Multiple sequence alignment - TraesCS6D01G157100

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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 TraesCS6D01G157100 chr6D 100.000 2333 0 0 1 2333 133226565 133224233 0.000000e+00 4309.0
1 TraesCS6D01G157100 chr6B 93.224 2376 70 30 1 2333 231682851 231680524 0.000000e+00 3411.0
2 TraesCS6D01G157100 chr6A 92.029 1819 68 28 545 2333 172130867 172129096 0.000000e+00 2484.0
3 TraesCS6D01G157100 chr6A 84.393 519 48 12 1 513 172131704 172131213 1.620000e-131 479.0
4 TraesCS6D01G157100 chr6A 89.286 84 8 1 2184 2267 93910633 93910551 1.140000e-18 104.0
5 TraesCS6D01G157100 chr2A 97.619 42 1 0 1334 1375 4969496 4969537 3.220000e-09 73.1
6 TraesCS6D01G157100 chr5B 95.455 44 2 0 1334 1377 116684127 116684084 1.160000e-08 71.3
7 TraesCS6D01G157100 chr2D 95.455 44 2 0 1334 1377 299891063 299891106 1.160000e-08 71.3
8 TraesCS6D01G157100 chr2D 97.561 41 1 0 1334 1374 449065543 449065583 1.160000e-08 71.3
9 TraesCS6D01G157100 chr2D 97.561 41 1 0 1334 1374 578045465 578045505 1.160000e-08 71.3
10 TraesCS6D01G157100 chr2D 97.561 41 1 0 1334 1374 578312020 578312060 1.160000e-08 71.3
11 TraesCS6D01G157100 chr1D 97.561 41 1 0 1334 1374 77013413 77013453 1.160000e-08 71.3
12 TraesCS6D01G157100 chr5D 100.000 36 0 0 2298 2333 479618903 479618868 1.500000e-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 TraesCS6D01G157100 chr6D 133224233 133226565 2332 True 4309.0 4309 100.000 1 2333 1 chr6D.!!$R1 2332
1 TraesCS6D01G157100 chr6B 231680524 231682851 2327 True 3411.0 3411 93.224 1 2333 1 chr6B.!!$R1 2332
2 TraesCS6D01G157100 chr6A 172129096 172131704 2608 True 1481.5 2484 88.211 1 2333 2 chr6A.!!$R2 2332

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
836 1184 0.460109 GGCGCCATTTTTCCATCCAC 60.46 55.0 24.8 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 2292 1.202256 TGCGATCACCGTGTCTACATC 60.202 52.381 0.0 0.0 41.15 3.06 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
45 46 6.612863 TCTGAATATCCAGAGAGGTCAAATCA 59.387 38.462 0.00 0.00 38.18 2.57
96 97 5.246883 AGCAAATAAAGAACCTTGAAGGCAT 59.753 36.000 11.96 0.00 39.63 4.40
234 239 1.001378 GCATGACCTTTGTTTGCTCGT 60.001 47.619 0.00 0.00 33.52 4.18
235 240 2.225491 GCATGACCTTTGTTTGCTCGTA 59.775 45.455 0.00 0.00 33.52 3.43
338 343 5.123227 CACAACAGGGTACAGAAGAAGAAA 58.877 41.667 0.00 0.00 0.00 2.52
434 450 1.197721 CAGATCAGGCGTGTCAAAACC 59.802 52.381 6.26 0.00 0.00 3.27
439 455 0.681564 AGGCGTGTCAAAACCCACAA 60.682 50.000 0.00 0.00 0.00 3.33
470 497 6.922957 AGATTTTGAATAATTTGTGTGCGTGT 59.077 30.769 0.00 0.00 0.00 4.49
471 498 5.879948 TTTGAATAATTTGTGTGCGTGTG 57.120 34.783 0.00 0.00 0.00 3.82
472 499 3.304257 TGAATAATTTGTGTGCGTGTGC 58.696 40.909 0.00 0.00 43.20 4.57
534 590 3.616956 TTGTACTCTCCATCTTGCTGG 57.383 47.619 0.00 0.00 37.66 4.85
550 891 5.181245 TCTTGCTGGATTAACTAACAAGCAC 59.819 40.000 0.00 0.00 34.48 4.40
613 961 3.246226 CAGATAGCGGTGCAATCTACAAC 59.754 47.826 0.00 0.00 0.00 3.32
623 971 2.032550 GCAATCTACAACGCATCAGCAT 59.967 45.455 0.00 0.00 42.27 3.79
624 972 3.488047 GCAATCTACAACGCATCAGCATT 60.488 43.478 0.00 0.00 42.27 3.56
659 1007 1.450312 CACGACAGGATCAAGGGCC 60.450 63.158 0.00 0.00 0.00 5.80
715 1063 3.121688 AGAGGATGGAGCCAAGAGAAAT 58.878 45.455 0.00 0.00 0.00 2.17
828 1176 2.635443 CCTGACCGGCGCCATTTTT 61.635 57.895 28.98 4.35 0.00 1.94
836 1184 0.460109 GGCGCCATTTTTCCATCCAC 60.460 55.000 24.80 0.00 0.00 4.02
951 1309 6.903883 GTGGACTTTACATACACCACATAG 57.096 41.667 0.00 0.00 44.58 2.23
954 1317 6.439375 TGGACTTTACATACACCACATAGAGT 59.561 38.462 0.00 0.00 0.00 3.24
959 1322 3.132289 ACATACACCACATAGAGTTCCGG 59.868 47.826 0.00 0.00 0.00 5.14
969 1332 3.959991 GAGTTCCGGTCAGGCCAGC 62.960 68.421 5.01 0.00 40.77 4.85
1152 1515 2.042762 AGGTGCTGCCCTGGGATA 59.957 61.111 19.27 3.10 38.26 2.59
1491 1857 7.390718 ACTCCTACTTATTTCAAACATGGACAC 59.609 37.037 0.00 0.00 0.00 3.67
1530 1897 5.063817 GCCCAAAAGCAAATGAACATATGTC 59.936 40.000 9.23 3.74 0.00 3.06
1538 1905 5.220265 GCAAATGAACATATGTCAAAAGGCG 60.220 40.000 9.23 0.00 0.00 5.52
1845 2225 3.923425 ACCTACCCTCCCTTTCAGAAATT 59.077 43.478 0.00 0.00 0.00 1.82
1912 2292 4.516698 AGCTAAATCCTCATGTTTATGGCG 59.483 41.667 0.00 0.00 34.97 5.69
2176 2569 3.830192 GCCTTCAATGCCAGCGGG 61.830 66.667 0.00 0.00 37.18 6.13
2195 2588 1.737816 CGTCGACGATAACCCCCAT 59.262 57.895 33.35 0.00 43.02 4.00
2200 2593 2.436542 TCGACGATAACCCCCATGAATT 59.563 45.455 0.00 0.00 0.00 2.17
2214 2607 9.002061 ACCCCCATGAATTGAAATTAATGTTAT 57.998 29.630 10.79 0.00 36.08 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 0.537188 AATCGGGCTGTCTCGACATT 59.463 50.000 0.00 0.00 41.01 2.71
338 343 0.601841 ATGGCTTCGGTTTCGTCGTT 60.602 50.000 0.00 0.00 37.69 3.85
380 388 2.108075 TGCATCAAGACCCTTCAGGAAA 59.892 45.455 0.00 0.00 39.89 3.13
434 450 3.749665 TTCAAAATCTTGGGCTTGTGG 57.250 42.857 0.00 0.00 33.01 4.17
439 455 7.388500 CACACAAATTATTCAAAATCTTGGGCT 59.612 33.333 0.00 0.00 33.01 5.19
534 590 5.505165 TCGTTCGTGCTTGTTAGTTAATC 57.495 39.130 0.00 0.00 0.00 1.75
586 927 2.689553 TTGCACCGCTATCTGAATCA 57.310 45.000 0.00 0.00 0.00 2.57
613 961 1.298413 GCTGCTGAATGCTGATGCG 60.298 57.895 0.00 0.00 42.27 4.73
623 971 2.281970 CACCAGGCTGCTGCTGAA 60.282 61.111 15.64 0.00 39.59 3.02
640 988 2.109126 GCCCTTGATCCTGTCGTGC 61.109 63.158 0.00 0.00 0.00 5.34
659 1007 1.059838 CGTCATGTCATGCTGTGCG 59.940 57.895 8.03 4.08 0.00 5.34
703 1051 2.564504 GCCTGGAAAATTTCTCTTGGCT 59.435 45.455 17.15 0.00 35.44 4.75
715 1063 3.687698 GCATAAACTACTCGCCTGGAAAA 59.312 43.478 0.00 0.00 0.00 2.29
828 1176 0.322816 GCTCAAGCCTTGTGGATGGA 60.323 55.000 4.04 0.00 34.57 3.41
836 1184 0.667487 TCTCGTTCGCTCAAGCCTTG 60.667 55.000 0.00 0.00 37.91 3.61
945 1303 1.471676 GCCTGACCGGAACTCTATGTG 60.472 57.143 9.46 0.00 33.16 3.21
949 1307 1.077805 TGGCCTGACCGGAACTCTA 59.922 57.895 9.46 0.00 43.94 2.43
959 1322 2.125512 CACTACCGCTGGCCTGAC 60.126 66.667 14.77 3.95 0.00 3.51
969 1332 2.481449 GCACCTGGTATCTTCACTACCG 60.481 54.545 0.00 0.00 41.35 4.02
1207 1570 1.153469 GGAAGGAAGCCGAGCTCTG 60.153 63.158 12.85 6.45 38.25 3.35
1530 1897 1.002468 CAGTTCCAGACACGCCTTTTG 60.002 52.381 0.00 0.00 0.00 2.44
1538 1905 4.212214 GTGACAAGAATCAGTTCCAGACAC 59.788 45.833 0.00 0.00 34.81 3.67
1588 1966 6.681729 AACTATTCTGGTAGGAGTTTCACA 57.318 37.500 0.00 0.00 0.00 3.58
1589 1967 9.099454 CATTAACTATTCTGGTAGGAGTTTCAC 57.901 37.037 0.00 0.00 32.75 3.18
1590 1968 8.822805 ACATTAACTATTCTGGTAGGAGTTTCA 58.177 33.333 0.00 0.00 32.75 2.69
1591 1969 9.668497 AACATTAACTATTCTGGTAGGAGTTTC 57.332 33.333 0.00 0.00 32.75 2.78
1592 1970 9.668497 GAACATTAACTATTCTGGTAGGAGTTT 57.332 33.333 0.00 0.00 32.75 2.66
1593 1971 9.047947 AGAACATTAACTATTCTGGTAGGAGTT 57.952 33.333 0.00 0.00 31.47 3.01
1594 1972 8.478877 CAGAACATTAACTATTCTGGTAGGAGT 58.521 37.037 13.66 0.00 43.66 3.85
1595 1973 8.879342 CAGAACATTAACTATTCTGGTAGGAG 57.121 38.462 13.66 0.00 43.66 3.69
1881 2261 7.721286 AACATGAGGATTTAGCTCTTAATCG 57.279 36.000 0.00 0.00 32.73 3.34
1912 2292 1.202256 TGCGATCACCGTGTCTACATC 60.202 52.381 0.00 0.00 41.15 3.06
2176 2569 2.279054 GGGGGTTATCGTCGACGC 60.279 66.667 32.19 18.11 39.60 5.19
2200 2593 8.811017 TGCCCTTCTTTCATAACATTAATTTCA 58.189 29.630 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.