Multiple sequence alignment - TraesCS3B01G472900

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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 TraesCS3B01G472900 chr3B 100.000 2549 0 0 1 2549 722334141 722336689 0 4708
1 TraesCS3B01G472900 chr3B 95.785 1993 72 12 560 2549 703251163 703253146 0 3205
2 TraesCS3B01G472900 chr2B 95.756 2003 77 8 551 2549 596962054 596964052 0 3221
3 TraesCS3B01G472900 chr2B 95.779 1990 74 9 563 2549 36241847 36243829 0 3201
4 TraesCS3B01G472900 chr2B 95.552 2001 77 9 556 2549 602077195 602075200 0 3192
5 TraesCS3B01G472900 chr2B 97.699 565 13 0 1 565 7257424 7256860 0 972
6 TraesCS3B01G472900 chr2B 97.699 565 13 0 1 565 157662253 157661689 0 972
7 TraesCS3B01G472900 chr5B 95.884 1992 76 6 560 2549 446193260 446191273 0 3219
8 TraesCS3B01G472900 chr5B 95.825 1988 74 7 566 2549 269389473 269391455 0 3203
9 TraesCS3B01G472900 chr5B 98.053 565 11 0 1 565 526889951 526889387 0 983
10 TraesCS3B01G472900 chr5B 98.053 565 11 0 1 565 538648256 538647692 0 983
11 TraesCS3B01G472900 chr5B 97.699 565 13 0 1 565 362253718 362254282 0 972
12 TraesCS3B01G472900 chr1B 95.974 1987 70 8 565 2549 498442420 498440442 0 3217
13 TraesCS3B01G472900 chr1B 97.876 565 12 0 1 565 399252054 399252618 0 977
14 TraesCS3B01G472900 chr1B 97.699 565 13 0 1 565 502296598 502297162 0 972
15 TraesCS3B01G472900 chr7B 95.921 1986 72 8 566 2549 718488474 718486496 0 3210
16 TraesCS3B01G472900 chr7B 95.643 1997 75 9 559 2549 621924184 621926174 0 3195
17 TraesCS3B01G472900 chr7B 97.699 565 13 0 1 565 98954918 98955482 0 972
18 TraesCS3B01G472900 chr7B 92.401 658 43 4 1 656 256806919 256807571 0 931


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 TraesCS3B01G472900 chr3B 722334141 722336689 2548 False 4708 4708 100.000 1 2549 1 chr3B.!!$F2 2548
1 TraesCS3B01G472900 chr3B 703251163 703253146 1983 False 3205 3205 95.785 560 2549 1 chr3B.!!$F1 1989
2 TraesCS3B01G472900 chr2B 596962054 596964052 1998 False 3221 3221 95.756 551 2549 1 chr2B.!!$F2 1998
3 TraesCS3B01G472900 chr2B 36241847 36243829 1982 False 3201 3201 95.779 563 2549 1 chr2B.!!$F1 1986
4 TraesCS3B01G472900 chr2B 602075200 602077195 1995 True 3192 3192 95.552 556 2549 1 chr2B.!!$R3 1993
5 TraesCS3B01G472900 chr2B 7256860 7257424 564 True 972 972 97.699 1 565 1 chr2B.!!$R1 564
6 TraesCS3B01G472900 chr2B 157661689 157662253 564 True 972 972 97.699 1 565 1 chr2B.!!$R2 564
7 TraesCS3B01G472900 chr5B 446191273 446193260 1987 True 3219 3219 95.884 560 2549 1 chr5B.!!$R1 1989
8 TraesCS3B01G472900 chr5B 269389473 269391455 1982 False 3203 3203 95.825 566 2549 1 chr5B.!!$F1 1983
9 TraesCS3B01G472900 chr5B 526889387 526889951 564 True 983 983 98.053 1 565 1 chr5B.!!$R2 564
10 TraesCS3B01G472900 chr5B 538647692 538648256 564 True 983 983 98.053 1 565 1 chr5B.!!$R3 564
11 TraesCS3B01G472900 chr5B 362253718 362254282 564 False 972 972 97.699 1 565 1 chr5B.!!$F2 564
12 TraesCS3B01G472900 chr1B 498440442 498442420 1978 True 3217 3217 95.974 565 2549 1 chr1B.!!$R1 1984
13 TraesCS3B01G472900 chr1B 399252054 399252618 564 False 977 977 97.876 1 565 1 chr1B.!!$F1 564
14 TraesCS3B01G472900 chr1B 502296598 502297162 564 False 972 972 97.699 1 565 1 chr1B.!!$F2 564
15 TraesCS3B01G472900 chr7B 718486496 718488474 1978 True 3210 3210 95.921 566 2549 1 chr7B.!!$R1 1983
16 TraesCS3B01G472900 chr7B 621924184 621926174 1990 False 3195 3195 95.643 559 2549 1 chr7B.!!$F3 1990
17 TraesCS3B01G472900 chr7B 98954918 98955482 564 False 972 972 97.699 1 565 1 chr7B.!!$F1 564
18 TraesCS3B01G472900 chr7B 256806919 256807571 652 False 931 931 92.401 1 656 1 chr7B.!!$F2 655

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
133 134 0.246635 CGGTGTCCTTACCCAGTGAG 59.753 60.0 0.00 0.00 37.44 3.51 F
1067 1070 0.459237 CGTGTGGAGATGCCTGTCTC 60.459 60.0 3.08 3.08 43.10 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1117 1120 0.037605 GGACGATTGTGGTTCCTCGT 60.038 55.0 4.07 4.07 46.09 4.18 R
2165 2173 1.251527 AAACACCACAAACCCACGCA 61.252 50.0 0.00 0.00 0.00 5.24 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
133 134 0.246635 CGGTGTCCTTACCCAGTGAG 59.753 60.000 0.00 0.00 37.44 3.51
183 184 5.913137 TTGTTGCCATCGAGGATAAAAAT 57.087 34.783 0.00 0.00 41.22 1.82
692 695 1.615107 GAACTTTGGCGTCTCCGTCG 61.615 60.000 0.00 0.00 43.03 5.12
732 735 0.546747 CCTTACAGGTGGGACCAGGA 60.547 60.000 0.00 0.00 41.95 3.86
738 741 2.930562 GTGGGACCAGGAGGCAGT 60.931 66.667 0.00 0.00 39.06 4.40
805 808 1.669115 GCAGAGAGCCGTTGAGCAA 60.669 57.895 0.00 0.00 37.23 3.91
844 847 2.650163 GCTATATTAGCGGGCGACG 58.350 57.895 0.00 0.00 42.62 5.12
1006 1009 1.227205 GCTCCGAGCTCCATGTCTG 60.227 63.158 13.42 0.00 38.45 3.51
1041 1044 3.071206 ACCTCGCGGATGCAGAGT 61.071 61.111 6.13 0.00 42.97 3.24
1067 1070 0.459237 CGTGTGGAGATGCCTGTCTC 60.459 60.000 3.08 3.08 43.10 3.36
1117 1120 3.390967 TGATCAGAGGGTTTCTCACACAA 59.609 43.478 0.00 0.00 44.81 3.33
1329 1332 1.153978 CGAATGGTTGCGCATGCTT 60.154 52.632 12.75 2.41 43.34 3.91
1490 1493 4.103943 ACCCATTTGCAAATACTTTTGGGT 59.896 37.500 32.30 32.30 42.09 4.51
2021 2028 1.599797 GTGGTGTTTAGGGCTGCGT 60.600 57.895 0.00 0.00 0.00 5.24
2044 2051 1.755380 GTAACCGCTAGGACAGATGGT 59.245 52.381 0.00 0.00 41.02 3.55
2165 2173 2.363297 GGGACTCGAACCCAAGACT 58.637 57.895 18.78 0.00 46.05 3.24
2388 2399 0.729140 GTATGTTTGCACTGCCACGC 60.729 55.000 0.00 0.00 0.00 5.34
2404 2415 2.406130 CACGCGGTTTTGGTTAGAGTA 58.594 47.619 12.47 0.00 0.00 2.59
2539 2553 6.696411 TCTTTTGAATGACAACCACAAGTTT 58.304 32.000 6.36 0.00 36.18 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.856145 ATTCGAAGAGACTTGCAAAGATAAT 57.144 32.000 3.35 0.00 43.32 1.28
133 134 0.315251 GTGCCTTGCAACCCTTTCTC 59.685 55.000 0.00 0.00 41.47 2.87
183 184 9.631257 CTCATGCAATATGATATAAACCCCATA 57.369 33.333 0.00 0.00 0.00 2.74
408 410 5.689383 ACAAATTACTGTCGAGCAATTGT 57.311 34.783 7.40 0.00 0.00 2.71
576 579 2.488347 GGACACCACTAAGGGCAAAAGA 60.488 50.000 0.00 0.00 43.89 2.52
738 741 2.165437 GTCTGAATAAAATTGGCCGCCA 59.835 45.455 8.43 8.43 0.00 5.69
805 808 0.464373 CACACCCGCAATGGCTCTAT 60.464 55.000 0.00 0.00 38.10 1.98
906 909 2.512515 CTAGCTTCCCACTGCCGC 60.513 66.667 0.00 0.00 0.00 6.53
911 914 0.545309 TCCACAGCTAGCTTCCCACT 60.545 55.000 16.46 0.00 0.00 4.00
1067 1070 2.317609 CGGCACCACGGAAAGACAG 61.318 63.158 0.00 0.00 0.00 3.51
1117 1120 0.037605 GGACGATTGTGGTTCCTCGT 60.038 55.000 4.07 4.07 46.09 4.18
1329 1332 2.197324 GCCACTGTGGTTTGGGGA 59.803 61.111 26.48 0.00 40.46 4.81
1490 1493 6.926826 CAGTGCGATTACCATACCTACAAATA 59.073 38.462 0.00 0.00 0.00 1.40
1636 1639 4.963318 TCAACATGGTCACTTCTTCTCT 57.037 40.909 0.00 0.00 0.00 3.10
1801 1805 4.857037 GGTCTTTGATTTAAATCACGGTGC 59.143 41.667 26.69 16.44 44.54 5.01
2021 2028 1.927487 TCTGTCCTAGCGGTTACCAA 58.073 50.000 1.13 0.00 0.00 3.67
2044 2051 4.431378 TCCCTACCCATGTCAAACTCTTA 58.569 43.478 0.00 0.00 0.00 2.10
2109 2117 1.686052 TGTGCATTTTCCACCCTTCAC 59.314 47.619 0.00 0.00 32.30 3.18
2165 2173 1.251527 AAACACCACAAACCCACGCA 61.252 50.000 0.00 0.00 0.00 5.24
2388 2399 3.660865 AGTGCTACTCTAACCAAAACCG 58.339 45.455 0.00 0.00 0.00 4.44
2514 2528 6.279513 ACTTGTGGTTGTCATTCAAAAGAA 57.720 33.333 10.89 0.00 37.81 2.52


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

AutoCloner maintained by Alex Coulton.