Multiple sequence alignment - TraesCS1A01G000700

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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 TraesCS1A01G000700 chr1A 100.000 2378 0 0 1 2378 170969 168592 0.000000e+00 4392
1 TraesCS1A01G000700 chr1A 96.316 2389 76 6 1 2378 9080 6693 0.000000e+00 3914
2 TraesCS1A01G000700 chr1A 96.191 2389 79 3 1 2378 403222 400835 0.000000e+00 3897
3 TraesCS1A01G000700 chr1A 96.151 2390 80 6 1 2378 243381 240992 0.000000e+00 3893
4 TraesCS1A01G000700 chrUn 96.653 2390 68 3 1 2378 245706835 245704446 0.000000e+00 3960
5 TraesCS1A01G000700 chrUn 96.485 2390 72 3 1 2378 291536207 291533818 0.000000e+00 3938
6 TraesCS1A01G000700 chrUn 96.444 2390 73 3 1 2378 67500241 67502630 0.000000e+00 3932
7 TraesCS1A01G000700 chrUn 96.067 2390 71 4 1 2378 67510017 67512395 0.000000e+00 3871
8 TraesCS1A01G000700 chrUn 96.521 2328 69 3 63 2378 67491604 67493931 0.000000e+00 3840
9 TraesCS1A01G000700 chrUn 96.809 2131 56 3 260 2378 220750768 220752898 0.000000e+00 3548
10 TraesCS1A01G000700 chrUn 96.623 2132 60 3 259 2378 237320907 237318776 0.000000e+00 3528
11 TraesCS1A01G000700 chrUn 96.780 1211 28 5 1 1200 424675253 424676463 0.000000e+00 2010
12 TraesCS1A01G000700 chrUn 96.799 1187 27 5 1 1176 416971677 416970491 0.000000e+00 1971
13 TraesCS1A01G000700 chrUn 94.957 575 18 5 1 564 398203199 398203773 0.000000e+00 891
14 TraesCS1A01G000700 chrUn 94.643 504 16 5 1 493 395166274 395166777 0.000000e+00 771
15 TraesCS1A01G000700 chrUn 93.782 386 14 4 1 376 433643359 433643744 2.650000e-159 571
16 TraesCS1A01G000700 chrUn 93.684 380 14 4 1 370 420752541 420752162 5.740000e-156 560
17 TraesCS1A01G000700 chr5D 96.444 2390 73 3 1 2378 18999691 18997302 0.000000e+00 3932
18 TraesCS1A01G000700 chr1B 95.983 2390 83 7 1 2378 544610106 544607718 0.000000e+00 3869


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 TraesCS1A01G000700 chr1A 168592 170969 2377 True 4392 4392 100.000 1 2378 1 chr1A.!!$R2 2377
1 TraesCS1A01G000700 chr1A 6693 9080 2387 True 3914 3914 96.316 1 2378 1 chr1A.!!$R1 2377
2 TraesCS1A01G000700 chr1A 400835 403222 2387 True 3897 3897 96.191 1 2378 1 chr1A.!!$R4 2377
3 TraesCS1A01G000700 chr1A 240992 243381 2389 True 3893 3893 96.151 1 2378 1 chr1A.!!$R3 2377
4 TraesCS1A01G000700 chrUn 245704446 245706835 2389 True 3960 3960 96.653 1 2378 1 chrUn.!!$R2 2377
5 TraesCS1A01G000700 chrUn 291533818 291536207 2389 True 3938 3938 96.485 1 2378 1 chrUn.!!$R3 2377
6 TraesCS1A01G000700 chrUn 67500241 67502630 2389 False 3932 3932 96.444 1 2378 1 chrUn.!!$F2 2377
7 TraesCS1A01G000700 chrUn 67510017 67512395 2378 False 3871 3871 96.067 1 2378 1 chrUn.!!$F3 2377
8 TraesCS1A01G000700 chrUn 67491604 67493931 2327 False 3840 3840 96.521 63 2378 1 chrUn.!!$F1 2315
9 TraesCS1A01G000700 chrUn 220750768 220752898 2130 False 3548 3548 96.809 260 2378 1 chrUn.!!$F4 2118
10 TraesCS1A01G000700 chrUn 237318776 237320907 2131 True 3528 3528 96.623 259 2378 1 chrUn.!!$R1 2119
11 TraesCS1A01G000700 chrUn 424675253 424676463 1210 False 2010 2010 96.780 1 1200 1 chrUn.!!$F7 1199
12 TraesCS1A01G000700 chrUn 416970491 416971677 1186 True 1971 1971 96.799 1 1176 1 chrUn.!!$R4 1175
13 TraesCS1A01G000700 chrUn 398203199 398203773 574 False 891 891 94.957 1 564 1 chrUn.!!$F6 563
14 TraesCS1A01G000700 chrUn 395166274 395166777 503 False 771 771 94.643 1 493 1 chrUn.!!$F5 492
15 TraesCS1A01G000700 chr5D 18997302 18999691 2389 True 3932 3932 96.444 1 2378 1 chr5D.!!$R1 2377
16 TraesCS1A01G000700 chr1B 544607718 544610106 2388 True 3869 3869 95.983 1 2378 1 chr1B.!!$R1 2377

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
218 219 0.107508 CCACCAAGATCTGCACCGAT 60.108 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 1825 0.03392 CATCGGGAATCAGGATGCGA 59.966 55.0 0.0 0.0 34.76 5.1 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
31 32 2.047274 CGTCAACCGCCACATCCT 60.047 61.111 0.00 0.00 0.00 3.24
89 90 1.202359 TGCACGTGATTGCGCTATCTA 60.202 47.619 27.59 14.45 46.20 1.98
165 166 2.605257 TGGAACCTTTCTCCTCTTCGA 58.395 47.619 0.00 0.00 33.77 3.71
218 219 0.107508 CCACCAAGATCTGCACCGAT 60.108 55.000 0.00 0.00 0.00 4.18
224 225 1.141881 GATCTGCACCGATGACCGT 59.858 57.895 0.00 0.00 36.31 4.83
398 409 3.343617 GGATTTCGACTTCCATGACCAA 58.656 45.455 7.75 0.00 31.99 3.67
400 411 2.178912 TTCGACTTCCATGACCAACC 57.821 50.000 0.00 0.00 0.00 3.77
869 882 3.403038 CAACTCGAACCCTTCACAGAAT 58.597 45.455 0.00 0.00 0.00 2.40
956 969 0.316204 TTTCAGAACCCGTCGACTCC 59.684 55.000 14.70 0.00 0.00 3.85
998 1011 2.980562 CGTGTTTCAAGACGGGTCA 58.019 52.632 1.41 0.00 41.37 4.02
1490 1505 0.553819 AGGACGCCTCTCCAGACTAT 59.446 55.000 0.00 0.00 31.94 2.12
1501 1516 4.711399 TCTCCAGACTATAATTCGGACGA 58.289 43.478 0.00 0.00 0.00 4.20
1530 1545 0.465705 CCGATTCTCAAGCTGGGCTA 59.534 55.000 0.00 0.00 38.25 3.93
1617 1632 2.094130 GCTTAAACTCAGCGGGTAGTCT 60.094 50.000 0.00 0.00 0.00 3.24
1656 1671 3.299050 TCGAAGCGACATGTGGTTT 57.701 47.368 9.60 9.60 0.00 3.27
1665 1680 2.479389 CGACATGTGGTTTGTTTGCTGT 60.479 45.455 1.15 0.00 0.00 4.40
1679 1694 0.592637 TGCTGTGTCATTTTGAGGCG 59.407 50.000 0.00 0.00 0.00 5.52
1808 1823 3.053849 GCGAGACGAGGGACCAGAC 62.054 68.421 0.00 0.00 0.00 3.51
1810 1825 1.674980 GAGACGAGGGACCAGACGT 60.675 63.158 9.02 9.02 41.57 4.34
1967 1983 2.469826 CAGGTATCGCATTTCGCTACA 58.530 47.619 0.00 0.00 40.44 2.74
2009 2025 2.292016 CGAGATATCTGTTGCCGAGAGT 59.708 50.000 10.74 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.064979 GGGTTAAGATTTCCCGAGCCA 60.065 52.381 0.00 0.0 0.00 4.75
72 73 1.599667 CGGTAGATAGCGCAATCACGT 60.600 52.381 11.47 0.0 40.41 4.49
261 262 3.733507 ATGAGTAGGAGGGCGCGGA 62.734 63.158 8.83 0.0 0.00 5.54
320 331 0.923358 TAGCCCCGAAAATGGATGGT 59.077 50.000 0.00 0.0 0.00 3.55
398 409 1.207329 GTCGATTAAGACAGCAGGGGT 59.793 52.381 0.00 0.0 40.65 4.95
400 411 1.207089 TGGTCGATTAAGACAGCAGGG 59.793 52.381 0.00 0.0 42.62 4.45
869 882 3.536917 CGCTGGCCGACCCTGATA 61.537 66.667 0.00 0.0 40.02 2.15
956 969 0.036952 AAGGAGTCTGACATGCGTGG 60.037 55.000 11.36 0.0 0.00 4.94
1490 1505 0.457166 CGGCTGTGTCGTCCGAATTA 60.457 55.000 0.00 0.0 45.53 1.40
1501 1516 3.665675 GAGAATCGGGCGGCTGTGT 62.666 63.158 18.34 6.7 0.00 3.72
1530 1545 3.069318 GGCGAGAGAACCGGGAGT 61.069 66.667 6.32 0.0 0.00 3.85
1541 1556 0.034186 TTCCCCTAGTAACGGCGAGA 60.034 55.000 16.62 0.0 0.00 4.04
1571 1586 3.828875 AAATAGGCGGAGGAGAAGAAG 57.171 47.619 0.00 0.0 0.00 2.85
1648 1663 2.495270 TGACACAGCAAACAAACCACAT 59.505 40.909 0.00 0.0 0.00 3.21
1653 1668 5.220453 CCTCAAAATGACACAGCAAACAAAC 60.220 40.000 0.00 0.0 0.00 2.93
1656 1671 3.737663 GCCTCAAAATGACACAGCAAACA 60.738 43.478 0.00 0.0 0.00 2.83
1665 1680 2.097954 GCATGATCGCCTCAAAATGACA 59.902 45.455 0.00 0.0 37.44 3.58
1808 1823 1.951130 CGGGAATCAGGATGCGACG 60.951 63.158 0.00 0.0 34.76 5.12
1810 1825 0.033920 CATCGGGAATCAGGATGCGA 59.966 55.000 0.00 0.0 34.76 5.10
1967 1983 2.402305 GCTCTCGCATCGATGAAGAAT 58.598 47.619 29.20 0.0 34.61 2.40
1997 2013 0.813610 CCACACAACTCTCGGCAACA 60.814 55.000 0.00 0.0 0.00 3.33
2009 2025 6.338214 TGCAAAGCTATTTAATCCACACAA 57.662 33.333 0.00 0.0 0.00 3.33


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

AutoCloner maintained by Alex Coulton.