Multiple sequence alignment - TraesCS1A01G216300

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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 TraesCS1A01G216300 chr1A 100.000 2239 0 0 722 2960 382253426 382251188 0.000000e+00 4135
1 TraesCS1A01G216300 chr1A 100.000 433 0 0 1 433 382254147 382253715 0.000000e+00 800
2 TraesCS1A01G216300 chr1D 95.219 2280 55 11 722 2960 305230255 305227989 0.000000e+00 3557
3 TraesCS1A01G216300 chr1D 91.532 248 15 3 186 433 305230718 305230477 1.310000e-88 337
4 TraesCS1A01G216300 chr1B 93.621 2273 67 31 722 2951 412242772 412245009 0.000000e+00 3323
5 TraesCS1A01G216300 chr1B 92.800 250 11 4 186 433 412242305 412242549 3.630000e-94 355


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 TraesCS1A01G216300 chr1A 382251188 382254147 2959 True 2467.5 4135 100.0000 1 2960 2 chr1A.!!$R1 2959
1 TraesCS1A01G216300 chr1D 305227989 305230718 2729 True 1947.0 3557 93.3755 186 2960 2 chr1D.!!$R1 2774
2 TraesCS1A01G216300 chr1B 412242305 412245009 2704 False 1839.0 3323 93.2105 186 2951 2 chr1B.!!$F1 2765

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
121 122 0.251073 GAAACCCTAACCCTAGCGCA 59.749 55.0 11.47 0.00 0.0 6.09 F
122 123 0.252197 AAACCCTAACCCTAGCGCAG 59.748 55.0 11.47 4.88 0.0 5.18 F
1017 1026 0.396417 CCATGTCCTCCTCCTCGTCT 60.396 60.0 0.00 0.00 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1500 1.063417 CCCCTGGGCTTGATCTTGATT 60.063 52.381 7.39 0.0 0.0 2.57 R
1830 1839 1.220206 CTGGGTGCGCTTCATCTCT 59.780 57.895 9.73 0.0 0.0 3.10 R
2860 2922 0.613853 CACCCTCCTCAAGTCCGGTA 60.614 60.000 0.00 0.0 0.0 4.02 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
19 20 2.299993 TGAGCGGAATACTCAGCAAG 57.700 50.000 0.00 0.00 44.36 4.01
20 21 1.824852 TGAGCGGAATACTCAGCAAGA 59.175 47.619 0.00 0.00 44.36 3.02
21 22 2.233676 TGAGCGGAATACTCAGCAAGAA 59.766 45.455 0.00 0.00 44.36 2.52
22 23 2.605366 GAGCGGAATACTCAGCAAGAAC 59.395 50.000 0.00 0.00 44.36 3.01
23 24 1.666189 GCGGAATACTCAGCAAGAACC 59.334 52.381 0.00 0.00 41.84 3.62
24 25 2.935238 GCGGAATACTCAGCAAGAACCA 60.935 50.000 0.00 0.00 41.84 3.67
25 26 2.932614 CGGAATACTCAGCAAGAACCAG 59.067 50.000 0.00 0.00 0.00 4.00
26 27 3.617531 CGGAATACTCAGCAAGAACCAGT 60.618 47.826 0.00 0.00 0.00 4.00
27 28 4.327680 GGAATACTCAGCAAGAACCAGTT 58.672 43.478 0.00 0.00 0.00 3.16
28 29 4.393371 GGAATACTCAGCAAGAACCAGTTC 59.607 45.833 2.19 2.19 39.78 3.01
36 37 2.070639 AGAACCAGTTCTCCCAGCC 58.929 57.895 7.23 0.00 46.13 4.85
37 38 0.768221 AGAACCAGTTCTCCCAGCCA 60.768 55.000 7.23 0.00 46.13 4.75
38 39 0.322008 GAACCAGTTCTCCCAGCCAG 60.322 60.000 3.25 0.00 36.69 4.85
39 40 2.045536 CCAGTTCTCCCAGCCAGC 60.046 66.667 0.00 0.00 0.00 4.85
40 41 2.435586 CAGTTCTCCCAGCCAGCG 60.436 66.667 0.00 0.00 0.00 5.18
41 42 2.604686 AGTTCTCCCAGCCAGCGA 60.605 61.111 0.00 0.00 0.00 4.93
42 43 2.217038 AGTTCTCCCAGCCAGCGAA 61.217 57.895 0.00 0.00 0.00 4.70
43 44 2.035442 GTTCTCCCAGCCAGCGAAC 61.035 63.158 0.00 0.00 0.00 3.95
44 45 2.515979 TTCTCCCAGCCAGCGAACA 61.516 57.895 0.00 0.00 0.00 3.18
45 46 2.435586 CTCCCAGCCAGCGAACAG 60.436 66.667 0.00 0.00 0.00 3.16
46 47 3.965539 CTCCCAGCCAGCGAACAGG 62.966 68.421 0.00 0.00 0.00 4.00
48 49 4.020617 CCAGCCAGCGAACAGGGA 62.021 66.667 0.00 0.00 0.00 4.20
49 50 2.270205 CAGCCAGCGAACAGGGAT 59.730 61.111 0.00 0.00 0.00 3.85
50 51 1.377725 CAGCCAGCGAACAGGGATT 60.378 57.895 0.00 0.00 0.00 3.01
51 52 1.377725 AGCCAGCGAACAGGGATTG 60.378 57.895 0.00 0.00 0.00 2.67
52 53 3.056313 GCCAGCGAACAGGGATTGC 62.056 63.158 0.00 0.00 0.00 3.56
53 54 2.753966 CCAGCGAACAGGGATTGCG 61.754 63.158 0.00 0.00 0.00 4.85
55 56 4.179579 GCGAACAGGGATTGCGCC 62.180 66.667 4.18 0.00 41.65 6.53
56 57 3.864686 CGAACAGGGATTGCGCCG 61.865 66.667 4.18 0.00 0.00 6.46
57 58 2.746277 GAACAGGGATTGCGCCGT 60.746 61.111 4.18 0.00 0.00 5.68
58 59 2.746277 AACAGGGATTGCGCCGTC 60.746 61.111 4.18 2.17 0.00 4.79
73 74 4.400961 GTCGCCCTCCTTGCTGCT 62.401 66.667 0.00 0.00 0.00 4.24
74 75 4.399395 TCGCCCTCCTTGCTGCTG 62.399 66.667 0.00 0.00 0.00 4.41
77 78 4.355720 CCCTCCTTGCTGCTGCCA 62.356 66.667 13.47 0.57 38.71 4.92
78 79 2.282674 CCTCCTTGCTGCTGCCAA 60.283 61.111 13.47 6.69 38.71 4.52
79 80 1.904865 CCTCCTTGCTGCTGCCAAA 60.905 57.895 13.47 0.62 38.71 3.28
80 81 1.255667 CCTCCTTGCTGCTGCCAAAT 61.256 55.000 13.47 0.00 38.71 2.32
81 82 0.606604 CTCCTTGCTGCTGCCAAATT 59.393 50.000 13.47 0.00 38.71 1.82
82 83 0.604578 TCCTTGCTGCTGCCAAATTC 59.395 50.000 13.47 0.00 38.71 2.17
83 84 0.319083 CCTTGCTGCTGCCAAATTCA 59.681 50.000 13.47 0.00 38.71 2.57
84 85 1.270412 CCTTGCTGCTGCCAAATTCAA 60.270 47.619 13.47 0.00 38.71 2.69
85 86 2.485903 CTTGCTGCTGCCAAATTCAAA 58.514 42.857 13.47 0.00 38.71 2.69
86 87 1.868469 TGCTGCTGCCAAATTCAAAC 58.132 45.000 13.47 0.00 38.71 2.93
87 88 1.150827 GCTGCTGCCAAATTCAAACC 58.849 50.000 3.85 0.00 0.00 3.27
88 89 1.540797 GCTGCTGCCAAATTCAAACCA 60.541 47.619 3.85 0.00 0.00 3.67
89 90 2.137523 CTGCTGCCAAATTCAAACCAC 58.862 47.619 0.00 0.00 0.00 4.16
90 91 1.202627 TGCTGCCAAATTCAAACCACC 60.203 47.619 0.00 0.00 0.00 4.61
91 92 1.877680 GCTGCCAAATTCAAACCACCC 60.878 52.381 0.00 0.00 0.00 4.61
92 93 1.693606 CTGCCAAATTCAAACCACCCT 59.306 47.619 0.00 0.00 0.00 4.34
93 94 1.691434 TGCCAAATTCAAACCACCCTC 59.309 47.619 0.00 0.00 0.00 4.30
94 95 1.336795 GCCAAATTCAAACCACCCTCG 60.337 52.381 0.00 0.00 0.00 4.63
95 96 1.960689 CCAAATTCAAACCACCCTCGT 59.039 47.619 0.00 0.00 0.00 4.18
96 97 2.288152 CCAAATTCAAACCACCCTCGTG 60.288 50.000 0.00 0.00 39.91 4.35
97 98 2.621055 CAAATTCAAACCACCCTCGTGA 59.379 45.455 0.00 0.00 43.14 4.35
98 99 2.649531 ATTCAAACCACCCTCGTGAA 57.350 45.000 0.00 0.00 43.14 3.18
99 100 1.961793 TTCAAACCACCCTCGTGAAG 58.038 50.000 0.00 0.00 43.14 3.02
100 101 0.834612 TCAAACCACCCTCGTGAAGT 59.165 50.000 0.00 0.00 43.14 3.01
101 102 2.040939 TCAAACCACCCTCGTGAAGTA 58.959 47.619 0.00 0.00 43.14 2.24
102 103 2.036733 TCAAACCACCCTCGTGAAGTAG 59.963 50.000 0.00 0.00 43.14 2.57
103 104 2.005370 AACCACCCTCGTGAAGTAGA 57.995 50.000 0.00 0.00 43.14 2.59
104 105 2.005370 ACCACCCTCGTGAAGTAGAA 57.995 50.000 0.00 0.00 43.14 2.10
105 106 2.322658 ACCACCCTCGTGAAGTAGAAA 58.677 47.619 0.00 0.00 43.14 2.52
106 107 2.036862 ACCACCCTCGTGAAGTAGAAAC 59.963 50.000 0.00 0.00 43.14 2.78
107 108 2.612221 CCACCCTCGTGAAGTAGAAACC 60.612 54.545 0.00 0.00 43.14 3.27
108 109 1.622312 ACCCTCGTGAAGTAGAAACCC 59.378 52.381 0.00 0.00 0.00 4.11
109 110 1.900486 CCCTCGTGAAGTAGAAACCCT 59.100 52.381 0.00 0.00 0.00 4.34
110 111 3.094572 CCCTCGTGAAGTAGAAACCCTA 58.905 50.000 0.00 0.00 0.00 3.53
111 112 3.512724 CCCTCGTGAAGTAGAAACCCTAA 59.487 47.826 0.00 0.00 0.00 2.69
112 113 4.492611 CCTCGTGAAGTAGAAACCCTAAC 58.507 47.826 0.00 0.00 0.00 2.34
113 114 4.492611 CTCGTGAAGTAGAAACCCTAACC 58.507 47.826 0.00 0.00 0.00 2.85
114 115 3.259123 TCGTGAAGTAGAAACCCTAACCC 59.741 47.826 0.00 0.00 0.00 4.11
115 116 3.260128 CGTGAAGTAGAAACCCTAACCCT 59.740 47.826 0.00 0.00 0.00 4.34
116 117 4.463891 CGTGAAGTAGAAACCCTAACCCTA 59.536 45.833 0.00 0.00 0.00 3.53
117 118 5.393896 CGTGAAGTAGAAACCCTAACCCTAG 60.394 48.000 0.00 0.00 0.00 3.02
118 119 4.468868 TGAAGTAGAAACCCTAACCCTAGC 59.531 45.833 0.00 0.00 0.00 3.42
119 120 3.029570 AGTAGAAACCCTAACCCTAGCG 58.970 50.000 0.00 0.00 0.00 4.26
120 121 0.540454 AGAAACCCTAACCCTAGCGC 59.460 55.000 0.00 0.00 0.00 5.92
121 122 0.251073 GAAACCCTAACCCTAGCGCA 59.749 55.000 11.47 0.00 0.00 6.09
122 123 0.252197 AAACCCTAACCCTAGCGCAG 59.748 55.000 11.47 4.88 0.00 5.18
123 124 1.623542 AACCCTAACCCTAGCGCAGG 61.624 60.000 11.47 14.49 45.07 4.85
131 132 4.528674 CTAGCGCAGGAGCACAAT 57.471 55.556 11.47 0.00 42.27 2.71
132 133 2.305405 CTAGCGCAGGAGCACAATC 58.695 57.895 11.47 0.00 42.27 2.67
133 134 1.485838 CTAGCGCAGGAGCACAATCG 61.486 60.000 11.47 0.00 42.27 3.34
134 135 4.527157 GCGCAGGAGCACAATCGC 62.527 66.667 0.30 0.00 42.27 4.58
135 136 3.869272 CGCAGGAGCACAATCGCC 61.869 66.667 0.00 0.00 42.27 5.54
136 137 2.437359 GCAGGAGCACAATCGCCT 60.437 61.111 0.00 0.00 41.58 5.52
137 138 2.467826 GCAGGAGCACAATCGCCTC 61.468 63.158 0.00 0.00 41.58 4.70
138 139 1.078918 CAGGAGCACAATCGCCTCA 60.079 57.895 0.00 0.00 33.86 3.86
139 140 1.078848 AGGAGCACAATCGCCTCAC 60.079 57.895 0.00 0.00 29.99 3.51
140 141 2.456119 GGAGCACAATCGCCTCACG 61.456 63.158 0.00 0.00 45.62 4.35
151 152 2.520982 CCTCACGATCGCCCCCTA 60.521 66.667 16.60 0.00 0.00 3.53
152 153 2.728817 CTCACGATCGCCCCCTAC 59.271 66.667 16.60 0.00 0.00 3.18
153 154 2.836360 TCACGATCGCCCCCTACC 60.836 66.667 16.60 0.00 0.00 3.18
154 155 4.280494 CACGATCGCCCCCTACCG 62.280 72.222 16.60 0.00 0.00 4.02
159 160 3.761690 ATCGCCCCCTACCGCCTTA 62.762 63.158 0.00 0.00 0.00 2.69
160 161 3.925090 CGCCCCCTACCGCCTTAG 61.925 72.222 0.00 0.00 0.00 2.18
161 162 2.767073 GCCCCCTACCGCCTTAGT 60.767 66.667 0.00 0.00 0.00 2.24
162 163 3.103091 GCCCCCTACCGCCTTAGTG 62.103 68.421 0.00 0.00 0.00 2.74
163 164 1.688187 CCCCCTACCGCCTTAGTGT 60.688 63.158 0.00 0.00 0.00 3.55
164 165 1.269703 CCCCCTACCGCCTTAGTGTT 61.270 60.000 0.00 0.00 0.00 3.32
165 166 0.616891 CCCCTACCGCCTTAGTGTTT 59.383 55.000 0.00 0.00 0.00 2.83
166 167 1.406477 CCCCTACCGCCTTAGTGTTTC 60.406 57.143 0.00 0.00 0.00 2.78
167 168 1.406477 CCCTACCGCCTTAGTGTTTCC 60.406 57.143 0.00 0.00 0.00 3.13
168 169 1.553704 CCTACCGCCTTAGTGTTTCCT 59.446 52.381 0.00 0.00 0.00 3.36
169 170 2.027469 CCTACCGCCTTAGTGTTTCCTT 60.027 50.000 0.00 0.00 0.00 3.36
170 171 3.196254 CCTACCGCCTTAGTGTTTCCTTA 59.804 47.826 0.00 0.00 0.00 2.69
171 172 3.049708 ACCGCCTTAGTGTTTCCTTAC 57.950 47.619 0.00 0.00 0.00 2.34
172 173 1.997606 CCGCCTTAGTGTTTCCTTACG 59.002 52.381 0.00 0.00 0.00 3.18
173 174 2.611224 CCGCCTTAGTGTTTCCTTACGT 60.611 50.000 0.00 0.00 0.00 3.57
174 175 2.410730 CGCCTTAGTGTTTCCTTACGTG 59.589 50.000 0.00 0.00 0.00 4.49
175 176 2.740447 GCCTTAGTGTTTCCTTACGTGG 59.260 50.000 0.00 0.00 0.00 4.94
176 177 3.804759 GCCTTAGTGTTTCCTTACGTGGT 60.805 47.826 0.00 0.00 0.00 4.16
177 178 3.744426 CCTTAGTGTTTCCTTACGTGGTG 59.256 47.826 0.00 0.00 0.00 4.17
178 179 2.249844 AGTGTTTCCTTACGTGGTGG 57.750 50.000 0.00 0.00 0.00 4.61
179 180 1.764134 AGTGTTTCCTTACGTGGTGGA 59.236 47.619 0.00 0.00 0.00 4.02
180 181 1.869132 GTGTTTCCTTACGTGGTGGAC 59.131 52.381 0.00 0.00 0.00 4.02
181 182 1.202675 TGTTTCCTTACGTGGTGGACC 60.203 52.381 0.00 0.00 0.00 4.46
182 183 0.397564 TTTCCTTACGTGGTGGACCC 59.602 55.000 0.00 0.00 34.29 4.46
183 184 0.472352 TTCCTTACGTGGTGGACCCT 60.472 55.000 0.00 0.00 34.29 4.34
184 185 0.901580 TCCTTACGTGGTGGACCCTC 60.902 60.000 0.00 0.00 34.29 4.30
196 197 2.040412 GTGGACCCTCAAAATCAGGACT 59.960 50.000 0.00 0.00 31.91 3.85
197 198 3.263425 GTGGACCCTCAAAATCAGGACTA 59.737 47.826 0.00 0.00 31.91 2.59
211 212 2.747989 CAGGACTAGAGTGCTTCGTACA 59.252 50.000 0.29 0.00 44.54 2.90
234 236 6.690957 ACAACACGTTTGTCACTTATCATTTG 59.309 34.615 9.39 0.00 33.55 2.32
235 237 5.757886 ACACGTTTGTCACTTATCATTTGG 58.242 37.500 0.00 0.00 0.00 3.28
240 242 7.976734 ACGTTTGTCACTTATCATTTGGAAAAA 59.023 29.630 0.00 0.00 0.00 1.94
241 243 8.977505 CGTTTGTCACTTATCATTTGGAAAAAT 58.022 29.630 0.00 0.00 0.00 1.82
267 269 6.581171 AAAGAAAAACCAGATTAGCAGAGG 57.419 37.500 0.00 0.00 0.00 3.69
1017 1026 0.396417 CCATGTCCTCCTCCTCGTCT 60.396 60.000 0.00 0.00 0.00 4.18
1329 1338 2.432563 CCCACCGCCACCTACAAA 59.567 61.111 0.00 0.00 0.00 2.83
1338 1347 1.087771 CCACCTACAAATCCGGCGTC 61.088 60.000 6.01 0.00 0.00 5.19
1368 1377 0.457851 ACAAGATCGAGAAGCTCCGG 59.542 55.000 0.00 0.00 0.00 5.14
1491 1500 3.749870 GCCAGCCCCAACCCCATA 61.750 66.667 0.00 0.00 0.00 2.74
1830 1839 0.324738 AGAAGGAGCGGATGGAGTCA 60.325 55.000 0.00 0.00 0.00 3.41
1975 1990 2.217510 TTGAGAACTAGAGCTCCGGT 57.782 50.000 10.93 6.73 0.00 5.28
2051 2066 0.390078 CTGCTGCTCCTGTCAGTCAG 60.390 60.000 0.00 4.65 43.27 3.51
2082 2097 7.987458 TGACTTGTGATGTTTCTACTCTTCTTT 59.013 33.333 0.00 0.00 0.00 2.52
2352 2384 4.092279 TCAACAGTCTCTCACTCATGGAT 58.908 43.478 0.00 0.00 30.26 3.41
2354 2386 5.716703 TCAACAGTCTCTCACTCATGGATAA 59.283 40.000 0.00 0.00 30.26 1.75
2377 2409 1.322442 GTTATGGATGGCCCTTGCTC 58.678 55.000 0.00 0.00 37.74 4.26
2396 2428 4.184629 GCTCAACTATCAACTGGGTACTG 58.815 47.826 0.00 0.00 0.00 2.74
2486 2518 0.035820 TGAACTATCAACCGGGCACC 60.036 55.000 6.32 0.00 37.72 5.01
2679 2723 8.352942 ACAATATTTGTTCTTCTCAACCTTGAC 58.647 33.333 0.00 0.00 42.22 3.18
2823 2885 8.735692 TCTAATGATATGCTTTTCATGACACA 57.264 30.769 0.00 0.00 36.63 3.72
2860 2922 3.517901 TCAAATCAACGACCCTCCTATGT 59.482 43.478 0.00 0.00 0.00 2.29
2943 3006 3.388676 AGAAGATCAGCCTCATGGAAGAG 59.611 47.826 0.00 0.00 34.57 2.85
2954 3017 0.253327 ATGGAAGAGGCGAACCCTTC 59.747 55.000 0.00 0.00 46.60 3.46
2955 3018 1.078356 GGAAGAGGCGAACCCTTCC 60.078 63.158 13.23 13.23 46.60 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.824852 TCTTGCTGAGTATTCCGCTCA 59.175 47.619 3.46 0.00 40.28 4.26
1 2 2.586258 TCTTGCTGAGTATTCCGCTC 57.414 50.000 3.46 0.00 34.94 5.03
3 4 1.666189 GGTTCTTGCTGAGTATTCCGC 59.334 52.381 0.00 0.00 34.50 5.54
4 5 2.932614 CTGGTTCTTGCTGAGTATTCCG 59.067 50.000 0.00 0.00 0.00 4.30
5 6 3.944087 ACTGGTTCTTGCTGAGTATTCC 58.056 45.455 0.00 0.00 0.00 3.01
6 7 5.241662 AGAACTGGTTCTTGCTGAGTATTC 58.758 41.667 9.85 0.00 46.95 1.75
7 8 5.234466 AGAACTGGTTCTTGCTGAGTATT 57.766 39.130 9.85 0.00 46.95 1.89
8 9 4.899352 AGAACTGGTTCTTGCTGAGTAT 57.101 40.909 9.85 0.00 46.95 2.12
19 20 0.322008 CTGGCTGGGAGAACTGGTTC 60.322 60.000 5.43 5.43 39.78 3.62
20 21 1.763770 CTGGCTGGGAGAACTGGTT 59.236 57.895 0.00 0.00 0.00 3.67
21 22 2.900106 GCTGGCTGGGAGAACTGGT 61.900 63.158 0.00 0.00 0.00 4.00
22 23 2.045536 GCTGGCTGGGAGAACTGG 60.046 66.667 0.00 0.00 0.00 4.00
23 24 2.435586 CGCTGGCTGGGAGAACTG 60.436 66.667 2.10 0.00 0.00 3.16
24 25 2.217038 TTCGCTGGCTGGGAGAACT 61.217 57.895 10.79 0.00 38.86 3.01
25 26 2.035442 GTTCGCTGGCTGGGAGAAC 61.035 63.158 10.79 8.40 38.86 3.01
26 27 2.347490 GTTCGCTGGCTGGGAGAA 59.653 61.111 10.79 0.43 38.86 2.87
27 28 2.922503 TGTTCGCTGGCTGGGAGA 60.923 61.111 10.79 0.59 38.86 3.71
28 29 2.435586 CTGTTCGCTGGCTGGGAG 60.436 66.667 10.79 0.00 38.86 4.30
29 30 4.020617 CCTGTTCGCTGGCTGGGA 62.021 66.667 7.05 7.05 35.75 4.37
31 32 2.826777 AATCCCTGTTCGCTGGCTGG 62.827 60.000 0.00 0.00 35.18 4.85
32 33 1.377725 AATCCCTGTTCGCTGGCTG 60.378 57.895 0.00 0.00 35.18 4.85
33 34 1.377725 CAATCCCTGTTCGCTGGCT 60.378 57.895 0.00 0.00 35.18 4.75
34 35 3.056313 GCAATCCCTGTTCGCTGGC 62.056 63.158 0.00 0.00 35.18 4.85
35 36 2.753966 CGCAATCCCTGTTCGCTGG 61.754 63.158 0.00 0.00 36.14 4.85
36 37 2.787249 CGCAATCCCTGTTCGCTG 59.213 61.111 0.00 0.00 0.00 5.18
37 38 3.127533 GCGCAATCCCTGTTCGCT 61.128 61.111 0.30 0.00 42.19 4.93
38 39 4.179579 GGCGCAATCCCTGTTCGC 62.180 66.667 10.83 0.00 44.39 4.70
39 40 3.864686 CGGCGCAATCCCTGTTCG 61.865 66.667 10.83 0.00 0.00 3.95
40 41 2.746277 ACGGCGCAATCCCTGTTC 60.746 61.111 10.83 0.00 0.00 3.18
41 42 2.746277 GACGGCGCAATCCCTGTT 60.746 61.111 10.83 0.00 0.00 3.16
56 57 4.400961 AGCAGCAAGGAGGGCGAC 62.401 66.667 0.00 0.00 36.08 5.19
57 58 4.399395 CAGCAGCAAGGAGGGCGA 62.399 66.667 0.00 0.00 36.08 5.54
60 61 3.873679 TTGGCAGCAGCAAGGAGGG 62.874 63.158 2.65 0.00 44.61 4.30
61 62 1.255667 ATTTGGCAGCAGCAAGGAGG 61.256 55.000 2.65 0.00 44.61 4.30
62 63 0.606604 AATTTGGCAGCAGCAAGGAG 59.393 50.000 2.65 0.00 44.61 3.69
63 64 0.604578 GAATTTGGCAGCAGCAAGGA 59.395 50.000 2.65 0.00 44.61 3.36
64 65 0.319083 TGAATTTGGCAGCAGCAAGG 59.681 50.000 2.65 0.00 44.61 3.61
65 66 2.157834 TTGAATTTGGCAGCAGCAAG 57.842 45.000 2.65 0.00 44.61 4.01
66 67 2.211806 GTTTGAATTTGGCAGCAGCAA 58.788 42.857 2.65 0.00 44.61 3.91
67 68 1.540797 GGTTTGAATTTGGCAGCAGCA 60.541 47.619 2.65 0.00 44.61 4.41
68 69 1.150827 GGTTTGAATTTGGCAGCAGC 58.849 50.000 0.00 0.00 41.10 5.25
69 70 2.137523 GTGGTTTGAATTTGGCAGCAG 58.862 47.619 0.00 0.00 0.00 4.24
70 71 1.202627 GGTGGTTTGAATTTGGCAGCA 60.203 47.619 0.00 0.00 0.00 4.41
71 72 1.511850 GGTGGTTTGAATTTGGCAGC 58.488 50.000 0.00 0.00 0.00 5.25
72 73 1.693606 AGGGTGGTTTGAATTTGGCAG 59.306 47.619 0.00 0.00 0.00 4.85
73 74 1.691434 GAGGGTGGTTTGAATTTGGCA 59.309 47.619 0.00 0.00 0.00 4.92
74 75 1.336795 CGAGGGTGGTTTGAATTTGGC 60.337 52.381 0.00 0.00 0.00 4.52
75 76 1.960689 ACGAGGGTGGTTTGAATTTGG 59.039 47.619 0.00 0.00 0.00 3.28
76 77 2.621055 TCACGAGGGTGGTTTGAATTTG 59.379 45.455 0.00 0.00 44.50 2.32
77 78 2.938838 TCACGAGGGTGGTTTGAATTT 58.061 42.857 0.00 0.00 44.50 1.82
78 79 2.649531 TCACGAGGGTGGTTTGAATT 57.350 45.000 0.00 0.00 44.50 2.17
79 80 2.158667 ACTTCACGAGGGTGGTTTGAAT 60.159 45.455 0.00 0.00 44.50 2.57
80 81 1.210967 ACTTCACGAGGGTGGTTTGAA 59.789 47.619 0.00 0.00 44.50 2.69
81 82 0.834612 ACTTCACGAGGGTGGTTTGA 59.165 50.000 0.00 0.00 44.50 2.69
82 83 2.036733 TCTACTTCACGAGGGTGGTTTG 59.963 50.000 0.00 0.00 44.50 2.93
83 84 2.322658 TCTACTTCACGAGGGTGGTTT 58.677 47.619 0.00 0.00 44.50 3.27
84 85 2.005370 TCTACTTCACGAGGGTGGTT 57.995 50.000 0.00 0.00 44.50 3.67
85 86 2.005370 TTCTACTTCACGAGGGTGGT 57.995 50.000 0.00 0.00 44.50 4.16
86 87 2.612221 GGTTTCTACTTCACGAGGGTGG 60.612 54.545 0.00 0.00 44.50 4.61
87 88 2.612221 GGGTTTCTACTTCACGAGGGTG 60.612 54.545 0.00 0.00 45.78 4.61
88 89 1.622312 GGGTTTCTACTTCACGAGGGT 59.378 52.381 0.00 0.00 0.00 4.34
89 90 1.900486 AGGGTTTCTACTTCACGAGGG 59.100 52.381 0.00 0.00 0.00 4.30
90 91 4.492611 GTTAGGGTTTCTACTTCACGAGG 58.507 47.826 0.00 0.00 0.00 4.63
91 92 4.492611 GGTTAGGGTTTCTACTTCACGAG 58.507 47.826 0.00 0.00 0.00 4.18
92 93 3.259123 GGGTTAGGGTTTCTACTTCACGA 59.741 47.826 0.00 0.00 0.00 4.35
93 94 3.260128 AGGGTTAGGGTTTCTACTTCACG 59.740 47.826 0.00 0.00 0.00 4.35
94 95 4.904895 AGGGTTAGGGTTTCTACTTCAC 57.095 45.455 0.00 0.00 0.00 3.18
95 96 4.468868 GCTAGGGTTAGGGTTTCTACTTCA 59.531 45.833 0.00 0.00 0.00 3.02
96 97 4.441217 CGCTAGGGTTAGGGTTTCTACTTC 60.441 50.000 0.00 0.00 35.67 3.01
97 98 3.450096 CGCTAGGGTTAGGGTTTCTACTT 59.550 47.826 0.00 0.00 35.67 2.24
98 99 3.029570 CGCTAGGGTTAGGGTTTCTACT 58.970 50.000 0.00 0.00 35.67 2.57
99 100 2.482664 GCGCTAGGGTTAGGGTTTCTAC 60.483 54.545 8.77 0.00 40.82 2.59
100 101 1.758862 GCGCTAGGGTTAGGGTTTCTA 59.241 52.381 8.77 0.00 40.82 2.10
101 102 0.540454 GCGCTAGGGTTAGGGTTTCT 59.460 55.000 8.77 0.00 40.82 2.52
102 103 0.251073 TGCGCTAGGGTTAGGGTTTC 59.749 55.000 9.73 0.00 40.82 2.78
103 104 0.252197 CTGCGCTAGGGTTAGGGTTT 59.748 55.000 9.73 0.00 40.82 3.27
104 105 1.623542 CCTGCGCTAGGGTTAGGGTT 61.624 60.000 9.73 0.00 43.33 4.11
105 106 2.064581 CCTGCGCTAGGGTTAGGGT 61.065 63.158 9.73 0.00 43.33 4.34
106 107 2.822399 CCTGCGCTAGGGTTAGGG 59.178 66.667 9.73 8.80 43.33 3.53
118 119 3.869272 GGCGATTGTGCTCCTGCG 61.869 66.667 0.00 0.00 43.34 5.18
119 120 2.437359 AGGCGATTGTGCTCCTGC 60.437 61.111 0.00 0.00 40.20 4.85
120 121 1.078918 TGAGGCGATTGTGCTCCTG 60.079 57.895 0.00 0.00 34.52 3.86
121 122 1.078848 GTGAGGCGATTGTGCTCCT 60.079 57.895 0.00 0.00 34.52 3.69
122 123 2.456119 CGTGAGGCGATTGTGCTCC 61.456 63.158 0.00 0.00 44.77 4.70
123 124 1.446099 TCGTGAGGCGATTGTGCTC 60.446 57.895 0.00 0.00 45.68 4.26
124 125 2.656646 TCGTGAGGCGATTGTGCT 59.343 55.556 0.00 0.00 45.68 4.40
134 135 2.520982 TAGGGGGCGATCGTGAGG 60.521 66.667 17.81 0.00 0.00 3.86
135 136 2.728817 GTAGGGGGCGATCGTGAG 59.271 66.667 17.81 0.00 0.00 3.51
136 137 2.836360 GGTAGGGGGCGATCGTGA 60.836 66.667 17.81 0.00 0.00 4.35
137 138 4.280494 CGGTAGGGGGCGATCGTG 62.280 72.222 17.81 0.00 0.00 4.35
141 142 3.761690 TAAGGCGGTAGGGGGCGAT 62.762 63.158 0.00 0.00 34.74 4.58
142 143 4.462133 TAAGGCGGTAGGGGGCGA 62.462 66.667 0.00 0.00 34.74 5.54
143 144 3.925090 CTAAGGCGGTAGGGGGCG 61.925 72.222 0.00 0.00 34.74 6.13
144 145 2.767073 ACTAAGGCGGTAGGGGGC 60.767 66.667 3.76 0.00 0.00 5.80
145 146 1.269703 AACACTAAGGCGGTAGGGGG 61.270 60.000 5.65 0.00 0.00 5.40
146 147 0.616891 AAACACTAAGGCGGTAGGGG 59.383 55.000 5.65 0.00 0.00 4.79
147 148 1.406477 GGAAACACTAAGGCGGTAGGG 60.406 57.143 0.00 0.00 0.00 3.53
148 149 1.553704 AGGAAACACTAAGGCGGTAGG 59.446 52.381 3.76 0.00 0.00 3.18
149 150 3.329929 AAGGAAACACTAAGGCGGTAG 57.670 47.619 0.00 0.00 0.00 3.18
150 151 3.367292 CGTAAGGAAACACTAAGGCGGTA 60.367 47.826 0.00 0.00 0.00 4.02
151 152 2.611224 CGTAAGGAAACACTAAGGCGGT 60.611 50.000 0.00 0.00 0.00 5.68
152 153 1.997606 CGTAAGGAAACACTAAGGCGG 59.002 52.381 0.00 0.00 0.00 6.13
153 154 2.410730 CACGTAAGGAAACACTAAGGCG 59.589 50.000 0.00 0.00 46.39 5.52
154 155 2.740447 CCACGTAAGGAAACACTAAGGC 59.260 50.000 0.00 0.00 46.39 4.35
155 156 3.744426 CACCACGTAAGGAAACACTAAGG 59.256 47.826 0.00 0.00 46.39 2.69
156 157 3.744426 CCACCACGTAAGGAAACACTAAG 59.256 47.826 0.00 0.00 46.39 2.18
157 158 3.387374 TCCACCACGTAAGGAAACACTAA 59.613 43.478 0.00 0.00 46.39 2.24
158 159 2.964464 TCCACCACGTAAGGAAACACTA 59.036 45.455 0.00 0.00 46.39 2.74
159 160 1.764134 TCCACCACGTAAGGAAACACT 59.236 47.619 0.00 0.00 46.39 3.55
160 161 1.869132 GTCCACCACGTAAGGAAACAC 59.131 52.381 4.58 0.00 46.39 3.32
161 162 1.202675 GGTCCACCACGTAAGGAAACA 60.203 52.381 4.58 0.00 46.39 2.83
162 163 1.516161 GGTCCACCACGTAAGGAAAC 58.484 55.000 4.58 0.00 46.39 2.78
163 164 0.397564 GGGTCCACCACGTAAGGAAA 59.602 55.000 4.58 0.00 46.39 3.13
164 165 0.472352 AGGGTCCACCACGTAAGGAA 60.472 55.000 4.58 0.00 43.89 3.36
165 166 0.901580 GAGGGTCCACCACGTAAGGA 60.902 60.000 0.00 0.00 43.89 3.36
166 167 1.189524 TGAGGGTCCACCACGTAAGG 61.190 60.000 0.00 0.00 43.89 2.69
167 168 0.682852 TTGAGGGTCCACCACGTAAG 59.317 55.000 0.00 0.00 43.89 2.34
168 169 1.129917 TTTGAGGGTCCACCACGTAA 58.870 50.000 0.00 0.00 43.89 3.18
169 170 1.129917 TTTTGAGGGTCCACCACGTA 58.870 50.000 0.00 0.00 43.89 3.57
170 171 0.476771 ATTTTGAGGGTCCACCACGT 59.523 50.000 0.00 0.00 43.89 4.49
171 172 1.165270 GATTTTGAGGGTCCACCACG 58.835 55.000 0.00 0.00 43.89 4.94
172 173 2.162681 CTGATTTTGAGGGTCCACCAC 58.837 52.381 0.00 0.00 43.89 4.16
173 174 1.075374 CCTGATTTTGAGGGTCCACCA 59.925 52.381 0.00 0.00 43.89 4.17
174 175 1.354368 TCCTGATTTTGAGGGTCCACC 59.646 52.381 0.00 0.00 40.67 4.61
175 176 2.040412 AGTCCTGATTTTGAGGGTCCAC 59.960 50.000 0.00 0.00 0.00 4.02
176 177 2.348472 AGTCCTGATTTTGAGGGTCCA 58.652 47.619 0.00 0.00 0.00 4.02
177 178 3.775316 TCTAGTCCTGATTTTGAGGGTCC 59.225 47.826 0.00 0.00 0.00 4.46
178 179 4.468153 ACTCTAGTCCTGATTTTGAGGGTC 59.532 45.833 0.00 0.00 0.00 4.46
179 180 4.223923 CACTCTAGTCCTGATTTTGAGGGT 59.776 45.833 0.00 0.00 0.00 4.34
180 181 4.764172 CACTCTAGTCCTGATTTTGAGGG 58.236 47.826 0.00 0.00 0.00 4.30
181 182 4.081198 AGCACTCTAGTCCTGATTTTGAGG 60.081 45.833 0.00 0.00 0.00 3.86
182 183 5.083533 AGCACTCTAGTCCTGATTTTGAG 57.916 43.478 0.00 0.00 0.00 3.02
183 184 5.482908 GAAGCACTCTAGTCCTGATTTTGA 58.517 41.667 0.00 0.00 0.00 2.69
184 185 4.328440 CGAAGCACTCTAGTCCTGATTTTG 59.672 45.833 0.00 0.00 0.00 2.44
211 212 6.038825 TCCAAATGATAAGTGACAAACGTGTT 59.961 34.615 0.00 0.00 38.41 3.32
241 243 8.576442 CCTCTGCTAATCTGGTTTTTCTTTTTA 58.424 33.333 0.00 0.00 0.00 1.52
242 244 7.436933 CCTCTGCTAATCTGGTTTTTCTTTTT 58.563 34.615 0.00 0.00 0.00 1.94
254 256 1.070445 CCGGCCCTCTGCTAATCTG 59.930 63.158 0.00 0.00 40.92 2.90
267 269 4.128388 CGATTTGGGTTGCCGGCC 62.128 66.667 26.77 9.46 0.00 6.13
367 369 0.107214 GGGCACTCGAATTCCATCCA 60.107 55.000 0.00 0.00 0.00 3.41
368 370 1.160329 CGGGCACTCGAATTCCATCC 61.160 60.000 0.00 0.00 0.00 3.51
369 371 0.179084 TCGGGCACTCGAATTCCATC 60.179 55.000 0.00 0.00 36.12 3.51
370 372 0.469917 ATCGGGCACTCGAATTCCAT 59.530 50.000 0.00 0.00 42.69 3.41
397 399 0.035343 CGTCTCCTTTCCTTTCCCCC 60.035 60.000 0.00 0.00 0.00 5.40
1017 1026 1.579932 GACGTCGTCCTGCTTGAGA 59.420 57.895 14.60 0.00 0.00 3.27
1338 1347 2.360350 ATCTTGTGGCGGCACTGG 60.360 61.111 37.33 28.74 0.00 4.00
1491 1500 1.063417 CCCCTGGGCTTGATCTTGATT 60.063 52.381 7.39 0.00 0.00 2.57
1830 1839 1.220206 CTGGGTGCGCTTCATCTCT 59.780 57.895 9.73 0.00 0.00 3.10
1870 1879 1.800713 GGAACGCCTCGACGAAGAC 60.801 63.158 0.00 0.00 36.70 3.01
2051 2066 5.641209 AGTAGAAACATCACAAGTCATCAGC 59.359 40.000 0.00 0.00 0.00 4.26
2082 2097 7.925483 CACTTCTTAAATCAACCATCCAAACAA 59.075 33.333 0.00 0.00 0.00 2.83
2336 2368 7.856145 AACAAATTATCCATGAGTGAGAGAC 57.144 36.000 0.00 0.00 0.00 3.36
2340 2372 8.681486 TCCATAACAAATTATCCATGAGTGAG 57.319 34.615 0.00 0.00 0.00 3.51
2352 2384 4.100808 GCAAGGGCCATCCATAACAAATTA 59.899 41.667 6.18 0.00 38.24 1.40
2354 2386 2.435437 GCAAGGGCCATCCATAACAAAT 59.565 45.455 6.18 0.00 38.24 2.32
2377 2409 5.147330 TCACAGTACCCAGTTGATAGTTG 57.853 43.478 0.00 0.00 0.00 3.16
2655 2699 7.725844 AGGTCAAGGTTGAGAAGAACAAATATT 59.274 33.333 0.00 0.00 37.98 1.28
2772 2834 8.659925 ATCATACACAAGATGAAGCTTCTAAG 57.340 34.615 26.09 13.94 36.90 2.18
2852 2914 2.623889 CCTCAAGTCCGGTACATAGGAG 59.376 54.545 0.00 0.94 37.18 3.69
2860 2922 0.613853 CACCCTCCTCAAGTCCGGTA 60.614 60.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.