Multiple sequence alignment - TraesCS6A01G246900

Loading Multiple Alignment...

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 TraesCS6A01G246900 chr6A 100.000 2896 0 0 1 2896 457682489 457685384 0.000000e+00 5349.0
1 TraesCS6A01G246900 chr6A 100.000 281 0 0 3274 3554 457685762 457686042 1.460000e-143 520.0
2 TraesCS6A01G246900 chr6A 90.000 270 27 0 163 432 607984239 607984508 2.030000e-92 350.0
3 TraesCS6A01G246900 chr6D 95.765 2456 87 8 445 2896 320225515 320227957 0.000000e+00 3943.0
4 TraesCS6A01G246900 chr6D 93.972 282 16 1 3274 3554 320227999 320228280 3.280000e-115 425.0
5 TraesCS6A01G246900 chr6B 95.265 2471 97 9 430 2893 502487080 502484623 0.000000e+00 3897.0
6 TraesCS6A01G246900 chr6B 93.594 281 17 1 3275 3554 502484579 502484299 5.490000e-113 418.0
7 TraesCS6A01G246900 chr6B 84.247 146 21 2 1 146 87040573 87040430 1.330000e-29 141.0
8 TraesCS6A01G246900 chr3B 88.727 275 31 0 164 438 327046363 327046637 1.580000e-88 337.0
9 TraesCS6A01G246900 chr3A 89.394 264 28 0 167 430 385436490 385436227 2.040000e-87 333.0
10 TraesCS6A01G246900 chr3A 87.636 275 33 1 161 434 10313287 10313561 5.730000e-83 318.0
11 TraesCS6A01G246900 chr7A 89.394 264 27 1 167 430 669771032 669770770 7.350000e-87 331.0
12 TraesCS6A01G246900 chr7A 83.893 149 17 1 2 143 33427733 33427881 6.190000e-28 135.0
13 TraesCS6A01G246900 chr5B 89.057 265 27 2 167 430 94680426 94680689 9.510000e-86 327.0
14 TraesCS6A01G246900 chr5B 84.314 153 17 3 1 146 465823379 465823531 3.700000e-30 143.0
15 TraesCS6A01G246900 chr5B 84.564 149 16 1 2 143 24677890 24678038 1.330000e-29 141.0
16 TraesCS6A01G246900 chr5B 83.562 146 17 3 8 146 7561074 7561219 2.880000e-26 130.0
17 TraesCS6A01G246900 chr4A 88.433 268 31 0 165 432 173721623 173721890 1.230000e-84 324.0
18 TraesCS6A01G246900 chr4A 87.636 275 32 2 157 430 200056296 200056023 5.730000e-83 318.0
19 TraesCS6A01G246900 chr1A 87.868 272 33 0 165 436 564178823 564179094 1.590000e-83 320.0
20 TraesCS6A01G246900 chr4B 84.967 153 16 1 1 146 17484165 17484013 7.950000e-32 148.0
21 TraesCS6A01G246900 chr4B 100.000 28 0 0 582 609 262409843 262409816 6.000000e-03 52.8
22 TraesCS6A01G246900 chr5A 84.667 150 16 1 1 143 53144031 53144180 3.700000e-30 143.0
23 TraesCS6A01G246900 chr7B 83.893 149 17 1 2 143 17663575 17663723 6.190000e-28 135.0
24 TraesCS6A01G246900 chr5D 82.051 156 18 6 1 148 56559268 56559115 1.340000e-24 124.0


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 TraesCS6A01G246900 chr6A 457682489 457686042 3553 False 2934.5 5349 100.0000 1 3554 2 chr6A.!!$F2 3553
1 TraesCS6A01G246900 chr6D 320225515 320228280 2765 False 2184.0 3943 94.8685 445 3554 2 chr6D.!!$F1 3109
2 TraesCS6A01G246900 chr6B 502484299 502487080 2781 True 2157.5 3897 94.4295 430 3554 2 chr6B.!!$R2 3124

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
184 185 0.253160 AAGGCTGGTCATAGTGGGGA 60.253 55.0 0.00 0.00 0.0 4.81 F
185 186 0.692419 AGGCTGGTCATAGTGGGGAG 60.692 60.0 0.00 0.00 0.0 4.30 F
1951 1955 0.184211 TGATCTGGACATGGCATGGG 59.816 55.0 29.49 16.55 33.6 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1074 1078 0.179156 CAGCAATCACCGCATTCCAC 60.179 55.0 0.00 0.00 0.00 4.02 R
1998 2002 0.473755 TACCGTACCCAGCGAGGATA 59.526 55.0 1.68 0.00 41.22 2.59 R
2822 2830 0.695347 AATATAGGGAGGCCTGCTGC 59.305 55.0 24.77 8.42 40.16 5.25 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
44 45 7.588497 AAAACTCATAAGAAAAGGCTTGTCT 57.412 32.000 14.33 14.33 0.00 3.41
45 46 7.588497 AAACTCATAAGAAAAGGCTTGTCTT 57.412 32.000 30.04 30.04 35.77 3.01
46 47 6.809630 ACTCATAAGAAAAGGCTTGTCTTC 57.190 37.500 30.86 17.17 33.70 2.87
47 48 6.538263 ACTCATAAGAAAAGGCTTGTCTTCT 58.462 36.000 30.86 21.01 33.70 2.85
48 49 7.680730 ACTCATAAGAAAAGGCTTGTCTTCTA 58.319 34.615 30.86 18.16 33.70 2.10
49 50 8.157476 ACTCATAAGAAAAGGCTTGTCTTCTAA 58.843 33.333 30.86 17.51 33.70 2.10
50 51 8.553459 TCATAAGAAAAGGCTTGTCTTCTAAG 57.447 34.615 30.86 19.93 33.70 2.18
51 52 8.375506 TCATAAGAAAAGGCTTGTCTTCTAAGA 58.624 33.333 30.86 21.45 33.70 2.10
52 53 8.663911 CATAAGAAAAGGCTTGTCTTCTAAGAG 58.336 37.037 30.86 14.53 35.32 2.85
53 54 6.426646 AGAAAAGGCTTGTCTTCTAAGAGA 57.573 37.500 14.33 0.00 35.32 3.10
54 55 6.831976 AGAAAAGGCTTGTCTTCTAAGAGAA 58.168 36.000 14.33 2.73 36.14 2.87
68 69 7.581213 TTCTAAGAGAAGACCAGAGATGATC 57.419 40.000 0.00 0.00 29.50 2.92
69 70 6.667661 TCTAAGAGAAGACCAGAGATGATCA 58.332 40.000 0.00 0.00 0.00 2.92
70 71 5.596836 AAGAGAAGACCAGAGATGATCAC 57.403 43.478 0.00 0.00 0.00 3.06
71 72 4.870636 AGAGAAGACCAGAGATGATCACT 58.129 43.478 0.00 0.00 0.00 3.41
72 73 5.271598 AGAGAAGACCAGAGATGATCACTT 58.728 41.667 0.00 0.00 0.00 3.16
73 74 6.430864 AGAGAAGACCAGAGATGATCACTTA 58.569 40.000 0.00 0.00 0.00 2.24
74 75 6.547141 AGAGAAGACCAGAGATGATCACTTAG 59.453 42.308 0.00 0.00 0.00 2.18
75 76 4.935352 AGACCAGAGATGATCACTTAGC 57.065 45.455 0.00 0.00 0.00 3.09
76 77 4.285020 AGACCAGAGATGATCACTTAGCA 58.715 43.478 0.00 0.00 0.00 3.49
77 78 4.099266 AGACCAGAGATGATCACTTAGCAC 59.901 45.833 0.00 0.00 0.00 4.40
78 79 3.771479 ACCAGAGATGATCACTTAGCACA 59.229 43.478 0.00 0.00 0.00 4.57
79 80 4.223700 ACCAGAGATGATCACTTAGCACAA 59.776 41.667 0.00 0.00 0.00 3.33
80 81 5.104610 ACCAGAGATGATCACTTAGCACAAT 60.105 40.000 0.00 0.00 0.00 2.71
81 82 6.098838 ACCAGAGATGATCACTTAGCACAATA 59.901 38.462 0.00 0.00 0.00 1.90
82 83 7.160049 CCAGAGATGATCACTTAGCACAATAT 58.840 38.462 0.00 0.00 0.00 1.28
83 84 7.117956 CCAGAGATGATCACTTAGCACAATATG 59.882 40.741 0.00 0.00 0.00 1.78
84 85 7.656542 CAGAGATGATCACTTAGCACAATATGT 59.343 37.037 0.00 0.00 0.00 2.29
85 86 7.871973 AGAGATGATCACTTAGCACAATATGTC 59.128 37.037 0.00 0.00 0.00 3.06
86 87 7.733969 AGATGATCACTTAGCACAATATGTCT 58.266 34.615 0.00 0.00 0.00 3.41
87 88 8.209584 AGATGATCACTTAGCACAATATGTCTT 58.790 33.333 0.00 0.00 0.00 3.01
88 89 9.481340 GATGATCACTTAGCACAATATGTCTTA 57.519 33.333 0.00 0.00 0.00 2.10
89 90 8.648557 TGATCACTTAGCACAATATGTCTTAC 57.351 34.615 0.00 0.00 0.00 2.34
90 91 7.710907 TGATCACTTAGCACAATATGTCTTACC 59.289 37.037 0.00 0.00 0.00 2.85
91 92 6.941857 TCACTTAGCACAATATGTCTTACCA 58.058 36.000 0.00 0.00 0.00 3.25
92 93 6.816640 TCACTTAGCACAATATGTCTTACCAC 59.183 38.462 0.00 0.00 0.00 4.16
93 94 5.810587 ACTTAGCACAATATGTCTTACCACG 59.189 40.000 0.00 0.00 0.00 4.94
94 95 4.202245 AGCACAATATGTCTTACCACGT 57.798 40.909 0.00 0.00 0.00 4.49
95 96 4.575885 AGCACAATATGTCTTACCACGTT 58.424 39.130 0.00 0.00 0.00 3.99
96 97 5.001232 AGCACAATATGTCTTACCACGTTT 58.999 37.500 0.00 0.00 0.00 3.60
97 98 5.472137 AGCACAATATGTCTTACCACGTTTT 59.528 36.000 0.00 0.00 0.00 2.43
98 99 6.651643 AGCACAATATGTCTTACCACGTTTTA 59.348 34.615 0.00 0.00 0.00 1.52
99 100 7.173562 AGCACAATATGTCTTACCACGTTTTAA 59.826 33.333 0.00 0.00 0.00 1.52
100 101 7.804129 GCACAATATGTCTTACCACGTTTTAAA 59.196 33.333 0.00 0.00 0.00 1.52
101 102 9.325150 CACAATATGTCTTACCACGTTTTAAAG 57.675 33.333 0.00 0.00 0.00 1.85
102 103 9.275398 ACAATATGTCTTACCACGTTTTAAAGA 57.725 29.630 0.00 0.00 0.00 2.52
103 104 9.537848 CAATATGTCTTACCACGTTTTAAAGAC 57.462 33.333 16.93 16.93 43.98 3.01
104 105 9.498176 AATATGTCTTACCACGTTTTAAAGACT 57.502 29.630 21.15 13.67 44.02 3.24
106 107 7.935338 TGTCTTACCACGTTTTAAAGACTAG 57.065 36.000 21.15 0.00 44.02 2.57
107 108 7.491682 TGTCTTACCACGTTTTAAAGACTAGT 58.508 34.615 21.15 0.00 44.02 2.57
108 109 7.981225 TGTCTTACCACGTTTTAAAGACTAGTT 59.019 33.333 21.15 0.00 44.02 2.24
109 110 9.463443 GTCTTACCACGTTTTAAAGACTAGTTA 57.537 33.333 16.67 0.00 41.68 2.24
110 111 9.683069 TCTTACCACGTTTTAAAGACTAGTTAG 57.317 33.333 0.00 0.00 0.00 2.34
111 112 9.468532 CTTACCACGTTTTAAAGACTAGTTAGT 57.531 33.333 0.00 0.00 39.71 2.24
112 113 9.816354 TTACCACGTTTTAAAGACTAGTTAGTT 57.184 29.630 0.00 0.00 36.50 2.24
114 115 9.987272 ACCACGTTTTAAAGACTAGTTAGTTAT 57.013 29.630 0.00 0.00 36.50 1.89
140 141 7.667575 AAAGATAAGGCTAAGAGATGACTCA 57.332 36.000 0.00 0.00 44.79 3.41
141 142 7.854166 AAGATAAGGCTAAGAGATGACTCAT 57.146 36.000 0.00 0.00 44.79 2.90
142 143 7.854166 AGATAAGGCTAAGAGATGACTCATT 57.146 36.000 0.00 0.00 44.79 2.57
143 144 8.948401 AGATAAGGCTAAGAGATGACTCATTA 57.052 34.615 0.00 0.00 44.79 1.90
144 145 9.545928 AGATAAGGCTAAGAGATGACTCATTAT 57.454 33.333 0.00 0.00 44.79 1.28
147 148 8.484214 AAGGCTAAGAGATGACTCATTATACA 57.516 34.615 0.00 0.00 44.79 2.29
148 149 8.663209 AGGCTAAGAGATGACTCATTATACAT 57.337 34.615 0.00 0.00 44.79 2.29
149 150 8.530311 AGGCTAAGAGATGACTCATTATACATG 58.470 37.037 0.00 0.00 44.79 3.21
150 151 7.277539 GGCTAAGAGATGACTCATTATACATGC 59.722 40.741 0.00 0.00 44.79 4.06
151 152 7.277539 GCTAAGAGATGACTCATTATACATGCC 59.722 40.741 0.00 0.00 44.79 4.40
152 153 6.047511 AGAGATGACTCATTATACATGCCC 57.952 41.667 0.00 0.00 44.79 5.36
153 154 5.784390 AGAGATGACTCATTATACATGCCCT 59.216 40.000 0.00 0.00 44.79 5.19
154 155 6.271857 AGAGATGACTCATTATACATGCCCTT 59.728 38.462 0.00 0.00 44.79 3.95
155 156 7.455953 AGAGATGACTCATTATACATGCCCTTA 59.544 37.037 0.00 0.00 44.79 2.69
156 157 7.619050 AGATGACTCATTATACATGCCCTTAG 58.381 38.462 0.00 0.00 0.00 2.18
157 158 6.994421 TGACTCATTATACATGCCCTTAGA 57.006 37.500 0.00 0.00 0.00 2.10
158 159 7.559335 TGACTCATTATACATGCCCTTAGAT 57.441 36.000 0.00 0.00 0.00 1.98
159 160 8.664669 TGACTCATTATACATGCCCTTAGATA 57.335 34.615 0.00 0.00 0.00 1.98
160 161 8.753133 TGACTCATTATACATGCCCTTAGATAG 58.247 37.037 0.00 0.00 0.00 2.08
161 162 7.560368 ACTCATTATACATGCCCTTAGATAGC 58.440 38.462 0.00 0.00 0.00 2.97
162 163 7.401493 ACTCATTATACATGCCCTTAGATAGCT 59.599 37.037 0.00 0.00 0.00 3.32
163 164 8.838649 TCATTATACATGCCCTTAGATAGCTA 57.161 34.615 0.00 0.00 0.00 3.32
164 165 9.439461 TCATTATACATGCCCTTAGATAGCTAT 57.561 33.333 5.76 5.76 0.00 2.97
168 169 6.552445 ACATGCCCTTAGATAGCTATAAGG 57.448 41.667 21.49 21.49 45.15 2.69
169 170 5.104735 ACATGCCCTTAGATAGCTATAAGGC 60.105 44.000 22.48 20.28 44.51 4.35
170 171 4.689062 TGCCCTTAGATAGCTATAAGGCT 58.311 43.478 22.48 12.12 44.51 4.58
171 172 4.467795 TGCCCTTAGATAGCTATAAGGCTG 59.532 45.833 22.48 14.48 44.51 4.85
172 173 4.141824 GCCCTTAGATAGCTATAAGGCTGG 60.142 50.000 22.48 13.97 44.51 4.85
173 174 5.026790 CCCTTAGATAGCTATAAGGCTGGT 58.973 45.833 22.48 0.00 44.51 4.00
174 175 5.128008 CCCTTAGATAGCTATAAGGCTGGTC 59.872 48.000 22.48 3.95 44.51 4.02
175 176 5.717178 CCTTAGATAGCTATAAGGCTGGTCA 59.283 44.000 18.25 0.00 41.10 4.02
176 177 6.382570 CCTTAGATAGCTATAAGGCTGGTCAT 59.617 42.308 18.25 0.00 41.10 3.06
177 178 7.561722 CCTTAGATAGCTATAAGGCTGGTCATA 59.438 40.741 18.25 0.00 41.10 2.15
178 179 8.526667 TTAGATAGCTATAAGGCTGGTCATAG 57.473 38.462 6.13 0.00 43.01 2.23
179 180 6.498538 AGATAGCTATAAGGCTGGTCATAGT 58.501 40.000 6.13 0.00 43.01 2.12
180 181 4.881019 AGCTATAAGGCTGGTCATAGTG 57.119 45.455 0.00 0.00 41.43 2.74
181 182 3.580458 AGCTATAAGGCTGGTCATAGTGG 59.420 47.826 0.00 0.00 41.43 4.00
182 183 3.307059 GCTATAAGGCTGGTCATAGTGGG 60.307 52.174 0.00 0.00 0.00 4.61
183 184 1.507140 TAAGGCTGGTCATAGTGGGG 58.493 55.000 0.00 0.00 0.00 4.96
184 185 0.253160 AAGGCTGGTCATAGTGGGGA 60.253 55.000 0.00 0.00 0.00 4.81
185 186 0.692419 AGGCTGGTCATAGTGGGGAG 60.692 60.000 0.00 0.00 0.00 4.30
186 187 0.983378 GGCTGGTCATAGTGGGGAGT 60.983 60.000 0.00 0.00 0.00 3.85
187 188 1.691482 GGCTGGTCATAGTGGGGAGTA 60.691 57.143 0.00 0.00 0.00 2.59
188 189 2.116238 GCTGGTCATAGTGGGGAGTAA 58.884 52.381 0.00 0.00 0.00 2.24
189 190 2.158943 GCTGGTCATAGTGGGGAGTAAC 60.159 54.545 0.00 0.00 0.00 2.50
190 191 3.375699 CTGGTCATAGTGGGGAGTAACT 58.624 50.000 0.00 0.00 0.00 2.24
191 192 3.775316 CTGGTCATAGTGGGGAGTAACTT 59.225 47.826 0.00 0.00 0.00 2.66
192 193 4.950361 TGGTCATAGTGGGGAGTAACTTA 58.050 43.478 0.00 0.00 0.00 2.24
193 194 5.535029 TGGTCATAGTGGGGAGTAACTTAT 58.465 41.667 0.00 0.00 0.00 1.73
194 195 6.685541 TGGTCATAGTGGGGAGTAACTTATA 58.314 40.000 0.00 0.00 0.00 0.98
195 196 6.552350 TGGTCATAGTGGGGAGTAACTTATAC 59.448 42.308 0.00 0.00 0.00 1.47
196 197 6.781507 GGTCATAGTGGGGAGTAACTTATACT 59.218 42.308 0.00 0.00 0.00 2.12
197 198 7.946776 GGTCATAGTGGGGAGTAACTTATACTA 59.053 40.741 0.00 0.00 0.00 1.82
198 199 9.012161 GTCATAGTGGGGAGTAACTTATACTAG 57.988 40.741 0.00 0.00 0.00 2.57
199 200 8.730948 TCATAGTGGGGAGTAACTTATACTAGT 58.269 37.037 0.00 0.00 0.00 2.57
200 201 8.794553 CATAGTGGGGAGTAACTTATACTAGTG 58.205 40.741 5.39 0.00 0.00 2.74
201 202 6.739664 AGTGGGGAGTAACTTATACTAGTGT 58.260 40.000 5.39 0.39 0.00 3.55
202 203 6.832900 AGTGGGGAGTAACTTATACTAGTGTC 59.167 42.308 5.39 0.00 0.00 3.67
203 204 6.604795 GTGGGGAGTAACTTATACTAGTGTCA 59.395 42.308 5.39 0.00 0.00 3.58
204 205 7.287235 GTGGGGAGTAACTTATACTAGTGTCAT 59.713 40.741 5.39 0.00 0.00 3.06
205 206 7.287005 TGGGGAGTAACTTATACTAGTGTCATG 59.713 40.741 5.39 0.00 0.00 3.07
206 207 7.146648 GGGAGTAACTTATACTAGTGTCATGC 58.853 42.308 5.39 0.00 0.00 4.06
207 208 7.201884 GGGAGTAACTTATACTAGTGTCATGCA 60.202 40.741 5.39 0.00 0.00 3.96
208 209 8.361139 GGAGTAACTTATACTAGTGTCATGCAT 58.639 37.037 5.39 0.00 0.00 3.96
225 226 7.588497 TCATGCATATGACACTAGTCTAAGT 57.412 36.000 6.97 0.00 45.20 2.24
226 227 8.011844 TCATGCATATGACACTAGTCTAAGTT 57.988 34.615 6.97 0.00 45.20 2.66
227 228 9.131791 TCATGCATATGACACTAGTCTAAGTTA 57.868 33.333 6.97 0.00 45.20 2.24
228 229 9.920133 CATGCATATGACACTAGTCTAAGTTAT 57.080 33.333 6.97 0.00 45.20 1.89
304 305 8.718102 TTAATAGTTTGTAGACTCATCTTGCC 57.282 34.615 0.00 0.00 36.29 4.52
305 306 4.899352 AGTTTGTAGACTCATCTTGCCT 57.101 40.909 0.00 0.00 36.29 4.75
306 307 5.234466 AGTTTGTAGACTCATCTTGCCTT 57.766 39.130 0.00 0.00 36.29 4.35
307 308 4.999950 AGTTTGTAGACTCATCTTGCCTTG 59.000 41.667 0.00 0.00 36.29 3.61
308 309 4.890158 TTGTAGACTCATCTTGCCTTGA 57.110 40.909 0.00 0.00 36.29 3.02
309 310 4.890158 TGTAGACTCATCTTGCCTTGAA 57.110 40.909 0.00 0.00 36.29 2.69
310 311 5.227569 TGTAGACTCATCTTGCCTTGAAA 57.772 39.130 0.00 0.00 36.29 2.69
311 312 5.620206 TGTAGACTCATCTTGCCTTGAAAA 58.380 37.500 0.00 0.00 36.29 2.29
312 313 6.061441 TGTAGACTCATCTTGCCTTGAAAAA 58.939 36.000 0.00 0.00 36.29 1.94
313 314 5.444663 AGACTCATCTTGCCTTGAAAAAC 57.555 39.130 0.00 0.00 0.00 2.43
314 315 4.023707 AGACTCATCTTGCCTTGAAAAACG 60.024 41.667 0.00 0.00 0.00 3.60
315 316 2.982470 CTCATCTTGCCTTGAAAAACGC 59.018 45.455 0.00 0.00 0.00 4.84
316 317 2.622942 TCATCTTGCCTTGAAAAACGCT 59.377 40.909 0.00 0.00 0.00 5.07
317 318 3.818210 TCATCTTGCCTTGAAAAACGCTA 59.182 39.130 0.00 0.00 0.00 4.26
318 319 4.458989 TCATCTTGCCTTGAAAAACGCTAT 59.541 37.500 0.00 0.00 0.00 2.97
319 320 4.159377 TCTTGCCTTGAAAAACGCTATG 57.841 40.909 0.00 0.00 0.00 2.23
320 321 3.568007 TCTTGCCTTGAAAAACGCTATGT 59.432 39.130 0.00 0.00 0.00 2.29
321 322 4.037446 TCTTGCCTTGAAAAACGCTATGTT 59.963 37.500 0.00 0.00 44.59 2.71
322 323 5.239744 TCTTGCCTTGAAAAACGCTATGTTA 59.760 36.000 0.00 0.00 40.84 2.41
323 324 5.637006 TGCCTTGAAAAACGCTATGTTAT 57.363 34.783 0.00 0.00 40.84 1.89
324 325 6.745159 TGCCTTGAAAAACGCTATGTTATA 57.255 33.333 0.00 0.00 40.84 0.98
325 326 6.781138 TGCCTTGAAAAACGCTATGTTATAG 58.219 36.000 0.00 0.00 40.84 1.31
326 327 6.373216 TGCCTTGAAAAACGCTATGTTATAGT 59.627 34.615 0.00 0.00 40.84 2.12
327 328 7.549842 TGCCTTGAAAAACGCTATGTTATAGTA 59.450 33.333 0.00 0.00 40.84 1.82
328 329 8.392612 GCCTTGAAAAACGCTATGTTATAGTAA 58.607 33.333 0.00 0.00 40.84 2.24
329 330 9.698617 CCTTGAAAAACGCTATGTTATAGTAAC 57.301 33.333 0.00 0.00 40.84 2.50
428 429 8.684520 TCTAAGTTACTTTCACTATGACTAGCC 58.315 37.037 1.94 0.00 0.00 3.93
451 452 3.708563 AAGTGTTCGGACCAATGTTTG 57.291 42.857 0.00 0.00 0.00 2.93
485 486 9.762933 TTATAACGGTTTAACTGAGTTACAACT 57.237 29.630 11.24 0.00 43.16 3.16
486 487 6.990341 AACGGTTTAACTGAGTTACAACTT 57.010 33.333 11.24 5.46 39.88 2.66
487 488 9.762933 ATAACGGTTTAACTGAGTTACAACTTA 57.237 29.630 11.24 14.89 39.88 2.24
502 503 9.439500 AGTTACAACTTACAAGTACACTCAAAA 57.561 29.630 0.00 0.00 38.57 2.44
507 508 9.490663 CAACTTACAAGTACACTCAAAAAGAAG 57.509 33.333 0.00 0.00 38.57 2.85
530 534 2.436646 AAGATCCAAGCACCCGCG 60.437 61.111 0.00 0.00 45.49 6.46
620 624 1.078426 CAAGAACGCGATCCCCCTT 60.078 57.895 15.93 0.00 0.00 3.95
676 680 3.892104 TAACGTCCGGCCACCTCCT 62.892 63.158 2.24 0.00 0.00 3.69
711 715 1.751927 CCCCTCTTCATGCTGCACC 60.752 63.158 3.57 0.00 0.00 5.01
812 816 1.977544 CCTCCGCTCCTATACCGGG 60.978 68.421 6.32 0.00 42.18 5.73
1074 1078 2.353839 AACCGTTCGGTCGTGTCG 60.354 61.111 17.19 0.00 37.57 4.35
1164 1168 2.282180 GTTGGTGATGGTGCCGGT 60.282 61.111 1.90 0.00 0.00 5.28
1179 1183 3.645975 GGTGTTGACCGTGCCACG 61.646 66.667 10.95 10.95 42.11 4.94
1191 1195 0.235665 GTGCCACGATTGTGTCTGTG 59.764 55.000 12.19 0.00 44.92 3.66
1809 1813 0.323178 CACTTGCAAGCATCCTCCCT 60.323 55.000 26.27 0.04 0.00 4.20
1817 1821 1.302033 GCATCCTCCCTGCGTATGG 60.302 63.158 0.00 0.00 0.00 2.74
1844 1848 1.294659 GCGGACCTGAGACAAGCAAG 61.295 60.000 0.00 0.00 0.00 4.01
1898 1902 1.202302 TCTTCGGAGCACATCGATCAC 60.202 52.381 0.00 0.00 35.25 3.06
1951 1955 0.184211 TGATCTGGACATGGCATGGG 59.816 55.000 29.49 16.55 33.60 4.00
1998 2002 0.185901 ATGTTGTTGCCTGGACCACT 59.814 50.000 0.00 0.00 0.00 4.00
2025 2029 1.669049 CTGGGTACGGTATGCACGGA 61.669 60.000 0.00 0.00 35.23 4.69
2055 2059 4.645535 GAACTGCCATCCTGCTATATGAA 58.354 43.478 0.00 0.00 0.00 2.57
2057 2061 3.392285 ACTGCCATCCTGCTATATGAACA 59.608 43.478 0.00 0.00 0.00 3.18
2072 2076 1.168714 GAACAGATGGTGGAGTTGGC 58.831 55.000 0.00 0.00 0.00 4.52
2094 2098 2.654912 GAAGCCGAACACCGTGACG 61.655 63.158 5.28 10.22 36.31 4.35
2098 2102 1.589461 CCGAACACCGTGACGTTCA 60.589 57.895 5.28 0.00 41.28 3.18
2215 2219 0.965866 CGAGCACTACCTGTCCCTGA 60.966 60.000 0.00 0.00 0.00 3.86
2224 2228 1.114627 CCTGTCCCTGATCGACATGA 58.885 55.000 0.00 0.00 39.43 3.07
2260 2264 1.383248 ATCAAGGAGGCCTACCGCT 60.383 57.895 12.85 2.40 42.76 5.52
2286 2290 2.880268 CAAAGATATGCCATTCGAGCCA 59.120 45.455 0.00 0.00 0.00 4.75
2298 2302 2.485677 CGAGCCAAGTACCTCGGTA 58.514 57.895 10.36 0.00 45.20 4.02
2388 2392 0.603707 TGTTTGAGCTTGAGCCGGAG 60.604 55.000 5.05 0.00 43.38 4.63
2402 2406 4.515404 GGAGAACACCGGGAATCG 57.485 61.111 6.32 0.00 38.88 3.34
2406 2410 1.203052 GAGAACACCGGGAATCGTGTA 59.797 52.381 6.32 0.00 34.50 2.90
2458 2462 4.405680 ACAGATGGAACGATGTTCAGGATA 59.594 41.667 11.39 0.00 0.00 2.59
2461 2465 4.336889 TGGAACGATGTTCAGGATATCC 57.663 45.455 14.41 14.41 0.00 2.59
2479 2483 3.281727 TCCGGAAAATGATGGGAAGAG 57.718 47.619 0.00 0.00 0.00 2.85
2484 2488 3.053320 GGAAAATGATGGGAAGAGAGGGT 60.053 47.826 0.00 0.00 0.00 4.34
2521 2525 2.093658 GGATCTAGTTTGGTCGAGGCAA 60.094 50.000 0.00 0.00 0.00 4.52
2573 2577 2.996621 AGAATGTAAGTCTTGCACTCGC 59.003 45.455 5.43 0.00 38.70 5.03
2582 2586 1.405463 TCTTGCACTCGCGTCAGATAT 59.595 47.619 5.77 0.00 42.97 1.63
2593 2597 4.443063 TCGCGTCAGATATTATCAAAACGG 59.557 41.667 5.77 12.64 33.93 4.44
2688 2693 3.735240 TGTTTTGATGCTGCAACGATTTC 59.265 39.130 6.36 0.00 0.00 2.17
2738 2743 2.098298 GTGGTAGCGCGCATGTTG 59.902 61.111 35.10 0.00 0.00 3.33
2804 2812 1.368268 TTGGTCAAAAGCCCCTCCCT 61.368 55.000 0.00 0.00 0.00 4.20
2822 2830 1.371337 CTGGACGTGGTGGCATCATG 61.371 60.000 18.21 18.21 0.00 3.07
3316 3324 3.748568 CGAGAAAGGAAGGAAGGAAACAG 59.251 47.826 0.00 0.00 0.00 3.16
3342 3350 2.991250 AGCATCAACCATGGTGAGTAC 58.009 47.619 20.60 8.76 41.89 2.73
3346 3354 1.977854 TCAACCATGGTGAGTACAGCT 59.022 47.619 20.60 0.00 43.81 4.24
3360 3368 4.826556 AGTACAGCTCAACCTCATTCTTC 58.173 43.478 0.00 0.00 0.00 2.87
3418 3427 4.481463 GGTGTGTGTTAACATGTTATGGC 58.519 43.478 18.69 12.32 38.92 4.40
3420 3429 3.168193 GTGTGTTAACATGTTATGGCGC 58.832 45.455 18.69 16.87 38.92 6.53
3421 3430 2.162608 TGTGTTAACATGTTATGGCGCC 59.837 45.455 22.73 22.73 33.60 6.53
3432 3441 2.196997 TATGGCGCCTCCTTGTTGCT 62.197 55.000 29.70 1.76 35.26 3.91
3449 3458 1.207377 GCTAGTCGAATTCCGCGTCC 61.207 60.000 4.92 0.00 38.37 4.79
3468 3477 2.404186 GGAATGGCCGTTTCCGACC 61.404 63.158 18.52 8.76 37.10 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 8.011844 AGACAAGCCTTTTCTTATGAGTTTTT 57.988 30.769 0.00 0.00 0.00 1.94
20 21 7.588497 AGACAAGCCTTTTCTTATGAGTTTT 57.412 32.000 0.00 0.00 0.00 2.43
21 22 7.503902 AGAAGACAAGCCTTTTCTTATGAGTTT 59.496 33.333 5.86 0.00 29.54 2.66
22 23 7.001073 AGAAGACAAGCCTTTTCTTATGAGTT 58.999 34.615 5.86 0.00 29.54 3.01
23 24 6.538263 AGAAGACAAGCCTTTTCTTATGAGT 58.462 36.000 5.86 0.00 29.54 3.41
24 25 8.553459 TTAGAAGACAAGCCTTTTCTTATGAG 57.447 34.615 10.02 0.00 32.54 2.90
25 26 8.375506 TCTTAGAAGACAAGCCTTTTCTTATGA 58.624 33.333 10.02 2.36 32.54 2.15
26 27 8.553459 TCTTAGAAGACAAGCCTTTTCTTATG 57.447 34.615 10.02 0.00 32.54 1.90
27 28 8.598041 TCTCTTAGAAGACAAGCCTTTTCTTAT 58.402 33.333 5.86 5.86 32.54 1.73
28 29 7.963532 TCTCTTAGAAGACAAGCCTTTTCTTA 58.036 34.615 5.86 0.00 32.54 2.10
29 30 6.831976 TCTCTTAGAAGACAAGCCTTTTCTT 58.168 36.000 5.57 5.57 32.54 2.52
30 31 6.426646 TCTCTTAGAAGACAAGCCTTTTCT 57.573 37.500 0.00 0.00 34.51 2.52
44 45 7.068103 GTGATCATCTCTGGTCTTCTCTTAGAA 59.932 40.741 0.00 0.00 33.37 2.10
45 46 6.545666 GTGATCATCTCTGGTCTTCTCTTAGA 59.454 42.308 0.00 0.00 33.37 2.10
46 47 6.547141 AGTGATCATCTCTGGTCTTCTCTTAG 59.453 42.308 0.00 0.00 33.37 2.18
47 48 6.430864 AGTGATCATCTCTGGTCTTCTCTTA 58.569 40.000 0.00 0.00 33.37 2.10
48 49 5.271598 AGTGATCATCTCTGGTCTTCTCTT 58.728 41.667 0.00 0.00 33.37 2.85
49 50 4.870636 AGTGATCATCTCTGGTCTTCTCT 58.129 43.478 0.00 0.00 33.37 3.10
50 51 5.596836 AAGTGATCATCTCTGGTCTTCTC 57.403 43.478 0.00 0.00 33.37 2.87
51 52 5.068987 GCTAAGTGATCATCTCTGGTCTTCT 59.931 44.000 0.00 0.00 33.37 2.85
52 53 5.163468 TGCTAAGTGATCATCTCTGGTCTTC 60.163 44.000 0.00 0.00 33.37 2.87
53 54 4.713814 TGCTAAGTGATCATCTCTGGTCTT 59.286 41.667 0.00 0.00 33.37 3.01
54 55 4.099266 GTGCTAAGTGATCATCTCTGGTCT 59.901 45.833 0.00 0.00 33.37 3.85
55 56 4.142071 TGTGCTAAGTGATCATCTCTGGTC 60.142 45.833 0.00 0.00 32.76 4.02
56 57 3.771479 TGTGCTAAGTGATCATCTCTGGT 59.229 43.478 0.00 0.00 0.00 4.00
57 58 4.397481 TGTGCTAAGTGATCATCTCTGG 57.603 45.455 0.00 0.00 0.00 3.86
58 59 7.656542 ACATATTGTGCTAAGTGATCATCTCTG 59.343 37.037 0.00 0.00 0.00 3.35
59 60 7.733969 ACATATTGTGCTAAGTGATCATCTCT 58.266 34.615 0.00 0.00 0.00 3.10
60 61 7.871973 AGACATATTGTGCTAAGTGATCATCTC 59.128 37.037 0.00 0.00 0.00 2.75
61 62 7.733969 AGACATATTGTGCTAAGTGATCATCT 58.266 34.615 0.00 0.00 0.00 2.90
62 63 7.959689 AGACATATTGTGCTAAGTGATCATC 57.040 36.000 0.00 0.00 0.00 2.92
63 64 9.265901 GTAAGACATATTGTGCTAAGTGATCAT 57.734 33.333 0.00 0.00 0.00 2.45
64 65 7.710907 GGTAAGACATATTGTGCTAAGTGATCA 59.289 37.037 0.00 0.00 0.00 2.92
65 66 7.710907 TGGTAAGACATATTGTGCTAAGTGATC 59.289 37.037 0.00 0.00 0.00 2.92
66 67 7.495934 GTGGTAAGACATATTGTGCTAAGTGAT 59.504 37.037 0.00 0.00 0.00 3.06
67 68 6.816640 GTGGTAAGACATATTGTGCTAAGTGA 59.183 38.462 0.00 0.00 0.00 3.41
68 69 6.237835 CGTGGTAAGACATATTGTGCTAAGTG 60.238 42.308 0.00 0.00 0.00 3.16
69 70 5.810587 CGTGGTAAGACATATTGTGCTAAGT 59.189 40.000 0.00 0.00 0.00 2.24
70 71 5.810587 ACGTGGTAAGACATATTGTGCTAAG 59.189 40.000 0.00 0.00 0.00 2.18
71 72 5.726397 ACGTGGTAAGACATATTGTGCTAA 58.274 37.500 0.00 0.00 0.00 3.09
72 73 5.333299 ACGTGGTAAGACATATTGTGCTA 57.667 39.130 0.00 0.00 0.00 3.49
73 74 4.202245 ACGTGGTAAGACATATTGTGCT 57.798 40.909 0.00 0.00 0.00 4.40
74 75 4.939509 AACGTGGTAAGACATATTGTGC 57.060 40.909 0.00 0.00 0.00 4.57
75 76 9.325150 CTTTAAAACGTGGTAAGACATATTGTG 57.675 33.333 0.00 0.00 0.00 3.33
76 77 9.275398 TCTTTAAAACGTGGTAAGACATATTGT 57.725 29.630 0.00 0.00 0.00 2.71
77 78 9.537848 GTCTTTAAAACGTGGTAAGACATATTG 57.462 33.333 19.62 0.00 42.51 1.90
78 79 9.498176 AGTCTTTAAAACGTGGTAAGACATATT 57.502 29.630 23.37 9.51 44.35 1.28
80 81 9.630098 CTAGTCTTTAAAACGTGGTAAGACATA 57.370 33.333 23.37 15.76 44.35 2.29
81 82 8.146412 ACTAGTCTTTAAAACGTGGTAAGACAT 58.854 33.333 23.37 15.59 44.35 3.06
82 83 7.491682 ACTAGTCTTTAAAACGTGGTAAGACA 58.508 34.615 23.37 14.26 44.35 3.41
83 84 7.936950 ACTAGTCTTTAAAACGTGGTAAGAC 57.063 36.000 18.06 18.06 43.01 3.01
84 85 9.683069 CTAACTAGTCTTTAAAACGTGGTAAGA 57.317 33.333 0.00 0.00 0.00 2.10
85 86 9.468532 ACTAACTAGTCTTTAAAACGTGGTAAG 57.531 33.333 0.00 0.00 0.00 2.34
86 87 9.816354 AACTAACTAGTCTTTAAAACGTGGTAA 57.184 29.630 0.00 0.00 34.99 2.85
88 89 9.987272 ATAACTAACTAGTCTTTAAAACGTGGT 57.013 29.630 0.00 0.00 34.99 4.16
114 115 9.201989 TGAGTCATCTCTTAGCCTTATCTTTAA 57.798 33.333 0.00 0.00 40.98 1.52
115 116 8.768501 TGAGTCATCTCTTAGCCTTATCTTTA 57.231 34.615 0.00 0.00 40.98 1.85
116 117 7.667575 TGAGTCATCTCTTAGCCTTATCTTT 57.332 36.000 0.00 0.00 40.98 2.52
117 118 7.854166 ATGAGTCATCTCTTAGCCTTATCTT 57.146 36.000 0.00 0.00 40.98 2.40
118 119 7.854166 AATGAGTCATCTCTTAGCCTTATCT 57.146 36.000 5.98 0.00 40.98 1.98
121 122 9.588096 TGTATAATGAGTCATCTCTTAGCCTTA 57.412 33.333 5.98 0.00 40.98 2.69
122 123 8.484214 TGTATAATGAGTCATCTCTTAGCCTT 57.516 34.615 5.98 0.00 40.98 4.35
123 124 8.530311 CATGTATAATGAGTCATCTCTTAGCCT 58.470 37.037 5.98 0.00 40.98 4.58
124 125 7.277539 GCATGTATAATGAGTCATCTCTTAGCC 59.722 40.741 5.98 0.00 40.98 3.93
125 126 7.277539 GGCATGTATAATGAGTCATCTCTTAGC 59.722 40.741 5.98 6.00 40.98 3.09
126 127 7.763528 GGGCATGTATAATGAGTCATCTCTTAG 59.236 40.741 5.98 0.00 40.98 2.18
127 128 7.455953 AGGGCATGTATAATGAGTCATCTCTTA 59.544 37.037 5.98 0.00 40.98 2.10
128 129 6.271857 AGGGCATGTATAATGAGTCATCTCTT 59.728 38.462 5.98 0.00 40.98 2.85
129 130 5.784390 AGGGCATGTATAATGAGTCATCTCT 59.216 40.000 5.98 0.00 40.98 3.10
130 131 6.047511 AGGGCATGTATAATGAGTCATCTC 57.952 41.667 5.98 0.00 40.79 2.75
131 132 6.445451 AAGGGCATGTATAATGAGTCATCT 57.555 37.500 5.98 0.00 0.00 2.90
132 133 7.615403 TCTAAGGGCATGTATAATGAGTCATC 58.385 38.462 5.98 0.00 0.00 2.92
133 134 7.559335 TCTAAGGGCATGTATAATGAGTCAT 57.441 36.000 0.00 0.00 0.00 3.06
134 135 6.994421 TCTAAGGGCATGTATAATGAGTCA 57.006 37.500 0.00 0.00 0.00 3.41
135 136 7.708752 GCTATCTAAGGGCATGTATAATGAGTC 59.291 40.741 0.00 0.00 0.00 3.36
136 137 7.401493 AGCTATCTAAGGGCATGTATAATGAGT 59.599 37.037 0.00 0.00 0.00 3.41
137 138 7.790027 AGCTATCTAAGGGCATGTATAATGAG 58.210 38.462 0.00 0.00 0.00 2.90
138 139 7.739995 AGCTATCTAAGGGCATGTATAATGA 57.260 36.000 0.00 0.00 0.00 2.57
142 143 9.368416 CCTTATAGCTATCTAAGGGCATGTATA 57.632 37.037 20.98 0.00 40.13 1.47
143 144 7.202047 GCCTTATAGCTATCTAAGGGCATGTAT 60.202 40.741 26.30 0.00 42.80 2.29
144 145 6.098409 GCCTTATAGCTATCTAAGGGCATGTA 59.902 42.308 26.30 0.00 42.80 2.29
145 146 5.104735 GCCTTATAGCTATCTAAGGGCATGT 60.105 44.000 26.30 0.00 42.80 3.21
146 147 5.130145 AGCCTTATAGCTATCTAAGGGCATG 59.870 44.000 26.30 9.75 42.70 4.06
147 148 5.130145 CAGCCTTATAGCTATCTAAGGGCAT 59.870 44.000 26.30 12.65 42.61 4.40
148 149 4.467795 CAGCCTTATAGCTATCTAAGGGCA 59.532 45.833 26.30 1.75 42.61 5.36
149 150 4.141824 CCAGCCTTATAGCTATCTAAGGGC 60.142 50.000 26.30 21.82 42.61 5.19
150 151 5.026790 ACCAGCCTTATAGCTATCTAAGGG 58.973 45.833 26.30 16.98 42.61 3.95
151 152 5.717178 TGACCAGCCTTATAGCTATCTAAGG 59.283 44.000 23.15 23.15 42.61 2.69
152 153 6.842437 TGACCAGCCTTATAGCTATCTAAG 57.158 41.667 10.16 9.26 42.61 2.18
153 154 8.116669 ACTATGACCAGCCTTATAGCTATCTAA 58.883 37.037 10.16 0.00 42.61 2.10
154 155 7.558081 CACTATGACCAGCCTTATAGCTATCTA 59.442 40.741 10.16 0.00 42.61 1.98
155 156 6.379703 CACTATGACCAGCCTTATAGCTATCT 59.620 42.308 10.16 0.00 42.61 1.98
156 157 6.406400 CCACTATGACCAGCCTTATAGCTATC 60.406 46.154 10.16 0.00 42.61 2.08
157 158 5.423610 CCACTATGACCAGCCTTATAGCTAT 59.576 44.000 11.77 11.77 42.61 2.97
158 159 4.772624 CCACTATGACCAGCCTTATAGCTA 59.227 45.833 0.00 0.00 42.61 3.32
159 160 3.580458 CCACTATGACCAGCCTTATAGCT 59.420 47.826 0.00 0.00 46.45 3.32
160 161 3.307059 CCCACTATGACCAGCCTTATAGC 60.307 52.174 0.00 0.00 0.00 2.97
161 162 3.261897 CCCCACTATGACCAGCCTTATAG 59.738 52.174 0.00 0.00 0.00 1.31
162 163 3.116512 TCCCCACTATGACCAGCCTTATA 60.117 47.826 0.00 0.00 0.00 0.98
163 164 2.057922 CCCCACTATGACCAGCCTTAT 58.942 52.381 0.00 0.00 0.00 1.73
164 165 1.009060 TCCCCACTATGACCAGCCTTA 59.991 52.381 0.00 0.00 0.00 2.69
165 166 0.253160 TCCCCACTATGACCAGCCTT 60.253 55.000 0.00 0.00 0.00 4.35
166 167 0.692419 CTCCCCACTATGACCAGCCT 60.692 60.000 0.00 0.00 0.00 4.58
167 168 0.983378 ACTCCCCACTATGACCAGCC 60.983 60.000 0.00 0.00 0.00 4.85
168 169 1.789523 TACTCCCCACTATGACCAGC 58.210 55.000 0.00 0.00 0.00 4.85
169 170 3.375699 AGTTACTCCCCACTATGACCAG 58.624 50.000 0.00 0.00 0.00 4.00
170 171 3.484953 AGTTACTCCCCACTATGACCA 57.515 47.619 0.00 0.00 0.00 4.02
171 172 6.781507 AGTATAAGTTACTCCCCACTATGACC 59.218 42.308 0.00 0.00 0.00 4.02
172 173 7.836479 AGTATAAGTTACTCCCCACTATGAC 57.164 40.000 0.00 0.00 0.00 3.06
173 174 8.730948 ACTAGTATAAGTTACTCCCCACTATGA 58.269 37.037 0.00 0.00 0.00 2.15
174 175 8.794553 CACTAGTATAAGTTACTCCCCACTATG 58.205 40.741 0.00 0.00 0.00 2.23
175 176 8.509441 ACACTAGTATAAGTTACTCCCCACTAT 58.491 37.037 0.00 0.00 0.00 2.12
176 177 7.876371 ACACTAGTATAAGTTACTCCCCACTA 58.124 38.462 0.00 0.00 0.00 2.74
177 178 6.739664 ACACTAGTATAAGTTACTCCCCACT 58.260 40.000 0.00 0.00 0.00 4.00
178 179 6.604795 TGACACTAGTATAAGTTACTCCCCAC 59.395 42.308 0.00 0.00 0.00 4.61
179 180 6.734532 TGACACTAGTATAAGTTACTCCCCA 58.265 40.000 0.00 0.00 0.00 4.96
180 181 7.659186 CATGACACTAGTATAAGTTACTCCCC 58.341 42.308 0.00 0.00 0.00 4.81
181 182 7.146648 GCATGACACTAGTATAAGTTACTCCC 58.853 42.308 0.00 0.00 0.00 4.30
182 183 7.713750 TGCATGACACTAGTATAAGTTACTCC 58.286 38.462 0.00 0.00 0.00 3.85
201 202 7.588497 ACTTAGACTAGTGTCATATGCATGA 57.412 36.000 10.16 0.00 45.20 3.07
202 203 9.920133 ATAACTTAGACTAGTGTCATATGCATG 57.080 33.333 10.16 0.00 45.20 4.06
278 279 9.162764 GGCAAGATGAGTCTACAAACTATTAAA 57.837 33.333 0.00 0.00 33.30 1.52
279 280 8.540388 AGGCAAGATGAGTCTACAAACTATTAA 58.460 33.333 0.00 0.00 33.30 1.40
280 281 8.079211 AGGCAAGATGAGTCTACAAACTATTA 57.921 34.615 0.00 0.00 33.30 0.98
281 282 6.951971 AGGCAAGATGAGTCTACAAACTATT 58.048 36.000 0.00 0.00 33.30 1.73
282 283 6.552445 AGGCAAGATGAGTCTACAAACTAT 57.448 37.500 0.00 0.00 33.30 2.12
283 284 6.014584 TCAAGGCAAGATGAGTCTACAAACTA 60.015 38.462 0.00 0.00 33.30 2.24
284 285 4.899352 AGGCAAGATGAGTCTACAAACT 57.101 40.909 0.00 0.00 33.30 2.66
285 286 4.997395 TCAAGGCAAGATGAGTCTACAAAC 59.003 41.667 0.00 0.00 33.30 2.93
286 287 5.227569 TCAAGGCAAGATGAGTCTACAAA 57.772 39.130 0.00 0.00 33.30 2.83
287 288 4.890158 TCAAGGCAAGATGAGTCTACAA 57.110 40.909 0.00 0.00 33.30 2.41
288 289 4.890158 TTCAAGGCAAGATGAGTCTACA 57.110 40.909 0.00 0.00 33.30 2.74
289 290 6.374578 GTTTTTCAAGGCAAGATGAGTCTAC 58.625 40.000 0.00 0.00 33.30 2.59
290 291 5.179368 CGTTTTTCAAGGCAAGATGAGTCTA 59.821 40.000 0.00 0.00 33.30 2.59
291 292 4.023707 CGTTTTTCAAGGCAAGATGAGTCT 60.024 41.667 0.00 0.00 35.82 3.24
292 293 4.222114 CGTTTTTCAAGGCAAGATGAGTC 58.778 43.478 0.00 0.00 0.00 3.36
293 294 3.550842 GCGTTTTTCAAGGCAAGATGAGT 60.551 43.478 0.00 0.00 42.35 3.41
294 295 2.982470 GCGTTTTTCAAGGCAAGATGAG 59.018 45.455 0.00 0.00 42.35 2.90
295 296 2.622942 AGCGTTTTTCAAGGCAAGATGA 59.377 40.909 2.80 0.00 44.73 2.92
296 297 3.017265 AGCGTTTTTCAAGGCAAGATG 57.983 42.857 2.80 0.00 44.73 2.90
297 298 4.218417 ACATAGCGTTTTTCAAGGCAAGAT 59.782 37.500 2.80 0.00 44.73 2.40
298 299 3.568007 ACATAGCGTTTTTCAAGGCAAGA 59.432 39.130 2.80 0.00 44.73 3.02
299 300 3.900941 ACATAGCGTTTTTCAAGGCAAG 58.099 40.909 2.80 0.00 44.73 4.01
300 301 4.314740 AACATAGCGTTTTTCAAGGCAA 57.685 36.364 2.80 0.00 44.73 4.52
301 302 5.637006 ATAACATAGCGTTTTTCAAGGCA 57.363 34.783 2.80 0.00 44.73 4.75
302 303 6.782150 ACTATAACATAGCGTTTTTCAAGGC 58.218 36.000 0.00 0.00 42.99 4.35
303 304 9.698617 GTTACTATAACATAGCGTTTTTCAAGG 57.301 33.333 0.00 0.00 39.14 3.61
402 403 8.684520 GGCTAGTCATAGTGAAAGTAACTTAGA 58.315 37.037 0.00 0.00 0.00 2.10
403 404 8.688151 AGGCTAGTCATAGTGAAAGTAACTTAG 58.312 37.037 0.00 0.00 0.00 2.18
404 405 8.591114 AGGCTAGTCATAGTGAAAGTAACTTA 57.409 34.615 0.00 0.00 0.00 2.24
405 406 7.483580 AGGCTAGTCATAGTGAAAGTAACTT 57.516 36.000 0.00 0.00 0.00 2.66
406 407 8.591114 TTAGGCTAGTCATAGTGAAAGTAACT 57.409 34.615 0.00 0.00 0.00 2.24
407 408 9.303537 CTTTAGGCTAGTCATAGTGAAAGTAAC 57.696 37.037 0.00 0.00 0.00 2.50
408 409 9.032624 ACTTTAGGCTAGTCATAGTGAAAGTAA 57.967 33.333 0.00 0.00 36.55 2.24
409 410 8.467598 CACTTTAGGCTAGTCATAGTGAAAGTA 58.532 37.037 14.65 0.00 36.38 2.24
410 411 7.038941 ACACTTTAGGCTAGTCATAGTGAAAGT 60.039 37.037 22.34 12.92 37.55 2.66
411 412 7.324178 ACACTTTAGGCTAGTCATAGTGAAAG 58.676 38.462 22.34 12.45 36.08 2.62
412 413 7.241042 ACACTTTAGGCTAGTCATAGTGAAA 57.759 36.000 22.34 3.57 36.08 2.69
413 414 6.852420 ACACTTTAGGCTAGTCATAGTGAA 57.148 37.500 22.34 0.00 36.08 3.18
414 415 6.404403 CGAACACTTTAGGCTAGTCATAGTGA 60.404 42.308 22.34 0.00 36.08 3.41
415 416 5.744345 CGAACACTTTAGGCTAGTCATAGTG 59.256 44.000 16.94 16.94 37.95 2.74
416 417 5.163540 CCGAACACTTTAGGCTAGTCATAGT 60.164 44.000 0.00 0.00 0.00 2.12
417 418 5.067413 TCCGAACACTTTAGGCTAGTCATAG 59.933 44.000 0.00 0.00 0.00 2.23
418 419 4.951715 TCCGAACACTTTAGGCTAGTCATA 59.048 41.667 0.00 0.00 0.00 2.15
419 420 3.767673 TCCGAACACTTTAGGCTAGTCAT 59.232 43.478 0.00 0.00 0.00 3.06
420 421 3.057033 GTCCGAACACTTTAGGCTAGTCA 60.057 47.826 0.00 0.00 0.00 3.41
421 422 3.509740 GTCCGAACACTTTAGGCTAGTC 58.490 50.000 0.00 0.00 0.00 2.59
422 423 2.233186 GGTCCGAACACTTTAGGCTAGT 59.767 50.000 0.00 0.00 0.00 2.57
423 424 2.232941 TGGTCCGAACACTTTAGGCTAG 59.767 50.000 0.00 0.00 0.00 3.42
424 425 2.250031 TGGTCCGAACACTTTAGGCTA 58.750 47.619 0.00 0.00 0.00 3.93
425 426 1.053424 TGGTCCGAACACTTTAGGCT 58.947 50.000 0.00 0.00 0.00 4.58
426 427 1.886886 TTGGTCCGAACACTTTAGGC 58.113 50.000 0.00 0.00 0.00 3.93
427 428 3.408634 ACATTGGTCCGAACACTTTAGG 58.591 45.455 0.00 0.00 0.00 2.69
428 429 5.212194 CAAACATTGGTCCGAACACTTTAG 58.788 41.667 0.00 0.00 0.00 1.85
482 483 8.674607 CCTTCTTTTTGAGTGTACTTGTAAGTT 58.325 33.333 2.20 0.00 40.37 2.66
483 484 8.044908 TCCTTCTTTTTGAGTGTACTTGTAAGT 58.955 33.333 2.51 2.51 42.91 2.24
484 485 8.336080 GTCCTTCTTTTTGAGTGTACTTGTAAG 58.664 37.037 0.00 0.00 0.00 2.34
485 486 7.281549 GGTCCTTCTTTTTGAGTGTACTTGTAA 59.718 37.037 0.00 0.00 0.00 2.41
486 487 6.764560 GGTCCTTCTTTTTGAGTGTACTTGTA 59.235 38.462 0.00 0.00 0.00 2.41
487 488 5.589050 GGTCCTTCTTTTTGAGTGTACTTGT 59.411 40.000 0.00 0.00 0.00 3.16
502 503 2.355209 GCTTGGATCTTCGGTCCTTCTT 60.355 50.000 0.00 0.00 36.68 2.52
507 508 0.744771 GGTGCTTGGATCTTCGGTCC 60.745 60.000 0.00 0.00 36.26 4.46
530 534 1.201429 TTCAGGAACAGAGGAGGGCC 61.201 60.000 0.00 0.00 0.00 5.80
536 540 4.653341 AGGAGTATCATTCAGGAACAGAGG 59.347 45.833 0.00 0.00 36.25 3.69
655 659 4.462280 GGTGGCCGGACGTTAGGG 62.462 72.222 5.05 4.52 0.00 3.53
676 680 0.761187 GGGATGGATGCTGCTGTAGA 59.239 55.000 0.00 0.00 0.00 2.59
731 735 3.537206 GAGCAGGTTGTGGGCGTCT 62.537 63.158 0.00 0.00 0.00 4.18
812 816 2.203480 TCCTTGTGGTGGCCAAGC 60.203 61.111 7.24 1.56 38.36 4.01
826 830 1.681327 TAAAGAGCGACGGCCTCCT 60.681 57.895 0.00 0.00 41.24 3.69
1045 1049 2.548587 GAACGGTTCTGCATCGCACG 62.549 60.000 13.49 0.00 33.79 5.34
1074 1078 0.179156 CAGCAATCACCGCATTCCAC 60.179 55.000 0.00 0.00 0.00 4.02
1164 1168 1.227704 AATCGTGGCACGGTCAACA 60.228 52.632 36.30 18.99 42.81 3.33
1179 1183 0.520404 CTGGCAGCACAGACACAATC 59.480 55.000 0.00 0.00 40.97 2.67
1210 1214 4.834496 TCTTCCAATGCTCAAATTCTTGGT 59.166 37.500 0.00 0.00 38.02 3.67
1695 1699 3.506455 TGCGACTATAACCAGAGATAGCC 59.494 47.826 0.00 0.00 0.00 3.93
1817 1821 1.066587 CTCAGGTCCGCGGATTCTC 59.933 63.158 33.58 18.48 0.00 2.87
1824 1828 2.811317 GCTTGTCTCAGGTCCGCG 60.811 66.667 0.00 0.00 0.00 6.46
1898 1902 5.445939 GCATACACATCGACTAAACCAGTTG 60.446 44.000 0.00 0.00 37.72 3.16
1935 1939 2.276409 GCCCATGCCATGTCCAGA 59.724 61.111 3.63 0.00 0.00 3.86
1951 1955 1.516603 GTAGCCCGTCGAAGAGTGC 60.517 63.158 0.00 0.00 36.95 4.40
1998 2002 0.473755 TACCGTACCCAGCGAGGATA 59.526 55.000 1.68 0.00 41.22 2.59
2055 2059 1.003355 CGCCAACTCCACCATCTGT 60.003 57.895 0.00 0.00 0.00 3.41
2057 2061 2.224159 ACCGCCAACTCCACCATCT 61.224 57.895 0.00 0.00 0.00 2.90
2132 2136 1.137086 GCTGAAGGCCTTCGTCTATCA 59.863 52.381 34.49 19.03 42.28 2.15
2194 2198 0.966370 AGGGACAGGTAGTGCTCGAC 60.966 60.000 0.00 0.00 38.81 4.20
2215 2219 1.439353 GCACGCCCAATCATGTCGAT 61.439 55.000 0.00 0.00 35.12 3.59
2224 2228 4.431131 CCTCCCAGCACGCCCAAT 62.431 66.667 0.00 0.00 0.00 3.16
2260 2264 5.049198 GCTCGAATGGCATATCTTTGATGAA 60.049 40.000 0.00 0.00 0.00 2.57
2286 2290 1.273438 ACACCCCATACCGAGGTACTT 60.273 52.381 3.83 0.00 41.55 2.24
2298 2302 2.162906 ACCCAGCAGAACACCCCAT 61.163 57.895 0.00 0.00 0.00 4.00
2368 2372 0.603707 TCCGGCTCAAGCTCAAACAG 60.604 55.000 0.00 0.00 41.70 3.16
2370 2374 0.320771 TCTCCGGCTCAAGCTCAAAC 60.321 55.000 0.00 0.00 41.70 2.93
2388 2392 1.067354 AGTACACGATTCCCGGTGTTC 60.067 52.381 0.00 0.00 43.93 3.18
2402 2406 5.701290 GCATATATGTTCCCAAGGAGTACAC 59.299 44.000 14.14 0.00 31.21 2.90
2406 2410 4.747931 GCAGCATATATGTTCCCAAGGAGT 60.748 45.833 14.14 0.00 31.21 3.85
2458 2462 3.459598 TCTCTTCCCATCATTTTCCGGAT 59.540 43.478 4.15 0.00 0.00 4.18
2461 2465 3.209410 CCTCTCTTCCCATCATTTTCCG 58.791 50.000 0.00 0.00 0.00 4.30
2479 2483 2.622436 CGGTTCTTTGATGAGACCCTC 58.378 52.381 0.00 0.00 0.00 4.30
2484 2488 3.107601 AGATCCCGGTTCTTTGATGAGA 58.892 45.455 0.00 0.00 0.00 3.27
2521 2525 1.202758 TGTTCGGCATTGTTCAGACCT 60.203 47.619 0.00 0.00 0.00 3.85
2573 2577 8.889849 AAAAACCGTTTTGATAATATCTGACG 57.110 30.769 9.98 12.84 35.58 4.35
2633 2638 7.752518 TGGGGTGGTGTATATTTACTCTTAA 57.247 36.000 0.00 0.00 0.00 1.85
2634 2639 7.348801 ACATGGGGTGGTGTATATTTACTCTTA 59.651 37.037 0.00 0.00 0.00 2.10
2646 2651 0.119561 AGGGTACATGGGGTGGTGTA 59.880 55.000 0.00 0.00 0.00 2.90
2653 2658 2.883026 TCAAAACAAGGGTACATGGGG 58.117 47.619 0.00 0.00 0.00 4.96
2688 2693 0.334676 AGACAGACCCTCCCTCAGAG 59.665 60.000 0.00 0.00 42.83 3.35
2738 2743 3.430236 CCAGAAACTTTTGTGTCCAACCC 60.430 47.826 0.00 0.00 37.38 4.11
2804 2812 1.377072 CATGATGCCACCACGTCCA 60.377 57.895 0.00 0.00 0.00 4.02
2822 2830 0.695347 AATATAGGGAGGCCTGCTGC 59.305 55.000 24.77 8.42 40.16 5.25
3316 3324 2.165030 CACCATGGTTGATGCTTTCTCC 59.835 50.000 16.84 0.00 0.00 3.71
3342 3350 2.746362 GTGGAAGAATGAGGTTGAGCTG 59.254 50.000 0.00 0.00 0.00 4.24
3360 3368 2.288395 GGTTCCTTGAACAGCATTGTGG 60.288 50.000 9.01 0.00 43.54 4.17
3393 3402 2.738587 ACATGTTAACACACACCCCA 57.261 45.000 11.22 0.00 35.03 4.96
3399 3408 3.168193 GCGCCATAACATGTTAACACAC 58.832 45.455 21.57 8.61 35.03 3.82
3418 3427 1.078759 CGACTAGCAACAAGGAGGCG 61.079 60.000 0.00 0.00 33.45 5.52
3420 3429 2.743636 TTCGACTAGCAACAAGGAGG 57.256 50.000 0.00 0.00 0.00 4.30
3421 3430 3.619038 GGAATTCGACTAGCAACAAGGAG 59.381 47.826 0.00 0.00 0.00 3.69
3432 3441 1.063006 CGGACGCGGAATTCGACTA 59.937 57.895 12.47 0.00 42.43 2.59
3463 3472 1.608590 ACTTGAGTTTGCATTGGTCGG 59.391 47.619 0.00 0.00 0.00 4.79
3468 3477 3.318839 TCCTGGAACTTGAGTTTGCATTG 59.681 43.478 0.00 0.00 38.56 2.82


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

AutoCloner maintained by Alex Coulton.