Multiple sequence alignment - TraesCS5D01G479100

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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 TraesCS5D01G479100 chr5D 100.000 2560 0 0 747 3306 517446096 517448655 0.000000e+00 4728
1 TraesCS5D01G479100 chr5D 100.000 378 0 0 1 378 517445350 517445727 0.000000e+00 699
2 TraesCS5D01G479100 chr5B 94.309 2618 67 33 748 3306 650030041 650032635 0.000000e+00 3934
3 TraesCS5D01G479100 chr5B 84.697 379 15 9 10 378 650029645 650029990 4.090000e-89 339
4 TraesCS5D01G479100 chr5A 93.812 2634 70 43 748 3306 644858857 644861472 0.000000e+00 3875
5 TraesCS5D01G479100 chr5A 91.406 384 16 4 1 378 644858427 644858799 8.180000e-141 510


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 TraesCS5D01G479100 chr5D 517445350 517448655 3305 False 2713.5 4728 100.000 1 3306 2 chr5D.!!$F1 3305
1 TraesCS5D01G479100 chr5B 650029645 650032635 2990 False 2136.5 3934 89.503 10 3306 2 chr5B.!!$F1 3296
2 TraesCS5D01G479100 chr5A 644858427 644861472 3045 False 2192.5 3875 92.609 1 3306 2 chr5A.!!$F1 3305

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
110 111 0.670239 GCAAGGCAAAACATTCCCCG 60.670 55.000 0.00 0.0 0.00 5.73 F
276 293 1.152440 GCCCCTAGAGCCAGCTAGA 60.152 63.158 0.00 0.0 40.20 2.43 F
961 1004 2.045926 GGCGTGATCAAGGCACCT 60.046 61.111 26.23 0.0 41.59 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1056 1099 0.679640 GCCACATGGATCCCACGAAA 60.680 55.000 9.9 0.0 35.80 3.46 R
1289 1335 1.669115 CACGAGGGCACAGGACTTG 60.669 63.158 0.0 0.0 0.00 3.16 R
2350 2407 1.197721 GCCATATGCAACCGTATCAGC 59.802 52.381 0.0 0.0 40.77 4.26 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
25 26 2.491271 GGTGGATAGAGAGGGACCTACC 60.491 59.091 0.00 0.00 38.08 3.18
110 111 0.670239 GCAAGGCAAAACATTCCCCG 60.670 55.000 0.00 0.00 0.00 5.73
276 293 1.152440 GCCCCTAGAGCCAGCTAGA 60.152 63.158 0.00 0.00 40.20 2.43
781 798 2.267006 CACCCACATGCGCTCTCT 59.733 61.111 9.73 0.00 0.00 3.10
946 989 2.955614 TGTTAGTTAGCTTGACGAGGC 58.044 47.619 0.00 0.00 0.00 4.70
959 1002 2.456119 CGAGGCGTGATCAAGGCAC 61.456 63.158 30.86 24.90 41.59 5.01
961 1004 2.045926 GGCGTGATCAAGGCACCT 60.046 61.111 26.23 0.00 41.59 4.00
1056 1099 2.363406 GCCATGCTGCCTCCCTTT 60.363 61.111 0.00 0.00 0.00 3.11
1289 1335 4.508861 GGCATGCAATTTCATTACACATCC 59.491 41.667 21.36 0.00 0.00 3.51
1455 1506 2.711895 ATCCCCATGAGTAGCTAGCT 57.288 50.000 23.12 23.12 0.00 3.32
1456 1507 1.709578 TCCCCATGAGTAGCTAGCTG 58.290 55.000 27.68 9.95 0.00 4.24
1462 1513 3.068732 CCATGAGTAGCTAGCTGTGCTAA 59.931 47.826 27.68 15.07 43.50 3.09
1573 1624 5.798132 TGCTATCATCCTATGAATGACACC 58.202 41.667 0.00 0.00 43.50 4.16
2239 2292 4.154347 CTCGTGGAGAGGCAGGGC 62.154 72.222 0.00 0.00 43.20 5.19
2340 2397 4.671569 CGGCGGCCATAGCTCCTC 62.672 72.222 20.71 0.00 39.73 3.71
2341 2398 3.550431 GGCGGCCATAGCTCCTCA 61.550 66.667 15.62 0.00 39.73 3.86
2343 2400 1.670406 GCGGCCATAGCTCCTCATG 60.670 63.158 2.24 0.00 39.73 3.07
2344 2401 1.004080 CGGCCATAGCTCCTCATGG 60.004 63.158 2.24 8.64 43.90 3.66
2345 2402 1.762522 CGGCCATAGCTCCTCATGGT 61.763 60.000 13.55 0.00 43.14 3.55
2346 2403 1.352083 GGCCATAGCTCCTCATGGTA 58.648 55.000 13.55 0.00 43.14 3.25
2347 2404 1.912043 GGCCATAGCTCCTCATGGTAT 59.088 52.381 13.55 0.00 43.14 2.73
2348 2405 2.093235 GGCCATAGCTCCTCATGGTATC 60.093 54.545 13.55 2.58 43.14 2.24
2349 2406 2.568956 GCCATAGCTCCTCATGGTATCA 59.431 50.000 13.55 0.00 43.14 2.15
2350 2407 3.369261 GCCATAGCTCCTCATGGTATCAG 60.369 52.174 13.55 0.00 43.14 2.90
2438 2505 6.416455 CAGCGTGTTAATTTGCTTTCAAAGTA 59.584 34.615 0.00 0.00 44.47 2.24
2511 2582 2.254152 ATGGCTGACTCTCCTTGGTA 57.746 50.000 0.00 0.00 0.00 3.25
2533 2604 7.093988 TGGTAATGCCAATATGCCATGTATAAC 60.094 37.037 0.00 0.00 45.94 1.89
2629 2705 2.167693 GCAAACCCAGCCCCTAAAATAC 59.832 50.000 0.00 0.00 0.00 1.89
2753 2832 6.252233 TCCCACAAGTCCATTTTTGATCATA 58.748 36.000 0.00 0.00 0.00 2.15
2755 2834 8.058235 TCCCACAAGTCCATTTTTGATCATATA 58.942 33.333 0.00 0.00 0.00 0.86
2756 2835 8.863086 CCCACAAGTCCATTTTTGATCATATAT 58.137 33.333 0.00 0.00 0.00 0.86
2758 2837 9.188588 CACAAGTCCATTTTTGATCATATATGC 57.811 33.333 7.92 0.00 0.00 3.14
2759 2838 9.139734 ACAAGTCCATTTTTGATCATATATGCT 57.860 29.630 7.92 0.00 0.00 3.79
2760 2839 9.406828 CAAGTCCATTTTTGATCATATATGCTG 57.593 33.333 7.92 1.01 0.00 4.41
2761 2840 7.600065 AGTCCATTTTTGATCATATATGCTGC 58.400 34.615 7.92 0.00 0.00 5.25
2840 2942 1.836802 TGTAGCAATGCATGGCAAGA 58.163 45.000 27.59 9.89 43.62 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.196766 AGTGAAACCCGGGTAGGTCC 61.197 60.000 30.52 17.07 40.05 4.46
25 26 1.904287 TGGATGAAAGTGAAACCCGG 58.096 50.000 0.00 0.00 37.80 5.73
110 111 2.646175 TACGCTGGCTCACACTCCC 61.646 63.158 0.00 0.00 0.00 4.30
245 262 0.554305 TAGGGGCGGTAGAGATGTCA 59.446 55.000 0.00 0.00 0.00 3.58
276 293 2.532715 ATGGGAGGTGGTGCTGGT 60.533 61.111 0.00 0.00 0.00 4.00
746 763 3.244911 GGGTGGATAGAGAGAGAGAGAGG 60.245 56.522 0.00 0.00 0.00 3.69
755 772 1.269988 CGCATGTGGGTGGATAGAGAG 60.270 57.143 0.00 0.00 0.00 3.20
781 798 0.612732 TAAACGGGGCTTCGAGGAGA 60.613 55.000 0.00 0.00 0.00 3.71
946 989 1.811266 CCGAGGTGCCTTGATCACG 60.811 63.158 7.04 0.00 35.39 4.35
959 1002 1.064946 CTAGAGCTTCACGCCGAGG 59.935 63.158 0.00 0.00 40.39 4.63
961 1004 2.490217 GCTAGAGCTTCACGCCGA 59.510 61.111 0.00 0.00 40.39 5.54
980 1023 1.529478 CCCGCCAGAGCTAGCTAGA 60.529 63.158 25.15 0.00 36.60 2.43
1056 1099 0.679640 GCCACATGGATCCCACGAAA 60.680 55.000 9.90 0.00 35.80 3.46
1065 1108 2.124570 GCCGACTGCCACATGGAT 60.125 61.111 0.87 0.00 37.39 3.41
1101 1147 2.683933 TCCTCCTCGGACAAGGCC 60.684 66.667 0.00 0.00 36.69 5.19
1289 1335 1.669115 CACGAGGGCACAGGACTTG 60.669 63.158 0.00 0.00 0.00 3.16
1455 1506 1.970640 TGAGCTGAGAACCTTAGCACA 59.029 47.619 12.24 9.44 44.06 4.57
1456 1507 2.615869 CTGAGCTGAGAACCTTAGCAC 58.384 52.381 12.24 7.22 44.06 4.40
1462 1513 2.433970 GGATTAGCTGAGCTGAGAACCT 59.566 50.000 18.79 0.00 40.10 3.50
1573 1624 2.879646 CCTAACCTGACCTAGCTAGTCG 59.120 54.545 19.31 7.67 37.04 4.18
1678 1731 2.289467 AGGGTAGAGAGGAGAAGGTGA 58.711 52.381 0.00 0.00 0.00 4.02
2304 2357 1.443802 GGCCGGCTAGCTGATTAATC 58.556 55.000 28.56 8.60 0.00 1.75
2307 2360 2.734591 CGGCCGGCTAGCTGATTA 59.265 61.111 28.56 0.00 42.00 1.75
2345 2402 3.751479 ATGCAACCGTATCAGCTGATA 57.249 42.857 28.69 28.69 36.05 2.15
2346 2403 2.627515 ATGCAACCGTATCAGCTGAT 57.372 45.000 30.85 30.85 38.51 2.90
2347 2404 3.392882 CATATGCAACCGTATCAGCTGA 58.607 45.455 20.79 20.79 0.00 4.26
2348 2405 2.481568 CCATATGCAACCGTATCAGCTG 59.518 50.000 7.63 7.63 0.00 4.24
2349 2406 2.771089 CCATATGCAACCGTATCAGCT 58.229 47.619 0.00 0.00 0.00 4.24
2350 2407 1.197721 GCCATATGCAACCGTATCAGC 59.802 52.381 0.00 0.00 40.77 4.26
2563 2639 5.415701 TGATTAAAGCTCAAGCAAACCCTAG 59.584 40.000 4.59 0.00 45.16 3.02
2629 2705 8.382030 TGTGCATATATTCTGACATTAACTGG 57.618 34.615 0.00 0.00 0.00 4.00
2979 3092 7.504911 CCTCTCCTCCATATTCAAACAATCAAT 59.495 37.037 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.