Multiple sequence alignment - TraesCS6A01G285000

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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 TraesCS6A01G285000 chr6A 100.000 3968 0 0 1 3968 516407630 516411597 0.000000e+00 7328
1 TraesCS6A01G285000 chr6D 96.607 3478 72 22 1 3464 375014976 375018421 0.000000e+00 5727
2 TraesCS6A01G285000 chr6D 87.783 221 10 4 3748 3968 375018663 375018866 3.960000e-60 243
3 TraesCS6A01G285000 chr6D 87.027 185 6 7 3459 3640 375018447 375018616 4.050000e-45 193
4 TraesCS6A01G285000 chr6D 95.833 72 3 0 3683 3754 102978798 102978869 2.510000e-22 117
5 TraesCS6A01G285000 chr6B 96.336 3493 89 15 1 3464 561691486 561694968 0.000000e+00 5705
6 TraesCS6A01G285000 chr6B 95.536 224 8 2 3459 3681 561694994 561695216 1.360000e-94 357
7 TraesCS6A01G285000 chr6B 95.833 216 8 1 3753 3968 561695209 561695423 8.160000e-92 348
8 TraesCS6A01G285000 chr7A 93.182 88 3 3 3681 3767 6373196 6373281 4.160000e-25 126
9 TraesCS6A01G285000 chr7A 93.590 78 5 0 3679 3756 664986999 664986922 2.510000e-22 117
10 TraesCS6A01G285000 chr4D 96.154 78 2 1 3681 3757 365394714 365394637 4.160000e-25 126
11 TraesCS6A01G285000 chr3D 95.946 74 3 0 3681 3754 416188743 416188670 1.940000e-23 121
12 TraesCS6A01G285000 chr4A 93.671 79 5 0 3676 3754 714078200 714078278 6.970000e-23 119
13 TraesCS6A01G285000 chr3B 94.737 76 4 0 3679 3754 52905643 52905568 6.970000e-23 119
14 TraesCS6A01G285000 chr3A 93.671 79 5 0 3676 3754 474212706 474212784 6.970000e-23 119
15 TraesCS6A01G285000 chr5A 93.421 76 5 0 3679 3754 44109607 44109532 3.240000e-21 113


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 TraesCS6A01G285000 chr6A 516407630 516411597 3967 False 7328.000000 7328 100.000000 1 3968 1 chr6A.!!$F1 3967
1 TraesCS6A01G285000 chr6D 375014976 375018866 3890 False 2054.333333 5727 90.472333 1 3968 3 chr6D.!!$F2 3967
2 TraesCS6A01G285000 chr6B 561691486 561695423 3937 False 2136.666667 5705 95.901667 1 3968 3 chr6B.!!$F1 3967

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
27 28 0.958382 TGTTTACCCACTCGCATGGC 60.958 55.000 0.00 0.0 38.55 4.40 F
1488 1509 0.398664 CCCCAGAAGGTACCTCCGAT 60.399 60.000 16.64 0.0 41.99 4.18 F
2232 2259 1.963338 GGCCGGATATGCTGCTGTC 60.963 63.158 5.05 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 1615 1.001293 GGCATCAGTGTCAGTGTCAGA 59.999 52.381 7.54 0.0 0.0 3.27 R
2665 2692 0.673333 TCAGCGCATACCACAACCAG 60.673 55.000 11.47 0.0 0.0 4.00 R
3694 3788 0.106116 ACTATGGGAGAGGGTCGGAC 60.106 60.000 0.00 0.0 0.0 4.79 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
17 18 4.804806 GCCGTTCCTGTTTACCCA 57.195 55.556 0.00 0.00 0.00 4.51
27 28 0.958382 TGTTTACCCACTCGCATGGC 60.958 55.000 0.00 0.00 38.55 4.40
88 89 1.877443 CACGATTCGGGAGTGGTTTTT 59.123 47.619 11.29 0.00 28.17 1.94
130 131 1.577328 AATGTTTGAGCGACGCTGGG 61.577 55.000 29.85 0.00 39.88 4.45
303 304 2.403586 GCAAGATGCGCCGTTACC 59.596 61.111 4.18 0.00 31.71 2.85
331 332 2.092323 GATGCCGCCTTTTCCTAGTTT 58.908 47.619 0.00 0.00 0.00 2.66
346 347 3.887110 CCTAGTTTCCCGAGGTTTTGTTT 59.113 43.478 0.00 0.00 31.67 2.83
436 438 9.762933 ATGTTTGTTGTCTGTTTGCTTATTATT 57.237 25.926 0.00 0.00 0.00 1.40
528 531 6.597280 AGACATTCTTTCATTCTGAAGTAGGC 59.403 38.462 0.00 0.00 37.70 3.93
686 703 5.178797 TGCTGCCAGTCTTATTTTACTCTC 58.821 41.667 0.00 0.00 0.00 3.20
731 748 1.008538 CTGGGCGTGTTTTGTGCTC 60.009 57.895 0.00 0.00 0.00 4.26
1032 1053 3.003482 GCTGGATATTCTCTGCTTTGCTG 59.997 47.826 0.00 0.00 0.00 4.41
1036 1057 0.886563 ATTCTCTGCTTTGCTGGTGC 59.113 50.000 0.00 0.00 40.20 5.01
1488 1509 0.398664 CCCCAGAAGGTACCTCCGAT 60.399 60.000 16.64 0.00 41.99 4.18
1593 1614 5.338708 GGAAGGAATGGAAGTGATCTCAGAA 60.339 44.000 0.00 0.00 0.00 3.02
1594 1615 5.972327 AGGAATGGAAGTGATCTCAGAAT 57.028 39.130 0.00 0.00 0.00 2.40
1785 1812 8.950208 AGAAGGAGCAGATTACTTTTACATAC 57.050 34.615 0.00 0.00 0.00 2.39
2070 2097 2.352127 GCCAACCTCATCAAAGCTGTTC 60.352 50.000 0.00 0.00 0.00 3.18
2085 2112 4.655963 AGCTGTTCTGTGTTATGATTGGT 58.344 39.130 0.00 0.00 0.00 3.67
2091 2118 3.259625 TCTGTGTTATGATTGGTGACGGA 59.740 43.478 0.00 0.00 0.00 4.69
2175 2202 2.758423 TGCGTCTAGAGGAATGCTGTTA 59.242 45.455 16.47 0.00 0.00 2.41
2232 2259 1.963338 GGCCGGATATGCTGCTGTC 60.963 63.158 5.05 0.00 0.00 3.51
2424 2451 3.444034 TCTCCTTGTGGTTCTGTATCTCG 59.556 47.826 0.00 0.00 34.23 4.04
2523 2550 8.367156 CAAATACCAAGAGAAATCCCTTCAAAA 58.633 33.333 0.00 0.00 36.40 2.44
2665 2692 0.595095 CCTTGTTGTGCTCCTTCTGC 59.405 55.000 0.00 0.00 0.00 4.26
2712 2739 4.446385 TCTGTTGTTCTTACGTACATGCAC 59.554 41.667 0.00 0.00 0.00 4.57
2817 2844 6.808008 ATCAACTACTTGGTGTTTGATCTG 57.192 37.500 0.00 0.00 34.34 2.90
2886 2913 4.438472 GCTTTCATTGTCTCTCTTGCCATC 60.438 45.833 0.00 0.00 0.00 3.51
2952 2979 7.497909 TCTTTTGTTCACTACCTTTTCTCGAAT 59.502 33.333 0.00 0.00 0.00 3.34
3192 3230 9.195411 GTTGATGCAAATGTTCTCTTAAAATCA 57.805 29.630 0.00 0.00 0.00 2.57
3207 3245 4.666928 AAAATCATGAATTTTGCCACGC 57.333 36.364 0.00 0.00 44.15 5.34
3214 3252 2.037620 AATTTTGCCACGCCCTTGCA 62.038 50.000 0.00 0.00 37.32 4.08
3277 3316 4.569719 AGGTTTGTCACGGGAGATTTAT 57.430 40.909 0.00 0.00 0.00 1.40
3337 3376 4.213482 GTGTTTCTCATGGACGCTAGTTTT 59.787 41.667 0.00 0.00 0.00 2.43
3353 3392 5.460091 GCTAGTTTTTGCTTTTCTGACTTGG 59.540 40.000 0.00 0.00 0.00 3.61
3384 3423 6.712095 TGCCCAAGATTCTGTATGTCATAATC 59.288 38.462 0.00 0.00 38.84 1.75
3413 3452 8.934023 CCTTTCCTAATTAGGCATGGTAATTA 57.066 34.615 24.52 2.64 43.31 1.40
3414 3453 9.533831 CCTTTCCTAATTAGGCATGGTAATTAT 57.466 33.333 24.52 0.00 43.31 1.28
3501 3572 4.640771 TTCATTAGGTTGCTCCTCTGTT 57.359 40.909 4.41 0.00 44.42 3.16
3609 3682 4.628081 CATATCGCACCATAATTTCGACG 58.372 43.478 0.00 0.00 31.74 5.12
3640 3713 2.032924 CCATATCGCCCCGTTTCTTTTC 59.967 50.000 0.00 0.00 0.00 2.29
3641 3714 1.741528 TATCGCCCCGTTTCTTTTCC 58.258 50.000 0.00 0.00 0.00 3.13
3681 3775 6.597672 TGCATAATGTTCAAAGGTAGGTAGTG 59.402 38.462 0.00 0.00 0.00 2.74
3682 3776 6.598064 GCATAATGTTCAAAGGTAGGTAGTGT 59.402 38.462 0.00 0.00 0.00 3.55
3683 3777 7.120726 GCATAATGTTCAAAGGTAGGTAGTGTT 59.879 37.037 0.00 0.00 0.00 3.32
3684 3778 6.877611 AATGTTCAAAGGTAGGTAGTGTTG 57.122 37.500 0.00 0.00 0.00 3.33
3685 3779 4.710324 TGTTCAAAGGTAGGTAGTGTTGG 58.290 43.478 0.00 0.00 0.00 3.77
3686 3780 4.409574 TGTTCAAAGGTAGGTAGTGTTGGA 59.590 41.667 0.00 0.00 0.00 3.53
3687 3781 4.884668 TCAAAGGTAGGTAGTGTTGGAG 57.115 45.455 0.00 0.00 0.00 3.86
3688 3782 4.228824 TCAAAGGTAGGTAGTGTTGGAGT 58.771 43.478 0.00 0.00 0.00 3.85
3689 3783 5.396485 TCAAAGGTAGGTAGTGTTGGAGTA 58.604 41.667 0.00 0.00 0.00 2.59
3690 3784 6.021030 TCAAAGGTAGGTAGTGTTGGAGTAT 58.979 40.000 0.00 0.00 0.00 2.12
3691 3785 5.934402 AAGGTAGGTAGTGTTGGAGTATG 57.066 43.478 0.00 0.00 0.00 2.39
3692 3786 5.202746 AGGTAGGTAGTGTTGGAGTATGA 57.797 43.478 0.00 0.00 0.00 2.15
3693 3787 5.778542 AGGTAGGTAGTGTTGGAGTATGAT 58.221 41.667 0.00 0.00 0.00 2.45
3694 3788 5.598830 AGGTAGGTAGTGTTGGAGTATGATG 59.401 44.000 0.00 0.00 0.00 3.07
3695 3789 5.363005 GGTAGGTAGTGTTGGAGTATGATGT 59.637 44.000 0.00 0.00 0.00 3.06
3696 3790 5.599999 AGGTAGTGTTGGAGTATGATGTC 57.400 43.478 0.00 0.00 0.00 3.06
3697 3791 4.406003 AGGTAGTGTTGGAGTATGATGTCC 59.594 45.833 0.00 0.00 0.00 4.02
3698 3792 3.526931 AGTGTTGGAGTATGATGTCCG 57.473 47.619 0.00 0.00 35.37 4.79
3699 3793 3.096852 AGTGTTGGAGTATGATGTCCGA 58.903 45.455 0.00 0.00 35.37 4.55
3700 3794 3.119101 AGTGTTGGAGTATGATGTCCGAC 60.119 47.826 8.43 8.43 44.71 4.79
3701 3795 2.167693 TGTTGGAGTATGATGTCCGACC 59.832 50.000 11.49 0.00 44.08 4.79
3702 3796 1.410004 TGGAGTATGATGTCCGACCC 58.590 55.000 0.00 0.00 35.37 4.46
3703 3797 1.063190 TGGAGTATGATGTCCGACCCT 60.063 52.381 0.00 0.00 35.37 4.34
3704 3798 1.614413 GGAGTATGATGTCCGACCCTC 59.386 57.143 0.00 0.00 0.00 4.30
3705 3799 2.588620 GAGTATGATGTCCGACCCTCT 58.411 52.381 0.00 0.00 0.00 3.69
3706 3800 2.554893 GAGTATGATGTCCGACCCTCTC 59.445 54.545 0.00 0.00 0.00 3.20
3707 3801 1.614413 GTATGATGTCCGACCCTCTCC 59.386 57.143 0.00 0.00 0.00 3.71
3708 3802 0.760945 ATGATGTCCGACCCTCTCCC 60.761 60.000 0.00 0.00 0.00 4.30
3709 3803 1.381327 GATGTCCGACCCTCTCCCA 60.381 63.158 0.00 0.00 0.00 4.37
3710 3804 0.760945 GATGTCCGACCCTCTCCCAT 60.761 60.000 0.00 0.00 0.00 4.00
3711 3805 0.561184 ATGTCCGACCCTCTCCCATA 59.439 55.000 0.00 0.00 0.00 2.74
3712 3806 0.106167 TGTCCGACCCTCTCCCATAG 60.106 60.000 0.00 0.00 0.00 2.23
3713 3807 0.106116 GTCCGACCCTCTCCCATAGT 60.106 60.000 0.00 0.00 0.00 2.12
3714 3808 0.635009 TCCGACCCTCTCCCATAGTT 59.365 55.000 0.00 0.00 0.00 2.24
3715 3809 1.041437 CCGACCCTCTCCCATAGTTC 58.959 60.000 0.00 0.00 0.00 3.01
3716 3810 0.669077 CGACCCTCTCCCATAGTTCG 59.331 60.000 0.00 0.00 0.00 3.95
3717 3811 1.041437 GACCCTCTCCCATAGTTCGG 58.959 60.000 0.00 0.00 0.00 4.30
3718 3812 0.635009 ACCCTCTCCCATAGTTCGGA 59.365 55.000 0.00 0.00 0.00 4.55
3719 3813 1.041437 CCCTCTCCCATAGTTCGGAC 58.959 60.000 0.00 0.00 0.00 4.79
3720 3814 1.411787 CCCTCTCCCATAGTTCGGACT 60.412 57.143 0.00 0.00 39.97 3.85
3721 3815 2.389715 CCTCTCCCATAGTTCGGACTT 58.610 52.381 0.00 0.00 37.33 3.01
3722 3816 2.766828 CCTCTCCCATAGTTCGGACTTT 59.233 50.000 0.00 0.00 37.33 2.66
3723 3817 3.197983 CCTCTCCCATAGTTCGGACTTTT 59.802 47.826 0.00 0.00 37.33 2.27
3724 3818 4.184629 CTCTCCCATAGTTCGGACTTTTG 58.815 47.826 0.00 0.04 37.33 2.44
3725 3819 3.055385 TCTCCCATAGTTCGGACTTTTGG 60.055 47.826 15.47 15.47 37.55 3.28
3726 3820 2.907696 TCCCATAGTTCGGACTTTTGGA 59.092 45.455 21.45 13.44 38.94 3.53
3727 3821 3.521937 TCCCATAGTTCGGACTTTTGGAT 59.478 43.478 21.45 0.00 38.94 3.41
3728 3822 3.627577 CCCATAGTTCGGACTTTTGGATG 59.372 47.826 21.45 10.82 38.94 3.51
3729 3823 4.513442 CCATAGTTCGGACTTTTGGATGA 58.487 43.478 16.87 0.00 38.94 2.92
3730 3824 4.572389 CCATAGTTCGGACTTTTGGATGAG 59.428 45.833 16.87 0.37 38.94 2.90
3731 3825 3.771577 AGTTCGGACTTTTGGATGAGT 57.228 42.857 0.00 0.00 29.87 3.41
3732 3826 4.086706 AGTTCGGACTTTTGGATGAGTT 57.913 40.909 0.00 0.00 29.87 3.01
3733 3827 3.815401 AGTTCGGACTTTTGGATGAGTTG 59.185 43.478 0.00 0.00 29.87 3.16
3734 3828 2.778299 TCGGACTTTTGGATGAGTTGG 58.222 47.619 0.00 0.00 0.00 3.77
3735 3829 1.200020 CGGACTTTTGGATGAGTTGGC 59.800 52.381 0.00 0.00 0.00 4.52
3736 3830 2.519013 GGACTTTTGGATGAGTTGGCT 58.481 47.619 0.00 0.00 0.00 4.75
3737 3831 2.229784 GGACTTTTGGATGAGTTGGCTG 59.770 50.000 0.00 0.00 0.00 4.85
3738 3832 2.229784 GACTTTTGGATGAGTTGGCTGG 59.770 50.000 0.00 0.00 0.00 4.85
3739 3833 2.158475 ACTTTTGGATGAGTTGGCTGGA 60.158 45.455 0.00 0.00 0.00 3.86
3740 3834 2.205022 TTTGGATGAGTTGGCTGGAG 57.795 50.000 0.00 0.00 0.00 3.86
3741 3835 0.322816 TTGGATGAGTTGGCTGGAGC 60.323 55.000 0.00 0.00 41.14 4.70
3742 3836 1.300963 GGATGAGTTGGCTGGAGCA 59.699 57.895 0.20 0.00 44.36 4.26
3743 3837 0.106819 GGATGAGTTGGCTGGAGCAT 60.107 55.000 0.20 0.00 44.36 3.79
3744 3838 1.022735 GATGAGTTGGCTGGAGCATG 58.977 55.000 0.20 0.00 44.36 4.06
3745 3839 0.622136 ATGAGTTGGCTGGAGCATGA 59.378 50.000 0.00 0.00 44.36 3.07
3746 3840 0.401356 TGAGTTGGCTGGAGCATGAA 59.599 50.000 0.00 0.00 44.36 2.57
3747 3841 1.005097 TGAGTTGGCTGGAGCATGAAT 59.995 47.619 0.00 0.00 44.36 2.57
3748 3842 2.097825 GAGTTGGCTGGAGCATGAATT 58.902 47.619 0.00 0.00 44.36 2.17
3749 3843 2.097825 AGTTGGCTGGAGCATGAATTC 58.902 47.619 0.00 0.00 44.36 2.17
3750 3844 1.820519 GTTGGCTGGAGCATGAATTCA 59.179 47.619 11.26 11.26 44.36 2.57
3751 3845 2.219080 TGGCTGGAGCATGAATTCAA 57.781 45.000 13.09 0.00 44.36 2.69
3752 3846 2.742348 TGGCTGGAGCATGAATTCAAT 58.258 42.857 13.09 1.32 44.36 2.57
3753 3847 3.900971 TGGCTGGAGCATGAATTCAATA 58.099 40.909 13.09 0.00 44.36 1.90
3754 3848 3.887110 TGGCTGGAGCATGAATTCAATAG 59.113 43.478 13.09 6.87 44.36 1.73
3755 3849 3.887716 GGCTGGAGCATGAATTCAATAGT 59.112 43.478 13.09 0.00 44.36 2.12
3756 3850 4.340381 GGCTGGAGCATGAATTCAATAGTT 59.660 41.667 13.09 3.68 44.36 2.24
3757 3851 5.532406 GGCTGGAGCATGAATTCAATAGTTA 59.468 40.000 13.09 0.00 44.36 2.24
3758 3852 6.293845 GGCTGGAGCATGAATTCAATAGTTAG 60.294 42.308 13.09 8.64 44.36 2.34
3759 3853 6.261826 GCTGGAGCATGAATTCAATAGTTAGT 59.738 38.462 13.09 0.00 41.59 2.24
3776 3870 4.696402 AGTTAGTCCTGAGAACACTACTCG 59.304 45.833 0.00 0.00 37.22 4.18
3937 4034 1.131126 GTGACAGTGAAATGGCGGATG 59.869 52.381 0.00 0.00 0.00 3.51
3954 4051 4.731773 GCGGATGTATCTCTTTTTGCCTTG 60.732 45.833 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 2.511600 CCACTCCCGAATCGTGGC 60.512 66.667 0.82 0.00 41.39 5.01
69 70 1.877443 CAAAAACCACTCCCGAATCGT 59.123 47.619 0.82 0.00 0.00 3.73
88 89 0.106868 TCGGCTCGACCCTAGAATCA 60.107 55.000 0.00 0.00 33.26 2.57
130 131 2.745492 GTGGCACTGGAGCTGCTC 60.745 66.667 21.17 21.17 34.84 4.26
303 304 4.923942 AGGCGGCATCCATCAGCG 62.924 66.667 13.08 0.00 0.00 5.18
331 332 0.464013 TCGCAAACAAAACCTCGGGA 60.464 50.000 0.00 0.00 0.00 5.14
346 347 3.473647 CCCAGGGAGATGCTCGCA 61.474 66.667 0.00 0.00 44.32 5.10
434 436 8.365060 TCTTTTACCATCCATCATGAAACAAT 57.635 30.769 0.00 0.00 33.80 2.71
435 437 7.773489 TCTTTTACCATCCATCATGAAACAA 57.227 32.000 0.00 0.00 33.80 2.83
436 438 7.574779 CGTTCTTTTACCATCCATCATGAAACA 60.575 37.037 0.00 0.00 33.80 2.83
528 531 5.281727 TCTCTGTAAGCAGCATAACATACG 58.718 41.667 0.00 0.00 42.29 3.06
686 703 2.224257 GCTAAGCCTCAAGGAGGATCAG 60.224 54.545 16.22 6.39 46.28 2.90
757 776 4.622933 GCAAAGAAAGGTTCAAACAGGGTT 60.623 41.667 0.00 0.00 0.00 4.11
1032 1053 1.336240 GCCATCACAAGAAACAGCACC 60.336 52.381 0.00 0.00 0.00 5.01
1036 1057 2.486982 CAGGAGCCATCACAAGAAACAG 59.513 50.000 0.00 0.00 0.00 3.16
1488 1509 9.685276 AATTTCAGGTGATTAATGATGTAGACA 57.315 29.630 0.00 0.00 0.00 3.41
1593 1614 2.354503 GGCATCAGTGTCAGTGTCAGAT 60.355 50.000 7.54 0.00 0.00 2.90
1594 1615 1.001293 GGCATCAGTGTCAGTGTCAGA 59.999 52.381 7.54 0.00 0.00 3.27
1785 1812 5.907391 GTCACTGTTTACAAATTCAACCTCG 59.093 40.000 0.00 0.00 0.00 4.63
2070 2097 3.595173 TCCGTCACCAATCATAACACAG 58.405 45.455 0.00 0.00 0.00 3.66
2085 2112 2.635915 ACCCAGAATTTGTACTCCGTCA 59.364 45.455 0.00 0.00 0.00 4.35
2091 2118 3.199071 TCGCCATACCCAGAATTTGTACT 59.801 43.478 0.00 0.00 0.00 2.73
2094 2121 2.799126 TCGCCATACCCAGAATTTGT 57.201 45.000 0.00 0.00 0.00 2.83
2175 2202 8.618385 AGCATATAAAGGAATATCATCCCTGTT 58.382 33.333 0.00 0.00 40.59 3.16
2232 2259 1.561643 TTACAGTCCTCCAGAGCCTG 58.438 55.000 9.68 9.68 34.26 4.85
2424 2451 1.209747 CCTAGAAGGGTAAGTGGCACC 59.790 57.143 15.27 0.00 35.15 5.01
2523 2550 7.232127 CCAAATATGAGGAGCCATGAGTAATTT 59.768 37.037 0.00 0.00 0.00 1.82
2665 2692 0.673333 TCAGCGCATACCACAACCAG 60.673 55.000 11.47 0.00 0.00 4.00
2817 2844 0.676151 CTGGCCCACTCAAGCTTCTC 60.676 60.000 0.00 0.00 0.00 2.87
2886 2913 1.759445 ACAGTCCCAGTAGCTAGCATG 59.241 52.381 18.83 12.22 0.00 4.06
2952 2979 5.787953 TTTGCCTTCAATCAATCTTGACA 57.212 34.783 0.00 0.00 40.49 3.58
3179 3216 9.206870 GTGGCAAAATTCATGATTTTAAGAGAA 57.793 29.630 14.25 0.00 44.16 2.87
3192 3230 0.975887 AAGGGCGTGGCAAAATTCAT 59.024 45.000 0.00 0.00 0.00 2.57
3214 3252 3.055530 TGGAACAAACAATTGCACAAGGT 60.056 39.130 5.05 0.00 40.34 3.50
3230 3268 8.021898 ATCTTGGAAAAGAGAAAAATGGAACA 57.978 30.769 0.00 0.00 35.59 3.18
3337 3376 5.738783 GCAAATACCCAAGTCAGAAAAGCAA 60.739 40.000 0.00 0.00 0.00 3.91
3353 3392 5.594317 ACATACAGAATCTTGGGCAAATACC 59.406 40.000 0.00 0.00 0.00 2.73
3415 3454 8.903820 GGAATAATAACATAAAGCACTTCACCT 58.096 33.333 0.00 0.00 0.00 4.00
3416 3455 8.903820 AGGAATAATAACATAAAGCACTTCACC 58.096 33.333 0.00 0.00 0.00 4.02
3444 3484 2.346766 ACATGCCACTGACAGTCAAA 57.653 45.000 4.74 0.00 0.00 2.69
3452 3492 4.081642 GGAGTAACTAGAACATGCCACTGA 60.082 45.833 0.00 0.00 0.00 3.41
3501 3572 8.879759 CAACTTTAACTCAAGTAAAGTGACTGA 58.120 33.333 9.63 0.00 41.50 3.41
3543 3616 7.173218 GTGAACTTCAGAATAATGGAACTGTCA 59.827 37.037 0.00 0.00 0.00 3.58
3609 3682 1.679032 GGGCGATATGGGCATAGAACC 60.679 57.143 13.23 0.00 0.00 3.62
3641 3714 1.039233 ATGCATCAGCGAAAAGGGGG 61.039 55.000 0.00 0.00 46.23 5.40
3681 3775 2.483188 GGGTCGGACATCATACTCCAAC 60.483 54.545 10.76 0.00 0.00 3.77
3682 3776 1.760613 GGGTCGGACATCATACTCCAA 59.239 52.381 10.76 0.00 0.00 3.53
3683 3777 1.063190 AGGGTCGGACATCATACTCCA 60.063 52.381 10.76 0.00 0.00 3.86
3684 3778 1.614413 GAGGGTCGGACATCATACTCC 59.386 57.143 10.76 0.00 0.00 3.85
3685 3779 2.554893 GAGAGGGTCGGACATCATACTC 59.445 54.545 10.76 7.16 0.00 2.59
3686 3780 2.588620 GAGAGGGTCGGACATCATACT 58.411 52.381 10.76 0.47 0.00 2.12
3687 3781 1.614413 GGAGAGGGTCGGACATCATAC 59.386 57.143 10.76 3.93 0.00 2.39
3688 3782 1.480683 GGGAGAGGGTCGGACATCATA 60.481 57.143 10.76 0.00 0.00 2.15
3689 3783 0.760945 GGGAGAGGGTCGGACATCAT 60.761 60.000 10.76 0.00 0.00 2.45
3690 3784 1.381327 GGGAGAGGGTCGGACATCA 60.381 63.158 10.76 0.00 0.00 3.07
3691 3785 0.760945 ATGGGAGAGGGTCGGACATC 60.761 60.000 10.76 7.42 0.00 3.06
3692 3786 0.561184 TATGGGAGAGGGTCGGACAT 59.439 55.000 10.76 0.00 0.00 3.06
3693 3787 0.106167 CTATGGGAGAGGGTCGGACA 60.106 60.000 10.76 0.00 0.00 4.02
3694 3788 0.106116 ACTATGGGAGAGGGTCGGAC 60.106 60.000 0.00 0.00 0.00 4.79
3695 3789 0.635009 AACTATGGGAGAGGGTCGGA 59.365 55.000 0.00 0.00 0.00 4.55
3696 3790 1.041437 GAACTATGGGAGAGGGTCGG 58.959 60.000 0.00 0.00 0.00 4.79
3697 3791 0.669077 CGAACTATGGGAGAGGGTCG 59.331 60.000 0.00 0.00 0.00 4.79
3698 3792 1.041437 CCGAACTATGGGAGAGGGTC 58.959 60.000 0.00 0.00 0.00 4.46
3699 3793 0.635009 TCCGAACTATGGGAGAGGGT 59.365 55.000 0.00 0.00 0.00 4.34
3700 3794 1.041437 GTCCGAACTATGGGAGAGGG 58.959 60.000 0.00 0.00 33.66 4.30
3701 3795 2.074729 AGTCCGAACTATGGGAGAGG 57.925 55.000 0.00 0.00 33.66 3.69
3702 3796 4.184629 CAAAAGTCCGAACTATGGGAGAG 58.815 47.826 0.00 0.00 33.66 3.20
3703 3797 3.055385 CCAAAAGTCCGAACTATGGGAGA 60.055 47.826 0.00 0.00 38.25 3.71
3704 3798 3.055385 TCCAAAAGTCCGAACTATGGGAG 60.055 47.826 6.69 0.00 40.51 4.30
3705 3799 2.907696 TCCAAAAGTCCGAACTATGGGA 59.092 45.455 6.69 0.00 40.51 4.37
3706 3800 3.343941 TCCAAAAGTCCGAACTATGGG 57.656 47.619 6.69 0.00 40.51 4.00
3707 3801 4.513442 TCATCCAAAAGTCCGAACTATGG 58.487 43.478 0.65 0.65 41.05 2.74
3708 3802 5.178797 ACTCATCCAAAAGTCCGAACTATG 58.821 41.667 0.00 0.00 33.48 2.23
3709 3803 5.422214 ACTCATCCAAAAGTCCGAACTAT 57.578 39.130 0.00 0.00 33.48 2.12
3710 3804 4.884668 ACTCATCCAAAAGTCCGAACTA 57.115 40.909 0.00 0.00 33.48 2.24
3711 3805 3.771577 ACTCATCCAAAAGTCCGAACT 57.228 42.857 0.00 0.00 37.32 3.01
3712 3806 3.058224 CCAACTCATCCAAAAGTCCGAAC 60.058 47.826 0.00 0.00 0.00 3.95
3713 3807 3.146066 CCAACTCATCCAAAAGTCCGAA 58.854 45.455 0.00 0.00 0.00 4.30
3714 3808 2.778299 CCAACTCATCCAAAAGTCCGA 58.222 47.619 0.00 0.00 0.00 4.55
3715 3809 1.200020 GCCAACTCATCCAAAAGTCCG 59.800 52.381 0.00 0.00 0.00 4.79
3716 3810 2.229784 CAGCCAACTCATCCAAAAGTCC 59.770 50.000 0.00 0.00 0.00 3.85
3717 3811 2.229784 CCAGCCAACTCATCCAAAAGTC 59.770 50.000 0.00 0.00 0.00 3.01
3718 3812 2.158475 TCCAGCCAACTCATCCAAAAGT 60.158 45.455 0.00 0.00 0.00 2.66
3719 3813 2.490903 CTCCAGCCAACTCATCCAAAAG 59.509 50.000 0.00 0.00 0.00 2.27
3720 3814 2.517959 CTCCAGCCAACTCATCCAAAA 58.482 47.619 0.00 0.00 0.00 2.44
3721 3815 1.887956 GCTCCAGCCAACTCATCCAAA 60.888 52.381 0.00 0.00 34.31 3.28
3722 3816 0.322816 GCTCCAGCCAACTCATCCAA 60.323 55.000 0.00 0.00 34.31 3.53
3723 3817 1.300963 GCTCCAGCCAACTCATCCA 59.699 57.895 0.00 0.00 34.31 3.41
3724 3818 0.106819 ATGCTCCAGCCAACTCATCC 60.107 55.000 0.00 0.00 41.18 3.51
3725 3819 1.022735 CATGCTCCAGCCAACTCATC 58.977 55.000 0.00 0.00 41.18 2.92
3726 3820 0.622136 TCATGCTCCAGCCAACTCAT 59.378 50.000 0.00 0.00 41.18 2.90
3727 3821 0.401356 TTCATGCTCCAGCCAACTCA 59.599 50.000 0.00 0.00 41.18 3.41
3728 3822 1.760192 ATTCATGCTCCAGCCAACTC 58.240 50.000 0.00 0.00 41.18 3.01
3729 3823 2.097825 GAATTCATGCTCCAGCCAACT 58.902 47.619 0.00 0.00 41.18 3.16
3730 3824 1.820519 TGAATTCATGCTCCAGCCAAC 59.179 47.619 3.38 0.00 41.18 3.77
3731 3825 2.219080 TGAATTCATGCTCCAGCCAA 57.781 45.000 3.38 0.00 41.18 4.52
3732 3826 2.219080 TTGAATTCATGCTCCAGCCA 57.781 45.000 9.40 0.00 41.18 4.75
3733 3827 3.887716 ACTATTGAATTCATGCTCCAGCC 59.112 43.478 9.40 0.00 41.18 4.85
3734 3828 5.511234 AACTATTGAATTCATGCTCCAGC 57.489 39.130 9.40 0.00 42.50 4.85
3735 3829 7.041508 GGACTAACTATTGAATTCATGCTCCAG 60.042 40.741 9.40 6.08 0.00 3.86
3736 3830 6.767902 GGACTAACTATTGAATTCATGCTCCA 59.232 38.462 9.40 0.00 0.00 3.86
3737 3831 6.995091 AGGACTAACTATTGAATTCATGCTCC 59.005 38.462 9.40 5.38 0.00 4.70
3738 3832 7.712639 TCAGGACTAACTATTGAATTCATGCTC 59.287 37.037 9.40 0.00 0.00 4.26
3739 3833 7.568349 TCAGGACTAACTATTGAATTCATGCT 58.432 34.615 9.40 0.00 0.00 3.79
3740 3834 7.712639 TCTCAGGACTAACTATTGAATTCATGC 59.287 37.037 9.40 0.00 0.00 4.06
3741 3835 9.605275 TTCTCAGGACTAACTATTGAATTCATG 57.395 33.333 9.40 5.60 0.00 3.07
3742 3836 9.606631 GTTCTCAGGACTAACTATTGAATTCAT 57.393 33.333 9.40 2.50 0.00 2.57
3743 3837 8.593679 TGTTCTCAGGACTAACTATTGAATTCA 58.406 33.333 3.38 3.38 0.00 2.57
3744 3838 8.874816 GTGTTCTCAGGACTAACTATTGAATTC 58.125 37.037 0.00 0.00 0.00 2.17
3745 3839 8.598041 AGTGTTCTCAGGACTAACTATTGAATT 58.402 33.333 0.00 0.00 0.00 2.17
3746 3840 8.140112 AGTGTTCTCAGGACTAACTATTGAAT 57.860 34.615 0.00 0.00 0.00 2.57
3747 3841 7.540474 AGTGTTCTCAGGACTAACTATTGAA 57.460 36.000 0.00 0.00 0.00 2.69
3748 3842 7.889073 AGTAGTGTTCTCAGGACTAACTATTGA 59.111 37.037 0.00 0.00 0.00 2.57
3749 3843 8.057536 AGTAGTGTTCTCAGGACTAACTATTG 57.942 38.462 0.00 0.00 0.00 1.90
3750 3844 7.066043 CGAGTAGTGTTCTCAGGACTAACTATT 59.934 40.741 0.00 0.00 32.79 1.73
3751 3845 6.539464 CGAGTAGTGTTCTCAGGACTAACTAT 59.461 42.308 0.00 0.00 32.79 2.12
3752 3846 5.873712 CGAGTAGTGTTCTCAGGACTAACTA 59.126 44.000 0.00 0.00 32.79 2.24
3753 3847 4.696402 CGAGTAGTGTTCTCAGGACTAACT 59.304 45.833 0.00 0.00 32.79 2.24
3754 3848 4.142643 CCGAGTAGTGTTCTCAGGACTAAC 60.143 50.000 0.00 0.00 32.06 2.34
3755 3849 4.008330 CCGAGTAGTGTTCTCAGGACTAA 58.992 47.826 0.00 0.00 32.06 2.24
3756 3850 3.008813 ACCGAGTAGTGTTCTCAGGACTA 59.991 47.826 0.00 0.00 33.42 2.59
3757 3851 2.224818 ACCGAGTAGTGTTCTCAGGACT 60.225 50.000 0.00 0.00 33.42 3.85
3758 3852 2.161030 ACCGAGTAGTGTTCTCAGGAC 58.839 52.381 0.00 0.00 33.42 3.85
3759 3853 2.581216 ACCGAGTAGTGTTCTCAGGA 57.419 50.000 0.00 0.00 33.42 3.86
3776 3870 6.017109 ACATCAGATTTCATTAATGCGGTACC 60.017 38.462 10.76 0.16 0.00 3.34
3884 3978 7.148523 GCACAAATGGTTTACTAGTACCACTAC 60.149 40.741 17.88 5.10 46.50 2.73
3885 3979 6.875195 GCACAAATGGTTTACTAGTACCACTA 59.125 38.462 17.88 9.26 46.50 2.74
3886 3980 5.704053 GCACAAATGGTTTACTAGTACCACT 59.296 40.000 17.88 6.33 46.50 4.00
3887 3981 5.704053 AGCACAAATGGTTTACTAGTACCAC 59.296 40.000 17.88 10.48 46.50 4.16
3888 3982 6.300703 AAGCACAAATGGTTTACTAGTACCA 58.699 36.000 17.83 17.83 44.10 3.25
3889 3983 6.812879 AAGCACAAATGGTTTACTAGTACC 57.187 37.500 0.91 4.90 44.10 3.34


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

AutoCloner maintained by Alex Coulton.