Multiple sequence alignment - TraesCS5D01G494900

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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 TraesCS5D01G494900 chr5D 100.000 3974 0 0 1 3974 526686396 526690369 0.000000e+00 7339.0
1 TraesCS5D01G494900 chr5D 87.079 178 20 2 3767 3942 526752802 526752978 8.710000e-47 198.0
2 TraesCS5D01G494900 chr5D 89.535 86 8 1 1 85 381780123 381780038 1.510000e-19 108.0
3 TraesCS5D01G494900 chr5D 89.535 86 7 2 1 84 479526392 479526477 1.510000e-19 108.0
4 TraesCS5D01G494900 chr5A 91.859 3599 165 56 444 3974 653847478 653851016 0.000000e+00 4905.0
5 TraesCS5D01G494900 chr5B 92.881 2978 89 48 228 3169 662453387 662456277 0.000000e+00 4211.0
6 TraesCS5D01G494900 chr5B 94.691 810 37 5 3166 3974 662456398 662457202 0.000000e+00 1253.0
7 TraesCS5D01G494900 chr2A 93.103 87 4 2 1 85 137133661 137133575 4.170000e-25 126.0
8 TraesCS5D01G494900 chr6D 92.857 84 4 2 1 82 396461631 396461548 1.940000e-23 121.0
9 TraesCS5D01G494900 chr6D 96.774 31 1 0 114 144 34737975 34737945 7.000000e-03 52.8
10 TraesCS5D01G494900 chr1A 90.909 88 5 2 1 85 396263506 396263419 9.020000e-22 115.0
11 TraesCS5D01G494900 chr4D 90.698 86 6 2 1 84 351675778 351675863 3.250000e-21 113.0
12 TraesCS5D01G494900 chr3D 89.247 93 7 3 3 93 535730197 535730106 3.250000e-21 113.0
13 TraesCS5D01G494900 chr2B 91.667 84 4 3 1 82 68259044 68259126 3.250000e-21 113.0
14 TraesCS5D01G494900 chr1D 90.000 90 5 4 1 88 486887596 486887509 3.250000e-21 113.0
15 TraesCS5D01G494900 chr7B 100.000 31 0 0 114 144 693794912 693794882 1.540000e-04 58.4


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 TraesCS5D01G494900 chr5D 526686396 526690369 3973 False 7339 7339 100.000 1 3974 1 chr5D.!!$F2 3973
1 TraesCS5D01G494900 chr5A 653847478 653851016 3538 False 4905 4905 91.859 444 3974 1 chr5A.!!$F1 3530
2 TraesCS5D01G494900 chr5B 662453387 662457202 3815 False 2732 4211 93.786 228 3974 2 chr5B.!!$F1 3746

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
299 300 0.038251 AGAAGATTCGTCGTGCAGCA 60.038 50.0 0.0 0.0 0.00 4.41 F
300 301 0.368227 GAAGATTCGTCGTGCAGCAG 59.632 55.0 0.0 0.0 0.00 4.24 F
1725 1809 0.108585 ACGGTGTCAACTGCATCCTT 59.891 50.0 0.0 0.0 35.97 3.36 F
2742 2826 0.179094 TTCTCAACGTGGTCGCTTGT 60.179 50.0 0.0 0.0 41.18 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 1588 0.108089 CTCTGTCTGCTGCTGCTGAT 60.108 55.0 23.97 0.0 46.12 2.90 R
2094 2178 0.322366 TTCTGATGAACGGGCATGCA 60.322 50.0 21.36 0.0 0.00 3.96 R
2823 2907 0.605589 CCGACTCTTGAAGCAGAGGT 59.394 55.0 4.05 0.0 44.23 3.85 R
3631 3850 0.951558 TTTCAAAGCGCTGTTCTCCC 59.048 50.0 12.58 0.0 0.00 4.30 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
17 18 2.438795 GCCCCCACGCCGATTTTA 60.439 61.111 0.00 0.00 0.00 1.52
18 19 2.478033 GCCCCCACGCCGATTTTAG 61.478 63.158 0.00 0.00 0.00 1.85
19 20 2.478033 CCCCCACGCCGATTTTAGC 61.478 63.158 0.00 0.00 0.00 3.09
24 25 4.293626 CGCCGATTTTAGCGCCGG 62.294 66.667 15.00 15.00 46.50 6.13
46 47 2.124487 CCCCAGGCGGCGATTTTA 60.124 61.111 12.98 0.00 0.00 1.52
47 48 2.478033 CCCCAGGCGGCGATTTTAC 61.478 63.158 12.98 0.00 0.00 2.01
48 49 1.747367 CCCAGGCGGCGATTTTACA 60.747 57.895 12.98 0.00 0.00 2.41
49 50 1.427819 CCAGGCGGCGATTTTACAC 59.572 57.895 12.98 0.00 0.00 2.90
50 51 1.060308 CAGGCGGCGATTTTACACG 59.940 57.895 12.98 0.00 0.00 4.49
57 58 3.146783 CGATTTTACACGCCCCTGA 57.853 52.632 0.00 0.00 0.00 3.86
58 59 1.444836 CGATTTTACACGCCCCTGAA 58.555 50.000 0.00 0.00 0.00 3.02
59 60 1.396996 CGATTTTACACGCCCCTGAAG 59.603 52.381 0.00 0.00 0.00 3.02
60 61 1.743394 GATTTTACACGCCCCTGAAGG 59.257 52.381 0.00 0.00 0.00 3.46
78 79 2.486966 GCCAACGGCTGAAGATGC 59.513 61.111 0.00 0.00 46.69 3.91
79 80 2.042831 GCCAACGGCTGAAGATGCT 61.043 57.895 0.00 0.00 46.69 3.79
80 81 1.986575 GCCAACGGCTGAAGATGCTC 61.987 60.000 0.00 0.00 46.69 4.26
81 82 0.392193 CCAACGGCTGAAGATGCTCT 60.392 55.000 0.00 0.00 0.00 4.09
82 83 1.134699 CCAACGGCTGAAGATGCTCTA 60.135 52.381 0.00 0.00 0.00 2.43
83 84 2.621338 CAACGGCTGAAGATGCTCTAA 58.379 47.619 0.00 0.00 0.00 2.10
84 85 2.593346 ACGGCTGAAGATGCTCTAAG 57.407 50.000 0.00 0.00 0.00 2.18
85 86 1.827969 ACGGCTGAAGATGCTCTAAGT 59.172 47.619 0.00 0.00 0.00 2.24
86 87 3.024547 ACGGCTGAAGATGCTCTAAGTA 58.975 45.455 0.00 0.00 0.00 2.24
87 88 3.181485 ACGGCTGAAGATGCTCTAAGTAC 60.181 47.826 0.00 0.00 0.00 2.73
88 89 3.181486 CGGCTGAAGATGCTCTAAGTACA 60.181 47.826 0.00 0.00 0.00 2.90
89 90 4.116238 GGCTGAAGATGCTCTAAGTACAC 58.884 47.826 0.00 0.00 0.00 2.90
90 91 4.382040 GGCTGAAGATGCTCTAAGTACACA 60.382 45.833 0.00 0.00 0.00 3.72
91 92 4.803088 GCTGAAGATGCTCTAAGTACACAG 59.197 45.833 0.00 0.00 0.00 3.66
92 93 5.623368 GCTGAAGATGCTCTAAGTACACAGT 60.623 44.000 0.00 0.00 0.00 3.55
93 94 5.714047 TGAAGATGCTCTAAGTACACAGTG 58.286 41.667 0.00 0.00 0.00 3.66
94 95 4.116747 AGATGCTCTAAGTACACAGTGC 57.883 45.455 0.00 11.65 33.10 4.40
95 96 3.511540 AGATGCTCTAAGTACACAGTGCA 59.488 43.478 19.32 19.32 43.17 4.57
96 97 3.026630 TGCTCTAAGTACACAGTGCAC 57.973 47.619 9.40 9.40 36.62 4.57
97 98 2.288825 TGCTCTAAGTACACAGTGCACC 60.289 50.000 14.63 0.00 36.62 5.01
98 99 2.931320 GCTCTAAGTACACAGTGCACCC 60.931 54.545 14.63 0.00 32.81 4.61
99 100 2.563179 CTCTAAGTACACAGTGCACCCT 59.437 50.000 14.63 0.00 0.00 4.34
100 101 2.299013 TCTAAGTACACAGTGCACCCTG 59.701 50.000 14.63 11.51 38.45 4.45
101 102 1.128200 AAGTACACAGTGCACCCTGA 58.872 50.000 14.63 0.00 36.30 3.86
102 103 0.681733 AGTACACAGTGCACCCTGAG 59.318 55.000 14.63 7.60 36.30 3.35
103 104 0.320771 GTACACAGTGCACCCTGAGG 60.321 60.000 14.63 7.05 36.30 3.86
140 141 3.540211 CAACGGCTGGAGATGTTCT 57.460 52.632 0.00 0.00 0.00 3.01
141 142 2.672961 CAACGGCTGGAGATGTTCTA 57.327 50.000 0.00 0.00 0.00 2.10
142 143 2.972625 CAACGGCTGGAGATGTTCTAA 58.027 47.619 0.00 0.00 0.00 2.10
143 144 2.932614 CAACGGCTGGAGATGTTCTAAG 59.067 50.000 0.00 0.00 0.00 2.18
144 145 2.180276 ACGGCTGGAGATGTTCTAAGT 58.820 47.619 0.00 0.00 0.00 2.24
145 146 3.362706 ACGGCTGGAGATGTTCTAAGTA 58.637 45.455 0.00 0.00 0.00 2.24
146 147 3.130693 ACGGCTGGAGATGTTCTAAGTAC 59.869 47.826 0.00 0.00 0.00 2.73
147 148 3.130516 CGGCTGGAGATGTTCTAAGTACA 59.869 47.826 0.00 0.00 0.00 2.90
148 149 4.434520 GGCTGGAGATGTTCTAAGTACAC 58.565 47.826 0.00 0.00 0.00 2.90
149 150 4.081642 GGCTGGAGATGTTCTAAGTACACA 60.082 45.833 0.00 0.00 0.00 3.72
150 151 5.105752 GCTGGAGATGTTCTAAGTACACAG 58.894 45.833 0.00 0.00 0.00 3.66
151 152 5.336849 GCTGGAGATGTTCTAAGTACACAGT 60.337 44.000 0.00 0.00 0.00 3.55
152 153 6.025749 TGGAGATGTTCTAAGTACACAGTG 57.974 41.667 0.00 0.00 0.00 3.66
153 154 4.865365 GGAGATGTTCTAAGTACACAGTGC 59.135 45.833 0.00 0.00 0.00 4.40
154 155 5.468540 AGATGTTCTAAGTACACAGTGCA 57.531 39.130 0.00 0.00 0.00 4.57
155 156 5.230942 AGATGTTCTAAGTACACAGTGCAC 58.769 41.667 9.40 9.40 0.00 4.57
156 157 3.724374 TGTTCTAAGTACACAGTGCACC 58.276 45.455 14.63 0.00 0.00 5.01
157 158 2.717580 TCTAAGTACACAGTGCACCG 57.282 50.000 14.63 5.70 0.00 4.94
158 159 1.271379 TCTAAGTACACAGTGCACCGG 59.729 52.381 14.63 9.04 0.00 5.28
159 160 1.271379 CTAAGTACACAGTGCACCGGA 59.729 52.381 14.63 0.00 0.00 5.14
160 161 0.685097 AAGTACACAGTGCACCGGAT 59.315 50.000 14.63 0.00 0.00 4.18
161 162 0.246635 AGTACACAGTGCACCGGATC 59.753 55.000 14.63 0.00 0.00 3.36
162 163 0.739813 GTACACAGTGCACCGGATCC 60.740 60.000 14.63 0.00 0.00 3.36
163 164 0.902984 TACACAGTGCACCGGATCCT 60.903 55.000 14.63 0.00 0.00 3.24
164 165 0.902984 ACACAGTGCACCGGATCCTA 60.903 55.000 14.63 0.00 0.00 2.94
165 166 0.249120 CACAGTGCACCGGATCCTAA 59.751 55.000 14.63 0.00 0.00 2.69
166 167 0.981183 ACAGTGCACCGGATCCTAAA 59.019 50.000 14.63 0.00 0.00 1.85
167 168 1.349688 ACAGTGCACCGGATCCTAAAA 59.650 47.619 14.63 0.00 0.00 1.52
168 169 2.224670 ACAGTGCACCGGATCCTAAAAA 60.225 45.455 14.63 0.00 0.00 1.94
188 189 3.775661 AAAAAGTACACAGTGCACCAC 57.224 42.857 14.63 4.18 34.10 4.16
189 190 1.675552 AAAGTACACAGTGCACCACC 58.324 50.000 14.63 0.00 34.49 4.61
190 191 0.531974 AAGTACACAGTGCACCACCG 60.532 55.000 14.63 2.17 34.49 4.94
191 192 2.280524 TACACAGTGCACCACCGC 60.281 61.111 14.63 0.00 34.49 5.68
192 193 3.095347 TACACAGTGCACCACCGCA 62.095 57.895 14.63 0.00 40.32 5.69
213 214 3.283684 TGCCGGTGCAAAACGAGG 61.284 61.111 1.90 0.00 46.66 4.63
214 215 4.700365 GCCGGTGCAAAACGAGGC 62.700 66.667 1.90 4.30 43.12 4.70
215 216 3.283684 CCGGTGCAAAACGAGGCA 61.284 61.111 8.11 0.00 37.77 4.75
216 217 2.718731 CGGTGCAAAACGAGGCAA 59.281 55.556 0.00 0.00 42.45 4.52
217 218 1.370414 CGGTGCAAAACGAGGCAAG 60.370 57.895 0.00 0.00 42.45 4.01
218 219 1.733526 GGTGCAAAACGAGGCAAGT 59.266 52.632 0.00 0.00 42.45 3.16
219 220 0.948678 GGTGCAAAACGAGGCAAGTA 59.051 50.000 0.00 0.00 42.45 2.24
220 221 1.069227 GGTGCAAAACGAGGCAAGTAG 60.069 52.381 0.00 0.00 42.45 2.57
221 222 0.591170 TGCAAAACGAGGCAAGTAGC 59.409 50.000 0.00 0.00 44.65 3.58
242 243 3.305110 CGTAACACCAAAAATGAGCCAC 58.695 45.455 0.00 0.00 0.00 5.01
252 253 0.928505 AATGAGCCACCCATCCATCA 59.071 50.000 0.00 0.00 0.00 3.07
253 254 0.928505 ATGAGCCACCCATCCATCAA 59.071 50.000 0.00 0.00 0.00 2.57
254 255 0.928505 TGAGCCACCCATCCATCAAT 59.071 50.000 0.00 0.00 0.00 2.57
255 256 1.133699 TGAGCCACCCATCCATCAATC 60.134 52.381 0.00 0.00 0.00 2.67
256 257 1.144503 GAGCCACCCATCCATCAATCT 59.855 52.381 0.00 0.00 0.00 2.40
257 258 1.144503 AGCCACCCATCCATCAATCTC 59.855 52.381 0.00 0.00 0.00 2.75
265 266 1.595382 CCATCAATCTCCCGCCGTC 60.595 63.158 0.00 0.00 0.00 4.79
271 272 1.683418 AATCTCCCGCCGTCTAACCC 61.683 60.000 0.00 0.00 0.00 4.11
288 289 3.606826 CGCGAGCGGAGAAGATTC 58.393 61.111 9.90 0.00 35.56 2.52
291 292 1.203600 GCGAGCGGAGAAGATTCGTC 61.204 60.000 0.00 0.00 34.05 4.20
293 294 0.099082 GAGCGGAGAAGATTCGTCGT 59.901 55.000 10.51 1.55 32.89 4.34
297 298 1.272781 GGAGAAGATTCGTCGTGCAG 58.727 55.000 0.00 0.00 0.00 4.41
298 299 0.642800 GAGAAGATTCGTCGTGCAGC 59.357 55.000 0.00 0.00 0.00 5.25
299 300 0.038251 AGAAGATTCGTCGTGCAGCA 60.038 50.000 0.00 0.00 0.00 4.41
300 301 0.368227 GAAGATTCGTCGTGCAGCAG 59.632 55.000 0.00 0.00 0.00 4.24
301 302 1.630244 AAGATTCGTCGTGCAGCAGC 61.630 55.000 0.00 0.00 42.57 5.25
313 314 2.280389 AGCAGCACGTGGTGACTG 60.280 61.111 42.62 28.36 45.66 3.51
353 354 2.395353 CCCCATTCCCTTCTCCCCC 61.395 68.421 0.00 0.00 0.00 5.40
368 369 4.159108 CCCCGCTACCTCCTCCCT 62.159 72.222 0.00 0.00 0.00 4.20
369 370 2.522193 CCCGCTACCTCCTCCCTC 60.522 72.222 0.00 0.00 0.00 4.30
370 371 2.522193 CCGCTACCTCCTCCCTCC 60.522 72.222 0.00 0.00 0.00 4.30
371 372 2.604152 CGCTACCTCCTCCCTCCT 59.396 66.667 0.00 0.00 0.00 3.69
372 373 1.529713 CGCTACCTCCTCCCTCCTC 60.530 68.421 0.00 0.00 0.00 3.71
429 430 2.124736 CAATCCCCGTCGCCACAT 60.125 61.111 0.00 0.00 0.00 3.21
431 432 3.733344 AATCCCCGTCGCCACATCG 62.733 63.158 0.00 0.00 0.00 3.84
462 473 8.771920 TTATTATTACTGCCGGTAATCTGATG 57.228 34.615 12.11 0.00 44.98 3.07
688 716 1.306226 AGCCTCGGGGTTTCTAGCT 60.306 57.895 1.62 0.00 34.45 3.32
734 762 1.739067 CTCCCGCGATTTCTTTTCCT 58.261 50.000 8.23 0.00 0.00 3.36
739 767 3.057526 CCCGCGATTTCTTTTCCTTTTCT 60.058 43.478 8.23 0.00 0.00 2.52
762 790 4.680237 CGCCTCTCCCACGCAACA 62.680 66.667 0.00 0.00 0.00 3.33
764 792 2.046892 CCTCTCCCACGCAACAGG 60.047 66.667 0.00 0.00 0.00 4.00
765 793 2.743928 CTCTCCCACGCAACAGGC 60.744 66.667 0.00 0.00 39.90 4.85
780 808 2.503546 GGCTGCTACTGGCCTCTC 59.496 66.667 3.32 0.00 44.48 3.20
783 811 1.821936 CTGCTACTGGCCTCTCCTG 59.178 63.158 3.32 0.00 40.92 3.86
797 825 0.622665 CTCCTGGGTCCTGCAAGAAT 59.377 55.000 0.00 0.00 34.07 2.40
830 861 1.644509 GGTTGATTTTCCCTGCCCTT 58.355 50.000 0.00 0.00 0.00 3.95
913 972 2.671963 GGAGGTGGGGTTTGCGTC 60.672 66.667 0.00 0.00 0.00 5.19
974 1039 1.633852 CGGCAGCAGAGTCTTCAAGC 61.634 60.000 0.00 0.00 0.00 4.01
1017 1086 1.026718 CCATGGGTTCTTGCGAGGAC 61.027 60.000 2.85 3.42 0.00 3.85
1099 1168 1.842381 CTTCTCCCTCCACCACCACC 61.842 65.000 0.00 0.00 0.00 4.61
1104 1173 2.431683 CTCCACCACCACCACCAG 59.568 66.667 0.00 0.00 0.00 4.00
1110 1179 2.906897 CACCACCACCAGCACCAC 60.907 66.667 0.00 0.00 0.00 4.16
1504 1588 1.839994 GAGGATCCCCTGACATGTTCA 59.160 52.381 8.55 0.00 44.53 3.18
1513 1597 2.081462 CTGACATGTTCATCAGCAGCA 58.919 47.619 0.00 0.00 36.22 4.41
1514 1598 2.081462 TGACATGTTCATCAGCAGCAG 58.919 47.619 0.00 0.00 0.00 4.24
1515 1599 0.809385 ACATGTTCATCAGCAGCAGC 59.191 50.000 0.00 0.00 42.56 5.25
1539 1623 1.073897 GAGCTCCTGCCAGTTGGTT 59.926 57.895 0.87 0.00 40.80 3.67
1725 1809 0.108585 ACGGTGTCAACTGCATCCTT 59.891 50.000 0.00 0.00 35.97 3.36
1740 1824 4.749310 CTTCAGTCGCCGCTGCCT 62.749 66.667 4.07 0.00 36.49 4.75
1941 2025 1.528586 CAGATTAGGCGGCATTCTTCG 59.471 52.381 13.08 0.00 0.00 3.79
1980 2064 0.533755 AGAGGCTGGCGCATTACATC 60.534 55.000 10.83 2.30 38.10 3.06
2058 2142 3.411351 GCGCGGCGAACTTCTTCA 61.411 61.111 28.54 0.00 0.00 3.02
2094 2178 9.512588 CTGAAAATATTCAAGCTATATGGGACT 57.487 33.333 0.00 0.00 44.64 3.85
2112 2196 0.745486 CTGCATGCCCGTTCATCAGA 60.745 55.000 16.68 0.00 30.37 3.27
2229 2313 1.614903 CAGTGGCCAATCTTCTTGCAA 59.385 47.619 7.24 0.00 0.00 4.08
2421 2505 1.000283 GATGCCATCCGAGTCGAAGAT 60.000 52.381 15.64 6.27 40.67 2.40
2524 2608 1.950973 GAGCCCGAGGAAGACAGTCC 61.951 65.000 0.00 0.00 38.03 3.85
2589 2673 2.825532 GGTTGTCAATGGCACCTACAAT 59.174 45.455 11.89 0.00 33.10 2.71
2640 2724 4.357325 AGGCTCTGTTCTATTTCTCCTCA 58.643 43.478 0.00 0.00 0.00 3.86
2742 2826 0.179094 TTCTCAACGTGGTCGCTTGT 60.179 50.000 0.00 0.00 41.18 3.16
2823 2907 2.602676 GGCAGGGTTCAGGCAGGTA 61.603 63.158 0.00 0.00 0.00 3.08
2877 2961 7.042389 GCAAGATACAAGGTAATCAAGAGCTAC 60.042 40.741 0.00 0.00 0.00 3.58
3037 3121 9.748708 TTTTTCTTTGATCGAATTTTCATCACT 57.251 25.926 0.00 0.00 30.28 3.41
3038 3122 9.748708 TTTTCTTTGATCGAATTTTCATCACTT 57.251 25.926 0.00 0.00 30.28 3.16
3248 3459 9.687210 CTGATTTTTCATTTCTCAGTTCAATGA 57.313 29.630 0.00 0.00 35.56 2.57
3286 3497 5.348179 GCTGCTGAGTGATATATTAGCTGTG 59.652 44.000 0.00 0.00 34.12 3.66
3441 3654 6.382869 AGAAAATCTCGGGAAAATGCATAG 57.617 37.500 0.00 0.00 0.00 2.23
3467 3680 2.945080 TCTCCAATCTCCATGCATCC 57.055 50.000 0.00 0.00 0.00 3.51
3554 3767 3.701205 ATGCACAAGGATACACACTCA 57.299 42.857 0.00 0.00 41.41 3.41
3609 3828 5.415415 CACTTATGCTCCTTAACTGATGC 57.585 43.478 0.00 0.00 0.00 3.91
3631 3850 1.528309 AAAACCGGGCTGTGACCTG 60.528 57.895 6.32 0.00 35.68 4.00
3659 3878 2.904932 CAGCGCTTTGAAATCTTTCGTC 59.095 45.455 7.50 0.00 40.01 4.20
3776 3995 6.214191 TCAGAATGATAGTCCTCAAGTGTC 57.786 41.667 0.00 0.00 42.56 3.67
3778 3997 6.041511 CAGAATGATAGTCCTCAAGTGTCTG 58.958 44.000 0.00 0.00 39.69 3.51
3779 3998 5.719085 AGAATGATAGTCCTCAAGTGTCTGT 59.281 40.000 0.00 0.00 0.00 3.41
3780 3999 5.590530 ATGATAGTCCTCAAGTGTCTGTC 57.409 43.478 0.00 0.00 0.00 3.51
3783 4002 1.689273 AGTCCTCAAGTGTCTGTCCAC 59.311 52.381 0.00 0.00 35.53 4.02
3784 4003 1.412710 GTCCTCAAGTGTCTGTCCACA 59.587 52.381 0.00 0.00 37.82 4.17
3785 4004 1.688735 TCCTCAAGTGTCTGTCCACAG 59.311 52.381 0.00 0.00 45.08 3.66
3800 4019 3.189287 GTCCACAGAAATACAGTTGCAGG 59.811 47.826 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.438795 TAAAATCGGCGTGGGGGC 60.439 61.111 6.85 0.00 37.98 5.80
1 2 2.478033 GCTAAAATCGGCGTGGGGG 61.478 63.158 6.85 0.00 0.00 5.40
2 3 2.819552 CGCTAAAATCGGCGTGGGG 61.820 63.158 6.85 0.00 45.34 4.96
3 4 2.707039 CGCTAAAATCGGCGTGGG 59.293 61.111 6.85 0.00 45.34 4.61
9 10 2.895372 AGCCGGCGCTAAAATCGG 60.895 61.111 23.20 15.00 46.08 4.18
30 31 1.747367 TGTAAAATCGCCGCCTGGG 60.747 57.895 0.00 0.00 39.58 4.45
31 32 1.427819 GTGTAAAATCGCCGCCTGG 59.572 57.895 0.00 0.00 38.77 4.45
32 33 1.060308 CGTGTAAAATCGCCGCCTG 59.940 57.895 0.00 0.00 0.00 4.85
33 34 2.746803 GCGTGTAAAATCGCCGCCT 61.747 57.895 0.00 0.00 45.54 5.52
34 35 2.277057 GCGTGTAAAATCGCCGCC 60.277 61.111 0.00 0.00 45.54 6.13
39 40 1.396996 CTTCAGGGGCGTGTAAAATCG 59.603 52.381 0.00 0.00 0.00 3.34
40 41 1.743394 CCTTCAGGGGCGTGTAAAATC 59.257 52.381 0.00 0.00 0.00 2.17
41 42 1.834188 CCTTCAGGGGCGTGTAAAAT 58.166 50.000 0.00 0.00 0.00 1.82
42 43 3.332706 CCTTCAGGGGCGTGTAAAA 57.667 52.632 0.00 0.00 0.00 1.52
62 63 2.093216 GAGCATCTTCAGCCGTTGG 58.907 57.895 0.00 0.00 0.00 3.77
71 72 7.818148 GTGCACTGTGTACTTAGAGCATCTTC 61.818 46.154 19.74 7.92 41.30 2.87
72 73 6.080173 GTGCACTGTGTACTTAGAGCATCTT 61.080 44.000 19.74 0.00 41.30 2.40
73 74 4.619394 GTGCACTGTGTACTTAGAGCATCT 60.619 45.833 19.74 0.00 41.30 2.90
74 75 3.614616 GTGCACTGTGTACTTAGAGCATC 59.385 47.826 19.74 12.05 41.30 3.91
75 76 3.589988 GTGCACTGTGTACTTAGAGCAT 58.410 45.455 19.74 0.00 41.30 3.79
76 77 2.288825 GGTGCACTGTGTACTTAGAGCA 60.289 50.000 24.55 14.37 38.01 4.26
77 78 2.338500 GGTGCACTGTGTACTTAGAGC 58.662 52.381 24.55 6.91 33.35 4.09
78 79 2.563179 AGGGTGCACTGTGTACTTAGAG 59.437 50.000 24.55 0.00 33.35 2.43
79 80 2.299013 CAGGGTGCACTGTGTACTTAGA 59.701 50.000 24.55 0.00 33.35 2.10
80 81 2.299013 TCAGGGTGCACTGTGTACTTAG 59.701 50.000 24.55 15.57 39.48 2.18
81 82 2.299013 CTCAGGGTGCACTGTGTACTTA 59.701 50.000 24.55 9.87 39.48 2.24
82 83 1.070758 CTCAGGGTGCACTGTGTACTT 59.929 52.381 24.55 13.09 39.48 2.24
83 84 0.681733 CTCAGGGTGCACTGTGTACT 59.318 55.000 24.55 6.93 39.48 2.73
84 85 0.320771 CCTCAGGGTGCACTGTGTAC 60.321 60.000 18.99 18.99 39.48 2.90
85 86 1.480212 CCCTCAGGGTGCACTGTGTA 61.480 60.000 17.98 1.30 38.25 2.90
86 87 2.822637 CCCTCAGGGTGCACTGTGT 61.823 63.158 17.98 0.00 38.25 3.72
87 88 2.033141 CCCTCAGGGTGCACTGTG 59.967 66.667 17.98 14.18 38.25 3.66
122 123 2.672961 TAGAACATCTCCAGCCGTTG 57.327 50.000 0.00 0.00 0.00 4.10
123 124 2.567615 ACTTAGAACATCTCCAGCCGTT 59.432 45.455 0.00 0.00 0.00 4.44
124 125 2.180276 ACTTAGAACATCTCCAGCCGT 58.820 47.619 0.00 0.00 0.00 5.68
125 126 2.969628 ACTTAGAACATCTCCAGCCG 57.030 50.000 0.00 0.00 0.00 5.52
126 127 4.081642 TGTGTACTTAGAACATCTCCAGCC 60.082 45.833 0.00 0.00 0.00 4.85
127 128 5.073311 TGTGTACTTAGAACATCTCCAGC 57.927 43.478 0.00 0.00 0.00 4.85
128 129 6.096036 CACTGTGTACTTAGAACATCTCCAG 58.904 44.000 0.00 0.00 0.00 3.86
129 130 5.566826 GCACTGTGTACTTAGAACATCTCCA 60.567 44.000 9.86 0.00 0.00 3.86
130 131 4.865365 GCACTGTGTACTTAGAACATCTCC 59.135 45.833 9.86 0.00 0.00 3.71
131 132 5.346281 GTGCACTGTGTACTTAGAACATCTC 59.654 44.000 19.74 0.00 30.04 2.75
132 133 5.230942 GTGCACTGTGTACTTAGAACATCT 58.769 41.667 19.74 0.00 30.04 2.90
133 134 4.389077 GGTGCACTGTGTACTTAGAACATC 59.611 45.833 24.55 4.99 33.35 3.06
134 135 4.315803 GGTGCACTGTGTACTTAGAACAT 58.684 43.478 24.55 0.00 33.35 2.71
135 136 3.724374 GGTGCACTGTGTACTTAGAACA 58.276 45.455 24.55 2.37 33.35 3.18
136 137 2.729882 CGGTGCACTGTGTACTTAGAAC 59.270 50.000 24.55 9.19 33.35 3.01
137 138 2.288579 CCGGTGCACTGTGTACTTAGAA 60.289 50.000 24.55 0.00 33.35 2.10
138 139 1.271379 CCGGTGCACTGTGTACTTAGA 59.729 52.381 24.55 0.00 33.35 2.10
139 140 1.271379 TCCGGTGCACTGTGTACTTAG 59.729 52.381 24.55 16.81 33.35 2.18
140 141 1.330234 TCCGGTGCACTGTGTACTTA 58.670 50.000 24.55 10.59 33.35 2.24
141 142 0.685097 ATCCGGTGCACTGTGTACTT 59.315 50.000 24.55 8.27 33.35 2.24
142 143 0.246635 GATCCGGTGCACTGTGTACT 59.753 55.000 24.55 8.36 33.35 2.73
143 144 0.739813 GGATCCGGTGCACTGTGTAC 60.740 60.000 23.77 18.99 31.96 2.90
144 145 0.902984 AGGATCCGGTGCACTGTGTA 60.903 55.000 23.77 9.74 0.00 2.90
145 146 0.902984 TAGGATCCGGTGCACTGTGT 60.903 55.000 23.77 12.01 0.00 3.72
146 147 0.249120 TTAGGATCCGGTGCACTGTG 59.751 55.000 23.77 15.12 0.00 3.66
147 148 0.981183 TTTAGGATCCGGTGCACTGT 59.019 50.000 23.77 6.71 0.00 3.55
148 149 2.107950 TTTTAGGATCCGGTGCACTG 57.892 50.000 19.25 19.25 0.00 3.66
149 150 2.871096 TTTTTAGGATCCGGTGCACT 57.129 45.000 17.98 0.00 0.00 4.40
168 169 2.425668 GGTGGTGCACTGTGTACTTTTT 59.574 45.455 24.55 0.00 33.35 1.94
169 170 2.021457 GGTGGTGCACTGTGTACTTTT 58.979 47.619 24.55 0.00 33.35 2.27
170 171 1.675552 GGTGGTGCACTGTGTACTTT 58.324 50.000 24.55 0.00 33.35 2.66
171 172 0.531974 CGGTGGTGCACTGTGTACTT 60.532 55.000 24.55 0.00 36.14 2.24
172 173 1.069090 CGGTGGTGCACTGTGTACT 59.931 57.895 24.55 0.00 36.14 2.73
173 174 2.604174 GCGGTGGTGCACTGTGTAC 61.604 63.158 18.99 18.99 42.21 2.90
174 175 2.280524 GCGGTGGTGCACTGTGTA 60.281 61.111 17.98 1.30 42.21 2.90
175 176 4.481617 TGCGGTGGTGCACTGTGT 62.482 61.111 17.98 0.00 42.21 3.72
197 198 4.700365 GCCTCGTTTTGCACCGGC 62.700 66.667 0.00 0.00 41.68 6.13
198 199 2.731587 CTTGCCTCGTTTTGCACCGG 62.732 60.000 0.00 0.00 37.18 5.28
199 200 1.370414 CTTGCCTCGTTTTGCACCG 60.370 57.895 0.00 0.00 37.18 4.94
200 201 0.948678 TACTTGCCTCGTTTTGCACC 59.051 50.000 0.00 0.00 37.18 5.01
201 202 1.663161 GCTACTTGCCTCGTTTTGCAC 60.663 52.381 0.00 0.00 37.18 4.57
202 203 0.591170 GCTACTTGCCTCGTTTTGCA 59.409 50.000 0.00 0.00 35.15 4.08
203 204 0.452784 CGCTACTTGCCTCGTTTTGC 60.453 55.000 0.00 0.00 38.78 3.68
204 205 0.865769 ACGCTACTTGCCTCGTTTTG 59.134 50.000 0.00 0.00 38.78 2.44
205 206 2.443887 TACGCTACTTGCCTCGTTTT 57.556 45.000 0.00 0.00 38.78 2.43
206 207 2.064014 GTTACGCTACTTGCCTCGTTT 58.936 47.619 0.00 0.00 38.78 3.60
207 208 1.000060 TGTTACGCTACTTGCCTCGTT 60.000 47.619 0.00 0.00 38.78 3.85
208 209 0.599558 TGTTACGCTACTTGCCTCGT 59.400 50.000 0.00 0.00 38.78 4.18
209 210 0.989890 GTGTTACGCTACTTGCCTCG 59.010 55.000 0.00 0.00 38.78 4.63
210 211 1.337447 TGGTGTTACGCTACTTGCCTC 60.337 52.381 0.00 0.00 38.78 4.70
211 212 0.682852 TGGTGTTACGCTACTTGCCT 59.317 50.000 0.00 0.00 38.78 4.75
212 213 1.515081 TTGGTGTTACGCTACTTGCC 58.485 50.000 0.00 0.00 38.78 4.52
213 214 3.612472 TTTTGGTGTTACGCTACTTGC 57.388 42.857 0.00 0.00 38.57 4.01
214 215 5.753744 TCATTTTTGGTGTTACGCTACTTG 58.246 37.500 0.00 0.00 0.00 3.16
215 216 5.562113 GCTCATTTTTGGTGTTACGCTACTT 60.562 40.000 0.00 0.00 0.00 2.24
216 217 4.083484 GCTCATTTTTGGTGTTACGCTACT 60.083 41.667 0.00 0.00 0.00 2.57
217 218 4.156182 GCTCATTTTTGGTGTTACGCTAC 58.844 43.478 0.00 0.00 0.00 3.58
218 219 3.189702 GGCTCATTTTTGGTGTTACGCTA 59.810 43.478 0.00 0.00 0.00 4.26
219 220 2.030274 GGCTCATTTTTGGTGTTACGCT 60.030 45.455 0.00 0.00 0.00 5.07
220 221 2.287909 TGGCTCATTTTTGGTGTTACGC 60.288 45.455 0.00 0.00 0.00 4.42
221 222 3.305110 GTGGCTCATTTTTGGTGTTACG 58.695 45.455 0.00 0.00 0.00 3.18
222 223 3.554129 GGGTGGCTCATTTTTGGTGTTAC 60.554 47.826 0.00 0.00 0.00 2.50
223 224 2.630580 GGGTGGCTCATTTTTGGTGTTA 59.369 45.455 0.00 0.00 0.00 2.41
224 225 1.416030 GGGTGGCTCATTTTTGGTGTT 59.584 47.619 0.00 0.00 0.00 3.32
225 226 1.047801 GGGTGGCTCATTTTTGGTGT 58.952 50.000 0.00 0.00 0.00 4.16
226 227 1.047002 TGGGTGGCTCATTTTTGGTG 58.953 50.000 0.00 0.00 0.00 4.17
242 243 0.607489 GCGGGAGATTGATGGATGGG 60.607 60.000 0.00 0.00 0.00 4.00
252 253 1.683418 GGGTTAGACGGCGGGAGATT 61.683 60.000 13.24 0.00 0.00 2.40
253 254 2.132352 GGGTTAGACGGCGGGAGAT 61.132 63.158 13.24 0.00 0.00 2.75
254 255 2.757099 GGGTTAGACGGCGGGAGA 60.757 66.667 13.24 0.00 0.00 3.71
255 256 4.203076 CGGGTTAGACGGCGGGAG 62.203 72.222 13.24 0.00 0.00 4.30
271 272 2.289375 CGAATCTTCTCCGCTCGCG 61.289 63.158 0.00 0.00 39.44 5.87
297 298 4.017877 GCAGTCACCACGTGCTGC 62.018 66.667 23.71 23.71 46.66 5.25
298 299 3.705638 CGCAGTCACCACGTGCTG 61.706 66.667 10.91 13.03 39.12 4.41
299 300 4.221422 ACGCAGTCACCACGTGCT 62.221 61.111 10.91 0.00 29.74 4.40
353 354 2.522193 GGAGGGAGGAGGTAGCGG 60.522 72.222 0.00 0.00 0.00 5.52
355 356 1.152419 GGAGGAGGGAGGAGGTAGC 60.152 68.421 0.00 0.00 0.00 3.58
356 357 1.002242 AGGGAGGAGGGAGGAGGTAG 61.002 65.000 0.00 0.00 0.00 3.18
357 358 1.000041 GAGGGAGGAGGGAGGAGGTA 61.000 65.000 0.00 0.00 0.00 3.08
358 359 2.204705 AGGGAGGAGGGAGGAGGT 60.205 66.667 0.00 0.00 0.00 3.85
359 360 2.612251 GAGGGAGGAGGGAGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
360 361 2.612251 GGAGGGAGGAGGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
361 362 3.430497 CGGAGGGAGGAGGGAGGA 61.430 72.222 0.00 0.00 0.00 3.71
362 363 3.430497 TCGGAGGGAGGAGGGAGG 61.430 72.222 0.00 0.00 0.00 4.30
363 364 2.197324 CTCGGAGGGAGGAGGGAG 59.803 72.222 0.00 0.00 39.22 4.30
364 365 2.286962 TCTCGGAGGGAGGAGGGA 60.287 66.667 4.96 0.00 43.34 4.20
365 366 2.123640 GTCTCGGAGGGAGGAGGG 60.124 72.222 4.96 0.00 43.34 4.30
366 367 2.517402 CGTCTCGGAGGGAGGAGG 60.517 72.222 4.96 0.00 43.34 4.30
367 368 1.820481 GTCGTCTCGGAGGGAGGAG 60.820 68.421 4.96 0.00 43.34 3.69
368 369 2.271497 GTCGTCTCGGAGGGAGGA 59.729 66.667 4.96 0.00 43.34 3.71
369 370 2.829458 GGTCGTCTCGGAGGGAGG 60.829 72.222 4.96 0.00 43.34 4.30
370 371 2.045242 TGGTCGTCTCGGAGGGAG 60.045 66.667 4.96 0.00 44.58 4.30
371 372 2.045242 CTGGTCGTCTCGGAGGGA 60.045 66.667 4.96 0.42 0.00 4.20
372 373 3.141488 CCTGGTCGTCTCGGAGGG 61.141 72.222 4.96 0.00 0.00 4.30
399 400 2.825836 GATTGCGCCACCTCCTGG 60.826 66.667 4.18 0.00 44.08 4.45
400 401 2.825836 GGATTGCGCCACCTCCTG 60.826 66.667 4.18 0.00 0.00 3.86
401 402 4.115199 GGGATTGCGCCACCTCCT 62.115 66.667 4.18 0.00 0.00 3.69
431 432 5.447624 ACCGGCAGTAATAATAAAATGGC 57.552 39.130 0.00 0.00 0.00 4.40
462 473 1.040339 AGTGGAGCGGGAGTGATCTC 61.040 60.000 0.00 0.00 39.76 2.75
616 644 2.616458 GGGTGATTGGTGGGGAGCT 61.616 63.158 0.00 0.00 0.00 4.09
734 762 4.329545 AGAGGCGGCGGCAGAAAA 62.330 61.111 34.87 0.00 42.47 2.29
764 792 2.063378 AGGAGAGGCCAGTAGCAGC 61.063 63.158 5.01 0.00 46.50 5.25
765 793 1.684386 CCAGGAGAGGCCAGTAGCAG 61.684 65.000 5.01 0.00 46.50 4.24
780 808 0.329261 TGATTCTTGCAGGACCCAGG 59.671 55.000 0.00 0.00 0.00 4.45
783 811 0.038166 TGGTGATTCTTGCAGGACCC 59.962 55.000 0.00 0.00 0.00 4.46
830 861 1.071699 CGAACTGGACAAGAAAGGGGA 59.928 52.381 0.00 0.00 0.00 4.81
913 972 2.661504 CGAGATCTCGCAGTACTCAG 57.338 55.000 30.41 2.44 46.50 3.35
956 1021 0.604780 TGCTTGAAGACTCTGCTGCC 60.605 55.000 0.00 0.00 0.00 4.85
974 1039 0.905357 ACGATCCACCTCCTTCCTTG 59.095 55.000 0.00 0.00 0.00 3.61
1099 1168 2.981909 CTGCTGGTGGTGCTGGTG 60.982 66.667 0.00 0.00 0.00 4.17
1504 1588 0.108089 CTCTGTCTGCTGCTGCTGAT 60.108 55.000 23.97 0.00 46.12 2.90
1539 1623 1.218047 CTTCACGGAATCGCAGGGA 59.782 57.895 0.00 0.00 40.63 4.20
1980 2064 2.663188 GCCTCGAGCCCATTAGCG 60.663 66.667 6.99 0.00 38.01 4.26
2094 2178 0.322366 TTCTGATGAACGGGCATGCA 60.322 50.000 21.36 0.00 0.00 3.96
2112 2196 4.466370 TCATTCGAGTAGAACCTGGACATT 59.534 41.667 0.00 0.00 42.39 2.71
2421 2505 3.018423 TCATCCTTGTCGATCCTGAGA 57.982 47.619 0.00 0.00 0.00 3.27
2524 2608 4.115401 TCATCTTCCTGATCGTGTTCAG 57.885 45.455 1.72 1.72 42.31 3.02
2589 2673 2.379634 CGTCACGAAGAATGGCGCA 61.380 57.895 10.83 0.00 38.49 6.09
2640 2724 1.202200 GCTTCGAGCATGTCGTAGAGT 60.202 52.381 20.10 0.00 46.12 3.24
2742 2826 4.316823 ACCCTCTCCGTGCCCTCA 62.317 66.667 0.00 0.00 0.00 3.86
2823 2907 0.605589 CCGACTCTTGAAGCAGAGGT 59.394 55.000 4.05 0.00 44.23 3.85
2877 2961 1.067142 TCGACGAAGAAATCCCTGTGG 60.067 52.381 0.00 0.00 0.00 4.17
3248 3459 2.022195 CAGCAGCTCATATGCACCTTT 58.978 47.619 0.00 0.00 46.31 3.11
3286 3497 5.454232 CCACACGAATTTTATCATTTACGCC 59.546 40.000 0.00 0.00 0.00 5.68
3317 3528 2.191802 GACTCAGATCTGATGCACACG 58.808 52.381 25.30 14.13 39.13 4.49
3441 3654 3.004524 GCATGGAGATTGGAGAAGCAATC 59.995 47.826 0.00 0.00 37.90 2.67
3461 3674 4.104579 TGAAAATAGCCTCCTATGGATGCA 59.895 41.667 14.42 0.00 44.01 3.96
3467 3680 7.934855 ATAATGCTGAAAATAGCCTCCTATG 57.065 36.000 0.00 0.00 43.02 2.23
3587 3800 4.274459 GGCATCAGTTAAGGAGCATAAGTG 59.726 45.833 0.00 0.00 35.80 3.16
3609 3828 1.228124 TCACAGCCCGGTTTTGAGG 60.228 57.895 0.00 0.00 0.00 3.86
3631 3850 0.951558 TTTCAAAGCGCTGTTCTCCC 59.048 50.000 12.58 0.00 0.00 4.30
3761 3980 3.511934 GTGGACAGACACTTGAGGACTAT 59.488 47.826 0.00 0.00 38.32 2.12
3763 3982 1.689273 GTGGACAGACACTTGAGGACT 59.311 52.381 0.00 0.00 38.32 3.85
3776 3995 3.814842 TGCAACTGTATTTCTGTGGACAG 59.185 43.478 0.00 0.00 43.97 3.51
3778 3997 3.189287 CCTGCAACTGTATTTCTGTGGAC 59.811 47.826 0.00 0.00 0.00 4.02
3779 3998 3.072330 TCCTGCAACTGTATTTCTGTGGA 59.928 43.478 0.00 0.00 0.00 4.02
3780 3999 3.411446 TCCTGCAACTGTATTTCTGTGG 58.589 45.455 0.00 0.00 0.00 4.17
3783 4002 7.988737 TGATAATTCCTGCAACTGTATTTCTG 58.011 34.615 0.00 0.00 0.00 3.02
3784 4003 8.757982 ATGATAATTCCTGCAACTGTATTTCT 57.242 30.769 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.