Multiple sequence alignment - TraesCS5D01G073800

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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 TraesCS5D01G073800 chr5D 100.000 2183 0 0 1 2183 72902330 72900148 0.000000e+00 4032
1 TraesCS5D01G073800 chr5A 95.032 2194 85 15 1 2183 67471143 67468963 0.000000e+00 3426
2 TraesCS5D01G073800 chr5B 93.491 2197 94 21 1 2183 79804819 79802658 0.000000e+00 3219
3 TraesCS5D01G073800 chr3B 87.886 875 79 14 1323 2183 125783006 125783867 0.000000e+00 1003
4 TraesCS5D01G073800 chr3D 88.224 501 57 2 1245 1744 79509240 79509739 4.010000e-167 597
5 TraesCS5D01G073800 chr3D 86.801 447 42 10 1741 2183 79509835 79510268 1.170000e-132 483
6 TraesCS5D01G073800 chr3D 80.727 275 32 11 869 1134 79508895 79509157 6.150000e-46 195


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 TraesCS5D01G073800 chr5D 72900148 72902330 2182 True 4032 4032 100.000000 1 2183 1 chr5D.!!$R1 2182
1 TraesCS5D01G073800 chr5A 67468963 67471143 2180 True 3426 3426 95.032000 1 2183 1 chr5A.!!$R1 2182
2 TraesCS5D01G073800 chr5B 79802658 79804819 2161 True 3219 3219 93.491000 1 2183 1 chr5B.!!$R1 2182
3 TraesCS5D01G073800 chr3B 125783006 125783867 861 False 1003 1003 87.886000 1323 2183 1 chr3B.!!$F1 860
4 TraesCS5D01G073800 chr3D 79508895 79510268 1373 False 425 597 85.250667 869 2183 3 chr3D.!!$F1 1314

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
982 1002 0.602372 GGGCCTCAGCGATTCATCTC 60.602 60.0 0.84 0.0 41.24 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 2060 2.774439 ACCCGATTATCAATTTGCGC 57.226 45.0 0.0 0.0 0.0 6.09 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
321 322 4.770362 TGGGGCTCGATGGACCGA 62.770 66.667 0.00 0.00 34.56 4.69
327 328 1.516386 CTCGATGGACCGAACACCG 60.516 63.158 0.00 0.00 38.17 4.94
329 330 3.186047 GATGGACCGAACACCGCG 61.186 66.667 0.00 0.00 36.84 6.46
371 372 2.733593 GTGTCGGTGCAGGACGTC 60.734 66.667 7.13 7.13 37.22 4.34
439 440 3.244579 CGCTTTCCGTAGCCAAGTTATAC 59.755 47.826 0.00 0.00 37.90 1.47
451 452 0.978151 AGTTATACCCCACGTGCACA 59.022 50.000 18.64 0.00 0.00 4.57
455 456 0.605319 ATACCCCACGTGCACACAAG 60.605 55.000 18.64 2.44 0.00 3.16
457 458 1.821759 CCCCACGTGCACACAAGAA 60.822 57.895 18.64 0.00 0.00 2.52
511 514 2.814336 GGTGAAGTTCTCCATGGTGAAC 59.186 50.000 36.25 36.25 44.27 3.18
555 560 5.812127 TGCACATGTATTACTAGCACAAGAG 59.188 40.000 0.00 0.00 0.00 2.85
675 680 6.518208 TGATCATCATTGCAACAAGATCAA 57.482 33.333 22.72 12.79 37.89 2.57
676 681 6.926313 TGATCATCATTGCAACAAGATCAAA 58.074 32.000 22.72 9.47 37.89 2.69
711 716 2.305927 ACAGAGTTGTTCCCATCCGAAT 59.694 45.455 0.00 0.00 32.28 3.34
718 723 5.532406 AGTTGTTCCCATCCGAATCATATTG 59.468 40.000 0.00 0.00 0.00 1.90
833 838 2.492881 TCGCACAACTTATCCGGACTTA 59.507 45.455 6.12 0.00 0.00 2.24
955 970 3.195825 AGTCCAGAACAGCATACTACACC 59.804 47.826 0.00 0.00 0.00 4.16
958 974 3.449018 CCAGAACAGCATACTACACCTCT 59.551 47.826 0.00 0.00 0.00 3.69
975 991 0.687757 TCTAACAGGGCCTCAGCGAT 60.688 55.000 0.95 0.00 41.24 4.58
982 1002 0.602372 GGGCCTCAGCGATTCATCTC 60.602 60.000 0.84 0.00 41.24 2.75
991 1011 5.482006 TCAGCGATTCATCTCAAGAAGAAA 58.518 37.500 2.20 0.00 37.61 2.52
993 1013 6.091849 TCAGCGATTCATCTCAAGAAGAAAAG 59.908 38.462 2.20 1.70 37.61 2.27
1252 1279 2.954684 CGGGGCTGTACTTGCAGGA 61.955 63.158 1.40 0.00 37.00 3.86
1553 1581 2.534757 GCATCGTTAAGTTCTCTACCGC 59.465 50.000 0.00 0.00 0.00 5.68
1603 1631 2.047655 CCAACACCGCGGCTCTTA 60.048 61.111 28.58 0.00 0.00 2.10
1630 1658 4.362279 CACAGGGAACAATGTGTTGAAAG 58.638 43.478 0.00 0.00 41.28 2.62
1883 2014 2.290260 ACTGAAGGGCACGAATGATCAA 60.290 45.455 0.00 0.00 0.00 2.57
1884 2015 2.083774 TGAAGGGCACGAATGATCAAC 58.916 47.619 0.00 0.00 0.00 3.18
1921 2052 2.496070 TGGTACCAGACAAGATCCTTCG 59.504 50.000 11.60 0.00 0.00 3.79
1929 2060 5.766150 AGACAAGATCCTTCGTCTGATAG 57.234 43.478 3.82 0.00 37.34 2.08
2075 2206 7.333528 AGTCAGCAAGTTTGTTCTTATTTCA 57.666 32.000 0.00 0.00 0.00 2.69
2081 2220 8.337532 AGCAAGTTTGTTCTTATTTCAAAATGC 58.662 29.630 14.83 14.83 41.25 3.56
2088 2227 9.545105 TTGTTCTTATTTCAAAATGCTCATTGT 57.455 25.926 0.00 0.00 0.00 2.71
2122 2262 7.475137 CCAAAAAGGTTATGGTCTTATGGAA 57.525 36.000 0.00 0.00 34.61 3.53
2123 2263 7.547227 CCAAAAAGGTTATGGTCTTATGGAAG 58.453 38.462 0.00 0.00 34.61 3.46
2124 2264 7.396055 CCAAAAAGGTTATGGTCTTATGGAAGA 59.604 37.037 0.00 0.00 39.47 2.87
2125 2265 8.971073 CAAAAAGGTTATGGTCTTATGGAAGAT 58.029 33.333 0.00 0.00 43.58 2.40
2126 2266 8.753497 AAAAGGTTATGGTCTTATGGAAGATC 57.247 34.615 0.00 0.00 43.58 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 4.988716 ACCCACTCCTCGCCGTGA 62.989 66.667 0.00 0.00 33.04 4.35
439 440 1.380403 TTTCTTGTGTGCACGTGGGG 61.380 55.000 18.88 1.42 0.00 4.96
511 514 4.274705 TGCAACTGTACAAGTACAACCATG 59.725 41.667 13.45 10.63 44.47 3.66
514 517 3.623960 TGTGCAACTGTACAAGTACAACC 59.376 43.478 13.45 4.17 44.47 3.77
522 525 7.064134 GCTAGTAATACATGTGCAACTGTACAA 59.936 37.037 9.11 1.83 43.49 2.41
555 560 0.868406 CCTTCGAACCTGTGAGTTGC 59.132 55.000 0.00 0.00 0.00 4.17
675 680 2.169352 ACTCTGTCTGTGCTCTTGTGTT 59.831 45.455 0.00 0.00 0.00 3.32
676 681 1.759445 ACTCTGTCTGTGCTCTTGTGT 59.241 47.619 0.00 0.00 0.00 3.72
711 716 0.669619 CAATGCTGCGGCCAATATGA 59.330 50.000 16.57 0.00 37.74 2.15
718 723 0.249031 GTATTTCCAATGCTGCGGCC 60.249 55.000 16.57 0.00 37.74 6.13
955 970 1.142748 CGCTGAGGCCCTGTTAGAG 59.857 63.158 0.00 0.00 34.44 2.43
958 974 0.178068 GAATCGCTGAGGCCCTGTTA 59.822 55.000 0.00 0.00 34.44 2.41
966 982 3.449528 TCTTGAGATGAATCGCTGAGG 57.550 47.619 0.00 0.00 0.00 3.86
975 991 7.735917 TCCTGTACTTTTCTTCTTGAGATGAA 58.264 34.615 5.51 5.51 36.72 2.57
982 1002 5.471456 AGCACATCCTGTACTTTTCTTCTTG 59.529 40.000 0.00 0.00 0.00 3.02
991 1011 3.583086 ACCTTGTAGCACATCCTGTACTT 59.417 43.478 0.00 0.00 0.00 2.24
993 1013 3.262420 CACCTTGTAGCACATCCTGTAC 58.738 50.000 0.00 0.00 0.00 2.90
1184 1210 5.535783 TGCAATTCTGGACAGATGAAAAGAA 59.464 36.000 2.42 0.00 37.29 2.52
1186 1212 5.381174 TGCAATTCTGGACAGATGAAAAG 57.619 39.130 2.42 0.00 37.29 2.27
1205 1231 5.645067 CCATTCTCAGTAAATCTGTCTTGCA 59.355 40.000 0.00 0.00 43.97 4.08
1252 1279 4.140536 CAAGAACTCAAGCTTTTCCTCCT 58.859 43.478 0.00 0.00 0.00 3.69
1553 1581 5.591877 AGCAGATATTACAAAAGGCTTCCAG 59.408 40.000 0.00 0.00 0.00 3.86
1599 1627 3.517296 TTGTTCCCTGTGGCATTAAGA 57.483 42.857 0.00 0.00 0.00 2.10
1603 1631 1.619827 CACATTGTTCCCTGTGGCATT 59.380 47.619 0.00 0.00 39.24 3.56
1609 1637 3.384467 CCTTTCAACACATTGTTCCCTGT 59.616 43.478 0.00 0.00 38.77 4.00
1630 1658 1.061546 TCACAACTGACCTAACCCCC 58.938 55.000 0.00 0.00 0.00 5.40
1883 2014 3.933861 ACCAAAGGTCACTTGAAGAGT 57.066 42.857 0.00 0.00 39.89 3.24
1884 2015 4.065789 GGTACCAAAGGTCACTTGAAGAG 58.934 47.826 7.15 0.00 36.93 2.85
1921 2052 6.011879 CGATTATCAATTTGCGCTATCAGAC 58.988 40.000 9.73 0.00 0.00 3.51
1929 2060 2.774439 ACCCGATTATCAATTTGCGC 57.226 45.000 0.00 0.00 0.00 6.09
2033 2164 7.487484 TGCTGACTTTTGAAATATTGAACACA 58.513 30.769 0.00 0.00 0.00 3.72
2081 2220 8.524870 CCTTTTTGGTTAGATCAAACAATGAG 57.475 34.615 8.53 9.02 43.31 2.90


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

AutoCloner maintained by Alex Coulton.