Multiple sequence alignment - TraesCS2D01G322700

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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 TraesCS2D01G322700 chr2D 100.000 2780 0 0 1 2780 414400608 414403387 0.000000e+00 5134
1 TraesCS2D01G322700 chr2B 93.604 2830 115 35 1 2780 488007994 488010807 0.000000e+00 4163
2 TraesCS2D01G322700 chr2A 92.185 2009 106 24 814 2780 581577065 581579064 0.000000e+00 2793
3 TraesCS2D01G322700 chr2A 86.317 782 46 23 3 757 581565976 581566723 0.000000e+00 795
4 TraesCS2D01G322700 chr5D 85.109 826 69 27 989 1781 513978159 513978963 0.000000e+00 795
5 TraesCS2D01G322700 chr5A 92.079 404 32 0 1378 1781 641733449 641733852 1.120000e-158 569
6 TraesCS2D01G322700 chr5A 85.846 325 30 9 989 1300 641733086 641733407 5.740000e-87 331
7 TraesCS2D01G322700 chr5B 91.832 404 33 0 1378 1781 644890066 644890469 5.200000e-157 564
8 TraesCS2D01G322700 chr5B 85.044 341 22 17 989 1300 644889684 644890024 1.240000e-83 320
9 TraesCS2D01G322700 chr6B 82.258 186 29 3 1593 1778 39324848 39324667 1.030000e-34 158


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 TraesCS2D01G322700 chr2D 414400608 414403387 2779 False 5134 5134 100.0000 1 2780 1 chr2D.!!$F1 2779
1 TraesCS2D01G322700 chr2B 488007994 488010807 2813 False 4163 4163 93.6040 1 2780 1 chr2B.!!$F1 2779
2 TraesCS2D01G322700 chr2A 581577065 581579064 1999 False 2793 2793 92.1850 814 2780 1 chr2A.!!$F2 1966
3 TraesCS2D01G322700 chr2A 581565976 581566723 747 False 795 795 86.3170 3 757 1 chr2A.!!$F1 754
4 TraesCS2D01G322700 chr5D 513978159 513978963 804 False 795 795 85.1090 989 1781 1 chr5D.!!$F1 792
5 TraesCS2D01G322700 chr5A 641733086 641733852 766 False 450 569 88.9625 989 1781 2 chr5A.!!$F1 792
6 TraesCS2D01G322700 chr5B 644889684 644890469 785 False 442 564 88.4380 989 1781 2 chr5B.!!$F1 792

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
160 161 0.109919 CAACGATGAGACCGACGACA 60.110 55.0 0.00 0.0 0.00 4.35 F
834 924 0.244450 AGCACATCGGCACAATTTGG 59.756 50.0 0.78 0.0 35.83 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 1842 1.194098 CTGCAACTTCTCGAAGCTGTG 59.806 52.381 10.65 6.59 41.99 3.66 R
2435 2659 0.325933 CATGCTTGGGTGGAGACTCA 59.674 55.000 4.53 0.00 0.00 3.41 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
160 161 0.109919 CAACGATGAGACCGACGACA 60.110 55.000 0.00 0.00 0.00 4.35
238 239 2.286732 ATGGCTGCTTCTCCCCCT 60.287 61.111 0.00 0.00 0.00 4.79
239 240 2.381941 ATGGCTGCTTCTCCCCCTC 61.382 63.158 0.00 0.00 0.00 4.30
240 241 2.690510 GGCTGCTTCTCCCCCTCT 60.691 66.667 0.00 0.00 0.00 3.69
241 242 2.741055 GGCTGCTTCTCCCCCTCTC 61.741 68.421 0.00 0.00 0.00 3.20
242 243 2.741055 GCTGCTTCTCCCCCTCTCC 61.741 68.421 0.00 0.00 0.00 3.71
243 244 2.041265 TGCTTCTCCCCCTCTCCC 59.959 66.667 0.00 0.00 0.00 4.30
244 245 3.157949 GCTTCTCCCCCTCTCCCG 61.158 72.222 0.00 0.00 0.00 5.14
245 246 2.444895 CTTCTCCCCCTCTCCCGG 60.445 72.222 0.00 0.00 0.00 5.73
246 247 4.798682 TTCTCCCCCTCTCCCGGC 62.799 72.222 0.00 0.00 0.00 6.13
302 304 0.892358 AGTGGAATGTGTGCTGGCAG 60.892 55.000 10.94 10.94 0.00 4.85
370 411 1.298014 GGTCAGCTCAGACAAGGGG 59.702 63.158 6.54 0.00 40.29 4.79
408 449 5.805728 ACAAGAGAACGGTCCAGATTTTAT 58.194 37.500 0.00 0.00 0.00 1.40
413 454 4.469945 AGAACGGTCCAGATTTTATCCAGA 59.530 41.667 0.00 0.00 0.00 3.86
480 531 0.391130 GGCTATCGTTGACACCTGCA 60.391 55.000 0.00 0.00 0.00 4.41
486 537 1.526917 GTTGACACCTGCAGGCTGT 60.527 57.895 33.06 30.88 39.32 4.40
489 540 1.121407 TGACACCTGCAGGCTGTAGT 61.121 55.000 33.06 21.73 39.32 2.73
496 547 2.437359 CAGGCTGTAGTGCAGGGC 60.437 66.667 10.44 3.57 45.14 5.19
526 600 5.557576 CCTCTCAAGGAACCATATGATCA 57.442 43.478 3.65 0.00 46.67 2.92
533 607 3.004839 AGGAACCATATGATCAGTCGTCG 59.995 47.826 3.65 0.00 0.00 5.12
597 671 1.135333 GAAAACTTGGGTTCACGGCAA 59.865 47.619 0.00 0.00 34.14 4.52
598 672 0.744281 AAACTTGGGTTCACGGCAAG 59.256 50.000 0.00 0.00 34.14 4.01
599 673 1.106944 AACTTGGGTTCACGGCAAGG 61.107 55.000 0.00 0.00 0.00 3.61
600 674 2.909965 TTGGGTTCACGGCAAGGC 60.910 61.111 0.00 0.00 0.00 4.35
601 675 3.723097 TTGGGTTCACGGCAAGGCA 62.723 57.895 0.00 0.00 0.00 4.75
602 676 2.909965 GGGTTCACGGCAAGGCAA 60.910 61.111 0.00 0.00 0.00 4.52
661 735 4.820897 TGCCATGAAGTACTCAACTACTG 58.179 43.478 0.00 0.00 37.50 2.74
792 882 9.892130 GTATTTCCTTCATAAGAGAAGAAAGGA 57.108 33.333 5.34 0.00 46.18 3.36
805 895 2.716217 AGAAAGGAAAGAATGGCCGAG 58.284 47.619 0.00 0.00 0.00 4.63
834 924 0.244450 AGCACATCGGCACAATTTGG 59.756 50.000 0.78 0.00 35.83 3.28
846 936 0.538118 CAATTTGGCATGGTCCCCTG 59.462 55.000 0.00 0.00 0.00 4.45
993 1107 2.900273 GCGCTATCCAGTCCCACA 59.100 61.111 0.00 0.00 0.00 4.17
1134 1275 0.901124 CAGCTTGCCTCAGTCTAGGT 59.099 55.000 0.00 0.00 39.02 3.08
1314 1480 7.015682 CCCATACATACTATATCACCTCATCCC 59.984 44.444 0.00 0.00 0.00 3.85
1614 1790 2.792290 CGACAAGCTCATCACCGCG 61.792 63.158 0.00 0.00 0.00 6.46
1615 1791 1.446099 GACAAGCTCATCACCGCGA 60.446 57.895 8.23 0.00 0.00 5.87
1620 1796 1.227089 GCTCATCACCGCGACAGAT 60.227 57.895 8.23 4.71 0.00 2.90
1666 1842 1.153349 CTAGCCAACCGCCTCTTCC 60.153 63.158 0.00 0.00 38.78 3.46
1738 1914 2.100128 AGGATCCTGCTATGCTGACT 57.900 50.000 15.29 0.00 0.00 3.41
1793 1969 0.972883 GCCTAGCCAGTATCCAGGAG 59.027 60.000 0.00 0.00 0.00 3.69
1951 2175 2.297033 ACAAGCCAAGCCATAACAACAG 59.703 45.455 0.00 0.00 0.00 3.16
2285 2509 5.942236 ACTTGACAGTGAATTGACTGCATAT 59.058 36.000 22.89 5.35 46.28 1.78
2372 2596 1.441016 CCGAGCAGCAAAACGAAGC 60.441 57.895 0.00 0.00 0.00 3.86
2413 2637 0.037232 GAAGACACTTCCGGGGACAG 60.037 60.000 0.00 0.00 0.00 3.51
2435 2659 4.578928 AGGTTCACAAACATTAGCGTCTTT 59.421 37.500 0.00 0.00 37.10 2.52
2461 2685 1.904865 CACCCAAGCATGGCTGTGT 60.905 57.895 1.35 0.00 46.09 3.72
2462 2686 0.608856 CACCCAAGCATGGCTGTGTA 60.609 55.000 1.35 0.00 46.09 2.90
2484 2708 5.959618 ATACAAGGAAAACAGTTGTAGGC 57.040 39.130 0.00 0.00 39.40 3.93
2705 2929 7.696453 GTGCTATTGATGTTACAAATGTACACC 59.304 37.037 0.00 0.00 33.44 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 1.361668 CCAAGTCCCATCGCAACTCG 61.362 60.000 0.00 0.00 40.15 4.18
238 239 3.024356 AGGGAGAGAGCCGGGAGA 61.024 66.667 2.18 0.00 0.00 3.71
239 240 2.520741 GAGGGAGAGAGCCGGGAG 60.521 72.222 2.18 0.00 0.00 4.30
240 241 3.024356 AGAGGGAGAGAGCCGGGA 61.024 66.667 2.18 0.00 0.00 5.14
241 242 2.520741 GAGAGGGAGAGAGCCGGG 60.521 72.222 2.18 0.00 0.00 5.73
242 243 2.520741 GGAGAGGGAGAGAGCCGG 60.521 72.222 0.00 0.00 0.00 6.13
243 244 2.904866 CGGAGAGGGAGAGAGCCG 60.905 72.222 0.00 0.00 0.00 5.52
244 245 2.520741 CCGGAGAGGGAGAGAGCC 60.521 72.222 0.00 0.00 35.97 4.70
408 449 1.070758 GCTCCACTGTTTCACTCTGGA 59.929 52.381 0.00 0.00 0.00 3.86
480 531 4.087892 CGCCCTGCACTACAGCCT 62.088 66.667 0.00 0.00 45.78 4.58
496 547 2.581354 CCTTGAGAGGAGCACCCG 59.419 66.667 0.00 0.00 46.74 5.28
519 585 3.440522 GGATGGATCGACGACTGATCATA 59.559 47.826 0.00 8.82 43.21 2.15
526 600 0.464013 AGACGGATGGATCGACGACT 60.464 55.000 0.00 0.00 0.00 4.18
533 607 1.762957 TCCAAAGGAGACGGATGGATC 59.237 52.381 0.00 0.00 36.65 3.36
599 673 1.262683 GTAGCGAGAGAATGGCATTGC 59.737 52.381 19.07 14.08 34.56 3.56
600 674 1.524355 CGTAGCGAGAGAATGGCATTG 59.476 52.381 19.07 3.66 34.56 2.82
601 675 1.137086 ACGTAGCGAGAGAATGGCATT 59.863 47.619 13.54 13.54 34.56 3.56
602 676 0.747255 ACGTAGCGAGAGAATGGCAT 59.253 50.000 0.00 0.00 34.56 4.40
661 735 6.144078 TGTACTCTGAAAAAGGAAAAAGGC 57.856 37.500 0.00 0.00 0.00 4.35
792 882 0.400213 TCCACACTCGGCCATTCTTT 59.600 50.000 2.24 0.00 0.00 2.52
805 895 1.359848 CCGATGTGCTTACTCCACAC 58.640 55.000 0.00 0.00 45.00 3.82
846 936 2.731587 ATTTGTGTTGGACGCGCTGC 62.732 55.000 5.73 0.00 0.00 5.25
937 1036 3.230976 TGACTGGTGTGAGAAAGAGCTA 58.769 45.455 0.00 0.00 0.00 3.32
993 1107 4.047059 GTGCTTGCCATGTGCGCT 62.047 61.111 9.73 0.00 45.60 5.92
1314 1480 6.002082 TCTCTAGGAATGAAATGCATCATGG 58.998 40.000 0.00 0.00 39.90 3.66
1446 1622 2.044946 AAGCTTGGCCCGATGTCC 60.045 61.111 0.00 0.00 0.00 4.02
1614 1790 1.519455 CTTGGCGTCGGGATCTGTC 60.519 63.158 0.00 0.00 0.00 3.51
1615 1791 2.579201 CTTGGCGTCGGGATCTGT 59.421 61.111 0.00 0.00 0.00 3.41
1666 1842 1.194098 CTGCAACTTCTCGAAGCTGTG 59.806 52.381 10.65 6.59 41.99 3.66
1738 1914 3.008375 ACTTCCTGCAGTATGAGCTTTGA 59.992 43.478 13.81 0.00 39.69 2.69
1970 2194 9.567848 TCAGCCTTTTATTTTATTCTAAAAGCG 57.432 29.630 8.55 4.95 40.86 4.68
2256 2480 3.251004 GTCAATTCACTGTCAAGTCCCAC 59.749 47.826 0.00 0.00 32.98 4.61
2285 2509 3.866066 GCAGCTTGTCACAAGGATGAGTA 60.866 47.826 19.35 0.00 0.00 2.59
2413 2637 4.483476 AAGACGCTAATGTTTGTGAACC 57.517 40.909 0.00 0.00 34.80 3.62
2435 2659 0.325933 CATGCTTGGGTGGAGACTCA 59.674 55.000 4.53 0.00 0.00 3.41
2461 2685 6.653320 CAGCCTACAACTGTTTTCCTTGTATA 59.347 38.462 0.00 0.00 31.59 1.47
2462 2686 5.473504 CAGCCTACAACTGTTTTCCTTGTAT 59.526 40.000 0.00 0.00 31.59 2.29
2705 2929 5.452078 TTGCTATCCCTTTGTTTTGTGAG 57.548 39.130 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.