Multiple sequence alignment - TraesCS6B01G031100

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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 TraesCS6B01G031100 chr6B 100.000 2654 0 0 1 2654 18454337 18451684 0.000000e+00 4902
1 TraesCS6B01G031100 chr6B 88.304 684 70 2 945 1627 18837252 18837926 0.000000e+00 811
2 TraesCS6B01G031100 chr6B 87.988 666 66 2 910 1562 18639039 18638375 0.000000e+00 774
3 TraesCS6B01G031100 chr6B 86.050 724 71 6 910 1626 18770709 18771409 0.000000e+00 750
4 TraesCS6B01G031100 chr6B 83.887 782 98 21 845 1624 9932493 9933248 0.000000e+00 721
5 TraesCS6B01G031100 chr7B 99.318 1027 7 0 1628 2654 99794902 99795928 0.000000e+00 1858
6 TraesCS6B01G031100 chr7B 99.124 1027 9 0 1628 2654 125246954 125247980 0.000000e+00 1847
7 TraesCS6B01G031100 chr7B 98.929 1027 11 0 1628 2654 125283009 125284035 0.000000e+00 1836
8 TraesCS6B01G031100 chr7B 98.637 1027 14 0 1628 2654 125316890 125317916 0.000000e+00 1820
9 TraesCS6B01G031100 chr5A 99.124 1027 7 1 1628 2654 698855913 698856937 0.000000e+00 1845
10 TraesCS6B01G031100 chr3A 98.929 1027 11 0 1628 2654 738332037 738333063 0.000000e+00 1836
11 TraesCS6B01G031100 chr3A 98.637 1027 13 1 1628 2654 691767354 691768379 0.000000e+00 1818
12 TraesCS6B01G031100 chrUn 98.637 1027 14 0 1628 2654 360479091 360478065 0.000000e+00 1820
13 TraesCS6B01G031100 chrUn 91.033 658 51 7 973 1627 71129792 71129140 0.000000e+00 881
14 TraesCS6B01G031100 chr4B 98.637 1027 11 1 1628 2654 30593705 30592682 0.000000e+00 1816
15 TraesCS6B01G031100 chr6A 88.839 896 90 6 733 1625 11648822 11649710 0.000000e+00 1092
16 TraesCS6B01G031100 chr6A 91.161 758 41 8 1 733 11630469 11631225 0.000000e+00 1005
17 TraesCS6B01G031100 chr6A 87.201 836 77 9 733 1545 11700808 11701636 0.000000e+00 924
18 TraesCS6B01G031100 chr6D 90.885 768 41 14 1 741 10296553 10297318 0.000000e+00 1003
19 TraesCS6B01G031100 chr6D 86.942 919 88 10 733 1627 10302181 10303091 0.000000e+00 1003
20 TraesCS6B01G031100 chr6D 85.610 549 73 5 1083 1627 9932682 9932136 2.960000e-159 571
21 TraesCS6B01G031100 chr3D 82.280 886 99 17 1 840 608397729 608398602 0.000000e+00 713
22 TraesCS6B01G031100 chr1A 78.750 640 67 27 134 725 13176163 13175545 5.400000e-97 364


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 TraesCS6B01G031100 chr6B 18451684 18454337 2653 True 4902 4902 100.000 1 2654 1 chr6B.!!$R1 2653
1 TraesCS6B01G031100 chr6B 18837252 18837926 674 False 811 811 88.304 945 1627 1 chr6B.!!$F3 682
2 TraesCS6B01G031100 chr6B 18638375 18639039 664 True 774 774 87.988 910 1562 1 chr6B.!!$R2 652
3 TraesCS6B01G031100 chr6B 18770709 18771409 700 False 750 750 86.050 910 1626 1 chr6B.!!$F2 716
4 TraesCS6B01G031100 chr6B 9932493 9933248 755 False 721 721 83.887 845 1624 1 chr6B.!!$F1 779
5 TraesCS6B01G031100 chr7B 99794902 99795928 1026 False 1858 1858 99.318 1628 2654 1 chr7B.!!$F1 1026
6 TraesCS6B01G031100 chr7B 125246954 125247980 1026 False 1847 1847 99.124 1628 2654 1 chr7B.!!$F2 1026
7 TraesCS6B01G031100 chr7B 125283009 125284035 1026 False 1836 1836 98.929 1628 2654 1 chr7B.!!$F3 1026
8 TraesCS6B01G031100 chr7B 125316890 125317916 1026 False 1820 1820 98.637 1628 2654 1 chr7B.!!$F4 1026
9 TraesCS6B01G031100 chr5A 698855913 698856937 1024 False 1845 1845 99.124 1628 2654 1 chr5A.!!$F1 1026
10 TraesCS6B01G031100 chr3A 738332037 738333063 1026 False 1836 1836 98.929 1628 2654 1 chr3A.!!$F2 1026
11 TraesCS6B01G031100 chr3A 691767354 691768379 1025 False 1818 1818 98.637 1628 2654 1 chr3A.!!$F1 1026
12 TraesCS6B01G031100 chrUn 360478065 360479091 1026 True 1820 1820 98.637 1628 2654 1 chrUn.!!$R2 1026
13 TraesCS6B01G031100 chrUn 71129140 71129792 652 True 881 881 91.033 973 1627 1 chrUn.!!$R1 654
14 TraesCS6B01G031100 chr4B 30592682 30593705 1023 True 1816 1816 98.637 1628 2654 1 chr4B.!!$R1 1026
15 TraesCS6B01G031100 chr6A 11648822 11649710 888 False 1092 1092 88.839 733 1625 1 chr6A.!!$F2 892
16 TraesCS6B01G031100 chr6A 11630469 11631225 756 False 1005 1005 91.161 1 733 1 chr6A.!!$F1 732
17 TraesCS6B01G031100 chr6A 11700808 11701636 828 False 924 924 87.201 733 1545 1 chr6A.!!$F3 812
18 TraesCS6B01G031100 chr6D 10296553 10297318 765 False 1003 1003 90.885 1 741 1 chr6D.!!$F1 740
19 TraesCS6B01G031100 chr6D 10302181 10303091 910 False 1003 1003 86.942 733 1627 1 chr6D.!!$F2 894
20 TraesCS6B01G031100 chr6D 9932136 9932682 546 True 571 571 85.610 1083 1627 1 chr6D.!!$R1 544
21 TraesCS6B01G031100 chr3D 608397729 608398602 873 False 713 713 82.280 1 840 1 chr3D.!!$F1 839
22 TraesCS6B01G031100 chr1A 13175545 13176163 618 True 364 364 78.750 134 725 1 chr1A.!!$R1 591

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
535 586 0.099968 CCAACGCTGCAATGATCCTG 59.900 55.0 0.0 0.0 0.0 3.86 F
582 635 0.674581 CTTCAGAGGCATTGACGGCA 60.675 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1603 1726 1.832912 GGAAGATGACCCCGAGCAT 59.167 57.895 0.0 0.0 0.0 3.79 R
2151 2274 3.896888 TCAACATGACCCTGCTGAAATTT 59.103 39.130 0.0 0.0 0.0 1.82 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
40 41 1.477553 ACTTTGGGATCGCATGCATT 58.522 45.000 19.57 3.40 0.00 3.56
116 118 1.470098 GCTGAATGTACTGGCCAACTG 59.530 52.381 7.01 0.00 0.00 3.16
130 132 2.101582 GCCAACTGTCGAGAGGATATGT 59.898 50.000 14.79 0.00 0.00 2.29
136 138 3.576118 CTGTCGAGAGGATATGTGGGATT 59.424 47.826 0.62 0.00 0.00 3.01
317 337 5.835819 TGAAGGAGGAAGGTCTAGTCATATG 59.164 44.000 0.00 0.00 0.00 1.78
402 424 1.526887 GATGGGGCATTCTCCACGA 59.473 57.895 0.00 0.00 35.67 4.35
445 467 0.617413 ATGGTTCTGAGGAGGCACTG 59.383 55.000 0.00 0.00 41.55 3.66
455 477 1.571460 GAGGCACTGTGAAAGCGTG 59.429 57.895 12.86 0.00 41.55 5.34
510 552 5.987347 AGAATTGCATGCAATAATGTAAGGC 59.013 36.000 38.60 21.02 44.86 4.35
535 586 0.099968 CCAACGCTGCAATGATCCTG 59.900 55.000 0.00 0.00 0.00 3.86
548 601 7.062322 TGCAATGATCCTGTTATAGTCCAATT 58.938 34.615 0.00 0.00 0.00 2.32
566 619 4.934602 CCAATTGGACTCTTCAGACTCTTC 59.065 45.833 20.50 0.00 37.39 2.87
567 620 5.512060 CCAATTGGACTCTTCAGACTCTTCA 60.512 44.000 20.50 0.00 37.39 3.02
582 635 0.674581 CTTCAGAGGCATTGACGGCA 60.675 55.000 0.00 0.00 0.00 5.69
617 670 4.675976 ATTTAACCCGGTCGACATATGA 57.324 40.909 18.91 0.00 0.00 2.15
618 671 4.468765 TTTAACCCGGTCGACATATGAA 57.531 40.909 18.91 0.94 0.00 2.57
697 750 5.590530 AATTAAGCGTGGGCAAAATATGA 57.409 34.783 0.00 0.00 43.41 2.15
712 765 4.955811 AATATGATAGCAGGTCGGTTGA 57.044 40.909 0.00 0.00 0.00 3.18
752 808 6.496144 TGAGAGTACTACTGTATGGCTAGA 57.504 41.667 0.00 0.00 0.00 2.43
763 819 5.222442 ACTGTATGGCTAGATAGAGGTCCAT 60.222 44.000 0.00 0.00 37.92 3.41
775 831 1.272490 GAGGTCCATCGTGTGTGAAGA 59.728 52.381 0.00 0.00 0.00 2.87
822 878 8.488651 AACCCTATTCACGTAGAATAAAACTG 57.511 34.615 16.10 8.32 45.87 3.16
897 992 4.087182 GAGGGTATCCGAGATGGTCATTA 58.913 47.826 0.00 0.00 39.52 1.90
898 993 4.489737 AGGGTATCCGAGATGGTCATTAA 58.510 43.478 0.00 0.00 39.52 1.40
942 1037 3.112075 CCGCACGCACGACAGATT 61.112 61.111 0.00 0.00 34.06 2.40
943 1038 1.803922 CCGCACGCACGACAGATTA 60.804 57.895 0.00 0.00 34.06 1.75
954 1049 4.326205 CACGACAGATTAAGTTGCGATTG 58.674 43.478 0.00 0.00 0.00 2.67
997 1096 3.551496 CTGCCTGCGGAGGGTTTCA 62.551 63.158 25.56 12.72 40.19 2.69
1212 1333 2.893398 GGTCTCACCTTCCGCGAT 59.107 61.111 8.23 0.00 34.73 4.58
1293 1414 2.034685 CCTTCTTGACGTCTGTCTCACA 59.965 50.000 17.92 0.00 45.70 3.58
1533 1656 0.744414 GCTGCGAATTCCCTGCACTA 60.744 55.000 14.86 0.00 34.42 2.74
1724 1847 1.207329 ACCGGAGAGAAAAGGAATCGG 59.793 52.381 9.46 0.00 41.65 4.18
2171 2294 6.418057 TTTAAATTTCAGCAGGGTCATGTT 57.582 33.333 0.00 0.00 0.00 2.71
2493 2616 7.942341 TGAGGAACAAGTTAGTGTGGATATTTT 59.058 33.333 0.00 0.00 0.00 1.82
2546 2669 4.161565 ACAAAGCGAGGGACATATTAGTGA 59.838 41.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 118 3.862642 GCAATCCCACATATCCTCTCGAC 60.863 52.174 0.00 0.00 0.00 4.20
130 132 1.744522 CAACATGATGACGCAATCCCA 59.255 47.619 0.00 0.00 0.00 4.37
136 138 3.080319 TCCAAATCAACATGATGACGCA 58.920 40.909 7.94 0.00 37.15 5.24
263 279 8.543774 GCATCTTCCCCTTAATGATATCTTCTA 58.456 37.037 3.98 0.00 0.00 2.10
317 337 1.608283 GCCAGGTTACCACACTCTCAC 60.608 57.143 3.51 0.00 0.00 3.51
402 424 3.958147 CTGCCGCTGTTCCATCCGT 62.958 63.158 0.00 0.00 0.00 4.69
444 466 3.114809 CAGCAAAAATCACGCTTTCACA 58.885 40.909 0.00 0.00 32.48 3.58
445 467 2.097250 GCAGCAAAAATCACGCTTTCAC 60.097 45.455 0.00 0.00 32.48 3.18
501 543 1.530323 GTTGGACCGTGCCTTACATT 58.470 50.000 0.00 0.00 0.00 2.71
510 552 2.616330 ATTGCAGCGTTGGACCGTG 61.616 57.895 0.16 0.00 0.00 4.94
548 601 4.078537 CTCTGAAGAGTCTGAAGAGTCCA 58.921 47.826 18.24 3.53 43.73 4.02
566 619 2.485677 ATTGCCGTCAATGCCTCTG 58.514 52.632 0.00 0.00 41.12 3.35
582 635 4.014406 GGGTTAAATTGTCTCCGGTCATT 58.986 43.478 0.00 0.00 0.00 2.57
617 670 3.159213 TCATCTCAGCCACCAAATGTT 57.841 42.857 0.00 0.00 0.00 2.71
618 671 2.885135 TCATCTCAGCCACCAAATGT 57.115 45.000 0.00 0.00 0.00 2.71
697 750 4.755266 ATAAAGTCAACCGACCTGCTAT 57.245 40.909 0.00 0.00 43.73 2.97
752 808 2.735151 TCACACACGATGGACCTCTAT 58.265 47.619 0.00 0.00 0.00 1.98
763 819 2.095213 GCACAAGTTTCTTCACACACGA 59.905 45.455 0.00 0.00 0.00 4.35
775 831 6.273071 GTTACAATTGAAGAGGCACAAGTTT 58.727 36.000 13.59 0.00 0.00 2.66
822 878 9.010366 GTTTCATTCTTTTTGCGAGGATAATAC 57.990 33.333 0.00 0.00 0.00 1.89
897 992 1.618343 CAATTTCCAAAGCCCGGACTT 59.382 47.619 0.73 0.00 30.29 3.01
898 993 1.256812 CAATTTCCAAAGCCCGGACT 58.743 50.000 0.73 0.00 30.29 3.85
942 1037 2.156891 GCGTCAAGACAATCGCAACTTA 59.843 45.455 0.00 0.00 46.40 2.24
943 1038 1.069906 GCGTCAAGACAATCGCAACTT 60.070 47.619 0.00 0.00 46.40 2.66
954 1049 3.173240 GCTCCGTCGCGTCAAGAC 61.173 66.667 5.77 0.00 35.41 3.01
997 1096 2.548920 GCCTCGATCGGAAATCCATCTT 60.549 50.000 16.41 0.00 35.14 2.40
1293 1414 1.071471 CGCCTCCAACACACTCCTT 59.929 57.895 0.00 0.00 0.00 3.36
1522 1645 1.902508 CAACCTCTCTAGTGCAGGGAA 59.097 52.381 12.13 0.00 31.61 3.97
1603 1726 1.832912 GGAAGATGACCCCGAGCAT 59.167 57.895 0.00 0.00 0.00 3.79
1724 1847 7.657336 TCCAAAGTTACAGAAAATCAATGGAC 58.343 34.615 0.00 0.00 0.00 4.02
2151 2274 3.896888 TCAACATGACCCTGCTGAAATTT 59.103 39.130 0.00 0.00 0.00 1.82
2171 2294 7.618117 TGGATGTATACTTTCTACCTGAACTCA 59.382 37.037 4.17 0.00 33.88 3.41
2546 2669 4.498493 TCTTCCATTTTAGGCCCCTTTTT 58.502 39.130 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.