Multiple sequence alignment - TraesCS1A01G153200

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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 TraesCS1A01G153200 chr1A 100.000 1896 0 0 861 2756 266885943 266887838 0.000000e+00 3502
1 TraesCS1A01G153200 chr1A 100.000 521 0 0 1 521 266885083 266885603 0.000000e+00 963
2 TraesCS1A01G153200 chr6B 98.175 1315 16 3 861 2171 482807165 482808475 0.000000e+00 2289
3 TraesCS1A01G153200 chr6B 98.584 1271 14 2 905 2171 482844098 482842828 0.000000e+00 2244
4 TraesCS1A01G153200 chr6B 89.251 1135 99 8 939 2053 653232600 653233731 0.000000e+00 1399
5 TraesCS1A01G153200 chr6B 98.472 589 9 0 2168 2756 482817476 482816888 0.000000e+00 1038
6 TraesCS1A01G153200 chr6B 98.302 589 10 0 2168 2756 482837109 482836521 0.000000e+00 1033
7 TraesCS1A01G153200 chr6B 97.808 365 3 1 162 521 482826491 482826127 2.330000e-175 625
8 TraesCS1A01G153200 chrUn 97.888 1326 9 2 861 2171 289564922 289563601 0.000000e+00 2276
9 TraesCS1A01G153200 chrUn 96.610 1239 16 4 918 2155 424834178 424832965 0.000000e+00 2032
10 TraesCS1A01G153200 chrUn 98.302 589 9 1 2168 2756 289560338 289559751 0.000000e+00 1031
11 TraesCS1A01G153200 chrUn 97.283 368 9 1 154 521 377222544 377222178 8.380000e-175 623
12 TraesCS1A01G153200 chr6A 97.719 1315 14 4 861 2171 73513166 73514468 0.000000e+00 2248
13 TraesCS1A01G153200 chr6A 96.910 1327 25 7 861 2171 158421502 158420176 0.000000e+00 2209
14 TraesCS1A01G153200 chr6A 91.237 1221 74 12 863 2053 33376350 33377567 0.000000e+00 1631
15 TraesCS1A01G153200 chr6A 98.472 589 9 0 2168 2756 73517584 73518172 0.000000e+00 1038
16 TraesCS1A01G153200 chr6A 98.333 360 5 1 163 521 73512227 73512586 5.010000e-177 630
17 TraesCS1A01G153200 chr6A 96.267 375 13 1 148 521 47630242 47630616 5.040000e-172 614
18 TraesCS1A01G153200 chr7B 97.972 1282 11 1 905 2171 75059456 75058175 0.000000e+00 2209
19 TraesCS1A01G153200 chr7B 98.642 589 8 0 2168 2756 75051007 75050419 0.000000e+00 1044
20 TraesCS1A01G153200 chr7B 98.472 589 9 0 2168 2756 628742922 628743510 0.000000e+00 1038
21 TraesCS1A01G153200 chr7B 98.361 366 5 1 157 521 628737686 628738051 2.310000e-180 641
22 TraesCS1A01G153200 chr7B 97.260 365 5 1 162 521 75060401 75060037 5.040000e-172 614
23 TraesCS1A01G153200 chr2A 98.322 1192 17 1 864 2055 167356271 167355083 0.000000e+00 2087
24 TraesCS1A01G153200 chr2A 91.412 1211 75 11 863 2053 111441776 111442977 0.000000e+00 1633
25 TraesCS1A01G153200 chr2A 98.642 589 8 0 2168 2756 70019937 70019349 0.000000e+00 1044
26 TraesCS1A01G153200 chr2A 97.784 361 6 2 162 521 70025660 70025301 3.010000e-174 621
27 TraesCS1A01G153200 chr3B 93.180 1217 54 11 861 2053 680330807 680329596 0.000000e+00 1760
28 TraesCS1A01G153200 chr2B 90.909 1232 80 13 861 2066 723353334 723352109 0.000000e+00 1626
29 TraesCS1A01G153200 chr2B 98.472 589 9 0 2168 2756 615343211 615342623 0.000000e+00 1038
30 TraesCS1A01G153200 chr2B 98.889 360 4 0 162 521 616527988 616527629 0.000000e+00 643
31 TraesCS1A01G153200 chr3A 98.642 589 8 0 2168 2756 742304739 742305327 0.000000e+00 1044
32 TraesCS1A01G153200 chr5A 97.541 366 4 1 161 521 641774211 641773846 3.010000e-174 621
33 TraesCS1A01G153200 chr1D 92.547 161 12 0 1 161 211632952 211633112 5.940000e-57 231


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 TraesCS1A01G153200 chr1A 266885083 266887838 2755 False 2232.500000 3502 100.000000 1 2756 2 chr1A.!!$F1 2755
1 TraesCS1A01G153200 chr6B 482807165 482808475 1310 False 2289.000000 2289 98.175000 861 2171 1 chr6B.!!$F1 1310
2 TraesCS1A01G153200 chr6B 482842828 482844098 1270 True 2244.000000 2244 98.584000 905 2171 1 chr6B.!!$R4 1266
3 TraesCS1A01G153200 chr6B 653232600 653233731 1131 False 1399.000000 1399 89.251000 939 2053 1 chr6B.!!$F2 1114
4 TraesCS1A01G153200 chr6B 482816888 482817476 588 True 1038.000000 1038 98.472000 2168 2756 1 chr6B.!!$R1 588
5 TraesCS1A01G153200 chr6B 482836521 482837109 588 True 1033.000000 1033 98.302000 2168 2756 1 chr6B.!!$R3 588
6 TraesCS1A01G153200 chrUn 424832965 424834178 1213 True 2032.000000 2032 96.610000 918 2155 1 chrUn.!!$R2 1237
7 TraesCS1A01G153200 chrUn 289559751 289564922 5171 True 1653.500000 2276 98.095000 861 2756 2 chrUn.!!$R3 1895
8 TraesCS1A01G153200 chr6A 158420176 158421502 1326 True 2209.000000 2209 96.910000 861 2171 1 chr6A.!!$R1 1310
9 TraesCS1A01G153200 chr6A 33376350 33377567 1217 False 1631.000000 1631 91.237000 863 2053 1 chr6A.!!$F1 1190
10 TraesCS1A01G153200 chr6A 73512227 73518172 5945 False 1305.333333 2248 98.174667 163 2756 3 chr6A.!!$F3 2593
11 TraesCS1A01G153200 chr7B 75058175 75060401 2226 True 1411.500000 2209 97.616000 162 2171 2 chr7B.!!$R2 2009
12 TraesCS1A01G153200 chr7B 75050419 75051007 588 True 1044.000000 1044 98.642000 2168 2756 1 chr7B.!!$R1 588
13 TraesCS1A01G153200 chr7B 628742922 628743510 588 False 1038.000000 1038 98.472000 2168 2756 1 chr7B.!!$F2 588
14 TraesCS1A01G153200 chr2A 167355083 167356271 1188 True 2087.000000 2087 98.322000 864 2055 1 chr2A.!!$R3 1191
15 TraesCS1A01G153200 chr2A 111441776 111442977 1201 False 1633.000000 1633 91.412000 863 2053 1 chr2A.!!$F1 1190
16 TraesCS1A01G153200 chr2A 70019349 70019937 588 True 1044.000000 1044 98.642000 2168 2756 1 chr2A.!!$R1 588
17 TraesCS1A01G153200 chr3B 680329596 680330807 1211 True 1760.000000 1760 93.180000 861 2053 1 chr3B.!!$R1 1192
18 TraesCS1A01G153200 chr2B 723352109 723353334 1225 True 1626.000000 1626 90.909000 861 2066 1 chr2B.!!$R3 1205
19 TraesCS1A01G153200 chr2B 615342623 615343211 588 True 1038.000000 1038 98.472000 2168 2756 1 chr2B.!!$R1 588
20 TraesCS1A01G153200 chr3A 742304739 742305327 588 False 1044.000000 1044 98.642000 2168 2756 1 chr3A.!!$F1 588

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
50 51 0.040425 CGCCAAAACCAGCACTACAC 60.040 55.0 0.0 0.0 0.0 2.90 F
51 52 1.028905 GCCAAAACCAGCACTACACA 58.971 50.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1087 1866 2.032681 GAACCGGTGCAGCTCCTT 59.967 61.111 8.52 1.8 0.00 3.36 R
2338 7405 5.183713 TGCATTCCAGTTGAACTTCCTTATG 59.816 40.000 0.00 0.0 35.31 1.90 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
18 19 2.551996 GGGGCCTTATTAGGGAGCA 58.448 57.895 0.84 0.00 42.25 4.26
19 20 0.850784 GGGGCCTTATTAGGGAGCAA 59.149 55.000 0.84 0.00 42.25 3.91
20 21 1.478837 GGGGCCTTATTAGGGAGCAAC 60.479 57.143 0.84 0.00 42.25 4.17
21 22 1.214424 GGGCCTTATTAGGGAGCAACA 59.786 52.381 0.84 0.00 42.25 3.33
22 23 2.158460 GGGCCTTATTAGGGAGCAACAT 60.158 50.000 0.84 0.00 42.25 2.71
23 24 3.566351 GGCCTTATTAGGGAGCAACATT 58.434 45.455 0.00 0.00 42.25 2.71
24 25 3.960755 GGCCTTATTAGGGAGCAACATTT 59.039 43.478 0.00 0.00 42.25 2.32
25 26 5.137551 GGCCTTATTAGGGAGCAACATTTA 58.862 41.667 0.00 0.00 42.25 1.40
26 27 5.596772 GGCCTTATTAGGGAGCAACATTTAA 59.403 40.000 0.00 0.00 42.25 1.52
27 28 6.267699 GGCCTTATTAGGGAGCAACATTTAAT 59.732 38.462 0.00 0.00 42.25 1.40
28 29 7.371159 GCCTTATTAGGGAGCAACATTTAATC 58.629 38.462 0.00 0.00 42.25 1.75
29 30 7.014230 GCCTTATTAGGGAGCAACATTTAATCA 59.986 37.037 0.00 0.00 42.25 2.57
30 31 9.082313 CCTTATTAGGGAGCAACATTTAATCAT 57.918 33.333 0.00 0.00 37.94 2.45
32 33 6.618287 TTAGGGAGCAACATTTAATCATCG 57.382 37.500 0.00 0.00 0.00 3.84
33 34 3.316308 AGGGAGCAACATTTAATCATCGC 59.684 43.478 0.00 0.00 0.00 4.58
34 35 3.550842 GGGAGCAACATTTAATCATCGCC 60.551 47.826 0.00 0.00 0.00 5.54
35 36 3.066621 GGAGCAACATTTAATCATCGCCA 59.933 43.478 0.00 0.00 0.00 5.69
36 37 4.439974 GGAGCAACATTTAATCATCGCCAA 60.440 41.667 0.00 0.00 0.00 4.52
37 38 5.070770 AGCAACATTTAATCATCGCCAAA 57.929 34.783 0.00 0.00 0.00 3.28
38 39 5.477510 AGCAACATTTAATCATCGCCAAAA 58.522 33.333 0.00 0.00 0.00 2.44
39 40 5.348451 AGCAACATTTAATCATCGCCAAAAC 59.652 36.000 0.00 0.00 0.00 2.43
40 41 5.445806 GCAACATTTAATCATCGCCAAAACC 60.446 40.000 0.00 0.00 0.00 3.27
41 42 5.398603 ACATTTAATCATCGCCAAAACCA 57.601 34.783 0.00 0.00 0.00 3.67
42 43 5.410067 ACATTTAATCATCGCCAAAACCAG 58.590 37.500 0.00 0.00 0.00 4.00
43 44 3.502191 TTAATCATCGCCAAAACCAGC 57.498 42.857 0.00 0.00 0.00 4.85
44 45 1.255882 AATCATCGCCAAAACCAGCA 58.744 45.000 0.00 0.00 0.00 4.41
45 46 0.527565 ATCATCGCCAAAACCAGCAC 59.472 50.000 0.00 0.00 0.00 4.40
46 47 0.537143 TCATCGCCAAAACCAGCACT 60.537 50.000 0.00 0.00 0.00 4.40
47 48 1.164411 CATCGCCAAAACCAGCACTA 58.836 50.000 0.00 0.00 0.00 2.74
48 49 1.135689 CATCGCCAAAACCAGCACTAC 60.136 52.381 0.00 0.00 0.00 2.73
49 50 0.179043 TCGCCAAAACCAGCACTACA 60.179 50.000 0.00 0.00 0.00 2.74
50 51 0.040425 CGCCAAAACCAGCACTACAC 60.040 55.000 0.00 0.00 0.00 2.90
51 52 1.028905 GCCAAAACCAGCACTACACA 58.971 50.000 0.00 0.00 0.00 3.72
52 53 1.269051 GCCAAAACCAGCACTACACAC 60.269 52.381 0.00 0.00 0.00 3.82
53 54 2.020720 CCAAAACCAGCACTACACACA 58.979 47.619 0.00 0.00 0.00 3.72
54 55 2.425312 CCAAAACCAGCACTACACACAA 59.575 45.455 0.00 0.00 0.00 3.33
55 56 3.068024 CCAAAACCAGCACTACACACAAT 59.932 43.478 0.00 0.00 0.00 2.71
56 57 4.277174 CCAAAACCAGCACTACACACAATA 59.723 41.667 0.00 0.00 0.00 1.90
57 58 5.048083 CCAAAACCAGCACTACACACAATAT 60.048 40.000 0.00 0.00 0.00 1.28
58 59 5.627499 AAACCAGCACTACACACAATATG 57.373 39.130 0.00 0.00 0.00 1.78
59 60 3.009723 ACCAGCACTACACACAATATGC 58.990 45.455 0.00 0.00 0.00 3.14
60 61 3.273434 CCAGCACTACACACAATATGCT 58.727 45.455 0.00 0.00 43.96 3.79
62 63 4.206477 AGCACTACACACAATATGCTGA 57.794 40.909 0.00 0.00 41.67 4.26
63 64 4.774124 AGCACTACACACAATATGCTGAT 58.226 39.130 0.00 0.00 41.67 2.90
64 65 5.188434 AGCACTACACACAATATGCTGATT 58.812 37.500 0.00 0.00 41.67 2.57
65 66 5.649395 AGCACTACACACAATATGCTGATTT 59.351 36.000 0.00 0.00 41.67 2.17
66 67 6.151648 AGCACTACACACAATATGCTGATTTT 59.848 34.615 0.00 0.00 41.67 1.82
67 68 6.808212 GCACTACACACAATATGCTGATTTTT 59.192 34.615 0.00 0.00 0.00 1.94
68 69 7.967854 GCACTACACACAATATGCTGATTTTTA 59.032 33.333 0.00 0.00 0.00 1.52
71 72 7.760131 ACACACAATATGCTGATTTTTATGC 57.240 32.000 0.00 0.00 0.00 3.14
72 73 7.321908 ACACACAATATGCTGATTTTTATGCA 58.678 30.769 0.00 0.00 39.83 3.96
73 74 7.490079 ACACACAATATGCTGATTTTTATGCAG 59.510 33.333 0.00 0.00 38.87 4.41
74 75 7.703197 CACACAATATGCTGATTTTTATGCAGA 59.297 33.333 0.00 0.00 38.87 4.26
75 76 8.418662 ACACAATATGCTGATTTTTATGCAGAT 58.581 29.630 0.00 0.00 38.73 2.90
76 77 8.699749 CACAATATGCTGATTTTTATGCAGATG 58.300 33.333 0.00 0.00 37.42 2.90
77 78 8.635328 ACAATATGCTGATTTTTATGCAGATGA 58.365 29.630 0.00 0.00 37.42 2.92
78 79 9.639601 CAATATGCTGATTTTTATGCAGATGAT 57.360 29.630 0.00 0.00 37.42 2.45
82 83 7.998580 TGCTGATTTTTATGCAGATGATTACA 58.001 30.769 0.00 0.00 0.00 2.41
83 84 8.468399 TGCTGATTTTTATGCAGATGATTACAA 58.532 29.630 0.00 0.00 0.00 2.41
84 85 9.304731 GCTGATTTTTATGCAGATGATTACAAA 57.695 29.630 0.00 0.00 0.00 2.83
93 94 6.554419 TGCAGATGATTACAAAACATAGTGC 58.446 36.000 0.00 0.00 35.99 4.40
94 95 6.375174 TGCAGATGATTACAAAACATAGTGCT 59.625 34.615 0.00 0.00 36.21 4.40
95 96 7.552330 TGCAGATGATTACAAAACATAGTGCTA 59.448 33.333 0.00 0.00 36.21 3.49
96 97 8.562892 GCAGATGATTACAAAACATAGTGCTAT 58.437 33.333 0.00 0.00 34.30 2.97
102 103 9.503427 GATTACAAAACATAGTGCTATTTGTCC 57.497 33.333 10.74 2.80 30.86 4.02
103 104 6.892658 ACAAAACATAGTGCTATTTGTCCA 57.107 33.333 0.00 0.00 0.00 4.02
104 105 7.466746 ACAAAACATAGTGCTATTTGTCCAT 57.533 32.000 0.00 0.00 0.00 3.41
105 106 7.315142 ACAAAACATAGTGCTATTTGTCCATG 58.685 34.615 0.00 0.00 0.00 3.66
106 107 5.505173 AACATAGTGCTATTTGTCCATGC 57.495 39.130 0.00 0.00 0.00 4.06
107 108 4.525996 ACATAGTGCTATTTGTCCATGCA 58.474 39.130 0.00 0.00 0.00 3.96
113 114 4.779696 TGCTATTTGTCCATGCACATAGA 58.220 39.130 2.20 0.00 33.35 1.98
114 115 4.818005 TGCTATTTGTCCATGCACATAGAG 59.182 41.667 2.20 0.24 33.35 2.43
115 116 5.059161 GCTATTTGTCCATGCACATAGAGA 58.941 41.667 6.10 0.00 33.35 3.10
116 117 5.528690 GCTATTTGTCCATGCACATAGAGAA 59.471 40.000 6.10 0.00 33.35 2.87
117 118 5.824904 ATTTGTCCATGCACATAGAGAAC 57.175 39.130 0.00 0.00 0.00 3.01
118 119 4.558226 TTGTCCATGCACATAGAGAACT 57.442 40.909 0.00 0.00 0.00 3.01
119 120 4.558226 TGTCCATGCACATAGAGAACTT 57.442 40.909 0.00 0.00 0.00 2.66
120 121 4.910195 TGTCCATGCACATAGAGAACTTT 58.090 39.130 0.00 0.00 0.00 2.66
121 122 5.316167 TGTCCATGCACATAGAGAACTTTT 58.684 37.500 0.00 0.00 0.00 2.27
122 123 5.412594 TGTCCATGCACATAGAGAACTTTTC 59.587 40.000 0.00 0.00 0.00 2.29
123 124 5.645497 GTCCATGCACATAGAGAACTTTTCT 59.355 40.000 0.00 0.00 44.21 2.52
124 125 5.645067 TCCATGCACATAGAGAACTTTTCTG 59.355 40.000 0.00 0.00 40.87 3.02
125 126 5.330295 CATGCACATAGAGAACTTTTCTGC 58.670 41.667 0.00 0.00 40.87 4.26
126 127 4.645535 TGCACATAGAGAACTTTTCTGCT 58.354 39.130 0.00 0.00 40.87 4.24
127 128 5.065914 TGCACATAGAGAACTTTTCTGCTT 58.934 37.500 0.00 0.00 40.87 3.91
128 129 5.180117 TGCACATAGAGAACTTTTCTGCTTC 59.820 40.000 0.00 0.00 40.87 3.86
129 130 5.411053 GCACATAGAGAACTTTTCTGCTTCT 59.589 40.000 0.00 0.00 40.87 2.85
130 131 6.072783 GCACATAGAGAACTTTTCTGCTTCTT 60.073 38.462 0.00 0.00 40.87 2.52
131 132 7.118390 GCACATAGAGAACTTTTCTGCTTCTTA 59.882 37.037 0.00 0.00 40.87 2.10
132 133 8.993121 CACATAGAGAACTTTTCTGCTTCTTAA 58.007 33.333 0.00 0.00 40.87 1.85
133 134 9.561069 ACATAGAGAACTTTTCTGCTTCTTAAA 57.439 29.630 0.00 0.00 40.87 1.52
135 136 9.785982 ATAGAGAACTTTTCTGCTTCTTAAAGT 57.214 29.630 0.00 0.00 40.87 2.66
137 138 8.961634 AGAGAACTTTTCTGCTTCTTAAAGTTT 58.038 29.630 11.64 0.00 45.62 2.66
138 139 9.574458 GAGAACTTTTCTGCTTCTTAAAGTTTT 57.426 29.630 11.64 7.41 45.62 2.43
139 140 9.574458 AGAACTTTTCTGCTTCTTAAAGTTTTC 57.426 29.630 11.64 2.94 45.62 2.29
140 141 9.574458 GAACTTTTCTGCTTCTTAAAGTTTTCT 57.426 29.630 11.64 0.00 45.62 2.52
141 142 9.574458 AACTTTTCTGCTTCTTAAAGTTTTCTC 57.426 29.630 0.00 0.00 44.16 2.87
142 143 8.961634 ACTTTTCTGCTTCTTAAAGTTTTCTCT 58.038 29.630 0.00 0.00 37.50 3.10
146 147 8.608844 TCTGCTTCTTAAAGTTTTCTCTAAGG 57.391 34.615 0.00 0.00 32.88 2.69
147 148 8.211629 TCTGCTTCTTAAAGTTTTCTCTAAGGT 58.788 33.333 0.00 0.00 32.88 3.50
148 149 8.379457 TGCTTCTTAAAGTTTTCTCTAAGGTC 57.621 34.615 0.00 0.00 32.88 3.85
149 150 7.990886 TGCTTCTTAAAGTTTTCTCTAAGGTCA 59.009 33.333 0.00 0.00 32.88 4.02
150 151 9.004717 GCTTCTTAAAGTTTTCTCTAAGGTCAT 57.995 33.333 0.00 0.00 32.88 3.06
220 221 2.225066 GGTCCAGATCGTCCTATACCCT 60.225 54.545 0.00 0.00 0.00 4.34
319 320 4.404654 GGCCCGTCGACGTACGTT 62.405 66.667 33.49 6.19 41.27 3.99
2372 7439 4.768448 TCAACTGGAATGCATTCACTTCAT 59.232 37.500 34.08 16.10 38.53 2.57
2380 7447 4.365899 TGCATTCACTTCATGATTCTGC 57.634 40.909 0.00 1.53 37.11 4.26
2394 7461 5.535753 TGATTCTGCTTATCGGAGATTGA 57.464 39.130 0.00 0.00 45.12 2.57
2590 7657 4.771114 TCACCGGTCCAAAATATGATCT 57.229 40.909 2.59 0.00 0.00 2.75
2637 7704 3.637229 GAGGAACTGGACGGAAGATATGA 59.363 47.826 0.00 0.00 41.55 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.850784 TTGCTCCCTAATAAGGCCCC 59.149 55.000 0.00 0.00 42.14 5.80
1 2 1.214424 TGTTGCTCCCTAATAAGGCCC 59.786 52.381 0.00 0.00 42.14 5.80
2 3 2.729028 TGTTGCTCCCTAATAAGGCC 57.271 50.000 0.00 0.00 42.14 5.19
3 4 6.709018 TTAAATGTTGCTCCCTAATAAGGC 57.291 37.500 0.00 0.00 42.14 4.35
4 5 8.463930 TGATTAAATGTTGCTCCCTAATAAGG 57.536 34.615 0.00 0.00 43.25 2.69
6 7 8.783093 CGATGATTAAATGTTGCTCCCTAATAA 58.217 33.333 0.00 0.00 0.00 1.40
7 8 7.094805 GCGATGATTAAATGTTGCTCCCTAATA 60.095 37.037 0.00 0.00 0.00 0.98
8 9 6.294176 GCGATGATTAAATGTTGCTCCCTAAT 60.294 38.462 0.00 0.00 0.00 1.73
9 10 5.008613 GCGATGATTAAATGTTGCTCCCTAA 59.991 40.000 0.00 0.00 0.00 2.69
10 11 4.515191 GCGATGATTAAATGTTGCTCCCTA 59.485 41.667 0.00 0.00 0.00 3.53
11 12 3.316308 GCGATGATTAAATGTTGCTCCCT 59.684 43.478 0.00 0.00 0.00 4.20
12 13 3.550842 GGCGATGATTAAATGTTGCTCCC 60.551 47.826 0.00 0.00 0.00 4.30
13 14 3.066621 TGGCGATGATTAAATGTTGCTCC 59.933 43.478 0.00 0.00 0.00 4.70
14 15 4.291540 TGGCGATGATTAAATGTTGCTC 57.708 40.909 0.00 0.00 0.00 4.26
15 16 4.717233 TTGGCGATGATTAAATGTTGCT 57.283 36.364 0.00 0.00 0.00 3.91
16 17 5.445806 GGTTTTGGCGATGATTAAATGTTGC 60.446 40.000 0.00 0.00 0.00 4.17
17 18 5.636965 TGGTTTTGGCGATGATTAAATGTTG 59.363 36.000 0.00 0.00 0.00 3.33
18 19 5.788450 TGGTTTTGGCGATGATTAAATGTT 58.212 33.333 0.00 0.00 0.00 2.71
19 20 5.398603 TGGTTTTGGCGATGATTAAATGT 57.601 34.783 0.00 0.00 0.00 2.71
20 21 4.268405 GCTGGTTTTGGCGATGATTAAATG 59.732 41.667 0.00 0.00 0.00 2.32
21 22 4.081752 TGCTGGTTTTGGCGATGATTAAAT 60.082 37.500 0.00 0.00 0.00 1.40
22 23 3.256879 TGCTGGTTTTGGCGATGATTAAA 59.743 39.130 0.00 0.00 0.00 1.52
23 24 2.822561 TGCTGGTTTTGGCGATGATTAA 59.177 40.909 0.00 0.00 0.00 1.40
24 25 2.163412 GTGCTGGTTTTGGCGATGATTA 59.837 45.455 0.00 0.00 0.00 1.75
25 26 1.067635 GTGCTGGTTTTGGCGATGATT 60.068 47.619 0.00 0.00 0.00 2.57
26 27 0.527565 GTGCTGGTTTTGGCGATGAT 59.472 50.000 0.00 0.00 0.00 2.45
27 28 0.537143 AGTGCTGGTTTTGGCGATGA 60.537 50.000 0.00 0.00 0.00 2.92
28 29 1.135689 GTAGTGCTGGTTTTGGCGATG 60.136 52.381 0.00 0.00 0.00 3.84
29 30 1.165270 GTAGTGCTGGTTTTGGCGAT 58.835 50.000 0.00 0.00 0.00 4.58
30 31 0.179043 TGTAGTGCTGGTTTTGGCGA 60.179 50.000 0.00 0.00 0.00 5.54
31 32 0.040425 GTGTAGTGCTGGTTTTGGCG 60.040 55.000 0.00 0.00 0.00 5.69
32 33 1.028905 TGTGTAGTGCTGGTTTTGGC 58.971 50.000 0.00 0.00 0.00 4.52
33 34 2.020720 TGTGTGTAGTGCTGGTTTTGG 58.979 47.619 0.00 0.00 0.00 3.28
34 35 3.773860 TTGTGTGTAGTGCTGGTTTTG 57.226 42.857 0.00 0.00 0.00 2.44
35 36 5.564651 GCATATTGTGTGTAGTGCTGGTTTT 60.565 40.000 0.00 0.00 0.00 2.43
36 37 4.082787 GCATATTGTGTGTAGTGCTGGTTT 60.083 41.667 0.00 0.00 0.00 3.27
37 38 3.440173 GCATATTGTGTGTAGTGCTGGTT 59.560 43.478 0.00 0.00 0.00 3.67
38 39 3.009723 GCATATTGTGTGTAGTGCTGGT 58.990 45.455 0.00 0.00 0.00 4.00
39 40 3.273434 AGCATATTGTGTGTAGTGCTGG 58.727 45.455 0.00 0.00 40.99 4.85
41 42 4.206477 TCAGCATATTGTGTGTAGTGCT 57.794 40.909 0.00 0.00 43.07 4.40
42 43 5.490139 AATCAGCATATTGTGTGTAGTGC 57.510 39.130 0.00 0.00 0.00 4.40
45 46 8.961092 GCATAAAAATCAGCATATTGTGTGTAG 58.039 33.333 0.00 0.00 0.00 2.74
46 47 8.465201 TGCATAAAAATCAGCATATTGTGTGTA 58.535 29.630 0.00 0.00 31.05 2.90
47 48 7.321908 TGCATAAAAATCAGCATATTGTGTGT 58.678 30.769 0.00 0.00 31.05 3.72
48 49 7.703197 TCTGCATAAAAATCAGCATATTGTGTG 59.297 33.333 0.00 0.00 36.28 3.82
49 50 7.774134 TCTGCATAAAAATCAGCATATTGTGT 58.226 30.769 0.00 0.00 36.28 3.72
50 51 8.699749 CATCTGCATAAAAATCAGCATATTGTG 58.300 33.333 0.00 0.00 36.28 3.33
51 52 8.635328 TCATCTGCATAAAAATCAGCATATTGT 58.365 29.630 0.00 0.00 36.28 2.71
52 53 9.639601 ATCATCTGCATAAAAATCAGCATATTG 57.360 29.630 0.00 0.00 36.28 1.90
56 57 8.635328 TGTAATCATCTGCATAAAAATCAGCAT 58.365 29.630 0.00 0.00 36.28 3.79
57 58 7.998580 TGTAATCATCTGCATAAAAATCAGCA 58.001 30.769 0.00 0.00 35.43 4.41
58 59 8.861033 TTGTAATCATCTGCATAAAAATCAGC 57.139 30.769 0.00 0.00 0.00 4.26
67 68 8.344831 GCACTATGTTTTGTAATCATCTGCATA 58.655 33.333 0.00 0.00 31.48 3.14
68 69 7.067859 AGCACTATGTTTTGTAATCATCTGCAT 59.932 33.333 0.00 0.00 32.54 3.96
69 70 6.375174 AGCACTATGTTTTGTAATCATCTGCA 59.625 34.615 0.00 0.00 32.54 4.41
70 71 6.789262 AGCACTATGTTTTGTAATCATCTGC 58.211 36.000 0.00 0.00 0.00 4.26
76 77 9.503427 GGACAAATAGCACTATGTTTTGTAATC 57.497 33.333 7.51 0.00 29.29 1.75
77 78 9.019656 TGGACAAATAGCACTATGTTTTGTAAT 57.980 29.630 7.51 0.00 29.29 1.89
78 79 8.397575 TGGACAAATAGCACTATGTTTTGTAA 57.602 30.769 7.51 0.07 29.29 2.41
79 80 7.987750 TGGACAAATAGCACTATGTTTTGTA 57.012 32.000 7.51 0.00 29.29 2.41
80 81 6.892658 TGGACAAATAGCACTATGTTTTGT 57.107 33.333 7.32 7.32 30.84 2.83
81 82 6.254157 GCATGGACAAATAGCACTATGTTTTG 59.746 38.462 0.00 0.00 0.00 2.44
82 83 6.071447 TGCATGGACAAATAGCACTATGTTTT 60.071 34.615 0.00 0.00 0.00 2.43
83 84 5.418524 TGCATGGACAAATAGCACTATGTTT 59.581 36.000 0.00 0.00 0.00 2.83
84 85 4.949238 TGCATGGACAAATAGCACTATGTT 59.051 37.500 0.00 0.00 0.00 2.71
85 86 4.525996 TGCATGGACAAATAGCACTATGT 58.474 39.130 0.00 0.00 0.00 2.29
91 92 4.779696 TCTATGTGCATGGACAAATAGCA 58.220 39.130 24.45 9.36 37.65 3.49
92 93 5.059161 TCTCTATGTGCATGGACAAATAGC 58.941 41.667 24.45 0.00 37.65 2.97
93 94 6.765036 AGTTCTCTATGTGCATGGACAAATAG 59.235 38.462 24.45 20.30 38.66 1.73
94 95 6.653020 AGTTCTCTATGTGCATGGACAAATA 58.347 36.000 24.45 11.91 0.00 1.40
95 96 5.503927 AGTTCTCTATGTGCATGGACAAAT 58.496 37.500 24.45 11.35 0.00 2.32
96 97 4.910195 AGTTCTCTATGTGCATGGACAAA 58.090 39.130 24.45 10.60 0.00 2.83
97 98 4.558226 AGTTCTCTATGTGCATGGACAA 57.442 40.909 24.45 12.24 0.00 3.18
98 99 4.558226 AAGTTCTCTATGTGCATGGACA 57.442 40.909 22.95 22.95 0.00 4.02
99 100 5.645497 AGAAAAGTTCTCTATGTGCATGGAC 59.355 40.000 10.90 10.90 34.07 4.02
100 101 5.645067 CAGAAAAGTTCTCTATGTGCATGGA 59.355 40.000 0.00 0.00 38.11 3.41
101 102 5.675575 GCAGAAAAGTTCTCTATGTGCATGG 60.676 44.000 0.00 0.00 38.11 3.66
102 103 5.123502 AGCAGAAAAGTTCTCTATGTGCATG 59.876 40.000 0.00 0.00 38.11 4.06
103 104 5.251764 AGCAGAAAAGTTCTCTATGTGCAT 58.748 37.500 0.00 0.00 38.11 3.96
104 105 4.645535 AGCAGAAAAGTTCTCTATGTGCA 58.354 39.130 0.00 0.00 38.11 4.57
105 106 5.411053 AGAAGCAGAAAAGTTCTCTATGTGC 59.589 40.000 0.00 0.00 38.11 4.57
106 107 7.432350 AAGAAGCAGAAAAGTTCTCTATGTG 57.568 36.000 0.00 0.00 38.11 3.21
107 108 9.561069 TTTAAGAAGCAGAAAAGTTCTCTATGT 57.439 29.630 0.00 0.00 38.11 2.29
109 110 9.785982 ACTTTAAGAAGCAGAAAAGTTCTCTAT 57.214 29.630 0.00 0.00 38.65 1.98
110 111 9.614792 AACTTTAAGAAGCAGAAAAGTTCTCTA 57.385 29.630 0.00 0.00 44.63 2.43
111 112 8.512966 AACTTTAAGAAGCAGAAAAGTTCTCT 57.487 30.769 0.00 0.00 44.63 3.10
112 113 9.574458 AAAACTTTAAGAAGCAGAAAAGTTCTC 57.426 29.630 11.23 0.00 46.19 2.87
113 114 9.574458 GAAAACTTTAAGAAGCAGAAAAGTTCT 57.426 29.630 11.23 0.00 46.19 3.01
114 115 9.574458 AGAAAACTTTAAGAAGCAGAAAAGTTC 57.426 29.630 11.23 2.64 46.19 3.01
116 117 8.961634 AGAGAAAACTTTAAGAAGCAGAAAAGT 58.038 29.630 0.00 0.00 42.40 2.66
120 121 9.057089 CCTTAGAGAAAACTTTAAGAAGCAGAA 57.943 33.333 0.00 0.00 36.29 3.02
121 122 8.211629 ACCTTAGAGAAAACTTTAAGAAGCAGA 58.788 33.333 0.00 0.00 36.29 4.26
122 123 8.384607 ACCTTAGAGAAAACTTTAAGAAGCAG 57.615 34.615 0.00 0.00 36.29 4.24
123 124 7.990886 TGACCTTAGAGAAAACTTTAAGAAGCA 59.009 33.333 0.00 0.00 36.29 3.91
124 125 8.379457 TGACCTTAGAGAAAACTTTAAGAAGC 57.621 34.615 0.00 0.00 36.29 3.86
144 145 9.482175 AGAAGAAGTGTTACTAGAATATGACCT 57.518 33.333 0.00 0.00 0.00 3.85
148 149 9.239002 CCGAAGAAGAAGTGTTACTAGAATATG 57.761 37.037 0.00 0.00 0.00 1.78
149 150 8.968969 ACCGAAGAAGAAGTGTTACTAGAATAT 58.031 33.333 0.00 0.00 0.00 1.28
150 151 8.345724 ACCGAAGAAGAAGTGTTACTAGAATA 57.654 34.615 0.00 0.00 0.00 1.75
151 152 7.229581 ACCGAAGAAGAAGTGTTACTAGAAT 57.770 36.000 0.00 0.00 0.00 2.40
152 153 6.645790 ACCGAAGAAGAAGTGTTACTAGAA 57.354 37.500 0.00 0.00 0.00 2.10
153 154 6.712095 TGTACCGAAGAAGAAGTGTTACTAGA 59.288 38.462 0.00 0.00 0.00 2.43
154 155 6.906659 TGTACCGAAGAAGAAGTGTTACTAG 58.093 40.000 0.00 0.00 0.00 2.57
155 156 6.882610 TGTACCGAAGAAGAAGTGTTACTA 57.117 37.500 0.00 0.00 0.00 1.82
156 157 5.779529 TGTACCGAAGAAGAAGTGTTACT 57.220 39.130 0.00 0.00 0.00 2.24
157 158 5.176406 GGTTGTACCGAAGAAGAAGTGTTAC 59.824 44.000 0.00 0.00 0.00 2.50
158 159 5.291971 GGTTGTACCGAAGAAGAAGTGTTA 58.708 41.667 0.00 0.00 0.00 2.41
159 160 4.124970 GGTTGTACCGAAGAAGAAGTGTT 58.875 43.478 0.00 0.00 0.00 3.32
160 161 3.493873 GGGTTGTACCGAAGAAGAAGTGT 60.494 47.826 0.00 0.00 39.83 3.55
319 320 6.201425 ACAGTAAAAAGAAAATGCGTAGACGA 59.799 34.615 6.19 0.00 43.02 4.20
372 374 4.373116 ACCGACGCGCTTGACCAT 62.373 61.111 5.73 0.00 0.00 3.55
1087 1866 2.032681 GAACCGGTGCAGCTCCTT 59.967 61.111 8.52 1.80 0.00 3.36
2338 7405 5.183713 TGCATTCCAGTTGAACTTCCTTATG 59.816 40.000 0.00 0.00 35.31 1.90
2372 7439 5.535753 TCAATCTCCGATAAGCAGAATCA 57.464 39.130 0.00 0.00 0.00 2.57
2394 7461 0.462759 GCCGTCCTGCAGAAGCTTAT 60.463 55.000 17.39 0.00 42.74 1.73
2552 7619 2.508526 GTGATTGGTTGCACCTTCTCT 58.491 47.619 6.83 0.00 39.58 3.10
2637 7704 5.241949 AGTCGTATTTGTCTCTTCTCACAGT 59.758 40.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.