Multiple sequence alignment - TraesCS2B01G138000

Loading Multiple Alignment...

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 TraesCS2B01G138000 chr2B 100.000 2903 0 0 1 2903 104894262 104897164 0.000000e+00 5361.0
1 TraesCS2B01G138000 chr2B 83.591 2066 272 39 1 2018 105372499 105374545 0.000000e+00 1875.0
2 TraesCS2B01G138000 chr2B 96.319 163 6 0 2069 2231 546830167 546830329 4.770000e-68 268.0
3 TraesCS2B01G138000 chr2B 96.825 63 2 0 2841 2903 105381505 105381567 3.960000e-19 106.0
4 TraesCS2B01G138000 chr2D 92.254 2001 128 11 1 1976 66462827 66460829 0.000000e+00 2811.0
5 TraesCS2B01G138000 chr2D 84.236 2068 266 34 1 2023 65719044 65716992 0.000000e+00 1958.0
6 TraesCS2B01G138000 chr2D 94.196 448 20 2 2462 2903 66460730 66460283 0.000000e+00 678.0
7 TraesCS2B01G138000 chr2D 91.005 189 12 3 2058 2244 305514861 305515046 1.730000e-62 250.0
8 TraesCS2B01G138000 chr2D 96.825 63 2 0 2841 2903 65715655 65715593 3.960000e-19 106.0
9 TraesCS2B01G138000 chr2D 90.323 62 6 0 791 852 66118846 66118907 6.670000e-12 82.4
10 TraesCS2B01G138000 chr2A 91.490 1986 143 11 2 1963 68503840 68505823 0.000000e+00 2708.0
11 TraesCS2B01G138000 chr2A 82.640 2068 287 41 2 2019 68811400 68813445 0.000000e+00 1764.0
12 TraesCS2B01G138000 chr2A 88.131 396 25 4 2229 2624 68505959 68506332 4.410000e-123 451.0
13 TraesCS2B01G138000 chr2A 90.099 303 20 5 2610 2903 68506603 68506904 4.540000e-103 385.0
14 TraesCS2B01G138000 chr2A 93.529 170 11 0 2062 2231 722494951 722495120 1.340000e-63 254.0
15 TraesCS2B01G138000 chr2A 95.161 124 6 0 1947 2070 68505837 68505960 2.280000e-46 196.0
16 TraesCS2B01G138000 chr2A 95.238 63 3 0 2841 2903 68821990 68822052 1.840000e-17 100.0
17 TraesCS2B01G138000 chr5B 95.679 162 7 0 2069 2230 539322883 539322722 7.980000e-66 261.0
18 TraesCS2B01G138000 chr6D 95.092 163 8 0 2068 2230 394588596 394588758 1.030000e-64 257.0
19 TraesCS2B01G138000 chr5D 95.092 163 8 0 2068 2230 254008287 254008449 1.030000e-64 257.0
20 TraesCS2B01G138000 chr4B 94.611 167 8 1 2069 2235 483266540 483266375 1.030000e-64 257.0
21 TraesCS2B01G138000 chr7B 91.257 183 15 1 2064 2246 54315520 54315701 6.210000e-62 248.0
22 TraesCS2B01G138000 chr7D 90.909 187 12 5 2061 2245 579049525 579049342 2.230000e-61 246.0


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 TraesCS2B01G138000 chr2B 104894262 104897164 2902 False 5361.0 5361 100.00000 1 2903 1 chr2B.!!$F1 2902
1 TraesCS2B01G138000 chr2B 105372499 105374545 2046 False 1875.0 1875 83.59100 1 2018 1 chr2B.!!$F2 2017
2 TraesCS2B01G138000 chr2D 66460283 66462827 2544 True 1744.5 2811 93.22500 1 2903 2 chr2D.!!$R2 2902
3 TraesCS2B01G138000 chr2D 65715593 65719044 3451 True 1032.0 1958 90.53050 1 2903 2 chr2D.!!$R1 2902
4 TraesCS2B01G138000 chr2A 68811400 68813445 2045 False 1764.0 1764 82.64000 2 2019 1 chr2A.!!$F1 2017
5 TraesCS2B01G138000 chr2A 68503840 68506904 3064 False 935.0 2708 91.22025 2 2903 4 chr2A.!!$F4 2901

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
845 890 0.032813 AGCCATGCCCTAACTGCATT 60.033 50.0 0.0 0.0 46.91 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 2585 0.394899 CTGAGGAGGCATTGGGTTCC 60.395 60.0 0.0 0.0 0.0 3.62 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
36 39 1.559065 CCTAAGTGCGGAAGGGGGAA 61.559 60.000 0.00 0.00 0.00 3.97
114 117 5.630061 TCGTTTACGAATTGATGTAGTCGA 58.370 37.500 1.95 0.00 46.30 4.20
123 126 0.525668 GATGTAGTCGACGTGGCCAG 60.526 60.000 5.11 2.58 0.00 4.85
133 136 0.038166 ACGTGGCCAGAATCACCAAT 59.962 50.000 5.11 0.00 34.63 3.16
171 175 0.463833 GGACAGGGGACGGCAAATAG 60.464 60.000 0.00 0.00 0.00 1.73
234 238 1.156736 CACTCGGCCTACCAAGTTTG 58.843 55.000 0.00 0.00 34.57 2.93
244 248 0.459489 ACCAAGTTTGCGCAACATGT 59.541 45.000 24.99 12.84 37.93 3.21
245 249 0.854062 CCAAGTTTGCGCAACATGTG 59.146 50.000 24.99 17.46 37.93 3.21
300 304 1.831726 GGGACGGCTAGGGAGTACC 60.832 68.421 0.00 0.00 40.67 3.34
326 330 6.757897 TGAACCTAGCCAAAAGATGTTATG 57.242 37.500 0.00 0.00 0.00 1.90
333 337 7.285401 CCTAGCCAAAAGATGTTATGTATGGTT 59.715 37.037 0.00 0.00 0.00 3.67
385 390 2.586792 GCCCTTGCTCGAGATGGT 59.413 61.111 18.75 0.00 33.53 3.55
409 417 1.547675 CCACACCAAGGGCTACAACAT 60.548 52.381 0.00 0.00 0.00 2.71
417 425 1.064463 AGGGCTACAACATCCACCATG 60.064 52.381 0.00 0.00 38.64 3.66
452 474 5.965486 TCTTATCACATTAGCTCCTCCCTA 58.035 41.667 0.00 0.00 0.00 3.53
462 484 0.905357 CTCCTCCCTACCACCACAAG 59.095 60.000 0.00 0.00 0.00 3.16
519 544 0.103608 TTTCCAAGGGGAGGAAGGGA 60.104 55.000 0.00 0.00 46.01 4.20
544 569 6.013293 ACAAGAATCTAGCTTTTAGTCAGGGT 60.013 38.462 0.00 0.00 0.00 4.34
578 603 3.947834 GACTCAATGTCCAAATACCCAGG 59.052 47.826 0.00 0.00 39.69 4.45
604 629 9.341899 GCGTCTTTCATTATCTTTACAACAAAT 57.658 29.630 0.00 0.00 0.00 2.32
630 655 7.110155 ACAAATGGGTACGAGACAAAATAGAT 58.890 34.615 0.00 0.00 0.00 1.98
679 704 7.483018 CATCCCCTAGAGCTATATATACCCAT 58.517 42.308 0.00 0.00 0.00 4.00
698 723 2.105528 GCCGGGCAAATGCAGATG 59.894 61.111 15.62 0.00 44.36 2.90
760 786 3.734360 ACCAAATAATCCCCCATCCTCAT 59.266 43.478 0.00 0.00 0.00 2.90
778 804 7.959658 TCCTCATCATTCATTAACAACCATT 57.040 32.000 0.00 0.00 0.00 3.16
825 870 5.197224 TCCCATCCTCAACATTCTTTCAT 57.803 39.130 0.00 0.00 0.00 2.57
841 886 2.936919 TCATAGCCATGCCCTAACTG 57.063 50.000 0.00 0.00 31.73 3.16
845 890 0.032813 AGCCATGCCCTAACTGCATT 60.033 50.000 0.00 0.00 46.91 3.56
898 946 5.103129 TCCCCCATATCCAACATTCTTTCAT 60.103 40.000 0.00 0.00 0.00 2.57
900 948 6.435277 CCCCCATATCCAACATTCTTTCATAG 59.565 42.308 0.00 0.00 0.00 2.23
907 955 4.646040 CCAACATTCTTTCATAGCCATGGA 59.354 41.667 18.40 0.00 32.61 3.41
991 1041 5.299279 AGAGTTTGTTGTGTGTGATTAAGGG 59.701 40.000 0.00 0.00 0.00 3.95
1028 1087 4.644685 ACTGGACATGTATAAAATGGTGGC 59.355 41.667 0.00 0.00 0.00 5.01
1029 1088 4.604156 TGGACATGTATAAAATGGTGGCA 58.396 39.130 0.00 0.00 0.00 4.92
1464 1523 0.742281 GCCAGATCTGCTTCTTCGCA 60.742 55.000 17.76 0.00 38.40 5.10
1496 1555 4.200283 GCTCAGGAGCGAGGACCG 62.200 72.222 5.41 0.00 45.29 4.79
1635 1694 0.109086 CTCCACAGCTGTTCGACGAT 60.109 55.000 18.94 0.00 0.00 3.73
1643 1702 0.736325 CTGTTCGACGATGTCACCCC 60.736 60.000 0.00 0.00 32.09 4.95
1662 1721 1.228245 GCAGGCCACTCCAAACAGA 60.228 57.895 5.01 0.00 37.29 3.41
1806 1865 1.766494 TAATGGCGTACGAGGAGGAA 58.234 50.000 21.65 0.00 0.00 3.36
1816 1878 0.257616 CGAGGAGGAAGAGGAGGACT 59.742 60.000 0.00 0.00 0.00 3.85
1898 1960 6.183810 AGATCTCATCATGGACTTTATGCA 57.816 37.500 0.00 0.00 0.00 3.96
2039 2131 1.227823 TGTTCAAGCAGTGGGTCCG 60.228 57.895 0.00 0.00 0.00 4.79
2040 2132 1.966451 GTTCAAGCAGTGGGTCCGG 60.966 63.158 0.00 0.00 0.00 5.14
2046 2138 2.750350 CAGTGGGTCCGGAAAGCT 59.250 61.111 5.23 0.00 0.00 3.74
2070 2162 7.315247 TGTGTGCATGGTTCTTATTACATAC 57.685 36.000 0.00 0.00 0.00 2.39
2073 2165 8.122952 GTGTGCATGGTTCTTATTACATACTTC 58.877 37.037 0.00 0.00 0.00 3.01
2074 2166 7.282224 TGTGCATGGTTCTTATTACATACTTCC 59.718 37.037 0.00 0.00 0.00 3.46
2075 2167 7.499232 GTGCATGGTTCTTATTACATACTTCCT 59.501 37.037 0.00 0.00 0.00 3.36
2076 2168 7.715249 TGCATGGTTCTTATTACATACTTCCTC 59.285 37.037 0.00 0.00 0.00 3.71
2077 2169 7.173390 GCATGGTTCTTATTACATACTTCCTCC 59.827 40.741 0.00 0.00 0.00 4.30
2078 2170 6.812998 TGGTTCTTATTACATACTTCCTCCG 58.187 40.000 0.00 0.00 0.00 4.63
2079 2171 6.381994 TGGTTCTTATTACATACTTCCTCCGT 59.618 38.462 0.00 0.00 0.00 4.69
2080 2172 7.093201 TGGTTCTTATTACATACTTCCTCCGTT 60.093 37.037 0.00 0.00 0.00 4.44
2081 2173 7.437565 GGTTCTTATTACATACTTCCTCCGTTC 59.562 40.741 0.00 0.00 0.00 3.95
2082 2174 7.047460 TCTTATTACATACTTCCTCCGTTCC 57.953 40.000 0.00 0.00 0.00 3.62
2083 2175 6.837568 TCTTATTACATACTTCCTCCGTTCCT 59.162 38.462 0.00 0.00 0.00 3.36
2084 2176 8.000709 TCTTATTACATACTTCCTCCGTTCCTA 58.999 37.037 0.00 0.00 0.00 2.94
2085 2177 8.537728 TTATTACATACTTCCTCCGTTCCTAA 57.462 34.615 0.00 0.00 0.00 2.69
2086 2178 6.855763 TTACATACTTCCTCCGTTCCTAAA 57.144 37.500 0.00 0.00 0.00 1.85
2087 2179 5.952347 ACATACTTCCTCCGTTCCTAAAT 57.048 39.130 0.00 0.00 0.00 1.40
2088 2180 8.537728 TTACATACTTCCTCCGTTCCTAAATA 57.462 34.615 0.00 0.00 0.00 1.40
2089 2181 7.613551 ACATACTTCCTCCGTTCCTAAATAT 57.386 36.000 0.00 0.00 0.00 1.28
2090 2182 8.716674 ACATACTTCCTCCGTTCCTAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
2091 2183 9.151177 ACATACTTCCTCCGTTCCTAAATATAA 57.849 33.333 0.00 0.00 0.00 0.98
2092 2184 9.640963 CATACTTCCTCCGTTCCTAAATATAAG 57.359 37.037 0.00 0.00 0.00 1.73
2093 2185 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
2094 2186 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
2095 2187 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
2096 2188 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
2097 2189 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
2098 2190 9.425248 TCCTCCGTTCCTAAATATAAGTCTTTA 57.575 33.333 0.00 0.00 0.00 1.85
2118 2210 9.699703 GTCTTTATAGAGATTTCACTATGGACC 57.300 37.037 7.52 0.00 33.08 4.46
2119 2211 9.434275 TCTTTATAGAGATTTCACTATGGACCA 57.566 33.333 0.00 0.00 33.08 4.02
2120 2212 9.482627 CTTTATAGAGATTTCACTATGGACCAC 57.517 37.037 0.00 0.00 33.08 4.16
2121 2213 8.547481 TTATAGAGATTTCACTATGGACCACA 57.453 34.615 0.00 0.00 33.08 4.17
2122 2214 5.965033 AGAGATTTCACTATGGACCACAT 57.035 39.130 0.00 0.00 43.68 3.21
2123 2215 8.727100 ATAGAGATTTCACTATGGACCACATA 57.273 34.615 0.00 0.00 41.03 2.29
2124 2216 6.821388 AGAGATTTCACTATGGACCACATAC 58.179 40.000 0.00 0.00 41.03 2.39
2125 2217 5.601662 AGATTTCACTATGGACCACATACG 58.398 41.667 0.00 0.00 41.03 3.06
2126 2218 3.812156 TTCACTATGGACCACATACGG 57.188 47.619 0.00 0.00 41.03 4.02
2127 2219 3.021177 TCACTATGGACCACATACGGA 57.979 47.619 0.00 0.00 41.03 4.69
2128 2220 3.572642 TCACTATGGACCACATACGGAT 58.427 45.455 0.00 0.00 41.03 4.18
2129 2221 3.320826 TCACTATGGACCACATACGGATG 59.679 47.826 5.94 5.94 41.03 3.51
2131 2223 4.279922 CACTATGGACCACATACGGATGTA 59.720 45.833 14.23 0.00 44.82 2.29
2132 2224 5.047306 CACTATGGACCACATACGGATGTAT 60.047 44.000 14.23 4.48 44.82 2.29
2147 2239 9.719355 ATACGGATGTATGTAGATGCATTTTAA 57.281 29.630 0.00 0.00 39.81 1.52
2148 2240 8.445275 ACGGATGTATGTAGATGCATTTTAAA 57.555 30.769 0.00 0.00 35.26 1.52
2149 2241 8.559536 ACGGATGTATGTAGATGCATTTTAAAG 58.440 33.333 0.00 0.00 35.26 1.85
2150 2242 8.559536 CGGATGTATGTAGATGCATTTTAAAGT 58.440 33.333 0.00 0.00 35.26 2.66
2151 2243 9.669353 GGATGTATGTAGATGCATTTTAAAGTG 57.331 33.333 0.00 6.35 35.26 3.16
2162 2254 9.455847 GATGCATTTTAAAGTGTAGATTCATCC 57.544 33.333 11.77 0.00 0.00 3.51
2163 2255 8.347004 TGCATTTTAAAGTGTAGATTCATCCA 57.653 30.769 11.77 0.00 0.00 3.41
2164 2256 8.970020 TGCATTTTAAAGTGTAGATTCATCCAT 58.030 29.630 11.77 0.00 0.00 3.41
2165 2257 9.807649 GCATTTTAAAGTGTAGATTCATCCATT 57.192 29.630 11.77 0.00 0.00 3.16
2169 2261 9.638239 TTTAAAGTGTAGATTCATCCATTTTGC 57.362 29.630 0.00 0.00 0.00 3.68
2170 2262 7.472334 AAAGTGTAGATTCATCCATTTTGCT 57.528 32.000 0.00 0.00 0.00 3.91
2171 2263 7.472334 AAGTGTAGATTCATCCATTTTGCTT 57.528 32.000 0.00 0.00 0.00 3.91
2172 2264 7.093322 AGTGTAGATTCATCCATTTTGCTTC 57.907 36.000 0.00 0.00 0.00 3.86
2173 2265 5.967674 GTGTAGATTCATCCATTTTGCTTCG 59.032 40.000 0.00 0.00 0.00 3.79
2174 2266 5.647658 TGTAGATTCATCCATTTTGCTTCGT 59.352 36.000 0.00 0.00 0.00 3.85
2175 2267 6.821160 TGTAGATTCATCCATTTTGCTTCGTA 59.179 34.615 0.00 0.00 0.00 3.43
2176 2268 6.949352 AGATTCATCCATTTTGCTTCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
2177 2269 6.732154 AGATTCATCCATTTTGCTTCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
2178 2270 5.895636 TTCATCCATTTTGCTTCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
2179 2271 6.993786 TTCATCCATTTTGCTTCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
2180 2272 6.603237 TCATCCATTTTGCTTCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
2181 2273 6.112734 TCATCCATTTTGCTTCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
2182 2274 6.257849 TCATCCATTTTGCTTCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
2183 2275 4.873827 TCCATTTTGCTTCGTATGTAGTCC 59.126 41.667 0.00 0.00 0.00 3.85
2184 2276 4.634004 CCATTTTGCTTCGTATGTAGTCCA 59.366 41.667 0.00 0.00 0.00 4.02
2185 2277 5.296780 CCATTTTGCTTCGTATGTAGTCCAT 59.703 40.000 0.00 0.00 37.58 3.41
2186 2278 6.481976 CCATTTTGCTTCGTATGTAGTCCATA 59.518 38.462 0.00 0.00 34.86 2.74
2187 2279 7.307396 CCATTTTGCTTCGTATGTAGTCCATAG 60.307 40.741 0.00 0.00 36.71 2.23
2188 2280 5.847111 TTGCTTCGTATGTAGTCCATAGT 57.153 39.130 0.00 0.00 36.71 2.12
2189 2281 5.183014 TGCTTCGTATGTAGTCCATAGTG 57.817 43.478 0.00 0.00 36.71 2.74
2190 2282 4.885325 TGCTTCGTATGTAGTCCATAGTGA 59.115 41.667 0.00 0.00 36.71 3.41
2191 2283 5.358725 TGCTTCGTATGTAGTCCATAGTGAA 59.641 40.000 0.00 0.00 36.71 3.18
2192 2284 6.127563 TGCTTCGTATGTAGTCCATAGTGAAA 60.128 38.462 0.00 0.00 36.71 2.69
2193 2285 6.924060 GCTTCGTATGTAGTCCATAGTGAAAT 59.076 38.462 0.00 0.00 36.71 2.17
2194 2286 7.115095 GCTTCGTATGTAGTCCATAGTGAAATC 59.885 40.741 0.00 0.00 36.71 2.17
2195 2287 7.818997 TCGTATGTAGTCCATAGTGAAATCT 57.181 36.000 0.00 0.00 36.71 2.40
2196 2288 7.872881 TCGTATGTAGTCCATAGTGAAATCTC 58.127 38.462 0.00 0.00 36.71 2.75
2197 2289 7.720074 TCGTATGTAGTCCATAGTGAAATCTCT 59.280 37.037 0.00 0.00 36.71 3.10
2198 2290 8.018520 CGTATGTAGTCCATAGTGAAATCTCTC 58.981 40.741 0.00 0.00 36.71 3.20
2199 2291 6.716934 TGTAGTCCATAGTGAAATCTCTCC 57.283 41.667 0.00 0.00 0.00 3.71
2200 2292 6.194967 TGTAGTCCATAGTGAAATCTCTCCA 58.805 40.000 0.00 0.00 0.00 3.86
2201 2293 6.667848 TGTAGTCCATAGTGAAATCTCTCCAA 59.332 38.462 0.00 0.00 0.00 3.53
2202 2294 6.627087 AGTCCATAGTGAAATCTCTCCAAA 57.373 37.500 0.00 0.00 0.00 3.28
2203 2295 6.648192 AGTCCATAGTGAAATCTCTCCAAAG 58.352 40.000 0.00 0.00 0.00 2.77
2204 2296 6.441924 AGTCCATAGTGAAATCTCTCCAAAGA 59.558 38.462 0.00 0.00 0.00 2.52
2205 2297 6.536941 GTCCATAGTGAAATCTCTCCAAAGAC 59.463 42.308 0.00 0.00 0.00 3.01
2206 2298 6.441924 TCCATAGTGAAATCTCTCCAAAGACT 59.558 38.462 0.00 0.00 0.00 3.24
2207 2299 7.038017 TCCATAGTGAAATCTCTCCAAAGACTT 60.038 37.037 0.00 0.00 0.00 3.01
2208 2300 8.260818 CCATAGTGAAATCTCTCCAAAGACTTA 58.739 37.037 0.00 0.00 0.00 2.24
2209 2301 9.829507 CATAGTGAAATCTCTCCAAAGACTTAT 57.170 33.333 0.00 0.00 0.00 1.73
2220 2312 9.250624 CTCTCCAAAGACTTATATTTAGGAACG 57.749 37.037 0.00 0.00 0.00 3.95
2221 2313 8.202137 TCTCCAAAGACTTATATTTAGGAACGG 58.798 37.037 0.00 0.00 0.00 4.44
2222 2314 8.081517 TCCAAAGACTTATATTTAGGAACGGA 57.918 34.615 0.00 0.00 0.00 4.69
2223 2315 8.202137 TCCAAAGACTTATATTTAGGAACGGAG 58.798 37.037 0.00 0.00 0.00 4.63
2224 2316 7.441458 CCAAAGACTTATATTTAGGAACGGAGG 59.559 40.741 0.00 0.00 0.00 4.30
2225 2317 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2226 2318 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2227 2319 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2228 2320 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2229 2321 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2230 2322 7.954620 ACTTATATTTAGGAACGGAGGGAGTAT 59.045 37.037 0.00 0.00 0.00 2.12
2231 2323 4.957684 ATTTAGGAACGGAGGGAGTATG 57.042 45.455 0.00 0.00 0.00 2.39
2232 2324 3.393426 TTAGGAACGGAGGGAGTATGT 57.607 47.619 0.00 0.00 0.00 2.29
2292 2384 1.911766 GGTCCTCAGGAACGTCCCA 60.912 63.158 0.00 0.00 37.19 4.37
2378 2470 6.082338 CGATGGAGATTTACAATGCTATTGC 58.918 40.000 8.27 0.00 40.20 3.56
2423 2515 3.607741 TGTTTTATCCGTCGGGCAAATA 58.392 40.909 12.29 4.02 0.00 1.40
2446 2538 8.823220 ATATGTAATGTTTCCCTAAGCACTTT 57.177 30.769 0.00 0.00 0.00 2.66
2511 2603 1.139498 TGGAACCCAATGCCTCCTCA 61.139 55.000 0.00 0.00 0.00 3.86
2706 3093 8.768019 AGTAACCACAATAAGTAAAGACGAAAC 58.232 33.333 0.00 0.00 0.00 2.78
2710 3097 7.496591 ACCACAATAAGTAAAGACGAAACAAGA 59.503 33.333 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 39 1.305201 CACGCATAAAATACGGCCCT 58.695 50.000 0.00 0.00 0.00 5.19
114 117 0.038166 ATTGGTGATTCTGGCCACGT 59.962 50.000 0.00 0.00 34.30 4.49
123 126 9.382244 GCTATTTGTTCGTATTATTGGTGATTC 57.618 33.333 0.00 0.00 0.00 2.52
133 136 5.893687 TGTCCTCGCTATTTGTTCGTATTA 58.106 37.500 0.00 0.00 0.00 0.98
234 238 0.663867 TGCACAATCACATGTTGCGC 60.664 50.000 13.27 0.00 35.72 6.09
300 304 3.502211 ACATCTTTTGGCTAGGTTCAACG 59.498 43.478 0.00 0.00 0.00 4.10
333 337 3.134574 ACACGAGCCATTTGGTCTAAA 57.865 42.857 0.00 0.00 39.38 1.85
385 390 1.462432 TAGCCCTTGGTGTGGTGGA 60.462 57.895 0.00 0.00 0.00 4.02
409 417 1.530419 GGGTTGTGCACATGGTGGA 60.530 57.895 22.39 0.45 33.64 4.02
417 425 3.081061 TGTGATAAGATGGGTTGTGCAC 58.919 45.455 10.75 10.75 0.00 4.57
452 474 0.321671 CCATCTCGTCTTGTGGTGGT 59.678 55.000 0.00 0.00 37.53 4.16
462 484 3.949113 GGGACTAGGATATCCATCTCGTC 59.051 52.174 23.81 18.44 36.65 4.20
519 544 6.013293 ACCCTGACTAAAAGCTAGATTCTTGT 60.013 38.462 0.00 0.00 0.00 3.16
544 569 4.380531 GACATTGAGTCTCCAACAAGACA 58.619 43.478 6.79 0.00 46.65 3.41
578 603 8.722342 TTTGTTGTAAAGATAATGAAAGACGC 57.278 30.769 0.00 0.00 0.00 5.19
604 629 7.613585 TCTATTTTGTCTCGTACCCATTTGTA 58.386 34.615 0.00 0.00 0.00 2.41
630 655 4.523083 GGTGATTAGCATTGGGTGAGTTA 58.477 43.478 0.00 0.00 0.00 2.24
679 704 3.961225 ATCTGCATTTGCCCGGCCA 62.961 57.895 7.03 0.00 41.18 5.36
698 723 1.134818 TGCGGTGTATGGAGATGTGTC 60.135 52.381 0.00 0.00 0.00 3.67
760 786 5.999205 AGGCAATGGTTGTTAATGAATGA 57.001 34.783 0.00 0.00 0.00 2.57
778 804 7.182817 TGATTTAGACTAAAAGCTCTAGGCA 57.817 36.000 11.57 0.00 44.79 4.75
825 870 2.306124 TGCAGTTAGGGCATGGCTA 58.694 52.632 19.78 6.77 36.11 3.93
898 946 3.026707 TGTGTAGCTAGTCCATGGCTA 57.973 47.619 6.96 11.00 45.19 3.93
900 948 2.691409 TTGTGTAGCTAGTCCATGGC 57.309 50.000 6.96 2.00 35.14 4.40
907 955 5.804639 TCATGGACATTTTGTGTAGCTAGT 58.195 37.500 0.00 0.00 42.36 2.57
991 1041 1.880027 GTCCAGTTCCATGGTTGTCAC 59.120 52.381 12.58 2.38 41.43 3.67
1050 1109 2.577593 GGGTCGGTCAGCTGGTAC 59.422 66.667 15.13 5.33 0.00 3.34
1464 1523 3.575351 GAGCTCGCGGGTGAAGTGT 62.575 63.158 8.30 0.00 0.00 3.55
1643 1702 2.594303 TGTTTGGAGTGGCCTGCG 60.594 61.111 3.32 0.00 37.63 5.18
1662 1721 0.467384 ATAGGCTCAGCATGCGAAGT 59.533 50.000 13.01 1.73 34.76 3.01
1816 1878 2.953648 TCGCATAGTGGACGGATTTAGA 59.046 45.455 0.00 0.00 0.00 2.10
1898 1960 4.719026 TGTCATACCTCGGATACCTAGT 57.281 45.455 0.00 0.00 0.00 2.57
2039 2131 0.675633 AACCATGCACACAGCTTTCC 59.324 50.000 0.00 0.00 45.94 3.13
2040 2132 1.610522 AGAACCATGCACACAGCTTTC 59.389 47.619 0.00 0.00 45.94 2.62
2046 2138 7.109501 AGTATGTAATAAGAACCATGCACACA 58.890 34.615 0.00 0.00 0.00 3.72
2070 2162 7.953752 AGACTTATATTTAGGAACGGAGGAAG 58.046 38.462 0.00 0.00 0.00 3.46
2092 2184 9.699703 GGTCCATAGTGAAATCTCTATAAAGAC 57.300 37.037 5.06 10.50 33.04 3.01
2093 2185 9.434275 TGGTCCATAGTGAAATCTCTATAAAGA 57.566 33.333 5.06 1.84 33.04 2.52
2094 2186 9.482627 GTGGTCCATAGTGAAATCTCTATAAAG 57.517 37.037 0.00 0.00 33.04 1.85
2095 2187 8.988060 TGTGGTCCATAGTGAAATCTCTATAAA 58.012 33.333 0.00 0.00 33.04 1.40
2096 2188 8.547481 TGTGGTCCATAGTGAAATCTCTATAA 57.453 34.615 0.00 0.00 33.04 0.98
2097 2189 8.727100 ATGTGGTCCATAGTGAAATCTCTATA 57.273 34.615 0.00 0.00 33.04 1.31
2098 2190 7.623999 ATGTGGTCCATAGTGAAATCTCTAT 57.376 36.000 0.00 0.37 34.17 1.98
2099 2191 7.255486 CGTATGTGGTCCATAGTGAAATCTCTA 60.255 40.741 0.00 0.00 36.71 2.43
2100 2192 5.965033 ATGTGGTCCATAGTGAAATCTCT 57.035 39.130 0.00 0.00 29.82 3.10
2101 2193 5.692204 CGTATGTGGTCCATAGTGAAATCTC 59.308 44.000 0.00 0.00 36.71 2.75
2102 2194 5.453339 CCGTATGTGGTCCATAGTGAAATCT 60.453 44.000 0.00 0.00 36.71 2.40
2103 2195 4.750098 CCGTATGTGGTCCATAGTGAAATC 59.250 45.833 0.00 0.00 36.71 2.17
2104 2196 4.407621 TCCGTATGTGGTCCATAGTGAAAT 59.592 41.667 0.00 0.00 36.71 2.17
2105 2197 3.770388 TCCGTATGTGGTCCATAGTGAAA 59.230 43.478 0.00 0.00 36.71 2.69
2106 2198 3.367321 TCCGTATGTGGTCCATAGTGAA 58.633 45.455 0.00 0.00 36.71 3.18
2107 2199 3.021177 TCCGTATGTGGTCCATAGTGA 57.979 47.619 0.00 0.00 36.71 3.41
2108 2200 3.069586 ACATCCGTATGTGGTCCATAGTG 59.930 47.826 0.00 0.00 44.79 2.74
2109 2201 3.305720 ACATCCGTATGTGGTCCATAGT 58.694 45.455 0.00 0.00 44.79 2.12
2110 2202 5.410924 CATACATCCGTATGTGGTCCATAG 58.589 45.833 3.56 0.00 46.70 2.23
2111 2203 5.400066 CATACATCCGTATGTGGTCCATA 57.600 43.478 3.56 0.00 46.70 2.74
2112 2204 4.271696 CATACATCCGTATGTGGTCCAT 57.728 45.455 3.56 0.00 46.70 3.41
2113 2205 3.744238 CATACATCCGTATGTGGTCCA 57.256 47.619 3.56 0.00 46.70 4.02
2121 2213 9.719355 TTAAAATGCATCTACATACATCCGTAT 57.281 29.630 0.00 0.00 38.96 3.06
2122 2214 9.549078 TTTAAAATGCATCTACATACATCCGTA 57.451 29.630 0.00 0.00 0.00 4.02
2123 2215 8.445275 TTTAAAATGCATCTACATACATCCGT 57.555 30.769 0.00 0.00 0.00 4.69
2124 2216 8.559536 ACTTTAAAATGCATCTACATACATCCG 58.440 33.333 0.00 0.00 0.00 4.18
2125 2217 9.669353 CACTTTAAAATGCATCTACATACATCC 57.331 33.333 0.00 0.00 0.00 3.51
2136 2228 9.455847 GGATGAATCTACACTTTAAAATGCATC 57.544 33.333 0.00 7.39 31.21 3.91
2137 2229 8.970020 TGGATGAATCTACACTTTAAAATGCAT 58.030 29.630 0.00 0.00 0.00 3.96
2138 2230 8.347004 TGGATGAATCTACACTTTAAAATGCA 57.653 30.769 0.00 0.00 0.00 3.96
2139 2231 9.807649 AATGGATGAATCTACACTTTAAAATGC 57.192 29.630 0.00 0.00 0.00 3.56
2143 2235 9.638239 GCAAAATGGATGAATCTACACTTTAAA 57.362 29.630 0.00 0.00 0.00 1.52
2144 2236 9.023962 AGCAAAATGGATGAATCTACACTTTAA 57.976 29.630 0.00 0.00 0.00 1.52
2145 2237 8.579850 AGCAAAATGGATGAATCTACACTTTA 57.420 30.769 0.00 0.00 0.00 1.85
2146 2238 7.472334 AGCAAAATGGATGAATCTACACTTT 57.528 32.000 0.00 0.00 0.00 2.66
2147 2239 7.472334 AAGCAAAATGGATGAATCTACACTT 57.528 32.000 0.00 0.00 0.00 3.16
2148 2240 6.183360 CGAAGCAAAATGGATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
2149 2241 5.967674 CGAAGCAAAATGGATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
2150 2242 5.647658 ACGAAGCAAAATGGATGAATCTACA 59.352 36.000 0.00 0.00 0.00 2.74
2151 2243 6.124088 ACGAAGCAAAATGGATGAATCTAC 57.876 37.500 0.00 0.00 0.00 2.59
2152 2244 7.498900 ACATACGAAGCAAAATGGATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
2153 2245 6.319658 ACATACGAAGCAAAATGGATGAATCT 59.680 34.615 0.00 0.00 0.00 2.40
2154 2246 6.498304 ACATACGAAGCAAAATGGATGAATC 58.502 36.000 0.00 0.00 0.00 2.52
2155 2247 6.455360 ACATACGAAGCAAAATGGATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
2156 2248 5.895636 ACATACGAAGCAAAATGGATGAA 57.104 34.783 0.00 0.00 0.00 2.57
2157 2249 6.112734 ACTACATACGAAGCAAAATGGATGA 58.887 36.000 0.00 0.00 0.00 2.92
2158 2250 6.363577 ACTACATACGAAGCAAAATGGATG 57.636 37.500 0.00 0.00 0.00 3.51
2159 2251 5.527582 GGACTACATACGAAGCAAAATGGAT 59.472 40.000 0.00 0.00 0.00 3.41
2160 2252 4.873827 GGACTACATACGAAGCAAAATGGA 59.126 41.667 0.00 0.00 0.00 3.41
2161 2253 4.634004 TGGACTACATACGAAGCAAAATGG 59.366 41.667 0.00 0.00 0.00 3.16
2162 2254 5.794687 TGGACTACATACGAAGCAAAATG 57.205 39.130 0.00 0.00 0.00 2.32
2163 2255 7.224753 CACTATGGACTACATACGAAGCAAAAT 59.775 37.037 0.00 0.00 41.03 1.82
2164 2256 6.533723 CACTATGGACTACATACGAAGCAAAA 59.466 38.462 0.00 0.00 41.03 2.44
2165 2257 6.040247 CACTATGGACTACATACGAAGCAAA 58.960 40.000 0.00 0.00 41.03 3.68
2166 2258 5.358725 TCACTATGGACTACATACGAAGCAA 59.641 40.000 0.00 0.00 41.03 3.91
2167 2259 4.885325 TCACTATGGACTACATACGAAGCA 59.115 41.667 0.00 0.00 41.03 3.91
2168 2260 5.434352 TCACTATGGACTACATACGAAGC 57.566 43.478 0.00 0.00 41.03 3.86
2169 2261 8.353684 AGATTTCACTATGGACTACATACGAAG 58.646 37.037 0.00 0.00 41.03 3.79
2170 2262 8.234136 AGATTTCACTATGGACTACATACGAA 57.766 34.615 0.00 0.00 41.03 3.85
2171 2263 7.720074 AGAGATTTCACTATGGACTACATACGA 59.280 37.037 0.00 0.00 41.03 3.43
2172 2264 7.877003 AGAGATTTCACTATGGACTACATACG 58.123 38.462 0.00 0.00 41.03 3.06
2173 2265 8.301002 GGAGAGATTTCACTATGGACTACATAC 58.699 40.741 0.00 0.00 41.03 2.39
2174 2266 8.004801 TGGAGAGATTTCACTATGGACTACATA 58.995 37.037 0.00 0.00 41.03 2.29
2175 2267 6.841229 TGGAGAGATTTCACTATGGACTACAT 59.159 38.462 0.00 0.00 43.68 2.29
2176 2268 6.194967 TGGAGAGATTTCACTATGGACTACA 58.805 40.000 0.00 0.00 0.00 2.74
2177 2269 6.716934 TGGAGAGATTTCACTATGGACTAC 57.283 41.667 0.00 0.00 0.00 2.73
2178 2270 7.619698 TCTTTGGAGAGATTTCACTATGGACTA 59.380 37.037 0.00 0.00 0.00 2.59
2179 2271 6.441924 TCTTTGGAGAGATTTCACTATGGACT 59.558 38.462 0.00 0.00 0.00 3.85
2180 2272 6.536941 GTCTTTGGAGAGATTTCACTATGGAC 59.463 42.308 0.00 0.00 31.07 4.02
2181 2273 6.441924 AGTCTTTGGAGAGATTTCACTATGGA 59.558 38.462 0.00 0.00 31.07 3.41
2182 2274 6.648192 AGTCTTTGGAGAGATTTCACTATGG 58.352 40.000 0.00 0.00 31.07 2.74
2183 2275 9.829507 ATAAGTCTTTGGAGAGATTTCACTATG 57.170 33.333 0.00 0.00 31.07 2.23
2194 2286 9.250624 CGTTCCTAAATATAAGTCTTTGGAGAG 57.749 37.037 0.00 0.00 31.07 3.20
2195 2287 8.202137 CCGTTCCTAAATATAAGTCTTTGGAGA 58.798 37.037 0.00 0.00 0.00 3.71
2196 2288 8.202137 TCCGTTCCTAAATATAAGTCTTTGGAG 58.798 37.037 0.00 0.00 0.00 3.86
2197 2289 8.081517 TCCGTTCCTAAATATAAGTCTTTGGA 57.918 34.615 0.00 0.00 0.00 3.53
2198 2290 7.441458 CCTCCGTTCCTAAATATAAGTCTTTGG 59.559 40.741 0.00 0.00 0.00 3.28
2199 2291 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
2200 2292 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2201 2293 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2202 2294 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2203 2295 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2204 2296 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2205 2297 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2206 2298 7.731688 ACATACTCCCTCCGTTCCTAAATATAA 59.268 37.037 0.00 0.00 0.00 0.98
2207 2299 7.243824 ACATACTCCCTCCGTTCCTAAATATA 58.756 38.462 0.00 0.00 0.00 0.86
2208 2300 6.082707 ACATACTCCCTCCGTTCCTAAATAT 58.917 40.000 0.00 0.00 0.00 1.28
2209 2301 5.461327 ACATACTCCCTCCGTTCCTAAATA 58.539 41.667 0.00 0.00 0.00 1.40
2210 2302 4.296056 ACATACTCCCTCCGTTCCTAAAT 58.704 43.478 0.00 0.00 0.00 1.40
2211 2303 3.716431 ACATACTCCCTCCGTTCCTAAA 58.284 45.455 0.00 0.00 0.00 1.85
2212 2304 3.393426 ACATACTCCCTCCGTTCCTAA 57.607 47.619 0.00 0.00 0.00 2.69
2213 2305 4.736611 ATACATACTCCCTCCGTTCCTA 57.263 45.455 0.00 0.00 0.00 2.94
2214 2306 3.614568 ATACATACTCCCTCCGTTCCT 57.385 47.619 0.00 0.00 0.00 3.36
2215 2307 5.997384 ATTATACATACTCCCTCCGTTCC 57.003 43.478 0.00 0.00 0.00 3.62
2216 2308 6.147328 GCAAATTATACATACTCCCTCCGTTC 59.853 42.308 0.00 0.00 0.00 3.95
2217 2309 5.995897 GCAAATTATACATACTCCCTCCGTT 59.004 40.000 0.00 0.00 0.00 4.44
2218 2310 5.071250 TGCAAATTATACATACTCCCTCCGT 59.929 40.000 0.00 0.00 0.00 4.69
2219 2311 5.547465 TGCAAATTATACATACTCCCTCCG 58.453 41.667 0.00 0.00 0.00 4.63
2220 2312 6.942576 ACATGCAAATTATACATACTCCCTCC 59.057 38.462 0.00 0.00 0.00 4.30
2221 2313 7.148573 CGACATGCAAATTATACATACTCCCTC 60.149 40.741 0.00 0.00 0.00 4.30
2222 2314 6.650807 CGACATGCAAATTATACATACTCCCT 59.349 38.462 0.00 0.00 0.00 4.20
2223 2315 6.426937 ACGACATGCAAATTATACATACTCCC 59.573 38.462 0.00 0.00 0.00 4.30
2224 2316 7.290842 CACGACATGCAAATTATACATACTCC 58.709 38.462 0.00 0.00 0.00 3.85
2259 2351 1.285962 AGGACCTACTACCGCCACTTA 59.714 52.381 0.00 0.00 0.00 2.24
2273 2365 1.609794 GGGACGTTCCTGAGGACCT 60.610 63.158 5.31 0.00 36.57 3.85
2292 2384 5.537295 TGACCAGGTACGCTATACACATATT 59.463 40.000 0.00 0.00 0.00 1.28
2423 2515 7.539034 AAAAGTGCTTAGGGAAACATTACAT 57.461 32.000 0.00 0.00 0.00 2.29
2461 2553 9.914834 ACAATTGTATATAAGTGCTTAGGGAAA 57.085 29.630 9.97 0.00 0.00 3.13
2462 2554 9.914834 AACAATTGTATATAAGTGCTTAGGGAA 57.085 29.630 12.39 0.00 0.00 3.97
2463 2555 9.914834 AAACAATTGTATATAAGTGCTTAGGGA 57.085 29.630 12.39 0.00 0.00 4.20
2468 2560 9.638239 CCACAAAACAATTGTATATAAGTGCTT 57.362 29.630 12.39 1.63 0.00 3.91
2469 2561 9.019656 TCCACAAAACAATTGTATATAAGTGCT 57.980 29.630 12.39 0.00 0.00 4.40
2470 2562 9.632807 TTCCACAAAACAATTGTATATAAGTGC 57.367 29.630 12.39 0.00 0.00 4.40
2493 2585 0.394899 CTGAGGAGGCATTGGGTTCC 60.395 60.000 0.00 0.00 0.00 3.62
2498 2590 0.622665 AGGAACTGAGGAGGCATTGG 59.377 55.000 0.00 0.00 37.18 3.16
2572 2664 6.037172 GGCACGTATGAATCACATTTCTAACT 59.963 38.462 0.00 0.00 40.07 2.24


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

AutoCloner maintained by Alex Coulton.