Multiple sequence alignment - TraesCS2B01G555600

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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 TraesCS2B01G555600 chr2B 100.000 2846 0 0 1 2846 750153070 750155915 0 5256
1 TraesCS2B01G555600 chr2B 94.672 2834 144 7 2 2830 129687580 129684749 0 4390
2 TraesCS2B01G555600 chr2B 94.670 2833 140 9 2 2830 136082731 136085556 0 4385
3 TraesCS2B01G555600 chr2B 94.637 2834 142 9 2 2830 200675179 200672351 0 4383
4 TraesCS2B01G555600 chr2B 94.601 2834 144 8 2 2830 227967731 227970560 0 4377
5 TraesCS2B01G555600 chr6B 94.811 2833 141 5 1 2830 545402163 545399334 0 4412
6 TraesCS2B01G555600 chr7B 94.741 2833 141 8 2 2830 203052017 203054845 0 4399
7 TraesCS2B01G555600 chr5B 94.622 2845 145 7 1 2841 691258544 691255704 0 4399
8 TraesCS2B01G555600 chr5B 94.705 2833 144 6 2 2830 192551743 192548913 0 4396
9 TraesCS2B01G555600 chr3B 94.707 2834 144 6 1 2830 66989267 66992098 0 4397


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 TraesCS2B01G555600 chr2B 750153070 750155915 2845 False 5256 5256 100.000 1 2846 1 chr2B.!!$F3 2845
1 TraesCS2B01G555600 chr2B 129684749 129687580 2831 True 4390 4390 94.672 2 2830 1 chr2B.!!$R1 2828
2 TraesCS2B01G555600 chr2B 136082731 136085556 2825 False 4385 4385 94.670 2 2830 1 chr2B.!!$F1 2828
3 TraesCS2B01G555600 chr2B 200672351 200675179 2828 True 4383 4383 94.637 2 2830 1 chr2B.!!$R2 2828
4 TraesCS2B01G555600 chr2B 227967731 227970560 2829 False 4377 4377 94.601 2 2830 1 chr2B.!!$F2 2828
5 TraesCS2B01G555600 chr6B 545399334 545402163 2829 True 4412 4412 94.811 1 2830 1 chr6B.!!$R1 2829
6 TraesCS2B01G555600 chr7B 203052017 203054845 2828 False 4399 4399 94.741 2 2830 1 chr7B.!!$F1 2828
7 TraesCS2B01G555600 chr5B 691255704 691258544 2840 True 4399 4399 94.622 1 2841 1 chr5B.!!$R2 2840
8 TraesCS2B01G555600 chr5B 192548913 192551743 2830 True 4396 4396 94.705 2 2830 1 chr5B.!!$R1 2828
9 TraesCS2B01G555600 chr3B 66989267 66992098 2831 False 4397 4397 94.707 1 2830 1 chr3B.!!$F1 2829

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
554 557 0.883833 ATTTGTTGGAGGCGCTCAAG 59.116 50.0 7.64 0.0 31.08 3.02 F
1097 1108 0.030101 GAATGGACGGAGCGAGAGAG 59.970 60.0 0.00 0.0 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1415 1.035932 CCTCCTCGGCTCGGTAGAAA 61.036 60.0 0.0 0.0 0.00 2.52 R
2136 2148 1.541310 CGACACTAGGGGCTTCACCA 61.541 60.0 0.0 0.0 42.05 4.17 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
192 193 4.402056 TCCGGATTCCTGAGTGATTTAC 57.598 45.455 0.00 0.00 0.00 2.01
344 347 3.893763 CCTCGCGACGCTGAGGAT 61.894 66.667 36.01 0.00 45.13 3.24
502 505 2.045926 GGGCAAGACCATGACGCT 60.046 61.111 0.00 0.00 42.05 5.07
554 557 0.883833 ATTTGTTGGAGGCGCTCAAG 59.116 50.000 7.64 0.00 31.08 3.02
729 732 1.271840 TAGCCCCTGATGCTCGGTTT 61.272 55.000 0.00 0.00 40.23 3.27
818 824 1.826720 CAATATGGGTTTGCAGGCTGT 59.173 47.619 17.16 0.00 0.00 4.40
1053 1064 1.197430 CCCTGAAGGAGGCTGTGTCT 61.197 60.000 0.00 0.00 41.19 3.41
1064 1075 3.865929 CTGTGTCTGCGGCCGAACT 62.866 63.158 33.48 0.00 0.00 3.01
1097 1108 0.030101 GAATGGACGGAGCGAGAGAG 59.970 60.000 0.00 0.00 0.00 3.20
1202 1213 1.153667 GAGAGTCCGAGCTTGCCTG 60.154 63.158 0.00 0.00 0.00 4.85
1225 1236 1.600636 CTCGAAAGTGCCAAGGCCA 60.601 57.895 5.01 0.00 41.09 5.36
1555 1566 1.770658 CCATGAAGGGCCTCATAGTCA 59.229 52.381 6.46 6.97 34.20 3.41
1736 1747 1.751924 GGAGAGGCTTATCACTGACGT 59.248 52.381 0.00 0.00 0.00 4.34
1828 1839 3.112205 GCGGATGAGTGCCCCAGAT 62.112 63.158 0.00 0.00 0.00 2.90
2191 2205 2.190578 GCTATCCACGCCTTGGCT 59.809 61.111 10.12 0.00 46.47 4.75
2214 2228 3.195661 GACATTATCCGGTTCTTCGCTT 58.804 45.455 0.00 0.00 0.00 4.68
2442 2456 6.065976 ACTATTGACCCAAGACATGATTCA 57.934 37.500 0.00 0.00 0.00 2.57
2466 2480 8.138074 TCAGAGCCGATTCATATAATGCTATAC 58.862 37.037 0.00 0.00 0.00 1.47
2540 2554 1.682087 GGAACATAAGCCCCTGGTGTC 60.682 57.143 0.00 0.00 0.00 3.67
2588 2602 5.515270 GTGCAAGATGTCATTGATGAACATG 59.485 40.000 11.24 0.00 38.75 3.21
2677 2693 3.126831 GCAGAGCGATACAAATAGTGCT 58.873 45.455 0.00 0.00 34.96 4.40
2710 2726 9.670442 AAGGGATAGGACTTAATTAGACATGTA 57.330 33.333 0.00 0.00 0.00 2.29
2776 2793 2.029623 TGCTCGTAATAGAGACCACCC 58.970 52.381 0.00 0.00 40.57 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.003051 GACCCTTCAGCCTCCCCTA 59.997 63.158 0.00 0.00 0.00 3.53
62 63 0.104144 TTCCCCTCTTGGACCCTTCA 60.104 55.000 0.00 0.00 35.39 3.02
158 159 4.701171 AGGAATCCGGATACTTACGATCTC 59.299 45.833 19.48 7.14 0.00 2.75
192 193 8.633075 ACACTATGTGACACAAAAAGAAATTG 57.367 30.769 13.23 7.36 36.96 2.32
536 539 1.172180 CCTTGAGCGCCTCCAACAAA 61.172 55.000 2.29 0.00 0.00 2.83
554 557 2.272146 TCCTTGATGGAAGCGCCC 59.728 61.111 2.29 0.00 42.94 6.13
595 598 2.373169 AGCTGAACCTTCTGAATCACCA 59.627 45.455 0.00 0.00 0.00 4.17
729 732 1.679153 GGCTTTTCTTTCCGAACACCA 59.321 47.619 0.00 0.00 0.00 4.17
818 824 3.006756 GCGGCAGAGGTCAGTAGCA 62.007 63.158 0.00 0.00 0.00 3.49
1053 1064 3.430862 GCATTGAGTTCGGCCGCA 61.431 61.111 23.51 6.92 0.00 5.69
1161 1172 1.517257 CTTCGAGTCGCGCTCCAAT 60.517 57.895 19.89 0.00 41.10 3.16
1202 1213 1.301677 CTTGGCACTTTCGAGAGCCC 61.302 60.000 11.43 8.13 46.45 5.19
1404 1415 1.035932 CCTCCTCGGCTCGGTAGAAA 61.036 60.000 0.00 0.00 0.00 2.52
1849 1860 2.826428 CGCACAGGATAACACATAGCT 58.174 47.619 0.00 0.00 0.00 3.32
2136 2148 1.541310 CGACACTAGGGGCTTCACCA 61.541 60.000 0.00 0.00 42.05 4.17
2214 2228 3.531538 CCTAAAGACTTATGCCGCTTCA 58.468 45.455 0.00 0.00 0.00 3.02
2385 2399 2.231235 GCTCCCATGTTTTGGTACCTTG 59.769 50.000 14.36 1.52 44.83 3.61
2442 2456 7.142021 CGTATAGCATTATATGAATCGGCTCT 58.858 38.462 0.00 0.00 32.67 4.09
2496 2510 4.126437 CGCATTATGGTGTGATAAGTCCA 58.874 43.478 0.00 0.00 0.00 4.02
2677 2693 6.824958 ATTAAGTCCTATCCCTTGCTTACA 57.175 37.500 0.00 0.00 0.00 2.41
2691 2707 7.235812 GGAGGGATACATGTCTAATTAAGTCCT 59.764 40.741 0.00 0.00 39.74 3.85
2696 2712 7.316393 CCTGGAGGGATACATGTCTAATTAA 57.684 40.000 0.00 0.00 37.23 1.40
2766 2783 4.621269 AACACTCGGGTGGTCTCT 57.379 55.556 21.67 0.00 46.85 3.10


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

AutoCloner maintained by Alex Coulton.