Multiple sequence alignment - TraesCS6D01G185300

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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 TraesCS6D01G185300 chr6D 100.000 3199 0 0 1 3199 238727462 238724264 0 5908
1 TraesCS6D01G185300 chr6D 98.423 634 10 0 1 634 90824178 90823545 0 1116
2 TraesCS6D01G185300 chr6D 98.423 634 10 0 1 634 337086382 337087015 0 1116
3 TraesCS6D01G185300 chr6D 98.265 634 11 0 1 634 20038975 20038342 0 1110
4 TraesCS6D01G185300 chr1A 92.621 2575 173 12 634 3199 355025369 355027935 0 3687
5 TraesCS6D01G185300 chr3D 96.004 2252 75 12 634 2878 448148501 448150744 0 3646
6 TraesCS6D01G185300 chr3D 97.823 643 13 1 1 643 535632937 535633578 0 1109
7 TraesCS6D01G185300 chr5D 91.457 2540 192 21 634 3161 179127411 179129937 0 3465
8 TraesCS6D01G185300 chr5D 98.268 635 11 0 1 635 367650439 367649805 0 1112
9 TraesCS6D01G185300 chr5D 97.966 639 12 1 1 639 345502102 345501465 0 1107
10 TraesCS6D01G185300 chr4A 91.008 2580 206 22 634 3199 113197957 113200524 0 3456
11 TraesCS6D01G185300 chr2D 91.342 2518 171 37 634 3127 290211340 290208846 0 3398
12 TraesCS6D01G185300 chr2D 98.425 635 10 0 1 635 76792907 76793541 0 1118
13 TraesCS6D01G185300 chr6A 90.465 2580 220 19 634 3199 481855519 481852952 0 3378
14 TraesCS6D01G185300 chr6A 90.318 2582 222 22 634 3199 481860064 481857495 0 3358
15 TraesCS6D01G185300 chr1B 90.546 2507 201 29 711 3199 617347364 617349852 0 3284
16 TraesCS6D01G185300 chr7B 90.375 2504 215 18 711 3199 122446501 122448993 0 3265
17 TraesCS6D01G185300 chr4D 98.425 635 10 0 1 635 490116374 490117008 0 1118
18 TraesCS6D01G185300 chr7D 98.268 635 11 0 1 635 593456771 593457405 0 1112


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 TraesCS6D01G185300 chr6D 238724264 238727462 3198 True 5908 5908 100.0000 1 3199 1 chr6D.!!$R3 3198
1 TraesCS6D01G185300 chr6D 90823545 90824178 633 True 1116 1116 98.4230 1 634 1 chr6D.!!$R2 633
2 TraesCS6D01G185300 chr6D 337086382 337087015 633 False 1116 1116 98.4230 1 634 1 chr6D.!!$F1 633
3 TraesCS6D01G185300 chr6D 20038342 20038975 633 True 1110 1110 98.2650 1 634 1 chr6D.!!$R1 633
4 TraesCS6D01G185300 chr1A 355025369 355027935 2566 False 3687 3687 92.6210 634 3199 1 chr1A.!!$F1 2565
5 TraesCS6D01G185300 chr3D 448148501 448150744 2243 False 3646 3646 96.0040 634 2878 1 chr3D.!!$F1 2244
6 TraesCS6D01G185300 chr3D 535632937 535633578 641 False 1109 1109 97.8230 1 643 1 chr3D.!!$F2 642
7 TraesCS6D01G185300 chr5D 179127411 179129937 2526 False 3465 3465 91.4570 634 3161 1 chr5D.!!$F1 2527
8 TraesCS6D01G185300 chr5D 367649805 367650439 634 True 1112 1112 98.2680 1 635 1 chr5D.!!$R2 634
9 TraesCS6D01G185300 chr5D 345501465 345502102 637 True 1107 1107 97.9660 1 639 1 chr5D.!!$R1 638
10 TraesCS6D01G185300 chr4A 113197957 113200524 2567 False 3456 3456 91.0080 634 3199 1 chr4A.!!$F1 2565
11 TraesCS6D01G185300 chr2D 290208846 290211340 2494 True 3398 3398 91.3420 634 3127 1 chr2D.!!$R1 2493
12 TraesCS6D01G185300 chr2D 76792907 76793541 634 False 1118 1118 98.4250 1 635 1 chr2D.!!$F1 634
13 TraesCS6D01G185300 chr6A 481852952 481860064 7112 True 3368 3378 90.3915 634 3199 2 chr6A.!!$R1 2565
14 TraesCS6D01G185300 chr1B 617347364 617349852 2488 False 3284 3284 90.5460 711 3199 1 chr1B.!!$F1 2488
15 TraesCS6D01G185300 chr7B 122446501 122448993 2492 False 3265 3265 90.3750 711 3199 1 chr7B.!!$F1 2488
16 TraesCS6D01G185300 chr4D 490116374 490117008 634 False 1118 1118 98.4250 1 635 1 chr4D.!!$F1 634
17 TraesCS6D01G185300 chr7D 593456771 593457405 634 False 1112 1112 98.2680 1 635 1 chr7D.!!$F1 634

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
61 62 4.054780 ACTCGTACCGTAATGCATGATT 57.945 40.909 0.00 0.0 0.00 2.57 F
419 420 4.388485 TGATGTGATCCCGTTATCAATGG 58.612 43.478 0.00 0.0 37.61 3.16 F
444 445 5.102953 TCCAATGTCCATAGTCAGGAAAG 57.897 43.478 0.00 0.0 36.80 2.62 F
1244 1249 5.403766 GTGAATACGAGAGCTTGTATGATGG 59.596 44.000 10.37 0.0 39.46 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1244 1249 0.984995 AGCCTTGTACCTCTCCCAAC 59.015 55.000 0.00 0.0 0.00 3.77 R
1287 1292 1.215673 TCTAACCATCTCTCGAGCCCT 59.784 52.381 7.81 0.0 0.00 5.19 R
1360 5911 1.926426 AATAGCTCCACCCACTGCCC 61.926 60.000 0.00 0.0 0.00 5.36 R
2882 7458 1.918293 ACAAGCCACCGATCCAGGA 60.918 57.895 0.00 0.0 34.73 3.86 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
25 26 8.848474 CCCAATACCTTATTCAATCTCGTTAT 57.152 34.615 0.00 0.00 0.00 1.89
61 62 4.054780 ACTCGTACCGTAATGCATGATT 57.945 40.909 0.00 0.00 0.00 2.57
97 98 4.697352 ACTTGGTCACATTGAGCTCATTAC 59.303 41.667 19.04 9.14 44.58 1.89
419 420 4.388485 TGATGTGATCCCGTTATCAATGG 58.612 43.478 0.00 0.00 37.61 3.16
444 445 5.102953 TCCAATGTCCATAGTCAGGAAAG 57.897 43.478 0.00 0.00 36.80 2.62
938 943 5.710099 TGAAACCTAGTCTTATTGCTTTGGG 59.290 40.000 0.00 0.00 0.00 4.12
1244 1249 5.403766 GTGAATACGAGAGCTTGTATGATGG 59.596 44.000 10.37 0.00 39.46 3.51
1360 5911 2.284684 ACACTCGAGCTTACGTCGATAG 59.715 50.000 13.61 0.00 45.00 2.08
1366 5917 0.384669 GCTTACGTCGATAGGGCAGT 59.615 55.000 0.00 0.00 0.00 4.40
1516 6067 5.046807 TCACTTCATCTCAGCAAGAATCTCA 60.047 40.000 0.00 0.00 37.61 3.27
1529 6080 6.712095 AGCAAGAATCTCATACACAAAAGTCA 59.288 34.615 0.00 0.00 0.00 3.41
1861 6412 3.204306 TGATGAGGTGGATTCAGATGC 57.796 47.619 0.00 0.00 0.00 3.91
1956 6507 7.181125 ACTTGGTATCTTCAATTGAGGTAGTCT 59.819 37.037 16.29 3.87 0.00 3.24
2225 6781 3.766591 ACAGAGTTCGAGATGACATTCCT 59.233 43.478 0.00 0.00 0.00 3.36
2335 6892 4.712476 AGAGAAGCAAAAAGAGAAGAGCA 58.288 39.130 0.00 0.00 0.00 4.26
2449 7011 7.879160 ACATGCTGAAATCAAATGTTATTTGGT 59.121 29.630 12.72 4.63 32.51 3.67
2569 7138 8.668510 AAACTAGTGATCTACATATTGCTTGG 57.331 34.615 0.00 0.00 0.00 3.61
2577 7146 2.963432 ACATATTGCTTGGTTTGCTGC 58.037 42.857 0.00 0.00 0.00 5.25
2817 7388 9.358872 GATGATTCTTGTTTCCTTTTGTATTCC 57.641 33.333 0.00 0.00 0.00 3.01
2882 7458 5.560724 ACCTAACAGTAGCATGTCATGTTT 58.439 37.500 14.26 6.03 35.77 2.83
2917 7493 3.507233 GCTTGTGAAATCTGGTTGGATCA 59.493 43.478 0.00 0.00 0.00 2.92
3087 7665 4.841813 TGGTATGTTCCTTTGGTGAGACTA 59.158 41.667 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.442706 ACTTGCCGATAACGAGATTGAAT 58.557 39.130 0.00 0.00 42.66 2.57
25 26 1.338973 ACGAGTAAAGTGACTTGCCGA 59.661 47.619 0.00 0.00 34.59 5.54
97 98 1.794701 CCACTCGGTAATGCATCATCG 59.205 52.381 0.00 0.00 0.00 3.84
203 204 2.017049 GGTGGCTATAAAGGTGCACTG 58.983 52.381 17.98 0.15 0.00 3.66
419 420 3.144506 CCTGACTATGGACATTGGATGC 58.855 50.000 0.00 0.00 0.00 3.91
444 445 4.805719 TCGTTGATCAACAGATAGTCATGC 59.194 41.667 32.06 6.59 41.20 4.06
719 722 9.209048 TCAGAAAGTTAGTATCCTAATAAGCCA 57.791 33.333 0.00 0.00 35.67 4.75
938 943 3.442273 TCCTCCAAACTGTTGTTGTTGAC 59.558 43.478 0.00 0.00 36.39 3.18
1125 1130 5.536538 AGCTCGTGATATCTCATTCCAACTA 59.463 40.000 3.98 0.00 32.98 2.24
1244 1249 0.984995 AGCCTTGTACCTCTCCCAAC 59.015 55.000 0.00 0.00 0.00 3.77
1287 1292 1.215673 TCTAACCATCTCTCGAGCCCT 59.784 52.381 7.81 0.00 0.00 5.19
1360 5911 1.926426 AATAGCTCCACCCACTGCCC 61.926 60.000 0.00 0.00 0.00 5.36
1366 5917 4.042311 TCTTGTTTGTAATAGCTCCACCCA 59.958 41.667 0.00 0.00 0.00 4.51
1399 5950 4.139786 ACTCTCAATCAGCAGAAAAGCAA 58.860 39.130 0.00 0.00 36.85 3.91
1516 6067 6.828785 AGAAACTGGTTCTGACTTTTGTGTAT 59.171 34.615 7.25 0.00 45.29 2.29
1956 6507 7.364232 CCTGAGATAGTTAGGAAGAAGCTTCAA 60.364 40.741 27.57 10.45 33.33 2.69
2106 6662 3.068873 AGAATGCCCTCTAAGTCATCGAC 59.931 47.826 0.00 0.00 0.00 4.20
2335 6892 4.502962 GCTTGATCACTCTCTAAGTTGCT 58.497 43.478 0.00 0.00 35.45 3.91
2569 7138 4.301628 AGCTTTCACTAATTGCAGCAAAC 58.698 39.130 12.97 0.00 34.92 2.93
2637 7206 7.769044 GGTGTATCAAGGTAAGAGCAGAAAATA 59.231 37.037 0.00 0.00 0.00 1.40
2882 7458 1.918293 ACAAGCCACCGATCCAGGA 60.918 57.895 0.00 0.00 34.73 3.86
3129 7710 6.098679 TGCAGAAATATAACATTGTGGTTGC 58.901 36.000 0.00 0.00 32.29 4.17


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

AutoCloner maintained by Alex Coulton.