Multiple sequence alignment - TraesCS3A01G460700

Loading Multiple Alignment...

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 TraesCS3A01G460700 chr3A 100.000 2453 0 0 1 2453 696643727 696646179 0.000000e+00 4530
1 TraesCS3A01G460700 chr3A 97.007 2138 29 7 347 2453 730380822 730378689 0.000000e+00 3561
2 TraesCS3A01G460700 chr3A 96.645 2116 37 7 370 2453 102793536 102795649 0.000000e+00 3483
3 TraesCS3A01G460700 chr3A 94.722 360 18 1 1 360 122929984 122930342 2.130000e-155 558
4 TraesCS3A01G460700 chr3A 78.979 333 47 17 324 639 748243362 748243688 3.200000e-49 206
5 TraesCS3A01G460700 chr6A 96.034 353 13 1 1 353 60222075 60221724 7.610000e-160 573
6 TraesCS3A01G460700 chr6A 95.028 362 15 2 1 360 456346125 456345765 1.270000e-157 566
7 TraesCS3A01G460700 chr1A 95.068 365 11 5 1 360 4887598 4887960 3.540000e-158 568
8 TraesCS3A01G460700 chr1A 95.198 354 15 2 1 353 407355056 407354704 2.130000e-155 558
9 TraesCS3A01G460700 chr1A 94.444 360 20 0 1 360 583480142 583480501 2.760000e-154 555
10 TraesCS3A01G460700 chr5A 94.737 361 16 3 1 360 32207609 32207967 2.130000e-155 558
11 TraesCS3A01G460700 chr5A 94.460 361 18 2 1 360 289462203 289461844 2.760000e-154 555
12 TraesCS3A01G460700 chr2A 94.722 360 15 3 1 360 775634357 775634712 7.660000e-155 556
13 TraesCS3A01G460700 chr2B 78.169 284 44 14 369 637 623335614 623335894 5.430000e-37 165


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 TraesCS3A01G460700 chr3A 696643727 696646179 2452 False 4530 4530 100.000 1 2453 1 chr3A.!!$F3 2452
1 TraesCS3A01G460700 chr3A 730378689 730380822 2133 True 3561 3561 97.007 347 2453 1 chr3A.!!$R1 2106
2 TraesCS3A01G460700 chr3A 102793536 102795649 2113 False 3483 3483 96.645 370 2453 1 chr3A.!!$F1 2083

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
80 81 0.035343 GTGTGGGGACTAAAGGCCTC 60.035 60.0 5.23 0.0 0.00 4.70 F
123 124 0.891904 GAACCGGTGCTAAAGGGCAA 60.892 55.0 8.52 0.0 44.18 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 1452 1.001815 CACAATTCGTTGTTCCGCCTT 60.002 47.619 0.00 0.0 31.86 4.35 R
1628 1651 3.136443 TCACCTTTGAACCAGTCAGACAT 59.864 43.478 2.66 0.0 37.61 3.06 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 2.819550 AACCGGGCTATAGCACCG 59.180 61.111 31.50 31.50 46.81 4.94
20 21 2.819550 CGGGCTATAGCACCGGTT 59.180 61.111 31.12 0.00 44.99 4.44
21 22 1.145377 CGGGCTATAGCACCGGTTT 59.855 57.895 31.12 0.00 44.99 3.27
22 23 1.157870 CGGGCTATAGCACCGGTTTG 61.158 60.000 31.12 12.97 44.99 2.93
23 24 0.107361 GGGCTATAGCACCGGTTTGT 60.107 55.000 25.53 0.00 44.36 2.83
24 25 1.139455 GGGCTATAGCACCGGTTTGTA 59.861 52.381 25.53 0.00 44.36 2.41
25 26 2.420408 GGGCTATAGCACCGGTTTGTAA 60.420 50.000 25.53 0.00 44.36 2.41
26 27 2.870411 GGCTATAGCACCGGTTTGTAAG 59.130 50.000 25.53 0.90 44.36 2.34
27 28 2.870411 GCTATAGCACCGGTTTGTAAGG 59.130 50.000 20.01 0.00 41.59 2.69
28 29 1.746470 ATAGCACCGGTTTGTAAGGC 58.254 50.000 2.97 2.83 0.00 4.35
29 30 0.321830 TAGCACCGGTTTGTAAGGCC 60.322 55.000 2.97 0.00 0.00 5.19
30 31 2.632544 GCACCGGTTTGTAAGGCCC 61.633 63.158 2.97 0.00 0.00 5.80
31 32 1.074248 CACCGGTTTGTAAGGCCCT 59.926 57.895 2.97 0.00 0.00 5.19
32 33 0.538746 CACCGGTTTGTAAGGCCCTT 60.539 55.000 2.97 0.00 0.00 3.95
33 34 0.186630 ACCGGTTTGTAAGGCCCTTT 59.813 50.000 0.00 0.00 0.00 3.11
34 35 1.424684 ACCGGTTTGTAAGGCCCTTTA 59.575 47.619 0.00 0.00 0.00 1.85
35 36 2.089201 CCGGTTTGTAAGGCCCTTTAG 58.911 52.381 0.00 0.00 0.00 1.85
36 37 2.553685 CCGGTTTGTAAGGCCCTTTAGT 60.554 50.000 0.00 0.00 0.00 2.24
37 38 2.486592 CGGTTTGTAAGGCCCTTTAGTG 59.513 50.000 0.00 0.00 0.00 2.74
38 39 2.230508 GGTTTGTAAGGCCCTTTAGTGC 59.769 50.000 0.00 0.00 0.00 4.40
43 44 2.035155 GGCCCTTTAGTGCCGGTT 59.965 61.111 1.90 0.00 38.00 4.44
44 45 2.044555 GGCCCTTTAGTGCCGGTTC 61.045 63.158 1.90 0.00 38.00 3.62
45 46 2.396157 GCCCTTTAGTGCCGGTTCG 61.396 63.158 1.90 0.00 0.00 3.95
62 63 3.520187 CGGTAACCGGCACTAAAGT 57.480 52.632 0.00 0.00 44.15 2.66
63 64 1.073177 CGGTAACCGGCACTAAAGTG 58.927 55.000 0.00 5.73 44.15 3.16
64 65 1.606224 CGGTAACCGGCACTAAAGTGT 60.606 52.381 0.00 0.00 44.15 3.55
65 66 3.745341 CGGTAACCGGCACTAAAGTGTG 61.745 54.545 0.00 5.04 44.15 3.82
76 77 4.324267 CACTAAAGTGTGGGGACTAAAGG 58.676 47.826 1.81 0.00 40.96 3.11
77 78 2.287977 AAAGTGTGGGGACTAAAGGC 57.712 50.000 0.00 0.00 0.00 4.35
78 79 0.404426 AAGTGTGGGGACTAAAGGCC 59.596 55.000 0.00 0.00 0.00 5.19
79 80 0.475828 AGTGTGGGGACTAAAGGCCT 60.476 55.000 0.00 0.00 0.00 5.19
80 81 0.035343 GTGTGGGGACTAAAGGCCTC 60.035 60.000 5.23 0.00 0.00 4.70
81 82 1.205460 TGTGGGGACTAAAGGCCTCC 61.205 60.000 5.23 1.56 0.00 4.30
82 83 1.618447 TGGGGACTAAAGGCCTCCC 60.618 63.158 17.10 17.10 42.88 4.30
83 84 3.332395 GGGACTAAAGGCCTCCCC 58.668 66.667 14.91 12.34 38.20 4.81
94 95 2.047830 AGGCCTCCCCTTTTAGTATCG 58.952 52.381 0.00 0.00 43.06 2.92
95 96 1.071857 GGCCTCCCCTTTTAGTATCGG 59.928 57.143 0.00 0.00 0.00 4.18
96 97 1.767088 GCCTCCCCTTTTAGTATCGGT 59.233 52.381 0.00 0.00 0.00 4.69
97 98 2.172082 GCCTCCCCTTTTAGTATCGGTT 59.828 50.000 0.00 0.00 0.00 4.44
98 99 3.743584 GCCTCCCCTTTTAGTATCGGTTC 60.744 52.174 0.00 0.00 0.00 3.62
99 100 3.181457 CCTCCCCTTTTAGTATCGGTTCC 60.181 52.174 0.00 0.00 0.00 3.62
100 101 2.431782 TCCCCTTTTAGTATCGGTTCCG 59.568 50.000 4.74 4.74 0.00 4.30
101 102 2.207590 CCCTTTTAGTATCGGTTCCGC 58.792 52.381 6.35 0.00 0.00 5.54
102 103 2.419021 CCCTTTTAGTATCGGTTCCGCA 60.419 50.000 6.35 0.00 0.00 5.69
103 104 2.606272 CCTTTTAGTATCGGTTCCGCAC 59.394 50.000 6.35 6.98 0.00 5.34
104 105 1.912001 TTTAGTATCGGTTCCGCACG 58.088 50.000 6.35 0.00 0.00 5.34
105 106 1.093972 TTAGTATCGGTTCCGCACGA 58.906 50.000 6.35 0.00 43.85 4.35
106 107 1.093972 TAGTATCGGTTCCGCACGAA 58.906 50.000 6.35 0.00 42.88 3.85
112 113 3.708734 GTTCCGCACGAACCGGTG 61.709 66.667 8.52 0.00 44.46 4.94
119 120 2.159181 CACGAACCGGTGCTAAAGG 58.841 57.895 8.52 0.00 0.00 3.11
120 121 1.004200 ACGAACCGGTGCTAAAGGG 60.004 57.895 8.52 0.00 0.00 3.95
121 122 2.396157 CGAACCGGTGCTAAAGGGC 61.396 63.158 8.52 0.00 0.00 5.19
122 123 1.302993 GAACCGGTGCTAAAGGGCA 60.303 57.895 8.52 0.00 40.15 5.36
123 124 0.891904 GAACCGGTGCTAAAGGGCAA 60.892 55.000 8.52 0.00 44.18 4.52
124 125 1.176619 AACCGGTGCTAAAGGGCAAC 61.177 55.000 8.52 0.00 45.46 4.17
137 138 4.012895 GCAACCACGTGGCACGAG 62.013 66.667 42.65 34.61 46.05 4.18
138 139 4.012895 CAACCACGTGGCACGAGC 62.013 66.667 42.65 4.67 46.05 5.03
149 150 4.760047 CACGAGCCAGTTCCGGGG 62.760 72.222 0.00 0.00 0.00 5.73
163 164 3.342477 GGGGGCAGGGAGCTCTTT 61.342 66.667 14.64 0.00 45.61 2.52
164 165 2.001269 GGGGGCAGGGAGCTCTTTA 61.001 63.158 14.64 0.00 45.61 1.85
165 166 1.529309 GGGGCAGGGAGCTCTTTAG 59.471 63.158 14.64 2.75 45.61 1.85
166 167 1.275421 GGGGCAGGGAGCTCTTTAGT 61.275 60.000 14.64 0.00 45.61 2.24
167 168 1.497161 GGGCAGGGAGCTCTTTAGTA 58.503 55.000 14.64 0.00 41.91 1.82
168 169 1.139256 GGGCAGGGAGCTCTTTAGTAC 59.861 57.143 14.64 0.00 41.91 2.73
169 170 1.139256 GGCAGGGAGCTCTTTAGTACC 59.861 57.143 14.64 4.13 44.79 3.34
170 171 1.202428 GCAGGGAGCTCTTTAGTACCG 60.202 57.143 14.64 2.61 41.15 4.02
171 172 1.409427 CAGGGAGCTCTTTAGTACCGG 59.591 57.143 14.64 0.00 0.00 5.28
172 173 1.006878 AGGGAGCTCTTTAGTACCGGT 59.993 52.381 13.98 13.98 0.00 5.28
173 174 1.829849 GGGAGCTCTTTAGTACCGGTT 59.170 52.381 15.04 0.00 0.00 4.44
174 175 2.418334 GGGAGCTCTTTAGTACCGGTTG 60.418 54.545 15.04 0.00 0.00 3.77
175 176 2.418334 GGAGCTCTTTAGTACCGGTTGG 60.418 54.545 15.04 0.00 42.84 3.77
192 193 3.637184 GGTGACACCAACCGGTATT 57.363 52.632 20.14 0.00 46.94 1.89
193 194 2.766345 GGTGACACCAACCGGTATTA 57.234 50.000 20.14 0.00 46.94 0.98
194 195 3.056588 GGTGACACCAACCGGTATTAA 57.943 47.619 20.14 0.00 46.94 1.40
195 196 3.410508 GGTGACACCAACCGGTATTAAA 58.589 45.455 20.14 0.00 46.94 1.52
196 197 3.819902 GGTGACACCAACCGGTATTAAAA 59.180 43.478 20.14 0.00 46.94 1.52
197 198 4.083164 GGTGACACCAACCGGTATTAAAAG 60.083 45.833 20.14 0.00 46.94 2.27
198 199 4.073549 TGACACCAACCGGTATTAAAAGG 58.926 43.478 8.00 4.11 46.94 3.11
199 200 4.074259 GACACCAACCGGTATTAAAAGGT 58.926 43.478 8.00 4.79 46.94 3.50
200 201 4.472496 ACACCAACCGGTATTAAAAGGTT 58.528 39.130 8.00 0.00 46.94 3.50
204 205 3.090210 ACCGGTATTAAAAGGTTGGGG 57.910 47.619 4.49 0.00 32.17 4.96
205 206 2.291735 ACCGGTATTAAAAGGTTGGGGG 60.292 50.000 4.49 0.00 32.17 5.40
223 224 3.603158 GGGGGTTTTGCGTTTATGATT 57.397 42.857 0.00 0.00 0.00 2.57
224 225 3.932822 GGGGGTTTTGCGTTTATGATTT 58.067 40.909 0.00 0.00 0.00 2.17
225 226 3.930229 GGGGGTTTTGCGTTTATGATTTC 59.070 43.478 0.00 0.00 0.00 2.17
226 227 4.322424 GGGGGTTTTGCGTTTATGATTTCT 60.322 41.667 0.00 0.00 0.00 2.52
227 228 5.234752 GGGGTTTTGCGTTTATGATTTCTT 58.765 37.500 0.00 0.00 0.00 2.52
228 229 5.699001 GGGGTTTTGCGTTTATGATTTCTTT 59.301 36.000 0.00 0.00 0.00 2.52
229 230 6.203915 GGGGTTTTGCGTTTATGATTTCTTTT 59.796 34.615 0.00 0.00 0.00 2.27
230 231 7.254966 GGGGTTTTGCGTTTATGATTTCTTTTT 60.255 33.333 0.00 0.00 0.00 1.94
231 232 7.796660 GGGTTTTGCGTTTATGATTTCTTTTTC 59.203 33.333 0.00 0.00 0.00 2.29
232 233 8.331742 GGTTTTGCGTTTATGATTTCTTTTTCA 58.668 29.630 0.00 0.00 0.00 2.69
233 234 9.862585 GTTTTGCGTTTATGATTTCTTTTTCAT 57.137 25.926 0.00 0.00 36.57 2.57
266 267 9.631639 GTGTGTTTTCCATTTAATTCTTTTTCG 57.368 29.630 0.00 0.00 0.00 3.46
267 268 9.372369 TGTGTTTTCCATTTAATTCTTTTTCGT 57.628 25.926 0.00 0.00 0.00 3.85
271 272 9.709600 TTTTCCATTTAATTCTTTTTCGTTTGC 57.290 25.926 0.00 0.00 0.00 3.68
272 273 8.655651 TTCCATTTAATTCTTTTTCGTTTGCT 57.344 26.923 0.00 0.00 0.00 3.91
273 274 8.071122 TCCATTTAATTCTTTTTCGTTTGCTG 57.929 30.769 0.00 0.00 0.00 4.41
274 275 7.170658 TCCATTTAATTCTTTTTCGTTTGCTGG 59.829 33.333 0.00 0.00 0.00 4.85
275 276 7.042119 CCATTTAATTCTTTTTCGTTTGCTGGT 60.042 33.333 0.00 0.00 0.00 4.00
276 277 8.973378 CATTTAATTCTTTTTCGTTTGCTGGTA 58.027 29.630 0.00 0.00 0.00 3.25
277 278 9.705290 ATTTAATTCTTTTTCGTTTGCTGGTAT 57.295 25.926 0.00 0.00 0.00 2.73
278 279 9.535878 TTTAATTCTTTTTCGTTTGCTGGTATT 57.464 25.926 0.00 0.00 0.00 1.89
279 280 9.535878 TTAATTCTTTTTCGTTTGCTGGTATTT 57.464 25.926 0.00 0.00 0.00 1.40
280 281 8.432110 AATTCTTTTTCGTTTGCTGGTATTTT 57.568 26.923 0.00 0.00 0.00 1.82
281 282 9.535878 AATTCTTTTTCGTTTGCTGGTATTTTA 57.464 25.926 0.00 0.00 0.00 1.52
282 283 7.917720 TCTTTTTCGTTTGCTGGTATTTTAC 57.082 32.000 0.00 0.00 0.00 2.01
283 284 6.633634 TCTTTTTCGTTTGCTGGTATTTTACG 59.366 34.615 0.00 0.00 0.00 3.18
284 285 5.670149 TTTCGTTTGCTGGTATTTTACGA 57.330 34.783 0.00 0.00 35.11 3.43
285 286 5.866335 TTCGTTTGCTGGTATTTTACGAT 57.134 34.783 0.00 0.00 36.58 3.73
286 287 6.964741 TTCGTTTGCTGGTATTTTACGATA 57.035 33.333 0.00 0.00 36.58 2.92
287 288 6.335176 TCGTTTGCTGGTATTTTACGATAC 57.665 37.500 0.00 0.00 32.39 2.24
288 289 5.004630 TCGTTTGCTGGTATTTTACGATACG 59.995 40.000 0.00 0.00 34.11 3.06
289 290 5.495502 GTTTGCTGGTATTTTACGATACGG 58.504 41.667 0.00 0.00 34.11 4.02
290 291 3.125316 TGCTGGTATTTTACGATACGGC 58.875 45.455 0.00 0.00 34.11 5.68
291 292 3.125316 GCTGGTATTTTACGATACGGCA 58.875 45.455 0.00 0.00 34.78 5.69
292 293 3.744426 GCTGGTATTTTACGATACGGCAT 59.256 43.478 0.00 0.00 34.78 4.40
293 294 4.925054 GCTGGTATTTTACGATACGGCATA 59.075 41.667 0.00 0.00 34.78 3.14
294 295 5.579511 GCTGGTATTTTACGATACGGCATAT 59.420 40.000 0.00 0.00 34.78 1.78
295 296 6.091713 GCTGGTATTTTACGATACGGCATATT 59.908 38.462 0.00 0.00 34.78 1.28
296 297 7.354025 TGGTATTTTACGATACGGCATATTG 57.646 36.000 0.00 0.00 34.11 1.90
297 298 6.930164 TGGTATTTTACGATACGGCATATTGT 59.070 34.615 0.00 0.00 40.49 2.71
298 299 8.087136 TGGTATTTTACGATACGGCATATTGTA 58.913 33.333 0.00 0.00 38.61 2.41
299 300 8.375465 GGTATTTTACGATACGGCATATTGTAC 58.625 37.037 0.28 0.00 39.11 2.90
300 301 7.949903 ATTTTACGATACGGCATATTGTACA 57.050 32.000 0.28 0.00 39.11 2.90
301 302 6.752335 TTTACGATACGGCATATTGTACAC 57.248 37.500 0.28 0.00 39.11 2.90
302 303 3.302555 ACGATACGGCATATTGTACACG 58.697 45.455 0.00 0.00 36.29 4.49
303 304 3.243168 ACGATACGGCATATTGTACACGT 60.243 43.478 11.07 11.07 36.29 4.49
304 305 3.732219 CGATACGGCATATTGTACACGTT 59.268 43.478 11.48 1.87 35.97 3.99
305 306 4.911033 CGATACGGCATATTGTACACGTTA 59.089 41.667 11.48 0.00 35.97 3.18
306 307 5.570206 CGATACGGCATATTGTACACGTTAT 59.430 40.000 11.48 0.00 35.97 1.89
307 308 6.451960 CGATACGGCATATTGTACACGTTATG 60.452 42.308 11.48 11.92 35.97 1.90
308 309 3.246699 ACGGCATATTGTACACGTTATGC 59.753 43.478 23.74 23.74 43.85 3.14
309 310 3.246463 CGGCATATTGTACACGTTATGCA 59.754 43.478 28.30 6.62 45.50 3.96
310 311 4.084066 CGGCATATTGTACACGTTATGCAT 60.084 41.667 28.30 3.79 45.50 3.96
311 312 5.119434 CGGCATATTGTACACGTTATGCATA 59.881 40.000 28.30 1.16 45.50 3.14
312 313 6.183360 CGGCATATTGTACACGTTATGCATAT 60.183 38.462 28.30 13.38 45.50 1.78
313 314 7.009723 CGGCATATTGTACACGTTATGCATATA 59.990 37.037 28.30 11.01 45.50 0.86
314 315 8.826710 GGCATATTGTACACGTTATGCATATAT 58.173 33.333 28.30 12.34 45.50 0.86
343 344 9.667107 AAATAGAATTTCAAGTAGAACCGATCA 57.333 29.630 0.00 0.00 35.56 2.92
344 345 9.838339 AATAGAATTTCAAGTAGAACCGATCAT 57.162 29.630 0.00 0.00 35.56 2.45
379 380 3.438297 AGGGATTGTCTATTCGTCACG 57.562 47.619 0.00 0.00 0.00 4.35
386 387 1.402968 GTCTATTCGTCACGCAGGGTA 59.597 52.381 0.00 0.00 0.00 3.69
388 389 2.691526 TCTATTCGTCACGCAGGGTAAT 59.308 45.455 0.00 0.00 0.00 1.89
658 660 4.217550 CGAGGTAAAAGGGAGCAAAAATCA 59.782 41.667 0.00 0.00 0.00 2.57
893 916 5.571791 TCATTCATAATGGCTGATCCTCA 57.428 39.130 0.12 0.00 39.38 3.86
1377 1400 8.204160 CAGTTCTGTTATTGTAGGTATCCATCA 58.796 37.037 0.00 0.00 0.00 3.07
1554 1577 6.068461 TGAACATGGGGCTAGTTTGTAATA 57.932 37.500 0.00 0.00 0.00 0.98
2265 2298 1.546923 TGATCCGAGCGGTTTCAACTA 59.453 47.619 8.96 0.00 36.47 2.24
2309 2342 1.734477 CAGTCTCCACGGCGAACAG 60.734 63.158 16.62 5.59 0.00 3.16
2395 2429 3.556213 CGTTGTGAGTGTTTATCTCCCCA 60.556 47.826 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.819550 CGGTGCTATAGCCCGGTT 59.180 61.111 31.12 0.00 44.99 4.44
3 4 1.145377 AAACCGGTGCTATAGCCCG 59.855 57.895 31.50 31.50 46.81 6.13
4 5 0.107361 ACAAACCGGTGCTATAGCCC 60.107 55.000 21.84 19.43 41.18 5.19
5 6 2.607631 TACAAACCGGTGCTATAGCC 57.392 50.000 21.84 12.70 41.18 3.93
6 7 2.870411 CCTTACAAACCGGTGCTATAGC 59.130 50.000 18.18 18.18 42.50 2.97
7 8 2.870411 GCCTTACAAACCGGTGCTATAG 59.130 50.000 8.52 3.38 0.00 1.31
8 9 2.420408 GGCCTTACAAACCGGTGCTATA 60.420 50.000 8.52 0.00 0.00 1.31
9 10 1.680860 GGCCTTACAAACCGGTGCTAT 60.681 52.381 8.52 0.00 0.00 2.97
10 11 0.321830 GGCCTTACAAACCGGTGCTA 60.322 55.000 8.52 0.00 0.00 3.49
11 12 1.602605 GGCCTTACAAACCGGTGCT 60.603 57.895 8.52 0.00 0.00 4.40
12 13 2.632544 GGGCCTTACAAACCGGTGC 61.633 63.158 8.52 4.77 0.00 5.01
13 14 0.538746 AAGGGCCTTACAAACCGGTG 60.539 55.000 19.37 0.00 0.00 4.94
14 15 0.186630 AAAGGGCCTTACAAACCGGT 59.813 50.000 21.25 0.00 0.00 5.28
15 16 2.089201 CTAAAGGGCCTTACAAACCGG 58.911 52.381 21.25 0.00 0.00 5.28
16 17 2.486592 CACTAAAGGGCCTTACAAACCG 59.513 50.000 21.25 5.60 0.00 4.44
17 18 2.230508 GCACTAAAGGGCCTTACAAACC 59.769 50.000 21.25 3.14 0.00 3.27
18 19 2.230508 GGCACTAAAGGGCCTTACAAAC 59.769 50.000 21.25 9.49 46.74 2.93
19 20 2.521126 GGCACTAAAGGGCCTTACAAA 58.479 47.619 21.25 4.81 46.74 2.83
20 21 2.209690 GGCACTAAAGGGCCTTACAA 57.790 50.000 21.25 7.47 46.74 2.41
21 22 3.970205 GGCACTAAAGGGCCTTACA 57.030 52.632 21.25 9.80 46.74 2.41
26 27 2.035155 AACCGGCACTAAAGGGCC 59.965 61.111 13.51 13.51 46.80 5.80
27 28 2.396157 CGAACCGGCACTAAAGGGC 61.396 63.158 0.00 0.00 0.00 5.19
28 29 1.743995 CCGAACCGGCACTAAAGGG 60.744 63.158 0.00 0.00 41.17 3.95
29 30 3.884900 CCGAACCGGCACTAAAGG 58.115 61.111 0.00 0.00 41.17 3.11
41 42 4.945824 CACTTTAGTGCCGGTTACCGAAC 61.946 52.174 26.59 21.33 43.81 3.95
42 43 2.867251 CACTTTAGTGCCGGTTACCGAA 60.867 50.000 26.59 10.31 43.81 4.30
43 44 1.337074 CACTTTAGTGCCGGTTACCGA 60.337 52.381 26.59 2.64 43.81 4.69
44 45 1.073177 CACTTTAGTGCCGGTTACCG 58.927 55.000 17.88 17.88 40.97 4.02
55 56 3.244805 GCCTTTAGTCCCCACACTTTAGT 60.245 47.826 0.00 0.00 0.00 2.24
56 57 3.344515 GCCTTTAGTCCCCACACTTTAG 58.655 50.000 0.00 0.00 0.00 1.85
57 58 2.040679 GGCCTTTAGTCCCCACACTTTA 59.959 50.000 0.00 0.00 0.00 1.85
58 59 1.203013 GGCCTTTAGTCCCCACACTTT 60.203 52.381 0.00 0.00 0.00 2.66
59 60 0.404426 GGCCTTTAGTCCCCACACTT 59.596 55.000 0.00 0.00 0.00 3.16
60 61 0.475828 AGGCCTTTAGTCCCCACACT 60.476 55.000 0.00 0.00 0.00 3.55
61 62 0.035343 GAGGCCTTTAGTCCCCACAC 60.035 60.000 6.77 0.00 0.00 3.82
62 63 1.205460 GGAGGCCTTTAGTCCCCACA 61.205 60.000 6.77 0.00 0.00 4.17
63 64 1.608154 GGAGGCCTTTAGTCCCCAC 59.392 63.158 6.77 0.00 0.00 4.61
64 65 1.618447 GGGAGGCCTTTAGTCCCCA 60.618 63.158 18.09 0.00 43.91 4.96
65 66 3.332395 GGGAGGCCTTTAGTCCCC 58.668 66.667 14.91 12.11 43.91 4.81
67 68 1.000496 AAAGGGGAGGCCTTTAGTCC 59.000 55.000 6.77 2.24 35.97 3.85
68 69 2.901338 AAAAGGGGAGGCCTTTAGTC 57.099 50.000 6.77 0.00 36.61 2.59
69 70 3.266374 ACTAAAAGGGGAGGCCTTTAGT 58.734 45.455 16.30 16.30 36.61 2.24
70 71 5.622180 GATACTAAAAGGGGAGGCCTTTAG 58.378 45.833 6.77 12.40 36.61 1.85
71 72 4.102054 CGATACTAAAAGGGGAGGCCTTTA 59.898 45.833 6.77 0.00 36.61 1.85
72 73 3.118000 CGATACTAAAAGGGGAGGCCTTT 60.118 47.826 6.77 0.00 38.90 3.11
73 74 2.438392 CGATACTAAAAGGGGAGGCCTT 59.562 50.000 6.77 0.00 0.00 4.35
74 75 2.047830 CGATACTAAAAGGGGAGGCCT 58.952 52.381 3.86 3.86 0.00 5.19
75 76 1.071857 CCGATACTAAAAGGGGAGGCC 59.928 57.143 0.00 0.00 0.00 5.19
76 77 1.767088 ACCGATACTAAAAGGGGAGGC 59.233 52.381 0.00 0.00 0.00 4.70
77 78 3.181457 GGAACCGATACTAAAAGGGGAGG 60.181 52.174 0.00 0.00 0.00 4.30
78 79 3.492137 CGGAACCGATACTAAAAGGGGAG 60.492 52.174 7.53 0.00 42.83 4.30
79 80 2.431782 CGGAACCGATACTAAAAGGGGA 59.568 50.000 7.53 0.00 42.83 4.81
80 81 2.830104 CGGAACCGATACTAAAAGGGG 58.170 52.381 7.53 0.00 42.83 4.79
81 82 2.207590 GCGGAACCGATACTAAAAGGG 58.792 52.381 17.63 0.00 42.83 3.95
82 83 2.606272 GTGCGGAACCGATACTAAAAGG 59.394 50.000 17.63 0.00 42.83 3.11
83 84 2.280708 CGTGCGGAACCGATACTAAAAG 59.719 50.000 17.63 0.00 42.83 2.27
84 85 2.094803 TCGTGCGGAACCGATACTAAAA 60.095 45.455 17.63 0.00 42.83 1.52
85 86 1.472082 TCGTGCGGAACCGATACTAAA 59.528 47.619 17.63 1.73 42.83 1.85
86 87 1.093972 TCGTGCGGAACCGATACTAA 58.906 50.000 17.63 3.85 42.83 2.24
87 88 1.093972 TTCGTGCGGAACCGATACTA 58.906 50.000 17.63 4.60 42.83 1.82
88 89 1.885157 TTCGTGCGGAACCGATACT 59.115 52.632 17.63 0.00 42.83 2.12
89 90 4.481870 TTCGTGCGGAACCGATAC 57.518 55.556 17.63 12.97 42.83 2.24
101 102 1.296056 CCCTTTAGCACCGGTTCGTG 61.296 60.000 2.97 0.00 36.80 4.35
102 103 1.004200 CCCTTTAGCACCGGTTCGT 60.004 57.895 2.97 0.00 0.00 3.85
103 104 2.396157 GCCCTTTAGCACCGGTTCG 61.396 63.158 2.97 0.00 0.00 3.95
104 105 0.891904 TTGCCCTTTAGCACCGGTTC 60.892 55.000 2.97 0.00 43.97 3.62
105 106 1.151908 TTGCCCTTTAGCACCGGTT 59.848 52.632 2.97 0.00 43.97 4.44
106 107 1.602605 GTTGCCCTTTAGCACCGGT 60.603 57.895 0.00 0.00 43.97 5.28
107 108 2.340328 GGTTGCCCTTTAGCACCGG 61.340 63.158 0.00 0.00 43.97 5.28
108 109 1.602323 TGGTTGCCCTTTAGCACCG 60.602 57.895 0.00 0.00 43.97 4.94
109 110 1.862602 CGTGGTTGCCCTTTAGCACC 61.863 60.000 0.00 0.00 43.97 5.01
110 111 1.170290 ACGTGGTTGCCCTTTAGCAC 61.170 55.000 0.00 0.00 43.97 4.40
111 112 1.149627 ACGTGGTTGCCCTTTAGCA 59.850 52.632 0.00 0.00 42.17 3.49
112 113 1.579429 CACGTGGTTGCCCTTTAGC 59.421 57.895 7.95 0.00 0.00 3.09
113 114 1.862602 GCCACGTGGTTGCCCTTTAG 61.863 60.000 33.92 6.07 37.57 1.85
114 115 1.899534 GCCACGTGGTTGCCCTTTA 60.900 57.895 33.92 0.00 37.57 1.85
115 116 3.223589 GCCACGTGGTTGCCCTTT 61.224 61.111 33.92 0.00 37.57 3.11
116 117 4.514585 TGCCACGTGGTTGCCCTT 62.515 61.111 33.92 0.00 37.57 3.95
120 121 4.012895 CTCGTGCCACGTGGTTGC 62.013 66.667 33.92 20.95 43.14 4.17
121 122 4.012895 GCTCGTGCCACGTGGTTG 62.013 66.667 33.92 23.28 43.14 3.77
132 133 4.760047 CCCCGGAACTGGCTCGTG 62.760 72.222 0.73 0.00 0.00 4.35
146 147 1.988982 CTAAAGAGCTCCCTGCCCCC 61.989 65.000 10.93 0.00 44.23 5.40
147 148 1.275421 ACTAAAGAGCTCCCTGCCCC 61.275 60.000 10.93 0.00 44.23 5.80
148 149 1.139256 GTACTAAAGAGCTCCCTGCCC 59.861 57.143 10.93 0.00 44.23 5.36
149 150 1.139256 GGTACTAAAGAGCTCCCTGCC 59.861 57.143 10.93 0.29 44.23 4.85
150 151 1.202428 CGGTACTAAAGAGCTCCCTGC 60.202 57.143 10.93 0.00 43.29 4.85
151 152 1.409427 CCGGTACTAAAGAGCTCCCTG 59.591 57.143 10.93 0.94 0.00 4.45
152 153 1.006878 ACCGGTACTAAAGAGCTCCCT 59.993 52.381 4.49 0.00 0.00 4.20
153 154 1.482954 ACCGGTACTAAAGAGCTCCC 58.517 55.000 4.49 1.06 0.00 4.30
154 155 2.418334 CCAACCGGTACTAAAGAGCTCC 60.418 54.545 8.00 0.00 0.00 4.70
155 156 2.233186 ACCAACCGGTACTAAAGAGCTC 59.767 50.000 8.00 5.27 46.71 4.09
156 157 2.028385 CACCAACCGGTACTAAAGAGCT 60.028 50.000 8.00 0.00 46.94 4.09
157 158 2.028748 TCACCAACCGGTACTAAAGAGC 60.029 50.000 8.00 0.00 46.94 4.09
158 159 3.006110 TGTCACCAACCGGTACTAAAGAG 59.994 47.826 8.00 0.00 46.94 2.85
159 160 2.964464 TGTCACCAACCGGTACTAAAGA 59.036 45.455 8.00 0.00 46.94 2.52
160 161 3.062042 GTGTCACCAACCGGTACTAAAG 58.938 50.000 8.00 0.00 46.94 1.85
161 162 2.224257 GGTGTCACCAACCGGTACTAAA 60.224 50.000 17.59 0.00 46.94 1.85
162 163 1.344114 GGTGTCACCAACCGGTACTAA 59.656 52.381 17.59 0.00 46.94 2.24
163 164 0.968405 GGTGTCACCAACCGGTACTA 59.032 55.000 17.59 0.00 46.94 1.82
164 165 1.750297 GGTGTCACCAACCGGTACT 59.250 57.895 17.59 0.00 46.94 2.73
165 166 4.366603 GGTGTCACCAACCGGTAC 57.633 61.111 17.59 1.54 46.94 3.34
183 184 3.433343 CCCCAACCTTTTAATACCGGTT 58.567 45.455 15.04 0.00 40.19 4.44
184 185 2.291735 CCCCCAACCTTTTAATACCGGT 60.292 50.000 13.98 13.98 0.00 5.28
185 186 2.380941 CCCCCAACCTTTTAATACCGG 58.619 52.381 0.00 0.00 0.00 5.28
203 204 3.603158 AATCATAAACGCAAAACCCCC 57.397 42.857 0.00 0.00 0.00 5.40
204 205 4.816392 AGAAATCATAAACGCAAAACCCC 58.184 39.130 0.00 0.00 0.00 4.95
205 206 6.779115 AAAGAAATCATAAACGCAAAACCC 57.221 33.333 0.00 0.00 0.00 4.11
206 207 8.331742 TGAAAAAGAAATCATAAACGCAAAACC 58.668 29.630 0.00 0.00 0.00 3.27
207 208 9.862585 ATGAAAAAGAAATCATAAACGCAAAAC 57.137 25.926 0.00 0.00 34.61 2.43
240 241 9.631639 CGAAAAAGAATTAAATGGAAAACACAC 57.368 29.630 0.00 0.00 0.00 3.82
241 242 9.372369 ACGAAAAAGAATTAAATGGAAAACACA 57.628 25.926 0.00 0.00 0.00 3.72
245 246 9.709600 GCAAACGAAAAAGAATTAAATGGAAAA 57.290 25.926 0.00 0.00 0.00 2.29
246 247 9.103861 AGCAAACGAAAAAGAATTAAATGGAAA 57.896 25.926 0.00 0.00 0.00 3.13
247 248 8.547069 CAGCAAACGAAAAAGAATTAAATGGAA 58.453 29.630 0.00 0.00 0.00 3.53
248 249 7.170658 CCAGCAAACGAAAAAGAATTAAATGGA 59.829 33.333 0.00 0.00 0.00 3.41
249 250 7.042119 ACCAGCAAACGAAAAAGAATTAAATGG 60.042 33.333 0.00 0.00 0.00 3.16
250 251 7.850501 ACCAGCAAACGAAAAAGAATTAAATG 58.149 30.769 0.00 0.00 0.00 2.32
251 252 9.705290 ATACCAGCAAACGAAAAAGAATTAAAT 57.295 25.926 0.00 0.00 0.00 1.40
252 253 9.535878 AATACCAGCAAACGAAAAAGAATTAAA 57.464 25.926 0.00 0.00 0.00 1.52
253 254 9.535878 AAATACCAGCAAACGAAAAAGAATTAA 57.464 25.926 0.00 0.00 0.00 1.40
254 255 9.535878 AAAATACCAGCAAACGAAAAAGAATTA 57.464 25.926 0.00 0.00 0.00 1.40
255 256 8.432110 AAAATACCAGCAAACGAAAAAGAATT 57.568 26.923 0.00 0.00 0.00 2.17
256 257 8.974408 GTAAAATACCAGCAAACGAAAAAGAAT 58.026 29.630 0.00 0.00 0.00 2.40
257 258 7.166142 CGTAAAATACCAGCAAACGAAAAAGAA 59.834 33.333 0.00 0.00 0.00 2.52
258 259 6.633634 CGTAAAATACCAGCAAACGAAAAAGA 59.366 34.615 0.00 0.00 0.00 2.52
259 260 6.633634 TCGTAAAATACCAGCAAACGAAAAAG 59.366 34.615 0.00 0.00 35.23 2.27
260 261 6.493116 TCGTAAAATACCAGCAAACGAAAAA 58.507 32.000 0.00 0.00 35.23 1.94
261 262 6.057627 TCGTAAAATACCAGCAAACGAAAA 57.942 33.333 0.00 0.00 35.23 2.29
262 263 5.670149 TCGTAAAATACCAGCAAACGAAA 57.330 34.783 0.00 0.00 35.23 3.46
263 264 5.866335 ATCGTAAAATACCAGCAAACGAA 57.134 34.783 0.00 0.00 40.71 3.85
264 265 5.004630 CGTATCGTAAAATACCAGCAAACGA 59.995 40.000 0.00 0.00 41.45 3.85
265 266 5.185341 CGTATCGTAAAATACCAGCAAACG 58.815 41.667 0.00 0.00 0.00 3.60
266 267 5.495502 CCGTATCGTAAAATACCAGCAAAC 58.504 41.667 0.00 0.00 0.00 2.93
267 268 4.034279 GCCGTATCGTAAAATACCAGCAAA 59.966 41.667 0.00 0.00 32.30 3.68
268 269 3.556775 GCCGTATCGTAAAATACCAGCAA 59.443 43.478 0.00 0.00 32.30 3.91
269 270 3.125316 GCCGTATCGTAAAATACCAGCA 58.875 45.455 0.00 0.00 32.30 4.41
270 271 3.125316 TGCCGTATCGTAAAATACCAGC 58.875 45.455 0.00 0.00 32.49 4.85
271 272 7.117236 ACAATATGCCGTATCGTAAAATACCAG 59.883 37.037 0.00 0.00 0.00 4.00
272 273 6.930164 ACAATATGCCGTATCGTAAAATACCA 59.070 34.615 0.00 0.00 0.00 3.25
273 274 7.355332 ACAATATGCCGTATCGTAAAATACC 57.645 36.000 0.00 0.00 0.00 2.73
274 275 8.914654 TGTACAATATGCCGTATCGTAAAATAC 58.085 33.333 0.00 0.00 0.00 1.89
275 276 8.914654 GTGTACAATATGCCGTATCGTAAAATA 58.085 33.333 0.00 0.00 0.00 1.40
276 277 7.358600 CGTGTACAATATGCCGTATCGTAAAAT 60.359 37.037 0.00 0.00 0.00 1.82
277 278 6.074941 CGTGTACAATATGCCGTATCGTAAAA 60.075 38.462 0.00 0.00 0.00 1.52
278 279 5.399006 CGTGTACAATATGCCGTATCGTAAA 59.601 40.000 0.00 0.00 0.00 2.01
279 280 4.911033 CGTGTACAATATGCCGTATCGTAA 59.089 41.667 0.00 0.00 0.00 3.18
280 281 4.024133 ACGTGTACAATATGCCGTATCGTA 60.024 41.667 0.00 0.00 33.10 3.43
281 282 3.243168 ACGTGTACAATATGCCGTATCGT 60.243 43.478 0.00 0.00 0.00 3.73
282 283 3.302555 ACGTGTACAATATGCCGTATCG 58.697 45.455 0.00 0.00 0.00 2.92
283 284 6.669032 GCATAACGTGTACAATATGCCGTATC 60.669 42.308 24.97 8.73 42.92 2.24
284 285 5.119588 GCATAACGTGTACAATATGCCGTAT 59.880 40.000 24.97 12.54 42.92 3.06
285 286 4.445052 GCATAACGTGTACAATATGCCGTA 59.555 41.667 24.97 10.13 42.92 4.02
286 287 3.246699 GCATAACGTGTACAATATGCCGT 59.753 43.478 24.97 15.95 42.92 5.68
287 288 3.246463 TGCATAACGTGTACAATATGCCG 59.754 43.478 28.59 18.09 46.28 5.69
288 289 4.804608 TGCATAACGTGTACAATATGCC 57.195 40.909 28.59 18.92 46.28 4.40
317 318 9.667107 TGATCGGTTCTACTTGAAATTCTATTT 57.333 29.630 0.00 0.00 36.30 1.40
318 319 9.838339 ATGATCGGTTCTACTTGAAATTCTATT 57.162 29.630 0.00 0.00 36.30 1.73
360 361 1.859080 GCGTGACGAATAGACAATCCC 59.141 52.381 10.10 0.00 0.00 3.85
361 362 2.535984 CTGCGTGACGAATAGACAATCC 59.464 50.000 10.10 0.00 0.00 3.01
362 363 2.535984 CCTGCGTGACGAATAGACAATC 59.464 50.000 10.10 0.00 0.00 2.67
388 389 5.044476 TGGCTGGGGTGAAGAATAAGAATTA 60.044 40.000 0.00 0.00 33.48 1.40
560 562 4.120946 ACTTCTCTCTTCTGGTGTAGGT 57.879 45.455 0.00 0.00 0.00 3.08
893 916 0.541530 TCTGCACACTCTCTCCTGCT 60.542 55.000 0.00 0.00 0.00 4.24
1429 1452 1.001815 CACAATTCGTTGTTCCGCCTT 60.002 47.619 0.00 0.00 31.86 4.35
1628 1651 3.136443 TCACCTTTGAACCAGTCAGACAT 59.864 43.478 2.66 0.00 37.61 3.06
1983 2006 6.045955 TGGTCAAAATTTACCTGCACTTTTC 58.954 36.000 10.72 0.00 36.67 2.29
2309 2342 1.282875 GCCACCTTTCACTTCGTGC 59.717 57.895 0.00 0.00 32.98 5.34


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

AutoCloner maintained by Alex Coulton.