Multiple sequence alignment - TraesCS3A01G507000

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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 TraesCS3A01G507000 chr3A 100.000 2537 0 0 1 2537 728245353 728247889 0.000000e+00 4686
1 TraesCS3A01G507000 chr3A 80.193 934 160 19 990 1902 158591037 158590108 0.000000e+00 676
2 TraesCS3A01G507000 chr3A 91.093 247 13 3 1 247 728101931 728102168 2.430000e-85 326
3 TraesCS3A01G507000 chr6A 99.514 2262 11 0 276 2537 485768990 485771251 0.000000e+00 4117
4 TraesCS3A01G507000 chr2B 98.945 2274 24 0 264 2537 72972042 72969769 0.000000e+00 4067
5 TraesCS3A01G507000 chr2B 79.178 1508 266 38 994 2470 242541261 242542751 0.000000e+00 1002
6 TraesCS3A01G507000 chr7A 79.507 1054 179 27 987 2026 11242864 11243894 0.000000e+00 715
7 TraesCS3A01G507000 chr3B 79.380 1033 177 24 987 2004 31196682 31197693 0.000000e+00 695
8 TraesCS3A01G507000 chr3D 78.253 1053 196 23 987 2026 379587574 379586542 0.000000e+00 645
9 TraesCS3A01G507000 chr7B 85.398 226 25 4 23 247 712737262 712737044 7.060000e-56 228
10 TraesCS3A01G507000 chr7D 84.549 233 26 6 16 247 618322973 618322750 3.290000e-54 222
11 TraesCS3A01G507000 chr5A 84.120 233 25 6 16 247 94799898 94800119 5.500000e-52 215
12 TraesCS3A01G507000 chr5A 82.273 220 29 6 32 247 702987782 702987569 5.580000e-42 182
13 TraesCS3A01G507000 chr5B 84.305 223 23 8 27 247 427334520 427334308 9.200000e-50 207
14 TraesCS3A01G507000 chr5B 82.805 221 29 5 28 247 112531205 112530993 3.330000e-44 189
15 TraesCS3A01G507000 chr2D 83.193 238 22 8 16 247 579606887 579606662 4.280000e-48 202
16 TraesCS3A01G507000 chr4D 81.982 222 27 7 32 247 506726342 506726128 2.590000e-40 176


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 TraesCS3A01G507000 chr3A 728245353 728247889 2536 False 4686 4686 100.000 1 2537 1 chr3A.!!$F2 2536
1 TraesCS3A01G507000 chr3A 158590108 158591037 929 True 676 676 80.193 990 1902 1 chr3A.!!$R1 912
2 TraesCS3A01G507000 chr6A 485768990 485771251 2261 False 4117 4117 99.514 276 2537 1 chr6A.!!$F1 2261
3 TraesCS3A01G507000 chr2B 72969769 72972042 2273 True 4067 4067 98.945 264 2537 1 chr2B.!!$R1 2273
4 TraesCS3A01G507000 chr2B 242541261 242542751 1490 False 1002 1002 79.178 994 2470 1 chr2B.!!$F1 1476
5 TraesCS3A01G507000 chr7A 11242864 11243894 1030 False 715 715 79.507 987 2026 1 chr7A.!!$F1 1039
6 TraesCS3A01G507000 chr3B 31196682 31197693 1011 False 695 695 79.380 987 2004 1 chr3B.!!$F1 1017
7 TraesCS3A01G507000 chr3D 379586542 379587574 1032 True 645 645 78.253 987 2026 1 chr3D.!!$R1 1039

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
39 40 0.252012 AGCCACAGTGAGGAGTAGCT 60.252 55.0 11.2 0.0 0.00 3.32 F
67 68 0.478072 AACATGGGTCCAACTCAGCA 59.522 50.0 0.0 0.0 28.45 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1159 1164 0.037326 AGATGTTCAGCTTTCGCCGA 60.037 50.000 0.0 0.0 36.6 5.54 R
1863 1883 2.022195 CTACCGCTACTTCCTGCACTA 58.978 52.381 0.0 0.0 0.0 2.74 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
23 24 5.346181 ACTAGGTTTTCATCAGACTAGCC 57.654 43.478 0.00 0.00 33.10 3.93
24 25 4.777896 ACTAGGTTTTCATCAGACTAGCCA 59.222 41.667 0.00 0.00 33.10 4.75
25 26 3.944087 AGGTTTTCATCAGACTAGCCAC 58.056 45.455 0.00 0.00 0.00 5.01
26 27 3.327757 AGGTTTTCATCAGACTAGCCACA 59.672 43.478 0.00 0.00 0.00 4.17
27 28 3.686726 GGTTTTCATCAGACTAGCCACAG 59.313 47.826 0.00 0.00 0.00 3.66
28 29 4.319177 GTTTTCATCAGACTAGCCACAGT 58.681 43.478 0.00 0.00 0.00 3.55
29 30 3.599730 TTCATCAGACTAGCCACAGTG 57.400 47.619 0.00 0.00 0.00 3.66
30 31 2.807676 TCATCAGACTAGCCACAGTGA 58.192 47.619 0.62 0.00 0.00 3.41
31 32 2.757314 TCATCAGACTAGCCACAGTGAG 59.243 50.000 0.62 0.00 0.00 3.51
32 33 1.550327 TCAGACTAGCCACAGTGAGG 58.450 55.000 0.62 1.62 0.00 3.86
33 34 1.075536 TCAGACTAGCCACAGTGAGGA 59.924 52.381 11.20 0.00 0.00 3.71
34 35 1.476085 CAGACTAGCCACAGTGAGGAG 59.524 57.143 11.20 2.32 0.00 3.69
35 36 1.076350 AGACTAGCCACAGTGAGGAGT 59.924 52.381 11.20 5.73 0.00 3.85
36 37 2.309162 AGACTAGCCACAGTGAGGAGTA 59.691 50.000 11.20 0.24 0.00 2.59
37 38 2.685897 GACTAGCCACAGTGAGGAGTAG 59.314 54.545 11.20 11.81 0.00 2.57
38 39 1.407258 CTAGCCACAGTGAGGAGTAGC 59.593 57.143 11.20 0.00 0.00 3.58
39 40 0.252012 AGCCACAGTGAGGAGTAGCT 60.252 55.000 11.20 0.00 0.00 3.32
40 41 0.610687 GCCACAGTGAGGAGTAGCTT 59.389 55.000 11.20 0.00 0.00 3.74
41 42 1.404851 GCCACAGTGAGGAGTAGCTTC 60.405 57.143 11.20 0.00 0.00 3.86
42 43 1.895798 CCACAGTGAGGAGTAGCTTCA 59.104 52.381 0.62 0.00 0.00 3.02
43 44 2.094286 CCACAGTGAGGAGTAGCTTCAG 60.094 54.545 0.62 0.00 32.76 3.02
44 45 2.560542 CACAGTGAGGAGTAGCTTCAGT 59.439 50.000 0.00 0.00 36.77 3.41
45 46 3.759086 CACAGTGAGGAGTAGCTTCAGTA 59.241 47.826 0.00 0.00 34.35 2.74
46 47 4.013728 ACAGTGAGGAGTAGCTTCAGTAG 58.986 47.826 0.00 0.00 34.35 2.57
47 48 4.013728 CAGTGAGGAGTAGCTTCAGTAGT 58.986 47.826 0.00 0.00 34.35 2.73
48 49 5.186942 CAGTGAGGAGTAGCTTCAGTAGTA 58.813 45.833 0.00 0.00 34.35 1.82
49 50 5.648526 CAGTGAGGAGTAGCTTCAGTAGTAA 59.351 44.000 0.00 0.00 34.35 2.24
50 51 5.648960 AGTGAGGAGTAGCTTCAGTAGTAAC 59.351 44.000 0.00 0.00 34.79 2.50
51 52 5.415077 GTGAGGAGTAGCTTCAGTAGTAACA 59.585 44.000 0.00 0.00 32.76 2.41
52 53 6.095720 GTGAGGAGTAGCTTCAGTAGTAACAT 59.904 42.308 0.00 0.00 32.76 2.71
53 54 6.095580 TGAGGAGTAGCTTCAGTAGTAACATG 59.904 42.308 0.00 0.00 0.00 3.21
54 55 5.361285 AGGAGTAGCTTCAGTAGTAACATGG 59.639 44.000 0.00 0.00 0.00 3.66
55 56 5.452077 GGAGTAGCTTCAGTAGTAACATGGG 60.452 48.000 0.00 0.00 0.00 4.00
56 57 5.024118 AGTAGCTTCAGTAGTAACATGGGT 58.976 41.667 0.00 0.00 0.00 4.51
57 58 4.473477 AGCTTCAGTAGTAACATGGGTC 57.527 45.455 0.00 0.00 0.00 4.46
58 59 3.197983 AGCTTCAGTAGTAACATGGGTCC 59.802 47.826 0.00 0.00 0.00 4.46
59 60 3.055385 GCTTCAGTAGTAACATGGGTCCA 60.055 47.826 0.00 0.00 0.00 4.02
60 61 4.564821 GCTTCAGTAGTAACATGGGTCCAA 60.565 45.833 0.00 0.00 0.00 3.53
61 62 4.546829 TCAGTAGTAACATGGGTCCAAC 57.453 45.455 0.00 0.00 0.00 3.77
62 63 4.164981 TCAGTAGTAACATGGGTCCAACT 58.835 43.478 0.00 0.00 0.00 3.16
63 64 4.222145 TCAGTAGTAACATGGGTCCAACTC 59.778 45.833 0.00 0.00 0.00 3.01
64 65 4.020573 CAGTAGTAACATGGGTCCAACTCA 60.021 45.833 0.00 0.00 30.24 3.41
65 66 3.703001 AGTAACATGGGTCCAACTCAG 57.297 47.619 0.00 0.00 28.45 3.35
66 67 2.084546 GTAACATGGGTCCAACTCAGC 58.915 52.381 0.00 0.00 28.45 4.26
67 68 0.478072 AACATGGGTCCAACTCAGCA 59.522 50.000 0.00 0.00 28.45 4.41
68 69 0.478072 ACATGGGTCCAACTCAGCAA 59.522 50.000 0.00 0.00 28.45 3.91
69 70 1.133513 ACATGGGTCCAACTCAGCAAA 60.134 47.619 0.00 0.00 28.45 3.68
70 71 2.173519 CATGGGTCCAACTCAGCAAAT 58.826 47.619 0.00 0.00 28.45 2.32
71 72 2.380064 TGGGTCCAACTCAGCAAATT 57.620 45.000 0.00 0.00 0.00 1.82
72 73 2.676748 TGGGTCCAACTCAGCAAATTT 58.323 42.857 0.00 0.00 0.00 1.82
73 74 2.364970 TGGGTCCAACTCAGCAAATTTG 59.635 45.455 14.03 14.03 0.00 2.32
93 94 5.929058 TTGCATAGGTGGCAATGATTTAA 57.071 34.783 1.90 0.00 45.57 1.52
94 95 6.482898 TTGCATAGGTGGCAATGATTTAAT 57.517 33.333 1.90 0.00 45.57 1.40
95 96 5.845103 TGCATAGGTGGCAATGATTTAATG 58.155 37.500 1.90 0.00 38.54 1.90
96 97 5.597594 TGCATAGGTGGCAATGATTTAATGA 59.402 36.000 1.90 0.00 38.54 2.57
97 98 6.268158 TGCATAGGTGGCAATGATTTAATGAT 59.732 34.615 1.90 0.00 38.54 2.45
98 99 6.588756 GCATAGGTGGCAATGATTTAATGATG 59.411 38.462 1.90 0.00 0.00 3.07
99 100 7.524202 GCATAGGTGGCAATGATTTAATGATGA 60.524 37.037 1.90 0.00 0.00 2.92
100 101 6.795144 AGGTGGCAATGATTTAATGATGAA 57.205 33.333 0.00 0.00 0.00 2.57
101 102 7.185318 AGGTGGCAATGATTTAATGATGAAA 57.815 32.000 0.00 0.00 0.00 2.69
102 103 7.622713 AGGTGGCAATGATTTAATGATGAAAA 58.377 30.769 0.00 0.00 0.00 2.29
103 104 8.102047 AGGTGGCAATGATTTAATGATGAAAAA 58.898 29.630 0.00 0.00 0.00 1.94
104 105 8.392612 GGTGGCAATGATTTAATGATGAAAAAG 58.607 33.333 0.00 0.00 0.00 2.27
105 106 9.153721 GTGGCAATGATTTAATGATGAAAAAGA 57.846 29.630 0.00 0.00 0.00 2.52
106 107 9.893634 TGGCAATGATTTAATGATGAAAAAGAT 57.106 25.926 0.00 0.00 0.00 2.40
118 119 9.696917 AATGATGAAAAAGATGGTTTGAGTAAC 57.303 29.630 0.00 0.00 35.94 2.50
119 120 8.231692 TGATGAAAAAGATGGTTTGAGTAACA 57.768 30.769 0.00 0.00 38.55 2.41
120 121 8.859090 TGATGAAAAAGATGGTTTGAGTAACAT 58.141 29.630 0.00 0.00 38.55 2.71
123 124 8.296713 TGAAAAAGATGGTTTGAGTAACATAGC 58.703 33.333 0.00 0.00 38.55 2.97
124 125 8.409358 AAAAAGATGGTTTGAGTAACATAGCT 57.591 30.769 0.00 0.00 38.55 3.32
125 126 9.515226 AAAAAGATGGTTTGAGTAACATAGCTA 57.485 29.630 0.00 0.00 38.55 3.32
126 127 9.686683 AAAAGATGGTTTGAGTAACATAGCTAT 57.313 29.630 0.00 0.00 38.55 2.97
128 129 9.988815 AAGATGGTTTGAGTAACATAGCTATAG 57.011 33.333 5.77 3.92 38.55 1.31
129 130 9.148879 AGATGGTTTGAGTAACATAGCTATAGT 57.851 33.333 5.77 4.56 38.55 2.12
130 131 9.765795 GATGGTTTGAGTAACATAGCTATAGTT 57.234 33.333 18.92 18.92 38.55 2.24
154 155 8.541899 TTACTCATACTATGGGTAACATCACA 57.458 34.615 15.04 0.00 46.27 3.58
155 156 6.817184 ACTCATACTATGGGTAACATCACAC 58.183 40.000 0.00 0.00 43.54 3.82
156 157 6.382859 ACTCATACTATGGGTAACATCACACA 59.617 38.462 0.00 0.00 43.54 3.72
157 158 7.071196 ACTCATACTATGGGTAACATCACACAT 59.929 37.037 0.00 0.00 43.54 3.21
158 159 8.485578 TCATACTATGGGTAACATCACACATA 57.514 34.615 0.00 0.00 40.79 2.29
159 160 9.100197 TCATACTATGGGTAACATCACACATAT 57.900 33.333 0.00 0.00 42.44 1.78
164 165 9.817809 CTATGGGTAACATCACACATATATACC 57.182 37.037 0.00 0.00 42.44 2.73
165 166 7.619512 TGGGTAACATCACACATATATACCA 57.380 36.000 0.00 0.00 34.58 3.25
166 167 8.035448 TGGGTAACATCACACATATATACCAA 57.965 34.615 0.00 0.00 34.58 3.67
167 168 8.154203 TGGGTAACATCACACATATATACCAAG 58.846 37.037 0.00 0.00 34.58 3.61
168 169 8.372459 GGGTAACATCACACATATATACCAAGA 58.628 37.037 0.00 0.00 34.58 3.02
169 170 9.424319 GGTAACATCACACATATATACCAAGAG 57.576 37.037 0.00 0.00 33.42 2.85
172 173 9.770097 AACATCACACATATATACCAAGAGAAG 57.230 33.333 0.00 0.00 0.00 2.85
173 174 9.147732 ACATCACACATATATACCAAGAGAAGA 57.852 33.333 0.00 0.00 0.00 2.87
176 177 9.367160 TCACACATATATACCAAGAGAAGATGA 57.633 33.333 0.00 0.00 0.00 2.92
177 178 9.636879 CACACATATATACCAAGAGAAGATGAG 57.363 37.037 0.00 0.00 0.00 2.90
178 179 9.373450 ACACATATATACCAAGAGAAGATGAGT 57.627 33.333 0.00 0.00 0.00 3.41
187 188 8.560124 ACCAAGAGAAGATGAGTTTATATCCT 57.440 34.615 0.00 0.00 0.00 3.24
188 189 9.661954 ACCAAGAGAAGATGAGTTTATATCCTA 57.338 33.333 0.00 0.00 0.00 2.94
217 218 9.693739 AAATGAAGTGTTGGATAATACCATACA 57.306 29.630 0.00 0.00 39.82 2.29
218 219 9.866655 AATGAAGTGTTGGATAATACCATACAT 57.133 29.630 0.00 0.00 39.82 2.29
232 233 7.735326 ATACCATACATATCTTACTCCCCAC 57.265 40.000 0.00 0.00 0.00 4.61
233 234 5.727630 ACCATACATATCTTACTCCCCACT 58.272 41.667 0.00 0.00 0.00 4.00
234 235 6.871035 ACCATACATATCTTACTCCCCACTA 58.129 40.000 0.00 0.00 0.00 2.74
235 236 7.488205 ACCATACATATCTTACTCCCCACTAT 58.512 38.462 0.00 0.00 0.00 2.12
236 237 8.630091 ACCATACATATCTTACTCCCCACTATA 58.370 37.037 0.00 0.00 0.00 1.31
237 238 9.137459 CCATACATATCTTACTCCCCACTATAG 57.863 40.741 0.00 0.00 0.00 1.31
238 239 9.922477 CATACATATCTTACTCCCCACTATAGA 57.078 37.037 6.78 0.00 0.00 1.98
240 241 7.415086 ACATATCTTACTCCCCACTATAGAGG 58.585 42.308 6.78 8.10 31.70 3.69
241 242 5.952161 ATCTTACTCCCCACTATAGAGGT 57.048 43.478 14.29 0.00 31.70 3.85
242 243 8.558312 CATATCTTACTCCCCACTATAGAGGTA 58.442 40.741 14.29 2.62 31.70 3.08
243 244 6.451292 TCTTACTCCCCACTATAGAGGTAG 57.549 45.833 14.29 12.87 31.70 3.18
244 245 5.915900 TCTTACTCCCCACTATAGAGGTAGT 59.084 44.000 18.82 18.82 35.34 2.73
245 246 7.084943 TCTTACTCCCCACTATAGAGGTAGTA 58.915 42.308 17.42 17.42 33.29 1.82
246 247 7.573994 TCTTACTCCCCACTATAGAGGTAGTAA 59.426 40.741 24.22 24.22 34.50 2.24
247 248 6.603110 ACTCCCCACTATAGAGGTAGTAAA 57.397 41.667 14.29 0.00 33.29 2.01
248 249 6.989894 ACTCCCCACTATAGAGGTAGTAAAA 58.010 40.000 14.29 0.00 33.29 1.52
249 250 7.425003 ACTCCCCACTATAGAGGTAGTAAAAA 58.575 38.462 14.29 0.00 33.29 1.94
250 251 8.072480 ACTCCCCACTATAGAGGTAGTAAAAAT 58.928 37.037 14.29 0.00 33.29 1.82
251 252 8.258850 TCCCCACTATAGAGGTAGTAAAAATG 57.741 38.462 14.29 0.00 33.29 2.32
252 253 7.847848 TCCCCACTATAGAGGTAGTAAAAATGT 59.152 37.037 14.29 0.00 33.29 2.71
253 254 9.151177 CCCCACTATAGAGGTAGTAAAAATGTA 57.849 37.037 14.29 0.00 33.29 2.29
262 263 9.392259 AGAGGTAGTAAAAATGTAATTGTAGCC 57.608 33.333 0.00 0.00 36.10 3.93
437 438 5.625197 GCTGTTCTGCATAATCCACCAATTT 60.625 40.000 0.00 0.00 0.00 1.82
931 932 3.760684 GCTGTCAAACCAATTGGAGAGAT 59.239 43.478 31.22 4.95 39.62 2.75
1096 1100 3.427573 AGGAAAGTGGTAAAAATCGGGG 58.572 45.455 0.00 0.00 0.00 5.73
1159 1164 3.118371 GGGGAAACTGTTGTCGGATAGAT 60.118 47.826 0.00 0.00 0.00 1.98
1863 1883 3.763057 AGGCGGTTTTTGGAGAAGTAAT 58.237 40.909 0.00 0.00 0.00 1.89
2479 2508 2.674754 GAACTGCCGGGGATTGGA 59.325 61.111 2.18 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.248477 TGGCTAGTCTGATGAAAACCTAGTT 59.752 40.000 0.00 0.00 0.00 2.24
1 2 4.777896 TGGCTAGTCTGATGAAAACCTAGT 59.222 41.667 0.00 0.00 0.00 2.57
2 3 5.112686 GTGGCTAGTCTGATGAAAACCTAG 58.887 45.833 0.00 0.00 0.00 3.02
3 4 4.530553 TGTGGCTAGTCTGATGAAAACCTA 59.469 41.667 0.00 0.00 0.00 3.08
4 5 3.327757 TGTGGCTAGTCTGATGAAAACCT 59.672 43.478 0.00 0.00 0.00 3.50
6 7 4.153117 CACTGTGGCTAGTCTGATGAAAAC 59.847 45.833 0.00 0.00 0.00 2.43
7 8 4.040339 TCACTGTGGCTAGTCTGATGAAAA 59.960 41.667 8.11 0.00 0.00 2.29
8 9 3.578282 TCACTGTGGCTAGTCTGATGAAA 59.422 43.478 8.11 0.00 0.00 2.69
9 10 3.165071 TCACTGTGGCTAGTCTGATGAA 58.835 45.455 8.11 0.00 0.00 2.57
10 11 2.757314 CTCACTGTGGCTAGTCTGATGA 59.243 50.000 8.11 0.00 0.00 2.92
11 12 2.159128 CCTCACTGTGGCTAGTCTGATG 60.159 54.545 8.11 0.00 0.00 3.07
12 13 2.106566 CCTCACTGTGGCTAGTCTGAT 58.893 52.381 8.11 0.00 0.00 2.90
13 14 1.075536 TCCTCACTGTGGCTAGTCTGA 59.924 52.381 8.11 0.00 0.00 3.27
14 15 1.476085 CTCCTCACTGTGGCTAGTCTG 59.524 57.143 8.11 0.00 0.00 3.51
15 16 1.076350 ACTCCTCACTGTGGCTAGTCT 59.924 52.381 8.11 0.00 0.00 3.24
16 17 1.551452 ACTCCTCACTGTGGCTAGTC 58.449 55.000 8.11 0.00 0.00 2.59
17 18 2.729194 CTACTCCTCACTGTGGCTAGT 58.271 52.381 8.11 10.69 0.00 2.57
18 19 1.407258 GCTACTCCTCACTGTGGCTAG 59.593 57.143 8.11 5.44 37.62 3.42
19 20 1.006043 AGCTACTCCTCACTGTGGCTA 59.994 52.381 8.11 0.00 46.44 3.93
20 21 0.252012 AGCTACTCCTCACTGTGGCT 60.252 55.000 8.11 3.86 44.20 4.75
21 22 0.610687 AAGCTACTCCTCACTGTGGC 59.389 55.000 8.11 1.41 40.27 5.01
22 23 1.895798 TGAAGCTACTCCTCACTGTGG 59.104 52.381 8.11 0.00 0.00 4.17
23 24 2.560542 ACTGAAGCTACTCCTCACTGTG 59.439 50.000 0.17 0.17 0.00 3.66
24 25 2.883026 ACTGAAGCTACTCCTCACTGT 58.117 47.619 0.00 0.00 0.00 3.55
25 26 4.013728 ACTACTGAAGCTACTCCTCACTG 58.986 47.826 0.00 0.00 0.00 3.66
26 27 4.310022 ACTACTGAAGCTACTCCTCACT 57.690 45.455 0.00 0.00 0.00 3.41
27 28 5.415077 TGTTACTACTGAAGCTACTCCTCAC 59.585 44.000 0.00 0.00 0.00 3.51
28 29 5.567430 TGTTACTACTGAAGCTACTCCTCA 58.433 41.667 0.00 0.00 0.00 3.86
29 30 6.460399 CCATGTTACTACTGAAGCTACTCCTC 60.460 46.154 0.00 0.00 0.00 3.71
30 31 5.361285 CCATGTTACTACTGAAGCTACTCCT 59.639 44.000 0.00 0.00 0.00 3.69
31 32 5.452077 CCCATGTTACTACTGAAGCTACTCC 60.452 48.000 0.00 0.00 0.00 3.85
32 33 5.127356 ACCCATGTTACTACTGAAGCTACTC 59.873 44.000 0.00 0.00 0.00 2.59
33 34 5.024118 ACCCATGTTACTACTGAAGCTACT 58.976 41.667 0.00 0.00 0.00 2.57
34 35 5.340439 ACCCATGTTACTACTGAAGCTAC 57.660 43.478 0.00 0.00 0.00 3.58
35 36 4.404715 GGACCCATGTTACTACTGAAGCTA 59.595 45.833 0.00 0.00 0.00 3.32
36 37 3.197983 GGACCCATGTTACTACTGAAGCT 59.802 47.826 0.00 0.00 0.00 3.74
37 38 3.055385 TGGACCCATGTTACTACTGAAGC 60.055 47.826 0.00 0.00 0.00 3.86
38 39 4.819105 TGGACCCATGTTACTACTGAAG 57.181 45.455 0.00 0.00 0.00 3.02
39 40 4.595781 AGTTGGACCCATGTTACTACTGAA 59.404 41.667 0.00 0.00 0.00 3.02
40 41 4.164981 AGTTGGACCCATGTTACTACTGA 58.835 43.478 0.00 0.00 0.00 3.41
41 42 4.020573 TGAGTTGGACCCATGTTACTACTG 60.021 45.833 0.00 0.00 0.00 2.74
42 43 4.164981 TGAGTTGGACCCATGTTACTACT 58.835 43.478 0.00 0.00 0.00 2.57
43 44 4.504858 CTGAGTTGGACCCATGTTACTAC 58.495 47.826 0.00 0.00 0.00 2.73
44 45 3.055385 GCTGAGTTGGACCCATGTTACTA 60.055 47.826 0.00 0.00 0.00 1.82
45 46 2.290323 GCTGAGTTGGACCCATGTTACT 60.290 50.000 0.00 0.00 0.00 2.24
46 47 2.084546 GCTGAGTTGGACCCATGTTAC 58.915 52.381 0.00 0.00 0.00 2.50
47 48 1.702401 TGCTGAGTTGGACCCATGTTA 59.298 47.619 0.00 0.00 0.00 2.41
48 49 0.478072 TGCTGAGTTGGACCCATGTT 59.522 50.000 0.00 0.00 0.00 2.71
49 50 0.478072 TTGCTGAGTTGGACCCATGT 59.522 50.000 0.00 0.00 0.00 3.21
50 51 1.619654 TTTGCTGAGTTGGACCCATG 58.380 50.000 0.00 0.00 0.00 3.66
51 52 2.610438 ATTTGCTGAGTTGGACCCAT 57.390 45.000 0.00 0.00 0.00 4.00
52 53 2.364970 CAAATTTGCTGAGTTGGACCCA 59.635 45.455 5.01 0.00 0.00 4.51
53 54 3.030668 CAAATTTGCTGAGTTGGACCC 57.969 47.619 5.01 0.00 0.00 4.46
72 73 5.597594 TCATTAAATCATTGCCACCTATGCA 59.402 36.000 0.00 0.00 36.84 3.96
73 74 6.088016 TCATTAAATCATTGCCACCTATGC 57.912 37.500 0.00 0.00 0.00 3.14
74 75 7.888424 TCATCATTAAATCATTGCCACCTATG 58.112 34.615 0.00 0.00 0.00 2.23
75 76 8.481492 TTCATCATTAAATCATTGCCACCTAT 57.519 30.769 0.00 0.00 0.00 2.57
76 77 7.894753 TTCATCATTAAATCATTGCCACCTA 57.105 32.000 0.00 0.00 0.00 3.08
77 78 6.795144 TTCATCATTAAATCATTGCCACCT 57.205 33.333 0.00 0.00 0.00 4.00
78 79 7.846644 TTTTCATCATTAAATCATTGCCACC 57.153 32.000 0.00 0.00 0.00 4.61
79 80 9.153721 TCTTTTTCATCATTAAATCATTGCCAC 57.846 29.630 0.00 0.00 0.00 5.01
80 81 9.893634 ATCTTTTTCATCATTAAATCATTGCCA 57.106 25.926 0.00 0.00 0.00 4.92
92 93 9.696917 GTTACTCAAACCATCTTTTTCATCATT 57.303 29.630 0.00 0.00 31.38 2.57
93 94 8.859090 TGTTACTCAAACCATCTTTTTCATCAT 58.141 29.630 0.00 0.00 37.27 2.45
94 95 8.231692 TGTTACTCAAACCATCTTTTTCATCA 57.768 30.769 0.00 0.00 37.27 3.07
97 98 8.296713 GCTATGTTACTCAAACCATCTTTTTCA 58.703 33.333 0.00 0.00 37.27 2.69
98 99 8.515414 AGCTATGTTACTCAAACCATCTTTTTC 58.485 33.333 0.00 0.00 37.27 2.29
99 100 8.409358 AGCTATGTTACTCAAACCATCTTTTT 57.591 30.769 0.00 0.00 37.27 1.94
100 101 9.686683 ATAGCTATGTTACTCAAACCATCTTTT 57.313 29.630 5.15 0.00 37.27 2.27
102 103 9.988815 CTATAGCTATGTTACTCAAACCATCTT 57.011 33.333 16.77 0.00 37.27 2.40
103 104 9.148879 ACTATAGCTATGTTACTCAAACCATCT 57.851 33.333 16.77 0.00 37.27 2.90
104 105 9.765795 AACTATAGCTATGTTACTCAAACCATC 57.234 33.333 16.77 0.00 37.27 3.51
129 130 8.418662 GTGTGATGTTACCCATAGTATGAGTAA 58.581 37.037 11.93 11.93 32.10 2.24
130 131 7.562088 TGTGTGATGTTACCCATAGTATGAGTA 59.438 37.037 11.91 6.07 32.56 2.59
131 132 6.382859 TGTGTGATGTTACCCATAGTATGAGT 59.617 38.462 11.91 7.13 32.56 3.41
132 133 6.816136 TGTGTGATGTTACCCATAGTATGAG 58.184 40.000 11.91 0.35 32.56 2.90
133 134 6.800072 TGTGTGATGTTACCCATAGTATGA 57.200 37.500 11.91 0.00 32.56 2.15
138 139 9.817809 GGTATATATGTGTGATGTTACCCATAG 57.182 37.037 0.00 0.00 32.56 2.23
139 140 9.327731 TGGTATATATGTGTGATGTTACCCATA 57.672 33.333 0.00 0.00 32.56 2.74
140 141 8.213489 TGGTATATATGTGTGATGTTACCCAT 57.787 34.615 0.00 0.00 36.13 4.00
141 142 7.619512 TGGTATATATGTGTGATGTTACCCA 57.380 36.000 0.00 0.00 0.00 4.51
142 143 8.372459 TCTTGGTATATATGTGTGATGTTACCC 58.628 37.037 0.00 0.00 0.00 3.69
143 144 9.424319 CTCTTGGTATATATGTGTGATGTTACC 57.576 37.037 0.00 0.00 0.00 2.85
146 147 9.770097 CTTCTCTTGGTATATATGTGTGATGTT 57.230 33.333 0.00 0.00 0.00 2.71
147 148 9.147732 TCTTCTCTTGGTATATATGTGTGATGT 57.852 33.333 0.00 0.00 0.00 3.06
150 151 9.367160 TCATCTTCTCTTGGTATATATGTGTGA 57.633 33.333 0.00 0.00 0.00 3.58
151 152 9.636879 CTCATCTTCTCTTGGTATATATGTGTG 57.363 37.037 0.00 0.00 0.00 3.82
152 153 9.373450 ACTCATCTTCTCTTGGTATATATGTGT 57.627 33.333 0.00 0.00 0.00 3.72
161 162 9.661954 AGGATATAAACTCATCTTCTCTTGGTA 57.338 33.333 0.00 0.00 0.00 3.25
162 163 8.560124 AGGATATAAACTCATCTTCTCTTGGT 57.440 34.615 0.00 0.00 0.00 3.67
191 192 9.693739 TGTATGGTATTATCCAACACTTCATTT 57.306 29.630 0.00 0.00 41.09 2.32
192 193 9.866655 ATGTATGGTATTATCCAACACTTCATT 57.133 29.630 0.00 0.00 41.09 2.57
206 207 9.263446 GTGGGGAGTAAGATATGTATGGTATTA 57.737 37.037 0.00 0.00 0.00 0.98
207 208 7.962003 AGTGGGGAGTAAGATATGTATGGTATT 59.038 37.037 0.00 0.00 0.00 1.89
208 209 7.488205 AGTGGGGAGTAAGATATGTATGGTAT 58.512 38.462 0.00 0.00 0.00 2.73
209 210 6.871035 AGTGGGGAGTAAGATATGTATGGTA 58.129 40.000 0.00 0.00 0.00 3.25
210 211 5.727630 AGTGGGGAGTAAGATATGTATGGT 58.272 41.667 0.00 0.00 0.00 3.55
211 212 7.979786 ATAGTGGGGAGTAAGATATGTATGG 57.020 40.000 0.00 0.00 0.00 2.74
212 213 9.922477 TCTATAGTGGGGAGTAAGATATGTATG 57.078 37.037 0.00 0.00 0.00 2.39
214 215 8.558312 CCTCTATAGTGGGGAGTAAGATATGTA 58.442 40.741 12.29 0.00 0.00 2.29
215 216 7.019761 ACCTCTATAGTGGGGAGTAAGATATGT 59.980 40.741 21.82 0.00 33.22 2.29
216 217 7.415086 ACCTCTATAGTGGGGAGTAAGATATG 58.585 42.308 21.82 0.00 33.22 1.78
217 218 7.606892 ACCTCTATAGTGGGGAGTAAGATAT 57.393 40.000 21.82 0.00 33.22 1.63
218 219 7.743139 ACTACCTCTATAGTGGGGAGTAAGATA 59.257 40.741 22.09 6.34 34.02 1.98
219 220 5.952161 ACCTCTATAGTGGGGAGTAAGAT 57.048 43.478 21.82 0.00 33.22 2.40
220 221 5.915900 ACTACCTCTATAGTGGGGAGTAAGA 59.084 44.000 22.09 0.00 34.02 2.10
221 222 6.203526 ACTACCTCTATAGTGGGGAGTAAG 57.796 45.833 22.09 13.26 34.02 2.34
222 223 7.712142 TTACTACCTCTATAGTGGGGAGTAA 57.288 40.000 28.26 28.26 38.03 2.24
223 224 7.712142 TTTACTACCTCTATAGTGGGGAGTA 57.288 40.000 23.32 23.32 36.09 2.59
224 225 6.603110 TTTACTACCTCTATAGTGGGGAGT 57.397 41.667 24.72 24.72 36.09 3.85
225 226 7.909485 TTTTTACTACCTCTATAGTGGGGAG 57.091 40.000 21.82 20.04 36.09 4.30
226 227 7.847848 ACATTTTTACTACCTCTATAGTGGGGA 59.152 37.037 21.82 11.28 36.09 4.81
227 228 8.030913 ACATTTTTACTACCTCTATAGTGGGG 57.969 38.462 21.82 16.35 36.09 4.96
236 237 9.392259 GGCTACAATTACATTTTTACTACCTCT 57.608 33.333 0.00 0.00 0.00 3.69
237 238 9.169592 TGGCTACAATTACATTTTTACTACCTC 57.830 33.333 0.00 0.00 0.00 3.85
238 239 9.174166 CTGGCTACAATTACATTTTTACTACCT 57.826 33.333 0.00 0.00 0.00 3.08
239 240 8.953313 ACTGGCTACAATTACATTTTTACTACC 58.047 33.333 0.00 0.00 0.00 3.18
240 241 9.983804 GACTGGCTACAATTACATTTTTACTAC 57.016 33.333 0.00 0.00 0.00 2.73
241 242 9.169592 GGACTGGCTACAATTACATTTTTACTA 57.830 33.333 0.00 0.00 0.00 1.82
242 243 7.148306 CGGACTGGCTACAATTACATTTTTACT 60.148 37.037 0.00 0.00 0.00 2.24
243 244 6.964934 CGGACTGGCTACAATTACATTTTTAC 59.035 38.462 0.00 0.00 0.00 2.01
244 245 6.655848 ACGGACTGGCTACAATTACATTTTTA 59.344 34.615 0.00 0.00 0.00 1.52
245 246 5.475564 ACGGACTGGCTACAATTACATTTTT 59.524 36.000 0.00 0.00 0.00 1.94
246 247 5.007682 ACGGACTGGCTACAATTACATTTT 58.992 37.500 0.00 0.00 0.00 1.82
247 248 4.585879 ACGGACTGGCTACAATTACATTT 58.414 39.130 0.00 0.00 0.00 2.32
248 249 4.189231 GACGGACTGGCTACAATTACATT 58.811 43.478 0.00 0.00 0.00 2.71
249 250 3.431766 GGACGGACTGGCTACAATTACAT 60.432 47.826 0.00 0.00 0.00 2.29
250 251 2.093869 GGACGGACTGGCTACAATTACA 60.094 50.000 0.00 0.00 0.00 2.41
251 252 2.093869 TGGACGGACTGGCTACAATTAC 60.094 50.000 0.00 0.00 0.00 1.89
252 253 2.093869 GTGGACGGACTGGCTACAATTA 60.094 50.000 0.00 0.00 0.00 1.40
253 254 0.981183 TGGACGGACTGGCTACAATT 59.019 50.000 0.00 0.00 0.00 2.32
254 255 0.249398 GTGGACGGACTGGCTACAAT 59.751 55.000 0.00 0.00 0.00 2.71
255 256 1.116536 TGTGGACGGACTGGCTACAA 61.117 55.000 3.38 0.00 0.00 2.41
256 257 1.532078 TGTGGACGGACTGGCTACA 60.532 57.895 1.42 1.42 0.00 2.74
257 258 1.080025 GTGTGGACGGACTGGCTAC 60.080 63.158 0.00 0.00 0.00 3.58
258 259 2.632544 CGTGTGGACGGACTGGCTA 61.633 63.158 0.00 0.00 42.18 3.93
259 260 3.991051 CGTGTGGACGGACTGGCT 61.991 66.667 0.00 0.00 42.18 4.75
437 438 5.752036 AGAGTGGTTGAGATTGATGAGAA 57.248 39.130 0.00 0.00 0.00 2.87
897 898 0.318699 TTGACAGCTCGACGAACTGG 60.319 55.000 26.87 12.73 35.70 4.00
931 932 0.813610 CTGTCTTTCGCCACCACACA 60.814 55.000 0.00 0.00 0.00 3.72
1096 1100 5.176223 CCACTGTCATGAAGTTTGCATTTTC 59.824 40.000 0.00 0.00 0.00 2.29
1159 1164 0.037326 AGATGTTCAGCTTTCGCCGA 60.037 50.000 0.00 0.00 36.60 5.54
1534 1542 3.582647 AGTGGTACAGTGATGTCCATTCA 59.417 43.478 0.00 0.00 42.47 2.57
1863 1883 2.022195 CTACCGCTACTTCCTGCACTA 58.978 52.381 0.00 0.00 0.00 2.74
2479 2508 4.171103 GGACTGCCGGGCCGTTAT 62.171 66.667 26.32 7.09 30.75 1.89


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

AutoCloner maintained by Alex Coulton.