Multiple sequence alignment - TraesCS7A01G290100

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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 TraesCS7A01G290100 chr7A 100.000 2438 0 0 1 2438 352293030 352295467 0.000000e+00 4503
1 TraesCS7A01G290100 chr5D 93.988 2445 136 8 1 2437 6232465 6234906 0.000000e+00 3690
2 TraesCS7A01G290100 chr5D 94.557 2076 105 6 1 2071 483803994 483806066 0.000000e+00 3201
3 TraesCS7A01G290100 chr3B 93.944 2444 139 7 1 2438 201496785 201494345 0.000000e+00 3685
4 TraesCS7A01G290100 chr3B 93.878 196 10 2 85 278 231953409 231953604 6.590000e-76 294
5 TraesCS7A01G290100 chr1D 93.788 2447 129 10 1 2438 254480763 254478331 0.000000e+00 3655
6 TraesCS7A01G290100 chr1D 94.151 2291 126 8 154 2438 180352115 180354403 0.000000e+00 3482
7 TraesCS7A01G290100 chr1D 92.162 2105 140 11 342 2438 244792092 244790005 0.000000e+00 2950
8 TraesCS7A01G290100 chr1D 91.619 2100 152 11 346 2438 244212129 244210047 0.000000e+00 2881
9 TraesCS7A01G290100 chr6D 92.507 1815 124 10 6 1816 210721578 210723384 0.000000e+00 2588
10 TraesCS7A01G290100 chrUn 94.727 1593 81 3 389 1978 386522344 386523936 0.000000e+00 2473
11 TraesCS7A01G290100 chrUn 95.018 1365 65 3 267 1629 407032912 407031549 0.000000e+00 2141
12 TraesCS7A01G290100 chrUn 93.946 958 43 6 1484 2438 397678311 397677366 0.000000e+00 1434
13 TraesCS7A01G290100 chrUn 91.026 78 4 3 1527 1602 231546318 231546242 4.290000e-18 102
14 TraesCS7A01G290100 chr2B 93.422 1429 79 8 1 1425 474938633 474937216 0.000000e+00 2104
15 TraesCS7A01G290100 chr2B 96.377 138 5 0 1421 1558 474928181 474928044 6.780000e-56 228
16 TraesCS7A01G290100 chr2D 94.637 1324 65 4 1 1321 643857125 643855805 0.000000e+00 2047
17 TraesCS7A01G290100 chr1A 94.539 824 42 3 1618 2438 554444322 554445145 0.000000e+00 1269
18 TraesCS7A01G290100 chr4A 92.130 648 44 4 5 649 309272252 309272895 0.000000e+00 907
19 TraesCS7A01G290100 chr4A 93.609 532 32 1 1909 2438 665560764 665560233 0.000000e+00 793
20 TraesCS7A01G290100 chr7D 90.994 644 54 3 1798 2438 88617453 88618095 0.000000e+00 865


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 TraesCS7A01G290100 chr7A 352293030 352295467 2437 False 4503 4503 100.000 1 2438 1 chr7A.!!$F1 2437
1 TraesCS7A01G290100 chr5D 6232465 6234906 2441 False 3690 3690 93.988 1 2437 1 chr5D.!!$F1 2436
2 TraesCS7A01G290100 chr5D 483803994 483806066 2072 False 3201 3201 94.557 1 2071 1 chr5D.!!$F2 2070
3 TraesCS7A01G290100 chr3B 201494345 201496785 2440 True 3685 3685 93.944 1 2438 1 chr3B.!!$R1 2437
4 TraesCS7A01G290100 chr1D 254478331 254480763 2432 True 3655 3655 93.788 1 2438 1 chr1D.!!$R3 2437
5 TraesCS7A01G290100 chr1D 180352115 180354403 2288 False 3482 3482 94.151 154 2438 1 chr1D.!!$F1 2284
6 TraesCS7A01G290100 chr1D 244790005 244792092 2087 True 2950 2950 92.162 342 2438 1 chr1D.!!$R2 2096
7 TraesCS7A01G290100 chr1D 244210047 244212129 2082 True 2881 2881 91.619 346 2438 1 chr1D.!!$R1 2092
8 TraesCS7A01G290100 chr6D 210721578 210723384 1806 False 2588 2588 92.507 6 1816 1 chr6D.!!$F1 1810
9 TraesCS7A01G290100 chrUn 386522344 386523936 1592 False 2473 2473 94.727 389 1978 1 chrUn.!!$F1 1589
10 TraesCS7A01G290100 chrUn 407031549 407032912 1363 True 2141 2141 95.018 267 1629 1 chrUn.!!$R3 1362
11 TraesCS7A01G290100 chrUn 397677366 397678311 945 True 1434 1434 93.946 1484 2438 1 chrUn.!!$R2 954
12 TraesCS7A01G290100 chr2B 474937216 474938633 1417 True 2104 2104 93.422 1 1425 1 chr2B.!!$R2 1424
13 TraesCS7A01G290100 chr2D 643855805 643857125 1320 True 2047 2047 94.637 1 1321 1 chr2D.!!$R1 1320
14 TraesCS7A01G290100 chr1A 554444322 554445145 823 False 1269 1269 94.539 1618 2438 1 chr1A.!!$F1 820
15 TraesCS7A01G290100 chr4A 309272252 309272895 643 False 907 907 92.130 5 649 1 chr4A.!!$F1 644
16 TraesCS7A01G290100 chr4A 665560233 665560764 531 True 793 793 93.609 1909 2438 1 chr4A.!!$R1 529
17 TraesCS7A01G290100 chr7D 88617453 88618095 642 False 865 865 90.994 1798 2438 1 chr7D.!!$F1 640

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
94 96 0.039472 TTGCTAAAGCTCATGGGGCA 59.961 50.0 12.59 2.28 42.66 5.36 F
518 523 0.393448 TTGACGATTTGACCGACCCA 59.607 50.0 0.00 0.00 0.00 4.51 F
1117 1126 2.530958 ATTACCAACTCACGCCCCCG 62.531 60.0 0.00 0.00 41.14 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1106 1115 0.176219 TATGTTAACGGGGGCGTGAG 59.824 55.000 0.26 0.0 0.0 3.51 R
1321 1330 1.247567 ACCAAATCTTTCGCACCCAG 58.752 50.000 0.00 0.0 0.0 4.45 R
2062 2088 1.348036 GGCCCTTATCCTCATTACGCT 59.652 52.381 0.00 0.0 0.0 5.07 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
93 95 1.068127 CATTGCTAAAGCTCATGGGGC 59.932 52.381 3.26 0.00 42.66 5.80
94 96 0.039472 TTGCTAAAGCTCATGGGGCA 59.961 50.000 12.59 2.28 42.66 5.36
105 108 3.273434 CTCATGGGGCATATCCGTATTG 58.727 50.000 0.00 0.00 34.94 1.90
115 118 4.262721 GCATATCCGTATTGGGTGGAGTAA 60.263 45.833 0.00 0.00 38.76 2.24
130 133 5.011227 GGTGGAGTAAGGGAATAGACTCATC 59.989 48.000 3.54 0.00 40.10 2.92
135 138 5.604650 AGTAAGGGAATAGACTCATCAAGGG 59.395 44.000 0.00 0.00 0.00 3.95
236 241 1.622811 GGCCAAATGAATGAACCACCA 59.377 47.619 0.00 0.00 0.00 4.17
438 443 4.058721 ACAGAAATGGGTTCTTTGCAAC 57.941 40.909 0.00 0.00 44.64 4.17
500 505 4.530710 TCGAGCAGTTTATGTACCTGTT 57.469 40.909 0.00 0.00 0.00 3.16
518 523 0.393448 TTGACGATTTGACCGACCCA 59.607 50.000 0.00 0.00 0.00 4.51
530 536 2.991540 GACCCAGCCCTGCCAAAC 60.992 66.667 0.00 0.00 0.00 2.93
583 589 5.044550 ACTTTCCAGAGGATTAGCTTCCAAT 60.045 40.000 7.20 0.00 38.32 3.16
584 590 6.158695 ACTTTCCAGAGGATTAGCTTCCAATA 59.841 38.462 7.20 0.00 38.32 1.90
732 738 5.185454 TCAGGACATTATCGCAATTCTTGT 58.815 37.500 0.00 0.00 0.00 3.16
811 817 3.059188 AGCGTTTCTTATCACAACCGTTG 60.059 43.478 9.80 9.80 0.00 4.10
815 821 6.420588 CGTTTCTTATCACAACCGTTGTTTA 58.579 36.000 14.36 6.43 43.23 2.01
875 883 3.055385 TGCTCTTGCGGAAACTATTAGGT 60.055 43.478 0.00 0.00 43.34 3.08
996 1004 2.611518 AGAAGAGGAGAACAAATCGCG 58.388 47.619 0.00 0.00 0.00 5.87
1117 1126 2.530958 ATTACCAACTCACGCCCCCG 62.531 60.000 0.00 0.00 41.14 5.73
1154 1163 7.789831 AGTAGATATGGGTCCTTTGAGAATACA 59.210 37.037 0.00 0.00 0.00 2.29
1156 1165 4.927267 ATGGGTCCTTTGAGAATACACA 57.073 40.909 0.00 0.00 0.00 3.72
1177 1186 3.328382 TCCTCAACGACCAATGGTTAG 57.672 47.619 6.30 6.84 35.25 2.34
1178 1187 2.635915 TCCTCAACGACCAATGGTTAGT 59.364 45.455 6.30 7.55 35.25 2.24
1248 1257 4.717877 TCATTGTAGGAAATGATGCGGAT 58.282 39.130 0.00 0.00 40.72 4.18
1321 1330 4.327627 CCGAAGCTAACTTGAGTAAAGCTC 59.672 45.833 16.60 11.36 42.83 4.09
1322 1331 5.164954 CGAAGCTAACTTGAGTAAAGCTCT 58.835 41.667 16.60 10.02 42.83 4.09
1327 1336 3.409026 ACTTGAGTAAAGCTCTGGGTG 57.591 47.619 0.00 0.00 44.41 4.61
1350 1359 4.475944 CGAAAGATTTGGTTGAAGCGAAT 58.524 39.130 9.44 9.44 32.75 3.34
1459 1471 8.576442 GTTGATACAAAGAAAAATGGAAGAGGA 58.424 33.333 0.00 0.00 0.00 3.71
1558 1570 4.387026 TGGATTTGAACCAATGACTCCT 57.613 40.909 0.00 0.00 34.25 3.69
1559 1571 5.512942 TGGATTTGAACCAATGACTCCTA 57.487 39.130 0.00 0.00 34.25 2.94
1560 1572 6.078456 TGGATTTGAACCAATGACTCCTAT 57.922 37.500 0.00 0.00 34.25 2.57
1571 1583 6.323996 ACCAATGACTCCTATCGTATGAAAGA 59.676 38.462 0.00 0.00 0.00 2.52
1584 1596 8.798748 ATCGTATGAAAGAAATACTCTAACCG 57.201 34.615 0.00 0.00 32.46 4.44
1608 1620 6.562270 CGCTGAGTTAAGTAGGCAATTTATCG 60.562 42.308 7.45 0.00 0.00 2.92
1629 1641 3.365472 GCCACAAAGGAAGACCCATTAT 58.635 45.455 0.00 0.00 41.22 1.28
1630 1642 4.532834 GCCACAAAGGAAGACCCATTATA 58.467 43.478 0.00 0.00 41.22 0.98
1676 1688 6.442564 TCCCTTTTCTAAGCAATACCACTCTA 59.557 38.462 0.00 0.00 0.00 2.43
1843 1857 3.645884 GGTAGAGCAACTCGTTTACACA 58.354 45.455 0.00 0.00 35.36 3.72
1889 1903 9.918630 GGAGCTTATTATGCAATGAACATAATT 57.081 29.630 12.66 0.00 44.44 1.40
1907 1921 8.570096 ACATAATTGATCTGATTGCAAAATCG 57.430 30.769 1.71 0.00 31.94 3.34
1989 2015 3.760684 GAGTCTGATTCAGGTGCCAATTT 59.239 43.478 13.59 0.00 31.51 1.82
2031 2057 7.119387 AGAACCCTTATGGATTTTCTAGTTGG 58.881 38.462 0.00 0.00 38.00 3.77
2062 2088 3.951563 ATCCAGCCCACTAAATGCTAA 57.048 42.857 0.00 0.00 33.16 3.09
2091 2117 3.916035 GAGGATAAGGGCCTCCAAAAAT 58.084 45.455 6.46 0.00 44.96 1.82
2162 2188 5.613329 ACTCTAGTAGTGGAACGATAGAGG 58.387 45.833 10.75 0.00 44.78 3.69
2164 2190 3.014304 AGTAGTGGAACGATAGAGGCA 57.986 47.619 0.00 0.00 45.86 4.75
2240 2266 7.778382 AGGTAATCCTACTTTGAAACACTTTGT 59.222 33.333 0.00 0.00 43.12 2.83
2252 2278 6.966021 TGAAACACTTTGTTATTGCTCCTAC 58.034 36.000 0.00 0.00 40.14 3.18
2295 2323 1.811778 TCAGAGCATAGGGAGCCATT 58.188 50.000 0.00 0.00 0.00 3.16
2296 2324 1.696336 TCAGAGCATAGGGAGCCATTC 59.304 52.381 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 34 9.823647 CATGATCAGTACTGTTTTACCTAATCT 57.176 33.333 21.99 3.14 0.00 2.40
35 37 8.141298 TCCATGATCAGTACTGTTTTACCTAA 57.859 34.615 21.99 0.05 0.00 2.69
93 95 5.477607 TTACTCCACCCAATACGGATATG 57.522 43.478 0.00 0.00 36.56 1.78
94 96 4.530946 CCTTACTCCACCCAATACGGATAT 59.469 45.833 0.00 0.00 36.56 1.63
105 108 3.642377 GAGTCTATTCCCTTACTCCACCC 59.358 52.174 0.00 0.00 33.74 4.61
115 118 4.286813 TCCCTTGATGAGTCTATTCCCT 57.713 45.455 0.00 0.00 0.00 4.20
195 200 4.830600 GCCATAGACTAGAGCTACCTTTCT 59.169 45.833 0.00 0.00 0.00 2.52
196 201 4.021807 GGCCATAGACTAGAGCTACCTTTC 60.022 50.000 0.00 0.00 0.00 2.62
236 241 3.652055 ACCAACTCTCATATGAGCTCCT 58.348 45.455 25.27 3.56 41.80 3.69
278 283 9.778741 TGCTTATTAACATCTCGGAAATATTCT 57.221 29.630 0.00 0.00 0.00 2.40
348 353 1.133325 AGCGGATACCTCTGATCCTGT 60.133 52.381 0.52 0.00 40.77 4.00
411 416 6.016610 TGCAAAGAACCCATTTCTGTACTAAC 60.017 38.462 0.00 0.00 44.41 2.34
438 443 8.576442 TCCCTTTTTAGTAGAAGCAATTCTTTG 58.424 33.333 0.00 0.00 34.56 2.77
481 486 4.091509 CGTCAACAGGTACATAAACTGCTC 59.908 45.833 0.00 0.00 35.70 4.26
500 505 0.037697 CTGGGTCGGTCAAATCGTCA 60.038 55.000 0.00 0.00 0.00 4.35
518 523 2.123468 AAACGGTTTGGCAGGGCT 60.123 55.556 5.12 0.00 0.00 5.19
528 534 2.753296 CATCCAAATGTGCAAACGGTT 58.247 42.857 0.00 0.00 0.00 4.44
530 536 1.070038 GCATCCAAATGTGCAAACGG 58.930 50.000 0.00 0.00 40.94 4.44
532 538 4.178545 AGTAGCATCCAAATGTGCAAAC 57.821 40.909 0.00 0.00 43.63 2.93
583 589 8.958060 AAGGATCTACTGCTGGATAAATACTA 57.042 34.615 0.00 0.00 0.00 1.82
584 590 7.863901 AAGGATCTACTGCTGGATAAATACT 57.136 36.000 0.00 0.00 0.00 2.12
668 674 8.795842 TGTAAAGTTTCCTTAACTCTTTGTGA 57.204 30.769 0.00 0.00 46.34 3.58
732 738 7.681259 TCCTCTTCTGATAATTCATCCAAGA 57.319 36.000 0.00 0.00 33.56 3.02
786 792 3.370978 CGGTTGTGATAAGAAACGCTCAT 59.629 43.478 0.00 0.00 0.00 2.90
811 817 6.745116 ACCAGTAAAAACTTCTGCCATAAAC 58.255 36.000 0.00 0.00 0.00 2.01
815 821 5.140454 AGAACCAGTAAAAACTTCTGCCAT 58.860 37.500 0.00 0.00 0.00 4.40
907 915 0.919710 AATCCTGTTCAGGTAGGCCC 59.080 55.000 17.00 0.00 34.00 5.80
1012 1020 9.686683 AATTTGCTTAGGAGTCAGTACATAAAT 57.313 29.630 0.00 0.00 0.00 1.40
1034 1042 9.492973 CTTTCACTTCACAATCCCAAATAATTT 57.507 29.630 0.00 0.00 0.00 1.82
1106 1115 0.176219 TATGTTAACGGGGGCGTGAG 59.824 55.000 0.26 0.00 0.00 3.51
1107 1116 0.176219 CTATGTTAACGGGGGCGTGA 59.824 55.000 0.26 0.00 0.00 4.35
1117 1126 7.038941 AGGACCCATATCTACTGCTATGTTAAC 60.039 40.741 0.00 0.00 0.00 2.01
1154 1163 1.351017 ACCATTGGTCGTTGAGGATGT 59.649 47.619 1.37 0.00 0.00 3.06
1156 1165 2.879103 AACCATTGGTCGTTGAGGAT 57.121 45.000 9.22 0.00 33.12 3.24
1177 1186 1.805945 CGCTCCACAGAACCGCTAC 60.806 63.158 0.00 0.00 0.00 3.58
1178 1187 2.571757 CGCTCCACAGAACCGCTA 59.428 61.111 0.00 0.00 0.00 4.26
1231 1240 3.004734 CCCAAATCCGCATCATTTCCTAC 59.995 47.826 0.00 0.00 0.00 3.18
1248 1257 4.656575 TCCGGATCAATATCACTACCCAAA 59.343 41.667 0.00 0.00 33.41 3.28
1321 1330 1.247567 ACCAAATCTTTCGCACCCAG 58.752 50.000 0.00 0.00 0.00 4.45
1322 1331 1.339610 CAACCAAATCTTTCGCACCCA 59.660 47.619 0.00 0.00 0.00 4.51
1327 1336 1.978782 CGCTTCAACCAAATCTTTCGC 59.021 47.619 0.00 0.00 0.00 4.70
1412 1423 6.878923 TCAACTATAAACCACTGGATTGTCTG 59.121 38.462 0.71 0.00 0.00 3.51
1482 1494 3.412386 AGCATTGGACTTACTTCGCTTT 58.588 40.909 0.00 0.00 0.00 3.51
1558 1570 9.888878 CGGTTAGAGTATTTCTTTCATACGATA 57.111 33.333 0.00 0.00 37.36 2.92
1559 1571 7.381678 GCGGTTAGAGTATTTCTTTCATACGAT 59.618 37.037 0.00 0.00 37.36 3.73
1560 1572 6.694411 GCGGTTAGAGTATTTCTTTCATACGA 59.306 38.462 0.00 0.00 37.36 3.43
1571 1583 6.932947 ACTTAACTCAGCGGTTAGAGTATTT 58.067 36.000 7.89 0.00 43.88 1.40
1584 1596 6.650372 CGATAAATTGCCTACTTAACTCAGC 58.350 40.000 0.00 0.00 0.00 4.26
1608 1620 1.632589 AATGGGTCTTCCTTTGTGGC 58.367 50.000 0.00 0.00 36.20 5.01
1800 1813 4.021016 CCGAACTGAGCTATAGCCCTTATT 60.021 45.833 21.17 9.51 43.38 1.40
1889 1903 5.587443 AGACATCGATTTTGCAATCAGATCA 59.413 36.000 0.00 0.00 39.14 2.92
1895 1909 7.243487 TGAAGTAAGACATCGATTTTGCAATC 58.757 34.615 0.00 0.00 36.20 2.67
1927 1941 4.890581 GGCTACTGTTCTCCTATTCTCTCA 59.109 45.833 0.00 0.00 0.00 3.27
1967 1981 2.479566 TTGGCACCTGAATCAGACTC 57.520 50.000 12.53 0.00 32.44 3.36
1989 2015 5.670361 AGGGTTCTATTTGATTAGGCACCTA 59.330 40.000 0.00 0.00 0.00 3.08
2023 2049 7.202066 GGCTGGATATTTACCTTACCAACTAGA 60.202 40.741 0.00 0.00 0.00 2.43
2031 2057 5.306114 AGTGGGCTGGATATTTACCTTAC 57.694 43.478 0.00 0.00 0.00 2.34
2062 2088 1.348036 GGCCCTTATCCTCATTACGCT 59.652 52.381 0.00 0.00 0.00 5.07
2144 2170 2.688958 GTGCCTCTATCGTTCCACTACT 59.311 50.000 0.00 0.00 0.00 2.57
2146 2172 2.029623 GGTGCCTCTATCGTTCCACTA 58.970 52.381 0.00 0.00 0.00 2.74
2162 2188 5.391312 AATCAACCTAAGTGAAATGGTGC 57.609 39.130 0.00 0.00 32.53 5.01
2195 2221 3.309296 CCTAGATTTAGGTCTGCCTCCA 58.691 50.000 0.95 0.00 45.64 3.86
2213 2239 9.280174 CAAAGTGTTTCAAAGTAGGATTACCTA 57.720 33.333 0.00 0.00 45.83 3.08
2224 2250 6.756542 GGAGCAATAACAAAGTGTTTCAAAGT 59.243 34.615 0.00 0.00 41.45 2.66
2272 2300 1.419387 GGCTCCCTATGCTCTGATTGT 59.581 52.381 0.00 0.00 0.00 2.71
2284 2312 5.222130 GGAAAGATAATGGAATGGCTCCCTA 60.222 44.000 0.00 0.00 44.69 3.53
2354 2382 2.437200 TTTTGCATTGGGCTCTTTCG 57.563 45.000 0.00 0.00 45.15 3.46


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

AutoCloner maintained by Alex Coulton.