Multiple sequence alignment - TraesCS6A01G279900

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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 TraesCS6A01G279900 chr6A 100.000 2249 0 0 1 2249 508000567 508002815 0 4154
1 TraesCS6A01G279900 chr6A 96.673 1082 32 3 1 1081 349779534 349780612 0 1796
2 TraesCS6A01G279900 chr3A 96.309 2249 73 7 1 2249 50435225 50437463 0 3685
3 TraesCS6A01G279900 chr3A 96.481 1080 34 4 1 1079 657439404 657440480 0 1781
4 TraesCS6A01G279900 chr1A 95.467 2250 85 8 1 2249 527084309 527082076 0 3574
5 TraesCS6A01G279900 chr2A 96.398 2110 74 2 141 2249 94221952 94224060 0 3474
6 TraesCS6A01G279900 chr2A 95.673 1710 72 2 1 1709 65084521 65086229 0 2747
7 TraesCS6A01G279900 chr5A 95.996 1823 71 2 429 2249 554347662 554349484 0 2961
8 TraesCS6A01G279900 chr5A 96.529 1354 47 0 896 2249 560882915 560881562 0 2241
9 TraesCS6A01G279900 chr6D 96.357 1647 54 3 1 1646 196357615 196359256 0 2704
10 TraesCS6A01G279900 chr7A 94.972 1591 78 2 379 1968 724636562 724638151 0 2494
11 TraesCS6A01G279900 chr6B 94.601 1352 69 3 901 2249 131761702 131760352 0 2089
12 TraesCS6A01G279900 chr1B 94.732 1044 53 2 1206 2249 552389896 552388855 0 1622
13 TraesCS6A01G279900 chr2D 95.618 890 39 0 1360 2249 464801694 464800805 0 1428


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 TraesCS6A01G279900 chr6A 508000567 508002815 2248 False 4154 4154 100.000 1 2249 1 chr6A.!!$F2 2248
1 TraesCS6A01G279900 chr6A 349779534 349780612 1078 False 1796 1796 96.673 1 1081 1 chr6A.!!$F1 1080
2 TraesCS6A01G279900 chr3A 50435225 50437463 2238 False 3685 3685 96.309 1 2249 1 chr3A.!!$F1 2248
3 TraesCS6A01G279900 chr3A 657439404 657440480 1076 False 1781 1781 96.481 1 1079 1 chr3A.!!$F2 1078
4 TraesCS6A01G279900 chr1A 527082076 527084309 2233 True 3574 3574 95.467 1 2249 1 chr1A.!!$R1 2248
5 TraesCS6A01G279900 chr2A 94221952 94224060 2108 False 3474 3474 96.398 141 2249 1 chr2A.!!$F2 2108
6 TraesCS6A01G279900 chr2A 65084521 65086229 1708 False 2747 2747 95.673 1 1709 1 chr2A.!!$F1 1708
7 TraesCS6A01G279900 chr5A 554347662 554349484 1822 False 2961 2961 95.996 429 2249 1 chr5A.!!$F1 1820
8 TraesCS6A01G279900 chr5A 560881562 560882915 1353 True 2241 2241 96.529 896 2249 1 chr5A.!!$R1 1353
9 TraesCS6A01G279900 chr6D 196357615 196359256 1641 False 2704 2704 96.357 1 1646 1 chr6D.!!$F1 1645
10 TraesCS6A01G279900 chr7A 724636562 724638151 1589 False 2494 2494 94.972 379 1968 1 chr7A.!!$F1 1589
11 TraesCS6A01G279900 chr6B 131760352 131761702 1350 True 2089 2089 94.601 901 2249 1 chr6B.!!$R1 1348
12 TraesCS6A01G279900 chr1B 552388855 552389896 1041 True 1622 1622 94.732 1206 2249 1 chr1B.!!$R1 1043
13 TraesCS6A01G279900 chr2D 464800805 464801694 889 True 1428 1428 95.618 1360 2249 1 chr2D.!!$R1 889

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
929 933 2.107041 TTTGGTCGCCGGTCTGATGT 62.107 55.0 1.9 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 1922 5.749596 TTGGGAATGCAGTGTATAAATCG 57.25 39.13 0.0 0.0 0.0 3.34 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
121 122 5.046878 TGGTTCAGCTCTCGGTAATTTAAGA 60.047 40.000 0.00 0.0 0.00 2.10
146 147 9.151471 GATTCTGTATAAATTTGGCGCTATCTA 57.849 33.333 7.64 0.0 0.00 1.98
158 159 6.852420 TGGCGCTATCTATACCTATTTCTT 57.148 37.500 7.64 0.0 0.00 2.52
482 485 8.255111 TGTGTATACCTTGATTCAGAGATCAT 57.745 34.615 0.00 0.0 36.05 2.45
484 487 9.553064 GTGTATACCTTGATTCAGAGATCATTT 57.447 33.333 0.00 0.0 36.05 2.32
531 534 7.170828 CGTACTGCACAATTATGCTATTTCCTA 59.829 37.037 10.54 0.0 46.28 2.94
863 866 4.530946 CAGGTAAAGGAGGGAACAGTTCTA 59.469 45.833 13.13 0.0 0.00 2.10
929 933 2.107041 TTTGGTCGCCGGTCTGATGT 62.107 55.000 1.90 0.0 0.00 3.06
1106 1113 2.091541 CGCCTTTTCCTTTGCCAGATA 58.908 47.619 0.00 0.0 0.00 1.98
1147 1154 2.297895 ACCTCAGGGTGGCGCATTA 61.298 57.895 10.83 0.0 45.43 1.90
1230 1237 3.509967 TGTTGATTCTCTCCGTGCTCTTA 59.490 43.478 0.00 0.0 0.00 2.10
1347 1354 0.103937 GCCCAGATTCCTCGACTGAG 59.896 60.000 1.78 0.0 42.18 3.35
1428 1435 2.684881 CTGCATTACCACCACCATTCTC 59.315 50.000 0.00 0.0 0.00 2.87
1533 1540 9.552114 CATTGACAAGTCAGAACAAGATAAATC 57.448 33.333 2.87 0.0 41.13 2.17
1666 1673 8.689061 ACATACGTCTGTACTATTGATGGTTAA 58.311 33.333 4.56 0.0 32.26 2.01
2063 2070 9.219603 ACTTATAGTGCATATTCGCATTGTATT 57.780 29.630 0.00 0.0 45.26 1.89
2208 2215 3.540314 AGAGTGAATCCATGAGACTGC 57.460 47.619 0.00 0.0 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 7.986085 AGATAGCGCCAAATTTATACAGAAT 57.014 32.000 2.29 0.00 0.00 2.40
158 159 6.539173 ACACCAAATTTGTCTACCTATGTCA 58.461 36.000 16.73 0.00 0.00 3.58
482 485 7.936584 ACGGTTTTTCTGAATCAAGATGTAAA 58.063 30.769 0.00 0.00 0.00 2.01
484 487 7.876068 AGTACGGTTTTTCTGAATCAAGATGTA 59.124 33.333 0.00 0.00 0.00 2.29
531 534 2.815589 GCTGGGGTGTTCTTCTCATGTT 60.816 50.000 0.00 0.00 0.00 2.71
747 750 8.217111 TCCATGGCAATCTAACTTATGATGTTA 58.783 33.333 6.96 0.00 0.00 2.41
863 866 0.035630 GGATCACCTGCAGAGTGCTT 60.036 55.000 22.98 15.72 45.31 3.91
929 933 3.197766 ACCAACTAGCAGCAGTAGCAATA 59.802 43.478 0.00 0.00 45.49 1.90
1106 1113 2.505982 CCGCCGATCTCCCAATGT 59.494 61.111 0.00 0.00 0.00 2.71
1230 1237 2.452600 CTCACCTAGGAGGAGAAGCT 57.547 55.000 22.73 0.00 37.67 3.74
1347 1354 3.317150 GCACAAAAGTCAATAGGCCAAC 58.683 45.455 5.01 0.00 0.00 3.77
1428 1435 7.039434 TGGCAGGATTCAGATACTATTGTAGAG 60.039 40.741 0.00 0.00 31.51 2.43
1533 1540 5.682943 TCTCAAATTCGTAAACCCACTTG 57.317 39.130 0.00 0.00 0.00 3.16
1605 1612 3.454858 ACTCAAAGAAGATGCTAGGGGA 58.545 45.455 0.00 0.00 0.00 4.81
1666 1673 7.545965 GTCACTCAAGTGCATAACTAACAGTAT 59.454 37.037 5.25 0.00 45.25 2.12
1692 1699 6.835819 TGATCTTATTATCCTACAGACCCG 57.164 41.667 0.00 0.00 0.00 5.28
1915 1922 5.749596 TTGGGAATGCAGTGTATAAATCG 57.250 39.130 0.00 0.00 0.00 3.34
2063 2070 9.716556 ATACAGGAGAAAAGGACTAAGATTCTA 57.283 33.333 0.00 0.00 30.89 2.10


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

AutoCloner maintained by Alex Coulton.