Multiple sequence alignment - TraesCS1B01G355000

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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 TraesCS1B01G355000 chr1B 100.000 3092 0 0 1 3092 584619439 584622530 0.000000e+00 5710.0
1 TraesCS1B01G355000 chr1B 98.804 3093 23 3 1 3092 584574078 584577157 0.000000e+00 5494.0
2 TraesCS1B01G355000 chr1B 88.779 2023 113 36 386 2369 584778732 584780679 0.000000e+00 2374.0
3 TraesCS1B01G355000 chr1B 87.759 1928 150 40 645 2543 584603477 584605347 0.000000e+00 2176.0
4 TraesCS1B01G355000 chr1B 86.150 2065 142 49 386 2400 584761445 584763415 0.000000e+00 2097.0
5 TraesCS1B01G355000 chr1B 87.642 1853 155 38 645 2477 584653911 584655709 0.000000e+00 2085.0
6 TraesCS1B01G355000 chr1B 89.108 1570 90 23 835 2369 584797948 584799471 0.000000e+00 1877.0
7 TraesCS1B01G355000 chr1B 90.370 1028 70 16 1525 2543 584566230 584567237 0.000000e+00 1323.0
8 TraesCS1B01G355000 chr1B 97.840 324 7 0 2769 3092 584538281 584538604 7.490000e-156 560.0
9 TraesCS1B01G355000 chr1B 87.660 470 25 15 386 846 584797095 584797540 1.640000e-142 516.0
10 TraesCS1B01G355000 chr1B 94.737 285 12 1 403 687 584752447 584752728 1.020000e-119 440.0
11 TraesCS1B01G355000 chr1B 89.130 276 29 1 11 285 584752173 584752448 2.950000e-90 342.0
12 TraesCS1B01G355000 chr1B 83.575 207 32 1 2540 2746 664609894 664609690 3.150000e-45 193.0
13 TraesCS1B01G355000 chr1D 88.986 2052 135 43 372 2378 433092019 433094024 0.000000e+00 2453.0
14 TraesCS1B01G355000 chr1D 89.771 1789 116 33 721 2503 433060330 433062057 0.000000e+00 2228.0
15 TraesCS1B01G355000 chr1D 91.525 295 21 4 39 332 433091732 433092023 1.340000e-108 403.0
16 TraesCS1B01G355000 chr1D 89.610 77 8 0 209 285 433129493 433129569 7.060000e-17 99.0
17 TraesCS1B01G355000 chr1A 89.785 1674 96 32 845 2500 531366891 531368507 0.000000e+00 2074.0
18 TraesCS1B01G355000 chr1A 91.504 1436 90 14 978 2402 531513133 531514547 0.000000e+00 1947.0
19 TraesCS1B01G355000 chr1A 90.377 1434 110 21 978 2402 531561962 531563376 0.000000e+00 1858.0
20 TraesCS1B01G355000 chr1A 88.889 828 58 17 17 841 531561106 531561902 0.000000e+00 989.0
21 TraesCS1B01G355000 chr1A 90.923 650 47 10 11 655 531501619 531502261 0.000000e+00 863.0
22 TraesCS1B01G355000 chr1A 85.714 266 13 7 617 876 531502261 531502507 1.100000e-64 257.0
23 TraesCS1B01G355000 chr1A 84.259 108 8 7 434 532 531510042 531510149 2.540000e-16 97.1
24 TraesCS1B01G355000 chr1A 91.837 49 2 1 2495 2541 24130321 24130369 1.990000e-07 67.6
25 TraesCS1B01G355000 chr3B 82.273 1997 216 82 384 2321 647944507 647942590 0.000000e+00 1600.0
26 TraesCS1B01G355000 chr3B 78.979 1156 130 63 384 1499 647969914 647968832 0.000000e+00 684.0
27 TraesCS1B01G355000 chr3B 84.058 207 31 1 2540 2746 697080622 697080826 6.760000e-47 198.0
28 TraesCS1B01G355000 chr3B 100.000 39 0 0 2505 2543 571808570 571808532 4.280000e-09 73.1
29 TraesCS1B01G355000 chr3A 82.050 2000 208 87 384 2321 628220798 628218888 0.000000e+00 1565.0
30 TraesCS1B01G355000 chr6A 84.698 562 65 10 963 1518 616689143 616688597 2.710000e-150 542.0
31 TraesCS1B01G355000 chr6A 92.105 76 6 0 812 887 616689241 616689166 1.170000e-19 108.0
32 TraesCS1B01G355000 chr7D 84.058 207 31 1 2540 2746 536119056 536118852 6.760000e-47 198.0
33 TraesCS1B01G355000 chr5B 84.390 205 28 3 2543 2746 404146006 404145805 6.760000e-47 198.0
34 TraesCS1B01G355000 chr4A 84.058 207 31 1 2540 2746 742969159 742968955 6.760000e-47 198.0
35 TraesCS1B01G355000 chr4A 83.575 207 32 1 2540 2746 727800057 727800261 3.150000e-45 193.0
36 TraesCS1B01G355000 chr2D 84.058 207 31 1 2540 2746 91799111 91798907 6.760000e-47 198.0
37 TraesCS1B01G355000 chr2D 100.000 39 0 0 2505 2543 326362689 326362727 4.280000e-09 73.1
38 TraesCS1B01G355000 chr5A 83.575 207 32 1 2540 2746 563891866 563891662 3.150000e-45 193.0
39 TraesCS1B01G355000 chr3D 76.955 243 41 9 2505 2746 487249379 487249151 1.160000e-24 124.0
40 TraesCS1B01G355000 chr3D 100.000 39 0 0 2505 2543 488391436 488391398 4.280000e-09 73.1
41 TraesCS1B01G355000 chr2A 100.000 39 0 0 2505 2543 391353312 391353274 4.280000e-09 73.1


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 TraesCS1B01G355000 chr1B 584619439 584622530 3091 False 5710.00 5710 100.0000 1 3092 1 chr1B.!!$F5 3091
1 TraesCS1B01G355000 chr1B 584574078 584577157 3079 False 5494.00 5494 98.8040 1 3092 1 chr1B.!!$F3 3091
2 TraesCS1B01G355000 chr1B 584778732 584780679 1947 False 2374.00 2374 88.7790 386 2369 1 chr1B.!!$F8 1983
3 TraesCS1B01G355000 chr1B 584603477 584605347 1870 False 2176.00 2176 87.7590 645 2543 1 chr1B.!!$F4 1898
4 TraesCS1B01G355000 chr1B 584761445 584763415 1970 False 2097.00 2097 86.1500 386 2400 1 chr1B.!!$F7 2014
5 TraesCS1B01G355000 chr1B 584653911 584655709 1798 False 2085.00 2085 87.6420 645 2477 1 chr1B.!!$F6 1832
6 TraesCS1B01G355000 chr1B 584566230 584567237 1007 False 1323.00 1323 90.3700 1525 2543 1 chr1B.!!$F2 1018
7 TraesCS1B01G355000 chr1B 584797095 584799471 2376 False 1196.50 1877 88.3840 386 2369 2 chr1B.!!$F10 1983
8 TraesCS1B01G355000 chr1B 584752173 584752728 555 False 391.00 440 91.9335 11 687 2 chr1B.!!$F9 676
9 TraesCS1B01G355000 chr1D 433060330 433062057 1727 False 2228.00 2228 89.7710 721 2503 1 chr1D.!!$F1 1782
10 TraesCS1B01G355000 chr1D 433091732 433094024 2292 False 1428.00 2453 90.2555 39 2378 2 chr1D.!!$F3 2339
11 TraesCS1B01G355000 chr1A 531366891 531368507 1616 False 2074.00 2074 89.7850 845 2500 1 chr1A.!!$F2 1655
12 TraesCS1B01G355000 chr1A 531561106 531563376 2270 False 1423.50 1858 89.6330 17 2402 2 chr1A.!!$F5 2385
13 TraesCS1B01G355000 chr1A 531510042 531514547 4505 False 1022.05 1947 87.8815 434 2402 2 chr1A.!!$F4 1968
14 TraesCS1B01G355000 chr1A 531501619 531502507 888 False 560.00 863 88.3185 11 876 2 chr1A.!!$F3 865
15 TraesCS1B01G355000 chr3B 647942590 647944507 1917 True 1600.00 1600 82.2730 384 2321 1 chr3B.!!$R2 1937
16 TraesCS1B01G355000 chr3B 647968832 647969914 1082 True 684.00 684 78.9790 384 1499 1 chr3B.!!$R3 1115
17 TraesCS1B01G355000 chr3A 628218888 628220798 1910 True 1565.00 1565 82.0500 384 2321 1 chr3A.!!$R1 1937
18 TraesCS1B01G355000 chr6A 616688597 616689241 644 True 325.00 542 88.4015 812 1518 2 chr6A.!!$R1 706

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
1999 5136 0.25077 GTGGTGGGAGGACAAGTTCC 60.251 60.0 0.0 0.0 46.33 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2924 6133 1.896465 AGCGTCCAGAGCTAGTTTTCT 59.104 47.619 0.0 0.0 44.05 2.52 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
1999 5136 0.250770 GTGGTGGGAGGACAAGTTCC 60.251 60.000 0.00 0.0 46.33 3.62
2071 5208 1.649664 CCAGATCAGGAAGAACTGCG 58.350 55.000 0.00 0.0 43.60 5.18
2234 5439 2.119457 CTGCGTGCCTTTGTTCTTTTC 58.881 47.619 0.00 0.0 0.00 2.29
2477 5686 2.611971 CGATGACCGGAAAAGGAACTGA 60.612 50.000 9.46 0.0 34.09 3.41
2564 5773 3.565482 TGCTCGCATTATTCCTGGATTTC 59.435 43.478 0.00 0.0 0.00 2.17
2604 5813 0.038159 CGTGTTCAGTGGGAGGAGAC 60.038 60.000 0.00 0.0 0.00 3.36
2608 5817 0.966920 TTCAGTGGGAGGAGACGTTC 59.033 55.000 0.00 0.0 0.00 3.95
2676 5885 8.099537 AGATGATATGTGTCAGTTCAGTCTTTT 58.900 33.333 0.00 0.0 0.00 2.27
2942 6151 5.411781 ACAATAGAAAACTAGCTCTGGACG 58.588 41.667 0.00 0.0 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1999 5136 2.022195 CATCTTCACCATGGCCTTCTG 58.978 52.381 13.04 1.70 0.00 3.02
2071 5208 2.018542 TAGTAGTGGTTGATTGCGCC 57.981 50.000 4.18 0.00 0.00 6.53
2234 5439 9.793252 CTAGAATTGAACCATGAATAACCAAAG 57.207 33.333 0.00 0.00 0.00 2.77
2564 5773 3.354397 GCATCGCCGAAAATCTTACAAG 58.646 45.455 0.00 0.00 0.00 3.16
2604 5813 0.029035 CCTCGTAGTCGATGGGAACG 59.971 60.000 0.00 0.00 45.21 3.95
2608 5817 1.065928 GTGCCTCGTAGTCGATGGG 59.934 63.158 0.00 0.00 45.21 4.00
2611 5820 0.680280 ACTGGTGCCTCGTAGTCGAT 60.680 55.000 0.00 0.00 45.21 3.59
2626 5835 3.480470 AGATTGACAAAGTCACCACTGG 58.520 45.455 0.00 0.00 42.60 4.00
2676 5885 2.696707 CCTACCGGTATAAGCACTTCCA 59.303 50.000 16.25 0.00 0.00 3.53
2765 5974 2.568090 CGGTTCATGGCCAAGTGC 59.432 61.111 10.96 2.48 40.16 4.40
2896 6105 8.614469 TGTTTTTGGACTTTTCAGAAAAACAT 57.386 26.923 14.04 0.00 42.94 2.71
2897 6106 8.438676 TTGTTTTTGGACTTTTCAGAAAAACA 57.561 26.923 14.04 14.04 44.27 2.83
2915 6124 8.568794 GTCCAGAGCTAGTTTTCTATTGTTTTT 58.431 33.333 0.00 0.00 0.00 1.94
2924 6133 1.896465 AGCGTCCAGAGCTAGTTTTCT 59.104 47.619 0.00 0.00 44.05 2.52
3044 6253 6.221659 TCAGCATGCTCTCTAATATGTCTTG 58.778 40.000 19.68 1.29 34.76 3.02


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

AutoCloner maintained by Alex Coulton.