Multiple sequence alignment - TraesCS6B01G276100

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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 TraesCS6B01G276100 chr6B 100.000 2945 0 0 1 2945 499579636 499576692 0.000000e+00 5439
1 TraesCS6B01G276100 chr6A 93.596 2998 120 20 2 2941 461643956 461646939 0.000000e+00 4407
2 TraesCS6B01G276100 chr6D 94.085 2485 76 23 501 2944 324247954 324250408 0.000000e+00 3709
3 TraesCS6B01G276100 chr6D 93.933 445 27 0 2 446 324247186 324247630 0.000000e+00 673
4 TraesCS6B01G276100 chr2D 75.783 958 147 60 993 1918 524932529 524931625 3.530000e-109 405
5 TraesCS6B01G276100 chr2B 75.472 954 163 50 993 1918 620861719 620860809 1.640000e-107 399
6 TraesCS6B01G276100 chr2A 75.584 942 138 65 993 1918 670315092 670314227 5.960000e-102 381


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 TraesCS6B01G276100 chr6B 499576692 499579636 2944 True 5439 5439 100.000 1 2945 1 chr6B.!!$R1 2944
1 TraesCS6B01G276100 chr6A 461643956 461646939 2983 False 4407 4407 93.596 2 2941 1 chr6A.!!$F1 2939
2 TraesCS6B01G276100 chr6D 324247186 324250408 3222 False 2191 3709 94.009 2 2944 2 chr6D.!!$F1 2942
3 TraesCS6B01G276100 chr2D 524931625 524932529 904 True 405 405 75.783 993 1918 1 chr2D.!!$R1 925
4 TraesCS6B01G276100 chr2B 620860809 620861719 910 True 399 399 75.472 993 1918 1 chr2B.!!$R1 925
5 TraesCS6B01G276100 chr2A 670314227 670315092 865 True 381 381 75.584 993 1918 1 chr2A.!!$R1 925

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
469 470 0.108585 GGTGTGATGAGTGTGTGGGT 59.891 55.0 0.0 0.0 0.0 4.51 F
507 777 0.331616 AGGGGGTGTGTAAAGGATGC 59.668 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1848 0.673644 AATACCTTCTTGCACGCGCT 60.674 50.0 5.73 0.0 39.64 5.92 R
2464 2840 0.951558 GCGAAAGAAAGGAGGCAACA 59.048 50.0 0.00 0.0 41.41 3.33 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
25 26 2.553904 CCACTCTCCAAAGATGTGGCTT 60.554 50.000 0.00 0.00 40.60 4.35
90 91 2.365768 GTGGGAGGGAGAGGGGTC 60.366 72.222 0.00 0.00 0.00 4.46
105 106 1.683938 GGGGTCGGTTTTAGGGAATGG 60.684 57.143 0.00 0.00 0.00 3.16
152 153 5.064314 TGCCAAATTGGGATGATCTATCA 57.936 39.130 14.59 0.00 38.19 2.15
158 159 2.038659 TGGGATGATCTATCACGTGCA 58.961 47.619 11.67 1.72 42.41 4.57
166 167 2.606108 TCTATCACGTGCACATGTGTC 58.394 47.619 26.01 18.27 45.84 3.67
173 174 1.720805 GTGCACATGTGTCGGTGATA 58.279 50.000 26.01 0.44 37.18 2.15
178 179 3.676049 GCACATGTGTCGGTGATAGAGAA 60.676 47.826 26.01 0.00 37.18 2.87
179 180 4.494484 CACATGTGTCGGTGATAGAGAAA 58.506 43.478 18.03 0.00 37.18 2.52
189 190 3.118738 GGTGATAGAGAAAGGCGAAGGAA 60.119 47.826 0.00 0.00 0.00 3.36
192 193 6.281405 GTGATAGAGAAAGGCGAAGGAATAA 58.719 40.000 0.00 0.00 0.00 1.40
208 209 6.426646 AGGAATAAGCTCATCTTTCGGTAT 57.573 37.500 0.00 0.00 36.25 2.73
394 395 0.779997 AAGGGGTCATGCTCACCTTT 59.220 50.000 15.37 3.29 38.31 3.11
396 397 1.147817 AGGGGTCATGCTCACCTTTTT 59.852 47.619 5.83 0.00 33.96 1.94
415 416 3.590720 TTGCACGCAGATCGAATAATG 57.409 42.857 0.00 0.00 41.67 1.90
439 440 2.059541 GTAACAAGTCACGCTCACTCC 58.940 52.381 0.00 0.00 0.00 3.85
446 447 2.891580 AGTCACGCTCACTCCTAAAAGA 59.108 45.455 0.00 0.00 0.00 2.52
463 464 3.777106 AAGACATGGTGTGATGAGTGT 57.223 42.857 0.00 0.00 0.00 3.55
469 470 0.108585 GGTGTGATGAGTGTGTGGGT 59.891 55.000 0.00 0.00 0.00 4.51
470 471 1.229428 GTGTGATGAGTGTGTGGGTG 58.771 55.000 0.00 0.00 0.00 4.61
471 472 0.836606 TGTGATGAGTGTGTGGGTGT 59.163 50.000 0.00 0.00 0.00 4.16
472 473 1.211703 TGTGATGAGTGTGTGGGTGTT 59.788 47.619 0.00 0.00 0.00 3.32
473 474 1.603802 GTGATGAGTGTGTGGGTGTTG 59.396 52.381 0.00 0.00 0.00 3.33
474 475 1.211703 TGATGAGTGTGTGGGTGTTGT 59.788 47.619 0.00 0.00 0.00 3.32
480 481 1.275421 TGTGTGGGTGTTGTGAGGGA 61.275 55.000 0.00 0.00 0.00 4.20
507 777 0.331616 AGGGGGTGTGTAAAGGATGC 59.668 55.000 0.00 0.00 0.00 3.91
510 780 2.640184 GGGGTGTGTAAAGGATGCTAC 58.360 52.381 0.00 0.00 0.00 3.58
763 1035 5.238868 AGCACATCTGTGATTTGATATGCTC 59.761 40.000 14.31 0.00 46.48 4.26
822 1096 1.262950 CAATGGAAAGTGTCAACGCGA 59.737 47.619 15.93 0.00 0.00 5.87
831 1105 6.143278 GGAAAGTGTCAACGCGAAATTAAAAT 59.857 34.615 15.93 0.00 0.00 1.82
921 1197 1.198759 TTCTAACTTCCCCCGCAGCT 61.199 55.000 0.00 0.00 0.00 4.24
1341 1645 3.753434 CCGCTGAGCTCGGTGTCT 61.753 66.667 29.42 0.00 41.85 3.41
1347 1651 2.983930 GAGCTCGGTGTCTGACGCT 61.984 63.158 19.60 13.16 0.00 5.07
1522 1848 1.300311 CGTACACGGTTCCAGTGCA 60.300 57.895 11.46 0.00 42.94 4.57
1560 1886 0.252103 TCCGTTCCTACCAGGCTCTT 60.252 55.000 0.00 0.00 34.61 2.85
1692 2024 1.152819 CGAGGGGGACGAGGACATA 60.153 63.158 0.00 0.00 0.00 2.29
1970 2314 1.270550 GCATTCCGGCTAATCCCAATG 59.729 52.381 0.00 0.00 35.87 2.82
1983 2327 1.010046 TCCCAATGGAGGAGGTGATCT 59.990 52.381 0.00 0.00 35.03 2.75
2091 2461 1.804151 GGCAGTCAATTTGCTCGTACA 59.196 47.619 0.92 0.00 41.27 2.90
2120 2490 8.214405 TCGATTCCGTTGATCTGTTTTTACAGA 61.214 37.037 10.11 10.11 42.46 3.41
2149 2519 6.479095 AAACTGTTGATGTTGGTTTTGTTG 57.521 33.333 0.00 0.00 0.00 3.33
2398 2768 4.955450 TGGAGTAGAGTAGAGTAGACGAGT 59.045 45.833 0.00 0.00 0.00 4.18
2464 2840 2.401583 TTGCTCTGTGTCTGTGTTGT 57.598 45.000 0.00 0.00 0.00 3.32
2610 2996 3.324713 GCCCCAGCCACATACTCT 58.675 61.111 0.00 0.00 0.00 3.24
2611 2997 1.153086 GCCCCAGCCACATACTCTG 60.153 63.158 0.00 0.00 0.00 3.35
2695 3088 2.067932 TAACAGCCAGCCAACCAGCT 62.068 55.000 0.00 0.00 46.45 4.24
2829 3237 2.516888 CCCAGTCGGAGGTTGGTGT 61.517 63.158 3.36 0.00 0.00 4.16
2831 3239 1.445942 CAGTCGGAGGTTGGTGTGT 59.554 57.895 0.00 0.00 0.00 3.72
2847 3255 2.123897 GTGGTGGTGGTGGTGCTT 60.124 61.111 0.00 0.00 0.00 3.91
2851 3259 1.961277 GTGGTGGTGGTGCTTCGAG 60.961 63.158 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.980765 ACATCTTTGGAGAGTGGAGCA 59.019 47.619 0.00 0.00 34.85 4.26
90 91 1.551452 TTGCCCATTCCCTAAAACCG 58.449 50.000 0.00 0.00 0.00 4.44
152 153 2.108157 ACCGACACATGTGCACGT 59.892 55.556 29.85 19.95 33.99 4.49
158 159 4.382040 CCTTTCTCTATCACCGACACATGT 60.382 45.833 0.00 0.00 0.00 3.21
166 167 2.464865 CTTCGCCTTTCTCTATCACCG 58.535 52.381 0.00 0.00 0.00 4.94
173 174 3.198853 AGCTTATTCCTTCGCCTTTCTCT 59.801 43.478 0.00 0.00 0.00 3.10
178 179 3.135530 AGATGAGCTTATTCCTTCGCCTT 59.864 43.478 0.00 0.00 0.00 4.35
179 180 2.703007 AGATGAGCTTATTCCTTCGCCT 59.297 45.455 0.00 0.00 0.00 5.52
189 190 6.150318 CGTGTATACCGAAAGATGAGCTTAT 58.850 40.000 0.00 0.00 35.24 1.73
192 193 3.795826 GCGTGTATACCGAAAGATGAGCT 60.796 47.826 15.19 0.00 0.00 4.09
208 209 2.672188 CACGTTTTTCATGGCGTGTA 57.328 45.000 6.60 0.00 46.30 2.90
359 360 2.225369 CCCCTTTCCTCAAACCCTTCAT 60.225 50.000 0.00 0.00 0.00 2.57
394 395 3.373748 ACATTATTCGATCTGCGTGCAAA 59.626 39.130 0.00 0.00 41.80 3.68
396 397 2.284952 CACATTATTCGATCTGCGTGCA 59.715 45.455 0.00 0.00 41.80 4.57
415 416 2.034001 GTGAGCGTGACTTGTTACACAC 60.034 50.000 0.00 0.00 36.91 3.82
439 440 5.702670 ACACTCATCACACCATGTCTTTTAG 59.297 40.000 0.00 0.00 0.00 1.85
446 447 2.497138 CACACACTCATCACACCATGT 58.503 47.619 0.00 0.00 0.00 3.21
463 464 1.705002 CCTCCCTCACAACACCCACA 61.705 60.000 0.00 0.00 0.00 4.17
487 488 1.682087 GCATCCTTTACACACCCCCTC 60.682 57.143 0.00 0.00 0.00 4.30
488 489 0.331616 GCATCCTTTACACACCCCCT 59.668 55.000 0.00 0.00 0.00 4.79
489 490 0.331616 AGCATCCTTTACACACCCCC 59.668 55.000 0.00 0.00 0.00 5.40
490 491 2.238898 AGTAGCATCCTTTACACACCCC 59.761 50.000 0.00 0.00 0.00 4.95
491 492 3.629142 AGTAGCATCCTTTACACACCC 57.371 47.619 0.00 0.00 0.00 4.61
492 493 5.462398 CGATTAGTAGCATCCTTTACACACC 59.538 44.000 0.00 0.00 0.00 4.16
493 494 6.040878 ACGATTAGTAGCATCCTTTACACAC 58.959 40.000 0.00 0.00 0.00 3.82
494 495 6.216801 ACGATTAGTAGCATCCTTTACACA 57.783 37.500 0.00 0.00 0.00 3.72
495 496 5.398711 CGACGATTAGTAGCATCCTTTACAC 59.601 44.000 0.00 0.00 0.00 2.90
507 777 4.433805 GCAACCACAAACGACGATTAGTAG 60.434 45.833 0.00 0.00 0.00 2.57
510 780 2.720590 CGCAACCACAAACGACGATTAG 60.721 50.000 0.00 0.00 0.00 1.73
714 986 7.116075 TGCTTGATATTTTCCAGCCTTAACTA 58.884 34.615 0.00 0.00 41.36 2.24
921 1197 0.038526 GACGGGAGCAAACGAGAGAA 60.039 55.000 0.00 0.00 0.00 2.87
1155 1453 0.666374 TCTTGAAGCTGACGTCGTCA 59.334 50.000 25.51 25.51 40.50 4.35
1522 1848 0.673644 AATACCTTCTTGCACGCGCT 60.674 50.000 5.73 0.00 39.64 5.92
1970 2314 1.118838 CACCTCAGATCACCTCCTCC 58.881 60.000 0.00 0.00 0.00 4.30
1983 2327 5.667172 TCTTGGATGGATTTATCTCACCTCA 59.333 40.000 0.00 0.00 0.00 3.86
2091 2461 5.880054 AAACAGATCAACGGAATCGAATT 57.120 34.783 0.00 0.00 40.11 2.17
2120 2490 9.097257 CAAAACCAACATCAACAGTTTAGAATT 57.903 29.630 0.00 0.00 30.80 2.17
2124 2494 7.673776 GCAACAAAACCAACATCAACAGTTTAG 60.674 37.037 0.00 0.00 30.80 1.85
2140 2510 5.765072 TTTAAACGAACAGCAACAAAACC 57.235 34.783 0.00 0.00 0.00 3.27
2149 2519 5.291293 TCCATAGCTTTTAAACGAACAGC 57.709 39.130 0.00 1.34 0.00 4.40
2277 2647 1.484038 GGCTATGCAAACATGGGGAA 58.516 50.000 0.00 0.00 37.04 3.97
2398 2768 4.093472 TGGACACTAGGCAAAAGCTTAA 57.907 40.909 0.00 0.00 0.00 1.85
2464 2840 0.951558 GCGAAAGAAAGGAGGCAACA 59.048 50.000 0.00 0.00 41.41 3.33
2598 2984 0.100682 CGTACGCAGAGTATGTGGCT 59.899 55.000 0.52 0.00 44.07 4.75
2610 2996 0.171007 GCAACCTAGTACCGTACGCA 59.829 55.000 10.49 0.00 0.00 5.24
2611 2997 0.171007 TGCAACCTAGTACCGTACGC 59.829 55.000 10.49 0.00 0.00 4.42
2695 3088 7.361713 CGTTTCTCCATAAACAAAGAATGGCTA 60.362 37.037 0.00 0.00 40.05 3.93
2814 3217 1.445942 CACACACCAACCTCCGACT 59.554 57.895 0.00 0.00 0.00 4.18
2816 3219 2.067605 ACCACACACCAACCTCCGA 61.068 57.895 0.00 0.00 0.00 4.55
2829 3237 2.902423 GAAGCACCACCACCACCACA 62.902 60.000 0.00 0.00 0.00 4.17
2831 3239 2.194597 GAAGCACCACCACCACCA 59.805 61.111 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.