Multiple sequence alignment - TraesCS2A01G124300

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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 TraesCS2A01G124300 chr2A 100.000 3300 0 0 1 3300 73202137 73198838 0.000000e+00 6095
1 TraesCS2A01G124300 chr2A 97.458 118 3 0 1 118 382780000 382779883 5.580000e-48 202
2 TraesCS2A01G124300 chr2B 94.328 2521 90 28 801 3300 111690448 111687960 0.000000e+00 3814
3 TraesCS2A01G124300 chr2D 93.158 2543 102 24 792 3300 73855449 73852945 0.000000e+00 3666
4 TraesCS2A01G124300 chr2D 89.823 678 67 2 108 785 122707793 122708468 0.000000e+00 869
5 TraesCS2A01G124300 chr1D 89.282 905 54 17 1086 1968 404760036 404759153 0.000000e+00 1094
6 TraesCS2A01G124300 chr5D 93.088 680 44 3 108 786 416078282 416078959 0.000000e+00 992
7 TraesCS2A01G124300 chr5A 86.736 671 87 2 112 781 291179536 291180205 0.000000e+00 745
8 TraesCS2A01G124300 chr5A 97.458 118 3 0 1 118 144610208 144610091 5.580000e-48 202
9 TraesCS2A01G124300 chr3A 86.391 676 88 3 108 781 33447425 33448098 0.000000e+00 736
10 TraesCS2A01G124300 chr3A 97.458 118 3 0 1 118 393347492 393347609 5.580000e-48 202
11 TraesCS2A01G124300 chr1A 85.714 686 87 7 108 787 31132623 31131943 0.000000e+00 713
12 TraesCS2A01G124300 chr1A 100.000 110 0 0 1 110 35913266 35913157 1.550000e-48 204
13 TraesCS2A01G124300 chr1A 100.000 110 0 0 1 110 52192492 52192601 1.550000e-48 204
14 TraesCS2A01G124300 chr1A 97.458 118 3 0 1 118 72653930 72653813 5.580000e-48 202
15 TraesCS2A01G124300 chr4A 85.609 681 92 4 108 785 37291511 37292188 0.000000e+00 710
16 TraesCS2A01G124300 chr7A 92.941 340 24 0 448 787 699035903 699036242 2.290000e-136 496
17 TraesCS2A01G124300 chr7A 98.305 118 2 0 1 118 548284460 548284577 1.200000e-49 207
18 TraesCS2A01G124300 chr7A 97.458 118 3 0 1 118 391065990 391065873 5.580000e-48 202
19 TraesCS2A01G124300 chr7A 99.091 110 1 0 1 110 195300221 195300330 7.220000e-47 198
20 TraesCS2A01G124300 chr6D 80.000 635 123 3 108 740 163934864 163934232 1.790000e-127 466


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 TraesCS2A01G124300 chr2A 73198838 73202137 3299 True 6095 6095 100.000 1 3300 1 chr2A.!!$R1 3299
1 TraesCS2A01G124300 chr2B 111687960 111690448 2488 True 3814 3814 94.328 801 3300 1 chr2B.!!$R1 2499
2 TraesCS2A01G124300 chr2D 73852945 73855449 2504 True 3666 3666 93.158 792 3300 1 chr2D.!!$R1 2508
3 TraesCS2A01G124300 chr2D 122707793 122708468 675 False 869 869 89.823 108 785 1 chr2D.!!$F1 677
4 TraesCS2A01G124300 chr1D 404759153 404760036 883 True 1094 1094 89.282 1086 1968 1 chr1D.!!$R1 882
5 TraesCS2A01G124300 chr5D 416078282 416078959 677 False 992 992 93.088 108 786 1 chr5D.!!$F1 678
6 TraesCS2A01G124300 chr5A 291179536 291180205 669 False 745 745 86.736 112 781 1 chr5A.!!$F1 669
7 TraesCS2A01G124300 chr3A 33447425 33448098 673 False 736 736 86.391 108 781 1 chr3A.!!$F1 673
8 TraesCS2A01G124300 chr1A 31131943 31132623 680 True 713 713 85.714 108 787 1 chr1A.!!$R1 679
9 TraesCS2A01G124300 chr4A 37291511 37292188 677 False 710 710 85.609 108 785 1 chr4A.!!$F1 677
10 TraesCS2A01G124300 chr6D 163934232 163934864 632 True 466 466 80.000 108 740 1 chr6D.!!$R1 632

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
874 879 0.106708 AGAAGAAACCGCACTCAGCA 59.893 50.0 0.0 0.0 46.13 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2486 2543 1.665679 AGCAATTACAGGATTCGCACG 59.334 47.619 0.0 0.0 0.0 5.34 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
20 21 2.924903 TGTAGTCGACGTTCACATGAC 58.075 47.619 10.46 0.00 0.00 3.06
21 22 2.291190 TGTAGTCGACGTTCACATGACA 59.709 45.455 10.46 2.13 32.08 3.58
22 23 1.767289 AGTCGACGTTCACATGACAC 58.233 50.000 10.46 0.00 32.08 3.67
23 24 0.782384 GTCGACGTTCACATGACACC 59.218 55.000 0.00 0.00 0.00 4.16
24 25 0.386113 TCGACGTTCACATGACACCA 59.614 50.000 0.00 0.00 0.00 4.17
25 26 0.506932 CGACGTTCACATGACACCAC 59.493 55.000 0.00 0.00 0.00 4.16
26 27 1.865865 GACGTTCACATGACACCACT 58.134 50.000 0.00 0.00 0.00 4.00
27 28 2.606065 CGACGTTCACATGACACCACTA 60.606 50.000 0.00 0.00 0.00 2.74
28 29 2.987149 GACGTTCACATGACACCACTAG 59.013 50.000 0.00 0.00 0.00 2.57
29 30 2.626266 ACGTTCACATGACACCACTAGA 59.374 45.455 0.00 0.00 0.00 2.43
30 31 3.245797 CGTTCACATGACACCACTAGAG 58.754 50.000 0.00 0.00 0.00 2.43
31 32 3.589988 GTTCACATGACACCACTAGAGG 58.410 50.000 4.44 4.44 0.00 3.69
32 33 2.179427 TCACATGACACCACTAGAGGG 58.821 52.381 11.20 7.36 0.00 4.30
33 34 2.179427 CACATGACACCACTAGAGGGA 58.821 52.381 11.20 0.00 0.00 4.20
34 35 2.768527 CACATGACACCACTAGAGGGAT 59.231 50.000 11.20 0.00 0.00 3.85
35 36 2.768527 ACATGACACCACTAGAGGGATG 59.231 50.000 11.20 9.05 0.00 3.51
36 37 2.919772 TGACACCACTAGAGGGATGA 57.080 50.000 11.20 0.00 0.00 2.92
37 38 2.457598 TGACACCACTAGAGGGATGAC 58.542 52.381 11.20 2.30 0.00 3.06
38 39 2.225267 TGACACCACTAGAGGGATGACA 60.225 50.000 11.20 4.78 0.00 3.58
39 40 2.832129 GACACCACTAGAGGGATGACAA 59.168 50.000 11.20 0.00 0.00 3.18
40 41 2.567615 ACACCACTAGAGGGATGACAAC 59.432 50.000 11.20 0.00 0.00 3.32
41 42 2.567169 CACCACTAGAGGGATGACAACA 59.433 50.000 11.20 0.00 0.00 3.33
42 43 3.198635 CACCACTAGAGGGATGACAACAT 59.801 47.826 11.20 0.00 39.67 2.71
43 44 4.405680 CACCACTAGAGGGATGACAACATA 59.594 45.833 11.20 0.00 36.82 2.29
44 45 4.406003 ACCACTAGAGGGATGACAACATAC 59.594 45.833 11.20 0.00 36.82 2.39
45 46 4.405680 CCACTAGAGGGATGACAACATACA 59.594 45.833 0.00 0.00 38.99 2.29
46 47 5.070981 CCACTAGAGGGATGACAACATACAT 59.929 44.000 0.00 0.00 38.99 2.29
47 48 6.219473 CACTAGAGGGATGACAACATACATC 58.781 44.000 0.00 0.00 45.23 3.06
50 51 5.282055 GAGGGATGACAACATACATCTCA 57.718 43.478 0.00 0.00 42.66 3.27
51 52 5.862845 GAGGGATGACAACATACATCTCAT 58.137 41.667 0.00 0.00 42.66 2.90
52 53 5.862845 AGGGATGACAACATACATCTCATC 58.137 41.667 0.00 0.00 43.84 2.92
53 54 5.367644 AGGGATGACAACATACATCTCATCA 59.632 40.000 0.00 0.00 43.84 3.07
54 55 6.057533 GGGATGACAACATACATCTCATCAA 58.942 40.000 0.00 0.00 41.82 2.57
55 56 6.543465 GGGATGACAACATACATCTCATCAAA 59.457 38.462 0.00 0.00 41.82 2.69
56 57 7.067372 GGGATGACAACATACATCTCATCAAAA 59.933 37.037 0.00 0.00 41.82 2.44
57 58 8.627403 GGATGACAACATACATCTCATCAAAAT 58.373 33.333 0.00 0.00 41.50 1.82
61 62 9.803130 GACAACATACATCTCATCAAAATATCG 57.197 33.333 0.00 0.00 0.00 2.92
62 63 9.546428 ACAACATACATCTCATCAAAATATCGA 57.454 29.630 0.00 0.00 0.00 3.59
65 66 8.703336 ACATACATCTCATCAAAATATCGAACG 58.297 33.333 0.00 0.00 0.00 3.95
66 67 8.915654 CATACATCTCATCAAAATATCGAACGA 58.084 33.333 0.00 0.00 0.00 3.85
67 68 7.770801 ACATCTCATCAAAATATCGAACGAA 57.229 32.000 0.12 0.00 0.00 3.85
68 69 8.370493 ACATCTCATCAAAATATCGAACGAAT 57.630 30.769 0.12 0.00 0.00 3.34
69 70 9.476202 ACATCTCATCAAAATATCGAACGAATA 57.524 29.630 0.12 0.00 0.00 1.75
70 71 9.732893 CATCTCATCAAAATATCGAACGAATAC 57.267 33.333 0.12 0.00 0.00 1.89
71 72 8.294341 TCTCATCAAAATATCGAACGAATACC 57.706 34.615 0.12 0.00 0.00 2.73
72 73 7.923878 TCTCATCAAAATATCGAACGAATACCA 59.076 33.333 0.12 0.00 0.00 3.25
73 74 8.426881 TCATCAAAATATCGAACGAATACCAA 57.573 30.769 0.12 0.00 0.00 3.67
74 75 8.884726 TCATCAAAATATCGAACGAATACCAAA 58.115 29.630 0.12 0.00 0.00 3.28
75 76 9.663904 CATCAAAATATCGAACGAATACCAAAT 57.336 29.630 0.12 0.00 0.00 2.32
77 78 9.710979 TCAAAATATCGAACGAATACCAAATTC 57.289 29.630 0.12 0.00 0.00 2.17
78 79 9.497030 CAAAATATCGAACGAATACCAAATTCA 57.503 29.630 0.12 0.00 0.00 2.57
79 80 9.498307 AAAATATCGAACGAATACCAAATTCAC 57.502 29.630 0.12 0.00 0.00 3.18
80 81 7.780008 ATATCGAACGAATACCAAATTCACA 57.220 32.000 0.12 0.00 0.00 3.58
81 82 6.677781 ATCGAACGAATACCAAATTCACAT 57.322 33.333 0.12 0.00 0.00 3.21
82 83 5.863898 TCGAACGAATACCAAATTCACATG 58.136 37.500 0.00 0.00 0.00 3.21
83 84 5.639931 TCGAACGAATACCAAATTCACATGA 59.360 36.000 0.00 0.00 0.00 3.07
84 85 5.732647 CGAACGAATACCAAATTCACATGAC 59.267 40.000 0.00 0.00 0.00 3.06
85 86 6.402118 CGAACGAATACCAAATTCACATGACT 60.402 38.462 0.00 0.00 0.00 3.41
86 87 7.201487 CGAACGAATACCAAATTCACATGACTA 60.201 37.037 0.00 0.00 0.00 2.59
87 88 7.303634 ACGAATACCAAATTCACATGACTAC 57.696 36.000 0.00 0.00 0.00 2.73
88 89 7.103641 ACGAATACCAAATTCACATGACTACT 58.896 34.615 0.00 0.00 0.00 2.57
89 90 7.606456 ACGAATACCAAATTCACATGACTACTT 59.394 33.333 0.00 0.00 0.00 2.24
90 91 9.093970 CGAATACCAAATTCACATGACTACTTA 57.906 33.333 0.00 0.00 0.00 2.24
94 95 8.438676 ACCAAATTCACATGACTACTTATAGC 57.561 34.615 0.00 0.00 30.75 2.97
95 96 8.046708 ACCAAATTCACATGACTACTTATAGCA 58.953 33.333 0.00 0.00 30.75 3.49
96 97 8.892723 CCAAATTCACATGACTACTTATAGCAA 58.107 33.333 0.00 0.00 30.75 3.91
97 98 9.926751 CAAATTCACATGACTACTTATAGCAAG 57.073 33.333 0.00 0.00 30.75 4.01
98 99 9.890629 AAATTCACATGACTACTTATAGCAAGA 57.109 29.630 0.00 0.00 30.75 3.02
99 100 8.879342 ATTCACATGACTACTTATAGCAAGAC 57.121 34.615 0.00 0.00 30.75 3.01
100 101 7.646548 TCACATGACTACTTATAGCAAGACT 57.353 36.000 0.00 0.00 30.75 3.24
101 102 8.067751 TCACATGACTACTTATAGCAAGACTT 57.932 34.615 0.00 0.00 30.75 3.01
102 103 8.191446 TCACATGACTACTTATAGCAAGACTTC 58.809 37.037 0.00 0.00 30.75 3.01
103 104 8.194104 CACATGACTACTTATAGCAAGACTTCT 58.806 37.037 0.00 0.00 30.75 2.85
104 105 8.410141 ACATGACTACTTATAGCAAGACTTCTC 58.590 37.037 0.00 0.00 30.75 2.87
105 106 7.336161 TGACTACTTATAGCAAGACTTCTCC 57.664 40.000 0.00 0.00 30.75 3.71
106 107 6.321690 TGACTACTTATAGCAAGACTTCTCCC 59.678 42.308 0.00 0.00 30.75 4.30
136 137 5.448654 TCTGGTTAGCAAGGAATAATGCAT 58.551 37.500 0.00 0.00 0.00 3.96
144 145 4.798263 GCAAGGAATAATGCATGTGATGGG 60.798 45.833 0.00 0.00 0.00 4.00
203 204 5.402630 AGTTGTCAACTTAATGGGGGAATT 58.597 37.500 12.62 0.00 39.04 2.17
237 238 3.607741 TGGTCGGAAACACAAACTAACA 58.392 40.909 0.00 0.00 0.00 2.41
298 299 3.492337 GGGTGGGTGAAAGTCAATGTAA 58.508 45.455 0.00 0.00 0.00 2.41
310 311 3.871594 AGTCAATGTAAATGGAGCTACGC 59.128 43.478 0.00 0.00 0.00 4.42
374 375 1.339920 CCATGTGGGCGCATATATGGA 60.340 52.381 26.44 2.79 37.79 3.41
404 405 3.833650 TGTCATTTCCTTCCAATGTGCAT 59.166 39.130 0.00 0.00 33.91 3.96
424 425 0.532862 CAACCCAGCGACAGTTGAGT 60.533 55.000 6.20 0.00 42.76 3.41
427 428 1.623811 ACCCAGCGACAGTTGAGTTAT 59.376 47.619 0.00 0.00 0.00 1.89
435 436 3.412386 GACAGTTGAGTTATGGGCTTGT 58.588 45.455 0.00 0.00 0.00 3.16
470 471 3.124560 GTCTGGCGGAAGAGCTAAATAC 58.875 50.000 0.00 0.00 37.29 1.89
576 577 0.976641 TCGTGGAGGAAGTCAAGCAT 59.023 50.000 0.00 0.00 0.00 3.79
735 736 2.346803 CATGTGGTTTCGGACGAGATT 58.653 47.619 0.00 0.00 0.00 2.40
799 803 5.717038 AAAAGAAAAACGAAGCATGGTTG 57.283 34.783 16.18 9.89 0.00 3.77
814 818 2.166829 TGGTTGCGGATTTTGTAGCAT 58.833 42.857 0.00 0.00 39.50 3.79
817 821 3.179048 GTTGCGGATTTTGTAGCATTCC 58.821 45.455 0.00 0.00 39.50 3.01
826 830 6.367422 GGATTTTGTAGCATTCCGAGATAGAG 59.633 42.308 0.00 0.00 0.00 2.43
874 879 0.106708 AGAAGAAACCGCACTCAGCA 59.893 50.000 0.00 0.00 46.13 4.41
875 880 0.514691 GAAGAAACCGCACTCAGCAG 59.485 55.000 0.00 0.00 46.13 4.24
876 881 1.510480 AAGAAACCGCACTCAGCAGC 61.510 55.000 0.00 0.00 46.13 5.25
877 882 1.963338 GAAACCGCACTCAGCAGCT 60.963 57.895 0.00 0.00 46.13 4.24
931 936 1.219124 CATCTAGCCACACTGCGGT 59.781 57.895 0.00 0.00 36.02 5.68
1134 1149 4.851214 AGGCGGCTCCTCTCCTCC 62.851 72.222 5.25 0.00 43.20 4.30
1233 1248 5.774690 TCTGGATGAAAACTTTGGTGCTTAT 59.225 36.000 0.00 0.00 0.00 1.73
1234 1249 6.267471 TCTGGATGAAAACTTTGGTGCTTATT 59.733 34.615 0.00 0.00 0.00 1.40
1235 1250 7.450014 TCTGGATGAAAACTTTGGTGCTTATTA 59.550 33.333 0.00 0.00 0.00 0.98
1245 1261 1.061566 GGTGCTTATTACGTTGCGGTC 59.938 52.381 0.00 0.00 0.00 4.79
1424 1440 6.594788 ACTGTTCCTGCAATGTTTGATTAT 57.405 33.333 0.00 0.00 0.00 1.28
1434 1453 8.800370 TGCAATGTTTGATTATACTTCACCTA 57.200 30.769 0.00 0.00 0.00 3.08
1435 1454 9.407380 TGCAATGTTTGATTATACTTCACCTAT 57.593 29.630 0.00 0.00 0.00 2.57
1436 1455 9.669353 GCAATGTTTGATTATACTTCACCTATG 57.331 33.333 0.00 0.00 0.00 2.23
1475 1494 6.073276 TGTTCGTATATGTGCTATTTGCCATC 60.073 38.462 0.00 0.00 42.00 3.51
1496 1516 3.258372 TCGAGAGTGGTCTGTATTTGCTT 59.742 43.478 0.00 0.00 30.97 3.91
1521 1541 0.105964 CCACCGAAGTCCAAGTCACA 59.894 55.000 0.00 0.00 0.00 3.58
1539 1559 5.121768 AGTCACAGCCGTTCATTTGTAATAC 59.878 40.000 0.00 0.00 0.00 1.89
1571 1592 3.737559 TGCATGGGTAAAAGAGACCAT 57.262 42.857 0.00 0.00 44.17 3.55
1711 1762 4.373156 ACCTCCCATGCATAAATAGGAC 57.627 45.455 18.39 0.00 0.00 3.85
1712 1763 3.983410 ACCTCCCATGCATAAATAGGACT 59.017 43.478 18.39 0.68 0.00 3.85
1713 1764 5.162637 ACCTCCCATGCATAAATAGGACTA 58.837 41.667 18.39 0.00 0.00 2.59
1714 1765 5.792712 ACCTCCCATGCATAAATAGGACTAT 59.207 40.000 18.39 0.00 0.00 2.12
1715 1766 6.965866 ACCTCCCATGCATAAATAGGACTATA 59.034 38.462 18.39 0.00 0.00 1.31
1716 1767 7.126421 ACCTCCCATGCATAAATAGGACTATAG 59.874 40.741 18.39 0.00 0.00 1.31
1717 1768 7.419518 CCTCCCATGCATAAATAGGACTATAGG 60.420 44.444 0.00 0.00 0.00 2.57
1718 1769 7.196187 TCCCATGCATAAATAGGACTATAGGA 58.804 38.462 0.00 0.00 0.00 2.94
1726 1777 5.476091 AATAGGACTATAGGAGCTGCAAC 57.524 43.478 8.35 0.00 0.00 4.17
1909 1961 3.023119 TGGTTGCACTTTCTGACAACAT 58.977 40.909 9.40 0.00 43.23 2.71
2020 2075 6.288294 TCTACTGTTGCAAGACATGTTACTT 58.712 36.000 0.00 0.00 0.00 2.24
2037 2092 3.863142 ACTTGAAGCTGCCATGATTTC 57.137 42.857 0.00 0.00 0.00 2.17
2114 2170 4.320494 GGTTGTAATTGTTGACTGCTGGAG 60.320 45.833 0.00 0.00 0.00 3.86
2116 2172 1.251251 AATTGTTGACTGCTGGAGCC 58.749 50.000 0.00 0.00 41.18 4.70
2125 2181 2.034687 GCTGGAGCCTGCCAAAGA 59.965 61.111 7.10 0.00 37.52 2.52
2203 2259 4.869861 GTGTTTTGATGGTTTGCTTCTGTT 59.130 37.500 0.00 0.00 0.00 3.16
2391 2448 6.116806 AGTAGGAGTAGTATCCATGATAGCG 58.883 44.000 0.00 0.00 42.26 4.26
2984 3043 8.856247 GTTTATTTTCGCCAGTAACTTTTATGG 58.144 33.333 0.00 0.00 35.84 2.74
3213 3272 3.608073 GTGGCGTGCAAGAAATAATGTTC 59.392 43.478 2.99 0.00 0.00 3.18
3221 3280 7.201291 CGTGCAAGAAATAATGTTCAGTTCATG 60.201 37.037 0.00 0.00 0.00 3.07
3242 3301 1.202952 TCTGGGGCCGTATTGTTTTGT 60.203 47.619 0.00 0.00 0.00 2.83
3250 3309 5.333721 GGGCCGTATTGTTTTGTCATTTTTG 60.334 40.000 0.00 0.00 0.00 2.44
3252 3311 6.351749 GCCGTATTGTTTTGTCATTTTTGTC 58.648 36.000 0.00 0.00 0.00 3.18
3253 3312 6.200097 GCCGTATTGTTTTGTCATTTTTGTCT 59.800 34.615 0.00 0.00 0.00 3.41
3255 3314 8.055402 CCGTATTGTTTTGTCATTTTTGTCTTG 58.945 33.333 0.00 0.00 0.00 3.02
3256 3315 8.802856 CGTATTGTTTTGTCATTTTTGTCTTGA 58.197 29.630 0.00 0.00 0.00 3.02
3264 3326 5.063691 TGTCATTTTTGTCTTGACGTTACGT 59.936 36.000 11.12 11.12 45.10 3.57
3278 3342 7.704991 TGACGTTACGTTATAACTTTAGTCG 57.295 36.000 12.82 11.78 41.37 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.291190 TGTCATGTGAACGTCGACTACA 59.709 45.455 14.70 13.11 0.00 2.74
1 2 2.655474 GTGTCATGTGAACGTCGACTAC 59.345 50.000 14.70 7.93 0.00 2.73
2 3 2.351060 GGTGTCATGTGAACGTCGACTA 60.351 50.000 14.70 0.00 0.00 2.59
3 4 1.602165 GGTGTCATGTGAACGTCGACT 60.602 52.381 14.70 0.00 0.00 4.18
4 5 0.782384 GGTGTCATGTGAACGTCGAC 59.218 55.000 5.18 5.18 0.00 4.20
5 6 0.386113 TGGTGTCATGTGAACGTCGA 59.614 50.000 0.00 0.00 0.00 4.20
6 7 0.506932 GTGGTGTCATGTGAACGTCG 59.493 55.000 0.00 0.00 0.00 5.12
7 8 1.865865 AGTGGTGTCATGTGAACGTC 58.134 50.000 0.00 0.00 0.00 4.34
8 9 2.626266 TCTAGTGGTGTCATGTGAACGT 59.374 45.455 0.00 0.00 0.00 3.99
9 10 3.245797 CTCTAGTGGTGTCATGTGAACG 58.754 50.000 0.00 0.00 0.00 3.95
10 11 3.589988 CCTCTAGTGGTGTCATGTGAAC 58.410 50.000 2.47 0.00 0.00 3.18
11 12 2.567169 CCCTCTAGTGGTGTCATGTGAA 59.433 50.000 9.90 0.00 0.00 3.18
12 13 2.179427 CCCTCTAGTGGTGTCATGTGA 58.821 52.381 9.90 0.00 0.00 3.58
13 14 2.179427 TCCCTCTAGTGGTGTCATGTG 58.821 52.381 9.90 0.00 0.00 3.21
14 15 2.623418 TCCCTCTAGTGGTGTCATGT 57.377 50.000 9.90 0.00 0.00 3.21
15 16 3.033909 TCATCCCTCTAGTGGTGTCATG 58.966 50.000 9.90 6.55 0.00 3.07
16 17 3.034635 GTCATCCCTCTAGTGGTGTCAT 58.965 50.000 9.90 0.00 0.00 3.06
17 18 2.225267 TGTCATCCCTCTAGTGGTGTCA 60.225 50.000 9.90 4.18 0.00 3.58
18 19 2.457598 TGTCATCCCTCTAGTGGTGTC 58.542 52.381 9.90 1.84 0.00 3.67
19 20 2.567615 GTTGTCATCCCTCTAGTGGTGT 59.432 50.000 9.90 0.00 0.00 4.16
20 21 2.567169 TGTTGTCATCCCTCTAGTGGTG 59.433 50.000 9.90 2.99 0.00 4.17
21 22 2.902608 TGTTGTCATCCCTCTAGTGGT 58.097 47.619 9.90 0.00 0.00 4.16
22 23 4.405680 TGTATGTTGTCATCCCTCTAGTGG 59.594 45.833 3.70 3.70 35.70 4.00
23 24 5.598416 TGTATGTTGTCATCCCTCTAGTG 57.402 43.478 0.00 0.00 35.70 2.74
24 25 6.139671 AGATGTATGTTGTCATCCCTCTAGT 58.860 40.000 0.00 0.00 40.63 2.57
25 26 6.266330 TGAGATGTATGTTGTCATCCCTCTAG 59.734 42.308 0.00 0.00 40.63 2.43
26 27 6.136155 TGAGATGTATGTTGTCATCCCTCTA 58.864 40.000 0.00 0.00 40.63 2.43
27 28 4.964897 TGAGATGTATGTTGTCATCCCTCT 59.035 41.667 0.00 0.00 40.63 3.69
28 29 5.282055 TGAGATGTATGTTGTCATCCCTC 57.718 43.478 0.00 0.00 40.63 4.30
29 30 5.367644 TGATGAGATGTATGTTGTCATCCCT 59.632 40.000 7.88 0.00 41.86 4.20
30 31 5.614308 TGATGAGATGTATGTTGTCATCCC 58.386 41.667 7.88 0.00 41.86 3.85
31 32 7.558161 TTTGATGAGATGTATGTTGTCATCC 57.442 36.000 7.88 0.00 41.86 3.51
35 36 9.803130 CGATATTTTGATGAGATGTATGTTGTC 57.197 33.333 0.00 0.00 0.00 3.18
36 37 9.546428 TCGATATTTTGATGAGATGTATGTTGT 57.454 29.630 0.00 0.00 0.00 3.32
39 40 8.703336 CGTTCGATATTTTGATGAGATGTATGT 58.297 33.333 0.00 0.00 0.00 2.29
40 41 8.915654 TCGTTCGATATTTTGATGAGATGTATG 58.084 33.333 0.00 0.00 0.00 2.39
41 42 9.476202 TTCGTTCGATATTTTGATGAGATGTAT 57.524 29.630 0.00 0.00 0.00 2.29
42 43 8.865590 TTCGTTCGATATTTTGATGAGATGTA 57.134 30.769 0.00 0.00 0.00 2.29
43 44 7.770801 TTCGTTCGATATTTTGATGAGATGT 57.229 32.000 0.00 0.00 0.00 3.06
44 45 9.732893 GTATTCGTTCGATATTTTGATGAGATG 57.267 33.333 0.00 0.00 0.00 2.90
45 46 8.926710 GGTATTCGTTCGATATTTTGATGAGAT 58.073 33.333 0.00 0.00 0.00 2.75
46 47 7.923878 TGGTATTCGTTCGATATTTTGATGAGA 59.076 33.333 0.00 0.00 0.00 3.27
47 48 8.072238 TGGTATTCGTTCGATATTTTGATGAG 57.928 34.615 0.00 0.00 0.00 2.90
48 49 8.426881 TTGGTATTCGTTCGATATTTTGATGA 57.573 30.769 0.00 0.00 0.00 2.92
49 50 9.663904 ATTTGGTATTCGTTCGATATTTTGATG 57.336 29.630 0.00 0.00 0.00 3.07
51 52 9.710979 GAATTTGGTATTCGTTCGATATTTTGA 57.289 29.630 0.00 0.00 0.00 2.69
52 53 9.497030 TGAATTTGGTATTCGTTCGATATTTTG 57.503 29.630 0.00 0.00 0.00 2.44
53 54 9.498307 GTGAATTTGGTATTCGTTCGATATTTT 57.502 29.630 0.00 0.00 0.00 1.82
54 55 8.670135 TGTGAATTTGGTATTCGTTCGATATTT 58.330 29.630 0.00 0.00 0.00 1.40
55 56 8.203937 TGTGAATTTGGTATTCGTTCGATATT 57.796 30.769 0.00 0.00 0.00 1.28
56 57 7.780008 TGTGAATTTGGTATTCGTTCGATAT 57.220 32.000 0.00 0.00 0.00 1.63
57 58 7.492994 TCATGTGAATTTGGTATTCGTTCGATA 59.507 33.333 0.00 0.00 0.00 2.92
58 59 6.315144 TCATGTGAATTTGGTATTCGTTCGAT 59.685 34.615 0.00 0.00 0.00 3.59
59 60 5.639931 TCATGTGAATTTGGTATTCGTTCGA 59.360 36.000 0.00 0.00 0.00 3.71
60 61 5.732647 GTCATGTGAATTTGGTATTCGTTCG 59.267 40.000 0.00 0.00 0.00 3.95
61 62 6.842163 AGTCATGTGAATTTGGTATTCGTTC 58.158 36.000 0.00 0.00 0.00 3.95
62 63 6.817765 AGTCATGTGAATTTGGTATTCGTT 57.182 33.333 0.00 0.00 0.00 3.85
63 64 7.103641 AGTAGTCATGTGAATTTGGTATTCGT 58.896 34.615 0.00 0.00 0.00 3.85
64 65 7.539712 AGTAGTCATGTGAATTTGGTATTCG 57.460 36.000 0.00 0.00 0.00 3.34
68 69 9.542462 GCTATAAGTAGTCATGTGAATTTGGTA 57.458 33.333 0.00 0.00 0.00 3.25
69 70 8.046708 TGCTATAAGTAGTCATGTGAATTTGGT 58.953 33.333 0.00 0.00 0.00 3.67
70 71 8.437360 TGCTATAAGTAGTCATGTGAATTTGG 57.563 34.615 0.00 0.00 0.00 3.28
71 72 9.926751 CTTGCTATAAGTAGTCATGTGAATTTG 57.073 33.333 0.00 0.00 0.00 2.32
72 73 9.890629 TCTTGCTATAAGTAGTCATGTGAATTT 57.109 29.630 0.00 0.00 0.00 1.82
73 74 9.319143 GTCTTGCTATAAGTAGTCATGTGAATT 57.681 33.333 0.00 0.00 0.00 2.17
74 75 8.700051 AGTCTTGCTATAAGTAGTCATGTGAAT 58.300 33.333 0.00 0.00 0.00 2.57
75 76 8.067751 AGTCTTGCTATAAGTAGTCATGTGAA 57.932 34.615 0.00 0.00 0.00 3.18
76 77 7.646548 AGTCTTGCTATAAGTAGTCATGTGA 57.353 36.000 0.00 0.00 0.00 3.58
77 78 8.194104 AGAAGTCTTGCTATAAGTAGTCATGTG 58.806 37.037 0.00 0.00 0.00 3.21
78 79 8.299990 AGAAGTCTTGCTATAAGTAGTCATGT 57.700 34.615 0.00 0.00 0.00 3.21
79 80 7.865385 GGAGAAGTCTTGCTATAAGTAGTCATG 59.135 40.741 0.00 0.00 0.00 3.07
80 81 7.014808 GGGAGAAGTCTTGCTATAAGTAGTCAT 59.985 40.741 0.00 0.00 0.00 3.06
81 82 6.321690 GGGAGAAGTCTTGCTATAAGTAGTCA 59.678 42.308 0.00 0.00 0.00 3.41
82 83 6.321690 TGGGAGAAGTCTTGCTATAAGTAGTC 59.678 42.308 0.00 0.00 0.00 2.59
83 84 6.195700 TGGGAGAAGTCTTGCTATAAGTAGT 58.804 40.000 0.00 0.00 0.00 2.73
84 85 6.716934 TGGGAGAAGTCTTGCTATAAGTAG 57.283 41.667 0.00 0.00 0.00 2.57
85 86 6.463049 GCATGGGAGAAGTCTTGCTATAAGTA 60.463 42.308 0.00 0.00 0.00 2.24
86 87 5.686124 GCATGGGAGAAGTCTTGCTATAAGT 60.686 44.000 0.00 0.00 0.00 2.24
87 88 4.754114 GCATGGGAGAAGTCTTGCTATAAG 59.246 45.833 0.00 0.00 0.00 1.73
88 89 4.708177 GCATGGGAGAAGTCTTGCTATAA 58.292 43.478 0.00 0.00 0.00 0.98
89 90 3.243873 CGCATGGGAGAAGTCTTGCTATA 60.244 47.826 3.11 0.00 0.00 1.31
90 91 2.484417 CGCATGGGAGAAGTCTTGCTAT 60.484 50.000 3.11 0.00 0.00 2.97
91 92 1.134699 CGCATGGGAGAAGTCTTGCTA 60.135 52.381 3.11 0.00 0.00 3.49
92 93 0.392193 CGCATGGGAGAAGTCTTGCT 60.392 55.000 3.11 0.00 0.00 3.91
93 94 1.986575 GCGCATGGGAGAAGTCTTGC 61.987 60.000 14.90 0.00 0.00 4.01
94 95 0.392193 AGCGCATGGGAGAAGTCTTG 60.392 55.000 14.90 0.00 0.00 3.02
95 96 0.107945 GAGCGCATGGGAGAAGTCTT 60.108 55.000 14.90 0.00 0.00 3.01
96 97 0.975040 AGAGCGCATGGGAGAAGTCT 60.975 55.000 14.90 0.00 0.00 3.24
97 98 0.809241 CAGAGCGCATGGGAGAAGTC 60.809 60.000 14.90 1.60 0.00 3.01
98 99 1.220206 CAGAGCGCATGGGAGAAGT 59.780 57.895 14.90 0.00 0.00 3.01
99 100 1.523258 CCAGAGCGCATGGGAGAAG 60.523 63.158 20.71 0.00 33.94 2.85
100 101 1.841302 AACCAGAGCGCATGGGAGAA 61.841 55.000 28.65 0.00 42.48 2.87
101 102 0.975556 TAACCAGAGCGCATGGGAGA 60.976 55.000 28.65 14.70 42.48 3.71
102 103 0.531532 CTAACCAGAGCGCATGGGAG 60.532 60.000 28.65 22.05 42.48 4.30
103 104 1.522092 CTAACCAGAGCGCATGGGA 59.478 57.895 28.65 18.06 42.48 4.37
104 105 2.182842 GCTAACCAGAGCGCATGGG 61.183 63.158 28.65 19.92 42.48 4.00
105 106 1.026182 TTGCTAACCAGAGCGCATGG 61.026 55.000 25.17 25.17 45.99 3.66
106 107 0.376152 CTTGCTAACCAGAGCGCATG 59.624 55.000 11.47 8.07 45.99 4.06
136 137 2.702478 CCTCTATCTTCTGCCCATCACA 59.298 50.000 0.00 0.00 0.00 3.58
144 145 1.683917 TCCGCTTCCTCTATCTTCTGC 59.316 52.381 0.00 0.00 0.00 4.26
219 220 5.644636 AGTTCTTGTTAGTTTGTGTTTCCGA 59.355 36.000 0.00 0.00 0.00 4.55
237 238 4.503714 TTTCTCCTTCACCACAGTTCTT 57.496 40.909 0.00 0.00 0.00 2.52
374 375 3.833650 TGGAAGGAAATGACATGTTGCAT 59.166 39.130 0.00 0.00 0.00 3.96
379 380 4.322198 GCACATTGGAAGGAAATGACATGT 60.322 41.667 0.00 0.00 38.21 3.21
404 405 0.249868 CTCAACTGTCGCTGGGTTGA 60.250 55.000 0.00 0.00 44.35 3.18
435 436 1.098869 CCAGACGAGCTGCTTCTCTA 58.901 55.000 2.53 0.00 43.50 2.43
470 471 2.478894 GTCTCAATGTGTACGTTGGGTG 59.521 50.000 14.58 7.56 42.47 4.61
514 515 3.515901 TCCTTCCCTTTACTCTGAAGCTC 59.484 47.826 0.00 0.00 34.31 4.09
576 577 1.227342 TTTCACGCGATGCAAGCAGA 61.227 50.000 15.93 10.72 34.19 4.26
799 803 2.105323 CGGAATGCTACAAAATCCGC 57.895 50.000 0.00 0.00 45.41 5.54
814 818 3.574396 CCCATTACTGCTCTATCTCGGAA 59.426 47.826 0.00 0.00 0.00 4.30
817 821 2.353208 GGCCCATTACTGCTCTATCTCG 60.353 54.545 0.00 0.00 0.00 4.04
818 822 2.353208 CGGCCCATTACTGCTCTATCTC 60.353 54.545 0.00 0.00 0.00 2.75
819 823 1.620819 CGGCCCATTACTGCTCTATCT 59.379 52.381 0.00 0.00 0.00 1.98
820 824 1.344763 ACGGCCCATTACTGCTCTATC 59.655 52.381 0.00 0.00 0.00 2.08
821 825 1.344763 GACGGCCCATTACTGCTCTAT 59.655 52.381 0.00 0.00 0.00 1.98
846 850 1.661112 GCGGTTTCTTCTCTCCATTCG 59.339 52.381 0.00 0.00 0.00 3.34
874 879 2.162681 CCATTTTCTCCGTGGAAAGCT 58.837 47.619 0.00 0.00 36.69 3.74
875 880 1.202348 CCCATTTTCTCCGTGGAAAGC 59.798 52.381 0.00 0.00 36.69 3.51
876 881 1.202348 GCCCATTTTCTCCGTGGAAAG 59.798 52.381 0.00 0.00 36.69 2.62
877 882 1.253100 GCCCATTTTCTCCGTGGAAA 58.747 50.000 0.00 0.00 34.94 3.13
908 913 1.065854 GCAGTGTGGCTAGATGAAGGT 60.066 52.381 0.00 0.00 0.00 3.50
931 936 5.656416 GGAATGGATGGGAAAATCAGTGTAA 59.344 40.000 0.00 0.00 0.00 2.41
1019 1025 4.951963 GGAAGGATCTCGCGGCGG 62.952 72.222 23.46 13.27 0.00 6.13
1020 1026 3.832720 GAGGAAGGATCTCGCGGCG 62.833 68.421 17.70 17.70 0.00 6.46
1021 1027 2.028337 GAGGAAGGATCTCGCGGC 59.972 66.667 6.13 0.00 0.00 6.53
1233 1248 2.356075 CCACGGACCGCAACGTAA 60.356 61.111 15.39 0.00 42.04 3.18
1234 1249 3.271706 CTCCACGGACCGCAACGTA 62.272 63.158 15.39 0.00 42.04 3.57
1235 1250 4.657824 CTCCACGGACCGCAACGT 62.658 66.667 15.39 0.00 45.25 3.99
1434 1453 2.493278 CGAACAAAGGGGCTTCATTCAT 59.507 45.455 0.00 0.00 0.00 2.57
1435 1454 1.885887 CGAACAAAGGGGCTTCATTCA 59.114 47.619 0.00 0.00 0.00 2.57
1436 1455 1.886542 ACGAACAAAGGGGCTTCATTC 59.113 47.619 0.00 0.00 0.00 2.67
1437 1456 1.995376 ACGAACAAAGGGGCTTCATT 58.005 45.000 0.00 0.00 0.00 2.57
1475 1494 3.238108 AGCAAATACAGACCACTCTCG 57.762 47.619 0.00 0.00 0.00 4.04
1496 1516 3.698040 GACTTGGACTTCGGTGGATACTA 59.302 47.826 0.00 0.00 37.61 1.82
1521 1541 5.676079 GCACATGTATTACAAATGAACGGCT 60.676 40.000 0.00 0.00 0.00 5.52
1711 1762 5.847304 TGAGTTATGTTGCAGCTCCTATAG 58.153 41.667 1.17 0.00 0.00 1.31
1712 1763 5.869649 TGAGTTATGTTGCAGCTCCTATA 57.130 39.130 1.17 0.00 0.00 1.31
1713 1764 4.760530 TGAGTTATGTTGCAGCTCCTAT 57.239 40.909 1.17 0.00 0.00 2.57
1714 1765 4.253685 GTTGAGTTATGTTGCAGCTCCTA 58.746 43.478 1.17 0.00 0.00 2.94
1715 1766 3.077359 GTTGAGTTATGTTGCAGCTCCT 58.923 45.455 1.17 0.00 0.00 3.69
1716 1767 2.162408 GGTTGAGTTATGTTGCAGCTCC 59.838 50.000 1.17 0.00 0.00 4.70
1717 1768 3.077359 AGGTTGAGTTATGTTGCAGCTC 58.923 45.455 1.17 0.00 0.00 4.09
1718 1769 2.816087 CAGGTTGAGTTATGTTGCAGCT 59.184 45.455 1.17 0.00 0.00 4.24
1726 1777 8.511604 AGTAATGATTTCCAGGTTGAGTTATG 57.488 34.615 0.00 0.00 0.00 1.90
1983 2038 7.561021 TGCAACAGTAGAAGAAACAATAACA 57.439 32.000 0.00 0.00 0.00 2.41
2020 2075 2.519771 AGGAAATCATGGCAGCTTCA 57.480 45.000 0.00 0.00 0.00 3.02
2091 2147 3.568007 TCCAGCAGTCAACAATTACAACC 59.432 43.478 0.00 0.00 0.00 3.77
2102 2158 2.033141 GCAGGCTCCAGCAGTCAA 59.967 61.111 0.03 0.00 44.36 3.18
2114 2170 2.924421 AGCTAATAGTCTTTGGCAGGC 58.076 47.619 0.00 0.00 35.72 4.85
2116 2172 4.937620 TGTGAAGCTAATAGTCTTTGGCAG 59.062 41.667 0.00 0.00 35.72 4.85
2125 2181 6.013293 AGGGAAACTTCTGTGAAGCTAATAGT 60.013 38.462 7.17 0.00 0.00 2.12
2271 2328 2.036098 CATTGCCAGCTGGGTGGA 59.964 61.111 33.46 6.73 40.44 4.02
2478 2535 3.585990 GATTCGCACGGCCATGGG 61.586 66.667 15.13 9.98 0.00 4.00
2486 2543 1.665679 AGCAATTACAGGATTCGCACG 59.334 47.619 0.00 0.00 0.00 5.34
2984 3043 2.411904 CTCCAGCTCTTCAACTCACAC 58.588 52.381 0.00 0.00 0.00 3.82
3213 3272 1.746615 CGGCCCCAGACATGAACTG 60.747 63.158 0.00 8.62 35.43 3.16
3221 3280 1.201414 CAAAACAATACGGCCCCAGAC 59.799 52.381 0.00 0.00 0.00 3.51
3242 3301 5.721876 ACGTAACGTCAAGACAAAAATGA 57.278 34.783 0.72 0.00 33.69 2.57
3250 3309 9.118236 ACTAAAGTTATAACGTAACGTCAAGAC 57.882 33.333 9.91 0.00 39.99 3.01
3252 3311 8.299981 CGACTAAAGTTATAACGTAACGTCAAG 58.700 37.037 9.91 2.50 39.99 3.02
3253 3312 7.270365 CCGACTAAAGTTATAACGTAACGTCAA 59.730 37.037 9.91 0.00 39.99 3.18
3255 3314 6.959311 TCCGACTAAAGTTATAACGTAACGTC 59.041 38.462 9.91 11.87 39.99 4.34
3256 3315 6.837992 TCCGACTAAAGTTATAACGTAACGT 58.162 36.000 9.91 5.26 43.97 3.99


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

AutoCloner maintained by Alex Coulton.