Multiple sequence alignment - TraesCS1B01G424200

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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 TraesCS1B01G424200 chr1B 100.000 3268 0 0 1 3268 647447562 647444295 0 6035
1 TraesCS1B01G424200 chr1B 93.978 3288 146 8 3 3268 554956072 554952815 0 4927
2 TraesCS1B01G424200 chr1B 94.519 2828 118 7 463 3268 400394916 400397728 0 4329
3 TraesCS1B01G424200 chr1B 95.949 469 18 1 1 468 91407290 91407758 0 760
4 TraesCS1B01G424200 chr1B 95.949 469 17 2 1 468 400390346 400390813 0 760
5 TraesCS1B01G424200 chr1B 95.309 469 20 2 1 468 400392175 400392642 0 743
6 TraesCS1B01G424200 chr5B 94.554 2828 116 9 463 3268 92697791 92700602 0 4335
7 TraesCS1B01G424200 chr5B 95.551 472 17 2 1 468 92695933 92696404 0 752
8 TraesCS1B01G424200 chr6B 94.372 2825 131 6 466 3268 692864047 692866865 0 4311
9 TraesCS1B01G424200 chr6B 96.162 469 17 1 1 468 692861273 692861741 0 765
10 TraesCS1B01G424200 chr4A 94.059 2828 146 5 463 3268 656355851 656358678 0 4272
11 TraesCS1B01G424200 chr4A 93.980 2824 148 5 467 3268 656148557 656151380 0 4253
12 TraesCS1B01G424200 chr4A 93.425 2829 159 8 463 3268 655846760 655849584 0 4169
13 TraesCS1B01G424200 chr4A 93.319 2829 162 7 463 3268 655893911 655896735 0 4152
14 TraesCS1B01G424200 chr4B 93.887 2830 126 10 463 3268 16568025 16570831 0 4224
15 TraesCS1B01G424200 chr4B 92.786 1414 80 4 1877 3268 560073062 560074475 0 2026
16 TraesCS1B01G424200 chr4B 96.802 469 14 1 1 468 127526938 127527406 0 782
17 TraesCS1B01G424200 chr4B 95.949 469 18 1 1 468 127527852 127528320 0 760
18 TraesCS1B01G424200 chr3B 93.600 2828 159 7 463 3268 729227190 729230017 0 4200
19 TraesCS1B01G424200 chr3B 93.302 1702 83 8 1590 3268 746767969 746766276 0 2483
20 TraesCS1B01G424200 chr2B 92.966 2829 174 7 463 3268 177237189 177240015 0 4098
21 TraesCS1B01G424200 chr7B 95.522 469 20 1 1 468 529765006 529764538 0 749


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 TraesCS1B01G424200 chr1B 647444295 647447562 3267 True 6035.0 6035 100.0000 1 3268 1 chr1B.!!$R2 3267
1 TraesCS1B01G424200 chr1B 554952815 554956072 3257 True 4927.0 4927 93.9780 3 3268 1 chr1B.!!$R1 3265
2 TraesCS1B01G424200 chr1B 400390346 400397728 7382 False 1944.0 4329 95.2590 1 3268 3 chr1B.!!$F2 3267
3 TraesCS1B01G424200 chr5B 92695933 92700602 4669 False 2543.5 4335 95.0525 1 3268 2 chr5B.!!$F1 3267
4 TraesCS1B01G424200 chr6B 692861273 692866865 5592 False 2538.0 4311 95.2670 1 3268 2 chr6B.!!$F1 3267
5 TraesCS1B01G424200 chr4A 656355851 656358678 2827 False 4272.0 4272 94.0590 463 3268 1 chr4A.!!$F4 2805
6 TraesCS1B01G424200 chr4A 656148557 656151380 2823 False 4253.0 4253 93.9800 467 3268 1 chr4A.!!$F3 2801
7 TraesCS1B01G424200 chr4A 655846760 655849584 2824 False 4169.0 4169 93.4250 463 3268 1 chr4A.!!$F1 2805
8 TraesCS1B01G424200 chr4A 655893911 655896735 2824 False 4152.0 4152 93.3190 463 3268 1 chr4A.!!$F2 2805
9 TraesCS1B01G424200 chr4B 16568025 16570831 2806 False 4224.0 4224 93.8870 463 3268 1 chr4B.!!$F1 2805
10 TraesCS1B01G424200 chr4B 560073062 560074475 1413 False 2026.0 2026 92.7860 1877 3268 1 chr4B.!!$F2 1391
11 TraesCS1B01G424200 chr4B 127526938 127528320 1382 False 771.0 782 96.3755 1 468 2 chr4B.!!$F3 467
12 TraesCS1B01G424200 chr3B 729227190 729230017 2827 False 4200.0 4200 93.6000 463 3268 1 chr3B.!!$F1 2805
13 TraesCS1B01G424200 chr3B 746766276 746767969 1693 True 2483.0 2483 93.3020 1590 3268 1 chr3B.!!$R1 1678
14 TraesCS1B01G424200 chr2B 177237189 177240015 2826 False 4098.0 4098 92.9660 463 3268 1 chr2B.!!$F1 2805

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
474 5504 0.036765 TGGATGTAGGCACGGTTGTC 60.037 55.0 0.00 0.0 0.00 3.18 F
1130 6162 0.400213 AAAGAGGTTGGCATCCACGA 59.600 50.0 16.58 0.0 30.78 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 7071 1.402896 GGATGGATCACGCTCCCTGA 61.403 60.0 0.0 0.0 34.12 3.86 R
2568 7625 0.107312 CCAATCCTGCCACTCCTCAG 60.107 60.0 0.0 0.0 0.00 3.35 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
314 318 1.129624 GTGTGTTTTGTGCAGTCACGA 59.870 47.619 0.00 0.00 46.01 4.35
373 377 0.323633 TCATTGGTCCGACTACCCGA 60.324 55.000 0.00 0.00 38.90 5.14
377 381 2.142356 TGGTCCGACTACCCGATTTA 57.858 50.000 0.00 0.00 38.90 1.40
474 5504 0.036765 TGGATGTAGGCACGGTTGTC 60.037 55.000 0.00 0.00 0.00 3.18
587 5617 1.895798 TCAGAGAGCATTGGTCGTTCT 59.104 47.619 10.02 6.08 35.00 3.01
606 5636 0.955905 TGTAGTAGCAGCGTGTGTCA 59.044 50.000 0.00 0.00 0.00 3.58
667 5697 2.752903 TCTGAACGCAGTGCACTCTATA 59.247 45.455 18.64 0.57 37.76 1.31
721 5753 7.296628 TGGTTTAGGCAAGAACATTTGTTAT 57.703 32.000 0.00 0.00 38.56 1.89
824 5856 1.010013 CGCGAGCGCATGTCTACTA 60.010 57.895 11.47 0.00 42.06 1.82
866 5898 3.319198 GTCCAACGGCCTCCTCCA 61.319 66.667 0.00 0.00 0.00 3.86
1094 6126 4.760047 CCCCGGTCAGAAGCACGG 62.760 72.222 0.00 0.00 45.57 4.94
1130 6162 0.400213 AAAGAGGTTGGCATCCACGA 59.600 50.000 16.58 0.00 30.78 4.35
1235 6267 3.118884 GGCTCGTACCCTCAGTTTATCAA 60.119 47.826 0.00 0.00 0.00 2.57
1260 6292 5.453339 CGTTGATGTTGAGTATACCAGGGAT 60.453 44.000 0.00 0.00 0.00 3.85
1264 6296 4.358214 TGTTGAGTATACCAGGGATGACA 58.642 43.478 0.00 0.00 0.00 3.58
1337 6369 1.540363 GGTATACCACATCACCGCTGG 60.540 57.143 17.44 0.00 35.64 4.85
1474 6506 9.771534 GTTTCTGAAGTAGATAAAGCAGGATAT 57.228 33.333 0.00 0.00 34.80 1.63
1588 6620 4.127171 TGTTCTAGTGCACTTTCTGTTCC 58.873 43.478 27.06 5.95 0.00 3.62
1602 6634 6.985059 ACTTTCTGTTCCAGTGTAGTTTCTAC 59.015 38.462 0.59 0.59 32.61 2.59
1670 6703 3.067742 CGTGGGTAAGGAGTACATAGGTG 59.932 52.174 0.00 0.00 34.01 4.00
1675 6708 5.878669 GGGTAAGGAGTACATAGGTGTTTTG 59.121 44.000 0.00 0.00 39.77 2.44
1929 6963 6.652481 CAGTATTGAAGGTGACAAAGAGATGT 59.348 38.462 0.00 0.00 35.90 3.06
2309 7344 2.371841 ACTGGTCATGGAGTTGCTTGTA 59.628 45.455 0.00 0.00 0.00 2.41
2367 7402 6.645790 AGTTTAGTTCTGTTAGGACGAAGA 57.354 37.500 0.00 0.00 0.00 2.87
2379 7414 6.872020 TGTTAGGACGAAGAAGTTTCTAATGG 59.128 38.462 0.00 0.00 36.28 3.16
2380 7415 5.740290 AGGACGAAGAAGTTTCTAATGGA 57.260 39.130 0.00 0.00 36.28 3.41
2381 7416 5.725362 AGGACGAAGAAGTTTCTAATGGAG 58.275 41.667 0.00 0.00 36.28 3.86
2568 7625 2.551270 CACACAAGCGCGACTTCC 59.449 61.111 12.10 0.00 36.04 3.46
2620 7677 0.679505 ACGCAGTTAGAGAGGCACAA 59.320 50.000 0.00 0.00 37.78 3.33
2650 7707 2.361483 TAGAGCCGCCGGTGTGTA 60.361 61.111 15.14 0.00 0.00 2.90
2764 7827 3.567397 AGGTGAGCTCCGAATACATAGT 58.433 45.455 12.15 0.00 0.00 2.12
2765 7828 3.961408 AGGTGAGCTCCGAATACATAGTT 59.039 43.478 12.15 0.00 0.00 2.24
2792 7855 0.453793 CACGGTTTGGAAGTGTGCAA 59.546 50.000 0.00 0.00 32.56 4.08
2837 7900 2.939103 GGGCATGTAAGAGTCATCACAC 59.061 50.000 0.00 0.00 0.00 3.82
2842 7905 4.316205 TGTAAGAGTCATCACACGTGTT 57.684 40.909 20.79 2.55 0.00 3.32
2860 7923 2.497675 TGTTATGTGAGAGAGGCACCTC 59.502 50.000 8.74 8.74 43.03 3.85
2891 7954 1.490069 TGCAAGCCATAGGATGCACTA 59.510 47.619 11.35 0.00 40.37 2.74
2972 8035 3.248266 GTCACACATTAGGTACGTGGAC 58.752 50.000 0.00 0.00 34.91 4.02
3062 8251 7.709947 AGCAACTATCAATATTGTGGATGTTG 58.290 34.615 22.23 22.23 37.98 3.33
3155 8345 2.316867 CGCGTGTTCTGGCATCACA 61.317 57.895 0.00 6.61 33.04 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
196 200 4.645535 ACATGTGCAGTGACTCTTACATT 58.354 39.130 0.00 0.00 32.55 2.71
314 318 1.003928 TGCATCCAGAGAGTGCACAAT 59.996 47.619 21.04 6.57 43.30 2.71
346 350 1.450312 CGGACCAATGACTCTGCCC 60.450 63.158 0.00 0.00 0.00 5.36
373 377 6.094325 TCACTTCACAAACGTGGTTCTTAAAT 59.906 34.615 0.00 0.00 34.98 1.40
377 381 3.126343 GTCACTTCACAAACGTGGTTCTT 59.874 43.478 0.00 0.00 34.98 2.52
474 5504 4.321217 CACGCTCGTAACTCTAAAGACTTG 59.679 45.833 0.00 0.00 0.00 3.16
587 5617 0.955905 TGACACACGCTGCTACTACA 59.044 50.000 0.00 0.00 0.00 2.74
606 5636 0.321996 GAACTCCTCGCACCTTTCCT 59.678 55.000 0.00 0.00 0.00 3.36
721 5753 5.163804 CCGTCAAATCGTCCAATTAATCACA 60.164 40.000 0.00 0.00 0.00 3.58
824 5856 0.815734 CTCGTCGTGGTAATGAGGGT 59.184 55.000 0.00 0.00 0.00 4.34
1130 6162 3.299503 ACAACATCCAGCTTTTCCTTGT 58.700 40.909 0.00 0.00 0.00 3.16
1217 6249 3.841643 ACGTTGATAAACTGAGGGTACG 58.158 45.455 0.00 0.00 0.00 3.67
1235 6267 4.382685 CCCTGGTATACTCAACATCAACGT 60.383 45.833 2.25 0.00 0.00 3.99
1474 6506 7.223584 TGATCTGGTGAGTCAAGTTCAAAATA 58.776 34.615 0.00 0.00 0.00 1.40
1588 6620 8.993121 AGAACATCAAATGTAGAAACTACACTG 58.007 33.333 12.74 12.66 44.07 3.66
1602 6634 8.539770 ACTGAACTACACTAGAACATCAAATG 57.460 34.615 0.00 0.00 0.00 2.32
1670 6703 8.745464 TTTTGGTAGTTACACTTGAACAAAAC 57.255 30.769 0.00 0.00 32.42 2.43
1798 6831 5.233083 TGGATCCATCAAGTATCCATCAC 57.767 43.478 11.44 0.00 43.27 3.06
1929 6963 1.946768 CTCCAAACCAGAACTTCGCAA 59.053 47.619 0.00 0.00 0.00 4.85
2037 7071 1.402896 GGATGGATCACGCTCCCTGA 61.403 60.000 0.00 0.00 34.12 3.86
2128 7163 6.202762 CGCTGCATACTCAATGAGGTAATTAA 59.797 38.462 15.38 0.00 37.86 1.40
2129 7164 5.696270 CGCTGCATACTCAATGAGGTAATTA 59.304 40.000 15.38 0.00 37.86 1.40
2309 7344 6.560253 ACAATAGAAACGACAAGCAGAAAT 57.440 33.333 0.00 0.00 0.00 2.17
2367 7402 7.665559 TCACATAAGCAACTCCATTAGAAACTT 59.334 33.333 0.00 0.00 0.00 2.66
2379 7414 7.190920 ACTACAAACTTCACATAAGCAACTC 57.809 36.000 0.00 0.00 0.00 3.01
2380 7415 7.568199 AACTACAAACTTCACATAAGCAACT 57.432 32.000 0.00 0.00 0.00 3.16
2381 7416 7.700656 ACAAACTACAAACTTCACATAAGCAAC 59.299 33.333 0.00 0.00 0.00 4.17
2568 7625 0.107312 CCAATCCTGCCACTCCTCAG 60.107 60.000 0.00 0.00 0.00 3.35
2584 7641 1.468985 CGTATTCCAACCCATGCCAA 58.531 50.000 0.00 0.00 0.00 4.52
2620 7677 1.337260 CGGCTCTACAGACTGCAAACT 60.337 52.381 1.25 0.00 0.00 2.66
2650 7707 1.755380 GCCTCCGACACCTACACTAAT 59.245 52.381 0.00 0.00 0.00 1.73
2764 7827 1.129917 TCCAAACCGTGACCCTGTAA 58.870 50.000 0.00 0.00 0.00 2.41
2765 7828 1.071071 CTTCCAAACCGTGACCCTGTA 59.929 52.381 0.00 0.00 0.00 2.74
2792 7855 0.381801 CTGTCGCACAACCTTTGCTT 59.618 50.000 0.00 0.00 37.87 3.91
2837 7900 2.263077 GTGCCTCTCTCACATAACACG 58.737 52.381 0.00 0.00 34.73 4.49
2842 7905 1.064685 TCGAGGTGCCTCTCTCACATA 60.065 52.381 15.40 0.00 40.69 2.29
2891 7954 3.050619 GTCTCTTCACAAACGTCACGAT 58.949 45.455 2.91 0.00 0.00 3.73
2972 8035 1.133253 CGTGATTTCTGTGCCTGCG 59.867 57.895 0.00 0.00 0.00 5.18
3062 8251 3.735591 TGCTTCTGGTACCACACTTTAC 58.264 45.455 11.60 0.00 0.00 2.01
3155 8345 2.759114 CCACACCACTCCATGCCT 59.241 61.111 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.