Multiple sequence alignment - TraesCS4A01G144800

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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 TraesCS4A01G144800 chr4A 100.000 2594 0 0 1 2594 246658659 246656066 0 4791
1 TraesCS4A01G144800 chr7D 98.306 2598 40 4 1 2594 381923965 381926562 0 4551
2 TraesCS4A01G144800 chr7D 98.229 2598 42 4 1 2594 203499963 203502560 0 4540
3 TraesCS4A01G144800 chr7D 98.153 2599 43 4 1 2594 382050042 382052640 0 4529
4 TraesCS4A01G144800 chr7D 97.964 2603 41 6 1 2594 381973803 381971204 0 4503
5 TraesCS4A01G144800 chr5A 98.307 2599 39 4 1 2594 19248880 19246282 0 4551
6 TraesCS4A01G144800 chr6D 98.037 2598 47 4 1 2594 124517486 124520083 0 4512
7 TraesCS4A01G144800 chr7B 97.959 2597 45 4 1 2594 716878816 716876225 0 4495
8 TraesCS4A01G144800 chr1A 97.768 2598 49 5 1 2594 498691263 498688671 0 4468


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 TraesCS4A01G144800 chr4A 246656066 246658659 2593 True 4791 4791 100.000 1 2594 1 chr4A.!!$R1 2593
1 TraesCS4A01G144800 chr7D 381923965 381926562 2597 False 4551 4551 98.306 1 2594 1 chr7D.!!$F2 2593
2 TraesCS4A01G144800 chr7D 203499963 203502560 2597 False 4540 4540 98.229 1 2594 1 chr7D.!!$F1 2593
3 TraesCS4A01G144800 chr7D 382050042 382052640 2598 False 4529 4529 98.153 1 2594 1 chr7D.!!$F3 2593
4 TraesCS4A01G144800 chr7D 381971204 381973803 2599 True 4503 4503 97.964 1 2594 1 chr7D.!!$R1 2593
5 TraesCS4A01G144800 chr5A 19246282 19248880 2598 True 4551 4551 98.307 1 2594 1 chr5A.!!$R1 2593
6 TraesCS4A01G144800 chr6D 124517486 124520083 2597 False 4512 4512 98.037 1 2594 1 chr6D.!!$F1 2593
7 TraesCS4A01G144800 chr7B 716876225 716878816 2591 True 4495 4495 97.959 1 2594 1 chr7B.!!$R1 2593
8 TraesCS4A01G144800 chr1A 498688671 498691263 2592 True 4468 4468 97.768 1 2594 1 chr1A.!!$R1 2593

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
664 668 1.078214 GGTCCATGTAGCTGCTGCA 60.078 57.895 22.3 22.3 42.74 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2464 2475 0.106419 TTGAAGCCCCCAACGTTCTT 60.106 50.0 0.0 0.0 0.0 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
66 67 2.867624 TGGATTGTTTCTGCTTCTGCT 58.132 42.857 0.00 0.00 40.48 4.24
97 98 2.590092 CCTCGCCCCTTCCGAATT 59.410 61.111 0.00 0.00 33.92 2.17
111 112 3.828921 TCCGAATTCTTCTCCGATCCTA 58.171 45.455 3.52 0.00 0.00 2.94
230 231 3.654414 GCGAGAGGAAGAAAGAAAGTCA 58.346 45.455 0.00 0.00 0.00 3.41
451 454 4.913968 AGGTGCATATCCCTTACCACTAAT 59.086 41.667 0.00 0.00 33.88 1.73
664 668 1.078214 GGTCCATGTAGCTGCTGCA 60.078 57.895 22.30 22.30 42.74 4.41
1241 1246 6.709018 TCATAGTTCGATTGGACATGTAGA 57.291 37.500 0.00 0.00 0.00 2.59
1349 1354 3.482156 AGATGCATTCGCCATAGTTCT 57.518 42.857 0.00 0.00 37.32 3.01
1418 1423 6.183360 GCTCTAGCCAAAACGAATCCTATTTT 60.183 38.462 0.00 0.00 34.31 1.82
1419 1424 7.316544 TCTAGCCAAAACGAATCCTATTTTC 57.683 36.000 0.00 0.00 0.00 2.29
1453 1458 7.770433 CCTTCTCCATTACAATGTTCTCATACA 59.230 37.037 0.00 0.00 34.60 2.29
1463 1468 7.624549 ACAATGTTCTCATACACAGGAATACT 58.375 34.615 0.00 0.00 33.49 2.12
1672 1677 2.361757 CAGTTGCAACACAGATGGGAAA 59.638 45.455 30.11 0.00 0.00 3.13
1741 1746 4.480115 TCCATATCCTTGTACGAGTCCAT 58.520 43.478 9.32 1.33 0.00 3.41
1983 1988 5.720371 TGTGATACAACCCTTTCCATTTG 57.280 39.130 0.00 0.00 0.00 2.32
2100 2105 3.748298 GCACGGAGAAATAAAGAAGTGC 58.252 45.455 1.51 1.51 45.03 4.40
2352 2363 0.395448 GCAGAGGGTCCGTAGTACCT 60.395 60.000 0.00 0.00 36.45 3.08
2378 2389 2.916355 TGGAGTGATCCAGTAGCCC 58.084 57.895 0.00 0.00 34.33 5.19
2453 2464 4.781087 ACATTTACAGAGCTTACCCCTGTA 59.219 41.667 7.86 7.86 41.01 2.74
2464 2475 0.190069 ACCCCTGTACAGTGTCTGGA 59.810 55.000 21.18 0.00 35.51 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 1.365699 GCGAGGCCTTCATTTCGTTA 58.634 50.000 6.77 0.00 35.61 3.18
97 98 4.335874 CGAGAACTTTAGGATCGGAGAAGA 59.664 45.833 4.44 0.00 43.58 2.87
212 213 5.762711 GCTCTTTGACTTTCTTTCTTCCTCT 59.237 40.000 0.00 0.00 0.00 3.69
230 231 3.394719 GACAAAGGAGAAGACGCTCTTT 58.605 45.455 0.00 0.00 36.73 2.52
451 454 1.292223 CCTTCGTCGAGCCTTTCCA 59.708 57.895 0.00 0.00 0.00 3.53
664 668 4.410400 GCTGCTTAGTGGGCGGGT 62.410 66.667 0.00 0.00 36.65 5.28
675 679 2.034687 ATGCCGAACCTGCTGCTT 59.965 55.556 0.00 0.00 0.00 3.91
789 793 2.174363 TCACGTAACTCCACTCTCGA 57.826 50.000 0.00 0.00 0.00 4.04
1037 1042 2.957402 AGAAAGGAATGCAGTCACCA 57.043 45.000 16.99 0.00 0.00 4.17
1044 1049 1.405105 GGCGCAATAGAAAGGAATGCA 59.595 47.619 10.83 0.00 36.84 3.96
1148 1153 5.996513 CCTAAGATCATAGAAGCAATGCTGT 59.003 40.000 9.14 1.52 39.62 4.40
1241 1246 9.261180 CACATGAGAAACCAGTACGAATATAAT 57.739 33.333 0.00 0.00 0.00 1.28
1349 1354 0.036199 ACGGGTTTGCCGTAATGCTA 60.036 50.000 0.00 0.00 42.28 3.49
1418 1423 3.958147 TGTAATGGAGAAGGTCATAGCGA 59.042 43.478 0.00 0.00 0.00 4.93
1419 1424 4.322080 TGTAATGGAGAAGGTCATAGCG 57.678 45.455 0.00 0.00 0.00 4.26
1624 1629 2.125673 GCTACGTGTCCGGTGCAT 60.126 61.111 0.00 0.00 38.78 3.96
1672 1677 1.406069 CCCTGTCTTTCGTAGCATGCT 60.406 52.381 25.99 25.99 0.00 3.79
1741 1746 5.163550 CCAGGTTCATCTCGTGTAGTGATTA 60.164 44.000 0.00 0.00 31.32 1.75
1843 1848 2.680429 GTCGTTCCAACAACCGACA 58.320 52.632 6.20 0.00 46.53 4.35
1983 1988 2.254350 GCCGTTCTTTCCCAACGC 59.746 61.111 0.00 0.00 44.27 4.84
2072 2077 1.580059 TATTTCTCCGTGCCCCTTCT 58.420 50.000 0.00 0.00 0.00 2.85
2100 2105 4.521062 CTCGGCTGCTTCTCCCCG 62.521 72.222 0.00 0.00 41.97 5.73
2352 2363 1.351076 TGGATCACTCCAGTGCTTCA 58.649 50.000 1.49 0.00 46.95 3.02
2378 2389 1.522569 CACTTCTAGGCCCCTTCCG 59.477 63.158 0.00 0.00 0.00 4.30
2453 2464 2.550978 CAACGTTCTTCCAGACACTGT 58.449 47.619 0.00 0.00 0.00 3.55
2464 2475 0.106419 TTGAAGCCCCCAACGTTCTT 60.106 50.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.