Multiple sequence alignment - TraesCS7A01G498200
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 | TraesCS7A01G498200 | chr7A | 100.000 | 9646 | 0 | 0 | 1 | 9646 | 688694088 | 688684443 | 0.000000e+00 | 17813.0 |
1 | TraesCS7A01G498200 | chr7A | 80.942 | 892 | 102 | 28 | 7971 | 8847 | 688457232 | 688456394 | 2.270000e-180 | 643.0 |
2 | TraesCS7A01G498200 | chr7A | 81.096 | 529 | 60 | 19 | 7971 | 8488 | 688663185 | 688662686 | 4.230000e-103 | 387.0 |
3 | TraesCS7A01G498200 | chr7A | 80.583 | 515 | 65 | 22 | 7484 | 7974 | 688457817 | 688457314 | 1.980000e-96 | 364.0 |
4 | TraesCS7A01G498200 | chr7A | 83.288 | 371 | 48 | 10 | 8119 | 8486 | 688627292 | 688626933 | 7.220000e-86 | 329.0 |
5 | TraesCS7A01G498200 | chr7A | 85.809 | 303 | 26 | 10 | 9316 | 9611 | 688625965 | 688625673 | 1.220000e-78 | 305.0 |
6 | TraesCS7A01G498200 | chr7A | 83.270 | 263 | 25 | 9 | 6597 | 6857 | 688459549 | 688459304 | 3.510000e-54 | 224.0 |
7 | TraesCS7A01G498200 | chr7A | 85.520 | 221 | 20 | 8 | 9316 | 9532 | 688638930 | 688638718 | 4.530000e-53 | 220.0 |
8 | TraesCS7A01G498200 | chr7A | 88.095 | 168 | 12 | 6 | 8563 | 8725 | 688662656 | 688662492 | 9.890000e-45 | 193.0 |
9 | TraesCS7A01G498200 | chr7A | 74.629 | 607 | 68 | 40 | 8889 | 9453 | 688662071 | 688661509 | 1.280000e-43 | 189.0 |
10 | TraesCS7A01G498200 | chr7A | 85.430 | 151 | 18 | 3 | 7972 | 8122 | 688641090 | 688640944 | 4.670000e-33 | 154.0 |
11 | TraesCS7A01G498200 | chr7A | 84.810 | 79 | 10 | 2 | 8802 | 8879 | 688662483 | 688662406 | 2.890000e-10 | 78.7 |
12 | TraesCS7A01G498200 | chr7D | 96.462 | 5285 | 157 | 15 | 3517 | 8792 | 595728496 | 595723233 | 0.000000e+00 | 8696.0 |
13 | TraesCS7A01G498200 | chr7D | 95.064 | 2512 | 91 | 20 | 1 | 2504 | 595731731 | 595729245 | 0.000000e+00 | 3921.0 |
14 | TraesCS7A01G498200 | chr7D | 97.486 | 716 | 16 | 1 | 2805 | 3518 | 595729246 | 595728531 | 0.000000e+00 | 1221.0 |
15 | TraesCS7A01G498200 | chr7D | 85.369 | 786 | 50 | 22 | 8900 | 9646 | 595722748 | 595721989 | 0.000000e+00 | 754.0 |
16 | TraesCS7A01G498200 | chr7D | 80.624 | 898 | 100 | 27 | 7973 | 8847 | 595578345 | 595577499 | 2.290000e-175 | 627.0 |
17 | TraesCS7A01G498200 | chr7D | 82.749 | 371 | 51 | 6 | 8119 | 8486 | 595613555 | 595613195 | 1.560000e-82 | 318.0 |
18 | TraesCS7A01G498200 | chr7D | 86.184 | 304 | 21 | 12 | 9316 | 9610 | 595612252 | 595611961 | 9.410000e-80 | 309.0 |
19 | TraesCS7A01G498200 | chr7D | 81.935 | 310 | 39 | 6 | 6597 | 6903 | 595581364 | 595581069 | 7.480000e-61 | 246.0 |
20 | TraesCS7A01G498200 | chr7D | 82.818 | 291 | 21 | 10 | 8563 | 8848 | 595665559 | 595665293 | 5.820000e-57 | 233.0 |
21 | TraesCS7A01G498200 | chr7D | 74.633 | 682 | 82 | 52 | 8900 | 9543 | 595664911 | 595664283 | 5.870000e-52 | 217.0 |
22 | TraesCS7A01G498200 | chr7D | 81.655 | 278 | 32 | 3 | 7718 | 7976 | 595666651 | 595666374 | 7.590000e-51 | 213.0 |
23 | TraesCS7A01G498200 | chr7D | 76.728 | 434 | 59 | 19 | 7084 | 7488 | 595606037 | 595605617 | 4.570000e-48 | 204.0 |
24 | TraesCS7A01G498200 | chr7D | 92.647 | 136 | 6 | 2 | 8754 | 8889 | 595723234 | 595723103 | 9.890000e-45 | 193.0 |
25 | TraesCS7A01G498200 | chr7D | 83.333 | 192 | 10 | 10 | 8889 | 9076 | 595612601 | 595612428 | 3.610000e-34 | 158.0 |
26 | TraesCS7A01G498200 | chr7D | 94.898 | 98 | 4 | 1 | 7393 | 7490 | 595531873 | 595531777 | 1.680000e-32 | 152.0 |
27 | TraesCS7A01G498200 | chr7D | 91.045 | 67 | 6 | 0 | 6953 | 7019 | 595580493 | 595580427 | 3.710000e-14 | 91.6 |
28 | TraesCS7A01G498200 | chr7B | 96.308 | 4659 | 121 | 19 | 3517 | 8163 | 673309504 | 673304885 | 0.000000e+00 | 7603.0 |
29 | TraesCS7A01G498200 | chr7B | 93.034 | 2541 | 117 | 24 | 1 | 2504 | 673312654 | 673310137 | 0.000000e+00 | 3657.0 |
30 | TraesCS7A01G498200 | chr7B | 91.168 | 702 | 41 | 9 | 8193 | 8889 | 673304885 | 673304200 | 0.000000e+00 | 933.0 |
31 | TraesCS7A01G498200 | chr7B | 97.148 | 526 | 15 | 0 | 2992 | 3517 | 673310065 | 673309540 | 0.000000e+00 | 889.0 |
32 | TraesCS7A01G498200 | chr7B | 86.090 | 798 | 49 | 15 | 8903 | 9646 | 673303885 | 673303096 | 0.000000e+00 | 802.0 |
33 | TraesCS7A01G498200 | chr7B | 82.367 | 845 | 115 | 20 | 7971 | 8798 | 672915088 | 672914261 | 0.000000e+00 | 704.0 |
34 | TraesCS7A01G498200 | chr7B | 80.778 | 900 | 94 | 32 | 7973 | 8854 | 672841824 | 672840986 | 1.770000e-176 | 630.0 |
35 | TraesCS7A01G498200 | chr7B | 79.038 | 520 | 65 | 22 | 7484 | 7974 | 672842411 | 672841907 | 5.620000e-82 | 316.0 |
36 | TraesCS7A01G498200 | chr7B | 81.671 | 371 | 54 | 6 | 8119 | 8486 | 673124011 | 673123652 | 7.320000e-76 | 296.0 |
37 | TraesCS7A01G498200 | chr7B | 85.016 | 307 | 25 | 13 | 9311 | 9611 | 673122695 | 673122404 | 9.480000e-75 | 292.0 |
38 | TraesCS7A01G498200 | chr7B | 83.453 | 278 | 27 | 12 | 6749 | 7019 | 672843771 | 672843506 | 3.480000e-59 | 241.0 |
39 | TraesCS7A01G498200 | chr7B | 75.129 | 583 | 71 | 44 | 8900 | 9453 | 673135925 | 673135388 | 1.270000e-48 | 206.0 |
40 | TraesCS7A01G498200 | chr7B | 84.653 | 202 | 16 | 4 | 8900 | 9090 | 672913663 | 672913466 | 4.600000e-43 | 187.0 |
41 | TraesCS7A01G498200 | chr7B | 94.872 | 78 | 4 | 0 | 2805 | 2882 | 673310138 | 673310061 | 1.320000e-23 | 122.0 |
42 | TraesCS7A01G498200 | chr7B | 87.952 | 83 | 9 | 1 | 8797 | 8879 | 673136346 | 673136265 | 7.970000e-16 | 97.1 |
43 | TraesCS7A01G498200 | chr4A | 96.078 | 306 | 11 | 1 | 2502 | 2806 | 209332212 | 209331907 | 1.870000e-136 | 497.0 |
44 | TraesCS7A01G498200 | chr4A | 95.098 | 306 | 14 | 1 | 2502 | 2806 | 486117719 | 486118024 | 1.880000e-131 | 481.0 |
45 | TraesCS7A01G498200 | chr4A | 94.481 | 308 | 16 | 1 | 2500 | 2806 | 628560850 | 628561157 | 3.150000e-129 | 473.0 |
46 | TraesCS7A01G498200 | chr3A | 94.771 | 306 | 15 | 1 | 2502 | 2806 | 545355077 | 545354772 | 8.770000e-130 | 475.0 |
47 | TraesCS7A01G498200 | chr6A | 93.910 | 312 | 17 | 2 | 2498 | 2808 | 12373223 | 12372913 | 4.080000e-128 | 470.0 |
48 | TraesCS7A01G498200 | chr4D | 94.444 | 306 | 16 | 1 | 2502 | 2806 | 444466644 | 444466339 | 4.080000e-128 | 470.0 |
49 | TraesCS7A01G498200 | chr4D | 100.000 | 30 | 0 | 0 | 3912 | 3941 | 123635851 | 123635880 | 1.000000e-03 | 56.5 |
50 | TraesCS7A01G498200 | chr2A | 94.156 | 308 | 17 | 1 | 2503 | 2809 | 540047976 | 540047669 | 1.470000e-127 | 468.0 |
51 | TraesCS7A01G498200 | chr2A | 93.871 | 310 | 17 | 2 | 2502 | 2809 | 565266902 | 565266593 | 5.280000e-127 | 466.0 |
52 | TraesCS7A01G498200 | chr2A | 82.135 | 459 | 57 | 19 | 1820 | 2275 | 714211858 | 714211422 | 4.260000e-98 | 370.0 |
53 | TraesCS7A01G498200 | chr5B | 92.260 | 323 | 22 | 3 | 2498 | 2819 | 383920928 | 383920608 | 1.140000e-123 | 455.0 |
54 | TraesCS7A01G498200 | chr2B | 90.226 | 266 | 25 | 1 | 2002 | 2267 | 692167160 | 692166896 | 7.170000e-91 | 346.0 |
55 | TraesCS7A01G498200 | chr2D | 90.421 | 261 | 24 | 1 | 2002 | 2262 | 576195691 | 576195432 | 9.280000e-90 | 342.0 |
56 | TraesCS7A01G498200 | chrUn | 100.000 | 30 | 0 | 0 | 3912 | 3941 | 86461787 | 86461816 | 1.000000e-03 | 56.5 |
57 | TraesCS7A01G498200 | chrUn | 100.000 | 30 | 0 | 0 | 3912 | 3941 | 222673487 | 222673458 | 1.000000e-03 | 56.5 |
58 | TraesCS7A01G498200 | chrUn | 100.000 | 30 | 0 | 0 | 3912 | 3941 | 229496815 | 229496786 | 1.000000e-03 | 56.5 |
59 | TraesCS7A01G498200 | chrUn | 100.000 | 30 | 0 | 0 | 3912 | 3941 | 237101258 | 237101229 | 1.000000e-03 | 56.5 |
60 | TraesCS7A01G498200 | chr6D | 100.000 | 30 | 0 | 0 | 3912 | 3941 | 168781986 | 168782015 | 1.000000e-03 | 56.5 |
61 | TraesCS7A01G498200 | chr1D | 100.000 | 30 | 0 | 0 | 3912 | 3941 | 141328896 | 141328867 | 1.000000e-03 | 56.5 |
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 | TraesCS7A01G498200 | chr7A | 688684443 | 688694088 | 9645 | True | 17813.000000 | 17813 | 100.000000 | 1 | 9646 | 1 | chr7A.!!$R1 | 9645 |
1 | TraesCS7A01G498200 | chr7A | 688456394 | 688459549 | 3155 | True | 410.333333 | 643 | 81.598333 | 6597 | 8847 | 3 | chr7A.!!$R2 | 2250 |
2 | TraesCS7A01G498200 | chr7A | 688625673 | 688627292 | 1619 | True | 317.000000 | 329 | 84.548500 | 8119 | 9611 | 2 | chr7A.!!$R3 | 1492 |
3 | TraesCS7A01G498200 | chr7A | 688661509 | 688663185 | 1676 | True | 211.925000 | 387 | 82.157500 | 7971 | 9453 | 4 | chr7A.!!$R5 | 1482 |
4 | TraesCS7A01G498200 | chr7D | 595721989 | 595731731 | 9742 | True | 2957.000000 | 8696 | 93.405600 | 1 | 9646 | 5 | chr7D.!!$R6 | 9645 |
5 | TraesCS7A01G498200 | chr7D | 595577499 | 595581364 | 3865 | True | 321.533333 | 627 | 84.534667 | 6597 | 8847 | 3 | chr7D.!!$R3 | 2250 |
6 | TraesCS7A01G498200 | chr7D | 595611961 | 595613555 | 1594 | True | 261.666667 | 318 | 84.088667 | 8119 | 9610 | 3 | chr7D.!!$R4 | 1491 |
7 | TraesCS7A01G498200 | chr7D | 595664283 | 595666651 | 2368 | True | 221.000000 | 233 | 79.702000 | 7718 | 9543 | 3 | chr7D.!!$R5 | 1825 |
8 | TraesCS7A01G498200 | chr7B | 673303096 | 673312654 | 9558 | True | 2334.333333 | 7603 | 93.103333 | 1 | 9646 | 6 | chr7B.!!$R5 | 9645 |
9 | TraesCS7A01G498200 | chr7B | 672913466 | 672915088 | 1622 | True | 445.500000 | 704 | 83.510000 | 7971 | 9090 | 2 | chr7B.!!$R2 | 1119 |
10 | TraesCS7A01G498200 | chr7B | 672840986 | 672843771 | 2785 | True | 395.666667 | 630 | 81.089667 | 6749 | 8854 | 3 | chr7B.!!$R1 | 2105 |
11 | TraesCS7A01G498200 | chr7B | 673122404 | 673124011 | 1607 | True | 294.000000 | 296 | 83.343500 | 8119 | 9611 | 2 | chr7B.!!$R3 | 1492 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
518 | 532 | 0.102844 | TCTGCTTTTGTTGCCACAGC | 59.897 | 50.000 | 0.00 | 0.0 | 40.48 | 4.40 | F |
554 | 568 | 0.171231 | GTTGCCCTGAAAGCGGAATC | 59.829 | 55.000 | 0.00 | 0.0 | 0.00 | 2.52 | F |
1934 | 1971 | 0.392461 | TACCTTCACCATGCCTTCGC | 60.392 | 55.000 | 0.00 | 0.0 | 0.00 | 4.70 | F |
2579 | 2617 | 0.981183 | AGGCCACCAACAGTAATCGA | 59.019 | 50.000 | 5.01 | 0.0 | 0.00 | 3.59 | F |
2580 | 2618 | 1.066143 | AGGCCACCAACAGTAATCGAG | 60.066 | 52.381 | 5.01 | 0.0 | 0.00 | 4.04 | F |
2583 | 2621 | 1.338674 | CCACCAACAGTAATCGAGGCA | 60.339 | 52.381 | 0.00 | 0.0 | 0.00 | 4.75 | F |
2782 | 2820 | 1.349688 | TGTAATCCGAGTTTGTGGCCT | 59.650 | 47.619 | 3.32 | 0.0 | 0.00 | 5.19 | F |
3217 | 3257 | 1.610038 | CACTGAATGCTTCCACTTGCA | 59.390 | 47.619 | 0.00 | 0.0 | 43.67 | 4.08 | F |
4682 | 4760 | 2.143602 | CTCCTTTTCCCCCATATCCCA | 58.856 | 52.381 | 0.00 | 0.0 | 0.00 | 4.37 | F |
5592 | 5673 | 1.153005 | GCTGGCATTCAGGAGGGAG | 60.153 | 63.158 | 0.00 | 0.0 | 43.54 | 4.30 | F |
6155 | 6240 | 1.250328 | TGAGTTGGCTCATTGCTTGG | 58.750 | 50.000 | 0.00 | 0.0 | 45.94 | 3.61 | F |
8224 | 10231 | 0.178953 | ATGGGCCTGACTGCAAAAGT | 60.179 | 50.000 | 4.53 | 0.0 | 43.85 | 2.66 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1934 | 1971 | 1.229428 | TGAAGCAGAAAAGTCGGCAG | 58.771 | 50.000 | 0.00 | 0.00 | 46.27 | 4.85 | R |
2079 | 2116 | 1.473434 | GCCATAACCTCCCTCTTGACG | 60.473 | 57.143 | 0.00 | 0.00 | 0.00 | 4.35 | R |
2762 | 2800 | 1.349688 | AGGCCACAAACTCGGATTACA | 59.650 | 47.619 | 5.01 | 0.00 | 0.00 | 2.41 | R |
4435 | 4513 | 0.747283 | CTTGCAGGATGGGCTCTCAC | 60.747 | 60.000 | 0.00 | 0.00 | 35.86 | 3.51 | R |
4682 | 4760 | 9.359653 | CAGAGATTATATGTTTCCCCTTGAAAT | 57.640 | 33.333 | 0.00 | 0.00 | 44.44 | 2.17 | R |
4711 | 4789 | 7.257722 | TCATGAGAAAAGGAGACAAAACAAAC | 58.742 | 34.615 | 0.00 | 0.00 | 0.00 | 2.93 | R |
4840 | 4918 | 2.751436 | GCAGATCGCAAGGCCCAA | 60.751 | 61.111 | 0.00 | 0.00 | 41.79 | 4.12 | R |
5412 | 5493 | 5.185828 | GGGCACACTTTCCAGAATTATCTTT | 59.814 | 40.000 | 0.00 | 0.00 | 32.03 | 2.52 | R |
5759 | 5840 | 0.321564 | CACGGATTGCTTCCAGTCCA | 60.322 | 55.000 | 6.14 | 0.00 | 45.43 | 4.02 | R |
7692 | 9278 | 1.067213 | GCTCTCTGTCTGTCTCCCAAC | 60.067 | 57.143 | 0.00 | 0.00 | 0.00 | 3.77 | R |
8305 | 10312 | 1.279271 | ACTCAGAATTTACTGCCGGCT | 59.721 | 47.619 | 29.70 | 11.31 | 37.75 | 5.52 | R |
9115 | 12149 | 0.466124 | GCTCTACTAGGGGCCAACAG | 59.534 | 60.000 | 4.39 | 0.68 | 0.00 | 3.16 | 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.