Multiple sequence alignment - TraesCS6A01G192400

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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 TraesCS6A01G192400 chr6A 100.000 2432 0 0 1 2432 260125596 260128027 0.000000e+00 4492
1 TraesCS6A01G192400 chr6A 95.599 2454 84 7 1 2432 271184654 271182203 0.000000e+00 3912
2 TraesCS6A01G192400 chrUn 96.745 2458 54 7 1 2432 93417140 93419597 0.000000e+00 4072
3 TraesCS6A01G192400 chrUn 95.850 1470 35 8 1 1444 327660672 327662141 0.000000e+00 2353
4 TraesCS6A01G192400 chr5D 96.705 2458 54 7 1 2432 560879676 560877220 0.000000e+00 4065
5 TraesCS6A01G192400 chr5D 96.418 2457 57 9 1 2432 503213110 503210660 0.000000e+00 4021
6 TraesCS6A01G192400 chr1D 96.626 2460 54 9 1 2432 144237914 144235456 0.000000e+00 4056
7 TraesCS6A01G192400 chr3B 96.055 2459 67 11 1 2432 201521882 201519427 0.000000e+00 3976
8 TraesCS6A01G192400 chr3B 87.113 194 12 6 2252 2432 825408892 825409085 8.810000e-50 207
9 TraesCS6A01G192400 chr1A 94.943 2452 98 17 1 2432 168443416 168445861 0.000000e+00 3818
10 TraesCS6A01G192400 chr7A 90.942 2451 163 17 1 2432 352186873 352189283 0.000000e+00 3241
11 TraesCS6A01G192400 chr7A 95.810 1599 56 6 838 2432 201367984 201369575 0.000000e+00 2571
12 TraesCS6A01G192400 chr3A 95.708 1864 61 10 1 1848 672915133 672916993 0.000000e+00 2981
13 TraesCS6A01G192400 chr3A 94.428 682 30 5 1 677 471792807 471792129 0.000000e+00 1042
14 TraesCS6A01G192400 chr2D 95.850 1470 35 8 1 1444 272799026 272800495 0.000000e+00 2353
15 TraesCS6A01G192400 chr4A 95.234 1238 33 8 1 1214 722779684 722780919 0.000000e+00 1936
16 TraesCS6A01G192400 chr6D 97.285 663 13 4 1 658 168246410 168245748 0.000000e+00 1120
17 TraesCS6A01G192400 chr7B 94.492 236 11 2 2197 2432 459813610 459813377 1.780000e-96 363
18 TraesCS6A01G192400 chr2A 97.674 86 2 0 2321 2406 364460279 364460364 5.420000e-32 148


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 TraesCS6A01G192400 chr6A 260125596 260128027 2431 False 4492 4492 100.000 1 2432 1 chr6A.!!$F1 2431
1 TraesCS6A01G192400 chr6A 271182203 271184654 2451 True 3912 3912 95.599 1 2432 1 chr6A.!!$R1 2431
2 TraesCS6A01G192400 chrUn 93417140 93419597 2457 False 4072 4072 96.745 1 2432 1 chrUn.!!$F1 2431
3 TraesCS6A01G192400 chrUn 327660672 327662141 1469 False 2353 2353 95.850 1 1444 1 chrUn.!!$F2 1443
4 TraesCS6A01G192400 chr5D 560877220 560879676 2456 True 4065 4065 96.705 1 2432 1 chr5D.!!$R2 2431
5 TraesCS6A01G192400 chr5D 503210660 503213110 2450 True 4021 4021 96.418 1 2432 1 chr5D.!!$R1 2431
6 TraesCS6A01G192400 chr1D 144235456 144237914 2458 True 4056 4056 96.626 1 2432 1 chr1D.!!$R1 2431
7 TraesCS6A01G192400 chr3B 201519427 201521882 2455 True 3976 3976 96.055 1 2432 1 chr3B.!!$R1 2431
8 TraesCS6A01G192400 chr1A 168443416 168445861 2445 False 3818 3818 94.943 1 2432 1 chr1A.!!$F1 2431
9 TraesCS6A01G192400 chr7A 352186873 352189283 2410 False 3241 3241 90.942 1 2432 1 chr7A.!!$F2 2431
10 TraesCS6A01G192400 chr7A 201367984 201369575 1591 False 2571 2571 95.810 838 2432 1 chr7A.!!$F1 1594
11 TraesCS6A01G192400 chr3A 672915133 672916993 1860 False 2981 2981 95.708 1 1848 1 chr3A.!!$F1 1847
12 TraesCS6A01G192400 chr3A 471792129 471792807 678 True 1042 1042 94.428 1 677 1 chr3A.!!$R1 676
13 TraesCS6A01G192400 chr2D 272799026 272800495 1469 False 2353 2353 95.850 1 1444 1 chr2D.!!$F1 1443
14 TraesCS6A01G192400 chr4A 722779684 722780919 1235 False 1936 1936 95.234 1 1214 1 chr4A.!!$F1 1213
15 TraesCS6A01G192400 chr6D 168245748 168246410 662 True 1120 1120 97.285 1 658 1 chr6D.!!$R1 657

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
394 405 0.738975 TCGGCTAGAGAATGACACCG 59.261 55.0 0.0 0.0 40.47 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 1688 0.591659 GTGTCCGCTTGACCTTTTCC 59.408 55.0 1.37 0.0 43.78 3.13 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
394 405 0.738975 TCGGCTAGAGAATGACACCG 59.261 55.000 0.00 0.00 40.47 4.94
413 424 5.307196 ACACCGTCATCCTAGGCTATATTTT 59.693 40.000 2.96 0.00 0.00 1.82
505 516 4.693283 TGATTCAAGCAAGGGACGTATAG 58.307 43.478 0.00 0.00 0.00 1.31
530 541 9.015146 AGTTTATAGACTTCCCCATAAGGATTT 57.985 33.333 0.00 0.00 38.24 2.17
781 844 5.066505 GGCATGGACGAATTAGAGTCATTTT 59.933 40.000 0.00 0.00 39.01 1.82
817 880 6.727394 AGCATAAACAAAGACAGGGGTAATA 58.273 36.000 0.00 0.00 0.00 0.98
953 1018 7.369551 ACCCTGAAACGGATATCTTTGTATA 57.630 36.000 2.05 0.00 0.00 1.47
1066 1135 5.235616 CGTATTGGTTTACGTAGGAATGCAT 59.764 40.000 0.00 0.00 39.98 3.96
1140 1209 7.801716 TGTTCAAGCTAGTTTCAACAATACT 57.198 32.000 6.31 0.00 0.00 2.12
1215 1284 4.082733 GGTACTTGTGGATTCAAAAGCTCC 60.083 45.833 3.56 3.35 40.94 4.70
1235 1304 3.523157 TCCAGAAAAGCATCACCCTATGA 59.477 43.478 0.00 0.00 43.13 2.15
1258 1327 4.569943 TGGTCAAAGAACAGCAGTAGATC 58.430 43.478 0.00 0.00 0.00 2.75
1268 1337 6.717540 AGAACAGCAGTAGATCCTATTCGTAT 59.282 38.462 0.00 0.00 0.00 3.06
1313 1382 0.621609 ATGGTAAAGGGCGCTGGTAA 59.378 50.000 7.64 0.00 0.00 2.85
1374 1443 6.418819 GTGGTATGCGATTAAGTTGTATACGT 59.581 38.462 0.00 0.00 39.43 3.57
1382 1451 8.697067 GCGATTAAGTTGTATACGTGATGTAAT 58.303 33.333 0.00 0.00 36.44 1.89
1402 1471 2.185004 ACCTATGCCGCATAATGGAC 57.815 50.000 20.27 0.00 0.00 4.02
1619 1688 1.200020 GTTTCATTCTGTCCCCGCTTG 59.800 52.381 0.00 0.00 0.00 4.01
1679 1748 6.455780 GCGAAGAGCTTTACTTGGAGAAATAC 60.456 42.308 0.00 0.00 44.04 1.89
1902 1971 4.989168 GCCTTCCGTAGAAATCGTTGATAT 59.011 41.667 0.00 0.00 0.00 1.63
1952 2021 7.520798 AGAGCCCATTGATTTCTGTATTGATA 58.479 34.615 0.00 0.00 0.00 2.15
1992 2061 4.705023 TCGTGGATATCAGACAGAACTCAA 59.295 41.667 4.83 0.00 0.00 3.02
2159 2232 3.879892 CCCTAAGGAAGCACTTTATGAGC 59.120 47.826 0.00 0.00 33.47 4.26
2166 2239 9.159086 TAAGGAAGCACTTTATGAGCCTTCTCA 62.159 40.741 0.00 0.00 41.17 3.27
2235 2308 4.260253 GGGCGCTAGTTTCGAAGAAAATAG 60.260 45.833 19.41 19.41 45.90 1.73
2413 2486 6.371825 CACTATTGGACCTTTTGAGTAAGACC 59.628 42.308 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 44 3.547054 ATAAATTCGTAAGCCGGGTCA 57.453 42.857 6.62 0.00 37.11 4.02
309 320 7.170998 CCTTCGAAAGTTACTTTTGCTTCTCTA 59.829 37.037 17.72 0.00 35.47 2.43
394 405 9.660180 CTTTCCTAAAATATAGCCTAGGATGAC 57.340 37.037 14.75 0.00 39.67 3.06
413 424 9.717942 GTATAGAACTAGACCGTATCTTTCCTA 57.282 37.037 0.00 0.00 39.04 2.94
447 458 4.015730 TCAATTTTGACCCTATCCCCCATT 60.016 41.667 0.00 0.00 31.01 3.16
505 516 9.067986 CAAATCCTTATGGGGAAGTCTATAAAC 57.932 37.037 0.00 0.00 39.02 2.01
760 823 7.560368 AGAGAAAATGACTCTAATTCGTCCAT 58.440 34.615 0.00 0.00 42.03 3.41
781 844 7.277981 GTCTTTGTTTATGCTTCGGATTAGAGA 59.722 37.037 0.00 0.00 0.00 3.10
924 989 7.120726 ACAAAGATATCCGTTTCAGGGTAAAAG 59.879 37.037 0.00 0.00 29.46 2.27
1027 1096 3.181524 CCAATACGCACTTTCTTACGTGG 60.182 47.826 0.00 0.00 39.43 4.94
1066 1135 5.006941 GTGCACTCTTCCGTAAACTAAAACA 59.993 40.000 10.32 0.00 0.00 2.83
1235 1304 4.623932 TCTACTGCTGTTCTTTGACCAT 57.376 40.909 0.09 0.00 0.00 3.55
1258 1327 6.143438 CGTTGCAAACCTACTATACGAATAGG 59.857 42.308 0.00 0.00 46.28 2.57
1313 1382 2.498167 GTAATGCGGCATCTCTTCCAT 58.502 47.619 16.98 0.03 0.00 3.41
1354 1423 6.700081 ACATCACGTATACAACTTAATCGCAT 59.300 34.615 3.32 0.00 0.00 4.73
1374 1443 4.551702 ATGCGGCATAGGTATTACATCA 57.448 40.909 14.96 0.00 0.00 3.07
1382 1451 2.353307 CGTCCATTATGCGGCATAGGTA 60.353 50.000 20.78 8.82 0.00 3.08
1619 1688 0.591659 GTGTCCGCTTGACCTTTTCC 59.408 55.000 1.37 0.00 43.78 3.13
1679 1748 3.424829 GCACGTGTGATACATGTTCCTTG 60.425 47.826 18.38 0.00 45.33 3.61
1723 1792 9.143155 TCAATACCTGCTATTGTAGAATACTCA 57.857 33.333 4.62 0.00 43.54 3.41
1902 1971 4.224147 TCAAGTTAGCTATAGGTTGTGCCA 59.776 41.667 10.19 0.00 40.61 4.92
1952 2021 5.380900 TCCACGATCTCTCTTGATCTGTAT 58.619 41.667 0.00 0.00 40.32 2.29
2078 2150 8.786826 AGTATCTCGTGTTTTTCATTTCCATA 57.213 30.769 0.00 0.00 0.00 2.74
2235 2308 2.107726 AGGGGTGGAGTAAACCTGTTTC 59.892 50.000 0.00 0.00 37.85 2.78


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

AutoCloner maintained by Alex Coulton.