Multiple sequence alignment - TraesCS3D01G045000
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 | TraesCS3D01G045000 | chr3D | 100.000 | 6802 | 0 | 0 | 1 | 6802 | 17352565 | 17359366 | 0.000000e+00 | 12562.0 |
1 | TraesCS3D01G045000 | chr3D | 83.323 | 1643 | 153 | 62 | 4574 | 6132 | 17538372 | 17536767 | 0.000000e+00 | 1404.0 |
2 | TraesCS3D01G045000 | chr3D | 89.159 | 618 | 61 | 3 | 1256 | 1871 | 17541258 | 17540645 | 0.000000e+00 | 765.0 |
3 | TraesCS3D01G045000 | chr3D | 80.819 | 1001 | 129 | 42 | 4654 | 5622 | 17671034 | 17670065 | 0.000000e+00 | 726.0 |
4 | TraesCS3D01G045000 | chr3D | 78.049 | 861 | 133 | 29 | 3365 | 4205 | 17355075 | 17355899 | 6.130000e-135 | 492.0 |
5 | TraesCS3D01G045000 | chr3D | 78.049 | 861 | 133 | 29 | 2511 | 3335 | 17355929 | 17356769 | 6.130000e-135 | 492.0 |
6 | TraesCS3D01G045000 | chr3D | 77.551 | 784 | 133 | 26 | 1044 | 1814 | 17538072 | 17537319 | 3.770000e-117 | 433.0 |
7 | TraesCS3D01G045000 | chr3D | 77.452 | 785 | 127 | 30 | 1037 | 1811 | 17357428 | 17358172 | 2.270000e-114 | 424.0 |
8 | TraesCS3D01G045000 | chr3D | 85.287 | 401 | 56 | 2 | 4870 | 5270 | 18793228 | 18793625 | 1.770000e-110 | 411.0 |
9 | TraesCS3D01G045000 | chr3D | 95.500 | 200 | 9 | 0 | 6279 | 6478 | 1876473 | 1876274 | 3.060000e-83 | 320.0 |
10 | TraesCS3D01G045000 | chr3D | 95.050 | 202 | 9 | 1 | 6279 | 6479 | 378782479 | 378782680 | 3.960000e-82 | 316.0 |
11 | TraesCS3D01G045000 | chr3D | 76.224 | 715 | 78 | 50 | 4268 | 4949 | 11331494 | 11332149 | 1.860000e-75 | 294.0 |
12 | TraesCS3D01G045000 | chr3D | 76.726 | 391 | 74 | 13 | 1073 | 1462 | 18793251 | 18793625 | 1.160000e-47 | 202.0 |
13 | TraesCS3D01G045000 | chr3D | 91.667 | 144 | 9 | 1 | 1114 | 1257 | 17541743 | 17541603 | 5.380000e-46 | 196.0 |
14 | TraesCS3D01G045000 | chr3D | 83.516 | 182 | 23 | 3 | 4362 | 4543 | 17671468 | 17671294 | 5.460000e-36 | 163.0 |
15 | TraesCS3D01G045000 | chr3D | 80.925 | 173 | 21 | 3 | 6484 | 6645 | 595079857 | 595079686 | 7.160000e-25 | 126.0 |
16 | TraesCS3D01G045000 | chr3B | 81.779 | 2294 | 270 | 79 | 3517 | 5718 | 24927294 | 24929531 | 0.000000e+00 | 1784.0 |
17 | TraesCS3D01G045000 | chr3B | 87.666 | 1281 | 97 | 27 | 619 | 1868 | 24925189 | 24926439 | 0.000000e+00 | 1434.0 |
18 | TraesCS3D01G045000 | chr3B | 83.890 | 689 | 107 | 4 | 4896 | 5582 | 30498358 | 30499044 | 0.000000e+00 | 654.0 |
19 | TraesCS3D01G045000 | chr3B | 83.309 | 695 | 103 | 9 | 4896 | 5582 | 30200045 | 30200734 | 4.480000e-176 | 628.0 |
20 | TraesCS3D01G045000 | chr3B | 82.663 | 721 | 112 | 8 | 4870 | 5582 | 29776931 | 29777646 | 1.610000e-175 | 627.0 |
21 | TraesCS3D01G045000 | chr3B | 80.725 | 690 | 115 | 12 | 4870 | 5550 | 30508987 | 30509667 | 7.820000e-144 | 521.0 |
22 | TraesCS3D01G045000 | chr3B | 91.099 | 191 | 15 | 2 | 341 | 529 | 24924899 | 24925089 | 2.430000e-64 | 257.0 |
23 | TraesCS3D01G045000 | chr3B | 82.520 | 246 | 31 | 8 | 6482 | 6718 | 821480270 | 821480028 | 8.940000e-49 | 206.0 |
24 | TraesCS3D01G045000 | chr3B | 82.648 | 219 | 31 | 4 | 3353 | 3569 | 24927096 | 24927309 | 3.240000e-43 | 187.0 |
25 | TraesCS3D01G045000 | chr3B | 94.737 | 95 | 5 | 0 | 162 | 256 | 24924740 | 24924834 | 1.530000e-31 | 148.0 |
26 | TraesCS3D01G045000 | chr3A | 87.795 | 1483 | 108 | 31 | 4277 | 5720 | 19492160 | 19490712 | 0.000000e+00 | 1668.0 |
27 | TraesCS3D01G045000 | chr3A | 87.932 | 1185 | 100 | 23 | 905 | 2055 | 19494786 | 19493611 | 0.000000e+00 | 1356.0 |
28 | TraesCS3D01G045000 | chr3A | 85.128 | 1096 | 115 | 27 | 2281 | 3335 | 19493293 | 19492205 | 0.000000e+00 | 1077.0 |
29 | TraesCS3D01G045000 | chr3A | 81.105 | 1032 | 146 | 30 | 4574 | 5584 | 19275343 | 19276346 | 0.000000e+00 | 780.0 |
30 | TraesCS3D01G045000 | chr3A | 77.808 | 1469 | 173 | 81 | 4303 | 5718 | 25994495 | 25993127 | 0.000000e+00 | 765.0 |
31 | TraesCS3D01G045000 | chr3A | 80.599 | 902 | 149 | 17 | 3365 | 4247 | 19493057 | 19492163 | 0.000000e+00 | 673.0 |
32 | TraesCS3D01G045000 | chr3A | 75.979 | 970 | 163 | 40 | 845 | 1787 | 19491773 | 19490847 | 2.910000e-118 | 436.0 |
33 | TraesCS3D01G045000 | chr3A | 83.232 | 495 | 44 | 17 | 5717 | 6192 | 19490681 | 19490207 | 1.060000e-112 | 418.0 |
34 | TraesCS3D01G045000 | chr3A | 95.025 | 201 | 9 | 1 | 6279 | 6478 | 690792772 | 690792972 | 1.420000e-81 | 315.0 |
35 | TraesCS3D01G045000 | chr3A | 90.173 | 173 | 11 | 3 | 5716 | 5886 | 19352833 | 19353001 | 3.190000e-53 | 220.0 |
36 | TraesCS3D01G045000 | chr3A | 86.842 | 76 | 8 | 2 | 5722 | 5796 | 25993094 | 25993020 | 4.370000e-12 | 84.2 |
37 | TraesCS3D01G045000 | chr6D | 96.040 | 202 | 6 | 2 | 6276 | 6476 | 155841818 | 155841618 | 1.830000e-85 | 327.0 |
38 | TraesCS3D01G045000 | chr6D | 95.522 | 201 | 9 | 0 | 6279 | 6479 | 389653552 | 389653352 | 8.510000e-84 | 322.0 |
39 | TraesCS3D01G045000 | chr6D | 80.081 | 246 | 39 | 8 | 6479 | 6716 | 10420115 | 10420358 | 2.520000e-39 | 174.0 |
40 | TraesCS3D01G045000 | chr6D | 78.571 | 252 | 32 | 14 | 6482 | 6718 | 292373851 | 292374095 | 5.500000e-31 | 147.0 |
41 | TraesCS3D01G045000 | chr2D | 95.074 | 203 | 10 | 0 | 6276 | 6478 | 458171872 | 458172074 | 3.060000e-83 | 320.0 |
42 | TraesCS3D01G045000 | chr2D | 79.435 | 248 | 39 | 10 | 6482 | 6721 | 422881367 | 422881124 | 1.520000e-36 | 165.0 |
43 | TraesCS3D01G045000 | chr2A | 95.025 | 201 | 9 | 1 | 6279 | 6478 | 769618682 | 769618482 | 1.420000e-81 | 315.0 |
44 | TraesCS3D01G045000 | chr1A | 95.025 | 201 | 9 | 1 | 6279 | 6478 | 586372725 | 586372925 | 1.420000e-81 | 315.0 |
45 | TraesCS3D01G045000 | chr1A | 83.468 | 248 | 29 | 8 | 6483 | 6721 | 533318239 | 533317995 | 3.190000e-53 | 220.0 |
46 | TraesCS3D01G045000 | chr5D | 93.720 | 207 | 12 | 1 | 6270 | 6476 | 487979075 | 487979280 | 6.630000e-80 | 309.0 |
47 | TraesCS3D01G045000 | chr5A | 82.540 | 252 | 29 | 9 | 6479 | 6718 | 702190684 | 702190932 | 2.490000e-49 | 207.0 |
48 | TraesCS3D01G045000 | chr5A | 79.116 | 249 | 40 | 8 | 6482 | 6721 | 563220536 | 563220291 | 1.960000e-35 | 161.0 |
49 | TraesCS3D01G045000 | chr7D | 79.681 | 251 | 34 | 7 | 6479 | 6714 | 610805281 | 610805529 | 1.520000e-36 | 165.0 |
50 | TraesCS3D01G045000 | chr6B | 80.085 | 236 | 36 | 8 | 6489 | 6716 | 19132016 | 19132248 | 1.520000e-36 | 165.0 |
51 | TraesCS3D01G045000 | chr2B | 78.000 | 250 | 29 | 16 | 6482 | 6722 | 662899997 | 662899765 | 4.280000e-27 | 134.0 |
52 | TraesCS3D01G045000 | chr4B | 93.333 | 60 | 3 | 1 | 6663 | 6722 | 604867435 | 604867493 | 3.380000e-13 | 87.9 |
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 | TraesCS3D01G045000 | chr3D | 17352565 | 17359366 | 6801 | False | 12562.000000 | 12562 | 100.000000 | 1 | 6802 | 1 | chr3D.!!$F2 | 6801 |
1 | TraesCS3D01G045000 | chr3D | 17536767 | 17541743 | 4976 | True | 699.500000 | 1404 | 85.425000 | 1044 | 6132 | 4 | chr3D.!!$R3 | 5088 |
2 | TraesCS3D01G045000 | chr3D | 17355075 | 17358172 | 3097 | False | 469.333333 | 492 | 77.850000 | 1037 | 4205 | 3 | chr3D.!!$F4 | 3168 |
3 | TraesCS3D01G045000 | chr3D | 17670065 | 17671468 | 1403 | True | 444.500000 | 726 | 82.167500 | 4362 | 5622 | 2 | chr3D.!!$R4 | 1260 |
4 | TraesCS3D01G045000 | chr3D | 11331494 | 11332149 | 655 | False | 294.000000 | 294 | 76.224000 | 4268 | 4949 | 1 | chr3D.!!$F1 | 681 |
5 | TraesCS3D01G045000 | chr3B | 24924740 | 24929531 | 4791 | False | 762.000000 | 1784 | 87.585800 | 162 | 5718 | 5 | chr3B.!!$F5 | 5556 |
6 | TraesCS3D01G045000 | chr3B | 30498358 | 30499044 | 686 | False | 654.000000 | 654 | 83.890000 | 4896 | 5582 | 1 | chr3B.!!$F3 | 686 |
7 | TraesCS3D01G045000 | chr3B | 30200045 | 30200734 | 689 | False | 628.000000 | 628 | 83.309000 | 4896 | 5582 | 1 | chr3B.!!$F2 | 686 |
8 | TraesCS3D01G045000 | chr3B | 29776931 | 29777646 | 715 | False | 627.000000 | 627 | 82.663000 | 4870 | 5582 | 1 | chr3B.!!$F1 | 712 |
9 | TraesCS3D01G045000 | chr3B | 30508987 | 30509667 | 680 | False | 521.000000 | 521 | 80.725000 | 4870 | 5550 | 1 | chr3B.!!$F4 | 680 |
10 | TraesCS3D01G045000 | chr3A | 19490207 | 19494786 | 4579 | True | 938.000000 | 1668 | 83.444167 | 845 | 6192 | 6 | chr3A.!!$R1 | 5347 |
11 | TraesCS3D01G045000 | chr3A | 19275343 | 19276346 | 1003 | False | 780.000000 | 780 | 81.105000 | 4574 | 5584 | 1 | chr3A.!!$F1 | 1010 |
12 | TraesCS3D01G045000 | chr3A | 25993020 | 25994495 | 1475 | True | 424.600000 | 765 | 82.325000 | 4303 | 5796 | 2 | chr3A.!!$R2 | 1493 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
882 | 948 | 0.035598 | TTCGCATTCCCCTTTCGTCA | 59.964 | 50.0 | 0.00 | 0.0 | 0.00 | 4.35 | F |
1878 | 2322 | 0.096976 | CTTTCGCGGTATGGTTGCAG | 59.903 | 55.0 | 6.13 | 0.0 | 0.00 | 4.41 | F |
1910 | 2354 | 0.108756 | GTTGCACTAGTCGGGAGGTC | 60.109 | 60.0 | 0.00 | 0.0 | 0.00 | 3.85 | F |
1915 | 2359 | 0.179051 | ACTAGTCGGGAGGTCTAGCG | 60.179 | 60.0 | 0.00 | 0.0 | 37.87 | 4.26 | F |
1916 | 2360 | 0.179051 | CTAGTCGGGAGGTCTAGCGT | 60.179 | 60.0 | 0.00 | 0.0 | 32.05 | 5.07 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1881 | 2325 | 0.652592 | CTAGTGCAACGCTGGTATGC | 59.347 | 55.000 | 0.00 | 0.0 | 45.86 | 3.14 | R |
5632 | 7598 | 1.660575 | GATATGGCCGTCCACGTCG | 60.661 | 63.158 | 0.00 | 0.0 | 46.92 | 5.12 | R |
5678 | 7648 | 0.905357 | ACGAACCAGGGAGGAAGATG | 59.095 | 55.000 | 0.00 | 0.0 | 41.22 | 2.90 | R |
5731 | 7742 | 0.179018 | AAATCTCCATGGGCCTACGC | 60.179 | 55.000 | 13.02 | 0.0 | 0.00 | 4.42 | R |
5803 | 7826 | 0.109458 | TGTACTCAGCGTGTTAGCCG | 60.109 | 55.000 | 0.00 | 0.0 | 38.01 | 5.52 | 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.