Multiple sequence alignment - TraesCS5B01G336800

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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 TraesCS5B01G336800 chr5B 100.000 2569 0 0 1 2569 520082186 520084754 0.000000e+00 4745
1 TraesCS5B01G336800 chr5B 92.926 721 51 0 1 721 53652956 53652236 0.000000e+00 1050
2 TraesCS5B01G336800 chr5A 86.518 1617 104 48 819 2385 546162282 546163834 0.000000e+00 1674
3 TraesCS5B01G336800 chr5A 93.620 721 46 0 1 721 45752496 45751776 0.000000e+00 1077
4 TraesCS5B01G336800 chr5A 90.909 121 6 3 819 934 546161459 546161579 9.520000e-35 158
5 TraesCS5B01G336800 chr5A 90.909 121 6 3 819 934 546161905 546162025 9.520000e-35 158
6 TraesCS5B01G336800 chr7B 95.978 721 27 2 1 721 41489651 41488933 0.000000e+00 1170
7 TraesCS5B01G336800 chr4B 94.861 720 36 1 1 720 483052945 483052227 0.000000e+00 1123
8 TraesCS5B01G336800 chr4B 94.583 720 37 2 1 720 369929430 369928713 0.000000e+00 1112
9 TraesCS5B01G336800 chr6B 93.776 723 44 1 1 723 33077186 33076465 0.000000e+00 1085
10 TraesCS5B01G336800 chr3B 94.302 702 38 2 20 720 722455368 722454668 0.000000e+00 1074
11 TraesCS5B01G336800 chr5D 86.518 1031 67 21 819 1820 430545287 430546274 0.000000e+00 1068
12 TraesCS5B01G336800 chr5D 92.879 660 37 7 1805 2458 430546290 430546945 0.000000e+00 950
13 TraesCS5B01G336800 chr5D 90.385 104 10 0 2457 2560 430546998 430547101 1.240000e-28 137
14 TraesCS5B01G336800 chr2B 92.936 722 50 1 1 722 89438765 89439485 0.000000e+00 1050
15 TraesCS5B01G336800 chr3A 92.233 721 52 2 1 721 737131888 737132604 0.000000e+00 1018


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 TraesCS5B01G336800 chr5B 520082186 520084754 2568 False 4745.000000 4745 100.000000 1 2569 1 chr5B.!!$F1 2568
1 TraesCS5B01G336800 chr5B 53652236 53652956 720 True 1050.000000 1050 92.926000 1 721 1 chr5B.!!$R1 720
2 TraesCS5B01G336800 chr5A 45751776 45752496 720 True 1077.000000 1077 93.620000 1 721 1 chr5A.!!$R1 720
3 TraesCS5B01G336800 chr5A 546161459 546163834 2375 False 663.333333 1674 89.445333 819 2385 3 chr5A.!!$F1 1566
4 TraesCS5B01G336800 chr7B 41488933 41489651 718 True 1170.000000 1170 95.978000 1 721 1 chr7B.!!$R1 720
5 TraesCS5B01G336800 chr4B 483052227 483052945 718 True 1123.000000 1123 94.861000 1 720 1 chr4B.!!$R2 719
6 TraesCS5B01G336800 chr4B 369928713 369929430 717 True 1112.000000 1112 94.583000 1 720 1 chr4B.!!$R1 719
7 TraesCS5B01G336800 chr6B 33076465 33077186 721 True 1085.000000 1085 93.776000 1 723 1 chr6B.!!$R1 722
8 TraesCS5B01G336800 chr3B 722454668 722455368 700 True 1074.000000 1074 94.302000 20 720 1 chr3B.!!$R1 700
9 TraesCS5B01G336800 chr5D 430545287 430547101 1814 False 718.333333 1068 89.927333 819 2560 3 chr5D.!!$F1 1741
10 TraesCS5B01G336800 chr2B 89438765 89439485 720 False 1050.000000 1050 92.936000 1 722 1 chr2B.!!$F1 721
11 TraesCS5B01G336800 chr3A 737131888 737132604 716 False 1018.000000 1018 92.233000 1 721 1 chr3A.!!$F1 720

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
763 771 0.248661 CGTGCGTATCTGGAGTGAGG 60.249 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 2574 0.038526 ACGGATTCACGTCCAGACAC 60.039 55.0 0.0 0.0 45.08 3.67 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
105 106 6.373779 CGATCCATGAGCAAATATACCAAAC 58.626 40.000 0.00 0.00 0.00 2.93
126 127 2.352651 CTCCATTTCAGGTACATGCGTG 59.647 50.000 3.82 3.82 0.00 5.34
145 146 6.859017 TGCGTGTATTCAGTCTTACATAAGA 58.141 36.000 0.00 0.00 39.82 2.10
169 170 5.703130 AGAACTGGAAGCTATCAAAACTGTC 59.297 40.000 0.00 0.00 37.60 3.51
287 289 1.684248 GGGGAAGTAGACACGGCTCTA 60.684 57.143 0.00 0.00 0.00 2.43
319 322 2.729194 TCAAGAGACTCTACTGGCCTC 58.271 52.381 5.14 0.00 0.00 4.70
387 391 0.671781 ACTCTTGAGTGCATGGCGAC 60.672 55.000 2.11 0.00 0.00 5.19
401 405 4.003788 CGACCAGGGAGGCGTTGT 62.004 66.667 0.00 0.00 43.14 3.32
432 436 5.163854 CGGATGACCTGAATGTTTCAACTAC 60.164 44.000 0.00 0.00 39.58 2.73
464 468 1.524863 CGACTCGAAGGTGGTGGTCT 61.525 60.000 0.00 0.00 0.00 3.85
596 600 4.562789 CGAATATCGAAGCTCACAAACTCA 59.437 41.667 0.00 0.00 43.74 3.41
735 743 2.603915 AAAAACATGCGGTGCTTGC 58.396 47.368 4.78 0.00 37.23 4.01
736 744 0.879839 AAAAACATGCGGTGCTTGCC 60.880 50.000 4.78 0.00 37.23 4.52
737 745 1.747325 AAAACATGCGGTGCTTGCCT 61.747 50.000 4.78 0.00 37.23 4.75
738 746 1.747325 AAACATGCGGTGCTTGCCTT 61.747 50.000 4.78 0.00 37.23 4.35
739 747 1.747325 AACATGCGGTGCTTGCCTTT 61.747 50.000 4.78 0.00 37.23 3.11
740 748 0.893270 ACATGCGGTGCTTGCCTTTA 60.893 50.000 4.78 0.00 37.23 1.85
741 749 0.456653 CATGCGGTGCTTGCCTTTAC 60.457 55.000 0.00 0.00 0.00 2.01
742 750 1.595093 ATGCGGTGCTTGCCTTTACC 61.595 55.000 0.00 0.00 0.00 2.85
744 752 2.566529 GGTGCTTGCCTTTACCGC 59.433 61.111 0.00 0.00 0.00 5.68
745 753 2.175811 GTGCTTGCCTTTACCGCG 59.824 61.111 0.00 0.00 0.00 6.46
746 754 2.281208 TGCTTGCCTTTACCGCGT 60.281 55.556 4.92 0.00 0.00 6.01
747 755 2.175811 GCTTGCCTTTACCGCGTG 59.824 61.111 4.92 0.00 0.00 5.34
748 756 2.175811 CTTGCCTTTACCGCGTGC 59.824 61.111 4.92 0.00 0.00 5.34
749 757 3.645157 CTTGCCTTTACCGCGTGCG 62.645 63.158 4.92 7.38 39.44 5.34
750 758 4.973055 TGCCTTTACCGCGTGCGT 62.973 61.111 13.70 0.00 37.81 5.24
751 759 2.810458 GCCTTTACCGCGTGCGTA 60.810 61.111 13.70 0.00 37.81 4.42
752 760 2.169146 GCCTTTACCGCGTGCGTAT 61.169 57.895 13.70 3.55 37.81 3.06
753 761 1.922189 CCTTTACCGCGTGCGTATC 59.078 57.895 13.70 0.00 37.81 2.24
754 762 0.526954 CCTTTACCGCGTGCGTATCT 60.527 55.000 13.70 0.00 37.81 1.98
755 763 0.570734 CTTTACCGCGTGCGTATCTG 59.429 55.000 13.70 0.00 37.81 2.90
756 764 0.802994 TTTACCGCGTGCGTATCTGG 60.803 55.000 13.70 0.00 37.81 3.86
757 765 1.655885 TTACCGCGTGCGTATCTGGA 61.656 55.000 13.70 0.00 37.81 3.86
758 766 2.055310 TACCGCGTGCGTATCTGGAG 62.055 60.000 13.70 0.00 37.81 3.86
759 767 2.102357 CGCGTGCGTATCTGGAGT 59.898 61.111 6.00 0.00 34.35 3.85
760 768 2.224217 CGCGTGCGTATCTGGAGTG 61.224 63.158 6.00 0.00 34.35 3.51
761 769 1.138883 GCGTGCGTATCTGGAGTGA 59.861 57.895 0.00 0.00 0.00 3.41
762 770 0.867753 GCGTGCGTATCTGGAGTGAG 60.868 60.000 0.00 0.00 0.00 3.51
763 771 0.248661 CGTGCGTATCTGGAGTGAGG 60.249 60.000 0.00 0.00 0.00 3.86
764 772 0.528684 GTGCGTATCTGGAGTGAGGC 60.529 60.000 0.00 0.00 0.00 4.70
765 773 1.299468 GCGTATCTGGAGTGAGGCG 60.299 63.158 0.00 0.00 0.00 5.52
766 774 1.299468 CGTATCTGGAGTGAGGCGC 60.299 63.158 0.00 0.00 0.00 6.53
767 775 1.299468 GTATCTGGAGTGAGGCGCG 60.299 63.158 0.00 0.00 0.00 6.86
768 776 2.490148 TATCTGGAGTGAGGCGCGG 61.490 63.158 8.83 0.00 0.00 6.46
792 800 4.403976 GGAACAGCCGATCGAGAC 57.596 61.111 18.66 5.62 0.00 3.36
793 801 1.586564 GGAACAGCCGATCGAGACG 60.587 63.158 18.66 4.45 0.00 4.18
799 807 2.024871 CCGATCGAGACGGTGCTC 59.975 66.667 18.66 0.00 44.57 4.26
805 813 4.891566 GAGACGGTGCTCGAACAT 57.108 55.556 7.01 0.00 42.43 2.71
806 814 2.363807 GAGACGGTGCTCGAACATG 58.636 57.895 7.01 0.00 42.43 3.21
807 815 1.687494 GAGACGGTGCTCGAACATGC 61.687 60.000 7.01 0.00 42.43 4.06
808 816 3.071459 GACGGTGCTCGAACATGCG 62.071 63.158 7.01 0.00 42.43 4.73
809 817 3.853330 CGGTGCTCGAACATGCGG 61.853 66.667 0.00 0.00 42.43 5.69
810 818 2.742372 GGTGCTCGAACATGCGGT 60.742 61.111 0.00 0.00 0.00 5.68
811 819 2.476051 GTGCTCGAACATGCGGTG 59.524 61.111 0.00 0.00 0.00 4.94
812 820 3.422303 TGCTCGAACATGCGGTGC 61.422 61.111 0.00 0.00 33.97 5.01
813 821 3.121030 GCTCGAACATGCGGTGCT 61.121 61.111 0.00 0.00 0.00 4.40
814 822 2.680913 GCTCGAACATGCGGTGCTT 61.681 57.895 0.00 0.00 0.00 3.91
815 823 1.421485 CTCGAACATGCGGTGCTTC 59.579 57.895 0.00 0.00 0.00 3.86
816 824 1.970917 CTCGAACATGCGGTGCTTCC 61.971 60.000 0.00 0.00 0.00 3.46
817 825 2.877691 GAACATGCGGTGCTTCCC 59.122 61.111 0.00 0.00 0.00 3.97
907 1742 3.764466 CTCCACGAGAAGCGGGCT 61.764 66.667 0.00 0.00 43.67 5.19
977 1812 7.268212 TCTCTCCCTCCTATATATACGTGTT 57.732 40.000 0.00 0.00 0.00 3.32
1027 1864 1.407258 CTCCTTCCAAGCTCTACTCGG 59.593 57.143 0.00 0.00 0.00 4.63
1031 1868 0.323451 TCCAAGCTCTACTCGGCTCA 60.323 55.000 0.00 0.00 37.87 4.26
1048 1885 3.784883 CTCACAAACGAAAGAGCAGAG 57.215 47.619 0.00 0.00 0.00 3.35
1049 1886 1.867233 TCACAAACGAAAGAGCAGAGC 59.133 47.619 0.00 0.00 0.00 4.09
1050 1887 1.599071 CACAAACGAAAGAGCAGAGCA 59.401 47.619 0.00 0.00 0.00 4.26
1051 1888 1.869767 ACAAACGAAAGAGCAGAGCAG 59.130 47.619 0.00 0.00 0.00 4.24
1056 1893 2.195096 CGAAAGAGCAGAGCAGATCAG 58.805 52.381 0.00 0.00 0.00 2.90
1074 1911 2.357323 TCAGATCAGATCAGCGTGAGTC 59.643 50.000 13.14 0.00 0.00 3.36
1081 1918 0.179089 ATCAGCGTGAGTCTGCATCC 60.179 55.000 9.99 0.00 35.94 3.51
1085 1922 2.125912 GTGAGTCTGCATCCGCGT 60.126 61.111 4.92 0.00 42.97 6.01
1089 1926 2.202743 GTCTGCATCCGCGTGCTA 60.203 61.111 20.48 7.97 45.27 3.49
1136 1976 3.909258 TTTCCTCGTCGTGCTCGCC 62.909 63.158 2.69 0.00 36.96 5.54
1208 2048 6.183360 CCATTTCACATCTCCCATCTCTTTTC 60.183 42.308 0.00 0.00 0.00 2.29
1213 2053 5.477984 CACATCTCCCATCTCTTTTCCAAAA 59.522 40.000 0.00 0.00 0.00 2.44
1271 2111 5.246883 TCCACAGAAAAGATCTCTGATGACA 59.753 40.000 15.32 0.00 42.51 3.58
1310 2150 3.940852 TGTTGGCTAACTGCATCTGTATG 59.059 43.478 14.47 0.00 45.15 2.39
1316 2156 8.361169 TGGCTAACTGCATCTGTATGTATATA 57.639 34.615 0.00 0.00 45.15 0.86
1353 2193 9.758651 ACTACGTGTTTATAATTCTATGCATGA 57.241 29.630 10.16 1.87 0.00 3.07
1442 2282 4.329545 TGCGTCAACCAGAGCCCC 62.330 66.667 0.00 0.00 0.00 5.80
1527 2367 3.695060 CGAGATGTGTACCAAGGAGTAGT 59.305 47.826 0.00 0.00 0.00 2.73
1536 2393 3.588569 ACCAAGGAGTAGTCTGGTCTTT 58.411 45.455 5.80 0.00 0.00 2.52
1583 2445 7.883311 ACCACCAATAAATCCATATGTAGCTAC 59.117 37.037 17.30 17.30 0.00 3.58
1624 2489 4.096532 AGGAGTATATATGCATGTCGTCGG 59.903 45.833 10.16 0.00 0.00 4.79
1712 2588 4.866508 AAAGATAGTGTCTGGACGTGAA 57.133 40.909 0.00 0.00 37.23 3.18
1726 2603 3.242804 GGACGTGAATCCGTTTTGTTTCA 60.243 43.478 0.00 0.00 41.98 2.69
1741 2618 6.558771 TTTGTTTCATCGTGATCTGATTGT 57.441 33.333 0.00 0.00 0.00 2.71
1742 2619 7.665561 TTTGTTTCATCGTGATCTGATTGTA 57.334 32.000 0.00 0.00 0.00 2.41
1743 2620 7.848223 TTGTTTCATCGTGATCTGATTGTAT 57.152 32.000 0.00 0.00 0.00 2.29
1744 2621 8.940768 TTGTTTCATCGTGATCTGATTGTATA 57.059 30.769 0.00 0.00 0.00 1.47
1745 2622 9.546428 TTGTTTCATCGTGATCTGATTGTATAT 57.454 29.630 0.00 0.00 0.00 0.86
1786 2669 3.309682 TCATCGACCTTCGCATGATTTTC 59.690 43.478 0.00 0.00 40.21 2.29
1999 2915 2.333926 TGAAATCGGTTAGCTCGTGTG 58.666 47.619 0.00 0.00 0.00 3.82
2058 2975 3.434641 ACTTGACGATGAGCATTGTTGAG 59.565 43.478 4.92 8.25 35.64 3.02
2213 3131 4.035102 GCCCGGCCAAGAGAGGTT 62.035 66.667 2.24 0.00 0.00 3.50
2300 3238 2.016318 CTGTGAGTTTGTTGAGCCACA 58.984 47.619 0.00 0.00 34.03 4.17
2424 3374 1.635844 AGATGTAATGCGTCGCGAAA 58.364 45.000 12.06 0.00 38.14 3.46
2431 3381 1.922570 ATGCGTCGCGAAATACTTCT 58.077 45.000 12.06 0.00 0.00 2.85
2435 3385 1.641577 GTCGCGAAATACTTCTGCCT 58.358 50.000 12.06 0.00 31.55 4.75
2436 3386 1.588861 GTCGCGAAATACTTCTGCCTC 59.411 52.381 12.06 0.00 31.55 4.70
2437 3387 1.203758 TCGCGAAATACTTCTGCCTCA 59.796 47.619 6.20 0.00 31.55 3.86
2470 3478 5.012354 GGGGTATACTTCGACCATTCCATTA 59.988 44.000 2.25 0.00 37.47 1.90
2484 3492 7.461749 ACCATTCCATTATAGGTCCACATAAG 58.538 38.462 0.00 0.00 0.00 1.73
2543 3551 5.936054 AGATCATGCTTTATAGAAATGCGC 58.064 37.500 0.00 0.00 0.00 6.09
2544 3552 5.704515 AGATCATGCTTTATAGAAATGCGCT 59.295 36.000 9.73 0.00 0.00 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 2.352651 CACGCATGTACCTGAAATGGAG 59.647 50.000 1.92 0.00 0.00 3.86
126 127 9.522804 CCAGTTCTCTTATGTAAGACTGAATAC 57.477 37.037 15.90 4.77 37.63 1.89
145 146 5.625150 ACAGTTTTGATAGCTTCCAGTTCT 58.375 37.500 0.00 0.00 0.00 3.01
169 170 3.051392 GCCATCCCGCCTCGTTTTG 62.051 63.158 0.00 0.00 0.00 2.44
287 289 4.526262 AGAGTCTCTTGATATTGCCGCTAT 59.474 41.667 0.00 0.00 0.00 2.97
387 391 4.410400 GGGACAACGCCTCCCTGG 62.410 72.222 5.56 0.00 43.93 4.45
432 436 2.022129 GAGTCGGACGCCACTTGTG 61.022 63.158 1.89 0.00 0.00 3.33
464 468 5.394738 AGGATTATTGTCTCGGATGTCCTA 58.605 41.667 0.00 0.00 32.13 2.94
554 558 0.931005 GAGCTCCTAAATTCGTGGCG 59.069 55.000 0.87 0.00 0.00 5.69
592 596 2.939103 GGATAAAGCATGCTTCGTGAGT 59.061 45.455 32.01 18.17 34.84 3.41
596 600 2.717639 AGGGATAAAGCATGCTTCGT 57.282 45.000 32.01 22.83 34.84 3.85
722 730 0.456653 GTAAAGGCAAGCACCGCATG 60.457 55.000 0.00 0.00 33.69 4.06
723 731 1.595093 GGTAAAGGCAAGCACCGCAT 61.595 55.000 0.00 0.00 33.69 4.73
724 732 2.265182 GGTAAAGGCAAGCACCGCA 61.265 57.895 0.00 0.00 33.69 5.69
725 733 2.566529 GGTAAAGGCAAGCACCGC 59.433 61.111 0.00 0.00 33.69 5.68
726 734 2.867472 CGGTAAAGGCAAGCACCG 59.133 61.111 7.19 7.19 46.85 4.94
727 735 2.566529 GCGGTAAAGGCAAGCACC 59.433 61.111 0.00 0.00 0.00 5.01
728 736 2.175811 CGCGGTAAAGGCAAGCAC 59.824 61.111 0.00 0.00 0.00 4.40
729 737 2.281208 ACGCGGTAAAGGCAAGCA 60.281 55.556 12.47 0.00 0.00 3.91
730 738 2.175811 CACGCGGTAAAGGCAAGC 59.824 61.111 12.47 0.00 0.00 4.01
731 739 2.175811 GCACGCGGTAAAGGCAAG 59.824 61.111 12.47 0.00 0.00 4.01
732 740 3.718097 CGCACGCGGTAAAGGCAA 61.718 61.111 12.47 0.00 35.56 4.52
733 741 2.839043 ATACGCACGCGGTAAAGGCA 62.839 55.000 16.70 0.00 44.69 4.75
734 742 2.085928 GATACGCACGCGGTAAAGGC 62.086 60.000 16.70 2.96 44.69 4.35
735 743 0.526954 AGATACGCACGCGGTAAAGG 60.527 55.000 16.70 0.00 44.69 3.11
736 744 0.570734 CAGATACGCACGCGGTAAAG 59.429 55.000 16.70 0.00 44.69 1.85
737 745 0.802994 CCAGATACGCACGCGGTAAA 60.803 55.000 16.70 0.00 44.69 2.01
738 746 1.226745 CCAGATACGCACGCGGTAA 60.227 57.895 16.70 1.03 44.69 2.85
739 747 2.055310 CTCCAGATACGCACGCGGTA 62.055 60.000 16.70 3.20 44.69 4.02
740 748 3.411418 CTCCAGATACGCACGCGGT 62.411 63.158 16.70 0.39 44.69 5.68
741 749 2.655364 CTCCAGATACGCACGCGG 60.655 66.667 16.70 0.00 44.69 6.46
742 750 2.102357 ACTCCAGATACGCACGCG 59.898 61.111 10.36 10.36 46.03 6.01
743 751 0.867753 CTCACTCCAGATACGCACGC 60.868 60.000 0.00 0.00 0.00 5.34
744 752 0.248661 CCTCACTCCAGATACGCACG 60.249 60.000 0.00 0.00 0.00 5.34
745 753 0.528684 GCCTCACTCCAGATACGCAC 60.529 60.000 0.00 0.00 0.00 5.34
746 754 1.816537 GCCTCACTCCAGATACGCA 59.183 57.895 0.00 0.00 0.00 5.24
747 755 1.299468 CGCCTCACTCCAGATACGC 60.299 63.158 0.00 0.00 0.00 4.42
748 756 1.299468 GCGCCTCACTCCAGATACG 60.299 63.158 0.00 0.00 0.00 3.06
749 757 1.299468 CGCGCCTCACTCCAGATAC 60.299 63.158 0.00 0.00 0.00 2.24
750 758 2.490148 CCGCGCCTCACTCCAGATA 61.490 63.158 0.00 0.00 0.00 1.98
751 759 3.842923 CCGCGCCTCACTCCAGAT 61.843 66.667 0.00 0.00 0.00 2.90
775 783 1.586564 CGTCTCGATCGGCTGTTCC 60.587 63.158 16.41 0.00 0.00 3.62
776 784 1.586564 CCGTCTCGATCGGCTGTTC 60.587 63.158 16.41 0.00 41.48 3.18
777 785 2.490217 CCGTCTCGATCGGCTGTT 59.510 61.111 16.41 0.00 41.48 3.16
788 796 1.687494 GCATGTTCGAGCACCGTCTC 61.687 60.000 3.33 0.00 39.75 3.36
789 797 1.738099 GCATGTTCGAGCACCGTCT 60.738 57.895 3.33 0.00 39.75 4.18
790 798 2.778679 GCATGTTCGAGCACCGTC 59.221 61.111 3.33 0.00 39.75 4.79
791 799 3.112075 CGCATGTTCGAGCACCGT 61.112 61.111 3.33 0.00 39.75 4.83
792 800 3.853330 CCGCATGTTCGAGCACCG 61.853 66.667 3.33 10.42 40.25 4.94
793 801 2.742372 ACCGCATGTTCGAGCACC 60.742 61.111 3.33 0.00 0.00 5.01
794 802 2.476051 CACCGCATGTTCGAGCAC 59.524 61.111 3.33 0.00 0.00 4.40
795 803 3.422303 GCACCGCATGTTCGAGCA 61.422 61.111 3.86 3.86 33.06 4.26
796 804 2.568935 GAAGCACCGCATGTTCGAGC 62.569 60.000 0.00 0.00 0.00 5.03
797 805 1.421485 GAAGCACCGCATGTTCGAG 59.579 57.895 0.00 0.00 0.00 4.04
798 806 2.032634 GGAAGCACCGCATGTTCGA 61.033 57.895 0.00 0.00 0.00 3.71
799 807 2.480555 GGAAGCACCGCATGTTCG 59.519 61.111 0.00 0.00 0.00 3.95
800 808 1.244019 AAGGGAAGCACCGCATGTTC 61.244 55.000 0.00 0.00 40.11 3.18
801 809 1.228552 AAGGGAAGCACCGCATGTT 60.229 52.632 0.00 0.00 40.11 2.71
802 810 1.675641 GAAGGGAAGCACCGCATGT 60.676 57.895 0.00 0.00 40.11 3.21
803 811 1.372087 GAGAAGGGAAGCACCGCATG 61.372 60.000 0.00 0.00 40.11 4.06
804 812 1.078143 GAGAAGGGAAGCACCGCAT 60.078 57.895 0.00 0.00 40.11 4.73
805 813 2.347490 GAGAAGGGAAGCACCGCA 59.653 61.111 0.00 0.00 40.11 5.69
806 814 2.436824 GGAGAAGGGAAGCACCGC 60.437 66.667 0.00 0.00 40.11 5.68
807 815 0.391793 GAAGGAGAAGGGAAGCACCG 60.392 60.000 0.00 0.00 40.11 4.94
808 816 0.988063 AGAAGGAGAAGGGAAGCACC 59.012 55.000 0.00 0.00 38.08 5.01
809 817 1.065782 GGAGAAGGAGAAGGGAAGCAC 60.066 57.143 0.00 0.00 0.00 4.40
810 818 1.280457 GGAGAAGGAGAAGGGAAGCA 58.720 55.000 0.00 0.00 0.00 3.91
811 819 0.544223 GGGAGAAGGAGAAGGGAAGC 59.456 60.000 0.00 0.00 0.00 3.86
812 820 0.827368 CGGGAGAAGGAGAAGGGAAG 59.173 60.000 0.00 0.00 0.00 3.46
813 821 0.412244 TCGGGAGAAGGAGAAGGGAA 59.588 55.000 0.00 0.00 34.75 3.97
814 822 0.637195 ATCGGGAGAAGGAGAAGGGA 59.363 55.000 0.00 0.00 45.37 4.20
815 823 1.044611 GATCGGGAGAAGGAGAAGGG 58.955 60.000 0.00 0.00 45.37 3.95
816 824 0.671251 CGATCGGGAGAAGGAGAAGG 59.329 60.000 7.38 0.00 45.37 3.46
817 825 0.031449 GCGATCGGGAGAAGGAGAAG 59.969 60.000 18.30 0.00 45.37 2.85
842 850 3.488090 GGCTGTTACGCCTGTCGC 61.488 66.667 10.11 0.00 46.63 5.19
907 1742 1.108776 CGGAATCTCCTAACGACCCA 58.891 55.000 0.00 0.00 33.30 4.51
945 1780 0.553862 AGGAGGGAGAGAGGTGGAGA 60.554 60.000 0.00 0.00 0.00 3.71
1006 1841 1.407258 CGAGTAGAGCTTGGAAGGAGG 59.593 57.143 0.00 0.00 0.00 4.30
1031 1868 1.869767 CTGCTCTGCTCTTTCGTTTGT 59.130 47.619 0.00 0.00 0.00 2.83
1049 1886 3.004524 TCACGCTGATCTGATCTGATCTG 59.995 47.826 30.92 30.11 42.30 2.90
1050 1887 3.220940 TCACGCTGATCTGATCTGATCT 58.779 45.455 30.92 16.25 42.30 2.75
1051 1888 3.004629 ACTCACGCTGATCTGATCTGATC 59.995 47.826 27.10 27.10 42.19 2.92
1056 1893 2.730069 CAGACTCACGCTGATCTGATC 58.270 52.381 10.72 10.72 35.74 2.92
1067 1904 3.250323 CGCGGATGCAGACTCACG 61.250 66.667 0.00 0.00 42.97 4.35
1089 1926 0.250513 GTTCTCCTCTCCATTGGCGT 59.749 55.000 0.00 0.00 0.00 5.68
1136 1976 3.130160 GCAGGGCTTGCGAGAAGG 61.130 66.667 5.64 0.00 44.09 3.46
1167 2007 0.967380 ATGGAAGGGGAGCAAAAGCG 60.967 55.000 0.00 0.00 0.00 4.68
1170 2010 2.632512 GTGAAATGGAAGGGGAGCAAAA 59.367 45.455 0.00 0.00 0.00 2.44
1171 2011 2.247358 GTGAAATGGAAGGGGAGCAAA 58.753 47.619 0.00 0.00 0.00 3.68
1172 2012 1.146774 TGTGAAATGGAAGGGGAGCAA 59.853 47.619 0.00 0.00 0.00 3.91
1213 2053 7.950124 TGTAAAGGGGAAGAATGAGATCTTTTT 59.050 33.333 0.00 0.00 39.70 1.94
1224 2064 6.394345 AACAGAGATGTAAAGGGGAAGAAT 57.606 37.500 0.00 0.00 0.00 2.40
1265 2105 8.746922 ACAAACATACAAACATCATTGTCATC 57.253 30.769 0.00 0.00 42.33 2.92
1271 2111 6.523840 AGCCAACAAACATACAAACATCATT 58.476 32.000 0.00 0.00 0.00 2.57
1330 2170 9.882996 CATTCATGCATAGAATTATAAACACGT 57.117 29.630 16.73 0.00 33.64 4.49
1442 2282 4.268687 GACTTGAGCACCAGGTCG 57.731 61.111 5.82 0.00 45.10 4.79
1527 2367 5.962031 TCCCTAGCTAATAACAAAGACCAGA 59.038 40.000 0.00 0.00 0.00 3.86
1536 2393 2.674420 ACGCCTCCCTAGCTAATAACA 58.326 47.619 0.00 0.00 0.00 2.41
1697 2573 0.243907 CGGATTCACGTCCAGACACT 59.756 55.000 0.00 0.00 38.21 3.55
1698 2574 0.038526 ACGGATTCACGTCCAGACAC 60.039 55.000 0.00 0.00 45.08 3.67
1699 2575 2.347630 ACGGATTCACGTCCAGACA 58.652 52.632 0.00 0.00 45.08 3.41
1712 2588 4.695455 AGATCACGATGAAACAAAACGGAT 59.305 37.500 0.00 0.00 0.00 4.18
1742 2619 9.624373 GATGAAGAATCTGGCCAACATATATAT 57.376 33.333 7.01 0.00 32.01 0.86
1743 2620 7.765819 CGATGAAGAATCTGGCCAACATATATA 59.234 37.037 7.01 0.00 32.61 0.86
1744 2621 6.596888 CGATGAAGAATCTGGCCAACATATAT 59.403 38.462 7.01 0.00 32.61 0.86
1745 2622 5.934043 CGATGAAGAATCTGGCCAACATATA 59.066 40.000 7.01 0.00 32.61 0.86
1746 2623 4.758674 CGATGAAGAATCTGGCCAACATAT 59.241 41.667 7.01 0.00 32.61 1.78
1908 2822 8.646900 AGCCACCAAGTTCTGATTTAAAATTTA 58.353 29.630 0.00 0.00 0.00 1.40
1915 2829 4.985538 AGAAGCCACCAAGTTCTGATTTA 58.014 39.130 0.00 0.00 0.00 1.40
1999 2915 1.303091 AATCGCGTACAAACCAGGCC 61.303 55.000 5.77 0.00 0.00 5.19
2205 3123 1.633774 TCTTCCGCTTCAACCTCTCT 58.366 50.000 0.00 0.00 0.00 3.10
2265 3203 3.381908 ACTCACAGATGTAACCGATCCTC 59.618 47.826 0.00 0.00 0.00 3.71
2278 3216 2.880890 GTGGCTCAACAAACTCACAGAT 59.119 45.455 0.00 0.00 0.00 2.90
2300 3238 0.882474 CTATCCTACGCTAGCGCCTT 59.118 55.000 35.63 19.88 44.19 4.35
2337 3287 0.529773 CTGCCGAGCTTTACGCCATA 60.530 55.000 0.00 0.00 40.39 2.74
2396 3346 4.201589 CGACGCATTACATCTTTTTCTCGT 60.202 41.667 0.00 0.00 0.00 4.18
2405 3355 1.635844 TTTCGCGACGCATTACATCT 58.364 45.000 21.35 0.00 0.00 2.90
2445 3399 2.970640 GGAATGGTCGAAGTATACCCCT 59.029 50.000 0.00 0.00 34.69 4.79
2522 3530 5.954296 AGCGCATTTCTATAAAGCATGAT 57.046 34.783 11.47 0.00 0.00 2.45
2523 3531 7.439157 AATAGCGCATTTCTATAAAGCATGA 57.561 32.000 11.47 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.