Multiple sequence alignment - TraesCS3A01G012900

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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 TraesCS3A01G012900 chr3A 100.000 4350 0 0 1 4350 9613880 9609531 0.000000e+00 8034.0
1 TraesCS3A01G012900 chr3A 97.499 2399 47 7 1154 3541 9780875 9783271 0.000000e+00 4085.0
2 TraesCS3A01G012900 chr3A 96.763 865 22 3 1 859 9779394 9780258 0.000000e+00 1437.0
3 TraesCS3A01G012900 chr3A 98.113 265 3 1 902 1164 9780253 9780517 1.100000e-125 460.0
4 TraesCS3A01G012900 chr3D 95.411 2070 79 10 1 2062 4168631 4170692 0.000000e+00 3282.0
5 TraesCS3A01G012900 chr3D 86.840 2082 179 42 1 2062 4076593 4074587 0.000000e+00 2239.0
6 TraesCS3A01G012900 chr3D 93.763 1459 78 7 2072 3524 4073806 4072355 0.000000e+00 2178.0
7 TraesCS3A01G012900 chr3D 93.442 1479 72 4 2067 3541 4171277 4172734 0.000000e+00 2170.0
8 TraesCS3A01G012900 chr3D 87.692 780 27 16 3541 4261 4072290 4071521 0.000000e+00 845.0
9 TraesCS3A01G012900 chr3D 97.959 49 1 0 4246 4294 4071506 4071458 7.750000e-13 86.1
10 TraesCS3A01G012900 chrUn 94.293 1472 80 1 2070 3541 246337618 246336151 0.000000e+00 2250.0
11 TraesCS3A01G012900 chrUn 94.317 1179 54 7 892 2062 246339297 246338124 0.000000e+00 1794.0
12 TraesCS3A01G012900 chrUn 87.112 869 43 17 3541 4350 246336113 246335255 0.000000e+00 920.0
13 TraesCS3A01G012900 chrUn 84.427 899 101 15 1 885 246340214 246339341 0.000000e+00 848.0
14 TraesCS3A01G012900 chrUn 79.151 1060 208 13 2261 3313 238779954 238778901 0.000000e+00 721.0
15 TraesCS3A01G012900 chrUn 79.186 1057 207 13 2261 3310 240356320 240357370 0.000000e+00 721.0
16 TraesCS3A01G012900 chrUn 95.968 248 10 0 1639 1886 469290951 469290704 1.880000e-108 403.0
17 TraesCS3A01G012900 chr3B 94.293 1472 80 1 2070 3541 6391718 6390251 0.000000e+00 2250.0
18 TraesCS3A01G012900 chr3B 94.317 1179 54 7 892 2062 6393397 6392224 0.000000e+00 1794.0
19 TraesCS3A01G012900 chr3B 88.028 852 82 9 2688 3523 13947142 13947989 0.000000e+00 990.0
20 TraesCS3A01G012900 chr3B 87.112 869 43 17 3541 4350 6390213 6389355 0.000000e+00 920.0
21 TraesCS3A01G012900 chr3B 92.593 621 40 4 2070 2686 13940812 13941430 0.000000e+00 887.0
22 TraesCS3A01G012900 chr3B 84.427 899 101 15 1 885 6394314 6393441 0.000000e+00 848.0
23 TraesCS3A01G012900 chr3B 94.769 497 15 2 1 486 6667174 6667670 0.000000e+00 763.0
24 TraesCS3A01G012900 chr3B 93.786 515 19 5 1557 2062 13939561 13940071 0.000000e+00 761.0
25 TraesCS3A01G012900 chr3B 96.154 234 9 0 411 644 13939283 13939516 2.450000e-102 383.0
26 TraesCS3A01G012900 chr3B 89.767 215 10 4 528 742 6667662 6667864 9.280000e-67 265.0
27 TraesCS3A01G012900 chr3B 96.721 61 1 1 783 842 6667856 6667916 2.770000e-17 100.0
28 TraesCS3A01G012900 chr3B 100.000 28 0 0 4321 4348 31785186 31785213 8.000000e-03 52.8
29 TraesCS3A01G012900 chr6A 92.019 1466 101 6 2086 3541 609884788 609883329 0.000000e+00 2045.0
30 TraesCS3A01G012900 chr6A 91.034 1015 64 15 909 1904 609886616 609885610 0.000000e+00 1345.0
31 TraesCS3A01G012900 chr6A 87.736 106 11 2 1958 2062 609885607 609885503 5.910000e-24 122.0
32 TraesCS3A01G012900 chr1B 78.195 133 27 2 376 507 9597473 9597342 2.790000e-12 84.2
33 TraesCS3A01G012900 chr2D 100.000 30 0 0 4313 4342 63756903 63756932 6.080000e-04 56.5


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 TraesCS3A01G012900 chr3A 9609531 9613880 4349 True 8034.000000 8034 100.000000 1 4350 1 chr3A.!!$R1 4349
1 TraesCS3A01G012900 chr3A 9779394 9783271 3877 False 1994.000000 4085 97.458333 1 3541 3 chr3A.!!$F1 3540
2 TraesCS3A01G012900 chr3D 4168631 4172734 4103 False 2726.000000 3282 94.426500 1 3541 2 chr3D.!!$F1 3540
3 TraesCS3A01G012900 chr3D 4071458 4076593 5135 True 1337.025000 2239 91.563500 1 4294 4 chr3D.!!$R1 4293
4 TraesCS3A01G012900 chrUn 246335255 246340214 4959 True 1453.000000 2250 90.037250 1 4350 4 chrUn.!!$R3 4349
5 TraesCS3A01G012900 chrUn 238778901 238779954 1053 True 721.000000 721 79.151000 2261 3313 1 chrUn.!!$R1 1052
6 TraesCS3A01G012900 chrUn 240356320 240357370 1050 False 721.000000 721 79.186000 2261 3310 1 chrUn.!!$F1 1049
7 TraesCS3A01G012900 chr3B 6389355 6394314 4959 True 1453.000000 2250 90.037250 1 4350 4 chr3B.!!$R1 4349
8 TraesCS3A01G012900 chr3B 13947142 13947989 847 False 990.000000 990 88.028000 2688 3523 1 chr3B.!!$F1 835
9 TraesCS3A01G012900 chr3B 13939283 13941430 2147 False 677.000000 887 94.177667 411 2686 3 chr3B.!!$F4 2275
10 TraesCS3A01G012900 chr3B 6667174 6667916 742 False 376.000000 763 93.752333 1 842 3 chr3B.!!$F3 841
11 TraesCS3A01G012900 chr6A 609883329 609886616 3287 True 1170.666667 2045 90.263000 909 3541 3 chr6A.!!$R1 2632

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
624 636 1.270412 ACGTGGAAATGCAACGGAGTA 60.270 47.619 12.10 0.00 45.00 2.59 F
1122 1198 1.088340 CATCCAGGTGCAGCGAAGAG 61.088 60.000 10.78 0.00 0.00 2.85 F
2555 4008 3.144657 TGCTGGAGAATTCAAAGAGCA 57.855 42.857 8.44 11.94 32.73 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2555 4008 8.591114 ACTTCATTCATGAATTCTTCTCCATT 57.409 30.769 18.41 0.00 44.92 3.16 R
3058 4511 4.476113 TCAATCCATGGATCTGAGTTCCTT 59.524 41.667 27.45 5.89 33.08 3.36 R
4078 5646 1.041447 ATCTACACCCGTCCCCTTCG 61.041 60.000 0.00 0.00 0.00 3.79 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
95 99 2.957402 AGGCTCAACATTCTGAACCA 57.043 45.000 0.00 0.00 34.53 3.67
231 235 3.364565 GCCCATTTAACCGTACGCATATG 60.365 47.826 10.49 8.18 0.00 1.78
237 241 6.957984 TTTAACCGTACGCATATGTAACAA 57.042 33.333 10.49 0.00 0.00 2.83
624 636 1.270412 ACGTGGAAATGCAACGGAGTA 60.270 47.619 12.10 0.00 45.00 2.59
625 637 2.006888 CGTGGAAATGCAACGGAGTAT 58.993 47.619 0.00 0.00 45.00 2.12
1122 1198 1.088340 CATCCAGGTGCAGCGAAGAG 61.088 60.000 10.78 0.00 0.00 2.85
2555 4008 3.144657 TGCTGGAGAATTCAAAGAGCA 57.855 42.857 8.44 11.94 32.73 4.26
3058 4511 2.939640 GCTGGAAATGGTTAGCGGAAGA 60.940 50.000 0.00 0.00 0.00 2.87
3186 4639 2.863137 CGCAAGAAGAGAAGGATACAGC 59.137 50.000 0.00 0.00 43.02 4.40
3414 4867 5.409520 CACTGAGACTTAATTTGCTGCAGTA 59.590 40.000 16.64 8.31 33.27 2.74
3415 4868 5.997746 ACTGAGACTTAATTTGCTGCAGTAA 59.002 36.000 13.67 13.67 32.86 2.24
3416 4869 6.656693 ACTGAGACTTAATTTGCTGCAGTAAT 59.343 34.615 18.31 13.31 32.86 1.89
3491 4961 2.389962 TGGTAAACTGTACGGCATCC 57.610 50.000 0.23 0.51 0.00 3.51
3498 4969 2.394632 ACTGTACGGCATCCCTTCATA 58.605 47.619 0.23 0.00 0.00 2.15
3556 5075 2.223711 ACACCGTGTTTCAGAAATTGCC 60.224 45.455 0.00 0.00 0.00 4.52
3647 5179 1.745087 CACAACAGACTGCAAACTGGT 59.255 47.619 19.28 12.88 38.30 4.00
3648 5180 2.942376 CACAACAGACTGCAAACTGGTA 59.058 45.455 19.28 0.00 38.30 3.25
3649 5181 3.002656 CACAACAGACTGCAAACTGGTAG 59.997 47.826 19.28 12.23 38.30 3.18
3692 5224 3.431922 TGTCGCTTACCATGTACTAGC 57.568 47.619 0.00 0.00 0.00 3.42
3694 5226 1.335810 TCGCTTACCATGTACTAGCCG 59.664 52.381 0.00 0.00 0.00 5.52
3696 5228 1.684983 GCTTACCATGTACTAGCCGGA 59.315 52.381 5.05 0.00 0.00 5.14
3697 5229 2.545322 GCTTACCATGTACTAGCCGGAC 60.545 54.545 5.05 0.00 0.00 4.79
3739 5272 2.107141 CGTCTCCTTGCCGGATCC 59.893 66.667 5.05 0.00 42.12 3.36
3740 5273 2.427245 CGTCTCCTTGCCGGATCCT 61.427 63.158 5.05 0.00 42.12 3.24
3763 5321 2.630580 GCTCGGAAGGAATCCTACTCAT 59.369 50.000 0.46 0.00 46.98 2.90
3816 5374 0.976641 ATGCACACGAGAGAAAGGGA 59.023 50.000 0.00 0.00 0.00 4.20
3829 5387 3.064412 AGAAAGGGAAAGGAGGAGGTTT 58.936 45.455 0.00 0.00 0.00 3.27
3912 5475 4.828925 GCTCAGGCACGGGAGAGC 62.829 72.222 10.68 10.68 45.50 4.09
4007 5572 2.836360 TCCGTCGGGGAGTATGGC 60.836 66.667 12.29 0.00 40.94 4.40
4078 5646 0.890683 CTTCTGTGAAATGTGGGGCC 59.109 55.000 0.00 0.00 0.00 5.80
4261 5890 4.274950 ACAGTGGAACATTTTCTTGGTACG 59.725 41.667 0.00 0.00 44.52 3.67
4347 5976 9.558396 ACATTTTTCAAATACACATTGGACATT 57.442 25.926 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 99 5.109903 GTTGAGTACCACGCAATCTTATCT 58.890 41.667 0.00 0.00 39.89 1.98
189 193 2.159254 GCTGCCTTTGTCAGTTGTTCAA 60.159 45.455 0.00 0.00 34.21 2.69
231 235 9.371136 TGAGATCAGATTACATGTTCTTGTTAC 57.629 33.333 2.30 0.00 29.10 2.50
237 241 7.799081 TGGATTGAGATCAGATTACATGTTCT 58.201 34.615 2.30 0.00 33.77 3.01
624 636 4.815308 GCATCTGTAAAGCTCTCATGACAT 59.185 41.667 0.00 0.00 0.00 3.06
625 637 4.186926 GCATCTGTAAAGCTCTCATGACA 58.813 43.478 0.00 0.00 0.00 3.58
1122 1198 3.409026 AATCGGATCTCTATTGTGCCC 57.591 47.619 0.00 0.00 0.00 5.36
2555 4008 8.591114 ACTTCATTCATGAATTCTTCTCCATT 57.409 30.769 18.41 0.00 44.92 3.16
3058 4511 4.476113 TCAATCCATGGATCTGAGTTCCTT 59.524 41.667 27.45 5.89 33.08 3.36
3186 4639 1.337447 CCACAATGGCCAGCTTTCTTG 60.337 52.381 13.05 12.42 0.00 3.02
3211 4664 0.883833 GGTTCCACTGAATGCACCAG 59.116 55.000 14.38 14.38 37.64 4.00
3357 4810 2.681706 ACATTCAGAGTCGCAGTGAAG 58.318 47.619 0.00 0.00 33.83 3.02
3416 4869 9.620259 TGTCATACACAATACAATAGGCATTTA 57.380 29.630 0.00 0.00 29.30 1.40
3491 4961 5.142265 CGATTGCGATGTTTCATATGAAGG 58.858 41.667 17.28 7.86 40.82 3.46
3498 4969 2.223112 GCAGACGATTGCGATGTTTCAT 60.223 45.455 0.00 0.00 41.64 2.57
3647 5179 7.190335 ACTATTTACCATGGCTTGTACACTA 57.810 36.000 13.04 0.00 0.00 2.74
3648 5180 6.062258 ACTATTTACCATGGCTTGTACACT 57.938 37.500 13.04 0.00 0.00 3.55
3649 5181 6.150474 ACAACTATTTACCATGGCTTGTACAC 59.850 38.462 13.04 0.00 0.00 2.90
3692 5224 3.382111 AGTGAGGCTGAAGTCCGG 58.618 61.111 0.00 0.00 0.00 5.14
3763 5321 4.263550 TGTGCCTACTTAATTACCTTGGCA 60.264 41.667 13.92 13.92 45.51 4.92
3956 5519 3.992317 GCGATCTAGACCGCCCCC 61.992 72.222 21.39 0.00 45.06 5.40
4078 5646 1.041447 ATCTACACCCGTCCCCTTCG 61.041 60.000 0.00 0.00 0.00 3.79
4146 5725 9.651913 AAAACTGAAGAAATGCTGAAAAACTTA 57.348 25.926 0.00 0.00 0.00 2.24
4147 5726 8.552083 AAAACTGAAGAAATGCTGAAAAACTT 57.448 26.923 0.00 0.00 0.00 2.66
4237 5836 4.654091 ACCAAGAAAATGTTCCACTGTG 57.346 40.909 0.00 0.00 33.92 3.66
4321 5950 9.558396 AATGTCCAATGTGTATTTGAAAAATGT 57.442 25.926 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.