Multiple sequence alignment - TraesCS6A01G091100
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 | TraesCS6A01G091100 | chr6A | 100.000 | 5832 | 0 | 0 | 319 | 6150 | 59782631 | 59788462 | 0.000000e+00 | 10770.0 |
1 | TraesCS6A01G091100 | chr6A | 87.874 | 2573 | 239 | 39 | 3382 | 5890 | 59708729 | 59711292 | 0.000000e+00 | 2955.0 |
2 | TraesCS6A01G091100 | chr6A | 84.611 | 1787 | 222 | 33 | 3317 | 5060 | 59676069 | 59677845 | 0.000000e+00 | 1727.0 |
3 | TraesCS6A01G091100 | chr6A | 91.421 | 373 | 25 | 3 | 991 | 1362 | 59808223 | 59808589 | 7.110000e-139 | 505.0 |
4 | TraesCS6A01G091100 | chr6A | 86.970 | 330 | 26 | 7 | 2016 | 2330 | 59809306 | 59809633 | 7.580000e-94 | 355.0 |
5 | TraesCS6A01G091100 | chr6A | 84.118 | 340 | 32 | 10 | 1450 | 1767 | 59708108 | 59708447 | 5.990000e-80 | 309.0 |
6 | TraesCS6A01G091100 | chr6A | 86.047 | 258 | 27 | 6 | 2349 | 2605 | 59809700 | 59809949 | 1.020000e-67 | 268.0 |
7 | TraesCS6A01G091100 | chr6A | 91.912 | 136 | 11 | 0 | 5900 | 6035 | 59711358 | 59711493 | 2.260000e-44 | 191.0 |
8 | TraesCS6A01G091100 | chr6A | 100.000 | 82 | 0 | 0 | 1 | 82 | 59782313 | 59782394 | 1.070000e-32 | 152.0 |
9 | TraesCS6A01G091100 | chr6A | 87.611 | 113 | 14 | 0 | 6038 | 6150 | 582917329 | 582917217 | 1.390000e-26 | 132.0 |
10 | TraesCS6A01G091100 | chr6A | 92.000 | 50 | 3 | 1 | 5610 | 5659 | 59814590 | 59814638 | 1.110000e-07 | 69.4 |
11 | TraesCS6A01G091100 | chr6A | 82.667 | 75 | 6 | 6 | 5258 | 5326 | 59346430 | 59346503 | 6.660000e-05 | 60.2 |
12 | TraesCS6A01G091100 | chr6D | 96.200 | 2842 | 90 | 6 | 2881 | 5705 | 45208346 | 45211186 | 0.000000e+00 | 4634.0 |
13 | TraesCS6A01G091100 | chr6D | 88.442 | 2561 | 242 | 34 | 3382 | 5892 | 45203446 | 45206002 | 0.000000e+00 | 3040.0 |
14 | TraesCS6A01G091100 | chr6D | 85.003 | 1667 | 206 | 27 | 3426 | 5060 | 44505976 | 44507630 | 0.000000e+00 | 1653.0 |
15 | TraesCS6A01G091100 | chr6D | 84.754 | 1666 | 211 | 26 | 3426 | 5060 | 44736206 | 44737859 | 0.000000e+00 | 1629.0 |
16 | TraesCS6A01G091100 | chr6D | 94.000 | 900 | 47 | 3 | 3589 | 4487 | 45479905 | 45480798 | 0.000000e+00 | 1356.0 |
17 | TraesCS6A01G091100 | chr6D | 92.282 | 596 | 32 | 5 | 921 | 1504 | 45206238 | 45206831 | 0.000000e+00 | 833.0 |
18 | TraesCS6A01G091100 | chr6D | 92.759 | 580 | 20 | 7 | 2231 | 2810 | 45207454 | 45208011 | 0.000000e+00 | 819.0 |
19 | TraesCS6A01G091100 | chr6D | 92.290 | 428 | 28 | 3 | 5612 | 6035 | 45211653 | 45212079 | 2.450000e-168 | 603.0 |
20 | TraesCS6A01G091100 | chr6D | 95.860 | 314 | 12 | 1 | 1871 | 2184 | 45207135 | 45207447 | 1.980000e-139 | 507.0 |
21 | TraesCS6A01G091100 | chr6D | 90.860 | 372 | 28 | 1 | 991 | 1362 | 45478087 | 45478452 | 1.540000e-135 | 494.0 |
22 | TraesCS6A01G091100 | chr6D | 87.147 | 389 | 45 | 3 | 933 | 1317 | 45202264 | 45202651 | 2.630000e-118 | 436.0 |
23 | TraesCS6A01G091100 | chr6D | 87.915 | 331 | 24 | 5 | 2016 | 2330 | 45479174 | 45479504 | 5.820000e-100 | 375.0 |
24 | TraesCS6A01G091100 | chr6D | 86.826 | 334 | 28 | 8 | 1450 | 1767 | 45202831 | 45203164 | 5.860000e-95 | 359.0 |
25 | TraesCS6A01G091100 | chr6D | 94.860 | 214 | 11 | 0 | 1554 | 1767 | 45206923 | 45207136 | 9.880000e-88 | 335.0 |
26 | TraesCS6A01G091100 | chr6D | 86.047 | 258 | 27 | 6 | 2349 | 2605 | 45479571 | 45479820 | 1.020000e-67 | 268.0 |
27 | TraesCS6A01G091100 | chr6D | 90.299 | 134 | 13 | 0 | 660 | 793 | 459356285 | 459356152 | 6.340000e-40 | 176.0 |
28 | TraesCS6A01G091100 | chr6D | 86.331 | 139 | 12 | 3 | 511 | 647 | 45212546 | 45212679 | 1.790000e-30 | 145.0 |
29 | TraesCS6A01G091100 | chr6D | 83.908 | 87 | 8 | 6 | 5612 | 5695 | 45482067 | 45482150 | 1.840000e-10 | 78.7 |
30 | TraesCS6A01G091100 | chr6D | 84.375 | 64 | 4 | 5 | 5258 | 5315 | 44507824 | 44507887 | 2.390000e-04 | 58.4 |
31 | TraesCS6A01G091100 | chr6D | 84.375 | 64 | 4 | 5 | 5258 | 5315 | 44738052 | 44738115 | 2.390000e-04 | 58.4 |
32 | TraesCS6A01G091100 | chr6B | 93.526 | 2873 | 106 | 20 | 2881 | 5705 | 113846091 | 113848931 | 0.000000e+00 | 4202.0 |
33 | TraesCS6A01G091100 | chr6B | 88.660 | 1896 | 179 | 22 | 4166 | 6035 | 113783435 | 113785320 | 0.000000e+00 | 2278.0 |
34 | TraesCS6A01G091100 | chr6B | 85.210 | 1359 | 168 | 20 | 3727 | 5060 | 113771078 | 113772428 | 0.000000e+00 | 1365.0 |
35 | TraesCS6A01G091100 | chr6B | 90.370 | 540 | 27 | 3 | 1125 | 1664 | 113843649 | 113844163 | 0.000000e+00 | 686.0 |
36 | TraesCS6A01G091100 | chr6B | 92.947 | 397 | 21 | 3 | 5640 | 6033 | 113849362 | 113849754 | 6.920000e-159 | 571.0 |
37 | TraesCS6A01G091100 | chr6B | 83.291 | 395 | 49 | 12 | 5612 | 5999 | 114028276 | 114028660 | 1.270000e-91 | 348.0 |
38 | TraesCS6A01G091100 | chr6B | 85.928 | 334 | 31 | 8 | 1450 | 1767 | 113781771 | 113782104 | 5.900000e-90 | 342.0 |
39 | TraesCS6A01G091100 | chr6B | 84.308 | 325 | 35 | 6 | 937 | 1258 | 113780910 | 113781221 | 2.790000e-78 | 303.0 |
40 | TraesCS6A01G091100 | chr6B | 96.154 | 130 | 5 | 0 | 984 | 1113 | 113843464 | 113843593 | 4.830000e-51 | 213.0 |
41 | TraesCS6A01G091100 | chr6B | 88.182 | 110 | 13 | 0 | 511 | 620 | 113850120 | 113850229 | 1.390000e-26 | 132.0 |
42 | TraesCS6A01G091100 | chr6B | 97.101 | 69 | 1 | 1 | 2460 | 2527 | 113844192 | 113844260 | 1.400000e-21 | 115.0 |
43 | TraesCS6A01G091100 | chr6B | 84.375 | 64 | 4 | 5 | 5258 | 5315 | 113657787 | 113657850 | 2.390000e-04 | 58.4 |
44 | TraesCS6A01G091100 | chr5D | 96.491 | 114 | 4 | 0 | 1763 | 1876 | 521523688 | 521523801 | 8.140000e-44 | 189.0 |
45 | TraesCS6A01G091100 | chr5D | 88.889 | 135 | 15 | 0 | 660 | 794 | 330702999 | 330703133 | 3.810000e-37 | 167.0 |
46 | TraesCS6A01G091100 | chr4A | 91.241 | 137 | 12 | 0 | 660 | 796 | 140763864 | 140764000 | 2.930000e-43 | 187.0 |
47 | TraesCS6A01G091100 | chr4A | 94.872 | 117 | 5 | 1 | 1765 | 1880 | 720526580 | 720526696 | 1.360000e-41 | 182.0 |
48 | TraesCS6A01G091100 | chrUn | 94.872 | 117 | 5 | 1 | 1765 | 1880 | 51053148 | 51053032 | 1.360000e-41 | 182.0 |
49 | TraesCS6A01G091100 | chrUn | 94.872 | 117 | 5 | 1 | 1765 | 1880 | 342353519 | 342353403 | 1.360000e-41 | 182.0 |
50 | TraesCS6A01G091100 | chrUn | 94.828 | 116 | 5 | 1 | 1757 | 1872 | 77885381 | 77885267 | 4.900000e-41 | 180.0 |
51 | TraesCS6A01G091100 | chrUn | 86.842 | 114 | 14 | 1 | 6038 | 6150 | 42175456 | 42175343 | 6.470000e-25 | 126.0 |
52 | TraesCS6A01G091100 | chr7B | 95.575 | 113 | 5 | 0 | 1763 | 1875 | 297402183 | 297402295 | 1.360000e-41 | 182.0 |
53 | TraesCS6A01G091100 | chr7B | 94.783 | 115 | 6 | 0 | 1765 | 1879 | 730205113 | 730205227 | 4.900000e-41 | 180.0 |
54 | TraesCS6A01G091100 | chr7B | 89.552 | 134 | 14 | 0 | 661 | 794 | 96812038 | 96812171 | 2.950000e-38 | 171.0 |
55 | TraesCS6A01G091100 | chr7B | 97.297 | 37 | 1 | 0 | 991 | 1027 | 684367701 | 684367737 | 5.150000e-06 | 63.9 |
56 | TraesCS6A01G091100 | chr2D | 94.783 | 115 | 5 | 1 | 1758 | 1872 | 111321520 | 111321407 | 1.760000e-40 | 178.0 |
57 | TraesCS6A01G091100 | chr2D | 94.017 | 117 | 7 | 0 | 1764 | 1880 | 593429590 | 593429706 | 1.760000e-40 | 178.0 |
58 | TraesCS6A01G091100 | chr7D | 89.630 | 135 | 14 | 0 | 661 | 795 | 577917702 | 577917836 | 8.200000e-39 | 172.0 |
59 | TraesCS6A01G091100 | chr7D | 88.889 | 135 | 15 | 0 | 660 | 794 | 315668054 | 315667920 | 3.810000e-37 | 167.0 |
60 | TraesCS6A01G091100 | chr7D | 86.842 | 114 | 15 | 0 | 6037 | 6150 | 400297895 | 400298008 | 1.800000e-25 | 128.0 |
61 | TraesCS6A01G091100 | chr7D | 85.714 | 56 | 8 | 0 | 790 | 845 | 111749196 | 111749251 | 6.660000e-05 | 60.2 |
62 | TraesCS6A01G091100 | chr3D | 90.698 | 129 | 12 | 0 | 666 | 794 | 452657885 | 452658013 | 8.200000e-39 | 172.0 |
63 | TraesCS6A01G091100 | chr3D | 90.000 | 130 | 13 | 0 | 666 | 795 | 424623475 | 424623604 | 1.060000e-37 | 169.0 |
64 | TraesCS6A01G091100 | chr3D | 87.500 | 112 | 14 | 0 | 6039 | 6150 | 500223179 | 500223068 | 5.000000e-26 | 130.0 |
65 | TraesCS6A01G091100 | chr2B | 87.500 | 144 | 15 | 3 | 660 | 803 | 105905975 | 105905835 | 4.930000e-36 | 163.0 |
66 | TraesCS6A01G091100 | chr3A | 89.474 | 114 | 12 | 0 | 6037 | 6150 | 725923636 | 725923749 | 1.790000e-30 | 145.0 |
67 | TraesCS6A01G091100 | chr4D | 88.496 | 113 | 13 | 0 | 6038 | 6150 | 484720786 | 484720674 | 2.990000e-28 | 137.0 |
68 | TraesCS6A01G091100 | chr4D | 89.623 | 106 | 10 | 1 | 6038 | 6143 | 484719539 | 484719643 | 3.870000e-27 | 134.0 |
69 | TraesCS6A01G091100 | chr1D | 89.524 | 105 | 10 | 1 | 6038 | 6142 | 411190944 | 411190841 | 1.390000e-26 | 132.0 |
70 | TraesCS6A01G091100 | chr1D | 85.455 | 55 | 8 | 0 | 791 | 845 | 81062712 | 81062658 | 2.390000e-04 | 58.4 |
71 | TraesCS6A01G091100 | chr1A | 86.726 | 113 | 13 | 2 | 6039 | 6150 | 22538753 | 22538642 | 2.330000e-24 | 124.0 |
72 | TraesCS6A01G091100 | chr1A | 90.909 | 55 | 5 | 0 | 791 | 845 | 59128239 | 59128293 | 2.380000e-09 | 75.0 |
73 | TraesCS6A01G091100 | chr5B | 89.091 | 55 | 6 | 0 | 791 | 845 | 681782131 | 681782185 | 1.110000e-07 | 69.4 |
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 | TraesCS6A01G091100 | chr6A | 59782313 | 59788462 | 6149 | False | 5461.000000 | 10770 | 100.000000 | 1 | 6150 | 2 | chr6A.!!$F5 | 6149 |
1 | TraesCS6A01G091100 | chr6A | 59676069 | 59677845 | 1776 | False | 1727.000000 | 1727 | 84.611000 | 3317 | 5060 | 1 | chr6A.!!$F2 | 1743 |
2 | TraesCS6A01G091100 | chr6A | 59708108 | 59711493 | 3385 | False | 1151.666667 | 2955 | 87.968000 | 1450 | 6035 | 3 | chr6A.!!$F4 | 4585 |
3 | TraesCS6A01G091100 | chr6A | 59808223 | 59809949 | 1726 | False | 376.000000 | 505 | 88.146000 | 991 | 2605 | 3 | chr6A.!!$F6 | 1614 |
4 | TraesCS6A01G091100 | chr6D | 45202264 | 45212679 | 10415 | False | 1171.100000 | 4634 | 91.299700 | 511 | 6035 | 10 | chr6D.!!$F3 | 5524 |
5 | TraesCS6A01G091100 | chr6D | 44505976 | 44507887 | 1911 | False | 855.700000 | 1653 | 84.689000 | 3426 | 5315 | 2 | chr6D.!!$F1 | 1889 |
6 | TraesCS6A01G091100 | chr6D | 44736206 | 44738115 | 1909 | False | 843.700000 | 1629 | 84.564500 | 3426 | 5315 | 2 | chr6D.!!$F2 | 1889 |
7 | TraesCS6A01G091100 | chr6D | 45478087 | 45482150 | 4063 | False | 514.340000 | 1356 | 88.546000 | 991 | 5695 | 5 | chr6D.!!$F4 | 4704 |
8 | TraesCS6A01G091100 | chr6B | 113771078 | 113772428 | 1350 | False | 1365.000000 | 1365 | 85.210000 | 3727 | 5060 | 1 | chr6B.!!$F2 | 1333 |
9 | TraesCS6A01G091100 | chr6B | 113843464 | 113850229 | 6765 | False | 986.500000 | 4202 | 93.046667 | 511 | 6033 | 6 | chr6B.!!$F5 | 5522 |
10 | TraesCS6A01G091100 | chr6B | 113780910 | 113785320 | 4410 | False | 974.333333 | 2278 | 86.298667 | 937 | 6035 | 3 | chr6B.!!$F4 | 5098 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
424 | 425 | 0.038159 | GGAGCATAGCGAGCCGTAAT | 60.038 | 55.000 | 0.0 | 0.0 | 0.00 | 1.89 | F |
1720 | 5461 | 0.249868 | TATATGTGCCGCTGCCTGTC | 60.250 | 55.000 | 0.0 | 0.0 | 36.33 | 3.51 | F |
2126 | 6079 | 0.171455 | GTGCTGACGTGTAGAGGAGG | 59.829 | 60.000 | 0.0 | 0.0 | 0.00 | 4.30 | F |
2830 | 7250 | 0.734253 | CGTGGCTTGGAAGTCTCTCG | 60.734 | 60.000 | 0.0 | 0.0 | 0.00 | 4.04 | F |
3099 | 8590 | 1.067582 | GTAGGGATTGACTCGGGCG | 59.932 | 63.158 | 0.0 | 0.0 | 0.00 | 6.13 | F |
3258 | 8749 | 1.068055 | GTTTTGCTGCACTCCCATCAG | 60.068 | 52.381 | 0.0 | 0.0 | 0.00 | 2.90 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1767 | 5508 | 0.179065 | GTAATTCCGAACGGAGGGGG | 60.179 | 60.000 | 15.34 | 0.00 | 46.06 | 5.40 | R |
2876 | 7944 | 0.539986 | TCGAAAGAAATCTCCCGGGG | 59.460 | 55.000 | 23.50 | 12.05 | 37.03 | 5.73 | R |
3238 | 8729 | 0.961019 | TGATGGGAGTGCAGCAAAAC | 59.039 | 50.000 | 0.00 | 0.00 | 0.00 | 2.43 | R |
4631 | 10516 | 4.500603 | AGATTTGCTGCAAAGACTCAAG | 57.499 | 40.909 | 28.86 | 0.00 | 36.76 | 3.02 | R |
4684 | 10569 | 6.258507 | TCATGACATTTGTTATCCTCATGTCG | 59.741 | 38.462 | 0.00 | 0.00 | 39.59 | 4.35 | R |
5256 | 11145 | 2.303022 | ACTTCATCCGGTGACATCAAGT | 59.697 | 45.455 | 0.00 | 2.23 | 36.32 | 3.16 | 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.