Multiple sequence alignment - TraesCS2A01G158100

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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 TraesCS2A01G158100 chr2A 100.000 1973 0 0 1 1973 105031782 105033754 0.000000e+00 3644.0
1 TraesCS2A01G158100 chr2A 100.000 1077 0 0 2297 3373 105034078 105035154 0.000000e+00 1989.0
2 TraesCS2A01G158100 chr2A 88.235 1122 116 10 861 1973 104970006 104971120 0.000000e+00 1327.0
3 TraesCS2A01G158100 chr2A 95.401 761 33 2 2613 3373 105041822 105042580 0.000000e+00 1210.0
4 TraesCS2A01G158100 chr2A 94.118 289 17 0 2324 2612 104971118 104971406 1.110000e-119 440.0
5 TraesCS2A01G158100 chr2A 92.715 151 10 1 154 303 89921032 89920882 2.040000e-52 217.0
6 TraesCS2A01G158100 chr2A 94.737 38 2 0 809 846 252088172 252088209 3.630000e-05 60.2
7 TraesCS2A01G158100 chr2B 89.643 1120 105 4 861 1973 158642454 158643569 0.000000e+00 1415.0
8 TraesCS2A01G158100 chr2B 86.151 556 70 7 1421 1973 158780761 158781312 8.060000e-166 593.0
9 TraesCS2A01G158100 chr2B 86.142 534 39 17 311 817 158779997 158780522 8.230000e-151 544.0
10 TraesCS2A01G158100 chr2B 94.810 289 15 0 2324 2612 158781310 158781598 5.130000e-123 451.0
11 TraesCS2A01G158100 chr2B 92.233 309 24 0 2304 2612 158643574 158643882 4.000000e-119 438.0
12 TraesCS2A01G158100 chr2B 88.696 115 10 2 155 266 737933928 737933814 1.630000e-28 137.0
13 TraesCS2A01G158100 chr2B 97.917 48 1 0 1 48 158779926 158779973 2.160000e-12 84.2
14 TraesCS2A01G158100 chr3A 95.916 759 31 0 2608 3366 137219974 137220732 0.000000e+00 1230.0
15 TraesCS2A01G158100 chr3A 100.000 28 0 0 818 845 711130463 711130436 6.000000e-03 52.8
16 TraesCS2A01G158100 chr5A 95.144 762 35 2 2613 3373 574020795 574020035 0.000000e+00 1201.0
17 TraesCS2A01G158100 chr5A 95.007 761 37 1 2613 3373 677268320 677267561 0.000000e+00 1194.0
18 TraesCS2A01G158100 chrUn 95.358 754 35 0 2613 3366 311926901 311927654 0.000000e+00 1199.0
19 TraesCS2A01G158100 chr4A 95.364 755 34 1 2613 3366 577027362 577028116 0.000000e+00 1199.0
20 TraesCS2A01G158100 chr4A 95.358 754 35 0 2613 3366 681088769 681088016 0.000000e+00 1199.0
21 TraesCS2A01G158100 chr7A 95.007 761 38 0 2613 3373 513395998 513396758 0.000000e+00 1195.0
22 TraesCS2A01G158100 chr7A 89.024 164 13 2 147 310 515162032 515162190 7.380000e-47 198.0
23 TraesCS2A01G158100 chr1A 95.007 761 37 1 2613 3373 512730829 512730070 0.000000e+00 1194.0
24 TraesCS2A01G158100 chr1A 90.244 41 4 0 806 846 522508139 522508179 2.000000e-03 54.7
25 TraesCS2A01G158100 chr2D 83.243 1110 136 36 890 1973 109000776 109001861 0.000000e+00 974.0
26 TraesCS2A01G158100 chr2D 83.302 1066 153 17 928 1973 109043357 109044417 0.000000e+00 959.0
27 TraesCS2A01G158100 chr2D 96.712 365 12 0 1255 1619 109107345 109107709 2.880000e-170 608.0
28 TraesCS2A01G158100 chr2D 95.139 288 14 0 2324 2611 109001859 109002146 3.970000e-124 455.0
29 TraesCS2A01G158100 chr2D 95.769 260 11 0 2353 2612 109120414 109120673 1.450000e-113 420.0
30 TraesCS2A01G158100 chr2D 96.429 224 7 1 1694 1916 109113269 109113492 5.320000e-98 368.0
31 TraesCS2A01G158100 chr2D 79.433 564 61 28 305 817 109000200 109000759 6.930000e-92 348.0
32 TraesCS2A01G158100 chr2D 90.708 226 8 3 304 522 109106391 109106610 4.260000e-74 289.0
33 TraesCS2A01G158100 chr2D 95.484 155 6 1 1 155 109106247 109106400 2.600000e-61 246.0
34 TraesCS2A01G158100 chr2D 89.209 139 15 0 2474 2612 109392189 109392327 1.240000e-39 174.0
35 TraesCS2A01G158100 chr2D 92.105 114 9 0 2358 2471 109365992 109366105 9.690000e-36 161.0
36 TraesCS2A01G158100 chr2D 92.308 91 7 0 2522 2612 109046362 109046452 2.730000e-26 130.0
37 TraesCS2A01G158100 chr2D 98.077 52 1 0 1614 1665 109113219 109113270 1.290000e-14 91.6
38 TraesCS2A01G158100 chr2D 100.000 33 0 0 814 846 574413525 574413557 1.010000e-05 62.1
39 TraesCS2A01G158100 chr2D 94.737 38 2 0 809 846 256675495 256675458 3.630000e-05 60.2
40 TraesCS2A01G158100 chr5D 94.040 151 9 0 155 305 339984512 339984362 2.620000e-56 230.0
41 TraesCS2A01G158100 chr5D 93.846 130 7 1 155 283 312056351 312056480 9.550000e-46 195.0
42 TraesCS2A01G158100 chr6A 91.333 150 12 1 155 303 446722354 446722503 1.590000e-48 204.0
43 TraesCS2A01G158100 chr6B 93.443 122 7 1 180 300 171422664 171422785 2.670000e-41 180.0
44 TraesCS2A01G158100 chr3D 87.417 151 9 3 154 303 276746871 276746730 7.490000e-37 165.0
45 TraesCS2A01G158100 chr4D 91.667 48 2 2 814 860 277415930 277415976 7.810000e-07 65.8
46 TraesCS2A01G158100 chr4D 100.000 33 0 0 814 846 173574369 173574401 1.010000e-05 62.1
47 TraesCS2A01G158100 chr5B 91.111 45 2 2 803 846 571189471 571189428 3.630000e-05 60.2
48 TraesCS2A01G158100 chr7D 86.538 52 6 1 795 846 154233668 154233618 4.700000e-04 56.5


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 TraesCS2A01G158100 chr2A 105031782 105035154 3372 False 2816.500000 3644 100.000000 1 3373 2 chr2A.!!$F4 3372
1 TraesCS2A01G158100 chr2A 105041822 105042580 758 False 1210.000000 1210 95.401000 2613 3373 1 chr2A.!!$F1 760
2 TraesCS2A01G158100 chr2A 104970006 104971406 1400 False 883.500000 1327 91.176500 861 2612 2 chr2A.!!$F3 1751
3 TraesCS2A01G158100 chr2B 158642454 158643882 1428 False 926.500000 1415 90.938000 861 2612 2 chr2B.!!$F1 1751
4 TraesCS2A01G158100 chr2B 158779926 158781598 1672 False 418.050000 593 91.255000 1 2612 4 chr2B.!!$F2 2611
5 TraesCS2A01G158100 chr3A 137219974 137220732 758 False 1230.000000 1230 95.916000 2608 3366 1 chr3A.!!$F1 758
6 TraesCS2A01G158100 chr5A 574020035 574020795 760 True 1201.000000 1201 95.144000 2613 3373 1 chr5A.!!$R1 760
7 TraesCS2A01G158100 chr5A 677267561 677268320 759 True 1194.000000 1194 95.007000 2613 3373 1 chr5A.!!$R2 760
8 TraesCS2A01G158100 chrUn 311926901 311927654 753 False 1199.000000 1199 95.358000 2613 3366 1 chrUn.!!$F1 753
9 TraesCS2A01G158100 chr4A 577027362 577028116 754 False 1199.000000 1199 95.364000 2613 3366 1 chr4A.!!$F1 753
10 TraesCS2A01G158100 chr4A 681088016 681088769 753 True 1199.000000 1199 95.358000 2613 3366 1 chr4A.!!$R1 753
11 TraesCS2A01G158100 chr7A 513395998 513396758 760 False 1195.000000 1195 95.007000 2613 3373 1 chr7A.!!$F1 760
12 TraesCS2A01G158100 chr1A 512730070 512730829 759 True 1194.000000 1194 95.007000 2613 3373 1 chr1A.!!$R1 760
13 TraesCS2A01G158100 chr2D 109000200 109002146 1946 False 592.333333 974 85.938333 305 2611 3 chr2D.!!$F5 2306
14 TraesCS2A01G158100 chr2D 109043357 109046452 3095 False 544.500000 959 87.805000 928 2612 2 chr2D.!!$F6 1684
15 TraesCS2A01G158100 chr2D 109106247 109107709 1462 False 381.000000 608 94.301333 1 1619 3 chr2D.!!$F7 1618

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
201 202 0.102481 ACACGATATCCAGCGGACAC 59.898 55.0 0.0 0.0 38.05 3.67 F
289 290 0.109919 TCGTCTGGAATCGTCGTGTG 60.110 55.0 0.0 0.0 0.00 3.82 F
290 291 0.386858 CGTCTGGAATCGTCGTGTGT 60.387 55.0 0.0 0.0 0.00 3.72 F
1755 2114 0.759959 TGACGGTGCCTCCTTGTTAA 59.240 50.0 0.0 0.0 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2297 0.368907 GTACGCACAGGCACGTATTG 59.631 55.000 0.00 0.0 45.46 1.90 R
1943 2302 1.065102 AGTATAGTACGCACAGGCACG 59.935 52.381 0.00 0.0 41.24 5.34 R
2296 2657 3.953612 ACATTTTCATCAGGTGTGTGTGT 59.046 39.130 0.00 0.0 0.00 3.72 R
3094 5178 2.167075 TGATCGATCGCATCTGGCATAT 59.833 45.455 20.03 0.0 45.17 1.78 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
50 51 2.691409 TTCCGAGCCCAATAGTTCAG 57.309 50.000 0.00 0.00 0.00 3.02
81 82 1.903860 AGTACAATACAGGCCCGTGAA 59.096 47.619 0.49 0.00 0.00 3.18
149 150 4.068282 CTGCGCTGCACGTGTCTG 62.068 66.667 18.38 13.80 46.11 3.51
150 151 4.889856 TGCGCTGCACGTGTCTGT 62.890 61.111 18.38 0.00 46.11 3.41
151 152 3.640000 GCGCTGCACGTGTCTGTT 61.640 61.111 18.38 0.00 46.11 3.16
152 153 2.546321 CGCTGCACGTGTCTGTTC 59.454 61.111 18.38 0.00 36.87 3.18
153 154 2.939022 GCTGCACGTGTCTGTTCC 59.061 61.111 18.38 0.00 0.00 3.62
154 155 2.607892 GCTGCACGTGTCTGTTCCC 61.608 63.158 18.38 0.00 0.00 3.97
155 156 2.279851 TGCACGTGTCTGTTCCCG 60.280 61.111 18.38 0.00 0.00 5.14
156 157 2.028484 GCACGTGTCTGTTCCCGA 59.972 61.111 18.38 0.00 0.00 5.14
157 158 1.593209 GCACGTGTCTGTTCCCGAA 60.593 57.895 18.38 0.00 0.00 4.30
158 159 1.155424 GCACGTGTCTGTTCCCGAAA 61.155 55.000 18.38 0.00 0.00 3.46
159 160 0.580104 CACGTGTCTGTTCCCGAAAC 59.420 55.000 7.58 0.00 38.43 2.78
160 161 0.462789 ACGTGTCTGTTCCCGAAACT 59.537 50.000 0.00 0.00 38.76 2.66
161 162 0.859232 CGTGTCTGTTCCCGAAACTG 59.141 55.000 2.95 2.73 38.76 3.16
162 163 0.586802 GTGTCTGTTCCCGAAACTGC 59.413 55.000 2.95 0.00 38.76 4.40
163 164 0.468226 TGTCTGTTCCCGAAACTGCT 59.532 50.000 2.95 0.00 38.76 4.24
164 165 1.149148 GTCTGTTCCCGAAACTGCTC 58.851 55.000 2.95 0.00 38.76 4.26
165 166 1.048601 TCTGTTCCCGAAACTGCTCT 58.951 50.000 2.95 0.00 38.76 4.09
166 167 2.029290 GTCTGTTCCCGAAACTGCTCTA 60.029 50.000 2.95 0.00 38.76 2.43
167 168 2.832129 TCTGTTCCCGAAACTGCTCTAT 59.168 45.455 2.95 0.00 38.76 1.98
168 169 4.021229 TCTGTTCCCGAAACTGCTCTATA 58.979 43.478 2.95 0.00 38.76 1.31
169 170 4.098044 TCTGTTCCCGAAACTGCTCTATAG 59.902 45.833 0.00 0.00 38.76 1.31
170 171 4.021229 TGTTCCCGAAACTGCTCTATAGA 58.979 43.478 1.69 1.69 38.76 1.98
171 172 4.142227 TGTTCCCGAAACTGCTCTATAGAC 60.142 45.833 0.00 0.00 38.76 2.59
172 173 2.617308 TCCCGAAACTGCTCTATAGACG 59.383 50.000 0.00 0.00 0.00 4.18
173 174 2.617308 CCCGAAACTGCTCTATAGACGA 59.383 50.000 0.00 0.00 0.00 4.20
174 175 3.548415 CCCGAAACTGCTCTATAGACGAC 60.548 52.174 0.00 0.00 0.00 4.34
175 176 3.064958 CCGAAACTGCTCTATAGACGACA 59.935 47.826 0.00 0.00 0.00 4.35
176 177 4.029704 CGAAACTGCTCTATAGACGACAC 58.970 47.826 0.00 0.00 0.00 3.67
177 178 4.201832 CGAAACTGCTCTATAGACGACACT 60.202 45.833 0.00 0.00 0.00 3.55
178 179 5.642686 GAAACTGCTCTATAGACGACACTT 58.357 41.667 0.00 0.00 0.00 3.16
179 180 4.886247 ACTGCTCTATAGACGACACTTC 57.114 45.455 0.00 0.00 0.00 3.01
180 181 4.262617 ACTGCTCTATAGACGACACTTCA 58.737 43.478 0.00 0.00 0.00 3.02
181 182 4.884744 ACTGCTCTATAGACGACACTTCAT 59.115 41.667 0.00 0.00 0.00 2.57
182 183 6.056236 ACTGCTCTATAGACGACACTTCATA 58.944 40.000 0.00 0.00 0.00 2.15
183 184 6.017770 ACTGCTCTATAGACGACACTTCATAC 60.018 42.308 0.00 0.00 0.00 2.39
184 185 5.820947 TGCTCTATAGACGACACTTCATACA 59.179 40.000 0.00 0.00 0.00 2.29
185 186 6.137415 GCTCTATAGACGACACTTCATACAC 58.863 44.000 0.00 0.00 0.00 2.90
186 187 6.283161 TCTATAGACGACACTTCATACACG 57.717 41.667 0.00 0.00 0.00 4.49
187 188 6.044682 TCTATAGACGACACTTCATACACGA 58.955 40.000 0.00 0.00 0.00 4.35
188 189 5.752892 ATAGACGACACTTCATACACGAT 57.247 39.130 0.00 0.00 0.00 3.73
189 190 6.856135 ATAGACGACACTTCATACACGATA 57.144 37.500 0.00 0.00 0.00 2.92
190 191 5.752892 AGACGACACTTCATACACGATAT 57.247 39.130 0.00 0.00 0.00 1.63
191 192 5.749620 AGACGACACTTCATACACGATATC 58.250 41.667 0.00 0.00 0.00 1.63
192 193 4.856664 ACGACACTTCATACACGATATCC 58.143 43.478 0.00 0.00 0.00 2.59
193 194 4.337274 ACGACACTTCATACACGATATCCA 59.663 41.667 0.00 0.00 0.00 3.41
194 195 4.912187 CGACACTTCATACACGATATCCAG 59.088 45.833 0.00 0.00 0.00 3.86
195 196 4.621991 ACACTTCATACACGATATCCAGC 58.378 43.478 0.00 0.00 0.00 4.85
196 197 3.670523 CACTTCATACACGATATCCAGCG 59.329 47.826 0.00 0.00 40.09 5.18
197 198 3.245797 CTTCATACACGATATCCAGCGG 58.754 50.000 0.00 0.00 38.05 5.52
198 199 2.510613 TCATACACGATATCCAGCGGA 58.489 47.619 0.00 0.00 38.05 5.54
199 200 2.228103 TCATACACGATATCCAGCGGAC 59.772 50.000 0.00 0.00 38.05 4.79
200 201 1.682740 TACACGATATCCAGCGGACA 58.317 50.000 0.00 0.00 38.05 4.02
201 202 0.102481 ACACGATATCCAGCGGACAC 59.898 55.000 0.00 0.00 38.05 3.67
202 203 0.385751 CACGATATCCAGCGGACACT 59.614 55.000 0.00 0.00 38.05 3.55
203 204 1.112113 ACGATATCCAGCGGACACTT 58.888 50.000 0.00 0.00 38.05 3.16
204 205 1.480954 ACGATATCCAGCGGACACTTT 59.519 47.619 0.00 0.00 38.05 2.66
205 206 2.691526 ACGATATCCAGCGGACACTTTA 59.308 45.455 0.00 0.00 38.05 1.85
206 207 3.321111 ACGATATCCAGCGGACACTTTAT 59.679 43.478 0.00 0.00 38.05 1.40
207 208 3.921021 CGATATCCAGCGGACACTTTATC 59.079 47.826 0.00 3.27 32.98 1.75
208 209 2.622064 ATCCAGCGGACACTTTATCC 57.378 50.000 0.00 0.00 32.98 2.59
209 210 1.271856 TCCAGCGGACACTTTATCCA 58.728 50.000 0.00 0.00 35.83 3.41
210 211 1.626321 TCCAGCGGACACTTTATCCAA 59.374 47.619 0.00 0.00 35.83 3.53
211 212 1.737793 CCAGCGGACACTTTATCCAAC 59.262 52.381 0.00 0.00 35.83 3.77
212 213 1.393539 CAGCGGACACTTTATCCAACG 59.606 52.381 0.00 0.00 35.83 4.10
213 214 0.725117 GCGGACACTTTATCCAACGG 59.275 55.000 0.00 0.00 35.83 4.44
214 215 1.942586 GCGGACACTTTATCCAACGGT 60.943 52.381 0.00 0.00 35.83 4.83
215 216 1.730064 CGGACACTTTATCCAACGGTG 59.270 52.381 0.00 0.00 35.83 4.94
232 233 2.046507 GGACCTGTCCTGCTGCTG 60.047 66.667 9.11 0.00 46.16 4.41
233 234 2.046507 GACCTGTCCTGCTGCTGG 60.047 66.667 18.44 18.44 0.00 4.85
234 235 3.618780 GACCTGTCCTGCTGCTGGG 62.619 68.421 23.07 14.41 0.00 4.45
236 237 4.340246 CTGTCCTGCTGCTGGGCA 62.340 66.667 27.55 27.55 40.15 5.36
237 238 4.648626 TGTCCTGCTGCTGGGCAC 62.649 66.667 26.12 17.23 37.29 5.01
238 239 4.341783 GTCCTGCTGCTGGGCACT 62.342 66.667 23.06 0.00 37.29 4.40
239 240 4.340246 TCCTGCTGCTGGGCACTG 62.340 66.667 23.07 0.00 37.29 3.66
245 246 4.289101 TGCTGGGCACTGCATGGT 62.289 61.111 17.43 0.00 45.06 3.55
246 247 3.755628 GCTGGGCACTGCATGGTG 61.756 66.667 13.60 1.82 40.80 4.17
247 248 2.282674 CTGGGCACTGCATGGTGT 60.283 61.111 2.82 0.00 39.21 4.16
248 249 2.598099 TGGGCACTGCATGGTGTG 60.598 61.111 2.82 3.92 39.21 3.82
249 250 2.282391 GGGCACTGCATGGTGTGA 60.282 61.111 7.92 0.00 39.21 3.58
250 251 1.679977 GGGCACTGCATGGTGTGAT 60.680 57.895 7.92 0.00 39.21 3.06
251 252 1.660560 GGGCACTGCATGGTGTGATC 61.661 60.000 7.92 0.00 39.21 2.92
252 253 0.679002 GGCACTGCATGGTGTGATCT 60.679 55.000 7.92 0.00 39.21 2.75
253 254 1.171308 GCACTGCATGGTGTGATCTT 58.829 50.000 7.92 0.00 39.21 2.40
254 255 1.131883 GCACTGCATGGTGTGATCTTC 59.868 52.381 7.92 0.00 39.21 2.87
255 256 2.708051 CACTGCATGGTGTGATCTTCT 58.292 47.619 0.00 0.00 36.38 2.85
256 257 2.418976 CACTGCATGGTGTGATCTTCTG 59.581 50.000 0.00 0.00 36.38 3.02
257 258 1.400846 CTGCATGGTGTGATCTTCTGC 59.599 52.381 0.00 0.00 0.00 4.26
258 259 1.271488 TGCATGGTGTGATCTTCTGCA 60.271 47.619 0.00 0.00 35.93 4.41
259 260 2.022195 GCATGGTGTGATCTTCTGCAT 58.978 47.619 0.00 0.00 0.00 3.96
260 261 2.033049 GCATGGTGTGATCTTCTGCATC 59.967 50.000 0.00 0.00 0.00 3.91
261 262 2.014335 TGGTGTGATCTTCTGCATCG 57.986 50.000 0.00 0.00 0.00 3.84
262 263 1.276138 TGGTGTGATCTTCTGCATCGT 59.724 47.619 0.00 0.00 0.00 3.73
263 264 1.929836 GGTGTGATCTTCTGCATCGTC 59.070 52.381 0.00 0.00 0.00 4.20
264 265 2.417924 GGTGTGATCTTCTGCATCGTCT 60.418 50.000 0.00 0.00 0.00 4.18
265 266 3.257393 GTGTGATCTTCTGCATCGTCTT 58.743 45.455 0.00 0.00 0.00 3.01
266 267 3.305629 GTGTGATCTTCTGCATCGTCTTC 59.694 47.826 0.00 0.00 0.00 2.87
267 268 3.056607 TGTGATCTTCTGCATCGTCTTCA 60.057 43.478 0.00 0.00 0.00 3.02
268 269 3.928992 GTGATCTTCTGCATCGTCTTCAA 59.071 43.478 0.00 0.00 0.00 2.69
269 270 4.389992 GTGATCTTCTGCATCGTCTTCAAA 59.610 41.667 0.00 0.00 0.00 2.69
270 271 5.064452 GTGATCTTCTGCATCGTCTTCAAAT 59.936 40.000 0.00 0.00 0.00 2.32
271 272 5.292834 TGATCTTCTGCATCGTCTTCAAATC 59.707 40.000 0.00 0.00 0.00 2.17
272 273 3.614176 TCTTCTGCATCGTCTTCAAATCG 59.386 43.478 0.00 0.00 0.00 3.34
273 274 2.959516 TCTGCATCGTCTTCAAATCGT 58.040 42.857 0.00 0.00 0.00 3.73
274 275 2.923655 TCTGCATCGTCTTCAAATCGTC 59.076 45.455 0.00 0.00 0.00 4.20
275 276 2.926200 CTGCATCGTCTTCAAATCGTCT 59.074 45.455 0.00 0.00 0.00 4.18
276 277 2.667969 TGCATCGTCTTCAAATCGTCTG 59.332 45.455 0.00 0.00 0.00 3.51
277 278 2.029728 GCATCGTCTTCAAATCGTCTGG 59.970 50.000 0.00 0.00 0.00 3.86
278 279 3.511699 CATCGTCTTCAAATCGTCTGGA 58.488 45.455 0.00 0.00 0.00 3.86
279 280 3.653539 TCGTCTTCAAATCGTCTGGAA 57.346 42.857 0.00 0.00 0.00 3.53
280 281 4.188247 TCGTCTTCAAATCGTCTGGAAT 57.812 40.909 0.00 0.00 0.00 3.01
281 282 4.174009 TCGTCTTCAAATCGTCTGGAATC 58.826 43.478 0.00 0.00 0.00 2.52
282 283 3.000674 CGTCTTCAAATCGTCTGGAATCG 60.001 47.826 0.00 0.00 0.00 3.34
283 284 3.927142 GTCTTCAAATCGTCTGGAATCGT 59.073 43.478 0.00 0.00 0.00 3.73
284 285 4.031878 GTCTTCAAATCGTCTGGAATCGTC 59.968 45.833 0.00 0.00 0.00 4.20
285 286 2.526077 TCAAATCGTCTGGAATCGTCG 58.474 47.619 0.00 0.00 0.00 5.12
286 287 2.094906 TCAAATCGTCTGGAATCGTCGT 60.095 45.455 0.00 0.00 0.00 4.34
287 288 1.909376 AATCGTCTGGAATCGTCGTG 58.091 50.000 0.00 0.00 0.00 4.35
288 289 0.809385 ATCGTCTGGAATCGTCGTGT 59.191 50.000 0.00 0.00 0.00 4.49
289 290 0.109919 TCGTCTGGAATCGTCGTGTG 60.110 55.000 0.00 0.00 0.00 3.82
290 291 0.386858 CGTCTGGAATCGTCGTGTGT 60.387 55.000 0.00 0.00 0.00 3.72
291 292 1.135888 CGTCTGGAATCGTCGTGTGTA 60.136 52.381 0.00 0.00 0.00 2.90
292 293 2.477357 CGTCTGGAATCGTCGTGTGTAT 60.477 50.000 0.00 0.00 0.00 2.29
293 294 3.242511 CGTCTGGAATCGTCGTGTGTATA 60.243 47.826 0.00 0.00 0.00 1.47
294 295 4.280461 GTCTGGAATCGTCGTGTGTATAG 58.720 47.826 0.00 0.00 0.00 1.31
295 296 3.043586 CTGGAATCGTCGTGTGTATAGC 58.956 50.000 0.00 0.00 0.00 2.97
296 297 2.424246 TGGAATCGTCGTGTGTATAGCA 59.576 45.455 0.00 0.00 0.00 3.49
297 298 3.043586 GGAATCGTCGTGTGTATAGCAG 58.956 50.000 0.00 0.00 0.00 4.24
298 299 2.776312 ATCGTCGTGTGTATAGCAGG 57.224 50.000 0.00 0.00 0.00 4.85
299 300 1.741528 TCGTCGTGTGTATAGCAGGA 58.258 50.000 0.00 0.00 0.00 3.86
300 301 1.399440 TCGTCGTGTGTATAGCAGGAC 59.601 52.381 14.91 14.91 43.87 3.85
301 302 1.400846 CGTCGTGTGTATAGCAGGACT 59.599 52.381 19.20 0.00 44.62 3.85
302 303 2.539142 CGTCGTGTGTATAGCAGGACTC 60.539 54.545 19.20 4.33 44.62 3.36
303 304 1.669265 TCGTGTGTATAGCAGGACTCG 59.331 52.381 0.00 0.00 0.00 4.18
323 324 1.550976 GTCTGTTCCCTTCCTCACGAT 59.449 52.381 0.00 0.00 0.00 3.73
367 374 4.597507 TGTACTGTTCTTCCCCAGATCTTT 59.402 41.667 0.00 0.00 32.93 2.52
370 377 4.019771 ACTGTTCTTCCCCAGATCTTTCTC 60.020 45.833 0.00 0.00 32.93 2.87
371 378 4.171234 TGTTCTTCCCCAGATCTTTCTCT 58.829 43.478 0.00 0.00 0.00 3.10
372 379 5.342017 TGTTCTTCCCCAGATCTTTCTCTA 58.658 41.667 0.00 0.00 0.00 2.43
385 395 7.558444 CAGATCTTTCTCTACTACTGGTACCTT 59.442 40.741 14.36 2.42 0.00 3.50
525 572 8.795786 TGAAGTTCAGATATTTTTGTTTTCGG 57.204 30.769 0.08 0.00 0.00 4.30
539 594 6.394025 TTGTTTTCGGCCTAGTTTATGTTT 57.606 33.333 0.00 0.00 0.00 2.83
541 596 6.807789 TGTTTTCGGCCTAGTTTATGTTTTT 58.192 32.000 0.00 0.00 0.00 1.94
574 629 5.289917 GTCTTGCTAGAGCTACTTTAGTTGC 59.710 44.000 8.02 8.02 44.91 4.17
718 784 9.679661 TCAACTGCTATTTCTAATGTTGGATTA 57.320 29.630 0.00 0.00 35.46 1.75
719 785 9.941664 CAACTGCTATTTCTAATGTTGGATTAG 57.058 33.333 0.00 0.00 33.96 1.73
720 786 9.905713 AACTGCTATTTCTAATGTTGGATTAGA 57.094 29.630 0.00 0.00 38.44 2.10
791 861 7.202526 CGTAATTTTGGTCATGGCTTATGAAT 58.797 34.615 0.00 0.00 46.85 2.57
798 868 7.716799 TGGTCATGGCTTATGAATAACTTTT 57.283 32.000 0.00 0.00 46.85 2.27
824 894 7.545489 AGCATACACTAGTTTTGTACTACTCC 58.455 38.462 0.00 0.00 38.33 3.85
825 895 6.755607 GCATACACTAGTTTTGTACTACTCCC 59.244 42.308 0.00 0.00 38.33 4.30
826 896 7.363617 GCATACACTAGTTTTGTACTACTCCCT 60.364 40.741 0.00 0.00 38.33 4.20
827 897 6.587206 ACACTAGTTTTGTACTACTCCCTC 57.413 41.667 0.00 0.00 38.33 4.30
828 898 6.313324 ACACTAGTTTTGTACTACTCCCTCT 58.687 40.000 0.00 0.00 38.33 3.69
829 899 6.208994 ACACTAGTTTTGTACTACTCCCTCTG 59.791 42.308 0.00 0.00 38.33 3.35
830 900 6.208994 CACTAGTTTTGTACTACTCCCTCTGT 59.791 42.308 0.00 0.00 38.33 3.41
831 901 5.725325 AGTTTTGTACTACTCCCTCTGTC 57.275 43.478 0.00 0.00 34.56 3.51
832 902 4.527427 AGTTTTGTACTACTCCCTCTGTCC 59.473 45.833 0.00 0.00 34.56 4.02
833 903 2.822707 TGTACTACTCCCTCTGTCCC 57.177 55.000 0.00 0.00 0.00 4.46
834 904 1.997791 TGTACTACTCCCTCTGTCCCA 59.002 52.381 0.00 0.00 0.00 4.37
835 905 2.585900 TGTACTACTCCCTCTGTCCCAT 59.414 50.000 0.00 0.00 0.00 4.00
836 906 3.789840 TGTACTACTCCCTCTGTCCCATA 59.210 47.826 0.00 0.00 0.00 2.74
837 907 4.231195 TGTACTACTCCCTCTGTCCCATAA 59.769 45.833 0.00 0.00 0.00 1.90
838 908 4.561254 ACTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
839 909 5.681494 ACTACTCCCTCTGTCCCATAATA 57.319 43.478 0.00 0.00 0.00 0.98
840 910 6.234404 ACTACTCCCTCTGTCCCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
841 911 7.358255 ACTACTCCCTCTGTCCCATAATATA 57.642 40.000 0.00 0.00 0.00 0.86
842 912 7.776745 ACTACTCCCTCTGTCCCATAATATAA 58.223 38.462 0.00 0.00 0.00 0.98
843 913 7.896496 ACTACTCCCTCTGTCCCATAATATAAG 59.104 40.741 0.00 0.00 0.00 1.73
844 914 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
845 915 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
846 916 7.116089 TCCCTCTGTCCCATAATATAAGAGA 57.884 40.000 0.00 0.00 33.14 3.10
847 917 7.185565 TCCCTCTGTCCCATAATATAAGAGAG 58.814 42.308 0.00 0.00 33.14 3.20
848 918 7.019659 TCCCTCTGTCCCATAATATAAGAGAGA 59.980 40.741 0.00 3.33 33.14 3.10
849 919 7.123547 CCCTCTGTCCCATAATATAAGAGAGAC 59.876 44.444 0.00 0.00 33.14 3.36
850 920 7.893302 CCTCTGTCCCATAATATAAGAGAGACT 59.107 40.741 0.00 0.00 33.14 3.24
851 921 8.642935 TCTGTCCCATAATATAAGAGAGACTG 57.357 38.462 0.00 0.00 0.00 3.51
852 922 8.448816 TCTGTCCCATAATATAAGAGAGACTGA 58.551 37.037 0.00 0.00 0.00 3.41
853 923 8.642935 TGTCCCATAATATAAGAGAGACTGAG 57.357 38.462 0.00 0.00 0.00 3.35
854 924 7.671819 TGTCCCATAATATAAGAGAGACTGAGG 59.328 40.741 0.00 0.00 0.00 3.86
855 925 7.123547 GTCCCATAATATAAGAGAGACTGAGGG 59.876 44.444 0.00 0.00 0.00 4.30
856 926 7.019659 TCCCATAATATAAGAGAGACTGAGGGA 59.980 40.741 0.00 0.00 35.82 4.20
857 927 7.341769 CCCATAATATAAGAGAGACTGAGGGAG 59.658 44.444 0.00 0.00 0.00 4.30
858 928 7.893302 CCATAATATAAGAGAGACTGAGGGAGT 59.107 40.741 0.00 0.00 37.76 3.85
859 929 9.967451 CATAATATAAGAGAGACTGAGGGAGTA 57.033 37.037 0.00 0.00 33.83 2.59
865 935 5.531198 AGAGAGACTGAGGGAGTAGTACTA 58.469 45.833 1.88 0.00 33.83 1.82
880 956 7.808856 GGAGTAGTACTATGTTATGCTTGCTAC 59.191 40.741 5.75 0.00 0.00 3.58
885 961 9.078990 AGTACTATGTTATGCTTGCTACTGATA 57.921 33.333 0.00 0.00 0.00 2.15
913 989 2.803386 CCTGTGTGTGTATGCGTGTTTA 59.197 45.455 0.00 0.00 0.00 2.01
989 1066 1.338484 TGCTGTCTGTTGCTCATCCTC 60.338 52.381 0.00 0.00 0.00 3.71
1016 1093 2.415893 GCGAAATGGTGATCCTTTGTGG 60.416 50.000 0.00 0.00 32.50 4.17
1051 1128 5.335976 GCTCCTTCGGTTCATTCTGAATTTT 60.336 40.000 0.00 0.00 38.79 1.82
1078 1155 2.420547 GGATGGCTATCACTCAACAGCA 60.421 50.000 12.54 0.00 35.69 4.41
1099 1176 3.511146 CACCAGAATGCCTTACCATTTGT 59.489 43.478 0.00 0.00 35.67 2.83
1142 1219 3.633525 AGAAAGCAAAACAGACATCAGCA 59.366 39.130 0.00 0.00 0.00 4.41
1165 1330 3.196007 CGATTACCTTCGCAAAAAGCA 57.804 42.857 0.00 0.00 46.13 3.91
1171 1336 2.119457 CCTTCGCAAAAAGCACTTCAC 58.881 47.619 0.00 0.00 46.13 3.18
1243 1415 7.976175 AGCTAAATTATTAGTTTTGCCTGCTTC 59.024 33.333 12.13 0.00 40.59 3.86
1291 1627 8.477984 TTGCAAGCAATATATTCTTTGGAAAC 57.522 30.769 16.45 5.56 34.90 2.78
1382 1725 3.685550 GCTCTTAATGCCCTAGCCTTCAA 60.686 47.826 0.00 0.00 38.69 2.69
1445 1803 7.333528 TGCCCTCTGTTATGATGTAAATTTC 57.666 36.000 0.00 0.00 0.00 2.17
1575 1934 1.112916 TCGTCTTCTGCCCACAGTGA 61.113 55.000 0.62 0.00 44.77 3.41
1627 1986 8.206867 CCCTGATGAGATACTATCAAAACTCAA 58.793 37.037 0.00 0.00 37.79 3.02
1655 2014 6.095860 TGGAAGAATCTGATGCCTTTTACATG 59.904 38.462 6.90 0.00 0.00 3.21
1667 2026 3.624861 CCTTTTACATGCTAGAGCTGTGG 59.375 47.826 13.49 0.00 42.66 4.17
1672 2031 2.005451 CATGCTAGAGCTGTGGACAAC 58.995 52.381 0.00 0.00 42.66 3.32
1707 2066 9.823647 TTAGTTCCTCTTTGCTAGATAAGAATG 57.176 33.333 0.00 0.00 30.55 2.67
1714 2073 3.384668 TGCTAGATAAGAATGCTGCGAC 58.615 45.455 0.00 0.00 0.00 5.19
1723 2082 4.672587 AGAATGCTGCGACCTTAATCTA 57.327 40.909 0.00 0.00 0.00 1.98
1744 2103 2.671396 ACTTAATCGATGTTGACGGTGC 59.329 45.455 0.00 0.00 0.00 5.01
1755 2114 0.759959 TGACGGTGCCTCCTTGTTAA 59.240 50.000 0.00 0.00 0.00 2.01
1902 2261 2.044123 AATCTGGATCGGCCTTGAAC 57.956 50.000 0.00 0.00 37.63 3.18
1927 2286 5.187186 CAGGTACACTATCCACCTAGTTGTT 59.813 44.000 0.00 0.00 40.77 2.83
1933 2292 5.120208 CACTATCCACCTAGTTGTTTGTTCG 59.880 44.000 0.00 0.00 29.41 3.95
1935 2294 1.877443 CCACCTAGTTGTTTGTTCGGG 59.123 52.381 0.00 0.00 0.00 5.14
1938 2297 0.879090 CTAGTTGTTTGTTCGGGGCC 59.121 55.000 0.00 0.00 0.00 5.80
1943 2302 1.249407 TGTTTGTTCGGGGCCAATAC 58.751 50.000 4.39 0.00 0.00 1.89
1952 2311 3.187058 GGCCAATACGTGCCTGTG 58.813 61.111 7.35 0.00 44.46 3.66
1954 2313 2.784596 CCAATACGTGCCTGTGCG 59.215 61.111 0.00 0.00 41.78 5.34
2328 2689 5.840693 ACCTGATGAAAATGTTCTTCCCTTT 59.159 36.000 8.61 0.00 37.20 3.11
2329 2690 6.161381 CCTGATGAAAATGTTCTTCCCTTTG 58.839 40.000 8.61 0.00 37.20 2.77
2432 2793 2.836981 ACACCTGAAGATCTTGAGGGAG 59.163 50.000 35.09 29.24 46.34 4.30
2459 2820 3.003480 GAGCTCAAGTTCAGCGGTTTAT 58.997 45.455 9.40 0.00 42.14 1.40
2470 2831 4.808558 TCAGCGGTTTATAGTACACGTTT 58.191 39.130 0.00 0.00 0.00 3.60
2480 2841 3.173668 AGTACACGTTTGACAAGCTCA 57.826 42.857 0.00 0.00 0.00 4.26
2668 4751 7.508977 AGTTGAGGGATAAATTTTGGTTCTTGA 59.491 33.333 0.00 0.00 0.00 3.02
2699 4782 7.923888 TCAAGTTCTTCATAATGATAAGCAGC 58.076 34.615 0.00 0.00 0.00 5.25
2849 4932 0.613260 TGATTCGACACAAGGGGAGG 59.387 55.000 0.00 0.00 0.00 4.30
2975 5059 3.996363 GTGGTAACGGTGGTAAAAGGTAG 59.004 47.826 0.00 0.00 42.51 3.18
3048 5132 5.798434 GCAACGGAAAAGTAAATAAGCGAAT 59.202 36.000 0.00 0.00 0.00 3.34
3093 5177 3.055530 GGCAATGGATCGGTGATAGAGAT 60.056 47.826 0.00 0.00 0.00 2.75
3094 5178 4.160439 GGCAATGGATCGGTGATAGAGATA 59.840 45.833 0.00 0.00 0.00 1.98
3101 5185 5.536538 GGATCGGTGATAGAGATATATGCCA 59.463 44.000 0.00 0.00 0.00 4.92
3147 5231 5.030147 TCATAACCTAGGGTGACACAGAAT 58.970 41.667 10.48 0.00 35.34 2.40
3200 5284 7.979537 GGCATGTATTCCGAATATAGTCATACA 59.020 37.037 11.78 11.78 31.90 2.29
3332 5416 4.022068 ACCAAAGCATTAACACATGGTGAG 60.022 41.667 2.98 0.00 38.22 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.636206 GCTCGGAAAATGTACTCCATCTTT 59.364 41.667 0.00 0.00 31.75 2.52
50 51 6.704937 GGCCTGTATTGTACTGTATTTCCTAC 59.295 42.308 0.00 0.00 0.00 3.18
107 108 0.169672 GCCGTGCTCTACTTACGACA 59.830 55.000 0.00 0.00 40.01 4.35
147 148 2.743636 TAGAGCAGTTTCGGGAACAG 57.256 50.000 1.33 0.00 40.84 3.16
148 149 4.021229 TCTATAGAGCAGTTTCGGGAACA 58.979 43.478 1.33 0.00 40.84 3.18
149 150 4.361420 GTCTATAGAGCAGTTTCGGGAAC 58.639 47.826 1.64 0.00 38.58 3.62
150 151 3.066342 CGTCTATAGAGCAGTTTCGGGAA 59.934 47.826 1.64 0.00 0.00 3.97
151 152 2.617308 CGTCTATAGAGCAGTTTCGGGA 59.383 50.000 1.64 0.00 0.00 5.14
152 153 2.617308 TCGTCTATAGAGCAGTTTCGGG 59.383 50.000 1.64 0.00 0.00 5.14
153 154 3.064958 TGTCGTCTATAGAGCAGTTTCGG 59.935 47.826 1.64 0.00 0.00 4.30
154 155 4.029704 GTGTCGTCTATAGAGCAGTTTCG 58.970 47.826 1.64 1.50 0.00 3.46
155 156 5.238006 AGTGTCGTCTATAGAGCAGTTTC 57.762 43.478 1.64 0.00 0.00 2.78
156 157 5.183331 TGAAGTGTCGTCTATAGAGCAGTTT 59.817 40.000 16.57 9.15 0.00 2.66
157 158 4.700692 TGAAGTGTCGTCTATAGAGCAGTT 59.299 41.667 15.92 15.92 0.00 3.16
158 159 4.262617 TGAAGTGTCGTCTATAGAGCAGT 58.737 43.478 1.64 3.37 0.00 4.40
159 160 4.884458 TGAAGTGTCGTCTATAGAGCAG 57.116 45.455 1.64 0.00 0.00 4.24
160 161 5.820947 TGTATGAAGTGTCGTCTATAGAGCA 59.179 40.000 1.64 0.20 0.00 4.26
161 162 6.137415 GTGTATGAAGTGTCGTCTATAGAGC 58.863 44.000 1.64 0.00 0.00 4.09
162 163 6.200475 TCGTGTATGAAGTGTCGTCTATAGAG 59.800 42.308 1.64 0.00 0.00 2.43
163 164 6.044682 TCGTGTATGAAGTGTCGTCTATAGA 58.955 40.000 0.00 0.00 0.00 1.98
164 165 6.283161 TCGTGTATGAAGTGTCGTCTATAG 57.717 41.667 0.00 0.00 0.00 1.31
165 166 6.856135 ATCGTGTATGAAGTGTCGTCTATA 57.144 37.500 0.00 0.00 0.00 1.31
166 167 5.752892 ATCGTGTATGAAGTGTCGTCTAT 57.247 39.130 0.00 0.00 0.00 1.98
167 168 6.073385 GGATATCGTGTATGAAGTGTCGTCTA 60.073 42.308 0.00 0.00 0.00 2.59
168 169 5.277876 GGATATCGTGTATGAAGTGTCGTCT 60.278 44.000 0.00 0.00 0.00 4.18
169 170 4.910456 GGATATCGTGTATGAAGTGTCGTC 59.090 45.833 0.00 0.00 0.00 4.20
170 171 4.337274 TGGATATCGTGTATGAAGTGTCGT 59.663 41.667 0.00 0.00 0.00 4.34
171 172 4.855531 TGGATATCGTGTATGAAGTGTCG 58.144 43.478 0.00 0.00 0.00 4.35
172 173 4.681942 GCTGGATATCGTGTATGAAGTGTC 59.318 45.833 0.00 0.00 0.00 3.67
173 174 4.621991 GCTGGATATCGTGTATGAAGTGT 58.378 43.478 0.00 0.00 0.00 3.55
174 175 3.670523 CGCTGGATATCGTGTATGAAGTG 59.329 47.826 0.00 0.00 0.00 3.16
175 176 3.305403 CCGCTGGATATCGTGTATGAAGT 60.305 47.826 0.00 0.00 0.00 3.01
176 177 3.057526 TCCGCTGGATATCGTGTATGAAG 60.058 47.826 0.00 0.00 0.00 3.02
177 178 2.888414 TCCGCTGGATATCGTGTATGAA 59.112 45.455 0.00 0.00 0.00 2.57
178 179 2.228103 GTCCGCTGGATATCGTGTATGA 59.772 50.000 0.00 0.00 32.73 2.15
179 180 2.030274 TGTCCGCTGGATATCGTGTATG 60.030 50.000 0.00 0.00 32.73 2.39
180 181 2.030185 GTGTCCGCTGGATATCGTGTAT 60.030 50.000 0.00 0.00 32.73 2.29
181 182 1.335810 GTGTCCGCTGGATATCGTGTA 59.664 52.381 0.00 0.00 32.73 2.90
182 183 0.102481 GTGTCCGCTGGATATCGTGT 59.898 55.000 0.00 0.00 32.73 4.49
183 184 0.385751 AGTGTCCGCTGGATATCGTG 59.614 55.000 0.00 0.00 32.73 4.35
184 185 1.112113 AAGTGTCCGCTGGATATCGT 58.888 50.000 0.00 0.00 32.73 3.73
185 186 2.225068 AAAGTGTCCGCTGGATATCG 57.775 50.000 0.00 0.00 32.73 2.92
186 187 4.246458 GGATAAAGTGTCCGCTGGATATC 58.754 47.826 0.00 0.00 32.73 1.63
187 188 3.646162 TGGATAAAGTGTCCGCTGGATAT 59.354 43.478 0.67 0.00 38.64 1.63
188 189 3.035363 TGGATAAAGTGTCCGCTGGATA 58.965 45.455 0.67 0.00 38.64 2.59
189 190 1.837439 TGGATAAAGTGTCCGCTGGAT 59.163 47.619 0.67 0.00 38.64 3.41
190 191 1.271856 TGGATAAAGTGTCCGCTGGA 58.728 50.000 0.00 0.00 38.64 3.86
191 192 1.737793 GTTGGATAAAGTGTCCGCTGG 59.262 52.381 0.00 0.00 38.64 4.85
192 193 1.393539 CGTTGGATAAAGTGTCCGCTG 59.606 52.381 0.00 0.00 38.64 5.18
193 194 1.674817 CCGTTGGATAAAGTGTCCGCT 60.675 52.381 0.00 0.00 38.64 5.52
194 195 0.725117 CCGTTGGATAAAGTGTCCGC 59.275 55.000 0.00 0.00 38.64 5.54
195 196 1.730064 CACCGTTGGATAAAGTGTCCG 59.270 52.381 0.00 0.00 38.64 4.79
216 217 2.046507 CCAGCAGCAGGACAGGTC 60.047 66.667 0.00 0.00 0.00 3.85
217 218 3.644606 CCCAGCAGCAGGACAGGT 61.645 66.667 5.14 0.00 0.00 4.00
219 220 4.340246 TGCCCAGCAGCAGGACAG 62.340 66.667 5.14 0.00 38.00 3.51
220 221 4.648626 GTGCCCAGCAGCAGGACA 62.649 66.667 5.14 0.00 45.14 4.02
221 222 4.341783 AGTGCCCAGCAGCAGGAC 62.342 66.667 5.14 0.00 45.14 3.85
222 223 4.340246 CAGTGCCCAGCAGCAGGA 62.340 66.667 5.14 0.00 45.14 3.86
225 226 4.671590 ATGCAGTGCCCAGCAGCA 62.672 61.111 13.72 6.04 44.94 4.41
226 227 4.129737 CATGCAGTGCCCAGCAGC 62.130 66.667 13.72 0.00 44.94 5.25
227 228 3.449227 CCATGCAGTGCCCAGCAG 61.449 66.667 13.72 0.00 44.94 4.24
228 229 4.289101 ACCATGCAGTGCCCAGCA 62.289 61.111 13.72 0.00 45.92 4.41
229 230 3.755628 CACCATGCAGTGCCCAGC 61.756 66.667 13.72 0.00 0.00 4.85
230 231 2.282674 ACACCATGCAGTGCCCAG 60.283 61.111 13.72 3.08 41.67 4.45
231 232 2.429235 ATCACACCATGCAGTGCCCA 62.429 55.000 13.72 0.00 41.67 5.36
232 233 1.660560 GATCACACCATGCAGTGCCC 61.661 60.000 13.72 2.63 41.67 5.36
233 234 0.679002 AGATCACACCATGCAGTGCC 60.679 55.000 13.72 0.00 41.67 5.01
234 235 1.131883 GAAGATCACACCATGCAGTGC 59.868 52.381 8.58 8.58 41.67 4.40
235 236 2.418976 CAGAAGATCACACCATGCAGTG 59.581 50.000 4.64 4.64 43.65 3.66
236 237 2.708051 CAGAAGATCACACCATGCAGT 58.292 47.619 0.00 0.00 0.00 4.40
237 238 1.400846 GCAGAAGATCACACCATGCAG 59.599 52.381 0.00 0.00 32.58 4.41
238 239 1.271488 TGCAGAAGATCACACCATGCA 60.271 47.619 0.00 0.00 39.67 3.96
239 240 1.456296 TGCAGAAGATCACACCATGC 58.544 50.000 0.00 0.00 0.00 4.06
240 241 2.287103 CGATGCAGAAGATCACACCATG 59.713 50.000 0.00 0.00 0.00 3.66
241 242 2.093288 ACGATGCAGAAGATCACACCAT 60.093 45.455 0.00 0.00 0.00 3.55
242 243 1.276138 ACGATGCAGAAGATCACACCA 59.724 47.619 0.00 0.00 0.00 4.17
243 244 1.929836 GACGATGCAGAAGATCACACC 59.070 52.381 0.00 0.00 0.00 4.16
244 245 2.886081 AGACGATGCAGAAGATCACAC 58.114 47.619 0.00 0.00 0.00 3.82
245 246 3.056607 TGAAGACGATGCAGAAGATCACA 60.057 43.478 0.00 0.00 0.00 3.58
246 247 3.515630 TGAAGACGATGCAGAAGATCAC 58.484 45.455 0.00 0.00 0.00 3.06
247 248 3.874392 TGAAGACGATGCAGAAGATCA 57.126 42.857 0.00 0.00 0.00 2.92
248 249 5.556006 CGATTTGAAGACGATGCAGAAGATC 60.556 44.000 0.00 0.00 0.00 2.75
249 250 4.269603 CGATTTGAAGACGATGCAGAAGAT 59.730 41.667 0.00 0.00 0.00 2.40
250 251 3.614176 CGATTTGAAGACGATGCAGAAGA 59.386 43.478 0.00 0.00 0.00 2.87
251 252 3.369147 ACGATTTGAAGACGATGCAGAAG 59.631 43.478 0.00 0.00 0.00 2.85
252 253 3.325870 ACGATTTGAAGACGATGCAGAA 58.674 40.909 0.00 0.00 0.00 3.02
253 254 2.923655 GACGATTTGAAGACGATGCAGA 59.076 45.455 0.00 0.00 0.00 4.26
254 255 2.926200 AGACGATTTGAAGACGATGCAG 59.074 45.455 0.00 0.00 0.00 4.41
255 256 2.667969 CAGACGATTTGAAGACGATGCA 59.332 45.455 0.00 0.00 0.00 3.96
256 257 2.029728 CCAGACGATTTGAAGACGATGC 59.970 50.000 0.00 0.00 0.00 3.91
257 258 3.511699 TCCAGACGATTTGAAGACGATG 58.488 45.455 0.00 0.00 0.00 3.84
258 259 3.868757 TCCAGACGATTTGAAGACGAT 57.131 42.857 0.00 0.00 0.00 3.73
259 260 3.653539 TTCCAGACGATTTGAAGACGA 57.346 42.857 0.00 0.00 0.00 4.20
260 261 3.000674 CGATTCCAGACGATTTGAAGACG 60.001 47.826 0.00 0.00 0.00 4.18
261 262 3.927142 ACGATTCCAGACGATTTGAAGAC 59.073 43.478 0.00 0.00 0.00 3.01
262 263 4.174009 GACGATTCCAGACGATTTGAAGA 58.826 43.478 0.00 0.00 0.00 2.87
263 264 3.000674 CGACGATTCCAGACGATTTGAAG 60.001 47.826 0.00 0.00 0.00 3.02
264 265 2.921121 CGACGATTCCAGACGATTTGAA 59.079 45.455 0.00 0.00 0.00 2.69
265 266 2.094906 ACGACGATTCCAGACGATTTGA 60.095 45.455 0.00 0.00 0.00 2.69
266 267 2.028045 CACGACGATTCCAGACGATTTG 59.972 50.000 0.00 0.00 0.00 2.32
267 268 2.259618 CACGACGATTCCAGACGATTT 58.740 47.619 0.00 0.00 0.00 2.17
268 269 1.201647 ACACGACGATTCCAGACGATT 59.798 47.619 0.00 0.00 0.00 3.34
269 270 0.809385 ACACGACGATTCCAGACGAT 59.191 50.000 0.00 0.00 0.00 3.73
270 271 0.109919 CACACGACGATTCCAGACGA 60.110 55.000 0.00 0.00 0.00 4.20
271 272 0.386858 ACACACGACGATTCCAGACG 60.387 55.000 0.00 0.00 0.00 4.18
272 273 2.624316 TACACACGACGATTCCAGAC 57.376 50.000 0.00 0.00 0.00 3.51
273 274 3.242969 GCTATACACACGACGATTCCAGA 60.243 47.826 0.00 0.00 0.00 3.86
274 275 3.043586 GCTATACACACGACGATTCCAG 58.956 50.000 0.00 0.00 0.00 3.86
275 276 2.424246 TGCTATACACACGACGATTCCA 59.576 45.455 0.00 0.00 0.00 3.53
276 277 3.043586 CTGCTATACACACGACGATTCC 58.956 50.000 0.00 0.00 0.00 3.01
277 278 3.043586 CCTGCTATACACACGACGATTC 58.956 50.000 0.00 0.00 0.00 2.52
278 279 2.686405 TCCTGCTATACACACGACGATT 59.314 45.455 0.00 0.00 0.00 3.34
279 280 2.033049 GTCCTGCTATACACACGACGAT 59.967 50.000 0.00 0.00 0.00 3.73
280 281 1.399440 GTCCTGCTATACACACGACGA 59.601 52.381 0.00 0.00 0.00 4.20
281 282 1.400846 AGTCCTGCTATACACACGACG 59.599 52.381 0.00 0.00 31.09 5.12
282 283 2.539142 CGAGTCCTGCTATACACACGAC 60.539 54.545 0.00 0.00 0.00 4.34
283 284 1.669265 CGAGTCCTGCTATACACACGA 59.331 52.381 0.00 0.00 0.00 4.35
284 285 1.400846 ACGAGTCCTGCTATACACACG 59.599 52.381 0.00 0.00 0.00 4.49
285 286 2.683867 AGACGAGTCCTGCTATACACAC 59.316 50.000 0.00 0.00 0.00 3.82
286 287 2.683362 CAGACGAGTCCTGCTATACACA 59.317 50.000 0.00 0.00 0.00 3.72
287 288 2.683867 ACAGACGAGTCCTGCTATACAC 59.316 50.000 0.00 0.00 35.14 2.90
288 289 3.000684 ACAGACGAGTCCTGCTATACA 57.999 47.619 0.00 0.00 35.14 2.29
289 290 3.243134 GGAACAGACGAGTCCTGCTATAC 60.243 52.174 0.00 0.00 35.14 1.47
290 291 2.950309 GGAACAGACGAGTCCTGCTATA 59.050 50.000 0.00 0.00 35.14 1.31
291 292 1.751924 GGAACAGACGAGTCCTGCTAT 59.248 52.381 0.00 0.00 35.14 2.97
292 293 1.174783 GGAACAGACGAGTCCTGCTA 58.825 55.000 0.00 0.00 35.14 3.49
293 294 1.536943 GGGAACAGACGAGTCCTGCT 61.537 60.000 0.00 0.00 35.14 4.24
294 295 1.079750 GGGAACAGACGAGTCCTGC 60.080 63.158 0.00 0.00 35.14 4.85
295 296 0.969894 AAGGGAACAGACGAGTCCTG 59.030 55.000 0.00 0.00 37.64 3.86
296 297 1.258676 GAAGGGAACAGACGAGTCCT 58.741 55.000 0.00 0.00 0.00 3.85
297 298 0.246910 GGAAGGGAACAGACGAGTCC 59.753 60.000 0.00 0.00 0.00 3.85
298 299 1.202817 GAGGAAGGGAACAGACGAGTC 59.797 57.143 0.00 0.00 0.00 3.36
299 300 1.258676 GAGGAAGGGAACAGACGAGT 58.741 55.000 0.00 0.00 0.00 4.18
300 301 1.067495 GTGAGGAAGGGAACAGACGAG 60.067 57.143 0.00 0.00 0.00 4.18
301 302 0.966920 GTGAGGAAGGGAACAGACGA 59.033 55.000 0.00 0.00 0.00 4.20
302 303 0.388649 CGTGAGGAAGGGAACAGACG 60.389 60.000 0.00 0.00 0.00 4.18
303 304 0.966920 TCGTGAGGAAGGGAACAGAC 59.033 55.000 0.00 0.00 0.00 3.51
323 324 1.582968 GACGACGGCTTCAGGTACA 59.417 57.895 0.00 0.00 0.00 2.90
367 374 6.550163 AGAAACAAGGTACCAGTAGTAGAGA 58.450 40.000 15.94 0.00 0.00 3.10
370 377 6.127675 GGAGAGAAACAAGGTACCAGTAGTAG 60.128 46.154 15.94 0.00 0.00 2.57
371 378 5.713861 GGAGAGAAACAAGGTACCAGTAGTA 59.286 44.000 15.94 0.00 0.00 1.82
372 379 4.527427 GGAGAGAAACAAGGTACCAGTAGT 59.473 45.833 15.94 3.65 0.00 2.73
385 395 1.132849 TGTGGGAGAGGGAGAGAAACA 60.133 52.381 0.00 0.00 0.00 2.83
525 572 4.789784 TCGCACAAAAACATAAACTAGGC 58.210 39.130 0.00 0.00 0.00 3.93
539 594 2.135139 CTAGCAAGACACTCGCACAAA 58.865 47.619 0.00 0.00 0.00 2.83
541 596 0.958822 TCTAGCAAGACACTCGCACA 59.041 50.000 0.00 0.00 0.00 4.57
678 744 0.324614 AGTTGACATGCATCCGTGGA 59.675 50.000 0.00 0.00 32.11 4.02
718 784 5.848286 TGAACAGGGCATATTCCATATCT 57.152 39.130 0.00 0.00 0.00 1.98
719 785 5.359009 CCATGAACAGGGCATATTCCATATC 59.641 44.000 0.00 0.00 0.00 1.63
720 786 5.266788 CCATGAACAGGGCATATTCCATAT 58.733 41.667 0.00 0.00 0.00 1.78
798 868 8.680903 GGAGTAGTACAAAACTAGTGTATGCTA 58.319 37.037 2.52 0.00 43.17 3.49
829 899 7.123547 CCCTCAGTCTCTCTTATATTATGGGAC 59.876 44.444 0.00 0.00 0.00 4.46
830 900 7.019659 TCCCTCAGTCTCTCTTATATTATGGGA 59.980 40.741 0.00 0.00 34.55 4.37
831 901 7.185565 TCCCTCAGTCTCTCTTATATTATGGG 58.814 42.308 0.00 0.00 0.00 4.00
832 902 7.893302 ACTCCCTCAGTCTCTCTTATATTATGG 59.107 40.741 0.00 0.00 0.00 2.74
833 903 8.877864 ACTCCCTCAGTCTCTCTTATATTATG 57.122 38.462 0.00 0.00 0.00 1.90
835 905 9.173231 ACTACTCCCTCAGTCTCTCTTATATTA 57.827 37.037 0.00 0.00 36.43 0.98
836 906 8.052621 ACTACTCCCTCAGTCTCTCTTATATT 57.947 38.462 0.00 0.00 36.43 1.28
837 907 7.642094 ACTACTCCCTCAGTCTCTCTTATAT 57.358 40.000 0.00 0.00 36.43 0.86
838 908 7.790798 AGTACTACTCCCTCAGTCTCTCTTATA 59.209 40.741 0.00 0.00 36.43 0.98
839 909 5.987019 ACTACTCCCTCAGTCTCTCTTAT 57.013 43.478 0.00 0.00 36.43 1.73
840 910 5.965705 AGTACTACTCCCTCAGTCTCTCTTA 59.034 44.000 0.00 0.00 36.43 2.10
841 911 4.786454 AGTACTACTCCCTCAGTCTCTCTT 59.214 45.833 0.00 0.00 36.43 2.85
842 912 4.368067 AGTACTACTCCCTCAGTCTCTCT 58.632 47.826 0.00 0.00 36.43 3.10
843 913 4.765813 AGTACTACTCCCTCAGTCTCTC 57.234 50.000 0.00 0.00 36.43 3.20
844 914 5.668535 ACATAGTACTACTCCCTCAGTCTCT 59.331 44.000 4.31 0.00 36.43 3.10
845 915 5.932455 ACATAGTACTACTCCCTCAGTCTC 58.068 45.833 4.31 0.00 36.43 3.36
846 916 5.979656 ACATAGTACTACTCCCTCAGTCT 57.020 43.478 4.31 0.00 36.43 3.24
847 917 7.308710 GCATAACATAGTACTACTCCCTCAGTC 60.309 44.444 4.31 0.00 36.43 3.51
848 918 6.490721 GCATAACATAGTACTACTCCCTCAGT 59.509 42.308 4.31 0.00 39.41 3.41
849 919 6.717540 AGCATAACATAGTACTACTCCCTCAG 59.282 42.308 4.31 0.00 0.00 3.35
850 920 6.611785 AGCATAACATAGTACTACTCCCTCA 58.388 40.000 4.31 0.00 0.00 3.86
851 921 7.371936 CAAGCATAACATAGTACTACTCCCTC 58.628 42.308 4.31 0.00 0.00 4.30
852 922 6.239345 GCAAGCATAACATAGTACTACTCCCT 60.239 42.308 4.31 0.00 0.00 4.20
853 923 5.927115 GCAAGCATAACATAGTACTACTCCC 59.073 44.000 4.31 0.00 0.00 4.30
854 924 6.750148 AGCAAGCATAACATAGTACTACTCC 58.250 40.000 4.31 0.00 0.00 3.85
855 925 8.569641 AGTAGCAAGCATAACATAGTACTACTC 58.430 37.037 4.31 0.00 33.21 2.59
856 926 8.353684 CAGTAGCAAGCATAACATAGTACTACT 58.646 37.037 4.31 0.00 37.64 2.57
857 927 8.350722 TCAGTAGCAAGCATAACATAGTACTAC 58.649 37.037 4.31 0.00 0.00 2.73
858 928 8.459911 TCAGTAGCAAGCATAACATAGTACTA 57.540 34.615 4.77 4.77 0.00 1.82
859 929 7.348080 TCAGTAGCAAGCATAACATAGTACT 57.652 36.000 0.00 0.00 0.00 2.73
865 935 8.455903 AACAATATCAGTAGCAAGCATAACAT 57.544 30.769 0.00 0.00 0.00 2.71
880 956 4.326826 ACACACACAGGGAACAATATCAG 58.673 43.478 0.00 0.00 0.00 2.90
885 961 2.819608 GCATACACACACAGGGAACAAT 59.180 45.455 0.00 0.00 0.00 2.71
940 1016 8.525316 TGTTACACAAATAAGATACTCGAAGGA 58.475 33.333 0.00 0.00 0.00 3.36
989 1066 3.535561 AGGATCACCATTTCGCTGTAAG 58.464 45.455 0.00 0.00 38.94 2.34
1016 1093 3.927481 GAAGGAGCAGGGTGGCCAC 62.927 68.421 28.57 28.57 0.00 5.01
1051 1128 5.366477 TGTTGAGTGATAGCCATCCAGATAA 59.634 40.000 0.00 0.00 0.00 1.75
1078 1155 3.511146 CACAAATGGTAAGGCATTCTGGT 59.489 43.478 0.00 0.00 0.00 4.00
1099 1176 2.151202 GATGTTCCTTTCGGTTGAGCA 58.849 47.619 0.00 0.00 0.00 4.26
1164 1329 5.096169 CGAGACATACCTTGTAGTGAAGTG 58.904 45.833 0.00 0.00 39.18 3.16
1165 1330 4.765856 ACGAGACATACCTTGTAGTGAAGT 59.234 41.667 0.00 0.00 39.18 3.01
1227 1397 2.264005 TCCGAAGCAGGCAAAACTAA 57.736 45.000 0.00 0.00 0.00 2.24
1229 1399 0.883833 CATCCGAAGCAGGCAAAACT 59.116 50.000 0.00 0.00 0.00 2.66
1243 1415 4.485016 AGGAACTACTGCAAATGCATCCG 61.485 47.826 15.54 5.69 45.18 4.18
1291 1627 6.466308 TGATTTACACGATTCACTGTGAAG 57.534 37.500 25.40 16.45 40.05 3.02
1382 1725 5.123227 ACAGTACTGCTACACAACATTTGT 58.877 37.500 22.90 0.00 46.75 2.83
1575 1934 5.468409 CGCTATTGGGAAATGTTTTTGGTTT 59.532 36.000 0.00 0.00 0.00 3.27
1627 1986 6.616237 AAAAGGCATCAGATTCTTCCAATT 57.384 33.333 0.00 0.00 0.00 2.32
1655 2014 2.755655 TCTAGTTGTCCACAGCTCTAGC 59.244 50.000 0.00 0.00 38.40 3.42
1667 2026 7.457024 AGAGGAACTAAGTTCTCTAGTTGTC 57.543 40.000 6.25 3.77 41.55 3.18
1672 2031 6.930731 AGCAAAGAGGAACTAAGTTCTCTAG 58.069 40.000 0.00 0.00 41.55 2.43
1706 2065 3.887621 AAGTAGATTAAGGTCGCAGCA 57.112 42.857 0.00 0.00 0.00 4.41
1707 2066 5.117287 CGATTAAGTAGATTAAGGTCGCAGC 59.883 44.000 0.00 0.00 36.81 5.25
1714 2073 8.691727 CGTCAACATCGATTAAGTAGATTAAGG 58.308 37.037 0.00 0.00 36.81 2.69
1723 2082 2.671396 GCACCGTCAACATCGATTAAGT 59.329 45.455 0.00 0.00 0.00 2.24
1744 2103 5.181433 GCTGGTACTCTTTTTAACAAGGAGG 59.819 44.000 1.66 0.00 0.00 4.30
1755 2114 5.440610 CCCATAGATTGCTGGTACTCTTTT 58.559 41.667 0.00 0.00 0.00 2.27
1801 2160 2.420058 AGGAAGGAATTGTAAGGGCG 57.580 50.000 0.00 0.00 0.00 6.13
1805 2164 7.653311 CCACTTTGAAAAGGAAGGAATTGTAAG 59.347 37.037 7.65 0.00 40.31 2.34
1902 2261 3.912248 ACTAGGTGGATAGTGTACCTGG 58.088 50.000 5.46 5.07 44.22 4.45
1927 2286 0.956410 CACGTATTGGCCCCGAACAA 60.956 55.000 0.00 0.00 0.00 2.83
1938 2297 0.368907 GTACGCACAGGCACGTATTG 59.631 55.000 0.00 0.00 45.46 1.90
1943 2302 1.065102 AGTATAGTACGCACAGGCACG 59.935 52.381 0.00 0.00 41.24 5.34
2296 2657 3.953612 ACATTTTCATCAGGTGTGTGTGT 59.046 39.130 0.00 0.00 0.00 3.72
2297 2658 4.572985 ACATTTTCATCAGGTGTGTGTG 57.427 40.909 0.00 0.00 0.00 3.82
2298 2659 4.889409 AGAACATTTTCATCAGGTGTGTGT 59.111 37.500 0.00 0.00 33.72 3.72
2299 2660 5.443185 AGAACATTTTCATCAGGTGTGTG 57.557 39.130 0.00 0.00 33.72 3.82
2300 2661 5.010012 GGAAGAACATTTTCATCAGGTGTGT 59.990 40.000 0.00 0.00 32.12 3.72
2301 2662 5.464168 GGAAGAACATTTTCATCAGGTGTG 58.536 41.667 0.00 0.00 32.12 3.82
2302 2663 4.524328 GGGAAGAACATTTTCATCAGGTGT 59.476 41.667 0.00 0.00 32.12 4.16
2344 2705 3.260632 TCCATGAACCTGATCTTCAACGA 59.739 43.478 0.00 0.00 31.48 3.85
2395 2756 0.657840 GTGTATTCCGTGCTCCATGC 59.342 55.000 0.00 0.00 43.25 4.06
2459 2820 4.202080 ACTGAGCTTGTCAAACGTGTACTA 60.202 41.667 0.00 0.00 33.60 1.82
2480 2841 1.228063 CCTCACCAAGCAGCACACT 60.228 57.895 0.00 0.00 0.00 3.55
2598 4681 3.495629 CCATCTAGCAATGCTTGAGGCTA 60.496 47.826 21.88 2.13 42.66 3.93
2699 4782 8.792830 TTCTTTGAGTCACTTGGGATTTATAG 57.207 34.615 0.00 0.00 0.00 1.31
2753 4836 7.393515 ACTTGTGGGTTATCAAGACTATTTTCC 59.606 37.037 11.07 0.00 42.22 3.13
2975 5059 8.856247 CACCAAAAATATTACTTTTTCTACCGC 58.144 33.333 0.00 0.00 36.45 5.68
3048 5132 6.872020 GCCTACGAGCTTTCCATATATTGTTA 59.128 38.462 0.00 0.00 0.00 2.41
3093 5177 3.381272 TGATCGATCGCATCTGGCATATA 59.619 43.478 20.03 0.00 45.17 0.86
3094 5178 2.167075 TGATCGATCGCATCTGGCATAT 59.833 45.455 20.03 0.00 45.17 1.78
3101 5185 4.233005 CTGTTACATGATCGATCGCATCT 58.767 43.478 20.03 0.00 0.00 2.90
3200 5284 5.726980 TGCAAGTTCTTTTCCATAAGCAT 57.273 34.783 0.00 0.00 0.00 3.79
3332 5416 4.863131 CCGTAGTTTGAGGAGTTCATGTAC 59.137 45.833 0.00 0.00 35.27 2.90


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

AutoCloner maintained by Alex Coulton.