Multiple sequence alignment - TraesCS3B01G306900

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 TraesCS3B01G306900 chr3B 100.000 2691 0 0 1 2691 492757005 492759695 0.000000e+00 4970.0
1 TraesCS3B01G306900 chr3B 90.390 385 24 3 2320 2691 492416153 492415769 6.690000e-136 494.0
2 TraesCS3B01G306900 chr3B 92.784 97 3 3 2043 2139 492416237 492416145 1.300000e-28 137.0
3 TraesCS3B01G306900 chr3D 92.891 1702 96 18 311 2008 378200145 378201825 0.000000e+00 2449.0
4 TraesCS3B01G306900 chr3D 88.636 308 34 1 2 308 378199186 378199493 9.100000e-100 374.0
5 TraesCS3B01G306900 chr3D 90.734 259 17 3 2440 2691 378216788 378217046 3.320000e-89 339.0
6 TraesCS3B01G306900 chr3D 94.074 135 4 3 2005 2139 378213196 378213326 4.540000e-48 202.0
7 TraesCS3B01G306900 chr3D 86.364 132 1 1 2328 2442 378216415 378216546 7.820000e-26 128.0
8 TraesCS3B01G306900 chr3A 92.725 976 53 7 976 1945 502278652 502279615 0.000000e+00 1393.0
9 TraesCS3B01G306900 chr3A 91.116 968 63 16 2 965 502272354 502273302 0.000000e+00 1290.0
10 TraesCS3B01G306900 chr3A 89.451 237 18 3 2462 2691 502280470 502280706 2.620000e-75 292.0
11 TraesCS3B01G306900 chr3A 92.000 200 10 4 1942 2139 502279888 502280083 2.640000e-70 276.0
12 TraesCS3B01G306900 chr3A 88.608 158 1 1 2320 2460 502280075 502280232 2.750000e-40 176.0
13 TraesCS3B01G306900 chr4A 91.758 182 13 2 2140 2321 617655797 617655618 4.450000e-63 252.0
14 TraesCS3B01G306900 chr7B 94.969 159 7 1 2140 2298 538575000 538575157 5.750000e-62 248.0
15 TraesCS3B01G306900 chr7B 84.492 187 18 5 2142 2319 35253842 35254026 9.900000e-40 174.0
16 TraesCS3B01G306900 chr7A 91.257 183 13 3 2140 2320 49270158 49269977 2.070000e-61 246.0
17 TraesCS3B01G306900 chr2B 94.872 156 8 0 2139 2294 4933836 4933681 7.440000e-61 244.0
18 TraesCS3B01G306900 chr4D 88.649 185 12 4 2142 2322 503741855 503741676 1.620000e-52 217.0
19 TraesCS3B01G306900 chr5B 88.288 111 5 1 2217 2319 273155550 273155440 2.810000e-25 126.0
20 TraesCS3B01G306900 chr1D 79.104 134 24 4 471 603 302995442 302995312 3.690000e-14 89.8
21 TraesCS3B01G306900 chr2A 91.489 47 4 0 467 513 156770760 156770806 6.220000e-07 65.8
22 TraesCS3B01G306900 chr2A 91.489 47 4 0 467 513 156773755 156773801 6.220000e-07 65.8


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 TraesCS3B01G306900 chr3B 492757005 492759695 2690 False 4970.00 4970 100.000000 1 2691 1 chr3B.!!$F1 2690
1 TraesCS3B01G306900 chr3D 378199186 378201825 2639 False 1411.50 2449 90.763500 2 2008 2 chr3D.!!$F1 2006
2 TraesCS3B01G306900 chr3D 378213196 378217046 3850 False 223.00 339 90.390667 2005 2691 3 chr3D.!!$F2 686
3 TraesCS3B01G306900 chr3A 502272354 502273302 948 False 1290.00 1290 91.116000 2 965 1 chr3A.!!$F1 963
4 TraesCS3B01G306900 chr3A 502278652 502280706 2054 False 534.25 1393 90.696000 976 2691 4 chr3A.!!$F2 1715

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
55 56 0.392863 CCATCTGTTGCCATGTCCGA 60.393 55.000 0.0 0.0 0.00 4.55 F
893 1566 1.003118 TGTTCCACCATAGGTCAGCAC 59.997 52.381 0.0 0.0 31.02 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1675 2351 0.179078 CATCTCAGAGCACCAGAGCC 60.179 60.0 0.0 0.0 34.23 4.70 R
2175 3132 0.036010 CAGTTCAGGAATCAGCCCGT 60.036 55.0 0.0 0.0 0.00 5.28 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
44 45 2.025887 CCAAACCCTAGCTCCATCTGTT 60.026 50.000 0.00 0.00 0.00 3.16
55 56 0.392863 CCATCTGTTGCCATGTCCGA 60.393 55.000 0.00 0.00 0.00 4.55
137 138 4.096681 TCCTATGCCGATTAGTCCATGAT 58.903 43.478 0.00 0.00 0.00 2.45
333 984 2.980568 TGCCGTTAAGGTGTCCTTATG 58.019 47.619 8.75 5.55 44.38 1.90
389 1040 6.645884 TGTTTAGGGGCTCTATTTTAGGAA 57.354 37.500 0.00 0.00 0.00 3.36
393 1044 8.270030 GTTTAGGGGCTCTATTTTAGGAAGTAA 58.730 37.037 0.00 0.00 0.00 2.24
515 1167 6.392354 GGATTTTCAAGCATGACAAATCTGA 58.608 36.000 23.20 0.00 39.60 3.27
516 1168 7.039882 GGATTTTCAAGCATGACAAATCTGAT 58.960 34.615 23.20 0.00 39.60 2.90
539 1191 9.844790 TGATGTTTGAGATGACAAATTATGTTC 57.155 29.630 0.00 0.00 44.12 3.18
560 1212 3.857665 TCTCGCGAGTATGACAATGTTTC 59.142 43.478 33.33 0.00 0.00 2.78
562 1214 4.242475 TCGCGAGTATGACAATGTTTCTT 58.758 39.130 3.71 0.00 0.00 2.52
563 1215 5.404096 TCGCGAGTATGACAATGTTTCTTA 58.596 37.500 3.71 0.00 0.00 2.10
564 1216 5.287752 TCGCGAGTATGACAATGTTTCTTAC 59.712 40.000 3.71 0.00 0.00 2.34
654 1327 4.095410 TGCCATCAAATTTGTAGCGAAG 57.905 40.909 17.47 3.15 0.00 3.79
656 1329 4.098416 GCCATCAAATTTGTAGCGAAGTC 58.902 43.478 17.47 0.00 0.00 3.01
658 1331 4.438744 CCATCAAATTTGTAGCGAAGTCCC 60.439 45.833 17.47 0.00 0.00 4.46
659 1332 4.015872 TCAAATTTGTAGCGAAGTCCCT 57.984 40.909 17.47 0.00 0.00 4.20
660 1333 4.000988 TCAAATTTGTAGCGAAGTCCCTC 58.999 43.478 17.47 0.00 0.00 4.30
661 1334 2.295253 ATTTGTAGCGAAGTCCCTCG 57.705 50.000 0.00 0.00 41.84 4.63
791 1464 1.403249 CCGCAAGAAAATCCAGCTTGG 60.403 52.381 0.00 0.00 39.42 3.61
893 1566 1.003118 TGTTCCACCATAGGTCAGCAC 59.997 52.381 0.00 0.00 31.02 4.40
935 1608 1.152881 GCATCCAATCCCGCCTCTT 60.153 57.895 0.00 0.00 0.00 2.85
1216 1892 6.446318 TCGTCGATATTGTCATCATGAATCA 58.554 36.000 0.00 0.00 0.00 2.57
1366 2042 2.754658 CTAGAGGACGCCGGTGGT 60.755 66.667 21.14 10.24 0.00 4.16
1567 2243 4.864334 CCGGACATGAGCCCTGGC 62.864 72.222 0.00 0.00 42.33 4.85
1568 2244 4.100084 CGGACATGAGCCCTGGCA 62.100 66.667 11.38 0.00 44.88 4.92
1647 2323 2.000447 GTTGGACTTGGACGTGATAGC 59.000 52.381 0.00 0.00 0.00 2.97
1675 2351 1.065926 GTAGTCGTGGGGGTTTTAGGG 60.066 57.143 0.00 0.00 0.00 3.53
1710 2386 0.030369 GATGGCGTACGAATCGGACT 59.970 55.000 21.65 0.00 38.73 3.85
1711 2388 1.265095 GATGGCGTACGAATCGGACTA 59.735 52.381 21.65 2.81 38.73 2.59
1753 2430 0.321653 GGTGTGGTCTGTGGATGGTC 60.322 60.000 0.00 0.00 0.00 4.02
1782 2459 1.459592 GTGTGATACGCTGTTGGTGTC 59.540 52.381 0.00 0.00 39.59 3.67
1881 2558 2.343101 TGGATACTGAAGCCGTTTTCG 58.657 47.619 0.00 0.00 39.67 3.46
1889 2566 3.132160 TGAAGCCGTTTTCGTGATTACA 58.868 40.909 0.00 0.00 42.35 2.41
1935 2613 8.992835 AATCTTTTTCTTGAGATATGGTTTGC 57.007 30.769 0.00 0.00 32.52 3.68
1980 2935 6.627087 ATTCTGACCCATCTTCACTTAGAA 57.373 37.500 0.00 0.00 34.41 2.10
2139 3096 7.144722 TGGCATGTAGTATGTTCTTTGAAAG 57.855 36.000 0.00 0.00 0.00 2.62
2140 3097 6.939730 TGGCATGTAGTATGTTCTTTGAAAGA 59.060 34.615 3.02 3.02 35.26 2.52
2141 3098 7.119699 TGGCATGTAGTATGTTCTTTGAAAGAG 59.880 37.037 7.76 0.00 39.03 2.85
2142 3099 7.119846 GGCATGTAGTATGTTCTTTGAAAGAGT 59.880 37.037 7.76 1.90 39.03 3.24
2143 3100 8.507249 GCATGTAGTATGTTCTTTGAAAGAGTT 58.493 33.333 7.76 0.42 39.03 3.01
2147 3104 9.170584 GTAGTATGTTCTTTGAAAGAGTTTTGC 57.829 33.333 7.76 0.00 39.03 3.68
2148 3105 8.000780 AGTATGTTCTTTGAAAGAGTTTTGCT 57.999 30.769 7.76 1.84 39.03 3.91
2149 3106 9.120538 AGTATGTTCTTTGAAAGAGTTTTGCTA 57.879 29.630 7.76 0.00 39.03 3.49
2150 3107 9.387123 GTATGTTCTTTGAAAGAGTTTTGCTAG 57.613 33.333 7.76 0.00 39.03 3.42
2151 3108 7.624360 TGTTCTTTGAAAGAGTTTTGCTAGA 57.376 32.000 7.76 0.00 39.03 2.43
2154 3111 5.815740 TCTTTGAAAGAGTTTTGCTAGACGT 59.184 36.000 3.02 0.00 32.71 4.34
2155 3112 6.982141 TCTTTGAAAGAGTTTTGCTAGACGTA 59.018 34.615 3.02 0.00 32.71 3.57
2158 3115 3.213249 AGAGTTTTGCTAGACGTACGG 57.787 47.619 21.06 2.24 0.00 4.02
2159 3116 2.816087 AGAGTTTTGCTAGACGTACGGA 59.184 45.455 21.06 3.34 0.00 4.69
2163 3120 1.171308 TTGCTAGACGTACGGAGCTT 58.829 50.000 27.89 7.68 34.81 3.74
2164 3121 1.171308 TGCTAGACGTACGGAGCTTT 58.829 50.000 27.89 7.02 34.81 3.51
2165 3122 2.358957 TGCTAGACGTACGGAGCTTTA 58.641 47.619 27.89 13.76 34.81 1.85
2166 3123 2.096496 TGCTAGACGTACGGAGCTTTAC 59.904 50.000 27.89 13.59 34.81 2.01
2167 3124 2.096496 GCTAGACGTACGGAGCTTTACA 59.904 50.000 23.63 4.28 32.33 2.41
2168 3125 3.243002 GCTAGACGTACGGAGCTTTACAT 60.243 47.826 23.63 0.26 32.33 2.29
2169 3126 4.024556 GCTAGACGTACGGAGCTTTACATA 60.025 45.833 23.63 3.44 32.33 2.29
2170 3127 4.970662 AGACGTACGGAGCTTTACATAA 57.029 40.909 21.06 0.00 0.00 1.90
2171 3128 4.918037 AGACGTACGGAGCTTTACATAAG 58.082 43.478 21.06 0.00 0.00 1.73
2173 3130 5.586243 AGACGTACGGAGCTTTACATAAGTA 59.414 40.000 21.06 0.00 0.00 2.24
2175 3132 7.442364 AGACGTACGGAGCTTTACATAAGTATA 59.558 37.037 21.06 0.00 0.00 1.47
2176 3133 7.355778 ACGTACGGAGCTTTACATAAGTATAC 58.644 38.462 21.06 0.00 0.00 1.47
2177 3134 6.517714 CGTACGGAGCTTTACATAAGTATACG 59.482 42.308 7.57 0.00 0.00 3.06
2178 3135 5.766222 ACGGAGCTTTACATAAGTATACGG 58.234 41.667 0.00 0.00 0.00 4.02
2181 3138 5.279356 GGAGCTTTACATAAGTATACGGGCT 60.279 44.000 0.00 0.00 0.00 5.19
2182 3139 5.539048 AGCTTTACATAAGTATACGGGCTG 58.461 41.667 0.00 0.00 0.00 4.85
2183 3140 5.303589 AGCTTTACATAAGTATACGGGCTGA 59.696 40.000 0.00 0.00 0.00 4.26
2184 3141 6.014499 AGCTTTACATAAGTATACGGGCTGAT 60.014 38.462 0.00 0.00 0.00 2.90
2185 3142 6.649557 GCTTTACATAAGTATACGGGCTGATT 59.350 38.462 0.00 0.00 0.00 2.57
2186 3143 7.148623 GCTTTACATAAGTATACGGGCTGATTC 60.149 40.741 0.00 0.00 0.00 2.52
2187 3144 5.148651 ACATAAGTATACGGGCTGATTCC 57.851 43.478 0.00 0.00 0.00 3.01
2188 3145 4.838986 ACATAAGTATACGGGCTGATTCCT 59.161 41.667 0.00 0.00 0.00 3.36
2189 3146 3.753294 AAGTATACGGGCTGATTCCTG 57.247 47.619 0.00 0.00 38.47 3.86
2194 3151 0.036010 ACGGGCTGATTCCTGAACTG 60.036 55.000 0.00 0.00 36.35 3.16
2195 3152 0.745845 CGGGCTGATTCCTGAACTGG 60.746 60.000 0.00 0.00 34.34 4.00
2196 3153 1.034292 GGGCTGATTCCTGAACTGGC 61.034 60.000 0.00 0.00 0.00 4.85
2197 3154 1.372087 GGCTGATTCCTGAACTGGCG 61.372 60.000 0.00 0.00 0.00 5.69
2198 3155 1.986575 GCTGATTCCTGAACTGGCGC 61.987 60.000 0.00 0.00 0.00 6.53
2201 3158 1.298859 GATTCCTGAACTGGCGCGTT 61.299 55.000 8.43 0.00 0.00 4.84
2202 3159 0.889186 ATTCCTGAACTGGCGCGTTT 60.889 50.000 8.43 0.00 0.00 3.60
2203 3160 1.098712 TTCCTGAACTGGCGCGTTTT 61.099 50.000 8.43 0.00 0.00 2.43
2205 3162 0.589223 CCTGAACTGGCGCGTTTTAA 59.411 50.000 8.43 0.00 0.00 1.52
2206 3163 1.662026 CCTGAACTGGCGCGTTTTAAC 60.662 52.381 8.43 0.00 0.00 2.01
2207 3164 0.308376 TGAACTGGCGCGTTTTAACC 59.692 50.000 8.43 0.00 0.00 2.85
2208 3165 0.723459 GAACTGGCGCGTTTTAACCG 60.723 55.000 8.43 0.00 0.00 4.44
2209 3166 2.120355 AACTGGCGCGTTTTAACCGG 62.120 55.000 8.43 0.00 34.56 5.28
2210 3167 2.280660 TGGCGCGTTTTAACCGGA 60.281 55.556 9.46 0.00 0.00 5.14
2212 3169 2.202083 GCGCGTTTTAACCGGACG 60.202 61.111 9.46 8.66 39.61 4.79
2213 3170 2.656807 GCGCGTTTTAACCGGACGA 61.657 57.895 15.97 0.00 38.99 4.20
2214 3171 1.851978 CGCGTTTTAACCGGACGAA 59.148 52.632 15.97 0.23 38.99 3.85
2216 3173 1.719295 CGCGTTTTAACCGGACGAAAG 60.719 52.381 15.97 5.28 38.99 2.62
2218 3175 1.866601 CGTTTTAACCGGACGAAAGGT 59.133 47.619 9.46 0.00 43.68 3.50
2219 3176 2.348779 CGTTTTAACCGGACGAAAGGTG 60.349 50.000 9.46 0.00 41.21 4.00
2220 3177 2.871633 GTTTTAACCGGACGAAAGGTGA 59.128 45.455 9.46 0.00 41.21 4.02
2222 3179 0.604578 TAACCGGACGAAAGGTGAGG 59.395 55.000 9.46 0.00 41.21 3.86
2223 3180 2.108278 AACCGGACGAAAGGTGAGGG 62.108 60.000 9.46 0.00 41.21 4.30
2224 3181 2.434359 CGGACGAAAGGTGAGGGC 60.434 66.667 0.00 0.00 0.00 5.19
2225 3182 2.434359 GGACGAAAGGTGAGGGCG 60.434 66.667 0.00 0.00 0.00 6.13
2226 3183 2.434359 GACGAAAGGTGAGGGCGG 60.434 66.667 0.00 0.00 0.00 6.13
2227 3184 4.699522 ACGAAAGGTGAGGGCGGC 62.700 66.667 0.00 0.00 0.00 6.53
2249 3206 4.390048 ACACGGGTGAAAATCGGG 57.610 55.556 5.71 0.00 0.00 5.14
2250 3207 1.302993 ACACGGGTGAAAATCGGGG 60.303 57.895 5.71 0.00 0.00 5.73
2269 3226 3.602205 GGGGGCCTGAAGAGAATTTAT 57.398 47.619 0.84 0.00 0.00 1.40
2270 3227 3.225940 GGGGGCCTGAAGAGAATTTATG 58.774 50.000 0.84 0.00 0.00 1.90
2271 3228 3.225940 GGGGCCTGAAGAGAATTTATGG 58.774 50.000 0.84 0.00 0.00 2.74
2273 3230 4.536765 GGGCCTGAAGAGAATTTATGGAA 58.463 43.478 0.84 0.00 0.00 3.53
2275 3232 4.582240 GGCCTGAAGAGAATTTATGGAAGG 59.418 45.833 0.00 0.00 0.00 3.46
2276 3233 4.582240 GCCTGAAGAGAATTTATGGAAGGG 59.418 45.833 0.00 0.00 0.00 3.95
2277 3234 5.760131 CCTGAAGAGAATTTATGGAAGGGT 58.240 41.667 0.00 0.00 0.00 4.34
2278 3235 6.190587 CCTGAAGAGAATTTATGGAAGGGTT 58.809 40.000 0.00 0.00 0.00 4.11
2279 3236 6.665248 CCTGAAGAGAATTTATGGAAGGGTTT 59.335 38.462 0.00 0.00 0.00 3.27
2280 3237 7.363268 CCTGAAGAGAATTTATGGAAGGGTTTG 60.363 40.741 0.00 0.00 0.00 2.93
2282 3239 8.167392 TGAAGAGAATTTATGGAAGGGTTTGTA 58.833 33.333 0.00 0.00 0.00 2.41
2283 3240 8.581253 AAGAGAATTTATGGAAGGGTTTGTAG 57.419 34.615 0.00 0.00 0.00 2.74
2284 3241 6.603599 AGAGAATTTATGGAAGGGTTTGTAGC 59.396 38.462 0.00 0.00 0.00 3.58
2285 3242 6.252995 AGAATTTATGGAAGGGTTTGTAGCA 58.747 36.000 0.00 0.00 0.00 3.49
2286 3243 6.378280 AGAATTTATGGAAGGGTTTGTAGCAG 59.622 38.462 0.00 0.00 0.00 4.24
2287 3244 2.514458 ATGGAAGGGTTTGTAGCAGG 57.486 50.000 0.00 0.00 0.00 4.85
2288 3245 0.251165 TGGAAGGGTTTGTAGCAGGC 60.251 55.000 0.00 0.00 0.00 4.85
2289 3246 0.965866 GGAAGGGTTTGTAGCAGGCC 60.966 60.000 0.00 0.00 0.00 5.19
2290 3247 0.038310 GAAGGGTTTGTAGCAGGCCT 59.962 55.000 0.00 0.00 0.00 5.19
2291 3248 0.251341 AAGGGTTTGTAGCAGGCCTG 60.251 55.000 29.34 29.34 0.00 4.85
2292 3249 1.074951 GGGTTTGTAGCAGGCCTGT 59.925 57.895 32.81 21.44 0.00 4.00
2293 3250 0.326927 GGGTTTGTAGCAGGCCTGTA 59.673 55.000 32.81 20.43 0.00 2.74
2294 3251 1.271707 GGGTTTGTAGCAGGCCTGTAA 60.272 52.381 32.81 18.96 0.00 2.41
2306 3263 2.723273 GGCCTGTAAAAGCCTGTATGT 58.277 47.619 0.00 0.00 46.14 2.29
2307 3264 2.423538 GGCCTGTAAAAGCCTGTATGTG 59.576 50.000 0.00 0.00 46.14 3.21
2308 3265 3.081804 GCCTGTAAAAGCCTGTATGTGT 58.918 45.455 0.00 0.00 0.00 3.72
2310 3267 4.332819 GCCTGTAAAAGCCTGTATGTGTAG 59.667 45.833 0.00 0.00 0.00 2.74
2311 3268 4.332819 CCTGTAAAAGCCTGTATGTGTAGC 59.667 45.833 0.00 0.00 0.00 3.58
2314 3271 5.943416 TGTAAAAGCCTGTATGTGTAGCATT 59.057 36.000 0.00 0.00 38.94 3.56
2316 3273 5.982890 AAAGCCTGTATGTGTAGCATTTT 57.017 34.783 0.00 0.00 38.94 1.82
2317 3274 5.982890 AAGCCTGTATGTGTAGCATTTTT 57.017 34.783 0.00 0.00 38.94 1.94
2318 3275 5.314923 AGCCTGTATGTGTAGCATTTTTG 57.685 39.130 0.00 0.00 38.94 2.44
2449 6567 3.243704 TGGCCTTTGCATGTAGTGTTTTC 60.244 43.478 3.32 0.00 40.13 2.29
2484 6838 9.673454 AGGTTCTATGTAAATTTTTCGACAAAC 57.327 29.630 0.00 0.00 0.00 2.93
2485 6839 9.673454 GGTTCTATGTAAATTTTTCGACAAACT 57.327 29.630 0.00 0.00 0.00 2.66
2535 6889 2.871182 TACATCTAGCCTCTGCAACG 57.129 50.000 0.00 0.00 41.13 4.10
2539 6893 0.528017 TCTAGCCTCTGCAACGTCAG 59.472 55.000 0.00 0.00 41.13 3.51
2585 6942 4.202264 ACGAGAGAAAAAGAAGAAGGCTGA 60.202 41.667 0.00 0.00 0.00 4.26
2614 6973 3.756802 CCAATGTGGCCAACGTGA 58.243 55.556 7.24 0.00 0.00 4.35
2625 6984 0.251916 CCAACGTGATAGGGGCAAGA 59.748 55.000 0.00 0.00 0.00 3.02
2640 6999 4.565652 GGGGCAAGAGTGTTCTGATCTTTA 60.566 45.833 0.00 0.00 32.79 1.85
2641 7000 5.003804 GGGCAAGAGTGTTCTGATCTTTAA 58.996 41.667 0.00 0.00 32.79 1.52
2675 7036 1.425066 TGCTGATTTGGGTGGAGAACT 59.575 47.619 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.224695 TGGAGTAGAGAGGACACGACAA 60.225 50.000 0.00 0.00 0.00 3.18
44 45 2.606213 TCCCACTCGGACATGGCA 60.606 61.111 0.00 0.00 34.86 4.92
55 56 2.174639 TCAATGTCACCAAACTCCCACT 59.825 45.455 0.00 0.00 0.00 4.00
65 66 1.355381 AGCTCCCAATCAATGTCACCA 59.645 47.619 0.00 0.00 0.00 4.17
67 68 2.019984 GGAGCTCCCAATCAATGTCAC 58.980 52.381 23.19 0.00 34.14 3.67
187 188 2.261361 CACTCGACACATGCCGGA 59.739 61.111 5.05 0.00 0.00 5.14
281 283 3.450115 GCCAGGGACGACGCTACT 61.450 66.667 3.90 0.00 37.53 2.57
333 984 5.163784 GGCGTCCCAATTCTTAAGTCTTAAC 60.164 44.000 1.63 0.00 0.00 2.01
516 1168 8.229811 CGAGAACATAATTTGTCATCTCAAACA 58.770 33.333 15.22 0.00 40.19 2.83
539 1191 3.859961 AGAAACATTGTCATACTCGCGAG 59.140 43.478 33.45 33.45 0.00 5.03
560 1212 6.238374 CGGGATTTGCCATGTTTACTAGTAAG 60.238 42.308 14.73 5.15 38.95 2.34
562 1214 5.120399 CGGGATTTGCCATGTTTACTAGTA 58.880 41.667 0.00 0.00 38.95 1.82
563 1215 3.945285 CGGGATTTGCCATGTTTACTAGT 59.055 43.478 0.00 0.00 38.95 2.57
564 1216 3.315191 CCGGGATTTGCCATGTTTACTAG 59.685 47.826 0.00 0.00 38.95 2.57
601 1253 6.023357 TGCAAGCATAGCAAAGATTTTACA 57.977 33.333 0.00 0.00 39.39 2.41
666 1339 7.820044 TTGTGACTTCGCTACAAAAATTTTT 57.180 28.000 10.41 10.41 31.95 1.94
667 1340 7.757624 TCTTTGTGACTTCGCTACAAAAATTTT 59.242 29.630 0.00 0.00 41.91 1.82
668 1341 7.254852 TCTTTGTGACTTCGCTACAAAAATTT 58.745 30.769 0.00 0.00 41.91 1.82
669 1342 6.791303 TCTTTGTGACTTCGCTACAAAAATT 58.209 32.000 0.00 0.00 41.91 1.82
670 1343 6.371809 TCTTTGTGACTTCGCTACAAAAAT 57.628 33.333 0.00 0.00 41.91 1.82
671 1344 5.804692 TCTTTGTGACTTCGCTACAAAAA 57.195 34.783 0.00 0.00 41.91 1.94
672 1345 5.804692 TTCTTTGTGACTTCGCTACAAAA 57.195 34.783 0.00 0.00 41.91 2.44
673 1346 5.804692 TTTCTTTGTGACTTCGCTACAAA 57.195 34.783 0.00 0.00 40.73 2.83
674 1347 5.583061 TCTTTTCTTTGTGACTTCGCTACAA 59.417 36.000 0.00 0.00 32.93 2.41
675 1348 5.113383 TCTTTTCTTTGTGACTTCGCTACA 58.887 37.500 0.00 0.00 0.00 2.74
676 1349 5.462398 TCTCTTTTCTTTGTGACTTCGCTAC 59.538 40.000 0.00 0.00 0.00 3.58
677 1350 5.597806 TCTCTTTTCTTTGTGACTTCGCTA 58.402 37.500 0.00 0.00 0.00 4.26
678 1351 4.442706 TCTCTTTTCTTTGTGACTTCGCT 58.557 39.130 0.00 0.00 0.00 4.93
679 1352 4.795970 TCTCTTTTCTTTGTGACTTCGC 57.204 40.909 0.00 0.00 0.00 4.70
680 1353 5.523916 TCCTTCTCTTTTCTTTGTGACTTCG 59.476 40.000 0.00 0.00 0.00 3.79
681 1354 6.927294 TCCTTCTCTTTTCTTTGTGACTTC 57.073 37.500 0.00 0.00 0.00 3.01
682 1355 7.703058 TTTCCTTCTCTTTTCTTTGTGACTT 57.297 32.000 0.00 0.00 0.00 3.01
683 1356 7.629437 GCTTTTCCTTCTCTTTTCTTTGTGACT 60.629 37.037 0.00 0.00 0.00 3.41
684 1357 6.473778 GCTTTTCCTTCTCTTTTCTTTGTGAC 59.526 38.462 0.00 0.00 0.00 3.67
685 1358 6.378280 AGCTTTTCCTTCTCTTTTCTTTGTGA 59.622 34.615 0.00 0.00 0.00 3.58
686 1359 6.567959 AGCTTTTCCTTCTCTTTTCTTTGTG 58.432 36.000 0.00 0.00 0.00 3.33
687 1360 6.782082 AGCTTTTCCTTCTCTTTTCTTTGT 57.218 33.333 0.00 0.00 0.00 2.83
688 1361 8.159344 TCTAGCTTTTCCTTCTCTTTTCTTTG 57.841 34.615 0.00 0.00 0.00 2.77
791 1464 2.578495 CTTCGTTGAATCAGTTGCTGC 58.422 47.619 0.00 0.00 0.00 5.25
893 1566 2.329539 ATAGGCACGCTGGATGTGGG 62.330 60.000 0.00 0.00 37.80 4.61
935 1608 5.014860 TCCGGGAAGTGATAGATATGGTAGA 59.985 44.000 0.00 0.00 0.00 2.59
1186 1862 1.337071 TGACAATATCGACGAGGAGGC 59.663 52.381 3.01 0.00 0.00 4.70
1216 1892 6.494893 ACATGCATGTACGATTTACACTTT 57.505 33.333 30.50 0.00 39.68 2.66
1567 2243 2.885644 CGCGACATCCCCTCGTTG 60.886 66.667 0.00 0.00 33.51 4.10
1568 2244 4.814294 GCGCGACATCCCCTCGTT 62.814 66.667 12.10 0.00 33.51 3.85
1647 2323 4.824166 CCACGACTACGCCGACGG 62.824 72.222 10.29 10.29 46.04 4.79
1657 2333 1.494716 CCCCTAAAACCCCCACGACT 61.495 60.000 0.00 0.00 0.00 4.18
1675 2351 0.179078 CATCTCAGAGCACCAGAGCC 60.179 60.000 0.00 0.00 34.23 4.70
1710 2386 1.202325 ACAGCACGAACACAACGTCTA 60.202 47.619 0.00 0.00 42.07 2.59
1711 2388 0.459585 ACAGCACGAACACAACGTCT 60.460 50.000 0.00 0.00 42.07 4.18
1753 2430 2.058798 AGCGTATCACACAACGAACAG 58.941 47.619 0.00 0.00 41.55 3.16
1782 2459 9.436957 AACTCCTTGAACTACATATAACAACTG 57.563 33.333 0.00 0.00 0.00 3.16
1881 2558 7.291411 AGTCCTGGTATCACTATGTAATCAC 57.709 40.000 0.00 0.00 0.00 3.06
1889 2566 7.072562 AGATTCAGAAGTCCTGGTATCACTAT 58.927 38.462 0.00 0.00 43.12 2.12
1935 2613 7.601508 AGAATTTCGGGTGTTAACTAACTGTAG 59.398 37.037 7.22 0.00 37.12 2.74
2027 2982 1.667154 GGAGGAAAAATCCAGCGCCC 61.667 60.000 2.29 0.00 36.79 6.13
2139 3096 3.169733 CTCCGTACGTCTAGCAAAACTC 58.830 50.000 15.21 0.00 0.00 3.01
2140 3097 2.670509 GCTCCGTACGTCTAGCAAAACT 60.671 50.000 22.19 0.00 35.05 2.66
2141 3098 1.652619 GCTCCGTACGTCTAGCAAAAC 59.347 52.381 22.19 0.95 35.05 2.43
2142 3099 1.542915 AGCTCCGTACGTCTAGCAAAA 59.457 47.619 26.24 0.00 37.44 2.44
2143 3100 1.171308 AGCTCCGTACGTCTAGCAAA 58.829 50.000 26.24 0.82 37.44 3.68
2144 3101 1.171308 AAGCTCCGTACGTCTAGCAA 58.829 50.000 26.24 1.96 37.44 3.91
2145 3102 1.171308 AAAGCTCCGTACGTCTAGCA 58.829 50.000 26.24 1.99 37.44 3.49
2146 3103 2.096496 TGTAAAGCTCCGTACGTCTAGC 59.904 50.000 20.52 20.52 35.16 3.42
2147 3104 4.548991 ATGTAAAGCTCCGTACGTCTAG 57.451 45.455 15.21 9.59 0.00 2.43
2148 3105 5.586243 ACTTATGTAAAGCTCCGTACGTCTA 59.414 40.000 15.21 0.00 0.00 2.59
2149 3106 4.397417 ACTTATGTAAAGCTCCGTACGTCT 59.603 41.667 15.21 5.34 0.00 4.18
2150 3107 4.666237 ACTTATGTAAAGCTCCGTACGTC 58.334 43.478 15.21 2.93 0.00 4.34
2151 3108 4.708726 ACTTATGTAAAGCTCCGTACGT 57.291 40.909 15.21 0.00 0.00 3.57
2154 3111 6.072508 CCCGTATACTTATGTAAAGCTCCGTA 60.073 42.308 0.56 0.00 31.80 4.02
2155 3112 5.278660 CCCGTATACTTATGTAAAGCTCCGT 60.279 44.000 0.56 0.00 31.80 4.69
2158 3115 5.634020 CAGCCCGTATACTTATGTAAAGCTC 59.366 44.000 0.56 0.00 31.80 4.09
2159 3116 5.303589 TCAGCCCGTATACTTATGTAAAGCT 59.696 40.000 0.56 0.00 31.80 3.74
2163 3120 6.495872 AGGAATCAGCCCGTATACTTATGTAA 59.504 38.462 0.56 0.00 31.80 2.41
2164 3121 6.014647 AGGAATCAGCCCGTATACTTATGTA 58.985 40.000 0.56 0.00 0.00 2.29
2165 3122 4.838986 AGGAATCAGCCCGTATACTTATGT 59.161 41.667 0.56 0.00 0.00 2.29
2166 3123 5.047306 TCAGGAATCAGCCCGTATACTTATG 60.047 44.000 0.56 0.00 0.00 1.90
2167 3124 5.084519 TCAGGAATCAGCCCGTATACTTAT 58.915 41.667 0.56 0.00 0.00 1.73
2168 3125 4.476297 TCAGGAATCAGCCCGTATACTTA 58.524 43.478 0.56 0.00 0.00 2.24
2169 3126 3.305720 TCAGGAATCAGCCCGTATACTT 58.694 45.455 0.56 0.00 0.00 2.24
2170 3127 2.958818 TCAGGAATCAGCCCGTATACT 58.041 47.619 0.56 0.00 0.00 2.12
2171 3128 3.069729 AGTTCAGGAATCAGCCCGTATAC 59.930 47.826 0.00 0.00 0.00 1.47
2173 3130 2.119495 AGTTCAGGAATCAGCCCGTAT 58.881 47.619 0.00 0.00 0.00 3.06
2175 3132 0.036010 CAGTTCAGGAATCAGCCCGT 60.036 55.000 0.00 0.00 0.00 5.28
2176 3133 0.745845 CCAGTTCAGGAATCAGCCCG 60.746 60.000 0.00 0.00 0.00 6.13
2177 3134 1.034292 GCCAGTTCAGGAATCAGCCC 61.034 60.000 0.00 0.00 0.00 5.19
2178 3135 1.372087 CGCCAGTTCAGGAATCAGCC 61.372 60.000 0.00 0.00 0.00 4.85
2181 3138 1.741401 CGCGCCAGTTCAGGAATCA 60.741 57.895 0.00 0.00 0.00 2.57
2182 3139 1.298859 AACGCGCCAGTTCAGGAATC 61.299 55.000 5.73 0.00 0.00 2.52
2183 3140 0.889186 AAACGCGCCAGTTCAGGAAT 60.889 50.000 5.73 0.00 32.43 3.01
2184 3141 1.098712 AAAACGCGCCAGTTCAGGAA 61.099 50.000 5.73 0.00 32.43 3.36
2185 3142 0.249953 TAAAACGCGCCAGTTCAGGA 60.250 50.000 5.73 0.00 32.43 3.86
2186 3143 0.589223 TTAAAACGCGCCAGTTCAGG 59.411 50.000 5.73 0.00 32.43 3.86
2187 3144 1.662026 GGTTAAAACGCGCCAGTTCAG 60.662 52.381 5.73 0.00 32.43 3.02
2188 3145 0.308376 GGTTAAAACGCGCCAGTTCA 59.692 50.000 5.73 0.00 32.43 3.18
2189 3146 0.723459 CGGTTAAAACGCGCCAGTTC 60.723 55.000 5.73 0.00 32.43 3.01
2194 3151 2.174107 GTCCGGTTAAAACGCGCC 59.826 61.111 5.73 0.00 0.00 6.53
2195 3152 2.156846 TTCGTCCGGTTAAAACGCGC 62.157 55.000 5.73 0.00 36.40 6.86
2196 3153 0.231790 TTTCGTCCGGTTAAAACGCG 59.768 50.000 3.53 3.53 36.40 6.01
2197 3154 1.398832 CCTTTCGTCCGGTTAAAACGC 60.399 52.381 7.70 0.00 36.40 4.84
2198 3155 1.866601 ACCTTTCGTCCGGTTAAAACG 59.133 47.619 0.00 3.33 37.74 3.60
2201 3158 2.548493 CCTCACCTTTCGTCCGGTTAAA 60.548 50.000 0.00 0.00 0.00 1.52
2202 3159 1.001181 CCTCACCTTTCGTCCGGTTAA 59.999 52.381 0.00 0.00 0.00 2.01
2203 3160 0.604578 CCTCACCTTTCGTCCGGTTA 59.395 55.000 0.00 0.00 0.00 2.85
2205 3162 2.580601 CCCTCACCTTTCGTCCGGT 61.581 63.158 0.00 0.00 0.00 5.28
2206 3163 2.264794 CCCTCACCTTTCGTCCGG 59.735 66.667 0.00 0.00 0.00 5.14
2207 3164 2.434359 GCCCTCACCTTTCGTCCG 60.434 66.667 0.00 0.00 0.00 4.79
2208 3165 2.434359 CGCCCTCACCTTTCGTCC 60.434 66.667 0.00 0.00 0.00 4.79
2209 3166 2.434359 CCGCCCTCACCTTTCGTC 60.434 66.667 0.00 0.00 0.00 4.20
2210 3167 4.699522 GCCGCCCTCACCTTTCGT 62.700 66.667 0.00 0.00 0.00 3.85
2230 3187 1.582610 CCCGATTTTCACCCGTGTGG 61.583 60.000 0.00 0.00 42.98 4.17
2231 3188 1.582610 CCCCGATTTTCACCCGTGTG 61.583 60.000 0.00 0.00 44.18 3.82
2233 3190 2.043980 CCCCCGATTTTCACCCGTG 61.044 63.158 0.00 0.00 0.00 4.94
2234 3191 2.353573 CCCCCGATTTTCACCCGT 59.646 61.111 0.00 0.00 0.00 5.28
2249 3206 3.225940 CATAAATTCTCTTCAGGCCCCC 58.774 50.000 0.00 0.00 0.00 5.40
2250 3207 3.117512 TCCATAAATTCTCTTCAGGCCCC 60.118 47.826 0.00 0.00 0.00 5.80
2252 3209 4.582240 CCTTCCATAAATTCTCTTCAGGCC 59.418 45.833 0.00 0.00 0.00 5.19
2253 3210 4.582240 CCCTTCCATAAATTCTCTTCAGGC 59.418 45.833 0.00 0.00 0.00 4.85
2254 3211 5.760131 ACCCTTCCATAAATTCTCTTCAGG 58.240 41.667 0.00 0.00 0.00 3.86
2255 3212 7.177392 ACAAACCCTTCCATAAATTCTCTTCAG 59.823 37.037 0.00 0.00 0.00 3.02
2256 3213 7.010160 ACAAACCCTTCCATAAATTCTCTTCA 58.990 34.615 0.00 0.00 0.00 3.02
2257 3214 7.468141 ACAAACCCTTCCATAAATTCTCTTC 57.532 36.000 0.00 0.00 0.00 2.87
2258 3215 7.122799 GCTACAAACCCTTCCATAAATTCTCTT 59.877 37.037 0.00 0.00 0.00 2.85
2260 3217 6.377146 TGCTACAAACCCTTCCATAAATTCTC 59.623 38.462 0.00 0.00 0.00 2.87
2261 3218 6.252995 TGCTACAAACCCTTCCATAAATTCT 58.747 36.000 0.00 0.00 0.00 2.40
2262 3219 6.405842 CCTGCTACAAACCCTTCCATAAATTC 60.406 42.308 0.00 0.00 0.00 2.17
2263 3220 5.422012 CCTGCTACAAACCCTTCCATAAATT 59.578 40.000 0.00 0.00 0.00 1.82
2264 3221 4.956075 CCTGCTACAAACCCTTCCATAAAT 59.044 41.667 0.00 0.00 0.00 1.40
2265 3222 4.340617 CCTGCTACAAACCCTTCCATAAA 58.659 43.478 0.00 0.00 0.00 1.40
2268 3225 1.616994 GCCTGCTACAAACCCTTCCAT 60.617 52.381 0.00 0.00 0.00 3.41
2269 3226 0.251165 GCCTGCTACAAACCCTTCCA 60.251 55.000 0.00 0.00 0.00 3.53
2270 3227 0.965866 GGCCTGCTACAAACCCTTCC 60.966 60.000 0.00 0.00 0.00 3.46
2271 3228 0.038310 AGGCCTGCTACAAACCCTTC 59.962 55.000 3.11 0.00 0.00 3.46
2273 3230 1.380302 CAGGCCTGCTACAAACCCT 59.620 57.895 22.33 0.00 0.00 4.34
2275 3232 2.194201 TTACAGGCCTGCTACAAACC 57.806 50.000 33.06 0.00 0.00 3.27
2276 3233 3.611766 GCTTTTACAGGCCTGCTACAAAC 60.612 47.826 33.06 13.19 0.00 2.93
2277 3234 2.556622 GCTTTTACAGGCCTGCTACAAA 59.443 45.455 33.06 22.33 0.00 2.83
2278 3235 2.159382 GCTTTTACAGGCCTGCTACAA 58.841 47.619 33.06 19.59 0.00 2.41
2279 3236 1.613255 GGCTTTTACAGGCCTGCTACA 60.613 52.381 33.06 13.95 44.48 2.74
2280 3237 1.095600 GGCTTTTACAGGCCTGCTAC 58.904 55.000 33.06 15.56 44.48 3.58
2282 3239 4.423231 GGCTTTTACAGGCCTGCT 57.577 55.556 33.06 21.13 44.48 4.24
2288 3245 4.332819 GCTACACATACAGGCTTTTACAGG 59.667 45.833 0.00 0.00 0.00 4.00
2289 3246 4.935205 TGCTACACATACAGGCTTTTACAG 59.065 41.667 0.00 0.00 0.00 2.74
2290 3247 4.900684 TGCTACACATACAGGCTTTTACA 58.099 39.130 0.00 0.00 0.00 2.41
2291 3248 6.436843 AATGCTACACATACAGGCTTTTAC 57.563 37.500 0.00 0.00 38.34 2.01
2292 3249 7.461182 AAAATGCTACACATACAGGCTTTTA 57.539 32.000 0.00 0.00 38.34 1.52
2293 3250 5.982890 AAATGCTACACATACAGGCTTTT 57.017 34.783 0.00 0.00 38.34 2.27
2294 3251 5.982890 AAAATGCTACACATACAGGCTTT 57.017 34.783 0.00 0.00 38.34 3.51
2302 3259 9.979578 ATTTCAAAGACAAAAATGCTACACATA 57.020 25.926 0.00 0.00 38.34 2.29
2304 3261 7.763528 ACATTTCAAAGACAAAAATGCTACACA 59.236 29.630 6.90 0.00 41.76 3.72
2305 3262 8.057742 CACATTTCAAAGACAAAAATGCTACAC 58.942 33.333 6.90 0.00 41.76 2.90
2306 3263 7.763528 ACACATTTCAAAGACAAAAATGCTACA 59.236 29.630 6.90 0.00 41.76 2.74
2307 3264 8.057742 CACACATTTCAAAGACAAAAATGCTAC 58.942 33.333 6.90 0.00 41.76 3.58
2308 3265 7.224362 CCACACATTTCAAAGACAAAAATGCTA 59.776 33.333 6.90 0.00 41.76 3.49
2310 3267 6.036953 TCCACACATTTCAAAGACAAAAATGC 59.963 34.615 6.90 0.00 41.76 3.56
2311 3268 7.536895 TCCACACATTTCAAAGACAAAAATG 57.463 32.000 5.71 5.71 43.02 2.32
2314 3271 7.326454 TCATTCCACACATTTCAAAGACAAAA 58.674 30.769 0.00 0.00 0.00 2.44
2316 3273 6.462552 TCATTCCACACATTTCAAAGACAA 57.537 33.333 0.00 0.00 0.00 3.18
2317 3274 6.462552 TTCATTCCACACATTTCAAAGACA 57.537 33.333 0.00 0.00 0.00 3.41
2318 3275 7.439056 ACATTTCATTCCACACATTTCAAAGAC 59.561 33.333 0.00 0.00 0.00 3.01
2535 6889 5.651530 TCGAGTTGGTCTTGATATTCTGAC 58.348 41.667 0.00 0.00 32.12 3.51
2539 6893 5.517054 GTGTCTCGAGTTGGTCTTGATATTC 59.483 44.000 13.13 0.00 36.15 1.75
2610 6969 0.537188 ACACTCTTGCCCCTATCACG 59.463 55.000 0.00 0.00 0.00 4.35
2614 6973 2.551270 TCAGAACACTCTTGCCCCTAT 58.449 47.619 0.00 0.00 0.00 2.57
2625 6984 9.730705 TGATTCTCATTTAAAGATCAGAACACT 57.269 29.630 0.00 0.00 0.00 3.55
2640 6999 6.127703 CCAAATCAGCAGAGTGATTCTCATTT 60.128 38.462 0.00 0.00 44.72 2.32
2641 7000 5.357314 CCAAATCAGCAGAGTGATTCTCATT 59.643 40.000 0.00 0.00 44.72 2.57
2657 7018 1.815003 GCAGTTCTCCACCCAAATCAG 59.185 52.381 0.00 0.00 0.00 2.90
2658 7019 1.425066 AGCAGTTCTCCACCCAAATCA 59.575 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.