Multiple sequence alignment - TraesCS6B01G052000

Loading Multiple Alignment...

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 TraesCS6B01G052000 chr6B 100.000 2202 0 0 584 2785 31075580 31073379 0.000000e+00 4067.0
1 TraesCS6B01G052000 chr6B 94.078 591 25 4 586 1167 144854161 144854750 0.000000e+00 889.0
2 TraesCS6B01G052000 chr6B 100.000 261 0 0 1 261 31076163 31075903 1.500000e-132 483.0
3 TraesCS6B01G052000 chr6B 98.496 133 2 0 1 133 31129848 31129716 4.640000e-58 235.0
4 TraesCS6B01G052000 chr6B 98.496 133 2 0 1 133 31140281 31140149 4.640000e-58 235.0
5 TraesCS6B01G052000 chr6B 98.496 133 2 0 1 133 31150721 31150589 4.640000e-58 235.0
6 TraesCS6B01G052000 chr6B 98.496 133 2 0 1 133 31213207 31213075 4.640000e-58 235.0
7 TraesCS6B01G052000 chr6B 97.744 133 3 0 1 133 31120329 31120197 2.160000e-56 230.0
8 TraesCS6B01G052000 chr6B 97.744 133 3 0 1 133 31172503 31172371 2.160000e-56 230.0
9 TraesCS6B01G052000 chr6B 97.744 133 3 0 1 133 31182936 31182804 2.160000e-56 230.0
10 TraesCS6B01G052000 chr6B 96.992 133 4 0 1 133 31110063 31109931 1.000000e-54 224.0
11 TraesCS6B01G052000 chr6B 96.992 133 4 0 1 133 31193177 31193045 1.000000e-54 224.0
12 TraesCS6B01G052000 chr1B 97.231 2203 56 3 586 2785 507366431 507364231 0.000000e+00 3725.0
13 TraesCS6B01G052000 chr1B 97.159 1936 44 2 861 2785 14779199 14777264 0.000000e+00 3260.0
14 TraesCS6B01G052000 chr1B 95.836 1897 60 13 590 2483 306680743 306678863 0.000000e+00 3048.0
15 TraesCS6B01G052000 chr1B 94.982 279 14 0 590 868 14780071 14779793 3.290000e-119 438.0
16 TraesCS6B01G052000 chr1B 96.183 131 4 1 132 261 507366618 507366488 2.170000e-51 213.0
17 TraesCS6B01G052000 chr1B 96.124 129 5 0 133 261 306680933 306680805 7.820000e-51 211.0
18 TraesCS6B01G052000 chr5A 96.879 2211 59 4 584 2785 112143021 112140812 0.000000e+00 3692.0
19 TraesCS6B01G052000 chr5A 83.142 611 63 14 1021 1618 624112632 624113215 3.180000e-144 521.0
20 TraesCS6B01G052000 chr5A 92.222 90 2 2 1683 1767 624113349 624113438 3.770000e-24 122.0
21 TraesCS6B01G052000 chr2B 97.280 1765 42 2 1027 2785 191737590 191735826 0.000000e+00 2988.0
22 TraesCS6B01G052000 chr2B 93.014 501 26 1 584 1075 191738072 191737572 0.000000e+00 723.0
23 TraesCS6B01G052000 chr2B 95.736 258 10 1 586 843 797909324 797909580 5.550000e-112 414.0
24 TraesCS6B01G052000 chr2B 92.466 146 8 3 117 261 191738257 191738114 3.640000e-49 206.0
25 TraesCS6B01G052000 chr5B 96.949 1770 33 4 1021 2785 549714679 549716432 0.000000e+00 2950.0
26 TraesCS6B01G052000 chr5B 94.208 587 23 5 590 1167 513728754 513728170 0.000000e+00 885.0
27 TraesCS6B01G052000 chr5B 94.929 493 21 2 586 1075 549714212 549714703 0.000000e+00 769.0
28 TraesCS6B01G052000 chr5B 82.660 940 85 33 858 1766 620947885 620948777 0.000000e+00 761.0
29 TraesCS6B01G052000 chr3B 98.845 1039 12 0 1747 2785 807233579 807234617 0.000000e+00 1853.0
30 TraesCS6B01G052000 chr3B 96.765 742 20 2 981 1718 807232844 807233585 0.000000e+00 1234.0
31 TraesCS6B01G052000 chr3B 95.110 409 16 1 584 992 807231978 807232382 2.340000e-180 641.0
32 TraesCS6B01G052000 chr3B 96.923 130 4 0 132 261 807231797 807231926 4.670000e-53 219.0
33 TraesCS6B01G052000 chrUn 96.804 438 14 0 2348 2785 283592860 283593297 0.000000e+00 732.0
34 TraesCS6B01G052000 chrUn 95.706 326 13 1 584 909 283591707 283592031 8.840000e-145 523.0
35 TraesCS6B01G052000 chrUn 95.455 132 5 1 128 258 387538641 387538510 2.810000e-50 209.0
36 TraesCS6B01G052000 chrUn 95.455 132 5 1 128 258 407200612 407200743 2.810000e-50 209.0
37 TraesCS6B01G052000 chr3D 95.034 443 17 2 2348 2785 424489179 424489621 0.000000e+00 691.0
38 TraesCS6B01G052000 chr7B 92.777 443 27 2 2348 2785 584641884 584641442 1.090000e-178 636.0
39 TraesCS6B01G052000 chr4D 95.855 386 16 0 1965 2350 2861272 2861657 2.360000e-175 625.0
40 TraesCS6B01G052000 chr4B 95.855 386 16 0 1968 2353 28238558 28238173 2.360000e-175 625.0
41 TraesCS6B01G052000 chr4B 96.850 127 4 0 132 258 647697982 647697856 2.170000e-51 213.0
42 TraesCS6B01G052000 chr4B 86.869 198 11 5 1769 1951 28239753 28239556 1.010000e-49 207.0
43 TraesCS6B01G052000 chr4A 96.850 127 4 0 132 258 716724541 716724667 2.170000e-51 213.0
44 TraesCS6B01G052000 chr2A 96.154 130 4 1 133 261 707029430 707029301 7.820000e-51 211.0
45 TraesCS6B01G052000 chr2A 83.246 191 20 9 1763 1949 21167985 21167803 6.170000e-37 165.0
46 TraesCS6B01G052000 chr6D 81.915 188 29 4 1763 1949 446751390 446751573 1.340000e-33 154.0
47 TraesCS6B01G052000 chr2D 82.199 191 22 9 1763 1949 20333184 20333366 1.340000e-33 154.0
48 TraesCS6B01G052000 chr5D 92.982 57 0 1 1711 1767 499684135 499684187 2.300000e-11 80.5


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 TraesCS6B01G052000 chr6B 31073379 31076163 2784 True 2275.000000 4067 100.000000 1 2785 2 chr6B.!!$R10 2784
1 TraesCS6B01G052000 chr6B 144854161 144854750 589 False 889.000000 889 94.078000 586 1167 1 chr6B.!!$F1 581
2 TraesCS6B01G052000 chr1B 507364231 507366618 2387 True 1969.000000 3725 96.707000 132 2785 2 chr1B.!!$R3 2653
3 TraesCS6B01G052000 chr1B 14777264 14780071 2807 True 1849.000000 3260 96.070500 590 2785 2 chr1B.!!$R1 2195
4 TraesCS6B01G052000 chr1B 306678863 306680933 2070 True 1629.500000 3048 95.980000 133 2483 2 chr1B.!!$R2 2350
5 TraesCS6B01G052000 chr5A 112140812 112143021 2209 True 3692.000000 3692 96.879000 584 2785 1 chr5A.!!$R1 2201
6 TraesCS6B01G052000 chr5A 624112632 624113438 806 False 321.500000 521 87.682000 1021 1767 2 chr5A.!!$F1 746
7 TraesCS6B01G052000 chr2B 191735826 191738257 2431 True 1305.666667 2988 94.253333 117 2785 3 chr2B.!!$R1 2668
8 TraesCS6B01G052000 chr5B 549714212 549716432 2220 False 1859.500000 2950 95.939000 586 2785 2 chr5B.!!$F2 2199
9 TraesCS6B01G052000 chr5B 513728170 513728754 584 True 885.000000 885 94.208000 590 1167 1 chr5B.!!$R1 577
10 TraesCS6B01G052000 chr5B 620947885 620948777 892 False 761.000000 761 82.660000 858 1766 1 chr5B.!!$F1 908
11 TraesCS6B01G052000 chr3B 807231797 807234617 2820 False 986.750000 1853 96.910750 132 2785 4 chr3B.!!$F1 2653
12 TraesCS6B01G052000 chrUn 283591707 283593297 1590 False 627.500000 732 96.255000 584 2785 2 chrUn.!!$F2 2201
13 TraesCS6B01G052000 chr4B 28238173 28239753 1580 True 416.000000 625 91.362000 1769 2353 2 chr4B.!!$R2 584

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
46 47 0.610687 GGAGACCACAAGGAGACAGG 59.389 60.000 0.0 0.0 38.69 4.00 F
48 49 1.003233 GACCACAAGGAGACAGGGC 60.003 63.158 0.0 0.0 38.69 5.19 F
72 73 1.548719 TGGACACCACCAGAACGATAG 59.451 52.381 0.0 0.0 37.25 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1235 2864 2.885113 TGAGCATCACCGTCGGAG 59.115 61.111 20.51 10.94 42.56 4.63 R
1414 3055 4.679373 ATCTACCATGCTCACTACTTGG 57.321 45.455 0.00 0.00 38.11 3.61 R
1966 3764 5.321516 CGTTAATGGTAAAACAGTGCTAGC 58.678 41.667 8.10 8.10 0.00 3.42 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
26 27 8.601845 TCATATGAACGAAACAAAAAGAGAGA 57.398 30.769 1.98 0.00 0.00 3.10
27 28 8.712363 TCATATGAACGAAACAAAAAGAGAGAG 58.288 33.333 1.98 0.00 0.00 3.20
28 29 5.734855 TGAACGAAACAAAAAGAGAGAGG 57.265 39.130 0.00 0.00 0.00 3.69
29 30 5.424757 TGAACGAAACAAAAAGAGAGAGGA 58.575 37.500 0.00 0.00 0.00 3.71
30 31 5.523916 TGAACGAAACAAAAAGAGAGAGGAG 59.476 40.000 0.00 0.00 0.00 3.69
31 32 5.277857 ACGAAACAAAAAGAGAGAGGAGA 57.722 39.130 0.00 0.00 0.00 3.71
32 33 5.051153 ACGAAACAAAAAGAGAGAGGAGAC 58.949 41.667 0.00 0.00 0.00 3.36
33 34 4.449405 CGAAACAAAAAGAGAGAGGAGACC 59.551 45.833 0.00 0.00 0.00 3.85
34 35 5.368989 GAAACAAAAAGAGAGAGGAGACCA 58.631 41.667 0.00 0.00 0.00 4.02
35 36 4.344359 ACAAAAAGAGAGAGGAGACCAC 57.656 45.455 0.00 0.00 0.00 4.16
36 37 3.711704 ACAAAAAGAGAGAGGAGACCACA 59.288 43.478 0.00 0.00 0.00 4.17
37 38 4.164221 ACAAAAAGAGAGAGGAGACCACAA 59.836 41.667 0.00 0.00 0.00 3.33
38 39 4.615588 AAAAGAGAGAGGAGACCACAAG 57.384 45.455 0.00 0.00 0.00 3.16
39 40 2.230130 AGAGAGAGGAGACCACAAGG 57.770 55.000 0.00 0.00 42.21 3.61
40 41 1.713647 AGAGAGAGGAGACCACAAGGA 59.286 52.381 0.00 0.00 38.69 3.36
41 42 2.099405 GAGAGAGGAGACCACAAGGAG 58.901 57.143 0.00 0.00 38.69 3.69
42 43 1.713647 AGAGAGGAGACCACAAGGAGA 59.286 52.381 0.00 0.00 38.69 3.71
43 44 1.822371 GAGAGGAGACCACAAGGAGAC 59.178 57.143 0.00 0.00 38.69 3.36
44 45 1.148027 AGAGGAGACCACAAGGAGACA 59.852 52.381 0.00 0.00 38.69 3.41
45 46 1.548269 GAGGAGACCACAAGGAGACAG 59.452 57.143 0.00 0.00 38.69 3.51
46 47 0.610687 GGAGACCACAAGGAGACAGG 59.389 60.000 0.00 0.00 38.69 4.00
47 48 0.610687 GAGACCACAAGGAGACAGGG 59.389 60.000 0.00 0.00 38.69 4.45
48 49 1.003233 GACCACAAGGAGACAGGGC 60.003 63.158 0.00 0.00 38.69 5.19
49 50 2.046892 CCACAAGGAGACAGGGCG 60.047 66.667 0.00 0.00 36.89 6.13
50 51 2.743928 CACAAGGAGACAGGGCGC 60.744 66.667 0.00 0.00 0.00 6.53
51 52 4.379243 ACAAGGAGACAGGGCGCG 62.379 66.667 0.00 0.00 0.00 6.86
52 53 4.379243 CAAGGAGACAGGGCGCGT 62.379 66.667 8.43 0.00 0.00 6.01
53 54 4.379243 AAGGAGACAGGGCGCGTG 62.379 66.667 8.43 3.70 0.00 5.34
69 70 3.957919 TGGACACCACCAGAACGA 58.042 55.556 0.00 0.00 34.77 3.85
70 71 2.447630 TGGACACCACCAGAACGAT 58.552 52.632 0.00 0.00 34.77 3.73
71 72 1.634960 TGGACACCACCAGAACGATA 58.365 50.000 0.00 0.00 34.77 2.92
72 73 1.548719 TGGACACCACCAGAACGATAG 59.451 52.381 0.00 0.00 37.25 2.08
73 74 1.822990 GGACACCACCAGAACGATAGA 59.177 52.381 0.00 0.00 41.38 1.98
74 75 2.159226 GGACACCACCAGAACGATAGAG 60.159 54.545 0.00 0.00 41.38 2.43
75 76 2.753452 GACACCACCAGAACGATAGAGA 59.247 50.000 0.00 0.00 41.38 3.10
76 77 3.162666 ACACCACCAGAACGATAGAGAA 58.837 45.455 0.00 0.00 41.38 2.87
77 78 3.576982 ACACCACCAGAACGATAGAGAAA 59.423 43.478 0.00 0.00 41.38 2.52
78 79 4.223032 ACACCACCAGAACGATAGAGAAAT 59.777 41.667 0.00 0.00 41.38 2.17
79 80 5.421056 ACACCACCAGAACGATAGAGAAATA 59.579 40.000 0.00 0.00 41.38 1.40
80 81 6.070995 ACACCACCAGAACGATAGAGAAATAA 60.071 38.462 0.00 0.00 41.38 1.40
81 82 6.816640 CACCACCAGAACGATAGAGAAATAAA 59.183 38.462 0.00 0.00 41.38 1.40
82 83 6.817140 ACCACCAGAACGATAGAGAAATAAAC 59.183 38.462 0.00 0.00 41.38 2.01
83 84 6.258068 CCACCAGAACGATAGAGAAATAAACC 59.742 42.308 0.00 0.00 41.38 3.27
84 85 6.816640 CACCAGAACGATAGAGAAATAAACCA 59.183 38.462 0.00 0.00 41.38 3.67
85 86 7.010552 CACCAGAACGATAGAGAAATAAACCAG 59.989 40.741 0.00 0.00 41.38 4.00
86 87 7.042335 CCAGAACGATAGAGAAATAAACCAGT 58.958 38.462 0.00 0.00 41.38 4.00
87 88 8.195436 CCAGAACGATAGAGAAATAAACCAGTA 58.805 37.037 0.00 0.00 41.38 2.74
88 89 9.239002 CAGAACGATAGAGAAATAAACCAGTAG 57.761 37.037 0.00 0.00 41.38 2.57
89 90 7.921745 AGAACGATAGAGAAATAAACCAGTAGC 59.078 37.037 0.00 0.00 41.38 3.58
90 91 6.207213 ACGATAGAGAAATAAACCAGTAGCG 58.793 40.000 0.00 0.00 41.38 4.26
91 92 6.039047 ACGATAGAGAAATAAACCAGTAGCGA 59.961 38.462 0.00 0.00 41.38 4.93
92 93 6.916387 CGATAGAGAAATAAACCAGTAGCGAA 59.084 38.462 0.00 0.00 39.76 4.70
93 94 7.113684 CGATAGAGAAATAAACCAGTAGCGAAG 59.886 40.741 0.00 0.00 39.76 3.79
127 128 7.784633 TTTTATGATATCAAGCGACATCACA 57.215 32.000 9.99 0.00 37.88 3.58
128 129 7.784633 TTTATGATATCAAGCGACATCACAA 57.215 32.000 9.99 0.00 37.88 3.33
129 130 7.784633 TTATGATATCAAGCGACATCACAAA 57.215 32.000 9.99 0.00 37.88 2.83
621 643 1.658994 AAAAACCAGAACTCGCACGA 58.341 45.000 0.00 0.00 0.00 4.35
673 695 3.024547 ACCTACGATATGTGACTGCAGT 58.975 45.455 21.88 21.88 0.00 4.40
686 708 2.125912 GCAGTCGCACCAGATCGT 60.126 61.111 0.00 0.00 38.36 3.73
730 752 2.721167 CGGACGAGATCCCAAGCCA 61.721 63.158 0.00 0.00 46.04 4.75
865 1520 2.713770 GGATACGTCGCTGCGAGA 59.286 61.111 26.68 14.13 36.23 4.04
1125 2753 2.364448 GAGGAGGAGAGGGGCGTT 60.364 66.667 0.00 0.00 0.00 4.84
1168 2796 2.039624 AGATGGTCTCTGGCGGGT 59.960 61.111 0.00 0.00 31.12 5.28
1209 2838 2.167918 GTGAAGCGTGCGTTCGTC 59.832 61.111 3.76 0.00 0.00 4.20
1428 3069 1.066143 CGGAACCCAAGTAGTGAGCAT 60.066 52.381 0.00 0.00 0.00 3.79
1452 3104 3.784701 AGATTCTCTGTACGTTCGCAT 57.215 42.857 0.00 0.00 0.00 4.73
1458 3110 4.989044 TCTCTGTACGTTCGCATAAATCA 58.011 39.130 0.00 0.00 0.00 2.57
1675 3349 6.658816 TGTATTTTCAGCTGTATGGATGTTGT 59.341 34.615 14.67 0.00 0.00 3.32
1799 3574 4.689071 TGTCATAATTTATCACGTCCGCT 58.311 39.130 0.00 0.00 0.00 5.52
1892 3681 2.975851 GACTCATTTGTTTTGCTGCTCG 59.024 45.455 0.00 0.00 0.00 5.03
1966 3764 7.060633 GGCACAAATAAACTTTCACTCATTACG 59.939 37.037 0.00 0.00 0.00 3.18
1986 4757 4.571919 ACGCTAGCACTGTTTTACCATTA 58.428 39.130 16.45 0.00 0.00 1.90
2090 4861 4.885907 ACATGCACTGCTGCTTCTAATTAT 59.114 37.500 1.98 0.00 44.57 1.28
2549 5323 4.733077 TTTCCAGGACCATTGTTTCCTA 57.267 40.909 4.22 0.00 40.52 2.94
2659 5441 2.670148 GGAGGGTTGATCGCTGGGT 61.670 63.158 0.00 0.00 39.46 4.51
2699 5481 2.167487 GCCAGGAGGAACAAGAGTAGAG 59.833 54.545 0.00 0.00 36.89 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.601845 TCTCTCTTTTTGTTTCGTTCATATGA 57.398 30.769 0.00 0.00 0.00 2.15
4 5 7.214381 TCCTCTCTCTTTTTGTTTCGTTCATA 58.786 34.615 0.00 0.00 0.00 2.15
5 6 6.055588 TCCTCTCTCTTTTTGTTTCGTTCAT 58.944 36.000 0.00 0.00 0.00 2.57
6 7 5.424757 TCCTCTCTCTTTTTGTTTCGTTCA 58.575 37.500 0.00 0.00 0.00 3.18
7 8 5.753921 TCTCCTCTCTCTTTTTGTTTCGTTC 59.246 40.000 0.00 0.00 0.00 3.95
8 9 5.524281 GTCTCCTCTCTCTTTTTGTTTCGTT 59.476 40.000 0.00 0.00 0.00 3.85
9 10 5.051153 GTCTCCTCTCTCTTTTTGTTTCGT 58.949 41.667 0.00 0.00 0.00 3.85
10 11 4.449405 GGTCTCCTCTCTCTTTTTGTTTCG 59.551 45.833 0.00 0.00 0.00 3.46
11 12 5.237561 GTGGTCTCCTCTCTCTTTTTGTTTC 59.762 44.000 0.00 0.00 0.00 2.78
12 13 5.126779 GTGGTCTCCTCTCTCTTTTTGTTT 58.873 41.667 0.00 0.00 0.00 2.83
13 14 4.164221 TGTGGTCTCCTCTCTCTTTTTGTT 59.836 41.667 0.00 0.00 0.00 2.83
14 15 3.711704 TGTGGTCTCCTCTCTCTTTTTGT 59.288 43.478 0.00 0.00 0.00 2.83
15 16 4.342862 TGTGGTCTCCTCTCTCTTTTTG 57.657 45.455 0.00 0.00 0.00 2.44
16 17 4.202409 CCTTGTGGTCTCCTCTCTCTTTTT 60.202 45.833 0.00 0.00 0.00 1.94
17 18 3.326297 CCTTGTGGTCTCCTCTCTCTTTT 59.674 47.826 0.00 0.00 0.00 2.27
18 19 2.903135 CCTTGTGGTCTCCTCTCTCTTT 59.097 50.000 0.00 0.00 0.00 2.52
19 20 2.110899 TCCTTGTGGTCTCCTCTCTCTT 59.889 50.000 0.00 0.00 34.23 2.85
20 21 1.713647 TCCTTGTGGTCTCCTCTCTCT 59.286 52.381 0.00 0.00 34.23 3.10
21 22 2.099405 CTCCTTGTGGTCTCCTCTCTC 58.901 57.143 0.00 0.00 34.23 3.20
22 23 1.713647 TCTCCTTGTGGTCTCCTCTCT 59.286 52.381 0.00 0.00 34.23 3.10
23 24 1.822371 GTCTCCTTGTGGTCTCCTCTC 59.178 57.143 0.00 0.00 34.23 3.20
24 25 1.148027 TGTCTCCTTGTGGTCTCCTCT 59.852 52.381 0.00 0.00 34.23 3.69
25 26 1.548269 CTGTCTCCTTGTGGTCTCCTC 59.452 57.143 0.00 0.00 34.23 3.71
26 27 1.638529 CTGTCTCCTTGTGGTCTCCT 58.361 55.000 0.00 0.00 34.23 3.69
27 28 0.610687 CCTGTCTCCTTGTGGTCTCC 59.389 60.000 0.00 0.00 34.23 3.71
28 29 0.610687 CCCTGTCTCCTTGTGGTCTC 59.389 60.000 0.00 0.00 34.23 3.36
29 30 1.484444 GCCCTGTCTCCTTGTGGTCT 61.484 60.000 0.00 0.00 34.23 3.85
30 31 1.003233 GCCCTGTCTCCTTGTGGTC 60.003 63.158 0.00 0.00 34.23 4.02
31 32 2.883828 CGCCCTGTCTCCTTGTGGT 61.884 63.158 0.00 0.00 34.23 4.16
32 33 2.046892 CGCCCTGTCTCCTTGTGG 60.047 66.667 0.00 0.00 0.00 4.17
33 34 2.743928 GCGCCCTGTCTCCTTGTG 60.744 66.667 0.00 0.00 0.00 3.33
34 35 4.379243 CGCGCCCTGTCTCCTTGT 62.379 66.667 0.00 0.00 0.00 3.16
35 36 4.379243 ACGCGCCCTGTCTCCTTG 62.379 66.667 5.73 0.00 0.00 3.61
36 37 4.379243 CACGCGCCCTGTCTCCTT 62.379 66.667 5.73 0.00 0.00 3.36
52 53 1.548719 CTATCGTTCTGGTGGTGTCCA 59.451 52.381 0.00 0.00 36.00 4.02
53 54 1.822990 TCTATCGTTCTGGTGGTGTCC 59.177 52.381 0.00 0.00 0.00 4.02
54 55 2.753452 TCTCTATCGTTCTGGTGGTGTC 59.247 50.000 0.00 0.00 0.00 3.67
55 56 2.803956 TCTCTATCGTTCTGGTGGTGT 58.196 47.619 0.00 0.00 0.00 4.16
56 57 3.868757 TTCTCTATCGTTCTGGTGGTG 57.131 47.619 0.00 0.00 0.00 4.17
57 58 6.540438 TTATTTCTCTATCGTTCTGGTGGT 57.460 37.500 0.00 0.00 0.00 4.16
58 59 6.258068 GGTTTATTTCTCTATCGTTCTGGTGG 59.742 42.308 0.00 0.00 0.00 4.61
59 60 6.816640 TGGTTTATTTCTCTATCGTTCTGGTG 59.183 38.462 0.00 0.00 0.00 4.17
60 61 6.942976 TGGTTTATTTCTCTATCGTTCTGGT 58.057 36.000 0.00 0.00 0.00 4.00
61 62 7.042335 ACTGGTTTATTTCTCTATCGTTCTGG 58.958 38.462 0.00 0.00 0.00 3.86
62 63 9.239002 CTACTGGTTTATTTCTCTATCGTTCTG 57.761 37.037 0.00 0.00 0.00 3.02
63 64 7.921745 GCTACTGGTTTATTTCTCTATCGTTCT 59.078 37.037 0.00 0.00 0.00 3.01
64 65 7.096558 CGCTACTGGTTTATTTCTCTATCGTTC 60.097 40.741 0.00 0.00 0.00 3.95
65 66 6.696148 CGCTACTGGTTTATTTCTCTATCGTT 59.304 38.462 0.00 0.00 0.00 3.85
66 67 6.039047 TCGCTACTGGTTTATTTCTCTATCGT 59.961 38.462 0.00 0.00 0.00 3.73
67 68 6.436261 TCGCTACTGGTTTATTTCTCTATCG 58.564 40.000 0.00 0.00 0.00 2.92
68 69 7.095982 GCTTCGCTACTGGTTTATTTCTCTATC 60.096 40.741 0.00 0.00 0.00 2.08
69 70 6.702282 GCTTCGCTACTGGTTTATTTCTCTAT 59.298 38.462 0.00 0.00 0.00 1.98
70 71 6.040878 GCTTCGCTACTGGTTTATTTCTCTA 58.959 40.000 0.00 0.00 0.00 2.43
71 72 4.870991 GCTTCGCTACTGGTTTATTTCTCT 59.129 41.667 0.00 0.00 0.00 3.10
72 73 4.630069 TGCTTCGCTACTGGTTTATTTCTC 59.370 41.667 0.00 0.00 0.00 2.87
73 74 4.575885 TGCTTCGCTACTGGTTTATTTCT 58.424 39.130 0.00 0.00 0.00 2.52
74 75 4.939509 TGCTTCGCTACTGGTTTATTTC 57.060 40.909 0.00 0.00 0.00 2.17
75 76 5.183140 ACATTGCTTCGCTACTGGTTTATTT 59.817 36.000 0.00 0.00 0.00 1.40
76 77 4.700213 ACATTGCTTCGCTACTGGTTTATT 59.300 37.500 0.00 0.00 0.00 1.40
77 78 4.261801 ACATTGCTTCGCTACTGGTTTAT 58.738 39.130 0.00 0.00 0.00 1.40
78 79 3.670625 ACATTGCTTCGCTACTGGTTTA 58.329 40.909 0.00 0.00 0.00 2.01
79 80 2.504367 ACATTGCTTCGCTACTGGTTT 58.496 42.857 0.00 0.00 0.00 3.27
80 81 2.185004 ACATTGCTTCGCTACTGGTT 57.815 45.000 0.00 0.00 0.00 3.67
81 82 3.543680 ATACATTGCTTCGCTACTGGT 57.456 42.857 0.00 0.00 0.00 4.00
82 83 6.545504 AAATATACATTGCTTCGCTACTGG 57.454 37.500 0.00 0.00 0.00 4.00
83 84 9.533983 CATAAAATATACATTGCTTCGCTACTG 57.466 33.333 0.00 0.00 0.00 2.74
84 85 9.489084 TCATAAAATATACATTGCTTCGCTACT 57.511 29.630 0.00 0.00 0.00 2.57
108 109 6.493449 TTTTTGTGATGTCGCTTGATATCA 57.507 33.333 0.00 0.00 44.79 2.15
109 110 7.412853 AGATTTTTGTGATGTCGCTTGATATC 58.587 34.615 0.00 0.00 39.81 1.63
110 111 7.281774 AGAGATTTTTGTGATGTCGCTTGATAT 59.718 33.333 0.00 0.00 0.00 1.63
111 112 6.595326 AGAGATTTTTGTGATGTCGCTTGATA 59.405 34.615 0.00 0.00 0.00 2.15
112 113 5.413833 AGAGATTTTTGTGATGTCGCTTGAT 59.586 36.000 0.00 0.00 0.00 2.57
113 114 4.756642 AGAGATTTTTGTGATGTCGCTTGA 59.243 37.500 0.00 0.00 0.00 3.02
114 115 5.039480 AGAGATTTTTGTGATGTCGCTTG 57.961 39.130 0.00 0.00 0.00 4.01
115 116 5.934625 AGTAGAGATTTTTGTGATGTCGCTT 59.065 36.000 0.00 0.00 0.00 4.68
116 117 5.482908 AGTAGAGATTTTTGTGATGTCGCT 58.517 37.500 0.00 0.00 0.00 4.93
117 118 5.220491 GGAGTAGAGATTTTTGTGATGTCGC 60.220 44.000 0.00 0.00 0.00 5.19
118 119 6.102663 AGGAGTAGAGATTTTTGTGATGTCG 58.897 40.000 0.00 0.00 0.00 4.35
119 120 9.606631 ATTAGGAGTAGAGATTTTTGTGATGTC 57.393 33.333 0.00 0.00 0.00 3.06
120 121 9.388506 CATTAGGAGTAGAGATTTTTGTGATGT 57.611 33.333 0.00 0.00 0.00 3.06
121 122 9.388506 ACATTAGGAGTAGAGATTTTTGTGATG 57.611 33.333 0.00 0.00 0.00 3.07
122 123 9.606631 GACATTAGGAGTAGAGATTTTTGTGAT 57.393 33.333 0.00 0.00 0.00 3.06
123 124 8.816894 AGACATTAGGAGTAGAGATTTTTGTGA 58.183 33.333 0.00 0.00 0.00 3.58
124 125 9.092876 GAGACATTAGGAGTAGAGATTTTTGTG 57.907 37.037 0.00 0.00 0.00 3.33
125 126 8.816894 TGAGACATTAGGAGTAGAGATTTTTGT 58.183 33.333 0.00 0.00 0.00 2.83
126 127 9.311916 CTGAGACATTAGGAGTAGAGATTTTTG 57.688 37.037 0.00 0.00 0.00 2.44
127 128 9.041354 ACTGAGACATTAGGAGTAGAGATTTTT 57.959 33.333 0.00 0.00 0.00 1.94
128 129 8.602472 ACTGAGACATTAGGAGTAGAGATTTT 57.398 34.615 0.00 0.00 0.00 1.82
129 130 8.474025 CAACTGAGACATTAGGAGTAGAGATTT 58.526 37.037 0.00 0.00 0.00 2.17
621 643 2.992114 AGGGCAGTCTCGCTCGTT 60.992 61.111 0.00 0.00 37.50 3.85
673 695 4.492160 GGCGACGATCTGGTGCGA 62.492 66.667 0.00 0.00 0.00 5.10
730 752 2.695970 CCGGGAGAGGAGGAGGAGT 61.696 68.421 0.00 0.00 0.00 3.85
844 878 2.713770 GCAGCGACGTATCCGAGA 59.286 61.111 0.00 0.00 37.88 4.04
936 1648 0.266152 CCTCCTCCCATACCCAGTCT 59.734 60.000 0.00 0.00 0.00 3.24
939 1651 1.056700 CCACCTCCTCCCATACCCAG 61.057 65.000 0.00 0.00 0.00 4.45
1168 2796 4.783621 GCTGCCCGCCTCATCACA 62.784 66.667 0.00 0.00 0.00 3.58
1222 2851 4.214327 CGGAGAGAAGAGCGCCCC 62.214 72.222 2.29 0.00 0.00 5.80
1235 2864 2.885113 TGAGCATCACCGTCGGAG 59.115 61.111 20.51 10.94 42.56 4.63
1414 3055 4.679373 ATCTACCATGCTCACTACTTGG 57.321 45.455 0.00 0.00 38.11 3.61
1458 3110 9.784531 ATTACTGCTGTAATTAGTAGCAATGAT 57.215 29.630 19.83 12.35 44.35 2.45
1675 3349 8.408043 AACATCATTCAGTATTCCTCAAACAA 57.592 30.769 0.00 0.00 0.00 2.83
1799 3574 8.698973 TCCAAACTACAGTCCAAAAATCATTA 57.301 30.769 0.00 0.00 0.00 1.90
1892 3681 5.698545 CCATTCTTCTCGTCTCAATATTCCC 59.301 44.000 0.00 0.00 0.00 3.97
1966 3764 5.321516 CGTTAATGGTAAAACAGTGCTAGC 58.678 41.667 8.10 8.10 0.00 3.42
1986 4757 6.150307 TGTTAACATATTCACAATGCTCCGTT 59.850 34.615 3.59 0.00 0.00 4.44
2549 5323 5.655090 TGATTTTCAGATTGCATCACTGGAT 59.345 36.000 12.85 7.15 33.19 3.41
2659 5441 1.517039 CTACTCGTGCAGCGCATCA 60.517 57.895 11.47 3.33 41.91 3.07
2699 5481 1.342175 ACCTACAGGCTACAGTCCTCC 60.342 57.143 0.00 0.00 39.32 4.30


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

AutoCloner maintained by Alex Coulton.