Multiple sequence alignment - TraesCS3D01G179100

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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 TraesCS3D01G179100 chr3D 100.000 2903 0 0 1 2903 160882257 160885159 0.000000e+00 5361
1 TraesCS3D01G179100 chr3D 95.109 184 7 2 421 602 142708770 142708587 3.660000e-74 289
2 TraesCS3D01G179100 chr3A 88.875 2346 201 27 598 2903 189340634 189338309 0.000000e+00 2832
3 TraesCS3D01G179100 chr3A 88.249 417 48 1 4 419 189341046 189340630 5.590000e-137 497
4 TraesCS3D01G179100 chr3B 96.035 1362 51 2 599 1959 237605205 237606564 0.000000e+00 2213
5 TraesCS3D01G179100 chr3B 94.112 968 44 9 1946 2903 237623133 237624097 0.000000e+00 1459
6 TraesCS3D01G179100 chr3B 94.524 420 22 1 1 419 237604789 237605208 0.000000e+00 647
7 TraesCS3D01G179100 chr7D 93.137 204 10 4 398 599 161844372 161844573 2.190000e-76 296
8 TraesCS3D01G179100 chr5D 95.213 188 7 2 414 599 121102665 121102478 2.190000e-76 296
9 TraesCS3D01G179100 chr5D 95.652 184 6 2 418 599 130661326 130661509 7.870000e-76 294
10 TraesCS3D01G179100 chr5B 94.792 192 7 3 410 599 447830854 447830664 2.190000e-76 296
11 TraesCS3D01G179100 chr4D 95.187 187 7 2 415 599 503922021 503922207 7.870000e-76 294
12 TraesCS3D01G179100 chr6D 93.434 198 9 4 408 602 427225065 427225261 1.020000e-74 291
13 TraesCS3D01G179100 chr2D 94.241 191 8 3 411 599 516411003 516410814 3.660000e-74 289
14 TraesCS3D01G179100 chr2D 92.929 198 10 4 407 602 26038974 26038779 4.730000e-73 285


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 TraesCS3D01G179100 chr3D 160882257 160885159 2902 False 5361.0 5361 100.0000 1 2903 1 chr3D.!!$F1 2902
1 TraesCS3D01G179100 chr3A 189338309 189341046 2737 True 1664.5 2832 88.5620 4 2903 2 chr3A.!!$R1 2899
2 TraesCS3D01G179100 chr3B 237623133 237624097 964 False 1459.0 1459 94.1120 1946 2903 1 chr3B.!!$F1 957
3 TraesCS3D01G179100 chr3B 237604789 237606564 1775 False 1430.0 2213 95.2795 1 1959 2 chr3B.!!$F2 1958

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
537 540 0.035725 CCCTCCCGTTTGGTTCCTAC 60.036 60.0 0.0 0.0 34.77 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2440 2462 0.242825 TAGACGCACGGTTGAAGAGG 59.757 55.0 0.0 0.0 0.0 3.69 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
77 78 6.109359 CCTATCTTCAAACTTCGTCTCCATT 58.891 40.000 0.00 0.00 0.00 3.16
145 146 3.736483 GCTGGGCGTGGATATGTG 58.264 61.111 0.00 0.00 0.00 3.21
204 206 2.493675 TCTTCTCGACAATGTCAGAGGG 59.506 50.000 23.92 19.02 35.57 4.30
236 238 6.380274 TCTCCACTTCTACCGAAATATTGACT 59.620 38.462 0.00 0.00 0.00 3.41
314 316 0.955905 AAACCAAATTGACCCGTCCG 59.044 50.000 0.00 0.00 0.00 4.79
320 322 2.550606 CAAATTGACCCGTCCGAAAGAA 59.449 45.455 0.00 0.00 0.00 2.52
331 333 4.201783 CCGTCCGAAAGAATAAATGGTGTC 60.202 45.833 0.00 0.00 0.00 3.67
415 418 2.420022 GCATGCACCGACTAAACAATCT 59.580 45.455 14.21 0.00 0.00 2.40
416 419 3.728864 GCATGCACCGACTAAACAATCTG 60.729 47.826 14.21 0.00 0.00 2.90
417 420 3.394674 TGCACCGACTAAACAATCTGA 57.605 42.857 0.00 0.00 0.00 3.27
418 421 3.325870 TGCACCGACTAAACAATCTGAG 58.674 45.455 0.00 0.00 0.00 3.35
419 422 3.006430 TGCACCGACTAAACAATCTGAGA 59.994 43.478 0.00 0.00 0.00 3.27
420 423 3.614616 GCACCGACTAAACAATCTGAGAG 59.385 47.826 0.00 0.00 0.00 3.20
421 424 4.177026 CACCGACTAAACAATCTGAGAGG 58.823 47.826 0.00 0.00 0.00 3.69
422 425 3.195825 ACCGACTAAACAATCTGAGAGGG 59.804 47.826 0.00 0.00 0.00 4.30
423 426 3.195825 CCGACTAAACAATCTGAGAGGGT 59.804 47.826 0.00 0.00 0.00 4.34
424 427 4.177026 CGACTAAACAATCTGAGAGGGTG 58.823 47.826 0.00 0.00 0.00 4.61
425 428 4.322049 CGACTAAACAATCTGAGAGGGTGT 60.322 45.833 0.00 0.00 0.00 4.16
426 429 5.153950 ACTAAACAATCTGAGAGGGTGTC 57.846 43.478 0.00 0.00 0.00 3.67
427 430 4.841246 ACTAAACAATCTGAGAGGGTGTCT 59.159 41.667 0.00 0.00 38.71 3.41
428 431 3.692257 AACAATCTGAGAGGGTGTCTG 57.308 47.619 0.00 0.00 34.71 3.51
429 432 1.905215 ACAATCTGAGAGGGTGTCTGG 59.095 52.381 0.00 0.00 34.71 3.86
430 433 1.905215 CAATCTGAGAGGGTGTCTGGT 59.095 52.381 0.00 0.00 34.71 4.00
431 434 2.304180 CAATCTGAGAGGGTGTCTGGTT 59.696 50.000 0.00 0.00 34.71 3.67
432 435 1.633774 TCTGAGAGGGTGTCTGGTTC 58.366 55.000 0.00 0.00 34.71 3.62
433 436 1.133167 TCTGAGAGGGTGTCTGGTTCA 60.133 52.381 0.00 0.00 34.71 3.18
434 437 1.274728 CTGAGAGGGTGTCTGGTTCAG 59.725 57.143 0.00 0.00 34.71 3.02
435 438 1.133167 TGAGAGGGTGTCTGGTTCAGA 60.133 52.381 0.00 0.00 38.25 3.27
436 439 1.971357 GAGAGGGTGTCTGGTTCAGAA 59.029 52.381 0.00 0.00 42.46 3.02
437 440 1.974236 AGAGGGTGTCTGGTTCAGAAG 59.026 52.381 0.00 0.00 42.46 2.85
438 441 1.694696 GAGGGTGTCTGGTTCAGAAGT 59.305 52.381 0.00 0.00 42.46 3.01
439 442 1.694696 AGGGTGTCTGGTTCAGAAGTC 59.305 52.381 0.00 0.00 42.46 3.01
440 443 1.270893 GGGTGTCTGGTTCAGAAGTCC 60.271 57.143 0.00 3.27 42.46 3.85
441 444 1.694696 GGTGTCTGGTTCAGAAGTCCT 59.305 52.381 0.00 0.00 42.46 3.85
442 445 2.897969 GGTGTCTGGTTCAGAAGTCCTA 59.102 50.000 0.00 0.00 42.46 2.94
443 446 3.056465 GGTGTCTGGTTCAGAAGTCCTAG 60.056 52.174 0.00 0.00 42.46 3.02
444 447 3.056465 GTGTCTGGTTCAGAAGTCCTAGG 60.056 52.174 0.82 0.82 42.46 3.02
445 448 3.181422 TGTCTGGTTCAGAAGTCCTAGGA 60.181 47.826 7.62 7.62 42.46 2.94
446 449 3.193903 GTCTGGTTCAGAAGTCCTAGGAC 59.806 52.174 31.29 31.29 42.46 3.85
505 508 9.022884 TCTTTAGTAGAGTCTTTTTCTAGTCCC 57.977 37.037 0.00 0.00 33.84 4.46
506 509 8.953223 TTTAGTAGAGTCTTTTTCTAGTCCCT 57.047 34.615 0.00 0.00 33.84 4.20
507 510 6.844097 AGTAGAGTCTTTTTCTAGTCCCTG 57.156 41.667 0.00 0.00 0.00 4.45
508 511 6.316513 AGTAGAGTCTTTTTCTAGTCCCTGT 58.683 40.000 0.00 0.00 0.00 4.00
509 512 7.468496 AGTAGAGTCTTTTTCTAGTCCCTGTA 58.532 38.462 0.00 0.00 0.00 2.74
510 513 6.844097 AGAGTCTTTTTCTAGTCCCTGTAG 57.156 41.667 0.00 0.00 0.00 2.74
511 514 6.553857 AGAGTCTTTTTCTAGTCCCTGTAGA 58.446 40.000 0.00 0.00 0.00 2.59
512 515 7.011382 AGAGTCTTTTTCTAGTCCCTGTAGAA 58.989 38.462 0.00 0.00 35.21 2.10
513 516 7.509659 AGAGTCTTTTTCTAGTCCCTGTAGAAA 59.490 37.037 1.96 1.96 42.24 2.52
519 522 5.997384 TCTAGTCCCTGTAGAAAAAGTCC 57.003 43.478 0.00 0.00 0.00 3.85
520 523 4.776308 TCTAGTCCCTGTAGAAAAAGTCCC 59.224 45.833 0.00 0.00 0.00 4.46
521 524 3.599348 AGTCCCTGTAGAAAAAGTCCCT 58.401 45.455 0.00 0.00 0.00 4.20
522 525 3.583526 AGTCCCTGTAGAAAAAGTCCCTC 59.416 47.826 0.00 0.00 0.00 4.30
523 526 2.910977 TCCCTGTAGAAAAAGTCCCTCC 59.089 50.000 0.00 0.00 0.00 4.30
524 527 2.026169 CCCTGTAGAAAAAGTCCCTCCC 60.026 54.545 0.00 0.00 0.00 4.30
525 528 2.354805 CCTGTAGAAAAAGTCCCTCCCG 60.355 54.545 0.00 0.00 0.00 5.14
526 529 2.302157 CTGTAGAAAAAGTCCCTCCCGT 59.698 50.000 0.00 0.00 0.00 5.28
527 530 2.707257 TGTAGAAAAAGTCCCTCCCGTT 59.293 45.455 0.00 0.00 0.00 4.44
528 531 3.136992 TGTAGAAAAAGTCCCTCCCGTTT 59.863 43.478 0.00 0.00 0.00 3.60
529 532 2.583143 AGAAAAAGTCCCTCCCGTTTG 58.417 47.619 0.00 0.00 0.00 2.93
530 533 1.611977 GAAAAAGTCCCTCCCGTTTGG 59.388 52.381 0.00 0.00 0.00 3.28
531 534 0.554305 AAAAGTCCCTCCCGTTTGGT 59.446 50.000 0.00 0.00 34.77 3.67
532 535 0.554305 AAAGTCCCTCCCGTTTGGTT 59.446 50.000 0.00 0.00 34.77 3.67
533 536 0.109913 AAGTCCCTCCCGTTTGGTTC 59.890 55.000 0.00 0.00 34.77 3.62
534 537 1.303074 GTCCCTCCCGTTTGGTTCC 60.303 63.158 0.00 0.00 34.77 3.62
535 538 1.462627 TCCCTCCCGTTTGGTTCCT 60.463 57.895 0.00 0.00 34.77 3.36
536 539 0.178897 TCCCTCCCGTTTGGTTCCTA 60.179 55.000 0.00 0.00 34.77 2.94
537 540 0.035725 CCCTCCCGTTTGGTTCCTAC 60.036 60.000 0.00 0.00 34.77 3.18
538 541 0.390735 CCTCCCGTTTGGTTCCTACG 60.391 60.000 9.03 9.03 34.77 3.51
542 545 3.900446 CGTTTGGTTCCTACGGACT 57.100 52.632 8.41 0.00 0.00 3.85
543 546 2.159327 CGTTTGGTTCCTACGGACTT 57.841 50.000 8.41 0.00 0.00 3.01
544 547 2.486918 CGTTTGGTTCCTACGGACTTT 58.513 47.619 8.41 0.00 0.00 2.66
545 548 2.874086 CGTTTGGTTCCTACGGACTTTT 59.126 45.455 8.41 0.00 0.00 2.27
546 549 3.313249 CGTTTGGTTCCTACGGACTTTTT 59.687 43.478 8.41 0.00 0.00 1.94
547 550 4.511082 CGTTTGGTTCCTACGGACTTTTTA 59.489 41.667 8.41 0.00 0.00 1.52
548 551 5.333568 CGTTTGGTTCCTACGGACTTTTTAG 60.334 44.000 8.41 0.00 0.00 1.85
549 552 4.276058 TGGTTCCTACGGACTTTTTAGG 57.724 45.455 0.00 0.00 34.69 2.69
550 553 3.008266 TGGTTCCTACGGACTTTTTAGGG 59.992 47.826 0.00 0.00 34.23 3.53
551 554 3.261643 GGTTCCTACGGACTTTTTAGGGA 59.738 47.826 0.00 0.00 34.23 4.20
552 555 4.080695 GGTTCCTACGGACTTTTTAGGGAT 60.081 45.833 0.00 0.00 34.23 3.85
553 556 5.494724 GTTCCTACGGACTTTTTAGGGATT 58.505 41.667 0.00 0.00 34.23 3.01
554 557 5.767277 TCCTACGGACTTTTTAGGGATTT 57.233 39.130 0.00 0.00 34.23 2.17
555 558 6.130692 TCCTACGGACTTTTTAGGGATTTT 57.869 37.500 0.00 0.00 34.23 1.82
556 559 6.545567 TCCTACGGACTTTTTAGGGATTTTT 58.454 36.000 0.00 0.00 34.23 1.94
591 594 5.779922 GGACTAAAAATCCCTGAACCAAAC 58.220 41.667 0.00 0.00 0.00 2.93
592 595 5.303333 GGACTAAAAATCCCTGAACCAAACA 59.697 40.000 0.00 0.00 0.00 2.83
593 596 6.156748 ACTAAAAATCCCTGAACCAAACAC 57.843 37.500 0.00 0.00 0.00 3.32
594 597 4.415881 AAAAATCCCTGAACCAAACACC 57.584 40.909 0.00 0.00 0.00 4.16
595 598 2.009681 AATCCCTGAACCAAACACCC 57.990 50.000 0.00 0.00 0.00 4.61
596 599 0.114364 ATCCCTGAACCAAACACCCC 59.886 55.000 0.00 0.00 0.00 4.95
597 600 1.533033 CCCTGAACCAAACACCCCC 60.533 63.158 0.00 0.00 0.00 5.40
620 623 3.899980 TGAGGCTCAGATGCTATACATGT 59.100 43.478 14.43 2.69 39.84 3.21
688 691 1.618487 TGCATGCACCAACATCTTGA 58.382 45.000 18.46 0.00 0.00 3.02
713 716 7.008941 AGCTAATTAAGTAGGGGTAAGATCGA 58.991 38.462 11.62 0.00 0.00 3.59
719 722 8.716674 TTAAGTAGGGGTAAGATCGATAACAT 57.283 34.615 0.00 0.00 0.00 2.71
809 812 6.725834 AGGGAATAGTTGTTGTGGAATTCAAT 59.274 34.615 7.93 0.00 0.00 2.57
859 862 2.232941 TCGTTTTCTAGCCCGACAATCT 59.767 45.455 0.00 0.00 0.00 2.40
860 863 3.444742 TCGTTTTCTAGCCCGACAATCTA 59.555 43.478 0.00 0.00 0.00 1.98
880 883 6.205101 TCTAAATCTACCTCCGTCTTTCAC 57.795 41.667 0.00 0.00 0.00 3.18
982 985 0.757561 GCTCTCCTCCCTCCCACTAC 60.758 65.000 0.00 0.00 0.00 2.73
1045 1048 2.519541 TCTCCCTCGCCCTCATCG 60.520 66.667 0.00 0.00 0.00 3.84
1088 1091 3.636231 CTCCTCCGTTGCCCACCA 61.636 66.667 0.00 0.00 0.00 4.17
1131 1136 1.809619 CCGCTTTCGCATCCTTCGA 60.810 57.895 0.00 0.00 35.30 3.71
1213 1218 1.379977 CCCACCTCTCGCCTACTCA 60.380 63.158 0.00 0.00 0.00 3.41
1315 1320 6.213802 CCCTTTATTCTTATCCCTCCCTCTAC 59.786 46.154 0.00 0.00 0.00 2.59
1464 1469 1.374758 GCAGTCGAGAACCACCCAG 60.375 63.158 0.00 0.00 0.00 4.45
1482 1487 0.679505 AGCACTTGTTAGCGGAGACA 59.320 50.000 0.00 0.00 35.48 3.41
1725 1730 2.700773 GCATCTCGGGGTGGCAAAC 61.701 63.158 0.00 0.00 0.00 2.93
1731 1736 1.969589 CGGGGTGGCAAACAGGTAC 60.970 63.158 0.00 0.00 0.00 3.34
1733 1738 1.228033 GGGTGGCAAACAGGTACGT 60.228 57.895 0.00 0.00 0.00 3.57
1786 1791 2.367567 GGGACAGGTCGAAGGCATAATA 59.632 50.000 0.00 0.00 0.00 0.98
1855 1860 0.908198 GGCCATTGAGGAGACAGAGT 59.092 55.000 0.00 0.00 41.22 3.24
1967 1973 6.426633 TGATCGTCTGAATTAATGTGTGTTGT 59.573 34.615 0.00 0.00 0.00 3.32
1984 1990 3.901222 TGTTGTTCAGATGTCACCCTCTA 59.099 43.478 0.00 0.00 0.00 2.43
2012 2018 9.509956 AACAGTTAGTTGTATGTGGCTAAATTA 57.490 29.630 0.00 0.00 39.49 1.40
2162 2168 3.624900 CCATGCATCAACATCATTCGTC 58.375 45.455 0.00 0.00 0.00 4.20
2194 2200 1.684450 GGACCAAAAATCCAACGGTGT 59.316 47.619 0.00 0.00 36.15 4.16
2206 2212 2.417651 CCAACGGTGTACATATGGTCGT 60.418 50.000 7.80 6.48 0.00 4.34
2214 2220 2.779755 ACATATGGTCGTGCTGGAAA 57.220 45.000 7.80 0.00 0.00 3.13
2269 2290 9.088987 AGGCTAGTTTTTATCAAAAATCCTTGA 57.911 29.630 0.61 0.00 41.85 3.02
2338 2359 2.610438 ATCCCATGCAAAGGTCACTT 57.390 45.000 7.67 0.00 38.99 3.16
2404 2426 4.002906 TGTCGCTACCTGAAGTTTCATT 57.997 40.909 0.00 0.00 36.46 2.57
2554 2576 8.699749 GTTTCGGATGAACCTTTTTCAAAATAG 58.300 33.333 0.00 0.00 32.71 1.73
2609 2631 7.770801 AAAAAGCACAATTGTCCTTCTTTAC 57.229 32.000 15.03 0.00 0.00 2.01
2631 2653 4.397417 ACTTTTCTGGAAGCATATCTGTGC 59.603 41.667 0.00 0.00 45.38 4.57
2757 2780 4.242475 TGTGGAAGTATAGTTGTGCTTCG 58.758 43.478 0.00 0.00 40.41 3.79
2759 2782 3.259064 GGAAGTATAGTTGTGCTTCGCA 58.741 45.455 0.00 0.00 40.41 5.10
2819 2860 6.410914 CACTCGAAAACACAACTGTATTTCAC 59.589 38.462 15.16 2.80 32.55 3.18
2829 2870 2.806244 ACTGTATTTCACCGTGAAGCAC 59.194 45.455 13.51 14.64 37.70 4.40
2855 2896 0.371645 GCTTTTCCAGACGATGCTCG 59.628 55.000 0.00 4.36 46.93 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.275418 GTTCCCCATGGTCGGCAT 59.725 61.111 11.73 0.00 0.00 4.40
21 22 3.003482 GCAGATCCGATCTACTAACGTGT 59.997 47.826 10.65 0.00 37.58 4.49
77 78 5.353394 AAGATGATTACGCCAAGAAGGTA 57.647 39.130 0.00 0.00 40.61 3.08
173 175 2.897436 TGTCGAGAAGATGGATGCAAG 58.103 47.619 0.00 0.00 0.00 4.01
204 206 2.094130 CGGTAGAAGTGGAGACCCTTTC 60.094 54.545 0.00 0.00 0.00 2.62
236 238 0.536233 TTTAGCTGCAAGGCGGACAA 60.536 50.000 1.02 0.00 37.02 3.18
314 316 5.095490 CCTTGCGACACCATTTATTCTTTC 58.905 41.667 0.00 0.00 0.00 2.62
320 322 1.762708 CCCCTTGCGACACCATTTAT 58.237 50.000 0.00 0.00 0.00 1.40
415 418 1.133167 TCTGAACCAGACACCCTCTCA 60.133 52.381 0.00 0.00 35.39 3.27
416 419 1.633774 TCTGAACCAGACACCCTCTC 58.366 55.000 0.00 0.00 35.39 3.20
417 420 1.974236 CTTCTGAACCAGACACCCTCT 59.026 52.381 0.00 0.00 40.46 3.69
418 421 1.694696 ACTTCTGAACCAGACACCCTC 59.305 52.381 0.00 0.00 40.46 4.30
419 422 1.694696 GACTTCTGAACCAGACACCCT 59.305 52.381 0.00 0.00 40.46 4.34
420 423 1.270893 GGACTTCTGAACCAGACACCC 60.271 57.143 0.00 0.00 40.46 4.61
421 424 1.694696 AGGACTTCTGAACCAGACACC 59.305 52.381 0.00 1.67 40.46 4.16
422 425 3.056465 CCTAGGACTTCTGAACCAGACAC 60.056 52.174 1.05 0.00 40.46 3.67
423 426 3.165875 CCTAGGACTTCTGAACCAGACA 58.834 50.000 1.05 0.00 40.46 3.41
424 427 3.193903 GTCCTAGGACTTCTGAACCAGAC 59.806 52.174 31.12 3.26 41.57 3.51
425 428 3.432378 GTCCTAGGACTTCTGAACCAGA 58.568 50.000 31.12 0.00 41.57 3.86
426 429 3.878160 GTCCTAGGACTTCTGAACCAG 57.122 52.381 31.12 0.00 41.57 4.00
479 482 9.022884 GGGACTAGAAAAAGACTCTACTAAAGA 57.977 37.037 0.00 0.00 0.00 2.52
480 483 9.027202 AGGGACTAGAAAAAGACTCTACTAAAG 57.973 37.037 0.00 0.00 36.02 1.85
481 484 8.804204 CAGGGACTAGAAAAAGACTCTACTAAA 58.196 37.037 0.00 0.00 36.02 1.85
482 485 7.949006 ACAGGGACTAGAAAAAGACTCTACTAA 59.051 37.037 0.00 0.00 36.02 2.24
483 486 7.468496 ACAGGGACTAGAAAAAGACTCTACTA 58.532 38.462 0.00 0.00 36.02 1.82
484 487 6.316513 ACAGGGACTAGAAAAAGACTCTACT 58.683 40.000 0.00 0.00 36.02 2.57
485 488 6.593268 ACAGGGACTAGAAAAAGACTCTAC 57.407 41.667 0.00 0.00 36.02 2.59
486 489 7.696981 TCTACAGGGACTAGAAAAAGACTCTA 58.303 38.462 0.00 0.00 36.02 2.43
487 490 6.553857 TCTACAGGGACTAGAAAAAGACTCT 58.446 40.000 0.00 0.00 36.02 3.24
488 491 6.837471 TCTACAGGGACTAGAAAAAGACTC 57.163 41.667 0.00 0.00 36.02 3.36
489 492 7.613551 TTTCTACAGGGACTAGAAAAAGACT 57.386 36.000 0.00 0.00 37.31 3.24
490 493 8.672823 TTTTTCTACAGGGACTAGAAAAAGAC 57.327 34.615 16.61 0.00 46.05 3.01
494 497 7.222161 GGACTTTTTCTACAGGGACTAGAAAA 58.778 38.462 0.00 8.58 43.60 2.29
495 498 6.239800 GGGACTTTTTCTACAGGGACTAGAAA 60.240 42.308 0.00 0.00 38.08 2.52
496 499 5.247792 GGGACTTTTTCTACAGGGACTAGAA 59.752 44.000 0.00 0.00 36.02 2.10
497 500 4.776308 GGGACTTTTTCTACAGGGACTAGA 59.224 45.833 0.00 0.00 36.02 2.43
498 501 4.778427 AGGGACTTTTTCTACAGGGACTAG 59.222 45.833 0.00 0.00 28.08 2.57
499 502 4.759953 AGGGACTTTTTCTACAGGGACTA 58.240 43.478 0.00 0.00 28.08 2.59
500 503 3.583526 GAGGGACTTTTTCTACAGGGACT 59.416 47.826 0.00 0.00 41.55 3.85
501 504 3.307550 GGAGGGACTTTTTCTACAGGGAC 60.308 52.174 0.00 0.00 41.55 4.46
502 505 2.910977 GGAGGGACTTTTTCTACAGGGA 59.089 50.000 0.00 0.00 41.55 4.20
503 506 2.026169 GGGAGGGACTTTTTCTACAGGG 60.026 54.545 0.00 0.00 41.55 4.45
504 507 2.354805 CGGGAGGGACTTTTTCTACAGG 60.355 54.545 0.00 0.00 41.55 4.00
505 508 2.302157 ACGGGAGGGACTTTTTCTACAG 59.698 50.000 0.00 0.00 41.55 2.74
506 509 2.332117 ACGGGAGGGACTTTTTCTACA 58.668 47.619 0.00 0.00 41.55 2.74
507 510 3.413846 AACGGGAGGGACTTTTTCTAC 57.586 47.619 0.00 0.00 41.55 2.59
508 511 3.497227 CCAAACGGGAGGGACTTTTTCTA 60.497 47.826 0.00 0.00 41.55 2.10
509 512 2.583143 CAAACGGGAGGGACTTTTTCT 58.417 47.619 0.00 0.00 41.55 2.52
510 513 1.611977 CCAAACGGGAGGGACTTTTTC 59.388 52.381 0.00 0.00 41.55 2.29
511 514 1.063492 ACCAAACGGGAGGGACTTTTT 60.063 47.619 0.00 0.00 41.55 1.94
512 515 0.554305 ACCAAACGGGAGGGACTTTT 59.446 50.000 0.00 0.00 41.55 2.27
513 516 0.554305 AACCAAACGGGAGGGACTTT 59.446 50.000 0.00 0.00 41.55 2.66
514 517 0.109913 GAACCAAACGGGAGGGACTT 59.890 55.000 0.00 0.00 41.55 3.01
516 519 1.303074 GGAACCAAACGGGAGGGAC 60.303 63.158 0.00 0.00 41.15 4.46
517 520 0.178897 TAGGAACCAAACGGGAGGGA 60.179 55.000 0.00 0.00 41.15 4.20
518 521 0.035725 GTAGGAACCAAACGGGAGGG 60.036 60.000 0.00 0.00 41.15 4.30
519 522 0.390735 CGTAGGAACCAAACGGGAGG 60.391 60.000 9.72 0.00 41.15 4.30
520 523 3.132863 CGTAGGAACCAAACGGGAG 57.867 57.895 9.72 0.00 41.15 4.30
568 571 5.303333 TGTTTGGTTCAGGGATTTTTAGTCC 59.697 40.000 0.00 0.00 34.92 3.85
569 572 6.213677 GTGTTTGGTTCAGGGATTTTTAGTC 58.786 40.000 0.00 0.00 0.00 2.59
570 573 5.069914 GGTGTTTGGTTCAGGGATTTTTAGT 59.930 40.000 0.00 0.00 0.00 2.24
571 574 5.510690 GGGTGTTTGGTTCAGGGATTTTTAG 60.511 44.000 0.00 0.00 0.00 1.85
572 575 4.345547 GGGTGTTTGGTTCAGGGATTTTTA 59.654 41.667 0.00 0.00 0.00 1.52
573 576 3.135712 GGGTGTTTGGTTCAGGGATTTTT 59.864 43.478 0.00 0.00 0.00 1.94
574 577 2.703536 GGGTGTTTGGTTCAGGGATTTT 59.296 45.455 0.00 0.00 0.00 1.82
575 578 2.325484 GGGTGTTTGGTTCAGGGATTT 58.675 47.619 0.00 0.00 0.00 2.17
576 579 1.482365 GGGGTGTTTGGTTCAGGGATT 60.482 52.381 0.00 0.00 0.00 3.01
577 580 0.114364 GGGGTGTTTGGTTCAGGGAT 59.886 55.000 0.00 0.00 0.00 3.85
578 581 1.539665 GGGGTGTTTGGTTCAGGGA 59.460 57.895 0.00 0.00 0.00 4.20
579 582 1.533033 GGGGGTGTTTGGTTCAGGG 60.533 63.158 0.00 0.00 0.00 4.45
580 583 0.827507 CAGGGGGTGTTTGGTTCAGG 60.828 60.000 0.00 0.00 0.00 3.86
581 584 0.184933 TCAGGGGGTGTTTGGTTCAG 59.815 55.000 0.00 0.00 0.00 3.02
582 585 0.184933 CTCAGGGGGTGTTTGGTTCA 59.815 55.000 0.00 0.00 0.00 3.18
583 586 0.539669 CCTCAGGGGGTGTTTGGTTC 60.540 60.000 0.00 0.00 0.00 3.62
584 587 1.541672 CCTCAGGGGGTGTTTGGTT 59.458 57.895 0.00 0.00 0.00 3.67
585 588 3.146828 GCCTCAGGGGGTGTTTGGT 62.147 63.158 0.00 0.00 35.12 3.67
586 589 2.283173 GCCTCAGGGGGTGTTTGG 60.283 66.667 0.00 0.00 35.12 3.28
587 590 2.846532 AGCCTCAGGGGGTGTTTG 59.153 61.111 0.00 0.00 45.16 2.93
593 596 3.117452 GCATCTGAGCCTCAGGGGG 62.117 68.421 21.14 11.87 44.39 5.40
594 597 0.762082 TAGCATCTGAGCCTCAGGGG 60.762 60.000 21.14 14.19 44.39 4.79
595 598 1.350071 ATAGCATCTGAGCCTCAGGG 58.650 55.000 21.14 14.53 44.39 4.45
596 599 2.896044 TGTATAGCATCTGAGCCTCAGG 59.104 50.000 21.14 7.69 44.39 3.86
597 600 4.021280 ACATGTATAGCATCTGAGCCTCAG 60.021 45.833 15.79 15.79 45.59 3.35
652 655 3.829886 TGCATACCGAAGAAAGCTTTG 57.170 42.857 18.30 4.02 33.61 2.77
688 691 7.008941 TCGATCTTACCCCTACTTAATTAGCT 58.991 38.462 0.00 0.00 0.00 3.32
713 716 7.441458 GGAGAGCCAAAGTACGATTAATGTTAT 59.559 37.037 0.00 0.00 0.00 1.89
719 722 5.046878 TGAAGGAGAGCCAAAGTACGATTAA 60.047 40.000 0.00 0.00 36.29 1.40
809 812 3.695606 GGCGTGAGGTGGAGCTCA 61.696 66.667 17.19 4.42 0.00 4.26
859 862 4.990257 CGTGAAAGACGGAGGTAGATTTA 58.010 43.478 0.00 0.00 44.85 1.40
860 863 3.846360 CGTGAAAGACGGAGGTAGATTT 58.154 45.455 0.00 0.00 44.85 2.17
1045 1048 3.462678 GTGGGAGAGGGAGGCGAC 61.463 72.222 0.00 0.00 0.00 5.19
1088 1091 2.961893 TTAGTGTGCGCGGGGGATT 61.962 57.895 8.83 0.00 0.00 3.01
1102 1107 1.223187 CGAAAGCGGTGGTTGTTAGT 58.777 50.000 0.00 0.00 0.00 2.24
1131 1136 3.430929 GGAGTATGCGAAAGAGTGGATGT 60.431 47.826 0.00 0.00 0.00 3.06
1213 1218 1.625508 GGGAGGTAGGAGGGTGAATGT 60.626 57.143 0.00 0.00 0.00 2.71
1464 1469 1.726853 ATGTCTCCGCTAACAAGTGC 58.273 50.000 0.00 0.00 0.00 4.40
1725 1730 1.438651 CACCATCAACCACGTACCTG 58.561 55.000 0.00 0.00 0.00 4.00
1731 1736 2.361104 CCCCCACCATCAACCACG 60.361 66.667 0.00 0.00 0.00 4.94
1733 1738 1.660019 AACACCCCCACCATCAACCA 61.660 55.000 0.00 0.00 0.00 3.67
1786 1791 3.503365 CATCATATGAACCCCCAATGCT 58.497 45.455 9.99 0.00 0.00 3.79
1984 1990 7.811117 TTAGCCACATACAACTAACTGTTTT 57.189 32.000 0.00 0.00 36.63 2.43
2162 2168 2.144833 TTTGGTCCAAGCATGCGCAG 62.145 55.000 18.32 9.45 42.27 5.18
2194 2200 3.196901 ACTTTCCAGCACGACCATATGTA 59.803 43.478 1.24 0.00 0.00 2.29
2206 2212 2.803133 CGACTCAACAGACTTTCCAGCA 60.803 50.000 0.00 0.00 0.00 4.41
2275 2296 9.809096 TTCAAATTTATTGTGACTTGTTTAGCA 57.191 25.926 0.00 0.00 0.00 3.49
2310 2331 4.854436 ACCTTTGCATGGGATATCCTCTAT 59.146 41.667 21.18 10.61 36.20 1.98
2338 2359 3.961480 ATCACCACGAGAGAATGTGAA 57.039 42.857 0.00 0.00 38.82 3.18
2377 2398 2.263077 CTTCAGGTAGCGACATGTGTC 58.737 52.381 11.33 3.07 38.52 3.67
2440 2462 0.242825 TAGACGCACGGTTGAAGAGG 59.757 55.000 0.00 0.00 0.00 3.69
2565 2587 6.641169 TTTTTGGTTTCTGGCTTTTTGTTT 57.359 29.167 0.00 0.00 0.00 2.83
2609 2631 4.918037 GCACAGATATGCTTCCAGAAAAG 58.082 43.478 0.00 0.00 42.62 2.27
2721 2744 2.928801 TCCACAGCTGTGCTTTTCTA 57.071 45.000 36.38 14.80 44.34 2.10
2734 2757 4.327357 CGAAGCACAACTATACTTCCACAG 59.673 45.833 0.00 0.00 36.08 3.66
2757 2780 6.978080 TGGTTCTCAAAAGTAAATTGAACTGC 59.022 34.615 0.00 0.00 36.43 4.40
2759 2782 7.973944 GTGTGGTTCTCAAAAGTAAATTGAACT 59.026 33.333 0.00 0.00 36.43 3.01
2829 2870 1.860078 GTCTGGAAAAGCACGGTCG 59.140 57.895 0.00 0.00 0.00 4.79
2830 2871 0.599204 TCGTCTGGAAAAGCACGGTC 60.599 55.000 0.00 0.00 33.19 4.79


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

AutoCloner maintained by Alex Coulton.