Multiple sequence alignment - TraesCS5B01G127400

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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 TraesCS5B01G127400 chr5B 100.000 4133 0 0 1 4133 232625662 232629794 0.000000e+00 7633
1 TraesCS5B01G127400 chr5D 97.987 3527 54 5 611 4133 216623314 216626827 0.000000e+00 6104
2 TraesCS5B01G127400 chr5D 91.613 465 26 7 3 462 216622516 216622972 7.540000e-177 630
3 TraesCS5B01G127400 chr5D 94.400 125 7 0 461 585 216623134 216623258 4.220000e-45 193
4 TraesCS5B01G127400 chr5A 98.080 3437 59 4 701 4133 286671664 286675097 0.000000e+00 5975
5 TraesCS5B01G127400 chr5A 90.212 613 47 9 3 611 286670849 286671452 0.000000e+00 787


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 TraesCS5B01G127400 chr5B 232625662 232629794 4132 False 7633 7633 100.000000 1 4133 1 chr5B.!!$F1 4132
1 TraesCS5B01G127400 chr5D 216622516 216626827 4311 False 2309 6104 94.666667 3 4133 3 chr5D.!!$F1 4130
2 TraesCS5B01G127400 chr5A 286670849 286675097 4248 False 3381 5975 94.146000 3 4133 2 chr5A.!!$F1 4130

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
795 1088 0.696501 AGCACCCCGGTACTCAAAAT 59.303 50.0 0.0 0.0 0.00 1.82 F
1566 1859 0.252197 GTCAAGGTGTCGCCCCTTAT 59.748 55.0 0.0 0.0 40.35 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2659 2952 0.748367 GCTTTCCTTAGAAGCCCCCG 60.748 60.000 0.0 0.0 42.79 5.73 R
3135 3428 3.578716 AGACGATCCTTTCTTGAAGACCA 59.421 43.478 0.0 0.0 37.57 4.02 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
60 63 1.308998 AACACTTGCCCTTGAAGACG 58.691 50.000 0.00 0.00 0.00 4.18
73 76 4.387256 CCTTGAAGACGCTCTAAGTGAAAG 59.613 45.833 0.00 0.00 0.00 2.62
95 98 5.580022 AGGATAGCTTGTGTGGGTTATTTT 58.420 37.500 0.00 0.00 0.00 1.82
115 118 1.256812 ATAAAGGCCAAGTGGTGTGC 58.743 50.000 5.01 0.00 37.57 4.57
149 152 9.691362 GCAAAAGAGTAAGGACATTTTCAAATA 57.309 29.630 0.00 0.00 29.27 1.40
182 185 6.738114 TGTGAATTTTGCTAAAGGTCTTCAG 58.262 36.000 7.37 0.00 0.00 3.02
203 206 9.428097 CTTCAGTGATATTAATGAATCCGATGA 57.572 33.333 10.32 0.00 34.61 2.92
250 253 5.299279 CCACGCACAAATCCCTATAAAGATT 59.701 40.000 0.00 0.00 34.18 2.40
332 335 8.006298 TCAAAGTCTAAGCATCCTTTCAAAAA 57.994 30.769 0.00 0.00 32.47 1.94
374 382 3.851976 ATATTAGGCGAGGAAGCGTAG 57.148 47.619 0.00 0.00 38.48 3.51
470 641 7.921214 TGCTAGCTGTGAACTATAGTTTGTATC 59.079 37.037 18.96 7.04 38.56 2.24
512 683 2.069465 ATCGTTGCGCCAAACAAGCA 62.069 50.000 4.18 0.00 39.33 3.91
517 688 1.005340 TGCGCCAAACAAGCAAAAAG 58.995 45.000 4.18 0.00 38.01 2.27
585 756 1.300971 TGAAGCTGCTCATCGTTGCC 61.301 55.000 1.00 0.00 0.00 4.52
586 757 1.986575 GAAGCTGCTCATCGTTGCCC 61.987 60.000 1.00 0.00 0.00 5.36
617 870 8.589335 AAGGTACATACGATACAAATAAGCTG 57.411 34.615 0.00 0.00 0.00 4.24
665 918 3.391296 TGAGAGGGTCAAATATAGCCACC 59.609 47.826 0.00 0.00 36.95 4.61
666 919 3.391296 GAGAGGGTCAAATATAGCCACCA 59.609 47.826 0.00 0.00 36.95 4.17
680 933 3.164268 AGCCACCATGCACATTTTTCTA 58.836 40.909 0.00 0.00 0.00 2.10
689 942 6.974622 CCATGCACATTTTTCTATAGAACACC 59.025 38.462 14.85 1.17 33.13 4.16
694 947 5.708230 ACATTTTTCTATAGAACACCCGCAA 59.292 36.000 14.85 2.32 33.13 4.85
734 1027 2.542020 TTCGCAGGTTCAGACATCAA 57.458 45.000 0.00 0.00 0.00 2.57
748 1041 5.649395 TCAGACATCAACCCAGATGAAATTC 59.351 40.000 10.59 0.00 46.51 2.17
795 1088 0.696501 AGCACCCCGGTACTCAAAAT 59.303 50.000 0.00 0.00 0.00 1.82
818 1111 6.770286 TGGAATTTCCCTAATGCTATCTCT 57.230 37.500 12.90 0.00 35.03 3.10
839 1132 3.924114 TTTTCGGAAGAGCCCATATGA 57.076 42.857 3.65 0.00 43.69 2.15
851 1144 9.852091 GAAGAGCCCATATGAAATCAAATTATC 57.148 33.333 3.65 0.00 0.00 1.75
1070 1363 2.444706 TATCTGCAGCCTCCGCCT 60.445 61.111 9.47 0.00 34.57 5.52
1095 1388 2.355837 TCATCGCCGGCGCTTATC 60.356 61.111 42.78 2.90 39.59 1.75
1137 1430 1.276622 ACCCATTCGCCTCACTACTT 58.723 50.000 0.00 0.00 0.00 2.24
1566 1859 0.252197 GTCAAGGTGTCGCCCCTTAT 59.748 55.000 0.00 0.00 40.35 1.73
1896 2189 1.394917 CAAGCGTCAGCCTTCACATAC 59.605 52.381 0.00 0.00 46.67 2.39
2010 2303 4.873827 ACGGTGGTGACATACAATACATTC 59.126 41.667 0.00 0.00 46.14 2.67
2510 2803 4.214986 TGATGCCGAGTGGAATTTCTTA 57.785 40.909 0.00 0.00 31.51 2.10
2659 2952 4.266976 GCTTGATTCATGCACATTGTAAGC 59.733 41.667 17.08 8.22 35.13 3.09
3001 3294 1.151899 TGGGTGGAGGCTGTAAGGT 60.152 57.895 0.00 0.00 0.00 3.50
3009 3302 2.347731 GAGGCTGTAAGGTTGTACTGC 58.652 52.381 0.00 5.86 44.05 4.40
3135 3428 3.505386 TGTTGTTTTGGGTGCATAGGAT 58.495 40.909 0.00 0.00 0.00 3.24
3321 3614 3.840666 TGACACTCTGGATAAAGGAGCTT 59.159 43.478 0.00 0.00 0.00 3.74
3403 3696 4.803329 ATTTCCTCCTGGTCATATGCTT 57.197 40.909 0.00 0.00 34.23 3.91
3424 3717 3.814504 ATGGTCATGGAGAAACAACCT 57.185 42.857 0.00 0.00 0.00 3.50
3557 3850 8.408601 AGCTTCAACAATAACATATAGGCTTTG 58.591 33.333 0.00 0.00 0.00 2.77
3776 4072 2.817258 CTCAACCGGTATCAGCCAAAAA 59.183 45.455 8.00 0.00 0.00 1.94
3941 4237 2.753043 GGGACTGCCGACCTACGA 60.753 66.667 0.00 0.00 45.77 3.43
3965 4261 3.947868 ACTGCATTCTGCTCATTACACT 58.052 40.909 0.34 0.00 45.31 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.798776 CGGACAGCACAAGGTTGATC 59.201 55.000 0.00 0.00 0.00 2.92
1 2 2.932663 CGGACAGCACAAGGTTGAT 58.067 52.632 0.00 0.00 0.00 2.57
55 58 4.810191 ATCCTTTCACTTAGAGCGTCTT 57.190 40.909 0.00 0.00 0.00 3.01
60 63 5.293079 CACAAGCTATCCTTTCACTTAGAGC 59.707 44.000 0.00 0.00 0.00 4.09
73 76 5.914898 AAAATAACCCACACAAGCTATCC 57.085 39.130 0.00 0.00 0.00 2.59
95 98 2.442413 GCACACCACTTGGCCTTTATA 58.558 47.619 3.32 0.00 39.32 0.98
115 118 3.994392 TCCTTACTCTTTTGCTAAGTGCG 59.006 43.478 0.00 0.00 46.63 5.34
203 206 0.691078 ACGGGGAGGTGCACTATCAT 60.691 55.000 17.98 0.00 0.00 2.45
274 277 7.780745 TGTTAGGTAGGAGGAAACATTTTTCAA 59.219 33.333 6.67 0.00 42.72 2.69
360 368 1.516603 GTGTCTACGCTTCCTCGCC 60.517 63.158 0.00 0.00 0.00 5.54
411 419 6.417635 TGTTCGCATGTTTTTCTTTCTCAATC 59.582 34.615 0.00 0.00 0.00 2.67
416 424 5.296780 TCTCTGTTCGCATGTTTTTCTTTCT 59.703 36.000 0.00 0.00 0.00 2.52
470 641 6.974932 TGAGCAACTTCATTAGCTTTCTAG 57.025 37.500 0.00 0.00 37.48 2.43
512 683 8.599792 TCACAGCTAGTAAACCCTATACTTTTT 58.400 33.333 0.00 0.00 35.34 1.94
517 688 7.110043 AGTTCACAGCTAGTAAACCCTATAC 57.890 40.000 0.00 0.00 0.00 1.47
596 767 9.758651 ATCAACAGCTTATTTGTATCGTATGTA 57.241 29.630 0.00 0.00 0.00 2.29
603 774 6.563422 TGCCAATCAACAGCTTATTTGTATC 58.437 36.000 0.00 0.00 0.00 2.24
665 918 6.974622 GGGTGTTCTATAGAAAAATGTGCATG 59.025 38.462 16.73 0.00 35.58 4.06
666 919 6.183360 CGGGTGTTCTATAGAAAAATGTGCAT 60.183 38.462 16.73 0.00 35.58 3.96
680 933 2.871453 AGGTTTTTGCGGGTGTTCTAT 58.129 42.857 0.00 0.00 0.00 1.98
694 947 7.278868 TGCGAATTTCACACAAAAATAGGTTTT 59.721 29.630 0.00 0.00 40.16 2.43
734 1027 5.677319 TCGAACTAGAATTTCATCTGGGT 57.323 39.130 0.00 0.00 32.64 4.51
748 1041 3.000727 ACCGGCTCAAAAATCGAACTAG 58.999 45.455 0.00 0.00 0.00 2.57
783 1076 4.705023 AGGGAAATTCCATTTTGAGTACCG 59.295 41.667 14.68 0.00 38.64 4.02
784 1077 7.712204 TTAGGGAAATTCCATTTTGAGTACC 57.288 36.000 14.68 0.00 38.64 3.34
795 1088 6.770286 AGAGATAGCATTAGGGAAATTCCA 57.230 37.500 14.68 0.00 38.64 3.53
818 1111 4.229304 TCATATGGGCTCTTCCGAAAAA 57.771 40.909 2.13 0.00 34.94 1.94
839 1132 4.261031 GCTACGGCCGTGATAATTTGATTT 60.261 41.667 40.02 10.90 0.00 2.17
1095 1388 2.123597 TCGTGATACGGGGGAGGG 60.124 66.667 1.24 0.00 42.81 4.30
1137 1430 1.152610 CGGAGGGGGATCGGAAGTA 60.153 63.158 0.00 0.00 0.00 2.24
1511 1804 2.485122 CGGAAAGGCATTGCGTCC 59.515 61.111 8.22 9.09 46.39 4.79
1566 1859 1.713937 CGCAGTTGCACACCTTGACA 61.714 55.000 4.84 0.00 42.21 3.58
2010 2303 8.305046 TCCCTCTTTTAAATAACCCATGAATG 57.695 34.615 0.00 0.00 0.00 2.67
2124 2417 6.237915 GCTTCAAATTACATGCCTTACAATGC 60.238 38.462 0.00 0.00 0.00 3.56
2659 2952 0.748367 GCTTTCCTTAGAAGCCCCCG 60.748 60.000 0.00 0.00 42.79 5.73
3009 3302 6.122850 TGAATACCTTTCTGATGCATTTCG 57.877 37.500 0.00 0.00 0.00 3.46
3135 3428 3.578716 AGACGATCCTTTCTTGAAGACCA 59.421 43.478 0.00 0.00 37.57 4.02
3321 3614 6.295249 TGTGTTATCTGTCTGGAAATCACAA 58.705 36.000 0.00 0.00 0.00 3.33
3403 3696 4.843728 GAGGTTGTTTCTCCATGACCATA 58.156 43.478 0.00 0.00 0.00 2.74
3776 4072 9.378551 TGCAGTTTAATCTCATAAATAGACGTT 57.621 29.630 0.00 0.00 0.00 3.99
3965 4261 0.762418 AGGTGATCGGTGGTTTCACA 59.238 50.000 4.85 0.00 45.32 3.58


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

AutoCloner maintained by Alex Coulton.