Multiple sequence alignment - TraesCS1A01G305600

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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 TraesCS1A01G305600 chr1A 100.000 2446 0 0 1 2446 498052317 498054762 0.000000e+00 4518
1 TraesCS1A01G305600 chr1B 93.753 2193 86 24 1 2187 540724183 540726330 0.000000e+00 3243
2 TraesCS1A01G305600 chr1B 97.059 204 4 2 2244 2446 540726327 540726529 2.330000e-90 342
3 TraesCS1A01G305600 chr1D 96.314 1709 44 4 747 2446 402829350 402831048 0.000000e+00 2789
4 TraesCS1A01G305600 chr1D 98.288 292 3 1 325 616 402829056 402829345 6.030000e-141 510
5 TraesCS1A01G305600 chr1D 94.654 318 13 3 1 315 402828597 402828913 7.860000e-135 490
6 TraesCS1A01G305600 chr6A 95.506 89 3 1 2176 2264 524351914 524352001 9.120000e-30 141


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 TraesCS1A01G305600 chr1A 498052317 498054762 2445 False 4518.0 4518 100.000000 1 2446 1 chr1A.!!$F1 2445
1 TraesCS1A01G305600 chr1B 540724183 540726529 2346 False 1792.5 3243 95.406000 1 2446 2 chr1B.!!$F1 2445
2 TraesCS1A01G305600 chr1D 402828597 402831048 2451 False 1263.0 2789 96.418667 1 2446 3 chr1D.!!$F1 2445

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
609 754 0.037326 TGACGCTTAGTTGCCTCTGG 60.037 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2192 0.034059 AAGACTCAAGAGCACCCACG 59.966 55.0 0.0 0.0 0.0 4.94 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
91 92 5.099042 TCCTTTAGCTACTCATTGGGAAC 57.901 43.478 0.00 0.0 0.00 3.62
173 174 7.038231 ACAGTAAGGCTCTCATAGGTTTTAGTT 60.038 37.037 0.00 0.0 0.00 2.24
280 283 0.316841 TGCTGATGACTGTGCACGTA 59.683 50.000 13.13 0.0 0.00 3.57
305 309 7.315247 TGTGTAGCATGGTATGTCAATTTAC 57.685 36.000 8.06 0.0 0.00 2.01
306 310 7.109501 TGTGTAGCATGGTATGTCAATTTACT 58.890 34.615 8.06 0.0 0.00 2.24
307 311 8.261522 TGTGTAGCATGGTATGTCAATTTACTA 58.738 33.333 8.06 0.0 0.00 1.82
308 312 9.273016 GTGTAGCATGGTATGTCAATTTACTAT 57.727 33.333 8.06 0.0 0.00 2.12
309 313 9.489084 TGTAGCATGGTATGTCAATTTACTATC 57.511 33.333 8.06 0.0 0.00 2.08
310 314 9.712305 GTAGCATGGTATGTCAATTTACTATCT 57.288 33.333 8.06 0.0 0.00 1.98
609 754 0.037326 TGACGCTTAGTTGCCTCTGG 60.037 55.000 0.00 0.0 0.00 3.86
628 773 2.169352 TGGATCTTTGCCAGTCTAGAGC 59.831 50.000 0.00 0.0 0.00 4.09
649 794 2.846827 CCTTTTCTGATGGAGGGGTACT 59.153 50.000 0.00 0.0 0.00 2.73
678 823 7.923414 AAAATTCTAATGGAGGAGTACACAC 57.077 36.000 0.00 0.0 0.00 3.82
679 824 6.620877 AATTCTAATGGAGGAGTACACACA 57.379 37.500 0.00 0.0 0.00 3.72
686 831 3.646162 TGGAGGAGTACACACAGTGAATT 59.354 43.478 7.81 0.0 36.96 2.17
713 858 9.408069 GACCTCGTTAACCAGATAATGTTATAG 57.592 37.037 1.33 0.0 0.00 1.31
850 995 4.695455 TGCTTTGGTCTAAGAATCTTTCCG 59.305 41.667 0.00 0.0 0.00 4.30
876 1021 9.447040 GTTGTCAATAAAACTGAAGTTCCTTAC 57.553 33.333 0.00 0.0 37.25 2.34
896 1041 7.051000 CCTTACTCTCTTATCCTTTTTCCCAG 58.949 42.308 0.00 0.0 0.00 4.45
1242 1388 7.037730 CCCACATCCTAATCTCAATATTCCTCT 60.038 40.741 0.00 0.0 0.00 3.69
1244 1390 7.758980 CACATCCTAATCTCAATATTCCTCTCG 59.241 40.741 0.00 0.0 0.00 4.04
1684 1832 7.970061 TGATTTTGCTCTCTTTTTCATATTCCG 59.030 33.333 0.00 0.0 0.00 4.30
1829 1977 1.915141 CAGGATTTGTCTGCCTGGTT 58.085 50.000 0.00 0.0 44.24 3.67
1830 1978 2.242043 CAGGATTTGTCTGCCTGGTTT 58.758 47.619 0.00 0.0 44.24 3.27
1831 1979 2.629617 CAGGATTTGTCTGCCTGGTTTT 59.370 45.455 0.00 0.0 44.24 2.43
1914 2062 5.893897 AAAGTTGATGATGCTCTCTTTCC 57.106 39.130 0.00 0.0 0.00 3.13
1950 2098 4.161377 ACCAAAACTTGCACCAACTTATGT 59.839 37.500 0.00 0.0 0.00 2.29
1972 2120 6.962182 TGTTGGATATTGTCATTCTTCCTCT 58.038 36.000 0.00 0.0 0.00 3.69
1990 2138 6.479972 TCCTCTTTTGTTTGAGTCTGACTA 57.520 37.500 10.86 0.0 0.00 2.59
1991 2139 6.884832 TCCTCTTTTGTTTGAGTCTGACTAA 58.115 36.000 10.86 0.0 0.00 2.24
2028 2176 5.412594 AGGTGCTGTATGAGTAATTGTTGTG 59.587 40.000 0.00 0.0 0.00 3.33
2044 2192 6.385649 TTGTTGTGTAACCTTTCTTCATCC 57.614 37.500 0.00 0.0 35.92 3.51
2056 2204 0.036010 CTTCATCCGTGGGTGCTCTT 60.036 55.000 0.00 0.0 0.00 2.85
2319 2475 1.416030 GCCACACCAATTGTTTCCCTT 59.584 47.619 4.43 0.0 35.67 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 9.940166 AAAGAAAGTTATGTTACAAACTTACCG 57.060 29.630 18.41 0.00 43.35 4.02
173 174 3.678056 ATACAGAGCAAACGTTCTCCA 57.322 42.857 12.09 1.19 0.00 3.86
208 211 9.362151 GAATGGGGAAATAAATCTGTGGTATTA 57.638 33.333 0.00 0.00 0.00 0.98
210 213 7.287696 GTGAATGGGGAAATAAATCTGTGGTAT 59.712 37.037 0.00 0.00 0.00 2.73
280 283 7.775093 AGTAAATTGACATACCATGCTACACAT 59.225 33.333 0.00 0.00 40.66 3.21
316 320 8.547967 AATAAACTGAAGCAAGTATCTCGAAA 57.452 30.769 0.00 0.00 0.00 3.46
317 321 8.547967 AAATAAACTGAAGCAAGTATCTCGAA 57.452 30.769 0.00 0.00 0.00 3.71
318 322 8.547967 AAAATAAACTGAAGCAAGTATCTCGA 57.452 30.769 0.00 0.00 0.00 4.04
319 323 7.905493 GGAAAATAAACTGAAGCAAGTATCTCG 59.095 37.037 0.00 0.00 0.00 4.04
320 324 8.951243 AGGAAAATAAACTGAAGCAAGTATCTC 58.049 33.333 0.00 0.00 0.00 2.75
321 325 8.870075 AGGAAAATAAACTGAAGCAAGTATCT 57.130 30.769 0.00 0.00 0.00 1.98
487 632 3.719268 ACAACTGAATATGCTCCCACA 57.281 42.857 0.00 0.00 0.00 4.17
609 754 2.433970 AGGCTCTAGACTGGCAAAGATC 59.566 50.000 8.07 0.00 27.68 2.75
628 773 2.846827 AGTACCCCTCCATCAGAAAAGG 59.153 50.000 0.00 0.00 0.00 3.11
678 823 4.062293 TGGTTAACGAGGTCAATTCACTG 58.938 43.478 0.00 0.00 0.00 3.66
679 824 4.039973 TCTGGTTAACGAGGTCAATTCACT 59.960 41.667 16.45 0.00 0.00 3.41
686 831 5.670792 ACATTATCTGGTTAACGAGGTCA 57.329 39.130 16.45 2.65 0.00 4.02
713 858 7.169308 CAGCTGCATCAGATTCATTTATTTTCC 59.831 37.037 0.00 0.00 32.44 3.13
876 1021 6.597280 CACTTCTGGGAAAAAGGATAAGAGAG 59.403 42.308 0.00 0.00 0.00 3.20
914 1059 6.497954 AGGATGATTGGAAAAGGAACAAATCA 59.502 34.615 0.00 0.00 0.00 2.57
1242 1388 1.669115 GAAAGCTGGAGTGCTGCGA 60.669 57.895 7.83 0.00 43.24 5.10
1244 1390 0.888285 ACAGAAAGCTGGAGTGCTGC 60.888 55.000 5.33 5.33 46.60 5.25
1371 1517 5.468072 GCATCACATAACCAATAGACCAGAG 59.532 44.000 0.00 0.00 0.00 3.35
1497 1643 7.277760 GTGTCACATAAGAGCACATATACACAA 59.722 37.037 0.00 0.00 34.12 3.33
1516 1664 3.799366 ACAAATCTAACCACGTGTCACA 58.201 40.909 15.65 0.00 0.00 3.58
1517 1665 4.806342 AACAAATCTAACCACGTGTCAC 57.194 40.909 15.65 0.00 0.00 3.67
1684 1832 8.723942 AAGTGACTAATGTTAATCTGATCACC 57.276 34.615 0.00 0.00 35.61 4.02
1744 1892 2.676471 AGGCGAAATGTGGCACCC 60.676 61.111 16.26 7.73 0.00 4.61
1829 1977 4.650734 TGCTGTTGATCAGTACCATCAAA 58.349 39.130 15.94 8.55 45.23 2.69
1830 1978 4.284829 TGCTGTTGATCAGTACCATCAA 57.715 40.909 11.96 11.96 45.23 2.57
1831 1979 3.979101 TGCTGTTGATCAGTACCATCA 57.021 42.857 0.00 1.70 45.23 3.07
1914 2062 5.280945 CAAGTTTTGGTGTATGTTGTCCTG 58.719 41.667 0.00 0.00 0.00 3.86
1950 2098 8.742777 CAAAAGAGGAAGAATGACAATATCCAA 58.257 33.333 0.00 0.00 0.00 3.53
2028 2176 3.007635 CCCACGGATGAAGAAAGGTTAC 58.992 50.000 0.00 0.00 0.00 2.50
2044 2192 0.034059 AAGACTCAAGAGCACCCACG 59.966 55.000 0.00 0.00 0.00 4.94
2208 2364 1.067295 AGACCCACCTCAGCAATCAA 58.933 50.000 0.00 0.00 0.00 2.57
2300 2456 3.387699 AGAAAGGGAAACAATTGGTGTGG 59.612 43.478 10.83 0.00 40.60 4.17
2301 2457 4.670896 AGAAAGGGAAACAATTGGTGTG 57.329 40.909 10.83 0.00 40.60 3.82
2319 2475 4.637276 TCACGAGGTCAAATTGCTTAGAA 58.363 39.130 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.