Multiple sequence alignment - TraesCS5D01G345700

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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 TraesCS5D01G345700 chr5D 100.000 2282 0 0 1 2282 432424552 432422271 0.000000e+00 4215
1 TraesCS5D01G345700 chr5D 97.944 2043 40 2 1 2041 503220147 503218105 0.000000e+00 3539
2 TraesCS5D01G345700 chr5D 97.846 2043 42 2 1 2041 503276297 503278339 0.000000e+00 3528
3 TraesCS5D01G345700 chr5D 97.406 2043 51 2 1 2041 6190869 6188827 0.000000e+00 3478
4 TraesCS5D01G345700 chr1A 97.994 2044 37 4 1 2041 554514177 554512135 0.000000e+00 3544
5 TraesCS5D01G345700 chrUn 97.846 2043 42 2 1 2041 346594565 346596607 0.000000e+00 3528
6 TraesCS5D01G345700 chrUn 97.553 2043 47 3 1 2041 216516674 216518715 0.000000e+00 3493
7 TraesCS5D01G345700 chrUn 98.361 244 4 0 2039 2282 114878468 114878225 1.620000e-116 429
8 TraesCS5D01G345700 chr3B 97.797 2043 43 2 1 2041 201528953 201526911 0.000000e+00 3522
9 TraesCS5D01G345700 chr3B 97.951 244 4 1 2039 2282 201557867 201557625 2.710000e-114 422
10 TraesCS5D01G345700 chr6D 97.699 2043 45 2 1 2041 168256855 168254813 0.000000e+00 3511
11 TraesCS5D01G345700 chr3D 97.651 2043 43 4 1 2041 589277616 589279655 0.000000e+00 3502
12 TraesCS5D01G345700 chr5B 98.770 244 3 0 2039 2282 429039550 429039793 3.480000e-118 435
13 TraesCS5D01G345700 chr5B 98.361 244 4 0 2039 2282 432879628 432879871 1.620000e-116 429
14 TraesCS5D01G345700 chr5B 97.934 242 5 0 2039 2280 413610360 413610601 9.750000e-114 420
15 TraesCS5D01G345700 chr2D 98.770 244 3 0 2039 2282 33936754 33936997 3.480000e-118 435
16 TraesCS5D01G345700 chr2D 98.361 244 4 0 2039 2282 630273229 630273472 1.620000e-116 429
17 TraesCS5D01G345700 chr5A 98.361 244 4 0 2039 2282 482026465 482026222 1.620000e-116 429
18 TraesCS5D01G345700 chr1D 98.361 244 4 0 2039 2282 254419673 254419916 1.620000e-116 429


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 TraesCS5D01G345700 chr5D 432422271 432424552 2281 True 4215 4215 100.000 1 2282 1 chr5D.!!$R2 2281
1 TraesCS5D01G345700 chr5D 503218105 503220147 2042 True 3539 3539 97.944 1 2041 1 chr5D.!!$R3 2040
2 TraesCS5D01G345700 chr5D 503276297 503278339 2042 False 3528 3528 97.846 1 2041 1 chr5D.!!$F1 2040
3 TraesCS5D01G345700 chr5D 6188827 6190869 2042 True 3478 3478 97.406 1 2041 1 chr5D.!!$R1 2040
4 TraesCS5D01G345700 chr1A 554512135 554514177 2042 True 3544 3544 97.994 1 2041 1 chr1A.!!$R1 2040
5 TraesCS5D01G345700 chrUn 346594565 346596607 2042 False 3528 3528 97.846 1 2041 1 chrUn.!!$F2 2040
6 TraesCS5D01G345700 chrUn 216516674 216518715 2041 False 3493 3493 97.553 1 2041 1 chrUn.!!$F1 2040
7 TraesCS5D01G345700 chr3B 201526911 201528953 2042 True 3522 3522 97.797 1 2041 1 chr3B.!!$R1 2040
8 TraesCS5D01G345700 chr6D 168254813 168256855 2042 True 3511 3511 97.699 1 2041 1 chr6D.!!$R1 2040
9 TraesCS5D01G345700 chr3D 589277616 589279655 2039 False 3502 3502 97.651 1 2041 1 chr3D.!!$F1 2040

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
817 818 1.937191 ATTTGCGGGTTCAATCCCTT 58.063 45.0 0.25 0.0 44.95 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 1906 1.001378 GGTTCTGTGCGTGCTTCAAAT 60.001 47.619 0.0 0.0 0.0 2.32 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
69 70 5.250235 GTGCTACAAGATCTAGTGCACTA 57.750 43.478 24.63 24.63 43.79 2.74
134 135 4.894705 TGTCTTTACAAGGTAAAAACCCCC 59.105 41.667 3.64 0.00 30.91 5.40
187 188 4.657814 TCTTGTGGAATAAGAAGCCCTT 57.342 40.909 0.00 0.00 41.30 3.95
201 202 5.254115 AGAAGCCCTTGTACCTTAATGAAC 58.746 41.667 0.00 0.00 0.00 3.18
406 407 9.046296 CAAGGAATATACGTCTTTCTGCTAAAT 57.954 33.333 0.00 0.00 0.00 1.40
542 543 7.440556 TGCTAAAGAGAAATGATCACTATGAGC 59.559 37.037 0.00 2.57 32.94 4.26
585 586 7.337942 GGATCCATTCCAAATAGCGAGAATTAT 59.662 37.037 6.95 0.00 44.74 1.28
611 612 4.222336 TCTTGATCCCTCTCAATCTCTCC 58.778 47.826 0.00 0.00 34.76 3.71
813 814 4.181309 TGGTAAATTTGCGGGTTCAATC 57.819 40.909 0.00 0.00 0.00 2.67
817 818 1.937191 ATTTGCGGGTTCAATCCCTT 58.063 45.000 0.25 0.00 44.95 3.95
1370 1373 3.012518 CCCTAGACAGGCAAGTGAAATG 58.987 50.000 0.00 0.00 41.08 2.32
1387 1390 7.995289 AGTGAAATGCAATCCACGAAATAATA 58.005 30.769 0.00 0.00 34.93 0.98
1802 1806 3.140519 ACCTCTACGGGATAGACCTCAAT 59.859 47.826 0.00 0.00 34.80 2.57
2003 2007 5.182001 GTCAGAGGCAAATTGAAAGCTAAGA 59.818 40.000 0.00 0.00 0.00 2.10
2037 2041 2.197599 CCCGGGGGAAAATAGGGC 59.802 66.667 14.71 0.00 37.50 5.19
2041 2045 0.033503 CGGGGGAAAATAGGGCTGTT 60.034 55.000 0.00 0.00 0.00 3.16
2042 2046 1.618616 CGGGGGAAAATAGGGCTGTTT 60.619 52.381 0.00 0.00 0.00 2.83
2043 2047 2.546899 GGGGGAAAATAGGGCTGTTTT 58.453 47.619 0.00 0.00 36.75 2.43
2044 2048 2.236146 GGGGGAAAATAGGGCTGTTTTG 59.764 50.000 0.00 0.00 34.72 2.44
2045 2049 2.354704 GGGGAAAATAGGGCTGTTTTGC 60.355 50.000 0.00 0.00 39.78 3.68
2046 2050 2.567169 GGGAAAATAGGGCTGTTTTGCT 59.433 45.455 0.00 0.00 40.15 3.91
2047 2051 3.588955 GGAAAATAGGGCTGTTTTGCTG 58.411 45.455 0.00 0.00 38.35 4.41
2048 2052 3.258123 GGAAAATAGGGCTGTTTTGCTGA 59.742 43.478 0.00 0.00 38.35 4.26
2049 2053 4.081476 GGAAAATAGGGCTGTTTTGCTGAT 60.081 41.667 0.00 0.00 38.35 2.90
2050 2054 5.127031 GGAAAATAGGGCTGTTTTGCTGATA 59.873 40.000 0.00 0.00 38.35 2.15
2051 2055 6.183360 GGAAAATAGGGCTGTTTTGCTGATAT 60.183 38.462 0.00 0.00 38.35 1.63
2052 2056 6.796785 AAATAGGGCTGTTTTGCTGATATT 57.203 33.333 0.00 0.00 0.00 1.28
2053 2057 6.796785 AATAGGGCTGTTTTGCTGATATTT 57.203 33.333 0.00 0.00 0.00 1.40
2054 2058 4.460948 AGGGCTGTTTTGCTGATATTTG 57.539 40.909 0.00 0.00 0.00 2.32
2055 2059 2.931969 GGGCTGTTTTGCTGATATTTGC 59.068 45.455 0.00 0.00 0.00 3.68
2056 2060 3.587923 GGCTGTTTTGCTGATATTTGCA 58.412 40.909 0.31 0.31 37.42 4.08
2057 2061 3.615496 GGCTGTTTTGCTGATATTTGCAG 59.385 43.478 4.26 0.00 40.46 4.41
2058 2062 3.615496 GCTGTTTTGCTGATATTTGCAGG 59.385 43.478 0.00 0.00 40.46 4.85
2059 2063 4.813027 CTGTTTTGCTGATATTTGCAGGT 58.187 39.130 0.00 0.00 40.46 4.00
2060 2064 5.212532 TGTTTTGCTGATATTTGCAGGTT 57.787 34.783 0.00 0.00 40.46 3.50
2061 2065 5.229423 TGTTTTGCTGATATTTGCAGGTTC 58.771 37.500 0.00 0.00 40.46 3.62
2062 2066 5.221402 TGTTTTGCTGATATTTGCAGGTTCA 60.221 36.000 0.00 0.00 40.46 3.18
2063 2067 5.664294 TTTGCTGATATTTGCAGGTTCAT 57.336 34.783 0.00 0.00 40.46 2.57
2064 2068 5.664294 TTGCTGATATTTGCAGGTTCATT 57.336 34.783 0.00 0.00 40.46 2.57
2065 2069 6.772360 TTGCTGATATTTGCAGGTTCATTA 57.228 33.333 0.00 0.00 40.46 1.90
2066 2070 6.772360 TGCTGATATTTGCAGGTTCATTAA 57.228 33.333 0.00 0.00 34.84 1.40
2067 2071 7.350744 TGCTGATATTTGCAGGTTCATTAAT 57.649 32.000 0.00 0.00 34.84 1.40
2068 2072 7.784037 TGCTGATATTTGCAGGTTCATTAATT 58.216 30.769 0.00 0.00 34.84 1.40
2069 2073 8.259411 TGCTGATATTTGCAGGTTCATTAATTT 58.741 29.630 0.00 0.00 34.84 1.82
2070 2074 9.101655 GCTGATATTTGCAGGTTCATTAATTTT 57.898 29.630 0.00 0.00 34.00 1.82
2098 2102 7.754851 TTTACCTCATAAGGGAAACAAAGTC 57.245 36.000 0.00 0.00 46.72 3.01
2099 2103 4.946784 CCTCATAAGGGAAACAAAGTCG 57.053 45.455 0.00 0.00 39.21 4.18
2100 2104 4.324267 CCTCATAAGGGAAACAAAGTCGT 58.676 43.478 0.00 0.00 39.21 4.34
2101 2105 4.760204 CCTCATAAGGGAAACAAAGTCGTT 59.240 41.667 0.00 0.00 39.21 3.85
2102 2106 5.935789 CCTCATAAGGGAAACAAAGTCGTTA 59.064 40.000 0.00 0.00 39.21 3.18
2103 2107 6.092259 CCTCATAAGGGAAACAAAGTCGTTAG 59.908 42.308 0.00 0.00 39.21 2.34
2104 2108 5.935789 TCATAAGGGAAACAAAGTCGTTAGG 59.064 40.000 0.00 0.00 0.00 2.69
2105 2109 3.851458 AGGGAAACAAAGTCGTTAGGT 57.149 42.857 0.00 0.00 0.00 3.08
2106 2110 3.473625 AGGGAAACAAAGTCGTTAGGTG 58.526 45.455 0.00 0.00 0.00 4.00
2107 2111 2.551032 GGGAAACAAAGTCGTTAGGTGG 59.449 50.000 0.00 0.00 0.00 4.61
2108 2112 3.208594 GGAAACAAAGTCGTTAGGTGGT 58.791 45.455 0.00 0.00 0.00 4.16
2109 2113 4.379652 GGAAACAAAGTCGTTAGGTGGTA 58.620 43.478 0.00 0.00 0.00 3.25
2110 2114 4.999311 GGAAACAAAGTCGTTAGGTGGTAT 59.001 41.667 0.00 0.00 0.00 2.73
2111 2115 6.165577 GGAAACAAAGTCGTTAGGTGGTATA 58.834 40.000 0.00 0.00 0.00 1.47
2112 2116 6.091305 GGAAACAAAGTCGTTAGGTGGTATAC 59.909 42.308 0.00 0.00 0.00 1.47
2113 2117 5.990120 ACAAAGTCGTTAGGTGGTATACT 57.010 39.130 2.25 0.00 0.00 2.12
2114 2118 7.466746 AACAAAGTCGTTAGGTGGTATACTA 57.533 36.000 2.25 0.00 0.00 1.82
2115 2119 7.651027 ACAAAGTCGTTAGGTGGTATACTAT 57.349 36.000 2.25 0.00 0.00 2.12
2116 2120 8.752005 ACAAAGTCGTTAGGTGGTATACTATA 57.248 34.615 2.25 0.00 0.00 1.31
2117 2121 9.359653 ACAAAGTCGTTAGGTGGTATACTATAT 57.640 33.333 2.25 0.00 0.00 0.86
2118 2122 9.837525 CAAAGTCGTTAGGTGGTATACTATATC 57.162 37.037 2.25 0.00 0.00 1.63
2119 2123 9.804977 AAAGTCGTTAGGTGGTATACTATATCT 57.195 33.333 2.25 0.00 0.00 1.98
2155 2159 7.721286 AGAATTCCTTCTAATGACTTATGCG 57.279 36.000 0.65 0.00 40.00 4.73
2156 2160 7.275920 AGAATTCCTTCTAATGACTTATGCGT 58.724 34.615 0.65 0.00 40.00 5.24
2157 2161 7.770897 AGAATTCCTTCTAATGACTTATGCGTT 59.229 33.333 0.65 0.00 40.00 4.84
2158 2162 6.903883 TTCCTTCTAATGACTTATGCGTTC 57.096 37.500 0.00 0.00 0.00 3.95
2159 2163 6.222038 TCCTTCTAATGACTTATGCGTTCT 57.778 37.500 0.00 0.00 0.00 3.01
2160 2164 6.042777 TCCTTCTAATGACTTATGCGTTCTG 58.957 40.000 0.00 0.00 0.00 3.02
2161 2165 5.812642 CCTTCTAATGACTTATGCGTTCTGT 59.187 40.000 0.00 0.00 0.00 3.41
2162 2166 6.313905 CCTTCTAATGACTTATGCGTTCTGTT 59.686 38.462 0.00 0.00 0.00 3.16
2163 2167 7.491372 CCTTCTAATGACTTATGCGTTCTGTTA 59.509 37.037 0.00 0.00 0.00 2.41
2164 2168 8.942338 TTCTAATGACTTATGCGTTCTGTTAT 57.058 30.769 0.00 0.00 0.00 1.89
2165 2169 8.575565 TCTAATGACTTATGCGTTCTGTTATC 57.424 34.615 0.00 0.00 0.00 1.75
2166 2170 8.194769 TCTAATGACTTATGCGTTCTGTTATCA 58.805 33.333 0.00 0.00 0.00 2.15
2167 2171 7.792374 AATGACTTATGCGTTCTGTTATCAT 57.208 32.000 0.00 0.00 0.00 2.45
2168 2172 7.792374 ATGACTTATGCGTTCTGTTATCATT 57.208 32.000 0.00 0.00 0.00 2.57
2169 2173 7.609760 TGACTTATGCGTTCTGTTATCATTT 57.390 32.000 0.00 0.00 0.00 2.32
2170 2174 7.684670 TGACTTATGCGTTCTGTTATCATTTC 58.315 34.615 0.00 0.00 0.00 2.17
2171 2175 7.016361 ACTTATGCGTTCTGTTATCATTTCC 57.984 36.000 0.00 0.00 0.00 3.13
2172 2176 6.597672 ACTTATGCGTTCTGTTATCATTTCCA 59.402 34.615 0.00 0.00 0.00 3.53
2173 2177 5.895636 ATGCGTTCTGTTATCATTTCCAA 57.104 34.783 0.00 0.00 0.00 3.53
2174 2178 5.041951 TGCGTTCTGTTATCATTTCCAAC 57.958 39.130 0.00 0.00 0.00 3.77
2175 2179 4.759693 TGCGTTCTGTTATCATTTCCAACT 59.240 37.500 0.00 0.00 0.00 3.16
2176 2180 5.088739 GCGTTCTGTTATCATTTCCAACTG 58.911 41.667 0.00 0.00 0.00 3.16
2177 2181 5.631026 CGTTCTGTTATCATTTCCAACTGG 58.369 41.667 0.00 0.00 0.00 4.00
2178 2182 5.411361 CGTTCTGTTATCATTTCCAACTGGA 59.589 40.000 0.00 0.00 43.73 3.86
2179 2183 6.402550 CGTTCTGTTATCATTTCCAACTGGAG 60.403 42.308 0.00 0.00 46.36 3.86
2180 2184 5.500234 TCTGTTATCATTTCCAACTGGAGG 58.500 41.667 0.00 0.00 46.36 4.30
2181 2185 5.250543 TCTGTTATCATTTCCAACTGGAGGA 59.749 40.000 0.00 0.00 46.36 3.71
2182 2186 6.069440 TCTGTTATCATTTCCAACTGGAGGAT 60.069 38.462 11.81 11.81 46.36 3.24
2183 2187 6.122277 TGTTATCATTTCCAACTGGAGGATC 58.878 40.000 10.92 0.00 46.36 3.36
2201 2205 7.767250 GAGGATCCCTTAATCCAATTAAAGG 57.233 40.000 8.55 2.06 46.56 3.11
2202 2206 7.480222 AGGATCCCTTAATCCAATTAAAGGA 57.520 36.000 8.55 10.64 46.56 3.36
2203 2207 7.530435 AGGATCCCTTAATCCAATTAAAGGAG 58.470 38.462 8.55 0.00 44.32 3.69
2204 2208 6.721668 GGATCCCTTAATCCAATTAAAGGAGG 59.278 42.308 0.00 3.36 44.32 4.30
2205 2209 6.918951 TCCCTTAATCCAATTAAAGGAGGA 57.081 37.500 5.91 4.37 39.32 3.71
2206 2210 7.480222 TCCCTTAATCCAATTAAAGGAGGAT 57.520 36.000 5.91 0.00 39.32 3.24
2207 2211 8.523009 ATCCCTTAATCCAATTAAAGGAGGATT 58.477 33.333 12.78 10.08 44.32 3.01
2208 2212 9.020644 TCCCTTAATCCAATTAAAGGAGGATTA 57.979 33.333 8.29 8.29 46.16 1.75
2209 2213 9.828691 CCCTTAATCCAATTAAAGGAGGATTAT 57.171 33.333 12.09 0.00 46.65 1.28
2225 2229 9.796242 AGGAGGATTATAAATGGATAGATGTCT 57.204 33.333 0.00 0.00 0.00 3.41
2235 2239 8.827832 AAATGGATAGATGTCTTTGATTTCCA 57.172 30.769 0.00 0.00 35.39 3.53
2236 2240 7.814264 ATGGATAGATGTCTTTGATTTCCAC 57.186 36.000 0.00 0.00 33.86 4.02
2237 2241 6.962182 TGGATAGATGTCTTTGATTTCCACT 58.038 36.000 0.00 0.00 0.00 4.00
2238 2242 6.825213 TGGATAGATGTCTTTGATTTCCACTG 59.175 38.462 0.00 0.00 0.00 3.66
2239 2243 6.261826 GGATAGATGTCTTTGATTTCCACTGG 59.738 42.308 0.00 0.00 0.00 4.00
2240 2244 5.246981 AGATGTCTTTGATTTCCACTGGA 57.753 39.130 0.00 0.00 0.00 3.86
2241 2245 5.251764 AGATGTCTTTGATTTCCACTGGAG 58.748 41.667 0.00 0.00 31.21 3.86
2242 2246 4.705110 TGTCTTTGATTTCCACTGGAGA 57.295 40.909 0.00 0.00 31.21 3.71
2243 2247 5.246981 TGTCTTTGATTTCCACTGGAGAT 57.753 39.130 0.57 0.57 31.21 2.75
2244 2248 5.634118 TGTCTTTGATTTCCACTGGAGATT 58.366 37.500 2.67 0.00 31.21 2.40
2245 2249 5.474532 TGTCTTTGATTTCCACTGGAGATTG 59.525 40.000 2.67 0.00 31.21 2.67
2246 2250 5.012239 TCTTTGATTTCCACTGGAGATTGG 58.988 41.667 2.67 0.00 31.21 3.16
2247 2251 3.370840 TGATTTCCACTGGAGATTGGG 57.629 47.619 2.67 0.00 33.25 4.12
2248 2252 2.918934 TGATTTCCACTGGAGATTGGGA 59.081 45.455 2.67 0.00 33.25 4.37
2249 2253 3.333381 TGATTTCCACTGGAGATTGGGAA 59.667 43.478 2.67 0.00 34.71 3.97
2250 2254 4.017222 TGATTTCCACTGGAGATTGGGAAT 60.017 41.667 2.67 0.00 42.90 3.01
2251 2255 3.652057 TTCCACTGGAGATTGGGAATC 57.348 47.619 0.00 0.00 38.20 2.52
2252 2256 1.486310 TCCACTGGAGATTGGGAATCG 59.514 52.381 0.00 0.00 42.75 3.34
2253 2257 1.486310 CCACTGGAGATTGGGAATCGA 59.514 52.381 0.00 0.00 42.75 3.59
2254 2258 2.105477 CCACTGGAGATTGGGAATCGAT 59.895 50.000 0.00 0.00 42.75 3.59
2255 2259 3.136763 CACTGGAGATTGGGAATCGATG 58.863 50.000 0.00 0.00 42.75 3.84
2256 2260 2.105477 ACTGGAGATTGGGAATCGATGG 59.895 50.000 0.00 0.00 42.75 3.51
2257 2261 2.369860 CTGGAGATTGGGAATCGATGGA 59.630 50.000 0.00 0.00 42.75 3.41
2258 2262 2.104792 TGGAGATTGGGAATCGATGGAC 59.895 50.000 0.00 0.00 42.75 4.02
2259 2263 2.370189 GGAGATTGGGAATCGATGGACT 59.630 50.000 0.00 0.00 42.75 3.85
2260 2264 3.181450 GGAGATTGGGAATCGATGGACTT 60.181 47.826 0.00 0.00 42.75 3.01
2261 2265 4.455606 GAGATTGGGAATCGATGGACTTT 58.544 43.478 0.00 0.00 42.75 2.66
2262 2266 4.455606 AGATTGGGAATCGATGGACTTTC 58.544 43.478 0.00 0.00 42.75 2.62
2263 2267 3.712016 TTGGGAATCGATGGACTTTCA 57.288 42.857 0.00 0.00 0.00 2.69
2264 2268 3.931907 TGGGAATCGATGGACTTTCAT 57.068 42.857 0.00 0.00 0.00 2.57
2265 2269 4.235079 TGGGAATCGATGGACTTTCATT 57.765 40.909 0.00 0.00 0.00 2.57
2266 2270 5.366482 TGGGAATCGATGGACTTTCATTA 57.634 39.130 0.00 0.00 0.00 1.90
2267 2271 5.368145 TGGGAATCGATGGACTTTCATTAG 58.632 41.667 0.00 0.00 0.00 1.73
2268 2272 4.757149 GGGAATCGATGGACTTTCATTAGG 59.243 45.833 0.00 0.00 0.00 2.69
2269 2273 5.454755 GGGAATCGATGGACTTTCATTAGGA 60.455 44.000 0.00 0.00 0.00 2.94
2270 2274 6.234177 GGAATCGATGGACTTTCATTAGGAT 58.766 40.000 0.00 0.00 0.00 3.24
2271 2275 6.370166 GGAATCGATGGACTTTCATTAGGATC 59.630 42.308 0.00 0.00 0.00 3.36
2272 2276 6.678568 ATCGATGGACTTTCATTAGGATCT 57.321 37.500 0.00 0.00 0.00 2.75
2273 2277 7.782897 ATCGATGGACTTTCATTAGGATCTA 57.217 36.000 0.00 0.00 0.00 1.98
2274 2278 7.782897 TCGATGGACTTTCATTAGGATCTAT 57.217 36.000 0.00 0.00 0.00 1.98
2275 2279 8.195165 TCGATGGACTTTCATTAGGATCTATT 57.805 34.615 0.00 0.00 0.00 1.73
2276 2280 8.651389 TCGATGGACTTTCATTAGGATCTATTT 58.349 33.333 0.00 0.00 0.00 1.40
2277 2281 9.277783 CGATGGACTTTCATTAGGATCTATTTT 57.722 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 5.104109 TCCATACTAAAGGATTTGGGTCCAG 60.104 44.000 0.00 0.00 41.28 3.86
90 91 9.533831 AAGACAATGTTCCATACTAAAGGATTT 57.466 29.630 0.00 0.00 43.42 2.17
118 119 4.752621 ATACTGGGGGTTTTTACCTTGT 57.247 40.909 0.00 0.00 0.00 3.16
120 121 6.661740 TCATATACTGGGGGTTTTTACCTT 57.338 37.500 0.00 0.00 0.00 3.50
122 123 7.120716 TCTTTCATATACTGGGGGTTTTTACC 58.879 38.462 0.00 0.00 0.00 2.85
134 135 8.680903 AGCACCTTTTCATTCTTTCATATACTG 58.319 33.333 0.00 0.00 0.00 2.74
187 188 5.933463 ACGATTTTCCGTTCATTAAGGTACA 59.067 36.000 0.00 0.00 40.17 2.90
332 333 3.408634 CAAACCTCGTGTGGGACTAATT 58.591 45.455 0.00 0.00 0.00 1.40
542 543 5.933617 TGGATCCAATTCTATTGAGTCTGG 58.066 41.667 13.46 0.00 0.00 3.86
585 586 5.904169 AGAGATTGAGAGGGATCAAGAATCA 59.096 40.000 0.00 0.00 42.20 2.57
611 612 4.501229 CCTCTCTGGATCCTCGAATTGAAG 60.501 50.000 14.23 0.00 38.35 3.02
813 814 0.321564 TTCGTGTGCATCCAGAAGGG 60.322 55.000 0.00 0.00 34.83 3.95
817 818 1.374125 CCGTTCGTGTGCATCCAGA 60.374 57.895 0.00 0.00 0.00 3.86
1351 1354 3.076621 TGCATTTCACTTGCCTGTCTAG 58.923 45.455 0.00 0.00 39.39 2.43
1370 1373 7.144722 TGGATCATATTATTTCGTGGATTGC 57.855 36.000 0.00 0.00 0.00 3.56
1387 1390 1.149174 GGTGCCGTCCATGGATCAT 59.851 57.895 19.62 0.00 0.00 2.45
1741 1745 5.100259 GTGATCGATTTCTAGGTTTCGTCA 58.900 41.667 0.00 8.49 33.52 4.35
1802 1806 4.695396 TGCCGTTACTCAACAGTTTTCTA 58.305 39.130 0.00 0.00 34.05 2.10
1902 1906 1.001378 GGTTCTGTGCGTGCTTCAAAT 60.001 47.619 0.00 0.00 0.00 2.32
2003 2007 2.173996 CCGGGGGTCATAATTACCACTT 59.826 50.000 0.00 0.00 40.51 3.16
2037 2041 4.813027 ACCTGCAAATATCAGCAAAACAG 58.187 39.130 3.95 0.00 40.73 3.16
2041 2045 5.664294 ATGAACCTGCAAATATCAGCAAA 57.336 34.783 3.95 0.00 40.73 3.68
2042 2046 5.664294 AATGAACCTGCAAATATCAGCAA 57.336 34.783 3.95 0.00 40.73 3.91
2043 2047 6.772360 TTAATGAACCTGCAAATATCAGCA 57.228 33.333 2.53 2.53 39.25 4.41
2044 2048 8.652810 AAATTAATGAACCTGCAAATATCAGC 57.347 30.769 0.00 0.00 0.00 4.26
2071 2075 9.154632 ACTTTGTTTCCCTTATGAGGTAAAAAT 57.845 29.630 2.39 0.00 41.85 1.82
2072 2076 8.541899 ACTTTGTTTCCCTTATGAGGTAAAAA 57.458 30.769 2.39 0.00 41.85 1.94
2073 2077 7.040961 CGACTTTGTTTCCCTTATGAGGTAAAA 60.041 37.037 2.39 0.48 41.85 1.52
2074 2078 6.428771 CGACTTTGTTTCCCTTATGAGGTAAA 59.571 38.462 2.39 0.00 41.85 2.01
2075 2079 5.935789 CGACTTTGTTTCCCTTATGAGGTAA 59.064 40.000 2.39 0.00 41.85 2.85
2076 2080 5.012354 ACGACTTTGTTTCCCTTATGAGGTA 59.988 40.000 2.39 0.00 41.85 3.08
2077 2081 4.202430 ACGACTTTGTTTCCCTTATGAGGT 60.202 41.667 2.39 0.00 41.85 3.85
2078 2082 4.324267 ACGACTTTGTTTCCCTTATGAGG 58.676 43.478 0.00 0.00 43.15 3.86
2079 2083 5.941948 AACGACTTTGTTTCCCTTATGAG 57.058 39.130 0.00 0.00 0.00 2.90
2080 2084 5.935789 CCTAACGACTTTGTTTCCCTTATGA 59.064 40.000 0.00 0.00 33.32 2.15
2081 2085 5.704053 ACCTAACGACTTTGTTTCCCTTATG 59.296 40.000 0.00 0.00 33.32 1.90
2082 2086 5.704053 CACCTAACGACTTTGTTTCCCTTAT 59.296 40.000 0.00 0.00 33.32 1.73
2083 2087 5.058490 CACCTAACGACTTTGTTTCCCTTA 58.942 41.667 0.00 0.00 33.32 2.69
2084 2088 3.881089 CACCTAACGACTTTGTTTCCCTT 59.119 43.478 0.00 0.00 33.32 3.95
2085 2089 3.473625 CACCTAACGACTTTGTTTCCCT 58.526 45.455 0.00 0.00 33.32 4.20
2086 2090 2.551032 CCACCTAACGACTTTGTTTCCC 59.449 50.000 0.00 0.00 33.32 3.97
2087 2091 3.208594 ACCACCTAACGACTTTGTTTCC 58.791 45.455 0.00 0.00 33.32 3.13
2088 2092 6.870439 AGTATACCACCTAACGACTTTGTTTC 59.130 38.462 0.00 0.00 33.32 2.78
2089 2093 6.762333 AGTATACCACCTAACGACTTTGTTT 58.238 36.000 0.00 0.00 33.32 2.83
2090 2094 6.350629 AGTATACCACCTAACGACTTTGTT 57.649 37.500 0.00 0.00 35.86 2.83
2091 2095 5.990120 AGTATACCACCTAACGACTTTGT 57.010 39.130 0.00 0.00 0.00 2.83
2092 2096 9.837525 GATATAGTATACCACCTAACGACTTTG 57.162 37.037 0.00 0.00 0.00 2.77
2093 2097 9.804977 AGATATAGTATACCACCTAACGACTTT 57.195 33.333 0.00 0.00 0.00 2.66
2129 2133 9.261180 CGCATAAGTCATTAGAAGGAATTCTAA 57.739 33.333 11.64 11.64 44.68 2.10
2130 2134 8.421784 ACGCATAAGTCATTAGAAGGAATTCTA 58.578 33.333 5.23 0.00 29.58 2.10
2131 2135 7.275920 ACGCATAAGTCATTAGAAGGAATTCT 58.724 34.615 5.23 0.00 29.58 2.40
2132 2136 7.484035 ACGCATAAGTCATTAGAAGGAATTC 57.516 36.000 0.00 0.00 29.58 2.17
2133 2137 7.770897 AGAACGCATAAGTCATTAGAAGGAATT 59.229 33.333 0.00 0.00 31.74 2.17
2134 2138 7.225538 CAGAACGCATAAGTCATTAGAAGGAAT 59.774 37.037 0.00 0.00 0.00 3.01
2135 2139 6.535150 CAGAACGCATAAGTCATTAGAAGGAA 59.465 38.462 0.00 0.00 0.00 3.36
2136 2140 6.042777 CAGAACGCATAAGTCATTAGAAGGA 58.957 40.000 0.00 0.00 0.00 3.36
2137 2141 5.812642 ACAGAACGCATAAGTCATTAGAAGG 59.187 40.000 0.00 0.00 0.00 3.46
2138 2142 6.893958 ACAGAACGCATAAGTCATTAGAAG 57.106 37.500 0.00 0.00 0.00 2.85
2139 2143 8.942338 ATAACAGAACGCATAAGTCATTAGAA 57.058 30.769 0.00 0.00 0.00 2.10
2140 2144 8.194769 TGATAACAGAACGCATAAGTCATTAGA 58.805 33.333 0.00 0.00 0.00 2.10
2141 2145 8.352752 TGATAACAGAACGCATAAGTCATTAG 57.647 34.615 0.00 0.00 0.00 1.73
2142 2146 8.887036 ATGATAACAGAACGCATAAGTCATTA 57.113 30.769 0.00 0.00 0.00 1.90
2143 2147 7.792374 ATGATAACAGAACGCATAAGTCATT 57.208 32.000 0.00 0.00 0.00 2.57
2144 2148 7.792374 AATGATAACAGAACGCATAAGTCAT 57.208 32.000 0.00 0.00 0.00 3.06
2145 2149 7.201609 GGAAATGATAACAGAACGCATAAGTCA 60.202 37.037 0.00 0.00 0.00 3.41
2146 2150 7.126398 GGAAATGATAACAGAACGCATAAGTC 58.874 38.462 0.00 0.00 0.00 3.01
2147 2151 6.597672 TGGAAATGATAACAGAACGCATAAGT 59.402 34.615 0.00 0.00 0.00 2.24
2148 2152 7.015226 TGGAAATGATAACAGAACGCATAAG 57.985 36.000 0.00 0.00 0.00 1.73
2149 2153 6.993786 TGGAAATGATAACAGAACGCATAA 57.006 33.333 0.00 0.00 0.00 1.90
2150 2154 6.597672 AGTTGGAAATGATAACAGAACGCATA 59.402 34.615 0.00 0.00 0.00 3.14
2151 2155 5.415701 AGTTGGAAATGATAACAGAACGCAT 59.584 36.000 0.00 0.00 0.00 4.73
2152 2156 4.759693 AGTTGGAAATGATAACAGAACGCA 59.240 37.500 0.00 0.00 0.00 5.24
2153 2157 5.088739 CAGTTGGAAATGATAACAGAACGC 58.911 41.667 0.00 0.00 0.00 4.84
2154 2158 5.411361 TCCAGTTGGAAATGATAACAGAACG 59.589 40.000 0.00 0.00 42.18 3.95
2155 2159 6.127897 CCTCCAGTTGGAAATGATAACAGAAC 60.128 42.308 1.99 0.00 44.91 3.01
2156 2160 5.945784 CCTCCAGTTGGAAATGATAACAGAA 59.054 40.000 1.99 0.00 44.91 3.02
2157 2161 5.250543 TCCTCCAGTTGGAAATGATAACAGA 59.749 40.000 1.99 0.00 44.91 3.41
2158 2162 5.500234 TCCTCCAGTTGGAAATGATAACAG 58.500 41.667 1.99 0.00 44.91 3.16
2159 2163 5.512942 TCCTCCAGTTGGAAATGATAACA 57.487 39.130 1.99 0.00 44.91 2.41
2160 2164 5.532779 GGATCCTCCAGTTGGAAATGATAAC 59.467 44.000 3.84 0.00 44.91 1.89
2161 2165 5.399038 GGGATCCTCCAGTTGGAAATGATAA 60.399 44.000 12.58 0.00 44.91 1.75
2162 2166 4.104738 GGGATCCTCCAGTTGGAAATGATA 59.895 45.833 12.58 0.00 44.91 2.15
2163 2167 3.117360 GGGATCCTCCAGTTGGAAATGAT 60.117 47.826 12.58 5.04 44.91 2.45
2164 2168 2.242196 GGGATCCTCCAGTTGGAAATGA 59.758 50.000 12.58 0.42 44.91 2.57
2165 2169 2.243221 AGGGATCCTCCAGTTGGAAATG 59.757 50.000 12.58 0.00 44.91 2.32
2166 2170 2.577970 AGGGATCCTCCAGTTGGAAAT 58.422 47.619 12.58 0.00 44.91 2.17
2167 2171 2.059756 AGGGATCCTCCAGTTGGAAA 57.940 50.000 12.58 0.00 44.91 3.13
2168 2172 2.059756 AAGGGATCCTCCAGTTGGAA 57.940 50.000 12.58 0.00 44.91 3.53
2169 2173 2.961536 TAAGGGATCCTCCAGTTGGA 57.038 50.000 12.58 0.18 43.08 3.53
2170 2174 3.181439 GGATTAAGGGATCCTCCAGTTGG 60.181 52.174 12.58 0.00 41.96 3.77
2171 2175 3.459598 TGGATTAAGGGATCCTCCAGTTG 59.540 47.826 14.21 0.00 44.85 3.16
2172 2176 3.747852 TGGATTAAGGGATCCTCCAGTT 58.252 45.455 14.21 3.12 44.85 3.16
2173 2177 3.438131 TGGATTAAGGGATCCTCCAGT 57.562 47.619 14.21 0.00 44.85 4.00
2174 2178 5.330648 AATTGGATTAAGGGATCCTCCAG 57.669 43.478 16.78 0.00 44.85 3.86
2175 2179 6.857083 TTAATTGGATTAAGGGATCCTCCA 57.143 37.500 14.21 14.21 44.85 3.86
2176 2180 7.767250 CTTTAATTGGATTAAGGGATCCTCC 57.233 40.000 12.58 10.85 44.85 4.30
2199 2203 9.796242 AGACATCTATCCATTTATAATCCTCCT 57.204 33.333 0.00 0.00 0.00 3.69
2209 2213 9.919416 TGGAAATCAAAGACATCTATCCATTTA 57.081 29.630 0.00 0.00 29.93 1.40
2210 2214 8.689972 GTGGAAATCAAAGACATCTATCCATTT 58.310 33.333 0.00 0.00 36.86 2.32
2211 2215 8.057623 AGTGGAAATCAAAGACATCTATCCATT 58.942 33.333 0.00 0.00 36.86 3.16
2212 2216 7.501559 CAGTGGAAATCAAAGACATCTATCCAT 59.498 37.037 0.00 0.00 36.86 3.41
2213 2217 6.825213 CAGTGGAAATCAAAGACATCTATCCA 59.175 38.462 0.00 0.00 32.33 3.41
2214 2218 6.261826 CCAGTGGAAATCAAAGACATCTATCC 59.738 42.308 1.68 0.00 0.00 2.59
2215 2219 7.050377 TCCAGTGGAAATCAAAGACATCTATC 58.950 38.462 10.20 0.00 0.00 2.08
2216 2220 6.962182 TCCAGTGGAAATCAAAGACATCTAT 58.038 36.000 10.20 0.00 0.00 1.98
2217 2221 6.213397 TCTCCAGTGGAAATCAAAGACATCTA 59.787 38.462 14.17 0.00 0.00 1.98
2218 2222 5.013495 TCTCCAGTGGAAATCAAAGACATCT 59.987 40.000 14.17 0.00 0.00 2.90
2219 2223 5.248640 TCTCCAGTGGAAATCAAAGACATC 58.751 41.667 14.17 0.00 0.00 3.06
2220 2224 5.246981 TCTCCAGTGGAAATCAAAGACAT 57.753 39.130 14.17 0.00 0.00 3.06
2221 2225 4.705110 TCTCCAGTGGAAATCAAAGACA 57.295 40.909 14.17 0.00 0.00 3.41
2222 2226 5.105997 CCAATCTCCAGTGGAAATCAAAGAC 60.106 44.000 14.17 0.00 37.03 3.01
2223 2227 5.012239 CCAATCTCCAGTGGAAATCAAAGA 58.988 41.667 14.17 5.38 37.03 2.52
2224 2228 4.159135 CCCAATCTCCAGTGGAAATCAAAG 59.841 45.833 14.17 0.00 37.03 2.77
2225 2229 4.088634 CCCAATCTCCAGTGGAAATCAAA 58.911 43.478 14.17 0.00 37.03 2.69
2226 2230 3.333381 TCCCAATCTCCAGTGGAAATCAA 59.667 43.478 14.17 0.00 37.03 2.57
2227 2231 2.918934 TCCCAATCTCCAGTGGAAATCA 59.081 45.455 14.17 0.00 37.03 2.57
2228 2232 3.652057 TCCCAATCTCCAGTGGAAATC 57.348 47.619 14.17 0.00 37.03 2.17
2229 2233 4.540715 GATTCCCAATCTCCAGTGGAAAT 58.459 43.478 14.17 7.99 38.50 2.17
2230 2234 3.622206 CGATTCCCAATCTCCAGTGGAAA 60.622 47.826 14.17 0.00 38.50 3.13
2231 2235 2.092968 CGATTCCCAATCTCCAGTGGAA 60.093 50.000 14.17 4.93 39.28 3.53
2232 2236 1.486310 CGATTCCCAATCTCCAGTGGA 59.514 52.381 12.40 12.40 37.03 4.02
2233 2237 1.486310 TCGATTCCCAATCTCCAGTGG 59.514 52.381 1.40 1.40 35.73 4.00
2234 2238 2.988010 TCGATTCCCAATCTCCAGTG 57.012 50.000 0.00 0.00 35.73 3.66
2235 2239 2.105477 CCATCGATTCCCAATCTCCAGT 59.895 50.000 0.00 0.00 35.73 4.00
2236 2240 2.369860 TCCATCGATTCCCAATCTCCAG 59.630 50.000 0.00 0.00 35.73 3.86
2237 2241 2.104792 GTCCATCGATTCCCAATCTCCA 59.895 50.000 0.00 0.00 35.73 3.86
2238 2242 2.370189 AGTCCATCGATTCCCAATCTCC 59.630 50.000 0.00 0.00 35.73 3.71
2239 2243 3.760580 AGTCCATCGATTCCCAATCTC 57.239 47.619 0.00 0.00 35.73 2.75
2240 2244 4.080356 TGAAAGTCCATCGATTCCCAATCT 60.080 41.667 0.00 0.00 35.73 2.40
2241 2245 4.199310 TGAAAGTCCATCGATTCCCAATC 58.801 43.478 0.00 0.00 34.52 2.67
2242 2246 4.235079 TGAAAGTCCATCGATTCCCAAT 57.765 40.909 0.00 0.00 0.00 3.16
2243 2247 3.712016 TGAAAGTCCATCGATTCCCAA 57.288 42.857 0.00 0.00 0.00 4.12
2244 2248 3.931907 ATGAAAGTCCATCGATTCCCA 57.068 42.857 0.00 0.00 0.00 4.37
2245 2249 4.757149 CCTAATGAAAGTCCATCGATTCCC 59.243 45.833 0.00 0.00 0.00 3.97
2246 2250 5.611374 TCCTAATGAAAGTCCATCGATTCC 58.389 41.667 0.00 0.00 0.00 3.01
2247 2251 7.158021 AGATCCTAATGAAAGTCCATCGATTC 58.842 38.462 0.00 0.00 0.00 2.52
2248 2252 7.072263 AGATCCTAATGAAAGTCCATCGATT 57.928 36.000 0.00 0.00 0.00 3.34
2249 2253 6.678568 AGATCCTAATGAAAGTCCATCGAT 57.321 37.500 0.00 0.00 0.00 3.59
2250 2254 7.782897 ATAGATCCTAATGAAAGTCCATCGA 57.217 36.000 0.00 0.00 0.00 3.59
2251 2255 8.839310 AAATAGATCCTAATGAAAGTCCATCG 57.161 34.615 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.