Multiple sequence alignment - TraesCS6D01G059900
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 | TraesCS6D01G059900 | chr6D | 100.000 | 2357 | 0 | 0 | 1 | 2357 | 28035668 | 28033312 | 0.000000e+00 | 4353 |
1 | TraesCS6D01G059900 | chr6D | 94.726 | 474 | 24 | 1 | 155 | 627 | 435992569 | 435992096 | 0.000000e+00 | 736 |
2 | TraesCS6D01G059900 | chr6D | 96.620 | 355 | 12 | 0 | 2002 | 2356 | 435992066 | 435991712 | 7.260000e-165 | 590 |
3 | TraesCS6D01G059900 | chr6D | 93.388 | 121 | 4 | 1 | 2037 | 2153 | 9156178 | 9156298 | 2.410000e-40 | 176 |
4 | TraesCS6D01G059900 | chr2D | 96.649 | 1343 | 43 | 2 | 627 | 1967 | 73126872 | 73125530 | 0.000000e+00 | 2230 |
5 | TraesCS6D01G059900 | chr2D | 95.926 | 1350 | 49 | 6 | 624 | 1970 | 621748800 | 621750146 | 0.000000e+00 | 2183 |
6 | TraesCS6D01G059900 | chr2D | 96.901 | 355 | 11 | 0 | 2002 | 2356 | 113496227 | 113495873 | 1.560000e-166 | 595 |
7 | TraesCS6D01G059900 | chr1D | 96.511 | 1347 | 43 | 4 | 627 | 1970 | 60171816 | 60170471 | 0.000000e+00 | 2224 |
8 | TraesCS6D01G059900 | chr1D | 95.697 | 1348 | 52 | 6 | 627 | 1970 | 247505758 | 247504413 | 0.000000e+00 | 2163 |
9 | TraesCS6D01G059900 | chr1D | 95.818 | 1339 | 49 | 7 | 626 | 1962 | 205134698 | 205133365 | 0.000000e+00 | 2156 |
10 | TraesCS6D01G059900 | chr3D | 95.991 | 1347 | 51 | 3 | 623 | 1966 | 584701397 | 584700051 | 0.000000e+00 | 2185 |
11 | TraesCS6D01G059900 | chr7D | 95.979 | 1343 | 50 | 4 | 623 | 1963 | 497560903 | 497562243 | 0.000000e+00 | 2178 |
12 | TraesCS6D01G059900 | chr7D | 95.775 | 1349 | 54 | 3 | 627 | 1972 | 50081832 | 50080484 | 0.000000e+00 | 2172 |
13 | TraesCS6D01G059900 | chr7D | 85.684 | 475 | 49 | 10 | 155 | 627 | 375971251 | 375970794 | 1.270000e-132 | 483 |
14 | TraesCS6D01G059900 | chr5D | 95.899 | 1341 | 52 | 3 | 626 | 1964 | 275171749 | 275170410 | 0.000000e+00 | 2169 |
15 | TraesCS6D01G059900 | chr4D | 95.570 | 474 | 20 | 1 | 155 | 627 | 36620511 | 36620038 | 0.000000e+00 | 758 |
16 | TraesCS6D01G059900 | chr4D | 95.359 | 474 | 21 | 1 | 155 | 627 | 416829170 | 416828697 | 0.000000e+00 | 752 |
17 | TraesCS6D01G059900 | chr4D | 96.620 | 355 | 12 | 0 | 2002 | 2356 | 36620008 | 36619654 | 7.260000e-165 | 590 |
18 | TraesCS6D01G059900 | chr4D | 96.848 | 349 | 10 | 1 | 2008 | 2356 | 416828661 | 416828314 | 1.210000e-162 | 582 |
19 | TraesCS6D01G059900 | chr7A | 95.148 | 474 | 20 | 2 | 155 | 627 | 612424512 | 612424041 | 0.000000e+00 | 745 |
20 | TraesCS6D01G059900 | chr7A | 97.183 | 355 | 10 | 0 | 2002 | 2356 | 612424011 | 612423657 | 3.350000e-168 | 601 |
21 | TraesCS6D01G059900 | chr7A | 87.282 | 401 | 47 | 4 | 155 | 553 | 422476917 | 422476519 | 2.760000e-124 | 455 |
22 | TraesCS6D01G059900 | chr7B | 94.515 | 474 | 18 | 2 | 155 | 627 | 665305087 | 665304621 | 0.000000e+00 | 725 |
23 | TraesCS6D01G059900 | chr7B | 97.746 | 355 | 8 | 0 | 2002 | 2356 | 665304591 | 665304237 | 1.550000e-171 | 612 |
24 | TraesCS6D01G059900 | chr7B | 88.529 | 401 | 42 | 4 | 155 | 553 | 370264861 | 370264463 | 1.270000e-132 | 483 |
25 | TraesCS6D01G059900 | chr4B | 94.816 | 463 | 23 | 1 | 166 | 627 | 399068605 | 399069067 | 0.000000e+00 | 721 |
26 | TraesCS6D01G059900 | chr4B | 95.493 | 355 | 14 | 2 | 2002 | 2356 | 399069097 | 399069449 | 1.220000e-157 | 566 |
27 | TraesCS6D01G059900 | chr6B | 94.872 | 117 | 6 | 0 | 2037 | 2153 | 16984056 | 16984172 | 1.440000e-42 | 183 |
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 | TraesCS6D01G059900 | chr6D | 28033312 | 28035668 | 2356 | True | 4353.0 | 4353 | 100.0000 | 1 | 2357 | 1 | chr6D.!!$R1 | 2356 |
1 | TraesCS6D01G059900 | chr6D | 435991712 | 435992569 | 857 | True | 663.0 | 736 | 95.6730 | 155 | 2356 | 2 | chr6D.!!$R2 | 2201 |
2 | TraesCS6D01G059900 | chr2D | 73125530 | 73126872 | 1342 | True | 2230.0 | 2230 | 96.6490 | 627 | 1967 | 1 | chr2D.!!$R1 | 1340 |
3 | TraesCS6D01G059900 | chr2D | 621748800 | 621750146 | 1346 | False | 2183.0 | 2183 | 95.9260 | 624 | 1970 | 1 | chr2D.!!$F1 | 1346 |
4 | TraesCS6D01G059900 | chr1D | 60170471 | 60171816 | 1345 | True | 2224.0 | 2224 | 96.5110 | 627 | 1970 | 1 | chr1D.!!$R1 | 1343 |
5 | TraesCS6D01G059900 | chr1D | 247504413 | 247505758 | 1345 | True | 2163.0 | 2163 | 95.6970 | 627 | 1970 | 1 | chr1D.!!$R3 | 1343 |
6 | TraesCS6D01G059900 | chr1D | 205133365 | 205134698 | 1333 | True | 2156.0 | 2156 | 95.8180 | 626 | 1962 | 1 | chr1D.!!$R2 | 1336 |
7 | TraesCS6D01G059900 | chr3D | 584700051 | 584701397 | 1346 | True | 2185.0 | 2185 | 95.9910 | 623 | 1966 | 1 | chr3D.!!$R1 | 1343 |
8 | TraesCS6D01G059900 | chr7D | 497560903 | 497562243 | 1340 | False | 2178.0 | 2178 | 95.9790 | 623 | 1963 | 1 | chr7D.!!$F1 | 1340 |
9 | TraesCS6D01G059900 | chr7D | 50080484 | 50081832 | 1348 | True | 2172.0 | 2172 | 95.7750 | 627 | 1972 | 1 | chr7D.!!$R1 | 1345 |
10 | TraesCS6D01G059900 | chr5D | 275170410 | 275171749 | 1339 | True | 2169.0 | 2169 | 95.8990 | 626 | 1964 | 1 | chr5D.!!$R1 | 1338 |
11 | TraesCS6D01G059900 | chr4D | 36619654 | 36620511 | 857 | True | 674.0 | 758 | 96.0950 | 155 | 2356 | 2 | chr4D.!!$R1 | 2201 |
12 | TraesCS6D01G059900 | chr4D | 416828314 | 416829170 | 856 | True | 667.0 | 752 | 96.1035 | 155 | 2356 | 2 | chr4D.!!$R2 | 2201 |
13 | TraesCS6D01G059900 | chr7A | 612423657 | 612424512 | 855 | True | 673.0 | 745 | 96.1655 | 155 | 2356 | 2 | chr7A.!!$R2 | 2201 |
14 | TraesCS6D01G059900 | chr7B | 665304237 | 665305087 | 850 | True | 668.5 | 725 | 96.1305 | 155 | 2356 | 2 | chr7B.!!$R2 | 2201 |
15 | TraesCS6D01G059900 | chr4B | 399068605 | 399069449 | 844 | False | 643.5 | 721 | 95.1545 | 166 | 2356 | 2 | chr4B.!!$F1 | 2190 |
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. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
688 | 690 | 0.031585 | GACGATGCATACGGCCACTA | 59.968 | 55.0 | 18.34 | 0.0 | 43.89 | 2.74 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1973 | 1985 | 1.549203 | AACATTCACATGGGTCAGCC | 58.451 | 50.0 | 0.0 | 0.0 | 34.27 | 4.85 | 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. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
24 | 25 | 4.854361 | CACTGATGAGTAATGAGTGCAC | 57.146 | 45.455 | 9.40 | 9.40 | 42.48 | 4.57 |
25 | 26 | 4.502016 | CACTGATGAGTAATGAGTGCACT | 58.498 | 43.478 | 21.88 | 21.88 | 42.48 | 4.40 |
26 | 27 | 4.565962 | CACTGATGAGTAATGAGTGCACTC | 59.434 | 45.833 | 35.04 | 35.04 | 42.48 | 3.51 |
27 | 28 | 4.465660 | ACTGATGAGTAATGAGTGCACTCT | 59.534 | 41.667 | 38.81 | 26.30 | 43.25 | 3.24 |
28 | 29 | 5.654209 | ACTGATGAGTAATGAGTGCACTCTA | 59.346 | 40.000 | 38.81 | 27.86 | 43.25 | 2.43 |
29 | 30 | 5.895928 | TGATGAGTAATGAGTGCACTCTAC | 58.104 | 41.667 | 38.81 | 32.39 | 43.25 | 2.59 |
30 | 31 | 5.418840 | TGATGAGTAATGAGTGCACTCTACA | 59.581 | 40.000 | 38.81 | 28.13 | 43.25 | 2.74 |
31 | 32 | 5.722021 | TGAGTAATGAGTGCACTCTACAA | 57.278 | 39.130 | 38.81 | 24.27 | 43.25 | 2.41 |
32 | 33 | 5.714047 | TGAGTAATGAGTGCACTCTACAAG | 58.286 | 41.667 | 38.81 | 0.00 | 43.25 | 3.16 |
33 | 34 | 5.078411 | AGTAATGAGTGCACTCTACAAGG | 57.922 | 43.478 | 38.81 | 0.00 | 43.25 | 3.61 |
34 | 35 | 4.528596 | AGTAATGAGTGCACTCTACAAGGT | 59.471 | 41.667 | 38.81 | 19.44 | 43.25 | 3.50 |
35 | 36 | 4.357918 | AATGAGTGCACTCTACAAGGTT | 57.642 | 40.909 | 38.81 | 21.71 | 43.25 | 3.50 |
36 | 37 | 5.483685 | AATGAGTGCACTCTACAAGGTTA | 57.516 | 39.130 | 38.81 | 21.25 | 43.25 | 2.85 |
37 | 38 | 4.521130 | TGAGTGCACTCTACAAGGTTAG | 57.479 | 45.455 | 38.81 | 0.00 | 43.25 | 2.34 |
38 | 39 | 3.254892 | GAGTGCACTCTACAAGGTTAGC | 58.745 | 50.000 | 34.54 | 8.49 | 39.81 | 3.09 |
39 | 40 | 2.028020 | AGTGCACTCTACAAGGTTAGCC | 60.028 | 50.000 | 15.25 | 0.00 | 0.00 | 3.93 |
40 | 41 | 1.278127 | TGCACTCTACAAGGTTAGCCC | 59.722 | 52.381 | 0.00 | 0.00 | 34.57 | 5.19 |
42 | 43 | 2.764572 | GCACTCTACAAGGTTAGCCCTA | 59.235 | 50.000 | 0.00 | 0.00 | 45.47 | 3.53 |
43 | 44 | 3.430513 | GCACTCTACAAGGTTAGCCCTAC | 60.431 | 52.174 | 0.00 | 0.00 | 45.47 | 3.18 |
44 | 45 | 4.024670 | CACTCTACAAGGTTAGCCCTACT | 58.975 | 47.826 | 0.00 | 0.00 | 45.47 | 2.57 |
45 | 46 | 4.024670 | ACTCTACAAGGTTAGCCCTACTG | 58.975 | 47.826 | 0.00 | 0.00 | 45.47 | 2.74 |
46 | 47 | 2.764572 | TCTACAAGGTTAGCCCTACTGC | 59.235 | 50.000 | 0.00 | 0.00 | 45.47 | 4.40 |
47 | 48 | 0.618981 | ACAAGGTTAGCCCTACTGCC | 59.381 | 55.000 | 0.00 | 0.00 | 45.47 | 4.85 |
48 | 49 | 0.618458 | CAAGGTTAGCCCTACTGCCA | 59.382 | 55.000 | 0.00 | 0.00 | 45.47 | 4.92 |
49 | 50 | 1.212935 | CAAGGTTAGCCCTACTGCCAT | 59.787 | 52.381 | 0.00 | 0.00 | 45.47 | 4.40 |
50 | 51 | 1.596496 | AGGTTAGCCCTACTGCCATT | 58.404 | 50.000 | 0.00 | 0.00 | 43.87 | 3.16 |
51 | 52 | 1.212935 | AGGTTAGCCCTACTGCCATTG | 59.787 | 52.381 | 0.00 | 0.00 | 43.87 | 2.82 |
52 | 53 | 1.680338 | GTTAGCCCTACTGCCATTGG | 58.320 | 55.000 | 0.00 | 0.00 | 0.00 | 3.16 |
53 | 54 | 1.064685 | GTTAGCCCTACTGCCATTGGT | 60.065 | 52.381 | 4.26 | 0.00 | 0.00 | 3.67 |
54 | 55 | 2.171870 | GTTAGCCCTACTGCCATTGGTA | 59.828 | 50.000 | 4.26 | 0.00 | 0.00 | 3.25 |
55 | 56 | 0.546598 | AGCCCTACTGCCATTGGTAC | 59.453 | 55.000 | 4.26 | 0.00 | 0.00 | 3.34 |
56 | 57 | 0.546598 | GCCCTACTGCCATTGGTACT | 59.453 | 55.000 | 4.26 | 0.00 | 0.00 | 2.73 |
57 | 58 | 1.747206 | GCCCTACTGCCATTGGTACTG | 60.747 | 57.143 | 4.26 | 0.00 | 0.00 | 2.74 |
58 | 59 | 1.837439 | CCCTACTGCCATTGGTACTGA | 59.163 | 52.381 | 4.26 | 0.00 | 0.00 | 3.41 |
59 | 60 | 2.238646 | CCCTACTGCCATTGGTACTGAA | 59.761 | 50.000 | 4.26 | 0.00 | 0.00 | 3.02 |
60 | 61 | 3.270877 | CCTACTGCCATTGGTACTGAAC | 58.729 | 50.000 | 4.26 | 0.00 | 0.00 | 3.18 |
61 | 62 | 3.055094 | CCTACTGCCATTGGTACTGAACT | 60.055 | 47.826 | 4.26 | 0.00 | 0.00 | 3.01 |
62 | 63 | 4.161565 | CCTACTGCCATTGGTACTGAACTA | 59.838 | 45.833 | 4.26 | 0.00 | 0.00 | 2.24 |
63 | 64 | 3.939066 | ACTGCCATTGGTACTGAACTAC | 58.061 | 45.455 | 4.26 | 0.00 | 0.00 | 2.73 |
64 | 65 | 3.583086 | ACTGCCATTGGTACTGAACTACT | 59.417 | 43.478 | 4.26 | 0.00 | 0.00 | 2.57 |
65 | 66 | 3.935203 | CTGCCATTGGTACTGAACTACTG | 59.065 | 47.826 | 4.26 | 0.00 | 0.00 | 2.74 |
66 | 67 | 3.580895 | TGCCATTGGTACTGAACTACTGA | 59.419 | 43.478 | 4.26 | 0.00 | 0.00 | 3.41 |
67 | 68 | 3.933332 | GCCATTGGTACTGAACTACTGAC | 59.067 | 47.826 | 4.26 | 0.00 | 0.00 | 3.51 |
68 | 69 | 4.562757 | GCCATTGGTACTGAACTACTGACA | 60.563 | 45.833 | 4.26 | 0.00 | 0.00 | 3.58 |
69 | 70 | 5.547465 | CCATTGGTACTGAACTACTGACAA | 58.453 | 41.667 | 0.00 | 0.00 | 0.00 | 3.18 |
70 | 71 | 6.173339 | CCATTGGTACTGAACTACTGACAAT | 58.827 | 40.000 | 0.00 | 0.00 | 0.00 | 2.71 |
71 | 72 | 6.655003 | CCATTGGTACTGAACTACTGACAATT | 59.345 | 38.462 | 0.00 | 0.00 | 0.00 | 2.32 |
72 | 73 | 7.822334 | CCATTGGTACTGAACTACTGACAATTA | 59.178 | 37.037 | 0.00 | 0.00 | 0.00 | 1.40 |
73 | 74 | 9.383519 | CATTGGTACTGAACTACTGACAATTAT | 57.616 | 33.333 | 0.00 | 0.00 | 0.00 | 1.28 |
74 | 75 | 8.997621 | TTGGTACTGAACTACTGACAATTATC | 57.002 | 34.615 | 0.00 | 0.00 | 0.00 | 1.75 |
75 | 76 | 8.362464 | TGGTACTGAACTACTGACAATTATCT | 57.638 | 34.615 | 0.00 | 0.00 | 0.00 | 1.98 |
76 | 77 | 8.812972 | TGGTACTGAACTACTGACAATTATCTT | 58.187 | 33.333 | 0.00 | 0.00 | 0.00 | 2.40 |
77 | 78 | 9.654663 | GGTACTGAACTACTGACAATTATCTTT | 57.345 | 33.333 | 0.00 | 0.00 | 0.00 | 2.52 |
80 | 81 | 9.372369 | ACTGAACTACTGACAATTATCTTTAGC | 57.628 | 33.333 | 0.00 | 0.00 | 0.00 | 3.09 |
81 | 82 | 9.593134 | CTGAACTACTGACAATTATCTTTAGCT | 57.407 | 33.333 | 0.00 | 0.00 | 0.00 | 3.32 |
108 | 109 | 7.776618 | TTCTCTTTTATCTATAGCATCCCGA | 57.223 | 36.000 | 0.00 | 0.00 | 0.00 | 5.14 |
109 | 110 | 7.776618 | TCTCTTTTATCTATAGCATCCCGAA | 57.223 | 36.000 | 0.00 | 0.00 | 0.00 | 4.30 |
110 | 111 | 7.831753 | TCTCTTTTATCTATAGCATCCCGAAG | 58.168 | 38.462 | 0.00 | 0.00 | 0.00 | 3.79 |
131 | 132 | 8.459521 | CGAAGGTGACAAAATTTTATATTGCA | 57.540 | 30.769 | 2.44 | 0.00 | 0.00 | 4.08 |
132 | 133 | 9.086336 | CGAAGGTGACAAAATTTTATATTGCAT | 57.914 | 29.630 | 2.44 | 0.00 | 0.00 | 3.96 |
134 | 135 | 8.721019 | AGGTGACAAAATTTTATATTGCATGG | 57.279 | 30.769 | 2.44 | 0.00 | 0.00 | 3.66 |
135 | 136 | 8.320617 | AGGTGACAAAATTTTATATTGCATGGT | 58.679 | 29.630 | 2.44 | 0.00 | 0.00 | 3.55 |
136 | 137 | 8.945057 | GGTGACAAAATTTTATATTGCATGGTT | 58.055 | 29.630 | 2.44 | 0.00 | 0.00 | 3.67 |
137 | 138 | 9.757859 | GTGACAAAATTTTATATTGCATGGTTG | 57.242 | 29.630 | 2.44 | 0.00 | 0.00 | 3.77 |
138 | 139 | 9.499479 | TGACAAAATTTTATATTGCATGGTTGT | 57.501 | 25.926 | 2.44 | 0.00 | 0.00 | 3.32 |
151 | 152 | 8.907222 | ATTGCATGGTTGTAAATTTCTCTTTT | 57.093 | 26.923 | 0.00 | 0.00 | 30.96 | 2.27 |
152 | 153 | 7.712264 | TGCATGGTTGTAAATTTCTCTTTTG | 57.288 | 32.000 | 0.00 | 0.00 | 0.00 | 2.44 |
153 | 154 | 7.271511 | TGCATGGTTGTAAATTTCTCTTTTGT | 58.728 | 30.769 | 0.00 | 0.00 | 0.00 | 2.83 |
243 | 244 | 4.463891 | ACATATTTTCTCCCACAAAGGCAG | 59.536 | 41.667 | 0.00 | 0.00 | 35.39 | 4.85 |
244 | 245 | 1.039856 | TTTTCTCCCACAAAGGCAGC | 58.960 | 50.000 | 0.00 | 0.00 | 35.39 | 5.25 |
287 | 288 | 1.000955 | GATGACCGTGTCTCTGTGGTT | 59.999 | 52.381 | 5.77 | 0.00 | 34.12 | 3.67 |
297 | 298 | 0.397941 | CTCTGTGGTTGAGGCCTTGA | 59.602 | 55.000 | 6.77 | 0.00 | 0.00 | 3.02 |
307 | 308 | 1.704628 | TGAGGCCTTGATCTTGGTCAA | 59.295 | 47.619 | 6.77 | 0.00 | 36.70 | 3.18 |
327 | 328 | 2.622436 | AGAGTGTTTATTCGCTCAGGC | 58.378 | 47.619 | 9.37 | 0.00 | 44.43 | 4.85 |
350 | 351 | 5.106277 | GCCGCTTAGTGGAAGAATAACTTTT | 60.106 | 40.000 | 16.92 | 0.00 | 39.13 | 2.27 |
373 | 374 | 6.486253 | TGTGCAGAGTGACATTTCTATTTC | 57.514 | 37.500 | 0.00 | 0.00 | 0.00 | 2.17 |
393 | 394 | 6.567687 | TTTCGACTGCAAGGAATCAAAATA | 57.432 | 33.333 | 0.00 | 0.00 | 39.30 | 1.40 |
454 | 456 | 9.281371 | CAGGATTGAGAATAGATTATGCTTTCA | 57.719 | 33.333 | 0.00 | 0.00 | 0.00 | 2.69 |
544 | 546 | 8.607713 | TCCAGTAGATACCATTTTTGAGGTAAA | 58.392 | 33.333 | 0.00 | 0.00 | 43.14 | 2.01 |
593 | 595 | 3.485877 | GCATATTCTTTGAGACCGTGCAC | 60.486 | 47.826 | 6.82 | 6.82 | 30.17 | 4.57 |
688 | 690 | 0.031585 | GACGATGCATACGGCCACTA | 59.968 | 55.000 | 18.34 | 0.00 | 43.89 | 2.74 |
802 | 804 | 1.725641 | TGATGCAGTGGTGTCGAATC | 58.274 | 50.000 | 0.00 | 0.00 | 0.00 | 2.52 |
951 | 953 | 1.696336 | CTTCCACCGATCCATCTCCAT | 59.304 | 52.381 | 0.00 | 0.00 | 0.00 | 3.41 |
1031 | 1033 | 4.379243 | CTCGACCACCCTGCGCTT | 62.379 | 66.667 | 9.73 | 0.00 | 0.00 | 4.68 |
1048 | 1050 | 1.001020 | TTGTCCATCCAGCCGCATT | 60.001 | 52.632 | 0.00 | 0.00 | 0.00 | 3.56 |
1112 | 1114 | 4.049186 | GTCAATGACGCGGTAGATACAAT | 58.951 | 43.478 | 12.47 | 0.00 | 0.00 | 2.71 |
1136 | 1138 | 2.162906 | ACCACCTGGCAACCTCCAT | 61.163 | 57.895 | 0.00 | 0.00 | 39.32 | 3.41 |
1149 | 1151 | 1.338107 | CCTCCATACCATCGCCACTA | 58.662 | 55.000 | 0.00 | 0.00 | 0.00 | 2.74 |
1309 | 1311 | 1.229853 | AGGGGTTCGAGGGTGGATT | 60.230 | 57.895 | 0.00 | 0.00 | 0.00 | 3.01 |
1369 | 1372 | 1.086067 | CAAGTGACATCGCCGATGCT | 61.086 | 55.000 | 25.90 | 12.87 | 43.15 | 3.79 |
1380 | 1383 | 2.514592 | CGATGCTGGGCCGAACAT | 60.515 | 61.111 | 2.96 | 2.96 | 0.00 | 2.71 |
1401 | 1404 | 0.250166 | CCGACCAAAGTTTCCTCCGT | 60.250 | 55.000 | 0.00 | 0.00 | 0.00 | 4.69 |
1991 | 2003 | 3.271250 | GGCTGACCCATGTGAATGT | 57.729 | 52.632 | 0.00 | 0.00 | 0.00 | 2.71 |
1992 | 2004 | 1.549203 | GGCTGACCCATGTGAATGTT | 58.451 | 50.000 | 0.00 | 0.00 | 0.00 | 2.71 |
1993 | 2005 | 2.722094 | GGCTGACCCATGTGAATGTTA | 58.278 | 47.619 | 0.00 | 0.00 | 0.00 | 2.41 |
1994 | 2006 | 3.290710 | GGCTGACCCATGTGAATGTTAT | 58.709 | 45.455 | 0.00 | 0.00 | 0.00 | 1.89 |
1995 | 2007 | 3.316308 | GGCTGACCCATGTGAATGTTATC | 59.684 | 47.826 | 0.00 | 0.00 | 0.00 | 1.75 |
1996 | 2008 | 3.947196 | GCTGACCCATGTGAATGTTATCA | 59.053 | 43.478 | 0.00 | 0.00 | 0.00 | 2.15 |
1997 | 2009 | 4.581824 | GCTGACCCATGTGAATGTTATCAT | 59.418 | 41.667 | 0.00 | 0.00 | 35.59 | 2.45 |
1998 | 2010 | 5.764686 | GCTGACCCATGTGAATGTTATCATA | 59.235 | 40.000 | 0.00 | 0.00 | 33.49 | 2.15 |
1999 | 2011 | 6.432162 | GCTGACCCATGTGAATGTTATCATAT | 59.568 | 38.462 | 0.00 | 0.00 | 32.13 | 1.78 |
2000 | 2012 | 7.607607 | GCTGACCCATGTGAATGTTATCATATA | 59.392 | 37.037 | 0.00 | 0.00 | 30.99 | 0.86 |
2091 | 2103 | 7.982354 | AGCCTACTAATTAGCTAGAACAAGTTG | 59.018 | 37.037 | 12.54 | 0.00 | 0.00 | 3.16 |
2156 | 2168 | 5.692115 | TTGTTGATATTCAGTCCTAGCCA | 57.308 | 39.130 | 0.00 | 0.00 | 0.00 | 4.75 |
2165 | 2177 | 2.438021 | TCAGTCCTAGCCACACAAAACT | 59.562 | 45.455 | 0.00 | 0.00 | 0.00 | 2.66 |
2332 | 2344 | 9.881529 | TTTTTACCTTAACAAGTTACATTAGCG | 57.118 | 29.630 | 0.00 | 0.00 | 0.00 | 4.26 |
2356 | 2368 | 6.140737 | CGATGTGTAAAAGTTTGTCAAAGCTC | 59.859 | 38.462 | 0.00 | 0.00 | 0.00 | 4.09 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
1 | 2 | 4.692625 | GTGCACTCATTACTCATCAGTGTT | 59.307 | 41.667 | 10.32 | 0.00 | 36.38 | 3.32 |
5 | 6 | 5.008619 | AGAGTGCACTCATTACTCATCAG | 57.991 | 43.478 | 40.25 | 0.00 | 45.21 | 2.90 |
6 | 7 | 5.418840 | TGTAGAGTGCACTCATTACTCATCA | 59.581 | 40.000 | 40.25 | 23.33 | 45.21 | 3.07 |
7 | 8 | 5.895928 | TGTAGAGTGCACTCATTACTCATC | 58.104 | 41.667 | 40.25 | 21.56 | 45.21 | 2.92 |
8 | 9 | 5.921962 | TGTAGAGTGCACTCATTACTCAT | 57.078 | 39.130 | 40.25 | 23.67 | 45.21 | 2.90 |
9 | 10 | 5.336770 | CCTTGTAGAGTGCACTCATTACTCA | 60.337 | 44.000 | 40.25 | 26.51 | 45.21 | 3.41 |
10 | 11 | 5.105752 | CCTTGTAGAGTGCACTCATTACTC | 58.894 | 45.833 | 40.25 | 24.75 | 45.21 | 2.59 |
11 | 12 | 4.528596 | ACCTTGTAGAGTGCACTCATTACT | 59.471 | 41.667 | 40.25 | 25.63 | 45.21 | 2.24 |
12 | 13 | 4.822026 | ACCTTGTAGAGTGCACTCATTAC | 58.178 | 43.478 | 40.25 | 33.11 | 45.21 | 1.89 |
13 | 14 | 5.483685 | AACCTTGTAGAGTGCACTCATTA | 57.516 | 39.130 | 40.25 | 25.96 | 45.21 | 1.90 |
14 | 15 | 4.357918 | AACCTTGTAGAGTGCACTCATT | 57.642 | 40.909 | 40.25 | 26.95 | 45.21 | 2.57 |
15 | 16 | 4.621747 | GCTAACCTTGTAGAGTGCACTCAT | 60.622 | 45.833 | 40.25 | 28.70 | 45.21 | 2.90 |
16 | 17 | 3.306088 | GCTAACCTTGTAGAGTGCACTCA | 60.306 | 47.826 | 40.25 | 26.48 | 45.21 | 3.41 |
17 | 18 | 3.254892 | GCTAACCTTGTAGAGTGCACTC | 58.745 | 50.000 | 34.82 | 34.82 | 43.17 | 3.51 |
18 | 19 | 2.028020 | GGCTAACCTTGTAGAGTGCACT | 60.028 | 50.000 | 21.88 | 21.88 | 0.00 | 4.40 |
19 | 20 | 2.347731 | GGCTAACCTTGTAGAGTGCAC | 58.652 | 52.381 | 9.40 | 9.40 | 0.00 | 4.57 |
20 | 21 | 1.278127 | GGGCTAACCTTGTAGAGTGCA | 59.722 | 52.381 | 0.00 | 0.00 | 35.85 | 4.57 |
21 | 22 | 2.025589 | GGGCTAACCTTGTAGAGTGC | 57.974 | 55.000 | 0.00 | 0.00 | 35.85 | 4.40 |
32 | 33 | 1.680338 | CAATGGCAGTAGGGCTAACC | 58.320 | 55.000 | 0.00 | 0.00 | 43.83 | 2.85 |
33 | 34 | 1.064685 | ACCAATGGCAGTAGGGCTAAC | 60.065 | 52.381 | 0.00 | 0.00 | 43.83 | 2.34 |
34 | 35 | 1.295020 | ACCAATGGCAGTAGGGCTAA | 58.705 | 50.000 | 0.00 | 0.00 | 43.83 | 3.09 |
35 | 36 | 1.766496 | GTACCAATGGCAGTAGGGCTA | 59.234 | 52.381 | 0.00 | 0.00 | 43.83 | 3.93 |
36 | 37 | 0.546598 | GTACCAATGGCAGTAGGGCT | 59.453 | 55.000 | 0.00 | 0.00 | 43.83 | 5.19 |
37 | 38 | 0.546598 | AGTACCAATGGCAGTAGGGC | 59.453 | 55.000 | 0.00 | 0.00 | 43.73 | 5.19 |
38 | 39 | 1.837439 | TCAGTACCAATGGCAGTAGGG | 59.163 | 52.381 | 0.00 | 0.00 | 0.00 | 3.53 |
39 | 40 | 3.055094 | AGTTCAGTACCAATGGCAGTAGG | 60.055 | 47.826 | 0.00 | 0.00 | 0.00 | 3.18 |
40 | 41 | 4.207891 | AGTTCAGTACCAATGGCAGTAG | 57.792 | 45.455 | 0.00 | 0.00 | 0.00 | 2.57 |
41 | 42 | 4.775780 | AGTAGTTCAGTACCAATGGCAGTA | 59.224 | 41.667 | 0.00 | 0.00 | 0.00 | 2.74 |
42 | 43 | 3.583086 | AGTAGTTCAGTACCAATGGCAGT | 59.417 | 43.478 | 0.00 | 0.00 | 0.00 | 4.40 |
43 | 44 | 3.935203 | CAGTAGTTCAGTACCAATGGCAG | 59.065 | 47.826 | 0.00 | 0.00 | 0.00 | 4.85 |
44 | 45 | 3.580895 | TCAGTAGTTCAGTACCAATGGCA | 59.419 | 43.478 | 0.00 | 0.00 | 0.00 | 4.92 |
45 | 46 | 3.933332 | GTCAGTAGTTCAGTACCAATGGC | 59.067 | 47.826 | 0.00 | 0.00 | 0.00 | 4.40 |
46 | 47 | 5.147330 | TGTCAGTAGTTCAGTACCAATGG | 57.853 | 43.478 | 0.00 | 0.00 | 0.00 | 3.16 |
47 | 48 | 7.672983 | AATTGTCAGTAGTTCAGTACCAATG | 57.327 | 36.000 | 0.00 | 0.00 | 0.00 | 2.82 |
48 | 49 | 9.601217 | GATAATTGTCAGTAGTTCAGTACCAAT | 57.399 | 33.333 | 0.00 | 0.00 | 0.00 | 3.16 |
49 | 50 | 8.812972 | AGATAATTGTCAGTAGTTCAGTACCAA | 58.187 | 33.333 | 4.92 | 0.00 | 0.00 | 3.67 |
50 | 51 | 8.362464 | AGATAATTGTCAGTAGTTCAGTACCA | 57.638 | 34.615 | 4.92 | 0.00 | 0.00 | 3.25 |
51 | 52 | 9.654663 | AAAGATAATTGTCAGTAGTTCAGTACC | 57.345 | 33.333 | 4.92 | 0.00 | 0.00 | 3.34 |
54 | 55 | 9.372369 | GCTAAAGATAATTGTCAGTAGTTCAGT | 57.628 | 33.333 | 4.92 | 0.00 | 0.00 | 3.41 |
55 | 56 | 9.593134 | AGCTAAAGATAATTGTCAGTAGTTCAG | 57.407 | 33.333 | 4.92 | 0.00 | 0.00 | 3.02 |
82 | 83 | 8.816894 | TCGGGATGCTATAGATAAAAGAGAAAT | 58.183 | 33.333 | 3.21 | 0.00 | 0.00 | 2.17 |
83 | 84 | 8.190326 | TCGGGATGCTATAGATAAAAGAGAAA | 57.810 | 34.615 | 3.21 | 0.00 | 0.00 | 2.52 |
84 | 85 | 7.776618 | TCGGGATGCTATAGATAAAAGAGAA | 57.223 | 36.000 | 3.21 | 0.00 | 0.00 | 2.87 |
85 | 86 | 7.093727 | CCTTCGGGATGCTATAGATAAAAGAGA | 60.094 | 40.741 | 3.21 | 0.00 | 37.25 | 3.10 |
86 | 87 | 7.038659 | CCTTCGGGATGCTATAGATAAAAGAG | 58.961 | 42.308 | 3.21 | 0.00 | 37.25 | 2.85 |
87 | 88 | 6.497259 | ACCTTCGGGATGCTATAGATAAAAGA | 59.503 | 38.462 | 3.21 | 0.00 | 38.77 | 2.52 |
88 | 89 | 6.591834 | CACCTTCGGGATGCTATAGATAAAAG | 59.408 | 42.308 | 3.21 | 0.00 | 38.77 | 2.27 |
89 | 90 | 6.269077 | TCACCTTCGGGATGCTATAGATAAAA | 59.731 | 38.462 | 3.21 | 0.00 | 38.77 | 1.52 |
90 | 91 | 5.778241 | TCACCTTCGGGATGCTATAGATAAA | 59.222 | 40.000 | 3.21 | 0.00 | 38.77 | 1.40 |
91 | 92 | 5.185249 | GTCACCTTCGGGATGCTATAGATAA | 59.815 | 44.000 | 3.21 | 0.00 | 38.77 | 1.75 |
92 | 93 | 4.705507 | GTCACCTTCGGGATGCTATAGATA | 59.294 | 45.833 | 3.21 | 0.00 | 38.77 | 1.98 |
93 | 94 | 3.511934 | GTCACCTTCGGGATGCTATAGAT | 59.488 | 47.826 | 3.21 | 0.00 | 38.77 | 1.98 |
94 | 95 | 2.891580 | GTCACCTTCGGGATGCTATAGA | 59.108 | 50.000 | 3.21 | 0.00 | 38.77 | 1.98 |
95 | 96 | 2.628178 | TGTCACCTTCGGGATGCTATAG | 59.372 | 50.000 | 0.00 | 0.00 | 38.77 | 1.31 |
96 | 97 | 2.673258 | TGTCACCTTCGGGATGCTATA | 58.327 | 47.619 | 0.00 | 0.00 | 38.77 | 1.31 |
97 | 98 | 1.496060 | TGTCACCTTCGGGATGCTAT | 58.504 | 50.000 | 0.00 | 0.00 | 38.77 | 2.97 |
98 | 99 | 1.271856 | TTGTCACCTTCGGGATGCTA | 58.728 | 50.000 | 0.00 | 0.00 | 38.77 | 3.49 |
99 | 100 | 0.400213 | TTTGTCACCTTCGGGATGCT | 59.600 | 50.000 | 0.00 | 0.00 | 38.77 | 3.79 |
100 | 101 | 1.243902 | TTTTGTCACCTTCGGGATGC | 58.756 | 50.000 | 0.00 | 0.00 | 38.77 | 3.91 |
101 | 102 | 4.519540 | AAATTTTGTCACCTTCGGGATG | 57.480 | 40.909 | 0.00 | 0.00 | 38.77 | 3.51 |
102 | 103 | 6.850752 | ATAAAATTTTGTCACCTTCGGGAT | 57.149 | 33.333 | 13.76 | 0.00 | 38.77 | 3.85 |
103 | 104 | 7.948034 | ATATAAAATTTTGTCACCTTCGGGA | 57.052 | 32.000 | 13.76 | 0.00 | 38.77 | 5.14 |
104 | 105 | 7.010091 | GCAATATAAAATTTTGTCACCTTCGGG | 59.990 | 37.037 | 13.76 | 0.00 | 41.87 | 5.14 |
105 | 106 | 7.543868 | TGCAATATAAAATTTTGTCACCTTCGG | 59.456 | 33.333 | 13.76 | 0.00 | 0.00 | 4.30 |
106 | 107 | 8.459521 | TGCAATATAAAATTTTGTCACCTTCG | 57.540 | 30.769 | 13.76 | 0.00 | 0.00 | 3.79 |
108 | 109 | 9.165035 | CCATGCAATATAAAATTTTGTCACCTT | 57.835 | 29.630 | 13.76 | 0.00 | 0.00 | 3.50 |
109 | 110 | 8.320617 | ACCATGCAATATAAAATTTTGTCACCT | 58.679 | 29.630 | 13.76 | 0.00 | 0.00 | 4.00 |
110 | 111 | 8.491331 | ACCATGCAATATAAAATTTTGTCACC | 57.509 | 30.769 | 13.76 | 0.00 | 0.00 | 4.02 |
111 | 112 | 9.757859 | CAACCATGCAATATAAAATTTTGTCAC | 57.242 | 29.630 | 13.76 | 0.00 | 0.00 | 3.67 |
112 | 113 | 9.499479 | ACAACCATGCAATATAAAATTTTGTCA | 57.501 | 25.926 | 13.76 | 1.86 | 0.00 | 3.58 |
125 | 126 | 9.995003 | AAAAGAGAAATTTACAACCATGCAATA | 57.005 | 25.926 | 0.00 | 0.00 | 0.00 | 1.90 |
126 | 127 | 8.776470 | CAAAAGAGAAATTTACAACCATGCAAT | 58.224 | 29.630 | 0.00 | 0.00 | 0.00 | 3.56 |
127 | 128 | 7.768120 | ACAAAAGAGAAATTTACAACCATGCAA | 59.232 | 29.630 | 0.00 | 0.00 | 0.00 | 4.08 |
128 | 129 | 7.271511 | ACAAAAGAGAAATTTACAACCATGCA | 58.728 | 30.769 | 0.00 | 0.00 | 0.00 | 3.96 |
129 | 130 | 7.653311 | AGACAAAAGAGAAATTTACAACCATGC | 59.347 | 33.333 | 0.00 | 0.00 | 0.00 | 4.06 |
164 | 165 | 7.496346 | AAATGAGGACACCTAGAGACATAAA | 57.504 | 36.000 | 0.00 | 0.00 | 31.76 | 1.40 |
287 | 288 | 1.361204 | TGACCAAGATCAAGGCCTCA | 58.639 | 50.000 | 5.23 | 0.00 | 0.00 | 3.86 |
297 | 298 | 5.122396 | GCGAATAAACACTCTTGACCAAGAT | 59.878 | 40.000 | 12.29 | 1.32 | 45.40 | 2.40 |
307 | 308 | 2.622436 | GCCTGAGCGAATAAACACTCT | 58.378 | 47.619 | 0.00 | 0.00 | 0.00 | 3.24 |
327 | 328 | 6.072673 | ACAAAAGTTATTCTTCCACTAAGCGG | 60.073 | 38.462 | 0.00 | 0.00 | 35.02 | 5.52 |
350 | 351 | 5.120674 | CGAAATAGAAATGTCACTCTGCACA | 59.879 | 40.000 | 0.00 | 0.00 | 0.00 | 4.57 |
373 | 374 | 4.635765 | TCCTATTTTGATTCCTTGCAGTCG | 59.364 | 41.667 | 0.00 | 0.00 | 0.00 | 4.18 |
393 | 394 | 2.270434 | TAAAGCCTCCTGGTCATCCT | 57.730 | 50.000 | 0.00 | 0.00 | 35.27 | 3.24 |
454 | 456 | 5.065914 | TGCTTTCAGTAGCATGAAAACTCT | 58.934 | 37.500 | 0.00 | 0.00 | 45.80 | 3.24 |
544 | 546 | 7.014230 | AGCGGTAATTAATATTCACAGCCATTT | 59.986 | 33.333 | 0.00 | 0.00 | 0.00 | 2.32 |
802 | 804 | 3.132289 | TCTGTTTGGTATTAGGCTCGGAG | 59.868 | 47.826 | 0.00 | 0.00 | 0.00 | 4.63 |
951 | 953 | 0.526211 | CTGTGCGTCAGTACCTGCTA | 59.474 | 55.000 | 0.00 | 0.00 | 39.17 | 3.49 |
1031 | 1033 | 1.451927 | GAATGCGGCTGGATGGACA | 60.452 | 57.895 | 0.00 | 0.00 | 0.00 | 4.02 |
1070 | 1072 | 4.758251 | CGAGTGGTGGCGGCATGA | 62.758 | 66.667 | 17.19 | 1.04 | 0.00 | 3.07 |
1136 | 1138 | 1.399714 | CTCCAGTAGTGGCGATGGTA | 58.600 | 55.000 | 12.14 | 0.00 | 44.60 | 3.25 |
1149 | 1151 | 1.755008 | GGCTCCGAGTAGCTCCAGT | 60.755 | 63.158 | 0.00 | 0.00 | 42.37 | 4.00 |
1334 | 1337 | 0.320073 | CTTGACGCCGTTACCCTTCA | 60.320 | 55.000 | 0.00 | 0.00 | 0.00 | 3.02 |
1380 | 1383 | 0.536460 | GGAGGAAACTTTGGTCGGCA | 60.536 | 55.000 | 0.00 | 0.00 | 44.43 | 5.69 |
1401 | 1404 | 1.303898 | TTGGTGGCATAGGATGGGAA | 58.696 | 50.000 | 0.00 | 0.00 | 0.00 | 3.97 |
1598 | 1602 | 3.583086 | TCTGGATCCTTTCTTCGGACTTT | 59.417 | 43.478 | 14.23 | 0.00 | 32.41 | 2.66 |
1599 | 1603 | 3.173965 | TCTGGATCCTTTCTTCGGACTT | 58.826 | 45.455 | 14.23 | 0.00 | 32.41 | 3.01 |
1973 | 1985 | 1.549203 | AACATTCACATGGGTCAGCC | 58.451 | 50.000 | 0.00 | 0.00 | 34.27 | 4.85 |
1974 | 1986 | 3.947196 | TGATAACATTCACATGGGTCAGC | 59.053 | 43.478 | 0.00 | 0.00 | 34.27 | 4.26 |
1975 | 1987 | 7.991084 | ATATGATAACATTCACATGGGTCAG | 57.009 | 36.000 | 0.00 | 0.00 | 37.87 | 3.51 |
2091 | 2103 | 8.779354 | AACAAATAACATCTACCTCTTGACTC | 57.221 | 34.615 | 0.00 | 0.00 | 0.00 | 3.36 |
2094 | 2106 | 9.793259 | AAAGAACAAATAACATCTACCTCTTGA | 57.207 | 29.630 | 0.00 | 0.00 | 0.00 | 3.02 |
2156 | 2168 | 1.663695 | AGTGTAGCGCAGTTTTGTGT | 58.336 | 45.000 | 11.47 | 0.00 | 37.15 | 3.72 |
2165 | 2177 | 6.103330 | TCATTATAAGTGAAAGTGTAGCGCA | 58.897 | 36.000 | 11.47 | 0.00 | 0.00 | 6.09 |
2273 | 2285 | 4.820716 | CCATTTTTCATTGCTGGGAAACAA | 59.179 | 37.500 | 0.00 | 0.00 | 33.10 | 2.83 |
2311 | 2323 | 6.877322 | ACATCGCTAATGTAACTTGTTAAGGT | 59.123 | 34.615 | 0.15 | 0.00 | 46.95 | 3.50 |
2332 | 2344 | 7.381744 | GAGCTTTGACAAACTTTTACACATC | 57.618 | 36.000 | 0.00 | 0.00 | 0.00 | 3.06 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.