00 0.00 2.74
2164 2346 5.857268 ACTTCTGCCAAAATGCAATACTTT 58.143 33.333 0.00 0.00 41.51 2.66
2167 2349 5.466393 ACAAACTTCTGCCAAAATGCAATAC 59.534 36.000 0.00 0.00 41.51 1.89
2172 2359 4.880886 AAACAAACTTCTGCCAAAATGC 57.119 36.364 0.00 0.00 0.00 3.56
2186 2373 6.512297 ACACCTGGTTGATATCAAAACAAAC 58.488 36.000 19.55 7.04 37.63 2.93
2199 2386 1.843851 ACTCCAAGAACACCTGGTTGA 59.156 47.619 0.00 0.00 40.63 3.18
2205 2392 6.670027 AGACAGATTATACTCCAAGAACACCT 59.330 38.462 0.00 0.00 0.00 4.00
2206 2393 6.879400 AGACAGATTATACTCCAAGAACACC 58.121 40.000 0.00 0.00 0.00 4.16
2223 2410 6.774656 AGATGAAGGTGAAAAACAAGACAGAT 59.225 34.615 0.00 0.00 0.00 2.90
2229 2416 6.438763 GGTACAGATGAAGGTGAAAAACAAG 58.561 40.000 0.00 0.00 0.00 3.16
2320 2511 4.069232 TCTCTGCTTCGGCCGGTG 62.069 66.667 27.83 19.15 40.91 4.94
2329 2520 1.670406 CAAGCCAGCGTCTCTGCTT 60.670 57.895 0.00 0.00 44.46 3.91
2474 2671 4.256920 CACATTCTACAGGGTTCAGAAGG 58.743 47.826 0.00 0.00 36.45 3.46
2490 2687 2.159234 GTCAGAGCAAGCTCACACATTC 59.841 50.000 22.68 3.90 44.99 2.67
2572 2770 1.745653 GAAGTTGTAGAATGGCAGGGC 59.254 52.381 0.00 0.00 0.00 5.19
2682 2880 1.179174 GGTTTGGTCAGCCCTTCCAC 61.179 60.000 0.00 0.00 0.00 4.02
2700 2898 5.047802 ACAACTTCCTAATGTTCATTGCAGG 60.048 40.000 8.11 7.84 0.00 4.85
2761 2960 6.111382 ACATCTCTTGATACATCTGGTGTTG 58.889 40.000 0.00 0.00 42.29 3.33
2791 2992 3.820467 TGGCAGTGAAAAACATGTCCTAG 59.180 43.478 0.00 0.00 0.00 3.02
2951 3182 5.491070 TCATCTACCCATCTCACACTTTTG 58.509 41.667 0.00 0.00 0.00 2.44
3068 3302 3.921677 AGAGAAAATTGCATTGTGCCAG 58.078 40.909 0.00 0.00 44.23 4.85
3071 3305 5.056894 AGAGAGAGAAAATTGCATTGTGC 57.943 39.130 0.00 0.00 45.29 4.57
3093 3327 0.742635 ATGTGTGTGTGTGTGTGCGA 60.743 50.000 0.00 0.00 0.00 5.10
3094 3328 0.589479 CATGTGTGTGTGTGTGTGCG 60.589 55.000 0.00 0.00 0.00 5.34
3095 3329 0.731994 TCATGTGTGTGTGTGTGTGC 59.268 50.000 0.00 0.00 0.00 4.57
3096 3330 1.736681 TGTCATGTGTGTGTGTGTGTG 59.263 47.619 0.00 0.00 0.00 3.82
3097 3331 2.106477 TGTCATGTGTGTGTGTGTGT 57.894 45.000 0.00 0.00 0.00 3.72
3098 3332 2.477694 GGTTGTCATGTGTGTGTGTGTG 60.478 50.000 0.00 0.00 0.00 3.82
3099 3333 1.742831 GGTTGTCATGTGTGTGTGTGT 59.257 47.619 0.00 0.00 0.00 3.72
3100 3334 2.016318 AGGTTGTCATGTGTGTGTGTG 58.984 47.619 0.00 0.00 0.00 3.82
3146 3389 6.748333 TTTATCTGGATTTTGCTCTCAGTG 57.252 37.500 0.00 0.00 0.00 3.66
3149 3392 6.151648 CCTGTTTTATCTGGATTTTGCTCTCA 59.848 38.462 0.00 0.00 0.00 3.27
3150 3393 6.151817 ACCTGTTTTATCTGGATTTTGCTCTC 59.848 38.462 0.00 0.00 0.00 3.20
3171 3694 6.124088 AGAAATAAGCTTGCGATTAACCTG 57.876 37.500 9.86 0.00 0.00 4.00
3181 3704 5.447573 GCTACATGCTAGAAATAAGCTTGC 58.552 41.667 9.86 2.12 44.62 4.01
3228 3754 9.233649 CTCTTCTCTTCGGTACTGGTATATTAT 57.766 37.037 0.85 0.00 0.00 1.28
3234 3760 4.564782 TCTCTTCTCTTCGGTACTGGTA 57.435 45.455 0.85 0.00 0.00 3.25
3239 3765 4.228317 GTGTGTTCTCTTCTCTTCGGTAC 58.772 47.826 0.00 0.00 0.00 3.34
3384 3911 1.532437 CGCTTGAGTTTGATGCTGTCA 59.468 47.619 0.00 0.00 34.25 3.58
3390 3917 2.349817 GGACACACGCTTGAGTTTGATG 60.350 50.000 0.00 0.00 0.00 3.07
3422 3949 1.538666 GGCTGGTCATAGGCCCATT 59.461 57.895 0.00 0.00 39.96 3.16
3426 3953 1.227674 CTTCGGCTGGTCATAGGCC 60.228 63.158 0.00 0.00 39.88 5.19
3546 4073 1.478105 CTCGTCTGTGTCATCATGGGA 59.522 52.381 0.00 0.00 0.00 4.37
3666 4193 2.202960 TTGCAGGTATACGGCGGC 60.203 61.111 13.24 0.00 43.71 6.53


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

AutoCloner maintained by Alex Coulton.