Multiple sequence alignment - TraesCS1D01G169600

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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 TraesCS1D01G169600 chr1D 100.000 2602 0 0 1 2602 244198033 244195432 0 4806
1 TraesCS1D01G169600 chr1D 95.477 2609 100 12 1 2602 244765228 244762631 0 4148
2 TraesCS1D01G169600 chr1D 94.504 2620 115 14 1 2602 254473543 254470935 0 4013
3 TraesCS1D01G169600 chr3B 95.115 2620 102 13 1 2600 201489860 201487247 0 4106
4 TraesCS1D01G169600 chr3A 94.950 2614 112 13 1 2602 524025317 524022712 0 4078
5 TraesCS1D01G169600 chr5D 94.697 2621 104 20 3 2602 503327634 503325028 0 4037
6 TraesCS1D01G169600 chr5D 94.432 2622 114 19 1 2602 6239157 6241766 0 4004
7 TraesCS1D01G169600 chr7B 94.514 2625 114 15 1 2602 662740885 662743502 0 4023
8 TraesCS1D01G169600 chr3D 94.430 2639 99 19 1 2602 24162309 24159682 0 4015
9 TraesCS1D01G169600 chr4A 92.508 2616 159 25 1 2602 205015291 205017883 0 3711


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 TraesCS1D01G169600 chr1D 244195432 244198033 2601 True 4806 4806 100.000 1 2602 1 chr1D.!!$R1 2601
1 TraesCS1D01G169600 chr1D 244762631 244765228 2597 True 4148 4148 95.477 1 2602 1 chr1D.!!$R2 2601
2 TraesCS1D01G169600 chr1D 254470935 254473543 2608 True 4013 4013 94.504 1 2602 1 chr1D.!!$R3 2601
3 TraesCS1D01G169600 chr3B 201487247 201489860 2613 True 4106 4106 95.115 1 2600 1 chr3B.!!$R1 2599
4 TraesCS1D01G169600 chr3A 524022712 524025317 2605 True 4078 4078 94.950 1 2602 1 chr3A.!!$R1 2601
5 TraesCS1D01G169600 chr5D 503325028 503327634 2606 True 4037 4037 94.697 3 2602 1 chr5D.!!$R1 2599
6 TraesCS1D01G169600 chr5D 6239157 6241766 2609 False 4004 4004 94.432 1 2602 1 chr5D.!!$F1 2601
7 TraesCS1D01G169600 chr7B 662740885 662743502 2617 False 4023 4023 94.514 1 2602 1 chr7B.!!$F1 2601
8 TraesCS1D01G169600 chr3D 24159682 24162309 2627 True 4015 4015 94.430 1 2602 1 chr3D.!!$R1 2601
9 TraesCS1D01G169600 chr4A 205015291 205017883 2592 False 3711 3711 92.508 1 2602 1 chr4A.!!$F1 2601

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
711 716 5.949735 TCAAATCCGATAGTTGGCTTTTTC 58.05 37.5 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 1675 0.770948 AGTTCGGGGAAAGGGGAAGT 60.771 55.0 0.0 0.0 0.0 3.01 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
72 73 7.503566 GGATTCCTTCTGTAATTTCATCCATCA 59.496 37.037 0.00 0.0 0.00 3.07
355 357 9.542462 TTTTATTTACTCTGGATCTATGTTCCG 57.458 33.333 0.00 0.0 35.94 4.30
374 376 8.725405 TGTTCCGCTTAGTGAAATATTAATCA 57.275 30.769 0.00 0.0 0.00 2.57
711 716 5.949735 TCAAATCCGATAGTTGGCTTTTTC 58.050 37.500 0.00 0.0 0.00 2.29
734 740 7.731882 TCTTCTCTATCGATGTTCTACGAAT 57.268 36.000 8.54 0.0 41.65 3.34
736 742 8.927721 TCTTCTCTATCGATGTTCTACGAATAG 58.072 37.037 8.54 0.0 41.65 1.73
1198 1231 8.304596 TCTGACAGAACGACAATTACTTAGATT 58.695 33.333 1.64 0.0 0.00 2.40
1233 1266 4.249661 TGGAAAAGCAAAAAGGTCAACAC 58.750 39.130 0.00 0.0 0.00 3.32
1303 1336 3.358111 TCGATTGGGTATGGCTTCAAA 57.642 42.857 0.00 0.0 0.00 2.69
1328 1362 1.990160 CTGGGGCCCGCCAATTAGTA 61.990 60.000 19.83 0.0 37.98 1.82
1341 1375 6.073222 CCGCCAATTAGTAAACCATAGACATC 60.073 42.308 0.00 0.0 0.00 3.06
1433 1467 7.169140 ACGAAACATAAACAAAGATCAAAAGGC 59.831 33.333 0.00 0.0 0.00 4.35
1455 1489 5.985530 GGCCTGGTTCAAAATTATATTGCTC 59.014 40.000 0.00 0.0 0.00 4.26
1641 1675 7.950124 AGGAAAGGTTCATAGAATTTTCTTCCA 59.050 33.333 0.00 0.0 38.70 3.53
1786 1820 9.733556 ATGTGTCTTTTTCATACCACAGTAATA 57.266 29.630 0.00 0.0 36.39 0.98
1951 1985 3.742385 TCGAACCCTCGGTAAACAAAAT 58.258 40.909 0.00 0.0 45.49 1.82
2143 2182 8.370940 TCATCTAAGTGGAAGGATACATGATTC 58.629 37.037 0.00 0.0 41.41 2.52
2144 2183 7.921041 TCTAAGTGGAAGGATACATGATTCT 57.079 36.000 0.00 0.0 41.41 2.40
2145 2184 8.324191 TCTAAGTGGAAGGATACATGATTCTT 57.676 34.615 0.00 0.0 35.91 2.52
2283 2329 7.134815 CCTTAGAATTCGGTTTGCATAAGATG 58.865 38.462 0.00 0.0 0.00 2.90
2470 2527 4.226427 AGGATACAATTTGAGCTGAGCA 57.774 40.909 7.39 0.0 41.41 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.977739 AGAACAGGGAAATGAGGATATGGA 59.022 41.667 0.00 0.00 0.00 3.41
22 23 4.141274 TGGTCTCAAAGAACAGGGAAATGA 60.141 41.667 0.00 0.00 36.94 2.57
343 345 8.764524 ATATTTCACTAAGCGGAACATAGATC 57.235 34.615 0.00 0.00 0.00 2.75
850 870 5.341169 AGTACCCCAACATGGAATTTCATT 58.659 37.500 0.00 0.00 40.96 2.57
863 884 6.489022 AGTGAAATCAACTAAAGTACCCCAAC 59.511 38.462 0.00 0.00 0.00 3.77
1113 1146 6.421202 AGACGAATACGATATTGCTCCTTTTC 59.579 38.462 0.00 0.00 42.66 2.29
1198 1231 4.875544 GCTTTTCCAGCGATATGTACAA 57.124 40.909 0.00 0.00 39.29 2.41
1233 1266 6.148150 TCAAGTAATTGTAGTAAAACCTGGCG 59.852 38.462 2.43 0.00 0.00 5.69
1418 1452 2.962859 ACCAGGCCTTTTGATCTTTGT 58.037 42.857 0.00 0.00 0.00 2.83
1433 1467 7.111247 TGGAGCAATATAATTTTGAACCAGG 57.889 36.000 0.00 0.00 31.90 4.45
1455 1489 2.851195 CAATTTCCCTAGGTCCGATGG 58.149 52.381 8.29 0.00 0.00 3.51
1533 1567 2.108970 GAGACCGACCCACTTCCTATT 58.891 52.381 0.00 0.00 0.00 1.73
1641 1675 0.770948 AGTTCGGGGAAAGGGGAAGT 60.771 55.000 0.00 0.00 0.00 3.01
1771 1805 9.975218 TCTCTATAGCATATTACTGTGGTATGA 57.025 33.333 14.52 6.47 37.62 2.15
2145 2184 5.768317 AGCAAGCGCAATTTCTAGTAAAAA 58.232 33.333 11.47 0.00 42.27 1.94
2256 2302 4.701956 ATGCAAACCGAATTCTAAGGTG 57.298 40.909 3.52 0.00 38.44 4.00
2283 2329 2.983402 TCGATAGTATGGTGTAGCGC 57.017 50.000 0.00 0.00 37.40 5.92


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

AutoCloner maintained by Alex Coulton.