Multiple sequence alignment - TraesCS3B01G561500

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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 TraesCS3B01G561500 chr3B 100.000 2642 0 0 1 2642 795065817 795068458 0.000000e+00 4879
1 TraesCS3B01G561500 chr2B 98.401 2626 34 4 22 2642 57160088 57157466 0.000000e+00 4610
2 TraesCS3B01G561500 chr2B 89.442 1326 90 23 818 2136 241246402 241247684 0.000000e+00 1628
3 TraesCS3B01G561500 chr2B 84.976 619 64 17 26 627 240790587 240789981 3.760000e-168 601
4 TraesCS3B01G561500 chr6B 98.363 2626 35 4 22 2642 168770345 168772967 0.000000e+00 4604
5 TraesCS3B01G561500 chr2A 97.754 2627 50 6 22 2642 395713884 395711261 0.000000e+00 4516
6 TraesCS3B01G561500 chr2A 97.181 2625 38 8 22 2642 405466741 405469333 0.000000e+00 4405
7 TraesCS3B01G561500 chr7B 98.015 1965 34 3 680 2642 49030996 49029035 0.000000e+00 3408
8 TraesCS3B01G561500 chr7B 98.397 624 7 3 22 643 49031789 49031167 0.000000e+00 1094
9 TraesCS3B01G561500 chr3A 98.231 1865 28 3 780 2642 699162148 699164009 0.000000e+00 3256
10 TraesCS3B01G561500 chr3A 98.342 1508 16 5 22 1523 699160633 699162137 0.000000e+00 2638
11 TraesCS3B01G561500 chr6D 90.315 1332 74 24 818 2137 384291459 384290171 0.000000e+00 1694
12 TraesCS3B01G561500 chr7A 89.224 1327 91 20 818 2136 299380503 299379221 0.000000e+00 1611
13 TraesCS3B01G561500 chr7A 91.602 512 35 6 2134 2642 498729399 498728893 0.000000e+00 701
14 TraesCS3B01G561500 chr5D 91.211 512 37 7 2134 2642 390800798 390800292 0.000000e+00 689
15 TraesCS3B01G561500 chr5D 82.543 527 36 23 1613 2137 390801558 390801086 1.890000e-111 412
16 TraesCS3B01G561500 chr5A 90.680 515 39 6 2134 2642 119067014 119067525 0.000000e+00 676
17 TraesCS3B01G561500 chr7D 85.137 619 65 15 25 627 76120543 76119936 2.250000e-170 608
18 TraesCS3B01G561500 chr7D 85.137 619 65 10 25 627 623453341 623452734 2.250000e-170 608
19 TraesCS3B01G561500 chr1B 86.515 482 36 15 1658 2137 235375848 235375394 1.090000e-138 503


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 TraesCS3B01G561500 chr3B 795065817 795068458 2641 False 4879.0 4879 100.0000 1 2642 1 chr3B.!!$F1 2641
1 TraesCS3B01G561500 chr2B 57157466 57160088 2622 True 4610.0 4610 98.4010 22 2642 1 chr2B.!!$R1 2620
2 TraesCS3B01G561500 chr2B 241246402 241247684 1282 False 1628.0 1628 89.4420 818 2136 1 chr2B.!!$F1 1318
3 TraesCS3B01G561500 chr2B 240789981 240790587 606 True 601.0 601 84.9760 26 627 1 chr2B.!!$R2 601
4 TraesCS3B01G561500 chr6B 168770345 168772967 2622 False 4604.0 4604 98.3630 22 2642 1 chr6B.!!$F1 2620
5 TraesCS3B01G561500 chr2A 395711261 395713884 2623 True 4516.0 4516 97.7540 22 2642 1 chr2A.!!$R1 2620
6 TraesCS3B01G561500 chr2A 405466741 405469333 2592 False 4405.0 4405 97.1810 22 2642 1 chr2A.!!$F1 2620
7 TraesCS3B01G561500 chr7B 49029035 49031789 2754 True 2251.0 3408 98.2060 22 2642 2 chr7B.!!$R1 2620
8 TraesCS3B01G561500 chr3A 699160633 699164009 3376 False 2947.0 3256 98.2865 22 2642 2 chr3A.!!$F1 2620
9 TraesCS3B01G561500 chr6D 384290171 384291459 1288 True 1694.0 1694 90.3150 818 2137 1 chr6D.!!$R1 1319
10 TraesCS3B01G561500 chr7A 299379221 299380503 1282 True 1611.0 1611 89.2240 818 2136 1 chr7A.!!$R1 1318
11 TraesCS3B01G561500 chr7A 498728893 498729399 506 True 701.0 701 91.6020 2134 2642 1 chr7A.!!$R2 508
12 TraesCS3B01G561500 chr5D 390800292 390801558 1266 True 550.5 689 86.8770 1613 2642 2 chr5D.!!$R1 1029
13 TraesCS3B01G561500 chr5A 119067014 119067525 511 False 676.0 676 90.6800 2134 2642 1 chr5A.!!$F1 508
14 TraesCS3B01G561500 chr7D 76119936 76120543 607 True 608.0 608 85.1370 25 627 1 chr7D.!!$R1 602
15 TraesCS3B01G561500 chr7D 623452734 623453341 607 True 608.0 608 85.1370 25 627 1 chr7D.!!$R2 602

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
20 21 0.675522 TTTACCACTGCGCTAAGGCC 60.676 55.0 9.73 0.0 34.44 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2303 3576 4.690748 TCTTGGAAGCAAGATAAGTTCGTG 59.309 41.667 0.0 0.0 36.39 4.35 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
19 20 0.727398 CTTTACCACTGCGCTAAGGC 59.273 55.000 9.73 0.00 0.00 4.35
20 21 0.675522 TTTACCACTGCGCTAAGGCC 60.676 55.000 9.73 0.00 34.44 5.19
269 274 7.528205 CCTAAGGGAGTCATGGTACAGTTTTTA 60.528 40.741 0.00 0.00 36.68 1.52
637 660 4.389890 TTGACATGCCCAATTATCAAGC 57.610 40.909 0.00 0.00 0.00 4.01
693 850 5.998363 CCCCTCTGAAAAGGTATATTGCTAC 59.002 44.000 0.00 0.00 34.34 3.58
748 905 8.474006 AAACAAACTTTAGACAATTGGTTGAC 57.526 30.769 10.83 0.00 38.71 3.18
752 909 7.418337 AACTTTAGACAATTGGTTGACCTTT 57.582 32.000 10.83 0.00 38.71 3.11
815 972 8.991810 CCTACGTTTACTAATACAAATTTTGCG 58.008 33.333 9.04 3.54 0.00 4.85
1122 1284 5.757850 AATTGTGACTCAGAAACACCTTC 57.242 39.130 0.00 0.00 34.18 3.46
1662 2584 0.803740 GACGTCGTCTACTGAAGCCT 59.196 55.000 18.09 0.00 0.00 4.58
2303 3576 3.405170 AATGAATTCGACAACATCCGC 57.595 42.857 0.04 0.00 0.00 5.54
2418 3691 3.456280 TGTTTTCTCCAAAATGCAGCAC 58.544 40.909 0.00 0.00 33.98 4.40
2440 3713 2.610438 ACCTTCCATTTGGAGCACAT 57.390 45.000 0.00 0.00 46.36 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.727398 GCCTTAGCGCAGTGGTAAAG 59.273 55.000 11.47 2.53 39.86 1.85
1 2 0.675522 GGCCTTAGCGCAGTGGTAAA 60.676 55.000 11.47 0.00 39.86 2.01
2 3 1.078708 GGCCTTAGCGCAGTGGTAA 60.079 57.895 11.47 5.53 41.24 2.85
3 4 2.287274 TGGCCTTAGCGCAGTGGTA 61.287 57.895 11.47 0.00 41.24 3.25
4 5 3.636231 TGGCCTTAGCGCAGTGGT 61.636 61.111 11.47 0.00 41.24 4.16
5 6 3.127533 GTGGCCTTAGCGCAGTGG 61.128 66.667 11.47 9.34 41.24 4.00
6 7 1.672356 AAGTGGCCTTAGCGCAGTG 60.672 57.895 11.47 0.00 41.24 3.66
7 8 1.672356 CAAGTGGCCTTAGCGCAGT 60.672 57.895 11.47 0.00 41.24 4.40
8 9 3.044059 GCAAGTGGCCTTAGCGCAG 62.044 63.158 11.47 0.00 41.24 5.18
9 10 2.178876 TAGCAAGTGGCCTTAGCGCA 62.179 55.000 11.47 0.00 46.50 6.09
10 11 1.024579 TTAGCAAGTGGCCTTAGCGC 61.025 55.000 3.32 0.00 46.50 5.92
11 12 1.448985 TTTAGCAAGTGGCCTTAGCG 58.551 50.000 3.32 0.00 46.50 4.26
12 13 2.755103 ACATTTAGCAAGTGGCCTTAGC 59.245 45.455 3.32 2.79 46.50 3.09
13 14 4.265073 AGACATTTAGCAAGTGGCCTTAG 58.735 43.478 3.32 0.00 46.50 2.18
14 15 4.019321 AGAGACATTTAGCAAGTGGCCTTA 60.019 41.667 3.32 0.00 46.50 2.69
15 16 3.084786 GAGACATTTAGCAAGTGGCCTT 58.915 45.455 3.32 0.00 46.50 4.35
16 17 2.307098 AGAGACATTTAGCAAGTGGCCT 59.693 45.455 3.32 0.00 46.50 5.19
17 18 2.716217 AGAGACATTTAGCAAGTGGCC 58.284 47.619 0.00 0.00 46.50 5.36
18 19 3.119708 CCAAGAGACATTTAGCAAGTGGC 60.120 47.826 0.00 0.00 45.30 5.01
19 20 3.441572 CCCAAGAGACATTTAGCAAGTGG 59.558 47.826 0.00 0.00 0.00 4.00
20 21 4.074970 ACCCAAGAGACATTTAGCAAGTG 58.925 43.478 0.00 0.00 0.00 3.16
545 564 2.097036 TGAATCAGAAGGCTGCATTGG 58.903 47.619 3.50 0.00 42.01 3.16
693 850 2.533266 ATGAGCGCCCTACTACATTG 57.467 50.000 2.29 0.00 0.00 2.82
748 905 2.062971 AGGTGCAGATATGCCAAAGG 57.937 50.000 10.32 0.00 0.00 3.11
752 909 3.862877 AACATAGGTGCAGATATGCCA 57.137 42.857 10.32 0.00 33.53 4.92
2303 3576 4.690748 TCTTGGAAGCAAGATAAGTTCGTG 59.309 41.667 0.00 0.00 36.39 4.35
2418 3691 3.420893 TGTGCTCCAAATGGAAGGTAAG 58.579 45.455 3.35 0.00 44.91 2.34


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

AutoCloner maintained by Alex Coulton.