Multiple sequence alignment - TraesCS4D01G327400

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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 TraesCS4D01G327400 chr4D 100.000 3975 0 0 1 3975 486776386 486772412 0.000000e+00 7341.0
1 TraesCS4D01G327400 chr4D 96.842 95 2 1 462 556 89424066 89423973 1.480000e-34 158.0
2 TraesCS4D01G327400 chr4B 93.654 3388 135 19 587 3966 621441139 621437824 0.000000e+00 4992.0
3 TraesCS4D01G327400 chr4B 86.498 474 19 15 4 455 621442964 621442514 2.780000e-131 479.0
4 TraesCS4D01G327400 chr5A 93.101 1551 54 18 765 2307 667107177 667105672 0.000000e+00 2222.0
5 TraesCS4D01G327400 chr5A 88.527 1351 85 38 2300 3617 667105647 667104334 0.000000e+00 1572.0
6 TraesCS4D01G327400 chr5A 82.957 487 34 20 1 463 667107933 667107472 1.040000e-105 394.0
7 TraesCS4D01G327400 chr5A 87.755 196 8 6 587 771 667107464 667107274 8.650000e-52 215.0
8 TraesCS4D01G327400 chr5A 96.842 95 3 0 462 556 320214237 320214331 4.110000e-35 159.0
9 TraesCS4D01G327400 chr6B 91.453 117 8 2 469 584 561700716 561700601 4.110000e-35 159.0
10 TraesCS4D01G327400 chr5D 96.842 95 3 0 462 556 279302881 279302787 4.110000e-35 159.0
11 TraesCS4D01G327400 chr5D 90.741 54 1 2 549 599 241841808 241841756 7.130000e-08 69.4
12 TraesCS4D01G327400 chr7A 93.396 106 5 2 452 556 498937189 498937293 5.320000e-34 156.0
13 TraesCS4D01G327400 chr5B 94.118 102 4 2 457 556 313151782 313151883 1.910000e-33 154.0
14 TraesCS4D01G327400 chr5B 100.000 29 0 0 3470 3498 36072064 36072092 2.000000e-03 54.7
15 TraesCS4D01G327400 chr3B 90.000 120 10 1 467 586 5745790 5745673 1.910000e-33 154.0
16 TraesCS4D01G327400 chr3B 89.831 118 8 3 469 584 408630977 408630862 8.900000e-32 148.0
17 TraesCS4D01G327400 chrUn 89.831 118 10 2 469 584 27488164 27488281 2.470000e-32 150.0
18 TraesCS4D01G327400 chr2B 95.455 44 1 1 549 592 104712467 104712509 7.130000e-08 69.4
19 TraesCS4D01G327400 chr6D 91.837 49 2 2 549 596 353051926 353051879 2.560000e-07 67.6


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 TraesCS4D01G327400 chr4D 486772412 486776386 3974 True 7341.00 7341 100.000 1 3975 1 chr4D.!!$R2 3974
1 TraesCS4D01G327400 chr4B 621437824 621442964 5140 True 2735.50 4992 90.076 4 3966 2 chr4B.!!$R1 3962
2 TraesCS4D01G327400 chr5A 667104334 667107933 3599 True 1100.75 2222 88.085 1 3617 4 chr5A.!!$R1 3616

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
915 2313 0.806492 GGTGAATCTTCGCTCCGGTC 60.806 60.0 0.00 0.0 37.80 4.79 F
916 2314 0.806492 GTGAATCTTCGCTCCGGTCC 60.806 60.0 0.00 0.0 34.94 4.46 F
1794 3196 1.313812 ACGAAGGGTACGAGCTCCTG 61.314 60.0 8.47 0.0 34.70 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 3433 0.607489 ACGTACGTACCCAGAGCACT 60.607 55.000 21.41 0.00 0.00 4.40 R
2641 4079 2.334946 CCACTGGTTCACCATGGCG 61.335 63.158 13.04 1.26 46.46 5.69 R
3599 5065 0.169009 GAATGAACAGCTCCGGCAAC 59.831 55.000 0.00 0.00 41.70 4.17 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 91 2.029666 ACGCTGCTGACTGACCAC 59.970 61.111 0.00 0.00 0.00 4.16
110 124 4.338400 TCGTGGAGACAGGTTATGATACTG 59.662 45.833 0.00 0.00 46.12 2.74
133 147 4.572389 GCGATGGGCTATTGGTAATCATAG 59.428 45.833 0.00 0.00 39.11 2.23
183 198 6.622427 AGCCTAACTCCTGTTGTTTACTAT 57.378 37.500 0.00 0.00 37.59 2.12
184 199 6.407202 AGCCTAACTCCTGTTGTTTACTATG 58.593 40.000 0.00 0.00 37.59 2.23
185 200 6.212791 AGCCTAACTCCTGTTGTTTACTATGA 59.787 38.462 0.00 0.00 37.59 2.15
187 202 7.612677 CCTAACTCCTGTTGTTTACTATGAGT 58.387 38.462 0.00 0.00 37.59 3.41
188 203 8.746530 CCTAACTCCTGTTGTTTACTATGAGTA 58.253 37.037 0.00 0.00 37.59 2.59
189 204 9.570488 CTAACTCCTGTTGTTTACTATGAGTAC 57.430 37.037 0.00 0.00 37.59 2.73
190 205 7.534723 ACTCCTGTTGTTTACTATGAGTACA 57.465 36.000 0.00 0.00 32.02 2.90
191 206 7.376615 ACTCCTGTTGTTTACTATGAGTACAC 58.623 38.462 0.00 0.00 33.27 2.90
192 207 7.014905 ACTCCTGTTGTTTACTATGAGTACACA 59.985 37.037 0.00 0.00 38.99 3.72
193 208 7.149973 TCCTGTTGTTTACTATGAGTACACAC 58.850 38.462 5.36 3.26 40.04 3.82
194 209 6.367969 CCTGTTGTTTACTATGAGTACACACC 59.632 42.308 5.36 0.63 40.04 4.16
195 210 6.818233 TGTTGTTTACTATGAGTACACACCA 58.182 36.000 5.36 2.94 40.04 4.17
196 211 7.273712 TGTTGTTTACTATGAGTACACACCAA 58.726 34.615 5.36 0.00 40.04 3.67
197 212 7.225145 TGTTGTTTACTATGAGTACACACCAAC 59.775 37.037 5.36 3.36 40.04 3.77
198 213 7.058023 TGTTTACTATGAGTACACACCAACT 57.942 36.000 0.00 0.00 36.71 3.16
199 214 6.926826 TGTTTACTATGAGTACACACCAACTG 59.073 38.462 0.00 0.00 36.71 3.16
200 215 6.659745 TTACTATGAGTACACACCAACTGT 57.340 37.500 0.00 0.00 28.93 3.55
282 299 0.837691 ACACAGGAGACCTCATGCCA 60.838 55.000 11.09 0.00 44.38 4.92
326 343 1.028905 ATCCACACACAAAACCCACG 58.971 50.000 0.00 0.00 0.00 4.94
463 505 6.948886 AGATGCTAGCTGCCTTATACTACTAA 59.051 38.462 17.23 0.00 42.00 2.24
467 509 7.147794 TGCTAGCTGCCTTATACTACTAACAAA 60.148 37.037 17.23 0.00 42.00 2.83
468 510 7.873505 GCTAGCTGCCTTATACTACTAACAAAT 59.126 37.037 7.70 0.00 35.15 2.32
471 513 8.925338 AGCTGCCTTATACTACTAACAAATACT 58.075 33.333 0.00 0.00 0.00 2.12
472 514 9.194271 GCTGCCTTATACTACTAACAAATACTC 57.806 37.037 0.00 0.00 0.00 2.59
473 515 9.694137 CTGCCTTATACTACTAACAAATACTCC 57.306 37.037 0.00 0.00 0.00 3.85
474 516 8.645110 TGCCTTATACTACTAACAAATACTCCC 58.355 37.037 0.00 0.00 0.00 4.30
475 517 8.868103 GCCTTATACTACTAACAAATACTCCCT 58.132 37.037 0.00 0.00 0.00 4.20
478 520 5.848833 ACTACTAACAAATACTCCCTCCG 57.151 43.478 0.00 0.00 0.00 4.63
479 521 5.267587 ACTACTAACAAATACTCCCTCCGT 58.732 41.667 0.00 0.00 0.00 4.69
481 523 5.082251 ACTAACAAATACTCCCTCCGTTC 57.918 43.478 0.00 0.00 0.00 3.95
482 524 3.345508 AACAAATACTCCCTCCGTTCC 57.654 47.619 0.00 0.00 0.00 3.62
483 525 2.547990 ACAAATACTCCCTCCGTTCCT 58.452 47.619 0.00 0.00 0.00 3.36
484 526 3.716431 ACAAATACTCCCTCCGTTCCTA 58.284 45.455 0.00 0.00 0.00 2.94
485 527 4.098894 ACAAATACTCCCTCCGTTCCTAA 58.901 43.478 0.00 0.00 0.00 2.69
486 528 4.533311 ACAAATACTCCCTCCGTTCCTAAA 59.467 41.667 0.00 0.00 0.00 1.85
487 529 5.191124 ACAAATACTCCCTCCGTTCCTAAAT 59.809 40.000 0.00 0.00 0.00 1.40
488 530 6.384886 ACAAATACTCCCTCCGTTCCTAAATA 59.615 38.462 0.00 0.00 0.00 1.40
490 532 8.591072 CAAATACTCCCTCCGTTCCTAAATATA 58.409 37.037 0.00 0.00 0.00 0.86
491 533 8.731591 AATACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
493 535 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
494 536 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
495 537 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
496 538 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
497 539 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
498 540 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
499 541 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
516 558 9.466497 AAGTCTTTTTAGAGATTCCAATATGCA 57.534 29.630 0.00 0.00 0.00 3.96
517 559 8.897752 AGTCTTTTTAGAGATTCCAATATGCAC 58.102 33.333 0.00 0.00 0.00 4.57
518 560 8.897752 GTCTTTTTAGAGATTCCAATATGCACT 58.102 33.333 0.00 0.00 0.00 4.40
521 563 9.679661 TTTTTAGAGATTCCAATATGCACTACA 57.320 29.630 0.00 0.00 0.00 2.74
522 564 9.851686 TTTTAGAGATTCCAATATGCACTACAT 57.148 29.630 0.00 0.00 43.18 2.29
524 566 9.929180 TTAGAGATTCCAATATGCACTACATAC 57.071 33.333 0.00 0.00 43.99 2.39
525 567 7.093354 AGAGATTCCAATATGCACTACATACG 58.907 38.462 0.00 0.00 43.99 3.06
526 568 6.166279 AGATTCCAATATGCACTACATACGG 58.834 40.000 0.00 0.00 43.99 4.02
527 569 5.538849 TTCCAATATGCACTACATACGGA 57.461 39.130 0.00 0.00 43.99 4.69
530 572 4.306600 CAATATGCACTACATACGGAGCA 58.693 43.478 0.00 0.00 43.99 4.26
531 573 2.979814 ATGCACTACATACGGAGCAA 57.020 45.000 0.00 0.00 37.17 3.91
532 574 2.753055 TGCACTACATACGGAGCAAA 57.247 45.000 0.00 0.00 0.00 3.68
533 575 3.046968 TGCACTACATACGGAGCAAAA 57.953 42.857 0.00 0.00 0.00 2.44
535 577 3.373748 TGCACTACATACGGAGCAAAATG 59.626 43.478 0.00 0.00 0.00 2.32
536 578 3.621268 GCACTACATACGGAGCAAAATGA 59.379 43.478 0.00 0.00 0.00 2.57
537 579 4.260375 GCACTACATACGGAGCAAAATGAG 60.260 45.833 0.00 0.00 0.00 2.90
538 580 4.870426 CACTACATACGGAGCAAAATGAGT 59.130 41.667 0.00 0.00 0.00 3.41
539 581 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
540 582 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
541 583 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
542 584 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
544 586 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
545 587 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
546 588 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
547 589 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
548 590 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
575 617 9.211485 TCTAAAAAGACTTACATTTAGGAACGG 57.789 33.333 13.94 0.00 36.48 4.44
576 618 9.211485 CTAAAAAGACTTACATTTAGGAACGGA 57.789 33.333 8.91 0.00 33.69 4.69
577 619 7.668525 AAAAGACTTACATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
579 621 5.721232 AGACTTACATTTAGGAACGGAGTG 58.279 41.667 0.00 0.00 45.00 3.51
580 622 5.479375 AGACTTACATTTAGGAACGGAGTGA 59.521 40.000 0.00 0.00 45.00 3.41
581 623 5.721232 ACTTACATTTAGGAACGGAGTGAG 58.279 41.667 0.00 0.00 45.00 3.51
583 625 6.435277 ACTTACATTTAGGAACGGAGTGAGTA 59.565 38.462 0.00 0.00 45.00 2.59
584 626 5.326200 ACATTTAGGAACGGAGTGAGTAG 57.674 43.478 0.00 0.00 45.00 2.57
585 627 4.771054 ACATTTAGGAACGGAGTGAGTAGT 59.229 41.667 0.00 0.00 45.00 2.73
914 2312 1.218316 GGTGAATCTTCGCTCCGGT 59.782 57.895 0.00 0.00 37.80 5.28
915 2313 0.806492 GGTGAATCTTCGCTCCGGTC 60.806 60.000 0.00 0.00 37.80 4.79
916 2314 0.806492 GTGAATCTTCGCTCCGGTCC 60.806 60.000 0.00 0.00 34.94 4.46
917 2315 1.589196 GAATCTTCGCTCCGGTCCG 60.589 63.158 3.60 3.60 0.00 4.79
979 2378 3.535629 TTCCCTCACAGGCAGCACG 62.536 63.158 0.00 0.00 32.73 5.34
1120 2522 2.125106 CCACCAGCTTCGCCTACC 60.125 66.667 0.00 0.00 0.00 3.18
1579 2981 4.373116 GGCAGGTCGACGCCTTCA 62.373 66.667 22.67 0.00 45.29 3.02
1794 3196 1.313812 ACGAAGGGTACGAGCTCCTG 61.314 60.000 8.47 0.00 34.70 3.86
2107 3509 9.877178 ATACAACTTTTTCACCAAATTAACACA 57.123 25.926 0.00 0.00 0.00 3.72
2168 3570 7.094720 GGAGTAGTATTACGTATGCAGATCACT 60.095 40.741 0.00 0.00 34.88 3.41
2268 3674 1.676615 CCATGCAAAATTCCACCAGCC 60.677 52.381 0.00 0.00 0.00 4.85
2315 3753 9.208022 CGAATCATTTTAATGGATAGAGCACTA 57.792 33.333 2.85 0.00 37.03 2.74
2318 3756 8.262601 TCATTTTAATGGATAGAGCACTAGGA 57.737 34.615 2.85 0.00 37.03 2.94
2320 3758 6.672266 TTTAATGGATAGAGCACTAGGAGG 57.328 41.667 0.00 0.00 31.78 4.30
2322 3760 3.517296 TGGATAGAGCACTAGGAGGAG 57.483 52.381 0.00 0.00 31.78 3.69
2323 3761 2.786445 TGGATAGAGCACTAGGAGGAGT 59.214 50.000 0.00 0.00 31.78 3.85
2324 3762 3.205507 TGGATAGAGCACTAGGAGGAGTT 59.794 47.826 0.00 0.00 31.78 3.01
2339 3777 6.122964 AGGAGGAGTTATACAAGAAAATGGC 58.877 40.000 0.00 0.00 0.00 4.40
2371 3809 4.767578 TTTCCAGGAGATGATCTTCAGG 57.232 45.455 5.84 5.84 30.37 3.86
2830 4268 3.338250 TCCCTGGCCATGACCACC 61.338 66.667 5.51 0.00 35.33 4.61
2839 4277 4.388499 ATGACCACCGTGACCGCC 62.388 66.667 0.00 0.00 0.00 6.13
2989 4430 4.050934 TGATGTGCTCGTCGCGGT 62.051 61.111 6.13 0.00 43.27 5.68
3038 4479 2.621407 CCCACCGTCCCTACTACAGTAA 60.621 54.545 0.00 0.00 0.00 2.24
3203 4661 0.593618 TGTGAGCGTGAGAGTGACTC 59.406 55.000 3.98 3.98 45.11 3.36
3293 4751 2.054687 TAGTACACCGTTGCTTGTCG 57.945 50.000 0.00 0.00 0.00 4.35
3327 4785 1.276705 ACGTGTTTTGGCTTTTGGGTT 59.723 42.857 0.00 0.00 0.00 4.11
3335 4793 1.367471 GCTTTTGGGTTGCACTCCC 59.633 57.895 16.75 16.75 44.81 4.30
3364 4825 5.580297 CAGCAACAGTTTTGTGGTTTTATGT 59.420 36.000 0.00 0.00 37.67 2.29
3397 4858 6.976934 TCTTAAAGGAATGGCAGAGTTTTT 57.023 33.333 0.00 0.00 0.00 1.94
3429 4890 5.297029 GGGTTTGCTGAACATTAGATACCTC 59.703 44.000 6.01 0.00 40.13 3.85
3509 4972 2.439960 ATGAGGAACGCCGGCCATA 61.440 57.895 23.46 0.23 39.96 2.74
3599 5065 3.721706 GGAGGGGAGGTGCAGGTG 61.722 72.222 0.00 0.00 0.00 4.00
3600 5066 2.930562 GAGGGGAGGTGCAGGTGT 60.931 66.667 0.00 0.00 0.00 4.16
3612 5079 3.560251 AGGTGTTGCCGGAGCTGT 61.560 61.111 5.05 0.00 43.70 4.40
3617 5084 0.537143 TGTTGCCGGAGCTGTTCATT 60.537 50.000 5.05 0.00 40.80 2.57
3618 5085 0.169009 GTTGCCGGAGCTGTTCATTC 59.831 55.000 5.05 0.00 40.80 2.67
3619 5086 1.298157 TTGCCGGAGCTGTTCATTCG 61.298 55.000 5.05 0.00 40.80 3.34
3638 5105 2.042261 GGGGGTGGCTTAGAGGGA 59.958 66.667 0.00 0.00 0.00 4.20
3646 5113 2.140792 GCTTAGAGGGATGGCCGGA 61.141 63.158 5.05 0.00 33.83 5.14
3728 5195 3.072468 GTCGACCGACCATGGGGA 61.072 66.667 18.09 0.25 39.08 4.81
3737 5204 2.354729 CCATGGGGAACGAAGGCA 59.645 61.111 2.85 0.00 35.59 4.75
3738 5205 1.304052 CCATGGGGAACGAAGGCAA 60.304 57.895 2.85 0.00 35.59 4.52
3740 5207 0.609131 CATGGGGAACGAAGGCAAGT 60.609 55.000 0.00 0.00 0.00 3.16
3749 5216 1.202758 ACGAAGGCAAGTGATTGGTCA 60.203 47.619 0.00 0.00 0.00 4.02
3778 5245 1.324005 GGGGAGAGGAGGAACTGTCG 61.324 65.000 0.00 0.00 41.55 4.35
3780 5247 1.251527 GGAGAGGAGGAACTGTCGCA 61.252 60.000 0.00 0.00 41.55 5.10
3783 5250 1.228894 AGGAGGAACTGTCGCAGGA 60.229 57.895 10.80 0.00 41.55 3.86
3791 5258 0.318762 ACTGTCGCAGGAGGAGAAAC 59.681 55.000 10.80 0.00 35.51 2.78
3811 5278 7.160726 AGAAACAAGAAAGAGAGGATGAAGAG 58.839 38.462 0.00 0.00 0.00 2.85
3827 5294 0.534877 AGAGGAACAATGCACGCACA 60.535 50.000 0.00 0.00 0.00 4.57
3832 5299 0.945265 AACAATGCACGCACAATGGC 60.945 50.000 0.00 0.00 0.00 4.40
3833 5300 1.080366 CAATGCACGCACAATGGCT 60.080 52.632 0.00 0.00 0.00 4.75
3902 5369 3.384467 CCAGAAAGGTGTCCAAACAATGT 59.616 43.478 0.00 0.00 37.08 2.71
3942 5409 4.359706 GGAACTCAAACGTGCTCAAAAAT 58.640 39.130 0.00 0.00 0.00 1.82
3943 5410 4.207019 GGAACTCAAACGTGCTCAAAAATG 59.793 41.667 0.00 0.00 0.00 2.32
3973 5440 4.575973 GGATCGGCTGCCAGGCAT 62.576 66.667 16.64 10.59 41.44 4.40
3974 5441 3.285215 GATCGGCTGCCAGGCATG 61.285 66.667 16.64 10.54 41.44 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 124 2.778299 TGATTACCAATAGCCCATCGC 58.222 47.619 0.00 0.00 37.98 4.58
133 147 2.702847 GTGTCACACACCCTTGGTC 58.297 57.895 2.00 0.00 43.05 4.02
190 205 0.107214 CCACAGTCCACAGTTGGTGT 60.107 55.000 0.00 0.00 46.44 4.16
192 207 0.107214 CACCACAGTCCACAGTTGGT 60.107 55.000 0.00 0.00 44.35 3.67
193 208 0.819259 CCACCACAGTCCACAGTTGG 60.819 60.000 0.00 0.00 45.56 3.77
194 209 0.107214 ACCACCACAGTCCACAGTTG 60.107 55.000 0.00 0.00 0.00 3.16
195 210 0.107214 CACCACCACAGTCCACAGTT 60.107 55.000 0.00 0.00 0.00 3.16
196 211 1.526887 CACCACCACAGTCCACAGT 59.473 57.895 0.00 0.00 0.00 3.55
197 212 1.893808 GCACCACCACAGTCCACAG 60.894 63.158 0.00 0.00 0.00 3.66
198 213 1.993701 ATGCACCACCACAGTCCACA 61.994 55.000 0.00 0.00 0.00 4.17
199 214 0.036164 TATGCACCACCACAGTCCAC 59.964 55.000 0.00 0.00 0.00 4.02
200 215 0.991146 ATATGCACCACCACAGTCCA 59.009 50.000 0.00 0.00 0.00 4.02
201 216 1.065491 TGATATGCACCACCACAGTCC 60.065 52.381 0.00 0.00 0.00 3.85
202 217 2.401583 TGATATGCACCACCACAGTC 57.598 50.000 0.00 0.00 0.00 3.51
282 299 0.173935 CAATCATTGGTGCGTGGCAT 59.826 50.000 0.00 0.00 41.91 4.40
326 343 9.409312 CTTCTCTTGAGATGATATCATGTGTAC 57.591 37.037 22.86 7.99 36.57 2.90
463 505 2.547990 AGGAACGGAGGGAGTATTTGT 58.452 47.619 0.00 0.00 0.00 2.83
467 509 7.954620 ACTTATATTTAGGAACGGAGGGAGTAT 59.045 37.037 0.00 0.00 0.00 2.12
468 510 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
469 511 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
471 513 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
472 514 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
473 515 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
490 532 9.466497 TGCATATTGGAATCTCTAAAAAGACTT 57.534 29.630 0.00 0.00 0.00 3.01
491 533 8.897752 GTGCATATTGGAATCTCTAAAAAGACT 58.102 33.333 0.00 0.00 0.00 3.24
495 537 9.679661 TGTAGTGCATATTGGAATCTCTAAAAA 57.320 29.630 0.00 0.00 0.00 1.94
496 538 9.851686 ATGTAGTGCATATTGGAATCTCTAAAA 57.148 29.630 0.00 0.00 35.74 1.52
498 540 9.929180 GTATGTAGTGCATATTGGAATCTCTAA 57.071 33.333 4.13 0.00 41.58 2.10
499 541 8.244113 CGTATGTAGTGCATATTGGAATCTCTA 58.756 37.037 4.13 0.00 41.58 2.43
500 542 7.093354 CGTATGTAGTGCATATTGGAATCTCT 58.907 38.462 4.13 0.00 41.58 3.10
501 543 6.311445 CCGTATGTAGTGCATATTGGAATCTC 59.689 42.308 13.70 0.00 41.58 2.75
504 546 6.109156 TCCGTATGTAGTGCATATTGGAAT 57.891 37.500 17.17 0.00 40.92 3.01
507 549 3.679980 GCTCCGTATGTAGTGCATATTGG 59.320 47.826 13.08 13.08 41.58 3.16
508 550 4.306600 TGCTCCGTATGTAGTGCATATTG 58.693 43.478 4.13 1.10 41.58 1.90
509 551 4.600692 TGCTCCGTATGTAGTGCATATT 57.399 40.909 4.13 0.00 41.58 1.28
510 552 4.600692 TTGCTCCGTATGTAGTGCATAT 57.399 40.909 4.13 0.00 41.58 1.78
511 553 4.394439 TTTGCTCCGTATGTAGTGCATA 57.606 40.909 0.00 0.00 38.94 3.14
512 554 2.979814 TTGCTCCGTATGTAGTGCAT 57.020 45.000 0.00 0.00 41.42 3.96
513 555 2.753055 TTTGCTCCGTATGTAGTGCA 57.247 45.000 0.00 0.00 0.00 4.57
514 556 3.621268 TCATTTTGCTCCGTATGTAGTGC 59.379 43.478 0.00 0.00 0.00 4.40
515 557 4.870426 ACTCATTTTGCTCCGTATGTAGTG 59.130 41.667 0.00 0.00 0.00 2.74
516 558 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
517 559 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
518 560 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
520 562 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
521 563 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
522 564 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
523 565 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
524 566 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
525 567 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
526 568 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
549 591 9.211485 CCGTTCCTAAATGTAAGTCTTTTTAGA 57.789 33.333 13.43 2.40 0.00 2.10
550 592 9.211485 TCCGTTCCTAAATGTAAGTCTTTTTAG 57.789 33.333 7.75 7.75 0.00 1.85
551 593 9.211485 CTCCGTTCCTAAATGTAAGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
552 594 7.718314 ACTCCGTTCCTAAATGTAAGTCTTTTT 59.282 33.333 0.00 0.00 0.00 1.94
553 595 7.172703 CACTCCGTTCCTAAATGTAAGTCTTTT 59.827 37.037 0.00 0.00 0.00 2.27
554 596 6.649557 CACTCCGTTCCTAAATGTAAGTCTTT 59.350 38.462 0.00 0.00 0.00 2.52
555 597 6.014840 TCACTCCGTTCCTAAATGTAAGTCTT 60.015 38.462 0.00 0.00 0.00 3.01
556 598 5.479375 TCACTCCGTTCCTAAATGTAAGTCT 59.521 40.000 0.00 0.00 0.00 3.24
558 600 5.245526 ACTCACTCCGTTCCTAAATGTAAGT 59.754 40.000 0.00 0.00 0.00 2.24
559 601 5.721232 ACTCACTCCGTTCCTAAATGTAAG 58.279 41.667 0.00 0.00 0.00 2.34
561 603 5.948162 ACTACTCACTCCGTTCCTAAATGTA 59.052 40.000 0.00 0.00 0.00 2.29
562 604 4.771054 ACTACTCACTCCGTTCCTAAATGT 59.229 41.667 0.00 0.00 0.00 2.71
563 605 5.326200 ACTACTCACTCCGTTCCTAAATG 57.674 43.478 0.00 0.00 0.00 2.32
564 606 6.662663 ACTTACTACTCACTCCGTTCCTAAAT 59.337 38.462 0.00 0.00 0.00 1.40
565 607 6.006449 ACTTACTACTCACTCCGTTCCTAAA 58.994 40.000 0.00 0.00 0.00 1.85
566 608 5.564550 ACTTACTACTCACTCCGTTCCTAA 58.435 41.667 0.00 0.00 0.00 2.69
567 609 5.171339 ACTTACTACTCACTCCGTTCCTA 57.829 43.478 0.00 0.00 0.00 2.94
569 611 4.940654 ACTACTTACTACTCACTCCGTTCC 59.059 45.833 0.00 0.00 0.00 3.62
571 613 5.312079 ACACTACTTACTACTCACTCCGTT 58.688 41.667 0.00 0.00 0.00 4.44
572 614 4.904241 ACACTACTTACTACTCACTCCGT 58.096 43.478 0.00 0.00 0.00 4.69
573 615 5.876612 AACACTACTTACTACTCACTCCG 57.123 43.478 0.00 0.00 0.00 4.63
574 616 9.612066 AGTATAACACTACTTACTACTCACTCC 57.388 37.037 0.00 0.00 34.98 3.85
746 2042 1.211457 CTCAGTTTGGAGGCTAGGCAT 59.789 52.381 19.70 3.40 0.00 4.40
894 2292 1.153823 CGGAGCGAAGATTCACCGT 60.154 57.895 11.82 0.00 35.20 4.83
923 2321 4.678309 GCGGTATTTATAGGAGCTAGCCAG 60.678 50.000 12.13 0.00 0.00 4.85
924 2322 3.194968 GCGGTATTTATAGGAGCTAGCCA 59.805 47.826 12.13 0.00 0.00 4.75
925 2323 3.430513 GGCGGTATTTATAGGAGCTAGCC 60.431 52.174 12.13 2.59 0.00 3.93
929 2327 1.907255 GGGGCGGTATTTATAGGAGCT 59.093 52.381 0.00 0.00 0.00 4.09
958 2357 2.045536 CTGCCTGTGAGGGAAGCC 60.046 66.667 0.00 0.00 34.40 4.35
979 2378 4.389576 CGGACTTTGCTGCGGTGC 62.390 66.667 0.00 0.00 0.00 5.01
1230 2632 2.585247 GGGATGGCACGTCGTAGC 60.585 66.667 0.00 4.37 0.00 3.58
1794 3196 1.002011 GCACCAGTTCTCCTTCCCC 60.002 63.158 0.00 0.00 0.00 4.81
2031 3433 0.607489 ACGTACGTACCCAGAGCACT 60.607 55.000 21.41 0.00 0.00 4.40
2107 3509 6.569035 CGATGCCATGCTGATAATTTATGTGT 60.569 38.462 0.00 0.00 0.00 3.72
2202 3604 2.507769 GCTCATTGGCCGCTTTGC 60.508 61.111 0.00 0.00 0.00 3.68
2218 3620 4.553815 GCTAGCTTTTAAAAAGTGCTACGC 59.446 41.667 7.70 15.32 33.70 4.42
2231 3633 3.717707 CATGGACGCTAGCTAGCTTTTA 58.282 45.455 36.02 22.67 46.85 1.52
2268 3674 9.170584 GATTCGGAACTAAACAAAGAAGAAAAG 57.829 33.333 0.00 0.00 0.00 2.27
2315 3753 6.122964 GCCATTTTCTTGTATAACTCCTCCT 58.877 40.000 0.00 0.00 0.00 3.69
2318 3756 4.881850 CCGCCATTTTCTTGTATAACTCCT 59.118 41.667 0.00 0.00 0.00 3.69
2320 3758 4.335594 AGCCGCCATTTTCTTGTATAACTC 59.664 41.667 0.00 0.00 0.00 3.01
2322 3760 4.142469 ACAGCCGCCATTTTCTTGTATAAC 60.142 41.667 0.00 0.00 0.00 1.89
2323 3761 4.013728 ACAGCCGCCATTTTCTTGTATAA 58.986 39.130 0.00 0.00 0.00 0.98
2324 3762 3.616219 ACAGCCGCCATTTTCTTGTATA 58.384 40.909 0.00 0.00 0.00 1.47
2641 4079 2.334946 CCACTGGTTCACCATGGCG 61.335 63.158 13.04 1.26 46.46 5.69
2839 4277 3.736224 AGCAGGGTGGCCATCCAG 61.736 66.667 36.54 29.79 44.48 3.86
3013 4454 2.519119 TAGTAGGGACGGTGGGTGGG 62.519 65.000 0.00 0.00 0.00 4.61
3015 4456 0.612732 TGTAGTAGGGACGGTGGGTG 60.613 60.000 0.00 0.00 0.00 4.61
3203 4661 1.202806 ACACCATGTGGAACCTCACTG 60.203 52.381 5.96 0.00 37.94 3.66
3293 4751 2.748461 ACACGTGCACATTTACACAC 57.252 45.000 17.22 0.00 36.57 3.82
3327 4785 2.451191 TTGCTGAGGTGGGAGTGCA 61.451 57.895 0.00 0.00 0.00 4.57
3335 4793 2.480073 CCACAAAACTGTTGCTGAGGTG 60.480 50.000 9.20 5.23 0.00 4.00
3364 4825 5.888161 GCCATTCCTTTAAGATTCAGGAGAA 59.112 40.000 0.00 0.00 38.00 2.87
3397 4858 1.686052 GTTCAGCAAACCCAACCATGA 59.314 47.619 0.00 0.00 31.20 3.07
3438 4901 5.122396 GCAGAAAAAGTGACTTCCGTGATAT 59.878 40.000 0.00 0.00 0.00 1.63
3439 4902 4.451096 GCAGAAAAAGTGACTTCCGTGATA 59.549 41.667 0.00 0.00 0.00 2.15
3440 4903 3.251004 GCAGAAAAAGTGACTTCCGTGAT 59.749 43.478 0.00 0.00 0.00 3.06
3447 4910 2.286418 CGCTTCGCAGAAAAAGTGACTT 60.286 45.455 0.00 0.00 45.90 3.01
3533 4999 3.937062 CGCCGGTTATCGCTTGCC 61.937 66.667 1.90 0.00 37.59 4.52
3536 5002 3.441011 CTCCCGCCGGTTATCGCTT 62.441 63.158 1.90 0.00 37.59 4.68
3562 5028 3.340789 GCCCTCGCGTCAAGTTTT 58.659 55.556 5.77 0.00 0.00 2.43
3595 5061 3.120086 AACAGCTCCGGCAACACCT 62.120 57.895 0.00 0.00 41.70 4.00
3598 5064 0.537143 AATGAACAGCTCCGGCAACA 60.537 50.000 0.00 0.00 41.70 3.33
3599 5065 0.169009 GAATGAACAGCTCCGGCAAC 59.831 55.000 0.00 0.00 41.70 4.17
3600 5066 1.298157 CGAATGAACAGCTCCGGCAA 61.298 55.000 0.00 0.00 41.70 4.52
3603 5070 1.815421 CCCGAATGAACAGCTCCGG 60.815 63.158 0.00 0.00 36.98 5.14
3648 5115 4.659874 CGTCGTGTTGGCCGTTGC 62.660 66.667 0.00 0.00 0.00 4.17
3677 5144 0.324460 CCTCACCCTACCTCGACCTT 60.324 60.000 0.00 0.00 0.00 3.50
3714 5181 2.125269 CGTTCCCCATGGTCGGTC 60.125 66.667 11.73 3.45 0.00 4.79
3719 5186 2.075355 TTGCCTTCGTTCCCCATGGT 62.075 55.000 11.73 0.00 0.00 3.55
3728 5195 1.880027 GACCAATCACTTGCCTTCGTT 59.120 47.619 0.00 0.00 0.00 3.85
3740 5207 1.374125 CCTCACGCGTGACCAATCA 60.374 57.895 36.40 15.83 35.46 2.57
3759 5226 1.324005 CGACAGTTCCTCCTCTCCCC 61.324 65.000 0.00 0.00 0.00 4.81
3762 5229 0.172352 CTGCGACAGTTCCTCCTCTC 59.828 60.000 0.00 0.00 0.00 3.20
3764 5231 1.216710 CCTGCGACAGTTCCTCCTC 59.783 63.158 6.19 0.00 0.00 3.71
3765 5232 1.228894 TCCTGCGACAGTTCCTCCT 60.229 57.895 6.19 0.00 0.00 3.69
3770 5237 0.603569 TTCTCCTCCTGCGACAGTTC 59.396 55.000 6.19 0.00 0.00 3.01
3778 5245 3.744660 TCTTTCTTGTTTCTCCTCCTGC 58.255 45.455 0.00 0.00 0.00 4.85
3780 5247 4.285775 CCTCTCTTTCTTGTTTCTCCTCCT 59.714 45.833 0.00 0.00 0.00 3.69
3783 5250 5.545723 TCATCCTCTCTTTCTTGTTTCTCCT 59.454 40.000 0.00 0.00 0.00 3.69
3791 5258 5.674052 TCCTCTTCATCCTCTCTTTCTTG 57.326 43.478 0.00 0.00 0.00 3.02
3811 5278 1.062258 CATTGTGCGTGCATTGTTCC 58.938 50.000 0.00 0.00 0.00 3.62
3827 5294 2.498481 CCATCAACATCCAACAGCCATT 59.502 45.455 0.00 0.00 0.00 3.16
3832 5299 1.739466 CGGTCCATCAACATCCAACAG 59.261 52.381 0.00 0.00 0.00 3.16
3833 5300 1.349357 TCGGTCCATCAACATCCAACA 59.651 47.619 0.00 0.00 0.00 3.33
3884 5351 4.262420 GGCATACATTGTTTGGACACCTTT 60.262 41.667 8.94 0.00 34.98 3.11
3897 5364 2.036958 TCTCAACGGGGCATACATTG 57.963 50.000 0.00 0.00 0.00 2.82
3942 5409 3.969250 GATCCGCCGCCCAAACTCA 62.969 63.158 0.00 0.00 0.00 3.41
3943 5410 3.202706 GATCCGCCGCCCAAACTC 61.203 66.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.