Multiple sequence alignment - TraesCS7B01G189200

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 TraesCS7B01G189200 chr7B 100.000 3590 0 0 1 3590 322492219 322488630 0.000000e+00 6630.0
1 TraesCS7B01G189200 chr7D 96.941 2909 74 10 685 3590 363051738 363048842 0.000000e+00 4865.0
2 TraesCS7B01G189200 chr7D 91.725 713 50 6 1 711 363052444 363051739 0.000000e+00 981.0
3 TraesCS7B01G189200 chr7D 85.135 74 9 2 3509 3582 80739436 80739365 1.380000e-09 75.0
4 TraesCS7B01G189200 chr7A 96.669 2852 74 12 749 3590 394759950 394762790 0.000000e+00 4721.0
5 TraesCS7B01G189200 chr7A 83.529 85 11 3 3508 3590 127450809 127450726 3.840000e-10 76.8
6 TraesCS7B01G189200 chr2D 89.005 764 78 5 1 763 587269834 587269076 0.000000e+00 941.0
7 TraesCS7B01G189200 chr2D 87.160 771 88 9 1 768 479318829 479318067 0.000000e+00 865.0
8 TraesCS7B01G189200 chr3B 88.621 747 77 7 2 746 182466500 182467240 0.000000e+00 902.0
9 TraesCS7B01G189200 chr5D 87.792 770 88 5 1 768 458001337 458000572 0.000000e+00 896.0
10 TraesCS7B01G189200 chr5D 87.834 748 84 6 1 747 56803182 56803923 0.000000e+00 870.0
11 TraesCS7B01G189200 chr5D 100.000 32 0 0 3509 3540 241960244 241960213 3.870000e-05 60.2
12 TraesCS7B01G189200 chr6D 86.750 800 99 6 1 798 311598974 311598180 0.000000e+00 883.0
13 TraesCS7B01G189200 chr6D 86.573 782 100 3 1 782 93632303 93633079 0.000000e+00 857.0
14 TraesCS7B01G189200 chr4D 87.270 762 87 7 9 769 447929259 447930011 0.000000e+00 861.0
15 TraesCS7B01G189200 chr4D 83.529 85 9 5 3509 3590 363683969 363683887 1.380000e-09 75.0
16 TraesCS7B01G189200 chrUn 96.503 429 6 4 2674 3102 476912478 476912897 0.000000e+00 701.0
17 TraesCS7B01G189200 chr3A 92.857 70 5 0 3521 3590 749277817 749277886 6.340000e-18 102.0
18 TraesCS7B01G189200 chr2B 87.805 82 8 2 3509 3590 688373121 688373042 1.060000e-15 95.3
19 TraesCS7B01G189200 chr4A 83.133 83 13 1 3509 3590 101743396 101743478 1.380000e-09 75.0


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 TraesCS7B01G189200 chr7B 322488630 322492219 3589 True 6630 6630 100.000 1 3590 1 chr7B.!!$R1 3589
1 TraesCS7B01G189200 chr7D 363048842 363052444 3602 True 2923 4865 94.333 1 3590 2 chr7D.!!$R2 3589
2 TraesCS7B01G189200 chr7A 394759950 394762790 2840 False 4721 4721 96.669 749 3590 1 chr7A.!!$F1 2841
3 TraesCS7B01G189200 chr2D 587269076 587269834 758 True 941 941 89.005 1 763 1 chr2D.!!$R2 762
4 TraesCS7B01G189200 chr2D 479318067 479318829 762 True 865 865 87.160 1 768 1 chr2D.!!$R1 767
5 TraesCS7B01G189200 chr3B 182466500 182467240 740 False 902 902 88.621 2 746 1 chr3B.!!$F1 744
6 TraesCS7B01G189200 chr5D 458000572 458001337 765 True 896 896 87.792 1 768 1 chr5D.!!$R2 767
7 TraesCS7B01G189200 chr5D 56803182 56803923 741 False 870 870 87.834 1 747 1 chr5D.!!$F1 746
8 TraesCS7B01G189200 chr6D 311598180 311598974 794 True 883 883 86.750 1 798 1 chr6D.!!$R1 797
9 TraesCS7B01G189200 chr6D 93632303 93633079 776 False 857 857 86.573 1 782 1 chr6D.!!$F1 781
10 TraesCS7B01G189200 chr4D 447929259 447930011 752 False 861 861 87.270 9 769 1 chr4D.!!$F1 760

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
357 362 0.394565 CAATGGGATCCGGAGACCTC 59.605 60.0 23.24 10.94 0.0 3.85 F
543 548 0.790207 CGACATTGACCAACTCACGG 59.210 55.0 0.00 0.00 0.0 4.94 F
1225 1269 0.179111 CGCTTCCTTCCACGCTCATA 60.179 55.0 0.00 0.00 0.0 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1225 1269 0.399233 AGGAGGCCTAGGCGAAGAAT 60.399 55.000 27.24 8.68 43.06 2.40 R
1915 1960 1.558756 CAGAGACCCCATGAAGCTCTT 59.441 52.381 0.00 0.00 33.94 2.85 R
3175 3220 0.037326 TAGTGGTGAAAGCCTCGCAG 60.037 55.000 0.00 0.00 36.17 5.18 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
42 43 4.257731 TGACACGCTTTCTTTGGCATATA 58.742 39.130 0.00 0.00 0.00 0.86
63 64 1.484653 CCCGGGTCTCACAATGACATA 59.515 52.381 14.18 0.00 36.26 2.29
106 107 5.857822 GTTGTTTACGAGGCTAACTGAAT 57.142 39.130 0.00 0.00 0.00 2.57
131 132 4.989875 AAGCTCATCCTTGCCACTATAT 57.010 40.909 0.00 0.00 0.00 0.86
132 133 6.439636 AAAGCTCATCCTTGCCACTATATA 57.560 37.500 0.00 0.00 0.00 0.86
175 176 2.827755 TGGGCTACTATCTGGTTGACA 58.172 47.619 0.00 0.00 0.00 3.58
176 177 2.500098 TGGGCTACTATCTGGTTGACAC 59.500 50.000 0.00 0.00 0.00 3.67
194 195 4.140686 TGACACTATCTATCCTCCATGGGT 60.141 45.833 13.02 0.00 36.20 4.51
214 215 3.146066 GTTACCTTTGTCAGCACCATCA 58.854 45.455 0.00 0.00 0.00 3.07
219 220 3.006110 CCTTTGTCAGCACCATCACAAAT 59.994 43.478 0.00 0.00 37.92 2.32
357 362 0.394565 CAATGGGATCCGGAGACCTC 59.605 60.000 23.24 10.94 0.00 3.85
380 385 1.349688 GGGAGGTGGTGACATGTTGTA 59.650 52.381 0.00 0.00 46.14 2.41
472 477 3.049344 GGGTGATCCTATCCAACTTCCT 58.951 50.000 0.00 0.00 0.00 3.36
486 491 0.905357 CTTCCTGACCAGAATCCGGT 59.095 55.000 0.00 0.00 40.30 5.28
530 535 6.645827 TCAAATGCATCAACAAATTCGACATT 59.354 30.769 0.00 0.00 0.00 2.71
543 548 0.790207 CGACATTGACCAACTCACGG 59.210 55.000 0.00 0.00 0.00 4.94
555 560 3.965539 CTCACGGGCAGCTGAAGGG 62.966 68.421 20.43 8.75 0.00 3.95
664 670 1.813896 CATGCGGCTATTTGAACGTG 58.186 50.000 0.00 0.00 0.00 4.49
732 767 4.196971 ACTTAAAAGGTCGGATGTATGCC 58.803 43.478 0.00 0.00 0.00 4.40
774 809 6.748333 TCTTTTGCATCCTTGTCTATGAAG 57.252 37.500 0.00 0.00 0.00 3.02
795 830 2.232941 GTGGTCCCTCTATTCGTGAACA 59.767 50.000 0.00 0.00 0.00 3.18
813 848 3.369546 ACAGAGAAAATTTGCGGGTTG 57.630 42.857 0.00 0.00 0.00 3.77
824 859 2.332654 GCGGGTTGCGATTGGAGTT 61.333 57.895 0.00 0.00 0.00 3.01
920 964 1.702957 CTCTGTTACCTGAAACCCCCA 59.297 52.381 0.00 0.00 0.00 4.96
931 975 4.526348 ACCCCCAAAAACGGGCGT 62.526 61.111 0.00 0.00 45.90 5.68
1225 1269 0.179111 CGCTTCCTTCCACGCTCATA 60.179 55.000 0.00 0.00 0.00 2.15
1333 1377 2.987547 TCGACGAAACGCCTCCCT 60.988 61.111 0.00 0.00 0.00 4.20
1751 1796 5.824624 AGAATGATCTTTATGCGTGGAATGT 59.175 36.000 0.00 0.00 29.15 2.71
1915 1960 0.111639 GAGGTTTGGGCTGTGGGTTA 59.888 55.000 0.00 0.00 0.00 2.85
2061 2106 2.823747 AGACGTGGTATCTTACAGTGCA 59.176 45.455 0.00 0.00 0.00 4.57
2594 2639 2.408050 GGTGCTGGCTGAATAGATACG 58.592 52.381 0.00 0.00 0.00 3.06
2650 2695 6.262496 TGGTCAGTCGATAACTCAACCTATAG 59.738 42.308 0.00 0.00 39.82 1.31
2822 2867 9.618890 TGAGAAATTCCAATCATTACTAAGGAG 57.381 33.333 0.00 0.00 0.00 3.69
2840 2885 8.011290 ACTAAGGAGGTACATTATGGTCTGTAT 58.989 37.037 0.00 0.00 31.06 2.29
2845 2890 7.246171 AGGTACATTATGGTCTGTATCCATC 57.754 40.000 0.53 0.00 43.58 3.51
2846 2891 6.787458 AGGTACATTATGGTCTGTATCCATCA 59.213 38.462 0.53 0.00 43.58 3.07
2847 2892 6.874134 GGTACATTATGGTCTGTATCCATCAC 59.126 42.308 0.53 0.00 43.58 3.06
2848 2893 5.869579 ACATTATGGTCTGTATCCATCACC 58.130 41.667 0.53 0.00 43.58 4.02
2849 2894 5.608437 ACATTATGGTCTGTATCCATCACCT 59.392 40.000 0.53 0.00 43.58 4.00
2850 2895 6.101734 ACATTATGGTCTGTATCCATCACCTT 59.898 38.462 0.53 0.00 43.58 3.50
2851 2896 6.575244 TTATGGTCTGTATCCATCACCTTT 57.425 37.500 0.53 0.00 43.58 3.11
2852 2897 4.487714 TGGTCTGTATCCATCACCTTTC 57.512 45.455 0.00 0.00 0.00 2.62
2853 2898 3.843619 TGGTCTGTATCCATCACCTTTCA 59.156 43.478 0.00 0.00 0.00 2.69
2881 2926 7.337942 ACCTTTCACTCAATTCATGTATCTTCC 59.662 37.037 0.00 0.00 0.00 3.46
2920 2965 6.309009 CAGTTGTACACTAGCTATGTGACTTG 59.691 42.308 22.25 13.90 38.65 3.16
2969 3014 3.871006 TGCGTCTCCATAAATAGCTGTTG 59.129 43.478 0.00 0.00 0.00 3.33
2971 3016 4.025647 GCGTCTCCATAAATAGCTGTTGAC 60.026 45.833 0.00 0.00 0.00 3.18
3118 3163 4.224370 ACGGTTAGGATTACAGGTCACAAT 59.776 41.667 0.00 0.00 0.00 2.71
3261 3306 6.325028 CAGGAGTGATTTCTGGAGAAGGTATA 59.675 42.308 0.00 0.00 35.21 1.47
3477 3522 2.672874 TGGCATTTTCTTGATCGACTCG 59.327 45.455 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.679389 AGCGTGTCAAATCCAAAGATCT 58.321 40.909 0.00 0.00 0.00 2.75
42 43 1.125093 TGTCATTGTGAGACCCGGGT 61.125 55.000 30.81 30.81 35.15 5.28
63 64 2.476686 CGATGATCGTTGCAGCACATTT 60.477 45.455 6.68 0.00 34.72 2.32
99 100 5.566230 GCAAGGATGAGCTTTTCATTCAGTT 60.566 40.000 0.00 0.00 46.51 3.16
106 107 1.888512 GTGGCAAGGATGAGCTTTTCA 59.111 47.619 0.00 0.00 40.85 2.69
131 132 7.716560 CCATCTTGTACTCATGTCCATTGATTA 59.283 37.037 0.00 0.00 0.00 1.75
132 133 6.544931 CCATCTTGTACTCATGTCCATTGATT 59.455 38.462 0.00 0.00 0.00 2.57
175 176 5.078006 AGGTAACCCATGGAGGATAGATAGT 59.922 44.000 15.22 0.00 41.22 2.12
176 177 5.594777 AGGTAACCCATGGAGGATAGATAG 58.405 45.833 15.22 0.00 41.22 2.08
194 195 3.146066 GTGATGGTGCTGACAAAGGTAA 58.854 45.455 0.00 0.00 0.00 2.85
214 215 2.380064 TTCTGGCCAACTGGATTTGT 57.620 45.000 7.01 0.00 37.39 2.83
250 252 5.895636 TTCTTGTTGCTTCTTGACTTTGA 57.104 34.783 0.00 0.00 0.00 2.69
357 362 1.375908 CATGTCACCACCTCCCACG 60.376 63.158 0.00 0.00 0.00 4.94
368 373 6.784176 TGTGCATAATCATACAACATGTCAC 58.216 36.000 0.00 0.00 0.00 3.67
380 385 5.333568 CGACGATCATGTTGTGCATAATCAT 60.334 40.000 0.00 2.65 32.84 2.45
530 535 2.425592 CTGCCCGTGAGTTGGTCA 59.574 61.111 0.00 0.00 0.00 4.02
543 548 0.179051 CAGATCTCCCTTCAGCTGCC 60.179 60.000 9.47 0.00 0.00 4.85
555 560 4.561938 CCCAGAGATGCTCAATCAGATCTC 60.562 50.000 0.00 0.00 40.74 2.75
664 670 0.168128 GTCGCATGCAAAGGGTACAC 59.832 55.000 19.57 0.00 0.00 2.90
732 767 1.095228 AATGGCATCCAACCGTAGCG 61.095 55.000 0.00 0.00 36.95 4.26
747 782 4.796038 AGACAAGGATGCAAAAGAATGG 57.204 40.909 0.00 0.00 0.00 3.16
774 809 2.232941 TGTTCACGAATAGAGGGACCAC 59.767 50.000 0.00 0.00 0.00 4.16
795 830 1.335872 CGCAACCCGCAAATTTTCTCT 60.336 47.619 0.00 0.00 42.60 3.10
816 851 7.484557 GGCTAAACCAAAAGGCAACTCCAAT 62.485 44.000 0.00 0.00 43.57 3.16
818 853 4.815132 GGCTAAACCAAAAGGCAACTCCA 61.815 47.826 0.00 0.00 43.57 3.86
820 855 3.026630 GGCTAAACCAAAAGGCAACTC 57.973 47.619 0.00 0.00 43.57 3.01
855 899 2.419667 TCGGAAACTTTTGGTCGATCC 58.580 47.619 0.00 0.00 0.00 3.36
868 912 7.534239 CAGTAGCTAAAACTCAAAATCGGAAAC 59.466 37.037 0.00 0.00 0.00 2.78
920 964 0.591170 CATGACTGACGCCCGTTTTT 59.409 50.000 0.00 0.00 0.00 1.94
931 975 1.267574 GGGAGGGCAGACATGACTGA 61.268 60.000 26.07 0.00 39.94 3.41
1225 1269 0.399233 AGGAGGCCTAGGCGAAGAAT 60.399 55.000 27.24 8.68 43.06 2.40
1505 1549 2.897641 GAAGAGCTCGATGGCGCTGT 62.898 60.000 7.64 0.00 41.18 4.40
1751 1796 6.696441 TTTGTGCATAGCATGTAATCATCA 57.304 33.333 0.00 0.00 41.91 3.07
1915 1960 1.558756 CAGAGACCCCATGAAGCTCTT 59.441 52.381 0.00 0.00 33.94 2.85
2061 2106 2.053865 CCCGCAGCCCACAATCATT 61.054 57.895 0.00 0.00 0.00 2.57
2258 2303 2.279741 CCATGATGGTGTAGTGTTCCG 58.720 52.381 2.54 0.00 31.35 4.30
2650 2695 4.035675 CGATCACCCTAAAATTTGAGGAGC 59.964 45.833 21.81 5.20 34.46 4.70
2840 2885 3.117701 TGAAAGGTGTGAAAGGTGATGGA 60.118 43.478 0.00 0.00 0.00 3.41
2845 2890 3.278574 TGAGTGAAAGGTGTGAAAGGTG 58.721 45.455 0.00 0.00 0.00 4.00
2846 2891 3.644966 TGAGTGAAAGGTGTGAAAGGT 57.355 42.857 0.00 0.00 0.00 3.50
2847 2892 5.067674 TGAATTGAGTGAAAGGTGTGAAAGG 59.932 40.000 0.00 0.00 0.00 3.11
2848 2893 6.135290 TGAATTGAGTGAAAGGTGTGAAAG 57.865 37.500 0.00 0.00 0.00 2.62
2849 2894 6.096705 ACATGAATTGAGTGAAAGGTGTGAAA 59.903 34.615 0.00 0.00 0.00 2.69
2850 2895 5.593909 ACATGAATTGAGTGAAAGGTGTGAA 59.406 36.000 0.00 0.00 0.00 3.18
2851 2896 5.132502 ACATGAATTGAGTGAAAGGTGTGA 58.867 37.500 0.00 0.00 0.00 3.58
2852 2897 5.443185 ACATGAATTGAGTGAAAGGTGTG 57.557 39.130 0.00 0.00 0.00 3.82
2853 2898 7.170965 AGATACATGAATTGAGTGAAAGGTGT 58.829 34.615 0.00 0.00 0.00 4.16
2954 2999 4.109766 TCGTCGTCAACAGCTATTTATGG 58.890 43.478 0.00 0.00 0.00 2.74
2969 3014 4.669318 TGAGAAATATGGACTTCGTCGTC 58.331 43.478 0.00 0.00 32.65 4.20
2971 3016 6.090898 ACTTTTGAGAAATATGGACTTCGTCG 59.909 38.462 0.00 0.00 32.65 5.12
3152 3197 8.365647 GCAGAAGATTCCATTTCATCCATTTAT 58.634 33.333 0.00 0.00 0.00 1.40
3175 3220 0.037326 TAGTGGTGAAAGCCTCGCAG 60.037 55.000 0.00 0.00 36.17 5.18
3477 3522 1.985684 GTGCCTGAAAATAAAGCGCAC 59.014 47.619 11.47 0.00 35.20 5.34


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

AutoCloner maintained by Alex Coulton.