Multiple sequence alignment - TraesCS4B01G167900

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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 TraesCS4B01G167900 chr4B 100.000 2486 0 0 1 2486 366945759 366948244 0.000000e+00 4591.0
1 TraesCS4B01G167900 chr4B 83.264 968 148 5 565 1519 599443189 599442223 0.000000e+00 878.0
2 TraesCS4B01G167900 chr4A 95.425 1530 60 6 1 1521 192620902 192619374 0.000000e+00 2429.0
3 TraesCS4B01G167900 chr4A 95.514 691 24 1 1803 2486 192618919 192618229 0.000000e+00 1098.0
4 TraesCS4B01G167900 chr4A 91.667 108 5 2 1534 1641 192619305 192619202 1.990000e-31 147.0
5 TraesCS4B01G167900 chr4A 92.308 78 6 0 485 562 591452555 591452632 7.270000e-21 111.0
6 TraesCS4B01G167900 chr4A 93.333 75 5 0 488 562 592264874 592264800 7.270000e-21 111.0
7 TraesCS4B01G167900 chr4A 93.333 75 5 0 488 562 592602292 592602218 7.270000e-21 111.0
8 TraesCS4B01G167900 chr4A 93.333 75 5 0 488 562 592891412 592891338 7.270000e-21 111.0
9 TraesCS4B01G167900 chr4A 93.333 75 5 0 488 562 593162882 593162808 7.270000e-21 111.0
10 TraesCS4B01G167900 chr4A 90.566 53 5 0 1559 1611 362094815 362094763 1.230000e-08 71.3
11 TraesCS4B01G167900 chr4D 93.883 1177 60 9 1 1169 296732137 296733309 0.000000e+00 1764.0
12 TraesCS4B01G167900 chr4D 93.684 855 30 9 1642 2486 296737890 296738730 0.000000e+00 1258.0
13 TraesCS4B01G167900 chr4D 94.444 108 2 2 1534 1641 296737742 296737845 1.980000e-36 163.0
14 TraesCS4B01G167900 chr7D 87.384 967 110 6 565 1519 309505580 309504614 0.000000e+00 1099.0
15 TraesCS4B01G167900 chr7D 85.391 972 117 9 566 1521 615446431 615445469 0.000000e+00 985.0
16 TraesCS4B01G167900 chr7B 87.371 966 109 7 567 1519 304962253 304963218 0.000000e+00 1096.0
17 TraesCS4B01G167900 chr7B 86.229 472 55 4 565 1027 622267675 622267205 1.030000e-138 503.0
18 TraesCS4B01G167900 chr7B 88.153 287 24 6 1641 1920 594412363 594412646 1.420000e-87 333.0
19 TraesCS4B01G167900 chr7B 87.633 283 27 3 1642 1918 266388797 266388517 3.080000e-84 322.0
20 TraesCS4B01G167900 chr7B 87.726 277 26 6 1642 1912 301607122 301607396 1.440000e-82 316.0
21 TraesCS4B01G167900 chr7A 87.280 967 109 8 566 1519 372201741 372200776 0.000000e+00 1092.0
22 TraesCS4B01G167900 chr7A 87.279 283 29 2 1642 1918 534403421 534403140 1.440000e-82 316.0
23 TraesCS4B01G167900 chr2A 85.729 967 122 7 565 1519 339093486 339094448 0.000000e+00 1007.0
24 TraesCS4B01G167900 chr2A 87.234 282 29 2 1642 1917 350776678 350776958 5.160000e-82 315.0
25 TraesCS4B01G167900 chr2A 94.805 77 4 0 489 565 414294304 414294380 1.210000e-23 121.0
26 TraesCS4B01G167900 chr2D 84.592 967 136 7 565 1519 373891185 373890220 0.000000e+00 948.0
27 TraesCS4B01G167900 chr2D 83.060 974 153 5 569 1530 218037955 218036982 0.000000e+00 874.0
28 TraesCS4B01G167900 chr2D 87.018 285 29 3 1642 1920 24923486 24923768 5.160000e-82 315.0
29 TraesCS4B01G167900 chr3B 83.275 855 127 10 679 1519 615776817 615775965 0.000000e+00 773.0
30 TraesCS4B01G167900 chr6B 83.247 776 115 10 565 1329 150283724 150282953 0.000000e+00 699.0
31 TraesCS4B01G167900 chr6B 89.085 284 23 7 1643 1920 532165311 532165592 1.830000e-91 346.0
32 TraesCS4B01G167900 chr6D 88.172 279 23 5 1642 1912 15375885 15375609 8.580000e-85 324.0
33 TraesCS4B01G167900 chr1A 87.413 286 23 5 1642 1916 67685797 67686080 1.440000e-82 316.0
34 TraesCS4B01G167900 chr1A 81.215 181 19 14 211 382 482858782 482858608 5.580000e-27 132.0
35 TraesCS4B01G167900 chr1D 92.593 81 6 0 488 568 468029976 468029896 1.560000e-22 117.0
36 TraesCS4B01G167900 chr2B 88.095 84 8 2 1534 1617 232782346 232782265 5.660000e-17 99.0
37 TraesCS4B01G167900 chr5A 92.857 56 4 0 1559 1614 486064800 486064745 5.700000e-12 82.4
38 TraesCS4B01G167900 chr5D 94.872 39 1 1 1578 1615 50997955 50997917 2.670000e-05 60.2


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 TraesCS4B01G167900 chr4B 366945759 366948244 2485 False 4591.000000 4591 100.000 1 2486 1 chr4B.!!$F1 2485
1 TraesCS4B01G167900 chr4B 599442223 599443189 966 True 878.000000 878 83.264 565 1519 1 chr4B.!!$R1 954
2 TraesCS4B01G167900 chr4A 192618229 192620902 2673 True 1224.666667 2429 94.202 1 2486 3 chr4A.!!$R6 2485
3 TraesCS4B01G167900 chr4D 296732137 296733309 1172 False 1764.000000 1764 93.883 1 1169 1 chr4D.!!$F1 1168
4 TraesCS4B01G167900 chr4D 296737742 296738730 988 False 710.500000 1258 94.064 1534 2486 2 chr4D.!!$F2 952
5 TraesCS4B01G167900 chr7D 309504614 309505580 966 True 1099.000000 1099 87.384 565 1519 1 chr7D.!!$R1 954
6 TraesCS4B01G167900 chr7D 615445469 615446431 962 True 985.000000 985 85.391 566 1521 1 chr7D.!!$R2 955
7 TraesCS4B01G167900 chr7B 304962253 304963218 965 False 1096.000000 1096 87.371 567 1519 1 chr7B.!!$F2 952
8 TraesCS4B01G167900 chr7A 372200776 372201741 965 True 1092.000000 1092 87.280 566 1519 1 chr7A.!!$R1 953
9 TraesCS4B01G167900 chr2A 339093486 339094448 962 False 1007.000000 1007 85.729 565 1519 1 chr2A.!!$F1 954
10 TraesCS4B01G167900 chr2D 373890220 373891185 965 True 948.000000 948 84.592 565 1519 1 chr2D.!!$R2 954
11 TraesCS4B01G167900 chr2D 218036982 218037955 973 True 874.000000 874 83.060 569 1530 1 chr2D.!!$R1 961
12 TraesCS4B01G167900 chr3B 615775965 615776817 852 True 773.000000 773 83.275 679 1519 1 chr3B.!!$R1 840
13 TraesCS4B01G167900 chr6B 150282953 150283724 771 True 699.000000 699 83.247 565 1329 1 chr6B.!!$R1 764

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
758 766 0.107897 CATGGTCGTCGGGAATGGAA 60.108 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 2096 1.343884 TGGCAATATTTGGGAAGGGGG 60.344 52.381 0.0 0.0 0.0 5.4 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
23 24 5.973158 GGAAATTGCACAAATACACAACAC 58.027 37.500 0.00 0.00 0.00 3.32
47 48 3.755378 TGTTAAGTGACTAGAGGGACGAC 59.245 47.826 0.00 0.00 0.00 4.34
189 191 7.587037 TTGAAAAGATCTGAACAATTCCAGT 57.413 32.000 0.00 0.00 0.00 4.00
206 208 5.178096 TCCAGTAATTCAAGCCATCTTCA 57.822 39.130 0.00 0.00 0.00 3.02
207 209 4.943705 TCCAGTAATTCAAGCCATCTTCAC 59.056 41.667 0.00 0.00 0.00 3.18
319 322 8.785946 CAGAAATGTCCAAAATTTAAAATGGCT 58.214 29.630 11.30 2.39 32.87 4.75
458 465 7.446931 TGAATATTATAATTGGCTCGGCTCAAA 59.553 33.333 2.68 0.00 0.00 2.69
483 490 1.063764 GCCGTCCGTCTAGTCACTTAG 59.936 57.143 0.00 0.00 0.00 2.18
488 495 4.002316 GTCCGTCTAGTCACTTAGAGTGT 58.998 47.826 7.85 0.00 46.03 3.55
528 535 2.444766 AGAGCTAGGGAATGGGAATTGG 59.555 50.000 0.00 0.00 0.00 3.16
534 541 1.697284 GGAATGGGAATTGGAGAGGC 58.303 55.000 0.00 0.00 0.00 4.70
701 709 2.579738 GGCTCGACCTCCAGTTCC 59.420 66.667 0.00 0.00 34.51 3.62
758 766 0.107897 CATGGTCGTCGGGAATGGAA 60.108 55.000 0.00 0.00 0.00 3.53
934 955 0.808755 TGCACGAGATCGCTCAGTAA 59.191 50.000 1.39 0.00 44.43 2.24
935 956 1.201414 TGCACGAGATCGCTCAGTAAA 59.799 47.619 1.39 0.00 44.43 2.01
1150 1172 2.203280 CCAACCAGGACCGTTGCA 60.203 61.111 6.71 0.00 39.42 4.08
1758 1883 4.339814 GTCTAGTCTCTCGTCAATTCCCAT 59.660 45.833 0.00 0.00 0.00 4.00
1789 1914 5.186198 ACAAGGGAATACAATTTCTCCTCG 58.814 41.667 0.00 0.00 30.59 4.63
1874 2083 9.042450 TGTCTAATCTCAATACAACTCCCTAAA 57.958 33.333 0.00 0.00 0.00 1.85
1887 2096 5.695424 ACTCCCTAAACTAAACTCCCATC 57.305 43.478 0.00 0.00 0.00 3.51
1912 2121 4.080413 CCCTTCCCAAATATTGCCAAACAT 60.080 41.667 0.00 0.00 0.00 2.71
2063 2272 2.883026 TGTTACCTCAACCCCAAATGG 58.117 47.619 0.00 0.00 36.20 3.16
2072 2281 3.829601 TCAACCCCAAATGGTGTGTATTC 59.170 43.478 0.00 0.00 39.05 1.75
2078 2287 3.233578 CAAATGGTGTGTATTCGTGCAC 58.766 45.455 6.82 6.82 36.26 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.458295 TCGTCCCTCTAGTCACTTAACAAG 59.542 45.833 0.00 0.00 0.00 3.16
47 48 1.805345 CTTGGCTCAGCTCAAGTCAAG 59.195 52.381 19.98 19.98 46.49 3.02
189 191 8.806429 TTGATTAGTGAAGATGGCTTGAATTA 57.194 30.769 0.00 0.00 33.61 1.40
206 208 7.841222 AGGCTAAAAATTCCCAGATTGATTAGT 59.159 33.333 0.00 0.00 30.12 2.24
207 209 8.242729 AGGCTAAAAATTCCCAGATTGATTAG 57.757 34.615 0.00 0.00 0.00 1.73
427 434 8.082242 GCCGAGCCAATTATAATATTCAAAGTT 58.918 33.333 0.00 0.00 0.00 2.66
458 465 1.593296 GACTAGACGGACGGCTTGGT 61.593 60.000 5.00 5.47 34.01 3.67
483 490 0.396556 ACCCCCAACCAAACACACTC 60.397 55.000 0.00 0.00 0.00 3.51
488 495 4.668636 CTCTAATTACCCCCAACCAAACA 58.331 43.478 0.00 0.00 0.00 2.83
528 535 2.440539 TTTGAAGTCTCGTGCCTCTC 57.559 50.000 0.00 0.00 0.00 3.20
758 766 2.822637 CCCATAGCAGGGCGGTCAT 61.823 63.158 0.00 0.00 43.10 3.06
848 869 2.649034 GTCCGCCACTGTTCTCGA 59.351 61.111 0.00 0.00 0.00 4.04
902 923 3.127533 GTGCAGGCCTAGGTTGCG 61.128 66.667 25.46 9.64 40.62 4.85
934 955 2.651382 TGATCTGCCATAGCTGCATT 57.349 45.000 1.02 0.00 40.80 3.56
935 956 2.437413 CATGATCTGCCATAGCTGCAT 58.563 47.619 1.02 0.00 40.80 3.96
1150 1172 1.835927 GCCAACCTCTCTGCAGTCCT 61.836 60.000 14.67 0.00 0.00 3.85
1523 1548 1.984570 TCCGAGGACAAGCAGGAGG 60.985 63.158 0.00 0.00 0.00 4.30
1525 1550 2.636412 CGTCCGAGGACAAGCAGGA 61.636 63.158 20.75 0.00 44.77 3.86
1530 1555 2.921754 GTTACAATCGTCCGAGGACAAG 59.078 50.000 20.75 10.01 44.77 3.16
1531 1556 2.559668 AGTTACAATCGTCCGAGGACAA 59.440 45.455 20.75 4.10 44.77 3.18
1532 1557 2.165167 AGTTACAATCGTCCGAGGACA 58.835 47.619 20.75 9.41 44.77 4.02
1573 1654 5.662211 CAAAGGACCTTTGCATTTCTTTG 57.338 39.130 29.32 7.35 43.07 2.77
1614 1695 2.871096 TCCGCCTAACCAAACAATCT 57.129 45.000 0.00 0.00 0.00 2.40
1615 1696 3.428862 CCAATCCGCCTAACCAAACAATC 60.429 47.826 0.00 0.00 0.00 2.67
1758 1883 6.739331 AATTGTATTCCCTTGTTTGGTTCA 57.261 33.333 0.00 0.00 0.00 3.18
1874 2083 2.206223 GAAGGGGGATGGGAGTTTAGT 58.794 52.381 0.00 0.00 0.00 2.24
1887 2096 1.343884 TGGCAATATTTGGGAAGGGGG 60.344 52.381 0.00 0.00 0.00 5.40
1912 2121 1.423541 AGGTCCCATGTGTTAACAGCA 59.576 47.619 8.98 10.58 40.39 4.41
2015 2224 9.588096 AAAACTACAACTCTAAGGGATTTCAAT 57.412 29.630 0.00 0.00 0.00 2.57
2063 2272 2.806244 AGGAAAGTGCACGAATACACAC 59.194 45.455 12.01 0.00 39.30 3.82
2072 2281 2.699954 ACCATTAGAGGAAAGTGCACG 58.300 47.619 12.01 0.00 0.00 5.34
2271 2480 3.262420 GAGTTGTTGATATGTCAGCCGT 58.738 45.455 3.93 0.00 34.98 5.68
2273 2482 5.393962 GTTTGAGTTGTTGATATGTCAGCC 58.606 41.667 3.93 0.00 34.98 4.85
2274 2483 5.082059 CGTTTGAGTTGTTGATATGTCAGC 58.918 41.667 0.00 0.00 35.39 4.26


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

AutoCloner maintained by Alex Coulton.