Multiple sequence alignment - TraesCS5D01G456300

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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 TraesCS5D01G456300 chr5D 100.000 2525 0 0 1 2525 503208843 503211367 0.000000e+00 4663
1 TraesCS5D01G456300 chr5D 99.254 2280 16 1 246 2525 560875649 560877927 0.000000e+00 4115
2 TraesCS5D01G456300 chr5D 98.246 2281 37 3 246 2525 329193132 329195410 0.000000e+00 3988
3 TraesCS5D01G456300 chr5D 99.222 257 0 1 1 255 6197853 6197597 1.770000e-126 462
4 TraesCS5D01G456300 chr5D 99.600 250 1 0 1 250 503209359 503209608 8.230000e-125 457
5 TraesCS5D01G456300 chr5D 99.200 250 2 0 1 250 560875920 560876169 3.830000e-123 451
6 TraesCS5D01G456300 chr3B 99.034 2277 19 2 246 2522 201517858 201520131 0.000000e+00 4080
7 TraesCS5D01G456300 chr3B 99.600 250 1 0 1 250 201518129 201518378 8.230000e-125 457
8 TraesCS5D01G456300 chr3B 89.035 228 12 6 1784 1998 825409119 825408892 1.150000e-68 270
9 TraesCS5D01G456300 chr3B 97.297 111 3 0 1984 2094 47547333 47547223 3.320000e-44 189
10 TraesCS5D01G456300 chr3B 100.000 96 0 0 1965 2060 303758671 303758766 7.180000e-41 178
11 TraesCS5D01G456300 chr4D 97.588 2280 49 4 246 2525 19919668 19921941 0.000000e+00 3901
12 TraesCS5D01G456300 chr6A 97.500 2280 50 2 246 2525 260129592 260127320 0.000000e+00 3888
13 TraesCS5D01G456300 chr7A 94.781 2280 89 7 246 2525 352190852 352188603 0.000000e+00 3524
14 TraesCS5D01G456300 chrUn 99.359 1715 11 0 811 2525 93420604 93418890 0.000000e+00 3107
15 TraesCS5D01G456300 chrUn 99.325 1630 10 1 487 2116 383641864 383640236 0.000000e+00 2948
16 TraesCS5D01G456300 chrUn 99.222 257 0 1 1 255 383641834 383641578 1.770000e-126 462
17 TraesCS5D01G456300 chrUn 98.833 257 1 1 1 255 93421413 93421157 8.230000e-125 457
18 TraesCS5D01G456300 chr5A 97.132 1604 44 2 246 1848 283489599 283487997 0.000000e+00 2706
19 TraesCS5D01G456300 chr1D 99.222 257 0 1 1 255 206073913 206073657 1.770000e-126 462
20 TraesCS5D01G456300 chr1D 99.600 250 1 0 1 250 254501449 254501698 8.230000e-125 457
21 TraesCS5D01G456300 chr7B 98.444 257 2 1 1 255 102630196 102629940 3.830000e-123 451


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 TraesCS5D01G456300 chr5D 503208843 503211367 2524 False 2560.0 4663 99.8000 1 2525 2 chr5D.!!$F2 2524
1 TraesCS5D01G456300 chr5D 329193132 329195410 2278 False 3988.0 3988 98.2460 246 2525 1 chr5D.!!$F1 2279
2 TraesCS5D01G456300 chr5D 560875649 560877927 2278 False 2283.0 4115 99.2270 1 2525 2 chr5D.!!$F3 2524
3 TraesCS5D01G456300 chr3B 201517858 201520131 2273 False 2268.5 4080 99.3170 1 2522 2 chr3B.!!$F2 2521
4 TraesCS5D01G456300 chr4D 19919668 19921941 2273 False 3901.0 3901 97.5880 246 2525 1 chr4D.!!$F1 2279
5 TraesCS5D01G456300 chr6A 260127320 260129592 2272 True 3888.0 3888 97.5000 246 2525 1 chr6A.!!$R1 2279
6 TraesCS5D01G456300 chr7A 352188603 352190852 2249 True 3524.0 3524 94.7810 246 2525 1 chr7A.!!$R1 2279
7 TraesCS5D01G456300 chrUn 93418890 93421413 2523 True 1782.0 3107 99.0960 1 2525 2 chrUn.!!$R1 2524
8 TraesCS5D01G456300 chrUn 383640236 383641864 1628 True 1705.0 2948 99.2735 1 2116 2 chrUn.!!$R2 2115
9 TraesCS5D01G456300 chr5A 283487997 283489599 1602 True 2706.0 2706 97.1320 246 1848 1 chr5A.!!$R1 1602

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
99 100 0.461693 TGCATCGATTGTGATCCGCA 60.462 50.0 0.0 0.00 0.00 5.69 F
100 101 0.657312 GCATCGATTGTGATCCGCAA 59.343 50.0 0.0 2.88 38.24 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1256 1258 5.031066 CCACTCGGGTAATATTTCCAGAA 57.969 43.478 13.39 1.2 0.0 3.02 R
1711 2235 5.957842 ACTCTCGTTTTAAATCCATTGCA 57.042 34.783 0.00 0.0 0.0 4.08 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
25 26 4.871993 GTCATGTGACATGATCCAGTTC 57.128 45.455 28.59 12.12 44.18 3.01
26 27 4.511527 GTCATGTGACATGATCCAGTTCT 58.488 43.478 28.59 0.00 44.18 3.01
27 28 4.569966 GTCATGTGACATGATCCAGTTCTC 59.430 45.833 28.59 10.77 44.18 2.87
28 29 4.468868 TCATGTGACATGATCCAGTTCTCT 59.531 41.667 23.25 0.00 0.00 3.10
29 30 5.658190 TCATGTGACATGATCCAGTTCTCTA 59.342 40.000 23.25 0.00 0.00 2.43
30 31 6.325804 TCATGTGACATGATCCAGTTCTCTAT 59.674 38.462 23.25 0.00 0.00 1.98
31 32 6.550938 TGTGACATGATCCAGTTCTCTATT 57.449 37.500 0.00 0.00 0.00 1.73
32 33 6.950842 TGTGACATGATCCAGTTCTCTATTT 58.049 36.000 0.00 0.00 0.00 1.40
33 34 8.078060 TGTGACATGATCCAGTTCTCTATTTA 57.922 34.615 0.00 0.00 0.00 1.40
34 35 8.708378 TGTGACATGATCCAGTTCTCTATTTAT 58.292 33.333 0.00 0.00 0.00 1.40
35 36 9.553064 GTGACATGATCCAGTTCTCTATTTATT 57.447 33.333 0.00 0.00 0.00 1.40
87 88 4.807443 TGCATTCATTTTCTTTGCATCGA 58.193 34.783 0.00 0.00 38.32 3.59
88 89 5.412640 TGCATTCATTTTCTTTGCATCGAT 58.587 33.333 0.00 0.00 38.32 3.59
89 90 5.870433 TGCATTCATTTTCTTTGCATCGATT 59.130 32.000 0.00 0.00 38.32 3.34
90 91 6.182634 GCATTCATTTTCTTTGCATCGATTG 58.817 36.000 0.00 0.00 33.58 2.67
91 92 6.183360 GCATTCATTTTCTTTGCATCGATTGT 60.183 34.615 0.00 0.00 33.58 2.71
92 93 6.693761 TTCATTTTCTTTGCATCGATTGTG 57.306 33.333 0.00 0.00 0.00 3.33
93 94 6.011476 TCATTTTCTTTGCATCGATTGTGA 57.989 33.333 0.00 0.00 0.00 3.58
94 95 6.623486 TCATTTTCTTTGCATCGATTGTGAT 58.377 32.000 0.00 0.00 0.00 3.06
95 96 6.748658 TCATTTTCTTTGCATCGATTGTGATC 59.251 34.615 0.00 0.00 0.00 2.92
96 97 4.621068 TTCTTTGCATCGATTGTGATCC 57.379 40.909 0.00 0.00 0.00 3.36
97 98 2.609002 TCTTTGCATCGATTGTGATCCG 59.391 45.455 0.00 0.00 0.00 4.18
98 99 0.657312 TTGCATCGATTGTGATCCGC 59.343 50.000 0.00 0.00 0.00 5.54
99 100 0.461693 TGCATCGATTGTGATCCGCA 60.462 50.000 0.00 0.00 0.00 5.69
100 101 0.657312 GCATCGATTGTGATCCGCAA 59.343 50.000 0.00 2.88 38.24 4.85
101 102 1.265095 GCATCGATTGTGATCCGCAAT 59.735 47.619 11.03 11.03 45.53 3.56
102 103 2.480037 GCATCGATTGTGATCCGCAATA 59.520 45.455 11.15 0.67 43.36 1.90
103 104 3.665323 GCATCGATTGTGATCCGCAATAC 60.665 47.826 11.15 6.23 43.36 1.89
104 105 3.452755 TCGATTGTGATCCGCAATACT 57.547 42.857 11.15 0.00 43.36 2.12
105 106 4.577834 TCGATTGTGATCCGCAATACTA 57.422 40.909 11.15 0.84 43.36 1.82
106 107 5.134202 TCGATTGTGATCCGCAATACTAT 57.866 39.130 11.15 0.00 43.36 2.12
107 108 5.161358 TCGATTGTGATCCGCAATACTATC 58.839 41.667 11.15 3.71 43.36 2.08
108 109 4.030641 CGATTGTGATCCGCAATACTATCG 59.969 45.833 11.15 10.36 43.36 2.92
109 110 3.297830 TGTGATCCGCAATACTATCGG 57.702 47.619 0.00 0.00 44.16 4.18
116 117 5.518848 TCCGCAATACTATCGGAGTAAAA 57.481 39.130 0.00 0.00 46.12 1.52
117 118 5.526115 TCCGCAATACTATCGGAGTAAAAG 58.474 41.667 0.00 0.00 46.12 2.27
118 119 5.300034 TCCGCAATACTATCGGAGTAAAAGA 59.700 40.000 0.00 0.00 46.12 2.52
119 120 5.981315 CCGCAATACTATCGGAGTAAAAGAA 59.019 40.000 2.78 0.00 43.96 2.52
120 121 6.144080 CCGCAATACTATCGGAGTAAAAGAAG 59.856 42.308 2.78 0.00 43.96 2.85
121 122 6.144080 CGCAATACTATCGGAGTAAAAGAAGG 59.856 42.308 2.78 0.00 43.96 3.46
122 123 6.424207 GCAATACTATCGGAGTAAAAGAAGGG 59.576 42.308 2.78 0.00 43.96 3.95
123 124 7.686127 GCAATACTATCGGAGTAAAAGAAGGGA 60.686 40.741 2.78 0.00 43.96 4.20
124 125 8.368668 CAATACTATCGGAGTAAAAGAAGGGAT 58.631 37.037 2.78 0.00 43.96 3.85
125 126 6.408107 ACTATCGGAGTAAAAGAAGGGATC 57.592 41.667 0.00 0.00 36.27 3.36
126 127 6.137559 ACTATCGGAGTAAAAGAAGGGATCT 58.862 40.000 0.00 0.00 36.85 2.75
127 128 7.296098 ACTATCGGAGTAAAAGAAGGGATCTA 58.704 38.462 0.00 0.00 34.94 1.98
128 129 7.783596 ACTATCGGAGTAAAAGAAGGGATCTAA 59.216 37.037 0.00 0.00 34.94 2.10
129 130 6.466885 TCGGAGTAAAAGAAGGGATCTAAG 57.533 41.667 0.00 0.00 37.42 2.18
130 131 5.363005 TCGGAGTAAAAGAAGGGATCTAAGG 59.637 44.000 0.00 0.00 37.42 2.69
131 132 5.363005 CGGAGTAAAAGAAGGGATCTAAGGA 59.637 44.000 0.00 0.00 37.42 3.36
132 133 6.127140 CGGAGTAAAAGAAGGGATCTAAGGAA 60.127 42.308 0.00 0.00 37.42 3.36
133 134 7.276658 GGAGTAAAAGAAGGGATCTAAGGAAG 58.723 42.308 0.00 0.00 37.42 3.46
134 135 7.125963 GGAGTAAAAGAAGGGATCTAAGGAAGA 59.874 40.741 0.00 0.00 37.42 2.87
135 136 8.450780 AGTAAAAGAAGGGATCTAAGGAAGAA 57.549 34.615 0.00 0.00 37.42 2.52
136 137 9.063484 AGTAAAAGAAGGGATCTAAGGAAGAAT 57.937 33.333 0.00 0.00 37.42 2.40
137 138 9.114952 GTAAAAGAAGGGATCTAAGGAAGAATG 57.885 37.037 0.00 0.00 37.42 2.67
138 139 6.899892 AAGAAGGGATCTAAGGAAGAATGT 57.100 37.500 0.00 0.00 37.42 2.71
139 140 7.996758 AAGAAGGGATCTAAGGAAGAATGTA 57.003 36.000 0.00 0.00 37.42 2.29
140 141 7.610580 AGAAGGGATCTAAGGAAGAATGTAG 57.389 40.000 0.00 0.00 37.89 2.74
141 142 6.556874 AGAAGGGATCTAAGGAAGAATGTAGG 59.443 42.308 0.00 0.00 37.89 3.18
142 143 4.595350 AGGGATCTAAGGAAGAATGTAGGC 59.405 45.833 0.00 0.00 37.89 3.93
143 144 4.595350 GGGATCTAAGGAAGAATGTAGGCT 59.405 45.833 0.00 0.00 37.89 4.58
144 145 5.780793 GGGATCTAAGGAAGAATGTAGGCTA 59.219 44.000 0.00 0.00 37.89 3.93
145 146 6.270231 GGGATCTAAGGAAGAATGTAGGCTAA 59.730 42.308 0.00 0.00 37.89 3.09
146 147 7.202102 GGGATCTAAGGAAGAATGTAGGCTAAA 60.202 40.741 0.00 0.00 37.89 1.85
147 148 7.658167 GGATCTAAGGAAGAATGTAGGCTAAAC 59.342 40.741 0.00 0.00 37.89 2.01
148 149 7.735326 TCTAAGGAAGAATGTAGGCTAAACT 57.265 36.000 0.00 0.00 0.00 2.66
149 150 8.147244 TCTAAGGAAGAATGTAGGCTAAACTT 57.853 34.615 0.00 0.00 0.00 2.66
150 151 8.603304 TCTAAGGAAGAATGTAGGCTAAACTTT 58.397 33.333 0.00 0.00 0.00 2.66
151 152 9.232473 CTAAGGAAGAATGTAGGCTAAACTTTT 57.768 33.333 0.00 0.00 0.00 2.27
152 153 8.478775 AAGGAAGAATGTAGGCTAAACTTTTT 57.521 30.769 0.00 0.00 0.00 1.94
153 154 7.886338 AGGAAGAATGTAGGCTAAACTTTTTG 58.114 34.615 0.00 0.00 0.00 2.44
154 155 7.724061 AGGAAGAATGTAGGCTAAACTTTTTGA 59.276 33.333 0.00 0.00 0.00 2.69
155 156 8.523658 GGAAGAATGTAGGCTAAACTTTTTGAT 58.476 33.333 0.00 0.00 0.00 2.57
156 157 9.914131 GAAGAATGTAGGCTAAACTTTTTGATT 57.086 29.630 0.00 0.00 0.00 2.57
202 203 9.981114 ATATTTTGTTTGGAGGTAAGAAACTTG 57.019 29.630 0.00 0.00 32.01 3.16
203 204 4.911514 TGTTTGGAGGTAAGAAACTTGC 57.088 40.909 0.00 0.00 32.01 4.01
204 205 3.314080 TGTTTGGAGGTAAGAAACTTGCG 59.686 43.478 0.00 0.00 32.01 4.85
205 206 3.478857 TTGGAGGTAAGAAACTTGCGA 57.521 42.857 0.00 0.00 0.00 5.10
206 207 3.695830 TGGAGGTAAGAAACTTGCGAT 57.304 42.857 0.00 0.00 0.00 4.58
207 208 4.811969 TGGAGGTAAGAAACTTGCGATA 57.188 40.909 0.00 0.00 0.00 2.92
208 209 5.353394 TGGAGGTAAGAAACTTGCGATAT 57.647 39.130 0.00 0.00 0.00 1.63
209 210 5.741011 TGGAGGTAAGAAACTTGCGATATT 58.259 37.500 0.00 0.00 0.00 1.28
210 211 5.584649 TGGAGGTAAGAAACTTGCGATATTG 59.415 40.000 0.00 0.00 0.00 1.90
211 212 5.815740 GGAGGTAAGAAACTTGCGATATTGA 59.184 40.000 0.00 0.00 0.00 2.57
212 213 6.018669 GGAGGTAAGAAACTTGCGATATTGAG 60.019 42.308 0.00 0.00 0.00 3.02
213 214 5.817816 AGGTAAGAAACTTGCGATATTGAGG 59.182 40.000 0.00 0.00 0.00 3.86
214 215 5.007724 GGTAAGAAACTTGCGATATTGAGGG 59.992 44.000 0.00 0.00 0.00 4.30
215 216 3.545703 AGAAACTTGCGATATTGAGGGG 58.454 45.455 0.00 0.00 0.00 4.79
216 217 3.199946 AGAAACTTGCGATATTGAGGGGA 59.800 43.478 0.00 0.00 0.00 4.81
217 218 3.864789 AACTTGCGATATTGAGGGGAT 57.135 42.857 0.00 0.00 0.00 3.85
218 219 4.974645 AACTTGCGATATTGAGGGGATA 57.025 40.909 0.00 0.00 0.00 2.59
219 220 4.974645 ACTTGCGATATTGAGGGGATAA 57.025 40.909 0.00 0.00 0.00 1.75
220 221 5.304686 ACTTGCGATATTGAGGGGATAAA 57.695 39.130 0.00 0.00 0.00 1.40
221 222 5.880901 ACTTGCGATATTGAGGGGATAAAT 58.119 37.500 0.00 0.00 0.00 1.40
222 223 7.016153 ACTTGCGATATTGAGGGGATAAATA 57.984 36.000 0.00 0.00 0.00 1.40
223 224 6.879458 ACTTGCGATATTGAGGGGATAAATAC 59.121 38.462 0.00 0.00 0.00 1.89
224 225 5.741011 TGCGATATTGAGGGGATAAATACC 58.259 41.667 0.00 0.00 0.00 2.73
225 226 5.249622 TGCGATATTGAGGGGATAAATACCA 59.750 40.000 0.00 0.00 29.87 3.25
226 227 6.177610 GCGATATTGAGGGGATAAATACCAA 58.822 40.000 0.00 0.00 29.87 3.67
227 228 6.093633 GCGATATTGAGGGGATAAATACCAAC 59.906 42.308 0.00 0.00 29.87 3.77
228 229 7.394816 CGATATTGAGGGGATAAATACCAACT 58.605 38.462 0.00 0.00 29.87 3.16
229 230 8.537016 CGATATTGAGGGGATAAATACCAACTA 58.463 37.037 0.00 0.00 29.87 2.24
233 234 7.699709 TGAGGGGATAAATACCAACTAATCA 57.300 36.000 0.00 0.00 29.87 2.57
234 235 8.108378 TGAGGGGATAAATACCAACTAATCAA 57.892 34.615 0.00 0.00 29.87 2.57
235 236 8.217799 TGAGGGGATAAATACCAACTAATCAAG 58.782 37.037 0.00 0.00 29.87 3.02
236 237 8.344939 AGGGGATAAATACCAACTAATCAAGA 57.655 34.615 0.00 0.00 29.87 3.02
237 238 8.440771 AGGGGATAAATACCAACTAATCAAGAG 58.559 37.037 0.00 0.00 29.87 2.85
238 239 8.437575 GGGGATAAATACCAACTAATCAAGAGA 58.562 37.037 0.00 0.00 29.87 3.10
239 240 9.274206 GGGATAAATACCAACTAATCAAGAGAC 57.726 37.037 0.00 0.00 0.00 3.36
240 241 9.832445 GGATAAATACCAACTAATCAAGAGACA 57.168 33.333 0.00 0.00 0.00 3.41
244 245 8.954950 AATACCAACTAATCAAGAGACATGAG 57.045 34.615 0.00 0.00 0.00 2.90
1147 1149 2.203139 CCGCATGGCCCAACGATA 60.203 61.111 10.76 0.00 0.00 2.92
1256 1258 1.160137 GCAGATCCGTTTGCAACTCT 58.840 50.000 0.00 0.00 40.02 3.24
1568 2087 5.767168 ACCGTGAAGTACCATAGGTATCTAC 59.233 44.000 0.00 0.00 40.54 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.468868 AGAGAACTGGATCATGTCACATGA 59.531 41.667 22.76 22.76 0.00 3.07
6 7 4.767478 AGAGAACTGGATCATGTCACATG 58.233 43.478 11.96 11.96 0.00 3.21
7 8 6.744175 ATAGAGAACTGGATCATGTCACAT 57.256 37.500 0.00 0.00 0.00 3.21
8 9 6.550938 AATAGAGAACTGGATCATGTCACA 57.449 37.500 0.00 0.00 0.00 3.58
9 10 9.553064 AATAAATAGAGAACTGGATCATGTCAC 57.447 33.333 0.00 0.00 0.00 3.67
66 67 5.961395 ATCGATGCAAAGAAAATGAATGC 57.039 34.783 0.00 0.00 37.52 3.56
67 68 7.062488 TCACAATCGATGCAAAGAAAATGAATG 59.938 33.333 0.00 0.00 0.00 2.67
68 69 7.092079 TCACAATCGATGCAAAGAAAATGAAT 58.908 30.769 0.00 0.00 0.00 2.57
69 70 6.445475 TCACAATCGATGCAAAGAAAATGAA 58.555 32.000 0.00 0.00 0.00 2.57
70 71 6.011476 TCACAATCGATGCAAAGAAAATGA 57.989 33.333 0.00 0.00 0.00 2.57
71 72 6.020121 GGATCACAATCGATGCAAAGAAAATG 60.020 38.462 0.00 0.00 34.17 2.32
72 73 6.038356 GGATCACAATCGATGCAAAGAAAAT 58.962 36.000 0.00 0.00 34.17 1.82
73 74 5.401550 GGATCACAATCGATGCAAAGAAAA 58.598 37.500 0.00 0.00 34.17 2.29
74 75 4.437255 CGGATCACAATCGATGCAAAGAAA 60.437 41.667 0.00 0.00 33.65 2.52
75 76 3.063861 CGGATCACAATCGATGCAAAGAA 59.936 43.478 0.00 0.00 33.65 2.52
76 77 2.609002 CGGATCACAATCGATGCAAAGA 59.391 45.455 0.00 0.00 33.65 2.52
77 78 2.852143 GCGGATCACAATCGATGCAAAG 60.852 50.000 0.00 0.00 33.65 2.77
78 79 1.063912 GCGGATCACAATCGATGCAAA 59.936 47.619 0.00 0.00 33.65 3.68
79 80 0.657312 GCGGATCACAATCGATGCAA 59.343 50.000 0.00 0.00 33.65 4.08
80 81 0.461693 TGCGGATCACAATCGATGCA 60.462 50.000 0.00 0.00 33.65 3.96
81 82 0.657312 TTGCGGATCACAATCGATGC 59.343 50.000 0.00 0.00 32.24 3.91
82 83 3.742882 AGTATTGCGGATCACAATCGATG 59.257 43.478 14.45 0.00 38.62 3.84
83 84 3.995199 AGTATTGCGGATCACAATCGAT 58.005 40.909 14.45 0.00 38.62 3.59
84 85 3.452755 AGTATTGCGGATCACAATCGA 57.547 42.857 14.45 0.00 38.62 3.59
85 86 4.030641 CGATAGTATTGCGGATCACAATCG 59.969 45.833 14.45 10.06 38.62 3.34
86 87 5.441700 CGATAGTATTGCGGATCACAATC 57.558 43.478 14.45 8.42 38.62 2.67
95 96 5.526115 TCTTTTACTCCGATAGTATTGCGG 58.474 41.667 4.30 4.30 46.08 5.69
96 97 6.144080 CCTTCTTTTACTCCGATAGTATTGCG 59.856 42.308 0.00 0.00 40.41 4.85
97 98 6.424207 CCCTTCTTTTACTCCGATAGTATTGC 59.576 42.308 0.00 0.00 40.41 3.56
98 99 7.723324 TCCCTTCTTTTACTCCGATAGTATTG 58.277 38.462 0.00 0.00 40.41 1.90
99 100 7.909485 TCCCTTCTTTTACTCCGATAGTATT 57.091 36.000 0.00 0.00 40.41 1.89
100 101 7.951245 AGATCCCTTCTTTTACTCCGATAGTAT 59.049 37.037 0.00 0.00 40.41 2.12
101 102 7.296098 AGATCCCTTCTTTTACTCCGATAGTA 58.704 38.462 0.00 0.00 39.80 1.82
102 103 6.137559 AGATCCCTTCTTTTACTCCGATAGT 58.862 40.000 0.00 0.00 42.62 2.12
103 104 6.658188 AGATCCCTTCTTTTACTCCGATAG 57.342 41.667 0.00 0.00 0.00 2.08
104 105 7.232941 CCTTAGATCCCTTCTTTTACTCCGATA 59.767 40.741 0.00 0.00 35.79 2.92
105 106 6.042208 CCTTAGATCCCTTCTTTTACTCCGAT 59.958 42.308 0.00 0.00 35.79 4.18
106 107 5.363005 CCTTAGATCCCTTCTTTTACTCCGA 59.637 44.000 0.00 0.00 35.79 4.55
107 108 5.363005 TCCTTAGATCCCTTCTTTTACTCCG 59.637 44.000 0.00 0.00 35.79 4.63
108 109 6.809976 TCCTTAGATCCCTTCTTTTACTCC 57.190 41.667 0.00 0.00 35.79 3.85
109 110 8.080363 TCTTCCTTAGATCCCTTCTTTTACTC 57.920 38.462 0.00 0.00 35.79 2.59
110 111 8.450780 TTCTTCCTTAGATCCCTTCTTTTACT 57.549 34.615 0.00 0.00 35.79 2.24
111 112 9.114952 CATTCTTCCTTAGATCCCTTCTTTTAC 57.885 37.037 0.00 0.00 35.79 2.01
112 113 8.836735 ACATTCTTCCTTAGATCCCTTCTTTTA 58.163 33.333 0.00 0.00 35.79 1.52
113 114 7.703755 ACATTCTTCCTTAGATCCCTTCTTTT 58.296 34.615 0.00 0.00 35.79 2.27
114 115 7.277405 ACATTCTTCCTTAGATCCCTTCTTT 57.723 36.000 0.00 0.00 35.79 2.52
115 116 6.899892 ACATTCTTCCTTAGATCCCTTCTT 57.100 37.500 0.00 0.00 35.79 2.52
116 117 6.556874 CCTACATTCTTCCTTAGATCCCTTCT 59.443 42.308 0.00 0.00 38.57 2.85
117 118 6.742926 GCCTACATTCTTCCTTAGATCCCTTC 60.743 46.154 0.00 0.00 31.54 3.46
118 119 5.072464 GCCTACATTCTTCCTTAGATCCCTT 59.928 44.000 0.00 0.00 31.54 3.95
119 120 4.595350 GCCTACATTCTTCCTTAGATCCCT 59.405 45.833 0.00 0.00 31.54 4.20
120 121 4.595350 AGCCTACATTCTTCCTTAGATCCC 59.405 45.833 0.00 0.00 31.54 3.85
121 122 5.816955 AGCCTACATTCTTCCTTAGATCC 57.183 43.478 0.00 0.00 31.54 3.36
122 123 8.425703 AGTTTAGCCTACATTCTTCCTTAGATC 58.574 37.037 0.00 0.00 31.54 2.75
123 124 8.325477 AGTTTAGCCTACATTCTTCCTTAGAT 57.675 34.615 0.00 0.00 31.54 1.98
124 125 7.735326 AGTTTAGCCTACATTCTTCCTTAGA 57.265 36.000 0.00 0.00 0.00 2.10
125 126 8.794335 AAAGTTTAGCCTACATTCTTCCTTAG 57.206 34.615 0.00 0.00 0.00 2.18
126 127 9.582648 AAAAAGTTTAGCCTACATTCTTCCTTA 57.417 29.630 0.00 0.00 0.00 2.69
127 128 8.360390 CAAAAAGTTTAGCCTACATTCTTCCTT 58.640 33.333 0.00 0.00 0.00 3.36
128 129 7.724061 TCAAAAAGTTTAGCCTACATTCTTCCT 59.276 33.333 0.00 0.00 0.00 3.36
129 130 7.882179 TCAAAAAGTTTAGCCTACATTCTTCC 58.118 34.615 0.00 0.00 0.00 3.46
130 131 9.914131 AATCAAAAAGTTTAGCCTACATTCTTC 57.086 29.630 0.00 0.00 0.00 2.87
176 177 9.981114 CAAGTTTCTTACCTCCAAACAAAATAT 57.019 29.630 0.00 0.00 33.26 1.28
177 178 7.923878 GCAAGTTTCTTACCTCCAAACAAAATA 59.076 33.333 0.00 0.00 33.26 1.40
178 179 6.761242 GCAAGTTTCTTACCTCCAAACAAAAT 59.239 34.615 0.00 0.00 33.26 1.82
179 180 6.103330 GCAAGTTTCTTACCTCCAAACAAAA 58.897 36.000 0.00 0.00 33.26 2.44
180 181 5.656480 GCAAGTTTCTTACCTCCAAACAAA 58.344 37.500 0.00 0.00 33.26 2.83
181 182 4.201970 CGCAAGTTTCTTACCTCCAAACAA 60.202 41.667 0.00 0.00 33.26 2.83
182 183 3.314080 CGCAAGTTTCTTACCTCCAAACA 59.686 43.478 0.00 0.00 33.26 2.83
183 184 3.562557 TCGCAAGTTTCTTACCTCCAAAC 59.437 43.478 0.00 0.00 39.48 2.93
184 185 3.811083 TCGCAAGTTTCTTACCTCCAAA 58.189 40.909 0.00 0.00 39.48 3.28
185 186 3.478857 TCGCAAGTTTCTTACCTCCAA 57.521 42.857 0.00 0.00 39.48 3.53
186 187 3.695830 ATCGCAAGTTTCTTACCTCCA 57.304 42.857 0.00 0.00 39.48 3.86
187 188 5.815740 TCAATATCGCAAGTTTCTTACCTCC 59.184 40.000 0.00 0.00 39.48 4.30
188 189 6.018669 CCTCAATATCGCAAGTTTCTTACCTC 60.019 42.308 0.00 0.00 39.48 3.85
189 190 5.817816 CCTCAATATCGCAAGTTTCTTACCT 59.182 40.000 0.00 0.00 39.48 3.08
190 191 5.007724 CCCTCAATATCGCAAGTTTCTTACC 59.992 44.000 0.00 0.00 39.48 2.85
191 192 5.007724 CCCCTCAATATCGCAAGTTTCTTAC 59.992 44.000 0.00 0.00 39.48 2.34
192 193 5.104693 TCCCCTCAATATCGCAAGTTTCTTA 60.105 40.000 0.00 0.00 39.48 2.10
193 194 3.947834 CCCCTCAATATCGCAAGTTTCTT 59.052 43.478 0.00 0.00 39.48 2.52
194 195 3.199946 TCCCCTCAATATCGCAAGTTTCT 59.800 43.478 0.00 0.00 39.48 2.52
195 196 3.541632 TCCCCTCAATATCGCAAGTTTC 58.458 45.455 0.00 0.00 39.48 2.78
196 197 3.644966 TCCCCTCAATATCGCAAGTTT 57.355 42.857 0.00 0.00 39.48 2.66
197 198 3.864789 ATCCCCTCAATATCGCAAGTT 57.135 42.857 0.00 0.00 39.48 2.66
198 199 4.974645 TTATCCCCTCAATATCGCAAGT 57.025 40.909 0.00 0.00 39.48 3.16
199 200 6.316390 GGTATTTATCCCCTCAATATCGCAAG 59.684 42.308 0.00 0.00 0.00 4.01
200 201 6.177610 GGTATTTATCCCCTCAATATCGCAA 58.822 40.000 0.00 0.00 0.00 4.85
201 202 5.249622 TGGTATTTATCCCCTCAATATCGCA 59.750 40.000 0.00 0.00 0.00 5.10
202 203 5.741011 TGGTATTTATCCCCTCAATATCGC 58.259 41.667 0.00 0.00 0.00 4.58
203 204 7.394816 AGTTGGTATTTATCCCCTCAATATCG 58.605 38.462 0.00 0.00 0.00 2.92
207 208 8.732854 TGATTAGTTGGTATTTATCCCCTCAAT 58.267 33.333 0.00 0.00 0.00 2.57
208 209 8.108378 TGATTAGTTGGTATTTATCCCCTCAA 57.892 34.615 0.00 0.00 0.00 3.02
209 210 7.699709 TGATTAGTTGGTATTTATCCCCTCA 57.300 36.000 0.00 0.00 0.00 3.86
210 211 8.437575 TCTTGATTAGTTGGTATTTATCCCCTC 58.562 37.037 0.00 0.00 0.00 4.30
211 212 8.344939 TCTTGATTAGTTGGTATTTATCCCCT 57.655 34.615 0.00 0.00 0.00 4.79
212 213 8.437575 TCTCTTGATTAGTTGGTATTTATCCCC 58.562 37.037 0.00 0.00 0.00 4.81
213 214 9.274206 GTCTCTTGATTAGTTGGTATTTATCCC 57.726 37.037 0.00 0.00 0.00 3.85
214 215 9.832445 TGTCTCTTGATTAGTTGGTATTTATCC 57.168 33.333 0.00 0.00 0.00 2.59
218 219 9.388506 CTCATGTCTCTTGATTAGTTGGTATTT 57.611 33.333 0.00 0.00 0.00 1.40
219 220 8.762645 TCTCATGTCTCTTGATTAGTTGGTATT 58.237 33.333 0.00 0.00 0.00 1.89
220 221 8.200792 GTCTCATGTCTCTTGATTAGTTGGTAT 58.799 37.037 0.00 0.00 0.00 2.73
221 222 7.178451 TGTCTCATGTCTCTTGATTAGTTGGTA 59.822 37.037 0.00 0.00 0.00 3.25
222 223 6.014242 TGTCTCATGTCTCTTGATTAGTTGGT 60.014 38.462 0.00 0.00 0.00 3.67
223 224 6.401394 TGTCTCATGTCTCTTGATTAGTTGG 58.599 40.000 0.00 0.00 0.00 3.77
224 225 7.895975 TTGTCTCATGTCTCTTGATTAGTTG 57.104 36.000 0.00 0.00 0.00 3.16
225 226 9.593134 GTATTGTCTCATGTCTCTTGATTAGTT 57.407 33.333 0.00 0.00 0.00 2.24
226 227 8.753133 TGTATTGTCTCATGTCTCTTGATTAGT 58.247 33.333 0.00 0.00 0.00 2.24
227 228 9.591792 TTGTATTGTCTCATGTCTCTTGATTAG 57.408 33.333 0.00 0.00 0.00 1.73
228 229 9.942850 TTTGTATTGTCTCATGTCTCTTGATTA 57.057 29.630 0.00 0.00 0.00 1.75
229 230 8.853077 TTTGTATTGTCTCATGTCTCTTGATT 57.147 30.769 0.00 0.00 0.00 2.57
231 232 9.591792 CTATTTGTATTGTCTCATGTCTCTTGA 57.408 33.333 0.00 0.00 0.00 3.02
232 233 9.376075 ACTATTTGTATTGTCTCATGTCTCTTG 57.624 33.333 0.00 0.00 0.00 3.02
233 234 9.950496 AACTATTTGTATTGTCTCATGTCTCTT 57.050 29.630 0.00 0.00 0.00 2.85
234 235 9.376075 CAACTATTTGTATTGTCTCATGTCTCT 57.624 33.333 0.00 0.00 0.00 3.10
235 236 9.371136 TCAACTATTTGTATTGTCTCATGTCTC 57.629 33.333 0.00 0.00 34.02 3.36
236 237 9.725019 TTCAACTATTTGTATTGTCTCATGTCT 57.275 29.630 0.00 0.00 34.02 3.41
237 238 9.979270 CTTCAACTATTTGTATTGTCTCATGTC 57.021 33.333 0.00 0.00 34.02 3.06
238 239 9.507329 ACTTCAACTATTTGTATTGTCTCATGT 57.493 29.630 0.00 0.00 34.02 3.21
1256 1258 5.031066 CCACTCGGGTAATATTTCCAGAA 57.969 43.478 13.39 1.20 0.00 3.02
1568 2087 8.480643 AGATTCACTTGGAAGTAACTATTTCG 57.519 34.615 0.00 0.00 39.30 3.46
1711 2235 5.957842 ACTCTCGTTTTAAATCCATTGCA 57.042 34.783 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.