Multiple sequence alignment - TraesCS4D01G292200

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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 TraesCS4D01G292200 chr4D 100.000 2111 0 0 1 2111 463401419 463403529 0.000000e+00 3899.0
1 TraesCS4D01G292200 chr4D 86.885 427 32 20 858 1270 477914171 477914587 6.870000e-125 457.0
2 TraesCS4D01G292200 chr4D 84.259 432 47 17 874 1298 456124202 456124619 3.260000e-108 401.0
3 TraesCS4D01G292200 chr4B 89.210 2039 138 52 120 2111 579389775 579391778 0.000000e+00 2471.0
4 TraesCS4D01G292200 chr4B 94.512 492 27 0 106 597 579102441 579102932 0.000000e+00 760.0
5 TraesCS4D01G292200 chr4B 88.480 625 46 18 1463 2080 579103904 579104509 0.000000e+00 732.0
6 TraesCS4D01G292200 chr4B 92.391 460 27 8 858 1315 579103347 579103800 0.000000e+00 649.0
7 TraesCS4D01G292200 chr4B 91.096 292 23 3 874 1163 604141371 604141661 1.960000e-105 392.0
8 TraesCS4D01G292200 chr4A 88.102 1370 98 42 787 2111 6033760 6032411 0.000000e+00 1567.0
9 TraesCS4D01G292200 chr4A 87.169 717 32 25 10 697 6034631 6033946 0.000000e+00 760.0
10 TraesCS4D01G292200 chr4A 85.242 454 46 13 857 1305 21844250 21844687 4.130000e-122 448.0
11 TraesCS4D01G292200 chr4A 86.500 400 38 12 880 1275 11622990 11622603 1.940000e-115 425.0
12 TraesCS4D01G292200 chr4A 92.982 285 18 2 880 1163 684615227 684615510 4.190000e-112 414.0
13 TraesCS4D01G292200 chr2D 90.741 54 2 2 463 516 343164749 343164799 3.760000e-08 69.4


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 TraesCS4D01G292200 chr4D 463401419 463403529 2110 False 3899.000000 3899 100.000000 1 2111 1 chr4D.!!$F2 2110
1 TraesCS4D01G292200 chr4B 579389775 579391778 2003 False 2471.000000 2471 89.210000 120 2111 1 chr4B.!!$F1 1991
2 TraesCS4D01G292200 chr4B 579102441 579104509 2068 False 713.666667 760 91.794333 106 2080 3 chr4B.!!$F3 1974
3 TraesCS4D01G292200 chr4A 6032411 6034631 2220 True 1163.500000 1567 87.635500 10 2111 2 chr4A.!!$R2 2101

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
734 856 0.110644 GCTGTCGGTCGCTTTCTTTG 60.111 55.0 0.0 0.0 0.0 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 2148 1.623311 TGGATCGTTTCAGAAGGCAGA 59.377 47.619 0.0 0.0 0.0 4.26 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
22 23 5.072040 CCCTTGTCAAAGAACAAACAAGT 57.928 39.130 11.76 0.00 44.45 3.16
31 32 6.797995 TCAAAGAACAAACAAGTAACAACGTC 59.202 34.615 0.00 0.00 0.00 4.34
43 44 2.203015 AACGTCGCAACACCAGCT 60.203 55.556 0.00 0.00 0.00 4.24
45 46 0.531090 AACGTCGCAACACCAGCTAA 60.531 50.000 0.00 0.00 0.00 3.09
46 47 0.944311 ACGTCGCAACACCAGCTAAG 60.944 55.000 0.00 0.00 0.00 2.18
47 48 1.497722 GTCGCAACACCAGCTAAGC 59.502 57.895 0.00 0.00 0.00 3.09
48 49 1.070615 TCGCAACACCAGCTAAGCA 59.929 52.632 0.00 0.00 0.00 3.91
49 50 1.207593 CGCAACACCAGCTAAGCAC 59.792 57.895 0.00 0.00 0.00 4.40
50 51 1.506309 CGCAACACCAGCTAAGCACA 61.506 55.000 0.00 0.00 0.00 4.57
96 100 2.965147 GCAAGTGCAATGGCGTCGA 61.965 57.895 0.00 0.00 45.35 4.20
97 101 1.133253 CAAGTGCAATGGCGTCGAG 59.867 57.895 0.00 0.00 45.35 4.04
98 102 2.680913 AAGTGCAATGGCGTCGAGC 61.681 57.895 0.00 0.00 45.35 5.03
272 277 4.735132 GTGCACGCCGCCACTCTA 62.735 66.667 0.00 0.00 41.33 2.43
281 286 2.809010 GCCACTCTACTCTCCGCC 59.191 66.667 0.00 0.00 0.00 6.13
299 304 1.872234 CCTCGCGTCCATGTACACG 60.872 63.158 5.77 0.00 39.09 4.49
497 517 2.413142 GCTGCTGGCCATGTTCCTC 61.413 63.158 5.51 0.00 34.27 3.71
642 729 3.771160 CCGTGGACGAGAAGGGGG 61.771 72.222 0.00 0.00 43.02 5.40
718 840 3.435327 TGCCGTGTGTTTAAATAGAGCTG 59.565 43.478 0.00 0.00 0.00 4.24
732 854 0.667792 GAGCTGTCGGTCGCTTTCTT 60.668 55.000 0.00 0.00 36.45 2.52
734 856 0.110644 GCTGTCGGTCGCTTTCTTTG 60.111 55.000 0.00 0.00 0.00 2.77
753 885 4.952262 TTGCATATTGTCTGAACAGCTC 57.048 40.909 0.00 0.00 36.57 4.09
768 919 5.926542 TGAACAGCTCTCACAAATACAGTAC 59.073 40.000 0.00 0.00 0.00 2.73
769 920 5.468540 ACAGCTCTCACAAATACAGTACA 57.531 39.130 0.00 0.00 0.00 2.90
771 922 5.011125 ACAGCTCTCACAAATACAGTACAGT 59.989 40.000 0.00 0.00 0.00 3.55
773 924 7.090808 CAGCTCTCACAAATACAGTACAGTAA 58.909 38.462 1.93 0.00 0.00 2.24
778 929 9.214957 TCTCACAAATACAGTACAGTAATTTGG 57.785 33.333 22.16 16.24 32.74 3.28
822 1155 4.646492 ACAGAAACCAAGCTCAGTTTTCAT 59.354 37.500 13.52 3.46 36.36 2.57
834 1167 9.651913 AAGCTCAGTTTTCATTTTGTTCTAAAA 57.348 25.926 0.00 0.00 0.00 1.52
866 1201 5.185635 CCAAAGCCATCAGGAAGAACAAATA 59.814 40.000 0.00 0.00 36.89 1.40
878 1213 8.792633 CAGGAAGAACAAATATTCCACTTGTTA 58.207 33.333 6.02 0.00 44.11 2.41
1089 1425 2.969628 AAGGTATGCTTCTCTCCGTG 57.030 50.000 0.00 0.00 0.00 4.94
1242 1584 3.601685 CCGTTTGCTTGGGCCGTT 61.602 61.111 0.00 0.00 37.74 4.44
1368 1727 5.902981 TCTTTTGTTTTCACGCGTACATTAC 59.097 36.000 13.44 7.58 0.00 1.89
1370 1729 4.377911 TGTTTTCACGCGTACATTACTG 57.622 40.909 13.44 0.00 0.00 2.74
1493 1869 3.835790 TTTGGTTCCTCGCGGTGGG 62.836 63.158 6.13 6.82 0.00 4.61
1697 2085 3.852286 ACGTGTGTCTCGGCAAATAATA 58.148 40.909 0.00 0.00 0.00 0.98
1785 2173 2.749076 CCTTCTGAAACGATCCATGCAA 59.251 45.455 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.113684 CGTTGTTACTTGTTTGTTCTTTGACAA 59.886 33.333 0.00 0.00 37.73 3.18
4 5 6.579292 CGTTGTTACTTGTTTGTTCTTTGACA 59.421 34.615 0.00 0.00 0.00 3.58
5 6 6.579666 ACGTTGTTACTTGTTTGTTCTTTGAC 59.420 34.615 0.00 0.00 0.00 3.18
6 7 6.670233 ACGTTGTTACTTGTTTGTTCTTTGA 58.330 32.000 0.00 0.00 0.00 2.69
7 8 6.236838 CGACGTTGTTACTTGTTTGTTCTTTG 60.237 38.462 0.00 0.00 0.00 2.77
8 9 5.791480 CGACGTTGTTACTTGTTTGTTCTTT 59.209 36.000 0.00 0.00 0.00 2.52
20 21 0.932399 GGTGTTGCGACGTTGTTACT 59.068 50.000 4.37 0.00 0.00 2.24
21 22 0.651551 TGGTGTTGCGACGTTGTTAC 59.348 50.000 4.37 3.77 0.00 2.50
22 23 0.931702 CTGGTGTTGCGACGTTGTTA 59.068 50.000 4.37 0.00 0.00 2.41
31 32 1.207593 GTGCTTAGCTGGTGTTGCG 59.792 57.895 5.60 0.00 35.28 4.85
43 44 0.673985 AGCTGTCTGTCGTGTGCTTA 59.326 50.000 0.00 0.00 0.00 3.09
45 46 1.006805 GAGCTGTCTGTCGTGTGCT 60.007 57.895 0.00 0.00 0.00 4.40
46 47 2.024319 GGAGCTGTCTGTCGTGTGC 61.024 63.158 0.00 0.00 0.00 4.57
47 48 0.665670 CTGGAGCTGTCTGTCGTGTG 60.666 60.000 0.00 0.00 0.00 3.82
48 49 1.662608 CTGGAGCTGTCTGTCGTGT 59.337 57.895 0.00 0.00 0.00 4.49
49 50 1.735920 GCTGGAGCTGTCTGTCGTG 60.736 63.158 0.00 0.00 38.21 4.35
50 51 2.653702 GCTGGAGCTGTCTGTCGT 59.346 61.111 0.00 0.00 38.21 4.34
103 107 3.388703 CTCAGGCTGGAGCTGGAGC 62.389 68.421 15.73 0.00 41.70 4.70
104 108 2.733669 CCTCAGGCTGGAGCTGGAG 61.734 68.421 15.73 2.22 41.70 3.86
105 109 2.686470 CCTCAGGCTGGAGCTGGA 60.686 66.667 15.73 0.00 41.70 3.86
106 110 2.686470 TCCTCAGGCTGGAGCTGG 60.686 66.667 15.73 9.47 41.70 4.85
107 111 2.901813 CTCCTCAGGCTGGAGCTG 59.098 66.667 15.73 0.00 43.67 4.24
269 274 2.516460 GCGAGGGCGGAGAGTAGA 60.516 66.667 0.00 0.00 38.16 2.59
281 286 4.088421 GTGTACATGGACGCGAGG 57.912 61.111 15.93 0.00 0.00 4.63
620 707 3.966026 CTTCTCGTCCACGGGCGTC 62.966 68.421 10.29 0.00 40.23 5.19
621 708 4.052229 CTTCTCGTCCACGGGCGT 62.052 66.667 10.29 0.00 40.23 5.68
622 709 4.796231 CCTTCTCGTCCACGGGCG 62.796 72.222 3.04 3.04 40.23 6.13
623 710 4.452733 CCCTTCTCGTCCACGGGC 62.453 72.222 0.00 0.00 40.23 6.13
624 711 3.771160 CCCCTTCTCGTCCACGGG 61.771 72.222 0.00 0.00 42.17 5.28
625 712 3.771160 CCCCCTTCTCGTCCACGG 61.771 72.222 0.00 0.00 40.29 4.94
626 713 4.452733 GCCCCCTTCTCGTCCACG 62.453 72.222 0.00 0.00 41.45 4.94
627 714 4.452733 CGCCCCCTTCTCGTCCAC 62.453 72.222 0.00 0.00 0.00 4.02
628 715 4.689549 TCGCCCCCTTCTCGTCCA 62.690 66.667 0.00 0.00 0.00 4.02
718 840 0.517316 ATGCAAAGAAAGCGACCGAC 59.483 50.000 0.00 0.00 33.85 4.79
732 854 4.582869 AGAGCTGTTCAGACAATATGCAA 58.417 39.130 0.00 0.00 34.85 4.08
734 856 4.033817 GTGAGAGCTGTTCAGACAATATGC 59.966 45.833 0.00 0.00 34.85 3.14
753 885 8.999431 ACCAAATTACTGTACTGTATTTGTGAG 58.001 33.333 24.90 18.96 0.00 3.51
768 919 8.154649 ACAGTAGAACTTGAACCAAATTACTG 57.845 34.615 6.34 6.34 30.52 2.74
769 920 8.621286 CAACAGTAGAACTTGAACCAAATTACT 58.379 33.333 0.00 0.00 0.00 2.24
771 922 8.740123 TCAACAGTAGAACTTGAACCAAATTA 57.260 30.769 0.00 0.00 0.00 1.40
773 924 7.639113 TTCAACAGTAGAACTTGAACCAAAT 57.361 32.000 0.00 0.00 0.00 2.32
777 928 7.724305 TGTATTCAACAGTAGAACTTGAACC 57.276 36.000 0.00 0.00 30.47 3.62
808 1141 9.651913 TTTTAGAACAAAATGAAAACTGAGCTT 57.348 25.926 0.00 0.00 0.00 3.74
834 1167 3.966665 TCCTGATGGCTTTGGTTTTCTTT 59.033 39.130 0.00 0.00 0.00 2.52
1089 1425 1.068121 ATATAAGCAGACCCAGGGCC 58.932 55.000 4.91 0.00 0.00 5.80
1113 1449 1.612442 CGGAAGGGAGGGGAAGACA 60.612 63.158 0.00 0.00 0.00 3.41
1120 1456 3.474570 CCAGAGCGGAAGGGAGGG 61.475 72.222 0.00 0.00 36.56 4.30
1191 1530 2.434134 CCGAGAAAACGACCGAGCG 61.434 63.158 0.00 0.00 35.09 5.03
1192 1531 1.071567 CTCCGAGAAAACGACCGAGC 61.072 60.000 0.00 0.00 35.09 5.03
1194 1533 1.582968 CCTCCGAGAAAACGACCGA 59.417 57.895 0.00 0.00 35.09 4.69
1196 1535 2.092882 CGCCTCCGAGAAAACGACC 61.093 63.158 0.00 0.00 36.29 4.79
1197 1536 1.080974 TCGCCTCCGAGAAAACGAC 60.081 57.895 0.00 0.00 38.82 4.34
1198 1537 3.357919 TCGCCTCCGAGAAAACGA 58.642 55.556 0.00 0.00 38.82 3.85
1226 1568 2.354539 CAACGGCCCAAGCAAACG 60.355 61.111 0.00 0.00 42.56 3.60
1242 1584 1.366111 GCGCTCGGCCTTATTCAACA 61.366 55.000 0.00 0.00 34.80 3.33
1348 1706 4.270566 ACAGTAATGTACGCGTGAAAACAA 59.729 37.500 24.59 0.64 0.00 2.83
1349 1707 3.803231 ACAGTAATGTACGCGTGAAAACA 59.197 39.130 24.59 18.85 0.00 2.83
1493 1869 2.507324 GCCTCGTCACCTTCTCGC 60.507 66.667 0.00 0.00 0.00 5.03
1697 2085 9.311425 AGTCCCAGATATTATAGGGTAGATACT 57.689 37.037 11.51 6.44 42.12 2.12
1760 2148 1.623311 TGGATCGTTTCAGAAGGCAGA 59.377 47.619 0.00 0.00 0.00 4.26
1887 2276 7.039011 TGTCTCCTCAGTCACATTTGTATAAGT 60.039 37.037 0.00 0.00 0.00 2.24
1888 2277 7.323420 TGTCTCCTCAGTCACATTTGTATAAG 58.677 38.462 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.