Multiple sequence alignment - TraesCS4A01G153000

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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 TraesCS4A01G153000 chr4A 100.000 2237 0 0 1 2237 309490583 309488347 0 4132
1 TraesCS4A01G153000 chr5D 96.564 2241 69 7 1 2237 6177700 6175464 0 3705
2 TraesCS4A01G153000 chr5D 96.435 533 13 3 1 528 28034102 28034633 0 874
3 TraesCS4A01G153000 chr2D 96.344 2243 70 8 1 2237 638423723 638425959 0 3677
4 TraesCS4A01G153000 chr1D 96.255 2243 74 8 1 2237 254434248 254436486 0 3668
5 TraesCS4A01G153000 chr1D 95.026 1709 74 6 531 2237 51872191 51870492 0 2675
6 TraesCS4A01G153000 chr4B 95.274 2243 98 7 1 2237 308680552 308678312 0 3548
7 TraesCS4A01G153000 chr4D 92.883 2248 138 14 1 2237 207069014 207066778 0 3245
8 TraesCS4A01G153000 chr2A 95.049 2040 87 11 45 2073 32525820 32527856 0 3195
9 TraesCS4A01G153000 chr3D 92.321 2240 138 11 1 2236 235618120 235620329 0 3153
10 TraesCS4A01G153000 chr5A 95.313 1963 77 8 287 2237 657451090 657453049 0 3101


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 TraesCS4A01G153000 chr4A 309488347 309490583 2236 True 4132 4132 100.000 1 2237 1 chr4A.!!$R1 2236
1 TraesCS4A01G153000 chr5D 6175464 6177700 2236 True 3705 3705 96.564 1 2237 1 chr5D.!!$R1 2236
2 TraesCS4A01G153000 chr5D 28034102 28034633 531 False 874 874 96.435 1 528 1 chr5D.!!$F1 527
3 TraesCS4A01G153000 chr2D 638423723 638425959 2236 False 3677 3677 96.344 1 2237 1 chr2D.!!$F1 2236
4 TraesCS4A01G153000 chr1D 254434248 254436486 2238 False 3668 3668 96.255 1 2237 1 chr1D.!!$F1 2236
5 TraesCS4A01G153000 chr1D 51870492 51872191 1699 True 2675 2675 95.026 531 2237 1 chr1D.!!$R1 1706
6 TraesCS4A01G153000 chr4B 308678312 308680552 2240 True 3548 3548 95.274 1 2237 1 chr4B.!!$R1 2236
7 TraesCS4A01G153000 chr4D 207066778 207069014 2236 True 3245 3245 92.883 1 2237 1 chr4D.!!$R1 2236
8 TraesCS4A01G153000 chr2A 32525820 32527856 2036 False 3195 3195 95.049 45 2073 1 chr2A.!!$F1 2028
9 TraesCS4A01G153000 chr3D 235618120 235620329 2209 False 3153 3153 92.321 1 2236 1 chr3D.!!$F1 2235
10 TraesCS4A01G153000 chr5A 657451090 657453049 1959 False 3101 3101 95.313 287 2237 1 chr5A.!!$F1 1950

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
934 945 0.349091 ACCTCTAAGGGGCCCCAATA 59.651 55.0 42.48 30.85 40.58 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 1828 4.402056 TTTCTAATCCTCCAAGCTACCG 57.598 45.455 0.0 0.0 0.0 4.02 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
73 74 3.737559 AAGCCCATGTATGAACAAGGA 57.262 42.857 1.53 0.00 45.48 3.36
76 77 4.613437 AGCCCATGTATGAACAAGGATTT 58.387 39.130 1.53 0.00 45.48 2.17
135 138 1.368558 AGGGCTAGGGGGAAGTTCTAA 59.631 52.381 2.25 0.00 0.00 2.10
162 165 3.965379 TTCCGTACTTTGTATCTGGCA 57.035 42.857 0.00 0.00 0.00 4.92
229 232 4.760047 CACGCTTCTGGGACCCGG 62.760 72.222 13.92 13.92 0.00 5.73
318 321 9.824534 CAATTTTGGGTATTCACTTAATTTTGC 57.175 29.630 0.00 0.00 0.00 3.68
365 368 6.779860 AGTACTCAAGGCTCTTTATTTTGGA 58.220 36.000 0.00 0.00 0.00 3.53
449 459 9.847224 CTTAGTCCCAGTGTTATATTTGGTTAT 57.153 33.333 0.00 0.00 0.00 1.89
485 495 0.476771 TTTGGTGGAGAAGGGTGGAC 59.523 55.000 0.00 0.00 0.00 4.02
541 551 2.354604 GGGCATGTATGGTTGGGTTTTG 60.355 50.000 0.00 0.00 0.00 2.44
553 563 6.942976 TGGTTGGGTTTTGTTTGTGTATTTA 58.057 32.000 0.00 0.00 0.00 1.40
556 566 6.222038 TGGGTTTTGTTTGTGTATTTAGCA 57.778 33.333 0.00 0.00 0.00 3.49
623 633 3.629398 GCATTTGTATGGTCTGGAGAAGG 59.371 47.826 0.00 0.00 32.15 3.46
710 720 7.276658 TGGTTCAATAATACAGCTTATCCGAA 58.723 34.615 0.00 0.00 0.00 4.30
820 831 1.274703 ATCCGCTCAAGGACCCACAT 61.275 55.000 0.00 0.00 44.07 3.21
839 850 9.847224 ACCCACATGTTTAGGTAAATATCTAAG 57.153 33.333 9.69 0.00 31.15 2.18
869 880 3.010138 CCAACTGGGGAGGTTATCTTTGA 59.990 47.826 0.00 0.00 0.00 2.69
934 945 0.349091 ACCTCTAAGGGGCCCCAATA 59.651 55.000 42.48 30.85 40.58 1.90
982 994 4.666512 AGACATACAACCTTGGCAAGAAT 58.333 39.130 28.18 13.12 0.00 2.40
985 997 4.832266 ACATACAACCTTGGCAAGAATGAA 59.168 37.500 28.18 10.91 0.00 2.57
990 1002 1.131883 CCTTGGCAAGAATGAAGCTCG 59.868 52.381 28.18 3.67 0.00 5.03
1042 1054 1.889829 CTTTAAATTCCGTGGGTGGCA 59.110 47.619 0.00 0.00 0.00 4.92
1196 1208 5.048083 CAGGTTTTGAAAAGGGAATCGATCA 60.048 40.000 0.00 0.00 0.00 2.92
1198 1210 6.211384 AGGTTTTGAAAAGGGAATCGATCATT 59.789 34.615 0.00 0.00 0.00 2.57
1210 1222 8.163408 AGGGAATCGATCATTATTTGGAACATA 58.837 33.333 0.00 0.00 39.30 2.29
1452 1474 1.414181 CCGGAGCTATCAACCACTCAT 59.586 52.381 0.00 0.00 0.00 2.90
1477 1499 3.454858 TCTCTCCACAGCCTAATCCTTT 58.545 45.455 0.00 0.00 0.00 3.11
1910 1940 2.291605 ACCCCTTGTATTTGCTTCTCCC 60.292 50.000 0.00 0.00 0.00 4.30
1911 1941 2.024941 CCCCTTGTATTTGCTTCTCCCT 60.025 50.000 0.00 0.00 0.00 4.20
1929 1959 6.980577 TCTCCCTATGGTTGGTCAAATAATT 58.019 36.000 0.00 0.00 0.00 1.40
1990 2021 6.293571 GGACTAGTCTTTCTCGTAGCTATTCC 60.294 46.154 21.88 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 9.032624 AGAGTAGCTAAGTGTGGAAGTAAAATA 57.967 33.333 0.00 0.00 0.00 1.40
135 138 7.065443 GCCAGATACAAAGTACGGAAAAGTATT 59.935 37.037 0.00 0.00 0.00 1.89
162 165 4.163458 TGCGGAGGAAATTAGGTGAAGTAT 59.837 41.667 0.00 0.00 0.00 2.12
318 321 5.669164 AGAAGAAAAGCACCTAGACCTAG 57.331 43.478 0.00 0.00 0.00 3.02
365 368 3.587506 GGGCCAAGGTATCATATACACCT 59.412 47.826 4.39 0.00 44.66 4.00
449 459 8.770010 TCCACCAAAAGGAGATTTTAGTAAAA 57.230 30.769 10.39 10.39 39.11 1.52
541 551 6.644592 TGCCAAATTCTGCTAAATACACAAAC 59.355 34.615 1.47 0.00 0.00 2.93
553 563 6.945218 TGGTTAAAATATGCCAAATTCTGCT 58.055 32.000 1.47 0.00 0.00 4.24
623 633 8.705048 AGCAGCTAAACTATAAGACAAGTAAC 57.295 34.615 0.00 0.00 0.00 2.50
710 720 2.356741 CCGGTGGGTCCATAAAACTCAT 60.357 50.000 0.00 0.00 35.57 2.90
754 764 9.930693 CTGGTCTCTAACTAGAAAAGTAAATGT 57.069 33.333 0.00 0.00 38.71 2.71
820 831 9.569122 GGAATGCCTTAGATATTTACCTAAACA 57.431 33.333 0.00 0.00 0.00 2.83
982 994 4.560128 GTCATATATTCTGCCGAGCTTCA 58.440 43.478 0.00 0.00 0.00 3.02
985 997 2.234908 GGGTCATATATTCTGCCGAGCT 59.765 50.000 0.00 0.00 0.00 4.09
990 1002 2.076863 GCGTGGGTCATATATTCTGCC 58.923 52.381 0.00 0.00 0.00 4.85
1042 1054 3.576118 ACTGCATTGATCTCGGTAGCTAT 59.424 43.478 0.00 0.00 0.00 2.97
1168 1180 5.105756 CGATTCCCTTTTCAAAACCTGCTAT 60.106 40.000 0.00 0.00 0.00 2.97
1346 1366 9.522804 TGCTTATTGAATACGTTTGTTTCTTTT 57.477 25.926 0.00 0.00 0.00 2.27
1411 1433 5.541098 GGTCTTGAAAACCGGTATAGTTG 57.459 43.478 8.00 0.00 0.00 3.16
1452 1474 2.550277 TTAGGCTGTGGAGAGATGGA 57.450 50.000 0.00 0.00 0.00 3.41
1703 1726 6.902416 AGGGGTTTAATCATGAATCCATTGAA 59.098 34.615 0.00 0.00 26.81 2.69
1757 1784 9.838339 CTACATATTTGATCCCTCACTTAAACT 57.162 33.333 0.00 0.00 0.00 2.66
1798 1828 4.402056 TTTCTAATCCTCCAAGCTACCG 57.598 45.455 0.00 0.00 0.00 4.02
1929 1959 7.610692 TGATGTACCGGAAAATACACCATTTTA 59.389 33.333 9.46 0.00 44.98 1.52
1936 1966 7.442969 TCCATAATGATGTACCGGAAAATACAC 59.557 37.037 9.46 2.35 34.24 2.90
2115 2148 6.233434 TGAAAGAGAAGAGCTAGCAATTCAA 58.767 36.000 25.05 8.18 0.00 2.69
2116 2149 5.798132 TGAAAGAGAAGAGCTAGCAATTCA 58.202 37.500 25.05 16.05 0.00 2.57


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

AutoCloner maintained by Alex Coulton.