Multiple sequence alignment - TraesCS4A01G179000

Loading Multiple Alignment...

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 TraesCS4A01G179000 chr4A 100.000 3640 0 0 1 3640 452342153 452345792 0.000000e+00 6722
1 TraesCS4A01G179000 chr4D 97.249 2581 67 4 786 3362 120865326 120867906 0.000000e+00 4370
2 TraesCS4A01G179000 chr4D 95.948 765 20 5 1 757 120864506 120865267 0.000000e+00 1230
3 TraesCS4A01G179000 chr4D 94.815 135 6 1 3361 3495 120867940 120868073 3.680000e-50 209
4 TraesCS4A01G179000 chr4B 94.646 2596 94 18 786 3361 183603211 183605781 0.000000e+00 3982
5 TraesCS4A01G179000 chr4B 92.327 782 21 10 1 759 183602387 183603152 0.000000e+00 1075
6 TraesCS4A01G179000 chr4B 89.216 102 8 2 3439 3537 183605923 183606024 1.370000e-24 124
7 TraesCS4A01G179000 chr5A 97.345 113 2 1 3529 3640 85158000 85157888 1.330000e-44 191
8 TraesCS4A01G179000 chr5A 97.345 113 2 1 3529 3640 524033090 524032978 1.330000e-44 191
9 TraesCS4A01G179000 chr5A 96.460 113 3 1 3529 3640 375570830 375570718 6.210000e-43 185
10 TraesCS4A01G179000 chr3A 97.345 113 2 1 3529 3640 52460104 52460216 1.330000e-44 191
11 TraesCS4A01G179000 chr2A 97.345 113 2 1 3529 3640 71692773 71692661 1.330000e-44 191
12 TraesCS4A01G179000 chr1B 97.321 112 3 0 3529 3640 69253908 69253797 1.330000e-44 191
13 TraesCS4A01G179000 chr6A 96.460 113 3 1 3529 3640 57658489 57658377 6.210000e-43 185
14 TraesCS4A01G179000 chr5B 96.460 113 3 1 3529 3640 342183089 342183201 6.210000e-43 185
15 TraesCS4A01G179000 chr7B 95.652 115 3 2 3527 3640 516264876 516264763 2.230000e-42 183


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 TraesCS4A01G179000 chr4A 452342153 452345792 3639 False 6722.000000 6722 100.000 1 3640 1 chr4A.!!$F1 3639
1 TraesCS4A01G179000 chr4D 120864506 120868073 3567 False 1936.333333 4370 96.004 1 3495 3 chr4D.!!$F1 3494
2 TraesCS4A01G179000 chr4B 183602387 183606024 3637 False 1727.000000 3982 92.063 1 3537 3 chr4B.!!$F1 3536

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
56 57 0.242017 GGCGCTGTTGCTTTCAGATT 59.758 50.0 7.64 0.0 36.97 2.40 F
1558 1635 0.101399 CACCCTTCTCTCGATGGACG 59.899 60.0 0.00 0.0 44.09 4.79 F
1686 1763 1.111715 GCTCTGATGGCCAAATCCCC 61.112 60.0 10.96 0.0 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1763 1.241990 TGTCCTCGTCTTCCTCCACG 61.242 60.0 0.0 0.0 37.36 4.94 R
2427 2504 0.463654 TCCCATTCTGATTTCGCCGG 60.464 55.0 0.0 0.0 0.00 6.13 R
3614 3766 0.833949 TTGCCCCTGTTTTTCAACCC 59.166 50.0 0.0 0.0 31.02 4.11 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
39 40 3.019564 AGATCCTTGTGCTAATTGTGGC 58.980 45.455 0.00 0.00 0.00 5.01
56 57 0.242017 GGCGCTGTTGCTTTCAGATT 59.758 50.000 7.64 0.00 36.97 2.40
77 78 3.850752 TGAAACTAATTGAAGGCCCCAA 58.149 40.909 10.19 10.19 0.00 4.12
190 191 5.930135 AGCTGGTAGGTATTACAATCCAAG 58.070 41.667 0.00 0.00 33.73 3.61
381 400 1.536709 GCCGATGCATCAATTTCACCC 60.537 52.381 25.70 0.00 37.47 4.61
392 411 5.416271 TCAATTTCACCCACTCCTACTAC 57.584 43.478 0.00 0.00 0.00 2.73
393 412 5.091552 TCAATTTCACCCACTCCTACTACT 58.908 41.667 0.00 0.00 0.00 2.57
394 413 5.046591 TCAATTTCACCCACTCCTACTACTG 60.047 44.000 0.00 0.00 0.00 2.74
411 430 7.436673 CCTACTACTGCTCTTGTGTTTATCATC 59.563 40.741 0.00 0.00 0.00 2.92
495 514 4.213906 GGATTTGTTTGTCTGGCCAAAATG 59.786 41.667 7.01 0.00 36.17 2.32
629 653 3.895704 AAGGGTAAAGCAAAAGAGGGA 57.104 42.857 0.00 0.00 0.00 4.20
675 699 8.777865 AAGGAAAAGTGAAAAAGAAAAGGAAG 57.222 30.769 0.00 0.00 0.00 3.46
752 776 2.817056 GCTCATCCCCTCTCCCAGC 61.817 68.421 0.00 0.00 0.00 4.85
757 781 3.478274 CCCCTCTCCCAGCTGAGC 61.478 72.222 17.39 0.00 32.22 4.26
758 782 2.365370 CCCTCTCCCAGCTGAGCT 60.365 66.667 17.39 0.00 40.77 4.09
860 923 3.786368 TTCTCCCACATCACAACATCA 57.214 42.857 0.00 0.00 0.00 3.07
897 960 6.573664 TCTCTTCTCTTCTCTTCAGACAAG 57.426 41.667 0.00 0.00 0.00 3.16
906 969 4.564041 TCTCTTCAGACAAGAACATCAGC 58.436 43.478 0.00 0.00 0.00 4.26
909 972 1.081892 CAGACAAGAACATCAGCCCG 58.918 55.000 0.00 0.00 0.00 6.13
935 1000 6.812160 TCTTCTTAAGTAGGAATTCAGTTCGC 59.188 38.462 7.93 0.00 37.73 4.70
959 1024 4.039092 TGCTGCCTCCTTGCCCTC 62.039 66.667 0.00 0.00 0.00 4.30
960 1025 3.726144 GCTGCCTCCTTGCCCTCT 61.726 66.667 0.00 0.00 0.00 3.69
978 1055 5.596772 GCCCTCTCCCTTGATAGATATAGAC 59.403 48.000 0.00 0.00 0.00 2.59
1467 1544 2.956964 CCGCACGAGAATCTCCGC 60.957 66.667 4.47 6.94 0.00 5.54
1558 1635 0.101399 CACCCTTCTCTCGATGGACG 59.899 60.000 0.00 0.00 44.09 4.79
1686 1763 1.111715 GCTCTGATGGCCAAATCCCC 61.112 60.000 10.96 0.00 0.00 4.81
1848 1925 2.203451 CTGCCCAGGATGATGGCC 60.203 66.667 0.00 0.00 41.97 5.36
1945 2022 4.021544 AGAGTCAGAGTGTTCTTGACCATC 60.022 45.833 0.00 0.00 34.65 3.51
1947 2024 4.285517 AGTCAGAGTGTTCTTGACCATCAT 59.714 41.667 0.64 0.00 34.65 2.45
2087 2164 2.024941 GGATCAAGGGGTGGAACATCTT 60.025 50.000 0.00 0.00 44.52 2.40
2088 2165 3.564352 GGATCAAGGGGTGGAACATCTTT 60.564 47.826 0.00 0.00 44.52 2.52
2325 2402 2.803285 ATGGCTTAGGGAGGATGAGA 57.197 50.000 0.00 0.00 0.00 3.27
2426 2503 0.107017 ATCGGAGGTGCCCAATTCAG 60.107 55.000 0.00 0.00 0.00 3.02
2427 2504 2.409870 CGGAGGTGCCCAATTCAGC 61.410 63.158 0.00 0.00 0.00 4.26
2584 2661 2.624838 GCCTTGGCTACAATGTGCATAT 59.375 45.455 4.11 0.00 35.73 1.78
2599 2676 4.772100 TGTGCATATCTATGGTAGCTAGCA 59.228 41.667 26.55 26.55 38.16 3.49
2896 2973 6.441093 TGGATCTTGTTTGATATTGACAGC 57.559 37.500 0.00 0.00 0.00 4.40
2914 2991 1.701704 GCAAGAAAATTGCAGGGTCG 58.298 50.000 7.67 0.00 44.34 4.79
2919 2996 2.293399 AGAAAATTGCAGGGTCGTTGTC 59.707 45.455 0.00 0.00 0.00 3.18
2957 3034 3.384789 GCCAGGTTTTCTTCCTCTTTTGT 59.615 43.478 0.00 0.00 32.37 2.83
2984 3061 0.736053 GTTGTGTGCCGTTTCTTCCA 59.264 50.000 0.00 0.00 0.00 3.53
3062 3143 7.004225 CGTCTTCACGTTCTTCATTTCTTAAG 58.996 38.462 0.00 0.00 41.42 1.85
3063 3144 6.792726 GTCTTCACGTTCTTCATTTCTTAAGC 59.207 38.462 0.00 0.00 0.00 3.09
3198 3281 7.857885 CCTATCGCATTTCCTTTCTTATGTTTC 59.142 37.037 0.00 0.00 0.00 2.78
3288 3372 3.564644 CCCAGCATCTAAATTCTGCTCAG 59.435 47.826 0.00 0.00 44.09 3.35
3321 3405 1.234806 ATCATAACCCCAGGCACCAT 58.765 50.000 0.00 0.00 0.00 3.55
3387 3506 2.290896 TGTCTATTTGCAGTTGGAGGGG 60.291 50.000 0.00 0.00 0.00 4.79
3390 3509 0.613012 ATTTGCAGTTGGAGGGGAGC 60.613 55.000 0.00 0.00 0.00 4.70
3418 3537 9.490663 GTATCTGTTTCAAATTCATAACGAAGG 57.509 33.333 0.00 0.00 36.95 3.46
3463 3615 4.180057 CAGAAGCAGCCTTAACTACTCAG 58.820 47.826 0.00 0.00 0.00 3.35
3516 3668 3.122948 CGAAACAAGGTTCGGTATGTCTG 59.877 47.826 12.15 0.00 45.21 3.51
3517 3669 2.094762 ACAAGGTTCGGTATGTCTGC 57.905 50.000 0.00 0.00 0.00 4.26
3520 3672 1.447140 GGTTCGGTATGTCTGCGCA 60.447 57.895 10.98 10.98 0.00 6.09
3537 3689 1.470098 CGCAGCAACCTTAAGAGCATT 59.530 47.619 3.36 0.00 0.00 3.56
3538 3690 2.677836 CGCAGCAACCTTAAGAGCATTA 59.322 45.455 3.36 0.00 0.00 1.90
3539 3691 3.485877 CGCAGCAACCTTAAGAGCATTAC 60.486 47.826 3.36 0.00 0.00 1.89
3540 3692 3.691609 GCAGCAACCTTAAGAGCATTACT 59.308 43.478 3.36 0.00 0.00 2.24
3541 3693 4.876107 GCAGCAACCTTAAGAGCATTACTA 59.124 41.667 3.36 0.00 0.00 1.82
3542 3694 5.007136 GCAGCAACCTTAAGAGCATTACTAG 59.993 44.000 3.36 0.00 0.00 2.57
3543 3695 6.109359 CAGCAACCTTAAGAGCATTACTAGT 58.891 40.000 3.36 0.00 0.00 2.57
3544 3696 7.265673 CAGCAACCTTAAGAGCATTACTAGTA 58.734 38.462 3.36 0.00 0.00 1.82
3545 3697 7.436673 CAGCAACCTTAAGAGCATTACTAGTAG 59.563 40.741 3.36 0.00 0.00 2.57
3546 3698 7.342284 AGCAACCTTAAGAGCATTACTAGTAGA 59.658 37.037 3.36 0.00 0.00 2.59
3547 3699 7.980099 GCAACCTTAAGAGCATTACTAGTAGAA 59.020 37.037 3.36 0.00 0.00 2.10
3548 3700 9.303537 CAACCTTAAGAGCATTACTAGTAGAAC 57.696 37.037 3.36 0.00 0.00 3.01
3549 3701 8.009622 ACCTTAAGAGCATTACTAGTAGAACC 57.990 38.462 3.36 0.00 0.00 3.62
3550 3702 7.069702 ACCTTAAGAGCATTACTAGTAGAACCC 59.930 40.741 3.36 0.00 0.00 4.11
3551 3703 7.288158 CCTTAAGAGCATTACTAGTAGAACCCT 59.712 40.741 3.36 0.00 0.00 4.34
3552 3704 6.718522 AAGAGCATTACTAGTAGAACCCTC 57.281 41.667 3.59 6.41 0.00 4.30
3553 3705 5.767670 AGAGCATTACTAGTAGAACCCTCA 58.232 41.667 3.59 0.00 0.00 3.86
3554 3706 6.195700 AGAGCATTACTAGTAGAACCCTCAA 58.804 40.000 3.59 0.00 0.00 3.02
3555 3707 6.668283 AGAGCATTACTAGTAGAACCCTCAAA 59.332 38.462 3.59 0.00 0.00 2.69
3556 3708 7.345914 AGAGCATTACTAGTAGAACCCTCAAAT 59.654 37.037 3.59 0.00 0.00 2.32
3557 3709 7.501844 AGCATTACTAGTAGAACCCTCAAATC 58.498 38.462 3.59 0.00 0.00 2.17
3558 3710 6.706716 GCATTACTAGTAGAACCCTCAAATCC 59.293 42.308 3.59 0.00 0.00 3.01
3559 3711 7.419172 GCATTACTAGTAGAACCCTCAAATCCT 60.419 40.741 3.59 0.00 0.00 3.24
3560 3712 7.657023 TTACTAGTAGAACCCTCAAATCCTC 57.343 40.000 3.59 0.00 0.00 3.71
3561 3713 5.590818 ACTAGTAGAACCCTCAAATCCTCA 58.409 41.667 3.59 0.00 0.00 3.86
3562 3714 6.023603 ACTAGTAGAACCCTCAAATCCTCAA 58.976 40.000 3.59 0.00 0.00 3.02
3563 3715 5.843019 AGTAGAACCCTCAAATCCTCAAA 57.157 39.130 0.00 0.00 0.00 2.69
3564 3716 5.561679 AGTAGAACCCTCAAATCCTCAAAC 58.438 41.667 0.00 0.00 0.00 2.93
3565 3717 3.412386 AGAACCCTCAAATCCTCAAACG 58.588 45.455 0.00 0.00 0.00 3.60
3566 3718 1.534729 ACCCTCAAATCCTCAAACGC 58.465 50.000 0.00 0.00 0.00 4.84
3567 3719 1.073923 ACCCTCAAATCCTCAAACGCT 59.926 47.619 0.00 0.00 0.00 5.07
3568 3720 1.740025 CCCTCAAATCCTCAAACGCTC 59.260 52.381 0.00 0.00 0.00 5.03
3569 3721 2.426522 CCTCAAATCCTCAAACGCTCA 58.573 47.619 0.00 0.00 0.00 4.26
3570 3722 2.160417 CCTCAAATCCTCAAACGCTCAC 59.840 50.000 0.00 0.00 0.00 3.51
3571 3723 3.070018 CTCAAATCCTCAAACGCTCACT 58.930 45.455 0.00 0.00 0.00 3.41
3572 3724 4.245660 CTCAAATCCTCAAACGCTCACTA 58.754 43.478 0.00 0.00 0.00 2.74
3573 3725 4.245660 TCAAATCCTCAAACGCTCACTAG 58.754 43.478 0.00 0.00 0.00 2.57
3574 3726 2.301577 ATCCTCAAACGCTCACTAGC 57.698 50.000 0.00 0.00 45.86 3.42
3585 3737 2.696506 GCTCACTAGCGTTTTAAGGGT 58.303 47.619 0.00 0.00 39.39 4.34
3586 3738 2.671888 GCTCACTAGCGTTTTAAGGGTC 59.328 50.000 0.00 0.00 39.39 4.46
3587 3739 3.259902 CTCACTAGCGTTTTAAGGGTCC 58.740 50.000 0.00 0.00 0.00 4.46
3588 3740 2.633967 TCACTAGCGTTTTAAGGGTCCA 59.366 45.455 0.00 0.00 0.00 4.02
3589 3741 3.071312 TCACTAGCGTTTTAAGGGTCCAA 59.929 43.478 0.00 0.00 0.00 3.53
3590 3742 3.816523 CACTAGCGTTTTAAGGGTCCAAA 59.183 43.478 0.00 0.00 0.00 3.28
3591 3743 4.276431 CACTAGCGTTTTAAGGGTCCAAAA 59.724 41.667 0.00 0.00 0.00 2.44
3592 3744 4.888823 ACTAGCGTTTTAAGGGTCCAAAAA 59.111 37.500 0.00 0.00 0.00 1.94
3593 3745 4.948341 AGCGTTTTAAGGGTCCAAAAAT 57.052 36.364 0.00 0.00 0.00 1.82
3594 3746 4.627058 AGCGTTTTAAGGGTCCAAAAATG 58.373 39.130 11.93 11.93 33.99 2.32
3595 3747 4.342665 AGCGTTTTAAGGGTCCAAAAATGA 59.657 37.500 16.88 0.00 33.09 2.57
3596 3748 5.011635 AGCGTTTTAAGGGTCCAAAAATGAT 59.988 36.000 16.88 11.44 33.09 2.45
3597 3749 5.347635 GCGTTTTAAGGGTCCAAAAATGATC 59.652 40.000 16.88 0.00 33.09 2.92
3598 3750 6.687604 CGTTTTAAGGGTCCAAAAATGATCT 58.312 36.000 11.28 0.00 33.09 2.75
3599 3751 7.151976 CGTTTTAAGGGTCCAAAAATGATCTT 58.848 34.615 11.28 0.00 33.09 2.40
3600 3752 7.655732 CGTTTTAAGGGTCCAAAAATGATCTTT 59.344 33.333 11.28 0.00 33.09 2.52
3601 3753 9.337396 GTTTTAAGGGTCCAAAAATGATCTTTT 57.663 29.630 0.88 0.88 0.00 2.27
3602 3754 9.913310 TTTTAAGGGTCCAAAAATGATCTTTTT 57.087 25.926 12.28 12.28 32.38 1.94
3620 3772 4.451629 TTTTTGCACTTTTACGGGTTGA 57.548 36.364 0.00 0.00 0.00 3.18
3621 3773 4.451629 TTTTGCACTTTTACGGGTTGAA 57.548 36.364 0.00 0.00 0.00 2.69
3622 3774 4.451629 TTTGCACTTTTACGGGTTGAAA 57.548 36.364 0.00 0.00 0.00 2.69
3623 3775 4.451629 TTGCACTTTTACGGGTTGAAAA 57.548 36.364 0.00 0.00 0.00 2.29
3624 3776 4.451629 TGCACTTTTACGGGTTGAAAAA 57.548 36.364 0.00 0.00 0.00 1.94
3625 3777 4.174762 TGCACTTTTACGGGTTGAAAAAC 58.825 39.130 0.00 0.00 0.00 2.43
3626 3778 4.174762 GCACTTTTACGGGTTGAAAAACA 58.825 39.130 0.00 0.00 32.77 2.83
3627 3779 4.266739 GCACTTTTACGGGTTGAAAAACAG 59.733 41.667 0.00 0.00 32.77 3.16
3628 3780 4.801516 CACTTTTACGGGTTGAAAAACAGG 59.198 41.667 0.00 0.00 32.77 4.00
3629 3781 4.142116 ACTTTTACGGGTTGAAAAACAGGG 60.142 41.667 0.00 0.00 32.77 4.45
3630 3782 1.984066 TACGGGTTGAAAAACAGGGG 58.016 50.000 0.00 0.00 32.77 4.79
3631 3783 1.365999 CGGGTTGAAAAACAGGGGC 59.634 57.895 0.00 0.00 32.77 5.80
3632 3784 1.395826 CGGGTTGAAAAACAGGGGCA 61.396 55.000 0.00 0.00 32.77 5.36
3633 3785 0.833949 GGGTTGAAAAACAGGGGCAA 59.166 50.000 0.00 0.00 32.77 4.52
3634 3786 1.210722 GGGTTGAAAAACAGGGGCAAA 59.789 47.619 0.00 0.00 32.77 3.68
3635 3787 2.560504 GGTTGAAAAACAGGGGCAAAG 58.439 47.619 0.00 0.00 30.22 2.77
3636 3788 2.169561 GGTTGAAAAACAGGGGCAAAGA 59.830 45.455 0.00 0.00 30.22 2.52
3637 3789 3.181455 GGTTGAAAAACAGGGGCAAAGAT 60.181 43.478 0.00 0.00 30.22 2.40
3638 3790 4.450976 GTTGAAAAACAGGGGCAAAGATT 58.549 39.130 0.00 0.00 0.00 2.40
3639 3791 5.454045 GGTTGAAAAACAGGGGCAAAGATTA 60.454 40.000 0.00 0.00 30.22 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.975410 TCAATCTGAAAGCAACAGCG 57.025 45.000 0.00 0.00 35.61 5.18
56 57 3.534357 TGGGGCCTTCAATTAGTTTCA 57.466 42.857 0.84 0.00 0.00 2.69
77 78 0.251832 ATGGTCTGGACTCGACTGGT 60.252 55.000 0.67 0.00 0.00 4.00
179 180 2.961741 TGTGCTTTGCCTTGGATTGTAA 59.038 40.909 0.00 0.00 0.00 2.41
190 191 1.493134 GCTTGTGCTTGTGCTTTGCC 61.493 55.000 0.00 0.00 40.48 4.52
271 286 6.324254 TGCATCATGAATGATAATTTCCACCA 59.676 34.615 0.00 0.00 45.23 4.17
381 400 3.508012 ACACAAGAGCAGTAGTAGGAGTG 59.492 47.826 0.00 0.00 0.00 3.51
392 411 6.094464 TGAATGGATGATAAACACAAGAGCAG 59.906 38.462 0.00 0.00 0.00 4.24
393 412 5.945191 TGAATGGATGATAAACACAAGAGCA 59.055 36.000 0.00 0.00 0.00 4.26
394 413 6.094603 AGTGAATGGATGATAAACACAAGAGC 59.905 38.462 0.00 0.00 0.00 4.09
495 514 2.832129 TCCCACATCTGTGTCTAGTTCC 59.168 50.000 9.33 0.00 44.21 3.62
520 539 8.980610 TCATTTGCTTTAACATTTCACTTCATG 58.019 29.630 0.00 0.00 0.00 3.07
568 592 3.066621 TGTTGCACATTCCAGAACAACTC 59.933 43.478 10.88 0.00 38.50 3.01
573 597 3.316308 ACTCTTGTTGCACATTCCAGAAC 59.684 43.478 0.00 0.00 0.00 3.01
629 653 1.151810 TTGCCCCTGTCCCTCTTCT 60.152 57.895 0.00 0.00 0.00 2.85
675 699 0.744771 GTGATGGCGACCTCTTTCCC 60.745 60.000 0.00 0.00 0.00 3.97
782 806 9.719355 TGTGTTGTATTCTTGTATCTATTGTGT 57.281 29.630 0.00 0.00 0.00 3.72
860 923 8.264347 AGAAGAGAAGAGAAGAAAGAAACTTGT 58.736 33.333 0.00 0.00 0.00 3.16
897 960 2.100605 AAGAAGACGGGCTGATGTTC 57.899 50.000 0.00 0.00 0.00 3.18
906 969 5.974108 TGAATTCCTACTTAAGAAGACGGG 58.026 41.667 10.09 2.21 0.00 5.28
909 972 7.201453 GCGAACTGAATTCCTACTTAAGAAGAC 60.201 40.741 10.09 0.00 33.26 3.01
935 1000 1.304713 AAGGAGGCAGCACCATTGG 60.305 57.895 0.00 0.00 43.14 3.16
959 1024 7.106890 TCGTCTGTCTATATCTATCAAGGGAG 58.893 42.308 0.00 0.00 0.00 4.30
960 1025 7.017319 TCGTCTGTCTATATCTATCAAGGGA 57.983 40.000 0.00 0.00 0.00 4.20
978 1055 2.920227 GCTCACTCACTTCACTCGTCTG 60.920 54.545 0.00 0.00 0.00 3.51
1305 1382 3.071874 TGGTGGATGTGGTCTTTCATC 57.928 47.619 0.00 0.00 39.49 2.92
1686 1763 1.241990 TGTCCTCGTCTTCCTCCACG 61.242 60.000 0.00 0.00 37.36 4.94
1848 1925 4.424566 GCATTGGCAGTGGCACCG 62.425 66.667 20.46 14.13 43.71 4.94
1945 2022 1.451567 CCTGCTCCCACTGCTGATG 60.452 63.158 0.00 0.00 0.00 3.07
1947 2024 3.324930 CCCTGCTCCCACTGCTGA 61.325 66.667 0.00 0.00 0.00 4.26
2087 2164 6.544928 TGCTCTTCTTATGTATGAGACCAA 57.455 37.500 0.00 0.00 0.00 3.67
2088 2165 5.452496 GCTGCTCTTCTTATGTATGAGACCA 60.452 44.000 0.00 0.00 0.00 4.02
2244 2321 2.653726 CCCATTGCTGCACCACTATTA 58.346 47.619 0.00 0.00 0.00 0.98
2269 2346 2.841988 GCTCCTCCTCCCGCTCAT 60.842 66.667 0.00 0.00 0.00 2.90
2325 2402 5.337652 CCTCTCGAGTAAAACCTCATCCTTT 60.338 44.000 13.13 0.00 0.00 3.11
2426 2503 1.356624 CCATTCTGATTTCGCCGGC 59.643 57.895 19.07 19.07 0.00 6.13
2427 2504 0.463654 TCCCATTCTGATTTCGCCGG 60.464 55.000 0.00 0.00 0.00 6.13
2584 2661 5.574188 TCTGATGATGCTAGCTACCATAGA 58.426 41.667 17.23 10.23 0.00 1.98
2599 2676 9.638176 AGCCTATAAAAAGTTGATTCTGATGAT 57.362 29.630 0.00 0.00 0.00 2.45
2689 2766 3.594232 TCCCAAGCCCAGTAGGAAATAAA 59.406 43.478 0.00 0.00 38.24 1.40
2896 2973 3.052036 CAACGACCCTGCAATTTTCTTG 58.948 45.455 0.00 0.00 0.00 3.02
2914 2991 1.159285 TGCTGCTATGCTGTGACAAC 58.841 50.000 0.00 0.00 0.00 3.32
2939 3016 7.010460 CACAATGAACAAAAGAGGAAGAAAACC 59.990 37.037 0.00 0.00 0.00 3.27
2957 3034 1.098869 ACGGCACACAACACAATGAA 58.901 45.000 0.00 0.00 0.00 2.57
2984 3061 6.848562 ACCCATAGATTTAGGATTTCTGGT 57.151 37.500 0.00 0.00 0.00 4.00
3062 3143 3.428534 CCTTTCAAAAACATAAGCACGGC 59.571 43.478 0.00 0.00 0.00 5.68
3063 3144 3.428534 GCCTTTCAAAAACATAAGCACGG 59.571 43.478 0.00 0.00 0.00 4.94
3128 3211 4.412796 TGATCTGATTTACCCAGCAGAG 57.587 45.455 0.00 0.00 40.34 3.35
3198 3281 9.608617 CTGCTATTTACATATTGCTTCATTCTG 57.391 33.333 0.00 0.00 0.00 3.02
3214 3297 4.336433 TCAAGGCATCAAGCTGCTATTTAC 59.664 41.667 0.90 0.00 44.79 2.01
3288 3372 4.259356 GGTTATGATAATCCCCTTACGGC 58.741 47.826 0.00 0.00 0.00 5.68
3321 3405 7.279981 CACAATCCATTCAACTTAGATTCGGTA 59.720 37.037 0.00 0.00 0.00 4.02
3387 3506 9.495754 GTTATGAATTTGAAACAGATACAGCTC 57.504 33.333 0.00 0.00 0.00 4.09
3463 3615 6.036577 TGGCCTGGAATCAAATTAACTTTC 57.963 37.500 3.32 0.00 0.00 2.62
3495 3647 3.120304 GCAGACATACCGAACCTTGTTTC 60.120 47.826 0.00 0.00 0.00 2.78
3507 3659 1.425428 GTTGCTGCGCAGACATACC 59.575 57.895 40.21 21.45 40.61 2.73
3516 3668 1.135523 GCTCTTAAGGTTGCTGCGC 59.864 57.895 0.00 0.00 0.00 6.09
3517 3669 1.089920 ATGCTCTTAAGGTTGCTGCG 58.910 50.000 1.85 0.00 0.00 5.18
3520 3672 6.301169 ACTAGTAATGCTCTTAAGGTTGCT 57.699 37.500 1.85 5.01 0.00 3.91
3527 3679 7.837689 TGAGGGTTCTACTAGTAATGCTCTTAA 59.162 37.037 3.76 0.00 0.00 1.85
3533 3685 6.706716 GGATTTGAGGGTTCTACTAGTAATGC 59.293 42.308 3.76 0.00 0.00 3.56
3537 3689 6.738635 TGAGGATTTGAGGGTTCTACTAGTA 58.261 40.000 1.89 1.89 0.00 1.82
3538 3690 5.590818 TGAGGATTTGAGGGTTCTACTAGT 58.409 41.667 0.00 0.00 0.00 2.57
3539 3691 6.546428 TTGAGGATTTGAGGGTTCTACTAG 57.454 41.667 0.00 0.00 0.00 2.57
3540 3692 6.573680 CGTTTGAGGATTTGAGGGTTCTACTA 60.574 42.308 0.00 0.00 0.00 1.82
3541 3693 5.561679 GTTTGAGGATTTGAGGGTTCTACT 58.438 41.667 0.00 0.00 0.00 2.57
3542 3694 4.392138 CGTTTGAGGATTTGAGGGTTCTAC 59.608 45.833 0.00 0.00 0.00 2.59
3543 3695 4.575885 CGTTTGAGGATTTGAGGGTTCTA 58.424 43.478 0.00 0.00 0.00 2.10
3544 3696 3.412386 CGTTTGAGGATTTGAGGGTTCT 58.588 45.455 0.00 0.00 0.00 3.01
3545 3697 2.095212 GCGTTTGAGGATTTGAGGGTTC 60.095 50.000 0.00 0.00 0.00 3.62
3546 3698 1.886542 GCGTTTGAGGATTTGAGGGTT 59.113 47.619 0.00 0.00 0.00 4.11
3547 3699 1.073923 AGCGTTTGAGGATTTGAGGGT 59.926 47.619 0.00 0.00 0.00 4.34
3548 3700 1.740025 GAGCGTTTGAGGATTTGAGGG 59.260 52.381 0.00 0.00 0.00 4.30
3549 3701 2.160417 GTGAGCGTTTGAGGATTTGAGG 59.840 50.000 0.00 0.00 0.00 3.86
3550 3702 3.070018 AGTGAGCGTTTGAGGATTTGAG 58.930 45.455 0.00 0.00 0.00 3.02
3551 3703 3.126001 AGTGAGCGTTTGAGGATTTGA 57.874 42.857 0.00 0.00 0.00 2.69
3552 3704 3.181516 GCTAGTGAGCGTTTGAGGATTTG 60.182 47.826 0.00 0.00 39.39 2.32
3553 3705 3.003480 GCTAGTGAGCGTTTGAGGATTT 58.997 45.455 0.00 0.00 39.39 2.17
3554 3706 2.622436 GCTAGTGAGCGTTTGAGGATT 58.378 47.619 0.00 0.00 39.39 3.01
3555 3707 2.301577 GCTAGTGAGCGTTTGAGGAT 57.698 50.000 0.00 0.00 39.39 3.24
3556 3708 3.814577 GCTAGTGAGCGTTTGAGGA 57.185 52.632 0.00 0.00 39.39 3.71
3565 3717 2.671888 GACCCTTAAAACGCTAGTGAGC 59.328 50.000 10.99 0.00 46.00 4.26
3566 3718 3.259902 GGACCCTTAAAACGCTAGTGAG 58.740 50.000 10.99 0.00 0.00 3.51
3567 3719 2.633967 TGGACCCTTAAAACGCTAGTGA 59.366 45.455 10.99 0.00 0.00 3.41
3568 3720 3.048337 TGGACCCTTAAAACGCTAGTG 57.952 47.619 0.59 0.59 0.00 2.74
3569 3721 3.775261 TTGGACCCTTAAAACGCTAGT 57.225 42.857 0.00 0.00 0.00 2.57
3570 3722 5.441709 TTTTTGGACCCTTAAAACGCTAG 57.558 39.130 0.00 0.00 0.00 3.42
3571 3723 5.535406 TCATTTTTGGACCCTTAAAACGCTA 59.465 36.000 0.00 0.00 0.00 4.26
3572 3724 4.342665 TCATTTTTGGACCCTTAAAACGCT 59.657 37.500 0.00 0.00 0.00 5.07
3573 3725 4.623002 TCATTTTTGGACCCTTAAAACGC 58.377 39.130 0.00 0.00 0.00 4.84
3574 3726 6.687604 AGATCATTTTTGGACCCTTAAAACG 58.312 36.000 0.00 0.00 0.00 3.60
3575 3727 8.902540 AAAGATCATTTTTGGACCCTTAAAAC 57.097 30.769 0.00 0.00 0.00 2.43
3576 3728 9.913310 AAAAAGATCATTTTTGGACCCTTAAAA 57.087 25.926 2.87 0.00 31.05 1.52
3599 3751 4.451629 TCAACCCGTAAAAGTGCAAAAA 57.548 36.364 0.00 0.00 0.00 1.94
3600 3752 4.451629 TTCAACCCGTAAAAGTGCAAAA 57.548 36.364 0.00 0.00 0.00 2.44
3601 3753 4.451629 TTTCAACCCGTAAAAGTGCAAA 57.548 36.364 0.00 0.00 0.00 3.68
3602 3754 4.451629 TTTTCAACCCGTAAAAGTGCAA 57.548 36.364 0.00 0.00 0.00 4.08
3603 3755 4.174762 GTTTTTCAACCCGTAAAAGTGCA 58.825 39.130 0.00 0.00 0.00 4.57
3604 3756 4.174762 TGTTTTTCAACCCGTAAAAGTGC 58.825 39.130 0.00 0.00 31.02 4.40
3605 3757 4.801516 CCTGTTTTTCAACCCGTAAAAGTG 59.198 41.667 0.00 0.00 31.02 3.16
3606 3758 4.142116 CCCTGTTTTTCAACCCGTAAAAGT 60.142 41.667 0.00 0.00 31.02 2.66
3607 3759 4.364860 CCCTGTTTTTCAACCCGTAAAAG 58.635 43.478 0.00 0.00 31.02 2.27
3608 3760 3.132467 CCCCTGTTTTTCAACCCGTAAAA 59.868 43.478 0.00 0.00 31.02 1.52
3609 3761 2.694109 CCCCTGTTTTTCAACCCGTAAA 59.306 45.455 0.00 0.00 31.02 2.01
3610 3762 2.308690 CCCCTGTTTTTCAACCCGTAA 58.691 47.619 0.00 0.00 31.02 3.18
3611 3763 1.984066 CCCCTGTTTTTCAACCCGTA 58.016 50.000 0.00 0.00 31.02 4.02
3612 3764 1.396607 GCCCCTGTTTTTCAACCCGT 61.397 55.000 0.00 0.00 31.02 5.28
3613 3765 1.365999 GCCCCTGTTTTTCAACCCG 59.634 57.895 0.00 0.00 31.02 5.28
3614 3766 0.833949 TTGCCCCTGTTTTTCAACCC 59.166 50.000 0.00 0.00 31.02 4.11
3615 3767 2.169561 TCTTTGCCCCTGTTTTTCAACC 59.830 45.455 0.00 0.00 31.02 3.77
3616 3768 3.535280 TCTTTGCCCCTGTTTTTCAAC 57.465 42.857 0.00 0.00 0.00 3.18
3617 3769 4.769345 AATCTTTGCCCCTGTTTTTCAA 57.231 36.364 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.