Multiple sequence alignment - TraesCS6A01G332700
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 | TraesCS6A01G332700 | chr6A | 100.000 | 8193 | 0 | 0 | 1 | 8193 | 564268930 | 564260738 | 0.000000e+00 | 15130.0 |
1 | TraesCS6A01G332700 | chr6A | 96.400 | 250 | 6 | 1 | 5240 | 5489 | 586578721 | 586578475 | 7.650000e-110 | 409.0 |
2 | TraesCS6A01G332700 | chr4A | 98.955 | 4881 | 41 | 5 | 195 | 5066 | 668259975 | 668264854 | 0.000000e+00 | 8722.0 |
3 | TraesCS6A01G332700 | chr4A | 98.832 | 4880 | 48 | 4 | 195 | 5066 | 668212913 | 668217791 | 0.000000e+00 | 8687.0 |
4 | TraesCS6A01G332700 | chr4A | 98.832 | 4880 | 48 | 4 | 195 | 5066 | 668220699 | 668225577 | 0.000000e+00 | 8687.0 |
5 | TraesCS6A01G332700 | chr4A | 98.811 | 4880 | 47 | 6 | 195 | 5066 | 668186127 | 668191003 | 0.000000e+00 | 8680.0 |
6 | TraesCS6A01G332700 | chr4A | 98.709 | 4880 | 54 | 4 | 195 | 5066 | 668228581 | 668233459 | 0.000000e+00 | 8654.0 |
7 | TraesCS6A01G332700 | chr4A | 98.668 | 4879 | 56 | 4 | 195 | 5066 | 668178246 | 668183122 | 0.000000e+00 | 8641.0 |
8 | TraesCS6A01G332700 | chr7B | 98.423 | 4884 | 69 | 3 | 190 | 5066 | 537538710 | 537543592 | 0.000000e+00 | 8586.0 |
9 | TraesCS6A01G332700 | chr7B | 91.525 | 413 | 28 | 6 | 7046 | 7454 | 692302595 | 692302186 | 5.550000e-156 | 562.0 |
10 | TraesCS6A01G332700 | chr7B | 90.617 | 405 | 29 | 8 | 7045 | 7445 | 730403674 | 730403275 | 5.630000e-146 | 529.0 |
11 | TraesCS6A01G332700 | chr7B | 96.691 | 272 | 7 | 2 | 6772 | 7041 | 692303197 | 692302926 | 1.250000e-122 | 451.0 |
12 | TraesCS6A01G332700 | chr7B | 94.891 | 274 | 7 | 3 | 6775 | 7041 | 730404285 | 730404012 | 9.830000e-114 | 422.0 |
13 | TraesCS6A01G332700 | chr7B | 86.316 | 285 | 29 | 6 | 7706 | 7980 | 181408295 | 181408011 | 1.340000e-77 | 302.0 |
14 | TraesCS6A01G332700 | chr7A | 98.302 | 4887 | 74 | 4 | 189 | 5067 | 443976732 | 443971847 | 0.000000e+00 | 8556.0 |
15 | TraesCS6A01G332700 | chr7A | 96.414 | 251 | 6 | 1 | 5240 | 5490 | 9210695 | 9210448 | 2.130000e-110 | 411.0 |
16 | TraesCS6A01G332700 | chr7A | 96.414 | 251 | 6 | 2 | 5240 | 5490 | 463707622 | 463707869 | 2.130000e-110 | 411.0 |
17 | TraesCS6A01G332700 | chr3A | 98.014 | 4884 | 88 | 4 | 191 | 5066 | 679657206 | 679652324 | 0.000000e+00 | 8473.0 |
18 | TraesCS6A01G332700 | chr3A | 96.414 | 251 | 7 | 2 | 5240 | 5490 | 394385369 | 394385121 | 5.920000e-111 | 412.0 |
19 | TraesCS6A01G332700 | chr3A | 96.063 | 254 | 7 | 1 | 5240 | 5493 | 58275059 | 58274809 | 2.130000e-110 | 411.0 |
20 | TraesCS6A01G332700 | chr3A | 85.911 | 291 | 26 | 10 | 7703 | 7980 | 712651150 | 712650862 | 6.220000e-76 | 296.0 |
21 | TraesCS6A01G332700 | chr3A | 83.432 | 169 | 21 | 6 | 7516 | 7680 | 41061824 | 41061989 | 5.120000e-32 | 150.0 |
22 | TraesCS6A01G332700 | chr5D | 91.761 | 886 | 55 | 7 | 5487 | 6355 | 355431111 | 355431995 | 0.000000e+00 | 1216.0 |
23 | TraesCS6A01G332700 | chr5D | 92.840 | 405 | 20 | 3 | 6638 | 7041 | 355432497 | 355432893 | 5.510000e-161 | 579.0 |
24 | TraesCS6A01G332700 | chr5D | 90.032 | 311 | 20 | 5 | 7140 | 7450 | 355454762 | 355455061 | 7.710000e-105 | 392.0 |
25 | TraesCS6A01G332700 | chr5D | 88.070 | 285 | 24 | 8 | 7706 | 7980 | 485395261 | 485394977 | 6.130000e-86 | 329.0 |
26 | TraesCS6A01G332700 | chr5D | 93.780 | 209 | 12 | 1 | 6350 | 6558 | 355432091 | 355432298 | 6.170000e-81 | 313.0 |
27 | TraesCS6A01G332700 | chr5D | 90.588 | 170 | 13 | 2 | 5067 | 5234 | 355430932 | 355431100 | 1.070000e-53 | 222.0 |
28 | TraesCS6A01G332700 | chr2B | 95.058 | 688 | 20 | 6 | 6357 | 7041 | 34145354 | 34146030 | 0.000000e+00 | 1070.0 |
29 | TraesCS6A01G332700 | chr2B | 88.204 | 763 | 54 | 11 | 5486 | 6216 | 34144431 | 34145189 | 0.000000e+00 | 878.0 |
30 | TraesCS6A01G332700 | chr2B | 91.045 | 402 | 30 | 4 | 7047 | 7445 | 572755952 | 572756350 | 9.360000e-149 | 538.0 |
31 | TraesCS6A01G332700 | chr2B | 97.004 | 267 | 4 | 1 | 6775 | 7041 | 572755350 | 572755612 | 5.830000e-121 | 446.0 |
32 | TraesCS6A01G332700 | chr2B | 86.572 | 283 | 27 | 7 | 7706 | 7977 | 43228726 | 43229008 | 1.340000e-77 | 302.0 |
33 | TraesCS6A01G332700 | chr2B | 93.878 | 147 | 6 | 1 | 6209 | 6355 | 34145152 | 34145295 | 1.380000e-52 | 219.0 |
34 | TraesCS6A01G332700 | chr2B | 85.915 | 213 | 20 | 9 | 7462 | 7668 | 631168640 | 631168432 | 1.380000e-52 | 219.0 |
35 | TraesCS6A01G332700 | chr2B | 86.935 | 199 | 19 | 7 | 7474 | 7669 | 157991885 | 157991691 | 4.980000e-52 | 217.0 |
36 | TraesCS6A01G332700 | chr2B | 93.431 | 137 | 7 | 1 | 53 | 189 | 34144119 | 34144253 | 1.390000e-47 | 202.0 |
37 | TraesCS6A01G332700 | chr2B | 79.667 | 300 | 39 | 14 | 5666 | 5945 | 550972093 | 550972390 | 6.490000e-46 | 196.0 |
38 | TraesCS6A01G332700 | chr2B | 85.938 | 64 | 9 | 0 | 7065 | 7128 | 788531779 | 788531716 | 1.480000e-07 | 69.4 |
39 | TraesCS6A01G332700 | chr3B | 89.049 | 694 | 49 | 15 | 5666 | 6355 | 119346112 | 119345442 | 0.000000e+00 | 835.0 |
40 | TraesCS6A01G332700 | chr3B | 91.646 | 407 | 27 | 5 | 7042 | 7445 | 815965604 | 815966006 | 2.580000e-154 | 556.0 |
41 | TraesCS6A01G332700 | chr3B | 93.143 | 350 | 21 | 3 | 6357 | 6703 | 119345343 | 119344994 | 2.040000e-140 | 510.0 |
42 | TraesCS6A01G332700 | chr3B | 93.860 | 342 | 12 | 5 | 6701 | 7041 | 119334663 | 119334330 | 2.640000e-139 | 507.0 |
43 | TraesCS6A01G332700 | chr3B | 89.894 | 376 | 30 | 8 | 7045 | 7417 | 119310236 | 119309866 | 2.070000e-130 | 477.0 |
44 | TraesCS6A01G332700 | chr3B | 98.507 | 268 | 3 | 1 | 6775 | 7041 | 815965002 | 815965269 | 9.630000e-129 | 472.0 |
45 | TraesCS6A01G332700 | chr3B | 86.316 | 285 | 25 | 8 | 7706 | 7977 | 544545846 | 544546129 | 1.730000e-76 | 298.0 |
46 | TraesCS6A01G332700 | chr3B | 96.951 | 164 | 5 | 0 | 5487 | 5650 | 119354942 | 119354779 | 8.100000e-70 | 276.0 |
47 | TraesCS6A01G332700 | chr3B | 81.159 | 276 | 32 | 13 | 5689 | 5945 | 496171026 | 496171300 | 3.880000e-48 | 204.0 |
48 | TraesCS6A01G332700 | chr3B | 92.754 | 138 | 8 | 1 | 53 | 190 | 119355246 | 119355111 | 1.800000e-46 | 198.0 |
49 | TraesCS6A01G332700 | chr3B | 80.797 | 276 | 32 | 15 | 5689 | 5945 | 496228251 | 496228524 | 6.490000e-46 | 196.0 |
50 | TraesCS6A01G332700 | chr3B | 94.340 | 53 | 2 | 1 | 1 | 52 | 119355272 | 119355220 | 6.820000e-11 | 80.5 |
51 | TraesCS6A01G332700 | chr5B | 90.594 | 404 | 32 | 4 | 7045 | 7445 | 584888110 | 584887710 | 1.570000e-146 | 531.0 |
52 | TraesCS6A01G332700 | chr5B | 97.761 | 268 | 5 | 1 | 6775 | 7041 | 584888714 | 584888447 | 2.080000e-125 | 460.0 |
53 | TraesCS6A01G332700 | chr5B | 87.189 | 281 | 23 | 10 | 7706 | 7975 | 340615701 | 340615423 | 2.870000e-79 | 307.0 |
54 | TraesCS6A01G332700 | chr5B | 86.500 | 200 | 24 | 3 | 7470 | 7668 | 507982937 | 507983134 | 4.980000e-52 | 217.0 |
55 | TraesCS6A01G332700 | chr5B | 85.354 | 198 | 24 | 5 | 7474 | 7669 | 80196079 | 80195885 | 5.010000e-47 | 200.0 |
56 | TraesCS6A01G332700 | chr5B | 85.354 | 198 | 24 | 5 | 7474 | 7669 | 80600560 | 80600366 | 5.010000e-47 | 200.0 |
57 | TraesCS6A01G332700 | chr5A | 96.400 | 250 | 6 | 1 | 5240 | 5489 | 137286203 | 137286449 | 7.650000e-110 | 409.0 |
58 | TraesCS6A01G332700 | chr5A | 96.016 | 251 | 7 | 1 | 5240 | 5490 | 210736053 | 210736300 | 9.900000e-109 | 405.0 |
59 | TraesCS6A01G332700 | chr2A | 96.032 | 252 | 7 | 1 | 5239 | 5490 | 81244437 | 81244189 | 2.750000e-109 | 407.0 |
60 | TraesCS6A01G332700 | chrUn | 95.669 | 254 | 8 | 1 | 5240 | 5493 | 1525676 | 1525426 | 9.900000e-109 | 405.0 |
61 | TraesCS6A01G332700 | chrUn | 84.360 | 211 | 23 | 10 | 7474 | 7680 | 92772778 | 92772574 | 1.800000e-46 | 198.0 |
62 | TraesCS6A01G332700 | chr1D | 78.323 | 632 | 66 | 27 | 6394 | 6968 | 455631549 | 455630932 | 7.870000e-90 | 342.0 |
63 | TraesCS6A01G332700 | chr1D | 86.473 | 207 | 21 | 7 | 7468 | 7671 | 41299268 | 41299470 | 3.850000e-53 | 220.0 |
64 | TraesCS6A01G332700 | chr1D | 80.934 | 257 | 40 | 6 | 6005 | 6258 | 455632208 | 455631958 | 2.330000e-45 | 195.0 |
65 | TraesCS6A01G332700 | chr3D | 88.070 | 285 | 21 | 7 | 7706 | 7977 | 418215942 | 418216226 | 7.930000e-85 | 326.0 |
66 | TraesCS6A01G332700 | chr3D | 86.268 | 284 | 30 | 7 | 7706 | 7980 | 283311634 | 283311351 | 4.810000e-77 | 300.0 |
67 | TraesCS6A01G332700 | chr3D | 88.119 | 202 | 17 | 7 | 7474 | 7672 | 166501407 | 166501210 | 4.940000e-57 | 233.0 |
68 | TraesCS6A01G332700 | chr3D | 85.294 | 204 | 23 | 7 | 7468 | 7668 | 8906128 | 8906327 | 3.880000e-48 | 204.0 |
69 | TraesCS6A01G332700 | chr2D | 87.589 | 282 | 27 | 5 | 7707 | 7980 | 56324321 | 56324040 | 3.690000e-83 | 320.0 |
70 | TraesCS6A01G332700 | chr2D | 81.230 | 309 | 44 | 11 | 7680 | 7977 | 564703786 | 564704091 | 3.820000e-58 | 237.0 |
71 | TraesCS6A01G332700 | chr4B | 79.000 | 300 | 40 | 13 | 5666 | 5945 | 504337726 | 504338022 | 5.050000e-42 | 183.0 |
72 | TraesCS6A01G332700 | chr4B | 78.667 | 300 | 41 | 14 | 5666 | 5945 | 434104414 | 434104710 | 2.350000e-40 | 178.0 |
73 | TraesCS6A01G332700 | chr4B | 79.422 | 277 | 36 | 13 | 5689 | 5945 | 266621335 | 266621610 | 8.450000e-40 | 176.0 |
74 | TraesCS6A01G332700 | chr6B | 79.556 | 225 | 35 | 10 | 7462 | 7680 | 14387807 | 14387588 | 5.120000e-32 | 150.0 |
75 | TraesCS6A01G332700 | chr6B | 87.903 | 124 | 5 | 4 | 8077 | 8192 | 634330761 | 634330640 | 3.990000e-28 | 137.0 |
76 | TraesCS6A01G332700 | chr6D | 86.400 | 125 | 7 | 4 | 8077 | 8193 | 420957399 | 420957277 | 2.400000e-25 | 128.0 |
77 | TraesCS6A01G332700 | chr6D | 88.525 | 61 | 3 | 3 | 8136 | 8193 | 420936565 | 420936506 | 4.100000e-08 | 71.3 |
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 | TraesCS6A01G332700 | chr6A | 564260738 | 564268930 | 8192 | True | 15130.00 | 15130 | 100.00000 | 1 | 8193 | 1 | chr6A.!!$R1 | 8192 |
1 | TraesCS6A01G332700 | chr4A | 668259975 | 668264854 | 4879 | False | 8722.00 | 8722 | 98.95500 | 195 | 5066 | 1 | chr4A.!!$F1 | 4871 |
2 | TraesCS6A01G332700 | chr4A | 668212913 | 668233459 | 20546 | False | 8676.00 | 8687 | 98.79100 | 195 | 5066 | 3 | chr4A.!!$F3 | 4871 |
3 | TraesCS6A01G332700 | chr4A | 668178246 | 668191003 | 12757 | False | 8660.50 | 8680 | 98.73950 | 195 | 5066 | 2 | chr4A.!!$F2 | 4871 |
4 | TraesCS6A01G332700 | chr7B | 537538710 | 537543592 | 4882 | False | 8586.00 | 8586 | 98.42300 | 190 | 5066 | 1 | chr7B.!!$F1 | 4876 |
5 | TraesCS6A01G332700 | chr7B | 692302186 | 692303197 | 1011 | True | 506.50 | 562 | 94.10800 | 6772 | 7454 | 2 | chr7B.!!$R2 | 682 |
6 | TraesCS6A01G332700 | chr7B | 730403275 | 730404285 | 1010 | True | 475.50 | 529 | 92.75400 | 6775 | 7445 | 2 | chr7B.!!$R3 | 670 |
7 | TraesCS6A01G332700 | chr7A | 443971847 | 443976732 | 4885 | True | 8556.00 | 8556 | 98.30200 | 189 | 5067 | 1 | chr7A.!!$R2 | 4878 |
8 | TraesCS6A01G332700 | chr3A | 679652324 | 679657206 | 4882 | True | 8473.00 | 8473 | 98.01400 | 191 | 5066 | 1 | chr3A.!!$R3 | 4875 |
9 | TraesCS6A01G332700 | chr5D | 355430932 | 355432893 | 1961 | False | 582.50 | 1216 | 92.24225 | 5067 | 7041 | 4 | chr5D.!!$F2 | 1974 |
10 | TraesCS6A01G332700 | chr2B | 34144119 | 34146030 | 1911 | False | 592.25 | 1070 | 92.64275 | 53 | 7041 | 4 | chr2B.!!$F3 | 6988 |
11 | TraesCS6A01G332700 | chr2B | 572755350 | 572756350 | 1000 | False | 492.00 | 538 | 94.02450 | 6775 | 7445 | 2 | chr2B.!!$F4 | 670 |
12 | TraesCS6A01G332700 | chr3B | 119344994 | 119346112 | 1118 | True | 672.50 | 835 | 91.09600 | 5666 | 6703 | 2 | chr3B.!!$R3 | 1037 |
13 | TraesCS6A01G332700 | chr3B | 815965002 | 815966006 | 1004 | False | 514.00 | 556 | 95.07650 | 6775 | 7445 | 2 | chr3B.!!$F4 | 670 |
14 | TraesCS6A01G332700 | chr5B | 584887710 | 584888714 | 1004 | True | 495.50 | 531 | 94.17750 | 6775 | 7445 | 2 | chr5B.!!$R4 | 670 |
15 | TraesCS6A01G332700 | chr1D | 455630932 | 455632208 | 1276 | True | 268.50 | 342 | 79.62850 | 6005 | 6968 | 2 | chr1D.!!$R1 | 963 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
162 | 163 | 0.033796 | TGTACCCGTCCTACAGGAGG | 60.034 | 60.000 | 10.41 | 10.41 | 46.49 | 4.30 | F |
235 | 237 | 0.101759 | GCTACGGACCAAGCGATACA | 59.898 | 55.000 | 0.31 | 0.00 | 0.00 | 2.29 | F |
524 | 527 | 0.251634 | GAAGCTTGAGGACTGGAGGG | 59.748 | 60.000 | 2.10 | 0.00 | 0.00 | 4.30 | F |
914 | 917 | 3.881688 | GCATGCCTCTGAATCTACATGTT | 59.118 | 43.478 | 6.36 | 0.00 | 37.73 | 2.71 | F |
2322 | 10118 | 4.103357 | CAGGTATGTCTACTACACAACGC | 58.897 | 47.826 | 0.00 | 0.00 | 42.09 | 4.84 | F |
2893 | 10692 | 5.047377 | TGGAAAATACTCCTGTTGCAAATCC | 60.047 | 40.000 | 0.00 | 0.00 | 36.35 | 3.01 | F |
4409 | 20094 | 0.657312 | TGAGTCTGCACTTGTTTGCG | 59.343 | 50.000 | 0.00 | 0.00 | 46.20 | 4.85 | F |
5112 | 20798 | 0.032952 | TTGCGGATACATACGGAGCC | 59.967 | 55.000 | 0.00 | 0.00 | 35.37 | 4.70 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1486 | 9282 | 0.674895 | AGCCTTCGCTTCACATGGAC | 60.675 | 55.000 | 0.00 | 0.00 | 45.55 | 4.02 | R |
1891 | 9687 | 5.927281 | AATAGAGCACATCCAAGCAAAAT | 57.073 | 34.783 | 0.00 | 0.00 | 0.00 | 1.82 | R |
2322 | 10118 | 5.021033 | AGAAGGCATTCATACTCTCACTG | 57.979 | 43.478 | 14.34 | 0.00 | 37.94 | 3.66 | R |
2554 | 10350 | 6.873997 | ACTTCCGATCACAATACATCTTGTA | 58.126 | 36.000 | 0.00 | 0.00 | 37.25 | 2.41 | R |
4409 | 20094 | 3.196469 | TCTTGTCAGGACATGTCATCTCC | 59.804 | 47.826 | 26.47 | 10.22 | 41.52 | 3.71 | R |
5074 | 20760 | 3.632145 | GCAATGTTCGGATACCAAGGATT | 59.368 | 43.478 | 0.00 | 0.00 | 0.00 | 3.01 | R |
5248 | 20943 | 0.109365 | TTCGGCAAATCCAATGTGCG | 60.109 | 50.000 | 0.00 | 0.00 | 39.22 | 5.34 | R |
7253 | 23800 | 0.320858 | TGCGCACGTCTCCCAAATTA | 60.321 | 50.000 | 5.66 | 0.00 | 0.00 | 1.40 | 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.