Multiple sequence alignment - TraesCS5B01G074900

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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 TraesCS5B01G074900 chr5B 100.000 4783 0 0 1 4783 89230959 89235741 0.000000e+00 8833
1 TraesCS5B01G074900 chr5D 96.553 2988 84 10 888 3860 80370665 80373648 0.000000e+00 4929
2 TraesCS5B01G074900 chr5D 95.604 910 27 6 3885 4783 80373643 80374550 0.000000e+00 1447
3 TraesCS5B01G074900 chr5A 95.712 2962 94 11 888 3828 76907577 76910526 0.000000e+00 4735
4 TraesCS5B01G074900 chr5A 95.460 859 26 6 3936 4783 76910568 76911424 0.000000e+00 1358
5 TraesCS5B01G074900 chr1A 92.412 738 44 5 1 733 437726217 437726947 0.000000e+00 1042
6 TraesCS5B01G074900 chr1A 91.964 112 8 1 777 887 437726930 437727041 6.410000e-34 156
7 TraesCS5B01G074900 chr3A 90.663 739 50 8 1 733 21407516 21406791 0.000000e+00 965
8 TraesCS5B01G074900 chr2D 88.095 84 9 1 805 887 81995453 81995536 1.100000e-16 99


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 TraesCS5B01G074900 chr5B 89230959 89235741 4782 False 8833.0 8833 100.0000 1 4783 1 chr5B.!!$F1 4782
1 TraesCS5B01G074900 chr5D 80370665 80374550 3885 False 3188.0 4929 96.0785 888 4783 2 chr5D.!!$F1 3895
2 TraesCS5B01G074900 chr5A 76907577 76911424 3847 False 3046.5 4735 95.5860 888 4783 2 chr5A.!!$F1 3895
3 TraesCS5B01G074900 chr1A 437726217 437727041 824 False 599.0 1042 92.1880 1 887 2 chr1A.!!$F1 886
4 TraesCS5B01G074900 chr3A 21406791 21407516 725 True 965.0 965 90.6630 1 733 1 chr3A.!!$R1 732

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
735 742 0.105408 ATAACCCGCACCGTATCACC 59.895 55.000 0.00 0.00 0.00 4.02 F
752 759 0.178947 ACCCTCAAAATCCCCGCAAA 60.179 50.000 0.00 0.00 0.00 3.68 F
1707 1727 0.322187 CCCCGGAATCAAAAGACGGT 60.322 55.000 0.73 0.00 42.81 4.83 F
1837 1857 2.042831 AGTGATTGCGCCTGCTTCC 61.043 57.895 4.18 0.00 43.34 3.46 F
2060 2083 3.375299 AGCTTATGATTTGTTCGCCTGTC 59.625 43.478 0.00 0.00 0.00 3.51 F
3693 3725 1.303643 ACTTTGGGTAGCTGCAGGC 60.304 57.895 17.12 7.98 42.19 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1700 0.036765 TTGATTCCGGGGAGAACACG 60.037 55.000 0.00 0.0 0.00 4.49 R
1815 1835 0.679002 AGCAGGCGCAATCACTGATT 60.679 50.000 10.83 0.0 42.27 2.57 R
3667 3699 1.421646 AGCTACCCAAAGTCAGCTGTT 59.578 47.619 14.67 0.0 42.60 3.16 R
3693 3725 4.588899 TGTAATCACATGGAAGTTGGGAG 58.411 43.478 0.00 0.0 28.22 4.30 R
3734 3766 4.876107 CAGGCAAATAGTTGGTACAGTAGG 59.124 45.833 4.91 0.0 42.39 3.18 R
4682 4723 0.036732 TCAGTCAACATCCTGCCACC 59.963 55.000 0.00 0.0 0.00 4.61 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
89 91 2.819608 AGCTACCGACAACAAATTGCAT 59.180 40.909 0.00 0.00 39.66 3.96
162 164 5.726560 TCCTCCAACTATATCATCAAGGGA 58.273 41.667 0.00 0.00 0.00 4.20
302 304 0.733150 TACCTCTCGCACGATGTCAG 59.267 55.000 0.00 0.00 0.00 3.51
308 310 2.887568 GCACGATGTCAGGCCTCG 60.888 66.667 0.00 5.93 40.33 4.63
310 312 3.071206 ACGATGTCAGGCCTCGCT 61.071 61.111 0.00 0.00 38.51 4.93
324 326 2.292267 CCTCGCTGAATGGCTAACAAT 58.708 47.619 0.00 0.00 0.00 2.71
373 380 2.122813 CCCCTAGCACCCCGATCT 60.123 66.667 0.00 0.00 0.00 2.75
384 391 3.292460 CACCCCGATCTAGAACTCTCTT 58.708 50.000 0.00 0.00 32.70 2.85
395 402 9.877178 GATCTAGAACTCTCTTCCAAAAATACA 57.123 33.333 0.00 0.00 32.70 2.29
442 449 3.302480 GGATATAAGTCAGCGCGTTTGTG 60.302 47.826 8.43 0.31 0.00 3.33
504 511 2.028476 TGTCAATACGCTAACCTGTGCT 60.028 45.455 0.00 0.00 0.00 4.40
508 515 2.649331 TACGCTAACCTGTGCTTCTC 57.351 50.000 0.00 0.00 0.00 2.87
544 551 8.816894 TCTTCTTGTTCTTCTACTTATCCACAT 58.183 33.333 0.00 0.00 0.00 3.21
548 555 6.330278 TGTTCTTCTACTTATCCACATGACG 58.670 40.000 0.00 0.00 0.00 4.35
599 606 2.094494 CACGTCCTGAGCAGTTATGACT 60.094 50.000 0.00 0.00 36.25 3.41
650 657 3.664486 CAGACACGCTAGTATTCATACGC 59.336 47.826 0.00 0.00 38.28 4.42
660 667 7.688167 CGCTAGTATTCATACGCAAATAAATGG 59.312 37.037 0.00 0.00 38.28 3.16
661 668 8.717821 GCTAGTATTCATACGCAAATAAATGGA 58.282 33.333 0.00 0.00 38.28 3.41
676 683 3.180449 TGGAACATGACCCACTCCT 57.820 52.632 0.00 0.00 0.00 3.69
677 684 0.692476 TGGAACATGACCCACTCCTG 59.308 55.000 0.00 0.00 0.00 3.86
718 725 1.491668 TTCACCTCGGCCTGCTAATA 58.508 50.000 0.00 0.00 0.00 0.98
719 726 1.491668 TCACCTCGGCCTGCTAATAA 58.508 50.000 0.00 0.00 0.00 1.40
720 727 1.138266 TCACCTCGGCCTGCTAATAAC 59.862 52.381 0.00 0.00 0.00 1.89
721 728 0.468648 ACCTCGGCCTGCTAATAACC 59.531 55.000 0.00 0.00 0.00 2.85
722 729 0.250338 CCTCGGCCTGCTAATAACCC 60.250 60.000 0.00 0.00 0.00 4.11
723 730 0.600255 CTCGGCCTGCTAATAACCCG 60.600 60.000 0.00 0.00 37.21 5.28
724 731 2.251642 CGGCCTGCTAATAACCCGC 61.252 63.158 0.00 0.00 0.00 6.13
725 732 1.153046 GGCCTGCTAATAACCCGCA 60.153 57.895 0.00 0.00 0.00 5.69
726 733 1.444917 GGCCTGCTAATAACCCGCAC 61.445 60.000 0.00 0.00 0.00 5.34
727 734 1.444917 GCCTGCTAATAACCCGCACC 61.445 60.000 0.00 0.00 0.00 5.01
728 735 1.157870 CCTGCTAATAACCCGCACCG 61.158 60.000 0.00 0.00 0.00 4.94
729 736 0.461339 CTGCTAATAACCCGCACCGT 60.461 55.000 0.00 0.00 0.00 4.83
730 737 0.822811 TGCTAATAACCCGCACCGTA 59.177 50.000 0.00 0.00 0.00 4.02
731 738 1.413445 TGCTAATAACCCGCACCGTAT 59.587 47.619 0.00 0.00 0.00 3.06
732 739 2.064014 GCTAATAACCCGCACCGTATC 58.936 52.381 0.00 0.00 0.00 2.24
733 740 2.546373 GCTAATAACCCGCACCGTATCA 60.546 50.000 0.00 0.00 0.00 2.15
734 741 1.944032 AATAACCCGCACCGTATCAC 58.056 50.000 0.00 0.00 0.00 3.06
735 742 0.105408 ATAACCCGCACCGTATCACC 59.895 55.000 0.00 0.00 0.00 4.02
736 743 1.958902 TAACCCGCACCGTATCACCC 61.959 60.000 0.00 0.00 0.00 4.61
737 744 3.467226 CCCGCACCGTATCACCCT 61.467 66.667 0.00 0.00 0.00 4.34
738 745 2.106332 CCGCACCGTATCACCCTC 59.894 66.667 0.00 0.00 0.00 4.30
739 746 2.717044 CCGCACCGTATCACCCTCA 61.717 63.158 0.00 0.00 0.00 3.86
740 747 1.216977 CGCACCGTATCACCCTCAA 59.783 57.895 0.00 0.00 0.00 3.02
741 748 0.390603 CGCACCGTATCACCCTCAAA 60.391 55.000 0.00 0.00 0.00 2.69
742 749 1.816074 GCACCGTATCACCCTCAAAA 58.184 50.000 0.00 0.00 0.00 2.44
743 750 2.365582 GCACCGTATCACCCTCAAAAT 58.634 47.619 0.00 0.00 0.00 1.82
744 751 2.354821 GCACCGTATCACCCTCAAAATC 59.645 50.000 0.00 0.00 0.00 2.17
745 752 2.943033 CACCGTATCACCCTCAAAATCC 59.057 50.000 0.00 0.00 0.00 3.01
746 753 2.092592 ACCGTATCACCCTCAAAATCCC 60.093 50.000 0.00 0.00 0.00 3.85
747 754 2.572290 CGTATCACCCTCAAAATCCCC 58.428 52.381 0.00 0.00 0.00 4.81
748 755 2.572290 GTATCACCCTCAAAATCCCCG 58.428 52.381 0.00 0.00 0.00 5.73
749 756 0.395724 ATCACCCTCAAAATCCCCGC 60.396 55.000 0.00 0.00 0.00 6.13
750 757 1.304052 CACCCTCAAAATCCCCGCA 60.304 57.895 0.00 0.00 0.00 5.69
751 758 0.897863 CACCCTCAAAATCCCCGCAA 60.898 55.000 0.00 0.00 0.00 4.85
752 759 0.178947 ACCCTCAAAATCCCCGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
753 760 0.972883 CCCTCAAAATCCCCGCAAAA 59.027 50.000 0.00 0.00 0.00 2.44
754 761 1.346068 CCCTCAAAATCCCCGCAAAAA 59.654 47.619 0.00 0.00 0.00 1.94
794 801 2.695127 AAATAACCCGCACCGTATCA 57.305 45.000 0.00 0.00 0.00 2.15
796 803 0.825410 ATAACCCGCACCGTATCACA 59.175 50.000 0.00 0.00 0.00 3.58
800 807 1.809619 CCGCACCGTATCACACAGG 60.810 63.158 0.00 0.00 0.00 4.00
803 810 1.596934 CACCGTATCACACAGGGCT 59.403 57.895 0.00 0.00 0.00 5.19
820 828 8.656806 ACACAGGGCTTATATTAAGTAGCAATA 58.343 33.333 0.00 0.00 35.36 1.90
871 879 1.144716 ATCGCGTGCCATCATGTCT 59.855 52.632 5.77 0.00 0.00 3.41
896 904 5.441709 AAAATTCACGTCCGTGGTTTTAT 57.558 34.783 22.68 10.18 45.43 1.40
1357 1368 1.982958 TCTAGGTTCACTTTCCCCACC 59.017 52.381 0.00 0.00 0.00 4.61
1385 1405 4.326826 CTTGGTGATTCCTTACTGCTCAA 58.673 43.478 0.00 0.00 37.07 3.02
1395 1415 3.684788 CCTTACTGCTCAACGTTGCTTAT 59.315 43.478 23.47 9.81 0.00 1.73
1402 1422 3.489047 GCTCAACGTTGCTTATTTTGCAA 59.511 39.130 23.47 0.00 46.48 4.08
1434 1454 4.376340 ACGATCCCTTGAAATGAATTGC 57.624 40.909 0.00 0.00 0.00 3.56
1438 1458 5.589192 GATCCCTTGAAATGAATTGCTGAG 58.411 41.667 0.00 0.00 0.00 3.35
1445 1465 2.401583 ATGAATTGCTGAGGCGTGTA 57.598 45.000 0.00 0.00 42.25 2.90
1455 1475 1.272313 TGAGGCGTGTACTCTAGGGTT 60.272 52.381 0.00 0.00 35.98 4.11
1653 1673 2.418976 GAGTTTGTTGCCGGGAGATAAC 59.581 50.000 2.18 5.82 0.00 1.89
1680 1700 2.097142 GCACATTGCCTCTCTTGATGAC 59.903 50.000 0.00 0.00 37.42 3.06
1690 1710 2.231478 TCTCTTGATGACGTGTTCTCCC 59.769 50.000 0.00 0.00 0.00 4.30
1707 1727 0.322187 CCCCGGAATCAAAAGACGGT 60.322 55.000 0.73 0.00 42.81 4.83
1734 1754 2.596776 GCTGAGGGAGCTAGTTGGA 58.403 57.895 0.00 0.00 45.21 3.53
1837 1857 2.042831 AGTGATTGCGCCTGCTTCC 61.043 57.895 4.18 0.00 43.34 3.46
1910 1930 5.808540 TCGGTGATTAAAGTCAGATTTACCG 59.191 40.000 9.58 9.58 34.43 4.02
2029 2049 6.213677 TCTGCAACAGTAAAGGTATATAGCG 58.786 40.000 6.30 0.00 32.61 4.26
2035 2055 7.299246 ACAGTAAAGGTATATAGCGGATGTT 57.701 36.000 6.30 1.11 0.00 2.71
2036 2056 8.413309 ACAGTAAAGGTATATAGCGGATGTTA 57.587 34.615 6.30 0.31 0.00 2.41
2038 2058 8.737175 CAGTAAAGGTATATAGCGGATGTTAGA 58.263 37.037 6.30 0.00 0.00 2.10
2039 2059 8.958506 AGTAAAGGTATATAGCGGATGTTAGAG 58.041 37.037 6.30 0.00 0.00 2.43
2060 2083 3.375299 AGCTTATGATTTGTTCGCCTGTC 59.625 43.478 0.00 0.00 0.00 3.51
2284 2307 8.642935 TTTGTTGAATTGTATTCCTGATACCA 57.357 30.769 0.00 0.00 39.96 3.25
2401 2424 5.221501 TGCACGACTAAGGGTAAGTAAGTTT 60.222 40.000 0.00 0.00 0.00 2.66
2774 2797 5.485620 TCAGTGAATCAGAACTCCAGAATG 58.514 41.667 0.00 0.00 0.00 2.67
2981 3004 5.134725 AGGCTGATGTCTTTATCCCAATT 57.865 39.130 0.00 0.00 0.00 2.32
3067 3096 6.379988 ACTGAACCTTTGGATGTTACAACTTT 59.620 34.615 0.00 0.00 0.00 2.66
3171 3200 7.945033 TTTTCTTGTTCATTTTGATAGTGCC 57.055 32.000 0.00 0.00 0.00 5.01
3546 3575 7.680730 TCTGCCATATTCTTAGAATTACCCTC 58.319 38.462 13.00 0.00 0.00 4.30
3693 3725 1.303643 ACTTTGGGTAGCTGCAGGC 60.304 57.895 17.12 7.98 42.19 4.85
3734 3766 7.981789 TGATTACAGTATTCTGATTGGTCTCAC 59.018 37.037 6.32 0.00 43.76 3.51
3829 3862 7.112528 TGTGCTGTATAAACTTTTGTACTCG 57.887 36.000 9.25 3.54 36.22 4.18
3865 3898 8.970691 ATCTATTACACTGTTGCATTTGTTTC 57.029 30.769 0.00 0.00 0.00 2.78
3866 3899 8.165239 TCTATTACACTGTTGCATTTGTTTCT 57.835 30.769 0.00 0.00 0.00 2.52
3867 3900 8.629158 TCTATTACACTGTTGCATTTGTTTCTT 58.371 29.630 0.00 0.00 0.00 2.52
3868 3901 9.248291 CTATTACACTGTTGCATTTGTTTCTTT 57.752 29.630 0.00 0.00 0.00 2.52
4163 4198 6.713450 TGTTACTCCTACACATTTTCTTTCCC 59.287 38.462 0.00 0.00 0.00 3.97
4213 4248 5.743398 TCTTTGACTGTCATTTTCTTTTGCG 59.257 36.000 11.86 0.00 0.00 4.85
4238 4273 2.234908 AGGCGCATTGTCTCTTCTACTT 59.765 45.455 10.83 0.00 0.00 2.24
4360 4401 2.101575 GCATGTGCATGTGCTCGG 59.898 61.111 16.29 1.10 42.66 4.63
4562 4603 5.820947 TGATGATGATGATGTCAAGACAAGG 59.179 40.000 7.02 0.00 45.41 3.61
4682 4723 8.602328 TGTCTAATTTTCAAAATGTTTGCAGTG 58.398 29.630 0.00 0.00 0.00 3.66
4685 4726 5.542616 TTTTCAAAATGTTTGCAGTGGTG 57.457 34.783 0.00 0.00 0.00 4.17
4727 4768 2.296190 GGAACCAGTGAAAATTTCCGCT 59.704 45.455 3.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 164 7.248976 TCAGAGGGTGGATAACAGATATGTAT 58.751 38.462 0.00 0.00 0.00 2.29
252 254 3.190874 GACCAAACCGACAAATTTGCAA 58.809 40.909 18.12 0.00 34.99 4.08
308 310 6.423905 TCGACTATTATTGTTAGCCATTCAGC 59.576 38.462 0.00 0.00 0.00 4.26
310 312 6.929049 CCTCGACTATTATTGTTAGCCATTCA 59.071 38.462 0.00 0.00 0.00 2.57
324 326 6.228258 AGTTGCTTGTTTTCCTCGACTATTA 58.772 36.000 0.00 0.00 0.00 0.98
373 380 8.647796 TGTCTGTATTTTTGGAAGAGAGTTCTA 58.352 33.333 0.00 0.00 31.96 2.10
384 391 5.652014 CCCTTAGCATGTCTGTATTTTTGGA 59.348 40.000 0.00 0.00 0.00 3.53
395 402 1.899814 TGTTCGTCCCTTAGCATGTCT 59.100 47.619 0.00 0.00 0.00 3.41
504 511 3.181465 ACAAGAAGAGCAGAAACGGAGAA 60.181 43.478 0.00 0.00 0.00 2.87
508 515 3.134458 AGAACAAGAAGAGCAGAAACGG 58.866 45.455 0.00 0.00 0.00 4.44
544 551 1.788258 CTCTTCTTCAAGCTGCGTCA 58.212 50.000 0.00 0.00 0.00 4.35
622 629 2.048444 TACTAGCGTGTCTGGTAGGG 57.952 55.000 5.15 0.00 42.73 3.53
650 657 6.284891 AGTGGGTCATGTTCCATTTATTTG 57.715 37.500 11.66 0.00 35.28 2.32
676 683 3.208594 ACGTAGCGATATACCTCACACA 58.791 45.455 0.00 0.00 0.00 3.72
677 684 3.892918 ACGTAGCGATATACCTCACAC 57.107 47.619 0.00 0.00 0.00 3.82
718 725 2.266689 GGTGATACGGTGCGGGTT 59.733 61.111 0.00 0.00 0.00 4.11
719 726 3.777910 GGGTGATACGGTGCGGGT 61.778 66.667 0.00 0.00 0.00 5.28
720 727 3.441011 GAGGGTGATACGGTGCGGG 62.441 68.421 0.00 0.00 0.00 6.13
721 728 2.106332 GAGGGTGATACGGTGCGG 59.894 66.667 0.00 0.00 0.00 5.69
722 729 0.390603 TTTGAGGGTGATACGGTGCG 60.391 55.000 0.00 0.00 0.00 5.34
723 730 1.816074 TTTTGAGGGTGATACGGTGC 58.184 50.000 0.00 0.00 0.00 5.01
724 731 2.943033 GGATTTTGAGGGTGATACGGTG 59.057 50.000 0.00 0.00 0.00 4.94
725 732 2.092592 GGGATTTTGAGGGTGATACGGT 60.093 50.000 0.00 0.00 0.00 4.83
726 733 2.572290 GGGATTTTGAGGGTGATACGG 58.428 52.381 0.00 0.00 0.00 4.02
727 734 2.572290 GGGGATTTTGAGGGTGATACG 58.428 52.381 0.00 0.00 0.00 3.06
728 735 2.572290 CGGGGATTTTGAGGGTGATAC 58.428 52.381 0.00 0.00 0.00 2.24
729 736 1.133915 GCGGGGATTTTGAGGGTGATA 60.134 52.381 0.00 0.00 0.00 2.15
730 737 0.395724 GCGGGGATTTTGAGGGTGAT 60.396 55.000 0.00 0.00 0.00 3.06
731 738 1.001393 GCGGGGATTTTGAGGGTGA 60.001 57.895 0.00 0.00 0.00 4.02
732 739 0.897863 TTGCGGGGATTTTGAGGGTG 60.898 55.000 0.00 0.00 0.00 4.61
733 740 0.178947 TTTGCGGGGATTTTGAGGGT 60.179 50.000 0.00 0.00 0.00 4.34
734 741 0.972883 TTTTGCGGGGATTTTGAGGG 59.027 50.000 0.00 0.00 0.00 4.30
735 742 2.829741 TTTTTGCGGGGATTTTGAGG 57.170 45.000 0.00 0.00 0.00 3.86
773 780 3.127376 GTGATACGGTGCGGGTTATTTTT 59.873 43.478 0.00 0.00 0.00 1.94
774 781 2.679336 GTGATACGGTGCGGGTTATTTT 59.321 45.455 0.00 0.00 0.00 1.82
775 782 2.282407 GTGATACGGTGCGGGTTATTT 58.718 47.619 0.00 0.00 0.00 1.40
776 783 1.207570 TGTGATACGGTGCGGGTTATT 59.792 47.619 0.00 0.00 0.00 1.40
777 784 0.825410 TGTGATACGGTGCGGGTTAT 59.175 50.000 0.00 0.00 0.00 1.89
778 785 0.108709 GTGTGATACGGTGCGGGTTA 60.109 55.000 0.00 0.00 0.00 2.85
794 801 6.494666 TGCTACTTAATATAAGCCCTGTGT 57.505 37.500 0.00 0.00 33.99 3.72
796 803 7.824779 GCTATTGCTACTTAATATAAGCCCTGT 59.175 37.037 0.00 0.00 33.99 4.00
800 807 7.253684 CGTCGCTATTGCTACTTAATATAAGCC 60.254 40.741 2.66 0.00 36.97 4.35
803 810 6.249893 CGCGTCGCTATTGCTACTTAATATAA 59.750 38.462 16.36 0.00 36.97 0.98
896 904 6.014012 ACTCCCTCCGATCCAAAATTTAAAA 58.986 36.000 0.00 0.00 0.00 1.52
1083 1094 2.686835 AGGTGGAGGAGGAGCAGC 60.687 66.667 0.00 0.00 0.00 5.25
1240 1251 4.344865 TTCCCGAACAGCTGGGCC 62.345 66.667 19.93 0.00 45.60 5.80
1339 1350 2.127651 AGGTGGGGAAAGTGAACCTA 57.872 50.000 0.00 0.00 39.48 3.08
1357 1368 5.335976 GCAGTAAGGAATCACCAAGGAAAAG 60.336 44.000 0.00 0.00 42.04 2.27
1395 1415 6.864165 GGGATCGTAACAATAAGTTTGCAAAA 59.136 34.615 14.67 0.00 41.64 2.44
1402 1422 7.989416 TTTCAAGGGATCGTAACAATAAGTT 57.011 32.000 0.00 0.00 44.27 2.66
1434 1454 1.025812 CCCTAGAGTACACGCCTCAG 58.974 60.000 0.00 0.00 0.00 3.35
1438 1458 0.459759 GCAACCCTAGAGTACACGCC 60.460 60.000 0.00 0.00 0.00 5.68
1445 1465 1.352083 TTGCAGAGCAACCCTAGAGT 58.648 50.000 0.00 0.00 43.99 3.24
1455 1475 6.293790 GCATCTCATGTATAAATTGCAGAGCA 60.294 38.462 0.00 0.00 36.47 4.26
1467 1487 3.006859 CCTTGGACCGCATCTCATGTATA 59.993 47.826 0.00 0.00 0.00 1.47
1680 1700 0.036765 TTGATTCCGGGGAGAACACG 60.037 55.000 0.00 0.00 0.00 4.49
1690 1710 1.803334 TCACCGTCTTTTGATTCCGG 58.197 50.000 0.00 0.00 40.22 5.14
1707 1727 2.203983 TCCCTCAGCCTGCCTTCA 60.204 61.111 0.00 0.00 0.00 3.02
1734 1754 6.013032 CCCTCCCAGTATCATCAGTAATCATT 60.013 42.308 0.00 0.00 0.00 2.57
1815 1835 0.679002 AGCAGGCGCAATCACTGATT 60.679 50.000 10.83 0.00 42.27 2.57
1830 1850 3.655486 TGACAATTTGCAATGGAAGCAG 58.345 40.909 0.00 0.00 43.75 4.24
1910 1930 9.478019 CAATCTGAAGAACGTATCAAATGTAAC 57.522 33.333 0.00 0.00 0.00 2.50
2029 2049 7.348201 CGAACAAATCATAAGCTCTAACATCC 58.652 38.462 0.00 0.00 0.00 3.51
2035 2055 4.811024 CAGGCGAACAAATCATAAGCTCTA 59.189 41.667 0.00 0.00 0.00 2.43
2036 2056 3.624861 CAGGCGAACAAATCATAAGCTCT 59.375 43.478 0.00 0.00 0.00 4.09
2038 2058 3.347216 ACAGGCGAACAAATCATAAGCT 58.653 40.909 0.00 0.00 0.00 3.74
2039 2059 3.685058 GACAGGCGAACAAATCATAAGC 58.315 45.455 0.00 0.00 0.00 3.09
2273 2296 8.778059 ACCAGTTAGAATAAATGGTATCAGGAA 58.222 33.333 17.39 0.00 42.37 3.36
2491 2514 7.528481 CTGCAAGCAATTAATGAAAGCAATA 57.472 32.000 0.00 0.00 32.54 1.90
2527 2550 9.967451 TGGAAATTAATGACCTGTAAGATTACA 57.033 29.630 5.38 5.38 41.06 2.41
2774 2797 1.559831 GTGTGCCTTGTGCTTTCAAC 58.440 50.000 0.00 0.00 42.00 3.18
2793 2816 6.718454 ACAGATCAATTTTCTTCTGAGACG 57.282 37.500 5.84 0.00 38.25 4.18
2981 3004 6.586344 AGCTATAAAGACAATGAAGCAGCTA 58.414 36.000 0.00 0.00 34.08 3.32
3171 3200 7.215789 AGTTATCAATAGCTCACTGAATCAGG 58.784 38.462 15.38 3.94 35.51 3.86
3667 3699 1.421646 AGCTACCCAAAGTCAGCTGTT 59.578 47.619 14.67 0.00 42.60 3.16
3693 3725 4.588899 TGTAATCACATGGAAGTTGGGAG 58.411 43.478 0.00 0.00 28.22 4.30
3734 3766 4.876107 CAGGCAAATAGTTGGTACAGTAGG 59.124 45.833 4.91 0.00 42.39 3.18
3804 3836 7.569297 CGAGTACAAAAGTTTATACAGCACAA 58.431 34.615 10.85 0.00 0.00 3.33
3860 3893 7.862372 GCATAAGAGTGACAAATGAAAGAAACA 59.138 33.333 0.00 0.00 0.00 2.83
3861 3894 7.862372 TGCATAAGAGTGACAAATGAAAGAAAC 59.138 33.333 0.00 0.00 0.00 2.78
3862 3895 7.939782 TGCATAAGAGTGACAAATGAAAGAAA 58.060 30.769 0.00 0.00 0.00 2.52
3863 3896 7.509141 TGCATAAGAGTGACAAATGAAAGAA 57.491 32.000 0.00 0.00 0.00 2.52
3864 3897 7.692460 ATGCATAAGAGTGACAAATGAAAGA 57.308 32.000 0.00 0.00 0.00 2.52
3865 3898 8.242053 AGAATGCATAAGAGTGACAAATGAAAG 58.758 33.333 0.00 0.00 0.00 2.62
3866 3899 8.024865 CAGAATGCATAAGAGTGACAAATGAAA 58.975 33.333 0.00 0.00 0.00 2.69
3867 3900 7.391275 TCAGAATGCATAAGAGTGACAAATGAA 59.609 33.333 0.00 0.00 34.76 2.57
3868 3901 6.880529 TCAGAATGCATAAGAGTGACAAATGA 59.119 34.615 0.00 0.00 34.76 2.57
4148 4183 4.536765 ACTGTCTGGGAAAGAAAATGTGT 58.463 39.130 0.00 0.00 36.40 3.72
4156 4191 4.232091 AGGACTTAACTGTCTGGGAAAGA 58.768 43.478 0.00 0.00 37.16 2.52
4163 4198 6.207810 ACTGTAGAGAAGGACTTAACTGTCTG 59.792 42.308 0.00 0.00 37.16 3.51
4213 4248 1.328986 GAAGAGACAATGCGCCTAAGC 59.671 52.381 4.18 0.00 37.71 3.09
4360 4401 1.518903 GGGTTCAGCAGCACCAAGAC 61.519 60.000 0.00 0.00 32.11 3.01
4552 4593 1.429930 TAGGTGTGCCCTTGTCTTGA 58.570 50.000 0.00 0.00 42.73 3.02
4562 4603 1.886542 CTTGGGAACTTTAGGTGTGCC 59.113 52.381 0.00 0.00 0.00 5.01
4618 4659 5.597182 AGCATCAATCAACATTCATAAGCCT 59.403 36.000 0.00 0.00 0.00 4.58
4682 4723 0.036732 TCAGTCAACATCCTGCCACC 59.963 55.000 0.00 0.00 0.00 4.61
4685 4726 1.002430 TGACTCAGTCAACATCCTGCC 59.998 52.381 4.55 0.00 39.78 4.85
4727 4768 3.198417 GGGAACATAACTTCCGGTCCTTA 59.802 47.826 0.00 0.00 40.80 2.69


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

AutoCloner maintained by Alex Coulton.