Multiple sequence alignment - TraesCS2D01G184000

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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 TraesCS2D01G184000 chr2D 100.000 2627 0 0 1 2627 129267169 129269795 0.000000e+00 4852.0
1 TraesCS2D01G184000 chr2A 93.593 1389 66 7 281 1665 136086060 136087429 0.000000e+00 2050.0
2 TraesCS2D01G184000 chr2A 93.814 291 9 1 2225 2506 136088122 136088412 1.870000e-116 429.0
3 TraesCS2D01G184000 chr2A 88.889 288 24 5 1 288 136085626 136085905 5.380000e-92 348.0
4 TraesCS2D01G184000 chr2A 91.781 73 6 0 2555 2627 136089045 136089117 4.630000e-18 102.0
5 TraesCS2D01G184000 chr2B 92.572 1252 55 19 598 1823 182861324 182862563 0.000000e+00 1762.0
6 TraesCS2D01G184000 chr2B 92.027 439 21 9 2201 2627 182863073 182863509 2.890000e-169 604.0
7 TraesCS2D01G184000 chr2B 89.593 221 22 1 1 220 182720377 182720597 1.990000e-71 279.0
8 TraesCS2D01G184000 chr2B 94.656 131 7 0 224 354 182722293 182722423 1.230000e-48 204.0
9 TraesCS2D01G184000 chr2B 95.238 63 3 0 395 457 182845867 182845929 1.660000e-17 100.0
10 TraesCS2D01G184000 chr3A 81.818 154 28 0 1116 1269 30362574 30362727 2.120000e-26 130.0
11 TraesCS2D01G184000 chr5A 79.235 183 37 1 172 354 291281165 291281346 2.740000e-25 126.0
12 TraesCS2D01G184000 chr3B 95.349 43 2 0 2193 2235 3075938 3075980 4.690000e-08 69.4
13 TraesCS2D01G184000 chr3B 97.143 35 1 0 2193 2227 140262859 140262893 2.820000e-05 60.2
14 TraesCS2D01G184000 chr6B 94.872 39 2 0 2192 2230 717901571 717901533 7.850000e-06 62.1
15 TraesCS2D01G184000 chr6B 97.143 35 1 0 2193 2227 682857060 682857094 2.820000e-05 60.2
16 TraesCS2D01G184000 chr6A 93.023 43 1 2 2189 2231 113516761 113516721 7.850000e-06 62.1
17 TraesCS2D01G184000 chr1A 97.222 36 1 0 2193 2228 5514220 5514185 7.850000e-06 62.1
18 TraesCS2D01G184000 chr5D 97.143 35 1 0 2192 2226 283352183 283352149 2.820000e-05 60.2
19 TraesCS2D01G184000 chr5B 97.143 35 1 0 2193 2227 344531873 344531907 2.820000e-05 60.2


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 TraesCS2D01G184000 chr2D 129267169 129269795 2626 False 4852.00 4852 100.00000 1 2627 1 chr2D.!!$F1 2626
1 TraesCS2D01G184000 chr2A 136085626 136089117 3491 False 732.25 2050 92.01925 1 2627 4 chr2A.!!$F1 2626
2 TraesCS2D01G184000 chr2B 182861324 182863509 2185 False 1183.00 1762 92.29950 598 2627 2 chr2B.!!$F3 2029
3 TraesCS2D01G184000 chr2B 182720377 182722423 2046 False 241.50 279 92.12450 1 354 2 chr2B.!!$F2 353

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
380 2244 0.180406 GCAAAGATAGCGGAAGGGGA 59.82 55.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 4712 0.179134 ATCAACGACTAGTGCGCTCC 60.179 55.0 9.73 0.0 0.0 4.7 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
61 63 0.656205 CGCGTTCCTTTGTTTCCACG 60.656 55.000 0.00 0.00 0.00 4.94
179 189 2.859165 TTGACCTCTGGAATGACCAC 57.141 50.000 0.00 0.00 44.64 4.16
180 190 0.608130 TGACCTCTGGAATGACCACG 59.392 55.000 0.00 0.00 44.64 4.94
181 191 0.608640 GACCTCTGGAATGACCACGT 59.391 55.000 0.00 0.00 44.64 4.49
182 192 1.822990 GACCTCTGGAATGACCACGTA 59.177 52.381 0.00 0.00 44.64 3.57
183 193 1.549170 ACCTCTGGAATGACCACGTAC 59.451 52.381 0.00 0.00 44.64 3.67
184 194 1.548719 CCTCTGGAATGACCACGTACA 59.451 52.381 0.00 0.00 44.64 2.90
185 195 2.607187 CTCTGGAATGACCACGTACAC 58.393 52.381 0.00 0.00 44.64 2.90
222 1924 1.050988 AGCCATGCCATACCTCTCGT 61.051 55.000 0.00 0.00 0.00 4.18
370 2234 3.947196 TGTAGCCAACCATGCAAAGATAG 59.053 43.478 0.00 0.00 0.00 2.08
372 2236 1.534595 GCCAACCATGCAAAGATAGCG 60.535 52.381 0.00 0.00 33.85 4.26
380 2244 0.180406 GCAAAGATAGCGGAAGGGGA 59.820 55.000 0.00 0.00 0.00 4.81
381 2245 1.811941 GCAAAGATAGCGGAAGGGGAG 60.812 57.143 0.00 0.00 0.00 4.30
411 2275 1.268032 CGGAGTTTTATGCGATGGTGC 60.268 52.381 0.00 0.00 35.89 5.01
434 2298 5.220491 GCTTATGTGGAAGAACTCATTCGAC 60.220 44.000 0.00 0.00 40.04 4.20
442 2306 6.096846 TGGAAGAACTCATTCGACTATGATGA 59.903 38.462 0.39 0.00 40.04 2.92
448 2312 9.430838 GAACTCATTCGACTATGATGAATTTTG 57.569 33.333 0.39 0.00 34.24 2.44
462 2326 5.013568 TGAATTTTGCCATGCCATTCTAG 57.986 39.130 0.00 0.00 0.00 2.43
465 2329 4.981806 TTTTGCCATGCCATTCTAGTAC 57.018 40.909 0.00 0.00 0.00 2.73
474 2339 2.628657 GCCATTCTAGTACTCCCACGAT 59.371 50.000 0.00 0.00 0.00 3.73
478 2343 4.978083 TTCTAGTACTCCCACGATTCAC 57.022 45.455 0.00 0.00 0.00 3.18
481 2346 2.253610 AGTACTCCCACGATTCACCAA 58.746 47.619 0.00 0.00 0.00 3.67
504 2369 3.080300 TCTCCACCACACAAACAAACT 57.920 42.857 0.00 0.00 0.00 2.66
520 2385 8.141268 ACAAACAAACTAATAGTTTCCACATGG 58.859 33.333 14.84 5.68 44.47 3.66
532 2397 6.607019 AGTTTCCACATGGGTTTAAGACTTA 58.393 36.000 0.00 0.00 38.11 2.24
537 2402 4.941873 CACATGGGTTTAAGACTTACTCCC 59.058 45.833 19.40 19.40 0.00 4.30
544 2409 7.886446 TGGGTTTAAGACTTACTCCCATTTTAG 59.114 37.037 22.66 0.00 38.51 1.85
546 2411 8.727910 GGTTTAAGACTTACTCCCATTTTAGTG 58.272 37.037 0.00 0.00 0.00 2.74
547 2412 9.498176 GTTTAAGACTTACTCCCATTTTAGTGA 57.502 33.333 0.00 0.00 0.00 3.41
548 2413 9.498176 TTTAAGACTTACTCCCATTTTAGTGAC 57.502 33.333 0.00 0.00 0.00 3.67
549 2414 6.936968 AGACTTACTCCCATTTTAGTGACT 57.063 37.500 0.00 0.00 0.00 3.41
629 2496 0.605319 TGAACTTGCCGTGATGTCCC 60.605 55.000 0.00 0.00 0.00 4.46
714 2581 3.296709 AACCGCGGTCCTGCTACAG 62.297 63.158 34.29 0.00 0.00 2.74
890 2757 2.273538 TAGCCGACTACTCTCCATCC 57.726 55.000 0.00 0.00 0.00 3.51
941 2808 3.050275 GCCACTTCTGACCGGCAC 61.050 66.667 0.00 0.00 44.25 5.01
956 2823 0.251341 GGCACAATCCCCTGTTCTGT 60.251 55.000 0.00 0.00 0.00 3.41
1056 2923 3.304251 GTCAGCAGGACCTCCTCC 58.696 66.667 0.00 0.00 46.65 4.30
1504 3371 1.443702 CTCGACGACGCCATTGTCA 60.444 57.895 1.48 0.00 41.37 3.58
1505 3372 0.802222 CTCGACGACGCCATTGTCAT 60.802 55.000 1.48 0.00 41.37 3.06
1517 3384 0.815734 ATTGTCATGAAGCCTGCTGC 59.184 50.000 0.00 0.00 41.71 5.25
1563 3430 0.898789 GTCTGGTTCAGGGAGGTCGA 60.899 60.000 0.00 0.00 31.51 4.20
1646 3513 1.742761 TTATGTTCAGAGGCTGCAGC 58.257 50.000 30.88 30.88 41.14 5.25
1665 3532 7.437267 GCTGCAGCAAATAAATTCTCATTGTAT 59.563 33.333 33.36 0.00 41.59 2.29
1666 3533 9.955208 CTGCAGCAAATAAATTCTCATTGTATA 57.045 29.630 0.00 0.00 0.00 1.47
1667 3534 9.955208 TGCAGCAAATAAATTCTCATTGTATAG 57.045 29.630 0.00 0.00 0.00 1.31
1690 4099 3.314357 AGCCAGTTTTAACTTGGTCGAAC 59.686 43.478 0.00 0.00 37.08 3.95
1694 4103 3.942748 AGTTTTAACTTGGTCGAACTGCA 59.057 39.130 0.33 0.00 35.21 4.41
1756 4187 0.819259 GGGTCTGCAGTTCTGCACAA 60.819 55.000 21.30 11.18 40.23 3.33
1791 4222 3.895232 ATGTAATCTTGCTCGTGGAGT 57.105 42.857 0.00 0.00 31.39 3.85
1842 4400 5.734720 TCTTTCTACTTGCCCTCAACATAG 58.265 41.667 0.00 0.00 0.00 2.23
1846 4404 3.788227 ACTTGCCCTCAACATAGTCAA 57.212 42.857 0.00 0.00 0.00 3.18
1853 4411 3.370846 CCCTCAACATAGTCAATGCCTCA 60.371 47.826 0.00 0.00 39.39 3.86
1888 4447 5.358160 ACATTCTTTCTACTTGGCCTATTGC 59.642 40.000 3.32 0.00 40.16 3.56
1893 4452 5.950544 TTCTACTTGGCCTATTGCTCTTA 57.049 39.130 3.32 0.00 40.92 2.10
1911 4470 7.466805 TGCTCTTAATTTCGACAAATGATCTG 58.533 34.615 0.00 0.00 32.18 2.90
1913 4472 7.850003 GCTCTTAATTTCGACAAATGATCTGAG 59.150 37.037 0.00 0.00 32.18 3.35
1936 4541 0.668706 CAGCACTCGGTGTTGGAGAG 60.669 60.000 11.27 0.00 40.24 3.20
1941 4546 1.202651 ACTCGGTGTTGGAGAGTTTGG 60.203 52.381 0.00 0.00 41.93 3.28
1942 4547 0.534203 TCGGTGTTGGAGAGTTTGGC 60.534 55.000 0.00 0.00 0.00 4.52
1965 4570 2.024868 CGACGGTGGCGTGATGAAA 61.025 57.895 0.00 0.00 0.00 2.69
1981 4586 3.719268 TGAAACTGATGGTGCTATGGT 57.281 42.857 0.00 0.00 0.00 3.55
1987 4592 1.561076 TGATGGTGCTATGGTCAAGCT 59.439 47.619 0.00 0.00 40.73 3.74
1991 4596 1.676014 GGTGCTATGGTCAAGCTTCGT 60.676 52.381 0.00 0.00 40.73 3.85
1993 4598 2.094417 GTGCTATGGTCAAGCTTCGTTC 59.906 50.000 0.00 0.00 40.73 3.95
1994 4599 1.324736 GCTATGGTCAAGCTTCGTTCG 59.675 52.381 0.00 0.00 37.01 3.95
1995 4600 1.927174 CTATGGTCAAGCTTCGTTCGG 59.073 52.381 0.00 0.00 0.00 4.30
1996 4601 1.298859 ATGGTCAAGCTTCGTTCGGC 61.299 55.000 0.00 0.00 0.00 5.54
1997 4602 2.677979 GGTCAAGCTTCGTTCGGCC 61.678 63.158 0.00 0.00 0.00 6.13
1998 4603 1.668151 GTCAAGCTTCGTTCGGCCT 60.668 57.895 0.00 0.00 0.00 5.19
1999 4604 1.667830 TCAAGCTTCGTTCGGCCTG 60.668 57.895 0.00 0.00 0.00 4.85
2000 4605 3.050275 AAGCTTCGTTCGGCCTGC 61.050 61.111 0.00 0.00 0.00 4.85
2001 4606 3.537206 AAGCTTCGTTCGGCCTGCT 62.537 57.895 0.00 0.00 0.00 4.24
2002 4607 3.793144 GCTTCGTTCGGCCTGCTG 61.793 66.667 0.00 0.00 0.00 4.41
2003 4608 3.793144 CTTCGTTCGGCCTGCTGC 61.793 66.667 0.00 0.00 40.16 5.25
2004 4609 4.314440 TTCGTTCGGCCTGCTGCT 62.314 61.111 0.00 0.00 40.92 4.24
2005 4610 4.742201 TCGTTCGGCCTGCTGCTC 62.742 66.667 0.00 0.00 40.92 4.26
2007 4612 4.704833 GTTCGGCCTGCTGCTCCA 62.705 66.667 0.00 0.00 40.92 3.86
2008 4613 3.952508 TTCGGCCTGCTGCTCCAA 61.953 61.111 0.00 0.00 40.92 3.53
2009 4614 3.907260 TTCGGCCTGCTGCTCCAAG 62.907 63.158 0.00 0.00 40.92 3.61
2010 4615 4.711949 CGGCCTGCTGCTCCAAGT 62.712 66.667 0.00 0.00 40.92 3.16
2011 4616 2.282745 GGCCTGCTGCTCCAAGTT 60.283 61.111 0.00 0.00 40.92 2.66
2012 4617 2.338785 GGCCTGCTGCTCCAAGTTC 61.339 63.158 0.00 0.00 40.92 3.01
2013 4618 1.601759 GCCTGCTGCTCCAAGTTCA 60.602 57.895 0.00 0.00 36.87 3.18
2014 4619 1.584380 GCCTGCTGCTCCAAGTTCAG 61.584 60.000 0.00 0.00 36.87 3.02
2015 4620 0.959372 CCTGCTGCTCCAAGTTCAGG 60.959 60.000 0.00 0.00 35.68 3.86
2016 4621 1.584380 CTGCTGCTCCAAGTTCAGGC 61.584 60.000 0.00 0.00 0.00 4.85
2017 4622 1.601759 GCTGCTCCAAGTTCAGGCA 60.602 57.895 0.00 0.00 0.00 4.75
2018 4623 2.552802 CTGCTCCAAGTTCAGGCAG 58.447 57.895 0.00 0.00 43.03 4.85
2019 4624 0.959372 CTGCTCCAAGTTCAGGCAGG 60.959 60.000 10.76 0.00 44.32 4.85
2020 4625 1.676967 GCTCCAAGTTCAGGCAGGG 60.677 63.158 0.00 0.00 0.00 4.45
2021 4626 1.676967 CTCCAAGTTCAGGCAGGGC 60.677 63.158 0.00 0.00 0.00 5.19
2022 4627 3.058160 CCAAGTTCAGGCAGGGCG 61.058 66.667 0.00 0.00 0.00 6.13
2023 4628 3.058160 CAAGTTCAGGCAGGGCGG 61.058 66.667 0.00 0.00 0.00 6.13
2024 4629 3.570212 AAGTTCAGGCAGGGCGGT 61.570 61.111 0.00 0.00 0.00 5.68
2025 4630 3.850098 AAGTTCAGGCAGGGCGGTG 62.850 63.158 0.00 0.00 0.00 4.94
2032 4637 4.840005 GCAGGGCGGTGGCTACTC 62.840 72.222 0.00 0.00 39.81 2.59
2033 4638 3.077556 CAGGGCGGTGGCTACTCT 61.078 66.667 0.00 0.00 39.81 3.24
2034 4639 3.077556 AGGGCGGTGGCTACTCTG 61.078 66.667 0.00 0.00 39.81 3.35
2035 4640 3.391382 GGGCGGTGGCTACTCTGT 61.391 66.667 0.00 0.00 39.81 3.41
2036 4641 2.056223 GGGCGGTGGCTACTCTGTA 61.056 63.158 0.00 0.00 39.81 2.74
2037 4642 1.437986 GGCGGTGGCTACTCTGTAG 59.562 63.158 0.00 0.77 39.81 2.74
2038 4643 1.321074 GGCGGTGGCTACTCTGTAGT 61.321 60.000 0.00 0.00 39.81 2.73
2039 4644 1.386533 GCGGTGGCTACTCTGTAGTA 58.613 55.000 0.00 0.00 37.15 1.82
2040 4645 1.065251 GCGGTGGCTACTCTGTAGTAC 59.935 57.143 0.00 0.00 37.15 2.73
2041 4646 1.329906 CGGTGGCTACTCTGTAGTACG 59.670 57.143 0.00 3.50 37.15 3.67
2042 4647 2.363683 GGTGGCTACTCTGTAGTACGT 58.636 52.381 0.00 0.00 37.15 3.57
2043 4648 2.751806 GGTGGCTACTCTGTAGTACGTT 59.248 50.000 0.00 0.00 37.15 3.99
2044 4649 3.427233 GGTGGCTACTCTGTAGTACGTTG 60.427 52.174 0.00 0.00 37.15 4.10
2045 4650 2.751259 TGGCTACTCTGTAGTACGTTGG 59.249 50.000 0.00 0.00 37.15 3.77
2046 4651 2.751806 GGCTACTCTGTAGTACGTTGGT 59.248 50.000 0.00 0.00 37.15 3.67
2047 4652 3.181502 GGCTACTCTGTAGTACGTTGGTC 60.182 52.174 0.00 0.00 37.15 4.02
2048 4653 3.688673 GCTACTCTGTAGTACGTTGGTCT 59.311 47.826 0.00 0.00 37.15 3.85
2049 4654 4.155644 GCTACTCTGTAGTACGTTGGTCTT 59.844 45.833 0.00 0.00 37.15 3.01
2050 4655 5.335504 GCTACTCTGTAGTACGTTGGTCTTT 60.336 44.000 0.00 0.00 37.15 2.52
2051 4656 5.118642 ACTCTGTAGTACGTTGGTCTTTC 57.881 43.478 0.00 0.00 32.84 2.62
2052 4657 4.022503 ACTCTGTAGTACGTTGGTCTTTCC 60.023 45.833 0.00 0.00 32.84 3.13
2053 4658 3.058016 TCTGTAGTACGTTGGTCTTTCCG 60.058 47.826 0.00 0.00 39.52 4.30
2054 4659 2.030007 TGTAGTACGTTGGTCTTTCCGG 60.030 50.000 0.00 0.00 39.52 5.14
2055 4660 1.331214 AGTACGTTGGTCTTTCCGGA 58.669 50.000 0.00 0.00 39.52 5.14
2056 4661 1.000171 AGTACGTTGGTCTTTCCGGAC 60.000 52.381 1.83 0.00 39.52 4.79
2082 4688 2.232941 TCTGGTTCTGGTTGTATCGGTC 59.767 50.000 0.00 0.00 0.00 4.79
2084 4690 2.635915 TGGTTCTGGTTGTATCGGTCTT 59.364 45.455 0.00 0.00 0.00 3.01
2089 4695 1.887854 TGGTTGTATCGGTCTTCGTCA 59.112 47.619 0.00 0.00 40.32 4.35
2096 4702 4.456911 TGTATCGGTCTTCGTCAGTAACTT 59.543 41.667 0.00 0.00 40.32 2.66
2099 4705 3.567164 TCGGTCTTCGTCAGTAACTTCTT 59.433 43.478 0.00 0.00 40.32 2.52
2100 4706 4.037208 TCGGTCTTCGTCAGTAACTTCTTT 59.963 41.667 0.00 0.00 40.32 2.52
2101 4707 4.743644 CGGTCTTCGTCAGTAACTTCTTTT 59.256 41.667 0.00 0.00 0.00 2.27
2102 4708 5.233689 CGGTCTTCGTCAGTAACTTCTTTTT 59.766 40.000 0.00 0.00 0.00 1.94
2103 4709 6.418819 CGGTCTTCGTCAGTAACTTCTTTTTA 59.581 38.462 0.00 0.00 0.00 1.52
2104 4710 7.358187 CGGTCTTCGTCAGTAACTTCTTTTTAG 60.358 40.741 0.00 0.00 0.00 1.85
2105 4711 7.095732 GGTCTTCGTCAGTAACTTCTTTTTAGG 60.096 40.741 0.00 0.00 0.00 2.69
2106 4712 6.927381 TCTTCGTCAGTAACTTCTTTTTAGGG 59.073 38.462 0.00 0.00 0.00 3.53
2107 4713 5.544650 TCGTCAGTAACTTCTTTTTAGGGG 58.455 41.667 0.00 0.00 0.00 4.79
2108 4714 5.305128 TCGTCAGTAACTTCTTTTTAGGGGA 59.695 40.000 0.00 0.00 0.00 4.81
2109 4715 5.638234 CGTCAGTAACTTCTTTTTAGGGGAG 59.362 44.000 0.00 0.00 0.00 4.30
2112 4718 1.822506 ACTTCTTTTTAGGGGAGCGC 58.177 50.000 0.00 0.00 0.00 5.92
2140 4746 4.454504 GTCGTTGATCCCAAGTGTATTGTT 59.545 41.667 0.00 0.00 32.06 2.83
2145 4751 6.367374 TGATCCCAAGTGTATTGTTCACTA 57.633 37.500 0.00 0.00 44.03 2.74
2182 4788 5.020795 TGTATTGTCCACTGGAAGCTACTA 58.979 41.667 0.00 0.00 37.60 1.82
2184 4790 3.170991 TGTCCACTGGAAGCTACTACT 57.829 47.619 0.00 0.00 37.60 2.57
2188 4794 2.624557 CCACTGGAAGCTACTACTCCCT 60.625 54.545 0.00 0.00 37.60 4.20
2190 4796 3.100671 ACTGGAAGCTACTACTCCCTTG 58.899 50.000 0.00 0.00 37.60 3.61
2196 4836 3.944087 AGCTACTACTCCCTTGCAAAAG 58.056 45.455 0.00 0.97 0.00 2.27
2198 4838 1.523758 ACTACTCCCTTGCAAAAGCG 58.476 50.000 0.00 0.00 0.00 4.68
2199 4839 1.202770 ACTACTCCCTTGCAAAAGCGT 60.203 47.619 0.00 0.00 0.00 5.07
2212 4852 8.128582 CCTTGCAAAAGCGTTCTTATATTATGA 58.871 33.333 0.00 0.00 31.02 2.15
2215 4855 8.335356 TGCAAAAGCGTTCTTATATTATGAGAC 58.665 33.333 0.00 0.00 31.02 3.36
2217 4857 7.639162 AAAGCGTTCTTATATTATGAGACGG 57.361 36.000 15.32 6.59 31.02 4.79
2220 4860 6.430308 AGCGTTCTTATATTATGAGACGGAGA 59.570 38.462 15.32 0.00 0.00 3.71
2227 4870 9.878667 CTTATATTATGAGACGGAGAGAGTAGA 57.121 37.037 0.00 0.00 0.00 2.59
2234 4877 4.323417 AGACGGAGAGAGTAGATAGCATG 58.677 47.826 0.00 0.00 0.00 4.06
2241 4884 6.152661 GGAGAGAGTAGATAGCATGCAGTTAT 59.847 42.308 21.98 9.14 0.00 1.89
2459 5111 6.684613 GCATCTCTACTCCGGGTTAAATAACA 60.685 42.308 0.00 0.00 37.92 2.41
2493 5145 2.901839 AGTTCAGGCGGGTTAGTTAGAA 59.098 45.455 0.00 0.00 0.00 2.10
2540 5192 1.577328 AAGTCGTCATTGCCCGCAAG 61.577 55.000 8.27 1.10 39.47 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 119 0.944311 CTCGGACACGGGACAGTTTG 60.944 60.000 0.00 0.00 45.57 2.93
169 171 1.722011 CAGGTGTACGTGGTCATTCC 58.278 55.000 0.00 0.00 0.00 3.01
170 172 1.076332 GCAGGTGTACGTGGTCATTC 58.924 55.000 0.00 0.00 32.80 2.67
178 188 2.355837 CACGCTGCAGGTGTACGT 60.356 61.111 17.12 13.13 36.83 3.57
179 189 2.355837 ACACGCTGCAGGTGTACG 60.356 61.111 28.54 19.97 46.16 3.67
183 193 0.592247 GTTTTGACACGCTGCAGGTG 60.592 55.000 24.89 24.89 41.15 4.00
184 194 1.029408 TGTTTTGACACGCTGCAGGT 61.029 50.000 17.12 8.98 0.00 4.00
185 195 0.317269 CTGTTTTGACACGCTGCAGG 60.317 55.000 17.12 8.27 0.00 4.85
263 1965 1.801771 GCTACACATGTTTGCACGGTA 59.198 47.619 0.00 0.00 0.00 4.02
265 1967 0.590682 TGCTACACATGTTTGCACGG 59.409 50.000 11.63 0.00 33.66 4.94
354 2218 2.016318 TCCGCTATCTTTGCATGGTTG 58.984 47.619 0.00 0.00 0.00 3.77
370 2234 4.883354 CATGCCCTCCCCTTCCGC 62.883 72.222 0.00 0.00 0.00 5.54
372 2236 2.308722 TGTCATGCCCTCCCCTTCC 61.309 63.158 0.00 0.00 0.00 3.46
380 2244 0.110486 AAAACTCCGTGTCATGCCCT 59.890 50.000 0.00 0.00 0.00 5.19
381 2245 1.816074 TAAAACTCCGTGTCATGCCC 58.184 50.000 0.00 0.00 0.00 5.36
411 2275 6.102663 AGTCGAATGAGTTCTTCCACATAAG 58.897 40.000 0.00 0.00 32.00 1.73
434 2298 4.951254 TGGCATGGCAAAATTCATCATAG 58.049 39.130 21.13 0.00 0.00 2.23
442 2306 5.658190 AGTACTAGAATGGCATGGCAAAATT 59.342 36.000 27.04 16.13 0.00 1.82
448 2312 2.551071 GGGAGTACTAGAATGGCATGGC 60.551 54.545 13.29 13.29 0.00 4.40
462 2326 2.289195 TGTTGGTGAATCGTGGGAGTAC 60.289 50.000 0.00 0.00 0.00 2.73
465 2329 2.009774 GATGTTGGTGAATCGTGGGAG 58.990 52.381 0.00 0.00 0.00 4.30
474 2339 1.492599 TGTGGTGGAGATGTTGGTGAA 59.507 47.619 0.00 0.00 0.00 3.18
478 2343 1.979855 TTGTGTGGTGGAGATGTTGG 58.020 50.000 0.00 0.00 0.00 3.77
481 2346 2.727123 TGTTTGTGTGGTGGAGATGT 57.273 45.000 0.00 0.00 0.00 3.06
504 2369 8.387813 AGTCTTAAACCCATGTGGAAACTATTA 58.612 33.333 0.00 0.00 37.39 0.98
520 2385 8.727910 CACTAAAATGGGAGTAAGTCTTAAACC 58.272 37.037 0.00 1.37 0.00 3.27
532 2397 6.537660 GCGTTTATAGTCACTAAAATGGGAGT 59.462 38.462 0.00 0.00 0.00 3.85
570 2437 3.671008 TGCAGCGTACTCCTTTCTTAA 57.329 42.857 0.00 0.00 0.00 1.85
571 2438 3.056107 ACATGCAGCGTACTCCTTTCTTA 60.056 43.478 0.00 0.00 0.00 2.10
572 2439 2.289694 ACATGCAGCGTACTCCTTTCTT 60.290 45.455 0.00 0.00 0.00 2.52
573 2440 1.276421 ACATGCAGCGTACTCCTTTCT 59.724 47.619 0.00 0.00 0.00 2.52
574 2441 1.726853 ACATGCAGCGTACTCCTTTC 58.273 50.000 0.00 0.00 0.00 2.62
575 2442 2.076863 GAACATGCAGCGTACTCCTTT 58.923 47.619 0.00 0.00 0.00 3.11
576 2443 1.676014 GGAACATGCAGCGTACTCCTT 60.676 52.381 6.84 0.00 0.00 3.36
577 2444 0.108138 GGAACATGCAGCGTACTCCT 60.108 55.000 6.84 0.00 0.00 3.69
578 2445 1.421410 CGGAACATGCAGCGTACTCC 61.421 60.000 0.00 4.61 0.00 3.85
579 2446 0.736325 ACGGAACATGCAGCGTACTC 60.736 55.000 0.00 0.00 0.00 2.59
648 2515 2.687935 GGCGGCAATTCTGAAAATCCTA 59.312 45.455 3.07 0.00 0.00 2.94
672 2539 4.425520 GTCTATTCCTTCAGTCCAAGTCG 58.574 47.826 0.00 0.00 0.00 4.18
941 2808 3.689347 TCAATGACAGAACAGGGGATTG 58.311 45.455 0.00 0.00 0.00 2.67
956 2823 3.881089 AGCTGATCGAATTGCATCAATGA 59.119 39.130 9.03 0.00 34.04 2.57
1122 2989 1.153289 GATGTGCGCCATCTCCAGT 60.153 57.895 23.41 0.00 45.50 4.00
1504 3371 1.744368 CACTCGCAGCAGGCTTCAT 60.744 57.895 0.00 0.00 41.67 2.57
1505 3372 2.357881 CACTCGCAGCAGGCTTCA 60.358 61.111 0.00 0.00 41.67 3.02
1517 3384 3.168604 CACTCGCACTCGCACTCG 61.169 66.667 0.00 0.00 38.40 4.18
1532 3399 2.821366 CCAGACCATGCCTCGCAC 60.821 66.667 0.00 0.00 43.04 5.34
1533 3400 2.803155 GAACCAGACCATGCCTCGCA 62.803 60.000 0.00 0.00 44.86 5.10
1534 3401 2.045926 AACCAGACCATGCCTCGC 60.046 61.111 0.00 0.00 0.00 5.03
1535 3402 0.742281 CTGAACCAGACCATGCCTCG 60.742 60.000 0.00 0.00 32.44 4.63
1536 3403 0.393537 CCTGAACCAGACCATGCCTC 60.394 60.000 0.00 0.00 32.44 4.70
1537 3404 1.687612 CCTGAACCAGACCATGCCT 59.312 57.895 0.00 0.00 32.44 4.75
1665 3532 4.039488 TCGACCAAGTTAAAACTGGCTCTA 59.961 41.667 0.00 0.00 39.66 2.43
1666 3533 3.139077 CGACCAAGTTAAAACTGGCTCT 58.861 45.455 0.00 0.00 39.66 4.09
1667 3534 3.135994 TCGACCAAGTTAAAACTGGCTC 58.864 45.455 0.00 0.00 39.66 4.70
1690 4099 8.514136 TTGGATTACGAAATTAAAACTTGCAG 57.486 30.769 0.00 0.00 0.00 4.41
1694 4103 9.471084 CCACTTTGGATTACGAAATTAAAACTT 57.529 29.630 0.00 0.00 40.96 2.66
1699 4108 5.105675 GGGCCACTTTGGATTACGAAATTAA 60.106 40.000 4.39 0.00 40.96 1.40
1700 4109 4.399934 GGGCCACTTTGGATTACGAAATTA 59.600 41.667 4.39 0.00 40.96 1.40
1709 4126 2.250924 CTTTGAGGGCCACTTTGGATT 58.749 47.619 6.18 0.00 40.96 3.01
1756 4187 7.068716 GCAAGATTACATTCCTGGGATAAGTTT 59.931 37.037 0.00 0.00 0.00 2.66
1791 4222 3.066342 GGTAGTTGATTCGATCGTCTCCA 59.934 47.826 15.94 6.58 0.00 3.86
1859 4418 6.071320 AGGCCAAGTAGAAAGAATGTTTTCT 58.929 36.000 5.01 9.04 46.27 2.52
1860 4419 6.332735 AGGCCAAGTAGAAAGAATGTTTTC 57.667 37.500 5.01 0.00 37.34 2.29
1880 4439 5.734855 TGTCGAAATTAAGAGCAATAGGC 57.265 39.130 0.00 0.00 45.30 3.93
1888 4447 7.850003 GCTCAGATCATTTGTCGAAATTAAGAG 59.150 37.037 0.00 0.00 28.65 2.85
1893 4452 4.701651 TGGCTCAGATCATTTGTCGAAATT 59.298 37.500 0.00 0.00 28.65 1.82
1911 4470 2.740055 CACCGAGTGCTGTGGCTC 60.740 66.667 0.00 0.00 39.59 4.70
1913 4472 2.591715 AACACCGAGTGCTGTGGC 60.592 61.111 4.23 0.00 36.98 5.01
1936 4541 4.324991 ACCGTCGAGGGGCCAAAC 62.325 66.667 26.71 0.00 46.96 2.93
1965 4570 2.681976 GCTTGACCATAGCACCATCAGT 60.682 50.000 0.00 0.00 38.51 3.41
1981 4586 1.667830 CAGGCCGAACGAAGCTTGA 60.668 57.895 2.10 0.00 38.27 3.02
1987 4592 4.314440 AGCAGCAGGCCGAACGAA 62.314 61.111 0.00 0.00 46.50 3.85
1991 4596 3.907260 CTTGGAGCAGCAGGCCGAA 62.907 63.158 0.00 0.00 46.50 4.30
1993 4598 4.711949 ACTTGGAGCAGCAGGCCG 62.712 66.667 0.00 0.00 46.50 6.13
1994 4599 2.282745 AACTTGGAGCAGCAGGCC 60.283 61.111 0.00 0.00 46.50 5.19
1995 4600 1.584380 CTGAACTTGGAGCAGCAGGC 61.584 60.000 0.00 0.00 45.30 4.85
1996 4601 0.959372 CCTGAACTTGGAGCAGCAGG 60.959 60.000 0.00 0.00 37.21 4.85
1997 4602 1.584380 GCCTGAACTTGGAGCAGCAG 61.584 60.000 0.00 0.00 0.00 4.24
1998 4603 1.601759 GCCTGAACTTGGAGCAGCA 60.602 57.895 0.00 0.00 0.00 4.41
1999 4604 1.584380 CTGCCTGAACTTGGAGCAGC 61.584 60.000 0.00 0.00 43.84 5.25
2000 4605 2.552802 CTGCCTGAACTTGGAGCAG 58.447 57.895 0.00 0.00 44.31 4.24
2001 4606 1.073722 CCTGCCTGAACTTGGAGCA 59.926 57.895 0.00 0.00 0.00 4.26
2002 4607 1.676967 CCCTGCCTGAACTTGGAGC 60.677 63.158 0.00 0.00 0.00 4.70
2003 4608 1.676967 GCCCTGCCTGAACTTGGAG 60.677 63.158 0.00 0.00 0.00 3.86
2004 4609 2.436109 GCCCTGCCTGAACTTGGA 59.564 61.111 0.00 0.00 0.00 3.53
2005 4610 3.058160 CGCCCTGCCTGAACTTGG 61.058 66.667 0.00 0.00 0.00 3.61
2006 4611 3.058160 CCGCCCTGCCTGAACTTG 61.058 66.667 0.00 0.00 0.00 3.16
2007 4612 3.570212 ACCGCCCTGCCTGAACTT 61.570 61.111 0.00 0.00 0.00 2.66
2008 4613 4.335647 CACCGCCCTGCCTGAACT 62.336 66.667 0.00 0.00 0.00 3.01
2015 4620 4.840005 GAGTAGCCACCGCCCTGC 62.840 72.222 0.00 0.00 34.57 4.85
2016 4621 3.077556 AGAGTAGCCACCGCCCTG 61.078 66.667 0.00 0.00 34.57 4.45
2017 4622 2.509931 TACAGAGTAGCCACCGCCCT 62.510 60.000 0.00 0.00 34.57 5.19
2018 4623 2.017559 CTACAGAGTAGCCACCGCCC 62.018 65.000 0.00 0.00 34.57 6.13
2019 4624 1.321074 ACTACAGAGTAGCCACCGCC 61.321 60.000 4.20 0.00 32.65 6.13
2020 4625 1.065251 GTACTACAGAGTAGCCACCGC 59.935 57.143 4.20 0.00 38.88 5.68
2021 4626 1.329906 CGTACTACAGAGTAGCCACCG 59.670 57.143 4.20 0.00 38.88 4.94
2022 4627 2.363683 ACGTACTACAGAGTAGCCACC 58.636 52.381 4.20 0.00 38.88 4.61
2023 4628 3.427233 CCAACGTACTACAGAGTAGCCAC 60.427 52.174 4.20 2.65 38.88 5.01
2024 4629 2.751259 CCAACGTACTACAGAGTAGCCA 59.249 50.000 4.20 0.00 38.88 4.75
2025 4630 2.751806 ACCAACGTACTACAGAGTAGCC 59.248 50.000 4.20 0.00 38.88 3.93
2026 4631 3.688673 AGACCAACGTACTACAGAGTAGC 59.311 47.826 4.20 0.00 38.88 3.58
2027 4632 5.876612 AAGACCAACGTACTACAGAGTAG 57.123 43.478 2.79 2.79 38.88 2.57
2028 4633 5.182001 GGAAAGACCAACGTACTACAGAGTA 59.818 44.000 0.00 0.00 36.49 2.59
2029 4634 4.022503 GGAAAGACCAACGTACTACAGAGT 60.023 45.833 0.00 0.00 37.92 3.24
2030 4635 4.483311 GGAAAGACCAACGTACTACAGAG 58.517 47.826 0.00 0.00 38.79 3.35
2031 4636 3.058016 CGGAAAGACCAACGTACTACAGA 60.058 47.826 0.00 0.00 38.90 3.41
2032 4637 3.240069 CGGAAAGACCAACGTACTACAG 58.760 50.000 0.00 0.00 38.90 2.74
2033 4638 2.030007 CCGGAAAGACCAACGTACTACA 60.030 50.000 0.00 0.00 38.90 2.74
2034 4639 2.228822 TCCGGAAAGACCAACGTACTAC 59.771 50.000 0.00 0.00 38.90 2.73
2035 4640 2.228822 GTCCGGAAAGACCAACGTACTA 59.771 50.000 5.23 0.00 38.90 1.82
2036 4641 1.000171 GTCCGGAAAGACCAACGTACT 60.000 52.381 5.23 0.00 38.90 2.73
2037 4642 1.422388 GTCCGGAAAGACCAACGTAC 58.578 55.000 5.23 0.00 38.90 3.67
2038 4643 3.892200 GTCCGGAAAGACCAACGTA 57.108 52.632 5.23 0.00 38.90 3.57
2039 4644 4.764896 GTCCGGAAAGACCAACGT 57.235 55.556 5.23 0.00 38.90 3.99
2055 4660 1.768888 AACCAGAACCAGACGGGGT 60.769 57.895 0.00 0.00 45.04 4.95
2056 4661 1.302511 CAACCAGAACCAGACGGGG 60.303 63.158 0.00 0.00 42.91 5.73
2057 4662 0.682852 TACAACCAGAACCAGACGGG 59.317 55.000 0.00 0.00 44.81 5.28
2082 4688 6.147328 CCCCTAAAAAGAAGTTACTGACGAAG 59.853 42.308 0.00 0.00 0.00 3.79
2084 4690 5.305128 TCCCCTAAAAAGAAGTTACTGACGA 59.695 40.000 0.00 0.00 0.00 4.20
2089 4695 4.576879 CGCTCCCCTAAAAAGAAGTTACT 58.423 43.478 0.00 0.00 0.00 2.24
2096 4702 0.690762 AGTGCGCTCCCCTAAAAAGA 59.309 50.000 9.73 0.00 0.00 2.52
2099 4705 1.206371 GACTAGTGCGCTCCCCTAAAA 59.794 52.381 9.73 0.00 0.00 1.52
2100 4706 0.822164 GACTAGTGCGCTCCCCTAAA 59.178 55.000 9.73 0.00 0.00 1.85
2101 4707 1.381928 CGACTAGTGCGCTCCCCTAA 61.382 60.000 9.73 0.00 0.00 2.69
2102 4708 1.822613 CGACTAGTGCGCTCCCCTA 60.823 63.158 9.73 2.79 0.00 3.53
2103 4709 3.141488 CGACTAGTGCGCTCCCCT 61.141 66.667 9.73 1.58 0.00 4.79
2104 4710 3.003113 AACGACTAGTGCGCTCCCC 62.003 63.158 9.73 0.00 0.00 4.81
2105 4711 1.805945 CAACGACTAGTGCGCTCCC 60.806 63.158 9.73 0.00 0.00 4.30
2106 4712 0.179134 ATCAACGACTAGTGCGCTCC 60.179 55.000 9.73 0.00 0.00 4.70
2107 4713 1.192793 GATCAACGACTAGTGCGCTC 58.807 55.000 9.73 4.74 0.00 5.03
2108 4714 0.179134 GGATCAACGACTAGTGCGCT 60.179 55.000 9.73 4.58 0.00 5.92
2109 4715 1.146358 GGGATCAACGACTAGTGCGC 61.146 60.000 0.00 0.00 0.00 6.09
2112 4718 3.254060 CACTTGGGATCAACGACTAGTG 58.746 50.000 0.00 0.00 0.00 2.74
2161 4767 5.269991 AGTAGTAGCTTCCAGTGGACAATA 58.730 41.667 12.69 1.66 0.00 1.90
2190 4796 7.527516 CGTCTCATAATATAAGAACGCTTTTGC 59.472 37.037 0.00 0.00 43.23 3.68
2196 4836 6.609533 TCTCCGTCTCATAATATAAGAACGC 58.390 40.000 0.00 0.00 0.00 4.84
2198 4838 9.005777 ACTCTCTCCGTCTCATAATATAAGAAC 57.994 37.037 0.00 0.00 0.00 3.01
2212 4852 4.323417 CATGCTATCTACTCTCTCCGTCT 58.677 47.826 0.00 0.00 0.00 4.18
2215 4855 2.816672 TGCATGCTATCTACTCTCTCCG 59.183 50.000 20.33 0.00 0.00 4.63
2217 4857 5.452078 AACTGCATGCTATCTACTCTCTC 57.548 43.478 20.33 0.00 0.00 3.20
2220 4860 6.907853 TGATAACTGCATGCTATCTACTCT 57.092 37.500 20.33 0.00 0.00 3.24
2241 4884 3.799366 TCGTTAGAAAGCAACCAGTTGA 58.201 40.909 14.56 0.00 42.93 3.18
2459 5111 3.026694 GCCTGAACTATTGCCAATTCCT 58.973 45.455 0.00 0.00 0.00 3.36
2580 5816 9.912634 AATACACATAAACAAAAATGGTCAGAG 57.087 29.630 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.