Multiple sequence alignment - TraesCS3D01G433500

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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 TraesCS3D01G433500 chr3D 100.000 2549 0 0 1 2549 546485400 546487948 0.000000e+00 4708
1 TraesCS3D01G433500 chr3D 90.078 383 32 4 210 591 546480320 546480697 2.280000e-135 492
2 TraesCS3D01G433500 chr3D 86.404 228 17 4 1 216 546480061 546480286 1.180000e-58 237
3 TraesCS3D01G433500 chr1D 95.561 1960 76 9 596 2549 25464319 25466273 0.000000e+00 3127
4 TraesCS3D01G433500 chr5D 94.383 1976 80 19 588 2549 44511933 44513891 0.000000e+00 3005
5 TraesCS3D01G433500 chr2D 94.433 1958 80 12 599 2549 84780830 84782765 0.000000e+00 2985
6 TraesCS3D01G433500 chr2D 96.604 265 8 1 2286 2549 331198906 331199170 3.010000e-119 438
7 TraesCS3D01G433500 chrUn 94.904 1923 69 19 639 2549 43407879 43409784 0.000000e+00 2981
8 TraesCS3D01G433500 chr4D 94.193 1963 90 15 595 2549 78732770 78730824 0.000000e+00 2972
9 TraesCS3D01G433500 chr4D 96.935 261 6 1 2289 2549 43271015 43270757 1.080000e-118 436
10 TraesCS3D01G433500 chr3B 93.944 1965 91 15 595 2549 370213880 370215826 0.000000e+00 2944
11 TraesCS3D01G433500 chr3B 90.674 386 28 6 216 595 723511324 723511707 8.140000e-140 507
12 TraesCS3D01G433500 chr3B 88.696 230 15 2 2 220 723511067 723511296 1.160000e-68 270
13 TraesCS3D01G433500 chr1B 93.524 1961 116 10 596 2549 593290586 593288630 0.000000e+00 2907
14 TraesCS3D01G433500 chr7B 93.147 1970 112 15 587 2549 9595583 9597536 0.000000e+00 2868
15 TraesCS3D01G433500 chr7B 94.656 262 14 0 2288 2549 523523336 523523075 8.490000e-110 407
16 TraesCS3D01G433500 chr5B 92.695 1848 122 8 596 2433 548612963 548611119 0.000000e+00 2652
17 TraesCS3D01G433500 chr6B 95.455 264 11 1 2286 2549 59431924 59431662 1.090000e-113 420
18 TraesCS3D01G433500 chr6B 93.657 268 15 1 2282 2549 709809997 709809732 1.420000e-107 399
19 TraesCS3D01G433500 chr3A 90.614 277 22 4 270 542 683256837 683257113 5.180000e-97 364
20 TraesCS3D01G433500 chr3A 86.266 233 19 9 1 226 683256108 683256334 9.110000e-60 241
21 TraesCS3D01G433500 chr3A 87.079 178 18 4 210 385 683262106 683262280 2.000000e-46 196


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 TraesCS3D01G433500 chr3D 546485400 546487948 2548 False 4708.0 4708 100.000 1 2549 1 chr3D.!!$F1 2548
1 TraesCS3D01G433500 chr3D 546480061 546480697 636 False 364.5 492 88.241 1 591 2 chr3D.!!$F2 590
2 TraesCS3D01G433500 chr1D 25464319 25466273 1954 False 3127.0 3127 95.561 596 2549 1 chr1D.!!$F1 1953
3 TraesCS3D01G433500 chr5D 44511933 44513891 1958 False 3005.0 3005 94.383 588 2549 1 chr5D.!!$F1 1961
4 TraesCS3D01G433500 chr2D 84780830 84782765 1935 False 2985.0 2985 94.433 599 2549 1 chr2D.!!$F1 1950
5 TraesCS3D01G433500 chrUn 43407879 43409784 1905 False 2981.0 2981 94.904 639 2549 1 chrUn.!!$F1 1910
6 TraesCS3D01G433500 chr4D 78730824 78732770 1946 True 2972.0 2972 94.193 595 2549 1 chr4D.!!$R2 1954
7 TraesCS3D01G433500 chr3B 370213880 370215826 1946 False 2944.0 2944 93.944 595 2549 1 chr3B.!!$F1 1954
8 TraesCS3D01G433500 chr3B 723511067 723511707 640 False 388.5 507 89.685 2 595 2 chr3B.!!$F2 593
9 TraesCS3D01G433500 chr1B 593288630 593290586 1956 True 2907.0 2907 93.524 596 2549 1 chr1B.!!$R1 1953
10 TraesCS3D01G433500 chr7B 9595583 9597536 1953 False 2868.0 2868 93.147 587 2549 1 chr7B.!!$F1 1962
11 TraesCS3D01G433500 chr5B 548611119 548612963 1844 True 2652.0 2652 92.695 596 2433 1 chr5B.!!$R1 1837
12 TraesCS3D01G433500 chr3A 683256108 683257113 1005 False 302.5 364 88.440 1 542 2 chr3A.!!$F2 541

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
939 1435 0.461163 CGAGAGAGAGAGAGCACGGA 60.461 60.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 2831 0.586802 GGAAAACCACTCTCACACGC 59.413 55.0 0.0 0.0 0.0 5.34 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
31 32 6.772605 ACATGCTCTCCAATATGTATGCTTA 58.227 36.000 0.00 0.00 32.41 3.09
170 181 7.643123 AGAAAACCAAGTACTCCATCCATATT 58.357 34.615 0.00 0.00 0.00 1.28
171 182 7.775561 AGAAAACCAAGTACTCCATCCATATTC 59.224 37.037 0.00 0.00 0.00 1.75
172 183 5.215252 ACCAAGTACTCCATCCATATTCG 57.785 43.478 0.00 0.00 0.00 3.34
196 207 5.414454 GGAAAACATAGGTTGTGAGCATGTA 59.586 40.000 0.00 0.00 38.99 2.29
205 216 5.643777 AGGTTGTGAGCATGTATTCAGTTAC 59.356 40.000 0.00 0.00 0.00 2.50
336 810 4.305769 ACTGCGCAAAATATTCAAAAGCA 58.694 34.783 13.05 0.00 0.00 3.91
338 812 5.409214 ACTGCGCAAAATATTCAAAAGCATT 59.591 32.000 13.05 0.38 0.00 3.56
354 828 2.441001 AGCATTAGACATGGAGGAAGGG 59.559 50.000 0.00 0.00 0.00 3.95
557 1038 6.471519 CGCAAATCATCTTCTCTTTCCATTTC 59.528 38.462 0.00 0.00 0.00 2.17
635 1116 1.523711 CAGTGGTGTCCGTGTGCTT 60.524 57.895 0.00 0.00 0.00 3.91
717 1198 1.006102 CCGTGAACTCTGCCGTCTT 60.006 57.895 0.00 0.00 0.00 3.01
747 1228 1.164041 ACGTTTTGACTCGGCCCTTG 61.164 55.000 0.00 0.00 0.00 3.61
862 1343 2.867368 CGTTGCGGGTGTGCTATATAAA 59.133 45.455 0.00 0.00 35.36 1.40
863 1344 3.059868 CGTTGCGGGTGTGCTATATAAAG 60.060 47.826 0.00 0.00 35.36 1.85
864 1345 2.489971 TGCGGGTGTGCTATATAAAGC 58.510 47.619 0.00 0.00 43.08 3.51
888 1374 4.969196 CACACAGCGGCGGTGACT 62.969 66.667 41.06 23.73 39.53 3.41
939 1435 0.461163 CGAGAGAGAGAGAGCACGGA 60.461 60.000 0.00 0.00 0.00 4.69
1193 1689 2.353208 GGGCAATTGCACCATTTTCGTA 60.353 45.455 30.32 0.00 44.36 3.43
1413 1909 4.526262 ACTGACAGAGAGCTAGTTGTTGAT 59.474 41.667 10.08 0.00 0.00 2.57
1504 2003 5.329399 ACTTTTGGGCATTTGTAGGTATGA 58.671 37.500 0.00 0.00 0.00 2.15
2049 2562 6.458210 AGACCAAAATGTCATGGAAAATGTC 58.542 36.000 0.00 0.00 39.12 3.06
2161 2682 4.914177 AAATGAAGGGTGGAAAATGCAT 57.086 36.364 0.00 0.00 0.00 3.96
2204 2725 4.309950 GAACCCAGGACCGCGTGT 62.310 66.667 4.92 1.93 0.00 4.49
2219 2740 1.794437 GCGTGTGTTTGTGGCGTTTAA 60.794 47.619 0.00 0.00 0.00 1.52
2309 2830 2.226437 GTGAGACCGTGAATGTTTGCAT 59.774 45.455 0.00 0.00 36.80 3.96
2310 2831 2.226200 TGAGACCGTGAATGTTTGCATG 59.774 45.455 0.00 0.00 35.15 4.06
2390 2927 1.533625 ACGTATGTTTGCACTGCCAT 58.466 45.000 0.00 0.00 0.00 4.40
2485 3025 6.389830 TTTGCATGTTAGTTCATGACTTGT 57.610 33.333 10.28 0.00 45.41 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.018537 TGGCTACACATACATACAGAACTATT 57.981 34.615 0.00 0.00 0.00 1.73
40 41 7.315247 TGTTTTGATGGCTACACATACATAC 57.685 36.000 0.00 0.00 0.00 2.39
154 165 6.126883 TGTTTTCCGAATATGGATGGAGTACT 60.127 38.462 0.00 0.00 38.00 2.73
170 181 3.071479 GCTCACAACCTATGTTTTCCGA 58.929 45.455 0.00 0.00 41.46 4.55
171 182 2.811431 TGCTCACAACCTATGTTTTCCG 59.189 45.455 0.00 0.00 41.46 4.30
172 183 4.218417 ACATGCTCACAACCTATGTTTTCC 59.782 41.667 0.00 0.00 41.46 3.13
205 216 9.541143 ACACATTAGTTCCAAATTTTAAAGGTG 57.459 29.630 0.00 1.59 0.00 4.00
257 310 8.558312 TGTTCTAACATATGTATAAAACCCCCA 58.442 33.333 9.21 0.00 33.17 4.96
258 311 8.983702 TGTTCTAACATATGTATAAAACCCCC 57.016 34.615 9.21 0.00 33.17 5.40
336 810 2.781667 AGCCCTTCCTCCATGTCTAAT 58.218 47.619 0.00 0.00 0.00 1.73
338 812 2.270434 AAGCCCTTCCTCCATGTCTA 57.730 50.000 0.00 0.00 0.00 2.59
481 960 2.101249 CTCCTCCACTGAGATTGAGAGC 59.899 54.545 0.00 0.00 41.42 4.09
484 963 2.830923 ACACTCCTCCACTGAGATTGAG 59.169 50.000 0.00 0.00 41.42 3.02
543 1024 7.068226 ACGAAAGGAAAAGAAATGGAAAGAGAA 59.932 33.333 0.00 0.00 0.00 2.87
557 1038 5.744666 TCACAACCTAACGAAAGGAAAAG 57.255 39.130 13.57 4.28 39.15 2.27
635 1116 1.277842 TCGCATCTGAGGGCAAAACTA 59.722 47.619 5.18 0.00 0.00 2.24
717 1198 2.296831 TCAAAACGTTGACCTGACGA 57.703 45.000 0.00 0.00 42.82 4.20
869 1350 4.961511 TCACCGCCGCTGTGTGTC 62.962 66.667 13.78 0.00 35.25 3.67
871 1352 3.567478 TAGTCACCGCCGCTGTGTG 62.567 63.158 13.78 6.53 35.25 3.82
872 1353 3.299977 TAGTCACCGCCGCTGTGT 61.300 61.111 13.78 0.00 35.25 3.72
873 1354 2.809601 GTAGTCACCGCCGCTGTG 60.810 66.667 8.53 8.53 35.01 3.66
888 1374 4.129737 GTGCTCTCTGCCGCCGTA 62.130 66.667 0.00 0.00 42.00 4.02
895 1381 2.807045 CACCGACGTGCTCTCTGC 60.807 66.667 0.00 0.00 43.25 4.26
939 1435 1.557269 CCACAGCTAGCTTCCCACCT 61.557 60.000 16.46 0.00 0.00 4.00
1029 1525 4.575973 GCCCGGCTCTGCATCCAT 62.576 66.667 0.71 0.00 0.00 3.41
1193 1689 2.636830 CATTGCTCAAAGATCCCGACT 58.363 47.619 0.00 0.00 0.00 4.18
1413 1909 6.688073 ACCTTCTTCTTCAACATCCTAAGA 57.312 37.500 0.00 0.00 0.00 2.10
1504 2003 5.645929 TCAACATTACAACCAGTGCGATTAT 59.354 36.000 0.00 0.00 0.00 1.28
1669 2170 7.946776 TCTGAATTCCTCATTTCTTCTCCTTTT 59.053 33.333 2.27 0.00 32.14 2.27
2049 2562 2.819477 CCTCTACCAGAGCTGAGGG 58.181 63.158 7.49 0.97 40.98 4.30
2204 2725 1.066303 CAGCCTTAAACGCCACAAACA 59.934 47.619 0.00 0.00 0.00 2.83
2309 2830 1.295792 GAAAACCACTCTCACACGCA 58.704 50.000 0.00 0.00 0.00 5.24
2310 2831 0.586802 GGAAAACCACTCTCACACGC 59.413 55.000 0.00 0.00 0.00 5.34
2390 2927 5.815581 AGTGCCACTCTAACCAAAATCATA 58.184 37.500 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.