Multiple sequence alignment - TraesCS5D01G546800

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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 TraesCS5D01G546800 chr5D 100.000 2558 0 0 1 2558 555230788 555233345 0 4724
1 TraesCS5D01G546800 chrUn 97.039 2567 67 6 1 2558 246703764 246701198 0 4311
2 TraesCS5D01G546800 chr6B 97.038 2566 68 5 1 2558 128896751 128894186 0 4311
3 TraesCS5D01G546800 chr7B 96.921 2566 71 5 1 2558 698133379 698130814 0 4294
4 TraesCS5D01G546800 chr7B 96.921 2566 71 5 1 2558 742930717 742933282 0 4294
5 TraesCS5D01G546800 chr7B 96.532 2566 81 6 1 2558 716802613 716800048 0 4239
6 TraesCS5D01G546800 chr3D 96.648 2566 77 6 1 2558 202630988 202628424 0 4253
7 TraesCS5D01G546800 chr5B 96.532 2566 79 7 1 2558 127825766 127823203 0 4237
8 TraesCS5D01G546800 chr5B 96.454 2566 82 6 1 2558 713088993 713091557 0 4226
9 TraesCS5D01G546800 chr2D 96.415 2566 84 5 1 2558 18020457 18017892 0 4222


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 TraesCS5D01G546800 chr5D 555230788 555233345 2557 False 4724 4724 100.000 1 2558 1 chr5D.!!$F1 2557
1 TraesCS5D01G546800 chrUn 246701198 246703764 2566 True 4311 4311 97.039 1 2558 1 chrUn.!!$R1 2557
2 TraesCS5D01G546800 chr6B 128894186 128896751 2565 True 4311 4311 97.038 1 2558 1 chr6B.!!$R1 2557
3 TraesCS5D01G546800 chr7B 698130814 698133379 2565 True 4294 4294 96.921 1 2558 1 chr7B.!!$R1 2557
4 TraesCS5D01G546800 chr7B 742930717 742933282 2565 False 4294 4294 96.921 1 2558 1 chr7B.!!$F1 2557
5 TraesCS5D01G546800 chr7B 716800048 716802613 2565 True 4239 4239 96.532 1 2558 1 chr7B.!!$R2 2557
6 TraesCS5D01G546800 chr3D 202628424 202630988 2564 True 4253 4253 96.648 1 2558 1 chr3D.!!$R1 2557
7 TraesCS5D01G546800 chr5B 127823203 127825766 2563 True 4237 4237 96.532 1 2558 1 chr5B.!!$R1 2557
8 TraesCS5D01G546800 chr5B 713088993 713091557 2564 False 4226 4226 96.454 1 2558 1 chr5B.!!$F1 2557
9 TraesCS5D01G546800 chr2D 18017892 18020457 2565 True 4222 4222 96.415 1 2558 1 chr2D.!!$R1 2557

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
465 468 0.396435 ACCACCATGTCGCTCTTTCA 59.604 50.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2143 0.102481 GACCGCGGTCAGATGTATGT 59.898 55.0 44.88 15.05 44.02 2.29 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
160 161 0.843343 AAAAAGGACCCTCCCCGCTA 60.843 55.000 0.00 0.00 37.19 4.26
164 165 3.161450 GACCCTCCCCGCTATGCA 61.161 66.667 0.00 0.00 0.00 3.96
173 174 1.837051 CCGCTATGCACCCCTCCTA 60.837 63.158 0.00 0.00 0.00 2.94
258 260 4.012374 AGTTCTCAATCATTTCGTGGCAT 58.988 39.130 0.00 0.00 0.00 4.40
323 325 7.040271 GGAGGAAGCTTAGATAAGAGAATACGT 60.040 40.741 0.00 0.00 35.33 3.57
378 381 1.407258 CGAGAAAAAGTGTTTGGCCCA 59.593 47.619 0.00 0.00 0.00 5.36
394 397 1.140852 GCCCAAGCCAAAAAGAGGTTT 59.859 47.619 0.00 0.00 0.00 3.27
454 457 3.202097 GGGAACAACAAAAACCACCATG 58.798 45.455 0.00 0.00 0.00 3.66
465 468 0.396435 ACCACCATGTCGCTCTTTCA 59.604 50.000 0.00 0.00 0.00 2.69
472 475 4.520492 ACCATGTCGCTCTTTCATTTCTTT 59.480 37.500 0.00 0.00 0.00 2.52
971 976 1.306654 TGGTCGATTAGGGGGTGCT 60.307 57.895 0.00 0.00 0.00 4.40
994 999 5.660460 TGAAATAGCTAGAACTGAATGCGA 58.340 37.500 0.00 0.00 0.00 5.10
1021 1026 8.986477 AAGTATGGAAAAACATCTTGTAATGC 57.014 30.769 0.00 0.00 32.39 3.56
1244 1249 2.618709 GCACCAAAAGTTGTAGAGCTGT 59.381 45.455 0.00 0.00 0.00 4.40
1273 1278 3.807553 TCATATCGAGCCATTGAAGCAA 58.192 40.909 0.00 0.00 0.00 3.91
1279 1284 1.371635 GCCATTGAAGCAACGCGTT 60.372 52.632 20.79 20.79 0.00 4.84
1303 1308 3.632145 GGCTACAATCGGACAATTCCATT 59.368 43.478 0.00 0.00 43.00 3.16
1418 1423 5.542848 ATGGGAAGAGGAAAAGGAAATCT 57.457 39.130 0.00 0.00 0.00 2.40
1435 1440 0.400213 TCTGACGGGTTGGATTGCTT 59.600 50.000 0.00 0.00 0.00 3.91
1598 1604 1.000896 CTGGGCCGGGACTCAAAAT 60.001 57.895 3.77 0.00 0.00 1.82
1606 1612 3.445805 GCCGGGACTCAAAATAATTTGGA 59.554 43.478 2.18 0.00 44.88 3.53
1636 1642 0.034896 TTCCTGAACGAGGGAAGTGC 59.965 55.000 0.00 0.00 43.06 4.40
1807 1816 2.820059 AGAGAAGCGTGATGTTGTCA 57.180 45.000 0.00 0.00 0.00 3.58
1830 1839 7.756272 GTCATGTTGTCAGCAATCAAATTATCA 59.244 33.333 0.00 0.00 36.92 2.15
2007 2017 5.888161 GGTATTGAAGTTCCTGATGGTCATT 59.112 40.000 0.00 0.00 34.23 2.57
2032 2042 4.625800 CCTTCGAAAGGCCCTCTG 57.374 61.111 0.00 0.00 42.78 3.35
2073 2083 1.039856 ATGCTTGGTTTGAGCGGTTT 58.960 45.000 0.00 0.00 43.02 3.27
2091 2101 2.878406 GTTTAGCTCTGTGGTTCAAGCA 59.122 45.455 0.00 0.00 34.82 3.91
2108 2118 4.019860 TCAAGCAGCTGGTTTCTCTTCTAT 60.020 41.667 27.77 0.59 32.86 1.98
2133 2143 1.955778 CATGACCCTGCACTTTTCACA 59.044 47.619 0.00 0.00 0.00 3.58
2217 2227 5.104817 TGGAGATGATCAGAAGTACATTGCA 60.105 40.000 0.09 0.00 0.00 4.08
2285 2295 7.820648 TGATTTTCTCTCAGTTATTTTCTGGC 58.179 34.615 0.00 0.00 34.15 4.85
2360 2370 3.055530 ACTCAGGATTTGATCTCACGCTT 60.056 43.478 0.00 0.00 34.68 4.68
2396 2406 2.742372 CACTGCCGCTACACCCAC 60.742 66.667 0.00 0.00 0.00 4.61
2417 2427 2.048444 GAGCTCCATCTCCAATTGCA 57.952 50.000 0.87 0.00 0.00 4.08
2425 2435 3.136443 CCATCTCCAATTGCACCCTAGTA 59.864 47.826 0.00 0.00 0.00 1.82
2528 2538 1.913778 TGCTCATGCAGTCCACATTT 58.086 45.000 0.00 0.00 45.31 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 6.265304 AGGGTCCTTTTTAGTAGATGACTCT 58.735 40.000 0.00 0.00 39.81 3.24
160 161 4.263068 CGAATAATTCTAGGAGGGGTGCAT 60.263 45.833 0.00 0.00 0.00 3.96
164 165 3.902467 GACCGAATAATTCTAGGAGGGGT 59.098 47.826 0.00 0.00 0.00 4.95
173 174 7.807977 AAGTATTGCATGACCGAATAATTCT 57.192 32.000 0.00 0.00 0.00 2.40
225 226 2.297698 TTGAGAACTAGGACGGGTCA 57.702 50.000 0.75 0.00 0.00 4.02
258 260 3.164977 TGGTTCAGCCACACCCGA 61.165 61.111 0.00 0.00 43.61 5.14
378 381 5.147767 AGTGGATAAACCTCTTTTTGGCTT 58.852 37.500 0.00 0.00 39.14 4.35
394 397 2.288666 GCTTGGCGAATGAAGTGGATA 58.711 47.619 0.00 0.00 0.00 2.59
454 457 4.222114 CACCAAAGAAATGAAAGAGCGAC 58.778 43.478 0.00 0.00 0.00 5.19
465 468 6.731292 AAAAGAAGGTAGCACCAAAGAAAT 57.269 33.333 7.86 0.00 41.95 2.17
491 494 2.245379 CCCCAACCCCATCCCTTGA 61.245 63.158 0.00 0.00 0.00 3.02
535 538 1.726853 CTAGGAGTTGTTTCCAGGCG 58.273 55.000 0.00 0.00 39.84 5.52
539 542 4.640771 ATTGAGCTAGGAGTTGTTTCCA 57.359 40.909 0.00 0.00 39.84 3.53
683 686 6.270815 CGTACGGAATTATCCTCTTTCTCAA 58.729 40.000 7.57 0.00 44.17 3.02
765 770 7.263496 ACCGACTCAATTAAGGTATTAGTGTC 58.737 38.462 0.00 0.00 32.76 3.67
804 809 7.122353 AGCAATCAGAGAAGCACTTTGATAAAT 59.878 33.333 14.00 4.52 45.58 1.40
971 976 5.660460 TCGCATTCAGTTCTAGCTATTTCA 58.340 37.500 0.00 0.00 0.00 2.69
1021 1026 9.173939 GAGCATAATCGATTTTCTGGTTAAATG 57.826 33.333 17.19 10.43 0.00 2.32
1244 1249 3.793797 TGGCTCGATATGAAAGACGAA 57.206 42.857 0.00 0.00 34.50 3.85
1273 1278 2.098233 CGATTGTAGCCCAACGCGT 61.098 57.895 5.58 5.58 44.76 6.01
1279 1284 2.639065 GAATTGTCCGATTGTAGCCCA 58.361 47.619 0.00 0.00 0.00 5.36
1303 1308 2.279741 GAATTGTCCGCTCATAGCACA 58.720 47.619 0.00 0.00 42.58 4.57
1385 1390 4.350245 TCCTCTTCCCATTCGAACTTCTA 58.650 43.478 0.00 0.00 0.00 2.10
1418 1423 0.179004 ACAAGCAATCCAACCCGTCA 60.179 50.000 0.00 0.00 0.00 4.35
1598 1604 6.831353 TCAGGAACAAACACTTCTCCAAATTA 59.169 34.615 0.00 0.00 0.00 1.40
1606 1612 3.869065 TCGTTCAGGAACAAACACTTCT 58.131 40.909 12.22 0.00 41.20 2.85
1636 1642 4.775236 CTCCCTATCCCTCTTTGTCTTTG 58.225 47.826 0.00 0.00 0.00 2.77
1748 1757 1.373435 CTGTCACTTTACCGGGCCA 59.627 57.895 6.32 0.00 0.00 5.36
1844 1853 5.426504 ACAGAAATTGAAACAATGCAACCA 58.573 33.333 0.00 0.00 0.00 3.67
1851 1860 9.903682 CAGAGTATGAACAGAAATTGAAACAAT 57.096 29.630 0.00 0.00 0.00 2.71
1897 1906 5.718130 TCCATTTGAGAGATTTGCCAAGATT 59.282 36.000 0.00 0.00 0.00 2.40
2054 2064 1.039856 AAACCGCTCAAACCAAGCAT 58.960 45.000 0.00 0.00 39.81 3.79
2073 2083 1.609061 GCTGCTTGAACCACAGAGCTA 60.609 52.381 0.00 0.00 35.40 3.32
2091 2101 4.019860 TGCTCAATAGAAGAGAAACCAGCT 60.020 41.667 0.00 0.00 35.09 4.24
2108 2118 0.111061 AAGTGCAGGGTCATGCTCAA 59.889 50.000 9.01 0.00 46.63 3.02
2133 2143 0.102481 GACCGCGGTCAGATGTATGT 59.898 55.000 44.88 15.05 44.02 2.29
2217 2227 8.250332 TGCTCACTCAACTTTTTCTTAACAAAT 58.750 29.630 0.00 0.00 0.00 2.32
2285 2295 9.297586 CATCATTAGTTTGATCAACCTCAATTG 57.702 33.333 8.99 0.00 35.20 2.32
2360 2370 5.105877 GCAGTGTGTGTATCAGTAAGACCTA 60.106 44.000 0.00 0.00 0.00 3.08
2417 2427 5.043582 TCAAGAGGAGTACCATTACTAGGGT 60.044 44.000 0.00 0.00 38.77 4.34
2451 2461 3.556513 CCTACAAGATGACGATAGCGAC 58.443 50.000 7.69 0.19 41.64 5.19
2528 2538 3.627395 ACCACTGACAAACTGACTGAA 57.373 42.857 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.