Multiple sequence alignment - TraesCS1B01G091500

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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 TraesCS1B01G091500 chr1B 100.000 2453 0 0 1 2453 92871054 92873506 0.000000e+00 4530
1 TraesCS1B01G091500 chr1A 88.058 2152 157 42 1 2127 56616882 56618958 0.000000e+00 2459
2 TraesCS1B01G091500 chr1D 90.693 1644 85 29 263 1876 57476333 57477938 0.000000e+00 2126
3 TraesCS1B01G091500 chr1D 78.824 595 81 34 1879 2448 57477975 57478549 2.320000e-95 359


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 TraesCS1B01G091500 chr1B 92871054 92873506 2452 False 4530.0 4530 100.0000 1 2453 1 chr1B.!!$F1 2452
1 TraesCS1B01G091500 chr1A 56616882 56618958 2076 False 2459.0 2459 88.0580 1 2127 1 chr1A.!!$F1 2126
2 TraesCS1B01G091500 chr1D 57476333 57478549 2216 False 1242.5 2126 84.7585 263 2448 2 chr1D.!!$F1 2185

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
221 222 0.033366 GACGCTGGGCCAACAAAAAT 59.967 50.0 8.04 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 1672 0.528684 GAGCACAGGACACGATAGGC 60.529 60.0 0.0 0.0 43.77 3.93 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
27 28 0.668535 GAAGAGTTTGCCACACCACC 59.331 55.000 0.00 0.00 0.00 4.61
34 35 0.256177 TTGCCACACCACCTGTACAA 59.744 50.000 0.00 0.00 0.00 2.41
35 36 0.179032 TGCCACACCACCTGTACAAG 60.179 55.000 0.00 0.00 0.00 3.16
36 37 0.179029 GCCACACCACCTGTACAAGT 60.179 55.000 0.00 0.00 0.00 3.16
38 39 2.762745 CCACACCACCTGTACAAGTAC 58.237 52.381 0.00 3.47 36.63 2.73
43 44 4.222145 ACACCACCTGTACAAGTACATAGG 59.778 45.833 12.95 13.49 44.15 2.57
47 48 6.127140 ACCACCTGTACAAGTACATAGGAATC 60.127 42.308 19.53 0.00 44.15 2.52
55 56 8.814553 GTACAAGTACATAGGAATCGTCCTGGA 61.815 44.444 5.51 0.00 43.60 3.86
69 70 4.954202 TCGTCCTGGAATCTACATACAAGT 59.046 41.667 0.00 0.00 0.00 3.16
83 84 5.689819 ACATACAAGTTTCTGAAATCGCAC 58.310 37.500 6.06 0.00 0.00 5.34
85 86 4.900635 ACAAGTTTCTGAAATCGCACTT 57.099 36.364 6.06 2.58 0.00 3.16
91 92 2.699954 TCTGAAATCGCACTTTCTCCC 58.300 47.619 8.84 0.00 36.34 4.30
92 93 2.303022 TCTGAAATCGCACTTTCTCCCT 59.697 45.455 8.84 0.00 36.34 4.20
94 95 2.038426 TGAAATCGCACTTTCTCCCTGA 59.962 45.455 8.84 0.00 36.34 3.86
99 100 1.394917 CGCACTTTCTCCCTGAATTCG 59.605 52.381 0.04 0.00 34.24 3.34
101 102 3.074412 GCACTTTCTCCCTGAATTCGAA 58.926 45.455 0.00 0.00 34.24 3.71
116 117 9.840427 CCTGAATTCGAACAAACTTATTTACAT 57.160 29.630 0.00 0.00 0.00 2.29
164 165 5.569059 GCGTTTGGTTGATTAGTTGAGAATG 59.431 40.000 0.00 0.00 0.00 2.67
194 195 3.284617 TGCATCTGAAATGACCCATCTG 58.715 45.455 0.00 0.00 0.00 2.90
207 208 0.176680 CCATCTGTTGCCTAGACGCT 59.823 55.000 0.00 0.00 0.00 5.07
221 222 0.033366 GACGCTGGGCCAACAAAAAT 59.967 50.000 8.04 0.00 0.00 1.82
223 224 1.689273 ACGCTGGGCCAACAAAAATTA 59.311 42.857 8.04 0.00 0.00 1.40
224 225 2.065512 CGCTGGGCCAACAAAAATTAC 58.934 47.619 8.04 0.00 0.00 1.89
228 229 4.688879 GCTGGGCCAACAAAAATTACTAAC 59.311 41.667 8.04 0.00 0.00 2.34
229 230 5.740513 GCTGGGCCAACAAAAATTACTAACA 60.741 40.000 8.04 0.00 0.00 2.41
230 231 6.426646 TGGGCCAACAAAAATTACTAACAT 57.573 33.333 2.13 0.00 0.00 2.71
231 232 6.459923 TGGGCCAACAAAAATTACTAACATC 58.540 36.000 2.13 0.00 0.00 3.06
232 233 6.042093 TGGGCCAACAAAAATTACTAACATCA 59.958 34.615 2.13 0.00 0.00 3.07
265 268 5.220586 CCACTTACCACTATGTGCATTAACG 60.221 44.000 0.00 0.00 31.34 3.18
292 295 0.461339 GCTTGGTAGGATTTCGGCGA 60.461 55.000 4.99 4.99 0.00 5.54
304 307 2.288961 TTCGGCGAAACTAGATGGAC 57.711 50.000 21.53 0.00 0.00 4.02
305 308 1.471119 TCGGCGAAACTAGATGGACT 58.529 50.000 7.35 0.00 0.00 3.85
317 320 9.344309 GAAACTAGATGGACTTATAGCGAATAC 57.656 37.037 0.00 0.00 0.00 1.89
321 324 4.866508 TGGACTTATAGCGAATACCCTG 57.133 45.455 0.00 0.00 0.00 4.45
368 371 8.896744 CAAAAGTGCAATAGAAAGATATCTCCA 58.103 33.333 5.51 0.00 0.00 3.86
369 372 9.466497 AAAAGTGCAATAGAAAGATATCTCCAA 57.534 29.630 5.51 0.00 0.00 3.53
370 373 9.466497 AAAGTGCAATAGAAAGATATCTCCAAA 57.534 29.630 5.51 0.00 0.00 3.28
371 374 8.674263 AGTGCAATAGAAAGATATCTCCAAAG 57.326 34.615 5.51 0.00 0.00 2.77
372 375 7.228308 AGTGCAATAGAAAGATATCTCCAAAGC 59.772 37.037 5.51 5.77 0.00 3.51
373 376 6.203530 TGCAATAGAAAGATATCTCCAAAGCG 59.796 38.462 5.51 0.00 0.00 4.68
405 408 1.678970 GCCCATGACAGGTTGTCCC 60.679 63.158 6.74 0.00 46.40 4.46
406 409 2.078452 CCCATGACAGGTTGTCCCT 58.922 57.895 6.74 0.00 46.40 4.20
460 463 1.607225 ATACCCAGAATGCCCTCCAA 58.393 50.000 0.00 0.00 31.97 3.53
541 544 0.766674 TATGCATTAGAGCCCCCGGT 60.767 55.000 3.54 0.00 0.00 5.28
546 549 0.912487 ATTAGAGCCCCCGGTGTTGA 60.912 55.000 0.00 0.00 0.00 3.18
578 581 2.235898 CAGCTAAGTCCTGCTCTCCTTT 59.764 50.000 0.00 0.00 37.44 3.11
579 582 2.499693 AGCTAAGTCCTGCTCTCCTTTC 59.500 50.000 0.00 0.00 33.90 2.62
590 609 2.304470 GCTCTCCTTTCCTTTCAGTCCT 59.696 50.000 0.00 0.00 0.00 3.85
786 805 3.490759 CCGATGAAGCTGCGCGTT 61.491 61.111 8.43 0.00 0.00 4.84
897 916 4.346418 CCATCCAGCCTCTAGTTGATTAGT 59.654 45.833 0.00 0.00 0.00 2.24
898 917 5.540337 CCATCCAGCCTCTAGTTGATTAGTA 59.460 44.000 0.00 0.00 0.00 1.82
899 918 6.295011 CCATCCAGCCTCTAGTTGATTAGTAG 60.295 46.154 0.00 0.00 0.00 2.57
921 940 1.291877 CCAGCCTCGTTTCTTCCACG 61.292 60.000 0.00 0.00 39.08 4.94
932 951 3.478857 TTCTTCCACGTTCTTGCCTTA 57.521 42.857 0.00 0.00 0.00 2.69
933 952 2.762745 TCTTCCACGTTCTTGCCTTAC 58.237 47.619 0.00 0.00 0.00 2.34
948 967 0.106894 CTTACTCCTTCCCGCCATCC 59.893 60.000 0.00 0.00 0.00 3.51
960 979 2.436417 CCGCCATCCAAGAAAAGAGAA 58.564 47.619 0.00 0.00 0.00 2.87
961 980 3.019564 CCGCCATCCAAGAAAAGAGAAT 58.980 45.455 0.00 0.00 0.00 2.40
963 982 4.082026 CCGCCATCCAAGAAAAGAGAATTT 60.082 41.667 0.00 0.00 0.00 1.82
964 983 5.098211 CGCCATCCAAGAAAAGAGAATTTC 58.902 41.667 0.00 0.00 39.16 2.17
997 1016 1.153429 GGATCAAGAACCCGACCGG 60.153 63.158 0.00 0.00 37.81 5.28
1245 1264 1.371558 GACCGAGCTGACCAAGGTT 59.628 57.895 0.00 0.00 36.52 3.50
1341 1360 1.224592 GATCTTCCATGTGGCCGGT 59.775 57.895 1.90 0.00 34.44 5.28
1368 1387 1.123077 TTGACATCCCAGAGATCCCG 58.877 55.000 0.00 0.00 30.59 5.14
1401 1420 2.035626 CCATGGCAGTCCCCGTTT 59.964 61.111 0.00 0.00 0.00 3.60
1499 1528 0.254462 TTGCGCCACCATGGATAAGA 59.746 50.000 21.47 0.00 40.96 2.10
1500 1529 0.254462 TGCGCCACCATGGATAAGAA 59.746 50.000 21.47 0.00 40.96 2.52
1515 1544 5.586243 TGGATAAGAAGTTGCTGATTACTGC 59.414 40.000 0.00 0.00 40.53 4.40
1516 1545 5.819901 GGATAAGAAGTTGCTGATTACTGCT 59.180 40.000 0.00 0.00 40.71 4.24
1517 1546 6.238320 GGATAAGAAGTTGCTGATTACTGCTG 60.238 42.308 0.00 0.00 40.71 4.41
1518 1547 2.746362 AGAAGTTGCTGATTACTGCTGC 59.254 45.455 0.00 0.00 40.71 5.25
1519 1548 2.189594 AGTTGCTGATTACTGCTGCA 57.810 45.000 0.88 0.88 40.71 4.41
1534 1563 1.735386 CTGCACTACTGCTGCTGAAT 58.265 50.000 13.69 0.00 44.57 2.57
1536 1565 2.864946 CTGCACTACTGCTGCTGAATAG 59.135 50.000 13.69 7.88 44.57 1.73
1539 1568 4.100035 TGCACTACTGCTGCTGAATAGTAT 59.900 41.667 13.69 0.00 44.57 2.12
1544 1573 7.380870 CACTACTGCTGCTGAATAGTATTAGTG 59.619 40.741 13.69 12.62 37.52 2.74
1590 1619 8.958175 TGTTTAATTATGGTTTGATTCGTGTC 57.042 30.769 0.00 0.00 0.00 3.67
1598 1627 3.485216 GGTTTGATTCGTGTCGCTTATGG 60.485 47.826 0.00 0.00 0.00 2.74
1645 1674 8.986477 ACTTATTTTGTGATTGTAATCTTGCC 57.014 30.769 6.21 0.00 36.39 4.52
1646 1675 8.806146 ACTTATTTTGTGATTGTAATCTTGCCT 58.194 29.630 6.21 0.00 36.39 4.75
1650 1679 6.603237 TTGTGATTGTAATCTTGCCTATCG 57.397 37.500 6.21 0.00 36.39 2.92
1651 1680 5.670485 TGTGATTGTAATCTTGCCTATCGT 58.330 37.500 6.21 0.00 36.39 3.73
1652 1681 5.523552 TGTGATTGTAATCTTGCCTATCGTG 59.476 40.000 6.21 0.00 36.39 4.35
1657 1686 2.898729 ATCTTGCCTATCGTGTCCTG 57.101 50.000 0.00 0.00 0.00 3.86
1666 1695 0.818296 ATCGTGTCCTGTGCTCCTAC 59.182 55.000 0.00 0.00 0.00 3.18
1693 1722 8.156820 CCAGTGGATATGGATAAGAACAATGTA 58.843 37.037 1.68 0.00 40.51 2.29
1713 1744 1.830279 ATTGATGTGGTGGAGCACAG 58.170 50.000 16.10 0.00 35.86 3.66
1733 1765 2.017049 GCGGATTGTGCCTATCTTTGT 58.983 47.619 0.00 0.00 0.00 2.83
1748 1780 9.503427 GCCTATCTTTGTGTTGATTTGTAATAC 57.497 33.333 0.00 0.00 0.00 1.89
1802 1836 9.518906 TGCATCAAATTATTTAGCTATGTGTTG 57.481 29.630 0.00 0.00 0.00 3.33
1805 1839 9.956720 ATCAAATTATTTAGCTATGTGTTGCTC 57.043 29.630 0.00 0.00 40.35 4.26
1916 1988 7.163001 AGTCTCCTTTTGCCAAAATTAGATC 57.837 36.000 13.99 9.75 0.00 2.75
1957 2037 6.173339 TCTGAATGCACTCCTTTTTACCTAG 58.827 40.000 0.00 0.00 0.00 3.02
1966 2046 7.985752 GCACTCCTTTTTACCTAGTATATGTGT 59.014 37.037 0.00 0.00 0.00 3.72
1994 2074 2.355108 CCTGTGATGACCGGAGAATTGT 60.355 50.000 9.46 0.00 0.00 2.71
2000 2080 6.263392 TGTGATGACCGGAGAATTGTTAAAAA 59.737 34.615 9.46 0.00 0.00 1.94
2001 2081 7.040062 TGTGATGACCGGAGAATTGTTAAAAAT 60.040 33.333 9.46 0.00 0.00 1.82
2005 2085 6.265649 TGACCGGAGAATTGTTAAAAATCCAA 59.734 34.615 9.46 0.00 0.00 3.53
2007 2087 7.501844 ACCGGAGAATTGTTAAAAATCCAAAA 58.498 30.769 9.46 0.00 0.00 2.44
2035 2115 2.092484 TGCCATACTCTAGCATTTGCCA 60.092 45.455 0.00 0.00 43.38 4.92
2043 2123 4.037208 ACTCTAGCATTTGCCATTGTATGC 59.963 41.667 0.00 0.00 43.38 3.14
2051 2132 7.932491 AGCATTTGCCATTGTATGCATATTTTA 59.068 29.630 10.16 0.00 44.38 1.52
2052 2133 8.723311 GCATTTGCCATTGTATGCATATTTTAT 58.277 29.630 10.16 0.00 42.18 1.40
2057 2138 9.519191 TGCCATTGTATGCATATTTTATACTCT 57.481 29.630 10.16 0.00 31.31 3.24
2067 2148 8.514594 TGCATATTTTATACTCTAGCATTTGCC 58.485 33.333 0.00 0.00 43.38 4.52
2068 2149 8.514594 GCATATTTTATACTCTAGCATTTGCCA 58.485 33.333 0.00 0.00 43.38 4.92
2122 2203 8.001549 CGTTTATTGTGATTGGCTTTTGTTTAC 58.998 33.333 0.00 0.00 0.00 2.01
2133 2214 4.333926 GGCTTTTGTTTACAACATTGGCAA 59.666 37.500 0.68 0.68 41.79 4.52
2150 2237 2.419297 GGCAACCACCAATGTTGTTCAA 60.419 45.455 5.19 0.00 43.86 2.69
2151 2238 2.607180 GCAACCACCAATGTTGTTCAAC 59.393 45.455 8.52 8.52 43.86 3.18
2154 2241 4.817318 ACCACCAATGTTGTTCAACTTT 57.183 36.364 15.18 12.38 0.00 2.66
2155 2242 4.502962 ACCACCAATGTTGTTCAACTTTG 58.497 39.130 24.41 24.41 37.48 2.77
2156 2243 3.309410 CCACCAATGTTGTTCAACTTTGC 59.691 43.478 25.24 2.40 36.84 3.68
2157 2244 3.309410 CACCAATGTTGTTCAACTTTGCC 59.691 43.478 25.24 1.84 36.84 4.52
2158 2245 3.197549 ACCAATGTTGTTCAACTTTGCCT 59.802 39.130 25.24 15.93 36.84 4.75
2159 2246 4.404073 ACCAATGTTGTTCAACTTTGCCTA 59.596 37.500 25.24 5.76 36.84 3.93
2213 2300 6.933521 GTGATATCCATTGTATCTGCTCTGTT 59.066 38.462 0.00 0.00 31.38 3.16
2216 2303 4.517285 TCCATTGTATCTGCTCTGTTTCC 58.483 43.478 0.00 0.00 0.00 3.13
2217 2304 3.310774 CCATTGTATCTGCTCTGTTTCCG 59.689 47.826 0.00 0.00 0.00 4.30
2218 2305 2.010145 TGTATCTGCTCTGTTTCCGC 57.990 50.000 0.00 0.00 0.00 5.54
2219 2306 1.291132 GTATCTGCTCTGTTTCCGCC 58.709 55.000 0.00 0.00 0.00 6.13
2220 2307 0.178068 TATCTGCTCTGTTTCCGCCC 59.822 55.000 0.00 0.00 0.00 6.13
2221 2308 2.543067 ATCTGCTCTGTTTCCGCCCC 62.543 60.000 0.00 0.00 0.00 5.80
2222 2309 3.249189 TGCTCTGTTTCCGCCCCT 61.249 61.111 0.00 0.00 0.00 4.79
2223 2310 1.899437 CTGCTCTGTTTCCGCCCCTA 61.899 60.000 0.00 0.00 0.00 3.53
2224 2311 1.449778 GCTCTGTTTCCGCCCCTAC 60.450 63.158 0.00 0.00 0.00 3.18
2225 2312 1.900545 GCTCTGTTTCCGCCCCTACT 61.901 60.000 0.00 0.00 0.00 2.57
2226 2313 0.175989 CTCTGTTTCCGCCCCTACTC 59.824 60.000 0.00 0.00 0.00 2.59
2228 2315 1.601419 CTGTTTCCGCCCCTACTCGA 61.601 60.000 0.00 0.00 0.00 4.04
2229 2316 1.186917 TGTTTCCGCCCCTACTCGAA 61.187 55.000 0.00 0.00 0.00 3.71
2230 2317 0.177373 GTTTCCGCCCCTACTCGAAT 59.823 55.000 0.00 0.00 0.00 3.34
2232 2319 0.974010 TTCCGCCCCTACTCGAATGT 60.974 55.000 0.00 0.00 0.00 2.71
2233 2320 0.974010 TCCGCCCCTACTCGAATGTT 60.974 55.000 0.00 0.00 0.00 2.71
2234 2321 0.107848 CCGCCCCTACTCGAATGTTT 60.108 55.000 0.00 0.00 0.00 2.83
2235 2322 1.006832 CGCCCCTACTCGAATGTTTG 58.993 55.000 0.00 0.00 0.00 2.93
2236 2323 1.674817 CGCCCCTACTCGAATGTTTGT 60.675 52.381 0.00 0.00 0.00 2.83
2237 2324 2.417651 CGCCCCTACTCGAATGTTTGTA 60.418 50.000 0.00 0.00 0.00 2.41
2238 2325 3.740141 CGCCCCTACTCGAATGTTTGTAT 60.740 47.826 0.00 0.00 0.00 2.29
2312 2403 4.313282 AGTCCGTTAAGGTGTTAAGCTTC 58.687 43.478 0.00 0.00 43.03 3.86
2313 2404 4.040095 AGTCCGTTAAGGTGTTAAGCTTCT 59.960 41.667 0.00 0.00 43.03 2.85
2314 2405 5.244626 AGTCCGTTAAGGTGTTAAGCTTCTA 59.755 40.000 0.00 0.00 43.03 2.10
2315 2406 5.575995 GTCCGTTAAGGTGTTAAGCTTCTAG 59.424 44.000 0.00 0.00 43.03 2.43
2316 2407 4.329256 CCGTTAAGGTGTTAAGCTTCTAGC 59.671 45.833 0.00 0.01 43.03 3.42
2317 2408 5.853702 CCGTTAAGGTGTTAAGCTTCTAGCT 60.854 44.000 0.00 2.66 44.56 3.32
2318 2409 7.605524 CCGTTAAGGTGTTAAGCTTCTAGCTC 61.606 46.154 0.00 0.00 42.86 4.09
2329 2420 3.512680 GCTTCTAGCTCGCTTCTTAACA 58.487 45.455 0.00 0.00 38.45 2.41
2330 2421 3.927142 GCTTCTAGCTCGCTTCTTAACAA 59.073 43.478 0.00 0.00 38.45 2.83
2331 2422 4.389077 GCTTCTAGCTCGCTTCTTAACAAA 59.611 41.667 0.00 0.00 38.45 2.83
2332 2423 5.669111 GCTTCTAGCTCGCTTCTTAACAAAC 60.669 44.000 0.00 0.00 38.45 2.93
2333 2424 5.135508 TCTAGCTCGCTTCTTAACAAACT 57.864 39.130 0.00 0.00 0.00 2.66
2334 2425 4.923871 TCTAGCTCGCTTCTTAACAAACTG 59.076 41.667 0.00 0.00 0.00 3.16
2360 2469 6.719370 AGTCAATCATTGGTTTTAGCTTACCA 59.281 34.615 10.09 10.09 42.48 3.25
2376 2485 4.377124 GCTTACCAAACAAGCTAACGAGTC 60.377 45.833 0.00 0.00 44.04 3.36
2385 2494 0.522705 GCTAACGAGTCGCACGATCA 60.523 55.000 13.59 0.00 34.70 2.92
2406 2515 8.328864 CGATCAAACTTGTTAAGCTCCTAATAC 58.671 37.037 0.00 0.00 0.00 1.89
2413 2522 7.717875 ACTTGTTAAGCTCCTAATACAACACAA 59.282 33.333 0.00 0.00 0.00 3.33
2424 2533 8.952278 TCCTAATACAACACAACACATATTTCC 58.048 33.333 0.00 0.00 0.00 3.13
2430 2539 8.635765 ACAACACAACACATATTTCCTATCTT 57.364 30.769 0.00 0.00 0.00 2.40
2444 2553 8.617290 ATTTCCTATCTTAAGTGACAACGTTT 57.383 30.769 0.00 0.00 0.00 3.60
2446 2555 9.545105 TTTCCTATCTTAAGTGACAACGTTTAA 57.455 29.630 0.00 0.00 0.00 1.52
2447 2556 9.715121 TTCCTATCTTAAGTGACAACGTTTAAT 57.285 29.630 0.00 0.00 0.00 1.40
2448 2557 9.146984 TCCTATCTTAAGTGACAACGTTTAATG 57.853 33.333 0.00 0.00 0.00 1.90
2449 2558 8.388103 CCTATCTTAAGTGACAACGTTTAATGG 58.612 37.037 0.00 0.00 0.00 3.16
2450 2559 5.992729 TCTTAAGTGACAACGTTTAATGGC 58.007 37.500 0.00 0.00 0.00 4.40
2451 2560 5.527951 TCTTAAGTGACAACGTTTAATGGCA 59.472 36.000 0.00 0.00 30.44 4.92
2452 2561 4.846779 AAGTGACAACGTTTAATGGCAT 57.153 36.364 0.00 0.00 36.84 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.388547 GTGGTGTGGCAAACTCTTCA 58.611 50.000 7.91 0.00 0.00 3.02
8 9 0.668535 GGTGGTGTGGCAAACTCTTC 59.331 55.000 7.91 0.00 0.00 2.87
27 28 6.207213 GGACGATTCCTATGTACTTGTACAG 58.793 44.000 17.01 6.51 39.13 2.74
43 44 6.085555 TGTATGTAGATTCCAGGACGATTC 57.914 41.667 0.00 0.00 0.00 2.52
47 48 5.263968 ACTTGTATGTAGATTCCAGGACG 57.736 43.478 0.00 0.00 0.00 4.79
55 56 8.391106 GCGATTTCAGAAACTTGTATGTAGATT 58.609 33.333 0.00 0.00 0.00 2.40
56 57 7.549134 TGCGATTTCAGAAACTTGTATGTAGAT 59.451 33.333 0.00 0.00 0.00 1.98
69 70 3.502211 GGGAGAAAGTGCGATTTCAGAAA 59.498 43.478 13.89 0.00 40.86 2.52
83 84 5.239525 AGTTTGTTCGAATTCAGGGAGAAAG 59.760 40.000 0.00 0.00 40.22 2.62
85 86 4.714632 AGTTTGTTCGAATTCAGGGAGAA 58.285 39.130 0.00 0.00 41.28 2.87
129 130 0.876399 ACCAAACGCCGGTGAATAAC 59.124 50.000 24.59 0.00 34.69 1.89
139 140 3.500680 TCTCAACTAATCAACCAAACGCC 59.499 43.478 0.00 0.00 0.00 5.68
142 143 7.040409 AGGACATTCTCAACTAATCAACCAAAC 60.040 37.037 0.00 0.00 0.00 2.93
164 165 4.024218 GTCATTTCAGATGCAGCATAGGAC 60.024 45.833 8.22 6.01 0.00 3.85
194 195 2.820037 GCCCAGCGTCTAGGCAAC 60.820 66.667 10.41 0.00 46.34 4.17
207 208 5.871396 TGTTAGTAATTTTTGTTGGCCCA 57.129 34.783 0.00 0.00 0.00 5.36
241 244 5.220586 CGTTAATGCACATAGTGGTAAGTGG 60.221 44.000 0.00 0.00 33.64 4.00
244 247 5.113383 TCCGTTAATGCACATAGTGGTAAG 58.887 41.667 0.00 0.00 33.64 2.34
253 256 3.193267 AGCAAACATCCGTTAATGCACAT 59.807 39.130 0.00 0.00 40.04 3.21
254 257 2.556189 AGCAAACATCCGTTAATGCACA 59.444 40.909 0.00 0.00 40.04 4.57
255 258 3.216147 AGCAAACATCCGTTAATGCAC 57.784 42.857 0.00 0.00 40.04 4.57
265 268 4.438744 CGAAATCCTACCAAGCAAACATCC 60.439 45.833 0.00 0.00 0.00 3.51
292 295 8.305317 GGTATTCGCTATAAGTCCATCTAGTTT 58.695 37.037 0.00 0.00 0.00 2.66
304 307 4.691216 GGAAAGCAGGGTATTCGCTATAAG 59.309 45.833 0.00 0.00 34.11 1.73
305 308 4.347000 AGGAAAGCAGGGTATTCGCTATAA 59.653 41.667 0.00 0.00 34.11 0.98
317 320 2.281761 ACACGCAGGAAAGCAGGG 60.282 61.111 0.00 0.00 0.00 4.45
321 324 3.744559 TTCCACACGCAGGAAAGC 58.255 55.556 1.75 0.00 41.94 3.51
357 360 8.561738 TTTTAACTTCGCTTTGGAGATATCTT 57.438 30.769 6.70 0.00 0.00 2.40
405 408 1.508088 GTGGGCGGCATTTTCTGAG 59.492 57.895 12.47 0.00 0.00 3.35
406 409 1.976474 GGTGGGCGGCATTTTCTGA 60.976 57.895 12.47 0.00 0.00 3.27
460 463 6.265304 GGAGAGGGTCTATTTATAGGTGGAT 58.735 44.000 0.00 0.00 0.00 3.41
541 544 2.221169 AGCTGCAAATCGAAGTCAACA 58.779 42.857 1.02 0.00 0.00 3.33
546 549 3.003480 GGACTTAGCTGCAAATCGAAGT 58.997 45.455 1.02 7.96 32.26 3.01
572 575 4.092116 ACAAGGACTGAAAGGAAAGGAG 57.908 45.455 0.00 0.00 39.30 3.69
575 578 4.646572 AGCTACAAGGACTGAAAGGAAAG 58.353 43.478 0.00 0.00 39.30 2.62
578 581 3.904339 AGAAGCTACAAGGACTGAAAGGA 59.096 43.478 0.00 0.00 39.30 3.36
579 582 4.278975 AGAAGCTACAAGGACTGAAAGG 57.721 45.455 0.00 0.00 39.30 3.11
610 629 0.173708 CGGAACAGGGAGTAGACTGC 59.826 60.000 0.00 0.00 38.25 4.40
863 882 2.513666 TGGATGGATGCGGCGTTC 60.514 61.111 9.37 6.07 0.00 3.95
897 916 2.431057 GGAAGAAACGAGGCTGGATCTA 59.569 50.000 2.65 0.00 0.00 1.98
898 917 1.208293 GGAAGAAACGAGGCTGGATCT 59.792 52.381 2.65 3.73 0.00 2.75
899 918 1.066143 TGGAAGAAACGAGGCTGGATC 60.066 52.381 2.65 1.30 0.00 3.36
921 940 2.712709 GGGAAGGAGTAAGGCAAGAAC 58.287 52.381 0.00 0.00 0.00 3.01
932 951 1.915078 CTTGGATGGCGGGAAGGAGT 61.915 60.000 0.00 0.00 0.00 3.85
933 952 1.153086 CTTGGATGGCGGGAAGGAG 60.153 63.158 0.00 0.00 0.00 3.69
960 979 6.077322 TGATCCAAGAACCAGAAAAGGAAAT 58.923 36.000 0.00 0.00 0.00 2.17
961 980 5.454062 TGATCCAAGAACCAGAAAAGGAAA 58.546 37.500 0.00 0.00 0.00 3.13
963 982 4.722526 TGATCCAAGAACCAGAAAAGGA 57.277 40.909 0.00 0.00 0.00 3.36
964 983 5.072741 TCTTGATCCAAGAACCAGAAAAGG 58.927 41.667 6.91 0.00 45.84 3.11
1350 1369 0.760567 CCGGGATCTCTGGGATGTCA 60.761 60.000 0.00 0.00 38.27 3.58
1359 1378 4.144727 AGCGGGTCCGGGATCTCT 62.145 66.667 7.34 2.14 40.19 3.10
1499 1528 2.227388 GTGCAGCAGTAATCAGCAACTT 59.773 45.455 0.00 0.00 36.91 2.66
1500 1529 1.808945 GTGCAGCAGTAATCAGCAACT 59.191 47.619 0.00 0.00 36.91 3.16
1518 1547 7.380870 CACTAATACTATTCAGCAGCAGTAGTG 59.619 40.741 0.00 0.00 0.00 2.74
1519 1548 7.429633 CACTAATACTATTCAGCAGCAGTAGT 58.570 38.462 0.00 0.00 0.00 2.73
1534 1563 9.865321 CCAAACAAACTAGTAGCACTAATACTA 57.135 33.333 0.00 0.00 35.20 1.82
1536 1565 8.543862 ACCAAACAAACTAGTAGCACTAATAC 57.456 34.615 0.00 0.00 29.00 1.89
1539 1568 7.049133 TGAACCAAACAAACTAGTAGCACTAA 58.951 34.615 0.00 0.00 29.00 2.24
1544 1573 6.313744 ACATGAACCAAACAAACTAGTAGC 57.686 37.500 0.00 0.00 0.00 3.58
1590 1619 4.866508 TGGTCTAGGATTACCATAAGCG 57.133 45.455 0.00 0.00 40.84 4.68
1643 1672 0.528684 GAGCACAGGACACGATAGGC 60.529 60.000 0.00 0.00 43.77 3.93
1645 1674 1.107114 AGGAGCACAGGACACGATAG 58.893 55.000 0.00 0.00 46.19 2.08
1646 1675 2.022195 GTAGGAGCACAGGACACGATA 58.978 52.381 0.00 0.00 0.00 2.92
1647 1676 0.818296 GTAGGAGCACAGGACACGAT 59.182 55.000 0.00 0.00 0.00 3.73
1649 1678 1.215647 GGTAGGAGCACAGGACACG 59.784 63.158 0.00 0.00 0.00 4.49
1650 1679 1.192146 TGGGTAGGAGCACAGGACAC 61.192 60.000 0.00 0.00 0.00 3.67
1651 1680 0.904865 CTGGGTAGGAGCACAGGACA 60.905 60.000 0.00 0.00 0.00 4.02
1652 1681 0.905337 ACTGGGTAGGAGCACAGGAC 60.905 60.000 0.32 0.00 35.34 3.85
1657 1686 1.789523 TATCCACTGGGTAGGAGCAC 58.210 55.000 0.00 0.00 37.34 4.40
1666 1695 5.567037 TGTTCTTATCCATATCCACTGGG 57.433 43.478 0.00 0.00 34.36 4.45
1693 1722 2.165167 CTGTGCTCCACCACATCAATT 58.835 47.619 0.00 0.00 44.05 2.32
1704 1735 1.672030 CACAATCCGCTGTGCTCCA 60.672 57.895 0.00 0.00 40.26 3.86
1713 1744 2.017049 ACAAAGATAGGCACAATCCGC 58.983 47.619 0.00 0.00 0.00 5.54
1714 1745 3.009723 ACACAAAGATAGGCACAATCCG 58.990 45.455 0.00 0.00 0.00 4.18
1733 1765 8.628630 TGTCAAGATGGTATTACAAATCAACA 57.371 30.769 9.92 8.35 0.00 3.33
1748 1780 8.324306 ACATATATAGGTTCCATGTCAAGATGG 58.676 37.037 0.00 0.00 43.96 3.51
1802 1836 2.294233 TCAATCAAACACTTGCCAGAGC 59.706 45.455 0.00 0.00 40.48 4.09
1805 1839 6.607735 AAAATTCAATCAAACACTTGCCAG 57.392 33.333 0.00 0.00 32.14 4.85
1916 1988 4.743057 TCAGATACAATCCCTGTGAGTG 57.257 45.455 0.00 0.00 44.51 3.51
1957 2037 6.593770 TCATCACAGGTTCACAACACATATAC 59.406 38.462 0.00 0.00 0.00 1.47
1966 2046 1.542328 CCGGTCATCACAGGTTCACAA 60.542 52.381 0.00 0.00 33.37 3.33
2020 2100 4.037208 GCATACAATGGCAAATGCTAGAGT 59.963 41.667 15.77 4.95 41.16 3.24
2051 2132 4.843220 GCAATGGCAAATGCTAGAGTAT 57.157 40.909 18.12 0.00 41.70 2.12
2086 2167 7.571026 CCAATCACAATAAACGCAAATTTTCA 58.429 30.769 0.00 0.00 0.00 2.69
2133 2214 4.502962 CAAAGTTGAACAACATTGGTGGT 58.497 39.130 20.51 0.00 42.74 4.16
2143 2230 7.990886 CCTATACCTATAGGCAAAGTTGAACAA 59.009 37.037 19.25 0.00 46.22 2.83
2193 2280 5.128919 GGAAACAGAGCAGATACAATGGAT 58.871 41.667 0.00 0.00 0.00 3.41
2198 2285 2.346803 GCGGAAACAGAGCAGATACAA 58.653 47.619 0.00 0.00 0.00 2.41
2213 2300 0.974010 ACATTCGAGTAGGGGCGGAA 60.974 55.000 0.00 0.00 0.00 4.30
2216 2303 1.006832 CAAACATTCGAGTAGGGGCG 58.993 55.000 0.00 0.00 0.00 6.13
2217 2304 2.109425 ACAAACATTCGAGTAGGGGC 57.891 50.000 0.00 0.00 0.00 5.80
2218 2305 8.342634 CAAATAATACAAACATTCGAGTAGGGG 58.657 37.037 0.00 0.00 0.00 4.79
2219 2306 7.855904 GCAAATAATACAAACATTCGAGTAGGG 59.144 37.037 0.00 0.00 0.00 3.53
2220 2307 8.612619 AGCAAATAATACAAACATTCGAGTAGG 58.387 33.333 0.00 0.00 0.00 3.18
2283 2374 8.886719 GCTTAACACCTTAACGGACTAATTTAT 58.113 33.333 0.00 0.00 36.31 1.40
2286 2377 6.470278 AGCTTAACACCTTAACGGACTAATT 58.530 36.000 0.00 0.00 36.31 1.40
2290 2381 4.040095 AGAAGCTTAACACCTTAACGGACT 59.960 41.667 0.00 0.00 36.31 3.85
2293 2384 4.329256 GCTAGAAGCTTAACACCTTAACGG 59.671 45.833 0.00 0.00 38.45 4.44
2308 2399 3.512680 TGTTAAGAAGCGAGCTAGAAGC 58.487 45.455 0.00 0.00 42.84 3.86
2312 2403 4.923871 TCAGTTTGTTAAGAAGCGAGCTAG 59.076 41.667 0.00 0.00 0.00 3.42
2313 2404 4.878439 TCAGTTTGTTAAGAAGCGAGCTA 58.122 39.130 0.00 0.00 0.00 3.32
2314 2405 3.728845 TCAGTTTGTTAAGAAGCGAGCT 58.271 40.909 0.00 0.00 0.00 4.09
2315 2406 3.495001 ACTCAGTTTGTTAAGAAGCGAGC 59.505 43.478 15.13 0.00 0.00 5.03
2316 2407 4.745125 TGACTCAGTTTGTTAAGAAGCGAG 59.255 41.667 14.27 14.27 0.00 5.03
2317 2408 4.689071 TGACTCAGTTTGTTAAGAAGCGA 58.311 39.130 0.00 0.00 0.00 4.93
2318 2409 5.403897 TTGACTCAGTTTGTTAAGAAGCG 57.596 39.130 0.00 0.00 0.00 4.68
2319 2410 6.959361 TGATTGACTCAGTTTGTTAAGAAGC 58.041 36.000 0.00 0.00 0.00 3.86
2320 2411 9.390795 CAATGATTGACTCAGTTTGTTAAGAAG 57.609 33.333 0.00 0.00 37.28 2.85
2321 2412 8.352201 CCAATGATTGACTCAGTTTGTTAAGAA 58.648 33.333 6.76 0.00 37.28 2.52
2322 2413 7.502226 ACCAATGATTGACTCAGTTTGTTAAGA 59.498 33.333 6.76 0.00 37.28 2.10
2323 2414 7.651808 ACCAATGATTGACTCAGTTTGTTAAG 58.348 34.615 6.76 0.00 37.28 1.85
2324 2415 7.581213 ACCAATGATTGACTCAGTTTGTTAA 57.419 32.000 6.76 0.00 37.28 2.01
2325 2416 7.581213 AACCAATGATTGACTCAGTTTGTTA 57.419 32.000 6.76 0.00 37.28 2.41
2326 2417 6.469782 AACCAATGATTGACTCAGTTTGTT 57.530 33.333 6.76 0.00 37.28 2.83
2327 2418 6.469782 AAACCAATGATTGACTCAGTTTGT 57.530 33.333 6.76 0.00 37.28 2.83
2328 2419 7.115378 GCTAAAACCAATGATTGACTCAGTTTG 59.885 37.037 6.76 0.00 37.28 2.93
2329 2420 7.014615 AGCTAAAACCAATGATTGACTCAGTTT 59.985 33.333 6.76 5.33 37.28 2.66
2330 2421 6.491403 AGCTAAAACCAATGATTGACTCAGTT 59.509 34.615 6.76 0.00 37.28 3.16
2331 2422 6.006449 AGCTAAAACCAATGATTGACTCAGT 58.994 36.000 6.76 0.00 37.28 3.41
2332 2423 6.506500 AGCTAAAACCAATGATTGACTCAG 57.493 37.500 6.76 0.00 37.28 3.35
2333 2424 6.899393 AAGCTAAAACCAATGATTGACTCA 57.101 33.333 6.76 0.00 38.53 3.41
2334 2425 7.094377 TGGTAAGCTAAAACCAATGATTGACTC 60.094 37.037 6.76 0.00 42.74 3.36
2360 2469 1.525619 GTGCGACTCGTTAGCTTGTTT 59.474 47.619 0.00 0.00 0.00 2.83
2370 2479 0.039437 AGTTTGATCGTGCGACTCGT 60.039 50.000 0.00 0.00 0.00 4.18
2376 2485 2.902484 GCTTAACAAGTTTGATCGTGCG 59.098 45.455 0.00 0.00 0.00 5.34
2385 2494 8.565416 GTGTTGTATTAGGAGCTTAACAAGTTT 58.435 33.333 0.00 0.00 0.00 2.66
2424 2533 7.903431 GCCATTAAACGTTGTCACTTAAGATAG 59.097 37.037 10.09 0.00 0.00 2.08
2430 2539 5.950758 ATGCCATTAAACGTTGTCACTTA 57.049 34.783 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.