Multiple sequence alignment - TraesCS5D01G338700

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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 TraesCS5D01G338700 chr5D 100.000 2565 0 0 1 2565 428306267 428308831 0.000000e+00 4737.0
1 TraesCS5D01G338700 chr5D 81.687 415 55 15 766 1173 428374745 428375145 2.460000e-85 326.0
2 TraesCS5D01G338700 chr5D 78.491 530 82 17 1205 1716 428038231 428038746 4.120000e-83 318.0
3 TraesCS5D01G338700 chr5D 85.926 135 11 6 2097 2228 428376061 428376190 1.240000e-28 137.0
4 TraesCS5D01G338700 chr5A 92.694 2587 133 21 1 2565 543713247 543715799 0.000000e+00 3679.0
5 TraesCS5D01G338700 chr5A 79.952 419 56 14 766 1173 543916279 543916680 1.500000e-72 283.0
6 TraesCS5D01G338700 chr5A 81.073 354 49 10 1228 1568 542527211 542527559 1.510000e-67 267.0
7 TraesCS5D01G338700 chr5A 76.966 178 29 9 2101 2272 541941107 541941278 9.770000e-15 91.6
8 TraesCS5D01G338700 chr5B 95.622 1462 55 5 1 1458 517502652 517504108 0.000000e+00 2337.0
9 TraesCS5D01G338700 chr5B 86.926 1002 90 25 1517 2500 517504432 517505410 0.000000e+00 1086.0
10 TraesCS5D01G338700 chr5B 82.951 305 37 8 1205 1501 517247084 517247381 7.040000e-66 261.0
11 TraesCS5D01G338700 chr5B 83.399 253 30 3 922 1174 517557148 517557388 9.240000e-55 224.0


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 TraesCS5D01G338700 chr5D 428306267 428308831 2564 False 4737.0 4737 100.0000 1 2565 1 chr5D.!!$F2 2564
1 TraesCS5D01G338700 chr5D 428038231 428038746 515 False 318.0 318 78.4910 1205 1716 1 chr5D.!!$F1 511
2 TraesCS5D01G338700 chr5D 428374745 428376190 1445 False 231.5 326 83.8065 766 2228 2 chr5D.!!$F3 1462
3 TraesCS5D01G338700 chr5A 543713247 543715799 2552 False 3679.0 3679 92.6940 1 2565 1 chr5A.!!$F3 2564
4 TraesCS5D01G338700 chr5B 517502652 517505410 2758 False 1711.5 2337 91.2740 1 2500 2 chr5B.!!$F3 2499

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
235 237 0.856641 GTTGCGTTCGCTACTGACAA 59.143 50.0 20.06 2.85 34.88 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 2115 0.627451 TGCAGGCAGGGATTGATCTT 59.373 50.0 0.0 0.0 0.0 2.4 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
120 121 3.551551 GAAAAACGGGTGAGAATTGTCG 58.448 45.455 0.00 0.00 0.00 4.35
127 128 1.066430 GGTGAGAATTGTCGTGCCCTA 60.066 52.381 0.00 0.00 0.00 3.53
132 133 4.764823 TGAGAATTGTCGTGCCCTAAAAAT 59.235 37.500 0.00 0.00 0.00 1.82
235 237 0.856641 GTTGCGTTCGCTACTGACAA 59.143 50.000 20.06 2.85 34.88 3.18
246 248 7.411480 CGTTCGCTACTGACAATTTAGAATTCA 60.411 37.037 8.44 0.00 0.00 2.57
262 264 2.511600 CAGGCGTGGAATCCGACC 60.512 66.667 0.00 0.00 32.41 4.79
346 348 8.914011 GGGTTAAGATATTGCTTGGAGTATTTT 58.086 33.333 0.00 0.00 0.00 1.82
435 437 5.754406 TCAGTAAAAACCTGAATCGACGAAA 59.246 36.000 0.00 0.00 36.07 3.46
457 459 2.819608 CTCATTGGTTTGATCACCGGTT 59.180 45.455 2.97 0.00 40.09 4.44
459 461 2.350057 TTGGTTTGATCACCGGTTCA 57.650 45.000 2.97 4.10 40.09 3.18
502 504 4.142004 ACCTACTCGTGTGAATATCCAACC 60.142 45.833 0.00 0.00 0.00 3.77
591 593 1.128692 ACGAAATTTGTAGAGCTGCGC 59.871 47.619 0.00 0.00 0.00 6.09
635 637 2.222886 CCGATAGTCGTCTGATCTGGT 58.777 52.381 0.00 0.00 38.40 4.00
646 648 1.745653 CTGATCTGGTGACGTGCTAGA 59.254 52.381 0.00 0.00 0.00 2.43
795 797 5.180117 CCAAATCAATTCCAGGCTATACGAG 59.820 44.000 0.00 0.00 0.00 4.18
941 952 4.522722 ACCAAAGAAAGAGTAGACGAGG 57.477 45.455 0.00 0.00 0.00 4.63
1016 1027 5.414454 CCAATCGTCCAAGAAATTCCTACAA 59.586 40.000 0.00 0.00 0.00 2.41
1486 1555 0.891373 TTCGAGCAGTCCTCTCCTTG 59.109 55.000 0.00 0.00 38.49 3.61
1514 1586 1.341531 CGGGAGGAATCGCTATCACTT 59.658 52.381 0.00 0.00 0.00 3.16
1522 1852 5.473846 AGGAATCGCTATCACTTTCGATCTA 59.526 40.000 0.00 0.00 40.29 1.98
1770 2117 3.257561 CGCCTGCGGTCGATCAAG 61.258 66.667 3.07 0.00 35.56 3.02
1771 2118 2.184322 GCCTGCGGTCGATCAAGA 59.816 61.111 0.00 0.00 0.00 3.02
1772 2119 1.227380 GCCTGCGGTCGATCAAGAT 60.227 57.895 0.00 0.00 0.00 2.40
1896 2243 0.736053 TGTTTATCGGATTTGGGCGC 59.264 50.000 0.00 0.00 0.00 6.53
1928 2275 1.789078 CTGCTGTCTGCGCTGGTTTT 61.789 55.000 14.70 0.00 46.63 2.43
1945 2292 6.697641 TGGTTTTGGAGTCCTATTTCTAGT 57.302 37.500 11.33 0.00 0.00 2.57
2047 2403 1.508088 CAATGCCTTGTTCTCCGGC 59.492 57.895 0.00 0.00 44.02 6.13
2143 2499 0.179189 GAGTCCAATTTGCTTCCGCG 60.179 55.000 0.00 0.00 39.65 6.46
2155 2517 4.776322 TCCGCGGCATTGGAGTGG 62.776 66.667 23.51 0.00 36.92 4.00
2237 2602 1.531748 CTTCCATGCCACCCGGTAT 59.468 57.895 0.00 0.00 38.30 2.73
2344 2713 5.163774 CGATCGAGCTTATCATCTGAGATGA 60.164 44.000 25.64 25.64 0.00 2.92
2345 2714 5.369685 TCGAGCTTATCATCTGAGATGAC 57.630 43.478 25.92 13.93 0.00 3.06
2346 2715 5.069318 TCGAGCTTATCATCTGAGATGACT 58.931 41.667 25.92 18.17 0.00 3.41
2347 2716 5.181056 TCGAGCTTATCATCTGAGATGACTC 59.819 44.000 25.92 23.32 42.88 3.36
2367 2736 0.180642 ATGACTGATGAGGCTGCAGG 59.819 55.000 17.12 0.00 34.05 4.85
2482 2859 3.378427 TGATACTGTGAGACATGACCTCG 59.622 47.826 0.00 0.00 33.51 4.63
2518 2895 4.128925 ACTGCAAGATTCATCGAGCTAA 57.871 40.909 0.00 0.00 37.43 3.09
2535 2912 1.265095 CTAACACCGATGATGCATGCC 59.735 52.381 16.68 0.28 0.00 4.40
2536 2913 0.680601 AACACCGATGATGCATGCCA 60.681 50.000 16.68 7.22 0.00 4.92
2537 2914 0.466739 ACACCGATGATGCATGCCAT 60.467 50.000 16.68 12.33 36.70 4.40
2538 2915 0.039527 CACCGATGATGCATGCCATG 60.040 55.000 16.68 0.00 33.29 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 4.631377 GGCAATTTCTGATTTTTAGGGCAC 59.369 41.667 0.00 0.00 0.00 5.01
127 128 5.248934 TCTGGGATGGCAATTTCTGATTTTT 59.751 36.000 0.00 0.00 0.00 1.94
132 133 3.454719 TTCTGGGATGGCAATTTCTGA 57.545 42.857 0.00 0.00 0.00 3.27
235 237 4.580580 GGATTCCACGCCTGAATTCTAAAT 59.419 41.667 7.05 0.00 32.74 1.40
246 248 2.683933 AGGTCGGATTCCACGCCT 60.684 61.111 3.09 3.87 34.60 5.52
262 264 1.376424 AGTGAACGCCCTCATGCAG 60.376 57.895 0.00 0.00 0.00 4.41
371 373 3.736433 CGGTTCAATGTGTGGCTTTTCAA 60.736 43.478 0.00 0.00 0.00 2.69
378 380 1.240256 TTACCGGTTCAATGTGTGGC 58.760 50.000 15.04 0.00 0.00 5.01
435 437 2.224769 ACCGGTGATCAAACCAATGAGT 60.225 45.455 6.12 0.00 40.53 3.41
502 504 9.494479 CTGCTTAGTTTCATACACATTGTTATG 57.506 33.333 10.33 10.33 37.79 1.90
591 593 4.135153 CGGCTGGAGGTCCTCACG 62.135 72.222 20.72 14.19 36.82 4.35
646 648 1.208052 AGTGCGTCCAATCAGCTATGT 59.792 47.619 0.00 0.00 0.00 2.29
941 952 1.541452 GGCTAATTTCGCCTCCTCTCC 60.541 57.143 10.31 0.00 44.17 3.71
980 991 1.078497 CGATTGGTGTGGCTGGCTA 60.078 57.895 2.00 0.00 0.00 3.93
982 993 2.672996 ACGATTGGTGTGGCTGGC 60.673 61.111 0.00 0.00 0.00 4.85
1556 1890 2.229784 GGATTCAGCTCCAACCAACAAG 59.770 50.000 0.00 0.00 35.24 3.16
1557 1891 2.238521 GGATTCAGCTCCAACCAACAA 58.761 47.619 0.00 0.00 35.24 2.83
1558 1892 1.144708 TGGATTCAGCTCCAACCAACA 59.855 47.619 0.00 0.00 42.36 3.33
1559 1893 1.909700 TGGATTCAGCTCCAACCAAC 58.090 50.000 0.00 0.00 42.36 3.77
1767 2114 1.030457 GCAGGCAGGGATTGATCTTG 58.970 55.000 0.00 0.00 0.00 3.02
1768 2115 0.627451 TGCAGGCAGGGATTGATCTT 59.373 50.000 0.00 0.00 0.00 2.40
1769 2116 0.851469 ATGCAGGCAGGGATTGATCT 59.149 50.000 0.00 0.00 0.00 2.75
1770 2117 0.959553 CATGCAGGCAGGGATTGATC 59.040 55.000 0.00 0.00 0.00 2.92
1771 2118 1.113517 GCATGCAGGCAGGGATTGAT 61.114 55.000 20.11 0.00 0.00 2.57
1772 2119 1.755395 GCATGCAGGCAGGGATTGA 60.755 57.895 20.11 0.00 0.00 2.57
1896 2243 4.363990 AGCAGTGCACCTCGTCGG 62.364 66.667 19.20 0.00 39.35 4.79
1945 2292 6.296026 ACCACAAGCAGAGTAAACATTTCTA 58.704 36.000 0.00 0.00 0.00 2.10
2034 2390 2.434359 GACCGCCGGAGAACAAGG 60.434 66.667 11.71 0.00 0.00 3.61
2047 2403 1.654105 GAACTATGAGTTGCACGACCG 59.346 52.381 0.00 0.00 38.80 4.79
2143 2499 1.379044 CAGTCCCCACTCCAATGCC 60.379 63.158 0.00 0.00 0.00 4.40
2155 2517 1.739049 CAGCTCGATCCTCAGTCCC 59.261 63.158 0.00 0.00 0.00 4.46
2312 2681 6.544197 AGATGATAAGCTCGATCGTGGTATAT 59.456 38.462 20.60 18.05 0.00 0.86
2313 2682 5.880887 AGATGATAAGCTCGATCGTGGTATA 59.119 40.000 20.60 14.92 0.00 1.47
2346 2715 0.906775 TGCAGCCTCATCAGTCATGA 59.093 50.000 0.00 0.00 39.39 3.07
2347 2716 1.300481 CTGCAGCCTCATCAGTCATG 58.700 55.000 0.00 0.00 0.00 3.07
2348 2717 0.180642 CCTGCAGCCTCATCAGTCAT 59.819 55.000 8.66 0.00 0.00 3.06
2349 2718 1.196766 ACCTGCAGCCTCATCAGTCA 61.197 55.000 8.66 0.00 0.00 3.41
2350 2719 0.826715 TACCTGCAGCCTCATCAGTC 59.173 55.000 8.66 0.00 0.00 3.51
2367 2736 7.907563 GCATCAGAAAGCTCAGAGTAAATTTAC 59.092 37.037 18.77 18.77 0.00 2.01
2482 2859 3.944422 TGCAGTTGAAGAACGAACTTC 57.056 42.857 15.32 15.32 44.31 3.01
2518 2895 0.466739 ATGGCATGCATCATCGGTGT 60.467 50.000 21.36 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.