Multiple sequence alignment - TraesCS5B01G119600

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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 TraesCS5B01G119600 chr5B 100.000 2192 0 0 1 2192 211740284 211738093 0.000000e+00 4048.0
1 TraesCS5B01G119600 chr5B 92.593 81 6 0 753 833 541950960 541950880 1.370000e-22 117.0
2 TraesCS5B01G119600 chr5A 93.988 1497 43 17 689 2140 214955953 214954459 0.000000e+00 2222.0
3 TraesCS5B01G119600 chr5A 87.565 193 24 0 1 193 214889900 214890092 7.880000e-55 224.0
4 TraesCS5B01G119600 chr5A 83.537 164 26 1 1 164 214890139 214890301 3.770000e-33 152.0
5 TraesCS5B01G119600 chr5A 93.506 77 5 0 753 829 561975658 561975582 4.950000e-22 115.0
6 TraesCS5B01G119600 chr5A 84.762 105 13 1 177 281 570787584 570787483 3.850000e-18 102.0
7 TraesCS5B01G119600 chr5D 94.617 966 31 9 600 1549 200788137 200787177 0.000000e+00 1476.0
8 TraesCS5B01G119600 chr5D 96.552 580 16 3 1616 2192 200787130 200786552 0.000000e+00 957.0
9 TraesCS5B01G119600 chr5D 90.929 463 42 0 9 471 200790207 200789745 6.650000e-175 623.0
10 TraesCS5B01G119600 chr5D 90.750 400 28 6 379 778 200789740 200789350 1.930000e-145 525.0
11 TraesCS5B01G119600 chr5D 87.742 155 16 1 600 754 200788508 200788357 6.220000e-41 178.0
12 TraesCS5B01G119600 chr5D 92.593 81 6 0 753 833 444902178 444902098 1.370000e-22 117.0
13 TraesCS5B01G119600 chrUn 94.215 242 7 2 1358 1592 471412444 471412685 1.600000e-96 363.0
14 TraesCS5B01G119600 chr4D 78.084 616 104 22 1 603 80957070 80957667 5.750000e-96 361.0
15 TraesCS5B01G119600 chr4A 77.814 613 107 22 1 603 490585789 490586382 3.460000e-93 351.0
16 TraesCS5B01G119600 chr4A 74.781 571 101 31 52 601 60009636 60009088 1.320000e-52 217.0
17 TraesCS5B01G119600 chr4B 75.614 611 107 24 1 603 113881724 113882300 4.640000e-67 265.0
18 TraesCS5B01G119600 chr7D 76.455 378 63 18 9 378 563674622 563674981 4.810000e-42 182.0
19 TraesCS5B01G119600 chr7B 77.500 240 42 7 139 378 613431157 613431384 1.370000e-27 134.0
20 TraesCS5B01G119600 chr3B 96.053 76 3 0 753 828 798525844 798525919 8.220000e-25 124.0
21 TraesCS5B01G119600 chr3B 91.228 57 5 0 1 57 685651427 685651483 6.490000e-11 78.7
22 TraesCS5B01G119600 chr3B 89.474 57 6 0 1 57 685622857 685622913 3.020000e-09 73.1
23 TraesCS5B01G119600 chr3A 95.946 74 3 0 753 826 726123444 726123517 1.060000e-23 121.0
24 TraesCS5B01G119600 chr3A 93.243 74 5 0 754 827 659020118 659020191 2.300000e-20 110.0
25 TraesCS5B01G119600 chr3D 93.421 76 5 0 753 828 595076871 595076946 1.780000e-21 113.0


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 TraesCS5B01G119600 chr5B 211738093 211740284 2191 True 4048.0 4048 100.000 1 2192 1 chr5B.!!$R1 2191
1 TraesCS5B01G119600 chr5A 214954459 214955953 1494 True 2222.0 2222 93.988 689 2140 1 chr5A.!!$R1 1451
2 TraesCS5B01G119600 chr5D 200786552 200790207 3655 True 751.8 1476 92.118 9 2192 5 chr5D.!!$R2 2183
3 TraesCS5B01G119600 chr4D 80957070 80957667 597 False 361.0 361 78.084 1 603 1 chr4D.!!$F1 602
4 TraesCS5B01G119600 chr4A 490585789 490586382 593 False 351.0 351 77.814 1 603 1 chr4A.!!$F1 602
5 TraesCS5B01G119600 chr4A 60009088 60009636 548 True 217.0 217 74.781 52 601 1 chr4A.!!$R1 549
6 TraesCS5B01G119600 chr4B 113881724 113882300 576 False 265.0 265 75.614 1 603 1 chr4B.!!$F1 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
251 265 0.101399 CTCCTACGCGACTGCTCATT 59.899 55.0 15.93 0.0 39.65 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 2964 0.396435 ACCATCCAGTCGTTCAAGCA 59.604 50.0 0.0 0.0 0.0 3.91 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
70 71 1.640428 CTAGCCGCAACGAGAATCAA 58.360 50.000 0.00 0.00 33.17 2.57
90 91 2.713895 ATCGCATCTCTACATCCACG 57.286 50.000 0.00 0.00 0.00 4.94
103 108 2.593468 ATCCACGCCCGTCATTCCTG 62.593 60.000 0.00 0.00 0.00 3.86
110 115 0.321564 CCCGTCATTCCTGTTGCTGA 60.322 55.000 0.00 0.00 0.00 4.26
160 165 0.942410 CACGTACACAGTTGACGGGG 60.942 60.000 8.50 0.00 40.84 5.73
217 222 0.106318 ACGGTAGAGGGGCGATTAGT 60.106 55.000 0.00 0.00 0.00 2.24
251 265 0.101399 CTCCTACGCGACTGCTCATT 59.899 55.000 15.93 0.00 39.65 2.57
285 299 1.516386 CCGCTGCATCGTCTACGTT 60.516 57.895 9.34 0.00 40.80 3.99
440 560 4.371786 TCGCTTATGCCTCTCATGTTTAG 58.628 43.478 0.00 0.00 36.63 1.85
444 565 5.008118 GCTTATGCCTCTCATGTTTAGTTCC 59.992 44.000 0.00 0.00 36.63 3.62
517 644 5.406780 GTGCATGCTTATCTAGAGCGTAATT 59.593 40.000 20.33 0.00 43.02 1.40
554 681 6.812879 TTCTATCAATGCCATGATCATGAC 57.187 37.500 32.71 24.03 41.20 3.06
560 687 8.873186 ATCAATGCCATGATCATGACTATTTA 57.127 30.769 32.71 20.32 41.20 1.40
613 740 9.573133 CTATTTATTCAACACTTTCAACCCATC 57.427 33.333 0.00 0.00 0.00 3.51
638 765 2.158740 GGGGGAGGATAAAGAGAGCAAC 60.159 54.545 0.00 0.00 0.00 4.17
710 837 9.362539 GCAAATTCATTGAAGAGTGTTTGATAT 57.637 29.630 19.31 0.00 41.85 1.63
719 846 8.918202 TGAAGAGTGTTTGATATACCAAAAGT 57.082 30.769 0.00 0.00 37.72 2.66
874 2397 2.926838 CTCCTTCTTTAGTCTTCTGCGC 59.073 50.000 0.00 0.00 0.00 6.09
922 2445 6.561614 TCTCTTGTCGTTATATCCAAGACAC 58.438 40.000 0.00 0.00 40.91 3.67
995 2523 1.519719 GGAAGAGGTCATCTGCGCT 59.480 57.895 9.73 0.00 38.67 5.92
1010 2538 3.474570 GCTCGGGATGGAGGCAGT 61.475 66.667 0.00 0.00 34.56 4.40
1074 2602 2.364448 GAGGAGGAGAAGGGCCGT 60.364 66.667 0.00 0.00 0.00 5.68
1302 2831 0.746063 TTGATGCAATGGATTCCGCC 59.254 50.000 0.00 0.00 0.00 6.13
1435 2964 4.402155 TGCTTCAGTGTTCCTTTGTTCATT 59.598 37.500 0.00 0.00 0.00 2.57
1543 3079 0.877743 GGAACAAGAAGCTCAGGTGC 59.122 55.000 0.00 0.00 0.00 5.01
1613 3149 4.101430 TCTGCCTTGGCTTCTTTCAAAATT 59.899 37.500 13.18 0.00 0.00 1.82
1622 3176 4.318050 GCTTCTTTCAAAATTGGCAACGAC 60.318 41.667 0.00 0.00 42.51 4.34
1679 3234 3.461831 TCCCAAGAGGAAGAGACCAAAAA 59.538 43.478 0.00 0.00 43.78 1.94
1832 3387 5.614308 TGGATAACCAGATATTCACAGCAG 58.386 41.667 0.00 0.00 41.77 4.24
2063 3618 1.133199 TGCCATTGGGTGAAAGGAAGT 60.133 47.619 4.53 0.00 36.17 3.01
2148 3703 9.965824 AAGGGCAAATAAATGTTAGATAAATCG 57.034 29.630 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 2.864097 GCGTGGATGTAGAGATGCGATT 60.864 50.000 0.00 0.00 0.00 3.34
90 91 1.675641 AGCAACAGGAATGACGGGC 60.676 57.895 0.00 0.00 0.00 6.13
150 155 0.614134 GACCTACTCCCCCGTCAACT 60.614 60.000 0.00 0.00 0.00 3.16
160 165 2.614734 CGGGGTTTCAAAGACCTACTCC 60.615 54.545 0.00 0.00 37.34 3.85
251 265 2.332514 GGACGTGGACGAACGACA 59.667 61.111 14.87 0.00 46.49 4.35
285 299 1.992667 GTGACGATGAAGACGATGCAA 59.007 47.619 0.00 0.00 34.70 4.08
289 303 2.814269 CATGGTGACGATGAAGACGAT 58.186 47.619 0.94 0.00 34.70 3.73
399 422 2.626743 CGAGTTATACCCTCCAATCGGT 59.373 50.000 0.00 0.00 36.08 4.69
440 560 2.673326 GCTGGTACCACTAAGACGGAAC 60.673 54.545 11.60 0.00 0.00 3.62
444 565 3.380637 ACATAGCTGGTACCACTAAGACG 59.619 47.826 22.41 10.73 0.00 4.18
613 740 2.630580 CTCTCTTTATCCTCCCCCGAAG 59.369 54.545 0.00 0.00 0.00 3.79
656 783 9.723601 AAAAGCTCCTAAAATAATGAATTTGCA 57.276 25.926 0.00 0.00 37.85 4.08
662 789 9.553064 TTTGCAAAAAGCTCCTAAAATAATGAA 57.447 25.926 10.02 0.00 45.94 2.57
666 793 9.553064 TGAATTTGCAAAAAGCTCCTAAAATAA 57.447 25.926 17.19 0.00 45.94 1.40
668 795 8.625786 ATGAATTTGCAAAAAGCTCCTAAAAT 57.374 26.923 17.19 0.00 45.94 1.82
674 801 5.927954 TCAATGAATTTGCAAAAAGCTCC 57.072 34.783 17.19 2.84 45.94 4.70
675 802 7.042254 ACTCTTCAATGAATTTGCAAAAAGCTC 60.042 33.333 17.19 10.84 45.94 4.09
677 804 6.849305 CACTCTTCAATGAATTTGCAAAAAGC 59.151 34.615 17.19 8.97 45.96 3.51
828 2351 0.817634 TGGGTTGGACGCAGACAAAG 60.818 55.000 0.00 0.00 36.06 2.77
874 2397 1.493311 GGAACGCAAGAAGACGCAG 59.507 57.895 0.00 0.00 43.62 5.18
922 2445 3.358076 GAGACGACGGGGAAGGCTG 62.358 68.421 0.00 0.00 0.00 4.85
995 2523 3.083349 CCACTGCCTCCATCCCGA 61.083 66.667 0.00 0.00 0.00 5.14
1074 2602 1.764854 GGATCCGTGGCCCCTCTTA 60.765 63.158 0.00 0.00 0.00 2.10
1302 2831 9.087424 TCGTCTCATATTTTGATTGTTACAGAG 57.913 33.333 0.00 0.00 32.72 3.35
1435 2964 0.396435 ACCATCCAGTCGTTCAAGCA 59.604 50.000 0.00 0.00 0.00 3.91
1505 3041 8.924511 TTGTTCCTGGAAATATTATCCATCTC 57.075 34.615 11.40 0.00 45.57 2.75
1543 3079 2.275318 GAAGAAGGGACGCTTCAGATG 58.725 52.381 28.01 0.00 41.69 2.90
1613 3149 2.481185 GGTCGAAATTAAGTCGTTGCCA 59.519 45.455 10.20 0.00 39.52 4.92
1622 3176 6.743575 AGGTCAATCTTGGTCGAAATTAAG 57.256 37.500 0.00 0.00 0.00 1.85
1668 3223 6.184789 TGTAACAAGGTTCTTTTTGGTCTCT 58.815 36.000 0.00 0.00 0.00 3.10
1679 3234 6.767524 TGTGAAATGTTGTAACAAGGTTCT 57.232 33.333 1.10 0.00 43.03 3.01
1761 3316 1.827344 TCAGATCACCACTGTAGCTGG 59.173 52.381 0.00 0.00 36.81 4.85
1832 3387 3.482110 CGTAAGCTTCAACTGCAAAACAC 59.518 43.478 0.00 0.00 0.00 3.32
2135 3690 6.931838 ACACCTTGAGACGATTTATCTAACA 58.068 36.000 0.00 0.00 0.00 2.41
2148 3703 3.997021 CACATTGTCCTACACCTTGAGAC 59.003 47.826 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.