Multiple sequence alignment - TraesCS6B01G216700

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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 TraesCS6B01G216700 chr6B 100.000 1480 0 0 1629 3108 297486390 297484911 0 2734
1 TraesCS6B01G216700 chr6B 96.917 1492 34 6 1629 3108 596630174 596631665 0 2490
2 TraesCS6B01G216700 chr6B 100.000 1211 0 0 1 1211 297488018 297486808 0 2237
3 TraesCS6B01G216700 chr6B 97.195 1212 30 4 1 1211 596628846 596630054 0 2047
4 TraesCS6B01G216700 chrUn 96.986 1493 32 6 1629 3108 222678829 222677337 0 2495
5 TraesCS6B01G216700 chrUn 96.919 1493 33 6 1629 3108 86450447 86451939 0 2490
6 TraesCS6B01G216700 chrUn 96.917 1492 34 6 1629 3108 86456447 86457938 0 2490
7 TraesCS6B01G216700 chrUn 97.442 1212 27 4 1 1211 86449119 86450327 0 2063
8 TraesCS6B01G216700 chrUn 97.360 1212 29 3 1 1211 222680158 222678949 0 2058
9 TraesCS6B01G216700 chrUn 97.277 1212 29 4 1 1211 86455119 86456327 0 2052
10 TraesCS6B01G216700 chr5B 96.919 1493 33 6 1629 3108 533067995 533069487 0 2490
11 TraesCS6B01G216700 chr5B 97.525 1212 27 3 1 1211 533066666 533067875 0 2069
12 TraesCS6B01G216700 chr1A 96.919 1493 33 6 1629 3108 238118817 238120309 0 2490
13 TraesCS6B01G216700 chr1A 96.852 1493 34 6 1629 3108 238122738 238124230 0 2484
14 TraesCS6B01G216700 chr1A 97.442 1212 28 3 1 1211 238117487 238118696 0 2063
15 TraesCS6B01G216700 chr1A 97.195 1212 30 4 1 1211 238121410 238122618 0 2047
16 TraesCS6B01G216700 chr3B 96.787 1494 34 8 1629 3108 92327713 92329206 0 2481
17 TraesCS6B01G216700 chr3B 97.195 1212 31 3 1 1211 92326384 92327593 0 2047
18 TraesCS6B01G216700 chr4D 96.586 1494 37 6 1629 3108 123433599 123435092 0 2464
19 TraesCS6B01G216700 chr7B 97.195 1212 31 3 1 1211 742925243 742926452 0 2047


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 TraesCS6B01G216700 chr6B 297484911 297488018 3107 True 2485.50 2734 100.00000 1 3108 2 chr6B.!!$R1 3107
1 TraesCS6B01G216700 chr6B 596628846 596631665 2819 False 2268.50 2490 97.05600 1 3108 2 chr6B.!!$F1 3107
2 TraesCS6B01G216700 chrUn 222677337 222680158 2821 True 2276.50 2495 97.17300 1 3108 2 chrUn.!!$R1 3107
3 TraesCS6B01G216700 chrUn 86449119 86457938 8819 False 2273.75 2490 97.13875 1 3108 4 chrUn.!!$F1 3107
4 TraesCS6B01G216700 chr5B 533066666 533069487 2821 False 2279.50 2490 97.22200 1 3108 2 chr5B.!!$F1 3107
5 TraesCS6B01G216700 chr1A 238117487 238124230 6743 False 2271.00 2490 97.10200 1 3108 4 chr1A.!!$F1 3107
6 TraesCS6B01G216700 chr3B 92326384 92329206 2822 False 2264.00 2481 96.99100 1 3108 2 chr3B.!!$F1 3107
7 TraesCS6B01G216700 chr4D 123433599 123435092 1493 False 2464.00 2464 96.58600 1629 3108 1 chr4D.!!$F1 1479
8 TraesCS6B01G216700 chr7B 742925243 742926452 1209 False 2047.00 2047 97.19500 1 1211 1 chr7B.!!$F1 1210

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
415 416 0.166814 GTGCTTCTTTAGTGCCGCTG 59.833 55.000 0.00 0.0 0.00 5.18 F
1140 1144 0.678395 TTACGCGTTACTGGTTCCCA 59.322 50.000 20.78 0.0 0.00 4.37 F
1981 1988 1.134098 CCGGATATCTGGTGCCAAACT 60.134 52.381 20.98 0.0 37.62 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 1951 1.228124 CGGGGTGTGGAAAGAGCAA 60.228 57.895 0.00 0.0 0.0 3.91 R
2064 5992 2.168521 CCGCTTTCCCTCATTCTACTCA 59.831 50.000 0.00 0.0 0.0 3.41 R
2922 12859 2.615986 TGGCCTTCTCACTAGTGGTA 57.384 50.000 22.48 8.4 0.0 3.25 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
40 41 3.496884 CGGTCCGAACTCAATTTCAAGAA 59.503 43.478 4.91 0.00 0.00 2.52
67 68 1.202568 TCTATCTCGCATGTGGCCAAG 60.203 52.381 7.24 0.00 40.31 3.61
207 208 3.321682 CCTTGTTTTGGTCATGTCCACAT 59.678 43.478 11.47 0.00 37.20 3.21
217 218 1.203052 CATGTCCACATGCCTTTCCAC 59.797 52.381 6.75 0.00 45.92 4.02
275 276 7.168219 TGCATAATTCTACTTCTTGAACCACT 58.832 34.615 0.00 0.00 0.00 4.00
360 361 2.694628 AGCACACTTTTGAAAGGCATCA 59.305 40.909 8.23 0.00 40.31 3.07
411 412 1.661112 CTAGCGTGCTTCTTTAGTGCC 59.339 52.381 0.00 0.00 0.00 5.01
415 416 0.166814 GTGCTTCTTTAGTGCCGCTG 59.833 55.000 0.00 0.00 0.00 5.18
517 518 5.988310 TGATTTTGATCATGAAGTTGGCT 57.012 34.783 0.00 0.00 0.00 4.75
542 543 5.012239 TGGACTTTGGAATTGATTCTGGAG 58.988 41.667 3.94 2.75 37.00 3.86
564 565 2.660064 CCACCTGCTTAGGACGCCT 61.660 63.158 0.00 3.87 37.71 5.52
589 590 2.301296 CTGCTCAGGACGATCCCATTAT 59.699 50.000 0.00 0.00 37.19 1.28
599 600 5.770162 GGACGATCCCATTATGGATTTTCTT 59.230 40.000 13.63 0.00 45.25 2.52
677 678 5.833406 TCATGAAGAACAAAAGCAGAACA 57.167 34.783 0.00 0.00 0.00 3.18
693 694 5.127682 AGCAGAACAAACCTTCAAAATGAGT 59.872 36.000 0.00 0.00 0.00 3.41
980 984 5.492524 AGAAATGGTCCCAGAGAAAGGAATA 59.507 40.000 0.00 0.00 32.81 1.75
992 996 6.534793 CAGAGAAAGGAATAAGTCTCTTCAGC 59.465 42.308 0.00 0.00 43.36 4.26
1140 1144 0.678395 TTACGCGTTACTGGTTCCCA 59.322 50.000 20.78 0.00 0.00 4.37
1188 1192 8.274322 GCTAAACCCTTTATTACCCTACCTTTA 58.726 37.037 0.00 0.00 0.00 1.85
1945 1951 2.494073 TGGTTTTTCCGCTTTTCACAGT 59.506 40.909 0.00 0.00 39.52 3.55
1981 1988 1.134098 CCGGATATCTGGTGCCAAACT 60.134 52.381 20.98 0.00 37.62 2.66
1984 1991 3.356290 GGATATCTGGTGCCAAACTGTT 58.644 45.455 2.05 0.00 0.00 3.16
2048 5976 5.528043 TGTGGCATTGATTGTACAAGTTT 57.472 34.783 14.65 0.00 33.22 2.66
2054 5982 6.074356 GGCATTGATTGTACAAGTTTGTGAAC 60.074 38.462 14.65 0.03 42.31 3.18
2059 5987 4.223556 TGTACAAGTTTGTGAACAGGGA 57.776 40.909 7.73 0.00 42.31 4.20
2064 5992 3.814504 AGTTTGTGAACAGGGATGGAT 57.185 42.857 0.00 0.00 38.26 3.41
2209 6140 7.507616 AGACGGAATCTCAGATAAGAACCTAAT 59.492 37.037 0.00 0.00 28.16 1.73
2443 6381 0.827368 TGCATATCCCGTGTGTGCTA 59.173 50.000 0.00 0.00 36.78 3.49
2530 6468 2.472695 TCGCAGCTGTTAGTGGAAAT 57.527 45.000 16.64 0.00 0.00 2.17
2740 12677 5.362263 AGCTACTAAGTCAAAACGTCCAAA 58.638 37.500 0.00 0.00 0.00 3.28
2851 12788 4.428209 AGAGATCACAAGCGTTATCAGTG 58.572 43.478 0.00 0.00 29.58 3.66
2854 12791 3.660501 TCACAAGCGTTATCAGTGTCT 57.339 42.857 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 3.788227 TTTCACTACTCTTGGCCACAT 57.212 42.857 3.88 0.00 0.00 3.21
207 208 3.695830 ATAAAGACGAGTGGAAAGGCA 57.304 42.857 0.00 0.00 0.00 4.75
217 218 5.003590 CGGAAGAAAGACGAATAAAGACGAG 59.996 44.000 0.00 0.00 0.00 4.18
275 276 4.862902 TCCATTTTCAAAAGCGGATTCA 57.137 36.364 0.53 0.00 0.00 2.57
411 412 1.284657 AAGCATCTGATCGAACAGCG 58.715 50.000 17.19 11.71 42.69 5.18
415 416 5.292834 TCAATGAGAAAGCATCTGATCGAAC 59.707 40.000 0.00 0.00 38.96 3.95
517 518 5.012239 CCAGAATCAATTCCAAAGTCCAGA 58.988 41.667 0.00 0.00 37.51 3.86
542 543 3.015145 TCCTAAGCAGGTGGGGGC 61.015 66.667 0.00 0.00 43.18 5.80
589 590 2.069775 TGTCCCCCTCAAGAAAATCCA 58.930 47.619 0.00 0.00 0.00 3.41
599 600 2.525629 TCAAGCGTGTCCCCCTCA 60.526 61.111 0.00 0.00 0.00 3.86
664 665 4.799564 TGAAGGTTTGTTCTGCTTTTGT 57.200 36.364 0.00 0.00 0.00 2.83
677 678 6.391227 ACGATTCACTCATTTTGAAGGTTT 57.609 33.333 0.00 0.00 36.44 3.27
693 694 8.673711 CCCTCAACATCTTTTTATTACGATTCA 58.326 33.333 0.00 0.00 0.00 2.57
716 718 1.883322 AACTACTACCCTCGCCCCCT 61.883 60.000 0.00 0.00 0.00 4.79
783 787 0.475475 TGCTAATCCCCCAGCATGAG 59.525 55.000 0.00 0.00 42.68 2.90
784 788 0.475475 CTGCTAATCCCCCAGCATGA 59.525 55.000 0.00 0.00 46.15 3.07
786 790 1.723128 CCCTGCTAATCCCCCAGCAT 61.723 60.000 0.00 0.00 46.15 3.79
980 984 2.665603 GCCGGGCTGAAGAGACTT 59.334 61.111 12.87 0.00 0.00 3.01
1140 1144 6.956497 AGCTAATGGAGAAATTGACTCTTCT 58.044 36.000 11.09 0.00 34.58 2.85
1810 1814 5.447846 CGATGGAATGAACAAAATACGAACG 59.552 40.000 0.00 0.00 0.00 3.95
1909 1913 7.290118 CGGAAAAACCATCAAAACAATGATTC 58.710 34.615 0.00 0.00 37.96 2.52
1914 1918 4.702831 AGCGGAAAAACCATCAAAACAAT 58.297 34.783 0.00 0.00 38.90 2.71
1916 1920 3.810310 AGCGGAAAAACCATCAAAACA 57.190 38.095 0.00 0.00 38.90 2.83
1945 1951 1.228124 CGGGGTGTGGAAAGAGCAA 60.228 57.895 0.00 0.00 0.00 3.91
1981 1988 6.001460 CGAATATATAAGGAAAGGGGCAACA 58.999 40.000 0.00 0.00 39.74 3.33
1984 1991 6.636454 ATCGAATATATAAGGAAAGGGGCA 57.364 37.500 0.00 0.00 0.00 5.36
2048 5976 2.269023 ACTCATCCATCCCTGTTCACA 58.731 47.619 0.00 0.00 0.00 3.58
2054 5982 4.020396 CCTCATTCTACTCATCCATCCCTG 60.020 50.000 0.00 0.00 0.00 4.45
2059 5987 5.455899 GCTTTCCCTCATTCTACTCATCCAT 60.456 44.000 0.00 0.00 0.00 3.41
2064 5992 2.168521 CCGCTTTCCCTCATTCTACTCA 59.831 50.000 0.00 0.00 0.00 3.41
2209 6140 2.555325 TGAAGGAGTCGCGAAACTTCTA 59.445 45.455 31.05 21.65 33.79 2.10
2443 6381 3.959449 GGTCTAGGAGAACCCGAAACTAT 59.041 47.826 0.00 0.00 40.87 2.12
2521 6459 9.983024 TTAGAACCAATTTCCATATTTCCACTA 57.017 29.630 0.00 0.00 34.32 2.74
2530 6468 6.951198 TGGCTCTTTTAGAACCAATTTCCATA 59.049 34.615 0.00 0.00 37.52 2.74
2555 6493 7.293535 ACCAACCATATCTCTTATCCTTAGCTT 59.706 37.037 0.00 0.00 0.00 3.74
2561 12498 5.456763 GCCAACCAACCATATCTCTTATCCT 60.457 44.000 0.00 0.00 0.00 3.24
2693 12630 7.977853 GCTATGTGATTTTTCACTTTGATCCAT 59.022 33.333 7.55 0.00 40.97 3.41
2694 12631 7.177216 AGCTATGTGATTTTTCACTTTGATCCA 59.823 33.333 7.55 0.00 40.97 3.41
2740 12677 3.966665 GTCCCTCTTGATCTCCATTCTCT 59.033 47.826 0.00 0.00 0.00 3.10
2851 12788 9.562583 CCTTTTTATAGATAGATGCGTCTAGAC 57.437 37.037 19.95 13.18 40.16 2.59
2854 12791 9.298250 ACTCCTTTTTATAGATAGATGCGTCTA 57.702 33.333 17.80 17.80 41.03 2.59
2905 12842 4.487714 TGGTATCAATCCTTGACTCCAC 57.512 45.455 9.36 0.30 43.48 4.02
2922 12859 2.615986 TGGCCTTCTCACTAGTGGTA 57.384 50.000 22.48 8.40 0.00 3.25


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

AutoCloner maintained by Alex Coulton.