Multiple sequence alignment - TraesCS6B01G052700

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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 TraesCS6B01G052700 chr6B 100.000 2763 0 0 1 2763 32171126 32173888 0.000000e+00 5103
1 TraesCS6B01G052700 chr6B 92.491 1092 60 7 534 1624 32024005 32025075 0.000000e+00 1543
2 TraesCS6B01G052700 chr6B 85.569 1282 147 21 1510 2763 31869197 31870468 0.000000e+00 1308
3 TraesCS6B01G052700 chr6B 94.307 808 44 1 817 1624 31793112 31793917 0.000000e+00 1236
4 TraesCS6B01G052700 chr6B 87.706 911 84 15 1510 2402 32087057 32087957 0.000000e+00 1037
5 TraesCS6B01G052700 chr6B 86.610 941 90 24 1626 2547 31842562 31843485 0.000000e+00 1007
6 TraesCS6B01G052700 chr6B 85.851 940 97 21 1626 2547 32074220 32075141 0.000000e+00 966
7 TraesCS6B01G052700 chr6B 94.626 521 28 0 990 1510 32075907 32076427 0.000000e+00 808
8 TraesCS6B01G052700 chr6B 94.050 521 31 0 990 1510 31844251 31844771 0.000000e+00 791
9 TraesCS6B01G052700 chr6B 92.308 286 19 3 534 817 31783855 31784139 1.190000e-108 403
10 TraesCS6B01G052700 chr6B 97.854 233 5 0 1 233 376984854 376985086 1.190000e-108 403
11 TraesCS6B01G052700 chr6B 97.021 235 5 2 1 233 538427586 538427820 7.170000e-106 394
12 TraesCS6B01G052700 chr6B 84.270 178 15 8 258 426 32023709 32023882 7.920000e-36 161
13 TraesCS6B01G052700 chr6A 94.680 2237 93 15 539 2763 18624633 18626855 0.000000e+00 3448
14 TraesCS6B01G052700 chr6A 82.456 171 27 3 258 426 18624365 18624534 2.220000e-31 147
15 TraesCS6B01G052700 chr6D 97.451 1530 28 8 534 2063 17891997 17893515 0.000000e+00 2599
16 TraesCS6B01G052700 chr6D 96.483 654 21 2 2111 2763 17893509 17894161 0.000000e+00 1079
17 TraesCS6B01G052700 chr6D 91.830 306 15 4 244 539 17891661 17891966 4.260000e-113 418
18 TraesCS6B01G052700 chr6D 96.596 235 6 2 1 233 184826414 184826648 3.340000e-104 388
19 TraesCS6B01G052700 chr1B 97.925 241 3 2 1 240 236960921 236960682 1.530000e-112 416
20 TraesCS6B01G052700 chr1B 97.854 233 5 0 1 233 543025240 543025008 1.190000e-108 403
21 TraesCS6B01G052700 chr1B 80.143 559 69 20 946 1498 623505711 623505189 2.010000e-101 379
22 TraesCS6B01G052700 chr5B 97.835 231 4 1 3 233 134072709 134072480 5.540000e-107 398
23 TraesCS6B01G052700 chr5D 97.009 234 6 1 1 233 380661214 380661447 2.580000e-105 392
24 TraesCS6B01G052700 chr5D 96.596 235 6 2 1 233 256855397 256855163 3.340000e-104 388
25 TraesCS6B01G052700 chr4D 96.596 235 6 2 1 233 300007104 300006870 3.340000e-104 388
26 TraesCS6B01G052700 chr3B 85.581 215 22 4 2545 2750 779624850 779625064 1.670000e-52 217
27 TraesCS6B01G052700 chr1D 82.883 222 28 4 2538 2750 33418281 33418501 1.010000e-44 191
28 TraesCS6B01G052700 chr7B 82.243 214 27 5 2544 2747 667384485 667384273 1.020000e-39 174


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 TraesCS6B01G052700 chr6B 32171126 32173888 2762 False 5103.000000 5103 100.000000 1 2763 1 chr6B.!!$F5 2762
1 TraesCS6B01G052700 chr6B 31869197 31870468 1271 False 1308.000000 1308 85.569000 1510 2763 1 chr6B.!!$F3 1253
2 TraesCS6B01G052700 chr6B 31793112 31793917 805 False 1236.000000 1236 94.307000 817 1624 1 chr6B.!!$F2 807
3 TraesCS6B01G052700 chr6B 32087057 32087957 900 False 1037.000000 1037 87.706000 1510 2402 1 chr6B.!!$F4 892
4 TraesCS6B01G052700 chr6B 31842562 31844771 2209 False 899.000000 1007 90.330000 990 2547 2 chr6B.!!$F8 1557
5 TraesCS6B01G052700 chr6B 32074220 32076427 2207 False 887.000000 966 90.238500 990 2547 2 chr6B.!!$F10 1557
6 TraesCS6B01G052700 chr6B 32023709 32025075 1366 False 852.000000 1543 88.380500 258 1624 2 chr6B.!!$F9 1366
7 TraesCS6B01G052700 chr6A 18624365 18626855 2490 False 1797.500000 3448 88.568000 258 2763 2 chr6A.!!$F1 2505
8 TraesCS6B01G052700 chr6D 17891661 17894161 2500 False 1365.333333 2599 95.254667 244 2763 3 chr6D.!!$F2 2519
9 TraesCS6B01G052700 chr1B 623505189 623505711 522 True 379.000000 379 80.143000 946 1498 1 chr1B.!!$R3 552

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
210 211 0.109179 TTGCCAAATCTCATGCGTGC 60.109 50.0 0.0 0.0 0.0 5.34 F
1317 1397 0.179108 GTGGCTACGGTGGTCTCATC 60.179 60.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 1420 0.030504 CTTGCGACACACCATTGCAA 59.969 50.0 0.00 0.0 42.84 4.08 R
2305 3260 0.388659 ACGCATGCCACAACAACAAT 59.611 45.0 13.15 0.0 0.00 2.71 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
31 32 9.717942 TGCCATTATTTGTTTTTACTTTATGCT 57.282 25.926 0.00 0.00 0.00 3.79
42 43 7.611821 TTTTACTTTATGCTTTACAACGCAC 57.388 32.000 0.00 0.00 39.21 5.34
44 45 5.176407 ACTTTATGCTTTACAACGCACAA 57.824 34.783 0.00 0.00 39.21 3.33
46 47 6.212955 ACTTTATGCTTTACAACGCACAATT 58.787 32.000 0.00 0.00 39.21 2.32
47 48 6.362283 ACTTTATGCTTTACAACGCACAATTC 59.638 34.615 0.00 0.00 39.21 2.17
48 49 3.006659 TGCTTTACAACGCACAATTCC 57.993 42.857 0.00 0.00 0.00 3.01
51 52 3.364621 GCTTTACAACGCACAATTCCATG 59.635 43.478 0.00 0.00 0.00 3.66
52 53 4.793071 CTTTACAACGCACAATTCCATGA 58.207 39.130 0.00 0.00 0.00 3.07
53 54 4.837896 TTACAACGCACAATTCCATGAA 57.162 36.364 0.00 0.00 0.00 2.57
54 55 3.940209 ACAACGCACAATTCCATGAAT 57.060 38.095 0.00 0.00 33.25 2.57
55 56 3.836949 ACAACGCACAATTCCATGAATC 58.163 40.909 0.00 0.00 30.29 2.52
56 57 3.507233 ACAACGCACAATTCCATGAATCT 59.493 39.130 0.00 0.00 30.29 2.40
58 59 5.182950 ACAACGCACAATTCCATGAATCTTA 59.817 36.000 0.00 0.00 30.29 2.10
59 60 5.895636 ACGCACAATTCCATGAATCTTAA 57.104 34.783 0.00 0.00 30.29 1.85
61 62 6.686630 ACGCACAATTCCATGAATCTTAAAA 58.313 32.000 0.00 0.00 30.29 1.52
62 63 7.322664 ACGCACAATTCCATGAATCTTAAAAT 58.677 30.769 0.00 0.00 30.29 1.82
64 65 8.961092 CGCACAATTCCATGAATCTTAAAATAG 58.039 33.333 0.00 0.00 30.29 1.73
146 147 9.729281 ACAAACATCTACATCATGCATATATGA 57.271 29.630 21.83 8.89 41.00 2.15
150 151 8.755977 ACATCTACATCATGCATATATGACTCA 58.244 33.333 21.83 5.50 39.68 3.41
151 152 9.595823 CATCTACATCATGCATATATGACTCAA 57.404 33.333 21.83 7.90 39.68 3.02
154 155 7.683437 ACATCATGCATATATGACTCAAAGG 57.317 36.000 21.83 3.18 39.68 3.11
155 156 7.229308 ACATCATGCATATATGACTCAAAGGT 58.771 34.615 21.83 3.71 39.68 3.50
157 158 9.223099 CATCATGCATATATGACTCAAAGGTTA 57.777 33.333 17.10 0.00 39.68 2.85
158 159 8.607441 TCATGCATATATGACTCAAAGGTTAC 57.393 34.615 17.10 0.00 32.39 2.50
161 162 8.382030 TGCATATATGACTCAAAGGTTACATG 57.618 34.615 17.10 0.00 0.00 3.21
162 163 7.041167 TGCATATATGACTCAAAGGTTACATGC 60.041 37.037 17.10 0.00 34.58 4.06
164 165 9.710900 CATATATGACTCAAAGGTTACATGCTA 57.289 33.333 6.92 0.00 0.00 3.49
167 168 9.935241 ATATGACTCAAAGGTTACATGCTATAG 57.065 33.333 0.00 0.00 0.00 1.31
168 169 7.182817 TGACTCAAAGGTTACATGCTATAGT 57.817 36.000 0.84 0.00 0.00 2.12
169 170 7.041721 TGACTCAAAGGTTACATGCTATAGTG 58.958 38.462 0.84 0.00 0.00 2.74
170 171 6.947464 ACTCAAAGGTTACATGCTATAGTGT 58.053 36.000 0.84 1.50 0.00 3.55
171 172 6.818644 ACTCAAAGGTTACATGCTATAGTGTG 59.181 38.462 0.84 3.54 0.00 3.82
173 174 5.693769 AAGGTTACATGCTATAGTGTGGT 57.306 39.130 0.84 0.00 0.00 4.16
174 175 6.801718 AAGGTTACATGCTATAGTGTGGTA 57.198 37.500 0.84 0.00 0.00 3.25
175 176 6.996180 AGGTTACATGCTATAGTGTGGTAT 57.004 37.500 0.84 0.00 0.00 2.73
176 177 7.374975 AGGTTACATGCTATAGTGTGGTATT 57.625 36.000 0.84 0.00 0.00 1.89
178 179 8.930527 AGGTTACATGCTATAGTGTGGTATTTA 58.069 33.333 0.84 0.00 0.00 1.40
179 180 9.720769 GGTTACATGCTATAGTGTGGTATTTAT 57.279 33.333 0.84 0.00 0.00 1.40
195 196 9.040939 GTGGTATTTATTCATAATTTGGTTGCC 57.959 33.333 0.00 0.00 0.00 4.52
196 197 8.762645 TGGTATTTATTCATAATTTGGTTGCCA 58.237 29.630 0.00 0.00 0.00 4.92
206 207 2.747396 TTGGTTGCCAAATCTCATGC 57.253 45.000 0.00 0.00 40.92 4.06
207 208 0.527113 TGGTTGCCAAATCTCATGCG 59.473 50.000 0.00 0.00 0.00 4.73
210 211 0.109179 TTGCCAAATCTCATGCGTGC 60.109 50.000 0.00 0.00 0.00 5.34
211 212 1.242665 TGCCAAATCTCATGCGTGCA 61.243 50.000 0.00 0.00 0.00 4.57
214 215 2.190161 CCAAATCTCATGCGTGCAATG 58.810 47.619 0.00 0.00 0.00 2.82
225 226 4.789977 TGCAATGCACGTGTACCT 57.210 50.000 18.38 0.33 31.71 3.08
226 227 3.917072 TGCAATGCACGTGTACCTA 57.083 47.368 18.38 0.00 31.71 3.08
228 229 1.801771 TGCAATGCACGTGTACCTAAC 59.198 47.619 18.38 2.42 31.71 2.34
229 230 2.073816 GCAATGCACGTGTACCTAACT 58.926 47.619 18.38 0.00 0.00 2.24
231 232 3.306166 GCAATGCACGTGTACCTAACTAG 59.694 47.826 18.38 0.00 0.00 2.57
232 233 4.491676 CAATGCACGTGTACCTAACTAGT 58.508 43.478 18.38 0.00 0.00 2.57
233 234 3.837213 TGCACGTGTACCTAACTAGTC 57.163 47.619 18.38 0.00 0.00 2.59
234 235 2.489329 TGCACGTGTACCTAACTAGTCC 59.511 50.000 18.38 0.00 0.00 3.85
235 236 2.751806 GCACGTGTACCTAACTAGTCCT 59.248 50.000 18.38 0.00 0.00 3.85
237 238 4.034975 GCACGTGTACCTAACTAGTCCTAG 59.965 50.000 18.38 0.00 39.04 3.02
239 240 6.341316 CACGTGTACCTAACTAGTCCTAGTA 58.659 44.000 7.58 0.00 44.96 1.82
240 241 6.478344 CACGTGTACCTAACTAGTCCTAGTAG 59.522 46.154 7.58 5.92 44.96 2.57
241 242 6.155393 ACGTGTACCTAACTAGTCCTAGTAGT 59.845 42.308 7.38 8.19 44.96 2.73
243 244 6.259829 GTGTACCTAACTAGTCCTAGTAGTGC 59.740 46.154 7.38 9.36 44.96 4.40
244 245 4.790937 ACCTAACTAGTCCTAGTAGTGCC 58.209 47.826 7.38 0.00 44.96 5.01
245 246 4.143543 CCTAACTAGTCCTAGTAGTGCCC 58.856 52.174 7.38 0.00 44.96 5.36
278 279 2.343758 GGTTGCCGTCTGAGAGCA 59.656 61.111 0.00 0.00 33.97 4.26
339 340 0.940126 GATTTGCGCATCAGATCCGT 59.060 50.000 12.75 0.00 31.94 4.69
351 352 1.986378 CAGATCCGTTGACTCACGTTC 59.014 52.381 0.00 0.00 38.57 3.95
355 356 1.135527 TCCGTTGACTCACGTTCTGTT 59.864 47.619 0.00 0.00 38.57 3.16
420 425 5.189180 GTTCCTGGAGAATGTTAGCTCAAT 58.811 41.667 0.00 0.00 36.69 2.57
520 561 5.514204 CGTTGATCAGTACCTAAACTAACCG 59.486 44.000 0.00 0.00 0.00 4.44
726 806 3.499918 GCACTATCTCCCATAATGCACAC 59.500 47.826 0.00 0.00 0.00 3.82
729 809 0.463654 TCTCCCATAATGCACACGCC 60.464 55.000 0.00 0.00 37.32 5.68
850 930 1.346395 TGCAAACCGTATCACAGGTCT 59.654 47.619 0.00 0.00 40.37 3.85
851 931 2.000447 GCAAACCGTATCACAGGTCTC 59.000 52.381 0.00 0.00 40.37 3.36
925 1005 7.148137 CCTCTCATCAATCAATCACATTCACAA 60.148 37.037 0.00 0.00 0.00 3.33
1204 1284 9.922477 TGTTCCTTCTATCTACATAAGAGAAGA 57.078 33.333 10.71 0.00 38.15 2.87
1213 1293 8.719645 ATCTACATAAGAGAAGATACTTGCCT 57.280 34.615 0.00 0.00 37.74 4.75
1214 1294 9.815306 ATCTACATAAGAGAAGATACTTGCCTA 57.185 33.333 0.00 0.00 37.74 3.93
1215 1295 9.815306 TCTACATAAGAGAAGATACTTGCCTAT 57.185 33.333 0.00 0.00 0.00 2.57
1218 1298 8.709308 ACATAAGAGAAGATACTTGCCTATTGT 58.291 33.333 0.00 0.00 0.00 2.71
1219 1299 8.986847 CATAAGAGAAGATACTTGCCTATTGTG 58.013 37.037 0.00 0.00 0.00 3.33
1220 1300 5.363939 AGAGAAGATACTTGCCTATTGTGC 58.636 41.667 0.00 0.00 0.00 4.57
1221 1301 5.102953 AGAAGATACTTGCCTATTGTGCA 57.897 39.130 0.00 0.00 36.84 4.57
1224 1304 4.139786 AGATACTTGCCTATTGTGCATGG 58.860 43.478 0.00 0.00 38.76 3.66
1225 1305 2.512692 ACTTGCCTATTGTGCATGGA 57.487 45.000 0.00 0.00 38.76 3.41
1227 1307 4.169059 ACTTGCCTATTGTGCATGGATA 57.831 40.909 0.00 0.00 38.76 2.59
1229 1309 4.339247 ACTTGCCTATTGTGCATGGATAAC 59.661 41.667 0.00 0.00 38.76 1.89
1230 1310 3.221771 TGCCTATTGTGCATGGATAACC 58.778 45.455 0.00 0.00 32.85 2.85
1262 1342 6.327279 TGTCATATGTAATAGGTCGTCCTG 57.673 41.667 11.77 0.00 44.81 3.86
1263 1343 6.066032 TGTCATATGTAATAGGTCGTCCTGA 58.934 40.000 11.77 0.00 44.81 3.86
1264 1344 6.206829 TGTCATATGTAATAGGTCGTCCTGAG 59.793 42.308 11.77 0.00 44.81 3.35
1266 1346 2.029623 TGTAATAGGTCGTCCTGAGCC 58.970 52.381 11.77 0.00 46.44 4.70
1267 1347 1.340568 GTAATAGGTCGTCCTGAGCCC 59.659 57.143 11.77 0.00 46.44 5.19
1268 1348 1.392710 AATAGGTCGTCCTGAGCCCG 61.393 60.000 11.77 0.00 46.44 6.13
1269 1349 2.280404 ATAGGTCGTCCTGAGCCCGA 62.280 60.000 11.77 0.00 46.44 5.14
1270 1350 2.888464 TAGGTCGTCCTGAGCCCGAG 62.888 65.000 11.77 0.00 46.44 4.63
1271 1351 2.750637 GTCGTCCTGAGCCCGAGA 60.751 66.667 0.00 0.00 0.00 4.04
1272 1352 2.438614 TCGTCCTGAGCCCGAGAG 60.439 66.667 0.00 0.00 0.00 3.20
1273 1353 4.200283 CGTCCTGAGCCCGAGAGC 62.200 72.222 0.00 0.00 0.00 4.09
1274 1354 3.071206 GTCCTGAGCCCGAGAGCA 61.071 66.667 0.00 0.00 34.23 4.26
1275 1355 3.071206 TCCTGAGCCCGAGAGCAC 61.071 66.667 0.00 0.00 34.23 4.40
1276 1356 3.385384 CCTGAGCCCGAGAGCACA 61.385 66.667 0.00 0.00 34.23 4.57
1278 1358 1.395045 CCTGAGCCCGAGAGCACATA 61.395 60.000 0.00 0.00 32.80 2.29
1280 1360 1.299468 GAGCCCGAGAGCACATACG 60.299 63.158 0.00 0.00 34.23 3.06
1281 1361 1.725557 GAGCCCGAGAGCACATACGA 61.726 60.000 0.00 0.00 34.23 3.43
1282 1362 1.141019 GCCCGAGAGCACATACGAA 59.859 57.895 0.00 0.00 0.00 3.85
1283 1363 0.872021 GCCCGAGAGCACATACGAAG 60.872 60.000 0.00 0.00 0.00 3.79
1286 1366 2.389059 CCGAGAGCACATACGAAGATG 58.611 52.381 0.00 0.00 0.00 2.90
1287 1367 2.389059 CGAGAGCACATACGAAGATGG 58.611 52.381 0.00 0.00 0.00 3.51
1289 1369 1.202580 AGAGCACATACGAAGATGGCC 60.203 52.381 0.00 0.00 0.00 5.36
1290 1370 0.541392 AGCACATACGAAGATGGCCA 59.459 50.000 8.56 8.56 0.00 5.36
1291 1371 1.141657 AGCACATACGAAGATGGCCAT 59.858 47.619 20.96 20.96 0.00 4.40
1292 1372 1.532868 GCACATACGAAGATGGCCATC 59.467 52.381 34.48 34.48 38.09 3.51
1293 1373 1.794701 CACATACGAAGATGGCCATCG 59.205 52.381 34.48 28.46 42.48 3.84
1295 1375 0.392706 ATACGAAGATGGCCATCGCA 59.607 50.000 34.48 19.79 42.48 5.10
1297 1377 1.353103 CGAAGATGGCCATCGCAAC 59.647 57.895 34.48 24.97 42.48 4.17
1298 1378 1.353103 GAAGATGGCCATCGCAACG 59.647 57.895 34.48 0.00 42.48 4.10
1301 1381 3.112126 GATGGCCATCGCAACGTGG 62.112 63.158 29.34 0.00 38.55 4.94
1305 1385 3.089784 CCATCGCAACGTGGCTAC 58.910 61.111 14.16 0.00 0.00 3.58
1314 1394 2.181021 CGTGGCTACGGTGGTCTC 59.819 66.667 15.64 0.00 46.23 3.36
1316 1396 1.898154 GTGGCTACGGTGGTCTCAT 59.102 57.895 0.00 0.00 0.00 2.90
1317 1397 0.179108 GTGGCTACGGTGGTCTCATC 60.179 60.000 0.00 0.00 0.00 2.92
1318 1398 0.613572 TGGCTACGGTGGTCTCATCA 60.614 55.000 0.00 0.00 0.00 3.07
1320 1400 1.139058 GGCTACGGTGGTCTCATCATT 59.861 52.381 0.00 0.00 0.00 2.57
1322 1402 3.553096 GGCTACGGTGGTCTCATCATTAG 60.553 52.174 0.00 0.00 0.00 1.73
1323 1403 3.318275 GCTACGGTGGTCTCATCATTAGA 59.682 47.826 0.00 0.00 0.00 2.10
1343 1423 8.853345 CATTAGATGACAACAAACTTACATTGC 58.147 33.333 0.00 0.00 0.00 3.56
1344 1424 6.389830 AGATGACAACAAACTTACATTGCA 57.610 33.333 0.00 0.00 0.00 4.08
1348 1428 5.752472 TGACAACAAACTTACATTGCAATGG 59.248 36.000 35.85 23.59 40.70 3.16
1349 1429 5.669477 ACAACAAACTTACATTGCAATGGT 58.331 33.333 35.85 24.17 40.70 3.55
1350 1430 5.523188 ACAACAAACTTACATTGCAATGGTG 59.477 36.000 35.85 27.02 40.70 4.17
1351 1431 5.275067 ACAAACTTACATTGCAATGGTGT 57.725 34.783 35.85 27.56 40.70 4.16
1352 1432 5.049167 ACAAACTTACATTGCAATGGTGTG 58.951 37.500 35.85 29.47 40.70 3.82
1353 1433 4.935352 AACTTACATTGCAATGGTGTGT 57.065 36.364 35.85 25.83 40.70 3.72
1354 1434 4.503741 ACTTACATTGCAATGGTGTGTC 57.496 40.909 35.85 0.00 40.70 3.67
1357 1437 0.039346 CATTGCAATGGTGTGTCGCA 60.039 50.000 28.34 0.00 32.78 5.10
1358 1438 0.672889 ATTGCAATGGTGTGTCGCAA 59.327 45.000 12.09 0.00 45.70 4.85
1359 1439 0.030504 TTGCAATGGTGTGTCGCAAG 59.969 50.000 0.00 0.00 37.64 4.01
1362 1442 0.888736 CAATGGTGTGTCGCAAGGGA 60.889 55.000 0.00 0.00 38.47 4.20
1363 1443 0.038166 AATGGTGTGTCGCAAGGGAT 59.962 50.000 0.00 0.00 38.47 3.85
1364 1444 0.038166 ATGGTGTGTCGCAAGGGATT 59.962 50.000 0.00 0.00 38.47 3.01
1365 1445 0.888736 TGGTGTGTCGCAAGGGATTG 60.889 55.000 0.00 0.00 38.47 2.67
1366 1446 0.889186 GGTGTGTCGCAAGGGATTGT 60.889 55.000 0.00 0.00 38.47 2.71
1367 1447 0.238289 GTGTGTCGCAAGGGATTGTG 59.762 55.000 0.00 0.00 38.47 3.33
1368 1448 0.179032 TGTGTCGCAAGGGATTGTGT 60.179 50.000 1.90 0.00 34.31 3.72
1369 1449 0.238289 GTGTCGCAAGGGATTGTGTG 59.762 55.000 1.90 0.00 34.31 3.82
1371 1451 0.517316 GTCGCAAGGGATTGTGTGAC 59.483 55.000 2.01 2.01 45.07 3.67
1372 1452 0.605319 TCGCAAGGGATTGTGTGACC 60.605 55.000 1.90 0.00 34.31 4.02
1374 1454 1.327303 GCAAGGGATTGTGTGACCAA 58.673 50.000 0.00 0.00 0.00 3.67
1375 1455 1.686052 GCAAGGGATTGTGTGACCAAA 59.314 47.619 0.00 0.00 0.00 3.28
1376 1456 2.288395 GCAAGGGATTGTGTGACCAAAG 60.288 50.000 0.00 0.00 0.00 2.77
1377 1457 2.292828 AGGGATTGTGTGACCAAAGG 57.707 50.000 0.00 0.00 0.00 3.11
1378 1458 1.499007 AGGGATTGTGTGACCAAAGGT 59.501 47.619 0.00 0.00 39.44 3.50
1379 1459 1.613437 GGGATTGTGTGACCAAAGGTG 59.387 52.381 0.00 0.00 35.25 4.00
1380 1460 2.582052 GGATTGTGTGACCAAAGGTGA 58.418 47.619 0.00 0.00 35.25 4.02
1381 1461 2.955660 GGATTGTGTGACCAAAGGTGAA 59.044 45.455 0.00 0.00 35.25 3.18
1382 1462 3.243401 GGATTGTGTGACCAAAGGTGAAC 60.243 47.826 0.00 0.00 35.25 3.18
1383 1463 1.757682 TGTGTGACCAAAGGTGAACC 58.242 50.000 0.00 0.00 35.25 3.62
1384 1464 0.661020 GTGTGACCAAAGGTGAACCG 59.339 55.000 0.00 0.00 42.08 4.44
1385 1465 1.098712 TGTGACCAAAGGTGAACCGC 61.099 55.000 0.00 0.00 42.08 5.68
1386 1466 1.098712 GTGACCAAAGGTGAACCGCA 61.099 55.000 0.00 0.00 42.08 5.69
1387 1467 0.179004 TGACCAAAGGTGAACCGCAT 60.179 50.000 0.00 0.00 42.08 4.73
1388 1468 0.240945 GACCAAAGGTGAACCGCATG 59.759 55.000 0.00 0.00 42.08 4.06
1389 1469 1.080569 CCAAAGGTGAACCGCATGC 60.081 57.895 7.91 7.91 42.08 4.06
1390 1470 1.080569 CAAAGGTGAACCGCATGCC 60.081 57.895 13.15 0.00 42.08 4.40
1391 1471 1.530419 AAAGGTGAACCGCATGCCA 60.530 52.632 13.15 0.42 42.08 4.92
1392 1472 1.112315 AAAGGTGAACCGCATGCCAA 61.112 50.000 13.15 0.00 42.08 4.52
1393 1473 0.899717 AAGGTGAACCGCATGCCAAT 60.900 50.000 13.15 0.00 42.08 3.16
1394 1474 1.139520 GGTGAACCGCATGCCAATC 59.860 57.895 13.15 8.16 0.00 2.67
1396 1476 0.457035 GTGAACCGCATGCCAATCAT 59.543 50.000 13.15 0.00 35.31 2.45
1397 1477 1.135024 GTGAACCGCATGCCAATCATT 60.135 47.619 13.15 0.00 31.79 2.57
1398 1478 1.135053 TGAACCGCATGCCAATCATTG 60.135 47.619 13.15 0.00 31.79 2.82
1399 1479 0.460635 AACCGCATGCCAATCATTGC 60.461 50.000 13.15 0.00 31.79 3.56
1400 1480 1.324740 ACCGCATGCCAATCATTGCT 61.325 50.000 13.15 0.00 31.79 3.91
1404 1484 2.222931 CGCATGCCAATCATTGCTTTTG 60.223 45.455 13.15 0.00 31.79 2.44
1405 1485 2.477189 GCATGCCAATCATTGCTTTTGC 60.477 45.455 6.36 0.00 38.61 3.68
1406 1486 3.006940 CATGCCAATCATTGCTTTTGCT 58.993 40.909 0.00 0.00 38.81 3.91
1408 1488 6.716879 CATGCCAATCATTGCTTTTGCTGC 62.717 45.833 0.00 0.00 38.81 5.25
1416 1496 2.452767 GCTTTTGCTGCCTCAATGC 58.547 52.632 0.00 0.00 43.35 3.56
1417 1497 1.349259 GCTTTTGCTGCCTCAATGCG 61.349 55.000 0.00 0.00 43.35 4.73
1418 1498 1.349259 CTTTTGCTGCCTCAATGCGC 61.349 55.000 0.00 0.00 0.00 6.09
1419 1499 2.768503 TTTTGCTGCCTCAATGCGCC 62.769 55.000 4.18 0.00 32.42 6.53
1437 1517 1.611519 CCGGGAGCACCTTGTTTTAA 58.388 50.000 0.00 0.00 36.97 1.52
1438 1518 2.167662 CCGGGAGCACCTTGTTTTAAT 58.832 47.619 0.00 0.00 36.97 1.40
1439 1519 2.560981 CCGGGAGCACCTTGTTTTAATT 59.439 45.455 0.00 0.00 36.97 1.40
1440 1520 3.366985 CCGGGAGCACCTTGTTTTAATTC 60.367 47.826 0.00 0.00 36.97 2.17
1441 1521 3.366985 CGGGAGCACCTTGTTTTAATTCC 60.367 47.826 0.00 0.00 36.97 3.01
1442 1522 3.576550 GGGAGCACCTTGTTTTAATTCCA 59.423 43.478 0.00 0.00 35.85 3.53
1443 1523 4.321974 GGGAGCACCTTGTTTTAATTCCAG 60.322 45.833 0.00 0.00 35.85 3.86
1444 1524 4.522789 GGAGCACCTTGTTTTAATTCCAGA 59.477 41.667 0.00 0.00 0.00 3.86
1445 1525 5.185828 GGAGCACCTTGTTTTAATTCCAGAT 59.814 40.000 0.00 0.00 0.00 2.90
1446 1526 6.295292 GGAGCACCTTGTTTTAATTCCAGATT 60.295 38.462 0.00 0.00 0.00 2.40
1447 1527 6.458210 AGCACCTTGTTTTAATTCCAGATTG 58.542 36.000 0.00 0.00 0.00 2.67
1448 1528 5.639082 GCACCTTGTTTTAATTCCAGATTGG 59.361 40.000 0.00 0.00 39.43 3.16
1463 1543 5.045359 TCCAGATTGGATTGTCAGAGTCAAT 60.045 40.000 0.00 0.00 42.67 2.57
1465 1545 4.639310 AGATTGGATTGTCAGAGTCAATGC 59.361 41.667 0.00 0.00 41.60 3.56
1466 1546 2.715046 TGGATTGTCAGAGTCAATGCC 58.285 47.619 7.45 4.76 40.92 4.40
1467 1547 2.019984 GGATTGTCAGAGTCAATGCCC 58.980 52.381 0.00 0.00 37.55 5.36
1470 1550 1.896220 TGTCAGAGTCAATGCCCAAC 58.104 50.000 0.00 0.00 0.00 3.77
1471 1551 1.421268 TGTCAGAGTCAATGCCCAACT 59.579 47.619 0.00 0.00 0.00 3.16
1472 1552 2.637382 TGTCAGAGTCAATGCCCAACTA 59.363 45.455 0.00 0.00 0.00 2.24
1473 1553 3.264193 TGTCAGAGTCAATGCCCAACTAT 59.736 43.478 0.00 0.00 0.00 2.12
1475 1555 2.357009 CAGAGTCAATGCCCAACTATGC 59.643 50.000 0.00 0.00 0.00 3.14
1476 1556 1.678101 GAGTCAATGCCCAACTATGCC 59.322 52.381 0.00 0.00 0.00 4.40
1478 1558 1.134946 GTCAATGCCCAACTATGCCAC 59.865 52.381 0.00 0.00 0.00 5.01
1479 1559 0.461135 CAATGCCCAACTATGCCACC 59.539 55.000 0.00 0.00 0.00 4.61
1481 1561 0.396139 ATGCCCAACTATGCCACCAG 60.396 55.000 0.00 0.00 0.00 4.00
1482 1562 1.754234 GCCCAACTATGCCACCAGG 60.754 63.158 0.00 0.00 38.23 4.45
1483 1563 1.998530 CCCAACTATGCCACCAGGA 59.001 57.895 0.00 0.00 36.89 3.86
1485 1565 1.272425 CCCAACTATGCCACCAGGAAA 60.272 52.381 0.00 0.00 36.89 3.13
1487 1567 3.099141 CCAACTATGCCACCAGGAAAAT 58.901 45.455 0.00 0.00 36.89 1.82
1488 1568 4.277476 CCAACTATGCCACCAGGAAAATA 58.723 43.478 0.00 0.00 36.89 1.40
1489 1569 4.709397 CCAACTATGCCACCAGGAAAATAA 59.291 41.667 0.00 0.00 36.89 1.40
1490 1570 5.163519 CCAACTATGCCACCAGGAAAATAAG 60.164 44.000 0.00 0.00 36.89 1.73
1491 1571 4.536765 ACTATGCCACCAGGAAAATAAGG 58.463 43.478 0.00 0.00 36.89 2.69
1493 1573 1.431243 TGCCACCAGGAAAATAAGGGT 59.569 47.619 0.00 0.00 36.89 4.34
1494 1574 1.824852 GCCACCAGGAAAATAAGGGTG 59.175 52.381 0.00 0.00 46.63 4.61
1495 1575 2.821625 GCCACCAGGAAAATAAGGGTGT 60.822 50.000 8.17 0.00 45.85 4.16
1496 1576 2.825532 CCACCAGGAAAATAAGGGTGTG 59.174 50.000 8.17 0.00 45.85 3.82
1497 1577 2.231235 CACCAGGAAAATAAGGGTGTGC 59.769 50.000 0.00 0.00 43.08 4.57
1498 1578 2.158385 ACCAGGAAAATAAGGGTGTGCA 60.158 45.455 0.00 0.00 0.00 4.57
1500 1580 3.323403 CCAGGAAAATAAGGGTGTGCAAA 59.677 43.478 0.00 0.00 0.00 3.68
1502 1582 4.039124 CAGGAAAATAAGGGTGTGCAAAGT 59.961 41.667 0.00 0.00 0.00 2.66
1505 1585 5.336451 GGAAAATAAGGGTGTGCAAAGTAGG 60.336 44.000 0.00 0.00 0.00 3.18
1507 1587 4.650972 ATAAGGGTGTGCAAAGTAGGAA 57.349 40.909 0.00 0.00 0.00 3.36
1508 1588 3.306472 AAGGGTGTGCAAAGTAGGAAA 57.694 42.857 0.00 0.00 0.00 3.13
1509 1589 3.525800 AGGGTGTGCAAAGTAGGAAAT 57.474 42.857 0.00 0.00 0.00 2.17
1510 1590 4.650972 AGGGTGTGCAAAGTAGGAAATA 57.349 40.909 0.00 0.00 0.00 1.40
1511 1591 4.589908 AGGGTGTGCAAAGTAGGAAATAG 58.410 43.478 0.00 0.00 0.00 1.73
1512 1592 3.694566 GGGTGTGCAAAGTAGGAAATAGG 59.305 47.826 0.00 0.00 0.00 2.57
1551 2501 5.448654 TCTATGCAATTTGAGTAATGGGCT 58.551 37.500 0.00 0.00 31.87 5.19
1689 2639 6.158598 GGAAAAATGTGTATGTGAGCATTGT 58.841 36.000 0.00 0.00 36.58 2.71
1736 2686 9.625747 TCTTCTATGTTATATTTTGTGCATCCA 57.374 29.630 0.00 0.00 0.00 3.41
1849 2800 7.158099 ACCTATTTTGTTGGAAGAGCATAAC 57.842 36.000 0.00 0.00 0.00 1.89
2074 3029 4.643784 ACCAAATTTCAGCCAATGCAAAAA 59.356 33.333 0.00 0.00 41.13 1.94
2305 3260 5.799536 TGAGGAGAGGAGGGGATATAAAAA 58.200 41.667 0.00 0.00 0.00 1.94
2307 3262 6.857222 TGAGGAGAGGAGGGGATATAAAAATT 59.143 38.462 0.00 0.00 0.00 1.82
2382 3337 0.174845 CGTCAGCCCTAACATTCGGA 59.825 55.000 0.00 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.533153 GCGTTGTAAAGCATAAAGTAAAAACAA 58.467 29.630 0.00 0.00 0.00 2.83
15 16 7.701078 TGCGTTGTAAAGCATAAAGTAAAAACA 59.299 29.630 1.13 0.00 38.59 2.83
16 17 7.994343 GTGCGTTGTAAAGCATAAAGTAAAAAC 59.006 33.333 8.36 0.00 45.69 2.43
18 19 7.194278 TGTGCGTTGTAAAGCATAAAGTAAAA 58.806 30.769 8.36 0.00 45.69 1.52
20 21 6.301687 TGTGCGTTGTAAAGCATAAAGTAA 57.698 33.333 8.36 0.00 45.69 2.24
23 24 6.183359 GGAATTGTGCGTTGTAAAGCATAAAG 60.183 38.462 15.58 0.00 44.97 1.85
24 25 5.631512 GGAATTGTGCGTTGTAAAGCATAAA 59.368 36.000 15.58 10.70 44.97 1.40
25 26 5.157781 GGAATTGTGCGTTGTAAAGCATAA 58.842 37.500 14.43 14.43 45.64 1.90
26 27 4.216472 TGGAATTGTGCGTTGTAAAGCATA 59.784 37.500 8.36 3.46 45.69 3.14
29 30 3.006659 TGGAATTGTGCGTTGTAAAGC 57.993 42.857 0.00 0.00 0.00 3.51
30 31 4.793071 TCATGGAATTGTGCGTTGTAAAG 58.207 39.130 0.00 0.00 0.00 1.85
31 32 4.837896 TCATGGAATTGTGCGTTGTAAA 57.162 36.364 0.00 0.00 0.00 2.01
32 33 4.837896 TTCATGGAATTGTGCGTTGTAA 57.162 36.364 0.00 0.00 0.00 2.41
33 34 4.699735 AGATTCATGGAATTGTGCGTTGTA 59.300 37.500 0.00 0.00 31.89 2.41
34 35 3.507233 AGATTCATGGAATTGTGCGTTGT 59.493 39.130 0.00 0.00 31.89 3.32
37 38 5.895636 TTAAGATTCATGGAATTGTGCGT 57.104 34.783 0.00 0.00 31.89 5.24
38 39 7.760131 ATTTTAAGATTCATGGAATTGTGCG 57.240 32.000 0.00 0.00 31.89 5.34
113 114 9.926158 TGCATGATGTAGATGTTTGTTTAATTT 57.074 25.926 0.00 0.00 0.00 1.82
120 121 9.729281 TCATATATGCATGATGTAGATGTTTGT 57.271 29.630 10.16 0.00 29.93 2.83
121 122 9.983804 GTCATATATGCATGATGTAGATGTTTG 57.016 33.333 10.16 0.00 37.28 2.93
122 123 9.955102 AGTCATATATGCATGATGTAGATGTTT 57.045 29.630 10.16 0.00 37.28 2.83
123 124 9.597170 GAGTCATATATGCATGATGTAGATGTT 57.403 33.333 10.16 0.00 37.28 2.71
124 125 8.755977 TGAGTCATATATGCATGATGTAGATGT 58.244 33.333 10.16 0.00 37.28 3.06
125 126 9.595823 TTGAGTCATATATGCATGATGTAGATG 57.404 33.333 10.16 1.90 37.28 2.90
127 128 9.649167 CTTTGAGTCATATATGCATGATGTAGA 57.351 33.333 10.16 0.00 37.28 2.59
128 129 8.880750 CCTTTGAGTCATATATGCATGATGTAG 58.119 37.037 10.16 5.77 37.28 2.74
130 131 7.229308 ACCTTTGAGTCATATATGCATGATGT 58.771 34.615 10.16 0.00 37.28 3.06
131 132 7.683437 ACCTTTGAGTCATATATGCATGATG 57.317 36.000 10.16 12.77 37.28 3.07
133 134 8.210265 TGTAACCTTTGAGTCATATATGCATGA 58.790 33.333 10.16 0.00 32.50 3.07
134 135 8.382030 TGTAACCTTTGAGTCATATATGCATG 57.618 34.615 10.16 0.00 0.00 4.06
135 136 9.006839 CATGTAACCTTTGAGTCATATATGCAT 57.993 33.333 3.79 3.79 0.00 3.96
136 137 7.041167 GCATGTAACCTTTGAGTCATATATGCA 60.041 37.037 19.40 0.00 37.62 3.96
137 138 7.173907 AGCATGTAACCTTTGAGTCATATATGC 59.826 37.037 17.80 17.80 37.82 3.14
138 139 8.613060 AGCATGTAACCTTTGAGTCATATATG 57.387 34.615 6.36 6.36 0.00 1.78
143 144 7.712639 CACTATAGCATGTAACCTTTGAGTCAT 59.287 37.037 0.00 0.00 0.00 3.06
144 145 7.041721 CACTATAGCATGTAACCTTTGAGTCA 58.958 38.462 0.00 0.00 0.00 3.41
145 146 7.010552 CACACTATAGCATGTAACCTTTGAGTC 59.989 40.741 0.00 0.00 0.00 3.36
146 147 6.818644 CACACTATAGCATGTAACCTTTGAGT 59.181 38.462 0.00 0.00 0.00 3.41
150 151 6.062258 ACCACACTATAGCATGTAACCTTT 57.938 37.500 0.00 0.00 0.00 3.11
151 152 5.693769 ACCACACTATAGCATGTAACCTT 57.306 39.130 0.00 0.00 0.00 3.50
168 169 9.593134 GCAACCAAATTATGAATAAATACCACA 57.407 29.630 0.00 0.00 0.00 4.17
169 170 9.040939 GGCAACCAAATTATGAATAAATACCAC 57.959 33.333 0.00 0.00 0.00 4.16
170 171 8.762645 TGGCAACCAAATTATGAATAAATACCA 58.237 29.630 0.00 0.00 0.00 3.25
171 172 9.606631 TTGGCAACCAAATTATGAATAAATACC 57.393 29.630 0.00 0.00 40.92 2.73
187 188 1.067706 CGCATGAGATTTGGCAACCAA 60.068 47.619 0.00 0.00 42.29 3.67
189 190 0.527565 ACGCATGAGATTTGGCAACC 59.472 50.000 2.50 0.00 0.00 3.77
190 191 1.621107 CACGCATGAGATTTGGCAAC 58.379 50.000 2.50 0.00 0.00 4.17
191 192 0.109179 GCACGCATGAGATTTGGCAA 60.109 50.000 2.50 0.00 0.00 4.52
192 193 1.242665 TGCACGCATGAGATTTGGCA 61.243 50.000 2.50 2.24 0.00 4.92
193 194 0.109179 TTGCACGCATGAGATTTGGC 60.109 50.000 2.50 0.00 0.00 4.52
195 196 1.586578 GCATTGCACGCATGAGATTTG 59.413 47.619 2.50 0.00 0.00 2.32
196 197 1.202817 TGCATTGCACGCATGAGATTT 59.797 42.857 7.38 0.00 33.55 2.17
199 200 3.984352 TGCATTGCACGCATGAGA 58.016 50.000 7.38 0.00 33.55 3.27
210 211 4.491676 ACTAGTTAGGTACACGTGCATTG 58.508 43.478 17.22 0.00 0.00 2.82
211 212 4.381292 GGACTAGTTAGGTACACGTGCATT 60.381 45.833 17.22 0.00 0.00 3.56
214 215 2.751806 AGGACTAGTTAGGTACACGTGC 59.248 50.000 17.22 0.00 0.00 5.34
215 216 5.181748 ACTAGGACTAGTTAGGTACACGTG 58.818 45.833 15.48 15.48 43.35 4.49
216 217 5.428184 ACTAGGACTAGTTAGGTACACGT 57.572 43.478 6.19 0.00 43.35 4.49
218 219 6.259829 GCACTACTAGGACTAGTTAGGTACAC 59.740 46.154 16.37 4.96 43.35 2.90
219 220 6.352516 GCACTACTAGGACTAGTTAGGTACA 58.647 44.000 16.37 0.00 43.35 2.90
220 221 5.762711 GGCACTACTAGGACTAGTTAGGTAC 59.237 48.000 16.37 8.66 43.35 3.34
221 222 5.163152 GGGCACTACTAGGACTAGTTAGGTA 60.163 48.000 16.37 0.00 43.35 3.08
222 223 4.386200 GGGCACTACTAGGACTAGTTAGGT 60.386 50.000 16.37 10.64 43.35 3.08
223 224 4.143543 GGGCACTACTAGGACTAGTTAGG 58.856 52.174 16.37 10.11 43.35 2.69
224 225 4.141205 AGGGGCACTACTAGGACTAGTTAG 60.141 50.000 16.37 13.24 43.35 2.34
225 226 3.790408 AGGGGCACTACTAGGACTAGTTA 59.210 47.826 16.37 3.67 43.35 2.24
226 227 2.586368 AGGGGCACTACTAGGACTAGTT 59.414 50.000 16.37 0.00 43.35 2.24
228 229 3.753815 GTAGGGGCACTACTAGGACTAG 58.246 54.545 19.61 4.86 46.89 2.57
229 230 3.872459 GTAGGGGCACTACTAGGACTA 57.128 52.381 19.61 0.00 46.89 2.59
238 239 1.229272 AACCGGTGTAGGGGCACTA 60.229 57.895 8.52 0.00 39.21 2.74
239 240 2.528378 AACCGGTGTAGGGGCACT 60.528 61.111 8.52 0.00 39.21 4.40
240 241 2.359478 CAACCGGTGTAGGGGCAC 60.359 66.667 8.52 0.00 38.56 5.01
241 242 2.850130 ACAACCGGTGTAGGGGCA 60.850 61.111 8.52 0.00 39.29 5.36
278 279 2.487762 ACATCATCGGCGTCAATTGTTT 59.512 40.909 6.85 0.00 0.00 2.83
328 329 2.188524 CGTGAGTCAACGGATCTGATG 58.811 52.381 9.00 7.05 39.89 3.07
329 330 2.568696 CGTGAGTCAACGGATCTGAT 57.431 50.000 9.00 0.00 39.89 2.90
351 352 2.054687 ACATTTCACATGCGCAACAG 57.945 45.000 17.11 10.55 0.00 3.16
355 356 1.068402 CAGGAACATTTCACATGCGCA 60.068 47.619 14.96 14.96 0.00 6.09
552 628 6.868339 CCAACTCAAGGAAAAACATCCATAAC 59.132 38.462 0.00 0.00 42.27 1.89
726 806 1.529226 TATTTCCTGTGTTGTGGGCG 58.471 50.000 0.00 0.00 0.00 6.13
729 809 4.396166 GGTGAGATATTTCCTGTGTTGTGG 59.604 45.833 0.00 0.00 0.00 4.17
779 859 7.658179 TGCGATTGGATTGAGAATATTAGTC 57.342 36.000 0.00 0.00 0.00 2.59
850 930 9.244292 CTTATATATACAAGCTAGGACCACAGA 57.756 37.037 0.00 0.00 0.00 3.41
851 931 8.470805 CCTTATATATACAAGCTAGGACCACAG 58.529 40.741 0.00 0.00 0.00 3.66
925 1005 9.736414 ATAACTATCAGGTACATAGATACGTGT 57.264 33.333 0.00 0.00 40.32 4.49
1200 1280 5.278169 CCATGCACAATAGGCAAGTATCTTC 60.278 44.000 0.00 0.00 45.60 2.87
1201 1281 4.581824 CCATGCACAATAGGCAAGTATCTT 59.418 41.667 0.00 0.00 45.60 2.40
1203 1283 4.136796 TCCATGCACAATAGGCAAGTATC 58.863 43.478 0.00 0.00 45.60 2.24
1204 1284 4.169059 TCCATGCACAATAGGCAAGTAT 57.831 40.909 0.00 0.00 45.60 2.12
1205 1285 3.643199 TCCATGCACAATAGGCAAGTA 57.357 42.857 0.00 0.00 45.60 2.24
1206 1286 2.512692 TCCATGCACAATAGGCAAGT 57.487 45.000 0.00 0.00 45.60 3.16
1207 1287 4.261741 GGTTATCCATGCACAATAGGCAAG 60.262 45.833 0.00 0.00 45.60 4.01
1208 1288 3.636300 GGTTATCCATGCACAATAGGCAA 59.364 43.478 0.00 0.00 45.60 4.52
1209 1289 3.221771 GGTTATCCATGCACAATAGGCA 58.778 45.455 0.00 0.00 46.66 4.75
1210 1290 3.221771 TGGTTATCCATGCACAATAGGC 58.778 45.455 0.00 0.00 39.03 3.93
1237 1317 7.886446 TCAGGACGACCTATTACATATGACATA 59.114 37.037 10.38 0.00 45.94 2.29
1238 1318 6.719829 TCAGGACGACCTATTACATATGACAT 59.280 38.462 10.38 3.28 45.94 3.06
1240 1320 6.570672 TCAGGACGACCTATTACATATGAC 57.429 41.667 10.38 0.00 45.94 3.06
1241 1321 5.183331 GCTCAGGACGACCTATTACATATGA 59.817 44.000 10.38 0.00 45.94 2.15
1242 1322 5.403246 GCTCAGGACGACCTATTACATATG 58.597 45.833 6.01 0.00 45.94 1.78
1244 1324 3.825014 GGCTCAGGACGACCTATTACATA 59.175 47.826 6.01 0.00 45.94 2.29
1247 1327 1.340568 GGGCTCAGGACGACCTATTAC 59.659 57.143 6.01 0.00 45.94 1.89
1248 1328 1.700955 GGGCTCAGGACGACCTATTA 58.299 55.000 6.01 0.00 45.94 0.98
1253 1333 3.827898 CTCGGGCTCAGGACGACC 61.828 72.222 0.00 0.00 32.66 4.79
1254 1334 2.750637 TCTCGGGCTCAGGACGAC 60.751 66.667 0.00 0.00 32.66 4.34
1255 1335 2.438614 CTCTCGGGCTCAGGACGA 60.439 66.667 0.00 0.00 35.14 4.20
1257 1337 3.071206 TGCTCTCGGGCTCAGGAC 61.071 66.667 0.00 0.00 0.00 3.85
1258 1338 3.071206 GTGCTCTCGGGCTCAGGA 61.071 66.667 0.00 0.00 0.00 3.86
1259 1339 1.395045 TATGTGCTCTCGGGCTCAGG 61.395 60.000 0.00 0.00 38.73 3.86
1260 1340 0.249238 GTATGTGCTCTCGGGCTCAG 60.249 60.000 0.00 0.00 38.73 3.35
1261 1341 1.816537 GTATGTGCTCTCGGGCTCA 59.183 57.895 0.00 0.00 39.47 4.26
1262 1342 1.299468 CGTATGTGCTCTCGGGCTC 60.299 63.158 0.00 0.00 0.00 4.70
1263 1343 1.320344 TTCGTATGTGCTCTCGGGCT 61.320 55.000 0.00 0.00 0.00 5.19
1264 1344 0.872021 CTTCGTATGTGCTCTCGGGC 60.872 60.000 0.00 0.00 0.00 6.13
1266 1346 2.389059 CATCTTCGTATGTGCTCTCGG 58.611 52.381 0.00 0.00 0.00 4.63
1267 1347 2.389059 CCATCTTCGTATGTGCTCTCG 58.611 52.381 0.00 0.00 0.00 4.04
1268 1348 2.131183 GCCATCTTCGTATGTGCTCTC 58.869 52.381 0.00 0.00 0.00 3.20
1269 1349 1.202580 GGCCATCTTCGTATGTGCTCT 60.203 52.381 0.00 0.00 0.00 4.09
1270 1350 1.221414 GGCCATCTTCGTATGTGCTC 58.779 55.000 0.00 0.00 0.00 4.26
1271 1351 0.541392 TGGCCATCTTCGTATGTGCT 59.459 50.000 0.00 0.00 0.00 4.40
1272 1352 1.532868 GATGGCCATCTTCGTATGTGC 59.467 52.381 34.20 7.66 35.04 4.57
1273 1353 1.794701 CGATGGCCATCTTCGTATGTG 59.205 52.381 36.51 18.28 37.98 3.21
1274 1354 1.873903 GCGATGGCCATCTTCGTATGT 60.874 52.381 36.51 5.98 42.67 2.29
1275 1355 0.792640 GCGATGGCCATCTTCGTATG 59.207 55.000 36.51 22.99 42.67 2.39
1276 1356 0.392706 TGCGATGGCCATCTTCGTAT 59.607 50.000 36.51 7.61 42.67 3.06
1278 1358 1.078497 TTGCGATGGCCATCTTCGT 60.078 52.632 36.51 9.27 42.67 3.85
1280 1360 1.353103 CGTTGCGATGGCCATCTTC 59.647 57.895 36.51 28.36 38.85 2.87
1281 1361 1.377202 ACGTTGCGATGGCCATCTT 60.377 52.632 36.51 10.95 38.85 2.40
1282 1362 2.108514 CACGTTGCGATGGCCATCT 61.109 57.895 36.51 18.97 38.85 2.90
1283 1363 2.404789 CACGTTGCGATGGCCATC 59.595 61.111 32.34 32.34 38.85 3.51
1289 1369 2.695055 CGTAGCCACGTTGCGATG 59.305 61.111 5.91 2.65 43.31 3.84
1290 1370 2.508439 CCGTAGCCACGTTGCGAT 60.508 61.111 5.91 0.00 46.96 4.58
1291 1371 3.980989 ACCGTAGCCACGTTGCGA 61.981 61.111 5.91 0.00 46.96 5.10
1292 1372 3.773630 CACCGTAGCCACGTTGCG 61.774 66.667 5.91 0.00 46.96 4.85
1293 1373 3.419759 CCACCGTAGCCACGTTGC 61.420 66.667 2.86 2.86 46.96 4.17
1295 1375 2.151049 GAGACCACCGTAGCCACGTT 62.151 60.000 3.55 0.00 46.96 3.99
1298 1378 0.179108 GATGAGACCACCGTAGCCAC 60.179 60.000 0.00 0.00 0.00 5.01
1301 1381 2.604046 AATGATGAGACCACCGTAGC 57.396 50.000 0.00 0.00 0.00 3.58
1317 1397 8.853345 GCAATGTAAGTTTGTTGTCATCTAATG 58.147 33.333 0.00 0.00 0.00 1.90
1318 1398 8.575589 TGCAATGTAAGTTTGTTGTCATCTAAT 58.424 29.630 0.00 0.00 0.00 1.73
1320 1400 7.503521 TGCAATGTAAGTTTGTTGTCATCTA 57.496 32.000 0.00 0.00 0.00 1.98
1322 1402 7.359431 CCATTGCAATGTAAGTTTGTTGTCATC 60.359 37.037 31.87 0.00 34.60 2.92
1323 1403 6.424509 CCATTGCAATGTAAGTTTGTTGTCAT 59.575 34.615 31.87 0.00 34.60 3.06
1325 1405 5.752955 ACCATTGCAATGTAAGTTTGTTGTC 59.247 36.000 31.87 0.00 34.60 3.18
1326 1406 5.523188 CACCATTGCAATGTAAGTTTGTTGT 59.477 36.000 31.87 18.34 34.60 3.32
1327 1407 5.523188 ACACCATTGCAATGTAAGTTTGTTG 59.477 36.000 31.87 17.77 34.60 3.33
1328 1408 5.523188 CACACCATTGCAATGTAAGTTTGTT 59.477 36.000 31.87 12.56 34.60 2.83
1329 1409 5.049167 CACACCATTGCAATGTAAGTTTGT 58.951 37.500 31.87 21.62 34.60 2.83
1330 1410 5.049167 ACACACCATTGCAATGTAAGTTTG 58.951 37.500 31.87 26.07 34.60 2.93
1331 1411 5.275067 ACACACCATTGCAATGTAAGTTT 57.725 34.783 31.87 19.19 34.60 2.66
1334 1414 3.491356 CGACACACCATTGCAATGTAAG 58.509 45.455 31.87 23.69 34.60 2.34
1337 1417 0.039256 GCGACACACCATTGCAATGT 60.039 50.000 31.87 18.84 34.60 2.71
1338 1418 0.039346 TGCGACACACCATTGCAATG 60.039 50.000 28.91 28.91 33.40 2.82
1340 1420 0.030504 CTTGCGACACACCATTGCAA 59.969 50.000 0.00 0.00 42.84 4.08
1341 1421 1.653667 CTTGCGACACACCATTGCA 59.346 52.632 0.00 0.00 34.56 4.08
1342 1422 1.081242 CCTTGCGACACACCATTGC 60.081 57.895 0.00 0.00 0.00 3.56
1343 1423 0.888736 TCCCTTGCGACACACCATTG 60.889 55.000 0.00 0.00 0.00 2.82
1344 1424 0.038166 ATCCCTTGCGACACACCATT 59.962 50.000 0.00 0.00 0.00 3.16
1348 1428 0.238289 CACAATCCCTTGCGACACAC 59.762 55.000 0.00 0.00 35.69 3.82
1349 1429 0.179032 ACACAATCCCTTGCGACACA 60.179 50.000 0.00 0.00 35.69 3.72
1350 1430 0.238289 CACACAATCCCTTGCGACAC 59.762 55.000 0.00 0.00 35.69 3.67
1351 1431 0.107643 TCACACAATCCCTTGCGACA 59.892 50.000 0.00 0.00 35.69 4.35
1352 1432 0.517316 GTCACACAATCCCTTGCGAC 59.483 55.000 0.00 0.00 35.69 5.19
1353 1433 0.605319 GGTCACACAATCCCTTGCGA 60.605 55.000 0.00 0.00 35.69 5.10
1354 1434 0.888736 TGGTCACACAATCCCTTGCG 60.889 55.000 0.00 0.00 35.69 4.85
1357 1437 2.091333 ACCTTTGGTCACACAATCCCTT 60.091 45.455 0.00 0.00 0.00 3.95
1358 1438 1.499007 ACCTTTGGTCACACAATCCCT 59.501 47.619 0.00 0.00 0.00 4.20
1359 1439 1.613437 CACCTTTGGTCACACAATCCC 59.387 52.381 0.00 0.00 31.02 3.85
1362 1442 2.693074 GGTTCACCTTTGGTCACACAAT 59.307 45.455 0.00 0.00 31.02 2.71
1363 1443 2.096248 GGTTCACCTTTGGTCACACAA 58.904 47.619 0.00 0.00 31.02 3.33
1364 1444 1.757682 GGTTCACCTTTGGTCACACA 58.242 50.000 0.00 0.00 31.02 3.72
1365 1445 0.661020 CGGTTCACCTTTGGTCACAC 59.339 55.000 0.00 0.00 31.02 3.82
1366 1446 1.098712 GCGGTTCACCTTTGGTCACA 61.099 55.000 0.00 0.00 31.02 3.58
1367 1447 1.098712 TGCGGTTCACCTTTGGTCAC 61.099 55.000 0.00 0.00 31.02 3.67
1368 1448 0.179004 ATGCGGTTCACCTTTGGTCA 60.179 50.000 0.00 0.00 31.02 4.02
1369 1449 0.240945 CATGCGGTTCACCTTTGGTC 59.759 55.000 0.00 0.00 31.02 4.02
1371 1451 1.080569 GCATGCGGTTCACCTTTGG 60.081 57.895 0.00 0.00 0.00 3.28
1372 1452 1.080569 GGCATGCGGTTCACCTTTG 60.081 57.895 12.44 0.00 0.00 2.77
1374 1454 0.899717 ATTGGCATGCGGTTCACCTT 60.900 50.000 12.44 0.00 0.00 3.50
1375 1455 1.304381 ATTGGCATGCGGTTCACCT 60.304 52.632 12.44 0.00 0.00 4.00
1376 1456 1.139520 GATTGGCATGCGGTTCACC 59.860 57.895 12.44 0.00 0.00 4.02
1377 1457 0.457035 ATGATTGGCATGCGGTTCAC 59.543 50.000 12.44 0.00 35.42 3.18
1378 1458 1.135053 CAATGATTGGCATGCGGTTCA 60.135 47.619 12.44 13.87 37.28 3.18
1379 1459 1.563111 CAATGATTGGCATGCGGTTC 58.437 50.000 12.44 8.42 37.28 3.62
1380 1460 0.460635 GCAATGATTGGCATGCGGTT 60.461 50.000 12.44 0.00 37.28 4.44
1381 1461 1.142314 GCAATGATTGGCATGCGGT 59.858 52.632 12.44 0.00 37.28 5.68
1382 1462 0.179094 AAGCAATGATTGGCATGCGG 60.179 50.000 12.44 0.00 37.28 5.69
1383 1463 1.647346 AAAGCAATGATTGGCATGCG 58.353 45.000 12.44 0.00 37.28 4.73
1384 1464 2.477189 GCAAAAGCAATGATTGGCATGC 60.477 45.455 9.90 9.90 37.28 4.06
1385 1465 3.006940 AGCAAAAGCAATGATTGGCATG 58.993 40.909 7.35 0.00 37.28 4.06
1386 1466 3.006940 CAGCAAAAGCAATGATTGGCAT 58.993 40.909 7.35 0.00 39.43 4.40
1387 1467 2.418692 CAGCAAAAGCAATGATTGGCA 58.581 42.857 7.35 0.00 0.00 4.92
1388 1468 1.129811 GCAGCAAAAGCAATGATTGGC 59.870 47.619 7.35 1.39 0.00 4.52
1389 1469 1.735571 GGCAGCAAAAGCAATGATTGG 59.264 47.619 7.35 0.00 0.00 3.16
1390 1470 2.671396 GAGGCAGCAAAAGCAATGATTG 59.329 45.455 0.00 0.00 0.00 2.67
1391 1471 2.300723 TGAGGCAGCAAAAGCAATGATT 59.699 40.909 0.00 0.00 0.00 2.57
1392 1472 1.897133 TGAGGCAGCAAAAGCAATGAT 59.103 42.857 0.00 0.00 0.00 2.45
1393 1473 1.330234 TGAGGCAGCAAAAGCAATGA 58.670 45.000 0.00 0.00 0.00 2.57
1394 1474 2.157834 TTGAGGCAGCAAAAGCAATG 57.842 45.000 0.00 0.00 0.00 2.82
1396 1476 1.874739 GCATTGAGGCAGCAAAAGCAA 60.875 47.619 0.00 0.00 34.80 3.91
1397 1477 0.320073 GCATTGAGGCAGCAAAAGCA 60.320 50.000 0.00 0.00 34.80 3.91
1398 1478 1.349259 CGCATTGAGGCAGCAAAAGC 61.349 55.000 0.00 9.32 32.77 3.51
1399 1479 1.349259 GCGCATTGAGGCAGCAAAAG 61.349 55.000 0.30 0.00 34.83 2.27
1400 1480 1.373246 GCGCATTGAGGCAGCAAAA 60.373 52.632 0.30 0.00 34.83 2.44
1417 1497 0.891904 TAAAACAAGGTGCTCCCGGC 60.892 55.000 0.00 0.00 38.74 6.13
1418 1498 1.611519 TTAAAACAAGGTGCTCCCGG 58.388 50.000 0.00 0.00 38.74 5.73
1419 1499 3.366985 GGAATTAAAACAAGGTGCTCCCG 60.367 47.826 0.00 0.00 38.74 5.14
1420 1500 3.576550 TGGAATTAAAACAAGGTGCTCCC 59.423 43.478 0.00 0.00 0.00 4.30
1422 1502 5.705609 TCTGGAATTAAAACAAGGTGCTC 57.294 39.130 0.00 0.00 0.00 4.26
1423 1503 6.458210 CAATCTGGAATTAAAACAAGGTGCT 58.542 36.000 0.00 0.00 0.00 4.40
1424 1504 5.639082 CCAATCTGGAATTAAAACAAGGTGC 59.361 40.000 0.00 0.00 40.96 5.01
1440 1520 4.212143 TGACTCTGACAATCCAATCTGG 57.788 45.455 0.00 0.00 39.43 3.86
1441 1521 5.448768 GCATTGACTCTGACAATCCAATCTG 60.449 44.000 0.00 0.00 36.07 2.90
1442 1522 4.639310 GCATTGACTCTGACAATCCAATCT 59.361 41.667 0.00 0.00 36.07 2.40
1443 1523 4.201990 GGCATTGACTCTGACAATCCAATC 60.202 45.833 0.00 0.00 36.07 2.67
1444 1524 3.698040 GGCATTGACTCTGACAATCCAAT 59.302 43.478 0.00 0.00 36.07 3.16
1445 1525 3.084039 GGCATTGACTCTGACAATCCAA 58.916 45.455 0.00 0.00 36.07 3.53
1446 1526 2.618816 GGGCATTGACTCTGACAATCCA 60.619 50.000 0.00 0.00 36.07 3.41
1447 1527 2.019984 GGGCATTGACTCTGACAATCC 58.980 52.381 0.00 0.00 36.07 3.01
1448 1528 2.715046 TGGGCATTGACTCTGACAATC 58.285 47.619 0.00 0.00 36.07 2.67
1450 1530 2.158623 AGTTGGGCATTGACTCTGACAA 60.159 45.455 0.00 0.00 0.00 3.18
1451 1531 1.421268 AGTTGGGCATTGACTCTGACA 59.579 47.619 0.00 0.00 0.00 3.58
1452 1532 2.191128 AGTTGGGCATTGACTCTGAC 57.809 50.000 0.00 0.00 0.00 3.51
1454 1534 2.357009 GCATAGTTGGGCATTGACTCTG 59.643 50.000 0.00 0.00 0.00 3.35
1456 1536 1.678101 GGCATAGTTGGGCATTGACTC 59.322 52.381 0.00 0.00 0.00 3.36
1457 1537 1.005805 TGGCATAGTTGGGCATTGACT 59.994 47.619 0.00 0.00 35.74 3.41
1463 1543 1.001020 CTGGTGGCATAGTTGGGCA 60.001 57.895 0.00 0.00 38.62 5.36
1465 1545 0.331278 TTCCTGGTGGCATAGTTGGG 59.669 55.000 0.00 0.00 0.00 4.12
1466 1546 2.214376 TTTCCTGGTGGCATAGTTGG 57.786 50.000 0.00 0.00 0.00 3.77
1467 1547 5.163519 CCTTATTTTCCTGGTGGCATAGTTG 60.164 44.000 0.00 0.00 0.00 3.16
1470 1550 3.891366 CCCTTATTTTCCTGGTGGCATAG 59.109 47.826 0.00 0.00 0.00 2.23
1471 1551 3.270960 ACCCTTATTTTCCTGGTGGCATA 59.729 43.478 0.00 0.00 0.00 3.14
1472 1552 2.044353 ACCCTTATTTTCCTGGTGGCAT 59.956 45.455 0.00 0.00 0.00 4.40
1473 1553 1.431243 ACCCTTATTTTCCTGGTGGCA 59.569 47.619 0.00 0.00 0.00 4.92
1478 1558 2.524306 TGCACACCCTTATTTTCCTGG 58.476 47.619 0.00 0.00 0.00 4.45
1479 1559 4.039124 ACTTTGCACACCCTTATTTTCCTG 59.961 41.667 0.00 0.00 0.00 3.86
1481 1561 4.600692 ACTTTGCACACCCTTATTTTCC 57.399 40.909 0.00 0.00 0.00 3.13
1482 1562 5.475564 TCCTACTTTGCACACCCTTATTTTC 59.524 40.000 0.00 0.00 0.00 2.29
1483 1563 5.390387 TCCTACTTTGCACACCCTTATTTT 58.610 37.500 0.00 0.00 0.00 1.82
1485 1565 4.650972 TCCTACTTTGCACACCCTTATT 57.349 40.909 0.00 0.00 0.00 1.40
1487 1567 4.440826 TTTCCTACTTTGCACACCCTTA 57.559 40.909 0.00 0.00 0.00 2.69
1488 1568 3.306472 TTTCCTACTTTGCACACCCTT 57.694 42.857 0.00 0.00 0.00 3.95
1489 1569 3.525800 ATTTCCTACTTTGCACACCCT 57.474 42.857 0.00 0.00 0.00 4.34
1490 1570 3.694566 CCTATTTCCTACTTTGCACACCC 59.305 47.826 0.00 0.00 0.00 4.61
1491 1571 4.332828 ACCTATTTCCTACTTTGCACACC 58.667 43.478 0.00 0.00 0.00 4.16
1493 1573 8.644374 ATTAAACCTATTTCCTACTTTGCACA 57.356 30.769 0.00 0.00 0.00 4.57
1494 1574 9.923143 AAATTAAACCTATTTCCTACTTTGCAC 57.077 29.630 0.00 0.00 0.00 4.57
1495 1575 9.921637 CAAATTAAACCTATTTCCTACTTTGCA 57.078 29.630 0.00 0.00 0.00 4.08
1496 1576 9.923143 ACAAATTAAACCTATTTCCTACTTTGC 57.077 29.630 0.00 0.00 0.00 3.68
1849 2800 3.851955 GCCTTGATGGGCCATCTG 58.148 61.111 38.44 30.41 45.92 2.90
1897 2848 9.631452 ACGATGTCATGATAAATATCTGTACAG 57.369 33.333 17.17 17.17 33.88 2.74
2122 3077 5.220381 CGTCTATAAAGAAGCGCCTATCAA 58.780 41.667 2.29 0.00 32.16 2.57
2153 3108 4.623932 TCTTCCTTCAACACACTGCTAT 57.376 40.909 0.00 0.00 0.00 2.97
2305 3260 0.388659 ACGCATGCCACAACAACAAT 59.611 45.000 13.15 0.00 0.00 2.71
2307 3262 1.358402 GACGCATGCCACAACAACA 59.642 52.632 13.15 0.00 0.00 3.33
2382 3337 5.491439 AGGGGTACTCCTTAATTAGTTGCTT 59.509 40.000 9.09 0.00 32.13 3.91
2417 3372 1.334384 ACAAAAAGGGGCCTTTGCGT 61.334 50.000 14.63 4.58 44.50 5.24
2471 3426 2.298158 CTAGCCCGCGACACCTGATT 62.298 60.000 8.23 0.00 0.00 2.57
2728 3684 7.961326 AAATTGCATATTTCAGTAGGGTCTT 57.039 32.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.