Multiple sequence alignment - TraesCS3D01G504500

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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 TraesCS3D01G504500 chr3D 100.000 3097 0 0 1 3097 591984714 591987810 0.000000e+00 5720
1 TraesCS3D01G504500 chr7A 94.963 2462 73 27 1 2431 84768202 84765761 0.000000e+00 3812
2 TraesCS3D01G504500 chr7A 94.228 1975 71 22 482 2431 107623464 107621508 0.000000e+00 2976
3 TraesCS3D01G504500 chr7A 96.434 673 17 6 2426 3095 107621471 107620803 0.000000e+00 1103
4 TraesCS3D01G504500 chr7A 94.815 675 14 10 2426 3095 84765724 84765066 0.000000e+00 1033
5 TraesCS3D01G504500 chr7A 95.142 494 16 6 1 487 107623990 107623498 0.000000e+00 773
6 TraesCS3D01G504500 chr3A 94.261 2457 83 30 1 2431 202637737 202640161 0.000000e+00 3703
7 TraesCS3D01G504500 chr3A 93.796 677 16 15 2426 3095 202640198 202640855 0.000000e+00 994
8 TraesCS3D01G504500 chr6A 94.551 1982 59 27 482 2431 194724465 194722501 0.000000e+00 3016
9 TraesCS3D01G504500 chr6A 94.615 1820 60 18 482 2274 194747391 194745583 0.000000e+00 2784
10 TraesCS3D01G504500 chr6A 94.505 1820 60 19 482 2274 194775248 194773442 0.000000e+00 2771
11 TraesCS3D01G504500 chr6A 95.691 673 22 6 2426 3095 194722464 194721796 0.000000e+00 1075
12 TraesCS3D01G504500 chr6A 97.331 487 11 2 1 487 194747910 194747426 0.000000e+00 826
13 TraesCS3D01G504500 chr6A 96.920 487 12 3 1 487 194775766 194775283 0.000000e+00 813
14 TraesCS3D01G504500 chr6A 96.894 483 14 1 5 487 194724981 194724500 0.000000e+00 808
15 TraesCS3D01G504500 chr3B 85.643 2013 184 48 482 2431 757875724 757873754 0.000000e+00 2019
16 TraesCS3D01G504500 chr3B 91.803 488 27 7 1 487 757876234 757875759 0.000000e+00 667
17 TraesCS3D01G504500 chr3B 91.958 286 20 3 2811 3095 757884778 757884495 6.220000e-107 398
18 TraesCS3D01G504500 chr3B 91.579 285 22 2 2811 3095 757873368 757873086 2.900000e-105 392
19 TraesCS3D01G504500 chr3B 85.083 362 19 19 2427 2760 757873717 757873363 1.380000e-88 337


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 TraesCS3D01G504500 chr3D 591984714 591987810 3096 False 5720.000000 5720 100.0000 1 3097 1 chr3D.!!$F1 3096
1 TraesCS3D01G504500 chr7A 84765066 84768202 3136 True 2422.500000 3812 94.8890 1 3095 2 chr7A.!!$R1 3094
2 TraesCS3D01G504500 chr7A 107620803 107623990 3187 True 1617.333333 2976 95.2680 1 3095 3 chr7A.!!$R2 3094
3 TraesCS3D01G504500 chr3A 202637737 202640855 3118 False 2348.500000 3703 94.0285 1 3095 2 chr3A.!!$F1 3094
4 TraesCS3D01G504500 chr6A 194745583 194747910 2327 True 1805.000000 2784 95.9730 1 2274 2 chr6A.!!$R2 2273
5 TraesCS3D01G504500 chr6A 194773442 194775766 2324 True 1792.000000 2771 95.7125 1 2274 2 chr6A.!!$R3 2273
6 TraesCS3D01G504500 chr6A 194721796 194724981 3185 True 1633.000000 3016 95.7120 5 3095 3 chr6A.!!$R1 3090
7 TraesCS3D01G504500 chr3B 757873086 757876234 3148 True 853.750000 2019 88.5270 1 3095 4 chr3B.!!$R2 3094

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
393 404 3.445096 GCAGCAAAAGGAATCCAGTACAT 59.555 43.478 0.61 0.0 0.0 2.29 F
1098 1165 2.101640 AAGCAAATGAAACCCCACCT 57.898 45.000 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 1836 2.832733 TGCATTGAAATCCATTGGCTCA 59.167 40.909 0.0 0.0 0.0 4.26 R
2533 2712 1.539388 GATGCCACACGGAAAACATGA 59.461 47.619 0.0 0.0 0.0 3.07 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
393 404 3.445096 GCAGCAAAAGGAATCCAGTACAT 59.555 43.478 0.61 0.0 0.00 2.29
459 474 6.942532 AAGTGCTCTCTGTTTTGTTAATCA 57.057 33.333 0.00 0.0 0.00 2.57
597 653 9.897744 GATGATTTTTACAACACAAATCTCTCA 57.102 29.630 0.00 0.0 37.66 3.27
973 1040 8.265055 AGAATTGGGTAACTCGATGAAAATAGA 58.735 33.333 0.00 0.0 0.00 1.98
1004 1071 4.757149 GTCCAGGCCTATGTCATAAATGTC 59.243 45.833 3.98 0.0 0.00 3.06
1007 1074 6.328934 TCCAGGCCTATGTCATAAATGTCTAA 59.671 38.462 3.98 0.0 0.00 2.10
1098 1165 2.101640 AAGCAAATGAAACCCCACCT 57.898 45.000 0.00 0.0 0.00 4.00
1099 1166 2.101640 AGCAAATGAAACCCCACCTT 57.898 45.000 0.00 0.0 0.00 3.50
1100 1167 2.407562 AGCAAATGAAACCCCACCTTT 58.592 42.857 0.00 0.0 0.00 3.11
1550 1641 7.501515 GCACGTTTTATTTTCTGGATTCTTTG 58.498 34.615 0.00 0.0 0.00 2.77
1680 1774 6.403866 TTTCCTGCAAACATCAGTAAATGT 57.596 33.333 0.00 0.0 41.60 2.71
1828 1929 3.135994 ACGAAACCAAACATCTACGCTT 58.864 40.909 0.00 0.0 0.00 4.68
1912 2019 5.106078 TGTTCACAAACACCTGTACCTTTTC 60.106 40.000 0.00 0.0 40.45 2.29
2088 2213 1.689273 AGAAGCGTGTCAAGGAGTTCT 59.311 47.619 0.00 0.0 0.00 3.01
2325 2454 9.008965 TGTATCAAACACATAGTTAGCAATTGT 57.991 29.630 7.40 0.0 40.26 2.71
2387 2516 3.559238 CAGAATGTACACCCTTGTTGC 57.441 47.619 0.00 0.0 37.15 4.17
2391 2520 3.780804 ATGTACACCCTTGTTGCTGTA 57.219 42.857 0.00 0.0 37.15 2.74
2393 2522 2.701423 TGTACACCCTTGTTGCTGTAGA 59.299 45.455 0.00 0.0 37.15 2.59
2623 2830 1.694696 GACACAAAGGTCACCCTCTCT 59.305 52.381 0.00 0.0 41.56 3.10
2718 2927 4.770795 AGGTTCAGATCCACCTAAAATCG 58.229 43.478 7.00 0.0 41.97 3.34
2939 3152 3.118992 GGAGGAGAAACAATGCCCATTTC 60.119 47.826 0.00 0.0 33.40 2.17
2971 3184 6.094464 TCTCATAATGCAAGGAAACACTCATG 59.906 38.462 0.00 0.0 0.00 3.07
3031 3244 4.412796 TTGTTTCCCATCATTTGTGCAA 57.587 36.364 0.00 0.0 0.00 4.08
3056 3269 6.318648 ACAACAGAGTTTTCAGTTCATAAGCA 59.681 34.615 0.00 0.0 31.50 3.91
3086 3299 4.070716 AGAGGAAGAGAAACATGCAACAG 58.929 43.478 0.00 0.0 0.00 3.16
3089 3302 4.276926 AGGAAGAGAAACATGCAACAGTTC 59.723 41.667 0.00 0.0 0.00 3.01
3095 3308 3.818961 AACATGCAACAGTTCTCATCG 57.181 42.857 0.00 0.0 0.00 3.84
3096 3309 2.771089 ACATGCAACAGTTCTCATCGT 58.229 42.857 0.00 0.0 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 179 4.406003 TCTGCTATTTCAGGACTACCTTCC 59.594 45.833 0.00 0.00 45.36 3.46
597 653 2.907458 AACTGCTTGGCCTTCCTAAT 57.093 45.000 3.32 0.00 0.00 1.73
902 969 9.453058 TTGTCAATCAAAACTGCAGGTTTGCTA 62.453 37.037 40.17 29.38 46.18 3.49
933 1000 2.415893 CCAATTCTCCAAATGTGGCGAC 60.416 50.000 0.00 0.00 45.54 5.19
948 1015 8.433421 TCTATTTTCATCGAGTTACCCAATTC 57.567 34.615 0.00 0.00 0.00 2.17
950 1017 7.445402 CCATCTATTTTCATCGAGTTACCCAAT 59.555 37.037 0.00 0.00 0.00 3.16
1007 1074 9.420118 TGATTTTCATTAAATAGGTGCCTACAT 57.580 29.630 0.00 0.00 36.59 2.29
1742 1836 2.832733 TGCATTGAAATCCATTGGCTCA 59.167 40.909 0.00 0.00 0.00 4.26
1743 1837 3.530265 TGCATTGAAATCCATTGGCTC 57.470 42.857 0.00 0.00 0.00 4.70
1828 1929 7.791029 AGCAAAAGGAGTCAGGAAAAATAAAA 58.209 30.769 0.00 0.00 0.00 1.52
1912 2019 5.577945 GTGAAAATGCCACAATCAATACTGG 59.422 40.000 0.00 0.00 34.81 4.00
2088 2213 5.772393 CATATGGGGTTAACCTATAGGCA 57.228 43.478 23.69 7.06 44.74 4.75
2136 2261 6.214191 TCCTGTCACAAACATAAAGCAAAA 57.786 33.333 0.00 0.00 37.23 2.44
2367 2496 3.058016 CAGCAACAAGGGTGTACATTCTG 60.058 47.826 0.00 0.00 36.80 3.02
2387 2516 6.613271 AGAGGGGGCATATATATGTTCTACAG 59.387 42.308 21.10 0.00 36.11 2.74
2391 2520 9.920230 ATAATAGAGGGGGCATATATATGTTCT 57.080 33.333 21.10 17.04 36.11 3.01
2423 2559 7.486870 ACATTACCGAGTGAAAAAGAACAAAAC 59.513 33.333 0.00 0.00 0.00 2.43
2533 2712 1.539388 GATGCCACACGGAAAACATGA 59.461 47.619 0.00 0.00 0.00 3.07
2718 2927 5.232838 CAGGAAAAACTCAAACATGAGCAAC 59.767 40.000 0.00 0.00 39.42 4.17
2939 3152 7.541783 TGTTTCCTTGCATTATGAGAAAAATCG 59.458 33.333 0.00 0.00 0.00 3.34
2971 3184 3.565482 TGTTGCTGTTGGTCTTGATCTTC 59.435 43.478 0.00 0.00 0.00 2.87
3031 3244 6.318648 TGCTTATGAACTGAAAACTCTGTTGT 59.681 34.615 2.61 0.00 33.07 3.32
3063 3276 4.067896 TGTTGCATGTTTCTCTTCCTCTC 58.932 43.478 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.