Multiple sequence alignment - TraesCS6B01G427400

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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 TraesCS6B01G427400 chr6B 100.000 2687 0 0 1 2687 696021999 696019313 0.000000e+00 4963
1 TraesCS6B01G427400 chr6B 83.307 1917 232 48 655 2506 696100307 696098414 0.000000e+00 1687
2 TraesCS6B01G427400 chr6B 83.051 649 80 14 2053 2687 696096879 696096247 1.810000e-156 562
3 TraesCS6B01G427400 chr6A 92.823 2271 131 11 433 2687 604456475 604454221 0.000000e+00 3262
4 TraesCS6B01G427400 chr6A 84.845 1940 220 43 655 2537 604574051 604572129 0.000000e+00 1886
5 TraesCS6B01G427400 chr6A 87.461 319 23 7 1 318 604456769 604456467 4.260000e-93 351
6 TraesCS6B01G427400 chr6D 92.281 2267 141 14 433 2687 457591416 457589172 0.000000e+00 3186
7 TraesCS6B01G427400 chr6D 84.384 2094 239 44 653 2687 457636819 457634755 0.000000e+00 1975
8 TraesCS6B01G427400 chr6D 85.580 319 23 9 1 318 457591704 457591408 2.010000e-81 313
9 TraesCS6B01G427400 chr2A 80.478 1296 180 41 695 1951 23878559 23879820 0.000000e+00 924
10 TraesCS6B01G427400 chr2A 80.976 1209 167 35 782 1951 23828232 23829416 0.000000e+00 900
11 TraesCS6B01G427400 chr2D 80.354 1298 186 42 691 1951 21642210 21643475 0.000000e+00 920
12 TraesCS6B01G427400 chr2D 80.139 1299 188 40 691 1951 21681021 21682287 0.000000e+00 905


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 TraesCS6B01G427400 chr6B 696019313 696021999 2686 True 4963.0 4963 100.0000 1 2687 1 chr6B.!!$R1 2686
1 TraesCS6B01G427400 chr6B 696096247 696100307 4060 True 1124.5 1687 83.1790 655 2687 2 chr6B.!!$R2 2032
2 TraesCS6B01G427400 chr6A 604572129 604574051 1922 True 1886.0 1886 84.8450 655 2537 1 chr6A.!!$R1 1882
3 TraesCS6B01G427400 chr6A 604454221 604456769 2548 True 1806.5 3262 90.1420 1 2687 2 chr6A.!!$R2 2686
4 TraesCS6B01G427400 chr6D 457634755 457636819 2064 True 1975.0 1975 84.3840 653 2687 1 chr6D.!!$R1 2034
5 TraesCS6B01G427400 chr6D 457589172 457591704 2532 True 1749.5 3186 88.9305 1 2687 2 chr6D.!!$R2 2686
6 TraesCS6B01G427400 chr2A 23878559 23879820 1261 False 924.0 924 80.4780 695 1951 1 chr2A.!!$F2 1256
7 TraesCS6B01G427400 chr2A 23828232 23829416 1184 False 900.0 900 80.9760 782 1951 1 chr2A.!!$F1 1169
8 TraesCS6B01G427400 chr2D 21642210 21643475 1265 False 920.0 920 80.3540 691 1951 1 chr2D.!!$F1 1260
9 TraesCS6B01G427400 chr2D 21681021 21682287 1266 False 905.0 905 80.1390 691 1951 1 chr2D.!!$F2 1260

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
247 249 0.038166 GTGGGGATGAAAGGCTCACA 59.962 55.0 0.0 0.0 36.69 3.58 F
374 376 0.181114 TGCAGATGACACATAGGGCC 59.819 55.0 0.0 0.0 0.00 5.80 F
376 378 0.250038 CAGATGACACATAGGGCCGG 60.250 60.0 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1466 0.748729 GGTCGAGATCGTCCCACTCT 60.749 60.000 7.20 0.0 40.73 3.24 R
1440 1511 1.227556 GTGCACGAAGTCCAGTGGT 60.228 57.895 9.54 0.0 41.61 4.16 R
2331 4441 1.369091 CGGCGGAAATTGCTAGTGCT 61.369 55.000 0.00 0.0 40.48 4.40 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
28 29 6.603237 TGTATCTGCAAATACATGTAGCAC 57.397 37.500 8.83 4.72 37.24 4.40
56 57 9.618410 CTCGATTGTGTAAAACAACAAAAATTC 57.382 29.630 0.00 0.00 44.97 2.17
68 69 9.934190 AAACAACAAAAATTCAATATCTGTTGC 57.066 25.926 14.11 0.00 43.66 4.17
69 70 8.659925 ACAACAAAAATTCAATATCTGTTGCA 57.340 26.923 14.11 0.00 43.66 4.08
122 123 5.009631 CCAACCACCAAGATGTGATTAGAA 58.990 41.667 0.00 0.00 38.55 2.10
192 194 3.724508 TTTGGCGCTTTGATTTCTCAA 57.275 38.095 7.64 0.00 39.62 3.02
198 200 4.142600 GGCGCTTTGATTTCTCAATAGTGT 60.143 41.667 7.64 0.00 40.95 3.55
202 204 6.026513 GCTTTGATTTCTCAATAGTGTGAGC 58.973 40.000 0.00 0.00 44.01 4.26
213 215 5.997129 TCAATAGTGTGAGCATTCTTCACAA 59.003 36.000 9.39 0.00 44.53 3.33
217 219 3.058639 GTGTGAGCATTCTTCACAAGGTC 60.059 47.826 9.39 0.00 44.53 3.85
237 239 4.034246 CACCTCTCGTGGGGATGA 57.966 61.111 11.10 0.00 38.96 2.92
238 240 2.286826 CACCTCTCGTGGGGATGAA 58.713 57.895 11.10 0.00 38.96 2.57
239 241 0.613260 CACCTCTCGTGGGGATGAAA 59.387 55.000 11.10 0.00 38.96 2.69
240 242 0.905357 ACCTCTCGTGGGGATGAAAG 59.095 55.000 11.10 0.00 0.00 2.62
241 243 0.179000 CCTCTCGTGGGGATGAAAGG 59.821 60.000 0.00 0.00 0.00 3.11
242 244 0.462759 CTCTCGTGGGGATGAAAGGC 60.463 60.000 0.00 0.00 0.00 4.35
243 245 0.909610 TCTCGTGGGGATGAAAGGCT 60.910 55.000 0.00 0.00 0.00 4.58
244 246 0.462759 CTCGTGGGGATGAAAGGCTC 60.463 60.000 0.00 0.00 0.00 4.70
245 247 1.198094 TCGTGGGGATGAAAGGCTCA 61.198 55.000 0.00 0.00 38.81 4.26
246 248 1.026718 CGTGGGGATGAAAGGCTCAC 61.027 60.000 0.00 0.00 36.69 3.51
247 249 0.038166 GTGGGGATGAAAGGCTCACA 59.962 55.000 0.00 0.00 36.69 3.58
308 310 2.630098 CTGACGAGTGGGTCCATGATAT 59.370 50.000 0.00 0.00 36.07 1.63
309 311 2.365293 TGACGAGTGGGTCCATGATATG 59.635 50.000 0.00 0.00 36.07 1.78
324 326 5.793817 CATGATATGGAGATAACGGGTTGA 58.206 41.667 0.00 0.00 0.00 3.18
325 327 5.468540 TGATATGGAGATAACGGGTTGAG 57.531 43.478 0.00 0.00 0.00 3.02
326 328 5.144832 TGATATGGAGATAACGGGTTGAGA 58.855 41.667 0.00 0.00 0.00 3.27
327 329 5.780282 TGATATGGAGATAACGGGTTGAGAT 59.220 40.000 0.00 0.00 0.00 2.75
328 330 4.608948 ATGGAGATAACGGGTTGAGATC 57.391 45.455 0.00 0.00 0.00 2.75
329 331 2.698797 TGGAGATAACGGGTTGAGATCC 59.301 50.000 0.00 0.00 0.00 3.36
330 332 2.966516 GGAGATAACGGGTTGAGATCCT 59.033 50.000 0.00 0.00 0.00 3.24
331 333 3.006003 GGAGATAACGGGTTGAGATCCTC 59.994 52.174 0.00 0.00 0.00 3.71
332 334 3.892588 GAGATAACGGGTTGAGATCCTCT 59.107 47.826 0.00 0.00 0.00 3.69
333 335 3.639094 AGATAACGGGTTGAGATCCTCTG 59.361 47.826 0.00 0.00 0.00 3.35
334 336 0.250513 AACGGGTTGAGATCCTCTGC 59.749 55.000 0.00 0.00 0.00 4.26
335 337 0.904865 ACGGGTTGAGATCCTCTGCA 60.905 55.000 0.00 0.00 0.00 4.41
336 338 0.250234 CGGGTTGAGATCCTCTGCAA 59.750 55.000 0.00 0.00 0.00 4.08
337 339 1.134280 CGGGTTGAGATCCTCTGCAAT 60.134 52.381 0.00 0.00 0.00 3.56
338 340 2.103094 CGGGTTGAGATCCTCTGCAATA 59.897 50.000 0.00 0.00 0.00 1.90
339 341 3.737850 GGGTTGAGATCCTCTGCAATAG 58.262 50.000 0.00 0.00 0.00 1.73
340 342 3.135530 GGGTTGAGATCCTCTGCAATAGT 59.864 47.826 0.00 0.00 0.00 2.12
341 343 4.125703 GGTTGAGATCCTCTGCAATAGTG 58.874 47.826 0.00 0.00 0.00 2.74
357 359 6.400579 CAATAGTGCATAGTGCTATAGTGC 57.599 41.667 0.84 3.57 45.31 4.40
358 360 5.728637 ATAGTGCATAGTGCTATAGTGCA 57.271 39.130 10.10 10.10 45.31 4.57
359 361 3.987547 AGTGCATAGTGCTATAGTGCAG 58.012 45.455 13.54 0.00 45.32 4.41
360 362 3.638627 AGTGCATAGTGCTATAGTGCAGA 59.361 43.478 13.54 0.00 45.32 4.26
361 363 4.282957 AGTGCATAGTGCTATAGTGCAGAT 59.717 41.667 13.54 5.13 45.32 2.90
362 364 4.388165 GTGCATAGTGCTATAGTGCAGATG 59.612 45.833 13.54 8.91 45.32 2.90
363 365 4.281688 TGCATAGTGCTATAGTGCAGATGA 59.718 41.667 10.10 0.00 45.31 2.92
364 366 4.624882 GCATAGTGCTATAGTGCAGATGAC 59.375 45.833 7.26 4.15 44.20 3.06
365 367 5.776744 CATAGTGCTATAGTGCAGATGACA 58.223 41.667 0.84 0.00 44.20 3.58
366 368 4.052159 AGTGCTATAGTGCAGATGACAC 57.948 45.455 0.84 0.00 44.20 3.67
367 369 3.448660 AGTGCTATAGTGCAGATGACACA 59.551 43.478 0.84 0.00 44.20 3.72
368 370 4.100653 AGTGCTATAGTGCAGATGACACAT 59.899 41.667 0.84 0.00 44.20 3.21
369 371 5.302823 AGTGCTATAGTGCAGATGACACATA 59.697 40.000 0.84 5.50 44.20 2.29
370 372 5.632764 GTGCTATAGTGCAGATGACACATAG 59.367 44.000 0.84 12.03 44.20 2.23
371 373 5.167121 GCTATAGTGCAGATGACACATAGG 58.833 45.833 0.84 0.00 40.59 2.57
372 374 2.996249 AGTGCAGATGACACATAGGG 57.004 50.000 0.00 0.00 40.59 3.53
373 375 1.134280 AGTGCAGATGACACATAGGGC 60.134 52.381 0.00 0.00 40.59 5.19
374 376 0.181114 TGCAGATGACACATAGGGCC 59.819 55.000 0.00 0.00 0.00 5.80
375 377 0.882042 GCAGATGACACATAGGGCCG 60.882 60.000 0.00 0.00 0.00 6.13
376 378 0.250038 CAGATGACACATAGGGCCGG 60.250 60.000 0.00 0.00 0.00 6.13
377 379 1.071471 GATGACACATAGGGCCGGG 59.929 63.158 2.18 0.00 0.00 5.73
378 380 1.692749 ATGACACATAGGGCCGGGT 60.693 57.895 2.18 0.00 0.00 5.28
379 381 1.696097 ATGACACATAGGGCCGGGTC 61.696 60.000 2.18 5.45 0.00 4.46
380 382 3.087906 ACACATAGGGCCGGGTCC 61.088 66.667 10.47 10.47 0.00 4.46
381 383 3.087253 CACATAGGGCCGGGTCCA 61.087 66.667 21.90 6.34 0.00 4.02
382 384 3.087906 ACATAGGGCCGGGTCCAC 61.088 66.667 21.90 4.43 0.00 4.02
383 385 3.087253 CATAGGGCCGGGTCCACA 61.087 66.667 21.90 7.52 0.00 4.17
384 386 3.087906 ATAGGGCCGGGTCCACAC 61.088 66.667 21.90 0.00 0.00 3.82
385 387 3.935456 ATAGGGCCGGGTCCACACA 62.935 63.158 21.90 1.79 0.00 3.72
388 390 4.572571 GGCCGGGTCCACACAACA 62.573 66.667 2.18 0.00 0.00 3.33
389 391 2.978010 GCCGGGTCCACACAACAG 60.978 66.667 2.18 0.00 0.00 3.16
390 392 2.978010 CCGGGTCCACACAACAGC 60.978 66.667 0.00 0.00 0.00 4.40
391 393 3.345808 CGGGTCCACACAACAGCG 61.346 66.667 0.00 0.00 0.00 5.18
392 394 2.110213 GGGTCCACACAACAGCGA 59.890 61.111 0.00 0.00 0.00 4.93
393 395 2.251642 GGGTCCACACAACAGCGAC 61.252 63.158 0.00 0.00 0.00 5.19
394 396 2.251642 GGTCCACACAACAGCGACC 61.252 63.158 0.00 0.00 36.52 4.79
395 397 2.279851 TCCACACAACAGCGACCG 60.280 61.111 0.00 0.00 0.00 4.79
396 398 2.587753 CCACACAACAGCGACCGT 60.588 61.111 0.00 0.00 0.00 4.83
397 399 1.300311 CCACACAACAGCGACCGTA 60.300 57.895 0.00 0.00 0.00 4.02
398 400 1.554042 CCACACAACAGCGACCGTAC 61.554 60.000 0.00 0.00 0.00 3.67
399 401 0.596600 CACACAACAGCGACCGTACT 60.597 55.000 0.00 0.00 0.00 2.73
400 402 0.596600 ACACAACAGCGACCGTACTG 60.597 55.000 0.00 0.50 39.86 2.74
401 403 1.006571 ACAACAGCGACCGTACTGG 60.007 57.895 6.12 2.71 46.41 4.00
402 404 1.287815 CAACAGCGACCGTACTGGA 59.712 57.895 10.17 0.00 42.00 3.86
403 405 1.007336 CAACAGCGACCGTACTGGAC 61.007 60.000 10.17 4.00 42.00 4.02
416 418 2.802787 ACTGGACGATGTGCTATAGC 57.197 50.000 18.18 18.18 42.50 2.97
430 432 4.729227 GCTATAGCAGAGGATCCTAACC 57.271 50.000 16.16 1.92 41.59 2.85
431 433 3.449377 GCTATAGCAGAGGATCCTAACCC 59.551 52.174 16.16 1.49 41.59 4.11
436 438 0.470268 AGAGGATCCTAACCCGGAGC 60.470 60.000 16.16 0.00 38.73 4.70
454 456 6.053005 CCGGAGCTAACCAATATGAAAACTA 58.947 40.000 0.00 0.00 0.00 2.24
470 472 8.876275 ATGAAAACTATGAATTTGCGCATTAT 57.124 26.923 12.75 5.14 0.00 1.28
475 477 6.895898 ACTATGAATTTGCGCATTATCTCAG 58.104 36.000 12.75 12.43 0.00 3.35
495 497 1.811558 GCGTCCTCCATATGCACATGT 60.812 52.381 3.92 0.00 0.00 3.21
512 514 3.252458 ACATGTAGCACGCTCGATATGTA 59.748 43.478 0.00 0.00 0.00 2.29
548 550 4.932200 ACAACACAGAAACTATGCTAGAGC 59.068 41.667 0.00 0.00 42.50 4.09
589 591 5.327616 TGGAGACGGAAAATATAACGACA 57.672 39.130 0.00 0.00 0.00 4.35
592 594 6.477688 TGGAGACGGAAAATATAACGACAATC 59.522 38.462 0.00 0.00 0.00 2.67
612 614 6.183360 ACAATCCTAGAGTTGCTCTTAGTACG 60.183 42.308 3.87 0.00 41.50 3.67
624 626 4.210955 GCTCTTAGTACGTAGCGTGAGTAT 59.789 45.833 0.00 0.00 41.39 2.12
642 644 7.478322 GTGAGTATAAAATGACGTACTCCTGA 58.522 38.462 8.04 0.00 41.32 3.86
658 664 7.275123 CGTACTCCTGAACAAACTTATAGTTCC 59.725 40.741 0.00 0.00 37.47 3.62
710 717 9.494271 CTTACATAGCATACATCACCAGTTAAT 57.506 33.333 0.00 0.00 0.00 1.40
743 755 2.223112 GCGGCAAACTAGTCATGTCATG 60.223 50.000 6.47 6.47 0.00 3.07
914 959 7.201848 GGACTTTGGAATCATTCAGCAATATGA 60.202 37.037 0.00 0.00 35.43 2.15
915 960 8.070034 ACTTTGGAATCATTCAGCAATATGAA 57.930 30.769 0.00 0.00 43.04 2.57
995 1051 0.456824 CAGATCACGCACAGTACGCT 60.457 55.000 0.00 0.00 0.00 5.07
1002 1058 1.724623 ACGCACAGTACGCTTACAATG 59.275 47.619 2.93 1.82 0.00 2.82
1003 1059 1.060553 CGCACAGTACGCTTACAATGG 59.939 52.381 2.93 0.00 0.00 3.16
1004 1060 1.202031 GCACAGTACGCTTACAATGGC 60.202 52.381 2.93 0.00 0.00 4.40
1005 1061 1.396996 CACAGTACGCTTACAATGGCC 59.603 52.381 0.00 0.00 0.00 5.36
1006 1062 1.278127 ACAGTACGCTTACAATGGCCT 59.722 47.619 3.32 0.00 0.00 5.19
1007 1063 1.933853 CAGTACGCTTACAATGGCCTC 59.066 52.381 3.32 0.00 0.00 4.70
1060 1116 3.912496 TCCAGATACACCCATTGACAG 57.088 47.619 0.00 0.00 0.00 3.51
1066 1122 1.296392 CACCCATTGACAGCCGAGA 59.704 57.895 0.00 0.00 0.00 4.04
1167 1235 1.903877 TAGCTCAGCTCCTGCCAACC 61.904 60.000 0.00 0.00 40.44 3.77
1185 1253 3.918544 GGCACGGTGTTGGCATAT 58.081 55.556 10.24 0.00 41.65 1.78
1194 1262 2.285083 GTGTTGGCATATCAGGCGTTA 58.715 47.619 0.00 0.00 36.77 3.18
1266 1334 2.203294 GGGGTGCTGGTTGTCGTT 60.203 61.111 0.00 0.00 0.00 3.85
1293 1361 2.732412 TCTTGTGCCTCTTCTTCTCG 57.268 50.000 0.00 0.00 0.00 4.04
1305 1373 1.315690 TCTTCTCGTTCACCGACAGT 58.684 50.000 0.00 0.00 41.60 3.55
1398 1466 2.038007 AGCGAGGAGGAGAGGCAA 59.962 61.111 0.00 0.00 0.00 4.52
1688 1759 5.914716 AGGTGGTCCATCCCATAAATTAGTA 59.085 40.000 0.00 0.00 36.74 1.82
1786 1875 1.005975 GCTCAATCGGATTTGACGACG 60.006 52.381 0.00 0.00 43.78 5.12
1837 1927 7.814107 GCTTGATTGTATCATGTTGGAGAAAAA 59.186 33.333 0.00 0.00 39.39 1.94
1900 1995 5.983118 CCATGGTTCTTTTGTAAACAAGGAC 59.017 40.000 2.57 0.00 34.98 3.85
1935 2030 7.145323 GTCCAAAGCAAGTGTACAATTATGTT 58.855 34.615 8.43 0.00 41.05 2.71
1975 2072 2.301583 CTCCCAGGCTTATTAGAGCTCC 59.698 54.545 10.93 0.00 42.32 4.70
1993 2090 2.364970 CTCCCCATTCACTTTGTTTGCA 59.635 45.455 0.00 0.00 0.00 4.08
2001 2098 4.389890 TCACTTTGTTTGCATCAAGCTT 57.610 36.364 0.00 0.00 45.94 3.74
2211 4314 6.715347 AACACCTAAATCAATTGGATAGGC 57.285 37.500 21.81 0.00 35.82 3.93
2221 4324 1.679139 TTGGATAGGCGCCATTTCAG 58.321 50.000 31.54 0.00 34.90 3.02
2271 4381 0.242825 CGGTGTAAGAAGCGGAGTGA 59.757 55.000 0.00 0.00 37.40 3.41
2367 4477 2.209273 GCCGTTGGATTTGCTGTTTTT 58.791 42.857 0.00 0.00 0.00 1.94
2379 4489 2.171003 GCTGTTTTTGGCATCCCTAGT 58.829 47.619 0.00 0.00 0.00 2.57
2409 4519 1.597797 CCTTGTCAATGCGCCCATGT 61.598 55.000 4.18 0.00 0.00 3.21
2447 4557 2.106166 CTCTGCAGAATGGGCTAAGGAT 59.894 50.000 18.85 0.00 35.86 3.24
2462 4572 4.360431 CTAAGGATTAGGATGGCGTTGCC 61.360 52.174 0.00 0.00 46.25 4.52
2498 4608 4.261909 CCCATAGCAAAATCAGAAGCATCC 60.262 45.833 0.00 0.00 0.00 3.51
2516 4626 0.321564 CCGGTTGATTCAGGTCTGCA 60.322 55.000 0.00 0.00 0.00 4.41
2551 4664 3.206866 ACCCTCTACTATGCTACCAAGGA 59.793 47.826 0.00 0.00 0.00 3.36
2556 4669 1.137086 ACTATGCTACCAAGGACTGCG 59.863 52.381 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.493057 CGAGTGTGCTACATGTATTTGCAG 60.493 45.833 16.16 2.96 34.15 4.41
56 57 6.401047 AATTGAGGGATGCAACAGATATTG 57.599 37.500 0.00 0.00 0.00 1.90
62 63 3.947910 ACAAATTGAGGGATGCAACAG 57.052 42.857 0.00 0.00 0.00 3.16
64 65 5.414454 TGTACTACAAATTGAGGGATGCAAC 59.586 40.000 0.00 0.00 0.00 4.17
68 69 8.908786 ACATATGTACTACAAATTGAGGGATG 57.091 34.615 6.56 0.00 0.00 3.51
99 100 4.588899 TCTAATCACATCTTGGTGGTTGG 58.411 43.478 2.28 0.00 41.90 3.77
122 123 2.636403 GGTACAACCACACTCCTAACCT 59.364 50.000 0.00 0.00 38.42 3.50
153 154 5.226194 CAAAATTTGGGGTTTGATCCTCA 57.774 39.130 0.00 0.00 36.96 3.86
192 194 4.940046 CCTTGTGAAGAATGCTCACACTAT 59.060 41.667 5.31 0.00 43.04 2.12
198 200 2.553028 GGGACCTTGTGAAGAATGCTCA 60.553 50.000 0.00 0.00 0.00 4.26
226 228 1.198094 TGAGCCTTTCATCCCCACGA 61.198 55.000 0.00 0.00 0.00 4.35
231 233 1.396653 CCATGTGAGCCTTTCATCCC 58.603 55.000 0.00 0.00 38.29 3.85
232 234 1.396653 CCCATGTGAGCCTTTCATCC 58.603 55.000 0.00 0.00 38.29 3.51
234 236 1.002069 TCCCCATGTGAGCCTTTCAT 58.998 50.000 0.00 0.00 38.29 2.57
235 237 1.002069 ATCCCCATGTGAGCCTTTCA 58.998 50.000 0.00 0.00 0.00 2.69
236 238 1.396653 CATCCCCATGTGAGCCTTTC 58.603 55.000 0.00 0.00 0.00 2.62
237 239 0.032813 CCATCCCCATGTGAGCCTTT 60.033 55.000 0.00 0.00 0.00 3.11
238 240 0.920763 TCCATCCCCATGTGAGCCTT 60.921 55.000 0.00 0.00 0.00 4.35
239 241 0.920763 TTCCATCCCCATGTGAGCCT 60.921 55.000 0.00 0.00 0.00 4.58
240 242 0.466922 CTTCCATCCCCATGTGAGCC 60.467 60.000 0.00 0.00 0.00 4.70
241 243 0.466922 CCTTCCATCCCCATGTGAGC 60.467 60.000 0.00 0.00 0.00 4.26
242 244 0.184451 CCCTTCCATCCCCATGTGAG 59.816 60.000 0.00 0.00 0.00 3.51
243 245 1.288508 CCCCTTCCATCCCCATGTGA 61.289 60.000 0.00 0.00 0.00 3.58
244 246 1.231068 CCCCTTCCATCCCCATGTG 59.769 63.158 0.00 0.00 0.00 3.21
245 247 2.014550 CCCCCTTCCATCCCCATGT 61.015 63.158 0.00 0.00 0.00 3.21
246 248 2.937650 CCCCCTTCCATCCCCATG 59.062 66.667 0.00 0.00 0.00 3.66
287 289 0.826715 ATCATGGACCCACTCGTCAG 59.173 55.000 0.00 0.00 34.24 3.51
308 310 2.698797 GGATCTCAACCCGTTATCTCCA 59.301 50.000 0.00 0.00 0.00 3.86
309 311 2.966516 AGGATCTCAACCCGTTATCTCC 59.033 50.000 0.00 0.00 0.00 3.71
310 312 4.245845 GAGGATCTCAACCCGTTATCTC 57.754 50.000 0.00 0.00 0.00 2.75
341 343 4.624882 GTCATCTGCACTATAGCACTATGC 59.375 45.833 0.00 2.46 45.46 3.14
342 344 5.632764 GTGTCATCTGCACTATAGCACTATG 59.367 44.000 0.00 0.00 40.11 2.23
343 345 5.302823 TGTGTCATCTGCACTATAGCACTAT 59.697 40.000 0.00 0.00 40.11 2.12
344 346 4.644685 TGTGTCATCTGCACTATAGCACTA 59.355 41.667 0.00 0.00 40.11 2.74
345 347 3.448660 TGTGTCATCTGCACTATAGCACT 59.551 43.478 0.00 0.00 40.11 4.40
346 348 3.785486 TGTGTCATCTGCACTATAGCAC 58.215 45.455 0.00 0.00 40.11 4.40
347 349 4.677673 ATGTGTCATCTGCACTATAGCA 57.322 40.909 0.00 0.00 43.35 3.49
348 350 5.167121 CCTATGTGTCATCTGCACTATAGC 58.833 45.833 0.00 0.00 37.70 2.97
349 351 5.718146 CCCTATGTGTCATCTGCACTATAG 58.282 45.833 0.00 0.00 37.70 1.31
350 352 4.021104 GCCCTATGTGTCATCTGCACTATA 60.021 45.833 0.00 0.00 37.70 1.31
351 353 3.244353 GCCCTATGTGTCATCTGCACTAT 60.244 47.826 0.00 0.00 37.70 2.12
352 354 2.103094 GCCCTATGTGTCATCTGCACTA 59.897 50.000 0.00 0.00 37.70 2.74
353 355 1.134280 GCCCTATGTGTCATCTGCACT 60.134 52.381 0.00 0.00 37.70 4.40
354 356 1.303309 GCCCTATGTGTCATCTGCAC 58.697 55.000 0.00 0.00 37.37 4.57
355 357 0.181114 GGCCCTATGTGTCATCTGCA 59.819 55.000 0.00 0.00 0.00 4.41
356 358 0.882042 CGGCCCTATGTGTCATCTGC 60.882 60.000 0.00 0.00 0.00 4.26
357 359 0.250038 CCGGCCCTATGTGTCATCTG 60.250 60.000 0.00 0.00 0.00 2.90
358 360 1.410850 CCCGGCCCTATGTGTCATCT 61.411 60.000 0.00 0.00 0.00 2.90
359 361 1.071471 CCCGGCCCTATGTGTCATC 59.929 63.158 0.00 0.00 0.00 2.92
360 362 1.692749 ACCCGGCCCTATGTGTCAT 60.693 57.895 0.00 0.00 0.00 3.06
361 363 2.285069 ACCCGGCCCTATGTGTCA 60.285 61.111 0.00 0.00 0.00 3.58
362 364 2.504519 GACCCGGCCCTATGTGTC 59.495 66.667 0.00 0.00 0.00 3.67
363 365 3.087906 GGACCCGGCCCTATGTGT 61.088 66.667 0.00 0.00 0.00 3.72
364 366 3.087253 TGGACCCGGCCCTATGTG 61.087 66.667 11.68 0.00 0.00 3.21
365 367 3.087906 GTGGACCCGGCCCTATGT 61.088 66.667 11.68 0.00 0.00 2.29
366 368 3.087253 TGTGGACCCGGCCCTATG 61.087 66.667 11.68 0.00 0.00 2.23
367 369 3.087906 GTGTGGACCCGGCCCTAT 61.088 66.667 11.68 0.00 0.00 2.57
368 370 4.642488 TGTGTGGACCCGGCCCTA 62.642 66.667 11.68 0.00 0.00 3.53
371 373 4.572571 TGTTGTGTGGACCCGGCC 62.573 66.667 0.00 0.00 0.00 6.13
372 374 2.978010 CTGTTGTGTGGACCCGGC 60.978 66.667 0.00 0.00 0.00 6.13
373 375 2.978010 GCTGTTGTGTGGACCCGG 60.978 66.667 0.00 0.00 0.00 5.73
374 376 3.345808 CGCTGTTGTGTGGACCCG 61.346 66.667 0.00 0.00 0.00 5.28
375 377 2.110213 TCGCTGTTGTGTGGACCC 59.890 61.111 0.00 0.00 0.00 4.46
376 378 2.251642 GGTCGCTGTTGTGTGGACC 61.252 63.158 0.00 0.00 0.00 4.46
377 379 2.594962 CGGTCGCTGTTGTGTGGAC 61.595 63.158 0.00 0.00 0.00 4.02
378 380 1.736365 TACGGTCGCTGTTGTGTGGA 61.736 55.000 0.00 0.00 0.00 4.02
379 381 1.300311 TACGGTCGCTGTTGTGTGG 60.300 57.895 0.00 0.00 0.00 4.17
380 382 0.596600 AGTACGGTCGCTGTTGTGTG 60.597 55.000 0.00 0.00 0.00 3.82
381 383 0.596600 CAGTACGGTCGCTGTTGTGT 60.597 55.000 4.95 0.00 0.00 3.72
382 384 1.282248 CCAGTACGGTCGCTGTTGTG 61.282 60.000 10.39 0.00 0.00 3.33
383 385 1.006571 CCAGTACGGTCGCTGTTGT 60.007 57.895 10.39 0.00 0.00 3.32
384 386 1.007336 GTCCAGTACGGTCGCTGTTG 61.007 60.000 10.39 0.00 35.57 3.33
385 387 1.288127 GTCCAGTACGGTCGCTGTT 59.712 57.895 10.39 0.00 35.57 3.16
386 388 2.960170 GTCCAGTACGGTCGCTGT 59.040 61.111 10.39 0.00 35.57 4.40
387 389 1.989966 ATCGTCCAGTACGGTCGCTG 61.990 60.000 14.63 5.87 42.73 5.18
388 390 1.748122 ATCGTCCAGTACGGTCGCT 60.748 57.895 14.63 6.33 42.73 4.93
389 391 1.585521 CATCGTCCAGTACGGTCGC 60.586 63.158 14.63 3.60 42.73 5.19
390 392 0.522705 CACATCGTCCAGTACGGTCG 60.523 60.000 13.75 13.75 42.73 4.79
391 393 0.801067 GCACATCGTCCAGTACGGTC 60.801 60.000 0.00 0.00 42.73 4.79
393 395 6.892358 GCTATAGCACATCGTCCAGTACGG 62.892 54.167 20.01 0.00 45.66 4.02
394 396 3.909722 GCTATAGCACATCGTCCAGTACG 60.910 52.174 20.01 0.00 46.38 3.67
395 397 3.566523 GCTATAGCACATCGTCCAGTAC 58.433 50.000 20.01 0.00 41.59 2.73
396 398 3.917329 GCTATAGCACATCGTCCAGTA 57.083 47.619 20.01 0.00 41.59 2.74
397 399 2.802787 GCTATAGCACATCGTCCAGT 57.197 50.000 20.01 0.00 41.59 4.00
409 411 3.449377 GGGTTAGGATCCTCTGCTATAGC 59.551 52.174 20.22 18.18 42.50 2.97
410 412 3.697045 CGGGTTAGGATCCTCTGCTATAG 59.303 52.174 20.22 0.00 0.00 1.31
411 413 3.563697 CCGGGTTAGGATCCTCTGCTATA 60.564 52.174 20.22 0.00 0.00 1.31
412 414 2.530701 CGGGTTAGGATCCTCTGCTAT 58.469 52.381 20.22 0.00 0.00 2.97
413 415 1.480683 CCGGGTTAGGATCCTCTGCTA 60.481 57.143 20.22 0.00 0.00 3.49
414 416 0.760945 CCGGGTTAGGATCCTCTGCT 60.761 60.000 20.22 0.00 0.00 4.24
415 417 0.759436 TCCGGGTTAGGATCCTCTGC 60.759 60.000 20.22 9.52 34.92 4.26
416 418 1.333177 CTCCGGGTTAGGATCCTCTG 58.667 60.000 20.22 9.25 39.96 3.35
417 419 0.470268 GCTCCGGGTTAGGATCCTCT 60.470 60.000 20.22 0.00 39.96 3.69
418 420 0.470268 AGCTCCGGGTTAGGATCCTC 60.470 60.000 20.22 4.44 39.96 3.71
419 421 0.858369 TAGCTCCGGGTTAGGATCCT 59.142 55.000 20.48 20.48 39.96 3.24
420 422 1.343789 GTTAGCTCCGGGTTAGGATCC 59.656 57.143 2.48 2.48 39.96 3.36
421 423 1.343789 GGTTAGCTCCGGGTTAGGATC 59.656 57.143 0.00 0.00 39.96 3.36
422 424 1.343681 TGGTTAGCTCCGGGTTAGGAT 60.344 52.381 0.00 0.00 39.96 3.24
423 425 0.041535 TGGTTAGCTCCGGGTTAGGA 59.958 55.000 0.00 0.00 38.80 2.94
424 426 0.906775 TTGGTTAGCTCCGGGTTAGG 59.093 55.000 0.00 0.00 0.00 2.69
425 427 4.039973 TCATATTGGTTAGCTCCGGGTTAG 59.960 45.833 0.00 0.00 0.00 2.34
426 428 3.968649 TCATATTGGTTAGCTCCGGGTTA 59.031 43.478 0.00 0.00 0.00 2.85
427 429 2.775384 TCATATTGGTTAGCTCCGGGTT 59.225 45.455 0.00 0.00 0.00 4.11
428 430 2.404559 TCATATTGGTTAGCTCCGGGT 58.595 47.619 0.00 0.00 0.00 5.28
429 431 3.485463 TTCATATTGGTTAGCTCCGGG 57.515 47.619 0.00 0.00 0.00 5.73
430 432 4.881850 AGTTTTCATATTGGTTAGCTCCGG 59.118 41.667 0.00 0.00 0.00 5.14
431 433 7.441157 TCATAGTTTTCATATTGGTTAGCTCCG 59.559 37.037 0.00 0.00 0.00 4.63
454 456 4.543692 GCTGAGATAATGCGCAAATTCAT 58.456 39.130 17.11 2.91 0.00 2.57
470 472 0.676184 GCATATGGAGGACGCTGAGA 59.324 55.000 4.56 0.00 0.00 3.27
475 477 0.870393 CATGTGCATATGGAGGACGC 59.130 55.000 15.17 0.00 0.00 5.19
477 479 3.070018 GCTACATGTGCATATGGAGGAC 58.930 50.000 30.27 15.43 39.06 3.85
495 497 5.355910 TCCATAATACATATCGAGCGTGCTA 59.644 40.000 0.00 0.00 0.00 3.49
512 514 3.587061 TCTGTGTTGTCCACCTCCATAAT 59.413 43.478 0.00 0.00 43.85 1.28
531 533 5.659463 AGAACAGCTCTAGCATAGTTTCTG 58.341 41.667 4.54 0.00 45.16 3.02
548 550 6.746364 GTCTCCATAACGTGTACTAAGAACAG 59.254 42.308 0.00 0.00 0.00 3.16
589 591 5.887035 ACGTACTAAGAGCAACTCTAGGATT 59.113 40.000 0.00 0.00 40.28 3.01
592 594 5.277442 GCTACGTACTAAGAGCAACTCTAGG 60.277 48.000 0.93 0.00 40.28 3.02
612 614 6.909357 AGTACGTCATTTTATACTCACGCTAC 59.091 38.462 0.00 0.00 0.00 3.58
624 626 6.987992 AGTTTGTTCAGGAGTACGTCATTTTA 59.012 34.615 0.00 0.00 0.00 1.52
642 644 6.464530 AGGAAGGGGAACTATAAGTTTGTT 57.535 37.500 0.00 0.00 38.80 2.83
658 664 2.586792 CAGGAAGGCGAGGAAGGG 59.413 66.667 0.00 0.00 0.00 3.95
743 755 9.543783 AGTTGTAATAACTTATAGCCAACTAGC 57.456 33.333 13.66 0.00 0.00 3.42
792 810 2.689646 GTGGACTTCAACTCACTAGCC 58.310 52.381 0.00 0.00 0.00 3.93
850 877 4.907010 GTGTTGATTAGTCTCGCTCGATAG 59.093 45.833 0.00 0.00 0.00 2.08
1003 1059 0.461163 GAAGAAGAAGAGGCCGAGGC 60.461 60.000 5.37 5.37 41.06 4.70
1004 1060 1.136110 GAGAAGAAGAAGAGGCCGAGG 59.864 57.143 0.00 0.00 0.00 4.63
1005 1061 1.136110 GGAGAAGAAGAAGAGGCCGAG 59.864 57.143 0.00 0.00 0.00 4.63
1006 1062 1.187087 GGAGAAGAAGAAGAGGCCGA 58.813 55.000 0.00 0.00 0.00 5.54
1007 1063 0.179124 CGGAGAAGAAGAAGAGGCCG 60.179 60.000 0.00 0.00 0.00 6.13
1060 1116 1.207377 GCGGTCGTTATCTTCTCGGC 61.207 60.000 0.00 0.00 0.00 5.54
1066 1122 1.435577 GTGGTTGCGGTCGTTATCTT 58.564 50.000 0.00 0.00 0.00 2.40
1167 1235 2.047151 GATATGCCAACACCGTGCCG 62.047 60.000 0.00 0.00 0.00 5.69
1194 1262 1.375523 GTTGGTGAAGGACGGCGAT 60.376 57.895 16.62 0.00 0.00 4.58
1398 1466 0.748729 GGTCGAGATCGTCCCACTCT 60.749 60.000 7.20 0.00 40.73 3.24
1440 1511 1.227556 GTGCACGAAGTCCAGTGGT 60.228 57.895 9.54 0.00 41.61 4.16
1443 1514 2.661866 GCGTGCACGAAGTCCAGT 60.662 61.111 41.19 0.00 41.61 4.00
1975 2072 3.992643 TGATGCAAACAAAGTGAATGGG 58.007 40.909 0.00 0.00 0.00 4.00
2271 4381 8.629821 ATCTAAATGTATATATGTGGCCTCCT 57.370 34.615 3.32 0.00 0.00 3.69
2320 4430 4.392921 TTGCTAGTGCTCTAAGATGGAC 57.607 45.455 0.00 0.00 40.48 4.02
2331 4441 1.369091 CGGCGGAAATTGCTAGTGCT 61.369 55.000 0.00 0.00 40.48 4.40
2367 4477 2.447408 TCTAACGACTAGGGATGCCA 57.553 50.000 5.86 0.00 0.00 4.92
2379 4489 3.270027 CATTGACAAGGGCATCTAACGA 58.730 45.455 0.00 0.00 0.00 3.85
2409 4519 1.764723 AGAGAATGATGATCCACGGCA 59.235 47.619 0.00 0.00 0.00 5.69
2462 4572 1.271597 GCTATGGGAATAGTGGCCCTG 60.272 57.143 0.00 0.00 44.96 4.45
2498 4608 1.081892 CTGCAGACCTGAATCAACCG 58.918 55.000 8.42 0.00 0.00 4.44
2537 4647 1.409064 TCGCAGTCCTTGGTAGCATAG 59.591 52.381 0.00 0.00 0.00 2.23
2556 4669 2.866085 AATGCTCTGGCGAGGCTGTC 62.866 60.000 0.00 0.00 42.25 3.51
2593 4706 6.251801 CGATTCACACGTTGTAAAAGGTTTTT 59.748 34.615 0.00 0.00 0.00 1.94
2595 4708 5.064962 TCGATTCACACGTTGTAAAAGGTTT 59.935 36.000 0.00 0.00 0.00 3.27
2596 4709 4.571580 TCGATTCACACGTTGTAAAAGGTT 59.428 37.500 0.00 0.00 0.00 3.50
2597 4710 4.121317 TCGATTCACACGTTGTAAAAGGT 58.879 39.130 0.00 0.00 0.00 3.50
2598 4711 4.446385 TCTCGATTCACACGTTGTAAAAGG 59.554 41.667 0.00 0.00 0.00 3.11
2599 4712 5.570262 TCTCGATTCACACGTTGTAAAAG 57.430 39.130 0.00 0.00 0.00 2.27
2600 4713 5.970140 TTCTCGATTCACACGTTGTAAAA 57.030 34.783 0.00 0.00 0.00 1.52
2601 4714 5.692654 TCATTCTCGATTCACACGTTGTAAA 59.307 36.000 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.