Multiple sequence alignment - TraesCS7A01G211900

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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 TraesCS7A01G211900 chr7A 100.000 4160 0 0 1 4160 174912389 174916548 0.000000e+00 7683.0
1 TraesCS7A01G211900 chr7A 97.895 190 4 0 1 190 293097229 293097040 3.100000e-86 329.0
2 TraesCS7A01G211900 chr7A 97.895 190 3 1 1 189 563349149 563348960 1.120000e-85 327.0
3 TraesCS7A01G211900 chr7A 95.098 204 7 3 1 203 105757547 105757346 6.710000e-83 318.0
4 TraesCS7A01G211900 chr7A 100.000 48 0 0 2164 2211 174914477 174914524 5.730000e-14 89.8
5 TraesCS7A01G211900 chr7A 100.000 48 0 0 2089 2136 174914552 174914599 5.730000e-14 89.8
6 TraesCS7A01G211900 chr7B 92.291 2309 83 30 230 2491 138249801 138252061 0.000000e+00 3190.0
7 TraesCS7A01G211900 chr7B 92.626 1424 75 10 2505 3905 138252275 138253691 0.000000e+00 2021.0
8 TraesCS7A01G211900 chr7B 85.149 202 21 6 3965 4160 138253699 138253897 9.120000e-47 198.0
9 TraesCS7A01G211900 chr7D 94.283 1889 81 15 218 2090 172252628 172254505 0.000000e+00 2865.0
10 TraesCS7A01G211900 chr7D 91.383 1265 84 15 2908 4160 172255439 172256690 0.000000e+00 1709.0
11 TraesCS7A01G211900 chr7D 97.757 758 16 1 2153 2909 172254520 172255277 0.000000e+00 1304.0
12 TraesCS7A01G211900 chr3B 97.917 192 4 0 1 192 742450107 742449916 2.400000e-87 333.0
13 TraesCS7A01G211900 chr3B 97.884 189 4 0 1 189 12174827 12175015 1.120000e-85 327.0
14 TraesCS7A01G211900 chr3B 97.884 189 4 0 1 189 661163743 661163931 1.120000e-85 327.0
15 TraesCS7A01G211900 chr2A 97.884 189 4 0 1 189 84977717 84977529 1.120000e-85 327.0
16 TraesCS7A01G211900 chr1B 97.884 189 4 0 1 189 152079677 152079865 1.120000e-85 327.0
17 TraesCS7A01G211900 chrUn 95.545 202 7 2 1 202 40974998 40974799 5.190000e-84 322.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G211900 chr7A 174912389 174916548 4159 False 2620.866667 7683 100.000000 1 4160 3 chr7A.!!$F1 4159
1 TraesCS7A01G211900 chr7B 138249801 138253897 4096 False 1803.000000 3190 90.022000 230 4160 3 chr7B.!!$F1 3930
2 TraesCS7A01G211900 chr7D 172252628 172256690 4062 False 1959.333333 2865 94.474333 218 4160 3 chr7D.!!$F1 3942

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
106 107 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.0 34.43 6.53 F
153 154 0.179234 TCAAAGTTGGAGCACGTGGA 59.821 50.000 18.88 0.0 0.00 4.02 F
1318 1361 0.687427 GGGGTTCATGGATTGTGGGG 60.687 60.000 0.00 0.0 0.00 4.96 F
1488 1531 1.474143 GGTGATAGGCAGCAAGGAGAC 60.474 57.143 0.00 0.0 44.31 3.36 F
2339 2390 2.111384 AGTTGAGGTATGATGTCCGCT 58.889 47.619 0.00 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1233 1276 0.318762 AGAACGAGGAGAACTGGTGC 59.681 55.0 0.00 0.0 38.24 5.01 R
2003 2054 0.539986 TCCCTCCGAACCTGTATTGC 59.460 55.0 0.00 0.0 0.00 3.56 R
2268 2319 0.106708 TCTCATCCAGCATAACGGCC 59.893 55.0 0.00 0.0 0.00 6.13 R
2958 3373 0.987294 ATACAGAACTGCACCAGGCT 59.013 50.0 1.46 0.0 45.15 4.58 R
3571 3989 1.291184 CGCGGAGTGTGAATCTTGCA 61.291 55.0 0.00 0.0 0.00 4.08 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
24 25 7.136289 TGACCATAAATTTAACCAACGAGAC 57.864 36.000 1.21 0.00 0.00 3.36
25 26 6.149807 TGACCATAAATTTAACCAACGAGACC 59.850 38.462 1.21 0.00 0.00 3.85
26 27 6.005198 ACCATAAATTTAACCAACGAGACCA 58.995 36.000 1.21 0.00 0.00 4.02
27 28 6.490721 ACCATAAATTTAACCAACGAGACCAA 59.509 34.615 1.21 0.00 0.00 3.67
28 29 6.804783 CCATAAATTTAACCAACGAGACCAAC 59.195 38.462 1.21 0.00 0.00 3.77
29 30 7.308951 CCATAAATTTAACCAACGAGACCAACT 60.309 37.037 1.21 0.00 0.00 3.16
30 31 5.432885 AATTTAACCAACGAGACCAACTG 57.567 39.130 0.00 0.00 0.00 3.16
31 32 1.873698 TAACCAACGAGACCAACTGC 58.126 50.000 0.00 0.00 0.00 4.40
32 33 1.157870 AACCAACGAGACCAACTGCG 61.158 55.000 0.00 0.00 0.00 5.18
33 34 2.317609 CCAACGAGACCAACTGCGG 61.318 63.158 0.00 0.00 0.00 5.69
34 35 2.665185 AACGAGACCAACTGCGGC 60.665 61.111 0.00 0.00 0.00 6.53
41 42 4.697756 CCAACTGCGGCGGGAGAA 62.698 66.667 19.55 0.00 35.29 2.87
42 43 2.668212 CAACTGCGGCGGGAGAAA 60.668 61.111 19.55 0.00 35.29 2.52
43 44 2.112297 AACTGCGGCGGGAGAAAA 59.888 55.556 19.55 0.00 35.29 2.29
44 45 1.527380 AACTGCGGCGGGAGAAAAA 60.527 52.632 19.55 0.00 35.29 1.94
99 100 9.722056 ACGAATTCACTGATATAATTTTTGCTC 57.278 29.630 6.22 0.00 0.00 4.26
100 101 9.173939 CGAATTCACTGATATAATTTTTGCTCC 57.826 33.333 6.22 0.00 0.00 4.70
101 102 9.468532 GAATTCACTGATATAATTTTTGCTCCC 57.531 33.333 0.00 0.00 0.00 4.30
102 103 6.618287 TCACTGATATAATTTTTGCTCCCG 57.382 37.500 0.00 0.00 0.00 5.14
103 104 5.008613 TCACTGATATAATTTTTGCTCCCGC 59.991 40.000 0.00 0.00 0.00 6.13
104 105 4.278419 ACTGATATAATTTTTGCTCCCGCC 59.722 41.667 0.00 0.00 34.43 6.13
105 106 3.252215 TGATATAATTTTTGCTCCCGCCG 59.748 43.478 0.00 0.00 34.43 6.46
106 107 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
107 108 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
108 109 2.093537 AATTTTTGCTCCCGCCGCAA 62.094 50.000 0.00 0.00 44.83 4.85
109 110 1.887344 ATTTTTGCTCCCGCCGCAAT 61.887 50.000 5.33 0.00 45.67 3.56
110 111 2.485188 TTTTTGCTCCCGCCGCAATC 62.485 55.000 5.33 0.00 45.67 2.67
111 112 4.713735 TTGCTCCCGCCGCAATCA 62.714 61.111 0.00 0.00 41.97 2.57
114 115 2.892425 CTCCCGCCGCAATCAGTC 60.892 66.667 0.00 0.00 0.00 3.51
115 116 3.376935 CTCCCGCCGCAATCAGTCT 62.377 63.158 0.00 0.00 0.00 3.24
116 117 2.436646 CCCGCCGCAATCAGTCTT 60.437 61.111 0.00 0.00 0.00 3.01
117 118 2.753966 CCCGCCGCAATCAGTCTTG 61.754 63.158 0.00 0.00 0.00 3.02
118 119 2.753966 CCGCCGCAATCAGTCTTGG 61.754 63.158 0.00 0.00 0.00 3.61
119 120 2.034879 CGCCGCAATCAGTCTTGGT 61.035 57.895 0.00 0.00 0.00 3.67
120 121 0.739462 CGCCGCAATCAGTCTTGGTA 60.739 55.000 0.00 0.00 0.00 3.25
121 122 1.009829 GCCGCAATCAGTCTTGGTAG 58.990 55.000 0.00 0.00 0.00 3.18
122 123 1.676014 GCCGCAATCAGTCTTGGTAGT 60.676 52.381 0.00 0.00 0.00 2.73
123 124 2.699954 CCGCAATCAGTCTTGGTAGTT 58.300 47.619 0.00 0.00 0.00 2.24
124 125 3.857052 CCGCAATCAGTCTTGGTAGTTA 58.143 45.455 0.00 0.00 0.00 2.24
125 126 4.250464 CCGCAATCAGTCTTGGTAGTTAA 58.750 43.478 0.00 0.00 0.00 2.01
126 127 4.693566 CCGCAATCAGTCTTGGTAGTTAAA 59.306 41.667 0.00 0.00 0.00 1.52
127 128 5.354234 CCGCAATCAGTCTTGGTAGTTAAAT 59.646 40.000 0.00 0.00 0.00 1.40
128 129 6.128007 CCGCAATCAGTCTTGGTAGTTAAATT 60.128 38.462 0.00 0.00 0.00 1.82
129 130 7.305474 CGCAATCAGTCTTGGTAGTTAAATTT 58.695 34.615 0.00 0.00 0.00 1.82
130 131 8.447833 CGCAATCAGTCTTGGTAGTTAAATTTA 58.552 33.333 0.00 0.00 0.00 1.40
131 132 9.556030 GCAATCAGTCTTGGTAGTTAAATTTAC 57.444 33.333 0.00 0.00 0.00 2.01
132 133 9.755064 CAATCAGTCTTGGTAGTTAAATTTACG 57.245 33.333 0.00 0.00 0.00 3.18
133 134 7.894376 TCAGTCTTGGTAGTTAAATTTACGG 57.106 36.000 0.00 0.00 0.00 4.02
134 135 7.444299 TCAGTCTTGGTAGTTAAATTTACGGT 58.556 34.615 0.00 0.00 0.00 4.83
135 136 7.599998 TCAGTCTTGGTAGTTAAATTTACGGTC 59.400 37.037 0.00 0.00 0.00 4.79
136 137 7.385752 CAGTCTTGGTAGTTAAATTTACGGTCA 59.614 37.037 0.00 0.00 0.00 4.02
137 138 7.933033 AGTCTTGGTAGTTAAATTTACGGTCAA 59.067 33.333 0.00 0.00 0.00 3.18
138 139 8.558700 GTCTTGGTAGTTAAATTTACGGTCAAA 58.441 33.333 0.00 0.00 0.00 2.69
139 140 8.776470 TCTTGGTAGTTAAATTTACGGTCAAAG 58.224 33.333 0.00 0.00 0.00 2.77
140 141 8.449251 TTGGTAGTTAAATTTACGGTCAAAGT 57.551 30.769 0.00 0.00 0.00 2.66
141 142 8.449251 TGGTAGTTAAATTTACGGTCAAAGTT 57.551 30.769 0.00 0.00 31.36 2.66
142 143 8.344098 TGGTAGTTAAATTTACGGTCAAAGTTG 58.656 33.333 0.00 0.00 29.44 3.16
143 144 7.804600 GGTAGTTAAATTTACGGTCAAAGTTGG 59.195 37.037 0.00 0.00 29.44 3.77
144 145 7.571080 AGTTAAATTTACGGTCAAAGTTGGA 57.429 32.000 0.00 0.00 29.44 3.53
145 146 7.645402 AGTTAAATTTACGGTCAAAGTTGGAG 58.355 34.615 0.00 0.00 29.44 3.86
146 147 4.499037 AATTTACGGTCAAAGTTGGAGC 57.501 40.909 0.00 0.00 0.00 4.70
147 148 2.623878 TTACGGTCAAAGTTGGAGCA 57.376 45.000 10.02 0.00 33.16 4.26
148 149 1.873698 TACGGTCAAAGTTGGAGCAC 58.126 50.000 10.02 0.00 33.16 4.40
149 150 1.157870 ACGGTCAAAGTTGGAGCACG 61.158 55.000 10.02 4.18 33.16 5.34
150 151 1.157870 CGGTCAAAGTTGGAGCACGT 61.158 55.000 10.02 0.00 33.16 4.49
151 152 0.307760 GGTCAAAGTTGGAGCACGTG 59.692 55.000 12.28 12.28 33.16 4.49
152 153 0.307760 GTCAAAGTTGGAGCACGTGG 59.692 55.000 18.88 0.00 0.00 4.94
153 154 0.179234 TCAAAGTTGGAGCACGTGGA 59.821 50.000 18.88 0.00 0.00 4.02
154 155 1.202758 TCAAAGTTGGAGCACGTGGAT 60.203 47.619 18.88 0.00 0.00 3.41
155 156 2.037902 TCAAAGTTGGAGCACGTGGATA 59.962 45.455 18.88 0.00 0.00 2.59
156 157 2.386661 AAGTTGGAGCACGTGGATAG 57.613 50.000 18.88 0.00 0.00 2.08
157 158 1.557099 AGTTGGAGCACGTGGATAGA 58.443 50.000 18.88 0.00 0.00 1.98
158 159 1.478510 AGTTGGAGCACGTGGATAGAG 59.521 52.381 18.88 0.00 0.00 2.43
159 160 1.476891 GTTGGAGCACGTGGATAGAGA 59.523 52.381 18.88 0.00 0.00 3.10
160 161 1.847328 TGGAGCACGTGGATAGAGAA 58.153 50.000 18.88 0.00 0.00 2.87
161 162 2.176045 TGGAGCACGTGGATAGAGAAA 58.824 47.619 18.88 0.00 0.00 2.52
162 163 2.166459 TGGAGCACGTGGATAGAGAAAG 59.834 50.000 18.88 0.00 0.00 2.62
163 164 2.197577 GAGCACGTGGATAGAGAAAGC 58.802 52.381 18.88 0.00 0.00 3.51
164 165 1.550524 AGCACGTGGATAGAGAAAGCA 59.449 47.619 18.88 0.00 0.00 3.91
165 166 1.661112 GCACGTGGATAGAGAAAGCAC 59.339 52.381 18.88 0.00 0.00 4.40
166 167 2.675317 GCACGTGGATAGAGAAAGCACT 60.675 50.000 18.88 0.00 0.00 4.40
167 168 3.428999 GCACGTGGATAGAGAAAGCACTA 60.429 47.826 18.88 0.00 0.00 2.74
168 169 4.106197 CACGTGGATAGAGAAAGCACTAC 58.894 47.826 7.95 0.00 0.00 2.73
169 170 3.762288 ACGTGGATAGAGAAAGCACTACA 59.238 43.478 0.00 0.00 0.00 2.74
170 171 4.402793 ACGTGGATAGAGAAAGCACTACAT 59.597 41.667 0.00 0.00 0.00 2.29
171 172 5.105310 ACGTGGATAGAGAAAGCACTACATT 60.105 40.000 0.00 0.00 0.00 2.71
172 173 5.233050 CGTGGATAGAGAAAGCACTACATTG 59.767 44.000 0.00 0.00 0.00 2.82
173 174 6.109359 GTGGATAGAGAAAGCACTACATTGT 58.891 40.000 0.00 0.00 0.00 2.71
174 175 6.036517 GTGGATAGAGAAAGCACTACATTGTG 59.963 42.308 0.00 0.00 40.62 3.33
175 176 5.525378 GGATAGAGAAAGCACTACATTGTGG 59.475 44.000 0.00 0.00 38.31 4.17
176 177 4.623932 AGAGAAAGCACTACATTGTGGA 57.376 40.909 7.20 0.00 38.31 4.02
177 178 4.973168 AGAGAAAGCACTACATTGTGGAA 58.027 39.130 7.20 0.00 38.31 3.53
178 179 5.564550 AGAGAAAGCACTACATTGTGGAAT 58.435 37.500 7.20 0.00 38.31 3.01
179 180 5.413833 AGAGAAAGCACTACATTGTGGAATG 59.586 40.000 7.20 0.00 44.11 2.67
180 181 4.460382 AGAAAGCACTACATTGTGGAATGG 59.540 41.667 7.20 0.00 43.00 3.16
181 182 3.719268 AGCACTACATTGTGGAATGGA 57.281 42.857 7.20 0.00 43.00 3.41
185 186 3.931907 CTACATTGTGGAATGGAGGGA 57.068 47.619 0.00 0.00 44.23 4.20
186 187 2.814805 ACATTGTGGAATGGAGGGAG 57.185 50.000 0.00 0.00 43.00 4.30
187 188 1.995542 ACATTGTGGAATGGAGGGAGT 59.004 47.619 0.00 0.00 43.00 3.85
188 189 3.189606 ACATTGTGGAATGGAGGGAGTA 58.810 45.455 0.00 0.00 43.00 2.59
189 190 3.591527 ACATTGTGGAATGGAGGGAGTAA 59.408 43.478 0.00 0.00 43.00 2.24
190 191 4.202441 CATTGTGGAATGGAGGGAGTAAG 58.798 47.826 0.00 0.00 36.12 2.34
191 192 3.199442 TGTGGAATGGAGGGAGTAAGA 57.801 47.619 0.00 0.00 0.00 2.10
192 193 3.736094 TGTGGAATGGAGGGAGTAAGAT 58.264 45.455 0.00 0.00 0.00 2.40
193 194 3.455910 TGTGGAATGGAGGGAGTAAGATG 59.544 47.826 0.00 0.00 0.00 2.90
194 195 3.456277 GTGGAATGGAGGGAGTAAGATGT 59.544 47.826 0.00 0.00 0.00 3.06
195 196 4.080299 GTGGAATGGAGGGAGTAAGATGTT 60.080 45.833 0.00 0.00 0.00 2.71
196 197 4.540099 TGGAATGGAGGGAGTAAGATGTTT 59.460 41.667 0.00 0.00 0.00 2.83
197 198 5.126779 GGAATGGAGGGAGTAAGATGTTTC 58.873 45.833 0.00 0.00 0.00 2.78
198 199 5.104318 GGAATGGAGGGAGTAAGATGTTTCT 60.104 44.000 0.00 0.00 0.00 2.52
199 200 4.826274 TGGAGGGAGTAAGATGTTTCTG 57.174 45.455 0.00 0.00 30.72 3.02
200 201 4.168101 TGGAGGGAGTAAGATGTTTCTGT 58.832 43.478 0.00 0.00 30.72 3.41
201 202 5.338632 TGGAGGGAGTAAGATGTTTCTGTA 58.661 41.667 0.00 0.00 30.72 2.74
202 203 5.422331 TGGAGGGAGTAAGATGTTTCTGTAG 59.578 44.000 0.00 0.00 30.72 2.74
203 204 5.163395 GGAGGGAGTAAGATGTTTCTGTAGG 60.163 48.000 0.00 0.00 30.72 3.18
204 205 4.162509 AGGGAGTAAGATGTTTCTGTAGGC 59.837 45.833 0.00 0.00 30.72 3.93
205 206 4.162509 GGGAGTAAGATGTTTCTGTAGGCT 59.837 45.833 0.00 0.00 30.72 4.58
206 207 5.363005 GGGAGTAAGATGTTTCTGTAGGCTA 59.637 44.000 0.00 0.00 30.72 3.93
207 208 6.461788 GGGAGTAAGATGTTTCTGTAGGCTAG 60.462 46.154 0.00 0.00 30.72 3.42
208 209 6.097129 GGAGTAAGATGTTTCTGTAGGCTAGT 59.903 42.308 0.00 0.00 30.72 2.57
209 210 7.363968 GGAGTAAGATGTTTCTGTAGGCTAGTT 60.364 40.741 0.00 0.00 30.72 2.24
210 211 7.908453 AGTAAGATGTTTCTGTAGGCTAGTTT 58.092 34.615 0.00 0.00 30.72 2.66
211 212 9.032624 AGTAAGATGTTTCTGTAGGCTAGTTTA 57.967 33.333 0.00 0.00 30.72 2.01
212 213 9.649167 GTAAGATGTTTCTGTAGGCTAGTTTAA 57.351 33.333 0.00 0.00 30.72 1.52
214 215 9.569122 AAGATGTTTCTGTAGGCTAGTTTAAAA 57.431 29.630 0.00 0.00 30.72 1.52
215 216 9.569122 AGATGTTTCTGTAGGCTAGTTTAAAAA 57.431 29.630 0.00 0.00 0.00 1.94
354 356 9.582431 ACATGCAAAAAGATCATGATTTCTTAG 57.418 29.630 10.14 5.85 39.80 2.18
412 424 1.842562 CATGGTCAAGATCCACCTCCT 59.157 52.381 7.44 0.00 37.81 3.69
413 425 1.573108 TGGTCAAGATCCACCTCCTC 58.427 55.000 7.44 0.00 33.36 3.71
480 492 4.419921 GCACCTACCCCAACCCCG 62.420 72.222 0.00 0.00 0.00 5.73
482 494 2.608678 ACCTACCCCAACCCCGAC 60.609 66.667 0.00 0.00 0.00 4.79
522 540 2.892425 CCCGATGCGCCTCTGAAC 60.892 66.667 4.18 0.00 0.00 3.18
544 562 1.344763 AGTACCACTCCAGTCAAGTGC 59.655 52.381 0.00 0.00 42.26 4.40
725 767 2.504681 CGCATTTTGCCGTCCAGC 60.505 61.111 0.00 0.00 41.12 4.85
751 793 1.139853 GCTAGACCCCATTGACCTCTG 59.860 57.143 0.00 0.00 0.00 3.35
807 849 1.070309 CACTCTCGTTGCTTTCACTGC 60.070 52.381 0.00 0.00 0.00 4.40
829 871 9.357652 ACTGCACTGCATTTGTTTATTTATTAG 57.642 29.630 3.64 0.00 38.13 1.73
830 872 9.357652 CTGCACTGCATTTGTTTATTTATTAGT 57.642 29.630 3.64 0.00 38.13 2.24
858 900 2.396590 TTGGATTTACTCGGCTCACC 57.603 50.000 0.00 0.00 0.00 4.02
876 918 1.021968 CCGGATTCCCTTTTAAGCGG 58.978 55.000 0.00 0.00 0.00 5.52
937 980 4.742201 GGTCTGAAGCAGCGCCGA 62.742 66.667 2.29 0.00 0.00 5.54
944 987 1.361668 GAAGCAGCGCCGAATCTCAA 61.362 55.000 2.29 0.00 0.00 3.02
948 991 0.798776 CAGCGCCGAATCTCAAACTT 59.201 50.000 2.29 0.00 0.00 2.66
949 992 1.999735 CAGCGCCGAATCTCAAACTTA 59.000 47.619 2.29 0.00 0.00 2.24
950 993 2.000447 AGCGCCGAATCTCAAACTTAC 59.000 47.619 2.29 0.00 0.00 2.34
987 1030 2.234908 CAGATTTCGGTCTTCCAGGAGT 59.765 50.000 0.00 0.00 0.00 3.85
994 1037 1.971357 GGTCTTCCAGGAGTGACAGAA 59.029 52.381 20.00 0.00 0.00 3.02
1038 1081 2.464459 CGCCGCTGATTTGGAGGAC 61.464 63.158 0.00 0.00 0.00 3.85
1170 1213 2.045926 CCGTTCCCTCCTGGCTTG 60.046 66.667 0.00 0.00 0.00 4.01
1233 1276 4.127171 ACACTAACGCTATGCTTAATGGG 58.873 43.478 0.00 0.00 0.00 4.00
1317 1360 1.037030 CGGGGTTCATGGATTGTGGG 61.037 60.000 0.00 0.00 0.00 4.61
1318 1361 0.687427 GGGGTTCATGGATTGTGGGG 60.687 60.000 0.00 0.00 0.00 4.96
1377 1420 4.284178 CCATGATGGATCACCCTTTTTCT 58.716 43.478 5.27 0.00 40.96 2.52
1387 1430 3.073946 TCACCCTTTTTCTAGGAACCCTG 59.926 47.826 0.00 0.00 37.50 4.45
1488 1531 1.474143 GGTGATAGGCAGCAAGGAGAC 60.474 57.143 0.00 0.00 44.31 3.36
1658 1701 7.224753 CCTGTTATATAGCTGAATTTGTGTCGT 59.775 37.037 0.00 0.00 0.00 4.34
1659 1702 7.905126 TGTTATATAGCTGAATTTGTGTCGTG 58.095 34.615 0.00 0.00 0.00 4.35
1664 1707 5.186996 AGCTGAATTTGTGTCGTGATTTT 57.813 34.783 0.00 0.00 0.00 1.82
1683 1726 8.450964 GTGATTTTGATGGAACTTAGAATTCGA 58.549 33.333 0.00 0.00 0.00 3.71
1726 1769 2.749621 GGTGAAGCATGTACAAGAAGGG 59.250 50.000 0.00 0.00 0.00 3.95
1771 1814 2.816087 TGCAAAGCAGGAGAAAGATGAC 59.184 45.455 0.00 0.00 33.32 3.06
1774 1817 2.663826 AGCAGGAGAAAGATGACGAC 57.336 50.000 0.00 0.00 0.00 4.34
1799 1842 2.503895 AGATGAACCAAAGAGGCCTG 57.496 50.000 12.00 0.00 43.14 4.85
1955 1998 4.202131 CCGAGTTATCTTCCCTGAACTACC 60.202 50.000 0.00 0.00 32.37 3.18
1980 2031 9.141400 CCTTTATCGAATGGTATTTCTAGCTAC 57.859 37.037 0.00 0.00 0.00 3.58
2003 2054 9.599322 CTACTTAGCTTCAGTGTTATTTGTTTG 57.401 33.333 8.23 0.00 0.00 2.93
2090 2141 7.954835 TGGTTGTAGTAAAGTAAGCACTTCTA 58.045 34.615 0.00 0.00 44.41 2.10
2097 2148 8.779354 AGTAAAGTAAGCACTTCTAAATGAGG 57.221 34.615 0.00 0.00 44.41 3.86
2098 2149 8.594550 AGTAAAGTAAGCACTTCTAAATGAGGA 58.405 33.333 0.00 0.00 44.41 3.71
2099 2150 9.216117 GTAAAGTAAGCACTTCTAAATGAGGAA 57.784 33.333 0.00 0.00 44.41 3.36
2100 2151 7.913674 AAGTAAGCACTTCTAAATGAGGAAG 57.086 36.000 0.00 0.00 41.25 3.46
2102 2153 7.100409 AGTAAGCACTTCTAAATGAGGAAGTC 58.900 38.462 5.52 2.66 45.95 3.01
2103 2154 5.489792 AGCACTTCTAAATGAGGAAGTCA 57.510 39.130 5.52 0.00 45.95 3.41
2104 2155 5.486526 AGCACTTCTAAATGAGGAAGTCAG 58.513 41.667 5.52 0.00 45.95 3.51
2105 2156 4.094146 GCACTTCTAAATGAGGAAGTCAGC 59.906 45.833 5.52 4.48 45.95 4.26
2106 2157 5.240891 CACTTCTAAATGAGGAAGTCAGCA 58.759 41.667 5.52 0.00 45.95 4.41
2107 2158 5.121454 CACTTCTAAATGAGGAAGTCAGCAC 59.879 44.000 5.52 0.00 45.95 4.40
2108 2159 5.012561 ACTTCTAAATGAGGAAGTCAGCACT 59.987 40.000 0.00 0.00 45.95 4.40
2109 2160 5.489792 TCTAAATGAGGAAGTCAGCACTT 57.510 39.130 0.00 0.00 46.21 3.16
2110 2161 5.869579 TCTAAATGAGGAAGTCAGCACTTT 58.130 37.500 0.00 0.00 43.37 2.66
2111 2162 6.299141 TCTAAATGAGGAAGTCAGCACTTTT 58.701 36.000 0.00 0.00 43.37 2.27
2112 2163 5.859205 AAATGAGGAAGTCAGCACTTTTT 57.141 34.783 0.00 0.00 43.37 1.94
2113 2164 6.959639 AAATGAGGAAGTCAGCACTTTTTA 57.040 33.333 0.00 0.00 43.37 1.52
2114 2165 6.566197 AATGAGGAAGTCAGCACTTTTTAG 57.434 37.500 0.00 0.00 43.37 1.85
2115 2166 3.815401 TGAGGAAGTCAGCACTTTTTAGC 59.185 43.478 0.00 0.00 43.37 3.09
2116 2167 4.068599 GAGGAAGTCAGCACTTTTTAGCT 58.931 43.478 0.00 0.00 43.37 3.32
2185 2236 4.457257 GCTAAATGAGGAAGTCAGCACTTT 59.543 41.667 0.00 0.00 43.37 2.66
2244 2295 4.560035 CCATTCGCTATTTTCACAAGCAAG 59.440 41.667 0.00 0.00 35.98 4.01
2339 2390 2.111384 AGTTGAGGTATGATGTCCGCT 58.889 47.619 0.00 0.00 0.00 5.52
2390 2442 4.913924 GCTCTTTGCTGTAATGTGAACTTG 59.086 41.667 0.00 0.00 38.95 3.16
2958 3373 9.771140 AGAGAGTACCTTCTAGATTTCCTTTAA 57.229 33.333 0.00 0.00 0.00 1.52
2963 3378 6.418946 ACCTTCTAGATTTCCTTTAAGCCTG 58.581 40.000 0.00 0.00 0.00 4.85
3126 3541 2.230130 TTGGGATGCCTTTTACCCTG 57.770 50.000 4.35 0.00 42.49 4.45
3132 3547 4.714802 GGGATGCCTTTTACCCTGTTTAAT 59.285 41.667 0.00 0.00 39.28 1.40
3138 3553 5.186992 GCCTTTTACCCTGTTTAATGACCAT 59.813 40.000 0.00 0.00 0.00 3.55
3149 3564 8.252417 CCTGTTTAATGACCATGAATCAAATGA 58.748 33.333 0.00 0.00 0.00 2.57
3187 3602 0.816018 TTCCGCAACCGAAGCAAGAA 60.816 50.000 0.00 0.00 36.29 2.52
3202 3617 2.165437 GCAAGAAATCATAACGGGCCAA 59.835 45.455 4.39 0.00 0.00 4.52
3245 3660 2.032178 GTGAGCTTGTTGACACTGTTCC 59.968 50.000 0.00 0.00 0.00 3.62
3248 3663 2.017049 GCTTGTTGACACTGTTCCACT 58.983 47.619 0.00 0.00 0.00 4.00
3275 3690 5.359756 TCGCATTTGAGCACTGAAGTATAT 58.640 37.500 0.00 0.00 0.00 0.86
3278 3693 5.528690 GCATTTGAGCACTGAAGTATATCCA 59.471 40.000 0.00 0.00 0.00 3.41
3328 3743 6.688637 CAATATTGGAATCAGCACTTGAGA 57.311 37.500 7.62 0.00 39.68 3.27
3358 3773 2.270434 AGGCCCTTTCCTCAGATGTA 57.730 50.000 0.00 0.00 0.00 2.29
3363 3778 3.372025 GCCCTTTCCTCAGATGTACCATT 60.372 47.826 0.00 0.00 0.00 3.16
3392 3807 0.032615 AGGAAGCTGGAGATCCGACT 60.033 55.000 0.00 0.00 38.31 4.18
3393 3808 0.387565 GGAAGCTGGAGATCCGACTC 59.612 60.000 0.00 0.00 39.43 3.36
3422 3837 3.350833 GTCCACATGGAGATTTCAAGCT 58.649 45.455 0.00 0.00 46.49 3.74
3433 3851 6.375455 TGGAGATTTCAAGCTTTACATTCTCC 59.625 38.462 23.12 23.12 44.46 3.71
3434 3852 6.601217 GGAGATTTCAAGCTTTACATTCTCCT 59.399 38.462 22.85 5.17 42.14 3.69
3435 3853 7.201688 GGAGATTTCAAGCTTTACATTCTCCTC 60.202 40.741 22.85 11.35 42.14 3.71
3609 4027 4.933400 CCGCGGTATAATATAACAGCCTTT 59.067 41.667 19.50 0.00 33.92 3.11
3611 4029 5.163893 CGCGGTATAATATAACAGCCTTTGG 60.164 44.000 0.00 0.00 33.92 3.28
3630 4048 7.527457 CCTTTGGTTTGTTAGTTGCTAGTATC 58.473 38.462 0.00 0.00 0.00 2.24
3669 4091 7.617041 AGAATCTTTGTTGTACTTCTATGGC 57.383 36.000 0.00 0.00 0.00 4.40
3722 4144 8.567285 ACTGGTTTTCGATTTCTTGAGAATAT 57.433 30.769 0.00 0.00 33.54 1.28
3723 4145 9.014297 ACTGGTTTTCGATTTCTTGAGAATATT 57.986 29.630 0.00 0.00 33.54 1.28
3771 4205 3.278574 TGTGTGGAAGAAACAGTGAAGG 58.721 45.455 0.00 0.00 0.00 3.46
3857 4292 5.814705 CCTCATCTGAACTTGGATAGTTGAC 59.185 44.000 0.00 0.00 47.00 3.18
3858 4293 6.358974 TCATCTGAACTTGGATAGTTGACA 57.641 37.500 0.00 0.00 47.00 3.58
3863 4298 7.279615 TCTGAACTTGGATAGTTGACAAAAGA 58.720 34.615 2.79 0.00 47.00 2.52
3866 4301 8.567948 TGAACTTGGATAGTTGACAAAAGAATC 58.432 33.333 2.79 2.26 47.00 2.52
3867 4302 8.463930 AACTTGGATAGTTGACAAAAGAATCA 57.536 30.769 2.79 0.00 45.33 2.57
3878 4313 6.629128 TGACAAAAGAATCAAAGAAACTGCA 58.371 32.000 0.00 0.00 0.00 4.41
3884 4319 8.953368 AAAGAATCAAAGAAACTGCAAATCTT 57.047 26.923 3.22 3.22 35.00 2.40
3920 4355 2.481854 CTCAAGGGAAGATCATGAGCG 58.518 52.381 5.12 0.00 32.05 5.03
3943 4378 5.004630 CGTAGTCAGTCGAGTAGAACTACAG 59.995 48.000 24.62 18.11 39.16 2.74
4030 4480 5.048504 TGAATCTCAAATGAGTTCTGCAACC 60.049 40.000 10.06 0.00 42.60 3.77
4150 4600 7.116075 TCATCAAAGCCTAGCCTTAATTACAA 58.884 34.615 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.149807 TGGTCTCGTTGGTTAAATTTATGGTC 59.850 38.462 0.00 0.00 0.00 4.02
2 3 6.005198 TGGTCTCGTTGGTTAAATTTATGGT 58.995 36.000 0.00 0.00 0.00 3.55
3 4 6.503589 TGGTCTCGTTGGTTAAATTTATGG 57.496 37.500 0.00 0.00 0.00 2.74
4 5 7.537306 CAGTTGGTCTCGTTGGTTAAATTTATG 59.463 37.037 0.00 0.00 0.00 1.90
5 6 7.590279 CAGTTGGTCTCGTTGGTTAAATTTAT 58.410 34.615 0.00 0.00 0.00 1.40
7 8 5.735070 GCAGTTGGTCTCGTTGGTTAAATTT 60.735 40.000 0.00 0.00 0.00 1.82
8 9 4.261447 GCAGTTGGTCTCGTTGGTTAAATT 60.261 41.667 0.00 0.00 0.00 1.82
9 10 3.252458 GCAGTTGGTCTCGTTGGTTAAAT 59.748 43.478 0.00 0.00 0.00 1.40
11 12 2.215196 GCAGTTGGTCTCGTTGGTTAA 58.785 47.619 0.00 0.00 0.00 2.01
13 14 1.157870 CGCAGTTGGTCTCGTTGGTT 61.158 55.000 0.00 0.00 0.00 3.67
14 15 1.594293 CGCAGTTGGTCTCGTTGGT 60.594 57.895 0.00 0.00 0.00 3.67
15 16 2.317609 CCGCAGTTGGTCTCGTTGG 61.318 63.158 0.00 0.00 0.00 3.77
16 17 2.954753 GCCGCAGTTGGTCTCGTTG 61.955 63.158 0.00 0.00 0.00 4.10
17 18 2.665185 GCCGCAGTTGGTCTCGTT 60.665 61.111 0.00 0.00 0.00 3.85
24 25 4.697756 TTCTCCCGCCGCAGTTGG 62.698 66.667 0.00 0.00 0.00 3.77
25 26 1.791103 TTTTTCTCCCGCCGCAGTTG 61.791 55.000 0.00 0.00 0.00 3.16
26 27 1.527380 TTTTTCTCCCGCCGCAGTT 60.527 52.632 0.00 0.00 0.00 3.16
27 28 2.112297 TTTTTCTCCCGCCGCAGT 59.888 55.556 0.00 0.00 0.00 4.40
73 74 9.722056 GAGCAAAAATTATATCAGTGAATTCGT 57.278 29.630 0.00 0.00 0.00 3.85
74 75 9.173939 GGAGCAAAAATTATATCAGTGAATTCG 57.826 33.333 0.00 0.00 0.00 3.34
75 76 9.468532 GGGAGCAAAAATTATATCAGTGAATTC 57.531 33.333 0.00 0.00 0.00 2.17
76 77 8.137437 CGGGAGCAAAAATTATATCAGTGAATT 58.863 33.333 0.00 0.00 0.00 2.17
77 78 7.651808 CGGGAGCAAAAATTATATCAGTGAAT 58.348 34.615 0.00 0.00 0.00 2.57
78 79 7.026631 CGGGAGCAAAAATTATATCAGTGAA 57.973 36.000 0.00 0.00 0.00 3.18
79 80 6.618287 CGGGAGCAAAAATTATATCAGTGA 57.382 37.500 0.00 0.00 0.00 3.41
97 98 2.859273 AAGACTGATTGCGGCGGGAG 62.859 60.000 9.78 0.00 0.00 4.30
98 99 2.954684 AAGACTGATTGCGGCGGGA 61.955 57.895 9.78 0.00 0.00 5.14
99 100 2.436646 AAGACTGATTGCGGCGGG 60.437 61.111 9.78 0.00 0.00 6.13
100 101 2.753966 CCAAGACTGATTGCGGCGG 61.754 63.158 9.78 0.00 0.00 6.13
101 102 0.739462 TACCAAGACTGATTGCGGCG 60.739 55.000 0.51 0.51 0.00 6.46
102 103 1.009829 CTACCAAGACTGATTGCGGC 58.990 55.000 0.00 0.00 0.00 6.53
103 104 2.386661 ACTACCAAGACTGATTGCGG 57.613 50.000 0.00 0.00 0.00 5.69
104 105 5.856126 TTTAACTACCAAGACTGATTGCG 57.144 39.130 0.00 0.00 0.00 4.85
105 106 9.556030 GTAAATTTAACTACCAAGACTGATTGC 57.444 33.333 0.00 0.00 0.00 3.56
106 107 9.755064 CGTAAATTTAACTACCAAGACTGATTG 57.245 33.333 0.00 0.00 0.00 2.67
107 108 8.943002 CCGTAAATTTAACTACCAAGACTGATT 58.057 33.333 0.00 0.00 0.00 2.57
108 109 8.098912 ACCGTAAATTTAACTACCAAGACTGAT 58.901 33.333 0.00 0.00 0.00 2.90
109 110 7.444299 ACCGTAAATTTAACTACCAAGACTGA 58.556 34.615 0.00 0.00 0.00 3.41
110 111 7.385752 TGACCGTAAATTTAACTACCAAGACTG 59.614 37.037 0.00 0.00 0.00 3.51
111 112 7.444299 TGACCGTAAATTTAACTACCAAGACT 58.556 34.615 0.00 0.00 0.00 3.24
112 113 7.656707 TGACCGTAAATTTAACTACCAAGAC 57.343 36.000 0.00 0.00 0.00 3.01
113 114 8.674263 TTTGACCGTAAATTTAACTACCAAGA 57.326 30.769 0.00 0.00 0.00 3.02
114 115 8.562052 ACTTTGACCGTAAATTTAACTACCAAG 58.438 33.333 0.00 2.45 0.00 3.61
115 116 8.449251 ACTTTGACCGTAAATTTAACTACCAA 57.551 30.769 0.00 0.00 0.00 3.67
116 117 8.344098 CAACTTTGACCGTAAATTTAACTACCA 58.656 33.333 0.00 0.00 0.00 3.25
117 118 7.804600 CCAACTTTGACCGTAAATTTAACTACC 59.195 37.037 0.00 0.00 0.00 3.18
118 119 8.558700 TCCAACTTTGACCGTAAATTTAACTAC 58.441 33.333 0.00 0.00 0.00 2.73
119 120 8.674263 TCCAACTTTGACCGTAAATTTAACTA 57.326 30.769 0.00 0.00 0.00 2.24
120 121 7.571080 TCCAACTTTGACCGTAAATTTAACT 57.429 32.000 0.00 0.00 0.00 2.24
121 122 6.361481 GCTCCAACTTTGACCGTAAATTTAAC 59.639 38.462 0.00 0.00 0.00 2.01
122 123 6.039493 TGCTCCAACTTTGACCGTAAATTTAA 59.961 34.615 0.00 0.00 0.00 1.52
123 124 5.531659 TGCTCCAACTTTGACCGTAAATTTA 59.468 36.000 0.00 0.00 0.00 1.40
124 125 4.339814 TGCTCCAACTTTGACCGTAAATTT 59.660 37.500 0.00 0.00 0.00 1.82
125 126 3.886505 TGCTCCAACTTTGACCGTAAATT 59.113 39.130 0.00 0.00 0.00 1.82
126 127 3.252458 GTGCTCCAACTTTGACCGTAAAT 59.748 43.478 0.00 0.00 0.00 1.40
127 128 2.614983 GTGCTCCAACTTTGACCGTAAA 59.385 45.455 0.00 0.00 0.00 2.01
128 129 2.215196 GTGCTCCAACTTTGACCGTAA 58.785 47.619 0.00 0.00 0.00 3.18
129 130 1.870580 CGTGCTCCAACTTTGACCGTA 60.871 52.381 0.00 0.00 0.00 4.02
130 131 1.157870 CGTGCTCCAACTTTGACCGT 61.158 55.000 0.00 0.00 0.00 4.83
131 132 1.157870 ACGTGCTCCAACTTTGACCG 61.158 55.000 0.00 0.00 0.00 4.79
132 133 0.307760 CACGTGCTCCAACTTTGACC 59.692 55.000 0.82 0.00 0.00 4.02
133 134 0.307760 CCACGTGCTCCAACTTTGAC 59.692 55.000 10.91 0.00 0.00 3.18
134 135 0.179234 TCCACGTGCTCCAACTTTGA 59.821 50.000 10.91 0.00 0.00 2.69
135 136 1.238439 ATCCACGTGCTCCAACTTTG 58.762 50.000 10.91 0.00 0.00 2.77
136 137 2.301870 TCTATCCACGTGCTCCAACTTT 59.698 45.455 10.91 0.00 0.00 2.66
137 138 1.899814 TCTATCCACGTGCTCCAACTT 59.100 47.619 10.91 0.00 0.00 2.66
138 139 1.478510 CTCTATCCACGTGCTCCAACT 59.521 52.381 10.91 0.00 0.00 3.16
139 140 1.476891 TCTCTATCCACGTGCTCCAAC 59.523 52.381 10.91 0.00 0.00 3.77
140 141 1.847328 TCTCTATCCACGTGCTCCAA 58.153 50.000 10.91 0.00 0.00 3.53
141 142 1.847328 TTCTCTATCCACGTGCTCCA 58.153 50.000 10.91 0.00 0.00 3.86
142 143 2.815478 CTTTCTCTATCCACGTGCTCC 58.185 52.381 10.91 0.00 0.00 4.70
143 144 2.197577 GCTTTCTCTATCCACGTGCTC 58.802 52.381 10.91 0.00 0.00 4.26
144 145 1.550524 TGCTTTCTCTATCCACGTGCT 59.449 47.619 10.91 1.67 0.00 4.40
145 146 1.661112 GTGCTTTCTCTATCCACGTGC 59.339 52.381 10.91 0.00 0.00 5.34
146 147 3.238108 AGTGCTTTCTCTATCCACGTG 57.762 47.619 9.08 9.08 0.00 4.49
147 148 3.762288 TGTAGTGCTTTCTCTATCCACGT 59.238 43.478 0.00 0.00 0.00 4.49
148 149 4.371855 TGTAGTGCTTTCTCTATCCACG 57.628 45.455 0.00 0.00 0.00 4.94
149 150 6.036517 CACAATGTAGTGCTTTCTCTATCCAC 59.963 42.308 0.00 0.00 32.04 4.02
150 151 6.108687 CACAATGTAGTGCTTTCTCTATCCA 58.891 40.000 0.00 0.00 32.04 3.41
151 152 5.525378 CCACAATGTAGTGCTTTCTCTATCC 59.475 44.000 0.00 0.00 38.18 2.59
152 153 6.341316 TCCACAATGTAGTGCTTTCTCTATC 58.659 40.000 0.00 0.00 38.18 2.08
153 154 6.299805 TCCACAATGTAGTGCTTTCTCTAT 57.700 37.500 0.00 0.00 38.18 1.98
154 155 5.738619 TCCACAATGTAGTGCTTTCTCTA 57.261 39.130 0.00 0.00 38.18 2.43
155 156 4.623932 TCCACAATGTAGTGCTTTCTCT 57.376 40.909 0.00 0.00 38.18 3.10
156 157 5.392380 CCATTCCACAATGTAGTGCTTTCTC 60.392 44.000 0.00 0.00 38.22 2.87
157 158 4.460382 CCATTCCACAATGTAGTGCTTTCT 59.540 41.667 0.00 0.00 38.22 2.52
158 159 4.458989 TCCATTCCACAATGTAGTGCTTTC 59.541 41.667 0.00 0.00 38.22 2.62
159 160 4.406456 TCCATTCCACAATGTAGTGCTTT 58.594 39.130 0.00 0.00 38.22 3.51
160 161 4.012374 CTCCATTCCACAATGTAGTGCTT 58.988 43.478 0.00 0.00 38.22 3.91
161 162 3.614092 CTCCATTCCACAATGTAGTGCT 58.386 45.455 0.00 0.00 38.22 4.40
162 163 2.684881 CCTCCATTCCACAATGTAGTGC 59.315 50.000 0.00 0.00 38.22 4.40
163 164 3.054434 TCCCTCCATTCCACAATGTAGTG 60.054 47.826 0.00 0.00 38.22 2.74
164 165 3.189606 TCCCTCCATTCCACAATGTAGT 58.810 45.455 0.00 0.00 38.22 2.73
165 166 3.200825 ACTCCCTCCATTCCACAATGTAG 59.799 47.826 0.00 0.00 38.22 2.74
166 167 3.189606 ACTCCCTCCATTCCACAATGTA 58.810 45.455 0.00 0.00 38.22 2.29
167 168 1.995542 ACTCCCTCCATTCCACAATGT 59.004 47.619 0.00 0.00 38.22 2.71
168 169 2.814805 ACTCCCTCCATTCCACAATG 57.185 50.000 0.00 0.00 39.45 2.82
169 170 4.111577 TCTTACTCCCTCCATTCCACAAT 58.888 43.478 0.00 0.00 0.00 2.71
170 171 3.526899 TCTTACTCCCTCCATTCCACAA 58.473 45.455 0.00 0.00 0.00 3.33
171 172 3.199442 TCTTACTCCCTCCATTCCACA 57.801 47.619 0.00 0.00 0.00 4.17
172 173 3.456277 ACATCTTACTCCCTCCATTCCAC 59.544 47.826 0.00 0.00 0.00 4.02
173 174 3.736094 ACATCTTACTCCCTCCATTCCA 58.264 45.455 0.00 0.00 0.00 3.53
174 175 4.779993 AACATCTTACTCCCTCCATTCC 57.220 45.455 0.00 0.00 0.00 3.01
175 176 5.819901 CAGAAACATCTTACTCCCTCCATTC 59.180 44.000 0.00 0.00 0.00 2.67
176 177 5.251700 ACAGAAACATCTTACTCCCTCCATT 59.748 40.000 0.00 0.00 0.00 3.16
177 178 4.785376 ACAGAAACATCTTACTCCCTCCAT 59.215 41.667 0.00 0.00 0.00 3.41
178 179 4.168101 ACAGAAACATCTTACTCCCTCCA 58.832 43.478 0.00 0.00 0.00 3.86
179 180 4.828072 ACAGAAACATCTTACTCCCTCC 57.172 45.455 0.00 0.00 0.00 4.30
180 181 5.682730 GCCTACAGAAACATCTTACTCCCTC 60.683 48.000 0.00 0.00 0.00 4.30
181 182 4.162509 GCCTACAGAAACATCTTACTCCCT 59.837 45.833 0.00 0.00 0.00 4.20
182 183 4.162509 AGCCTACAGAAACATCTTACTCCC 59.837 45.833 0.00 0.00 0.00 4.30
183 184 5.346181 AGCCTACAGAAACATCTTACTCC 57.654 43.478 0.00 0.00 0.00 3.85
184 185 7.102847 ACTAGCCTACAGAAACATCTTACTC 57.897 40.000 0.00 0.00 0.00 2.59
185 186 7.483580 AACTAGCCTACAGAAACATCTTACT 57.516 36.000 0.00 0.00 0.00 2.24
186 187 9.649167 TTAAACTAGCCTACAGAAACATCTTAC 57.351 33.333 0.00 0.00 0.00 2.34
188 189 9.569122 TTTTAAACTAGCCTACAGAAACATCTT 57.431 29.630 0.00 0.00 0.00 2.40
189 190 9.569122 TTTTTAAACTAGCCTACAGAAACATCT 57.431 29.630 0.00 0.00 0.00 2.90
225 226 9.463902 TCCCGTGATAAAAAGGTTATCATAAAA 57.536 29.630 10.95 0.00 41.66 1.52
226 227 9.116067 CTCCCGTGATAAAAAGGTTATCATAAA 57.884 33.333 10.95 0.26 41.66 1.40
227 228 7.227910 GCTCCCGTGATAAAAAGGTTATCATAA 59.772 37.037 10.95 0.00 41.66 1.90
228 229 6.708949 GCTCCCGTGATAAAAAGGTTATCATA 59.291 38.462 10.95 0.24 41.66 2.15
368 370 8.645814 TGGATGGAGAACACGTATACTATAAT 57.354 34.615 0.56 0.00 0.00 1.28
369 371 8.520351 CATGGATGGAGAACACGTATACTATAA 58.480 37.037 0.56 0.00 0.00 0.98
370 372 8.051901 CATGGATGGAGAACACGTATACTATA 57.948 38.462 0.56 0.00 0.00 1.31
371 373 6.925211 CATGGATGGAGAACACGTATACTAT 58.075 40.000 0.56 0.00 0.00 2.12
480 492 2.779072 GGGGATGGGGATTGGGGTC 61.779 68.421 0.00 0.00 0.00 4.46
482 494 2.097978 GATGGGGATGGGGATTGGGG 62.098 65.000 0.00 0.00 0.00 4.96
522 540 3.367498 GCACTTGACTGGAGTGGTACTAG 60.367 52.174 6.41 0.00 43.63 2.57
725 767 1.140852 TCAATGGGGTCTAGCCAATCG 59.859 52.381 0.00 0.00 39.65 3.34
751 793 0.108851 ATGGTGCGCCGAAAATTTCC 60.109 50.000 12.58 0.00 37.67 3.13
858 900 1.400494 CACCGCTTAAAAGGGAATCCG 59.600 52.381 8.24 0.00 41.06 4.18
937 980 6.127196 TGCCAACAAAAGGTAAGTTTGAGATT 60.127 34.615 4.03 0.00 38.05 2.40
944 987 3.552068 GCGATGCCAACAAAAGGTAAGTT 60.552 43.478 0.00 0.00 0.00 2.66
948 991 1.539388 CTGCGATGCCAACAAAAGGTA 59.461 47.619 0.00 0.00 0.00 3.08
949 992 0.314935 CTGCGATGCCAACAAAAGGT 59.685 50.000 0.00 0.00 0.00 3.50
950 993 0.597568 TCTGCGATGCCAACAAAAGG 59.402 50.000 0.00 0.00 0.00 3.11
987 1030 2.688507 GTCTCCATTTCGCTTCTGTCA 58.311 47.619 0.00 0.00 0.00 3.58
994 1037 2.166459 TCTCATTCGTCTCCATTTCGCT 59.834 45.455 0.00 0.00 0.00 4.93
1038 1081 3.058160 CCGCTGGGCTGGTTCTTG 61.058 66.667 0.00 0.00 0.00 3.02
1198 1241 1.003233 GTTAGTGTTGGTCTCCCCCAG 59.997 57.143 0.00 0.00 35.49 4.45
1215 1258 2.875933 GTGCCCATTAAGCATAGCGTTA 59.124 45.455 0.00 0.00 43.29 3.18
1233 1276 0.318762 AGAACGAGGAGAACTGGTGC 59.681 55.000 0.00 0.00 38.24 5.01
1387 1430 4.004982 TCGTTTTGGAAACTACCCATAGC 58.995 43.478 2.53 0.00 33.04 2.97
1488 1531 1.432514 CACCATGTGAACTCTCGGTG 58.567 55.000 0.00 0.00 38.11 4.94
1658 1701 8.560355 TCGAATTCTAAGTTCCATCAAAATCA 57.440 30.769 3.52 0.00 0.00 2.57
1664 1707 8.792830 AGAAAATCGAATTCTAAGTTCCATCA 57.207 30.769 13.40 0.00 35.43 3.07
1683 1726 4.202441 CCCACGATCCTTCATGAGAAAAT 58.798 43.478 0.00 0.00 32.35 1.82
1771 1814 3.493129 TCTTTGGTTCATCTTTGTCGTCG 59.507 43.478 0.00 0.00 0.00 5.12
1774 1817 3.365364 GCCTCTTTGGTTCATCTTTGTCG 60.365 47.826 0.00 0.00 38.35 4.35
1799 1842 2.224769 TGGACTTTCTGGATGTCCCAAC 60.225 50.000 16.16 0.00 46.81 3.77
1955 1998 9.915629 AGTAGCTAGAAATACCATTCGATAAAG 57.084 33.333 0.00 0.00 34.46 1.85
1980 2031 6.917477 TGCAAACAAATAACACTGAAGCTAAG 59.083 34.615 0.00 0.00 0.00 2.18
2003 2054 0.539986 TCCCTCCGAACCTGTATTGC 59.460 55.000 0.00 0.00 0.00 3.56
2090 2141 5.859205 AAAAAGTGCTGACTTCCTCATTT 57.141 34.783 0.00 0.00 41.87 2.32
2093 2144 3.815401 GCTAAAAAGTGCTGACTTCCTCA 59.185 43.478 0.00 0.00 41.87 3.86
2094 2145 4.068599 AGCTAAAAAGTGCTGACTTCCTC 58.931 43.478 0.00 0.00 41.87 3.71
2095 2146 4.092116 AGCTAAAAAGTGCTGACTTCCT 57.908 40.909 0.00 0.00 41.87 3.36
2103 2154 9.495572 GGAGATAATATACAGCTAAAAAGTGCT 57.504 33.333 0.00 0.00 40.54 4.40
2104 2155 9.273016 TGGAGATAATATACAGCTAAAAAGTGC 57.727 33.333 0.00 0.00 0.00 4.40
2114 2165 9.994432 GCAATAATTGTGGAGATAATATACAGC 57.006 33.333 0.00 0.00 0.00 4.40
2121 2172 9.812347 TTCTATGGCAATAATTGTGGAGATAAT 57.188 29.630 0.00 0.00 0.00 1.28
2122 2173 9.639563 TTTCTATGGCAATAATTGTGGAGATAA 57.360 29.630 0.00 0.00 0.00 1.75
2268 2319 0.106708 TCTCATCCAGCATAACGGCC 59.893 55.000 0.00 0.00 0.00 6.13
2339 2390 6.568869 AGCTGCAAACAATGTTACAAGTTTA 58.431 32.000 15.32 4.80 33.30 2.01
2390 2442 4.036734 CCAATATGCACATACAGGGTCAAC 59.963 45.833 0.00 0.00 0.00 3.18
2958 3373 0.987294 ATACAGAACTGCACCAGGCT 59.013 50.000 1.46 0.00 45.15 4.58
2963 3378 4.261801 ACCACATAATACAGAACTGCACC 58.738 43.478 1.46 0.00 0.00 5.01
3132 3547 7.959658 AGGTTTATCATTTGATTCATGGTCA 57.040 32.000 0.00 0.00 36.05 4.02
3138 3553 7.465353 TGCTCAAGGTTTATCATTTGATTCA 57.535 32.000 0.00 0.00 36.05 2.57
3149 3564 5.239525 GCGGAATCTATTGCTCAAGGTTTAT 59.760 40.000 0.00 0.00 0.00 1.40
3187 3602 3.864789 ATCTCTTGGCCCGTTATGATT 57.135 42.857 0.00 0.00 0.00 2.57
3202 3617 6.543465 TCACATGTTGTTCTGTTGAAATCTCT 59.457 34.615 0.00 0.00 33.52 3.10
3275 3690 7.002250 TCAACAATTAAGCAATTTGGATGGA 57.998 32.000 0.00 0.00 31.82 3.41
3278 3693 8.949177 GGAAATCAACAATTAAGCAATTTGGAT 58.051 29.630 0.00 0.00 31.82 3.41
3310 3725 5.131642 AGGATATCTCAAGTGCTGATTCCAA 59.868 40.000 2.05 0.00 32.14 3.53
3358 3773 3.026694 GCTTCCTCCAATAGCAAATGGT 58.973 45.455 0.00 0.00 37.94 3.55
3363 3778 1.915489 TCCAGCTTCCTCCAATAGCAA 59.085 47.619 0.00 0.00 37.37 3.91
3392 3807 2.348104 CCATGTGGACGTCCCGAGA 61.348 63.158 31.19 13.23 37.93 4.04
3393 3808 2.184322 CCATGTGGACGTCCCGAG 59.816 66.667 31.19 17.63 37.93 4.63
3422 3837 9.280174 ACGTAAATTTTCAGAGGAGAATGTAAA 57.720 29.630 0.00 0.00 29.11 2.01
3516 3934 5.773091 TGAACTAGATGGTACCCAGATACA 58.227 41.667 10.07 0.00 36.75 2.29
3571 3989 1.291184 CGCGGAGTGTGAATCTTGCA 61.291 55.000 0.00 0.00 0.00 4.08
3609 4027 5.636121 CACGATACTAGCAACTAACAAACCA 59.364 40.000 0.00 0.00 0.00 3.67
3611 4029 6.805271 TCTCACGATACTAGCAACTAACAAAC 59.195 38.462 0.00 0.00 0.00 2.93
3630 4048 6.201806 ACAAAGATTCTTCTTTCACTCTCACG 59.798 38.462 0.00 0.00 46.88 4.35
3648 4070 5.355350 GCAGCCATAGAAGTACAACAAAGAT 59.645 40.000 0.00 0.00 0.00 2.40
3722 4144 3.930229 ACGCGCTGAAAATACACTCATAA 59.070 39.130 5.73 0.00 0.00 1.90
3723 4145 3.305897 CACGCGCTGAAAATACACTCATA 59.694 43.478 5.73 0.00 0.00 2.15
3724 4146 2.094258 CACGCGCTGAAAATACACTCAT 59.906 45.455 5.73 0.00 0.00 2.90
3725 4147 1.459209 CACGCGCTGAAAATACACTCA 59.541 47.619 5.73 0.00 0.00 3.41
3727 4149 1.790755 TCACGCGCTGAAAATACACT 58.209 45.000 5.73 0.00 0.00 3.55
3729 4151 4.331443 ACATAATCACGCGCTGAAAATACA 59.669 37.500 5.73 0.00 30.60 2.29
3730 4152 4.666176 CACATAATCACGCGCTGAAAATAC 59.334 41.667 5.73 0.00 30.60 1.89
3816 4251 4.053469 TGAGGCGATCACGATGAAAATA 57.947 40.909 0.00 0.00 42.66 1.40
3854 4289 6.629128 TGCAGTTTCTTTGATTCTTTTGTCA 58.371 32.000 0.00 0.00 0.00 3.58
3857 4292 8.823818 AGATTTGCAGTTTCTTTGATTCTTTTG 58.176 29.630 0.00 0.00 0.00 2.44
3858 4293 8.953368 AGATTTGCAGTTTCTTTGATTCTTTT 57.047 26.923 0.00 0.00 0.00 2.27
3863 4298 8.496707 AAACAAGATTTGCAGTTTCTTTGATT 57.503 26.923 5.43 0.00 28.81 2.57
3866 4301 6.253298 TCGAAACAAGATTTGCAGTTTCTTTG 59.747 34.615 18.92 9.56 44.55 2.77
3867 4302 6.253512 GTCGAAACAAGATTTGCAGTTTCTTT 59.746 34.615 18.92 2.97 44.55 2.52
3878 4313 5.519722 AGCAAATTCGTCGAAACAAGATTT 58.480 33.333 12.40 4.06 0.00 2.17
3884 4319 3.303725 CCTTGAGCAAATTCGTCGAAACA 60.304 43.478 12.40 3.52 0.00 2.83
3920 4355 6.098679 TCTGTAGTTCTACTCGACTGACTAC 58.901 44.000 10.65 0.00 0.00 2.73
3943 4378 7.960793 ACTACGTAGTTCAACATGCTAAATTC 58.039 34.615 22.45 0.00 37.78 2.17
4004 4440 5.311265 TGCAGAACTCATTTGAGATTCAGT 58.689 37.500 14.29 0.00 44.74 3.41
4006 4442 5.048504 GGTTGCAGAACTCATTTGAGATTCA 60.049 40.000 14.29 2.61 44.74 2.57
4007 4443 5.048504 TGGTTGCAGAACTCATTTGAGATTC 60.049 40.000 14.29 12.65 44.74 2.52
4030 4480 7.087409 TGTATCCAGAGCAAAATTGTATGTG 57.913 36.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.