Multiple sequence alignment - TraesCS3B01G558600

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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 TraesCS3B01G558600 chr3B 100.000 2549 0 0 1 2549 792938821 792941369 0.000000e+00 4708
1 TraesCS3B01G558600 chr3B 94.992 599 28 2 1 597 792881134 792881732 0.000000e+00 939
2 TraesCS3B01G558600 chr3B 95.151 598 22 3 1 597 62611876 62612467 0.000000e+00 937
3 TraesCS3B01G558600 chr3B 94.482 598 26 5 1 597 436612058 436612649 0.000000e+00 915
4 TraesCS3B01G558600 chr6B 95.774 1964 73 8 593 2549 527993582 527991622 0.000000e+00 3158
5 TraesCS3B01G558600 chr6B 93.122 378 24 2 595 971 478999962 479000338 1.030000e-153 553
6 TraesCS3B01G558600 chr5B 95.197 1957 77 12 598 2549 76431899 76429955 0.000000e+00 3077
7 TraesCS3B01G558600 chr1B 95.046 1958 75 10 598 2549 189219500 189221441 0.000000e+00 3059
8 TraesCS3B01G558600 chr1B 94.570 1989 69 18 598 2549 581717561 581715575 0.000000e+00 3038
9 TraesCS3B01G558600 chr4A 94.710 1985 69 14 598 2549 705529252 705527271 0.000000e+00 3051
10 TraesCS3B01G558600 chr4A 95.213 1922 70 14 634 2549 598584614 598582709 0.000000e+00 3020
11 TraesCS3B01G558600 chr4A 94.482 598 27 4 1 597 610787024 610787616 0.000000e+00 917
12 TraesCS3B01G558600 chr2B 94.038 1996 76 13 588 2549 667899795 667897809 0.000000e+00 2987
13 TraesCS3B01G558600 chr2B 95.318 598 20 4 1 597 383428872 383428282 0.000000e+00 942
14 TraesCS3B01G558600 chr2B 94.816 598 28 3 1 597 772889892 772890487 0.000000e+00 929
15 TraesCS3B01G558600 chr2B 94.622 595 28 2 1 594 566600734 566601325 0.000000e+00 918
16 TraesCS3B01G558600 chr2B 94.324 599 31 3 1 597 756235521 756236118 0.000000e+00 915
17 TraesCS3B01G558600 chr7B 94.348 1964 70 25 622 2549 708943230 708941272 0.000000e+00 2974
18 TraesCS3B01G558600 chr7B 96.654 1614 46 5 940 2549 12494308 12492699 0.000000e+00 2675
19 TraesCS3B01G558600 chr7B 96.594 1615 48 5 940 2549 720988819 720987207 0.000000e+00 2671
20 TraesCS3B01G558600 chr3A 89.362 1128 85 12 598 1723 120653865 120654959 0.000000e+00 1386
21 TraesCS3B01G558600 chr4B 94.333 600 31 3 1 597 330949805 330950404 0.000000e+00 917
22 TraesCS3B01G558600 chr2A 89.852 542 49 4 598 1138 695806752 695806216 0.000000e+00 691
23 TraesCS3B01G558600 chr2D 93.600 375 22 2 598 971 64508698 64509071 2.220000e-155 558


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 TraesCS3B01G558600 chr3B 792938821 792941369 2548 False 4708 4708 100.000 1 2549 1 chr3B.!!$F4 2548
1 TraesCS3B01G558600 chr3B 792881134 792881732 598 False 939 939 94.992 1 597 1 chr3B.!!$F3 596
2 TraesCS3B01G558600 chr3B 62611876 62612467 591 False 937 937 95.151 1 597 1 chr3B.!!$F1 596
3 TraesCS3B01G558600 chr3B 436612058 436612649 591 False 915 915 94.482 1 597 1 chr3B.!!$F2 596
4 TraesCS3B01G558600 chr6B 527991622 527993582 1960 True 3158 3158 95.774 593 2549 1 chr6B.!!$R1 1956
5 TraesCS3B01G558600 chr5B 76429955 76431899 1944 True 3077 3077 95.197 598 2549 1 chr5B.!!$R1 1951
6 TraesCS3B01G558600 chr1B 189219500 189221441 1941 False 3059 3059 95.046 598 2549 1 chr1B.!!$F1 1951
7 TraesCS3B01G558600 chr1B 581715575 581717561 1986 True 3038 3038 94.570 598 2549 1 chr1B.!!$R1 1951
8 TraesCS3B01G558600 chr4A 705527271 705529252 1981 True 3051 3051 94.710 598 2549 1 chr4A.!!$R2 1951
9 TraesCS3B01G558600 chr4A 598582709 598584614 1905 True 3020 3020 95.213 634 2549 1 chr4A.!!$R1 1915
10 TraesCS3B01G558600 chr4A 610787024 610787616 592 False 917 917 94.482 1 597 1 chr4A.!!$F1 596
11 TraesCS3B01G558600 chr2B 667897809 667899795 1986 True 2987 2987 94.038 588 2549 1 chr2B.!!$R2 1961
12 TraesCS3B01G558600 chr2B 383428282 383428872 590 True 942 942 95.318 1 597 1 chr2B.!!$R1 596
13 TraesCS3B01G558600 chr2B 772889892 772890487 595 False 929 929 94.816 1 597 1 chr2B.!!$F3 596
14 TraesCS3B01G558600 chr2B 566600734 566601325 591 False 918 918 94.622 1 594 1 chr2B.!!$F1 593
15 TraesCS3B01G558600 chr2B 756235521 756236118 597 False 915 915 94.324 1 597 1 chr2B.!!$F2 596
16 TraesCS3B01G558600 chr7B 708941272 708943230 1958 True 2974 2974 94.348 622 2549 1 chr7B.!!$R2 1927
17 TraesCS3B01G558600 chr7B 12492699 12494308 1609 True 2675 2675 96.654 940 2549 1 chr7B.!!$R1 1609
18 TraesCS3B01G558600 chr7B 720987207 720988819 1612 True 2671 2671 96.594 940 2549 1 chr7B.!!$R3 1609
19 TraesCS3B01G558600 chr3A 120653865 120654959 1094 False 1386 1386 89.362 598 1723 1 chr3A.!!$F1 1125
20 TraesCS3B01G558600 chr4B 330949805 330950404 599 False 917 917 94.333 1 597 1 chr4B.!!$F1 596
21 TraesCS3B01G558600 chr2A 695806216 695806752 536 True 691 691 89.852 598 1138 1 chr2A.!!$R1 540

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
687 691 0.250597 GTTTTGCCCCTAGTCCGTGT 60.251 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2507 2815 1.925972 GAGGGGGTGAGAAGCCCTT 60.926 63.158 12.46 5.11 45.39 3.95 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
91 92 4.389374 GTTTTGAGAGGAGATGGTGTTGA 58.611 43.478 0.00 0.00 0.00 3.18
271 272 2.437895 GTCCCGTAAGCTTGCCCC 60.438 66.667 9.86 0.00 0.00 5.80
272 273 2.609610 TCCCGTAAGCTTGCCCCT 60.610 61.111 9.86 0.00 0.00 4.79
323 325 1.080354 AGAAGATGGACACCGGGGA 59.920 57.895 12.96 0.00 0.00 4.81
345 347 2.374342 CCAGGGGGTCCAGGAGAT 59.626 66.667 0.00 0.00 41.82 2.75
495 499 3.423539 TTTGGAGCTGTGCAGAATAGT 57.576 42.857 3.02 0.00 0.00 2.12
620 624 5.190925 GGGGTTAATTATCCTTTTGCCCTTT 59.809 40.000 11.51 0.00 34.29 3.11
687 691 0.250597 GTTTTGCCCCTAGTCCGTGT 60.251 55.000 0.00 0.00 0.00 4.49
714 718 3.195661 GACTCGTTCTGTGAACTTTGGT 58.804 45.455 8.51 2.84 0.00 3.67
865 873 1.967779 TGGCGGCTGTGCTATATTAGA 59.032 47.619 11.43 0.00 34.52 2.10
888 896 3.807631 GACAGCAGCGGTGACCACA 62.808 63.158 20.69 0.00 34.87 4.17
900 908 0.823769 TGACCACAGCGACAGAGAGT 60.824 55.000 0.00 0.00 0.00 3.24
1179 1304 1.422402 GGGGTAAGAATCGGGGCAATA 59.578 52.381 0.00 0.00 0.00 1.90
1245 1370 0.603707 CCGTGTTCATGCAGGTGACT 60.604 55.000 0.00 0.00 46.44 3.41
1246 1371 0.792640 CGTGTTCATGCAGGTGACTC 59.207 55.000 0.00 0.00 40.21 3.36
1329 1454 1.153978 CGAATGGTTGCGCATGCTT 60.154 52.632 12.75 2.41 43.34 3.91
1338 1463 2.639327 GCGCATGCTTCCCCAAACT 61.639 57.895 17.13 0.00 38.39 2.66
1385 1510 1.115467 GAAGAGATGGAGGGCGAAGA 58.885 55.000 0.00 0.00 0.00 2.87
1711 1838 8.355169 TGGAGAATTCAGAAACTTTTGATCAAG 58.645 33.333 8.41 0.11 0.00 3.02
1730 1857 6.140303 TCAAGGAAATGCAGCTAATGAATC 57.860 37.500 0.00 0.00 0.00 2.52
2177 2479 2.342279 CTCGAACCCAAGACCGCA 59.658 61.111 0.00 0.00 0.00 5.69
2236 2538 2.107204 AGGACAGATGGCAAGAGTTTGT 59.893 45.455 0.00 0.00 36.65 2.83
2237 2539 3.327757 AGGACAGATGGCAAGAGTTTGTA 59.672 43.478 0.00 0.00 36.65 2.41
2412 2718 2.289547 CCACGTGGTTTTGGTTAGAGTG 59.710 50.000 26.95 0.00 0.00 3.51
2447 2754 2.948979 TGTTAGAGTGGCACTTGGTTTG 59.051 45.455 22.98 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 5.826737 GGTCAATCTCCATCAACATCTTCAT 59.173 40.000 0.00 0.00 0.00 2.57
135 136 2.559698 TCACCAACGTCATCACCAAT 57.440 45.000 0.00 0.00 0.00 3.16
175 176 1.228154 GTTCTGCCGGGGACACTTT 60.228 57.895 2.18 0.00 0.00 2.66
345 347 2.596631 CTACTAGGCGCGCCCCTA 60.597 66.667 44.47 30.08 36.41 3.53
458 462 3.053991 TCCAAAAGTCCTGAAACTCCACA 60.054 43.478 0.00 0.00 0.00 4.17
495 499 5.122519 GGAAAAGGAGCAAACATTGGAAAA 58.877 37.500 0.00 0.00 0.00 2.29
620 624 0.322648 CTGAGCAGATGGACACCACA 59.677 55.000 0.00 0.00 35.80 4.17
687 691 1.299850 CACAGAACGAGTCGGTGCA 60.300 57.895 18.30 0.00 43.94 4.57
714 718 1.338107 ATGTTGACCTGACGGAGACA 58.662 50.000 0.00 0.00 0.00 3.41
888 896 2.751913 CGCCGTACTCTCTGTCGCT 61.752 63.158 0.00 0.00 0.00 4.93
917 925 0.746204 ATCGTGCTCTCGCTCTCTCA 60.746 55.000 0.00 0.00 36.97 3.27
936 945 1.609501 AGCTAGCTTCCCACCGTCA 60.610 57.895 12.68 0.00 0.00 4.35
938 947 1.913762 ACAGCTAGCTTCCCACCGT 60.914 57.895 16.46 5.02 0.00 4.83
968 1064 1.079405 GAACGGGATCTCAACGCCA 60.079 57.895 0.00 0.00 0.00 5.69
1098 1223 0.602905 GTGTGTGAGAAACCCTCCGG 60.603 60.000 0.00 0.00 41.25 5.14
1245 1370 1.069513 TCGACCCAAAGAAAGAAGCGA 59.930 47.619 0.00 0.00 0.00 4.93
1246 1371 1.508632 TCGACCCAAAGAAAGAAGCG 58.491 50.000 0.00 0.00 0.00 4.68
1329 1454 2.203480 GCCACTGCAGTTTGGGGA 60.203 61.111 18.94 0.00 37.47 4.81
1385 1510 1.201181 CTAGCTCTCTGTCAGTGCGTT 59.799 52.381 0.00 0.00 44.91 4.84
1687 1814 8.571336 TCCTTGATCAAAAGTTTCTGAATTCTC 58.429 33.333 9.88 0.00 0.00 2.87
1711 1838 5.924825 GGAATGATTCATTAGCTGCATTTCC 59.075 40.000 11.79 2.72 33.90 3.13
1730 1857 4.931002 CCTTAATTGTTTGGCTGTGGAATG 59.069 41.667 0.00 0.00 0.00 2.67
1946 2245 2.607499 TGTGCATTTTCCACCCTTCAT 58.393 42.857 0.00 0.00 32.30 2.57
2177 2479 2.604139 CCCTAAACACCACAAACCCAT 58.396 47.619 0.00 0.00 0.00 4.00
2236 2538 8.570038 TGTATACATTTCTTCCCTACCCATTA 57.430 34.615 0.08 0.00 0.00 1.90
2237 2539 7.460214 TGTATACATTTCTTCCCTACCCATT 57.540 36.000 0.08 0.00 0.00 3.16
2447 2754 7.835634 TGCAAATTTATTCCGTTTAAATCCC 57.164 32.000 0.00 0.00 30.79 3.85
2507 2815 1.925972 GAGGGGGTGAGAAGCCCTT 60.926 63.158 12.46 5.11 45.39 3.95


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

AutoCloner maintained by Alex Coulton.