Multiple sequence alignment - TraesCS5A01G230200

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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 TraesCS5A01G230200 chr5A 100.000 3230 0 0 1 3230 445246106 445242877 0.000000e+00 5965
1 TraesCS5A01G230200 chr5B 93.035 2814 124 31 450 3230 405596758 405593984 0.000000e+00 4045
2 TraesCS5A01G230200 chr5D 91.209 3003 145 41 299 3230 345956950 345959904 0.000000e+00 3973
3 TraesCS5A01G230200 chr5D 90.909 176 14 2 124 298 280384140 280384314 5.390000e-58 235
4 TraesCS5A01G230200 chr3A 92.857 168 12 0 132 299 40914889 40915056 8.950000e-61 244
5 TraesCS5A01G230200 chr3A 89.423 104 11 0 3 106 674471820 674471923 7.270000e-27 132
6 TraesCS5A01G230200 chr7D 91.061 179 16 0 119 297 522510490 522510312 3.220000e-60 243
7 TraesCS5A01G230200 chr7D 91.329 173 15 0 130 302 23497761 23497589 1.500000e-58 237
8 TraesCS5A01G230200 chr3B 91.011 178 16 0 123 300 190902138 190901961 1.160000e-59 241
9 TraesCS5A01G230200 chr3D 92.308 169 12 1 129 297 410304829 410304662 4.160000e-59 239
10 TraesCS5A01G230200 chr3D 90.960 177 15 1 133 309 412074652 412074477 1.500000e-58 237
11 TraesCS5A01G230200 chr1D 91.813 171 14 0 133 303 404282251 404282081 4.160000e-59 239
12 TraesCS5A01G230200 chr4D 90.556 180 13 3 120 298 109243692 109243868 5.390000e-58 235


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 TraesCS5A01G230200 chr5A 445242877 445246106 3229 True 5965 5965 100.000 1 3230 1 chr5A.!!$R1 3229
1 TraesCS5A01G230200 chr5B 405593984 405596758 2774 True 4045 4045 93.035 450 3230 1 chr5B.!!$R1 2780
2 TraesCS5A01G230200 chr5D 345956950 345959904 2954 False 3973 3973 91.209 299 3230 1 chr5D.!!$F2 2931

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
866 906 0.031994 CTTCCAACCGCAACCAAAGG 59.968 55.0 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2507 2586 0.322975 AGAGTGTCATGACAGCCCAC 59.677 55.0 28.54 16.16 42.74 4.61 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 6.411630 TGAAACGGTCATAAAATTACCTCG 57.588 37.500 0.00 0.00 0.00 4.63
88 89 5.352016 TGAAACGGTCATAAAATTACCTCGG 59.648 40.000 0.00 0.00 0.00 4.63
89 90 3.800531 ACGGTCATAAAATTACCTCGGG 58.199 45.455 0.00 0.00 0.00 5.14
90 91 3.198417 ACGGTCATAAAATTACCTCGGGT 59.802 43.478 1.14 1.14 40.16 5.28
91 92 4.405358 ACGGTCATAAAATTACCTCGGGTA 59.595 41.667 0.00 0.00 37.09 3.69
106 107 9.603921 TTACCTCGGGTAAAGAATAACTTATTG 57.396 33.333 11.65 0.00 44.06 1.90
107 108 7.854337 ACCTCGGGTAAAGAATAACTTATTGA 58.146 34.615 0.00 0.00 37.93 2.57
108 109 8.323567 ACCTCGGGTAAAGAATAACTTATTGAA 58.676 33.333 0.00 0.00 37.93 2.69
109 110 9.338622 CCTCGGGTAAAGAATAACTTATTGAAT 57.661 33.333 0.00 0.00 37.93 2.57
111 112 9.893634 TCGGGTAAAGAATAACTTATTGAATGA 57.106 29.630 0.00 0.00 37.93 2.57
147 148 7.966246 ACTATATACTACTCACTCTGTTCCG 57.034 40.000 0.00 0.00 0.00 4.30
148 149 7.733969 ACTATATACTACTCACTCTGTTCCGA 58.266 38.462 0.00 0.00 0.00 4.55
149 150 8.209584 ACTATATACTACTCACTCTGTTCCGAA 58.790 37.037 0.00 0.00 0.00 4.30
150 151 7.876936 ATATACTACTCACTCTGTTCCGAAA 57.123 36.000 0.00 0.00 0.00 3.46
151 152 6.777213 ATACTACTCACTCTGTTCCGAAAT 57.223 37.500 0.00 0.00 0.00 2.17
152 153 7.876936 ATACTACTCACTCTGTTCCGAAATA 57.123 36.000 0.00 0.00 0.00 1.40
153 154 6.777213 ACTACTCACTCTGTTCCGAAATAT 57.223 37.500 0.00 0.00 0.00 1.28
154 155 7.876936 ACTACTCACTCTGTTCCGAAATATA 57.123 36.000 0.00 0.00 0.00 0.86
155 156 8.289939 ACTACTCACTCTGTTCCGAAATATAA 57.710 34.615 0.00 0.00 0.00 0.98
156 157 8.407064 ACTACTCACTCTGTTCCGAAATATAAG 58.593 37.037 0.00 0.00 0.00 1.73
157 158 7.171630 ACTCACTCTGTTCCGAAATATAAGT 57.828 36.000 0.00 0.00 0.00 2.24
158 159 7.259161 ACTCACTCTGTTCCGAAATATAAGTC 58.741 38.462 0.00 0.00 0.00 3.01
159 160 7.122948 ACTCACTCTGTTCCGAAATATAAGTCT 59.877 37.037 0.00 0.00 0.00 3.24
160 161 7.837863 TCACTCTGTTCCGAAATATAAGTCTT 58.162 34.615 0.00 0.00 0.00 3.01
161 162 8.311836 TCACTCTGTTCCGAAATATAAGTCTTT 58.688 33.333 0.00 0.00 0.00 2.52
162 163 8.936864 CACTCTGTTCCGAAATATAAGTCTTTT 58.063 33.333 0.00 0.00 0.00 2.27
163 164 9.503399 ACTCTGTTCCGAAATATAAGTCTTTTT 57.497 29.630 0.00 0.00 0.00 1.94
180 181 9.750125 AAGTCTTTTTAGACATTTCAAATGGAC 57.250 29.630 14.70 8.92 41.02 4.02
181 182 9.136323 AGTCTTTTTAGACATTTCAAATGGACT 57.864 29.630 14.70 14.18 41.02 3.85
186 187 9.959749 TTTTAGACATTTCAAATGGACTACAAC 57.040 29.630 14.70 0.00 0.00 3.32
187 188 8.684386 TTAGACATTTCAAATGGACTACAACA 57.316 30.769 14.70 1.25 0.00 3.33
188 189 7.765695 AGACATTTCAAATGGACTACAACAT 57.234 32.000 14.70 0.00 0.00 2.71
189 190 8.862325 AGACATTTCAAATGGACTACAACATA 57.138 30.769 14.70 0.00 0.00 2.29
190 191 8.730680 AGACATTTCAAATGGACTACAACATAC 58.269 33.333 14.70 0.00 0.00 2.39
191 192 7.526608 ACATTTCAAATGGACTACAACATACG 58.473 34.615 14.70 0.00 0.00 3.06
192 193 6.489127 TTTCAAATGGACTACAACATACGG 57.511 37.500 0.00 0.00 0.00 4.02
193 194 5.408880 TCAAATGGACTACAACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
194 195 5.984725 TCAAATGGACTACAACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
195 196 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
197 198 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
198 199 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
243 244 9.490663 GTAAATTCATTCATTTTACTCTGGACG 57.509 33.333 0.00 0.00 34.51 4.79
244 245 7.687941 AATTCATTCATTTTACTCTGGACGT 57.312 32.000 0.00 0.00 0.00 4.34
245 246 8.786826 AATTCATTCATTTTACTCTGGACGTA 57.213 30.769 0.00 0.00 0.00 3.57
246 247 7.827819 TTCATTCATTTTACTCTGGACGTAG 57.172 36.000 0.00 0.00 0.00 3.51
263 264 5.517322 ACGTAGTCACCTATTGGAATCTC 57.483 43.478 0.00 0.00 29.74 2.75
264 265 5.202004 ACGTAGTCACCTATTGGAATCTCT 58.798 41.667 0.00 0.00 29.74 3.10
265 266 6.363065 ACGTAGTCACCTATTGGAATCTCTA 58.637 40.000 0.00 0.00 29.74 2.43
266 267 6.832384 ACGTAGTCACCTATTGGAATCTCTAA 59.168 38.462 0.00 0.00 29.74 2.10
267 268 7.341256 ACGTAGTCACCTATTGGAATCTCTAAA 59.659 37.037 0.00 0.00 29.74 1.85
268 269 8.195436 CGTAGTCACCTATTGGAATCTCTAAAA 58.805 37.037 0.00 0.00 37.04 1.52
269 270 9.886132 GTAGTCACCTATTGGAATCTCTAAAAA 57.114 33.333 0.00 0.00 37.04 1.94
271 272 8.826765 AGTCACCTATTGGAATCTCTAAAAAGA 58.173 33.333 0.00 0.00 37.04 2.52
272 273 8.884726 GTCACCTATTGGAATCTCTAAAAAGAC 58.115 37.037 0.00 0.00 37.04 3.01
273 274 8.826765 TCACCTATTGGAATCTCTAAAAAGACT 58.173 33.333 0.00 0.00 37.04 3.24
274 275 9.454859 CACCTATTGGAATCTCTAAAAAGACTT 57.545 33.333 0.00 0.00 37.04 3.01
292 293 9.908152 AAAAGACTTATATTTTGAAACGAAGGG 57.092 29.630 0.00 0.00 28.15 3.95
293 294 8.857694 AAGACTTATATTTTGAAACGAAGGGA 57.142 30.769 0.00 0.00 0.00 4.20
294 295 8.494016 AGACTTATATTTTGAAACGAAGGGAG 57.506 34.615 0.00 0.00 0.00 4.30
295 296 8.101419 AGACTTATATTTTGAAACGAAGGGAGT 58.899 33.333 0.00 0.00 0.00 3.85
296 297 9.374838 GACTTATATTTTGAAACGAAGGGAGTA 57.625 33.333 0.00 0.00 0.00 2.59
297 298 9.159364 ACTTATATTTTGAAACGAAGGGAGTAC 57.841 33.333 0.00 0.00 0.00 2.73
303 304 9.901172 ATTTTGAAACGAAGGGAGTACTATATT 57.099 29.630 0.00 0.00 0.00 1.28
312 313 7.148154 CGAAGGGAGTACTATATTGATGGAGAG 60.148 44.444 0.00 0.00 0.00 3.20
345 354 5.367945 TTTCCAATAATTACCGAGCCTCT 57.632 39.130 0.00 0.00 0.00 3.69
352 361 3.596940 ATTACCGAGCCTCTTAGGAGA 57.403 47.619 2.89 0.00 41.86 3.71
381 390 6.678655 GCCAAAGTTTCGTTTTTAGTGGTACT 60.679 38.462 0.00 0.00 0.00 2.73
382 391 7.467131 GCCAAAGTTTCGTTTTTAGTGGTACTA 60.467 37.037 0.00 0.00 0.00 1.82
383 392 7.852454 CCAAAGTTTCGTTTTTAGTGGTACTAC 59.148 37.037 0.19 0.19 28.93 2.73
400 409 4.697756 CCTTTCACGCCTCCGCCA 62.698 66.667 0.00 0.00 38.22 5.69
413 422 1.898574 CCGCCAAGCAGAAACTGGT 60.899 57.895 0.00 0.00 44.48 4.00
446 455 0.034337 GTTCCGTAGTTCCACCAGCA 59.966 55.000 0.00 0.00 0.00 4.41
447 456 0.759959 TTCCGTAGTTCCACCAGCAA 59.240 50.000 0.00 0.00 0.00 3.91
448 457 0.320374 TCCGTAGTTCCACCAGCAAG 59.680 55.000 0.00 0.00 0.00 4.01
449 458 0.034896 CCGTAGTTCCACCAGCAAGT 59.965 55.000 0.00 0.00 0.00 3.16
450 459 1.542547 CCGTAGTTCCACCAGCAAGTT 60.543 52.381 0.00 0.00 0.00 2.66
453 462 3.303791 CGTAGTTCCACCAGCAAGTTTTC 60.304 47.826 0.00 0.00 0.00 2.29
455 464 4.164843 AGTTCCACCAGCAAGTTTTCTA 57.835 40.909 0.00 0.00 0.00 2.10
456 465 4.137543 AGTTCCACCAGCAAGTTTTCTAG 58.862 43.478 0.00 0.00 0.00 2.43
463 472 6.430451 CACCAGCAAGTTTTCTAGTACTTTG 58.570 40.000 0.00 0.00 32.50 2.77
515 547 7.415206 GCCATTCAGAATCCACGTAGTATTTTT 60.415 37.037 0.00 0.00 41.61 1.94
693 733 2.351738 GCCAGGATTTCCAACAACTTCG 60.352 50.000 0.00 0.00 38.89 3.79
717 757 3.009805 ACCCATACGCTATTTATTCCCCC 59.990 47.826 0.00 0.00 0.00 5.40
718 758 3.265995 CCCATACGCTATTTATTCCCCCT 59.734 47.826 0.00 0.00 0.00 4.79
778 818 1.567357 GGAGAAGAGGCAGAAGGTCT 58.433 55.000 0.00 0.00 0.00 3.85
853 893 8.514594 CAATCTTACTGCATTAGTTTCTTCCAA 58.485 33.333 0.00 0.00 40.89 3.53
866 906 0.031994 CTTCCAACCGCAACCAAAGG 59.968 55.000 0.00 0.00 0.00 3.11
935 975 2.146342 CGGCTATGTTCATCCATGTCC 58.854 52.381 0.00 0.00 0.00 4.02
1018 1067 0.401738 AATGTGTGTCCAGAGGGGTG 59.598 55.000 0.00 0.00 38.11 4.61
1050 1099 3.518705 CAGGCATCTTAGATGGGCTCTAT 59.481 47.826 21.90 0.00 36.35 1.98
1054 1103 1.895798 TCTTAGATGGGCTCTATGGCG 59.104 52.381 0.00 0.00 42.84 5.69
1056 1105 0.969149 TAGATGGGCTCTATGGCGTG 59.031 55.000 0.00 0.00 42.84 5.34
1064 1113 1.945387 CTCTATGGCGTGCAGATTGT 58.055 50.000 0.00 0.00 0.00 2.71
1071 1120 1.416049 CGTGCAGATTGTTCGTCGG 59.584 57.895 0.00 0.00 0.00 4.79
1077 1126 4.690719 ATTGTTCGTCGGCCGCCA 62.691 61.111 23.51 8.75 36.19 5.69
1213 1262 4.141620 GGTGAGCTTCCATTAATCAGGAGA 60.142 45.833 0.00 0.00 34.91 3.71
1248 1314 1.375268 GACTGAGCTGACACCCTGC 60.375 63.158 0.00 0.00 39.67 4.85
1254 1320 2.186826 GCTGACACCCTGCGTTTGT 61.187 57.895 0.00 0.00 0.00 2.83
1317 1383 0.471617 AGCCCATCCACTGTAGCATC 59.528 55.000 0.00 0.00 0.00 3.91
1336 1402 0.659427 CACATGTATGGCAGCTTCCG 59.341 55.000 0.00 0.00 0.00 4.30
1359 1425 4.028490 CCTGCCCAGCAACCGGTA 62.028 66.667 8.00 0.00 38.41 4.02
1376 1447 3.428316 CCGGTACCACAATATTTGCCAAC 60.428 47.826 13.54 0.00 0.00 3.77
1403 1474 2.943033 CCTCTTGTCTGACGGTTTTGTT 59.057 45.455 2.98 0.00 0.00 2.83
1405 1476 4.342772 CTCTTGTCTGACGGTTTTGTTTG 58.657 43.478 2.98 0.00 0.00 2.93
1424 1496 0.737219 GATCAGGTGACAAGCATGCC 59.263 55.000 15.66 0.00 0.00 4.40
1487 1559 1.669115 CCTTGGACTGCAGACACCG 60.669 63.158 23.35 11.67 0.00 4.94
1514 1586 5.291614 GCAAGACATCTTCTGAGACAAGATC 59.708 44.000 0.00 0.00 38.33 2.75
1523 1595 6.370994 TCTTCTGAGACAAGATCATTCTTTGC 59.629 38.462 0.00 0.00 40.28 3.68
1524 1596 5.802465 TCTGAGACAAGATCATTCTTTGCT 58.198 37.500 0.00 0.00 40.28 3.91
1525 1597 5.873712 TCTGAGACAAGATCATTCTTTGCTC 59.126 40.000 0.00 3.01 40.28 4.26
1527 1599 6.939622 TGAGACAAGATCATTCTTTGCTCTA 58.060 36.000 0.00 0.00 40.28 2.43
1531 1603 8.675504 AGACAAGATCATTCTTTGCTCTATTTG 58.324 33.333 0.00 0.00 40.28 2.32
1547 1619 8.506437 TGCTCTATTTGTTTCTGAGTTTGTATG 58.494 33.333 0.00 0.00 0.00 2.39
1731 1803 5.123820 GCTGGTGAGTCATATTTTTGCACTA 59.876 40.000 0.00 0.00 0.00 2.74
1810 1883 2.795329 CAGTGTTTATCCAGGGCAGTT 58.205 47.619 0.00 0.00 0.00 3.16
1935 2008 2.726821 TCCAAATGACCTGGCAGATTC 58.273 47.619 17.94 12.39 33.63 2.52
1982 2055 2.031769 TGATCAGCAAACTCGCTTGTTG 60.032 45.455 0.00 3.36 41.38 3.33
2082 2160 2.147150 GTTGAACCAGAGCTCAGAACC 58.853 52.381 17.77 2.51 0.00 3.62
2157 2235 2.223525 CGACGATTACTTCCCAGAGACC 60.224 54.545 0.00 0.00 0.00 3.85
2273 2351 6.948353 GCTATCAACGAATAGCTGATTTCAA 58.052 36.000 16.50 0.00 46.94 2.69
2351 2430 7.340232 ACGGTGTACAGAATAGGTTACATAGAA 59.660 37.037 0.00 0.00 0.00 2.10
2352 2431 7.861372 CGGTGTACAGAATAGGTTACATAGAAG 59.139 40.741 0.00 0.00 0.00 2.85
2353 2432 8.910944 GGTGTACAGAATAGGTTACATAGAAGA 58.089 37.037 0.00 0.00 0.00 2.87
2354 2433 9.953697 GTGTACAGAATAGGTTACATAGAAGAG 57.046 37.037 0.00 0.00 0.00 2.85
2355 2434 9.916360 TGTACAGAATAGGTTACATAGAAGAGA 57.084 33.333 0.00 0.00 0.00 3.10
2358 2437 9.702253 ACAGAATAGGTTACATAGAAGAGAGAA 57.298 33.333 0.00 0.00 0.00 2.87
2359 2438 9.959749 CAGAATAGGTTACATAGAAGAGAGAAC 57.040 37.037 0.00 0.00 0.00 3.01
2360 2439 9.702253 AGAATAGGTTACATAGAAGAGAGAACA 57.298 33.333 0.00 0.00 0.00 3.18
2380 2459 5.733620 ACAGGAGCATTGTTCAAATTGAT 57.266 34.783 0.00 0.00 0.00 2.57
2382 2461 6.624423 ACAGGAGCATTGTTCAAATTGATAC 58.376 36.000 0.00 0.00 0.00 2.24
2390 2469 7.814107 GCATTGTTCAAATTGATACCAGAAGAA 59.186 33.333 0.00 0.00 0.00 2.52
2443 2522 5.074584 AGGAAAATGAGACGAACTAGGTC 57.925 43.478 0.00 0.00 34.62 3.85
2474 2553 6.690098 GTGCATGTAGTTCTGCTATGATTTTG 59.310 38.462 0.00 0.00 39.16 2.44
2475 2554 5.684626 GCATGTAGTTCTGCTATGATTTTGC 59.315 40.000 0.00 0.00 35.49 3.68
2497 2576 8.472683 TTGCATTGGTGTTTAATTATTACTGC 57.527 30.769 0.00 0.00 0.00 4.40
2500 2579 7.165812 GCATTGGTGTTTAATTATTACTGCGAG 59.834 37.037 0.00 0.00 0.00 5.03
2525 2604 0.674895 GGTGGGCTGTCATGACACTC 60.675 60.000 24.56 19.90 36.21 3.51
2592 2671 7.334421 GCTTCAAAGACCTCATCATTACAACTA 59.666 37.037 0.00 0.00 0.00 2.24
2593 2672 9.388506 CTTCAAAGACCTCATCATTACAACTAT 57.611 33.333 0.00 0.00 0.00 2.12
2714 2793 9.513906 TCAAATGTATCATGTTCTAACCTTGAA 57.486 29.630 0.00 0.00 0.00 2.69
2758 2837 3.305950 GCATAATTCCACAGTTGCACCAA 60.306 43.478 0.00 0.00 0.00 3.67
2794 2873 3.076621 TGTGTGGCAGACTGATCATTTC 58.923 45.455 16.26 0.00 0.00 2.17
2871 2950 1.081242 CACCTGATGGTTGCAACGC 60.081 57.895 22.67 15.82 46.05 4.84
2872 2951 2.268076 ACCTGATGGTTGCAACGCC 61.268 57.895 22.67 11.22 46.05 5.68
2873 2952 2.568090 CTGATGGTTGCAACGCCC 59.432 61.111 22.67 10.46 0.00 6.13
2876 2955 2.522923 ATGGTTGCAACGCCCCAA 60.523 55.556 22.67 5.01 33.50 4.12
2877 2956 1.887344 GATGGTTGCAACGCCCCAAT 61.887 55.000 22.67 9.36 33.50 3.16
2989 3068 7.876936 AGACAATTTGTTGAGATCATGCTAT 57.123 32.000 3.08 0.00 0.00 2.97
3122 3201 2.352651 CGCATACATGTTTGACAGGAGG 59.647 50.000 18.99 0.00 33.56 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 7.225145 CCGAGGTAATTTTATGACCGTTTCATA 59.775 37.037 0.88 0.88 43.70 2.15
64 65 5.352016 CCGAGGTAATTTTATGACCGTTTCA 59.648 40.000 0.00 0.00 38.35 2.69
65 66 5.220719 CCCGAGGTAATTTTATGACCGTTTC 60.221 44.000 0.00 0.00 38.35 2.78
66 67 4.637091 CCCGAGGTAATTTTATGACCGTTT 59.363 41.667 0.00 0.00 38.35 3.60
67 68 4.193865 CCCGAGGTAATTTTATGACCGTT 58.806 43.478 0.00 0.00 38.35 4.44
68 69 3.198417 ACCCGAGGTAATTTTATGACCGT 59.802 43.478 0.00 0.00 38.35 4.83
69 70 3.800531 ACCCGAGGTAATTTTATGACCG 58.199 45.455 0.00 0.00 38.35 4.79
70 71 7.049754 TCTTTACCCGAGGTAATTTTATGACC 58.950 38.462 13.97 0.00 45.95 4.02
71 72 8.496707 TTCTTTACCCGAGGTAATTTTATGAC 57.503 34.615 13.97 0.00 45.95 3.06
76 77 9.524496 AAGTTATTCTTTACCCGAGGTAATTTT 57.476 29.630 13.97 5.43 45.95 1.82
80 81 9.603921 CAATAAGTTATTCTTTACCCGAGGTAA 57.396 33.333 5.10 10.41 45.16 2.85
81 82 8.980596 TCAATAAGTTATTCTTTACCCGAGGTA 58.019 33.333 5.10 0.00 36.05 3.08
82 83 7.854337 TCAATAAGTTATTCTTTACCCGAGGT 58.146 34.615 5.10 1.14 37.36 3.85
83 84 8.726870 TTCAATAAGTTATTCTTTACCCGAGG 57.273 34.615 5.10 0.00 37.56 4.63
85 86 9.893634 TCATTCAATAAGTTATTCTTTACCCGA 57.106 29.630 5.10 0.00 37.56 5.14
121 122 9.486497 CGGAACAGAGTGAGTAGTATATAGTAA 57.514 37.037 0.00 0.00 0.00 2.24
122 123 8.864087 TCGGAACAGAGTGAGTAGTATATAGTA 58.136 37.037 0.00 0.00 0.00 1.82
123 124 7.733969 TCGGAACAGAGTGAGTAGTATATAGT 58.266 38.462 0.00 0.00 0.00 2.12
124 125 8.604640 TTCGGAACAGAGTGAGTAGTATATAG 57.395 38.462 0.00 0.00 0.00 1.31
125 126 8.969260 TTTCGGAACAGAGTGAGTAGTATATA 57.031 34.615 0.00 0.00 0.00 0.86
126 127 7.876936 TTTCGGAACAGAGTGAGTAGTATAT 57.123 36.000 0.00 0.00 0.00 0.86
127 128 7.876936 ATTTCGGAACAGAGTGAGTAGTATA 57.123 36.000 0.00 0.00 0.00 1.47
128 129 6.777213 ATTTCGGAACAGAGTGAGTAGTAT 57.223 37.500 0.00 0.00 0.00 2.12
129 130 7.876936 ATATTTCGGAACAGAGTGAGTAGTA 57.123 36.000 0.00 0.00 0.00 1.82
130 131 6.777213 ATATTTCGGAACAGAGTGAGTAGT 57.223 37.500 0.00 0.00 0.00 2.73
131 132 8.407064 ACTTATATTTCGGAACAGAGTGAGTAG 58.593 37.037 0.00 0.00 0.00 2.57
132 133 8.289939 ACTTATATTTCGGAACAGAGTGAGTA 57.710 34.615 0.00 0.00 0.00 2.59
133 134 7.122948 AGACTTATATTTCGGAACAGAGTGAGT 59.877 37.037 0.00 0.00 0.00 3.41
134 135 7.484975 AGACTTATATTTCGGAACAGAGTGAG 58.515 38.462 0.00 0.00 0.00 3.51
135 136 7.406031 AGACTTATATTTCGGAACAGAGTGA 57.594 36.000 0.00 0.00 0.00 3.41
136 137 8.480643 AAAGACTTATATTTCGGAACAGAGTG 57.519 34.615 0.00 0.00 0.00 3.51
137 138 9.503399 AAAAAGACTTATATTTCGGAACAGAGT 57.497 29.630 0.00 0.00 0.00 3.24
154 155 9.750125 GTCCATTTGAAATGTCTAAAAAGACTT 57.250 29.630 15.93 0.00 39.41 3.01
155 156 9.136323 AGTCCATTTGAAATGTCTAAAAAGACT 57.864 29.630 15.93 14.21 39.41 3.24
160 161 9.959749 GTTGTAGTCCATTTGAAATGTCTAAAA 57.040 29.630 15.93 14.59 0.00 1.52
161 162 9.126151 TGTTGTAGTCCATTTGAAATGTCTAAA 57.874 29.630 15.93 10.39 0.00 1.85
162 163 8.684386 TGTTGTAGTCCATTTGAAATGTCTAA 57.316 30.769 15.93 4.89 0.00 2.10
163 164 8.862325 ATGTTGTAGTCCATTTGAAATGTCTA 57.138 30.769 15.93 13.97 0.00 2.59
164 165 7.765695 ATGTTGTAGTCCATTTGAAATGTCT 57.234 32.000 15.93 14.81 0.00 3.41
165 166 7.692291 CGTATGTTGTAGTCCATTTGAAATGTC 59.308 37.037 15.93 9.10 0.00 3.06
166 167 7.361713 CCGTATGTTGTAGTCCATTTGAAATGT 60.362 37.037 15.93 1.43 0.00 2.71
167 168 6.966632 CCGTATGTTGTAGTCCATTTGAAATG 59.033 38.462 10.84 10.84 0.00 2.32
168 169 6.882140 TCCGTATGTTGTAGTCCATTTGAAAT 59.118 34.615 0.00 0.00 0.00 2.17
169 170 6.231951 TCCGTATGTTGTAGTCCATTTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
170 171 5.795972 TCCGTATGTTGTAGTCCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
171 172 5.408880 TCCGTATGTTGTAGTCCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
172 173 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
173 174 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
174 175 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
175 176 6.455647 CATACATCCGTATGTTGTAGTCCAT 58.544 40.000 0.00 0.00 46.70 3.41
176 177 5.838529 CATACATCCGTATGTTGTAGTCCA 58.161 41.667 0.00 0.00 46.70 4.02
217 218 9.490663 CGTCCAGAGTAAAATGAATGAATTTAC 57.509 33.333 0.00 0.00 38.95 2.01
218 219 9.226606 ACGTCCAGAGTAAAATGAATGAATTTA 57.773 29.630 0.00 0.00 0.00 1.40
219 220 8.110860 ACGTCCAGAGTAAAATGAATGAATTT 57.889 30.769 0.00 0.00 0.00 1.82
220 221 7.687941 ACGTCCAGAGTAAAATGAATGAATT 57.312 32.000 0.00 0.00 0.00 2.17
221 222 8.041323 ACTACGTCCAGAGTAAAATGAATGAAT 58.959 33.333 0.00 0.00 0.00 2.57
222 223 7.383687 ACTACGTCCAGAGTAAAATGAATGAA 58.616 34.615 0.00 0.00 0.00 2.57
223 224 6.931838 ACTACGTCCAGAGTAAAATGAATGA 58.068 36.000 0.00 0.00 0.00 2.57
224 225 6.811665 TGACTACGTCCAGAGTAAAATGAATG 59.188 38.462 0.00 0.00 0.00 2.67
225 226 6.812160 GTGACTACGTCCAGAGTAAAATGAAT 59.188 38.462 0.00 0.00 0.00 2.57
226 227 6.154445 GTGACTACGTCCAGAGTAAAATGAA 58.846 40.000 0.00 0.00 0.00 2.57
227 228 5.336213 GGTGACTACGTCCAGAGTAAAATGA 60.336 44.000 0.00 0.00 0.00 2.57
228 229 4.863131 GGTGACTACGTCCAGAGTAAAATG 59.137 45.833 0.00 0.00 0.00 2.32
229 230 4.771054 AGGTGACTACGTCCAGAGTAAAAT 59.229 41.667 0.00 0.00 40.61 1.82
230 231 4.147321 AGGTGACTACGTCCAGAGTAAAA 58.853 43.478 0.00 0.00 40.61 1.52
231 232 3.759581 AGGTGACTACGTCCAGAGTAAA 58.240 45.455 0.00 0.00 40.61 2.01
232 233 3.430042 AGGTGACTACGTCCAGAGTAA 57.570 47.619 0.00 0.00 40.61 2.24
246 247 8.884726 GTCTTTTTAGAGATTCCAATAGGTGAC 58.115 37.037 0.00 0.00 35.89 3.67
247 248 8.826765 AGTCTTTTTAGAGATTCCAATAGGTGA 58.173 33.333 0.00 0.00 35.89 4.02
248 249 9.454859 AAGTCTTTTTAGAGATTCCAATAGGTG 57.545 33.333 0.00 0.00 35.89 4.00
266 267 9.908152 CCCTTCGTTTCAAAATATAAGTCTTTT 57.092 29.630 0.00 0.00 0.00 2.27
267 268 9.292195 TCCCTTCGTTTCAAAATATAAGTCTTT 57.708 29.630 0.00 0.00 0.00 2.52
268 269 8.857694 TCCCTTCGTTTCAAAATATAAGTCTT 57.142 30.769 0.00 0.00 0.00 3.01
269 270 8.101419 ACTCCCTTCGTTTCAAAATATAAGTCT 58.899 33.333 0.00 0.00 0.00 3.24
270 271 8.265165 ACTCCCTTCGTTTCAAAATATAAGTC 57.735 34.615 0.00 0.00 0.00 3.01
271 272 9.159364 GTACTCCCTTCGTTTCAAAATATAAGT 57.841 33.333 0.00 0.00 0.00 2.24
272 273 9.379791 AGTACTCCCTTCGTTTCAAAATATAAG 57.620 33.333 0.00 0.00 0.00 1.73
277 278 9.901172 AATATAGTACTCCCTTCGTTTCAAAAT 57.099 29.630 0.00 0.00 0.00 1.82
278 279 9.158233 CAATATAGTACTCCCTTCGTTTCAAAA 57.842 33.333 0.00 0.00 0.00 2.44
279 280 8.533657 TCAATATAGTACTCCCTTCGTTTCAAA 58.466 33.333 0.00 0.00 0.00 2.69
280 281 8.070034 TCAATATAGTACTCCCTTCGTTTCAA 57.930 34.615 0.00 0.00 0.00 2.69
281 282 7.649533 TCAATATAGTACTCCCTTCGTTTCA 57.350 36.000 0.00 0.00 0.00 2.69
282 283 7.599245 CCATCAATATAGTACTCCCTTCGTTTC 59.401 40.741 0.00 0.00 0.00 2.78
283 284 7.289317 TCCATCAATATAGTACTCCCTTCGTTT 59.711 37.037 0.00 0.00 0.00 3.60
284 285 6.781014 TCCATCAATATAGTACTCCCTTCGTT 59.219 38.462 0.00 0.00 0.00 3.85
285 286 6.312529 TCCATCAATATAGTACTCCCTTCGT 58.687 40.000 0.00 0.00 0.00 3.85
286 287 6.659668 TCTCCATCAATATAGTACTCCCTTCG 59.340 42.308 0.00 0.00 0.00 3.79
287 288 7.891183 TCTCTCCATCAATATAGTACTCCCTTC 59.109 40.741 0.00 0.00 0.00 3.46
288 289 7.770662 TCTCTCCATCAATATAGTACTCCCTT 58.229 38.462 0.00 0.00 0.00 3.95
289 290 7.019153 ACTCTCTCCATCAATATAGTACTCCCT 59.981 40.741 0.00 0.00 0.00 4.20
290 291 7.179269 ACTCTCTCCATCAATATAGTACTCCC 58.821 42.308 0.00 0.00 0.00 4.30
291 292 9.391006 CTACTCTCTCCATCAATATAGTACTCC 57.609 40.741 0.00 0.00 0.00 3.85
295 296 9.402320 GCATCTACTCTCTCCATCAATATAGTA 57.598 37.037 0.00 0.00 0.00 1.82
296 297 7.892771 TGCATCTACTCTCTCCATCAATATAGT 59.107 37.037 0.00 0.00 0.00 2.12
297 298 8.291191 TGCATCTACTCTCTCCATCAATATAG 57.709 38.462 0.00 0.00 0.00 1.31
303 304 5.221601 GGAAATGCATCTACTCTCTCCATCA 60.222 44.000 0.00 0.00 0.00 3.07
312 313 8.230486 CGGTAATTATTGGAAATGCATCTACTC 58.770 37.037 0.00 0.00 0.00 2.59
345 354 3.660865 GAAACTTTGGCGAGTCTCCTAA 58.339 45.455 0.00 0.00 0.00 2.69
352 361 3.497297 AAAAACGAAACTTTGGCGAGT 57.503 38.095 0.00 0.00 0.00 4.18
381 390 2.263540 GCGGAGGCGTGAAAGGTA 59.736 61.111 0.00 0.00 0.00 3.08
400 409 1.152963 ACCGCACCAGTTTCTGCTT 60.153 52.632 0.00 0.00 0.00 3.91
433 442 4.164843 AGAAAACTTGCTGGTGGAACTA 57.835 40.909 0.00 0.00 36.74 2.24
446 455 7.065443 AGACGCAAACAAAGTACTAGAAAACTT 59.935 33.333 0.00 0.30 37.54 2.66
447 456 6.537660 AGACGCAAACAAAGTACTAGAAAACT 59.462 34.615 0.00 0.00 0.00 2.66
448 457 6.712549 AGACGCAAACAAAGTACTAGAAAAC 58.287 36.000 0.00 0.00 0.00 2.43
449 458 6.913873 AGACGCAAACAAAGTACTAGAAAA 57.086 33.333 0.00 0.00 0.00 2.29
450 459 6.913873 AAGACGCAAACAAAGTACTAGAAA 57.086 33.333 0.00 0.00 0.00 2.52
453 462 7.164858 CGATTAAGACGCAAACAAAGTACTAG 58.835 38.462 0.00 0.00 0.00 2.57
455 464 5.912528 CGATTAAGACGCAAACAAAGTACT 58.087 37.500 0.00 0.00 0.00 2.73
565 597 2.623889 CTCGGTCCGAATATCCTCTTGT 59.376 50.000 16.23 0.00 34.74 3.16
567 599 1.614413 GCTCGGTCCGAATATCCTCTT 59.386 52.381 16.23 0.00 34.74 2.85
597 634 3.602513 CTTCCCTCTGCTGCAGCGT 62.603 63.158 32.11 0.00 45.83 5.07
668 708 3.439540 TTGGAAATCCTGGCGCGC 61.440 61.111 25.94 25.94 36.82 6.86
693 733 3.439129 GGGAATAAATAGCGTATGGGTGC 59.561 47.826 0.00 0.00 0.00 5.01
853 893 1.133915 TCTTCTTCCTTTGGTTGCGGT 60.134 47.619 0.00 0.00 0.00 5.68
866 906 7.805542 GGTGAGCTCTAACAAATTTTCTTCTTC 59.194 37.037 16.19 0.00 0.00 2.87
1038 1087 1.750930 CACGCCATAGAGCCCATCT 59.249 57.895 0.00 0.00 42.47 2.90
1050 1099 1.565156 GACGAACAATCTGCACGCCA 61.565 55.000 0.00 0.00 0.00 5.69
1054 1103 1.132640 GCCGACGAACAATCTGCAC 59.867 57.895 0.00 0.00 0.00 4.57
1056 1105 2.785258 GGCCGACGAACAATCTGC 59.215 61.111 0.00 0.00 0.00 4.26
1077 1126 2.281761 CCTTTGCTCGGTGCCTGT 60.282 61.111 0.00 0.00 42.00 4.00
1085 1134 2.477845 CAGCTTCGCCTTTGCTCG 59.522 61.111 0.00 0.00 34.51 5.03
1101 1150 2.431683 GTGAAGCTGGTCTGGGCA 59.568 61.111 0.00 0.00 0.00 5.36
1103 1152 1.903877 ATCGGTGAAGCTGGTCTGGG 61.904 60.000 0.00 0.00 0.00 4.45
1106 1155 0.108615 CGAATCGGTGAAGCTGGTCT 60.109 55.000 0.00 0.00 0.00 3.85
1213 1262 2.620115 CAGTCTGGTGTTGAGTGCATTT 59.380 45.455 0.00 0.00 0.00 2.32
1248 1314 2.283086 TCGTCTGCAGTTGTTACAAACG 59.717 45.455 14.67 12.68 35.13 3.60
1254 1320 2.469826 CACAGTCGTCTGCAGTTGTTA 58.530 47.619 14.67 0.00 44.77 2.41
1317 1383 0.659427 CGGAAGCTGCCATACATGTG 59.341 55.000 12.53 0.00 0.00 3.21
1342 1408 4.028490 TACCGGTTGCTGGGCAGG 62.028 66.667 15.04 0.00 40.61 4.85
1359 1425 4.561326 GCTTCAGTTGGCAAATATTGTGGT 60.561 41.667 0.00 0.00 0.00 4.16
1376 1447 1.671261 CCGTCAGACAAGAGGCTTCAG 60.671 57.143 0.41 0.00 0.00 3.02
1403 1474 1.814394 GCATGCTTGTCACCTGATCAA 59.186 47.619 11.37 0.00 0.00 2.57
1405 1476 0.737219 GGCATGCTTGTCACCTGATC 59.263 55.000 18.92 0.00 0.00 2.92
1424 1496 4.092675 ACAACATTTGCAAAAGTTTCACCG 59.907 37.500 25.57 17.65 28.44 4.94
1487 1559 3.056250 TGTCTCAGAAGATGTCTTGCCTC 60.056 47.826 0.00 0.00 36.11 4.70
1514 1586 8.295288 ACTCAGAAACAAATAGAGCAAAGAATG 58.705 33.333 0.00 0.00 0.00 2.67
1547 1619 3.484721 GCGGCACCGACTTTTCTTATTAC 60.485 47.826 14.43 0.00 42.83 1.89
1629 1701 0.035458 GGGAGGAATGATACAGGCCG 59.965 60.000 0.00 0.00 0.00 6.13
1731 1803 9.211485 CAAATTCTGATAATTGAACAGCCTTTT 57.789 29.630 0.00 0.00 0.00 2.27
1781 1854 5.652014 CCCTGGATAAACACTGCATAGAAAA 59.348 40.000 0.00 0.00 0.00 2.29
1810 1883 3.491766 AGTCCTGGGTTCTCATTCCTA 57.508 47.619 0.00 0.00 0.00 2.94
1935 2008 8.925161 TTGAAATGGTTTGTTTTAGACAGAAG 57.075 30.769 0.00 0.00 39.94 2.85
1982 2055 6.808704 AGTTTTCTTTCAACAAAGACTTGCTC 59.191 34.615 0.00 0.00 46.38 4.26
2009 2082 9.213799 GCCATTTAAACAGTTTGATTTATCCAA 57.786 29.630 8.93 0.00 0.00 3.53
2030 2103 0.539438 TGCGAAGGAAACCTGCCATT 60.539 50.000 0.00 0.00 32.13 3.16
2082 2160 3.932710 ACATCTTGTGCAGGTTATGTACG 59.067 43.478 0.00 0.00 46.57 3.67
2264 2342 8.517062 ACTCCTTCTGGATAAATTGAAATCAG 57.483 34.615 0.00 0.00 42.29 2.90
2273 2351 7.936301 GCTGAATCTAACTCCTTCTGGATAAAT 59.064 37.037 0.00 0.00 42.29 1.40
2327 2406 8.910944 TCTTCTATGTAACCTATTCTGTACACC 58.089 37.037 0.00 0.00 0.00 4.16
2351 2430 3.936564 GAACAATGCTCCTGTTCTCTCT 58.063 45.455 14.84 0.00 46.01 3.10
2357 2436 5.534207 TCAATTTGAACAATGCTCCTGTT 57.466 34.783 0.00 0.00 39.69 3.16
2358 2437 5.733620 ATCAATTTGAACAATGCTCCTGT 57.266 34.783 2.68 0.00 0.00 4.00
2359 2438 6.038356 GGTATCAATTTGAACAATGCTCCTG 58.962 40.000 2.68 0.00 0.00 3.86
2360 2439 5.716228 TGGTATCAATTTGAACAATGCTCCT 59.284 36.000 2.68 0.00 0.00 3.69
2380 2459 6.096987 AGAGATACGAAAGCATTCTTCTGGTA 59.903 38.462 0.00 0.00 33.17 3.25
2382 2461 5.355596 AGAGATACGAAAGCATTCTTCTGG 58.644 41.667 0.00 0.00 33.17 3.86
2390 2469 6.214191 TCTTTCTGAGAGATACGAAAGCAT 57.786 37.500 0.00 0.00 41.11 3.79
2443 2522 2.413765 GCAGAACTACATGCACAAGCTG 60.414 50.000 0.00 0.00 42.11 4.24
2474 2553 6.970043 TCGCAGTAATAATTAAACACCAATGC 59.030 34.615 0.00 0.00 0.00 3.56
2475 2554 8.394877 TCTCGCAGTAATAATTAAACACCAATG 58.605 33.333 0.00 0.00 0.00 2.82
2504 2583 2.044946 GTCATGACAGCCCACCCC 60.045 66.667 21.07 0.00 0.00 4.95
2507 2586 0.322975 AGAGTGTCATGACAGCCCAC 59.677 55.000 28.54 16.16 42.74 4.61
2525 2604 9.423061 CCACCTTAATTCATTTTTGTAGGAAAG 57.577 33.333 0.00 0.00 0.00 2.62
2548 2627 3.027974 AGCGTAAACTTCTCTGTCCAC 57.972 47.619 0.00 0.00 0.00 4.02
2714 2793 2.154462 CCAGTTTCCATCTTCGCTGTT 58.846 47.619 0.00 0.00 0.00 3.16
2715 2794 1.072331 ACCAGTTTCCATCTTCGCTGT 59.928 47.619 0.00 0.00 0.00 4.40
2758 2837 4.021544 TGCCACACACTTTCTTTTGACTTT 60.022 37.500 0.00 0.00 0.00 2.66
2871 2950 2.124570 CGAGGGAGCACATTGGGG 60.125 66.667 0.00 0.00 0.00 4.96
2872 2951 1.153289 CTCGAGGGAGCACATTGGG 60.153 63.158 3.91 0.00 32.61 4.12
2873 2952 0.036010 AACTCGAGGGAGCACATTGG 60.036 55.000 18.41 0.00 44.48 3.16
2876 2955 0.534412 CAGAACTCGAGGGAGCACAT 59.466 55.000 18.41 0.00 44.48 3.21
2877 2956 0.539669 TCAGAACTCGAGGGAGCACA 60.540 55.000 18.41 0.00 44.48 4.57
2964 3043 8.969260 ATAGCATGATCTCAACAAATTGTCTA 57.031 30.769 0.00 0.00 37.11 2.59
2966 3045 7.700505 TGATAGCATGATCTCAACAAATTGTC 58.299 34.615 0.00 0.00 37.11 3.18
2980 3059 3.819337 GACCAGCATGTTGATAGCATGAT 59.181 43.478 11.60 0.00 44.60 2.45
2989 3068 2.254546 AAACGAGACCAGCATGTTGA 57.745 45.000 11.60 0.00 0.00 3.18
3090 3169 0.742990 ATGTATGCGGGTGTTGGTCG 60.743 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.