Multiple sequence alignment - TraesCS4A01G021400

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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 TraesCS4A01G021400 chr4A 100.000 2193 0 0 1596 3788 15124496 15126688 0.000000e+00 4050
1 TraesCS4A01G021400 chr4A 100.000 1294 0 0 1 1294 15122901 15124194 0.000000e+00 2390
2 TraesCS4A01G021400 chr4A 82.561 453 76 2 2944 3396 559067761 559068210 2.740000e-106 396
3 TraesCS4A01G021400 chr4B 93.197 2205 94 20 1596 3788 565090974 565093134 0.000000e+00 3190
4 TraesCS4A01G021400 chr4B 94.127 630 34 2 1 630 573692740 573692114 0.000000e+00 955
5 TraesCS4A01G021400 chr4B 91.238 525 25 3 784 1294 565090429 565090946 0.000000e+00 695
6 TraesCS4A01G021400 chr4B 79.956 454 86 4 2944 3396 59236273 59236722 2.820000e-86 329
7 TraesCS4A01G021400 chr4B 79.887 353 63 6 2944 3293 59226828 59227175 6.280000e-63 252
8 TraesCS4A01G021400 chr4D 91.134 2222 94 37 1596 3788 451683185 451685332 0.000000e+00 2916
9 TraesCS4A01G021400 chr4D 89.753 527 33 3 782 1294 451682648 451683167 0.000000e+00 654
10 TraesCS4A01G021400 chr4D 80.702 456 79 7 2944 3396 40567674 40568123 2.800000e-91 346
11 TraesCS4A01G021400 chr4D 87.215 219 17 6 630 848 451640097 451640304 4.890000e-59 239
12 TraesCS4A01G021400 chr3A 96.502 629 21 1 1 629 178184399 178183772 0.000000e+00 1038
13 TraesCS4A01G021400 chr6A 96.184 629 22 2 1 629 163208718 163209344 0.000000e+00 1027
14 TraesCS4A01G021400 chr2D 95.873 630 25 1 1 630 562708735 562708107 0.000000e+00 1018
15 TraesCS4A01G021400 chr2D 85.737 631 87 3 1 630 68622350 68622978 0.000000e+00 664
16 TraesCS4A01G021400 chr2D 85.420 631 89 3 1 630 68585198 68585826 0.000000e+00 652
17 TraesCS4A01G021400 chr5D 89.219 640 67 2 1 639 330765826 330766464 0.000000e+00 798
18 TraesCS4A01G021400 chr5B 88.254 630 73 1 1 630 513650625 513649997 0.000000e+00 752
19 TraesCS4A01G021400 chr6B 84.370 627 96 2 1 627 646235065 646235689 6.950000e-172 614


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 TraesCS4A01G021400 chr4A 15122901 15126688 3787 False 3220.0 4050 100.0000 1 3788 2 chr4A.!!$F2 3787
1 TraesCS4A01G021400 chr4B 565090429 565093134 2705 False 1942.5 3190 92.2175 784 3788 2 chr4B.!!$F3 3004
2 TraesCS4A01G021400 chr4B 573692114 573692740 626 True 955.0 955 94.1270 1 630 1 chr4B.!!$R1 629
3 TraesCS4A01G021400 chr4D 451682648 451685332 2684 False 1785.0 2916 90.4435 782 3788 2 chr4D.!!$F3 3006
4 TraesCS4A01G021400 chr3A 178183772 178184399 627 True 1038.0 1038 96.5020 1 629 1 chr3A.!!$R1 628
5 TraesCS4A01G021400 chr6A 163208718 163209344 626 False 1027.0 1027 96.1840 1 629 1 chr6A.!!$F1 628
6 TraesCS4A01G021400 chr2D 562708107 562708735 628 True 1018.0 1018 95.8730 1 630 1 chr2D.!!$R1 629
7 TraesCS4A01G021400 chr2D 68622350 68622978 628 False 664.0 664 85.7370 1 630 1 chr2D.!!$F2 629
8 TraesCS4A01G021400 chr2D 68585198 68585826 628 False 652.0 652 85.4200 1 630 1 chr2D.!!$F1 629
9 TraesCS4A01G021400 chr5D 330765826 330766464 638 False 798.0 798 89.2190 1 639 1 chr5D.!!$F1 638
10 TraesCS4A01G021400 chr5B 513649997 513650625 628 True 752.0 752 88.2540 1 630 1 chr5B.!!$R1 629
11 TraesCS4A01G021400 chr6B 646235065 646235689 624 False 614.0 614 84.3700 1 627 1 chr6B.!!$F1 626

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
703 704 0.182775 AAACAAAGCCCAGACGGTCT 59.817 50.0 4.45 4.45 0.00 3.85 F
732 733 0.253044 CCATATATGGGCCCGTCAGG 59.747 60.0 23.23 14.42 44.31 3.86 F
2362 2393 0.392706 ATGGTCAGAGTGTGCACGAA 59.607 50.0 13.13 0.00 36.20 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 1974 0.471022 TGCACCGGGGAGAGCATATA 60.471 55.000 8.67 0.0 31.05 0.86 R
2382 2413 0.944386 GCATGGTCAAGTGTTCACGT 59.056 50.000 0.00 0.0 0.00 4.49 R
3579 3621 2.283101 TACCACGTGTACCGGGCT 60.283 61.111 15.65 0.0 39.18 5.19 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
123 124 0.742505 CAAGATACGGCGTCCACCTA 59.257 55.000 19.21 0.00 0.00 3.08
163 164 0.253044 AGGACAACCCCGATCACATG 59.747 55.000 0.00 0.00 36.73 3.21
221 222 4.288105 ACTCCTGTTTCAGTGAATGGAGAT 59.712 41.667 33.26 23.00 37.36 2.75
422 423 5.581126 TGCACAACTCAAAACAAAGATCT 57.419 34.783 0.00 0.00 0.00 2.75
668 669 8.614469 AAAAATGATTTATTGCCGAAAAGGAA 57.386 26.923 0.00 0.00 45.00 3.36
669 670 8.614469 AAAATGATTTATTGCCGAAAAGGAAA 57.386 26.923 0.00 0.00 43.11 3.13
670 671 7.595311 AATGATTTATTGCCGAAAAGGAAAC 57.405 32.000 0.00 0.00 41.32 2.78
671 672 6.090483 TGATTTATTGCCGAAAAGGAAACA 57.910 33.333 0.00 0.00 41.32 2.83
672 673 6.696411 TGATTTATTGCCGAAAAGGAAACAT 58.304 32.000 0.00 0.00 41.32 2.71
673 674 6.589523 TGATTTATTGCCGAAAAGGAAACATG 59.410 34.615 0.00 0.00 41.32 3.21
674 675 5.713792 TTATTGCCGAAAAGGAAACATGA 57.286 34.783 0.00 0.00 41.32 3.07
675 676 4.806640 ATTGCCGAAAAGGAAACATGAT 57.193 36.364 0.00 0.00 41.32 2.45
676 677 4.599047 TTGCCGAAAAGGAAACATGATT 57.401 36.364 0.00 0.00 45.00 2.57
677 678 4.173036 TGCCGAAAAGGAAACATGATTC 57.827 40.909 7.15 7.15 45.00 2.52
678 679 3.571828 TGCCGAAAAGGAAACATGATTCA 59.428 39.130 16.48 0.00 45.00 2.57
679 680 4.220382 TGCCGAAAAGGAAACATGATTCAT 59.780 37.500 16.48 7.52 45.00 2.57
680 681 5.417266 TGCCGAAAAGGAAACATGATTCATA 59.583 36.000 16.48 0.00 45.00 2.15
681 682 6.071672 TGCCGAAAAGGAAACATGATTCATAA 60.072 34.615 16.48 0.00 45.00 1.90
682 683 6.253512 GCCGAAAAGGAAACATGATTCATAAC 59.746 38.462 16.48 5.12 45.00 1.89
683 684 6.468956 CCGAAAAGGAAACATGATTCATAACG 59.531 38.462 16.48 14.22 45.00 3.18
684 685 7.240674 CGAAAAGGAAACATGATTCATAACGA 58.759 34.615 16.48 0.00 0.00 3.85
685 686 7.748683 CGAAAAGGAAACATGATTCATAACGAA 59.251 33.333 16.48 0.00 38.22 3.85
686 687 9.405587 GAAAAGGAAACATGATTCATAACGAAA 57.594 29.630 16.48 0.00 37.12 3.46
687 688 8.742554 AAAGGAAACATGATTCATAACGAAAC 57.257 30.769 16.48 0.00 37.12 2.78
688 689 7.447374 AGGAAACATGATTCATAACGAAACA 57.553 32.000 16.48 0.00 40.29 2.83
689 690 7.881142 AGGAAACATGATTCATAACGAAACAA 58.119 30.769 16.48 0.00 39.54 2.83
690 691 8.356657 AGGAAACATGATTCATAACGAAACAAA 58.643 29.630 16.48 0.00 39.54 2.83
691 692 8.638565 GGAAACATGATTCATAACGAAACAAAG 58.361 33.333 16.48 0.00 39.54 2.77
692 693 7.566858 AACATGATTCATAACGAAACAAAGC 57.433 32.000 0.00 0.00 39.54 3.51
693 694 6.092748 ACATGATTCATAACGAAACAAAGCC 58.907 36.000 0.00 0.00 39.54 4.35
694 695 5.054390 TGATTCATAACGAAACAAAGCCC 57.946 39.130 0.00 0.00 37.12 5.19
695 696 4.520874 TGATTCATAACGAAACAAAGCCCA 59.479 37.500 0.00 0.00 37.12 5.36
696 697 4.497473 TTCATAACGAAACAAAGCCCAG 57.503 40.909 0.00 0.00 0.00 4.45
697 698 3.745799 TCATAACGAAACAAAGCCCAGA 58.254 40.909 0.00 0.00 0.00 3.86
698 699 3.500680 TCATAACGAAACAAAGCCCAGAC 59.499 43.478 0.00 0.00 0.00 3.51
699 700 0.661020 AACGAAACAAAGCCCAGACG 59.339 50.000 0.00 0.00 0.00 4.18
700 701 1.164041 ACGAAACAAAGCCCAGACGG 61.164 55.000 0.00 0.00 0.00 4.79
701 702 1.164041 CGAAACAAAGCCCAGACGGT 61.164 55.000 0.00 0.00 0.00 4.83
702 703 0.591659 GAAACAAAGCCCAGACGGTC 59.408 55.000 0.00 0.00 0.00 4.79
703 704 0.182775 AAACAAAGCCCAGACGGTCT 59.817 50.000 4.45 4.45 0.00 3.85
704 705 0.535102 AACAAAGCCCAGACGGTCTG 60.535 55.000 27.29 27.29 43.91 3.51
717 718 3.845259 GTCTGGCCGGCGTCCATA 61.845 66.667 22.54 0.00 32.37 2.74
718 719 2.842462 TCTGGCCGGCGTCCATAT 60.842 61.111 22.54 0.00 32.37 1.78
719 720 1.532078 TCTGGCCGGCGTCCATATA 60.532 57.895 22.54 0.00 32.37 0.86
720 721 0.902984 TCTGGCCGGCGTCCATATAT 60.903 55.000 22.54 0.00 32.37 0.86
721 722 0.740868 CTGGCCGGCGTCCATATATG 60.741 60.000 22.54 5.68 32.37 1.78
729 730 3.855159 GTCCATATATGGGCCCGTC 57.145 57.895 27.86 0.00 46.74 4.79
730 731 0.981183 GTCCATATATGGGCCCGTCA 59.019 55.000 27.86 10.60 46.74 4.35
731 732 1.066143 GTCCATATATGGGCCCGTCAG 60.066 57.143 27.86 8.86 46.74 3.51
732 733 0.253044 CCATATATGGGCCCGTCAGG 59.747 60.000 23.23 14.42 44.31 3.86
751 752 2.108157 GCCGCATCCACGACCATA 59.892 61.111 0.00 0.00 34.06 2.74
752 753 2.244651 GCCGCATCCACGACCATAC 61.245 63.158 0.00 0.00 34.06 2.39
753 754 1.949133 CCGCATCCACGACCATACG 60.949 63.158 0.00 0.00 39.31 3.06
754 755 1.065109 CGCATCCACGACCATACGA 59.935 57.895 0.00 0.00 37.03 3.43
755 756 0.526739 CGCATCCACGACCATACGAA 60.527 55.000 0.00 0.00 37.03 3.85
756 757 0.928229 GCATCCACGACCATACGAAC 59.072 55.000 0.00 0.00 37.03 3.95
757 758 1.567504 CATCCACGACCATACGAACC 58.432 55.000 0.00 0.00 37.03 3.62
758 759 1.136305 CATCCACGACCATACGAACCT 59.864 52.381 0.00 0.00 37.03 3.50
759 760 1.259609 TCCACGACCATACGAACCTT 58.740 50.000 0.00 0.00 37.03 3.50
760 761 1.203052 TCCACGACCATACGAACCTTC 59.797 52.381 0.00 0.00 37.03 3.46
761 762 1.636988 CACGACCATACGAACCTTCC 58.363 55.000 0.00 0.00 37.03 3.46
762 763 1.067425 CACGACCATACGAACCTTCCA 60.067 52.381 0.00 0.00 37.03 3.53
763 764 1.203994 ACGACCATACGAACCTTCCAG 59.796 52.381 0.00 0.00 37.03 3.86
764 765 1.475280 CGACCATACGAACCTTCCAGA 59.525 52.381 0.00 0.00 35.09 3.86
765 766 2.479730 CGACCATACGAACCTTCCAGAG 60.480 54.545 0.00 0.00 35.09 3.35
766 767 2.496470 GACCATACGAACCTTCCAGAGT 59.504 50.000 0.00 0.00 0.00 3.24
767 768 2.496470 ACCATACGAACCTTCCAGAGTC 59.504 50.000 0.00 0.00 0.00 3.36
768 769 2.159085 CCATACGAACCTTCCAGAGTCC 60.159 54.545 0.00 0.00 0.00 3.85
769 770 2.297698 TACGAACCTTCCAGAGTCCA 57.702 50.000 0.00 0.00 0.00 4.02
770 771 1.645710 ACGAACCTTCCAGAGTCCAT 58.354 50.000 0.00 0.00 0.00 3.41
771 772 2.816411 ACGAACCTTCCAGAGTCCATA 58.184 47.619 0.00 0.00 0.00 2.74
772 773 3.375699 ACGAACCTTCCAGAGTCCATAT 58.624 45.455 0.00 0.00 0.00 1.78
773 774 3.385111 ACGAACCTTCCAGAGTCCATATC 59.615 47.826 0.00 0.00 0.00 1.63
774 775 3.639094 CGAACCTTCCAGAGTCCATATCT 59.361 47.826 0.00 0.00 0.00 1.98
775 776 4.261825 CGAACCTTCCAGAGTCCATATCTC 60.262 50.000 0.00 0.00 0.00 2.75
776 777 3.582164 ACCTTCCAGAGTCCATATCTCC 58.418 50.000 0.00 0.00 32.93 3.71
777 778 2.903135 CCTTCCAGAGTCCATATCTCCC 59.097 54.545 0.00 0.00 32.93 4.30
778 779 3.581101 CTTCCAGAGTCCATATCTCCCA 58.419 50.000 0.00 0.00 32.93 4.37
779 780 3.931241 TCCAGAGTCCATATCTCCCAT 57.069 47.619 0.00 0.00 32.93 4.00
780 781 3.514539 TCCAGAGTCCATATCTCCCATG 58.485 50.000 0.00 0.00 32.93 3.66
809 810 8.809468 AATAACCCTGAAAAGAAATCTACTCC 57.191 34.615 0.00 0.00 0.00 3.85
810 811 4.833390 ACCCTGAAAAGAAATCTACTCCG 58.167 43.478 0.00 0.00 0.00 4.63
811 812 4.286291 ACCCTGAAAAGAAATCTACTCCGT 59.714 41.667 0.00 0.00 0.00 4.69
812 813 5.482878 ACCCTGAAAAGAAATCTACTCCGTA 59.517 40.000 0.00 0.00 0.00 4.02
826 827 7.984422 TCTACTCCGTATCCGTGATTAATAA 57.016 36.000 0.00 0.00 0.00 1.40
835 836 5.509605 TCCGTGATTAATAATGCGAATCG 57.490 39.130 0.00 0.00 33.18 3.34
881 882 4.033776 CCATGCAGGTGGGTCCGT 62.034 66.667 0.00 0.00 41.99 4.69
996 1010 4.338539 ACCGTCTCGTCACCGCAC 62.339 66.667 0.00 0.00 0.00 5.34
1215 1230 2.677337 TCGTCGACATACATAACGTCCA 59.323 45.455 17.16 0.00 35.04 4.02
1272 1287 3.068691 TTCCTGTCGGAGGCGGAG 61.069 66.667 0.00 0.00 44.34 4.63
1285 1300 2.885113 CGGAGTGCGATCACCTCA 59.115 61.111 0.00 0.00 44.16 3.86
1642 1657 0.659427 ACATTCCATCGCTCGCAATG 59.341 50.000 0.00 0.00 0.00 2.82
1805 1826 1.512694 CCTTCGGCTTTTCATGGCC 59.487 57.895 0.00 0.00 44.43 5.36
1861 1882 2.296752 CGATCTGTCTCATCCATCTGCT 59.703 50.000 0.00 0.00 0.00 4.24
1938 1969 2.830370 GCTGCCACAGGGTATGCC 60.830 66.667 0.00 0.00 36.17 4.40
1965 1996 3.075005 GCTCTCCCCGGTGCACTA 61.075 66.667 17.98 0.00 0.00 2.74
1984 2015 1.987704 AAACTCAACGCACGCTGCAA 61.988 50.000 0.00 0.00 45.36 4.08
1985 2016 1.987704 AACTCAACGCACGCTGCAAA 61.988 50.000 0.00 0.00 45.36 3.68
1986 2017 1.723542 CTCAACGCACGCTGCAAAG 60.724 57.895 0.00 0.00 45.36 2.77
1987 2018 2.024588 CAACGCACGCTGCAAAGT 59.975 55.556 0.00 0.00 45.36 2.66
1988 2019 2.024588 AACGCACGCTGCAAAGTG 59.975 55.556 14.72 14.72 45.36 3.16
2003 2034 5.523013 GCAAAGTGCAAAGTGTAAACAAA 57.477 34.783 0.00 0.00 44.26 2.83
2004 2035 5.312838 GCAAAGTGCAAAGTGTAAACAAAC 58.687 37.500 0.00 0.00 44.26 2.93
2005 2036 5.120053 GCAAAGTGCAAAGTGTAAACAAACT 59.880 36.000 0.00 0.00 44.26 2.66
2006 2037 6.347321 GCAAAGTGCAAAGTGTAAACAAACTT 60.347 34.615 0.00 0.00 44.26 2.66
2007 2038 6.704512 AAGTGCAAAGTGTAAACAAACTTG 57.295 33.333 0.00 0.00 36.75 3.16
2008 2039 4.625311 AGTGCAAAGTGTAAACAAACTTGC 59.375 37.500 13.83 13.83 36.75 4.01
2009 2040 4.387256 GTGCAAAGTGTAAACAAACTTGCA 59.613 37.500 17.17 17.17 40.97 4.08
2017 2048 8.130307 AGTGTAAACAAACTTGCATTTCAATC 57.870 30.769 0.00 0.00 33.57 2.67
2021 2052 7.614124 AAACAAACTTGCATTTCAATCTTGT 57.386 28.000 0.00 0.00 39.25 3.16
2025 2056 6.849588 AACTTGCATTTCAATCTTGTTTCC 57.150 33.333 0.00 0.00 33.57 3.13
2026 2057 4.984161 ACTTGCATTTCAATCTTGTTTCCG 59.016 37.500 0.00 0.00 33.57 4.30
2124 2155 1.079819 CGACTTCATCCGGCACACT 60.080 57.895 0.00 0.00 0.00 3.55
2201 2232 2.180769 CGACGTCAAGATGGGCGA 59.819 61.111 17.16 0.00 0.00 5.54
2246 2277 3.953766 ACGTACTAATCGCAGATCTGTG 58.046 45.455 27.01 27.01 45.12 3.66
2260 2291 3.963374 AGATCTGTGTTCCTAGCTGCATA 59.037 43.478 1.02 0.00 0.00 3.14
2266 2297 5.928976 TGTGTTCCTAGCTGCATACATATT 58.071 37.500 1.02 0.00 0.00 1.28
2288 2319 5.779241 TTCATTCTTCCCAACCTATGACT 57.221 39.130 0.00 0.00 0.00 3.41
2362 2393 0.392706 ATGGTCAGAGTGTGCACGAA 59.607 50.000 13.13 0.00 36.20 3.85
2382 2413 4.506758 GAAGTGGGTACGCAGGTAATAAA 58.493 43.478 13.62 0.00 0.00 1.40
2387 2418 3.510719 GGTACGCAGGTAATAAACGTGA 58.489 45.455 0.00 0.00 44.95 4.35
2395 2426 5.049954 GCAGGTAATAAACGTGAACACTTGA 60.050 40.000 0.00 0.00 44.95 3.02
2408 2439 2.636830 ACACTTGACCATGCAGATAGC 58.363 47.619 0.00 0.00 45.96 2.97
2440 2474 3.504520 TCTTGATGTGACGCACTACACTA 59.495 43.478 10.54 0.00 37.81 2.74
2571 2605 4.148825 AGCTGCCCCGTGATCGAC 62.149 66.667 0.00 0.00 39.71 4.20
2731 2765 1.520787 CGCTACATGGTCGGAACCC 60.521 63.158 0.00 0.00 45.83 4.11
2793 2827 3.259064 CACCGGTACACTGTAGATTTGG 58.741 50.000 6.87 0.00 0.00 3.28
2837 2871 8.184192 CACTGACTGGCTAATCGAAATAAAAAT 58.816 33.333 0.00 0.00 0.00 1.82
2838 2872 9.391006 ACTGACTGGCTAATCGAAATAAAAATA 57.609 29.630 0.00 0.00 0.00 1.40
2882 2916 6.528014 TTGTTATGTACAAATATACGGCCG 57.472 37.500 26.86 26.86 43.58 6.13
2885 2919 6.587226 TGTTATGTACAAATATACGGCCGATC 59.413 38.462 35.90 7.59 32.64 3.69
2936 2978 4.368808 CGTTCACGTGCCCTTGCG 62.369 66.667 11.67 4.89 41.78 4.85
3045 3087 0.320683 TGATCCTCTGCACGTGGTTG 60.321 55.000 18.88 0.00 0.00 3.77
3069 3111 4.671590 TCGTGGCTCGACCTCCCA 62.672 66.667 7.67 0.00 44.01 4.37
3213 3255 2.107750 ATGCTCATCCGGCACTCG 59.892 61.111 0.00 0.00 42.69 4.18
3731 3773 4.814294 GCGGCCGTCGTGGAAGAT 62.814 66.667 28.70 0.00 42.00 2.40
3754 3796 2.669569 GCTTCCGCAGCTTGTCCA 60.670 61.111 0.00 0.00 46.27 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 1.268234 GCATAACCACAATGAGCGAGC 60.268 52.381 0.00 0.00 0.00 5.03
221 222 1.543802 GGATGGGATTTGCACGTTGAA 59.456 47.619 0.00 0.00 0.00 2.69
422 423 7.622502 TCCTCCAATCATCAATCTCATCTAA 57.377 36.000 0.00 0.00 0.00 2.10
602 603 3.885724 TCGAGAGTATGTCAATGGCAA 57.114 42.857 0.00 0.00 0.00 4.52
643 644 8.614469 TTCCTTTTCGGCAATAAATCATTTTT 57.386 26.923 0.00 0.00 0.00 1.94
644 645 8.503196 GTTTCCTTTTCGGCAATAAATCATTTT 58.497 29.630 0.00 0.00 0.00 1.82
645 646 7.659390 TGTTTCCTTTTCGGCAATAAATCATTT 59.341 29.630 0.00 0.00 0.00 2.32
646 647 7.158021 TGTTTCCTTTTCGGCAATAAATCATT 58.842 30.769 0.00 0.00 0.00 2.57
647 648 6.696411 TGTTTCCTTTTCGGCAATAAATCAT 58.304 32.000 0.00 0.00 0.00 2.45
648 649 6.090483 TGTTTCCTTTTCGGCAATAAATCA 57.910 33.333 0.00 0.00 0.00 2.57
649 650 6.811170 TCATGTTTCCTTTTCGGCAATAAATC 59.189 34.615 0.00 0.00 0.00 2.17
650 651 6.696411 TCATGTTTCCTTTTCGGCAATAAAT 58.304 32.000 0.00 0.00 0.00 1.40
651 652 6.090483 TCATGTTTCCTTTTCGGCAATAAA 57.910 33.333 0.00 0.00 0.00 1.40
652 653 5.713792 TCATGTTTCCTTTTCGGCAATAA 57.286 34.783 0.00 0.00 0.00 1.40
653 654 5.913137 ATCATGTTTCCTTTTCGGCAATA 57.087 34.783 0.00 0.00 0.00 1.90
654 655 4.806640 ATCATGTTTCCTTTTCGGCAAT 57.193 36.364 0.00 0.00 0.00 3.56
655 656 4.038522 TGAATCATGTTTCCTTTTCGGCAA 59.961 37.500 12.81 0.00 0.00 4.52
656 657 3.571828 TGAATCATGTTTCCTTTTCGGCA 59.428 39.130 12.81 0.00 0.00 5.69
657 658 4.173036 TGAATCATGTTTCCTTTTCGGC 57.827 40.909 12.81 0.00 0.00 5.54
658 659 6.468956 CGTTATGAATCATGTTTCCTTTTCGG 59.531 38.462 12.81 0.00 0.00 4.30
659 660 7.240674 TCGTTATGAATCATGTTTCCTTTTCG 58.759 34.615 12.81 10.93 0.00 3.46
660 661 8.964420 TTCGTTATGAATCATGTTTCCTTTTC 57.036 30.769 12.81 1.67 0.00 2.29
661 662 9.191995 GTTTCGTTATGAATCATGTTTCCTTTT 57.808 29.630 12.81 0.61 36.22 2.27
662 663 8.356657 TGTTTCGTTATGAATCATGTTTCCTTT 58.643 29.630 12.81 2.64 36.22 3.11
663 664 7.881142 TGTTTCGTTATGAATCATGTTTCCTT 58.119 30.769 12.81 4.71 36.22 3.36
664 665 7.447374 TGTTTCGTTATGAATCATGTTTCCT 57.553 32.000 12.81 6.76 36.22 3.36
665 666 8.514136 TTTGTTTCGTTATGAATCATGTTTCC 57.486 30.769 12.81 0.00 36.45 3.13
666 667 8.155923 GCTTTGTTTCGTTATGAATCATGTTTC 58.844 33.333 5.91 9.21 36.45 2.78
667 668 7.116233 GGCTTTGTTTCGTTATGAATCATGTTT 59.884 33.333 5.91 0.00 36.45 2.83
668 669 6.586082 GGCTTTGTTTCGTTATGAATCATGTT 59.414 34.615 5.91 0.00 36.45 2.71
669 670 6.092748 GGCTTTGTTTCGTTATGAATCATGT 58.907 36.000 5.91 0.00 36.45 3.21
670 671 5.516339 GGGCTTTGTTTCGTTATGAATCATG 59.484 40.000 5.91 0.00 36.45 3.07
671 672 5.184864 TGGGCTTTGTTTCGTTATGAATCAT 59.815 36.000 0.00 0.00 36.45 2.45
672 673 4.520874 TGGGCTTTGTTTCGTTATGAATCA 59.479 37.500 0.00 0.00 36.22 2.57
673 674 5.054390 TGGGCTTTGTTTCGTTATGAATC 57.946 39.130 0.00 0.00 36.22 2.52
674 675 4.764823 TCTGGGCTTTGTTTCGTTATGAAT 59.235 37.500 0.00 0.00 36.22 2.57
675 676 4.023536 GTCTGGGCTTTGTTTCGTTATGAA 60.024 41.667 0.00 0.00 33.85 2.57
676 677 3.500680 GTCTGGGCTTTGTTTCGTTATGA 59.499 43.478 0.00 0.00 0.00 2.15
677 678 3.666902 CGTCTGGGCTTTGTTTCGTTATG 60.667 47.826 0.00 0.00 0.00 1.90
678 679 2.482721 CGTCTGGGCTTTGTTTCGTTAT 59.517 45.455 0.00 0.00 0.00 1.89
679 680 1.868498 CGTCTGGGCTTTGTTTCGTTA 59.132 47.619 0.00 0.00 0.00 3.18
680 681 0.661020 CGTCTGGGCTTTGTTTCGTT 59.339 50.000 0.00 0.00 0.00 3.85
681 682 1.164041 CCGTCTGGGCTTTGTTTCGT 61.164 55.000 0.00 0.00 0.00 3.85
682 683 1.164041 ACCGTCTGGGCTTTGTTTCG 61.164 55.000 0.00 0.00 40.62 3.46
683 684 0.591659 GACCGTCTGGGCTTTGTTTC 59.408 55.000 0.00 0.00 41.70 2.78
684 685 2.715536 GACCGTCTGGGCTTTGTTT 58.284 52.632 0.00 0.00 41.70 2.83
685 686 4.475527 GACCGTCTGGGCTTTGTT 57.524 55.556 0.00 0.00 41.70 2.83
700 701 1.812686 TATATGGACGCCGGCCAGAC 61.813 60.000 20.34 8.15 39.11 3.51
701 702 0.902984 ATATATGGACGCCGGCCAGA 60.903 55.000 20.34 15.28 39.11 3.86
702 703 0.740868 CATATATGGACGCCGGCCAG 60.741 60.000 20.34 10.83 39.11 4.85
703 704 1.295101 CATATATGGACGCCGGCCA 59.705 57.895 17.27 17.27 40.24 5.36
704 705 4.201951 CATATATGGACGCCGGCC 57.798 61.111 23.46 0.00 0.00 6.13
714 715 3.861341 CCTGACGGGCCCATATATG 57.139 57.895 24.92 6.57 0.00 1.78
733 734 3.783478 TATGGTCGTGGATGCGGCG 62.783 63.158 0.51 0.51 37.35 6.46
734 735 2.108157 TATGGTCGTGGATGCGGC 59.892 61.111 0.00 0.00 35.51 6.53
735 736 1.949133 CGTATGGTCGTGGATGCGG 60.949 63.158 0.00 0.00 0.00 5.69
736 737 0.526739 TTCGTATGGTCGTGGATGCG 60.527 55.000 0.00 0.00 0.00 4.73
737 738 0.928229 GTTCGTATGGTCGTGGATGC 59.072 55.000 0.00 0.00 0.00 3.91
738 739 1.136305 AGGTTCGTATGGTCGTGGATG 59.864 52.381 0.00 0.00 0.00 3.51
739 740 1.481871 AGGTTCGTATGGTCGTGGAT 58.518 50.000 0.00 0.00 0.00 3.41
740 741 1.203052 GAAGGTTCGTATGGTCGTGGA 59.797 52.381 0.00 0.00 0.00 4.02
741 742 1.636988 GAAGGTTCGTATGGTCGTGG 58.363 55.000 0.00 0.00 0.00 4.94
742 743 1.067425 TGGAAGGTTCGTATGGTCGTG 60.067 52.381 0.00 0.00 0.00 4.35
743 744 1.203994 CTGGAAGGTTCGTATGGTCGT 59.796 52.381 0.00 0.00 0.00 4.34
744 745 1.475280 TCTGGAAGGTTCGTATGGTCG 59.525 52.381 0.00 0.00 0.00 4.79
745 746 2.496470 ACTCTGGAAGGTTCGTATGGTC 59.504 50.000 0.00 0.00 0.00 4.02
746 747 2.496470 GACTCTGGAAGGTTCGTATGGT 59.504 50.000 0.00 0.00 0.00 3.55
747 748 2.159085 GGACTCTGGAAGGTTCGTATGG 60.159 54.545 0.00 0.00 0.00 2.74
748 749 2.496070 TGGACTCTGGAAGGTTCGTATG 59.504 50.000 0.00 0.00 0.00 2.39
749 750 2.816411 TGGACTCTGGAAGGTTCGTAT 58.184 47.619 0.00 0.00 0.00 3.06
750 751 2.297698 TGGACTCTGGAAGGTTCGTA 57.702 50.000 0.00 0.00 0.00 3.43
751 752 1.645710 ATGGACTCTGGAAGGTTCGT 58.354 50.000 0.00 0.00 0.00 3.85
752 753 3.639094 AGATATGGACTCTGGAAGGTTCG 59.361 47.826 0.00 0.00 0.00 3.95
753 754 4.039852 GGAGATATGGACTCTGGAAGGTTC 59.960 50.000 0.00 0.00 35.10 3.62
754 755 3.970640 GGAGATATGGACTCTGGAAGGTT 59.029 47.826 0.00 0.00 35.10 3.50
755 756 3.582164 GGAGATATGGACTCTGGAAGGT 58.418 50.000 0.00 0.00 35.10 3.50
756 757 2.903135 GGGAGATATGGACTCTGGAAGG 59.097 54.545 0.00 0.00 35.10 3.46
757 758 3.581101 TGGGAGATATGGACTCTGGAAG 58.419 50.000 0.00 0.00 35.10 3.46
758 759 3.706389 TGGGAGATATGGACTCTGGAA 57.294 47.619 0.00 0.00 35.10 3.53
759 760 3.142787 TCATGGGAGATATGGACTCTGGA 59.857 47.826 0.00 0.00 35.10 3.86
760 761 3.514539 TCATGGGAGATATGGACTCTGG 58.485 50.000 0.00 0.00 35.10 3.86
761 762 5.758790 AATCATGGGAGATATGGACTCTG 57.241 43.478 0.00 0.00 35.10 3.35
762 763 9.566331 TTATTAATCATGGGAGATATGGACTCT 57.434 33.333 0.00 0.00 35.10 3.24
763 764 9.606631 GTTATTAATCATGGGAGATATGGACTC 57.393 37.037 0.00 0.00 0.00 3.36
764 765 8.552296 GGTTATTAATCATGGGAGATATGGACT 58.448 37.037 0.00 0.00 0.00 3.85
765 766 7.775561 GGGTTATTAATCATGGGAGATATGGAC 59.224 40.741 0.00 0.00 0.00 4.02
766 767 7.688534 AGGGTTATTAATCATGGGAGATATGGA 59.311 37.037 0.00 0.00 0.00 3.41
767 768 7.776969 CAGGGTTATTAATCATGGGAGATATGG 59.223 40.741 0.00 0.00 0.00 2.74
768 769 8.551440 TCAGGGTTATTAATCATGGGAGATATG 58.449 37.037 1.83 0.00 0.00 1.78
769 770 8.700145 TCAGGGTTATTAATCATGGGAGATAT 57.300 34.615 1.83 0.00 0.00 1.63
770 771 8.518720 TTCAGGGTTATTAATCATGGGAGATA 57.481 34.615 1.83 0.00 0.00 1.98
771 772 7.406620 TTCAGGGTTATTAATCATGGGAGAT 57.593 36.000 1.83 0.00 0.00 2.75
772 773 6.840090 TTCAGGGTTATTAATCATGGGAGA 57.160 37.500 1.83 0.00 0.00 3.71
773 774 7.779798 TCTTTTCAGGGTTATTAATCATGGGAG 59.220 37.037 1.83 0.00 0.00 4.30
774 775 7.647827 TCTTTTCAGGGTTATTAATCATGGGA 58.352 34.615 1.83 0.00 0.00 4.37
775 776 7.896383 TCTTTTCAGGGTTATTAATCATGGG 57.104 36.000 1.83 0.00 0.00 4.00
810 811 7.111139 CGATTCGCATTATTAATCACGGATAC 58.889 38.462 0.00 1.72 31.37 2.24
811 812 6.809689 ACGATTCGCATTATTAATCACGGATA 59.190 34.615 5.86 0.00 31.37 2.59
812 813 5.637810 ACGATTCGCATTATTAATCACGGAT 59.362 36.000 5.86 5.57 31.37 4.18
835 836 0.863799 GACGGGTTTCCTTGACGAAC 59.136 55.000 0.00 0.00 0.00 3.95
881 882 6.365970 TGAAAGGGCAATTTTAATAAGCCA 57.634 33.333 16.07 0.00 46.96 4.75
996 1010 4.431131 AACAGGGGAGCCATGCGG 62.431 66.667 0.00 0.00 39.09 5.69
998 1012 2.440980 GGAACAGGGGAGCCATGC 60.441 66.667 0.00 0.00 39.09 4.06
1153 1167 2.760385 GAGGAGGGTGGAGGTCGG 60.760 72.222 0.00 0.00 0.00 4.79
1154 1168 2.760385 GGAGGAGGGTGGAGGTCG 60.760 72.222 0.00 0.00 0.00 4.79
1155 1169 2.760385 CGGAGGAGGGTGGAGGTC 60.760 72.222 0.00 0.00 0.00 3.85
1187 1202 1.741528 TGTATGTCGACGAGCCTGTA 58.258 50.000 11.62 0.00 0.00 2.74
1192 1207 2.712969 GACGTTATGTATGTCGACGAGC 59.287 50.000 11.62 3.64 37.20 5.03
1215 1230 2.270205 CGGCACAGAGGGAAGCAT 59.730 61.111 0.00 0.00 0.00 3.79
1621 1636 1.089481 TTGCGAGCGATGGAATGTCC 61.089 55.000 0.00 0.00 36.96 4.02
1642 1657 2.022346 CACGCAGATCACGCATGC 59.978 61.111 7.91 7.91 36.60 4.06
1793 1814 2.100991 CTCGCGGCCATGAAAAGC 59.899 61.111 6.13 0.00 0.00 3.51
1805 1826 2.436646 AAATGGACCTGCCTCGCG 60.437 61.111 0.00 0.00 37.63 5.87
1861 1882 6.127054 CCACAACTTGGTCCTAGATGAGATAA 60.127 42.308 15.68 0.00 41.10 1.75
1890 1921 1.470051 GGCGATCCTCTCCTCTATCC 58.530 60.000 0.00 0.00 0.00 2.59
1943 1974 0.471022 TGCACCGGGGAGAGCATATA 60.471 55.000 8.67 0.00 31.05 0.86
1944 1975 1.766059 TGCACCGGGGAGAGCATAT 60.766 57.895 8.67 0.00 31.05 1.78
1965 1996 2.327940 GCAGCGTGCGTTGAGTTT 59.672 55.556 12.31 0.00 31.71 2.66
1984 2015 5.120053 GCAAGTTTGTTTACACTTTGCACTT 59.880 36.000 14.89 0.00 37.01 3.16
1985 2016 4.625311 GCAAGTTTGTTTACACTTTGCACT 59.375 37.500 14.89 0.00 37.01 4.40
1986 2017 4.387256 TGCAAGTTTGTTTACACTTTGCAC 59.613 37.500 16.99 0.72 39.52 4.57
1987 2018 4.560128 TGCAAGTTTGTTTACACTTTGCA 58.440 34.783 16.99 16.99 40.80 4.08
1988 2019 5.717038 ATGCAAGTTTGTTTACACTTTGC 57.283 34.783 13.73 13.73 37.28 3.68
1989 2020 7.737395 TGAAATGCAAGTTTGTTTACACTTTG 58.263 30.769 0.00 0.00 30.48 2.77
1990 2021 7.897575 TGAAATGCAAGTTTGTTTACACTTT 57.102 28.000 0.00 0.00 30.48 2.66
1991 2022 7.897575 TTGAAATGCAAGTTTGTTTACACTT 57.102 28.000 0.00 0.00 33.29 3.16
1992 2023 7.981225 AGATTGAAATGCAAGTTTGTTTACACT 59.019 29.630 0.00 0.00 40.42 3.55
1993 2024 8.130307 AGATTGAAATGCAAGTTTGTTTACAC 57.870 30.769 0.00 0.00 40.42 2.90
1994 2025 8.602328 CAAGATTGAAATGCAAGTTTGTTTACA 58.398 29.630 0.00 0.00 40.42 2.41
1995 2026 8.603181 ACAAGATTGAAATGCAAGTTTGTTTAC 58.397 29.630 0.00 0.00 40.81 2.01
1996 2027 8.715191 ACAAGATTGAAATGCAAGTTTGTTTA 57.285 26.923 0.00 0.00 40.81 2.01
1997 2028 7.614124 ACAAGATTGAAATGCAAGTTTGTTT 57.386 28.000 0.00 0.00 40.81 2.83
1998 2029 7.614124 AACAAGATTGAAATGCAAGTTTGTT 57.386 28.000 10.84 10.84 43.96 2.83
1999 2030 7.201635 GGAAACAAGATTGAAATGCAAGTTTGT 60.202 33.333 0.00 1.42 43.18 2.83
2000 2031 7.127686 GGAAACAAGATTGAAATGCAAGTTTG 58.872 34.615 0.00 0.00 40.42 2.93
2001 2032 6.018832 CGGAAACAAGATTGAAATGCAAGTTT 60.019 34.615 0.00 0.00 40.42 2.66
2002 2033 5.463061 CGGAAACAAGATTGAAATGCAAGTT 59.537 36.000 0.00 0.00 40.42 2.66
2003 2034 4.984161 CGGAAACAAGATTGAAATGCAAGT 59.016 37.500 0.00 0.00 40.42 3.16
2004 2035 5.221880 TCGGAAACAAGATTGAAATGCAAG 58.778 37.500 0.00 0.00 40.42 4.01
2005 2036 5.193663 TCGGAAACAAGATTGAAATGCAA 57.806 34.783 0.00 0.00 41.53 4.08
2006 2037 4.844998 TCGGAAACAAGATTGAAATGCA 57.155 36.364 0.00 0.00 0.00 3.96
2007 2038 5.117592 CAGTTCGGAAACAAGATTGAAATGC 59.882 40.000 0.00 0.00 37.88 3.56
2008 2039 5.117592 GCAGTTCGGAAACAAGATTGAAATG 59.882 40.000 0.00 0.00 37.88 2.32
2009 2040 5.221224 TGCAGTTCGGAAACAAGATTGAAAT 60.221 36.000 0.00 0.00 37.88 2.17
2017 2048 3.354089 ACATTGCAGTTCGGAAACAAG 57.646 42.857 0.00 0.00 37.88 3.16
2021 2052 1.339610 CCCAACATTGCAGTTCGGAAA 59.660 47.619 0.00 0.00 32.28 3.13
2025 2056 1.659233 TGCCCAACATTGCAGTTCG 59.341 52.632 0.00 0.00 32.77 3.95
2246 2277 7.678947 ATGAAATATGTATGCAGCTAGGAAC 57.321 36.000 0.00 0.00 0.00 3.62
2260 2291 8.281531 TCATAGGTTGGGAAGAATGAAATATGT 58.718 33.333 0.00 0.00 0.00 2.29
2266 2297 5.779241 AGTCATAGGTTGGGAAGAATGAA 57.221 39.130 0.00 0.00 0.00 2.57
2320 2351 2.250939 CGTCTTTGGGCTGCAACGA 61.251 57.895 0.50 0.00 32.17 3.85
2362 2393 3.676873 CGTTTATTACCTGCGTACCCACT 60.677 47.826 0.00 0.00 0.00 4.00
2382 2413 0.944386 GCATGGTCAAGTGTTCACGT 59.056 50.000 0.00 0.00 0.00 4.49
2387 2418 3.012518 GCTATCTGCATGGTCAAGTGTT 58.987 45.455 0.00 0.00 42.31 3.32
2395 2426 5.090139 AGATACTAAGGCTATCTGCATGGT 58.910 41.667 0.00 0.00 45.15 3.55
2408 2439 4.979197 GCGTCACATCAAGAGATACTAAGG 59.021 45.833 0.00 0.00 31.88 2.69
2440 2474 7.682021 GCAAAAGAAATCAGTACTCCAAAGTGT 60.682 37.037 0.00 0.00 36.92 3.55
2502 2536 1.676967 GGGGTGCAGGCTGAAGAAG 60.677 63.158 20.86 0.00 0.00 2.85
2694 2728 3.423154 GGGTTCTTGGCGCACTCG 61.423 66.667 10.83 0.00 39.07 4.18
2776 2810 7.448748 ACAATTTCCAAATCTACAGTGTACC 57.551 36.000 0.00 0.00 0.00 3.34
2782 2816 7.546358 TGCCATTACAATTTCCAAATCTACAG 58.454 34.615 0.00 0.00 0.00 2.74
2879 2913 3.885484 ATGATTTGTTGATCGATCGGC 57.115 42.857 20.03 14.99 0.00 5.54
2880 2914 5.160699 ACAATGATTTGTTGATCGATCGG 57.839 39.130 20.03 0.00 43.57 4.18
2882 2916 5.200454 CGGACAATGATTTGTTGATCGATC 58.800 41.667 18.72 18.72 46.01 3.69
2885 2919 3.487376 CCCGGACAATGATTTGTTGATCG 60.487 47.826 0.73 0.00 46.01 3.69
2907 2941 0.725784 CGTGAACGTGATTGCCTTGC 60.726 55.000 0.00 0.00 34.11 4.01
2970 3012 1.978580 ACCAGGAAGGACAAGTACCTG 59.021 52.381 0.00 0.00 45.09 4.00
3029 3071 2.425592 CCAACCACGTGCAGAGGA 59.574 61.111 10.91 0.00 34.46 3.71
3125 3167 4.776322 TCATGAACCCGCGGCTGG 62.776 66.667 22.85 9.35 0.00 4.85
3127 3169 2.436646 CTTCATGAACCCGCGGCT 60.437 61.111 22.85 9.05 0.00 5.52
3579 3621 2.283101 TACCACGTGTACCGGGCT 60.283 61.111 15.65 0.00 39.18 5.19


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

AutoCloner maintained by Alex Coulton.