Multiple sequence alignment - TraesCS6B01G256800

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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 TraesCS6B01G256800 chr6B 100.000 2246 0 0 1 2246 461333580 461331335 0.000000e+00 4148
1 TraesCS6B01G256800 chr3A 95.200 1604 59 10 545 2134 105557758 105556159 0.000000e+00 2519
2 TraesCS6B01G256800 chr5D 95.072 1603 61 8 545 2134 299973307 299971710 0.000000e+00 2507
3 TraesCS6B01G256800 chr5D 94.694 1602 70 7 545 2134 503338638 503340236 0.000000e+00 2473
4 TraesCS6B01G256800 chr5D 94.625 1600 71 8 545 2134 503312703 503314297 0.000000e+00 2464
5 TraesCS6B01G256800 chr5D 94.448 1603 69 10 545 2128 6254085 6252484 0.000000e+00 2449
6 TraesCS6B01G256800 chr7B 95.012 1604 62 8 545 2134 662755835 662754236 0.000000e+00 2503
7 TraesCS6B01G256800 chr7B 92.308 117 9 0 2130 2246 627458110 627457994 1.380000e-37 167
8 TraesCS6B01G256800 chr5B 95.012 1604 61 8 545 2133 57515926 57514327 0.000000e+00 2501
9 TraesCS6B01G256800 chr1B 94.885 1603 65 8 545 2134 633716171 633717769 0.000000e+00 2490
10 TraesCS6B01G256800 chr1B 88.095 126 11 4 5 127 93950475 93950351 1.800000e-31 147
11 TraesCS6B01G256800 chrUn 94.694 1602 69 9 545 2134 261569495 261567898 0.000000e+00 2473
12 TraesCS6B01G256800 chrUn 94.672 976 41 6 545 1512 445187307 445188279 0.000000e+00 1504
13 TraesCS6B01G256800 chr1D 94.309 1599 80 9 545 2134 51832763 51831167 0.000000e+00 2438
14 TraesCS6B01G256800 chr3B 95.068 1480 57 8 545 2011 101924075 101925551 0.000000e+00 2314
15 TraesCS6B01G256800 chr1A 94.603 630 26 4 545 1169 554481457 554482083 0.000000e+00 968
16 TraesCS6B01G256800 chr6A 92.453 530 23 7 1 519 421754571 421755094 0.000000e+00 741
17 TraesCS6B01G256800 chr6A 97.436 117 3 0 2130 2246 493043936 493044052 1.360000e-47 200
18 TraesCS6B01G256800 chr6D 91.228 456 28 6 1 444 296195117 296195572 5.300000e-171 610
19 TraesCS6B01G256800 chr4D 93.772 289 15 3 545 831 19889611 19889898 4.430000e-117 431
20 TraesCS6B01G256800 chr7D 97.391 230 4 2 545 773 614829526 614829754 7.520000e-105 390
21 TraesCS6B01G256800 chr7D 96.957 230 5 2 545 773 614768611 614768839 3.500000e-103 385
22 TraesCS6B01G256800 chr7D 88.496 113 12 1 5 117 511057087 511056976 3.890000e-28 135
23 TraesCS6B01G256800 chr2B 94.545 110 5 1 1 110 569017345 569017237 3.840000e-38 169
24 TraesCS6B01G256800 chr2A 94.340 106 5 1 5 110 628582720 628582616 6.420000e-36 161
25 TraesCS6B01G256800 chr2A 87.302 126 12 4 5 127 115430555 115430431 8.360000e-30 141
26 TraesCS6B01G256800 chr2D 91.509 106 8 1 5 110 484327080 484326976 6.460000e-31 145
27 TraesCS6B01G256800 chr7A 86.508 126 13 4 5 127 611767913 611767789 3.890000e-28 135


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 TraesCS6B01G256800 chr6B 461331335 461333580 2245 True 4148 4148 100.000 1 2246 1 chr6B.!!$R1 2245
1 TraesCS6B01G256800 chr3A 105556159 105557758 1599 True 2519 2519 95.200 545 2134 1 chr3A.!!$R1 1589
2 TraesCS6B01G256800 chr5D 299971710 299973307 1597 True 2507 2507 95.072 545 2134 1 chr5D.!!$R2 1589
3 TraesCS6B01G256800 chr5D 503338638 503340236 1598 False 2473 2473 94.694 545 2134 1 chr5D.!!$F2 1589
4 TraesCS6B01G256800 chr5D 503312703 503314297 1594 False 2464 2464 94.625 545 2134 1 chr5D.!!$F1 1589
5 TraesCS6B01G256800 chr5D 6252484 6254085 1601 True 2449 2449 94.448 545 2128 1 chr5D.!!$R1 1583
6 TraesCS6B01G256800 chr7B 662754236 662755835 1599 True 2503 2503 95.012 545 2134 1 chr7B.!!$R2 1589
7 TraesCS6B01G256800 chr5B 57514327 57515926 1599 True 2501 2501 95.012 545 2133 1 chr5B.!!$R1 1588
8 TraesCS6B01G256800 chr1B 633716171 633717769 1598 False 2490 2490 94.885 545 2134 1 chr1B.!!$F1 1589
9 TraesCS6B01G256800 chrUn 261567898 261569495 1597 True 2473 2473 94.694 545 2134 1 chrUn.!!$R1 1589
10 TraesCS6B01G256800 chrUn 445187307 445188279 972 False 1504 1504 94.672 545 1512 1 chrUn.!!$F1 967
11 TraesCS6B01G256800 chr1D 51831167 51832763 1596 True 2438 2438 94.309 545 2134 1 chr1D.!!$R1 1589
12 TraesCS6B01G256800 chr3B 101924075 101925551 1476 False 2314 2314 95.068 545 2011 1 chr3B.!!$F1 1466
13 TraesCS6B01G256800 chr1A 554481457 554482083 626 False 968 968 94.603 545 1169 1 chr1A.!!$F1 624
14 TraesCS6B01G256800 chr6A 421754571 421755094 523 False 741 741 92.453 1 519 1 chr6A.!!$F1 518

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
142 143 0.315869 AAACACGCGTCGCTGAAAAG 60.316 50.0 9.86 0.0 0.0 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1861 0.180406 ACTCGCACACACTCCCTTTT 59.82 50.0 0.0 0.0 0.0 2.27 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
60 61 1.375523 GTAGTTCACCAGGGCCACG 60.376 63.158 6.18 0.00 0.00 4.94
104 105 1.521906 ACGGCTGCACGTAACACAA 60.522 52.632 13.14 0.00 46.58 3.33
106 107 0.384230 CGGCTGCACGTAACACAAAG 60.384 55.000 0.50 0.00 0.00 2.77
110 111 2.849502 GCTGCACGTAACACAAAGACAC 60.850 50.000 0.00 0.00 0.00 3.67
142 143 0.315869 AAACACGCGTCGCTGAAAAG 60.316 50.000 9.86 0.00 0.00 2.27
147 148 1.623081 CGCGTCGCTGAAAAGCCTTA 61.623 55.000 16.36 0.00 0.00 2.69
150 151 0.442699 GTCGCTGAAAAGCCTTACCG 59.557 55.000 0.00 0.00 0.00 4.02
172 173 1.785041 GCAGCACAGAACCAAAGCGA 61.785 55.000 0.00 0.00 0.00 4.93
175 176 1.444119 GCACAGAACCAAAGCGACCA 61.444 55.000 0.00 0.00 0.00 4.02
200 210 2.822255 TACCATCTTTGCGGCGGC 60.822 61.111 9.78 9.68 40.52 6.53
272 282 2.038975 AGGAGCTAGGGTTCGGCA 59.961 61.111 0.00 0.00 0.00 5.69
367 377 1.751351 CCGATGCAGGTCAGAGAGTTA 59.249 52.381 0.00 0.00 0.00 2.24
388 398 3.791640 GGGGGTTTCTGGGCTTTG 58.208 61.111 0.00 0.00 0.00 2.77
399 409 5.659440 TTCTGGGCTTTGGAATGAATAAC 57.341 39.130 0.00 0.00 0.00 1.89
406 416 3.935818 TTGGAATGAATAACGGGCCTA 57.064 42.857 0.84 0.00 0.00 3.93
424 434 3.260740 CCTAGTAGAGTCGTCGTTCACT 58.739 50.000 0.00 0.00 0.00 3.41
429 439 2.070783 AGAGTCGTCGTTCACTCTCTC 58.929 52.381 8.79 0.00 45.16 3.20
430 440 2.070783 GAGTCGTCGTTCACTCTCTCT 58.929 52.381 5.55 0.00 36.80 3.10
431 441 2.070783 AGTCGTCGTTCACTCTCTCTC 58.929 52.381 0.00 0.00 0.00 3.20
432 442 2.070783 GTCGTCGTTCACTCTCTCTCT 58.929 52.381 0.00 0.00 0.00 3.10
433 443 2.093152 GTCGTCGTTCACTCTCTCTCTC 59.907 54.545 0.00 0.00 0.00 3.20
434 444 1.395608 CGTCGTTCACTCTCTCTCTCC 59.604 57.143 0.00 0.00 0.00 3.71
456 466 3.701040 CCTATTGGGCTTATGTGCAAACT 59.299 43.478 0.00 0.00 34.04 2.66
470 480 5.016173 TGTGCAAACTATCCAAATTAGGCT 58.984 37.500 0.00 0.00 0.00 4.58
519 531 3.194005 GGACCAAATCCTCAATCGCTA 57.806 47.619 0.00 0.00 45.22 4.26
520 532 3.744660 GGACCAAATCCTCAATCGCTAT 58.255 45.455 0.00 0.00 45.22 2.97
521 533 4.137543 GGACCAAATCCTCAATCGCTATT 58.862 43.478 0.00 0.00 45.22 1.73
522 534 4.214332 GGACCAAATCCTCAATCGCTATTC 59.786 45.833 0.00 0.00 45.22 1.75
523 535 4.780815 ACCAAATCCTCAATCGCTATTCA 58.219 39.130 0.00 0.00 0.00 2.57
524 536 4.576463 ACCAAATCCTCAATCGCTATTCAC 59.424 41.667 0.00 0.00 0.00 3.18
525 537 4.023707 CCAAATCCTCAATCGCTATTCACC 60.024 45.833 0.00 0.00 0.00 4.02
526 538 4.696479 AATCCTCAATCGCTATTCACCT 57.304 40.909 0.00 0.00 0.00 4.00
527 539 3.735237 TCCTCAATCGCTATTCACCTC 57.265 47.619 0.00 0.00 0.00 3.85
528 540 3.031013 TCCTCAATCGCTATTCACCTCA 58.969 45.455 0.00 0.00 0.00 3.86
529 541 3.450817 TCCTCAATCGCTATTCACCTCAA 59.549 43.478 0.00 0.00 0.00 3.02
530 542 4.081142 TCCTCAATCGCTATTCACCTCAAA 60.081 41.667 0.00 0.00 0.00 2.69
531 543 4.635765 CCTCAATCGCTATTCACCTCAAAA 59.364 41.667 0.00 0.00 0.00 2.44
532 544 5.123820 CCTCAATCGCTATTCACCTCAAAAA 59.876 40.000 0.00 0.00 0.00 1.94
572 584 6.773685 GCCTAGAGTTGTAGGAGAGAGAATAA 59.226 42.308 6.53 0.00 42.18 1.40
574 586 9.362151 CCTAGAGTTGTAGGAGAGAGAATAAAT 57.638 37.037 0.00 0.00 42.18 1.40
768 781 9.424659 GCAAACAAAATAGAAGAAACAAATGTG 57.575 29.630 0.00 0.00 0.00 3.21
772 785 9.086336 ACAAAATAGAAGAAACAAATGTGTGTG 57.914 29.630 0.00 0.00 38.27 3.82
773 786 8.542132 CAAAATAGAAGAAACAAATGTGTGTGG 58.458 33.333 0.00 0.00 38.27 4.17
774 787 4.654091 AGAAGAAACAAATGTGTGTGGG 57.346 40.909 0.00 0.00 38.27 4.61
775 788 3.384467 AGAAGAAACAAATGTGTGTGGGG 59.616 43.478 0.00 0.00 38.27 4.96
776 789 2.038659 AGAAACAAATGTGTGTGGGGG 58.961 47.619 0.00 0.00 38.27 5.40
998 1022 2.803956 TGGACACGAGGAACTACTCAT 58.196 47.619 0.00 0.00 41.55 2.90
1016 1040 8.489489 ACTACTCATCATGAATCCACTAATTGT 58.511 33.333 0.00 0.00 0.00 2.71
1019 1043 7.613022 ACTCATCATGAATCCACTAATTGTTGT 59.387 33.333 0.00 0.00 0.00 3.32
1091 1115 3.775316 CCTGGAGTTGGTCAAGGTACTAT 59.225 47.826 0.00 0.00 41.29 2.12
1403 1434 4.754311 TCGGGACAGATAATACCCCATTA 58.246 43.478 0.00 0.00 39.20 1.90
1492 1523 9.731819 CTTAGTTTAGGAAAGTGGAAAGTTTTC 57.268 33.333 0.00 0.00 36.46 2.29
1563 1594 2.404923 TTCACCGGTCAAACAAGACA 57.595 45.000 2.59 0.00 40.29 3.41
1567 1598 4.452825 TCACCGGTCAAACAAGACATAAA 58.547 39.130 2.59 0.00 40.29 1.40
1739 1776 3.439857 TTTTTAGCTCACTGGCCATCT 57.560 42.857 5.51 1.17 0.00 2.90
1743 1780 1.818785 GCTCACTGGCCATCTGCTC 60.819 63.158 5.51 0.00 40.92 4.26
1814 1851 6.887013 TCTAACTGTAGTGGTTGGTGTTTTA 58.113 36.000 0.00 0.00 0.00 1.52
1851 1889 3.119602 GGAGTGTGTGCGAGTTGTCTATA 60.120 47.826 0.00 0.00 0.00 1.31
1949 1987 3.546670 GCACGATCTCGACGAATTACTTT 59.453 43.478 6.60 0.00 43.02 2.66
1951 1989 5.228635 GCACGATCTCGACGAATTACTTTTA 59.771 40.000 6.60 0.00 43.02 1.52
1992 2030 3.278574 TGGAAGAACCATAGCATTTCGG 58.721 45.455 0.00 0.00 44.64 4.30
2053 2091 5.147330 AGAATGTGAGACCATTAACACGA 57.853 39.130 0.00 0.00 35.24 4.35
2081 2119 3.807209 GCTAAACTGCTTGAAGTCCAGGA 60.807 47.826 5.12 0.00 0.00 3.86
2135 2173 6.688637 AGTATTAGTGCCGAATTTAAACCC 57.311 37.500 0.00 0.00 0.00 4.11
2136 2174 6.420638 AGTATTAGTGCCGAATTTAAACCCT 58.579 36.000 0.00 0.00 0.00 4.34
2137 2175 7.567458 AGTATTAGTGCCGAATTTAAACCCTA 58.433 34.615 0.00 0.00 0.00 3.53
2138 2176 6.688637 ATTAGTGCCGAATTTAAACCCTAC 57.311 37.500 0.00 0.00 0.00 3.18
2139 2177 4.023726 AGTGCCGAATTTAAACCCTACA 57.976 40.909 0.00 0.00 0.00 2.74
2140 2178 4.007659 AGTGCCGAATTTAAACCCTACAG 58.992 43.478 0.00 0.00 0.00 2.74
2141 2179 3.754850 GTGCCGAATTTAAACCCTACAGT 59.245 43.478 0.00 0.00 0.00 3.55
2142 2180 4.004982 TGCCGAATTTAAACCCTACAGTC 58.995 43.478 0.00 0.00 0.00 3.51
2143 2181 4.004982 GCCGAATTTAAACCCTACAGTCA 58.995 43.478 0.00 0.00 0.00 3.41
2144 2182 4.094442 GCCGAATTTAAACCCTACAGTCAG 59.906 45.833 0.00 0.00 0.00 3.51
2145 2183 4.634443 CCGAATTTAAACCCTACAGTCAGG 59.366 45.833 0.00 0.00 35.26 3.86
2146 2184 5.243207 CGAATTTAAACCCTACAGTCAGGT 58.757 41.667 0.00 0.00 33.44 4.00
2147 2185 5.704053 CGAATTTAAACCCTACAGTCAGGTT 59.296 40.000 1.92 1.92 45.79 3.50
2150 2188 2.951229 AACCCTACAGTCAGGTTTGG 57.049 50.000 1.92 0.00 41.07 3.28
2151 2189 1.815757 ACCCTACAGTCAGGTTTGGT 58.184 50.000 0.00 0.00 33.44 3.67
2152 2190 2.132686 ACCCTACAGTCAGGTTTGGTT 58.867 47.619 0.00 0.00 33.44 3.67
2153 2191 2.512476 ACCCTACAGTCAGGTTTGGTTT 59.488 45.455 0.00 0.00 33.44 3.27
2154 2192 3.053170 ACCCTACAGTCAGGTTTGGTTTT 60.053 43.478 0.00 0.00 33.44 2.43
2155 2193 3.958147 CCCTACAGTCAGGTTTGGTTTTT 59.042 43.478 0.00 0.00 33.44 1.94
2156 2194 4.037565 CCCTACAGTCAGGTTTGGTTTTTC 59.962 45.833 0.00 0.00 33.44 2.29
2157 2195 4.642885 CCTACAGTCAGGTTTGGTTTTTCA 59.357 41.667 0.00 0.00 0.00 2.69
2158 2196 4.718940 ACAGTCAGGTTTGGTTTTTCAG 57.281 40.909 0.00 0.00 0.00 3.02
2159 2197 3.447229 ACAGTCAGGTTTGGTTTTTCAGG 59.553 43.478 0.00 0.00 0.00 3.86
2160 2198 3.699038 CAGTCAGGTTTGGTTTTTCAGGA 59.301 43.478 0.00 0.00 0.00 3.86
2161 2199 4.159506 CAGTCAGGTTTGGTTTTTCAGGAA 59.840 41.667 0.00 0.00 0.00 3.36
2162 2200 4.962362 AGTCAGGTTTGGTTTTTCAGGAAT 59.038 37.500 0.00 0.00 0.00 3.01
2163 2201 6.040391 CAGTCAGGTTTGGTTTTTCAGGAATA 59.960 38.462 0.00 0.00 0.00 1.75
2164 2202 6.782494 AGTCAGGTTTGGTTTTTCAGGAATAT 59.218 34.615 0.00 0.00 0.00 1.28
2165 2203 6.868339 GTCAGGTTTGGTTTTTCAGGAATATG 59.132 38.462 0.00 0.00 0.00 1.78
2166 2204 6.780031 TCAGGTTTGGTTTTTCAGGAATATGA 59.220 34.615 0.00 0.00 0.00 2.15
2167 2205 7.039784 TCAGGTTTGGTTTTTCAGGAATATGAG 60.040 37.037 0.00 0.00 0.00 2.90
2168 2206 6.211384 AGGTTTGGTTTTTCAGGAATATGAGG 59.789 38.462 0.00 0.00 0.00 3.86
2169 2207 6.398095 GTTTGGTTTTTCAGGAATATGAGGG 58.602 40.000 0.00 0.00 0.00 4.30
2170 2208 5.269554 TGGTTTTTCAGGAATATGAGGGT 57.730 39.130 0.00 0.00 0.00 4.34
2171 2209 5.650283 TGGTTTTTCAGGAATATGAGGGTT 58.350 37.500 0.00 0.00 0.00 4.11
2172 2210 5.480073 TGGTTTTTCAGGAATATGAGGGTTG 59.520 40.000 0.00 0.00 0.00 3.77
2173 2211 5.410924 GTTTTTCAGGAATATGAGGGTTGC 58.589 41.667 0.00 0.00 0.00 4.17
2174 2212 2.620251 TCAGGAATATGAGGGTTGCG 57.380 50.000 0.00 0.00 0.00 4.85
2175 2213 1.837439 TCAGGAATATGAGGGTTGCGT 59.163 47.619 0.00 0.00 0.00 5.24
2176 2214 1.942657 CAGGAATATGAGGGTTGCGTG 59.057 52.381 0.00 0.00 0.00 5.34
2177 2215 1.134098 AGGAATATGAGGGTTGCGTGG 60.134 52.381 0.00 0.00 0.00 4.94
2178 2216 1.308998 GAATATGAGGGTTGCGTGGG 58.691 55.000 0.00 0.00 0.00 4.61
2179 2217 0.916086 AATATGAGGGTTGCGTGGGA 59.084 50.000 0.00 0.00 0.00 4.37
2180 2218 1.140312 ATATGAGGGTTGCGTGGGAT 58.860 50.000 0.00 0.00 0.00 3.85
2181 2219 0.468226 TATGAGGGTTGCGTGGGATC 59.532 55.000 0.00 0.00 0.00 3.36
2182 2220 1.274703 ATGAGGGTTGCGTGGGATCT 61.275 55.000 0.00 0.00 0.00 2.75
2183 2221 0.616395 TGAGGGTTGCGTGGGATCTA 60.616 55.000 0.00 0.00 0.00 1.98
2184 2222 0.105039 GAGGGTTGCGTGGGATCTAG 59.895 60.000 0.00 0.00 0.00 2.43
2185 2223 1.523938 GGGTTGCGTGGGATCTAGC 60.524 63.158 0.00 0.00 0.00 3.42
2186 2224 1.522569 GGTTGCGTGGGATCTAGCT 59.477 57.895 0.00 0.00 0.00 3.32
2187 2225 0.530870 GGTTGCGTGGGATCTAGCTC 60.531 60.000 0.00 0.00 0.00 4.09
2188 2226 0.175760 GTTGCGTGGGATCTAGCTCA 59.824 55.000 0.00 0.00 0.00 4.26
2189 2227 0.461548 TTGCGTGGGATCTAGCTCAG 59.538 55.000 0.00 0.00 0.00 3.35
2190 2228 1.300542 GCGTGGGATCTAGCTCAGC 60.301 63.158 0.00 0.00 0.00 4.26
2191 2229 2.021068 GCGTGGGATCTAGCTCAGCA 62.021 60.000 0.00 0.00 0.00 4.41
2192 2230 0.031857 CGTGGGATCTAGCTCAGCAG 59.968 60.000 0.00 0.00 0.00 4.24
2193 2231 0.392336 GTGGGATCTAGCTCAGCAGG 59.608 60.000 0.00 0.00 0.00 4.85
2194 2232 0.031716 TGGGATCTAGCTCAGCAGGT 60.032 55.000 0.00 0.00 0.00 4.00
2195 2233 0.392336 GGGATCTAGCTCAGCAGGTG 59.608 60.000 0.00 0.00 0.00 4.00
2196 2234 1.407936 GGATCTAGCTCAGCAGGTGA 58.592 55.000 0.00 1.52 0.00 4.02
2197 2235 1.759445 GGATCTAGCTCAGCAGGTGAA 59.241 52.381 0.00 0.00 33.60 3.18
2198 2236 2.368221 GGATCTAGCTCAGCAGGTGAAT 59.632 50.000 0.00 0.00 33.60 2.57
2199 2237 3.181456 GGATCTAGCTCAGCAGGTGAATT 60.181 47.826 0.00 0.00 33.60 2.17
2200 2238 3.988976 TCTAGCTCAGCAGGTGAATTT 57.011 42.857 0.00 0.00 33.60 1.82
2201 2239 3.866651 TCTAGCTCAGCAGGTGAATTTC 58.133 45.455 0.00 0.00 33.60 2.17
2202 2240 2.574006 AGCTCAGCAGGTGAATTTCA 57.426 45.000 0.00 0.00 33.60 2.69
2203 2241 2.867624 AGCTCAGCAGGTGAATTTCAA 58.132 42.857 0.00 0.00 33.60 2.69
2204 2242 2.818432 AGCTCAGCAGGTGAATTTCAAG 59.182 45.455 0.00 0.00 33.60 3.02
2205 2243 2.670509 GCTCAGCAGGTGAATTTCAAGC 60.671 50.000 3.41 6.20 33.60 4.01
2206 2244 1.888512 TCAGCAGGTGAATTTCAAGCC 59.111 47.619 0.00 0.00 29.64 4.35
2207 2245 1.614903 CAGCAGGTGAATTTCAAGCCA 59.385 47.619 0.00 0.00 0.00 4.75
2208 2246 1.615392 AGCAGGTGAATTTCAAGCCAC 59.385 47.619 0.00 0.00 0.00 5.01
2209 2247 1.615392 GCAGGTGAATTTCAAGCCACT 59.385 47.619 0.00 0.00 0.00 4.00
2210 2248 2.036346 GCAGGTGAATTTCAAGCCACTT 59.964 45.455 0.00 0.00 0.00 3.16
2211 2249 3.645884 CAGGTGAATTTCAAGCCACTTG 58.354 45.455 0.00 0.81 42.25 3.16
2212 2250 3.318839 CAGGTGAATTTCAAGCCACTTGA 59.681 43.478 5.94 5.94 46.93 3.02
2220 2258 3.648339 TCAAGCCACTTGAAGCAAATC 57.352 42.857 7.54 0.00 45.84 2.17
2221 2259 3.225104 TCAAGCCACTTGAAGCAAATCT 58.775 40.909 7.54 0.00 45.84 2.40
2222 2260 3.005050 TCAAGCCACTTGAAGCAAATCTG 59.995 43.478 7.54 0.00 45.84 2.90
2223 2261 2.590821 AGCCACTTGAAGCAAATCTGT 58.409 42.857 0.00 0.00 0.00 3.41
2224 2262 3.754965 AGCCACTTGAAGCAAATCTGTA 58.245 40.909 0.00 0.00 0.00 2.74
2225 2263 3.503748 AGCCACTTGAAGCAAATCTGTAC 59.496 43.478 0.00 0.00 0.00 2.90
2226 2264 3.253188 GCCACTTGAAGCAAATCTGTACA 59.747 43.478 0.00 0.00 0.00 2.90
2227 2265 4.787598 CCACTTGAAGCAAATCTGTACAC 58.212 43.478 0.00 0.00 0.00 2.90
2228 2266 4.275689 CCACTTGAAGCAAATCTGTACACA 59.724 41.667 0.00 0.00 0.00 3.72
2229 2267 5.221028 CCACTTGAAGCAAATCTGTACACAA 60.221 40.000 0.00 0.00 0.00 3.33
2230 2268 6.441274 CACTTGAAGCAAATCTGTACACAAT 58.559 36.000 0.00 0.00 0.00 2.71
2231 2269 6.361481 CACTTGAAGCAAATCTGTACACAATG 59.639 38.462 0.00 0.00 0.00 2.82
2232 2270 4.797471 TGAAGCAAATCTGTACACAATGC 58.203 39.130 9.13 9.13 0.00 3.56
2233 2271 4.277921 TGAAGCAAATCTGTACACAATGCA 59.722 37.500 16.11 0.00 0.00 3.96
2234 2272 4.852134 AGCAAATCTGTACACAATGCAA 57.148 36.364 16.11 0.00 0.00 4.08
2235 2273 5.395682 AGCAAATCTGTACACAATGCAAT 57.604 34.783 16.11 0.00 0.00 3.56
2236 2274 5.786311 AGCAAATCTGTACACAATGCAATT 58.214 33.333 16.11 0.00 36.63 2.32
2237 2275 5.865552 AGCAAATCTGTACACAATGCAATTC 59.134 36.000 16.11 0.00 31.22 2.17
2238 2276 5.062558 GCAAATCTGTACACAATGCAATTCC 59.937 40.000 11.31 0.00 31.22 3.01
2239 2277 5.981088 AATCTGTACACAATGCAATTCCA 57.019 34.783 0.00 0.00 31.22 3.53
2240 2278 5.571784 ATCTGTACACAATGCAATTCCAG 57.428 39.130 0.00 0.00 31.22 3.86
2241 2279 4.397420 TCTGTACACAATGCAATTCCAGT 58.603 39.130 0.00 0.00 31.22 4.00
2242 2280 4.216042 TCTGTACACAATGCAATTCCAGTG 59.784 41.667 0.00 0.00 31.22 3.66
2243 2281 2.443887 ACACAATGCAATTCCAGTGC 57.556 45.000 0.00 0.00 42.55 4.40
2244 2282 1.001181 ACACAATGCAATTCCAGTGCC 59.999 47.619 0.00 0.00 41.49 5.01
2245 2283 1.274167 CACAATGCAATTCCAGTGCCT 59.726 47.619 0.00 0.00 41.49 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.648102 CGCCTCGTCGTCATCGTC 60.648 66.667 0.00 0.00 38.33 4.20
60 61 4.547905 TTCGTCGAGATCGGGCGC 62.548 66.667 0.00 0.00 40.29 6.53
97 98 3.460103 GAGGTTCGGTGTCTTTGTGTTA 58.540 45.455 0.00 0.00 0.00 2.41
101 102 0.462789 ACGAGGTTCGGTGTCTTTGT 59.537 50.000 3.37 0.00 45.59 2.83
104 105 0.748450 TTGACGAGGTTCGGTGTCTT 59.252 50.000 3.37 0.00 45.59 3.01
106 107 1.259770 GTTTTGACGAGGTTCGGTGTC 59.740 52.381 3.37 0.00 45.59 3.67
110 111 0.231279 CGTGTTTTGACGAGGTTCGG 59.769 55.000 3.37 0.00 45.59 4.30
142 143 2.820037 GTGCTGCTCCGGTAAGGC 60.820 66.667 0.00 3.22 40.77 4.35
147 148 2.031163 GTTCTGTGCTGCTCCGGT 59.969 61.111 0.00 0.00 0.00 5.28
150 151 0.595095 CTTTGGTTCTGTGCTGCTCC 59.405 55.000 0.00 0.00 0.00 4.70
172 173 3.259064 CAAAGATGGTACGTCGATTGGT 58.741 45.455 0.00 0.00 0.00 3.67
175 176 1.924524 CGCAAAGATGGTACGTCGATT 59.075 47.619 0.00 0.00 0.00 3.34
179 180 1.713830 GCCGCAAAGATGGTACGTC 59.286 57.895 0.00 0.00 0.00 4.34
272 282 2.610727 GCCTTTATAATCCGCTCTCGCT 60.611 50.000 0.00 0.00 0.00 4.93
376 386 5.336372 CGTTATTCATTCCAAAGCCCAGAAA 60.336 40.000 0.00 0.00 0.00 2.52
388 398 3.487120 ACTAGGCCCGTTATTCATTCC 57.513 47.619 0.00 0.00 0.00 3.01
399 409 1.497223 CGACGACTCTACTAGGCCCG 61.497 65.000 0.00 0.00 0.00 6.13
406 416 3.042871 AGAGTGAACGACGACTCTACT 57.957 47.619 14.14 9.79 45.73 2.57
434 444 3.701040 AGTTTGCACATAAGCCCAATAGG 59.299 43.478 0.00 0.00 39.47 2.57
445 455 6.833416 AGCCTAATTTGGATAGTTTGCACATA 59.167 34.615 10.34 0.00 0.00 2.29
470 480 0.698238 ACTGCTACTTCATGGGCCAA 59.302 50.000 11.89 0.00 0.00 4.52
533 545 6.604795 ACAACTCTAGGCTATGCATGATTTTT 59.395 34.615 10.16 0.00 0.00 1.94
534 546 6.125029 ACAACTCTAGGCTATGCATGATTTT 58.875 36.000 10.16 0.00 0.00 1.82
535 547 5.688807 ACAACTCTAGGCTATGCATGATTT 58.311 37.500 10.16 0.00 0.00 2.17
536 548 5.301835 ACAACTCTAGGCTATGCATGATT 57.698 39.130 10.16 0.00 0.00 2.57
537 549 4.970860 ACAACTCTAGGCTATGCATGAT 57.029 40.909 10.16 0.00 0.00 2.45
538 550 4.281941 CCTACAACTCTAGGCTATGCATGA 59.718 45.833 10.16 0.00 0.00 3.07
539 551 4.281941 TCCTACAACTCTAGGCTATGCATG 59.718 45.833 10.16 0.26 34.25 4.06
540 552 4.483950 TCCTACAACTCTAGGCTATGCAT 58.516 43.478 3.79 3.79 34.25 3.96
541 553 3.891977 CTCCTACAACTCTAGGCTATGCA 59.108 47.826 0.00 0.00 34.25 3.96
542 554 4.145807 TCTCCTACAACTCTAGGCTATGC 58.854 47.826 0.00 0.00 34.25 3.14
543 555 5.626142 TCTCTCCTACAACTCTAGGCTATG 58.374 45.833 0.00 0.00 34.25 2.23
620 632 6.401537 AGTATAGATCTAGCCTGACTCCAT 57.598 41.667 8.70 0.00 0.00 3.41
673 686 3.697166 AGTGGAAACCCGCATAAAAGAT 58.303 40.909 0.00 0.00 36.68 2.40
822 842 8.543774 AGAAGCGAATTCCATATCCATATAACT 58.456 33.333 0.00 0.00 38.84 2.24
843 863 5.810587 TGAATTGTCCGAACTACATAGAAGC 59.189 40.000 0.00 0.00 0.00 3.86
975 995 3.385433 TGAGTAGTTCCTCGTGTCCAAAA 59.615 43.478 0.00 0.00 34.04 2.44
979 999 2.753452 TGATGAGTAGTTCCTCGTGTCC 59.247 50.000 0.00 0.00 34.04 4.02
998 1022 6.209192 AGCAACAACAATTAGTGGATTCATGA 59.791 34.615 0.00 0.00 0.00 3.07
1016 1040 3.318839 AGCAGCAATAACAGAAGCAACAA 59.681 39.130 0.00 0.00 0.00 2.83
1019 1043 2.229543 CCAGCAGCAATAACAGAAGCAA 59.770 45.455 0.00 0.00 0.00 3.91
1091 1115 2.550855 CCTTCTACAGCTTGTCCTGCAA 60.551 50.000 0.00 0.00 36.29 4.08
1403 1434 2.839228 ACTCAACTCAGCCCTTCCTAT 58.161 47.619 0.00 0.00 0.00 2.57
1442 1473 5.392703 GGACGGGAAATAAAAAGGTGATCAC 60.393 44.000 17.91 17.91 0.00 3.06
1445 1476 4.930696 AGGACGGGAAATAAAAAGGTGAT 58.069 39.130 0.00 0.00 0.00 3.06
1453 1484 7.256494 TCCTAAACTAAGGACGGGAAATAAA 57.744 36.000 0.00 0.00 40.86 1.40
1739 1776 2.443260 TAAGCCCGAAACTGCGAGCA 62.443 55.000 0.00 0.00 37.48 4.26
1743 1780 1.329599 GGTATTAAGCCCGAAACTGCG 59.670 52.381 0.00 0.00 0.00 5.18
1824 1861 0.180406 ACTCGCACACACTCCCTTTT 59.820 50.000 0.00 0.00 0.00 2.27
1992 2030 7.214467 TCAAAGTTGATTTACCAATGAGTCC 57.786 36.000 0.00 0.00 31.01 3.85
2121 2159 4.004982 TGACTGTAGGGTTTAAATTCGGC 58.995 43.478 0.00 0.00 0.00 5.54
2134 2172 4.642885 TGAAAAACCAAACCTGACTGTAGG 59.357 41.667 0.00 0.00 43.71 3.18
2135 2173 5.221048 CCTGAAAAACCAAACCTGACTGTAG 60.221 44.000 0.00 0.00 0.00 2.74
2136 2174 4.642885 CCTGAAAAACCAAACCTGACTGTA 59.357 41.667 0.00 0.00 0.00 2.74
2137 2175 3.447229 CCTGAAAAACCAAACCTGACTGT 59.553 43.478 0.00 0.00 0.00 3.55
2138 2176 3.699038 TCCTGAAAAACCAAACCTGACTG 59.301 43.478 0.00 0.00 0.00 3.51
2139 2177 3.976015 TCCTGAAAAACCAAACCTGACT 58.024 40.909 0.00 0.00 0.00 3.41
2140 2178 4.729227 TTCCTGAAAAACCAAACCTGAC 57.271 40.909 0.00 0.00 0.00 3.51
2141 2179 6.780031 TCATATTCCTGAAAAACCAAACCTGA 59.220 34.615 0.00 0.00 0.00 3.86
2142 2180 6.991938 TCATATTCCTGAAAAACCAAACCTG 58.008 36.000 0.00 0.00 0.00 4.00
2143 2181 6.211384 CCTCATATTCCTGAAAAACCAAACCT 59.789 38.462 0.00 0.00 0.00 3.50
2144 2182 6.398095 CCTCATATTCCTGAAAAACCAAACC 58.602 40.000 0.00 0.00 0.00 3.27
2145 2183 6.014584 ACCCTCATATTCCTGAAAAACCAAAC 60.015 38.462 0.00 0.00 0.00 2.93
2146 2184 6.081356 ACCCTCATATTCCTGAAAAACCAAA 58.919 36.000 0.00 0.00 0.00 3.28
2147 2185 5.650283 ACCCTCATATTCCTGAAAAACCAA 58.350 37.500 0.00 0.00 0.00 3.67
2148 2186 5.269554 ACCCTCATATTCCTGAAAAACCA 57.730 39.130 0.00 0.00 0.00 3.67
2149 2187 5.624509 GCAACCCTCATATTCCTGAAAAACC 60.625 44.000 0.00 0.00 0.00 3.27
2150 2188 5.410924 GCAACCCTCATATTCCTGAAAAAC 58.589 41.667 0.00 0.00 0.00 2.43
2151 2189 4.157656 CGCAACCCTCATATTCCTGAAAAA 59.842 41.667 0.00 0.00 0.00 1.94
2152 2190 3.694072 CGCAACCCTCATATTCCTGAAAA 59.306 43.478 0.00 0.00 0.00 2.29
2153 2191 3.278574 CGCAACCCTCATATTCCTGAAA 58.721 45.455 0.00 0.00 0.00 2.69
2154 2192 2.238646 ACGCAACCCTCATATTCCTGAA 59.761 45.455 0.00 0.00 0.00 3.02
2155 2193 1.837439 ACGCAACCCTCATATTCCTGA 59.163 47.619 0.00 0.00 0.00 3.86
2156 2194 1.942657 CACGCAACCCTCATATTCCTG 59.057 52.381 0.00 0.00 0.00 3.86
2157 2195 1.134098 CCACGCAACCCTCATATTCCT 60.134 52.381 0.00 0.00 0.00 3.36
2158 2196 1.308998 CCACGCAACCCTCATATTCC 58.691 55.000 0.00 0.00 0.00 3.01
2159 2197 1.134220 TCCCACGCAACCCTCATATTC 60.134 52.381 0.00 0.00 0.00 1.75
2160 2198 0.916086 TCCCACGCAACCCTCATATT 59.084 50.000 0.00 0.00 0.00 1.28
2161 2199 1.072331 GATCCCACGCAACCCTCATAT 59.928 52.381 0.00 0.00 0.00 1.78
2162 2200 0.468226 GATCCCACGCAACCCTCATA 59.532 55.000 0.00 0.00 0.00 2.15
2163 2201 1.224592 GATCCCACGCAACCCTCAT 59.775 57.895 0.00 0.00 0.00 2.90
2164 2202 0.616395 TAGATCCCACGCAACCCTCA 60.616 55.000 0.00 0.00 0.00 3.86
2165 2203 0.105039 CTAGATCCCACGCAACCCTC 59.895 60.000 0.00 0.00 0.00 4.30
2166 2204 1.972660 GCTAGATCCCACGCAACCCT 61.973 60.000 0.00 0.00 0.00 4.34
2167 2205 1.523938 GCTAGATCCCACGCAACCC 60.524 63.158 0.00 0.00 0.00 4.11
2168 2206 0.530870 GAGCTAGATCCCACGCAACC 60.531 60.000 0.00 0.00 0.00 3.77
2169 2207 0.175760 TGAGCTAGATCCCACGCAAC 59.824 55.000 5.36 0.00 0.00 4.17
2170 2208 0.461548 CTGAGCTAGATCCCACGCAA 59.538 55.000 5.36 0.00 0.00 4.85
2171 2209 2.021068 GCTGAGCTAGATCCCACGCA 62.021 60.000 5.36 0.00 0.00 5.24
2172 2210 1.300542 GCTGAGCTAGATCCCACGC 60.301 63.158 5.36 0.00 0.00 5.34
2173 2211 0.031857 CTGCTGAGCTAGATCCCACG 59.968 60.000 5.83 0.00 0.00 4.94
2174 2212 0.392336 CCTGCTGAGCTAGATCCCAC 59.608 60.000 5.83 0.00 0.00 4.61
2175 2213 0.031716 ACCTGCTGAGCTAGATCCCA 60.032 55.000 5.83 2.02 0.00 4.37
2176 2214 0.392336 CACCTGCTGAGCTAGATCCC 59.608 60.000 5.83 0.00 0.00 3.85
2177 2215 1.407936 TCACCTGCTGAGCTAGATCC 58.592 55.000 5.83 0.00 0.00 3.36
2178 2216 3.749665 ATTCACCTGCTGAGCTAGATC 57.250 47.619 5.83 0.00 0.00 2.75
2179 2217 4.080695 TGAAATTCACCTGCTGAGCTAGAT 60.081 41.667 5.83 0.00 0.00 1.98
2180 2218 3.261643 TGAAATTCACCTGCTGAGCTAGA 59.738 43.478 5.83 0.00 0.00 2.43
2181 2219 3.603532 TGAAATTCACCTGCTGAGCTAG 58.396 45.455 5.83 1.28 0.00 3.42
2182 2220 3.701205 TGAAATTCACCTGCTGAGCTA 57.299 42.857 5.83 0.00 0.00 3.32
2183 2221 2.574006 TGAAATTCACCTGCTGAGCT 57.426 45.000 5.83 0.00 0.00 4.09
2184 2222 2.670509 GCTTGAAATTCACCTGCTGAGC 60.671 50.000 0.00 0.00 0.00 4.26
2185 2223 2.094854 GGCTTGAAATTCACCTGCTGAG 60.095 50.000 12.19 0.93 0.00 3.35
2186 2224 1.888512 GGCTTGAAATTCACCTGCTGA 59.111 47.619 12.19 0.00 0.00 4.26
2187 2225 1.614903 TGGCTTGAAATTCACCTGCTG 59.385 47.619 12.19 0.00 0.00 4.41
2188 2226 1.615392 GTGGCTTGAAATTCACCTGCT 59.385 47.619 12.19 0.00 0.00 4.24
2189 2227 1.615392 AGTGGCTTGAAATTCACCTGC 59.385 47.619 0.00 0.84 0.00 4.85
2190 2228 3.318839 TCAAGTGGCTTGAAATTCACCTG 59.681 43.478 8.89 0.00 45.84 4.00
2191 2229 3.565307 TCAAGTGGCTTGAAATTCACCT 58.435 40.909 8.89 0.00 45.84 4.00
2200 2238 3.005050 CAGATTTGCTTCAAGTGGCTTGA 59.995 43.478 7.41 7.41 46.93 3.02
2201 2239 3.243636 ACAGATTTGCTTCAAGTGGCTTG 60.244 43.478 2.71 2.71 42.25 4.01
2202 2240 2.961062 ACAGATTTGCTTCAAGTGGCTT 59.039 40.909 0.00 0.00 0.00 4.35
2203 2241 2.590821 ACAGATTTGCTTCAAGTGGCT 58.409 42.857 0.00 0.00 0.00 4.75
2204 2242 3.253188 TGTACAGATTTGCTTCAAGTGGC 59.747 43.478 0.00 0.00 0.00 5.01
2205 2243 4.275689 TGTGTACAGATTTGCTTCAAGTGG 59.724 41.667 0.00 0.00 0.00 4.00
2206 2244 5.422666 TGTGTACAGATTTGCTTCAAGTG 57.577 39.130 0.00 0.00 0.00 3.16
2207 2245 6.441274 CATTGTGTACAGATTTGCTTCAAGT 58.559 36.000 0.00 0.00 0.00 3.16
2208 2246 5.344128 GCATTGTGTACAGATTTGCTTCAAG 59.656 40.000 16.55 0.00 0.00 3.02
2209 2247 5.221204 TGCATTGTGTACAGATTTGCTTCAA 60.221 36.000 21.37 9.94 0.00 2.69
2210 2248 4.277921 TGCATTGTGTACAGATTTGCTTCA 59.722 37.500 21.37 6.49 0.00 3.02
2211 2249 4.797471 TGCATTGTGTACAGATTTGCTTC 58.203 39.130 21.37 0.08 0.00 3.86
2212 2250 4.852134 TGCATTGTGTACAGATTTGCTT 57.148 36.364 21.37 0.00 0.00 3.91
2213 2251 4.852134 TTGCATTGTGTACAGATTTGCT 57.148 36.364 21.37 0.00 0.00 3.91
2214 2252 5.062558 GGAATTGCATTGTGTACAGATTTGC 59.937 40.000 16.82 16.82 0.00 3.68
2215 2253 6.157904 TGGAATTGCATTGTGTACAGATTTG 58.842 36.000 0.00 0.00 0.00 2.32
2216 2254 6.015180 ACTGGAATTGCATTGTGTACAGATTT 60.015 34.615 0.00 0.00 0.00 2.17
2217 2255 5.477984 ACTGGAATTGCATTGTGTACAGATT 59.522 36.000 0.00 0.00 0.00 2.40
2218 2256 5.012239 ACTGGAATTGCATTGTGTACAGAT 58.988 37.500 0.00 0.00 0.00 2.90
2219 2257 4.216042 CACTGGAATTGCATTGTGTACAGA 59.784 41.667 8.84 0.00 0.00 3.41
2220 2258 4.478699 CACTGGAATTGCATTGTGTACAG 58.521 43.478 8.84 0.00 0.00 2.74
2221 2259 3.305267 GCACTGGAATTGCATTGTGTACA 60.305 43.478 16.64 0.00 39.93 2.90
2222 2260 3.244976 GCACTGGAATTGCATTGTGTAC 58.755 45.455 16.64 1.52 39.93 2.90
2223 2261 2.230992 GGCACTGGAATTGCATTGTGTA 59.769 45.455 16.64 0.00 42.12 2.90
2224 2262 1.001181 GGCACTGGAATTGCATTGTGT 59.999 47.619 16.64 1.90 42.12 3.72
2225 2263 1.274167 AGGCACTGGAATTGCATTGTG 59.726 47.619 16.64 14.79 42.12 3.33
2226 2264 1.636148 AGGCACTGGAATTGCATTGT 58.364 45.000 16.64 2.93 42.12 2.71


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

AutoCloner maintained by Alex Coulton.