Multiple sequence alignment - TraesCS4B01G238500

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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 TraesCS4B01G238500 chr4B 100.000 4245 0 0 1 4245 495582658 495578414 0.000000e+00 7840.0
1 TraesCS4B01G238500 chr2B 98.344 4046 54 5 205 4245 449213532 449209495 0.000000e+00 7088.0
2 TraesCS4B01G238500 chr2B 98.293 4043 54 4 205 4245 234535356 234531327 0.000000e+00 7070.0
3 TraesCS4B01G238500 chr3B 98.243 4042 62 4 205 4245 6004966 6000933 0.000000e+00 7062.0
4 TraesCS4B01G238500 chr3B 98.218 4041 65 2 205 4245 92290943 92286910 0.000000e+00 7057.0
5 TraesCS4B01G238500 chr3B 87.156 109 9 3 18 122 750322933 750322826 7.460000e-23 119.0
6 TraesCS4B01G238500 chr1B 98.194 4041 65 3 205 4245 619189530 619185498 0.000000e+00 7051.0
7 TraesCS4B01G238500 chr6D 97.580 4050 78 7 205 4245 458922560 458918522 0.000000e+00 6918.0
8 TraesCS4B01G238500 chr7A 97.359 4052 86 7 205 4245 563516296 563512255 0.000000e+00 6870.0
9 TraesCS4B01G238500 chr7D 97.265 4022 87 10 232 4245 307045877 307049883 0.000000e+00 6796.0
10 TraesCS4B01G238500 chr6A 98.352 3520 51 2 205 3724 84403744 84400232 0.000000e+00 6172.0
11 TraesCS4B01G238500 chr2A 98.125 160 3 0 3772 3931 537269429 537269588 3.230000e-71 279.0
12 TraesCS4B01G238500 chr2A 97.143 105 2 1 4109 4212 24355093 24354989 4.360000e-40 176.0
13 TraesCS4B01G238500 chr6B 90.566 106 7 2 20 122 697461393 697461498 2.060000e-28 137.0
14 TraesCS4B01G238500 chr6B 81.731 104 17 2 20 122 445031258 445031360 7.560000e-13 86.1
15 TraesCS4B01G238500 chr4A 90.476 105 7 2 21 122 695493120 695493016 7.400000e-28 135.0
16 TraesCS4B01G238500 chr7B 85.577 104 13 1 20 121 703287316 703287419 1.610000e-19 108.0


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 TraesCS4B01G238500 chr4B 495578414 495582658 4244 True 7840 7840 100.000 1 4245 1 chr4B.!!$R1 4244
1 TraesCS4B01G238500 chr2B 449209495 449213532 4037 True 7088 7088 98.344 205 4245 1 chr2B.!!$R2 4040
2 TraesCS4B01G238500 chr2B 234531327 234535356 4029 True 7070 7070 98.293 205 4245 1 chr2B.!!$R1 4040
3 TraesCS4B01G238500 chr3B 6000933 6004966 4033 True 7062 7062 98.243 205 4245 1 chr3B.!!$R1 4040
4 TraesCS4B01G238500 chr3B 92286910 92290943 4033 True 7057 7057 98.218 205 4245 1 chr3B.!!$R2 4040
5 TraesCS4B01G238500 chr1B 619185498 619189530 4032 True 7051 7051 98.194 205 4245 1 chr1B.!!$R1 4040
6 TraesCS4B01G238500 chr6D 458918522 458922560 4038 True 6918 6918 97.580 205 4245 1 chr6D.!!$R1 4040
7 TraesCS4B01G238500 chr7A 563512255 563516296 4041 True 6870 6870 97.359 205 4245 1 chr7A.!!$R1 4040
8 TraesCS4B01G238500 chr7D 307045877 307049883 4006 False 6796 6796 97.265 232 4245 1 chr7D.!!$F1 4013
9 TraesCS4B01G238500 chr6A 84400232 84403744 3512 True 6172 6172 98.352 205 3724 1 chr6A.!!$R1 3519

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
62 63 0.034337 AAAAAGACCTCCGCGCACTA 59.966 50.0 8.75 0.00 0.00 2.74 F
65 66 0.034337 AAGACCTCCGCGCACTAAAA 59.966 50.0 8.75 0.00 0.00 1.52 F
107 108 0.169894 GCTCCAGCAAAAGCTGTAGC 59.830 55.0 17.07 17.07 41.19 3.58 F
125 126 0.781787 GCGCTAAAAGTTTTTGCCGG 59.218 50.0 23.09 14.26 0.00 6.13 F
2456 2471 0.109597 GCACGGTTTTGCATGAGAGG 60.110 55.0 0.00 0.00 42.49 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 1774 0.456312 CCACACTCCTTCGTAGACGC 60.456 60.000 0.00 0.0 39.60 5.19 R
1857 1864 3.782523 TGGGGATAGCATTTCTCTTCTGT 59.217 43.478 0.00 0.0 0.00 3.41 R
2223 2238 3.827722 TCAATCCTTTCGACCTTGGTTT 58.172 40.909 0.00 0.0 0.00 3.27 R
2650 2665 5.469373 TCATGCTTGTTTGAGTAATAGCG 57.531 39.130 0.00 0.0 32.19 4.26 R
3383 3398 4.258543 TGGTTCGGTATGGAATGAACTTC 58.741 43.478 4.23 0.0 40.34 3.01 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 3.314541 ACGTTCGGTCTTGCTAATTCT 57.685 42.857 0.00 0.00 0.00 2.40
21 22 4.445452 ACGTTCGGTCTTGCTAATTCTA 57.555 40.909 0.00 0.00 0.00 2.10
22 23 4.813027 ACGTTCGGTCTTGCTAATTCTAA 58.187 39.130 0.00 0.00 0.00 2.10
23 24 4.863131 ACGTTCGGTCTTGCTAATTCTAAG 59.137 41.667 0.00 0.00 0.00 2.18
24 25 5.100259 CGTTCGGTCTTGCTAATTCTAAGA 58.900 41.667 0.00 0.00 0.00 2.10
25 26 5.230306 CGTTCGGTCTTGCTAATTCTAAGAG 59.770 44.000 0.00 0.00 31.66 2.85
26 27 4.683832 TCGGTCTTGCTAATTCTAAGAGC 58.316 43.478 13.89 13.89 42.44 4.09
27 28 4.159693 TCGGTCTTGCTAATTCTAAGAGCA 59.840 41.667 19.50 10.93 44.73 4.26
28 29 5.053145 CGGTCTTGCTAATTCTAAGAGCAT 58.947 41.667 19.50 0.00 45.20 3.79
29 30 5.176590 CGGTCTTGCTAATTCTAAGAGCATC 59.823 44.000 19.50 8.15 45.20 3.91
43 44 3.827008 GAGCATCTCCAATAGACACCA 57.173 47.619 0.00 0.00 36.93 4.17
44 45 4.142609 GAGCATCTCCAATAGACACCAA 57.857 45.455 0.00 0.00 36.93 3.67
45 46 4.517285 GAGCATCTCCAATAGACACCAAA 58.483 43.478 0.00 0.00 36.93 3.28
46 47 4.922206 AGCATCTCCAATAGACACCAAAA 58.078 39.130 0.00 0.00 36.93 2.44
47 48 5.324409 AGCATCTCCAATAGACACCAAAAA 58.676 37.500 0.00 0.00 36.93 1.94
48 49 5.416952 AGCATCTCCAATAGACACCAAAAAG 59.583 40.000 0.00 0.00 36.93 2.27
49 50 5.415701 GCATCTCCAATAGACACCAAAAAGA 59.584 40.000 0.00 0.00 36.93 2.52
50 51 6.623767 GCATCTCCAATAGACACCAAAAAGAC 60.624 42.308 0.00 0.00 36.93 3.01
51 52 5.313712 TCTCCAATAGACACCAAAAAGACC 58.686 41.667 0.00 0.00 0.00 3.85
52 53 5.073144 TCTCCAATAGACACCAAAAAGACCT 59.927 40.000 0.00 0.00 0.00 3.85
53 54 5.313712 TCCAATAGACACCAAAAAGACCTC 58.686 41.667 0.00 0.00 0.00 3.85
54 55 4.459337 CCAATAGACACCAAAAAGACCTCC 59.541 45.833 0.00 0.00 0.00 4.30
55 56 2.256117 AGACACCAAAAAGACCTCCG 57.744 50.000 0.00 0.00 0.00 4.63
56 57 0.591659 GACACCAAAAAGACCTCCGC 59.408 55.000 0.00 0.00 0.00 5.54
57 58 1.164041 ACACCAAAAAGACCTCCGCG 61.164 55.000 0.00 0.00 0.00 6.46
58 59 2.258726 ACCAAAAAGACCTCCGCGC 61.259 57.895 0.00 0.00 0.00 6.86
59 60 2.258013 CCAAAAAGACCTCCGCGCA 61.258 57.895 8.75 0.00 0.00 6.09
60 61 1.082104 CAAAAAGACCTCCGCGCAC 60.082 57.895 8.75 0.00 0.00 5.34
61 62 1.227853 AAAAAGACCTCCGCGCACT 60.228 52.632 8.75 0.00 0.00 4.40
62 63 0.034337 AAAAAGACCTCCGCGCACTA 59.966 50.000 8.75 0.00 0.00 2.74
63 64 0.034337 AAAAGACCTCCGCGCACTAA 59.966 50.000 8.75 0.00 0.00 2.24
64 65 0.034337 AAAGACCTCCGCGCACTAAA 59.966 50.000 8.75 0.00 0.00 1.85
65 66 0.034337 AAGACCTCCGCGCACTAAAA 59.966 50.000 8.75 0.00 0.00 1.52
66 67 0.389948 AGACCTCCGCGCACTAAAAG 60.390 55.000 8.75 0.00 0.00 2.27
67 68 0.669625 GACCTCCGCGCACTAAAAGT 60.670 55.000 8.75 0.00 0.00 2.66
68 69 0.250166 ACCTCCGCGCACTAAAAGTT 60.250 50.000 8.75 0.00 0.00 2.66
69 70 0.872388 CCTCCGCGCACTAAAAGTTT 59.128 50.000 8.75 0.00 0.00 2.66
70 71 1.399727 CCTCCGCGCACTAAAAGTTTG 60.400 52.381 8.75 0.00 0.00 2.93
71 72 1.263217 CTCCGCGCACTAAAAGTTTGT 59.737 47.619 8.75 0.00 0.00 2.83
72 73 1.671845 TCCGCGCACTAAAAGTTTGTT 59.328 42.857 8.75 0.00 0.00 2.83
73 74 2.097791 TCCGCGCACTAAAAGTTTGTTT 59.902 40.909 8.75 0.00 0.00 2.83
74 75 2.855370 CCGCGCACTAAAAGTTTGTTTT 59.145 40.909 8.75 0.00 0.00 2.43
75 76 3.304826 CCGCGCACTAAAAGTTTGTTTTT 59.695 39.130 8.75 0.00 34.78 1.94
90 91 2.399856 TTTTTGACGCCGAACAGCT 58.600 47.368 0.00 0.00 0.00 4.24
91 92 0.306533 TTTTTGACGCCGAACAGCTC 59.693 50.000 0.00 0.00 0.00 4.09
92 93 1.503818 TTTTGACGCCGAACAGCTCC 61.504 55.000 0.00 0.00 0.00 4.70
93 94 2.652382 TTTGACGCCGAACAGCTCCA 62.652 55.000 0.00 0.00 0.00 3.86
94 95 2.811317 GACGCCGAACAGCTCCAG 60.811 66.667 0.00 0.00 0.00 3.86
97 98 2.669569 GCCGAACAGCTCCAGCAA 60.670 61.111 0.48 0.00 45.16 3.91
98 99 2.260869 GCCGAACAGCTCCAGCAAA 61.261 57.895 0.48 0.00 45.16 3.68
99 100 1.795170 GCCGAACAGCTCCAGCAAAA 61.795 55.000 0.48 0.00 45.16 2.44
100 101 0.239347 CCGAACAGCTCCAGCAAAAG 59.761 55.000 0.48 0.00 45.16 2.27
101 102 0.386478 CGAACAGCTCCAGCAAAAGC 60.386 55.000 0.48 0.00 45.16 3.51
104 105 4.916358 AGCTCCAGCAAAAGCTGT 57.084 50.000 15.42 0.00 46.78 4.40
106 107 1.818642 AGCTCCAGCAAAAGCTGTAG 58.181 50.000 15.42 10.67 46.78 2.74
107 108 0.169894 GCTCCAGCAAAAGCTGTAGC 59.830 55.000 17.07 17.07 41.19 3.58
108 109 3.444598 GCTCCAGCAAAAGCTGTAGCG 62.445 57.143 17.07 2.82 39.30 4.26
121 122 4.868581 GCTGTAGCGCTAAAAGTTTTTG 57.131 40.909 20.73 5.79 0.00 2.44
122 123 3.119628 GCTGTAGCGCTAAAAGTTTTTGC 59.880 43.478 20.73 20.45 0.00 3.68
123 124 3.634283 TGTAGCGCTAAAAGTTTTTGCC 58.366 40.909 20.73 17.18 0.00 4.52
124 125 1.766069 AGCGCTAAAAGTTTTTGCCG 58.234 45.000 23.09 19.18 0.00 5.69
125 126 0.781787 GCGCTAAAAGTTTTTGCCGG 59.218 50.000 23.09 14.26 0.00 6.13
126 127 0.781787 CGCTAAAAGTTTTTGCCGGC 59.218 50.000 22.73 22.73 0.00 6.13
127 128 1.859383 GCTAAAAGTTTTTGCCGGCA 58.141 45.000 29.03 29.03 0.00 5.69
128 129 1.792367 GCTAAAAGTTTTTGCCGGCAG 59.208 47.619 30.75 14.93 0.00 4.85
129 130 2.544903 GCTAAAAGTTTTTGCCGGCAGA 60.545 45.455 30.75 24.14 0.00 4.26
130 131 2.682155 AAAAGTTTTTGCCGGCAGAA 57.318 40.000 30.75 28.82 0.00 3.02
131 132 2.223537 AAAGTTTTTGCCGGCAGAAG 57.776 45.000 30.75 0.00 0.00 2.85
132 133 1.111277 AAGTTTTTGCCGGCAGAAGT 58.889 45.000 30.75 25.61 0.00 3.01
133 134 1.111277 AGTTTTTGCCGGCAGAAGTT 58.889 45.000 30.75 19.17 0.00 2.66
134 135 1.202405 AGTTTTTGCCGGCAGAAGTTG 60.202 47.619 30.75 0.00 0.00 3.16
135 136 0.820871 TTTTTGCCGGCAGAAGTTGT 59.179 45.000 30.75 0.00 0.00 3.32
136 137 1.681538 TTTTGCCGGCAGAAGTTGTA 58.318 45.000 30.75 9.52 0.00 2.41
137 138 1.904287 TTTGCCGGCAGAAGTTGTAT 58.096 45.000 30.75 0.00 0.00 2.29
138 139 1.904287 TTGCCGGCAGAAGTTGTATT 58.096 45.000 30.75 0.00 0.00 1.89
139 140 2.772077 TGCCGGCAGAAGTTGTATTA 57.228 45.000 29.03 0.00 0.00 0.98
140 141 3.060736 TGCCGGCAGAAGTTGTATTAA 57.939 42.857 29.03 0.00 0.00 1.40
141 142 3.413327 TGCCGGCAGAAGTTGTATTAAA 58.587 40.909 29.03 0.00 0.00 1.52
142 143 3.821600 TGCCGGCAGAAGTTGTATTAAAA 59.178 39.130 29.03 0.00 0.00 1.52
143 144 4.461081 TGCCGGCAGAAGTTGTATTAAAAT 59.539 37.500 29.03 0.00 0.00 1.82
144 145 4.798387 GCCGGCAGAAGTTGTATTAAAATG 59.202 41.667 24.80 0.00 0.00 2.32
145 146 5.392595 GCCGGCAGAAGTTGTATTAAAATGA 60.393 40.000 24.80 0.00 0.00 2.57
146 147 6.258160 CCGGCAGAAGTTGTATTAAAATGAG 58.742 40.000 0.00 0.00 0.00 2.90
147 148 5.739161 CGGCAGAAGTTGTATTAAAATGAGC 59.261 40.000 0.00 0.00 0.00 4.26
148 149 6.403636 CGGCAGAAGTTGTATTAAAATGAGCT 60.404 38.462 0.00 0.00 0.00 4.09
149 150 7.201609 CGGCAGAAGTTGTATTAAAATGAGCTA 60.202 37.037 0.00 0.00 0.00 3.32
150 151 8.125448 GGCAGAAGTTGTATTAAAATGAGCTAG 58.875 37.037 0.00 0.00 0.00 3.42
151 152 8.883731 GCAGAAGTTGTATTAAAATGAGCTAGA 58.116 33.333 0.00 0.00 0.00 2.43
181 182 9.080097 ACCATAATGTTACTACTGAGAGATACC 57.920 37.037 0.00 0.00 0.00 2.73
182 183 9.303116 CCATAATGTTACTACTGAGAGATACCT 57.697 37.037 0.00 0.00 0.00 3.08
185 186 8.694581 AATGTTACTACTGAGAGATACCTACC 57.305 38.462 0.00 0.00 0.00 3.18
186 187 7.448915 TGTTACTACTGAGAGATACCTACCT 57.551 40.000 0.00 0.00 0.00 3.08
187 188 7.507829 TGTTACTACTGAGAGATACCTACCTC 58.492 42.308 0.00 0.00 0.00 3.85
188 189 7.347748 TGTTACTACTGAGAGATACCTACCTCT 59.652 40.741 0.00 0.00 42.01 3.69
189 190 6.835029 ACTACTGAGAGATACCTACCTCTT 57.165 41.667 0.00 0.00 39.64 2.85
190 191 7.215743 ACTACTGAGAGATACCTACCTCTTT 57.784 40.000 0.00 0.00 39.64 2.52
191 192 8.334522 ACTACTGAGAGATACCTACCTCTTTA 57.665 38.462 0.00 0.00 39.64 1.85
192 193 8.780003 ACTACTGAGAGATACCTACCTCTTTAA 58.220 37.037 0.00 0.00 39.64 1.52
193 194 9.629878 CTACTGAGAGATACCTACCTCTTTAAA 57.370 37.037 0.00 0.00 39.64 1.52
194 195 8.528044 ACTGAGAGATACCTACCTCTTTAAAG 57.472 38.462 9.04 9.04 39.64 1.85
195 196 7.068962 ACTGAGAGATACCTACCTCTTTAAAGC 59.931 40.741 10.51 0.00 39.64 3.51
196 197 6.895756 TGAGAGATACCTACCTCTTTAAAGCA 59.104 38.462 10.51 0.00 39.64 3.91
197 198 7.068839 TGAGAGATACCTACCTCTTTAAAGCAG 59.931 40.741 10.51 8.62 39.64 4.24
198 199 5.919755 AGATACCTACCTCTTTAAAGCAGC 58.080 41.667 10.51 0.00 0.00 5.25
199 200 5.663556 AGATACCTACCTCTTTAAAGCAGCT 59.336 40.000 10.51 0.00 0.00 4.24
200 201 4.642466 ACCTACCTCTTTAAAGCAGCTT 57.358 40.909 10.51 0.21 0.00 3.74
201 202 4.580868 ACCTACCTCTTTAAAGCAGCTTC 58.419 43.478 8.48 0.00 0.00 3.86
202 203 4.287326 ACCTACCTCTTTAAAGCAGCTTCT 59.713 41.667 8.48 1.66 0.00 2.85
203 204 4.873259 CCTACCTCTTTAAAGCAGCTTCTC 59.127 45.833 8.48 0.00 0.00 2.87
252 253 1.068472 ACGTCGAGGTACTGCAGAAAG 60.068 52.381 23.35 5.43 41.55 2.62
255 256 3.650139 GTCGAGGTACTGCAGAAAGAAA 58.350 45.455 23.35 0.00 41.55 2.52
567 571 1.674322 CATCCCAAAAGCGTCCGGT 60.674 57.895 0.00 0.00 0.00 5.28
777 781 6.107901 AGAATCAATAGAAGGAGAATCGGG 57.892 41.667 0.00 0.00 34.37 5.14
824 828 9.554395 ACAAAAAGGAAAAGAAAGAGAAAACAA 57.446 25.926 0.00 0.00 0.00 2.83
1060 1064 9.582431 TCGACTCTACGAGAATTTTTATGAAAT 57.418 29.630 0.00 0.00 37.37 2.17
1159 1163 6.547510 TCTTCTGATCGATTCAACCTCTGATA 59.452 38.462 0.00 0.00 32.78 2.15
1558 1562 9.950496 AGGCTACTATGAAATATTTACTCATGG 57.050 33.333 10.20 9.73 35.03 3.66
1559 1563 9.167311 GGCTACTATGAAATATTTACTCATGGG 57.833 37.037 13.42 0.00 33.65 4.00
1767 1774 3.698040 CCTTTTCATCAATGGACTCCTGG 59.302 47.826 0.00 0.00 32.27 4.45
1857 1864 6.071616 GGGTTTTGCAAAACTCCATAGACATA 60.072 38.462 39.36 10.14 45.70 2.29
2223 2238 3.154710 TCTTTCTGACTTGCTCCTACGA 58.845 45.455 0.00 0.00 0.00 3.43
2297 2312 5.489249 AGGATTCCTCGAAAAGTTAAGGAC 58.511 41.667 0.00 0.00 37.64 3.85
2456 2471 0.109597 GCACGGTTTTGCATGAGAGG 60.110 55.000 0.00 0.00 42.49 3.69
2650 2665 3.320256 GCATGATTTTGGGGAATCTCCTC 59.680 47.826 0.00 0.00 37.60 3.71
2676 2691 7.308435 GCTATTACTCAAACAAGCATGAAACT 58.692 34.615 0.00 0.00 32.25 2.66
2978 2993 5.844004 TCGGAAAACTCTATCTATTCTGGC 58.156 41.667 0.00 0.00 0.00 4.85
2991 3006 2.046023 CTGGCGTGGATGGCAAGA 60.046 61.111 0.00 0.00 44.45 3.02
3032 3047 3.628008 TCAATAGGACTCCTTACGAGCA 58.372 45.455 1.94 0.00 43.01 4.26
3383 3398 3.528009 TCGACTCGATCATCAGATTCG 57.472 47.619 10.72 10.72 39.72 3.34
3617 3634 8.956533 TGAATCGAGAAATTGGATTGTACATA 57.043 30.769 0.00 0.00 34.78 2.29
3696 3713 6.451064 TCGAAGCTATTTGATGTCTGACTA 57.549 37.500 9.51 0.00 0.00 2.59
3736 3753 5.277857 AGAAGAGAACGAAAGGAGAACAA 57.722 39.130 0.00 0.00 0.00 2.83
4198 4217 4.775253 ACCCTTTTTCCTTCTCAAACAACA 59.225 37.500 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.314541 AGAATTAGCAAGACCGAACGT 57.685 42.857 0.00 0.00 0.00 3.99
1 2 5.100259 TCTTAGAATTAGCAAGACCGAACG 58.900 41.667 0.00 0.00 0.00 3.95
2 3 5.005875 GCTCTTAGAATTAGCAAGACCGAAC 59.994 44.000 0.00 0.00 36.26 3.95
3 4 5.109903 GCTCTTAGAATTAGCAAGACCGAA 58.890 41.667 0.00 0.00 36.26 4.30
4 5 4.159693 TGCTCTTAGAATTAGCAAGACCGA 59.840 41.667 0.00 0.00 42.96 4.69
5 6 4.433615 TGCTCTTAGAATTAGCAAGACCG 58.566 43.478 0.00 0.00 42.96 4.79
12 13 8.310382 TCTATTGGAGATGCTCTTAGAATTAGC 58.690 37.037 0.00 0.00 36.77 3.09
13 14 9.638239 GTCTATTGGAGATGCTCTTAGAATTAG 57.362 37.037 0.00 0.00 36.29 1.73
14 15 9.147732 TGTCTATTGGAGATGCTCTTAGAATTA 57.852 33.333 0.00 0.00 36.29 1.40
15 16 7.930865 GTGTCTATTGGAGATGCTCTTAGAATT 59.069 37.037 0.00 0.00 36.29 2.17
16 17 7.441017 GTGTCTATTGGAGATGCTCTTAGAAT 58.559 38.462 0.00 0.00 36.29 2.40
17 18 6.183360 GGTGTCTATTGGAGATGCTCTTAGAA 60.183 42.308 0.00 0.00 36.29 2.10
18 19 5.303078 GGTGTCTATTGGAGATGCTCTTAGA 59.697 44.000 0.00 0.00 36.29 2.10
19 20 5.069648 TGGTGTCTATTGGAGATGCTCTTAG 59.930 44.000 0.00 0.00 36.29 2.18
20 21 4.962362 TGGTGTCTATTGGAGATGCTCTTA 59.038 41.667 0.00 0.00 36.29 2.10
21 22 3.776969 TGGTGTCTATTGGAGATGCTCTT 59.223 43.478 0.00 0.00 36.29 2.85
22 23 3.378512 TGGTGTCTATTGGAGATGCTCT 58.621 45.455 0.00 0.00 36.29 4.09
23 24 3.827008 TGGTGTCTATTGGAGATGCTC 57.173 47.619 0.00 0.00 36.29 4.26
24 25 4.574674 TTTGGTGTCTATTGGAGATGCT 57.425 40.909 0.00 0.00 36.29 3.79
25 26 5.415701 TCTTTTTGGTGTCTATTGGAGATGC 59.584 40.000 0.00 0.00 36.29 3.91
26 27 6.127897 GGTCTTTTTGGTGTCTATTGGAGATG 60.128 42.308 0.00 0.00 36.29 2.90
27 28 5.946377 GGTCTTTTTGGTGTCTATTGGAGAT 59.054 40.000 0.00 0.00 36.29 2.75
28 29 5.073144 AGGTCTTTTTGGTGTCTATTGGAGA 59.927 40.000 0.00 0.00 0.00 3.71
29 30 5.316987 AGGTCTTTTTGGTGTCTATTGGAG 58.683 41.667 0.00 0.00 0.00 3.86
30 31 5.313712 GAGGTCTTTTTGGTGTCTATTGGA 58.686 41.667 0.00 0.00 0.00 3.53
31 32 4.459337 GGAGGTCTTTTTGGTGTCTATTGG 59.541 45.833 0.00 0.00 0.00 3.16
32 33 4.154195 CGGAGGTCTTTTTGGTGTCTATTG 59.846 45.833 0.00 0.00 0.00 1.90
33 34 4.324267 CGGAGGTCTTTTTGGTGTCTATT 58.676 43.478 0.00 0.00 0.00 1.73
34 35 3.868754 GCGGAGGTCTTTTTGGTGTCTAT 60.869 47.826 0.00 0.00 0.00 1.98
35 36 2.549349 GCGGAGGTCTTTTTGGTGTCTA 60.549 50.000 0.00 0.00 0.00 2.59
36 37 1.814248 GCGGAGGTCTTTTTGGTGTCT 60.814 52.381 0.00 0.00 0.00 3.41
37 38 0.591659 GCGGAGGTCTTTTTGGTGTC 59.408 55.000 0.00 0.00 0.00 3.67
38 39 1.164041 CGCGGAGGTCTTTTTGGTGT 61.164 55.000 0.00 0.00 0.00 4.16
39 40 1.574428 CGCGGAGGTCTTTTTGGTG 59.426 57.895 0.00 0.00 0.00 4.17
40 41 2.258726 GCGCGGAGGTCTTTTTGGT 61.259 57.895 8.83 0.00 0.00 3.67
41 42 2.258013 TGCGCGGAGGTCTTTTTGG 61.258 57.895 8.83 0.00 0.00 3.28
42 43 1.082104 GTGCGCGGAGGTCTTTTTG 60.082 57.895 8.83 0.00 0.00 2.44
43 44 0.034337 TAGTGCGCGGAGGTCTTTTT 59.966 50.000 8.83 0.00 0.00 1.94
44 45 0.034337 TTAGTGCGCGGAGGTCTTTT 59.966 50.000 8.83 0.00 0.00 2.27
45 46 0.034337 TTTAGTGCGCGGAGGTCTTT 59.966 50.000 8.83 0.00 0.00 2.52
46 47 0.034337 TTTTAGTGCGCGGAGGTCTT 59.966 50.000 8.83 0.00 0.00 3.01
47 48 0.389948 CTTTTAGTGCGCGGAGGTCT 60.390 55.000 8.83 0.38 0.00 3.85
48 49 0.669625 ACTTTTAGTGCGCGGAGGTC 60.670 55.000 8.83 0.00 0.00 3.85
49 50 0.250166 AACTTTTAGTGCGCGGAGGT 60.250 50.000 8.83 0.00 0.00 3.85
50 51 0.872388 AAACTTTTAGTGCGCGGAGG 59.128 50.000 8.83 0.00 0.00 4.30
51 52 1.263217 ACAAACTTTTAGTGCGCGGAG 59.737 47.619 8.83 0.00 0.00 4.63
52 53 1.301423 ACAAACTTTTAGTGCGCGGA 58.699 45.000 8.83 0.00 0.00 5.54
53 54 2.113910 AACAAACTTTTAGTGCGCGG 57.886 45.000 8.83 0.00 0.00 6.46
54 55 4.493074 AAAAACAAACTTTTAGTGCGCG 57.507 36.364 0.00 0.00 0.00 6.86
72 73 0.306533 GAGCTGTTCGGCGTCAAAAA 59.693 50.000 6.85 0.00 37.29 1.94
73 74 1.503818 GGAGCTGTTCGGCGTCAAAA 61.504 55.000 6.85 0.00 37.29 2.44
74 75 1.959226 GGAGCTGTTCGGCGTCAAA 60.959 57.895 6.85 0.00 37.29 2.69
75 76 2.357034 GGAGCTGTTCGGCGTCAA 60.357 61.111 6.85 0.00 37.29 3.18
76 77 3.573772 CTGGAGCTGTTCGGCGTCA 62.574 63.158 6.85 7.07 37.29 4.35
77 78 2.811317 CTGGAGCTGTTCGGCGTC 60.811 66.667 6.85 2.07 37.29 5.19
80 81 1.795170 TTTTGCTGGAGCTGTTCGGC 61.795 55.000 0.00 0.00 42.66 5.54
81 82 0.239347 CTTTTGCTGGAGCTGTTCGG 59.761 55.000 0.00 0.00 42.66 4.30
82 83 0.386478 GCTTTTGCTGGAGCTGTTCG 60.386 55.000 0.00 0.00 43.35 3.95
83 84 3.486285 GCTTTTGCTGGAGCTGTTC 57.514 52.632 0.00 0.00 43.35 3.18
94 95 2.611974 TTTAGCGCTACAGCTTTTGC 57.388 45.000 18.63 0.00 46.80 3.68
95 96 4.147219 ACTTTTAGCGCTACAGCTTTTG 57.853 40.909 18.63 4.43 46.80 2.44
96 97 4.830826 AACTTTTAGCGCTACAGCTTTT 57.169 36.364 18.63 4.21 46.80 2.27
97 98 4.830826 AAACTTTTAGCGCTACAGCTTT 57.169 36.364 18.63 14.51 46.80 3.51
98 99 4.830826 AAAACTTTTAGCGCTACAGCTT 57.169 36.364 18.63 10.81 46.80 3.74
100 101 3.119628 GCAAAAACTTTTAGCGCTACAGC 59.880 43.478 18.63 4.77 37.78 4.40
101 102 3.668656 GGCAAAAACTTTTAGCGCTACAG 59.331 43.478 18.63 18.01 0.00 2.74
102 103 3.634283 GGCAAAAACTTTTAGCGCTACA 58.366 40.909 18.63 8.18 0.00 2.74
103 104 2.655001 CGGCAAAAACTTTTAGCGCTAC 59.345 45.455 18.63 0.84 0.00 3.58
104 105 2.350964 CCGGCAAAAACTTTTAGCGCTA 60.351 45.455 14.45 14.45 0.00 4.26
105 106 1.601914 CCGGCAAAAACTTTTAGCGCT 60.602 47.619 17.26 17.26 0.00 5.92
106 107 0.781787 CCGGCAAAAACTTTTAGCGC 59.218 50.000 0.00 0.00 0.00 5.92
107 108 0.781787 GCCGGCAAAAACTTTTAGCG 59.218 50.000 24.80 0.00 0.00 4.26
108 109 1.792367 CTGCCGGCAAAAACTTTTAGC 59.208 47.619 32.09 0.00 0.00 3.09
109 110 3.363341 TCTGCCGGCAAAAACTTTTAG 57.637 42.857 32.09 14.71 0.00 1.85
110 111 3.131400 ACTTCTGCCGGCAAAAACTTTTA 59.869 39.130 32.09 2.57 0.00 1.52
111 112 2.093711 ACTTCTGCCGGCAAAAACTTTT 60.094 40.909 32.09 6.40 0.00 2.27
112 113 1.480545 ACTTCTGCCGGCAAAAACTTT 59.519 42.857 32.09 8.16 0.00 2.66
113 114 1.111277 ACTTCTGCCGGCAAAAACTT 58.889 45.000 32.09 7.90 0.00 2.66
114 115 1.111277 AACTTCTGCCGGCAAAAACT 58.889 45.000 32.09 10.53 0.00 2.66
115 116 1.208259 CAACTTCTGCCGGCAAAAAC 58.792 50.000 32.09 0.00 0.00 2.43
116 117 0.820871 ACAACTTCTGCCGGCAAAAA 59.179 45.000 32.09 24.79 0.00 1.94
117 118 1.681538 TACAACTTCTGCCGGCAAAA 58.318 45.000 32.09 24.00 0.00 2.44
118 119 1.904287 ATACAACTTCTGCCGGCAAA 58.096 45.000 32.09 24.01 0.00 3.68
119 120 1.904287 AATACAACTTCTGCCGGCAA 58.096 45.000 32.09 16.39 0.00 4.52
120 121 2.772077 TAATACAACTTCTGCCGGCA 57.228 45.000 30.59 30.59 0.00 5.69
121 122 4.428615 TTTTAATACAACTTCTGCCGGC 57.571 40.909 22.73 22.73 0.00 6.13
122 123 6.189677 TCATTTTAATACAACTTCTGCCGG 57.810 37.500 0.00 0.00 0.00 6.13
123 124 5.739161 GCTCATTTTAATACAACTTCTGCCG 59.261 40.000 0.00 0.00 0.00 5.69
124 125 6.856895 AGCTCATTTTAATACAACTTCTGCC 58.143 36.000 0.00 0.00 0.00 4.85
125 126 8.883731 TCTAGCTCATTTTAATACAACTTCTGC 58.116 33.333 0.00 0.00 0.00 4.26
155 156 9.080097 GGTATCTCTCAGTAGTAACATTATGGT 57.920 37.037 0.00 0.00 0.00 3.55
156 157 9.303116 AGGTATCTCTCAGTAGTAACATTATGG 57.697 37.037 0.00 0.00 0.00 2.74
159 160 9.790344 GGTAGGTATCTCTCAGTAGTAACATTA 57.210 37.037 0.00 0.00 0.00 1.90
160 161 8.504409 AGGTAGGTATCTCTCAGTAGTAACATT 58.496 37.037 0.00 0.00 0.00 2.71
161 162 8.048016 AGGTAGGTATCTCTCAGTAGTAACAT 57.952 38.462 0.00 0.00 0.00 2.71
162 163 7.347748 AGAGGTAGGTATCTCTCAGTAGTAACA 59.652 40.741 0.00 0.00 39.52 2.41
163 164 7.738847 AGAGGTAGGTATCTCTCAGTAGTAAC 58.261 42.308 0.00 0.00 39.52 2.50
164 165 7.934354 AGAGGTAGGTATCTCTCAGTAGTAA 57.066 40.000 0.00 0.00 39.52 2.24
165 166 7.934354 AAGAGGTAGGTATCTCTCAGTAGTA 57.066 40.000 0.14 0.00 42.73 1.82
166 167 6.835029 AAGAGGTAGGTATCTCTCAGTAGT 57.165 41.667 0.14 0.00 42.73 2.73
167 168 9.629878 TTTAAAGAGGTAGGTATCTCTCAGTAG 57.370 37.037 0.14 0.00 42.73 2.57
168 169 9.629878 CTTTAAAGAGGTAGGTATCTCTCAGTA 57.370 37.037 9.77 0.00 42.73 2.74
169 170 7.068962 GCTTTAAAGAGGTAGGTATCTCTCAGT 59.931 40.741 19.48 0.00 42.73 3.41
170 171 7.068839 TGCTTTAAAGAGGTAGGTATCTCTCAG 59.931 40.741 19.48 0.00 42.73 3.35
171 172 6.895756 TGCTTTAAAGAGGTAGGTATCTCTCA 59.104 38.462 19.48 0.00 42.73 3.27
172 173 7.349412 TGCTTTAAAGAGGTAGGTATCTCTC 57.651 40.000 19.48 0.00 42.73 3.20
173 174 6.183360 GCTGCTTTAAAGAGGTAGGTATCTCT 60.183 42.308 19.48 0.00 45.35 3.10
174 175 5.986741 GCTGCTTTAAAGAGGTAGGTATCTC 59.013 44.000 19.48 0.00 33.61 2.75
175 176 5.663556 AGCTGCTTTAAAGAGGTAGGTATCT 59.336 40.000 19.48 1.74 0.00 1.98
176 177 5.919755 AGCTGCTTTAAAGAGGTAGGTATC 58.080 41.667 19.48 0.00 0.00 2.24
177 178 5.959583 AGCTGCTTTAAAGAGGTAGGTAT 57.040 39.130 19.48 0.00 0.00 2.73
178 179 5.484290 AGAAGCTGCTTTAAAGAGGTAGGTA 59.516 40.000 19.48 0.00 0.00 3.08
179 180 4.287326 AGAAGCTGCTTTAAAGAGGTAGGT 59.713 41.667 19.48 12.31 0.00 3.08
180 181 4.837972 AGAAGCTGCTTTAAAGAGGTAGG 58.162 43.478 19.48 2.96 0.00 3.18
181 182 5.482908 TGAGAAGCTGCTTTAAAGAGGTAG 58.517 41.667 19.48 11.09 0.00 3.18
182 183 5.483685 TGAGAAGCTGCTTTAAAGAGGTA 57.516 39.130 19.48 1.13 0.00 3.08
183 184 4.357918 TGAGAAGCTGCTTTAAAGAGGT 57.642 40.909 19.48 14.55 0.00 3.85
184 185 5.647225 AGAATGAGAAGCTGCTTTAAAGAGG 59.353 40.000 19.48 10.80 0.00 3.69
185 186 6.740411 AGAATGAGAAGCTGCTTTAAAGAG 57.260 37.500 19.48 13.36 0.00 2.85
186 187 6.712095 TCAAGAATGAGAAGCTGCTTTAAAGA 59.288 34.615 19.48 3.58 0.00 2.52
187 188 6.906659 TCAAGAATGAGAAGCTGCTTTAAAG 58.093 36.000 17.10 11.02 0.00 1.85
188 189 6.882610 TCAAGAATGAGAAGCTGCTTTAAA 57.117 33.333 17.10 5.38 0.00 1.52
189 190 6.294176 GGTTCAAGAATGAGAAGCTGCTTTAA 60.294 38.462 17.10 5.75 38.74 1.52
190 191 5.182001 GGTTCAAGAATGAGAAGCTGCTTTA 59.818 40.000 17.10 6.86 38.74 1.85
191 192 4.022503 GGTTCAAGAATGAGAAGCTGCTTT 60.023 41.667 17.10 6.57 38.74 3.51
192 193 3.505293 GGTTCAAGAATGAGAAGCTGCTT 59.495 43.478 15.92 15.92 38.74 3.91
193 194 3.080319 GGTTCAAGAATGAGAAGCTGCT 58.920 45.455 0.00 0.00 38.74 4.24
194 195 3.484334 GGTTCAAGAATGAGAAGCTGC 57.516 47.619 0.00 0.00 38.74 5.25
197 198 5.471456 TGAAAGAGGTTCAAGAATGAGAAGC 59.529 40.000 0.00 0.00 43.43 3.86
252 253 7.662604 ATTGGATCAGATTTTGCAGTTTTTC 57.337 32.000 0.00 0.00 0.00 2.29
255 256 8.454570 AAAAATTGGATCAGATTTTGCAGTTT 57.545 26.923 15.01 0.87 36.06 2.66
302 303 5.579511 CGTCTTTCAGAATACGGTTAACCAT 59.420 40.000 24.14 12.32 33.33 3.55
503 507 5.489792 AGTGCTCTTCCTTGTTTAGATCA 57.510 39.130 0.00 0.00 0.00 2.92
567 571 9.921637 AACTTAATTTGAAAGCCATATTTCGAA 57.078 25.926 0.00 0.00 43.37 3.71
777 781 5.854157 TGTTTGTTTCGAGAAAGATATCGC 58.146 37.500 0.00 0.00 40.02 4.58
824 828 8.773033 AGGGCTAATTAGTTGATCATGATTTT 57.227 30.769 10.14 0.00 0.00 1.82
1060 1064 5.749596 TTGAAGAGAAGCAAATGAAACGA 57.250 34.783 0.00 0.00 0.00 3.85
1395 1399 4.527427 CCCCCTAGAGTAGCTGTTAATACC 59.473 50.000 0.00 0.00 0.00 2.73
1559 1563 3.513750 AAGAGCTTGCCCCACCCAC 62.514 63.158 0.00 0.00 0.00 4.61
1767 1774 0.456312 CCACACTCCTTCGTAGACGC 60.456 60.000 0.00 0.00 39.60 5.19
1857 1864 3.782523 TGGGGATAGCATTTCTCTTCTGT 59.217 43.478 0.00 0.00 0.00 3.41
2223 2238 3.827722 TCAATCCTTTCGACCTTGGTTT 58.172 40.909 0.00 0.00 0.00 3.27
2650 2665 5.469373 TCATGCTTGTTTGAGTAATAGCG 57.531 39.130 0.00 0.00 32.19 4.26
2676 2691 5.643348 CCTATGGACGAATATGCAAGCATAA 59.357 40.000 17.63 1.36 41.53 1.90
2978 2993 3.190878 GCCTTCTTGCCATCCACG 58.809 61.111 0.00 0.00 0.00 4.94
2991 3006 7.978099 ATTGAAACCAAGAAATATAGGCCTT 57.022 32.000 12.58 0.81 0.00 4.35
3383 3398 4.258543 TGGTTCGGTATGGAATGAACTTC 58.741 43.478 4.23 0.00 40.34 3.01
3696 3713 7.840931 TCTCTTCTTTCTTTTCTTTTTGCCTT 58.159 30.769 0.00 0.00 0.00 4.35
3736 3753 7.778382 ACAGGAGAGTTACCAAATACAAAGTTT 59.222 33.333 0.00 0.00 0.00 2.66
4198 4217 6.478129 TGGTATAAGGAAGGAAATCAAACGT 58.522 36.000 0.00 0.00 0.00 3.99


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

AutoCloner maintained by Alex Coulton.