Multiple sequence alignment - TraesCS4A01G171000

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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 TraesCS4A01G171000 chr4A 100.000 2528 0 0 1 2528 432419670 432422197 0 4669
1 TraesCS4A01G171000 chr2D 98.104 2532 44 3 1 2528 635037259 635039790 0 4407
2 TraesCS4A01G171000 chr7B 97.948 2534 46 4 1 2528 743066304 743068837 0 4386
3 TraesCS4A01G171000 chr7A 97.905 2530 50 3 1 2528 120828849 120826321 0 4375
4 TraesCS4A01G171000 chr2A 97.869 2534 48 3 1 2528 735172798 735175331 0 4375
5 TraesCS4A01G171000 chr5A 97.831 2536 47 5 1 2528 16623276 16620741 0 4372
6 TraesCS4A01G171000 chr5A 97.512 2532 56 4 1 2526 300048564 300051094 0 4320
7 TraesCS4A01G171000 chr3B 97.826 2530 52 3 1 2528 201635804 201633276 0 4364
8 TraesCS4A01G171000 chr5B 97.708 2530 53 4 1 2526 713046212 713043684 0 4346


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 TraesCS4A01G171000 chr4A 432419670 432422197 2527 False 4669 4669 100.000 1 2528 1 chr4A.!!$F1 2527
1 TraesCS4A01G171000 chr2D 635037259 635039790 2531 False 4407 4407 98.104 1 2528 1 chr2D.!!$F1 2527
2 TraesCS4A01G171000 chr7B 743066304 743068837 2533 False 4386 4386 97.948 1 2528 1 chr7B.!!$F1 2527
3 TraesCS4A01G171000 chr7A 120826321 120828849 2528 True 4375 4375 97.905 1 2528 1 chr7A.!!$R1 2527
4 TraesCS4A01G171000 chr2A 735172798 735175331 2533 False 4375 4375 97.869 1 2528 1 chr2A.!!$F1 2527
5 TraesCS4A01G171000 chr5A 16620741 16623276 2535 True 4372 4372 97.831 1 2528 1 chr5A.!!$R1 2527
6 TraesCS4A01G171000 chr5A 300048564 300051094 2530 False 4320 4320 97.512 1 2526 1 chr5A.!!$F1 2525
7 TraesCS4A01G171000 chr3B 201633276 201635804 2528 True 4364 4364 97.826 1 2528 1 chr3B.!!$R1 2527
8 TraesCS4A01G171000 chr5B 713043684 713046212 2528 True 4346 4346 97.708 1 2526 1 chr5B.!!$R1 2525

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
844 849 0.54851 GGGGCTAGCCTCATGACTTT 59.451 55.0 32.18 0.0 36.36 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2084 1.001641 GTCTCCACCTGCTGCCAAT 60.002 57.895 0.0 0.0 0.0 3.16 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
44 45 2.346099 TTACGTTAAACTCCGTCCGG 57.654 50.000 0.00 0.00 38.43 5.14
233 235 1.549170 GAGGTACCTTTTCTCGAGCCA 59.451 52.381 17.53 0.00 0.00 4.75
238 240 2.467880 ACCTTTTCTCGAGCCATCCTA 58.532 47.619 7.81 0.00 0.00 2.94
252 254 2.480419 CCATCCTATTTTCCGTCATCGC 59.520 50.000 0.00 0.00 35.54 4.58
268 270 2.831685 TCGCCTTCTTTAGAGTTGCA 57.168 45.000 0.00 0.00 0.00 4.08
337 339 7.348680 ACAGGCTTATCTATTTTATGGGGAT 57.651 36.000 0.00 0.00 0.00 3.85
397 399 1.302511 GCTCCTTCCACTGCCGAAA 60.303 57.895 0.00 0.00 0.00 3.46
662 664 1.084289 GGCGTAACAAAGCTACCTGG 58.916 55.000 0.00 0.00 0.00 4.45
694 696 3.065371 GGTGCACCTTAGATTGAAATCGG 59.935 47.826 29.12 0.00 40.35 4.18
746 748 8.873186 TTTAGAAAGATTCCCGGATAAAGTTT 57.127 30.769 0.73 1.29 0.00 2.66
844 849 0.548510 GGGGCTAGCCTCATGACTTT 59.451 55.000 32.18 0.00 36.36 2.66
1129 1134 2.183478 ACGATTGATTGGTCTGTGCA 57.817 45.000 0.00 0.00 0.00 4.57
1188 1193 5.533528 TCGGATACAATTCGATCCTTCTACA 59.466 40.000 11.62 0.00 39.69 2.74
1222 1227 0.400213 TGTGGAAAGCCTTCGATGGT 59.600 50.000 17.82 0.27 34.31 3.55
1437 1442 9.834628 GATCCTCTACTATTCTATGTTCTTTCG 57.165 37.037 0.00 0.00 0.00 3.46
1464 1469 2.446435 GTGCCAATCCCTATGTTGTGT 58.554 47.619 0.00 0.00 0.00 3.72
1743 1749 0.621571 TATGCAGGAAGGGGTGCTCT 60.622 55.000 0.00 0.00 40.54 4.09
1928 1937 4.753186 AGGGATAATCGTCCAGGTCTTAT 58.247 43.478 0.00 0.00 40.17 1.73
2040 2052 1.073098 AACAAACGGAGGGGAGGATT 58.927 50.000 0.00 0.00 0.00 3.01
2072 2084 7.698506 TCAGTAGAATTCCGAAGAAAGACTA 57.301 36.000 0.65 0.00 35.09 2.59
2141 2153 2.443016 AGGGTAGAGCTCGGCAGG 60.443 66.667 8.37 0.00 0.00 4.85
2168 2180 6.071560 GGTTCAAGAATAGGGTAGGGTTTTTG 60.072 42.308 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 235 2.368875 AGGCGATGACGGAAAATAGGAT 59.631 45.455 0.00 0.0 40.15 3.24
238 240 2.403252 AGAAGGCGATGACGGAAAAT 57.597 45.000 0.00 0.0 40.15 1.82
252 254 4.771590 TTGCATGCAACTCTAAAGAAGG 57.228 40.909 28.80 0.0 0.00 3.46
268 270 2.615447 CAATCGGCATCAGTAGTTGCAT 59.385 45.455 0.00 0.0 41.24 3.96
337 339 5.681639 TCTCATCCAAGATAGTGTCTCGTA 58.318 41.667 0.00 0.0 35.67 3.43
600 602 1.404391 GTCATAGCCGAAGTCGAAGGA 59.596 52.381 1.43 0.0 43.02 3.36
662 664 2.429927 AGGTGCACCTTGCCTTTTC 58.570 52.632 33.20 3.2 46.09 2.29
764 766 7.360522 CCCATGTATGCGCGTTTATTTAGATTA 60.361 37.037 7.78 0.0 0.00 1.75
803 805 3.519510 CCCCTGAATGAAGAAGTAGTGGA 59.480 47.826 0.00 0.0 0.00 4.02
1029 1034 6.436027 ACAGAGAATAGGACCACTTAGATCA 58.564 40.000 0.00 0.0 0.00 2.92
1073 1078 8.426569 TGAAGAATTTGGAATGAAAAGAGGAT 57.573 30.769 0.00 0.0 0.00 3.24
1437 1442 0.393808 TAGGGATTGGCACGCTTTCC 60.394 55.000 0.09 0.0 32.98 3.13
1464 1469 3.243670 CGAATAGAAGATGCTCAGCTCCA 60.244 47.826 0.00 0.0 0.00 3.86
1743 1749 1.354101 CACCCCCTACACACACCTAA 58.646 55.000 0.00 0.0 0.00 2.69
2040 2052 2.094390 CGGAATTCTACTGAACGGGTCA 60.094 50.000 5.23 0.0 34.71 4.02
2072 2084 1.001641 GTCTCCACCTGCTGCCAAT 60.002 57.895 0.00 0.0 0.00 3.16
2141 2153 2.442126 CCCTACCCTATTCTTGAACCCC 59.558 54.545 0.00 0.0 0.00 4.95
2148 2160 5.250982 CGTCAAAAACCCTACCCTATTCTT 58.749 41.667 0.00 0.0 0.00 2.52


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

AutoCloner maintained by Alex Coulton.