Multiple sequence alignment - TraesCS1B01G036400
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 | TraesCS1B01G036400 | chr1B | 100.000 | 6817 | 0 | 0 | 1 | 6817 | 17358093 | 17351277 | 0.000000e+00 | 12589.0 |
1 | TraesCS1B01G036400 | chr1B | 95.138 | 2674 | 79 | 23 | 1634 | 4266 | 16922342 | 16919679 | 0.000000e+00 | 4170.0 |
2 | TraesCS1B01G036400 | chr1B | 96.233 | 1858 | 55 | 7 | 4965 | 6817 | 16851515 | 16849668 | 0.000000e+00 | 3029.0 |
3 | TraesCS1B01G036400 | chr1B | 90.799 | 1576 | 79 | 28 | 5292 | 6808 | 16914927 | 16913359 | 0.000000e+00 | 2047.0 |
4 | TraesCS1B01G036400 | chr1B | 93.381 | 423 | 17 | 4 | 4877 | 5296 | 16919487 | 16919073 | 3.490000e-172 | 616.0 |
5 | TraesCS1B01G036400 | chr1B | 90.705 | 312 | 23 | 5 | 6161 | 6467 | 16742470 | 16742160 | 1.770000e-110 | 411.0 |
6 | TraesCS1B01G036400 | chr1B | 94.286 | 210 | 11 | 1 | 4347 | 4556 | 16919683 | 16919475 | 3.070000e-83 | 320.0 |
7 | TraesCS1B01G036400 | chr1B | 97.727 | 176 | 3 | 1 | 4553 | 4728 | 449828212 | 449828386 | 1.110000e-77 | 302.0 |
8 | TraesCS1B01G036400 | chr1B | 98.630 | 146 | 1 | 1 | 4735 | 4880 | 565662597 | 565662741 | 2.440000e-64 | 257.0 |
9 | TraesCS1B01G036400 | chr1A | 88.745 | 2319 | 152 | 43 | 1 | 2260 | 13675848 | 13673580 | 0.000000e+00 | 2736.0 |
10 | TraesCS1B01G036400 | chr1A | 95.159 | 1570 | 48 | 11 | 4877 | 6441 | 13671382 | 13669836 | 0.000000e+00 | 2453.0 |
11 | TraesCS1B01G036400 | chr1A | 84.412 | 1251 | 119 | 43 | 3322 | 4556 | 13672560 | 13671370 | 0.000000e+00 | 1160.0 |
12 | TraesCS1B01G036400 | chr1A | 92.371 | 485 | 26 | 7 | 2598 | 3071 | 13673048 | 13672564 | 0.000000e+00 | 680.0 |
13 | TraesCS1B01G036400 | chr1A | 90.064 | 312 | 25 | 5 | 6161 | 6467 | 13420451 | 13420141 | 3.830000e-107 | 399.0 |
14 | TraesCS1B01G036400 | chr1A | 86.667 | 300 | 22 | 3 | 2261 | 2546 | 13673338 | 13673043 | 3.970000e-82 | 316.0 |
15 | TraesCS1B01G036400 | chr1A | 98.830 | 171 | 2 | 0 | 4550 | 4720 | 208903961 | 208903791 | 8.590000e-79 | 305.0 |
16 | TraesCS1B01G036400 | chr1A | 78.065 | 155 | 32 | 2 | 4399 | 4553 | 490778264 | 490778112 | 5.630000e-16 | 97.1 |
17 | TraesCS1B01G036400 | chr1D | 88.939 | 1989 | 110 | 40 | 4877 | 6815 | 11545431 | 11543503 | 0.000000e+00 | 2353.0 |
18 | TraesCS1B01G036400 | chr1D | 91.267 | 1649 | 100 | 24 | 633 | 2246 | 11549594 | 11547955 | 0.000000e+00 | 2207.0 |
19 | TraesCS1B01G036400 | chr1D | 91.412 | 850 | 66 | 4 | 3711 | 4556 | 11546266 | 11545420 | 0.000000e+00 | 1158.0 |
20 | TraesCS1B01G036400 | chr1D | 90.270 | 555 | 38 | 12 | 2531 | 3071 | 11547346 | 11546794 | 0.000000e+00 | 712.0 |
21 | TraesCS1B01G036400 | chr1D | 88.400 | 500 | 37 | 7 | 1 | 497 | 11550152 | 11549671 | 3.540000e-162 | 582.0 |
22 | TraesCS1B01G036400 | chr1D | 78.710 | 155 | 31 | 2 | 4399 | 4553 | 276797528 | 276797376 | 1.210000e-17 | 102.0 |
23 | TraesCS1B01G036400 | chr1D | 77.419 | 155 | 33 | 2 | 4399 | 4553 | 225401965 | 225402117 | 2.620000e-14 | 91.6 |
24 | TraesCS1B01G036400 | chr1D | 80.328 | 122 | 20 | 4 | 4399 | 4518 | 250211940 | 250212059 | 9.420000e-14 | 89.8 |
25 | TraesCS1B01G036400 | chr3A | 88.912 | 478 | 38 | 12 | 5881 | 6351 | 750729541 | 750729072 | 5.930000e-160 | 575.0 |
26 | TraesCS1B01G036400 | chr3A | 78.736 | 348 | 66 | 8 | 2723 | 3065 | 740353103 | 740352759 | 6.880000e-55 | 226.0 |
27 | TraesCS1B01G036400 | chr3A | 90.076 | 131 | 10 | 3 | 5732 | 5862 | 750730107 | 750729980 | 4.230000e-37 | 167.0 |
28 | TraesCS1B01G036400 | chr3A | 80.255 | 157 | 27 | 4 | 4399 | 4553 | 561333726 | 561333880 | 1.550000e-21 | 115.0 |
29 | TraesCS1B01G036400 | chr3A | 97.059 | 34 | 1 | 0 | 4363 | 4396 | 497947285 | 497947252 | 2.660000e-04 | 58.4 |
30 | TraesCS1B01G036400 | chr3A | 92.105 | 38 | 3 | 0 | 5620 | 5657 | 750730244 | 750730207 | 3.000000e-03 | 54.7 |
31 | TraesCS1B01G036400 | chr3D | 80.294 | 477 | 64 | 24 | 3730 | 4201 | 608068168 | 608067717 | 3.940000e-87 | 333.0 |
32 | TraesCS1B01G036400 | chr3D | 78.917 | 351 | 60 | 8 | 2723 | 3065 | 608069134 | 608068790 | 6.880000e-55 | 226.0 |
33 | TraesCS1B01G036400 | chr3B | 80.086 | 467 | 63 | 23 | 3730 | 4191 | 817823902 | 817823461 | 3.070000e-83 | 320.0 |
34 | TraesCS1B01G036400 | chr3B | 96.703 | 182 | 5 | 1 | 4553 | 4734 | 168268209 | 168268389 | 1.110000e-77 | 302.0 |
35 | TraesCS1B01G036400 | chr3B | 79.429 | 350 | 60 | 9 | 2723 | 3065 | 817824720 | 817824376 | 3.180000e-58 | 237.0 |
36 | TraesCS1B01G036400 | chr3B | 86.935 | 199 | 24 | 2 | 5510 | 5706 | 817822329 | 817822131 | 8.900000e-54 | 222.0 |
37 | TraesCS1B01G036400 | chr7A | 98.830 | 171 | 2 | 0 | 4553 | 4723 | 639786703 | 639786533 | 8.590000e-79 | 305.0 |
38 | TraesCS1B01G036400 | chr7A | 80.645 | 155 | 24 | 6 | 4401 | 4553 | 665742352 | 665742502 | 1.550000e-21 | 115.0 |
39 | TraesCS1B01G036400 | chr5A | 98.824 | 170 | 2 | 0 | 4551 | 4720 | 439421078 | 439420909 | 3.090000e-78 | 303.0 |
40 | TraesCS1B01G036400 | chr5A | 97.740 | 177 | 2 | 2 | 4545 | 4720 | 680850638 | 680850813 | 3.090000e-78 | 303.0 |
41 | TraesCS1B01G036400 | chr5A | 81.013 | 158 | 25 | 5 | 4399 | 4553 | 493816056 | 493816211 | 3.340000e-23 | 121.0 |
42 | TraesCS1B01G036400 | chr5A | 80.851 | 141 | 25 | 2 | 2748 | 2887 | 484080636 | 484080497 | 7.230000e-20 | 110.0 |
43 | TraesCS1B01G036400 | chr5A | 97.059 | 34 | 1 | 0 | 4363 | 4396 | 691814720 | 691814687 | 2.660000e-04 | 58.4 |
44 | TraesCS1B01G036400 | chr4B | 91.228 | 228 | 13 | 4 | 3853 | 4076 | 406211170 | 406211394 | 3.090000e-78 | 303.0 |
45 | TraesCS1B01G036400 | chr4B | 84.390 | 205 | 18 | 4 | 3633 | 3825 | 406210971 | 406211173 | 9.030000e-44 | 189.0 |
46 | TraesCS1B01G036400 | chr6A | 98.266 | 173 | 2 | 1 | 4554 | 4726 | 64065217 | 64065388 | 1.110000e-77 | 302.0 |
47 | TraesCS1B01G036400 | chr6A | 97.727 | 176 | 2 | 2 | 4545 | 4720 | 582491251 | 582491078 | 1.110000e-77 | 302.0 |
48 | TraesCS1B01G036400 | chr6A | 97.059 | 34 | 1 | 0 | 4363 | 4396 | 77111291 | 77111258 | 2.660000e-04 | 58.4 |
49 | TraesCS1B01G036400 | chr4A | 96.648 | 179 | 4 | 2 | 4552 | 4730 | 3725996 | 3725820 | 5.170000e-76 | 296.0 |
50 | TraesCS1B01G036400 | chr4A | 100.000 | 137 | 0 | 0 | 4735 | 4871 | 229501633 | 229501769 | 3.160000e-63 | 254.0 |
51 | TraesCS1B01G036400 | chr4A | 84.034 | 119 | 18 | 1 | 4399 | 4517 | 286747778 | 286747661 | 5.590000e-21 | 113.0 |
52 | TraesCS1B01G036400 | chr4A | 77.576 | 165 | 33 | 4 | 4399 | 4563 | 742356810 | 742356650 | 5.630000e-16 | 97.1 |
53 | TraesCS1B01G036400 | chr7B | 98.013 | 151 | 2 | 1 | 4735 | 4884 | 183306551 | 183306701 | 1.890000e-65 | 261.0 |
54 | TraesCS1B01G036400 | chr7B | 96.178 | 157 | 3 | 3 | 4735 | 4890 | 624944871 | 624944717 | 3.160000e-63 | 254.0 |
55 | TraesCS1B01G036400 | chr2A | 99.306 | 144 | 0 | 1 | 4735 | 4878 | 385446466 | 385446608 | 6.780000e-65 | 259.0 |
56 | TraesCS1B01G036400 | chr2A | 97.143 | 35 | 1 | 0 | 4362 | 4396 | 25078412 | 25078378 | 7.380000e-05 | 60.2 |
57 | TraesCS1B01G036400 | chr5B | 100.000 | 139 | 0 | 0 | 4735 | 4873 | 128671441 | 128671579 | 2.440000e-64 | 257.0 |
58 | TraesCS1B01G036400 | chr5B | 94.479 | 163 | 6 | 3 | 4735 | 4894 | 554754512 | 554754674 | 1.470000e-61 | 248.0 |
59 | TraesCS1B01G036400 | chr5B | 80.142 | 141 | 26 | 2 | 2748 | 2887 | 460267522 | 460267383 | 3.360000e-18 | 104.0 |
60 | TraesCS1B01G036400 | chr5B | 97.143 | 35 | 1 | 0 | 4362 | 4396 | 562455992 | 562456026 | 7.380000e-05 | 60.2 |
61 | TraesCS1B01G036400 | chr2B | 97.351 | 151 | 1 | 3 | 4735 | 4885 | 522079021 | 522079168 | 3.160000e-63 | 254.0 |
62 | TraesCS1B01G036400 | chr2B | 97.931 | 145 | 1 | 2 | 4739 | 4881 | 316008066 | 316008210 | 4.080000e-62 | 250.0 |
63 | TraesCS1B01G036400 | chr2B | 84.615 | 156 | 17 | 7 | 4400 | 4553 | 740319119 | 740319269 | 1.530000e-31 | 148.0 |
64 | TraesCS1B01G036400 | chr2D | 81.132 | 159 | 25 | 4 | 4399 | 4556 | 627516638 | 627516484 | 9.280000e-24 | 122.0 |
65 | TraesCS1B01G036400 | chr2D | 80.255 | 157 | 25 | 5 | 4399 | 4553 | 393585419 | 393585571 | 5.590000e-21 | 113.0 |
66 | TraesCS1B01G036400 | chr2D | 81.955 | 133 | 23 | 1 | 4402 | 4534 | 16177849 | 16177718 | 2.010000e-20 | 111.0 |
67 | TraesCS1B01G036400 | chr2D | 79.618 | 157 | 28 | 4 | 4399 | 4554 | 50400568 | 50400721 | 7.230000e-20 | 110.0 |
68 | TraesCS1B01G036400 | chr2D | 97.143 | 35 | 1 | 0 | 4362 | 4396 | 637738387 | 637738353 | 7.380000e-05 | 60.2 |
69 | TraesCS1B01G036400 | chr6D | 80.769 | 156 | 26 | 4 | 4399 | 4553 | 123267960 | 123268112 | 1.200000e-22 | 119.0 |
70 | TraesCS1B01G036400 | chr6D | 81.618 | 136 | 22 | 2 | 4399 | 4534 | 402325126 | 402325258 | 7.230000e-20 | 110.0 |
71 | TraesCS1B01G036400 | chr6D | 78.431 | 153 | 31 | 2 | 4401 | 4553 | 117361953 | 117362103 | 1.560000e-16 | 99.0 |
72 | TraesCS1B01G036400 | chr6D | 80.672 | 119 | 19 | 4 | 4399 | 4515 | 35257889 | 35257773 | 9.420000e-14 | 89.8 |
73 | TraesCS1B01G036400 | chr6D | 78.295 | 129 | 21 | 7 | 4399 | 4523 | 35294436 | 35294311 | 7.330000e-10 | 76.8 |
74 | TraesCS1B01G036400 | chr6D | 88.000 | 50 | 4 | 1 | 4487 | 4536 | 109723171 | 109723124 | 2.660000e-04 | 58.4 |
75 | TraesCS1B01G036400 | chr4D | 80.519 | 154 | 27 | 2 | 4399 | 4552 | 428482010 | 428481860 | 1.550000e-21 | 115.0 |
76 | TraesCS1B01G036400 | chr4D | 82.727 | 110 | 15 | 3 | 4402 | 4509 | 316913470 | 316913363 | 2.020000e-15 | 95.3 |
77 | TraesCS1B01G036400 | chr4D | 78.761 | 113 | 20 | 4 | 4399 | 4509 | 19642523 | 19642633 | 9.480000e-09 | 73.1 |
78 | TraesCS1B01G036400 | chr5D | 80.851 | 141 | 25 | 2 | 2748 | 2887 | 383778004 | 383777865 | 7.230000e-20 | 110.0 |
79 | TraesCS1B01G036400 | chr5D | 78.710 | 155 | 28 | 4 | 4399 | 4553 | 38729872 | 38729723 | 1.560000e-16 | 99.0 |
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 | TraesCS1B01G036400 | chr1B | 17351277 | 17358093 | 6816 | True | 12589.000000 | 12589 | 100.000000 | 1 | 6817 | 1 | chr1B.!!$R4 | 6816 |
1 | TraesCS1B01G036400 | chr1B | 16849668 | 16851515 | 1847 | True | 3029.000000 | 3029 | 96.233000 | 4965 | 6817 | 1 | chr1B.!!$R2 | 1852 |
2 | TraesCS1B01G036400 | chr1B | 16913359 | 16914927 | 1568 | True | 2047.000000 | 2047 | 90.799000 | 5292 | 6808 | 1 | chr1B.!!$R3 | 1516 |
3 | TraesCS1B01G036400 | chr1B | 16919073 | 16922342 | 3269 | True | 1702.000000 | 4170 | 94.268333 | 1634 | 5296 | 3 | chr1B.!!$R5 | 3662 |
4 | TraesCS1B01G036400 | chr1A | 13669836 | 13675848 | 6012 | True | 1469.000000 | 2736 | 89.470800 | 1 | 6441 | 5 | chr1A.!!$R4 | 6440 |
5 | TraesCS1B01G036400 | chr1D | 11543503 | 11550152 | 6649 | True | 1402.400000 | 2353 | 90.057600 | 1 | 6815 | 5 | chr1D.!!$R2 | 6814 |
6 | TraesCS1B01G036400 | chr3A | 750729072 | 750730244 | 1172 | True | 265.566667 | 575 | 90.364333 | 5620 | 6351 | 3 | chr3A.!!$R3 | 731 |
7 | TraesCS1B01G036400 | chr3D | 608067717 | 608069134 | 1417 | True | 279.500000 | 333 | 79.605500 | 2723 | 4201 | 2 | chr3D.!!$R1 | 1478 |
8 | TraesCS1B01G036400 | chr3B | 817822131 | 817824720 | 2589 | True | 259.666667 | 320 | 82.150000 | 2723 | 5706 | 3 | chr3B.!!$R1 | 2983 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
393 | 408 | 0.036765 | TTGCGTCGGAGGCATACTTT | 60.037 | 50.000 | 24.01 | 0.0 | 38.88 | 2.66 | F |
739 | 758 | 0.042708 | GCATCTATGCGTCTGTTGCG | 60.043 | 55.000 | 0.00 | 0.0 | 44.67 | 4.85 | F |
1386 | 1446 | 0.325577 | TGGTGGCTGCTCTATCTGGA | 60.326 | 55.000 | 0.00 | 0.0 | 0.00 | 3.86 | F |
2001 | 2070 | 0.322008 | CAAGTCCTGTTCTGCCCTCC | 60.322 | 60.000 | 0.00 | 0.0 | 0.00 | 4.30 | F |
2332 | 2651 | 2.293399 | GCACACGAATCCTCCTTTGTTT | 59.707 | 45.455 | 0.00 | 0.0 | 0.00 | 2.83 | F |
3818 | 4855 | 1.537202 | GTTGCTGAACTGGATGGACAC | 59.463 | 52.381 | 0.00 | 0.0 | 0.00 | 3.67 | F |
4260 | 5317 | 0.036952 | ATGCTGCTTCACTACTGCGT | 60.037 | 50.000 | 0.00 | 0.0 | 33.87 | 5.24 | F |
4839 | 6306 | 0.037303 | ACCTCATGGTCACAAGGCAG | 59.963 | 55.000 | 0.00 | 0.0 | 44.78 | 4.85 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1401 | 1461 | 0.394565 | GCCCATTACCAGCTCTCGAT | 59.605 | 55.000 | 0.00 | 0.00 | 0.00 | 3.59 | R |
1983 | 2052 | 0.474660 | AGGAGGGCAGAACAGGACTT | 60.475 | 55.000 | 0.00 | 0.00 | 0.00 | 3.01 | R |
2613 | 3029 | 1.235724 | GGTCAGTACCCTGTGCAAAC | 58.764 | 55.000 | 0.00 | 0.00 | 40.21 | 2.93 | R |
3818 | 4855 | 0.025384 | CACGTACACAGCGCATGATG | 59.975 | 55.000 | 17.51 | 5.75 | 37.57 | 3.07 | R |
4093 | 5150 | 0.676466 | TTATCTGCTGCGTTGTGGGG | 60.676 | 55.000 | 0.00 | 0.00 | 0.00 | 4.96 | R |
4680 | 6147 | 0.036875 | GGTGAAGTCCTCCCCACTTG | 59.963 | 60.000 | 0.00 | 0.00 | 34.10 | 3.16 | R |
5356 | 6844 | 0.942962 | CAATCAAGATCTGCCGCTCC | 59.057 | 55.000 | 0.00 | 0.00 | 0.00 | 4.70 | R |
6714 | 8769 | 3.691118 | CACAAGGGTATGGACAGTTCATG | 59.309 | 47.826 | 4.35 | 0.00 | 0.00 | 3.07 | 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.