Multiple sequence alignment - TraesCS2A01G522000

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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 TraesCS2A01G522000 chr2A 100.000 2550 0 0 1 2550 744581429 744583978 0.000000e+00 4710
1 TraesCS2A01G522000 chr2A 96.232 1964 65 7 591 2550 677958479 677956521 0.000000e+00 3208
2 TraesCS2A01G522000 chr2A 94.842 1958 90 10 594 2547 677413613 677411663 0.000000e+00 3046
3 TraesCS2A01G522000 chr2A 93.177 1964 111 17 600 2550 213959518 213957565 0.000000e+00 2863
4 TraesCS2A01G522000 chr7A 96.313 1953 63 7 601 2550 36946200 36948146 0.000000e+00 3199
5 TraesCS2A01G522000 chr5B 96.164 1955 67 6 601 2550 3450172 3448221 0.000000e+00 3188
6 TraesCS2A01G522000 chr5A 95.850 1952 72 7 599 2549 689446509 689444566 0.000000e+00 3147
7 TraesCS2A01G522000 chr1B 95.536 1949 61 12 597 2538 645321433 645323362 0.000000e+00 3094
8 TraesCS2A01G522000 chr1B 84.091 176 21 6 478 650 410676847 410677018 2.030000e-36 163
9 TraesCS2A01G522000 chr7D 94.844 1959 82 15 599 2550 63995388 63997334 0.000000e+00 3040
10 TraesCS2A01G522000 chr3D 94.659 1966 88 15 591 2550 475106671 475108625 0.000000e+00 3033
11 TraesCS2A01G522000 chr3D 94.030 603 36 0 1 603 288033119 288032517 0.000000e+00 915
12 TraesCS2A01G522000 chr3D 87.865 684 71 11 3 680 385255017 385255694 0.000000e+00 793
13 TraesCS2A01G522000 chr2D 94.536 604 33 0 1 604 489725145 489724542 0.000000e+00 933
14 TraesCS2A01G522000 chr2D 94.040 604 36 0 1 604 378028476 378027873 0.000000e+00 917
15 TraesCS2A01G522000 chr1D 94.040 604 36 0 1 604 321294769 321294166 0.000000e+00 917
16 TraesCS2A01G522000 chr1D 93.874 604 36 1 1 603 211970624 211970021 0.000000e+00 909
17 TraesCS2A01G522000 chr6A 93.874 604 37 0 1 604 163189522 163188919 0.000000e+00 911
18 TraesCS2A01G522000 chr4A 93.874 604 37 0 1 604 464511284 464510681 0.000000e+00 911
19 TraesCS2A01G522000 chr1A 93.874 604 37 0 1 604 333944931 333944328 0.000000e+00 911
20 TraesCS2A01G522000 chr4D 93.709 604 38 0 1 604 234130388 234130991 0.000000e+00 905
21 TraesCS2A01G522000 chr2B 91.136 440 31 5 595 1029 13181546 13181982 7.860000e-165 590


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 TraesCS2A01G522000 chr2A 744581429 744583978 2549 False 4710 4710 100.000 1 2550 1 chr2A.!!$F1 2549
1 TraesCS2A01G522000 chr2A 677956521 677958479 1958 True 3208 3208 96.232 591 2550 1 chr2A.!!$R3 1959
2 TraesCS2A01G522000 chr2A 677411663 677413613 1950 True 3046 3046 94.842 594 2547 1 chr2A.!!$R2 1953
3 TraesCS2A01G522000 chr2A 213957565 213959518 1953 True 2863 2863 93.177 600 2550 1 chr2A.!!$R1 1950
4 TraesCS2A01G522000 chr7A 36946200 36948146 1946 False 3199 3199 96.313 601 2550 1 chr7A.!!$F1 1949
5 TraesCS2A01G522000 chr5B 3448221 3450172 1951 True 3188 3188 96.164 601 2550 1 chr5B.!!$R1 1949
6 TraesCS2A01G522000 chr5A 689444566 689446509 1943 True 3147 3147 95.850 599 2549 1 chr5A.!!$R1 1950
7 TraesCS2A01G522000 chr1B 645321433 645323362 1929 False 3094 3094 95.536 597 2538 1 chr1B.!!$F2 1941
8 TraesCS2A01G522000 chr7D 63995388 63997334 1946 False 3040 3040 94.844 599 2550 1 chr7D.!!$F1 1951
9 TraesCS2A01G522000 chr3D 475106671 475108625 1954 False 3033 3033 94.659 591 2550 1 chr3D.!!$F2 1959
10 TraesCS2A01G522000 chr3D 288032517 288033119 602 True 915 915 94.030 1 603 1 chr3D.!!$R1 602
11 TraesCS2A01G522000 chr3D 385255017 385255694 677 False 793 793 87.865 3 680 1 chr3D.!!$F1 677
12 TraesCS2A01G522000 chr2D 489724542 489725145 603 True 933 933 94.536 1 604 1 chr2D.!!$R2 603
13 TraesCS2A01G522000 chr2D 378027873 378028476 603 True 917 917 94.040 1 604 1 chr2D.!!$R1 603
14 TraesCS2A01G522000 chr1D 321294166 321294769 603 True 917 917 94.040 1 604 1 chr1D.!!$R2 603
15 TraesCS2A01G522000 chr1D 211970021 211970624 603 True 909 909 93.874 1 603 1 chr1D.!!$R1 602
16 TraesCS2A01G522000 chr6A 163188919 163189522 603 True 911 911 93.874 1 604 1 chr6A.!!$R1 603
17 TraesCS2A01G522000 chr4A 464510681 464511284 603 True 911 911 93.874 1 604 1 chr4A.!!$R1 603
18 TraesCS2A01G522000 chr1A 333944328 333944931 603 True 911 911 93.874 1 604 1 chr1A.!!$R1 603
19 TraesCS2A01G522000 chr4D 234130388 234130991 603 False 905 905 93.709 1 604 1 chr4D.!!$F1 603

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
713 715 0.318445 CCGACTCGTTCCGTGAACTT 60.318 55.0 12.8 0.79 40.05 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2514 2546 1.003051 GGGGGTGAGAAGCCCTCTA 59.997 63.158 12.46 0.0 43.38 2.43 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 4.273235 TGTGGATGACATATTGTTGATCGC 59.727 41.667 0.00 0.00 0.00 4.58
52 53 9.271828 ACATATTGTTGATCGCAAATGATACTA 57.728 29.630 19.16 6.10 35.42 1.82
127 128 4.238514 CCTCGGTGAAGCTGCTTATATAC 58.761 47.826 15.95 11.59 0.00 1.47
199 201 7.517614 TCACAAAGCACATACCTTGATAAAA 57.482 32.000 0.00 0.00 0.00 1.52
256 258 2.691011 GGGTTCTTGCCTGTGTTACAAA 59.309 45.455 0.00 0.00 0.00 2.83
257 259 3.490249 GGGTTCTTGCCTGTGTTACAAAC 60.490 47.826 0.00 0.00 0.00 2.93
259 261 4.497507 GGTTCTTGCCTGTGTTACAAACTC 60.498 45.833 0.00 0.00 0.00 3.01
354 356 6.994421 TCAGCCATAGGTTCTATCATGTAA 57.006 37.500 0.00 0.00 0.00 2.41
355 357 7.559335 TCAGCCATAGGTTCTATCATGTAAT 57.441 36.000 0.00 0.00 0.00 1.89
411 413 6.361768 GCTATTAGTTTAGCAGGGAGGTAT 57.638 41.667 0.00 0.00 43.33 2.73
420 422 6.630203 TTAGCAGGGAGGTATCAAAGTAAA 57.370 37.500 0.00 0.00 0.00 2.01
524 526 4.081420 AGGTGACAAAGAGCTCATCGTAAT 60.081 41.667 17.77 0.00 0.00 1.89
543 545 4.380841 AATAGGTTACGTCGATGCAAGA 57.619 40.909 4.06 0.00 0.00 3.02
713 715 0.318445 CCGACTCGTTCCGTGAACTT 60.318 55.000 12.80 0.79 40.05 2.66
723 725 0.600255 CCGTGAACTTTGCCGTCTCT 60.600 55.000 0.00 0.00 0.00 3.10
778 780 3.876589 GACCAGGCGGCAGAAACGA 62.877 63.158 13.08 0.00 34.57 3.85
822 824 2.197324 GTGGCTTGTGGGACCCAA 59.803 61.111 16.98 0.00 34.18 4.12
831 833 1.461268 TGGGACCCAACAGAGAGCA 60.461 57.895 12.05 0.00 0.00 4.26
908 910 2.343426 ACGGCGACAGAGAGCATGA 61.343 57.895 16.62 0.00 34.54 3.07
1171 1178 2.771943 AGCGAGAATGGGGTAAGAATCA 59.228 45.455 0.00 0.00 0.00 2.57
1322 1329 2.799017 AGAGCATGAAGAATGGTTGCA 58.201 42.857 0.00 0.00 46.95 4.08
1868 1882 8.948853 TCTTGCGTATTTTTCTGTTTTCTATG 57.051 30.769 0.00 0.00 0.00 2.23
1902 1916 6.882610 TTAGGCAGTAAATCATAATGCTGG 57.117 37.500 7.67 0.00 38.42 4.85
2083 2102 5.303971 CCAGGTGCCAAAATAAATGAACAA 58.696 37.500 0.00 0.00 0.00 2.83
2105 2124 8.546597 ACAATTTTTAAGGGCATTACATTGAC 57.453 30.769 17.67 0.00 0.00 3.18
2116 2136 7.602265 AGGGCATTACATTGACAAAAACATAAC 59.398 33.333 0.00 0.00 0.00 1.89
2239 2260 0.107456 CCGCTAGGACAGATGGCAAT 59.893 55.000 0.00 0.00 41.02 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 128 8.756927 TCTATCTTTATAGATCTTGATGCCCAG 58.243 37.037 0.00 0.00 39.34 4.45
146 147 8.301002 GTCCAATCTAGCGTCTTTATCTATCTT 58.699 37.037 0.00 0.00 0.00 2.40
155 156 4.691216 GTGAAAGTCCAATCTAGCGTCTTT 59.309 41.667 0.00 0.00 0.00 2.52
164 165 3.953612 TGTGCTTTGTGAAAGTCCAATCT 59.046 39.130 0.00 0.00 40.64 2.40
165 166 4.305989 TGTGCTTTGTGAAAGTCCAATC 57.694 40.909 0.00 0.00 40.64 2.67
316 318 4.492494 TGGCTGAAGCATAGAGAATGAA 57.508 40.909 4.43 0.00 44.36 2.57
323 325 3.969976 AGAACCTATGGCTGAAGCATAGA 59.030 43.478 16.63 0.31 44.36 1.98
354 356 4.640771 AGGTCTGGTACACAACATTGAT 57.359 40.909 0.00 0.00 0.00 2.57
355 357 5.554437 TTAGGTCTGGTACACAACATTGA 57.446 39.130 0.00 0.00 0.00 2.57
411 413 4.349636 TGATCCACTCCTGGTTTACTTTGA 59.650 41.667 0.00 0.00 38.90 2.69
420 422 2.043115 TGTCTAGTGATCCACTCCTGGT 59.957 50.000 2.55 0.00 41.21 4.00
524 526 4.380841 AATCTTGCATCGACGTAACCTA 57.619 40.909 0.00 0.00 0.00 3.08
543 545 3.198635 AGTCATCCGGATCAGTGTCAAAT 59.801 43.478 15.88 0.00 0.00 2.32
713 715 1.112916 TGACCTGACAGAGACGGCAA 61.113 55.000 3.32 0.00 0.00 4.52
778 780 4.279671 TGCAACGGTCTGAATAAAATTGGT 59.720 37.500 0.00 0.00 0.00 3.67
822 824 1.273048 CTCTGCTCAACTGCTCTCTGT 59.727 52.381 0.00 0.00 0.00 3.41
831 833 0.320247 CAACGGCTCTCTGCTCAACT 60.320 55.000 0.00 0.00 42.39 3.16
908 910 2.910479 TCTCGCCGTGGTCACTGT 60.910 61.111 0.00 0.00 0.00 3.55
1171 1178 1.338011 CGAAAATGGTGCAATTGCCCT 60.338 47.619 26.94 11.63 41.18 5.19
1322 1329 3.049674 CCGTTCGTGGCAGCATGT 61.050 61.111 0.00 0.00 39.31 3.21
1417 1424 6.044404 TCCTAACCTTCTTCTTCAACATCCTT 59.956 38.462 0.00 0.00 0.00 3.36
1590 1597 8.635328 ACTTTAACCAACATTTAAACTAGGTGG 58.365 33.333 15.83 15.83 0.00 4.61
1764 1778 2.621338 CTCTACGCTCTGAATTTGGCA 58.379 47.619 0.00 0.00 0.00 4.92
1868 1882 9.971922 ATGATTTACTGCCTAAATTAAATCAGC 57.028 29.630 16.48 0.00 46.40 4.26
1902 1916 8.593492 ATTCAATTAGCTTCCACAAAAAGTTC 57.407 30.769 0.00 0.00 0.00 3.01
2083 2102 9.566432 TTTTGTCAATGTAATGCCCTTAAAAAT 57.434 25.926 0.00 0.00 0.00 1.82
2239 2260 5.285401 TCCTTCCCTATCCATGTCAAAGTA 58.715 41.667 0.00 0.00 0.00 2.24
2252 2273 7.776745 TCACTATGTATACCTTCCTTCCCTAT 58.223 38.462 0.00 0.00 0.00 2.57
2346 2372 7.013178 CCCTCCAAAATTTAAGTGCAAAACAAT 59.987 33.333 0.00 0.00 0.00 2.71
2514 2546 1.003051 GGGGGTGAGAAGCCCTCTA 59.997 63.158 12.46 0.00 43.38 2.43


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

AutoCloner maintained by Alex Coulton.