Multiple sequence alignment - TraesCS2D01G171400

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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 TraesCS2D01G171400 chr2D 100.000 2418 0 0 1 2418 115150834 115148417 0.000000e+00 4466.0
1 TraesCS2D01G171400 chr2D 85.386 1567 197 19 844 2398 44139949 44138403 0.000000e+00 1596.0
2 TraesCS2D01G171400 chr2D 86.316 570 67 8 211 777 245074935 245075496 5.720000e-171 610.0
3 TraesCS2D01G171400 chr2D 80.556 612 102 11 113 713 522688390 522688995 2.830000e-124 455.0
4 TraesCS2D01G171400 chr2B 93.143 2421 144 15 4 2418 165779652 165777248 0.000000e+00 3531.0
5 TraesCS2D01G171400 chr2B 93.138 2419 147 12 4 2418 165929331 165926928 0.000000e+00 3530.0
6 TraesCS2D01G171400 chr2B 90.000 50 3 2 15 63 773873010 773873058 2.010000e-06 63.9
7 TraesCS2D01G171400 chr2A 92.222 2430 161 13 1 2418 116699600 116697187 0.000000e+00 3415.0
8 TraesCS2D01G171400 chr2A 92.079 2424 169 12 5 2418 116832462 116830052 0.000000e+00 3391.0
9 TraesCS2D01G171400 chr2A 85.281 462 67 1 120 581 693119313 693118853 2.180000e-130 475.0
10 TraesCS2D01G171400 chr4A 88.707 735 81 2 844 1577 735146447 735147180 0.000000e+00 896.0
11 TraesCS2D01G171400 chr4A 88.707 735 81 2 844 1577 735936559 735937292 0.000000e+00 896.0
12 TraesCS2D01G171400 chr4A 86.122 735 80 7 844 1577 736968624 736969337 0.000000e+00 773.0
13 TraesCS2D01G171400 chr4A 86.122 735 80 7 844 1577 736995739 736996452 0.000000e+00 773.0
14 TraesCS2D01G171400 chr7A 85.345 696 90 10 53 743 30158038 30157350 0.000000e+00 710.0
15 TraesCS2D01G171400 chr7D 79.938 643 113 13 91 729 35091791 35091161 2.190000e-125 459.0
16 TraesCS2D01G171400 chr7D 95.455 44 1 1 22 64 184642309 184642352 4.310000e-08 69.4
17 TraesCS2D01G171400 chr6A 78.437 691 116 27 54 726 73294457 73295132 1.030000e-113 420.0
18 TraesCS2D01G171400 chr5A 97.561 41 1 0 22 62 662538797 662538757 1.200000e-08 71.3
19 TraesCS2D01G171400 chr5A 93.333 45 1 2 15 59 175804726 175804768 5.580000e-07 65.8
20 TraesCS2D01G171400 chr5B 93.333 45 2 1 22 66 144857918 144857875 5.580000e-07 65.8


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 TraesCS2D01G171400 chr2D 115148417 115150834 2417 True 4466 4466 100.000 1 2418 1 chr2D.!!$R2 2417
1 TraesCS2D01G171400 chr2D 44138403 44139949 1546 True 1596 1596 85.386 844 2398 1 chr2D.!!$R1 1554
2 TraesCS2D01G171400 chr2D 245074935 245075496 561 False 610 610 86.316 211 777 1 chr2D.!!$F1 566
3 TraesCS2D01G171400 chr2D 522688390 522688995 605 False 455 455 80.556 113 713 1 chr2D.!!$F2 600
4 TraesCS2D01G171400 chr2B 165777248 165779652 2404 True 3531 3531 93.143 4 2418 1 chr2B.!!$R1 2414
5 TraesCS2D01G171400 chr2B 165926928 165929331 2403 True 3530 3530 93.138 4 2418 1 chr2B.!!$R2 2414
6 TraesCS2D01G171400 chr2A 116697187 116699600 2413 True 3415 3415 92.222 1 2418 1 chr2A.!!$R1 2417
7 TraesCS2D01G171400 chr2A 116830052 116832462 2410 True 3391 3391 92.079 5 2418 1 chr2A.!!$R2 2413
8 TraesCS2D01G171400 chr4A 735146447 735147180 733 False 896 896 88.707 844 1577 1 chr4A.!!$F1 733
9 TraesCS2D01G171400 chr4A 735936559 735937292 733 False 896 896 88.707 844 1577 1 chr4A.!!$F2 733
10 TraesCS2D01G171400 chr4A 736968624 736969337 713 False 773 773 86.122 844 1577 1 chr4A.!!$F3 733
11 TraesCS2D01G171400 chr4A 736995739 736996452 713 False 773 773 86.122 844 1577 1 chr4A.!!$F4 733
12 TraesCS2D01G171400 chr7A 30157350 30158038 688 True 710 710 85.345 53 743 1 chr7A.!!$R1 690
13 TraesCS2D01G171400 chr7D 35091161 35091791 630 True 459 459 79.938 91 729 1 chr7D.!!$R1 638
14 TraesCS2D01G171400 chr6A 73294457 73295132 675 False 420 420 78.437 54 726 1 chr6A.!!$F1 672

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
152 159 1.693062 TGCATGGCCACACTTGATTTT 59.307 42.857 8.16 0.0 0.0 1.82 F
1056 1088 1.451028 GCTCCTCATGCCACTCCAC 60.451 63.158 0.00 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1376 0.698818 CACTCCCCTTGGGTAAAGCT 59.301 55.000 4.84 0.0 44.74 3.74 R
2254 2295 1.066573 ACCATCTCACAAAGCTCGGAG 60.067 52.381 0.00 0.0 0.00 4.63 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
152 159 1.693062 TGCATGGCCACACTTGATTTT 59.307 42.857 8.16 0.00 0.00 1.82
188 195 4.569966 GTCTGGCTTTCTGTATGACTGATG 59.430 45.833 0.00 0.00 0.00 3.07
232 246 2.658373 TGAACGTATGTACATGGCGT 57.342 45.000 24.68 24.68 36.09 5.68
572 594 9.542462 TGTTTATATTTTAGGAAGGTGATCTCG 57.458 33.333 0.00 0.00 0.00 4.04
729 759 2.203938 TGGGAGGGGTGGTGAGAC 60.204 66.667 0.00 0.00 0.00 3.36
973 1005 6.514048 GCATCTTTTGTGTGCTCTCTTACTTT 60.514 38.462 0.00 0.00 36.02 2.66
1038 1070 9.961265 AATATGACAATCATGCTATGTTTTCTG 57.039 29.630 1.49 0.00 37.70 3.02
1056 1088 1.451028 GCTCCTCATGCCACTCCAC 60.451 63.158 0.00 0.00 0.00 4.02
1562 1603 4.917415 GGCTCAAAACACACACATGAATAC 59.083 41.667 0.00 0.00 0.00 1.89
1693 1734 5.061064 GTGTTCTTAGTGACTCGTTGCATAG 59.939 44.000 0.00 0.00 0.00 2.23
1694 1735 3.770666 TCTTAGTGACTCGTTGCATAGC 58.229 45.455 0.00 0.00 0.00 2.97
1695 1736 3.192633 TCTTAGTGACTCGTTGCATAGCA 59.807 43.478 0.00 0.00 36.47 3.49
1696 1737 2.455674 AGTGACTCGTTGCATAGCAA 57.544 45.000 0.00 0.00 46.80 3.91
1847 1888 7.763613 AGATATGAAAGAGGAGGCCATAAAAT 58.236 34.615 5.01 0.00 0.00 1.82
1966 2007 5.968254 ACATTCGTTTTGTAAACCCTTTGT 58.032 33.333 0.00 0.00 0.00 2.83
2204 2245 6.718522 TTGAGAAGGGTTTAAAATTTCGGT 57.281 33.333 0.00 0.00 0.00 4.69
2323 2364 9.654663 AACCATCAACTCTACTAGTGATAAAAC 57.345 33.333 5.39 0.00 38.88 2.43
2359 2400 8.206325 ACATGCTAGTCAAATGAACTTGATAG 57.794 34.615 0.00 0.00 37.63 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 141 5.389859 TTCTAAAATCAAGTGTGGCCATG 57.610 39.130 9.72 2.37 0.00 3.66
152 159 4.760530 AAGCCAGACATGCTACATTCTA 57.239 40.909 0.00 0.00 38.34 2.10
188 195 9.307121 CATGGACGAGGTCATATTATATTTCTC 57.693 37.037 0.00 0.00 33.68 2.87
206 213 4.356289 CATGTACATACGTTCATGGACGA 58.644 43.478 32.59 16.34 43.47 4.20
232 246 1.812686 CGGAAGGTGGGTCGTCAGAA 61.813 60.000 0.00 0.00 0.00 3.02
506 527 9.358872 GATAACCTTCCAAAACAAAATGAGATC 57.641 33.333 0.00 0.00 0.00 2.75
616 638 6.019640 CGTGGGTTGATTCATTTTAATCATGC 60.020 38.462 0.50 0.00 43.50 4.06
694 722 4.814967 TCCCACTGATTTTTCCCTTTCTT 58.185 39.130 0.00 0.00 0.00 2.52
729 759 3.192466 CCTGGTACTCCGGTTTTATTCG 58.808 50.000 0.00 0.00 38.38 3.34
890 922 8.512956 CCATGGATGATGATATCTGAAGAAAAC 58.487 37.037 5.56 0.00 33.31 2.43
973 1005 7.013083 GTCTCAAGTAATATACCGTCAGAAGGA 59.987 40.741 9.71 0.00 0.00 3.36
1015 1047 6.096423 AGCAGAAAACATAGCATGATTGTCAT 59.904 34.615 0.00 0.00 37.65 3.06
1038 1070 1.451028 GTGGAGTGGCATGAGGAGC 60.451 63.158 0.00 0.00 0.00 4.70
1337 1376 0.698818 CACTCCCCTTGGGTAAAGCT 59.301 55.000 4.84 0.00 44.74 3.74
1562 1603 6.757897 TTTAGAACATTGGCATGAGTTAGG 57.242 37.500 0.00 0.00 34.11 2.69
1693 1734 5.577835 TCTTGTTGTTGCGGATATATTTGC 58.422 37.500 3.81 3.81 0.00 3.68
1694 1735 8.633075 AATTCTTGTTGTTGCGGATATATTTG 57.367 30.769 0.00 0.00 0.00 2.32
1695 1736 9.301153 GAAATTCTTGTTGTTGCGGATATATTT 57.699 29.630 0.00 0.00 0.00 1.40
1696 1737 8.686334 AGAAATTCTTGTTGTTGCGGATATATT 58.314 29.630 0.00 0.00 0.00 1.28
1697 1738 8.225603 AGAAATTCTTGTTGTTGCGGATATAT 57.774 30.769 0.00 0.00 0.00 0.86
1847 1888 6.656632 TGGAAAATAATAGTTGTGTGCCAA 57.343 33.333 0.00 0.00 0.00 4.52
2031 2072 1.204704 TCAATATCGGCTCCGCTATGG 59.795 52.381 2.96 1.95 39.59 2.74
2086 2127 3.550030 CCCCGTTTCCGATTTGAATATGC 60.550 47.826 0.00 0.00 35.63 3.14
2089 2130 2.018515 GCCCCGTTTCCGATTTGAATA 58.981 47.619 0.00 0.00 35.63 1.75
2254 2295 1.066573 ACCATCTCACAAAGCTCGGAG 60.067 52.381 0.00 0.00 0.00 4.63
2323 2364 3.201290 GACTAGCATGTCCAACCATGAG 58.799 50.000 5.39 0.00 43.99 2.90
2328 2369 4.009675 TCATTTGACTAGCATGTCCAACC 58.990 43.478 6.64 0.00 36.21 3.77


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

AutoCloner maintained by Alex Coulton.