Multiple sequence alignment - TraesCS5B01G344600

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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 TraesCS5B01G344600 chr5B 100.000 2603 0 0 1 2603 527498294 527495692 0.000000e+00 4807
1 TraesCS5B01G344600 chr5B 88.876 1744 144 33 803 2532 527775422 527773715 0.000000e+00 2100
2 TraesCS5B01G344600 chr5B 77.113 1136 182 41 1053 2161 527609798 527608714 1.040000e-163 586
3 TraesCS5B01G344600 chr5B 97.368 228 5 1 1 228 670703794 670704020 1.130000e-103 387
4 TraesCS5B01G344600 chr5B 98.148 216 4 0 1 216 467125072 467124857 6.800000e-101 377
5 TraesCS5B01G344600 chr5B 98.131 214 4 0 1 214 315933894 315934107 8.800000e-100 374
6 TraesCS5B01G344600 chr5B 97.706 218 4 1 1 217 580280176 580279959 8.800000e-100 374
7 TraesCS5B01G344600 chr5B 86.404 228 26 4 2163 2387 590549841 590549616 7.200000e-61 244
8 TraesCS5B01G344600 chr5B 85.965 228 27 4 2163 2387 590538152 590537927 3.350000e-59 239
9 TraesCS5B01G344600 chr5B 84.722 216 28 5 2175 2387 703892196 703892409 7.300000e-51 211
10 TraesCS5B01G344600 chr5B 84.444 135 15 2 2391 2519 527787652 527787518 7.560000e-26 128
11 TraesCS5B01G344600 chr5D 96.687 1630 36 10 978 2603 434672440 434674055 0.000000e+00 2695
12 TraesCS5B01G344600 chr5D 85.599 993 85 13 791 1780 434554395 434553458 0.000000e+00 989
13 TraesCS5B01G344600 chr5D 79.610 1025 169 29 800 1795 434711357 434712370 0.000000e+00 699
14 TraesCS5B01G344600 chr5D 84.418 507 62 13 1595 2094 434577485 434576989 1.400000e-132 483
15 TraesCS5B01G344600 chr5D 78.327 789 136 21 791 1563 434578253 434577484 6.520000e-131 477
16 TraesCS5B01G344600 chr5D 91.954 348 12 6 215 561 434554961 434554629 8.430000e-130 473
17 TraesCS5B01G344600 chr5D 85.268 448 53 11 351 788 434710830 434711274 1.420000e-122 449
18 TraesCS5B01G344600 chr5D 92.140 229 16 2 523 751 434554629 434554403 3.230000e-84 322
19 TraesCS5B01G344600 chr5D 87.615 218 20 6 2181 2393 448129641 448129426 2.000000e-61 246
20 TraesCS5B01G344600 chr5D 88.265 196 20 2 1791 1984 434553410 434553216 5.600000e-57 231
21 TraesCS5B01G344600 chr5D 88.696 115 8 1 2412 2521 434604508 434604394 4.520000e-28 135
22 TraesCS5B01G344600 chr5D 97.333 75 2 0 2529 2603 434552866 434552792 7.560000e-26 128
23 TraesCS5B01G344600 chr5D 81.022 137 20 2 2391 2521 434570180 434570044 1.270000e-18 104
24 TraesCS5B01G344600 chr7B 99.057 212 2 0 1 212 32327741 32327952 5.260000e-102 381
25 TraesCS5B01G344600 chr4B 98.605 215 2 1 1 214 491804264 491804478 1.890000e-101 379
26 TraesCS5B01G344600 chrUn 98.140 215 4 0 1 215 325087211 325087425 2.450000e-100 375
27 TraesCS5B01G344600 chrUn 98.140 215 4 0 1 215 413410305 413410519 2.450000e-100 375
28 TraesCS5B01G344600 chr6B 98.131 214 4 0 1 214 91005284 91005497 8.800000e-100 374
29 TraesCS5B01G344600 chr6B 85.185 216 28 4 2175 2387 687328688 687328474 4.360000e-53 219
30 TraesCS5B01G344600 chr7D 87.168 226 25 3 2165 2387 535551711 535551487 1.200000e-63 254
31 TraesCS5B01G344600 chr2B 84.390 205 25 6 2162 2361 730087526 730087324 7.350000e-46 195


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 TraesCS5B01G344600 chr5B 527495692 527498294 2602 True 4807.0 4807 100.0000 1 2603 1 chr5B.!!$R2 2602
1 TraesCS5B01G344600 chr5B 527773715 527775422 1707 True 2100.0 2100 88.8760 803 2532 1 chr5B.!!$R4 1729
2 TraesCS5B01G344600 chr5B 527608714 527609798 1084 True 586.0 586 77.1130 1053 2161 1 chr5B.!!$R3 1108
3 TraesCS5B01G344600 chr5D 434672440 434674055 1615 False 2695.0 2695 96.6870 978 2603 1 chr5D.!!$F1 1625
4 TraesCS5B01G344600 chr5D 434710830 434712370 1540 False 574.0 699 82.4390 351 1795 2 chr5D.!!$F2 1444
5 TraesCS5B01G344600 chr5D 434576989 434578253 1264 True 480.0 483 81.3725 791 2094 2 chr5D.!!$R5 1303
6 TraesCS5B01G344600 chr5D 434552792 434554961 2169 True 428.6 989 91.0582 215 2603 5 chr5D.!!$R4 2388

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
301 302 0.038159 ACAGTAGTTGGCTCTCGTGC 60.038 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2018 0.96738 GCAGGCCAAGTGCATAGGTT 60.967 55.0 5.01 0.0 43.89 3.5 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
17 18 4.680487 CTCCTGGCGGTAGGTACT 57.320 61.111 0.00 0.00 46.37 2.73
18 19 2.897699 CTCCTGGCGGTAGGTACTT 58.102 57.895 0.00 0.00 41.75 2.24
19 20 2.062971 CTCCTGGCGGTAGGTACTTA 57.937 55.000 0.00 0.00 41.75 2.24
20 21 2.595238 CTCCTGGCGGTAGGTACTTAT 58.405 52.381 0.00 0.00 41.75 1.73
21 22 2.557490 CTCCTGGCGGTAGGTACTTATC 59.443 54.545 0.00 0.00 41.75 1.75
22 23 1.617357 CCTGGCGGTAGGTACTTATCC 59.383 57.143 0.00 0.00 41.75 2.59
23 24 2.313317 CTGGCGGTAGGTACTTATCCA 58.687 52.381 0.00 0.00 41.75 3.41
24 25 2.034124 TGGCGGTAGGTACTTATCCAC 58.966 52.381 0.00 0.00 41.75 4.02
25 26 1.000938 GGCGGTAGGTACTTATCCACG 60.001 57.143 0.00 0.00 41.75 4.94
26 27 1.678101 GCGGTAGGTACTTATCCACGT 59.322 52.381 0.00 0.00 41.75 4.49
27 28 2.287248 GCGGTAGGTACTTATCCACGTC 60.287 54.545 0.00 0.00 41.75 4.34
28 29 2.945008 CGGTAGGTACTTATCCACGTCA 59.055 50.000 0.00 0.00 41.75 4.35
29 30 3.003068 CGGTAGGTACTTATCCACGTCAG 59.997 52.174 0.00 0.00 41.75 3.51
30 31 3.243334 GGTAGGTACTTATCCACGTCAGC 60.243 52.174 0.00 0.00 41.75 4.26
31 32 1.404391 AGGTACTTATCCACGTCAGCG 59.596 52.381 0.00 0.00 39.38 5.18
32 33 1.197910 GTACTTATCCACGTCAGCGC 58.802 55.000 0.00 0.00 42.83 5.92
33 34 0.812549 TACTTATCCACGTCAGCGCA 59.187 50.000 11.47 0.00 42.83 6.09
34 35 0.458543 ACTTATCCACGTCAGCGCAG 60.459 55.000 11.47 0.00 42.83 5.18
35 36 0.458543 CTTATCCACGTCAGCGCAGT 60.459 55.000 11.47 0.27 42.83 4.40
36 37 0.457853 TTATCCACGTCAGCGCAGTC 60.458 55.000 11.47 0.00 42.83 3.51
37 38 1.591504 TATCCACGTCAGCGCAGTCA 61.592 55.000 11.47 0.00 42.83 3.41
38 39 2.434658 ATCCACGTCAGCGCAGTCAA 62.435 55.000 11.47 0.00 42.83 3.18
39 40 2.243957 CCACGTCAGCGCAGTCAAA 61.244 57.895 11.47 0.00 42.83 2.69
40 41 1.083401 CACGTCAGCGCAGTCAAAC 60.083 57.895 11.47 0.00 42.83 2.93
41 42 2.168621 CGTCAGCGCAGTCAAACG 59.831 61.111 11.47 3.42 0.00 3.60
42 43 2.551270 GTCAGCGCAGTCAAACGG 59.449 61.111 11.47 0.00 0.00 4.44
43 44 3.345808 TCAGCGCAGTCAAACGGC 61.346 61.111 11.47 0.00 35.94 5.68
44 45 4.389576 CAGCGCAGTCAAACGGCC 62.390 66.667 11.47 0.00 35.89 6.13
70 71 3.834799 CCTCCGTCGCACCCCTAC 61.835 72.222 0.00 0.00 0.00 3.18
71 72 3.834799 CTCCGTCGCACCCCTACC 61.835 72.222 0.00 0.00 0.00 3.18
78 79 4.875713 GCACCCCTACCGCCATGG 62.876 72.222 7.63 7.63 46.41 3.66
79 80 4.189580 CACCCCTACCGCCATGGG 62.190 72.222 15.13 3.37 44.64 4.00
97 98 2.338984 CCGTGGCGGTAGGCTATC 59.661 66.667 0.00 0.00 42.73 2.08
98 99 2.201022 CCGTGGCGGTAGGCTATCT 61.201 63.158 2.85 0.00 42.73 1.98
99 100 0.892358 CCGTGGCGGTAGGCTATCTA 60.892 60.000 2.85 0.00 42.73 1.98
100 101 0.956633 CGTGGCGGTAGGCTATCTAA 59.043 55.000 2.85 0.00 44.18 2.10
101 102 1.335689 CGTGGCGGTAGGCTATCTAAC 60.336 57.143 2.85 0.00 44.18 2.34
102 103 1.000618 GTGGCGGTAGGCTATCTAACC 59.999 57.143 2.85 2.59 44.18 2.85
103 104 0.607112 GGCGGTAGGCTATCTAACCC 59.393 60.000 2.85 0.00 42.94 4.11
104 105 1.630223 GCGGTAGGCTATCTAACCCT 58.370 55.000 2.85 0.00 39.11 4.34
105 106 2.556114 GGCGGTAGGCTATCTAACCCTA 60.556 54.545 2.85 0.00 42.94 3.53
106 107 2.491298 GCGGTAGGCTATCTAACCCTAC 59.509 54.545 2.85 7.39 46.60 3.18
109 110 1.630223 AGGCTATCTAACCCTACCGC 58.370 55.000 0.00 0.00 0.00 5.68
110 111 0.607112 GGCTATCTAACCCTACCGCC 59.393 60.000 0.00 0.00 0.00 6.13
111 112 0.243095 GCTATCTAACCCTACCGCCG 59.757 60.000 0.00 0.00 0.00 6.46
112 113 1.613836 CTATCTAACCCTACCGCCGT 58.386 55.000 0.00 0.00 0.00 5.68
113 114 2.783135 CTATCTAACCCTACCGCCGTA 58.217 52.381 0.00 0.00 0.00 4.02
114 115 1.613836 ATCTAACCCTACCGCCGTAG 58.386 55.000 5.35 5.35 41.55 3.51
127 128 3.912907 CGTAGGCCCTGGCGGTAG 61.913 72.222 0.00 0.00 43.06 3.18
128 129 4.237207 GTAGGCCCTGGCGGTAGC 62.237 72.222 0.00 0.00 43.06 3.58
138 139 4.390048 GCGGTAGCAAAAGGGTCA 57.610 55.556 0.00 0.00 44.35 4.02
139 140 2.636299 GCGGTAGCAAAAGGGTCAA 58.364 52.632 0.00 0.00 44.35 3.18
140 141 0.955905 GCGGTAGCAAAAGGGTCAAA 59.044 50.000 0.00 0.00 44.35 2.69
141 142 1.544246 GCGGTAGCAAAAGGGTCAAAT 59.456 47.619 0.00 0.00 44.35 2.32
142 143 2.415491 GCGGTAGCAAAAGGGTCAAATC 60.415 50.000 0.00 0.00 44.35 2.17
143 144 3.081804 CGGTAGCAAAAGGGTCAAATCT 58.918 45.455 0.00 0.00 0.00 2.40
144 145 3.127030 CGGTAGCAAAAGGGTCAAATCTC 59.873 47.826 0.00 0.00 0.00 2.75
145 146 3.127030 GGTAGCAAAAGGGTCAAATCTCG 59.873 47.826 0.00 0.00 0.00 4.04
146 147 3.140325 AGCAAAAGGGTCAAATCTCGA 57.860 42.857 0.00 0.00 0.00 4.04
147 148 3.486383 AGCAAAAGGGTCAAATCTCGAA 58.514 40.909 0.00 0.00 0.00 3.71
148 149 3.888930 AGCAAAAGGGTCAAATCTCGAAA 59.111 39.130 0.00 0.00 0.00 3.46
149 150 4.340950 AGCAAAAGGGTCAAATCTCGAAAA 59.659 37.500 0.00 0.00 0.00 2.29
150 151 5.047188 GCAAAAGGGTCAAATCTCGAAAAA 58.953 37.500 0.00 0.00 0.00 1.94
171 172 5.728637 AAAATTCAAACAGGGGTCAGATC 57.271 39.130 0.00 0.00 0.00 2.75
172 173 2.879103 TTCAAACAGGGGTCAGATCC 57.121 50.000 0.00 0.00 0.00 3.36
173 174 2.044793 TCAAACAGGGGTCAGATCCT 57.955 50.000 0.00 0.00 0.00 3.24
180 181 2.131023 AGGGGTCAGATCCTGAAATCC 58.869 52.381 0.00 1.92 42.46 3.01
181 182 2.131023 GGGGTCAGATCCTGAAATCCT 58.869 52.381 0.00 0.00 42.46 3.24
182 183 2.511637 GGGGTCAGATCCTGAAATCCTT 59.488 50.000 0.00 0.00 42.46 3.36
183 184 3.053320 GGGGTCAGATCCTGAAATCCTTT 60.053 47.826 0.00 0.00 42.46 3.11
184 185 4.203226 GGGTCAGATCCTGAAATCCTTTC 58.797 47.826 0.00 0.00 42.46 2.62
185 186 4.203226 GGTCAGATCCTGAAATCCTTTCC 58.797 47.826 0.00 0.00 42.46 3.13
186 187 4.324563 GGTCAGATCCTGAAATCCTTTCCA 60.325 45.833 0.00 0.00 42.46 3.53
187 188 5.256474 GTCAGATCCTGAAATCCTTTCCAA 58.744 41.667 0.00 0.00 42.46 3.53
188 189 5.711976 GTCAGATCCTGAAATCCTTTCCAAA 59.288 40.000 0.00 0.00 42.46 3.28
189 190 6.209391 GTCAGATCCTGAAATCCTTTCCAAAA 59.791 38.462 0.00 0.00 42.46 2.44
190 191 6.782000 TCAGATCCTGAAATCCTTTCCAAAAA 59.218 34.615 0.00 0.00 37.57 1.94
191 192 7.039504 TCAGATCCTGAAATCCTTTCCAAAAAG 60.040 37.037 0.00 0.00 37.57 2.27
192 193 7.793058 CAGATCCTGAAATCCTTTCCAAAAAGG 60.793 40.741 10.10 10.10 46.55 3.11
202 203 5.794687 CTTTCCAAAAAGGGTCAAAACAC 57.205 39.130 0.00 0.00 38.59 3.32
203 204 3.512033 TCCAAAAAGGGTCAAAACACG 57.488 42.857 0.00 0.00 38.24 4.49
204 205 3.090037 TCCAAAAAGGGTCAAAACACGA 58.910 40.909 0.00 0.00 38.24 4.35
205 206 3.510360 TCCAAAAAGGGTCAAAACACGAA 59.490 39.130 0.00 0.00 38.24 3.85
206 207 4.021368 TCCAAAAAGGGTCAAAACACGAAA 60.021 37.500 0.00 0.00 38.24 3.46
207 208 4.873259 CCAAAAAGGGTCAAAACACGAAAT 59.127 37.500 0.00 0.00 32.44 2.17
208 209 5.352846 CCAAAAAGGGTCAAAACACGAAATT 59.647 36.000 0.00 0.00 32.44 1.82
209 210 6.456315 CCAAAAAGGGTCAAAACACGAAATTC 60.456 38.462 0.00 0.00 32.44 2.17
210 211 3.619233 AGGGTCAAAACACGAAATTCG 57.381 42.857 14.35 14.35 46.93 3.34
211 212 2.292292 AGGGTCAAAACACGAAATTCGG 59.708 45.455 19.95 10.81 45.59 4.30
212 213 2.048498 GGTCAAAACACGAAATTCGGC 58.952 47.619 19.95 0.00 45.59 5.54
213 214 2.048498 GTCAAAACACGAAATTCGGCC 58.952 47.619 19.95 0.00 45.59 6.13
233 234 1.414061 CCCATACTCCCAGGGCTCTG 61.414 65.000 6.61 6.61 40.59 3.35
301 302 0.038159 ACAGTAGTTGGCTCTCGTGC 60.038 55.000 0.00 0.00 0.00 5.34
303 304 1.805945 GTAGTTGGCTCTCGTGCGG 60.806 63.158 0.00 0.00 0.00 5.69
477 493 3.827898 CTCGCTCTCCACCCGTCC 61.828 72.222 0.00 0.00 0.00 4.79
525 574 4.832608 CCCTAACGGCGGCTCACC 62.833 72.222 13.24 0.00 0.00 4.02
571 620 2.851102 CTCCGCCCCCATCTCCAT 60.851 66.667 0.00 0.00 0.00 3.41
586 635 8.785859 CCCCATCTCCATTTATATCCTAAATCT 58.214 37.037 0.00 0.00 0.00 2.40
623 672 2.749621 CCTCTATTCTTGTGCGGCTTTT 59.250 45.455 0.00 0.00 0.00 2.27
709 759 4.864704 TTTTCAGGGTTCAGTTAATGCC 57.135 40.909 0.00 0.00 0.00 4.40
757 808 1.004277 TGGCCCAGTTCATAGTGGAAC 59.996 52.381 0.00 0.00 46.20 3.62
770 821 8.739972 GTTCATAGTGGAACCTGTTAATCATTT 58.260 33.333 0.00 0.00 40.97 2.32
771 822 8.877864 TCATAGTGGAACCTGTTAATCATTTT 57.122 30.769 0.00 0.00 37.80 1.82
836 959 3.486383 TGTAACTTTGGCCTCTTTCTGG 58.514 45.455 3.32 0.00 0.00 3.86
849 972 4.465305 CCTCTTTCTGGAAATTCATGCCTT 59.535 41.667 0.00 0.00 0.00 4.35
929 1052 2.614520 CAACCGTGTGTGATTGTAACCA 59.385 45.455 0.00 0.00 0.00 3.67
994 1120 5.481824 AGATCACTCAAGTCAATAGTGTGGA 59.518 40.000 0.00 0.00 41.12 4.02
1136 1262 3.559069 CACATTGCATCTCTAACCCCAT 58.441 45.455 0.00 0.00 0.00 4.00
1413 1551 2.459442 GCAGAGCCTCATCGTGCAC 61.459 63.158 6.82 6.82 34.18 4.57
1461 1605 0.606673 GTGAGGAGGCCACCTTCAAC 60.607 60.000 23.79 17.18 40.73 3.18
1651 1795 3.601443 AGCTGCAAGTAAGACGAAGAT 57.399 42.857 1.02 0.00 35.30 2.40
1780 1945 1.811645 TTGTCAGCGATCGGGTGTCA 61.812 55.000 18.30 13.47 44.48 3.58
1800 2006 9.662947 GGTGTCATAAGTACTAGTAATGGTTTT 57.337 33.333 3.61 0.00 0.00 2.43
1812 2018 6.403866 AGTAATGGTTTTGATCAAACTGCA 57.596 33.333 20.35 3.23 43.95 4.41
1813 2019 6.815089 AGTAATGGTTTTGATCAAACTGCAA 58.185 32.000 20.35 8.05 43.95 4.08
1841 2047 4.580167 TGCACTTGGCCTGCTATAATTAAG 59.420 41.667 15.70 4.04 43.89 1.85
2240 2673 2.028112 TCGAATCCTGGGTTCTCACAAG 60.028 50.000 17.16 1.30 0.00 3.16
2387 2823 3.205733 ACTCCCCTTGGGTTGAGTTTTTA 59.794 43.478 10.53 0.00 44.74 1.52
2461 2897 2.224769 TGGATTCAGGGGTGTTCTTCAC 60.225 50.000 0.00 0.00 45.47 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.062971 TAAGTACCTACCGCCAGGAG 57.937 55.000 7.47 0.00 41.02 3.69
1 2 2.590821 GATAAGTACCTACCGCCAGGA 58.409 52.381 7.47 0.00 41.02 3.86
2 3 1.617357 GGATAAGTACCTACCGCCAGG 59.383 57.143 0.00 0.00 45.13 4.45
3 4 2.035576 GTGGATAAGTACCTACCGCCAG 59.964 54.545 0.00 0.00 0.00 4.85
4 5 2.034124 GTGGATAAGTACCTACCGCCA 58.966 52.381 0.00 0.00 0.00 5.69
5 6 1.000938 CGTGGATAAGTACCTACCGCC 60.001 57.143 0.00 0.00 0.00 6.13
6 7 1.678101 ACGTGGATAAGTACCTACCGC 59.322 52.381 0.00 0.00 0.00 5.68
7 8 2.945008 TGACGTGGATAAGTACCTACCG 59.055 50.000 0.00 0.00 0.00 4.02
8 9 3.243334 GCTGACGTGGATAAGTACCTACC 60.243 52.174 0.00 0.00 0.00 3.18
9 10 3.547613 CGCTGACGTGGATAAGTACCTAC 60.548 52.174 0.00 0.00 33.53 3.18
10 11 2.615447 CGCTGACGTGGATAAGTACCTA 59.385 50.000 0.00 0.00 33.53 3.08
11 12 1.404391 CGCTGACGTGGATAAGTACCT 59.596 52.381 0.00 0.00 33.53 3.08
12 13 1.836383 CGCTGACGTGGATAAGTACC 58.164 55.000 0.00 0.00 33.53 3.34
13 14 1.197910 GCGCTGACGTGGATAAGTAC 58.802 55.000 0.00 0.00 42.83 2.73
14 15 0.812549 TGCGCTGACGTGGATAAGTA 59.187 50.000 9.73 0.00 42.83 2.24
15 16 0.458543 CTGCGCTGACGTGGATAAGT 60.459 55.000 9.73 0.00 42.83 2.24
16 17 0.458543 ACTGCGCTGACGTGGATAAG 60.459 55.000 21.92 0.97 42.83 1.73
17 18 0.457853 GACTGCGCTGACGTGGATAA 60.458 55.000 21.92 0.00 42.83 1.75
18 19 1.138883 GACTGCGCTGACGTGGATA 59.861 57.895 21.92 0.00 42.83 2.59
19 20 2.125912 GACTGCGCTGACGTGGAT 60.126 61.111 21.92 0.00 42.83 3.41
20 21 2.636778 TTTGACTGCGCTGACGTGGA 62.637 55.000 21.92 0.00 42.83 4.02
21 22 2.243957 TTTGACTGCGCTGACGTGG 61.244 57.895 21.92 0.00 42.83 4.94
22 23 1.083401 GTTTGACTGCGCTGACGTG 60.083 57.895 21.92 0.63 42.83 4.49
23 24 2.585869 CGTTTGACTGCGCTGACGT 61.586 57.895 21.92 6.61 42.83 4.34
24 25 2.168621 CGTTTGACTGCGCTGACG 59.831 61.111 21.92 15.64 44.07 4.35
25 26 2.551270 CCGTTTGACTGCGCTGAC 59.449 61.111 21.92 15.42 0.00 3.51
26 27 3.345808 GCCGTTTGACTGCGCTGA 61.346 61.111 21.92 0.00 0.00 4.26
27 28 4.389576 GGCCGTTTGACTGCGCTG 62.390 66.667 13.23 13.23 0.00 5.18
53 54 3.834799 GTAGGGGTGCGACGGAGG 61.835 72.222 0.00 0.00 0.00 4.30
54 55 3.834799 GGTAGGGGTGCGACGGAG 61.835 72.222 0.00 0.00 0.00 4.63
61 62 4.875713 CCATGGCGGTAGGGGTGC 62.876 72.222 0.00 0.00 0.00 5.01
62 63 4.189580 CCCATGGCGGTAGGGGTG 62.190 72.222 6.09 0.00 36.91 4.61
81 82 0.956633 TTAGATAGCCTACCGCCACG 59.043 55.000 0.00 0.00 38.78 4.94
82 83 1.000618 GGTTAGATAGCCTACCGCCAC 59.999 57.143 0.00 0.00 38.78 5.01
83 84 1.335145 GGTTAGATAGCCTACCGCCA 58.665 55.000 0.00 0.00 38.78 5.69
84 85 0.607112 GGGTTAGATAGCCTACCGCC 59.393 60.000 0.00 0.00 41.39 6.13
91 92 0.607112 GGCGGTAGGGTTAGATAGCC 59.393 60.000 0.00 0.00 45.13 3.93
92 93 0.243095 CGGCGGTAGGGTTAGATAGC 59.757 60.000 0.00 0.00 0.00 2.97
93 94 1.613836 ACGGCGGTAGGGTTAGATAG 58.386 55.000 13.24 0.00 0.00 2.08
94 95 2.783135 CTACGGCGGTAGGGTTAGATA 58.217 52.381 20.62 0.00 42.02 1.98
95 96 1.613836 CTACGGCGGTAGGGTTAGAT 58.386 55.000 20.62 0.00 42.02 1.98
96 97 3.100545 CTACGGCGGTAGGGTTAGA 57.899 57.895 20.62 0.00 42.02 2.10
110 111 3.912907 CTACCGCCAGGGCCTACG 61.913 72.222 18.48 18.48 43.47 3.51
111 112 4.237207 GCTACCGCCAGGGCCTAC 62.237 72.222 5.28 0.00 43.47 3.18
112 113 4.789173 TGCTACCGCCAGGGCCTA 62.789 66.667 5.28 0.00 43.47 3.93
114 115 4.733542 TTTGCTACCGCCAGGGCC 62.734 66.667 4.42 0.00 43.47 5.80
115 116 2.675075 TTTTGCTACCGCCAGGGC 60.675 61.111 0.00 0.00 43.47 5.19
116 117 2.046285 CCTTTTGCTACCGCCAGGG 61.046 63.158 0.00 0.00 43.47 4.45
117 118 2.046285 CCCTTTTGCTACCGCCAGG 61.046 63.158 0.00 0.00 45.13 4.45
118 119 1.303317 ACCCTTTTGCTACCGCCAG 60.303 57.895 0.00 0.00 34.43 4.85
119 120 1.302993 GACCCTTTTGCTACCGCCA 60.303 57.895 0.00 0.00 34.43 5.69
120 121 0.891904 TTGACCCTTTTGCTACCGCC 60.892 55.000 0.00 0.00 34.43 6.13
121 122 0.955905 TTTGACCCTTTTGCTACCGC 59.044 50.000 0.00 0.00 0.00 5.68
122 123 3.081804 AGATTTGACCCTTTTGCTACCG 58.918 45.455 0.00 0.00 0.00 4.02
123 124 3.127030 CGAGATTTGACCCTTTTGCTACC 59.873 47.826 0.00 0.00 0.00 3.18
124 125 4.000988 TCGAGATTTGACCCTTTTGCTAC 58.999 43.478 0.00 0.00 0.00 3.58
125 126 4.280436 TCGAGATTTGACCCTTTTGCTA 57.720 40.909 0.00 0.00 0.00 3.49
126 127 3.140325 TCGAGATTTGACCCTTTTGCT 57.860 42.857 0.00 0.00 0.00 3.91
127 128 3.915437 TTCGAGATTTGACCCTTTTGC 57.085 42.857 0.00 0.00 0.00 3.68
148 149 5.012046 GGATCTGACCCCTGTTTGAATTTTT 59.988 40.000 0.00 0.00 0.00 1.94
149 150 4.528206 GGATCTGACCCCTGTTTGAATTTT 59.472 41.667 0.00 0.00 0.00 1.82
150 151 4.089361 GGATCTGACCCCTGTTTGAATTT 58.911 43.478 0.00 0.00 0.00 1.82
151 152 3.334881 AGGATCTGACCCCTGTTTGAATT 59.665 43.478 0.00 0.00 0.00 2.17
152 153 2.922283 AGGATCTGACCCCTGTTTGAAT 59.078 45.455 0.00 0.00 0.00 2.57
153 154 2.040278 CAGGATCTGACCCCTGTTTGAA 59.960 50.000 15.84 0.00 43.71 2.69
154 155 1.630369 CAGGATCTGACCCCTGTTTGA 59.370 52.381 15.84 0.00 43.71 2.69
155 156 2.119801 CAGGATCTGACCCCTGTTTG 57.880 55.000 15.84 0.00 43.71 2.93
160 161 2.131023 GGATTTCAGGATCTGACCCCT 58.869 52.381 0.00 0.00 40.46 4.79
161 162 2.131023 AGGATTTCAGGATCTGACCCC 58.869 52.381 0.00 0.37 40.46 4.95
162 163 3.941704 AAGGATTTCAGGATCTGACCC 57.058 47.619 0.00 0.68 40.46 4.46
180 181 4.328712 CGTGTTTTGACCCTTTTTGGAAAG 59.671 41.667 0.00 0.00 41.56 2.62
181 182 4.021368 TCGTGTTTTGACCCTTTTTGGAAA 60.021 37.500 0.00 0.00 38.35 3.13
182 183 3.510360 TCGTGTTTTGACCCTTTTTGGAA 59.490 39.130 0.00 0.00 38.35 3.53
183 184 3.090037 TCGTGTTTTGACCCTTTTTGGA 58.910 40.909 0.00 0.00 38.35 3.53
184 185 3.512033 TCGTGTTTTGACCCTTTTTGG 57.488 42.857 0.00 0.00 0.00 3.28
185 186 6.415798 AATTTCGTGTTTTGACCCTTTTTG 57.584 33.333 0.00 0.00 0.00 2.44
186 187 5.289917 CGAATTTCGTGTTTTGACCCTTTTT 59.710 36.000 10.61 0.00 34.72 1.94
187 188 4.801516 CGAATTTCGTGTTTTGACCCTTTT 59.198 37.500 10.61 0.00 34.72 2.27
188 189 4.356289 CGAATTTCGTGTTTTGACCCTTT 58.644 39.130 10.61 0.00 34.72 3.11
189 190 3.243267 CCGAATTTCGTGTTTTGACCCTT 60.243 43.478 16.89 0.00 38.40 3.95
190 191 2.292292 CCGAATTTCGTGTTTTGACCCT 59.708 45.455 16.89 0.00 38.40 4.34
191 192 2.657184 CCGAATTTCGTGTTTTGACCC 58.343 47.619 16.89 0.00 38.40 4.46
192 193 2.048498 GCCGAATTTCGTGTTTTGACC 58.952 47.619 16.89 0.00 38.40 4.02
193 194 2.048498 GGCCGAATTTCGTGTTTTGAC 58.952 47.619 16.89 0.00 38.40 3.18
194 195 1.001158 GGGCCGAATTTCGTGTTTTGA 60.001 47.619 16.89 0.00 38.40 2.69
195 196 1.414378 GGGCCGAATTTCGTGTTTTG 58.586 50.000 16.89 2.55 38.40 2.44
196 197 0.315886 GGGGCCGAATTTCGTGTTTT 59.684 50.000 16.89 0.00 38.40 2.43
197 198 1.529152 GGGGGCCGAATTTCGTGTTT 61.529 55.000 16.89 0.00 38.40 2.83
198 199 1.974875 GGGGGCCGAATTTCGTGTT 60.975 57.895 16.89 0.00 38.40 3.32
199 200 2.360726 GGGGGCCGAATTTCGTGT 60.361 61.111 16.89 0.00 38.40 4.49
200 201 0.464735 TATGGGGGCCGAATTTCGTG 60.465 55.000 16.89 9.83 38.40 4.35
201 202 0.464916 GTATGGGGGCCGAATTTCGT 60.465 55.000 16.89 0.10 38.40 3.85
202 203 0.179029 AGTATGGGGGCCGAATTTCG 60.179 55.000 11.81 11.81 40.07 3.46
203 204 1.605753 GAGTATGGGGGCCGAATTTC 58.394 55.000 0.00 0.00 0.00 2.17
204 205 0.185175 GGAGTATGGGGGCCGAATTT 59.815 55.000 0.00 0.00 0.00 1.82
205 206 1.716028 GGGAGTATGGGGGCCGAATT 61.716 60.000 0.00 0.00 0.00 2.17
206 207 2.154074 GGGAGTATGGGGGCCGAAT 61.154 63.158 0.00 0.00 0.00 3.34
207 208 2.770904 GGGAGTATGGGGGCCGAA 60.771 66.667 0.00 0.00 0.00 4.30
208 209 4.096816 TGGGAGTATGGGGGCCGA 62.097 66.667 0.00 0.00 0.00 5.54
209 210 3.560251 CTGGGAGTATGGGGGCCG 61.560 72.222 0.00 0.00 0.00 6.13
210 211 3.178611 CCTGGGAGTATGGGGGCC 61.179 72.222 0.00 0.00 0.00 5.80
211 212 3.178611 CCCTGGGAGTATGGGGGC 61.179 72.222 7.01 0.00 37.37 5.80
212 213 3.178611 GCCCTGGGAGTATGGGGG 61.179 72.222 19.27 0.00 41.19 5.40
213 214 2.039405 AGCCCTGGGAGTATGGGG 60.039 66.667 19.27 0.00 41.19 4.96
233 234 9.185680 ACCCCATAAACAAAGAAATATACAGAC 57.814 33.333 0.00 0.00 0.00 3.51
270 271 5.047660 AGCCAACTACTGTTTCAACACAAAA 60.048 36.000 0.00 0.00 34.70 2.44
477 493 3.916392 AAGAAGCGGTGAGGCGTCG 62.916 63.158 1.39 0.00 44.54 5.12
533 582 4.803426 CTCTCCGGCGGTGAGTGC 62.803 72.222 36.98 0.00 38.19 4.40
586 635 8.027524 AGAATAGAGGAAGCAAATCACATCTA 57.972 34.615 0.00 0.00 0.00 1.98
658 707 6.406400 CCCAAAACTGGTGTTGATTGAGTTAA 60.406 38.462 5.31 0.00 36.39 2.01
659 708 5.068460 CCCAAAACTGGTGTTGATTGAGTTA 59.932 40.000 5.31 0.00 36.39 2.24
662 711 3.636300 TCCCAAAACTGGTGTTGATTGAG 59.364 43.478 5.31 0.00 36.39 3.02
663 712 3.636679 TCCCAAAACTGGTGTTGATTGA 58.363 40.909 5.31 0.00 36.39 2.57
664 713 4.605640 ATCCCAAAACTGGTGTTGATTG 57.394 40.909 5.31 0.00 36.39 2.67
665 714 6.933514 AATATCCCAAAACTGGTGTTGATT 57.066 33.333 5.31 0.00 36.39 2.57
667 716 6.739331 AAAATATCCCAAAACTGGTGTTGA 57.261 33.333 5.31 0.00 36.39 3.18
668 717 6.989169 TGAAAAATATCCCAAAACTGGTGTTG 59.011 34.615 0.00 0.00 36.39 3.33
709 759 4.334759 CCATGAGCTTTACAGGATGAACTG 59.665 45.833 0.00 0.00 44.03 3.16
770 821 6.269769 AGGTTGGCTTTCAGATTGGAAAATAA 59.730 34.615 0.00 0.00 36.42 1.40
771 822 5.779771 AGGTTGGCTTTCAGATTGGAAAATA 59.220 36.000 0.00 0.00 36.42 1.40
775 826 2.892852 CAGGTTGGCTTTCAGATTGGAA 59.107 45.455 0.00 0.00 0.00 3.53
788 839 2.623416 ACAAAAGCTAGTTCAGGTTGGC 59.377 45.455 0.00 0.00 44.18 4.52
789 840 3.882888 TCACAAAAGCTAGTTCAGGTTGG 59.117 43.478 0.00 0.00 44.18 3.77
849 972 5.714333 TCACAGGAAAAAGCATGGCTATTTA 59.286 36.000 0.00 0.00 38.25 1.40
929 1052 3.200165 GCCAAGGTGGTAGAAATAGAGGT 59.800 47.826 0.00 0.00 40.46 3.85
1136 1262 5.364778 TCTGTTTGAAAGAATCGGTGAAGA 58.635 37.500 0.00 0.00 0.00 2.87
1612 1756 3.246619 GCTAGCTAGCTTAACTATGGCG 58.753 50.000 33.71 0.56 45.62 5.69
1651 1795 2.204291 AATGACCCTCCTGGCCCA 60.204 61.111 0.00 0.00 37.83 5.36
1812 2018 0.967380 GCAGGCCAAGTGCATAGGTT 60.967 55.000 5.01 0.00 43.89 3.50
1813 2019 1.379044 GCAGGCCAAGTGCATAGGT 60.379 57.895 5.01 0.00 43.89 3.08
1841 2047 5.334028 GCCAAGCAAATTCCATTGTACAAAC 60.334 40.000 13.23 0.00 32.80 2.93
1999 2207 6.762187 TGTGAATTTGTTCATTTCAGCATGTT 59.238 30.769 0.00 0.00 33.11 2.71
2240 2673 1.603739 ACAGCGAGGGGCCTTTTTC 60.604 57.895 0.84 0.00 45.17 2.29
2387 2823 7.657354 GCCTGAAAATACTCAAGGACAATTTTT 59.343 33.333 0.00 0.00 31.70 1.94


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

AutoCloner maintained by Alex Coulton.