Multiple sequence alignment - TraesCS6B01G346600

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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 TraesCS6B01G346600 chr6B 100.000 5162 0 0 1 5162 610803613 610808774 0.000000e+00 9533.0
1 TraesCS6B01G346600 chr6B 82.493 1388 189 38 3074 4427 103963362 103964729 0.000000e+00 1168.0
2 TraesCS6B01G346600 chr6B 99.454 366 2 0 1 366 718367381 718367746 0.000000e+00 665.0
3 TraesCS6B01G346600 chr6B 80.714 140 23 4 4838 4974 221401142 221401280 7.070000e-19 106.0
4 TraesCS6B01G346600 chr1A 98.583 5010 42 13 1 4984 184938712 184933706 0.000000e+00 8831.0
5 TraesCS6B01G346600 chr1A 86.869 396 44 5 910 1302 379191842 379192232 2.210000e-118 436.0
6 TraesCS6B01G346600 chr7B 97.141 5001 108 14 1 4974 574508606 574513598 0.000000e+00 8410.0
7 TraesCS6B01G346600 chr7A 96.006 3756 114 24 471 4216 255891137 255887408 0.000000e+00 6072.0
8 TraesCS6B01G346600 chr7A 94.246 2381 106 11 2612 4977 32589644 32587280 0.000000e+00 3609.0
9 TraesCS6B01G346600 chr7A 85.943 3315 400 38 910 4176 722321404 722318108 0.000000e+00 3480.0
10 TraesCS6B01G346600 chr7A 85.921 3317 397 45 910 4176 88961026 88957730 0.000000e+00 3474.0
11 TraesCS6B01G346600 chr7A 86.321 965 109 7 3349 4294 171878764 171877804 0.000000e+00 1029.0
12 TraesCS6B01G346600 chr7A 94.737 266 14 0 130 395 32589974 32589709 1.030000e-111 414.0
13 TraesCS6B01G346600 chr7A 94.030 134 8 0 1 134 32624543 32624410 2.440000e-48 204.0
14 TraesCS6B01G346600 chr5A 88.619 3418 339 36 909 4294 663072730 663076129 0.000000e+00 4111.0
15 TraesCS6B01G346600 chr5A 86.394 2080 247 22 910 2961 167893789 167891718 0.000000e+00 2241.0
16 TraesCS6B01G346600 chr5A 91.729 133 9 2 4843 4974 36865968 36866099 3.170000e-42 183.0
17 TraesCS6B01G346600 chrUn 98.273 2316 10 6 1 2296 340330971 340333276 0.000000e+00 4028.0
18 TraesCS6B01G346600 chrUn 98.479 1249 15 3 3733 4977 259654538 259653290 0.000000e+00 2198.0
19 TraesCS6B01G346600 chrUn 99.338 1058 7 0 2168 3225 445250912 445251969 0.000000e+00 1916.0
20 TraesCS6B01G346600 chrUn 86.121 1124 130 20 3074 4179 98277487 98276372 0.000000e+00 1188.0
21 TraesCS6B01G346600 chrUn 86.218 965 110 7 3349 4294 386814551 386813591 0.000000e+00 1024.0
22 TraesCS6B01G346600 chrUn 97.810 411 6 1 4302 4709 477615150 477614740 0.000000e+00 706.0
23 TraesCS6B01G346600 chrUn 81.548 168 27 4 4810 4975 62698328 62698163 9.020000e-28 135.0
24 TraesCS6B01G346600 chr7D 85.069 1969 253 31 1164 3103 299801742 299799786 0.000000e+00 1969.0
25 TraesCS6B01G346600 chr6A 83.133 1334 181 30 3074 4383 53257554 53256241 0.000000e+00 1177.0
26 TraesCS6B01G346600 chr6A 94.054 185 6 3 4970 5151 552757780 552757962 5.090000e-70 276.0
27 TraesCS6B01G346600 chr5D 85.345 116 11 2 774 889 475168513 475168622 1.170000e-21 115.0
28 TraesCS6B01G346600 chr6D 79.137 139 17 6 5023 5152 406334541 406334676 9.210000e-13 86.1


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 TraesCS6B01G346600 chr6B 610803613 610808774 5161 False 9533.0 9533 100.0000 1 5162 1 chr6B.!!$F3 5161
1 TraesCS6B01G346600 chr6B 103963362 103964729 1367 False 1168.0 1168 82.4930 3074 4427 1 chr6B.!!$F1 1353
2 TraesCS6B01G346600 chr1A 184933706 184938712 5006 True 8831.0 8831 98.5830 1 4984 1 chr1A.!!$R1 4983
3 TraesCS6B01G346600 chr7B 574508606 574513598 4992 False 8410.0 8410 97.1410 1 4974 1 chr7B.!!$F1 4973
4 TraesCS6B01G346600 chr7A 255887408 255891137 3729 True 6072.0 6072 96.0060 471 4216 1 chr7A.!!$R4 3745
5 TraesCS6B01G346600 chr7A 722318108 722321404 3296 True 3480.0 3480 85.9430 910 4176 1 chr7A.!!$R5 3266
6 TraesCS6B01G346600 chr7A 88957730 88961026 3296 True 3474.0 3474 85.9210 910 4176 1 chr7A.!!$R2 3266
7 TraesCS6B01G346600 chr7A 32587280 32589974 2694 True 2011.5 3609 94.4915 130 4977 2 chr7A.!!$R6 4847
8 TraesCS6B01G346600 chr7A 171877804 171878764 960 True 1029.0 1029 86.3210 3349 4294 1 chr7A.!!$R3 945
9 TraesCS6B01G346600 chr5A 663072730 663076129 3399 False 4111.0 4111 88.6190 909 4294 1 chr5A.!!$F2 3385
10 TraesCS6B01G346600 chr5A 167891718 167893789 2071 True 2241.0 2241 86.3940 910 2961 1 chr5A.!!$R1 2051
11 TraesCS6B01G346600 chrUn 340330971 340333276 2305 False 4028.0 4028 98.2730 1 2296 1 chrUn.!!$F1 2295
12 TraesCS6B01G346600 chrUn 259653290 259654538 1248 True 2198.0 2198 98.4790 3733 4977 1 chrUn.!!$R3 1244
13 TraesCS6B01G346600 chrUn 445250912 445251969 1057 False 1916.0 1916 99.3380 2168 3225 1 chrUn.!!$F2 1057
14 TraesCS6B01G346600 chrUn 98276372 98277487 1115 True 1188.0 1188 86.1210 3074 4179 1 chrUn.!!$R2 1105
15 TraesCS6B01G346600 chrUn 386813591 386814551 960 True 1024.0 1024 86.2180 3349 4294 1 chrUn.!!$R4 945
16 TraesCS6B01G346600 chr7D 299799786 299801742 1956 True 1969.0 1969 85.0690 1164 3103 1 chr7D.!!$R1 1939
17 TraesCS6B01G346600 chr6A 53256241 53257554 1313 True 1177.0 1177 83.1330 3074 4383 1 chr6A.!!$R1 1309

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
782 834 2.961062 ACAGCCTGCACTTTGAAAGATT 59.039 40.909 12.53 0.0 0.0 2.40 F
1545 1649 1.658686 GCACGTCCACCAACAAACCA 61.659 55.000 0.00 0.0 0.0 3.67 F
1782 1886 3.214328 GGATGGATAGGCGTTGTTTCAT 58.786 45.455 0.00 0.0 0.0 2.57 F
2504 2611 2.173569 ACTGTGAAGGGTTTCTTGCTCT 59.826 45.455 0.00 0.0 35.5 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 2342 0.250510 TCTGGCGCACATACACCAAA 60.251 50.000 10.83 0.0 0.00 3.28 R
2504 2611 3.568443 TGATACCGTTGCCCTCTGTATA 58.432 45.455 0.00 0.0 0.00 1.47 R
3587 3716 0.394488 TGCTCCCTCACGAGACTAGG 60.394 60.000 0.00 0.0 30.97 3.02 R
4388 4535 3.058016 GCAACACATGACACAGCAATACT 60.058 43.478 0.00 0.0 0.00 2.12 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
782 834 2.961062 ACAGCCTGCACTTTGAAAGATT 59.039 40.909 12.53 0.00 0.00 2.40
1369 1432 9.744468 ACATGAAAACAAGTTACTTTTATCCAC 57.256 29.630 0.00 0.00 0.00 4.02
1545 1649 1.658686 GCACGTCCACCAACAAACCA 61.659 55.000 0.00 0.00 0.00 3.67
1782 1886 3.214328 GGATGGATAGGCGTTGTTTCAT 58.786 45.455 0.00 0.00 0.00 2.57
2236 2342 7.614124 AAGAATGAAGTTGCAACAAATGTTT 57.386 28.000 30.11 15.11 35.83 2.83
2504 2611 2.173569 ACTGTGAAGGGTTTCTTGCTCT 59.826 45.455 0.00 0.00 35.50 4.09
3225 3339 3.844090 GGACAGCGGAGGAGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
4388 4535 4.535526 TCATCTCTTTCATCAACCGTGA 57.464 40.909 0.00 0.00 38.41 4.35
4653 4810 6.793505 TTTCCTTAGTTTGCCCAGTTTTAA 57.206 33.333 0.00 0.00 0.00 1.52
4801 4959 8.694540 CATATCATTAACAACTCCCATTCCAAA 58.305 33.333 0.00 0.00 0.00 3.28
4818 4976 2.237392 CCAAAACCCCTGAACCAAACAA 59.763 45.455 0.00 0.00 0.00 2.83
4974 5132 2.610374 TCAAACTACCAAACACGCTGTC 59.390 45.455 0.00 0.00 0.00 3.51
4977 5135 1.411246 ACTACCAAACACGCTGTCAGA 59.589 47.619 3.32 0.00 0.00 3.27
4979 5137 1.299541 ACCAAACACGCTGTCAGAAG 58.700 50.000 3.32 0.00 0.00 2.85
4982 5140 2.354510 CCAAACACGCTGTCAGAAGAAA 59.645 45.455 3.32 0.00 0.00 2.52
4983 5141 3.546815 CCAAACACGCTGTCAGAAGAAAG 60.547 47.826 3.32 0.00 31.84 2.62
4984 5142 2.890808 ACACGCTGTCAGAAGAAAGA 57.109 45.000 3.32 0.00 29.99 2.52
4985 5143 2.474816 ACACGCTGTCAGAAGAAAGAC 58.525 47.619 3.32 0.00 29.99 3.01
4986 5144 1.795286 CACGCTGTCAGAAGAAAGACC 59.205 52.381 3.32 0.00 29.99 3.85
4987 5145 1.412710 ACGCTGTCAGAAGAAAGACCA 59.587 47.619 3.32 0.00 29.99 4.02
4988 5146 2.158957 ACGCTGTCAGAAGAAAGACCAA 60.159 45.455 3.32 0.00 29.99 3.67
4989 5147 2.478134 CGCTGTCAGAAGAAAGACCAAG 59.522 50.000 3.32 0.00 29.99 3.61
4990 5148 3.733337 GCTGTCAGAAGAAAGACCAAGA 58.267 45.455 3.32 0.00 29.99 3.02
4991 5149 4.130118 GCTGTCAGAAGAAAGACCAAGAA 58.870 43.478 3.32 0.00 29.99 2.52
4992 5150 4.576463 GCTGTCAGAAGAAAGACCAAGAAA 59.424 41.667 3.32 0.00 29.99 2.52
4993 5151 5.066505 GCTGTCAGAAGAAAGACCAAGAAAA 59.933 40.000 3.32 0.00 29.99 2.29
4994 5152 6.436843 TGTCAGAAGAAAGACCAAGAAAAC 57.563 37.500 0.00 0.00 33.89 2.43
4995 5153 5.357032 TGTCAGAAGAAAGACCAAGAAAACC 59.643 40.000 0.00 0.00 33.89 3.27
4996 5154 4.574828 TCAGAAGAAAGACCAAGAAAACCG 59.425 41.667 0.00 0.00 0.00 4.44
4997 5155 3.883489 AGAAGAAAGACCAAGAAAACCGG 59.117 43.478 0.00 0.00 0.00 5.28
4998 5156 3.570912 AGAAAGACCAAGAAAACCGGA 57.429 42.857 9.46 0.00 0.00 5.14
4999 5157 4.100279 AGAAAGACCAAGAAAACCGGAT 57.900 40.909 9.46 0.00 0.00 4.18
5000 5158 4.072839 AGAAAGACCAAGAAAACCGGATC 58.927 43.478 9.46 3.11 0.00 3.36
5001 5159 2.491675 AGACCAAGAAAACCGGATCC 57.508 50.000 9.46 0.00 0.00 3.36
5002 5160 1.702957 AGACCAAGAAAACCGGATCCA 59.297 47.619 9.46 0.00 0.00 3.41
5003 5161 2.308866 AGACCAAGAAAACCGGATCCAT 59.691 45.455 9.46 0.00 0.00 3.41
5004 5162 3.089284 GACCAAGAAAACCGGATCCATT 58.911 45.455 9.46 2.11 0.00 3.16
5005 5163 2.825532 ACCAAGAAAACCGGATCCATTG 59.174 45.455 9.46 7.47 0.00 2.82
5006 5164 2.825532 CCAAGAAAACCGGATCCATTGT 59.174 45.455 9.46 2.41 0.00 2.71
5007 5165 3.258123 CCAAGAAAACCGGATCCATTGTT 59.742 43.478 9.46 8.93 0.00 2.83
5008 5166 4.262420 CCAAGAAAACCGGATCCATTGTTT 60.262 41.667 9.46 14.34 32.62 2.83
5009 5167 4.519540 AGAAAACCGGATCCATTGTTTG 57.480 40.909 19.19 0.14 31.73 2.93
5010 5168 4.148838 AGAAAACCGGATCCATTGTTTGA 58.851 39.130 19.19 0.00 31.73 2.69
5011 5169 4.772100 AGAAAACCGGATCCATTGTTTGAT 59.228 37.500 19.19 11.37 31.73 2.57
5012 5170 4.718940 AAACCGGATCCATTGTTTGATC 57.281 40.909 9.46 0.00 37.29 2.92
5013 5171 2.288666 ACCGGATCCATTGTTTGATCG 58.711 47.619 9.46 0.00 38.60 3.69
5014 5172 2.093181 ACCGGATCCATTGTTTGATCGA 60.093 45.455 9.46 0.00 38.60 3.59
5015 5173 3.141398 CCGGATCCATTGTTTGATCGAT 58.859 45.455 13.41 0.00 38.60 3.59
5016 5174 3.565482 CCGGATCCATTGTTTGATCGATT 59.435 43.478 13.41 0.00 38.60 3.34
5017 5175 4.319766 CCGGATCCATTGTTTGATCGATTC 60.320 45.833 13.41 0.00 38.60 2.52
5018 5176 4.273235 CGGATCCATTGTTTGATCGATTCA 59.727 41.667 13.41 0.00 38.60 2.57
5019 5177 5.049198 CGGATCCATTGTTTGATCGATTCAT 60.049 40.000 13.41 0.00 38.60 2.57
5020 5178 6.147656 CGGATCCATTGTTTGATCGATTCATA 59.852 38.462 13.41 0.00 38.60 2.15
5021 5179 7.301054 GGATCCATTGTTTGATCGATTCATAC 58.699 38.462 6.95 5.57 38.60 2.39
5022 5180 7.173907 GGATCCATTGTTTGATCGATTCATACT 59.826 37.037 6.95 0.00 38.60 2.12
5023 5181 7.482654 TCCATTGTTTGATCGATTCATACTC 57.517 36.000 0.00 0.00 37.25 2.59
5024 5182 6.200854 TCCATTGTTTGATCGATTCATACTCG 59.799 38.462 0.00 0.00 37.25 4.18
5025 5183 6.018751 CCATTGTTTGATCGATTCATACTCGT 60.019 38.462 0.00 0.00 37.25 4.18
5026 5184 7.169140 CCATTGTTTGATCGATTCATACTCGTA 59.831 37.037 0.00 0.00 37.25 3.43
5027 5185 7.445900 TTGTTTGATCGATTCATACTCGTAC 57.554 36.000 0.00 0.00 37.25 3.67
5028 5186 6.557110 TGTTTGATCGATTCATACTCGTACA 58.443 36.000 0.00 0.00 37.25 2.90
5029 5187 6.691388 TGTTTGATCGATTCATACTCGTACAG 59.309 38.462 0.00 0.00 37.25 2.74
5030 5188 5.358298 TGATCGATTCATACTCGTACAGG 57.642 43.478 0.00 0.00 37.40 4.00
5031 5189 3.620929 TCGATTCATACTCGTACAGGC 57.379 47.619 0.00 0.00 37.40 4.85
5032 5190 2.946990 TCGATTCATACTCGTACAGGCA 59.053 45.455 0.00 0.00 37.40 4.75
5033 5191 3.043586 CGATTCATACTCGTACAGGCAC 58.956 50.000 0.00 0.00 0.00 5.01
5034 5192 3.243101 CGATTCATACTCGTACAGGCACT 60.243 47.826 0.00 0.00 43.88 4.40
5035 5193 4.683832 GATTCATACTCGTACAGGCACTT 58.316 43.478 0.00 0.00 34.60 3.16
5036 5194 5.505159 CGATTCATACTCGTACAGGCACTTA 60.505 44.000 0.00 0.00 34.60 2.24
5037 5195 5.847111 TTCATACTCGTACAGGCACTTAT 57.153 39.130 0.00 0.00 34.60 1.73
5038 5196 5.434352 TCATACTCGTACAGGCACTTATC 57.566 43.478 0.00 0.00 34.60 1.75
5039 5197 4.885325 TCATACTCGTACAGGCACTTATCA 59.115 41.667 0.00 0.00 34.60 2.15
5040 5198 3.505464 ACTCGTACAGGCACTTATCAC 57.495 47.619 0.00 0.00 34.60 3.06
5041 5199 2.159421 ACTCGTACAGGCACTTATCACG 60.159 50.000 0.00 0.00 34.60 4.35
5042 5200 2.086094 TCGTACAGGCACTTATCACGA 58.914 47.619 0.00 0.00 34.60 4.35
5043 5201 2.096980 TCGTACAGGCACTTATCACGAG 59.903 50.000 0.00 0.00 34.60 4.18
5044 5202 2.096980 CGTACAGGCACTTATCACGAGA 59.903 50.000 0.00 0.00 34.60 4.04
5045 5203 2.656560 ACAGGCACTTATCACGAGAC 57.343 50.000 0.00 0.00 34.60 3.36
5046 5204 1.204941 ACAGGCACTTATCACGAGACC 59.795 52.381 0.00 0.00 34.60 3.85
5047 5205 1.204704 CAGGCACTTATCACGAGACCA 59.795 52.381 0.00 0.00 34.60 4.02
5048 5206 2.111384 AGGCACTTATCACGAGACCAT 58.889 47.619 0.00 0.00 27.25 3.55
5049 5207 2.101582 AGGCACTTATCACGAGACCATC 59.898 50.000 0.00 0.00 27.25 3.51
5050 5208 2.159099 GGCACTTATCACGAGACCATCA 60.159 50.000 0.00 0.00 0.00 3.07
5051 5209 2.860735 GCACTTATCACGAGACCATCAC 59.139 50.000 0.00 0.00 0.00 3.06
5052 5210 3.676049 GCACTTATCACGAGACCATCACA 60.676 47.826 0.00 0.00 0.00 3.58
5053 5211 4.686972 CACTTATCACGAGACCATCACAT 58.313 43.478 0.00 0.00 0.00 3.21
5054 5212 4.742167 CACTTATCACGAGACCATCACATC 59.258 45.833 0.00 0.00 0.00 3.06
5055 5213 2.898729 ATCACGAGACCATCACATCC 57.101 50.000 0.00 0.00 0.00 3.51
5056 5214 1.555967 TCACGAGACCATCACATCCA 58.444 50.000 0.00 0.00 0.00 3.41
5057 5215 1.478105 TCACGAGACCATCACATCCAG 59.522 52.381 0.00 0.00 0.00 3.86
5058 5216 1.478105 CACGAGACCATCACATCCAGA 59.522 52.381 0.00 0.00 0.00 3.86
5059 5217 1.478510 ACGAGACCATCACATCCAGAC 59.521 52.381 0.00 0.00 0.00 3.51
5060 5218 1.202463 CGAGACCATCACATCCAGACC 60.202 57.143 0.00 0.00 0.00 3.85
5061 5219 1.139853 GAGACCATCACATCCAGACCC 59.860 57.143 0.00 0.00 0.00 4.46
5062 5220 0.179073 GACCATCACATCCAGACCCG 60.179 60.000 0.00 0.00 0.00 5.28
5063 5221 0.617535 ACCATCACATCCAGACCCGA 60.618 55.000 0.00 0.00 0.00 5.14
5064 5222 0.179073 CCATCACATCCAGACCCGAC 60.179 60.000 0.00 0.00 0.00 4.79
5065 5223 0.536724 CATCACATCCAGACCCGACA 59.463 55.000 0.00 0.00 0.00 4.35
5066 5224 0.537188 ATCACATCCAGACCCGACAC 59.463 55.000 0.00 0.00 0.00 3.67
5067 5225 1.446099 CACATCCAGACCCGACACG 60.446 63.158 0.00 0.00 0.00 4.49
5068 5226 1.605451 ACATCCAGACCCGACACGA 60.605 57.895 0.00 0.00 0.00 4.35
5069 5227 1.153823 CATCCAGACCCGACACGAC 60.154 63.158 0.00 0.00 0.00 4.34
5070 5228 1.605451 ATCCAGACCCGACACGACA 60.605 57.895 0.00 0.00 0.00 4.35
5071 5229 1.183030 ATCCAGACCCGACACGACAA 61.183 55.000 0.00 0.00 0.00 3.18
5072 5230 1.068417 CCAGACCCGACACGACAAA 59.932 57.895 0.00 0.00 0.00 2.83
5073 5231 1.219522 CCAGACCCGACACGACAAAC 61.220 60.000 0.00 0.00 0.00 2.93
5074 5232 0.528901 CAGACCCGACACGACAAACA 60.529 55.000 0.00 0.00 0.00 2.83
5075 5233 0.176219 AGACCCGACACGACAAACAA 59.824 50.000 0.00 0.00 0.00 2.83
5076 5234 1.008329 GACCCGACACGACAAACAAA 58.992 50.000 0.00 0.00 0.00 2.83
5077 5235 1.397692 GACCCGACACGACAAACAAAA 59.602 47.619 0.00 0.00 0.00 2.44
5078 5236 1.811359 ACCCGACACGACAAACAAAAA 59.189 42.857 0.00 0.00 0.00 1.94
5110 5268 9.880157 TGAGTTATTTTTAGTTATTACTCGGCT 57.120 29.630 0.00 0.00 34.70 5.52
5112 5270 9.880157 AGTTATTTTTAGTTATTACTCGGCTCA 57.120 29.630 0.00 0.00 35.78 4.26
5113 5271 9.911980 GTTATTTTTAGTTATTACTCGGCTCAC 57.088 33.333 0.00 0.00 35.78 3.51
5114 5272 9.656040 TTATTTTTAGTTATTACTCGGCTCACA 57.344 29.630 0.00 0.00 35.78 3.58
5115 5273 6.956299 TTTTAGTTATTACTCGGCTCACAC 57.044 37.500 0.00 0.00 35.78 3.82
5116 5274 3.146618 AGTTATTACTCGGCTCACACG 57.853 47.619 0.00 0.00 0.00 4.49
5117 5275 2.751259 AGTTATTACTCGGCTCACACGA 59.249 45.455 0.00 0.00 38.79 4.35
5124 5282 2.955402 GGCTCACACGAGACGACT 59.045 61.111 0.00 0.00 42.34 4.18
5125 5283 1.154188 GGCTCACACGAGACGACTC 60.154 63.158 4.73 4.73 42.34 3.36
5143 5301 2.103538 GGCTATTCCGTGACGCGA 59.896 61.111 15.93 0.00 44.77 5.87
5144 5302 1.517694 GGCTATTCCGTGACGCGAA 60.518 57.895 15.93 5.38 44.77 4.70
5145 5303 1.079875 GGCTATTCCGTGACGCGAAA 61.080 55.000 15.93 0.00 44.77 3.46
5146 5304 0.024619 GCTATTCCGTGACGCGAAAC 59.975 55.000 15.93 9.71 44.77 2.78
5147 5305 1.625616 CTATTCCGTGACGCGAAACT 58.374 50.000 15.93 0.00 44.77 2.66
5148 5306 1.990563 CTATTCCGTGACGCGAAACTT 59.009 47.619 15.93 0.00 44.77 2.66
5149 5307 0.511221 ATTCCGTGACGCGAAACTTG 59.489 50.000 15.93 4.66 44.77 3.16
5150 5308 1.492319 TTCCGTGACGCGAAACTTGG 61.492 55.000 15.93 8.23 44.77 3.61
5151 5309 2.549282 CGTGACGCGAAACTTGGG 59.451 61.111 15.93 0.00 44.77 4.12
5152 5310 2.943653 GTGACGCGAAACTTGGGG 59.056 61.111 15.93 0.00 0.00 4.96
5153 5311 2.281208 TGACGCGAAACTTGGGGG 60.281 61.111 15.93 0.00 0.00 5.40
5154 5312 3.733960 GACGCGAAACTTGGGGGC 61.734 66.667 15.93 0.00 0.00 5.80
5155 5313 4.572571 ACGCGAAACTTGGGGGCA 62.573 61.111 15.93 0.00 0.00 5.36
5156 5314 3.061848 CGCGAAACTTGGGGGCAT 61.062 61.111 0.00 0.00 0.00 4.40
5157 5315 1.747367 CGCGAAACTTGGGGGCATA 60.747 57.895 0.00 0.00 0.00 3.14
5158 5316 1.101049 CGCGAAACTTGGGGGCATAT 61.101 55.000 0.00 0.00 0.00 1.78
5159 5317 0.385390 GCGAAACTTGGGGGCATATG 59.615 55.000 0.00 0.00 0.00 1.78
5160 5318 2.021723 GCGAAACTTGGGGGCATATGA 61.022 52.381 6.97 0.00 0.00 2.15
5161 5319 2.586425 CGAAACTTGGGGGCATATGAT 58.414 47.619 6.97 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
700 734 2.942376 CAAGGAAGCATACGCATAACCA 59.058 45.455 0.00 0.00 42.27 3.67
1369 1432 7.514125 GCATCAGCAGTAAAGAAAAATAATGCG 60.514 37.037 0.00 0.00 45.05 4.73
1545 1649 6.663093 TGTGTGCCATAAGATTATGTTTTCCT 59.337 34.615 10.77 0.00 39.04 3.36
2236 2342 0.250510 TCTGGCGCACATACACCAAA 60.251 50.000 10.83 0.00 0.00 3.28
2504 2611 3.568443 TGATACCGTTGCCCTCTGTATA 58.432 45.455 0.00 0.00 0.00 1.47
3225 3339 5.794687 TGTAGAATGTCAATAAGCAACCG 57.205 39.130 0.00 0.00 0.00 4.44
3587 3716 0.394488 TGCTCCCTCACGAGACTAGG 60.394 60.000 0.00 0.00 30.97 3.02
3731 3862 3.132289 GCTGGTAGGTTGTGCATCTACTA 59.868 47.826 14.53 10.28 35.15 1.82
4211 4351 9.468532 GAGTTTAAAAGAAAACGAGTAGTCCTA 57.531 33.333 0.00 0.00 42.83 2.94
4315 4459 7.649533 TGAACCAATCATTCAGCATATTTCT 57.350 32.000 0.00 0.00 32.34 2.52
4388 4535 3.058016 GCAACACATGACACAGCAATACT 60.058 43.478 0.00 0.00 0.00 2.12
4506 4657 8.621286 AGCATTTACCAAATAATGTACTACTGC 58.379 33.333 0.00 0.00 34.88 4.40
4515 4667 6.474427 CAGCTGACAGCATTTACCAAATAATG 59.526 38.462 28.43 9.40 45.56 1.90
4801 4959 2.115427 CCTTTGTTTGGTTCAGGGGTT 58.885 47.619 0.00 0.00 0.00 4.11
4818 4976 9.764363 GGAATTTGACAGAAAATTAACTTCCTT 57.236 29.630 0.00 0.00 39.31 3.36
4899 5057 2.916269 TGGTTGTGGGATTAGACATGGA 59.084 45.455 0.00 0.00 0.00 3.41
4974 5132 4.261197 CCGGTTTTCTTGGTCTTTCTTCTG 60.261 45.833 0.00 0.00 0.00 3.02
4977 5135 3.893521 TCCGGTTTTCTTGGTCTTTCTT 58.106 40.909 0.00 0.00 0.00 2.52
4979 5137 3.190744 GGATCCGGTTTTCTTGGTCTTTC 59.809 47.826 0.00 0.00 0.00 2.62
4982 5140 1.702957 TGGATCCGGTTTTCTTGGTCT 59.297 47.619 7.39 0.00 0.00 3.85
4983 5141 2.194201 TGGATCCGGTTTTCTTGGTC 57.806 50.000 7.39 0.00 0.00 4.02
4984 5142 2.825532 CAATGGATCCGGTTTTCTTGGT 59.174 45.455 7.39 0.00 0.00 3.67
4985 5143 2.825532 ACAATGGATCCGGTTTTCTTGG 59.174 45.455 7.39 0.00 0.00 3.61
4986 5144 4.519540 AACAATGGATCCGGTTTTCTTG 57.480 40.909 7.39 4.37 0.00 3.02
4987 5145 4.586841 TCAAACAATGGATCCGGTTTTCTT 59.413 37.500 20.19 3.94 31.57 2.52
4988 5146 4.148838 TCAAACAATGGATCCGGTTTTCT 58.851 39.130 20.19 4.23 31.57 2.52
4989 5147 4.513198 TCAAACAATGGATCCGGTTTTC 57.487 40.909 20.19 0.00 31.57 2.29
4990 5148 4.380444 CGATCAAACAATGGATCCGGTTTT 60.380 41.667 20.19 11.30 37.26 2.43
4991 5149 3.128589 CGATCAAACAATGGATCCGGTTT 59.871 43.478 18.14 18.14 37.26 3.27
4992 5150 2.682856 CGATCAAACAATGGATCCGGTT 59.317 45.455 7.39 8.76 37.26 4.44
4993 5151 2.093181 TCGATCAAACAATGGATCCGGT 60.093 45.455 7.39 2.24 37.26 5.28
4994 5152 2.560504 TCGATCAAACAATGGATCCGG 58.439 47.619 7.39 0.00 37.26 5.14
4995 5153 4.273235 TGAATCGATCAAACAATGGATCCG 59.727 41.667 7.39 0.00 37.26 4.18
4996 5154 5.756195 TGAATCGATCAAACAATGGATCC 57.244 39.130 4.20 4.20 37.26 3.36
4997 5155 8.092521 AGTATGAATCGATCAAACAATGGATC 57.907 34.615 0.00 0.00 42.54 3.36
4998 5156 7.095481 CGAGTATGAATCGATCAAACAATGGAT 60.095 37.037 0.00 0.00 42.54 3.41
4999 5157 6.200854 CGAGTATGAATCGATCAAACAATGGA 59.799 38.462 0.00 0.00 42.54 3.41
5000 5158 6.018751 ACGAGTATGAATCGATCAAACAATGG 60.019 38.462 0.00 0.00 42.54 3.16
5001 5159 6.937457 ACGAGTATGAATCGATCAAACAATG 58.063 36.000 0.00 0.00 42.54 2.82
5002 5160 7.704899 TGTACGAGTATGAATCGATCAAACAAT 59.295 33.333 0.00 0.00 42.54 2.71
5003 5161 7.030768 TGTACGAGTATGAATCGATCAAACAA 58.969 34.615 0.00 0.00 42.54 2.83
5004 5162 6.557110 TGTACGAGTATGAATCGATCAAACA 58.443 36.000 0.00 0.00 42.54 2.83
5005 5163 6.142480 CCTGTACGAGTATGAATCGATCAAAC 59.858 42.308 0.00 0.00 42.54 2.93
5006 5164 6.206498 CCTGTACGAGTATGAATCGATCAAA 58.794 40.000 0.00 0.00 42.54 2.69
5007 5165 5.758924 CCTGTACGAGTATGAATCGATCAA 58.241 41.667 0.00 0.00 42.54 2.57
5008 5166 4.320275 GCCTGTACGAGTATGAATCGATCA 60.320 45.833 0.00 0.00 42.76 2.92
5009 5167 4.159857 GCCTGTACGAGTATGAATCGATC 58.840 47.826 0.00 0.00 42.76 3.69
5010 5168 3.568430 TGCCTGTACGAGTATGAATCGAT 59.432 43.478 3.09 0.00 42.76 3.59
5011 5169 2.946990 TGCCTGTACGAGTATGAATCGA 59.053 45.455 3.09 0.00 42.76 3.59
5012 5170 3.043586 GTGCCTGTACGAGTATGAATCG 58.956 50.000 0.00 0.00 45.54 3.34
5013 5171 4.308899 AGTGCCTGTACGAGTATGAATC 57.691 45.455 0.00 0.00 0.00 2.52
5014 5172 4.737855 AAGTGCCTGTACGAGTATGAAT 57.262 40.909 0.00 0.00 0.00 2.57
5015 5173 5.358725 TGATAAGTGCCTGTACGAGTATGAA 59.641 40.000 0.00 0.00 0.00 2.57
5016 5174 4.885325 TGATAAGTGCCTGTACGAGTATGA 59.115 41.667 0.00 0.00 0.00 2.15
5017 5175 4.976731 GTGATAAGTGCCTGTACGAGTATG 59.023 45.833 0.00 0.00 0.00 2.39
5018 5176 4.261072 CGTGATAAGTGCCTGTACGAGTAT 60.261 45.833 0.00 0.00 32.36 2.12
5019 5177 3.064408 CGTGATAAGTGCCTGTACGAGTA 59.936 47.826 0.00 0.00 32.36 2.59
5020 5178 2.159421 CGTGATAAGTGCCTGTACGAGT 60.159 50.000 0.00 0.00 32.36 4.18
5021 5179 2.096980 TCGTGATAAGTGCCTGTACGAG 59.903 50.000 0.00 0.00 34.63 4.18
5022 5180 2.086094 TCGTGATAAGTGCCTGTACGA 58.914 47.619 0.00 0.00 36.83 3.43
5023 5181 2.096980 TCTCGTGATAAGTGCCTGTACG 59.903 50.000 0.00 0.00 0.00 3.67
5024 5182 3.436496 GTCTCGTGATAAGTGCCTGTAC 58.564 50.000 0.00 0.00 0.00 2.90
5025 5183 2.426024 GGTCTCGTGATAAGTGCCTGTA 59.574 50.000 0.00 0.00 0.00 2.74
5026 5184 1.204941 GGTCTCGTGATAAGTGCCTGT 59.795 52.381 0.00 0.00 0.00 4.00
5027 5185 1.204704 TGGTCTCGTGATAAGTGCCTG 59.795 52.381 0.00 0.00 0.00 4.85
5028 5186 1.557099 TGGTCTCGTGATAAGTGCCT 58.443 50.000 0.00 0.00 0.00 4.75
5029 5187 2.159099 TGATGGTCTCGTGATAAGTGCC 60.159 50.000 0.00 0.00 0.00 5.01
5030 5188 2.860735 GTGATGGTCTCGTGATAAGTGC 59.139 50.000 0.00 0.00 0.00 4.40
5031 5189 4.110036 TGTGATGGTCTCGTGATAAGTG 57.890 45.455 0.00 0.00 0.00 3.16
5032 5190 4.202161 GGATGTGATGGTCTCGTGATAAGT 60.202 45.833 0.00 0.00 0.00 2.24
5033 5191 4.202151 TGGATGTGATGGTCTCGTGATAAG 60.202 45.833 0.00 0.00 0.00 1.73
5034 5192 3.704061 TGGATGTGATGGTCTCGTGATAA 59.296 43.478 0.00 0.00 0.00 1.75
5035 5193 3.295973 TGGATGTGATGGTCTCGTGATA 58.704 45.455 0.00 0.00 0.00 2.15
5036 5194 2.102084 CTGGATGTGATGGTCTCGTGAT 59.898 50.000 0.00 0.00 0.00 3.06
5037 5195 1.478105 CTGGATGTGATGGTCTCGTGA 59.522 52.381 0.00 0.00 0.00 4.35
5038 5196 1.478105 TCTGGATGTGATGGTCTCGTG 59.522 52.381 0.00 0.00 0.00 4.35
5039 5197 1.478510 GTCTGGATGTGATGGTCTCGT 59.521 52.381 0.00 0.00 0.00 4.18
5040 5198 1.202463 GGTCTGGATGTGATGGTCTCG 60.202 57.143 0.00 0.00 0.00 4.04
5041 5199 1.139853 GGGTCTGGATGTGATGGTCTC 59.860 57.143 0.00 0.00 0.00 3.36
5042 5200 1.207791 GGGTCTGGATGTGATGGTCT 58.792 55.000 0.00 0.00 0.00 3.85
5043 5201 0.179073 CGGGTCTGGATGTGATGGTC 60.179 60.000 0.00 0.00 0.00 4.02
5044 5202 0.617535 TCGGGTCTGGATGTGATGGT 60.618 55.000 0.00 0.00 0.00 3.55
5045 5203 0.179073 GTCGGGTCTGGATGTGATGG 60.179 60.000 0.00 0.00 0.00 3.51
5046 5204 0.536724 TGTCGGGTCTGGATGTGATG 59.463 55.000 0.00 0.00 0.00 3.07
5047 5205 0.537188 GTGTCGGGTCTGGATGTGAT 59.463 55.000 0.00 0.00 0.00 3.06
5048 5206 1.873270 CGTGTCGGGTCTGGATGTGA 61.873 60.000 0.00 0.00 0.00 3.58
5049 5207 1.446099 CGTGTCGGGTCTGGATGTG 60.446 63.158 0.00 0.00 0.00 3.21
5050 5208 1.605451 TCGTGTCGGGTCTGGATGT 60.605 57.895 0.00 0.00 0.00 3.06
5051 5209 1.153823 GTCGTGTCGGGTCTGGATG 60.154 63.158 0.00 0.00 0.00 3.51
5052 5210 1.183030 TTGTCGTGTCGGGTCTGGAT 61.183 55.000 0.00 0.00 0.00 3.41
5053 5211 1.393487 TTTGTCGTGTCGGGTCTGGA 61.393 55.000 0.00 0.00 0.00 3.86
5054 5212 1.068417 TTTGTCGTGTCGGGTCTGG 59.932 57.895 0.00 0.00 0.00 3.86
5055 5213 0.528901 TGTTTGTCGTGTCGGGTCTG 60.529 55.000 0.00 0.00 0.00 3.51
5056 5214 0.176219 TTGTTTGTCGTGTCGGGTCT 59.824 50.000 0.00 0.00 0.00 3.85
5057 5215 1.008329 TTTGTTTGTCGTGTCGGGTC 58.992 50.000 0.00 0.00 0.00 4.46
5058 5216 1.451067 TTTTGTTTGTCGTGTCGGGT 58.549 45.000 0.00 0.00 0.00 5.28
5059 5217 2.546195 TTTTTGTTTGTCGTGTCGGG 57.454 45.000 0.00 0.00 0.00 5.14
5084 5242 9.880157 AGCCGAGTAATAACTAAAAATAACTCA 57.120 29.630 0.00 0.00 35.56 3.41
5086 5244 9.880157 TGAGCCGAGTAATAACTAAAAATAACT 57.120 29.630 0.00 0.00 35.56 2.24
5087 5245 9.911980 GTGAGCCGAGTAATAACTAAAAATAAC 57.088 33.333 0.00 0.00 35.56 1.89
5088 5246 9.656040 TGTGAGCCGAGTAATAACTAAAAATAA 57.344 29.630 0.00 0.00 35.56 1.40
5089 5247 9.090692 GTGTGAGCCGAGTAATAACTAAAAATA 57.909 33.333 0.00 0.00 35.56 1.40
5090 5248 7.201496 CGTGTGAGCCGAGTAATAACTAAAAAT 60.201 37.037 0.00 0.00 35.56 1.82
5091 5249 6.089820 CGTGTGAGCCGAGTAATAACTAAAAA 59.910 38.462 0.00 0.00 35.56 1.94
5092 5250 5.574055 CGTGTGAGCCGAGTAATAACTAAAA 59.426 40.000 0.00 0.00 35.56 1.52
5093 5251 5.097529 CGTGTGAGCCGAGTAATAACTAAA 58.902 41.667 0.00 0.00 35.56 1.85
5094 5252 4.395854 TCGTGTGAGCCGAGTAATAACTAA 59.604 41.667 0.00 0.00 35.56 2.24
5095 5253 3.940852 TCGTGTGAGCCGAGTAATAACTA 59.059 43.478 0.00 0.00 35.56 2.24
5096 5254 2.751259 TCGTGTGAGCCGAGTAATAACT 59.249 45.455 0.00 0.00 39.21 2.24
5097 5255 3.106672 CTCGTGTGAGCCGAGTAATAAC 58.893 50.000 1.87 0.00 45.09 1.89
5098 5256 3.416119 CTCGTGTGAGCCGAGTAATAA 57.584 47.619 1.87 0.00 45.09 1.40
5099 5257 5.069221 CGTCTCGTGTGAGCCGAGTAATA 62.069 52.174 9.34 0.00 45.96 0.98
5100 5258 4.380030 CGTCTCGTGTGAGCCGAGTAAT 62.380 54.545 9.34 0.00 45.96 1.89
5101 5259 3.118637 CGTCTCGTGTGAGCCGAGTAA 62.119 57.143 9.34 0.00 45.96 2.24
5102 5260 1.632948 CGTCTCGTGTGAGCCGAGTA 61.633 60.000 9.34 0.00 45.96 2.59
5103 5261 2.967473 CGTCTCGTGTGAGCCGAGT 61.967 63.158 9.34 0.00 45.96 4.18
5104 5262 2.202362 CGTCTCGTGTGAGCCGAG 60.202 66.667 3.56 3.56 45.96 4.63
5106 5264 2.502080 GTCGTCTCGTGTGAGCCG 60.502 66.667 0.00 0.00 44.53 5.52
5107 5265 1.154188 GAGTCGTCTCGTGTGAGCC 60.154 63.158 0.00 0.00 42.26 4.70
5108 5266 4.443784 GAGTCGTCTCGTGTGAGC 57.556 61.111 0.00 0.00 42.26 4.26
5116 5274 3.849619 GGAATAGCCGAGTCGTCTC 57.150 57.895 12.31 0.00 37.35 3.36
5126 5284 1.079875 TTTCGCGTCACGGAATAGCC 61.080 55.000 5.77 0.00 43.89 3.93
5127 5285 0.024619 GTTTCGCGTCACGGAATAGC 59.975 55.000 5.77 0.00 42.46 2.97
5128 5286 1.625616 AGTTTCGCGTCACGGAATAG 58.374 50.000 5.77 0.00 42.46 1.73
5129 5287 1.722464 CAAGTTTCGCGTCACGGAATA 59.278 47.619 5.77 0.00 42.46 1.75
5130 5288 0.511221 CAAGTTTCGCGTCACGGAAT 59.489 50.000 5.77 0.00 42.46 3.01
5131 5289 1.492319 CCAAGTTTCGCGTCACGGAA 61.492 55.000 5.77 0.00 43.89 4.30
5132 5290 1.952133 CCAAGTTTCGCGTCACGGA 60.952 57.895 5.77 0.00 43.89 4.69
5133 5291 2.549282 CCAAGTTTCGCGTCACGG 59.451 61.111 5.77 2.40 43.89 4.94
5134 5292 2.549282 CCCAAGTTTCGCGTCACG 59.451 61.111 5.77 0.00 45.62 4.35
5135 5293 2.613506 CCCCCAAGTTTCGCGTCAC 61.614 63.158 5.77 3.91 0.00 3.67
5136 5294 2.281208 CCCCCAAGTTTCGCGTCA 60.281 61.111 5.77 0.00 0.00 4.35
5137 5295 3.733960 GCCCCCAAGTTTCGCGTC 61.734 66.667 5.77 0.00 0.00 5.19
5138 5296 2.472414 TATGCCCCCAAGTTTCGCGT 62.472 55.000 5.77 0.00 0.00 6.01
5139 5297 1.101049 ATATGCCCCCAAGTTTCGCG 61.101 55.000 0.00 0.00 0.00 5.87
5140 5298 0.385390 CATATGCCCCCAAGTTTCGC 59.615 55.000 0.00 0.00 0.00 4.70
5141 5299 2.051334 TCATATGCCCCCAAGTTTCG 57.949 50.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.