Multiple sequence alignment - TraesCS3A01G058600

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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 TraesCS3A01G058600 chr3A 100.000 2879 0 0 1 2879 34994341 34991463 0.000000e+00 5317
1 TraesCS3A01G058600 chr3A 95.896 999 36 5 1884 2879 685503587 685504583 0.000000e+00 1613
2 TraesCS3A01G058600 chr5B 94.781 1897 85 7 1 1884 419520579 419522474 0.000000e+00 2942
3 TraesCS3A01G058600 chr5B 94.880 1875 82 7 23 1884 491849085 491850958 0.000000e+00 2918
4 TraesCS3A01G058600 chr2D 94.781 1897 85 7 1 1884 617965306 617967201 0.000000e+00 2942
5 TraesCS3A01G058600 chr2D 85.801 662 82 5 1 650 101557363 101558024 0.000000e+00 691
6 TraesCS3A01G058600 chr2B 94.781 1897 85 7 1 1884 795980318 795982213 0.000000e+00 2942
7 TraesCS3A01G058600 chr5A 95.340 1588 71 1 302 1886 138081798 138080211 0.000000e+00 2519
8 TraesCS3A01G058600 chr5A 95.833 1008 35 5 1878 2879 481242369 481243375 0.000000e+00 1622
9 TraesCS3A01G058600 chr5A 90.365 1204 112 2 684 1884 469664647 469665849 0.000000e+00 1578
10 TraesCS3A01G058600 chr5A 93.281 253 17 0 1 253 138082036 138081784 9.740000e-100 374
11 TraesCS3A01G058600 chr2A 97.186 995 28 0 1885 2879 51420000 51420994 0.000000e+00 1683
12 TraesCS3A01G058600 chr2A 96.396 999 32 2 1885 2879 88113520 88112522 0.000000e+00 1642
13 TraesCS3A01G058600 chr2A 95.996 999 36 3 1884 2879 36085209 36084212 0.000000e+00 1620
14 TraesCS3A01G058600 chr2A 95.721 1005 40 2 1878 2879 39506923 39507927 0.000000e+00 1615
15 TraesCS3A01G058600 chr7A 96.482 995 33 1 1885 2877 107417203 107418197 0.000000e+00 1642
16 TraesCS3A01G058600 chr7A 95.596 999 42 1 1882 2878 730265502 730264504 0.000000e+00 1600
17 TraesCS3A01G058600 chr7A 89.767 215 20 2 509 723 727383502 727383290 1.020000e-69 274
18 TraesCS3A01G058600 chr5D 90.542 1237 111 6 650 1884 467262774 467264006 0.000000e+00 1631
19 TraesCS3A01G058600 chr6A 95.992 998 38 1 1884 2879 31545682 31544685 0.000000e+00 1620
20 TraesCS3A01G058600 chr7B 89.992 1229 119 2 650 1874 59646075 59644847 0.000000e+00 1585
21 TraesCS3A01G058600 chr7B 89.306 1225 125 4 660 1884 664079252 664078034 0.000000e+00 1531
22 TraesCS3A01G058600 chr7B 82.373 590 58 19 73 650 664079868 664079313 3.360000e-129 472
23 TraesCS3A01G058600 chr7B 83.721 387 39 9 267 650 59646491 59646126 7.640000e-91 344


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 TraesCS3A01G058600 chr3A 34991463 34994341 2878 True 5317.0 5317 100.0000 1 2879 1 chr3A.!!$R1 2878
1 TraesCS3A01G058600 chr3A 685503587 685504583 996 False 1613.0 1613 95.8960 1884 2879 1 chr3A.!!$F1 995
2 TraesCS3A01G058600 chr5B 419520579 419522474 1895 False 2942.0 2942 94.7810 1 1884 1 chr5B.!!$F1 1883
3 TraesCS3A01G058600 chr5B 491849085 491850958 1873 False 2918.0 2918 94.8800 23 1884 1 chr5B.!!$F2 1861
4 TraesCS3A01G058600 chr2D 617965306 617967201 1895 False 2942.0 2942 94.7810 1 1884 1 chr2D.!!$F2 1883
5 TraesCS3A01G058600 chr2D 101557363 101558024 661 False 691.0 691 85.8010 1 650 1 chr2D.!!$F1 649
6 TraesCS3A01G058600 chr2B 795980318 795982213 1895 False 2942.0 2942 94.7810 1 1884 1 chr2B.!!$F1 1883
7 TraesCS3A01G058600 chr5A 481242369 481243375 1006 False 1622.0 1622 95.8330 1878 2879 1 chr5A.!!$F2 1001
8 TraesCS3A01G058600 chr5A 469664647 469665849 1202 False 1578.0 1578 90.3650 684 1884 1 chr5A.!!$F1 1200
9 TraesCS3A01G058600 chr5A 138080211 138082036 1825 True 1446.5 2519 94.3105 1 1886 2 chr5A.!!$R1 1885
10 TraesCS3A01G058600 chr2A 51420000 51420994 994 False 1683.0 1683 97.1860 1885 2879 1 chr2A.!!$F2 994
11 TraesCS3A01G058600 chr2A 88112522 88113520 998 True 1642.0 1642 96.3960 1885 2879 1 chr2A.!!$R2 994
12 TraesCS3A01G058600 chr2A 36084212 36085209 997 True 1620.0 1620 95.9960 1884 2879 1 chr2A.!!$R1 995
13 TraesCS3A01G058600 chr2A 39506923 39507927 1004 False 1615.0 1615 95.7210 1878 2879 1 chr2A.!!$F1 1001
14 TraesCS3A01G058600 chr7A 107417203 107418197 994 False 1642.0 1642 96.4820 1885 2877 1 chr7A.!!$F1 992
15 TraesCS3A01G058600 chr7A 730264504 730265502 998 True 1600.0 1600 95.5960 1882 2878 1 chr7A.!!$R2 996
16 TraesCS3A01G058600 chr5D 467262774 467264006 1232 False 1631.0 1631 90.5420 650 1884 1 chr5D.!!$F1 1234
17 TraesCS3A01G058600 chr6A 31544685 31545682 997 True 1620.0 1620 95.9920 1884 2879 1 chr6A.!!$R1 995
18 TraesCS3A01G058600 chr7B 664078034 664079868 1834 True 1001.5 1531 85.8395 73 1884 2 chr7B.!!$R2 1811
19 TraesCS3A01G058600 chr7B 59644847 59646491 1644 True 964.5 1585 86.8565 267 1874 2 chr7B.!!$R1 1607

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
369 382 0.390866 CTGCTGCTGTCGACATCCTT 60.391 55.000 20.40 0.00 0.00 3.36 F
912 987 0.605319 TTTGATCTGGACACACCGCC 60.605 55.000 0.00 0.00 42.61 6.13 F
1632 1714 1.003118 AGACATGTTTCTAAGGCGCCA 59.997 47.619 31.54 7.98 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 1816 0.178903 TAGACCCAGGACAAGCTGGT 60.179 55.0 0.00 0.0 39.00 4.00 R
1735 1817 0.250513 GTAGACCCAGGACAAGCTGG 59.749 60.0 0.00 0.0 40.28 4.85 R
2487 2569 0.613260 TTTGCAGAGCCGGACACTAT 59.387 50.0 5.05 0.0 0.00 2.12 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
60 61 3.072468 CCGCCTCCACCCTCGTTA 61.072 66.667 0.00 0.00 0.00 3.18
121 122 1.486211 ATCGTCTTCCCGGTCAGATT 58.514 50.000 0.00 0.00 0.00 2.40
128 129 1.578897 TCCCGGTCAGATTTGGATCA 58.421 50.000 0.00 0.00 34.60 2.92
187 188 4.329545 TGCCCACCCAGCTTCGTC 62.330 66.667 0.00 0.00 0.00 4.20
190 191 3.636231 CCACCCAGCTTCGTCCCA 61.636 66.667 0.00 0.00 0.00 4.37
369 382 0.390866 CTGCTGCTGTCGACATCCTT 60.391 55.000 20.40 0.00 0.00 3.36
489 502 4.514577 CCCGCTCCATCGTTCGCT 62.515 66.667 0.00 0.00 0.00 4.93
507 520 4.602259 GCCGCCGCACTAGCCATA 62.602 66.667 0.00 0.00 37.52 2.74
654 729 2.345244 CTCGCTGCTCCTGGTTGT 59.655 61.111 0.00 0.00 0.00 3.32
790 865 0.617935 TCGCCCTTCCATCAATGTGA 59.382 50.000 0.00 0.00 0.00 3.58
895 970 0.957395 CCGATGCACTGACTGCCTTT 60.957 55.000 0.00 0.00 46.51 3.11
908 983 1.808945 CTGCCTTTGATCTGGACACAC 59.191 52.381 0.00 0.00 0.00 3.82
912 987 0.605319 TTTGATCTGGACACACCGCC 60.605 55.000 0.00 0.00 42.61 6.13
1012 1087 5.011431 GGTGATGTCTCCATGATAGATGTGA 59.989 44.000 0.00 0.00 0.00 3.58
1146 1221 1.064389 GCCCCTCTTGCCAAACTAGAT 60.064 52.381 0.00 0.00 29.47 1.98
1153 1228 2.949177 TGCCAAACTAGATGTGGTGT 57.051 45.000 0.00 0.00 34.71 4.16
1246 1321 1.866015 TGACTCTGTCGATGGGGAAT 58.134 50.000 0.00 0.00 34.95 3.01
1300 1375 2.031012 CCTGTCAGTTGCCGCTGA 59.969 61.111 0.00 3.55 42.56 4.26
1327 1402 2.731571 CCGATTCCTTCCGGGAGCA 61.732 63.158 3.32 0.00 46.01 4.26
1412 1487 2.179427 GGAGCCCACTTTGCCTATTTT 58.821 47.619 0.00 0.00 0.00 1.82
1423 1498 4.888326 TTGCCTATTTTGATGGTGCTTT 57.112 36.364 0.00 0.00 0.00 3.51
1613 1695 3.616956 TGATGAGGTAGGTGCTTTGAG 57.383 47.619 0.00 0.00 0.00 3.02
1616 1698 2.325484 TGAGGTAGGTGCTTTGAGACA 58.675 47.619 0.00 0.00 0.00 3.41
1632 1714 1.003118 AGACATGTTTCTAAGGCGCCA 59.997 47.619 31.54 7.98 0.00 5.69
1734 1816 3.551496 CTTGCTCACCGGCTTGGGA 62.551 63.158 0.00 0.00 44.64 4.37
1735 1817 3.842925 TTGCTCACCGGCTTGGGAC 62.843 63.158 0.00 0.00 44.64 4.46
1753 1835 2.683916 CCAGCTTGTCCTGGGTCTA 58.316 57.895 0.26 0.00 46.93 2.59
1918 2000 2.521224 GCGGATCTCGGGTAGGGT 60.521 66.667 5.87 0.00 39.69 4.34
1988 2070 2.786777 GATGTTTTACCCAGGTTCGGT 58.213 47.619 0.00 0.00 37.40 4.69
2072 2154 5.498393 ACAAGAGTAGATCTACCACGAGAA 58.502 41.667 25.93 0.00 37.23 2.87
2114 2196 5.782331 AGAAGCTAGCCTATGGTATGATTGA 59.218 40.000 12.13 0.00 0.00 2.57
2360 2442 1.202615 GCTATCCGAACACCCCCTAAC 60.203 57.143 0.00 0.00 0.00 2.34
2487 2569 9.567776 TTCATAGAAGATTGTAAACACCAAGAA 57.432 29.630 0.00 0.00 0.00 2.52
2620 2704 7.524065 CCAAGTCCTTTACGAATCGTTTTTAT 58.476 34.615 15.21 0.00 41.54 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 155 3.733960 CAGGTCCAGCGTCGTCGA 61.734 66.667 6.17 0.00 39.71 4.20
505 518 1.651240 CGGCAAGCAAGTGCAGCTAT 61.651 55.000 16.73 0.00 46.81 2.97
506 519 2.327343 CGGCAAGCAAGTGCAGCTA 61.327 57.895 16.73 0.00 46.81 3.32
507 520 3.667282 CGGCAAGCAAGTGCAGCT 61.667 61.111 16.73 0.00 46.81 4.24
654 729 2.275089 CATCCACGCCAATCCCCA 59.725 61.111 0.00 0.00 0.00 4.96
895 970 2.662596 GGCGGTGTGTCCAGATCA 59.337 61.111 0.00 0.00 35.57 2.92
908 983 3.197790 CATGACAGAAGCGGGCGG 61.198 66.667 0.00 0.00 0.00 6.13
912 987 2.299993 TCTTAGCATGACAGAAGCGG 57.700 50.000 0.00 0.00 0.00 5.52
1129 1204 3.012518 CCACATCTAGTTTGGCAAGAGG 58.987 50.000 0.00 0.00 0.00 3.69
1146 1221 0.756294 AAGACACATCCGACACCACA 59.244 50.000 0.00 0.00 0.00 4.17
1153 1228 1.446099 GCAGCGAAGACACATCCGA 60.446 57.895 0.00 0.00 0.00 4.55
1246 1321 3.311990 AGAGATCTCCATACATGCCACA 58.688 45.455 19.30 0.00 0.00 4.17
1300 1375 1.407437 GGAAGGAATCGGCATGACAGT 60.407 52.381 0.00 0.00 0.00 3.55
1327 1402 3.560068 GTCACGACCTCAACAATGACTTT 59.440 43.478 0.00 0.00 34.86 2.66
1412 1487 2.259917 TCTCCTCAGAAAGCACCATCA 58.740 47.619 0.00 0.00 0.00 3.07
1613 1695 1.448985 TGGCGCCTTAGAAACATGTC 58.551 50.000 29.70 0.00 0.00 3.06
1616 1698 1.202348 GCTTTGGCGCCTTAGAAACAT 59.798 47.619 29.70 0.00 0.00 2.71
1632 1714 0.832135 TGAGAGACTGGACGGGCTTT 60.832 55.000 0.00 0.00 0.00 3.51
1734 1816 0.178903 TAGACCCAGGACAAGCTGGT 60.179 55.000 0.00 0.00 39.00 4.00
1735 1817 0.250513 GTAGACCCAGGACAAGCTGG 59.749 60.000 0.00 0.00 40.28 4.85
1753 1835 0.250901 AGGCAAGCAATCGTCTTGGT 60.251 50.000 5.10 5.78 40.79 3.67
1918 2000 1.674441 CTAGACGCATAGTTCGGGACA 59.326 52.381 0.00 0.00 0.00 4.02
2072 2154 3.200958 TCTAGGGTTTAGCCTCCTTGT 57.799 47.619 3.32 0.00 37.43 3.16
2114 2196 6.715280 ACAACTTCATCAACTCCATAGACAT 58.285 36.000 0.00 0.00 0.00 3.06
2360 2442 1.045911 GCTACTGAGGGAGTCCTGGG 61.046 65.000 9.58 0.04 45.05 4.45
2416 2498 2.035704 TGCAATGCCGAAGACAATTTGT 59.964 40.909 1.53 0.63 0.00 2.83
2487 2569 0.613260 TTTGCAGAGCCGGACACTAT 59.387 50.000 5.05 0.00 0.00 2.12
2693 2780 5.405571 CCGTATTGATGAGAATCCCGTAAAG 59.594 44.000 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.