Multiple sequence alignment - TraesCS2B01G427500

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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 TraesCS2B01G427500 chr2B 100.000 2570 0 0 1 2570 614826793 614829362 0.000000e+00 4747.0
1 TraesCS2B01G427500 chr2A 93.830 1329 61 11 519 1835 666318733 666320052 0.000000e+00 1980.0
2 TraesCS2B01G427500 chr2A 93.557 357 10 4 1830 2174 666320193 666320548 1.050000e-143 520.0
3 TraesCS2B01G427500 chr2A 87.841 403 45 3 2170 2570 666335216 666335616 1.080000e-128 470.0
4 TraesCS2B01G427500 chr2D 92.857 1232 47 17 474 1683 520743400 520742188 0.000000e+00 1749.0
5 TraesCS2B01G427500 chr2D 89.683 853 68 11 1732 2570 520741969 520741123 0.000000e+00 1070.0
6 TraesCS2B01G427500 chr2D 88.591 298 34 0 2273 2570 102819632 102819335 1.880000e-96 363.0
7 TraesCS2B01G427500 chr2D 87.059 255 20 8 1 242 520743925 520743671 2.520000e-70 276.0
8 TraesCS2B01G427500 chr5A 88.136 295 35 0 2273 2567 653095587 653095881 4.070000e-93 351.0
9 TraesCS2B01G427500 chr1B 87.584 298 37 0 2273 2570 192151400 192151103 1.890000e-91 346.0
10 TraesCS2B01G427500 chr1B 87.625 299 35 1 2272 2568 473435119 473435417 1.890000e-91 346.0
11 TraesCS2B01G427500 chr1D 88.014 292 34 1 2279 2570 405759496 405759206 6.810000e-91 344.0
12 TraesCS2B01G427500 chr7A 87.248 298 38 0 2273 2570 127878411 127878114 8.810000e-90 340.0
13 TraesCS2B01G427500 chr6D 87.248 298 38 0 2273 2570 388547974 388548271 8.810000e-90 340.0
14 TraesCS2B01G427500 chr7B 100.000 28 0 0 378 405 630784522 630784495 5.000000e-03 52.8


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 TraesCS2B01G427500 chr2B 614826793 614829362 2569 False 4747.000000 4747 100.000000 1 2570 1 chr2B.!!$F1 2569
1 TraesCS2B01G427500 chr2A 666318733 666320548 1815 False 1250.000000 1980 93.693500 519 2174 2 chr2A.!!$F2 1655
2 TraesCS2B01G427500 chr2D 520741123 520743925 2802 True 1031.666667 1749 89.866333 1 2570 3 chr2D.!!$R2 2569

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
437 451 0.321653 CAGCTTTAGGACGGCCAAGT 60.322 55.0 11.69 0.0 36.29 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2436 0.971386 AAGTCGACAATGGTACCGGT 59.029 50.0 19.5 13.98 0.0 5.28 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
89 90 1.912731 TGGTTGGAGCAAGTAGGCATA 59.087 47.619 0.00 0.00 35.83 3.14
97 109 4.443457 GGAGCAAGTAGGCATAGTCATCAA 60.443 45.833 0.00 0.00 35.83 2.57
117 129 9.559732 TCATCAACATATTGTATTACAGGGAAG 57.440 33.333 0.00 0.00 37.11 3.46
119 131 9.920946 ATCAACATATTGTATTACAGGGAAGTT 57.079 29.630 0.00 0.00 37.11 2.66
144 156 2.191400 CAAGAGAGGAAGGTGATGGGA 58.809 52.381 0.00 0.00 0.00 4.37
154 167 2.278245 AGGTGATGGGACTTGGATCAA 58.722 47.619 0.00 0.00 0.00 2.57
174 188 3.036452 ACCCATTTGCCATAGCTCATT 57.964 42.857 0.00 0.00 40.80 2.57
182 196 6.534475 TTTGCCATAGCTCATTGAGAATTT 57.466 33.333 17.87 2.32 40.80 1.82
202 216 9.880157 AGAATTTATTGCAATAAATCAGTTGCT 57.120 25.926 38.52 27.95 45.81 3.91
213 227 5.772825 AAATCAGTTGCTAGCACAAAGAA 57.227 34.783 19.17 0.00 0.00 2.52
216 230 5.173774 TCAGTTGCTAGCACAAAGAAAAG 57.826 39.130 19.17 0.34 0.00 2.27
228 242 3.954258 ACAAAGAAAAGTGGGAAGAGTGG 59.046 43.478 0.00 0.00 0.00 4.00
229 243 4.207165 CAAAGAAAAGTGGGAAGAGTGGA 58.793 43.478 0.00 0.00 0.00 4.02
236 250 1.760029 GTGGGAAGAGTGGATCTCCTC 59.240 57.143 0.00 0.00 43.71 3.71
242 256 1.562008 AGAGTGGATCTCCTCGTCTGA 59.438 52.381 0.00 0.00 43.71 3.27
243 257 1.673920 GAGTGGATCTCCTCGTCTGAC 59.326 57.143 0.00 0.00 37.22 3.51
244 258 1.004862 AGTGGATCTCCTCGTCTGACA 59.995 52.381 8.73 0.00 36.82 3.58
245 259 1.133407 GTGGATCTCCTCGTCTGACAC 59.867 57.143 8.73 0.00 36.82 3.67
246 260 0.741915 GGATCTCCTCGTCTGACACC 59.258 60.000 8.73 0.00 0.00 4.16
247 261 0.741915 GATCTCCTCGTCTGACACCC 59.258 60.000 8.73 0.00 0.00 4.61
248 262 0.684805 ATCTCCTCGTCTGACACCCC 60.685 60.000 8.73 0.00 0.00 4.95
249 263 2.283676 TCCTCGTCTGACACCCCC 60.284 66.667 8.73 0.00 0.00 5.40
250 264 2.283966 CCTCGTCTGACACCCCCT 60.284 66.667 8.73 0.00 0.00 4.79
251 265 1.913762 CCTCGTCTGACACCCCCTT 60.914 63.158 8.73 0.00 0.00 3.95
252 266 1.592223 CTCGTCTGACACCCCCTTC 59.408 63.158 8.73 0.00 0.00 3.46
253 267 0.900647 CTCGTCTGACACCCCCTTCT 60.901 60.000 8.73 0.00 0.00 2.85
254 268 0.406750 TCGTCTGACACCCCCTTCTA 59.593 55.000 8.73 0.00 0.00 2.10
255 269 0.531200 CGTCTGACACCCCCTTCTAC 59.469 60.000 8.73 0.00 0.00 2.59
256 270 1.640917 GTCTGACACCCCCTTCTACA 58.359 55.000 2.24 0.00 0.00 2.74
257 271 2.188817 GTCTGACACCCCCTTCTACAT 58.811 52.381 2.24 0.00 0.00 2.29
258 272 3.371965 GTCTGACACCCCCTTCTACATA 58.628 50.000 2.24 0.00 0.00 2.29
259 273 3.773119 GTCTGACACCCCCTTCTACATAA 59.227 47.826 2.24 0.00 0.00 1.90
260 274 4.030913 TCTGACACCCCCTTCTACATAAG 58.969 47.826 0.00 0.00 0.00 1.73
261 275 4.030913 CTGACACCCCCTTCTACATAAGA 58.969 47.826 0.00 0.00 0.00 2.10
262 276 4.431378 TGACACCCCCTTCTACATAAGAA 58.569 43.478 0.00 0.00 42.07 2.52
263 277 5.036916 TGACACCCCCTTCTACATAAGAAT 58.963 41.667 0.00 0.00 43.32 2.40
264 278 5.491078 TGACACCCCCTTCTACATAAGAATT 59.509 40.000 0.00 0.00 43.32 2.17
265 279 5.755849 ACACCCCCTTCTACATAAGAATTG 58.244 41.667 0.00 0.00 43.32 2.32
266 280 5.491078 ACACCCCCTTCTACATAAGAATTGA 59.509 40.000 0.00 0.00 43.32 2.57
267 281 6.160459 ACACCCCCTTCTACATAAGAATTGAT 59.840 38.462 0.00 0.00 43.32 2.57
268 282 7.062957 CACCCCCTTCTACATAAGAATTGATT 58.937 38.462 0.00 0.00 43.32 2.57
269 283 7.013655 CACCCCCTTCTACATAAGAATTGATTG 59.986 40.741 0.00 0.00 43.32 2.67
270 284 6.015940 CCCCCTTCTACATAAGAATTGATTGC 60.016 42.308 0.00 0.00 43.32 3.56
271 285 6.774656 CCCCTTCTACATAAGAATTGATTGCT 59.225 38.462 0.00 0.00 43.32 3.91
272 286 7.939039 CCCCTTCTACATAAGAATTGATTGCTA 59.061 37.037 0.00 0.00 43.32 3.49
277 291 6.630444 ACATAAGAATTGATTGCTAGGCAG 57.370 37.500 0.00 0.00 40.61 4.85
284 298 2.923121 TGATTGCTAGGCAGACCATTC 58.077 47.619 0.00 0.00 40.61 2.67
288 302 1.908619 TGCTAGGCAGACCATTCAGAA 59.091 47.619 0.00 0.00 39.06 3.02
297 311 4.701765 CAGACCATTCAGAAGGACATAGG 58.298 47.826 0.00 0.00 0.00 2.57
305 319 5.241403 TCAGAAGGACATAGGAAAAAGCA 57.759 39.130 0.00 0.00 0.00 3.91
333 347 4.677673 AAAATCATTTGCATCTAGGCCC 57.322 40.909 0.00 0.00 0.00 5.80
335 349 2.824689 TCATTTGCATCTAGGCCCAA 57.175 45.000 0.00 0.00 0.00 4.12
336 350 3.098774 TCATTTGCATCTAGGCCCAAA 57.901 42.857 0.00 1.46 0.00 3.28
337 351 3.439154 TCATTTGCATCTAGGCCCAAAA 58.561 40.909 0.00 0.00 31.80 2.44
338 352 4.032310 TCATTTGCATCTAGGCCCAAAAT 58.968 39.130 0.00 0.00 31.80 1.82
339 353 4.099881 TCATTTGCATCTAGGCCCAAAATC 59.900 41.667 0.00 0.00 31.80 2.17
340 354 3.386932 TTGCATCTAGGCCCAAAATCT 57.613 42.857 0.00 0.00 0.00 2.40
341 355 3.386932 TGCATCTAGGCCCAAAATCTT 57.613 42.857 0.00 0.00 0.00 2.40
342 356 4.518278 TGCATCTAGGCCCAAAATCTTA 57.482 40.909 0.00 0.00 0.00 2.10
343 357 5.065613 TGCATCTAGGCCCAAAATCTTAT 57.934 39.130 0.00 0.00 0.00 1.73
344 358 4.828939 TGCATCTAGGCCCAAAATCTTATG 59.171 41.667 0.00 0.00 0.00 1.90
345 359 4.829492 GCATCTAGGCCCAAAATCTTATGT 59.171 41.667 0.00 0.00 0.00 2.29
346 360 5.278660 GCATCTAGGCCCAAAATCTTATGTG 60.279 44.000 0.00 0.00 0.00 3.21
347 361 4.207165 TCTAGGCCCAAAATCTTATGTGC 58.793 43.478 0.00 0.00 0.00 4.57
348 362 3.105959 AGGCCCAAAATCTTATGTGCT 57.894 42.857 0.00 0.00 0.00 4.40
349 363 4.249638 AGGCCCAAAATCTTATGTGCTA 57.750 40.909 0.00 0.00 0.00 3.49
350 364 4.210331 AGGCCCAAAATCTTATGTGCTAG 58.790 43.478 0.00 0.00 0.00 3.42
351 365 3.243535 GGCCCAAAATCTTATGTGCTAGC 60.244 47.826 8.10 8.10 0.00 3.42
352 366 3.381272 GCCCAAAATCTTATGTGCTAGCA 59.619 43.478 14.93 14.93 0.00 3.49
353 367 4.498682 GCCCAAAATCTTATGTGCTAGCAG 60.499 45.833 20.03 6.07 0.00 4.24
354 368 4.883585 CCCAAAATCTTATGTGCTAGCAGA 59.116 41.667 20.03 18.88 0.00 4.26
355 369 5.533903 CCCAAAATCTTATGTGCTAGCAGAT 59.466 40.000 28.09 28.09 34.26 2.90
356 370 6.040166 CCCAAAATCTTATGTGCTAGCAGATT 59.960 38.462 29.85 23.51 32.10 2.40
375 389 5.755375 CAGATTTTGCGATTAGGAGCTCTTA 59.245 40.000 14.64 7.72 0.00 2.10
390 404 8.045176 AGGAGCTCTTAAATTGTGTTATGTTC 57.955 34.615 14.64 0.00 0.00 3.18
394 408 9.846248 AGCTCTTAAATTGTGTTATGTTCAATC 57.154 29.630 0.00 0.00 32.39 2.67
431 445 3.575965 AAAAATGCAGCTTTAGGACGG 57.424 42.857 0.00 0.00 0.00 4.79
437 451 0.321653 CAGCTTTAGGACGGCCAAGT 60.322 55.000 11.69 0.00 36.29 3.16
438 452 0.400594 AGCTTTAGGACGGCCAAGTT 59.599 50.000 11.69 0.00 36.29 2.66
459 473 4.437682 TTTTCTCCAGATTGGTGACACT 57.562 40.909 5.39 0.00 39.48 3.55
464 478 1.072173 CCAGATTGGTGACACTGGTGA 59.928 52.381 5.39 0.00 45.17 4.02
475 489 7.518028 TGGTGACACTGGTGAATGTATTCATG 61.518 42.308 10.20 7.30 41.62 3.07
492 598 9.394767 TGTATTCATGTGCACAAGATTAAGTAT 57.605 29.630 25.72 15.60 0.00 2.12
501 607 7.485913 GTGCACAAGATTAAGTATGATGGTTTG 59.514 37.037 13.17 0.00 0.00 2.93
504 610 8.028354 CACAAGATTAAGTATGATGGTTTGCAA 58.972 33.333 0.00 0.00 0.00 4.08
578 684 7.588888 ATTGCACCTCAAAACTTGCACAAGT 62.589 40.000 10.20 10.20 44.44 3.16
611 717 5.357314 CCATTTGCCAATTGCCATTTATCAA 59.643 36.000 0.00 0.00 40.16 2.57
637 743 4.202050 GCTCCATCTGTCGCCAAATTTATT 60.202 41.667 0.00 0.00 0.00 1.40
646 754 6.638610 TGTCGCCAAATTTATTGATCCAAAT 58.361 32.000 0.00 0.00 0.00 2.32
662 770 4.479158 TCCAAATGGCAAGGTCTTAAAGT 58.521 39.130 0.00 0.00 34.44 2.66
714 822 1.334689 GCAACTGTACGGCCAGAAAAC 60.335 52.381 2.24 0.00 36.30 2.43
731 839 3.394588 CGCATCACGCCACGTAAT 58.605 55.556 0.00 0.00 38.32 1.89
859 968 1.949847 AAGAGCGCTGGCACTACGAT 61.950 55.000 18.48 0.00 39.28 3.73
974 1088 3.657350 CACGACCCCACCCCCAAT 61.657 66.667 0.00 0.00 0.00 3.16
975 1089 3.335729 ACGACCCCACCCCCAATC 61.336 66.667 0.00 0.00 0.00 2.67
976 1090 4.123545 CGACCCCACCCCCAATCC 62.124 72.222 0.00 0.00 0.00 3.01
977 1091 2.617215 GACCCCACCCCCAATCCT 60.617 66.667 0.00 0.00 0.00 3.24
1017 1132 1.003839 CAGCTACCAAGTCGGCCAA 60.004 57.895 2.24 0.00 39.03 4.52
1018 1133 0.392998 CAGCTACCAAGTCGGCCAAT 60.393 55.000 2.24 0.00 39.03 3.16
1035 1150 2.632028 CCAATCCAACCAACCATCAACA 59.368 45.455 0.00 0.00 0.00 3.33
1068 1183 2.443016 CACTCCTCCTCCCTCCCG 60.443 72.222 0.00 0.00 0.00 5.14
1085 1200 0.395036 CCGCTTCTCTCTCTCTCCCA 60.395 60.000 0.00 0.00 0.00 4.37
1360 1482 2.049156 TTCGACGACAGCAGCCTG 60.049 61.111 0.00 0.00 44.80 4.85
1490 1618 1.272704 GGATCCCTTTTGCCACTTCCT 60.273 52.381 0.00 0.00 0.00 3.36
1622 1754 3.117794 TCTTCGCGGGTGTAAATATTCG 58.882 45.455 6.13 0.00 0.00 3.34
1655 1788 5.804979 TCTTCCAAAAGAAAAGAAAACAGCG 59.195 36.000 0.00 0.00 38.58 5.18
1659 1792 2.067365 AGAAAAGAAAACAGCGGGGT 57.933 45.000 0.00 0.00 0.00 4.95
1662 1795 2.882927 AAAGAAAACAGCGGGGTTTC 57.117 45.000 12.34 12.34 39.93 2.78
1689 1822 1.117994 CTGCATAGGAGCCAGTCAGA 58.882 55.000 0.00 0.00 0.00 3.27
1861 2331 4.321745 GCACGTCAAATAAGTTGCTGAATG 59.678 41.667 0.00 0.00 37.13 2.67
1894 2376 3.243002 GGCTTGTTGATATCTTGCAGAGC 60.243 47.826 3.98 10.52 0.00 4.09
1944 2436 1.281419 TGCTCCGTGGGATCCTTTTA 58.719 50.000 12.58 0.00 0.00 1.52
2060 2552 4.798882 ACGGATATGCCTTTTTATTGGGA 58.201 39.130 0.00 0.00 0.00 4.37
2133 2625 6.092670 CGGAAATCTATGGATAACGCATCAAT 59.907 38.462 0.00 0.00 35.11 2.57
2157 2649 4.764823 ACGCAACTTGGGAGAAAATATCAA 59.235 37.500 12.50 0.00 34.12 2.57
2178 2670 3.951563 AAACCAGGCCATTAGAGCATA 57.048 42.857 5.01 0.00 0.00 3.14
2181 2673 5.786121 AACCAGGCCATTAGAGCATATAT 57.214 39.130 5.01 0.00 0.00 0.86
2201 2693 0.725117 GCCCGTACTTGACAAATCCG 59.275 55.000 0.00 0.00 0.00 4.18
2202 2694 1.673626 GCCCGTACTTGACAAATCCGA 60.674 52.381 0.00 0.00 0.00 4.55
2216 2710 4.744316 CCGACCTTATACGGCCAC 57.256 61.111 2.24 0.00 42.55 5.01
2219 2713 1.068585 GACCTTATACGGCCACGGG 59.931 63.158 2.24 0.00 46.48 5.28
2256 2750 2.478033 CGGACGGCCCCTTATTTGC 61.478 63.158 0.00 0.00 0.00 3.68
2262 2756 2.837758 CCCCTTATTTGCCCCGCC 60.838 66.667 0.00 0.00 0.00 6.13
2268 2762 1.169661 TTATTTGCCCCGCCGCATAG 61.170 55.000 0.00 0.00 38.87 2.23
2302 2796 4.448537 TTTGTTTCTGGAATTATGCCGG 57.551 40.909 0.00 0.00 0.00 6.13
2340 2834 8.877864 ATACAACTATTGTTCTCATCCCAAAA 57.122 30.769 0.00 0.00 42.22 2.44
2377 2871 4.981806 TCAATTAAAGATTTCAGGCCGG 57.018 40.909 0.00 0.00 0.00 6.13
2380 2874 3.426787 TTAAAGATTTCAGGCCGGTCA 57.573 42.857 9.71 0.00 0.00 4.02
2381 2875 1.826385 AAAGATTTCAGGCCGGTCAG 58.174 50.000 9.71 0.00 0.00 3.51
2390 2884 2.485795 GGCCGGTCAGTTTGTGCAA 61.486 57.895 0.00 0.00 0.00 4.08
2391 2885 1.299089 GCCGGTCAGTTTGTGCAAC 60.299 57.895 1.90 0.00 35.32 4.17
2414 2908 9.529325 CAACGTTATCTACAAGATTATCTCCAA 57.471 33.333 0.00 0.00 36.20 3.53
2429 2923 8.918202 ATTATCTCCAAGTGTCTTGTAAACAA 57.082 30.769 8.37 0.00 0.00 2.83
2430 2924 8.740123 TTATCTCCAAGTGTCTTGTAAACAAA 57.260 30.769 8.37 0.00 35.15 2.83
2434 2928 5.708230 TCCAAGTGTCTTGTAAACAAACTGT 59.292 36.000 8.37 0.00 35.15 3.55
2445 2939 5.583061 TGTAAACAAACTGTGACCACTACTG 59.417 40.000 1.62 0.00 0.00 2.74
2483 2977 4.094442 CCCTACTCAAAGTGCGTTTATTCC 59.906 45.833 0.00 0.00 0.00 3.01
2486 2980 2.739913 CTCAAAGTGCGTTTATTCCGGA 59.260 45.455 0.00 0.00 0.00 5.14
2515 3009 9.935241 GGTTAATCTCTGATAATGCTCTCATAA 57.065 33.333 0.00 0.00 31.46 1.90
2532 3026 7.970061 GCTCTCATAACTTTTGAATGTATGCAA 59.030 33.333 0.00 0.00 0.00 4.08
2565 3059 6.200878 ACACTCAAAGATTTAAGAGGGGAA 57.799 37.500 0.00 0.00 35.86 3.97
2566 3060 6.794534 ACACTCAAAGATTTAAGAGGGGAAT 58.205 36.000 0.00 0.00 35.86 3.01
2567 3061 7.928873 ACACTCAAAGATTTAAGAGGGGAATA 58.071 34.615 0.00 0.00 35.86 1.75
2569 3063 9.413734 CACTCAAAGATTTAAGAGGGGAATATT 57.586 33.333 0.00 0.00 32.52 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.477253 ACACTACTCTGAGAGTCAAGTATGA 58.523 40.000 19.83 0.00 42.40 2.15
61 62 3.500343 ACTTGCTCCAACCAGCTAAATT 58.500 40.909 0.00 0.00 40.39 1.82
89 90 8.713971 TCCCTGTAATACAATATGTTGATGACT 58.286 33.333 9.40 0.00 38.71 3.41
97 109 7.060421 CCCAACTTCCCTGTAATACAATATGT 58.940 38.462 0.00 0.00 0.00 2.29
109 121 1.421646 CTCTTGTCCCAACTTCCCTGT 59.578 52.381 0.00 0.00 0.00 4.00
112 124 1.003696 CCTCTCTTGTCCCAACTTCCC 59.996 57.143 0.00 0.00 0.00 3.97
117 129 1.700186 ACCTTCCTCTCTTGTCCCAAC 59.300 52.381 0.00 0.00 0.00 3.77
119 131 1.132849 TCACCTTCCTCTCTTGTCCCA 60.133 52.381 0.00 0.00 0.00 4.37
144 156 1.901833 GGCAAATGGGTTGATCCAAGT 59.098 47.619 0.00 0.00 39.87 3.16
154 167 2.696707 CAATGAGCTATGGCAAATGGGT 59.303 45.455 3.10 0.00 41.70 4.51
198 212 3.068024 CCCACTTTTCTTTGTGCTAGCAA 59.932 43.478 21.29 7.26 33.26 3.91
202 216 4.787551 TCTTCCCACTTTTCTTTGTGCTA 58.212 39.130 0.00 0.00 33.26 3.49
205 219 4.202050 CCACTCTTCCCACTTTTCTTTGTG 60.202 45.833 0.00 0.00 0.00 3.33
207 221 4.207165 TCCACTCTTCCCACTTTTCTTTG 58.793 43.478 0.00 0.00 0.00 2.77
213 227 2.573915 GGAGATCCACTCTTCCCACTTT 59.426 50.000 0.00 0.00 44.37 2.66
216 230 1.760029 GAGGAGATCCACTCTTCCCAC 59.240 57.143 0.92 0.00 43.18 4.61
228 242 0.741915 GGGTGTCAGACGAGGAGATC 59.258 60.000 0.00 0.00 0.00 2.75
229 243 0.684805 GGGGTGTCAGACGAGGAGAT 60.685 60.000 0.00 0.00 0.00 2.75
236 250 0.531200 GTAGAAGGGGGTGTCAGACG 59.469 60.000 0.00 0.00 0.00 4.18
242 256 5.491078 TCAATTCTTATGTAGAAGGGGGTGT 59.509 40.000 0.00 0.00 45.69 4.16
243 257 6.001449 TCAATTCTTATGTAGAAGGGGGTG 57.999 41.667 0.00 0.00 45.69 4.61
244 258 6.848562 ATCAATTCTTATGTAGAAGGGGGT 57.151 37.500 0.00 0.00 45.69 4.95
245 259 6.015940 GCAATCAATTCTTATGTAGAAGGGGG 60.016 42.308 0.00 0.00 45.69 5.40
246 260 6.774656 AGCAATCAATTCTTATGTAGAAGGGG 59.225 38.462 0.00 0.00 45.69 4.79
247 261 7.814264 AGCAATCAATTCTTATGTAGAAGGG 57.186 36.000 0.00 0.00 45.69 3.95
248 262 8.997323 CCTAGCAATCAATTCTTATGTAGAAGG 58.003 37.037 0.00 0.00 45.69 3.46
249 263 8.502387 GCCTAGCAATCAATTCTTATGTAGAAG 58.498 37.037 0.00 0.00 45.69 2.85
250 264 7.992608 TGCCTAGCAATCAATTCTTATGTAGAA 59.007 33.333 0.00 0.00 40.52 2.10
251 265 7.508687 TGCCTAGCAATCAATTCTTATGTAGA 58.491 34.615 0.00 0.00 34.76 2.59
252 266 7.658982 TCTGCCTAGCAATCAATTCTTATGTAG 59.341 37.037 0.00 0.00 38.41 2.74
253 267 7.442364 GTCTGCCTAGCAATCAATTCTTATGTA 59.558 37.037 0.00 0.00 38.41 2.29
254 268 6.261826 GTCTGCCTAGCAATCAATTCTTATGT 59.738 38.462 0.00 0.00 38.41 2.29
255 269 6.293845 GGTCTGCCTAGCAATCAATTCTTATG 60.294 42.308 0.00 0.00 38.41 1.90
256 270 5.767168 GGTCTGCCTAGCAATCAATTCTTAT 59.233 40.000 0.00 0.00 38.41 1.73
257 271 5.126067 GGTCTGCCTAGCAATCAATTCTTA 58.874 41.667 0.00 0.00 38.41 2.10
258 272 3.950395 GGTCTGCCTAGCAATCAATTCTT 59.050 43.478 0.00 0.00 38.41 2.52
259 273 3.054139 TGGTCTGCCTAGCAATCAATTCT 60.054 43.478 0.00 0.00 38.41 2.40
260 274 3.282021 TGGTCTGCCTAGCAATCAATTC 58.718 45.455 0.00 0.00 38.41 2.17
261 275 3.370840 TGGTCTGCCTAGCAATCAATT 57.629 42.857 0.00 0.00 38.41 2.32
262 276 3.589951 ATGGTCTGCCTAGCAATCAAT 57.410 42.857 0.00 0.00 38.41 2.57
263 277 3.282021 GAATGGTCTGCCTAGCAATCAA 58.718 45.455 0.00 0.00 38.41 2.57
264 278 2.239402 TGAATGGTCTGCCTAGCAATCA 59.761 45.455 2.27 2.27 38.41 2.57
265 279 2.877168 CTGAATGGTCTGCCTAGCAATC 59.123 50.000 0.00 0.00 38.41 2.67
266 280 2.507058 TCTGAATGGTCTGCCTAGCAAT 59.493 45.455 0.00 0.00 38.41 3.56
267 281 1.908619 TCTGAATGGTCTGCCTAGCAA 59.091 47.619 0.00 0.00 38.41 3.91
268 282 1.571955 TCTGAATGGTCTGCCTAGCA 58.428 50.000 0.00 0.00 36.92 3.49
269 283 2.559440 CTTCTGAATGGTCTGCCTAGC 58.441 52.381 0.00 0.00 35.27 3.42
270 284 2.768527 TCCTTCTGAATGGTCTGCCTAG 59.231 50.000 0.00 0.00 35.27 3.02
271 285 2.501723 GTCCTTCTGAATGGTCTGCCTA 59.498 50.000 0.00 0.00 35.27 3.93
272 286 1.280421 GTCCTTCTGAATGGTCTGCCT 59.720 52.381 0.00 0.00 35.27 4.75
277 291 5.359194 TTCCTATGTCCTTCTGAATGGTC 57.641 43.478 0.00 0.00 0.00 4.02
284 298 5.248640 TCTGCTTTTTCCTATGTCCTTCTG 58.751 41.667 0.00 0.00 0.00 3.02
288 302 3.846588 TCCTCTGCTTTTTCCTATGTCCT 59.153 43.478 0.00 0.00 0.00 3.85
351 365 4.125703 AGAGCTCCTAATCGCAAAATCTG 58.874 43.478 10.93 0.00 0.00 2.90
352 366 4.414337 AGAGCTCCTAATCGCAAAATCT 57.586 40.909 10.93 0.00 0.00 2.40
353 367 6.604735 TTAAGAGCTCCTAATCGCAAAATC 57.395 37.500 10.93 0.00 0.00 2.17
354 368 7.573968 ATTTAAGAGCTCCTAATCGCAAAAT 57.426 32.000 10.93 0.00 0.00 1.82
355 369 7.094377 ACAATTTAAGAGCTCCTAATCGCAAAA 60.094 33.333 10.93 0.00 0.00 2.44
356 370 6.374333 ACAATTTAAGAGCTCCTAATCGCAAA 59.626 34.615 10.93 0.00 0.00 3.68
368 382 9.846248 GATTGAACATAACACAATTTAAGAGCT 57.154 29.630 0.00 0.00 34.94 4.09
411 425 2.352715 GCCGTCCTAAAGCTGCATTTTT 60.353 45.455 1.02 0.00 0.00 1.94
412 426 1.202348 GCCGTCCTAAAGCTGCATTTT 59.798 47.619 1.02 0.00 0.00 1.82
417 431 1.648467 CTTGGCCGTCCTAAAGCTGC 61.648 60.000 0.00 0.00 0.00 5.25
429 443 1.604604 TCTGGAGAAAAACTTGGCCG 58.395 50.000 0.00 0.00 0.00 6.13
430 444 3.306294 CCAATCTGGAGAAAAACTTGGCC 60.306 47.826 0.00 0.00 40.96 5.36
431 445 3.321968 ACCAATCTGGAGAAAAACTTGGC 59.678 43.478 0.00 0.00 40.96 4.52
437 451 4.580167 CAGTGTCACCAATCTGGAGAAAAA 59.420 41.667 0.00 0.00 40.96 1.94
438 452 4.136796 CAGTGTCACCAATCTGGAGAAAA 58.863 43.478 0.00 0.00 40.96 2.29
464 478 8.742777 ACTTAATCTTGTGCACATGAATACATT 58.257 29.630 31.63 23.88 34.39 2.71
475 489 6.683974 ACCATCATACTTAATCTTGTGCAC 57.316 37.500 10.75 10.75 0.00 4.57
504 610 2.028203 ACAAAGTTGCTTGCAAACAGGT 60.028 40.909 9.75 4.26 0.00 4.00
578 684 4.274459 GCAATTGGCAAATGGTTTGTACAA 59.726 37.500 16.49 3.59 42.56 2.41
611 717 3.474570 GGCGACAGATGGAGCCCT 61.475 66.667 8.95 0.00 43.54 5.19
637 743 2.905415 AGACCTTGCCATTTGGATCA 57.095 45.000 0.00 0.00 37.39 2.92
646 754 1.777878 TGGGACTTTAAGACCTTGCCA 59.222 47.619 12.61 1.83 30.67 4.92
662 770 1.609501 ACTGCTAGCCGACTTGGGA 60.610 57.895 13.29 0.00 38.63 4.37
698 806 1.225376 TGCGTTTTCTGGCCGTACAG 61.225 55.000 0.00 0.00 39.84 2.74
731 839 8.573035 GGTCAGTTTCTGTTTGGATTTAATGTA 58.427 33.333 0.00 0.00 32.61 2.29
754 863 5.935789 TGTGCAAACTTACTGTAATAGGGTC 59.064 40.000 0.00 0.00 0.00 4.46
859 968 1.068895 CTTGCAGTTTGGCACATTCCA 59.931 47.619 0.00 0.00 44.86 3.53
919 1033 3.009115 CGATGGGTGGGAGGTGGT 61.009 66.667 0.00 0.00 0.00 4.16
1017 1132 2.627699 GTGTGTTGATGGTTGGTTGGAT 59.372 45.455 0.00 0.00 0.00 3.41
1018 1133 2.028130 GTGTGTTGATGGTTGGTTGGA 58.972 47.619 0.00 0.00 0.00 3.53
1035 1150 1.070445 GTGCTGGAGTGAGCTGTGT 59.930 57.895 0.00 0.00 39.90 3.72
1068 1183 2.024414 GAGTGGGAGAGAGAGAGAAGC 58.976 57.143 0.00 0.00 0.00 3.86
1085 1200 3.753434 CTCGCCGACCAGCAGAGT 61.753 66.667 0.00 0.00 32.45 3.24
1147 1269 1.293683 ACTCCTCCTCCTCCTCCTCC 61.294 65.000 0.00 0.00 0.00 4.30
1148 1270 0.106217 CACTCCTCCTCCTCCTCCTC 60.106 65.000 0.00 0.00 0.00 3.71
1149 1271 2.015081 CACTCCTCCTCCTCCTCCT 58.985 63.158 0.00 0.00 0.00 3.69
1241 1363 3.431725 GAAAAGGTGCCGGAGCCG 61.432 66.667 5.05 1.06 38.69 5.52
1497 1625 1.898574 ACTCAAAGGGGCGCACAAG 60.899 57.895 13.89 2.58 0.00 3.16
1596 1727 4.776795 ATTTACACCCGCGAAGAAAAAT 57.223 36.364 8.23 5.27 0.00 1.82
1602 1733 2.861935 ACGAATATTTACACCCGCGAAG 59.138 45.455 8.23 0.00 0.00 3.79
1622 1754 4.712122 TTCTTTTGGAAGAACACCACAC 57.288 40.909 0.00 0.00 44.73 3.82
1655 1788 1.909700 TGCAGTTCATCAGAAACCCC 58.090 50.000 0.00 0.00 35.08 4.95
1659 1792 4.194640 GCTCCTATGCAGTTCATCAGAAA 58.805 43.478 0.00 0.00 36.63 2.52
1662 1795 2.158856 TGGCTCCTATGCAGTTCATCAG 60.159 50.000 0.00 0.00 36.63 2.90
1689 1822 4.910195 TCTGATAACCAAACAGACATGCT 58.090 39.130 0.00 0.00 36.04 3.79
1705 1838 6.472887 AGGAACTTGTTCCGAATTTCTGATA 58.527 36.000 22.18 0.00 45.64 2.15
1738 2062 3.126858 TGCACATTTGGAGCGTAGAAATC 59.873 43.478 0.00 0.00 0.00 2.17
1861 2331 7.593825 AGATATCAACAAGCCAACAAAGTAAC 58.406 34.615 5.32 0.00 0.00 2.50
1894 2376 3.738982 TCATAATAATGCCCAGACACGG 58.261 45.455 0.00 0.00 32.76 4.94
1914 2396 1.732259 CCACGGAGCAATACACTGTTC 59.268 52.381 0.00 0.00 0.00 3.18
1944 2436 0.971386 AAGTCGACAATGGTACCGGT 59.029 50.000 19.50 13.98 0.00 5.28
2133 2625 5.492895 TGATATTTTCTCCCAAGTTGCGTA 58.507 37.500 0.00 0.00 0.00 4.42
2157 2649 2.603075 TGCTCTAATGGCCTGGTTTT 57.397 45.000 3.32 0.00 0.00 2.43
2178 2670 4.134563 GGATTTGTCAAGTACGGGCATAT 58.865 43.478 0.00 0.00 0.00 1.78
2181 2673 1.816074 GGATTTGTCAAGTACGGGCA 58.184 50.000 0.00 0.00 0.00 5.36
2183 2675 1.997606 GTCGGATTTGTCAAGTACGGG 59.002 52.381 12.25 0.00 0.00 5.28
2187 2679 6.267817 CGTATAAGGTCGGATTTGTCAAGTA 58.732 40.000 0.00 0.00 0.00 2.24
2201 2693 1.068585 CCCGTGGCCGTATAAGGTC 59.931 63.158 1.90 1.90 36.18 3.85
2202 2694 3.097921 GCCCGTGGCCGTATAAGGT 62.098 63.158 6.57 0.00 44.06 3.50
2215 2709 4.388499 GTCCGTGGACATGCCCGT 62.388 66.667 14.10 0.00 44.02 5.28
2262 2756 2.704725 AAAACTGTTGTGGCTATGCG 57.295 45.000 0.00 0.00 0.00 4.73
2283 2777 3.278574 CTCCGGCATAATTCCAGAAACA 58.721 45.455 0.00 0.00 0.00 2.83
2284 2778 2.618709 CCTCCGGCATAATTCCAGAAAC 59.381 50.000 0.00 0.00 0.00 2.78
2299 2793 6.123045 AGTTGTATTATTAATCCCCTCCGG 57.877 41.667 0.00 0.00 0.00 5.14
2377 2871 4.468095 AGATAACGTTGCACAAACTGAC 57.532 40.909 11.99 0.00 36.56 3.51
2380 2874 5.756347 TCTTGTAGATAACGTTGCACAAACT 59.244 36.000 11.99 0.00 36.56 2.66
2381 2875 5.981174 TCTTGTAGATAACGTTGCACAAAC 58.019 37.500 11.99 2.47 35.25 2.93
2390 2884 8.915036 ACTTGGAGATAATCTTGTAGATAACGT 58.085 33.333 0.00 0.00 32.89 3.99
2391 2885 9.186323 CACTTGGAGATAATCTTGTAGATAACG 57.814 37.037 0.00 0.00 32.89 3.18
2414 2908 5.123344 GGTCACAGTTTGTTTACAAGACACT 59.877 40.000 11.55 4.30 37.15 3.55
2429 2923 2.303022 CCATCCAGTAGTGGTCACAGTT 59.697 50.000 16.36 0.00 45.28 3.16
2430 2924 1.902508 CCATCCAGTAGTGGTCACAGT 59.097 52.381 16.36 0.00 45.28 3.55
2434 2928 3.989056 TCATACCATCCAGTAGTGGTCA 58.011 45.455 16.36 0.00 45.30 4.02
2445 2939 5.091552 TGAGTAGGGGTTATCATACCATCC 58.908 45.833 0.00 0.00 40.09 3.51
2458 2952 0.763035 AACGCACTTTGAGTAGGGGT 59.237 50.000 0.00 0.00 28.03 4.95
2483 2977 6.708054 AGCATTATCAGAGATTAACCTTTCCG 59.292 38.462 0.00 0.00 0.00 4.30
2486 2980 8.489489 TGAGAGCATTATCAGAGATTAACCTTT 58.511 33.333 0.00 0.00 0.00 3.11
2515 3009 9.762933 ACTTAACAATTGCATACATTCAAAAGT 57.237 25.926 5.05 0.00 0.00 2.66
2526 3020 9.278978 TCTTTGAGTGTACTTAACAATTGCATA 57.721 29.630 5.05 0.00 40.63 3.14


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

AutoCloner maintained by Alex Coulton.