Multiple sequence alignment - TraesCS1B01G298400
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 | TraesCS1B01G298400 | chr1B | 100.000 | 7251 | 0 | 0 | 1 | 7251 | 519618560 | 519625810 | 0.000000e+00 | 13391.0 |
1 | TraesCS1B01G298400 | chr1B | 94.510 | 2623 | 79 | 13 | 1952 | 4517 | 518910057 | 518912671 | 0.000000e+00 | 3986.0 |
2 | TraesCS1B01G298400 | chr1B | 96.460 | 791 | 16 | 4 | 4501 | 5290 | 518912838 | 518913617 | 0.000000e+00 | 1295.0 |
3 | TraesCS1B01G298400 | chr1B | 97.841 | 602 | 13 | 0 | 1357 | 1958 | 518909305 | 518909906 | 0.000000e+00 | 1040.0 |
4 | TraesCS1B01G298400 | chr1B | 96.364 | 550 | 15 | 3 | 5297 | 5844 | 518913723 | 518914269 | 0.000000e+00 | 900.0 |
5 | TraesCS1B01G298400 | chr1B | 95.913 | 416 | 16 | 1 | 5844 | 6259 | 518914315 | 518914729 | 0.000000e+00 | 673.0 |
6 | TraesCS1B01G298400 | chr1B | 89.863 | 365 | 37 | 0 | 1 | 365 | 518813097 | 518813461 | 3.060000e-128 | 470.0 |
7 | TraesCS1B01G298400 | chr1B | 95.708 | 233 | 10 | 0 | 6031 | 6263 | 520100382 | 520100614 | 6.870000e-100 | 375.0 |
8 | TraesCS1B01G298400 | chr1B | 95.755 | 212 | 9 | 0 | 1339 | 1550 | 519619835 | 519620046 | 6.970000e-90 | 342.0 |
9 | TraesCS1B01G298400 | chr1B | 95.755 | 212 | 9 | 0 | 1276 | 1487 | 519619898 | 519620109 | 6.970000e-90 | 342.0 |
10 | TraesCS1B01G298400 | chr1B | 94.845 | 194 | 10 | 0 | 1294 | 1487 | 518909305 | 518909498 | 3.290000e-78 | 303.0 |
11 | TraesCS1B01G298400 | chr1B | 91.579 | 190 | 11 | 2 | 5844 | 6033 | 520100075 | 520100259 | 2.600000e-64 | 257.0 |
12 | TraesCS1B01G298400 | chr1B | 96.644 | 149 | 5 | 0 | 1402 | 1550 | 519619835 | 519619983 | 1.560000e-61 | 248.0 |
13 | TraesCS1B01G298400 | chr1B | 96.644 | 149 | 5 | 0 | 1276 | 1424 | 519619961 | 519620109 | 1.560000e-61 | 248.0 |
14 | TraesCS1B01G298400 | chr1B | 95.973 | 149 | 6 | 0 | 1276 | 1424 | 518909350 | 518909498 | 7.270000e-60 | 243.0 |
15 | TraesCS1B01G298400 | chr1B | 81.994 | 311 | 18 | 20 | 893 | 1166 | 518908669 | 518908978 | 5.660000e-56 | 230.0 |
16 | TraesCS1B01G298400 | chr1B | 93.893 | 131 | 8 | 0 | 1420 | 1550 | 518909305 | 518909435 | 1.600000e-46 | 198.0 |
17 | TraesCS1B01G298400 | chr1B | 94.958 | 119 | 5 | 1 | 5726 | 5844 | 520099847 | 520099964 | 1.240000e-42 | 185.0 |
18 | TraesCS1B01G298400 | chr1B | 97.674 | 86 | 2 | 0 | 1465 | 1550 | 519619835 | 519619920 | 1.630000e-31 | 148.0 |
19 | TraesCS1B01G298400 | chr1B | 97.674 | 86 | 2 | 0 | 1276 | 1361 | 519620024 | 519620109 | 1.630000e-31 | 148.0 |
20 | TraesCS1B01G298400 | chr1B | 96.512 | 86 | 3 | 0 | 1276 | 1361 | 518909413 | 518909498 | 7.580000e-30 | 143.0 |
21 | TraesCS1B01G298400 | chr1B | 94.118 | 85 | 5 | 0 | 363 | 447 | 440443756 | 440443840 | 5.900000e-26 | 130.0 |
22 | TraesCS1B01G298400 | chr1B | 91.954 | 87 | 7 | 0 | 361 | 447 | 91644893 | 91644979 | 9.880000e-24 | 122.0 |
23 | TraesCS1B01G298400 | chr1B | 91.954 | 87 | 7 | 0 | 361 | 447 | 407828956 | 407829042 | 9.880000e-24 | 122.0 |
24 | TraesCS1B01G298400 | chr1D | 93.303 | 2613 | 92 | 24 | 2196 | 4750 | 386471440 | 386474027 | 0.000000e+00 | 3779.0 |
25 | TraesCS1B01G298400 | chr1D | 95.982 | 1095 | 30 | 8 | 4752 | 5844 | 386474189 | 386475271 | 0.000000e+00 | 1766.0 |
26 | TraesCS1B01G298400 | chr1D | 92.637 | 421 | 21 | 4 | 5844 | 6263 | 386475383 | 386475794 | 1.350000e-166 | 597.0 |
27 | TraesCS1B01G298400 | chr1D | 91.594 | 345 | 17 | 8 | 1565 | 1901 | 386465880 | 386466220 | 3.960000e-127 | 466.0 |
28 | TraesCS1B01G298400 | chr1D | 89.879 | 247 | 24 | 1 | 119 | 365 | 386464431 | 386464676 | 4.220000e-82 | 316.0 |
29 | TraesCS1B01G298400 | chr1D | 86.667 | 210 | 18 | 8 | 438 | 639 | 21814066 | 21814273 | 2.630000e-54 | 224.0 |
30 | TraesCS1B01G298400 | chr1D | 86.667 | 210 | 15 | 11 | 438 | 639 | 262520355 | 262520151 | 3.410000e-53 | 220.0 |
31 | TraesCS1B01G298400 | chr1D | 85.833 | 120 | 11 | 4 | 2478 | 2595 | 386472228 | 386472343 | 9.880000e-24 | 122.0 |
32 | TraesCS1B01G298400 | chr1D | 90.566 | 53 | 5 | 0 | 1898 | 1950 | 386471322 | 386471374 | 3.630000e-08 | 71.3 |
33 | TraesCS1B01G298400 | chr7B | 90.892 | 1603 | 75 | 30 | 3588 | 5153 | 514515238 | 514513670 | 0.000000e+00 | 2085.0 |
34 | TraesCS1B01G298400 | chr7B | 92.380 | 1168 | 59 | 14 | 2445 | 3586 | 514516663 | 514515500 | 0.000000e+00 | 1637.0 |
35 | TraesCS1B01G298400 | chr7B | 90.413 | 1210 | 70 | 11 | 1953 | 3149 | 514517996 | 514516820 | 0.000000e+00 | 1550.0 |
36 | TraesCS1B01G298400 | chr7B | 94.648 | 654 | 31 | 3 | 5194 | 5844 | 514512994 | 514512342 | 0.000000e+00 | 1011.0 |
37 | TraesCS1B01G298400 | chr7B | 87.621 | 622 | 45 | 14 | 5844 | 6460 | 514512230 | 514511636 | 0.000000e+00 | 693.0 |
38 | TraesCS1B01G298400 | chr7B | 92.053 | 302 | 17 | 6 | 1655 | 1949 | 514518459 | 514518158 | 1.130000e-112 | 418.0 |
39 | TraesCS1B01G298400 | chr7B | 88.333 | 120 | 11 | 3 | 2478 | 2595 | 514516111 | 514515993 | 2.730000e-29 | 141.0 |
40 | TraesCS1B01G298400 | chr7B | 85.833 | 120 | 12 | 5 | 2478 | 2595 | 514516974 | 514516858 | 9.880000e-24 | 122.0 |
41 | TraesCS1B01G298400 | chr7B | 88.660 | 97 | 6 | 4 | 1565 | 1656 | 514518691 | 514518595 | 5.950000e-21 | 113.0 |
42 | TraesCS1B01G298400 | chr1A | 91.898 | 1444 | 49 | 12 | 2708 | 4103 | 486399850 | 486401273 | 0.000000e+00 | 1956.0 |
43 | TraesCS1B01G298400 | chr1A | 96.390 | 831 | 20 | 3 | 4913 | 5743 | 486403284 | 486404104 | 0.000000e+00 | 1360.0 |
44 | TraesCS1B01G298400 | chr1A | 94.471 | 832 | 36 | 4 | 4102 | 4926 | 486402223 | 486403051 | 0.000000e+00 | 1273.0 |
45 | TraesCS1B01G298400 | chr1A | 95.122 | 533 | 23 | 3 | 2187 | 2716 | 486389185 | 486389717 | 0.000000e+00 | 837.0 |
46 | TraesCS1B01G298400 | chr1A | 91.905 | 420 | 32 | 2 | 5844 | 6263 | 486411106 | 486411523 | 2.910000e-163 | 586.0 |
47 | TraesCS1B01G298400 | chr1A | 89.344 | 366 | 37 | 2 | 1 | 365 | 486386788 | 486387152 | 6.630000e-125 | 459.0 |
48 | TraesCS1B01G298400 | chr1A | 90.400 | 250 | 8 | 5 | 7003 | 7251 | 531372254 | 531372020 | 1.520000e-81 | 315.0 |
49 | TraesCS1B01G298400 | chr1A | 93.137 | 204 | 14 | 0 | 1949 | 2152 | 486388974 | 486389177 | 4.250000e-77 | 300.0 |
50 | TraesCS1B01G298400 | chr1A | 98.261 | 115 | 2 | 0 | 5730 | 5844 | 486410880 | 486410994 | 1.230000e-47 | 202.0 |
51 | TraesCS1B01G298400 | chr1A | 92.361 | 144 | 7 | 1 | 6317 | 6460 | 486411603 | 486411742 | 1.230000e-47 | 202.0 |
52 | TraesCS1B01G298400 | chr1A | 89.116 | 147 | 10 | 5 | 827 | 969 | 486388661 | 486388805 | 2.080000e-40 | 178.0 |
53 | TraesCS1B01G298400 | chr1A | 87.500 | 120 | 9 | 4 | 2478 | 2595 | 486400136 | 486400251 | 4.560000e-27 | 134.0 |
54 | TraesCS1B01G298400 | chr1A | 87.500 | 64 | 5 | 2 | 6272 | 6335 | 372550073 | 372550013 | 3.630000e-08 | 71.3 |
55 | TraesCS1B01G298400 | chr7A | 92.857 | 574 | 24 | 6 | 6679 | 7251 | 296574316 | 296573759 | 0.000000e+00 | 817.0 |
56 | TraesCS1B01G298400 | chr7A | 92.135 | 356 | 12 | 3 | 6897 | 7251 | 299252411 | 299252751 | 8.450000e-134 | 488.0 |
57 | TraesCS1B01G298400 | chr7A | 88.596 | 228 | 12 | 1 | 6465 | 6678 | 296574604 | 296574377 | 1.550000e-66 | 265.0 |
58 | TraesCS1B01G298400 | chr2A | 90.777 | 206 | 12 | 6 | 440 | 639 | 244909758 | 244909554 | 1.200000e-67 | 268.0 |
59 | TraesCS1B01G298400 | chr2A | 89.202 | 213 | 14 | 6 | 435 | 639 | 593720880 | 593720669 | 2.600000e-64 | 257.0 |
60 | TraesCS1B01G298400 | chr2A | 89.372 | 207 | 16 | 5 | 438 | 639 | 244828387 | 244828592 | 9.340000e-64 | 255.0 |
61 | TraesCS1B01G298400 | chr2A | 88.942 | 208 | 16 | 5 | 438 | 639 | 244908341 | 244908547 | 4.340000e-62 | 250.0 |
62 | TraesCS1B01G298400 | chr4D | 85.577 | 208 | 23 | 6 | 438 | 639 | 416131218 | 416131012 | 2.050000e-50 | 211.0 |
63 | TraesCS1B01G298400 | chr4D | 85.577 | 208 | 23 | 6 | 438 | 639 | 421204813 | 421204607 | 2.050000e-50 | 211.0 |
64 | TraesCS1B01G298400 | chr4D | 91.954 | 87 | 6 | 1 | 361 | 447 | 319063883 | 319063968 | 3.550000e-23 | 121.0 |
65 | TraesCS1B01G298400 | chr6B | 85.096 | 208 | 24 | 6 | 438 | 639 | 201209573 | 201209779 | 9.540000e-49 | 206.0 |
66 | TraesCS1B01G298400 | chr2D | 87.037 | 162 | 12 | 3 | 2593 | 2749 | 554694339 | 554694496 | 2.690000e-39 | 174.0 |
67 | TraesCS1B01G298400 | chr7D | 92.941 | 85 | 6 | 0 | 363 | 447 | 178507094 | 178507178 | 2.750000e-24 | 124.0 |
68 | TraesCS1B01G298400 | chr4B | 90.426 | 94 | 9 | 0 | 354 | 447 | 46010119 | 46010212 | 2.750000e-24 | 124.0 |
69 | TraesCS1B01G298400 | chr4B | 95.833 | 48 | 1 | 1 | 6269 | 6315 | 49514846 | 49514893 | 7.800000e-10 | 76.8 |
70 | TraesCS1B01G298400 | chr3D | 92.857 | 84 | 6 | 0 | 364 | 447 | 476397729 | 476397646 | 9.880000e-24 | 122.0 |
71 | TraesCS1B01G298400 | chr3D | 92.857 | 84 | 6 | 0 | 364 | 447 | 476404747 | 476404664 | 9.880000e-24 | 122.0 |
72 | TraesCS1B01G298400 | chr3D | 97.778 | 45 | 1 | 0 | 6272 | 6316 | 530356817 | 530356861 | 2.170000e-10 | 78.7 |
73 | TraesCS1B01G298400 | chr3D | 90.741 | 54 | 3 | 2 | 6272 | 6324 | 208707531 | 208707479 | 3.630000e-08 | 71.3 |
74 | TraesCS1B01G298400 | chr6D | 92.771 | 83 | 6 | 0 | 365 | 447 | 47326771 | 47326689 | 3.550000e-23 | 121.0 |
75 | TraesCS1B01G298400 | chr6D | 100.000 | 42 | 0 | 0 | 6272 | 6313 | 249445838 | 249445797 | 2.170000e-10 | 78.7 |
76 | TraesCS1B01G298400 | chr2B | 89.062 | 64 | 7 | 0 | 6274 | 6337 | 21651938 | 21651875 | 6.030000e-11 | 80.5 |
77 | TraesCS1B01G298400 | chr5D | 92.453 | 53 | 2 | 2 | 6272 | 6323 | 339105104 | 339105053 | 2.810000e-09 | 75.0 |
78 | TraesCS1B01G298400 | chr3B | 94.000 | 50 | 1 | 2 | 6265 | 6312 | 611171535 | 611171486 | 2.810000e-09 | 75.0 |
79 | TraesCS1B01G298400 | chr5A | 87.097 | 62 | 3 | 5 | 6272 | 6330 | 32129195 | 32129254 | 1.690000e-06 | 65.8 |
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 | TraesCS1B01G298400 | chr1B | 519618560 | 519625810 | 7250 | False | 13391.000000 | 13391 | 100.000000 | 1 | 7251 | 1 | chr1B.!!$F5 | 7250 |
1 | TraesCS1B01G298400 | chr1B | 518908669 | 518914729 | 6060 | False | 901.100000 | 3986 | 94.430500 | 893 | 6259 | 10 | chr1B.!!$F6 | 5366 |
2 | TraesCS1B01G298400 | chr1B | 520099847 | 520100614 | 767 | False | 272.333333 | 375 | 94.081667 | 5726 | 6263 | 3 | chr1B.!!$F8 | 537 |
3 | TraesCS1B01G298400 | chr1D | 386471322 | 386475794 | 4472 | False | 1267.060000 | 3779 | 91.664200 | 1898 | 6263 | 5 | chr1D.!!$F3 | 4365 |
4 | TraesCS1B01G298400 | chr1D | 386464431 | 386466220 | 1789 | False | 391.000000 | 466 | 90.736500 | 119 | 1901 | 2 | chr1D.!!$F2 | 1782 |
5 | TraesCS1B01G298400 | chr7B | 514511636 | 514518691 | 7055 | True | 863.333333 | 2085 | 90.092556 | 1565 | 6460 | 9 | chr7B.!!$R1 | 4895 |
6 | TraesCS1B01G298400 | chr1A | 486399850 | 486404104 | 4254 | False | 1180.750000 | 1956 | 92.564750 | 2478 | 5743 | 4 | chr1A.!!$F2 | 3265 |
7 | TraesCS1B01G298400 | chr1A | 486386788 | 486389717 | 2929 | False | 443.500000 | 837 | 91.679750 | 1 | 2716 | 4 | chr1A.!!$F1 | 2715 |
8 | TraesCS1B01G298400 | chr1A | 486410880 | 486411742 | 862 | False | 330.000000 | 586 | 94.175667 | 5730 | 6460 | 3 | chr1A.!!$F3 | 730 |
9 | TraesCS1B01G298400 | chr7A | 296573759 | 296574604 | 845 | True | 541.000000 | 817 | 90.726500 | 6465 | 7251 | 2 | chr7A.!!$R1 | 786 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
398 | 400 | 0.035739 | TGTGCCCTTAACTCGAACCC | 59.964 | 55.000 | 0.00 | 0.0 | 0.00 | 4.11 | F |
1099 | 2634 | 0.032403 | ATGACCGTCGTTGTTTCCGA | 59.968 | 50.000 | 0.00 | 0.0 | 0.00 | 4.55 | F |
1303 | 2863 | 0.104777 | TGATGCCTGCCTCCTCCTAT | 60.105 | 55.000 | 0.00 | 0.0 | 0.00 | 2.57 | F |
1304 | 2864 | 0.324285 | GATGCCTGCCTCCTCCTATG | 59.676 | 60.000 | 0.00 | 0.0 | 0.00 | 2.23 | F |
2060 | 4107 | 0.807667 | GACATGGTAGAGCTGCGGTG | 60.808 | 60.000 | 0.00 | 0.0 | 0.00 | 4.94 | F |
2109 | 4156 | 2.365068 | CGTGTGTTGACTCGCTCCG | 61.365 | 63.158 | 0.00 | 0.0 | 32.82 | 4.63 | F |
2529 | 4581 | 2.765699 | GAGAGGGAAAGAGAGACAGCAT | 59.234 | 50.000 | 0.00 | 0.0 | 0.00 | 3.79 | F |
3788 | 6997 | 0.111253 | AGCTTTTAGCCTGCCACACT | 59.889 | 50.000 | 0.00 | 0.0 | 43.77 | 3.55 | F |
4590 | 8968 | 0.176910 | TGGACGGCGATTATGAAGCA | 59.823 | 50.000 | 16.62 | 0.0 | 0.00 | 3.91 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1284 | 2844 | 0.104777 | ATAGGAGGAGGCAGGCATCA | 60.105 | 55.000 | 8.27 | 0.00 | 0.00 | 3.07 | R |
1987 | 4034 | 0.956902 | ATCGCTTGCTGCACATGACA | 60.957 | 50.000 | 0.00 | 0.00 | 43.06 | 3.58 | R |
2783 | 4844 | 2.002586 | TGAGAAATCTACAGCTTGCGC | 58.997 | 47.619 | 0.00 | 0.00 | 0.00 | 6.09 | R |
2871 | 4933 | 3.379372 | GCGCCGTATTCTCAGGGTATATA | 59.621 | 47.826 | 0.00 | 0.00 | 0.00 | 0.86 | R |
3413 | 6362 | 1.444933 | ATCACAAGACCAGTGGGGAA | 58.555 | 50.000 | 15.21 | 0.00 | 41.15 | 3.97 | R |
3415 | 6364 | 3.433306 | TTTATCACAAGACCAGTGGGG | 57.567 | 47.619 | 15.21 | 2.42 | 44.81 | 4.96 | R |
4247 | 8436 | 0.959372 | CTGGAGACCCGTCGTACAGT | 60.959 | 60.000 | 0.00 | 0.00 | 34.29 | 3.55 | R |
5290 | 10715 | 0.320334 | TGGCGCTCGAAACTGAATGA | 60.320 | 50.000 | 7.64 | 0.00 | 0.00 | 2.57 | R |
6259 | 12096 | 0.108329 | AGAAATGGTGCCCTACGTCG | 60.108 | 55.000 | 0.00 | 0.00 | 0.00 | 5.12 | 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.