Multiple sequence alignment - TraesCS4A01G190000

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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 TraesCS4A01G190000 chr4A 100.000 2513 0 0 1 2513 468651211 468653723 0.000000e+00 4641
1 TraesCS4A01G190000 chr4A 95.297 2488 100 11 28 2513 516667154 516664682 0.000000e+00 3930
2 TraesCS4A01G190000 chr5A 95.635 2520 97 8 1 2513 66112006 66114519 0.000000e+00 4032
3 TraesCS4A01G190000 chr2A 95.426 2514 106 6 1 2513 749465056 749467561 0.000000e+00 3997
4 TraesCS4A01G190000 chr2A 95.026 2513 111 11 3 2513 127168074 127170574 0.000000e+00 3936
5 TraesCS4A01G190000 chr2A 93.473 2298 128 14 1 2288 206090087 206092372 0.000000e+00 3393
6 TraesCS4A01G190000 chr2A 92.995 2284 147 11 5 2288 458999268 458996998 0.000000e+00 3319
7 TraesCS4A01G190000 chr7A 95.174 2507 109 10 7 2513 699083672 699081178 0.000000e+00 3949
8 TraesCS4A01G190000 chr7A 94.105 2290 120 11 1 2290 595120009 595122283 0.000000e+00 3467
9 TraesCS4A01G190000 chr7A 97.101 276 7 1 2238 2513 595122278 595122552 4.900000e-127 464
10 TraesCS4A01G190000 chr6A 93.624 2290 132 10 1 2290 54961585 54959310 0.000000e+00 3408
11 TraesCS4A01G190000 chr6A 96.875 384 11 1 2130 2513 573259027 573259409 2.110000e-180 641
12 TraesCS4A01G190000 chr6A 97.826 276 5 1 2238 2513 54959315 54959041 2.260000e-130 475


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 TraesCS4A01G190000 chr4A 468651211 468653723 2512 False 4641.0 4641 100.000 1 2513 1 chr4A.!!$F1 2512
1 TraesCS4A01G190000 chr4A 516664682 516667154 2472 True 3930.0 3930 95.297 28 2513 1 chr4A.!!$R1 2485
2 TraesCS4A01G190000 chr5A 66112006 66114519 2513 False 4032.0 4032 95.635 1 2513 1 chr5A.!!$F1 2512
3 TraesCS4A01G190000 chr2A 749465056 749467561 2505 False 3997.0 3997 95.426 1 2513 1 chr2A.!!$F3 2512
4 TraesCS4A01G190000 chr2A 127168074 127170574 2500 False 3936.0 3936 95.026 3 2513 1 chr2A.!!$F1 2510
5 TraesCS4A01G190000 chr2A 206090087 206092372 2285 False 3393.0 3393 93.473 1 2288 1 chr2A.!!$F2 2287
6 TraesCS4A01G190000 chr2A 458996998 458999268 2270 True 3319.0 3319 92.995 5 2288 1 chr2A.!!$R1 2283
7 TraesCS4A01G190000 chr7A 699081178 699083672 2494 True 3949.0 3949 95.174 7 2513 1 chr7A.!!$R1 2506
8 TraesCS4A01G190000 chr7A 595120009 595122552 2543 False 1965.5 3467 95.603 1 2513 2 chr7A.!!$F1 2512
9 TraesCS4A01G190000 chr6A 54959041 54961585 2544 True 1941.5 3408 95.725 1 2513 2 chr6A.!!$R1 2512

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
63 64 0.322546 GTCGGGGGCAATCAAGTTCT 60.323 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1884 0.040514 CGCATTCGAAGCAACAACCA 60.041 50.0 16.26 0.0 38.1 3.67 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
63 64 0.322546 GTCGGGGGCAATCAAGTTCT 60.323 55.000 0.00 0.00 0.00 3.01
81 82 4.080919 AGTTCTAATGTGCCTGCAGATACA 60.081 41.667 17.39 19.24 29.41 2.29
115 116 1.507140 CATTAGGAGTGCCACCCCTA 58.493 55.000 0.22 0.22 36.29 3.53
154 155 0.838987 GGTAGTTCACCCACCTCCCA 60.839 60.000 0.00 0.00 42.07 4.37
168 169 1.390565 CTCCCACGGAAGACTACGAT 58.609 55.000 6.49 0.00 0.00 3.73
188 189 1.002134 CCGAAGTCAGGGCCACAAT 60.002 57.895 6.18 0.00 0.00 2.71
214 215 6.406177 GGAACAGACCCAGTTGTACGATATTA 60.406 42.308 0.00 0.00 0.00 0.98
696 704 7.400339 TGAAGAAATATGTGAGTACTCCTTCCT 59.600 37.037 20.11 6.63 0.00 3.36
709 719 3.769300 ACTCCTTCCTTGTTTGCACTTTT 59.231 39.130 0.00 0.00 0.00 2.27
710 720 4.222810 ACTCCTTCCTTGTTTGCACTTTTT 59.777 37.500 0.00 0.00 0.00 1.94
784 794 1.016627 GTTTCATGCGGCATCAGCTA 58.983 50.000 13.53 0.00 41.70 3.32
787 797 1.524393 CATGCGGCATCAGCTACCA 60.524 57.895 13.53 0.00 41.70 3.25
1188 1203 3.040147 GTCAAAGAGACATGGAACCGA 57.960 47.619 0.00 0.00 46.77 4.69
1201 1216 2.159128 TGGAACCGACACTACGAAAACA 60.159 45.455 0.00 0.00 35.09 2.83
1307 1327 5.421374 TCATGTGCCATTTTACATCAATCCA 59.579 36.000 0.00 0.00 35.46 3.41
1308 1328 5.070770 TGTGCCATTTTACATCAATCCAC 57.929 39.130 0.00 0.00 0.00 4.02
1378 1398 3.135994 GTCCTTTTTGCGAGTTCACCTA 58.864 45.455 0.00 0.00 0.00 3.08
1408 1428 2.960384 TCTTTGTGAAGGACGGACTGTA 59.040 45.455 0.00 0.00 33.56 2.74
1471 1491 0.955428 TGTTCCCGCTGTCAATGCTC 60.955 55.000 0.00 0.00 0.00 4.26
1511 1531 4.938832 CCGGAAATTGTACACATGGAACTA 59.061 41.667 0.00 0.00 0.00 2.24
1517 1537 8.635765 AAATTGTACACATGGAACTAGTTGAT 57.364 30.769 14.14 1.73 0.00 2.57
1519 1539 4.935205 TGTACACATGGAACTAGTTGATGC 59.065 41.667 14.14 0.00 0.00 3.91
1533 1553 8.114331 ACTAGTTGATGCATGAAGATTTCAAA 57.886 30.769 2.46 0.00 43.95 2.69
1593 1613 7.172361 GCTGTCAAGAAAGTCTTCAAGAAGTAT 59.828 37.037 9.44 0.00 33.78 2.12
1631 1651 1.518572 CACACCGGACGCATACCTC 60.519 63.158 9.46 0.00 0.00 3.85
1748 1768 1.885388 CGCAGTGGTGGTTCGTGAA 60.885 57.895 0.00 0.00 0.00 3.18
1854 1874 9.734620 ATCATTATTATTTGTGGTTTCATCGTG 57.265 29.630 0.00 0.00 0.00 4.35
1864 1884 0.179032 TTTCATCGTGTGCACCACCT 60.179 50.000 15.69 0.00 41.26 4.00
1975 1996 4.768583 TCATTTGGCTGTTTTGCTTCTTT 58.231 34.783 0.00 0.00 0.00 2.52
2033 2055 4.481368 TTTGATCATGTAGCCGTAACCT 57.519 40.909 0.00 0.00 0.00 3.50
2034 2056 4.481368 TTGATCATGTAGCCGTAACCTT 57.519 40.909 0.00 0.00 0.00 3.50
2074 2098 3.544682 ACGTTACGCTTTTTCAACTTTGC 59.455 39.130 4.09 0.00 0.00 3.68
2228 2254 2.146342 AGAACACGGCAGATTCAACAG 58.854 47.619 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 6.652062 CAGATATTGTATCTGCAGGCACATTA 59.348 38.462 15.13 16.82 39.03 1.90
81 82 7.093112 GCACTCCTAATGGTATCCTCAGATATT 60.093 40.741 0.00 0.00 37.32 1.28
154 155 0.107508 TCGGGATCGTAGTCTTCCGT 60.108 55.000 0.00 0.00 38.70 4.69
168 169 3.319198 GTGGCCCTGACTTCGGGA 61.319 66.667 5.59 0.00 45.36 5.14
188 189 1.069513 CGTACAACTGGGTCTGTTCCA 59.930 52.381 0.00 0.00 0.00 3.53
214 215 2.423185 TCGCATTTCCAAATCGCTTGAT 59.577 40.909 0.00 0.00 37.17 2.57
275 276 4.935352 AAGAGCAAAGCAAAATGTGGTA 57.065 36.364 0.00 0.00 36.79 3.25
404 407 3.072330 TGGTTCTGTCCAAACATGAGCTA 59.928 43.478 0.00 0.00 34.13 3.32
747 757 4.218200 TGAAACATCTGCCACATAAACAGG 59.782 41.667 0.00 0.00 32.19 4.00
784 794 4.734398 TCAAAAAGTCAGTTTGCATGGT 57.266 36.364 0.00 0.00 36.19 3.55
787 797 6.968335 GCAAAAATCAAAAAGTCAGTTTGCAT 59.032 30.769 11.68 0.00 45.47 3.96
937 949 3.584406 ACATGAAGAACATCAGAGGGACA 59.416 43.478 0.00 0.00 37.07 4.02
947 959 5.779529 AGCAAAGTTCACATGAAGAACAT 57.220 34.783 25.92 17.44 45.93 2.71
1188 1203 3.624410 GGACCTTTGTGTTTTCGTAGTGT 59.376 43.478 0.00 0.00 0.00 3.55
1201 1216 4.647564 AATGACTGATCTGGACCTTTGT 57.352 40.909 4.49 0.00 0.00 2.83
1378 1398 5.163652 CCGTCCTTCACAAAGAAAAAGAGTT 60.164 40.000 0.00 0.00 35.40 3.01
1408 1428 4.666512 AGGTATTCCAACATGTGAAAGCT 58.333 39.130 0.00 3.61 35.89 3.74
1511 1531 7.095355 GCTTTTTGAAATCTTCATGCATCAACT 60.095 33.333 0.00 0.00 39.84 3.16
1517 1537 3.989167 CCGCTTTTTGAAATCTTCATGCA 59.011 39.130 0.00 0.00 39.84 3.96
1519 1539 4.622740 GGACCGCTTTTTGAAATCTTCATG 59.377 41.667 0.00 0.00 39.84 3.07
1593 1613 2.030096 TGTAACGCCACGTGATCACTTA 60.030 45.455 22.95 10.93 39.99 2.24
1864 1884 0.040514 CGCATTCGAAGCAACAACCA 60.041 50.000 16.26 0.00 38.10 3.67
1870 1890 1.082169 GTGCACGCATTCGAAGCAA 60.082 52.632 10.20 0.00 45.53 3.91
1907 1927 5.078411 ACCATGTCTGATGAACTACAGTC 57.922 43.478 0.00 0.00 35.84 3.51
2034 2056 1.599171 CGTGCATCAACCGCAGAAAAA 60.599 47.619 0.00 0.00 40.78 1.94
2074 2098 5.125257 TGTGTTGTGTGCAATATATGGGAAG 59.875 40.000 0.00 0.00 36.92 3.46
2228 2254 1.004277 TGGGTCTACCATCCTGTTTGC 59.996 52.381 0.81 0.00 46.80 3.68
2397 2515 0.179936 GACTCTTGAGGGGCATCAGG 59.820 60.000 2.55 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.