Multiple sequence alignment - TraesCS3D01G233100

Loading Multiple Alignment...

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 TraesCS3D01G233100 chr3D 100.000 2954 0 0 1 2954 321717979 321720932 0.000000e+00 5456.0
1 TraesCS3D01G233100 chr3B 96.863 2582 57 9 1 2562 398590870 398588293 0.000000e+00 4298.0
2 TraesCS3D01G233100 chr3B 93.017 358 13 6 2599 2944 398588198 398587841 2.030000e-141 512.0
3 TraesCS3D01G233100 chr3B 83.673 98 12 3 2674 2767 164483429 164483526 4.060000e-14 89.8
4 TraesCS3D01G233100 chr3A 95.885 2600 60 15 1 2571 403005576 403008157 0.000000e+00 4165.0
5 TraesCS3D01G233100 chr3A 88.557 402 28 6 2570 2954 403008186 403008586 3.450000e-129 472.0
6 TraesCS3D01G233100 chr7B 83.929 168 22 2 2605 2767 640082259 640082092 3.940000e-34 156.0
7 TraesCS3D01G233100 chr7B 83.929 168 22 2 2605 2767 640141154 640140987 3.940000e-34 156.0
8 TraesCS3D01G233100 chr7B 80.909 110 14 6 2455 2562 746049045 746048941 2.440000e-11 80.5
9 TraesCS3D01G233100 chr4B 83.333 168 23 2 2605 2767 556067349 556067516 1.830000e-32 150.0
10 TraesCS3D01G233100 chr1B 83.333 168 23 2 2605 2767 53263461 53263628 1.830000e-32 150.0
11 TraesCS3D01G233100 chr6B 82.286 175 26 2 2598 2767 76272178 76272352 2.370000e-31 147.0
12 TraesCS3D01G233100 chr7D 83.030 165 21 3 2608 2767 333705340 333705178 3.070000e-30 143.0
13 TraesCS3D01G233100 chr5D 81.982 111 14 5 2455 2562 215302114 215302007 4.060000e-14 89.8
14 TraesCS3D01G233100 chr2A 83.505 97 11 4 2455 2550 445716879 445716787 5.250000e-13 86.1
15 TraesCS3D01G233100 chr5B 79.464 112 18 4 2457 2566 503219503 503219611 1.140000e-09 75.0
16 TraesCS3D01G233100 chr6D 90.741 54 4 1 2510 2562 112433563 112433616 1.470000e-08 71.3
17 TraesCS3D01G233100 chr6D 81.395 86 10 5 2455 2538 383494823 383494904 6.830000e-07 65.8
18 TraesCS3D01G233100 chr5A 87.931 58 6 1 2510 2566 529090445 529090502 1.900000e-07 67.6


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 TraesCS3D01G233100 chr3D 321717979 321720932 2953 False 5456.0 5456 100.000 1 2954 1 chr3D.!!$F1 2953
1 TraesCS3D01G233100 chr3B 398587841 398590870 3029 True 2405.0 4298 94.940 1 2944 2 chr3B.!!$R1 2943
2 TraesCS3D01G233100 chr3A 403005576 403008586 3010 False 2318.5 4165 92.221 1 2954 2 chr3A.!!$F1 2953

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
732 756 0.788391 GACGGTTTTAGTGCCAGACG 59.212 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 2270 1.219646 TTACAACGCAGGGAAACGAC 58.78 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
423 444 1.215647 GCGGACCATGTCTCTTCGT 59.784 57.895 0.00 0.00 32.47 3.85
515 537 4.217754 TGTATTTTGGTTTGTCTGCGTC 57.782 40.909 0.00 0.00 0.00 5.19
690 714 3.343941 TCATTTCCAGACGGGTTAAGG 57.656 47.619 0.00 0.00 38.11 2.69
708 732 9.773328 GGGTTAAGGTTATTTTGTTTCGTATAC 57.227 33.333 0.00 0.00 0.00 1.47
715 739 7.414429 GGTTATTTTGTTTCGTATACCAGGGAC 60.414 40.741 0.00 0.00 0.00 4.46
732 756 0.788391 GACGGTTTTAGTGCCAGACG 59.212 55.000 0.00 0.00 0.00 4.18
826 853 2.075338 GCCTGCTAGAATATGCTGCTC 58.925 52.381 0.00 0.00 0.00 4.26
1284 1311 3.009723 CAATTGCCTTGATCAGTACCGT 58.990 45.455 0.00 0.00 36.97 4.83
1329 1356 0.333993 ATTCAGGGGCAGCAGAATGT 59.666 50.000 0.00 0.00 39.31 2.71
1356 1383 0.523519 GCCAGCAGCCAGTTAAACTC 59.476 55.000 0.00 0.00 34.35 3.01
1371 1398 5.880332 AGTTAAACTCGCATGTCCATTATGT 59.120 36.000 0.00 0.00 0.00 2.29
1526 1553 0.107508 CATCCTGCTGTCCGACCAAT 60.108 55.000 0.00 0.00 0.00 3.16
1773 1800 1.141881 CCCAGGTCGTCGATCAAGG 59.858 63.158 8.47 9.00 0.00 3.61
1983 2010 0.905357 GGTTAGCTCCCTTGCTCTCA 59.095 55.000 0.00 0.00 42.97 3.27
2123 2150 2.226437 GCAAGCAAGAAGAAATCACGGA 59.774 45.455 0.00 0.00 0.00 4.69
2243 2270 2.346803 CATGTTTGGTACTCCGGTGAG 58.653 52.381 11.17 0.00 44.62 3.51
2251 2278 4.573162 CTCCGGTGAGTCGTTTCC 57.427 61.111 0.00 0.00 33.70 3.13
2327 2354 7.661968 TGTAGTAATTGCATCTGAGTAGATCC 58.338 38.462 0.00 0.00 41.71 3.36
2429 2456 2.385013 TGGTCGATGACAGTGAATGG 57.615 50.000 0.00 0.00 33.68 3.16
2472 2499 7.083858 ACACGTGAGATGTTTTGGATATTTTG 58.916 34.615 25.01 0.00 0.00 2.44
2545 2572 5.400782 CGTGTCTACATACATCTGATTCAGC 59.599 44.000 8.89 0.00 0.00 4.26
2564 2627 6.727824 TCAGCAAAAGCTAGAACATCTAAC 57.272 37.500 0.00 0.00 0.00 2.34
2571 2634 8.436200 CAAAAGCTAGAACATCTAACACAGTAC 58.564 37.037 0.00 0.00 0.00 2.73
2750 2881 7.206981 TCAAGAAGTTGACTTGAAATCATCC 57.793 36.000 0.30 0.00 46.68 3.51
2846 2984 4.442052 CCTCCTAATGTCGTGTGTCATGAT 60.442 45.833 0.00 0.00 31.77 2.45
2882 3020 9.947669 CATTTTGAATTTTGCAAAGGTTAATCA 57.052 25.926 12.41 3.73 36.68 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
423 444 1.879380 CAAATTCTCCCACAGAACGCA 59.121 47.619 0.00 0.00 44.28 5.24
515 537 1.080839 CAACAATCCGGCCCAAACG 60.081 57.895 0.00 0.00 0.00 3.60
690 714 7.466805 GTCCCTGGTATACGAAACAAAATAAC 58.533 38.462 0.00 0.00 0.00 1.89
708 732 0.958876 GGCACTAAAACCGTCCCTGG 60.959 60.000 0.00 0.00 0.00 4.45
715 739 0.511221 CACGTCTGGCACTAAAACCG 59.489 55.000 0.00 0.00 0.00 4.44
732 756 3.969117 TCACAGACAAGCAATTCACAC 57.031 42.857 0.00 0.00 0.00 3.82
826 853 2.222819 GCAAGAGTTTAATCAGGTCGCG 60.223 50.000 0.00 0.00 0.00 5.87
1284 1311 2.188817 GAGGACTCCTTGGAGGCTTTA 58.811 52.381 20.64 0.00 34.61 1.85
1356 1383 1.261354 CCACGACATAATGGACATGCG 59.739 52.381 0.00 0.00 38.34 4.73
1518 1545 1.078426 GTCCACCTCCATTGGTCGG 60.078 63.158 1.86 7.35 38.45 4.79
1526 1553 2.297895 CGATTGGGGTCCACCTCCA 61.298 63.158 0.00 0.00 40.03 3.86
1773 1800 3.942115 GCTCCCCAACTAGAAGAATTGTC 59.058 47.826 0.00 0.00 0.00 3.18
1983 2010 2.943199 GCTGCTAGGCTTTTCAGTCCAT 60.943 50.000 0.00 0.00 0.00 3.41
2123 2150 2.526873 AGCTCCACCACGTTCCCT 60.527 61.111 0.00 0.00 0.00 4.20
2243 2270 1.219646 TTACAACGCAGGGAAACGAC 58.780 50.000 0.00 0.00 0.00 4.34
2251 2278 3.799420 GCTAGAGAGAATTACAACGCAGG 59.201 47.826 0.00 0.00 0.00 4.85
2327 2354 7.912383 ACAACAAATTCTTCAAATGCAGAAAG 58.088 30.769 0.00 0.00 31.58 2.62
2429 2456 2.413453 GTGTCTGAACGAAGGAGCATTC 59.587 50.000 0.00 0.00 0.00 2.67
2491 2518 8.627208 AGTATGTTCATTGATTTCAGTCAGTT 57.373 30.769 0.00 0.00 0.00 3.16
2545 2572 7.426929 ACTGTGTTAGATGTTCTAGCTTTTG 57.573 36.000 0.00 0.00 32.33 2.44
2564 2627 4.151689 CCCGTTCACAAATACAGTACTGTG 59.848 45.833 33.77 21.23 44.63 3.66
2571 2634 1.468520 CAGCCCCGTTCACAAATACAG 59.531 52.381 0.00 0.00 0.00 2.74
2665 2791 4.945543 ACATGGTCTTTAATTTACCGACCC 59.054 41.667 15.50 4.59 42.63 4.46
2666 2792 6.149807 TCAACATGGTCTTTAATTTACCGACC 59.850 38.462 12.94 12.94 43.37 4.79
2749 2880 7.433719 TGTCAAAGTAATTTGAAATTCACACGG 59.566 33.333 19.01 0.00 41.95 4.94
2750 2881 8.334016 TGTCAAAGTAATTTGAAATTCACACG 57.666 30.769 19.01 0.00 41.95 4.49
2846 2984 7.704271 TGCAAAATTCAAAATGAAGCATCAAA 58.296 26.923 0.00 0.00 40.05 2.69


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

AutoCloner maintained by Alex Coulton.