Multiple sequence alignment - TraesCS7D01G253700

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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 TraesCS7D01G253700 chr7D 100.000 2978 0 0 1 2978 230380967 230377990 0.000000e+00 5500.0
1 TraesCS7D01G253700 chr7A 94.665 2343 81 14 1 2306 242949481 242947146 0.000000e+00 3594.0
2 TraesCS7D01G253700 chr7A 92.937 623 26 4 2370 2978 242947145 242946527 0.000000e+00 891.0
3 TraesCS7D01G253700 chr7B 95.923 2232 57 11 772 2978 201261495 201259273 0.000000e+00 3587.0
4 TraesCS7D01G253700 chr7B 92.188 64 5 0 664 727 201261554 201261491 1.140000e-14 91.6


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 TraesCS7D01G253700 chr7D 230377990 230380967 2977 True 5500.0 5500 100.0000 1 2978 1 chr7D.!!$R1 2977
1 TraesCS7D01G253700 chr7A 242946527 242949481 2954 True 2242.5 3594 93.8010 1 2978 2 chr7A.!!$R1 2977
2 TraesCS7D01G253700 chr7B 201259273 201261554 2281 True 1839.3 3587 94.0555 664 2978 2 chr7B.!!$R1 2314

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
46 47 1.885887 CTTCCCAAAAGATGCGACCAA 59.114 47.619 0.0 0.0 0.00 3.67 F
220 227 2.964978 GCAAAGTGCGGGCTTCAT 59.035 55.556 0.0 0.0 31.71 2.57 F
1645 1683 2.642154 TAAAACCCTGCTTCGGTTCA 57.358 45.000 3.6 0.0 42.90 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 1683 0.905357 GGCAGGGAGTCAGTGTACAT 59.095 55.000 0.00 0.0 0.00 2.29 R
1656 1694 1.897225 CTCTGTCCACAGGCAGGGAG 61.897 65.000 6.87 0.0 43.91 4.30 R
2672 2727 2.750657 GGATGAGGTGCCAGGGGAG 61.751 68.421 0.00 0.0 0.00 4.30 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
46 47 1.885887 CTTCCCAAAAGATGCGACCAA 59.114 47.619 0.00 0.00 0.00 3.67
220 227 2.964978 GCAAAGTGCGGGCTTCAT 59.035 55.556 0.00 0.00 31.71 2.57
304 311 5.218885 CAGAGTTATAATCGAGAGGCACAG 58.781 45.833 0.00 0.00 0.00 3.66
338 345 4.264172 ACATGGGGAACTAATTAAGCCACA 60.264 41.667 0.00 5.60 36.31 4.17
363 370 6.150307 ACCGCAAAACAATAATACATGACTGA 59.850 34.615 0.00 0.00 0.00 3.41
365 372 6.468956 CGCAAAACAATAATACATGACTGACC 59.531 38.462 0.00 0.00 0.00 4.02
366 373 7.312154 GCAAAACAATAATACATGACTGACCA 58.688 34.615 0.00 0.00 0.00 4.02
367 374 7.485913 GCAAAACAATAATACATGACTGACCAG 59.514 37.037 0.00 0.00 0.00 4.00
520 527 4.870123 TTTAGCAATGGCATTGTTGTCT 57.130 36.364 33.64 25.36 44.61 3.41
521 528 4.439305 TTAGCAATGGCATTGTTGTCTC 57.561 40.909 33.64 19.79 44.61 3.36
572 579 5.221541 GGTGGTATTTTCAATGTGGGTGAAA 60.222 40.000 0.00 0.00 41.91 2.69
576 583 7.233553 TGGTATTTTCAATGTGGGTGAAATACA 59.766 33.333 14.80 0.00 42.82 2.29
577 584 8.257306 GGTATTTTCAATGTGGGTGAAATACAT 58.743 33.333 14.80 0.00 42.82 2.29
644 651 3.192922 GACGCGGGTGGAATTCGG 61.193 66.667 10.96 0.00 0.00 4.30
760 767 3.986006 ACGCGCCAACGAGGAAGA 61.986 61.111 5.73 0.00 44.04 2.87
885 892 9.871238 TTCAGTTGTTCAGTTCTATATAAGGTC 57.129 33.333 0.00 0.00 0.00 3.85
888 926 8.915036 AGTTGTTCAGTTCTATATAAGGTCGAT 58.085 33.333 0.00 0.00 0.00 3.59
911 949 9.631452 CGATTCAGATTGATATAGAGTTTGCTA 57.369 33.333 0.00 0.00 0.00 3.49
1446 1484 2.968574 GGACATAGAGAGCCATCTTGGA 59.031 50.000 0.00 0.00 40.96 3.53
1510 1548 3.372795 AAAGGCGAGACGTTTCACA 57.627 47.368 6.91 0.00 30.71 3.58
1645 1683 2.642154 TAAAACCCTGCTTCGGTTCA 57.358 45.000 3.60 0.00 42.90 3.18
1656 1694 2.412089 GCTTCGGTTCATGTACACTGAC 59.588 50.000 0.00 0.00 0.00 3.51
1668 1706 1.004080 CACTGACTCCCTGCCTGTG 60.004 63.158 0.00 0.00 0.00 3.66
1680 1718 1.217779 GCCTGTGGACAGAGAGCTC 59.782 63.158 5.27 5.27 46.59 4.09
1690 1728 0.181587 CAGAGAGCTCGGGGACTCTA 59.818 60.000 8.37 0.00 43.26 2.43
2194 2233 3.833650 TGGAGGAAATCGTGGTACAGTTA 59.166 43.478 0.00 0.00 41.80 2.24
2475 2517 5.705441 AGTTAAAATGAGAGAATTGCCGTGA 59.295 36.000 0.00 0.00 0.00 4.35
2538 2580 7.444183 TGATTTCCTAACAATCGTTTCACTCTT 59.556 33.333 0.00 0.00 36.52 2.85
2672 2727 3.055021 CCCTCCTTCCTTCCTTACTTCAC 60.055 52.174 0.00 0.00 0.00 3.18
2962 3017 6.978343 TGGAGACATCTTTATGGTTTTACG 57.022 37.500 0.00 0.00 37.43 3.18
2963 3018 6.703319 TGGAGACATCTTTATGGTTTTACGA 58.297 36.000 0.00 0.00 37.43 3.43
2972 3028 9.620660 ATCTTTATGGTTTTACGAAATGTGTTC 57.379 29.630 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 5.721000 TCCAGGACAAATAAGGCAAATTGAT 59.279 36.000 0.00 0.00 0.00 2.57
200 207 0.955428 TGAAGCCCGCACTTTGCTAG 60.955 55.000 0.00 0.00 42.25 3.42
232 239 4.949856 ACCTCGCAAAAATAGGTTCATCAT 59.050 37.500 0.00 0.00 40.82 2.45
282 289 4.279671 CCTGTGCCTCTCGATTATAACTCT 59.720 45.833 0.00 0.00 0.00 3.24
338 345 6.150307 TCAGTCATGTATTATTGTTTTGCGGT 59.850 34.615 0.00 0.00 0.00 5.68
363 370 1.303074 CATCAGTGGTGCTGCTGGT 60.303 57.895 0.00 0.00 44.66 4.00
365 372 3.587095 CCATCAGTGGTGCTGCTG 58.413 61.111 0.00 0.00 44.66 4.41
472 479 9.280456 AGAGTATTCCCTAAATTACTCCTTTCA 57.720 33.333 5.56 0.00 33.28 2.69
572 579 6.482524 TGGGCTAGTTCTCGACTATATGTAT 58.517 40.000 0.00 0.00 40.01 2.29
576 583 5.244189 TCTGGGCTAGTTCTCGACTATAT 57.756 43.478 0.00 0.00 40.01 0.86
577 584 4.701651 TCTGGGCTAGTTCTCGACTATA 57.298 45.455 0.00 0.00 40.01 1.31
754 761 1.305381 CCACTCCTCCCGTCTTCCT 60.305 63.158 0.00 0.00 0.00 3.36
785 792 3.255379 GTCGGAAGCTAAGGCGCG 61.255 66.667 0.00 0.00 44.37 6.86
884 891 8.363390 AGCAAACTCTATATCAATCTGAATCGA 58.637 33.333 0.00 0.00 0.00 3.59
885 892 8.531622 AGCAAACTCTATATCAATCTGAATCG 57.468 34.615 0.00 0.00 0.00 3.34
888 926 9.147732 TCCTAGCAAACTCTATATCAATCTGAA 57.852 33.333 0.00 0.00 0.00 3.02
1281 1319 2.768698 CTCCTAGAGCTGATGCCATTG 58.231 52.381 0.00 0.00 40.80 2.82
1446 1484 2.430610 GGAGCGATCCAGCAGACCT 61.431 63.158 16.44 0.00 40.15 3.85
1510 1548 2.746277 GAGAATTGCCCGGTGCGT 60.746 61.111 0.00 0.00 45.60 5.24
1579 1617 1.790755 GTGACACACGCCATTGTAGA 58.209 50.000 0.00 0.00 0.00 2.59
1645 1683 0.905357 GGCAGGGAGTCAGTGTACAT 59.095 55.000 0.00 0.00 0.00 2.29
1656 1694 1.897225 CTCTGTCCACAGGCAGGGAG 61.897 65.000 6.87 0.00 43.91 4.30
1668 1706 2.043852 TCCCCGAGCTCTCTGTCC 60.044 66.667 12.85 0.00 0.00 4.02
1680 1718 3.445450 CCATATCAGTGATAGAGTCCCCG 59.555 52.174 17.52 0.50 0.00 5.73
1690 1728 5.704515 GCAGATGCTTTACCATATCAGTGAT 59.295 40.000 11.12 11.12 38.21 3.06
2194 2233 4.346127 TGCACATCCATAGCTCTGTATCTT 59.654 41.667 0.00 0.00 0.00 2.40
2571 2613 8.906636 TCGTTAGCTATATATGGTTTTCGATC 57.093 34.615 0.00 0.00 0.00 3.69
2672 2727 2.750657 GGATGAGGTGCCAGGGGAG 61.751 68.421 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.