Multiple sequence alignment - TraesCS2A01G240700

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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 TraesCS2A01G240700 chr2A 100.000 2372 0 0 1 2372 335822606 335820235 0 4381
1 TraesCS2A01G240700 chr2A 97.808 2372 51 1 1 2372 335805874 335803504 0 4091
2 TraesCS2A01G240700 chr2A 97.829 1428 31 0 945 2372 726905314 726903887 0 2466
3 TraesCS2A01G240700 chr2A 99.031 929 9 0 1 929 726901700 726900772 0 1666
4 TraesCS2A01G240700 chr2A 98.708 929 12 0 1 929 651438664 651439592 0 1650
5 TraesCS2A01G240700 chr3A 97.969 1428 29 0 945 2372 66003992 66002565 0 2477
6 TraesCS2A01G240700 chr3A 98.924 929 10 0 1 929 66000725 65999797 0 1661
7 TraesCS2A01G240700 chr5D 97.899 1428 30 0 945 2372 503263635 503262208 0 2471
8 TraesCS2A01G240700 chr5D 97.759 1428 32 0 945 2372 503246413 503247840 0 2460
9 TraesCS2A01G240700 chr5D 98.708 929 12 0 1 929 503260022 503259094 0 1650
10 TraesCS2A01G240700 chr2D 97.759 1428 32 0 945 2372 272811105 272809678 0 2460
11 TraesCS2A01G240700 chr2D 97.549 1428 35 0 945 2372 591985750 591987177 0 2444
12 TraesCS2A01G240700 chr6D 97.689 1428 33 0 945 2372 389244681 389243254 0 2455
13 TraesCS2A01G240700 chr3D 97.549 1428 34 1 945 2372 589262385 589260959 0 2442
14 TraesCS2A01G240700 chr7B 98.924 929 10 0 1 929 622433215 622432287 0 1661
15 TraesCS2A01G240700 chr3B 98.924 929 10 0 1 929 201548055 201548983 0 1661
16 TraesCS2A01G240700 chr3B 98.924 929 10 0 1 929 201570032 201569104 0 1661
17 TraesCS2A01G240700 chr3B 98.924 929 10 0 1 929 813249123 813250051 0 1661


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 TraesCS2A01G240700 chr2A 335820235 335822606 2371 True 4381.0 4381 100.0000 1 2372 1 chr2A.!!$R2 2371
1 TraesCS2A01G240700 chr2A 335803504 335805874 2370 True 4091.0 4091 97.8080 1 2372 1 chr2A.!!$R1 2371
2 TraesCS2A01G240700 chr2A 726900772 726905314 4542 True 2066.0 2466 98.4300 1 2372 2 chr2A.!!$R3 2371
3 TraesCS2A01G240700 chr2A 651438664 651439592 928 False 1650.0 1650 98.7080 1 929 1 chr2A.!!$F1 928
4 TraesCS2A01G240700 chr3A 65999797 66003992 4195 True 2069.0 2477 98.4465 1 2372 2 chr3A.!!$R1 2371
5 TraesCS2A01G240700 chr5D 503246413 503247840 1427 False 2460.0 2460 97.7590 945 2372 1 chr5D.!!$F1 1427
6 TraesCS2A01G240700 chr5D 503259094 503263635 4541 True 2060.5 2471 98.3035 1 2372 2 chr5D.!!$R1 2371
7 TraesCS2A01G240700 chr2D 272809678 272811105 1427 True 2460.0 2460 97.7590 945 2372 1 chr2D.!!$R1 1427
8 TraesCS2A01G240700 chr2D 591985750 591987177 1427 False 2444.0 2444 97.5490 945 2372 1 chr2D.!!$F1 1427
9 TraesCS2A01G240700 chr6D 389243254 389244681 1427 True 2455.0 2455 97.6890 945 2372 1 chr6D.!!$R1 1427
10 TraesCS2A01G240700 chr3D 589260959 589262385 1426 True 2442.0 2442 97.5490 945 2372 1 chr3D.!!$R1 1427
11 TraesCS2A01G240700 chr7B 622432287 622433215 928 True 1661.0 1661 98.9240 1 929 1 chr7B.!!$R1 928
12 TraesCS2A01G240700 chr3B 201548055 201548983 928 False 1661.0 1661 98.9240 1 929 1 chr3B.!!$F1 928
13 TraesCS2A01G240700 chr3B 201569104 201570032 928 True 1661.0 1661 98.9240 1 929 1 chr3B.!!$R1 928
14 TraesCS2A01G240700 chr3B 813249123 813250051 928 False 1661.0 1661 98.9240 1 929 1 chr3B.!!$F2 928

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
186 187 0.324943 CCCACTTCACACCTCGGAAT 59.675 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 1457 0.460284 ACGCTTGTATTGCTCTCCCG 60.46 55.0 0.0 0.0 0.0 5.14 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
57 58 5.533903 AGCTCGATGCCAGAATGATAAAAAT 59.466 36.000 3.66 0.00 44.23 1.82
186 187 0.324943 CCCACTTCACACCTCGGAAT 59.675 55.000 0.00 0.00 0.00 3.01
275 276 1.484038 AGAGATCCAGTGGAGACAGC 58.516 55.000 18.69 10.12 44.46 4.40
436 437 2.928116 AGCGGACGTAAAGCTATTGAAC 59.072 45.455 9.71 0.00 39.74 3.18
539 540 1.826720 ACAAGGATAGCGAACGGGTTA 59.173 47.619 0.00 0.00 0.00 2.85
553 554 2.314246 CGGGTTACCTACTCCTAAGGG 58.686 57.143 0.00 0.00 38.54 3.95
574 575 4.504864 GGGTCAAAGCAAGCCCTTTAATTT 60.505 41.667 0.00 0.00 38.12 1.82
663 664 4.380233 CGAACCTACGACCAGTCAGTTAAT 60.380 45.833 0.00 0.00 31.04 1.40
666 667 5.259632 ACCTACGACCAGTCAGTTAATAGT 58.740 41.667 0.00 0.00 0.00 2.12
676 677 3.065095 GTCAGTTAATAGTCGACCGCTCT 59.935 47.826 13.01 0.93 0.00 4.09
685 686 1.025113 TCGACCGCTCTACCACTGAG 61.025 60.000 0.00 0.00 34.87 3.35
791 792 8.857694 TCTTTCGTAACTCCCATAATTTCTTT 57.142 30.769 0.00 0.00 0.00 2.52
808 809 0.759959 TTTGTAGTGGCTCCGTTCCA 59.240 50.000 0.00 0.00 0.00 3.53
960 961 3.039011 GGCTTCTCTATGGTAGAACCCA 58.961 50.000 0.00 0.00 37.50 4.51
1299 1300 5.415077 GCATAGATCTGGAGATTCCCAAATG 59.585 44.000 5.18 0.00 35.03 2.32
1349 1350 1.738350 CATGAGCAGGCAAGAGACAAG 59.262 52.381 0.00 0.00 0.00 3.16
1375 1376 5.047590 TGGCGAACTGAAACATCTTAGTAGA 60.048 40.000 0.00 0.00 34.21 2.59
1403 1404 4.984785 GGAAAAGAAAGCAAAAGCGATTCT 59.015 37.500 0.00 0.00 31.98 2.40
1430 1431 2.125106 GGCGAGCGAAATGGGAGT 60.125 61.111 0.00 0.00 0.00 3.85
1526 1527 2.436173 GCACCCTAGATGGCTAAAGTCT 59.564 50.000 0.00 0.00 0.00 3.24
1557 1558 1.067821 AGCATCACTAGCTTACGCTCC 59.932 52.381 0.00 0.00 45.15 4.70
1830 1831 2.686106 AACCCACCGGAGCCGTAT 60.686 61.111 9.46 0.00 37.81 3.06
2068 2069 3.391296 TGGACATCTAGGGATAAAGCACC 59.609 47.826 0.00 0.00 0.00 5.01
2144 2146 8.980481 ACTAGATATGACCCAAAAATAACAGG 57.020 34.615 0.00 0.00 0.00 4.00
2225 2227 1.635817 GGATCACCAGCTAAGGCCCA 61.636 60.000 0.00 0.00 39.73 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.722201 CGCAGGACCTCCCCTACAC 61.722 68.421 0.00 0.00 34.07 2.90
186 187 6.634805 CCTTTCTCTCTATAAGAACAGTGCA 58.365 40.000 0.00 0.00 32.64 4.57
275 276 1.684386 CCTCTGAGCTACAGGCCCAG 61.684 65.000 0.00 0.00 46.27 4.45
436 437 6.183360 CGACAAAAGGAAAGAGCATACCTAAG 60.183 42.308 0.00 0.00 32.06 2.18
539 540 2.838813 GCTTTGACCCTTAGGAGTAGGT 59.161 50.000 0.00 0.00 36.73 3.08
553 554 7.905604 ATTAAATTAAAGGGCTTGCTTTGAC 57.094 32.000 0.00 0.00 0.00 3.18
663 664 0.251354 AGTGGTAGAGCGGTCGACTA 59.749 55.000 23.78 17.32 0.00 2.59
666 667 1.002990 TCAGTGGTAGAGCGGTCGA 60.003 57.895 9.28 0.00 0.00 4.20
676 677 3.090037 GTTCCTCAGTAGCTCAGTGGTA 58.910 50.000 0.00 0.00 0.00 3.25
685 686 0.253327 CCCCCTTGTTCCTCAGTAGC 59.747 60.000 0.00 0.00 0.00 3.58
791 792 0.249120 CATGGAACGGAGCCACTACA 59.751 55.000 0.00 0.00 38.44 2.74
808 809 3.494332 GCTTCCCTATGAAATGAGGCAT 58.506 45.455 0.00 0.00 31.06 4.40
960 961 2.123077 CTCTCAGGCCTCCCCGAT 60.123 66.667 0.00 0.00 39.21 4.18
1299 1300 2.963101 AGGCAGTTTAAAAGGTTGACCC 59.037 45.455 0.00 0.00 36.42 4.46
1349 1350 1.160137 AGATGTTTCAGTTCGCCAGC 58.840 50.000 0.00 0.00 0.00 4.85
1375 1376 4.686972 GCTTTTGCTTTCTTTTCCTCTGT 58.313 39.130 0.00 0.00 43.35 3.41
1403 1404 3.933498 CGCTCGCCGCTACTACGA 61.933 66.667 0.00 0.00 36.13 3.43
1456 1457 0.460284 ACGCTTGTATTGCTCTCCCG 60.460 55.000 0.00 0.00 0.00 5.14
1526 1527 3.243434 GCTAGTGATGCTTTCGGCTACTA 60.243 47.826 0.00 0.00 42.39 1.82
1557 1558 2.417516 CCCATGCTACTCGGGTCG 59.582 66.667 0.00 0.00 35.03 4.79
1701 1702 0.880278 GAGCTCAGCACGGTTTCACA 60.880 55.000 9.40 0.00 0.00 3.58
1830 1831 3.490419 GCCCTATTAAGACTCGCTTTCGA 60.490 47.826 0.00 0.00 43.28 3.71
1926 1927 1.321074 ATCAGTCGGTTCGGACCTCC 61.321 60.000 12.11 0.39 44.20 4.30
1959 1960 1.633432 CCCCTAACCACAACTCATCCA 59.367 52.381 0.00 0.00 0.00 3.41
2068 2069 4.430423 GCAGCTCGCACCGAAACG 62.430 66.667 3.64 0.00 41.79 3.60
2144 2146 3.637273 ACTGGCCGACCTTGACCC 61.637 66.667 0.00 0.00 36.63 4.46
2225 2227 5.760253 CCTTTATCACTGAGCGGTCATTTAT 59.240 40.000 18.98 11.92 30.18 1.40
2343 2345 1.751437 GCTTAGCCCCGTTCATCTTT 58.249 50.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.