Multiple sequence alignment - TraesCS5D01G543500
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 | TraesCS5D01G543500 | chr5D | 100.000 | 7064 | 0 | 0 | 1 | 7064 | 553678093 | 553671030 | 0.000000e+00 | 13045.0 |
1 | TraesCS5D01G543500 | chr5D | 94.286 | 105 | 5 | 1 | 1 | 104 | 553658544 | 553658440 | 7.330000e-35 | 159.0 |
2 | TraesCS5D01G543500 | chr4A | 84.098 | 1635 | 223 | 23 | 3843 | 5460 | 615039703 | 615041317 | 0.000000e+00 | 1544.0 |
3 | TraesCS5D01G543500 | chr4A | 80.352 | 341 | 46 | 12 | 5979 | 6314 | 615042127 | 615042451 | 9.160000e-59 | 239.0 |
4 | TraesCS5D01G543500 | chr4A | 85.484 | 186 | 19 | 6 | 1 | 179 | 614871131 | 614871315 | 3.360000e-43 | 187.0 |
5 | TraesCS5D01G543500 | chr5B | 84.137 | 1431 | 169 | 34 | 4020 | 5440 | 697293924 | 697295306 | 0.000000e+00 | 1332.0 |
6 | TraesCS5D01G543500 | chr5B | 84.661 | 1017 | 131 | 17 | 4564 | 5566 | 697125070 | 697126075 | 0.000000e+00 | 990.0 |
7 | TraesCS5D01G543500 | chr5B | 81.989 | 1066 | 155 | 25 | 1481 | 2531 | 697287694 | 697288737 | 0.000000e+00 | 870.0 |
8 | TraesCS5D01G543500 | chr5B | 89.509 | 591 | 43 | 10 | 1 | 577 | 697118035 | 697118620 | 0.000000e+00 | 730.0 |
9 | TraesCS5D01G543500 | chr5B | 83.714 | 700 | 94 | 15 | 3800 | 4490 | 697124024 | 697124712 | 1.660000e-180 | 643.0 |
10 | TraesCS5D01G543500 | chr5B | 78.554 | 401 | 72 | 12 | 3630 | 4021 | 697290036 | 697290431 | 1.180000e-62 | 252.0 |
11 | TraesCS5D01G543500 | chr5B | 82.979 | 188 | 23 | 7 | 6435 | 6620 | 577082583 | 577082763 | 2.040000e-35 | 161.0 |
12 | TraesCS5D01G543500 | chr7B | 76.043 | 1749 | 313 | 71 | 3868 | 5576 | 709559127 | 709560809 | 0.000000e+00 | 811.0 |
13 | TraesCS5D01G543500 | chr7B | 81.732 | 843 | 131 | 12 | 4559 | 5383 | 709524952 | 709525789 | 0.000000e+00 | 682.0 |
14 | TraesCS5D01G543500 | chr7B | 75.517 | 1499 | 293 | 55 | 3894 | 5349 | 746051886 | 746053353 | 0.000000e+00 | 667.0 |
15 | TraesCS5D01G543500 | chr7D | 76.000 | 1750 | 287 | 78 | 3898 | 5587 | 616310755 | 616312431 | 0.000000e+00 | 782.0 |
16 | TraesCS5D01G543500 | chr7D | 93.258 | 178 | 11 | 1 | 6426 | 6603 | 381000225 | 381000401 | 1.950000e-65 | 261.0 |
17 | TraesCS5D01G543500 | chr7D | 95.890 | 146 | 5 | 1 | 6888 | 7033 | 71982515 | 71982371 | 1.180000e-57 | 235.0 |
18 | TraesCS5D01G543500 | chr7D | 93.631 | 157 | 8 | 2 | 6877 | 7033 | 570276796 | 570276642 | 4.260000e-57 | 233.0 |
19 | TraesCS5D01G543500 | chr7D | 87.709 | 179 | 21 | 1 | 6445 | 6622 | 483890736 | 483890558 | 2.580000e-49 | 207.0 |
20 | TraesCS5D01G543500 | chr7D | 82.857 | 70 | 10 | 2 | 1426 | 1495 | 520390475 | 520390408 | 2.130000e-05 | 62.1 |
21 | TraesCS5D01G543500 | chr2B | 79.134 | 1016 | 185 | 20 | 4556 | 5553 | 17594574 | 17593568 | 0.000000e+00 | 676.0 |
22 | TraesCS5D01G543500 | chr2B | 79.395 | 859 | 141 | 25 | 4549 | 5387 | 17396122 | 17395280 | 2.210000e-159 | 573.0 |
23 | TraesCS5D01G543500 | chr2B | 78.978 | 509 | 90 | 14 | 3854 | 4352 | 17595255 | 17594754 | 1.470000e-86 | 331.0 |
24 | TraesCS5D01G543500 | chr2B | 73.684 | 513 | 112 | 15 | 4556 | 5051 | 787800957 | 787800451 | 2.020000e-40 | 178.0 |
25 | TraesCS5D01G543500 | chr2B | 82.514 | 183 | 20 | 10 | 6435 | 6611 | 94807985 | 94808161 | 4.410000e-32 | 150.0 |
26 | TraesCS5D01G543500 | chr2B | 82.243 | 107 | 15 | 2 | 1371 | 1477 | 418269890 | 418269788 | 9.760000e-14 | 89.8 |
27 | TraesCS5D01G543500 | chr3D | 78.049 | 1066 | 165 | 41 | 1500 | 2546 | 539909599 | 539908584 | 6.060000e-170 | 608.0 |
28 | TraesCS5D01G543500 | chr3D | 95.376 | 173 | 7 | 1 | 6427 | 6599 | 472443017 | 472442846 | 2.510000e-69 | 274.0 |
29 | TraesCS5D01G543500 | chr3D | 96.364 | 165 | 6 | 0 | 6435 | 6599 | 2350724 | 2350560 | 9.030000e-69 | 272.0 |
30 | TraesCS5D01G543500 | chr3D | 94.253 | 174 | 8 | 2 | 6431 | 6604 | 250054187 | 250054016 | 1.510000e-66 | 265.0 |
31 | TraesCS5D01G543500 | chr3D | 96.479 | 142 | 4 | 1 | 6888 | 7029 | 604800440 | 604800300 | 4.260000e-57 | 233.0 |
32 | TraesCS5D01G543500 | chr3D | 83.333 | 210 | 29 | 6 | 6434 | 6641 | 59924215 | 59924420 | 9.350000e-44 | 189.0 |
33 | TraesCS5D01G543500 | chr3D | 97.297 | 37 | 1 | 0 | 1426 | 1462 | 236232984 | 236232948 | 5.920000e-06 | 63.9 |
34 | TraesCS5D01G543500 | chr2D | 76.775 | 831 | 147 | 31 | 4572 | 5370 | 11257567 | 11258383 | 2.360000e-114 | 424.0 |
35 | TraesCS5D01G543500 | chr2D | 77.279 | 691 | 123 | 26 | 4753 | 5426 | 11292141 | 11292814 | 6.690000e-100 | 375.0 |
36 | TraesCS5D01G543500 | chr2D | 95.238 | 168 | 8 | 0 | 6435 | 6602 | 120100091 | 120099924 | 4.200000e-67 | 267.0 |
37 | TraesCS5D01G543500 | chr2D | 95.775 | 142 | 5 | 1 | 6888 | 7029 | 136380372 | 136380512 | 1.980000e-55 | 228.0 |
38 | TraesCS5D01G543500 | chr2D | 90.654 | 107 | 8 | 2 | 3261 | 3366 | 622352010 | 622351905 | 2.660000e-29 | 141.0 |
39 | TraesCS5D01G543500 | chr7A | 82.150 | 493 | 76 | 9 | 4556 | 5042 | 709296236 | 709296722 | 5.100000e-111 | 412.0 |
40 | TraesCS5D01G543500 | chr7A | 87.295 | 244 | 29 | 2 | 5139 | 5380 | 709296795 | 709297038 | 1.940000e-70 | 278.0 |
41 | TraesCS5D01G543500 | chr7A | 95.105 | 143 | 7 | 0 | 6888 | 7030 | 495505227 | 495505369 | 7.130000e-55 | 226.0 |
42 | TraesCS5D01G543500 | chr7A | 77.679 | 112 | 23 | 2 | 1370 | 1480 | 315296362 | 315296252 | 4.570000e-07 | 67.6 |
43 | TraesCS5D01G543500 | chr4B | 95.455 | 176 | 8 | 0 | 6434 | 6609 | 97895048 | 97894873 | 1.500000e-71 | 281.0 |
44 | TraesCS5D01G543500 | chr1D | 95.833 | 168 | 7 | 0 | 6435 | 6602 | 403044476 | 403044309 | 9.030000e-69 | 272.0 |
45 | TraesCS5D01G543500 | chr1D | 82.857 | 210 | 31 | 4 | 6435 | 6641 | 315034929 | 315035136 | 4.350000e-42 | 183.0 |
46 | TraesCS5D01G543500 | chr1D | 91.262 | 103 | 9 | 0 | 3269 | 3371 | 31154862 | 31154760 | 2.660000e-29 | 141.0 |
47 | TraesCS5D01G543500 | chr1D | 89.720 | 107 | 9 | 2 | 3270 | 3375 | 258092058 | 258091953 | 1.240000e-27 | 135.0 |
48 | TraesCS5D01G543500 | chr6D | 93.889 | 180 | 10 | 1 | 6424 | 6602 | 119803528 | 119803707 | 3.250000e-68 | 270.0 |
49 | TraesCS5D01G543500 | chr6D | 95.804 | 143 | 6 | 0 | 6888 | 7030 | 426639432 | 426639290 | 1.530000e-56 | 231.0 |
50 | TraesCS5D01G543500 | chr6D | 78.723 | 94 | 17 | 3 | 1370 | 1462 | 223454552 | 223454461 | 7.650000e-05 | 60.2 |
51 | TraesCS5D01G543500 | chr5A | 93.785 | 177 | 11 | 0 | 6434 | 6610 | 436260735 | 436260559 | 4.200000e-67 | 267.0 |
52 | TraesCS5D01G543500 | chr5A | 83.684 | 190 | 26 | 4 | 6435 | 6623 | 37590761 | 37590946 | 2.620000e-39 | 174.0 |
53 | TraesCS5D01G543500 | chr5A | 80.000 | 95 | 12 | 7 | 1370 | 1461 | 95672442 | 95672352 | 5.920000e-06 | 63.9 |
54 | TraesCS5D01G543500 | chr4D | 97.183 | 142 | 4 | 0 | 6888 | 7029 | 17560313 | 17560454 | 2.550000e-59 | 241.0 |
55 | TraesCS5D01G543500 | chr4D | 97.183 | 142 | 3 | 1 | 6888 | 7029 | 507858228 | 507858368 | 9.160000e-59 | 239.0 |
56 | TraesCS5D01G543500 | chr4D | 79.787 | 94 | 16 | 3 | 1370 | 1462 | 152155305 | 152155214 | 1.640000e-06 | 65.8 |
57 | TraesCS5D01G543500 | chr3A | 85.586 | 222 | 24 | 5 | 2683 | 2902 | 674755095 | 674754880 | 7.130000e-55 | 226.0 |
58 | TraesCS5D01G543500 | chr3A | 89.720 | 107 | 10 | 1 | 3262 | 3367 | 7126828 | 7126934 | 1.240000e-27 | 135.0 |
59 | TraesCS5D01G543500 | chr2A | 95.105 | 143 | 6 | 1 | 6888 | 7030 | 207465078 | 207465219 | 2.560000e-54 | 224.0 |
60 | TraesCS5D01G543500 | chr2A | 72.745 | 510 | 113 | 20 | 4556 | 5051 | 771805383 | 771804886 | 1.590000e-31 | 148.0 |
61 | TraesCS5D01G543500 | chr2A | 97.297 | 37 | 1 | 0 | 1426 | 1462 | 106518122 | 106518086 | 5.920000e-06 | 63.9 |
62 | TraesCS5D01G543500 | chr3B | 75.000 | 464 | 93 | 17 | 3895 | 4350 | 1372869 | 1373317 | 7.230000e-45 | 193.0 |
63 | TraesCS5D01G543500 | chr3B | 89.286 | 140 | 15 | 0 | 2578 | 2717 | 715890897 | 715890758 | 7.280000e-40 | 176.0 |
64 | TraesCS5D01G543500 | chr3B | 90.566 | 106 | 9 | 1 | 3262 | 3366 | 4219307 | 4219202 | 9.550000e-29 | 139.0 |
65 | TraesCS5D01G543500 | chr3B | 89.623 | 106 | 10 | 1 | 3262 | 3366 | 5074752 | 5074647 | 4.450000e-27 | 134.0 |
66 | TraesCS5D01G543500 | chr3B | 83.133 | 83 | 6 | 7 | 6539 | 6620 | 524326234 | 524326309 | 1.270000e-07 | 69.4 |
67 | TraesCS5D01G543500 | chr1B | 82.857 | 210 | 31 | 4 | 6435 | 6641 | 426855320 | 426855527 | 4.350000e-42 | 183.0 |
68 | TraesCS5D01G543500 | chr1B | 90.654 | 107 | 9 | 1 | 3270 | 3375 | 354987434 | 354987540 | 2.660000e-29 | 141.0 |
69 | TraesCS5D01G543500 | chr1A | 92.784 | 97 | 7 | 0 | 3270 | 3366 | 489239018 | 489238922 | 2.660000e-29 | 141.0 |
70 | TraesCS5D01G543500 | chr1A | 90.476 | 105 | 9 | 1 | 3267 | 3370 | 385895955 | 385896059 | 3.440000e-28 | 137.0 |
71 | TraesCS5D01G543500 | chr1A | 81.111 | 90 | 13 | 4 | 1374 | 1461 | 478551102 | 478551015 | 1.270000e-07 | 69.4 |
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 | TraesCS5D01G543500 | chr5D | 553671030 | 553678093 | 7063 | True | 13045.0 | 13045 | 100.0000 | 1 | 7064 | 1 | chr5D.!!$R2 | 7063 |
1 | TraesCS5D01G543500 | chr4A | 615039703 | 615042451 | 2748 | False | 891.5 | 1544 | 82.2250 | 3843 | 6314 | 2 | chr4A.!!$F2 | 2471 |
2 | TraesCS5D01G543500 | chr5B | 697287694 | 697295306 | 7612 | False | 818.0 | 1332 | 81.5600 | 1481 | 5440 | 3 | chr5B.!!$F4 | 3959 |
3 | TraesCS5D01G543500 | chr5B | 697124024 | 697126075 | 2051 | False | 816.5 | 990 | 84.1875 | 3800 | 5566 | 2 | chr5B.!!$F3 | 1766 |
4 | TraesCS5D01G543500 | chr5B | 697118035 | 697118620 | 585 | False | 730.0 | 730 | 89.5090 | 1 | 577 | 1 | chr5B.!!$F2 | 576 |
5 | TraesCS5D01G543500 | chr7B | 709559127 | 709560809 | 1682 | False | 811.0 | 811 | 76.0430 | 3868 | 5576 | 1 | chr7B.!!$F2 | 1708 |
6 | TraesCS5D01G543500 | chr7B | 709524952 | 709525789 | 837 | False | 682.0 | 682 | 81.7320 | 4559 | 5383 | 1 | chr7B.!!$F1 | 824 |
7 | TraesCS5D01G543500 | chr7B | 746051886 | 746053353 | 1467 | False | 667.0 | 667 | 75.5170 | 3894 | 5349 | 1 | chr7B.!!$F3 | 1455 |
8 | TraesCS5D01G543500 | chr7D | 616310755 | 616312431 | 1676 | False | 782.0 | 782 | 76.0000 | 3898 | 5587 | 1 | chr7D.!!$F2 | 1689 |
9 | TraesCS5D01G543500 | chr2B | 17395280 | 17396122 | 842 | True | 573.0 | 573 | 79.3950 | 4549 | 5387 | 1 | chr2B.!!$R1 | 838 |
10 | TraesCS5D01G543500 | chr2B | 17593568 | 17595255 | 1687 | True | 503.5 | 676 | 79.0560 | 3854 | 5553 | 2 | chr2B.!!$R4 | 1699 |
11 | TraesCS5D01G543500 | chr3D | 539908584 | 539909599 | 1015 | True | 608.0 | 608 | 78.0490 | 1500 | 2546 | 1 | chr3D.!!$R5 | 1046 |
12 | TraesCS5D01G543500 | chr2D | 11257567 | 11258383 | 816 | False | 424.0 | 424 | 76.7750 | 4572 | 5370 | 1 | chr2D.!!$F1 | 798 |
13 | TraesCS5D01G543500 | chr2D | 11292141 | 11292814 | 673 | False | 375.0 | 375 | 77.2790 | 4753 | 5426 | 1 | chr2D.!!$F2 | 673 |
14 | TraesCS5D01G543500 | chr7A | 709296236 | 709297038 | 802 | False | 345.0 | 412 | 84.7225 | 4556 | 5380 | 2 | chr7A.!!$F2 | 824 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
717 | 729 | 0.039911 | AGCCGAGTAGAGTGGACCTT | 59.960 | 55.000 | 0.00 | 0.0 | 0.00 | 3.50 | F |
953 | 965 | 0.040058 | TCCCTTGCTTGCATCCACAT | 59.960 | 50.000 | 0.00 | 0.0 | 0.00 | 3.21 | F |
963 | 975 | 0.099436 | GCATCCACATCTTGTTCCGC | 59.901 | 55.000 | 0.00 | 0.0 | 0.00 | 5.54 | F |
966 | 978 | 0.109532 | TCCACATCTTGTTCCGCCAA | 59.890 | 50.000 | 0.00 | 0.0 | 0.00 | 4.52 | F |
970 | 982 | 0.109597 | CATCTTGTTCCGCCAACTGC | 60.110 | 55.000 | 0.00 | 0.0 | 35.79 | 4.40 | F |
2840 | 3065 | 0.178992 | CTGGGGCAAAGAACCAGTGA | 60.179 | 55.000 | 0.00 | 0.0 | 45.21 | 3.41 | F |
2936 | 3161 | 0.030773 | TCACGTGCTCACTCACACTC | 59.969 | 55.000 | 11.67 | 0.0 | 36.80 | 3.51 | F |
2937 | 3162 | 0.031314 | CACGTGCTCACTCACACTCT | 59.969 | 55.000 | 0.82 | 0.0 | 36.80 | 3.24 | F |
2938 | 3163 | 0.031314 | ACGTGCTCACTCACACTCTG | 59.969 | 55.000 | 0.00 | 0.0 | 36.80 | 3.35 | F |
2940 | 3165 | 0.033228 | GTGCTCACTCACACTCTGCT | 59.967 | 55.000 | 0.00 | 0.0 | 36.97 | 4.24 | F |
3384 | 3609 | 0.038744 | ACATGTTCTTCAGCCCCAGG | 59.961 | 55.000 | 0.00 | 0.0 | 0.00 | 4.45 | F |
3892 | 4761 | 0.463654 | TGCAGACAACACCCACACTC | 60.464 | 55.000 | 0.00 | 0.0 | 0.00 | 3.51 | F |
3893 | 4762 | 0.463654 | GCAGACAACACCCACACTCA | 60.464 | 55.000 | 0.00 | 0.0 | 0.00 | 3.41 | F |
5266 | 10053 | 1.446792 | CTGCGTGAATCCTGAGCGT | 60.447 | 57.895 | 0.00 | 0.0 | 0.00 | 5.07 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2004 | 2032 | 0.251354 | TCCAGCTCACCTGATTCAGC | 59.749 | 55.000 | 8.23 | 0.00 | 44.64 | 4.26 | R |
2917 | 3142 | 0.030773 | GAGTGTGAGTGAGCACGTGA | 59.969 | 55.000 | 22.23 | 0.00 | 41.63 | 4.35 | R |
2918 | 3143 | 0.031314 | AGAGTGTGAGTGAGCACGTG | 59.969 | 55.000 | 12.28 | 12.28 | 41.63 | 4.49 | R |
2919 | 3144 | 0.031314 | CAGAGTGTGAGTGAGCACGT | 59.969 | 55.000 | 0.00 | 0.00 | 41.63 | 4.49 | R |
2921 | 3146 | 0.033228 | AGCAGAGTGTGAGTGAGCAC | 59.967 | 55.000 | 0.00 | 0.00 | 39.22 | 4.40 | R |
4609 | 9306 | 0.036875 | GCCCATAGGAAATCCCCTCG | 59.963 | 60.000 | 0.00 | 0.00 | 37.74 | 4.63 | R |
4627 | 9324 | 0.100861 | GCTCGTGGAGGTACTGTAGC | 59.899 | 60.000 | 8.91 | 8.91 | 41.55 | 3.58 | R |
4872 | 9601 | 5.662456 | TGCATTAACATGAATGGGTGAATG | 58.338 | 37.500 | 0.00 | 0.00 | 37.31 | 2.67 | R |
5053 | 9804 | 5.067805 | GGGGCCTCAAAAGTTTATACAGATG | 59.932 | 44.000 | 0.84 | 0.00 | 0.00 | 2.90 | R |
5075 | 9844 | 3.010138 | TGACATGGTCTTTAGGAAAGGGG | 59.990 | 47.826 | 0.00 | 0.00 | 39.01 | 4.79 | R |
5169 | 9953 | 3.525268 | ACCTTGGTTCTTTTTGCAGTG | 57.475 | 42.857 | 0.00 | 0.00 | 0.00 | 3.66 | R |
5648 | 10583 | 2.348472 | TGGACTCTGAAACCATTCCCT | 58.652 | 47.619 | 0.00 | 0.00 | 34.49 | 4.20 | R |
6028 | 11181 | 2.579873 | CTGGATGTTGGGGCTTGATAG | 58.420 | 52.381 | 0.00 | 0.00 | 0.00 | 2.08 | R |
6917 | 12073 | 0.033601 | AATGGGACCATTTAGCGGCA | 60.034 | 50.000 | 10.71 | 0.00 | 43.32 | 5.69 | 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.