Multiple sequence alignment - TraesCS5B01G228200

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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 TraesCS5B01G228200 chr5B 100.000 3434 0 0 1 3434 405545961 405542528 0.000000e+00 6342.0
1 TraesCS5B01G228200 chr5B 90.652 1166 83 13 566 1711 391208082 391209241 0.000000e+00 1526.0
2 TraesCS5B01G228200 chr5B 84.343 198 19 11 1 191 391165286 391165478 2.100000e-42 183.0
3 TraesCS5B01G228200 chr5B 77.108 166 31 5 1762 1924 391297432 391297593 4.720000e-14 89.8
4 TraesCS5B01G228200 chr7B 94.111 3430 146 24 1 3411 165110386 165113778 0.000000e+00 5164.0
5 TraesCS5B01G228200 chr2B 94.199 3258 159 17 196 3434 690759413 690762659 0.000000e+00 4942.0
6 TraesCS5B01G228200 chr2B 96.859 191 6 0 1 191 690759115 690759305 1.540000e-83 320.0
7 TraesCS5B01G228200 chr4D 93.524 3258 176 26 196 3434 27525791 27529032 0.000000e+00 4815.0
8 TraesCS5B01G228200 chr4D 94.180 189 10 1 3 191 27525496 27525683 1.560000e-73 287.0
9 TraesCS5B01G228200 chr3B 92.815 2728 171 18 196 2908 69600059 69597342 0.000000e+00 3928.0
10 TraesCS5B01G228200 chr3B 92.322 534 38 1 2904 3434 69463824 69463291 0.000000e+00 756.0
11 TraesCS5B01G228200 chr3B 93.717 191 11 1 1 191 69600356 69600167 5.610000e-73 285.0
12 TraesCS5B01G228200 chr5D 90.306 2806 213 33 647 3434 546553384 546550620 0.000000e+00 3620.0
13 TraesCS5B01G228200 chr5D 91.790 1961 135 17 1476 3434 151200225 151198289 0.000000e+00 2706.0
14 TraesCS5B01G228200 chr5D 90.997 1655 118 23 208 1842 396230652 396229009 0.000000e+00 2202.0
15 TraesCS5B01G228200 chr5D 92.462 1300 78 12 196 1479 151214366 151213071 0.000000e+00 1840.0
16 TraesCS5B01G228200 chr5D 90.587 818 64 8 1967 2776 396229003 396228191 0.000000e+00 1072.0
17 TraesCS5B01G228200 chr5D 91.522 460 27 10 196 649 546562485 546562032 1.050000e-174 623.0
18 TraesCS5B01G228200 chr5D 91.623 191 15 1 1 191 151214663 151214474 2.630000e-66 263.0
19 TraesCS5B01G228200 chr5D 79.878 164 23 9 1767 1924 546486644 546486485 1.010000e-20 111.0
20 TraesCS5B01G228200 chr5D 95.238 42 2 0 8 49 396230824 396230783 2.210000e-07 67.6
21 TraesCS5B01G228200 chr7D 90.926 1653 121 21 208 1842 24391936 24393577 0.000000e+00 2194.0
22 TraesCS5B01G228200 chr5A 88.995 1472 136 11 1967 3434 544473745 544475194 0.000000e+00 1797.0
23 TraesCS5B01G228200 chr5A 91.912 1051 76 7 209 1254 544470110 544471156 0.000000e+00 1461.0
24 TraesCS5B01G228200 chr5A 89.691 194 16 4 1 191 544469823 544470015 9.520000e-61 244.0
25 TraesCS5B01G228200 chr5A 88.462 78 6 2 1767 1842 544473663 544473739 1.310000e-14 91.6
26 TraesCS5B01G228200 chr2D 89.915 1299 115 8 2121 3415 376967731 376969017 0.000000e+00 1659.0
27 TraesCS5B01G228200 chr2D 81.915 94 15 2 1804 1897 377029005 377029096 1.020000e-10 78.7
28 TraesCS5B01G228200 chr4B 87.547 1317 153 7 2121 3434 621551953 621553261 0.000000e+00 1513.0
29 TraesCS5B01G228200 chr4B 92.500 880 52 5 587 1453 621514851 621515729 0.000000e+00 1247.0
30 TraesCS5B01G228200 chr4B 86.316 95 12 1 1804 1898 621623836 621623929 6.060000e-18 102.0


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 TraesCS5B01G228200 chr5B 405542528 405545961 3433 True 6342.000000 6342 100.0000 1 3434 1 chr5B.!!$R1 3433
1 TraesCS5B01G228200 chr5B 391208082 391209241 1159 False 1526.000000 1526 90.6520 566 1711 1 chr5B.!!$F2 1145
2 TraesCS5B01G228200 chr7B 165110386 165113778 3392 False 5164.000000 5164 94.1110 1 3411 1 chr7B.!!$F1 3410
3 TraesCS5B01G228200 chr2B 690759115 690762659 3544 False 2631.000000 4942 95.5290 1 3434 2 chr2B.!!$F1 3433
4 TraesCS5B01G228200 chr4D 27525496 27529032 3536 False 2551.000000 4815 93.8520 3 3434 2 chr4D.!!$F1 3431
5 TraesCS5B01G228200 chr3B 69597342 69600356 3014 True 2106.500000 3928 93.2660 1 2908 2 chr3B.!!$R2 2907
6 TraesCS5B01G228200 chr3B 69463291 69463824 533 True 756.000000 756 92.3220 2904 3434 1 chr3B.!!$R1 530
7 TraesCS5B01G228200 chr5D 546550620 546553384 2764 True 3620.000000 3620 90.3060 647 3434 1 chr5D.!!$R3 2787
8 TraesCS5B01G228200 chr5D 151198289 151200225 1936 True 2706.000000 2706 91.7900 1476 3434 1 chr5D.!!$R1 1958
9 TraesCS5B01G228200 chr5D 396228191 396230824 2633 True 1113.866667 2202 92.2740 8 2776 3 chr5D.!!$R6 2768
10 TraesCS5B01G228200 chr5D 151213071 151214663 1592 True 1051.500000 1840 92.0425 1 1479 2 chr5D.!!$R5 1478
11 TraesCS5B01G228200 chr7D 24391936 24393577 1641 False 2194.000000 2194 90.9260 208 1842 1 chr7D.!!$F1 1634
12 TraesCS5B01G228200 chr5A 544469823 544475194 5371 False 898.400000 1797 89.7650 1 3434 4 chr5A.!!$F1 3433
13 TraesCS5B01G228200 chr2D 376967731 376969017 1286 False 1659.000000 1659 89.9150 2121 3415 1 chr2D.!!$F1 1294
14 TraesCS5B01G228200 chr4B 621551953 621553261 1308 False 1513.000000 1513 87.5470 2121 3434 1 chr4B.!!$F2 1313
15 TraesCS5B01G228200 chr4B 621514851 621515729 878 False 1247.000000 1247 92.5000 587 1453 1 chr4B.!!$F1 866

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
800 930 1.474077 GCCAGTGGATCATGAAACACC 59.526 52.381 22.24 14.06 34.5 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2710 4985 1.552337 ACTGTCATCTCCGCTGTCATT 59.448 47.619 0.0 0.0 0.0 2.57 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
155 159 7.234355 ACCATGGGAAAATCTCATATTAGGAC 58.766 38.462 18.09 0.00 34.84 3.85
261 369 8.850454 TTTTGTACTAGCAATTTGTTGAGAAC 57.150 30.769 0.00 0.00 0.00 3.01
361 470 3.066203 TCGCGCTAGAACTTCATGTATGA 59.934 43.478 5.56 0.00 34.44 2.15
697 827 9.884465 CTTTTTAAGTTGAACAAAGATCTCGAT 57.116 29.630 0.00 0.00 0.00 3.59
800 930 1.474077 GCCAGTGGATCATGAAACACC 59.526 52.381 22.24 14.06 34.50 4.16
858 988 5.957771 AGAGGCAAAATACCAGTAGATGA 57.042 39.130 0.00 0.00 0.00 2.92
1032 1165 2.045438 AATGGGGCGTGCGATGAA 60.045 55.556 0.00 0.00 0.00 2.57
1139 1273 4.512944 CACTGCTATTCTTCACACAAGTGT 59.487 41.667 0.00 0.00 46.01 3.55
1585 3815 6.451064 AGGTTAGAAACAGAAACAGGTTTG 57.549 37.500 1.52 0.00 37.35 2.93
1614 3845 8.845413 ACAAATTATGCCAAACACATTGTTAT 57.155 26.923 0.00 0.00 40.14 1.89
1628 3859 7.312899 ACACATTGTTATAAGTTTAGGCAAGC 58.687 34.615 0.00 0.00 0.00 4.01
1652 3883 6.653740 GCCATAGTATTAGGACCAACATAACC 59.346 42.308 0.00 0.00 0.00 2.85
1854 4112 9.906660 CAGAACATAACTTGCCTACATTTTTAA 57.093 29.630 0.00 0.00 0.00 1.52
2185 4454 6.562086 CGCCTTGCTTTTAGTTTTGATGAAAC 60.562 38.462 0.00 0.00 46.42 2.78
2290 4559 3.252458 GGTTGCCTGAAAGTTACGACAAT 59.748 43.478 0.00 0.00 0.00 2.71
2623 4898 1.557099 ACACGGCTCAAGTGAGGATA 58.443 50.000 10.25 0.00 42.29 2.59
2710 4985 0.113776 AGACAGTGGTAACTCGGGGA 59.886 55.000 0.00 0.00 32.98 4.81
2808 5088 4.325119 CTGAGGATGATGCCAATAAGGAG 58.675 47.826 0.00 0.00 41.22 3.69
2980 5260 4.202264 ACGAGACAGAGAAAGTTGGTGAAT 60.202 41.667 0.00 0.00 0.00 2.57
3199 5479 6.544622 CAAAATGACAACAAACAACAAGCAT 58.455 32.000 0.00 0.00 0.00 3.79
3223 5503 2.791383 TGCCACAGAAACATTTTCCG 57.209 45.000 0.00 0.00 0.00 4.30
3256 5536 5.551305 TGTCAAGATGGAGTTCAAGAAGA 57.449 39.130 0.00 0.00 0.00 2.87
3345 5626 3.194062 TGCGAGCACATTATTCGATCAA 58.806 40.909 0.00 0.00 36.49 2.57
3385 5666 6.378280 GGAGGAAAGAGAAATAGGCATCAAAA 59.622 38.462 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
361 470 0.808125 TTGCACACACTTTCGCACTT 59.192 45.000 0.00 0.00 33.29 3.16
366 475 4.143115 CCACTATAGTTGCACACACTTTCG 60.143 45.833 1.56 0.00 0.00 3.46
800 930 2.526304 TGAGACTTTTCTGGGTCGTG 57.474 50.000 0.00 0.00 37.52 4.35
858 988 5.132816 CCCCAAATCCTCCTAACACTATCTT 59.867 44.000 0.00 0.00 0.00 2.40
897 1027 9.696917 GATTCATTTCAAAACATACTTTCCTGT 57.303 29.630 0.00 0.00 0.00 4.00
1032 1165 1.039856 ACCAAGCACGCAGGAAATTT 58.960 45.000 7.43 0.00 0.00 1.82
1139 1273 7.985184 AGTCGCATATCTTGGTGTCTTTTATAA 59.015 33.333 0.00 0.00 0.00 0.98
1212 1346 0.319297 GGCAGCAAACAGCCTTCTTG 60.319 55.000 0.00 0.00 44.75 3.02
1231 1365 6.780706 ACTTACAACTAGATGGAAAACACG 57.219 37.500 4.89 0.00 0.00 4.49
1362 3587 8.635328 TCATCAACATCCAATGAATCCAAATAG 58.365 33.333 0.00 0.00 0.00 1.73
1585 3815 9.364989 ACAATGTGTTTGGCATAATTTGTATAC 57.635 29.630 0.00 0.00 39.80 1.47
1614 3845 8.154856 CCTAATACTATGGCTTGCCTAAACTTA 58.845 37.037 13.18 3.84 0.00 2.24
1628 3859 7.878127 CAGGTTATGTTGGTCCTAATACTATGG 59.122 40.741 0.00 0.00 0.00 2.74
1652 3883 4.264253 TCATATGTTTCTTCCACAGGCAG 58.736 43.478 1.90 0.00 0.00 4.85
1854 4112 9.840427 GCTATGTACAATACAGAACAACAAAAT 57.160 29.630 0.00 0.00 42.77 1.82
2059 4318 5.511888 CCTTGGATTTCACTTTGGATTTGCT 60.512 40.000 0.00 0.00 0.00 3.91
2108 4367 9.525409 CAACGCCATATAGGTAGTAATATAACC 57.475 37.037 0.00 0.00 40.61 2.85
2167 4436 7.202526 TGAGCTGGTTTCATCAAAACTAAAAG 58.797 34.615 0.00 0.00 45.48 2.27
2172 4441 4.889409 TCTTGAGCTGGTTTCATCAAAACT 59.111 37.500 0.00 0.00 45.48 2.66
2185 4454 4.612259 CGTGAAAATTCAGTCTTGAGCTGG 60.612 45.833 0.00 0.00 37.98 4.85
2290 4559 9.515226 ACTTTCTTGCTATTGGAACTTACATAA 57.485 29.630 0.00 0.00 0.00 1.90
2393 4665 4.435917 GCTTCTGCACACCAAAAACAAAAG 60.436 41.667 0.00 0.00 39.41 2.27
2431 4706 3.056678 GTGCACATTTCATGGACCATTCA 60.057 43.478 13.17 0.00 32.67 2.57
2608 4883 2.769095 ACTCCTTATCCTCACTTGAGCC 59.231 50.000 0.26 0.00 40.75 4.70
2623 4898 2.352814 CGTCCGACTTGAATGACTCCTT 60.353 50.000 0.00 0.00 0.00 3.36
2710 4985 1.552337 ACTGTCATCTCCGCTGTCATT 59.448 47.619 0.00 0.00 0.00 2.57
2728 5005 6.315642 GTGTTGTCATCATCATCATCTGAACT 59.684 38.462 0.00 0.00 37.44 3.01
2808 5088 2.079925 GTTTCATGTGGCTCCTCACTC 58.920 52.381 0.00 0.00 38.40 3.51
2980 5260 4.104086 ACTTGGTCCTCATTGTCCTCATA 58.896 43.478 0.00 0.00 0.00 2.15
3144 5424 2.787473 AATTTGATCCAGAGTCGCCA 57.213 45.000 0.00 0.00 0.00 5.69
3199 5479 4.022068 GGAAAATGTTTCTGTGGCATCTCA 60.022 41.667 0.00 0.00 0.00 3.27
3207 5487 9.840427 AAATCTATAACGGAAAATGTTTCTGTG 57.160 29.630 14.29 4.33 38.01 3.66
3256 5536 2.677914 CTTTTGAAAGGGGTCCCACTT 58.322 47.619 10.98 8.01 38.92 3.16
3289 5570 0.667993 CGCCCATCAAACACTTGTGT 59.332 50.000 0.00 0.00 33.94 3.72
3345 5626 0.673644 CCTCCTCGCGAAACACCATT 60.674 55.000 11.33 0.00 0.00 3.16
3385 5666 3.073650 GGGCATAACTCCTCAGGATTGAT 59.926 47.826 0.00 0.00 31.68 2.57


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

AutoCloner maintained by Alex Coulton.