Multiple sequence alignment - TraesCS3D01G179400

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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 TraesCS3D01G179400 chr3D 100.000 2100 0 0 1808 3907 161401874 161399775 0.000000e+00 3879.0
1 TraesCS3D01G179400 chr3D 88.283 2108 179 38 1817 3907 161596742 161594686 0.000000e+00 2462.0
2 TraesCS3D01G179400 chr3D 100.000 1104 0 0 1 1104 161403681 161402578 0.000000e+00 2039.0
3 TraesCS3D01G179400 chr3D 90.331 1572 106 29 2351 3907 161497955 161496415 0.000000e+00 2019.0
4 TraesCS3D01G179400 chr3D 91.837 1127 59 15 2 1104 161499714 161498597 0.000000e+00 1541.0
5 TraesCS3D01G179400 chr3D 90.341 528 33 7 1808 2332 161498531 161498019 0.000000e+00 676.0
6 TraesCS3D01G179400 chr3A 96.619 2100 71 0 1808 3907 190094665 190092566 0.000000e+00 3485.0
7 TraesCS3D01G179400 chr3A 87.747 2122 178 47 1817 3907 190229042 190226972 0.000000e+00 2403.0
8 TraesCS3D01G179400 chr3A 87.791 2105 175 49 1817 3890 191254024 191251971 0.000000e+00 2388.0
9 TraesCS3D01G179400 chr3A 89.727 1577 110 32 2351 3907 191006604 191005060 0.000000e+00 1967.0
10 TraesCS3D01G179400 chr3A 97.240 1087 26 2 2080 3166 188112420 188113502 0.000000e+00 1838.0
11 TraesCS3D01G179400 chr3A 88.387 1128 79 26 1 1104 191008794 191007695 0.000000e+00 1310.0
12 TraesCS3D01G179400 chr3A 93.381 846 50 5 1 843 188100229 188101071 0.000000e+00 1247.0
13 TraesCS3D01G179400 chr3A 95.473 751 19 12 3159 3907 188113380 188114117 0.000000e+00 1184.0
14 TraesCS3D01G179400 chr3A 88.622 958 75 17 1 943 190096114 190095176 0.000000e+00 1134.0
15 TraesCS3D01G179400 chr3A 89.205 528 39 7 1808 2332 191007629 191007117 0.000000e+00 643.0
16 TraesCS3D01G179400 chr3A 95.785 261 9 1 843 1101 188101147 188101407 1.680000e-113 420.0
17 TraesCS3D01G179400 chr3A 92.529 174 4 4 940 1104 190094903 190094730 1.400000e-59 241.0
18 TraesCS3D01G179400 chr3A 98.214 56 1 0 970 1025 190229119 190229064 8.930000e-17 99.0
19 TraesCS3D01G179400 chr3A 98.214 56 1 0 970 1025 191254101 191254046 8.930000e-17 99.0
20 TraesCS3D01G179400 chr3A 96.364 55 2 0 971 1025 190583047 190582993 1.490000e-14 91.6
21 TraesCS3D01G179400 chr3B 96.763 2101 33 8 1808 3907 237734324 237732258 0.000000e+00 3470.0
22 TraesCS3D01G179400 chr3B 88.127 2114 177 40 1815 3907 238113670 238111610 0.000000e+00 2446.0
23 TraesCS3D01G179400 chr3B 93.172 1567 79 13 2351 3907 237972968 237971420 0.000000e+00 2276.0
24 TraesCS3D01G179400 chr3B 95.935 1107 35 7 2 1104 237735490 237734390 0.000000e+00 1786.0
25 TraesCS3D01G179400 chr3B 87.871 775 71 8 1 753 237978111 237977338 0.000000e+00 889.0
26 TraesCS3D01G179400 chr3B 89.962 528 35 7 1808 2332 237973535 237973023 0.000000e+00 665.0
27 TraesCS3D01G179400 chr3B 91.620 179 4 2 937 1104 237973779 237973601 1.810000e-58 237.0
28 TraesCS3D01G179400 chr3B 85.047 107 1 3 850 941 237977215 237977109 1.160000e-15 95.3
29 TraesCS3D01G179400 chr6D 90.184 163 15 1 495 656 281926087 281926249 1.100000e-50 211.0
30 TraesCS3D01G179400 chr6D 100.000 35 0 0 809 843 452414538 452414572 9.060000e-07 65.8
31 TraesCS3D01G179400 chr4A 90.909 154 13 1 498 650 555535884 555536037 5.120000e-49 206.0
32 TraesCS3D01G179400 chr7D 77.957 186 28 10 663 843 579794562 579794385 1.920000e-18 104.0
33 TraesCS3D01G179400 chr2D 78.571 168 24 10 679 843 124318469 124318311 2.480000e-17 100.0


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 TraesCS3D01G179400 chr3D 161399775 161403681 3906 True 2959.000000 3879 100.000000 1 3907 2 chr3D.!!$R2 3906
1 TraesCS3D01G179400 chr3D 161594686 161596742 2056 True 2462.000000 2462 88.283000 1817 3907 1 chr3D.!!$R1 2090
2 TraesCS3D01G179400 chr3D 161496415 161499714 3299 True 1412.000000 2019 90.836333 2 3907 3 chr3D.!!$R3 3905
3 TraesCS3D01G179400 chr3A 190092566 190096114 3548 True 1620.000000 3485 92.590000 1 3907 3 chr3A.!!$R2 3906
4 TraesCS3D01G179400 chr3A 188112420 188114117 1697 False 1511.000000 1838 96.356500 2080 3907 2 chr3A.!!$F2 1827
5 TraesCS3D01G179400 chr3A 191005060 191008794 3734 True 1306.666667 1967 89.106333 1 3907 3 chr3A.!!$R4 3906
6 TraesCS3D01G179400 chr3A 190226972 190229119 2147 True 1251.000000 2403 92.980500 970 3907 2 chr3A.!!$R3 2937
7 TraesCS3D01G179400 chr3A 191251971 191254101 2130 True 1243.500000 2388 93.002500 970 3890 2 chr3A.!!$R5 2920
8 TraesCS3D01G179400 chr3A 188100229 188101407 1178 False 833.500000 1247 94.583000 1 1101 2 chr3A.!!$F1 1100
9 TraesCS3D01G179400 chr3B 237732258 237735490 3232 True 2628.000000 3470 96.349000 2 3907 2 chr3B.!!$R2 3905
10 TraesCS3D01G179400 chr3B 238111610 238113670 2060 True 2446.000000 2446 88.127000 1815 3907 1 chr3B.!!$R1 2092
11 TraesCS3D01G179400 chr3B 237971420 237978111 6691 True 832.460000 2276 89.534400 1 3907 5 chr3B.!!$R3 3906

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
105 124 0.753867 TTGGTCTACAACAGGACGCA 59.246 50.0 0.0 0.0 33.18 5.24 F
402 423 1.950973 GCCACCAAACCAAACCGTGT 61.951 55.0 0.0 0.0 0.00 4.49 F
2210 5879 1.293267 GCGATGACGAAAACCCCGAA 61.293 55.0 0.0 0.0 42.66 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 5621 1.786441 TGGAGGGTGGTGAGGAAAAAT 59.214 47.619 0.00 0.0 0.00 1.82 R
2394 6584 3.673594 CGATTCCGATATGGCCAGTAGAC 60.674 52.174 13.05 0.0 38.22 2.59 R
3275 7497 1.628846 ACAGTAGCGAACCCAAGGAAT 59.371 47.619 0.00 0.0 0.00 3.01 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
31 40 2.167900 AGCGTGGGACTTGGATTACTAC 59.832 50.000 0.00 0.00 0.00 2.73
32 41 2.093869 GCGTGGGACTTGGATTACTACA 60.094 50.000 0.00 0.00 0.00 2.74
33 42 3.518590 CGTGGGACTTGGATTACTACAC 58.481 50.000 0.00 0.00 0.00 2.90
34 43 3.056393 CGTGGGACTTGGATTACTACACA 60.056 47.826 0.00 0.00 0.00 3.72
35 44 4.251268 GTGGGACTTGGATTACTACACAC 58.749 47.826 0.00 0.00 0.00 3.82
36 45 4.020485 GTGGGACTTGGATTACTACACACT 60.020 45.833 0.00 0.00 0.00 3.55
37 46 4.020573 TGGGACTTGGATTACTACACACTG 60.021 45.833 0.00 0.00 0.00 3.66
38 47 4.222145 GGGACTTGGATTACTACACACTGA 59.778 45.833 0.00 0.00 0.00 3.41
59 68 9.366216 CACTGAAATCAATCATCAAAATCACAT 57.634 29.630 0.00 0.00 0.00 3.21
104 123 1.873698 TTTGGTCTACAACAGGACGC 58.126 50.000 0.00 0.00 39.19 5.19
105 124 0.753867 TTGGTCTACAACAGGACGCA 59.246 50.000 0.00 0.00 33.18 5.24
134 155 9.420551 GAGAATGAAAGAGCAAAAGAATTCATT 57.579 29.630 8.44 10.34 45.21 2.57
402 423 1.950973 GCCACCAAACCAAACCGTGT 61.951 55.000 0.00 0.00 0.00 4.49
525 553 3.535561 CCTAGTTTGGGAGCACAGTATG 58.464 50.000 0.00 0.00 46.00 2.39
677 716 2.645628 CGTGAGTGTTTCTCGGTTTG 57.354 50.000 0.00 0.00 45.46 2.93
683 722 4.698304 TGAGTGTTTCTCGGTTTGAAAAGT 59.302 37.500 0.00 0.00 45.46 2.66
741 781 6.585695 ACCTCAGTTTTGAAGATACTACGA 57.414 37.500 0.00 0.00 31.69 3.43
807 937 5.357742 AAGTCTTTGAAGCCATGGTTTTT 57.642 34.783 15.65 6.64 0.00 1.94
1961 5621 4.301505 GCCATCTTGAGCGGTGAA 57.698 55.556 0.00 0.00 0.00 3.18
2210 5879 1.293267 GCGATGACGAAAACCCCGAA 61.293 55.000 0.00 0.00 42.66 4.30
2394 6584 1.268032 GCATGCGAGTGGGTAATTTCG 60.268 52.381 0.00 0.00 36.23 3.46
3692 7929 4.155826 GTCAGTGTTAAGGCATGCATGTTA 59.844 41.667 26.79 15.76 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 40 8.644619 GTGATTTTGATGATTGATTTCAGTGTG 58.355 33.333 0.00 0.00 0.00 3.82
32 41 8.361889 TGTGATTTTGATGATTGATTTCAGTGT 58.638 29.630 0.00 0.00 0.00 3.55
33 42 8.751302 TGTGATTTTGATGATTGATTTCAGTG 57.249 30.769 0.00 0.00 0.00 3.66
34 43 9.582431 GATGTGATTTTGATGATTGATTTCAGT 57.418 29.630 0.00 0.00 0.00 3.41
35 44 9.581099 TGATGTGATTTTGATGATTGATTTCAG 57.419 29.630 0.00 0.00 0.00 3.02
36 45 9.930693 TTGATGTGATTTTGATGATTGATTTCA 57.069 25.926 0.00 0.00 0.00 2.69
104 123 6.263516 TCTTTTGCTCTTTCATTCTCCATG 57.736 37.500 0.00 0.00 0.00 3.66
105 124 6.906157 TTCTTTTGCTCTTTCATTCTCCAT 57.094 33.333 0.00 0.00 0.00 3.41
295 316 1.203038 TCATCCCCGCATATGCCAATT 60.203 47.619 21.77 0.76 37.91 2.32
338 359 4.424711 GACATGGGGAAGGCGGCA 62.425 66.667 13.08 0.00 0.00 5.69
525 553 7.937649 AGTTTTGGATTACTGTGGTTTTAGAC 58.062 34.615 0.00 0.00 0.00 2.59
1961 5621 1.786441 TGGAGGGTGGTGAGGAAAAAT 59.214 47.619 0.00 0.00 0.00 1.82
2394 6584 3.673594 CGATTCCGATATGGCCAGTAGAC 60.674 52.174 13.05 0.00 38.22 2.59
3275 7497 1.628846 ACAGTAGCGAACCCAAGGAAT 59.371 47.619 0.00 0.00 0.00 3.01
3552 7784 4.610945 AGTGCAAGAAACACTGCAAATAC 58.389 39.130 0.00 0.00 46.38 1.89
3632 7869 6.092533 CCTGTTTCAGCTTTTGACACAAATTT 59.907 34.615 0.00 0.00 43.75 1.82
3692 7929 3.221771 TGAACTTTGCTGTAACATGGCT 58.778 40.909 0.00 0.00 0.00 4.75
3858 8121 5.294799 GTGTATTTGCCGGACATGTATACAA 59.705 40.000 10.14 7.64 33.19 2.41
3872 8135 8.671384 TTATCTAATACCACTGTGTATTTGCC 57.329 34.615 15.61 0.00 40.79 4.52


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

AutoCloner maintained by Alex Coulton.