Multiple sequence alignment - TraesCS4A01G414400
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 pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
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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 primersListed 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. |
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Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.