Multiple sequence alignment - TraesCS2D01G433000

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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 TraesCS2D01G433000 chr2D 100.000 4601 0 0 1 4601 544852078 544847478 0.000000e+00 8497
1 TraesCS2D01G433000 chr2D 90.000 170 10 2 2208 2372 341699339 341699506 3.610000e-51 213
2 TraesCS2D01G433000 chr2D 97.647 85 2 0 2029 2113 164992768 164992684 3.710000e-31 147
3 TraesCS2D01G433000 chr2B 96.665 2249 57 7 2369 4601 651070442 651068196 0.000000e+00 3722
4 TraesCS2D01G433000 chr2B 93.103 1450 54 14 609 2031 651072052 651070622 0.000000e+00 2082
5 TraesCS2D01G433000 chr2B 93.989 183 10 1 2110 2292 651070626 651070445 4.530000e-70 276
6 TraesCS2D01G433000 chr2B 90.000 170 12 1 2208 2372 209091152 209091321 1.000000e-51 215
7 TraesCS2D01G433000 chr2B 89.412 170 13 2 2208 2372 174396582 174396751 4.660000e-50 209
8 TraesCS2D01G433000 chr2A 87.166 1909 135 38 201 2031 688634769 688636645 0.000000e+00 2067
9 TraesCS2D01G433000 chr2A 97.029 1077 30 2 2110 3186 688636641 688637715 0.000000e+00 1810
10 TraesCS2D01G433000 chr2A 98.316 891 14 1 3184 4073 688637759 688638649 0.000000e+00 1561
11 TraesCS2D01G433000 chr2A 96.091 307 11 1 4296 4601 688641135 688641441 2.470000e-137 499
12 TraesCS2D01G433000 chr2A 90.726 248 7 3 4069 4300 688640587 688640834 2.670000e-82 316
13 TraesCS2D01G433000 chr2A 88.235 119 11 3 4 120 688634585 688634702 6.210000e-29 139
14 TraesCS2D01G433000 chr6A 92.025 163 8 1 2208 2365 381088706 381088868 1.670000e-54 224
15 TraesCS2D01G433000 chr4D 90.588 170 11 1 2208 2372 313574202 313574371 2.150000e-53 220
16 TraesCS2D01G433000 chr4D 90.000 170 11 2 2208 2372 325108105 325107937 1.000000e-51 215
17 TraesCS2D01G433000 chr4A 90.000 170 12 1 2208 2372 146552018 146552187 1.000000e-51 215
18 TraesCS2D01G433000 chr4A 88.983 118 9 4 1997 2114 30142327 30142440 4.800000e-30 143
19 TraesCS2D01G433000 chr1B 89.412 170 13 3 2208 2372 211323054 211322885 4.660000e-50 209
20 TraesCS2D01G433000 chr1A 96.842 95 2 1 2019 2113 432840455 432840548 1.710000e-34 158
21 TraesCS2D01G433000 chr5D 96.703 91 3 0 2024 2114 373214661 373214571 7.970000e-33 152
22 TraesCS2D01G433000 chr5D 92.453 106 4 4 2018 2121 45483788 45483685 1.030000e-31 148
23 TraesCS2D01G433000 chr7A 94.845 97 3 2 2021 2115 664477198 664477294 2.870000e-32 150
24 TraesCS2D01G433000 chr6B 93.939 99 5 1 2015 2113 216509855 216509758 1.030000e-31 148
25 TraesCS2D01G433000 chr7D 92.308 104 5 2 2012 2113 510397860 510397758 1.330000e-30 145
26 TraesCS2D01G433000 chr3D 87.288 118 11 4 2001 2118 459472547 459472434 1.040000e-26 132


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 TraesCS2D01G433000 chr2D 544847478 544852078 4600 True 8497.000000 8497 100.000000 1 4601 1 chr2D.!!$R2 4600
1 TraesCS2D01G433000 chr2B 651068196 651072052 3856 True 2026.666667 3722 94.585667 609 4601 3 chr2B.!!$R1 3992
2 TraesCS2D01G433000 chr2A 688634585 688641441 6856 False 1065.333333 2067 92.927167 4 4601 6 chr2A.!!$F1 4597

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
208 238 0.179179 GAGGCACATGCTTCTTTCGC 60.179 55.000 8.62 0.0 42.93 4.70 F
240 270 0.313672 TTTTTCGTGGAGGCACATGC 59.686 50.000 0.00 0.0 41.14 4.06 F
920 997 0.469331 TTCTCTATCCATCCCGGCGT 60.469 55.000 6.01 0.0 33.14 5.68 F
1829 1950 0.038159 GACGTGTGCTCTAGCCAACT 60.038 55.000 0.00 0.0 41.18 3.16 F
2043 2164 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.0 0.00 4.37 F
2046 2167 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.0 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1264 1349 0.326264 ACACAATCTCAGGAGCACCC 59.674 55.000 0.00 0.0 36.73 4.61 R
1364 1459 0.480690 ACCACATGTTAACCAGGGCA 59.519 50.000 2.48 0.0 0.00 5.36 R
2243 2364 0.944999 TTCAGATCTAGCCTCCCCCT 59.055 55.000 0.00 0.0 0.00 4.79 R
2669 2790 2.379907 TCTTTCAGGGGCTCTTTGGATT 59.620 45.455 0.00 0.0 0.00 3.01 R
3399 3566 2.886913 TGGGCACATTCTGAAAATGGA 58.113 42.857 0.00 0.0 32.14 3.41 R
4095 6213 5.104259 ACCTCCTGAATAAATCTGTCACC 57.896 43.478 0.00 0.0 0.00 4.02 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
25 26 4.202182 GGTTTTCCCCTAGGTTTTGAACAC 60.202 45.833 8.29 7.90 0.00 3.32
26 27 3.955524 TTCCCCTAGGTTTTGAACACA 57.044 42.857 8.29 0.00 0.00 3.72
27 28 4.463050 TTCCCCTAGGTTTTGAACACAT 57.537 40.909 8.29 0.00 0.00 3.21
89 91 2.159627 GGTACAAATGTGCTTCTCGTGG 59.840 50.000 0.00 0.00 0.00 4.94
90 92 2.254546 ACAAATGTGCTTCTCGTGGA 57.745 45.000 0.00 0.00 0.00 4.02
136 165 2.289002 GCACAGATTTGCCTATCGGAAG 59.711 50.000 3.07 0.00 36.42 3.46
140 169 3.041946 AGATTTGCCTATCGGAAGGAGT 58.958 45.455 8.02 0.00 39.15 3.85
179 209 0.812014 TGTTTCGCGAGAGGCACAAA 60.812 50.000 9.59 0.00 43.84 2.83
186 216 1.978782 GCGAGAGGCACAAATTTTTCG 59.021 47.619 0.00 0.00 42.87 3.46
194 224 2.801342 GCACAAATTTTTCGTGGAGGCA 60.801 45.455 8.67 0.00 0.00 4.75
206 236 1.200948 GTGGAGGCACATGCTTCTTTC 59.799 52.381 14.72 0.71 45.19 2.62
208 238 0.179179 GAGGCACATGCTTCTTTCGC 60.179 55.000 8.62 0.00 42.93 4.70
209 239 1.512734 GGCACATGCTTCTTTCGCG 60.513 57.895 0.00 0.00 41.70 5.87
210 240 1.497278 GCACATGCTTCTTTCGCGA 59.503 52.632 3.71 3.71 38.21 5.87
211 241 0.519999 GCACATGCTTCTTTCGCGAG 60.520 55.000 9.59 0.00 38.21 5.03
212 242 1.070821 CACATGCTTCTTTCGCGAGA 58.929 50.000 9.59 3.35 39.20 4.04
213 243 4.306489 GCACATGCTTCTTTCGCGAGAA 62.306 50.000 9.59 9.85 42.82 2.87
224 254 3.347958 TTCGCGAGAAGCACAATTTTT 57.652 38.095 9.59 0.00 46.92 1.94
240 270 0.313672 TTTTTCGTGGAGGCACATGC 59.686 50.000 0.00 0.00 41.14 4.06
241 271 0.537143 TTTTCGTGGAGGCACATGCT 60.537 50.000 3.48 0.00 41.70 3.79
242 272 0.537143 TTTCGTGGAGGCACATGCTT 60.537 50.000 3.48 0.00 41.70 3.91
243 273 0.955428 TTCGTGGAGGCACATGCTTC 60.955 55.000 7.42 7.42 45.14 3.86
244 274 1.376424 CGTGGAGGCACATGCTTCT 60.376 57.895 14.72 0.00 45.19 2.85
245 275 0.957395 CGTGGAGGCACATGCTTCTT 60.957 55.000 14.72 0.00 45.19 2.52
246 276 1.251251 GTGGAGGCACATGCTTCTTT 58.749 50.000 14.72 0.00 45.19 2.52
247 277 1.200948 GTGGAGGCACATGCTTCTTTC 59.799 52.381 14.72 0.71 45.19 2.62
248 278 1.202915 TGGAGGCACATGCTTCTTTCA 60.203 47.619 14.72 3.17 45.19 2.69
264 294 2.595124 TTCACGAGAAGCACAACTCA 57.405 45.000 0.00 0.00 33.86 3.41
269 299 3.060003 CACGAGAAGCACAACTCAGAAAG 60.060 47.826 0.00 0.00 33.86 2.62
272 302 2.439507 AGAAGCACAACTCAGAAAGGGA 59.560 45.455 0.00 0.00 0.00 4.20
279 309 3.181490 ACAACTCAGAAAGGGAAAAACGC 60.181 43.478 0.00 0.00 0.00 4.84
301 353 4.271687 CGTTTGTTTTTCTTCCACGAGAG 58.728 43.478 0.00 0.00 0.00 3.20
302 354 4.598062 GTTTGTTTTTCTTCCACGAGAGG 58.402 43.478 0.00 0.00 0.00 3.69
303 355 3.553828 TGTTTTTCTTCCACGAGAGGT 57.446 42.857 0.00 0.00 0.00 3.85
310 362 4.025040 TCTTCCACGAGAGGTACAACTA 57.975 45.455 0.00 0.00 0.00 2.24
312 364 5.014858 TCTTCCACGAGAGGTACAACTATT 58.985 41.667 0.00 0.00 0.00 1.73
316 368 6.624423 TCCACGAGAGGTACAACTATTAAAC 58.376 40.000 0.00 0.00 0.00 2.01
317 369 5.809051 CCACGAGAGGTACAACTATTAAACC 59.191 44.000 0.00 0.00 0.00 3.27
318 370 5.809051 CACGAGAGGTACAACTATTAAACCC 59.191 44.000 0.00 0.00 0.00 4.11
319 371 5.039333 CGAGAGGTACAACTATTAAACCCG 58.961 45.833 0.00 0.00 0.00 5.28
320 372 5.163622 CGAGAGGTACAACTATTAAACCCGA 60.164 44.000 0.00 0.00 0.00 5.14
413 466 5.997129 TGTGAACATTCTTTACAGATCTGCA 59.003 36.000 22.83 7.16 0.00 4.41
414 467 6.486320 TGTGAACATTCTTTACAGATCTGCAA 59.514 34.615 22.83 13.69 0.00 4.08
415 468 7.013178 TGTGAACATTCTTTACAGATCTGCAAA 59.987 33.333 22.83 20.17 0.00 3.68
422 475 8.578308 TTCTTTACAGATCTGCAAACATTTTG 57.422 30.769 22.83 9.27 0.00 2.44
427 480 6.518493 ACAGATCTGCAAACATTTTGTGAAT 58.482 32.000 22.83 0.00 0.00 2.57
430 483 7.170151 CAGATCTGCAAACATTTTGTGAATTCA 59.830 33.333 10.38 3.38 0.00 2.57
434 487 7.658167 TCTGCAAACATTTTGTGAATTCATGAT 59.342 29.630 12.12 0.00 0.00 2.45
435 488 8.155821 TGCAAACATTTTGTGAATTCATGATT 57.844 26.923 12.12 3.71 0.00 2.57
467 540 9.696917 ACAAATTCACAAATAGTTTCTGGAATC 57.303 29.630 0.00 0.00 0.00 2.52
475 548 9.028284 ACAAATAGTTTCTGGAATCATGAACAT 57.972 29.630 0.00 0.00 0.00 2.71
480 553 8.822652 AGTTTCTGGAATCATGAACATTTTTC 57.177 30.769 0.00 0.00 0.00 2.29
483 556 7.213216 TCTGGAATCATGAACATTTTTCGAA 57.787 32.000 0.00 0.00 0.00 3.71
487 560 8.087136 TGGAATCATGAACATTTTTCGAATTCA 58.913 29.630 12.18 12.18 34.03 2.57
488 561 8.924691 GGAATCATGAACATTTTTCGAATTCAA 58.075 29.630 13.43 2.06 33.29 2.69
685 760 6.111768 AGCATATTCATCAAACTCACGAAC 57.888 37.500 0.00 0.00 0.00 3.95
723 798 9.190858 TGAGAACATTTTTAAAATTCGTGATGG 57.809 29.630 0.55 0.00 0.00 3.51
815 891 4.575885 GAAAGGAAATAAAAACAGGGGCC 58.424 43.478 0.00 0.00 0.00 5.80
920 997 0.469331 TTCTCTATCCATCCCGGCGT 60.469 55.000 6.01 0.00 33.14 5.68
975 1054 2.281970 GCTTTTCCGGTCCCCGTT 60.282 61.111 0.00 0.00 46.80 4.44
1032 1111 4.463879 CTCCCAGCACCTCGCCAG 62.464 72.222 0.00 0.00 44.04 4.85
1053 1132 3.130160 CAAGCAGCTCTTCCCGCC 61.130 66.667 0.00 0.00 31.27 6.13
1229 1314 1.961277 CCGCCACCTGTGAGTGAAC 60.961 63.158 0.00 0.00 40.34 3.18
1231 1316 1.600916 GCCACCTGTGAGTGAACCC 60.601 63.158 0.00 0.00 40.34 4.11
1264 1349 2.573369 CCATCTTTGCCATCCAGAGAG 58.427 52.381 0.00 0.00 38.00 3.20
1272 1357 1.828768 CATCCAGAGAGGGTGCTCC 59.171 63.158 0.00 0.00 42.79 4.70
1282 1367 0.617413 AGGGTGCTCCTGAGATTGTG 59.383 55.000 4.53 0.00 46.07 3.33
1323 1408 4.290196 AGTGGTAGAGAGTAGAGAAGGTGT 59.710 45.833 0.00 0.00 0.00 4.16
1348 1433 4.274214 ACCGATGCACATGATTCTTGTATG 59.726 41.667 0.00 0.00 0.00 2.39
1349 1434 4.216731 CGATGCACATGATTCTTGTATGC 58.783 43.478 0.00 6.55 0.00 3.14
1364 1459 8.792830 TTCTTGTATGCTGCTTAGATTAAAGT 57.207 30.769 0.00 0.00 0.00 2.66
1410 1524 6.851609 TGTGAAGCACATATAAATTGTGTCC 58.148 36.000 6.78 0.00 44.96 4.02
1466 1580 9.394477 GTGTGGTTTGATTTTGTTTAGATAGTC 57.606 33.333 0.00 0.00 0.00 2.59
1533 1647 4.947388 TCCCCTATTTGCATAATAATCGGC 59.053 41.667 0.00 0.00 0.00 5.54
1734 1855 2.526888 TTCGACCCATGGAGACTAGT 57.473 50.000 15.22 0.00 0.00 2.57
1747 1868 0.824759 GACTAGTTCCCATGTCGGCT 59.175 55.000 0.00 0.00 0.00 5.52
1760 1881 5.105756 CCCATGTCGGCTTTTTAGAAGAAAT 60.106 40.000 0.00 0.00 0.00 2.17
1761 1882 5.801947 CCATGTCGGCTTTTTAGAAGAAATG 59.198 40.000 0.00 0.00 0.00 2.32
1767 1888 3.854240 GCTTTTTAGAAGAAATGAGGCGC 59.146 43.478 0.00 0.00 0.00 6.53
1769 1890 2.038387 TTAGAAGAAATGAGGCGCCC 57.962 50.000 26.15 15.80 0.00 6.13
1806 1927 3.600898 AACGCGGGTGGGTAAGCTC 62.601 63.158 12.47 0.00 40.91 4.09
1829 1950 0.038159 GACGTGTGCTCTAGCCAACT 60.038 55.000 0.00 0.00 41.18 3.16
2038 2159 9.848710 TTATCTTCATATATAGTACTCCCTCCG 57.151 37.037 0.00 0.00 0.00 4.63
2039 2160 7.268212 TCTTCATATATAGTACTCCCTCCGT 57.732 40.000 0.00 0.00 0.00 4.69
2040 2161 7.337167 TCTTCATATATAGTACTCCCTCCGTC 58.663 42.308 0.00 0.00 0.00 4.79
2041 2162 5.999044 TCATATATAGTACTCCCTCCGTCC 58.001 45.833 0.00 0.00 0.00 4.79
2042 2163 3.735720 ATATAGTACTCCCTCCGTCCC 57.264 52.381 0.00 0.00 0.00 4.46
2043 2164 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
2044 2165 1.229131 TAGTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
2045 2166 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2046 2167 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2047 2168 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2048 2169 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2049 2170 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2050 2171 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2051 2172 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2052 2173 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2053 2174 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2054 2175 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2055 2176 5.024118 CCCTCCGTCCCATAATATAAGAGT 58.976 45.833 0.00 0.00 0.00 3.24
2056 2177 5.105310 CCCTCCGTCCCATAATATAAGAGTG 60.105 48.000 0.00 0.00 0.00 3.51
2057 2178 5.480772 CCTCCGTCCCATAATATAAGAGTGT 59.519 44.000 0.00 0.00 0.00 3.55
2058 2179 6.014499 CCTCCGTCCCATAATATAAGAGTGTT 60.014 42.308 0.00 0.00 0.00 3.32
2059 2180 7.369551 TCCGTCCCATAATATAAGAGTGTTT 57.630 36.000 0.00 0.00 0.00 2.83
2060 2181 7.798071 TCCGTCCCATAATATAAGAGTGTTTT 58.202 34.615 0.00 0.00 0.00 2.43
2061 2182 7.713507 TCCGTCCCATAATATAAGAGTGTTTTG 59.286 37.037 0.00 0.00 0.00 2.44
2062 2183 7.497909 CCGTCCCATAATATAAGAGTGTTTTGT 59.502 37.037 0.00 0.00 0.00 2.83
2063 2184 9.537192 CGTCCCATAATATAAGAGTGTTTTGTA 57.463 33.333 0.00 0.00 0.00 2.41
2088 2209 4.743644 ACTAGTGTAGTGTCAAAAACGCTC 59.256 41.667 0.00 0.00 45.69 5.03
2089 2210 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
2090 2211 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
2091 2212 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
2092 2213 5.989777 AGTGTAGTGTCAAAAACGCTCTTAT 59.010 36.000 0.00 0.00 45.69 1.73
2093 2214 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
2094 2215 7.817962 AGTGTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 0.00 0.00 45.69 0.86
2095 2216 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
2096 2217 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
2099 2220 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
2100 2221 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
2101 2222 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
2102 2223 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
2198 2319 7.616150 AGATCACTTAACTCTGGCTCTAAACTA 59.384 37.037 0.00 0.00 0.00 2.24
2243 2364 4.717279 AGCCTTTAGTCCCAAACAAGTA 57.283 40.909 0.00 0.00 0.00 2.24
2323 2444 3.850098 AAGCTTCCACGCACCCCTG 62.850 63.158 0.00 0.00 0.00 4.45
2326 2447 4.308458 TTCCACGCACCCCTGTCG 62.308 66.667 0.00 0.00 0.00 4.35
2784 2905 3.245518 TGCACTATGTAACTGCGTGAT 57.754 42.857 0.00 0.00 33.35 3.06
2986 3107 6.904954 ATTCGTAAAATTGCTGTTGTAACG 57.095 33.333 0.00 0.00 0.00 3.18
3399 3566 7.591854 TTTCTACCTCTATATCCTAGGCTCT 57.408 40.000 2.96 0.00 33.42 4.09
4160 6279 2.263895 TGTGCTTCTATAGGTGGGGT 57.736 50.000 0.00 0.00 0.00 4.95
4180 6299 6.889722 TGGGGTCTTTCATTACATTAGAAAGG 59.110 38.462 12.51 0.00 45.05 3.11
4347 6778 2.304092 GCCAATCCATGAGCTCATTGA 58.696 47.619 27.27 27.27 33.61 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.175284 TCAAAACCTAGGGGAAAACCGT 59.825 45.455 14.81 0.00 41.60 4.83
1 2 2.866351 TCAAAACCTAGGGGAAAACCG 58.134 47.619 14.81 0.00 41.60 4.44
2 3 3.962063 TGTTCAAAACCTAGGGGAAAACC 59.038 43.478 14.81 1.25 39.11 3.27
8 9 5.545063 AAAATGTGTTCAAAACCTAGGGG 57.455 39.130 14.81 0.00 38.88 4.79
61 63 3.146104 AGCACATTTGTACCTCTTGCT 57.854 42.857 0.00 0.00 34.04 3.91
62 64 3.503748 AGAAGCACATTTGTACCTCTTGC 59.496 43.478 0.00 0.00 0.00 4.01
64 66 3.997021 CGAGAAGCACATTTGTACCTCTT 59.003 43.478 0.00 0.00 0.00 2.85
77 79 2.029844 GTGCCTCCACGAGAAGCAC 61.030 63.158 14.82 14.82 39.31 4.40
89 91 0.108585 TGGAAGTGAACCTGTGCCTC 59.891 55.000 0.00 0.00 0.00 4.70
90 92 0.179018 GTGGAAGTGAACCTGTGCCT 60.179 55.000 0.00 0.00 0.00 4.75
158 187 0.812014 TGTGCCTCTCGCGAAACAAA 60.812 50.000 11.33 0.00 42.08 2.83
161 190 0.517316 ATTTGTGCCTCTCGCGAAAC 59.483 50.000 11.33 4.48 42.08 2.78
162 191 1.234821 AATTTGTGCCTCTCGCGAAA 58.765 45.000 11.33 0.00 42.08 3.46
164 193 1.234821 AAAATTTGTGCCTCTCGCGA 58.765 45.000 9.26 9.26 42.08 5.87
165 194 1.978782 GAAAAATTTGTGCCTCTCGCG 59.021 47.619 0.00 0.00 42.08 5.87
179 209 1.067635 GCATGTGCCTCCACGAAAAAT 60.068 47.619 0.00 0.00 45.04 1.82
186 216 1.200948 GAAAGAAGCATGTGCCTCCAC 59.799 52.381 0.57 0.00 43.38 4.02
194 224 1.728971 CTTCTCGCGAAAGAAGCATGT 59.271 47.619 20.76 0.00 44.13 3.21
221 251 0.313672 GCATGTGCCTCCACGAAAAA 59.686 50.000 0.00 0.00 45.04 1.94
222 252 0.537143 AGCATGTGCCTCCACGAAAA 60.537 50.000 0.57 0.00 45.04 2.29
223 253 0.537143 AAGCATGTGCCTCCACGAAA 60.537 50.000 0.57 0.00 45.04 3.46
224 254 0.955428 GAAGCATGTGCCTCCACGAA 60.955 55.000 0.57 0.00 45.04 3.85
225 255 1.375908 GAAGCATGTGCCTCCACGA 60.376 57.895 0.57 0.00 45.04 4.35
226 256 0.957395 AAGAAGCATGTGCCTCCACG 60.957 55.000 0.57 0.00 45.04 4.94
227 257 1.200948 GAAAGAAGCATGTGCCTCCAC 59.799 52.381 0.57 0.00 43.38 4.02
228 258 1.202915 TGAAAGAAGCATGTGCCTCCA 60.203 47.619 0.57 0.00 43.38 3.86
229 259 1.200948 GTGAAAGAAGCATGTGCCTCC 59.799 52.381 0.57 0.00 43.38 4.30
230 260 1.135859 CGTGAAAGAAGCATGTGCCTC 60.136 52.381 0.57 0.00 43.38 4.70
231 261 0.877071 CGTGAAAGAAGCATGTGCCT 59.123 50.000 0.57 0.00 43.38 4.75
232 262 0.874390 TCGTGAAAGAAGCATGTGCC 59.126 50.000 0.57 0.00 43.38 5.01
233 263 1.800586 TCTCGTGAAAGAAGCATGTGC 59.199 47.619 0.00 0.00 42.49 4.57
234 264 4.062853 CTTCTCGTGAAAGAAGCATGTG 57.937 45.455 1.12 0.00 44.13 3.21
241 271 3.531538 AGTTGTGCTTCTCGTGAAAGAA 58.468 40.909 1.12 0.00 34.22 2.52
242 272 3.123804 GAGTTGTGCTTCTCGTGAAAGA 58.876 45.455 1.12 0.00 0.00 2.52
243 273 2.866156 TGAGTTGTGCTTCTCGTGAAAG 59.134 45.455 1.12 0.00 33.88 2.62
244 274 2.866156 CTGAGTTGTGCTTCTCGTGAAA 59.134 45.455 1.12 0.00 33.88 2.69
245 275 2.100749 TCTGAGTTGTGCTTCTCGTGAA 59.899 45.455 0.00 0.00 33.88 3.18
246 276 1.681264 TCTGAGTTGTGCTTCTCGTGA 59.319 47.619 0.00 0.00 33.88 4.35
247 277 2.140065 TCTGAGTTGTGCTTCTCGTG 57.860 50.000 0.00 0.00 33.88 4.35
248 278 2.890808 TTCTGAGTTGTGCTTCTCGT 57.109 45.000 0.00 0.00 33.88 4.18
264 294 2.164827 ACAAACGCGTTTTTCCCTTTCT 59.835 40.909 33.05 7.10 0.00 2.52
279 309 4.267357 TCTCGTGGAAGAAAAACAAACG 57.733 40.909 0.00 0.00 0.00 3.60
291 321 6.839124 TTAATAGTTGTACCTCTCGTGGAA 57.161 37.500 0.00 0.00 0.00 3.53
301 353 7.671495 TTCTTTCGGGTTTAATAGTTGTACC 57.329 36.000 0.00 0.00 0.00 3.34
310 362 5.945191 TCGGGTATTTTCTTTCGGGTTTAAT 59.055 36.000 0.00 0.00 0.00 1.40
312 364 4.904241 TCGGGTATTTTCTTTCGGGTTTA 58.096 39.130 0.00 0.00 0.00 2.01
316 368 1.669265 GCTCGGGTATTTTCTTTCGGG 59.331 52.381 0.00 0.00 0.00 5.14
317 369 1.326548 CGCTCGGGTATTTTCTTTCGG 59.673 52.381 0.00 0.00 0.00 4.30
318 370 2.264813 TCGCTCGGGTATTTTCTTTCG 58.735 47.619 0.00 0.00 0.00 3.46
319 371 4.390909 TCTTTCGCTCGGGTATTTTCTTTC 59.609 41.667 0.00 0.00 0.00 2.62
320 372 4.320870 TCTTTCGCTCGGGTATTTTCTTT 58.679 39.130 0.00 0.00 0.00 2.52
386 439 8.668353 GCAGATCTGTAAAGAATGTTCACAATA 58.332 33.333 23.38 0.00 0.00 1.90
387 440 7.175467 TGCAGATCTGTAAAGAATGTTCACAAT 59.825 33.333 23.38 0.00 0.00 2.71
388 441 6.486320 TGCAGATCTGTAAAGAATGTTCACAA 59.514 34.615 23.38 0.00 0.00 3.33
389 442 5.997129 TGCAGATCTGTAAAGAATGTTCACA 59.003 36.000 23.38 5.31 0.00 3.58
390 443 6.486253 TGCAGATCTGTAAAGAATGTTCAC 57.514 37.500 23.38 2.74 0.00 3.18
391 444 7.013178 TGTTTGCAGATCTGTAAAGAATGTTCA 59.987 33.333 31.45 22.52 43.75 3.18
392 445 7.362662 TGTTTGCAGATCTGTAAAGAATGTTC 58.637 34.615 31.45 20.68 43.75 3.18
393 446 7.275888 TGTTTGCAGATCTGTAAAGAATGTT 57.724 32.000 31.45 0.00 43.75 2.71
394 447 6.882610 TGTTTGCAGATCTGTAAAGAATGT 57.117 33.333 31.45 0.00 43.75 2.71
395 448 8.752766 AAATGTTTGCAGATCTGTAAAGAATG 57.247 30.769 31.45 4.03 43.75 2.67
396 449 9.199982 CAAAATGTTTGCAGATCTGTAAAGAAT 57.800 29.630 31.45 25.08 43.75 2.40
397 450 8.196771 ACAAAATGTTTGCAGATCTGTAAAGAA 58.803 29.630 31.45 24.23 43.75 2.52
398 451 7.648908 CACAAAATGTTTGCAGATCTGTAAAGA 59.351 33.333 31.45 30.28 43.75 2.52
399 452 7.648908 TCACAAAATGTTTGCAGATCTGTAAAG 59.351 33.333 31.45 22.52 43.75 1.85
410 463 7.731882 ATCATGAATTCACAAAATGTTTGCA 57.268 28.000 11.07 0.00 0.00 4.08
450 523 9.865321 AATGTTCATGATTCCAGAAACTATTTG 57.135 29.630 0.00 0.00 0.00 2.32
467 540 9.699985 TGTTTTTGAATTCGAAAAATGTTCATG 57.300 25.926 27.55 0.00 39.96 3.07
505 578 9.589111 TTCACAAGTTTTAAAAAGTGTTATCCC 57.411 29.630 19.99 1.37 0.00 3.85
721 796 7.761704 TCAAACAAAAATCGAATCTCAAAACCA 59.238 29.630 0.00 0.00 0.00 3.67
723 798 9.965748 TTTCAAACAAAAATCGAATCTCAAAAC 57.034 25.926 0.00 0.00 0.00 2.43
837 913 1.962306 TAACGCACGGGACTTTGGC 60.962 57.895 0.00 0.00 0.00 4.52
899 976 1.070134 CGCCGGGATGGATAGAGAAAA 59.930 52.381 2.18 0.00 42.00 2.29
1032 1111 3.808656 GGAAGAGCTGCTTGGCGC 61.809 66.667 2.53 0.00 36.83 6.53
1086 1171 4.888325 AGAGCGGGGATCTGGGGG 62.888 72.222 0.00 0.00 0.00 5.40
1147 1232 0.390472 GAGCCGTGGAAGAAGACCAG 60.390 60.000 0.00 0.00 38.14 4.00
1231 1316 3.878667 GATGGGGGCCGAAGAGGG 61.879 72.222 0.00 0.00 41.48 4.30
1264 1349 0.326264 ACACAATCTCAGGAGCACCC 59.674 55.000 0.00 0.00 36.73 4.61
1272 1357 8.779303 CCAGTAGTAGTATCTACACAATCTCAG 58.221 40.741 9.16 0.00 41.68 3.35
1302 1387 4.931027 ACACCTTCTCTACTCTCTACCA 57.069 45.455 0.00 0.00 0.00 3.25
1303 1388 5.589855 GGTAACACCTTCTCTACTCTCTACC 59.410 48.000 0.00 0.00 34.73 3.18
1304 1389 5.294060 CGGTAACACCTTCTCTACTCTCTAC 59.706 48.000 0.00 0.00 35.66 2.59
1305 1390 5.188555 TCGGTAACACCTTCTCTACTCTCTA 59.811 44.000 0.00 0.00 35.66 2.43
1306 1391 4.019501 TCGGTAACACCTTCTCTACTCTCT 60.020 45.833 0.00 0.00 35.66 3.10
1307 1392 4.260170 TCGGTAACACCTTCTCTACTCTC 58.740 47.826 0.00 0.00 35.66 3.20
1323 1408 4.260985 ACAAGAATCATGTGCATCGGTAA 58.739 39.130 0.00 0.00 0.00 2.85
1348 1433 3.065925 CAGGGCACTTTAATCTAAGCAGC 59.934 47.826 0.00 0.00 0.00 5.25
1349 1434 3.629398 CCAGGGCACTTTAATCTAAGCAG 59.371 47.826 0.00 0.00 0.00 4.24
1364 1459 0.480690 ACCACATGTTAACCAGGGCA 59.519 50.000 2.48 0.00 0.00 5.36
1401 1496 4.003648 GGATCAGACGAAAGGACACAATT 58.996 43.478 0.00 0.00 0.00 2.32
1402 1497 3.007940 TGGATCAGACGAAAGGACACAAT 59.992 43.478 0.00 0.00 0.00 2.71
1403 1498 2.367241 TGGATCAGACGAAAGGACACAA 59.633 45.455 0.00 0.00 0.00 3.33
1410 1524 3.319137 TCCAGTTGGATCAGACGAAAG 57.681 47.619 0.00 0.00 39.78 2.62
1466 1580 4.626042 CCAATTCCTCCTAAGTCATCTCG 58.374 47.826 0.00 0.00 0.00 4.04
1478 1592 1.477553 TGCATTCTGCCAATTCCTCC 58.522 50.000 0.00 0.00 44.23 4.30
1533 1647 1.289109 AAATTGCCGAGACCACGACG 61.289 55.000 0.00 0.00 35.09 5.12
1734 1855 3.426787 TCTAAAAAGCCGACATGGGAA 57.573 42.857 0.00 0.00 38.63 3.97
1747 1868 3.192633 GGGCGCCTCATTTCTTCTAAAAA 59.807 43.478 28.56 0.00 0.00 1.94
1856 1977 2.602257 TGTCAGCCCATTGATACTCG 57.398 50.000 0.00 0.00 0.00 4.18
1862 1983 3.737559 ACCTTTATGTCAGCCCATTGA 57.262 42.857 0.00 0.00 0.00 2.57
2031 2152 5.222484 ACTCTTATATTATGGGACGGAGGGA 60.222 44.000 0.00 0.00 0.00 4.20
2032 2153 5.024118 ACTCTTATATTATGGGACGGAGGG 58.976 45.833 0.00 0.00 0.00 4.30
2033 2154 5.480772 ACACTCTTATATTATGGGACGGAGG 59.519 44.000 0.00 0.00 0.00 4.30
2034 2155 6.591750 ACACTCTTATATTATGGGACGGAG 57.408 41.667 0.00 0.00 0.00 4.63
2035 2156 6.989155 AACACTCTTATATTATGGGACGGA 57.011 37.500 0.00 0.00 0.00 4.69
2036 2157 7.497909 ACAAAACACTCTTATATTATGGGACGG 59.502 37.037 0.00 0.00 0.00 4.79
2037 2158 8.433421 ACAAAACACTCTTATATTATGGGACG 57.567 34.615 0.00 0.00 0.00 4.79
2065 2186 4.690122 AGCGTTTTTGACACTACACTAGT 58.310 39.130 0.00 0.00 40.28 2.57
2066 2187 4.982916 AGAGCGTTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
2067 2188 4.940463 AGAGCGTTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
2068 2189 3.793559 AGAGCGTTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
2069 2190 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
2070 2191 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
2073 2194 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
2074 2195 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
2075 2196 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
2076 2197 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
2077 2198 7.771361 TGTCCCATAATATAAGAGCGTTTTTGA 59.229 33.333 0.00 0.00 0.00 2.69
2078 2199 7.925993 TGTCCCATAATATAAGAGCGTTTTTG 58.074 34.615 0.00 0.00 0.00 2.44
2079 2200 7.990886 TCTGTCCCATAATATAAGAGCGTTTTT 59.009 33.333 0.00 0.00 0.00 1.94
2080 2201 7.506114 TCTGTCCCATAATATAAGAGCGTTTT 58.494 34.615 0.00 0.00 0.00 2.43
2081 2202 7.062749 TCTGTCCCATAATATAAGAGCGTTT 57.937 36.000 0.00 0.00 0.00 3.60
2082 2203 6.295349 CCTCTGTCCCATAATATAAGAGCGTT 60.295 42.308 0.00 0.00 0.00 4.84
2083 2204 5.186021 CCTCTGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.00 0.00 5.07
2084 2205 5.394663 CCCTCTGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.00 0.00 5.03
2085 2206 5.721960 TCCCTCTGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
2086 2207 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
2087 2208 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
2088 2209 7.674348 TGTACTCCCTCTGTCCCATAATATAAG 59.326 40.741 0.00 0.00 0.00 1.73
2089 2210 7.541074 TGTACTCCCTCTGTCCCATAATATAA 58.459 38.462 0.00 0.00 0.00 0.98
2090 2211 7.111136 TGTACTCCCTCTGTCCCATAATATA 57.889 40.000 0.00 0.00 0.00 0.86
2091 2212 5.977533 TGTACTCCCTCTGTCCCATAATAT 58.022 41.667 0.00 0.00 0.00 1.28
2092 2213 5.412617 TGTACTCCCTCTGTCCCATAATA 57.587 43.478 0.00 0.00 0.00 0.98
2093 2214 4.280789 TGTACTCCCTCTGTCCCATAAT 57.719 45.455 0.00 0.00 0.00 1.28
2094 2215 3.769189 TGTACTCCCTCTGTCCCATAA 57.231 47.619 0.00 0.00 0.00 1.90
2095 2216 3.769189 TTGTACTCCCTCTGTCCCATA 57.231 47.619 0.00 0.00 0.00 2.74
2096 2217 2.642171 TTGTACTCCCTCTGTCCCAT 57.358 50.000 0.00 0.00 0.00 4.00
2097 2218 2.409064 TTTGTACTCCCTCTGTCCCA 57.591 50.000 0.00 0.00 0.00 4.37
2098 2219 3.610911 CAATTTGTACTCCCTCTGTCCC 58.389 50.000 0.00 0.00 0.00 4.46
2099 2220 3.610911 CCAATTTGTACTCCCTCTGTCC 58.389 50.000 0.00 0.00 0.00 4.02
2100 2221 3.610911 CCCAATTTGTACTCCCTCTGTC 58.389 50.000 0.00 0.00 0.00 3.51
2101 2222 2.308866 CCCCAATTTGTACTCCCTCTGT 59.691 50.000 0.00 0.00 0.00 3.41
2102 2223 2.576191 TCCCCAATTTGTACTCCCTCTG 59.424 50.000 0.00 0.00 0.00 3.35
2103 2224 2.929301 TCCCCAATTTGTACTCCCTCT 58.071 47.619 0.00 0.00 0.00 3.69
2104 2225 3.202151 TCATCCCCAATTTGTACTCCCTC 59.798 47.826 0.00 0.00 0.00 4.30
2105 2226 3.197983 TCATCCCCAATTTGTACTCCCT 58.802 45.455 0.00 0.00 0.00 4.20
2106 2227 3.662759 TCATCCCCAATTTGTACTCCC 57.337 47.619 0.00 0.00 0.00 4.30
2107 2228 7.654022 TTTAATCATCCCCAATTTGTACTCC 57.346 36.000 0.00 0.00 0.00 3.85
2174 2295 6.613153 AGTTTAGAGCCAGAGTTAAGTGAT 57.387 37.500 0.00 0.00 0.00 3.06
2198 2319 8.655970 GCTTTCTTGTTGTTGTTGAACTAAAAT 58.344 29.630 0.00 0.00 32.79 1.82
2243 2364 0.944999 TTCAGATCTAGCCTCCCCCT 59.055 55.000 0.00 0.00 0.00 4.79
2298 2419 1.083806 TGCGTGGAAGCTTGCTATCG 61.084 55.000 19.34 19.28 38.13 2.92
2323 2444 2.673368 CACCAAAGAACTAGCCATCGAC 59.327 50.000 0.00 0.00 0.00 4.20
2326 2447 5.675538 AGTATCACCAAAGAACTAGCCATC 58.324 41.667 0.00 0.00 0.00 3.51
2546 2667 2.551721 CCTCAGCTCACTTTCACACCAT 60.552 50.000 0.00 0.00 0.00 3.55
2669 2790 2.379907 TCTTTCAGGGGCTCTTTGGATT 59.620 45.455 0.00 0.00 0.00 3.01
2784 2905 4.688879 CACCTTAATTAGCTCACAACACGA 59.311 41.667 0.00 0.00 0.00 4.35
2992 3113 3.757745 ATAACATGTGTAAAGGCACGC 57.242 42.857 0.00 0.00 41.94 5.34
3170 3291 7.062371 GCTATAACCAGTTATGCAGAACTATCG 59.938 40.741 25.20 17.33 37.57 2.92
3399 3566 2.886913 TGGGCACATTCTGAAAATGGA 58.113 42.857 0.00 0.00 32.14 3.41
4095 6213 5.104259 ACCTCCTGAATAAATCTGTCACC 57.896 43.478 0.00 0.00 0.00 4.02
4160 6279 9.120538 GTATGGCCTTTCTAATGTAATGAAAGA 57.879 33.333 3.32 0.00 45.42 2.52
4347 6778 3.366052 ACTGGTTGGTTCAAGACAAGT 57.634 42.857 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.