Multiple sequence alignment - TraesCS5A01G403800

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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 TraesCS5A01G403800 chr5A 100.000 2881 0 0 1 2881 596018775 596021655 0.000000e+00 5321.0
1 TraesCS5A01G403800 chr5B 88.937 1618 96 36 1305 2881 584113972 584115547 0.000000e+00 1919.0
2 TraesCS5A01G403800 chr5B 88.362 1160 66 38 37 1178 584112757 584113865 0.000000e+00 1330.0
3 TraesCS5A01G403800 chr5D 88.294 1606 102 44 1301 2864 476697029 476698590 0.000000e+00 1845.0
4 TraesCS5A01G403800 chr5D 92.935 1005 44 11 161 1158 476695943 476696927 0.000000e+00 1437.0
5 TraesCS5A01G403800 chr5D 100.000 38 0 0 20 57 476692783 476692820 1.430000e-08 71.3


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 TraesCS5A01G403800 chr5A 596018775 596021655 2880 False 5321.000000 5321 100.0000 1 2881 1 chr5A.!!$F1 2880
1 TraesCS5A01G403800 chr5B 584112757 584115547 2790 False 1624.500000 1919 88.6495 37 2881 2 chr5B.!!$F1 2844
2 TraesCS5A01G403800 chr5D 476692783 476698590 5807 False 1117.766667 1845 93.7430 20 2864 3 chr5D.!!$F1 2844

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
243 3334 0.033699 ATTCTTCCCCTCAAGGCTGC 60.034 55.0 0.00 0.0 0.0 5.25 F
1450 4582 0.613260 AACATGGCAGCTTCCTCGTA 59.387 50.0 3.45 0.0 0.0 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 4813 1.067565 ACAGTATCGACAGCACCTGTG 60.068 52.381 2.12 0.0 45.44 3.66 R
2612 5789 0.988832 TCCATGGGTAGGTGGTGAAC 59.011 55.000 13.02 0.0 36.84 3.18 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
57 58 7.968405 GCATAACCATTTCTAGATTGACGTTTT 59.032 33.333 0.00 0.00 0.00 2.43
64 65 4.832248 TCTAGATTGACGTTTTGGCTGAT 58.168 39.130 0.00 0.00 0.00 2.90
70 71 4.377839 TGACGTTTTGGCTGATGAAAAA 57.622 36.364 0.00 0.00 0.00 1.94
96 97 1.889170 GGGAGCACCTTTCTTTTCCTG 59.111 52.381 0.00 0.00 35.85 3.86
97 98 2.587522 GGAGCACCTTTCTTTTCCTGT 58.412 47.619 0.00 0.00 0.00 4.00
98 99 2.554462 GGAGCACCTTTCTTTTCCTGTC 59.446 50.000 0.00 0.00 0.00 3.51
99 100 3.214328 GAGCACCTTTCTTTTCCTGTCA 58.786 45.455 0.00 0.00 0.00 3.58
100 101 2.952310 AGCACCTTTCTTTTCCTGTCAC 59.048 45.455 0.00 0.00 0.00 3.67
218 3306 4.918129 GCCATCCAATGCGCGCAG 62.918 66.667 38.44 25.60 0.00 5.18
243 3334 0.033699 ATTCTTCCCCTCAAGGCTGC 60.034 55.000 0.00 0.00 0.00 5.25
257 3348 1.434773 AGGCTGCCATCCTATCCTCTA 59.565 52.381 22.65 0.00 30.79 2.43
258 3349 2.158097 AGGCTGCCATCCTATCCTCTAA 60.158 50.000 22.65 0.00 30.79 2.10
259 3350 2.027653 GGCTGCCATCCTATCCTCTAAC 60.028 54.545 15.17 0.00 0.00 2.34
266 3357 5.746361 GCCATCCTATCCTCTAACCCTTTTC 60.746 48.000 0.00 0.00 0.00 2.29
325 3417 3.007290 TCTCCACTCTCATCACAACTTGG 59.993 47.826 0.00 0.00 0.00 3.61
342 3434 3.031660 GGTCGAACAGTGACCGATC 57.968 57.895 12.88 9.72 45.82 3.69
343 3435 0.797249 GGTCGAACAGTGACCGATCG 60.797 60.000 8.51 8.51 45.82 3.69
557 3673 0.746063 AGACGTGTGGTTTACCGACA 59.254 50.000 0.00 0.00 39.43 4.35
561 3677 1.223187 GTGTGGTTTACCGACACTGG 58.777 55.000 18.84 0.00 41.02 4.00
673 3789 1.747355 CATGGCGATCAAAAGGCTCTT 59.253 47.619 0.00 0.00 0.00 2.85
683 3799 2.624838 CAAAAGGCTCTTGAGAAAGGCA 59.375 45.455 0.00 0.00 40.33 4.75
853 3969 5.600069 TCATCATTCCCTCCATATATCTCCG 59.400 44.000 0.00 0.00 0.00 4.63
858 3974 1.137872 CCTCCATATATCTCCGCTGCC 59.862 57.143 0.00 0.00 0.00 4.85
888 4004 1.247419 ATCGAGCCGGAGATAGCAGG 61.247 60.000 5.05 0.00 0.00 4.85
950 4066 4.849310 ACGGCTGCGTGTGTTGGT 62.849 61.111 0.00 0.00 0.00 3.67
951 4067 3.582120 CGGCTGCGTGTGTTGGTT 61.582 61.111 0.00 0.00 0.00 3.67
952 4068 2.331451 GGCTGCGTGTGTTGGTTC 59.669 61.111 0.00 0.00 0.00 3.62
953 4069 2.052237 GCTGCGTGTGTTGGTTCG 60.052 61.111 0.00 0.00 0.00 3.95
1158 4274 3.134623 CCTTCTGGTATGTACTCCATGCA 59.865 47.826 0.00 0.00 37.85 3.96
1159 4275 4.202398 CCTTCTGGTATGTACTCCATGCAT 60.202 45.833 0.00 0.00 37.85 3.96
1160 4276 4.341366 TCTGGTATGTACTCCATGCATG 57.659 45.455 20.19 20.19 37.85 4.06
1161 4277 2.810274 CTGGTATGTACTCCATGCATGC 59.190 50.000 21.69 11.82 37.85 4.06
1162 4278 2.439135 TGGTATGTACTCCATGCATGCT 59.561 45.455 21.69 7.98 37.85 3.79
1163 4279 3.117926 TGGTATGTACTCCATGCATGCTT 60.118 43.478 21.69 10.16 37.85 3.91
1182 4298 4.141846 TGCTTCTCTCTCTCTCTCTCTCTC 60.142 50.000 0.00 0.00 0.00 3.20
1183 4299 4.100808 GCTTCTCTCTCTCTCTCTCTCTCT 59.899 50.000 0.00 0.00 0.00 3.10
1184 4300 5.738783 GCTTCTCTCTCTCTCTCTCTCTCTC 60.739 52.000 0.00 0.00 0.00 3.20
1185 4301 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1186 4302 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1189 4305 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1190 4306 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1192 4308 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1194 4310 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1196 4312 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1197 4313 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1198 4314 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1201 4317 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1202 4318 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1203 4319 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1206 4322 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1207 4323 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1208 4324 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1210 4326 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1211 4327 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1212 4328 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1214 4330 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1215 4331 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1216 4332 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1217 4333 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1218 4334 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1219 4335 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1220 4336 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1223 4339 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1224 4340 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1225 4341 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1226 4342 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1227 4343 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1228 4344 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1230 4346 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1232 4348 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1233 4349 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1234 4350 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1235 4351 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1236 4352 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1237 4353 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1238 4354 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1239 4355 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1240 4356 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1241 4357 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1242 4358 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1243 4359 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1244 4360 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1245 4361 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1246 4362 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1247 4363 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1248 4364 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1249 4365 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
1250 4366 4.078922 TCTCTCTCTCTCTCTCTCTCTCCT 60.079 50.000 0.00 0.00 0.00 3.69
1255 4371 3.706594 TCTCTCTCTCTCTCTCCTGAGAC 59.293 52.174 0.00 0.00 43.73 3.36
1256 4372 3.449918 TCTCTCTCTCTCTCCTGAGACA 58.550 50.000 0.00 0.00 43.73 3.41
1259 4375 3.117926 TCTCTCTCTCTCCTGAGACATGG 60.118 52.174 0.00 0.00 43.73 3.66
1265 4381 3.261897 TCTCTCCTGAGACATGGAAAACC 59.738 47.826 0.00 0.00 43.73 3.27
1270 4386 3.304659 CCTGAGACATGGAAAACCAAACG 60.305 47.826 0.00 0.00 0.00 3.60
1271 4387 2.034053 TGAGACATGGAAAACCAAACGC 59.966 45.455 0.00 0.00 0.00 4.84
1273 4389 2.293399 AGACATGGAAAACCAAACGCTC 59.707 45.455 0.00 0.00 0.00 5.03
1274 4390 2.293399 GACATGGAAAACCAAACGCTCT 59.707 45.455 0.00 0.00 0.00 4.09
1275 4391 2.693074 ACATGGAAAACCAAACGCTCTT 59.307 40.909 0.00 0.00 0.00 2.85
1279 4395 4.927422 TGGAAAACCAAACGCTCTTAAAG 58.073 39.130 0.00 0.00 0.00 1.85
1280 4396 4.399934 TGGAAAACCAAACGCTCTTAAAGT 59.600 37.500 0.00 0.00 0.00 2.66
1281 4397 5.105675 TGGAAAACCAAACGCTCTTAAAGTT 60.106 36.000 0.00 0.00 0.00 2.66
1284 4400 8.291740 GGAAAACCAAACGCTCTTAAAGTTATA 58.708 33.333 0.00 0.00 0.00 0.98
1285 4401 9.836076 GAAAACCAAACGCTCTTAAAGTTATAT 57.164 29.630 0.00 0.00 0.00 0.86
1287 4403 8.788325 AACCAAACGCTCTTAAAGTTATATCT 57.212 30.769 0.00 0.00 0.00 1.98
1288 4404 8.421673 ACCAAACGCTCTTAAAGTTATATCTC 57.578 34.615 0.00 0.00 0.00 2.75
1289 4405 8.258708 ACCAAACGCTCTTAAAGTTATATCTCT 58.741 33.333 0.00 0.00 0.00 3.10
1290 4406 9.099454 CCAAACGCTCTTAAAGTTATATCTCTT 57.901 33.333 0.00 0.00 0.00 2.85
1294 4410 9.448294 ACGCTCTTAAAGTTATATCTCTTTACG 57.552 33.333 10.05 11.61 36.35 3.18
1295 4411 9.661187 CGCTCTTAAAGTTATATCTCTTTACGA 57.339 33.333 10.05 11.73 36.35 3.43
1321 4446 6.189133 AGGAGTACTATCTTTCTTTCTCCGT 58.811 40.000 0.00 0.00 43.16 4.69
1336 4461 7.792032 TCTTTCTCCGTAGACATGGAAATATT 58.208 34.615 0.00 0.00 39.44 1.28
1339 4464 7.303182 TCTCCGTAGACATGGAAATATTGAT 57.697 36.000 0.00 0.00 39.44 2.57
1342 4467 7.735917 TCCGTAGACATGGAAATATTGATCTT 58.264 34.615 0.00 0.00 36.88 2.40
1343 4468 7.872993 TCCGTAGACATGGAAATATTGATCTTC 59.127 37.037 0.00 0.00 36.88 2.87
1344 4469 7.875041 CCGTAGACATGGAAATATTGATCTTCT 59.125 37.037 0.00 0.00 31.77 2.85
1345 4470 9.265901 CGTAGACATGGAAATATTGATCTTCTT 57.734 33.333 0.00 0.00 0.00 2.52
1447 4579 1.670967 GCAAAACATGGCAGCTTCCTC 60.671 52.381 3.45 0.00 0.00 3.71
1450 4582 0.613260 AACATGGCAGCTTCCTCGTA 59.387 50.000 3.45 0.00 0.00 3.43
1603 4735 2.357952 CACACCACGTAGCTAGCATCTA 59.642 50.000 18.83 0.00 0.00 1.98
1681 4813 9.734620 TGCTGAACATATACAGAATAAATTTGC 57.265 29.630 0.00 0.00 36.38 3.68
1682 4814 9.734620 GCTGAACATATACAGAATAAATTTGCA 57.265 29.630 0.00 0.00 36.38 4.08
1888 5020 4.549155 CTCCAGGTGAGGTGAGGT 57.451 61.111 0.00 0.00 37.45 3.85
1889 5021 1.978473 CTCCAGGTGAGGTGAGGTG 59.022 63.158 0.00 0.00 37.45 4.00
1890 5022 0.542938 CTCCAGGTGAGGTGAGGTGA 60.543 60.000 0.00 0.00 37.45 4.02
1891 5023 0.542938 TCCAGGTGAGGTGAGGTGAG 60.543 60.000 0.00 0.00 0.00 3.51
1892 5024 1.548357 CCAGGTGAGGTGAGGTGAGG 61.548 65.000 0.00 0.00 0.00 3.86
1893 5025 1.229336 AGGTGAGGTGAGGTGAGGG 60.229 63.158 0.00 0.00 0.00 4.30
1894 5026 1.536662 GGTGAGGTGAGGTGAGGGT 60.537 63.158 0.00 0.00 0.00 4.34
1932 5064 2.183046 GCCAGACTCTGACTCGCC 59.817 66.667 7.69 0.00 32.44 5.54
1939 5071 4.724602 TCTGACTCGCCGCAGCAC 62.725 66.667 0.00 0.00 39.83 4.40
1940 5072 4.731612 CTGACTCGCCGCAGCACT 62.732 66.667 0.00 0.00 39.83 4.40
2011 5150 4.164843 AGCTGGAAGGTTTTGTACTCAA 57.835 40.909 0.00 0.00 46.63 3.02
2019 5158 8.482128 TGGAAGGTTTTGTACTCAAATTTCATT 58.518 29.630 0.00 0.00 42.14 2.57
2020 5159 9.325198 GGAAGGTTTTGTACTCAAATTTCATTT 57.675 29.630 0.00 0.00 42.14 2.32
2022 5161 9.883142 AAGGTTTTGTACTCAAATTTCATTTCA 57.117 25.926 0.00 0.00 42.14 2.69
2043 5182 5.918608 TCATAAACCTGCCTCTGACTAATC 58.081 41.667 0.00 0.00 0.00 1.75
2090 5256 3.244561 ACATTCCACTTTCCACACGATCT 60.245 43.478 0.00 0.00 0.00 2.75
2145 5313 4.569162 TGTTTTCGTTTCTGGTCAGTACAG 59.431 41.667 0.00 0.00 37.30 2.74
2151 5319 4.611355 CGTTTCTGGTCAGTACAGCATTTG 60.611 45.833 0.00 0.00 35.94 2.32
2163 5331 6.255237 CAGTACAGCATTTGTAGAGATCAGTG 59.745 42.308 0.00 0.00 42.75 3.66
2189 5357 5.164233 TCGAGAGTTTCTGCAGAAATACAG 58.836 41.667 37.03 27.70 44.69 2.74
2224 5393 6.534475 AGACGGAACAACATATGTAGGTAA 57.466 37.500 9.21 0.00 42.99 2.85
2258 5434 6.094186 TGGATGTTATGTTTTTGTAGCGCATA 59.906 34.615 11.47 0.00 0.00 3.14
2274 5450 4.883585 AGCGCATATTTCATTTTCTGAGGA 59.116 37.500 11.47 0.00 34.68 3.71
2275 5451 5.357878 AGCGCATATTTCATTTTCTGAGGAA 59.642 36.000 11.47 0.00 34.68 3.36
2338 5514 1.675483 GACATTCCGGCATGTGCAATA 59.325 47.619 24.80 0.00 44.36 1.90
2359 5535 3.658725 AGTGCTATCTTAGGGGTGTCAT 58.341 45.455 0.00 0.00 0.00 3.06
2382 5558 3.810941 GTCGGACAAATGTTGAGGTGTAA 59.189 43.478 2.62 0.00 0.00 2.41
2420 5596 4.378874 CGAAAAGCCTTTGCCTTCTCTTAG 60.379 45.833 0.00 0.00 38.69 2.18
2425 5601 5.004448 AGCCTTTGCCTTCTCTTAGTTAAC 58.996 41.667 0.00 0.00 38.69 2.01
2427 5603 5.240844 GCCTTTGCCTTCTCTTAGTTAACAA 59.759 40.000 8.61 0.00 0.00 2.83
2474 5650 7.626452 GCCTCACCACATTTTTATGAACTAGAC 60.626 40.741 0.00 0.00 0.00 2.59
2612 5789 1.656652 CCACCTTACCAAGCTCATCG 58.343 55.000 0.00 0.00 0.00 3.84
2614 5791 2.615493 CCACCTTACCAAGCTCATCGTT 60.615 50.000 0.00 0.00 0.00 3.85
2662 5839 4.744570 CGTCAAGCTGATAACTAGTTCCA 58.255 43.478 12.39 10.54 0.00 3.53
2668 5845 8.318412 TCAAGCTGATAACTAGTTCCACAATTA 58.682 33.333 12.39 0.00 0.00 1.40
2871 6050 7.806409 TCATAATGTATTTGTGACCCAGATG 57.194 36.000 0.00 0.00 31.29 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.067896 TCTCTCAGCGCTTGAAATTTTCT 58.932 39.130 7.50 0.00 34.81 2.52
1 2 4.410492 TCTCTCAGCGCTTGAAATTTTC 57.590 40.909 7.50 2.05 34.81 2.29
2 3 4.836125 TTCTCTCAGCGCTTGAAATTTT 57.164 36.364 7.50 0.00 34.81 1.82
3 4 4.380233 CCATTCTCTCAGCGCTTGAAATTT 60.380 41.667 7.50 0.00 34.81 1.82
4 5 3.128242 CCATTCTCTCAGCGCTTGAAATT 59.872 43.478 7.50 0.00 34.81 1.82
5 6 2.681848 CCATTCTCTCAGCGCTTGAAAT 59.318 45.455 7.50 9.00 34.81 2.17
6 7 2.079158 CCATTCTCTCAGCGCTTGAAA 58.921 47.619 7.50 7.14 34.81 2.69
7 8 1.676916 CCCATTCTCTCAGCGCTTGAA 60.677 52.381 7.50 10.73 34.81 2.69
8 9 0.107993 CCCATTCTCTCAGCGCTTGA 60.108 55.000 7.50 8.61 0.00 3.02
9 10 1.712977 GCCCATTCTCTCAGCGCTTG 61.713 60.000 7.50 3.52 0.00 4.01
10 11 1.451028 GCCCATTCTCTCAGCGCTT 60.451 57.895 7.50 0.00 0.00 4.68
11 12 2.188994 GCCCATTCTCTCAGCGCT 59.811 61.111 2.64 2.64 0.00 5.92
12 13 2.899339 GGCCCATTCTCTCAGCGC 60.899 66.667 0.00 0.00 0.00 5.92
13 14 2.587194 CGGCCCATTCTCTCAGCG 60.587 66.667 0.00 0.00 0.00 5.18
14 15 2.203126 CCGGCCCATTCTCTCAGC 60.203 66.667 0.00 0.00 0.00 4.26
15 16 2.203126 GCCGGCCCATTCTCTCAG 60.203 66.667 18.11 0.00 0.00 3.35
16 17 1.053835 TATGCCGGCCCATTCTCTCA 61.054 55.000 26.77 0.00 0.00 3.27
17 18 0.108585 TTATGCCGGCCCATTCTCTC 59.891 55.000 26.77 0.00 0.00 3.20
18 19 0.179018 GTTATGCCGGCCCATTCTCT 60.179 55.000 26.77 0.46 0.00 3.10
70 71 1.128188 AGAAAGGTGCTCCCTCCGTT 61.128 55.000 0.00 0.00 45.47 4.44
71 72 1.128188 AAGAAAGGTGCTCCCTCCGT 61.128 55.000 0.00 0.00 45.47 4.69
72 73 0.036875 AAAGAAAGGTGCTCCCTCCG 59.963 55.000 0.00 0.00 45.47 4.63
74 75 2.163509 GGAAAAGAAAGGTGCTCCCTC 58.836 52.381 0.00 0.00 45.47 4.30
76 77 1.889170 CAGGAAAAGAAAGGTGCTCCC 59.111 52.381 0.00 0.00 0.00 4.30
77 78 2.554462 GACAGGAAAAGAAAGGTGCTCC 59.446 50.000 0.00 0.00 0.00 4.70
78 79 3.003793 GTGACAGGAAAAGAAAGGTGCTC 59.996 47.826 0.00 0.00 0.00 4.26
79 80 2.952310 GTGACAGGAAAAGAAAGGTGCT 59.048 45.455 0.00 0.00 0.00 4.40
80 81 2.952310 AGTGACAGGAAAAGAAAGGTGC 59.048 45.455 0.00 0.00 0.00 5.01
81 82 3.947834 ACAGTGACAGGAAAAGAAAGGTG 59.052 43.478 0.00 0.00 0.00 4.00
82 83 3.947834 CACAGTGACAGGAAAAGAAAGGT 59.052 43.478 0.00 0.00 0.00 3.50
83 84 4.199310 TCACAGTGACAGGAAAAGAAAGG 58.801 43.478 0.00 0.00 0.00 3.11
86 87 3.621268 CGTTCACAGTGACAGGAAAAGAA 59.379 43.478 1.52 0.00 0.00 2.52
93 94 2.006888 ACAAACGTTCACAGTGACAGG 58.993 47.619 1.52 3.65 0.00 4.00
94 95 2.930040 AGACAAACGTTCACAGTGACAG 59.070 45.455 1.52 2.74 0.00 3.51
96 97 2.671396 ACAGACAAACGTTCACAGTGAC 59.329 45.455 1.52 0.00 0.00 3.67
97 98 2.927477 GACAGACAAACGTTCACAGTGA 59.073 45.455 0.00 0.00 0.00 3.41
98 99 2.930040 AGACAGACAAACGTTCACAGTG 59.070 45.455 0.00 0.00 0.00 3.66
99 100 3.247006 AGACAGACAAACGTTCACAGT 57.753 42.857 0.00 0.00 0.00 3.55
100 101 4.600012 AAAGACAGACAAACGTTCACAG 57.400 40.909 0.00 0.00 0.00 3.66
175 182 1.519234 GCATCGCGACAGACATGGA 60.519 57.895 12.93 0.00 0.00 3.41
177 184 0.247419 GTTGCATCGCGACAGACATG 60.247 55.000 12.93 5.73 42.10 3.21
178 185 1.361668 GGTTGCATCGCGACAGACAT 61.362 55.000 12.93 0.00 44.12 3.06
179 186 2.027073 GGTTGCATCGCGACAGACA 61.027 57.895 12.93 4.26 44.12 3.41
180 187 2.778679 GGTTGCATCGCGACAGAC 59.221 61.111 12.93 8.12 44.12 3.51
181 188 2.809174 CGGTTGCATCGCGACAGA 60.809 61.111 12.93 0.00 44.12 3.41
182 189 4.505217 GCGGTTGCATCGCGACAG 62.505 66.667 12.93 8.77 44.12 3.51
218 3306 2.363683 CTTGAGGGGAAGAATGTGCTC 58.636 52.381 0.00 0.00 0.00 4.26
243 3334 5.221945 GGAAAAGGGTTAGAGGATAGGATGG 60.222 48.000 0.00 0.00 0.00 3.51
257 3348 5.086621 ACAATATCTGCAAGGAAAAGGGTT 58.913 37.500 0.00 0.00 0.00 4.11
258 3349 4.677182 ACAATATCTGCAAGGAAAAGGGT 58.323 39.130 0.00 0.00 0.00 4.34
259 3350 4.201950 CGACAATATCTGCAAGGAAAAGGG 60.202 45.833 0.00 0.00 0.00 3.95
266 3357 3.499918 GGAATCCGACAATATCTGCAAGG 59.500 47.826 0.00 0.00 0.00 3.61
325 3417 0.167470 TCGATCGGTCACTGTTCGAC 59.833 55.000 16.41 0.00 33.90 4.20
340 3432 0.741326 CAGTGGTCTGGACGATCGAT 59.259 55.000 24.34 5.96 37.97 3.59
341 3433 2.180674 CAGTGGTCTGGACGATCGA 58.819 57.895 24.34 0.00 37.97 3.59
342 3434 4.794164 CAGTGGTCTGGACGATCG 57.206 61.111 14.88 14.88 37.97 3.69
412 3506 3.866356 GTCGTAACAAGGGGCGAC 58.134 61.111 0.00 0.00 44.93 5.19
527 3643 3.406361 CACGTCTGTGCACGCTCC 61.406 66.667 13.13 0.00 43.93 4.70
561 3677 4.631813 CACTGCCTAGACTATTGGTGAAAC 59.368 45.833 0.00 0.00 0.00 2.78
673 3789 4.648762 CCTCTAGATTCTCTGCCTTTCTCA 59.351 45.833 0.00 0.00 0.00 3.27
683 3799 6.921412 TGATTCCTCTTCCTCTAGATTCTCT 58.079 40.000 0.00 0.00 0.00 3.10
900 4016 4.008933 GCACACCTGTCGGCCTCT 62.009 66.667 0.00 0.00 0.00 3.69
953 4069 4.916293 TCTCATCCCATGCGCGCC 62.916 66.667 30.77 11.42 0.00 6.53
995 4111 2.762043 TCCCGCGATCCATCCACA 60.762 61.111 8.23 0.00 0.00 4.17
1158 4274 4.411540 AGAGAGAGAGAGAGAGAGAAGCAT 59.588 45.833 0.00 0.00 0.00 3.79
1159 4275 3.776969 AGAGAGAGAGAGAGAGAGAAGCA 59.223 47.826 0.00 0.00 0.00 3.91
1160 4276 4.100808 AGAGAGAGAGAGAGAGAGAGAAGC 59.899 50.000 0.00 0.00 0.00 3.86
1161 4277 5.598005 AGAGAGAGAGAGAGAGAGAGAGAAG 59.402 48.000 0.00 0.00 0.00 2.85
1162 4278 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
1163 4279 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1182 4298 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1183 4299 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1184 4300 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1185 4301 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1186 4302 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1189 4305 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1190 4306 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1192 4308 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1194 4310 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1196 4312 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1197 4313 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1198 4314 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1201 4317 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1202 4318 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1203 4319 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1206 4322 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1207 4323 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1208 4324 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1210 4326 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1211 4327 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1212 4328 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1214 4330 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1215 4331 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1216 4332 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1217 4333 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1218 4334 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1219 4335 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1220 4336 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1223 4339 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1224 4340 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1225 4341 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1226 4342 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
1227 4343 4.078922 AGGAGAGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
1228 4344 4.039004 CAGGAGAGAGAGAGAGAGAGAGAG 59.961 54.167 0.00 0.00 0.00 3.20
1230 4346 3.963374 TCAGGAGAGAGAGAGAGAGAGAG 59.037 52.174 0.00 0.00 0.00 3.20
1232 4348 3.963374 TCTCAGGAGAGAGAGAGAGAGAG 59.037 52.174 0.00 0.00 45.73 3.20
1233 4349 3.994317 TCTCAGGAGAGAGAGAGAGAGA 58.006 50.000 0.00 0.00 45.73 3.10
1240 4356 8.519029 GGTTTTCCATGTCTCAGGAGAGAGAG 62.519 50.000 0.00 0.00 45.99 3.20
1241 4357 6.798341 GGTTTTCCATGTCTCAGGAGAGAGA 61.798 48.000 0.00 0.00 46.72 3.10
1242 4358 4.622695 GGTTTTCCATGTCTCAGGAGAGAG 60.623 50.000 0.00 0.00 44.70 3.20
1243 4359 3.261897 GGTTTTCCATGTCTCAGGAGAGA 59.738 47.826 0.00 0.00 43.25 3.10
1244 4360 3.008375 TGGTTTTCCATGTCTCAGGAGAG 59.992 47.826 0.00 0.00 46.22 3.20
1245 4361 2.978978 TGGTTTTCCATGTCTCAGGAGA 59.021 45.455 0.00 0.00 46.22 3.71
1246 4362 3.423539 TGGTTTTCCATGTCTCAGGAG 57.576 47.619 0.00 0.00 46.22 3.69
1259 4375 9.836076 ATATAACTTTAAGAGCGTTTGGTTTTC 57.164 29.630 0.00 0.00 0.00 2.29
1284 4400 8.983702 AGATAGTACTCCTTTCGTAAAGAGAT 57.016 34.615 0.00 0.00 41.02 2.75
1285 4401 8.804912 AAGATAGTACTCCTTTCGTAAAGAGA 57.195 34.615 0.00 3.95 41.02 3.10
1287 4403 9.240734 AGAAAGATAGTACTCCTTTCGTAAAGA 57.759 33.333 27.28 1.63 46.10 2.52
1288 4404 9.857957 AAGAAAGATAGTACTCCTTTCGTAAAG 57.142 33.333 27.28 0.00 46.10 1.85
1290 4406 9.852091 GAAAGAAAGATAGTACTCCTTTCGTAA 57.148 33.333 27.28 2.82 46.10 3.18
1291 4407 9.240734 AGAAAGAAAGATAGTACTCCTTTCGTA 57.759 33.333 27.28 3.42 46.10 3.43
1292 4408 8.124808 AGAAAGAAAGATAGTACTCCTTTCGT 57.875 34.615 27.28 24.58 46.10 3.85
1293 4409 7.703197 GGAGAAAGAAAGATAGTACTCCTTTCG 59.297 40.741 27.28 0.00 46.10 3.46
1294 4410 7.703197 CGGAGAAAGAAAGATAGTACTCCTTTC 59.297 40.741 26.92 26.92 43.51 2.62
1295 4411 7.178805 ACGGAGAAAGAAAGATAGTACTCCTTT 59.821 37.037 17.86 17.86 40.01 3.11
1296 4412 6.664384 ACGGAGAAAGAAAGATAGTACTCCTT 59.336 38.462 0.00 1.31 40.01 3.36
1297 4413 6.189133 ACGGAGAAAGAAAGATAGTACTCCT 58.811 40.000 0.00 0.00 40.01 3.69
1298 4414 6.453926 ACGGAGAAAGAAAGATAGTACTCC 57.546 41.667 0.00 0.00 39.16 3.85
1299 4415 8.337532 GTCTACGGAGAAAGAAAGATAGTACTC 58.662 40.741 0.00 0.00 31.96 2.59
1447 4579 1.498865 GCAGGCCCATGATCGTTACG 61.499 60.000 0.00 0.00 0.00 3.18
1450 4582 1.452651 CAGCAGGCCCATGATCGTT 60.453 57.895 0.00 0.00 0.00 3.85
1603 4735 2.293877 GGGTATTGACACGAGGGGT 58.706 57.895 0.00 0.00 0.00 4.95
1681 4813 1.067565 ACAGTATCGACAGCACCTGTG 60.068 52.381 2.12 0.00 45.44 3.66
1844 4976 1.353091 ACCAGAGGTTGAAGAGGGAC 58.647 55.000 0.00 0.00 27.29 4.46
1885 5017 2.529389 GACCACCCACCCTCACCT 60.529 66.667 0.00 0.00 0.00 4.00
1886 5018 4.016706 CGACCACCCACCCTCACC 62.017 72.222 0.00 0.00 0.00 4.02
1887 5019 4.699522 GCGACCACCCACCCTCAC 62.700 72.222 0.00 0.00 0.00 3.51
1910 5042 2.179517 GTCAGAGTCTGGCGTCCG 59.820 66.667 19.99 0.00 31.51 4.79
1932 5064 1.732259 ACGGAATTTAGAAGTGCTGCG 59.268 47.619 0.00 0.00 0.00 5.18
1939 5071 8.569641 AGCTATACAGACTACGGAATTTAGAAG 58.430 37.037 0.00 0.00 0.00 2.85
1940 5072 8.350722 CAGCTATACAGACTACGGAATTTAGAA 58.649 37.037 0.00 0.00 0.00 2.10
2011 5150 7.178983 TCAGAGGCAGGTTTATGAAATGAAATT 59.821 33.333 0.00 0.00 38.98 1.82
2019 5158 5.755409 TTAGTCAGAGGCAGGTTTATGAA 57.245 39.130 0.00 0.00 0.00 2.57
2020 5159 5.425217 TGATTAGTCAGAGGCAGGTTTATGA 59.575 40.000 0.00 0.00 0.00 2.15
2021 5160 5.674525 TGATTAGTCAGAGGCAGGTTTATG 58.325 41.667 0.00 0.00 0.00 1.90
2022 5161 5.957771 TGATTAGTCAGAGGCAGGTTTAT 57.042 39.130 0.00 0.00 0.00 1.40
2043 5182 8.915654 GTTAACTTCAAACAATCCTTAATGCTG 58.084 33.333 0.00 0.00 0.00 4.41
2048 5187 9.974980 GGAATGTTAACTTCAAACAATCCTTAA 57.025 29.630 13.34 0.00 46.53 1.85
2090 5256 6.841601 ATAGAACCCTATTATGCAAAGAGCA 58.158 36.000 0.00 0.00 44.45 4.26
2145 5313 4.502282 CGAGACACTGATCTCTACAAATGC 59.498 45.833 10.45 0.00 42.63 3.56
2151 5319 4.439057 ACTCTCGAGACACTGATCTCTAC 58.561 47.826 12.08 0.00 42.63 2.59
2163 5331 2.999507 TCTGCAGAAACTCTCGAGAC 57.000 50.000 15.67 1.30 0.00 3.36
2189 5357 2.125350 CCGTCTTCAGCAGCCTCC 60.125 66.667 0.00 0.00 0.00 4.30
2224 5393 7.342799 ACAAAAACATAACATCCATCAGCCTAT 59.657 33.333 0.00 0.00 0.00 2.57
2338 5514 3.116096 TGACACCCCTAAGATAGCACT 57.884 47.619 0.00 0.00 0.00 4.40
2351 5527 1.468520 CATTTGTCCGACATGACACCC 59.531 52.381 1.09 0.00 44.55 4.61
2359 5535 2.217750 CACCTCAACATTTGTCCGACA 58.782 47.619 0.00 0.00 0.00 4.35
2382 5558 3.546218 GCTTTTCGCGTGTTTCTCTTTCT 60.546 43.478 5.77 0.00 0.00 2.52
2425 5601 8.248945 AGGCATTTGTTCTTAAGAGATCATTTG 58.751 33.333 5.12 8.29 33.00 2.32
2427 5603 7.613022 TGAGGCATTTGTTCTTAAGAGATCATT 59.387 33.333 5.12 0.00 33.00 2.57
2474 5650 7.012704 CACAATGGGTGGTCTCTTAATCTTATG 59.987 40.741 0.00 0.00 44.04 1.90
2612 5789 0.988832 TCCATGGGTAGGTGGTGAAC 59.011 55.000 13.02 0.00 36.84 3.18
2614 5791 2.689658 CTATCCATGGGTAGGTGGTGA 58.310 52.381 22.68 0.00 36.84 4.02


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

AutoCloner maintained by Alex Coulton.