Multiple sequence alignment - TraesCS5B01G470400

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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 TraesCS5B01G470400 chr5B 100.000 5694 0 0 491 6184 643665697 643671390 0.000000e+00 10515
1 TraesCS5B01G470400 chr5B 100.000 100 0 0 1 100 643665207 643665306 1.060000e-42 185
2 TraesCS5B01G470400 chr5D 93.371 3228 153 28 1220 4421 512769016 512772208 0.000000e+00 4719
3 TraesCS5B01G470400 chr5D 91.130 1725 72 16 4516 6184 512772373 512774072 0.000000e+00 2263
4 TraesCS5B01G470400 chr5D 92.950 766 24 12 497 1241 512768354 512769110 0.000000e+00 1088
5 TraesCS5B01G470400 chr5D 91.837 98 6 2 3 100 512768193 512768288 1.080000e-27 135
6 TraesCS5B01G470400 chr5A 94.902 1981 82 11 3218 5192 640941396 640943363 0.000000e+00 3081
7 TraesCS5B01G470400 chr5A 89.652 1092 65 18 1220 2304 640939511 640940561 0.000000e+00 1347
8 TraesCS5B01G470400 chr5A 93.246 844 45 8 2327 3163 640940556 640941394 0.000000e+00 1232
9 TraesCS5B01G470400 chr5A 94.126 749 28 7 5443 6184 640945694 640946433 0.000000e+00 1125
10 TraesCS5B01G470400 chr5A 89.384 471 40 7 777 1241 640939139 640939605 8.930000e-163 584
11 TraesCS5B01G470400 chr5A 86.667 240 11 7 497 724 640938897 640939127 4.790000e-61 246


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 TraesCS5B01G470400 chr5B 643665207 643671390 6183 False 5350.000000 10515 100.0000 1 6184 2 chr5B.!!$F1 6183
1 TraesCS5B01G470400 chr5D 512768193 512774072 5879 False 2051.250000 4719 92.3220 3 6184 4 chr5D.!!$F1 6181
2 TraesCS5B01G470400 chr5A 640938897 640946433 7536 False 1269.166667 3081 91.3295 497 6184 6 chr5A.!!$F1 5687

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
40 41 0.039617 CATCTCCGAGATCTGCCGTC 60.040 60.0 8.0 0.0 31.32 4.79 F
1229 1257 0.327576 GAGGATGGGGAGGGGAAGAA 60.328 60.0 0.0 0.0 0.00 2.52 F
1262 1290 0.327576 GAGGATGGGGAGGGGAAGAA 60.328 60.0 0.0 0.0 0.00 2.52 F
1264 1292 0.327576 GGATGGGGAGGGGAAGAAGA 60.328 60.0 0.0 0.0 0.00 2.87 F
1284 1312 0.327964 AGAAGAAGGGGGAGGATGGG 60.328 60.0 0.0 0.0 0.00 4.00 F
2951 2985 1.191489 AAAATTCACCCCCTTGCCCG 61.191 55.0 0.0 0.0 0.00 6.13 F
3429 3464 0.232303 CAACAACCTCGACGAACTGC 59.768 55.0 0.0 0.0 0.00 4.40 F
4404 4452 0.601558 TGTCGTACTTCTCACCTGGC 59.398 55.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1811 0.033601 ACCTGCAAACCACAGTGGAA 60.034 50.000 27.39 5.19 40.96 3.53 R
2335 2364 1.000827 AGATCGAGGCGTGCTCTTATG 60.001 52.381 0.00 0.00 0.00 1.90 R
3207 3241 1.282875 GCCGTTGCTTGTTCTCCAC 59.717 57.895 0.00 0.00 33.53 4.02 R
3273 3307 5.539582 TTAAAAGCCAATAGTACAGTGCG 57.460 39.130 0.00 0.00 0.00 5.34 R
3296 3331 6.435277 AGCCAGACAGATAATTCAACAAATGT 59.565 34.615 0.00 0.00 0.00 2.71 R
4720 4859 1.719709 GCGACCGAAAATGTAGCCC 59.280 57.895 0.00 0.00 0.00 5.19 R
5100 5239 1.086634 GCTTGGCTCTCCGTGATGAC 61.087 60.000 0.00 0.00 34.14 3.06 R
5788 8025 0.671251 CTCTCGATTCGGGGAGGAAG 59.329 60.000 6.03 0.00 0.00 3.46 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
40 41 0.039617 CATCTCCGAGATCTGCCGTC 60.040 60.000 8.00 0.00 31.32 4.79
43 44 4.271816 CCGAGATCTGCCGTCCCG 62.272 72.222 0.00 0.00 0.00 5.14
727 740 0.547954 AGGGTCTCCTCTTCCCAACC 60.548 60.000 0.00 0.00 39.80 3.77
754 767 2.816958 CGCCGTCAGAGCAGCAAT 60.817 61.111 0.00 0.00 0.00 3.56
897 922 2.756283 ACGGCGGAGGAGGAAGAG 60.756 66.667 13.24 0.00 0.00 2.85
903 928 2.008242 CGGAGGAGGAAGAGGATGAT 57.992 55.000 0.00 0.00 0.00 2.45
987 1015 3.203412 CCGACGGGAGAGGACGAG 61.203 72.222 5.81 0.00 34.06 4.18
990 1018 2.045143 ACGGGAGAGGACGAGGAC 60.045 66.667 0.00 0.00 0.00 3.85
1221 1249 1.772156 GAAGGGGGAGGATGGGGAG 60.772 68.421 0.00 0.00 0.00 4.30
1222 1250 3.369161 AAGGGGGAGGATGGGGAGG 62.369 68.421 0.00 0.00 0.00 4.30
1223 1251 4.928520 GGGGGAGGATGGGGAGGG 62.929 77.778 0.00 0.00 0.00 4.30
1224 1252 4.928520 GGGGAGGATGGGGAGGGG 62.929 77.778 0.00 0.00 0.00 4.79
1225 1253 3.791076 GGGAGGATGGGGAGGGGA 61.791 72.222 0.00 0.00 0.00 4.81
1226 1254 2.376842 GGAGGATGGGGAGGGGAA 59.623 66.667 0.00 0.00 0.00 3.97
1227 1255 1.772156 GGAGGATGGGGAGGGGAAG 60.772 68.421 0.00 0.00 0.00 3.46
1228 1256 1.318380 GAGGATGGGGAGGGGAAGA 59.682 63.158 0.00 0.00 0.00 2.87
1229 1257 0.327576 GAGGATGGGGAGGGGAAGAA 60.328 60.000 0.00 0.00 0.00 2.52
1230 1258 0.327964 AGGATGGGGAGGGGAAGAAG 60.328 60.000 0.00 0.00 0.00 2.85
1231 1259 0.327576 GGATGGGGAGGGGAAGAAGA 60.328 60.000 0.00 0.00 0.00 2.87
1232 1260 1.596496 GATGGGGAGGGGAAGAAGAA 58.404 55.000 0.00 0.00 0.00 2.52
1233 1261 1.492599 GATGGGGAGGGGAAGAAGAAG 59.507 57.143 0.00 0.00 0.00 2.85
1234 1262 0.496382 TGGGGAGGGGAAGAAGAAGA 59.504 55.000 0.00 0.00 0.00 2.87
1235 1263 1.132201 TGGGGAGGGGAAGAAGAAGAA 60.132 52.381 0.00 0.00 0.00 2.52
1236 1264 1.562008 GGGGAGGGGAAGAAGAAGAAG 59.438 57.143 0.00 0.00 0.00 2.85
1237 1265 2.552367 GGGAGGGGAAGAAGAAGAAGA 58.448 52.381 0.00 0.00 0.00 2.87
1238 1266 2.913617 GGGAGGGGAAGAAGAAGAAGAA 59.086 50.000 0.00 0.00 0.00 2.52
1239 1267 3.054728 GGGAGGGGAAGAAGAAGAAGAAG 60.055 52.174 0.00 0.00 0.00 2.85
1240 1268 3.054728 GGAGGGGAAGAAGAAGAAGAAGG 60.055 52.174 0.00 0.00 0.00 3.46
1241 1269 2.916269 AGGGGAAGAAGAAGAAGAAGGG 59.084 50.000 0.00 0.00 0.00 3.95
1242 1270 2.025793 GGGGAAGAAGAAGAAGAAGGGG 60.026 54.545 0.00 0.00 0.00 4.79
1243 1271 2.025793 GGGAAGAAGAAGAAGAAGGGGG 60.026 54.545 0.00 0.00 0.00 5.40
1244 1272 2.913617 GGAAGAAGAAGAAGAAGGGGGA 59.086 50.000 0.00 0.00 0.00 4.81
1245 1273 3.054728 GGAAGAAGAAGAAGAAGGGGGAG 60.055 52.174 0.00 0.00 0.00 4.30
1246 1274 2.556766 AGAAGAAGAAGAAGGGGGAGG 58.443 52.381 0.00 0.00 0.00 4.30
1247 1275 2.114506 AGAAGAAGAAGAAGGGGGAGGA 59.885 50.000 0.00 0.00 0.00 3.71
1248 1276 2.980699 AGAAGAAGAAGGGGGAGGAT 57.019 50.000 0.00 0.00 0.00 3.24
1249 1277 2.486716 AGAAGAAGAAGGGGGAGGATG 58.513 52.381 0.00 0.00 0.00 3.51
1250 1278 1.492599 GAAGAAGAAGGGGGAGGATGG 59.507 57.143 0.00 0.00 0.00 3.51
1251 1279 0.327964 AGAAGAAGGGGGAGGATGGG 60.328 60.000 0.00 0.00 0.00 4.00
1252 1280 1.309102 AAGAAGGGGGAGGATGGGG 60.309 63.158 0.00 0.00 0.00 4.96
1253 1281 1.848835 AAGAAGGGGGAGGATGGGGA 61.849 60.000 0.00 0.00 0.00 4.81
1254 1282 1.772156 GAAGGGGGAGGATGGGGAG 60.772 68.421 0.00 0.00 0.00 4.30
1255 1283 3.369161 AAGGGGGAGGATGGGGAGG 62.369 68.421 0.00 0.00 0.00 4.30
1256 1284 4.928520 GGGGGAGGATGGGGAGGG 62.929 77.778 0.00 0.00 0.00 4.30
1257 1285 4.928520 GGGGAGGATGGGGAGGGG 62.929 77.778 0.00 0.00 0.00 4.79
1258 1286 3.791076 GGGAGGATGGGGAGGGGA 61.791 72.222 0.00 0.00 0.00 4.81
1259 1287 2.376842 GGAGGATGGGGAGGGGAA 59.623 66.667 0.00 0.00 0.00 3.97
1260 1288 1.772156 GGAGGATGGGGAGGGGAAG 60.772 68.421 0.00 0.00 0.00 3.46
1261 1289 1.318380 GAGGATGGGGAGGGGAAGA 59.682 63.158 0.00 0.00 0.00 2.87
1262 1290 0.327576 GAGGATGGGGAGGGGAAGAA 60.328 60.000 0.00 0.00 0.00 2.52
1263 1291 0.327964 AGGATGGGGAGGGGAAGAAG 60.328 60.000 0.00 0.00 0.00 2.85
1264 1292 0.327576 GGATGGGGAGGGGAAGAAGA 60.328 60.000 0.00 0.00 0.00 2.87
1265 1293 1.596496 GATGGGGAGGGGAAGAAGAA 58.404 55.000 0.00 0.00 0.00 2.52
1266 1294 1.492599 GATGGGGAGGGGAAGAAGAAG 59.507 57.143 0.00 0.00 0.00 2.85
1267 1295 0.496382 TGGGGAGGGGAAGAAGAAGA 59.504 55.000 0.00 0.00 0.00 2.87
1268 1296 1.132201 TGGGGAGGGGAAGAAGAAGAA 60.132 52.381 0.00 0.00 0.00 2.52
1269 1297 1.562008 GGGGAGGGGAAGAAGAAGAAG 59.438 57.143 0.00 0.00 0.00 2.85
1270 1298 2.552367 GGGAGGGGAAGAAGAAGAAGA 58.448 52.381 0.00 0.00 0.00 2.87
1271 1299 2.913617 GGGAGGGGAAGAAGAAGAAGAA 59.086 50.000 0.00 0.00 0.00 2.52
1272 1300 3.054728 GGGAGGGGAAGAAGAAGAAGAAG 60.055 52.174 0.00 0.00 0.00 2.85
1273 1301 3.054728 GGAGGGGAAGAAGAAGAAGAAGG 60.055 52.174 0.00 0.00 0.00 3.46
1274 1302 2.916269 AGGGGAAGAAGAAGAAGAAGGG 59.084 50.000 0.00 0.00 0.00 3.95
1275 1303 2.025793 GGGGAAGAAGAAGAAGAAGGGG 60.026 54.545 0.00 0.00 0.00 4.79
1276 1304 2.025793 GGGAAGAAGAAGAAGAAGGGGG 60.026 54.545 0.00 0.00 0.00 5.40
1277 1305 2.913617 GGAAGAAGAAGAAGAAGGGGGA 59.086 50.000 0.00 0.00 0.00 4.81
1278 1306 3.054728 GGAAGAAGAAGAAGAAGGGGGAG 60.055 52.174 0.00 0.00 0.00 4.30
1279 1307 2.556766 AGAAGAAGAAGAAGGGGGAGG 58.443 52.381 0.00 0.00 0.00 4.30
1280 1308 2.114506 AGAAGAAGAAGAAGGGGGAGGA 59.885 50.000 0.00 0.00 0.00 3.71
1281 1309 2.980699 AGAAGAAGAAGGGGGAGGAT 57.019 50.000 0.00 0.00 0.00 3.24
1282 1310 2.486716 AGAAGAAGAAGGGGGAGGATG 58.513 52.381 0.00 0.00 0.00 3.51
1283 1311 1.492599 GAAGAAGAAGGGGGAGGATGG 59.507 57.143 0.00 0.00 0.00 3.51
1284 1312 0.327964 AGAAGAAGGGGGAGGATGGG 60.328 60.000 0.00 0.00 0.00 4.00
1285 1313 1.309102 AAGAAGGGGGAGGATGGGG 60.309 63.158 0.00 0.00 0.00 4.96
1286 1314 1.848835 AAGAAGGGGGAGGATGGGGA 61.849 60.000 0.00 0.00 0.00 4.81
1367 1395 3.245519 GCCGAGAAGGTAACATTTCGATC 59.754 47.826 0.00 0.00 43.70 3.69
1374 1402 7.538575 AGAAGGTAACATTTCGATCATTTTGG 58.461 34.615 0.00 0.00 41.41 3.28
1381 1409 6.389906 ACATTTCGATCATTTTGGTTCCTTC 58.610 36.000 0.00 0.00 0.00 3.46
1383 1411 4.027674 TCGATCATTTTGGTTCCTTCCA 57.972 40.909 0.00 0.00 35.49 3.53
1398 1426 2.864343 CCTTCCATTCGGTTCGTATGAC 59.136 50.000 8.15 0.00 36.92 3.06
1412 1440 2.862536 CGTATGACTGCATCTGTTCCAG 59.137 50.000 0.00 0.00 35.94 3.86
1442 1470 5.422012 GGTCCATAGATTTTGTTGATGGGTT 59.578 40.000 0.00 0.00 38.09 4.11
1528 1556 2.167281 AGGCTGCTGCGAGGTATATATG 59.833 50.000 9.65 0.00 40.82 1.78
1529 1557 2.093973 GGCTGCTGCGAGGTATATATGT 60.094 50.000 9.65 0.00 40.82 2.29
1545 1573 2.275134 ATGTTGACAGTGTGCATGGA 57.725 45.000 0.00 0.00 0.00 3.41
1551 1579 2.291089 TGACAGTGTGCATGGATGGAAT 60.291 45.455 0.00 0.00 0.00 3.01
1777 1806 2.363788 TGACTGTCCGCTGATGTTAC 57.636 50.000 5.17 0.00 0.00 2.50
1782 1811 5.086104 ACTGTCCGCTGATGTTACTATTT 57.914 39.130 0.00 0.00 0.00 1.40
1831 1860 2.165437 CCTGTCGAAGAGGAAGAGGAAG 59.835 54.545 5.93 0.00 36.95 3.46
1832 1861 3.085533 CTGTCGAAGAGGAAGAGGAAGA 58.914 50.000 0.00 0.00 36.95 2.87
1833 1862 3.085533 TGTCGAAGAGGAAGAGGAAGAG 58.914 50.000 0.00 0.00 36.95 2.85
1834 1863 2.425668 GTCGAAGAGGAAGAGGAAGAGG 59.574 54.545 0.00 0.00 36.95 3.69
1835 1864 2.309162 TCGAAGAGGAAGAGGAAGAGGA 59.691 50.000 0.00 0.00 0.00 3.71
1836 1865 3.093057 CGAAGAGGAAGAGGAAGAGGAA 58.907 50.000 0.00 0.00 0.00 3.36
1837 1866 3.130340 CGAAGAGGAAGAGGAAGAGGAAG 59.870 52.174 0.00 0.00 0.00 3.46
1838 1867 4.349365 GAAGAGGAAGAGGAAGAGGAAGA 58.651 47.826 0.00 0.00 0.00 2.87
1839 1868 3.981212 AGAGGAAGAGGAAGAGGAAGAG 58.019 50.000 0.00 0.00 0.00 2.85
1840 1869 3.031013 GAGGAAGAGGAAGAGGAAGAGG 58.969 54.545 0.00 0.00 0.00 3.69
1841 1870 2.657459 AGGAAGAGGAAGAGGAAGAGGA 59.343 50.000 0.00 0.00 0.00 3.71
1842 1871 3.078305 AGGAAGAGGAAGAGGAAGAGGAA 59.922 47.826 0.00 0.00 0.00 3.36
1890 1919 4.608948 AGGCGAAGAAGAAGAAGAAGAA 57.391 40.909 0.00 0.00 0.00 2.52
1917 1946 3.219928 GAGCCCGAGAGCGATCCA 61.220 66.667 0.00 0.00 40.82 3.41
1972 2001 5.712152 AGTGGGTTCAGATGACAAAAATC 57.288 39.130 0.00 0.00 0.00 2.17
2057 2086 3.678056 AAGGCTGTGAATCGTTGTAGA 57.322 42.857 0.00 0.00 0.00 2.59
2079 2108 1.699083 TGATGCTGACAAGGAGGTTGA 59.301 47.619 0.00 0.00 38.60 3.18
2147 2176 2.887152 GAGGTGGTCATTGCTTTCACTT 59.113 45.455 0.00 0.00 0.00 3.16
2229 2258 4.183865 TGTGATTAGCGACAAGGATCTTG 58.816 43.478 6.15 6.15 0.00 3.02
2293 2322 6.352222 CCTTCCCTAATTGTGTAGTCATCTGT 60.352 42.308 0.00 0.00 0.00 3.41
2296 2325 5.338381 CCCTAATTGTGTAGTCATCTGTGGT 60.338 44.000 0.00 0.00 0.00 4.16
2325 2354 6.979817 TGTTTTGCAACAGAATATATGATGGC 59.020 34.615 0.00 0.00 38.03 4.40
2335 2364 5.648092 AGAATATATGATGGCGCTTTTACCC 59.352 40.000 7.64 0.00 0.00 3.69
2345 2374 2.223272 GCGCTTTTACCCATAAGAGCAC 60.223 50.000 0.00 0.00 44.85 4.40
2367 2396 3.370978 CGCCTCGATCTTGTGTTATTTGT 59.629 43.478 0.00 0.00 0.00 2.83
2436 2465 8.467963 AAGCATTGGTTTGATGATACATATCA 57.532 30.769 4.11 4.11 45.78 2.15
2456 2489 9.858247 CATATCAATGCAAAATATTGTGCTTTC 57.142 29.630 26.90 3.52 41.48 2.62
2491 2524 5.964758 TCAATGGTTGCTGGATTATCAAAC 58.035 37.500 0.00 0.00 0.00 2.93
2498 2531 3.823873 TGCTGGATTATCAAACGTTTGGT 59.176 39.130 33.97 31.21 38.66 3.67
2499 2532 5.004448 TGCTGGATTATCAAACGTTTGGTA 58.996 37.500 33.97 30.18 38.66 3.25
2531 2564 9.726438 ATCTACTATGGTTAGTCAATTATTGGC 57.274 33.333 0.66 0.66 39.42 4.52
2584 2617 7.856145 ATCTCATTGCGAAGTAAGAAAAGAT 57.144 32.000 0.00 0.00 34.31 2.40
2585 2618 8.948631 ATCTCATTGCGAAGTAAGAAAAGATA 57.051 30.769 0.00 0.00 34.31 1.98
2720 2754 3.153919 TGCTTGTTGGACTATTGGTTCC 58.846 45.455 0.00 0.00 0.00 3.62
2739 2773 4.286297 TCCACCAGGAACTTGTTGATAG 57.714 45.455 0.00 0.00 42.23 2.08
2809 2843 3.382865 TCGATGCTGTAGATGAAGAAGCT 59.617 43.478 0.00 0.00 34.92 3.74
2839 2873 1.354368 CCCTCTTCAAGCCCTACCAAA 59.646 52.381 0.00 0.00 0.00 3.28
2901 2935 6.012858 AGTCCATGATACTTTCCACCTGTTAA 60.013 38.462 0.00 0.00 0.00 2.01
2951 2985 1.191489 AAAATTCACCCCCTTGCCCG 61.191 55.000 0.00 0.00 0.00 6.13
3029 3063 8.450964 GCATAAGACTATAACAGCTTGTTTTGA 58.549 33.333 6.82 0.00 41.45 2.69
3077 3111 3.609853 TGTAGCCTTGACATGTGAATCC 58.390 45.455 1.15 0.00 0.00 3.01
3273 3307 8.739039 TGCCTGATTTTACATATGTATATTGGC 58.261 33.333 25.51 25.51 32.95 4.52
3291 3325 1.369625 GCGCACTGTACTATTGGCTT 58.630 50.000 0.30 0.00 0.00 4.35
3296 3331 5.618195 GCGCACTGTACTATTGGCTTTTAAA 60.618 40.000 0.30 0.00 0.00 1.52
3297 3332 5.793457 CGCACTGTACTATTGGCTTTTAAAC 59.207 40.000 0.00 0.00 0.00 2.01
3298 3333 6.566942 CGCACTGTACTATTGGCTTTTAAACA 60.567 38.462 0.00 0.00 0.00 2.83
3403 3438 7.063780 CCAGGCATTCAGAAAAATGATGTAAAC 59.936 37.037 0.98 0.00 38.64 2.01
3428 3463 1.847818 TCAACAACCTCGACGAACTG 58.152 50.000 0.00 0.00 0.00 3.16
3429 3464 0.232303 CAACAACCTCGACGAACTGC 59.768 55.000 0.00 0.00 0.00 4.40
3478 3513 5.247110 TGCTGTCCTGAAAGACTTTCTAGAT 59.753 40.000 24.60 0.00 40.32 1.98
3520 3555 2.027007 TGACAGTGATGATGACATGGCA 60.027 45.455 2.18 2.18 36.82 4.92
3550 3585 3.261897 AGGACAACGAAGAAGATGATGGT 59.738 43.478 0.00 0.00 0.00 3.55
3586 3621 4.130286 AGTACTTACTGCTCTGATTGCC 57.870 45.455 0.00 0.00 34.72 4.52
3898 3933 4.706035 AGCACTCTGATGATGAGGAAATC 58.294 43.478 0.00 0.00 35.98 2.17
4021 4069 4.793201 AGTGTTAGTTCTTCCCTTTGCTT 58.207 39.130 0.00 0.00 0.00 3.91
4058 4106 6.926630 TTTTTATCCACCCTATGTGCTTTT 57.073 33.333 0.00 0.00 44.01 2.27
4273 4321 7.395772 TGATTAAAAACATGGCTGGTCATCTAA 59.604 33.333 0.00 0.00 0.00 2.10
4274 4322 5.649782 AAAAACATGGCTGGTCATCTAAG 57.350 39.130 0.00 0.00 0.00 2.18
4275 4323 4.307032 AAACATGGCTGGTCATCTAAGT 57.693 40.909 0.00 0.00 0.00 2.24
4282 4330 6.808321 TGGCTGGTCATCTAAGTATTACTT 57.192 37.500 13.36 13.36 41.97 2.24
4286 4334 9.609346 GGCTGGTCATCTAAGTATTACTTTTTA 57.391 33.333 14.00 1.84 39.51 1.52
4404 4452 0.601558 TGTCGTACTTCTCACCTGGC 59.398 55.000 0.00 0.00 0.00 4.85
4409 4457 2.230508 CGTACTTCTCACCTGGCTGTTA 59.769 50.000 0.00 0.00 0.00 2.41
4429 4477 9.626045 GCTGTTAATTAGCTGAAAGTTTGTAAT 57.374 29.630 9.83 0.00 38.14 1.89
4457 4505 8.479689 TGAATTGACTTCATATGGCAAATCATT 58.520 29.630 2.13 0.00 38.97 2.57
4507 4580 7.563724 TCACCTAGTAAAACCTGGACTTAAT 57.436 36.000 0.00 0.00 0.00 1.40
4510 4583 7.333672 CACCTAGTAAAACCTGGACTTAATCAC 59.666 40.741 0.00 0.00 0.00 3.06
4511 4584 7.237055 ACCTAGTAAAACCTGGACTTAATCACT 59.763 37.037 0.00 0.00 0.00 3.41
4512 4585 8.101419 CCTAGTAAAACCTGGACTTAATCACTT 58.899 37.037 0.00 0.00 0.00 3.16
4531 4664 7.973048 TCACTTAAACATGTACTATCCCTCT 57.027 36.000 0.00 0.00 0.00 3.69
4558 4691 9.319143 CATTGTTTTGTTAGGGAACATTTTGTA 57.681 29.630 0.00 0.00 44.96 2.41
4601 4734 3.176708 CAAGGCATTGCTGAGATTTTCG 58.823 45.455 8.82 0.00 0.00 3.46
4602 4735 2.440409 AGGCATTGCTGAGATTTTCGT 58.560 42.857 8.82 0.00 0.00 3.85
4603 4736 2.821969 AGGCATTGCTGAGATTTTCGTT 59.178 40.909 8.82 0.00 0.00 3.85
4610 4745 4.059511 TGCTGAGATTTTCGTTAAACCGA 58.940 39.130 0.00 0.00 34.52 4.69
4848 4987 5.581126 TCTTGTCATAATTCCAATGTGCC 57.419 39.130 0.00 0.00 0.00 5.01
4864 5003 4.504916 CCCAGAGGCAGAGTCGCG 62.505 72.222 0.00 0.00 0.00 5.87
4874 5013 0.872021 CAGAGTCGCGCATTCCCTAC 60.872 60.000 8.75 0.00 0.00 3.18
4897 5036 4.408993 TTCAGAAACATTCTCATGTGCG 57.591 40.909 0.00 0.00 43.34 5.34
4911 5050 2.046023 TGCGCCCTCATTCCACTG 60.046 61.111 4.18 0.00 0.00 3.66
5059 5198 3.423154 GCGCAGGTCAACTTCCGG 61.423 66.667 0.30 0.00 0.00 5.14
5214 5372 2.107950 TTGCTACCATGTACACCTGC 57.892 50.000 0.00 0.00 0.00 4.85
5328 5498 9.838339 ATTCTGTATCACCTTAGGTTTAAGATG 57.162 33.333 0.00 0.00 38.88 2.90
5467 7704 4.973055 TTGGTCAACGACGGCCCG 62.973 66.667 0.00 0.00 32.65 6.13
5626 7863 2.892425 CAGGATCGAAGGTGCGCC 60.892 66.667 8.71 8.71 0.00 6.53
5627 7864 4.162690 AGGATCGAAGGTGCGCCC 62.163 66.667 14.07 5.76 34.57 6.13
5690 7927 1.451387 CGGACCTCAAAATCCCCCG 60.451 63.158 0.00 0.00 0.00 5.73
5729 7966 2.722071 CTCTCGCGGTAAGAAGATCAC 58.278 52.381 6.13 0.00 0.00 3.06
5741 7978 0.178068 AAGATCACCCGTCCATTCCG 59.822 55.000 0.00 0.00 0.00 4.30
5749 7986 1.400494 CCCGTCCATTCCGTTCAATTC 59.600 52.381 0.00 0.00 0.00 2.17
5763 8000 1.398041 TCAATTCGCAGCTGAATTCGG 59.602 47.619 20.43 10.10 44.55 4.30
5807 8044 0.671251 CTTCCTCCCCGAATCGAGAG 59.329 60.000 3.36 9.82 0.00 3.20
5849 8086 4.647611 TCTGAGCTCCGGATTTTTGTTTA 58.352 39.130 12.15 0.00 0.00 2.01
5969 8206 0.760189 GCAGCTCCCATCTCTCCTCT 60.760 60.000 0.00 0.00 0.00 3.69
5970 8207 1.792115 CAGCTCCCATCTCTCCTCTT 58.208 55.000 0.00 0.00 0.00 2.85
5973 8210 1.327303 CTCCCATCTCTCCTCTTCCG 58.673 60.000 0.00 0.00 0.00 4.30
5974 8211 0.105964 TCCCATCTCTCCTCTTCCGG 60.106 60.000 0.00 0.00 0.00 5.14
5975 8212 0.105964 CCCATCTCTCCTCTTCCGGA 60.106 60.000 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.764369 TCGGAGATGGAATGAGGGGG 60.764 60.000 0.00 0.00 0.00 5.40
12 13 1.709578 TCTCGGAGATGGAATGAGGG 58.290 55.000 2.97 0.00 33.89 4.30
13 14 3.056678 CAGATCTCGGAGATGGAATGAGG 60.057 52.174 24.43 2.20 34.53 3.86
14 15 3.614630 GCAGATCTCGGAGATGGAATGAG 60.615 52.174 24.43 7.62 34.53 2.90
15 16 2.298446 GCAGATCTCGGAGATGGAATGA 59.702 50.000 24.43 0.00 34.53 2.57
25 26 2.833582 GGGACGGCAGATCTCGGA 60.834 66.667 8.50 0.00 0.00 4.55
40 41 2.844839 GAGGGTGAGGGGATCGGG 60.845 72.222 0.00 0.00 0.00 5.14
43 44 2.448736 GGGGAGGGTGAGGGGATC 60.449 72.222 0.00 0.00 0.00 3.36
603 616 1.925972 GGCCAGGGTTTCCTCCTCT 60.926 63.158 0.00 0.00 42.67 3.69
641 654 1.305046 TGGTTCGGAGGAGGAGGAC 60.305 63.158 0.00 0.00 0.00 3.85
642 655 1.305046 GTGGTTCGGAGGAGGAGGA 60.305 63.158 0.00 0.00 0.00 3.71
643 656 1.305381 AGTGGTTCGGAGGAGGAGG 60.305 63.158 0.00 0.00 0.00 4.30
711 724 0.547954 AGGGGTTGGGAAGAGGAGAC 60.548 60.000 0.00 0.00 0.00 3.36
884 909 1.617850 CATCATCCTCTTCCTCCTCCG 59.382 57.143 0.00 0.00 0.00 4.63
897 922 0.668706 CGAGCCCGTCATCATCATCC 60.669 60.000 0.00 0.00 0.00 3.51
969 994 3.677284 CTCGTCCTCTCCCGTCGGA 62.677 68.421 14.39 0.00 36.45 4.55
987 1015 1.739049 CAGCATCTCCTCCTCGTCC 59.261 63.158 0.00 0.00 0.00 4.79
990 1018 2.420890 GCCAGCATCTCCTCCTCG 59.579 66.667 0.00 0.00 0.00 4.63
1099 1127 2.167861 GCTCGACGTCCATCTTGGC 61.168 63.158 10.58 0.50 37.47 4.52
1100 1128 1.519455 GGCTCGACGTCCATCTTGG 60.519 63.158 10.58 0.00 39.43 3.61
1102 1130 2.490217 CGGCTCGACGTCCATCTT 59.510 61.111 10.58 0.00 0.00 2.40
1180 1208 2.644798 TCTTCTTCTTCCCCTTCCCTTG 59.355 50.000 0.00 0.00 0.00 3.61
1221 1249 2.025793 CCCCTTCTTCTTCTTCTTCCCC 60.026 54.545 0.00 0.00 0.00 4.81
1222 1250 2.025793 CCCCCTTCTTCTTCTTCTTCCC 60.026 54.545 0.00 0.00 0.00 3.97
1223 1251 2.913617 TCCCCCTTCTTCTTCTTCTTCC 59.086 50.000 0.00 0.00 0.00 3.46
1224 1252 3.054728 CCTCCCCCTTCTTCTTCTTCTTC 60.055 52.174 0.00 0.00 0.00 2.87
1225 1253 2.916269 CCTCCCCCTTCTTCTTCTTCTT 59.084 50.000 0.00 0.00 0.00 2.52
1226 1254 2.114506 TCCTCCCCCTTCTTCTTCTTCT 59.885 50.000 0.00 0.00 0.00 2.85
1227 1255 2.552367 TCCTCCCCCTTCTTCTTCTTC 58.448 52.381 0.00 0.00 0.00 2.87
1228 1256 2.743131 TCCTCCCCCTTCTTCTTCTT 57.257 50.000 0.00 0.00 0.00 2.52
1229 1257 2.486716 CATCCTCCCCCTTCTTCTTCT 58.513 52.381 0.00 0.00 0.00 2.85
1230 1258 1.492599 CCATCCTCCCCCTTCTTCTTC 59.507 57.143 0.00 0.00 0.00 2.87
1231 1259 1.601248 CCATCCTCCCCCTTCTTCTT 58.399 55.000 0.00 0.00 0.00 2.52
1232 1260 0.327964 CCCATCCTCCCCCTTCTTCT 60.328 60.000 0.00 0.00 0.00 2.85
1233 1261 1.356494 CCCCATCCTCCCCCTTCTTC 61.356 65.000 0.00 0.00 0.00 2.87
1234 1262 1.309102 CCCCATCCTCCCCCTTCTT 60.309 63.158 0.00 0.00 0.00 2.52
1235 1263 2.272170 TCCCCATCCTCCCCCTTCT 61.272 63.158 0.00 0.00 0.00 2.85
1236 1264 1.772156 CTCCCCATCCTCCCCCTTC 60.772 68.421 0.00 0.00 0.00 3.46
1237 1265 2.378522 CTCCCCATCCTCCCCCTT 59.621 66.667 0.00 0.00 0.00 3.95
1238 1266 3.795924 CCTCCCCATCCTCCCCCT 61.796 72.222 0.00 0.00 0.00 4.79
1239 1267 4.928520 CCCTCCCCATCCTCCCCC 62.929 77.778 0.00 0.00 0.00 5.40
1240 1268 4.928520 CCCCTCCCCATCCTCCCC 62.929 77.778 0.00 0.00 0.00 4.81
1241 1269 3.362946 TTCCCCTCCCCATCCTCCC 62.363 68.421 0.00 0.00 0.00 4.30
1242 1270 1.772156 CTTCCCCTCCCCATCCTCC 60.772 68.421 0.00 0.00 0.00 4.30
1243 1271 0.327576 TTCTTCCCCTCCCCATCCTC 60.328 60.000 0.00 0.00 0.00 3.71
1244 1272 0.327964 CTTCTTCCCCTCCCCATCCT 60.328 60.000 0.00 0.00 0.00 3.24
1245 1273 0.327576 TCTTCTTCCCCTCCCCATCC 60.328 60.000 0.00 0.00 0.00 3.51
1246 1274 1.492599 CTTCTTCTTCCCCTCCCCATC 59.507 57.143 0.00 0.00 0.00 3.51
1247 1275 1.082879 TCTTCTTCTTCCCCTCCCCAT 59.917 52.381 0.00 0.00 0.00 4.00
1248 1276 0.496382 TCTTCTTCTTCCCCTCCCCA 59.504 55.000 0.00 0.00 0.00 4.96
1249 1277 1.562008 CTTCTTCTTCTTCCCCTCCCC 59.438 57.143 0.00 0.00 0.00 4.81
1250 1278 2.552367 TCTTCTTCTTCTTCCCCTCCC 58.448 52.381 0.00 0.00 0.00 4.30
1251 1279 3.054728 CCTTCTTCTTCTTCTTCCCCTCC 60.055 52.174 0.00 0.00 0.00 4.30
1252 1280 3.054728 CCCTTCTTCTTCTTCTTCCCCTC 60.055 52.174 0.00 0.00 0.00 4.30
1253 1281 2.916269 CCCTTCTTCTTCTTCTTCCCCT 59.084 50.000 0.00 0.00 0.00 4.79
1254 1282 2.025793 CCCCTTCTTCTTCTTCTTCCCC 60.026 54.545 0.00 0.00 0.00 4.81
1255 1283 2.025793 CCCCCTTCTTCTTCTTCTTCCC 60.026 54.545 0.00 0.00 0.00 3.97
1256 1284 2.913617 TCCCCCTTCTTCTTCTTCTTCC 59.086 50.000 0.00 0.00 0.00 3.46
1257 1285 3.054728 CCTCCCCCTTCTTCTTCTTCTTC 60.055 52.174 0.00 0.00 0.00 2.87
1258 1286 2.916269 CCTCCCCCTTCTTCTTCTTCTT 59.084 50.000 0.00 0.00 0.00 2.52
1259 1287 2.114506 TCCTCCCCCTTCTTCTTCTTCT 59.885 50.000 0.00 0.00 0.00 2.85
1260 1288 2.552367 TCCTCCCCCTTCTTCTTCTTC 58.448 52.381 0.00 0.00 0.00 2.87
1261 1289 2.743131 TCCTCCCCCTTCTTCTTCTT 57.257 50.000 0.00 0.00 0.00 2.52
1262 1290 2.486716 CATCCTCCCCCTTCTTCTTCT 58.513 52.381 0.00 0.00 0.00 2.85
1263 1291 1.492599 CCATCCTCCCCCTTCTTCTTC 59.507 57.143 0.00 0.00 0.00 2.87
1264 1292 1.601248 CCATCCTCCCCCTTCTTCTT 58.399 55.000 0.00 0.00 0.00 2.52
1265 1293 0.327964 CCCATCCTCCCCCTTCTTCT 60.328 60.000 0.00 0.00 0.00 2.85
1266 1294 1.356494 CCCCATCCTCCCCCTTCTTC 61.356 65.000 0.00 0.00 0.00 2.87
1267 1295 1.309102 CCCCATCCTCCCCCTTCTT 60.309 63.158 0.00 0.00 0.00 2.52
1268 1296 2.272170 TCCCCATCCTCCCCCTTCT 61.272 63.158 0.00 0.00 0.00 2.85
1269 1297 1.772156 CTCCCCATCCTCCCCCTTC 60.772 68.421 0.00 0.00 0.00 3.46
1270 1298 2.378522 CTCCCCATCCTCCCCCTT 59.621 66.667 0.00 0.00 0.00 3.95
1271 1299 3.795924 CCTCCCCATCCTCCCCCT 61.796 72.222 0.00 0.00 0.00 4.79
1272 1300 4.928520 CCCTCCCCATCCTCCCCC 62.929 77.778 0.00 0.00 0.00 5.40
1273 1301 4.928520 CCCCTCCCCATCCTCCCC 62.929 77.778 0.00 0.00 0.00 4.81
1274 1302 3.362946 TTCCCCTCCCCATCCTCCC 62.363 68.421 0.00 0.00 0.00 4.30
1275 1303 1.772156 CTTCCCCTCCCCATCCTCC 60.772 68.421 0.00 0.00 0.00 4.30
1276 1304 0.327576 TTCTTCCCCTCCCCATCCTC 60.328 60.000 0.00 0.00 0.00 3.71
1277 1305 0.327964 CTTCTTCCCCTCCCCATCCT 60.328 60.000 0.00 0.00 0.00 3.24
1278 1306 0.327576 TCTTCTTCCCCTCCCCATCC 60.328 60.000 0.00 0.00 0.00 3.51
1279 1307 1.135960 CTCTTCTTCCCCTCCCCATC 58.864 60.000 0.00 0.00 0.00 3.51
1280 1308 0.327964 CCTCTTCTTCCCCTCCCCAT 60.328 60.000 0.00 0.00 0.00 4.00
1281 1309 1.082954 CCTCTTCTTCCCCTCCCCA 59.917 63.158 0.00 0.00 0.00 4.96
1282 1310 0.253207 TTCCTCTTCTTCCCCTCCCC 60.253 60.000 0.00 0.00 0.00 4.81
1283 1311 1.208706 CTTCCTCTTCTTCCCCTCCC 58.791 60.000 0.00 0.00 0.00 4.30
1284 1312 2.255770 TCTTCCTCTTCTTCCCCTCC 57.744 55.000 0.00 0.00 0.00 4.30
1285 1313 2.503765 CCTTCTTCCTCTTCTTCCCCTC 59.496 54.545 0.00 0.00 0.00 4.30
1286 1314 2.114506 TCCTTCTTCCTCTTCTTCCCCT 59.885 50.000 0.00 0.00 0.00 4.79
1367 1395 3.258123 ACCGAATGGAAGGAACCAAAATG 59.742 43.478 0.00 0.00 43.47 2.32
1374 1402 1.804601 ACGAACCGAATGGAAGGAAC 58.195 50.000 0.00 0.00 39.21 3.62
1381 1409 1.593006 GCAGTCATACGAACCGAATGG 59.407 52.381 0.00 0.00 42.84 3.16
1383 1411 2.665649 TGCAGTCATACGAACCGAAT 57.334 45.000 0.00 0.00 0.00 3.34
1412 1440 7.156876 TCAACAAAATCTATGGACCATTCAC 57.843 36.000 13.40 0.00 0.00 3.18
1422 1450 7.037438 CAGGAAACCCATCAACAAAATCTATG 58.963 38.462 0.00 0.00 0.00 2.23
1423 1451 6.725834 ACAGGAAACCCATCAACAAAATCTAT 59.274 34.615 0.00 0.00 0.00 1.98
1425 1453 4.901250 ACAGGAAACCCATCAACAAAATCT 59.099 37.500 0.00 0.00 0.00 2.40
1427 1455 4.202346 CCACAGGAAACCCATCAACAAAAT 60.202 41.667 0.00 0.00 0.00 1.82
1442 1470 1.303561 GCACATCAGCCCACAGGAA 60.304 57.895 0.00 0.00 33.47 3.36
1528 1556 1.200716 CCATCCATGCACACTGTCAAC 59.799 52.381 0.00 0.00 0.00 3.18
1529 1557 1.073603 TCCATCCATGCACACTGTCAA 59.926 47.619 0.00 0.00 0.00 3.18
1545 1573 7.067859 CACAAATCTAACACCATCTGATTCCAT 59.932 37.037 0.00 0.00 0.00 3.41
1551 1579 4.650734 TGCACAAATCTAACACCATCTGA 58.349 39.130 0.00 0.00 0.00 3.27
1582 1610 7.283127 TGCAGAGAACAAGATTAACAAGAAACT 59.717 33.333 0.00 0.00 0.00 2.66
1777 1806 4.549458 CTGCAAACCACAGTGGAAAATAG 58.451 43.478 27.39 13.81 40.96 1.73
1782 1811 0.033601 ACCTGCAAACCACAGTGGAA 60.034 50.000 27.39 5.19 40.96 3.53
1831 1860 3.031013 CCTCTTCCTCTTCCTCTTCCTC 58.969 54.545 0.00 0.00 0.00 3.71
1832 1861 2.657459 TCCTCTTCCTCTTCCTCTTCCT 59.343 50.000 0.00 0.00 0.00 3.36
1833 1862 3.108847 TCCTCTTCCTCTTCCTCTTCC 57.891 52.381 0.00 0.00 0.00 3.46
1834 1863 4.349365 TCTTCCTCTTCCTCTTCCTCTTC 58.651 47.826 0.00 0.00 0.00 2.87
1835 1864 4.352893 CTCTTCCTCTTCCTCTTCCTCTT 58.647 47.826 0.00 0.00 0.00 2.85
1836 1865 3.309848 CCTCTTCCTCTTCCTCTTCCTCT 60.310 52.174 0.00 0.00 0.00 3.69
1837 1866 3.031013 CCTCTTCCTCTTCCTCTTCCTC 58.969 54.545 0.00 0.00 0.00 3.71
1838 1867 2.657459 TCCTCTTCCTCTTCCTCTTCCT 59.343 50.000 0.00 0.00 0.00 3.36
1839 1868 3.108847 TCCTCTTCCTCTTCCTCTTCC 57.891 52.381 0.00 0.00 0.00 3.46
1840 1869 4.349365 TCTTCCTCTTCCTCTTCCTCTTC 58.651 47.826 0.00 0.00 0.00 2.87
1841 1870 4.412060 TCTTCCTCTTCCTCTTCCTCTT 57.588 45.455 0.00 0.00 0.00 2.85
1842 1871 4.045334 TCTTCTTCCTCTTCCTCTTCCTCT 59.955 45.833 0.00 0.00 0.00 3.69
2057 2086 3.087031 CAACCTCCTTGTCAGCATCATT 58.913 45.455 0.00 0.00 0.00 2.57
2136 2165 5.409520 CAGCATACTAGTCAAGTGAAAGCAA 59.590 40.000 0.00 0.00 39.39 3.91
2147 2176 4.617253 ACACCAAACAGCATACTAGTCA 57.383 40.909 0.00 0.00 0.00 3.41
2229 2258 4.873827 TGGAGATTTGCTACCACGTTTATC 59.126 41.667 0.00 0.00 0.00 1.75
2325 2354 2.030457 CGTGCTCTTATGGGTAAAAGCG 59.970 50.000 0.00 0.00 32.49 4.68
2335 2364 1.000827 AGATCGAGGCGTGCTCTTATG 60.001 52.381 0.00 0.00 0.00 1.90
2345 2374 3.370978 ACAAATAACACAAGATCGAGGCG 59.629 43.478 0.00 0.00 0.00 5.52
2384 2413 6.767524 TTGACATTGTGACACTTAGGTTTT 57.232 33.333 7.20 0.00 0.00 2.43
2385 2414 6.545666 TCATTGACATTGTGACACTTAGGTTT 59.454 34.615 7.20 0.00 0.00 3.27
2389 2418 6.580041 GCTTTCATTGACATTGTGACACTTAG 59.420 38.462 7.20 0.00 0.00 2.18
2436 2465 6.232692 ACAGGAAAGCACAATATTTTGCATT 58.767 32.000 24.44 19.76 41.48 3.56
2456 2489 3.742369 GCAACCATTGATTCAACAACAGG 59.258 43.478 0.15 2.30 35.68 4.00
2491 2524 8.388484 ACCATAGTAGATAGTACTACCAAACG 57.612 38.462 4.31 0.00 42.34 3.60
2523 2556 2.781403 AATCCTGGGCAGCCAATAAT 57.219 45.000 15.19 0.00 0.00 1.28
2531 2564 6.058553 TGAATCTATGATAATCCTGGGCAG 57.941 41.667 0.00 0.00 0.00 4.85
2584 2617 8.800370 TGACAGCCATTGAGTTTACATAATTA 57.200 30.769 0.00 0.00 0.00 1.40
2585 2618 7.701539 TGACAGCCATTGAGTTTACATAATT 57.298 32.000 0.00 0.00 0.00 1.40
2720 2754 5.613358 GAACTATCAACAAGTTCCTGGTG 57.387 43.478 4.94 0.00 44.60 4.17
2739 2773 9.552114 CATTGTCTTCATGTTTATCTTGAGAAC 57.448 33.333 0.00 0.00 33.00 3.01
2809 2843 1.836166 CTTGAAGAGGGAGGCAGATGA 59.164 52.381 0.00 0.00 0.00 2.92
2901 2935 9.485206 ACAGAAGATAAGTACGTTTGTAAATGT 57.515 29.630 0.00 7.31 40.88 2.71
3011 3045 8.236586 TGCTACAATCAAAACAAGCTGTTATAG 58.763 33.333 0.00 0.00 40.14 1.31
3017 3051 3.983344 GGTGCTACAATCAAAACAAGCTG 59.017 43.478 0.00 0.00 0.00 4.24
3029 3063 6.042638 AGAGATAATATGCGGTGCTACAAT 57.957 37.500 0.00 0.00 0.00 2.71
3206 3240 1.444119 GCCGTTGCTTGTTCTCCACA 61.444 55.000 0.00 0.00 33.53 4.17
3207 3241 1.282875 GCCGTTGCTTGTTCTCCAC 59.717 57.895 0.00 0.00 33.53 4.02
3273 3307 5.539582 TTAAAAGCCAATAGTACAGTGCG 57.460 39.130 0.00 0.00 0.00 5.34
3296 3331 6.435277 AGCCAGACAGATAATTCAACAAATGT 59.565 34.615 0.00 0.00 0.00 2.71
3297 3332 6.860080 AGCCAGACAGATAATTCAACAAATG 58.140 36.000 0.00 0.00 0.00 2.32
3298 3333 6.660521 TGAGCCAGACAGATAATTCAACAAAT 59.339 34.615 0.00 0.00 0.00 2.32
3403 3438 1.156736 GTCGAGGTTGTTGATGGGTG 58.843 55.000 0.00 0.00 0.00 4.61
3428 3463 1.814394 TGGACATGAATCACTTGCAGC 59.186 47.619 0.00 0.00 0.00 5.25
3429 3464 3.340928 TCTGGACATGAATCACTTGCAG 58.659 45.455 0.00 7.77 0.00 4.41
3478 3513 2.329267 TCCTCTTCCTCAGCTTCAACA 58.671 47.619 0.00 0.00 0.00 3.33
3520 3555 5.677567 TCTTCTTCGTTGTCCTTAAACCTT 58.322 37.500 0.00 0.00 0.00 3.50
3550 3585 8.668353 GCAGTAAGTACTTCATTTTCATCATCA 58.332 33.333 12.39 0.00 33.46 3.07
3586 3621 4.453819 ACTTCTTCTTCTTCAAATCCAGCG 59.546 41.667 0.00 0.00 0.00 5.18
3898 3933 3.204827 CGGGCCAAATGCTCCTCG 61.205 66.667 4.39 0.00 37.02 4.63
4021 4069 7.338449 GGGTGGATAAAAATTCTGTACTAGCAA 59.662 37.037 0.00 0.00 0.00 3.91
4102 4150 7.718314 TCTTCCAATGGAGATATGAATGAAGTG 59.282 37.037 0.86 0.00 31.21 3.16
4252 4300 5.079643 ACTTAGATGACCAGCCATGTTTTT 58.920 37.500 0.00 0.00 0.00 1.94
4292 4340 7.227910 AGCATTTCAAGATTTGCTGAAAACATT 59.772 29.630 6.50 0.00 43.44 2.71
4457 4505 3.429492 TCAATTTGGAGCAACATAGGCA 58.571 40.909 0.00 0.00 0.00 4.75
4507 4580 7.618117 TGAGAGGGATAGTACATGTTTAAGTGA 59.382 37.037 2.30 0.00 0.00 3.41
4510 4583 9.265901 CAATGAGAGGGATAGTACATGTTTAAG 57.734 37.037 2.30 0.00 0.00 1.85
4511 4584 8.768397 ACAATGAGAGGGATAGTACATGTTTAA 58.232 33.333 2.30 0.00 0.00 1.52
4512 4585 8.319057 ACAATGAGAGGGATAGTACATGTTTA 57.681 34.615 2.30 0.00 0.00 2.01
4513 4586 7.200434 ACAATGAGAGGGATAGTACATGTTT 57.800 36.000 2.30 0.00 0.00 2.83
4514 4587 6.814954 ACAATGAGAGGGATAGTACATGTT 57.185 37.500 2.30 0.00 0.00 2.71
4558 4691 3.005155 GCAAGTTGCAATGGAAGAGAACT 59.995 43.478 22.90 0.00 44.26 3.01
4601 4734 3.076079 TGAGGGGGAAATCGGTTTAAC 57.924 47.619 0.00 0.00 0.00 2.01
4602 4735 3.010808 ACATGAGGGGGAAATCGGTTTAA 59.989 43.478 0.00 0.00 0.00 1.52
4603 4736 2.578940 ACATGAGGGGGAAATCGGTTTA 59.421 45.455 0.00 0.00 0.00 2.01
4610 4745 3.334881 AGAGACAAACATGAGGGGGAAAT 59.665 43.478 0.00 0.00 0.00 2.17
4647 4786 4.519147 GAGAAAAGACGACTGCAAAGAAC 58.481 43.478 0.00 0.00 0.00 3.01
4720 4859 1.719709 GCGACCGAAAATGTAGCCC 59.280 57.895 0.00 0.00 0.00 5.19
4777 4916 3.444034 CCACATCCGAGTTACTCTCAGAA 59.556 47.826 10.83 0.00 42.88 3.02
4864 5003 5.841957 ATGTTTCTGAATGTAGGGAATGC 57.158 39.130 0.00 0.00 0.00 3.56
4874 5013 4.791676 CGCACATGAGAATGTTTCTGAATG 59.208 41.667 0.00 2.15 40.87 2.67
4897 5036 2.014068 GCTGTACAGTGGAATGAGGGC 61.014 57.143 23.44 2.20 0.00 5.19
4911 5050 2.125512 CGCCTGGTCCTGCTGTAC 60.126 66.667 0.00 0.00 0.00 2.90
5015 5154 3.672295 GAACAGGGAGGCGCCTGAG 62.672 68.421 38.41 22.17 37.48 3.35
5027 5166 2.507992 CGCAGGAGCTCGAACAGG 60.508 66.667 7.83 0.00 39.10 4.00
5059 5198 3.858989 GCTCTTGCTTCTCGGCGC 61.859 66.667 0.00 0.00 36.03 6.53
5100 5239 1.086634 GCTTGGCTCTCCGTGATGAC 61.087 60.000 0.00 0.00 34.14 3.06
5214 5372 6.737254 AAAATGTACTTCCACCGACATAAG 57.263 37.500 0.00 0.00 32.31 1.73
5328 5498 4.023792 TCAGAAACACACAGATGCACATTC 60.024 41.667 0.00 0.00 0.00 2.67
5407 5590 3.181458 GGTCTGGCCCATTATTAAGACGA 60.181 47.826 0.00 0.00 35.89 4.20
5410 5593 2.105821 CCGGTCTGGCCCATTATTAAGA 59.894 50.000 0.00 0.00 0.00 2.10
5467 7704 2.187163 GGAGCGGCTGGTAAGACC 59.813 66.667 7.50 0.00 39.22 3.85
5646 7883 1.442148 GGATCTCAGGTACGGCCAC 59.558 63.158 2.24 0.00 40.61 5.01
5647 7884 2.125326 CGGATCTCAGGTACGGCCA 61.125 63.158 2.24 0.00 40.61 5.36
5648 7885 1.797211 CTCGGATCTCAGGTACGGCC 61.797 65.000 0.00 0.00 37.58 6.13
5649 7886 1.655329 CTCGGATCTCAGGTACGGC 59.345 63.158 0.00 0.00 0.00 5.68
5650 7887 1.655329 GCTCGGATCTCAGGTACGG 59.345 63.158 0.00 0.00 0.00 4.02
5676 7913 2.828549 CGGCGGGGGATTTTGAGG 60.829 66.667 0.00 0.00 0.00 3.86
5729 7966 1.400494 GAATTGAACGGAATGGACGGG 59.600 52.381 0.00 0.00 35.23 5.28
5741 7978 2.842485 CGAATTCAGCTGCGAATTGAAC 59.158 45.455 25.52 15.79 43.86 3.18
5784 8021 2.365105 ATTCGGGGAGGAAGGCGA 60.365 61.111 0.00 0.00 0.00 5.54
5788 8025 0.671251 CTCTCGATTCGGGGAGGAAG 59.329 60.000 6.03 0.00 0.00 3.46
5807 8044 2.402640 ACGCGAATACTCCGAGAATC 57.597 50.000 15.93 0.00 0.00 2.52
5815 8052 2.113289 GAGCTCAGAACGCGAATACTC 58.887 52.381 15.93 6.29 0.00 2.59
5849 8086 4.575973 GCGGCTGCCATGGGAGAT 62.576 66.667 35.08 0.00 35.50 2.75
5911 8148 1.069090 CCGCCGGCTAGCATCTTAA 59.931 57.895 26.68 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.