Multiple sequence alignment - TraesCS6A01G287800

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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 TraesCS6A01G287800 chr6A 100.000 4803 0 0 1 4803 520390863 520395665 0.000000e+00 8870.0
1 TraesCS6A01G287800 chr6D 92.737 4227 181 57 1 4167 378733828 378737988 0.000000e+00 5989.0
2 TraesCS6A01G287800 chr6D 90.255 431 19 8 4383 4803 378738801 378739218 4.230000e-150 542.0
3 TraesCS6A01G287800 chr6B 94.837 2886 103 23 777 3638 565197203 565200066 0.000000e+00 4462.0
4 TraesCS6A01G287800 chr6B 90.629 747 41 10 3531 4253 565200072 565200813 0.000000e+00 965.0
5 TraesCS6A01G287800 chr6B 86.445 841 82 17 1 826 565196395 565197218 0.000000e+00 893.0
6 TraesCS6A01G287800 chr6B 93.559 295 14 2 4433 4727 565201202 565201491 7.380000e-118 435.0
7 TraesCS6A01G287800 chr7D 81.019 569 80 20 15 560 42383837 42383274 1.240000e-115 427.0
8 TraesCS6A01G287800 chr5D 81.734 542 66 20 1 523 310017710 310018237 5.750000e-114 422.0
9 TraesCS6A01G287800 chr3D 82.072 502 73 14 15 500 169890091 169889591 3.460000e-111 412.0
10 TraesCS6A01G287800 chr3D 78.559 569 105 14 1 560 8898364 8898924 4.570000e-95 359.0
11 TraesCS6A01G287800 chr7B 79.795 584 85 24 1 560 2559845 2560419 1.250000e-105 394.0
12 TraesCS6A01G287800 chr7B 85.758 330 41 5 26 349 197012214 197011885 1.280000e-90 344.0
13 TraesCS6A01G287800 chr3A 86.389 360 44 4 15 369 207247053 207246694 5.830000e-104 388.0
14 TraesCS6A01G287800 chr3B 86.792 53 6 1 650 701 644147155 644147103 1.870000e-04 58.4


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 TraesCS6A01G287800 chr6A 520390863 520395665 4802 False 8870.00 8870 100.0000 1 4803 1 chr6A.!!$F1 4802
1 TraesCS6A01G287800 chr6D 378733828 378739218 5390 False 3265.50 5989 91.4960 1 4803 2 chr6D.!!$F1 4802
2 TraesCS6A01G287800 chr6B 565196395 565201491 5096 False 1688.75 4462 91.3675 1 4727 4 chr6B.!!$F1 4726
3 TraesCS6A01G287800 chr7D 42383274 42383837 563 True 427.00 427 81.0190 15 560 1 chr7D.!!$R1 545
4 TraesCS6A01G287800 chr5D 310017710 310018237 527 False 422.00 422 81.7340 1 523 1 chr5D.!!$F1 522
5 TraesCS6A01G287800 chr3D 169889591 169890091 500 True 412.00 412 82.0720 15 500 1 chr3D.!!$R1 485
6 TraesCS6A01G287800 chr3D 8898364 8898924 560 False 359.00 359 78.5590 1 560 1 chr3D.!!$F1 559
7 TraesCS6A01G287800 chr7B 2559845 2560419 574 False 394.00 394 79.7950 1 560 1 chr7B.!!$F1 559

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
761 800 0.033504 CACTGAACGTGGGTAGCAGT 59.966 55.000 0.00 0.00 40.45 4.40 F
762 801 0.317479 ACTGAACGTGGGTAGCAGTC 59.683 55.000 0.00 0.00 37.35 3.51 F
1430 1503 0.544697 GGTTTAGGGGATTCGAGGCA 59.455 55.000 0.00 0.00 0.00 4.75 F
2411 2492 1.956477 GCCACATTTGCCACCTATAGG 59.044 52.381 17.73 17.73 42.17 2.57 F
3293 3389 1.549170 AGTAAGTACACCTGCTTCCCG 59.451 52.381 0.00 0.00 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 2119 1.220206 CCAACAGAGCCTCAGCGAT 59.780 57.895 0.00 0.0 46.67 4.58 R
2339 2419 1.243342 TGATGCAGAAGTTTGGCCCG 61.243 55.000 0.00 0.0 0.00 6.13 R
3012 3108 1.149148 GGCACCTTCGTGTCTTTCTC 58.851 55.000 0.00 0.0 41.62 2.87 R
3655 3873 0.029300 AGCATGTCAAACACACACGC 59.971 50.000 0.00 0.0 38.04 5.34 R
4736 5646 0.183492 CTTTGGGCTATGGGCTGCTA 59.817 55.000 1.86 0.0 41.46 3.49 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
115 119 6.488006 GCAAATGAAGGCTTAGATGGAGATAA 59.512 38.462 0.00 0.00 0.00 1.75
174 178 3.494048 CGAAGAAGCTTGATATGGAGGCT 60.494 47.826 2.10 0.00 34.52 4.58
328 334 2.426522 CCTTGGTTCGAGAAGATGCAA 58.573 47.619 0.00 0.00 0.00 4.08
365 374 4.582240 AGCTTGATGACTGATCTATGACGA 59.418 41.667 0.00 0.00 31.55 4.20
474 511 2.709170 CCAACCGTTGGTAAGTGCA 58.291 52.632 20.55 0.00 45.93 4.57
487 524 4.202419 TGGTAAGTGCACCAGTATGAACTT 60.202 41.667 14.63 4.60 43.76 2.66
523 562 0.249868 GCTAGCATGTATGTCGGCCA 60.250 55.000 10.63 0.00 0.00 5.36
575 614 3.728474 GCCACATGATCTCTGGCG 58.272 61.111 8.37 0.00 41.15 5.69
576 615 1.144716 GCCACATGATCTCTGGCGA 59.855 57.895 8.37 0.00 41.15 5.54
577 616 0.250209 GCCACATGATCTCTGGCGAT 60.250 55.000 8.37 0.00 41.15 4.58
578 617 1.793258 CCACATGATCTCTGGCGATC 58.207 55.000 0.00 0.00 40.13 3.69
579 618 1.343789 CCACATGATCTCTGGCGATCT 59.656 52.381 0.00 0.00 40.32 2.75
580 619 2.609984 CCACATGATCTCTGGCGATCTC 60.610 54.545 0.00 0.00 40.32 2.75
581 620 2.296752 CACATGATCTCTGGCGATCTCT 59.703 50.000 0.00 0.00 40.32 3.10
582 621 2.296752 ACATGATCTCTGGCGATCTCTG 59.703 50.000 0.00 0.00 40.32 3.35
583 622 1.326328 TGATCTCTGGCGATCTCTGG 58.674 55.000 0.00 0.00 40.32 3.86
584 623 0.038343 GATCTCTGGCGATCTCTGGC 60.038 60.000 0.00 0.00 37.43 4.85
590 629 4.899239 GCGATCTCTGGCCGTGGG 62.899 72.222 0.00 0.00 0.00 4.61
601 640 2.044555 GCCGTGGGCCCTTTCTAAC 61.045 63.158 25.70 10.79 44.06 2.34
613 652 6.872020 GGGCCCTTTCTAACTTTAAATTGTTC 59.128 38.462 17.04 0.00 0.00 3.18
618 657 8.925700 CCTTTCTAACTTTAAATTGTTCCATGC 58.074 33.333 0.00 0.00 0.00 4.06
620 659 7.209471 TCTAACTTTAAATTGTTCCATGCGT 57.791 32.000 0.00 0.00 0.00 5.24
622 661 5.446143 ACTTTAAATTGTTCCATGCGTGA 57.554 34.783 7.72 0.00 0.00 4.35
628 667 1.960417 TGTTCCATGCGTGAACAAGA 58.040 45.000 7.72 0.00 46.58 3.02
632 671 4.517075 TGTTCCATGCGTGAACAAGAATTA 59.483 37.500 7.72 0.00 46.58 1.40
659 698 1.220749 GCTCCAACATAGGCGGACA 59.779 57.895 0.00 0.00 0.00 4.02
686 725 0.970427 GGCAACCGACCCAAATGGAT 60.970 55.000 0.00 0.00 37.39 3.41
720 759 4.142752 CGAAGTACACGTCCAGTTAGATCA 60.143 45.833 0.00 0.00 0.00 2.92
734 773 0.530744 AGATCAGCGCGTTGGAGTTA 59.469 50.000 22.99 3.21 0.00 2.24
737 776 0.666274 TCAGCGCGTTGGAGTTACTG 60.666 55.000 22.99 10.45 0.00 2.74
747 786 4.628074 GTTGGAGTTACTGTTAGCACTGA 58.372 43.478 0.00 0.00 0.00 3.41
755 794 0.466543 TGTTAGCACTGAACGTGGGT 59.533 50.000 0.00 0.00 43.97 4.51
756 795 1.687660 TGTTAGCACTGAACGTGGGTA 59.312 47.619 0.00 0.00 43.97 3.69
757 796 2.288579 TGTTAGCACTGAACGTGGGTAG 60.289 50.000 0.00 0.00 43.97 3.18
758 797 0.245539 TAGCACTGAACGTGGGTAGC 59.754 55.000 0.00 0.00 43.97 3.58
759 798 1.301401 GCACTGAACGTGGGTAGCA 60.301 57.895 0.00 0.00 43.97 3.49
760 799 1.291877 GCACTGAACGTGGGTAGCAG 61.292 60.000 0.00 0.00 43.97 4.24
761 800 0.033504 CACTGAACGTGGGTAGCAGT 59.966 55.000 0.00 0.00 40.45 4.40
762 801 0.317479 ACTGAACGTGGGTAGCAGTC 59.683 55.000 0.00 0.00 37.35 3.51
763 802 0.603569 CTGAACGTGGGTAGCAGTCT 59.396 55.000 0.00 0.00 0.00 3.24
764 803 1.816835 CTGAACGTGGGTAGCAGTCTA 59.183 52.381 0.00 0.00 0.00 2.59
765 804 1.816835 TGAACGTGGGTAGCAGTCTAG 59.183 52.381 0.00 0.00 0.00 2.43
812 885 8.432110 TTGCCATTTAGAAAGAAAGAAAAACC 57.568 30.769 0.00 0.00 0.00 3.27
1368 1441 1.089481 ACGGCATGACCATAAGCACG 61.089 55.000 0.00 0.00 39.03 5.34
1380 1453 0.598158 TAAGCACGTTCCGCGACTTT 60.598 50.000 8.23 0.00 44.77 2.66
1430 1503 0.544697 GGTTTAGGGGATTCGAGGCA 59.455 55.000 0.00 0.00 0.00 4.75
1449 1522 4.164796 AGGCACTGGATTGACTGATGATAA 59.835 41.667 0.00 0.00 37.18 1.75
1595 1668 6.227522 TGTCTCGATTAACCATTTCAGTCAA 58.772 36.000 0.00 0.00 0.00 3.18
1763 1837 8.657074 AAAAGGGTGAAAACTATGTTTTTAGC 57.343 30.769 16.19 16.19 0.00 3.09
1854 1928 4.261280 CGGTTAGAGGCTTAGAGCTAACTC 60.261 50.000 17.45 10.14 41.99 3.01
1860 1934 6.811954 AGAGGCTTAGAGCTAACTCAATAAC 58.188 40.000 9.28 0.00 46.09 1.89
1895 1969 4.514401 GACTTATCAACACTCGGGGAATT 58.486 43.478 0.00 0.00 0.00 2.17
2039 2119 2.438021 ACAAGTTTACTGCTGGTCCAGA 59.562 45.455 23.77 6.94 36.67 3.86
2143 2223 8.245701 TGTATTTTGGCGAAATTTTATTCACC 57.754 30.769 17.45 0.00 38.80 4.02
2146 2226 3.843999 TGGCGAAATTTTATTCACCAGC 58.156 40.909 0.00 0.00 36.78 4.85
2307 2387 5.192176 TCATGTTGGCTCATGCTATGTAAA 58.808 37.500 14.85 0.00 43.18 2.01
2339 2419 5.048083 ACATATTGTGGTCATTGGTCAACAC 60.048 40.000 0.00 0.00 0.00 3.32
2411 2492 1.956477 GCCACATTTGCCACCTATAGG 59.044 52.381 17.73 17.73 42.17 2.57
2467 2548 8.074370 CACACAATAGATATTCTGCCAGAATTG 58.926 37.037 23.95 17.42 41.90 2.32
2562 2643 7.636150 ATTTCTAGAATCTGGATGGTTTGTG 57.364 36.000 5.89 0.00 0.00 3.33
2578 2659 6.074648 TGGTTTGTGATTTATCCTTGGTCTT 58.925 36.000 0.00 0.00 0.00 3.01
2654 2750 3.605634 TCCACGATTCAGTTACCCAATG 58.394 45.455 0.00 0.00 0.00 2.82
2755 2851 3.554934 ACAAACTTGACTTGCCTCATGA 58.445 40.909 0.00 0.00 0.00 3.07
2903 2999 6.027749 GCTTATTGACTTGAAATGTAACCCG 58.972 40.000 0.00 0.00 0.00 5.28
2904 3000 3.907894 TTGACTTGAAATGTAACCCGC 57.092 42.857 0.00 0.00 0.00 6.13
3012 3108 4.450419 CCTCACAAGCTACAACTTCAGAAG 59.550 45.833 8.77 8.77 0.00 2.85
3142 3238 2.290641 CGCTATTCATTTACCTGCACCC 59.709 50.000 0.00 0.00 0.00 4.61
3146 3242 3.737559 TTCATTTACCTGCACCCTGAT 57.262 42.857 0.00 0.00 0.00 2.90
3293 3389 1.549170 AGTAAGTACACCTGCTTCCCG 59.451 52.381 0.00 0.00 0.00 5.14
3362 3461 3.701040 AGTGTTTCATACCCATGGAATGC 59.299 43.478 15.22 4.98 44.97 3.56
3369 3468 4.160065 TCATACCCATGGAATGCAGTTTTG 59.840 41.667 15.22 3.46 44.97 2.44
3444 3543 2.093447 AGTGCTACTACCAATGTGAGGC 60.093 50.000 0.00 0.00 0.00 4.70
3466 3565 4.800914 GCGTGGTGATCATTCTATAGCCTT 60.801 45.833 0.00 0.00 0.00 4.35
3482 3581 4.547406 AGCCTTTACACGTTTCTTGTTC 57.453 40.909 0.00 0.00 0.00 3.18
3490 3590 2.351418 CACGTTTCTTGTTCTGCTGTGA 59.649 45.455 0.00 0.00 0.00 3.58
3491 3591 3.002656 CACGTTTCTTGTTCTGCTGTGAT 59.997 43.478 0.00 0.00 0.00 3.06
3492 3592 3.002656 ACGTTTCTTGTTCTGCTGTGATG 59.997 43.478 0.00 0.00 0.00 3.07
3493 3593 3.002656 CGTTTCTTGTTCTGCTGTGATGT 59.997 43.478 0.00 0.00 0.00 3.06
3494 3594 4.211164 CGTTTCTTGTTCTGCTGTGATGTA 59.789 41.667 0.00 0.00 0.00 2.29
3495 3595 5.444122 GTTTCTTGTTCTGCTGTGATGTAC 58.556 41.667 0.00 0.00 0.00 2.90
3580 3798 3.496870 CCTTAGTGGGGGCATGAATCTAC 60.497 52.174 0.00 0.00 0.00 2.59
3632 3850 3.011482 ACCACTAGGCTACTTAGGTGTCT 59.989 47.826 9.23 0.00 39.06 3.41
3655 3873 6.870439 TCTCTTGAGATGTTGTGTATCACTTG 59.130 38.462 0.00 0.00 35.11 3.16
3758 3976 0.898320 GCAGGGCTTAGAGAGTGACA 59.102 55.000 0.00 0.00 0.00 3.58
3794 4012 3.319245 GCAGAAAATGCGAAGGAGC 57.681 52.632 0.00 0.00 46.99 4.70
3799 4017 0.524862 AAAATGCGAAGGAGCTGCTG 59.475 50.000 9.14 0.00 38.13 4.41
3813 4031 1.590238 GCTGCTGTGATCATACGTGAC 59.410 52.381 0.00 0.00 37.14 3.67
3822 4040 1.216977 CATACGTGACGCCTTCCCA 59.783 57.895 4.25 0.00 0.00 4.37
3869 4105 3.417275 CTACCGAGTCCCAGCTGCG 62.417 68.421 8.66 5.90 0.00 5.18
3943 4179 5.390885 GCTATTCTTGTTGCGATTGAAGTCA 60.391 40.000 0.00 0.00 0.00 3.41
3969 4205 4.162690 GGTACCCCTGCTCTGGCG 62.163 72.222 0.00 0.00 42.25 5.69
4098 4335 9.520204 AATAAGATTCCATTTTTATTCTGCACG 57.480 29.630 0.00 0.00 0.00 5.34
4132 4369 3.373130 TCGTCGTCTAAGTGACCATAGTG 59.627 47.826 0.00 0.00 42.49 2.74
4134 4371 4.413087 GTCGTCTAAGTGACCATAGTGTG 58.587 47.826 0.00 0.00 42.49 3.82
4184 4423 9.237846 GTAAAACTTCCATCAAAAACTCTCAAG 57.762 33.333 0.00 0.00 0.00 3.02
4192 4431 7.025963 CCATCAAAAACTCTCAAGTATGAAGC 58.974 38.462 0.00 0.00 33.48 3.86
4193 4432 6.228273 TCAAAAACTCTCAAGTATGAAGCG 57.772 37.500 0.00 0.00 33.48 4.68
4194 4433 4.670227 AAAACTCTCAAGTATGAAGCGC 57.330 40.909 0.00 0.00 33.48 5.92
4195 4434 3.319137 AACTCTCAAGTATGAAGCGCA 57.681 42.857 11.47 0.00 33.48 6.09
4202 4441 3.133901 TCAAGTATGAAGCGCATTCCCTA 59.866 43.478 11.47 3.02 38.44 3.53
4213 4452 2.423538 CGCATTCCCTAGTTTCCCAAAG 59.576 50.000 0.00 0.00 0.00 2.77
4254 4495 2.614983 GTTGGCAAAAACTGACGGACTA 59.385 45.455 0.00 0.00 34.74 2.59
4283 4597 6.304126 ACGAATTATTTTGTACTTGAGTGCG 58.696 36.000 0.00 0.00 33.15 5.34
4290 4604 3.106242 TGTACTTGAGTGCGTGATGTT 57.894 42.857 0.00 0.00 33.15 2.71
4291 4605 3.462982 TGTACTTGAGTGCGTGATGTTT 58.537 40.909 0.00 0.00 33.15 2.83
4293 4607 1.002468 ACTTGAGTGCGTGATGTTTGC 60.002 47.619 0.00 0.00 0.00 3.68
4301 4615 1.417372 CGTGATGTTTGCGCCAAATT 58.583 45.000 4.18 0.00 35.74 1.82
4329 4667 9.427127 GAGTTTCGACATTAGATAAAATTCAGC 57.573 33.333 0.00 0.00 0.00 4.26
4334 4672 6.260936 CGACATTAGATAAAATTCAGCCCTGT 59.739 38.462 0.00 0.00 0.00 4.00
4339 4677 5.435291 AGATAAAATTCAGCCCTGTGAGAG 58.565 41.667 0.00 0.00 0.00 3.20
4347 4685 2.027377 CAGCCCTGTGAGAGAGTTTGAT 60.027 50.000 0.00 0.00 0.00 2.57
4348 4686 2.641815 AGCCCTGTGAGAGAGTTTGATT 59.358 45.455 0.00 0.00 0.00 2.57
4350 4688 4.287067 AGCCCTGTGAGAGAGTTTGATTTA 59.713 41.667 0.00 0.00 0.00 1.40
4352 4690 5.551233 CCCTGTGAGAGAGTTTGATTTACA 58.449 41.667 0.00 0.00 0.00 2.41
4354 4692 6.656693 CCCTGTGAGAGAGTTTGATTTACAAT 59.343 38.462 0.00 0.00 38.36 2.71
4355 4693 7.148340 CCCTGTGAGAGAGTTTGATTTACAATC 60.148 40.741 0.00 0.00 38.36 2.67
4358 4739 7.095649 TGTGAGAGAGTTTGATTTACAATCGTG 60.096 37.037 0.00 0.00 38.36 4.35
4380 4761 7.017645 CGTGAAGACACTATTGATTTTTCTGG 58.982 38.462 0.00 0.00 43.99 3.86
4413 5249 0.322322 TTGCCCCGACGACTACAATT 59.678 50.000 0.00 0.00 0.00 2.32
4426 5262 7.487189 CGACGACTACAATTAGGTTTGAACTAT 59.513 37.037 0.00 0.00 0.00 2.12
4428 5264 9.498176 ACGACTACAATTAGGTTTGAACTATTT 57.502 29.630 0.00 0.00 0.00 1.40
4429 5265 9.755064 CGACTACAATTAGGTTTGAACTATTTG 57.245 33.333 6.24 6.24 37.59 2.32
4474 5384 1.207089 TGACGAGCCAACCCTATTGAG 59.793 52.381 0.00 0.00 0.00 3.02
4571 5481 0.313987 CCAACCGACCCTTTTTGAGC 59.686 55.000 0.00 0.00 0.00 4.26
4577 5487 0.038801 GACCCTTTTTGAGCTGCAGC 60.039 55.000 31.53 31.53 42.49 5.25
4661 5571 0.510359 GGATTATTCAGCAGCGCTCG 59.490 55.000 7.13 4.46 36.40 5.03
4736 5646 1.560866 CCTCTCTCCAAAGGCTGGCT 61.561 60.000 0.00 0.00 45.98 4.75
4768 5678 1.546029 GCCCAAAGCTTGTTCCTTAGG 59.454 52.381 0.00 0.00 38.99 2.69
4769 5679 1.546029 CCCAAAGCTTGTTCCTTAGGC 59.454 52.381 0.00 0.00 0.00 3.93
4770 5680 1.546029 CCAAAGCTTGTTCCTTAGGCC 59.454 52.381 0.00 0.00 0.00 5.19
4787 5697 1.594293 CCGGCCGCACGATATTTCT 60.594 57.895 22.85 0.00 35.47 2.52
4792 5702 1.190323 GCCGCACGATATTTCTTCTCG 59.810 52.381 0.00 0.00 38.34 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.101249 CCTTCCAAAGTTGCTTGCAAGA 59.899 45.455 30.39 12.25 0.00 3.02
115 119 4.990526 TCCATCTCAAGCTTCTTCCTTTT 58.009 39.130 0.00 0.00 0.00 2.27
165 169 0.475475 CTTGCATCCCAGCCTCCATA 59.525 55.000 0.00 0.00 0.00 2.74
174 178 1.378882 GCATCTTCGCTTGCATCCCA 61.379 55.000 0.00 0.00 38.72 4.37
384 407 2.031919 TGGTCATGCCGTCACACC 59.968 61.111 0.00 0.00 41.21 4.16
390 413 4.735132 CGGTCGTGGTCATGCCGT 62.735 66.667 13.74 0.00 41.21 5.68
459 496 4.468007 GGTGCACTTACCAACGGT 57.532 55.556 17.98 0.00 40.54 4.83
474 511 6.959639 AAACATCACAAAGTTCATACTGGT 57.040 33.333 0.00 0.00 34.01 4.00
584 623 0.037734 AAGTTAGAAAGGGCCCACGG 59.962 55.000 27.56 0.00 0.00 4.94
587 626 5.841783 ACAATTTAAAGTTAGAAAGGGCCCA 59.158 36.000 27.56 0.00 0.00 5.36
590 629 7.438564 TGGAACAATTTAAAGTTAGAAAGGGC 58.561 34.615 0.00 0.00 31.92 5.19
613 652 4.853196 CACTTAATTCTTGTTCACGCATGG 59.147 41.667 0.00 0.00 0.00 3.66
618 657 4.219033 GGTGCACTTAATTCTTGTTCACG 58.781 43.478 17.98 0.00 30.77 4.35
620 659 3.304391 GCGGTGCACTTAATTCTTGTTCA 60.304 43.478 17.98 0.00 0.00 3.18
622 661 2.884639 AGCGGTGCACTTAATTCTTGTT 59.115 40.909 17.98 0.00 0.00 2.83
628 667 1.539827 GTTGGAGCGGTGCACTTAATT 59.460 47.619 17.98 0.00 0.00 1.40
632 671 0.036164 TATGTTGGAGCGGTGCACTT 59.964 50.000 17.98 2.54 0.00 3.16
703 742 1.135373 CGCTGATCTAACTGGACGTGT 60.135 52.381 0.00 0.00 0.00 4.49
704 743 1.550065 CGCTGATCTAACTGGACGTG 58.450 55.000 0.00 0.00 0.00 4.49
705 744 0.179134 GCGCTGATCTAACTGGACGT 60.179 55.000 0.00 0.00 0.00 4.34
712 751 0.924090 CTCCAACGCGCTGATCTAAC 59.076 55.000 11.83 0.00 0.00 2.34
715 754 0.530744 TAACTCCAACGCGCTGATCT 59.469 50.000 11.83 0.00 0.00 2.75
720 759 0.249741 AACAGTAACTCCAACGCGCT 60.250 50.000 5.73 0.00 0.00 5.92
747 786 1.920610 ACTAGACTGCTACCCACGTT 58.079 50.000 0.00 0.00 0.00 3.99
755 794 6.219417 AGTCGAAGTACTACTAGACTGCTA 57.781 41.667 18.92 0.00 41.49 3.49
756 795 5.088680 AGTCGAAGTACTACTAGACTGCT 57.911 43.478 18.92 4.12 41.49 4.24
757 796 6.272318 TCTAGTCGAAGTACTACTAGACTGC 58.728 44.000 22.08 0.00 43.85 4.40
758 797 8.700722 TTTCTAGTCGAAGTACTACTAGACTG 57.299 38.462 24.29 16.22 46.33 3.51
759 798 7.981225 CCTTTCTAGTCGAAGTACTACTAGACT 59.019 40.741 24.29 21.69 46.33 3.24
760 799 7.978975 TCCTTTCTAGTCGAAGTACTACTAGAC 59.021 40.741 24.29 17.42 46.33 2.59
761 800 8.072321 TCCTTTCTAGTCGAAGTACTACTAGA 57.928 38.462 22.08 22.08 45.61 2.43
762 801 8.891671 ATCCTTTCTAGTCGAAGTACTACTAG 57.108 38.462 19.16 19.16 42.52 2.57
763 802 9.107177 CAATCCTTTCTAGTCGAAGTACTACTA 57.893 37.037 0.00 0.00 32.21 1.82
764 803 7.415429 GCAATCCTTTCTAGTCGAAGTACTACT 60.415 40.741 0.00 0.00 32.21 2.57
765 804 6.692249 GCAATCCTTTCTAGTCGAAGTACTAC 59.308 42.308 0.00 0.00 32.21 2.73
812 885 6.015940 GTGATAATTAGGGGCAATCCTTTCTG 60.016 42.308 0.00 0.00 38.30 3.02
976 1049 3.081804 CGCTTGGGAAATTCTACAAGGT 58.918 45.455 22.21 0.00 40.37 3.50
1110 1183 5.418676 GAGAAGATCTCCTTGGACTTCTTG 58.581 45.833 16.83 0.00 44.41 3.02
1368 1441 1.866925 CAAGGGAAAGTCGCGGAAC 59.133 57.895 6.13 0.00 34.19 3.62
1430 1503 8.051535 ACAAATCTTATCATCAGTCAATCCAGT 58.948 33.333 0.00 0.00 0.00 4.00
1449 1522 3.057736 GCTCATCTGTGCAACACAAATCT 60.058 43.478 1.64 0.00 45.67 2.40
1595 1668 4.555689 ACATACATGCATTAAACCCCCAT 58.444 39.130 0.00 0.00 0.00 4.00
1819 1893 2.028476 CCTCTAACCGTCACACCAATCA 60.028 50.000 0.00 0.00 0.00 2.57
1860 1934 8.404000 AGTGTTGATAAGTCGGTAATGTACTAG 58.596 37.037 0.00 0.00 0.00 2.57
1872 1946 1.475280 TCCCCGAGTGTTGATAAGTCG 59.525 52.381 0.00 0.00 39.62 4.18
1895 1969 8.472007 AAGTAGGAAACACAAATACCATTGAA 57.528 30.769 0.00 0.00 34.38 2.69
2007 2087 6.142798 CAGCAGTAAACTTGTAGCAACAAATG 59.857 38.462 0.00 0.00 44.79 2.32
2039 2119 1.220206 CCAACAGAGCCTCAGCGAT 59.780 57.895 0.00 0.00 46.67 4.58
2140 2220 3.457234 TGAACATAAGATAGCGCTGGTG 58.543 45.455 22.90 11.56 0.00 4.17
2142 2222 3.062763 CCTGAACATAAGATAGCGCTGG 58.937 50.000 22.90 3.29 0.00 4.85
2143 2223 3.982475 TCCTGAACATAAGATAGCGCTG 58.018 45.455 22.90 4.28 0.00 5.18
2146 2226 7.919690 TGAAATTTCCTGAACATAAGATAGCG 58.080 34.615 15.48 0.00 0.00 4.26
2307 2387 8.448008 ACCAATGACCACAATATGTATTAGGAT 58.552 33.333 9.22 0.00 0.00 3.24
2339 2419 1.243342 TGATGCAGAAGTTTGGCCCG 61.243 55.000 0.00 0.00 0.00 6.13
2411 2492 9.436957 TCTGAAGAAATAATCAGTCCAAACTAC 57.563 33.333 3.03 0.00 33.25 2.73
2467 2548 6.892691 TGGACACAACAAAATTTGAACAAAC 58.107 32.000 13.19 0.37 32.51 2.93
2562 2643 5.183904 ACAAGTGCAAGACCAAGGATAAATC 59.816 40.000 0.00 0.00 0.00 2.17
2578 2659 5.906113 TTTTAGTTCCTTCAACAAGTGCA 57.094 34.783 0.00 0.00 37.48 4.57
2755 2851 3.562182 AGAAAAACATCGACCCTGGTTT 58.438 40.909 0.00 0.00 35.08 3.27
2903 2999 9.562583 TCAAAATATTTGGTTTCGTAACTATGC 57.437 29.630 0.39 0.00 34.59 3.14
2915 3011 6.916360 TTCAGCTCCTCAAAATATTTGGTT 57.084 33.333 0.39 0.00 0.00 3.67
3012 3108 1.149148 GGCACCTTCGTGTCTTTCTC 58.851 55.000 0.00 0.00 41.62 2.87
3142 3238 8.853077 TGTAGCAATTAATTGGATAGGATCAG 57.147 34.615 25.61 0.66 38.21 2.90
3146 3242 8.849168 CAACATGTAGCAATTAATTGGATAGGA 58.151 33.333 25.61 4.48 38.21 2.94
3207 3303 1.505353 GCCAGCATCTGCAAGTGAC 59.495 57.895 4.79 0.00 45.16 3.67
3293 3389 6.742109 TGGCTAGTGACGGTATCTATTTTAC 58.258 40.000 0.00 0.00 0.00 2.01
3362 3461 2.664424 CGGTTACCGCACATCAAAACTG 60.664 50.000 11.93 0.00 41.17 3.16
3444 3543 4.527509 AGGCTATAGAATGATCACCACG 57.472 45.455 3.21 0.00 0.00 4.94
3466 3565 3.936453 ACAGCAGAACAAGAAACGTGTAA 59.064 39.130 0.00 0.00 0.00 2.41
3482 3581 4.809673 TCTTGTACAGTACATCACAGCAG 58.190 43.478 14.34 7.06 38.68 4.24
3490 3590 6.863126 GCAAATGCTTTTCTTGTACAGTACAT 59.137 34.615 14.34 0.00 36.96 2.29
3491 3591 6.183360 TGCAAATGCTTTTCTTGTACAGTACA 60.183 34.615 9.51 9.51 42.66 2.90
3492 3592 6.205784 TGCAAATGCTTTTCTTGTACAGTAC 58.794 36.000 6.97 3.49 42.66 2.73
3493 3593 6.384258 TGCAAATGCTTTTCTTGTACAGTA 57.616 33.333 6.97 0.00 42.66 2.74
3494 3594 5.261209 TGCAAATGCTTTTCTTGTACAGT 57.739 34.783 6.97 0.00 42.66 3.55
3495 3595 4.682860 CCTGCAAATGCTTTTCTTGTACAG 59.317 41.667 6.97 0.00 42.66 2.74
3632 3850 5.409520 GCAAGTGATACACAACATCTCAAGA 59.590 40.000 4.75 0.00 36.74 3.02
3655 3873 0.029300 AGCATGTCAAACACACACGC 59.971 50.000 0.00 0.00 38.04 5.34
3758 3976 2.428890 CTGCCTTCTTATCCTCGTCACT 59.571 50.000 0.00 0.00 0.00 3.41
3794 4012 1.848608 CGTCACGTATGATCACAGCAG 59.151 52.381 0.00 0.00 37.14 4.24
3799 4017 1.852895 GAAGGCGTCACGTATGATCAC 59.147 52.381 0.00 0.00 37.14 3.06
3813 4031 0.320374 TGTGTAGACTTGGGAAGGCG 59.680 55.000 0.00 0.00 43.06 5.52
3822 4040 0.898320 AGCGCCATCTGTGTAGACTT 59.102 50.000 2.29 0.00 35.34 3.01
3932 4168 5.424121 ACCAGTTTTCTTGACTTCAATCG 57.576 39.130 0.00 0.00 35.02 3.34
3969 4205 6.544931 ACACCCTAGTAGAAACAAAAAGGAAC 59.455 38.462 0.00 0.00 0.00 3.62
4132 4369 3.972502 CCCTTTCGATTCGAACAAAACAC 59.027 43.478 20.38 0.00 45.64 3.32
4134 4371 2.977829 GCCCTTTCGATTCGAACAAAAC 59.022 45.455 20.38 6.63 45.64 2.43
4153 4392 4.864704 TTTGATGGAAGTTTTACAGGCC 57.135 40.909 0.00 0.00 0.00 5.19
4155 4394 7.716612 AGAGTTTTTGATGGAAGTTTTACAGG 58.283 34.615 0.00 0.00 0.00 4.00
4156 4395 8.405531 TGAGAGTTTTTGATGGAAGTTTTACAG 58.594 33.333 0.00 0.00 0.00 2.74
4184 4423 3.113260 ACTAGGGAATGCGCTTCATAC 57.887 47.619 9.73 4.80 38.40 2.39
4192 4431 2.122783 TTGGGAAACTAGGGAATGCG 57.877 50.000 0.00 0.00 0.00 4.73
4193 4432 3.697166 TCTTTGGGAAACTAGGGAATGC 58.303 45.455 0.00 0.00 0.00 3.56
4194 4433 6.664428 TTTTCTTTGGGAAACTAGGGAATG 57.336 37.500 0.00 0.00 42.80 2.67
4195 4434 7.248976 AGATTTTCTTTGGGAAACTAGGGAAT 58.751 34.615 0.00 0.00 42.80 3.01
4202 4441 7.601705 TGATGAAGATTTTCTTTGGGAAACT 57.398 32.000 0.00 0.00 42.80 2.66
4213 4452 6.527957 CCAACGCATTTTGATGAAGATTTTC 58.472 36.000 0.00 0.00 0.00 2.29
4283 4597 2.799412 TCAAATTTGGCGCAAACATCAC 59.201 40.909 17.90 0.00 36.13 3.06
4290 4604 2.123342 CGAAACTCAAATTTGGCGCAA 58.877 42.857 17.90 0.00 0.00 4.85
4291 4605 1.335182 TCGAAACTCAAATTTGGCGCA 59.665 42.857 17.90 0.00 0.00 6.09
4293 4607 2.993545 TGTCGAAACTCAAATTTGGCG 58.006 42.857 17.90 11.68 0.00 5.69
4329 4667 5.551233 TGTAAATCAAACTCTCTCACAGGG 58.449 41.667 0.00 0.00 0.00 4.45
4334 4672 7.151976 TCACGATTGTAAATCAAACTCTCTCA 58.848 34.615 0.00 0.00 39.62 3.27
4339 4677 7.530861 GTGTCTTCACGATTGTAAATCAAACTC 59.469 37.037 0.00 0.00 35.90 3.01
4352 4690 9.003658 AGAAAAATCAATAGTGTCTTCACGATT 57.996 29.630 0.00 2.00 45.69 3.34
4358 4739 7.308435 CACCCAGAAAAATCAATAGTGTCTTC 58.692 38.462 0.00 0.00 0.00 2.87
4426 5262 4.344102 CGACCCTCCATACCTAATCTCAAA 59.656 45.833 0.00 0.00 0.00 2.69
4428 5264 3.497332 CGACCCTCCATACCTAATCTCA 58.503 50.000 0.00 0.00 0.00 3.27
4429 5265 2.826725 CCGACCCTCCATACCTAATCTC 59.173 54.545 0.00 0.00 0.00 2.75
4430 5266 2.890814 CCGACCCTCCATACCTAATCT 58.109 52.381 0.00 0.00 0.00 2.40
4431 5267 1.275573 GCCGACCCTCCATACCTAATC 59.724 57.143 0.00 0.00 0.00 1.75
4571 5481 2.825836 GGAATGGGACGGCTGCAG 60.826 66.667 10.11 10.11 0.00 4.41
4577 5487 1.074775 TAGGAGGGGAATGGGACGG 60.075 63.158 0.00 0.00 0.00 4.79
4703 5613 1.797211 GAGAGGTCGGCCCATACTCG 61.797 65.000 0.08 0.00 34.66 4.18
4707 5617 1.152525 GGAGAGAGGTCGGCCCATA 60.153 63.158 0.08 0.00 34.66 2.74
4734 5644 2.033294 GGGCTATGGGCTGCTAGC 59.967 66.667 8.10 8.10 41.46 3.42
4736 5646 0.183492 CTTTGGGCTATGGGCTGCTA 59.817 55.000 1.86 0.00 41.46 3.49
4768 5678 3.236618 GAAATATCGTGCGGCCGGC 62.237 63.158 29.38 21.18 43.96 6.13
4769 5679 1.157870 AAGAAATATCGTGCGGCCGG 61.158 55.000 29.38 10.87 0.00 6.13
4770 5680 0.232303 GAAGAAATATCGTGCGGCCG 59.768 55.000 24.05 24.05 0.00 6.13


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

AutoCloner maintained by Alex Coulton.