Multiple sequence alignment - TraesCS4D01G137500

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 TraesCS4D01G137500 chr4D 100.000 2575 0 0 1 2575 123330827 123333401 0 4756
1 TraesCS4D01G137500 chr6D 98.835 2575 27 2 1 2575 124512883 124515454 0 4586
2 TraesCS4D01G137500 chr7D 98.757 2575 29 2 1 2575 203495358 203497929 0 4575
3 TraesCS4D01G137500 chr7D 98.447 2575 37 2 1 2575 381978403 381975832 0 4530
4 TraesCS4D01G137500 chr5A 98.104 2584 38 4 1 2575 19253500 19250919 0 4490
5 TraesCS4D01G137500 chr5A 97.981 2575 48 3 1 2575 238901412 238898842 0 4464
6 TraesCS4D01G137500 chr4A 98.137 2576 43 3 1 2575 67592139 67594710 0 4486
7 TraesCS4D01G137500 chr7B 97.987 2583 42 3 1 2575 716843191 716840611 0 4473
8 TraesCS4D01G137500 chr7B 97.988 2584 41 4 1 2575 716883432 716880851 0 4473
9 TraesCS4D01G137500 chr7B 97.909 2583 43 4 1 2575 742984793 742987372 0 4460


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 TraesCS4D01G137500 chr4D 123330827 123333401 2574 False 4756 4756 100.000 1 2575 1 chr4D.!!$F1 2574
1 TraesCS4D01G137500 chr6D 124512883 124515454 2571 False 4586 4586 98.835 1 2575 1 chr6D.!!$F1 2574
2 TraesCS4D01G137500 chr7D 203495358 203497929 2571 False 4575 4575 98.757 1 2575 1 chr7D.!!$F1 2574
3 TraesCS4D01G137500 chr7D 381975832 381978403 2571 True 4530 4530 98.447 1 2575 1 chr7D.!!$R1 2574
4 TraesCS4D01G137500 chr5A 19250919 19253500 2581 True 4490 4490 98.104 1 2575 1 chr5A.!!$R1 2574
5 TraesCS4D01G137500 chr5A 238898842 238901412 2570 True 4464 4464 97.981 1 2575 1 chr5A.!!$R2 2574
6 TraesCS4D01G137500 chr4A 67592139 67594710 2571 False 4486 4486 98.137 1 2575 1 chr4A.!!$F1 2574
7 TraesCS4D01G137500 chr7B 716840611 716843191 2580 True 4473 4473 97.987 1 2575 1 chr7B.!!$R1 2574
8 TraesCS4D01G137500 chr7B 716880851 716883432 2581 True 4473 4473 97.988 1 2575 1 chr7B.!!$R2 2574
9 TraesCS4D01G137500 chr7B 742984793 742987372 2579 False 4460 4460 97.909 1 2575 1 chr7B.!!$F1 2574

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
96 97 0.164002 GAAACCTCGCTTGTTCTCGC 59.836 55.0 0.0 0.0 0.0 5.03 F
214 215 3.576648 GCCTCAAGCGTATAGATACCAC 58.423 50.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1184 1.755621 CGAGAGGGATGATCCACTCCA 60.756 57.143 22.58 0.0 38.64 3.86 R
1902 1907 2.474410 TCTACTGACACTGAGCGAGA 57.526 50.000 0.00 0.0 0.00 4.04 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
84 85 5.472137 TGGTGCTTTGTATTGTAGAAACCTC 59.528 40.000 0.00 0.00 0.00 3.85
96 97 0.164002 GAAACCTCGCTTGTTCTCGC 59.836 55.000 0.00 0.00 0.00 5.03
162 163 4.680708 GCGGATGATTCCTGAAGAGTGTTA 60.681 45.833 0.00 0.00 40.17 2.41
214 215 3.576648 GCCTCAAGCGTATAGATACCAC 58.423 50.000 0.00 0.00 0.00 4.16
1179 1184 6.183360 GGGTTCAAGTTTCGATCGATATTTGT 60.183 38.462 28.90 10.69 29.86 2.83
1391 1396 2.158885 TCAATCATCCGGATTTACGCCA 60.159 45.455 16.19 0.00 43.76 5.69
1420 1425 5.188163 TCAACAGATTATGGTTTCGAGGGTA 59.812 40.000 0.00 0.00 0.00 3.69
1466 1471 5.269189 TCTGAGTGGATATGTGGAAGTACA 58.731 41.667 0.00 0.00 34.63 2.90
1519 1524 2.514458 ACCCATTGAGATGACCCAAC 57.486 50.000 0.00 0.00 35.16 3.77
1522 1527 3.245730 ACCCATTGAGATGACCCAACAAT 60.246 43.478 0.00 0.00 35.16 2.71
1523 1528 3.770933 CCCATTGAGATGACCCAACAATT 59.229 43.478 0.00 0.00 35.16 2.32
1902 1907 4.098501 GGAAACTATTGCCTATGCTTGCTT 59.901 41.667 0.00 0.00 38.71 3.91
1933 1938 6.043243 TCAGTGTCAGTAGAAGGGAAGAAAAT 59.957 38.462 0.00 0.00 0.00 1.82
2243 2252 9.770097 CAAATCTAATAGTTCCATCTGCTCTTA 57.230 33.333 0.00 0.00 0.00 2.10
2333 2342 3.239627 AAGGGGAGAGTGGCCGAGA 62.240 63.158 0.00 0.00 0.00 4.04
2360 2369 6.365247 GTCAAAAGCGACAGACTGTAAATCTA 59.635 38.462 8.41 0.00 35.88 1.98
2421 2430 6.015350 TCCCACTTGTTGTAGACTTAAGAGAG 60.015 42.308 10.09 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 0.383491 CAACTGTGCGAGAACAAGCG 60.383 55.000 0.00 0.0 35.87 4.68
162 163 7.573710 TGATTCATGTACTAGGCTTGGTATTT 58.426 34.615 0.00 0.0 0.00 1.40
214 215 7.437748 AGTAGCTTACCTATGCTTAAGATGTG 58.562 38.462 6.67 0.0 40.35 3.21
829 830 8.726988 TCCAAAACTGCACACTTTATATAGTTC 58.273 33.333 0.00 0.0 0.00 3.01
1147 1152 5.121768 CGATCGAAACTTGAACCCTTGTATT 59.878 40.000 10.26 0.0 0.00 1.89
1179 1184 1.755621 CGAGAGGGATGATCCACTCCA 60.756 57.143 22.58 0.0 38.64 3.86
1391 1396 9.658799 CCTCGAAACCATAATCTGTTGATATAT 57.341 33.333 0.00 0.0 31.70 0.86
1420 1425 7.119846 CAGAGGAAAGTCTTTTCGTAATGGATT 59.880 37.037 0.00 0.0 42.93 3.01
1466 1471 5.127845 ACACGTTTCTCTGGATCATCATAGT 59.872 40.000 0.00 0.0 0.00 2.12
1519 1524 7.447430 AGCAAAATCGAAATAGCGAAAAATTG 58.553 30.769 0.00 0.0 44.22 2.32
1522 1527 7.302524 ACTAGCAAAATCGAAATAGCGAAAAA 58.697 30.769 0.00 0.0 44.22 1.94
1523 1528 6.837992 ACTAGCAAAATCGAAATAGCGAAAA 58.162 32.000 0.00 0.0 44.22 2.29
1767 1772 3.480894 CTTTCGTATAGATCGAGACGCC 58.519 50.000 16.73 0.0 38.52 5.68
1902 1907 2.474410 TCTACTGACACTGAGCGAGA 57.526 50.000 0.00 0.0 0.00 4.04
1933 1938 6.414732 CATGTTCCTAAAAGGAGTGACCATA 58.585 40.000 0.00 0.0 46.73 2.74
2243 2252 3.373130 GCGGCCTTCGTTCTTAAGTTAAT 59.627 43.478 0.00 0.0 41.72 1.40
2333 2342 1.139058 ACAGTCTGTCGCTTTTGACCT 59.861 47.619 0.00 0.0 38.11 3.85
2360 2369 5.636543 CGAACCTACGTAGAAAACCTTCAAT 59.363 40.000 24.15 0.0 33.64 2.57
2421 2430 3.067074 GCTTCCGCCTACTTTCTCC 57.933 57.895 0.00 0.0 0.00 3.71
2482 2492 5.688823 CATACGAGAAAATTGCACTTCACA 58.311 37.500 0.00 0.0 0.00 3.58


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

AutoCloner maintained by Alex Coulton.