Multiple sequence alignment - TraesCS2B01G062400

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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 TraesCS2B01G062400 chr2B 100.000 2640 0 0 1 2640 29754553 29751914 0 4876
1 TraesCS2B01G062400 chr2B 91.632 1936 122 24 1 1926 47387771 47385866 0 2641
2 TraesCS2B01G062400 chr2B 89.945 1452 86 39 536 1983 717652611 717654006 0 1818
3 TraesCS2B01G062400 chr4B 94.197 2654 117 19 1 2640 74251922 74254552 0 4013
4 TraesCS2B01G062400 chr5B 95.484 2148 73 13 1 2126 428831273 428833418 0 3408
5 TraesCS2B01G062400 chr5B 97.440 1953 49 1 1 1952 428825822 428827774 0 3328
6 TraesCS2B01G062400 chr5B 94.045 2032 97 16 1 2022 548566789 548564772 0 3061
7 TraesCS2B01G062400 chr5B 93.506 693 38 7 1950 2640 428833445 428834132 0 1024
8 TraesCS2B01G062400 chr5B 92.208 693 44 6 1950 2640 530938829 530938145 0 972
9 TraesCS2B01G062400 chr7B 97.479 1983 49 1 1 1982 27326590 27328572 0 3384
10 TraesCS2B01G062400 chr7B 91.592 2010 111 38 1 1983 235458118 235456140 0 2723
11 TraesCS2B01G062400 chr7B 91.066 694 51 6 1950 2640 130335963 130336648 0 928
12 TraesCS2B01G062400 chr7B 90.674 697 51 6 1950 2640 235456091 235455403 0 915
13 TraesCS2B01G062400 chr6B 93.169 2108 114 15 1 2105 687514423 687512343 0 3068
14 TraesCS2B01G062400 chr6B 91.847 1987 109 33 1 1983 114144817 114142880 0 2723
15 TraesCS2B01G062400 chr6B 94.225 1749 89 8 1 1746 661051621 661053360 0 2660
16 TraesCS2B01G062400 chr6B 90.490 694 54 5 1950 2640 650644659 650643975 0 905
17 TraesCS2B01G062400 chr6A 93.490 1782 101 10 1 1779 74992217 74990448 0 2634
18 TraesCS2B01G062400 chr1B 89.731 1451 91 38 536 1983 550439539 550438144 0 1801
19 TraesCS2B01G062400 chr1B 91.342 693 50 6 1950 2640 550438095 550437411 0 939
20 TraesCS2B01G062400 chr1B 91.198 693 51 6 1950 2640 357900099 357899415 0 933
21 TraesCS2B01G062400 chr3B 91.631 693 41 8 1950 2640 16122419 16121742 0 942
22 TraesCS2B01G062400 chrUn 90.778 694 51 7 1950 2640 17580581 17581264 0 915


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 TraesCS2B01G062400 chr2B 29751914 29754553 2639 True 4876.000000 4876 100.000000 1 2640 1 chr2B.!!$R1 2639
1 TraesCS2B01G062400 chr2B 47385866 47387771 1905 True 2641.000000 2641 91.632000 1 1926 1 chr2B.!!$R2 1925
2 TraesCS2B01G062400 chr2B 717652611 717654006 1395 False 1818.000000 1818 89.945000 536 1983 1 chr2B.!!$F1 1447
3 TraesCS2B01G062400 chr4B 74251922 74254552 2630 False 4013.000000 4013 94.197000 1 2640 1 chr4B.!!$F1 2639
4 TraesCS2B01G062400 chr5B 548564772 548566789 2017 True 3061.000000 3061 94.045000 1 2022 1 chr5B.!!$R2 2021
5 TraesCS2B01G062400 chr5B 428825822 428834132 8310 False 2586.666667 3408 95.476667 1 2640 3 chr5B.!!$F1 2639
6 TraesCS2B01G062400 chr5B 530938145 530938829 684 True 972.000000 972 92.208000 1950 2640 1 chr5B.!!$R1 690
7 TraesCS2B01G062400 chr7B 27326590 27328572 1982 False 3384.000000 3384 97.479000 1 1982 1 chr7B.!!$F1 1981
8 TraesCS2B01G062400 chr7B 235455403 235458118 2715 True 1819.000000 2723 91.133000 1 2640 2 chr7B.!!$R1 2639
9 TraesCS2B01G062400 chr7B 130335963 130336648 685 False 928.000000 928 91.066000 1950 2640 1 chr7B.!!$F2 690
10 TraesCS2B01G062400 chr6B 687512343 687514423 2080 True 3068.000000 3068 93.169000 1 2105 1 chr6B.!!$R3 2104
11 TraesCS2B01G062400 chr6B 114142880 114144817 1937 True 2723.000000 2723 91.847000 1 1983 1 chr6B.!!$R1 1982
12 TraesCS2B01G062400 chr6B 661051621 661053360 1739 False 2660.000000 2660 94.225000 1 1746 1 chr6B.!!$F1 1745
13 TraesCS2B01G062400 chr6B 650643975 650644659 684 True 905.000000 905 90.490000 1950 2640 1 chr6B.!!$R2 690
14 TraesCS2B01G062400 chr6A 74990448 74992217 1769 True 2634.000000 2634 93.490000 1 1779 1 chr6A.!!$R1 1778
15 TraesCS2B01G062400 chr1B 550437411 550439539 2128 True 1370.000000 1801 90.536500 536 2640 2 chr1B.!!$R2 2104
16 TraesCS2B01G062400 chr1B 357899415 357900099 684 True 933.000000 933 91.198000 1950 2640 1 chr1B.!!$R1 690
17 TraesCS2B01G062400 chr3B 16121742 16122419 677 True 942.000000 942 91.631000 1950 2640 1 chr3B.!!$R1 690
18 TraesCS2B01G062400 chrUn 17580581 17581264 683 False 915.000000 915 90.778000 1950 2640 1 chrUn.!!$F1 690

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
753 6301 0.035458 GTGCTAGAGGTGCTTGTGGT 59.965 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 8385 0.327924 TTGGCGTCTGGATGTCCATT 59.672 50.0 1.54 0.0 46.46 3.16 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
66 67 0.877071 CTGCATTTGAGGTGCGTCTT 59.123 50.000 0.00 0.00 45.37 3.01
272 273 0.615331 CAGTGGCCTGAGTACCATGT 59.385 55.000 3.32 0.00 41.50 3.21
393 394 4.588528 ACTGGCATGAAACAATTTGGTAGT 59.411 37.500 0.00 0.00 0.00 2.73
542 543 1.630369 TGAATGAGGTGGAAGAGGTGG 59.370 52.381 0.00 0.00 0.00 4.61
543 544 1.630878 GAATGAGGTGGAAGAGGTGGT 59.369 52.381 0.00 0.00 0.00 4.16
553 554 1.275573 GAAGAGGTGGTAGTGGTGGTC 59.724 57.143 0.00 0.00 0.00 4.02
556 557 0.112995 AGGTGGTAGTGGTGGTCGTA 59.887 55.000 0.00 0.00 0.00 3.43
561 562 1.101331 GTAGTGGTGGTCGTAGAGGG 58.899 60.000 0.00 0.00 36.95 4.30
629 666 2.996621 GTGCTAGAGGTGCTAGTGTTTG 59.003 50.000 0.00 0.00 46.81 2.93
695 822 0.680280 GCTAGAGGTGGTGGTCGAGA 60.680 60.000 0.00 0.00 0.00 4.04
697 824 1.746220 CTAGAGGTGGTGGTCGAGAAG 59.254 57.143 0.00 0.00 0.00 2.85
748 6296 2.175878 CACAAGTGCTAGAGGTGCTT 57.824 50.000 0.00 0.00 0.00 3.91
751 6299 1.802960 CAAGTGCTAGAGGTGCTTGTG 59.197 52.381 0.00 0.00 33.83 3.33
753 6301 0.035458 GTGCTAGAGGTGCTTGTGGT 59.965 55.000 0.00 0.00 0.00 4.16
754 6302 0.321671 TGCTAGAGGTGCTTGTGGTC 59.678 55.000 0.00 0.00 0.00 4.02
755 6303 0.737715 GCTAGAGGTGCTTGTGGTCG 60.738 60.000 0.00 0.00 0.00 4.79
756 6304 0.108615 CTAGAGGTGCTTGTGGTCGG 60.109 60.000 0.00 0.00 0.00 4.79
757 6305 0.541063 TAGAGGTGCTTGTGGTCGGA 60.541 55.000 0.00 0.00 0.00 4.55
761 6399 1.374758 GTGCTTGTGGTCGGAGAGG 60.375 63.158 0.00 0.00 36.95 3.69
1540 7182 1.365368 GCAAAGAGAAGGAGGCTCGC 61.365 60.000 8.69 1.48 37.46 5.03
1629 7271 2.271173 GGGAAAGTGGCCCCGTAG 59.729 66.667 0.00 0.00 39.81 3.51
1677 7319 3.198068 CCGACATCGATGATGGACTTTT 58.802 45.455 31.33 5.71 43.60 2.27
1698 7342 6.698008 TTTGAGACTTTGTGTGTGATGAAT 57.302 33.333 0.00 0.00 0.00 2.57
1799 7475 8.554528 CGAGACTATTTGAGATTATGTGCAAAT 58.445 33.333 0.00 0.00 41.96 2.32
1980 7740 1.675641 AAGGTTCATGGCGTCTGGC 60.676 57.895 0.00 0.00 42.51 4.85
1983 7743 1.078848 GTTCATGGCGTCTGGCTCT 60.079 57.895 0.00 0.00 42.94 4.09
1991 7971 1.371183 CGTCTGGCTCTTCCCACAA 59.629 57.895 0.00 0.00 0.00 3.33
2032 8022 1.069090 TCTGGCTCGTTTTGCTCGT 59.931 52.632 0.00 0.00 0.00 4.18
2050 8041 2.217038 TGCAGGAGACCAGACACCC 61.217 63.158 0.00 0.00 0.00 4.61
2051 8042 2.217038 GCAGGAGACCAGACACCCA 61.217 63.158 0.00 0.00 0.00 4.51
2183 8385 2.889512 ACACCCTGTCTGATGTGTCTA 58.110 47.619 0.00 0.00 37.37 2.59
2228 8430 1.457831 GGCGTCTGGGTCCCTATCT 60.458 63.158 10.00 0.00 0.00 1.98
2243 8445 6.408662 GGTCCCTATCTAGAGAGCATTTTTGT 60.409 42.308 8.96 0.00 30.24 2.83
2323 8526 3.587951 CCCTCTCATCCATTCATCTCCAT 59.412 47.826 0.00 0.00 0.00 3.41
2344 8547 5.279910 CCATCTCTACCCCTCTCATTTCATC 60.280 48.000 0.00 0.00 0.00 2.92
2454 8664 1.463444 GGTTTCACCGTTGGATCTTCG 59.537 52.381 0.00 0.00 0.00 3.79
2543 8753 8.124808 ACTTTTGTGAAAACCCTAGTTTGTTA 57.875 30.769 0.00 0.00 45.54 2.41
2561 8771 8.504005 AGTTTGTTATCTTCGTGGTTTAATGAG 58.496 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 0.830444 ACTGGCACCACCGAGTCTTA 60.830 55.000 0.00 0.00 43.94 2.10
272 273 2.621070 GGTCTGGCCTAATATGAGGGA 58.379 52.381 8.32 0.00 37.06 4.20
542 543 1.101331 CCCTCTACGACCACCACTAC 58.899 60.000 0.00 0.00 0.00 2.73
543 544 0.994247 TCCCTCTACGACCACCACTA 59.006 55.000 0.00 0.00 0.00 2.74
553 554 0.603569 ACACTTGTGCTCCCTCTACG 59.396 55.000 0.10 0.00 0.00 3.51
556 557 0.683973 CTGACACTTGTGCTCCCTCT 59.316 55.000 0.10 0.00 0.00 3.69
561 562 1.506493 CACCTCTGACACTTGTGCTC 58.494 55.000 0.10 0.00 0.00 4.26
617 654 3.258622 ACTCCCTCTACAAACACTAGCAC 59.741 47.826 0.00 0.00 0.00 4.40
623 660 4.989168 CACTTGTACTCCCTCTACAAACAC 59.011 45.833 0.00 0.00 34.46 3.32
629 666 4.525024 TCTAGCACTTGTACTCCCTCTAC 58.475 47.826 0.00 0.00 0.00 2.59
695 822 1.059913 ACCTCTAGCACTTGTGCCTT 58.940 50.000 20.39 7.34 34.90 4.35
697 824 0.674895 CCACCTCTAGCACTTGTGCC 60.675 60.000 20.39 4.86 34.90 5.01
746 6294 0.390472 GCTTCCTCTCCGACCACAAG 60.390 60.000 0.00 0.00 0.00 3.16
748 6296 1.533033 TGCTTCCTCTCCGACCACA 60.533 57.895 0.00 0.00 0.00 4.17
751 6299 0.390472 CTTGTGCTTCCTCTCCGACC 60.390 60.000 0.00 0.00 0.00 4.79
753 6301 0.318441 CACTTGTGCTTCCTCTCCGA 59.682 55.000 0.00 0.00 0.00 4.55
754 6302 1.294659 GCACTTGTGCTTCCTCTCCG 61.295 60.000 17.36 0.00 0.00 4.63
755 6303 0.036022 AGCACTTGTGCTTCCTCTCC 59.964 55.000 20.95 0.00 43.52 3.71
756 6304 2.232452 TCTAGCACTTGTGCTTCCTCTC 59.768 50.000 29.37 0.00 43.52 3.20
757 6305 2.233431 CTCTAGCACTTGTGCTTCCTCT 59.767 50.000 29.37 10.28 43.52 3.69
761 6399 2.072298 CACCTCTAGCACTTGTGCTTC 58.928 52.381 29.37 1.49 43.52 3.86
1364 7005 5.988310 TCTTTTGGTACCTCGTGATCTAA 57.012 39.130 14.36 0.00 0.00 2.10
1540 7182 2.867109 TTCTTGCCCTCTCTTCTTGG 57.133 50.000 0.00 0.00 0.00 3.61
1629 7271 6.128254 GCCTTTTCCATTTGTCTACTGAGTAC 60.128 42.308 0.00 0.00 0.00 2.73
1677 7319 6.095300 ACAAATTCATCACACACAAAGTCTCA 59.905 34.615 0.00 0.00 0.00 3.27
1698 7342 1.798223 CGCAAGGTCTCGAATGACAAA 59.202 47.619 7.08 0.00 38.61 2.83
1799 7475 9.569167 CTAACTAGTCTCGAATGACAAACATAA 57.431 33.333 7.47 0.00 38.38 1.90
1980 7740 0.951040 GCGTCTGGTTGTGGGAAGAG 60.951 60.000 0.00 0.00 0.00 2.85
1983 7743 2.112297 GGCGTCTGGTTGTGGGAA 59.888 61.111 0.00 0.00 0.00 3.97
2032 8022 2.217038 GGGTGTCTGGTCTCCTGCA 61.217 63.158 0.00 0.00 0.00 4.41
2183 8385 0.327924 TTGGCGTCTGGATGTCCATT 59.672 50.000 1.54 0.00 46.46 3.16
2228 8430 9.944376 AACAGATAACTACAAAAATGCTCTCTA 57.056 29.630 0.00 0.00 0.00 2.43
2243 8445 9.914131 CGAATCTTATCCATCAACAGATAACTA 57.086 33.333 0.00 0.00 32.81 2.24
2323 8526 4.227197 GGATGAAATGAGAGGGGTAGAGA 58.773 47.826 0.00 0.00 0.00 3.10
2344 8547 1.417890 GGTGAGAGTGGGTGGATATGG 59.582 57.143 0.00 0.00 0.00 2.74
2454 8664 7.551617 TGATTTACCTTCTAGTTTCGAAATCCC 59.448 37.037 14.69 1.07 33.24 3.85
2543 8753 6.986817 CCTATGACTCATTAAACCACGAAGAT 59.013 38.462 0.00 0.00 0.00 2.40
2561 8771 9.685828 CAAATCTCTTAGTAGCTAACCTATGAC 57.314 37.037 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.