Multiple sequence alignment - TraesCS2A01G316100

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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 TraesCS2A01G316100 chr2A 100.000 2960 0 0 1 2960 541845525 541842566 0.000000e+00 5467
1 TraesCS2A01G316100 chr2B 95.271 2601 92 15 1 2573 477609591 477606994 0.000000e+00 4093
2 TraesCS2A01G316100 chr2B 95.178 394 11 2 2575 2960 477606959 477606566 1.510000e-172 616
3 TraesCS2A01G316100 chr2D 96.155 2445 65 9 1 2438 403506966 403504544 0.000000e+00 3967
4 TraesCS2A01G316100 chr2D 97.150 386 11 0 2575 2960 403502775 403502390 0.000000e+00 652


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 TraesCS2A01G316100 chr2A 541842566 541845525 2959 True 5467.0 5467 100.0000 1 2960 1 chr2A.!!$R1 2959
1 TraesCS2A01G316100 chr2B 477606566 477609591 3025 True 2354.5 4093 95.2245 1 2960 2 chr2B.!!$R1 2959
2 TraesCS2A01G316100 chr2D 403502390 403506966 4576 True 2309.5 3967 96.6525 1 2960 2 chr2D.!!$R1 2959

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
128 129 0.110486 CCTAGGGCACTTGTGGTGTT 59.890 55.0 0.0 0.0 46.86 3.32 F
130 131 0.548989 TAGGGCACTTGTGGTGTTGT 59.451 50.0 0.0 0.0 46.86 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 1932 0.620556 GGATCTTGCTTGTCTCCCCA 59.379 55.000 0.0 0.0 0.0 4.96 R
2074 2081 4.749245 ATCTTTTAAACCGCACACTCTG 57.251 40.909 0.0 0.0 0.0 3.35 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
128 129 0.110486 CCTAGGGCACTTGTGGTGTT 59.890 55.000 0.00 0.00 46.86 3.32
130 131 0.548989 TAGGGCACTTGTGGTGTTGT 59.451 50.000 0.00 0.00 46.86 3.32
252 253 4.946784 ATTAAGAAGTTGTTAGCTGGCG 57.053 40.909 0.00 0.00 0.00 5.69
271 272 0.662085 GCTGGCTATTCTTGCAGAGC 59.338 55.000 0.00 0.00 32.86 4.09
282 283 5.468540 TTCTTGCAGAGCTTTACTAGACA 57.531 39.130 0.00 0.00 0.00 3.41
328 329 8.355913 TGTATGACATTGTTTGATGTGCTTTAA 58.644 29.630 0.00 0.00 40.21 1.52
500 501 2.259917 AGGCTTTATTGCTTTTGCCCT 58.740 42.857 0.00 0.00 46.87 5.19
508 509 7.432350 TTTATTGCTTTTGCCCTAATTGTTG 57.568 32.000 0.00 0.00 46.87 3.33
604 605 9.125026 CCATGCTTCCTCACTAATAAAAGTAAT 57.875 33.333 0.00 0.00 0.00 1.89
742 744 5.716094 TGATTTTGAAGGTGATGAGCAATG 58.284 37.500 0.00 0.00 0.00 2.82
817 819 8.478775 TTCTGTATACAGTATAGCTCATGGTT 57.521 34.615 27.83 0.00 44.12 3.67
818 820 8.478775 TCTGTATACAGTATAGCTCATGGTTT 57.521 34.615 27.83 0.00 44.12 3.27
847 849 6.109320 AGTGCAAATTCATTTGTTGTTGTG 57.891 33.333 12.71 0.00 46.63 3.33
1045 1052 1.479323 ACTTATCAAGCCGGCGACTTA 59.521 47.619 23.20 9.47 0.00 2.24
1116 1123 5.352293 GGCAGCCAAGGAAAATAAATTGAAG 59.648 40.000 6.55 0.00 0.00 3.02
1632 1639 1.213926 ACAGGCTTGAATCCAGGATCC 59.786 52.381 2.48 2.48 0.00 3.36
2045 2052 3.876914 GCGGAACCACTATTCATGAATCA 59.123 43.478 23.95 10.13 32.50 2.57
2074 2081 2.147150 GCTTCTTTCTGGTCTGGTCAC 58.853 52.381 0.00 0.00 0.00 3.67
2313 2323 9.520515 AGTCAGACCATTTTGTTATATGTTTCT 57.479 29.630 0.00 0.00 0.00 2.52
2348 2358 7.234187 TGACATATTGCTCGACTTGTATTTC 57.766 36.000 0.00 0.00 0.00 2.17
2350 2360 5.810587 ACATATTGCTCGACTTGTATTTCGT 59.189 36.000 0.00 0.00 36.60 3.85
2357 2367 2.414138 CGACTTGTATTTCGTGGTTCCC 59.586 50.000 0.00 0.00 0.00 3.97
2361 2371 1.619827 TGTATTTCGTGGTTCCCGTCT 59.380 47.619 0.00 0.00 0.00 4.18
2372 2382 1.338890 TTCCCGTCTGGTGTTGTCCA 61.339 55.000 0.00 0.00 36.00 4.02
2379 2389 3.476552 GTCTGGTGTTGTCCAATCTCAA 58.523 45.455 0.00 0.00 37.01 3.02
2388 2398 3.753815 TGTCCAATCTCAATGTGCTGAA 58.246 40.909 0.00 0.00 0.00 3.02
2392 2402 4.768448 TCCAATCTCAATGTGCTGAATTGT 59.232 37.500 6.51 0.00 36.58 2.71
2494 4104 1.522668 CAAGGAGGCAATGAACACGA 58.477 50.000 0.00 0.00 0.00 4.35
2573 4183 2.061773 GGTGGCGATCTACATGATTCG 58.938 52.381 0.00 3.42 35.14 3.34
2600 4245 5.046014 AGGAGCTGGATGGTTCATCATATAC 60.046 44.000 9.68 0.00 42.13 1.47
2609 4254 6.048732 TGGTTCATCATATACACACACAGT 57.951 37.500 0.00 0.00 0.00 3.55
2627 4272 2.428530 CAGTTGACAGGGATCGAGATGA 59.571 50.000 0.00 0.00 0.00 2.92
2650 4295 4.008330 TCGCCCTTCTCTAAGATATACCG 58.992 47.826 0.00 0.00 34.37 4.02
2749 4394 2.047274 CCGAACACCGTGATGCCT 60.047 61.111 5.28 0.00 36.31 4.75
2874 4527 1.210478 GCCTGCCTCTTCTGGTATGAA 59.790 52.381 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 3.512329 AGCATGGATCTCAAAATGCAACA 59.488 39.130 8.96 0.00 46.21 3.33
130 131 4.020928 ACAAGCATGGATCTCAAAATGCAA 60.021 37.500 8.96 0.00 46.21 4.08
252 253 0.662085 GCTCTGCAAGAATAGCCAGC 59.338 55.000 0.00 0.00 46.34 4.85
282 283 4.579869 ACAGCAAGGACAAGTTCGATATT 58.420 39.130 0.00 0.00 0.00 1.28
337 338 4.363991 AGCAGAGATGAAAGGACAGTTT 57.636 40.909 0.00 0.00 0.00 2.66
341 342 4.774726 AGAGTAAGCAGAGATGAAAGGACA 59.225 41.667 0.00 0.00 0.00 4.02
468 469 7.290110 AGCAATAAAGCCTAAAGTTTGAACT 57.710 32.000 0.00 0.00 36.50 3.01
604 605 7.361438 AGGTCATGGATGGTTTATTATTTCCA 58.639 34.615 0.00 0.00 37.63 3.53
613 614 5.765510 AGCATTTAGGTCATGGATGGTTTA 58.234 37.500 0.00 0.00 0.00 2.01
614 615 4.613437 AGCATTTAGGTCATGGATGGTTT 58.387 39.130 0.00 0.00 0.00 3.27
742 744 7.759886 GGGTTTATTTTAAATCCTTCTGCTCAC 59.240 37.037 0.00 0.00 0.00 3.51
831 833 5.065859 TCACGACTCACAACAACAAATGAAT 59.934 36.000 0.00 0.00 0.00 2.57
847 849 6.648725 AGTTTGCTATAACAATCACGACTC 57.351 37.500 0.00 0.00 0.00 3.36
1045 1052 1.343782 TGCATCAGGAGGAGATGACCT 60.344 52.381 7.31 0.00 44.34 3.85
1116 1123 5.106277 CCAATCCTTTTTCTCCGAGGTTAAC 60.106 44.000 0.00 0.00 32.33 2.01
1632 1639 9.964354 TCAATAAGATAGTCCCCAATAATCATG 57.036 33.333 0.00 0.00 0.00 3.07
1925 1932 0.620556 GGATCTTGCTTGTCTCCCCA 59.379 55.000 0.00 0.00 0.00 4.96
2045 2052 5.125097 CAGACCAGAAAGAAGCATGCTAAAT 59.875 40.000 23.00 5.09 0.00 1.40
2074 2081 4.749245 ATCTTTTAAACCGCACACTCTG 57.251 40.909 0.00 0.00 0.00 3.35
2313 2323 7.750458 GTCGAGCAATATGTCAAAAGAAATTCA 59.250 33.333 0.00 0.00 0.00 2.57
2357 2367 2.069273 GAGATTGGACAACACCAGACG 58.931 52.381 0.00 0.00 41.19 4.18
2361 2371 3.569277 CACATTGAGATTGGACAACACCA 59.431 43.478 0.00 0.00 38.24 4.17
2372 2382 4.525487 ACCACAATTCAGCACATTGAGATT 59.475 37.500 8.93 0.00 35.51 2.40
2438 2448 7.500892 ACCTGATGACAAACTGTAACATGTTTA 59.499 33.333 17.78 5.75 35.01 2.01
2439 2449 6.321181 ACCTGATGACAAACTGTAACATGTTT 59.679 34.615 17.78 0.95 36.91 2.83
2441 2451 5.376625 ACCTGATGACAAACTGTAACATGT 58.623 37.500 0.00 0.00 0.00 3.21
2442 2452 5.947228 ACCTGATGACAAACTGTAACATG 57.053 39.130 0.00 0.00 0.00 3.21
2448 2477 4.067896 CTGCTTACCTGATGACAAACTGT 58.932 43.478 0.00 0.00 0.00 3.55
2573 4183 3.326006 TGATGAACCATCCAGCTCCTATC 59.674 47.826 4.69 0.00 39.87 2.08
2600 4245 2.146342 GATCCCTGTCAACTGTGTGTG 58.854 52.381 0.00 0.00 0.00 3.82
2627 4272 4.641094 CGGTATATCTTAGAGAAGGGCGAT 59.359 45.833 0.00 0.00 33.09 4.58
2650 4295 1.452833 GCTGCTGGGGAAGACCATC 60.453 63.158 0.00 0.00 42.91 3.51
2749 4394 2.664851 CTGGAGAACAACCGCGCA 60.665 61.111 8.75 0.00 0.00 6.09
2874 4527 0.606401 CCTTCCACGCCACTCACATT 60.606 55.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.