Multiple sequence alignment - TraesCS7A01G289200

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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 TraesCS7A01G289200 chr7A 100.000 2141 0 0 1 2141 352181629 352179489 0 3954
1 TraesCS7A01G289200 chr2D 95.026 2151 93 7 1 2141 272793671 272791525 0 3367
2 TraesCS7A01G289200 chr2D 94.103 2001 87 12 169 2141 272564345 272566342 0 3013
3 TraesCS7A01G289200 chr3D 94.421 2169 87 16 1 2141 589279320 589277158 0 3304
4 TraesCS7A01G289200 chr5D 94.191 2169 95 12 1 2141 503218440 503220605 0 3278
5 TraesCS7A01G289200 chr5D 93.868 2169 102 14 1 2141 503278004 503275839 0 3240
6 TraesCS7A01G289200 chr5D 93.638 2169 107 14 1 2141 6189162 6191327 0 3212
7 TraesCS7A01G289200 chr5D 94.051 1933 84 12 237 2141 446174242 446176171 0 2904
8 TraesCS7A01G289200 chr1A 94.191 2169 95 12 1 2141 554512470 554514635 0 3278
9 TraesCS7A01G289200 chr3B 94.099 2169 97 14 1 2141 201527246 201529411 0 3267
10 TraesCS7A01G289200 chr3B 94.349 1681 65 11 488 2141 101911885 101913562 0 2551
11 TraesCS7A01G289200 chr3A 94.050 2168 98 14 1 2141 672909785 672907622 0 3260
12 TraesCS7A01G289200 chr3A 93.865 2168 103 14 1 2141 594899402 594897238 0 3240
13 TraesCS7A01G289200 chrUn 94.004 2168 100 11 1 2141 216518380 216516216 0 3256
14 TraesCS7A01G289200 chrUn 93.816 1714 83 11 1 1692 346596272 346594560 0 2556
15 TraesCS7A01G289200 chr6D 93.963 2170 98 16 1 2141 168255148 168257313 0 3251


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 TraesCS7A01G289200 chr7A 352179489 352181629 2140 True 3954 3954 100.000 1 2141 1 chr7A.!!$R1 2140
1 TraesCS7A01G289200 chr2D 272791525 272793671 2146 True 3367 3367 95.026 1 2141 1 chr2D.!!$R1 2140
2 TraesCS7A01G289200 chr2D 272564345 272566342 1997 False 3013 3013 94.103 169 2141 1 chr2D.!!$F1 1972
3 TraesCS7A01G289200 chr3D 589277158 589279320 2162 True 3304 3304 94.421 1 2141 1 chr3D.!!$R1 2140
4 TraesCS7A01G289200 chr5D 503218440 503220605 2165 False 3278 3278 94.191 1 2141 1 chr5D.!!$F3 2140
5 TraesCS7A01G289200 chr5D 503275839 503278004 2165 True 3240 3240 93.868 1 2141 1 chr5D.!!$R1 2140
6 TraesCS7A01G289200 chr5D 6189162 6191327 2165 False 3212 3212 93.638 1 2141 1 chr5D.!!$F1 2140
7 TraesCS7A01G289200 chr5D 446174242 446176171 1929 False 2904 2904 94.051 237 2141 1 chr5D.!!$F2 1904
8 TraesCS7A01G289200 chr1A 554512470 554514635 2165 False 3278 3278 94.191 1 2141 1 chr1A.!!$F1 2140
9 TraesCS7A01G289200 chr3B 201527246 201529411 2165 False 3267 3267 94.099 1 2141 1 chr3B.!!$F2 2140
10 TraesCS7A01G289200 chr3B 101911885 101913562 1677 False 2551 2551 94.349 488 2141 1 chr3B.!!$F1 1653
11 TraesCS7A01G289200 chr3A 672907622 672909785 2163 True 3260 3260 94.050 1 2141 1 chr3A.!!$R2 2140
12 TraesCS7A01G289200 chr3A 594897238 594899402 2164 True 3240 3240 93.865 1 2141 1 chr3A.!!$R1 2140
13 TraesCS7A01G289200 chrUn 216516216 216518380 2164 True 3256 3256 94.004 1 2141 1 chrUn.!!$R1 2140
14 TraesCS7A01G289200 chrUn 346594560 346596272 1712 True 2556 2556 93.816 1 1692 1 chrUn.!!$R2 1691
15 TraesCS7A01G289200 chr6D 168255148 168257313 2165 False 3251 3251 93.963 1 2141 1 chr6D.!!$F1 2140


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
552 554 0.539986 TTTCCAGGTAGTCGATGGCC 59.46 55.0 0.0 0.0 33.92 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1780 1.059006 GGTCCCATGATCCTGAGCCT 61.059 60.0 0.0 0.0 0.0 4.58 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
25 26 4.638865 AGTTGAAACCACACTCAAAGGTAC 59.361 41.667 0.00 0.00 33.52 3.34
26 27 4.223556 TGAAACCACACTCAAAGGTACA 57.776 40.909 0.00 0.00 34.63 2.90
27 28 4.590918 TGAAACCACACTCAAAGGTACAA 58.409 39.130 0.00 0.00 34.63 2.41
172 173 7.771361 TGCATTTCAATTAGGGTCGTATTCTAA 59.229 33.333 0.00 0.00 0.00 2.10
178 179 9.151177 TCAATTAGGGTCGTATTCTAAGGTTAT 57.849 33.333 0.00 0.00 0.00 1.89
254 255 0.761802 GCTTATGACCTCCCCCTCTG 59.238 60.000 0.00 0.00 0.00 3.35
262 263 2.935481 TCCCCCTCTGTGCCTTGG 60.935 66.667 0.00 0.00 0.00 3.61
371 372 1.005867 TACGGTTCCCTTGCGTGTC 60.006 57.895 0.00 0.00 0.00 3.67
377 378 4.003788 CCCTTGCGTGTCCTCGGT 62.004 66.667 0.00 0.00 0.00 4.69
405 406 8.012957 AGGTGTTTTGTATAAATGTTTCACCA 57.987 30.769 16.92 0.00 42.43 4.17
519 521 2.770447 TGTATGGCCCAGAATAGGTCA 58.230 47.619 0.00 0.00 44.69 4.02
552 554 0.539986 TTTCCAGGTAGTCGATGGCC 59.460 55.000 0.00 0.00 33.92 5.36
591 593 6.661805 ACCTTAACACCAAAGAAGAGTTTGAA 59.338 34.615 0.00 0.00 39.40 2.69
647 649 9.793245 CCGATTCGACATTAAAAGTATATTGAC 57.207 33.333 7.83 0.00 0.00 3.18
662 664 9.474313 AAGTATATTGACTCTTGCCCAATAAAA 57.526 29.630 0.00 0.00 36.65 1.52
670 672 5.474876 ACTCTTGCCCAATAAAAGAAGACTG 59.525 40.000 0.00 0.00 29.93 3.51
713 734 7.323420 CGTATTTGATTCCATCCTATGCTCTA 58.677 38.462 0.00 0.00 0.00 2.43
721 742 4.968719 TCCATCCTATGCTCTAAGTTCCAA 59.031 41.667 0.00 0.00 0.00 3.53
743 764 9.841880 TCCAATATCGATAAGAATTCTAGTTCG 57.158 33.333 20.22 20.22 33.36 3.95
832 853 1.967066 CATGGATAGAGAGCCGGTTCT 59.033 52.381 22.00 22.00 31.83 3.01
834 855 2.865079 TGGATAGAGAGCCGGTTCTAG 58.135 52.381 21.86 0.00 31.83 2.43
843 864 4.198530 AGAGCCGGTTCTAGTAGACTTAC 58.801 47.826 20.45 0.00 0.00 2.34
854 875 6.421485 TCTAGTAGACTTACGGAATGTTCCT 58.579 40.000 9.90 0.70 45.33 3.36
864 885 1.535462 GGAATGTTCCTGTTCGTGTGG 59.465 52.381 4.53 0.00 44.11 4.17
868 889 1.691976 TGTTCCTGTTCGTGTGGATCT 59.308 47.619 0.00 0.00 0.00 2.75
958 979 5.739070 GCTTAACAGGGATCATCGTACATCA 60.739 44.000 0.00 0.00 0.00 3.07
1041 1062 6.639671 CGAGATGGAAAATATTCGGAGATC 57.360 41.667 0.00 0.00 36.36 2.75
1216 1237 2.280628 GATTGAACGACCAGGATCCAC 58.719 52.381 15.82 1.40 0.00 4.02
1229 1250 7.546250 ACCAGGATCCACTTACTTATGATAG 57.454 40.000 15.82 0.00 0.00 2.08
1230 1251 7.306013 ACCAGGATCCACTTACTTATGATAGA 58.694 38.462 15.82 0.00 0.00 1.98
1361 1382 2.921754 CTCGTGTGGGACTAATCGTTTC 59.078 50.000 0.00 0.00 0.00 2.78
1398 1419 0.382873 AAAAACCTGTTCGTTCCGCC 59.617 50.000 0.00 0.00 0.00 6.13
1431 1453 8.716674 ATCGGGTATTTTAGTGATAGGTTCTA 57.283 34.615 0.00 0.00 0.00 2.10
1517 1539 3.202373 AGGTACAAGGGCTTCTTATTCCC 59.798 47.826 0.00 0.00 40.36 3.97
1629 1651 1.419374 CACGAGTTCCAGTGCACTAC 58.581 55.000 21.20 14.73 0.00 2.73
1632 1654 2.037251 ACGAGTTCCAGTGCACTACATT 59.963 45.455 21.20 4.33 0.00 2.71
1672 1696 8.944029 CAATGAAGCTATCCATTAGTATTCCAG 58.056 37.037 8.11 0.00 32.31 3.86
1752 1780 3.267483 GTTTGCGAGCCAAGGTAAGATA 58.733 45.455 0.00 0.00 34.34 1.98
1799 1827 0.642156 TCAGATGGGAGGGGCTCTTA 59.358 55.000 0.00 0.00 0.00 2.10
1802 1830 3.116356 TCAGATGGGAGGGGCTCTTATAA 60.116 47.826 0.00 0.00 0.00 0.98
1840 1872 9.845214 AGTAATAACCCCATACAATCTATCTCT 57.155 33.333 0.00 0.00 0.00 3.10
1925 1957 3.340814 ACTTGGAACGAGCATGAAGAT 57.659 42.857 0.00 0.00 0.00 2.40
1973 2005 1.415672 TTTTCTGGAGGACCTGCCGT 61.416 55.000 10.94 0.00 43.43 5.68
2035 2067 4.645136 AGTGGATCGCTTCTTATGTACTCA 59.355 41.667 0.00 0.00 0.00 3.41
2040 2072 5.638596 TCGCTTCTTATGTACTCACTCAA 57.361 39.130 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.396790 TGTTGTACCTTTGAGTGTGGTTTC 59.603 41.667 0.00 0.00 35.48 2.78
12 13 4.583073 GGGAAATGTTGTACCTTTGAGTGT 59.417 41.667 0.00 0.00 0.00 3.55
96 97 8.926710 GGATGGTGAGAACAGATATATTTTACG 58.073 37.037 0.00 0.00 0.00 3.18
110 111 2.505819 ACACTATGGGGATGGTGAGAAC 59.494 50.000 5.65 0.00 36.65 3.01
154 155 9.151177 TCATAACCTTAGAATACGACCCTAATT 57.849 33.333 0.00 0.00 0.00 1.40
172 173 8.964533 AGACATATCTGGTAGAATCATAACCT 57.035 34.615 0.00 0.00 32.29 3.50
254 255 2.031870 GGAATCATTACCCCAAGGCAC 58.968 52.381 0.00 0.00 36.11 5.01
307 308 6.710295 TCCACGAAATAATTTGATCCATCGAT 59.290 34.615 0.00 0.00 33.61 3.59
310 311 7.596248 CCAATCCACGAAATAATTTGATCCATC 59.404 37.037 0.00 0.00 0.00 3.51
371 372 8.770828 CATTTATACAAAACACCTATACCGAGG 58.229 37.037 0.00 0.00 42.89 4.63
448 450 5.527582 CCTTCAACCGGGTTATTCTATCTTG 59.472 44.000 12.95 0.00 0.00 3.02
449 451 5.397559 CCCTTCAACCGGGTTATTCTATCTT 60.398 44.000 12.95 0.00 36.91 2.40
450 452 4.102681 CCCTTCAACCGGGTTATTCTATCT 59.897 45.833 12.95 0.00 36.91 1.98
451 453 4.386711 CCCTTCAACCGGGTTATTCTATC 58.613 47.826 12.95 0.00 36.91 2.08
552 554 4.154195 GTGTTAAGGTGGTAGCTGTGAATG 59.846 45.833 0.00 0.00 0.00 2.67
614 616 7.916552 ACTTTTAATGTCGAATCGGGATTTAG 58.083 34.615 1.76 3.57 0.00 1.85
616 618 6.753107 ACTTTTAATGTCGAATCGGGATTT 57.247 33.333 1.76 0.00 0.00 2.17
647 649 5.474876 ACAGTCTTCTTTTATTGGGCAAGAG 59.525 40.000 0.00 0.00 0.00 2.85
652 654 7.169813 CAGAAAAACAGTCTTCTTTTATTGGGC 59.830 37.037 0.00 0.00 29.29 5.36
662 664 8.560374 GCAGTATTTACAGAAAAACAGTCTTCT 58.440 33.333 0.00 0.00 31.99 2.85
785 806 9.848710 GAATCTCATCCATCATCCATACATAAT 57.151 33.333 0.00 0.00 0.00 1.28
854 875 3.959293 TCCTACTAGATCCACACGAACA 58.041 45.455 0.00 0.00 0.00 3.18
864 885 4.202223 TGCGGGTTCAATTCCTACTAGATC 60.202 45.833 0.00 0.00 0.00 2.75
868 889 3.985019 TTGCGGGTTCAATTCCTACTA 57.015 42.857 0.00 0.00 0.00 1.82
911 932 4.046286 TCCATGGCTGAATGGTTAAAGT 57.954 40.909 6.96 0.00 46.24 2.66
1041 1062 5.152623 TCCAGAGAGGTGTTTTCATAGTG 57.847 43.478 0.00 0.00 39.02 2.74
1229 1250 6.942532 TCCTTGTTATCAATGCCAACTATC 57.057 37.500 0.00 0.00 32.82 2.08
1230 1251 7.293073 AGATCCTTGTTATCAATGCCAACTAT 58.707 34.615 0.00 0.00 32.82 2.12
1501 1523 2.926329 TCTTGGGGAATAAGAAGCCCTT 59.074 45.455 0.00 0.00 41.72 3.95
1517 1539 3.181491 TGAAAAGGTGCTTTCGTTCTTGG 60.181 43.478 0.00 0.00 38.00 3.61
1588 1610 4.784177 GGTTATGGACCCGAATCCTTTAA 58.216 43.478 6.49 2.92 43.06 1.52
1629 1651 6.034256 GCTTCATTGCTAAGTGCTACAAAATG 59.966 38.462 0.00 0.00 43.37 2.32
1632 1654 4.761739 AGCTTCATTGCTAAGTGCTACAAA 59.238 37.500 0.00 0.00 42.10 2.83
1649 1671 7.855784 TCTGGAATACTAATGGATAGCTTCA 57.144 36.000 0.00 0.00 34.78 3.02
1752 1780 1.059006 GGTCCCATGATCCTGAGCCT 61.059 60.000 0.00 0.00 0.00 4.58
1839 1871 8.926710 CACGGTTGCCTCTTTATCTTTATATAG 58.073 37.037 0.00 0.00 0.00 1.31
1840 1872 8.426489 ACACGGTTGCCTCTTTATCTTTATATA 58.574 33.333 0.00 0.00 0.00 0.86
1861 1893 3.530910 AACCCGCTTCCTGACACGG 62.531 63.158 0.00 0.00 45.21 4.94
1943 1975 5.536538 GGTCCTCCAGAAAAACTCAAAAGAT 59.463 40.000 0.00 0.00 0.00 2.40
1962 1994 2.527951 GATCTTGCACGGCAGGTCCT 62.528 60.000 7.63 0.00 40.61 3.85
1973 2005 2.555227 GGGGAAGACCAAAGATCTTGCA 60.555 50.000 9.17 0.00 44.01 4.08



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

AutoCloner maintained by Alex Coulton.