Multiple sequence alignment - TraesCS5B01G179200

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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 TraesCS5B01G179200 chr5B 100.000 3029 0 0 1 3029 326919100 326916072 0.000000e+00 5594.0
1 TraesCS5B01G179200 chr5B 87.692 260 30 2 2697 2955 364139531 364139789 4.910000e-78 302.0
2 TraesCS5B01G179200 chr5A 93.991 2879 86 22 1 2846 380226644 380223820 0.000000e+00 4277.0
3 TraesCS5B01G179200 chr5A 96.154 182 6 1 2846 3027 380222999 380222819 2.280000e-76 296.0
4 TraesCS5B01G179200 chr5A 86.207 261 29 6 2697 2955 410512837 410513092 2.970000e-70 276.0
5 TraesCS5B01G179200 chr5D 95.481 2567 65 21 470 3029 287809216 287806694 0.000000e+00 4050.0
6 TraesCS5B01G179200 chr5D 86.935 398 18 6 1 387 287809594 287809220 1.680000e-112 416.0
7 TraesCS5B01G179200 chr5D 88.077 260 29 2 2697 2955 315935973 315936231 1.050000e-79 307.0
8 TraesCS5B01G179200 chr4B 85.714 266 36 2 2695 2959 317763549 317763285 2.300000e-71 279.0
9 TraesCS5B01G179200 chr3B 84.791 263 37 3 2694 2955 236510343 236510603 8.330000e-66 261.0
10 TraesCS5B01G179200 chr3B 83.333 174 28 1 2729 2901 7346454 7346627 3.130000e-35 159.0
11 TraesCS5B01G179200 chr3B 87.209 86 10 1 2871 2956 257099119 257099203 2.490000e-16 97.1
12 TraesCS5B01G179200 chr2D 85.771 253 29 4 2695 2947 218020931 218020686 8.330000e-66 261.0


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 TraesCS5B01G179200 chr5B 326916072 326919100 3028 True 5594.0 5594 100.0000 1 3029 1 chr5B.!!$R1 3028
1 TraesCS5B01G179200 chr5A 380222819 380226644 3825 True 2286.5 4277 95.0725 1 3027 2 chr5A.!!$R1 3026
2 TraesCS5B01G179200 chr5D 287806694 287809594 2900 True 2233.0 4050 91.2080 1 3029 2 chr5D.!!$R1 3028

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
157 163 0.535780 TTGTGCAGCCAACCAGAGAG 60.536 55.0 0.00 0.0 0.0 3.2 F
422 454 0.649475 GCTGTGCAGAGACGCTTATG 59.351 55.0 16.28 0.0 0.0 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1686 0.467290 GCTGGAACCAACCCTCAACA 60.467 55.000 0.0 0.0 0.00 3.33 R
2342 2384 2.353011 CCAAAGCATCTGGACGCAAATT 60.353 45.455 0.0 0.0 35.85 1.82 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
23 25 6.947376 ATCTTGGGGTTACTGTTACTACTT 57.053 37.500 0.00 0.00 0.00 2.24
26 28 7.844009 TCTTGGGGTTACTGTTACTACTTATG 58.156 38.462 0.00 0.00 0.00 1.90
28 30 7.174107 TGGGGTTACTGTTACTACTTATGAC 57.826 40.000 0.00 0.00 0.00 3.06
29 31 6.955851 TGGGGTTACTGTTACTACTTATGACT 59.044 38.462 0.00 0.00 0.00 3.41
30 32 7.123247 TGGGGTTACTGTTACTACTTATGACTC 59.877 40.741 0.00 0.00 0.00 3.36
31 33 7.123247 GGGGTTACTGTTACTACTTATGACTCA 59.877 40.741 0.00 0.00 0.00 3.41
157 163 0.535780 TTGTGCAGCCAACCAGAGAG 60.536 55.000 0.00 0.00 0.00 3.20
158 164 1.673665 GTGCAGCCAACCAGAGAGG 60.674 63.158 0.00 0.00 45.67 3.69
206 212 2.405892 ACGAATGAGCTGTTTTGTGC 57.594 45.000 0.00 0.00 0.00 4.57
225 231 1.603931 GCTGTTTGCCCTTTTGCTCTC 60.604 52.381 0.00 0.00 35.15 3.20
340 372 6.633500 TTTTGCAGTAATTAGTGTCAAGCT 57.367 33.333 19.15 0.00 30.41 3.74
357 389 6.092670 TGTCAAGCTGATTCTGCAGTAATTAC 59.907 38.462 14.67 7.57 38.17 1.89
394 426 6.407320 AATTGGGATACATAGGCATATGGT 57.593 37.500 21.39 10.31 42.72 3.55
422 454 0.649475 GCTGTGCAGAGACGCTTATG 59.351 55.000 16.28 0.00 0.00 1.90
423 455 1.737029 GCTGTGCAGAGACGCTTATGA 60.737 52.381 16.28 0.00 0.00 2.15
424 456 2.819115 CTGTGCAGAGACGCTTATGAT 58.181 47.619 4.50 0.00 0.00 2.45
434 468 7.415095 GCAGAGACGCTTATGATCTCATACTAT 60.415 40.741 0.00 0.00 41.18 2.12
436 470 9.845740 AGAGACGCTTATGATCTCATACTATAT 57.154 33.333 0.00 0.00 41.18 0.86
437 471 9.877137 GAGACGCTTATGATCTCATACTATATG 57.123 37.037 0.00 0.00 38.44 1.78
438 472 9.402320 AGACGCTTATGATCTCATACTATATGT 57.598 33.333 0.00 0.00 38.44 2.29
450 484 9.971922 TCTCATACTATATGTGTGTTGATTCAG 57.028 33.333 0.00 0.00 38.65 3.02
530 564 1.108727 TCAGCTTTGGTGCCTTGGTG 61.109 55.000 0.00 0.00 0.00 4.17
531 565 2.029518 GCTTTGGTGCCTTGGTGC 59.970 61.111 0.00 0.00 0.00 5.01
560 597 9.525826 TCTAGCTATACTCTCATGATTCATTGA 57.474 33.333 0.00 0.00 0.00 2.57
616 653 4.641541 TGACAAATGTGATCATAAGCCAGG 59.358 41.667 0.00 0.00 33.49 4.45
633 670 2.237143 CCAGGACAGCCAAGACATTAGA 59.763 50.000 0.00 0.00 36.29 2.10
681 718 3.397482 AGATCATGCTAAGCGCCTTAAG 58.603 45.455 2.29 0.00 38.05 1.85
708 745 4.870363 TGCTGCCTGTTGATTTTTCTAAC 58.130 39.130 0.00 0.00 0.00 2.34
711 748 3.568007 TGCCTGTTGATTTTTCTAACGCT 59.432 39.130 0.00 0.00 0.00 5.07
728 765 2.030893 ACGCTTCATGTTGTTGATGTGG 60.031 45.455 0.00 0.00 36.27 4.17
729 766 2.669113 CGCTTCATGTTGTTGATGTGGG 60.669 50.000 0.00 0.00 31.31 4.61
730 767 2.927871 GCTTCATGTTGTTGATGTGGGC 60.928 50.000 0.00 0.00 0.00 5.36
731 768 1.992538 TCATGTTGTTGATGTGGGCA 58.007 45.000 0.00 0.00 0.00 5.36
732 769 2.527497 TCATGTTGTTGATGTGGGCAT 58.473 42.857 0.00 0.00 38.18 4.40
906 945 7.814587 AGGCAAAATAAGTTGAAGAATACTTGC 59.185 33.333 0.00 0.00 36.16 4.01
1647 1686 0.881796 TCTCAGCAGTCGAATCACGT 59.118 50.000 0.00 0.00 43.13 4.49
1948 1987 2.785258 GTGAAACGGCATCGGAGC 59.215 61.111 0.00 0.00 41.39 4.70
1969 2008 4.452455 AGCAACTTAAGGATGAAAGTGACG 59.548 41.667 7.53 0.00 36.12 4.35
2011 2050 7.336427 AGGAGAAACAGAAGCTTATTTCATCTG 59.664 37.037 22.57 16.36 42.43 2.90
2165 2204 3.704800 ACAACTAGAAGGCCCTTTCTC 57.295 47.619 10.37 0.00 38.35 2.87
2232 2272 5.172687 TGTTTTATGGTAGGAGTGATGCA 57.827 39.130 0.00 0.00 0.00 3.96
2592 2634 4.638304 AGTCGTGCTTATGTTGTAACCTT 58.362 39.130 0.00 0.00 0.00 3.50
2721 2763 8.417884 ACTTCCTCCGTTTCAAAATAATTGAAA 58.582 29.630 11.21 11.21 43.62 2.69
3025 3893 3.605634 CACGAATCACCCATAACTGGAA 58.394 45.455 0.00 0.00 46.37 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 25 4.284829 TCACACAGGCAAATGAGTCATA 57.715 40.909 5.94 0.00 0.00 2.15
24 26 3.144657 TCACACAGGCAAATGAGTCAT 57.855 42.857 0.00 0.00 0.00 3.06
26 28 3.341823 AGATCACACAGGCAAATGAGTC 58.658 45.455 0.00 0.00 0.00 3.36
28 30 4.201891 GCTAAGATCACACAGGCAAATGAG 60.202 45.833 0.00 0.00 0.00 2.90
29 31 3.691118 GCTAAGATCACACAGGCAAATGA 59.309 43.478 0.00 0.00 0.00 2.57
30 32 3.486375 CGCTAAGATCACACAGGCAAATG 60.486 47.826 0.00 0.00 0.00 2.32
31 33 2.679837 CGCTAAGATCACACAGGCAAAT 59.320 45.455 0.00 0.00 0.00 2.32
157 163 1.812922 CTGCCACACGATCTCTGCC 60.813 63.158 0.00 0.00 0.00 4.85
158 164 0.179089 ATCTGCCACACGATCTCTGC 60.179 55.000 0.00 0.00 0.00 4.26
159 165 1.537776 GGATCTGCCACACGATCTCTG 60.538 57.143 0.00 0.00 36.97 3.35
160 166 0.749649 GGATCTGCCACACGATCTCT 59.250 55.000 0.00 0.00 36.97 3.10
192 198 2.878580 CAAACAGCACAAAACAGCTCA 58.121 42.857 0.00 0.00 39.50 4.26
194 200 1.643880 GCAAACAGCACAAAACAGCT 58.356 45.000 0.00 0.00 44.79 4.24
206 212 1.959282 AGAGAGCAAAAGGGCAAACAG 59.041 47.619 0.00 0.00 35.83 3.16
225 231 2.334838 CACCCTAAGTTTCCGACGAAG 58.665 52.381 0.00 0.00 0.00 3.79
411 443 9.877137 CATATAGTATGAGATCATAAGCGTCTC 57.123 37.037 4.15 0.00 40.18 3.36
424 456 9.971922 CTGAATCAACACACATATAGTATGAGA 57.028 33.333 4.12 0.00 0.00 3.27
434 468 5.620206 AGGACAACTGAATCAACACACATA 58.380 37.500 0.00 0.00 0.00 2.29
436 470 3.876914 GAGGACAACTGAATCAACACACA 59.123 43.478 0.00 0.00 0.00 3.72
437 471 3.876914 TGAGGACAACTGAATCAACACAC 59.123 43.478 0.00 0.00 0.00 3.82
438 472 4.149511 TGAGGACAACTGAATCAACACA 57.850 40.909 0.00 0.00 0.00 3.72
465 499 4.408921 TCTGATCCGGACCAACAGAATATT 59.591 41.667 21.69 0.00 35.20 1.28
616 653 2.935201 CTGCTCTAATGTCTTGGCTGTC 59.065 50.000 0.00 0.00 0.00 3.51
650 687 7.643528 CGCTTAGCATGATCTTAGACAATTA 57.356 36.000 4.70 0.00 0.00 1.40
681 718 0.886563 AATCAACAGGCAGCAAGAGC 59.113 50.000 0.00 0.00 42.56 4.09
708 745 2.587956 CCACATCAACAACATGAAGCG 58.412 47.619 0.00 0.00 32.06 4.68
711 748 2.314246 TGCCCACATCAACAACATGAA 58.686 42.857 0.00 0.00 32.06 2.57
729 766 7.175641 ACCAAATATAACTAAGATGGCAGATGC 59.824 37.037 0.00 0.00 41.14 3.91
730 767 8.509690 CACCAAATATAACTAAGATGGCAGATG 58.490 37.037 0.00 0.00 0.00 2.90
731 768 7.667219 CCACCAAATATAACTAAGATGGCAGAT 59.333 37.037 0.00 0.00 0.00 2.90
732 769 6.998074 CCACCAAATATAACTAAGATGGCAGA 59.002 38.462 0.00 0.00 0.00 4.26
733 770 6.294176 GCCACCAAATATAACTAAGATGGCAG 60.294 42.308 0.00 0.00 46.47 4.85
734 771 5.534654 GCCACCAAATATAACTAAGATGGCA 59.465 40.000 0.00 0.00 46.47 4.92
873 912 9.520515 TTCTTCAACTTATTTTGCCTCTAAGAT 57.479 29.630 0.00 0.00 0.00 2.40
906 945 7.664082 ATTCTAATGGAACTGCAAGATATCG 57.336 36.000 0.00 0.00 36.70 2.92
935 974 4.041567 ACATGAGAGACCAAACCATACACA 59.958 41.667 0.00 0.00 0.00 3.72
936 975 4.393062 CACATGAGAGACCAAACCATACAC 59.607 45.833 0.00 0.00 0.00 2.90
984 1023 3.387699 TCGCCATGAGACCAGATTATTCA 59.612 43.478 0.00 0.00 0.00 2.57
1428 1467 3.198417 TGAGGCTGAATGCAGAATCTGTA 59.802 43.478 12.29 7.92 45.17 2.74
1647 1686 0.467290 GCTGGAACCAACCCTCAACA 60.467 55.000 0.00 0.00 0.00 3.33
1948 1987 4.755123 ACCGTCACTTTCATCCTTAAGTTG 59.245 41.667 0.97 0.00 32.50 3.16
1969 2008 2.961741 TCTCCTCATCATACTCAGCACC 59.038 50.000 0.00 0.00 0.00 5.01
2165 2204 6.925211 TCCAGTAGAAATGAGTAACACAGAG 58.075 40.000 0.00 0.00 0.00 3.35
2232 2272 9.492973 AGGTATTGTATTACAAGTTTACAACGT 57.507 29.630 14.18 0.00 41.94 3.99
2342 2384 2.353011 CCAAAGCATCTGGACGCAAATT 60.353 45.455 0.00 0.00 35.85 1.82
2409 2451 3.010584 ACCACAGCTTGTTCCAAGGATAT 59.989 43.478 6.15 0.00 0.00 1.63
2416 2458 4.323417 CAAGTATACCACAGCTTGTTCCA 58.677 43.478 0.00 0.00 35.09 3.53
2559 2601 2.961526 AGCACGACTATCCGAAACAT 57.038 45.000 0.00 0.00 0.00 2.71
2561 2603 4.110482 ACATAAGCACGACTATCCGAAAC 58.890 43.478 0.00 0.00 0.00 2.78
2592 2634 1.490490 GTGAAGGGATCCATGCTACCA 59.510 52.381 15.23 1.25 0.00 3.25
2920 3788 8.293867 CCGTTCCAAAATAATTGAAGTTCTACA 58.706 33.333 4.17 0.00 0.00 2.74
2976 3844 3.209410 CTTGAGCCTGTTGAAGAACACT 58.791 45.455 0.00 0.00 37.15 3.55


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

AutoCloner maintained by Alex Coulton.