Multiple sequence alignment - TraesCS4D01G031000

Loading Multiple Alignment...

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 TraesCS4D01G031000 chr4D 100.000 2401 0 0 1 2401 14568682 14571082 0 4434
1 TraesCS4D01G031000 chr4D 85.791 2407 330 10 1 2401 449477952 449480352 0 2540
2 TraesCS4D01G031000 chr5A 92.590 2402 163 3 1 2401 293443244 293440857 0 3435
3 TraesCS4D01G031000 chr2B 91.639 2404 198 2 1 2401 59268724 59266321 0 3323
4 TraesCS4D01G031000 chr2B 86.088 2408 325 10 1 2401 795837360 795834956 0 2582
5 TraesCS4D01G031000 chr3D 87.099 2403 308 2 1 2401 541366144 541368546 0 2719
6 TraesCS4D01G031000 chr2D 86.891 2403 312 3 1 2401 293043073 293040672 0 2689
7 TraesCS4D01G031000 chr2D 87.121 2112 271 1 291 2401 13660499 13658388 0 2392
8 TraesCS4D01G031000 chr7A 85.774 2397 336 5 8 2401 637830266 637832660 0 2532
9 TraesCS4D01G031000 chr6B 83.534 2405 391 5 1 2401 584656125 584653722 0 2242


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 TraesCS4D01G031000 chr4D 14568682 14571082 2400 False 4434 4434 100.000 1 2401 1 chr4D.!!$F1 2400
1 TraesCS4D01G031000 chr4D 449477952 449480352 2400 False 2540 2540 85.791 1 2401 1 chr4D.!!$F2 2400
2 TraesCS4D01G031000 chr5A 293440857 293443244 2387 True 3435 3435 92.590 1 2401 1 chr5A.!!$R1 2400
3 TraesCS4D01G031000 chr2B 59266321 59268724 2403 True 3323 3323 91.639 1 2401 1 chr2B.!!$R1 2400
4 TraesCS4D01G031000 chr2B 795834956 795837360 2404 True 2582 2582 86.088 1 2401 1 chr2B.!!$R2 2400
5 TraesCS4D01G031000 chr3D 541366144 541368546 2402 False 2719 2719 87.099 1 2401 1 chr3D.!!$F1 2400
6 TraesCS4D01G031000 chr2D 293040672 293043073 2401 True 2689 2689 86.891 1 2401 1 chr2D.!!$R2 2400
7 TraesCS4D01G031000 chr2D 13658388 13660499 2111 True 2392 2392 87.121 291 2401 1 chr2D.!!$R1 2110
8 TraesCS4D01G031000 chr7A 637830266 637832660 2394 False 2532 2532 85.774 8 2401 1 chr7A.!!$F1 2393
9 TraesCS4D01G031000 chr6B 584653722 584656125 2403 True 2242 2242 83.534 1 2401 1 chr6B.!!$R1 2400

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
972 977 0.601558 TACGGAGTTGGAGCAGTGTC 59.398 55.0 0.0 0.0 37.78 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 1808 0.8951 TGAATGGGTGCTGAAGTGGC 60.895 55.0 0.0 0.0 0.0 5.01 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
70 71 0.603569 CGTCCCTACAGACACAAGCT 59.396 55.000 0.00 0.00 36.52 3.74
97 99 4.808364 GCTCAAAAATGAGATAGAGCGTCT 59.192 41.667 9.89 0.00 39.04 4.18
366 370 5.549619 CAGAGGGGGAGGAATATAAGACAAT 59.450 44.000 0.00 0.00 0.00 2.71
424 428 2.166821 TGTCATTTGGTTTGGCATGC 57.833 45.000 9.90 9.90 0.00 4.06
436 440 3.673484 GCATGCGCACCACCAACT 61.673 61.111 14.90 0.00 38.36 3.16
458 462 0.723414 CATAGGCGCAGTGACTTGTG 59.277 55.000 10.83 0.00 0.00 3.33
528 532 9.959749 TGACATTTTGGTATTCAGTAAAACTTC 57.040 29.630 0.00 0.00 0.00 3.01
539 543 3.068560 AGTAAAACTTCGGCGCAACATA 58.931 40.909 10.83 0.00 0.00 2.29
656 660 1.285667 TGGGGCATGTGATTGATGAGT 59.714 47.619 0.00 0.00 0.00 3.41
827 831 9.071276 TCTTCAACTTGCTAAAGAAGAATCATT 57.929 29.630 0.00 0.00 41.01 2.57
972 977 0.601558 TACGGAGTTGGAGCAGTGTC 59.398 55.000 0.00 0.00 37.78 3.67
1005 1012 3.069289 GCATCCGATTGCATACATGAGA 58.931 45.455 0.00 0.00 42.31 3.27
1009 1016 6.675026 CATCCGATTGCATACATGAGAAAAT 58.325 36.000 0.00 0.00 0.00 1.82
1033 1041 2.045536 CTCCCAAGCACAGAGGGC 60.046 66.667 0.00 0.00 42.52 5.19
1124 1132 7.093988 ACACCATGATGAATTTTTGATACGGAA 60.094 33.333 0.00 0.00 0.00 4.30
1221 1229 5.010213 GCTTCTGGGGTTGTGTTACAAAATA 59.990 40.000 0.00 0.00 40.15 1.40
1570 1578 1.664649 CGTCTCCGCAAGCTGTTCA 60.665 57.895 0.00 0.00 0.00 3.18
1650 1658 5.763204 CCAACAAGCTAAACCAGAAAGAGTA 59.237 40.000 0.00 0.00 0.00 2.59
1800 1808 1.284657 CACGCTATGCTCACTTCCTG 58.715 55.000 0.00 0.00 0.00 3.86
2113 2121 5.930135 AGTTCTGTTACAATTCCAGTCACT 58.070 37.500 0.00 0.00 0.00 3.41
2204 2212 1.747709 GCATCAGTGTGCAAGATCCT 58.252 50.000 11.34 0.00 44.43 3.24
2211 2219 2.836981 AGTGTGCAAGATCCTAGAGCTT 59.163 45.455 0.00 0.00 38.93 3.74
2225 2233 1.630878 AGAGCTTAAGGAGTGGTTGGG 59.369 52.381 4.29 0.00 0.00 4.12
2369 2377 4.424430 GTTGCAGCCGTACGTGCG 62.424 66.667 19.61 19.61 42.96 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.383825 GGTTGAGCTCCCTCTATTAACGA 59.616 47.826 12.15 0.00 38.93 3.85
21 22 4.362677 ACTGGTTGAGCTCCCTCTATTAA 58.637 43.478 12.15 0.00 38.93 1.40
70 71 6.183360 ACGCTCTATCTCATTTTTGAGCTCTA 60.183 38.462 16.19 4.09 43.06 2.43
335 339 2.935481 CTCCCCCTCTGCCAACCA 60.935 66.667 0.00 0.00 0.00 3.67
366 370 2.701423 TGCCCTGAGTGTGTAGTAAACA 59.299 45.455 0.00 0.00 35.06 2.83
424 428 1.468520 CCTATGAAAGTTGGTGGTGCG 59.531 52.381 0.00 0.00 0.00 5.34
436 440 2.076100 CAAGTCACTGCGCCTATGAAA 58.924 47.619 4.18 0.00 0.00 2.69
528 532 0.662619 ATGTTCCATATGTTGCGCCG 59.337 50.000 4.18 0.00 0.00 6.46
539 543 2.936993 GCACCTGACGAAGATGTTCCAT 60.937 50.000 0.00 0.00 0.00 3.41
656 660 1.418264 TGGATCCGTTGAAACTCCACA 59.582 47.619 7.39 0.00 29.10 4.17
827 831 5.181811 CAGTTTCAGCAGTCCATACAAATGA 59.818 40.000 0.00 0.00 34.84 2.57
835 840 3.423539 TTAGCAGTTTCAGCAGTCCAT 57.576 42.857 0.00 0.00 0.00 3.41
1005 1012 0.603065 GCTTGGGAGCCAACGATTTT 59.397 50.000 0.00 0.00 43.29 1.82
1033 1041 4.378459 GCATTCCTTTTCGTAAGTGGACAG 60.378 45.833 0.00 0.00 39.48 3.51
1124 1132 1.671845 GGACGAGACTACGCTGATCTT 59.328 52.381 0.00 0.00 36.70 2.40
1221 1229 0.538516 TTGCACCTTGCCGGTAACAT 60.539 50.000 0.00 0.00 46.94 2.71
1264 1272 4.812476 TTCATGGCGACGGCGAGG 62.812 66.667 18.90 5.63 41.24 4.63
1570 1578 0.471591 TGCTTCATTTTGGGCCAGGT 60.472 50.000 6.23 0.00 0.00 4.00
1650 1658 5.485620 GGTTCGAGTAAACCTGGATACTTT 58.514 41.667 14.81 2.71 44.45 2.66
1800 1808 0.895100 TGAATGGGTGCTGAAGTGGC 60.895 55.000 0.00 0.00 0.00 5.01
2097 2105 4.619863 GCCGAGTAGTGACTGGAATTGTAA 60.620 45.833 0.00 0.00 35.45 2.41
2113 2121 3.592059 GTGACATGTTTAAGGCCGAGTA 58.408 45.455 0.00 0.00 0.00 2.59
2204 2212 2.838202 CCCAACCACTCCTTAAGCTCTA 59.162 50.000 0.00 0.00 0.00 2.43
2211 2219 1.708551 CTTTCCCCCAACCACTCCTTA 59.291 52.381 0.00 0.00 0.00 2.69
2225 2233 1.546029 GTTGCATGGTCTTCCTTTCCC 59.454 52.381 0.00 0.00 34.23 3.97
2338 2346 3.419915 GCTGCAACTTGACGAATACATG 58.580 45.455 0.00 0.00 0.00 3.21
2369 2377 3.188786 GGCGATGCACTGACGACC 61.189 66.667 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.