Multiple sequence alignment - TraesCS5A01G337200

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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 TraesCS5A01G337200 chr5A 100.000 2498 0 0 1 2498 545646412 545643915 0.000000e+00 4614
1 TraesCS5A01G337200 chr5A 72.900 369 83 13 705 1062 445499519 445499881 7.300000e-21 111
2 TraesCS5A01G337200 chr6D 91.766 2514 172 13 12 2498 377187403 377189908 0.000000e+00 3463
3 TraesCS5A01G337200 chr6D 86.207 2059 243 27 468 2498 312812413 312810368 0.000000e+00 2191
4 TraesCS5A01G337200 chr1A 86.624 2026 244 19 12 2018 592546648 592548665 0.000000e+00 2215
5 TraesCS5A01G337200 chr1A 81.890 2529 388 36 1 2498 515117322 515119811 0.000000e+00 2069
6 TraesCS5A01G337200 chr1A 81.811 2529 390 36 1 2498 514861077 514863566 0.000000e+00 2058
7 TraesCS5A01G337200 chr1A 87.082 1556 192 6 12 1567 265638973 265637427 0.000000e+00 1751
8 TraesCS5A01G337200 chr1A 85.348 935 122 11 1573 2498 265628882 265627954 0.000000e+00 953
9 TraesCS5A01G337200 chr5D 82.857 2520 375 30 1 2498 88531849 88529365 0.000000e+00 2207
10 TraesCS5A01G337200 chr3A 82.153 2527 395 27 1 2498 32907266 32904767 0.000000e+00 2117
11 TraesCS5A01G337200 chr4A 80.330 2542 439 38 1 2498 547206118 547208642 0.000000e+00 1868
12 TraesCS5A01G337200 chr2D 80.245 2526 440 33 6 2498 250625308 250622809 0.000000e+00 1845
13 TraesCS5A01G337200 chr2D 93.320 1003 43 9 1505 2498 633446221 633445234 0.000000e+00 1459
14 TraesCS5A01G337200 chr2D 93.260 549 33 2 1949 2497 31903967 31903423 0.000000e+00 806
15 TraesCS5A01G337200 chr7D 89.857 1262 96 11 1264 2498 3718696 3719952 0.000000e+00 1592
16 TraesCS5A01G337200 chr3D 80.280 1785 320 20 6 1766 581411751 581409975 0.000000e+00 1317


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 TraesCS5A01G337200 chr5A 545643915 545646412 2497 True 4614 4614 100.000 1 2498 1 chr5A.!!$R1 2497
1 TraesCS5A01G337200 chr6D 377187403 377189908 2505 False 3463 3463 91.766 12 2498 1 chr6D.!!$F1 2486
2 TraesCS5A01G337200 chr6D 312810368 312812413 2045 True 2191 2191 86.207 468 2498 1 chr6D.!!$R1 2030
3 TraesCS5A01G337200 chr1A 592546648 592548665 2017 False 2215 2215 86.624 12 2018 1 chr1A.!!$F3 2006
4 TraesCS5A01G337200 chr1A 515117322 515119811 2489 False 2069 2069 81.890 1 2498 1 chr1A.!!$F2 2497
5 TraesCS5A01G337200 chr1A 514861077 514863566 2489 False 2058 2058 81.811 1 2498 1 chr1A.!!$F1 2497
6 TraesCS5A01G337200 chr1A 265637427 265638973 1546 True 1751 1751 87.082 12 1567 1 chr1A.!!$R2 1555
7 TraesCS5A01G337200 chr1A 265627954 265628882 928 True 953 953 85.348 1573 2498 1 chr1A.!!$R1 925
8 TraesCS5A01G337200 chr5D 88529365 88531849 2484 True 2207 2207 82.857 1 2498 1 chr5D.!!$R1 2497
9 TraesCS5A01G337200 chr3A 32904767 32907266 2499 True 2117 2117 82.153 1 2498 1 chr3A.!!$R1 2497
10 TraesCS5A01G337200 chr4A 547206118 547208642 2524 False 1868 1868 80.330 1 2498 1 chr4A.!!$F1 2497
11 TraesCS5A01G337200 chr2D 250622809 250625308 2499 True 1845 1845 80.245 6 2498 1 chr2D.!!$R2 2492
12 TraesCS5A01G337200 chr2D 633445234 633446221 987 True 1459 1459 93.320 1505 2498 1 chr2D.!!$R3 993
13 TraesCS5A01G337200 chr2D 31903423 31903967 544 True 806 806 93.260 1949 2497 1 chr2D.!!$R1 548
14 TraesCS5A01G337200 chr7D 3718696 3719952 1256 False 1592 1592 89.857 1264 2498 1 chr7D.!!$F1 1234
15 TraesCS5A01G337200 chr3D 581409975 581411751 1776 True 1317 1317 80.280 6 1766 1 chr3D.!!$R1 1760


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
175 182 0.03563 GAGATGCAGGCAACAGAGGT 60.036 55.0 0.0 0.0 41.41 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 1954 0.109532 TTGTTTGGCACCTCGATCCA 59.89 50.0 0.0 0.0 0.0 3.41 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
91 92 7.230027 AGTTCTTCAGTTTTTCCAGAGATCAT 58.770 34.615 0.00 0.00 0.00 2.45
175 182 0.035630 GAGATGCAGGCAACAGAGGT 60.036 55.000 0.00 0.00 41.41 3.85
210 217 1.623542 GGTGGGAGAGGGCGTAACAT 61.624 60.000 0.00 0.00 0.00 2.71
216 223 2.029623 GAGAGGGCGTAACATAGGTCA 58.970 52.381 0.00 0.00 0.00 4.02
381 394 0.037512 CTCCTCCTATGATGCAGCCG 60.038 60.000 0.00 0.00 0.00 5.52
475 488 6.414732 CCCAACTTCCAGTTTCAGTATATGA 58.585 40.000 0.00 0.00 36.03 2.15
489 502 1.976132 ATATGACAGCTGCGGCAGGT 61.976 55.000 27.50 27.50 43.33 4.00
523 536 6.815142 GCAATTTAGTCCAGCAAATCAGAATT 59.185 34.615 0.00 0.00 0.00 2.17
538 551 3.817084 TCAGAATTTGCAGTCAACTCAGG 59.183 43.478 0.00 0.00 30.75 3.86
548 561 1.869767 GTCAACTCAGGCAGTTCAGTG 59.130 52.381 0.00 0.00 44.14 3.66
645 658 9.435688 AAAAATAAAAATCAGGGTGTTGCTATC 57.564 29.630 0.00 0.00 0.00 2.08
680 699 1.135094 ATGCGTGAAGATGATCCCCT 58.865 50.000 0.00 0.00 0.00 4.79
688 707 5.626809 CGTGAAGATGATCCCCTTTTCACTA 60.627 44.000 17.02 0.00 41.16 2.74
703 723 7.417797 CCCTTTTCACTATGGACCCAAAATATG 60.418 40.741 0.00 0.00 0.00 1.78
729 749 2.434336 AGCCATCTGTTATAACTGCGGA 59.566 45.455 23.22 14.56 0.00 5.54
732 752 4.051922 CCATCTGTTATAACTGCGGACTC 58.948 47.826 16.33 0.00 0.00 3.36
905 925 3.058016 CACATTGAAACTAGTGGTGCAGG 60.058 47.826 0.00 0.00 0.00 4.85
909 929 1.282157 GAAACTAGTGGTGCAGGGGAT 59.718 52.381 0.00 0.00 0.00 3.85
921 941 0.393537 CAGGGGATTGTGAGTGGCTC 60.394 60.000 0.00 0.00 0.00 4.70
949 969 3.153919 GGCAATGTGGGACTTGTTCTTA 58.846 45.455 0.00 0.00 0.00 2.10
952 972 5.279456 GGCAATGTGGGACTTGTTCTTATTT 60.279 40.000 0.00 0.00 0.00 1.40
961 981 8.226112 TGGGACTTGTTCTTATTTAAAAGGGTA 58.774 33.333 0.00 0.00 0.00 3.69
1022 1042 1.002011 GGAAGACCAACAGGCCCTC 60.002 63.158 0.00 0.00 35.97 4.30
1145 1165 6.800890 AGGAAGGGGTAACAATATCTTTTGT 58.199 36.000 0.00 0.00 41.49 2.83
1205 1225 6.980593 TGACTGAAACTTGGATTGTTATTGG 58.019 36.000 0.00 0.00 0.00 3.16
1206 1226 6.775142 TGACTGAAACTTGGATTGTTATTGGA 59.225 34.615 0.00 0.00 0.00 3.53
1209 1229 6.310941 TGAAACTTGGATTGTTATTGGAGGA 58.689 36.000 0.00 0.00 0.00 3.71
1299 1319 8.121305 TCAACATTGACTGGCATACTATTTTT 57.879 30.769 0.00 0.00 31.01 1.94
1350 1370 1.203523 GTAGCTGTCAGAGACCCTGTG 59.796 57.143 3.32 0.00 43.38 3.66
1426 1446 2.550277 TTCTGTGGAGAGGGATGCTA 57.450 50.000 0.00 0.00 0.00 3.49
1462 1482 1.833630 CTGACAAGCCATCTGGACCTA 59.166 52.381 0.00 0.00 37.39 3.08
1563 1584 6.117488 GGAGGAGATGGATACTAGTACTAGC 58.883 48.000 26.54 12.84 36.66 3.42
1572 1593 6.610020 TGGATACTAGTACTAGCAACACCATT 59.390 38.462 26.54 9.04 36.66 3.16
1679 1724 2.108250 TCTTCTCCAAAGTTCAAGGGGG 59.892 50.000 0.00 0.00 0.00 5.40
1778 1829 1.901833 TGAGGCTGCTATCACACAAGA 59.098 47.619 0.00 0.00 0.00 3.02
1783 1834 3.529533 GCTGCTATCACACAAGATCACT 58.470 45.455 0.00 0.00 0.00 3.41
1806 1857 5.207354 TCTCTTCCTCAGAACATAGCTGAT 58.793 41.667 0.00 0.00 41.20 2.90
1826 1877 1.280457 AAAAACAAACAGTGGGGCCA 58.720 45.000 4.39 0.00 0.00 5.36
1868 1919 3.840666 AGCACTAGAAACAGGAAGGATGA 59.159 43.478 0.00 0.00 0.00 2.92
1899 1950 0.480690 TGCAAAAGGCCCAGGAACTA 59.519 50.000 0.00 0.00 43.89 2.24
1903 1954 3.007940 GCAAAAGGCCCAGGAACTAAAAT 59.992 43.478 0.00 0.00 33.52 1.82
2067 2127 4.152938 TGTGATCAAGAACATTGAGCTTCG 59.847 41.667 0.00 0.00 35.97 3.79
2251 2311 6.351202 CCTGGATTGAGGTCAAATATGCAAAA 60.351 38.462 0.00 0.00 39.55 2.44
2320 2380 6.122964 GGTCTATTTTGGAACATTAGAGGCT 58.877 40.000 0.00 0.00 39.30 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 2.141011 TACCCGACCTCCTCGACCAA 62.141 60.000 0.00 0.00 46.14 3.67
175 182 2.126882 CCACCACCATATCTTCCTCCA 58.873 52.381 0.00 0.00 0.00 3.86
210 217 1.074471 GAGGCAGGGGGATGACCTA 60.074 63.158 0.00 0.00 40.03 3.08
216 223 1.384643 GTAGTGGAGGCAGGGGGAT 60.385 63.158 0.00 0.00 0.00 3.85
381 394 4.697352 CCCTGATATTCGAACATGGGATTC 59.303 45.833 6.03 0.00 35.64 2.52
475 488 2.519302 AAAACCTGCCGCAGCTGT 60.519 55.556 16.64 5.66 40.80 4.40
489 502 5.163468 TGCTGGACTAAATTGCTGTTGAAAA 60.163 36.000 0.00 0.00 0.00 2.29
523 536 0.181114 ACTGCCTGAGTTGACTGCAA 59.819 50.000 0.00 0.00 0.00 4.08
529 542 1.811558 GCACTGAACTGCCTGAGTTGA 60.812 52.381 0.00 0.00 45.48 3.18
538 551 1.650912 CACCACTGCACTGAACTGC 59.349 57.895 0.00 0.00 37.70 4.40
548 561 0.868406 CGAAGAACTTCCACCACTGC 59.132 55.000 8.66 0.00 36.27 4.40
645 658 0.532417 GCATAGCACTCTGAGCCTGG 60.532 60.000 4.19 0.00 0.00 4.45
680 699 8.310382 CAACATATTTTGGGTCCATAGTGAAAA 58.690 33.333 0.00 0.00 0.00 2.29
688 707 3.706086 GCTCCAACATATTTTGGGTCCAT 59.294 43.478 18.43 0.00 45.49 3.41
703 723 4.035675 GCAGTTATAACAGATGGCTCCAAC 59.964 45.833 17.65 0.00 0.00 3.77
729 749 2.597455 CCAACAAAATGTCCAGGGAGT 58.403 47.619 0.00 0.00 0.00 3.85
732 752 1.047002 TGCCAACAAAATGTCCAGGG 58.953 50.000 0.00 0.00 0.00 4.45
905 925 2.134789 ATTGAGCCACTCACAATCCC 57.865 50.000 0.00 0.00 40.46 3.85
909 929 2.224018 GCCAAAATTGAGCCACTCACAA 60.224 45.455 0.00 0.00 40.46 3.33
921 941 3.405823 AGTCCCACATTGCCAAAATTG 57.594 42.857 0.00 0.00 0.00 2.32
961 981 7.791029 TGACCTAGCTCTTTTCCAAAAATTTT 58.209 30.769 0.00 0.00 0.00 1.82
1015 1035 1.403687 GGTCTTATCTGCGAGGGCCT 61.404 60.000 5.25 5.25 38.85 5.19
1022 1042 6.662414 TTTTGTCATAAGGTCTTATCTGCG 57.338 37.500 0.61 0.00 33.79 5.18
1145 1165 3.075882 AGGGTGTTCTCCATTCCAATCAA 59.924 43.478 0.00 0.00 0.00 2.57
1205 1225 3.903467 AGCCATTTAGGTGGAAATCCTC 58.097 45.455 0.44 0.00 42.02 3.71
1206 1226 5.373854 AGATAGCCATTTAGGTGGAAATCCT 59.626 40.000 0.44 0.00 42.02 3.24
1209 1229 5.835280 CCAAGATAGCCATTTAGGTGGAAAT 59.165 40.000 0.00 0.00 42.02 2.17
1299 1319 7.907389 TCCTGACTTTCTCATAAAAGCTTCTA 58.093 34.615 0.00 0.00 39.39 2.10
1350 1370 4.898861 ACAATCCTGTCTCTAGGGATCTTC 59.101 45.833 0.00 0.00 38.73 2.87
1426 1446 4.927267 TGTCAGAGGTGTTCCCAATATT 57.073 40.909 0.00 0.00 34.66 1.28
1494 1514 7.546250 AGAGTCAAATTCCTCTTCTGTCTAA 57.454 36.000 0.00 0.00 34.40 2.10
1495 1515 7.891183 ACTAGAGTCAAATTCCTCTTCTGTCTA 59.109 37.037 0.00 0.00 38.86 2.59
1563 1584 3.496331 AGTAACCTTGGGAATGGTGTTG 58.504 45.455 0.00 0.00 36.57 3.33
1572 1593 3.865571 AGAACCAGTAGTAACCTTGGGA 58.134 45.455 0.00 0.00 34.99 4.37
1679 1724 1.683385 GATAGCTTTTGGTCATGGGCC 59.317 52.381 0.00 0.00 0.00 5.80
1680 1725 2.360165 CAGATAGCTTTTGGTCATGGGC 59.640 50.000 0.00 0.00 0.00 5.36
1778 1829 5.068987 GCTATGTTCTGAGGAAGAGAGTGAT 59.931 44.000 0.00 0.00 36.72 3.06
1783 1834 4.604156 TCAGCTATGTTCTGAGGAAGAGA 58.396 43.478 0.00 0.00 35.81 3.10
1806 1857 2.467880 TGGCCCCACTGTTTGTTTTTA 58.532 42.857 0.00 0.00 0.00 1.52
1826 1877 0.546598 GGCCCTAGTAGCAACCACAT 59.453 55.000 0.00 0.00 0.00 3.21
1887 1938 2.525105 TCCATTTTAGTTCCTGGGCC 57.475 50.000 0.00 0.00 0.00 5.80
1899 1950 2.214376 TTGGCACCTCGATCCATTTT 57.786 45.000 0.00 0.00 0.00 1.82
1903 1954 0.109532 TTGTTTGGCACCTCGATCCA 59.890 50.000 0.00 0.00 0.00 3.41
1956 2016 7.237055 TGGAGATAAGAACATCATCATCCAGAT 59.763 37.037 0.00 0.00 37.48 2.90
2320 2380 5.777223 TGTTACATTTGATGGACCCATTCAA 59.223 36.000 2.68 6.44 36.70 2.69



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

AutoCloner maintained by Alex Coulton.