Multiple sequence alignment - TraesCS3D01G231600
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 | TraesCS3D01G231600 | chr3D | 100.000 | 4339 | 0 | 0 | 1 | 4339 | 317197816 | 317202154 | 0.000000e+00 | 8013.0 |
1 | TraesCS3D01G231600 | chr3D | 100.000 | 3831 | 0 | 0 | 4727 | 8557 | 317202542 | 317206372 | 0.000000e+00 | 7075.0 |
2 | TraesCS3D01G231600 | chr3D | 93.564 | 202 | 13 | 0 | 5580 | 5781 | 586958967 | 586959168 | 1.400000e-77 | 302.0 |
3 | TraesCS3D01G231600 | chr3D | 96.648 | 179 | 4 | 2 | 7887 | 8065 | 563837750 | 563837574 | 6.490000e-76 | 296.0 |
4 | TraesCS3D01G231600 | chr3A | 94.032 | 3770 | 139 | 28 | 603 | 4335 | 410114985 | 410111265 | 0.000000e+00 | 5637.0 |
5 | TraesCS3D01G231600 | chr3A | 92.951 | 2128 | 78 | 27 | 5782 | 7870 | 410110139 | 410108045 | 0.000000e+00 | 3033.0 |
6 | TraesCS3D01G231600 | chr3A | 97.552 | 858 | 20 | 1 | 4727 | 5583 | 410111237 | 410110380 | 0.000000e+00 | 1467.0 |
7 | TraesCS3D01G231600 | chr3A | 91.991 | 462 | 19 | 6 | 8055 | 8505 | 410108032 | 410107578 | 4.360000e-177 | 632.0 |
8 | TraesCS3D01G231600 | chr3A | 81.879 | 447 | 72 | 8 | 66 | 508 | 526856582 | 526857023 | 1.360000e-97 | 368.0 |
9 | TraesCS3D01G231600 | chr3A | 82.567 | 413 | 65 | 6 | 53 | 462 | 444285391 | 444285799 | 2.940000e-94 | 357.0 |
10 | TraesCS3D01G231600 | chr3B | 94.238 | 2204 | 85 | 10 | 620 | 2807 | 401810359 | 401808182 | 0.000000e+00 | 3328.0 |
11 | TraesCS3D01G231600 | chr3B | 93.551 | 1349 | 55 | 12 | 3002 | 4337 | 401808178 | 401806849 | 0.000000e+00 | 1980.0 |
12 | TraesCS3D01G231600 | chr3B | 95.223 | 1256 | 38 | 10 | 5782 | 7020 | 401805739 | 401804489 | 0.000000e+00 | 1967.0 |
13 | TraesCS3D01G231600 | chr3B | 97.322 | 859 | 21 | 1 | 4727 | 5583 | 401806838 | 401805980 | 0.000000e+00 | 1458.0 |
14 | TraesCS3D01G231600 | chr3B | 96.038 | 530 | 16 | 2 | 7074 | 7603 | 401804490 | 401803966 | 0.000000e+00 | 857.0 |
15 | TraesCS3D01G231600 | chr3B | 79.428 | 909 | 156 | 26 | 1325 | 2223 | 406649934 | 406650821 | 1.580000e-171 | 614.0 |
16 | TraesCS3D01G231600 | chr3B | 90.909 | 462 | 19 | 6 | 8055 | 8505 | 401803747 | 401803298 | 4.420000e-167 | 599.0 |
17 | TraesCS3D01G231600 | chr3B | 85.398 | 226 | 11 | 8 | 7648 | 7870 | 401803966 | 401803760 | 1.870000e-51 | 215.0 |
18 | TraesCS3D01G231600 | chr4D | 79.621 | 3008 | 369 | 142 | 714 | 3597 | 96912259 | 96909372 | 0.000000e+00 | 1934.0 |
19 | TraesCS3D01G231600 | chr4D | 90.371 | 862 | 76 | 6 | 4737 | 5592 | 96908425 | 96907565 | 0.000000e+00 | 1125.0 |
20 | TraesCS3D01G231600 | chr4D | 79.315 | 701 | 99 | 30 | 3641 | 4313 | 96909379 | 96908697 | 4.710000e-122 | 449.0 |
21 | TraesCS3D01G231600 | chr4D | 96.517 | 201 | 7 | 0 | 5579 | 5779 | 258893655 | 258893455 | 4.950000e-87 | 333.0 |
22 | TraesCS3D01G231600 | chr4D | 97.191 | 178 | 3 | 2 | 7879 | 8055 | 113186974 | 113187150 | 5.020000e-77 | 300.0 |
23 | TraesCS3D01G231600 | chr4D | 95.238 | 189 | 5 | 4 | 7878 | 8065 | 420144051 | 420143866 | 6.490000e-76 | 296.0 |
24 | TraesCS3D01G231600 | chr4D | 94.709 | 189 | 7 | 3 | 7865 | 8052 | 509818854 | 509819040 | 3.020000e-74 | 291.0 |
25 | TraesCS3D01G231600 | chr4A | 81.337 | 2438 | 298 | 90 | 1247 | 3591 | 479412044 | 479414417 | 0.000000e+00 | 1836.0 |
26 | TraesCS3D01G231600 | chr4A | 90.743 | 821 | 69 | 6 | 4769 | 5583 | 479416367 | 479417186 | 0.000000e+00 | 1088.0 |
27 | TraesCS3D01G231600 | chr4A | 86.986 | 876 | 87 | 12 | 4730 | 5592 | 497815650 | 497814789 | 0.000000e+00 | 961.0 |
28 | TraesCS3D01G231600 | chr4A | 83.455 | 550 | 79 | 6 | 55 | 603 | 200056288 | 200055750 | 1.280000e-137 | 501.0 |
29 | TraesCS3D01G231600 | chr4A | 79.571 | 700 | 98 | 27 | 3641 | 4310 | 479414416 | 479415100 | 7.830000e-125 | 459.0 |
30 | TraesCS3D01G231600 | chr4A | 92.883 | 281 | 20 | 0 | 53 | 333 | 516586135 | 516585855 | 8.000000e-110 | 409.0 |
31 | TraesCS3D01G231600 | chr4A | 77.312 | 692 | 107 | 35 | 2923 | 3597 | 497819876 | 497819218 | 6.310000e-96 | 363.0 |
32 | TraesCS3D01G231600 | chr4A | 80.255 | 471 | 66 | 13 | 3641 | 4090 | 497819216 | 497818752 | 6.400000e-86 | 329.0 |
33 | TraesCS3D01G231600 | chr4A | 85.217 | 115 | 16 | 1 | 3477 | 3591 | 479415141 | 479415254 | 5.430000e-22 | 117.0 |
34 | TraesCS3D01G231600 | chr4A | 94.000 | 50 | 3 | 0 | 6959 | 7008 | 497814516 | 497814467 | 9.210000e-10 | 76.8 |
35 | TraesCS3D01G231600 | chr4A | 85.938 | 64 | 7 | 2 | 8483 | 8546 | 101515665 | 101515604 | 5.540000e-07 | 67.6 |
36 | TraesCS3D01G231600 | chr4B | 79.225 | 1704 | 233 | 71 | 1971 | 3597 | 138305553 | 138303894 | 0.000000e+00 | 1074.0 |
37 | TraesCS3D01G231600 | chr4B | 90.363 | 799 | 70 | 6 | 4800 | 5592 | 138302844 | 138302047 | 0.000000e+00 | 1042.0 |
38 | TraesCS3D01G231600 | chr4B | 79.919 | 1240 | 141 | 65 | 714 | 1908 | 138306744 | 138305568 | 0.000000e+00 | 811.0 |
39 | TraesCS3D01G231600 | chr4B | 79.627 | 1232 | 170 | 51 | 6407 | 7588 | 138301117 | 138299917 | 0.000000e+00 | 809.0 |
40 | TraesCS3D01G231600 | chr4B | 84.142 | 618 | 76 | 17 | 1235 | 1840 | 119858920 | 119859527 | 5.760000e-161 | 579.0 |
41 | TraesCS3D01G231600 | chr4B | 91.228 | 57 | 4 | 1 | 8500 | 8556 | 581066330 | 581066385 | 9.210000e-10 | 76.8 |
42 | TraesCS3D01G231600 | chr7B | 85.814 | 860 | 111 | 10 | 4731 | 5583 | 665542936 | 665542081 | 0.000000e+00 | 902.0 |
43 | TraesCS3D01G231600 | chr7B | 91.176 | 272 | 23 | 1 | 333 | 603 | 107926339 | 107926068 | 1.360000e-97 | 368.0 |
44 | TraesCS3D01G231600 | chr7B | 94.340 | 53 | 3 | 0 | 8504 | 8556 | 488352249 | 488352301 | 1.980000e-11 | 82.4 |
45 | TraesCS3D01G231600 | chr7B | 89.286 | 56 | 6 | 0 | 8501 | 8556 | 83536237 | 83536292 | 4.290000e-08 | 71.3 |
46 | TraesCS3D01G231600 | chr5B | 84.890 | 867 | 112 | 14 | 4728 | 5583 | 93459332 | 93460190 | 0.000000e+00 | 857.0 |
47 | TraesCS3D01G231600 | chr2A | 84.755 | 551 | 83 | 1 | 54 | 603 | 693643025 | 693642475 | 1.260000e-152 | 551.0 |
48 | TraesCS3D01G231600 | chr5A | 84.139 | 517 | 71 | 7 | 4739 | 5245 | 684629502 | 684628987 | 2.780000e-134 | 490.0 |
49 | TraesCS3D01G231600 | chr5A | 93.659 | 205 | 12 | 1 | 5576 | 5779 | 688698211 | 688698415 | 1.080000e-78 | 305.0 |
50 | TraesCS3D01G231600 | chr5A | 94.444 | 198 | 10 | 1 | 5583 | 5779 | 357050962 | 357050765 | 3.880000e-78 | 303.0 |
51 | TraesCS3D01G231600 | chr6A | 81.555 | 553 | 84 | 12 | 55 | 603 | 421221864 | 421221326 | 2.840000e-119 | 440.0 |
52 | TraesCS3D01G231600 | chr6A | 95.122 | 41 | 2 | 0 | 2092 | 2132 | 549539526 | 549539486 | 1.990000e-06 | 65.8 |
53 | TraesCS3D01G231600 | chr2D | 82.724 | 492 | 74 | 10 | 54 | 539 | 339196798 | 339196312 | 2.210000e-115 | 427.0 |
54 | TraesCS3D01G231600 | chr2D | 94.554 | 202 | 11 | 0 | 5578 | 5779 | 647674604 | 647674805 | 6.450000e-81 | 313.0 |
55 | TraesCS3D01G231600 | chr2D | 96.133 | 181 | 6 | 1 | 7874 | 8054 | 252715232 | 252715053 | 2.340000e-75 | 294.0 |
56 | TraesCS3D01G231600 | chr2D | 96.154 | 52 | 0 | 2 | 8505 | 8556 | 5909192 | 5909241 | 5.500000e-12 | 84.2 |
57 | TraesCS3D01G231600 | chr1B | 92.908 | 282 | 20 | 0 | 52 | 333 | 558919895 | 558919614 | 2.220000e-110 | 411.0 |
58 | TraesCS3D01G231600 | chr1B | 92.657 | 286 | 20 | 1 | 51 | 336 | 660674443 | 660674727 | 2.220000e-110 | 411.0 |
59 | TraesCS3D01G231600 | chr1B | 79.342 | 547 | 104 | 9 | 57 | 598 | 612399941 | 612400483 | 8.110000e-100 | 375.0 |
60 | TraesCS3D01G231600 | chr7D | 93.382 | 272 | 17 | 1 | 333 | 603 | 583442202 | 583441931 | 1.340000e-107 | 401.0 |
61 | TraesCS3D01G231600 | chr7D | 92.336 | 274 | 20 | 1 | 331 | 603 | 123368358 | 123368085 | 1.040000e-103 | 388.0 |
62 | TraesCS3D01G231600 | chr7D | 90.842 | 273 | 24 | 1 | 329 | 600 | 326122829 | 326123101 | 1.760000e-96 | 364.0 |
63 | TraesCS3D01G231600 | chr7D | 95.918 | 49 | 1 | 1 | 8505 | 8553 | 295151127 | 295151080 | 2.560000e-10 | 78.7 |
64 | TraesCS3D01G231600 | chr7D | 91.071 | 56 | 5 | 0 | 8501 | 8556 | 340233596 | 340233651 | 9.210000e-10 | 76.8 |
65 | TraesCS3D01G231600 | chr6D | 91.176 | 272 | 23 | 1 | 333 | 603 | 183017157 | 183016886 | 1.360000e-97 | 368.0 |
66 | TraesCS3D01G231600 | chr6D | 94.554 | 202 | 10 | 1 | 5583 | 5784 | 181729733 | 181729533 | 2.320000e-80 | 311.0 |
67 | TraesCS3D01G231600 | chr6D | 96.154 | 182 | 5 | 2 | 7879 | 8060 | 115783102 | 115782923 | 6.490000e-76 | 296.0 |
68 | TraesCS3D01G231600 | chr6D | 95.122 | 41 | 2 | 0 | 2092 | 2132 | 403066780 | 403066740 | 1.990000e-06 | 65.8 |
69 | TraesCS3D01G231600 | chr7A | 94.146 | 205 | 9 | 2 | 5580 | 5784 | 504221549 | 504221348 | 8.340000e-80 | 309.0 |
70 | TraesCS3D01G231600 | chr7A | 95.833 | 48 | 2 | 0 | 8503 | 8550 | 571270589 | 571270542 | 2.560000e-10 | 78.7 |
71 | TraesCS3D01G231600 | chr5D | 91.593 | 226 | 15 | 4 | 5568 | 5791 | 362579277 | 362579500 | 8.340000e-80 | 309.0 |
72 | TraesCS3D01G231600 | chr5D | 96.610 | 177 | 6 | 0 | 7877 | 8053 | 466142342 | 466142518 | 2.340000e-75 | 294.0 |
73 | TraesCS3D01G231600 | chr5D | 96.629 | 178 | 4 | 2 | 7887 | 8063 | 486175133 | 486175309 | 2.340000e-75 | 294.0 |
74 | TraesCS3D01G231600 | chr5D | 95.604 | 182 | 6 | 2 | 7871 | 8052 | 508629017 | 508629196 | 3.020000e-74 | 291.0 |
75 | TraesCS3D01G231600 | chr6B | 91.943 | 211 | 15 | 2 | 5576 | 5785 | 347750841 | 347751050 | 2.340000e-75 | 294.0 |
76 | TraesCS3D01G231600 | chr6B | 85.714 | 70 | 6 | 4 | 2092 | 2159 | 604109806 | 604109739 | 4.290000e-08 | 71.3 |
77 | TraesCS3D01G231600 | chrUn | 93.103 | 58 | 4 | 0 | 1 | 58 | 314145583 | 314145526 | 1.530000e-12 | 86.1 |
78 | TraesCS3D01G231600 | chr2B | 97.917 | 48 | 1 | 0 | 8503 | 8550 | 140746874 | 140746827 | 5.500000e-12 | 84.2 |
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 | TraesCS3D01G231600 | chr3D | 317197816 | 317206372 | 8556 | False | 7544.000000 | 8013 | 100.000000 | 1 | 8557 | 2 | chr3D.!!$F2 | 8556 |
1 | TraesCS3D01G231600 | chr3A | 410107578 | 410114985 | 7407 | True | 2692.250000 | 5637 | 94.131500 | 603 | 8505 | 4 | chr3A.!!$R1 | 7902 |
2 | TraesCS3D01G231600 | chr3B | 401803298 | 401810359 | 7061 | True | 1486.285714 | 3328 | 93.239857 | 620 | 8505 | 7 | chr3B.!!$R1 | 7885 |
3 | TraesCS3D01G231600 | chr3B | 406649934 | 406650821 | 887 | False | 614.000000 | 614 | 79.428000 | 1325 | 2223 | 1 | chr3B.!!$F1 | 898 |
4 | TraesCS3D01G231600 | chr4D | 96907565 | 96912259 | 4694 | True | 1169.333333 | 1934 | 83.102333 | 714 | 5592 | 3 | chr4D.!!$R3 | 4878 |
5 | TraesCS3D01G231600 | chr4A | 479412044 | 479417186 | 5142 | False | 875.000000 | 1836 | 84.217000 | 1247 | 5583 | 4 | chr4A.!!$F1 | 4336 |
6 | TraesCS3D01G231600 | chr4A | 200055750 | 200056288 | 538 | True | 501.000000 | 501 | 83.455000 | 55 | 603 | 1 | chr4A.!!$R2 | 548 |
7 | TraesCS3D01G231600 | chr4A | 497814467 | 497819876 | 5409 | True | 432.450000 | 961 | 84.638250 | 2923 | 7008 | 4 | chr4A.!!$R4 | 4085 |
8 | TraesCS3D01G231600 | chr4B | 138299917 | 138306744 | 6827 | True | 934.000000 | 1074 | 82.283500 | 714 | 7588 | 4 | chr4B.!!$R1 | 6874 |
9 | TraesCS3D01G231600 | chr4B | 119858920 | 119859527 | 607 | False | 579.000000 | 579 | 84.142000 | 1235 | 1840 | 1 | chr4B.!!$F1 | 605 |
10 | TraesCS3D01G231600 | chr7B | 665542081 | 665542936 | 855 | True | 902.000000 | 902 | 85.814000 | 4731 | 5583 | 1 | chr7B.!!$R2 | 852 |
11 | TraesCS3D01G231600 | chr5B | 93459332 | 93460190 | 858 | False | 857.000000 | 857 | 84.890000 | 4728 | 5583 | 1 | chr5B.!!$F1 | 855 |
12 | TraesCS3D01G231600 | chr2A | 693642475 | 693643025 | 550 | True | 551.000000 | 551 | 84.755000 | 54 | 603 | 1 | chr2A.!!$R1 | 549 |
13 | TraesCS3D01G231600 | chr5A | 684628987 | 684629502 | 515 | True | 490.000000 | 490 | 84.139000 | 4739 | 5245 | 1 | chr5A.!!$R2 | 506 |
14 | TraesCS3D01G231600 | chr6A | 421221326 | 421221864 | 538 | True | 440.000000 | 440 | 81.555000 | 55 | 603 | 1 | chr6A.!!$R1 | 548 |
15 | TraesCS3D01G231600 | chr1B | 612399941 | 612400483 | 542 | False | 375.000000 | 375 | 79.342000 | 57 | 598 | 1 | chr1B.!!$F1 | 541 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
356 | 357 | 3.104512 | CTGGTCATAGTGGGGAGTAACA | 58.895 | 50.000 | 0.00 | 0.00 | 0.00 | 2.41 | F |
1119 | 1151 | 4.021981 | GCAATTTACTGCCTTTGTTCTCCT | 60.022 | 41.667 | 0.00 | 0.00 | 36.25 | 3.69 | F |
2174 | 2248 | 0.040157 | TTGATGAACTTGCTGTGCGC | 60.040 | 50.000 | 0.00 | 0.00 | 39.77 | 6.09 | F |
2492 | 2595 | 0.676782 | AATGGACGTTACTGGCCAGC | 60.677 | 55.000 | 33.06 | 15.65 | 33.26 | 4.85 | F |
4017 | 4983 | 1.295792 | GTTCCGAGCACTGTTGTCAA | 58.704 | 50.000 | 0.00 | 0.00 | 0.00 | 3.18 | F |
5678 | 9262 | 0.107831 | TTTGTACAGGGCAGACGCTT | 59.892 | 50.000 | 0.00 | 0.00 | 36.86 | 4.68 | F |
5679 | 9263 | 0.970640 | TTGTACAGGGCAGACGCTTA | 59.029 | 50.000 | 0.00 | 0.00 | 36.86 | 3.09 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1448 | 1498 | 0.323360 | CCTTCTGGGGGCAAAATCGA | 60.323 | 55.000 | 0.00 | 0.00 | 0.00 | 3.59 | R |
2478 | 2581 | 0.248289 | AATACGCTGGCCAGTAACGT | 59.752 | 50.000 | 30.74 | 30.74 | 40.53 | 3.99 | R |
3939 | 4900 | 0.172578 | TCAGAATCCCACACGCGTAG | 59.827 | 55.000 | 13.44 | 9.47 | 0.00 | 3.51 | R |
4211 | 7771 | 1.266718 | TGTTGTCCGAGAGCAAAATGC | 59.733 | 47.619 | 0.00 | 0.00 | 45.46 | 3.56 | R |
5746 | 9330 | 0.042731 | TGCTAGGTGCTTAGGGAGGT | 59.957 | 55.000 | 0.00 | 0.00 | 43.37 | 3.85 | R |
6722 | 10679 | 2.277084 | CACTACTCCACGGGCAAATAC | 58.723 | 52.381 | 0.00 | 0.00 | 0.00 | 1.89 | R |
7627 | 11645 | 2.309162 | TGGATAATCCAACGAAACCCCA | 59.691 | 45.455 | 0.00 | 0.00 | 45.00 | 4.96 | 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.