Multiple sequence alignment - TraesCS7D01G189600

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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 TraesCS7D01G189600 chr7D 100.000 4046 0 0 1 4046 142620184 142616139 0.000000e+00 7472.0
1 TraesCS7D01G189600 chr7D 96.507 687 15 4 1 681 550271821 550271138 0.000000e+00 1127.0
2 TraesCS7D01G189600 chr7D 92.647 68 3 2 3721 3788 98997902 98997837 3.330000e-16 97.1
3 TraesCS7D01G189600 chr7A 97.137 3074 63 13 958 4022 144611275 144608218 0.000000e+00 5166.0
4 TraesCS7D01G189600 chr7A 100.000 32 0 0 893 924 144611321 144611290 4.370000e-05 60.2
5 TraesCS7D01G189600 chr7B 96.769 2538 66 9 961 3494 106945136 106947661 0.000000e+00 4218.0
6 TraesCS7D01G189600 chr5D 96.652 687 14 6 1 681 432506015 432505332 0.000000e+00 1133.0
7 TraesCS7D01G189600 chr3D 96.512 688 17 3 1 682 578844171 578843485 0.000000e+00 1131.0
8 TraesCS7D01G189600 chr3D 96.081 689 22 5 1 686 7112819 7112133 0.000000e+00 1118.0
9 TraesCS7D01G189600 chr3D 95.702 698 20 5 1 692 524198803 524198110 0.000000e+00 1114.0
10 TraesCS7D01G189600 chr1D 95.845 698 20 6 1 691 61782056 61782751 0.000000e+00 1120.0
11 TraesCS7D01G189600 chr1D 95.954 692 19 5 1 686 495409392 495410080 0.000000e+00 1114.0
12 TraesCS7D01G189600 chr1D 89.744 78 7 1 3727 3804 393442175 393442099 9.250000e-17 99.0
13 TraesCS7D01G189600 chr4D 95.827 695 20 4 1 689 6919897 6920588 0.000000e+00 1114.0
14 TraesCS7D01G189600 chr4D 95.683 695 20 6 1 689 488740175 488740865 0.000000e+00 1109.0
15 TraesCS7D01G189600 chr4D 90.123 81 4 4 3713 3792 314659623 314659546 7.150000e-18 102.0
16 TraesCS7D01G189600 chr2B 91.429 70 4 2 3720 3788 552660112 552660044 1.200000e-15 95.3
17 TraesCS7D01G189600 chr2B 89.333 75 6 2 3726 3799 35362554 35362627 4.310000e-15 93.5
18 TraesCS7D01G189600 chr1B 88.608 79 8 1 3726 3804 529506319 529506396 1.200000e-15 95.3
19 TraesCS7D01G189600 chr1A 88.608 79 8 1 3726 3804 492198095 492198172 1.200000e-15 95.3
20 TraesCS7D01G189600 chr3B 91.304 69 2 3 3722 3788 576142300 576142234 1.550000e-14 91.6


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 TraesCS7D01G189600 chr7D 142616139 142620184 4045 True 7472.0 7472 100.0000 1 4046 1 chr7D.!!$R2 4045
1 TraesCS7D01G189600 chr7D 550271138 550271821 683 True 1127.0 1127 96.5070 1 681 1 chr7D.!!$R3 680
2 TraesCS7D01G189600 chr7A 144608218 144611321 3103 True 2613.1 5166 98.5685 893 4022 2 chr7A.!!$R1 3129
3 TraesCS7D01G189600 chr7B 106945136 106947661 2525 False 4218.0 4218 96.7690 961 3494 1 chr7B.!!$F1 2533
4 TraesCS7D01G189600 chr5D 432505332 432506015 683 True 1133.0 1133 96.6520 1 681 1 chr5D.!!$R1 680
5 TraesCS7D01G189600 chr3D 578843485 578844171 686 True 1131.0 1131 96.5120 1 682 1 chr3D.!!$R3 681
6 TraesCS7D01G189600 chr3D 7112133 7112819 686 True 1118.0 1118 96.0810 1 686 1 chr3D.!!$R1 685
7 TraesCS7D01G189600 chr3D 524198110 524198803 693 True 1114.0 1114 95.7020 1 692 1 chr3D.!!$R2 691
8 TraesCS7D01G189600 chr1D 61782056 61782751 695 False 1120.0 1120 95.8450 1 691 1 chr1D.!!$F1 690
9 TraesCS7D01G189600 chr1D 495409392 495410080 688 False 1114.0 1114 95.9540 1 686 1 chr1D.!!$F2 685
10 TraesCS7D01G189600 chr4D 6919897 6920588 691 False 1114.0 1114 95.8270 1 689 1 chr4D.!!$F1 688
11 TraesCS7D01G189600 chr4D 488740175 488740865 690 False 1109.0 1109 95.6830 1 689 1 chr4D.!!$F2 688

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
549 556 1.071471 GGGAGAGGGTGTGTGTGTG 59.929 63.158 0.0 0.0 0.00 3.82 F
1581 1592 0.600557 CTGTGAAGGACTCTGCGTCT 59.399 55.000 0.0 0.0 42.44 4.18 F
1875 1886 1.093159 CTGGAGATGTTTGCTCAGCC 58.907 55.000 0.0 0.0 34.07 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 1983 1.070445 TGGCATTTCCCAAAACAGCTG 59.930 47.619 13.48 13.48 32.32 4.24 R
2694 2705 0.598680 CAGATCGGTCCGGAGCAATC 60.599 60.000 31.39 27.65 0.00 2.67 R
3687 3702 1.478510 AGCGAGTGTTATGTCAGAGGG 59.521 52.381 0.00 0.00 0.00 4.30 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
467 472 2.557056 TCTCAGTTGGTAGTCTCCGTTG 59.443 50.000 0.00 0.00 0.00 4.10
548 555 1.074471 AGGGAGAGGGTGTGTGTGT 60.074 57.895 0.00 0.00 0.00 3.72
549 556 1.071471 GGGAGAGGGTGTGTGTGTG 59.929 63.158 0.00 0.00 0.00 3.82
691 702 7.650903 CGGGCGTTCTTCTAGTTAATATAAAGT 59.349 37.037 0.00 0.00 0.00 2.66
692 703 8.976471 GGGCGTTCTTCTAGTTAATATAAAGTC 58.024 37.037 0.00 0.00 0.00 3.01
693 704 8.689069 GGCGTTCTTCTAGTTAATATAAAGTCG 58.311 37.037 0.00 0.00 0.00 4.18
694 705 8.689069 GCGTTCTTCTAGTTAATATAAAGTCGG 58.311 37.037 0.00 0.00 0.00 4.79
695 706 9.941664 CGTTCTTCTAGTTAATATAAAGTCGGA 57.058 33.333 0.00 0.00 0.00 4.55
713 724 9.886132 AAAGTCGGACTAACATCTTTTATATGT 57.114 29.630 11.71 0.00 39.22 2.29
743 754 9.756571 AAGAATAGATAGATAGTAATCGTGGGT 57.243 33.333 0.00 0.00 37.19 4.51
744 755 9.398538 AGAATAGATAGATAGTAATCGTGGGTC 57.601 37.037 0.00 0.00 37.19 4.46
745 756 9.175312 GAATAGATAGATAGTAATCGTGGGTCA 57.825 37.037 0.00 0.00 37.19 4.02
746 757 9.702253 AATAGATAGATAGTAATCGTGGGTCAT 57.298 33.333 0.00 0.00 37.19 3.06
747 758 7.397892 AGATAGATAGTAATCGTGGGTCATG 57.602 40.000 0.00 0.00 37.19 3.07
748 759 4.873746 AGATAGTAATCGTGGGTCATGG 57.126 45.455 0.00 0.00 37.19 3.66
749 760 3.578716 AGATAGTAATCGTGGGTCATGGG 59.421 47.826 0.00 0.00 37.19 4.00
750 761 1.874129 AGTAATCGTGGGTCATGGGA 58.126 50.000 0.00 0.00 0.00 4.37
751 762 2.408565 AGTAATCGTGGGTCATGGGAT 58.591 47.619 0.00 0.00 0.00 3.85
752 763 3.583228 AGTAATCGTGGGTCATGGGATA 58.417 45.455 0.00 0.00 0.00 2.59
753 764 2.930826 AATCGTGGGTCATGGGATAC 57.069 50.000 0.00 0.00 0.00 2.24
754 765 1.801242 ATCGTGGGTCATGGGATACA 58.199 50.000 0.00 0.00 39.74 2.29
755 766 1.574263 TCGTGGGTCATGGGATACAA 58.426 50.000 0.00 0.00 39.74 2.41
756 767 1.909986 TCGTGGGTCATGGGATACAAA 59.090 47.619 0.00 0.00 39.74 2.83
757 768 2.306219 TCGTGGGTCATGGGATACAAAA 59.694 45.455 0.00 0.00 39.74 2.44
758 769 2.682856 CGTGGGTCATGGGATACAAAAG 59.317 50.000 0.00 0.00 39.74 2.27
759 770 3.697166 GTGGGTCATGGGATACAAAAGT 58.303 45.455 0.00 0.00 39.74 2.66
760 771 3.694566 GTGGGTCATGGGATACAAAAGTC 59.305 47.826 0.00 0.00 39.74 3.01
761 772 3.332187 TGGGTCATGGGATACAAAAGTCA 59.668 43.478 0.00 0.00 39.74 3.41
762 773 4.017591 TGGGTCATGGGATACAAAAGTCAT 60.018 41.667 0.00 0.00 39.74 3.06
763 774 5.192722 TGGGTCATGGGATACAAAAGTCATA 59.807 40.000 0.00 0.00 39.74 2.15
764 775 6.126215 TGGGTCATGGGATACAAAAGTCATAT 60.126 38.462 0.00 0.00 39.74 1.78
765 776 6.777580 GGGTCATGGGATACAAAAGTCATATT 59.222 38.462 0.00 0.00 39.74 1.28
766 777 7.942341 GGGTCATGGGATACAAAAGTCATATTA 59.058 37.037 0.00 0.00 39.74 0.98
767 778 9.349713 GGTCATGGGATACAAAAGTCATATTAA 57.650 33.333 0.00 0.00 39.74 1.40
769 780 9.913310 TCATGGGATACAAAAGTCATATTAACA 57.087 29.630 0.00 0.00 39.74 2.41
770 781 9.950680 CATGGGATACAAAAGTCATATTAACAC 57.049 33.333 0.00 0.00 39.74 3.32
771 782 8.203937 TGGGATACAAAAGTCATATTAACACG 57.796 34.615 0.00 0.00 39.74 4.49
772 783 7.825270 TGGGATACAAAAGTCATATTAACACGT 59.175 33.333 0.00 0.00 39.74 4.49
773 784 8.671028 GGGATACAAAAGTCATATTAACACGTT 58.329 33.333 0.00 0.00 39.74 3.99
885 896 8.530269 ACTTTGAAAAGGTATACTCGTAGTTG 57.470 34.615 2.25 0.00 40.31 3.16
886 897 7.601508 ACTTTGAAAAGGTATACTCGTAGTTGG 59.398 37.037 2.25 0.00 40.31 3.77
887 898 6.594788 TGAAAAGGTATACTCGTAGTTGGT 57.405 37.500 2.25 0.00 0.00 3.67
888 899 6.624423 TGAAAAGGTATACTCGTAGTTGGTC 58.376 40.000 2.25 0.00 0.00 4.02
889 900 6.209192 TGAAAAGGTATACTCGTAGTTGGTCA 59.791 38.462 2.25 0.00 0.00 4.02
890 901 6.594788 AAAGGTATACTCGTAGTTGGTCAA 57.405 37.500 2.25 0.00 0.00 3.18
891 902 6.594788 AAGGTATACTCGTAGTTGGTCAAA 57.405 37.500 2.25 0.00 0.00 2.69
924 935 3.186047 CGTCACCGGACAATCGCC 61.186 66.667 9.46 0.00 44.54 5.54
955 966 2.794910 CACAGTTGAACTCACCACGTAG 59.205 50.000 0.00 0.00 0.00 3.51
958 969 2.691526 AGTTGAACTCACCACGTAGTCA 59.308 45.455 0.00 0.00 41.61 3.41
959 970 2.787601 TGAACTCACCACGTAGTCAC 57.212 50.000 0.00 0.00 41.61 3.67
1254 1265 2.432628 GACGTAAGCGCTGCCAGT 60.433 61.111 12.58 9.45 42.83 4.00
1519 1530 0.822121 GGTCACCGGGTTCTTTGCTT 60.822 55.000 6.32 0.00 0.00 3.91
1581 1592 0.600557 CTGTGAAGGACTCTGCGTCT 59.399 55.000 0.00 0.00 42.44 4.18
1681 1692 2.485814 GTGAAAGACATGGACAAGGCTC 59.514 50.000 0.00 0.00 0.00 4.70
1875 1886 1.093159 CTGGAGATGTTTGCTCAGCC 58.907 55.000 0.00 0.00 34.07 4.85
2365 2376 1.956477 GGGCAATAACTGATGCGGAAT 59.044 47.619 0.00 0.00 43.47 3.01
2646 2657 3.311871 CAGCACTTGTCAATCTCATAGGC 59.688 47.826 0.00 0.00 0.00 3.93
2694 2705 2.744202 GGAGGTAATCAATAGCATGCCG 59.256 50.000 15.66 0.36 34.36 5.69
2758 2769 3.250744 TGTACGGCGAAGAAGAATGAAG 58.749 45.455 16.62 0.00 0.00 3.02
3114 3127 6.449635 AGATTGCAGTGTAGAAACAAACAA 57.550 33.333 0.00 0.00 37.36 2.83
3117 3130 8.629158 AGATTGCAGTGTAGAAACAAACAAATA 58.371 29.630 0.00 0.00 37.36 1.40
3365 3380 5.469479 GCTTATTTTGCTGGCTTTGTAAGA 58.531 37.500 0.00 0.00 0.00 2.10
3404 3419 3.756082 AGAAACATGGGGATAAGCCAA 57.244 42.857 0.00 0.00 38.95 4.52
3464 3479 6.292150 TGGTACACATGTGTTTTGATACTCA 58.708 36.000 34.66 20.51 41.83 3.41
3465 3480 6.768381 TGGTACACATGTGTTTTGATACTCAA 59.232 34.615 34.66 11.01 41.83 3.02
3466 3481 7.283354 TGGTACACATGTGTTTTGATACTCAAA 59.717 33.333 34.66 10.80 43.84 2.69
3467 3482 8.296713 GGTACACATGTGTTTTGATACTCAAAT 58.703 33.333 34.66 8.15 44.75 2.32
3524 3539 4.495422 ACCACGTTGTCACATTATCTCTC 58.505 43.478 0.00 0.00 0.00 3.20
3525 3540 4.220821 ACCACGTTGTCACATTATCTCTCT 59.779 41.667 0.00 0.00 0.00 3.10
3526 3541 4.800993 CCACGTTGTCACATTATCTCTCTC 59.199 45.833 0.00 0.00 0.00 3.20
3527 3542 5.402398 CACGTTGTCACATTATCTCTCTCA 58.598 41.667 0.00 0.00 0.00 3.27
3528 3543 5.863935 CACGTTGTCACATTATCTCTCTCAA 59.136 40.000 0.00 0.00 0.00 3.02
3566 3581 1.203441 AGGCCTGGCTGAACAGATCA 61.203 55.000 19.68 2.71 40.97 2.92
3577 3592 3.466836 TGAACAGATCACACAACAGGTC 58.533 45.455 0.00 0.00 31.50 3.85
3607 3622 7.334421 TCAAAGATTGGCACATAAGTTACTCTC 59.666 37.037 0.00 0.00 39.30 3.20
3612 3627 4.099573 TGGCACATAAGTTACTCTCCTAGC 59.900 45.833 0.00 0.00 0.00 3.42
3685 3700 8.623903 GCTTGATTACCTGTTTATGAATCATCA 58.376 33.333 0.00 0.00 36.64 3.07
3687 3702 8.450578 TGATTACCTGTTTATGAATCATCACC 57.549 34.615 0.00 0.00 38.69 4.02
3721 3736 3.244770 ACACTCGCTCCCCAAATTCTAAA 60.245 43.478 0.00 0.00 0.00 1.85
3723 3738 4.035675 CACTCGCTCCCCAAATTCTAAATC 59.964 45.833 0.00 0.00 0.00 2.17
3724 3739 3.202906 TCGCTCCCCAAATTCTAAATCG 58.797 45.455 0.00 0.00 0.00 3.34
3809 3824 8.329502 AGTTTTACAGATAGCCCTCAACTAAAT 58.670 33.333 0.00 0.00 0.00 1.40
3810 3825 8.613482 GTTTTACAGATAGCCCTCAACTAAATC 58.387 37.037 0.00 0.00 0.00 2.17
3811 3826 4.950050 ACAGATAGCCCTCAACTAAATCG 58.050 43.478 0.00 0.00 0.00 3.34
3825 3840 8.610248 TCAACTAAATCGGTATTTGACTTTGA 57.390 30.769 0.00 0.00 36.02 2.69
3851 3866 7.421530 AAAAATCCCATATTGTAGATCGTCG 57.578 36.000 0.00 0.00 0.00 5.12
3853 3868 2.230508 TCCCATATTGTAGATCGTCGCC 59.769 50.000 0.00 0.00 0.00 5.54
3881 3896 7.801547 AATTTCAACATGCTATTCTGAAACG 57.198 32.000 0.00 0.00 38.45 3.60
3882 3897 6.552859 TTTCAACATGCTATTCTGAAACGA 57.447 33.333 0.00 0.00 32.54 3.85
3903 3918 2.741985 CATGCTTCCGTCGCACCA 60.742 61.111 0.00 0.00 40.65 4.17
3934 3949 5.649831 AGCTTTGATCTTTTCTTATCCGCTT 59.350 36.000 0.00 0.00 0.00 4.68
4000 4021 0.966179 TTCTCTGGTGCTACGCAGAA 59.034 50.000 0.00 0.00 40.08 3.02
4025 4046 2.107141 CTCGGTTGGGCGAGGATC 59.893 66.667 0.00 0.00 0.00 3.36
4036 4057 4.522971 GAGGATCGGGTGCTTGAC 57.477 61.111 0.00 0.00 0.00 3.18
4037 4058 1.901085 GAGGATCGGGTGCTTGACT 59.099 57.895 0.00 0.00 0.00 3.41
4038 4059 0.179097 GAGGATCGGGTGCTTGACTC 60.179 60.000 0.00 0.00 0.00 3.36
4042 4063 3.550656 CGGGTGCTTGACTCGTTC 58.449 61.111 0.00 0.00 44.16 3.95
4043 4064 1.300620 CGGGTGCTTGACTCGTTCA 60.301 57.895 0.00 0.00 44.16 3.18
4044 4065 0.878523 CGGGTGCTTGACTCGTTCAA 60.879 55.000 0.00 2.90 44.16 2.69
4045 4066 0.586802 GGGTGCTTGACTCGTTCAAC 59.413 55.000 0.00 0.00 39.45 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
256 258 0.114560 TCTTCTCCTGTTCCCCGAGT 59.885 55.000 0.00 0.00 0.00 4.18
424 429 9.206690 TGAGACATTAGGAGTAGAGATCATTTT 57.793 33.333 0.00 0.00 0.00 1.82
467 472 1.135603 GTGGGACGAAAATAAACCCGC 60.136 52.381 0.00 0.00 43.04 6.13
661 668 0.677842 ACTAGAAGAACGCCCGTTGT 59.322 50.000 11.10 3.91 38.60 3.32
717 728 9.756571 ACCCACGATTACTATCTATCTATTCTT 57.243 33.333 0.00 0.00 0.00 2.52
718 729 9.398538 GACCCACGATTACTATCTATCTATTCT 57.601 37.037 0.00 0.00 0.00 2.40
719 730 9.175312 TGACCCACGATTACTATCTATCTATTC 57.825 37.037 0.00 0.00 0.00 1.75
720 731 9.702253 ATGACCCACGATTACTATCTATCTATT 57.298 33.333 0.00 0.00 0.00 1.73
721 732 9.126151 CATGACCCACGATTACTATCTATCTAT 57.874 37.037 0.00 0.00 0.00 1.98
722 733 7.556635 CCATGACCCACGATTACTATCTATCTA 59.443 40.741 0.00 0.00 0.00 1.98
723 734 6.378564 CCATGACCCACGATTACTATCTATCT 59.621 42.308 0.00 0.00 0.00 1.98
724 735 6.405953 CCCATGACCCACGATTACTATCTATC 60.406 46.154 0.00 0.00 0.00 2.08
725 736 5.422331 CCCATGACCCACGATTACTATCTAT 59.578 44.000 0.00 0.00 0.00 1.98
726 737 4.770531 CCCATGACCCACGATTACTATCTA 59.229 45.833 0.00 0.00 0.00 1.98
727 738 3.578716 CCCATGACCCACGATTACTATCT 59.421 47.826 0.00 0.00 0.00 1.98
728 739 3.576982 TCCCATGACCCACGATTACTATC 59.423 47.826 0.00 0.00 0.00 2.08
729 740 3.583228 TCCCATGACCCACGATTACTAT 58.417 45.455 0.00 0.00 0.00 2.12
730 741 3.035055 TCCCATGACCCACGATTACTA 57.965 47.619 0.00 0.00 0.00 1.82
731 742 1.874129 TCCCATGACCCACGATTACT 58.126 50.000 0.00 0.00 0.00 2.24
732 743 2.930826 ATCCCATGACCCACGATTAC 57.069 50.000 0.00 0.00 0.00 1.89
733 744 3.310193 TGTATCCCATGACCCACGATTA 58.690 45.455 0.00 0.00 0.00 1.75
734 745 2.123589 TGTATCCCATGACCCACGATT 58.876 47.619 0.00 0.00 0.00 3.34
735 746 1.801242 TGTATCCCATGACCCACGAT 58.199 50.000 0.00 0.00 0.00 3.73
736 747 1.574263 TTGTATCCCATGACCCACGA 58.426 50.000 0.00 0.00 0.00 4.35
737 748 2.411628 TTTGTATCCCATGACCCACG 57.588 50.000 0.00 0.00 0.00 4.94
738 749 3.694566 GACTTTTGTATCCCATGACCCAC 59.305 47.826 0.00 0.00 0.00 4.61
739 750 3.332187 TGACTTTTGTATCCCATGACCCA 59.668 43.478 0.00 0.00 0.00 4.51
740 751 3.963129 TGACTTTTGTATCCCATGACCC 58.037 45.455 0.00 0.00 0.00 4.46
741 752 7.823745 AATATGACTTTTGTATCCCATGACC 57.176 36.000 0.00 0.00 0.00 4.02
743 754 9.913310 TGTTAATATGACTTTTGTATCCCATGA 57.087 29.630 0.00 0.00 0.00 3.07
744 755 9.950680 GTGTTAATATGACTTTTGTATCCCATG 57.049 33.333 0.00 0.00 0.00 3.66
745 756 8.836413 CGTGTTAATATGACTTTTGTATCCCAT 58.164 33.333 0.00 0.00 0.00 4.00
746 757 7.825270 ACGTGTTAATATGACTTTTGTATCCCA 59.175 33.333 0.00 0.00 0.00 4.37
747 758 8.205131 ACGTGTTAATATGACTTTTGTATCCC 57.795 34.615 0.00 0.00 0.00 3.85
859 870 9.630098 CAACTACGAGTATACCTTTTCAAAGTA 57.370 33.333 0.00 0.00 34.20 2.24
860 871 7.601508 CCAACTACGAGTATACCTTTTCAAAGT 59.398 37.037 0.00 0.00 34.20 2.66
861 872 7.601508 ACCAACTACGAGTATACCTTTTCAAAG 59.398 37.037 0.00 0.00 35.79 2.77
862 873 7.444299 ACCAACTACGAGTATACCTTTTCAAA 58.556 34.615 0.00 0.00 0.00 2.69
863 874 6.996509 ACCAACTACGAGTATACCTTTTCAA 58.003 36.000 0.00 0.00 0.00 2.69
864 875 6.209192 TGACCAACTACGAGTATACCTTTTCA 59.791 38.462 0.00 0.00 0.00 2.69
865 876 6.624423 TGACCAACTACGAGTATACCTTTTC 58.376 40.000 0.00 0.00 0.00 2.29
866 877 6.594788 TGACCAACTACGAGTATACCTTTT 57.405 37.500 0.00 0.00 0.00 2.27
867 878 6.594788 TTGACCAACTACGAGTATACCTTT 57.405 37.500 0.00 0.00 0.00 3.11
868 879 6.594788 TTTGACCAACTACGAGTATACCTT 57.405 37.500 0.00 0.00 0.00 3.50
869 880 6.393171 GTTTTGACCAACTACGAGTATACCT 58.607 40.000 0.00 0.00 0.00 3.08
870 881 5.578336 GGTTTTGACCAACTACGAGTATACC 59.422 44.000 0.00 0.00 0.00 2.73
871 882 6.158598 TGGTTTTGACCAACTACGAGTATAC 58.841 40.000 0.00 0.00 36.74 1.47
872 883 6.343716 TGGTTTTGACCAACTACGAGTATA 57.656 37.500 0.00 0.00 36.74 1.47
873 884 5.217978 TGGTTTTGACCAACTACGAGTAT 57.782 39.130 0.00 0.00 36.74 2.12
874 885 4.669206 TGGTTTTGACCAACTACGAGTA 57.331 40.909 0.00 0.00 36.74 2.59
875 886 3.547054 TGGTTTTGACCAACTACGAGT 57.453 42.857 0.00 0.00 36.74 4.18
883 894 2.498078 GAGGTGGTTTGGTTTTGACCAA 59.502 45.455 6.91 6.91 46.95 3.67
884 895 2.104170 GAGGTGGTTTGGTTTTGACCA 58.896 47.619 0.00 0.00 40.95 4.02
885 896 2.104170 TGAGGTGGTTTGGTTTTGACC 58.896 47.619 0.00 0.00 0.00 4.02
886 897 3.517602 GTTGAGGTGGTTTGGTTTTGAC 58.482 45.455 0.00 0.00 0.00 3.18
887 898 2.164624 CGTTGAGGTGGTTTGGTTTTGA 59.835 45.455 0.00 0.00 0.00 2.69
888 899 2.094442 ACGTTGAGGTGGTTTGGTTTTG 60.094 45.455 0.00 0.00 0.00 2.44
889 900 2.164827 GACGTTGAGGTGGTTTGGTTTT 59.835 45.455 0.00 0.00 0.00 2.43
890 901 1.746787 GACGTTGAGGTGGTTTGGTTT 59.253 47.619 0.00 0.00 0.00 3.27
891 902 1.340211 TGACGTTGAGGTGGTTTGGTT 60.340 47.619 0.00 0.00 0.00 3.67
927 938 4.683334 GTTCAACTGTGCGCGGCC 62.683 66.667 8.83 0.00 0.00 6.13
928 939 3.579626 GAGTTCAACTGTGCGCGGC 62.580 63.158 8.83 0.00 0.00 6.53
929 940 2.243957 TGAGTTCAACTGTGCGCGG 61.244 57.895 8.83 4.06 0.00 6.46
930 941 1.083401 GTGAGTTCAACTGTGCGCG 60.083 57.895 0.00 0.00 0.00 6.86
931 942 1.279840 GGTGAGTTCAACTGTGCGC 59.720 57.895 0.00 0.00 0.00 6.09
932 943 0.304705 GTGGTGAGTTCAACTGTGCG 59.695 55.000 0.00 0.00 33.92 5.34
933 944 0.304705 CGTGGTGAGTTCAACTGTGC 59.695 55.000 0.00 0.00 33.92 4.57
934 945 1.651987 ACGTGGTGAGTTCAACTGTG 58.348 50.000 0.00 0.00 33.92 3.66
955 966 0.245813 GGGACTCTTGGGTACGTGAC 59.754 60.000 0.00 0.00 0.00 3.67
956 967 1.246056 CGGGACTCTTGGGTACGTGA 61.246 60.000 0.00 0.00 0.00 4.35
958 969 1.980772 CCGGGACTCTTGGGTACGT 60.981 63.158 0.00 0.00 0.00 3.57
959 970 1.679977 TCCGGGACTCTTGGGTACG 60.680 63.158 0.00 0.00 0.00 3.67
960 971 1.611474 GGTCCGGGACTCTTGGGTAC 61.611 65.000 25.39 2.98 32.47 3.34
961 972 1.305549 GGTCCGGGACTCTTGGGTA 60.306 63.158 25.39 0.00 32.47 3.69
962 973 2.606826 GGTCCGGGACTCTTGGGT 60.607 66.667 25.39 0.00 32.47 4.51
963 974 3.771160 CGGTCCGGGACTCTTGGG 61.771 72.222 25.39 5.94 32.47 4.12
964 975 4.452733 GCGGTCCGGGACTCTTGG 62.453 72.222 25.39 11.55 32.47 3.61
965 976 4.452733 GGCGGTCCGGGACTCTTG 62.453 72.222 25.39 14.26 32.47 3.02
1254 1265 1.876497 GCATGGAGGCGAAAAAGGCA 61.876 55.000 0.00 0.00 39.37 4.75
1519 1530 2.061220 CCTTGCTCACCTGACCAGA 58.939 57.895 0.00 0.00 0.00 3.86
1581 1592 1.766059 AGACACCAGTGTGCCCAGA 60.766 57.895 8.43 0.00 46.86 3.86
1664 1675 2.373169 TCAAGAGCCTTGTCCATGTCTT 59.627 45.455 12.71 0.00 0.00 3.01
1681 1692 5.618056 ATGAGTGTGTTGTAAGCATCAAG 57.382 39.130 0.00 0.00 0.00 3.02
1875 1886 3.243101 GCATCTCATCAAACAGCATCCTG 60.243 47.826 0.00 0.00 44.80 3.86
1972 1983 1.070445 TGGCATTTCCCAAAACAGCTG 59.930 47.619 13.48 13.48 32.32 4.24
2163 2174 6.638468 CACCAACTTCTAGCATCTTTGAAAAC 59.362 38.462 0.00 0.00 0.00 2.43
2646 2657 2.905075 TCATCAAGCTTACCATGTCGG 58.095 47.619 0.00 0.00 42.50 4.79
2694 2705 0.598680 CAGATCGGTCCGGAGCAATC 60.599 60.000 31.39 27.65 0.00 2.67
2758 2769 2.360852 AGCCATGTGAGCCAGTGC 60.361 61.111 0.00 0.00 37.95 4.40
2954 2965 1.482593 AGGTATCTCCTGCGTTGAAGG 59.517 52.381 0.00 0.00 46.19 3.46
3117 3130 9.129532 AGTCAAGAAGAATCAAAGACAGAAAAT 57.870 29.630 0.00 0.00 0.00 1.82
3365 3380 3.595758 GGCTTGTGCAACTGCCGT 61.596 61.111 8.94 0.00 44.14 5.68
3524 3539 2.845967 GCACACGTGTTTTTGAGTTGAG 59.154 45.455 20.79 4.05 0.00 3.02
3525 3540 2.226674 TGCACACGTGTTTTTGAGTTGA 59.773 40.909 20.79 0.00 0.00 3.18
3526 3541 2.590073 TGCACACGTGTTTTTGAGTTG 58.410 42.857 20.79 5.50 0.00 3.16
3527 3542 2.999507 TGCACACGTGTTTTTGAGTT 57.000 40.000 20.79 0.00 0.00 3.01
3528 3543 2.415357 CCTTGCACACGTGTTTTTGAGT 60.415 45.455 20.79 0.00 0.00 3.41
3555 3570 3.470709 ACCTGTTGTGTGATCTGTTCAG 58.529 45.455 0.00 0.00 34.17 3.02
3566 3581 3.897239 TCTTTGAATGGACCTGTTGTGT 58.103 40.909 0.00 0.00 0.00 3.72
3577 3592 5.969423 ACTTATGTGCCAATCTTTGAATGG 58.031 37.500 0.00 0.00 35.84 3.16
3607 3622 6.643770 GGCATAAACAAAATGATGATGCTAGG 59.356 38.462 9.09 0.00 38.56 3.02
3612 3627 9.806203 TTAGAAGGCATAAACAAAATGATGATG 57.194 29.630 0.00 0.00 0.00 3.07
3685 3700 1.825474 CGAGTGTTATGTCAGAGGGGT 59.175 52.381 0.00 0.00 0.00 4.95
3687 3702 1.478510 AGCGAGTGTTATGTCAGAGGG 59.521 52.381 0.00 0.00 0.00 4.30
3731 3746 2.060050 TCTTTTGCCTCCGTTTCCAA 57.940 45.000 0.00 0.00 0.00 3.53
3732 3747 2.286365 ATCTTTTGCCTCCGTTTCCA 57.714 45.000 0.00 0.00 0.00 3.53
3733 3748 3.317150 CAAATCTTTTGCCTCCGTTTCC 58.683 45.455 0.00 0.00 0.00 3.13
3734 3749 2.731451 GCAAATCTTTTGCCTCCGTTTC 59.269 45.455 12.74 0.00 39.38 2.78
3772 3787 8.856103 GGCTATCTGTAAAACTCTATTCTCTCT 58.144 37.037 0.00 0.00 0.00 3.10
3777 3792 7.727181 TGAGGGCTATCTGTAAAACTCTATTC 58.273 38.462 0.00 0.00 0.00 1.75
3809 3824 8.463607 GGGATTTTTATCAAAGTCAAATACCGA 58.536 33.333 0.00 0.00 29.98 4.69
3810 3825 8.247562 TGGGATTTTTATCAAAGTCAAATACCG 58.752 33.333 0.00 0.00 39.75 4.02
3825 3840 9.151471 CGACGATCTACAATATGGGATTTTTAT 57.849 33.333 0.00 0.00 0.00 1.40
3827 3842 6.073222 GCGACGATCTACAATATGGGATTTTT 60.073 38.462 0.00 0.00 0.00 1.94
3853 3868 9.844790 TTTCAGAATAGCATGTTGAAATTACAG 57.155 29.630 0.00 0.00 34.04 2.74
3882 3897 1.005037 TGCGACGGAAGCATGTCTT 60.005 52.632 0.00 0.00 40.01 3.01
3903 3918 1.609208 AAAGATCAAAGCTGGCGTGT 58.391 45.000 0.00 0.00 0.00 4.49
3934 3949 1.000506 GAGACAAAGCGGTGGTAGACA 59.999 52.381 0.00 0.00 0.00 3.41
4000 4021 4.003788 CCCAACCGAGGTGAGCGT 62.004 66.667 0.00 0.00 0.00 5.07
4022 4043 0.389948 AACGAGTCAAGCACCCGATC 60.390 55.000 0.00 0.00 0.00 3.69
4023 4044 0.389948 GAACGAGTCAAGCACCCGAT 60.390 55.000 0.00 0.00 0.00 4.18
4024 4045 1.006571 GAACGAGTCAAGCACCCGA 60.007 57.895 0.00 0.00 0.00 5.14
4025 4046 0.878523 TTGAACGAGTCAAGCACCCG 60.879 55.000 0.00 0.00 41.47 5.28
4026 4047 3.000815 TTGAACGAGTCAAGCACCC 57.999 52.632 0.00 0.00 41.47 4.61


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

AutoCloner maintained by Alex Coulton.