Multiple sequence alignment - TraesCS6D01G321800

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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 TraesCS6D01G321800 chr6D 100.000 3267 0 0 1 3267 429255234 429258500 0 6034
1 TraesCS6D01G321800 chr6D 97.374 2361 60 2 909 3267 411364464 411362104 0 4015
2 TraesCS6D01G321800 chr6D 98.348 908 14 1 1 908 429243029 429243935 0 1592
3 TraesCS6D01G321800 chr6D 98.018 908 18 0 1 908 350602782 350601875 0 1578
4 TraesCS6D01G321800 chr6D 97.912 910 19 0 1 910 266995827 266994918 0 1576
5 TraesCS6D01G321800 chr5D 97.203 2360 61 3 909 3267 539388323 539385968 0 3988
6 TraesCS6D01G321800 chr5D 97.817 916 19 1 1 915 273157640 273156725 0 1580
7 TraesCS6D01G321800 chr5D 98.018 908 18 0 1 908 304385620 304386527 0 1578
8 TraesCS6D01G321800 chr7D 97.076 2360 67 2 909 3267 518130445 518132803 0 3975
9 TraesCS6D01G321800 chr7D 96.525 2360 79 3 909 3267 610301129 610303486 0 3901
10 TraesCS6D01G321800 chr7D 97.800 909 20 0 1 909 479011847 479012755 0 1568
11 TraesCS6D01G321800 chr3D 97.039 2364 67 3 906 3267 335958157 335955795 0 3975
12 TraesCS6D01G321800 chr2D 96.907 2360 72 1 909 3267 534898989 534896630 0 3952
13 TraesCS6D01G321800 chr2D 96.907 2360 72 1 909 3267 536060536 536058177 0 3952
14 TraesCS6D01G321800 chr2D 97.907 908 19 0 1 908 610228200 610229107 0 1572
15 TraesCS6D01G321800 chr1D 96.864 2360 72 2 909 3267 466163786 466166144 0 3947
16 TraesCS6D01G321800 chr1D 96.616 2364 74 3 909 3267 366429983 366427621 0 3917
17 TraesCS6D01G321800 chr1D 97.800 909 19 1 1 908 232101773 232100865 0 1567
18 TraesCS6D01G321800 chr4D 97.802 910 18 2 1 908 491666432 491667341 0 1568


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 TraesCS6D01G321800 chr6D 429255234 429258500 3266 False 6034 6034 100.000 1 3267 1 chr6D.!!$F2 3266
1 TraesCS6D01G321800 chr6D 411362104 411364464 2360 True 4015 4015 97.374 909 3267 1 chr6D.!!$R3 2358
2 TraesCS6D01G321800 chr6D 429243029 429243935 906 False 1592 1592 98.348 1 908 1 chr6D.!!$F1 907
3 TraesCS6D01G321800 chr6D 350601875 350602782 907 True 1578 1578 98.018 1 908 1 chr6D.!!$R2 907
4 TraesCS6D01G321800 chr6D 266994918 266995827 909 True 1576 1576 97.912 1 910 1 chr6D.!!$R1 909
5 TraesCS6D01G321800 chr5D 539385968 539388323 2355 True 3988 3988 97.203 909 3267 1 chr5D.!!$R2 2358
6 TraesCS6D01G321800 chr5D 273156725 273157640 915 True 1580 1580 97.817 1 915 1 chr5D.!!$R1 914
7 TraesCS6D01G321800 chr5D 304385620 304386527 907 False 1578 1578 98.018 1 908 1 chr5D.!!$F1 907
8 TraesCS6D01G321800 chr7D 518130445 518132803 2358 False 3975 3975 97.076 909 3267 1 chr7D.!!$F2 2358
9 TraesCS6D01G321800 chr7D 610301129 610303486 2357 False 3901 3901 96.525 909 3267 1 chr7D.!!$F3 2358
10 TraesCS6D01G321800 chr7D 479011847 479012755 908 False 1568 1568 97.800 1 909 1 chr7D.!!$F1 908
11 TraesCS6D01G321800 chr3D 335955795 335958157 2362 True 3975 3975 97.039 906 3267 1 chr3D.!!$R1 2361
12 TraesCS6D01G321800 chr2D 534896630 534898989 2359 True 3952 3952 96.907 909 3267 1 chr2D.!!$R1 2358
13 TraesCS6D01G321800 chr2D 536058177 536060536 2359 True 3952 3952 96.907 909 3267 1 chr2D.!!$R2 2358
14 TraesCS6D01G321800 chr2D 610228200 610229107 907 False 1572 1572 97.907 1 908 1 chr2D.!!$F1 907
15 TraesCS6D01G321800 chr1D 466163786 466166144 2358 False 3947 3947 96.864 909 3267 1 chr1D.!!$F1 2358
16 TraesCS6D01G321800 chr1D 366427621 366429983 2362 True 3917 3917 96.616 909 3267 1 chr1D.!!$R2 2358
17 TraesCS6D01G321800 chr1D 232100865 232101773 908 True 1567 1567 97.800 1 908 1 chr1D.!!$R1 907
18 TraesCS6D01G321800 chr4D 491666432 491667341 909 False 1568 1568 97.802 1 908 1 chr4D.!!$F1 907

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
348 350 0.872388 ACAGCAACGGTCGGAAATTC 59.128 50.0 0.00 0.0 0.0 2.17 F
1220 1224 0.250640 AAGAGGGTCTGCAGCTTGTG 60.251 55.0 9.47 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2161 0.031585 GGTGGCGTACGCATCTATCA 59.968 55.0 37.99 23.94 44.11 2.15 R
3060 3073 0.253044 ACTGCATCCACGTGCCTAAT 59.747 50.0 10.91 0.00 44.43 1.73 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
47 48 4.451096 GTCTTCAAAGGTAACAAGCATCGA 59.549 41.667 0.00 0.00 41.41 3.59
272 273 5.470098 GCCCGACATGATAAGACATAAATGT 59.530 40.000 0.00 0.00 45.16 2.71
348 350 0.872388 ACAGCAACGGTCGGAAATTC 59.128 50.000 0.00 0.00 0.00 2.17
447 449 5.306678 AGTCAGAACAAATTCCTCAGAGACT 59.693 40.000 0.00 0.00 35.18 3.24
804 808 9.706691 TCGACTTTCTCTGTAAATATCAAACTT 57.293 29.630 0.00 0.00 0.00 2.66
1029 1033 2.129555 AACCATCTGCCAAGCGTCCT 62.130 55.000 0.00 0.00 0.00 3.85
1054 1058 3.053849 GAGACGTCCGACCAGAGCC 62.054 68.421 13.01 0.00 0.00 4.70
1213 1217 1.198713 GATCCTGAAGAGGGTCTGCA 58.801 55.000 0.00 0.00 45.28 4.41
1220 1224 0.250640 AAGAGGGTCTGCAGCTTGTG 60.251 55.000 9.47 0.00 0.00 3.33
1236 1240 0.902984 TGTGCCCTCAGTACATCGGT 60.903 55.000 0.00 0.00 36.01 4.69
1414 1418 4.948847 AGCTTTTCACCCTGAAATTTGAC 58.051 39.130 0.00 0.00 44.75 3.18
1587 1591 9.692749 CTTGATGTTCTAGTGTACTTTCTGTTA 57.307 33.333 0.00 0.00 0.00 2.41
1754 1758 5.928839 TGAACTCTGCATAGAAGTTTCTGAC 59.071 40.000 6.05 0.00 38.19 3.51
1928 1938 6.875726 CAGTATTGAAGGTGACAAAGAGATGA 59.124 38.462 0.00 0.00 0.00 2.92
1978 1988 3.507786 CGACAAGTACATCGACATCCAA 58.492 45.455 8.10 0.00 40.86 3.53
2151 2161 6.319658 CCAAATTACCTCATTGAGTATGCAGT 59.680 38.462 12.54 4.86 34.06 4.40
2296 2306 5.984926 ACGAAAACATAGAAAACTGGTCGTA 59.015 36.000 0.00 0.00 0.00 3.43
2333 2343 9.290988 TGTTTATGCTTGTCCTTTCTATTGTAA 57.709 29.630 0.00 0.00 0.00 2.41
2354 2364 8.165239 TGTAACAGGTTCGTAGTTTACTTCTA 57.835 34.615 0.00 0.00 0.00 2.10
2600 2611 0.473755 TGCTTCTTGAGGAGTGGCAA 59.526 50.000 0.00 0.00 33.64 4.52
2614 2625 4.102113 GCAAGAGTGGCATGGGTT 57.898 55.556 0.00 0.00 0.00 4.11
2623 2634 0.329931 TGGCATGGGTTGGAATACGT 59.670 50.000 0.00 0.00 0.00 3.57
2637 2648 5.138276 TGGAATACGTAGTTAGAGAGGCAT 58.862 41.667 0.08 0.00 37.78 4.40
2685 2697 0.542467 TGTGTTACTACAGGGGCCGA 60.542 55.000 0.00 0.00 34.24 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 273 5.365605 ACCTAACGGTCATATCATTGAAGGA 59.634 40.000 0.00 0.00 40.27 3.36
297 298 4.141390 CCAGCTGTCCCAAAATATCTACCT 60.141 45.833 13.81 0.00 0.00 3.08
348 350 4.962155 AGCCCTAAGGAATTTGATACTCG 58.038 43.478 0.00 0.00 33.47 4.18
1029 1033 2.281002 TCGGACGTCTCACCACGA 60.281 61.111 16.46 11.72 42.69 4.35
1054 1058 3.657835 GAACGTCGTCGACCTCGGG 62.658 68.421 23.67 7.65 40.62 5.14
1213 1217 0.987294 ATGTACTGAGGGCACAAGCT 59.013 50.000 0.00 0.00 41.70 3.74
1220 1224 0.249398 AACACCGATGTACTGAGGGC 59.751 55.000 0.00 0.00 38.45 5.19
1236 1240 3.383505 CCCTGGTATACTCGACATCAACA 59.616 47.826 2.25 0.00 0.00 3.33
1530 1534 9.651718 GAAAATAATCTCGTACATCAAATCCAC 57.348 33.333 0.00 0.00 0.00 4.02
1797 1805 5.337894 GGTGGATCCATCAAGTATCGATCAT 60.338 44.000 20.69 0.00 34.78 2.45
1928 1938 2.154462 CTCCAAACCAGAACTTCGCAT 58.846 47.619 0.00 0.00 0.00 4.73
1978 1988 2.568623 AAGGAACTCTCCATTTGCGT 57.431 45.000 0.00 0.00 45.24 5.24
2151 2161 0.031585 GGTGGCGTACGCATCTATCA 59.968 55.000 37.99 23.94 44.11 2.15
2296 2306 4.339247 ACAAGCATAAACACAAGCAACTCT 59.661 37.500 0.00 0.00 0.00 3.24
2333 2343 9.236006 TCTAATAGAAGTAAACTACGAACCTGT 57.764 33.333 0.00 0.00 0.00 4.00
2354 2364 7.602644 TGACATTAGAAACTGCTTCGTTCTAAT 59.397 33.333 10.60 10.60 39.22 1.73
2581 2592 0.473755 TTGCCACTCCTCAAGAAGCA 59.526 50.000 0.00 0.00 35.65 3.91
2600 2611 0.706433 ATTCCAACCCATGCCACTCT 59.294 50.000 0.00 0.00 0.00 3.24
2614 2625 4.529897 TGCCTCTCTAACTACGTATTCCA 58.470 43.478 0.00 0.00 0.00 3.53
2623 2634 4.714802 TGCAAACCTATGCCTCTCTAACTA 59.285 41.667 0.00 0.00 45.83 2.24
2637 2648 2.761208 GGCTCTAGAGACTGCAAACCTA 59.239 50.000 24.24 0.00 32.39 3.08
2685 2697 0.693049 AGACTTCCATTCCGTGCCTT 59.307 50.000 0.00 0.00 0.00 4.35
3035 3048 4.289312 GCCCCGCGACTCTTAAAA 57.711 55.556 8.23 0.00 0.00 1.52
3060 3073 0.253044 ACTGCATCCACGTGCCTAAT 59.747 50.000 10.91 0.00 44.43 1.73
3147 3160 4.281688 ACTTTTGAACATCCACAGGATTGG 59.718 41.667 0.00 0.00 39.79 3.16


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

AutoCloner maintained by Alex Coulton.