Multiple sequence alignment - TraesCS6D01G118400

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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 TraesCS6D01G118400 chr6D 100.000 2328 0 0 1 2328 83976678 83974351 0 4300
1 TraesCS6D01G118400 chr5A 98.026 2330 34 4 1 2328 300072978 300075297 0 4037
2 TraesCS6D01G118400 chrUn 97.983 2330 35 4 1 2328 189392538 189394857 0 4032
3 TraesCS6D01G118400 chr2A 97.940 2330 36 4 1 2328 618279957 618277638 0 4026
4 TraesCS6D01G118400 chr7D 97.767 2329 41 6 1 2328 203556346 203554028 0 4002
5 TraesCS6D01G118400 chr7D 97.725 2330 41 4 1 2328 626698491 626696172 0 3999
6 TraesCS6D01G118400 chr6A 97.767 2329 40 4 1 2328 289128631 289130948 0 4002
7 TraesCS6D01G118400 chr7B 97.725 2330 41 5 1 2328 743086198 743088517 0 3999
8 TraesCS6D01G118400 chr3B 97.681 2329 41 6 1 2328 92199603 92201919 0 3989
9 TraesCS6D01G118400 chr7A 97.558 2334 41 5 1 2328 4959837 4962160 0 3980


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 TraesCS6D01G118400 chr6D 83974351 83976678 2327 True 4300 4300 100.000 1 2328 1 chr6D.!!$R1 2327
1 TraesCS6D01G118400 chr5A 300072978 300075297 2319 False 4037 4037 98.026 1 2328 1 chr5A.!!$F1 2327
2 TraesCS6D01G118400 chrUn 189392538 189394857 2319 False 4032 4032 97.983 1 2328 1 chrUn.!!$F1 2327
3 TraesCS6D01G118400 chr2A 618277638 618279957 2319 True 4026 4026 97.940 1 2328 1 chr2A.!!$R1 2327
4 TraesCS6D01G118400 chr7D 203554028 203556346 2318 True 4002 4002 97.767 1 2328 1 chr7D.!!$R1 2327
5 TraesCS6D01G118400 chr7D 626696172 626698491 2319 True 3999 3999 97.725 1 2328 1 chr7D.!!$R2 2327
6 TraesCS6D01G118400 chr6A 289128631 289130948 2317 False 4002 4002 97.767 1 2328 1 chr6A.!!$F1 2327
7 TraesCS6D01G118400 chr7B 743086198 743088517 2319 False 3999 3999 97.725 1 2328 1 chr7B.!!$F1 2327
8 TraesCS6D01G118400 chr3B 92199603 92201919 2316 False 3989 3989 97.681 1 2328 1 chr3B.!!$F1 2327
9 TraesCS6D01G118400 chr7A 4959837 4962160 2323 False 3980 3980 97.558 1 2328 1 chr7A.!!$F1 2327

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
979 983 1.3382 GGAGTTCATTCAGCACCGAGT 60.338 52.381 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 1942 0.668706 CCACAAGCTCTGACCTGACG 60.669 60.0 0.0 0.0 0.0 4.35 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
157 158 3.081061 CTCACTCGCATATCTAGAGCCT 58.919 50.000 0.00 0.0 35.56 4.58
406 407 8.522830 CAACTTAAGGAATCTTTAGATTTGGCA 58.477 33.333 7.53 0.0 44.14 4.92
577 580 5.068591 TCAATCCAAAATCTCCGATCGTCTA 59.931 40.000 15.09 0.0 0.00 2.59
589 592 2.980476 CGATCGTCTATGATCCAAACCG 59.020 50.000 7.03 0.0 41.39 4.44
761 764 5.067023 GCTCAGTGAAATGGAATAAGGAAGG 59.933 44.000 0.00 0.0 0.00 3.46
819 822 2.452600 TGAGGTTTTCAAGCAAGGGT 57.547 45.000 0.00 0.0 31.34 4.34
863 866 5.947443 GAAGAATTCACATCAGAACCCTTG 58.053 41.667 8.44 0.0 46.62 3.61
892 895 2.291346 CCCCTTTTTACCCATCGGACTT 60.291 50.000 0.00 0.0 0.00 3.01
979 983 1.338200 GGAGTTCATTCAGCACCGAGT 60.338 52.381 0.00 0.0 0.00 4.18
1055 1059 2.679355 CGAAAGCCACATTCGTTTCA 57.321 45.000 0.82 0.0 43.41 2.69
1076 1080 0.391597 TTGAGGAAGTCACACGTCCC 59.608 55.000 5.15 0.0 46.06 4.46
1248 1253 5.965922 TGTGATCTATTCTCGTGTCACATT 58.034 37.500 3.42 0.0 40.47 2.71
1299 1304 4.095932 TCACTACTACCGCTTCTACACATG 59.904 45.833 0.00 0.0 0.00 3.21
1300 1305 2.295253 ACTACCGCTTCTACACATGC 57.705 50.000 0.00 0.0 0.00 4.06
1301 1306 1.548719 ACTACCGCTTCTACACATGCA 59.451 47.619 0.00 0.0 0.00 3.96
1302 1307 2.168521 ACTACCGCTTCTACACATGCAT 59.831 45.455 0.00 0.0 0.00 3.96
1424 1429 4.099419 TGAAAGTGAATAGGAGCATAGCGA 59.901 41.667 0.00 0.0 0.00 4.93
1482 1487 3.551890 GTCTTCTCGCGCAAATAAGATCA 59.448 43.478 8.75 0.0 0.00 2.92
1538 1543 1.153449 CCGCCCGCTCTCAATACAA 60.153 57.895 0.00 0.0 0.00 2.41
1642 1652 5.553123 TGTATAGCGAAACCTTTCCTTGAA 58.447 37.500 0.00 0.0 33.68 2.69
1685 1695 2.722094 AGCCGAGCTATCTATCCAGAG 58.278 52.381 0.00 0.0 36.99 3.35
1712 1722 4.226761 GTTGAACGAAGCGAATGGAAAAT 58.773 39.130 0.00 0.0 0.00 1.82
1800 1810 6.647067 CGATGTAAGATAGAAAGAATGGGGAC 59.353 42.308 0.00 0.0 0.00 4.46
1853 1863 5.341872 TCAATTCCAAATCATTTGCCGAT 57.658 34.783 4.40 0.0 39.31 4.18
1932 1942 3.059188 CGTGGGTGAATCAAGTACAACAC 60.059 47.826 0.00 0.0 0.00 3.32
2002 2012 5.836898 TCCACTCAACTAGGAAAGAAGTACA 59.163 40.000 0.00 0.0 0.00 2.90
2018 2028 5.243954 AGAAGTACACATTGCTGACTGACTA 59.756 40.000 0.00 0.0 0.00 2.59
2120 2130 1.169577 AGCACAGACTCTACTCACCG 58.830 55.000 0.00 0.0 0.00 4.94
2308 2318 1.009997 TTAGGGGTAAGAGGGGACGA 58.990 55.000 0.00 0.0 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 158 2.423892 GTGTCGTTCAGGAGAGATGCTA 59.576 50.000 0.00 0.00 0.00 3.49
406 407 3.107601 TGTGCCCTTTGAGTCTATAGCT 58.892 45.455 0.00 0.00 0.00 3.32
513 516 1.820519 AGTTACGAGTCGGGTAATGCA 59.179 47.619 18.30 0.00 32.94 3.96
577 580 3.264450 AGGAGAGTTTCGGTTTGGATCAT 59.736 43.478 0.00 0.00 0.00 2.45
761 764 5.416271 TCCCTTATCACACTACACTTTCC 57.584 43.478 0.00 0.00 0.00 3.13
863 866 0.895530 GGTAAAAAGGGGAAGCAGGC 59.104 55.000 0.00 0.00 0.00 4.85
892 895 5.410924 CGTAGGAGATCAAAATGTGAGTCA 58.589 41.667 0.00 0.00 40.43 3.41
979 983 0.730840 TTGAATCTACGCTCGCTCGA 59.269 50.000 3.28 0.00 0.00 4.04
1055 1059 2.550208 GGGACGTGTGACTTCCTCAAAT 60.550 50.000 0.00 0.00 36.81 2.32
1076 1080 9.726438 AATGAATCTCCTTATTTATAGGGAACG 57.274 33.333 2.70 0.00 37.96 3.95
1110 1115 6.206180 AGAAGAGGGGATTTCTGAAGAAAA 57.794 37.500 9.42 0.00 45.81 2.29
1111 1116 5.850046 AGAAGAGGGGATTTCTGAAGAAA 57.150 39.130 7.89 7.89 46.60 2.52
1112 1117 5.280727 GGAAGAAGAGGGGATTTCTGAAGAA 60.281 44.000 0.00 0.00 34.09 2.52
1113 1118 4.226168 GGAAGAAGAGGGGATTTCTGAAGA 59.774 45.833 0.00 0.00 34.09 2.87
1114 1119 4.227073 AGGAAGAAGAGGGGATTTCTGAAG 59.773 45.833 0.00 0.00 34.09 3.02
1248 1253 2.711009 TGGAGGGAGAAGAAAGAAAGCA 59.289 45.455 0.00 0.00 0.00 3.91
1299 1304 6.567050 TCCAGAATGCTTCTTTGATTTATGC 58.433 36.000 0.00 0.00 38.11 3.14
1302 1307 9.466497 ACTATTCCAGAATGCTTCTTTGATTTA 57.534 29.630 3.10 0.00 38.11 1.40
1319 1324 5.811399 TTAACGAAATGCCACTATTCCAG 57.189 39.130 0.00 0.00 0.00 3.86
1424 1429 1.541147 CGTGTTTGGCTTGGATGATGT 59.459 47.619 0.00 0.00 0.00 3.06
1538 1543 4.037446 GTCTTGTGAGAGAGAGTCACTTGT 59.963 45.833 4.96 0.00 44.02 3.16
1642 1652 7.148000 GGCTTCTATTAGCTGAGAATGGTTTTT 60.148 37.037 0.00 0.00 40.99 1.94
1685 1695 1.503818 TTCGCTTCGTTCAACCCTGC 61.504 55.000 0.00 0.00 0.00 4.85
1712 1722 8.646004 TCACAATGGATTTATGTTTTCTTTGGA 58.354 29.630 0.00 0.00 0.00 3.53
1800 1810 1.555533 AGAGGAAACCGAAGCCCTAAG 59.444 52.381 0.00 0.00 0.00 2.18
1853 1863 4.537135 AAAAGAGAAGTGAGTCCGCATA 57.463 40.909 0.00 0.00 0.00 3.14
1932 1942 0.668706 CCACAAGCTCTGACCTGACG 60.669 60.000 0.00 0.00 0.00 4.35
2002 2012 5.106948 CGTTCAAATAGTCAGTCAGCAATGT 60.107 40.000 0.00 0.00 0.00 2.71
2018 2028 8.351461 GCTACTAGTAACTAGGATCGTTCAAAT 58.649 37.037 3.76 0.00 38.30 2.32
2120 2130 1.777199 CGTAGGTGGAAAACGCGTC 59.223 57.895 14.44 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.