Multiple sequence alignment - TraesCS6D01G355900

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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 TraesCS6D01G355900 chr6D 100.000 2739 0 0 1 2739 450531761 450534499 0.000000e+00 5059
1 TraesCS6D01G355900 chr6D 95.143 2162 95 4 578 2739 36621602 36619451 0.000000e+00 3402
2 TraesCS6D01G355900 chr6D 96.501 543 16 2 1 543 463783067 463782528 0.000000e+00 894
3 TraesCS6D01G355900 chr4D 95.692 2739 98 7 1 2739 7132690 7135408 0.000000e+00 4386
4 TraesCS6D01G355900 chr3B 95.033 2738 116 11 1 2735 636124579 636127299 0.000000e+00 4285
5 TraesCS6D01G355900 chr1D 94.311 2742 135 10 2 2739 447334056 447331332 0.000000e+00 4180
6 TraesCS6D01G355900 chr1D 95.797 2165 83 7 578 2739 307842584 307840425 0.000000e+00 3487
7 TraesCS6D01G355900 chr1D 96.324 544 14 4 1 543 307843113 307842575 0.000000e+00 889
8 TraesCS6D01G355900 chr1D 91.168 351 23 8 1 349 484434767 484435111 1.150000e-128 470
9 TraesCS6D01G355900 chr1D 90.678 354 24 7 1 349 452270970 452271319 1.920000e-126 462
10 TraesCS6D01G355900 chr5D 94.941 2471 114 8 274 2739 45498636 45496172 0.000000e+00 3860
11 TraesCS6D01G355900 chr1A 92.600 2581 161 18 159 2739 372262198 372264748 0.000000e+00 3681
12 TraesCS6D01G355900 chr3D 95.847 2167 79 8 69 2233 53611129 53608972 0.000000e+00 3493
13 TraesCS6D01G355900 chr3D 97.727 132 3 0 2608 2739 53563984 53563853 7.630000e-56 228
14 TraesCS6D01G355900 chr7D 95.814 2150 75 4 596 2739 184206407 184204267 0.000000e+00 3458
15 TraesCS6D01G355900 chr7D 90.331 362 27 7 1 360 579739718 579740073 4.130000e-128 468
16 TraesCS6D01G355900 chr6B 94.049 2151 119 4 589 2739 84917510 84915369 0.000000e+00 3254


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 TraesCS6D01G355900 chr6D 450531761 450534499 2738 False 5059 5059 100.0000 1 2739 1 chr6D.!!$F1 2738
1 TraesCS6D01G355900 chr6D 36619451 36621602 2151 True 3402 3402 95.1430 578 2739 1 chr6D.!!$R1 2161
2 TraesCS6D01G355900 chr6D 463782528 463783067 539 True 894 894 96.5010 1 543 1 chr6D.!!$R2 542
3 TraesCS6D01G355900 chr4D 7132690 7135408 2718 False 4386 4386 95.6920 1 2739 1 chr4D.!!$F1 2738
4 TraesCS6D01G355900 chr3B 636124579 636127299 2720 False 4285 4285 95.0330 1 2735 1 chr3B.!!$F1 2734
5 TraesCS6D01G355900 chr1D 447331332 447334056 2724 True 4180 4180 94.3110 2 2739 1 chr1D.!!$R1 2737
6 TraesCS6D01G355900 chr1D 307840425 307843113 2688 True 2188 3487 96.0605 1 2739 2 chr1D.!!$R2 2738
7 TraesCS6D01G355900 chr5D 45496172 45498636 2464 True 3860 3860 94.9410 274 2739 1 chr5D.!!$R1 2465
8 TraesCS6D01G355900 chr1A 372262198 372264748 2550 False 3681 3681 92.6000 159 2739 1 chr1A.!!$F1 2580
9 TraesCS6D01G355900 chr3D 53608972 53611129 2157 True 3493 3493 95.8470 69 2233 1 chr3D.!!$R2 2164
10 TraesCS6D01G355900 chr7D 184204267 184206407 2140 True 3458 3458 95.8140 596 2739 1 chr7D.!!$R1 2143
11 TraesCS6D01G355900 chr6B 84915369 84917510 2141 True 3254 3254 94.0490 589 2739 1 chr6B.!!$R1 2150

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
198 199 3.118811 TGTGATAGATGACGCATGTTCCA 60.119 43.478 0.00 0.00 0.00 3.53 F
1054 1071 2.517875 GCCTACCGCTCGAGGGTA 60.518 66.667 25.69 24.29 38.99 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1272 1296 0.325933 CAATGTCCCCAGAGCAGTCA 59.674 55.0 0.00 0.0 0.0 3.41 R
1951 1978 1.293267 TACGCTGCGCCTTACCAAAC 61.293 55.0 23.51 0.0 0.0 2.93 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
188 189 5.220931 GGAGGCATTTGTTGTGATAGATGAC 60.221 44.000 0.00 0.00 0.00 3.06
198 199 3.118811 TGTGATAGATGACGCATGTTCCA 60.119 43.478 0.00 0.00 0.00 3.53
211 212 4.848562 CATGTTCCAATGCTATGATGCT 57.151 40.909 0.00 0.00 0.00 3.79
266 267 9.730705 TGGAGATGAATATTGGAGATATTTGTC 57.269 33.333 0.00 0.00 0.00 3.18
383 385 6.930722 TGCATGTAGTGTATGTTAGATGATGG 59.069 38.462 0.00 0.00 0.00 3.51
558 570 6.053632 TGTTATGCATCTATATGTCCCCTG 57.946 41.667 0.19 0.00 35.38 4.45
797 814 3.196469 TCTTCATTTCGACAGATGCTCCT 59.804 43.478 0.00 0.00 0.00 3.69
1054 1071 2.517875 GCCTACCGCTCGAGGGTA 60.518 66.667 25.69 24.29 38.99 3.69
1272 1296 1.893801 CTCACGGAGGTAGTGTTTCCT 59.106 52.381 0.00 0.00 40.28 3.36
1289 1313 1.270414 CCTGACTGCTCTGGGGACAT 61.270 60.000 0.00 0.00 41.51 3.06
1384 1408 5.305585 CCTACCTATACCGTTCGGTAAGTA 58.694 45.833 24.36 21.87 43.09 2.24
1595 1622 2.225791 TAGAGCGCGTGCATGGACTT 62.226 55.000 24.79 0.00 46.23 3.01
1941 1968 3.209097 ACTTGCCACAGCGCGTTT 61.209 55.556 8.43 0.00 44.31 3.60
1942 1969 2.026014 CTTGCCACAGCGCGTTTT 59.974 55.556 8.43 0.00 44.31 2.43
2416 2444 2.224066 GGAGTACGGACCCATCATGAAG 60.224 54.545 0.00 0.00 0.00 3.02
2461 2490 3.875727 TGTTTTCAACCGACGTTTGGATA 59.124 39.130 14.02 0.00 0.00 2.59
2632 2662 6.012658 TGGAGTTCATTTGCTTATGTTCAC 57.987 37.500 0.00 0.00 0.00 3.18
2666 2696 8.291191 TGATCCATATTGTGCTTATTGTTTCA 57.709 30.769 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 3.561503 CATCATAGCATTGGAACATGCG 58.438 45.455 0.00 0.00 43.75 4.73
198 199 7.400439 ACATCCAATACTAGCATCATAGCATT 58.600 34.615 0.00 0.00 36.85 3.56
383 385 4.014406 ACCCCGACAAAATCCAGTATTTC 58.986 43.478 0.00 0.00 36.76 2.17
467 471 4.464951 ACAACATCCAACATGCATCATCTT 59.535 37.500 0.00 0.00 0.00 2.40
692 706 4.969484 ACCACTCCGTTCTCAATAAAACT 58.031 39.130 0.00 0.00 0.00 2.66
756 773 7.504924 TGAAGACCCAAACAATTAGTAACTG 57.495 36.000 0.00 0.00 0.00 3.16
797 814 4.100084 CCCTCATCCGCAGTGGCA 62.100 66.667 0.00 0.00 41.24 4.92
919 936 4.427661 AGCTGAGTGGACGAGCGC 62.428 66.667 0.00 0.00 37.81 5.92
1054 1071 1.067283 CACTCGTCCTGTCAGAGCATT 60.067 52.381 0.00 0.00 35.56 3.56
1203 1227 2.122769 TCCACCACCCGAGGTTCA 60.123 61.111 0.00 0.00 40.77 3.18
1242 1266 3.033659 ACCTCCGTGAGAAGATACCAT 57.966 47.619 2.84 0.00 0.00 3.55
1272 1296 0.325933 CAATGTCCCCAGAGCAGTCA 59.674 55.000 0.00 0.00 0.00 3.41
1289 1313 1.688735 CGAGATACATCCAGAGGGCAA 59.311 52.381 0.00 0.00 0.00 4.52
1354 1378 0.608582 CGGTATAGGTAGGCGAGGCT 60.609 60.000 4.23 4.23 0.00 4.58
1595 1622 1.000607 GTCGCCATCTTCGCCATAGTA 60.001 52.381 0.00 0.00 0.00 1.82
1941 1968 2.123988 CTTACCAAACTGCGCGGCAA 62.124 55.000 18.15 0.00 38.41 4.52
1942 1969 2.592001 TTACCAAACTGCGCGGCA 60.592 55.556 18.15 5.56 36.92 5.69
1951 1978 1.293267 TACGCTGCGCCTTACCAAAC 61.293 55.000 23.51 0.00 0.00 2.93
2300 2328 2.683859 CGTCTGCCGTCGTCCACTA 61.684 63.158 0.00 0.00 0.00 2.74
2416 2444 8.379457 ACAGATAAAAACAACTTACCACTCTC 57.621 34.615 0.00 0.00 0.00 3.20
2461 2490 7.715249 TGAGTCAGTAGCACTAAAGTTGATTTT 59.285 33.333 0.00 0.00 32.01 1.82
2632 2662 5.301045 AGCACAATATGGATCAACTTCATGG 59.699 40.000 0.00 0.00 0.00 3.66
2666 2696 4.318332 TGACGAACTTCTGCAATGAGAAT 58.682 39.130 0.00 0.00 31.51 2.40


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

AutoCloner maintained by Alex Coulton.