Multiple sequence alignment - TraesCS6B01G392300

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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 TraesCS6B01G392300 chr6B 100.000 2549 0 0 1 2549 667350976 667348428 0 4708
1 TraesCS6B01G392300 chr6B 96.497 571 19 1 1 571 456878472 456877903 0 942
2 TraesCS6B01G392300 chr2D 94.500 2000 90 11 567 2548 64508693 64510690 0 3066
3 TraesCS6B01G392300 chr3B 94.162 1987 100 7 574 2548 804661034 804663016 0 3013
4 TraesCS6B01G392300 chr3B 93.373 1992 115 7 574 2548 687040068 687042059 0 2931
5 TraesCS6B01G392300 chr3B 93.029 1994 111 12 574 2547 723101531 723103516 0 2887
6 TraesCS6B01G392300 chr3B 96.510 573 18 1 1 571 39683599 39683027 0 946
7 TraesCS6B01G392300 chr3B 96.497 571 19 1 1 571 122732149 122732718 0 942
8 TraesCS6B01G392300 chr3B 96.497 571 19 1 1 571 142680552 142679983 0 942
9 TraesCS6B01G392300 chr3B 90.821 621 36 9 1942 2549 474241629 474241017 0 811
10 TraesCS6B01G392300 chrUn 93.553 2001 105 12 570 2548 60558709 60560707 0 2959
11 TraesCS6B01G392300 chrUn 88.902 847 32 16 1717 2548 368601967 368602766 0 987
12 TraesCS6B01G392300 chr4B 93.700 1984 110 7 574 2542 645967794 645965811 0 2957
13 TraesCS6B01G392300 chr4B 92.703 1987 104 19 574 2549 534922949 534920993 0 2828
14 TraesCS6B01G392300 chr4B 96.497 571 19 1 1 571 124888397 124888966 0 942
15 TraesCS6B01G392300 chr4B 96.497 571 18 2 1 571 139969370 139969938 0 942
16 TraesCS6B01G392300 chr4B 96.322 571 21 0 1 571 593903190 593902620 0 939
17 TraesCS6B01G392300 chr5B 93.574 1992 109 10 574 2549 26059376 26057388 0 2952
18 TraesCS6B01G392300 chr1B 93.474 1992 112 9 574 2548 542264942 542266932 0 2942
19 TraesCS6B01G392300 chr1B 96.673 571 17 2 1 571 36325565 36324997 0 948
20 TraesCS6B01G392300 chr1B 96.667 570 19 0 1 570 653107082 653106513 0 948
21 TraesCS6B01G392300 chr2B 93.320 1991 107 9 574 2546 666075771 666073789 0 2916
22 TraesCS6B01G392300 chr7B 91.182 2030 126 29 567 2548 22313608 22315632 0 2708
23 TraesCS6B01G392300 chr7B 92.246 619 30 6 1942 2549 708941707 708941096 0 861
24 TraesCS6B01G392300 chr3D 88.902 847 32 16 1717 2548 17559484 17560283 0 987
25 TraesCS6B01G392300 chr3D 88.902 847 32 16 1717 2548 17577437 17576638 0 987
26 TraesCS6B01G392300 chr5A 89.207 769 31 12 1791 2548 589653697 589652970 0 913


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 TraesCS6B01G392300 chr6B 667348428 667350976 2548 True 4708 4708 100.000 1 2549 1 chr6B.!!$R2 2548
1 TraesCS6B01G392300 chr6B 456877903 456878472 569 True 942 942 96.497 1 571 1 chr6B.!!$R1 570
2 TraesCS6B01G392300 chr2D 64508693 64510690 1997 False 3066 3066 94.500 567 2548 1 chr2D.!!$F1 1981
3 TraesCS6B01G392300 chr3B 804661034 804663016 1982 False 3013 3013 94.162 574 2548 1 chr3B.!!$F4 1974
4 TraesCS6B01G392300 chr3B 687040068 687042059 1991 False 2931 2931 93.373 574 2548 1 chr3B.!!$F2 1974
5 TraesCS6B01G392300 chr3B 723101531 723103516 1985 False 2887 2887 93.029 574 2547 1 chr3B.!!$F3 1973
6 TraesCS6B01G392300 chr3B 39683027 39683599 572 True 946 946 96.510 1 571 1 chr3B.!!$R1 570
7 TraesCS6B01G392300 chr3B 122732149 122732718 569 False 942 942 96.497 1 571 1 chr3B.!!$F1 570
8 TraesCS6B01G392300 chr3B 142679983 142680552 569 True 942 942 96.497 1 571 1 chr3B.!!$R2 570
9 TraesCS6B01G392300 chr3B 474241017 474241629 612 True 811 811 90.821 1942 2549 1 chr3B.!!$R3 607
10 TraesCS6B01G392300 chrUn 60558709 60560707 1998 False 2959 2959 93.553 570 2548 1 chrUn.!!$F1 1978
11 TraesCS6B01G392300 chrUn 368601967 368602766 799 False 987 987 88.902 1717 2548 1 chrUn.!!$F2 831
12 TraesCS6B01G392300 chr4B 645965811 645967794 1983 True 2957 2957 93.700 574 2542 1 chr4B.!!$R3 1968
13 TraesCS6B01G392300 chr4B 534920993 534922949 1956 True 2828 2828 92.703 574 2549 1 chr4B.!!$R1 1975
14 TraesCS6B01G392300 chr4B 124888397 124888966 569 False 942 942 96.497 1 571 1 chr4B.!!$F1 570
15 TraesCS6B01G392300 chr4B 139969370 139969938 568 False 942 942 96.497 1 571 1 chr4B.!!$F2 570
16 TraesCS6B01G392300 chr4B 593902620 593903190 570 True 939 939 96.322 1 571 1 chr4B.!!$R2 570
17 TraesCS6B01G392300 chr5B 26057388 26059376 1988 True 2952 2952 93.574 574 2549 1 chr5B.!!$R1 1975
18 TraesCS6B01G392300 chr1B 542264942 542266932 1990 False 2942 2942 93.474 574 2548 1 chr1B.!!$F1 1974
19 TraesCS6B01G392300 chr1B 36324997 36325565 568 True 948 948 96.673 1 571 1 chr1B.!!$R1 570
20 TraesCS6B01G392300 chr1B 653106513 653107082 569 True 948 948 96.667 1 570 1 chr1B.!!$R2 569
21 TraesCS6B01G392300 chr2B 666073789 666075771 1982 True 2916 2916 93.320 574 2546 1 chr2B.!!$R1 1972
22 TraesCS6B01G392300 chr7B 22313608 22315632 2024 False 2708 2708 91.182 567 2548 1 chr7B.!!$F1 1981
23 TraesCS6B01G392300 chr7B 708941096 708941707 611 True 861 861 92.246 1942 2549 1 chr7B.!!$R1 607
24 TraesCS6B01G392300 chr3D 17559484 17560283 799 False 987 987 88.902 1717 2548 1 chr3D.!!$F1 831
25 TraesCS6B01G392300 chr3D 17576638 17577437 799 True 987 987 88.902 1717 2548 1 chr3D.!!$R1 831
26 TraesCS6B01G392300 chr5A 589652970 589653697 727 True 913 913 89.207 1791 2548 1 chr5A.!!$R1 757

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
446 451 0.798776 CTTGGCAGCTAGTTTCACCG 59.201 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2014 0.670239 CCCAGCCGCACCAATTTTTC 60.67 55.0 0.0 0.0 0.0 2.29 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
31 32 4.276642 TCAATATTGTTGCATGGCAGGTA 58.723 39.130 14.97 0.00 40.61 3.08
224 228 3.446442 AGGATTCATGTGTCTTGCCTT 57.554 42.857 0.00 0.00 0.00 4.35
446 451 0.798776 CTTGGCAGCTAGTTTCACCG 59.201 55.000 0.00 0.00 0.00 4.94
572 577 6.316140 TCCAGTCAGTGTGATTACAATAATGC 59.684 38.462 0.00 0.00 38.82 3.56
766 771 5.577164 AGAGACGACCAATTTTATTCAGACG 59.423 40.000 0.00 0.00 0.00 4.18
778 783 3.636043 CAGACGGTTGCACGCGTT 61.636 61.111 10.22 0.00 37.37 4.84
804 809 2.435059 GACCCAACAGAGAGCCGC 60.435 66.667 0.00 0.00 0.00 6.53
858 863 1.293498 GGGTGACAGCGACAGTGAT 59.707 57.895 0.00 0.00 0.00 3.06
859 864 1.016130 GGGTGACAGCGACAGTGATG 61.016 60.000 0.00 0.00 0.00 3.07
1063 1102 2.494445 CGCGTGTGGAGATGCCTA 59.506 61.111 0.00 0.00 37.63 3.93
1152 1191 1.668919 CGTCCGTTCTATGTGTGCAGT 60.669 52.381 0.00 0.00 0.00 4.40
1349 1388 4.988598 CCGAACCGCAGTGGCTGT 62.989 66.667 0.00 0.00 43.94 4.40
1350 1389 3.716006 CGAACCGCAGTGGCTGTG 61.716 66.667 0.00 2.98 43.94 3.66
1397 1436 2.546321 CGAAGCACGCACTGACAC 59.454 61.111 0.00 0.00 34.51 3.67
1401 1440 0.250038 AAGCACGCACTGACACAGAT 60.250 50.000 5.76 0.00 35.18 2.90
1426 1465 2.421424 GCTGTTGAGCTTAGGATGTTGG 59.579 50.000 0.00 0.00 42.52 3.77
1491 1531 4.325972 CCATTTGCAAATACTTTTGGGCT 58.674 39.130 23.69 0.00 42.09 5.19
1522 1562 2.967362 TGGTAATCGCACTGGTTGTAG 58.033 47.619 0.00 0.00 0.00 2.74
1534 1574 4.578516 CACTGGTTGTAGTGTGGAAAATGA 59.421 41.667 0.00 0.00 42.38 2.57
1742 1789 7.342799 AGCTAATGAATTATTCCAGAGCCAAAA 59.657 33.333 14.32 0.00 30.90 2.44
1788 1835 9.627123 TTGGAGCTGTTAAATATTTAGTAGCAT 57.373 29.630 28.57 20.34 36.61 3.79
1965 2014 0.958091 TGAAGGGTGGAAAATGCACG 59.042 50.000 0.00 0.00 39.79 5.34
2025 2074 1.569548 TGGGTTTGTGGTGTTTAGGGA 59.430 47.619 0.00 0.00 0.00 4.20
2040 2089 0.907704 AGGGATGCACTGGTAACCGA 60.908 55.000 0.00 0.00 0.00 4.69
2176 2231 5.046950 AGTGGTTTTCCTTTGTTTTGCACTA 60.047 36.000 0.00 0.00 41.38 2.74
2276 2331 2.293399 GGTTAGAGTGGCACTTGGTTTG 59.707 50.000 22.98 0.00 0.00 2.93
2514 2593 2.060326 TAAGTTCGCGGACAGTTCAG 57.940 50.000 21.79 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.755686 GACATCCTTCATCCGGCTCT 59.244 55.000 0.00 0.0 0.00 4.09
262 266 5.940617 AGATGCATTAGCCATGGTAGTTTA 58.059 37.500 14.67 0.0 41.13 2.01
572 577 5.357032 ACTGAGGGCAAAAGGATAATTAACG 59.643 40.000 0.00 0.0 0.00 3.18
728 733 4.087892 CTCTGCCACCTGGTCCCG 62.088 72.222 0.00 0.0 37.57 5.14
778 783 4.196778 TGTTGGGTCCCGCAAGCA 62.197 61.111 2.65 0.0 36.99 3.91
804 809 1.485838 CGCAACGGCTCTATGCTCAG 61.486 60.000 0.00 0.0 42.39 3.35
843 848 0.387239 CGTCATCACTGTCGCTGTCA 60.387 55.000 0.00 0.0 0.00 3.58
851 856 1.270826 CTCTGTCACCGTCATCACTGT 59.729 52.381 0.00 0.0 0.00 3.55
858 863 1.660355 GTGCTCTCTGTCACCGTCA 59.340 57.895 0.00 0.0 0.00 4.35
859 864 1.442857 CGTGCTCTCTGTCACCGTC 60.443 63.158 0.00 0.0 0.00 4.79
1063 1102 2.341101 ACCGCGGACAGACGAAGAT 61.341 57.895 35.90 0.0 35.47 2.40
1088 1127 1.541310 AACCCTCCGATCAACGCTCA 61.541 55.000 0.00 0.0 41.07 4.26
1152 1191 2.438021 CCCGATTCTTACCCCATTCTCA 59.562 50.000 0.00 0.0 0.00 3.27
1198 1237 2.749076 TCAACCCATTGCTCAAAGATCG 59.251 45.455 0.00 0.0 35.63 3.69
1349 1388 4.069232 CTTCCGGAGCTCGTGCCA 62.069 66.667 3.34 0.0 40.80 4.92
1350 1389 3.296709 TTCTTCCGGAGCTCGTGCC 62.297 63.158 3.34 0.0 40.80 5.01
1426 1465 5.153950 TCAAGCTTCCTAACCTTCTTCTC 57.846 43.478 0.00 0.0 0.00 2.87
1491 1531 5.583061 CAGTGCGATTACCATACCTACAAAA 59.417 40.000 0.00 0.0 0.00 2.44
1522 1562 3.996363 GCCTTTCCATTCATTTTCCACAC 59.004 43.478 0.00 0.0 0.00 3.82
1526 1566 5.088680 TCATGCCTTTCCATTCATTTTCC 57.911 39.130 0.00 0.0 0.00 3.13
1534 1574 5.306160 CCTCCATAATTCATGCCTTTCCATT 59.694 40.000 0.00 0.0 32.84 3.16
1691 1738 8.301730 TGCATTTCATTGATCAAAAGTTTCTC 57.698 30.769 13.09 0.0 0.00 2.87
1936 1983 5.699097 TTTCCACCCTTCATTTTTAGACG 57.301 39.130 0.00 0.0 0.00 4.18
1965 2014 0.670239 CCCAGCCGCACCAATTTTTC 60.670 55.000 0.00 0.0 0.00 2.29
2025 2074 2.394632 TCCTATCGGTTACCAGTGCAT 58.605 47.619 1.13 0.0 0.00 3.96
2040 2089 5.649831 GTCAAACTCTTGCCATCTTTCCTAT 59.350 40.000 0.00 0.0 32.14 2.57
2046 2095 3.508793 CCATGTCAAACTCTTGCCATCTT 59.491 43.478 0.00 0.0 28.75 2.40
2176 2231 4.044308 ACCTTCCAACCCTCCAAAATTTT 58.956 39.130 0.00 0.0 0.00 1.82
2276 2331 8.839343 CATGCAAATTTATTCCCTTTAAATCCC 58.161 33.333 0.00 0.0 30.79 3.85
2484 2548 5.521010 TGTCCGCGAACTTATTATTGTAAGG 59.479 40.000 8.23 0.0 36.27 2.69
2514 2593 2.159627 GTCATGTTTCGTCATGTGTCCC 59.840 50.000 13.87 0.0 43.70 4.46


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

AutoCloner maintained by Alex Coulton.