Multiple sequence alignment - TraesCS5A01G524600

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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 TraesCS5A01G524600 chr5A 100.000 2912 0 0 1 2912 685196508 685193597 0 5378
1 TraesCS5A01G524600 chr5A 96.480 767 25 2 2147 2912 382997953 382997188 0 1266
2 TraesCS5A01G524600 chr5A 96.224 768 27 2 2147 2912 550778264 550777497 0 1256
3 TraesCS5A01G524600 chr5A 96.204 764 26 3 2147 2909 49631472 49632233 0 1247
4 TraesCS5A01G524600 chr7D 98.042 2145 40 2 1 2144 135768490 135770633 0 3727
5 TraesCS5A01G524600 chr7D 97.949 2145 42 2 1 2144 23562479 23564622 0 3716
6 TraesCS5A01G524600 chr7D 97.902 2145 43 2 1 2144 135764565 135762422 0 3711
7 TraesCS5A01G524600 chr7D 97.716 2145 47 2 1 2144 14171614 14169471 0 3688
8 TraesCS5A01G524600 chr7D 97.672 2148 48 2 1 2147 400292279 400290133 0 3688
9 TraesCS5A01G524600 chr6D 97.762 2145 45 3 1 2144 402531809 402529667 0 3692
10 TraesCS5A01G524600 chr2D 97.716 2145 45 3 1 2144 70659969 70657828 0 3687
11 TraesCS5A01G524600 chr2D 97.622 2145 49 2 1 2144 35062095 35059952 0 3677
12 TraesCS5A01G524600 chr5D 97.669 2145 48 2 1 2144 460677388 460679531 0 3683
13 TraesCS5A01G524600 chr2A 96.597 764 25 1 2147 2909 593876604 593877367 0 1266
14 TraesCS5A01G524600 chr2A 96.089 767 28 2 2147 2912 168058439 168057674 0 1249
15 TraesCS5A01G524600 chr1A 96.209 765 28 1 2149 2912 126142799 126143563 0 1251
16 TraesCS5A01G524600 chr1A 96.204 764 27 2 2147 2909 510890824 510891586 0 1249
17 TraesCS5A01G524600 chr6A 96.204 764 27 2 2147 2909 427392940 427393702 0 1249
18 TraesCS5A01G524600 chr6A 96.089 767 28 2 2147 2912 581214215 581213450 0 1249


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 TraesCS5A01G524600 chr5A 685193597 685196508 2911 True 5378 5378 100.000 1 2912 1 chr5A.!!$R3 2911
1 TraesCS5A01G524600 chr5A 382997188 382997953 765 True 1266 1266 96.480 2147 2912 1 chr5A.!!$R1 765
2 TraesCS5A01G524600 chr5A 550777497 550778264 767 True 1256 1256 96.224 2147 2912 1 chr5A.!!$R2 765
3 TraesCS5A01G524600 chr5A 49631472 49632233 761 False 1247 1247 96.204 2147 2909 1 chr5A.!!$F1 762
4 TraesCS5A01G524600 chr7D 135768490 135770633 2143 False 3727 3727 98.042 1 2144 1 chr7D.!!$F2 2143
5 TraesCS5A01G524600 chr7D 23562479 23564622 2143 False 3716 3716 97.949 1 2144 1 chr7D.!!$F1 2143
6 TraesCS5A01G524600 chr7D 135762422 135764565 2143 True 3711 3711 97.902 1 2144 1 chr7D.!!$R2 2143
7 TraesCS5A01G524600 chr7D 14169471 14171614 2143 True 3688 3688 97.716 1 2144 1 chr7D.!!$R1 2143
8 TraesCS5A01G524600 chr7D 400290133 400292279 2146 True 3688 3688 97.672 1 2147 1 chr7D.!!$R3 2146
9 TraesCS5A01G524600 chr6D 402529667 402531809 2142 True 3692 3692 97.762 1 2144 1 chr6D.!!$R1 2143
10 TraesCS5A01G524600 chr2D 70657828 70659969 2141 True 3687 3687 97.716 1 2144 1 chr2D.!!$R2 2143
11 TraesCS5A01G524600 chr2D 35059952 35062095 2143 True 3677 3677 97.622 1 2144 1 chr2D.!!$R1 2143
12 TraesCS5A01G524600 chr5D 460677388 460679531 2143 False 3683 3683 97.669 1 2144 1 chr5D.!!$F1 2143
13 TraesCS5A01G524600 chr2A 593876604 593877367 763 False 1266 1266 96.597 2147 2909 1 chr2A.!!$F1 762
14 TraesCS5A01G524600 chr2A 168057674 168058439 765 True 1249 1249 96.089 2147 2912 1 chr2A.!!$R1 765
15 TraesCS5A01G524600 chr1A 126142799 126143563 764 False 1251 1251 96.209 2149 2912 1 chr1A.!!$F1 763
16 TraesCS5A01G524600 chr1A 510890824 510891586 762 False 1249 1249 96.204 2147 2909 1 chr1A.!!$F2 762
17 TraesCS5A01G524600 chr6A 427392940 427393702 762 False 1249 1249 96.204 2147 2909 1 chr6A.!!$F1 762
18 TraesCS5A01G524600 chr6A 581213450 581214215 765 True 1249 1249 96.089 2147 2912 1 chr6A.!!$R1 765

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
669 671 0.538746 GAAGGGAAAACGCCAAGGGA 60.539 55.000 0.0 0.0 0.00 4.20 F
1632 1634 2.288334 GCCAAACACATTCATGTCAGCA 60.288 45.455 0.0 0.0 39.39 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1708 0.878523 TGCAACAGTCACAGGTACGC 60.879 55.0 0.0 0.0 0.0 4.42 R
2877 2883 0.747255 ATCGCATTCTAGCTGGTCGT 59.253 50.0 0.0 0.0 0.0 4.34 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 2.478872 TGAGGTAAGGCTGAGGCTAT 57.521 50.000 9.60 2.43 37.50 2.97
135 136 2.160417 GGAGCGATGGAGACTTGTTTTG 59.840 50.000 0.00 0.00 0.00 2.44
149 150 9.950680 GAGACTTGTTTTGATTAGAATTGTTGA 57.049 29.630 0.00 0.00 0.00 3.18
188 189 5.312895 TGCTAAACATAGTCTGGCTTTTCA 58.687 37.500 0.00 0.00 0.00 2.69
439 440 4.412843 TGTCATCTTGGACTGTACACCTA 58.587 43.478 0.00 0.00 38.61 3.08
480 481 6.299141 ACAAATGACTCTAATTGTGAGGTGT 58.701 36.000 12.73 7.24 34.88 4.16
661 663 3.551551 GTTCGAACATGAAGGGAAAACG 58.448 45.455 23.12 0.00 0.00 3.60
669 671 0.538746 GAAGGGAAAACGCCAAGGGA 60.539 55.000 0.00 0.00 0.00 4.20
674 676 2.375146 GGAAAACGCCAAGGGATACAT 58.625 47.619 0.00 0.00 39.74 2.29
700 702 7.224297 AGCAGACTACTTGAAACTAATCCAAA 58.776 34.615 0.00 0.00 0.00 3.28
757 759 7.287927 CCTGAACCTTACTCTTAGTGATATGGA 59.712 40.741 0.00 0.00 0.00 3.41
894 896 7.064134 TGACAGTTAAGTCTTTGTGTAACACTG 59.936 37.037 0.00 0.00 42.60 3.66
895 897 7.064253 GACAGTTAAGTCTTTGTGTAACACTGT 59.936 37.037 0.00 0.00 40.40 3.55
921 923 4.158025 TGGGAGAGTCGAATAAAGAGTGTC 59.842 45.833 0.00 0.00 32.50 3.67
1045 1047 3.366374 GGCTAGCGCACTTGAGAAATTTT 60.366 43.478 11.47 0.00 38.10 1.82
1188 1190 8.778358 GCCATCTCATATTTTAAGAAGTACAGG 58.222 37.037 0.00 0.00 0.00 4.00
1205 1207 2.549754 ACAGGAATGACGACTTTGCAAG 59.450 45.455 0.00 0.00 0.00 4.01
1318 1320 6.587206 TTGATGAAATTAGTGGCAATGACA 57.413 33.333 0.00 0.00 0.00 3.58
1473 1475 6.922957 GCATATTTGGTTTCTTGTTCAACTCA 59.077 34.615 0.00 0.00 0.00 3.41
1502 1504 4.235079 TGAAGTCCTTGGGTGATAATGG 57.765 45.455 0.00 0.00 0.00 3.16
1632 1634 2.288334 GCCAAACACATTCATGTCAGCA 60.288 45.455 0.00 0.00 39.39 4.41
1699 1701 8.437360 AAATGTCTCAATTGCTTATCGTATCA 57.563 30.769 0.00 0.00 0.00 2.15
1706 1708 9.378597 CTCAATTGCTTATCGTATCATTTTGAG 57.621 33.333 0.00 0.00 0.00 3.02
1743 1745 4.019792 TGCATCAGCTGAAAGGAGTTTA 57.980 40.909 22.50 0.00 42.74 2.01
1787 1789 8.519492 AAAAATTATTTGAGGTCAACGATGTG 57.481 30.769 0.00 0.00 35.28 3.21
1915 1917 5.062683 CGAAAGTCTCGTTTCACATGATCAT 59.937 40.000 1.18 1.18 42.89 2.45
1945 1947 8.571336 AGGTTAGCATGCTATTTCAATATGTTC 58.429 33.333 27.35 1.94 0.00 3.18
1953 1955 8.054152 TGCTATTTCAATATGTTCTTTCTGCA 57.946 30.769 0.00 0.00 0.00 4.41
2130 2132 2.045340 ACCGGGGCCTTCGAAATG 60.045 61.111 18.01 6.16 0.00 2.32
2140 2142 2.803492 GCCTTCGAAATGATAGAGCCGT 60.803 50.000 0.00 0.00 0.00 5.68
2144 2146 1.068588 CGAAATGATAGAGCCGTCCCA 59.931 52.381 0.00 0.00 0.00 4.37
2530 2534 2.787035 AGTCCCAGGGGAGTTTTGTTTA 59.213 45.455 7.47 0.00 45.01 2.01
2644 2648 2.994186 TGAGAATAACCCGCCTAACC 57.006 50.000 0.00 0.00 0.00 2.85
2707 2711 7.624360 TCGAGCATACAAAACAGGATATTTT 57.376 32.000 0.00 0.00 0.00 1.82
2848 2854 2.604046 AGCAGTATTCCCGCTTAGTG 57.396 50.000 0.00 0.00 29.87 2.74
2877 2883 2.108250 AGGCTAGCAAAAGACTGGGAAA 59.892 45.455 18.24 0.00 31.94 3.13
2890 2896 1.344065 TGGGAAACGACCAGCTAGAA 58.656 50.000 0.00 0.00 33.23 2.10
2891 2897 1.906574 TGGGAAACGACCAGCTAGAAT 59.093 47.619 0.00 0.00 33.23 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 8.922058 ATTTCACAGCATCAACAATTCTAATC 57.078 30.769 0.00 0.00 0.00 1.75
149 150 6.514947 TGTTTAGCAAGAAATTTCACAGCAT 58.485 32.000 19.99 11.70 0.00 3.79
439 440 2.254546 TGTTCTTGATGGCTCACGTT 57.745 45.000 0.00 0.00 0.00 3.99
661 663 2.370189 AGTCTGCTATGTATCCCTTGGC 59.630 50.000 0.00 0.00 0.00 4.52
674 676 7.476540 TGGATTAGTTTCAAGTAGTCTGCTA 57.523 36.000 0.00 0.00 0.00 3.49
757 759 4.584327 ACAGCTTTACCGCAAGATTTTT 57.416 36.364 0.00 0.00 43.02 1.94
894 896 5.163499 ACTCTTTATTCGACTCTCCCATCAC 60.163 44.000 0.00 0.00 0.00 3.06
895 897 4.956700 ACTCTTTATTCGACTCTCCCATCA 59.043 41.667 0.00 0.00 0.00 3.07
921 923 4.252073 GTGCTTGATATCTGATAGCCTGG 58.748 47.826 10.16 0.00 0.00 4.45
1045 1047 7.605691 CCAAATGACCATGCCAAGTAAAAATTA 59.394 33.333 0.00 0.00 0.00 1.40
1152 1154 9.639563 TTAAAATATGAGATGGCACCTTCAATA 57.360 29.630 5.47 3.77 0.00 1.90
1205 1207 5.637006 AGATCTCGCAATATCCAGACTAC 57.363 43.478 0.00 0.00 0.00 2.73
1318 1320 7.206687 TGCGTTTCTTCATTCTGGTTATTTTT 58.793 30.769 0.00 0.00 0.00 1.94
1382 1384 3.872511 TTGCAACATCAATCATCACCC 57.127 42.857 0.00 0.00 0.00 4.61
1473 1475 3.954258 CACCCAAGGACTTCAACTCTTTT 59.046 43.478 0.00 0.00 0.00 2.27
1502 1504 9.334693 CAAAATTAGTGCAACATCTTCTTAGAC 57.665 33.333 0.00 0.00 41.43 2.59
1699 1701 3.067106 CAGTCACAGGTACGCTCAAAAT 58.933 45.455 0.00 0.00 0.00 1.82
1706 1708 0.878523 TGCAACAGTCACAGGTACGC 60.879 55.000 0.00 0.00 0.00 4.42
1787 1789 5.809051 GCCAATCCATTCAATCTTTCTTGAC 59.191 40.000 0.00 0.00 34.96 3.18
1915 1917 4.854173 TGAAATAGCATGCTAACCTCCAA 58.146 39.130 30.06 8.32 31.73 3.53
1945 1947 6.258230 TCATGGAAGTTACAATGCAGAAAG 57.742 37.500 0.00 0.00 0.00 2.62
1953 1955 8.522830 CAAACCAAGTATCATGGAAGTTACAAT 58.477 33.333 0.00 0.00 40.56 2.71
2130 2132 0.892063 GATCCTGGGACGGCTCTATC 59.108 60.000 0.00 0.00 0.00 2.08
2140 2142 1.203300 TGACTTGACTGGATCCTGGGA 60.203 52.381 21.40 5.76 0.00 4.37
2144 2146 4.614475 TGAGTATGACTTGACTGGATCCT 58.386 43.478 14.23 0.00 0.00 3.24
2353 2355 9.132521 CATCTCTTGGTTGTTATGTTGAAAATC 57.867 33.333 0.00 0.00 0.00 2.17
2644 2648 1.831736 AGGGTTGTCCGTATCTTCCAG 59.168 52.381 0.00 0.00 41.52 3.86
2707 2711 5.186021 TGTGCCAAACTCTAAACCTTCAAAA 59.814 36.000 0.00 0.00 0.00 2.44
2848 2854 3.685272 GTCTTTTGCTAGCCTTCACCTAC 59.315 47.826 13.29 0.00 0.00 3.18
2877 2883 0.747255 ATCGCATTCTAGCTGGTCGT 59.253 50.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.