Multiple sequence alignment - TraesCS4A01G154900

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 TraesCS4A01G154900 chr4A 100.000 2141 0 0 1 2141 310738838 310740978 0.000000e+00 3954
1 TraesCS4A01G154900 chr5D 96.684 2141 71 0 1 2141 503218459 503220599 0.000000e+00 3561
2 TraesCS4A01G154900 chr5D 96.489 2136 75 0 1 2136 503277985 503275850 0.000000e+00 3530
3 TraesCS4A01G154900 chr1A 96.684 2141 71 0 1 2141 554512489 554514629 0.000000e+00 3561
4 TraesCS4A01G154900 chr3B 96.497 2141 75 0 1 2141 201527265 201529405 0.000000e+00 3539
5 TraesCS4A01G154900 chr3B 94.370 2007 110 3 135 2141 700786918 700784915 0.000000e+00 3077
6 TraesCS4A01G154900 chr3B 97.066 1670 49 0 472 2141 101911887 101913556 0.000000e+00 2813
7 TraesCS4A01G154900 chr3B 95.484 155 7 0 1 155 810706442 810706288 4.560000e-62 248
8 TraesCS4A01G154900 chr3A 96.497 2141 73 2 1 2141 672909766 672907628 0.000000e+00 3537
9 TraesCS4A01G154900 chr3D 96.579 2134 72 1 8 2141 589279296 589277164 0.000000e+00 3535
10 TraesCS4A01G154900 chr2A 95.787 2136 88 2 1 2135 335838869 335841003 0.000000e+00 3445


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 TraesCS4A01G154900 chr4A 310738838 310740978 2140 False 3954 3954 100.000 1 2141 1 chr4A.!!$F1 2140
1 TraesCS4A01G154900 chr5D 503218459 503220599 2140 False 3561 3561 96.684 1 2141 1 chr5D.!!$F1 2140
2 TraesCS4A01G154900 chr5D 503275850 503277985 2135 True 3530 3530 96.489 1 2136 1 chr5D.!!$R1 2135
3 TraesCS4A01G154900 chr1A 554512489 554514629 2140 False 3561 3561 96.684 1 2141 1 chr1A.!!$F1 2140
4 TraesCS4A01G154900 chr3B 201527265 201529405 2140 False 3539 3539 96.497 1 2141 1 chr3B.!!$F2 2140
5 TraesCS4A01G154900 chr3B 700784915 700786918 2003 True 3077 3077 94.370 135 2141 1 chr3B.!!$R1 2006
6 TraesCS4A01G154900 chr3B 101911887 101913556 1669 False 2813 2813 97.066 472 2141 1 chr3B.!!$F1 1669
7 TraesCS4A01G154900 chr3A 672907628 672909766 2138 True 3537 3537 96.497 1 2141 1 chr3A.!!$R1 2140
8 TraesCS4A01G154900 chr3D 589277164 589279296 2132 True 3535 3535 96.579 8 2141 1 chr3D.!!$R1 2133
9 TraesCS4A01G154900 chr2A 335838869 335841003 2134 False 3445 3445 95.787 1 2135 1 chr2A.!!$F1 2134

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
924 927 1.544246 GTTGGGCGCTTTAACCATTCT 59.456 47.619 7.64 0.0 33.63 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 1729 1.029681 GCTCACAAACCCCGAGTTTT 58.97 50.0 1.32 0.0 46.79 2.43 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
37 38 8.893563 TTCCCATTGATATAGGAACTTTTGTT 57.106 30.769 0.00 0.00 46.75 2.83
143 144 5.376854 AATGTATGCATTTCGATTAGGGC 57.623 39.130 3.54 0.00 42.19 5.19
145 146 2.363306 ATGCATTTCGATTAGGGCCA 57.637 45.000 6.18 0.00 0.00 5.36
386 387 5.921408 GGTGTTTTGTATAAATGTTTCGCCA 59.079 36.000 0.00 0.00 0.00 5.69
450 452 5.446260 AGTGGAATAGAATAACCCGGTTT 57.554 39.130 8.44 0.00 0.00 3.27
469 471 5.221106 CGGTTTAAGGGTAGTGATCATACGA 60.221 44.000 0.00 0.00 0.00 3.43
470 472 6.516194 CGGTTTAAGGGTAGTGATCATACGAT 60.516 42.308 0.00 0.00 33.31 3.73
487 489 8.376889 TCATACGATTGTAATGCATTGTATGT 57.623 30.769 27.39 18.92 39.11 2.29
590 592 5.476945 AGTTCGACCCAATGCTTTATTTCTT 59.523 36.000 0.00 0.00 0.00 2.52
593 595 5.102313 CGACCCAATGCTTTATTTCTTTCC 58.898 41.667 0.00 0.00 0.00 3.13
597 599 6.381133 ACCCAATGCTTTATTTCTTTCCTAGG 59.619 38.462 0.82 0.82 0.00 3.02
686 689 6.748333 ATACTGCATATTTGATTCCATCCG 57.252 37.500 0.00 0.00 0.00 4.18
711 714 2.467880 TCGACTTTCCCTCCTATGCTT 58.532 47.619 0.00 0.00 0.00 3.91
848 851 5.885912 GCCAGTTCCAATAGACTTATGGAAA 59.114 40.000 18.22 5.59 39.92 3.13
868 871 2.024868 TTCCCGTTCGTGTGCATCG 61.025 57.895 7.73 7.73 0.00 3.84
884 887 2.877168 GCATCGAGCAGGAATTGAATCT 59.123 45.455 0.00 0.00 44.79 2.40
924 927 1.544246 GTTGGGCGCTTTAACCATTCT 59.456 47.619 7.64 0.00 33.63 2.40
1039 1042 3.077359 GGAGATGGCAAATATTCGGAGG 58.923 50.000 0.00 0.00 0.00 4.30
1070 1073 0.396417 ACACCTCTCTGGATCCTCGG 60.396 60.000 14.23 8.36 39.71 4.63
1102 1105 6.042322 AGAGAGATTGAGAGGGATCAAGAATG 59.958 42.308 0.00 0.00 42.20 2.67
1262 1265 8.632679 GGCATTGATAACAAGGATCTAATGAAA 58.367 33.333 1.20 0.00 39.71 2.69
1308 1311 9.745880 CTTTAGCAGAAAGACGTATATTCCTTA 57.254 33.333 5.42 0.00 0.00 2.69
1480 1484 7.693536 GGTCAAATACCTAACGAAAAATTACGG 59.306 37.037 0.00 0.00 45.75 4.02
1530 1534 6.073222 GCTTCTTATTCCACAAGAACGAAAGA 60.073 38.462 0.00 0.00 37.15 2.52
1645 1649 6.276847 GTGCACTAGATCTTGTAGCACTTAT 58.723 40.000 31.71 5.45 45.24 1.73
1649 1653 7.168972 GCACTAGATCTTGTAGCACTTATCAAG 59.831 40.741 18.87 0.00 38.69 3.02
1653 1657 7.800092 AGATCTTGTAGCACTTATCAAGGAAT 58.200 34.615 0.00 0.00 38.13 3.01
1740 1744 4.721132 TCATAGAAAAACTCGGGGTTTGT 58.279 39.130 6.78 0.25 46.18 2.83
1813 1817 4.478686 AGGAGGGGCTCTTGTACAAAATAT 59.521 41.667 10.03 0.00 0.00 1.28
1889 1893 1.028905 TGTCAGGAAGCGGGTTTTTG 58.971 50.000 0.00 0.00 0.00 2.44
2003 2007 2.921221 AGATCTTTGGTCTTCCCCTGA 58.079 47.619 0.00 0.00 0.00 3.86
2119 2124 1.280710 TGGTGCAATCCTTACCGACAT 59.719 47.619 0.00 0.00 37.29 3.06
2126 2131 5.124776 TGCAATCCTTACCGACATAAAAAGG 59.875 40.000 0.00 0.00 38.44 3.11
2130 2135 5.623169 TCCTTACCGACATAAAAAGGTTGT 58.377 37.500 0.00 0.00 38.29 3.32
2136 2141 6.235664 ACCGACATAAAAAGGTTGTAGTCAT 58.764 36.000 0.00 0.00 32.17 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 8.528643 TGGTAGAATCGTAACCATAGAATATGG 58.471 37.037 13.15 13.15 44.54 2.74
145 146 9.529823 TCTGGTAGAATCGTAACCATAGAATAT 57.470 33.333 5.80 0.00 42.23 1.28
206 207 2.561419 GAGGTCATAAGCGCCTATACCA 59.439 50.000 18.62 0.00 31.89 3.25
450 452 6.971726 ACAATCGTATGATCACTACCCTTA 57.028 37.500 0.00 0.00 32.24 2.69
458 460 7.355017 ACAATGCATTACAATCGTATGATCAC 58.645 34.615 12.53 0.00 32.24 3.06
469 471 6.128486 TCTGGGACATACAATGCATTACAAT 58.872 36.000 12.53 3.14 38.20 2.71
470 472 5.504853 TCTGGGACATACAATGCATTACAA 58.495 37.500 12.53 0.60 38.20 2.41
515 517 1.115467 AGCCATCGACTACCTGGAAG 58.885 55.000 6.18 0.00 31.38 3.46
590 592 1.968493 CGAATCGGGATTCCCTAGGAA 59.032 52.381 19.63 3.05 46.39 3.36
686 689 4.750598 GCATAGGAGGGAAAGTCGATTTAC 59.249 45.833 0.00 0.00 0.00 2.01
711 714 7.648112 CGAATTCTTATCGATACTGGAACTCAA 59.352 37.037 4.16 0.00 42.76 3.02
784 787 7.557875 TCTCATCCATCATCCATACATAACA 57.442 36.000 0.00 0.00 0.00 2.41
848 851 0.949105 GATGCACACGAACGGGAACT 60.949 55.000 2.83 0.00 0.00 3.01
882 885 8.034215 CCAACTCATAATTGGTAAATTTGCAGA 58.966 33.333 8.59 0.00 41.55 4.26
884 887 7.102346 CCCAACTCATAATTGGTAAATTTGCA 58.898 34.615 8.59 0.00 44.46 4.08
924 927 1.685803 CCCTGTTAAGCATCCATGGCA 60.686 52.381 6.96 0.00 0.00 4.92
1018 1021 3.077359 CCTCCGAATATTTGCCATCTCC 58.923 50.000 0.00 0.00 0.00 3.71
1039 1042 4.932200 CCAGAGAGGTGTTTTCATAGTCAC 59.068 45.833 0.00 0.00 0.00 3.67
1070 1073 6.232581 TCCCTCTCAATCTCTCTTTCAATC 57.767 41.667 0.00 0.00 0.00 2.67
1102 1105 5.470098 TCCATTCCAAATAGCGAGAATTAGC 59.530 40.000 0.00 0.00 0.00 3.09
1205 1208 6.070424 GGTATCATAAGTAAATGGATCCCGGA 60.070 42.308 9.90 0.00 0.00 5.14
1308 1311 9.553064 GGAATAAGTGATTGTCTGATAATGAGT 57.447 33.333 4.27 0.00 0.00 3.41
1381 1384 0.589223 TAAGCGCAACGAAAAGGGTG 59.411 50.000 11.47 0.00 0.00 4.61
1645 1649 8.757307 AATACTAATGGATAGGGATTCCTTGA 57.243 34.615 0.00 0.00 41.56 3.02
1649 1653 7.037586 TGTGGAATACTAATGGATAGGGATTCC 60.038 40.741 16.66 16.66 46.35 3.01
1653 1657 8.982471 TTATGTGGAATACTAATGGATAGGGA 57.018 34.615 0.00 0.00 35.81 4.20
1725 1729 1.029681 GCTCACAAACCCCGAGTTTT 58.970 50.000 1.32 0.00 46.79 2.43
1731 1735 2.268076 CCTTGGCTCACAAACCCCG 61.268 63.158 0.00 0.00 38.91 5.73
1889 1893 2.619646 TCGAAGTACCTTTTGGCCAAAC 59.380 45.455 30.43 19.10 45.59 2.93
2071 2076 7.017651 AGCACCTTCTACTTATAATAGGCCATT 59.982 37.037 5.01 5.55 0.00 3.16
2083 2088 2.233922 GCACCAGAGCACCTTCTACTTA 59.766 50.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.