Multiple sequence alignment - TraesCS4B01G362800

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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 TraesCS4B01G362800 chr4B 100.000 2375 0 0 1 2375 651903068 651905442 0.000000e+00 4386.0
1 TraesCS4B01G362800 chr4B 91.197 284 17 2 1 284 441660528 441660803 1.720000e-101 379.0
2 TraesCS4B01G362800 chr4D 94.752 1372 51 5 304 1659 505238557 505237191 0.000000e+00 2115.0
3 TraesCS4B01G362800 chr4D 94.651 673 32 3 1704 2375 505236946 505236277 0.000000e+00 1040.0
4 TraesCS4B01G362800 chr5A 87.944 929 74 19 739 1637 689387365 689386445 0.000000e+00 1061.0
5 TraesCS4B01G362800 chr1D 93.770 305 17 2 1 305 435496173 435496475 7.740000e-125 457.0
6 TraesCS4B01G362800 chr1D 93.793 290 14 2 1 290 393016389 393016104 1.300000e-117 433.0
7 TraesCS4B01G362800 chr7D 93.464 306 17 2 1 306 50125770 50125468 3.600000e-123 451.0
8 TraesCS4B01G362800 chr7D 94.483 290 13 1 1 290 615804693 615804407 6.020000e-121 444.0
9 TraesCS4B01G362800 chr2B 94.828 290 13 1 1 290 743675656 743675943 3.600000e-123 451.0
10 TraesCS4B01G362800 chr2B 77.157 394 61 12 309 673 768806692 768806299 4.000000e-48 202.0
11 TraesCS4B01G362800 chr3D 94.138 290 16 1 1 290 573761960 573762248 7.790000e-120 440.0
12 TraesCS4B01G362800 chr3D 92.787 305 20 2 1 305 609267549 609267851 7.790000e-120 440.0
13 TraesCS4B01G362800 chr3D 93.793 290 16 2 1 290 594595862 594595575 3.630000e-118 435.0
14 TraesCS4B01G362800 chr6B 92.459 305 22 1 1 304 699619754 699619450 3.630000e-118 435.0
15 TraesCS4B01G362800 chr3B 80.645 248 36 7 24 269 35284791 35285028 5.210000e-42 182.0
16 TraesCS4B01G362800 chr3B 80.242 248 37 7 24 269 35208637 35208874 2.430000e-40 176.0
17 TraesCS4B01G362800 chr2D 82.326 215 29 1 309 514 19587318 19587532 6.750000e-41 178.0
18 TraesCS4B01G362800 chr2D 75.741 371 60 12 315 656 9879441 9879072 2.440000e-35 159.0
19 TraesCS4B01G362800 chr2A 75.134 374 62 12 309 652 9847911 9848283 1.900000e-31 147.0
20 TraesCS4B01G362800 chr2A 74.866 374 63 12 309 652 9395434 9395806 8.850000e-30 141.0
21 TraesCS4B01G362800 chr2A 86.538 52 7 0 315 366 9099699 9099648 9.170000e-05 58.4
22 TraesCS4B01G362800 chr5D 100.000 28 0 0 2123 2150 327982096 327982069 4.000000e-03 52.8


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 TraesCS4B01G362800 chr4B 651903068 651905442 2374 False 4386.0 4386 100.0000 1 2375 1 chr4B.!!$F2 2374
1 TraesCS4B01G362800 chr4D 505236277 505238557 2280 True 1577.5 2115 94.7015 304 2375 2 chr4D.!!$R1 2071
2 TraesCS4B01G362800 chr5A 689386445 689387365 920 True 1061.0 1061 87.9440 739 1637 1 chr5A.!!$R1 898

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
268 269 0.108472 CGACCCTTTAGTCCCGGTTC 60.108 60.0 0.0 0.0 32.91 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 1744 0.834612 TGTACCGATTGATGTCCCCC 59.165 55.0 0.0 0.0 0.0 5.4 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
27 28 9.046296 AGCTAGCTAACACAATATATGAAACAC 57.954 33.333 17.69 0.00 0.00 3.32
28 29 8.283291 GCTAGCTAACACAATATATGAAACACC 58.717 37.037 7.70 0.00 0.00 4.16
29 30 9.547753 CTAGCTAACACAATATATGAAACACCT 57.452 33.333 0.00 0.00 0.00 4.00
31 32 9.899661 AGCTAACACAATATATGAAACACCTAA 57.100 29.630 0.00 0.00 0.00 2.69
41 42 7.907841 ATATGAAACACCTAAATTAACCCCC 57.092 36.000 0.00 0.00 0.00 5.40
55 56 2.528127 CCCCCAAAACCCCCAACC 60.528 66.667 0.00 0.00 0.00 3.77
56 57 2.528127 CCCCAAAACCCCCAACCC 60.528 66.667 0.00 0.00 0.00 4.11
57 58 2.618139 CCCAAAACCCCCAACCCT 59.382 61.111 0.00 0.00 0.00 4.34
58 59 1.535444 CCCAAAACCCCCAACCCTC 60.535 63.158 0.00 0.00 0.00 4.30
59 60 1.535444 CCAAAACCCCCAACCCTCC 60.535 63.158 0.00 0.00 0.00 4.30
60 61 1.535444 CAAAACCCCCAACCCTCCC 60.535 63.158 0.00 0.00 0.00 4.30
61 62 2.797075 AAAACCCCCAACCCTCCCC 61.797 63.158 0.00 0.00 0.00 4.81
94 95 1.724545 AAAACTAAAACCCCAGCCCC 58.275 50.000 0.00 0.00 0.00 5.80
95 96 0.864659 AAACTAAAACCCCAGCCCCT 59.135 50.000 0.00 0.00 0.00 4.79
96 97 0.114364 AACTAAAACCCCAGCCCCTG 59.886 55.000 0.00 0.00 0.00 4.45
97 98 0.774491 ACTAAAACCCCAGCCCCTGA 60.774 55.000 0.00 0.00 32.44 3.86
98 99 0.407918 CTAAAACCCCAGCCCCTGAA 59.592 55.000 0.00 0.00 32.44 3.02
99 100 0.861155 TAAAACCCCAGCCCCTGAAA 59.139 50.000 0.00 0.00 32.44 2.69
100 101 0.193321 AAAACCCCAGCCCCTGAAAT 59.807 50.000 0.00 0.00 32.44 2.17
101 102 0.545071 AAACCCCAGCCCCTGAAATG 60.545 55.000 0.00 0.00 32.44 2.32
102 103 2.761213 CCCCAGCCCCTGAAATGC 60.761 66.667 0.00 0.00 32.44 3.56
103 104 2.361771 CCCAGCCCCTGAAATGCT 59.638 61.111 0.00 0.00 32.44 3.79
106 107 4.751431 AGCCCCTGAAATGCTGAC 57.249 55.556 0.00 0.00 33.23 3.51
107 108 1.377725 AGCCCCTGAAATGCTGACG 60.378 57.895 0.00 0.00 33.23 4.35
108 109 3.056313 GCCCCTGAAATGCTGACGC 62.056 63.158 0.00 0.00 0.00 5.19
109 110 2.753966 CCCCTGAAATGCTGACGCG 61.754 63.158 3.53 3.53 39.65 6.01
110 111 2.034879 CCCTGAAATGCTGACGCGT 61.035 57.895 13.85 13.85 39.65 6.01
111 112 1.133253 CCTGAAATGCTGACGCGTG 59.867 57.895 20.70 3.71 39.65 5.34
112 113 1.133253 CTGAAATGCTGACGCGTGG 59.867 57.895 20.70 10.85 39.65 4.94
113 114 1.291184 CTGAAATGCTGACGCGTGGA 61.291 55.000 20.70 4.37 39.65 4.02
114 115 0.673333 TGAAATGCTGACGCGTGGAT 60.673 50.000 20.70 7.22 39.65 3.41
115 116 0.247814 GAAATGCTGACGCGTGGATG 60.248 55.000 20.70 4.59 39.65 3.51
116 117 2.257286 AAATGCTGACGCGTGGATGC 62.257 55.000 20.70 15.70 39.65 3.91
119 120 2.434884 CTGACGCGTGGATGCCTT 60.435 61.111 20.70 0.00 0.00 4.35
120 121 2.031919 TGACGCGTGGATGCCTTT 59.968 55.556 20.70 0.00 0.00 3.11
121 122 1.577328 CTGACGCGTGGATGCCTTTT 61.577 55.000 20.70 0.00 0.00 2.27
122 123 1.154225 GACGCGTGGATGCCTTTTG 60.154 57.895 20.70 0.00 0.00 2.44
123 124 2.179018 CGCGTGGATGCCTTTTGG 59.821 61.111 0.00 0.00 44.18 3.28
124 125 2.625823 CGCGTGGATGCCTTTTGGT 61.626 57.895 0.00 0.00 42.99 3.67
125 126 1.212751 GCGTGGATGCCTTTTGGTC 59.787 57.895 0.00 0.00 42.99 4.02
126 127 1.883021 CGTGGATGCCTTTTGGTCC 59.117 57.895 0.00 0.00 42.99 4.46
127 128 1.595093 CGTGGATGCCTTTTGGTCCC 61.595 60.000 0.00 0.00 42.99 4.46
128 129 1.304052 TGGATGCCTTTTGGTCCCG 60.304 57.895 0.00 0.00 42.99 5.14
129 130 2.052104 GGATGCCTTTTGGTCCCGG 61.052 63.158 0.00 0.00 42.99 5.73
130 131 1.304134 GATGCCTTTTGGTCCCGGT 60.304 57.895 0.00 0.00 42.99 5.28
131 132 0.898326 GATGCCTTTTGGTCCCGGTT 60.898 55.000 0.00 0.00 42.99 4.44
132 133 1.184970 ATGCCTTTTGGTCCCGGTTG 61.185 55.000 0.00 0.00 42.99 3.77
133 134 2.570284 GCCTTTTGGTCCCGGTTGG 61.570 63.158 0.00 0.00 42.99 3.77
134 135 1.152631 CCTTTTGGTCCCGGTTGGT 60.153 57.895 0.00 0.00 34.77 3.67
135 136 1.460273 CCTTTTGGTCCCGGTTGGTG 61.460 60.000 0.00 0.00 34.77 4.17
136 137 0.753848 CTTTTGGTCCCGGTTGGTGT 60.754 55.000 0.00 0.00 34.77 4.16
137 138 0.752376 TTTTGGTCCCGGTTGGTGTC 60.752 55.000 0.00 0.00 34.77 3.67
138 139 1.923006 TTTGGTCCCGGTTGGTGTCA 61.923 55.000 0.00 0.00 34.77 3.58
139 140 2.281276 GGTCCCGGTTGGTGTCAC 60.281 66.667 0.00 0.00 34.77 3.67
140 141 2.281276 GTCCCGGTTGGTGTCACC 60.281 66.667 15.64 15.64 39.22 4.02
149 150 2.281276 GGTGTCACCAACCGGGAC 60.281 66.667 17.59 3.26 38.42 4.46
150 151 2.281276 GTGTCACCAACCGGGACC 60.281 66.667 6.32 0.00 41.15 4.46
151 152 2.768769 TGTCACCAACCGGGACCA 60.769 61.111 6.32 0.00 41.15 4.02
152 153 2.376165 TGTCACCAACCGGGACCAA 61.376 57.895 6.32 0.00 41.15 3.67
153 154 1.152922 GTCACCAACCGGGACCAAA 60.153 57.895 6.32 0.00 41.15 3.28
154 155 1.149627 TCACCAACCGGGACCAAAG 59.850 57.895 6.32 0.00 41.15 2.77
155 156 1.901464 CACCAACCGGGACCAAAGG 60.901 63.158 6.32 0.00 41.15 3.11
156 157 2.989253 CCAACCGGGACCAAAGGC 60.989 66.667 6.32 0.00 40.01 4.35
157 158 2.989253 CAACCGGGACCAAAGGCC 60.989 66.667 6.32 0.00 0.00 5.19
158 159 4.295199 AACCGGGACCAAAGGCCC 62.295 66.667 6.32 0.00 36.26 5.80
160 161 4.426313 CCGGGACCAAAGGCCCTC 62.426 72.222 0.00 0.00 37.05 4.30
161 162 4.426313 CGGGACCAAAGGCCCTCC 62.426 72.222 0.00 0.00 37.05 4.30
163 164 2.356667 GGACCAAAGGCCCTCCTG 59.643 66.667 0.00 0.00 43.40 3.86
164 165 2.361737 GACCAAAGGCCCTCCTGC 60.362 66.667 0.00 0.00 43.40 4.85
172 173 3.555324 GCCCTCCTGCCTAGGCTC 61.555 72.222 33.07 7.42 44.22 4.70
173 174 3.230245 CCCTCCTGCCTAGGCTCG 61.230 72.222 33.07 22.98 44.22 5.03
174 175 2.123683 CCTCCTGCCTAGGCTCGA 60.124 66.667 33.07 25.00 44.22 4.04
175 176 2.494530 CCTCCTGCCTAGGCTCGAC 61.495 68.421 33.07 5.82 44.22 4.20
176 177 2.829003 TCCTGCCTAGGCTCGACG 60.829 66.667 33.07 15.88 44.22 5.12
177 178 4.577246 CCTGCCTAGGCTCGACGC 62.577 72.222 33.07 6.63 42.51 5.19
178 179 3.826754 CTGCCTAGGCTCGACGCA 61.827 66.667 33.07 11.36 41.67 5.24
179 180 4.129737 TGCCTAGGCTCGACGCAC 62.130 66.667 33.07 2.70 41.67 5.34
180 181 4.874977 GCCTAGGCTCGACGCACC 62.875 72.222 27.17 0.00 41.67 5.01
181 182 4.554363 CCTAGGCTCGACGCACCG 62.554 72.222 0.00 0.00 41.67 4.94
182 183 4.554363 CTAGGCTCGACGCACCGG 62.554 72.222 0.00 0.00 41.67 5.28
199 200 3.134127 GCCACGTGAAGGCCCATC 61.134 66.667 19.30 0.00 46.50 3.51
200 201 2.671070 CCACGTGAAGGCCCATCT 59.329 61.111 19.30 0.00 0.00 2.90
201 202 1.746615 CCACGTGAAGGCCCATCTG 60.747 63.158 19.30 0.00 0.00 2.90
202 203 1.003355 CACGTGAAGGCCCATCTGT 60.003 57.895 10.90 0.00 0.00 3.41
203 204 1.021390 CACGTGAAGGCCCATCTGTC 61.021 60.000 10.90 0.00 0.00 3.51
204 205 1.450312 CGTGAAGGCCCATCTGTCC 60.450 63.158 0.00 0.00 0.00 4.02
205 206 1.077429 GTGAAGGCCCATCTGTCCC 60.077 63.158 0.00 0.00 0.00 4.46
206 207 2.190578 GAAGGCCCATCTGTCCCG 59.809 66.667 0.00 0.00 0.00 5.14
207 208 3.406595 GAAGGCCCATCTGTCCCGG 62.407 68.421 0.00 0.00 0.00 5.73
208 209 4.741239 AGGCCCATCTGTCCCGGT 62.741 66.667 0.00 0.00 0.00 5.28
209 210 3.728373 GGCCCATCTGTCCCGGTT 61.728 66.667 0.00 0.00 0.00 4.44
210 211 2.124695 GCCCATCTGTCCCGGTTC 60.125 66.667 0.00 0.00 0.00 3.62
211 212 2.186903 CCCATCTGTCCCGGTTCG 59.813 66.667 0.00 0.00 0.00 3.95
212 213 2.656069 CCCATCTGTCCCGGTTCGT 61.656 63.158 0.00 0.00 0.00 3.85
213 214 1.447838 CCATCTGTCCCGGTTCGTG 60.448 63.158 0.00 0.00 0.00 4.35
214 215 1.292223 CATCTGTCCCGGTTCGTGT 59.708 57.895 0.00 0.00 0.00 4.49
215 216 0.528924 CATCTGTCCCGGTTCGTGTA 59.471 55.000 0.00 0.00 0.00 2.90
216 217 1.067425 CATCTGTCCCGGTTCGTGTAA 60.067 52.381 0.00 0.00 0.00 2.41
217 218 0.599558 TCTGTCCCGGTTCGTGTAAG 59.400 55.000 0.00 0.00 0.00 2.34
218 219 0.599558 CTGTCCCGGTTCGTGTAAGA 59.400 55.000 0.00 0.00 0.00 2.10
219 220 1.000060 CTGTCCCGGTTCGTGTAAGAA 60.000 52.381 0.00 0.00 0.00 2.52
220 221 1.619827 TGTCCCGGTTCGTGTAAGAAT 59.380 47.619 0.00 0.00 32.25 2.40
221 222 2.265683 GTCCCGGTTCGTGTAAGAATC 58.734 52.381 0.00 0.00 32.25 2.52
225 226 2.660189 GGTTCGTGTAAGAATCGGGA 57.340 50.000 0.00 0.00 32.25 5.14
226 227 2.265683 GGTTCGTGTAAGAATCGGGAC 58.734 52.381 0.00 0.00 32.25 4.46
227 228 2.094338 GGTTCGTGTAAGAATCGGGACT 60.094 50.000 0.00 0.00 32.25 3.85
228 229 3.129287 GGTTCGTGTAAGAATCGGGACTA 59.871 47.826 0.00 0.00 32.25 2.59
229 230 4.380867 GGTTCGTGTAAGAATCGGGACTAA 60.381 45.833 0.00 0.00 32.25 2.24
230 231 4.627611 TCGTGTAAGAATCGGGACTAAG 57.372 45.455 0.00 0.00 0.00 2.18
231 232 3.379372 TCGTGTAAGAATCGGGACTAAGG 59.621 47.826 0.00 0.00 0.00 2.69
232 233 3.490419 CGTGTAAGAATCGGGACTAAGGG 60.490 52.174 0.00 0.00 0.00 3.95
233 234 3.036091 TGTAAGAATCGGGACTAAGGGG 58.964 50.000 0.00 0.00 0.00 4.79
234 235 0.837940 AAGAATCGGGACTAAGGGGC 59.162 55.000 0.00 0.00 0.00 5.80
235 236 1.054978 AGAATCGGGACTAAGGGGCC 61.055 60.000 0.00 0.00 44.23 5.80
240 241 3.810188 GGACTAAGGGGCCAGGGC 61.810 72.222 4.39 3.77 44.40 5.19
241 242 3.015145 GACTAAGGGGCCAGGGCA 61.015 66.667 16.36 0.00 44.11 5.36
242 243 2.287194 ACTAAGGGGCCAGGGCAT 60.287 61.111 16.36 2.77 44.11 4.40
243 244 1.935931 ACTAAGGGGCCAGGGCATT 60.936 57.895 16.36 11.41 44.11 3.56
244 245 0.626277 ACTAAGGGGCCAGGGCATTA 60.626 55.000 16.36 11.95 44.11 1.90
245 246 0.111253 CTAAGGGGCCAGGGCATTAG 59.889 60.000 16.36 17.21 44.11 1.73
246 247 0.626277 TAAGGGGCCAGGGCATTAGT 60.626 55.000 16.36 0.00 44.11 2.24
247 248 0.626277 AAGGGGCCAGGGCATTAGTA 60.626 55.000 16.36 0.00 44.11 1.82
248 249 0.626277 AGGGGCCAGGGCATTAGTAA 60.626 55.000 16.36 0.00 44.11 2.24
249 250 0.467474 GGGGCCAGGGCATTAGTAAC 60.467 60.000 16.36 0.00 44.11 2.50
250 251 0.818040 GGGCCAGGGCATTAGTAACG 60.818 60.000 16.36 0.00 44.11 3.18
251 252 0.179468 GGCCAGGGCATTAGTAACGA 59.821 55.000 13.10 0.00 44.11 3.85
252 253 1.296727 GCCAGGGCATTAGTAACGAC 58.703 55.000 5.20 0.00 41.49 4.34
253 254 1.949465 CCAGGGCATTAGTAACGACC 58.051 55.000 0.00 0.00 0.00 4.79
254 255 1.474498 CCAGGGCATTAGTAACGACCC 60.474 57.143 0.00 3.07 37.63 4.46
255 256 1.875488 AGGGCATTAGTAACGACCCT 58.125 50.000 11.72 11.72 42.97 4.34
256 257 2.093128 CAGGGCATTAGTAACGACCCTT 60.093 50.000 13.98 1.61 45.55 3.95
257 258 2.574824 AGGGCATTAGTAACGACCCTTT 59.425 45.455 11.72 0.00 45.55 3.11
258 259 3.776417 AGGGCATTAGTAACGACCCTTTA 59.224 43.478 11.72 0.00 45.55 1.85
259 260 4.124970 GGGCATTAGTAACGACCCTTTAG 58.875 47.826 8.75 0.00 34.34 1.85
260 261 4.383444 GGGCATTAGTAACGACCCTTTAGT 60.383 45.833 8.75 0.00 34.34 2.24
261 262 4.807834 GGCATTAGTAACGACCCTTTAGTC 59.192 45.833 0.00 0.00 0.00 2.59
262 263 4.807834 GCATTAGTAACGACCCTTTAGTCC 59.192 45.833 0.00 0.00 32.91 3.85
263 264 5.354767 CATTAGTAACGACCCTTTAGTCCC 58.645 45.833 0.00 0.00 32.91 4.46
264 265 1.821136 AGTAACGACCCTTTAGTCCCG 59.179 52.381 0.00 0.00 32.91 5.14
265 266 1.134995 GTAACGACCCTTTAGTCCCGG 60.135 57.143 0.00 0.00 32.91 5.73
266 267 0.833409 AACGACCCTTTAGTCCCGGT 60.833 55.000 0.00 0.00 32.91 5.28
267 268 0.833409 ACGACCCTTTAGTCCCGGTT 60.833 55.000 0.00 0.00 32.91 4.44
268 269 0.108472 CGACCCTTTAGTCCCGGTTC 60.108 60.000 0.00 0.00 32.91 3.62
269 270 0.978907 GACCCTTTAGTCCCGGTTCA 59.021 55.000 0.00 0.00 0.00 3.18
270 271 1.348696 GACCCTTTAGTCCCGGTTCAA 59.651 52.381 0.00 0.00 0.00 2.69
271 272 1.072806 ACCCTTTAGTCCCGGTTCAAC 59.927 52.381 0.00 0.00 0.00 3.18
272 273 1.072648 CCCTTTAGTCCCGGTTCAACA 59.927 52.381 0.00 0.00 0.00 3.33
273 274 2.487625 CCCTTTAGTCCCGGTTCAACAA 60.488 50.000 0.00 0.00 0.00 2.83
274 275 2.551032 CCTTTAGTCCCGGTTCAACAAC 59.449 50.000 0.00 0.00 0.00 3.32
281 282 4.563404 GGTTCAACAACCGGGACA 57.437 55.556 6.32 0.00 43.00 4.02
282 283 2.796500 GGTTCAACAACCGGGACAA 58.204 52.632 6.32 0.00 43.00 3.18
283 284 1.104630 GGTTCAACAACCGGGACAAA 58.895 50.000 6.32 0.00 43.00 2.83
284 285 1.684450 GGTTCAACAACCGGGACAAAT 59.316 47.619 6.32 0.00 43.00 2.32
285 286 2.544903 GGTTCAACAACCGGGACAAATG 60.545 50.000 6.32 0.00 43.00 2.32
286 287 1.323412 TCAACAACCGGGACAAATGG 58.677 50.000 6.32 0.00 0.00 3.16
287 288 0.319469 CAACAACCGGGACAAATGGC 60.319 55.000 6.32 0.00 0.00 4.40
288 289 1.468506 AACAACCGGGACAAATGGCC 61.469 55.000 6.32 0.00 44.61 5.36
296 297 1.644509 GGACAAATGGCCCCTTTTCT 58.355 50.000 0.00 0.00 37.19 2.52
297 298 2.815158 GGACAAATGGCCCCTTTTCTA 58.185 47.619 0.00 0.00 37.19 2.10
298 299 2.496070 GGACAAATGGCCCCTTTTCTAC 59.504 50.000 0.00 0.00 37.19 2.59
299 300 3.431415 GACAAATGGCCCCTTTTCTACT 58.569 45.455 0.00 0.00 0.00 2.57
300 301 4.569015 GGACAAATGGCCCCTTTTCTACTA 60.569 45.833 0.00 0.00 37.19 1.82
301 302 4.600062 ACAAATGGCCCCTTTTCTACTAG 58.400 43.478 0.00 0.00 0.00 2.57
302 303 4.044191 ACAAATGGCCCCTTTTCTACTAGT 59.956 41.667 0.00 0.00 0.00 2.57
311 312 4.562963 CCCTTTTCTACTAGTGTGTGGACC 60.563 50.000 5.39 0.00 0.00 4.46
369 370 2.420722 AGCGTTCTCGAACAAAAACCAA 59.579 40.909 10.10 0.00 41.20 3.67
474 475 1.134128 TGGTGGATGCGAGCATATGTT 60.134 47.619 10.85 0.00 36.70 2.71
547 548 3.149196 TGAAAAGGTAAAGCTGCTGAGG 58.851 45.455 1.35 0.00 0.00 3.86
585 597 2.639327 GCCCTCGCACTGCCAATTT 61.639 57.895 0.00 0.00 34.03 1.82
671 683 2.006056 GCTCACATGCGCTTCTTCTCT 61.006 52.381 9.73 0.00 0.00 3.10
691 703 4.087182 TCTAGGTGACGAAGACTGGAATT 58.913 43.478 0.00 0.00 0.00 2.17
837 849 2.680913 GGCCACACATGAGCACGAC 61.681 63.158 0.00 0.00 0.00 4.34
845 857 1.610673 ATGAGCACGACCACCTCCT 60.611 57.895 0.00 0.00 0.00 3.69
875 887 2.813179 GAGCCACATACGCGCCAAG 61.813 63.158 5.73 0.00 0.00 3.61
913 925 2.218759 CGCGAGCGCCCATATATAAATC 59.781 50.000 2.29 0.00 37.98 2.17
990 1010 8.948145 GTTCAGCTTCTACCGATAATCTATCTA 58.052 37.037 0.00 0.00 33.01 1.98
991 1011 8.725405 TCAGCTTCTACCGATAATCTATCTAG 57.275 38.462 0.00 0.00 33.01 2.43
992 1012 7.771361 TCAGCTTCTACCGATAATCTATCTAGG 59.229 40.741 0.00 0.00 33.01 3.02
993 1013 6.544564 AGCTTCTACCGATAATCTATCTAGGC 59.455 42.308 0.00 0.00 33.01 3.93
994 1014 6.544564 GCTTCTACCGATAATCTATCTAGGCT 59.455 42.308 0.00 0.00 33.01 4.58
997 1017 7.631007 TCTACCGATAATCTATCTAGGCTTCA 58.369 38.462 0.00 0.00 33.01 3.02
1303 1323 3.368531 CCGCTACTTCACTAAGAAAGGCT 60.369 47.826 0.00 0.00 35.40 4.58
1386 1406 4.867599 GGGTAGCGCGTCCTTCCG 62.868 72.222 19.72 0.00 0.00 4.30
1389 1409 3.057548 TAGCGCGTCCTTCCGTCA 61.058 61.111 8.43 0.00 0.00 4.35
1396 1416 0.455633 CGTCCTTCCGTCAACGTAGG 60.456 60.000 12.27 12.27 39.27 3.18
1421 1441 4.472286 CGCAAAAGTATGTTCAATCGGTT 58.528 39.130 0.00 0.00 0.00 4.44
1599 1647 2.974165 GCATATGCGTTTGTACTCTGC 58.026 47.619 12.82 0.00 0.00 4.26
1640 1688 8.902540 ATTTGCTTAGGATCGTGAAATATGTA 57.097 30.769 0.00 0.00 0.00 2.29
1662 1710 8.795786 TGTAGTAACTTGATTGTGCATTTTTC 57.204 30.769 0.00 0.00 0.00 2.29
1663 1711 8.629158 TGTAGTAACTTGATTGTGCATTTTTCT 58.371 29.630 0.00 0.00 0.00 2.52
1664 1712 9.463443 GTAGTAACTTGATTGTGCATTTTTCTT 57.537 29.630 0.00 0.00 0.00 2.52
1665 1713 8.947055 AGTAACTTGATTGTGCATTTTTCTTT 57.053 26.923 0.00 0.00 0.00 2.52
1666 1714 9.382275 AGTAACTTGATTGTGCATTTTTCTTTT 57.618 25.926 0.00 0.00 0.00 2.27
1667 1715 9.986833 GTAACTTGATTGTGCATTTTTCTTTTT 57.013 25.926 0.00 0.00 0.00 1.94
1669 1717 8.496707 ACTTGATTGTGCATTTTTCTTTTTCT 57.503 26.923 0.00 0.00 0.00 2.52
1670 1718 8.949177 ACTTGATTGTGCATTTTTCTTTTTCTT 58.051 25.926 0.00 0.00 0.00 2.52
1671 1719 9.777575 CTTGATTGTGCATTTTTCTTTTTCTTT 57.222 25.926 0.00 0.00 0.00 2.52
1690 1738 1.479709 TTTTTGTGTGTGTGAGGGGG 58.520 50.000 0.00 0.00 0.00 5.40
1727 1975 5.795972 TCAATCGGTACAACATCTGGTTTA 58.204 37.500 0.00 0.00 37.72 2.01
1792 2040 5.897377 ATAAAAGTGTGACTGGGTTATGC 57.103 39.130 0.00 0.00 0.00 3.14
1795 2043 2.260822 AGTGTGACTGGGTTATGCTCT 58.739 47.619 0.00 0.00 0.00 4.09
1840 2089 5.460748 CCGCTTTACTTAAACAAAGTTTGGG 59.539 40.000 19.45 2.87 46.61 4.12
1845 2094 9.463443 CTTTACTTAAACAAAGTTTGGGATCTG 57.537 33.333 19.45 7.65 46.61 2.90
1893 2142 1.668151 GTGACGAGTCCACCCAAGC 60.668 63.158 0.34 0.00 0.00 4.01
1909 2158 3.195698 GCATCACGGCGTTCCTCC 61.196 66.667 11.19 0.00 0.00 4.30
1913 2162 2.866523 ATCACGGCGTTCCTCCCCTA 62.867 60.000 11.19 0.00 0.00 3.53
1922 2171 2.030451 CGTTCCTCCCCTATACGCTTAC 60.030 54.545 0.00 0.00 0.00 2.34
1942 2191 2.731976 ACTCTAGCTAATTTATGCGCGC 59.268 45.455 27.26 27.26 0.00 6.86
1947 2196 1.385038 CTAATTTATGCGCGCCAACG 58.615 50.000 30.77 4.76 44.07 4.10
1975 2224 0.178533 ACGACGAACCCAAGAAACCA 59.821 50.000 0.00 0.00 0.00 3.67
1992 2241 1.069513 ACCATGAACTCCGTCAACGAA 59.930 47.619 3.71 0.00 43.02 3.85
2013 2262 3.834489 TTGAGCATCTCCTTGATCTCC 57.166 47.619 0.00 0.00 33.25 3.71
2131 2380 0.901827 TAGCTCGATGGCCAACTGAA 59.098 50.000 10.96 0.00 0.00 3.02
2142 2391 1.755179 CCAACTGAATAGCCCACCTG 58.245 55.000 0.00 0.00 0.00 4.00
2167 2416 1.152030 AGGACCTCCACTGCTTCCA 60.152 57.895 0.00 0.00 38.89 3.53
2174 2423 2.092538 CCTCCACTGCTTCCAGATCAAT 60.093 50.000 0.00 0.00 41.77 2.57
2196 2445 1.021202 CGTGTGGAAAGAACTGGCAA 58.979 50.000 0.00 0.00 0.00 4.52
2252 2501 3.902112 AGCCCCACCACCACCTTG 61.902 66.667 0.00 0.00 0.00 3.61
2329 2578 2.467880 GTGGTTCCCATCTCTGGACTA 58.532 52.381 0.00 0.00 46.37 2.59
2331 2580 3.070302 GTGGTTCCCATCTCTGGACTATC 59.930 52.174 0.00 0.00 46.37 2.08
2332 2581 2.635427 GGTTCCCATCTCTGGACTATCC 59.365 54.545 0.00 0.00 46.37 2.59
2359 2608 4.175337 TGCTATGGTGCCCTCGCC 62.175 66.667 0.00 0.00 43.16 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.046296 GTGTTTCATATATTGTGTTAGCTAGCT 57.954 33.333 23.12 23.12 0.00 3.32
2 3 8.283291 GGTGTTTCATATATTGTGTTAGCTAGC 58.717 37.037 6.62 6.62 0.00 3.42
3 4 9.547753 AGGTGTTTCATATATTGTGTTAGCTAG 57.452 33.333 0.00 0.00 0.00 3.42
5 6 9.899661 TTAGGTGTTTCATATATTGTGTTAGCT 57.100 29.630 0.00 0.00 0.00 3.32
15 16 9.596308 GGGGGTTAATTTAGGTGTTTCATATAT 57.404 33.333 0.00 0.00 0.00 0.86
16 17 8.999905 GGGGGTTAATTTAGGTGTTTCATATA 57.000 34.615 0.00 0.00 0.00 0.86
17 18 7.907841 GGGGGTTAATTTAGGTGTTTCATAT 57.092 36.000 0.00 0.00 0.00 1.78
38 39 2.528127 GGTTGGGGGTTTTGGGGG 60.528 66.667 0.00 0.00 0.00 5.40
39 40 2.528127 GGGTTGGGGGTTTTGGGG 60.528 66.667 0.00 0.00 0.00 4.96
40 41 1.535444 GAGGGTTGGGGGTTTTGGG 60.535 63.158 0.00 0.00 0.00 4.12
41 42 1.535444 GGAGGGTTGGGGGTTTTGG 60.535 63.158 0.00 0.00 0.00 3.28
42 43 1.535444 GGGAGGGTTGGGGGTTTTG 60.535 63.158 0.00 0.00 0.00 2.44
43 44 2.797075 GGGGAGGGTTGGGGGTTTT 61.797 63.158 0.00 0.00 0.00 2.43
44 45 3.197895 GGGGAGGGTTGGGGGTTT 61.198 66.667 0.00 0.00 0.00 3.27
74 75 2.051692 GGGGCTGGGGTTTTAGTTTTT 58.948 47.619 0.00 0.00 0.00 1.94
75 76 1.222039 AGGGGCTGGGGTTTTAGTTTT 59.778 47.619 0.00 0.00 0.00 2.43
76 77 0.864659 AGGGGCTGGGGTTTTAGTTT 59.135 50.000 0.00 0.00 0.00 2.66
77 78 0.114364 CAGGGGCTGGGGTTTTAGTT 59.886 55.000 0.00 0.00 0.00 2.24
78 79 0.774491 TCAGGGGCTGGGGTTTTAGT 60.774 55.000 0.00 0.00 31.51 2.24
79 80 0.407918 TTCAGGGGCTGGGGTTTTAG 59.592 55.000 0.00 0.00 31.51 1.85
80 81 0.861155 TTTCAGGGGCTGGGGTTTTA 59.139 50.000 0.00 0.00 31.51 1.52
81 82 0.193321 ATTTCAGGGGCTGGGGTTTT 59.807 50.000 0.00 0.00 31.51 2.43
82 83 0.545071 CATTTCAGGGGCTGGGGTTT 60.545 55.000 0.00 0.00 31.51 3.27
83 84 1.079073 CATTTCAGGGGCTGGGGTT 59.921 57.895 0.00 0.00 31.51 4.11
84 85 2.772924 CATTTCAGGGGCTGGGGT 59.227 61.111 0.00 0.00 31.51 4.95
85 86 2.761213 GCATTTCAGGGGCTGGGG 60.761 66.667 0.00 0.00 31.51 4.96
86 87 2.361771 AGCATTTCAGGGGCTGGG 59.638 61.111 0.00 0.00 36.34 4.45
89 90 1.377725 CGTCAGCATTTCAGGGGCT 60.378 57.895 0.00 0.00 38.70 5.19
90 91 3.056313 GCGTCAGCATTTCAGGGGC 62.056 63.158 0.00 0.00 44.35 5.80
91 92 2.753966 CGCGTCAGCATTTCAGGGG 61.754 63.158 0.00 0.00 45.49 4.79
92 93 2.034879 ACGCGTCAGCATTTCAGGG 61.035 57.895 5.58 0.00 45.49 4.45
93 94 1.133253 CACGCGTCAGCATTTCAGG 59.867 57.895 9.86 0.00 45.49 3.86
94 95 1.133253 CCACGCGTCAGCATTTCAG 59.867 57.895 9.86 0.00 45.49 3.02
95 96 0.673333 ATCCACGCGTCAGCATTTCA 60.673 50.000 9.86 0.00 45.49 2.69
96 97 0.247814 CATCCACGCGTCAGCATTTC 60.248 55.000 9.86 0.00 45.49 2.17
97 98 1.796151 CATCCACGCGTCAGCATTT 59.204 52.632 9.86 0.00 45.49 2.32
98 99 2.753966 GCATCCACGCGTCAGCATT 61.754 57.895 9.86 0.00 45.49 3.56
99 100 3.197790 GCATCCACGCGTCAGCAT 61.198 61.111 9.86 0.00 45.49 3.79
102 103 1.577328 AAAAGGCATCCACGCGTCAG 61.577 55.000 9.86 3.57 0.00 3.51
103 104 1.599518 AAAAGGCATCCACGCGTCA 60.600 52.632 9.86 0.00 0.00 4.35
104 105 1.154225 CAAAAGGCATCCACGCGTC 60.154 57.895 9.86 0.00 0.00 5.19
105 106 2.625823 CCAAAAGGCATCCACGCGT 61.626 57.895 5.58 5.58 0.00 6.01
106 107 2.179018 CCAAAAGGCATCCACGCG 59.821 61.111 3.53 3.53 0.00 6.01
107 108 1.212751 GACCAAAAGGCATCCACGC 59.787 57.895 0.00 0.00 0.00 5.34
108 109 1.595093 GGGACCAAAAGGCATCCACG 61.595 60.000 0.00 0.00 32.45 4.94
109 110 1.595093 CGGGACCAAAAGGCATCCAC 61.595 60.000 0.00 0.00 32.45 4.02
110 111 1.304052 CGGGACCAAAAGGCATCCA 60.304 57.895 0.00 0.00 32.45 3.41
111 112 2.052104 CCGGGACCAAAAGGCATCC 61.052 63.158 0.00 0.00 0.00 3.51
112 113 0.898326 AACCGGGACCAAAAGGCATC 60.898 55.000 6.32 0.00 0.00 3.91
113 114 1.155155 AACCGGGACCAAAAGGCAT 59.845 52.632 6.32 0.00 0.00 4.40
114 115 1.830408 CAACCGGGACCAAAAGGCA 60.830 57.895 6.32 0.00 0.00 4.75
115 116 2.570284 CCAACCGGGACCAAAAGGC 61.570 63.158 6.32 0.00 40.01 4.35
116 117 1.152631 ACCAACCGGGACCAAAAGG 60.153 57.895 6.32 0.00 41.15 3.11
117 118 0.753848 ACACCAACCGGGACCAAAAG 60.754 55.000 6.32 0.00 41.15 2.27
118 119 0.752376 GACACCAACCGGGACCAAAA 60.752 55.000 6.32 0.00 41.15 2.44
119 120 1.152922 GACACCAACCGGGACCAAA 60.153 57.895 6.32 0.00 41.15 3.28
120 121 2.376165 TGACACCAACCGGGACCAA 61.376 57.895 6.32 0.00 41.15 3.67
121 122 2.768769 TGACACCAACCGGGACCA 60.769 61.111 6.32 0.00 41.15 4.02
122 123 2.281276 GTGACACCAACCGGGACC 60.281 66.667 6.32 0.00 41.15 4.46
123 124 2.281276 GGTGACACCAACCGGGAC 60.281 66.667 20.14 0.00 38.42 4.46
132 133 2.281276 GTCCCGGTTGGTGACACC 60.281 66.667 18.28 18.28 42.67 4.16
133 134 2.281276 GGTCCCGGTTGGTGACAC 60.281 66.667 0.00 0.00 42.67 3.67
134 135 1.923006 TTTGGTCCCGGTTGGTGACA 61.923 55.000 0.00 0.00 37.25 3.58
135 136 1.152922 TTTGGTCCCGGTTGGTGAC 60.153 57.895 0.00 0.00 35.74 3.67
136 137 1.149627 CTTTGGTCCCGGTTGGTGA 59.850 57.895 0.00 0.00 34.77 4.02
137 138 1.901464 CCTTTGGTCCCGGTTGGTG 60.901 63.158 0.00 0.00 34.77 4.17
138 139 2.518933 CCTTTGGTCCCGGTTGGT 59.481 61.111 0.00 0.00 34.77 3.67
139 140 2.989253 GCCTTTGGTCCCGGTTGG 60.989 66.667 0.00 0.00 0.00 3.77
140 141 2.989253 GGCCTTTGGTCCCGGTTG 60.989 66.667 0.00 0.00 0.00 3.77
141 142 4.295199 GGGCCTTTGGTCCCGGTT 62.295 66.667 0.84 0.00 42.67 4.44
147 148 2.361737 GCAGGAGGGCCTTTGGTC 60.362 66.667 7.89 0.00 43.90 4.02
155 156 3.555324 GAGCCTAGGCAGGAGGGC 61.555 72.222 34.70 6.92 45.91 5.19
156 157 3.230245 CGAGCCTAGGCAGGAGGG 61.230 72.222 34.70 13.13 45.91 4.30
157 158 2.123683 TCGAGCCTAGGCAGGAGG 60.124 66.667 34.70 18.01 45.91 4.30
158 159 2.840066 CGTCGAGCCTAGGCAGGAG 61.840 68.421 34.70 21.32 45.91 3.69
159 160 2.829003 CGTCGAGCCTAGGCAGGA 60.829 66.667 34.70 26.46 45.91 3.86
160 161 4.577246 GCGTCGAGCCTAGGCAGG 62.577 72.222 34.70 24.66 45.77 4.85
183 184 1.746615 CAGATGGGCCTTCACGTGG 60.747 63.158 20.31 0.00 0.00 4.94
184 185 1.003355 ACAGATGGGCCTTCACGTG 60.003 57.895 20.31 9.94 0.00 4.49
185 186 1.296715 GACAGATGGGCCTTCACGT 59.703 57.895 20.31 16.10 0.00 4.49
186 187 1.450312 GGACAGATGGGCCTTCACG 60.450 63.158 20.31 13.29 0.00 4.35
187 188 1.077429 GGGACAGATGGGCCTTCAC 60.077 63.158 20.31 11.21 0.00 3.18
188 189 2.669133 CGGGACAGATGGGCCTTCA 61.669 63.158 20.31 0.00 0.00 3.02
189 190 2.190578 CGGGACAGATGGGCCTTC 59.809 66.667 11.32 11.32 0.00 3.46
190 191 3.411517 CCGGGACAGATGGGCCTT 61.412 66.667 4.53 0.00 0.00 4.35
191 192 4.741239 ACCGGGACAGATGGGCCT 62.741 66.667 6.32 0.00 0.00 5.19
192 193 3.699134 GAACCGGGACAGATGGGCC 62.699 68.421 6.32 0.00 0.00 5.80
193 194 2.124695 GAACCGGGACAGATGGGC 60.125 66.667 6.32 0.00 0.00 5.36
194 195 2.186903 CGAACCGGGACAGATGGG 59.813 66.667 6.32 0.00 0.00 4.00
195 196 1.447838 CACGAACCGGGACAGATGG 60.448 63.158 6.32 0.00 28.17 3.51
196 197 0.528924 TACACGAACCGGGACAGATG 59.471 55.000 6.32 0.00 32.98 2.90
197 198 1.203994 CTTACACGAACCGGGACAGAT 59.796 52.381 6.32 0.00 32.98 2.90
198 199 0.599558 CTTACACGAACCGGGACAGA 59.400 55.000 6.32 0.00 32.98 3.41
199 200 0.599558 TCTTACACGAACCGGGACAG 59.400 55.000 6.32 0.00 32.98 3.51
200 201 1.039068 TTCTTACACGAACCGGGACA 58.961 50.000 6.32 0.00 32.98 4.02
201 202 2.265683 GATTCTTACACGAACCGGGAC 58.734 52.381 6.32 0.00 32.98 4.46
202 203 1.135315 CGATTCTTACACGAACCGGGA 60.135 52.381 6.32 0.00 32.98 5.14
203 204 1.274596 CGATTCTTACACGAACCGGG 58.725 55.000 6.32 0.00 35.82 5.73
204 205 1.274596 CCGATTCTTACACGAACCGG 58.725 55.000 0.00 0.00 43.10 5.28
205 206 1.135315 TCCCGATTCTTACACGAACCG 60.135 52.381 0.00 0.00 29.74 4.44
206 207 2.094338 AGTCCCGATTCTTACACGAACC 60.094 50.000 0.00 0.00 0.00 3.62
207 208 3.227810 AGTCCCGATTCTTACACGAAC 57.772 47.619 0.00 0.00 0.00 3.95
208 209 4.142315 CCTTAGTCCCGATTCTTACACGAA 60.142 45.833 0.00 0.00 0.00 3.85
209 210 3.379372 CCTTAGTCCCGATTCTTACACGA 59.621 47.826 0.00 0.00 0.00 4.35
210 211 3.490419 CCCTTAGTCCCGATTCTTACACG 60.490 52.174 0.00 0.00 0.00 4.49
211 212 3.181468 CCCCTTAGTCCCGATTCTTACAC 60.181 52.174 0.00 0.00 0.00 2.90
212 213 3.036091 CCCCTTAGTCCCGATTCTTACA 58.964 50.000 0.00 0.00 0.00 2.41
213 214 2.224233 GCCCCTTAGTCCCGATTCTTAC 60.224 54.545 0.00 0.00 0.00 2.34
214 215 2.044758 GCCCCTTAGTCCCGATTCTTA 58.955 52.381 0.00 0.00 0.00 2.10
215 216 0.837940 GCCCCTTAGTCCCGATTCTT 59.162 55.000 0.00 0.00 0.00 2.52
216 217 1.054978 GGCCCCTTAGTCCCGATTCT 61.055 60.000 0.00 0.00 0.00 2.40
217 218 1.342672 TGGCCCCTTAGTCCCGATTC 61.343 60.000 0.00 0.00 0.00 2.52
218 219 1.307517 TGGCCCCTTAGTCCCGATT 60.308 57.895 0.00 0.00 0.00 3.34
219 220 1.766461 CTGGCCCCTTAGTCCCGAT 60.766 63.158 0.00 0.00 0.00 4.18
220 221 2.365105 CTGGCCCCTTAGTCCCGA 60.365 66.667 0.00 0.00 0.00 5.14
221 222 3.480133 CCTGGCCCCTTAGTCCCG 61.480 72.222 0.00 0.00 0.00 5.14
222 223 3.097162 CCCTGGCCCCTTAGTCCC 61.097 72.222 0.00 0.00 0.00 4.46
223 224 3.810188 GCCCTGGCCCCTTAGTCC 61.810 72.222 0.00 0.00 34.56 3.85
224 225 1.937924 AATGCCCTGGCCCCTTAGTC 61.938 60.000 5.57 0.00 41.09 2.59
225 226 0.626277 TAATGCCCTGGCCCCTTAGT 60.626 55.000 5.57 0.00 41.09 2.24
226 227 0.111253 CTAATGCCCTGGCCCCTTAG 59.889 60.000 5.57 6.76 41.09 2.18
227 228 0.626277 ACTAATGCCCTGGCCCCTTA 60.626 55.000 5.57 0.87 41.09 2.69
228 229 0.626277 TACTAATGCCCTGGCCCCTT 60.626 55.000 5.57 0.00 41.09 3.95
229 230 0.626277 TTACTAATGCCCTGGCCCCT 60.626 55.000 5.57 0.00 41.09 4.79
230 231 0.467474 GTTACTAATGCCCTGGCCCC 60.467 60.000 5.57 0.00 41.09 5.80
231 232 0.818040 CGTTACTAATGCCCTGGCCC 60.818 60.000 5.57 0.00 41.09 5.80
232 233 0.179468 TCGTTACTAATGCCCTGGCC 59.821 55.000 5.57 0.00 41.09 5.36
233 234 1.296727 GTCGTTACTAATGCCCTGGC 58.703 55.000 0.00 0.00 42.35 4.85
234 235 1.474498 GGGTCGTTACTAATGCCCTGG 60.474 57.143 10.85 0.00 33.56 4.45
235 236 1.485066 AGGGTCGTTACTAATGCCCTG 59.515 52.381 16.38 0.00 40.36 4.45
236 237 1.875488 AGGGTCGTTACTAATGCCCT 58.125 50.000 13.37 13.37 38.46 5.19
237 238 2.704464 AAGGGTCGTTACTAATGCCC 57.296 50.000 10.40 10.40 35.35 5.36
238 239 4.763073 ACTAAAGGGTCGTTACTAATGCC 58.237 43.478 0.00 0.00 0.00 4.40
239 240 4.807834 GGACTAAAGGGTCGTTACTAATGC 59.192 45.833 0.00 0.00 37.12 3.56
240 241 5.354767 GGGACTAAAGGGTCGTTACTAATG 58.645 45.833 0.00 0.00 37.12 1.90
241 242 4.098501 CGGGACTAAAGGGTCGTTACTAAT 59.901 45.833 0.00 0.00 37.12 1.73
242 243 3.443681 CGGGACTAAAGGGTCGTTACTAA 59.556 47.826 0.00 0.00 37.12 2.24
243 244 3.016736 CGGGACTAAAGGGTCGTTACTA 58.983 50.000 0.00 0.00 37.12 1.82
244 245 1.821136 CGGGACTAAAGGGTCGTTACT 59.179 52.381 0.00 0.00 37.12 2.24
245 246 1.134995 CCGGGACTAAAGGGTCGTTAC 60.135 57.143 0.00 0.00 37.12 2.50
246 247 1.185315 CCGGGACTAAAGGGTCGTTA 58.815 55.000 0.00 0.00 37.12 3.18
247 248 0.833409 ACCGGGACTAAAGGGTCGTT 60.833 55.000 6.32 0.00 37.12 3.85
248 249 0.833409 AACCGGGACTAAAGGGTCGT 60.833 55.000 6.32 0.00 37.12 4.34
249 250 0.108472 GAACCGGGACTAAAGGGTCG 60.108 60.000 6.32 0.00 37.12 4.79
250 251 0.978907 TGAACCGGGACTAAAGGGTC 59.021 55.000 6.32 0.00 41.92 4.46
251 252 1.072806 GTTGAACCGGGACTAAAGGGT 59.927 52.381 6.32 0.00 0.00 4.34
252 253 1.072648 TGTTGAACCGGGACTAAAGGG 59.927 52.381 6.32 0.00 0.00 3.95
253 254 2.551032 GTTGTTGAACCGGGACTAAAGG 59.449 50.000 6.32 0.00 0.00 3.11
254 255 2.551032 GGTTGTTGAACCGGGACTAAAG 59.449 50.000 6.32 0.00 42.47 1.85
255 256 2.574450 GGTTGTTGAACCGGGACTAAA 58.426 47.619 6.32 0.00 42.47 1.85
256 257 2.259266 GGTTGTTGAACCGGGACTAA 57.741 50.000 6.32 0.00 42.47 2.24
258 259 4.892002 GGTTGTTGAACCGGGACT 57.108 55.556 6.32 0.00 42.47 3.85
265 266 2.544903 CCATTTGTCCCGGTTGTTGAAC 60.545 50.000 0.00 0.00 0.00 3.18
266 267 1.683917 CCATTTGTCCCGGTTGTTGAA 59.316 47.619 0.00 0.00 0.00 2.69
267 268 1.323412 CCATTTGTCCCGGTTGTTGA 58.677 50.000 0.00 0.00 0.00 3.18
268 269 0.319469 GCCATTTGTCCCGGTTGTTG 60.319 55.000 0.00 0.00 0.00 3.33
269 270 1.468506 GGCCATTTGTCCCGGTTGTT 61.469 55.000 0.00 0.00 0.00 2.83
270 271 1.906333 GGCCATTTGTCCCGGTTGT 60.906 57.895 0.00 0.00 0.00 3.32
271 272 2.645192 GGGCCATTTGTCCCGGTTG 61.645 63.158 4.39 0.00 32.00 3.77
272 273 2.283604 GGGCCATTTGTCCCGGTT 60.284 61.111 4.39 0.00 32.00 4.44
273 274 4.376170 GGGGCCATTTGTCCCGGT 62.376 66.667 4.39 0.00 43.55 5.28
274 275 3.600410 AAGGGGCCATTTGTCCCGG 62.600 63.158 4.39 0.00 45.13 5.73
275 276 1.191489 AAAAGGGGCCATTTGTCCCG 61.191 55.000 17.94 0.00 45.13 5.14
276 277 0.613260 GAAAAGGGGCCATTTGTCCC 59.387 55.000 17.94 3.60 41.87 4.46
277 278 1.644509 AGAAAAGGGGCCATTTGTCC 58.355 50.000 17.94 9.59 0.00 4.02
278 279 3.431415 AGTAGAAAAGGGGCCATTTGTC 58.569 45.455 17.94 15.50 0.00 3.18
279 280 3.542969 AGTAGAAAAGGGGCCATTTGT 57.457 42.857 17.94 12.35 0.00 2.83
280 281 4.399303 CACTAGTAGAAAAGGGGCCATTTG 59.601 45.833 17.94 5.16 0.00 2.32
281 282 4.044191 ACACTAGTAGAAAAGGGGCCATTT 59.956 41.667 10.95 10.95 0.00 2.32
282 283 3.591977 ACACTAGTAGAAAAGGGGCCATT 59.408 43.478 4.39 0.00 0.00 3.16
283 284 3.054361 CACACTAGTAGAAAAGGGGCCAT 60.054 47.826 4.39 0.00 0.00 4.40
284 285 2.304761 CACACTAGTAGAAAAGGGGCCA 59.695 50.000 4.39 0.00 0.00 5.36
285 286 2.305052 ACACACTAGTAGAAAAGGGGCC 59.695 50.000 3.59 0.00 0.00 5.80
286 287 3.335579 CACACACTAGTAGAAAAGGGGC 58.664 50.000 3.59 0.00 0.00 5.80
287 288 3.581332 TCCACACACTAGTAGAAAAGGGG 59.419 47.826 3.59 1.70 0.00 4.79
288 289 4.562963 GGTCCACACACTAGTAGAAAAGGG 60.563 50.000 3.59 0.26 0.00 3.95
289 290 4.562963 GGGTCCACACACTAGTAGAAAAGG 60.563 50.000 3.59 0.00 0.00 3.11
290 291 4.039973 TGGGTCCACACACTAGTAGAAAAG 59.960 45.833 3.59 0.00 0.00 2.27
291 292 3.968649 TGGGTCCACACACTAGTAGAAAA 59.031 43.478 3.59 0.00 0.00 2.29
292 293 3.578978 TGGGTCCACACACTAGTAGAAA 58.421 45.455 3.59 0.00 0.00 2.52
293 294 3.247948 TGGGTCCACACACTAGTAGAA 57.752 47.619 3.59 0.00 0.00 2.10
294 295 2.984435 TGGGTCCACACACTAGTAGA 57.016 50.000 3.59 0.00 0.00 2.59
295 296 3.366396 AGATGGGTCCACACACTAGTAG 58.634 50.000 0.00 0.00 28.47 2.57
296 297 3.468071 AGATGGGTCCACACACTAGTA 57.532 47.619 0.00 0.00 28.47 1.82
297 298 2.327325 AGATGGGTCCACACACTAGT 57.673 50.000 0.00 0.00 28.47 2.57
298 299 2.101582 GCTAGATGGGTCCACACACTAG 59.898 54.545 11.34 11.34 35.76 2.57
299 300 2.108168 GCTAGATGGGTCCACACACTA 58.892 52.381 0.00 0.00 28.47 2.74
300 301 0.905357 GCTAGATGGGTCCACACACT 59.095 55.000 0.00 0.00 28.47 3.55
301 302 0.613260 TGCTAGATGGGTCCACACAC 59.387 55.000 0.00 0.00 28.47 3.82
302 303 1.357137 TTGCTAGATGGGTCCACACA 58.643 50.000 0.00 0.00 0.00 3.72
328 329 4.620332 CGCTTGAAAGGAATGGCCAAATAA 60.620 41.667 10.96 0.00 40.02 1.40
334 335 0.603065 AACGCTTGAAAGGAATGGCC 59.397 50.000 0.00 0.00 0.00 5.36
369 370 1.684248 GCATGGCCTTGTCATCCTTCT 60.684 52.381 19.05 0.00 0.00 2.85
398 399 1.409241 GCTTCCCAAGGCATCATCTGA 60.409 52.381 0.00 0.00 0.00 3.27
399 400 1.030457 GCTTCCCAAGGCATCATCTG 58.970 55.000 0.00 0.00 0.00 2.90
474 475 7.017551 AGAGGTAAACATGATATGGCCTATGAA 59.982 37.037 3.32 0.00 33.60 2.57
547 548 2.863704 GCCATTGTGCTCCAACAAGAAC 60.864 50.000 0.00 0.00 42.99 3.01
585 597 3.064682 CCAACACCGCATATGATCGAAAA 59.935 43.478 6.97 0.00 0.00 2.29
599 611 4.364415 TTTCTTTGAAACTCCAACACCG 57.636 40.909 0.00 0.00 0.00 4.94
671 683 3.576982 ACAATTCCAGTCTTCGTCACCTA 59.423 43.478 0.00 0.00 0.00 3.08
789 801 2.011222 GTTTTGGCATGCATGATTGGG 58.989 47.619 30.64 2.65 0.00 4.12
845 857 3.555324 TGGCTCGCCTTGGTCACA 61.555 61.111 9.65 0.00 36.94 3.58
875 887 3.070576 GGTGGCCATGCTTGTCCC 61.071 66.667 9.72 0.00 0.00 4.46
913 925 6.767423 TGTGTATGATGATCTATGTTTGTGGG 59.233 38.462 0.00 0.00 0.00 4.61
990 1010 0.924823 AGGATGCCATCTTGAAGCCT 59.075 50.000 4.41 0.00 0.00 4.58
991 1011 1.316651 GAGGATGCCATCTTGAAGCC 58.683 55.000 4.41 0.00 0.00 4.35
992 1012 0.942962 CGAGGATGCCATCTTGAAGC 59.057 55.000 4.41 0.00 0.00 3.86
993 1013 2.102084 TCTCGAGGATGCCATCTTGAAG 59.898 50.000 13.56 0.00 0.00 3.02
994 1014 2.110578 TCTCGAGGATGCCATCTTGAA 58.889 47.619 13.56 0.00 0.00 2.69
997 1017 2.906691 CTTCTCGAGGATGCCATCTT 57.093 50.000 13.56 0.00 0.00 2.40
1071 1091 2.032634 CACCGTGAATGTCACCGGG 61.033 63.158 6.32 10.68 44.20 5.73
1080 1100 0.840722 ACCCCTTCTCCACCGTGAAT 60.841 55.000 0.00 0.00 0.00 2.57
1113 1133 2.675772 GCCAGCTGCTTCTTGCCT 60.676 61.111 8.66 0.00 42.00 4.75
1386 1406 1.193874 CTTTTGCGGACCTACGTTGAC 59.806 52.381 0.00 0.00 35.98 3.18
1389 1409 2.818130 TACTTTTGCGGACCTACGTT 57.182 45.000 0.00 0.00 35.98 3.99
1396 1416 4.088648 CGATTGAACATACTTTTGCGGAC 58.911 43.478 0.00 0.00 0.00 4.79
1421 1441 3.691698 AACTACCAAAACCCAGGGAAA 57.308 42.857 14.54 0.00 0.00 3.13
1483 1503 2.738521 CCGGTCAAGAGTGGCGTG 60.739 66.667 0.00 0.00 0.00 5.34
1640 1688 8.947055 AAAGAAAAATGCACAATCAAGTTACT 57.053 26.923 0.00 0.00 0.00 2.24
1671 1719 1.479709 CCCCCTCACACACACAAAAA 58.520 50.000 0.00 0.00 0.00 1.94
1672 1720 3.199290 CCCCCTCACACACACAAAA 57.801 52.632 0.00 0.00 0.00 2.44
1673 1721 4.997884 CCCCCTCACACACACAAA 57.002 55.556 0.00 0.00 0.00 2.83
1696 1744 0.834612 TGTACCGATTGATGTCCCCC 59.165 55.000 0.00 0.00 0.00 5.40
1697 1745 2.285977 GTTGTACCGATTGATGTCCCC 58.714 52.381 0.00 0.00 0.00 4.81
1698 1746 2.980568 TGTTGTACCGATTGATGTCCC 58.019 47.619 0.00 0.00 0.00 4.46
1699 1747 4.271049 CAGATGTTGTACCGATTGATGTCC 59.729 45.833 0.00 0.00 0.00 4.02
1700 1748 4.271049 CCAGATGTTGTACCGATTGATGTC 59.729 45.833 0.00 0.00 0.00 3.06
1701 1749 4.191544 CCAGATGTTGTACCGATTGATGT 58.808 43.478 0.00 0.00 0.00 3.06
1702 1750 4.191544 ACCAGATGTTGTACCGATTGATG 58.808 43.478 0.00 0.00 0.00 3.07
1727 1975 6.286240 TGTGCAGAGTGAGTATTTATCTGT 57.714 37.500 0.00 0.00 39.63 3.41
1758 2006 7.913821 CAGTCACACTTTTATAGTAGCACGATA 59.086 37.037 0.00 0.00 34.56 2.92
1767 2015 6.598064 GCATAACCCAGTCACACTTTTATAGT 59.402 38.462 0.00 0.00 37.68 2.12
1816 2065 5.460748 CCCAAACTTTGTTTAAGTAAAGCGG 59.539 40.000 11.32 9.82 46.34 5.52
1878 2127 1.296715 GATGCTTGGGTGGACTCGT 59.703 57.895 0.00 0.00 0.00 4.18
1880 2129 1.021390 CGTGATGCTTGGGTGGACTC 61.021 60.000 0.00 0.00 0.00 3.36
1884 2133 3.443045 GCCGTGATGCTTGGGTGG 61.443 66.667 0.00 0.00 0.00 4.61
1922 2171 2.092838 GGCGCGCATAAATTAGCTAGAG 59.907 50.000 34.42 0.00 0.00 2.43
1942 2191 1.644913 GTCGTTGTGGGAACGTTGG 59.355 57.895 5.00 0.00 43.47 3.77
1947 2196 1.501337 GGGTTCGTCGTTGTGGGAAC 61.501 60.000 0.00 0.00 38.38 3.62
1954 2203 1.003223 GGTTTCTTGGGTTCGTCGTTG 60.003 52.381 0.00 0.00 0.00 4.10
1992 2241 3.975312 AGGAGATCAAGGAGATGCTCAAT 59.025 43.478 0.00 0.00 37.00 2.57
2013 2262 1.880027 GCTGTTGGACCCTGTTTACAG 59.120 52.381 2.86 2.86 43.40 2.74
2131 2380 2.196776 GGCATGCAGGTGGGCTAT 59.803 61.111 21.36 0.00 34.04 2.97
2142 2391 2.439156 GTGGAGGTCCTGGCATGC 60.439 66.667 9.90 9.90 36.82 4.06
2167 2416 4.271696 TCTTTCCACACGTCATTGATCT 57.728 40.909 0.00 0.00 0.00 2.75
2174 2423 1.948104 CCAGTTCTTTCCACACGTCA 58.052 50.000 0.00 0.00 0.00 4.35
2205 2454 2.098607 GGATCACAGTGGTGCATTCATG 59.901 50.000 0.00 0.00 44.87 3.07
2252 2501 1.804748 CAGTTTCAAAGTACGGGGAGC 59.195 52.381 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.