Multiple sequence alignment - TraesCS5D01G181400

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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 TraesCS5D01G181400 chr5D 100.000 3134 0 0 1 3134 281893356 281896489 0.000000e+00 5788.0
1 TraesCS5D01G181400 chr5A 92.179 2097 93 30 786 2867 374477357 374479397 0.000000e+00 2898.0
2 TraesCS5D01G181400 chr5A 87.405 786 47 25 1 751 374476526 374477294 0.000000e+00 856.0
3 TraesCS5D01G181400 chr5A 93.714 175 3 4 2865 3032 374480646 374480819 4.010000e-64 255.0
4 TraesCS5D01G181400 chr5A 97.403 77 2 0 3058 3134 374480816 374480892 7.050000e-27 132.0
5 TraesCS5D01G181400 chr5B 87.813 1715 89 48 1 1654 319904118 319905773 0.000000e+00 1899.0
6 TraesCS5D01G181400 chr5B 92.061 718 33 7 1698 2413 319905785 319906480 0.000000e+00 989.0
7 TraesCS5D01G181400 chr5B 88.055 586 28 18 2518 3065 319908261 319908842 0.000000e+00 656.0
8 TraesCS5D01G181400 chr5B 98.507 67 1 0 3068 3134 319908982 319909048 5.490000e-23 119.0
9 TraesCS5D01G181400 chr5B 92.593 54 4 0 2467 2520 319906548 319906601 9.320000e-11 78.7


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 TraesCS5D01G181400 chr5D 281893356 281896489 3133 False 5788.00 5788 100.00000 1 3134 1 chr5D.!!$F1 3133
1 TraesCS5D01G181400 chr5A 374476526 374480892 4366 False 1035.25 2898 92.67525 1 3134 4 chr5A.!!$F1 3133
2 TraesCS5D01G181400 chr5B 319904118 319909048 4930 False 748.34 1899 91.80580 1 3134 5 chr5B.!!$F1 3133

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
633 683 0.108804 GGCTCGGACGAACAGATTCA 60.109 55.0 0.0 0.0 34.14 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2303 0.173481 TCTCTTGGGCATCGTCGAAG 59.827 55.0 0.0 0.0 0.0 3.79 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
99 100 1.217001 TCATTGCCGGAATCGATTCG 58.783 50.000 27.21 21.87 37.67 3.34
150 170 1.974236 AGCCATATCCAGACCTACAGC 59.026 52.381 0.00 0.00 0.00 4.40
151 171 1.002544 GCCATATCCAGACCTACAGCC 59.997 57.143 0.00 0.00 0.00 4.85
164 184 3.329520 ACCTACAGCCAAGGTAACAATGA 59.670 43.478 0.53 0.00 45.69 2.57
166 186 4.576463 CCTACAGCCAAGGTAACAATGATC 59.424 45.833 0.00 0.00 41.41 2.92
167 187 4.032960 ACAGCCAAGGTAACAATGATCA 57.967 40.909 0.00 0.00 41.41 2.92
172 192 5.359009 AGCCAAGGTAACAATGATCAATCTG 59.641 40.000 0.00 0.04 41.41 2.90
173 193 5.585390 CCAAGGTAACAATGATCAATCTGC 58.415 41.667 0.00 0.00 41.41 4.26
175 195 6.459298 CCAAGGTAACAATGATCAATCTGCTC 60.459 42.308 0.00 0.00 41.41 4.26
177 197 6.054295 AGGTAACAATGATCAATCTGCTCTC 58.946 40.000 0.00 0.00 41.41 3.20
178 198 5.238214 GGTAACAATGATCAATCTGCTCTCC 59.762 44.000 0.00 0.00 0.00 3.71
179 199 3.818180 ACAATGATCAATCTGCTCTCCC 58.182 45.455 0.00 0.00 0.00 4.30
181 201 0.755079 TGATCAATCTGCTCTCCCCG 59.245 55.000 0.00 0.00 0.00 5.73
182 202 0.602372 GATCAATCTGCTCTCCCCGC 60.602 60.000 0.00 0.00 0.00 6.13
183 203 1.053264 ATCAATCTGCTCTCCCCGCT 61.053 55.000 0.00 0.00 0.00 5.52
184 204 1.227497 CAATCTGCTCTCCCCGCTC 60.227 63.158 0.00 0.00 0.00 5.03
185 205 2.439104 AATCTGCTCTCCCCGCTCC 61.439 63.158 0.00 0.00 0.00 4.70
189 209 3.145551 GCTCTCCCCGCTCCGTTA 61.146 66.667 0.00 0.00 0.00 3.18
190 210 2.718073 GCTCTCCCCGCTCCGTTAA 61.718 63.158 0.00 0.00 0.00 2.01
191 211 1.895238 CTCTCCCCGCTCCGTTAAA 59.105 57.895 0.00 0.00 0.00 1.52
192 212 0.464452 CTCTCCCCGCTCCGTTAAAT 59.536 55.000 0.00 0.00 0.00 1.40
193 213 1.684983 CTCTCCCCGCTCCGTTAAATA 59.315 52.381 0.00 0.00 0.00 1.40
194 214 2.299297 CTCTCCCCGCTCCGTTAAATAT 59.701 50.000 0.00 0.00 0.00 1.28
195 215 2.701951 TCTCCCCGCTCCGTTAAATATT 59.298 45.455 0.00 0.00 0.00 1.28
196 216 3.135167 TCTCCCCGCTCCGTTAAATATTT 59.865 43.478 5.89 5.89 0.00 1.40
197 217 4.344679 TCTCCCCGCTCCGTTAAATATTTA 59.655 41.667 3.71 3.71 0.00 1.40
198 218 5.012354 TCTCCCCGCTCCGTTAAATATTTAT 59.988 40.000 8.70 0.00 0.00 1.40
199 219 5.623169 TCCCCGCTCCGTTAAATATTTATT 58.377 37.500 8.70 0.00 0.00 1.40
208 228 9.113876 CTCCGTTAAATATTTATTTTGATCCGC 57.886 33.333 8.70 0.00 37.16 5.54
238 258 0.830648 TAGCTCGATGAAGGGGGTTG 59.169 55.000 0.00 0.00 0.00 3.77
269 292 0.808755 ATTCGTCGTTGCCATTTCCC 59.191 50.000 0.00 0.00 0.00 3.97
419 451 2.112691 ACTTTGGGGGAGAGAGAGAGAA 59.887 50.000 0.00 0.00 0.00 2.87
441 479 6.481644 AGAAAGATAGAACAATCGCATTCCTC 59.518 38.462 0.00 0.00 0.00 3.71
446 484 7.933577 AGATAGAACAATCGCATTCCTCATTAA 59.066 33.333 0.00 0.00 0.00 1.40
512 559 3.399330 TGTGCCTTGTACTACTGAAAGC 58.601 45.455 0.00 0.00 37.60 3.51
517 564 4.687483 GCCTTGTACTACTGAAAGCGTTTA 59.313 41.667 0.00 0.00 37.60 2.01
563 613 1.606668 TGTGCCGGCAAAAGTAGAAAG 59.393 47.619 34.66 0.00 0.00 2.62
582 632 7.380431 AGAAAGAAAAGAAGCATCATCAGAG 57.620 36.000 0.00 0.00 0.00 3.35
617 667 4.379243 CTCTGGAACGTGGCGGCT 62.379 66.667 11.43 0.00 0.00 5.52
633 683 0.108804 GGCTCGGACGAACAGATTCA 60.109 55.000 0.00 0.00 34.14 2.57
736 786 8.651389 TCTTCCCGAAGAATATTTACATGATCT 58.349 33.333 0.00 0.00 43.79 2.75
740 790 9.929180 CCCGAAGAATATTTACATGATCTAAGA 57.071 33.333 0.00 0.00 0.00 2.10
840 916 1.145598 CGATGGACCTGCAGATGCT 59.854 57.895 17.39 0.00 42.66 3.79
877 953 5.966742 AATAAAAGGGAGAGCAAAGACAC 57.033 39.130 0.00 0.00 0.00 3.67
930 1006 1.207329 ACTCGGAACCTTGGTAGATGC 59.793 52.381 0.00 0.00 0.00 3.91
946 1022 3.891049 AGATGCCATAACTCTTGTTCCC 58.109 45.455 0.00 0.00 37.59 3.97
948 1024 1.992557 TGCCATAACTCTTGTTCCCCT 59.007 47.619 0.00 0.00 37.59 4.79
949 1025 3.186283 TGCCATAACTCTTGTTCCCCTA 58.814 45.455 0.00 0.00 37.59 3.53
950 1026 3.785887 TGCCATAACTCTTGTTCCCCTAT 59.214 43.478 0.00 0.00 37.59 2.57
951 1027 4.972568 TGCCATAACTCTTGTTCCCCTATA 59.027 41.667 0.00 0.00 37.59 1.31
952 1028 5.610982 TGCCATAACTCTTGTTCCCCTATAT 59.389 40.000 0.00 0.00 37.59 0.86
953 1029 6.790461 TGCCATAACTCTTGTTCCCCTATATA 59.210 38.462 0.00 0.00 37.59 0.86
954 1030 7.461043 TGCCATAACTCTTGTTCCCCTATATAT 59.539 37.037 0.00 0.00 37.59 0.86
955 1031 8.989131 GCCATAACTCTTGTTCCCCTATATATA 58.011 37.037 0.00 0.00 37.59 0.86
1037 1113 4.976116 GCACTTTAAAGTTCATGTGTCCAC 59.024 41.667 18.25 0.00 37.08 4.02
1067 1143 3.369052 GGTGTTCCGACCATCATGTTCTA 60.369 47.826 0.00 0.00 35.88 2.10
1072 1148 7.065324 GTGTTCCGACCATCATGTTCTATTTAA 59.935 37.037 0.00 0.00 0.00 1.52
1112 1188 7.533426 ACTCTGTTTGCTATGTTTTCATCATC 58.467 34.615 0.00 0.00 41.25 2.92
1242 1318 1.909781 CCACTGGCAGGCCACAATT 60.910 57.895 20.34 0.00 41.89 2.32
1409 1485 1.360820 TCGTTGTTGCGAACTGTTCA 58.639 45.000 19.56 0.00 37.99 3.18
1482 1558 9.265901 AGTCGATGAATATGTCTTTAGGAAATG 57.734 33.333 0.00 0.00 0.00 2.32
1542 1618 8.555166 TTTTTGTAAAGTTGCTTCGTTATCTG 57.445 30.769 0.00 0.00 0.00 2.90
1546 1622 5.532025 AAAGTTGCTTCGTTATCTGCTAC 57.468 39.130 0.00 0.00 0.00 3.58
1552 1628 3.495001 GCTTCGTTATCTGCTACCCATTC 59.505 47.826 0.00 0.00 0.00 2.67
1564 1640 2.795231 ACCCATTCCAGTCAGATGTG 57.205 50.000 0.00 0.00 0.00 3.21
1597 1674 5.263968 TGCTACACCTGCTAAATAGAGAC 57.736 43.478 0.00 0.00 0.00 3.36
1678 1769 6.593382 AGAATAGATCTGTCAAACTCAGCAAC 59.407 38.462 5.18 0.00 36.88 4.17
1823 1916 9.667107 TTCAAATAGAATAACTGTCAAGTAGGG 57.333 33.333 0.00 0.00 34.77 3.53
1825 1918 6.808321 ATAGAATAACTGTCAAGTAGGGCA 57.192 37.500 0.00 0.00 34.77 5.36
1826 1919 5.091261 AGAATAACTGTCAAGTAGGGCAG 57.909 43.478 0.00 0.00 34.77 4.85
1827 1920 4.532521 AGAATAACTGTCAAGTAGGGCAGT 59.467 41.667 0.00 0.00 43.13 4.40
1830 1923 3.679824 ACTGTCAAGTAGGGCAGTTAC 57.320 47.619 0.00 0.00 38.86 2.50
1831 1924 3.240302 ACTGTCAAGTAGGGCAGTTACT 58.760 45.455 0.00 0.00 38.86 2.24
1832 1925 3.646637 ACTGTCAAGTAGGGCAGTTACTT 59.353 43.478 0.00 3.41 40.91 2.24
1833 1926 4.102681 ACTGTCAAGTAGGGCAGTTACTTT 59.897 41.667 0.00 0.00 38.85 2.66
1834 1927 4.385825 TGTCAAGTAGGGCAGTTACTTTG 58.614 43.478 5.81 3.74 38.85 2.77
1835 1928 4.101898 TGTCAAGTAGGGCAGTTACTTTGA 59.898 41.667 5.81 5.38 38.85 2.69
2088 2188 0.397816 AGAACCAGAGAGCCCGCTAT 60.398 55.000 0.00 0.00 0.00 2.97
2094 2194 0.825840 AGAGAGCCCGCTATGAGGAC 60.826 60.000 0.00 0.00 0.00 3.85
2151 2251 1.338960 TGATCGCTGCAAAGATGACCA 60.339 47.619 8.14 0.00 0.00 4.02
2181 2281 4.608951 GTGTAAGAGAACTTCTGTGTCGT 58.391 43.478 0.00 0.00 35.91 4.34
2203 2303 2.436824 GTTTCCCGCCCTCTGAGC 60.437 66.667 0.00 0.00 0.00 4.26
2227 2327 2.190578 GATGCCCAAGAGACCCCG 59.809 66.667 0.00 0.00 0.00 5.73
2276 2376 9.915629 TTTTTACTTGTGTACAGTTGTCAAAAT 57.084 25.926 0.00 0.00 0.00 1.82
2296 2396 6.816134 AAATTGGGTAATGTTTGCATTTCC 57.184 33.333 7.24 7.24 45.87 3.13
2300 2400 4.202264 TGGGTAATGTTTGCATTTCCGTTT 60.202 37.500 8.96 0.00 46.86 3.60
2301 2401 4.752604 GGGTAATGTTTGCATTTCCGTTTT 59.247 37.500 8.96 0.00 46.86 2.43
2302 2402 5.107259 GGGTAATGTTTGCATTTCCGTTTTC 60.107 40.000 8.96 0.00 46.86 2.29
2362 2462 9.077885 ACCTGTATGTATCAAGACAAAACATTT 57.922 29.630 0.00 0.00 32.23 2.32
2423 2551 3.368323 CCTTTTCATTTGTTGGATCCGGG 60.368 47.826 7.39 0.00 0.00 5.73
2428 2556 2.366640 TTTGTTGGATCCGGGTGAAA 57.633 45.000 7.39 0.00 0.00 2.69
2584 4374 2.092323 GTCTGCCCCGCTTCTAAAATT 58.908 47.619 0.00 0.00 0.00 1.82
2656 4448 1.833630 TGTCCTCCTGGCATTACTCTG 59.166 52.381 0.00 0.00 0.00 3.35
2706 4505 5.444176 AGCATTCTTTCTTTGGGAGGATAG 58.556 41.667 0.00 0.00 0.00 2.08
2731 4530 2.943345 GCTTGCACGTGTCTCACCG 61.943 63.158 18.38 2.09 0.00 4.94
2751 4550 0.375803 GTGTCGTGTGTGGGTTGAAC 59.624 55.000 0.00 0.00 0.00 3.18
2781 4580 2.050351 CACGACTTGTCCGCGAGT 60.050 61.111 8.23 1.67 41.84 4.18
2796 4595 0.647410 CGAGTGATGCATGAACGGAC 59.353 55.000 2.46 0.00 0.00 4.79
2797 4596 0.647410 GAGTGATGCATGAACGGACG 59.353 55.000 2.46 0.00 0.00 4.79
2845 4672 6.711277 AGAATGTTGATCAGGTAAGTAAGCA 58.289 36.000 0.00 0.00 0.00 3.91
2863 4690 0.035458 CAGACAGGGACACAGGGTTC 59.965 60.000 0.00 0.00 0.00 3.62
2902 5980 6.149142 AGTGCTTCATTTCTCTTTGCTTCTAG 59.851 38.462 0.00 0.00 0.00 2.43
3016 6100 0.530211 TTGCCACATTTGCACTGTGC 60.530 50.000 25.15 25.15 45.29 4.57
3038 6122 2.969821 ATGTGTGCCCCTGTAAGAAA 57.030 45.000 0.00 0.00 34.07 2.52
3046 6130 3.782523 TGCCCCTGTAAGAAAGAGATCAT 59.217 43.478 0.00 0.00 34.07 2.45
3047 6131 4.968719 TGCCCCTGTAAGAAAGAGATCATA 59.031 41.667 0.00 0.00 34.07 2.15
3051 6135 6.043706 CCCCTGTAAGAAAGAGATCATATGGT 59.956 42.308 2.13 0.00 34.07 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 4.350816 CAGGTGGGAATGGGATTATAGACA 59.649 45.833 0.00 0.00 0.00 3.41
49 50 3.330701 GCAGGTGGGAATGGGATTATAGA 59.669 47.826 0.00 0.00 0.00 1.98
99 100 0.731855 CCCCGAGAGAACGAACGAAC 60.732 60.000 0.14 0.00 35.09 3.95
129 149 2.028567 GCTGTAGGTCTGGATATGGCTC 60.029 54.545 0.00 0.00 0.00 4.70
134 154 2.975489 CCTTGGCTGTAGGTCTGGATAT 59.025 50.000 0.00 0.00 0.00 1.63
136 156 1.207791 CCTTGGCTGTAGGTCTGGAT 58.792 55.000 0.00 0.00 0.00 3.41
137 157 0.178903 ACCTTGGCTGTAGGTCTGGA 60.179 55.000 0.00 0.00 42.30 3.86
150 170 5.359009 AGCAGATTGATCATTGTTACCTTGG 59.641 40.000 0.00 0.00 0.00 3.61
151 171 6.318144 AGAGCAGATTGATCATTGTTACCTTG 59.682 38.462 0.00 0.00 34.77 3.61
157 177 4.205587 GGGAGAGCAGATTGATCATTGTT 58.794 43.478 0.00 0.00 34.77 2.83
159 179 3.147629 GGGGAGAGCAGATTGATCATTG 58.852 50.000 0.00 0.00 34.77 2.82
160 180 2.224475 CGGGGAGAGCAGATTGATCATT 60.224 50.000 0.00 0.00 34.77 2.57
161 181 1.347050 CGGGGAGAGCAGATTGATCAT 59.653 52.381 0.00 0.00 34.77 2.45
164 184 1.053264 AGCGGGGAGAGCAGATTGAT 61.053 55.000 0.00 0.00 37.01 2.57
166 186 1.227497 GAGCGGGGAGAGCAGATTG 60.227 63.158 0.00 0.00 37.01 2.67
167 187 2.439104 GGAGCGGGGAGAGCAGATT 61.439 63.158 0.00 0.00 37.01 2.40
172 192 2.234913 TTTAACGGAGCGGGGAGAGC 62.235 60.000 0.00 0.00 0.00 4.09
173 193 0.464452 ATTTAACGGAGCGGGGAGAG 59.536 55.000 0.00 0.00 0.00 3.20
175 195 2.833631 ATATTTAACGGAGCGGGGAG 57.166 50.000 0.00 0.00 0.00 4.30
177 197 5.952526 AATAAATATTTAACGGAGCGGGG 57.047 39.130 11.80 0.00 0.00 5.73
178 198 7.419204 TCAAAATAAATATTTAACGGAGCGGG 58.581 34.615 11.80 0.00 35.00 6.13
179 199 9.113876 GATCAAAATAAATATTTAACGGAGCGG 57.886 33.333 11.80 0.00 35.00 5.52
181 201 9.113876 CGGATCAAAATAAATATTTAACGGAGC 57.886 33.333 11.80 9.62 35.00 4.70
182 202 9.113876 GCGGATCAAAATAAATATTTAACGGAG 57.886 33.333 11.80 2.73 35.00 4.63
183 203 8.842280 AGCGGATCAAAATAAATATTTAACGGA 58.158 29.630 11.80 7.97 35.00 4.69
184 204 8.901748 CAGCGGATCAAAATAAATATTTAACGG 58.098 33.333 11.80 3.32 35.00 4.44
185 205 9.658475 TCAGCGGATCAAAATAAATATTTAACG 57.342 29.630 11.80 7.81 35.00 3.18
192 212 9.897744 GATGATTTCAGCGGATCAAAATAAATA 57.102 29.630 0.00 0.00 36.03 1.40
193 213 8.636213 AGATGATTTCAGCGGATCAAAATAAAT 58.364 29.630 0.00 0.00 37.34 1.40
194 214 7.999679 AGATGATTTCAGCGGATCAAAATAAA 58.000 30.769 0.00 0.00 37.34 1.40
195 215 7.572523 AGATGATTTCAGCGGATCAAAATAA 57.427 32.000 0.00 0.00 37.34 1.40
196 216 7.095060 GCTAGATGATTTCAGCGGATCAAAATA 60.095 37.037 0.00 0.00 37.34 1.40
197 217 6.293845 GCTAGATGATTTCAGCGGATCAAAAT 60.294 38.462 0.00 0.00 37.34 1.82
198 218 5.008019 GCTAGATGATTTCAGCGGATCAAAA 59.992 40.000 0.00 0.00 37.34 2.44
199 219 4.512944 GCTAGATGATTTCAGCGGATCAAA 59.487 41.667 0.00 0.00 37.34 2.69
238 258 3.765505 ACGACGAATCAAGAACGAAAC 57.234 42.857 0.00 0.00 0.00 2.78
269 292 3.252974 ACCAACCAATCTCTTCTAGCG 57.747 47.619 0.00 0.00 0.00 4.26
419 451 5.674525 TGAGGAATGCGATTGTTCTATCTT 58.325 37.500 0.00 0.00 0.00 2.40
467 505 8.562892 ACAATAATATTCTGAAGATTGAAGGCG 58.437 33.333 17.87 5.59 0.00 5.52
512 559 5.544650 TCTACTTTTCAGGTTCCCTAAACG 58.455 41.667 0.00 0.00 38.87 3.60
517 564 4.202567 TGCAATCTACTTTTCAGGTTCCCT 60.203 41.667 0.00 0.00 0.00 4.20
563 613 6.404513 CCCTTTCTCTGATGATGCTTCTTTTC 60.405 42.308 0.88 0.00 0.00 2.29
582 632 6.238648 TCCAGAGACAAAACTTATCCCTTTC 58.761 40.000 0.00 0.00 0.00 2.62
617 667 0.601057 TGCTGAATCTGTTCGTCCGA 59.399 50.000 0.00 0.00 37.15 4.55
633 683 3.019564 GGAATGGACTGTTAAGCATGCT 58.980 45.455 16.30 16.30 0.00 3.79
663 713 3.506067 CCACTAACATCCAGGAAACCAAC 59.494 47.826 0.00 0.00 0.00 3.77
752 802 6.435277 AGAGAAATTCCTACGTAACTACACCA 59.565 38.462 0.00 0.00 0.00 4.17
973 1049 6.315393 TCATGTGACAGATGAACTTGATGATG 59.685 38.462 12.58 0.00 0.00 3.07
974 1050 6.412214 TCATGTGACAGATGAACTTGATGAT 58.588 36.000 12.58 0.00 0.00 2.45
1037 1113 0.171007 GGTCGGAACACCAATGCATG 59.829 55.000 0.00 0.00 36.32 4.06
1077 1153 6.543831 ACATAGCAAACAGAGTTGAAGTTCTT 59.456 34.615 4.17 0.00 0.00 2.52
1078 1154 6.058183 ACATAGCAAACAGAGTTGAAGTTCT 58.942 36.000 4.17 0.00 0.00 3.01
1079 1155 6.305693 ACATAGCAAACAGAGTTGAAGTTC 57.694 37.500 0.00 0.00 0.00 3.01
1080 1156 6.699575 AACATAGCAAACAGAGTTGAAGTT 57.300 33.333 0.00 0.00 0.00 2.66
1081 1157 6.699575 AAACATAGCAAACAGAGTTGAAGT 57.300 33.333 0.00 0.00 0.00 3.01
1242 1318 2.679342 GCTGTCACCAGGGCCCATA 61.679 63.158 27.56 0.00 39.22 2.74
1409 1485 9.956640 AAGACTGAAGAGTAATCATGAGAAAAT 57.043 29.630 0.09 0.00 30.16 1.82
1542 1618 2.171448 ACATCTGACTGGAATGGGTAGC 59.829 50.000 0.00 0.00 0.00 3.58
1546 1622 2.795231 ACACATCTGACTGGAATGGG 57.205 50.000 0.00 0.00 0.00 4.00
1564 1640 3.125316 GCAGGTGTAGCATGTAACAGAAC 59.875 47.826 2.92 0.00 0.00 3.01
1597 1674 0.235665 ACGCTGTTGAAGAATGTGCG 59.764 50.000 0.00 0.00 46.02 5.34
1678 1769 1.184970 AAGCCCAATGGAACCAACCG 61.185 55.000 0.00 0.00 0.00 4.44
1822 1915 5.238650 TCAAAGTAGCTTCAAAGTAACTGCC 59.761 40.000 0.00 0.00 0.00 4.85
1823 1916 6.300354 TCAAAGTAGCTTCAAAGTAACTGC 57.700 37.500 0.00 0.00 0.00 4.40
1825 1918 7.859325 TGTTCAAAGTAGCTTCAAAGTAACT 57.141 32.000 0.00 0.00 0.00 2.24
1826 1919 8.958043 CATTGTTCAAAGTAGCTTCAAAGTAAC 58.042 33.333 0.00 0.00 0.00 2.50
1827 1920 7.647715 GCATTGTTCAAAGTAGCTTCAAAGTAA 59.352 33.333 0.00 0.00 0.00 2.24
1828 1921 7.013274 AGCATTGTTCAAAGTAGCTTCAAAGTA 59.987 33.333 0.00 0.00 0.00 2.24
1829 1922 5.979517 GCATTGTTCAAAGTAGCTTCAAAGT 59.020 36.000 0.00 0.00 0.00 2.66
1830 1923 6.143438 CAGCATTGTTCAAAGTAGCTTCAAAG 59.857 38.462 0.00 0.00 0.00 2.77
1831 1924 5.978919 CAGCATTGTTCAAAGTAGCTTCAAA 59.021 36.000 0.00 0.00 0.00 2.69
1832 1925 5.522456 CAGCATTGTTCAAAGTAGCTTCAA 58.478 37.500 0.00 0.00 0.00 2.69
1833 1926 4.557296 GCAGCATTGTTCAAAGTAGCTTCA 60.557 41.667 0.00 0.00 0.00 3.02
1834 1927 3.916776 GCAGCATTGTTCAAAGTAGCTTC 59.083 43.478 0.00 0.00 0.00 3.86
1835 1928 3.318839 TGCAGCATTGTTCAAAGTAGCTT 59.681 39.130 0.00 0.00 0.00 3.74
2151 2251 3.895232 AGTTCTCTTACACGATGCCAT 57.105 42.857 0.00 0.00 0.00 4.40
2203 2303 0.173481 TCTCTTGGGCATCGTCGAAG 59.827 55.000 0.00 0.00 0.00 3.79
2227 2327 4.207891 TGGTTCAGAGAAAGCCAGATAC 57.792 45.455 0.00 0.00 0.00 2.24
2276 2376 3.322254 ACGGAAATGCAAACATTACCCAA 59.678 39.130 0.00 0.00 45.90 4.12
2321 2421 0.838122 CAGGTCTTCAGGGACAGGGT 60.838 60.000 0.00 0.00 37.91 4.34
2362 2462 5.715070 ACGAAAACACCACAAATTCTTGAA 58.285 33.333 0.00 0.00 36.33 2.69
2423 2551 0.593128 ATTGACCAGCGCTGTTTCAC 59.407 50.000 33.75 19.69 0.00 3.18
2428 2556 1.174712 AAGCAATTGACCAGCGCTGT 61.175 50.000 33.75 22.41 32.14 4.40
2495 2623 0.543277 TGTCATCATCACCAGAGGGC 59.457 55.000 0.00 0.00 37.90 5.19
2503 2631 5.006455 GTCAGTCATCACATGTCATCATCAC 59.994 44.000 0.00 0.00 31.15 3.06
2656 4448 2.960170 CCTTTCTGGTGCTGCTGC 59.040 61.111 8.89 8.89 40.20 5.25
2706 4505 1.005630 ACACGTGCAAGCTCTCTCC 60.006 57.895 17.22 0.00 0.00 3.71
2731 4530 0.745128 TTCAACCCACACACGACACC 60.745 55.000 0.00 0.00 0.00 4.16
2781 4580 0.739462 GGTCGTCCGTTCATGCATCA 60.739 55.000 0.00 0.00 0.00 3.07
2796 4595 0.660488 CTCTCGTCCTCTGATGGTCG 59.340 60.000 6.51 6.51 39.35 4.79
2797 4596 1.757682 ACTCTCGTCCTCTGATGGTC 58.242 55.000 0.00 0.00 0.00 4.02
2827 4654 5.337571 CCTGTCTGCTTACTTACCTGATCAA 60.338 44.000 0.00 0.00 0.00 2.57
2845 4672 0.399949 TGAACCCTGTGTCCCTGTCT 60.400 55.000 0.00 0.00 0.00 3.41
2863 4690 5.268118 TGAAGCACTGGATGTATAGTCTG 57.732 43.478 0.00 0.00 0.00 3.51
2993 6077 2.823984 CAGTGCAAATGTGGCAAGAAA 58.176 42.857 0.00 0.00 43.91 2.52
3016 6100 1.206132 TCTTACAGGGGCACACATACG 59.794 52.381 0.00 0.00 0.00 3.06
3051 6135 0.754217 CTACGGCCAGCTGGTACCTA 60.754 60.000 32.81 18.03 37.57 3.08


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

AutoCloner maintained by Alex Coulton.