Multiple sequence alignment - TraesCS5B01G104900

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 TraesCS5B01G104900 chr5B 100.000 3652 0 0 1 3652 140737567 140733916 0.000000e+00 6745.0
1 TraesCS5B01G104900 chr5B 92.958 71 3 2 847 916 140741786 140741717 6.450000e-18 102.0
2 TraesCS5B01G104900 chr5D 96.783 2176 52 9 810 2977 127260417 127258252 0.000000e+00 3615.0
3 TraesCS5B01G104900 chr5D 95.781 640 17 7 3016 3652 127258082 127257450 0.000000e+00 1024.0
4 TraesCS5B01G104900 chr5D 91.429 70 6 0 847 916 127263368 127263299 3.000000e-16 97.1
5 TraesCS5B01G104900 chr5D 100.000 30 0 0 787 816 108341957 108341986 5.090000e-04 56.5
6 TraesCS5B01G104900 chr5A 94.537 1977 85 17 867 2835 142847437 142845476 0.000000e+00 3031.0
7 TraesCS5B01G104900 chr5A 93.701 635 29 6 3019 3652 142844021 142843397 0.000000e+00 941.0
8 TraesCS5B01G104900 chr5A 88.344 163 10 2 2819 2977 142844336 142844179 1.730000e-43 187.0
9 TraesCS5B01G104900 chr6B 93.376 785 40 10 1 784 45530938 45530165 0.000000e+00 1151.0
10 TraesCS5B01G104900 chr4D 92.985 784 53 2 1 784 69136077 69135296 0.000000e+00 1142.0
11 TraesCS5B01G104900 chr4D 90.141 71 4 2 2857 2927 418772437 418772504 5.020000e-14 89.8
12 TraesCS5B01G104900 chr2B 92.857 784 55 1 1 784 709045578 709044796 0.000000e+00 1136.0
13 TraesCS5B01G104900 chr2B 100.000 30 0 0 787 816 93897228 93897257 5.090000e-04 56.5
14 TraesCS5B01G104900 chr2B 97.059 34 0 1 787 819 148048335 148048302 5.090000e-04 56.5
15 TraesCS5B01G104900 chr2B 100.000 29 0 0 787 815 440597049 440597021 2.000000e-03 54.7
16 TraesCS5B01G104900 chr4A 92.730 784 54 3 1 784 673081825 673082605 0.000000e+00 1129.0
17 TraesCS5B01G104900 chr4A 91.720 785 47 8 1 784 631640560 631641327 0.000000e+00 1074.0
18 TraesCS5B01G104900 chr6D 92.229 785 51 5 1 784 144604096 144603321 0.000000e+00 1103.0
19 TraesCS5B01G104900 chr6D 96.970 33 1 0 787 819 107534890 107534922 5.090000e-04 56.5
20 TraesCS5B01G104900 chr6D 100.000 28 0 0 787 814 139307666 139307693 7.000000e-03 52.8
21 TraesCS5B01G104900 chr6D 100.000 28 0 0 787 814 457742275 457742248 7.000000e-03 52.8
22 TraesCS5B01G104900 chr7D 91.805 781 60 4 1 780 615885218 615885995 0.000000e+00 1085.0
23 TraesCS5B01G104900 chr2D 91.826 783 54 5 1 781 222851429 222852203 0.000000e+00 1083.0
24 TraesCS5B01G104900 chr2D 91.327 784 53 6 1 784 340278233 340277465 0.000000e+00 1057.0
25 TraesCS5B01G104900 chr4B 95.385 65 1 1 2857 2921 628556396 628556458 6.450000e-18 102.0
26 TraesCS5B01G104900 chr1D 93.846 65 2 1 2857 2921 206041004 206041066 3.000000e-16 97.1
27 TraesCS5B01G104900 chr1D 90.141 71 5 2 2857 2927 299928271 299928203 1.400000e-14 91.6
28 TraesCS5B01G104900 chr1D 100.000 28 0 0 787 814 407803077 407803104 7.000000e-03 52.8
29 TraesCS5B01G104900 chr7A 91.549 71 3 2 2857 2927 520786209 520786276 1.080000e-15 95.3
30 TraesCS5B01G104900 chr3D 91.549 71 2 3 2860 2930 548275702 548275636 1.080000e-15 95.3
31 TraesCS5B01G104900 chr3B 92.537 67 2 3 2859 2925 725843555 725843492 3.880000e-15 93.5
32 TraesCS5B01G104900 chr1A 100.000 28 0 0 787 814 281655829 281655856 7.000000e-03 52.8


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 TraesCS5B01G104900 chr5B 140733916 140737567 3651 True 6745.000000 6745 100.000000 1 3652 1 chr5B.!!$R1 3651
1 TraesCS5B01G104900 chr5D 127257450 127263368 5918 True 1578.700000 3615 94.664333 810 3652 3 chr5D.!!$R1 2842
2 TraesCS5B01G104900 chr5A 142843397 142847437 4040 True 1386.333333 3031 92.194000 867 3652 3 chr5A.!!$R1 2785
3 TraesCS5B01G104900 chr6B 45530165 45530938 773 True 1151.000000 1151 93.376000 1 784 1 chr6B.!!$R1 783
4 TraesCS5B01G104900 chr4D 69135296 69136077 781 True 1142.000000 1142 92.985000 1 784 1 chr4D.!!$R1 783
5 TraesCS5B01G104900 chr2B 709044796 709045578 782 True 1136.000000 1136 92.857000 1 784 1 chr2B.!!$R3 783
6 TraesCS5B01G104900 chr4A 673081825 673082605 780 False 1129.000000 1129 92.730000 1 784 1 chr4A.!!$F2 783
7 TraesCS5B01G104900 chr4A 631640560 631641327 767 False 1074.000000 1074 91.720000 1 784 1 chr4A.!!$F1 783
8 TraesCS5B01G104900 chr6D 144603321 144604096 775 True 1103.000000 1103 92.229000 1 784 1 chr6D.!!$R1 783
9 TraesCS5B01G104900 chr7D 615885218 615885995 777 False 1085.000000 1085 91.805000 1 780 1 chr7D.!!$F1 779
10 TraesCS5B01G104900 chr2D 222851429 222852203 774 False 1083.000000 1083 91.826000 1 781 1 chr2D.!!$F1 780
11 TraesCS5B01G104900 chr2D 340277465 340278233 768 True 1057.000000 1057 91.327000 1 784 1 chr2D.!!$R1 783

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
811 834 0.321298 GCCCGTTGGAGTTGCTCTAA 60.321 55.0 0.0 0.0 0.0 2.10 F
2033 4187 0.326264 GGGTGTGGAGCAAGATGAGT 59.674 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 4208 0.248336 TGCACTTATACTCGGCGTCG 60.248 55.0 1.15 1.15 37.82 5.12 R
3145 6592 0.107831 TTGTTCCTTCCCCGTCACAG 59.892 55.0 0.00 0.00 0.00 3.66 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
61 62 2.943978 CGTCCACTCCCCGCTCTTT 61.944 63.158 0.00 0.00 0.00 2.52
86 87 4.129737 CGCCTCCACCATCGTCGT 62.130 66.667 0.00 0.00 0.00 4.34
228 241 2.434884 CGTCCACTTCGCTGCCAT 60.435 61.111 0.00 0.00 0.00 4.40
426 439 4.828925 GACGCAGGAGGAGGCTGC 62.829 72.222 0.00 0.00 40.37 5.25
631 648 0.544833 TAGGTGGACTTTGGCCGGTA 60.545 55.000 1.90 0.00 0.00 4.02
805 828 3.047877 GTCGGCCCGTTGGAGTTG 61.048 66.667 1.63 0.00 0.00 3.16
810 833 1.295423 GCCCGTTGGAGTTGCTCTA 59.705 57.895 0.00 0.00 0.00 2.43
811 834 0.321298 GCCCGTTGGAGTTGCTCTAA 60.321 55.000 0.00 0.00 0.00 2.10
812 835 1.880646 GCCCGTTGGAGTTGCTCTAAA 60.881 52.381 0.00 0.00 33.06 1.85
813 836 2.711542 CCCGTTGGAGTTGCTCTAAAT 58.288 47.619 0.00 0.00 33.06 1.40
851 2994 2.693864 AGGCCTCTGACATGGGGG 60.694 66.667 0.00 0.00 0.00 5.40
1370 3524 0.964358 CCTGTCGACTTAGACCCCGT 60.964 60.000 17.92 0.00 40.26 5.28
1371 3525 0.886563 CTGTCGACTTAGACCCCGTT 59.113 55.000 17.92 0.00 40.26 4.44
1616 3770 1.164662 CCATGCTCAAGGAGATGGCG 61.165 60.000 0.00 0.00 33.88 5.69
1834 3988 3.272574 TCTCATGAAAGATGACAGGGC 57.727 47.619 0.00 0.00 0.00 5.19
1853 4007 1.257750 CGGTCCCAGACTGGATGACA 61.258 60.000 23.77 0.00 40.96 3.58
2033 4187 0.326264 GGGTGTGGAGCAAGATGAGT 59.674 55.000 0.00 0.00 0.00 3.41
2054 4208 3.003793 GTCAAACCTTCAGGAAGTTCAGC 59.996 47.826 5.01 0.00 38.94 4.26
2066 4220 1.226603 GTTCAGCGACGCCGAGTAT 60.227 57.895 17.79 0.00 38.22 2.12
2349 4503 2.504367 TGGAGTGCCTTAAGAAAGCAC 58.496 47.619 21.04 21.04 38.72 4.40
2392 4546 2.107546 AAACCCGCAACTCGTCGT 59.892 55.556 0.00 0.00 36.19 4.34
2393 4547 1.522130 AAACCCGCAACTCGTCGTT 60.522 52.632 0.00 0.00 36.19 3.85
2780 4934 5.105797 TGGCAGGCATAAACTTGAACTAATG 60.106 40.000 0.00 0.00 0.00 1.90
2783 4937 5.801947 CAGGCATAAACTTGAACTAATGCAC 59.198 40.000 7.33 0.00 41.08 4.57
2875 6189 4.816392 TGCAAGAGCGTTTAGATCACTAA 58.184 39.130 0.00 0.00 46.23 2.24
3014 6351 3.398406 TGCGAGCATTCAAGTGTAAAGA 58.602 40.909 0.00 0.00 0.00 2.52
3144 6591 1.132640 GGTTGCTAAACGCTGCTCG 59.867 57.895 0.00 0.00 45.38 5.03
3145 6592 1.509995 GTTGCTAAACGCTGCTCGC 60.510 57.895 0.00 0.00 43.23 5.03
3146 6593 1.667830 TTGCTAAACGCTGCTCGCT 60.668 52.632 0.00 0.00 43.23 4.93
3147 6594 1.900585 TTGCTAAACGCTGCTCGCTG 61.901 55.000 0.00 0.00 43.23 5.18
3148 6595 2.383527 GCTAAACGCTGCTCGCTGT 61.384 57.895 0.00 0.00 43.23 4.40
3149 6596 1.417592 CTAAACGCTGCTCGCTGTG 59.582 57.895 7.63 7.63 43.23 3.66
3150 6597 1.006688 TAAACGCTGCTCGCTGTGA 60.007 52.632 14.78 0.00 43.23 3.58
3151 6598 1.282248 TAAACGCTGCTCGCTGTGAC 61.282 55.000 14.78 0.00 43.23 3.67
3176 6623 5.445964 GGGAAGGAACAAGCTTCCATAATA 58.554 41.667 3.68 0.00 46.11 0.98
3190 6637 8.193438 AGCTTCCATAATAATTGCAGAAAAGTC 58.807 33.333 0.00 0.00 0.00 3.01
3191 6638 8.193438 GCTTCCATAATAATTGCAGAAAAGTCT 58.807 33.333 0.00 0.00 32.85 3.24
3206 6653 7.752686 GCAGAAAAGTCTTAACAGGAAATCATC 59.247 37.037 0.00 0.00 28.78 2.92
3315 6762 5.077564 TGAGTACTTCTCTAGAGTTGGCAA 58.922 41.667 19.21 0.00 43.13 4.52
3361 6808 4.253685 AGTTGACCAAACGATACATCTGG 58.746 43.478 0.00 0.00 44.04 3.86
3482 6931 2.450609 AAGCGCTTCTCGTTTCCTAA 57.549 45.000 18.98 0.00 36.97 2.69
3555 7004 4.211125 TCACTCATTTTGCCCACAACTTA 58.789 39.130 0.00 0.00 34.87 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
426 439 3.470888 CTGGTACGCTCCCAGGGG 61.471 72.222 5.33 0.92 44.77 4.79
631 648 5.806654 AAACATAAAGTGGCTGGTCAAAT 57.193 34.783 0.00 0.00 0.00 2.32
699 722 1.963855 CCCAAATGTGTCGGCGTGA 60.964 57.895 6.85 0.00 0.00 4.35
700 723 2.182614 GACCCAAATGTGTCGGCGTG 62.183 60.000 6.85 0.00 0.00 5.34
701 724 1.964373 GACCCAAATGTGTCGGCGT 60.964 57.895 6.85 0.00 0.00 5.68
707 730 1.303317 GAGGCCGACCCAAATGTGT 60.303 57.895 0.00 0.00 36.11 3.72
787 810 4.324991 AACTCCAACGGGCCGACC 62.325 66.667 35.78 0.00 0.00 4.79
788 811 3.047877 CAACTCCAACGGGCCGAC 61.048 66.667 35.78 0.00 0.00 4.79
791 814 2.180159 TAGAGCAACTCCAACGGGCC 62.180 60.000 0.00 0.00 0.00 5.80
793 816 2.178912 TTTAGAGCAACTCCAACGGG 57.821 50.000 0.00 0.00 0.00 5.28
794 817 4.935808 AGTTATTTAGAGCAACTCCAACGG 59.064 41.667 0.00 0.00 0.00 4.44
795 818 6.307155 CAAGTTATTTAGAGCAACTCCAACG 58.693 40.000 0.00 0.00 31.43 4.10
796 819 6.086871 GCAAGTTATTTAGAGCAACTCCAAC 58.913 40.000 0.00 0.00 31.43 3.77
797 820 5.183140 GGCAAGTTATTTAGAGCAACTCCAA 59.817 40.000 0.00 0.00 31.43 3.53
798 821 4.700213 GGCAAGTTATTTAGAGCAACTCCA 59.300 41.667 0.00 0.00 31.43 3.86
799 822 4.944317 AGGCAAGTTATTTAGAGCAACTCC 59.056 41.667 0.00 0.00 31.43 3.85
800 823 5.643777 TCAGGCAAGTTATTTAGAGCAACTC 59.356 40.000 0.00 0.00 31.43 3.01
801 824 5.560724 TCAGGCAAGTTATTTAGAGCAACT 58.439 37.500 0.00 0.00 34.03 3.16
802 825 5.880054 TCAGGCAAGTTATTTAGAGCAAC 57.120 39.130 0.00 0.00 0.00 4.17
805 828 4.853268 GCATCAGGCAAGTTATTTAGAGC 58.147 43.478 0.00 0.00 43.97 4.09
851 2994 1.699730 AAGGGCTGTGGGTACAAAAC 58.300 50.000 0.00 0.00 36.14 2.43
987 3141 3.594134 GGAGAGCATAGCTTCGCAATAT 58.406 45.455 9.44 0.00 39.88 1.28
988 3142 2.289072 GGGAGAGCATAGCTTCGCAATA 60.289 50.000 9.44 0.00 39.88 1.90
989 3143 1.542108 GGGAGAGCATAGCTTCGCAAT 60.542 52.381 9.44 0.00 39.88 3.56
990 3144 0.179073 GGGAGAGCATAGCTTCGCAA 60.179 55.000 9.44 0.00 39.88 4.85
1616 3770 4.468689 GTGAGGTACCCTGCGCCC 62.469 72.222 8.74 0.00 31.76 6.13
1679 3833 2.604686 ACCTTCTCCAGCTCGCCA 60.605 61.111 0.00 0.00 0.00 5.69
1834 3988 1.257750 TGTCATCCAGTCTGGGACCG 61.258 60.000 19.11 5.37 40.44 4.79
1841 3995 2.093075 CAGGCTGAATGTCATCCAGTCT 60.093 50.000 9.42 0.00 42.89 3.24
2033 4187 3.214328 GCTGAACTTCCTGAAGGTTTGA 58.786 45.455 11.34 0.00 38.71 2.69
2054 4208 0.248336 TGCACTTATACTCGGCGTCG 60.248 55.000 1.15 1.15 37.82 5.12
2066 4220 2.972625 AGCGAAGTAAGCATGCACTTA 58.027 42.857 21.98 7.93 35.17 2.24
2349 4503 2.490903 CCCATTTCTCCAAGCTTGACAG 59.509 50.000 28.05 20.94 0.00 3.51
2661 4815 5.997746 GCATCCAATCTAACACAGCCTATTA 59.002 40.000 0.00 0.00 0.00 0.98
2662 4816 4.823989 GCATCCAATCTAACACAGCCTATT 59.176 41.667 0.00 0.00 0.00 1.73
2783 4937 2.030893 TCAATTCCAAGAACGCAAGCTG 60.031 45.455 0.00 0.00 45.62 4.24
2830 6140 9.404848 TGCAGAGTACTTAGCTATAACTAAAGA 57.595 33.333 17.77 0.00 31.92 2.52
2844 6154 3.936372 AACGCTCTTGCAGAGTACTTA 57.064 42.857 12.71 0.00 44.12 2.24
2853 6163 3.319137 AGTGATCTAAACGCTCTTGCA 57.681 42.857 0.00 0.00 39.64 4.08
2854 6164 5.975410 ATTAGTGATCTAAACGCTCTTGC 57.025 39.130 0.00 0.00 39.23 4.01
2855 6165 9.088512 ACTAAATTAGTGATCTAAACGCTCTTG 57.911 33.333 4.66 0.00 39.23 3.02
2912 6228 1.142870 TGCTGTGTTTGCTACTCCCTT 59.857 47.619 0.00 0.00 0.00 3.95
3034 6481 7.451566 ACAAAACCCAGAGAGTATTTTAAGCAT 59.548 33.333 0.00 0.00 0.00 3.79
3050 6497 3.820467 TGCTCTTGATACACAAAACCCAG 59.180 43.478 0.00 0.00 38.08 4.45
3144 6591 1.671379 GTTCCTTCCCCGTCACAGC 60.671 63.158 0.00 0.00 0.00 4.40
3145 6592 0.107831 TTGTTCCTTCCCCGTCACAG 59.892 55.000 0.00 0.00 0.00 3.66
3146 6593 0.107831 CTTGTTCCTTCCCCGTCACA 59.892 55.000 0.00 0.00 0.00 3.58
3147 6594 1.235281 GCTTGTTCCTTCCCCGTCAC 61.235 60.000 0.00 0.00 0.00 3.67
3148 6595 1.072505 GCTTGTTCCTTCCCCGTCA 59.927 57.895 0.00 0.00 0.00 4.35
3149 6596 0.250770 AAGCTTGTTCCTTCCCCGTC 60.251 55.000 0.00 0.00 0.00 4.79
3150 6597 0.250770 GAAGCTTGTTCCTTCCCCGT 60.251 55.000 2.10 0.00 34.12 5.28
3151 6598 2.556286 GAAGCTTGTTCCTTCCCCG 58.444 57.895 2.10 0.00 34.12 5.73
3176 6623 6.959639 TCCTGTTAAGACTTTTCTGCAATT 57.040 33.333 0.00 0.00 29.98 2.32
3190 6637 5.277683 CGAGCATGGATGATTTCCTGTTAAG 60.278 44.000 0.00 0.00 45.68 1.85
3191 6638 4.576053 CGAGCATGGATGATTTCCTGTTAA 59.424 41.667 0.00 0.00 45.68 2.01
3390 6837 5.240623 CACTTTGGGTGTCTTGTTATGCTTA 59.759 40.000 0.00 0.00 40.79 3.09
3402 6849 2.639286 CGCAGCACTTTGGGTGTC 59.361 61.111 0.00 0.00 46.86 3.67
3482 6931 0.325296 TGGGACGTCTTCCTGCCTAT 60.325 55.000 16.46 0.00 45.09 2.57
3496 6945 0.179000 CATCTGGTACTGCCTGGGAC 59.821 60.000 0.00 0.00 38.35 4.46
3555 7004 5.079643 AGGGCATTTGTTGTTTCTATGTCT 58.920 37.500 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.