Multiple sequence alignment - TraesCS3B01G381600

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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 TraesCS3B01G381600 chr3B 100.000 2351 0 0 1 2351 599888924 599891274 0 4342
1 TraesCS3B01G381600 chr3B 94.970 835 39 1 1 832 417075961 417075127 0 1306
2 TraesCS3B01G381600 chr3D 96.691 1813 57 1 539 2348 189337636 189339448 0 3013
3 TraesCS3B01G381600 chr7D 97.185 1563 41 3 787 2348 468086063 468087623 0 2639
4 TraesCS3B01G381600 chr5D 88.536 2233 176 34 141 2348 17476951 17474774 0 2632
5 TraesCS3B01G381600 chr4D 96.358 1565 55 2 787 2351 270637894 270636332 0 2573
6 TraesCS3B01G381600 chr4D 96.075 1274 49 1 1076 2348 250328051 250329324 0 2074
7 TraesCS3B01G381600 chr3A 95.070 1562 61 3 787 2348 330458987 330460532 0 2444
8 TraesCS3B01G381600 chr3A 96.317 1059 34 2 1 1056 598349862 598350918 0 1735
9 TraesCS3B01G381600 chr3A 95.660 1060 32 5 1 1056 598406188 598407237 0 1690
10 TraesCS3B01G381600 chr3A 95.800 1000 38 2 1 997 598426424 598427422 0 1611
11 TraesCS3B01G381600 chr3A 95.329 835 36 1 1 832 330458157 330458991 0 1323
12 TraesCS3B01G381600 chr6B 94.633 1565 79 4 787 2351 522910254 522908695 0 2420
13 TraesCS3B01G381600 chr6B 95.450 1077 49 0 860 1936 250263843 250262767 0 1718
14 TraesCS3B01G381600 chr7B 94.591 1368 63 5 981 2348 355066507 355067863 0 2106
15 TraesCS3B01G381600 chr4A 88.287 1588 166 14 770 2348 216124679 216123103 0 1884
16 TraesCS3B01G381600 chr4A 95.724 842 31 3 1 839 362722239 362721400 0 1351
17 TraesCS3B01G381600 chr6A 94.599 1222 48 3 1129 2348 383201758 383202963 0 1875
18 TraesCS3B01G381600 chr1D 96.048 835 29 2 1 832 304624870 304624037 0 1356
19 TraesCS3B01G381600 chr4B 94.850 835 40 1 1 832 188057100 188056266 0 1301
20 TraesCS3B01G381600 chr5B 94.371 835 43 2 2 832 392521184 392522018 0 1279


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 TraesCS3B01G381600 chr3B 599888924 599891274 2350 False 4342.0 4342 100.0000 1 2351 1 chr3B.!!$F1 2350
1 TraesCS3B01G381600 chr3B 417075127 417075961 834 True 1306.0 1306 94.9700 1 832 1 chr3B.!!$R1 831
2 TraesCS3B01G381600 chr3D 189337636 189339448 1812 False 3013.0 3013 96.6910 539 2348 1 chr3D.!!$F1 1809
3 TraesCS3B01G381600 chr7D 468086063 468087623 1560 False 2639.0 2639 97.1850 787 2348 1 chr7D.!!$F1 1561
4 TraesCS3B01G381600 chr5D 17474774 17476951 2177 True 2632.0 2632 88.5360 141 2348 1 chr5D.!!$R1 2207
5 TraesCS3B01G381600 chr4D 270636332 270637894 1562 True 2573.0 2573 96.3580 787 2351 1 chr4D.!!$R1 1564
6 TraesCS3B01G381600 chr4D 250328051 250329324 1273 False 2074.0 2074 96.0750 1076 2348 1 chr4D.!!$F1 1272
7 TraesCS3B01G381600 chr3A 330458157 330460532 2375 False 1883.5 2444 95.1995 1 2348 2 chr3A.!!$F4 2347
8 TraesCS3B01G381600 chr3A 598349862 598350918 1056 False 1735.0 1735 96.3170 1 1056 1 chr3A.!!$F1 1055
9 TraesCS3B01G381600 chr3A 598406188 598407237 1049 False 1690.0 1690 95.6600 1 1056 1 chr3A.!!$F2 1055
10 TraesCS3B01G381600 chr3A 598426424 598427422 998 False 1611.0 1611 95.8000 1 997 1 chr3A.!!$F3 996
11 TraesCS3B01G381600 chr6B 522908695 522910254 1559 True 2420.0 2420 94.6330 787 2351 1 chr6B.!!$R2 1564
12 TraesCS3B01G381600 chr6B 250262767 250263843 1076 True 1718.0 1718 95.4500 860 1936 1 chr6B.!!$R1 1076
13 TraesCS3B01G381600 chr7B 355066507 355067863 1356 False 2106.0 2106 94.5910 981 2348 1 chr7B.!!$F1 1367
14 TraesCS3B01G381600 chr4A 216123103 216124679 1576 True 1884.0 1884 88.2870 770 2348 1 chr4A.!!$R1 1578
15 TraesCS3B01G381600 chr4A 362721400 362722239 839 True 1351.0 1351 95.7240 1 839 1 chr4A.!!$R2 838
16 TraesCS3B01G381600 chr6A 383201758 383202963 1205 False 1875.0 1875 94.5990 1129 2348 1 chr6A.!!$F1 1219
17 TraesCS3B01G381600 chr1D 304624037 304624870 833 True 1356.0 1356 96.0480 1 832 1 chr1D.!!$R1 831
18 TraesCS3B01G381600 chr4B 188056266 188057100 834 True 1301.0 1301 94.8500 1 832 1 chr4B.!!$R1 831
19 TraesCS3B01G381600 chr5B 392521184 392522018 834 False 1279.0 1279 94.3710 2 832 1 chr5B.!!$F1 830

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
203 207 1.953559 TTCTGTGTGTGCCTTCAGTC 58.046 50.000 0.0 0.0 0.0 3.51 F
735 756 3.135530 AGGATGATTAAGAGGCTGGTCAC 59.864 47.826 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1085 1152 2.239341 TTCTACATGCGCGCACAAGC 62.239 55.000 39.05 3.38 37.42 4.01 R
1905 1986 3.337358 TGTCCAATGCAGACATACAGTG 58.663 45.455 3.31 0.00 39.29 3.66 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
36 37 2.538790 TGCACTTTCCTGGTGGAGA 58.461 52.632 0.00 0.00 44.24 3.71
50 51 4.079253 TGGTGGAGAAGGAGCAAAATAAC 58.921 43.478 0.00 0.00 0.00 1.89
115 116 9.224267 TCAATTCTTTGTTTTGGTTTGAAATGA 57.776 25.926 0.00 0.00 34.32 2.57
196 200 4.036262 TCAGTTTTGTATTCTGTGTGTGCC 59.964 41.667 0.00 0.00 0.00 5.01
203 207 1.953559 TTCTGTGTGTGCCTTCAGTC 58.046 50.000 0.00 0.00 0.00 3.51
219 223 6.707608 GCCTTCAGTCAATCCTTCAAAATTTT 59.292 34.615 0.00 0.00 0.00 1.82
570 589 8.877864 TTTAATGTTTCCTGTTCTCCATATGT 57.122 30.769 1.24 0.00 0.00 2.29
571 590 8.506168 TTAATGTTTCCTGTTCTCCATATGTC 57.494 34.615 1.24 0.00 0.00 3.06
595 615 8.851416 GTCGTTAGTGTATAATAGCTGCTAATG 58.149 37.037 14.13 0.67 0.00 1.90
616 637 5.499139 TGTTTGCCTTCTGTACTTCTTTG 57.501 39.130 0.00 0.00 0.00 2.77
663 684 8.713708 AGTAGGACAATGCTAGATATAACTGT 57.286 34.615 0.00 0.00 0.00 3.55
735 756 3.135530 AGGATGATTAAGAGGCTGGTCAC 59.864 47.826 0.00 0.00 0.00 3.67
810 875 6.555360 CCTCCTTTAGGCTATCCTCTTTCTTA 59.445 42.308 0.00 0.00 43.06 2.10
894 959 8.477984 TTTCAAGTTGTTCTTTCCATTTTCTG 57.522 30.769 2.11 0.00 33.63 3.02
899 964 7.203218 AGTTGTTCTTTCCATTTTCTGTAAGC 58.797 34.615 0.00 0.00 0.00 3.09
1350 1418 7.878127 TCACCTTCTTATTTGTTCTCAGGTTAG 59.122 37.037 0.00 0.00 0.00 2.34
1353 1421 9.067986 CCTTCTTATTTGTTCTCAGGTTAGTTT 57.932 33.333 0.00 0.00 0.00 2.66
1486 1563 4.450976 TGACTGTTGTGTGCACTTCTTAT 58.549 39.130 19.41 0.00 0.00 1.73
1539 1618 6.542370 TCAGAAAAGAAAGAGACGGTTCAATT 59.458 34.615 0.00 0.00 0.00 2.32
1856 1935 8.971321 CAATGGTGCTAATGTTATGCTTATTTC 58.029 33.333 0.00 0.00 0.00 2.17
1905 1986 8.534778 CAAAATCTGCTTGAAGTTTTAACTGTC 58.465 33.333 0.00 0.00 39.66 3.51
1925 2006 3.372206 GTCACTGTATGTCTGCATTGGAC 59.628 47.826 0.00 0.00 36.58 4.02
1936 2017 3.258872 TCTGCATTGGACAATTTCTTGGG 59.741 43.478 0.00 0.00 36.64 4.12
1947 2028 5.018809 ACAATTTCTTGGGCTCATGTACAT 58.981 37.500 1.41 1.41 36.64 2.29
2006 2087 4.589216 TTCTTCTCAAAACAAGCCCATG 57.411 40.909 0.00 0.00 0.00 3.66
2028 2109 5.624159 TGGGAAGTATAATCAGGCATCTTG 58.376 41.667 0.00 0.00 0.00 3.02
2087 2168 4.281657 TGATATATCTGGATGGTCCGAGG 58.718 47.826 13.79 0.00 40.17 4.63
2155 2237 3.745797 GCCCTCCAGATTGTAGGAATGAC 60.746 52.174 0.00 0.00 32.57 3.06
2157 2239 3.455910 CCTCCAGATTGTAGGAATGACCA 59.544 47.826 0.00 0.00 42.04 4.02
2234 2316 8.045176 ACATACCTTCTAGCTCAATTTTTGTC 57.955 34.615 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.013050 GCCTCTGAGTTATTTTGCTCCTT 58.987 43.478 3.66 0.00 0.00 3.36
115 116 7.589993 ACAATCAAATAGGAGGAATTGAGGAT 58.410 34.615 0.00 0.00 35.47 3.24
219 223 7.037873 AGCCCTTTATAAACCCGATGTATCATA 60.038 37.037 0.00 0.00 0.00 2.15
570 589 8.573885 ACATTAGCAGCTATTATACACTAACGA 58.426 33.333 2.02 0.00 0.00 3.85
571 590 8.744008 ACATTAGCAGCTATTATACACTAACG 57.256 34.615 2.02 0.00 0.00 3.18
595 615 4.578928 TCCAAAGAAGTACAGAAGGCAAAC 59.421 41.667 0.00 0.00 0.00 2.93
616 637 5.241728 ACTCTTACCTTCAACAGCATTTTCC 59.758 40.000 0.00 0.00 0.00 3.13
663 684 3.889815 ACCTTCAGCAGCATATTAGCAA 58.110 40.909 0.00 0.00 36.85 3.91
735 756 3.181487 CCCAGTCAATTTATTTCCAGCCG 60.181 47.826 0.00 0.00 0.00 5.52
810 875 9.699410 TGAATAGGAGACAATAATTTCCAACAT 57.301 29.630 0.00 0.00 32.02 2.71
894 959 4.195225 ACTAACTGAAGGAGCTGCTTAC 57.805 45.455 21.43 14.29 0.00 2.34
899 964 4.399004 AGCATACTAACTGAAGGAGCTG 57.601 45.455 0.00 0.00 0.00 4.24
1085 1152 2.239341 TTCTACATGCGCGCACAAGC 62.239 55.000 39.05 3.38 37.42 4.01
1350 1418 5.536538 AGATGGGTTGAAAGAAGAAGGAAAC 59.463 40.000 0.00 0.00 0.00 2.78
1353 1421 4.599241 AGAGATGGGTTGAAAGAAGAAGGA 59.401 41.667 0.00 0.00 0.00 3.36
1467 1544 5.422666 TCAATAAGAAGTGCACACAACAG 57.577 39.130 21.04 1.79 0.00 3.16
1486 1563 7.615365 AGCAAATAACACTGGGATAATCTTCAA 59.385 33.333 0.00 0.00 0.00 2.69
1539 1618 5.358922 TCGATGTGATGATATGAAGCACAA 58.641 37.500 9.43 0.00 42.03 3.33
1789 1868 9.896263 GGACAAAATAACATGCAAATCAAAATT 57.104 25.926 0.00 0.00 0.00 1.82
1905 1986 3.337358 TGTCCAATGCAGACATACAGTG 58.663 45.455 3.31 0.00 39.29 3.66
1925 2006 5.587388 ATGTACATGAGCCCAAGAAATTG 57.413 39.130 7.78 0.00 0.00 2.32
1936 2017 4.274214 TCATGCAAGCTAATGTACATGAGC 59.726 41.667 30.80 30.80 44.12 4.26
1947 2028 5.622914 GCCAAGAAAAGATCATGCAAGCTAA 60.623 40.000 0.00 0.00 0.00 3.09
2006 2087 5.869579 TCAAGATGCCTGATTATACTTCCC 58.130 41.667 0.00 0.00 0.00 3.97
2028 2109 5.043248 TGCTAAAAGAAACTTTTGCAGCTC 58.957 37.500 21.40 5.87 40.48 4.09
2155 2237 6.092955 AGCATACATAGGAATTTTGCATGG 57.907 37.500 0.00 0.00 0.00 3.66
2157 2239 5.987347 GCAAGCATACATAGGAATTTTGCAT 59.013 36.000 0.00 0.00 38.50 3.96


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

AutoCloner maintained by Alex Coulton.