Multiple sequence alignment - TraesCS3B01G284500

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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 TraesCS3B01G284500 chr3B 100.000 3632 0 0 1 3632 455508428 455512059 0.000000e+00 6708
1 TraesCS3B01G284500 chr3B 98.018 2725 21 7 940 3632 463458549 463455826 0.000000e+00 4702
2 TraesCS3B01G284500 chr1D 96.214 1981 33 8 933 2878 198167115 198169088 0.000000e+00 3205
3 TraesCS3B01G284500 chr1D 96.570 758 20 2 2881 3632 198169132 198169889 0.000000e+00 1251
4 TraesCS3B01G284500 chr1D 89.894 940 89 5 1 937 138395764 138394828 0.000000e+00 1205
5 TraesCS3B01G284500 chr7A 94.874 1229 17 10 933 2121 471814603 471813381 0.000000e+00 1879
6 TraesCS3B01G284500 chr7A 96.266 723 10 3 2160 2878 471813390 471812681 0.000000e+00 1170
7 TraesCS3B01G284500 chr7A 92.647 748 21 7 2881 3623 471812637 471811919 0.000000e+00 1046
8 TraesCS3B01G284500 chr5D 90.628 939 84 4 1 937 241767347 241768283 0.000000e+00 1243
9 TraesCS3B01G284500 chr7D 90.354 933 84 5 8 937 163747606 163748535 0.000000e+00 1219
10 TraesCS3B01G284500 chr7D 90.106 940 87 5 1 937 68616264 68617200 0.000000e+00 1216
11 TraesCS3B01G284500 chr7D 90.302 928 88 2 11 937 421516042 421515116 0.000000e+00 1214
12 TraesCS3B01G284500 chr3D 90.096 939 90 3 1 937 21973515 21974452 0.000000e+00 1216
13 TraesCS3B01G284500 chr3D 90.247 933 86 4 1 930 415272425 415273355 0.000000e+00 1214
14 TraesCS3B01G284500 chr3D 90.032 933 87 5 7 937 81140075 81139147 0.000000e+00 1203
15 TraesCS3B01G284500 chr4D 90.150 934 87 5 8 937 292829893 292830825 0.000000e+00 1210
16 TraesCS3B01G284500 chr6B 82.614 903 116 25 1113 1980 652522678 652521782 0.000000e+00 760
17 TraesCS3B01G284500 chr6A 81.354 960 127 24 1047 1980 578701728 578700795 0.000000e+00 734
18 TraesCS3B01G284500 chr6A 79.663 949 144 26 1072 1980 578926006 578926945 3.960000e-179 638
19 TraesCS3B01G284500 chr6D 82.252 817 108 20 1189 1980 432672610 432671806 0.000000e+00 671
20 TraesCS3B01G284500 chr6D 79.509 937 124 33 1072 1980 432810541 432811437 4.010000e-169 604
21 TraesCS3B01G284500 chr2B 77.615 478 90 12 1267 1737 775770877 775770410 1.280000e-69 274
22 TraesCS3B01G284500 chr7B 79.577 284 56 2 2038 2320 12953014 12953296 6.150000e-48 202


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 TraesCS3B01G284500 chr3B 455508428 455512059 3631 False 6708 6708 100.000000 1 3632 1 chr3B.!!$F1 3631
1 TraesCS3B01G284500 chr3B 463455826 463458549 2723 True 4702 4702 98.018000 940 3632 1 chr3B.!!$R1 2692
2 TraesCS3B01G284500 chr1D 198167115 198169889 2774 False 2228 3205 96.392000 933 3632 2 chr1D.!!$F1 2699
3 TraesCS3B01G284500 chr1D 138394828 138395764 936 True 1205 1205 89.894000 1 937 1 chr1D.!!$R1 936
4 TraesCS3B01G284500 chr7A 471811919 471814603 2684 True 1365 1879 94.595667 933 3623 3 chr7A.!!$R1 2690
5 TraesCS3B01G284500 chr5D 241767347 241768283 936 False 1243 1243 90.628000 1 937 1 chr5D.!!$F1 936
6 TraesCS3B01G284500 chr7D 163747606 163748535 929 False 1219 1219 90.354000 8 937 1 chr7D.!!$F2 929
7 TraesCS3B01G284500 chr7D 68616264 68617200 936 False 1216 1216 90.106000 1 937 1 chr7D.!!$F1 936
8 TraesCS3B01G284500 chr7D 421515116 421516042 926 True 1214 1214 90.302000 11 937 1 chr7D.!!$R1 926
9 TraesCS3B01G284500 chr3D 21973515 21974452 937 False 1216 1216 90.096000 1 937 1 chr3D.!!$F1 936
10 TraesCS3B01G284500 chr3D 415272425 415273355 930 False 1214 1214 90.247000 1 930 1 chr3D.!!$F2 929
11 TraesCS3B01G284500 chr3D 81139147 81140075 928 True 1203 1203 90.032000 7 937 1 chr3D.!!$R1 930
12 TraesCS3B01G284500 chr4D 292829893 292830825 932 False 1210 1210 90.150000 8 937 1 chr4D.!!$F1 929
13 TraesCS3B01G284500 chr6B 652521782 652522678 896 True 760 760 82.614000 1113 1980 1 chr6B.!!$R1 867
14 TraesCS3B01G284500 chr6A 578700795 578701728 933 True 734 734 81.354000 1047 1980 1 chr6A.!!$R1 933
15 TraesCS3B01G284500 chr6A 578926006 578926945 939 False 638 638 79.663000 1072 1980 1 chr6A.!!$F1 908
16 TraesCS3B01G284500 chr6D 432671806 432672610 804 True 671 671 82.252000 1189 1980 1 chr6D.!!$R1 791
17 TraesCS3B01G284500 chr6D 432810541 432811437 896 False 604 604 79.509000 1072 1980 1 chr6D.!!$F1 908

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
856 866 0.108585 TGAGGGCAGAACTGGACAAC 59.891 55.0 3.99 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2879 3008 4.137116 TGCTGGTAATAACTACTGCTGG 57.863 45.455 0.0 0.0 33.86 4.85 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
103 106 3.884774 TCTTTGGGTGCGGCAGGT 61.885 61.111 1.18 0.00 0.00 4.00
119 123 1.750778 CAGGTGCGGCAGGATTTTTAT 59.249 47.619 1.18 0.00 0.00 1.40
162 169 1.390123 CACGACAGCAATTAGTCACGG 59.610 52.381 0.00 0.00 34.48 4.94
180 187 1.886886 GGTGACTCCGCCTGTAAAAA 58.113 50.000 0.00 0.00 39.82 1.94
191 198 2.863809 CCTGTAAAAACCACTGCTCCT 58.136 47.619 0.00 0.00 0.00 3.69
253 262 1.256812 CCAAAAGATTCACCCCGCTT 58.743 50.000 0.00 0.00 0.00 4.68
306 315 1.421382 CATTGCCTTTCAGCCGTTTG 58.579 50.000 0.00 0.00 0.00 2.93
320 329 0.389025 CGTTTGGCCCTCTTTGCTTT 59.611 50.000 0.00 0.00 0.00 3.51
434 443 2.381941 GGAGCTCAGGGCCAAGGAT 61.382 63.158 17.19 0.00 43.05 3.24
466 475 2.094234 GTGAGCTCAAGGAAGAGAGGAC 60.094 54.545 20.19 0.00 37.87 3.85
491 500 0.901827 TGCTCCTCCTTTATGTGCGA 59.098 50.000 0.00 0.00 0.00 5.10
543 552 1.338105 CCACCACAAAGATGCTCGAGA 60.338 52.381 18.75 1.31 0.00 4.04
629 639 2.577059 GGGCCAATCGTGACGAGA 59.423 61.111 14.71 0.00 39.91 4.04
706 716 2.954868 GATGCCTACCGTCGTGCG 60.955 66.667 0.00 0.00 40.95 5.34
798 808 4.163427 TCTGACCTGGTCTTCTTCTTCAT 58.837 43.478 26.03 0.00 33.15 2.57
811 821 9.691362 GTCTTCTTCTTCATCTATATCTCCAAC 57.309 37.037 0.00 0.00 0.00 3.77
813 823 7.220741 TCTTCTTCATCTATATCTCCAACGG 57.779 40.000 0.00 0.00 0.00 4.44
815 825 5.394738 TCTTCATCTATATCTCCAACGGGT 58.605 41.667 0.00 0.00 34.93 5.28
839 849 4.492160 GTCTCCGCGCGATGGTGA 62.492 66.667 34.63 18.64 0.00 4.02
847 857 2.268920 GCGATGGTGAGGGCAGAA 59.731 61.111 0.00 0.00 0.00 3.02
856 866 0.108585 TGAGGGCAGAACTGGACAAC 59.891 55.000 3.99 0.00 0.00 3.32
903 913 2.010582 GCCGAGCGAATCCTCTCAGT 62.011 60.000 0.00 0.00 0.00 3.41
913 923 0.323816 TCCTCTCAGTGCTCCGTCAT 60.324 55.000 0.00 0.00 0.00 3.06
922 932 0.527600 TGCTCCGTCATCGAAATCCG 60.528 55.000 0.00 0.00 39.71 4.18
968 978 2.222886 TCTCAATCCGAGTCGATCTCC 58.777 52.381 15.64 0.00 42.88 3.71
2879 3008 7.396540 ACCAATTTCATTATCCACTTCTGAC 57.603 36.000 0.00 0.00 0.00 3.51
2903 3073 6.126883 ACCAGCAGTAGTTATTACCAGCAATA 60.127 38.462 3.65 0.00 36.68 1.90
2920 3090 6.529477 CCAGCAATATGACTATATGAGTGACG 59.471 42.308 0.00 0.00 39.06 4.35
3250 3422 3.117663 ACATGGCCCCGTCTTAATAATGT 60.118 43.478 0.00 0.00 0.00 2.71
3303 3475 2.365293 ACTGCAGGATATATGTGTCGCA 59.635 45.455 19.93 0.00 0.00 5.10
3505 3678 9.995003 TGACTTGGTTTTCTTTATTTATTGCAT 57.005 25.926 0.00 0.00 0.00 3.96
3618 3797 3.453717 TCTTGCTTCTCATACTCATGGCT 59.546 43.478 0.00 0.00 32.61 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 85 3.670377 GCCGCACCCAAAGACCAC 61.670 66.667 0.00 0.00 0.00 4.16
162 169 1.534163 GGTTTTTACAGGCGGAGTCAC 59.466 52.381 0.00 0.00 0.00 3.67
180 187 1.059098 TCACATCAAGGAGCAGTGGT 58.941 50.000 0.00 0.00 0.00 4.16
191 198 4.035091 CCACTCAACGACTTTTCACATCAA 59.965 41.667 0.00 0.00 0.00 2.57
253 262 2.196229 GGAGGGAGCTAGCCGAGA 59.804 66.667 12.13 0.00 0.00 4.04
306 315 1.458398 GAGAGAAAGCAAAGAGGGCC 58.542 55.000 0.00 0.00 0.00 5.80
311 320 3.424703 CAATGGGGAGAGAAAGCAAAGA 58.575 45.455 0.00 0.00 0.00 2.52
320 329 2.119495 GGTAGAAGCAATGGGGAGAGA 58.881 52.381 0.00 0.00 0.00 3.10
458 467 1.336632 GGAGCATGGCAGTCCTCTCT 61.337 60.000 10.39 0.00 0.00 3.10
466 475 2.228059 CATAAAGGAGGAGCATGGCAG 58.772 52.381 0.00 0.00 0.00 4.85
491 500 4.292977 CTTTTGAAGCTCCGTGAACTTT 57.707 40.909 0.00 0.00 0.00 2.66
577 586 2.441348 TCGCCTGACCGCCTATCA 60.441 61.111 0.00 0.00 0.00 2.15
606 616 2.514592 CACGATTGGCCCGCTCAT 60.515 61.111 0.00 0.00 0.00 2.90
629 639 2.515071 GGCTGAGGCGATCCTGGAT 61.515 63.158 9.42 9.42 44.46 3.41
742 752 0.834261 TGAAGTCGATGGGGTGGTCA 60.834 55.000 0.00 0.00 0.00 4.02
776 786 3.576861 TGAAGAAGAAGACCAGGTCAGA 58.423 45.455 22.31 0.00 34.60 3.27
798 808 3.409570 CTCGACCCGTTGGAGATATAGA 58.590 50.000 0.00 0.00 34.81 1.98
839 849 1.071471 CGTTGTCCAGTTCTGCCCT 59.929 57.895 0.00 0.00 0.00 5.19
847 857 1.450211 CAACCCCTCGTTGTCCAGT 59.550 57.895 0.00 0.00 45.79 4.00
903 913 0.527600 CGGATTTCGATGACGGAGCA 60.528 55.000 0.00 0.00 42.43 4.26
922 932 2.100631 CCACTCCCATCGCACGAAC 61.101 63.158 0.00 0.00 0.00 3.95
930 940 3.200825 TGAGAAGAAATCCCACTCCCATC 59.799 47.826 0.00 0.00 0.00 3.51
968 978 4.394712 GGCCACTGGTCGGACCTG 62.395 72.222 26.67 26.67 42.22 4.00
1409 1477 0.593618 GATCTCGCAGGCATCGTCTA 59.406 55.000 0.00 0.00 0.00 2.59
2879 3008 4.137116 TGCTGGTAATAACTACTGCTGG 57.863 45.455 0.00 0.00 33.86 4.85
3232 3404 3.202829 TCACATTATTAAGACGGGGCC 57.797 47.619 0.00 0.00 0.00 5.80
3250 3422 3.938963 GCAAGGACGATAATCCAACTTCA 59.061 43.478 0.00 0.00 41.73 3.02
3303 3475 9.349713 TGGTCTATGAACACAAGAAAAATTAGT 57.650 29.630 0.00 0.00 0.00 2.24
3505 3678 9.757227 AAATTTCTGTTTTCGATAAAATCACCA 57.243 25.926 0.00 0.00 36.96 4.17


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

AutoCloner maintained by Alex Coulton.