Multiple sequence alignment - TraesCS3D01G167000

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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 TraesCS3D01G167000 chr3D 100.000 2155 0 0 884 3038 141410495 141412649 0.000000e+00 3980.0
1 TraesCS3D01G167000 chr3D 89.847 916 74 9 894 1802 147336118 147335215 0.000000e+00 1158.0
2 TraesCS3D01G167000 chr3D 89.606 914 77 10 894 1799 149544145 149545048 0.000000e+00 1146.0
3 TraesCS3D01G167000 chr3D 89.595 913 76 9 894 1799 149204984 149205884 0.000000e+00 1142.0
4 TraesCS3D01G167000 chr3D 100.000 460 0 0 1 460 141409612 141410071 0.000000e+00 850.0
5 TraesCS3D01G167000 chr3A 95.011 922 37 5 884 1799 159831894 159832812 0.000000e+00 1439.0
6 TraesCS3D01G167000 chr3A 91.240 879 34 13 1697 2542 159832636 159833504 0.000000e+00 1157.0
7 TraesCS3D01G167000 chr3A 91.768 826 56 8 984 1803 166923427 166924246 0.000000e+00 1138.0
8 TraesCS3D01G167000 chr3A 94.374 551 21 6 1697 2242 159431877 159432422 0.000000e+00 837.0
9 TraesCS3D01G167000 chr3A 94.861 467 19 3 2279 2742 159433420 159433884 0.000000e+00 725.0
10 TraesCS3D01G167000 chr3A 91.880 468 31 6 2555 3022 159429084 159429544 0.000000e+00 647.0
11 TraesCS3D01G167000 chr3A 93.317 404 23 4 2631 3034 159441414 159441813 7.250000e-166 593.0
12 TraesCS3D01G167000 chr3A 89.099 477 43 8 2548 3023 159833586 159834054 4.360000e-163 584.0
13 TraesCS3D01G167000 chr3A 92.593 405 22 8 2631 3034 159834501 159834898 2.630000e-160 575.0
14 TraesCS3D01G167000 chr3A 88.167 431 42 7 1 427 159831353 159831778 3.500000e-139 505.0
15 TraesCS3D01G167000 chr3A 84.069 408 31 15 2195 2569 159440982 159441388 2.230000e-96 363.0
16 TraesCS3D01G167000 chr3A 84.108 409 30 7 2195 2569 159834068 159834475 2.230000e-96 363.0
17 TraesCS3D01G167000 chr3A 97.561 41 0 1 2242 2282 159433369 159433408 5.430000e-08 69.4
18 TraesCS3D01G167000 chr3B 94.943 870 35 3 893 1756 203345641 203346507 0.000000e+00 1354.0
19 TraesCS3D01G167000 chr3B 94.541 806 40 3 970 1775 203549131 203549932 0.000000e+00 1242.0
20 TraesCS3D01G167000 chr3B 90.647 834 66 6 972 1799 221912453 221913280 0.000000e+00 1098.0
21 TraesCS3D01G167000 chr3B 91.414 792 37 10 1701 2461 203346389 203347180 0.000000e+00 1057.0
22 TraesCS3D01G167000 chr3B 90.891 494 35 7 2548 3038 203554469 203554955 0.000000e+00 654.0
23 TraesCS3D01G167000 chr3B 94.145 427 20 4 1697 2118 203549786 203550212 0.000000e+00 645.0
24 TraesCS3D01G167000 chr3B 90.814 479 34 7 2548 3023 203347854 203348325 1.540000e-177 632.0
25 TraesCS3D01G167000 chr3B 90.281 463 17 4 2108 2542 203553923 203554385 5.650000e-162 580.0
26 TraesCS3D01G167000 chr3B 92.519 401 26 4 2631 3031 203348781 203349177 3.400000e-159 571.0
27 TraesCS3D01G167000 chr3B 86.441 354 29 9 1697 2041 221913107 221913450 1.330000e-98 370.0
28 TraesCS3D01G167000 chr3B 86.207 348 31 9 1697 2041 221980587 221980920 8.010000e-96 361.0
29 TraesCS3D01G167000 chr3B 92.593 243 13 4 1 240 203344854 203345094 8.060000e-91 344.0
30 TraesCS3D01G167000 chr3B 85.028 354 34 10 1697 2041 215385825 215386168 2.900000e-90 342.0
31 TraesCS3D01G167000 chr3B 85.580 319 27 6 1697 2006 221458470 221458778 1.760000e-82 316.0
32 TraesCS3D01G167000 chr3B 81.579 418 33 12 2195 2569 203348339 203348755 3.810000e-79 305.0
33 TraesCS3D01G167000 chr3B 96.667 90 3 0 2453 2542 203347708 203347797 1.890000e-32 150.0
34 TraesCS3D01G167000 chr3B 98.684 76 1 0 2483 2558 221467572 221467647 5.280000e-28 135.0
35 TraesCS3D01G167000 chr3B 98.039 51 1 0 2066 2116 215386164 215386214 4.170000e-14 89.8
36 TraesCS3D01G167000 chr3B 98.039 51 1 0 2066 2116 215573074 215573124 4.170000e-14 89.8
37 TraesCS3D01G167000 chr3B 98.039 51 1 0 2066 2116 221466809 221466859 4.170000e-14 89.8
38 TraesCS3D01G167000 chr3B 98.039 51 1 0 2066 2116 221913446 221913496 4.170000e-14 89.8
39 TraesCS3D01G167000 chr6A 93.576 825 38 6 931 1755 146441660 146440851 0.000000e+00 1216.0
40 TraesCS3D01G167000 chr6A 89.481 713 49 14 2323 3023 146439015 146438317 0.000000e+00 878.0
41 TraesCS3D01G167000 chr6A 89.940 666 26 11 1697 2331 146440977 146440322 0.000000e+00 821.0
42 TraesCS3D01G167000 chr6A 91.649 467 31 7 2555 3021 146444195 146443737 9.180000e-180 640.0


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 TraesCS3D01G167000 chr3D 141409612 141412649 3037 False 2415.000000 3980 100.000000 1 3038 2 chr3D.!!$F3 3037
1 TraesCS3D01G167000 chr3D 147335215 147336118 903 True 1158.000000 1158 89.847000 894 1802 1 chr3D.!!$R1 908
2 TraesCS3D01G167000 chr3D 149544145 149545048 903 False 1146.000000 1146 89.606000 894 1799 1 chr3D.!!$F2 905
3 TraesCS3D01G167000 chr3D 149204984 149205884 900 False 1142.000000 1142 89.595000 894 1799 1 chr3D.!!$F1 905
4 TraesCS3D01G167000 chr3A 166923427 166924246 819 False 1138.000000 1138 91.768000 984 1803 1 chr3A.!!$F1 819
5 TraesCS3D01G167000 chr3A 159831353 159834898 3545 False 770.500000 1439 90.036333 1 3034 6 chr3A.!!$F4 3033
6 TraesCS3D01G167000 chr3A 159429084 159433884 4800 False 569.600000 837 94.669000 1697 3022 4 chr3A.!!$F2 1325
7 TraesCS3D01G167000 chr3A 159440982 159441813 831 False 478.000000 593 88.693000 2195 3034 2 chr3A.!!$F3 839
8 TraesCS3D01G167000 chr3B 203549131 203554955 5824 False 780.250000 1242 92.464500 970 3038 4 chr3B.!!$F5 2068
9 TraesCS3D01G167000 chr3B 203344854 203349177 4323 False 630.428571 1354 91.504143 1 3031 7 chr3B.!!$F4 3030
10 TraesCS3D01G167000 chr3B 221912453 221913496 1043 False 519.266667 1098 91.709000 972 2116 3 chr3B.!!$F8 1144
11 TraesCS3D01G167000 chr6A 146438317 146444195 5878 True 888.750000 1216 91.161500 931 3023 4 chr6A.!!$R1 2092

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
275 277 0.174162 TTTAGGAACCCTAGCGCGTC 59.826 55.0 8.43 0.0 37.42 5.19 F
1193 1243 0.168788 CGCAGGTACGTTCGTCCTAA 59.831 55.0 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1465 0.032815 GTAGGAGGGCTTCTCGATGC 59.967 60.0 0.0 0.0 43.34 3.91 R
2443 10117 0.250252 TGCTGACGAATGTGCCTTGA 60.250 50.0 0.0 0.0 0.00 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.059773 TCAGCCCATAAAAATGGTCCTT 57.940 40.909 3.84 0.00 40.06 3.36
32 33 4.098501 GCCCATAAAAATGGTCCTTCAGAG 59.901 45.833 3.84 0.00 40.06 3.35
111 112 1.514014 GCATGTTTGCCGCCTTACG 60.514 57.895 0.00 0.00 43.38 3.18
142 143 2.237392 CCAGCACTCCTAGGTAGCTTTT 59.763 50.000 18.31 1.44 32.35 2.27
169 170 1.859080 GTTGATCACGTAAGGATCGGC 59.141 52.381 0.00 2.49 42.95 5.54
177 178 0.249363 GTAAGGATCGGCCCGAAGAC 60.249 60.000 11.19 3.11 39.99 3.01
189 190 1.877443 CCCGAAGACCAATTCAACGTT 59.123 47.619 0.00 0.00 0.00 3.99
203 204 3.670625 TCAACGTTAGAAATCAGGTGGG 58.329 45.455 0.00 0.00 0.00 4.61
215 217 1.906574 TCAGGTGGGATTGGTGTAGAC 59.093 52.381 0.00 0.00 0.00 2.59
248 250 4.692475 AACCCTAGCGCGCCGTTT 62.692 61.111 30.33 12.34 0.00 3.60
249 251 4.692475 ACCCTAGCGCGCCGTTTT 62.692 61.111 30.33 11.88 0.00 2.43
252 254 4.160635 CTAGCGCGCCGTTTTGGG 62.161 66.667 30.33 5.16 38.63 4.12
259 261 0.311477 GCGCCGTTTTGGGAAGTTTA 59.689 50.000 0.00 0.00 38.63 2.01
272 274 2.277969 GAAGTTTAGGAACCCTAGCGC 58.722 52.381 0.00 0.00 37.42 5.92
273 275 0.175073 AGTTTAGGAACCCTAGCGCG 59.825 55.000 0.00 0.00 37.42 6.86
275 277 0.174162 TTTAGGAACCCTAGCGCGTC 59.826 55.000 8.43 0.00 37.42 5.19
309 311 5.401033 AGCGAGATTTCTTCATCGATTTG 57.599 39.130 0.00 0.00 37.35 2.32
314 316 7.061094 GCGAGATTTCTTCATCGATTTGTTTTT 59.939 33.333 0.00 0.00 37.35 1.94
315 317 8.360855 CGAGATTTCTTCATCGATTTGTTTTTG 58.639 33.333 0.00 0.00 37.35 2.44
316 318 8.524870 AGATTTCTTCATCGATTTGTTTTTGG 57.475 30.769 0.00 0.00 0.00 3.28
377 387 9.860650 TTACATATTAGAAATAGCACCAACCAT 57.139 29.630 0.00 0.00 0.00 3.55
382 392 3.199071 AGAAATAGCACCAACCATCCGTA 59.801 43.478 0.00 0.00 0.00 4.02
446 495 4.645692 AAAAATCGCGCCAACCAC 57.354 50.000 0.00 0.00 0.00 4.16
447 496 1.371145 AAAAATCGCGCCAACCACG 60.371 52.632 0.00 0.00 0.00 4.94
448 497 2.065906 AAAAATCGCGCCAACCACGT 62.066 50.000 0.00 0.00 0.00 4.49
451 500 1.229315 AATCGCGCCAACCACGTTAA 61.229 50.000 0.00 0.00 0.00 2.01
452 501 1.229315 ATCGCGCCAACCACGTTAAA 61.229 50.000 0.00 0.00 0.00 1.52
453 502 1.009900 CGCGCCAACCACGTTAAAA 60.010 52.632 0.00 0.00 0.00 1.52
953 1003 4.332828 CCTAGTTTCCGATCCCAACTTTT 58.667 43.478 4.61 0.00 32.88 2.27
1091 1141 3.033764 GGCGACGTGCGTCAAAGA 61.034 61.111 21.98 0.00 45.76 2.52
1101 1151 3.795638 GTCAAAGACGGGCGGATC 58.204 61.111 0.00 0.00 0.00 3.36
1102 1152 1.218316 GTCAAAGACGGGCGGATCT 59.782 57.895 0.00 0.00 0.00 2.75
1103 1153 0.391263 GTCAAAGACGGGCGGATCTT 60.391 55.000 0.00 1.93 36.73 2.40
1104 1154 0.323629 TCAAAGACGGGCGGATCTTT 59.676 50.000 13.02 13.02 44.19 2.52
1105 1155 0.727398 CAAAGACGGGCGGATCTTTC 59.273 55.000 14.76 0.00 42.03 2.62
1129 1179 1.583054 GGAAATCATCGAGTTCCCCG 58.417 55.000 11.24 0.00 46.90 5.73
1130 1180 0.938008 GAAATCATCGAGTTCCCCGC 59.062 55.000 0.00 0.00 31.57 6.13
1132 1182 2.644555 AATCATCGAGTTCCCCGCGG 62.645 60.000 21.04 21.04 36.95 6.46
1133 1183 4.143333 CATCGAGTTCCCCGCGGT 62.143 66.667 26.12 4.16 36.95 5.68
1134 1184 4.143333 ATCGAGTTCCCCGCGGTG 62.143 66.667 26.12 14.27 36.95 4.94
1173 1223 3.773630 CGCATCGTGTCCGCGTTT 61.774 61.111 4.92 0.00 43.86 3.60
1174 1224 2.095843 GCATCGTGTCCGCGTTTC 59.904 61.111 4.92 0.00 0.00 2.78
1175 1225 2.390288 CATCGTGTCCGCGTTTCG 59.610 61.111 4.92 4.59 38.08 3.46
1187 1237 1.409579 CGTTTCGCAGGTACGTTCG 59.590 57.895 0.00 1.07 0.00 3.95
1188 1238 1.270777 CGTTTCGCAGGTACGTTCGT 61.271 55.000 7.44 2.91 0.00 3.85
1189 1239 0.432361 GTTTCGCAGGTACGTTCGTC 59.568 55.000 7.44 0.00 0.00 4.20
1191 1241 1.518056 TTCGCAGGTACGTTCGTCCT 61.518 55.000 7.44 5.92 0.00 3.85
1192 1242 0.673333 TCGCAGGTACGTTCGTCCTA 60.673 55.000 7.44 0.00 0.00 2.94
1193 1243 0.168788 CGCAGGTACGTTCGTCCTAA 59.831 55.000 0.00 0.00 0.00 2.69
1194 1244 1.792993 CGCAGGTACGTTCGTCCTAAG 60.793 57.143 0.00 3.26 0.00 2.18
1197 1247 2.097825 AGGTACGTTCGTCCTAAGCAT 58.902 47.619 0.00 0.00 0.00 3.79
1199 1249 2.159338 GGTACGTTCGTCCTAAGCATCA 60.159 50.000 0.00 0.00 0.00 3.07
1200 1250 1.992170 ACGTTCGTCCTAAGCATCAC 58.008 50.000 0.00 0.00 0.00 3.06
1201 1251 1.278238 CGTTCGTCCTAAGCATCACC 58.722 55.000 0.00 0.00 0.00 4.02
1202 1252 1.653151 GTTCGTCCTAAGCATCACCC 58.347 55.000 0.00 0.00 0.00 4.61
1205 1255 0.537188 CGTCCTAAGCATCACCCTGT 59.463 55.000 0.00 0.00 0.00 4.00
1206 1256 1.740380 CGTCCTAAGCATCACCCTGTG 60.740 57.143 0.00 0.00 34.45 3.66
1207 1257 0.253044 TCCTAAGCATCACCCTGTGC 59.747 55.000 0.00 0.00 41.57 4.57
1211 1261 3.583383 GCATCACCCTGTGCTGAC 58.417 61.111 2.51 0.00 38.30 3.51
1213 1263 1.377725 CATCACCCTGTGCTGACCC 60.378 63.158 0.00 0.00 32.25 4.46
1214 1264 1.847506 ATCACCCTGTGCTGACCCA 60.848 57.895 0.00 0.00 32.98 4.51
1216 1266 1.075482 CACCCTGTGCTGACCCAAT 59.925 57.895 0.00 0.00 0.00 3.16
1217 1267 0.540365 CACCCTGTGCTGACCCAATT 60.540 55.000 0.00 0.00 0.00 2.32
1218 1268 0.188342 ACCCTGTGCTGACCCAATTT 59.812 50.000 0.00 0.00 0.00 1.82
1219 1269 1.341080 CCCTGTGCTGACCCAATTTT 58.659 50.000 0.00 0.00 0.00 1.82
1220 1270 1.001181 CCCTGTGCTGACCCAATTTTG 59.999 52.381 0.00 0.00 0.00 2.44
1221 1271 1.606224 CCTGTGCTGACCCAATTTTGC 60.606 52.381 0.00 0.00 0.00 3.68
1222 1272 1.068895 CTGTGCTGACCCAATTTTGCA 59.931 47.619 0.00 0.00 0.00 4.08
1226 1276 1.631405 CTGACCCAATTTTGCAGGGA 58.369 50.000 14.61 0.00 45.80 4.20
1229 1279 0.178924 ACCCAATTTTGCAGGGAGCT 60.179 50.000 14.61 0.00 45.80 4.09
1230 1280 0.533951 CCCAATTTTGCAGGGAGCTC 59.466 55.000 4.71 4.71 45.80 4.09
1231 1281 1.259609 CCAATTTTGCAGGGAGCTCA 58.740 50.000 17.19 0.00 45.94 4.26
1232 1282 1.067354 CCAATTTTGCAGGGAGCTCAC 60.067 52.381 17.19 13.15 45.94 3.51
1233 1283 1.067354 CAATTTTGCAGGGAGCTCACC 60.067 52.381 13.73 12.71 45.94 4.02
1235 1285 3.551496 TTTGCAGGGAGCTCACCGG 62.551 63.158 13.73 14.02 45.94 5.28
1257 1307 4.477975 CGGCAGGAGGACGTCGAC 62.478 72.222 9.92 5.18 45.26 4.20
1259 1309 4.477975 GCAGGAGGACGTCGACGG 62.478 72.222 37.89 21.11 44.95 4.79
1297 1347 2.816958 CGCTCTGGCTGCACGATT 60.817 61.111 0.50 0.00 36.09 3.34
1298 1348 2.806856 CGCTCTGGCTGCACGATTC 61.807 63.158 0.50 0.00 36.09 2.52
1299 1349 1.449246 GCTCTGGCTGCACGATTCT 60.449 57.895 0.50 0.00 35.22 2.40
1300 1350 1.023513 GCTCTGGCTGCACGATTCTT 61.024 55.000 0.50 0.00 35.22 2.52
1301 1351 0.725686 CTCTGGCTGCACGATTCTTG 59.274 55.000 0.50 0.00 0.00 3.02
1302 1352 0.674581 TCTGGCTGCACGATTCTTGG 60.675 55.000 0.50 0.00 0.00 3.61
1303 1353 2.262471 CTGGCTGCACGATTCTTGGC 62.262 60.000 0.50 0.00 0.00 4.52
1305 1355 1.136147 GCTGCACGATTCTTGGCTG 59.864 57.895 0.00 0.00 0.00 4.85
1306 1356 1.300971 GCTGCACGATTCTTGGCTGA 61.301 55.000 0.00 0.00 0.00 4.26
1307 1357 1.159285 CTGCACGATTCTTGGCTGAA 58.841 50.000 0.00 0.00 0.00 3.02
1311 1361 1.021390 ACGATTCTTGGCTGAAGGCG 61.021 55.000 0.00 12.85 44.42 5.52
1312 1362 1.709147 CGATTCTTGGCTGAAGGCGG 61.709 60.000 0.00 0.00 44.42 6.13
1313 1363 1.997928 GATTCTTGGCTGAAGGCGGC 61.998 60.000 0.00 0.00 45.89 6.53
1336 1386 3.068881 CGGGAGCAGGGAACAAGA 58.931 61.111 0.00 0.00 0.00 3.02
1337 1387 1.078848 CGGGAGCAGGGAACAAGAG 60.079 63.158 0.00 0.00 0.00 2.85
1338 1388 1.544825 CGGGAGCAGGGAACAAGAGA 61.545 60.000 0.00 0.00 0.00 3.10
1339 1389 0.251634 GGGAGCAGGGAACAAGAGAG 59.748 60.000 0.00 0.00 0.00 3.20
1343 1393 1.674057 CAGGGAACAAGAGAGGCGT 59.326 57.895 0.00 0.00 0.00 5.68
1344 1394 0.390472 CAGGGAACAAGAGAGGCGTC 60.390 60.000 0.00 0.00 0.00 5.19
1345 1395 1.079057 GGGAACAAGAGAGGCGTCC 60.079 63.158 2.06 0.00 0.00 4.79
1347 1397 2.048127 AACAAGAGAGGCGTCCGC 60.048 61.111 2.45 2.45 41.06 5.54
1348 1398 2.493907 GAACAAGAGAGGCGTCCGCT 62.494 60.000 11.82 2.09 41.60 5.52
1349 1399 2.100879 AACAAGAGAGGCGTCCGCTT 62.101 55.000 11.82 3.38 41.60 4.68
1351 1401 3.302347 AAGAGAGGCGTCCGCTTGG 62.302 63.158 11.82 0.00 41.60 3.61
1363 1413 4.643387 GCTTGGCCGTGGTGACCT 62.643 66.667 2.11 0.00 0.00 3.85
1364 1414 2.669569 CTTGGCCGTGGTGACCTG 60.670 66.667 2.11 0.00 0.00 4.00
1369 1419 3.706373 CCGTGGTGACCTGGGGAG 61.706 72.222 2.11 0.00 0.00 4.30
1370 1420 2.603473 CGTGGTGACCTGGGGAGA 60.603 66.667 2.11 0.00 0.00 3.71
1371 1421 2.943978 CGTGGTGACCTGGGGAGAC 61.944 68.421 2.11 0.00 0.00 3.36
1372 1422 1.536662 GTGGTGACCTGGGGAGACT 60.537 63.158 2.11 0.00 0.00 3.24
1374 1424 2.294078 GGTGACCTGGGGAGACTGG 61.294 68.421 0.00 0.00 35.76 4.00
1376 1426 2.450243 GACCTGGGGAGACTGGGA 59.550 66.667 0.00 0.00 34.12 4.37
1377 1427 1.003573 GACCTGGGGAGACTGGGAT 59.996 63.158 0.00 0.00 34.12 3.85
1378 1428 0.621862 GACCTGGGGAGACTGGGATT 60.622 60.000 0.00 0.00 34.12 3.01
1379 1429 0.916358 ACCTGGGGAGACTGGGATTG 60.916 60.000 0.00 0.00 34.12 2.67
1380 1430 1.225704 CTGGGGAGACTGGGATTGC 59.774 63.158 0.00 0.00 0.00 3.56
1383 1433 2.514824 GGAGACTGGGATTGCCGC 60.515 66.667 0.00 0.00 33.83 6.53
1386 1436 3.134127 GACTGGGATTGCCGCACC 61.134 66.667 0.00 0.00 33.84 5.01
1388 1438 2.440796 CTGGGATTGCCGCACCAT 60.441 61.111 1.89 0.00 33.84 3.55
1389 1439 2.755064 TGGGATTGCCGCACCATG 60.755 61.111 0.00 0.00 32.34 3.66
1390 1440 4.211502 GGGATTGCCGCACCATGC 62.212 66.667 0.00 0.00 40.69 4.06
1393 1443 3.459378 GATTGCCGCACCATGCTCG 62.459 63.158 0.00 0.00 42.25 5.03
1394 1444 3.974835 ATTGCCGCACCATGCTCGA 62.975 57.895 0.00 0.00 42.25 4.04
1397 1447 2.434884 CCGCACCATGCTCGAGTT 60.435 61.111 15.13 0.00 42.25 3.01
1399 1449 2.792290 CGCACCATGCTCGAGTTCG 61.792 63.158 15.13 2.20 42.25 3.95
1400 1450 1.446099 GCACCATGCTCGAGTTCGA 60.446 57.895 15.13 4.00 46.44 3.71
1408 1458 3.362797 TCGAGTTCGAGTGCCGCT 61.363 61.111 0.00 0.00 44.22 5.52
1409 1459 2.430921 CGAGTTCGAGTGCCGCTT 60.431 61.111 0.00 0.00 43.02 4.68
1410 1460 2.437343 CGAGTTCGAGTGCCGCTTC 61.437 63.158 0.00 0.00 43.02 3.86
1411 1461 1.372997 GAGTTCGAGTGCCGCTTCA 60.373 57.895 0.00 0.00 38.37 3.02
1412 1462 0.944311 GAGTTCGAGTGCCGCTTCAA 60.944 55.000 0.00 0.00 38.37 2.69
1414 1464 1.667830 TTCGAGTGCCGCTTCAAGG 60.668 57.895 0.00 0.00 38.37 3.61
1415 1465 3.121030 CGAGTGCCGCTTCAAGGG 61.121 66.667 0.00 0.00 0.00 3.95
1421 1471 2.125147 CCGCTTCAAGGGCATCGA 60.125 61.111 0.00 0.00 0.00 3.59
1422 1472 2.176273 CCGCTTCAAGGGCATCGAG 61.176 63.158 0.00 0.00 0.00 4.04
1423 1473 1.153568 CGCTTCAAGGGCATCGAGA 60.154 57.895 0.00 0.00 0.00 4.04
1426 1476 1.012841 CTTCAAGGGCATCGAGAAGC 58.987 55.000 0.00 0.00 30.64 3.86
1431 1481 2.110006 GGCATCGAGAAGCCCTCC 59.890 66.667 13.65 0.00 45.18 4.30
1432 1482 2.439104 GGCATCGAGAAGCCCTCCT 61.439 63.158 13.65 0.00 45.18 3.69
1435 1485 1.698506 CATCGAGAAGCCCTCCTACT 58.301 55.000 0.00 0.00 38.71 2.57
1437 1487 1.765230 TCGAGAAGCCCTCCTACTTC 58.235 55.000 0.00 0.00 42.13 3.01
1440 1490 2.312390 GAGAAGCCCTCCTACTTCGAT 58.688 52.381 0.00 0.00 45.56 3.59
1441 1491 2.295070 GAGAAGCCCTCCTACTTCGATC 59.705 54.545 0.00 0.00 45.56 3.69
1442 1492 2.032620 GAAGCCCTCCTACTTCGATCA 58.967 52.381 0.00 0.00 33.56 2.92
1443 1493 1.698506 AGCCCTCCTACTTCGATCAG 58.301 55.000 0.00 0.00 0.00 2.90
1445 1495 1.067821 GCCCTCCTACTTCGATCAGTG 59.932 57.143 0.00 0.00 0.00 3.66
1447 1497 2.656002 CCTCCTACTTCGATCAGTGGA 58.344 52.381 2.45 5.55 0.00 4.02
1448 1498 3.226777 CCTCCTACTTCGATCAGTGGAT 58.773 50.000 2.45 0.00 36.13 3.41
1449 1499 3.254657 CCTCCTACTTCGATCAGTGGATC 59.745 52.174 2.45 0.00 45.32 3.36
1461 1511 4.952071 TCAGTGGATCAATCTGAGGATC 57.048 45.455 11.58 11.58 39.31 3.36
1468 1518 2.412591 TCAATCTGAGGATCCCCTTCC 58.587 52.381 8.55 0.00 44.53 3.46
1469 1519 2.130193 CAATCTGAGGATCCCCTTCCA 58.870 52.381 8.55 0.00 44.53 3.53
1472 1522 1.694169 TGAGGATCCCCTTCCAGGC 60.694 63.158 8.55 0.00 44.53 4.85
1473 1523 1.694169 GAGGATCCCCTTCCAGGCA 60.694 63.158 8.55 0.00 44.53 4.75
1475 1525 2.194326 GATCCCCTTCCAGGCAGC 59.806 66.667 0.00 0.00 32.73 5.25
1509 1559 2.046892 CGGGTCAACCTGCAGGAG 60.047 66.667 39.19 28.12 38.94 3.69
1563 1613 3.357079 CTGCACTGCGGGTTGGAC 61.357 66.667 1.41 0.00 0.00 4.02
1565 1615 4.980805 GCACTGCGGGTTGGACGA 62.981 66.667 0.00 0.00 0.00 4.20
1566 1616 2.047274 CACTGCGGGTTGGACGAT 60.047 61.111 0.00 0.00 0.00 3.73
1567 1617 2.047274 ACTGCGGGTTGGACGATG 60.047 61.111 0.00 0.00 0.00 3.84
1568 1618 3.499737 CTGCGGGTTGGACGATGC 61.500 66.667 0.00 0.00 0.00 3.91
1572 1622 3.195698 GGGTTGGACGATGCGCTC 61.196 66.667 9.73 2.56 0.00 5.03
1573 1623 2.434185 GGTTGGACGATGCGCTCA 60.434 61.111 9.73 0.00 0.00 4.26
1574 1624 2.032634 GGTTGGACGATGCGCTCAA 61.033 57.895 9.73 0.98 0.00 3.02
1577 1627 1.565156 TTGGACGATGCGCTCAACAC 61.565 55.000 9.73 0.00 0.00 3.32
1578 1628 2.391821 GACGATGCGCTCAACACG 59.608 61.111 9.73 7.84 0.00 4.49
1579 1629 3.071459 GACGATGCGCTCAACACGG 62.071 63.158 9.73 0.00 0.00 4.94
1580 1630 4.505217 CGATGCGCTCAACACGGC 62.505 66.667 9.73 0.00 0.00 5.68
1601 1651 3.097461 GGCTGCTTGCTGAGATCAT 57.903 52.632 0.00 0.00 42.39 2.45
1602 1652 0.663688 GGCTGCTTGCTGAGATCATG 59.336 55.000 0.00 0.00 42.39 3.07
1603 1653 0.029567 GCTGCTTGCTGAGATCATGC 59.970 55.000 3.71 0.00 38.95 4.06
1604 1654 0.305009 CTGCTTGCTGAGATCATGCG 59.695 55.000 0.00 0.00 37.40 4.73
1605 1655 1.093496 TGCTTGCTGAGATCATGCGG 61.093 55.000 0.00 0.00 37.40 5.69
1606 1656 1.647629 CTTGCTGAGATCATGCGGC 59.352 57.895 0.00 1.17 36.93 6.53
1607 1657 2.102394 CTTGCTGAGATCATGCGGCG 62.102 60.000 0.51 0.51 39.23 6.46
1609 1659 2.586914 CTGAGATCATGCGGCGCA 60.587 61.111 38.09 38.09 44.86 6.09
1620 1670 2.892425 CGGCGCAGGGTCAAGATC 60.892 66.667 10.83 0.00 0.00 2.75
1621 1671 2.268920 GGCGCAGGGTCAAGATCA 59.731 61.111 10.83 0.00 0.00 2.92
1622 1672 2.109126 GGCGCAGGGTCAAGATCAC 61.109 63.158 10.83 0.00 0.00 3.06
1624 1674 1.296392 CGCAGGGTCAAGATCACCA 59.704 57.895 3.34 0.00 35.35 4.17
1625 1675 0.107508 CGCAGGGTCAAGATCACCAT 60.108 55.000 3.34 0.00 35.35 3.55
1626 1676 1.673168 GCAGGGTCAAGATCACCATC 58.327 55.000 3.34 0.00 35.35 3.51
1628 1678 2.636830 CAGGGTCAAGATCACCATCAC 58.363 52.381 3.34 0.00 35.35 3.06
1629 1679 1.561542 AGGGTCAAGATCACCATCACC 59.438 52.381 3.34 0.00 35.35 4.02
1630 1680 1.656652 GGTCAAGATCACCATCACCG 58.343 55.000 0.00 0.00 33.63 4.94
1631 1681 1.656652 GTCAAGATCACCATCACCGG 58.343 55.000 0.00 0.00 0.00 5.28
1633 1683 0.107508 CAAGATCACCATCACCGGCT 60.108 55.000 0.00 0.00 0.00 5.52
1634 1684 0.620556 AAGATCACCATCACCGGCTT 59.379 50.000 0.00 0.00 0.00 4.35
1635 1685 0.107508 AGATCACCATCACCGGCTTG 60.108 55.000 0.00 0.00 0.00 4.01
1636 1686 1.718757 GATCACCATCACCGGCTTGC 61.719 60.000 0.00 0.00 0.00 4.01
1638 1688 2.360350 ACCATCACCGGCTTGCTG 60.360 61.111 0.00 0.00 0.00 4.41
1639 1689 3.136123 CCATCACCGGCTTGCTGG 61.136 66.667 18.05 18.05 0.00 4.85
1640 1690 3.818787 CATCACCGGCTTGCTGGC 61.819 66.667 19.39 0.00 37.94 4.85
1664 1714 4.838152 GCCGCCGATCCAGCAGAA 62.838 66.667 3.53 0.00 0.00 3.02
1666 1716 3.267860 CGCCGATCCAGCAGAAGC 61.268 66.667 3.53 0.00 42.56 3.86
1667 1717 2.124983 GCCGATCCAGCAGAAGCA 60.125 61.111 0.00 0.00 45.49 3.91
1668 1718 2.178890 GCCGATCCAGCAGAAGCAG 61.179 63.158 0.00 0.00 45.49 4.24
1669 1719 2.178890 CCGATCCAGCAGAAGCAGC 61.179 63.158 0.00 0.00 45.49 5.25
1670 1720 1.449070 CGATCCAGCAGAAGCAGCA 60.449 57.895 0.00 0.00 45.49 4.41
1671 1721 1.429927 CGATCCAGCAGAAGCAGCAG 61.430 60.000 0.00 0.00 45.49 4.24
1672 1722 1.716826 GATCCAGCAGAAGCAGCAGC 61.717 60.000 0.00 0.00 45.49 5.25
1673 1723 3.441290 CCAGCAGAAGCAGCAGCC 61.441 66.667 0.00 0.00 45.49 4.85
1674 1724 2.360100 CAGCAGAAGCAGCAGCCT 60.360 61.111 0.00 0.00 45.49 4.58
1675 1725 2.360100 AGCAGAAGCAGCAGCCTG 60.360 61.111 0.00 0.00 45.49 4.85
1676 1726 3.441290 GCAGAAGCAGCAGCCTGG 61.441 66.667 8.91 0.00 43.56 4.45
1677 1727 3.441290 CAGAAGCAGCAGCCTGGC 61.441 66.667 11.65 11.65 43.56 4.85
1678 1728 3.962694 AGAAGCAGCAGCCTGGCA 61.963 61.111 22.65 0.00 43.56 4.92
1680 1730 4.591399 AAGCAGCAGCCTGGCACA 62.591 61.111 22.65 0.00 43.56 4.57
1693 1743 4.347453 GCACAAGCCCTTGCGGTG 62.347 66.667 7.88 7.66 44.94 4.94
1734 3342 1.746615 GCCGATCCAGCAGAAGCAA 60.747 57.895 0.00 0.00 45.49 3.91
1759 3367 3.605664 GCACAAGCCCTTGCGGTT 61.606 61.111 7.88 0.00 44.03 4.44
2043 3704 2.233271 CTGTGGAGCAACTGAACCAAT 58.767 47.619 0.00 0.00 34.11 3.16
2049 3710 2.086869 AGCAACTGAACCAATGATCCG 58.913 47.619 0.00 0.00 0.00 4.18
2589 10896 2.425592 CGTGGTGCTGGAAGTCCA 59.574 61.111 0.00 0.00 45.30 4.02
2608 10915 3.723154 TCCAGGGGGTACAGTTTAAAACT 59.277 43.478 0.00 0.00 37.61 2.66
2689 10999 6.017440 TCGTTCCTTTTATCCACTTTCAGTTG 60.017 38.462 0.00 0.00 0.00 3.16
2695 11006 6.959639 TTTATCCACTTTCAGTTGCTCTTT 57.040 33.333 0.00 0.00 0.00 2.52
2730 11041 1.888512 TGAGGCTTGCTTGGTTCATTC 59.111 47.619 0.00 0.00 0.00 2.67
2803 11115 7.144722 ACTTTCATCATATTTTCAGCGACAA 57.855 32.000 0.00 0.00 0.00 3.18
2804 11116 7.592938 ACTTTCATCATATTTTCAGCGACAAA 58.407 30.769 0.00 0.00 0.00 2.83
2856 12016 6.038603 TGTTGCTCTGATAGAATTATTGGTGC 59.961 38.462 0.00 0.00 0.00 5.01
2861 12021 5.827797 TCTGATAGAATTATTGGTGCCCAAC 59.172 40.000 8.59 0.00 46.95 3.77
2867 12027 2.612285 TATTGGTGCCCAACATCCAA 57.388 45.000 8.59 0.00 46.95 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.101415 CGTGATAGGGATTGCACTCTGA 59.899 50.000 3.88 0.00 0.00 3.27
72 73 1.078918 TCGACGGAGAAGGCGTCTA 60.079 57.895 2.07 0.00 36.41 2.59
111 112 1.818785 GAGTGCTGGCTCATGGCTC 60.819 63.158 6.20 0.00 41.46 4.70
142 143 2.549134 CCTTACGTGATCAACCACACCA 60.549 50.000 0.00 0.00 36.89 4.17
169 170 1.519408 ACGTTGAATTGGTCTTCGGG 58.481 50.000 0.00 0.00 0.00 5.14
177 178 6.086222 CACCTGATTTCTAACGTTGAATTGG 58.914 40.000 11.99 14.81 0.00 3.16
189 190 3.591527 ACACCAATCCCACCTGATTTCTA 59.408 43.478 0.00 0.00 32.71 2.10
203 204 3.055602 AGTTTACCCGGTCTACACCAATC 60.056 47.826 0.00 0.00 44.02 2.67
215 217 1.250328 GGTTCCCAAAGTTTACCCGG 58.750 55.000 0.00 0.00 0.00 5.73
247 249 4.507869 GCTAGGGTTCCTAAACTTCCCAAA 60.508 45.833 0.00 0.00 40.48 3.28
248 250 3.009805 GCTAGGGTTCCTAAACTTCCCAA 59.990 47.826 0.00 0.00 40.48 4.12
249 251 2.574824 GCTAGGGTTCCTAAACTTCCCA 59.425 50.000 0.00 0.00 40.48 4.37
252 254 2.277969 GCGCTAGGGTTCCTAAACTTC 58.722 52.381 8.77 0.00 35.49 3.01
259 261 3.823330 CGACGCGCTAGGGTTCCT 61.823 66.667 5.73 0.00 43.97 3.36
272 274 4.821589 GCTCCTTCCCTGGCGACG 62.822 72.222 0.00 0.00 0.00 5.12
286 288 5.006165 ACAAATCGATGAAGAAATCTCGCTC 59.994 40.000 0.00 0.00 32.36 5.03
309 311 4.039852 TGATTTGCTAGGGTTCCCAAAAAC 59.960 41.667 10.73 5.11 31.80 2.43
314 316 3.785887 ACTATGATTTGCTAGGGTTCCCA 59.214 43.478 10.73 0.00 0.00 4.37
315 317 4.103311 AGACTATGATTTGCTAGGGTTCCC 59.897 45.833 0.00 0.00 0.00 3.97
316 318 5.297569 AGACTATGATTTGCTAGGGTTCC 57.702 43.478 0.00 0.00 0.00 3.62
435 484 0.591741 TTTTTAACGTGGTTGGCGCG 60.592 50.000 0.00 0.00 0.00 6.86
888 937 1.287425 GATCGAAAACTAGGGCACGG 58.713 55.000 0.00 0.00 0.00 4.94
1085 1135 0.323629 AAAGATCCGCCCGTCTTTGA 59.676 50.000 5.76 0.00 41.67 2.69
1087 1137 0.392595 GGAAAGATCCGCCCGTCTTT 60.393 55.000 6.13 6.13 44.82 2.52
1088 1138 1.221021 GGAAAGATCCGCCCGTCTT 59.779 57.895 0.00 0.00 35.59 3.01
1089 1139 2.901042 GGAAAGATCCGCCCGTCT 59.099 61.111 0.00 0.00 35.59 4.18
1103 1153 1.207089 ACTCGATGATTTCCTGCGGAA 59.793 47.619 6.01 6.01 40.27 4.30
1104 1154 0.824109 ACTCGATGATTTCCTGCGGA 59.176 50.000 0.00 0.00 0.00 5.54
1105 1155 1.594862 GAACTCGATGATTTCCTGCGG 59.405 52.381 0.00 0.00 0.00 5.69
1107 1157 1.943340 GGGAACTCGATGATTTCCTGC 59.057 52.381 13.49 0.00 40.02 4.85
1108 1158 2.565841 GGGGAACTCGATGATTTCCTG 58.434 52.381 13.49 0.00 40.02 3.86
1109 1159 1.139058 CGGGGAACTCGATGATTTCCT 59.861 52.381 13.49 0.00 40.02 3.36
1110 1160 1.583054 CGGGGAACTCGATGATTTCC 58.417 55.000 7.25 7.25 39.61 3.13
1111 1161 0.938008 GCGGGGAACTCGATGATTTC 59.062 55.000 0.00 0.00 0.00 2.17
1112 1162 0.810031 CGCGGGGAACTCGATGATTT 60.810 55.000 0.00 0.00 0.00 2.17
1113 1163 1.227263 CGCGGGGAACTCGATGATT 60.227 57.895 0.00 0.00 0.00 2.57
1114 1164 2.417516 CGCGGGGAACTCGATGAT 59.582 61.111 0.00 0.00 0.00 2.45
1115 1165 3.833645 CCGCGGGGAACTCGATGA 61.834 66.667 20.10 0.00 34.06 2.92
1117 1167 4.143333 CACCGCGGGGAACTCGAT 62.143 66.667 31.76 0.57 36.97 3.59
1157 1207 2.095843 GAAACGCGGACACGATGC 59.904 61.111 12.47 0.00 44.60 3.91
1159 1209 3.475774 GCGAAACGCGGACACGAT 61.476 61.111 12.47 0.00 44.55 3.73
1171 1221 0.664166 GGACGAACGTACCTGCGAAA 60.664 55.000 0.00 0.00 35.59 3.46
1172 1222 1.081242 GGACGAACGTACCTGCGAA 60.081 57.895 0.00 0.00 35.59 4.70
1173 1223 0.673333 TAGGACGAACGTACCTGCGA 60.673 55.000 19.91 5.99 35.52 5.10
1174 1224 0.168788 TTAGGACGAACGTACCTGCG 59.831 55.000 19.91 4.14 35.52 5.18
1175 1225 1.905449 CTTAGGACGAACGTACCTGC 58.095 55.000 19.91 2.75 35.52 4.85
1177 1227 1.538047 TGCTTAGGACGAACGTACCT 58.462 50.000 17.06 17.06 37.76 3.08
1178 1228 2.159338 TGATGCTTAGGACGAACGTACC 60.159 50.000 5.93 6.80 0.00 3.34
1179 1229 2.850647 GTGATGCTTAGGACGAACGTAC 59.149 50.000 0.95 0.95 0.00 3.67
1180 1230 2.159338 GGTGATGCTTAGGACGAACGTA 60.159 50.000 0.00 0.00 0.00 3.57
1181 1231 1.403780 GGTGATGCTTAGGACGAACGT 60.404 52.381 0.00 0.00 0.00 3.99
1182 1232 1.278238 GGTGATGCTTAGGACGAACG 58.722 55.000 0.00 0.00 0.00 3.95
1183 1233 1.207329 AGGGTGATGCTTAGGACGAAC 59.793 52.381 0.00 0.00 0.00 3.95
1184 1234 1.207089 CAGGGTGATGCTTAGGACGAA 59.793 52.381 0.00 0.00 0.00 3.85
1185 1235 0.824109 CAGGGTGATGCTTAGGACGA 59.176 55.000 0.00 0.00 0.00 4.20
1186 1236 0.537188 ACAGGGTGATGCTTAGGACG 59.463 55.000 0.00 0.00 0.00 4.79
1187 1237 2.014068 GCACAGGGTGATGCTTAGGAC 61.014 57.143 0.00 0.00 38.84 3.85
1188 1238 0.253044 GCACAGGGTGATGCTTAGGA 59.747 55.000 0.00 0.00 38.84 2.94
1189 1239 2.785868 GCACAGGGTGATGCTTAGG 58.214 57.895 0.00 0.00 38.84 2.69
1199 1249 0.188342 AAATTGGGTCAGCACAGGGT 59.812 50.000 0.00 0.00 0.00 4.34
1200 1250 1.001181 CAAAATTGGGTCAGCACAGGG 59.999 52.381 0.00 0.00 0.00 4.45
1201 1251 1.606224 GCAAAATTGGGTCAGCACAGG 60.606 52.381 0.00 0.00 0.00 4.00
1202 1252 1.068895 TGCAAAATTGGGTCAGCACAG 59.931 47.619 0.00 0.00 0.00 3.66
1205 1255 0.680618 CCTGCAAAATTGGGTCAGCA 59.319 50.000 0.00 0.00 0.00 4.41
1206 1256 0.037046 CCCTGCAAAATTGGGTCAGC 60.037 55.000 0.00 0.00 36.32 4.26
1207 1257 1.547372 CTCCCTGCAAAATTGGGTCAG 59.453 52.381 7.78 0.00 41.58 3.51
1209 1259 0.247460 GCTCCCTGCAAAATTGGGTC 59.753 55.000 7.78 0.00 41.58 4.46
1210 1260 0.178924 AGCTCCCTGCAAAATTGGGT 60.179 50.000 7.78 0.00 45.94 4.51
1211 1261 0.533951 GAGCTCCCTGCAAAATTGGG 59.466 55.000 0.87 1.42 45.94 4.12
1213 1263 1.067354 GGTGAGCTCCCTGCAAAATTG 60.067 52.381 12.15 0.00 45.94 2.32
1214 1264 1.260544 GGTGAGCTCCCTGCAAAATT 58.739 50.000 12.15 0.00 45.94 1.82
1216 1266 1.600636 CGGTGAGCTCCCTGCAAAA 60.601 57.895 12.15 0.00 45.94 2.44
1217 1267 2.032528 CGGTGAGCTCCCTGCAAA 59.967 61.111 12.15 0.00 45.94 3.68
1218 1268 4.020617 CCGGTGAGCTCCCTGCAA 62.021 66.667 12.15 0.00 45.94 4.08
1221 1271 3.746949 GATGCCGGTGAGCTCCCTG 62.747 68.421 12.15 4.32 0.00 4.45
1222 1272 3.474570 GATGCCGGTGAGCTCCCT 61.475 66.667 12.15 0.00 0.00 4.20
1235 1285 4.899239 CGTCCTCCTGCCGGATGC 62.899 72.222 5.05 0.00 39.01 3.91
1236 1286 3.432051 GACGTCCTCCTGCCGGATG 62.432 68.421 5.05 0.00 42.12 3.51
1237 1287 3.148279 GACGTCCTCCTGCCGGAT 61.148 66.667 5.05 0.00 39.01 4.18
1241 1291 4.477975 CGTCGACGTCCTCCTGCC 62.478 72.222 29.08 0.00 34.11 4.85
1242 1292 4.477975 CCGTCGACGTCCTCCTGC 62.478 72.222 33.49 0.00 37.74 4.85
1243 1293 4.477975 GCCGTCGACGTCCTCCTG 62.478 72.222 33.49 18.76 37.74 3.86
1281 1331 1.023513 AAGAATCGTGCAGCCAGAGC 61.024 55.000 0.00 0.00 40.32 4.09
1284 1334 1.798735 CCAAGAATCGTGCAGCCAG 59.201 57.895 0.00 0.00 0.00 4.85
1285 1335 2.334946 GCCAAGAATCGTGCAGCCA 61.335 57.895 0.00 0.00 0.00 4.75
1286 1336 2.042831 AGCCAAGAATCGTGCAGCC 61.043 57.895 0.00 0.00 0.00 4.85
1287 1337 1.136147 CAGCCAAGAATCGTGCAGC 59.864 57.895 0.00 0.00 0.00 5.25
1291 1341 0.449388 GCCTTCAGCCAAGAATCGTG 59.551 55.000 0.00 0.00 33.29 4.35
1293 1343 1.709147 CCGCCTTCAGCCAAGAATCG 61.709 60.000 0.00 0.00 38.78 3.34
1294 1344 1.997928 GCCGCCTTCAGCCAAGAATC 61.998 60.000 0.00 0.00 38.78 2.52
1295 1345 2.048603 GCCGCCTTCAGCCAAGAAT 61.049 57.895 0.00 0.00 38.78 2.40
1296 1346 2.672996 GCCGCCTTCAGCCAAGAA 60.673 61.111 0.00 0.00 38.78 2.52
1317 1367 4.344865 TTGTTCCCTGCTCCCGCC 62.345 66.667 0.00 0.00 34.43 6.13
1320 1370 0.251634 CTCTCTTGTTCCCTGCTCCC 59.748 60.000 0.00 0.00 0.00 4.30
1321 1371 0.251634 CCTCTCTTGTTCCCTGCTCC 59.748 60.000 0.00 0.00 0.00 4.70
1323 1373 1.682257 GCCTCTCTTGTTCCCTGCT 59.318 57.895 0.00 0.00 0.00 4.24
1324 1374 1.743252 CGCCTCTCTTGTTCCCTGC 60.743 63.158 0.00 0.00 0.00 4.85
1325 1375 0.390472 GACGCCTCTCTTGTTCCCTG 60.390 60.000 0.00 0.00 0.00 4.45
1326 1376 1.545706 GGACGCCTCTCTTGTTCCCT 61.546 60.000 0.00 0.00 0.00 4.20
1327 1377 1.079057 GGACGCCTCTCTTGTTCCC 60.079 63.158 0.00 0.00 0.00 3.97
1328 1378 1.446272 CGGACGCCTCTCTTGTTCC 60.446 63.158 0.00 0.00 0.00 3.62
1329 1379 2.095252 GCGGACGCCTCTCTTGTTC 61.095 63.158 5.20 0.00 34.56 3.18
1330 1380 2.048127 GCGGACGCCTCTCTTGTT 60.048 61.111 5.20 0.00 34.56 2.83
1331 1381 2.574955 AAGCGGACGCCTCTCTTGT 61.575 57.895 13.63 0.00 43.17 3.16
1332 1382 2.097038 CAAGCGGACGCCTCTCTTG 61.097 63.158 13.63 7.12 43.17 3.02
1333 1383 2.262915 CAAGCGGACGCCTCTCTT 59.737 61.111 13.63 0.00 43.17 2.85
1347 1397 2.669569 CAGGTCACCACGGCCAAG 60.670 66.667 2.24 0.00 0.00 3.61
1348 1398 4.263572 CCAGGTCACCACGGCCAA 62.264 66.667 2.24 0.00 0.00 4.52
1352 1402 3.706373 CTCCCCAGGTCACCACGG 61.706 72.222 0.00 0.00 0.00 4.94
1354 1404 1.536662 AGTCTCCCCAGGTCACCAC 60.537 63.158 0.00 0.00 0.00 4.16
1355 1405 1.536418 CAGTCTCCCCAGGTCACCA 60.536 63.158 0.00 0.00 0.00 4.17
1356 1406 2.294078 CCAGTCTCCCCAGGTCACC 61.294 68.421 0.00 0.00 0.00 4.02
1357 1407 2.294078 CCCAGTCTCCCCAGGTCAC 61.294 68.421 0.00 0.00 0.00 3.67
1358 1408 1.826384 ATCCCAGTCTCCCCAGGTCA 61.826 60.000 0.00 0.00 0.00 4.02
1359 1409 0.621862 AATCCCAGTCTCCCCAGGTC 60.622 60.000 0.00 0.00 0.00 3.85
1360 1410 0.916358 CAATCCCAGTCTCCCCAGGT 60.916 60.000 0.00 0.00 0.00 4.00
1361 1411 1.918253 CAATCCCAGTCTCCCCAGG 59.082 63.158 0.00 0.00 0.00 4.45
1362 1412 1.225704 GCAATCCCAGTCTCCCCAG 59.774 63.158 0.00 0.00 0.00 4.45
1363 1413 2.308722 GGCAATCCCAGTCTCCCCA 61.309 63.158 0.00 0.00 0.00 4.96
1364 1414 2.597903 GGCAATCCCAGTCTCCCC 59.402 66.667 0.00 0.00 0.00 4.81
1366 1416 2.514824 GCGGCAATCCCAGTCTCC 60.515 66.667 0.00 0.00 0.00 3.71
1367 1417 2.109126 GTGCGGCAATCCCAGTCTC 61.109 63.158 3.23 0.00 0.00 3.36
1368 1418 2.045926 GTGCGGCAATCCCAGTCT 60.046 61.111 3.23 0.00 0.00 3.24
1369 1419 3.134127 GGTGCGGCAATCCCAGTC 61.134 66.667 3.23 0.00 0.00 3.51
1370 1420 3.286694 ATGGTGCGGCAATCCCAGT 62.287 57.895 14.94 3.12 0.00 4.00
1371 1421 2.440796 ATGGTGCGGCAATCCCAG 60.441 61.111 14.94 0.00 0.00 4.45
1372 1422 2.755064 CATGGTGCGGCAATCCCA 60.755 61.111 12.50 12.50 0.00 4.37
1383 1433 4.889427 TCGAACTCGAGCATGGTG 57.111 55.556 13.61 0.00 44.22 4.17
1393 1443 0.944311 TTGAAGCGGCACTCGAACTC 60.944 55.000 1.45 0.00 42.43 3.01
1394 1444 0.946221 CTTGAAGCGGCACTCGAACT 60.946 55.000 1.45 0.00 42.43 3.01
1395 1445 1.493311 CTTGAAGCGGCACTCGAAC 59.507 57.895 1.45 0.00 42.43 3.95
1397 1447 2.048222 CCTTGAAGCGGCACTCGA 60.048 61.111 1.45 0.00 42.43 4.04
1399 1449 3.435186 GCCCTTGAAGCGGCACTC 61.435 66.667 16.49 0.00 45.01 3.51
1404 1454 2.125147 TCGATGCCCTTGAAGCGG 60.125 61.111 0.00 0.00 0.00 5.52
1406 1456 1.012841 CTTCTCGATGCCCTTGAAGC 58.987 55.000 0.00 0.00 0.00 3.86
1407 1457 1.012841 GCTTCTCGATGCCCTTGAAG 58.987 55.000 4.45 4.45 37.69 3.02
1408 1458 0.392998 GGCTTCTCGATGCCCTTGAA 60.393 55.000 11.60 0.00 43.54 2.69
1409 1459 1.221840 GGCTTCTCGATGCCCTTGA 59.778 57.895 11.60 0.00 43.54 3.02
1410 1460 3.819188 GGCTTCTCGATGCCCTTG 58.181 61.111 11.60 0.00 43.54 3.61
1415 1465 0.032815 GTAGGAGGGCTTCTCGATGC 59.967 60.000 0.00 0.00 43.34 3.91
1416 1466 1.698506 AGTAGGAGGGCTTCTCGATG 58.301 55.000 0.00 0.00 43.34 3.84
1417 1467 2.312390 GAAGTAGGAGGGCTTCTCGAT 58.688 52.381 0.00 0.00 43.34 3.59
1418 1468 1.765230 GAAGTAGGAGGGCTTCTCGA 58.235 55.000 0.00 0.00 43.34 4.04
1420 1470 1.765230 TCGAAGTAGGAGGGCTTCTC 58.235 55.000 0.00 0.04 39.01 2.87
1421 1471 2.312390 GATCGAAGTAGGAGGGCTTCT 58.688 52.381 0.00 0.00 39.01 2.85
1422 1472 2.032620 TGATCGAAGTAGGAGGGCTTC 58.967 52.381 0.00 0.00 38.11 3.86
1423 1473 2.035632 CTGATCGAAGTAGGAGGGCTT 58.964 52.381 0.00 0.00 0.00 4.35
1426 1476 1.683917 CCACTGATCGAAGTAGGAGGG 59.316 57.143 0.00 0.00 0.00 4.30
1435 1485 9.348290 GATCCTCAGATTGATCCACTGATCGAA 62.348 44.444 11.88 0.00 43.16 3.71
1437 1487 5.850594 GATCCTCAGATTGATCCACTGATCG 60.851 48.000 11.88 7.45 40.72 3.69
1440 1490 4.952071 GATCCTCAGATTGATCCACTGA 57.048 45.455 11.25 11.25 38.16 3.41
1447 1497 2.985311 GGAAGGGGATCCTCAGATTGAT 59.015 50.000 15.83 0.00 44.07 2.57
1448 1498 2.293788 TGGAAGGGGATCCTCAGATTGA 60.294 50.000 15.83 0.00 44.07 2.57
1449 1499 2.106166 CTGGAAGGGGATCCTCAGATTG 59.894 54.545 15.83 0.00 44.07 2.67
1450 1500 2.416638 CTGGAAGGGGATCCTCAGATT 58.583 52.381 15.83 0.00 44.07 2.40
1451 1501 2.115337 CTGGAAGGGGATCCTCAGAT 57.885 55.000 15.83 0.00 44.07 2.90
1452 1502 3.642977 CTGGAAGGGGATCCTCAGA 57.357 57.895 15.83 0.00 44.07 3.27
1491 1541 4.329545 TCCTGCAGGTTGACCCGC 62.330 66.667 31.58 1.38 38.74 6.13
1493 1543 2.352805 CCTCCTGCAGGTTGACCC 59.647 66.667 31.58 0.00 37.53 4.46
1495 1545 2.743928 CGCCTCCTGCAGGTTGAC 60.744 66.667 31.58 18.11 45.61 3.18
1496 1546 4.020617 CCGCCTCCTGCAGGTTGA 62.021 66.667 31.58 12.65 45.61 3.18
1497 1547 4.335647 ACCGCCTCCTGCAGGTTG 62.336 66.667 31.58 23.33 45.61 3.77
1498 1548 4.021925 GACCGCCTCCTGCAGGTT 62.022 66.667 31.58 10.64 45.61 3.50
1545 1595 4.641645 TCCAACCCGCAGTGCAGG 62.642 66.667 16.12 16.12 31.46 4.85
1546 1596 3.357079 GTCCAACCCGCAGTGCAG 61.357 66.667 16.83 8.32 0.00 4.41
1548 1598 4.980805 TCGTCCAACCCGCAGTGC 62.981 66.667 4.58 4.58 0.00 4.40
1549 1599 2.047274 ATCGTCCAACCCGCAGTG 60.047 61.111 0.00 0.00 0.00 3.66
1550 1600 2.047274 CATCGTCCAACCCGCAGT 60.047 61.111 0.00 0.00 0.00 4.40
1551 1601 3.499737 GCATCGTCCAACCCGCAG 61.500 66.667 0.00 0.00 0.00 5.18
1555 1605 3.195698 GAGCGCATCGTCCAACCC 61.196 66.667 11.47 0.00 0.00 4.11
1556 1606 2.032634 TTGAGCGCATCGTCCAACC 61.033 57.895 11.47 0.00 0.00 3.77
1557 1607 1.132640 GTTGAGCGCATCGTCCAAC 59.867 57.895 11.47 9.78 35.63 3.77
1558 1608 1.301322 TGTTGAGCGCATCGTCCAA 60.301 52.632 11.47 0.58 0.00 3.53
1559 1609 2.027073 GTGTTGAGCGCATCGTCCA 61.027 57.895 11.47 0.00 0.00 4.02
1560 1610 2.778679 GTGTTGAGCGCATCGTCC 59.221 61.111 11.47 0.00 0.00 4.79
1562 1612 3.112075 CCGTGTTGAGCGCATCGT 61.112 61.111 11.47 0.00 0.00 3.73
1563 1613 4.505217 GCCGTGTTGAGCGCATCG 62.505 66.667 11.47 4.57 0.00 3.84
1564 1614 4.505217 CGCCGTGTTGAGCGCATC 62.505 66.667 11.47 4.91 46.50 3.91
1585 1635 0.305009 CGCATGATCTCAGCAAGCAG 59.695 55.000 0.00 0.00 0.00 4.24
1586 1636 1.093496 CCGCATGATCTCAGCAAGCA 61.093 55.000 0.00 0.00 0.00 3.91
1588 1638 1.647629 GCCGCATGATCTCAGCAAG 59.352 57.895 0.00 0.00 0.00 4.01
1592 1642 2.586914 TGCGCCGCATGATCTCAG 60.587 61.111 8.16 0.00 31.71 3.35
1593 1643 2.586914 CTGCGCCGCATGATCTCA 60.587 61.111 14.15 0.00 38.13 3.27
1594 1644 3.344215 CCTGCGCCGCATGATCTC 61.344 66.667 14.15 0.00 38.13 2.75
1603 1653 2.892425 GATCTTGACCCTGCGCCG 60.892 66.667 4.18 0.00 0.00 6.46
1604 1654 2.109126 GTGATCTTGACCCTGCGCC 61.109 63.158 4.18 0.00 0.00 6.53
1605 1655 2.109126 GGTGATCTTGACCCTGCGC 61.109 63.158 0.00 0.00 0.00 6.09
1606 1656 0.107508 ATGGTGATCTTGACCCTGCG 60.108 55.000 0.00 0.00 31.84 5.18
1607 1657 1.065199 TGATGGTGATCTTGACCCTGC 60.065 52.381 0.00 0.00 31.84 4.85
1609 1659 1.561542 GGTGATGGTGATCTTGACCCT 59.438 52.381 0.00 0.00 31.84 4.34
1615 1665 0.620556 AAGCCGGTGATGGTGATCTT 59.379 50.000 1.90 0.00 0.00 2.40
1616 1666 0.107508 CAAGCCGGTGATGGTGATCT 60.108 55.000 1.90 0.00 0.00 2.75
1617 1667 1.718757 GCAAGCCGGTGATGGTGATC 61.719 60.000 1.90 0.00 0.00 2.92
1618 1668 1.750399 GCAAGCCGGTGATGGTGAT 60.750 57.895 1.90 0.00 0.00 3.06
1619 1669 2.359850 GCAAGCCGGTGATGGTGA 60.360 61.111 1.90 0.00 0.00 4.02
1620 1670 2.360350 AGCAAGCCGGTGATGGTG 60.360 61.111 1.90 0.00 0.00 4.17
1621 1671 2.360350 CAGCAAGCCGGTGATGGT 60.360 61.111 1.90 2.43 46.47 3.55
1647 1697 4.838152 TTCTGCTGGATCGGCGGC 62.838 66.667 7.21 0.00 41.50 6.53
1648 1698 2.587194 CTTCTGCTGGATCGGCGG 60.587 66.667 7.21 10.66 42.96 6.13
1649 1699 3.267860 GCTTCTGCTGGATCGGCG 61.268 66.667 0.00 0.00 38.82 6.46
1650 1700 2.124983 TGCTTCTGCTGGATCGGC 60.125 61.111 2.84 2.84 40.48 5.54
1651 1701 2.178890 GCTGCTTCTGCTGGATCGG 61.179 63.158 0.00 0.00 40.48 4.18
1652 1702 1.429927 CTGCTGCTTCTGCTGGATCG 61.430 60.000 0.00 0.00 37.76 3.69
1654 1704 1.749638 GCTGCTGCTTCTGCTGGAT 60.750 57.895 8.53 0.00 37.76 3.41
1656 1706 3.441290 GGCTGCTGCTTCTGCTGG 61.441 66.667 15.64 0.00 40.48 4.85
1657 1707 2.360100 AGGCTGCTGCTTCTGCTG 60.360 61.111 15.64 0.00 40.48 4.41
1659 1709 3.441290 CCAGGCTGCTGCTTCTGC 61.441 66.667 15.64 0.00 39.59 4.26
1660 1710 3.441290 GCCAGGCTGCTGCTTCTG 61.441 66.667 15.64 13.98 39.59 3.02
1661 1711 3.962694 TGCCAGGCTGCTGCTTCT 61.963 61.111 14.15 1.96 39.59 2.85
1663 1713 4.591399 TGTGCCAGGCTGCTGCTT 62.591 61.111 14.15 4.74 39.59 3.91
1664 1714 4.591399 TTGTGCCAGGCTGCTGCT 62.591 61.111 14.15 0.00 39.59 4.24
1666 1716 4.052229 GCTTGTGCCAGGCTGCTG 62.052 66.667 14.15 0.00 33.60 4.41
1778 3398 4.783621 GCTGCTGGATCGGTGGCA 62.784 66.667 0.00 0.00 0.00 4.92
2014 3646 2.972713 AGTTGCTCCACAGGAAGTAAGA 59.027 45.455 0.00 0.00 32.08 2.10
2043 3704 0.982852 AATCCCAGCCTCACGGATCA 60.983 55.000 0.00 0.00 35.27 2.92
2049 3710 2.570135 GATTCTGAATCCCAGCCTCAC 58.430 52.381 17.62 0.00 42.62 3.51
2180 7567 2.844654 TTACATGCCCCATTGGTGAT 57.155 45.000 1.20 0.00 36.04 3.06
2443 10117 0.250252 TGCTGACGAATGTGCCTTGA 60.250 50.000 0.00 0.00 0.00 3.02
2608 10915 9.729023 CAAAAGTGTCATATTACAACAACTTCA 57.271 29.630 0.00 0.00 0.00 3.02
2803 11115 5.922544 CAGATTCAAAATCGCTCAGGTTTTT 59.077 36.000 0.00 0.00 40.00 1.94
2804 11116 5.464168 CAGATTCAAAATCGCTCAGGTTTT 58.536 37.500 0.00 0.00 43.46 2.43
2856 12016 2.489329 CTGTTAGCAGTTGGATGTTGGG 59.511 50.000 0.00 0.00 37.92 4.12
2861 12021 4.199432 AGTCTCTGTTAGCAGTTGGATG 57.801 45.455 6.47 0.00 43.05 3.51
2867 12027 4.262249 GGACAAGAAGTCTCTGTTAGCAGT 60.262 45.833 6.47 0.00 46.72 4.40


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

AutoCloner maintained by Alex Coulton.