Multiple sequence alignment - TraesCS1B01G422800

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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 TraesCS1B01G422800 chr1B 100.000 2445 0 0 1 2445 645568091 645565647 0.000000e+00 4516
1 TraesCS1B01G422800 chr1B 98.559 2221 26 3 230 2445 535837816 535840035 0.000000e+00 3919
2 TraesCS1B01G422800 chr2B 98.557 2218 31 1 229 2445 712297346 712299563 0.000000e+00 3917
3 TraesCS1B01G422800 chr6B 98.512 2218 31 2 230 2445 348821467 348819250 0.000000e+00 3912
4 TraesCS1B01G422800 chr6B 98.512 2217 32 1 230 2445 15303408 15305624 0.000000e+00 3910
5 TraesCS1B01G422800 chr5B 98.512 2218 31 2 230 2445 559122049 559124266 0.000000e+00 3912
6 TraesCS1B01G422800 chrUn 98.512 2217 32 1 230 2445 310459497 310457281 0.000000e+00 3910
7 TraesCS1B01G422800 chrUn 86.977 215 26 2 14 226 143845032 143844818 8.740000e-60 241
8 TraesCS1B01G422800 chrUn 86.385 213 28 1 15 226 81865114 81865326 5.260000e-57 231
9 TraesCS1B01G422800 chrUn 86.047 215 29 1 15 228 81881975 81882189 1.890000e-56 230
10 TraesCS1B01G422800 chr7B 98.512 2217 32 1 230 2445 666639397 666641613 0.000000e+00 3910
11 TraesCS1B01G422800 chr7B 98.512 2217 32 1 230 2445 693345619 693347835 0.000000e+00 3910
12 TraesCS1B01G422800 chr4B 98.467 2218 33 1 229 2445 613075985 613073768 0.000000e+00 3906
13 TraesCS1B01G422800 chr1D 91.064 235 20 1 1 235 467655394 467655161 1.410000e-82 316
14 TraesCS1B01G422800 chr1A 88.839 224 23 2 6 228 560252886 560253108 8.610000e-70 274
15 TraesCS1B01G422800 chr5D 88.372 215 23 2 14 226 520681782 520681568 8.670000e-65 257
16 TraesCS1B01G422800 chr7D 87.081 209 26 1 19 226 28285640 28285848 4.060000e-58 235
17 TraesCS1B01G422800 chr4A 86.512 215 27 2 14 226 656849323 656849537 4.060000e-58 235
18 TraesCS1B01G422800 chr4A 86.047 215 28 2 14 226 656847603 656847817 1.890000e-56 230


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 TraesCS1B01G422800 chr1B 645565647 645568091 2444 True 4516.0 4516 100.0000 1 2445 1 chr1B.!!$R1 2444
1 TraesCS1B01G422800 chr1B 535837816 535840035 2219 False 3919.0 3919 98.5590 230 2445 1 chr1B.!!$F1 2215
2 TraesCS1B01G422800 chr2B 712297346 712299563 2217 False 3917.0 3917 98.5570 229 2445 1 chr2B.!!$F1 2216
3 TraesCS1B01G422800 chr6B 348819250 348821467 2217 True 3912.0 3912 98.5120 230 2445 1 chr6B.!!$R1 2215
4 TraesCS1B01G422800 chr6B 15303408 15305624 2216 False 3910.0 3910 98.5120 230 2445 1 chr6B.!!$F1 2215
5 TraesCS1B01G422800 chr5B 559122049 559124266 2217 False 3912.0 3912 98.5120 230 2445 1 chr5B.!!$F1 2215
6 TraesCS1B01G422800 chrUn 310457281 310459497 2216 True 3910.0 3910 98.5120 230 2445 1 chrUn.!!$R2 2215
7 TraesCS1B01G422800 chr7B 666639397 666641613 2216 False 3910.0 3910 98.5120 230 2445 1 chr7B.!!$F1 2215
8 TraesCS1B01G422800 chr7B 693345619 693347835 2216 False 3910.0 3910 98.5120 230 2445 1 chr7B.!!$F2 2215
9 TraesCS1B01G422800 chr4B 613073768 613075985 2217 True 3906.0 3906 98.4670 229 2445 1 chr4B.!!$R1 2216
10 TraesCS1B01G422800 chr4A 656847603 656849537 1934 False 232.5 235 86.2795 14 226 2 chr4A.!!$F1 212

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
86 87 0.031111 TGATTCTCCCCACCTCCGAT 60.031 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 2352 0.03392 GGTGCCCAGCTTTTTCTTGG 59.966 55.0 0.0 0.0 0.0 3.61 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
22 23 3.009723 ACATTACATGGCTGTCTTTCCG 58.990 45.455 0.00 0.00 36.79 4.30
28 29 2.665603 GCTGTCTTTCCGCCTCCT 59.334 61.111 0.00 0.00 0.00 3.69
36 37 2.079925 CTTTCCGCCTCCTCAAGAAAG 58.920 52.381 0.00 0.00 37.98 2.62
37 38 1.056660 TTCCGCCTCCTCAAGAAAGT 58.943 50.000 0.00 0.00 0.00 2.66
38 39 0.608640 TCCGCCTCCTCAAGAAAGTC 59.391 55.000 0.00 0.00 0.00 3.01
39 40 0.610687 CCGCCTCCTCAAGAAAGTCT 59.389 55.000 0.00 0.00 0.00 3.24
40 41 1.404851 CCGCCTCCTCAAGAAAGTCTC 60.405 57.143 0.00 0.00 0.00 3.36
42 43 1.905894 GCCTCCTCAAGAAAGTCTCCT 59.094 52.381 0.00 0.00 0.00 3.69
44 45 3.618752 GCCTCCTCAAGAAAGTCTCCTTC 60.619 52.174 0.00 0.00 0.00 3.46
45 46 3.055458 CCTCCTCAAGAAAGTCTCCTTCC 60.055 52.174 0.00 0.00 0.00 3.46
46 47 3.837731 CTCCTCAAGAAAGTCTCCTTCCT 59.162 47.826 0.00 0.00 0.00 3.36
47 48 3.835395 TCCTCAAGAAAGTCTCCTTCCTC 59.165 47.826 0.00 0.00 0.00 3.71
48 49 3.055458 CCTCAAGAAAGTCTCCTTCCTCC 60.055 52.174 0.00 0.00 0.00 4.30
49 50 3.837731 CTCAAGAAAGTCTCCTTCCTCCT 59.162 47.826 0.00 0.00 0.00 3.69
50 51 3.580458 TCAAGAAAGTCTCCTTCCTCCTG 59.420 47.826 0.00 0.00 0.00 3.86
51 52 1.905894 AGAAAGTCTCCTTCCTCCTGC 59.094 52.381 0.00 0.00 0.00 4.85
52 53 0.988063 AAAGTCTCCTTCCTCCTGCC 59.012 55.000 0.00 0.00 0.00 4.85
53 54 1.261238 AAGTCTCCTTCCTCCTGCCG 61.261 60.000 0.00 0.00 0.00 5.69
54 55 3.077556 TCTCCTTCCTCCTGCCGC 61.078 66.667 0.00 0.00 0.00 6.53
55 56 4.168291 CTCCTTCCTCCTGCCGCC 62.168 72.222 0.00 0.00 0.00 6.13
76 77 3.782443 ACCGCCGGTGATTCTCCC 61.782 66.667 18.79 0.00 32.98 4.30
77 78 4.547367 CCGCCGGTGATTCTCCCC 62.547 72.222 18.79 0.00 0.00 4.81
78 79 3.781307 CGCCGGTGATTCTCCCCA 61.781 66.667 10.20 0.00 0.00 4.96
79 80 2.124695 GCCGGTGATTCTCCCCAC 60.125 66.667 1.90 0.00 0.00 4.61
80 81 2.590092 CCGGTGATTCTCCCCACC 59.410 66.667 0.00 0.00 46.99 4.61
83 84 1.915983 GGTGATTCTCCCCACCTCC 59.084 63.158 0.00 0.00 46.94 4.30
84 85 1.522569 GTGATTCTCCCCACCTCCG 59.477 63.158 0.00 0.00 0.00 4.63
85 86 0.976073 GTGATTCTCCCCACCTCCGA 60.976 60.000 0.00 0.00 0.00 4.55
86 87 0.031111 TGATTCTCCCCACCTCCGAT 60.031 55.000 0.00 0.00 0.00 4.18
87 88 0.394565 GATTCTCCCCACCTCCGATG 59.605 60.000 0.00 0.00 0.00 3.84
88 89 1.056700 ATTCTCCCCACCTCCGATGG 61.057 60.000 0.00 0.00 36.94 3.51
89 90 3.866582 CTCCCCACCTCCGATGGC 61.867 72.222 0.00 0.00 35.74 4.40
92 93 3.411517 CCCACCTCCGATGGCCTT 61.412 66.667 3.32 0.00 35.74 4.35
93 94 2.677228 CCACCTCCGATGGCCTTT 59.323 61.111 3.32 0.00 0.00 3.11
94 95 1.750399 CCACCTCCGATGGCCTTTG 60.750 63.158 3.32 0.53 0.00 2.77
95 96 1.750399 CACCTCCGATGGCCTTTGG 60.750 63.158 17.44 17.44 0.00 3.28
96 97 2.124151 CCTCCGATGGCCTTTGGG 60.124 66.667 21.99 12.12 0.00 4.12
106 107 3.966543 CCTTTGGGCCGTGGAGGT 61.967 66.667 0.00 0.00 43.70 3.85
107 108 2.672996 CTTTGGGCCGTGGAGGTG 60.673 66.667 0.00 0.00 43.70 4.00
108 109 4.966787 TTTGGGCCGTGGAGGTGC 62.967 66.667 0.00 0.00 43.70 5.01
115 116 3.461773 CGTGGAGGTGCGGAGGAT 61.462 66.667 0.00 0.00 0.00 3.24
116 117 2.501610 GTGGAGGTGCGGAGGATC 59.498 66.667 0.00 0.00 0.00 3.36
120 121 4.461119 AGGTGCGGAGGATCTCAA 57.539 55.556 0.00 0.00 28.04 3.02
121 122 1.901085 AGGTGCGGAGGATCTCAAC 59.099 57.895 0.00 0.00 28.04 3.18
122 123 1.153349 GGTGCGGAGGATCTCAACC 60.153 63.158 0.00 0.00 33.73 3.77
123 124 1.519455 GTGCGGAGGATCTCAACCG 60.519 63.158 12.99 12.99 46.74 4.44
125 126 3.211288 CGGAGGATCTCAACCGCT 58.789 61.111 0.00 0.00 38.98 5.52
126 127 1.066587 CGGAGGATCTCAACCGCTC 59.933 63.158 0.00 0.00 38.98 5.03
127 128 1.667154 CGGAGGATCTCAACCGCTCA 61.667 60.000 0.00 0.00 38.98 4.26
128 129 0.179097 GGAGGATCTCAACCGCTCAC 60.179 60.000 0.00 0.00 33.73 3.51
129 130 0.179097 GAGGATCTCAACCGCTCACC 60.179 60.000 0.00 0.00 0.00 4.02
130 131 1.519455 GGATCTCAACCGCTCACCG 60.519 63.158 0.00 0.00 0.00 4.94
151 152 2.679287 GGAGGGACCCGTTCTCGT 60.679 66.667 4.40 0.00 35.01 4.18
152 153 2.281295 GGAGGGACCCGTTCTCGTT 61.281 63.158 4.40 0.00 35.01 3.85
153 154 1.670015 GAGGGACCCGTTCTCGTTT 59.330 57.895 4.40 0.00 35.01 3.60
154 155 0.034476 GAGGGACCCGTTCTCGTTTT 59.966 55.000 4.40 0.00 35.01 2.43
155 156 0.471191 AGGGACCCGTTCTCGTTTTT 59.529 50.000 4.40 0.00 35.01 1.94
156 157 0.589708 GGGACCCGTTCTCGTTTTTG 59.410 55.000 0.00 0.00 35.01 2.44
157 158 1.302366 GGACCCGTTCTCGTTTTTGT 58.698 50.000 0.00 0.00 35.01 2.83
158 159 1.672363 GGACCCGTTCTCGTTTTTGTT 59.328 47.619 0.00 0.00 35.01 2.83
159 160 2.871633 GGACCCGTTCTCGTTTTTGTTA 59.128 45.455 0.00 0.00 35.01 2.41
160 161 3.059393 GGACCCGTTCTCGTTTTTGTTAG 60.059 47.826 0.00 0.00 35.01 2.34
161 162 2.874086 ACCCGTTCTCGTTTTTGTTAGG 59.126 45.455 0.00 0.00 35.01 2.69
162 163 2.874086 CCCGTTCTCGTTTTTGTTAGGT 59.126 45.455 0.00 0.00 35.01 3.08
163 164 3.313249 CCCGTTCTCGTTTTTGTTAGGTT 59.687 43.478 0.00 0.00 35.01 3.50
164 165 4.521010 CCGTTCTCGTTTTTGTTAGGTTC 58.479 43.478 0.00 0.00 35.01 3.62
165 166 4.034279 CCGTTCTCGTTTTTGTTAGGTTCA 59.966 41.667 0.00 0.00 35.01 3.18
166 167 5.447548 CCGTTCTCGTTTTTGTTAGGTTCAA 60.448 40.000 0.00 0.00 35.01 2.69
167 168 5.450066 CGTTCTCGTTTTTGTTAGGTTCAAC 59.550 40.000 0.00 0.00 0.00 3.18
168 169 5.146482 TCTCGTTTTTGTTAGGTTCAACG 57.854 39.130 0.00 0.00 38.64 4.10
169 170 4.630940 TCTCGTTTTTGTTAGGTTCAACGT 59.369 37.500 0.00 0.00 38.47 3.99
170 171 4.896080 TCGTTTTTGTTAGGTTCAACGTC 58.104 39.130 0.00 0.00 38.47 4.34
171 172 4.630940 TCGTTTTTGTTAGGTTCAACGTCT 59.369 37.500 0.00 0.00 38.47 4.18
172 173 5.122082 TCGTTTTTGTTAGGTTCAACGTCTT 59.878 36.000 0.00 0.00 38.47 3.01
173 174 5.226360 CGTTTTTGTTAGGTTCAACGTCTTG 59.774 40.000 0.00 0.00 33.90 3.02
174 175 4.886247 TTTGTTAGGTTCAACGTCTTGG 57.114 40.909 0.00 0.00 0.00 3.61
175 176 3.547054 TGTTAGGTTCAACGTCTTGGT 57.453 42.857 0.00 0.00 0.00 3.67
176 177 3.876341 TGTTAGGTTCAACGTCTTGGTT 58.124 40.909 0.00 0.00 0.00 3.67
177 178 3.623960 TGTTAGGTTCAACGTCTTGGTTG 59.376 43.478 0.00 0.00 46.70 3.77
178 179 1.675552 AGGTTCAACGTCTTGGTTGG 58.324 50.000 5.69 0.00 45.66 3.77
179 180 0.666374 GGTTCAACGTCTTGGTTGGG 59.334 55.000 5.69 0.00 45.66 4.12
180 181 0.666374 GTTCAACGTCTTGGTTGGGG 59.334 55.000 5.69 0.00 45.66 4.96
181 182 1.104577 TTCAACGTCTTGGTTGGGGC 61.105 55.000 5.69 0.00 45.66 5.80
182 183 1.528309 CAACGTCTTGGTTGGGGCT 60.528 57.895 0.00 0.00 42.73 5.19
183 184 1.528309 AACGTCTTGGTTGGGGCTG 60.528 57.895 0.00 0.00 0.00 4.85
184 185 2.113139 CGTCTTGGTTGGGGCTGT 59.887 61.111 0.00 0.00 0.00 4.40
185 186 2.260869 CGTCTTGGTTGGGGCTGTG 61.261 63.158 0.00 0.00 0.00 3.66
186 187 1.152756 GTCTTGGTTGGGGCTGTGT 60.153 57.895 0.00 0.00 0.00 3.72
187 188 1.152777 TCTTGGTTGGGGCTGTGTG 60.153 57.895 0.00 0.00 0.00 3.82
188 189 2.123511 TTGGTTGGGGCTGTGTGG 60.124 61.111 0.00 0.00 0.00 4.17
189 190 2.927201 CTTGGTTGGGGCTGTGTGGT 62.927 60.000 0.00 0.00 0.00 4.16
190 191 2.912025 GGTTGGGGCTGTGTGGTG 60.912 66.667 0.00 0.00 0.00 4.17
191 192 2.912025 GTTGGGGCTGTGTGGTGG 60.912 66.667 0.00 0.00 0.00 4.61
192 193 3.425014 TTGGGGCTGTGTGGTGGT 61.425 61.111 0.00 0.00 0.00 4.16
193 194 3.730028 TTGGGGCTGTGTGGTGGTG 62.730 63.158 0.00 0.00 0.00 4.17
194 195 4.974721 GGGGCTGTGTGGTGGTGG 62.975 72.222 0.00 0.00 0.00 4.61
197 198 4.927782 GCTGTGTGGTGGTGGCGA 62.928 66.667 0.00 0.00 0.00 5.54
198 199 2.032528 CTGTGTGGTGGTGGCGAT 59.967 61.111 0.00 0.00 0.00 4.58
199 200 2.281414 TGTGTGGTGGTGGCGATG 60.281 61.111 0.00 0.00 0.00 3.84
200 201 2.281484 GTGTGGTGGTGGCGATGT 60.281 61.111 0.00 0.00 0.00 3.06
201 202 2.031919 TGTGGTGGTGGCGATGTC 59.968 61.111 0.00 0.00 0.00 3.06
202 203 2.746277 GTGGTGGTGGCGATGTCC 60.746 66.667 0.00 0.00 0.00 4.02
203 204 4.028490 TGGTGGTGGCGATGTCCC 62.028 66.667 0.00 0.00 0.00 4.46
204 205 3.717294 GGTGGTGGCGATGTCCCT 61.717 66.667 0.00 0.00 0.00 4.20
205 206 2.125106 GTGGTGGCGATGTCCCTC 60.125 66.667 0.00 0.00 0.00 4.30
206 207 2.606213 TGGTGGCGATGTCCCTCA 60.606 61.111 0.00 0.00 0.00 3.86
207 208 2.187946 GGTGGCGATGTCCCTCAG 59.812 66.667 0.00 0.00 0.00 3.35
208 209 2.660064 GGTGGCGATGTCCCTCAGT 61.660 63.158 0.00 0.00 0.00 3.41
209 210 1.327690 GGTGGCGATGTCCCTCAGTA 61.328 60.000 0.00 0.00 0.00 2.74
210 211 0.103208 GTGGCGATGTCCCTCAGTAG 59.897 60.000 0.00 0.00 0.00 2.57
211 212 1.043116 TGGCGATGTCCCTCAGTAGG 61.043 60.000 0.00 0.00 43.25 3.18
408 409 2.758979 CGGTACTAATGAGAGTGGTGGT 59.241 50.000 0.00 0.00 0.00 4.16
647 649 7.759489 ATGATCACAAAGGTTAGCAACTTTA 57.241 32.000 0.00 0.00 35.32 1.85
1153 1159 3.619900 ATCTAGGAGGTATGTGAGCCA 57.380 47.619 0.00 0.00 0.00 4.75
1388 1395 9.013229 GGTATCATTATGCTGTTGGATCAATTA 57.987 33.333 0.00 0.00 0.00 1.40
1478 1485 8.534333 TTGTTTGTTGCATTTAAGTGTTGTAA 57.466 26.923 0.00 0.00 0.00 2.41
1548 1555 1.255882 TGAAAATGAGCCGGCAATGT 58.744 45.000 31.54 14.44 0.00 2.71
1694 1701 6.480320 GGTCGCAATTACTCTATGTCAAGAAT 59.520 38.462 0.00 0.00 0.00 2.40
2060 2352 0.460635 TACCCGAATTGCGTAGGTGC 60.461 55.000 0.00 0.00 35.69 5.01
2184 2476 3.383185 TGCTTCCAAAGGACAACGAATTT 59.617 39.130 0.00 0.00 0.00 1.82
2208 2500 2.587241 CGAGAGTACGTACGAAGCAAAC 59.413 50.000 24.41 9.50 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.188462 CGGAAAGACAGCCATGTAATGTA 58.812 43.478 0.00 0.00 44.81 2.29
1 2 3.009723 CGGAAAGACAGCCATGTAATGT 58.990 45.455 0.00 0.00 44.81 2.71
2 3 2.223340 GCGGAAAGACAGCCATGTAATG 60.223 50.000 0.00 0.00 46.21 1.90
3 4 2.017049 GCGGAAAGACAGCCATGTAAT 58.983 47.619 0.00 0.00 40.68 1.89
4 5 1.448985 GCGGAAAGACAGCCATGTAA 58.551 50.000 0.00 0.00 40.68 2.41
5 6 3.153024 GCGGAAAGACAGCCATGTA 57.847 52.632 0.00 0.00 40.68 2.29
6 7 3.987404 GCGGAAAGACAGCCATGT 58.013 55.556 0.00 0.00 44.31 3.21
11 12 1.448717 GAGGAGGCGGAAAGACAGC 60.449 63.158 0.00 0.00 38.89 4.40
12 13 0.321671 TTGAGGAGGCGGAAAGACAG 59.678 55.000 0.00 0.00 0.00 3.51
22 23 1.905894 AGGAGACTTTCTTGAGGAGGC 59.094 52.381 0.00 0.00 37.44 4.70
36 37 2.896443 CGGCAGGAGGAAGGAGAC 59.104 66.667 0.00 0.00 0.00 3.36
37 38 3.077556 GCGGCAGGAGGAAGGAGA 61.078 66.667 0.00 0.00 0.00 3.71
38 39 4.168291 GGCGGCAGGAGGAAGGAG 62.168 72.222 3.07 0.00 0.00 3.69
59 60 3.782443 GGGAGAATCACCGGCGGT 61.782 66.667 28.83 28.83 36.25 5.68
66 67 0.976073 TCGGAGGTGGGGAGAATCAC 60.976 60.000 0.00 0.00 38.30 3.06
67 68 0.031111 ATCGGAGGTGGGGAGAATCA 60.031 55.000 0.00 0.00 36.25 2.57
68 69 0.394565 CATCGGAGGTGGGGAGAATC 59.605 60.000 0.00 0.00 0.00 2.52
69 70 1.056700 CCATCGGAGGTGGGGAGAAT 61.057 60.000 0.00 0.00 32.98 2.40
70 71 1.689233 CCATCGGAGGTGGGGAGAA 60.689 63.158 0.00 0.00 32.98 2.87
71 72 2.041922 CCATCGGAGGTGGGGAGA 60.042 66.667 0.00 0.00 32.98 3.71
72 73 3.866582 GCCATCGGAGGTGGGGAG 61.867 72.222 1.16 0.00 37.22 4.30
75 76 2.983879 AAAGGCCATCGGAGGTGGG 61.984 63.158 5.01 0.00 37.22 4.61
76 77 1.750399 CAAAGGCCATCGGAGGTGG 60.750 63.158 5.01 0.00 39.80 4.61
77 78 1.750399 CCAAAGGCCATCGGAGGTG 60.750 63.158 5.01 0.00 0.00 4.00
78 79 2.677228 CCAAAGGCCATCGGAGGT 59.323 61.111 5.01 0.00 0.00 3.85
79 80 2.124151 CCCAAAGGCCATCGGAGG 60.124 66.667 5.01 0.00 0.00 4.30
89 90 3.966543 ACCTCCACGGCCCAAAGG 61.967 66.667 0.00 1.41 35.61 3.11
90 91 2.672996 CACCTCCACGGCCCAAAG 60.673 66.667 0.00 0.00 35.61 2.77
91 92 4.966787 GCACCTCCACGGCCCAAA 62.967 66.667 0.00 0.00 35.61 3.28
98 99 3.432051 GATCCTCCGCACCTCCACG 62.432 68.421 0.00 0.00 0.00 4.94
99 100 2.022240 GAGATCCTCCGCACCTCCAC 62.022 65.000 0.00 0.00 0.00 4.02
100 101 1.758514 GAGATCCTCCGCACCTCCA 60.759 63.158 0.00 0.00 0.00 3.86
101 102 1.330655 TTGAGATCCTCCGCACCTCC 61.331 60.000 0.00 0.00 0.00 4.30
102 103 0.179097 GTTGAGATCCTCCGCACCTC 60.179 60.000 0.00 0.00 0.00 3.85
103 104 1.617947 GGTTGAGATCCTCCGCACCT 61.618 60.000 0.00 0.00 0.00 4.00
104 105 1.153349 GGTTGAGATCCTCCGCACC 60.153 63.158 0.00 0.00 0.00 5.01
105 106 1.519455 CGGTTGAGATCCTCCGCAC 60.519 63.158 0.00 0.00 36.68 5.34
106 107 2.892640 CGGTTGAGATCCTCCGCA 59.107 61.111 0.00 0.00 36.68 5.69
108 109 1.066587 GAGCGGTTGAGATCCTCCG 59.933 63.158 9.91 9.91 44.86 4.63
109 110 0.179097 GTGAGCGGTTGAGATCCTCC 60.179 60.000 0.00 0.00 0.00 4.30
110 111 0.179097 GGTGAGCGGTTGAGATCCTC 60.179 60.000 0.00 0.00 0.00 3.71
111 112 1.901085 GGTGAGCGGTTGAGATCCT 59.099 57.895 0.00 0.00 0.00 3.24
112 113 1.519455 CGGTGAGCGGTTGAGATCC 60.519 63.158 0.00 0.00 0.00 3.36
113 114 1.519455 CCGGTGAGCGGTTGAGATC 60.519 63.158 15.93 0.00 0.00 2.75
114 115 2.579201 CCGGTGAGCGGTTGAGAT 59.421 61.111 15.93 0.00 0.00 2.75
115 116 4.373116 GCCGGTGAGCGGTTGAGA 62.373 66.667 24.77 0.00 0.00 3.27
134 135 1.824224 AAACGAGAACGGGTCCCTCC 61.824 60.000 6.29 0.00 44.46 4.30
135 136 0.034476 AAAACGAGAACGGGTCCCTC 59.966 55.000 6.29 0.00 44.46 4.30
136 137 0.471191 AAAAACGAGAACGGGTCCCT 59.529 50.000 6.29 0.00 44.46 4.20
137 138 0.589708 CAAAAACGAGAACGGGTCCC 59.410 55.000 0.00 0.00 44.46 4.46
138 139 1.302366 ACAAAAACGAGAACGGGTCC 58.698 50.000 0.00 0.00 44.46 4.46
139 140 3.059393 CCTAACAAAAACGAGAACGGGTC 60.059 47.826 0.00 0.00 44.46 4.46
140 141 2.874086 CCTAACAAAAACGAGAACGGGT 59.126 45.455 0.00 0.00 44.46 5.28
141 142 2.874086 ACCTAACAAAAACGAGAACGGG 59.126 45.455 0.00 0.00 44.46 5.28
142 143 4.034279 TGAACCTAACAAAAACGAGAACGG 59.966 41.667 0.00 0.00 44.46 4.44
143 144 5.146482 TGAACCTAACAAAAACGAGAACG 57.854 39.130 0.00 0.00 45.75 3.95
144 145 5.450066 CGTTGAACCTAACAAAAACGAGAAC 59.550 40.000 0.00 0.00 42.06 3.01
145 146 5.122082 ACGTTGAACCTAACAAAAACGAGAA 59.878 36.000 12.11 0.00 42.06 2.87
146 147 4.630940 ACGTTGAACCTAACAAAAACGAGA 59.369 37.500 12.11 0.00 42.06 4.04
147 148 4.900664 ACGTTGAACCTAACAAAAACGAG 58.099 39.130 12.11 0.00 42.06 4.18
148 149 4.630940 AGACGTTGAACCTAACAAAAACGA 59.369 37.500 12.11 0.00 42.06 3.85
149 150 4.900664 AGACGTTGAACCTAACAAAAACG 58.099 39.130 4.39 4.39 44.28 3.60
150 151 5.513849 CCAAGACGTTGAACCTAACAAAAAC 59.486 40.000 0.00 0.00 35.46 2.43
151 152 5.183522 ACCAAGACGTTGAACCTAACAAAAA 59.816 36.000 0.00 0.00 35.46 1.94
152 153 4.701171 ACCAAGACGTTGAACCTAACAAAA 59.299 37.500 0.00 0.00 35.46 2.44
153 154 4.263435 ACCAAGACGTTGAACCTAACAAA 58.737 39.130 0.00 0.00 35.46 2.83
154 155 3.876341 ACCAAGACGTTGAACCTAACAA 58.124 40.909 0.00 0.00 35.46 2.83
155 156 3.547054 ACCAAGACGTTGAACCTAACA 57.453 42.857 0.00 0.00 35.46 2.41
156 157 3.002965 CCAACCAAGACGTTGAACCTAAC 59.997 47.826 3.10 0.00 44.88 2.34
157 158 3.207778 CCAACCAAGACGTTGAACCTAA 58.792 45.455 3.10 0.00 44.88 2.69
158 159 2.485835 CCCAACCAAGACGTTGAACCTA 60.486 50.000 3.10 0.00 44.88 3.08
159 160 1.675552 CCAACCAAGACGTTGAACCT 58.324 50.000 3.10 0.00 44.88 3.50
160 161 0.666374 CCCAACCAAGACGTTGAACC 59.334 55.000 3.10 0.00 44.88 3.62
161 162 0.666374 CCCCAACCAAGACGTTGAAC 59.334 55.000 3.10 0.00 44.88 3.18
162 163 1.104577 GCCCCAACCAAGACGTTGAA 61.105 55.000 3.10 0.00 44.88 2.69
163 164 1.527380 GCCCCAACCAAGACGTTGA 60.527 57.895 3.10 0.00 44.88 3.18
164 165 1.528309 AGCCCCAACCAAGACGTTG 60.528 57.895 0.00 0.00 42.31 4.10
165 166 1.528309 CAGCCCCAACCAAGACGTT 60.528 57.895 0.00 0.00 0.00 3.99
166 167 2.113139 CAGCCCCAACCAAGACGT 59.887 61.111 0.00 0.00 0.00 4.34
167 168 2.113139 ACAGCCCCAACCAAGACG 59.887 61.111 0.00 0.00 0.00 4.18
168 169 1.152756 ACACAGCCCCAACCAAGAC 60.153 57.895 0.00 0.00 0.00 3.01
169 170 1.152777 CACACAGCCCCAACCAAGA 60.153 57.895 0.00 0.00 0.00 3.02
170 171 2.202395 CCACACAGCCCCAACCAAG 61.202 63.158 0.00 0.00 0.00 3.61
171 172 2.123511 CCACACAGCCCCAACCAA 60.124 61.111 0.00 0.00 0.00 3.67
172 173 3.425014 ACCACACAGCCCCAACCA 61.425 61.111 0.00 0.00 0.00 3.67
173 174 2.912025 CACCACACAGCCCCAACC 60.912 66.667 0.00 0.00 0.00 3.77
174 175 2.912025 CCACCACACAGCCCCAAC 60.912 66.667 0.00 0.00 0.00 3.77
175 176 3.425014 ACCACCACACAGCCCCAA 61.425 61.111 0.00 0.00 0.00 4.12
176 177 4.202574 CACCACCACACAGCCCCA 62.203 66.667 0.00 0.00 0.00 4.96
177 178 4.974721 CCACCACCACACAGCCCC 62.975 72.222 0.00 0.00 0.00 5.80
180 181 4.927782 TCGCCACCACCACACAGC 62.928 66.667 0.00 0.00 0.00 4.40
181 182 2.032528 ATCGCCACCACCACACAG 59.967 61.111 0.00 0.00 0.00 3.66
182 183 2.281414 CATCGCCACCACCACACA 60.281 61.111 0.00 0.00 0.00 3.72
183 184 2.281484 ACATCGCCACCACCACAC 60.281 61.111 0.00 0.00 0.00 3.82
184 185 2.031919 GACATCGCCACCACCACA 59.968 61.111 0.00 0.00 0.00 4.17
185 186 2.746277 GGACATCGCCACCACCAC 60.746 66.667 0.00 0.00 0.00 4.16
186 187 4.028490 GGGACATCGCCACCACCA 62.028 66.667 0.00 0.00 0.00 4.17
187 188 3.682292 GAGGGACATCGCCACCACC 62.682 68.421 0.00 0.00 0.00 4.61
188 189 2.125106 GAGGGACATCGCCACCAC 60.125 66.667 0.00 0.00 0.00 4.16
189 190 2.606213 TGAGGGACATCGCCACCA 60.606 61.111 0.00 0.00 0.00 4.17
190 191 1.327690 TACTGAGGGACATCGCCACC 61.328 60.000 0.00 0.00 0.00 4.61
191 192 0.103208 CTACTGAGGGACATCGCCAC 59.897 60.000 0.00 0.00 0.00 5.01
192 193 1.043116 CCTACTGAGGGACATCGCCA 61.043 60.000 0.00 0.00 39.48 5.69
193 194 0.755698 TCCTACTGAGGGACATCGCC 60.756 60.000 0.00 0.00 43.94 5.54
194 195 1.112113 TTCCTACTGAGGGACATCGC 58.888 55.000 0.00 0.00 43.94 4.58
195 196 5.730296 ATTATTCCTACTGAGGGACATCG 57.270 43.478 0.00 0.00 43.94 3.84
196 197 8.602472 AGATATTATTCCTACTGAGGGACATC 57.398 38.462 0.00 0.00 43.94 3.06
197 198 7.621683 GGAGATATTATTCCTACTGAGGGACAT 59.378 40.741 0.00 0.00 43.94 3.06
198 199 6.954684 GGAGATATTATTCCTACTGAGGGACA 59.045 42.308 0.00 0.00 43.94 4.02
199 200 6.381707 GGGAGATATTATTCCTACTGAGGGAC 59.618 46.154 0.00 0.00 43.94 4.46
200 201 6.047960 TGGGAGATATTATTCCTACTGAGGGA 59.952 42.308 0.00 0.00 43.94 4.20
201 202 6.264528 TGGGAGATATTATTCCTACTGAGGG 58.735 44.000 0.00 0.00 43.94 4.30
202 203 7.634649 GCATGGGAGATATTATTCCTACTGAGG 60.635 44.444 0.00 0.00 45.35 3.86
203 204 7.271511 GCATGGGAGATATTATTCCTACTGAG 58.728 42.308 0.00 0.00 33.85 3.35
204 205 6.156949 GGCATGGGAGATATTATTCCTACTGA 59.843 42.308 0.00 0.00 33.85 3.41
205 206 6.070021 TGGCATGGGAGATATTATTCCTACTG 60.070 42.308 0.00 0.00 33.85 2.74
206 207 6.032039 TGGCATGGGAGATATTATTCCTACT 58.968 40.000 0.00 0.00 33.85 2.57
207 208 6.069963 AGTGGCATGGGAGATATTATTCCTAC 60.070 42.308 0.00 0.00 33.85 3.18
208 209 6.032039 AGTGGCATGGGAGATATTATTCCTA 58.968 40.000 0.00 0.00 33.85 2.94
209 210 4.854436 AGTGGCATGGGAGATATTATTCCT 59.146 41.667 0.00 0.00 33.85 3.36
210 211 5.184892 AGTGGCATGGGAGATATTATTCC 57.815 43.478 0.00 0.00 0.00 3.01
211 212 6.951971 ACTAGTGGCATGGGAGATATTATTC 58.048 40.000 0.00 0.00 0.00 1.75
212 213 6.959606 ACTAGTGGCATGGGAGATATTATT 57.040 37.500 0.00 0.00 0.00 1.40
213 214 7.422512 TCTACTAGTGGCATGGGAGATATTAT 58.577 38.462 5.39 0.00 0.00 1.28
214 215 6.800890 TCTACTAGTGGCATGGGAGATATTA 58.199 40.000 5.39 0.00 0.00 0.98
215 216 5.655394 TCTACTAGTGGCATGGGAGATATT 58.345 41.667 5.39 0.00 0.00 1.28
216 217 5.276694 TCTACTAGTGGCATGGGAGATAT 57.723 43.478 5.39 0.00 0.00 1.63
217 218 4.741928 TCTACTAGTGGCATGGGAGATA 57.258 45.455 5.39 0.00 0.00 1.98
218 219 3.619900 TCTACTAGTGGCATGGGAGAT 57.380 47.619 5.39 0.00 0.00 2.75
219 220 3.398318 TTCTACTAGTGGCATGGGAGA 57.602 47.619 5.39 0.00 0.00 3.71
220 221 4.487714 TTTTCTACTAGTGGCATGGGAG 57.512 45.455 5.39 0.00 0.00 4.30
221 222 4.324254 CCTTTTTCTACTAGTGGCATGGGA 60.324 45.833 5.39 0.00 0.00 4.37
222 223 3.947834 CCTTTTTCTACTAGTGGCATGGG 59.052 47.826 5.39 0.00 0.00 4.00
223 224 3.947834 CCCTTTTTCTACTAGTGGCATGG 59.052 47.826 5.39 2.35 0.00 3.66
224 225 4.589908 ACCCTTTTTCTACTAGTGGCATG 58.410 43.478 5.39 0.00 0.00 4.06
225 226 4.288626 TGACCCTTTTTCTACTAGTGGCAT 59.711 41.667 5.39 0.00 0.00 4.40
226 227 3.649023 TGACCCTTTTTCTACTAGTGGCA 59.351 43.478 5.39 0.00 0.00 4.92
227 228 4.281898 TGACCCTTTTTCTACTAGTGGC 57.718 45.455 5.39 0.00 0.00 5.01
408 409 1.555075 GCCCAGACTGACAACATCCTA 59.445 52.381 3.32 0.00 0.00 2.94
1150 1156 0.526211 GGTCGGTTGGAATTTCTGGC 59.474 55.000 0.00 0.00 0.00 4.85
1153 1159 4.263771 ACAATAGGGTCGGTTGGAATTTCT 60.264 41.667 0.00 0.00 0.00 2.52
1548 1555 3.146847 AGAGCATCGGTCATCGTACATA 58.853 45.455 0.00 0.00 42.67 2.29
1694 1701 2.158885 TCAAACAGGTGGACGTGAATGA 60.159 45.455 6.48 7.04 35.83 2.57
2060 2352 0.033920 GGTGCCCAGCTTTTTCTTGG 59.966 55.000 0.00 0.00 0.00 3.61
2184 2476 1.645034 CTTCGTACGTACTCTCGGGA 58.355 55.000 22.55 9.13 34.94 5.14


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

AutoCloner maintained by Alex Coulton.