Multiple sequence alignment - TraesCS4D01G117000

Loading Multiple Alignment...

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 TraesCS4D01G117000 chr4D 100.000 2292 0 0 1 2292 97738905 97736614 0.000000e+00 4233.0
1 TraesCS4D01G117000 chr4D 98.651 1112 12 2 680 1788 98064005 98065116 0.000000e+00 1967.0
2 TraesCS4D01G117000 chr4D 98.036 1120 7 2 680 1784 98091219 98092338 0.000000e+00 1932.0
3 TraesCS4D01G117000 chr4D 98.532 681 9 1 1 681 157764083 157764762 0.000000e+00 1201.0
4 TraesCS4D01G117000 chr4D 98.532 681 9 1 1 681 157772141 157772820 0.000000e+00 1201.0
5 TraesCS4D01G117000 chr4D 98.091 681 5 2 1 681 97729661 97728989 0.000000e+00 1179.0
6 TraesCS4D01G117000 chr3D 98.281 1105 15 3 680 1782 519322955 519321853 0.000000e+00 1932.0
7 TraesCS4D01G117000 chr5B 94.689 1111 46 5 680 1782 52477613 52478718 0.000000e+00 1712.0
8 TraesCS4D01G117000 chr2D 98.542 686 7 2 1099 1782 7175153 7174469 0.000000e+00 1208.0
9 TraesCS4D01G117000 chr2D 98.396 374 6 0 680 1053 7175524 7175151 0.000000e+00 658.0
10 TraesCS4D01G117000 chr5D 98.678 681 6 3 1 681 399992212 399992889 0.000000e+00 1205.0
11 TraesCS4D01G117000 chr5D 97.451 510 8 1 1783 2292 399992880 399993384 0.000000e+00 865.0
12 TraesCS4D01G117000 chr6D 98.534 682 8 2 1 681 282003111 282002431 0.000000e+00 1203.0
13 TraesCS4D01G117000 chr6D 98.094 682 10 3 1 681 282011224 282010545 0.000000e+00 1184.0
14 TraesCS4D01G117000 chr6D 97.255 510 14 0 1783 2292 282002440 282001931 0.000000e+00 865.0
15 TraesCS4D01G117000 chr6D 96.863 510 15 1 1783 2292 345446668 345447176 0.000000e+00 852.0
16 TraesCS4D01G117000 chr6D 96.680 512 15 1 1783 2292 282010554 282010043 0.000000e+00 850.0
17 TraesCS4D01G117000 chr7A 98.251 686 10 1 1103 1786 725246835 725246150 0.000000e+00 1199.0
18 TraesCS4D01G117000 chr1D 98.387 682 9 2 1 681 200182093 200181413 0.000000e+00 1197.0
19 TraesCS4D01G117000 chr1D 96.760 679 19 3 1 678 124841953 124841277 0.000000e+00 1129.0
20 TraesCS4D01G117000 chr1D 97.446 509 13 0 1784 2292 200181421 200180913 0.000000e+00 869.0
21 TraesCS4D01G117000 chr1D 93.922 510 30 1 1783 2292 124841283 124840775 0.000000e+00 769.0
22 TraesCS4D01G117000 chr2A 96.476 681 22 2 1 680 79699232 79699911 0.000000e+00 1123.0
23 TraesCS4D01G117000 chr1A 93.725 510 32 0 1783 2292 497234026 497233517 0.000000e+00 765.0
24 TraesCS4D01G117000 chr6A 91.765 510 41 1 1783 2292 266869379 266868871 0.000000e+00 708.0
25 TraesCS4D01G117000 chr6A 91.569 510 42 1 1783 2292 266829549 266829041 0.000000e+00 702.0
26 TraesCS4D01G117000 chr6A 94.758 248 10 3 905 1152 116808543 116808787 1.280000e-102 383.0
27 TraesCS4D01G117000 chr6A 91.571 261 15 5 1494 1748 116810130 116810389 1.010000e-93 353.0
28 TraesCS4D01G117000 chr6A 88.197 305 15 5 1203 1507 116808790 116809073 6.060000e-91 344.0
29 TraesCS4D01G117000 chr6A 93.548 124 3 3 788 909 116802867 116802987 1.810000e-41 180.0
30 TraesCS4D01G117000 chr4A 82.861 671 70 25 1146 1782 576802245 576802904 5.530000e-156 560.0
31 TraesCS4D01G117000 chr6B 96.016 251 9 1 903 1152 644456949 644456699 7.620000e-110 407.0
32 TraesCS4D01G117000 chr6B 95.726 234 10 0 680 913 644457574 644457341 5.980000e-101 377.0
33 TraesCS4D01G117000 chr7B 80.714 140 17 8 680 815 686977830 686977963 1.450000e-17 100.0
34 TraesCS4D01G117000 chr7B 80.714 140 17 8 680 815 686990204 686990071 1.450000e-17 100.0
35 TraesCS4D01G117000 chr7B 80.147 136 20 6 668 799 645428190 645428322 6.740000e-16 95.3


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 TraesCS4D01G117000 chr4D 97736614 97738905 2291 True 4233 4233 100.000000 1 2292 1 chr4D.!!$R2 2291
1 TraesCS4D01G117000 chr4D 98064005 98065116 1111 False 1967 1967 98.651000 680 1788 1 chr4D.!!$F1 1108
2 TraesCS4D01G117000 chr4D 98091219 98092338 1119 False 1932 1932 98.036000 680 1784 1 chr4D.!!$F2 1104
3 TraesCS4D01G117000 chr4D 157764083 157764762 679 False 1201 1201 98.532000 1 681 1 chr4D.!!$F3 680
4 TraesCS4D01G117000 chr4D 157772141 157772820 679 False 1201 1201 98.532000 1 681 1 chr4D.!!$F4 680
5 TraesCS4D01G117000 chr4D 97728989 97729661 672 True 1179 1179 98.091000 1 681 1 chr4D.!!$R1 680
6 TraesCS4D01G117000 chr3D 519321853 519322955 1102 True 1932 1932 98.281000 680 1782 1 chr3D.!!$R1 1102
7 TraesCS4D01G117000 chr5B 52477613 52478718 1105 False 1712 1712 94.689000 680 1782 1 chr5B.!!$F1 1102
8 TraesCS4D01G117000 chr2D 7174469 7175524 1055 True 933 1208 98.469000 680 1782 2 chr2D.!!$R1 1102
9 TraesCS4D01G117000 chr5D 399992212 399993384 1172 False 1035 1205 98.064500 1 2292 2 chr5D.!!$F1 2291
10 TraesCS4D01G117000 chr6D 282001931 282003111 1180 True 1034 1203 97.894500 1 2292 2 chr6D.!!$R1 2291
11 TraesCS4D01G117000 chr6D 282010043 282011224 1181 True 1017 1184 97.387000 1 2292 2 chr6D.!!$R2 2291
12 TraesCS4D01G117000 chr6D 345446668 345447176 508 False 852 852 96.863000 1783 2292 1 chr6D.!!$F1 509
13 TraesCS4D01G117000 chr7A 725246150 725246835 685 True 1199 1199 98.251000 1103 1786 1 chr7A.!!$R1 683
14 TraesCS4D01G117000 chr1D 200180913 200182093 1180 True 1033 1197 97.916500 1 2292 2 chr1D.!!$R2 2291
15 TraesCS4D01G117000 chr1D 124840775 124841953 1178 True 949 1129 95.341000 1 2292 2 chr1D.!!$R1 2291
16 TraesCS4D01G117000 chr2A 79699232 79699911 679 False 1123 1123 96.476000 1 680 1 chr2A.!!$F1 679
17 TraesCS4D01G117000 chr1A 497233517 497234026 509 True 765 765 93.725000 1783 2292 1 chr1A.!!$R1 509
18 TraesCS4D01G117000 chr6A 266868871 266869379 508 True 708 708 91.765000 1783 2292 1 chr6A.!!$R2 509
19 TraesCS4D01G117000 chr6A 266829041 266829549 508 True 702 702 91.569000 1783 2292 1 chr6A.!!$R1 509
20 TraesCS4D01G117000 chr6A 116808543 116810389 1846 False 360 383 91.508667 905 1748 3 chr6A.!!$F2 843
21 TraesCS4D01G117000 chr4A 576802245 576802904 659 False 560 560 82.861000 1146 1782 1 chr4A.!!$F1 636
22 TraesCS4D01G117000 chr6B 644456699 644457574 875 True 392 407 95.871000 680 1152 2 chr6B.!!$R1 472

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
710 721 2.742372 CGTACAGCACAGTGGGGC 60.742 66.667 1.84 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 3755 1.280746 CGACACAAGCAGCAACAGG 59.719 57.895 0.0 0.0 0.0 4.0 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
710 721 2.742372 CGTACAGCACAGTGGGGC 60.742 66.667 1.84 0.0 0.00 5.80
925 1344 4.158764 AGGAAACGTGAGATCTGTTCCTAG 59.841 45.833 11.28 0.0 0.00 3.02
1303 1727 3.194116 ACATTTTGTGAGCCATAGCCTTG 59.806 43.478 0.00 0.0 41.25 3.61
1473 1901 6.150307 TGCATTCCGTCTTAATTTTAGCTTCA 59.850 34.615 0.00 0.0 0.00 3.02
1935 3476 0.667487 CACCAACTCGCAGTCGATGT 60.667 55.000 0.00 0.0 44.56 3.06
2211 3755 2.336809 CCGCCGCTGTCCTATCTC 59.663 66.667 0.00 0.0 0.00 2.75
2262 3806 4.819761 CGCTCGCCTTGCCTGCTA 62.820 66.667 0.00 0.0 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
444 455 0.614979 CAGAGGAAAGGGGAGACGGA 60.615 60.000 0.00 0.00 0.00 4.69
559 570 1.451747 GACGAGAGCGGTCTAGGGT 60.452 63.158 25.16 19.12 43.17 4.34
710 721 2.608970 AATCGAGTGGGGGCATTCGG 62.609 60.000 0.00 0.00 35.47 4.30
925 1344 7.823799 AGAAGATCTCACATTTCCTCTCTTTTC 59.176 37.037 0.00 0.00 0.00 2.29
1386 1814 6.151144 CACATTACCTTTTTCTTTCCTCCGAT 59.849 38.462 0.00 0.00 0.00 4.18
1561 3078 9.220767 ACTAATCACTTTAGACAAAATGACCTC 57.779 33.333 0.00 0.00 39.86 3.85
1981 3522 1.611851 AGGGAGGAGCTCACTGTGG 60.612 63.158 17.19 0.00 43.31 4.17
2204 3748 2.286872 CAAGCAGCAACAGGAGATAGG 58.713 52.381 0.00 0.00 0.00 2.57
2211 3755 1.280746 CGACACAAGCAGCAACAGG 59.719 57.895 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.