Multiple sequence alignment - TraesCS2B01G166900

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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 TraesCS2B01G166900 chr2B 100.000 2642 0 0 1 2642 139571538 139568897 0.000000e+00 4879
1 TraesCS2B01G166900 chr2A 92.483 1663 84 10 212 1865 86989499 86987869 0.000000e+00 2340
2 TraesCS2B01G166900 chr2A 89.251 828 59 18 1842 2642 86987923 86987099 0.000000e+00 1009
3 TraesCS2B01G166900 chr2D 92.561 1519 93 9 212 1722 86717807 86716301 0.000000e+00 2161
4 TraesCS2B01G166900 chr2D 85.000 200 15 4 1 193 86717989 86717798 3.470000e-44 189
5 TraesCS2B01G166900 chr2D 90.805 87 8 0 2556 2642 86715615 86715529 1.660000e-22 117


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 TraesCS2B01G166900 chr2B 139568897 139571538 2641 True 4879.000000 4879 100.000000 1 2642 1 chr2B.!!$R1 2641
1 TraesCS2B01G166900 chr2A 86987099 86989499 2400 True 1674.500000 2340 90.867000 212 2642 2 chr2A.!!$R1 2430
2 TraesCS2B01G166900 chr2D 86715529 86717989 2460 True 822.333333 2161 89.455333 1 2642 3 chr2D.!!$R1 2641

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
269 277 0.179076 GCCAAACCTTGCTTGCTGTT 60.179 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 1706 0.023103 GCACGCAAAACACAAACACG 59.977 50.0 0.0 0.0 0.0 4.49 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 0.517316 CGCAGTTTACCAGCAACCTC 59.483 55.000 0.00 0.00 0.00 3.85
21 22 1.266989 GCAGTTTACCAGCAACCTCAC 59.733 52.381 0.00 0.00 0.00 3.51
24 32 2.172717 AGTTTACCAGCAACCTCACAGT 59.827 45.455 0.00 0.00 0.00 3.55
40 48 2.266055 GTGGCAGGTCTCCCTTCG 59.734 66.667 0.00 0.00 39.89 3.79
44 52 1.446272 GCAGGTCTCCCTTCGTTCG 60.446 63.158 0.00 0.00 39.89 3.95
60 68 3.110178 CGTCGAAAGCCGGACACC 61.110 66.667 5.05 0.00 39.14 4.16
109 117 2.553028 GGTGCTTCAGTCCTCATTTCCA 60.553 50.000 0.00 0.00 0.00 3.53
111 119 3.760684 GTGCTTCAGTCCTCATTTCCAAT 59.239 43.478 0.00 0.00 0.00 3.16
131 139 6.723052 TCCAATGATGATCAGTCAGCTATAGA 59.277 38.462 3.21 0.00 41.28 1.98
132 140 7.399478 TCCAATGATGATCAGTCAGCTATAGAT 59.601 37.037 3.21 0.00 41.28 1.98
134 142 5.963594 TGATGATCAGTCAGCTATAGATGC 58.036 41.667 13.24 8.48 41.28 3.91
136 144 3.823304 TGATCAGTCAGCTATAGATGCGT 59.177 43.478 13.24 0.00 35.28 5.24
137 145 3.906014 TCAGTCAGCTATAGATGCGTC 57.094 47.619 13.24 0.00 35.28 5.19
138 146 3.214328 TCAGTCAGCTATAGATGCGTCA 58.786 45.455 13.24 0.00 35.28 4.35
139 147 3.823304 TCAGTCAGCTATAGATGCGTCAT 59.177 43.478 13.24 2.64 35.28 3.06
140 148 3.919197 CAGTCAGCTATAGATGCGTCATG 59.081 47.826 13.24 3.76 35.28 3.07
141 149 3.056962 AGTCAGCTATAGATGCGTCATGG 60.057 47.826 13.24 3.38 35.28 3.66
142 150 2.232208 TCAGCTATAGATGCGTCATGGG 59.768 50.000 13.24 0.00 35.28 4.00
143 151 1.066573 AGCTATAGATGCGTCATGGGC 60.067 52.381 8.99 7.21 35.28 5.36
147 155 1.051008 TAGATGCGTCATGGGCTCAT 58.949 50.000 8.99 0.00 0.00 2.90
171 179 4.047822 GCCTCTGAAATCTCATAGTCACG 58.952 47.826 0.00 0.00 0.00 4.35
179 187 7.768240 TGAAATCTCATAGTCACGCTACTTAA 58.232 34.615 0.00 0.00 31.59 1.85
183 191 5.878669 TCTCATAGTCACGCTACTTAACTGA 59.121 40.000 0.00 0.00 31.59 3.41
184 192 6.542735 TCTCATAGTCACGCTACTTAACTGAT 59.457 38.462 0.00 0.00 31.59 2.90
185 193 7.713942 TCTCATAGTCACGCTACTTAACTGATA 59.286 37.037 0.00 0.00 31.59 2.15
186 194 7.637229 TCATAGTCACGCTACTTAACTGATAC 58.363 38.462 0.00 0.00 31.59 2.24
187 195 5.892160 AGTCACGCTACTTAACTGATACA 57.108 39.130 0.00 0.00 0.00 2.29
188 196 6.452494 AGTCACGCTACTTAACTGATACAT 57.548 37.500 0.00 0.00 0.00 2.29
189 197 6.266323 AGTCACGCTACTTAACTGATACATG 58.734 40.000 0.00 0.00 0.00 3.21
190 198 6.095021 AGTCACGCTACTTAACTGATACATGA 59.905 38.462 0.00 0.00 0.00 3.07
191 199 6.415280 GTCACGCTACTTAACTGATACATGAG 59.585 42.308 0.00 0.00 0.00 2.90
192 200 6.095021 TCACGCTACTTAACTGATACATGAGT 59.905 38.462 0.00 0.00 0.00 3.41
193 201 6.752351 CACGCTACTTAACTGATACATGAGTT 59.248 38.462 0.00 0.72 37.90 3.01
194 202 7.275779 CACGCTACTTAACTGATACATGAGTTT 59.724 37.037 0.00 0.00 35.81 2.66
195 203 7.275779 ACGCTACTTAACTGATACATGAGTTTG 59.724 37.037 0.00 0.00 35.81 2.93
196 204 7.402640 GCTACTTAACTGATACATGAGTTTGC 58.597 38.462 0.00 0.00 35.81 3.68
197 205 6.743575 ACTTAACTGATACATGAGTTTGCC 57.256 37.500 0.00 0.00 35.81 4.52
198 206 6.476378 ACTTAACTGATACATGAGTTTGCCT 58.524 36.000 0.00 0.00 35.81 4.75
199 207 7.620880 ACTTAACTGATACATGAGTTTGCCTA 58.379 34.615 0.00 0.00 35.81 3.93
200 208 8.100791 ACTTAACTGATACATGAGTTTGCCTAA 58.899 33.333 0.00 0.00 35.81 2.69
201 209 8.856153 TTAACTGATACATGAGTTTGCCTAAA 57.144 30.769 0.00 0.00 35.81 1.85
202 210 7.759489 AACTGATACATGAGTTTGCCTAAAA 57.241 32.000 0.00 0.00 29.87 1.52
203 211 7.759489 ACTGATACATGAGTTTGCCTAAAAA 57.241 32.000 0.00 0.00 0.00 1.94
204 212 7.820648 ACTGATACATGAGTTTGCCTAAAAAG 58.179 34.615 0.00 0.00 0.00 2.27
205 213 7.665559 ACTGATACATGAGTTTGCCTAAAAAGA 59.334 33.333 0.00 0.00 0.00 2.52
206 214 8.402798 TGATACATGAGTTTGCCTAAAAAGAA 57.597 30.769 0.00 0.00 0.00 2.52
207 215 8.855110 TGATACATGAGTTTGCCTAAAAAGAAA 58.145 29.630 0.00 0.00 0.00 2.52
208 216 9.129209 GATACATGAGTTTGCCTAAAAAGAAAC 57.871 33.333 0.00 0.00 0.00 2.78
209 217 7.112452 ACATGAGTTTGCCTAAAAAGAAACT 57.888 32.000 0.00 0.00 40.49 2.66
210 218 7.555965 ACATGAGTTTGCCTAAAAAGAAACTT 58.444 30.769 0.00 0.00 38.46 2.66
246 254 8.210946 TCATAAGTCTCTGAAGTTCCTTTGAAA 58.789 33.333 0.00 0.00 30.79 2.69
264 272 3.626670 TGAAAATTGCCAAACCTTGCTTG 59.373 39.130 0.00 0.00 0.00 4.01
265 273 1.596603 AATTGCCAAACCTTGCTTGC 58.403 45.000 0.00 0.00 0.00 4.01
266 274 0.760572 ATTGCCAAACCTTGCTTGCT 59.239 45.000 0.00 0.00 0.00 3.91
267 275 0.179078 TTGCCAAACCTTGCTTGCTG 60.179 50.000 0.00 0.00 0.00 4.41
268 276 1.329171 TGCCAAACCTTGCTTGCTGT 61.329 50.000 0.00 0.00 0.00 4.40
269 277 0.179076 GCCAAACCTTGCTTGCTGTT 60.179 50.000 0.00 0.00 0.00 3.16
310 318 1.519455 GATCTTCACTCGCCACCCG 60.519 63.158 0.00 0.00 38.61 5.28
322 330 1.805428 GCCACCCGTGTCAGCAAAAT 61.805 55.000 0.00 0.00 0.00 1.82
448 459 2.751259 TCAACCAGTAGGCTAGTACGTG 59.249 50.000 0.60 0.84 39.06 4.49
449 460 1.101331 ACCAGTAGGCTAGTACGTGC 58.899 55.000 0.60 0.00 39.06 5.34
514 525 1.915228 GTCCAATCTAGGGGCAGCA 59.085 57.895 0.00 0.00 0.00 4.41
600 611 1.228552 TGCCTGCAAGAAACTCCCC 60.229 57.895 0.00 0.00 34.07 4.81
617 628 3.620488 TCCCCAGACAATTAATCTGCAC 58.380 45.455 11.71 0.00 41.97 4.57
672 683 4.096382 GTGTGCAGGTTTATAGATTGGTGG 59.904 45.833 0.00 0.00 0.00 4.61
689 700 1.273048 GTGGCATGAACAAGCAATCCA 59.727 47.619 0.00 0.00 0.00 3.41
694 705 3.841643 CATGAACAAGCAATCCAACCTC 58.158 45.455 0.00 0.00 0.00 3.85
712 723 6.327934 CAACCTCATCAATCATGAAAACTCC 58.672 40.000 0.00 0.00 41.25 3.85
713 724 4.952335 ACCTCATCAATCATGAAAACTCCC 59.048 41.667 0.00 0.00 41.25 4.30
725 736 6.953520 TCATGAAAACTCCCCATGAAACTATT 59.046 34.615 0.00 0.00 42.33 1.73
766 777 7.361201 CGCTGTCAGGATCTTAGAAAAATTTCA 60.361 37.037 8.47 0.00 39.61 2.69
786 797 3.895041 TCATATGTATGGACTTCGAGGCA 59.105 43.478 1.90 0.00 34.50 4.75
790 801 1.480954 GTATGGACTTCGAGGCAGGAA 59.519 52.381 0.00 0.00 0.00 3.36
791 802 0.250513 ATGGACTTCGAGGCAGGAAC 59.749 55.000 0.00 0.00 0.00 3.62
792 803 0.832135 TGGACTTCGAGGCAGGAACT 60.832 55.000 0.00 0.00 43.88 3.01
793 804 0.321996 GGACTTCGAGGCAGGAACTT 59.678 55.000 0.00 0.00 34.60 2.66
794 805 1.433534 GACTTCGAGGCAGGAACTTG 58.566 55.000 0.00 0.00 34.60 3.16
799 814 2.457598 TCGAGGCAGGAACTTGTATCT 58.542 47.619 0.00 0.00 34.60 1.98
817 832 2.250031 TCTTCTTGCAAATGTGGGCAT 58.750 42.857 0.00 0.00 40.17 4.40
825 840 2.166050 GCAAATGTGGGCATCATGTACA 59.834 45.455 0.00 0.00 33.50 2.90
848 863 8.806429 ACATCAATTTGGTCACTATCACATTA 57.194 30.769 0.00 0.00 0.00 1.90
869 884 8.141268 ACATTACAATTTACAACCAAGACAAGG 58.859 33.333 0.00 0.00 0.00 3.61
908 924 3.270877 AGTAAGCAACCGGATTAGCTTG 58.729 45.455 25.74 14.29 45.91 4.01
912 928 1.067915 GCAACCGGATTAGCTTGCAAA 60.068 47.619 17.53 0.00 39.09 3.68
913 929 2.417243 GCAACCGGATTAGCTTGCAAAT 60.417 45.455 17.53 0.00 39.09 2.32
933 949 6.352137 GCAAATTCCCATGGATTTCTTTAGGT 60.352 38.462 15.22 0.00 0.00 3.08
1023 1039 2.821969 GGAAGAAGGCATCAAAGAAGCA 59.178 45.455 0.00 0.00 0.00 3.91
1050 1066 1.658114 CAAGAAAGCAGCAGCAGCA 59.342 52.632 12.92 0.00 45.49 4.41
1051 1067 0.387367 CAAGAAAGCAGCAGCAGCAG 60.387 55.000 12.92 0.00 45.49 4.24
1101 1117 1.216977 CATGGCCGACTCCACGTTA 59.783 57.895 0.00 0.00 39.25 3.18
1179 1195 0.396435 TGCTCAACCCAATCGTGACT 59.604 50.000 0.00 0.00 0.00 3.41
1368 1384 3.055719 GACGACGACACCGGGGTA 61.056 66.667 10.83 0.00 40.78 3.69
1371 1387 2.334946 CGACGACACCGGGGTAAGA 61.335 63.158 10.83 0.00 40.78 2.10
1388 1404 5.245526 GGGTAAGAGACTTCTCCAAGTACAA 59.754 44.000 2.47 0.00 43.37 2.41
1524 1540 1.303561 GAAGCAGGTGGTCATGGCA 60.304 57.895 0.00 0.00 0.00 4.92
1744 1789 1.735571 AGTCGAGTTTTGTGTGCGTTT 59.264 42.857 0.00 0.00 0.00 3.60
1745 1790 2.160813 AGTCGAGTTTTGTGTGCGTTTT 59.839 40.909 0.00 0.00 0.00 2.43
1746 1791 2.912345 GTCGAGTTTTGTGTGCGTTTTT 59.088 40.909 0.00 0.00 0.00 1.94
1765 1810 2.254546 TTGTTCAGATGTGCCGTTCT 57.745 45.000 0.00 0.00 0.00 3.01
1768 1813 2.143122 GTTCAGATGTGCCGTTCTCAA 58.857 47.619 0.00 0.00 0.00 3.02
1775 1825 0.814010 GTGCCGTTCTCAAGTGGTGT 60.814 55.000 0.00 0.00 0.00 4.16
1867 1919 9.997482 GTACAAAAGTAAGTTCAATTCTGTTCA 57.003 29.630 0.00 0.00 0.00 3.18
1871 1923 9.450807 AAAAGTAAGTTCAATTCTGTTCATTCG 57.549 29.630 0.00 0.00 0.00 3.34
1872 1924 7.133891 AGTAAGTTCAATTCTGTTCATTCGG 57.866 36.000 0.00 0.00 0.00 4.30
1873 1925 6.934645 AGTAAGTTCAATTCTGTTCATTCGGA 59.065 34.615 0.00 0.00 0.00 4.55
1874 1926 6.633500 AAGTTCAATTCTGTTCATTCGGAA 57.367 33.333 0.00 0.00 37.16 4.30
1875 1927 6.633500 AGTTCAATTCTGTTCATTCGGAAA 57.367 33.333 0.00 0.00 37.23 3.13
1876 1928 7.038154 AGTTCAATTCTGTTCATTCGGAAAA 57.962 32.000 0.00 0.00 37.23 2.29
1877 1929 7.488322 AGTTCAATTCTGTTCATTCGGAAAAA 58.512 30.769 0.00 0.00 37.23 1.94
1906 1958 5.660864 TCAATTCTGTTCCCTTTTCTTGGTT 59.339 36.000 0.00 0.00 0.00 3.67
1908 1960 6.560003 ATTCTGTTCCCTTTTCTTGGTTTT 57.440 33.333 0.00 0.00 0.00 2.43
1984 2044 4.043435 AGGAAAACAGTAGCCAGGAAAGAT 59.957 41.667 0.00 0.00 0.00 2.40
1987 2047 6.433093 GGAAAACAGTAGCCAGGAAAGATAAA 59.567 38.462 0.00 0.00 0.00 1.40
1998 2058 6.447162 CCAGGAAAGATAAAAGGACACAAAC 58.553 40.000 0.00 0.00 0.00 2.93
1999 2059 6.142817 CAGGAAAGATAAAAGGACACAAACG 58.857 40.000 0.00 0.00 0.00 3.60
2000 2060 6.017440 CAGGAAAGATAAAAGGACACAAACGA 60.017 38.462 0.00 0.00 0.00 3.85
2001 2061 6.715264 AGGAAAGATAAAAGGACACAAACGAT 59.285 34.615 0.00 0.00 0.00 3.73
2004 2084 6.727824 AGATAAAAGGACACAAACGATCAG 57.272 37.500 0.00 0.00 0.00 2.90
2051 2131 9.506018 TGATCATCTTCTTCTTTTGATTGTACA 57.494 29.630 0.00 0.00 0.00 2.90
2163 2251 6.666678 TGAAGAAAGAATCCCATTGCTAGAT 58.333 36.000 0.00 0.00 0.00 1.98
2167 2255 5.393068 AAGAATCCCATTGCTAGATTGGA 57.607 39.130 0.00 0.00 30.52 3.53
2433 2525 2.749621 GTTGGAGAAATCGAACCATGCT 59.250 45.455 0.00 0.00 32.31 3.79
2614 2741 0.251253 TGTCATTGCTGCCACCATCA 60.251 50.000 0.00 0.00 0.00 3.07
2615 2742 0.454600 GTCATTGCTGCCACCATCAG 59.545 55.000 0.00 0.00 34.79 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 52 3.110178 CGGTGTCCGGCTTTCGAC 61.110 66.667 0.00 0.00 44.15 4.20
60 68 0.848942 CGGCGACAATGATCTCTTCG 59.151 55.000 0.00 0.00 0.00 3.79
89 97 2.783135 TGGAAATGAGGACTGAAGCAC 58.217 47.619 0.00 0.00 0.00 4.40
95 103 5.826208 TGATCATCATTGGAAATGAGGACTG 59.174 40.000 16.78 7.08 40.87 3.51
109 117 7.042950 GCATCTATAGCTGACTGATCATCATT 58.957 38.462 7.77 0.00 33.22 2.57
111 119 5.392811 CGCATCTATAGCTGACTGATCATCA 60.393 44.000 7.77 1.87 33.22 3.07
142 150 2.220313 GAGATTTCAGAGGCCATGAGC 58.780 52.381 5.01 2.77 42.60 4.26
143 151 3.555527 TGAGATTTCAGAGGCCATGAG 57.444 47.619 5.01 0.00 0.00 2.90
147 155 4.679373 GACTATGAGATTTCAGAGGCCA 57.321 45.455 12.05 0.00 43.49 5.36
151 159 4.930963 AGCGTGACTATGAGATTTCAGAG 58.069 43.478 6.35 6.35 45.87 3.35
171 179 7.402640 GCAAACTCATGTATCAGTTAAGTAGC 58.597 38.462 0.00 0.00 32.36 3.58
179 187 7.665559 TCTTTTTAGGCAAACTCATGTATCAGT 59.334 33.333 0.00 0.00 0.00 3.41
183 191 8.860088 AGTTTCTTTTTAGGCAAACTCATGTAT 58.140 29.630 0.00 0.00 34.66 2.29
184 192 8.232913 AGTTTCTTTTTAGGCAAACTCATGTA 57.767 30.769 0.00 0.00 34.66 2.29
185 193 7.112452 AGTTTCTTTTTAGGCAAACTCATGT 57.888 32.000 0.00 0.00 34.66 3.21
186 194 9.696917 ATAAGTTTCTTTTTAGGCAAACTCATG 57.303 29.630 0.00 0.00 37.96 3.07
192 200 9.921637 CCATGTATAAGTTTCTTTTTAGGCAAA 57.078 29.630 0.00 0.00 0.00 3.68
193 201 8.527810 CCCATGTATAAGTTTCTTTTTAGGCAA 58.472 33.333 0.00 0.00 0.00 4.52
194 202 7.672239 ACCCATGTATAAGTTTCTTTTTAGGCA 59.328 33.333 0.00 0.00 0.00 4.75
195 203 8.063200 ACCCATGTATAAGTTTCTTTTTAGGC 57.937 34.615 0.00 0.00 0.00 3.93
196 204 9.238368 TGACCCATGTATAAGTTTCTTTTTAGG 57.762 33.333 0.00 0.00 0.00 2.69
201 209 9.975218 ACTTATGACCCATGTATAAGTTTCTTT 57.025 29.630 12.39 0.00 42.07 2.52
202 210 9.614792 GACTTATGACCCATGTATAAGTTTCTT 57.385 33.333 16.34 0.00 43.74 2.52
203 211 8.993424 AGACTTATGACCCATGTATAAGTTTCT 58.007 33.333 16.34 10.79 43.74 2.52
204 212 9.262358 GAGACTTATGACCCATGTATAAGTTTC 57.738 37.037 16.34 16.00 43.74 2.78
205 213 8.993424 AGAGACTTATGACCCATGTATAAGTTT 58.007 33.333 16.34 13.13 43.74 2.66
206 214 8.424918 CAGAGACTTATGACCCATGTATAAGTT 58.575 37.037 16.34 10.40 43.74 2.66
207 215 7.785028 TCAGAGACTTATGACCCATGTATAAGT 59.215 37.037 15.69 15.69 45.37 2.24
208 216 8.183104 TCAGAGACTTATGACCCATGTATAAG 57.817 38.462 11.54 11.54 39.26 1.73
209 217 8.547481 TTCAGAGACTTATGACCCATGTATAA 57.453 34.615 0.00 0.00 0.00 0.98
210 218 7.785028 ACTTCAGAGACTTATGACCCATGTATA 59.215 37.037 0.00 0.00 0.00 1.47
246 254 1.141455 AGCAAGCAAGGTTTGGCAATT 59.859 42.857 0.00 0.00 0.00 2.32
264 272 1.672881 GGATATGTGACCAGCAACAGC 59.327 52.381 0.00 0.00 0.00 4.40
265 273 3.272574 AGGATATGTGACCAGCAACAG 57.727 47.619 0.00 0.00 0.00 3.16
266 274 3.719268 AAGGATATGTGACCAGCAACA 57.281 42.857 0.00 0.00 0.00 3.33
267 275 3.378427 GGAAAGGATATGTGACCAGCAAC 59.622 47.826 0.00 0.00 0.00 4.17
268 276 3.010027 TGGAAAGGATATGTGACCAGCAA 59.990 43.478 0.00 0.00 0.00 3.91
269 277 2.575735 TGGAAAGGATATGTGACCAGCA 59.424 45.455 0.00 0.00 0.00 4.41
310 318 3.631145 TGCTTGAGATTTTGCTGACAC 57.369 42.857 0.00 0.00 0.00 3.67
374 382 6.127786 GCACTTTCCTTAGAAAATCTGCAGAT 60.128 38.462 23.75 23.75 41.40 2.90
412 420 4.767409 ACTGGTTGAAATTAAGCCTTCTCC 59.233 41.667 0.00 0.00 0.00 3.71
448 459 4.571176 GCAAGTGTATTCTACTAAGTGGGC 59.429 45.833 0.00 0.00 0.00 5.36
449 460 5.730550 TGCAAGTGTATTCTACTAAGTGGG 58.269 41.667 0.00 0.00 0.00 4.61
514 525 6.311445 GTGAAAGACTACAATGTGATCGTGAT 59.689 38.462 0.00 0.00 0.00 3.06
600 611 3.935203 ACTCGGTGCAGATTAATTGTCTG 59.065 43.478 14.83 14.83 44.60 3.51
617 628 1.278172 CGTGTTGTGAGCTCACTCGG 61.278 60.000 38.81 24.50 46.69 4.63
672 683 2.028748 AGGTTGGATTGCTTGTTCATGC 60.029 45.455 4.14 4.14 0.00 4.06
689 700 5.420104 GGGAGTTTTCATGATTGATGAGGTT 59.580 40.000 0.00 0.00 42.24 3.50
694 705 5.361571 TCATGGGGAGTTTTCATGATTGATG 59.638 40.000 0.00 0.00 41.31 3.07
737 748 6.465439 TTTTCTAAGATCCTGACAGCGATA 57.535 37.500 0.00 0.00 0.00 2.92
766 777 3.259374 CCTGCCTCGAAGTCCATACATAT 59.741 47.826 0.00 0.00 0.00 1.78
769 780 0.824109 CCTGCCTCGAAGTCCATACA 59.176 55.000 0.00 0.00 0.00 2.29
770 781 1.112113 TCCTGCCTCGAAGTCCATAC 58.888 55.000 0.00 0.00 0.00 2.39
782 793 4.583871 CAAGAAGATACAAGTTCCTGCCT 58.416 43.478 0.00 0.00 0.00 4.75
786 797 6.491403 ACATTTGCAAGAAGATACAAGTTCCT 59.509 34.615 0.00 0.00 0.00 3.36
790 801 5.047802 CCCACATTTGCAAGAAGATACAAGT 60.048 40.000 0.00 0.00 0.00 3.16
791 802 5.404946 CCCACATTTGCAAGAAGATACAAG 58.595 41.667 0.00 0.00 0.00 3.16
792 803 4.321899 GCCCACATTTGCAAGAAGATACAA 60.322 41.667 0.00 0.00 0.00 2.41
793 804 3.193267 GCCCACATTTGCAAGAAGATACA 59.807 43.478 0.00 0.00 0.00 2.29
794 805 3.193267 TGCCCACATTTGCAAGAAGATAC 59.807 43.478 0.00 0.00 33.87 2.24
799 814 1.969208 TGATGCCCACATTTGCAAGAA 59.031 42.857 0.00 0.00 41.50 2.52
817 832 8.046107 TGATAGTGACCAAATTGATGTACATGA 58.954 33.333 14.43 0.68 0.00 3.07
825 840 8.806429 TGTAATGTGATAGTGACCAAATTGAT 57.194 30.769 0.00 0.00 0.00 2.57
848 863 6.040054 GGTACCTTGTCTTGGTTGTAAATTGT 59.960 38.462 4.06 0.00 38.88 2.71
869 884 5.816258 GCTTACTTGGGAGAAATAGTGGTAC 59.184 44.000 0.00 0.00 0.00 3.34
908 924 6.051074 CCTAAAGAAATCCATGGGAATTTGC 58.949 40.000 13.02 6.17 34.34 3.68
912 928 5.043432 TGGACCTAAAGAAATCCATGGGAAT 60.043 40.000 13.02 0.00 36.30 3.01
913 929 4.293634 TGGACCTAAAGAAATCCATGGGAA 59.706 41.667 13.02 0.00 36.30 3.97
933 949 7.881912 TTACCTATTTTATAGGCCATCTGGA 57.118 36.000 5.01 0.00 38.25 3.86
970 986 3.253061 GCTATCCCCTGCCCTCCC 61.253 72.222 0.00 0.00 0.00 4.30
1023 1039 1.938926 GCTGCTTTCTTGCTCGACTCT 60.939 52.381 0.00 0.00 0.00 3.24
1060 1076 2.983592 CACTTTGGTCCCGGTGCC 60.984 66.667 0.00 2.09 0.00 5.01
1065 1081 4.636435 ACGCCCACTTTGGTCCCG 62.636 66.667 0.00 0.00 35.17 5.14
1067 1083 1.303317 ATGACGCCCACTTTGGTCC 60.303 57.895 0.00 0.00 35.17 4.46
1095 1111 1.883084 GCCGATGCTCCCTAACGTG 60.883 63.158 0.00 0.00 33.53 4.49
1200 1216 2.978010 GTGACCACCCTGTTGGCG 60.978 66.667 0.00 0.00 40.77 5.69
1345 1361 4.380628 GGTGTCGTCGTCGTCGCT 62.381 66.667 7.01 0.00 36.31 4.93
1367 1383 5.775701 AGCTTGTACTTGGAGAAGTCTCTTA 59.224 40.000 8.19 0.00 41.75 2.10
1368 1384 4.591072 AGCTTGTACTTGGAGAAGTCTCTT 59.409 41.667 8.19 0.00 41.75 2.85
1371 1387 3.556004 GCAGCTTGTACTTGGAGAAGTCT 60.556 47.826 0.00 0.00 41.75 3.24
1401 1417 4.961511 AAGGCGTGCGCGAAGTCA 62.962 61.111 26.19 0.00 43.06 3.41
1688 1704 1.057005 CACGCAAAACACAAACACGTG 59.943 47.619 15.48 15.48 42.59 4.49
1690 1706 0.023103 GCACGCAAAACACAAACACG 59.977 50.000 0.00 0.00 0.00 4.49
1744 1789 2.948979 AGAACGGCACATCTGAACAAAA 59.051 40.909 0.00 0.00 0.00 2.44
1745 1790 2.548057 GAGAACGGCACATCTGAACAAA 59.452 45.455 0.00 0.00 0.00 2.83
1746 1791 2.143122 GAGAACGGCACATCTGAACAA 58.857 47.619 0.00 0.00 0.00 2.83
1747 1792 1.069978 TGAGAACGGCACATCTGAACA 59.930 47.619 0.00 0.00 0.00 3.18
1748 1793 1.795768 TGAGAACGGCACATCTGAAC 58.204 50.000 0.00 0.00 0.00 3.18
1749 1794 2.224281 ACTTGAGAACGGCACATCTGAA 60.224 45.455 0.00 0.00 0.00 3.02
1750 1795 1.344438 ACTTGAGAACGGCACATCTGA 59.656 47.619 0.00 0.00 0.00 3.27
1751 1796 1.462283 CACTTGAGAACGGCACATCTG 59.538 52.381 0.00 0.00 0.00 2.90
1752 1797 1.609061 CCACTTGAGAACGGCACATCT 60.609 52.381 0.00 0.00 0.00 2.90
1753 1798 0.798776 CCACTTGAGAACGGCACATC 59.201 55.000 0.00 0.00 0.00 3.06
1765 1810 2.820787 ACGAACCAAAAACACCACTTGA 59.179 40.909 0.00 0.00 0.00 3.02
1768 1813 1.399089 CGACGAACCAAAAACACCACT 59.601 47.619 0.00 0.00 0.00 4.00
1775 1825 1.774046 GACCCGCGACGAACCAAAAA 61.774 55.000 8.23 0.00 0.00 1.94
1875 1927 8.321353 AGAAAAGGGAACAGAATTGAACTTTTT 58.679 29.630 0.00 0.00 0.00 1.94
1876 1928 7.851228 AGAAAAGGGAACAGAATTGAACTTTT 58.149 30.769 0.00 0.00 0.00 2.27
1877 1929 7.423844 AGAAAAGGGAACAGAATTGAACTTT 57.576 32.000 0.00 0.00 0.00 2.66
1878 1930 7.267857 CAAGAAAAGGGAACAGAATTGAACTT 58.732 34.615 0.00 0.00 0.00 2.66
1879 1931 6.183360 CCAAGAAAAGGGAACAGAATTGAACT 60.183 38.462 0.00 0.00 0.00 3.01
1880 1932 5.985530 CCAAGAAAAGGGAACAGAATTGAAC 59.014 40.000 0.00 0.00 0.00 3.18
1881 1933 5.660864 ACCAAGAAAAGGGAACAGAATTGAA 59.339 36.000 0.00 0.00 0.00 2.69
1882 1934 5.208121 ACCAAGAAAAGGGAACAGAATTGA 58.792 37.500 0.00 0.00 0.00 2.57
1883 1935 5.535753 ACCAAGAAAAGGGAACAGAATTG 57.464 39.130 0.00 0.00 0.00 2.32
1884 1936 6.560003 AAACCAAGAAAAGGGAACAGAATT 57.440 33.333 0.00 0.00 0.00 2.17
1885 1937 6.560003 AAAACCAAGAAAAGGGAACAGAAT 57.440 33.333 0.00 0.00 0.00 2.40
1886 1938 7.669089 ATAAAACCAAGAAAAGGGAACAGAA 57.331 32.000 0.00 0.00 0.00 3.02
1887 1939 7.669089 AATAAAACCAAGAAAAGGGAACAGA 57.331 32.000 0.00 0.00 0.00 3.41
1888 1940 8.731275 AAAATAAAACCAAGAAAAGGGAACAG 57.269 30.769 0.00 0.00 0.00 3.16
1973 2033 4.079253 TGTGTCCTTTTATCTTTCCTGGC 58.921 43.478 0.00 0.00 0.00 4.85
1984 2044 4.130857 TGCTGATCGTTTGTGTCCTTTTA 58.869 39.130 0.00 0.00 0.00 1.52
1987 2047 2.254546 TGCTGATCGTTTGTGTCCTT 57.745 45.000 0.00 0.00 0.00 3.36
2022 2102 9.856488 ACAATCAAAAGAAGAAGATGATCATTG 57.144 29.630 10.14 0.87 30.76 2.82
2025 2105 9.506018 TGTACAATCAAAAGAAGAAGATGATCA 57.494 29.630 0.00 0.00 30.76 2.92
2028 2108 8.659491 CGATGTACAATCAAAAGAAGAAGATGA 58.341 33.333 0.00 0.00 0.00 2.92
2065 2145 4.116747 ACGGTTCACTGCAATTTTCAAA 57.883 36.364 0.00 0.00 0.00 2.69
2246 2338 9.349145 GAAGTAGAAGAGTTCTTGTCATTACTC 57.651 37.037 0.00 0.00 41.14 2.59
2284 2376 6.709846 TGGCTTGTTCCATTTCTTTAAATTGG 59.290 34.615 0.00 0.00 32.87 3.16
2303 2395 9.859427 TCTTATTTTCTAACAATGAATGGCTTG 57.141 29.630 0.00 0.00 0.00 4.01
2433 2525 6.029607 GCATCTTCTTTCGATTTGTTATGCA 58.970 36.000 12.56 0.00 36.79 3.96
2542 2634 2.376109 TCTTGACGAGGGTAGATGTCC 58.624 52.381 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.