Multiple sequence alignment - TraesCS5D01G246500

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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 TraesCS5D01G246500 chr5D 100.000 2578 0 0 1 2578 354506448 354503871 0.000000e+00 4761
1 TraesCS5D01G246500 chr5A 93.789 2415 92 25 193 2578 455469404 455467019 0.000000e+00 3576
2 TraesCS5D01G246500 chr5B 94.061 2374 70 19 250 2578 418816828 418814481 0.000000e+00 3537
3 TraesCS5D01G246500 chr5B 96.667 90 3 0 1 90 418816912 418816823 1.600000e-32 150
4 TraesCS5D01G246500 chr7D 81.037 1292 180 33 405 1676 11677290 11676044 0.000000e+00 968
5 TraesCS5D01G246500 chr4A 78.492 1167 171 47 542 1673 726112921 726114042 0.000000e+00 691
6 TraesCS5D01G246500 chr6A 84.066 364 40 6 2214 2577 42922690 42923035 4.110000e-88 335
7 TraesCS5D01G246500 chr7A 80.645 372 49 8 1182 1530 11104939 11104568 1.520000e-67 267


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 TraesCS5D01G246500 chr5D 354503871 354506448 2577 True 4761.0 4761 100.000 1 2578 1 chr5D.!!$R1 2577
1 TraesCS5D01G246500 chr5A 455467019 455469404 2385 True 3576.0 3576 93.789 193 2578 1 chr5A.!!$R1 2385
2 TraesCS5D01G246500 chr5B 418814481 418816912 2431 True 1843.5 3537 95.364 1 2578 2 chr5B.!!$R1 2577
3 TraesCS5D01G246500 chr7D 11676044 11677290 1246 True 968.0 968 81.037 405 1676 1 chr7D.!!$R1 1271
4 TraesCS5D01G246500 chr4A 726112921 726114042 1121 False 691.0 691 78.492 542 1673 1 chr4A.!!$F1 1131

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
239 240 0.036388 TCATCCCACGTTTCTCTGCC 60.036 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2215 0.68028 TGACAGTACGAGAGAGGGGC 60.68 60.0 0.0 0.0 0.0 5.8 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
55 56 2.316586 GCTCCCTTCCCCCATTCCA 61.317 63.158 0.00 0.00 0.00 3.53
58 59 0.423956 TCCCTTCCCCCATTCCACTA 59.576 55.000 0.00 0.00 0.00 2.74
61 62 2.422746 CCTTCCCCCATTCCACTATCT 58.577 52.381 0.00 0.00 0.00 1.98
84 85 0.629058 ACCCTCTCTCCCTCTCACTC 59.371 60.000 0.00 0.00 0.00 3.51
85 86 0.926293 CCCTCTCTCCCTCTCACTCT 59.074 60.000 0.00 0.00 0.00 3.24
86 87 1.410083 CCCTCTCTCCCTCTCACTCTG 60.410 61.905 0.00 0.00 0.00 3.35
87 88 1.392589 CTCTCTCCCTCTCACTCTGC 58.607 60.000 0.00 0.00 0.00 4.26
88 89 0.393673 TCTCTCCCTCTCACTCTGCG 60.394 60.000 0.00 0.00 0.00 5.18
89 90 0.679640 CTCTCCCTCTCACTCTGCGT 60.680 60.000 0.00 0.00 0.00 5.24
90 91 0.962855 TCTCCCTCTCACTCTGCGTG 60.963 60.000 0.00 0.00 45.18 5.34
105 106 3.713936 CGTGAATCGCCTGTACAGA 57.286 52.632 24.68 5.01 0.00 3.41
106 107 1.990799 CGTGAATCGCCTGTACAGAA 58.009 50.000 24.68 9.54 0.00 3.02
107 108 1.920574 CGTGAATCGCCTGTACAGAAG 59.079 52.381 24.68 16.45 0.00 2.85
108 109 2.271800 GTGAATCGCCTGTACAGAAGG 58.728 52.381 24.68 9.90 37.91 3.46
109 110 2.094182 GTGAATCGCCTGTACAGAAGGA 60.094 50.000 24.68 16.87 36.91 3.36
110 111 2.766263 TGAATCGCCTGTACAGAAGGAT 59.234 45.455 24.68 18.23 36.91 3.24
111 112 2.898729 ATCGCCTGTACAGAAGGATG 57.101 50.000 24.68 7.30 36.91 3.51
112 113 0.175760 TCGCCTGTACAGAAGGATGC 59.824 55.000 24.68 15.81 36.91 3.91
113 114 0.108186 CGCCTGTACAGAAGGATGCA 60.108 55.000 24.68 0.00 36.91 3.96
114 115 1.373570 GCCTGTACAGAAGGATGCAC 58.626 55.000 24.68 0.00 36.91 4.57
115 116 1.065854 GCCTGTACAGAAGGATGCACT 60.066 52.381 24.68 0.00 36.91 4.40
116 117 2.625737 CCTGTACAGAAGGATGCACTG 58.374 52.381 24.68 9.16 36.91 3.66
117 118 2.005451 CTGTACAGAAGGATGCACTGC 58.995 52.381 18.45 0.00 35.38 4.40
118 119 1.625315 TGTACAGAAGGATGCACTGCT 59.375 47.619 1.98 0.00 35.38 4.24
119 120 2.275318 GTACAGAAGGATGCACTGCTC 58.725 52.381 1.98 0.00 35.38 4.26
120 121 0.982704 ACAGAAGGATGCACTGCTCT 59.017 50.000 1.98 0.00 35.38 4.09
121 122 1.066286 ACAGAAGGATGCACTGCTCTC 60.066 52.381 1.98 0.00 35.38 3.20
122 123 0.540923 AGAAGGATGCACTGCTCTCC 59.459 55.000 12.77 12.77 33.48 3.71
123 124 0.463474 GAAGGATGCACTGCTCTCCC 60.463 60.000 15.61 6.54 33.66 4.30
124 125 2.202987 GGATGCACTGCTCTCCCG 60.203 66.667 1.98 0.00 0.00 5.14
125 126 2.581354 GATGCACTGCTCTCCCGT 59.419 61.111 1.98 0.00 0.00 5.28
126 127 1.520342 GATGCACTGCTCTCCCGTC 60.520 63.158 1.98 0.00 0.00 4.79
127 128 2.914777 GATGCACTGCTCTCCCGTCC 62.915 65.000 1.98 0.00 0.00 4.79
128 129 4.459089 GCACTGCTCTCCCGTCCC 62.459 72.222 0.00 0.00 0.00 4.46
129 130 3.775654 CACTGCTCTCCCGTCCCC 61.776 72.222 0.00 0.00 0.00 4.81
130 131 3.999285 ACTGCTCTCCCGTCCCCT 61.999 66.667 0.00 0.00 0.00 4.79
131 132 3.151022 CTGCTCTCCCGTCCCCTC 61.151 72.222 0.00 0.00 0.00 4.30
132 133 4.779733 TGCTCTCCCGTCCCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
134 135 4.862823 CTCTCCCGTCCCCTCCCC 62.863 77.778 0.00 0.00 0.00 4.81
139 140 4.499116 CCGTCCCCTCCCCCTCAT 62.499 72.222 0.00 0.00 0.00 2.90
140 141 2.844839 CGTCCCCTCCCCCTCATC 60.845 72.222 0.00 0.00 0.00 2.92
141 142 2.448736 GTCCCCTCCCCCTCATCC 60.449 72.222 0.00 0.00 0.00 3.51
142 143 2.628465 TCCCCTCCCCCTCATCCT 60.628 66.667 0.00 0.00 0.00 3.24
143 144 2.272170 TCCCCTCCCCCTCATCCTT 61.272 63.158 0.00 0.00 0.00 3.36
144 145 1.772156 CCCCTCCCCCTCATCCTTC 60.772 68.421 0.00 0.00 0.00 3.46
145 146 1.319799 CCCTCCCCCTCATCCTTCT 59.680 63.158 0.00 0.00 0.00 2.85
146 147 0.766288 CCCTCCCCCTCATCCTTCTC 60.766 65.000 0.00 0.00 0.00 2.87
147 148 0.766288 CCTCCCCCTCATCCTTCTCC 60.766 65.000 0.00 0.00 0.00 3.71
148 149 0.766288 CTCCCCCTCATCCTTCTCCC 60.766 65.000 0.00 0.00 0.00 4.30
149 150 2.143419 CCCCCTCATCCTTCTCCCG 61.143 68.421 0.00 0.00 0.00 5.14
150 151 1.383248 CCCCTCATCCTTCTCCCGT 60.383 63.158 0.00 0.00 0.00 5.28
151 152 1.403687 CCCCTCATCCTTCTCCCGTC 61.404 65.000 0.00 0.00 0.00 4.79
152 153 1.736586 CCTCATCCTTCTCCCGTCG 59.263 63.158 0.00 0.00 0.00 5.12
153 154 1.066587 CTCATCCTTCTCCCGTCGC 59.933 63.158 0.00 0.00 0.00 5.19
154 155 1.379977 TCATCCTTCTCCCGTCGCT 60.380 57.895 0.00 0.00 0.00 4.93
155 156 1.066587 CATCCTTCTCCCGTCGCTC 59.933 63.158 0.00 0.00 0.00 5.03
156 157 2.128507 ATCCTTCTCCCGTCGCTCC 61.129 63.158 0.00 0.00 0.00 4.70
157 158 2.575455 ATCCTTCTCCCGTCGCTCCT 62.575 60.000 0.00 0.00 0.00 3.69
158 159 2.776913 CCTTCTCCCGTCGCTCCTC 61.777 68.421 0.00 0.00 0.00 3.71
159 160 2.754658 TTCTCCCGTCGCTCCTCC 60.755 66.667 0.00 0.00 0.00 4.30
160 161 4.816984 TCTCCCGTCGCTCCTCCC 62.817 72.222 0.00 0.00 0.00 4.30
165 166 3.839432 CGTCGCTCCTCCCCCTTC 61.839 72.222 0.00 0.00 0.00 3.46
166 167 2.364448 GTCGCTCCTCCCCCTTCT 60.364 66.667 0.00 0.00 0.00 2.85
167 168 1.990614 GTCGCTCCTCCCCCTTCTT 60.991 63.158 0.00 0.00 0.00 2.52
168 169 1.686110 TCGCTCCTCCCCCTTCTTC 60.686 63.158 0.00 0.00 0.00 2.87
169 170 1.687493 CGCTCCTCCCCCTTCTTCT 60.687 63.158 0.00 0.00 0.00 2.85
170 171 1.681486 CGCTCCTCCCCCTTCTTCTC 61.681 65.000 0.00 0.00 0.00 2.87
171 172 1.341913 GCTCCTCCCCCTTCTTCTCC 61.342 65.000 0.00 0.00 0.00 3.71
172 173 0.341609 CTCCTCCCCCTTCTTCTCCT 59.658 60.000 0.00 0.00 0.00 3.69
173 174 0.340208 TCCTCCCCCTTCTTCTCCTC 59.660 60.000 0.00 0.00 0.00 3.71
174 175 0.692756 CCTCCCCCTTCTTCTCCTCC 60.693 65.000 0.00 0.00 0.00 4.30
175 176 0.341609 CTCCCCCTTCTTCTCCTCCT 59.658 60.000 0.00 0.00 0.00 3.69
176 177 0.340208 TCCCCCTTCTTCTCCTCCTC 59.660 60.000 0.00 0.00 0.00 3.71
177 178 0.692756 CCCCCTTCTTCTCCTCCTCC 60.693 65.000 0.00 0.00 0.00 4.30
178 179 0.692756 CCCCTTCTTCTCCTCCTCCC 60.693 65.000 0.00 0.00 0.00 4.30
179 180 0.692756 CCCTTCTTCTCCTCCTCCCC 60.693 65.000 0.00 0.00 0.00 4.81
180 181 0.043334 CCTTCTTCTCCTCCTCCCCA 59.957 60.000 0.00 0.00 0.00 4.96
181 182 1.199615 CTTCTTCTCCTCCTCCCCAC 58.800 60.000 0.00 0.00 0.00 4.61
182 183 0.614979 TTCTTCTCCTCCTCCCCACG 60.615 60.000 0.00 0.00 0.00 4.94
183 184 2.683933 TTCTCCTCCTCCCCACGC 60.684 66.667 0.00 0.00 0.00 5.34
184 185 3.239627 TTCTCCTCCTCCCCACGCT 62.240 63.158 0.00 0.00 0.00 5.07
185 186 3.151022 CTCCTCCTCCCCACGCTC 61.151 72.222 0.00 0.00 0.00 5.03
186 187 4.779733 TCCTCCTCCCCACGCTCC 62.780 72.222 0.00 0.00 0.00 4.70
187 188 4.787280 CCTCCTCCCCACGCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
188 189 3.151022 CTCCTCCCCACGCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
189 190 4.779733 TCCTCCCCACGCTCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
190 191 4.787280 CCTCCCCACGCTCCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
191 192 3.151022 CTCCCCACGCTCCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
192 193 4.779733 TCCCCACGCTCCTCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
195 196 3.382832 CCACGCTCCTCCTCCGTT 61.383 66.667 0.00 0.00 32.18 4.44
205 206 2.511600 CCTCCGTTGCCCGACATC 60.512 66.667 0.00 0.00 39.56 3.06
206 207 2.885644 CTCCGTTGCCCGACATCG 60.886 66.667 0.00 0.00 40.43 3.84
235 236 1.825474 TCTCCTCATCCCACGTTTCTC 59.175 52.381 0.00 0.00 0.00 2.87
239 240 0.036388 TCATCCCACGTTTCTCTGCC 60.036 55.000 0.00 0.00 0.00 4.85
243 244 1.237285 CCCACGTTTCTCTGCCCTTG 61.237 60.000 0.00 0.00 0.00 3.61
345 348 1.742761 TGATCTAAGTTGCTGCTGCC 58.257 50.000 13.47 0.00 38.71 4.85
401 416 6.029346 ACTGTTTGGCCTATGATTTCTTTG 57.971 37.500 3.32 0.00 0.00 2.77
446 461 2.540361 CCATGCTAAAACTGATCGCAGC 60.540 50.000 0.00 0.00 46.26 5.25
467 490 7.063780 CGCAGCTGATGTTTATGTATGATGATA 59.936 37.037 20.43 0.00 0.00 2.15
545 574 1.407258 CGTTTTTCTGTTGGGCTTGGA 59.593 47.619 0.00 0.00 0.00 3.53
726 761 7.068686 ACAAGGGCTAGAATTAGGAACTATC 57.931 40.000 0.00 0.00 42.38 2.08
749 784 2.100989 GTTCTGATCACCTACGGACCT 58.899 52.381 0.00 0.00 0.00 3.85
917 952 2.039418 CCATTCCTATCCACGAGGTCA 58.961 52.381 0.00 0.00 35.40 4.02
918 953 2.434336 CCATTCCTATCCACGAGGTCAA 59.566 50.000 0.00 0.00 35.40 3.18
964 999 0.746063 CTCTTTGTTTGTGCAGGCCA 59.254 50.000 5.01 0.00 0.00 5.36
982 1017 3.741476 CTGCTGCCGCTGGGAAAC 61.741 66.667 0.70 0.00 36.97 2.78
1022 1057 3.560105 TGTCCATCAGATCTCTCATCGT 58.440 45.455 0.00 0.00 0.00 3.73
1047 1082 1.143813 CCAGGTCCAGATATGCCCTT 58.856 55.000 0.00 0.00 0.00 3.95
1253 1300 3.637273 GGGGCTTGGACCACTCGT 61.637 66.667 0.00 0.00 27.52 4.18
1389 1463 0.390340 CAGGTGTCCGTGTCATGGAG 60.390 60.000 14.40 0.00 33.08 3.86
1924 2012 8.229811 CCATAGTTAAACCCTTGTAACGTAAAC 58.770 37.037 0.00 0.00 35.73 2.01
2122 2210 2.158652 ACCTAGCGTGATCCAGCTACTA 60.159 50.000 13.24 0.00 44.15 1.82
2127 2215 1.338337 CGTGATCCAGCTACTACCCTG 59.662 57.143 0.00 0.00 0.00 4.45
2332 2420 1.134220 TCGCCAAGGTCTTGTTCTTGT 60.134 47.619 9.51 0.00 38.83 3.16
2438 2526 1.137479 CCGCATTTGGCTCATTGGATT 59.863 47.619 0.00 0.00 41.67 3.01
2446 2534 1.215423 GGCTCATTGGATTGGTAGGGT 59.785 52.381 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.321282 AGGGAGAGAGGGTTAGAGATAGT 58.679 47.826 0.00 0.00 0.00 2.12
58 59 3.397955 GAGAGGGAGAGAGGGTTAGAGAT 59.602 52.174 0.00 0.00 0.00 2.75
61 62 2.242708 GTGAGAGGGAGAGAGGGTTAGA 59.757 54.545 0.00 0.00 0.00 2.10
87 88 1.920574 CTTCTGTACAGGCGATTCACG 59.079 52.381 22.48 0.00 45.66 4.35
88 89 2.094182 TCCTTCTGTACAGGCGATTCAC 60.094 50.000 22.48 0.00 0.00 3.18
89 90 2.176045 TCCTTCTGTACAGGCGATTCA 58.824 47.619 22.48 0.00 0.00 2.57
90 91 2.961526 TCCTTCTGTACAGGCGATTC 57.038 50.000 22.48 0.00 0.00 2.52
91 92 2.743183 GCATCCTTCTGTACAGGCGATT 60.743 50.000 22.48 3.14 0.00 3.34
92 93 1.202580 GCATCCTTCTGTACAGGCGAT 60.203 52.381 22.48 16.32 0.00 4.58
93 94 0.175760 GCATCCTTCTGTACAGGCGA 59.824 55.000 22.48 14.89 0.00 5.54
94 95 0.108186 TGCATCCTTCTGTACAGGCG 60.108 55.000 22.48 13.15 0.00 5.52
95 96 1.065854 AGTGCATCCTTCTGTACAGGC 60.066 52.381 22.48 16.30 34.59 4.85
96 97 2.625737 CAGTGCATCCTTCTGTACAGG 58.374 52.381 22.48 8.17 34.59 4.00
97 98 2.005451 GCAGTGCATCCTTCTGTACAG 58.995 52.381 17.17 17.17 34.59 2.74
98 99 1.625315 AGCAGTGCATCCTTCTGTACA 59.375 47.619 19.20 0.00 34.59 2.90
99 100 2.093764 AGAGCAGTGCATCCTTCTGTAC 60.094 50.000 19.20 0.00 32.58 2.90
100 101 2.167281 GAGAGCAGTGCATCCTTCTGTA 59.833 50.000 19.20 0.00 0.00 2.74
101 102 0.982704 AGAGCAGTGCATCCTTCTGT 59.017 50.000 19.20 0.00 0.00 3.41
102 103 1.654317 GAGAGCAGTGCATCCTTCTG 58.346 55.000 19.20 0.00 0.00 3.02
103 104 0.540923 GGAGAGCAGTGCATCCTTCT 59.459 55.000 24.74 15.78 34.99 2.85
104 105 0.463474 GGGAGAGCAGTGCATCCTTC 60.463 60.000 28.43 16.86 37.04 3.46
105 106 1.606531 GGGAGAGCAGTGCATCCTT 59.393 57.895 28.43 6.44 37.04 3.36
106 107 2.729479 CGGGAGAGCAGTGCATCCT 61.729 63.158 28.43 18.18 37.04 3.24
107 108 2.202987 CGGGAGAGCAGTGCATCC 60.203 66.667 24.25 24.25 36.41 3.51
108 109 1.520342 GACGGGAGAGCAGTGCATC 60.520 63.158 19.20 14.47 0.00 3.91
109 110 2.581354 GACGGGAGAGCAGTGCAT 59.419 61.111 19.20 5.04 0.00 3.96
110 111 3.695606 GGACGGGAGAGCAGTGCA 61.696 66.667 19.20 0.00 0.00 4.57
111 112 4.459089 GGGACGGGAGAGCAGTGC 62.459 72.222 7.13 7.13 0.00 4.40
112 113 3.775654 GGGGACGGGAGAGCAGTG 61.776 72.222 0.00 0.00 0.00 3.66
113 114 3.966930 GAGGGGACGGGAGAGCAGT 62.967 68.421 0.00 0.00 0.00 4.40
114 115 3.151022 GAGGGGACGGGAGAGCAG 61.151 72.222 0.00 0.00 0.00 4.24
115 116 4.779733 GGAGGGGACGGGAGAGCA 62.780 72.222 0.00 0.00 0.00 4.26
117 118 4.862823 GGGGAGGGGACGGGAGAG 62.863 77.778 0.00 0.00 0.00 3.20
122 123 4.499116 ATGAGGGGGAGGGGACGG 62.499 72.222 0.00 0.00 0.00 4.79
123 124 2.844839 GATGAGGGGGAGGGGACG 60.845 72.222 0.00 0.00 0.00 4.79
124 125 2.448736 GGATGAGGGGGAGGGGAC 60.449 72.222 0.00 0.00 0.00 4.46
125 126 2.271493 GAAGGATGAGGGGGAGGGGA 62.271 65.000 0.00 0.00 0.00 4.81
126 127 1.772156 GAAGGATGAGGGGGAGGGG 60.772 68.421 0.00 0.00 0.00 4.79
127 128 0.766288 GAGAAGGATGAGGGGGAGGG 60.766 65.000 0.00 0.00 0.00 4.30
128 129 0.766288 GGAGAAGGATGAGGGGGAGG 60.766 65.000 0.00 0.00 0.00 4.30
129 130 0.766288 GGGAGAAGGATGAGGGGGAG 60.766 65.000 0.00 0.00 0.00 4.30
130 131 1.318380 GGGAGAAGGATGAGGGGGA 59.682 63.158 0.00 0.00 0.00 4.81
131 132 2.143419 CGGGAGAAGGATGAGGGGG 61.143 68.421 0.00 0.00 0.00 5.40
132 133 1.383248 ACGGGAGAAGGATGAGGGG 60.383 63.158 0.00 0.00 0.00 4.79
133 134 1.739338 CGACGGGAGAAGGATGAGGG 61.739 65.000 0.00 0.00 0.00 4.30
134 135 1.736586 CGACGGGAGAAGGATGAGG 59.263 63.158 0.00 0.00 0.00 3.86
135 136 1.066587 GCGACGGGAGAAGGATGAG 59.933 63.158 0.00 0.00 0.00 2.90
136 137 1.379977 AGCGACGGGAGAAGGATGA 60.380 57.895 0.00 0.00 0.00 2.92
137 138 1.066587 GAGCGACGGGAGAAGGATG 59.933 63.158 0.00 0.00 0.00 3.51
138 139 2.128507 GGAGCGACGGGAGAAGGAT 61.129 63.158 0.00 0.00 0.00 3.24
139 140 2.754658 GGAGCGACGGGAGAAGGA 60.755 66.667 0.00 0.00 0.00 3.36
140 141 2.756283 AGGAGCGACGGGAGAAGG 60.756 66.667 0.00 0.00 0.00 3.46
141 142 2.776913 GGAGGAGCGACGGGAGAAG 61.777 68.421 0.00 0.00 0.00 2.85
142 143 2.754658 GGAGGAGCGACGGGAGAA 60.755 66.667 0.00 0.00 0.00 2.87
143 144 4.816984 GGGAGGAGCGACGGGAGA 62.817 72.222 0.00 0.00 0.00 3.71
148 149 3.839432 GAAGGGGGAGGAGCGACG 61.839 72.222 0.00 0.00 0.00 5.12
149 150 1.962321 GAAGAAGGGGGAGGAGCGAC 61.962 65.000 0.00 0.00 0.00 5.19
150 151 1.686110 GAAGAAGGGGGAGGAGCGA 60.686 63.158 0.00 0.00 0.00 4.93
151 152 1.681486 GAGAAGAAGGGGGAGGAGCG 61.681 65.000 0.00 0.00 0.00 5.03
152 153 1.341913 GGAGAAGAAGGGGGAGGAGC 61.342 65.000 0.00 0.00 0.00 4.70
153 154 0.341609 AGGAGAAGAAGGGGGAGGAG 59.658 60.000 0.00 0.00 0.00 3.69
154 155 0.340208 GAGGAGAAGAAGGGGGAGGA 59.660 60.000 0.00 0.00 0.00 3.71
155 156 0.692756 GGAGGAGAAGAAGGGGGAGG 60.693 65.000 0.00 0.00 0.00 4.30
156 157 0.341609 AGGAGGAGAAGAAGGGGGAG 59.658 60.000 0.00 0.00 0.00 4.30
157 158 0.340208 GAGGAGGAGAAGAAGGGGGA 59.660 60.000 0.00 0.00 0.00 4.81
158 159 0.692756 GGAGGAGGAGAAGAAGGGGG 60.693 65.000 0.00 0.00 0.00 5.40
159 160 0.692756 GGGAGGAGGAGAAGAAGGGG 60.693 65.000 0.00 0.00 0.00 4.79
160 161 0.692756 GGGGAGGAGGAGAAGAAGGG 60.693 65.000 0.00 0.00 0.00 3.95
161 162 0.043334 TGGGGAGGAGGAGAAGAAGG 59.957 60.000 0.00 0.00 0.00 3.46
162 163 1.199615 GTGGGGAGGAGGAGAAGAAG 58.800 60.000 0.00 0.00 0.00 2.85
163 164 0.614979 CGTGGGGAGGAGGAGAAGAA 60.615 60.000 0.00 0.00 0.00 2.52
164 165 1.000486 CGTGGGGAGGAGGAGAAGA 60.000 63.158 0.00 0.00 0.00 2.87
165 166 2.726351 GCGTGGGGAGGAGGAGAAG 61.726 68.421 0.00 0.00 0.00 2.85
166 167 2.683933 GCGTGGGGAGGAGGAGAA 60.684 66.667 0.00 0.00 0.00 2.87
167 168 3.663815 GAGCGTGGGGAGGAGGAGA 62.664 68.421 0.00 0.00 0.00 3.71
168 169 3.151022 GAGCGTGGGGAGGAGGAG 61.151 72.222 0.00 0.00 0.00 3.69
169 170 4.779733 GGAGCGTGGGGAGGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
170 171 4.787280 AGGAGCGTGGGGAGGAGG 62.787 72.222 0.00 0.00 0.00 4.30
171 172 3.151022 GAGGAGCGTGGGGAGGAG 61.151 72.222 0.00 0.00 0.00 3.69
172 173 4.779733 GGAGGAGCGTGGGGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
173 174 4.787280 AGGAGGAGCGTGGGGAGG 62.787 72.222 0.00 0.00 0.00 4.30
174 175 3.151022 GAGGAGGAGCGTGGGGAG 61.151 72.222 0.00 0.00 0.00 4.30
175 176 4.779733 GGAGGAGGAGCGTGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
178 179 3.382832 AACGGAGGAGGAGCGTGG 61.383 66.667 0.00 0.00 0.00 4.94
179 180 2.125912 CAACGGAGGAGGAGCGTG 60.126 66.667 0.00 0.00 0.00 5.34
180 181 4.070552 GCAACGGAGGAGGAGCGT 62.071 66.667 0.00 0.00 0.00 5.07
181 182 4.821589 GGCAACGGAGGAGGAGCG 62.822 72.222 0.00 0.00 0.00 5.03
182 183 4.475135 GGGCAACGGAGGAGGAGC 62.475 72.222 0.00 0.00 37.60 4.70
183 184 4.148825 CGGGCAACGGAGGAGGAG 62.149 72.222 0.00 0.00 39.75 3.69
184 185 4.689549 TCGGGCAACGGAGGAGGA 62.690 66.667 0.11 0.00 44.45 3.71
206 207 3.453070 GATGAGGAGAGTGGGCGGC 62.453 68.421 0.00 0.00 0.00 6.53
235 236 1.967319 ACACAGTTGTACAAGGGCAG 58.033 50.000 8.98 3.64 32.60 4.85
239 240 5.757886 CCACAATAACACAGTTGTACAAGG 58.242 41.667 8.98 7.09 36.48 3.61
243 244 5.121768 CCTAGCCACAATAACACAGTTGTAC 59.878 44.000 0.00 0.00 36.48 2.90
345 348 2.464865 GCACTGCATCTAAGGTAGTCG 58.535 52.381 0.00 0.00 0.00 4.18
441 456 5.178067 TCATCATACATAAACATCAGCTGCG 59.822 40.000 9.47 5.02 0.00 5.18
467 490 5.127031 ACAAACTAAGCAACAAAGACATGGT 59.873 36.000 0.00 0.00 0.00 3.55
749 784 1.875157 GCCATGTCGCTCTCATGCATA 60.875 52.381 0.00 0.00 40.63 3.14
917 952 7.394641 GGAAGAAAGTGATAAGAAGTCCCATTT 59.605 37.037 0.00 0.00 0.00 2.32
918 953 6.887002 GGAAGAAAGTGATAAGAAGTCCCATT 59.113 38.462 0.00 0.00 0.00 3.16
982 1017 0.820891 ATGGCTGCTGGCGATTAAGG 60.821 55.000 12.46 0.00 42.94 2.69
1022 1057 1.620323 CATATCTGGACCTGGATGCGA 59.380 52.381 0.00 0.00 0.00 5.10
1047 1082 2.244117 GAGAGATGGTGGAAGCGGCA 62.244 60.000 1.45 0.00 36.92 5.69
1253 1300 1.447140 CTGTACCTAAAGGCGCGCA 60.447 57.895 34.42 11.59 39.32 6.09
1389 1463 1.002502 GGAGTAACACACCTGCCCC 60.003 63.158 0.00 0.00 0.00 5.80
1623 1698 1.266989 CGGACCAAGAAAAAGAGGTGC 59.733 52.381 0.00 0.00 38.88 5.01
1924 2012 1.966451 GTGTCAAACCTCCCCAGCG 60.966 63.158 0.00 0.00 0.00 5.18
2122 2210 2.623450 TACGAGAGAGGGGCAGGGT 61.623 63.158 0.00 0.00 0.00 4.34
2127 2215 0.680280 TGACAGTACGAGAGAGGGGC 60.680 60.000 0.00 0.00 0.00 5.80
2241 2329 4.147449 CGACGCAGGAGGGATGCA 62.147 66.667 0.00 0.00 44.05 3.96
2332 2420 0.401395 GACATGGGGAGGATGGGGTA 60.401 60.000 0.00 0.00 0.00 3.69
2438 2526 2.136974 ACCCCTGTAAAACCCTACCA 57.863 50.000 0.00 0.00 0.00 3.25
2446 2534 8.226112 TCCATAGTTTCTAAAACCCCTGTAAAA 58.774 33.333 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.