Multiple sequence alignment - TraesCS1B01G281300

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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 TraesCS1B01G281300 chr1B 100.000 2351 0 0 1 2351 489557577 489559927 0.000000e+00 4342
1 TraesCS1B01G281300 chr1B 93.780 209 13 0 2142 2350 489571831 489572039 4.880000e-82 315
2 TraesCS1B01G281300 chr2D 91.257 2379 167 23 1 2351 536412 534047 0.000000e+00 3203
3 TraesCS1B01G281300 chr3B 93.632 2010 104 15 1 1995 808050649 808048649 0.000000e+00 2981
4 TraesCS1B01G281300 chr1D 92.938 2039 113 24 1 2017 116466587 116468616 0.000000e+00 2939
5 TraesCS1B01G281300 chr1D 88.442 199 15 4 1987 2177 33124492 33124690 1.400000e-57 233
6 TraesCS1B01G281300 chr1D 87.879 198 16 4 1987 2177 33176614 33176418 2.350000e-55 226
7 TraesCS1B01G281300 chr7D 92.734 2037 117 16 1 2017 558325758 558327783 0.000000e+00 2913
8 TraesCS1B01G281300 chr7D 89.867 375 30 3 1985 2351 558336981 558336607 2.110000e-130 475
9 TraesCS1B01G281300 chr7D 89.867 375 30 3 1985 2351 558338351 558337977 2.110000e-130 475
10 TraesCS1B01G281300 chr5A 89.757 2304 171 24 1 2277 293580084 293577819 0.000000e+00 2887
11 TraesCS1B01G281300 chr5A 92.250 2013 130 17 1 1996 21853807 21855810 0.000000e+00 2830
12 TraesCS1B01G281300 chr5A 92.284 1970 128 15 1 1954 21842468 21840507 0.000000e+00 2774
13 TraesCS1B01G281300 chr5A 83.136 338 39 7 1892 2220 293582836 293582508 2.290000e-75 292
14 TraesCS1B01G281300 chr6D 92.643 1998 124 19 1 1980 19452587 19454579 0.000000e+00 2854
15 TraesCS1B01G281300 chr6D 87.371 388 27 11 1974 2351 19454608 19454983 2.160000e-115 425
16 TraesCS1B01G281300 chr5B 92.236 2035 117 22 1 2017 544187296 544185285 0.000000e+00 2844
17 TraesCS1B01G281300 chr7B 92.197 2012 132 16 1 1996 613014463 613016465 0.000000e+00 2822
18 TraesCS1B01G281300 chr7B 89.947 378 27 5 1981 2351 747573483 747573856 5.880000e-131 477
19 TraesCS1B01G281300 chr2B 92.201 2013 130 20 1 1996 791908652 791910654 0.000000e+00 2822
20 TraesCS1B01G281300 chr2B 91.807 2014 135 19 1 1995 791868714 791866712 0.000000e+00 2778
21 TraesCS1B01G281300 chr2B 85.375 506 37 14 1883 2351 780735732 780735227 7.550000e-135 490
22 TraesCS1B01G281300 chr6A 92.292 1998 128 16 1 1981 531357173 531355185 0.000000e+00 2813
23 TraesCS1B01G281300 chr5D 91.123 2039 142 26 1 2017 407680633 407678612 0.000000e+00 2726
24 TraesCS1B01G281300 chr2A 86.509 971 102 18 1169 2120 44839054 44840014 0.000000e+00 1040
25 TraesCS1B01G281300 chr2A 83.226 1085 128 29 1205 2250 44839039 44837970 0.000000e+00 946
26 TraesCS1B01G281300 chr2A 89.397 481 38 8 1880 2349 689374153 689374631 5.590000e-166 593
27 TraesCS1B01G281300 chr4B 89.344 610 50 9 1756 2351 481636713 481636105 0.000000e+00 752
28 TraesCS1B01G281300 chr4B 89.648 483 30 7 1888 2351 481631477 481631958 4.320000e-167 597
29 TraesCS1B01G281300 chr4B 88.630 387 32 7 1974 2351 123875701 123875318 5.920000e-126 460
30 TraesCS1B01G281300 chrUn 95.714 210 9 0 2142 2351 117244172 117244381 2.890000e-89 339


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 TraesCS1B01G281300 chr1B 489557577 489559927 2350 False 4342.0 4342 100.0000 1 2351 1 chr1B.!!$F1 2350
1 TraesCS1B01G281300 chr2D 534047 536412 2365 True 3203.0 3203 91.2570 1 2351 1 chr2D.!!$R1 2350
2 TraesCS1B01G281300 chr3B 808048649 808050649 2000 True 2981.0 2981 93.6320 1 1995 1 chr3B.!!$R1 1994
3 TraesCS1B01G281300 chr1D 116466587 116468616 2029 False 2939.0 2939 92.9380 1 2017 1 chr1D.!!$F2 2016
4 TraesCS1B01G281300 chr7D 558325758 558327783 2025 False 2913.0 2913 92.7340 1 2017 1 chr7D.!!$F1 2016
5 TraesCS1B01G281300 chr7D 558336607 558338351 1744 True 475.0 475 89.8670 1985 2351 2 chr7D.!!$R1 366
6 TraesCS1B01G281300 chr5A 21853807 21855810 2003 False 2830.0 2830 92.2500 1 1996 1 chr5A.!!$F1 1995
7 TraesCS1B01G281300 chr5A 21840507 21842468 1961 True 2774.0 2774 92.2840 1 1954 1 chr5A.!!$R1 1953
8 TraesCS1B01G281300 chr5A 293577819 293582836 5017 True 1589.5 2887 86.4465 1 2277 2 chr5A.!!$R2 2276
9 TraesCS1B01G281300 chr6D 19452587 19454983 2396 False 1639.5 2854 90.0070 1 2351 2 chr6D.!!$F1 2350
10 TraesCS1B01G281300 chr5B 544185285 544187296 2011 True 2844.0 2844 92.2360 1 2017 1 chr5B.!!$R1 2016
11 TraesCS1B01G281300 chr7B 613014463 613016465 2002 False 2822.0 2822 92.1970 1 1996 1 chr7B.!!$F1 1995
12 TraesCS1B01G281300 chr2B 791908652 791910654 2002 False 2822.0 2822 92.2010 1 1996 1 chr2B.!!$F1 1995
13 TraesCS1B01G281300 chr2B 791866712 791868714 2002 True 2778.0 2778 91.8070 1 1995 1 chr2B.!!$R2 1994
14 TraesCS1B01G281300 chr2B 780735227 780735732 505 True 490.0 490 85.3750 1883 2351 1 chr2B.!!$R1 468
15 TraesCS1B01G281300 chr6A 531355185 531357173 1988 True 2813.0 2813 92.2920 1 1981 1 chr6A.!!$R1 1980
16 TraesCS1B01G281300 chr5D 407678612 407680633 2021 True 2726.0 2726 91.1230 1 2017 1 chr5D.!!$R1 2016
17 TraesCS1B01G281300 chr2A 44839054 44840014 960 False 1040.0 1040 86.5090 1169 2120 1 chr2A.!!$F1 951
18 TraesCS1B01G281300 chr2A 44837970 44839039 1069 True 946.0 946 83.2260 1205 2250 1 chr2A.!!$R1 1045
19 TraesCS1B01G281300 chr4B 481636105 481636713 608 True 752.0 752 89.3440 1756 2351 1 chr4B.!!$R2 595

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
838 3593 4.50771 GAACAGACTGTGAAGCCATATGA 58.492 43.478 9.33 0.0 0.0 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 5027 1.442769 CCATTGTCTCTCGGTTGGTG 58.557 55.0 0.0 0.0 0.0 4.17 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
293 3046 6.921914 AGAAGATGGAAATTTGCAAAGAGAG 58.078 36.000 16.71 0.00 30.51 3.20
434 3187 8.726988 GTTCTTAGGAATTGTAAACTATGCACA 58.273 33.333 0.00 0.00 33.71 4.57
577 3332 7.450634 AGGTCAAGAATTTAAAACCCCTAGAAC 59.549 37.037 0.00 0.00 0.00 3.01
631 3386 4.586841 AGACAGATGCATCTAAGGTAGGAC 59.413 45.833 28.27 14.19 34.85 3.85
682 3437 9.342308 CCAATAAATACTCTCCAAAAGCAGATA 57.658 33.333 0.00 0.00 0.00 1.98
715 3470 5.933617 TGCAGATATGCTTCAGGAAGTTAT 58.066 37.500 14.34 8.15 40.45 1.89
838 3593 4.507710 GAACAGACTGTGAAGCCATATGA 58.492 43.478 9.33 0.00 0.00 2.15
1176 3932 6.661805 GGTTCCAATATACCACCAAAAGAGAA 59.338 38.462 0.00 0.00 34.48 2.87
1334 4096 4.107798 ACCTGGCATATATTTGGAATGGGA 59.892 41.667 0.00 0.00 0.00 4.37
1427 4190 7.526142 AGTATAGATGATGCCTTACTTTCGA 57.474 36.000 0.00 0.00 0.00 3.71
1446 4209 3.640029 TCGACAAGAAAGGTGTTAGGACT 59.360 43.478 0.00 0.00 0.00 3.85
1522 4285 1.271543 CCTGCTTCATCAACTCCCACA 60.272 52.381 0.00 0.00 0.00 4.17
1629 4395 4.154918 GCTTGACCCTTTAGACAGTGAATG 59.845 45.833 0.00 0.00 0.00 2.67
1802 4595 7.626390 TGATGATGATCATATGGACATAGCAA 58.374 34.615 8.54 0.00 37.20 3.91
1813 4606 0.105862 ACATAGCAAGGCATGGGCAT 60.106 50.000 0.00 0.00 43.71 4.40
1837 4630 3.381590 GGCCTGAATAAAGCCCAAACTAG 59.618 47.826 0.00 0.00 41.00 2.57
1841 4634 6.017026 GCCTGAATAAAGCCCAAACTAGATAC 60.017 42.308 0.00 0.00 0.00 2.24
2051 4942 0.320508 TACGCATACACGGGCACAAA 60.321 50.000 0.00 0.00 37.37 2.83
2052 4943 0.958382 ACGCATACACGGGCACAAAT 60.958 50.000 0.00 0.00 37.37 2.32
2069 4960 6.158598 GCACAAATATTCTTGAAGGCAGAAA 58.841 36.000 0.00 0.00 0.00 2.52
2125 5016 1.151668 CCGAAGAGCAAAGACTGGTG 58.848 55.000 0.00 0.00 35.35 4.17
2155 5053 1.442769 CACCAACCGAGAGACAATGG 58.557 55.000 0.00 0.00 0.00 3.16
2259 5169 3.028850 GCATGTACCCTAGTAGGACACA 58.971 50.000 18.43 18.95 37.67 3.72
2325 5236 2.446802 CTCCCTAGGAGCCACCCC 60.447 72.222 11.48 0.00 43.29 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 2833 6.055588 GCAGGTGCATTCTTTAGACCTAATA 58.944 40.000 0.00 0.00 41.59 0.98
396 3149 9.185680 ACAATTCCTAAGAACTGTTGTAAAACT 57.814 29.630 0.00 0.00 39.31 2.66
547 3301 8.555896 AGGGGTTTTAAATTCTTGACCTTTTA 57.444 30.769 4.85 0.00 0.00 1.52
631 3386 2.012937 TGTTTTAGTATCGCACCCCG 57.987 50.000 0.00 0.00 38.61 5.73
893 3648 2.237143 TCCCAGCTATGGTGTCTTCAAG 59.763 50.000 1.67 0.00 46.10 3.02
1251 4012 7.014230 CCTTTTGGTATTTCAGTCTCTTTTGGA 59.986 37.037 0.00 0.00 34.07 3.53
1258 4019 7.228706 TGTTTCTCCTTTTGGTATTTCAGTCTC 59.771 37.037 0.00 0.00 41.38 3.36
1425 4188 3.991367 AGTCCTAACACCTTTCTTGTCG 58.009 45.455 0.00 0.00 0.00 4.35
1427 4190 6.936968 ATCTAGTCCTAACACCTTTCTTGT 57.063 37.500 0.00 0.00 0.00 3.16
1522 4285 2.105766 GAGCTTGATGCATCCCCTTTT 58.894 47.619 23.67 4.86 45.94 2.27
1774 4555 9.774413 GCTATGTCCATATGATCATCATCATTA 57.226 33.333 12.53 0.00 46.07 1.90
1864 4657 3.440162 TATAGGTCCTCCGCGCCCA 62.440 63.158 0.00 0.00 39.05 5.36
2043 4932 3.195396 TGCCTTCAAGAATATTTGTGCCC 59.805 43.478 0.00 0.00 0.00 5.36
2125 5016 2.985847 GTTGGTGGGCCTCTGTGC 60.986 66.667 4.53 0.00 35.27 4.57
2136 5027 1.442769 CCATTGTCTCTCGGTTGGTG 58.557 55.000 0.00 0.00 0.00 4.17
2155 5053 2.755836 TCTTTGCTTTCTTCACGTGC 57.244 45.000 11.67 0.00 0.00 5.34
2259 5169 2.027073 CACACGGTAGCATGCACGT 61.027 57.895 23.30 23.30 40.60 4.49
2325 5236 2.395654 GTCTCCTTTTATAGCCGCGAG 58.604 52.381 8.23 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.