Multiple sequence alignment - TraesCS2A01G239700

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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 TraesCS2A01G239700 chr2A 100.000 2636 0 0 1 2636 332948785 332946150 0.000000e+00 4868.0
1 TraesCS2A01G239700 chr2A 94.264 401 16 1 534 934 703515473 703515080 8.070000e-170 606.0
2 TraesCS2A01G239700 chr2A 94.987 379 19 0 2258 2636 358631728 358632106 1.750000e-166 595.0
3 TraesCS2A01G239700 chr2A 95.139 144 7 0 35 178 65286237 65286380 7.340000e-56 228.0
4 TraesCS2A01G239700 chr2A 97.895 95 2 0 2249 2343 65273992 65274086 5.840000e-37 165.0
5 TraesCS2A01G239700 chr2A 97.436 39 1 0 1 39 588451075 588451037 1.690000e-07 67.6
6 TraesCS2A01G239700 chrUn 98.185 2644 40 3 1 2636 189406575 189409218 0.000000e+00 4610.0
7 TraesCS2A01G239700 chrUn 97.957 2643 47 3 1 2636 251410020 251407378 0.000000e+00 4575.0
8 TraesCS2A01G239700 chr7D 97.916 2639 46 6 1 2636 382064169 382066801 0.000000e+00 4560.0
9 TraesCS2A01G239700 chr7D 97.730 2643 51 5 1 2636 626683744 626681104 0.000000e+00 4540.0
10 TraesCS2A01G239700 chr7B 97.844 2644 49 3 1 2636 644462935 644465578 0.000000e+00 4560.0


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 TraesCS2A01G239700 chr2A 332946150 332948785 2635 True 4868 4868 100.000 1 2636 1 chr2A.!!$R1 2635
1 TraesCS2A01G239700 chrUn 189406575 189409218 2643 False 4610 4610 98.185 1 2636 1 chrUn.!!$F1 2635
2 TraesCS2A01G239700 chrUn 251407378 251410020 2642 True 4575 4575 97.957 1 2636 1 chrUn.!!$R1 2635
3 TraesCS2A01G239700 chr7D 382064169 382066801 2632 False 4560 4560 97.916 1 2636 1 chr7D.!!$F1 2635
4 TraesCS2A01G239700 chr7D 626681104 626683744 2640 True 4540 4540 97.730 1 2636 1 chr7D.!!$R1 2635
5 TraesCS2A01G239700 chr7B 644462935 644465578 2643 False 4560 4560 97.844 1 2636 1 chr7B.!!$F1 2635

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
508 509 0.248012 TGCGTCTTTTATGCCTCGGA 59.752 50.0 0.0 0.0 39.57 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 1912 2.831333 CGAGACTCCATCCAAATCCAG 58.169 52.381 0.0 0.0 0.0 3.86 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
120 121 3.667497 TCCCATATAAGAAGCTCGCTG 57.333 47.619 0.00 0.00 0.00 5.18
332 333 1.301401 CTCTTTGTTGGACCGCCGA 60.301 57.895 0.00 0.00 36.79 5.54
508 509 0.248012 TGCGTCTTTTATGCCTCGGA 59.752 50.000 0.00 0.00 39.57 4.55
808 809 3.676324 GCGAAGTACTCTTGTGCACCTAT 60.676 47.826 15.69 0.00 34.12 2.57
919 920 2.267642 CTGCCGGATTTCGTCCCA 59.732 61.111 5.05 0.00 44.77 4.37
932 933 1.153429 GTCCCATCCGTAGCGCTTT 60.153 57.895 18.68 0.00 0.00 3.51
953 954 2.715532 GAAGTCACTCTGGCGTGGCA 62.716 60.000 0.00 0.00 41.80 4.92
959 960 3.300934 CTCTGGCGTGGCACTGCTA 62.301 63.158 25.34 20.99 0.00 3.49
1082 1083 2.582052 TGGAAACGCCTCACAATCTTT 58.418 42.857 0.00 0.00 37.63 2.52
1157 1158 4.957327 TGGTACCCCTAAAATTTGTATGCC 59.043 41.667 10.07 0.00 0.00 4.40
1255 1256 5.278660 GCTGGTGAATCACTGATCAAAAAGT 60.279 40.000 13.53 0.00 34.40 2.66
1358 1359 1.293763 TGTGGGATCCCTGGATGTAGA 59.706 52.381 31.05 4.98 34.60 2.59
1394 1395 5.106396 CGCTTCTTCTTCCACAAAGATTCAT 60.106 40.000 0.00 0.00 43.50 2.57
1437 1438 3.476552 ACTGAAGAAGATTTGGCGAACA 58.523 40.909 0.00 0.00 0.00 3.18
1449 1450 4.985538 TTGGCGAACAAAGAAAAAGGTA 57.014 36.364 0.00 0.00 35.79 3.08
1711 1712 5.809001 TGTTGAGGATCTTGCACTTATTCT 58.191 37.500 0.00 0.00 34.92 2.40
1911 1912 2.425668 ACACCAACCAACAAGTAAGTGC 59.574 45.455 0.00 0.00 0.00 4.40
2027 2028 1.501170 TGAATCCCCCTTCCAAACACA 59.499 47.619 0.00 0.00 0.00 3.72
2074 2076 7.093322 AGAAATGAGCAAGACCATATGTTTC 57.907 36.000 1.24 1.59 0.00 2.78
2455 2464 0.321653 GCCTGGTGGTTTCTGATCGT 60.322 55.000 0.00 0.00 35.27 3.73
2499 2508 1.209019 AGCTCTTCGCATGATCTGGTT 59.791 47.619 0.00 0.00 42.61 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 0.982704 ATCCAGCAGAGTGAAGCAGT 59.017 50.000 0.00 0.00 0.00 4.40
80 81 2.182791 CGACGCATCCAGCAGAGT 59.817 61.111 0.00 0.00 46.13 3.24
120 121 7.383843 ACAAAATGTTTGAATGATCGGGTAAAC 59.616 33.333 7.68 7.91 0.00 2.01
216 217 0.900182 TCCAGAGCGAAGAGAAGGCA 60.900 55.000 0.00 0.00 0.00 4.75
332 333 1.066918 GAGACCACCGTGTTCACGT 59.933 57.895 20.93 8.97 0.00 4.49
335 336 0.387929 GTCAGAGACCACCGTGTTCA 59.612 55.000 0.00 0.00 0.00 3.18
422 423 1.559682 GATGAGCCCACCAACTTCCTA 59.440 52.381 0.00 0.00 0.00 2.94
919 920 0.249398 ACTTCCAAAGCGCTACGGAT 59.751 50.000 23.98 10.98 0.00 4.18
932 933 1.367471 CACGCCAGAGTGACTTCCA 59.633 57.895 0.00 0.00 44.43 3.53
953 954 7.947332 TCCTATTGATCAGAAGTATCTAGCAGT 59.053 37.037 0.00 0.00 33.50 4.40
1049 1050 6.485313 TGAGGCGTTTCCATTACATAATAAGG 59.515 38.462 0.00 0.00 37.29 2.69
1061 1062 2.496899 AGATTGTGAGGCGTTTCCAT 57.503 45.000 0.00 0.00 37.29 3.41
1143 1144 7.408756 AAGCTCATCTGGCATACAAATTTTA 57.591 32.000 0.00 0.00 0.00 1.52
1157 1158 2.548875 GCAGTCCTGTAAGCTCATCTG 58.451 52.381 0.00 0.00 0.00 2.90
1255 1256 7.105588 TCGATGAAGAATCTCTCAAAAATCCA 58.894 34.615 0.00 0.00 32.61 3.41
1394 1395 4.811969 TCTATCCAAGCTCGGTTTTGTA 57.188 40.909 0.00 0.00 0.00 2.41
1711 1712 5.550011 TCTTGGCTATGTAAATATAGGGCCA 59.450 40.000 6.18 0.00 45.17 5.36
1911 1912 2.831333 CGAGACTCCATCCAAATCCAG 58.169 52.381 0.00 0.00 0.00 3.86
2027 2028 6.068853 TCTCATAAGGAATGGAGATTGGGTTT 60.069 38.462 0.00 0.00 36.15 3.27
2295 2304 8.567948 TCAAATTGTCTTACCTGAAAAGATGAC 58.432 33.333 0.00 0.00 35.53 3.06


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

AutoCloner maintained by Alex Coulton.