Multiple sequence alignment - TraesCS5A01G064900

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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 TraesCS5A01G064900 chr5A 100.000 2419 0 0 1 2419 70453142 70455560 0.000000e+00 4468
1 TraesCS5A01G064900 chr5A 80.220 182 24 11 624 799 650189106 650189281 2.520000e-25 126
2 TraesCS5A01G064900 chr5A 79.006 181 33 5 614 792 440763027 440762850 4.220000e-23 119
3 TraesCS5A01G064900 chr5D 93.938 1633 57 14 806 2418 75272431 75274041 0.000000e+00 2429
4 TraesCS5A01G064900 chr5B 92.613 1638 54 26 809 2419 83611812 83613409 0.000000e+00 2292
5 TraesCS5A01G064900 chr5B 92.941 85 4 1 723 805 686445108 686445192 3.270000e-24 122
6 TraesCS5A01G064900 chr2B 98.248 799 12 2 1 798 775002023 775001226 0.000000e+00 1397
7 TraesCS5A01G064900 chr2B 88.000 375 36 3 1 366 748591247 748590873 3.690000e-118 435
8 TraesCS5A01G064900 chr4A 86.358 843 79 17 1 810 575713445 575714284 0.000000e+00 887
9 TraesCS5A01G064900 chr4A 84.211 171 25 2 624 793 666990812 666990981 5.350000e-37 165
10 TraesCS5A01G064900 chr1A 85.348 819 90 17 1 792 139903749 139904564 0.000000e+00 821
11 TraesCS5A01G064900 chr6D 85.733 778 75 20 1 748 292712427 292711656 0.000000e+00 789
12 TraesCS5A01G064900 chr1B 89.646 367 37 1 1 367 17274918 17274553 1.310000e-127 466
13 TraesCS5A01G064900 chr1B 89.524 315 31 2 1 315 90186594 90186282 4.850000e-107 398
14 TraesCS5A01G064900 chr1B 80.220 182 31 5 614 793 113985291 113985469 5.430000e-27 132
15 TraesCS5A01G064900 chr6B 87.733 375 37 3 1 366 478471580 478471206 1.720000e-116 429
16 TraesCS5A01G064900 chr6B 91.304 92 4 4 723 811 142804557 142804647 3.270000e-24 122
17 TraesCS5A01G064900 chr7B 83.471 484 44 18 350 803 538057292 538057769 3.720000e-113 418
18 TraesCS5A01G064900 chr7B 89.841 315 31 1 1 315 538056980 538057293 1.040000e-108 403
19 TraesCS5A01G064900 chr6A 89.655 87 5 3 722 805 102110597 102110512 9.150000e-20 108
20 TraesCS5A01G064900 chr7A 77.907 172 34 4 624 793 586165279 586165448 1.180000e-18 104


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 TraesCS5A01G064900 chr5A 70453142 70455560 2418 False 4468.0 4468 100.000 1 2419 1 chr5A.!!$F1 2418
1 TraesCS5A01G064900 chr5D 75272431 75274041 1610 False 2429.0 2429 93.938 806 2418 1 chr5D.!!$F1 1612
2 TraesCS5A01G064900 chr5B 83611812 83613409 1597 False 2292.0 2292 92.613 809 2419 1 chr5B.!!$F1 1610
3 TraesCS5A01G064900 chr2B 775001226 775002023 797 True 1397.0 1397 98.248 1 798 1 chr2B.!!$R2 797
4 TraesCS5A01G064900 chr4A 575713445 575714284 839 False 887.0 887 86.358 1 810 1 chr4A.!!$F1 809
5 TraesCS5A01G064900 chr1A 139903749 139904564 815 False 821.0 821 85.348 1 792 1 chr1A.!!$F1 791
6 TraesCS5A01G064900 chr6D 292711656 292712427 771 True 789.0 789 85.733 1 748 1 chr6D.!!$R1 747
7 TraesCS5A01G064900 chr7B 538056980 538057769 789 False 410.5 418 86.656 1 803 2 chr7B.!!$F1 802

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
574 586 0.389948 GCGTGGACGAAGGATTGTCT 60.39 55.0 2.73 0.0 43.02 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1527 0.109689 GCGCAGAAGTCGACACTAGT 60.11 55.0 19.5 0.0 30.14 2.57 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
257 258 3.396911 GAGAGATGGACGCGTGCGA 62.397 63.158 25.71 15.1 42.83 5.10
574 586 0.389948 GCGTGGACGAAGGATTGTCT 60.390 55.000 2.73 0.0 43.02 3.41
686 714 6.708285 ACCACGAAATTACTATGGACTCTTT 58.292 36.000 0.00 0.0 34.38 2.52
943 973 2.824041 CGCCCCTTCCAATCACCG 60.824 66.667 0.00 0.0 0.00 4.94
946 976 2.824041 CCCTTCCAATCACCGCCG 60.824 66.667 0.00 0.0 0.00 6.46
1182 1212 2.377310 CGCACGGTAAGTCAACCCG 61.377 63.158 0.00 0.0 46.93 5.28
1187 1217 1.087771 CGGTAAGTCAACCCGATGCC 61.088 60.000 0.00 0.0 44.41 4.40
1247 1277 2.553602 TGTCCTCATGATGTTGTTGTGC 59.446 45.455 0.00 0.0 0.00 4.57
1248 1278 1.805943 TCCTCATGATGTTGTTGTGCG 59.194 47.619 0.00 0.0 0.00 5.34
1249 1279 1.609932 CTCATGATGTTGTTGTGCGC 58.390 50.000 0.00 0.0 0.00 6.09
1426 1456 5.048153 TGTCAGGATCGCTAATCTAATCG 57.952 43.478 0.00 0.0 34.56 3.34
1497 1527 9.733556 ATAGATGGTGAATTGTGTACTTTGTTA 57.266 29.630 0.00 0.0 0.00 2.41
1516 1546 0.109689 ACTAGTGTCGACTTCTGCGC 60.110 55.000 17.92 0.0 33.21 6.09
1592 1625 6.127897 GGGTCATAGATCCAACTTGTTTTCTG 60.128 42.308 0.00 0.0 32.11 3.02
1608 1641 3.370840 TTCTGTCTGGAAATGGATGGG 57.629 47.619 0.00 0.0 0.00 4.00
1609 1642 2.278245 TCTGTCTGGAAATGGATGGGT 58.722 47.619 0.00 0.0 0.00 4.51
1610 1643 2.025981 TCTGTCTGGAAATGGATGGGTG 60.026 50.000 0.00 0.0 0.00 4.61
1611 1644 1.710244 TGTCTGGAAATGGATGGGTGT 59.290 47.619 0.00 0.0 0.00 4.16
1612 1645 2.094675 GTCTGGAAATGGATGGGTGTG 58.905 52.381 0.00 0.0 0.00 3.82
1613 1646 1.710244 TCTGGAAATGGATGGGTGTGT 59.290 47.619 0.00 0.0 0.00 3.72
1624 1657 2.051334 TGGGTGTGTTTTCAGTGAGG 57.949 50.000 0.00 0.0 0.00 3.86
1699 1746 7.754069 TGAACAAAAACTGCATTTTCTGTAG 57.246 32.000 8.69 0.0 39.70 2.74
2027 2080 4.887071 TGTTGAGTGTTGGCTTTGTAGAAT 59.113 37.500 0.00 0.0 0.00 2.40
2039 2092 6.533723 TGGCTTTGTAGAATCGTATTACACTG 59.466 38.462 0.00 0.0 0.00 3.66
2040 2093 6.534079 GGCTTTGTAGAATCGTATTACACTGT 59.466 38.462 0.00 0.0 0.00 3.55
2070 2123 7.592903 GTCTCAAATGTTCAAAATGTCTTCTCC 59.407 37.037 0.00 0.0 0.00 3.71
2136 2190 8.032451 GCTATACCTTCTCTTCCTAATGCTAAG 58.968 40.741 0.00 0.0 0.00 2.18
2329 2383 2.798976 TGAACATGCACTCTTTTGGC 57.201 45.000 0.00 0.0 0.00 4.52
2333 2387 1.200716 ACATGCACTCTTTTGGCGATG 59.799 47.619 0.00 0.0 0.00 3.84
2377 2431 8.668368 TCATTTGAATGGAAGCTTGATGAGGTT 61.668 37.037 2.10 0.0 40.58 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.778993 GTGTTACTACGTCTGAAATTACATCTA 57.221 33.333 0.00 0.0 0.00 1.98
20 21 4.023792 TGGTACTGTGAGTGTGTTACTACG 60.024 45.833 0.00 0.0 40.53 3.51
34 35 3.605749 CTGCCCCGGTGGTACTGTG 62.606 68.421 0.00 0.0 36.04 3.66
257 258 0.741221 GGAGCCGAGAATGAAGCGTT 60.741 55.000 0.00 0.0 0.00 4.84
321 322 4.735132 CGCGCTTCTCCCGAACCA 62.735 66.667 5.56 0.0 0.00 3.67
512 524 1.407979 CGCTAACTCCTCCGGTTATGT 59.592 52.381 0.00 0.0 0.00 2.29
574 586 1.747367 CAAACCGCTAATCCCGCCA 60.747 57.895 0.00 0.0 0.00 5.69
930 960 3.508840 GCGGCGGTGATTGGAAGG 61.509 66.667 9.78 0.0 0.00 3.46
965 995 4.787280 AGGAGCGGGTGGAGGAGG 62.787 72.222 0.00 0.0 0.00 4.30
966 996 3.151022 GAGGAGCGGGTGGAGGAG 61.151 72.222 0.00 0.0 0.00 3.69
967 997 4.779733 GGAGGAGCGGGTGGAGGA 62.780 72.222 0.00 0.0 0.00 3.71
1187 1217 1.534595 GCAGTGCGAATGCCTAATTGG 60.535 52.381 0.00 0.0 41.78 3.16
1209 1239 2.224137 GGACATCAGATCGCCATCTCAA 60.224 50.000 0.00 0.0 37.25 3.02
1395 1425 0.172578 CGATCCTGACAAGTACGGCA 59.827 55.000 0.00 0.0 0.00 5.69
1426 1456 3.587797 TGGGATCACGACACTAACTTC 57.412 47.619 0.00 0.0 0.00 3.01
1471 1501 8.635765 AACAAAGTACACAATTCACCATCTAT 57.364 30.769 0.00 0.0 0.00 1.98
1497 1527 0.109689 GCGCAGAAGTCGACACTAGT 60.110 55.000 19.50 0.0 30.14 2.57
1592 1625 2.094675 CACACCCATCCATTTCCAGAC 58.905 52.381 0.00 0.0 0.00 3.51
1608 1641 1.388547 TGGCCTCACTGAAAACACAC 58.611 50.000 3.32 0.0 0.00 3.82
1609 1642 2.023673 CTTGGCCTCACTGAAAACACA 58.976 47.619 3.32 0.0 0.00 3.72
1610 1643 2.024414 ACTTGGCCTCACTGAAAACAC 58.976 47.619 3.32 0.0 0.00 3.32
1611 1644 2.435372 ACTTGGCCTCACTGAAAACA 57.565 45.000 3.32 0.0 0.00 2.83
1612 1645 4.911514 TTAACTTGGCCTCACTGAAAAC 57.088 40.909 3.32 0.0 0.00 2.43
1613 1646 5.841810 CAATTAACTTGGCCTCACTGAAAA 58.158 37.500 3.32 0.0 0.00 2.29
1699 1746 5.010922 TCACCATTGCAATATTAGCCCATTC 59.989 40.000 12.53 0.0 0.00 2.67
2027 2080 5.441709 TGAGACACAACAGTGTAATACGA 57.558 39.130 0.00 0.0 45.96 3.43
2039 2092 7.489113 AGACATTTTGAACATTTGAGACACAAC 59.511 33.333 0.00 0.0 38.29 3.32
2040 2093 7.546358 AGACATTTTGAACATTTGAGACACAA 58.454 30.769 0.00 0.0 36.65 3.33
2070 2123 6.607198 TGGGAAGAGATAAATGGGCTAAAAAG 59.393 38.462 0.00 0.0 0.00 2.27
2362 2416 3.760684 ACCATGAAACCTCATCAAGCTTC 59.239 43.478 0.00 0.0 40.49 3.86
2377 2431 8.887264 AATTGTTTTACTACCCATACCATGAA 57.113 30.769 0.00 0.0 0.00 2.57


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

AutoCloner maintained by Alex Coulton.