Multiple sequence alignment - TraesCS6A01G177100

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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 TraesCS6A01G177100 chr6A 100.000 4025 0 0 1 4025 196784981 196789005 0.000000e+00 7433.0
1 TraesCS6A01G177100 chr6B 96.997 4029 78 12 1 4025 262474451 262470462 0.000000e+00 6730.0
2 TraesCS6A01G177100 chr6D 96.364 4043 83 15 1 4025 149473305 149469309 0.000000e+00 6593.0
3 TraesCS6A01G177100 chr2D 84.519 478 36 15 3481 3941 49178746 49179202 4.780000e-119 438.0
4 TraesCS6A01G177100 chr2D 83.784 111 9 4 2032 2133 49178413 49178523 3.310000e-16 97.1


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 TraesCS6A01G177100 chr6A 196784981 196789005 4024 False 7433.00 7433 100.0000 1 4025 1 chr6A.!!$F1 4024
1 TraesCS6A01G177100 chr6B 262470462 262474451 3989 True 6730.00 6730 96.9970 1 4025 1 chr6B.!!$R1 4024
2 TraesCS6A01G177100 chr6D 149469309 149473305 3996 True 6593.00 6593 96.3640 1 4025 1 chr6D.!!$R1 4024
3 TraesCS6A01G177100 chr2D 49178413 49179202 789 False 267.55 438 84.1515 2032 3941 2 chr2D.!!$F1 1909

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
600 611 0.537188 CAGAGGATAGTTGTGCCCGT 59.463 55.000 0.00 0.00 0.00 5.28 F
615 626 1.268743 GCCCGTAGCAATTTCTCATGC 60.269 52.381 0.00 0.00 42.97 4.06 F
1107 1123 1.312815 GCAATGGGCACACCTATCTC 58.687 55.000 0.00 0.00 43.97 2.75 F
1202 1218 2.365635 CCCGTCCCCAGATGGTCT 60.366 66.667 0.00 0.00 46.44 3.85 F
1347 1363 3.281727 TTGAGGGTAGATGCATCCAAC 57.718 47.619 23.06 19.85 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 1497 4.739716 GTGTCAACTGTTTGCCATAAGTTG 59.260 41.667 7.85 7.85 46.98 3.16 R
2606 2631 4.851639 AGAAGACAGCTGGTTCCATTAT 57.148 40.909 19.93 1.69 0.00 1.28 R
2611 2636 5.249420 AGAATTAAGAAGACAGCTGGTTCC 58.751 41.667 19.93 4.50 0.00 3.62 R
2786 2811 9.383519 AGTTCAAGTAACATACTGAATACATGG 57.616 33.333 0.00 0.00 40.83 3.66 R
3357 3392 6.741992 TCCAGATTATTGCACACTTAACTG 57.258 37.500 0.00 0.00 0.00 3.16 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
80 81 3.864003 CCGGTTTTCTCCTTCGTCTAATC 59.136 47.826 0.00 0.00 0.00 1.75
81 82 4.381718 CCGGTTTTCTCCTTCGTCTAATCT 60.382 45.833 0.00 0.00 0.00 2.40
261 272 3.541713 CTAGAGTCTGGGGCGGGC 61.542 72.222 1.86 0.00 0.00 6.13
333 344 4.551702 TGATTAGCTGGTTGACTAAGCA 57.448 40.909 0.00 0.00 41.15 3.91
348 359 3.587506 ACTAAGCACCATAGTTTCCTGGT 59.412 43.478 0.00 0.00 46.68 4.00
406 417 9.536049 ACTAGAATAGACAGATCGTTCTGCTGC 62.536 44.444 20.79 11.91 46.61 5.25
415 426 1.692148 CGTTCTGCTGCGCGGATTTA 61.692 55.000 23.20 1.27 43.86 1.40
423 434 2.861935 GCTGCGCGGATTTACTAGTTTA 59.138 45.455 23.20 0.00 0.00 2.01
600 611 0.537188 CAGAGGATAGTTGTGCCCGT 59.463 55.000 0.00 0.00 0.00 5.28
615 626 1.268743 GCCCGTAGCAATTTCTCATGC 60.269 52.381 0.00 0.00 42.97 4.06
641 652 7.292292 CAAGTATTCTCGTCCGACTATTCTAG 58.708 42.308 0.00 0.00 0.00 2.43
642 653 6.523840 AGTATTCTCGTCCGACTATTCTAGT 58.476 40.000 0.00 0.00 42.86 2.57
834 845 8.512956 CCCATTCTGATCTATGATGAATTTGTC 58.487 37.037 0.00 0.00 0.00 3.18
921 932 9.449719 TCCTTGACAAGTTTAGATCTTTTATCC 57.550 33.333 14.03 0.00 0.00 2.59
947 963 7.099764 TGTTTTTAAGAACACATTGGCTCAAA 58.900 30.769 7.44 0.00 34.77 2.69
1107 1123 1.312815 GCAATGGGCACACCTATCTC 58.687 55.000 0.00 0.00 43.97 2.75
1202 1218 2.365635 CCCGTCCCCAGATGGTCT 60.366 66.667 0.00 0.00 46.44 3.85
1347 1363 3.281727 TTGAGGGTAGATGCATCCAAC 57.718 47.619 23.06 19.85 0.00 3.77
1481 1497 6.655078 ATGCCTGTTATGGAAATTATGGAC 57.345 37.500 0.00 0.00 0.00 4.02
1573 1589 4.929479 AGAGAGTCTTCAGTGTCTGGTAT 58.071 43.478 0.00 0.00 31.51 2.73
2092 2117 4.262377 CCCTATAGACAAGCACATCCTCAG 60.262 50.000 0.00 0.00 0.00 3.35
2125 2150 7.126733 ACAGTGGAGATATTTGTAGTAGGACT 58.873 38.462 0.00 0.00 0.00 3.85
2126 2151 7.068839 ACAGTGGAGATATTTGTAGTAGGACTG 59.931 40.741 0.00 0.00 0.00 3.51
2127 2152 7.285629 CAGTGGAGATATTTGTAGTAGGACTGA 59.714 40.741 0.00 0.00 0.00 3.41
2520 2545 3.508762 ACTTGACGCTCTGTATTAACCG 58.491 45.455 0.00 0.00 0.00 4.44
2535 2560 4.914177 TTAACCGTGTAGAAAGGGGAAT 57.086 40.909 0.00 0.00 0.00 3.01
2606 2631 5.011125 CCACTGAGTCAAAGGTCTCTTTCTA 59.989 44.000 0.00 0.00 40.92 2.10
2611 2636 9.311916 CTGAGTCAAAGGTCTCTTTCTATAATG 57.688 37.037 0.00 0.00 40.92 1.90
2634 2659 5.221925 TGGAACCAGCTGTCTTCTTAATTCT 60.222 40.000 13.81 0.00 0.00 2.40
2786 2811 2.473984 GCATGCTCAGCAAACAAGTTTC 59.526 45.455 11.37 0.00 43.62 2.78
2951 2976 3.034924 ACCGATGGTGTGCAATTGT 57.965 47.368 7.40 0.00 32.98 2.71
3122 3155 5.048364 CCATCAAACTTTGGTTCGTATCCAA 60.048 40.000 1.62 5.06 42.29 3.53
3357 3392 4.363138 CTGAACAAGGAAAACAAAGGAGC 58.637 43.478 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
261 272 0.953471 TCCCCGCATCAAGAACAACG 60.953 55.000 0.00 0.00 0.00 4.10
268 279 1.228063 CCTCCATCCCCGCATCAAG 60.228 63.158 0.00 0.00 0.00 3.02
348 359 1.415672 AAGCACCTTCGAACTGGGGA 61.416 55.000 9.77 0.00 0.00 4.81
358 369 0.591659 GTTCCCGAACAAGCACCTTC 59.408 55.000 2.69 0.00 40.84 3.46
406 417 6.581542 AGATCGAATAAACTAGTAAATCCGCG 59.418 38.462 0.00 0.00 0.00 6.46
415 426 7.536855 ACGAGAAACAGATCGAATAAACTAGT 58.463 34.615 1.13 0.00 41.40 2.57
423 434 3.759527 TCGACGAGAAACAGATCGAAT 57.240 42.857 0.00 0.00 41.40 3.34
438 449 2.352001 CGGGCTCGTACATCGACG 60.352 66.667 0.00 0.00 44.01 5.12
600 611 6.830324 AGAATACTTGGCATGAGAAATTGCTA 59.170 34.615 7.45 0.00 38.88 3.49
615 626 4.832590 ATAGTCGGACGAGAATACTTGG 57.167 45.455 1.89 0.00 32.13 3.61
641 652 7.811713 ACGAACTGACTGGTTTAATTACTAGAC 59.188 37.037 0.00 0.00 31.72 2.59
642 653 7.889469 ACGAACTGACTGGTTTAATTACTAGA 58.111 34.615 0.00 0.00 31.72 2.43
643 654 8.027771 AGACGAACTGACTGGTTTAATTACTAG 58.972 37.037 0.00 0.00 33.32 2.57
791 802 7.636150 AGAATGGGATTTCTGAAGTGTATTG 57.364 36.000 0.00 0.00 34.68 1.90
834 845 7.439356 ACACGGATGATACTATCACATTGAAAG 59.561 37.037 0.58 0.00 43.01 2.62
838 849 8.650714 CATAACACGGATGATACTATCACATTG 58.349 37.037 0.58 0.45 43.01 2.82
882 893 6.464222 ACTTGTCAAGGAGTATTGAATCGAA 58.536 36.000 16.85 0.00 40.72 3.71
883 894 6.037786 ACTTGTCAAGGAGTATTGAATCGA 57.962 37.500 16.85 0.00 40.72 3.59
884 895 6.727824 AACTTGTCAAGGAGTATTGAATCG 57.272 37.500 16.85 0.00 40.72 3.34
885 896 9.436957 TCTAAACTTGTCAAGGAGTATTGAATC 57.563 33.333 16.85 0.00 40.72 2.52
886 897 9.965902 ATCTAAACTTGTCAAGGAGTATTGAAT 57.034 29.630 16.85 0.00 40.72 2.57
896 907 9.454859 AGGATAAAAGATCTAAACTTGTCAAGG 57.545 33.333 16.85 0.00 0.00 3.61
921 932 6.272318 TGAGCCAATGTGTTCTTAAAAACAG 58.728 36.000 0.00 0.00 39.69 3.16
1107 1123 3.677121 GCAGACATGGATCATAGCTTACG 59.323 47.826 0.00 0.00 0.00 3.18
1202 1218 3.569210 CTGGGACCCAGCACACCA 61.569 66.667 27.72 0.00 45.13 4.17
1347 1363 1.815003 CAAAGCTGCCTTGTCCTAAGG 59.185 52.381 2.83 1.36 40.39 2.69
1438 1454 4.795278 GCATAACATAGAAGCTTGTGCAAC 59.205 41.667 2.10 0.00 42.74 4.17
1481 1497 4.739716 GTGTCAACTGTTTGCCATAAGTTG 59.260 41.667 7.85 7.85 46.98 3.16
1533 1549 7.777910 AGACTCTCTTCAAGCACTACAGTATAT 59.222 37.037 0.00 0.00 0.00 0.86
1554 1570 7.811117 ACTATATACCAGACACTGAAGACTC 57.189 40.000 0.00 0.00 32.44 3.36
1573 1589 6.558771 TGGCGTTAGCGAGTTATTACTATA 57.441 37.500 2.07 0.00 46.35 1.31
2092 2117 5.163540 ACAAATATCTCCACTGTCGTACTCC 60.164 44.000 0.00 0.00 0.00 3.85
2125 2150 5.681639 ACAGAAGCTTCATCATCATCATCA 58.318 37.500 27.57 0.00 0.00 3.07
2126 2151 7.820386 AGATACAGAAGCTTCATCATCATCATC 59.180 37.037 27.57 14.75 0.00 2.92
2127 2152 7.604545 CAGATACAGAAGCTTCATCATCATCAT 59.395 37.037 27.57 8.12 0.00 2.45
2432 2457 9.330063 CATAAATCCACTATTCTGAAGTAAGCA 57.670 33.333 0.00 0.00 0.00 3.91
2441 2466 8.830580 CACACTAACCATAAATCCACTATTCTG 58.169 37.037 0.00 0.00 0.00 3.02
2606 2631 4.851639 AGAAGACAGCTGGTTCCATTAT 57.148 40.909 19.93 1.69 0.00 1.28
2611 2636 5.249420 AGAATTAAGAAGACAGCTGGTTCC 58.751 41.667 19.93 4.50 0.00 3.62
2786 2811 9.383519 AGTTCAAGTAACATACTGAATACATGG 57.616 33.333 0.00 0.00 40.83 3.66
3357 3392 6.741992 TCCAGATTATTGCACACTTAACTG 57.258 37.500 0.00 0.00 0.00 3.16
3660 3701 9.976511 CCAAATAATCATTTAGCTGACATGAAT 57.023 29.630 0.00 0.00 32.96 2.57


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

AutoCloner maintained by Alex Coulton.