Multiple sequence alignment - TraesCS3D01G534300

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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 TraesCS3D01G534300 chr3D 100.000 3389 0 0 1 3389 609231242 609234630 0.000000e+00 6259
1 TraesCS3D01G534300 chr3A 96.028 2694 97 5 703 3389 742784455 742787145 0.000000e+00 4373
2 TraesCS3D01G534300 chr3A 89.145 304 28 4 401 702 742780937 742781237 1.150000e-99 374
3 TraesCS3D01G534300 chr3A 89.655 203 18 3 234 435 742618865 742619065 4.340000e-64 255
4 TraesCS3D01G534300 chr3B 94.876 2693 107 19 703 3389 819947918 819950585 0.000000e+00 4180
5 TraesCS3D01G534300 chr3B 85.794 359 36 3 1 358 819942372 819942716 1.920000e-97 366
6 TraesCS3D01G534300 chr3B 88.636 264 27 3 400 661 819942881 819943143 5.460000e-83 318
7 TraesCS3D01G534300 chr5A 76.672 673 113 35 1024 1677 605249002 605249649 1.950000e-87 333
8 TraesCS3D01G534300 chr5D 74.741 772 134 48 1024 1771 483810028 483810762 4.280000e-74 289
9 TraesCS3D01G534300 chr5D 74.656 509 102 19 1098 1604 564788511 564788994 2.060000e-47 200
10 TraesCS3D01G534300 chr5D 86.792 159 19 2 1121 1278 564752072 564751915 3.480000e-40 176
11 TraesCS3D01G534300 chr5D 89.209 139 13 2 1121 1258 564748973 564748836 4.500000e-39 172
12 TraesCS3D01G534300 chr5D 84.892 139 21 0 2238 2376 564758192 564758054 1.270000e-29 141
13 TraesCS3D01G534300 chr5D 91.250 80 7 0 2298 2377 564750483 564750404 3.580000e-20 110
14 TraesCS3D01G534300 chr7A 78.815 439 81 9 1980 2413 91497554 91497985 5.530000e-73 285
15 TraesCS3D01G534300 chr5B 85.294 170 23 2 1101 1269 708657682 708657514 1.250000e-39 174
16 TraesCS3D01G534300 chr5B 74.939 411 86 16 1980 2377 708453260 708452854 4.500000e-39 172
17 TraesCS3D01G534300 chr5B 87.857 140 17 0 2238 2377 708657407 708657268 7.520000e-37 165
18 TraesCS3D01G534300 chr5B 87.770 139 17 0 2238 2376 708674210 708674072 2.710000e-36 163
19 TraesCS3D01G534300 chr4A 83.916 143 21 2 1098 1239 606339571 606339712 5.900000e-28 135


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 TraesCS3D01G534300 chr3D 609231242 609234630 3388 False 6259.0 6259 100.0000 1 3389 1 chr3D.!!$F1 3388
1 TraesCS3D01G534300 chr3A 742780937 742787145 6208 False 2373.5 4373 92.5865 401 3389 2 chr3A.!!$F2 2988
2 TraesCS3D01G534300 chr3B 819947918 819950585 2667 False 4180.0 4180 94.8760 703 3389 1 chr3B.!!$F1 2686
3 TraesCS3D01G534300 chr3B 819942372 819943143 771 False 342.0 366 87.2150 1 661 2 chr3B.!!$F2 660
4 TraesCS3D01G534300 chr5A 605249002 605249649 647 False 333.0 333 76.6720 1024 1677 1 chr5A.!!$F1 653
5 TraesCS3D01G534300 chr5D 483810028 483810762 734 False 289.0 289 74.7410 1024 1771 1 chr5D.!!$F1 747

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
20 21 0.392193 GGTGGTCCAGCAGTCTGATG 60.392 60.0 16.35 11.25 42.95 3.07 F
296 298 0.456312 AGCAGTAGTCGTACGCTTGC 60.456 55.0 19.57 19.57 36.34 4.01 F
388 390 0.467290 TGGGGAGCACAACACTTTCC 60.467 55.0 0.00 0.00 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 5045 0.107945 GTGCCCAAGCGAAGAGAGAT 60.108 55.0 0.00 0.00 44.31 2.75 R
2232 5608 1.265454 AATCCACCAGGTCCTCGGAC 61.265 60.0 7.57 7.57 43.87 4.79 R
2668 6051 5.163581 TGCGTCTAGTAGACCAATCCTTAAC 60.164 44.0 21.92 0.00 42.12 2.01 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
20 21 0.392193 GGTGGTCCAGCAGTCTGATG 60.392 60.000 16.35 11.25 42.95 3.07
29 30 2.907910 GCAGTCTGATGCATTTTCGT 57.092 45.000 3.32 0.00 45.77 3.85
31 32 2.476854 GCAGTCTGATGCATTTTCGTCC 60.477 50.000 3.32 0.00 45.77 4.79
37 38 2.712984 TGCATTTTCGTCCAGTGCA 58.287 47.368 0.00 0.00 42.86 4.57
38 39 0.592637 TGCATTTTCGTCCAGTGCAG 59.407 50.000 0.00 0.00 40.51 4.41
45 46 1.597854 CGTCCAGTGCAGCCTTGAA 60.598 57.895 0.00 0.00 0.00 2.69
60 61 6.661669 CAGCCTTGAAAACAAAATTCATTCC 58.338 36.000 0.00 0.00 36.72 3.01
80 81 1.667724 CGCAAAGACCATAAGCTCCAG 59.332 52.381 0.00 0.00 0.00 3.86
83 84 3.376546 GCAAAGACCATAAGCTCCAGAAG 59.623 47.826 0.00 0.00 0.00 2.85
89 90 2.092753 CCATAAGCTCCAGAAGGAAGCA 60.093 50.000 0.00 0.00 45.19 3.91
108 109 6.259829 GGAAGCAGAGCAAACCAAATTAAAAA 59.740 34.615 0.00 0.00 0.00 1.94
110 111 8.900983 AAGCAGAGCAAACCAAATTAAAAATA 57.099 26.923 0.00 0.00 0.00 1.40
166 167 2.187239 TCCAGAGGAGATCTTGGCAT 57.813 50.000 6.32 0.00 35.47 4.40
173 174 2.306805 AGGAGATCTTGGCATGTCACAA 59.693 45.455 0.00 0.00 0.00 3.33
205 206 2.146342 AGCGAACACAGACCAAAGATG 58.854 47.619 0.00 0.00 0.00 2.90
214 215 1.615392 AGACCAAAGATGCTTTGCCAC 59.385 47.619 13.03 7.42 0.00 5.01
217 218 1.068895 CCAAAGATGCTTTGCCACACA 59.931 47.619 13.03 0.00 0.00 3.72
287 289 2.871182 TGAGGCATTAGCAGTAGTCG 57.129 50.000 0.00 0.00 44.61 4.18
291 293 2.033049 AGGCATTAGCAGTAGTCGTACG 59.967 50.000 9.53 9.53 44.61 3.67
296 298 0.456312 AGCAGTAGTCGTACGCTTGC 60.456 55.000 19.57 19.57 36.34 4.01
304 306 1.068816 GTCGTACGCTTGCCCAAATTT 60.069 47.619 11.24 0.00 0.00 1.82
305 307 1.609555 TCGTACGCTTGCCCAAATTTT 59.390 42.857 11.24 0.00 0.00 1.82
306 308 1.982913 CGTACGCTTGCCCAAATTTTC 59.017 47.619 0.52 0.00 0.00 2.29
307 309 2.351350 CGTACGCTTGCCCAAATTTTCT 60.351 45.455 0.52 0.00 0.00 2.52
308 310 2.438868 ACGCTTGCCCAAATTTTCTC 57.561 45.000 0.00 0.00 0.00 2.87
309 311 1.963515 ACGCTTGCCCAAATTTTCTCT 59.036 42.857 0.00 0.00 0.00 3.10
310 312 3.153919 ACGCTTGCCCAAATTTTCTCTA 58.846 40.909 0.00 0.00 0.00 2.43
311 313 3.191371 ACGCTTGCCCAAATTTTCTCTAG 59.809 43.478 0.00 0.00 0.00 2.43
312 314 3.191371 CGCTTGCCCAAATTTTCTCTAGT 59.809 43.478 0.00 0.00 0.00 2.57
313 315 4.321230 CGCTTGCCCAAATTTTCTCTAGTT 60.321 41.667 0.00 0.00 0.00 2.24
314 316 5.106317 CGCTTGCCCAAATTTTCTCTAGTTA 60.106 40.000 0.00 0.00 0.00 2.24
315 317 6.093404 GCTTGCCCAAATTTTCTCTAGTTAC 58.907 40.000 0.00 0.00 0.00 2.50
316 318 6.294508 GCTTGCCCAAATTTTCTCTAGTTACA 60.295 38.462 0.00 0.00 0.00 2.41
317 319 7.589958 TTGCCCAAATTTTCTCTAGTTACAA 57.410 32.000 0.00 0.00 0.00 2.41
318 320 6.977213 TGCCCAAATTTTCTCTAGTTACAAC 58.023 36.000 0.00 0.00 0.00 3.32
344 346 6.531503 TGTTATTGACCAACAACCAAAGAA 57.468 33.333 2.00 0.00 41.52 2.52
358 360 7.750769 ACAACCAAAGAAACACATGATTTTTG 58.249 30.769 0.00 2.73 0.00 2.44
361 363 5.239087 CCAAAGAAACACATGATTTTTGGGG 59.761 40.000 0.00 0.00 39.39 4.96
362 364 4.622260 AGAAACACATGATTTTTGGGGG 57.378 40.909 0.00 0.00 0.00 5.40
381 383 2.197324 TTGGGTGGGGAGCACAAC 59.803 61.111 0.00 0.00 0.00 3.32
382 384 2.694920 TTGGGTGGGGAGCACAACA 61.695 57.895 0.00 0.00 0.00 3.33
383 385 2.597510 GGGTGGGGAGCACAACAC 60.598 66.667 0.00 0.00 0.00 3.32
384 386 2.515901 GGTGGGGAGCACAACACT 59.484 61.111 7.22 0.00 34.42 3.55
385 387 1.152756 GGTGGGGAGCACAACACTT 60.153 57.895 7.22 0.00 34.42 3.16
386 388 0.755327 GGTGGGGAGCACAACACTTT 60.755 55.000 7.22 0.00 34.42 2.66
387 389 0.668535 GTGGGGAGCACAACACTTTC 59.331 55.000 0.00 0.00 0.00 2.62
388 390 0.467290 TGGGGAGCACAACACTTTCC 60.467 55.000 0.00 0.00 0.00 3.13
389 391 0.467290 GGGGAGCACAACACTTTCCA 60.467 55.000 0.00 0.00 0.00 3.53
390 392 1.398692 GGGAGCACAACACTTTCCAA 58.601 50.000 0.00 0.00 0.00 3.53
392 394 2.167487 GGGAGCACAACACTTTCCAAAA 59.833 45.455 0.00 0.00 0.00 2.44
393 395 3.447742 GGAGCACAACACTTTCCAAAAG 58.552 45.455 0.00 0.00 0.00 2.27
394 396 3.447742 GAGCACAACACTTTCCAAAAGG 58.552 45.455 4.60 0.00 0.00 3.11
397 399 2.929398 CACAACACTTTCCAAAAGGCAC 59.071 45.455 4.60 0.00 0.00 5.01
398 400 2.564947 ACAACACTTTCCAAAAGGCACA 59.435 40.909 4.60 0.00 0.00 4.57
424 549 2.290641 ACCTGCGAAATCATACCACCAA 60.291 45.455 0.00 0.00 0.00 3.67
431 556 5.527582 GCGAAATCATACCACCAAAGTAGAT 59.472 40.000 0.00 0.00 0.00 1.98
434 559 7.442364 CGAAATCATACCACCAAAGTAGATCAT 59.558 37.037 0.00 0.00 0.00 2.45
438 563 6.611236 TCATACCACCAAAGTAGATCATCTCA 59.389 38.462 0.00 0.00 0.00 3.27
458 584 9.595357 CATCTCATAAAATGATTTGATCGAGTG 57.405 33.333 11.26 7.75 38.85 3.51
466 592 3.189080 TGATTTGATCGAGTGCAAACCAG 59.811 43.478 11.50 0.00 36.89 4.00
496 622 7.124573 TGTAGCATCCATTTAGTAGTGTCAT 57.875 36.000 0.00 0.00 0.00 3.06
516 642 1.021390 GGGCAGATGTGAGGACAACG 61.021 60.000 0.00 0.00 35.11 4.10
542 668 7.256012 GGGTTTAACCAAATCAACCAGTTCATA 60.256 37.037 16.58 0.00 41.02 2.15
626 752 3.592898 CCAAACTTGGGATAAAGTGCC 57.407 47.619 0.09 0.00 44.70 5.01
633 759 2.647529 GGGATAAAGTGCCCAAAACG 57.352 50.000 0.00 0.00 44.07 3.60
638 764 2.577449 AAAGTGCCCAAAACGTGAAG 57.423 45.000 0.00 0.00 0.00 3.02
653 779 7.908193 AAACGTGAAGACAAATGATAAACAC 57.092 32.000 0.00 0.00 0.00 3.32
663 789 7.872483 AGACAAATGATAAACACATCCCAAAAC 59.128 33.333 0.00 0.00 0.00 2.43
664 790 6.644592 ACAAATGATAAACACATCCCAAAACG 59.355 34.615 0.00 0.00 0.00 3.60
685 811 4.156182 CGTGCTTTAACGGAGAAATTTCC 58.844 43.478 14.61 6.37 39.89 3.13
694 820 1.546029 GGAGAAATTTCCCAGCCACAC 59.454 52.381 14.61 0.00 0.00 3.82
704 4047 1.682702 CCCAGCCACACATCATGCTTA 60.683 52.381 0.00 0.00 30.08 3.09
769 4112 0.743688 TGCGTGCTGGTGTCAAATTT 59.256 45.000 0.00 0.00 0.00 1.82
772 4120 2.979813 GCGTGCTGGTGTCAAATTTTAG 59.020 45.455 0.00 0.00 0.00 1.85
779 4127 7.378728 GTGCTGGTGTCAAATTTTAGTAGTTTC 59.621 37.037 0.00 0.00 0.00 2.78
782 4130 8.659925 TGGTGTCAAATTTTAGTAGTTTCGTA 57.340 30.769 0.00 0.00 0.00 3.43
819 4167 1.461897 CAACCCAATACGTCGTCAACC 59.538 52.381 0.00 0.00 0.00 3.77
848 4196 3.283751 TCCTTCTCCTCATTCTCGACTC 58.716 50.000 0.00 0.00 0.00 3.36
867 4215 1.079438 GGATCGGATCCCTAGGGCT 59.921 63.158 24.42 14.66 43.88 5.19
884 4232 2.456577 GGCTAATTCCCTTGCTTCCAA 58.543 47.619 0.00 0.00 0.00 3.53
896 4244 0.537188 GCTTCCAATCCGTCTCCTCA 59.463 55.000 0.00 0.00 0.00 3.86
897 4245 1.740718 GCTTCCAATCCGTCTCCTCAC 60.741 57.143 0.00 0.00 0.00 3.51
899 4247 1.519455 CCAATCCGTCTCCTCACGC 60.519 63.158 0.00 0.00 38.52 5.34
900 4248 1.215382 CAATCCGTCTCCTCACGCA 59.785 57.895 0.00 0.00 38.52 5.24
910 4258 1.004560 CCTCACGCACACTCATGGT 60.005 57.895 0.00 0.00 0.00 3.55
940 4288 1.812922 CACCACGAGCAGCCTGATC 60.813 63.158 0.00 0.00 0.00 2.92
947 4295 2.590007 GCAGCCTGATCGCCGAAT 60.590 61.111 0.00 0.00 0.00 3.34
1003 4352 3.181501 GCAATCCAAATCGACGGAAATGA 60.182 43.478 15.19 0.00 34.22 2.57
1209 4582 2.049433 GGTACGTGCGTGCTGTCT 60.049 61.111 12.01 0.00 0.00 3.41
1420 4793 2.423446 CCATAGGTCTGGGCGAGC 59.577 66.667 0.00 0.00 40.43 5.03
1669 5045 7.452813 TCTTCATTATAGATGCTCCTGCTCTTA 59.547 37.037 0.00 0.00 40.48 2.10
1864 5240 3.855524 GCACTTGTTACATTTTGGGGTCG 60.856 47.826 0.00 0.00 0.00 4.79
2015 5391 1.267261 CCTTGTCTCTCGACGAGTGTT 59.733 52.381 23.41 0.00 46.14 3.32
2027 5403 4.333649 TCGACGAGTGTTATATTTCCGACT 59.666 41.667 0.00 0.00 0.00 4.18
2232 5608 1.003718 GGGACACCTTCAAGACCCG 60.004 63.158 0.00 0.00 0.00 5.28
2440 5816 8.093927 GTGGTGAGGATAATTCATTTTGGAAAA 58.906 33.333 0.00 0.00 0.00 2.29
2817 6200 6.527423 AGTTTTTAACGGAGGAGTATGACAA 58.473 36.000 0.00 0.00 36.23 3.18
2826 6209 5.749109 CGGAGGAGTATGACAAGTTTGATAC 59.251 44.000 0.00 0.00 0.00 2.24
2836 6219 7.825331 TGACAAGTTTGATACCCAAATTGTA 57.175 32.000 0.00 0.00 45.48 2.41
2967 6350 2.224523 GGGACATCATGGAAGGCGATAA 60.225 50.000 0.00 0.00 0.00 1.75
3231 6614 6.868339 GGAGGAAACCAAACATGTTATCTTTG 59.132 38.462 12.39 5.87 0.00 2.77
3243 6626 8.709386 ACATGTTATCTTTGATACACACTCTC 57.291 34.615 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.161012 ACGAAAATGCATCAGACTGCTG 59.839 45.455 0.00 1.81 42.75 4.41
15 16 2.730090 GCACTGGACGAAAATGCATCAG 60.730 50.000 0.00 3.55 36.30 2.90
20 21 0.730494 GCTGCACTGGACGAAAATGC 60.730 55.000 0.00 0.00 36.81 3.56
27 28 1.165907 TTTCAAGGCTGCACTGGACG 61.166 55.000 0.50 0.00 0.00 4.79
29 30 1.032014 GTTTTCAAGGCTGCACTGGA 58.968 50.000 0.50 0.00 0.00 3.86
31 32 2.582728 TTGTTTTCAAGGCTGCACTG 57.417 45.000 0.50 0.00 34.60 3.66
37 38 5.466393 CGGAATGAATTTTGTTTTCAAGGCT 59.534 36.000 0.00 0.00 41.09 4.58
38 39 5.678921 CGGAATGAATTTTGTTTTCAAGGC 58.321 37.500 0.00 0.00 41.09 4.35
45 46 5.236263 GGTCTTTGCGGAATGAATTTTGTTT 59.764 36.000 6.82 0.00 0.00 2.83
60 61 1.667724 CTGGAGCTTATGGTCTTTGCG 59.332 52.381 7.63 0.00 40.29 4.85
80 81 1.609208 TGGTTTGCTCTGCTTCCTTC 58.391 50.000 0.00 0.00 0.00 3.46
83 84 3.391506 AATTTGGTTTGCTCTGCTTCC 57.608 42.857 0.00 0.00 0.00 3.46
110 111 8.868522 TGTGGTCTCAAGATAAAAAGAATGAT 57.131 30.769 0.00 0.00 0.00 2.45
116 117 7.496529 TCAGTTGTGGTCTCAAGATAAAAAG 57.503 36.000 0.00 0.00 0.00 2.27
183 184 3.462483 TCTTTGGTCTGTGTTCGCTAA 57.538 42.857 0.00 0.00 0.00 3.09
184 185 3.325870 CATCTTTGGTCTGTGTTCGCTA 58.674 45.455 0.00 0.00 0.00 4.26
193 194 1.614903 TGGCAAAGCATCTTTGGTCTG 59.385 47.619 17.69 0.00 31.86 3.51
205 206 4.612932 TTTTTCAATTGTGTGGCAAAGC 57.387 36.364 5.13 0.00 40.91 3.51
233 234 1.813178 TGAAACAGAAACGGTGCAACA 59.187 42.857 0.98 0.00 39.98 3.33
266 268 3.133003 ACGACTACTGCTAATGCCTCATT 59.867 43.478 0.00 0.00 37.80 2.57
268 270 2.100197 ACGACTACTGCTAATGCCTCA 58.900 47.619 0.00 0.00 38.71 3.86
270 272 2.033049 CGTACGACTACTGCTAATGCCT 59.967 50.000 10.44 0.00 38.71 4.75
276 278 1.202110 GCAAGCGTACGACTACTGCTA 60.202 52.381 21.65 0.00 34.03 3.49
287 289 3.057526 AGAGAAAATTTGGGCAAGCGTAC 60.058 43.478 0.00 0.00 0.00 3.67
291 293 4.790765 ACTAGAGAAAATTTGGGCAAGC 57.209 40.909 0.00 0.00 0.00 4.01
296 298 9.463443 CAAAGTTGTAACTAGAGAAAATTTGGG 57.537 33.333 0.00 0.00 38.57 4.12
305 307 9.485206 GGTCAATAACAAAGTTGTAACTAGAGA 57.515 33.333 0.00 0.00 41.31 3.10
306 308 9.268268 TGGTCAATAACAAAGTTGTAACTAGAG 57.732 33.333 0.00 0.00 41.31 2.43
307 309 9.616156 TTGGTCAATAACAAAGTTGTAACTAGA 57.384 29.630 0.00 0.00 41.31 2.43
308 310 9.659830 GTTGGTCAATAACAAAGTTGTAACTAG 57.340 33.333 0.00 0.00 41.31 2.57
309 311 9.175312 TGTTGGTCAATAACAAAGTTGTAACTA 57.825 29.630 0.00 0.00 41.31 2.24
310 312 8.057536 TGTTGGTCAATAACAAAGTTGTAACT 57.942 30.769 0.00 0.00 41.31 2.24
311 313 8.588789 GTTGTTGGTCAATAACAAAGTTGTAAC 58.411 33.333 15.22 0.00 46.10 2.50
312 314 7.760340 GGTTGTTGGTCAATAACAAAGTTGTAA 59.240 33.333 19.59 0.00 46.10 2.41
313 315 7.093902 TGGTTGTTGGTCAATAACAAAGTTGTA 60.094 33.333 19.59 0.00 46.10 2.41
314 316 6.103330 GGTTGTTGGTCAATAACAAAGTTGT 58.897 36.000 19.59 0.00 46.10 3.32
315 317 6.102663 TGGTTGTTGGTCAATAACAAAGTTG 58.897 36.000 19.59 0.00 46.10 3.16
316 318 6.287589 TGGTTGTTGGTCAATAACAAAGTT 57.712 33.333 19.59 0.00 46.10 2.66
317 319 5.923733 TGGTTGTTGGTCAATAACAAAGT 57.076 34.783 19.59 0.00 46.10 2.66
318 320 7.038659 TCTTTGGTTGTTGGTCAATAACAAAG 58.961 34.615 22.61 22.61 46.10 2.77
361 363 4.678743 GTGCTCCCCACCCAACCC 62.679 72.222 0.00 0.00 38.55 4.11
362 364 3.444818 TTGTGCTCCCCACCCAACC 62.445 63.158 0.00 0.00 44.01 3.77
363 365 2.197324 TTGTGCTCCCCACCCAAC 59.803 61.111 0.00 0.00 44.01 3.77
364 366 2.197324 GTTGTGCTCCCCACCCAA 59.803 61.111 0.00 0.00 44.01 4.12
365 367 3.099841 TGTTGTGCTCCCCACCCA 61.100 61.111 0.00 0.00 44.01 4.51
366 368 2.597510 GTGTTGTGCTCCCCACCC 60.598 66.667 0.00 0.00 44.01 4.61
367 369 0.755327 AAAGTGTTGTGCTCCCCACC 60.755 55.000 2.43 0.00 44.01 4.61
368 370 0.668535 GAAAGTGTTGTGCTCCCCAC 59.331 55.000 0.00 0.00 44.90 4.61
370 372 0.467290 TGGAAAGTGTTGTGCTCCCC 60.467 55.000 0.00 0.00 0.00 4.81
371 373 1.398692 TTGGAAAGTGTTGTGCTCCC 58.601 50.000 0.00 0.00 0.00 4.30
372 374 3.447742 CTTTTGGAAAGTGTTGTGCTCC 58.552 45.455 0.00 0.00 0.00 4.70
373 375 3.447742 CCTTTTGGAAAGTGTTGTGCTC 58.552 45.455 0.37 0.00 44.07 4.26
374 376 2.418609 GCCTTTTGGAAAGTGTTGTGCT 60.419 45.455 0.37 0.00 44.07 4.40
375 377 1.933181 GCCTTTTGGAAAGTGTTGTGC 59.067 47.619 0.37 0.00 44.07 4.57
381 383 3.525268 AAGTGTGCCTTTTGGAAAGTG 57.475 42.857 0.37 0.00 44.07 3.16
382 384 4.142026 GGTTAAGTGTGCCTTTTGGAAAGT 60.142 41.667 0.37 0.00 44.07 2.66
383 385 4.099419 AGGTTAAGTGTGCCTTTTGGAAAG 59.901 41.667 0.00 0.00 44.07 2.62
384 386 4.027437 AGGTTAAGTGTGCCTTTTGGAAA 58.973 39.130 0.00 0.00 44.07 3.13
385 387 3.383185 CAGGTTAAGTGTGCCTTTTGGAA 59.617 43.478 0.00 0.00 44.07 3.53
386 388 2.955660 CAGGTTAAGTGTGCCTTTTGGA 59.044 45.455 0.00 0.00 44.07 3.53
387 389 2.545742 GCAGGTTAAGTGTGCCTTTTGG 60.546 50.000 0.00 0.00 44.18 3.28
388 390 2.742774 GCAGGTTAAGTGTGCCTTTTG 58.257 47.619 0.00 0.00 34.46 2.44
389 391 1.336755 CGCAGGTTAAGTGTGCCTTTT 59.663 47.619 0.00 0.00 34.46 2.27
390 392 0.951558 CGCAGGTTAAGTGTGCCTTT 59.048 50.000 0.00 0.00 34.46 3.11
392 394 0.107831 TTCGCAGGTTAAGTGTGCCT 59.892 50.000 0.00 0.00 33.42 4.75
393 395 0.948678 TTTCGCAGGTTAAGTGTGCC 59.051 50.000 0.00 0.00 33.42 5.01
394 396 2.225491 TGATTTCGCAGGTTAAGTGTGC 59.775 45.455 0.00 0.00 0.00 4.57
397 399 4.634004 TGGTATGATTTCGCAGGTTAAGTG 59.366 41.667 0.00 0.00 0.00 3.16
398 400 4.634443 GTGGTATGATTTCGCAGGTTAAGT 59.366 41.667 0.00 0.00 0.00 2.24
431 556 9.551734 ACTCGATCAAATCATTTTATGAGATGA 57.448 29.630 9.13 8.62 43.53 2.92
434 559 7.280652 TGCACTCGATCAAATCATTTTATGAGA 59.719 33.333 9.13 0.00 43.53 3.27
438 563 7.489113 GGTTTGCACTCGATCAAATCATTTTAT 59.511 33.333 11.11 0.00 34.41 1.40
446 571 3.149196 ACTGGTTTGCACTCGATCAAAT 58.851 40.909 9.72 0.00 35.06 2.32
453 579 1.129251 CATGCTACTGGTTTGCACTCG 59.871 52.381 0.00 0.00 39.63 4.18
458 584 2.083774 TGCTACATGCTACTGGTTTGC 58.916 47.619 0.00 0.00 43.37 3.68
466 592 7.116948 CACTACTAAATGGATGCTACATGCTAC 59.883 40.741 0.00 0.00 43.37 3.58
481 607 4.769688 TCTGCCCATGACACTACTAAATG 58.230 43.478 0.00 0.00 0.00 2.32
487 613 2.093500 TCACATCTGCCCATGACACTAC 60.093 50.000 0.00 0.00 0.00 2.73
488 614 2.169144 CTCACATCTGCCCATGACACTA 59.831 50.000 0.00 0.00 0.00 2.74
496 622 0.036732 GTTGTCCTCACATCTGCCCA 59.963 55.000 0.00 0.00 30.55 5.36
516 642 4.948341 ACTGGTTGATTTGGTTAAACCC 57.052 40.909 0.00 0.00 41.17 4.11
593 719 1.995376 AGTTTGGGATGGTCACCAAC 58.005 50.000 0.00 0.00 45.77 3.77
617 743 3.886505 TCTTCACGTTTTGGGCACTTTAT 59.113 39.130 0.00 0.00 0.00 1.40
626 752 7.433719 TGTTTATCATTTGTCTTCACGTTTTGG 59.566 33.333 0.00 0.00 0.00 3.28
628 754 7.971168 TGTGTTTATCATTTGTCTTCACGTTTT 59.029 29.630 0.00 0.00 0.00 2.43
629 755 7.476667 TGTGTTTATCATTTGTCTTCACGTTT 58.523 30.769 0.00 0.00 0.00 3.60
630 756 7.022055 TGTGTTTATCATTTGTCTTCACGTT 57.978 32.000 0.00 0.00 0.00 3.99
631 757 6.612247 TGTGTTTATCATTTGTCTTCACGT 57.388 33.333 0.00 0.00 0.00 4.49
632 758 6.742718 GGATGTGTTTATCATTTGTCTTCACG 59.257 38.462 0.00 0.00 0.00 4.35
633 759 7.029563 GGGATGTGTTTATCATTTGTCTTCAC 58.970 38.462 0.00 0.00 0.00 3.18
638 764 7.148820 CGTTTTGGGATGTGTTTATCATTTGTC 60.149 37.037 0.00 0.00 0.00 3.18
653 779 2.977169 CGTTAAAGCACGTTTTGGGATG 59.023 45.455 0.00 0.00 35.34 3.51
663 789 4.156182 GGAAATTTCTCCGTTAAAGCACG 58.844 43.478 17.42 0.00 40.02 5.34
664 790 4.022676 TGGGAAATTTCTCCGTTAAAGCAC 60.023 41.667 15.49 0.00 36.21 4.40
682 808 0.966875 GCATGATGTGTGGCTGGGAA 60.967 55.000 0.00 0.00 0.00 3.97
685 811 1.753930 TAAGCATGATGTGTGGCTGG 58.246 50.000 0.00 0.00 36.58 4.85
769 4112 1.750778 CGGGCCCTACGAAACTACTAA 59.249 52.381 22.43 0.00 0.00 2.24
772 4120 1.142531 CCGGGCCCTACGAAACTAC 59.857 63.158 22.43 0.00 0.00 2.73
799 4147 1.461897 GGTTGACGACGTATTGGGTTG 59.538 52.381 0.00 0.00 0.00 3.77
867 4215 3.287222 CGGATTGGAAGCAAGGGAATTA 58.713 45.455 0.00 0.00 0.00 1.40
884 4232 1.977009 TGTGCGTGAGGAGACGGAT 60.977 57.895 0.00 0.00 41.92 4.18
896 4244 2.669569 GCCACCATGAGTGTGCGT 60.670 61.111 11.73 0.00 45.74 5.24
899 4247 3.434319 GCCGCCACCATGAGTGTG 61.434 66.667 11.73 4.11 45.74 3.82
928 4276 2.985512 ATTCGGCGATCAGGCTGCTC 62.986 60.000 11.76 9.20 44.22 4.26
965 4313 3.541713 GCAGCGGTAGGGAGGAGG 61.542 72.222 0.00 0.00 0.00 4.30
966 4314 1.690219 ATTGCAGCGGTAGGGAGGAG 61.690 60.000 0.00 0.00 0.00 3.69
1434 4807 3.306294 GGGAAAGATGCAACCTTTTGAGG 60.306 47.826 15.64 0.00 34.33 3.86
1669 5045 0.107945 GTGCCCAAGCGAAGAGAGAT 60.108 55.000 0.00 0.00 44.31 2.75
1864 5240 3.618690 AGAAGAGGTGGAACATACAGC 57.381 47.619 0.00 0.00 44.52 4.40
2015 5391 8.582437 CAGACCCATAAAGTAGTCGGAAATATA 58.418 37.037 0.00 0.00 34.41 0.86
2027 5403 3.130734 AGGCTCCAGACCCATAAAGTA 57.869 47.619 0.00 0.00 0.00 2.24
2064 5440 3.584733 AAGTGAGCTTCTCCAGGTTTT 57.415 42.857 0.00 0.00 31.44 2.43
2109 5485 9.265901 GCTATGCTAATATTTGTTGAGAGAAGA 57.734 33.333 0.00 0.00 0.00 2.87
2179 5555 7.353414 TCTTAGATCTAGAATCCAACACCTG 57.647 40.000 2.02 0.00 0.00 4.00
2226 5602 3.659496 AGGTCCTCGGACGGGTCT 61.659 66.667 9.81 0.00 45.41 3.85
2232 5608 1.265454 AATCCACCAGGTCCTCGGAC 61.265 60.000 7.57 7.57 43.87 4.79
2668 6051 5.163581 TGCGTCTAGTAGACCAATCCTTAAC 60.164 44.000 21.92 0.00 42.12 2.01
2736 6119 1.423541 TCCACCCTTTAGCAAGCTTCA 59.576 47.619 0.00 0.00 0.00 3.02
2817 6200 8.052748 TGCTAGATACAATTTGGGTATCAAACT 58.947 33.333 13.80 0.70 46.72 2.66
2895 6278 6.877611 TCTCTTTGTTATTCCAAACCTCAC 57.122 37.500 0.00 0.00 31.38 3.51
3009 6392 9.064706 CATCTAGCACATTAATCATCCTTTTCT 57.935 33.333 0.00 0.00 0.00 2.52
3148 6531 4.840680 TCTTCAGTGATTTTCTCCTCAGGA 59.159 41.667 0.00 0.00 0.00 3.86
3231 6614 2.939103 GGGCACAATGAGAGTGTGTATC 59.061 50.000 6.09 0.00 46.58 2.24
3243 6626 0.331278 TTAGACCCAGGGGCACAATG 59.669 55.000 16.27 0.00 39.32 2.82
3336 6719 7.992754 AAGATGTCTAAATCAAGCTCAAACT 57.007 32.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.