Multiple sequence alignment - TraesCS1A01G098400

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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 TraesCS1A01G098400 chr1A 100.000 2318 0 0 1 2318 94772499 94774816 0 4281
1 TraesCS1A01G098400 chr6A 98.477 2232 32 1 1 2230 608884822 608882591 0 3932
2 TraesCS1A01G098400 chr6A 97.992 1843 32 2 476 2318 289129107 289130944 0 3193
3 TraesCS1A01G098400 chr7A 98.319 1844 30 1 476 2318 4960313 4962156 0 3232
4 TraesCS1A01G098400 chr7A 98.978 489 5 0 1 489 60109184 60109672 0 876
5 TraesCS1A01G098400 chr5A 98.265 1844 26 2 476 2318 300073455 300075293 0 3223
6 TraesCS1A01G098400 chrUn 98.156 1844 28 2 476 2318 189393015 189394853 0 3212
7 TraesCS1A01G098400 chrUn 98.978 489 5 0 1 489 273322488 273322976 0 876
8 TraesCS1A01G098400 chrUn 98.978 489 5 0 1 489 366017382 366017870 0 876
9 TraesCS1A01G098400 chr4A 98.101 1843 34 1 476 2318 67587057 67585216 0 3208
10 TraesCS1A01G098400 chr2A 98.102 1844 29 2 476 2318 618279480 618277642 0 3206
11 TraesCS1A01G098400 chr7B 97.995 1845 30 3 476 2318 743086674 743088513 0 3195
12 TraesCS1A01G098400 chr5B 97.995 1845 30 2 476 2318 679659372 679661211 0 3195
13 TraesCS1A01G098400 chr4D 98.978 489 5 0 1 489 123380881 123380393 0 876
14 TraesCS1A01G098400 chr4D 98.978 489 5 0 1 489 123591666 123591178 0 876
15 TraesCS1A01G098400 chr3D 98.978 489 5 0 1 489 523756929 523756441 0 876
16 TraesCS1A01G098400 chr2D 98.978 489 5 0 1 489 637323314 637323802 0 876
17 TraesCS1A01G098400 chr2D 98.773 489 6 0 1 489 635050311 635049823 0 870


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 TraesCS1A01G098400 chr1A 94772499 94774816 2317 False 4281 4281 100.000 1 2318 1 chr1A.!!$F1 2317
1 TraesCS1A01G098400 chr6A 608882591 608884822 2231 True 3932 3932 98.477 1 2230 1 chr6A.!!$R1 2229
2 TraesCS1A01G098400 chr6A 289129107 289130944 1837 False 3193 3193 97.992 476 2318 1 chr6A.!!$F1 1842
3 TraesCS1A01G098400 chr7A 4960313 4962156 1843 False 3232 3232 98.319 476 2318 1 chr7A.!!$F1 1842
4 TraesCS1A01G098400 chr5A 300073455 300075293 1838 False 3223 3223 98.265 476 2318 1 chr5A.!!$F1 1842
5 TraesCS1A01G098400 chrUn 189393015 189394853 1838 False 3212 3212 98.156 476 2318 1 chrUn.!!$F1 1842
6 TraesCS1A01G098400 chr4A 67585216 67587057 1841 True 3208 3208 98.101 476 2318 1 chr4A.!!$R1 1842
7 TraesCS1A01G098400 chr2A 618277642 618279480 1838 True 3206 3206 98.102 476 2318 1 chr2A.!!$R1 1842
8 TraesCS1A01G098400 chr7B 743086674 743088513 1839 False 3195 3195 97.995 476 2318 1 chr7B.!!$F1 1842
9 TraesCS1A01G098400 chr5B 679659372 679661211 1839 False 3195 3195 97.995 476 2318 1 chr5B.!!$F1 1842

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
596 597 2.558359 CTGTGATCCAAACCCAAACTCC 59.442 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1441 1447 0.809385 CGCGAGAAGACCCTTGACTA 59.191 55.0 0.0 0.0 0.0 2.59 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
364 365 6.761312 TGGAAGACCGTAGATTTTTCACTTA 58.239 36.000 0.00 0.00 39.42 2.24
458 459 6.996034 GGATAGAGATCTGCGGTAAACGAGT 61.996 48.000 0.00 0.00 37.18 4.18
596 597 2.558359 CTGTGATCCAAACCCAAACTCC 59.442 50.000 0.00 0.00 0.00 3.85
734 735 5.405269 GGTGAATACATGAAAAAGTGTTGCC 59.595 40.000 0.00 0.00 0.00 4.52
915 917 5.185056 TCGACTCACATTTTGATCTCCTACA 59.815 40.000 0.00 0.00 32.17 2.74
1014 1016 9.040939 CGTAGATTCAATATGTTGATTGTACCA 57.959 33.333 19.43 2.32 43.49 3.25
1022 1024 7.915293 ATATGTTGATTGTACCAAACGAAGA 57.085 32.000 0.00 0.00 0.00 2.87
1232 1238 3.805108 GCTGCCGGATGTGATCTATTCTT 60.805 47.826 5.05 0.00 0.00 2.52
1268 1274 6.239430 GCTTTCTTTCTTCTCCCTCCATTTTT 60.239 38.462 0.00 0.00 0.00 1.94
1326 1332 4.223477 AGCATTGTGGAATAGTGGCATTTT 59.777 37.500 0.00 0.00 0.00 1.82
1441 1447 1.308998 CAAGCCAAACACGTCTCCTT 58.691 50.000 0.00 0.00 0.00 3.36
1563 1569 8.359875 TCTCTCACAAGACAGAGAAAGATTAT 57.640 34.615 0.00 0.00 41.82 1.28
1788 1799 6.420903 CGATGGCGATGTAAGATAGAAAGAAA 59.579 38.462 0.00 0.00 40.82 2.52
1927 1938 4.035792 CGTGGGTGAATCAAGTACAACAAA 59.964 41.667 0.00 0.00 0.00 2.83
2075 2086 0.606673 GGTGGCCGAGAAGCTTCTTT 60.607 55.000 29.02 9.31 37.73 2.52
2148 2159 2.965831 CCTACGGAGGGAGAAATCATCA 59.034 50.000 5.47 0.00 39.48 3.07
2227 2238 5.876460 TGACTAAGGAGGCCGTAAAAATTAC 59.124 40.000 0.00 0.00 0.00 1.89
2301 2312 1.726352 AGTTAGGGGTAAGAGGGGACA 59.274 52.381 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.223200 TATGTTTACCCACGCCGCGA 62.223 55.000 21.79 0.00 0.00 5.87
388 389 3.030291 TGGCAATGTGTCAAGTCCTTTT 58.970 40.909 0.00 0.00 0.00 2.27
431 432 1.333177 ACCGCAGATCTCTATCCCAC 58.667 55.000 0.00 0.00 31.98 4.61
458 459 2.362397 CGGCACTCTTTAGAGGCTATCA 59.638 50.000 11.23 0.00 46.13 2.15
596 597 7.016661 ACTGTCTATATATCCAAAACTGGAGGG 59.983 40.741 0.00 0.00 41.88 4.30
706 707 5.710099 ACACTTTTTCATGTATTCACCCGAT 59.290 36.000 0.00 0.00 0.00 4.18
734 735 6.586344 TCCTTATTCCATTTCACTGAGCTAG 58.414 40.000 0.00 0.00 0.00 3.42
915 917 0.178990 GGGGGACTGTGAAAGCAAGT 60.179 55.000 0.00 0.00 0.00 3.16
1014 1016 5.180492 TCGTGATAAGGCAAATTCTTCGTTT 59.820 36.000 0.00 0.00 0.00 3.60
1022 1024 4.110036 GGCTTTCGTGATAAGGCAAATT 57.890 40.909 0.00 0.00 44.81 1.82
1232 1238 3.466836 AGAAAGAAAGCGATGTGACACA 58.533 40.909 11.41 11.41 0.00 3.72
1268 1274 4.520111 TGTGTAGAAGCGGTAGTAGTGAAA 59.480 41.667 0.00 0.00 0.00 2.69
1326 1332 9.290988 TCACTAAGAACATTTTAGCCATTAACA 57.709 29.630 0.00 0.00 32.58 2.41
1441 1447 0.809385 CGCGAGAAGACCCTTGACTA 59.191 55.000 0.00 0.00 0.00 2.59
1563 1569 4.436113 TGGATTGGATTGGATGAATCGA 57.564 40.909 0.00 0.00 41.45 3.59
1788 1799 1.689582 CCGAAGCCCTAACTCCCCT 60.690 63.158 0.00 0.00 0.00 4.79
1927 1938 1.356124 ACCACAAGCTCTGACCTGAT 58.644 50.000 0.00 0.00 0.00 2.90
2075 2086 2.203625 GCTTTTGGGGGCACTGGA 60.204 61.111 0.00 0.00 0.00 3.86
2148 2159 5.709594 CCTTTCAGGGGATGAGGATATTTT 58.290 41.667 0.00 0.00 39.68 1.82


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

AutoCloner maintained by Alex Coulton.