Multiple sequence alignment - TraesCS6A01G227500

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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 TraesCS6A01G227500 chr6A 100.000 2591 0 0 1 2591 428285748 428288338 0.000000e+00 4785
1 TraesCS6A01G227500 chr6A 97.098 1275 33 1 577 1847 608061677 608062951 0.000000e+00 2146
2 TraesCS6A01G227500 chr6A 96.921 747 17 4 1847 2591 602173270 602172528 0.000000e+00 1247
3 TraesCS6A01G227500 chr2A 97.509 1847 34 4 1 1847 461392444 461394278 0.000000e+00 3145
4 TraesCS6A01G227500 chr2A 97.055 747 12 5 1847 2591 668899993 668900731 0.000000e+00 1249
5 TraesCS6A01G227500 chr1A 97.293 1847 38 4 1 1847 302911992 302913826 0.000000e+00 3123
6 TraesCS6A01G227500 chr5A 97.155 1828 37 5 1 1826 680753331 680755145 0.000000e+00 3073
7 TraesCS6A01G227500 chr5A 94.641 1866 59 16 7 1847 701985502 701983653 0.000000e+00 2854
8 TraesCS6A01G227500 chr5A 94.917 1810 76 10 1 1810 647551288 647553081 0.000000e+00 2819
9 TraesCS6A01G227500 chr5A 96.671 751 17 7 1846 2591 11342200 11341453 0.000000e+00 1242
10 TraesCS6A01G227500 chr5A 96.174 758 22 7 1837 2591 56763136 56763889 0.000000e+00 1232
11 TraesCS6A01G227500 chr5A 98.551 69 1 0 7 75 680763031 680762963 3.500000e-24 122
12 TraesCS6A01G227500 chr7A 96.561 1861 38 14 1 1847 147920299 147918451 0.000000e+00 3059
13 TraesCS6A01G227500 chr7A 96.917 746 19 3 1847 2591 231883107 231883849 0.000000e+00 1247
14 TraesCS6A01G227500 chr3A 96.312 1844 32 12 7 1847 27908551 27906741 0.000000e+00 2996
15 TraesCS6A01G227500 chr3A 96.089 1841 59 8 7 1847 37633069 37634896 0.000000e+00 2988
16 TraesCS6A01G227500 chr4A 95.344 1847 71 9 1 1847 521945341 521947172 0.000000e+00 2920
17 TraesCS6A01G227500 chr3B 97.193 748 17 3 1847 2591 22534174 22533428 0.000000e+00 1262
18 TraesCS6A01G227500 chr7B 97.055 747 16 6 1847 2591 605693246 605693988 0.000000e+00 1253
19 TraesCS6A01G227500 chr7B 96.804 751 14 9 1847 2591 446392135 446391389 0.000000e+00 1245
20 TraesCS6A01G227500 chr6B 96.179 759 21 6 1838 2591 160700623 160699868 0.000000e+00 1234


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 TraesCS6A01G227500 chr6A 428285748 428288338 2590 False 4785 4785 100.000 1 2591 1 chr6A.!!$F1 2590
1 TraesCS6A01G227500 chr6A 608061677 608062951 1274 False 2146 2146 97.098 577 1847 1 chr6A.!!$F2 1270
2 TraesCS6A01G227500 chr6A 602172528 602173270 742 True 1247 1247 96.921 1847 2591 1 chr6A.!!$R1 744
3 TraesCS6A01G227500 chr2A 461392444 461394278 1834 False 3145 3145 97.509 1 1847 1 chr2A.!!$F1 1846
4 TraesCS6A01G227500 chr2A 668899993 668900731 738 False 1249 1249 97.055 1847 2591 1 chr2A.!!$F2 744
5 TraesCS6A01G227500 chr1A 302911992 302913826 1834 False 3123 3123 97.293 1 1847 1 chr1A.!!$F1 1846
6 TraesCS6A01G227500 chr5A 680753331 680755145 1814 False 3073 3073 97.155 1 1826 1 chr5A.!!$F3 1825
7 TraesCS6A01G227500 chr5A 701983653 701985502 1849 True 2854 2854 94.641 7 1847 1 chr5A.!!$R3 1840
8 TraesCS6A01G227500 chr5A 647551288 647553081 1793 False 2819 2819 94.917 1 1810 1 chr5A.!!$F2 1809
9 TraesCS6A01G227500 chr5A 11341453 11342200 747 True 1242 1242 96.671 1846 2591 1 chr5A.!!$R1 745
10 TraesCS6A01G227500 chr5A 56763136 56763889 753 False 1232 1232 96.174 1837 2591 1 chr5A.!!$F1 754
11 TraesCS6A01G227500 chr7A 147918451 147920299 1848 True 3059 3059 96.561 1 1847 1 chr7A.!!$R1 1846
12 TraesCS6A01G227500 chr7A 231883107 231883849 742 False 1247 1247 96.917 1847 2591 1 chr7A.!!$F1 744
13 TraesCS6A01G227500 chr3A 27906741 27908551 1810 True 2996 2996 96.312 7 1847 1 chr3A.!!$R1 1840
14 TraesCS6A01G227500 chr3A 37633069 37634896 1827 False 2988 2988 96.089 7 1847 1 chr3A.!!$F1 1840
15 TraesCS6A01G227500 chr4A 521945341 521947172 1831 False 2920 2920 95.344 1 1847 1 chr4A.!!$F1 1846
16 TraesCS6A01G227500 chr3B 22533428 22534174 746 True 1262 1262 97.193 1847 2591 1 chr3B.!!$R1 744
17 TraesCS6A01G227500 chr7B 605693246 605693988 742 False 1253 1253 97.055 1847 2591 1 chr7B.!!$F1 744
18 TraesCS6A01G227500 chr7B 446391389 446392135 746 True 1245 1245 96.804 1847 2591 1 chr7B.!!$R1 744
19 TraesCS6A01G227500 chr6B 160699868 160700623 755 True 1234 1234 96.179 1838 2591 1 chr6B.!!$R1 753

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
139 141 0.326595 TCGCTCACTCACTCTCTCCT 59.673 55.000 0.0 0.0 0.0 3.69 F
216 232 1.371183 CCGTCTTTGAGGTGGCTCA 59.629 57.895 0.0 0.0 0.0 4.26 F
504 531 3.509442 TCATGCTGAGTTGGGGATTTTT 58.491 40.909 0.0 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1178 1234 0.329596 CCTAAGCTTGGCCAACTCCT 59.670 55.0 16.05 8.42 0.00 3.69 R
1390 1452 2.283145 ATGCACCTCTGCTCTTTTGT 57.717 45.0 0.00 0.00 44.57 2.83 R
2255 2318 1.239968 GGAGGGCTGCTGAACACAAG 61.240 60.0 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
121 123 4.828925 GCGCTCACTCCCCTGCTC 62.829 72.222 0.00 0.00 0.00 4.26
139 141 0.326595 TCGCTCACTCACTCTCTCCT 59.673 55.000 0.00 0.00 0.00 3.69
216 232 1.371183 CCGTCTTTGAGGTGGCTCA 59.629 57.895 0.00 0.00 0.00 4.26
451 478 6.039382 GGGGTTTGATTGTAGGATTGATGTAC 59.961 42.308 0.00 0.00 0.00 2.90
504 531 3.509442 TCATGCTGAGTTGGGGATTTTT 58.491 40.909 0.00 0.00 0.00 1.94
712 739 4.102367 TGTTGCTTTTGAAGGGCCTTTAAT 59.898 37.500 22.41 0.00 0.00 1.40
1178 1234 5.241506 CCAGGCTTAAGAGTGAACATGAAAA 59.758 40.000 6.67 0.00 0.00 2.29
1345 1407 6.268847 ACTTGAGAAGAAGAAGAAGGAGCTAA 59.731 38.462 0.00 0.00 0.00 3.09
1390 1452 4.826733 TGCAGATGGAAAAGCTCAAACTTA 59.173 37.500 0.00 0.00 0.00 2.24
1572 1634 6.127786 GCAAGGAGAAGTTAGAGCAAATCAAT 60.128 38.462 0.00 0.00 0.00 2.57
1754 1816 9.383519 CTATGTTGTTAAGTTGTAGTGGATCAT 57.616 33.333 0.00 0.00 0.00 2.45
1856 1918 3.763557 ATGGATCTTGTGTTGGGGAAT 57.236 42.857 0.00 0.00 0.00 3.01
1864 1926 1.327303 GTGTTGGGGAATGTTGCAGA 58.673 50.000 0.00 0.00 0.00 4.26
1895 1957 4.841443 ATTTTTCCTACGGTTTCACCAC 57.159 40.909 0.00 0.00 38.47 4.16
2014 2076 3.251245 GTGATGATGGAGTCGTACTCGAT 59.749 47.826 10.59 10.59 45.96 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 112 3.386237 GTGAGCGAGCAGGGGAGT 61.386 66.667 0.00 0.00 0.00 3.85
111 113 3.073735 AGTGAGCGAGCAGGGGAG 61.074 66.667 0.00 0.00 0.00 4.30
112 114 3.071206 GAGTGAGCGAGCAGGGGA 61.071 66.667 0.00 0.00 0.00 4.81
113 115 3.385384 TGAGTGAGCGAGCAGGGG 61.385 66.667 0.00 0.00 0.00 4.79
114 116 2.125753 GTGAGTGAGCGAGCAGGG 60.126 66.667 0.00 0.00 0.00 4.45
115 117 1.153862 GAGTGAGTGAGCGAGCAGG 60.154 63.158 0.00 0.00 0.00 4.85
116 118 0.179166 GAGAGTGAGTGAGCGAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
117 119 0.607762 AGAGAGTGAGTGAGCGAGCA 60.608 55.000 0.00 0.00 0.00 4.26
118 120 0.098728 GAGAGAGTGAGTGAGCGAGC 59.901 60.000 0.00 0.00 0.00 5.03
119 121 0.732571 GGAGAGAGTGAGTGAGCGAG 59.267 60.000 0.00 0.00 0.00 5.03
120 122 0.326595 AGGAGAGAGTGAGTGAGCGA 59.673 55.000 0.00 0.00 0.00 4.93
121 123 1.135431 CAAGGAGAGAGTGAGTGAGCG 60.135 57.143 0.00 0.00 0.00 5.03
139 141 2.604686 AGGGGAGTGAGCGAGCAA 60.605 61.111 0.00 0.00 0.00 3.91
216 232 2.430367 GGCAAGGAGGTCAACGGT 59.570 61.111 0.00 0.00 0.00 4.83
451 478 2.688446 TGTACTGAGATGAACCCTAGCG 59.312 50.000 0.00 0.00 0.00 4.26
504 531 9.522804 ACGCTTCATTAAAAATGAACACTAAAA 57.477 25.926 10.27 0.00 34.66 1.52
517 544 8.673711 AGAATATACTTGCACGCTTCATTAAAA 58.326 29.630 0.00 0.00 0.00 1.52
712 739 3.748668 GCAGCCATAGAAATGCCTTCCTA 60.749 47.826 0.00 0.00 34.21 2.94
1009 1062 3.068024 ACAACACCACAATTCACACCATC 59.932 43.478 0.00 0.00 0.00 3.51
1178 1234 0.329596 CCTAAGCTTGGCCAACTCCT 59.670 55.000 16.05 8.42 0.00 3.69
1345 1407 3.589288 ACCTCCAACATAGCTTTCTCCTT 59.411 43.478 0.00 0.00 0.00 3.36
1390 1452 2.283145 ATGCACCTCTGCTCTTTTGT 57.717 45.000 0.00 0.00 44.57 2.83
1572 1634 2.373169 ACTTCAAGACTCAAGGATGGCA 59.627 45.455 0.00 0.00 0.00 4.92
1746 1808 8.715998 CAACACTTAATAGCATAGATGATCCAC 58.284 37.037 0.00 0.00 0.00 4.02
1785 1847 8.995027 TCCATTTTCCACTACATAATAGCATT 57.005 30.769 0.00 0.00 0.00 3.56
1895 1957 6.751425 GCTTAGATGAACTCATAGATGGATCG 59.249 42.308 0.00 0.00 36.57 3.69
2254 2317 1.860484 GAGGGCTGCTGAACACAAGC 61.860 60.000 0.00 0.00 0.00 4.01
2255 2318 1.239968 GGAGGGCTGCTGAACACAAG 61.240 60.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.