Multiple sequence alignment - TraesCS4D01G294900

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 TraesCS4D01G294900 chr4D 100.000 4526 0 0 1 4526 465071116 465066591 0.000000e+00 8359.0
1 TraesCS4D01G294900 chr4A 91.748 3781 206 47 238 3955 5403896 5407633 0.000000e+00 5156.0
2 TraesCS4D01G294900 chr4B 92.169 2337 111 32 1569 3886 581537877 581535594 0.000000e+00 3236.0
3 TraesCS4D01G294900 chr4B 86.654 1641 113 49 1 1587 581539585 581537997 0.000000e+00 1720.0
4 TraesCS4D01G294900 chr4B 98.969 97 1 0 3885 3981 581535480 581535384 1.670000e-39 174.0
5 TraesCS4D01G294900 chr6A 95.446 505 21 2 4023 4526 613602670 613602167 0.000000e+00 804.0
6 TraesCS4D01G294900 chr2B 95.437 504 21 2 4024 4526 625160178 625160680 0.000000e+00 802.0
7 TraesCS4D01G294900 chrUn 95.266 507 20 4 4022 4526 34421511 34422015 0.000000e+00 800.0
8 TraesCS4D01G294900 chr5D 94.942 514 16 10 4019 4526 188816164 188816673 0.000000e+00 797.0
9 TraesCS4D01G294900 chr5B 94.882 508 24 2 4020 4526 522850823 522851329 0.000000e+00 793.0
10 TraesCS4D01G294900 chr5B 91.304 46 3 1 3977 4022 326613551 326613595 1.360000e-05 62.1
11 TraesCS4D01G294900 chr1B 95.059 506 21 4 4023 4526 4080432 4079929 0.000000e+00 793.0
12 TraesCS4D01G294900 chr6B 95.059 506 20 5 4024 4526 213156724 213156221 0.000000e+00 791.0
13 TraesCS4D01G294900 chr2D 95.040 504 24 1 4024 4526 328330152 328330655 0.000000e+00 791.0
14 TraesCS4D01G294900 chr5A 94.695 509 23 4 4021 4526 560726524 560727031 0.000000e+00 787.0


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 TraesCS4D01G294900 chr4D 465066591 465071116 4525 True 8359 8359 100.000000 1 4526 1 chr4D.!!$R1 4525
1 TraesCS4D01G294900 chr4A 5403896 5407633 3737 False 5156 5156 91.748000 238 3955 1 chr4A.!!$F1 3717
2 TraesCS4D01G294900 chr4B 581535384 581539585 4201 True 1710 3236 92.597333 1 3981 3 chr4B.!!$R1 3980
3 TraesCS4D01G294900 chr6A 613602167 613602670 503 True 804 804 95.446000 4023 4526 1 chr6A.!!$R1 503
4 TraesCS4D01G294900 chr2B 625160178 625160680 502 False 802 802 95.437000 4024 4526 1 chr2B.!!$F1 502
5 TraesCS4D01G294900 chrUn 34421511 34422015 504 False 800 800 95.266000 4022 4526 1 chrUn.!!$F1 504
6 TraesCS4D01G294900 chr5D 188816164 188816673 509 False 797 797 94.942000 4019 4526 1 chr5D.!!$F1 507
7 TraesCS4D01G294900 chr5B 522850823 522851329 506 False 793 793 94.882000 4020 4526 1 chr5B.!!$F2 506
8 TraesCS4D01G294900 chr1B 4079929 4080432 503 True 793 793 95.059000 4023 4526 1 chr1B.!!$R1 503
9 TraesCS4D01G294900 chr6B 213156221 213156724 503 True 791 791 95.059000 4024 4526 1 chr6B.!!$R1 502
10 TraesCS4D01G294900 chr2D 328330152 328330655 503 False 791 791 95.040000 4024 4526 1 chr2D.!!$F1 502
11 TraesCS4D01G294900 chr5A 560726524 560727031 507 False 787 787 94.695000 4021 4526 1 chr5A.!!$F1 505

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
176 179 0.028505 CAGCAAGCTCACACACACAC 59.971 55.000 0.00 0.00 0.00 3.82 F
181 184 0.036483 AGCTCACACACACACACACA 60.036 50.000 0.00 0.00 0.00 3.72 F
182 185 0.096976 GCTCACACACACACACACAC 59.903 55.000 0.00 0.00 0.00 3.82 F
232 235 0.317020 GTCACGAAGCACAACCAAGC 60.317 55.000 0.00 0.00 0.00 4.01 F
1250 1296 0.386352 GTTTAAAACGGCGACTGGGC 60.386 55.000 16.62 0.00 37.98 5.36 F
1252 1298 0.606944 TTAAAACGGCGACTGGGCAT 60.607 50.000 16.62 0.00 42.43 4.40 F
1263 1309 0.625316 ACTGGGCATGGCATGTTAGA 59.375 50.000 26.94 9.40 0.00 2.10 F
1264 1310 1.005805 ACTGGGCATGGCATGTTAGAA 59.994 47.619 26.94 9.29 0.00 2.10 F
3132 3401 0.316204 GTGTTTGCATGAAGGCTGCT 59.684 50.000 0.00 0.00 40.34 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1373 0.253044 ATACGCCACTGAACCAGCAT 59.747 50.000 0.00 0.0 34.37 3.79 R
2109 2365 0.321653 GGTACTCCTTGGTGCCACAG 60.322 60.000 0.00 0.0 40.80 3.66 R
2179 2435 7.861629 TCTTGGTGTGATTAACTGATTATCCT 58.138 34.615 0.00 0.0 0.00 3.24 R
2190 2446 5.471797 TCGCTTGAATTCTTGGTGTGATTAA 59.528 36.000 7.05 0.0 0.00 1.40 R
2688 2957 0.883833 GCAGACTTCCCACCATTGTG 59.116 55.000 0.00 0.0 42.39 3.33 R
3024 3293 2.097466 ACTGGTGAAGTTGTTTGCGAAG 59.903 45.455 0.00 0.0 34.57 3.79 R
3132 3401 4.080751 TGACCATTCATGCTCTCATCTTCA 60.081 41.667 0.00 0.0 0.00 3.02 R
3432 3704 4.154737 TCCTGATTTTTCTGTTGCTCATCG 59.845 41.667 0.00 0.0 0.00 3.84 R
4007 4400 0.671163 TACAGTTTTAGGGTGCCGCG 60.671 55.000 0.00 0.0 0.00 6.46 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
37 38 7.830739 ACTTTTTGTCTGTTTTCATTCAGTCT 58.169 30.769 0.00 0.00 33.89 3.24
39 40 5.756195 TTGTCTGTTTTCATTCAGTCTGG 57.244 39.130 0.00 0.00 33.89 3.86
74 75 5.106475 CCACAAATTCAGAATGCCCAAAATG 60.106 40.000 0.00 0.00 34.76 2.32
100 101 1.271856 TCCACTATCAAACGCCTCCA 58.728 50.000 0.00 0.00 0.00 3.86
133 136 1.429463 AAGCAAGCGTACACAGCTAC 58.571 50.000 1.96 0.00 45.31 3.58
141 144 1.080093 TACACAGCTACCGCACAGC 60.080 57.895 0.00 0.00 39.10 4.40
167 170 1.005748 CACTCGGACAGCAAGCTCA 60.006 57.895 0.00 0.00 0.00 4.26
169 172 1.005748 CTCGGACAGCAAGCTCACA 60.006 57.895 0.00 0.00 0.00 3.58
170 173 1.287730 CTCGGACAGCAAGCTCACAC 61.288 60.000 0.00 0.00 0.00 3.82
171 174 1.595109 CGGACAGCAAGCTCACACA 60.595 57.895 0.00 0.00 0.00 3.72
172 175 1.835483 CGGACAGCAAGCTCACACAC 61.835 60.000 0.00 0.00 0.00 3.82
173 176 0.815213 GGACAGCAAGCTCACACACA 60.815 55.000 0.00 0.00 0.00 3.72
174 177 0.305922 GACAGCAAGCTCACACACAC 59.694 55.000 0.00 0.00 0.00 3.82
175 178 0.392863 ACAGCAAGCTCACACACACA 60.393 50.000 0.00 0.00 0.00 3.72
176 179 0.028505 CAGCAAGCTCACACACACAC 59.971 55.000 0.00 0.00 0.00 3.82
177 180 0.392863 AGCAAGCTCACACACACACA 60.393 50.000 0.00 0.00 0.00 3.72
178 181 0.248215 GCAAGCTCACACACACACAC 60.248 55.000 0.00 0.00 0.00 3.82
179 182 1.085893 CAAGCTCACACACACACACA 58.914 50.000 0.00 0.00 0.00 3.72
180 183 1.086696 AAGCTCACACACACACACAC 58.913 50.000 0.00 0.00 0.00 3.82
181 184 0.036483 AGCTCACACACACACACACA 60.036 50.000 0.00 0.00 0.00 3.72
182 185 0.096976 GCTCACACACACACACACAC 59.903 55.000 0.00 0.00 0.00 3.82
183 186 1.437625 CTCACACACACACACACACA 58.562 50.000 0.00 0.00 0.00 3.72
184 187 1.128507 CTCACACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
185 188 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
186 189 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
187 190 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
188 191 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
189 192 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
197 200 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
199 202 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
228 231 1.279840 GCAGTCACGAAGCACAACC 59.720 57.895 0.00 0.00 0.00 3.77
229 232 1.436195 GCAGTCACGAAGCACAACCA 61.436 55.000 0.00 0.00 0.00 3.67
231 234 1.003545 CAGTCACGAAGCACAACCAAG 60.004 52.381 0.00 0.00 0.00 3.61
232 235 0.317020 GTCACGAAGCACAACCAAGC 60.317 55.000 0.00 0.00 0.00 4.01
233 236 1.369209 CACGAAGCACAACCAAGCG 60.369 57.895 0.00 0.00 35.48 4.68
235 238 2.721231 GAAGCACAACCAAGCGCA 59.279 55.556 11.47 0.00 35.48 6.09
236 239 1.286880 GAAGCACAACCAAGCGCAT 59.713 52.632 11.47 0.00 35.48 4.73
458 464 9.512435 CATTTTTATTCATCAATCAGTCTGTCC 57.488 33.333 0.00 0.00 0.00 4.02
513 519 5.682234 TCAGTTAAGCATCTTGGAGATCA 57.318 39.130 0.00 0.00 31.32 2.92
528 534 0.938713 GATCATCCTCGACGTCGACT 59.061 55.000 34.97 19.91 44.22 4.18
530 536 1.062685 CATCCTCGACGTCGACTGG 59.937 63.158 34.97 32.28 44.22 4.00
537 543 0.457166 CGACGTCGACTGGCCAATTA 60.457 55.000 33.35 0.00 43.02 1.40
574 580 3.311106 GTGAAACATGACATGCACTTGG 58.689 45.455 15.49 0.00 36.32 3.61
644 651 2.748605 CGATCTCAGTAATCCCAGTGC 58.251 52.381 0.00 0.00 0.00 4.40
803 830 0.609131 AGAACATTCCGTGCCAAGGG 60.609 55.000 0.00 0.00 0.00 3.95
832 859 5.835280 ACCAGATTCTGATTCCACTGTTTTT 59.165 36.000 15.36 0.00 32.44 1.94
1029 1056 1.011333 CGTCGGAGGAAGAGTCTCTC 58.989 60.000 1.96 0.00 0.00 3.20
1117 1144 0.667184 CATGCCCGTGGTGAAAAAGC 60.667 55.000 0.00 0.00 0.00 3.51
1149 1195 2.509548 TCCAGGGAATCCAGGTATGTTG 59.490 50.000 0.09 0.00 40.31 3.33
1150 1196 2.301346 CAGGGAATCCAGGTATGTTGC 58.699 52.381 0.09 0.00 34.83 4.17
1151 1197 1.215423 AGGGAATCCAGGTATGTTGCC 59.785 52.381 0.09 0.00 34.83 4.52
1152 1198 1.215423 GGGAATCCAGGTATGTTGCCT 59.785 52.381 0.09 0.00 36.66 4.75
1153 1199 2.576615 GGAATCCAGGTATGTTGCCTC 58.423 52.381 0.00 0.00 33.31 4.70
1154 1200 2.092429 GGAATCCAGGTATGTTGCCTCA 60.092 50.000 0.00 0.00 33.31 3.86
1155 1201 3.620488 GAATCCAGGTATGTTGCCTCAA 58.380 45.455 0.00 0.00 33.31 3.02
1156 1202 2.489938 TCCAGGTATGTTGCCTCAAC 57.510 50.000 2.96 2.96 43.78 3.18
1157 1203 1.985159 TCCAGGTATGTTGCCTCAACT 59.015 47.619 10.52 0.65 43.85 3.16
1158 1204 2.027192 TCCAGGTATGTTGCCTCAACTC 60.027 50.000 10.52 2.70 43.85 3.01
1159 1205 2.290260 CCAGGTATGTTGCCTCAACTCA 60.290 50.000 10.52 0.00 43.85 3.41
1160 1206 3.411446 CAGGTATGTTGCCTCAACTCAA 58.589 45.455 10.52 0.00 43.85 3.02
1161 1207 3.438087 CAGGTATGTTGCCTCAACTCAAG 59.562 47.826 10.52 0.00 43.85 3.02
1162 1208 3.073062 AGGTATGTTGCCTCAACTCAAGT 59.927 43.478 10.52 0.00 43.85 3.16
1163 1209 3.821033 GGTATGTTGCCTCAACTCAAGTT 59.179 43.478 10.52 0.00 43.85 2.66
1170 1216 3.378112 TGCCTCAACTCAAGTTTCAACTG 59.622 43.478 0.00 0.00 39.66 3.16
1176 1222 6.744112 TCAACTCAAGTTTCAACTGTTGTTT 58.256 32.000 19.12 8.08 39.50 2.83
1227 1273 8.785946 CAATATAACAATGACATGCACCAGATA 58.214 33.333 0.00 0.00 0.00 1.98
1246 1292 6.311723 CAGATAAATGTTTAAAACGGCGACT 58.688 36.000 16.62 0.00 0.00 4.18
1247 1293 6.248420 CAGATAAATGTTTAAAACGGCGACTG 59.752 38.462 16.62 0.00 0.00 3.51
1248 1294 2.981400 ATGTTTAAAACGGCGACTGG 57.019 45.000 16.62 0.00 0.00 4.00
1249 1295 0.945813 TGTTTAAAACGGCGACTGGG 59.054 50.000 16.62 0.00 0.00 4.45
1250 1296 0.386352 GTTTAAAACGGCGACTGGGC 60.386 55.000 16.62 0.00 37.98 5.36
1251 1297 0.818445 TTTAAAACGGCGACTGGGCA 60.818 50.000 16.62 0.00 42.43 5.36
1252 1298 0.606944 TTAAAACGGCGACTGGGCAT 60.607 50.000 16.62 0.00 42.43 4.40
1253 1299 1.302383 TAAAACGGCGACTGGGCATG 61.302 55.000 16.62 0.00 42.43 4.06
1258 1304 3.896133 GCGACTGGGCATGGCATG 61.896 66.667 22.99 22.99 0.00 4.06
1259 1305 2.438975 CGACTGGGCATGGCATGT 60.439 61.111 26.94 17.80 0.00 3.21
1260 1306 2.048023 CGACTGGGCATGGCATGTT 61.048 57.895 26.94 8.15 0.00 2.71
1261 1307 0.747644 CGACTGGGCATGGCATGTTA 60.748 55.000 26.94 13.42 0.00 2.41
1262 1308 1.027357 GACTGGGCATGGCATGTTAG 58.973 55.000 26.94 22.39 0.00 2.34
1263 1309 0.625316 ACTGGGCATGGCATGTTAGA 59.375 50.000 26.94 9.40 0.00 2.10
1264 1310 1.005805 ACTGGGCATGGCATGTTAGAA 59.994 47.619 26.94 9.29 0.00 2.10
1265 1311 2.101783 CTGGGCATGGCATGTTAGAAA 58.898 47.619 26.94 8.01 0.00 2.52
1266 1312 2.100252 CTGGGCATGGCATGTTAGAAAG 59.900 50.000 26.94 13.09 0.00 2.62
1267 1313 1.202452 GGGCATGGCATGTTAGAAAGC 60.202 52.381 26.94 11.10 0.00 3.51
1268 1314 1.753073 GGCATGGCATGTTAGAAAGCT 59.247 47.619 26.94 0.00 0.00 3.74
1269 1315 2.167075 GGCATGGCATGTTAGAAAGCTT 59.833 45.455 26.94 0.00 0.00 3.74
1270 1316 3.442100 GCATGGCATGTTAGAAAGCTTC 58.558 45.455 26.94 3.65 0.00 3.86
1271 1317 3.119388 GCATGGCATGTTAGAAAGCTTCA 60.119 43.478 26.94 0.00 0.00 3.02
1272 1318 4.618927 GCATGGCATGTTAGAAAGCTTCAA 60.619 41.667 26.94 0.00 0.00 2.69
1273 1319 4.771590 TGGCATGTTAGAAAGCTTCAAG 57.228 40.909 0.00 0.00 0.00 3.02
1274 1320 4.144297 TGGCATGTTAGAAAGCTTCAAGT 58.856 39.130 0.00 0.00 0.00 3.16
1275 1321 4.584325 TGGCATGTTAGAAAGCTTCAAGTT 59.416 37.500 0.00 0.00 0.00 2.66
1276 1322 5.068987 TGGCATGTTAGAAAGCTTCAAGTTT 59.931 36.000 0.00 0.00 0.00 2.66
1277 1323 6.264292 TGGCATGTTAGAAAGCTTCAAGTTTA 59.736 34.615 0.00 0.00 0.00 2.01
1278 1324 7.039784 TGGCATGTTAGAAAGCTTCAAGTTTAT 60.040 33.333 0.00 0.00 0.00 1.40
1279 1325 7.486232 GGCATGTTAGAAAGCTTCAAGTTTATC 59.514 37.037 0.00 0.00 0.00 1.75
1280 1326 8.023128 GCATGTTAGAAAGCTTCAAGTTTATCA 58.977 33.333 0.00 0.00 0.00 2.15
1295 1341 6.545504 AGTTTATCATATCGTGCATGGTTC 57.454 37.500 5.98 0.00 0.00 3.62
1296 1342 6.054941 AGTTTATCATATCGTGCATGGTTCA 58.945 36.000 5.98 0.00 0.00 3.18
1297 1343 6.203530 AGTTTATCATATCGTGCATGGTTCAG 59.796 38.462 5.98 0.00 0.00 3.02
1309 1355 4.284490 TGCATGGTTCAGTAGAAAGTCTCT 59.716 41.667 0.00 0.00 35.08 3.10
1316 1362 9.310449 TGGTTCAGTAGAAAGTCTCTAGTTTAT 57.690 33.333 0.00 0.00 38.10 1.40
1326 1372 8.804688 AAAGTCTCTAGTTTATCATATCGTGC 57.195 34.615 0.00 0.00 0.00 5.34
1327 1373 7.511959 AGTCTCTAGTTTATCATATCGTGCA 57.488 36.000 0.00 0.00 0.00 4.57
1329 1375 8.026026 AGTCTCTAGTTTATCATATCGTGCATG 58.974 37.037 0.00 0.00 0.00 4.06
1332 1422 5.602458 AGTTTATCATATCGTGCATGCTG 57.398 39.130 20.33 11.68 0.00 4.41
1341 1431 1.582968 GTGCATGCTGGTTCAGTGG 59.417 57.895 20.33 0.00 33.43 4.00
1342 1432 2.270257 TGCATGCTGGTTCAGTGGC 61.270 57.895 20.33 0.00 33.43 5.01
1357 1447 3.131396 CAGTGGCGTATAGATTTGACCC 58.869 50.000 0.00 0.00 0.00 4.46
1360 1450 2.502130 TGGCGTATAGATTTGACCCACA 59.498 45.455 0.00 0.00 0.00 4.17
1424 1533 9.302345 TCTGCTATTAGTTCTATCAGTTTTTCG 57.698 33.333 0.00 0.00 0.00 3.46
1434 1543 9.314501 GTTCTATCAGTTTTTCGAAACATGTAC 57.685 33.333 10.79 4.39 35.20 2.90
1438 1547 5.237779 TCAGTTTTTCGAAACATGTACCTCC 59.762 40.000 10.79 0.00 35.20 4.30
1441 1550 5.621197 TTTTCGAAACATGTACCTCCATG 57.379 39.130 10.79 0.00 46.14 3.66
1442 1551 4.545208 TTCGAAACATGTACCTCCATGA 57.455 40.909 0.00 0.00 43.99 3.07
1446 1555 5.943416 TCGAAACATGTACCTCCATGATTTT 59.057 36.000 0.00 0.00 43.99 1.82
1450 1559 6.699575 ACATGTACCTCCATGATTTTAAGC 57.300 37.500 0.00 0.00 43.99 3.09
1453 1562 7.178274 ACATGTACCTCCATGATTTTAAGCAAA 59.822 33.333 0.00 0.00 43.99 3.68
1506 1621 9.553064 AGCTCATAGTATGAAGTATTTTCCAAG 57.447 33.333 13.74 0.00 39.11 3.61
1509 1624 9.109393 TCATAGTATGAAGTATTTTCCAAGTGC 57.891 33.333 10.50 0.00 36.11 4.40
1510 1625 6.422776 AGTATGAAGTATTTTCCAAGTGCG 57.577 37.500 0.00 0.00 0.00 5.34
1511 1626 5.938125 AGTATGAAGTATTTTCCAAGTGCGT 59.062 36.000 0.00 0.00 0.00 5.24
1515 1630 4.685169 AGTATTTTCCAAGTGCGTCATG 57.315 40.909 0.00 0.00 0.00 3.07
1517 1632 3.837213 ATTTTCCAAGTGCGTCATGAG 57.163 42.857 0.00 0.00 0.00 2.90
1518 1633 1.522668 TTTCCAAGTGCGTCATGAGG 58.477 50.000 11.07 11.07 0.00 3.86
1522 1637 1.879380 CCAAGTGCGTCATGAGGAAAA 59.121 47.619 19.26 0.98 0.00 2.29
1523 1638 2.095567 CCAAGTGCGTCATGAGGAAAAG 60.096 50.000 19.26 2.25 0.00 2.27
1534 1649 6.306356 CGTCATGAGGAAAAGTAAAGCAAATG 59.694 38.462 9.87 0.00 0.00 2.32
1562 1677 2.086869 CAAGTTCAGACCGCCAATCAT 58.913 47.619 0.00 0.00 0.00 2.45
1567 1682 4.336433 AGTTCAGACCGCCAATCATATTTG 59.664 41.667 0.00 0.00 0.00 2.32
1568 1683 4.149511 TCAGACCGCCAATCATATTTGA 57.850 40.909 0.00 0.00 36.00 2.69
1616 1869 9.434420 CAAAGGAATTGCAAATGGATACTAAAA 57.566 29.630 1.71 0.00 31.56 1.52
1693 1946 4.061596 ACTAGCTTGACAGAAACTGAAGC 58.938 43.478 13.53 13.53 39.81 3.86
1695 1948 1.599542 GCTTGACAGAAACTGAAGCGT 59.400 47.619 5.76 0.00 33.77 5.07
1700 1953 3.687212 TGACAGAAACTGAAGCGTTGAAA 59.313 39.130 5.76 0.00 35.18 2.69
1702 1956 4.412207 ACAGAAACTGAAGCGTTGAAAAC 58.588 39.130 5.76 0.00 38.15 2.43
1706 1960 6.452872 CAGAAACTGAAGCGTTGAAAACAAAG 60.453 38.462 0.00 0.00 39.43 2.77
1756 2012 6.891361 ACATTGGTTTCATGATGTCCATCTTA 59.109 34.615 12.57 2.09 38.60 2.10
1761 2017 6.769822 GGTTTCATGATGTCCATCTTACAGAT 59.230 38.462 8.61 0.00 38.60 2.90
1842 2098 2.265367 TGTGAAGTCTGCCATAAGGGA 58.735 47.619 0.00 0.00 40.01 4.20
1887 2143 1.227383 CCACAGGAGGGGGCATAAC 59.773 63.158 0.00 0.00 0.00 1.89
1926 2182 2.358003 AGAAGCAGCACTGACGCC 60.358 61.111 0.81 0.00 0.00 5.68
2079 2335 5.034797 CGATGTTCGAAGAAGTATGCTGTA 58.965 41.667 0.00 0.00 45.90 2.74
2109 2365 3.895232 TGGAAGGCTCACACTAAGATC 57.105 47.619 0.00 0.00 0.00 2.75
2169 2425 5.336150 TCTTCTCAAGGTATGCTTCTCAG 57.664 43.478 0.00 0.00 0.00 3.35
2173 2429 4.774726 TCTCAAGGTATGCTTCTCAGTTCT 59.225 41.667 0.00 0.00 0.00 3.01
2174 2430 5.078411 TCAAGGTATGCTTCTCAGTTCTC 57.922 43.478 0.00 0.00 0.00 2.87
2176 2432 4.464069 AGGTATGCTTCTCAGTTCTCAC 57.536 45.455 0.00 0.00 0.00 3.51
2177 2433 4.093011 AGGTATGCTTCTCAGTTCTCACT 58.907 43.478 0.00 0.00 0.00 3.41
2178 2434 4.530161 AGGTATGCTTCTCAGTTCTCACTT 59.470 41.667 0.00 0.00 0.00 3.16
2179 2435 5.717178 AGGTATGCTTCTCAGTTCTCACTTA 59.283 40.000 0.00 0.00 0.00 2.24
2180 2436 6.039616 GGTATGCTTCTCAGTTCTCACTTAG 58.960 44.000 0.00 0.00 0.00 2.18
2181 2437 4.527509 TGCTTCTCAGTTCTCACTTAGG 57.472 45.455 0.00 0.00 0.00 2.69
2182 2438 4.152647 TGCTTCTCAGTTCTCACTTAGGA 58.847 43.478 0.00 0.00 0.00 2.94
2183 2439 4.774726 TGCTTCTCAGTTCTCACTTAGGAT 59.225 41.667 0.00 0.00 0.00 3.24
2184 2440 5.952347 TGCTTCTCAGTTCTCACTTAGGATA 59.048 40.000 0.00 0.00 0.00 2.59
2185 2441 6.437477 TGCTTCTCAGTTCTCACTTAGGATAA 59.563 38.462 0.00 0.00 0.00 1.75
2186 2442 7.124901 TGCTTCTCAGTTCTCACTTAGGATAAT 59.875 37.037 0.00 0.00 0.00 1.28
2187 2443 7.651704 GCTTCTCAGTTCTCACTTAGGATAATC 59.348 40.741 0.00 0.00 0.00 1.75
2188 2444 8.595362 TTCTCAGTTCTCACTTAGGATAATCA 57.405 34.615 0.00 0.00 0.00 2.57
2189 2445 8.231692 TCTCAGTTCTCACTTAGGATAATCAG 57.768 38.462 0.00 0.00 0.00 2.90
2190 2446 7.836685 TCTCAGTTCTCACTTAGGATAATCAGT 59.163 37.037 0.00 0.00 0.00 3.41
2213 2469 3.837213 ATCACACCAAGAATTCAAGCG 57.163 42.857 8.44 0.00 0.00 4.68
2242 2498 7.390996 TGCATCATTAGCCATGAAAAACAAATT 59.609 29.630 0.00 0.00 45.45 1.82
2243 2499 7.906527 GCATCATTAGCCATGAAAAACAAATTC 59.093 33.333 0.00 0.00 45.45 2.17
2316 2580 7.116075 AGATGTAGACTGAAGTACTGACATCT 58.884 38.462 15.98 15.98 44.52 2.90
2318 2582 6.914259 TGTAGACTGAAGTACTGACATCTTG 58.086 40.000 0.00 0.00 0.00 3.02
2319 2583 6.715264 TGTAGACTGAAGTACTGACATCTTGA 59.285 38.462 0.00 0.00 0.00 3.02
2323 2589 8.976353 AGACTGAAGTACTGACATCTTGATTAT 58.024 33.333 0.00 0.00 0.00 1.28
2405 2671 5.120208 GCTTATGTCTCTGTTGCTTACGAAA 59.880 40.000 0.00 0.00 0.00 3.46
2406 2672 6.347402 GCTTATGTCTCTGTTGCTTACGAAAA 60.347 38.462 0.00 0.00 0.00 2.29
2456 2722 8.500753 TTCCATATTCACACAGTTTACATACC 57.499 34.615 0.00 0.00 0.00 2.73
2473 2742 6.468333 ACATACCATTTGAAGCAATGCATA 57.532 33.333 8.35 0.00 0.00 3.14
2531 2800 7.901322 TGGGAGTATCATATTAGACTAGCCATT 59.099 37.037 0.00 0.00 36.25 3.16
2564 2833 3.690139 CAGCCATGCCATTTAAAATGCAA 59.310 39.130 16.06 3.98 37.27 4.08
2566 2835 3.485546 GCCATGCCATTTAAAATGCAACG 60.486 43.478 16.06 11.35 37.27 4.10
2579 2848 4.385358 AATGCAACGTTTCTTGGAACTT 57.615 36.364 0.00 0.00 0.00 2.66
2688 2957 1.532604 GGGTTAACCACAGCCTTGCC 61.533 60.000 25.71 0.78 39.85 4.52
3009 3278 1.103398 GCCAGGATCCCATTTCACCG 61.103 60.000 8.55 0.00 0.00 4.94
3018 3287 2.134346 CCCATTTCACCGTTGCTTTTG 58.866 47.619 0.00 0.00 0.00 2.44
3024 3293 1.202359 TCACCGTTGCTTTTGAAAGGC 60.202 47.619 4.96 4.96 36.53 4.35
3132 3401 0.316204 GTGTTTGCATGAAGGCTGCT 59.684 50.000 0.00 0.00 40.34 4.24
3541 3813 4.104696 TCATGATGCTGTGATGCAAAAG 57.895 40.909 0.00 0.00 46.61 2.27
3565 3840 5.221783 GGGTTTCCTTACTCTGGTAGTTCAA 60.222 44.000 0.00 0.00 39.80 2.69
3570 3845 6.708285 TCCTTACTCTGGTAGTTCAATTTCC 58.292 40.000 0.00 0.00 39.80 3.13
3678 3955 8.783660 AATATGGTCAAGAACTAGAGATACCA 57.216 34.615 0.00 2.93 39.87 3.25
3679 3956 6.723298 ATGGTCAAGAACTAGAGATACCAG 57.277 41.667 0.00 0.00 39.01 4.00
3722 4000 7.439108 AAGTAGCCAGGTAATCTTATCAACT 57.561 36.000 0.00 0.00 0.00 3.16
3741 4019 1.289982 TTAATGGGGCCATTCGGGGA 61.290 55.000 4.39 0.00 44.50 4.81
3815 4093 6.459670 TTTGGAAGAAGTTGGTTCTAAACC 57.540 37.500 1.82 1.82 45.44 3.27
3956 4349 6.431722 TCTAGCCCTTGCCATAAACTTTAAT 58.568 36.000 0.00 0.00 38.69 1.40
3998 4391 3.805267 GAGCATCTCCAACAGGCG 58.195 61.111 0.00 0.00 0.00 5.52
3999 4392 2.437359 AGCATCTCCAACAGGCGC 60.437 61.111 0.00 0.00 0.00 6.53
4000 4393 3.869272 GCATCTCCAACAGGCGCG 61.869 66.667 0.00 0.00 0.00 6.86
4001 4394 3.869272 CATCTCCAACAGGCGCGC 61.869 66.667 25.94 25.94 0.00 6.86
4002 4395 4.393155 ATCTCCAACAGGCGCGCA 62.393 61.111 34.42 9.24 0.00 6.09
4003 4396 3.899981 ATCTCCAACAGGCGCGCAA 62.900 57.895 34.42 7.45 0.00 4.85
4004 4397 4.093952 CTCCAACAGGCGCGCAAG 62.094 66.667 34.42 25.82 43.44 4.01
4026 4419 0.671163 CGCGGCACCCTAAAACTGTA 60.671 55.000 0.00 0.00 0.00 2.74
4163 4559 2.187946 GCTCCTCCCCATGACACG 59.812 66.667 0.00 0.00 0.00 4.49
4269 4666 2.139323 TACATCGTGTGTCTAGCCCT 57.861 50.000 0.00 0.00 42.29 5.19
4418 4815 4.196193 CAAACTCCACCTTGGCGAATATA 58.804 43.478 0.00 0.00 37.47 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.756722 CAGACTGAATGAAAACAGACAAAAAGT 59.243 33.333 0.00 0.00 37.54 2.66
39 40 1.244019 AATTTGTGGCCCGACTCAGC 61.244 55.000 0.00 0.00 0.00 4.26
74 75 4.275936 AGGCGTTTGATAGTGGATTATTGC 59.724 41.667 0.00 0.00 0.00 3.56
100 101 2.350772 GCTTGCTTTCTGTGCGTGTTAT 60.351 45.455 0.00 0.00 0.00 1.89
141 144 4.293648 TGTCCGAGTGTGCGTGGG 62.294 66.667 0.00 0.00 0.00 4.61
167 170 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
169 172 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
170 173 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
171 174 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
172 175 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
173 176 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
174 177 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
175 178 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
176 179 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
177 180 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
178 181 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
179 182 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
180 183 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
181 184 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
182 185 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
183 186 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
184 187 0.179227 CGTGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
185 188 1.906994 GCGTGTGTGTGTGTGTGTGT 61.907 55.000 0.00 0.00 0.00 3.72
186 189 1.225991 GCGTGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
187 190 1.375396 AGCGTGTGTGTGTGTGTGT 60.375 52.632 0.00 0.00 0.00 3.72
188 191 1.060779 CAGCGTGTGTGTGTGTGTG 59.939 57.895 0.00 0.00 0.00 3.82
189 192 2.749865 GCAGCGTGTGTGTGTGTGT 61.750 57.895 0.00 0.00 0.00 3.72
228 231 4.842091 GCGGCCTCAATGCGCTTG 62.842 66.667 9.73 11.02 36.09 4.01
528 534 5.659079 CCTGGGTAAGTAAATTAATTGGCCA 59.341 40.000 0.00 0.00 0.00 5.36
530 536 5.659525 ACCCTGGGTAAGTAAATTAATTGGC 59.340 40.000 18.99 0.00 32.11 4.52
537 543 5.707495 TGTTTCACCCTGGGTAAGTAAATT 58.293 37.500 20.09 0.00 32.11 1.82
644 651 4.534103 AGATAGGCCCCTGATTTTAGCTAG 59.466 45.833 0.00 0.00 0.00 3.42
803 830 3.696548 GTGGAATCAGAATCTGGTTTCCC 59.303 47.826 27.37 18.97 40.28 3.97
832 859 4.208460 GCAATGCTCGCGTTTAGTATTAGA 59.792 41.667 5.77 0.00 29.57 2.10
981 1008 1.398692 TTGTTGTTGGGGACTTGAGC 58.601 50.000 0.00 0.00 0.00 4.26
1117 1144 1.320344 TTCCCTGGATGACCTCGTCG 61.320 60.000 0.00 0.00 34.95 5.12
1149 1195 3.378427 ACAGTTGAAACTTGAGTTGAGGC 59.622 43.478 0.00 0.00 38.44 4.70
1150 1196 5.106157 ACAACAGTTGAAACTTGAGTTGAGG 60.106 40.000 20.56 5.91 40.24 3.86
1151 1197 5.942872 ACAACAGTTGAAACTTGAGTTGAG 58.057 37.500 20.56 6.40 40.24 3.02
1152 1198 5.957842 ACAACAGTTGAAACTTGAGTTGA 57.042 34.783 20.56 0.00 40.24 3.18
1153 1199 6.420604 ACAAACAACAGTTGAAACTTGAGTTG 59.579 34.615 20.56 16.97 41.95 3.16
1154 1200 6.512297 ACAAACAACAGTTGAAACTTGAGTT 58.488 32.000 20.56 0.00 37.08 3.01
1155 1201 6.016276 AGACAAACAACAGTTGAAACTTGAGT 60.016 34.615 20.56 6.40 37.08 3.41
1156 1202 6.306356 CAGACAAACAACAGTTGAAACTTGAG 59.694 38.462 20.56 3.52 37.08 3.02
1157 1203 6.016693 TCAGACAAACAACAGTTGAAACTTGA 60.017 34.615 20.56 12.19 37.08 3.02
1158 1204 6.148948 TCAGACAAACAACAGTTGAAACTTG 58.851 36.000 20.56 16.93 37.08 3.16
1159 1205 6.325919 TCAGACAAACAACAGTTGAAACTT 57.674 33.333 20.56 0.53 37.08 2.66
1160 1206 5.957842 TCAGACAAACAACAGTTGAAACT 57.042 34.783 20.56 8.44 40.60 2.66
1161 1207 6.321717 TCATCAGACAAACAACAGTTGAAAC 58.678 36.000 20.56 6.48 0.00 2.78
1162 1208 6.507958 TCATCAGACAAACAACAGTTGAAA 57.492 33.333 20.56 0.00 0.00 2.69
1163 1209 6.072230 TGTTCATCAGACAAACAACAGTTGAA 60.072 34.615 20.56 0.00 30.39 2.69
1170 1216 4.028383 CGTGTGTTCATCAGACAAACAAC 58.972 43.478 1.83 3.16 39.84 3.32
1176 1222 1.217001 GCACGTGTGTTCATCAGACA 58.783 50.000 18.38 0.00 39.84 3.41
1215 1261 7.201427 CCGTTTTAAACATTTATCTGGTGCATG 60.201 37.037 8.61 0.00 0.00 4.06
1227 1273 3.551250 CCCAGTCGCCGTTTTAAACATTT 60.551 43.478 8.61 0.00 0.00 2.32
1246 1292 2.101783 CTTTCTAACATGCCATGCCCA 58.898 47.619 4.17 0.00 0.00 5.36
1247 1293 1.202452 GCTTTCTAACATGCCATGCCC 60.202 52.381 4.17 0.00 0.00 5.36
1248 1294 1.753073 AGCTTTCTAACATGCCATGCC 59.247 47.619 4.17 0.00 0.00 4.40
1249 1295 3.119388 TGAAGCTTTCTAACATGCCATGC 60.119 43.478 4.17 0.00 0.00 4.06
1250 1296 4.707030 TGAAGCTTTCTAACATGCCATG 57.293 40.909 2.40 2.40 0.00 3.66
1251 1297 4.768968 ACTTGAAGCTTTCTAACATGCCAT 59.231 37.500 0.00 0.00 0.00 4.40
1252 1298 4.144297 ACTTGAAGCTTTCTAACATGCCA 58.856 39.130 0.00 0.00 0.00 4.92
1253 1299 4.773323 ACTTGAAGCTTTCTAACATGCC 57.227 40.909 0.00 0.00 0.00 4.40
1254 1300 8.023128 TGATAAACTTGAAGCTTTCTAACATGC 58.977 33.333 0.00 0.00 0.00 4.06
1260 1306 9.817809 ACGATATGATAAACTTGAAGCTTTCTA 57.182 29.630 0.00 0.00 0.00 2.10
1261 1307 8.607459 CACGATATGATAAACTTGAAGCTTTCT 58.393 33.333 0.00 0.00 0.00 2.52
1262 1308 7.374491 GCACGATATGATAAACTTGAAGCTTTC 59.626 37.037 0.00 0.00 0.00 2.62
1263 1309 7.148255 TGCACGATATGATAAACTTGAAGCTTT 60.148 33.333 0.00 0.00 0.00 3.51
1264 1310 6.316140 TGCACGATATGATAAACTTGAAGCTT 59.684 34.615 0.00 0.00 0.00 3.74
1265 1311 5.817296 TGCACGATATGATAAACTTGAAGCT 59.183 36.000 0.00 0.00 0.00 3.74
1266 1312 6.048073 TGCACGATATGATAAACTTGAAGC 57.952 37.500 0.00 0.00 0.00 3.86
1267 1313 7.073883 CCATGCACGATATGATAAACTTGAAG 58.926 38.462 0.00 0.00 0.00 3.02
1268 1314 6.542005 ACCATGCACGATATGATAAACTTGAA 59.458 34.615 0.00 0.00 0.00 2.69
1269 1315 6.054941 ACCATGCACGATATGATAAACTTGA 58.945 36.000 0.00 0.00 0.00 3.02
1270 1316 6.304356 ACCATGCACGATATGATAAACTTG 57.696 37.500 0.00 0.00 0.00 3.16
1271 1317 6.542005 TGAACCATGCACGATATGATAAACTT 59.458 34.615 0.00 0.00 0.00 2.66
1272 1318 6.054941 TGAACCATGCACGATATGATAAACT 58.945 36.000 0.00 0.00 0.00 2.66
1273 1319 6.017934 ACTGAACCATGCACGATATGATAAAC 60.018 38.462 0.00 0.00 0.00 2.01
1274 1320 6.054941 ACTGAACCATGCACGATATGATAAA 58.945 36.000 0.00 0.00 0.00 1.40
1275 1321 5.610398 ACTGAACCATGCACGATATGATAA 58.390 37.500 0.00 0.00 0.00 1.75
1276 1322 5.213891 ACTGAACCATGCACGATATGATA 57.786 39.130 0.00 0.00 0.00 2.15
1277 1323 4.077300 ACTGAACCATGCACGATATGAT 57.923 40.909 0.00 0.00 0.00 2.45
1278 1324 3.541996 ACTGAACCATGCACGATATGA 57.458 42.857 0.00 0.00 0.00 2.15
1279 1325 4.620982 TCTACTGAACCATGCACGATATG 58.379 43.478 0.00 0.00 0.00 1.78
1280 1326 4.937201 TCTACTGAACCATGCACGATAT 57.063 40.909 0.00 0.00 0.00 1.63
1281 1327 4.729227 TTCTACTGAACCATGCACGATA 57.271 40.909 0.00 0.00 0.00 2.92
1282 1328 3.610040 TTCTACTGAACCATGCACGAT 57.390 42.857 0.00 0.00 0.00 3.73
1283 1329 3.244078 ACTTTCTACTGAACCATGCACGA 60.244 43.478 0.00 0.00 31.02 4.35
1309 1355 5.639082 CCAGCATGCACGATATGATAAACTA 59.361 40.000 21.98 0.00 31.97 2.24
1316 1362 2.212652 GAACCAGCATGCACGATATGA 58.787 47.619 21.98 0.00 31.97 2.15
1322 1368 1.208358 CACTGAACCAGCATGCACG 59.792 57.895 21.98 11.57 34.37 5.34
1325 1371 2.570181 GCCACTGAACCAGCATGC 59.430 61.111 10.51 10.51 34.37 4.06
1326 1372 0.673333 TACGCCACTGAACCAGCATG 60.673 55.000 0.00 0.00 34.37 4.06
1327 1373 0.253044 ATACGCCACTGAACCAGCAT 59.747 50.000 0.00 0.00 34.37 3.79
1329 1375 1.136305 TCTATACGCCACTGAACCAGC 59.864 52.381 0.00 0.00 34.37 4.85
1332 1422 4.270325 GTCAAATCTATACGCCACTGAACC 59.730 45.833 0.00 0.00 0.00 3.62
1341 1431 5.554822 TTTTGTGGGTCAAATCTATACGC 57.445 39.130 0.00 0.00 44.15 4.42
1377 1470 7.604927 AGCAGAAATGCATGTTAACAAAATGAT 59.395 29.630 13.23 0.00 37.25 2.45
1378 1471 6.930164 AGCAGAAATGCATGTTAACAAAATGA 59.070 30.769 13.23 0.00 37.25 2.57
1380 1473 9.439500 AATAGCAGAAATGCATGTTAACAAAAT 57.561 25.926 13.23 3.92 37.25 1.82
1381 1474 8.830201 AATAGCAGAAATGCATGTTAACAAAA 57.170 26.923 13.23 1.48 37.25 2.44
1385 1478 9.226345 GAACTAATAGCAGAAATGCATGTTAAC 57.774 33.333 0.00 0.00 37.25 2.01
1386 1479 9.177608 AGAACTAATAGCAGAAATGCATGTTAA 57.822 29.630 0.00 0.00 37.25 2.01
1392 1485 8.206867 ACTGATAGAACTAATAGCAGAAATGCA 58.793 33.333 5.34 0.00 38.61 3.96
1393 1486 8.600449 ACTGATAGAACTAATAGCAGAAATGC 57.400 34.615 5.34 0.00 38.61 3.56
1399 1492 9.302345 TCGAAAAACTGATAGAACTAATAGCAG 57.698 33.333 0.00 0.00 41.35 4.24
1408 1501 9.314501 GTACATGTTTCGAAAAACTGATAGAAC 57.685 33.333 13.10 0.00 44.23 3.01
1411 1504 8.029642 AGGTACATGTTTCGAAAAACTGATAG 57.970 34.615 13.10 0.09 44.23 2.08
1413 1506 6.072673 GGAGGTACATGTTTCGAAAAACTGAT 60.073 38.462 13.10 0.00 44.23 2.90
1414 1507 5.237779 GGAGGTACATGTTTCGAAAAACTGA 59.762 40.000 13.10 0.00 44.23 3.41
1424 1533 7.702348 GCTTAAAATCATGGAGGTACATGTTTC 59.298 37.037 2.30 0.00 46.39 2.78
1459 1568 4.142881 GCTGAACTCATTTAGGTTCGGTTC 60.143 45.833 13.69 0.00 45.38 3.62
1461 1570 3.008049 AGCTGAACTCATTTAGGTTCGGT 59.992 43.478 13.69 6.56 45.38 4.69
1462 1571 3.600388 AGCTGAACTCATTTAGGTTCGG 58.400 45.455 9.46 9.46 45.97 4.30
1501 1616 0.684535 TTCCTCATGACGCACTTGGA 59.315 50.000 0.00 0.00 0.00 3.53
1506 1621 4.712763 CTTTACTTTTCCTCATGACGCAC 58.287 43.478 0.00 0.00 0.00 5.34
1508 1623 3.188460 TGCTTTACTTTTCCTCATGACGC 59.812 43.478 0.00 0.00 0.00 5.19
1509 1624 5.356882 TTGCTTTACTTTTCCTCATGACG 57.643 39.130 0.00 0.00 0.00 4.35
1510 1625 6.587608 CCATTTGCTTTACTTTTCCTCATGAC 59.412 38.462 0.00 0.00 0.00 3.06
1511 1626 6.267471 ACCATTTGCTTTACTTTTCCTCATGA 59.733 34.615 0.00 0.00 0.00 3.07
1515 1630 7.215719 ACTACCATTTGCTTTACTTTTCCTC 57.784 36.000 0.00 0.00 0.00 3.71
1517 1632 7.923878 TGAAACTACCATTTGCTTTACTTTTCC 59.076 33.333 0.00 0.00 0.00 3.13
1518 1633 8.865590 TGAAACTACCATTTGCTTTACTTTTC 57.134 30.769 0.00 0.00 0.00 2.29
1522 1637 7.582667 ACTTGAAACTACCATTTGCTTTACT 57.417 32.000 0.00 0.00 0.00 2.24
1523 1638 7.918562 TGAACTTGAAACTACCATTTGCTTTAC 59.081 33.333 0.00 0.00 0.00 2.01
1534 1649 2.479275 GCGGTCTGAACTTGAAACTACC 59.521 50.000 0.00 0.00 0.00 3.18
1639 1892 9.742144 TGTTTTGGGTTAATCTAGCAATTAGTA 57.258 29.630 0.00 0.00 0.00 1.82
1640 1893 8.644374 TGTTTTGGGTTAATCTAGCAATTAGT 57.356 30.769 0.00 0.00 0.00 2.24
1668 1921 7.036220 GCTTCAGTTTCTGTCAAGCTAGTATA 58.964 38.462 12.65 0.00 37.17 1.47
1669 1922 5.872070 GCTTCAGTTTCTGTCAAGCTAGTAT 59.128 40.000 12.65 0.00 37.17 2.12
1670 1923 5.230942 GCTTCAGTTTCTGTCAAGCTAGTA 58.769 41.667 12.65 0.00 37.17 1.82
1671 1924 4.061596 GCTTCAGTTTCTGTCAAGCTAGT 58.938 43.478 12.65 0.00 37.17 2.57
1673 1926 3.059884 CGCTTCAGTTTCTGTCAAGCTA 58.940 45.455 15.73 0.00 37.84 3.32
1676 1929 3.309682 TCAACGCTTCAGTTTCTGTCAAG 59.690 43.478 0.00 0.00 32.61 3.02
1678 1931 2.899976 TCAACGCTTCAGTTTCTGTCA 58.100 42.857 0.00 0.00 32.61 3.58
1679 1932 3.944422 TTCAACGCTTCAGTTTCTGTC 57.056 42.857 0.00 0.00 32.61 3.51
1680 1933 4.083003 TGTTTTCAACGCTTCAGTTTCTGT 60.083 37.500 0.00 0.00 32.61 3.41
1693 1946 5.229921 TGGAACTCTCTTTGTTTTCAACG 57.770 39.130 0.00 0.00 39.73 4.10
1695 1948 7.090173 CAGTTTGGAACTCTCTTTGTTTTCAA 58.910 34.615 0.00 0.00 40.46 2.69
1700 1953 5.567138 CACAGTTTGGAACTCTCTTTGTT 57.433 39.130 0.00 0.00 40.46 2.83
1712 1966 9.711785 ACCAATGTTAGGTTACCACAGTTTGGA 62.712 40.741 22.92 0.00 41.91 3.53
1713 1967 7.639943 ACCAATGTTAGGTTACCACAGTTTGG 61.640 42.308 18.10 18.10 43.93 3.28
1714 1968 5.300792 ACCAATGTTAGGTTACCACAGTTTG 59.699 40.000 3.51 3.11 35.33 2.93
1715 1969 5.451354 ACCAATGTTAGGTTACCACAGTTT 58.549 37.500 3.51 0.00 35.33 2.66
1716 1970 5.056553 ACCAATGTTAGGTTACCACAGTT 57.943 39.130 3.51 0.00 35.33 3.16
1756 2012 1.633774 ACTTCCACGTCTGGATCTGT 58.366 50.000 0.00 0.00 46.64 3.41
1761 2017 2.089980 GCTACTACTTCCACGTCTGGA 58.910 52.381 0.00 0.00 45.68 3.86
1842 2098 3.103742 GAGGTTCTGGTCTCTCTGGAAT 58.896 50.000 0.00 0.00 0.00 3.01
1887 2143 1.664321 GCTTGAGCTTCCATGGCAGG 61.664 60.000 13.60 3.94 38.21 4.85
1926 2182 5.059833 GGGCAGATATACACCTTCTTCTTG 58.940 45.833 0.00 0.00 0.00 3.02
2022 2278 2.568546 TCTTCTCCCCATGCTTCCTA 57.431 50.000 0.00 0.00 0.00 2.94
2079 2335 3.245016 TGTGAGCCTTCCAATCAGATTGT 60.245 43.478 19.79 2.27 38.59 2.71
2109 2365 0.321653 GGTACTCCTTGGTGCCACAG 60.322 60.000 0.00 0.00 40.80 3.66
2173 2429 9.817809 GTGTGATTAACTGATTATCCTAAGTGA 57.182 33.333 0.00 0.00 0.00 3.41
2174 2430 9.046296 GGTGTGATTAACTGATTATCCTAAGTG 57.954 37.037 0.00 0.00 0.00 3.16
2176 2432 9.613428 TTGGTGTGATTAACTGATTATCCTAAG 57.387 33.333 0.00 0.00 0.00 2.18
2177 2433 9.613428 CTTGGTGTGATTAACTGATTATCCTAA 57.387 33.333 0.00 0.00 0.00 2.69
2178 2434 8.988060 TCTTGGTGTGATTAACTGATTATCCTA 58.012 33.333 0.00 0.00 0.00 2.94
2179 2435 7.861629 TCTTGGTGTGATTAACTGATTATCCT 58.138 34.615 0.00 0.00 0.00 3.24
2180 2436 8.506168 TTCTTGGTGTGATTAACTGATTATCC 57.494 34.615 0.00 0.00 0.00 2.59
2183 2439 9.513906 TGAATTCTTGGTGTGATTAACTGATTA 57.486 29.630 7.05 0.00 0.00 1.75
2184 2440 8.408043 TGAATTCTTGGTGTGATTAACTGATT 57.592 30.769 7.05 0.00 0.00 2.57
2185 2441 8.408043 TTGAATTCTTGGTGTGATTAACTGAT 57.592 30.769 7.05 0.00 0.00 2.90
2186 2442 7.522073 GCTTGAATTCTTGGTGTGATTAACTGA 60.522 37.037 7.05 0.00 0.00 3.41
2187 2443 6.583806 GCTTGAATTCTTGGTGTGATTAACTG 59.416 38.462 7.05 0.00 0.00 3.16
2188 2444 6.568462 CGCTTGAATTCTTGGTGTGATTAACT 60.568 38.462 7.05 0.00 0.00 2.24
2189 2445 5.569059 CGCTTGAATTCTTGGTGTGATTAAC 59.431 40.000 7.05 0.00 0.00 2.01
2190 2446 5.471797 TCGCTTGAATTCTTGGTGTGATTAA 59.528 36.000 7.05 0.00 0.00 1.40
2213 2469 6.535865 TGTTTTTCATGGCTAATGATGCATTC 59.464 34.615 0.00 0.00 44.84 2.67
2247 2503 9.631257 TGACATTAATGTTCATGTATCCTTGAT 57.369 29.630 21.63 0.00 41.95 2.57
2292 2556 7.328277 AGATGTCAGTACTTCAGTCTACATC 57.672 40.000 0.00 0.00 41.30 3.06
2344 2610 6.151691 GTGATTTTCAGTTGCAATTAGCTGA 58.848 36.000 12.13 12.13 45.94 4.26
2456 2722 5.984233 ATTGCTATGCATTGCTTCAAATG 57.016 34.783 28.73 0.00 38.76 2.32
2473 2742 4.646040 TGCCACAGATGCTAAAATATTGCT 59.354 37.500 0.00 0.00 0.00 3.91
2564 2833 5.576447 AAATGTCAAGTTCCAAGAAACGT 57.424 34.783 0.00 0.00 34.27 3.99
2566 2835 6.739112 AGCTAAATGTCAAGTTCCAAGAAAC 58.261 36.000 0.00 0.00 0.00 2.78
2579 2848 9.890629 ATTGACATAAAGTAGAGCTAAATGTCA 57.109 29.630 10.31 10.31 46.41 3.58
2688 2957 0.883833 GCAGACTTCCCACCATTGTG 59.116 55.000 0.00 0.00 42.39 3.33
3024 3293 2.097466 ACTGGTGAAGTTGTTTGCGAAG 59.903 45.455 0.00 0.00 34.57 3.79
3132 3401 4.080751 TGACCATTCATGCTCTCATCTTCA 60.081 41.667 0.00 0.00 0.00 3.02
3432 3704 4.154737 TCCTGATTTTTCTGTTGCTCATCG 59.845 41.667 0.00 0.00 0.00 3.84
3541 3813 4.285260 TGAACTACCAGAGTAAGGAAACCC 59.715 45.833 0.00 0.00 37.44 4.11
3565 3840 1.819632 CGGGCAGCTTAGCGGAAAT 60.820 57.895 8.81 0.00 34.64 2.17
3570 3845 4.148825 ACCTCGGGCAGCTTAGCG 62.149 66.667 0.00 0.00 34.64 4.26
3678 3955 7.814587 GCTACTTTCTGATTTTGCCAATAAACT 59.185 33.333 0.00 0.00 0.00 2.66
3679 3956 7.063426 GGCTACTTTCTGATTTTGCCAATAAAC 59.937 37.037 0.00 0.00 38.99 2.01
3722 4000 1.231641 CCCCGAATGGCCCCATTAA 59.768 57.895 12.27 0.00 45.50 1.40
3807 4085 6.001460 ACATTCACCGATTCAAGGTTTAGAA 58.999 36.000 0.00 0.00 40.59 2.10
3808 4086 5.556915 ACATTCACCGATTCAAGGTTTAGA 58.443 37.500 0.00 0.00 40.59 2.10
3810 4088 6.703319 TCTACATTCACCGATTCAAGGTTTA 58.297 36.000 0.00 0.00 40.59 2.01
3814 4092 5.586243 ACAATCTACATTCACCGATTCAAGG 59.414 40.000 0.00 0.00 0.00 3.61
3815 4093 6.668541 ACAATCTACATTCACCGATTCAAG 57.331 37.500 0.00 0.00 0.00 3.02
3981 4374 2.467826 GCGCCTGTTGGAGATGCTC 61.468 63.158 0.00 0.00 34.95 4.26
3982 4375 2.437359 GCGCCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 34.95 3.79
3983 4376 3.869272 CGCGCCTGTTGGAGATGC 61.869 66.667 0.00 0.00 34.95 3.91
3984 4377 3.869272 GCGCGCCTGTTGGAGATG 61.869 66.667 23.24 0.00 34.95 2.90
3985 4378 3.899981 TTGCGCGCCTGTTGGAGAT 62.900 57.895 30.77 0.00 34.95 2.75
3986 4379 4.617520 TTGCGCGCCTGTTGGAGA 62.618 61.111 30.77 2.53 34.95 3.71
3987 4380 4.093952 CTTGCGCGCCTGTTGGAG 62.094 66.667 30.77 10.72 36.16 3.86
4005 4398 4.454717 GTTTTAGGGTGCCGCGCG 62.455 66.667 25.67 25.67 34.93 6.86
4006 4399 3.053896 AGTTTTAGGGTGCCGCGC 61.054 61.111 0.00 0.00 0.00 6.86
4007 4400 0.671163 TACAGTTTTAGGGTGCCGCG 60.671 55.000 0.00 0.00 0.00 6.46
4008 4401 1.467342 CTTACAGTTTTAGGGTGCCGC 59.533 52.381 0.00 0.00 0.00 6.53
4009 4402 3.048337 TCTTACAGTTTTAGGGTGCCG 57.952 47.619 0.00 0.00 0.00 5.69
4010 4403 7.457024 TTTATTCTTACAGTTTTAGGGTGCC 57.543 36.000 0.00 0.00 0.00 5.01
4011 4404 8.188799 GGATTTATTCTTACAGTTTTAGGGTGC 58.811 37.037 0.00 0.00 0.00 5.01
4012 4405 8.395633 CGGATTTATTCTTACAGTTTTAGGGTG 58.604 37.037 0.00 0.00 0.00 4.61
4013 4406 8.323567 TCGGATTTATTCTTACAGTTTTAGGGT 58.676 33.333 0.00 0.00 0.00 4.34
4014 4407 8.726870 TCGGATTTATTCTTACAGTTTTAGGG 57.273 34.615 0.00 0.00 0.00 3.53
4015 4408 8.827677 CCTCGGATTTATTCTTACAGTTTTAGG 58.172 37.037 0.00 0.00 0.00 2.69
4016 4409 8.336080 GCCTCGGATTTATTCTTACAGTTTTAG 58.664 37.037 0.00 0.00 0.00 1.85
4017 4410 7.281549 GGCCTCGGATTTATTCTTACAGTTTTA 59.718 37.037 0.00 0.00 0.00 1.52
4018 4411 6.095021 GGCCTCGGATTTATTCTTACAGTTTT 59.905 38.462 0.00 0.00 0.00 2.43
4026 4419 2.745152 CGGTGGCCTCGGATTTATTCTT 60.745 50.000 3.32 0.00 0.00 2.52
4163 4559 1.885850 CGGGTGCGGTATTGTAGCC 60.886 63.158 0.00 0.00 38.55 3.93
4269 4666 5.734031 TCCTAGGCCTCTCATATATAGCA 57.266 43.478 9.68 0.00 0.00 3.49
4418 4815 1.420138 ACGAATTCAAGGTGGTGGAGT 59.580 47.619 6.22 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.