Multiple sequence alignment - TraesCS4A01G414400

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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 TraesCS4A01G414400 chr4A 100.000 3063 0 0 1 3063 684901343 684898281 0.000000e+00 5657.0
1 TraesCS4A01G414400 chr4A 94.203 759 29 6 2314 3063 440199930 440200682 0.000000e+00 1144.0
2 TraesCS4A01G414400 chr4D 85.341 1760 117 67 478 2155 478232257 478230557 0.000000e+00 1690.0
3 TraesCS4A01G414400 chr4D 92.510 761 29 9 2314 3063 64226178 64225435 0.000000e+00 1064.0
4 TraesCS4A01G414400 chr4D 92.116 761 27 10 2314 3063 173582091 173582829 0.000000e+00 1042.0
5 TraesCS4A01G414400 chr4D 91.316 760 33 12 2314 3063 381437638 381436902 0.000000e+00 1007.0
6 TraesCS4A01G414400 chr4D 89.910 446 45 0 1616 2061 489742328 489742773 2.650000e-160 575.0
7 TraesCS4A01G414400 chr4D 90.301 299 26 2 1224 1522 489741047 489741342 3.700000e-104 388.0
8 TraesCS4A01G414400 chr4D 96.296 54 2 0 1 54 478232936 478232883 4.210000e-14 89.8
9 TraesCS4A01G414400 chr4D 97.368 38 1 0 1086 1123 261757904 261757941 7.090000e-07 65.8
10 TraesCS4A01G414400 chr4D 95.122 41 2 0 1086 1126 474591323 474591283 7.090000e-07 65.8
11 TraesCS4A01G414400 chr4D 97.059 34 1 0 1093 1126 497132037 497132004 1.190000e-04 58.4
12 TraesCS4A01G414400 chr6D 94.203 759 25 8 2314 3063 55668790 55668042 0.000000e+00 1140.0
13 TraesCS4A01G414400 chr6D 91.853 761 33 10 2314 3063 340953278 340954020 0.000000e+00 1035.0
14 TraesCS4A01G414400 chr6D 95.556 45 2 0 1079 1123 21917154 21917198 4.240000e-09 73.1
15 TraesCS4A01G414400 chr6D 97.368 38 1 0 1086 1123 372822377 372822414 7.090000e-07 65.8
16 TraesCS4A01G414400 chr6D 95.122 41 2 0 1086 1126 473109101 473109061 7.090000e-07 65.8
17 TraesCS4A01G414400 chr6D 92.683 41 3 0 1086 1126 401298625 401298585 3.300000e-05 60.2
18 TraesCS4A01G414400 chr2D 93.939 759 29 7 2314 3063 325744637 325743887 0.000000e+00 1131.0
19 TraesCS4A01G414400 chr2D 92.257 762 28 11 2314 3063 592372966 592372224 0.000000e+00 1051.0
20 TraesCS4A01G414400 chr2D 91.304 759 36 5 2314 3063 78342213 78341476 0.000000e+00 1009.0
21 TraesCS4A01G414400 chr2D 97.436 39 1 0 1085 1123 154110674 154110712 1.970000e-07 67.6
22 TraesCS4A01G414400 chr5A 93.149 759 31 9 2314 3063 92448322 92449068 0.000000e+00 1094.0
23 TraesCS4A01G414400 chr5A 89.298 299 29 2 1224 1522 671191068 671191363 3.730000e-99 372.0
24 TraesCS4A01G414400 chr1D 93.149 759 29 8 2314 3063 234861776 234862520 0.000000e+00 1092.0
25 TraesCS4A01G414400 chr1D 90.646 759 44 8 2314 3063 49631128 49631868 0.000000e+00 983.0
26 TraesCS4A01G414400 chr1D 95.238 42 2 0 1085 1126 169367539 169367498 1.970000e-07 67.6
27 TraesCS4A01G414400 chr1D 90.000 50 5 0 1077 1126 45399311 45399262 7.090000e-07 65.8
28 TraesCS4A01G414400 chr1D 95.122 41 2 0 1086 1126 46112244 46112204 7.090000e-07 65.8
29 TraesCS4A01G414400 chr3D 92.773 761 25 8 2314 3063 94712815 94712074 0.000000e+00 1074.0
30 TraesCS4A01G414400 chr3D 90.333 600 31 8 2314 2903 614122187 614122769 0.000000e+00 761.0
31 TraesCS4A01G414400 chr7D 92.378 761 30 9 2314 3063 369901832 369901089 0.000000e+00 1059.0
32 TraesCS4A01G414400 chr7D 91.017 757 35 10 2314 3060 60233407 60232674 0.000000e+00 990.0
33 TraesCS4A01G414400 chr7D 86.852 540 61 9 1616 2150 539764434 539764968 2.030000e-166 595.0
34 TraesCS4A01G414400 chr7D 87.714 350 28 11 1180 1520 539761099 539761442 7.960000e-106 394.0
35 TraesCS4A01G414400 chr7D 95.238 42 2 0 1085 1126 468941647 468941606 1.970000e-07 67.6
36 TraesCS4A01G414400 chr7D 97.436 39 1 0 1085 1123 577826133 577826171 1.970000e-07 67.6
37 TraesCS4A01G414400 chr7D 95.238 42 2 0 1085 1126 586892612 586892571 1.970000e-07 67.6
38 TraesCS4A01G414400 chr1A 92.267 763 30 9 2314 3063 76806922 76806176 0.000000e+00 1055.0
39 TraesCS4A01G414400 chr5D 92.116 761 32 9 2314 3063 532712812 532712069 0.000000e+00 1048.0
40 TraesCS4A01G414400 chr5D 91.579 760 29 6 2314 3063 228521857 228521123 0.000000e+00 1016.0
41 TraesCS4A01G414400 chr4B 91.261 595 37 4 1616 2197 604532731 604532139 0.000000e+00 797.0
42 TraesCS4A01G414400 chr4B 89.262 447 48 0 1615 2061 628661271 628661717 7.420000e-156 560.0
43 TraesCS4A01G414400 chr4B 86.476 525 38 19 998 1522 604533363 604532872 2.080000e-151 545.0
44 TraesCS4A01G414400 chr4B 89.632 299 28 2 1224 1522 628660198 628660493 8.020000e-101 377.0
45 TraesCS4A01G414400 chr4B 88.652 141 11 5 659 794 604539097 604538957 1.890000e-37 167.0
46 TraesCS4A01G414400 chr4B 83.069 189 11 5 792 970 604533627 604533450 5.290000e-33 152.0
47 TraesCS4A01G414400 chr4B 90.826 109 9 1 581 689 604539207 604539100 8.850000e-31 145.0
48 TraesCS4A01G414400 chr4B 95.238 42 2 0 1082 1123 187359120 187359161 1.970000e-07 67.6
49 TraesCS4A01G414400 chr4B 89.796 49 5 0 1078 1126 566573984 566573936 2.550000e-06 63.9
50 TraesCS4A01G414400 chr7A 87.148 568 57 15 1616 2174 620934775 620935335 5.570000e-177 630.0
51 TraesCS4A01G414400 chr7A 89.441 322 31 2 1199 1520 620932401 620932719 1.320000e-108 403.0
52 TraesCS4A01G414400 chr7B 87.199 539 60 8 1616 2150 582655213 582655746 3.380000e-169 604.0
53 TraesCS4A01G414400 chr7B 88.509 322 34 2 1199 1520 582653150 582653468 1.330000e-103 387.0
54 TraesCS4A01G414400 chr7B 95.455 44 2 0 1083 1126 1816336 1816293 1.520000e-08 71.3
55 TraesCS4A01G414400 chr2A 91.083 314 15 3 2318 2623 422515262 422515570 2.200000e-111 412.0
56 TraesCS4A01G414400 chr1B 93.210 162 11 0 26 187 313450465 313450304 3.950000e-59 239.0
57 TraesCS4A01G414400 chr1B 95.349 43 2 0 1084 1126 457004101 457004059 5.480000e-08 69.4
58 TraesCS4A01G414400 chr1B 95.238 42 2 0 1085 1126 395249022 395248981 1.970000e-07 67.6
59 TraesCS4A01G414400 chr2B 93.878 49 3 0 1078 1126 545250762 545250714 1.180000e-09 75.0
60 TraesCS4A01G414400 chr2B 97.561 41 1 0 1083 1123 256148463 256148503 1.520000e-08 71.3
61 TraesCS4A01G414400 chr6B 97.619 42 1 0 1082 1123 226866952 226866993 4.240000e-09 73.1
62 TraesCS4A01G414400 chr6B 92.000 50 4 0 1077 1126 41377026 41376977 1.520000e-08 71.3
63 TraesCS4A01G414400 chr6B 95.238 42 2 0 1082 1123 143439800 143439841 1.970000e-07 67.6
64 TraesCS4A01G414400 chr6B 95.122 41 2 0 1086 1126 35376197 35376157 7.090000e-07 65.8
65 TraesCS4A01G414400 chr3B 97.561 41 1 0 1083 1123 50046413 50046453 1.520000e-08 71.3
66 TraesCS4A01G414400 chr5B 95.349 43 2 0 1081 1123 640282563 640282605 5.480000e-08 69.4
67 TraesCS4A01G414400 chr6A 95.238 42 2 0 1085 1126 422165689 422165648 1.970000e-07 67.6
68 TraesCS4A01G414400 chrUn 95.122 41 2 0 1086 1126 15981933 15981893 7.090000e-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 TraesCS4A01G414400 chr4A 684898281 684901343 3062 True 5657.0 5657 100.000000 1 3063 1 chr4A.!!$R1 3062
1 TraesCS4A01G414400 chr4A 440199930 440200682 752 False 1144.0 1144 94.203000 2314 3063 1 chr4A.!!$F1 749
2 TraesCS4A01G414400 chr4D 64225435 64226178 743 True 1064.0 1064 92.510000 2314 3063 1 chr4D.!!$R1 749
3 TraesCS4A01G414400 chr4D 173582091 173582829 738 False 1042.0 1042 92.116000 2314 3063 1 chr4D.!!$F1 749
4 TraesCS4A01G414400 chr4D 381436902 381437638 736 True 1007.0 1007 91.316000 2314 3063 1 chr4D.!!$R2 749
5 TraesCS4A01G414400 chr4D 478230557 478232936 2379 True 889.9 1690 90.818500 1 2155 2 chr4D.!!$R5 2154
6 TraesCS4A01G414400 chr4D 489741047 489742773 1726 False 481.5 575 90.105500 1224 2061 2 chr4D.!!$F3 837
7 TraesCS4A01G414400 chr6D 55668042 55668790 748 True 1140.0 1140 94.203000 2314 3063 1 chr6D.!!$R1 749
8 TraesCS4A01G414400 chr6D 340953278 340954020 742 False 1035.0 1035 91.853000 2314 3063 1 chr6D.!!$F2 749
9 TraesCS4A01G414400 chr2D 325743887 325744637 750 True 1131.0 1131 93.939000 2314 3063 1 chr2D.!!$R2 749
10 TraesCS4A01G414400 chr2D 592372224 592372966 742 True 1051.0 1051 92.257000 2314 3063 1 chr2D.!!$R3 749
11 TraesCS4A01G414400 chr2D 78341476 78342213 737 True 1009.0 1009 91.304000 2314 3063 1 chr2D.!!$R1 749
12 TraesCS4A01G414400 chr5A 92448322 92449068 746 False 1094.0 1094 93.149000 2314 3063 1 chr5A.!!$F1 749
13 TraesCS4A01G414400 chr1D 234861776 234862520 744 False 1092.0 1092 93.149000 2314 3063 1 chr1D.!!$F2 749
14 TraesCS4A01G414400 chr1D 49631128 49631868 740 False 983.0 983 90.646000 2314 3063 1 chr1D.!!$F1 749
15 TraesCS4A01G414400 chr3D 94712074 94712815 741 True 1074.0 1074 92.773000 2314 3063 1 chr3D.!!$R1 749
16 TraesCS4A01G414400 chr3D 614122187 614122769 582 False 761.0 761 90.333000 2314 2903 1 chr3D.!!$F1 589
17 TraesCS4A01G414400 chr7D 369901089 369901832 743 True 1059.0 1059 92.378000 2314 3063 1 chr7D.!!$R2 749
18 TraesCS4A01G414400 chr7D 60232674 60233407 733 True 990.0 990 91.017000 2314 3060 1 chr7D.!!$R1 746
19 TraesCS4A01G414400 chr7D 539761099 539764968 3869 False 494.5 595 87.283000 1180 2150 2 chr7D.!!$F2 970
20 TraesCS4A01G414400 chr1A 76806176 76806922 746 True 1055.0 1055 92.267000 2314 3063 1 chr1A.!!$R1 749
21 TraesCS4A01G414400 chr5D 532712069 532712812 743 True 1048.0 1048 92.116000 2314 3063 1 chr5D.!!$R2 749
22 TraesCS4A01G414400 chr5D 228521123 228521857 734 True 1016.0 1016 91.579000 2314 3063 1 chr5D.!!$R1 749
23 TraesCS4A01G414400 chr4B 604532139 604533627 1488 True 498.0 797 86.935333 792 2197 3 chr4B.!!$R2 1405
24 TraesCS4A01G414400 chr4B 628660198 628661717 1519 False 468.5 560 89.447000 1224 2061 2 chr4B.!!$F2 837
25 TraesCS4A01G414400 chr7A 620932401 620935335 2934 False 516.5 630 88.294500 1199 2174 2 chr7A.!!$F1 975
26 TraesCS4A01G414400 chr7B 582653150 582655746 2596 False 495.5 604 87.854000 1199 2150 2 chr7B.!!$F1 951


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
816 1244 0.035458 AGACACGGAAGGCCTCTTTG 59.965 55.0 5.23 3.66 32.52 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2316 6815 0.250553 ACCACCCAATACACCACACG 60.251 55.0 0.0 0.0 0.0 4.49 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)



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AutoCloner maintained by Alex Coulton.