Multiple sequence alignment - TraesCS2A01G223100

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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 TraesCS2A01G223100 chr2A 100.000 5351 0 0 1 5351 215747582 215752932 0.000000e+00 9882.0
1 TraesCS2A01G223100 chr2A 94.737 38 2 0 2783 2820 118444821 118444858 5.790000e-05 60.2
2 TraesCS2A01G223100 chr2D 96.172 5382 147 22 1 5351 198458649 198464002 0.000000e+00 8743.0
3 TraesCS2A01G223100 chr2D 94.737 38 2 0 2783 2820 116908939 116908976 5.790000e-05 60.2
4 TraesCS2A01G223100 chr2B 95.647 5330 148 27 1 5292 255050554 255055837 0.000000e+00 8480.0
5 TraesCS2A01G223100 chr2B 84.840 343 52 0 2164 2506 704119609 704119951 3.970000e-91 346.0
6 TraesCS2A01G223100 chr4B 85.423 343 46 4 2164 2504 467104322 467104662 2.370000e-93 353.0
7 TraesCS2A01G223100 chr4B 83.673 343 55 1 2164 2505 484587528 484587186 6.690000e-84 322.0
8 TraesCS2A01G223100 chr6B 84.211 342 53 1 2164 2504 71580083 71579742 1.110000e-86 331.0
9 TraesCS2A01G223100 chr6B 83.954 349 53 3 2164 2511 660635173 660635519 1.110000e-86 331.0
10 TraesCS2A01G223100 chr6B 82.535 355 59 3 2164 2516 680878191 680878544 5.200000e-80 309.0
11 TraesCS2A01G223100 chr6B 97.143 35 1 0 2786 2820 35701273 35701307 5.790000e-05 60.2
12 TraesCS2A01G223100 chr1B 83.333 348 54 3 2164 2510 431012493 431012837 8.650000e-83 318.0
13 TraesCS2A01G223100 chr3A 91.463 82 3 2 3622 3699 60433868 60433949 5.670000e-20 110.0
14 TraesCS2A01G223100 chr3A 86.486 74 4 2 3622 3694 12422015 12421947 5.750000e-10 76.8
15 TraesCS2A01G223100 chrUn 86.667 90 4 7 3613 3695 65136682 65136770 5.710000e-15 93.5
16 TraesCS2A01G223100 chr6D 87.838 74 5 4 3618 3689 294774925 294774854 3.430000e-12 84.2
17 TraesCS2A01G223100 chr4D 84.932 73 10 1 3618 3689 75264072 75264144 7.430000e-09 73.1
18 TraesCS2A01G223100 chr4A 82.474 97 4 8 3618 3701 599007942 599007846 7.430000e-09 73.1
19 TraesCS2A01G223100 chr5A 81.319 91 10 5 3613 3702 406534987 406535071 3.460000e-07 67.6
20 TraesCS2A01G223100 chr5B 97.143 35 1 0 2786 2820 234759829 234759863 5.790000e-05 60.2


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 TraesCS2A01G223100 chr2A 215747582 215752932 5350 False 9882 9882 100.000 1 5351 1 chr2A.!!$F2 5350
1 TraesCS2A01G223100 chr2D 198458649 198464002 5353 False 8743 8743 96.172 1 5351 1 chr2D.!!$F2 5350
2 TraesCS2A01G223100 chr2B 255050554 255055837 5283 False 8480 8480 95.647 1 5292 1 chr2B.!!$F1 5291

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
179 180 1.008875 TCGATGTGCTTGCTGACGTC 61.009 55.000 9.11 9.11 0.0 4.34 F
1257 1269 0.099613 ATGTGCGCTCTGTCTACTCG 59.900 55.000 9.73 0.00 0.0 4.18 F
1377 1389 1.038130 AGCTCGTGAGTAAGGCCGAT 61.038 55.000 0.00 0.00 0.0 4.18 F
2213 2226 0.250770 GCTCCTCGGTCTTTTGGGTT 60.251 55.000 0.00 0.00 0.0 4.11 F
3126 3140 1.466167 CTTGTGAGGAAGATGTTGGCG 59.534 52.381 0.00 0.00 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 2189 0.459063 GCAACCATTAAGCAGCTGCC 60.459 55.000 34.39 17.05 43.38 4.85 R
2198 2211 1.202770 AGGACAACCCAAAAGACCGAG 60.203 52.381 0.00 0.00 37.41 4.63 R
2408 2421 1.529865 GAGAACCGGACGAAAACCAAG 59.470 52.381 9.46 0.00 0.00 3.61 R
4144 4172 2.519377 TGTCCTTTATGGTATCCGCG 57.481 50.000 0.00 0.00 37.07 6.46 R
5074 5108 1.407936 AGCTCTCGTGCATAGTGGAT 58.592 50.000 0.00 0.00 34.99 3.41 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
41 42 2.147150 GTTCCTGCTCTGTCTTCAACC 58.853 52.381 0.00 0.00 0.00 3.77
179 180 1.008875 TCGATGTGCTTGCTGACGTC 61.009 55.000 9.11 9.11 0.00 4.34
210 211 1.139853 GATTGGGTCGCTCTTCCATCT 59.860 52.381 0.00 0.00 0.00 2.90
297 300 3.777106 TGATCTGACTGGAAAGCTTGT 57.223 42.857 0.00 0.00 0.00 3.16
388 392 7.708752 GCTCTCTACTTCTGCACTTGTATTTAT 59.291 37.037 0.00 0.00 0.00 1.40
395 399 9.236006 ACTTCTGCACTTGTATTTATCAATCTT 57.764 29.630 0.00 0.00 0.00 2.40
712 722 2.777094 GGCAACTGCTTCTTCTTCTCT 58.223 47.619 1.06 0.00 41.70 3.10
713 723 3.145286 GGCAACTGCTTCTTCTTCTCTT 58.855 45.455 1.06 0.00 41.70 2.85
714 724 4.319177 GGCAACTGCTTCTTCTTCTCTTA 58.681 43.478 1.06 0.00 41.70 2.10
769 779 3.712187 CTTCTAGATCCAGTTTCGGCTC 58.288 50.000 0.00 0.00 0.00 4.70
782 792 5.456822 CAGTTTCGGCTCTCTTTTCTTTTTG 59.543 40.000 0.00 0.00 0.00 2.44
845 855 1.068541 TGAGACGTGGATGAGTTCGTG 60.069 52.381 0.00 0.00 36.67 4.35
1257 1269 0.099613 ATGTGCGCTCTGTCTACTCG 59.900 55.000 9.73 0.00 0.00 4.18
1377 1389 1.038130 AGCTCGTGAGTAAGGCCGAT 61.038 55.000 0.00 0.00 0.00 4.18
1458 1470 2.234908 AGTGGAGTTCTGTGGAGCATAC 59.765 50.000 0.00 0.00 0.00 2.39
1551 1563 2.202810 GGGCACTACTCAGAGCGC 60.203 66.667 0.00 0.00 42.32 5.92
1590 1602 3.304257 GCAGAGGAGTTGTGAATGTTGTG 60.304 47.826 0.00 0.00 0.00 3.33
1638 1650 2.202743 CGCGATCTGAAGCCGGAA 60.203 61.111 5.05 0.00 0.00 4.30
1781 1793 4.610945 CATTTTGTTGTTGGACACCTCTC 58.389 43.478 0.00 0.00 0.00 3.20
2055 2068 8.468399 AGTAGAGAAGGAAAGTTTTCTATACCG 58.532 37.037 13.30 0.00 43.77 4.02
2128 2141 8.831715 CTAAGTTTGGGTTAGCATTGAAAATT 57.168 30.769 0.00 0.00 0.00 1.82
2156 2169 9.770097 ACATCTGATTCCATGTTAGTTACTATG 57.230 33.333 0.00 0.00 28.27 2.23
2176 2189 2.658593 CGCATAGGGAAGGCGTCG 60.659 66.667 0.00 0.00 45.27 5.12
2198 2211 1.133790 CAGCTGCTTAATGGTTGCTCC 59.866 52.381 0.00 0.00 0.00 4.70
2213 2226 0.250770 GCTCCTCGGTCTTTTGGGTT 60.251 55.000 0.00 0.00 0.00 4.11
2286 2299 2.061848 TCCAAGGTGTTCTCATTGGGA 58.938 47.619 14.97 0.00 42.05 4.37
2371 2384 2.355115 GGTGTGGTCATGGGGTCC 59.645 66.667 0.00 0.00 0.00 4.46
2408 2421 2.351726 GTCCGCATGTGGTCTATTTGTC 59.648 50.000 24.28 2.72 0.00 3.18
2438 2451 5.540400 TCGTCCGGTTCTCCATTAATTAT 57.460 39.130 0.00 0.00 0.00 1.28
2566 2580 3.334583 TTCTAGAGGCATTGCGACTTT 57.665 42.857 10.50 0.00 0.00 2.66
2635 2649 9.276590 TGTAGAATTGTAGCTCATGGAATTATG 57.723 33.333 0.00 0.00 0.00 1.90
2639 2653 5.294734 TGTAGCTCATGGAATTATGCAGA 57.705 39.130 0.00 0.00 0.00 4.26
2649 2663 6.899393 TGGAATTATGCAGAAAGTCTTTGT 57.101 33.333 1.60 0.00 0.00 2.83
2749 2763 8.752766 TTGTTCATGTGTACTAACTACTAAGC 57.247 34.615 0.00 0.00 0.00 3.09
3126 3140 1.466167 CTTGTGAGGAAGATGTTGGCG 59.534 52.381 0.00 0.00 0.00 5.69
3607 3621 2.011548 GCAGTTGATGGATGCGGTACA 61.012 52.381 0.00 0.00 0.00 2.90
3645 3659 5.222278 ACTCCCTCCGTCCCATAATATAT 57.778 43.478 0.00 0.00 0.00 0.86
3681 3707 7.060633 GCAGTTCAAAAACGTCTTACATTATGG 59.939 37.037 0.00 0.00 40.48 2.74
4096 4124 4.020839 ACCTTGCTTTAATGCAGCTTCATT 60.021 37.500 15.88 15.88 44.27 2.57
4144 4172 0.810648 TTGAGCATGAAATGGGCGAC 59.189 50.000 0.00 0.00 46.86 5.19
4227 4257 5.001232 TGGCAGTATTTTCTGACTACAACC 58.999 41.667 1.33 0.00 43.30 3.77
4494 4524 1.511850 CTCGTGCATGTTGTTCCTCA 58.488 50.000 5.68 0.00 0.00 3.86
4767 4797 2.123589 TGGGAGGACAAGAAGACACAA 58.876 47.619 0.00 0.00 0.00 3.33
4781 4811 3.836949 AGACACAACAGCAACAACAAAG 58.163 40.909 0.00 0.00 0.00 2.77
4856 4887 9.745880 TGAAACCGATAAGATAAGATACTGAAC 57.254 33.333 0.00 0.00 0.00 3.18
4858 4889 8.480133 AACCGATAAGATAAGATACTGAACCT 57.520 34.615 0.00 0.00 0.00 3.50
4868 4899 8.783660 ATAAGATACTGAACCTAAGTCATGGA 57.216 34.615 0.00 0.00 0.00 3.41
4877 4908 4.766375 ACCTAAGTCATGGATTTGGTACG 58.234 43.478 12.64 0.00 0.00 3.67
4896 4927 6.127394 TGGTACGTGGATAGCTAATTTACACA 60.127 38.462 8.54 0.00 0.00 3.72
4900 4931 5.006358 CGTGGATAGCTAATTTACACACACC 59.994 44.000 8.54 0.00 0.00 4.16
4901 4932 6.113411 GTGGATAGCTAATTTACACACACCT 58.887 40.000 0.00 0.00 0.00 4.00
4912 4943 1.980765 ACACACACCTCTGTCCATGAT 59.019 47.619 0.00 0.00 0.00 2.45
4925 4956 7.252612 TCTGTCCATGATTAGTTCTTTGGTA 57.747 36.000 0.00 0.00 32.94 3.25
4928 4959 9.613428 CTGTCCATGATTAGTTCTTTGGTAATA 57.387 33.333 0.00 0.00 32.94 0.98
4941 4972 9.550811 GTTCTTTGGTAATATTTTTGTCCTACG 57.449 33.333 0.00 0.00 0.00 3.51
4945 4976 8.441312 TTGGTAATATTTTTGTCCTACGGATC 57.559 34.615 0.00 0.00 32.73 3.36
4949 4980 9.543783 GTAATATTTTTGTCCTACGGATCTCTT 57.456 33.333 0.00 0.00 32.73 2.85
4969 5000 4.454504 TCTTTTAACGGACTTCTTCCATGC 59.545 41.667 0.00 0.00 46.29 4.06
4970 5001 3.695830 TTAACGGACTTCTTCCATGCT 57.304 42.857 0.00 0.00 46.29 3.79
5066 5100 6.161855 TCCTCTTTGATATTATGAGCACGT 57.838 37.500 0.00 0.00 0.00 4.49
5074 5108 7.784633 TGATATTATGAGCACGTTTCATTCA 57.215 32.000 15.29 10.94 36.68 2.57
5124 5158 6.595716 AGGTCTGAGTTGTATATGCTCAAAAC 59.404 38.462 0.00 0.00 38.58 2.43
5238 5282 6.156748 AGCCACATATCGTCTTAACATGTA 57.843 37.500 0.00 0.00 0.00 2.29
5310 5355 0.862490 CCGCGACATACAACAACACA 59.138 50.000 8.23 0.00 0.00 3.72
5338 5383 3.846360 ACTGTTGTCCTATAGAACACGC 58.154 45.455 0.00 0.00 36.50 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 1.684049 CCAAGTCCCGAGCTCTCCT 60.684 63.158 12.85 0.00 0.00 3.69
179 180 1.726853 GACCCAATCCACGAACAGAG 58.273 55.000 0.00 0.00 0.00 3.35
388 392 5.064198 ACGACACGAAAGTTGAAAAGATTGA 59.936 36.000 0.00 0.00 46.40 2.57
395 399 1.732809 TGCACGACACGAAAGTTGAAA 59.267 42.857 0.00 0.00 46.40 2.69
403 407 2.954316 AGAACATATGCACGACACGAA 58.046 42.857 1.58 0.00 0.00 3.85
711 721 5.012893 AGAACAGCAGAAGGGGAAAATAAG 58.987 41.667 0.00 0.00 0.00 1.73
712 722 4.998051 AGAACAGCAGAAGGGGAAAATAA 58.002 39.130 0.00 0.00 0.00 1.40
713 723 4.657814 AGAACAGCAGAAGGGGAAAATA 57.342 40.909 0.00 0.00 0.00 1.40
714 724 3.532641 AGAACAGCAGAAGGGGAAAAT 57.467 42.857 0.00 0.00 0.00 1.82
769 779 7.326968 AGAGACTGGAACAAAAAGAAAAGAG 57.673 36.000 0.00 0.00 38.70 2.85
1080 1092 2.166254 AGGAGGTGTTTGTGCTTGTTTG 59.834 45.455 0.00 0.00 0.00 2.93
1257 1269 1.541588 CTACCAAGTTCCTTGCCAAGC 59.458 52.381 0.00 0.00 39.85 4.01
1377 1389 1.431633 TCCCTGCGGATATCCTCCTTA 59.568 52.381 19.61 0.00 42.47 2.69
1458 1470 4.379243 ACGCTGCCCTTGTCCTCG 62.379 66.667 0.00 0.00 0.00 4.63
1485 1497 1.378250 GCCTGCACAGAGCTCCATT 60.378 57.895 10.93 0.00 45.94 3.16
1638 1650 0.531974 TGGTCGCGAGCAAGAAGTTT 60.532 50.000 36.10 0.00 35.69 2.66
1772 1784 2.497675 TCCAGTTGCTATGAGAGGTGTC 59.502 50.000 0.00 0.00 0.00 3.67
2035 2048 6.822170 ACCATCGGTATAGAAAACTTTCCTTC 59.178 38.462 0.00 0.00 34.02 3.46
2108 2121 9.213799 GATGTTAATTTTCAATGCTAACCCAAA 57.786 29.630 0.00 0.00 0.00 3.28
2156 2169 2.663188 CGCCTTCCCTATGCGCTC 60.663 66.667 9.73 0.00 41.95 5.03
2176 2189 0.459063 GCAACCATTAAGCAGCTGCC 60.459 55.000 34.39 17.05 43.38 4.85
2198 2211 1.202770 AGGACAACCCAAAAGACCGAG 60.203 52.381 0.00 0.00 37.41 4.63
2213 2226 4.037222 TGATAGGCTAAACCATGAGGACA 58.963 43.478 0.00 0.00 43.14 4.02
2286 2299 5.105351 TCACACATCTACATCACGAAGGAAT 60.105 40.000 0.00 0.00 0.00 3.01
2371 2384 2.359900 CGGACTTCTCCCAAATTCTGG 58.640 52.381 1.03 1.03 45.97 3.86
2385 2398 3.009723 CAAATAGACCACATGCGGACTT 58.990 45.455 9.98 0.00 33.04 3.01
2408 2421 1.529865 GAGAACCGGACGAAAACCAAG 59.470 52.381 9.46 0.00 0.00 3.61
2438 2451 2.614259 AGAAGAAGAGAGTTGCCCAGA 58.386 47.619 0.00 0.00 0.00 3.86
2543 2556 3.003480 AGTCGCAATGCCTCTAGAAAAC 58.997 45.455 0.00 0.00 0.00 2.43
2566 2580 6.484364 TGAAGCATGACTACCTCAATATCA 57.516 37.500 0.00 0.00 30.60 2.15
2635 2649 3.149436 TGCAACACAAAGACTTTCTGC 57.851 42.857 3.37 8.04 0.00 4.26
2649 2663 6.680810 CCATTCAGTCTTAATCTTTGCAACA 58.319 36.000 0.00 0.00 0.00 3.33
2749 2763 9.669353 CATTTTTCCTGATATATTTGGAAGACG 57.331 33.333 15.39 6.52 39.39 4.18
3126 3140 7.163001 ACTAATTCTTTTCTTTGGATCCTGC 57.837 36.000 14.23 0.00 0.00 4.85
3607 3621 4.484912 AGGGAGTAGTTCAGAAGAGTTGT 58.515 43.478 0.00 0.00 0.00 3.32
3723 3751 8.141298 TCAAGAGGTAGGTATACAATGTCAAA 57.859 34.615 5.01 0.00 33.21 2.69
3938 3966 5.763204 GTCTCACTGGTAAGGTTTGATGAAA 59.237 40.000 0.00 0.00 0.00 2.69
4096 4124 4.081972 GCAGTCTCCAGTTCATCTCTTGTA 60.082 45.833 0.00 0.00 0.00 2.41
4144 4172 2.519377 TGTCCTTTATGGTATCCGCG 57.481 50.000 0.00 0.00 37.07 6.46
4227 4257 6.572519 TCAAGAAAATGGAAGGAACAAACAG 58.427 36.000 0.00 0.00 0.00 3.16
4494 4524 6.318900 CAGAAGAAAGTAGGTCCAAAACACTT 59.681 38.462 0.00 0.00 0.00 3.16
4689 4719 7.336396 AGTATAAGATACCTTTTGCCGTCTTT 58.664 34.615 0.00 0.00 33.94 2.52
4767 4797 5.053145 TGTTTTTGTCTTTGTTGTTGCTGT 58.947 33.333 0.00 0.00 0.00 4.40
4781 4811 4.511454 GGATTGAAAGGCCTTGTTTTTGTC 59.489 41.667 21.33 11.55 0.00 3.18
4856 4887 4.570772 CACGTACCAAATCCATGACTTAGG 59.429 45.833 0.00 0.00 0.00 2.69
4858 4889 4.223255 TCCACGTACCAAATCCATGACTTA 59.777 41.667 0.00 0.00 0.00 2.24
4868 4899 7.988599 TGTAAATTAGCTATCCACGTACCAAAT 59.011 33.333 0.00 0.00 0.00 2.32
4877 4908 6.113411 AGGTGTGTGTAAATTAGCTATCCAC 58.887 40.000 0.00 0.00 0.00 4.02
4896 4927 4.780021 AGAACTAATCATGGACAGAGGTGT 59.220 41.667 0.00 0.00 40.71 4.16
4900 4931 6.176183 ACCAAAGAACTAATCATGGACAGAG 58.824 40.000 0.00 0.00 38.78 3.35
4901 4932 6.126863 ACCAAAGAACTAATCATGGACAGA 57.873 37.500 0.00 0.00 38.78 3.41
4939 4970 4.220163 AGAAGTCCGTTAAAAGAGATCCGT 59.780 41.667 0.00 0.00 0.00 4.69
4941 4972 5.581479 GGAAGAAGTCCGTTAAAAGAGATCC 59.419 44.000 0.00 0.00 36.40 3.36
4998 5029 7.823799 TGACATGAAAGAAGCACTGATAATGTA 59.176 33.333 0.00 0.00 0.00 2.29
5066 5100 4.512484 TCGTGCATAGTGGATGAATGAAA 58.488 39.130 0.00 0.00 36.33 2.69
5074 5108 1.407936 AGCTCTCGTGCATAGTGGAT 58.592 50.000 0.00 0.00 34.99 3.41
5124 5158 6.118170 AGGTTGTCCAACATCATCTAAGATG 58.882 40.000 11.89 4.08 42.85 2.90
5133 5167 3.576078 AGTGAAGGTTGTCCAACATCA 57.424 42.857 11.89 11.68 42.85 3.07
5238 5282 4.090090 ACAGTTAGGTGTAGCAGAGATGT 58.910 43.478 0.00 0.00 0.00 3.06
5292 5337 1.136363 CCTGTGTTGTTGTATGTCGCG 60.136 52.381 0.00 0.00 0.00 5.87


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

AutoCloner maintained by Alex Coulton.