Multiple sequence alignment - TraesCS5B01G476100

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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 TraesCS5B01G476100 chr5B 100.000 2546 0 0 1 2546 648608297 648610842 0.000000e+00 4702.0
1 TraesCS5B01G476100 chr5B 98.372 1167 18 1 461 1626 648284798 648283632 0.000000e+00 2049.0
2 TraesCS5B01G476100 chr5B 90.402 323 18 4 592 901 648293486 648293164 1.820000e-111 412.0
3 TraesCS5B01G476100 chr5B 90.809 272 18 5 333 603 648300050 648299785 8.660000e-95 357.0
4 TraesCS5B01G476100 chr5B 88.500 200 22 1 5 204 546192781 546192979 9.100000e-60 241.0
5 TraesCS5B01G476100 chr5B 95.455 132 6 0 333 464 648285251 648285120 7.140000e-51 211.0
6 TraesCS5B01G476100 chr5B 74.444 360 66 21 2178 2528 671342208 671342550 5.720000e-27 132.0
7 TraesCS5B01G476100 chr5D 92.382 1444 74 17 220 1639 515672309 515670878 0.000000e+00 2025.0
8 TraesCS5B01G476100 chr5D 82.781 151 24 2 2173 2321 270250718 270250868 1.590000e-27 134.0
9 TraesCS5B01G476100 chr5D 76.074 163 30 3 2082 2237 476040289 476040129 2.720000e-10 76.8
10 TraesCS5B01G476100 chr5A 82.850 1137 99 57 446 1546 643921814 643920738 0.000000e+00 931.0
11 TraesCS5B01G476100 chr7A 87.697 634 42 10 1945 2546 734916918 734917547 0.000000e+00 706.0
12 TraesCS5B01G476100 chr7A 87.037 216 24 3 7 222 712340685 712340474 9.100000e-60 241.0
13 TraesCS5B01G476100 chr2D 93.187 411 25 3 2138 2546 551837506 551837915 3.620000e-168 601.0
14 TraesCS5B01G476100 chr2D 95.195 333 13 2 1636 1967 551836879 551837209 8.070000e-145 523.0
15 TraesCS5B01G476100 chr2D 87.671 219 24 2 2 220 82102090 82102305 4.200000e-63 252.0
16 TraesCS5B01G476100 chr2D 87.907 215 23 2 7 221 584774621 584774410 1.510000e-62 250.0
17 TraesCS5B01G476100 chr2D 92.073 164 13 0 1966 2129 551837282 551837445 5.480000e-57 231.0
18 TraesCS5B01G476100 chr2D 78.161 261 44 11 2201 2452 179937361 179937105 1.220000e-33 154.0
19 TraesCS5B01G476100 chr2B 89.352 216 21 1 5 220 25269801 25269588 1.160000e-68 270.0
20 TraesCS5B01G476100 chr3D 88.426 216 22 2 7 222 394762798 394763010 9.040000e-65 257.0
21 TraesCS5B01G476100 chr3D 86.574 216 26 2 5 220 535702392 535702180 4.230000e-58 235.0
22 TraesCS5B01G476100 chr4B 86.758 219 23 5 5 222 412201571 412201358 3.270000e-59 239.0
23 TraesCS5B01G476100 chr7B 87.562 201 24 1 4 204 606848342 606848541 5.480000e-57 231.0
24 TraesCS5B01G476100 chr6A 92.500 40 2 1 2218 2257 61210723 61210761 3.540000e-04 56.5
25 TraesCS5B01G476100 chr1D 92.500 40 2 1 2218 2257 70603463 70603425 3.540000e-04 56.5
26 TraesCS5B01G476100 chr1D 100.000 29 0 0 2218 2246 153810507 153810479 1.000000e-03 54.7
27 TraesCS5B01G476100 chr1A 92.500 40 2 1 2218 2257 9208579 9208541 3.540000e-04 56.5


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 TraesCS5B01G476100 chr5B 648608297 648610842 2545 False 4702.000000 4702 100.0000 1 2546 1 chr5B.!!$F2 2545
1 TraesCS5B01G476100 chr5B 648283632 648285251 1619 True 1130.000000 2049 96.9135 333 1626 2 chr5B.!!$R3 1293
2 TraesCS5B01G476100 chr5D 515670878 515672309 1431 True 2025.000000 2025 92.3820 220 1639 1 chr5D.!!$R2 1419
3 TraesCS5B01G476100 chr5A 643920738 643921814 1076 True 931.000000 931 82.8500 446 1546 1 chr5A.!!$R1 1100
4 TraesCS5B01G476100 chr7A 734916918 734917547 629 False 706.000000 706 87.6970 1945 2546 1 chr7A.!!$F1 601
5 TraesCS5B01G476100 chr2D 551836879 551837915 1036 False 451.666667 601 93.4850 1636 2546 3 chr2D.!!$F2 910

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
106 107 0.034476 GGCGGTAGGCTGTATAACCC 59.966 60.0 0.0 0.0 42.94 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 2277 0.169672 CTTCAATTGCAGCCAGGACG 59.83 55.0 0.0 0.0 0.0 4.79 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
34 35 1.153429 GGTACCCATCCACGTCAGC 60.153 63.158 0.00 0.00 0.00 4.26
35 36 1.153429 GTACCCATCCACGTCAGCC 60.153 63.158 0.00 0.00 0.00 4.85
36 37 1.305802 TACCCATCCACGTCAGCCT 60.306 57.895 0.00 0.00 0.00 4.58
37 38 1.613317 TACCCATCCACGTCAGCCTG 61.613 60.000 0.00 0.00 0.00 4.85
38 39 2.124983 CCATCCACGTCAGCCTGG 60.125 66.667 0.00 0.00 0.00 4.45
39 40 2.124983 CATCCACGTCAGCCTGGG 60.125 66.667 0.00 0.00 0.00 4.45
40 41 4.101448 ATCCACGTCAGCCTGGGC 62.101 66.667 3.00 3.00 42.33 5.36
42 43 4.641645 CCACGTCAGCCTGGGCAA 62.642 66.667 14.39 0.00 44.88 4.52
43 44 2.594303 CACGTCAGCCTGGGCAAA 60.594 61.111 14.39 0.00 44.88 3.68
44 45 2.594592 ACGTCAGCCTGGGCAAAC 60.595 61.111 14.39 9.83 44.88 2.93
45 46 3.726517 CGTCAGCCTGGGCAAACG 61.727 66.667 18.80 18.80 44.88 3.60
46 47 3.365265 GTCAGCCTGGGCAAACGG 61.365 66.667 14.39 0.00 44.88 4.44
87 88 4.489771 CTACCGCCAGGCCCCTTG 62.490 72.222 5.63 0.00 42.76 3.61
98 99 4.489771 CCCCTTGGCGGTAGGCTG 62.490 72.222 0.00 0.00 44.18 4.85
99 100 3.717294 CCCTTGGCGGTAGGCTGT 61.717 66.667 0.00 0.00 44.18 4.40
100 101 2.363975 CCCTTGGCGGTAGGCTGTA 61.364 63.158 0.00 0.00 44.18 2.74
101 102 1.696097 CCCTTGGCGGTAGGCTGTAT 61.696 60.000 0.00 0.00 44.18 2.29
102 103 1.045407 CCTTGGCGGTAGGCTGTATA 58.955 55.000 0.00 0.00 44.18 1.47
103 104 1.414919 CCTTGGCGGTAGGCTGTATAA 59.585 52.381 0.00 0.00 44.18 0.98
104 105 2.480845 CTTGGCGGTAGGCTGTATAAC 58.519 52.381 0.00 0.00 44.18 1.89
105 106 0.754472 TGGCGGTAGGCTGTATAACC 59.246 55.000 0.00 0.00 44.18 2.85
106 107 0.034476 GGCGGTAGGCTGTATAACCC 59.966 60.000 0.00 0.00 42.94 4.11
107 108 1.046204 GCGGTAGGCTGTATAACCCT 58.954 55.000 0.00 0.00 39.11 4.34
108 109 2.242043 GCGGTAGGCTGTATAACCCTA 58.758 52.381 0.00 0.00 39.11 3.53
109 110 2.029560 GCGGTAGGCTGTATAACCCTAC 60.030 54.545 12.86 12.86 46.60 3.18
111 112 3.930634 GTAGGCTGTATAACCCTACCG 57.069 52.381 0.00 0.00 43.31 4.02
112 113 1.046204 AGGCTGTATAACCCTACCGC 58.954 55.000 0.00 0.00 32.84 5.68
113 114 0.034476 GGCTGTATAACCCTACCGCC 59.966 60.000 1.74 1.74 42.33 6.13
114 115 0.754472 GCTGTATAACCCTACCGCCA 59.246 55.000 0.00 0.00 0.00 5.69
115 116 1.270147 GCTGTATAACCCTACCGCCAG 60.270 57.143 0.00 0.00 0.00 4.85
116 117 2.313317 CTGTATAACCCTACCGCCAGA 58.687 52.381 0.00 0.00 0.00 3.86
117 118 2.296471 CTGTATAACCCTACCGCCAGAG 59.704 54.545 0.00 0.00 0.00 3.35
118 119 1.000618 GTATAACCCTACCGCCAGAGC 59.999 57.143 0.00 0.00 0.00 4.09
119 120 0.689745 ATAACCCTACCGCCAGAGCA 60.690 55.000 0.00 0.00 39.83 4.26
120 121 1.610554 TAACCCTACCGCCAGAGCAC 61.611 60.000 0.00 0.00 39.83 4.40
121 122 4.514577 CCCTACCGCCAGAGCACG 62.515 72.222 0.00 0.00 39.83 5.34
122 123 3.760035 CCTACCGCCAGAGCACGT 61.760 66.667 0.00 0.00 39.83 4.49
123 124 2.507102 CTACCGCCAGAGCACGTG 60.507 66.667 12.28 12.28 39.83 4.49
124 125 3.989698 CTACCGCCAGAGCACGTGG 62.990 68.421 18.88 0.30 39.83 4.94
134 135 3.339731 GCACGTGGCAGTAGCAAA 58.660 55.556 18.88 0.00 44.61 3.68
135 136 1.652012 GCACGTGGCAGTAGCAAAA 59.348 52.632 18.88 0.00 44.61 2.44
136 137 0.240945 GCACGTGGCAGTAGCAAAAT 59.759 50.000 18.88 0.00 44.61 1.82
137 138 1.967762 CACGTGGCAGTAGCAAAATG 58.032 50.000 7.95 0.00 44.61 2.32
138 139 0.881118 ACGTGGCAGTAGCAAAATGG 59.119 50.000 0.00 0.00 44.61 3.16
139 140 0.881118 CGTGGCAGTAGCAAAATGGT 59.119 50.000 0.00 0.00 44.61 3.55
140 141 1.135689 CGTGGCAGTAGCAAAATGGTC 60.136 52.381 0.00 0.00 44.61 4.02
141 142 1.135689 GTGGCAGTAGCAAAATGGTCG 60.136 52.381 0.00 0.00 44.61 4.79
142 143 1.271108 TGGCAGTAGCAAAATGGTCGA 60.271 47.619 0.00 0.00 44.61 4.20
143 144 1.810151 GGCAGTAGCAAAATGGTCGAA 59.190 47.619 0.00 0.00 44.61 3.71
144 145 2.423538 GGCAGTAGCAAAATGGTCGAAT 59.576 45.455 0.00 0.00 44.61 3.34
145 146 3.487544 GGCAGTAGCAAAATGGTCGAATC 60.488 47.826 0.00 0.00 44.61 2.52
146 147 3.487544 GCAGTAGCAAAATGGTCGAATCC 60.488 47.826 0.00 0.00 41.58 3.01
147 148 3.941483 CAGTAGCAAAATGGTCGAATCCT 59.059 43.478 0.00 0.00 0.00 3.24
148 149 3.941483 AGTAGCAAAATGGTCGAATCCTG 59.059 43.478 0.00 0.00 0.00 3.86
149 150 3.071874 AGCAAAATGGTCGAATCCTGA 57.928 42.857 0.00 0.00 0.00 3.86
150 151 3.624777 AGCAAAATGGTCGAATCCTGAT 58.375 40.909 0.00 0.00 0.00 2.90
151 152 4.019174 AGCAAAATGGTCGAATCCTGATT 58.981 39.130 0.00 0.00 0.00 2.57
152 153 4.463891 AGCAAAATGGTCGAATCCTGATTT 59.536 37.500 0.00 0.00 0.00 2.17
153 154 5.047092 AGCAAAATGGTCGAATCCTGATTTT 60.047 36.000 0.00 0.00 0.00 1.82
154 155 5.639082 GCAAAATGGTCGAATCCTGATTTTT 59.361 36.000 0.00 0.00 0.00 1.94
176 177 2.590092 CCAACCGGGGTCAGATCC 59.410 66.667 6.32 0.00 0.00 3.36
177 178 1.995626 CCAACCGGGGTCAGATCCT 60.996 63.158 6.32 0.00 0.00 3.24
178 179 1.221840 CAACCGGGGTCAGATCCTG 59.778 63.158 6.32 0.68 0.00 3.86
179 180 1.080354 AACCGGGGTCAGATCCTGA 59.920 57.895 10.57 0.00 38.25 3.86
180 181 0.546747 AACCGGGGTCAGATCCTGAA 60.547 55.000 10.57 0.00 42.46 3.02
181 182 0.326618 ACCGGGGTCAGATCCTGAAT 60.327 55.000 10.57 0.00 42.46 2.57
182 183 0.839946 CCGGGGTCAGATCCTGAATT 59.160 55.000 10.57 0.00 42.46 2.17
183 184 1.212935 CCGGGGTCAGATCCTGAATTT 59.787 52.381 10.57 0.00 42.46 1.82
184 185 2.292267 CGGGGTCAGATCCTGAATTTG 58.708 52.381 1.58 0.00 42.46 2.32
185 186 2.356125 CGGGGTCAGATCCTGAATTTGT 60.356 50.000 1.58 0.00 42.46 2.83
186 187 3.118408 CGGGGTCAGATCCTGAATTTGTA 60.118 47.826 1.58 0.00 42.46 2.41
187 188 4.444876 CGGGGTCAGATCCTGAATTTGTAT 60.445 45.833 1.58 0.00 42.46 2.29
188 189 4.823989 GGGGTCAGATCCTGAATTTGTATG 59.176 45.833 0.00 0.00 42.46 2.39
189 190 5.440610 GGGTCAGATCCTGAATTTGTATGT 58.559 41.667 0.00 0.00 42.46 2.29
190 191 6.409234 GGGGTCAGATCCTGAATTTGTATGTA 60.409 42.308 0.00 0.00 42.46 2.29
191 192 7.054124 GGGTCAGATCCTGAATTTGTATGTAA 58.946 38.462 0.00 0.00 42.46 2.41
192 193 7.556275 GGGTCAGATCCTGAATTTGTATGTAAA 59.444 37.037 0.00 0.00 42.46 2.01
193 194 8.956426 GGTCAGATCCTGAATTTGTATGTAAAA 58.044 33.333 0.00 0.00 42.46 1.52
196 197 9.793252 CAGATCCTGAATTTGTATGTAAAAAGG 57.207 33.333 0.00 0.00 32.44 3.11
197 198 8.971073 AGATCCTGAATTTGTATGTAAAAAGGG 58.029 33.333 0.00 0.00 0.00 3.95
198 199 8.664669 ATCCTGAATTTGTATGTAAAAAGGGT 57.335 30.769 0.00 0.00 0.00 4.34
199 200 8.117813 TCCTGAATTTGTATGTAAAAAGGGTC 57.882 34.615 0.00 0.00 0.00 4.46
200 201 7.726291 TCCTGAATTTGTATGTAAAAAGGGTCA 59.274 33.333 0.00 0.00 0.00 4.02
201 202 8.364142 CCTGAATTTGTATGTAAAAAGGGTCAA 58.636 33.333 0.00 0.00 0.00 3.18
202 203 9.757227 CTGAATTTGTATGTAAAAAGGGTCAAA 57.243 29.630 0.00 0.00 0.00 2.69
235 236 4.436998 CCCCGACTCGCAGGTCAC 62.437 72.222 6.82 0.00 36.12 3.67
252 253 2.419198 CCGGGGAGAAGATGCTCG 59.581 66.667 0.00 0.00 44.02 5.03
254 255 1.066587 CGGGGAGAAGATGCTCGTC 59.933 63.158 0.00 0.00 38.64 4.20
260 261 0.097325 AGAAGATGCTCGTCGACGAC 59.903 55.000 34.97 28.57 44.22 4.34
290 291 2.357517 CACCTCGACGCCAAGCTT 60.358 61.111 0.00 0.00 0.00 3.74
301 302 2.043625 CCAAGCTTGTGCACATGGT 58.956 52.632 26.33 26.33 42.74 3.55
306 307 1.499056 CTTGTGCACATGGTCGAGC 59.501 57.895 22.39 7.89 0.00 5.03
326 327 3.121030 GGCGAGCACTGCATCGTT 61.121 61.111 18.08 0.00 40.97 3.85
331 332 2.097160 GCACTGCATCGTTGAGCG 59.903 61.111 0.00 0.00 43.01 5.03
361 362 1.889530 GAGGGAACTGACCAGACGGG 61.890 65.000 3.76 0.00 44.43 5.28
511 837 2.087009 CGGTTCGAGCGTTCTGGAC 61.087 63.158 0.00 0.00 33.95 4.02
535 863 0.521735 GCCATGGTTGGTTCGTTCTC 59.478 55.000 14.67 0.00 45.57 2.87
536 864 1.882352 GCCATGGTTGGTTCGTTCTCT 60.882 52.381 14.67 0.00 45.57 3.10
537 865 2.504367 CCATGGTTGGTTCGTTCTCTT 58.496 47.619 2.57 0.00 38.30 2.85
538 866 2.226437 CCATGGTTGGTTCGTTCTCTTG 59.774 50.000 2.57 0.00 38.30 3.02
695 1033 3.799420 GTCCGATGAAGCAGTGAATCTAC 59.201 47.826 0.00 0.00 0.00 2.59
719 1057 0.893727 GTTTGCAGTGATCCCCGGTT 60.894 55.000 0.00 0.00 0.00 4.44
942 1326 2.598394 GCAAACCAGGCCTGCTGA 60.598 61.111 28.39 0.00 33.20 4.26
1131 1529 1.079819 CTACCTGCACGACACCCTG 60.080 63.158 0.00 0.00 0.00 4.45
1548 1946 0.467384 CCCTCCTGCACTACTGATGG 59.533 60.000 0.00 0.00 0.00 3.51
1629 2027 3.252215 TGAGGTTTTTATTGCTCCGTGTG 59.748 43.478 0.00 0.00 0.00 3.82
1662 2061 6.894339 AAAATCAACCGGATAAAACTGTCT 57.106 33.333 9.46 0.00 34.28 3.41
1690 2089 4.841617 TCCCTCTCCGCGCTCCAT 62.842 66.667 5.56 0.00 0.00 3.41
1706 2105 4.722700 ATGTGTCGCTGTGGGGCC 62.723 66.667 0.00 0.00 0.00 5.80
1731 2130 3.866582 CGCTCCCATCCCCTCCAC 61.867 72.222 0.00 0.00 0.00 4.02
1773 2172 1.215924 TCCTCCACCCGTTTCCTTTTT 59.784 47.619 0.00 0.00 0.00 1.94
1785 2184 5.069383 CCGTTTCCTTTTTCCCCTTTTCTAA 59.931 40.000 0.00 0.00 0.00 2.10
1814 2213 2.046892 GCAAAGGAGAGGCAGCGA 60.047 61.111 0.00 0.00 0.00 4.93
1818 2217 0.908198 AAAGGAGAGGCAGCGAAGAT 59.092 50.000 0.00 0.00 0.00 2.40
1877 2276 3.428862 CCAAGCGAGGTTGTTTGAAGTTT 60.429 43.478 13.05 0.00 32.49 2.66
1878 2277 3.692791 AGCGAGGTTGTTTGAAGTTTC 57.307 42.857 0.00 0.00 0.00 2.78
1906 2305 2.179018 CAATTGAAGCGCCACCGG 59.821 61.111 2.29 0.00 34.32 5.28
1919 2318 1.815421 CACCGGAGCTACATGGCAC 60.815 63.158 9.46 0.00 34.17 5.01
1920 2319 1.990060 ACCGGAGCTACATGGCACT 60.990 57.895 9.46 0.00 34.17 4.40
1992 2465 1.153823 GTCGTCGGCTGTGCTGTAT 60.154 57.895 0.00 0.00 36.18 2.29
2025 2499 1.980772 GGCTGCAAGGGAGCACAAT 60.981 57.895 11.76 0.00 40.11 2.71
2037 2511 0.544833 AGCACAATTGGGGCCATTGA 60.545 50.000 20.06 0.00 0.00 2.57
2207 2733 2.510906 CCGGGGCTGTAATGGAGG 59.489 66.667 0.00 0.00 0.00 4.30
2259 2785 4.338539 GTCGTCGTGCGGTGTCCT 62.339 66.667 0.00 0.00 41.72 3.85
2281 2808 1.405391 GCTTTTTGTGCTTGGTGTGGT 60.405 47.619 0.00 0.00 0.00 4.16
2286 2813 0.182299 TGTGCTTGGTGTGGTCATGA 59.818 50.000 0.00 0.00 0.00 3.07
2393 2920 0.179111 CGGCGGCTCTTGAAGATGTA 60.179 55.000 7.61 0.00 0.00 2.29
2455 2982 2.903855 GGATGTGCCATGGGAGCG 60.904 66.667 15.13 0.00 36.34 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.153429 GGCTGACGTGGATGGGTAC 60.153 63.158 0.00 0.00 0.00 3.34
18 19 1.305802 AGGCTGACGTGGATGGGTA 60.306 57.895 0.00 0.00 0.00 3.69
19 20 2.607750 AGGCTGACGTGGATGGGT 60.608 61.111 0.00 0.00 0.00 4.51
20 21 2.124983 CAGGCTGACGTGGATGGG 60.125 66.667 9.42 0.00 0.00 4.00
26 27 2.594303 TTTGCCCAGGCTGACGTG 60.594 61.111 17.94 2.45 42.51 4.49
27 28 2.594592 GTTTGCCCAGGCTGACGT 60.595 61.111 17.94 0.00 42.51 4.34
28 29 3.726517 CGTTTGCCCAGGCTGACG 61.727 66.667 17.94 13.68 42.51 4.35
29 30 3.365265 CCGTTTGCCCAGGCTGAC 61.365 66.667 17.94 8.37 42.51 3.51
70 71 4.489771 CAAGGGGCCTGGCGGTAG 62.490 72.222 13.40 0.00 0.00 3.18
81 82 4.489771 CAGCCTACCGCCAAGGGG 62.490 72.222 0.00 0.00 46.96 4.79
82 83 1.696097 ATACAGCCTACCGCCAAGGG 61.696 60.000 0.00 0.00 46.96 3.95
84 85 2.480845 GTTATACAGCCTACCGCCAAG 58.519 52.381 0.00 0.00 38.78 3.61
85 86 1.139455 GGTTATACAGCCTACCGCCAA 59.861 52.381 0.00 0.00 38.78 4.52
86 87 0.754472 GGTTATACAGCCTACCGCCA 59.246 55.000 0.00 0.00 38.78 5.69
87 88 0.034476 GGGTTATACAGCCTACCGCC 59.966 60.000 0.00 0.00 40.32 6.13
88 89 3.601277 GGGTTATACAGCCTACCGC 57.399 57.895 0.00 0.00 40.32 5.68
94 95 3.601277 GCGGTAGGGTTATACAGCC 57.399 57.895 0.00 0.00 44.40 4.85
95 96 0.754472 TGGCGGTAGGGTTATACAGC 59.246 55.000 1.14 1.14 43.45 4.40
96 97 2.296471 CTCTGGCGGTAGGGTTATACAG 59.704 54.545 0.00 0.00 0.00 2.74
97 98 2.313317 CTCTGGCGGTAGGGTTATACA 58.687 52.381 0.00 0.00 0.00 2.29
98 99 1.000618 GCTCTGGCGGTAGGGTTATAC 59.999 57.143 0.00 0.00 0.00 1.47
99 100 1.335145 GCTCTGGCGGTAGGGTTATA 58.665 55.000 0.00 0.00 0.00 0.98
100 101 0.689745 TGCTCTGGCGGTAGGGTTAT 60.690 55.000 0.00 0.00 42.25 1.89
101 102 1.305465 TGCTCTGGCGGTAGGGTTA 60.305 57.895 0.00 0.00 42.25 2.85
102 103 2.606519 TGCTCTGGCGGTAGGGTT 60.607 61.111 0.00 0.00 42.25 4.11
103 104 3.391382 GTGCTCTGGCGGTAGGGT 61.391 66.667 0.00 0.00 42.25 4.34
104 105 4.514577 CGTGCTCTGGCGGTAGGG 62.515 72.222 0.00 0.00 42.25 3.53
105 106 3.760035 ACGTGCTCTGGCGGTAGG 61.760 66.667 0.00 0.00 42.25 3.18
106 107 2.507102 CACGTGCTCTGGCGGTAG 60.507 66.667 0.82 0.00 42.25 3.18
107 108 4.063967 CCACGTGCTCTGGCGGTA 62.064 66.667 10.91 0.00 42.25 4.02
112 113 1.446792 CTACTGCCACGTGCTCTGG 60.447 63.158 10.91 0.00 42.00 3.86
113 114 2.097038 GCTACTGCCACGTGCTCTG 61.097 63.158 10.91 10.32 42.00 3.35
114 115 2.099652 TTGCTACTGCCACGTGCTCT 62.100 55.000 10.91 0.00 42.00 4.09
115 116 1.227999 TTTGCTACTGCCACGTGCTC 61.228 55.000 10.91 4.46 42.00 4.26
116 117 0.817634 TTTTGCTACTGCCACGTGCT 60.818 50.000 10.91 0.00 42.00 4.40
117 118 0.240945 ATTTTGCTACTGCCACGTGC 59.759 50.000 10.91 6.53 38.71 5.34
118 119 1.401409 CCATTTTGCTACTGCCACGTG 60.401 52.381 9.08 9.08 38.71 4.49
119 120 0.881118 CCATTTTGCTACTGCCACGT 59.119 50.000 0.00 0.00 38.71 4.49
120 121 0.881118 ACCATTTTGCTACTGCCACG 59.119 50.000 0.00 0.00 38.71 4.94
121 122 1.135689 CGACCATTTTGCTACTGCCAC 60.136 52.381 0.00 0.00 38.71 5.01
122 123 1.164411 CGACCATTTTGCTACTGCCA 58.836 50.000 0.00 0.00 38.71 4.92
123 124 1.448985 TCGACCATTTTGCTACTGCC 58.551 50.000 0.00 0.00 38.71 4.85
124 125 3.487544 GGATTCGACCATTTTGCTACTGC 60.488 47.826 0.00 0.00 40.20 4.40
125 126 3.941483 AGGATTCGACCATTTTGCTACTG 59.059 43.478 0.00 0.00 0.00 2.74
126 127 3.941483 CAGGATTCGACCATTTTGCTACT 59.059 43.478 0.00 0.00 0.00 2.57
127 128 3.938963 TCAGGATTCGACCATTTTGCTAC 59.061 43.478 0.00 0.00 0.00 3.58
128 129 4.214986 TCAGGATTCGACCATTTTGCTA 57.785 40.909 0.00 0.00 0.00 3.49
129 130 3.071874 TCAGGATTCGACCATTTTGCT 57.928 42.857 0.00 0.00 0.00 3.91
130 131 4.376340 AATCAGGATTCGACCATTTTGC 57.624 40.909 0.00 0.00 0.00 3.68
159 160 1.995626 AGGATCTGACCCCGGTTGG 60.996 63.158 0.00 0.00 0.00 3.77
160 161 1.221840 CAGGATCTGACCCCGGTTG 59.778 63.158 0.00 0.00 32.44 3.77
161 162 0.546747 TTCAGGATCTGACCCCGGTT 60.547 55.000 0.00 0.00 40.46 4.44
162 163 0.326618 ATTCAGGATCTGACCCCGGT 60.327 55.000 0.00 0.00 40.46 5.28
163 164 0.839946 AATTCAGGATCTGACCCCGG 59.160 55.000 0.00 0.00 40.46 5.73
164 165 2.292267 CAAATTCAGGATCTGACCCCG 58.708 52.381 0.00 0.00 40.46 5.73
165 166 3.372440 ACAAATTCAGGATCTGACCCC 57.628 47.619 0.00 0.00 40.46 4.95
166 167 5.440610 ACATACAAATTCAGGATCTGACCC 58.559 41.667 0.00 0.00 40.46 4.46
167 168 8.506168 TTTACATACAAATTCAGGATCTGACC 57.494 34.615 0.00 0.00 40.46 4.02
170 171 9.793252 CCTTTTTACATACAAATTCAGGATCTG 57.207 33.333 0.00 0.00 0.00 2.90
171 172 8.971073 CCCTTTTTACATACAAATTCAGGATCT 58.029 33.333 0.00 0.00 0.00 2.75
172 173 8.749354 ACCCTTTTTACATACAAATTCAGGATC 58.251 33.333 0.00 0.00 0.00 3.36
173 174 8.664669 ACCCTTTTTACATACAAATTCAGGAT 57.335 30.769 0.00 0.00 0.00 3.24
174 175 7.726291 TGACCCTTTTTACATACAAATTCAGGA 59.274 33.333 0.00 0.00 0.00 3.86
175 176 7.891561 TGACCCTTTTTACATACAAATTCAGG 58.108 34.615 0.00 0.00 0.00 3.86
176 177 9.757227 TTTGACCCTTTTTACATACAAATTCAG 57.243 29.630 0.00 0.00 0.00 3.02
203 204 4.713553 AGTCGGGGCAAAATTTCATTTTT 58.286 34.783 0.00 0.00 40.27 1.94
204 205 4.314961 GAGTCGGGGCAAAATTTCATTTT 58.685 39.130 0.00 0.00 42.81 1.82
205 206 3.613910 CGAGTCGGGGCAAAATTTCATTT 60.614 43.478 4.10 0.00 0.00 2.32
206 207 2.094752 CGAGTCGGGGCAAAATTTCATT 60.095 45.455 4.10 0.00 0.00 2.57
207 208 1.472480 CGAGTCGGGGCAAAATTTCAT 59.528 47.619 4.10 0.00 0.00 2.57
208 209 0.878416 CGAGTCGGGGCAAAATTTCA 59.122 50.000 4.10 0.00 0.00 2.69
209 210 0.456142 GCGAGTCGGGGCAAAATTTC 60.456 55.000 15.52 0.00 0.00 2.17
210 211 1.175983 TGCGAGTCGGGGCAAAATTT 61.176 50.000 15.52 0.00 35.98 1.82
211 212 1.586154 CTGCGAGTCGGGGCAAAATT 61.586 55.000 15.52 0.00 38.94 1.82
212 213 2.033448 TGCGAGTCGGGGCAAAAT 59.967 55.556 15.52 0.00 35.98 1.82
213 214 2.668212 CTGCGAGTCGGGGCAAAA 60.668 61.111 15.52 0.00 38.94 2.44
214 215 4.697756 CCTGCGAGTCGGGGCAAA 62.698 66.667 15.52 0.00 38.94 3.68
218 219 4.436998 GTGACCTGCGAGTCGGGG 62.437 72.222 15.52 0.00 45.92 5.73
235 236 2.356818 GACGAGCATCTTCTCCCCGG 62.357 65.000 0.00 0.00 29.60 5.73
266 267 4.803426 GCGTCGAGGTGCCTCCAG 62.803 72.222 12.20 5.50 39.77 3.86
278 279 3.648982 TGCACAAGCTTGGCGTCG 61.649 61.111 29.18 13.29 42.74 5.12
286 287 0.952497 CTCGACCATGTGCACAAGCT 60.952 55.000 25.72 6.61 42.74 3.74
287 288 1.499056 CTCGACCATGTGCACAAGC 59.501 57.895 25.72 12.12 42.57 4.01
290 291 2.738139 CGCTCGACCATGTGCACA 60.738 61.111 24.08 24.08 0.00 4.57
535 863 9.143631 GTAATTTTCAGATTCCACATTTCCAAG 57.856 33.333 0.00 0.00 0.00 3.61
536 864 8.646004 TGTAATTTTCAGATTCCACATTTCCAA 58.354 29.630 0.00 0.00 0.00 3.53
537 865 8.087750 GTGTAATTTTCAGATTCCACATTTCCA 58.912 33.333 0.00 0.00 29.39 3.53
538 866 8.306761 AGTGTAATTTTCAGATTCCACATTTCC 58.693 33.333 0.00 0.00 30.79 3.13
695 1033 0.883833 GGGATCACTGCAAACCTGTG 59.116 55.000 0.00 0.00 42.72 3.66
757 1095 1.402787 ATCAAGGCGCCTAAAATGGG 58.597 50.000 33.07 13.23 0.00 4.00
1548 1946 4.503910 AGGAAACAAGCAAACAAAACTCC 58.496 39.130 0.00 0.00 0.00 3.85
1629 2027 3.004944 TCCGGTTGATTTTAAACCAGCAC 59.995 43.478 0.00 0.00 46.24 4.40
1662 2061 1.867363 GGAGAGGGAGGCTTACAAGA 58.133 55.000 0.00 0.00 0.00 3.02
1706 2105 4.530857 GATGGGAGCGGTGGACGG 62.531 72.222 0.00 0.00 44.51 4.79
1722 2121 2.360423 GGAGAAGATAAGGTGGAGGGGA 60.360 54.545 0.00 0.00 0.00 4.81
1731 2130 0.315568 CGCTCGGGGAGAAGATAAGG 59.684 60.000 0.00 0.00 0.00 2.69
1773 2172 4.007659 GCTTGACGAATTAGAAAAGGGGA 58.992 43.478 0.00 0.00 0.00 4.81
1814 2213 3.743584 CGTGAGGATGAATCAGGCATCTT 60.744 47.826 0.00 0.00 41.39 2.40
1818 2217 3.766644 CGTGAGGATGAATCAGGCA 57.233 52.632 0.00 0.00 0.00 4.75
1877 2276 0.250684 TTCAATTGCAGCCAGGACGA 60.251 50.000 0.00 0.00 0.00 4.20
1878 2277 0.169672 CTTCAATTGCAGCCAGGACG 59.830 55.000 0.00 0.00 0.00 4.79
1906 2305 2.772287 GGGAATAGTGCCATGTAGCTC 58.228 52.381 0.00 0.00 34.72 4.09
1919 2318 1.564622 CGATGCAACGCGGGAATAG 59.435 57.895 12.47 0.00 0.00 1.73
1920 2319 3.712655 CGATGCAACGCGGGAATA 58.287 55.556 12.47 0.00 0.00 1.75
2025 2499 1.305213 GGAGCTTCAATGGCCCCAA 60.305 57.895 0.00 0.00 0.00 4.12
2077 2551 2.279517 CCACGGCGGTGCTCTATC 60.280 66.667 18.31 0.00 43.00 2.08
2144 2670 1.675310 CTCCATTGCAACCGAGGCA 60.675 57.895 14.22 0.00 40.00 4.75
2258 2784 2.349275 CACACCAAGCACAAAAAGCAAG 59.651 45.455 0.00 0.00 0.00 4.01
2259 2785 2.344950 CACACCAAGCACAAAAAGCAA 58.655 42.857 0.00 0.00 0.00 3.91
2281 2808 1.107945 CATTGCAGCCATGGTCATGA 58.892 50.000 14.67 0.00 41.20 3.07
2286 2813 2.056223 GCTCCATTGCAGCCATGGT 61.056 57.895 22.00 0.00 36.83 3.55
2330 2857 2.901840 CCATTGCATCGTCGGGGG 60.902 66.667 0.00 0.00 0.00 5.40
2455 2982 1.007387 CTTCCACCAAAGCAACGCC 60.007 57.895 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.