Multiple sequence alignment - TraesCS5B01G388100

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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 TraesCS5B01G388100 chr5B 100.000 2264 0 0 1 2264 567020821 567018558 0.000000e+00 4181
1 TraesCS5B01G388100 chr5A 94.330 2275 90 21 1 2264 581139944 581137698 0.000000e+00 3450
2 TraesCS5B01G388100 chr5D 93.704 2287 94 22 1 2261 460941802 460944064 0.000000e+00 3380
3 TraesCS5B01G388100 chr7D 81.231 325 59 2 12 335 531083962 531084285 6.200000e-66 261
4 TraesCS5B01G388100 chr7A 80.923 325 60 2 12 335 611496421 611496744 2.890000e-64 255
5 TraesCS5B01G388100 chr7B 80.615 325 61 2 12 335 571575737 571576060 1.340000e-62 250


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 TraesCS5B01G388100 chr5B 567018558 567020821 2263 True 4181 4181 100.000 1 2264 1 chr5B.!!$R1 2263
1 TraesCS5B01G388100 chr5A 581137698 581139944 2246 True 3450 3450 94.330 1 2264 1 chr5A.!!$R1 2263
2 TraesCS5B01G388100 chr5D 460941802 460944064 2262 False 3380 3380 93.704 1 2261 1 chr5D.!!$F1 2260

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
604 606 0.033504 ACTTCATCGGTCAAGCACGT 59.966 50.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 1479 0.236449 GACGGTACAAAAACTGGCCG 59.764 55.0 0.0 0.0 46.57 6.13 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
331 332 1.513622 GGAAGAGCTCCGAGTGGAC 59.486 63.158 10.93 0.00 40.17 4.02
443 444 2.964389 GCCAGCTCTCGAATCGCC 60.964 66.667 0.00 0.00 0.00 5.54
476 477 2.487428 CGGCAGTCGTCTGAGAGG 59.513 66.667 14.02 0.00 43.76 3.69
479 480 1.251527 GGCAGTCGTCTGAGAGGGAA 61.252 60.000 14.02 0.00 43.76 3.97
485 486 2.036089 GTCGTCTGAGAGGGAAAACACT 59.964 50.000 1.99 0.00 0.00 3.55
518 519 1.589196 GTCGCAGATCACGTAGCCC 60.589 63.158 7.86 0.00 40.67 5.19
521 522 1.217585 CGCAGATCACGTAGCCCATG 61.218 60.000 0.00 0.00 0.00 3.66
539 540 1.446272 GGAGACGCCTTTCAGACCG 60.446 63.158 0.00 0.00 0.00 4.79
578 580 5.482006 ACTGCAAGCAAGAAAGTTTTCTTT 58.518 33.333 15.27 2.26 46.11 2.52
594 596 7.381744 GTTTTCTTTCTCAAAACTTCATCGG 57.618 36.000 1.62 0.00 39.60 4.18
603 605 1.148310 AACTTCATCGGTCAAGCACG 58.852 50.000 0.00 0.00 0.00 5.34
604 606 0.033504 ACTTCATCGGTCAAGCACGT 59.966 50.000 0.00 0.00 0.00 4.49
694 697 2.702788 TTCCCGACGTAGATGCGCA 61.703 57.895 14.96 14.96 34.88 6.09
714 717 2.881111 TCCCGTCGATCTCTCCATAT 57.119 50.000 0.00 0.00 0.00 1.78
872 875 3.699411 AGAAGCTCTCATTTCAGCACT 57.301 42.857 0.00 0.00 38.18 4.40
873 876 3.336468 AGAAGCTCTCATTTCAGCACTG 58.664 45.455 0.00 0.00 38.18 3.66
875 878 1.627329 AGCTCTCATTTCAGCACTGGA 59.373 47.619 0.00 0.00 38.18 3.86
876 879 2.239150 AGCTCTCATTTCAGCACTGGAT 59.761 45.455 0.00 0.00 38.18 3.41
877 880 3.453717 AGCTCTCATTTCAGCACTGGATA 59.546 43.478 0.00 0.00 38.18 2.59
907 911 0.248843 TGAAATTTCAATGCCGGCCC 59.751 50.000 26.77 0.00 33.55 5.80
913 917 4.113815 CAATGCCGGCCCAGAGGA 62.114 66.667 26.77 2.60 33.47 3.71
914 918 4.115199 AATGCCGGCCCAGAGGAC 62.115 66.667 26.77 0.00 38.13 3.85
966 988 0.661020 GAACCTTGTGTCCAACCACG 59.339 55.000 0.00 0.00 38.20 4.94
1041 1063 3.390521 ACGGCCTTGATCTCGCCA 61.391 61.111 15.54 0.00 43.17 5.69
1137 1159 4.357947 GGCGTCGACAGCACCAGA 62.358 66.667 25.67 0.00 36.08 3.86
1441 1464 0.946221 ACGTCGCTGCCTTCAAGAAG 60.946 55.000 2.83 2.83 38.14 2.85
1455 1478 5.756849 CTTCAAGAAGGAGAAGAAACAAGC 58.243 41.667 1.86 0.00 42.95 4.01
1456 1479 4.137543 TCAAGAAGGAGAAGAAACAAGCC 58.862 43.478 0.00 0.00 0.00 4.35
1457 1480 2.772287 AGAAGGAGAAGAAACAAGCCG 58.228 47.619 0.00 0.00 0.00 5.52
1458 1481 1.807142 GAAGGAGAAGAAACAAGCCGG 59.193 52.381 0.00 0.00 0.00 6.13
1467 1490 0.539518 AAACAAGCCGGCCAGTTTTT 59.460 45.000 30.31 18.20 30.64 1.94
1512 1535 4.803426 CAGACCTCGGAGTGCGGC 62.803 72.222 3.57 0.00 0.00 6.53
1583 1606 4.082523 CTGCCCGTCGACCACCAT 62.083 66.667 10.58 0.00 0.00 3.55
1800 1834 6.962182 TCATGGAAAGTAACTGAGGATTCAT 58.038 36.000 0.00 0.00 31.68 2.57
1815 1849 9.599866 CTGAGGATTCATACTGTAATTGTTGTA 57.400 33.333 0.00 0.00 31.68 2.41
1816 1850 9.599866 TGAGGATTCATACTGTAATTGTTGTAG 57.400 33.333 0.00 0.00 0.00 2.74
1817 1851 8.964476 AGGATTCATACTGTAATTGTTGTAGG 57.036 34.615 0.00 0.00 0.00 3.18
1818 1852 8.548877 AGGATTCATACTGTAATTGTTGTAGGT 58.451 33.333 0.00 0.00 0.00 3.08
1819 1853 9.826574 GGATTCATACTGTAATTGTTGTAGGTA 57.173 33.333 0.00 0.00 0.00 3.08
1993 2027 2.892640 CCACGGAGAAGCATCGGA 59.107 61.111 0.00 0.00 0.00 4.55
2075 2109 3.700831 GAGGACGCGAGGAGGAGGA 62.701 68.421 15.93 0.00 0.00 3.71
2261 2295 3.287867 TCTTTCATGGAGATTCTGGGC 57.712 47.619 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 2.786495 CGACATCCTCAGGGTCCCG 61.786 68.421 0.99 0.00 0.00 5.14
331 332 2.747855 GCGCCTTGTTGGAGGAGG 60.748 66.667 0.00 0.00 39.25 4.30
387 388 1.305802 TACTGCTCACGGGGGACAT 60.306 57.895 0.00 0.00 0.00 3.06
470 471 1.343465 GTCGGAGTGTTTTCCCTCTCA 59.657 52.381 0.00 0.00 33.46 3.27
476 477 0.033090 ACCTCGTCGGAGTGTTTTCC 59.967 55.000 0.00 0.00 38.70 3.13
479 480 1.664306 GGACCTCGTCGGAGTGTTT 59.336 57.895 0.00 0.00 38.70 2.83
518 519 1.363744 GTCTGAAAGGCGTCTCCATG 58.636 55.000 0.00 0.00 37.29 3.66
521 522 1.446272 CGGTCTGAAAGGCGTCTCC 60.446 63.158 0.00 0.00 41.72 3.71
539 540 4.836125 TGCAGTTCCAGAAAGAATGAAC 57.164 40.909 0.00 0.00 37.86 3.18
578 580 3.498397 GCTTGACCGATGAAGTTTTGAGA 59.502 43.478 0.00 0.00 0.00 3.27
579 581 3.250762 TGCTTGACCGATGAAGTTTTGAG 59.749 43.478 0.00 0.00 0.00 3.02
580 582 3.003275 GTGCTTGACCGATGAAGTTTTGA 59.997 43.478 0.00 0.00 0.00 2.69
581 583 3.300009 GTGCTTGACCGATGAAGTTTTG 58.700 45.455 0.00 0.00 0.00 2.44
582 584 2.032030 CGTGCTTGACCGATGAAGTTTT 60.032 45.455 0.00 0.00 0.00 2.43
592 594 1.136085 CATTTGGTACGTGCTTGACCG 60.136 52.381 3.01 0.00 35.91 4.79
594 596 4.153475 ACATACATTTGGTACGTGCTTGAC 59.847 41.667 3.01 0.00 34.07 3.18
651 654 2.367202 GGTCTTGGCGAGGGGATCA 61.367 63.158 0.97 0.00 0.00 2.92
694 697 2.881111 TATGGAGAGATCGACGGGAT 57.119 50.000 0.00 0.00 38.35 3.85
819 822 3.118847 TCTCAAGCATCGAGAGCAAATCT 60.119 43.478 14.14 0.00 42.61 2.40
893 896 1.678635 CTCTGGGCCGGCATTGAAA 60.679 57.895 30.85 7.05 0.00 2.69
904 908 1.108776 TATGTGTACGTCCTCTGGGC 58.891 55.000 0.00 0.00 0.00 5.36
907 911 2.753452 ACTGGTATGTGTACGTCCTCTG 59.247 50.000 0.00 0.00 0.00 3.35
913 917 6.579666 TCTTCTTTACTGGTATGTGTACGT 57.420 37.500 0.00 0.00 0.00 3.57
914 918 6.475727 CCATCTTCTTTACTGGTATGTGTACG 59.524 42.308 0.00 0.00 0.00 3.67
915 919 6.258068 GCCATCTTCTTTACTGGTATGTGTAC 59.742 42.308 0.00 0.00 0.00 2.90
916 920 6.156256 AGCCATCTTCTTTACTGGTATGTGTA 59.844 38.462 0.00 0.00 0.00 2.90
1041 1063 2.688794 GGACGTCCTCGAGTCGCTT 61.689 63.158 27.64 8.14 40.62 4.68
1297 1319 1.376942 CCCAGCAGAGCAAGTCCAG 60.377 63.158 0.00 0.00 0.00 3.86
1441 1464 1.587043 GGCCGGCTTGTTTCTTCTCC 61.587 60.000 28.56 0.00 0.00 3.71
1454 1477 1.287815 GGTACAAAAACTGGCCGGC 59.712 57.895 21.18 21.18 0.00 6.13
1455 1478 1.167781 ACGGTACAAAAACTGGCCGG 61.168 55.000 11.02 11.02 45.91 6.13
1456 1479 0.236449 GACGGTACAAAAACTGGCCG 59.764 55.000 0.00 0.00 46.57 6.13
1457 1480 0.594602 GGACGGTACAAAAACTGGCC 59.405 55.000 0.00 0.00 46.65 5.36
1458 1481 1.310904 TGGACGGTACAAAAACTGGC 58.689 50.000 0.00 0.00 32.51 4.85
1467 1490 0.319211 CGCTCAACTTGGACGGTACA 60.319 55.000 0.00 0.00 0.00 2.90
1800 1834 7.879160 CCAAGGTTACCTACAACAATTACAGTA 59.121 37.037 3.55 0.00 31.13 2.74
1812 1846 1.349688 CCTGCACCAAGGTTACCTACA 59.650 52.381 3.55 0.00 31.13 2.74
1815 1849 1.074951 GCCTGCACCAAGGTTACCT 59.925 57.895 0.00 0.00 39.75 3.08
1816 1850 1.977009 GGCCTGCACCAAGGTTACC 60.977 63.158 0.00 0.00 39.75 2.85
1817 1851 1.228429 TGGCCTGCACCAAGGTTAC 60.228 57.895 3.32 0.00 39.75 2.50
1818 1852 1.074775 CTGGCCTGCACCAAGGTTA 59.925 57.895 3.32 0.00 39.86 2.85
1819 1853 2.203538 CTGGCCTGCACCAAGGTT 60.204 61.111 3.32 0.00 39.86 3.50
1852 1886 0.318441 TCTTCCTCTTCACCACTGCG 59.682 55.000 0.00 0.00 0.00 5.18
1974 2008 2.125552 CGATGCTTCTCCGTGGCA 60.126 61.111 0.00 0.00 40.32 4.92
1975 2009 2.892425 CCGATGCTTCTCCGTGGC 60.892 66.667 0.00 0.00 0.00 5.01
1978 2012 1.379977 TCCTCCGATGCTTCTCCGT 60.380 57.895 0.00 0.00 0.00 4.69
2219 2253 8.547967 AAGAAAGCTTAATTACAAGTCGATCA 57.452 30.769 0.00 0.00 31.07 2.92


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

AutoCloner maintained by Alex Coulton.