Multiple sequence alignment - TraesCS4A01G244700

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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 TraesCS4A01G244700 chr4A 100.000 2378 0 0 1 2378 554940585 554938208 0 4392
1 TraesCS4A01G244700 chrUn 97.248 2362 64 1 1 2361 245706824 245704463 0 4000
2 TraesCS4A01G244700 chrUn 97.036 2362 69 1 1 2361 67500252 67502613 0 3973
3 TraesCS4A01G244700 chrUn 96.994 2362 70 1 1 2361 291536196 291533835 0 3967
4 TraesCS4A01G244700 chrUn 96.952 2362 71 1 1 2361 229309471 229311832 0 3962
5 TraesCS4A01G244700 chrUn 96.782 2362 75 1 1 2361 199875580 199873219 0 3940
6 TraesCS4A01G244700 chrUn 96.782 2362 75 1 1 2361 199905500 199903139 0 3940
7 TraesCS4A01G244700 chr5D 96.994 2362 70 1 1 2361 18999680 18997319 0 3967
8 TraesCS4A01G244700 chr1A 96.867 2362 73 1 1 2362 403211 400851 0 3951
9 TraesCS4A01G244700 chr6B 96.825 2362 74 1 1 2361 111686033 111688394 0 3945


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 TraesCS4A01G244700 chr4A 554938208 554940585 2377 True 4392 4392 100.000 1 2378 1 chr4A.!!$R1 2377
1 TraesCS4A01G244700 chrUn 245704463 245706824 2361 True 4000 4000 97.248 1 2361 1 chrUn.!!$R3 2360
2 TraesCS4A01G244700 chrUn 67500252 67502613 2361 False 3973 3973 97.036 1 2361 1 chrUn.!!$F1 2360
3 TraesCS4A01G244700 chrUn 291533835 291536196 2361 True 3967 3967 96.994 1 2361 1 chrUn.!!$R4 2360
4 TraesCS4A01G244700 chrUn 229309471 229311832 2361 False 3962 3962 96.952 1 2361 1 chrUn.!!$F2 2360
5 TraesCS4A01G244700 chrUn 199873219 199875580 2361 True 3940 3940 96.782 1 2361 1 chrUn.!!$R1 2360
6 TraesCS4A01G244700 chrUn 199903139 199905500 2361 True 3940 3940 96.782 1 2361 1 chrUn.!!$R2 2360
7 TraesCS4A01G244700 chr5D 18997319 18999680 2361 True 3967 3967 96.994 1 2361 1 chr5D.!!$R1 2360
8 TraesCS4A01G244700 chr1A 400851 403211 2360 True 3951 3951 96.867 1 2362 1 chr1A.!!$R1 2361
9 TraesCS4A01G244700 chr6B 111686033 111688394 2361 False 3945 3945 96.825 1 2361 1 chr6B.!!$F1 2360

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
119 120 0.180406 GGATCGGCTTACCCATGTGT 59.82 55.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1805 1.00243 GGAATCAGGATGCGGCATCTA 59.998 52.381 34.29 23.15 40.39 1.98 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
119 120 0.180406 GGATCGGCTTACCCATGTGT 59.820 55.000 0.00 0.00 0.00 3.72
491 492 1.904990 TTCCGGTTCATCCCGCATCA 61.905 55.000 0.00 0.00 46.71 3.07
683 684 3.198635 CAGCTATCCTGAGGGAAACTTCA 59.801 47.826 0.00 0.00 45.78 3.02
792 793 2.821437 CCTCCACCAGAGTTTCCTCTA 58.179 52.381 0.00 0.00 46.52 2.43
822 823 1.675714 CGCTCAGGCATAGTTCACCAA 60.676 52.381 0.00 0.00 38.60 3.67
1150 1151 1.147376 CAACAGTCCACACCCCGAA 59.853 57.895 0.00 0.00 0.00 4.30
1156 1157 3.622826 CCACACCCCGAACCGAGT 61.623 66.667 0.00 0.00 0.00 4.18
1373 1374 0.547075 TTCCCAAACAACCCGACTCA 59.453 50.000 0.00 0.00 0.00 3.41
1528 1529 1.907739 CCCGATTCTCAAGCTGGGA 59.092 57.895 0.00 0.00 39.03 4.37
1609 1610 7.746475 CGCTTATTTATATGCTTAAACTCAGCC 59.254 37.037 6.20 0.00 36.33 4.85
1664 1665 1.882682 GACGTGCGCTTCGTTTGCTA 61.883 55.000 25.38 0.00 41.64 3.49
1804 1805 2.344203 CCTTGCGAGACGAGGGACT 61.344 63.158 1.22 0.00 45.41 3.85
2158 2160 3.462678 GAGGGGAGGTGGTCGAGC 61.463 72.222 7.89 7.89 0.00 5.03
2228 2230 0.736053 GCACGGTCTGTTTTGGTCAA 59.264 50.000 0.00 0.00 0.00 3.18
2234 2236 3.222603 GGTCTGTTTTGGTCAAGGTCAT 58.777 45.455 0.00 0.00 0.00 3.06
2278 2280 3.387374 TCACCTACGGAAACCTTGTTACA 59.613 43.478 0.00 0.00 0.00 2.41
2363 2365 4.337060 CCGTCGCCGCGATCCATA 62.337 66.667 20.03 0.00 38.42 2.74
2364 2366 2.801162 CGTCGCCGCGATCCATAG 60.801 66.667 20.03 3.14 38.42 2.23
2365 2367 3.106407 GTCGCCGCGATCCATAGC 61.106 66.667 20.03 0.00 38.42 2.97
2366 2368 3.601685 TCGCCGCGATCCATAGCA 61.602 61.111 12.39 0.00 0.00 3.49
2367 2369 2.433145 CGCCGCGATCCATAGCAT 60.433 61.111 8.23 0.00 0.00 3.79
2368 2370 1.153842 CGCCGCGATCCATAGCATA 60.154 57.895 8.23 0.00 0.00 3.14
2369 2371 1.413767 CGCCGCGATCCATAGCATAC 61.414 60.000 8.23 0.00 0.00 2.39
2370 2372 1.084370 GCCGCGATCCATAGCATACC 61.084 60.000 8.23 0.00 0.00 2.73
2371 2373 0.460284 CCGCGATCCATAGCATACCC 60.460 60.000 8.23 0.00 0.00 3.69
2372 2374 0.532573 CGCGATCCATAGCATACCCT 59.467 55.000 0.00 0.00 0.00 4.34
2373 2375 1.737029 CGCGATCCATAGCATACCCTG 60.737 57.143 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 233 4.662961 GGCCGCTGCAAAACCCAC 62.663 66.667 1.55 0.00 40.13 4.61
250 251 4.753662 TGAGTAGGAGGGCGCGGT 62.754 66.667 8.83 0.00 0.00 5.68
491 492 4.039124 CCATTTTTGGTAAGCAGAACTGGT 59.961 41.667 0.47 0.47 44.00 4.00
559 560 1.045407 AAATAGGTAGGATGGCGCGA 58.955 50.000 12.10 0.00 0.00 5.87
683 684 3.571590 CATCTAGTAGCTGGTTCCCTCT 58.428 50.000 0.00 0.00 0.00 3.69
948 949 1.874019 GACATGCGTGCGAGTCGAT 60.874 57.895 18.61 0.00 0.00 3.59
1034 1035 2.654877 GAAAGGCGTGTCCCTCGA 59.345 61.111 0.00 0.00 32.93 4.04
1126 1127 1.227556 GTGTGGACTGTTGTCGGCT 60.228 57.895 0.00 0.00 43.79 5.52
1150 1151 4.008933 GCTGGTCTGCCACTCGGT 62.009 66.667 0.00 0.00 40.46 4.69
1156 1157 2.033141 GCTCTTGCTGGTCTGCCA 59.967 61.111 0.00 0.00 43.73 4.92
1160 1161 3.151906 AACGGCTCTTGCTGGTCT 58.848 55.556 1.86 0.00 42.88 3.85
1373 1374 2.047274 CCACGAGGCACCGTCAAT 60.047 61.111 2.01 0.00 41.29 2.57
1417 1418 3.775654 CGCCTGGGAGGGTGAGAC 61.776 72.222 0.00 0.00 39.04 3.36
1440 1441 3.732849 GGCCCAAGTCCCCTGGAG 61.733 72.222 0.00 0.00 29.39 3.86
1528 1529 4.514577 CGAGCGAACCGGGAGCAT 62.515 66.667 17.92 5.56 0.00 3.79
1664 1665 2.905415 TGATGGCCTCAAAATGACCT 57.095 45.000 3.32 0.00 0.00 3.85
1804 1805 1.002430 GGAATCAGGATGCGGCATCTA 59.998 52.381 34.29 23.15 40.39 1.98
2228 2230 3.432749 CGGAAGGATCATTGTCATGACCT 60.433 47.826 22.85 8.14 42.46 3.85
2234 2236 2.028420 CTGCGGAAGGATCATTGTCA 57.972 50.000 0.00 0.00 0.00 3.58
2278 2280 8.490311 CCTTATCATTTAGAGGAAGGAGAAGTT 58.510 37.037 6.10 0.00 42.15 2.66


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

AutoCloner maintained by Alex Coulton.