Multiple sequence alignment - TraesCS7A01G008600
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 | TraesCS7A01G008600 | chr7A | 100.000 | 7241 | 0 | 0 | 1 | 7241 | 3851842 | 3844602 | 0.000000e+00 | 13372.0 |
1 | TraesCS7A01G008600 | chr7A | 94.265 | 3278 | 157 | 18 | 2457 | 5718 | 3538841 | 3535579 | 0.000000e+00 | 4983.0 |
2 | TraesCS7A01G008600 | chr7A | 82.788 | 703 | 87 | 19 | 2862 | 3540 | 3800868 | 3800176 | 1.340000e-166 | 597.0 |
3 | TraesCS7A01G008600 | chr7A | 87.222 | 360 | 37 | 2 | 2021 | 2380 | 3539363 | 3539013 | 1.130000e-107 | 401.0 |
4 | TraesCS7A01G008600 | chr7A | 91.391 | 151 | 12 | 1 | 2152 | 2302 | 2658064 | 2657915 | 9.520000e-49 | 206.0 |
5 | TraesCS7A01G008600 | chr7A | 95.876 | 97 | 4 | 0 | 2206 | 2302 | 2950618 | 2950714 | 2.700000e-34 | 158.0 |
6 | TraesCS7A01G008600 | chr7D | 95.571 | 4109 | 133 | 19 | 2428 | 6520 | 4015980 | 4011905 | 0.000000e+00 | 6534.0 |
7 | TraesCS7A01G008600 | chr7D | 84.633 | 1705 | 152 | 69 | 729 | 2380 | 4017782 | 4016135 | 0.000000e+00 | 1596.0 |
8 | TraesCS7A01G008600 | chr7D | 83.264 | 1201 | 131 | 40 | 3607 | 4774 | 3565440 | 3564277 | 0.000000e+00 | 1040.0 |
9 | TraesCS7A01G008600 | chr7D | 91.017 | 590 | 13 | 15 | 6549 | 7118 | 4011907 | 4011338 | 0.000000e+00 | 760.0 |
10 | TraesCS7A01G008600 | chr7D | 80.336 | 951 | 116 | 38 | 5902 | 6800 | 3563561 | 3562630 | 0.000000e+00 | 654.0 |
11 | TraesCS7A01G008600 | chr7D | 82.000 | 700 | 90 | 22 | 2862 | 3540 | 2664467 | 2663783 | 4.900000e-156 | 562.0 |
12 | TraesCS7A01G008600 | chr7D | 87.574 | 338 | 25 | 7 | 2457 | 2793 | 3620928 | 3620607 | 6.860000e-100 | 375.0 |
13 | TraesCS7A01G008600 | chr7D | 86.325 | 351 | 34 | 2 | 2618 | 2967 | 2507672 | 2507335 | 3.190000e-98 | 370.0 |
14 | TraesCS7A01G008600 | chr7D | 91.453 | 234 | 19 | 1 | 3307 | 3540 | 3418560 | 3418328 | 3.260000e-83 | 320.0 |
15 | TraesCS7A01G008600 | chr7D | 79.583 | 480 | 68 | 14 | 2862 | 3333 | 2675994 | 2675537 | 4.220000e-82 | 316.0 |
16 | TraesCS7A01G008600 | chr7D | 85.616 | 292 | 38 | 4 | 3271 | 3559 | 3609127 | 3608837 | 3.280000e-78 | 303.0 |
17 | TraesCS7A01G008600 | chr7D | 82.121 | 330 | 47 | 8 | 2862 | 3180 | 3420190 | 3419862 | 9.260000e-69 | 272.0 |
18 | TraesCS7A01G008600 | chr7D | 90.960 | 177 | 16 | 0 | 2618 | 2794 | 2676169 | 2675993 | 9.390000e-59 | 239.0 |
19 | TraesCS7A01G008600 | chr7D | 89.730 | 185 | 19 | 0 | 2618 | 2802 | 2664642 | 2664458 | 3.380000e-58 | 237.0 |
20 | TraesCS7A01G008600 | chr7D | 84.810 | 158 | 19 | 2 | 3142 | 3294 | 4005688 | 4005531 | 3.500000e-33 | 154.0 |
21 | TraesCS7A01G008600 | chr7D | 94.000 | 100 | 5 | 1 | 4794 | 4893 | 599718532 | 599718434 | 4.530000e-32 | 150.0 |
22 | TraesCS7A01G008600 | chr7D | 96.610 | 59 | 1 | 1 | 7183 | 7241 | 4011334 | 4011277 | 5.980000e-16 | 97.1 |
23 | TraesCS7A01G008600 | chr7D | 90.141 | 71 | 7 | 0 | 3859 | 3929 | 3608474 | 3608404 | 7.730000e-15 | 93.5 |
24 | TraesCS7A01G008600 | chr4A | 95.464 | 2293 | 74 | 8 | 2517 | 4803 | 741412393 | 741410125 | 0.000000e+00 | 3631.0 |
25 | TraesCS7A01G008600 | chr4A | 96.117 | 1339 | 35 | 2 | 2875 | 4212 | 741367998 | 741366676 | 0.000000e+00 | 2169.0 |
26 | TraesCS7A01G008600 | chr4A | 96.386 | 1273 | 24 | 6 | 3533 | 4803 | 742012791 | 742014043 | 0.000000e+00 | 2076.0 |
27 | TraesCS7A01G008600 | chr4A | 84.123 | 1795 | 144 | 69 | 642 | 2372 | 739595349 | 739597066 | 0.000000e+00 | 1605.0 |
28 | TraesCS7A01G008600 | chr4A | 82.783 | 1545 | 163 | 57 | 3271 | 4774 | 739598030 | 739599512 | 0.000000e+00 | 1284.0 |
29 | TraesCS7A01G008600 | chr4A | 91.315 | 829 | 56 | 6 | 4885 | 5699 | 742014042 | 742014868 | 0.000000e+00 | 1118.0 |
30 | TraesCS7A01G008600 | chr4A | 96.128 | 594 | 12 | 4 | 4214 | 4803 | 741366609 | 741366023 | 0.000000e+00 | 959.0 |
31 | TraesCS7A01G008600 | chr4A | 91.987 | 599 | 37 | 4 | 2378 | 2976 | 739597118 | 739597705 | 0.000000e+00 | 830.0 |
32 | TraesCS7A01G008600 | chr4A | 86.776 | 673 | 73 | 9 | 5091 | 5752 | 739599516 | 739600183 | 0.000000e+00 | 736.0 |
33 | TraesCS7A01G008600 | chr4A | 85.503 | 676 | 75 | 15 | 5091 | 5752 | 740154256 | 740153590 | 0.000000e+00 | 684.0 |
34 | TraesCS7A01G008600 | chr4A | 80.988 | 931 | 113 | 42 | 5610 | 6491 | 741181268 | 741182183 | 0.000000e+00 | 680.0 |
35 | TraesCS7A01G008600 | chr4A | 84.167 | 720 | 82 | 24 | 5747 | 6443 | 741365387 | 741364677 | 0.000000e+00 | 669.0 |
36 | TraesCS7A01G008600 | chr4A | 84.167 | 720 | 82 | 24 | 5747 | 6443 | 741409489 | 741408779 | 0.000000e+00 | 669.0 |
37 | TraesCS7A01G008600 | chr4A | 93.519 | 432 | 25 | 2 | 4885 | 5315 | 741366024 | 741365595 | 2.200000e-179 | 640.0 |
38 | TraesCS7A01G008600 | chr4A | 93.519 | 432 | 25 | 2 | 4885 | 5315 | 741410126 | 741409697 | 2.200000e-179 | 640.0 |
39 | TraesCS7A01G008600 | chr4A | 83.449 | 719 | 86 | 26 | 5747 | 6443 | 742014998 | 742015705 | 7.920000e-179 | 638.0 |
40 | TraesCS7A01G008600 | chr4A | 83.478 | 690 | 90 | 17 | 2862 | 3540 | 740133369 | 740132693 | 7.980000e-174 | 621.0 |
41 | TraesCS7A01G008600 | chr4A | 82.994 | 688 | 85 | 16 | 2862 | 3540 | 733809447 | 733810111 | 1.740000e-165 | 593.0 |
42 | TraesCS7A01G008600 | chr4A | 81.297 | 802 | 79 | 31 | 5747 | 6520 | 739600236 | 739600994 | 1.050000e-162 | 584.0 |
43 | TraesCS7A01G008600 | chr4A | 82.066 | 697 | 92 | 25 | 2862 | 3540 | 739610437 | 739611118 | 1.360000e-156 | 564.0 |
44 | TraesCS7A01G008600 | chr4A | 80.228 | 703 | 103 | 21 | 2862 | 3540 | 739758037 | 739757347 | 5.050000e-136 | 496.0 |
45 | TraesCS7A01G008600 | chr4A | 84.881 | 463 | 64 | 5 | 3083 | 3540 | 742024681 | 742025142 | 5.120000e-126 | 462.0 |
46 | TraesCS7A01G008600 | chr4A | 91.525 | 236 | 19 | 1 | 2686 | 2920 | 741178254 | 741178489 | 2.520000e-84 | 324.0 |
47 | TraesCS7A01G008600 | chr4A | 82.436 | 353 | 41 | 14 | 5784 | 6118 | 740153494 | 740153145 | 9.190000e-74 | 289.0 |
48 | TraesCS7A01G008600 | chr4A | 97.484 | 159 | 4 | 0 | 5594 | 5752 | 741365598 | 741365440 | 9.260000e-69 | 272.0 |
49 | TraesCS7A01G008600 | chr4A | 97.484 | 159 | 4 | 0 | 5594 | 5752 | 741409700 | 741409542 | 9.260000e-69 | 272.0 |
50 | TraesCS7A01G008600 | chr4A | 79.582 | 431 | 46 | 16 | 6538 | 6946 | 739990227 | 739989817 | 3.330000e-68 | 270.0 |
51 | TraesCS7A01G008600 | chr4A | 93.785 | 177 | 11 | 0 | 2618 | 2794 | 739610262 | 739610438 | 4.310000e-67 | 267.0 |
52 | TraesCS7A01G008600 | chr4A | 92.655 | 177 | 13 | 0 | 2618 | 2794 | 733809272 | 733809448 | 9.320000e-64 | 255.0 |
53 | TraesCS7A01G008600 | chr4A | 97.241 | 145 | 4 | 0 | 5608 | 5752 | 739997050 | 739996906 | 5.610000e-61 | 246.0 |
54 | TraesCS7A01G008600 | chr4A | 85.654 | 237 | 17 | 8 | 6523 | 6745 | 739603267 | 739603500 | 4.370000e-57 | 233.0 |
55 | TraesCS7A01G008600 | chr4A | 87.778 | 180 | 18 | 3 | 2866 | 3042 | 740498621 | 740498799 | 2.650000e-49 | 207.0 |
56 | TraesCS7A01G008600 | chr4A | 82.329 | 249 | 33 | 6 | 1881 | 2118 | 741048118 | 741048366 | 9.520000e-49 | 206.0 |
57 | TraesCS7A01G008600 | chr4A | 83.410 | 217 | 22 | 8 | 566 | 781 | 688787295 | 688787092 | 9.590000e-44 | 189.0 |
58 | TraesCS7A01G008600 | chr4A | 77.344 | 256 | 32 | 16 | 6523 | 6756 | 739601091 | 739601342 | 2.120000e-25 | 128.0 |
59 | TraesCS7A01G008600 | chr4A | 81.818 | 99 | 8 | 6 | 6832 | 6926 | 733826675 | 733826583 | 2.800000e-09 | 75.0 |
60 | TraesCS7A01G008600 | chrUn | 100.000 | 395 | 0 | 0 | 4830 | 5224 | 479299730 | 479300124 | 0.000000e+00 | 730.0 |
61 | TraesCS7A01G008600 | chrUn | 89.091 | 110 | 9 | 3 | 7000 | 7109 | 287061832 | 287061726 | 4.560000e-27 | 134.0 |
62 | TraesCS7A01G008600 | chr4B | 85.000 | 220 | 20 | 6 | 342 | 557 | 584073752 | 584073962 | 2.050000e-50 | 211.0 |
63 | TraesCS7A01G008600 | chr6A | 95.000 | 100 | 3 | 2 | 4799 | 4898 | 172113269 | 172113172 | 9.730000e-34 | 156.0 |
64 | TraesCS7A01G008600 | chr1A | 94.792 | 96 | 5 | 0 | 4799 | 4894 | 551438020 | 551437925 | 4.530000e-32 | 150.0 |
65 | TraesCS7A01G008600 | chr3B | 90.179 | 112 | 9 | 2 | 4783 | 4893 | 15111127 | 15111017 | 2.110000e-30 | 145.0 |
66 | TraesCS7A01G008600 | chr3B | 91.579 | 95 | 7 | 1 | 6998 | 7092 | 621537376 | 621537469 | 5.900000e-26 | 130.0 |
67 | TraesCS7A01G008600 | chr3A | 93.000 | 100 | 5 | 2 | 4795 | 4892 | 492755870 | 492755969 | 2.110000e-30 | 145.0 |
68 | TraesCS7A01G008600 | chr3A | 97.531 | 81 | 2 | 0 | 7004 | 7084 | 99426270 | 99426190 | 9.800000e-29 | 139.0 |
69 | TraesCS7A01G008600 | chr1D | 97.619 | 84 | 2 | 0 | 4890 | 4973 | 225405130 | 225405047 | 2.110000e-30 | 145.0 |
70 | TraesCS7A01G008600 | chr2A | 93.684 | 95 | 4 | 2 | 4878 | 4971 | 515955457 | 515955364 | 2.720000e-29 | 141.0 |
71 | TraesCS7A01G008600 | chr2A | 90.090 | 111 | 7 | 4 | 4783 | 4890 | 724029778 | 724029887 | 2.720000e-29 | 141.0 |
72 | TraesCS7A01G008600 | chr2A | 89.109 | 101 | 9 | 2 | 4791 | 4890 | 695156866 | 695156767 | 2.740000e-24 | 124.0 |
73 | TraesCS7A01G008600 | chr5D | 94.505 | 91 | 3 | 2 | 4881 | 4971 | 535711526 | 535711614 | 9.800000e-29 | 139.0 |
74 | TraesCS7A01G008600 | chr3D | 93.478 | 92 | 3 | 3 | 6998 | 7086 | 149291980 | 149292071 | 4.560000e-27 | 134.0 |
75 | TraesCS7A01G008600 | chr3D | 89.091 | 110 | 9 | 3 | 7000 | 7109 | 570116478 | 570116372 | 4.560000e-27 | 134.0 |
76 | TraesCS7A01G008600 | chr1B | 93.407 | 91 | 3 | 2 | 7005 | 7095 | 593927161 | 593927074 | 1.640000e-26 | 132.0 |
77 | TraesCS7A01G008600 | chr5B | 94.186 | 86 | 4 | 1 | 7000 | 7085 | 13722193 | 13722277 | 5.900000e-26 | 130.0 |
78 | TraesCS7A01G008600 | chr2D | 87.736 | 106 | 11 | 2 | 7005 | 7109 | 379699523 | 379699419 | 9.860000e-24 | 122.0 |
79 | TraesCS7A01G008600 | chr6B | 80.909 | 110 | 11 | 5 | 1186 | 1295 | 641468663 | 641468762 | 2.170000e-10 | 78.7 |
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 | TraesCS7A01G008600 | chr7A | 3844602 | 3851842 | 7240 | True | 13372.000000 | 13372 | 100.000000 | 1 | 7241 | 1 | chr7A.!!$R3 | 7240 |
1 | TraesCS7A01G008600 | chr7A | 3535579 | 3539363 | 3784 | True | 2692.000000 | 4983 | 90.743500 | 2021 | 5718 | 2 | chr7A.!!$R4 | 3697 |
2 | TraesCS7A01G008600 | chr7A | 3800176 | 3800868 | 692 | True | 597.000000 | 597 | 82.788000 | 2862 | 3540 | 1 | chr7A.!!$R2 | 678 |
3 | TraesCS7A01G008600 | chr7D | 4011277 | 4017782 | 6505 | True | 2246.775000 | 6534 | 91.957750 | 729 | 7241 | 4 | chr7D.!!$R10 | 6512 |
4 | TraesCS7A01G008600 | chr7D | 3562630 | 3565440 | 2810 | True | 847.000000 | 1040 | 81.800000 | 3607 | 6800 | 2 | chr7D.!!$R8 | 3193 |
5 | TraesCS7A01G008600 | chr7D | 2663783 | 2664642 | 859 | True | 399.500000 | 562 | 85.865000 | 2618 | 3540 | 2 | chr7D.!!$R5 | 922 |
6 | TraesCS7A01G008600 | chr7D | 3418328 | 3420190 | 1862 | True | 296.000000 | 320 | 86.787000 | 2862 | 3540 | 2 | chr7D.!!$R7 | 678 |
7 | TraesCS7A01G008600 | chr7D | 2675537 | 2676169 | 632 | True | 277.500000 | 316 | 85.271500 | 2618 | 3333 | 2 | chr7D.!!$R6 | 715 |
8 | TraesCS7A01G008600 | chr4A | 741408779 | 741412393 | 3614 | True | 1303.000000 | 3631 | 92.658500 | 2517 | 6443 | 4 | chr4A.!!$R9 | 3926 |
9 | TraesCS7A01G008600 | chr4A | 742012791 | 742015705 | 2914 | False | 1277.333333 | 2076 | 90.383333 | 3533 | 6443 | 3 | chr4A.!!$F8 | 2910 |
10 | TraesCS7A01G008600 | chr4A | 741364677 | 741367998 | 3321 | True | 941.800000 | 2169 | 93.483000 | 2875 | 6443 | 5 | chr4A.!!$R8 | 3568 |
11 | TraesCS7A01G008600 | chr4A | 739595349 | 739603500 | 8151 | False | 771.428571 | 1605 | 84.280571 | 642 | 6756 | 7 | chr4A.!!$F5 | 6114 |
12 | TraesCS7A01G008600 | chr4A | 740132693 | 740133369 | 676 | True | 621.000000 | 621 | 83.478000 | 2862 | 3540 | 1 | chr4A.!!$R6 | 678 |
13 | TraesCS7A01G008600 | chr4A | 741178254 | 741182183 | 3929 | False | 502.000000 | 680 | 86.256500 | 2686 | 6491 | 2 | chr4A.!!$F7 | 3805 |
14 | TraesCS7A01G008600 | chr4A | 739757347 | 739758037 | 690 | True | 496.000000 | 496 | 80.228000 | 2862 | 3540 | 1 | chr4A.!!$R3 | 678 |
15 | TraesCS7A01G008600 | chr4A | 740153145 | 740154256 | 1111 | True | 486.500000 | 684 | 83.969500 | 5091 | 6118 | 2 | chr4A.!!$R7 | 1027 |
16 | TraesCS7A01G008600 | chr4A | 733809272 | 733810111 | 839 | False | 424.000000 | 593 | 87.824500 | 2618 | 3540 | 2 | chr4A.!!$F4 | 922 |
17 | TraesCS7A01G008600 | chr4A | 739610262 | 739611118 | 856 | False | 415.500000 | 564 | 87.925500 | 2618 | 3540 | 2 | chr4A.!!$F6 | 922 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
844 | 861 | 0.036858 | GTGACCTCTCTGTGGCCTTC | 60.037 | 60.000 | 3.32 | 0.0 | 0.00 | 3.46 | F |
1457 | 1520 | 0.266152 | CCCCTCCTCTACCACCAGAT | 59.734 | 60.000 | 0.00 | 0.0 | 0.00 | 2.90 | F |
1865 | 1952 | 0.319405 | AAATTGGGACTGCTGCTTGC | 59.681 | 50.000 | 0.00 | 0.0 | 43.25 | 4.01 | F |
1866 | 1953 | 0.541296 | AATTGGGACTGCTGCTTGCT | 60.541 | 50.000 | 0.00 | 0.0 | 43.37 | 3.91 | F |
2454 | 2706 | 0.613260 | TTCCTGCACGGCTAGAACAT | 59.387 | 50.000 | 0.00 | 0.0 | 0.00 | 2.71 | F |
2807 | 3063 | 2.711009 | TGAAGGATTCCTGTCACCTGTT | 59.289 | 45.455 | 5.84 | 0.0 | 46.93 | 3.16 | F |
4778 | 8492 | 1.253100 | GGTTCGATTTGCAAAGGGGA | 58.747 | 50.000 | 18.19 | 11.2 | 0.00 | 4.81 | F |
5442 | 9249 | 0.461516 | CATGCAGGTGTCATCTCGCT | 60.462 | 55.000 | 0.00 | 0.0 | 0.00 | 4.93 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2795 | 3051 | 0.035458 | GAGGACCAACAGGTGACAGG | 59.965 | 60.000 | 0.00 | 0.0 | 35.25 | 4.00 | R |
3111 | 3449 | 1.222567 | ACTTCTGGGGTTCTTGTGGT | 58.777 | 50.000 | 0.00 | 0.0 | 0.00 | 4.16 | R |
3702 | 7303 | 0.033366 | GGGGCAAATGTTGTGTCCAC | 59.967 | 55.000 | 0.00 | 0.0 | 0.00 | 4.02 | R |
4201 | 7821 | 8.858003 | TCGAAATAGAAAGTACTGATGCTAAG | 57.142 | 34.615 | 0.00 | 0.0 | 0.00 | 2.18 | R |
4388 | 8095 | 4.997395 | TCAACAATCTAAAGTGCAGGAGTC | 59.003 | 41.667 | 0.00 | 0.0 | 0.00 | 3.36 | R |
4803 | 8591 | 8.081025 | CACTCTTATATTAGTTTACGGAGGGAC | 58.919 | 40.741 | 0.00 | 0.0 | 0.00 | 4.46 | R |
5782 | 9737 | 0.181350 | ATCTTAGGCAAGCCCTTCCG | 59.819 | 55.000 | 7.62 | 0.0 | 43.06 | 4.30 | R |
6281 | 10283 | 0.975556 | TAGCATCGCCAGACCAGGAA | 60.976 | 55.000 | 0.00 | 0.0 | 0.00 | 3.36 | 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.