Multiple sequence alignment - TraesCS5D01G343800

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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 TraesCS5D01G343800 chr5D 100.000 2330 0 0 1 2330 431628432 431626103 0.000000e+00 4303
1 TraesCS5D01G343800 chr5D 97.674 860 14 1 1 854 431634406 431633547 0.000000e+00 1472
2 TraesCS5D01G343800 chr5B 91.463 1476 76 19 891 2330 522499081 522500542 0.000000e+00 1982
3 TraesCS5D01G343800 chr5B 96.516 861 22 5 1 854 521249088 521248229 0.000000e+00 1417
4 TraesCS5D01G343800 chr5B 94.118 731 22 5 950 1674 521241486 521240771 0.000000e+00 1092
5 TraesCS5D01G343800 chr5B 95.833 240 10 0 2091 2330 521240772 521240533 2.810000e-104 388
6 TraesCS5D01G343800 chr6B 96.283 861 25 2 1 854 312031772 312032632 0.000000e+00 1406
7 TraesCS5D01G343800 chr6B 95.819 861 26 3 1 854 369609738 369608881 0.000000e+00 1382
8 TraesCS5D01G343800 chr6B 95.703 861 30 2 1 854 563534834 563535694 0.000000e+00 1378
9 TraesCS5D01G343800 chr6B 95.597 863 31 2 1 856 411200145 411199283 0.000000e+00 1376
10 TraesCS5D01G343800 chr6B 95.688 858 30 2 1 851 668227933 668228790 0.000000e+00 1373
11 TraesCS5D01G343800 chr4B 95.481 863 32 3 1 856 273471394 273470532 0.000000e+00 1371
12 TraesCS5D01G343800 chr1B 94.892 881 32 7 1 871 605485439 605484562 0.000000e+00 1365
13 TraesCS5D01G343800 chr5A 91.039 770 38 10 1584 2330 546885599 546886360 0.000000e+00 1011
14 TraesCS5D01G343800 chr5A 91.257 732 40 12 870 1590 546722966 546722248 0.000000e+00 976
15 TraesCS5D01G343800 chr5A 90.450 733 53 8 870 1594 546884853 546885576 0.000000e+00 950
16 TraesCS5D01G343800 chr5A 93.950 562 24 7 1641 2196 546718613 546718056 0.000000e+00 841
17 TraesCS5D01G343800 chr5A 91.912 136 10 1 2196 2330 546715123 546714988 3.060000e-44 189
18 TraesCS5D01G343800 chr1A 90.948 232 18 2 1684 1913 259970193 259969963 2.250000e-80 309
19 TraesCS5D01G343800 chr1D 87.603 242 14 7 1684 1921 204224161 204223932 1.370000e-67 267


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 TraesCS5D01G343800 chr5D 431626103 431628432 2329 True 4303.000000 4303 100.0000 1 2330 1 chr5D.!!$R1 2329
1 TraesCS5D01G343800 chr5D 431633547 431634406 859 True 1472.000000 1472 97.6740 1 854 1 chr5D.!!$R2 853
2 TraesCS5D01G343800 chr5B 522499081 522500542 1461 False 1982.000000 1982 91.4630 891 2330 1 chr5B.!!$F1 1439
3 TraesCS5D01G343800 chr5B 521248229 521249088 859 True 1417.000000 1417 96.5160 1 854 1 chr5B.!!$R1 853
4 TraesCS5D01G343800 chr5B 521240533 521241486 953 True 740.000000 1092 94.9755 950 2330 2 chr5B.!!$R2 1380
5 TraesCS5D01G343800 chr6B 312031772 312032632 860 False 1406.000000 1406 96.2830 1 854 1 chr6B.!!$F1 853
6 TraesCS5D01G343800 chr6B 369608881 369609738 857 True 1382.000000 1382 95.8190 1 854 1 chr6B.!!$R1 853
7 TraesCS5D01G343800 chr6B 563534834 563535694 860 False 1378.000000 1378 95.7030 1 854 1 chr6B.!!$F2 853
8 TraesCS5D01G343800 chr6B 411199283 411200145 862 True 1376.000000 1376 95.5970 1 856 1 chr6B.!!$R2 855
9 TraesCS5D01G343800 chr6B 668227933 668228790 857 False 1373.000000 1373 95.6880 1 851 1 chr6B.!!$F3 850
10 TraesCS5D01G343800 chr4B 273470532 273471394 862 True 1371.000000 1371 95.4810 1 856 1 chr4B.!!$R1 855
11 TraesCS5D01G343800 chr1B 605484562 605485439 877 True 1365.000000 1365 94.8920 1 871 1 chr1B.!!$R1 870
12 TraesCS5D01G343800 chr5A 546884853 546886360 1507 False 980.500000 1011 90.7445 870 2330 2 chr5A.!!$F1 1460
13 TraesCS5D01G343800 chr5A 546714988 546722966 7978 True 668.666667 976 92.3730 870 2330 3 chr5A.!!$R1 1460

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
743 750 3.381335 TCTCCACCTCCCTATGTTTACC 58.619 50.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 5283 0.671251 GGACATGTTTCGCACCCAAA 59.329 50.0 0.0 0.0 0.0 3.28 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
195 196 5.245531 TGCATTTATTGAGAAAGTCTCCGT 58.754 37.500 2.91 0.00 42.73 4.69
732 739 5.005628 AGAGGAACTATATCTCCACCTCC 57.994 47.826 0.00 0.00 41.55 4.30
741 748 7.776745 ACTATATCTCCACCTCCCTATGTTTA 58.223 38.462 0.00 0.00 0.00 2.01
743 750 3.381335 TCTCCACCTCCCTATGTTTACC 58.619 50.000 0.00 0.00 0.00 2.85
764 771 4.393062 ACCACACGATAGAATTGCAAGAAG 59.607 41.667 4.94 0.00 41.38 2.85
857 865 8.804912 AGGAAGAGAGTTAGACTTCGTTATAA 57.195 34.615 0.00 0.00 40.29 0.98
858 866 9.411189 AGGAAGAGAGTTAGACTTCGTTATAAT 57.589 33.333 0.00 0.00 40.29 1.28
859 867 9.453325 GGAAGAGAGTTAGACTTCGTTATAATG 57.547 37.037 0.00 0.00 40.29 1.90
925 933 5.277586 CGCTCTCTTCTACCTATACTGTGTG 60.278 48.000 0.00 0.00 0.00 3.82
926 934 5.591067 GCTCTCTTCTACCTATACTGTGTGT 59.409 44.000 0.00 0.00 0.00 3.72
1094 1110 0.962356 ACTCGATTGCCTTGCCCTTG 60.962 55.000 0.00 0.00 0.00 3.61
1117 1133 3.832490 TCTTTTCCATCTCTCTTCCACGA 59.168 43.478 0.00 0.00 0.00 4.35
1202 1223 1.399791 GCAAGAGCAATTCTTCTCCCG 59.600 52.381 0.00 0.00 44.34 5.14
1219 1240 0.397941 CCGGATATGCATGGACTGGT 59.602 55.000 10.16 0.00 0.00 4.00
1355 1382 6.330178 ACTAGGATGTGGTTAGAGAGTAGT 57.670 41.667 0.00 0.00 0.00 2.73
1356 1383 7.448915 ACTAGGATGTGGTTAGAGAGTAGTA 57.551 40.000 0.00 0.00 0.00 1.82
1357 1384 7.281841 ACTAGGATGTGGTTAGAGAGTAGTAC 58.718 42.308 0.00 0.00 0.00 2.73
1381 1408 8.567285 ACTAGCTGCTAATAAATTGACAGTTT 57.433 30.769 11.02 1.32 0.00 2.66
1454 1483 3.242446 GCTTGATCGCTAGTTTTAGGTGC 60.242 47.826 0.00 0.00 0.00 5.01
1494 1523 6.316890 TGTGTTGTGTTTTACTTTACCTCTCC 59.683 38.462 0.00 0.00 0.00 3.71
1635 5240 5.809001 TGCTTAGATCCAACAAATCTCACT 58.191 37.500 0.00 0.00 35.20 3.41
1657 5283 6.547141 CACTCATCTCTCTACTTCCTCAATCT 59.453 42.308 0.00 0.00 0.00 2.40
1678 5304 0.466372 TGGGTGCGAAACATGTCCAA 60.466 50.000 0.00 0.00 0.00 3.53
1690 5316 1.171308 ATGTCCAACATGCTCAGCAC 58.829 50.000 0.00 0.00 43.04 4.40
2116 5747 7.617723 TGGTAACCAATCACTAGCCAATATTTT 59.382 33.333 0.00 0.00 0.00 1.82
2231 8797 2.037251 AGTAAGTGCAGACATCCAACGT 59.963 45.455 0.00 0.00 0.00 3.99
2237 8803 3.307242 GTGCAGACATCCAACGTATCTTC 59.693 47.826 0.00 0.00 0.00 2.87
2247 8813 9.396022 ACATCCAACGTATCTTCTTGATTTAAT 57.604 29.630 0.00 0.00 36.65 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 7.953005 TCAATCTCATAAGCACCCATAAAAA 57.047 32.000 0.00 0.00 0.00 1.94
195 196 8.730680 GCAAAATATTAGTCTCTTCTTGGACAA 58.269 33.333 0.00 0.00 35.18 3.18
732 739 7.518370 GCAATTCTATCGTGTGGTAAACATAGG 60.518 40.741 0.00 0.00 41.97 2.57
741 748 3.937814 TCTTGCAATTCTATCGTGTGGT 58.062 40.909 0.00 0.00 0.00 4.16
743 750 4.093998 AGCTTCTTGCAATTCTATCGTGTG 59.906 41.667 0.00 0.00 45.94 3.82
925 933 3.543548 GCACTCTGCGAGACACAC 58.456 61.111 11.64 0.00 31.71 3.82
1094 1110 3.929610 CGTGGAAGAGAGATGGAAAAGAC 59.070 47.826 0.00 0.00 0.00 3.01
1202 1223 2.620115 CACAACCAGTCCATGCATATCC 59.380 50.000 0.00 0.00 0.00 2.59
1355 1382 9.667107 AAACTGTCAATTTATTAGCAGCTAGTA 57.333 29.630 1.49 0.97 0.00 1.82
1356 1383 8.454106 CAAACTGTCAATTTATTAGCAGCTAGT 58.546 33.333 1.49 2.07 0.00 2.57
1357 1384 8.668353 TCAAACTGTCAATTTATTAGCAGCTAG 58.332 33.333 1.49 0.00 0.00 3.42
1381 1408 4.339247 TGAGCGATACAGATGAACATCTCA 59.661 41.667 13.47 6.29 45.78 3.27
1454 1483 3.243035 ACAACACAACAACATGGTCATCG 60.243 43.478 0.00 0.00 0.00 3.84
1494 1523 4.704540 TCAACCAATATACAACCAAGGCAG 59.295 41.667 0.00 0.00 0.00 4.85
1635 5240 7.147759 CCAAAGATTGAGGAAGTAGAGAGATGA 60.148 40.741 0.00 0.00 0.00 2.92
1657 5283 0.671251 GGACATGTTTCGCACCCAAA 59.329 50.000 0.00 0.00 0.00 3.28
1690 5316 1.461127 GTGAAAGCAGTCCGCAAGTAG 59.539 52.381 0.00 0.00 46.13 2.57
2116 5747 5.237048 GGATGCTAAAATTTGACAAAGGCA 58.763 37.500 6.77 10.96 0.00 4.75
2237 8803 8.454106 CGAGGAAATATAGGCCATTAAATCAAG 58.546 37.037 5.01 0.00 0.00 3.02
2247 8813 5.367945 AAAAGTCGAGGAAATATAGGCCA 57.632 39.130 5.01 0.00 0.00 5.36
2287 8853 7.734924 ATGATAATGATAACATTGAGCGTGT 57.265 32.000 8.38 0.00 44.97 4.49


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

AutoCloner maintained by Alex Coulton.