Multiple sequence alignment - TraesCS5D01G125400

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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 TraesCS5D01G125400 chr5D 100.000 3022 0 0 592 3613 191907575 191904554 0.000000e+00 5581.0
1 TraesCS5D01G125400 chr5D 100.000 243 0 0 1 243 191908166 191907924 1.980000e-122 449.0
2 TraesCS5D01G125400 chr5A 92.038 2110 100 34 607 2701 229921747 229923803 0.000000e+00 2904.0
3 TraesCS5D01G125400 chr5A 95.614 912 32 4 2700 3611 229923846 229924749 0.000000e+00 1456.0
4 TraesCS5D01G125400 chr3B 88.269 1560 113 39 633 2172 586864683 586863174 0.000000e+00 1803.0
5 TraesCS5D01G125400 chr3B 90.838 513 30 8 2204 2702 586863175 586862666 0.000000e+00 671.0
6 TraesCS5D01G125400 chr3B 87.822 427 27 11 2700 3123 586862624 586862220 9.080000e-131 477.0
7 TraesCS5D01G125400 chr5B 93.031 1234 34 12 866 2092 196246055 196244867 0.000000e+00 1755.0
8 TraesCS5D01G125400 chr5B 94.639 914 34 5 2700 3613 196239901 196239003 0.000000e+00 1402.0
9 TraesCS5D01G125400 chr5B 98.217 617 9 2 2088 2702 196240557 196239941 0.000000e+00 1077.0
10 TraesCS5D01G125400 chr5B 96.889 225 5 2 607 831 196253084 196252862 3.410000e-100 375.0
11 TraesCS5D01G125400 chr3D 87.041 926 72 25 1264 2172 447634380 447633486 0.000000e+00 1002.0
12 TraesCS5D01G125400 chr3D 87.934 663 44 12 2735 3387 447632865 447632229 0.000000e+00 749.0
13 TraesCS5D01G125400 chr3D 89.453 512 33 10 2204 2698 447633487 447632980 8.520000e-176 627.0
14 TraesCS5D01G125400 chr3D 86.201 558 46 16 661 1215 447634908 447634379 3.130000e-160 575.0
15 TraesCS5D01G125400 chr3A 89.099 688 50 8 2700 3366 589373974 589373291 0.000000e+00 832.0
16 TraesCS5D01G125400 chr3A 88.785 642 47 12 1264 1888 589376216 589375583 0.000000e+00 763.0
17 TraesCS5D01G125400 chr3A 88.008 517 30 12 2204 2702 589374518 589374016 1.870000e-162 582.0
18 TraesCS5D01G125400 chr3A 91.081 370 28 5 850 1215 589376583 589376215 2.510000e-136 496.0
19 TraesCS5D01G125400 chr3A 88.559 236 17 4 1937 2172 589374742 589374517 9.880000e-71 278.0
20 TraesCS5D01G125400 chrUn 89.855 69 5 2 59 125 12994093 12994025 1.790000e-13 87.9


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 TraesCS5D01G125400 chr5D 191904554 191908166 3612 True 3015.000000 5581 100.000000 1 3613 2 chr5D.!!$R1 3612
1 TraesCS5D01G125400 chr5A 229921747 229924749 3002 False 2180.000000 2904 93.826000 607 3611 2 chr5A.!!$F1 3004
2 TraesCS5D01G125400 chr3B 586862220 586864683 2463 True 983.666667 1803 88.976333 633 3123 3 chr3B.!!$R1 2490
3 TraesCS5D01G125400 chr5B 196244867 196246055 1188 True 1755.000000 1755 93.031000 866 2092 1 chr5B.!!$R1 1226
4 TraesCS5D01G125400 chr5B 196239003 196240557 1554 True 1239.500000 1402 96.428000 2088 3613 2 chr5B.!!$R3 1525
5 TraesCS5D01G125400 chr3D 447632229 447634908 2679 True 738.250000 1002 87.657250 661 3387 4 chr3D.!!$R1 2726
6 TraesCS5D01G125400 chr3A 589373291 589376583 3292 True 590.200000 832 89.106400 850 3366 5 chr3A.!!$R1 2516

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
204 205 0.036010 ACATCTCGTTGCCCTTCCTG 60.036 55.0 0.0 0.0 0.0 3.86 F
842 847 0.306533 GGTGTAGTTGTTGTGTGGCG 59.693 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 1566 0.107557 ACACGGGGAAAAACACGTCT 60.108 50.0 0.0 0.0 37.48 4.18 R
2793 3733 0.592637 CATGTTCAACGCTTGGAGCA 59.407 50.0 0.5 0.0 42.58 4.26 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
139 140 3.782889 AAAGAAGGTTGTGTTCTGTGC 57.217 42.857 0.00 0.00 34.40 4.57
140 141 2.418368 AGAAGGTTGTGTTCTGTGCA 57.582 45.000 0.00 0.00 32.86 4.57
141 142 2.722094 AGAAGGTTGTGTTCTGTGCAA 58.278 42.857 0.00 0.00 32.86 4.08
142 143 3.290710 AGAAGGTTGTGTTCTGTGCAAT 58.709 40.909 0.00 0.00 32.86 3.56
143 144 3.701040 AGAAGGTTGTGTTCTGTGCAATT 59.299 39.130 0.00 0.00 32.86 2.32
144 145 3.715628 AGGTTGTGTTCTGTGCAATTC 57.284 42.857 0.00 0.00 0.00 2.17
145 146 3.023119 AGGTTGTGTTCTGTGCAATTCA 58.977 40.909 0.00 0.00 0.00 2.57
146 147 3.115554 GGTTGTGTTCTGTGCAATTCAC 58.884 45.455 0.00 0.00 45.82 3.18
147 148 3.181487 GGTTGTGTTCTGTGCAATTCACT 60.181 43.478 0.00 0.00 45.81 3.41
148 149 3.969117 TGTGTTCTGTGCAATTCACTC 57.031 42.857 0.00 0.00 45.81 3.51
149 150 2.287644 TGTGTTCTGTGCAATTCACTCG 59.712 45.455 0.00 0.00 45.81 4.18
150 151 1.872952 TGTTCTGTGCAATTCACTCGG 59.127 47.619 0.00 0.00 45.81 4.63
151 152 1.197721 GTTCTGTGCAATTCACTCGGG 59.802 52.381 0.00 0.00 45.81 5.14
152 153 0.321564 TCTGTGCAATTCACTCGGGG 60.322 55.000 0.00 0.00 45.81 5.73
153 154 0.321564 CTGTGCAATTCACTCGGGGA 60.322 55.000 0.00 0.00 45.81 4.81
154 155 0.109532 TGTGCAATTCACTCGGGGAA 59.890 50.000 0.00 0.00 45.81 3.97
155 156 1.243902 GTGCAATTCACTCGGGGAAA 58.756 50.000 0.00 0.00 42.38 3.13
156 157 1.611491 GTGCAATTCACTCGGGGAAAA 59.389 47.619 0.00 0.00 42.38 2.29
157 158 2.035321 GTGCAATTCACTCGGGGAAAAA 59.965 45.455 0.00 0.00 42.38 1.94
174 175 2.586648 AAAATCTCGTTGCCCTTCCT 57.413 45.000 0.00 0.00 0.00 3.36
175 176 2.586648 AAATCTCGTTGCCCTTCCTT 57.413 45.000 0.00 0.00 0.00 3.36
176 177 2.586648 AATCTCGTTGCCCTTCCTTT 57.413 45.000 0.00 0.00 0.00 3.11
177 178 2.586648 ATCTCGTTGCCCTTCCTTTT 57.413 45.000 0.00 0.00 0.00 2.27
178 179 2.358322 TCTCGTTGCCCTTCCTTTTT 57.642 45.000 0.00 0.00 0.00 1.94
198 199 4.759516 TTTTTAGAACATCTCGTTGCCC 57.240 40.909 0.00 0.00 38.19 5.36
199 200 3.695830 TTTAGAACATCTCGTTGCCCT 57.304 42.857 0.00 0.00 38.19 5.19
200 201 3.695830 TTAGAACATCTCGTTGCCCTT 57.304 42.857 0.00 0.00 38.19 3.95
201 202 2.100605 AGAACATCTCGTTGCCCTTC 57.899 50.000 0.00 0.00 38.19 3.46
202 203 1.087501 GAACATCTCGTTGCCCTTCC 58.912 55.000 0.00 0.00 38.19 3.46
203 204 0.693049 AACATCTCGTTGCCCTTCCT 59.307 50.000 0.00 0.00 36.12 3.36
204 205 0.036010 ACATCTCGTTGCCCTTCCTG 60.036 55.000 0.00 0.00 0.00 3.86
205 206 1.078143 ATCTCGTTGCCCTTCCTGC 60.078 57.895 0.00 0.00 0.00 4.85
206 207 2.859273 ATCTCGTTGCCCTTCCTGCG 62.859 60.000 0.00 0.00 0.00 5.18
207 208 3.589654 CTCGTTGCCCTTCCTGCGA 62.590 63.158 0.00 0.00 0.00 5.10
208 209 2.668212 CGTTGCCCTTCCTGCGAA 60.668 61.111 0.00 0.00 0.00 4.70
209 210 2.680913 CGTTGCCCTTCCTGCGAAG 61.681 63.158 0.00 0.00 44.47 3.79
224 225 2.481289 CGAAGCCTTTCCTTTCCTCT 57.519 50.000 0.00 0.00 0.00 3.69
225 226 2.351455 CGAAGCCTTTCCTTTCCTCTC 58.649 52.381 0.00 0.00 0.00 3.20
226 227 2.289694 CGAAGCCTTTCCTTTCCTCTCA 60.290 50.000 0.00 0.00 0.00 3.27
227 228 2.869101 AGCCTTTCCTTTCCTCTCAC 57.131 50.000 0.00 0.00 0.00 3.51
228 229 2.343625 AGCCTTTCCTTTCCTCTCACT 58.656 47.619 0.00 0.00 0.00 3.41
229 230 2.039613 AGCCTTTCCTTTCCTCTCACTG 59.960 50.000 0.00 0.00 0.00 3.66
230 231 2.039084 GCCTTTCCTTTCCTCTCACTGA 59.961 50.000 0.00 0.00 0.00 3.41
231 232 3.669536 CCTTTCCTTTCCTCTCACTGAC 58.330 50.000 0.00 0.00 0.00 3.51
232 233 3.558109 CCTTTCCTTTCCTCTCACTGACC 60.558 52.174 0.00 0.00 0.00 4.02
233 234 1.645710 TCCTTTCCTCTCACTGACCC 58.354 55.000 0.00 0.00 0.00 4.46
234 235 1.150135 TCCTTTCCTCTCACTGACCCT 59.850 52.381 0.00 0.00 0.00 4.34
235 236 1.552792 CCTTTCCTCTCACTGACCCTC 59.447 57.143 0.00 0.00 0.00 4.30
236 237 1.203523 CTTTCCTCTCACTGACCCTCG 59.796 57.143 0.00 0.00 0.00 4.63
237 238 1.251527 TTCCTCTCACTGACCCTCGC 61.252 60.000 0.00 0.00 0.00 5.03
238 239 2.716017 CCTCTCACTGACCCTCGCC 61.716 68.421 0.00 0.00 0.00 5.54
239 240 1.680651 CTCTCACTGACCCTCGCCT 60.681 63.158 0.00 0.00 0.00 5.52
240 241 1.228894 TCTCACTGACCCTCGCCTT 60.229 57.895 0.00 0.00 0.00 4.35
241 242 1.216710 CTCACTGACCCTCGCCTTC 59.783 63.158 0.00 0.00 0.00 3.46
242 243 2.125912 CACTGACCCTCGCCTTCG 60.126 66.667 0.00 0.00 0.00 3.79
612 613 0.663269 GGCGGCAAAAGAAGGTTTCG 60.663 55.000 3.07 0.00 34.02 3.46
668 669 3.869473 TTTAAGGACGCACGCCGCT 62.869 57.895 0.00 0.00 41.76 5.52
683 684 2.182842 CGCTGCTTAGGCCACATCC 61.183 63.158 5.01 0.00 37.74 3.51
706 709 2.294791 CTCTTAGGGTATCCGCACTCTG 59.705 54.545 0.00 0.00 38.33 3.35
776 781 8.999431 GTCCTCTCAAATAATCAAGTGTGTTTA 58.001 33.333 0.00 0.00 0.00 2.01
777 782 8.999431 TCCTCTCAAATAATCAAGTGTGTTTAC 58.001 33.333 0.00 0.00 0.00 2.01
808 813 1.076332 CGCTAGCTGTTTGTACCCAC 58.924 55.000 13.93 0.00 0.00 4.61
809 814 1.606994 CGCTAGCTGTTTGTACCCACA 60.607 52.381 13.93 0.00 0.00 4.17
810 815 2.076863 GCTAGCTGTTTGTACCCACAG 58.923 52.381 7.70 14.47 42.94 3.66
811 816 2.699954 CTAGCTGTTTGTACCCACAGG 58.300 52.381 18.47 3.82 40.77 4.00
842 847 0.306533 GGTGTAGTTGTTGTGTGGCG 59.693 55.000 0.00 0.00 0.00 5.69
876 882 7.549147 TTCTAGGTTAGGCTTACTGAAAAGA 57.451 36.000 3.43 0.00 0.00 2.52
887 894 8.743714 AGGCTTACTGAAAAGAATTCCATTTAG 58.256 33.333 0.65 6.46 0.00 1.85
910 917 4.960938 ACTTCTGTGAACAACTCTGCATA 58.039 39.130 0.00 0.00 0.00 3.14
951 959 4.832248 TCATATAATGCATCGGGAGAACC 58.168 43.478 0.00 0.00 45.37 3.62
1003 1013 7.424803 TCAACTCACAAGTTCAATTTGTATGG 58.575 34.615 0.00 0.00 43.99 2.74
1199 1212 3.451141 TTGCAATGTCGGCTTCTTTTT 57.549 38.095 0.00 0.00 0.00 1.94
1204 1217 6.682746 TGCAATGTCGGCTTCTTTTTATTTA 58.317 32.000 0.00 0.00 0.00 1.40
1304 1317 0.320421 GTGACGTACATGGTGCACCT 60.320 55.000 34.75 18.85 36.82 4.00
1399 1415 1.568118 TTGGGGGCCCTTACTAGTGC 61.568 60.000 24.38 2.13 36.94 4.40
1515 1531 2.870035 GCCAGTGTTAAACCAAATGGCC 60.870 50.000 0.00 0.00 40.81 5.36
1550 1566 7.053498 TGATAGTTGCTATGTTTGCATCCTAA 58.947 34.615 0.00 0.00 40.34 2.69
1697 1718 3.243907 GCCATGTGTACTCTCCATACTCC 60.244 52.174 0.00 0.00 0.00 3.85
2099 2942 7.563906 TGGTTTCTGAAATGTTGGAATCTTTT 58.436 30.769 6.06 0.00 0.00 2.27
2567 3420 6.423905 GCTTCCTTTGTTATTCTTTTGGAACC 59.576 38.462 0.00 0.00 36.70 3.62
2698 3560 0.888619 CGTCAGTGCTTAGGAGGTGA 59.111 55.000 0.00 0.00 0.00 4.02
2793 3733 9.023962 TGCATTCTCCAGTTTCAAACTTATTAT 57.976 29.630 0.00 0.00 40.46 1.28
2888 3830 6.561614 TCTTACCATTGAATCGTCACTAGTC 58.438 40.000 0.00 0.00 31.90 2.59
2955 3915 8.099364 TGTTTGTTTTCTATTCCTCTGATGAC 57.901 34.615 0.00 0.00 0.00 3.06
2961 3921 5.697473 TCTATTCCTCTGATGACATCGAC 57.303 43.478 10.79 0.00 0.00 4.20
2974 3935 7.649057 TGATGACATCGACGTATCTAAAATCT 58.351 34.615 10.79 0.00 0.00 2.40
3040 4001 4.149922 TCATCGACAATTTGTTCGTGACTC 59.850 41.667 3.08 0.00 0.00 3.36
3113 4074 7.230510 GGTAATCATATTGCAAGGGTGTCATTA 59.769 37.037 4.94 2.77 0.00 1.90
3307 4271 3.588842 ACAATCCACCTCTCTCATTTCCA 59.411 43.478 0.00 0.00 0.00 3.53
3390 4358 7.189512 AGCACGATCATGAAGTTTTATTTAGC 58.810 34.615 0.00 0.89 0.00 3.09
3425 4393 7.675962 TTCTGTATTATGCGTTTAAACTGGT 57.324 32.000 16.01 4.48 0.00 4.00
3554 4522 4.163078 AGAACCAGAATTCTCCATCGATGT 59.837 41.667 23.27 4.09 33.50 3.06
3584 4552 5.659440 TTGGATGGGCAGTATTTTTCTTC 57.341 39.130 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 4.806342 GAGTTACACTCGAAGGCAAAAA 57.194 40.909 0.00 0.00 35.28 1.94
117 118 4.021544 TGCACAGAACACAACCTTCTTTTT 60.022 37.500 0.00 0.00 0.00 1.94
118 119 3.509575 TGCACAGAACACAACCTTCTTTT 59.490 39.130 0.00 0.00 0.00 2.27
119 120 3.088532 TGCACAGAACACAACCTTCTTT 58.911 40.909 0.00 0.00 0.00 2.52
120 121 2.722094 TGCACAGAACACAACCTTCTT 58.278 42.857 0.00 0.00 0.00 2.52
121 122 2.418368 TGCACAGAACACAACCTTCT 57.582 45.000 0.00 0.00 0.00 2.85
122 123 3.715628 ATTGCACAGAACACAACCTTC 57.284 42.857 0.00 0.00 0.00 3.46
123 124 3.446873 TGAATTGCACAGAACACAACCTT 59.553 39.130 0.00 0.00 0.00 3.50
124 125 3.023119 TGAATTGCACAGAACACAACCT 58.977 40.909 0.00 0.00 0.00 3.50
125 126 3.115554 GTGAATTGCACAGAACACAACC 58.884 45.455 0.00 0.00 46.91 3.77
137 138 1.988293 TTTTCCCCGAGTGAATTGCA 58.012 45.000 0.00 0.00 0.00 4.08
154 155 2.876581 AGGAAGGGCAACGAGATTTTT 58.123 42.857 0.00 0.00 37.60 1.94
155 156 2.586648 AGGAAGGGCAACGAGATTTT 57.413 45.000 0.00 0.00 37.60 1.82
156 157 2.586648 AAGGAAGGGCAACGAGATTT 57.413 45.000 0.00 0.00 37.60 2.17
157 158 2.586648 AAAGGAAGGGCAACGAGATT 57.413 45.000 0.00 0.00 37.60 2.40
158 159 2.586648 AAAAGGAAGGGCAACGAGAT 57.413 45.000 0.00 0.00 37.60 2.75
159 160 2.358322 AAAAAGGAAGGGCAACGAGA 57.642 45.000 0.00 0.00 37.60 4.04
177 178 4.394729 AGGGCAACGAGATGTTCTAAAAA 58.605 39.130 0.00 0.00 39.29 1.94
178 179 4.015872 AGGGCAACGAGATGTTCTAAAA 57.984 40.909 0.00 0.00 39.29 1.52
179 180 3.695830 AGGGCAACGAGATGTTCTAAA 57.304 42.857 0.00 0.00 39.29 1.85
180 181 3.596214 GAAGGGCAACGAGATGTTCTAA 58.404 45.455 0.00 0.00 39.29 2.10
181 182 2.093658 GGAAGGGCAACGAGATGTTCTA 60.094 50.000 0.00 0.00 39.29 2.10
182 183 1.339151 GGAAGGGCAACGAGATGTTCT 60.339 52.381 0.00 0.00 39.29 3.01
183 184 1.087501 GGAAGGGCAACGAGATGTTC 58.912 55.000 0.00 0.00 39.29 3.18
184 185 0.693049 AGGAAGGGCAACGAGATGTT 59.307 50.000 0.00 0.00 43.09 2.71
185 186 0.036010 CAGGAAGGGCAACGAGATGT 60.036 55.000 0.00 0.00 37.60 3.06
186 187 1.372087 GCAGGAAGGGCAACGAGATG 61.372 60.000 0.00 0.00 37.60 2.90
187 188 1.078143 GCAGGAAGGGCAACGAGAT 60.078 57.895 0.00 0.00 37.60 2.75
188 189 2.347490 GCAGGAAGGGCAACGAGA 59.653 61.111 0.00 0.00 37.60 4.04
189 190 3.121030 CGCAGGAAGGGCAACGAG 61.121 66.667 0.00 0.00 37.60 4.18
190 191 3.171828 TTCGCAGGAAGGGCAACGA 62.172 57.895 0.00 0.00 37.60 3.85
191 192 2.668212 TTCGCAGGAAGGGCAACG 60.668 61.111 0.00 0.00 37.60 4.10
192 193 3.267974 CTTCGCAGGAAGGGCAAC 58.732 61.111 0.00 0.00 44.83 4.17
199 200 0.110486 AAGGAAAGGCTTCGCAGGAA 59.890 50.000 0.00 0.00 31.77 3.36
200 201 0.110486 AAAGGAAAGGCTTCGCAGGA 59.890 50.000 0.00 0.00 31.77 3.86
201 202 0.523519 GAAAGGAAAGGCTTCGCAGG 59.476 55.000 0.00 0.00 31.77 4.85
202 203 0.523519 GGAAAGGAAAGGCTTCGCAG 59.476 55.000 0.00 0.00 31.77 5.18
203 204 0.110486 AGGAAAGGAAAGGCTTCGCA 59.890 50.000 0.00 0.00 31.77 5.10
204 205 0.805614 GAGGAAAGGAAAGGCTTCGC 59.194 55.000 0.00 0.00 31.77 4.70
205 206 2.289694 TGAGAGGAAAGGAAAGGCTTCG 60.290 50.000 0.00 0.00 31.77 3.79
206 207 3.078097 GTGAGAGGAAAGGAAAGGCTTC 58.922 50.000 0.00 0.00 0.00 3.86
207 208 2.713708 AGTGAGAGGAAAGGAAAGGCTT 59.286 45.455 0.00 0.00 0.00 4.35
208 209 2.039613 CAGTGAGAGGAAAGGAAAGGCT 59.960 50.000 0.00 0.00 0.00 4.58
209 210 2.039084 TCAGTGAGAGGAAAGGAAAGGC 59.961 50.000 0.00 0.00 0.00 4.35
210 211 3.558109 GGTCAGTGAGAGGAAAGGAAAGG 60.558 52.174 0.00 0.00 0.00 3.11
211 212 3.558109 GGGTCAGTGAGAGGAAAGGAAAG 60.558 52.174 0.00 0.00 0.00 2.62
212 213 2.372172 GGGTCAGTGAGAGGAAAGGAAA 59.628 50.000 0.00 0.00 0.00 3.13
213 214 1.978580 GGGTCAGTGAGAGGAAAGGAA 59.021 52.381 0.00 0.00 0.00 3.36
214 215 1.150135 AGGGTCAGTGAGAGGAAAGGA 59.850 52.381 0.00 0.00 0.00 3.36
215 216 1.552792 GAGGGTCAGTGAGAGGAAAGG 59.447 57.143 0.00 0.00 0.00 3.11
216 217 1.203523 CGAGGGTCAGTGAGAGGAAAG 59.796 57.143 0.00 0.00 0.00 2.62
217 218 1.257743 CGAGGGTCAGTGAGAGGAAA 58.742 55.000 0.00 0.00 0.00 3.13
218 219 1.251527 GCGAGGGTCAGTGAGAGGAA 61.252 60.000 0.00 0.00 0.00 3.36
219 220 1.679305 GCGAGGGTCAGTGAGAGGA 60.679 63.158 0.00 0.00 0.00 3.71
220 221 2.716017 GGCGAGGGTCAGTGAGAGG 61.716 68.421 0.00 0.00 0.00 3.69
221 222 1.254284 AAGGCGAGGGTCAGTGAGAG 61.254 60.000 0.00 0.00 0.00 3.20
222 223 1.228894 AAGGCGAGGGTCAGTGAGA 60.229 57.895 0.00 0.00 0.00 3.27
223 224 1.216710 GAAGGCGAGGGTCAGTGAG 59.783 63.158 0.00 0.00 0.00 3.51
224 225 2.636412 CGAAGGCGAGGGTCAGTGA 61.636 63.158 0.00 0.00 40.82 3.41
225 226 2.125912 CGAAGGCGAGGGTCAGTG 60.126 66.667 0.00 0.00 40.82 3.66
591 592 2.693250 AAACCTTCTTTTGCCGCCGC 62.693 55.000 0.00 0.00 0.00 6.53
592 593 0.663269 GAAACCTTCTTTTGCCGCCG 60.663 55.000 0.00 0.00 0.00 6.46
593 594 0.663269 CGAAACCTTCTTTTGCCGCC 60.663 55.000 0.00 0.00 0.00 6.13
594 595 0.030235 ACGAAACCTTCTTTTGCCGC 59.970 50.000 0.00 0.00 0.00 6.53
595 596 1.659211 CGACGAAACCTTCTTTTGCCG 60.659 52.381 0.00 0.00 0.00 5.69
596 597 1.600485 TCGACGAAACCTTCTTTTGCC 59.400 47.619 0.00 0.00 0.00 4.52
597 598 3.537793 ATCGACGAAACCTTCTTTTGC 57.462 42.857 0.00 0.00 0.00 3.68
598 599 4.141680 CGAATCGACGAAACCTTCTTTTG 58.858 43.478 0.00 0.00 35.09 2.44
599 600 3.363673 GCGAATCGACGAAACCTTCTTTT 60.364 43.478 6.91 0.00 35.09 2.27
600 601 2.157085 GCGAATCGACGAAACCTTCTTT 59.843 45.455 6.91 0.00 35.09 2.52
601 602 1.725164 GCGAATCGACGAAACCTTCTT 59.275 47.619 6.91 0.00 35.09 2.52
602 603 1.347320 GCGAATCGACGAAACCTTCT 58.653 50.000 6.91 0.00 35.09 2.85
603 604 0.369248 GGCGAATCGACGAAACCTTC 59.631 55.000 6.91 0.00 35.09 3.46
604 605 2.452767 GGCGAATCGACGAAACCTT 58.547 52.632 6.91 0.00 35.09 3.50
605 606 4.180496 GGCGAATCGACGAAACCT 57.820 55.556 6.91 0.00 35.09 3.50
612 613 1.655959 GAGAGAGCGGCGAATCGAC 60.656 63.158 12.98 1.05 0.00 4.20
668 669 1.619363 AGGGGATGTGGCCTAAGCA 60.619 57.895 3.32 0.00 42.56 3.91
706 709 3.951663 ACCACCACATAAACCTAGAAGC 58.048 45.455 0.00 0.00 0.00 3.86
741 744 6.980978 TGATTATTTGAGAGGACGATGAGAAC 59.019 38.462 0.00 0.00 0.00 3.01
776 781 2.484651 CAGCTAGCGACCATATACGAGT 59.515 50.000 9.55 0.00 0.00 4.18
777 782 2.484651 ACAGCTAGCGACCATATACGAG 59.515 50.000 9.55 0.00 0.00 4.18
862 868 8.739972 TCTAAATGGAATTCTTTTCAGTAAGCC 58.260 33.333 5.23 0.00 33.67 4.35
876 882 8.352942 GTTGTTCACAGAAGTCTAAATGGAATT 58.647 33.333 0.00 0.00 38.98 2.17
887 894 3.198068 TGCAGAGTTGTTCACAGAAGTC 58.802 45.455 0.00 0.00 0.00 3.01
951 959 7.611855 TCTCTTTCTTTAGATAAAAGGCAAGGG 59.388 37.037 0.00 2.17 44.10 3.95
1003 1013 0.323629 TTCCCGATCACCTGTCCAAC 59.676 55.000 0.00 0.00 0.00 3.77
1199 1212 9.914834 AAACATGTTCCCTTGTAGCTATAAATA 57.085 29.630 12.39 0.00 0.00 1.40
1204 1217 5.648092 GTGAAACATGTTCCCTTGTAGCTAT 59.352 40.000 12.39 0.00 36.32 2.97
1304 1317 0.601558 GGTCTGCTACGGTGTTCAGA 59.398 55.000 0.00 0.00 33.64 3.27
1399 1415 7.396540 AAATATCTAAAACAGGGAAGCACAG 57.603 36.000 0.00 0.00 0.00 3.66
1489 1505 5.868801 CCATTTGGTTTAACACTGGCATAAG 59.131 40.000 0.00 0.00 0.00 1.73
1515 1531 6.286758 ACATAGCAACTATCATCCAGACTTG 58.713 40.000 0.00 0.00 0.00 3.16
1550 1566 0.107557 ACACGGGGAAAAACACGTCT 60.108 50.000 0.00 0.00 37.48 4.18
1660 1681 9.461312 AGTACACATGGCTAAAAAGATGATTTA 57.539 29.630 0.00 0.00 0.00 1.40
1697 1718 1.127817 CGTTACGACACAGCAAGCG 59.872 57.895 0.00 0.00 0.00 4.68
2041 2884 0.814010 GACAGCCACACTCAACGGTT 60.814 55.000 0.00 0.00 0.00 4.44
2384 3232 5.920273 CCCTAACAACATACAACAGCAAAAG 59.080 40.000 0.00 0.00 0.00 2.27
2387 3235 4.720046 TCCCTAACAACATACAACAGCAA 58.280 39.130 0.00 0.00 0.00 3.91
2567 3420 3.300009 GGCTGAAAATGAACAAGTGTCG 58.700 45.455 0.00 0.00 0.00 4.35
2698 3560 4.389374 CATGGTCACACTAACAGTCCTTT 58.611 43.478 0.00 0.00 0.00 3.11
2793 3733 0.592637 CATGTTCAACGCTTGGAGCA 59.407 50.000 0.50 0.00 42.58 4.26
2888 3830 5.898174 ACATGTGGAAGTTCAATGCATATG 58.102 37.500 0.00 9.50 41.33 1.78
2980 3941 5.644206 TGTGCTCAAAACCGCAATAGTTATA 59.356 36.000 0.00 0.00 37.97 0.98
3024 3985 4.552166 AACAGGAGTCACGAACAAATTG 57.448 40.909 0.00 0.00 0.00 2.32
3025 3986 5.820947 AGTTAACAGGAGTCACGAACAAATT 59.179 36.000 8.61 0.00 0.00 1.82
3040 4001 6.573664 TGGATGACAATTCAAGTTAACAGG 57.426 37.500 8.61 0.00 34.61 4.00
3113 4074 3.132289 CACTATAGGTCAACACCGATGGT 59.868 47.826 4.43 0.00 46.30 3.55
3307 4271 1.086696 CACGGAATTCGCAGGTCAAT 58.913 50.000 0.00 0.00 43.89 2.57
3408 4376 7.493743 TGAACTAACCAGTTTAAACGCATAA 57.506 32.000 12.54 0.00 45.18 1.90
3425 4393 8.531146 TGATGTGTATGTCTCTGATTGAACTAA 58.469 33.333 0.00 0.00 0.00 2.24
3554 4522 3.168035 ACTGCCCATCCAAACAATACA 57.832 42.857 0.00 0.00 0.00 2.29
3584 4552 8.915871 AATTTGAAATGAACACATAAGATCCG 57.084 30.769 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.