Multiple sequence alignment - TraesCS2A01G325300

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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 TraesCS2A01G325300 chr2A 100.000 2570 0 0 1 2570 555397897 555400466 0.000000e+00 4747.0
1 TraesCS2A01G325300 chr2A 88.482 929 80 14 1 922 375706374 375705466 0.000000e+00 1098.0
2 TraesCS2A01G325300 chr2A 98.120 585 11 0 1986 2570 43118533 43117949 0.000000e+00 1020.0
3 TraesCS2A01G325300 chr2A 79.900 602 107 13 965 1559 313162265 313162859 1.830000e-116 429.0
4 TraesCS2A01G325300 chr4B 93.328 1229 67 9 513 1729 638183726 638182501 0.000000e+00 1801.0
5 TraesCS2A01G325300 chr4B 92.969 256 16 2 1732 1986 638182434 638182180 3.120000e-99 372.0
6 TraesCS2A01G325300 chr4B 92.965 199 11 2 221 417 638216125 638215928 1.160000e-73 287.0
7 TraesCS2A01G325300 chr1B 94.889 763 37 2 796 1558 292417721 292418481 0.000000e+00 1192.0
8 TraesCS2A01G325300 chr1B 94.231 780 26 9 1 769 292416949 292417720 0.000000e+00 1173.0
9 TraesCS2A01G325300 chr1B 91.822 269 20 2 1729 1996 292418891 292419158 8.680000e-100 374.0
10 TraesCS2A01G325300 chr1B 94.444 162 8 1 1564 1725 292418663 292418823 5.490000e-62 248.0
11 TraesCS2A01G325300 chr1B 94.771 153 5 3 1557 1707 292418517 292418668 4.280000e-58 235.0
12 TraesCS2A01G325300 chr1B 100.000 33 0 0 1954 1986 499389958 499389926 7.680000e-06 62.1
13 TraesCS2A01G325300 chr3B 94.573 737 27 6 37 769 67913896 67914623 0.000000e+00 1127.0
14 TraesCS2A01G325300 chr3B 95.115 655 29 3 796 1450 67914624 67915275 0.000000e+00 1029.0
15 TraesCS2A01G325300 chr3B 87.891 256 18 8 1729 1983 67915602 67915845 3.240000e-74 289.0
16 TraesCS2A01G325300 chr3B 95.062 162 7 1 1564 1725 67915374 67915534 1.180000e-63 254.0
17 TraesCS2A01G325300 chr3B 94.340 106 5 1 1602 1707 67915275 67915379 7.360000e-36 161.0
18 TraesCS2A01G325300 chr4D 90.991 777 52 6 782 1558 262651023 262651781 0.000000e+00 1031.0
19 TraesCS2A01G325300 chr4D 93.265 490 21 7 296 784 262650301 262650779 0.000000e+00 712.0
20 TraesCS2A01G325300 chr4D 79.833 600 110 10 965 1559 396679093 396678500 6.570000e-116 427.0
21 TraesCS2A01G325300 chr4D 91.447 304 18 3 1 302 262649228 262649525 6.620000e-111 411.0
22 TraesCS2A01G325300 chr4D 91.667 252 17 4 1732 1983 262652054 262652301 1.890000e-91 346.0
23 TraesCS2A01G325300 chr4D 95.376 173 6 2 1557 1729 262651817 262651987 9.060000e-70 274.0
24 TraesCS2A01G325300 chr6A 98.291 585 10 0 1986 2570 380441014 380440430 0.000000e+00 1026.0
25 TraesCS2A01G325300 chr6A 98.120 585 11 0 1986 2570 441838953 441839537 0.000000e+00 1020.0
26 TraesCS2A01G325300 chr6A 79.112 608 115 11 965 1565 491375593 491374991 2.380000e-110 409.0
27 TraesCS2A01G325300 chr5A 97.949 585 12 0 1986 2570 411850563 411849979 0.000000e+00 1014.0
28 TraesCS2A01G325300 chr5A 97.949 585 12 0 1986 2570 621822908 621823492 0.000000e+00 1014.0
29 TraesCS2A01G325300 chr5A 97.949 585 12 0 1986 2570 675889024 675888440 0.000000e+00 1014.0
30 TraesCS2A01G325300 chr4A 97.949 585 12 0 1986 2570 5277169 5277753 0.000000e+00 1014.0
31 TraesCS2A01G325300 chr4A 97.949 585 12 0 1986 2570 513740379 513739795 0.000000e+00 1014.0
32 TraesCS2A01G325300 chr1A 97.949 585 12 0 1986 2570 107607157 107606573 0.000000e+00 1014.0
33 TraesCS2A01G325300 chr6D 80.167 600 109 9 965 1559 256231522 256232116 8.440000e-120 440.0
34 TraesCS2A01G325300 chr7B 79.333 600 114 9 965 1559 359258056 359258650 1.840000e-111 412.0
35 TraesCS2A01G325300 chr7A 97.297 37 1 0 1950 1986 408830388 408830352 2.130000e-06 63.9
36 TraesCS2A01G325300 chr5D 84.615 65 8 2 1923 1986 235251609 235251672 2.130000e-06 63.9


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 TraesCS2A01G325300 chr2A 555397897 555400466 2569 False 4747.0 4747 100.0000 1 2570 1 chr2A.!!$F2 2569
1 TraesCS2A01G325300 chr2A 375705466 375706374 908 True 1098.0 1098 88.4820 1 922 1 chr2A.!!$R2 921
2 TraesCS2A01G325300 chr2A 43117949 43118533 584 True 1020.0 1020 98.1200 1986 2570 1 chr2A.!!$R1 584
3 TraesCS2A01G325300 chr2A 313162265 313162859 594 False 429.0 429 79.9000 965 1559 1 chr2A.!!$F1 594
4 TraesCS2A01G325300 chr4B 638182180 638183726 1546 True 1086.5 1801 93.1485 513 1986 2 chr4B.!!$R2 1473
5 TraesCS2A01G325300 chr1B 292416949 292419158 2209 False 644.4 1192 94.0314 1 1996 5 chr1B.!!$F1 1995
6 TraesCS2A01G325300 chr3B 67913896 67915845 1949 False 572.0 1127 93.3962 37 1983 5 chr3B.!!$F1 1946
7 TraesCS2A01G325300 chr4D 262649228 262652301 3073 False 554.8 1031 92.5492 1 1983 5 chr4D.!!$F1 1982
8 TraesCS2A01G325300 chr4D 396678500 396679093 593 True 427.0 427 79.8330 965 1559 1 chr4D.!!$R1 594
9 TraesCS2A01G325300 chr6A 380440430 380441014 584 True 1026.0 1026 98.2910 1986 2570 1 chr6A.!!$R1 584
10 TraesCS2A01G325300 chr6A 441838953 441839537 584 False 1020.0 1020 98.1200 1986 2570 1 chr6A.!!$F1 584
11 TraesCS2A01G325300 chr6A 491374991 491375593 602 True 409.0 409 79.1120 965 1565 1 chr6A.!!$R2 600
12 TraesCS2A01G325300 chr5A 411849979 411850563 584 True 1014.0 1014 97.9490 1986 2570 1 chr5A.!!$R1 584
13 TraesCS2A01G325300 chr5A 621822908 621823492 584 False 1014.0 1014 97.9490 1986 2570 1 chr5A.!!$F1 584
14 TraesCS2A01G325300 chr5A 675888440 675889024 584 True 1014.0 1014 97.9490 1986 2570 1 chr5A.!!$R2 584
15 TraesCS2A01G325300 chr4A 5277169 5277753 584 False 1014.0 1014 97.9490 1986 2570 1 chr4A.!!$F1 584
16 TraesCS2A01G325300 chr4A 513739795 513740379 584 True 1014.0 1014 97.9490 1986 2570 1 chr4A.!!$R1 584
17 TraesCS2A01G325300 chr1A 107606573 107607157 584 True 1014.0 1014 97.9490 1986 2570 1 chr1A.!!$R1 584
18 TraesCS2A01G325300 chr6D 256231522 256232116 594 False 440.0 440 80.1670 965 1559 1 chr6D.!!$F1 594
19 TraesCS2A01G325300 chr7B 359258056 359258650 594 False 412.0 412 79.3330 965 1559 1 chr7B.!!$F1 594

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
428 1222 0.109723 GAAGTAACCCACAGGCCACA 59.89 55.0 5.01 0.0 36.11 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 3488 0.609957 CTTGCCATGGGAGAAGTGCA 60.61 55.0 15.13 0.0 0.0 4.57 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
59 60 8.034313 TCCTGTAATGCCTATAATTTCTGTCT 57.966 34.615 0.00 0.00 0.00 3.41
157 160 6.484364 TTCTCTGTGGTTGATGATATGCTA 57.516 37.500 0.00 0.00 0.00 3.49
337 1130 2.615912 CCTTAGCTTGCTATGTGCTTCC 59.384 50.000 2.99 0.00 43.37 3.46
341 1134 2.239654 AGCTTGCTATGTGCTTCCCTTA 59.760 45.455 0.00 0.00 43.37 2.69
423 1217 1.004745 AGCATGGAAGTAACCCACAGG 59.995 52.381 0.00 0.00 36.36 4.00
424 1218 1.463674 CATGGAAGTAACCCACAGGC 58.536 55.000 0.00 0.00 36.36 4.85
425 1219 0.331616 ATGGAAGTAACCCACAGGCC 59.668 55.000 0.00 0.00 36.36 5.19
426 1220 1.063070 TGGAAGTAACCCACAGGCCA 61.063 55.000 5.01 0.00 36.11 5.36
427 1221 0.608308 GGAAGTAACCCACAGGCCAC 60.608 60.000 5.01 0.00 36.11 5.01
428 1222 0.109723 GAAGTAACCCACAGGCCACA 59.890 55.000 5.01 0.00 36.11 4.17
429 1223 0.110486 AAGTAACCCACAGGCCACAG 59.890 55.000 5.01 0.00 36.11 3.66
453 1247 4.440525 CCAGTTTTCTTCATATGCGGCATT 60.441 41.667 21.99 6.32 0.00 3.56
562 1356 7.611855 ACAACCTAATATTAGCATTGGCCTATC 59.388 37.037 25.92 0.00 42.56 2.08
574 1368 6.156256 AGCATTGGCCTATCTATTATAACGGA 59.844 38.462 3.32 0.00 42.56 4.69
664 1460 5.123186 CACATCTTCCCTACGTTGCATAAAA 59.877 40.000 0.00 0.00 0.00 1.52
729 1525 6.555463 ATCGGAACCTTGATAAAACTCCTA 57.445 37.500 0.00 0.00 0.00 2.94
793 1863 6.701145 TCTGTTGTTGTTAAACCTATTGCA 57.299 33.333 0.00 0.00 35.25 4.08
863 1933 1.609208 AAGAGATGGTGTTTGCGCTT 58.391 45.000 9.73 0.00 0.00 4.68
871 1941 1.623359 GTGTTTGCGCTTGTTGTGAA 58.377 45.000 9.73 0.00 0.00 3.18
901 1971 7.523293 TTTATTTTCATTGCTGGAGAGAACA 57.477 32.000 0.00 0.00 0.00 3.18
902 1972 7.523293 TTATTTTCATTGCTGGAGAGAACAA 57.477 32.000 0.00 0.00 0.00 2.83
933 2003 4.640789 ATTTCGCAAATTTATACCGGCA 57.359 36.364 0.00 0.00 0.00 5.69
934 2004 4.640789 TTTCGCAAATTTATACCGGCAT 57.359 36.364 0.00 0.00 0.00 4.40
1018 2092 3.869246 AGCGATGGTCAAAATACCTTACG 59.131 43.478 0.00 0.00 40.44 3.18
1087 2161 5.009811 GCTGAGTACCGAACCAGAGTATATT 59.990 44.000 0.00 0.00 31.61 1.28
1088 2162 6.387041 TGAGTACCGAACCAGAGTATATTG 57.613 41.667 0.00 0.00 0.00 1.90
1151 2240 6.893554 CCCACATCATATGTTGGGAATGATAT 59.106 38.462 24.36 0.00 46.02 1.63
1169 2258 9.107177 GAATGATATGAATCGAATGGCTATTCT 57.893 33.333 19.16 2.18 40.43 2.40
1308 2397 3.258622 AGAAACTCGAGGAGGAAAATCGT 59.741 43.478 18.41 0.00 37.69 3.73
1324 2413 7.119846 AGGAAAATCGTTCTCTAAAACATGAGG 59.880 37.037 0.00 0.00 0.00 3.86
1343 2432 9.026121 ACATGAGGTTAATATAGCTAGGTACAG 57.974 37.037 3.24 0.00 0.00 2.74
1392 2481 7.114754 TCAGATCCATCAAGAACAAGCTAATT 58.885 34.615 0.00 0.00 0.00 1.40
1637 2902 5.767665 TGTTGTATTCTGCTCCTTTTGCTTA 59.232 36.000 0.00 0.00 0.00 3.09
1702 2967 5.654650 TCTCTTTAAACCAAGACTTGCCAAA 59.345 36.000 9.85 5.82 0.00 3.28
1730 3059 6.422344 TGTGTGTAAGAAGTAATGGTACCA 57.578 37.500 18.99 18.99 0.00 3.25
1817 3146 5.123227 CCGGTTATGGAAAAGAGCTGATAA 58.877 41.667 0.00 0.00 0.00 1.75
1947 3277 3.090210 TCAAAGCACACATGGGATCAT 57.910 42.857 0.00 0.00 0.00 2.45
1968 3299 3.064324 GCCTCTGCGCCATTTGGT 61.064 61.111 4.18 0.00 37.57 3.67
2092 3423 4.202172 TGTTATCCTCGATGGCAACGATAA 60.202 41.667 20.16 12.94 39.02 1.75
2127 3458 1.679898 CCCCTTCTGTCACTGGGTC 59.320 63.158 0.00 0.00 38.03 4.46
2157 3488 3.941483 CACAAGATCGAACCCAAAGCTAT 59.059 43.478 0.00 0.00 0.00 2.97
2179 3510 2.731572 CACTTCTCCCATGGCAAGAAT 58.268 47.619 21.49 12.74 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
289 292 9.614792 AGAGGAATACTATAATGGTGAAAACAC 57.385 33.333 0.00 0.00 0.00 3.32
337 1130 4.853924 ACAGGCTGTTGACATTTTAAGG 57.146 40.909 15.88 0.00 0.00 2.69
341 1134 6.010219 AGGTTATACAGGCTGTTGACATTTT 58.990 36.000 27.24 0.00 0.00 1.82
423 1217 1.032014 TGAAGAAAACTGGCTGTGGC 58.968 50.000 0.00 0.00 37.82 5.01
424 1218 4.676196 GCATATGAAGAAAACTGGCTGTGG 60.676 45.833 6.97 0.00 0.00 4.17
425 1219 4.418392 GCATATGAAGAAAACTGGCTGTG 58.582 43.478 6.97 0.00 0.00 3.66
426 1220 3.127548 CGCATATGAAGAAAACTGGCTGT 59.872 43.478 6.97 0.00 0.00 4.40
427 1221 3.488047 CCGCATATGAAGAAAACTGGCTG 60.488 47.826 6.97 0.00 0.00 4.85
428 1222 2.684881 CCGCATATGAAGAAAACTGGCT 59.315 45.455 6.97 0.00 0.00 4.75
429 1223 2.796032 GCCGCATATGAAGAAAACTGGC 60.796 50.000 6.97 1.31 0.00 4.85
453 1247 7.625395 GCCGTGAATTCTCATATTGTTTGTACA 60.625 37.037 7.05 0.00 33.05 2.90
793 1863 2.639839 ACAATGTGAGGTAGCCTGACTT 59.360 45.455 6.36 0.00 38.55 3.01
931 2001 6.207417 AGGGTAGCATGACAATAATACAATGC 59.793 38.462 0.00 0.00 0.00 3.56
933 2003 8.220559 AGAAGGGTAGCATGACAATAATACAAT 58.779 33.333 0.00 0.00 0.00 2.71
934 2004 7.498900 CAGAAGGGTAGCATGACAATAATACAA 59.501 37.037 0.00 0.00 0.00 2.41
1018 2092 5.665916 AAAAGAACATCCAACATCATCCC 57.334 39.130 0.00 0.00 0.00 3.85
1087 2161 3.807839 ACACACCCTGCTGCCACA 61.808 61.111 0.00 0.00 0.00 4.17
1088 2162 3.289834 CACACACCCTGCTGCCAC 61.290 66.667 0.00 0.00 0.00 5.01
1151 2240 3.554960 CCCGAGAATAGCCATTCGATTCA 60.555 47.826 0.00 0.00 44.51 2.57
1169 2258 2.835156 TGATCAACAGATTGTACCCCGA 59.165 45.455 0.00 0.00 37.11 5.14
1274 2363 1.135859 CGAGTTTCTTCATGGTGCTGC 60.136 52.381 0.00 0.00 0.00 5.25
1324 2413 9.413048 CTTCTTGCTGTACCTAGCTATATTAAC 57.587 37.037 6.73 0.00 44.01 2.01
1343 2432 6.551385 TCTTTGTCTTCATCTTCTTCTTGC 57.449 37.500 0.00 0.00 0.00 4.01
1702 2967 6.947464 ACCATTACTTCTTACACACATAGCT 58.053 36.000 0.00 0.00 0.00 3.32
1790 3119 2.093128 GCTCTTTTCCATAACCGGGAGA 60.093 50.000 6.32 0.00 35.46 3.71
1792 3121 1.913419 AGCTCTTTTCCATAACCGGGA 59.087 47.619 6.32 0.00 0.00 5.14
1968 3299 5.031066 ACTTAACTAGTTGACCTGTTGCA 57.969 39.130 18.56 0.00 31.29 4.08
1974 3305 9.895138 TCTGTTTTTAACTTAACTAGTTGACCT 57.105 29.630 18.56 3.20 46.46 3.85
2092 3423 1.595093 GGGCAGCAAGGCACGTATTT 61.595 55.000 0.00 0.00 46.44 1.40
2127 3458 2.069273 GTTCGATCTTGTGGTGTCCTG 58.931 52.381 0.00 0.00 0.00 3.86
2157 3488 0.609957 CTTGCCATGGGAGAAGTGCA 60.610 55.000 15.13 0.00 0.00 4.57
2447 3778 7.106239 CCTCCAATGAAGTGTGAGTAGTTTAT 58.894 38.462 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.