Multiple sequence alignment - TraesCS7B01G306300

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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 TraesCS7B01G306300 chr7B 100.000 3142 0 0 1 3142 549349486 549352627 0.000000e+00 5803
1 TraesCS7B01G306300 chr7D 95.534 3157 64 26 1 3142 516971133 516974227 0.000000e+00 4977
2 TraesCS7B01G306300 chr7A 93.426 3149 119 49 1 3116 591551928 591555021 0.000000e+00 4588
3 TraesCS7B01G306300 chr5B 88.623 167 17 2 1351 1516 504307106 504306941 5.310000e-48 202
4 TraesCS7B01G306300 chr5A 88.623 167 17 2 1351 1516 530302406 530302241 5.310000e-48 202
5 TraesCS7B01G306300 chr5D 88.024 167 18 2 1351 1516 417040867 417040702 2.470000e-46 196
6 TraesCS7B01G306300 chr3B 84.343 198 23 7 1354 1550 786970547 786970357 1.490000e-43 187


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 TraesCS7B01G306300 chr7B 549349486 549352627 3141 False 5803 5803 100.000 1 3142 1 chr7B.!!$F1 3141
1 TraesCS7B01G306300 chr7D 516971133 516974227 3094 False 4977 4977 95.534 1 3142 1 chr7D.!!$F1 3141
2 TraesCS7B01G306300 chr7A 591551928 591555021 3093 False 4588 4588 93.426 1 3116 1 chr7A.!!$F1 3115

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
696 713 0.106318 GTAACCGAGCCCCCTAGAGA 60.106 60.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 2637 0.254178 GAGAGAAGCTTCCCCATGCA 59.746 55.0 22.81 0.0 0.0 3.96 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
455 472 0.560688 CTCCTAAGCTCCTCCTCCCT 59.439 60.000 0.00 0.00 0.00 4.20
456 473 0.558712 TCCTAAGCTCCTCCTCCCTC 59.441 60.000 0.00 0.00 0.00 4.30
457 474 0.263172 CCTAAGCTCCTCCTCCCTCA 59.737 60.000 0.00 0.00 0.00 3.86
533 550 2.817258 AGGAGATCGAGAATTAGAGGCG 59.183 50.000 0.00 0.00 0.00 5.52
594 611 1.418637 GTGAGTACAAGTGGTTGGGGA 59.581 52.381 0.00 0.00 38.07 4.81
595 612 1.418637 TGAGTACAAGTGGTTGGGGAC 59.581 52.381 0.00 0.00 38.07 4.46
695 712 1.453762 CGTAACCGAGCCCCCTAGAG 61.454 65.000 0.00 0.00 35.63 2.43
696 713 0.106318 GTAACCGAGCCCCCTAGAGA 60.106 60.000 0.00 0.00 0.00 3.10
702 719 1.199615 GAGCCCCCTAGAGATATGCC 58.800 60.000 0.00 0.00 0.00 4.40
705 722 1.833332 GCCCCCTAGAGATATGCCAGT 60.833 57.143 0.00 0.00 0.00 4.00
755 772 6.348295 GCGTAGAAATCTGTGTATCTATCGGA 60.348 42.308 0.00 0.00 0.00 4.55
1027 1044 0.325203 GTTCTCTCTGAGGGGAGGCT 60.325 60.000 4.41 0.00 34.39 4.58
1254 1271 0.178900 AGTTCTTCTCCTCCGGGGTT 60.179 55.000 0.00 0.00 36.25 4.11
1399 1416 1.228245 GCCAAGAAGGACTGCACCA 60.228 57.895 0.00 0.00 41.22 4.17
1692 1709 8.577048 AGCTACTCAATTACAGTCTACAGTAA 57.423 34.615 1.29 1.29 33.43 2.24
1701 1718 9.654663 AATTACAGTCTACAGTAAAATCAGTCC 57.345 33.333 2.75 0.00 32.81 3.85
1711 1728 2.789409 AAATCAGTCCCTGCAGTACC 57.211 50.000 13.81 0.00 0.00 3.34
1732 1749 1.089920 CACTACTGCACCATTCAGGC 58.910 55.000 0.00 0.00 43.14 4.85
1733 1750 0.391661 ACTACTGCACCATTCAGGCG 60.392 55.000 0.00 0.00 43.14 5.52
1739 1756 1.452651 CACCATTCAGGCGGCTGAT 60.453 57.895 38.08 25.46 43.14 2.90
1865 1884 1.582968 GGAGTTCGCGTACCAGACA 59.417 57.895 12.54 0.00 0.00 3.41
1968 1987 1.676635 TCGTCAGGGGAGTACCACG 60.677 63.158 0.00 0.00 45.76 4.94
1979 1998 0.251209 AGTACCACGAGCTGACAGGA 60.251 55.000 4.26 0.00 0.00 3.86
2209 2228 0.960364 ATGGCGACCGAGTTGCATTT 60.960 50.000 15.37 0.84 44.12 2.32
2237 2256 3.128589 AGTCGAGAGCAAACAAAAGCAAA 59.871 39.130 0.00 0.00 0.00 3.68
2250 2269 0.524862 AAGCAAAGCCAAGCAGATCG 59.475 50.000 0.00 0.00 0.00 3.69
2410 2432 7.072177 TGGTGCAATTAAAGAGAGATAAACG 57.928 36.000 0.00 0.00 0.00 3.60
2603 2637 3.056250 TGGATTTGCTTTTGTGTGTGTGT 60.056 39.130 0.00 0.00 0.00 3.72
2604 2638 3.306703 GGATTTGCTTTTGTGTGTGTGTG 59.693 43.478 0.00 0.00 0.00 3.82
2659 2693 1.005294 GCTGCTCATTTTGTGGTGCG 61.005 55.000 0.00 0.00 32.87 5.34
2750 2784 3.756434 TCTGTTTAAGCAGCCAACCATAC 59.244 43.478 13.99 0.00 36.49 2.39
2858 2892 6.707290 TCTTTGGCTAATCTTTGCACTACTA 58.293 36.000 0.00 0.00 0.00 1.82
2871 2905 5.622346 TGCACTACTATCTCTCTCTCTCA 57.378 43.478 0.00 0.00 0.00 3.27
2872 2906 5.364778 TGCACTACTATCTCTCTCTCTCAC 58.635 45.833 0.00 0.00 0.00 3.51
2873 2907 4.755123 GCACTACTATCTCTCTCTCTCACC 59.245 50.000 0.00 0.00 0.00 4.02
2875 2909 4.972568 ACTACTATCTCTCTCTCTCACCCA 59.027 45.833 0.00 0.00 0.00 4.51
2876 2910 4.164843 ACTATCTCTCTCTCTCACCCAC 57.835 50.000 0.00 0.00 0.00 4.61
2877 2911 3.785887 ACTATCTCTCTCTCTCACCCACT 59.214 47.826 0.00 0.00 0.00 4.00
2878 2912 2.799126 TCTCTCTCTCTCACCCACTC 57.201 55.000 0.00 0.00 0.00 3.51
2879 2913 1.283613 TCTCTCTCTCTCACCCACTCC 59.716 57.143 0.00 0.00 0.00 3.85
2880 2914 0.333312 TCTCTCTCTCACCCACTCCC 59.667 60.000 0.00 0.00 0.00 4.30
2881 2915 0.334676 CTCTCTCTCACCCACTCCCT 59.665 60.000 0.00 0.00 0.00 4.20
2882 2916 0.333312 TCTCTCTCACCCACTCCCTC 59.667 60.000 0.00 0.00 0.00 4.30
2945 2979 2.436173 CCTCCTTTTCCTAGGGCACTAG 59.564 54.545 16.61 16.61 45.13 2.57
3018 3052 3.380320 CAGAAAATGGGAAATACCGACCC 59.620 47.826 0.00 0.00 43.51 4.46
3069 3107 6.401688 GGAATGTCAACAATGTGCATGATTTG 60.402 38.462 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
345 355 2.778278 GGGGAGGGATGATGGGCA 60.778 66.667 0.00 0.00 0.00 5.36
455 472 5.197451 GTTCTCTTCTCACTAGGAGGATGA 58.803 45.833 7.98 3.65 44.19 2.92
456 473 4.952957 TGTTCTCTTCTCACTAGGAGGATG 59.047 45.833 7.98 0.14 44.19 3.51
457 474 5.199982 TGTTCTCTTCTCACTAGGAGGAT 57.800 43.478 7.98 0.00 44.19 3.24
533 550 4.083003 CGTGAGGATAGGTAGCTTGATCTC 60.083 50.000 0.00 3.84 0.00 2.75
594 611 5.700450 AGGAAACTAGTTACTACCCCAAGGT 60.700 44.000 8.92 0.00 45.76 3.50
595 612 4.781621 AGGAAACTAGTTACTACCCCAAGG 59.218 45.833 8.92 0.00 40.61 3.61
596 613 7.179872 AGTTAGGAAACTAGTTACTACCCCAAG 59.820 40.741 8.92 0.00 44.26 3.61
597 614 7.018769 AGTTAGGAAACTAGTTACTACCCCAA 58.981 38.462 8.92 5.42 44.26 4.12
598 615 6.565036 AGTTAGGAAACTAGTTACTACCCCA 58.435 40.000 8.92 0.00 44.26 4.96
599 616 7.038729 ACAAGTTAGGAAACTAGTTACTACCCC 60.039 40.741 8.92 4.11 45.37 4.95
600 617 7.901029 ACAAGTTAGGAAACTAGTTACTACCC 58.099 38.462 8.92 5.79 45.37 3.69
695 712 2.324541 ACTCCTCCTCACTGGCATATC 58.675 52.381 0.00 0.00 35.26 1.63
696 713 2.485966 ACTCCTCCTCACTGGCATAT 57.514 50.000 0.00 0.00 35.26 1.78
702 719 2.828520 ACACACATACTCCTCCTCACTG 59.171 50.000 0.00 0.00 0.00 3.66
705 722 2.889512 ACACACACATACTCCTCCTCA 58.110 47.619 0.00 0.00 0.00 3.86
755 772 8.004215 AGATTAGACAGATCTACCACTGAGATT 58.996 37.037 0.00 0.00 37.15 2.40
889 906 5.721876 ACAAACACAAAACGAGACGAATA 57.278 34.783 0.00 0.00 0.00 1.75
890 907 4.609691 ACAAACACAAAACGAGACGAAT 57.390 36.364 0.00 0.00 0.00 3.34
892 909 3.552699 CCTACAAACACAAAACGAGACGA 59.447 43.478 0.00 0.00 0.00 4.20
893 910 3.552699 TCCTACAAACACAAAACGAGACG 59.447 43.478 0.00 0.00 0.00 4.18
895 912 4.124238 CCTCCTACAAACACAAAACGAGA 58.876 43.478 0.00 0.00 0.00 4.04
898 915 3.623960 TCACCTCCTACAAACACAAAACG 59.376 43.478 0.00 0.00 0.00 3.60
899 916 4.879545 TCTCACCTCCTACAAACACAAAAC 59.120 41.667 0.00 0.00 0.00 2.43
900 917 5.105567 TCTCACCTCCTACAAACACAAAA 57.894 39.130 0.00 0.00 0.00 2.44
1036 1053 2.042843 CCCGCTACCTCCTCCACT 60.043 66.667 0.00 0.00 0.00 4.00
1170 1187 1.276421 CATAGCTGGAACCCTATCCCG 59.724 57.143 0.00 0.00 38.82 5.14
1524 1541 3.594775 CTGTTGTTGGCTGCCGCA 61.595 61.111 14.98 12.74 38.10 5.69
1739 1756 3.578272 GCAAACACACCGTCGGCA 61.578 61.111 12.28 0.00 0.00 5.69
1883 1902 0.676782 GGATCCCCTTGAACGTGTGG 60.677 60.000 0.00 0.00 0.00 4.17
1955 1974 1.682684 CAGCTCGTGGTACTCCCCT 60.683 63.158 0.00 0.00 0.00 4.79
1957 1976 1.248785 TGTCAGCTCGTGGTACTCCC 61.249 60.000 0.00 0.00 0.00 4.30
2209 2228 3.953712 TGTTTGCTCTCGACTTGGATA 57.046 42.857 0.00 0.00 0.00 2.59
2219 2238 2.541346 GGCTTTGCTTTTGTTTGCTCTC 59.459 45.455 0.00 0.00 0.00 3.20
2220 2239 2.093553 TGGCTTTGCTTTTGTTTGCTCT 60.094 40.909 0.00 0.00 0.00 4.09
2237 2256 1.552337 TCTTCTTCGATCTGCTTGGCT 59.448 47.619 0.00 0.00 0.00 4.75
2250 2269 4.390297 CGGACAACAATTCTCCTCTTCTTC 59.610 45.833 0.00 0.00 0.00 2.87
2410 2432 7.550906 AGGAAGCAGTGATTAAGATACACTTTC 59.449 37.037 0.00 0.00 41.93 2.62
2562 2592 3.376859 TCCAAGCAAACAATACCATAGCG 59.623 43.478 0.00 0.00 0.00 4.26
2563 2593 4.981806 TCCAAGCAAACAATACCATAGC 57.018 40.909 0.00 0.00 0.00 2.97
2603 2637 0.254178 GAGAGAAGCTTCCCCATGCA 59.746 55.000 22.81 0.00 0.00 3.96
2604 2638 0.545646 AGAGAGAAGCTTCCCCATGC 59.454 55.000 22.81 6.99 0.00 4.06
2750 2784 3.698040 CCATCCCAAGGAACAAGAGAATG 59.302 47.826 0.00 0.00 34.34 2.67
2798 2832 4.041075 TGCTGTACTTTCCCTTGTGATGTA 59.959 41.667 0.00 0.00 0.00 2.29
2858 2892 2.091885 GGAGTGGGTGAGAGAGAGAGAT 60.092 54.545 0.00 0.00 0.00 2.75
2871 2905 0.629058 GAGAGAGAGAGGGAGTGGGT 59.371 60.000 0.00 0.00 0.00 4.51
2872 2906 0.926293 AGAGAGAGAGAGGGAGTGGG 59.074 60.000 0.00 0.00 0.00 4.61
2873 2907 3.045634 TCTAGAGAGAGAGAGGGAGTGG 58.954 54.545 0.00 0.00 0.00 4.00
3018 3052 6.348498 TCATTCCATGTGACTAGGTTGTATG 58.652 40.000 0.00 0.00 0.00 2.39
3069 3107 7.468922 AGTTTGCATGAAGTTTCTTAAAAGC 57.531 32.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.