Multiple sequence alignment - TraesCS3D01G220200

Loading Multiple Alignment...

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 TraesCS3D01G220200 chr3D 100.000 4013 0 0 1 4013 300572976 300568964 0.000000e+00 7411
1 TraesCS3D01G220200 chr3B 95.928 3315 90 8 735 4013 420872263 420875568 0.000000e+00 5332
2 TraesCS3D01G220200 chr3B 91.090 752 63 2 1 752 420797600 420798347 0.000000e+00 1014
3 TraesCS3D01G220200 chr3B 91.317 691 45 2 1 679 659460128 659460815 0.000000e+00 929
4 TraesCS3D01G220200 chr3A 94.198 3292 143 23 743 4013 434840393 434843657 0.000000e+00 4977
5 TraesCS3D01G220200 chr2B 93.523 633 41 0 1 633 90194107 90194739 0.000000e+00 942
6 TraesCS3D01G220200 chr2B 91.474 692 42 3 1 678 790304703 790304015 0.000000e+00 935
7 TraesCS3D01G220200 chr5D 93.207 633 40 1 1 633 413676003 413676632 0.000000e+00 928
8 TraesCS3D01G220200 chr4B 92.891 633 42 1 1 633 610119758 610120387 0.000000e+00 917
9 TraesCS3D01G220200 chr5B 91.001 689 46 5 1 677 387398804 387399488 0.000000e+00 915
10 TraesCS3D01G220200 chr4A 92.733 633 43 1 1 633 652092277 652091648 0.000000e+00 911
11 TraesCS3D01G220200 chr4A 92.744 634 41 3 1 633 724796622 724797251 0.000000e+00 911
12 TraesCS3D01G220200 chr7D 88.715 319 22 4 381 687 577958698 577959014 1.050000e-100 377


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 TraesCS3D01G220200 chr3D 300568964 300572976 4012 True 7411 7411 100.000 1 4013 1 chr3D.!!$R1 4012
1 TraesCS3D01G220200 chr3B 420872263 420875568 3305 False 5332 5332 95.928 735 4013 1 chr3B.!!$F2 3278
2 TraesCS3D01G220200 chr3B 420797600 420798347 747 False 1014 1014 91.090 1 752 1 chr3B.!!$F1 751
3 TraesCS3D01G220200 chr3B 659460128 659460815 687 False 929 929 91.317 1 679 1 chr3B.!!$F3 678
4 TraesCS3D01G220200 chr3A 434840393 434843657 3264 False 4977 4977 94.198 743 4013 1 chr3A.!!$F1 3270
5 TraesCS3D01G220200 chr2B 90194107 90194739 632 False 942 942 93.523 1 633 1 chr2B.!!$F1 632
6 TraesCS3D01G220200 chr2B 790304015 790304703 688 True 935 935 91.474 1 678 1 chr2B.!!$R1 677
7 TraesCS3D01G220200 chr5D 413676003 413676632 629 False 928 928 93.207 1 633 1 chr5D.!!$F1 632
8 TraesCS3D01G220200 chr4B 610119758 610120387 629 False 917 917 92.891 1 633 1 chr4B.!!$F1 632
9 TraesCS3D01G220200 chr5B 387398804 387399488 684 False 915 915 91.001 1 677 1 chr5B.!!$F1 676
10 TraesCS3D01G220200 chr4A 652091648 652092277 629 True 911 911 92.733 1 633 1 chr4A.!!$R1 632
11 TraesCS3D01G220200 chr4A 724796622 724797251 629 False 911 911 92.744 1 633 1 chr4A.!!$F1 632

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
447 451 0.744414 CCGCCATGAAAGACACCGAT 60.744 55.0 0.0 0.0 0.0 4.18 F
1265 1331 0.896940 ACCGCCTTCGTCTGGAACTA 60.897 55.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 1367 0.243365 GAACAACGCCAATGCATCCA 59.757 50.0 0.0 0.0 37.32 3.41 R
3083 3151 2.469274 ACTCTTCTCAGCCATGTGTG 57.531 50.0 0.0 0.0 0.00 3.82 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
39 40 1.804748 GGACCTCCAAAGTAGTTTGCG 59.195 52.381 16.26 10.35 41.64 4.85
74 75 5.817816 CCATAGCCGTTGAAAGAATTAGACT 59.182 40.000 0.00 0.00 0.00 3.24
77 78 4.000988 GCCGTTGAAAGAATTAGACTGGA 58.999 43.478 0.00 0.00 0.00 3.86
88 89 4.558226 ATTAGACTGGAGCAACATGTCA 57.442 40.909 0.00 0.00 0.00 3.58
127 128 1.301716 CAGAACTGACACCCCCACG 60.302 63.158 0.00 0.00 0.00 4.94
418 422 1.807755 CGGAGACACGATGCCATCAAT 60.808 52.381 5.40 0.00 35.47 2.57
446 450 1.375396 CCGCCATGAAAGACACCGA 60.375 57.895 0.00 0.00 0.00 4.69
447 451 0.744414 CCGCCATGAAAGACACCGAT 60.744 55.000 0.00 0.00 0.00 4.18
449 453 1.737838 GCCATGAAAGACACCGATGA 58.262 50.000 0.00 0.00 0.00 2.92
450 454 1.398390 GCCATGAAAGACACCGATGAC 59.602 52.381 0.00 0.00 0.00 3.06
485 489 1.527311 GAGGCAGATTTATTCGTCCGC 59.473 52.381 0.00 0.00 0.00 5.54
546 550 6.834168 ACAAATCCAAAACCTACCTACATG 57.166 37.500 0.00 0.00 0.00 3.21
680 698 2.010544 GCGGCTAGGGTAGGAAAACAC 61.011 57.143 0.00 0.00 0.00 3.32
684 702 2.940083 GCTAGGGTAGGAAAACACAGGC 60.940 54.545 0.00 0.00 0.00 4.85
763 781 7.767745 TGTAGTTTGTATTGTAACAACGACA 57.232 32.000 0.00 0.00 39.02 4.35
906 928 2.760092 ACAAAGGAAAGCAGAAGCACAA 59.240 40.909 0.00 0.00 45.49 3.33
1086 1146 1.819632 CCACCTAGACCAATGCGCC 60.820 63.158 4.18 0.00 0.00 6.53
1265 1331 0.896940 ACCGCCTTCGTCTGGAACTA 60.897 55.000 0.00 0.00 0.00 2.24
1301 1367 4.988598 CAGTTGCGACGCCCCTGT 62.989 66.667 18.69 0.00 0.00 4.00
1592 1658 2.288152 GGACTCTGATGATCTCGGCTTC 60.288 54.545 0.00 0.00 0.00 3.86
1674 1740 1.692519 ACTAAGCCGAACAAGGTCACT 59.307 47.619 0.00 0.00 0.00 3.41
1866 1932 5.532406 TCAGCTCATGCCAATAAGAAATACC 59.468 40.000 0.00 0.00 40.80 2.73
1905 1971 4.125703 TGATTGATGGGTTTGTGCAAAAC 58.874 39.130 13.01 13.01 37.28 2.43
2010 2076 3.632145 TCTTATCGTCATGTGCTCAGCTA 59.368 43.478 0.00 0.00 0.00 3.32
2190 2256 0.904649 TGTCCTGGACAGCTATGGTG 59.095 55.000 25.12 0.00 37.67 4.17
2963 3029 1.748591 GCAAGTAAGAGGGCTGATGGG 60.749 57.143 0.00 0.00 0.00 4.00
3050 3116 9.773328 AAATCATTGTTCGTACTTCATAATGTG 57.227 29.630 0.00 0.00 0.00 3.21
3083 3151 6.128661 TGCGAACACATGATTTGACTAGTAAC 60.129 38.462 0.00 0.00 0.00 2.50
3105 3173 4.118410 CACACATGGCTGAGAAGAGTATC 58.882 47.826 0.00 0.00 0.00 2.24
3201 3269 7.707624 TTCTTGATCATATTTTGGTTGCTCT 57.292 32.000 0.00 0.00 0.00 4.09
3303 3371 8.207545 GGAACTGAGATAAACTTGTCCATATCT 58.792 37.037 0.00 0.00 37.71 1.98
3678 3746 7.640597 TGATTTGATCTCTGATGCATCTTTT 57.359 32.000 26.32 7.91 0.00 2.27
3696 3764 5.055812 TCTTTTGGTTGTCCATGCATTTTC 58.944 37.500 0.00 0.00 43.91 2.29
3729 3797 9.435802 CGTACAATAGTCATAGACAGTACTTTC 57.564 37.037 0.47 0.47 34.60 2.62
3731 3799 8.277490 ACAATAGTCATAGACAGTACTTTCGA 57.723 34.615 3.43 0.00 34.60 3.71
3812 3880 2.549754 AGTTCAAATGCTCGTTGTCCAG 59.450 45.455 0.00 0.00 0.00 3.86
3847 3915 8.589629 GCTTTTCATACTTCATAATGCAAGTTG 58.410 33.333 0.00 0.00 34.60 3.16
3942 4013 7.495901 ACTCCACTGATAAGTTGATATGTGAG 58.504 38.462 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.084546 ACGGCTATGGTTTTGCTTCTC 58.915 47.619 0.00 0.00 0.00 2.87
74 75 1.302431 CCGGTGACATGTTGCTCCA 60.302 57.895 0.00 0.00 0.00 3.86
77 78 0.320771 GAGTCCGGTGACATGTTGCT 60.321 55.000 0.00 0.00 44.33 3.91
286 287 3.476031 CTGTCCCCGTTGCTGTGGT 62.476 63.158 0.00 0.00 0.00 4.16
418 422 4.812476 CATGGCGGCGTCTCGGAA 62.812 66.667 14.51 0.00 0.00 4.30
446 450 0.321671 CAACTCCACTCCCACGTCAT 59.678 55.000 0.00 0.00 0.00 3.06
447 451 0.757561 TCAACTCCACTCCCACGTCA 60.758 55.000 0.00 0.00 0.00 4.35
449 453 1.472662 CCTCAACTCCACTCCCACGT 61.473 60.000 0.00 0.00 0.00 4.49
450 454 1.293498 CCTCAACTCCACTCCCACG 59.707 63.158 0.00 0.00 0.00 4.94
656 674 2.762459 CCTACCCTAGCCGCCACA 60.762 66.667 0.00 0.00 0.00 4.17
658 676 0.910566 TTTTCCTACCCTAGCCGCCA 60.911 55.000 0.00 0.00 0.00 5.69
680 698 4.638865 TGAATGAATCACTCAGATTGCCTG 59.361 41.667 0.00 0.00 46.76 4.85
684 702 9.499585 GTTTACATGAATGAATCACTCAGATTG 57.500 33.333 0.00 0.00 46.76 2.67
763 781 3.499745 GGAGGTATGGAAACCAAACCACT 60.500 47.826 0.00 0.00 42.40 4.00
906 928 3.577667 CGAAATGCACAATGACAATGGT 58.422 40.909 0.00 0.00 0.00 3.55
1265 1331 3.260884 ACTGTTGTACCCTCGAATCATGT 59.739 43.478 0.00 0.00 0.00 3.21
1301 1367 0.243365 GAACAACGCCAATGCATCCA 59.757 50.000 0.00 0.00 37.32 3.41
1455 1521 1.196808 ACGAACACATCCGATGCAAAC 59.803 47.619 8.36 0.00 0.00 2.93
1813 1879 2.583319 CGCGTCCGACATGCATCT 60.583 61.111 0.00 0.00 36.74 2.90
1866 1932 5.459768 TCAATCAACGTGTTCCATGATTTG 58.540 37.500 7.91 5.35 39.74 2.32
1905 1971 1.017387 GTGCTTCCTTATGCTTCCCG 58.983 55.000 0.00 0.00 0.00 5.14
1977 2043 5.816258 ACATGACGATAAGAGACTTACGAGA 59.184 40.000 0.00 6.32 0.00 4.04
2010 2076 3.796111 TCTCCCTTTCTGAAGATCACCT 58.204 45.455 0.00 0.00 34.71 4.00
2190 2256 4.819630 TGAAGTCCTTTCACATAACCACAC 59.180 41.667 0.00 0.00 40.82 3.82
2358 2424 7.067859 AGCCATACGTCTGTTATTACACTCTTA 59.932 37.037 0.00 0.00 0.00 2.10
2369 2435 4.688879 CACTTTCAAGCCATACGTCTGTTA 59.311 41.667 0.00 0.00 0.00 2.41
2963 3029 5.078411 TGATTTCTCTACACCTCTGCTTC 57.922 43.478 0.00 0.00 0.00 3.86
3050 3116 4.864916 ATCATGTGTTCGCATGTAACTC 57.135 40.909 20.67 9.96 44.68 3.01
3058 3124 4.314961 ACTAGTCAAATCATGTGTTCGCA 58.685 39.130 0.00 0.00 0.00 5.10
3083 3151 2.469274 ACTCTTCTCAGCCATGTGTG 57.531 50.000 0.00 0.00 0.00 3.82
3201 3269 3.421919 TCATTCATTCAGTGCTGACCA 57.578 42.857 0.79 0.00 39.66 4.02
3419 3487 6.531439 CCGCAACTTCAACTATGTACTTAAC 58.469 40.000 0.00 0.00 0.00 2.01
3423 3491 3.000727 GCCGCAACTTCAACTATGTACT 58.999 45.455 0.00 0.00 0.00 2.73
3696 3764 9.122613 CTGTCTATGACTATTGTACGATTCATG 57.877 37.037 16.06 9.16 33.15 3.07
3729 3797 6.311723 ACTGCGGTGACTTTTTAATAAATCG 58.688 36.000 0.00 0.00 0.00 3.34
3731 3799 7.430441 ACAACTGCGGTGACTTTTTAATAAAT 58.570 30.769 0.00 0.00 0.00 1.40
3812 3880 7.644986 ATGAAGTATGAAAAGCGTCTATAGC 57.355 36.000 0.00 0.00 0.00 2.97
3857 3925 8.648557 TGTATGACTTACTAGTGAAATCATGC 57.351 34.615 17.73 16.90 33.84 4.06
3942 4013 8.276252 TGAACTACCAAATTAGGAGCAATAAC 57.724 34.615 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.