Multiple sequence alignment - TraesCS5A01G387900
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 | TraesCS5A01G387900 | chr5A | 100.000 | 5773 | 0 | 0 | 1 | 5773 | 584715273 | 584721045 | 0.000000e+00 | 10661.0 |
1 | TraesCS5A01G387900 | chr5A | 82.989 | 629 | 100 | 6 | 1890 | 2513 | 698646637 | 698646011 | 3.910000e-156 | 562.0 |
2 | TraesCS5A01G387900 | chr5A | 89.944 | 179 | 13 | 2 | 2662 | 2835 | 469102672 | 469102494 | 5.820000e-55 | 226.0 |
3 | TraesCS5A01G387900 | chr5A | 90.476 | 168 | 14 | 1 | 2662 | 2829 | 382961945 | 382961780 | 2.710000e-53 | 220.0 |
4 | TraesCS5A01G387900 | chr5A | 93.694 | 111 | 7 | 0 | 5269 | 5379 | 260334158 | 260334268 | 3.580000e-37 | 167.0 |
5 | TraesCS5A01G387900 | chr5A | 93.636 | 110 | 7 | 0 | 5268 | 5377 | 688927655 | 688927546 | 1.290000e-36 | 165.0 |
6 | TraesCS5A01G387900 | chr5A | 91.379 | 116 | 10 | 0 | 5268 | 5383 | 606350783 | 606350668 | 5.990000e-35 | 159.0 |
7 | TraesCS5A01G387900 | chr5A | 86.047 | 129 | 16 | 2 | 4971 | 5098 | 584859279 | 584859406 | 2.810000e-28 | 137.0 |
8 | TraesCS5A01G387900 | chr5A | 91.358 | 81 | 6 | 1 | 392 | 472 | 227926528 | 227926449 | 6.120000e-20 | 110.0 |
9 | TraesCS5A01G387900 | chr5B | 91.758 | 1650 | 81 | 23 | 3512 | 5142 | 571483938 | 571485551 | 0.000000e+00 | 2242.0 |
10 | TraesCS5A01G387900 | chr5B | 84.778 | 1465 | 148 | 30 | 3709 | 5142 | 571490668 | 571492088 | 0.000000e+00 | 1400.0 |
11 | TraesCS5A01G387900 | chr5B | 93.673 | 727 | 41 | 2 | 1887 | 2609 | 571480879 | 571481604 | 0.000000e+00 | 1083.0 |
12 | TraesCS5A01G387900 | chr5B | 91.195 | 795 | 47 | 12 | 1117 | 1889 | 571480060 | 571480853 | 0.000000e+00 | 1059.0 |
13 | TraesCS5A01G387900 | chr5B | 81.172 | 1041 | 117 | 29 | 3708 | 4722 | 571508829 | 571509816 | 0.000000e+00 | 763.0 |
14 | TraesCS5A01G387900 | chr5B | 91.536 | 319 | 20 | 5 | 3142 | 3455 | 387152098 | 387152414 | 3.200000e-117 | 433.0 |
15 | TraesCS5A01G387900 | chr5B | 85.610 | 410 | 48 | 8 | 4738 | 5144 | 571510083 | 571510484 | 2.490000e-113 | 420.0 |
16 | TraesCS5A01G387900 | chr5B | 86.335 | 161 | 14 | 3 | 1 | 161 | 571476417 | 571476569 | 9.950000e-38 | 169.0 |
17 | TraesCS5A01G387900 | chr5B | 84.000 | 125 | 14 | 5 | 2969 | 3093 | 571490285 | 571490403 | 1.310000e-21 | 115.0 |
18 | TraesCS5A01G387900 | chr5B | 93.333 | 75 | 5 | 0 | 392 | 466 | 460658924 | 460658998 | 1.700000e-20 | 111.0 |
19 | TraesCS5A01G387900 | chr5D | 83.122 | 1499 | 180 | 35 | 3671 | 5135 | 464395246 | 464396705 | 0.000000e+00 | 1299.0 |
20 | TraesCS5A01G387900 | chr5D | 93.676 | 759 | 41 | 2 | 1887 | 2645 | 464325574 | 464326325 | 0.000000e+00 | 1129.0 |
21 | TraesCS5A01G387900 | chr5D | 92.201 | 795 | 39 | 12 | 1117 | 1889 | 464324755 | 464325548 | 0.000000e+00 | 1103.0 |
22 | TraesCS5A01G387900 | chr5D | 90.520 | 538 | 39 | 7 | 4611 | 5142 | 464347634 | 464348165 | 0.000000e+00 | 701.0 |
23 | TraesCS5A01G387900 | chr5D | 90.614 | 277 | 15 | 5 | 5508 | 5773 | 464403110 | 464403386 | 1.980000e-94 | 357.0 |
24 | TraesCS5A01G387900 | chr5D | 84.639 | 319 | 24 | 14 | 2829 | 3144 | 464326333 | 464326629 | 1.570000e-75 | 294.0 |
25 | TraesCS5A01G387900 | chr5D | 87.912 | 182 | 18 | 3 | 2655 | 2835 | 104489784 | 104489962 | 1.630000e-50 | 211.0 |
26 | TraesCS5A01G387900 | chr5D | 89.032 | 155 | 6 | 1 | 5128 | 5271 | 464401561 | 464401715 | 1.280000e-41 | 182.0 |
27 | TraesCS5A01G387900 | chr5D | 92.913 | 127 | 5 | 2 | 5374 | 5498 | 464401712 | 464401836 | 1.280000e-41 | 182.0 |
28 | TraesCS5A01G387900 | chr5D | 87.770 | 139 | 11 | 4 | 2969 | 3107 | 464394941 | 464395073 | 2.150000e-34 | 158.0 |
29 | TraesCS5A01G387900 | chr5D | 87.805 | 82 | 10 | 0 | 391 | 472 | 268343147 | 268343066 | 4.760000e-16 | 97.1 |
30 | TraesCS5A01G387900 | chr2A | 78.412 | 1436 | 245 | 45 | 1119 | 2509 | 30222935 | 30224350 | 0.000000e+00 | 874.0 |
31 | TraesCS5A01G387900 | chr2A | 90.698 | 172 | 15 | 1 | 2662 | 2833 | 59330929 | 59331099 | 1.620000e-55 | 228.0 |
32 | TraesCS5A01G387900 | chr2A | 93.519 | 108 | 7 | 0 | 5270 | 5377 | 650256593 | 650256700 | 1.660000e-35 | 161.0 |
33 | TraesCS5A01G387900 | chr2A | 91.304 | 115 | 10 | 0 | 5270 | 5384 | 527504725 | 527504611 | 2.150000e-34 | 158.0 |
34 | TraesCS5A01G387900 | chr2A | 89.431 | 123 | 10 | 3 | 5262 | 5384 | 102329260 | 102329379 | 1.000000e-32 | 152.0 |
35 | TraesCS5A01G387900 | chr2D | 77.817 | 1429 | 255 | 42 | 1117 | 2509 | 28407749 | 28409151 | 0.000000e+00 | 826.0 |
36 | TraesCS5A01G387900 | chr2D | 92.727 | 110 | 8 | 0 | 5268 | 5377 | 637342564 | 637342673 | 5.990000e-35 | 159.0 |
37 | TraesCS5A01G387900 | chr2B | 77.645 | 1427 | 261 | 37 | 1117 | 2509 | 44942775 | 44941373 | 0.000000e+00 | 815.0 |
38 | TraesCS5A01G387900 | chr2B | 77.622 | 1430 | 256 | 44 | 1117 | 2509 | 45608344 | 45609746 | 0.000000e+00 | 809.0 |
39 | TraesCS5A01G387900 | chr2B | 77.289 | 1431 | 263 | 38 | 1117 | 2509 | 45642133 | 45640727 | 0.000000e+00 | 785.0 |
40 | TraesCS5A01G387900 | chr2B | 74.460 | 787 | 166 | 20 | 1755 | 2511 | 18320291 | 18319510 | 2.020000e-79 | 307.0 |
41 | TraesCS5A01G387900 | chr2B | 73.418 | 790 | 169 | 27 | 1755 | 2511 | 18386670 | 18385889 | 2.060000e-64 | 257.0 |
42 | TraesCS5A01G387900 | chr2B | 92.241 | 116 | 7 | 2 | 5270 | 5383 | 621062527 | 621062642 | 4.630000e-36 | 163.0 |
43 | TraesCS5A01G387900 | chr4D | 83.201 | 631 | 98 | 8 | 1890 | 2515 | 509838252 | 509837625 | 6.490000e-159 | 571.0 |
44 | TraesCS5A01G387900 | chr4D | 82.553 | 470 | 70 | 8 | 1125 | 1591 | 509839016 | 509838556 | 2.510000e-108 | 403.0 |
45 | TraesCS5A01G387900 | chr4B | 82.965 | 634 | 94 | 13 | 1890 | 2515 | 656892479 | 656893106 | 1.400000e-155 | 560.0 |
46 | TraesCS5A01G387900 | chr4B | 78.249 | 754 | 113 | 31 | 1122 | 1865 | 656891695 | 656892407 | 2.470000e-118 | 436.0 |
47 | TraesCS5A01G387900 | chr7D | 93.082 | 318 | 16 | 4 | 3142 | 3454 | 115140773 | 115141089 | 1.470000e-125 | 460.0 |
48 | TraesCS5A01G387900 | chr7D | 91.515 | 165 | 13 | 1 | 2662 | 2826 | 576654104 | 576654267 | 5.820000e-55 | 226.0 |
49 | TraesCS5A01G387900 | chr3D | 92.767 | 318 | 17 | 4 | 3142 | 3454 | 601009702 | 601010018 | 6.820000e-124 | 455.0 |
50 | TraesCS5A01G387900 | chr3D | 92.453 | 318 | 18 | 4 | 3142 | 3454 | 601035507 | 601035823 | 3.170000e-122 | 449.0 |
51 | TraesCS5A01G387900 | chr3D | 91.824 | 318 | 20 | 4 | 3142 | 3454 | 601018647 | 601018963 | 6.870000e-119 | 438.0 |
52 | TraesCS5A01G387900 | chr3D | 88.235 | 85 | 10 | 0 | 388 | 472 | 107672338 | 107672254 | 1.020000e-17 | 102.0 |
53 | TraesCS5A01G387900 | chr3A | 92.523 | 321 | 17 | 5 | 3142 | 3457 | 181668816 | 181669134 | 2.450000e-123 | 453.0 |
54 | TraesCS5A01G387900 | chr3A | 91.824 | 318 | 20 | 4 | 3142 | 3454 | 731579344 | 731579028 | 6.870000e-119 | 438.0 |
55 | TraesCS5A01G387900 | chr3A | 91.277 | 321 | 22 | 4 | 3142 | 3457 | 553946027 | 553946346 | 3.200000e-117 | 433.0 |
56 | TraesCS5A01G387900 | chr3B | 91.824 | 318 | 20 | 4 | 3142 | 3454 | 808278282 | 808278598 | 6.870000e-119 | 438.0 |
57 | TraesCS5A01G387900 | chr3B | 91.667 | 72 | 6 | 0 | 388 | 459 | 127932633 | 127932704 | 3.680000e-17 | 100.0 |
58 | TraesCS5A01G387900 | chr1B | 72.831 | 1406 | 299 | 58 | 1121 | 2482 | 557412403 | 557411037 | 2.510000e-108 | 403.0 |
59 | TraesCS5A01G387900 | chr6A | 91.954 | 174 | 13 | 1 | 2662 | 2835 | 64662417 | 64662245 | 5.780000e-60 | 243.0 |
60 | TraesCS5A01G387900 | chr6A | 87.582 | 153 | 18 | 1 | 9 | 161 | 251565851 | 251565700 | 5.950000e-40 | 176.0 |
61 | TraesCS5A01G387900 | chr6A | 87.179 | 78 | 9 | 1 | 881 | 957 | 108851916 | 108851839 | 2.870000e-13 | 87.9 |
62 | TraesCS5A01G387900 | chr6A | 84.416 | 77 | 11 | 1 | 882 | 957 | 251565274 | 251565198 | 2.230000e-09 | 75.0 |
63 | TraesCS5A01G387900 | chr1D | 75.941 | 478 | 98 | 13 | 1121 | 1588 | 413234463 | 413233993 | 4.500000e-56 | 230.0 |
64 | TraesCS5A01G387900 | chr1D | 90.419 | 167 | 15 | 1 | 2662 | 2828 | 42271754 | 42271589 | 9.740000e-53 | 219.0 |
65 | TraesCS5A01G387900 | chr1D | 80.791 | 177 | 26 | 6 | 4690 | 4865 | 243461882 | 243461713 | 1.310000e-26 | 132.0 |
66 | TraesCS5A01G387900 | chr1D | 90.361 | 83 | 7 | 1 | 390 | 472 | 205490289 | 205490370 | 2.200000e-19 | 108.0 |
67 | TraesCS5A01G387900 | chrUn | 75.770 | 487 | 98 | 16 | 1117 | 1587 | 12467689 | 12468171 | 1.620000e-55 | 228.0 |
68 | TraesCS5A01G387900 | chrUn | 86.747 | 83 | 11 | 0 | 390 | 472 | 79505465 | 79505383 | 6.160000e-15 | 93.5 |
69 | TraesCS5A01G387900 | chr7A | 89.560 | 182 | 14 | 3 | 2662 | 2838 | 543447842 | 543447661 | 5.820000e-55 | 226.0 |
70 | TraesCS5A01G387900 | chr7A | 90.058 | 171 | 15 | 2 | 2668 | 2836 | 84295677 | 84295847 | 2.710000e-53 | 220.0 |
71 | TraesCS5A01G387900 | chr7A | 93.519 | 108 | 7 | 0 | 5270 | 5377 | 188030228 | 188030335 | 1.660000e-35 | 161.0 |
72 | TraesCS5A01G387900 | chr7B | 91.765 | 85 | 7 | 0 | 388 | 472 | 511462090 | 511462174 | 1.020000e-22 | 119.0 |
73 | TraesCS5A01G387900 | chr1A | 90.361 | 83 | 7 | 1 | 391 | 472 | 463825451 | 463825369 | 2.200000e-19 | 108.0 |
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 | TraesCS5A01G387900 | chr5A | 584715273 | 584721045 | 5772 | False | 10661.000000 | 10661 | 100.00000 | 1 | 5773 | 1 | chr5A.!!$F2 | 5772 |
1 | TraesCS5A01G387900 | chr5A | 698646011 | 698646637 | 626 | True | 562.000000 | 562 | 82.98900 | 1890 | 2513 | 1 | chr5A.!!$R6 | 623 |
2 | TraesCS5A01G387900 | chr5B | 571476417 | 571485551 | 9134 | False | 1138.250000 | 2242 | 90.74025 | 1 | 5142 | 4 | chr5B.!!$F3 | 5141 |
3 | TraesCS5A01G387900 | chr5B | 571490285 | 571492088 | 1803 | False | 757.500000 | 1400 | 84.38900 | 2969 | 5142 | 2 | chr5B.!!$F4 | 2173 |
4 | TraesCS5A01G387900 | chr5B | 571508829 | 571510484 | 1655 | False | 591.500000 | 763 | 83.39100 | 3708 | 5144 | 2 | chr5B.!!$F5 | 1436 |
5 | TraesCS5A01G387900 | chr5D | 464324755 | 464326629 | 1874 | False | 842.000000 | 1129 | 90.17200 | 1117 | 3144 | 3 | chr5D.!!$F3 | 2027 |
6 | TraesCS5A01G387900 | chr5D | 464394941 | 464396705 | 1764 | False | 728.500000 | 1299 | 85.44600 | 2969 | 5135 | 2 | chr5D.!!$F4 | 2166 |
7 | TraesCS5A01G387900 | chr5D | 464347634 | 464348165 | 531 | False | 701.000000 | 701 | 90.52000 | 4611 | 5142 | 1 | chr5D.!!$F2 | 531 |
8 | TraesCS5A01G387900 | chr5D | 464401561 | 464403386 | 1825 | False | 240.333333 | 357 | 90.85300 | 5128 | 5773 | 3 | chr5D.!!$F5 | 645 |
9 | TraesCS5A01G387900 | chr2A | 30222935 | 30224350 | 1415 | False | 874.000000 | 874 | 78.41200 | 1119 | 2509 | 1 | chr2A.!!$F1 | 1390 |
10 | TraesCS5A01G387900 | chr2D | 28407749 | 28409151 | 1402 | False | 826.000000 | 826 | 77.81700 | 1117 | 2509 | 1 | chr2D.!!$F1 | 1392 |
11 | TraesCS5A01G387900 | chr2B | 44941373 | 44942775 | 1402 | True | 815.000000 | 815 | 77.64500 | 1117 | 2509 | 1 | chr2B.!!$R3 | 1392 |
12 | TraesCS5A01G387900 | chr2B | 45608344 | 45609746 | 1402 | False | 809.000000 | 809 | 77.62200 | 1117 | 2509 | 1 | chr2B.!!$F1 | 1392 |
13 | TraesCS5A01G387900 | chr2B | 45640727 | 45642133 | 1406 | True | 785.000000 | 785 | 77.28900 | 1117 | 2509 | 1 | chr2B.!!$R4 | 1392 |
14 | TraesCS5A01G387900 | chr2B | 18319510 | 18320291 | 781 | True | 307.000000 | 307 | 74.46000 | 1755 | 2511 | 1 | chr2B.!!$R1 | 756 |
15 | TraesCS5A01G387900 | chr2B | 18385889 | 18386670 | 781 | True | 257.000000 | 257 | 73.41800 | 1755 | 2511 | 1 | chr2B.!!$R2 | 756 |
16 | TraesCS5A01G387900 | chr4D | 509837625 | 509839016 | 1391 | True | 487.000000 | 571 | 82.87700 | 1125 | 2515 | 2 | chr4D.!!$R1 | 1390 |
17 | TraesCS5A01G387900 | chr4B | 656891695 | 656893106 | 1411 | False | 498.000000 | 560 | 80.60700 | 1122 | 2515 | 2 | chr4B.!!$F1 | 1393 |
18 | TraesCS5A01G387900 | chr1B | 557411037 | 557412403 | 1366 | True | 403.000000 | 403 | 72.83100 | 1121 | 2482 | 1 | chr1B.!!$R1 | 1361 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
523 | 524 | 0.036388 | GACAAGCAACTCCGGATGGA | 60.036 | 55.0 | 3.57 | 0.0 | 43.88 | 3.41 | F |
1058 | 1098 | 0.108138 | AAGCCACATCGAGCCTGTAC | 60.108 | 55.0 | 0.00 | 0.0 | 0.00 | 2.90 | F |
2553 | 5644 | 0.251297 | TCAGTTCTGGCACCCATTGG | 60.251 | 55.0 | 0.00 | 0.0 | 30.82 | 3.16 | F |
3317 | 6443 | 0.256752 | ATCTAGTGGCCAAGCATGCA | 59.743 | 50.0 | 21.98 | 0.0 | 0.00 | 3.96 | F |
3446 | 6572 | 0.183971 | TTGAGCCAACCGGAAAAGGA | 59.816 | 50.0 | 9.46 | 0.0 | 34.73 | 3.36 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1823 | 4854 | 2.511600 | ACGTAGCCTTGGCGCATC | 60.512 | 61.111 | 10.83 | 0.0 | 0.00 | 3.91 | R |
2609 | 5700 | 0.675633 | AAACAGATGGTGCCACAAGC | 59.324 | 50.000 | 0.00 | 0.0 | 44.14 | 4.01 | R |
3427 | 6553 | 0.183971 | TCCTTTTCCGGTTGGCTCAA | 59.816 | 50.000 | 0.00 | 0.0 | 34.14 | 3.02 | R |
4660 | 9900 | 0.247460 | CTGCACACCGAGATCAAGGA | 59.753 | 55.000 | 12.65 | 0.0 | 0.00 | 3.36 | R |
4887 | 10378 | 1.067846 | TCGTCTGTCAGTGGCATGTAC | 60.068 | 52.381 | 0.00 | 0.0 | 0.00 | 2.90 | 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.