Multiple sequence alignment - TraesCS7A01G369400
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 | TraesCS7A01G369400 | chr7A | 100.000 | 7519 | 0 | 0 | 1 | 7519 | 542967303 | 542974821 | 0.000000e+00 | 13886.0 |
1 | TraesCS7A01G369400 | chr7A | 86.196 | 2137 | 203 | 61 | 4257 | 6340 | 542817332 | 542819429 | 0.000000e+00 | 2228.0 |
2 | TraesCS7A01G369400 | chr7A | 86.408 | 515 | 47 | 15 | 40 | 547 | 542938500 | 542938998 | 6.640000e-150 | 542.0 |
3 | TraesCS7A01G369400 | chr7A | 85.656 | 244 | 11 | 7 | 989 | 1229 | 542812007 | 542812229 | 1.260000e-57 | 235.0 |
4 | TraesCS7A01G369400 | chr7A | 95.276 | 127 | 5 | 1 | 791 | 916 | 542939024 | 542939150 | 4.600000e-47 | 200.0 |
5 | TraesCS7A01G369400 | chr7A | 77.903 | 267 | 49 | 8 | 6908 | 7170 | 531106200 | 531105940 | 2.810000e-34 | 158.0 |
6 | TraesCS7A01G369400 | chr7A | 77.387 | 199 | 34 | 10 | 6908 | 7100 | 530938801 | 530938994 | 2.870000e-19 | 108.0 |
7 | TraesCS7A01G369400 | chr7A | 95.652 | 46 | 1 | 1 | 6581 | 6626 | 33027378 | 33027422 | 1.050000e-08 | 73.1 |
8 | TraesCS7A01G369400 | chr7B | 84.350 | 2147 | 237 | 62 | 4257 | 6363 | 479646714 | 479644627 | 0.000000e+00 | 2012.0 |
9 | TraesCS7A01G369400 | chr7B | 88.242 | 859 | 66 | 18 | 4292 | 5118 | 479621235 | 479620380 | 0.000000e+00 | 994.0 |
10 | TraesCS7A01G369400 | chr7B | 82.831 | 862 | 88 | 34 | 5186 | 6041 | 479620398 | 479619591 | 0.000000e+00 | 717.0 |
11 | TraesCS7A01G369400 | chr7B | 94.595 | 333 | 14 | 4 | 6042 | 6372 | 479619561 | 479619231 | 5.200000e-141 | 512.0 |
12 | TraesCS7A01G369400 | chr7B | 82.450 | 547 | 42 | 33 | 815 | 1345 | 479623550 | 479623042 | 5.390000e-116 | 429.0 |
13 | TraesCS7A01G369400 | chr7B | 86.275 | 255 | 14 | 6 | 988 | 1236 | 479652911 | 479652672 | 2.690000e-64 | 257.0 |
14 | TraesCS7A01G369400 | chr7B | 80.682 | 176 | 14 | 5 | 1444 | 1599 | 479623027 | 479622852 | 1.330000e-22 | 119.0 |
15 | TraesCS7A01G369400 | chr7B | 81.560 | 141 | 9 | 8 | 2436 | 2576 | 479621893 | 479621770 | 4.800000e-17 | 100.0 |
16 | TraesCS7A01G369400 | chr7B | 95.122 | 41 | 2 | 0 | 2527 | 2567 | 479651574 | 479651534 | 1.750000e-06 | 65.8 |
17 | TraesCS7A01G369400 | chr7B | 96.970 | 33 | 1 | 0 | 6442 | 6474 | 479619173 | 479619141 | 1.000000e-03 | 56.5 |
18 | TraesCS7A01G369400 | chr7D | 84.141 | 2188 | 227 | 66 | 4257 | 6370 | 457597535 | 457595394 | 0.000000e+00 | 2008.0 |
19 | TraesCS7A01G369400 | chr7D | 89.005 | 955 | 70 | 18 | 5426 | 6372 | 457226453 | 457225526 | 0.000000e+00 | 1149.0 |
20 | TraesCS7A01G369400 | chr7D | 89.057 | 859 | 67 | 14 | 4285 | 5118 | 457227712 | 457226856 | 0.000000e+00 | 1040.0 |
21 | TraesCS7A01G369400 | chr7D | 84.615 | 559 | 41 | 23 | 815 | 1345 | 457230811 | 457230270 | 1.450000e-141 | 514.0 |
22 | TraesCS7A01G369400 | chr7D | 85.459 | 392 | 53 | 4 | 1 | 389 | 264477651 | 264478041 | 9.080000e-109 | 405.0 |
23 | TraesCS7A01G369400 | chr7D | 90.455 | 220 | 19 | 2 | 3583 | 3800 | 63379823 | 63380042 | 9.550000e-74 | 289.0 |
24 | TraesCS7A01G369400 | chr7D | 87.712 | 236 | 26 | 2 | 5186 | 5421 | 457226874 | 457226642 | 9.610000e-69 | 272.0 |
25 | TraesCS7A01G369400 | chr7D | 86.747 | 249 | 12 | 8 | 988 | 1230 | 457603097 | 457602864 | 2.690000e-64 | 257.0 |
26 | TraesCS7A01G369400 | chr7D | 83.684 | 190 | 15 | 9 | 2389 | 2576 | 457229315 | 457229140 | 1.680000e-36 | 165.0 |
27 | TraesCS7A01G369400 | chr7D | 93.182 | 44 | 3 | 0 | 492 | 535 | 127223071 | 127223028 | 1.750000e-06 | 65.8 |
28 | TraesCS7A01G369400 | chr7D | 95.122 | 41 | 1 | 1 | 2527 | 2566 | 457601678 | 457601638 | 6.300000e-06 | 63.9 |
29 | TraesCS7A01G369400 | chr6B | 86.364 | 396 | 50 | 4 | 4 | 396 | 163947260 | 163946866 | 5.390000e-116 | 429.0 |
30 | TraesCS7A01G369400 | chr3B | 85.784 | 408 | 51 | 7 | 1 | 403 | 112905316 | 112905721 | 6.970000e-115 | 425.0 |
31 | TraesCS7A01G369400 | chr3B | 85.644 | 404 | 53 | 5 | 4 | 404 | 422314822 | 422314421 | 3.240000e-113 | 420.0 |
32 | TraesCS7A01G369400 | chr3B | 86.478 | 318 | 31 | 7 | 7190 | 7503 | 103727440 | 103727749 | 9.350000e-89 | 339.0 |
33 | TraesCS7A01G369400 | chr3B | 81.776 | 214 | 37 | 2 | 4686 | 4898 | 693075504 | 693075716 | 2.160000e-40 | 178.0 |
34 | TraesCS7A01G369400 | chr5D | 84.577 | 402 | 58 | 4 | 1 | 399 | 464405379 | 464405779 | 5.470000e-106 | 396.0 |
35 | TraesCS7A01G369400 | chr5D | 87.850 | 321 | 26 | 5 | 7187 | 7503 | 71910331 | 71910020 | 1.540000e-96 | 364.0 |
36 | TraesCS7A01G369400 | chr5D | 90.625 | 256 | 16 | 6 | 7267 | 7518 | 429964134 | 429964385 | 4.350000e-87 | 333.0 |
37 | TraesCS7A01G369400 | chr5D | 81.481 | 162 | 19 | 10 | 438 | 594 | 539985542 | 539985697 | 1.020000e-23 | 122.0 |
38 | TraesCS7A01G369400 | chr5D | 87.143 | 70 | 5 | 3 | 7078 | 7143 | 30610455 | 30610386 | 8.090000e-10 | 76.8 |
39 | TraesCS7A01G369400 | chr1A | 84.521 | 407 | 55 | 7 | 4 | 404 | 562118620 | 562118216 | 5.470000e-106 | 396.0 |
40 | TraesCS7A01G369400 | chr1A | 95.431 | 197 | 9 | 0 | 538 | 734 | 14796905 | 14796709 | 1.570000e-81 | 315.0 |
41 | TraesCS7A01G369400 | chr1A | 82.315 | 311 | 37 | 10 | 437 | 740 | 41071980 | 41071681 | 3.480000e-63 | 254.0 |
42 | TraesCS7A01G369400 | chr3A | 84.577 | 402 | 54 | 8 | 4 | 399 | 472765329 | 472764930 | 7.070000e-105 | 392.0 |
43 | TraesCS7A01G369400 | chr3A | 94.792 | 192 | 10 | 0 | 543 | 734 | 401557373 | 401557564 | 4.410000e-77 | 300.0 |
44 | TraesCS7A01G369400 | chr3A | 93.434 | 198 | 11 | 2 | 539 | 735 | 425145325 | 425145521 | 7.380000e-75 | 292.0 |
45 | TraesCS7A01G369400 | chr3A | 80.128 | 312 | 41 | 14 | 7187 | 7486 | 575334902 | 575335204 | 5.910000e-51 | 213.0 |
46 | TraesCS7A01G369400 | chr3A | 80.800 | 250 | 42 | 6 | 4686 | 4932 | 659527989 | 659528235 | 2.770000e-44 | 191.0 |
47 | TraesCS7A01G369400 | chr3A | 93.548 | 62 | 4 | 0 | 3819 | 3880 | 641172693 | 641172754 | 8.030000e-15 | 93.5 |
48 | TraesCS7A01G369400 | chr3A | 83.673 | 98 | 9 | 5 | 7078 | 7170 | 724135434 | 724135529 | 1.340000e-12 | 86.1 |
49 | TraesCS7A01G369400 | chr3A | 95.833 | 48 | 1 | 1 | 6581 | 6628 | 10266662 | 10266708 | 8.090000e-10 | 76.8 |
50 | TraesCS7A01G369400 | chr1D | 84.236 | 406 | 58 | 6 | 4 | 406 | 361102167 | 361101765 | 2.540000e-104 | 390.0 |
51 | TraesCS7A01G369400 | chr1D | 88.040 | 301 | 24 | 3 | 7209 | 7505 | 463164005 | 463163713 | 5.580000e-91 | 346.0 |
52 | TraesCS7A01G369400 | chr1D | 93.607 | 219 | 11 | 3 | 3584 | 3800 | 17161485 | 17161268 | 2.620000e-84 | 324.0 |
53 | TraesCS7A01G369400 | chr1D | 91.031 | 223 | 17 | 3 | 3580 | 3800 | 401204569 | 401204790 | 1.590000e-76 | 298.0 |
54 | TraesCS7A01G369400 | chr1D | 90.323 | 62 | 6 | 0 | 3819 | 3880 | 17161284 | 17161223 | 1.740000e-11 | 82.4 |
55 | TraesCS7A01G369400 | chr2D | 84.275 | 407 | 54 | 8 | 4 | 403 | 468165893 | 468165490 | 9.150000e-104 | 388.0 |
56 | TraesCS7A01G369400 | chr2D | 90.179 | 224 | 20 | 2 | 3579 | 3800 | 643797411 | 643797634 | 2.650000e-74 | 291.0 |
57 | TraesCS7A01G369400 | chr4B | 87.539 | 321 | 30 | 6 | 7187 | 7503 | 627441926 | 627442240 | 5.550000e-96 | 363.0 |
58 | TraesCS7A01G369400 | chr4B | 86.646 | 322 | 30 | 7 | 7187 | 7503 | 597303864 | 597303551 | 2.010000e-90 | 344.0 |
59 | TraesCS7A01G369400 | chr4B | 84.472 | 322 | 37 | 9 | 7187 | 7503 | 285531580 | 285531893 | 9.480000e-79 | 305.0 |
60 | TraesCS7A01G369400 | chr4B | 83.200 | 125 | 18 | 3 | 423 | 547 | 427278682 | 427278561 | 2.220000e-20 | 111.0 |
61 | TraesCS7A01G369400 | chr5A | 86.350 | 337 | 28 | 10 | 7187 | 7518 | 679127374 | 679127051 | 1.200000e-92 | 351.0 |
62 | TraesCS7A01G369400 | chr5A | 96.277 | 188 | 7 | 0 | 545 | 732 | 475465608 | 475465421 | 7.330000e-80 | 309.0 |
63 | TraesCS7A01G369400 | chr5A | 96.196 | 184 | 6 | 1 | 544 | 727 | 569174134 | 569174316 | 4.410000e-77 | 300.0 |
64 | TraesCS7A01G369400 | chr5A | 92.929 | 198 | 13 | 1 | 538 | 734 | 244431527 | 244431724 | 3.430000e-73 | 287.0 |
65 | TraesCS7A01G369400 | chr5A | 92.537 | 201 | 14 | 1 | 536 | 735 | 643571220 | 643571020 | 3.430000e-73 | 287.0 |
66 | TraesCS7A01G369400 | chr5A | 93.651 | 63 | 4 | 0 | 3819 | 3881 | 632556675 | 632556737 | 2.230000e-15 | 95.3 |
67 | TraesCS7A01G369400 | chr5A | 97.674 | 43 | 0 | 1 | 6584 | 6626 | 694522261 | 694522220 | 1.050000e-08 | 73.1 |
68 | TraesCS7A01G369400 | chr5A | 95.238 | 42 | 1 | 1 | 6584 | 6625 | 694543992 | 694543952 | 1.750000e-06 | 65.8 |
69 | TraesCS7A01G369400 | chr4A | 85.799 | 338 | 29 | 8 | 7189 | 7518 | 632977393 | 632977719 | 2.600000e-89 | 340.0 |
70 | TraesCS7A01G369400 | chr4A | 90.909 | 55 | 5 | 0 | 7176 | 7230 | 208256433 | 208256379 | 2.910000e-09 | 75.0 |
71 | TraesCS7A01G369400 | chr6D | 85.714 | 322 | 34 | 6 | 7187 | 7503 | 440650642 | 440650956 | 5.620000e-86 | 329.0 |
72 | TraesCS7A01G369400 | chr6A | 91.597 | 238 | 13 | 4 | 7272 | 7503 | 604838846 | 604839082 | 9.410000e-84 | 322.0 |
73 | TraesCS7A01G369400 | chr6A | 96.216 | 185 | 6 | 1 | 543 | 727 | 234189571 | 234189754 | 1.230000e-77 | 302.0 |
74 | TraesCS7A01G369400 | chr6A | 91.935 | 62 | 3 | 2 | 3819 | 3880 | 601962579 | 601962520 | 1.340000e-12 | 86.1 |
75 | TraesCS7A01G369400 | chr3D | 93.659 | 205 | 13 | 0 | 3593 | 3797 | 603709272 | 603709068 | 2.640000e-79 | 307.0 |
76 | TraesCS7A01G369400 | chr3D | 80.800 | 250 | 42 | 6 | 4686 | 4932 | 525334682 | 525334928 | 2.770000e-44 | 191.0 |
77 | TraesCS7A01G369400 | chr1B | 91.818 | 220 | 15 | 3 | 3574 | 3790 | 190292825 | 190293044 | 3.410000e-78 | 303.0 |
78 | TraesCS7A01G369400 | chr1B | 97.727 | 44 | 0 | 1 | 6584 | 6627 | 567366985 | 567366943 | 2.910000e-09 | 75.0 |
79 | TraesCS7A01G369400 | chr2A | 93.069 | 202 | 11 | 3 | 538 | 738 | 749623834 | 749623635 | 7.380000e-75 | 292.0 |
80 | TraesCS7A01G369400 | chr2A | 90.411 | 219 | 19 | 2 | 3584 | 3800 | 575349283 | 575349065 | 3.430000e-73 | 287.0 |
81 | TraesCS7A01G369400 | chr2A | 84.507 | 142 | 11 | 7 | 7176 | 7315 | 656245735 | 656245867 | 6.120000e-26 | 130.0 |
82 | TraesCS7A01G369400 | chr2A | 100.000 | 41 | 0 | 0 | 6581 | 6621 | 166057621 | 166057581 | 8.090000e-10 | 76.8 |
83 | TraesCS7A01G369400 | chrUn | 89.427 | 227 | 21 | 3 | 3576 | 3800 | 310932870 | 310933095 | 4.440000e-72 | 283.0 |
84 | TraesCS7A01G369400 | chrUn | 89.427 | 227 | 21 | 3 | 3576 | 3800 | 320954078 | 320953853 | 4.440000e-72 | 283.0 |
85 | TraesCS7A01G369400 | chrUn | 95.455 | 44 | 1 | 1 | 6584 | 6627 | 87948394 | 87948352 | 1.350000e-07 | 69.4 |
86 | TraesCS7A01G369400 | chr5B | 95.652 | 46 | 1 | 1 | 6581 | 6626 | 319327202 | 319327246 | 1.050000e-08 | 73.1 |
87 | TraesCS7A01G369400 | chr5B | 87.273 | 55 | 6 | 1 | 492 | 546 | 636899190 | 636899243 | 2.270000e-05 | 62.1 |
88 | TraesCS7A01G369400 | chr5B | 100.000 | 28 | 0 | 0 | 6584 | 6611 | 441075464 | 441075437 | 1.400000e-02 | 52.8 |
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 | TraesCS7A01G369400 | chr7A | 542967303 | 542974821 | 7518 | False | 13886.000000 | 13886 | 100.000000 | 1 | 7519 | 1 | chr7A.!!$F5 | 7518 |
1 | TraesCS7A01G369400 | chr7A | 542817332 | 542819429 | 2097 | False | 2228.000000 | 2228 | 86.196000 | 4257 | 6340 | 1 | chr7A.!!$F4 | 2083 |
2 | TraesCS7A01G369400 | chr7A | 542938500 | 542939150 | 650 | False | 371.000000 | 542 | 90.842000 | 40 | 916 | 2 | chr7A.!!$F6 | 876 |
3 | TraesCS7A01G369400 | chr7B | 479644627 | 479646714 | 2087 | True | 2012.000000 | 2012 | 84.350000 | 4257 | 6363 | 1 | chr7B.!!$R1 | 2106 |
4 | TraesCS7A01G369400 | chr7B | 479619141 | 479623550 | 4409 | True | 418.214286 | 994 | 86.761429 | 815 | 6474 | 7 | chr7B.!!$R2 | 5659 |
5 | TraesCS7A01G369400 | chr7D | 457595394 | 457597535 | 2141 | True | 2008.000000 | 2008 | 84.141000 | 4257 | 6370 | 1 | chr7D.!!$R2 | 2113 |
6 | TraesCS7A01G369400 | chr7D | 457225526 | 457230811 | 5285 | True | 628.000000 | 1149 | 86.814600 | 815 | 6372 | 5 | chr7D.!!$R3 | 5557 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
254 | 256 | 0.104934 | AGTGGAGGTGTCTCTTGGGT | 60.105 | 55.0 | 0.00 | 0.00 | 39.86 | 4.51 | F |
1424 | 1460 | 0.099436 | GGCGCAATCTACAAGCCAAG | 59.901 | 55.0 | 10.83 | 0.00 | 46.48 | 3.61 | F |
2588 | 3090 | 0.035739 | TGCCGGTAAAGTTCCCAGAC | 59.964 | 55.0 | 1.90 | 0.00 | 0.00 | 3.51 | F |
2998 | 3500 | 0.028770 | TTTCGTGAGCTTTGCAACGG | 59.971 | 50.0 | 0.00 | 0.00 | 39.87 | 4.44 | F |
3553 | 4055 | 0.035439 | CTAAACCACAGCCGGGTCAT | 60.035 | 55.0 | 1.27 | 0.00 | 37.77 | 3.06 | F |
3554 | 4056 | 0.035820 | TAAACCACAGCCGGGTCATC | 60.036 | 55.0 | 1.27 | 0.00 | 37.77 | 2.92 | F |
3931 | 4433 | 0.036010 | AACTCGACCAATGGCTGAGG | 60.036 | 55.0 | 20.73 | 7.45 | 0.00 | 3.86 | F |
4309 | 6034 | 0.109781 | GCACGGCTGTTATGTTGGTG | 60.110 | 55.0 | 0.00 | 0.00 | 0.00 | 4.17 | F |
4967 | 6726 | 0.171679 | ACACGTGAGACACAACGTGA | 59.828 | 50.0 | 28.56 | 0.00 | 46.20 | 4.35 | F |
5539 | 7504 | 0.321653 | AACGCATGGAGAGTTGGGTC | 60.322 | 55.0 | 0.00 | 0.00 | 38.89 | 4.46 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1680 | 1762 | 0.037697 | TACTCACGTGGATTGCGCTT | 60.038 | 50.0 | 17.00 | 0.0 | 0.00 | 4.68 | R |
2979 | 3481 | 0.028770 | CCGTTGCAAAGCTCACGAAA | 59.971 | 50.0 | 0.00 | 0.0 | 37.86 | 3.46 | R |
3534 | 4036 | 0.035439 | ATGACCCGGCTGTGGTTTAG | 60.035 | 55.0 | 0.00 | 0.0 | 35.85 | 1.85 | R |
3912 | 4414 | 0.036010 | CCTCAGCCATTGGTCGAGTT | 60.036 | 55.0 | 17.17 | 0.0 | 0.00 | 3.01 | R |
5173 | 6954 | 0.107410 | AACTCACCTGCACGGACAAA | 60.107 | 50.0 | 8.91 | 0.0 | 36.31 | 2.83 | R |
5182 | 6963 | 0.321653 | ATCCCGTGAAACTCACCTGC | 60.322 | 55.0 | 1.34 | 0.0 | 44.20 | 4.85 | R |
5600 | 7565 | 0.248458 | CGCACAAACAACAGTGGGTC | 60.248 | 55.0 | 0.00 | 0.0 | 41.89 | 4.46 | R |
5784 | 7771 | 0.311165 | CCGTGGGCTCGATGTAGTAG | 59.689 | 60.0 | 4.48 | 0.0 | 0.00 | 2.57 | R |
6405 | 8446 | 0.036952 | TTCTCTTGCTGCTTCCCTCG | 60.037 | 55.0 | 0.00 | 0.0 | 0.00 | 4.63 | R |
7254 | 9304 | 0.033208 | CCCCACATGGCCACATACTT | 60.033 | 55.0 | 8.16 | 0.0 | 34.99 | 2.24 | 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.