Multiple sequence alignment - TraesCS1A01G250500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G250500 chr1A 100.000 2730 0 0 1 2730 442153963 442156692 0.000000e+00 5042.0
1 TraesCS1A01G250500 chr1D 88.813 1171 78 27 1 1139 342488567 342489716 0.000000e+00 1387.0
2 TraesCS1A01G250500 chr1D 92.137 903 47 12 1243 2134 342489788 342490677 0.000000e+00 1253.0
3 TraesCS1A01G250500 chr1D 96.099 487 17 2 2246 2730 342490791 342491277 0.000000e+00 793.0
4 TraesCS1A01G250500 chr1B 90.532 940 54 16 1220 2134 458726781 458727710 0.000000e+00 1210.0
5 TraesCS1A01G250500 chr1B 88.655 714 52 14 443 1139 458726034 458726735 0.000000e+00 843.0
6 TraesCS1A01G250500 chr1B 94.650 486 24 2 2247 2730 458727764 458728249 0.000000e+00 752.0
7 TraesCS1A01G250500 chr1B 84.545 440 48 11 21 448 458684789 458685220 4.200000e-113 418.0
8 TraesCS1A01G250500 chr2A 93.333 45 2 1 2134 2178 650492490 650492447 6.310000e-07 65.8
9 TraesCS1A01G250500 chr7A 93.023 43 3 0 2135 2177 42710630 42710672 2.270000e-06 63.9
10 TraesCS1A01G250500 chr5B 95.122 41 0 2 2135 2175 17683038 17683076 2.270000e-06 63.9
11 TraesCS1A01G250500 chr4D 93.182 44 2 1 2134 2177 47539622 47539664 2.270000e-06 63.9
12 TraesCS1A01G250500 chr4B 97.297 37 1 0 2135 2171 515048794 515048830 2.270000e-06 63.9
13 TraesCS1A01G250500 chr4A 93.182 44 2 1 2135 2178 662811794 662811752 2.270000e-06 63.9
14 TraesCS1A01G250500 chr3A 93.182 44 2 1 2134 2177 170478385 170478427 2.270000e-06 63.9
15 TraesCS1A01G250500 chr3A 93.023 43 3 0 2135 2177 383085320 383085362 2.270000e-06 63.9
16 TraesCS1A01G250500 chrUn 91.304 46 3 1 2134 2178 88784691 88784646 8.160000e-06 62.1


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 TraesCS1A01G250500 chr1A 442153963 442156692 2729 False 5042.000000 5042 100.000000 1 2730 1 chr1A.!!$F1 2729
1 TraesCS1A01G250500 chr1D 342488567 342491277 2710 False 1144.333333 1387 92.349667 1 2730 3 chr1D.!!$F1 2729
2 TraesCS1A01G250500 chr1B 458726034 458728249 2215 False 935.000000 1210 91.279000 443 2730 3 chr1B.!!$F2 2287

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
218 230 0.031721 CACGGGGGTCGATACTAAGC 59.968 60.0 0.0 0.0 42.43 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2147 0.09473 GCAGCTGCGTTACCGTTTAG 59.905 55.0 25.23 0.0 36.15 1.85 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
43 44 2.599677 ACGGATCCTAGGAATGGAGAC 58.400 52.381 17.30 0.40 36.99 3.36
52 53 1.409427 AGGAATGGAGACGATCGGTTC 59.591 52.381 20.98 15.47 0.00 3.62
53 54 1.409427 GGAATGGAGACGATCGGTTCT 59.591 52.381 20.98 14.04 0.00 3.01
64 65 2.426024 CGATCGGTTCTTAGGGTCTTCA 59.574 50.000 7.38 0.00 0.00 3.02
76 82 4.148128 AGGGTCTTCATGTTATCAGCAG 57.852 45.455 0.00 0.00 0.00 4.24
81 87 4.208047 GTCTTCATGTTATCAGCAGCGTAG 59.792 45.833 0.00 0.00 0.00 3.51
115 121 2.076100 TCTCAAAGTTGTAGCATGCCG 58.924 47.619 15.66 0.00 0.00 5.69
140 152 1.868997 CGTTTGATCTTGCACCGCT 59.131 52.632 0.00 0.00 0.00 5.52
148 160 0.884704 TCTTGCACCGCTGAACCTTC 60.885 55.000 0.00 0.00 0.00 3.46
165 177 2.439409 CTTCACATCACATTGGCCTCA 58.561 47.619 3.32 0.00 0.00 3.86
166 178 2.583024 TCACATCACATTGGCCTCAA 57.417 45.000 3.32 0.00 37.28 3.02
167 179 2.874014 TCACATCACATTGGCCTCAAA 58.126 42.857 3.32 0.00 36.36 2.69
168 180 3.229293 TCACATCACATTGGCCTCAAAA 58.771 40.909 3.32 0.00 36.36 2.44
192 204 3.645884 AGCAACTTGTGATTGACATTGC 58.354 40.909 6.50 6.50 45.26 3.56
199 211 5.693104 ACTTGTGATTGACATTGCATTTGAC 59.307 36.000 4.32 0.00 33.40 3.18
200 212 5.197682 TGTGATTGACATTGCATTTGACA 57.802 34.783 4.32 1.84 0.00 3.58
202 214 4.088923 GTGATTGACATTGCATTTGACACG 59.911 41.667 4.32 0.00 0.00 4.49
205 217 0.602562 ACATTGCATTTGACACGGGG 59.397 50.000 4.32 0.00 0.00 5.73
206 218 0.108709 CATTGCATTTGACACGGGGG 60.109 55.000 0.00 0.00 0.00 5.40
207 219 0.541764 ATTGCATTTGACACGGGGGT 60.542 50.000 0.00 0.00 0.00 4.95
208 220 1.175983 TTGCATTTGACACGGGGGTC 61.176 55.000 0.00 0.00 38.29 4.46
210 222 1.004320 CATTTGACACGGGGGTCGA 60.004 57.895 0.00 0.00 40.72 4.20
211 223 0.392461 CATTTGACACGGGGGTCGAT 60.392 55.000 0.00 0.00 40.72 3.59
212 224 1.134640 CATTTGACACGGGGGTCGATA 60.135 52.381 0.00 0.00 40.72 2.92
213 225 0.247185 TTTGACACGGGGGTCGATAC 59.753 55.000 0.00 0.00 40.72 2.24
214 226 0.612732 TTGACACGGGGGTCGATACT 60.613 55.000 0.00 0.00 40.72 2.12
216 228 1.340893 TGACACGGGGGTCGATACTAA 60.341 52.381 0.00 0.00 40.72 2.24
217 229 1.336125 GACACGGGGGTCGATACTAAG 59.664 57.143 0.00 0.00 42.43 2.18
218 230 0.031721 CACGGGGGTCGATACTAAGC 59.968 60.000 0.00 0.00 42.43 3.09
286 299 3.750639 TTCGTTTTGAGCGTCAAACTT 57.249 38.095 11.15 0.00 45.03 2.66
287 300 3.046285 TCGTTTTGAGCGTCAAACTTG 57.954 42.857 11.15 6.24 45.03 3.16
288 301 2.108700 CGTTTTGAGCGTCAAACTTGG 58.891 47.619 11.15 1.29 45.03 3.61
322 335 5.971763 TCTAGCCAAGTTCTCTCATTCTTC 58.028 41.667 0.00 0.00 0.00 2.87
334 347 5.362143 TCTCTCATTCTTCAGATCGTGGAAT 59.638 40.000 0.00 0.00 0.00 3.01
338 351 4.760530 TTCTTCAGATCGTGGAATCCAT 57.239 40.909 4.81 0.00 35.28 3.41
343 356 3.129109 CAGATCGTGGAATCCATGTCTG 58.871 50.000 25.13 25.13 41.03 3.51
358 371 4.619320 CTGGCTTGCCCAACCCCA 62.619 66.667 9.35 0.00 44.81 4.96
370 383 2.091720 CCCAACCCCATGATCATCTTGA 60.092 50.000 4.86 0.00 0.00 3.02
377 390 7.100068 ACCCCATGATCATCTTGATATTTCT 57.900 36.000 4.86 0.00 37.20 2.52
458 474 3.701532 TCTGGTTTTGCGTTAAAGTGG 57.298 42.857 0.00 0.00 0.00 4.00
504 523 6.961554 GGTCAATCGCTAAGTTGTCATAAAAG 59.038 38.462 0.00 0.00 0.00 2.27
517 536 8.311109 AGTTGTCATAAAAGTTTTTGTTCCACT 58.689 29.630 6.10 0.86 0.00 4.00
519 538 9.495572 TTGTCATAAAAGTTTTTGTTCCACTTT 57.504 25.926 6.10 0.00 41.50 2.66
565 584 5.173854 CGAAAAAGATTGTTGGAAGTTCTGC 59.826 40.000 2.25 0.00 0.00 4.26
566 585 5.859205 AAAAGATTGTTGGAAGTTCTGCT 57.141 34.783 2.25 0.00 0.00 4.24
567 586 5.859205 AAAGATTGTTGGAAGTTCTGCTT 57.141 34.783 2.25 0.00 40.76 3.91
568 587 5.859205 AAGATTGTTGGAAGTTCTGCTTT 57.141 34.783 2.25 0.00 37.59 3.51
569 588 5.859205 AGATTGTTGGAAGTTCTGCTTTT 57.141 34.783 2.25 0.00 37.59 2.27
570 589 5.594926 AGATTGTTGGAAGTTCTGCTTTTG 58.405 37.500 2.25 0.00 37.59 2.44
582 601 1.001378 CTGCTTTTGACGGGTCCTTTG 60.001 52.381 0.00 0.00 0.00 2.77
681 700 3.328931 AGCATATCACCCTATTCACCTGG 59.671 47.826 0.00 0.00 0.00 4.45
741 765 0.179097 GAGATCCGTCCCTTGCAGAC 60.179 60.000 0.00 0.00 0.00 3.51
755 779 1.582968 CAGACCGCAAAAGCAGCAT 59.417 52.632 0.00 0.00 0.00 3.79
758 782 0.804989 GACCGCAAAAGCAGCATACT 59.195 50.000 0.00 0.00 0.00 2.12
759 783 2.006888 GACCGCAAAAGCAGCATACTA 58.993 47.619 0.00 0.00 0.00 1.82
761 785 1.064060 CCGCAAAAGCAGCATACTACC 59.936 52.381 0.00 0.00 0.00 3.18
762 786 2.009774 CGCAAAAGCAGCATACTACCT 58.990 47.619 0.00 0.00 0.00 3.08
848 885 1.448922 CGCCGACCTTTCCACCAAAA 61.449 55.000 0.00 0.00 0.00 2.44
897 935 2.278596 CCGATCACCACGCCGTAG 60.279 66.667 0.00 0.00 0.00 3.51
978 1016 1.833559 CGCATCGATCTCGTGTTCG 59.166 57.895 10.79 10.79 40.80 3.95
980 1018 1.812214 GCATCGATCTCGTGTTCGGC 61.812 60.000 15.51 9.70 40.80 5.54
1110 1150 1.550065 CCGTCAACTACAGCATCGAG 58.450 55.000 0.00 0.00 0.00 4.04
1116 1156 1.840737 ACTACAGCATCGAGGACAGT 58.159 50.000 0.00 0.00 0.00 3.55
1139 1179 0.108804 CACTCACGTAAGCCCATCGT 60.109 55.000 0.00 0.00 45.62 3.73
1140 1180 0.172803 ACTCACGTAAGCCCATCGTC 59.827 55.000 0.00 0.00 45.62 4.20
1141 1181 0.456221 CTCACGTAAGCCCATCGTCT 59.544 55.000 0.00 0.00 45.62 4.18
1146 1186 0.727398 GTAAGCCCATCGTCTGCAAC 59.273 55.000 0.00 0.00 0.00 4.17
1148 1188 2.045926 GCCCATCGTCTGCAACCT 60.046 61.111 0.00 0.00 0.00 3.50
1150 1190 1.599047 CCCATCGTCTGCAACCTCT 59.401 57.895 0.00 0.00 0.00 3.69
1151 1191 0.742281 CCCATCGTCTGCAACCTCTG 60.742 60.000 0.00 0.00 0.00 3.35
1152 1192 0.247460 CCATCGTCTGCAACCTCTGA 59.753 55.000 0.00 0.00 0.00 3.27
1153 1193 1.134580 CCATCGTCTGCAACCTCTGAT 60.135 52.381 0.00 0.00 0.00 2.90
1154 1194 2.200067 CATCGTCTGCAACCTCTGATC 58.800 52.381 0.00 0.00 0.00 2.92
1155 1195 1.256812 TCGTCTGCAACCTCTGATCA 58.743 50.000 0.00 0.00 0.00 2.92
1156 1196 1.203287 TCGTCTGCAACCTCTGATCAG 59.797 52.381 17.07 17.07 0.00 2.90
1158 1198 2.353109 CGTCTGCAACCTCTGATCAGAA 60.353 50.000 25.09 9.38 36.94 3.02
1161 1201 3.326006 TCTGCAACCTCTGATCAGAAGTT 59.674 43.478 27.00 27.00 41.39 2.66
1162 1202 3.668447 TGCAACCTCTGATCAGAAGTTC 58.332 45.455 28.94 23.42 39.39 3.01
1163 1203 3.071457 TGCAACCTCTGATCAGAAGTTCA 59.929 43.478 28.94 25.04 39.39 3.18
1164 1204 3.683822 GCAACCTCTGATCAGAAGTTCAG 59.316 47.826 28.94 21.72 39.39 3.02
1165 1205 4.562347 GCAACCTCTGATCAGAAGTTCAGA 60.562 45.833 28.94 7.39 44.34 3.27
1168 1208 3.883830 TCTGATCAGAAGTTCAGAGCC 57.116 47.619 23.17 3.06 42.66 4.70
1169 1209 3.439154 TCTGATCAGAAGTTCAGAGCCT 58.561 45.455 23.17 0.00 42.66 4.58
1170 1210 3.195182 TCTGATCAGAAGTTCAGAGCCTG 59.805 47.826 23.17 4.66 42.66 4.85
1171 1211 3.168292 TGATCAGAAGTTCAGAGCCTGA 58.832 45.455 10.55 2.35 38.87 3.86
1172 1212 3.580022 TGATCAGAAGTTCAGAGCCTGAA 59.420 43.478 10.55 12.03 46.50 3.02
1173 1213 8.244412 TCTGATCAGAAGTTCAGAGCCTGAAG 62.244 46.154 23.17 2.48 42.66 3.02
1181 1221 4.377839 TTCAGAGCCTGAAGAATACTCG 57.622 45.455 12.03 0.00 44.27 4.18
1182 1222 3.357203 TCAGAGCCTGAAGAATACTCGT 58.643 45.455 2.78 0.00 37.57 4.18
1183 1223 3.378742 TCAGAGCCTGAAGAATACTCGTC 59.621 47.826 2.78 0.00 37.57 4.20
1184 1224 3.380004 CAGAGCCTGAAGAATACTCGTCT 59.620 47.826 0.00 0.00 32.44 4.18
1185 1225 3.380004 AGAGCCTGAAGAATACTCGTCTG 59.620 47.826 0.00 0.00 31.92 3.51
1186 1226 3.093057 AGCCTGAAGAATACTCGTCTGT 58.907 45.455 0.00 0.00 31.92 3.41
1187 1227 3.511934 AGCCTGAAGAATACTCGTCTGTT 59.488 43.478 0.00 0.00 31.92 3.16
1188 1228 4.021016 AGCCTGAAGAATACTCGTCTGTTT 60.021 41.667 0.00 0.00 31.92 2.83
1189 1229 4.092091 GCCTGAAGAATACTCGTCTGTTTG 59.908 45.833 0.00 0.00 31.92 2.93
1190 1230 5.470368 CCTGAAGAATACTCGTCTGTTTGA 58.530 41.667 0.00 0.00 31.92 2.69
1191 1231 6.102663 CCTGAAGAATACTCGTCTGTTTGAT 58.897 40.000 0.00 0.00 31.92 2.57
1192 1232 6.254589 CCTGAAGAATACTCGTCTGTTTGATC 59.745 42.308 0.00 0.00 31.92 2.92
1193 1233 6.925211 TGAAGAATACTCGTCTGTTTGATCT 58.075 36.000 0.00 0.00 31.92 2.75
1194 1234 7.378966 TGAAGAATACTCGTCTGTTTGATCTT 58.621 34.615 0.00 0.00 31.92 2.40
1195 1235 7.329471 TGAAGAATACTCGTCTGTTTGATCTTG 59.671 37.037 0.00 0.00 31.92 3.02
1196 1236 6.692486 AGAATACTCGTCTGTTTGATCTTGT 58.308 36.000 0.00 0.00 0.00 3.16
1197 1237 6.809196 AGAATACTCGTCTGTTTGATCTTGTC 59.191 38.462 0.00 0.00 0.00 3.18
1198 1238 3.654414 ACTCGTCTGTTTGATCTTGTCC 58.346 45.455 0.00 0.00 0.00 4.02
1199 1239 3.322254 ACTCGTCTGTTTGATCTTGTCCT 59.678 43.478 0.00 0.00 0.00 3.85
1200 1240 3.653344 TCGTCTGTTTGATCTTGTCCTG 58.347 45.455 0.00 0.00 0.00 3.86
1201 1241 2.738846 CGTCTGTTTGATCTTGTCCTGG 59.261 50.000 0.00 0.00 0.00 4.45
1202 1242 3.744660 GTCTGTTTGATCTTGTCCTGGT 58.255 45.455 0.00 0.00 0.00 4.00
1203 1243 3.499918 GTCTGTTTGATCTTGTCCTGGTG 59.500 47.826 0.00 0.00 0.00 4.17
1204 1244 3.136443 TCTGTTTGATCTTGTCCTGGTGT 59.864 43.478 0.00 0.00 0.00 4.16
1205 1245 3.885297 CTGTTTGATCTTGTCCTGGTGTT 59.115 43.478 0.00 0.00 0.00 3.32
1206 1246 3.631686 TGTTTGATCTTGTCCTGGTGTTG 59.368 43.478 0.00 0.00 0.00 3.33
1207 1247 3.855255 TTGATCTTGTCCTGGTGTTGA 57.145 42.857 0.00 0.00 0.00 3.18
1208 1248 4.371624 TTGATCTTGTCCTGGTGTTGAT 57.628 40.909 0.00 0.00 0.00 2.57
1209 1249 3.678289 TGATCTTGTCCTGGTGTTGATG 58.322 45.455 0.00 0.00 0.00 3.07
1210 1250 2.566833 TCTTGTCCTGGTGTTGATGG 57.433 50.000 0.00 0.00 0.00 3.51
1211 1251 2.054021 TCTTGTCCTGGTGTTGATGGA 58.946 47.619 0.00 0.00 0.00 3.41
1212 1252 2.644299 TCTTGTCCTGGTGTTGATGGAT 59.356 45.455 0.00 0.00 0.00 3.41
1213 1253 2.495155 TGTCCTGGTGTTGATGGATG 57.505 50.000 0.00 0.00 0.00 3.51
1214 1254 1.704628 TGTCCTGGTGTTGATGGATGT 59.295 47.619 0.00 0.00 0.00 3.06
1215 1255 2.086869 GTCCTGGTGTTGATGGATGTG 58.913 52.381 0.00 0.00 0.00 3.21
1216 1256 0.813184 CCTGGTGTTGATGGATGTGC 59.187 55.000 0.00 0.00 0.00 4.57
1217 1257 1.536940 CTGGTGTTGATGGATGTGCA 58.463 50.000 0.00 0.00 0.00 4.57
1218 1258 2.097036 CTGGTGTTGATGGATGTGCAT 58.903 47.619 0.00 0.00 0.00 3.96
1226 1266 5.163632 TGTTGATGGATGTGCATGTATGTTC 60.164 40.000 0.00 0.00 0.00 3.18
1231 1271 4.035441 TGGATGTGCATGTATGTTCGATTG 59.965 41.667 0.00 0.00 0.00 2.67
1232 1272 4.035558 GGATGTGCATGTATGTTCGATTGT 59.964 41.667 0.00 0.00 0.00 2.71
1233 1273 5.449041 GGATGTGCATGTATGTTCGATTGTT 60.449 40.000 0.00 0.00 0.00 2.83
1234 1274 4.968626 TGTGCATGTATGTTCGATTGTTC 58.031 39.130 0.00 0.00 0.00 3.18
1239 1279 3.322369 TGTATGTTCGATTGTTCGTGCT 58.678 40.909 0.00 0.00 45.65 4.40
1240 1280 3.366724 TGTATGTTCGATTGTTCGTGCTC 59.633 43.478 0.00 0.00 45.65 4.26
1241 1281 0.781787 TGTTCGATTGTTCGTGCTCG 59.218 50.000 0.81 0.81 45.65 5.03
1470 1513 2.801631 CCTCCTCGCCATGGGACTC 61.802 68.421 15.13 0.00 0.00 3.36
1495 1538 0.883814 CAAGGAGATCAGCATCGGCC 60.884 60.000 0.00 0.00 42.56 6.13
1496 1539 1.053264 AAGGAGATCAGCATCGGCCT 61.053 55.000 0.00 0.00 42.56 5.19
1550 1593 6.758416 CAGTAAATCAATGGAGAATCTGTCGA 59.242 38.462 0.00 0.00 33.73 4.20
1551 1594 6.758886 AGTAAATCAATGGAGAATCTGTCGAC 59.241 38.462 9.11 9.11 33.73 4.20
1552 1595 3.526931 TCAATGGAGAATCTGTCGACC 57.473 47.619 14.12 0.00 33.73 4.79
1571 1614 1.340405 CCCCATCTCTTGTCCTTGTGG 60.340 57.143 0.00 0.00 0.00 4.17
1578 1621 3.971305 TCTCTTGTCCTTGTGGAACCTAA 59.029 43.478 0.00 0.00 45.18 2.69
1579 1622 4.597507 TCTCTTGTCCTTGTGGAACCTAAT 59.402 41.667 0.00 0.00 45.18 1.73
1585 1628 5.221682 TGTCCTTGTGGAACCTAATTAACGA 60.222 40.000 0.00 0.00 45.18 3.85
1586 1629 5.878669 GTCCTTGTGGAACCTAATTAACGAT 59.121 40.000 0.00 0.00 45.18 3.73
1588 1631 5.646360 CCTTGTGGAACCTAATTAACGATGT 59.354 40.000 0.00 0.00 34.36 3.06
1594 1637 7.280205 GTGGAACCTAATTAACGATGTTCATCT 59.720 37.037 10.44 0.00 35.09 2.90
1595 1638 7.279981 TGGAACCTAATTAACGATGTTCATCTG 59.720 37.037 10.44 7.02 35.09 2.90
1639 1682 1.154205 CGTTCACGATCATCCTGGCC 61.154 60.000 0.00 0.00 43.02 5.36
1721 1764 1.222936 CCCATGGGAGTCAGAGCAC 59.777 63.158 28.27 0.00 37.50 4.40
1727 1770 1.979693 GGAGTCAGAGCACGGGTCT 60.980 63.158 0.00 0.51 41.33 3.85
1795 1838 1.404391 GAAGGTGCAGCATCATCTTGG 59.596 52.381 19.63 0.00 37.52 3.61
1880 1950 2.034221 GGGGTTCTCAGGGTGTGC 59.966 66.667 0.00 0.00 0.00 4.57
1902 1972 1.608093 GCGCTTGCGGTGAAATTGTG 61.608 55.000 16.79 0.00 0.00 3.33
1943 2014 7.268659 GTGACGATCACATAATATGTCGAGTAC 59.731 40.741 16.37 9.78 46.22 2.73
1946 2017 8.657729 ACGATCACATAATATGTCGAGTACTAG 58.342 37.037 16.37 0.00 42.70 2.57
1947 2018 8.657729 CGATCACATAATATGTCGAGTACTAGT 58.342 37.037 2.41 0.00 42.70 2.57
2011 2082 8.479280 CAAAATCTGGCAAATATATAACGTTGC 58.521 33.333 11.99 15.61 44.43 4.17
2048 2119 4.131596 GCAAATATTACTACTTCCGGGCA 58.868 43.478 0.00 0.00 0.00 5.36
2144 2219 9.762933 AGCAGAGCTTTCACAATTTATTTTTAA 57.237 25.926 0.00 0.00 33.89 1.52
2148 2223 9.791838 GAGCTTTCACAATTTATTTTTAAACCG 57.208 29.630 0.00 0.00 0.00 4.44
2149 2224 8.769891 AGCTTTCACAATTTATTTTTAAACCGG 58.230 29.630 0.00 0.00 0.00 5.28
2150 2225 8.012809 GCTTTCACAATTTATTTTTAAACCGGG 58.987 33.333 6.32 0.00 0.00 5.73
2151 2226 7.422878 TTCACAATTTATTTTTAAACCGGGC 57.577 32.000 6.32 0.00 0.00 6.13
2152 2227 6.522054 TCACAATTTATTTTTAAACCGGGCA 58.478 32.000 6.32 0.00 0.00 5.36
2153 2228 7.162082 TCACAATTTATTTTTAAACCGGGCAT 58.838 30.769 6.32 0.00 0.00 4.40
2154 2229 7.661847 TCACAATTTATTTTTAAACCGGGCATT 59.338 29.630 6.32 0.00 0.00 3.56
2155 2230 8.936864 CACAATTTATTTTTAAACCGGGCATTA 58.063 29.630 6.32 0.00 0.00 1.90
2156 2231 8.937884 ACAATTTATTTTTAAACCGGGCATTAC 58.062 29.630 6.32 0.00 0.00 1.89
2157 2232 8.391859 CAATTTATTTTTAAACCGGGCATTACC 58.608 33.333 6.32 0.00 37.93 2.85
2170 2245 3.910989 GGCATTACCCCTTTCCATTACT 58.089 45.455 0.00 0.00 0.00 2.24
2179 2254 5.663556 ACCCCTTTCCATTACTTTCACAAAA 59.336 36.000 0.00 0.00 0.00 2.44
2181 2256 7.147391 ACCCCTTTCCATTACTTTCACAAAATT 60.147 33.333 0.00 0.00 0.00 1.82
2182 2257 7.173047 CCCCTTTCCATTACTTTCACAAAATTG 59.827 37.037 0.00 0.00 0.00 2.32
2220 2297 4.799564 TTTTTGGAGAAACACAAGCAGT 57.200 36.364 0.00 0.00 0.00 4.40
2225 2302 2.291741 GGAGAAACACAAGCAGTTCTGG 59.708 50.000 1.97 0.00 0.00 3.86
2231 2308 3.848726 ACACAAGCAGTTCTGGTTTTTG 58.151 40.909 13.45 14.69 0.00 2.44
2232 2309 3.258123 ACACAAGCAGTTCTGGTTTTTGT 59.742 39.130 13.45 15.20 0.00 2.83
2235 2312 4.107622 CAAGCAGTTCTGGTTTTTGTGAG 58.892 43.478 13.45 0.00 0.00 3.51
2237 2314 3.378427 AGCAGTTCTGGTTTTTGTGAGAC 59.622 43.478 0.00 0.00 0.00 3.36
2239 2316 4.202050 GCAGTTCTGGTTTTTGTGAGACAT 60.202 41.667 1.97 0.00 0.00 3.06
2240 2317 5.514279 CAGTTCTGGTTTTTGTGAGACATC 58.486 41.667 0.00 0.00 0.00 3.06
2241 2318 4.580580 AGTTCTGGTTTTTGTGAGACATCC 59.419 41.667 0.00 0.00 0.00 3.51
2242 2319 4.163441 TCTGGTTTTTGTGAGACATCCA 57.837 40.909 0.00 0.00 0.00 3.41
2244 2321 2.616376 TGGTTTTTGTGAGACATCCACG 59.384 45.455 0.00 0.00 37.34 4.94
2305 2427 1.080093 TGACGACCCGCATCAACTC 60.080 57.895 0.00 0.00 0.00 3.01
2312 2434 2.741985 CGCATCAACTCACGGGCA 60.742 61.111 0.00 0.00 0.00 5.36
2421 2543 2.047274 CGTGAGGTGGATGCCGTT 60.047 61.111 0.00 0.00 0.00 4.44
2428 2550 1.220749 GTGGATGCCGTTCCAGCTA 59.779 57.895 0.69 0.00 46.31 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.779529 TCCTAGGATCCGTTACATGTTAC 57.220 43.478 7.62 3.84 0.00 2.50
24 25 1.542030 CGTCTCCATTCCTAGGATCCG 59.458 57.143 13.57 3.93 33.99 4.18
43 44 2.426024 TGAAGACCCTAAGAACCGATCG 59.574 50.000 8.51 8.51 0.00 3.69
52 53 5.674525 TGCTGATAACATGAAGACCCTAAG 58.325 41.667 0.00 0.00 0.00 2.18
53 54 5.674525 CTGCTGATAACATGAAGACCCTAA 58.325 41.667 0.00 0.00 0.00 2.69
64 65 1.491670 CGCTACGCTGCTGATAACAT 58.508 50.000 0.00 0.00 0.00 2.71
76 82 1.464219 GAGTAGTAGGATCCGCTACGC 59.536 57.143 28.02 26.45 39.80 4.42
81 87 3.633065 ACTTTGAGAGTAGTAGGATCCGC 59.367 47.826 5.98 3.52 36.65 5.54
115 121 2.848302 GTGCAAGATCAAACGCAATAGC 59.152 45.455 0.00 0.00 35.87 2.97
133 145 1.237285 ATGTGAAGGTTCAGCGGTGC 61.237 55.000 10.38 0.00 37.98 5.01
140 152 2.557924 GCCAATGTGATGTGAAGGTTCA 59.442 45.455 0.00 0.00 34.20 3.18
148 160 3.663995 TTTTGAGGCCAATGTGATGTG 57.336 42.857 5.01 0.00 31.46 3.21
167 179 6.457257 GCAATGTCAATCACAAGTTGCTTTTT 60.457 34.615 1.81 0.00 43.42 1.94
168 180 5.006941 GCAATGTCAATCACAAGTTGCTTTT 59.993 36.000 1.81 0.00 43.42 2.27
192 204 0.392461 ATCGACCCCCGTGTCAAATG 60.392 55.000 0.00 0.00 39.75 2.32
199 211 0.031721 GCTTAGTATCGACCCCCGTG 59.968 60.000 0.00 0.00 39.75 4.94
200 212 0.106318 AGCTTAGTATCGACCCCCGT 60.106 55.000 0.00 0.00 39.75 5.28
202 214 2.557490 CACTAGCTTAGTATCGACCCCC 59.443 54.545 0.00 0.00 37.23 5.40
205 217 4.820716 TCCTTCACTAGCTTAGTATCGACC 59.179 45.833 0.00 0.00 37.23 4.79
206 218 6.374565 TTCCTTCACTAGCTTAGTATCGAC 57.625 41.667 0.00 0.00 37.23 4.20
207 219 7.284716 TGATTTCCTTCACTAGCTTAGTATCGA 59.715 37.037 0.00 0.00 37.23 3.59
208 220 7.426410 TGATTTCCTTCACTAGCTTAGTATCG 58.574 38.462 0.00 0.00 37.23 2.92
210 222 8.207545 CCTTGATTTCCTTCACTAGCTTAGTAT 58.792 37.037 0.00 0.00 37.23 2.12
211 223 7.556844 CCTTGATTTCCTTCACTAGCTTAGTA 58.443 38.462 0.00 0.00 37.23 1.82
212 224 6.410540 CCTTGATTTCCTTCACTAGCTTAGT 58.589 40.000 0.00 0.00 40.28 2.24
213 225 5.295540 GCCTTGATTTCCTTCACTAGCTTAG 59.704 44.000 0.00 0.00 0.00 2.18
214 226 5.045578 AGCCTTGATTTCCTTCACTAGCTTA 60.046 40.000 0.00 0.00 0.00 3.09
216 228 3.265479 AGCCTTGATTTCCTTCACTAGCT 59.735 43.478 0.00 0.00 0.00 3.32
217 229 3.615155 AGCCTTGATTTCCTTCACTAGC 58.385 45.455 0.00 0.00 0.00 3.42
218 230 5.238214 GCATAGCCTTGATTTCCTTCACTAG 59.762 44.000 0.00 0.00 0.00 2.57
271 284 1.946768 CCTCCAAGTTTGACGCTCAAA 59.053 47.619 8.47 8.47 43.37 2.69
287 300 1.362224 TGGCTAGATTATGGGCCTCC 58.638 55.000 4.53 0.00 44.36 4.30
288 301 2.373502 ACTTGGCTAGATTATGGGCCTC 59.626 50.000 4.53 0.00 44.36 4.70
322 335 3.129109 CAGACATGGATTCCACGATCTG 58.871 50.000 20.16 20.16 35.80 2.90
338 351 2.203480 GGTTGGGCAAGCCAGACA 60.203 61.111 13.87 0.00 37.98 3.41
370 383 9.930693 GATCAGGGTTTAACGAGATAGAAATAT 57.069 33.333 0.00 0.00 0.00 1.28
377 390 9.542462 CTTTATTGATCAGGGTTTAACGAGATA 57.458 33.333 0.00 0.00 0.00 1.98
382 395 6.436843 AGCTTTATTGATCAGGGTTTAACG 57.563 37.500 0.00 0.00 0.00 3.18
427 443 3.142174 GCAAAACCAGAAGTACTCAGCT 58.858 45.455 0.00 0.00 0.00 4.24
433 449 5.679792 CACTTTAACGCAAAACCAGAAGTAC 59.320 40.000 0.00 0.00 0.00 2.73
439 455 2.124122 GCCACTTTAACGCAAAACCAG 58.876 47.619 0.00 0.00 0.00 4.00
486 505 8.335256 ACAAAAACTTTTATGACAACTTAGCG 57.665 30.769 0.00 0.00 0.00 4.26
504 523 9.758651 AGTGGATTATTAAAGTGGAACAAAAAC 57.241 29.630 0.00 0.00 44.16 2.43
536 555 6.273071 ACTTCCAACAATCTTTTTCGAAAGG 58.727 36.000 10.98 8.43 0.00 3.11
565 584 1.880027 CTCCAAAGGACCCGTCAAAAG 59.120 52.381 0.00 0.00 0.00 2.27
566 585 1.477923 CCTCCAAAGGACCCGTCAAAA 60.478 52.381 0.00 0.00 46.67 2.44
567 586 0.109723 CCTCCAAAGGACCCGTCAAA 59.890 55.000 0.00 0.00 46.67 2.69
568 587 1.758592 CCTCCAAAGGACCCGTCAA 59.241 57.895 0.00 0.00 46.67 3.18
569 588 2.890766 GCCTCCAAAGGACCCGTCA 61.891 63.158 0.00 0.00 46.67 4.35
570 589 2.046217 GCCTCCAAAGGACCCGTC 60.046 66.667 0.00 0.00 46.67 4.79
637 656 2.490991 GTGGACACGGAAAGCTTTAGT 58.509 47.619 12.68 12.53 0.00 2.24
650 669 1.571919 GGTGATATGCTCGTGGACAC 58.428 55.000 0.00 0.00 0.00 3.67
681 700 3.479949 GGTCACGAATTCTTTTCTTCGC 58.520 45.455 3.52 0.00 46.11 4.70
697 716 2.358737 CTCCTTGCACGGGGTCAC 60.359 66.667 9.71 0.00 0.00 3.67
700 719 3.322466 CCTCTCCTTGCACGGGGT 61.322 66.667 9.27 0.00 0.00 4.95
755 779 2.385803 GAGTAAGCCAGCCAGGTAGTA 58.614 52.381 0.00 0.00 40.61 1.82
758 782 1.956629 GCGAGTAAGCCAGCCAGGTA 61.957 60.000 0.00 0.00 40.61 3.08
759 783 2.982130 CGAGTAAGCCAGCCAGGT 59.018 61.111 0.00 0.00 40.61 4.00
761 785 0.955428 TTTGCGAGTAAGCCAGCCAG 60.955 55.000 0.00 0.00 36.02 4.85
762 786 0.955428 CTTTGCGAGTAAGCCAGCCA 60.955 55.000 0.00 0.00 36.02 4.75
848 885 1.802636 CGCCACGGAAATGCATTCT 59.197 52.632 13.38 3.05 38.18 2.40
867 905 2.864343 GGTGATCGGCGGCATATATAAC 59.136 50.000 10.53 0.00 0.00 1.89
925 963 1.376553 GCTCAGCTCGCTCCCTTTT 60.377 57.895 0.00 0.00 0.00 2.27
966 1004 1.142778 GAGCTGCCGAACACGAGATC 61.143 60.000 0.00 0.00 0.00 2.75
995 1035 4.976925 CCCCGCTCGCCATGCTAG 62.977 72.222 0.00 0.00 0.00 3.42
1041 1081 4.115516 CGTACATGATGAGGTTCAGGAAG 58.884 47.826 0.00 0.00 32.03 3.46
1110 1150 2.357517 CGTGAGTGGGCACTGTCC 60.358 66.667 0.00 0.00 42.66 4.02
1139 1179 2.902486 ACTTCTGATCAGAGGTTGCAGA 59.098 45.455 29.26 11.24 44.02 4.26
1140 1180 3.331478 ACTTCTGATCAGAGGTTGCAG 57.669 47.619 29.26 21.97 44.02 4.41
1148 1188 3.195182 CAGGCTCTGAACTTCTGATCAGA 59.805 47.826 21.67 21.67 45.64 3.27
1150 1190 3.168292 TCAGGCTCTGAACTTCTGATCA 58.832 45.455 0.00 0.00 37.57 2.92
1151 1191 3.883830 TCAGGCTCTGAACTTCTGATC 57.116 47.619 2.78 0.00 37.57 2.92
1152 1192 3.837146 TCTTCAGGCTCTGAACTTCTGAT 59.163 43.478 12.03 0.00 44.27 2.90
1153 1193 3.234353 TCTTCAGGCTCTGAACTTCTGA 58.766 45.455 12.03 6.62 44.27 3.27
1154 1194 3.674528 TCTTCAGGCTCTGAACTTCTG 57.325 47.619 12.03 4.83 44.27 3.02
1155 1195 4.906747 ATTCTTCAGGCTCTGAACTTCT 57.093 40.909 12.03 0.00 44.27 2.85
1156 1196 5.729510 AGTATTCTTCAGGCTCTGAACTTC 58.270 41.667 12.03 4.32 44.27 3.01
1158 1198 4.142271 CGAGTATTCTTCAGGCTCTGAACT 60.142 45.833 12.03 8.99 44.27 3.01
1161 1201 3.357203 ACGAGTATTCTTCAGGCTCTGA 58.643 45.455 0.00 1.25 38.87 3.27
1162 1202 3.380004 AGACGAGTATTCTTCAGGCTCTG 59.620 47.826 0.00 0.00 0.00 3.35
1163 1203 3.380004 CAGACGAGTATTCTTCAGGCTCT 59.620 47.826 0.00 0.00 0.00 4.09
1164 1204 3.129638 ACAGACGAGTATTCTTCAGGCTC 59.870 47.826 0.00 0.00 0.00 4.70
1165 1205 3.093057 ACAGACGAGTATTCTTCAGGCT 58.907 45.455 0.00 0.00 0.00 4.58
1166 1206 3.512033 ACAGACGAGTATTCTTCAGGC 57.488 47.619 0.00 0.00 0.00 4.85
1167 1207 5.470368 TCAAACAGACGAGTATTCTTCAGG 58.530 41.667 0.00 0.00 0.00 3.86
1168 1208 7.032580 AGATCAAACAGACGAGTATTCTTCAG 58.967 38.462 0.00 0.00 0.00 3.02
1169 1209 6.925211 AGATCAAACAGACGAGTATTCTTCA 58.075 36.000 0.00 0.00 0.00 3.02
1170 1210 7.329717 ACAAGATCAAACAGACGAGTATTCTTC 59.670 37.037 0.00 0.00 0.00 2.87
1171 1211 7.155328 ACAAGATCAAACAGACGAGTATTCTT 58.845 34.615 0.00 0.00 0.00 2.52
1172 1212 6.692486 ACAAGATCAAACAGACGAGTATTCT 58.308 36.000 0.00 0.00 0.00 2.40
1173 1213 6.035112 GGACAAGATCAAACAGACGAGTATTC 59.965 42.308 0.00 0.00 0.00 1.75
1175 1215 5.186021 AGGACAAGATCAAACAGACGAGTAT 59.814 40.000 0.00 0.00 0.00 2.12
1176 1216 4.523173 AGGACAAGATCAAACAGACGAGTA 59.477 41.667 0.00 0.00 0.00 2.59
1177 1217 3.322254 AGGACAAGATCAAACAGACGAGT 59.678 43.478 0.00 0.00 0.00 4.18
1178 1218 3.677121 CAGGACAAGATCAAACAGACGAG 59.323 47.826 0.00 0.00 0.00 4.18
1179 1219 3.554960 CCAGGACAAGATCAAACAGACGA 60.555 47.826 0.00 0.00 0.00 4.20
1180 1220 2.738846 CCAGGACAAGATCAAACAGACG 59.261 50.000 0.00 0.00 0.00 4.18
1181 1221 3.499918 CACCAGGACAAGATCAAACAGAC 59.500 47.826 0.00 0.00 0.00 3.51
1182 1222 3.136443 ACACCAGGACAAGATCAAACAGA 59.864 43.478 0.00 0.00 0.00 3.41
1183 1223 3.480470 ACACCAGGACAAGATCAAACAG 58.520 45.455 0.00 0.00 0.00 3.16
1184 1224 3.576078 ACACCAGGACAAGATCAAACA 57.424 42.857 0.00 0.00 0.00 2.83
1185 1225 3.882888 TCAACACCAGGACAAGATCAAAC 59.117 43.478 0.00 0.00 0.00 2.93
1186 1226 4.163441 TCAACACCAGGACAAGATCAAA 57.837 40.909 0.00 0.00 0.00 2.69
1187 1227 3.855255 TCAACACCAGGACAAGATCAA 57.145 42.857 0.00 0.00 0.00 2.57
1188 1228 3.559811 CCATCAACACCAGGACAAGATCA 60.560 47.826 0.00 0.00 0.00 2.92
1189 1229 3.012518 CCATCAACACCAGGACAAGATC 58.987 50.000 0.00 0.00 0.00 2.75
1190 1230 2.644299 TCCATCAACACCAGGACAAGAT 59.356 45.455 0.00 0.00 0.00 2.40
1191 1231 2.054021 TCCATCAACACCAGGACAAGA 58.946 47.619 0.00 0.00 0.00 3.02
1192 1232 2.566833 TCCATCAACACCAGGACAAG 57.433 50.000 0.00 0.00 0.00 3.16
1193 1233 2.108075 ACATCCATCAACACCAGGACAA 59.892 45.455 0.00 0.00 32.04 3.18
1194 1234 1.704628 ACATCCATCAACACCAGGACA 59.295 47.619 0.00 0.00 32.04 4.02
1195 1235 2.086869 CACATCCATCAACACCAGGAC 58.913 52.381 0.00 0.00 32.04 3.85
1196 1236 1.614051 GCACATCCATCAACACCAGGA 60.614 52.381 0.00 0.00 34.12 3.86
1197 1237 0.813184 GCACATCCATCAACACCAGG 59.187 55.000 0.00 0.00 0.00 4.45
1198 1238 1.536940 TGCACATCCATCAACACCAG 58.463 50.000 0.00 0.00 0.00 4.00
1199 1239 1.819903 CATGCACATCCATCAACACCA 59.180 47.619 0.00 0.00 0.00 4.17
1200 1240 1.820519 ACATGCACATCCATCAACACC 59.179 47.619 0.00 0.00 0.00 4.16
1201 1241 4.096833 ACATACATGCACATCCATCAACAC 59.903 41.667 0.00 0.00 0.00 3.32
1202 1242 4.271661 ACATACATGCACATCCATCAACA 58.728 39.130 0.00 0.00 0.00 3.33
1203 1243 4.906065 ACATACATGCACATCCATCAAC 57.094 40.909 0.00 0.00 0.00 3.18
1204 1244 4.035441 CGAACATACATGCACATCCATCAA 59.965 41.667 0.00 0.00 0.00 2.57
1205 1245 3.560896 CGAACATACATGCACATCCATCA 59.439 43.478 0.00 0.00 0.00 3.07
1206 1246 3.809279 TCGAACATACATGCACATCCATC 59.191 43.478 0.00 0.00 0.00 3.51
1207 1247 3.807553 TCGAACATACATGCACATCCAT 58.192 40.909 0.00 0.00 0.00 3.41
1208 1248 3.258971 TCGAACATACATGCACATCCA 57.741 42.857 0.00 0.00 0.00 3.41
1209 1249 4.035558 ACAATCGAACATACATGCACATCC 59.964 41.667 0.00 0.00 0.00 3.51
1210 1250 5.160699 ACAATCGAACATACATGCACATC 57.839 39.130 0.00 0.00 0.00 3.06
1211 1251 5.565592 AACAATCGAACATACATGCACAT 57.434 34.783 0.00 0.00 0.00 3.21
1212 1252 4.968626 GAACAATCGAACATACATGCACA 58.031 39.130 0.00 0.00 0.00 4.57
1272 1315 0.108281 GGAAGTAGACCGGGAACAGC 60.108 60.000 6.32 0.00 0.00 4.40
1470 1513 2.806856 GCTGATCTCCTTGCACGCG 61.807 63.158 3.53 3.53 0.00 6.01
1506 1549 2.722094 TGGTGCTTAATTACCAGGCTG 58.278 47.619 7.75 7.75 41.80 4.85
1550 1593 1.352352 CACAAGGACAAGAGATGGGGT 59.648 52.381 0.00 0.00 0.00 4.95
1551 1594 1.340405 CCACAAGGACAAGAGATGGGG 60.340 57.143 0.00 0.00 36.89 4.96
1552 1595 1.630369 TCCACAAGGACAAGAGATGGG 59.370 52.381 0.00 0.00 39.61 4.00
1571 1614 8.116753 CACAGATGAACATCGTTAATTAGGTTC 58.883 37.037 8.79 9.37 42.48 3.62
1578 1621 5.700832 ACACACACAGATGAACATCGTTAAT 59.299 36.000 8.79 0.00 42.48 1.40
1579 1622 5.050431 CACACACACAGATGAACATCGTTAA 60.050 40.000 8.79 0.00 42.48 2.01
1585 1628 2.551032 CTGCACACACACAGATGAACAT 59.449 45.455 0.00 0.00 35.90 2.71
1586 1629 1.941975 CTGCACACACACAGATGAACA 59.058 47.619 0.00 0.00 35.90 3.18
1588 1631 0.946528 GCTGCACACACACAGATGAA 59.053 50.000 0.00 0.00 35.90 2.57
1721 1764 1.008424 CGACCGATCATCAGACCCG 60.008 63.158 0.00 0.00 0.00 5.28
1727 1770 1.064134 CTGCGTCGACCGATCATCA 59.936 57.895 10.58 0.00 39.56 3.07
1728 1771 1.658717 CCTGCGTCGACCGATCATC 60.659 63.158 10.58 0.00 39.56 2.92
1729 1772 2.413351 CCTGCGTCGACCGATCAT 59.587 61.111 10.58 0.00 39.56 2.45
1751 1794 0.608308 AGACCACACTCCATCGACGA 60.608 55.000 0.00 0.00 0.00 4.20
1795 1838 2.923020 CACGCAAACCAATAATCCTTGC 59.077 45.455 0.00 0.00 39.16 4.01
1880 1950 3.593551 ATTTCACCGCAAGCGCACG 62.594 57.895 11.47 10.64 38.40 5.34
1948 2019 9.178758 GACAGTCCCACAAATTAGAGAATAAAT 57.821 33.333 0.00 0.00 0.00 1.40
1949 2020 7.333423 CGACAGTCCCACAAATTAGAGAATAAA 59.667 37.037 0.00 0.00 0.00 1.40
2011 2082 7.924412 AGTAATATTTGCCAGATTTTGCATGAG 59.076 33.333 0.00 0.00 37.33 2.90
2048 2119 7.469260 GTTCAATACGCTGTTGTATAAATGGT 58.531 34.615 0.00 0.00 34.01 3.55
2076 2147 0.094730 GCAGCTGCGTTACCGTTTAG 59.905 55.000 25.23 0.00 36.15 1.85
2127 2202 6.990349 TGCCCGGTTTAAAAATAAATTGTGAA 59.010 30.769 0.00 0.00 0.00 3.18
2128 2203 6.522054 TGCCCGGTTTAAAAATAAATTGTGA 58.478 32.000 0.00 0.00 0.00 3.58
2129 2204 6.787085 TGCCCGGTTTAAAAATAAATTGTG 57.213 33.333 0.00 0.00 0.00 3.33
2130 2205 7.987750 AATGCCCGGTTTAAAAATAAATTGT 57.012 28.000 0.00 0.00 0.00 2.71
2131 2206 8.391859 GGTAATGCCCGGTTTAAAAATAAATTG 58.608 33.333 0.00 0.00 0.00 2.32
2132 2207 8.495361 GGTAATGCCCGGTTTAAAAATAAATT 57.505 30.769 0.00 0.00 0.00 1.82
2149 2224 3.910989 AGTAATGGAAAGGGGTAATGCC 58.089 45.455 0.00 0.00 0.00 4.40
2150 2225 5.420739 TGAAAGTAATGGAAAGGGGTAATGC 59.579 40.000 0.00 0.00 0.00 3.56
2151 2226 6.435904 TGTGAAAGTAATGGAAAGGGGTAATG 59.564 38.462 0.00 0.00 0.00 1.90
2152 2227 6.557568 TGTGAAAGTAATGGAAAGGGGTAAT 58.442 36.000 0.00 0.00 0.00 1.89
2153 2228 5.954757 TGTGAAAGTAATGGAAAGGGGTAA 58.045 37.500 0.00 0.00 0.00 2.85
2154 2229 5.586155 TGTGAAAGTAATGGAAAGGGGTA 57.414 39.130 0.00 0.00 0.00 3.69
2155 2230 4.463050 TGTGAAAGTAATGGAAAGGGGT 57.537 40.909 0.00 0.00 0.00 4.95
2156 2231 5.799827 TTTGTGAAAGTAATGGAAAGGGG 57.200 39.130 0.00 0.00 0.00 4.79
2157 2232 7.173047 CCAATTTTGTGAAAGTAATGGAAAGGG 59.827 37.037 0.00 0.00 0.00 3.95
2158 2233 7.930865 TCCAATTTTGTGAAAGTAATGGAAAGG 59.069 33.333 0.00 0.00 30.71 3.11
2159 2234 8.885494 TCCAATTTTGTGAAAGTAATGGAAAG 57.115 30.769 0.00 0.00 30.71 2.62
2160 2235 9.323985 CTTCCAATTTTGTGAAAGTAATGGAAA 57.676 29.630 0.00 0.00 37.09 3.13
2161 2236 7.440856 GCTTCCAATTTTGTGAAAGTAATGGAA 59.559 33.333 0.00 0.00 36.23 3.53
2162 2237 6.928492 GCTTCCAATTTTGTGAAAGTAATGGA 59.072 34.615 0.00 0.00 31.25 3.41
2163 2238 6.705381 TGCTTCCAATTTTGTGAAAGTAATGG 59.295 34.615 0.00 0.00 0.00 3.16
2164 2239 7.569957 GCTGCTTCCAATTTTGTGAAAGTAATG 60.570 37.037 0.00 0.00 0.00 1.90
2165 2240 6.424812 GCTGCTTCCAATTTTGTGAAAGTAAT 59.575 34.615 0.00 0.00 0.00 1.89
2166 2241 5.752955 GCTGCTTCCAATTTTGTGAAAGTAA 59.247 36.000 0.00 0.00 0.00 2.24
2167 2242 5.068987 AGCTGCTTCCAATTTTGTGAAAGTA 59.931 36.000 0.00 0.00 0.00 2.24
2168 2243 4.122046 GCTGCTTCCAATTTTGTGAAAGT 58.878 39.130 0.00 0.00 0.00 2.66
2169 2244 4.374399 AGCTGCTTCCAATTTTGTGAAAG 58.626 39.130 0.00 0.00 0.00 2.62
2170 2245 4.099881 AGAGCTGCTTCCAATTTTGTGAAA 59.900 37.500 2.53 0.00 0.00 2.69
2204 2279 2.291741 CCAGAACTGCTTGTGTTTCTCC 59.708 50.000 0.00 0.00 0.00 3.71
2220 2297 4.338118 GTGGATGTCTCACAAAAACCAGAA 59.662 41.667 0.00 0.00 35.39 3.02
2225 2302 4.545823 TTCGTGGATGTCTCACAAAAAC 57.454 40.909 0.00 0.00 35.03 2.43
2231 2308 3.729526 CACATTTCGTGGATGTCTCAC 57.270 47.619 0.00 0.00 42.34 3.51
2421 2543 3.461773 GCAGGCGTCCTAGCTGGA 61.462 66.667 0.00 0.00 43.86 3.86
2487 2609 3.400255 GGCGGGGAGTATAACTTTGATC 58.600 50.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.