Multiple sequence alignment - TraesCS4A01G028300

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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 TraesCS4A01G028300 chr4A 100.000 1909 0 0 541 2449 20259472 20261380 0.000000e+00 3526
1 TraesCS4A01G028300 chr4A 100.000 223 0 0 1 223 20258932 20259154 1.750000e-111 412
2 TraesCS4A01G028300 chr4A 94.949 99 4 1 1993 2091 709736512 709736415 1.170000e-33 154
3 TraesCS4A01G028300 chr4D 89.263 1872 88 52 644 2449 446916876 446915052 0.000000e+00 2239
4 TraesCS4A01G028300 chr4B 88.063 1977 112 51 541 2449 559288675 559286755 0.000000e+00 2230
5 TraesCS4A01G028300 chr3A 98.913 92 0 1 2004 2095 636154958 636154868 1.950000e-36 163
6 TraesCS4A01G028300 chr3A 91.667 120 5 5 1974 2090 636526418 636526301 7.010000e-36 161
7 TraesCS4A01G028300 chr2A 95.918 98 2 2 2000 2095 126483534 126483437 9.070000e-35 158
8 TraesCS4A01G028300 chr1D 95.000 100 5 0 2009 2108 306670169 306670268 9.070000e-35 158
9 TraesCS4A01G028300 chr1A 95.050 101 4 1 2009 2108 385352191 385352291 9.070000e-35 158
10 TraesCS4A01G028300 chr3D 95.876 97 2 2 1994 2088 498113504 498113600 3.260000e-34 156


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 TraesCS4A01G028300 chr4A 20258932 20261380 2448 False 1969 3526 100.000 1 2449 2 chr4A.!!$F1 2448
1 TraesCS4A01G028300 chr4D 446915052 446916876 1824 True 2239 2239 89.263 644 2449 1 chr4D.!!$R1 1805
2 TraesCS4A01G028300 chr4B 559286755 559288675 1920 True 2230 2230 88.063 541 2449 1 chr4B.!!$R1 1908

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
642 653 0.106217 CTCTCCTCTCACTCTCCCCC 60.106 65.0 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 1701 0.319727 CATGGATCTCTCTGCGCTCC 60.32 60.0 9.73 5.71 0.0 4.7 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
87 88 4.994471 TGCTGGGCGCACAGACTG 62.994 66.667 42.44 18.68 45.47 3.51
96 97 4.056125 CACAGACTGCGAGCCGGA 62.056 66.667 5.05 0.00 0.00 5.14
97 98 3.071206 ACAGACTGCGAGCCGGAT 61.071 61.111 5.05 0.00 0.00 4.18
98 99 2.185350 CAGACTGCGAGCCGGATT 59.815 61.111 5.05 0.00 0.00 3.01
99 100 2.169789 CAGACTGCGAGCCGGATTG 61.170 63.158 5.05 3.02 0.00 2.67
100 101 2.125512 GACTGCGAGCCGGATTGT 60.126 61.111 5.05 0.00 0.00 2.71
101 102 1.741770 GACTGCGAGCCGGATTGTT 60.742 57.895 5.05 0.00 0.00 2.83
102 103 1.970917 GACTGCGAGCCGGATTGTTG 61.971 60.000 5.05 2.28 0.00 3.33
103 104 3.386867 CTGCGAGCCGGATTGTTGC 62.387 63.158 5.05 2.41 0.00 4.17
104 105 4.179579 GCGAGCCGGATTGTTGCC 62.180 66.667 5.05 0.00 0.00 4.52
163 164 4.373116 GAGCGAGCCACACCCGAA 62.373 66.667 0.00 0.00 0.00 4.30
164 165 4.681978 AGCGAGCCACACCCGAAC 62.682 66.667 0.00 0.00 0.00 3.95
166 167 4.003788 CGAGCCACACCCGAACCT 62.004 66.667 0.00 0.00 0.00 3.50
167 168 2.047179 GAGCCACACCCGAACCTC 60.047 66.667 0.00 0.00 0.00 3.85
168 169 3.607370 GAGCCACACCCGAACCTCC 62.607 68.421 0.00 0.00 0.00 4.30
169 170 4.717313 GCCACACCCGAACCTCCC 62.717 72.222 0.00 0.00 0.00 4.30
170 171 3.246112 CCACACCCGAACCTCCCA 61.246 66.667 0.00 0.00 0.00 4.37
171 172 2.824880 CCACACCCGAACCTCCCAA 61.825 63.158 0.00 0.00 0.00 4.12
172 173 1.599797 CACACCCGAACCTCCCAAC 60.600 63.158 0.00 0.00 0.00 3.77
173 174 2.033602 CACCCGAACCTCCCAACC 59.966 66.667 0.00 0.00 0.00 3.77
174 175 2.448931 ACCCGAACCTCCCAACCA 60.449 61.111 0.00 0.00 0.00 3.67
175 176 2.079911 ACCCGAACCTCCCAACCAA 61.080 57.895 0.00 0.00 0.00 3.67
176 177 1.151908 CCCGAACCTCCCAACCAAA 59.848 57.895 0.00 0.00 0.00 3.28
177 178 0.893727 CCCGAACCTCCCAACCAAAG 60.894 60.000 0.00 0.00 0.00 2.77
178 179 1.524008 CCGAACCTCCCAACCAAAGC 61.524 60.000 0.00 0.00 0.00 3.51
179 180 1.524008 CGAACCTCCCAACCAAAGCC 61.524 60.000 0.00 0.00 0.00 4.35
180 181 1.524008 GAACCTCCCAACCAAAGCCG 61.524 60.000 0.00 0.00 0.00 5.52
181 182 3.373565 CCTCCCAACCAAAGCCGC 61.374 66.667 0.00 0.00 0.00 6.53
182 183 3.373565 CTCCCAACCAAAGCCGCC 61.374 66.667 0.00 0.00 0.00 6.13
183 184 3.868200 CTCCCAACCAAAGCCGCCT 62.868 63.158 0.00 0.00 0.00 5.52
184 185 3.373565 CCCAACCAAAGCCGCCTC 61.374 66.667 0.00 0.00 0.00 4.70
185 186 2.282462 CCAACCAAAGCCGCCTCT 60.282 61.111 0.00 0.00 0.00 3.69
186 187 1.002624 CCAACCAAAGCCGCCTCTA 60.003 57.895 0.00 0.00 0.00 2.43
187 188 1.305930 CCAACCAAAGCCGCCTCTAC 61.306 60.000 0.00 0.00 0.00 2.59
188 189 1.002502 AACCAAAGCCGCCTCTACC 60.003 57.895 0.00 0.00 0.00 3.18
189 190 2.124695 CCAAAGCCGCCTCTACCC 60.125 66.667 0.00 0.00 0.00 3.69
190 191 2.670148 CCAAAGCCGCCTCTACCCT 61.670 63.158 0.00 0.00 0.00 4.34
191 192 1.335132 CCAAAGCCGCCTCTACCCTA 61.335 60.000 0.00 0.00 0.00 3.53
192 193 0.539986 CAAAGCCGCCTCTACCCTAA 59.460 55.000 0.00 0.00 0.00 2.69
193 194 1.065709 CAAAGCCGCCTCTACCCTAAA 60.066 52.381 0.00 0.00 0.00 1.85
194 195 1.282382 AAGCCGCCTCTACCCTAAAA 58.718 50.000 0.00 0.00 0.00 1.52
195 196 1.282382 AGCCGCCTCTACCCTAAAAA 58.718 50.000 0.00 0.00 0.00 1.94
216 217 0.673985 AAAAACAAAGCCGCCTCTCC 59.326 50.000 0.00 0.00 0.00 3.71
217 218 1.179174 AAAACAAAGCCGCCTCTCCC 61.179 55.000 0.00 0.00 0.00 4.30
218 219 2.069165 AAACAAAGCCGCCTCTCCCT 62.069 55.000 0.00 0.00 0.00 4.20
219 220 2.124942 CAAAGCCGCCTCTCCCTC 60.125 66.667 0.00 0.00 0.00 4.30
220 221 3.403558 AAAGCCGCCTCTCCCTCC 61.404 66.667 0.00 0.00 0.00 4.30
221 222 4.722535 AAGCCGCCTCTCCCTCCA 62.723 66.667 0.00 0.00 0.00 3.86
580 581 4.602259 ACACCCACAGACACGGCG 62.602 66.667 4.80 4.80 0.00 6.46
582 583 3.991051 ACCCACAGACACGGCGAG 61.991 66.667 16.62 8.85 0.00 5.03
633 644 9.782900 TCTCTCTCTATATTATCTCTCCTCTCA 57.217 37.037 0.00 0.00 0.00 3.27
637 648 9.560860 TCTCTATATTATCTCTCCTCTCACTCT 57.439 37.037 0.00 0.00 0.00 3.24
642 653 0.106217 CTCTCCTCTCACTCTCCCCC 60.106 65.000 0.00 0.00 0.00 5.40
666 677 4.151883 CTCTCTCCCTCTCTCCTTTATGG 58.848 52.174 0.00 0.00 37.10 2.74
758 769 1.822186 ACACAAACGCCACTCCACC 60.822 57.895 0.00 0.00 0.00 4.61
865 885 1.815613 GCTTTGCTTTCTTCTCCCTCC 59.184 52.381 0.00 0.00 0.00 4.30
866 886 2.554124 GCTTTGCTTTCTTCTCCCTCCT 60.554 50.000 0.00 0.00 0.00 3.69
867 887 2.867109 TTGCTTTCTTCTCCCTCCTG 57.133 50.000 0.00 0.00 0.00 3.86
970 990 1.341531 GGGTGATACGAGATCTGGTGG 59.658 57.143 19.53 0.00 0.00 4.61
971 991 1.341531 GGTGATACGAGATCTGGTGGG 59.658 57.143 19.53 0.00 0.00 4.61
1126 1146 6.018588 CCGTGTTTCTTCGGCATTATATACAA 60.019 38.462 0.00 0.00 40.28 2.41
1452 1482 2.020131 CTCTTCATGCCATGACCGC 58.980 57.895 6.94 0.00 39.39 5.68
1503 1546 4.559063 CCCTGATGCTGCTCCCGG 62.559 72.222 0.00 0.00 0.00 5.73
1560 1603 1.445518 GAGCTAGCTCCTCAAGGCC 59.554 63.158 30.89 6.00 37.11 5.19
1566 1609 3.710722 CTCCTCAAGGCCACGGCT 61.711 66.667 5.01 0.00 41.24 5.52
1567 1610 3.965539 CTCCTCAAGGCCACGGCTG 62.966 68.421 5.01 0.00 38.81 4.85
1593 1636 2.352805 CACAAGGCCAGGAGGTCC 59.647 66.667 5.01 0.00 41.85 4.46
1637 1683 6.102615 AGAGGGATCTAGCTAGAGAAGAAGAA 59.897 42.308 26.64 2.63 35.50 2.52
1638 1684 6.306987 AGGGATCTAGCTAGAGAAGAAGAAG 58.693 44.000 26.64 0.00 35.50 2.85
1639 1685 6.102615 AGGGATCTAGCTAGAGAAGAAGAAGA 59.897 42.308 26.64 3.25 35.50 2.87
1640 1686 6.775629 GGGATCTAGCTAGAGAAGAAGAAGAA 59.224 42.308 26.64 1.16 35.50 2.52
1641 1687 7.040409 GGGATCTAGCTAGAGAAGAAGAAGAAG 60.040 44.444 26.64 0.00 35.50 2.85
1642 1688 7.719633 GGATCTAGCTAGAGAAGAAGAAGAAGA 59.280 40.741 26.64 1.92 35.50 2.87
1643 1689 9.120538 GATCTAGCTAGAGAAGAAGAAGAAGAA 57.879 37.037 26.64 0.00 35.50 2.52
1644 1690 8.506168 TCTAGCTAGAGAAGAAGAAGAAGAAG 57.494 38.462 19.72 0.00 0.00 2.85
1645 1691 8.325787 TCTAGCTAGAGAAGAAGAAGAAGAAGA 58.674 37.037 19.72 0.00 0.00 2.87
1646 1692 7.775053 AGCTAGAGAAGAAGAAGAAGAAGAA 57.225 36.000 0.00 0.00 0.00 2.52
1647 1693 7.830739 AGCTAGAGAAGAAGAAGAAGAAGAAG 58.169 38.462 0.00 0.00 0.00 2.85
1648 1694 7.669722 AGCTAGAGAAGAAGAAGAAGAAGAAGA 59.330 37.037 0.00 0.00 0.00 2.87
1655 1701 2.495669 AGAAGAAGAAGAAGAGGGAGCG 59.504 50.000 0.00 0.00 0.00 5.03
1678 1724 1.863267 CGCAGAGAGATCCATGGAAC 58.137 55.000 20.67 17.06 0.00 3.62
1761 1807 6.486993 AGTTCTTGGAGATTTTAACCAGTGTC 59.513 38.462 0.00 0.00 35.08 3.67
1762 1808 6.187727 TCTTGGAGATTTTAACCAGTGTCT 57.812 37.500 0.00 0.00 35.08 3.41
1766 1812 5.763204 TGGAGATTTTAACCAGTGTCTTGTC 59.237 40.000 0.00 0.00 0.00 3.18
1771 1842 0.874607 AACCAGTGTCTTGTCGTCGC 60.875 55.000 0.00 0.00 0.00 5.19
1839 1914 4.085733 TCTCTCTCTGGTTCTTCTCCTTG 58.914 47.826 0.00 0.00 0.00 3.61
1883 1964 3.364964 CGGTTTTGAGGAGTGATTTTCCG 60.365 47.826 0.00 0.00 39.77 4.30
1896 1977 7.198306 AGTGATTTTCCGACTAATTTTCGTT 57.802 32.000 7.99 0.00 34.56 3.85
1905 1986 9.806203 TTCCGACTAATTTTCGTTAATCTATGA 57.194 29.630 7.99 0.00 34.56 2.15
1906 1987 9.976511 TCCGACTAATTTTCGTTAATCTATGAT 57.023 29.630 7.99 0.00 34.56 2.45
1968 2052 2.233676 TCTGTTCGAGCATGCTTCCTTA 59.766 45.455 23.61 8.11 0.00 2.69
1973 2058 2.361119 TCGAGCATGCTTCCTTACGTAT 59.639 45.455 23.61 0.00 0.00 3.06
1980 2065 6.480320 AGCATGCTTCCTTACGTATAAAAGAG 59.520 38.462 16.30 0.37 0.00 2.85
1981 2066 6.650372 CATGCTTCCTTACGTATAAAAGAGC 58.350 40.000 12.78 10.55 0.00 4.09
1997 2082 3.550437 AGAGCCAGTATGCCAAACTAG 57.450 47.619 0.00 0.00 31.97 2.57
2091 2176 2.123342 GAATCTCTCAGGCGTCGATTG 58.877 52.381 0.00 0.00 0.00 2.67
2095 2181 1.656095 CTCTCAGGCGTCGATTGTTTC 59.344 52.381 0.00 0.00 0.00 2.78
2097 2183 0.672401 TCAGGCGTCGATTGTTTCCC 60.672 55.000 0.00 0.00 0.00 3.97
2100 2187 1.366854 GGCGTCGATTGTTTCCCTCC 61.367 60.000 0.00 0.00 0.00 4.30
2102 2189 1.944430 GCGTCGATTGTTTCCCTCCTT 60.944 52.381 0.00 0.00 0.00 3.36
2137 2224 6.201226 GGATCTCTCCAAATTTTCACTTCC 57.799 41.667 0.00 0.00 41.64 3.46
2139 2226 6.127786 GGATCTCTCCAAATTTTCACTTCCTG 60.128 42.308 0.00 0.00 41.64 3.86
2141 2228 4.473444 TCTCCAAATTTTCACTTCCTGCT 58.527 39.130 0.00 0.00 0.00 4.24
2144 2231 5.385198 TCCAAATTTTCACTTCCTGCTACT 58.615 37.500 0.00 0.00 0.00 2.57
2146 2233 6.430000 TCCAAATTTTCACTTCCTGCTACTAC 59.570 38.462 0.00 0.00 0.00 2.73
2147 2234 6.206634 CCAAATTTTCACTTCCTGCTACTACA 59.793 38.462 0.00 0.00 0.00 2.74
2148 2235 6.803154 AATTTTCACTTCCTGCTACTACAC 57.197 37.500 0.00 0.00 0.00 2.90
2185 2272 3.266772 TGGATGGAGCCTGTAATTGTTCT 59.733 43.478 0.00 0.00 0.00 3.01
2210 2297 1.139498 TTCCCTGGATCTTGTGGCCA 61.139 55.000 0.00 0.00 0.00 5.36
2213 2300 0.038744 CCTGGATCTTGTGGCCAGTT 59.961 55.000 5.11 0.00 46.05 3.16
2216 2303 1.144708 TGGATCTTGTGGCCAGTTCAA 59.855 47.619 5.11 6.36 0.00 2.69
2217 2304 2.225091 TGGATCTTGTGGCCAGTTCAAT 60.225 45.455 5.11 0.00 0.00 2.57
2218 2305 3.010027 TGGATCTTGTGGCCAGTTCAATA 59.990 43.478 5.11 0.00 0.00 1.90
2242 2329 1.821753 CACACCACACCCAAAGAAACA 59.178 47.619 0.00 0.00 0.00 2.83
2243 2330 2.232452 CACACCACACCCAAAGAAACAA 59.768 45.455 0.00 0.00 0.00 2.83
2244 2331 2.495669 ACACCACACCCAAAGAAACAAG 59.504 45.455 0.00 0.00 0.00 3.16
2245 2332 2.757868 CACCACACCCAAAGAAACAAGA 59.242 45.455 0.00 0.00 0.00 3.02
2246 2333 3.194542 CACCACACCCAAAGAAACAAGAA 59.805 43.478 0.00 0.00 0.00 2.52
2247 2334 3.835395 ACCACACCCAAAGAAACAAGAAA 59.165 39.130 0.00 0.00 0.00 2.52
2248 2335 4.180817 CCACACCCAAAGAAACAAGAAAC 58.819 43.478 0.00 0.00 0.00 2.78
2267 2354 5.246883 AGAAACAATCTCCCCCATGAAAAAG 59.753 40.000 0.00 0.00 30.46 2.27
2298 2385 6.360618 ACAATTTCTTATCCTCACTCCATCC 58.639 40.000 0.00 0.00 0.00 3.51
2299 2386 4.672587 TTTCTTATCCTCACTCCATCCG 57.327 45.455 0.00 0.00 0.00 4.18
2300 2387 3.314307 TCTTATCCTCACTCCATCCGT 57.686 47.619 0.00 0.00 0.00 4.69
2301 2388 3.643237 TCTTATCCTCACTCCATCCGTT 58.357 45.455 0.00 0.00 0.00 4.44
2380 2467 0.179200 CGCGTACAGAAAACCATGGC 60.179 55.000 13.04 0.00 0.00 4.40
2397 2496 0.756815 GGCTAGGCCCCCAAAAGATG 60.757 60.000 4.61 0.00 44.06 2.90
2402 2501 2.418083 GCCCCCAAAAGATGAGGCG 61.418 63.158 0.00 0.00 38.14 5.52
2403 2502 1.754234 CCCCCAAAAGATGAGGCGG 60.754 63.158 0.00 0.00 0.00 6.13
2417 2516 2.820037 GCGGGAACAGTAGCAGGC 60.820 66.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 2.842394 AATCCGGCTCGCAGTCTGTG 62.842 60.000 7.09 7.09 0.00 3.66
80 81 2.650116 AATCCGGCTCGCAGTCTGT 61.650 57.895 0.00 0.00 0.00 3.41
81 82 2.169789 CAATCCGGCTCGCAGTCTG 61.170 63.158 0.00 0.00 0.00 3.51
82 83 2.172483 AACAATCCGGCTCGCAGTCT 62.172 55.000 0.00 0.00 0.00 3.24
83 84 1.741770 AACAATCCGGCTCGCAGTC 60.742 57.895 0.00 0.00 0.00 3.51
84 85 2.034879 CAACAATCCGGCTCGCAGT 61.035 57.895 0.00 0.00 0.00 4.40
85 86 2.787249 CAACAATCCGGCTCGCAG 59.213 61.111 0.00 0.00 0.00 5.18
86 87 3.430862 GCAACAATCCGGCTCGCA 61.431 61.111 0.00 0.00 0.00 5.10
87 88 4.179579 GGCAACAATCCGGCTCGC 62.180 66.667 0.00 0.00 0.00 5.03
88 89 3.864686 CGGCAACAATCCGGCTCG 61.865 66.667 0.00 0.00 42.99 5.03
89 90 4.179579 GCGGCAACAATCCGGCTC 62.180 66.667 0.00 0.00 46.51 4.70
146 147 4.373116 TTCGGGTGTGGCTCGCTC 62.373 66.667 0.00 0.00 41.75 5.03
147 148 4.681978 GTTCGGGTGTGGCTCGCT 62.682 66.667 0.00 0.00 41.75 4.93
149 150 3.934391 GAGGTTCGGGTGTGGCTCG 62.934 68.421 0.00 0.00 43.78 5.03
150 151 2.047179 GAGGTTCGGGTGTGGCTC 60.047 66.667 0.00 0.00 0.00 4.70
151 152 3.637273 GGAGGTTCGGGTGTGGCT 61.637 66.667 0.00 0.00 0.00 4.75
152 153 4.717313 GGGAGGTTCGGGTGTGGC 62.717 72.222 0.00 0.00 0.00 5.01
153 154 2.824880 TTGGGAGGTTCGGGTGTGG 61.825 63.158 0.00 0.00 0.00 4.17
154 155 1.599797 GTTGGGAGGTTCGGGTGTG 60.600 63.158 0.00 0.00 0.00 3.82
155 156 2.826003 GGTTGGGAGGTTCGGGTGT 61.826 63.158 0.00 0.00 0.00 4.16
156 157 2.033602 GGTTGGGAGGTTCGGGTG 59.966 66.667 0.00 0.00 0.00 4.61
157 158 1.647334 TTTGGTTGGGAGGTTCGGGT 61.647 55.000 0.00 0.00 0.00 5.28
158 159 0.893727 CTTTGGTTGGGAGGTTCGGG 60.894 60.000 0.00 0.00 0.00 5.14
159 160 1.524008 GCTTTGGTTGGGAGGTTCGG 61.524 60.000 0.00 0.00 0.00 4.30
160 161 1.524008 GGCTTTGGTTGGGAGGTTCG 61.524 60.000 0.00 0.00 0.00 3.95
161 162 1.524008 CGGCTTTGGTTGGGAGGTTC 61.524 60.000 0.00 0.00 0.00 3.62
162 163 1.530655 CGGCTTTGGTTGGGAGGTT 60.531 57.895 0.00 0.00 0.00 3.50
163 164 2.115266 CGGCTTTGGTTGGGAGGT 59.885 61.111 0.00 0.00 0.00 3.85
164 165 3.373565 GCGGCTTTGGTTGGGAGG 61.374 66.667 0.00 0.00 0.00 4.30
165 166 3.373565 GGCGGCTTTGGTTGGGAG 61.374 66.667 0.00 0.00 0.00 4.30
166 167 3.860930 GAGGCGGCTTTGGTTGGGA 62.861 63.158 14.76 0.00 0.00 4.37
167 168 2.478335 TAGAGGCGGCTTTGGTTGGG 62.478 60.000 14.76 0.00 0.00 4.12
168 169 1.002624 TAGAGGCGGCTTTGGTTGG 60.003 57.895 14.76 0.00 0.00 3.77
169 170 1.305930 GGTAGAGGCGGCTTTGGTTG 61.306 60.000 14.76 0.00 0.00 3.77
170 171 1.002502 GGTAGAGGCGGCTTTGGTT 60.003 57.895 14.76 0.00 0.00 3.67
171 172 2.669240 GGTAGAGGCGGCTTTGGT 59.331 61.111 14.76 0.79 0.00 3.67
172 173 1.335132 TAGGGTAGAGGCGGCTTTGG 61.335 60.000 14.76 0.00 0.00 3.28
173 174 0.539986 TTAGGGTAGAGGCGGCTTTG 59.460 55.000 14.76 0.00 0.00 2.77
174 175 1.282382 TTTAGGGTAGAGGCGGCTTT 58.718 50.000 14.76 10.76 0.00 3.51
175 176 1.282382 TTTTAGGGTAGAGGCGGCTT 58.718 50.000 14.76 5.90 0.00 4.35
176 177 1.282382 TTTTTAGGGTAGAGGCGGCT 58.718 50.000 13.09 13.09 0.00 5.52
177 178 3.867549 TTTTTAGGGTAGAGGCGGC 57.132 52.632 0.00 0.00 0.00 6.53
197 198 0.673985 GGAGAGGCGGCTTTGTTTTT 59.326 50.000 14.76 0.00 0.00 1.94
198 199 1.179174 GGGAGAGGCGGCTTTGTTTT 61.179 55.000 14.76 0.00 0.00 2.43
199 200 1.603739 GGGAGAGGCGGCTTTGTTT 60.604 57.895 14.76 0.00 0.00 2.83
200 201 2.034221 GGGAGAGGCGGCTTTGTT 59.966 61.111 14.76 0.00 0.00 2.83
201 202 2.930562 AGGGAGAGGCGGCTTTGT 60.931 61.111 14.76 0.09 0.00 2.83
202 203 2.124942 GAGGGAGAGGCGGCTTTG 60.125 66.667 14.76 0.00 0.00 2.77
203 204 3.403558 GGAGGGAGAGGCGGCTTT 61.404 66.667 14.76 7.56 0.00 3.51
204 205 4.722535 TGGAGGGAGAGGCGGCTT 62.723 66.667 14.76 2.75 0.00 4.35
558 559 2.186826 GTGTCTGTGGGTGTGGTGC 61.187 63.158 0.00 0.00 0.00 5.01
559 560 1.887242 CGTGTCTGTGGGTGTGGTG 60.887 63.158 0.00 0.00 0.00 4.17
560 561 2.504032 CGTGTCTGTGGGTGTGGT 59.496 61.111 0.00 0.00 0.00 4.16
561 562 2.280797 CCGTGTCTGTGGGTGTGG 60.281 66.667 0.00 0.00 0.00 4.17
562 563 2.972505 GCCGTGTCTGTGGGTGTG 60.973 66.667 0.00 0.00 0.00 3.82
572 573 2.733593 GTGTGGTCTCGCCGTGTC 60.734 66.667 0.00 0.00 41.21 3.67
580 581 4.394712 CTGGGGCCGTGTGGTCTC 62.395 72.222 0.00 0.00 42.48 3.36
616 627 6.297594 GGGGAGAGTGAGAGGAGAGATAATAT 60.298 46.154 0.00 0.00 0.00 1.28
617 628 5.014755 GGGGAGAGTGAGAGGAGAGATAATA 59.985 48.000 0.00 0.00 0.00 0.98
618 629 4.202673 GGGGAGAGTGAGAGGAGAGATAAT 60.203 50.000 0.00 0.00 0.00 1.28
642 653 0.933700 AAGGAGAGAGGGAGAGAGGG 59.066 60.000 0.00 0.00 0.00 4.30
643 654 2.846665 AAAGGAGAGAGGGAGAGAGG 57.153 55.000 0.00 0.00 0.00 3.69
644 655 4.151883 CCATAAAGGAGAGAGGGAGAGAG 58.848 52.174 0.00 0.00 41.22 3.20
645 656 3.692772 GCCATAAAGGAGAGAGGGAGAGA 60.693 52.174 0.00 0.00 41.22 3.10
646 657 2.632512 GCCATAAAGGAGAGAGGGAGAG 59.367 54.545 0.00 0.00 41.22 3.20
647 658 2.248686 AGCCATAAAGGAGAGAGGGAGA 59.751 50.000 0.00 0.00 41.22 3.71
648 659 2.632512 GAGCCATAAAGGAGAGAGGGAG 59.367 54.545 0.00 0.00 41.22 4.30
649 660 2.683768 GAGCCATAAAGGAGAGAGGGA 58.316 52.381 0.00 0.00 41.22 4.20
650 661 1.696884 GGAGCCATAAAGGAGAGAGGG 59.303 57.143 0.00 0.00 41.22 4.30
651 662 1.342819 CGGAGCCATAAAGGAGAGAGG 59.657 57.143 0.00 0.00 41.22 3.69
694 705 0.818296 GCACGGAGTAGTCATGGACT 59.182 55.000 4.13 4.13 41.61 3.85
941 961 2.890371 GTATCACCCACCGAGCGT 59.110 61.111 0.00 0.00 0.00 5.07
946 966 1.001268 CAGATCTCGTATCACCCACCG 60.001 57.143 0.00 0.00 0.00 4.94
955 975 2.520069 CTAGCCCACCAGATCTCGTAT 58.480 52.381 0.00 0.00 0.00 3.06
1159 1179 1.938577 CTGCAGGAGACATACACATGC 59.061 52.381 5.57 0.00 44.37 4.06
1166 1186 0.252696 ACCCACCTGCAGGAGACATA 60.253 55.000 39.19 0.00 38.94 2.29
1167 1187 1.539869 ACCCACCTGCAGGAGACAT 60.540 57.895 39.19 13.98 38.94 3.06
1225 1247 3.362399 TACTGCTCCAGCGCTGCTC 62.362 63.158 31.96 20.98 45.83 4.26
1235 1257 1.668101 CCTCCCACGAGTACTGCTCC 61.668 65.000 0.00 0.00 41.10 4.70
1461 1491 2.289072 ACATATATGTGCAGACGGAGCC 60.289 50.000 17.60 0.00 40.03 4.70
1503 1546 2.960129 CGTAATGGCGGACCGAGC 60.960 66.667 20.50 0.00 39.70 5.03
1593 1636 4.962122 GTTGCCGTGCGTGTGCTG 62.962 66.667 0.00 0.00 43.34 4.41
1637 1683 1.190643 CCGCTCCCTCTTCTTCTTCT 58.809 55.000 0.00 0.00 0.00 2.85
1638 1684 1.136110 CTCCGCTCCCTCTTCTTCTTC 59.864 57.143 0.00 0.00 0.00 2.87
1639 1685 1.190643 CTCCGCTCCCTCTTCTTCTT 58.809 55.000 0.00 0.00 0.00 2.52
1640 1686 1.326951 GCTCCGCTCCCTCTTCTTCT 61.327 60.000 0.00 0.00 0.00 2.85
1641 1687 1.142965 GCTCCGCTCCCTCTTCTTC 59.857 63.158 0.00 0.00 0.00 2.87
1642 1688 2.716017 CGCTCCGCTCCCTCTTCTT 61.716 63.158 0.00 0.00 0.00 2.52
1643 1689 3.144193 CGCTCCGCTCCCTCTTCT 61.144 66.667 0.00 0.00 0.00 2.85
1655 1701 0.319727 CATGGATCTCTCTGCGCTCC 60.320 60.000 9.73 5.71 0.00 4.70
1678 1724 4.040217 TCCATGTTTGGTTTCTTTCCATGG 59.960 41.667 4.97 4.97 45.82 3.66
1761 1807 2.426183 CTTCGGACGCGACGACAAG 61.426 63.158 24.81 18.18 40.45 3.16
1762 1808 2.427905 CTTCGGACGCGACGACAA 60.428 61.111 24.81 13.82 40.45 3.18
1766 1812 4.099170 ACCTCTTCGGACGCGACG 62.099 66.667 15.93 17.74 36.31 5.12
1771 1842 0.677098 TCTCTCCACCTCTTCGGACG 60.677 60.000 0.00 0.00 36.31 4.79
1839 1914 2.357034 TTGGCTTGGCGACTCGAC 60.357 61.111 1.63 0.00 34.27 4.20
1915 1997 3.054875 TGAGGAAGATGTTGTCCATGAGG 60.055 47.826 0.00 0.00 36.28 3.86
1919 2001 4.849813 TGATGAGGAAGATGTTGTCCAT 57.150 40.909 0.00 0.00 36.28 3.41
1968 2052 4.141801 TGGCATACTGGCTCTTTTATACGT 60.142 41.667 0.00 0.00 44.10 3.57
1973 2058 4.662278 AGTTTGGCATACTGGCTCTTTTA 58.338 39.130 9.89 0.00 44.10 1.52
1980 2065 1.025041 GGCTAGTTTGGCATACTGGC 58.975 55.000 29.06 29.06 45.89 4.85
1981 2066 2.017049 GTGGCTAGTTTGGCATACTGG 58.983 52.381 19.08 17.13 44.18 4.00
1997 2082 1.215014 GCCAAAGCGTCTTTTGTGGC 61.215 55.000 13.96 13.96 36.54 5.01
2118 2205 4.522022 AGCAGGAAGTGAAAATTTGGAGAG 59.478 41.667 0.00 0.00 0.00 3.20
2131 2218 1.630148 GCGTGTAGTAGCAGGAAGTG 58.370 55.000 0.00 0.00 0.00 3.16
2135 2222 0.599558 AAACGCGTGTAGTAGCAGGA 59.400 50.000 14.98 0.00 0.00 3.86
2136 2223 1.389106 GAAAACGCGTGTAGTAGCAGG 59.611 52.381 14.98 0.00 0.00 4.85
2137 2224 1.389106 GGAAAACGCGTGTAGTAGCAG 59.611 52.381 14.98 0.00 0.00 4.24
2139 2226 1.421382 TGGAAAACGCGTGTAGTAGC 58.579 50.000 14.98 0.00 0.00 3.58
2141 2228 2.988493 GACATGGAAAACGCGTGTAGTA 59.012 45.455 14.98 0.00 0.00 1.82
2144 2231 1.795872 CAGACATGGAAAACGCGTGTA 59.204 47.619 14.98 0.00 0.00 2.90
2146 2233 3.366392 CAGACATGGAAAACGCGTG 57.634 52.632 14.98 0.00 0.00 5.34
2210 2297 3.211045 GTGTGGTGTGGTGTATTGAACT 58.789 45.455 0.00 0.00 0.00 3.01
2213 2300 1.202830 GGGTGTGGTGTGGTGTATTGA 60.203 52.381 0.00 0.00 0.00 2.57
2216 2303 0.847373 TTGGGTGTGGTGTGGTGTAT 59.153 50.000 0.00 0.00 0.00 2.29
2217 2304 0.624254 TTTGGGTGTGGTGTGGTGTA 59.376 50.000 0.00 0.00 0.00 2.90
2218 2305 0.682855 CTTTGGGTGTGGTGTGGTGT 60.683 55.000 0.00 0.00 0.00 4.16
2242 2329 4.402616 TTCATGGGGGAGATTGTTTCTT 57.597 40.909 0.00 0.00 33.74 2.52
2243 2330 4.402616 TTTCATGGGGGAGATTGTTTCT 57.597 40.909 0.00 0.00 37.41 2.52
2244 2331 5.012046 ACTTTTTCATGGGGGAGATTGTTTC 59.988 40.000 0.00 0.00 0.00 2.78
2245 2332 4.907269 ACTTTTTCATGGGGGAGATTGTTT 59.093 37.500 0.00 0.00 0.00 2.83
2246 2333 4.492646 ACTTTTTCATGGGGGAGATTGTT 58.507 39.130 0.00 0.00 0.00 2.83
2247 2334 4.132122 ACTTTTTCATGGGGGAGATTGT 57.868 40.909 0.00 0.00 0.00 2.71
2248 2335 4.527816 TGAACTTTTTCATGGGGGAGATTG 59.472 41.667 0.00 0.00 36.79 2.67
2267 2354 8.329203 AGTGAGGATAAGAAATTGTTCTGAAC 57.671 34.615 13.49 13.49 43.59 3.18
2298 2385 3.648982 TGCGCTTGTGCTGGAACG 61.649 61.111 9.73 0.00 36.97 3.95
2299 2386 2.050985 GTGCGCTTGTGCTGGAAC 60.051 61.111 9.73 0.00 36.97 3.62
2300 2387 2.203195 AGTGCGCTTGTGCTGGAA 60.203 55.556 9.73 0.00 36.97 3.53
2301 2388 2.666190 GAGTGCGCTTGTGCTGGA 60.666 61.111 9.73 0.00 36.97 3.86
2340 2427 3.312697 CGCTCATACTATATGCGGCTCTA 59.687 47.826 0.00 0.00 42.46 2.43
2380 2467 1.133668 CCTCATCTTTTGGGGGCCTAG 60.134 57.143 0.84 0.00 43.00 3.02
2397 2496 1.153549 CTGCTACTGTTCCCGCCTC 60.154 63.158 0.00 0.00 0.00 4.70
2402 2501 1.745653 GAAATGCCTGCTACTGTTCCC 59.254 52.381 0.00 0.00 0.00 3.97
2403 2502 1.745653 GGAAATGCCTGCTACTGTTCC 59.254 52.381 0.00 0.00 0.00 3.62
2417 2516 5.894393 TCTACACTCCTAGGAAGAGGAAATG 59.106 44.000 13.77 0.00 45.20 2.32


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

AutoCloner maintained by Alex Coulton.