Multiple sequence alignment - TraesCS2D01G540900
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 | TraesCS2D01G540900 | chr2D | 100.000 | 2523 | 0 | 0 | 1 | 2523 | 620322296 | 620319774 | 0.000000e+00 | 4660.0 |
1 | TraesCS2D01G540900 | chr4B | 92.868 | 2005 | 97 | 22 | 84 | 2059 | 637347225 | 637345238 | 0.000000e+00 | 2868.0 |
2 | TraesCS2D01G540900 | chr4B | 82.888 | 374 | 57 | 5 | 2156 | 2523 | 637344056 | 637343684 | 1.870000e-86 | 329.0 |
3 | TraesCS2D01G540900 | chr4B | 81.962 | 316 | 46 | 3 | 2209 | 2523 | 637344305 | 637344000 | 8.950000e-65 | 257.0 |
4 | TraesCS2D01G540900 | chr4B | 87.838 | 148 | 13 | 3 | 2375 | 2518 | 637344424 | 637344278 | 4.320000e-38 | 169.0 |
5 | TraesCS2D01G540900 | chr3B | 92.482 | 1902 | 109 | 19 | 433 | 2319 | 299750855 | 299748973 | 0.000000e+00 | 2689.0 |
6 | TraesCS2D01G540900 | chr3B | 92.767 | 318 | 19 | 2 | 124 | 438 | 299768355 | 299768039 | 8.230000e-125 | 457.0 |
7 | TraesCS2D01G540900 | chr3B | 89.174 | 351 | 28 | 1 | 2171 | 2521 | 299749150 | 299748810 | 1.790000e-116 | 429.0 |
8 | TraesCS2D01G540900 | chr3B | 80.278 | 360 | 62 | 8 | 2156 | 2512 | 299748864 | 299748511 | 1.920000e-66 | 263.0 |
9 | TraesCS2D01G540900 | chr1B | 93.968 | 1177 | 58 | 9 | 888 | 2059 | 12395791 | 12394623 | 0.000000e+00 | 1768.0 |
10 | TraesCS2D01G540900 | chr1B | 91.653 | 611 | 41 | 4 | 84 | 686 | 12396418 | 12395810 | 0.000000e+00 | 837.0 |
11 | TraesCS2D01G540900 | chr1B | 88.210 | 229 | 23 | 3 | 2297 | 2521 | 12393096 | 12392868 | 1.150000e-68 | 270.0 |
12 | TraesCS2D01G540900 | chr1B | 84.252 | 254 | 39 | 1 | 2209 | 2461 | 12393705 | 12393452 | 1.940000e-61 | 246.0 |
13 | TraesCS2D01G540900 | chr1B | 89.865 | 148 | 10 | 3 | 2375 | 2518 | 12393824 | 12393678 | 4.290000e-43 | 185.0 |
14 | TraesCS2D01G540900 | chr1B | 80.808 | 99 | 9 | 5 | 256 | 345 | 4857511 | 4857608 | 4.500000e-08 | 69.4 |
15 | TraesCS2D01G540900 | chr7A | 89.270 | 671 | 54 | 12 | 1325 | 1987 | 707987774 | 707988434 | 0.000000e+00 | 824.0 |
16 | TraesCS2D01G540900 | chr7A | 88.024 | 668 | 65 | 10 | 1327 | 1990 | 30225669 | 30225013 | 0.000000e+00 | 776.0 |
17 | TraesCS2D01G540900 | chr5A | 88.473 | 668 | 62 | 10 | 1327 | 1990 | 608038427 | 608037771 | 0.000000e+00 | 793.0 |
18 | TraesCS2D01G540900 | chr5A | 83.226 | 155 | 26 | 0 | 2158 | 2312 | 608036731 | 608036577 | 2.620000e-30 | 143.0 |
19 | TraesCS2D01G540900 | chr6B | 86.807 | 667 | 62 | 14 | 1325 | 1986 | 46409626 | 46408981 | 0.000000e+00 | 721.0 |
20 | TraesCS2D01G540900 | chr6B | 85.672 | 670 | 68 | 13 | 1328 | 1990 | 30418061 | 30417413 | 0.000000e+00 | 680.0 |
21 | TraesCS2D01G540900 | chr5B | 89.873 | 553 | 43 | 5 | 1325 | 1873 | 38456869 | 38456326 | 0.000000e+00 | 699.0 |
22 | TraesCS2D01G540900 | chr3D | 77.540 | 374 | 76 | 5 | 2155 | 2523 | 601999535 | 601999165 | 4.230000e-53 | 219.0 |
23 | TraesCS2D01G540900 | chr3D | 86.429 | 140 | 19 | 0 | 2175 | 2314 | 35686697 | 35686836 | 1.210000e-33 | 154.0 |
24 | TraesCS2D01G540900 | chr3A | 83.843 | 229 | 19 | 3 | 750 | 960 | 44580854 | 44581082 | 4.260000e-48 | 202.0 |
25 | TraesCS2D01G540900 | chr3A | 77.959 | 245 | 17 | 12 | 342 | 552 | 61240393 | 61240152 | 4.410000e-23 | 119.0 |
26 | TraesCS2D01G540900 | chr3A | 92.308 | 78 | 6 | 0 | 1169 | 1246 | 44583486 | 44583563 | 7.380000e-21 | 111.0 |
27 | TraesCS2D01G540900 | chr3A | 89.706 | 68 | 5 | 2 | 955 | 1020 | 44582838 | 44582771 | 4.470000e-13 | 86.1 |
28 | TraesCS2D01G540900 | chr5D | 93.636 | 110 | 7 | 0 | 1154 | 1263 | 450172210 | 450172319 | 5.580000e-37 | 165.0 |
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 | TraesCS2D01G540900 | chr2D | 620319774 | 620322296 | 2522 | True | 4660.00 | 4660 | 100.000000 | 1 | 2523 | 1 | chr2D.!!$R1 | 2522 |
1 | TraesCS2D01G540900 | chr4B | 637343684 | 637347225 | 3541 | True | 905.75 | 2868 | 86.389000 | 84 | 2523 | 4 | chr4B.!!$R1 | 2439 |
2 | TraesCS2D01G540900 | chr3B | 299748511 | 299750855 | 2344 | True | 1127.00 | 2689 | 87.311333 | 433 | 2521 | 3 | chr3B.!!$R2 | 2088 |
3 | TraesCS2D01G540900 | chr1B | 12392868 | 12396418 | 3550 | True | 661.20 | 1768 | 89.589600 | 84 | 2521 | 5 | chr1B.!!$R1 | 2437 |
4 | TraesCS2D01G540900 | chr7A | 707987774 | 707988434 | 660 | False | 824.00 | 824 | 89.270000 | 1325 | 1987 | 1 | chr7A.!!$F1 | 662 |
5 | TraesCS2D01G540900 | chr7A | 30225013 | 30225669 | 656 | True | 776.00 | 776 | 88.024000 | 1327 | 1990 | 1 | chr7A.!!$R1 | 663 |
6 | TraesCS2D01G540900 | chr5A | 608036577 | 608038427 | 1850 | True | 468.00 | 793 | 85.849500 | 1327 | 2312 | 2 | chr5A.!!$R1 | 985 |
7 | TraesCS2D01G540900 | chr6B | 46408981 | 46409626 | 645 | True | 721.00 | 721 | 86.807000 | 1325 | 1986 | 1 | chr6B.!!$R2 | 661 |
8 | TraesCS2D01G540900 | chr6B | 30417413 | 30418061 | 648 | True | 680.00 | 680 | 85.672000 | 1328 | 1990 | 1 | chr6B.!!$R1 | 662 |
9 | TraesCS2D01G540900 | chr5B | 38456326 | 38456869 | 543 | True | 699.00 | 699 | 89.873000 | 1325 | 1873 | 1 | chr5B.!!$R1 | 548 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
562 | 573 | 0.179032 | TAGGCAACGGCATACATGGG | 60.179 | 55.0 | 0.0 | 0.0 | 43.71 | 4.0 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2282 | 3939 | 0.402504 | TAGTCGTTTGGGCCCACAAT | 59.597 | 50.0 | 28.7 | 10.82 | 0.0 | 2.71 | 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 |
---|---|---|---|---|---|---|---|---|---|
27 | 28 | 9.930158 | TGTAAATACTTCTATTTTATTGCCCCT | 57.070 | 29.630 | 0.00 | 0.00 | 34.83 | 4.79 |
34 | 35 | 9.930158 | ACTTCTATTTTATTGCCCCTATGTTAA | 57.070 | 29.630 | 0.00 | 0.00 | 0.00 | 2.01 |
40 | 41 | 6.627395 | TTATTGCCCCTATGTTAATGAACG | 57.373 | 37.500 | 0.00 | 0.00 | 38.51 | 3.95 |
41 | 42 | 3.916359 | TGCCCCTATGTTAATGAACGA | 57.084 | 42.857 | 0.00 | 0.00 | 38.51 | 3.85 |
42 | 43 | 4.223556 | TGCCCCTATGTTAATGAACGAA | 57.776 | 40.909 | 0.00 | 0.00 | 38.51 | 3.85 |
43 | 44 | 4.787551 | TGCCCCTATGTTAATGAACGAAT | 58.212 | 39.130 | 0.00 | 0.00 | 38.51 | 3.34 |
44 | 45 | 4.819630 | TGCCCCTATGTTAATGAACGAATC | 59.180 | 41.667 | 0.00 | 0.00 | 38.51 | 2.52 |
45 | 46 | 4.819630 | GCCCCTATGTTAATGAACGAATCA | 59.180 | 41.667 | 0.00 | 0.00 | 43.67 | 2.57 |
46 | 47 | 5.298276 | GCCCCTATGTTAATGAACGAATCAA | 59.702 | 40.000 | 0.00 | 0.00 | 42.54 | 2.57 |
47 | 48 | 6.016276 | GCCCCTATGTTAATGAACGAATCAAT | 60.016 | 38.462 | 0.00 | 0.00 | 42.54 | 2.57 |
48 | 49 | 7.174253 | GCCCCTATGTTAATGAACGAATCAATA | 59.826 | 37.037 | 0.00 | 0.00 | 42.54 | 1.90 |
49 | 50 | 9.062524 | CCCCTATGTTAATGAACGAATCAATAA | 57.937 | 33.333 | 0.00 | 0.00 | 42.54 | 1.40 |
55 | 56 | 9.554724 | TGTTAATGAACGAATCAATAAAAGCTC | 57.445 | 29.630 | 0.00 | 0.00 | 42.54 | 4.09 |
56 | 57 | 9.010366 | GTTAATGAACGAATCAATAAAAGCTCC | 57.990 | 33.333 | 0.00 | 0.00 | 42.54 | 4.70 |
57 | 58 | 7.396540 | AATGAACGAATCAATAAAAGCTCCT | 57.603 | 32.000 | 0.00 | 0.00 | 42.54 | 3.69 |
58 | 59 | 8.506168 | AATGAACGAATCAATAAAAGCTCCTA | 57.494 | 30.769 | 0.00 | 0.00 | 42.54 | 2.94 |
59 | 60 | 8.682936 | ATGAACGAATCAATAAAAGCTCCTAT | 57.317 | 30.769 | 0.00 | 0.00 | 42.54 | 2.57 |
60 | 61 | 8.506168 | TGAACGAATCAATAAAAGCTCCTATT | 57.494 | 30.769 | 0.00 | 0.00 | 34.30 | 1.73 |
61 | 62 | 8.956426 | TGAACGAATCAATAAAAGCTCCTATTT | 58.044 | 29.630 | 0.00 | 0.00 | 34.30 | 1.40 |
62 | 63 | 9.439537 | GAACGAATCAATAAAAGCTCCTATTTC | 57.560 | 33.333 | 0.00 | 0.00 | 0.00 | 2.17 |
63 | 64 | 8.506168 | ACGAATCAATAAAAGCTCCTATTTCA | 57.494 | 30.769 | 0.00 | 0.00 | 0.00 | 2.69 |
64 | 65 | 8.616076 | ACGAATCAATAAAAGCTCCTATTTCAG | 58.384 | 33.333 | 0.00 | 0.00 | 0.00 | 3.02 |
65 | 66 | 8.830580 | CGAATCAATAAAAGCTCCTATTTCAGA | 58.169 | 33.333 | 0.00 | 0.00 | 0.00 | 3.27 |
67 | 68 | 8.688747 | ATCAATAAAAGCTCCTATTTCAGAGG | 57.311 | 34.615 | 0.00 | 0.00 | 35.17 | 3.69 |
68 | 69 | 7.861629 | TCAATAAAAGCTCCTATTTCAGAGGA | 58.138 | 34.615 | 0.00 | 0.00 | 40.95 | 3.71 |
69 | 70 | 8.328758 | TCAATAAAAGCTCCTATTTCAGAGGAA | 58.671 | 33.333 | 0.00 | 0.00 | 42.63 | 3.36 |
70 | 71 | 8.960591 | CAATAAAAGCTCCTATTTCAGAGGAAA | 58.039 | 33.333 | 0.00 | 0.00 | 46.36 | 3.13 |
71 | 72 | 9.533831 | AATAAAAGCTCCTATTTCAGAGGAAAA | 57.466 | 29.630 | 0.00 | 0.00 | 45.52 | 2.29 |
72 | 73 | 7.839680 | AAAAGCTCCTATTTCAGAGGAAAAA | 57.160 | 32.000 | 0.00 | 0.00 | 45.52 | 1.94 |
95 | 96 | 6.862944 | AAACATGTTTATGGCGAATTTACG | 57.137 | 33.333 | 22.10 | 0.00 | 38.66 | 3.18 |
118 | 119 | 1.540363 | CCGTCCATCCACCTTAATCGG | 60.540 | 57.143 | 0.00 | 0.00 | 0.00 | 4.18 |
120 | 121 | 2.037251 | CGTCCATCCACCTTAATCGGAT | 59.963 | 50.000 | 0.00 | 0.00 | 40.23 | 4.18 |
127 | 128 | 3.275617 | CACCTTAATCGGATGGTGGAA | 57.724 | 47.619 | 14.94 | 0.00 | 44.33 | 3.53 |
142 | 145 | 6.596497 | GGATGGTGGAAAAATAGAAGTTACGA | 59.404 | 38.462 | 0.00 | 0.00 | 0.00 | 3.43 |
156 | 159 | 7.101993 | AGAAGTTACGACGAGTTACAAAATG | 57.898 | 36.000 | 0.00 | 0.00 | 35.03 | 2.32 |
166 | 169 | 7.057149 | ACGAGTTACAAAATGAGAATTACGG | 57.943 | 36.000 | 0.00 | 0.00 | 0.00 | 4.02 |
197 | 200 | 1.941377 | TAACAGTGGGACCGGTACAT | 58.059 | 50.000 | 21.02 | 0.00 | 0.00 | 2.29 |
203 | 206 | 1.808343 | GTGGGACCGGTACATGTTTTC | 59.192 | 52.381 | 21.02 | 0.00 | 0.00 | 2.29 |
223 | 226 | 5.890424 | TTCGATGGGACCAGTTATTTTTC | 57.110 | 39.130 | 0.00 | 0.00 | 0.00 | 2.29 |
226 | 229 | 3.791953 | TGGGACCAGTTATTTTTCCGA | 57.208 | 42.857 | 0.00 | 0.00 | 0.00 | 4.55 |
258 | 261 | 4.760204 | TCCGTCTTGGAAAATTTCTCTTCC | 59.240 | 41.667 | 5.65 | 0.00 | 46.38 | 3.46 |
290 | 293 | 2.746277 | ACAGTTTCCGCGGCCATC | 60.746 | 61.111 | 23.51 | 10.76 | 0.00 | 3.51 |
402 | 405 | 1.760086 | ATCCCTGGTCTCGCTCCTG | 60.760 | 63.158 | 0.00 | 0.00 | 0.00 | 3.86 |
405 | 408 | 4.504916 | CTGGTCTCGCTCCTGCCG | 62.505 | 72.222 | 0.00 | 0.00 | 35.36 | 5.69 |
505 | 516 | 2.650116 | GCCTCCTCCGTTGAGCAGA | 61.650 | 63.158 | 0.00 | 0.00 | 37.29 | 4.26 |
549 | 560 | 2.589157 | CCAGTCCGTGGGTAGGCAA | 61.589 | 63.158 | 0.00 | 0.00 | 43.63 | 4.52 |
551 | 562 | 2.433664 | GTCCGTGGGTAGGCAACG | 60.434 | 66.667 | 0.00 | 0.00 | 46.39 | 4.10 |
562 | 573 | 0.179032 | TAGGCAACGGCATACATGGG | 60.179 | 55.000 | 0.00 | 0.00 | 43.71 | 4.00 |
609 | 620 | 3.553375 | TCCGATCCCATATTACCTCCA | 57.447 | 47.619 | 0.00 | 0.00 | 0.00 | 3.86 |
620 | 631 | 0.759959 | TTACCTCCAGCACGGTTCAA | 59.240 | 50.000 | 0.00 | 0.00 | 34.76 | 2.69 |
850 | 870 | 5.007234 | TGTTCTATTGTGAAGTCGGTGTTTG | 59.993 | 40.000 | 0.00 | 0.00 | 0.00 | 2.93 |
868 | 888 | 7.574967 | CGGTGTTTGCTATTTCTTCCTACAAAT | 60.575 | 37.037 | 0.00 | 0.00 | 0.00 | 2.32 |
1029 | 1059 | 7.068593 | ACAGTTGATCAATTGGAAGAACTGAAA | 59.931 | 33.333 | 28.17 | 3.52 | 44.14 | 2.69 |
1040 | 1070 | 2.310538 | AGAACTGAAAGCCCTTTGGTG | 58.689 | 47.619 | 0.00 | 0.00 | 37.60 | 4.17 |
1084 | 1114 | 6.830324 | TGATCTTTGGGGAATAACATCTGAAG | 59.170 | 38.462 | 0.00 | 0.00 | 0.00 | 3.02 |
1098 | 1128 | 9.917887 | ATAACATCTGAAGAATGGAAAGAGATT | 57.082 | 29.630 | 0.00 | 0.00 | 0.00 | 2.40 |
1127 | 1157 | 2.472029 | AGGAACAGACCCATCTACAGG | 58.528 | 52.381 | 0.00 | 0.00 | 32.25 | 4.00 |
1205 | 1235 | 5.758296 | AGTTACTGTACATATGCATTTCCCG | 59.242 | 40.000 | 3.54 | 0.00 | 0.00 | 5.14 |
1283 | 1313 | 2.555199 | CATTAAGAGGTGGAGGCTTCG | 58.445 | 52.381 | 0.00 | 0.00 | 0.00 | 3.79 |
1396 | 1433 | 4.445452 | AATTGCTTTACTCACCATGCTG | 57.555 | 40.909 | 0.00 | 0.00 | 0.00 | 4.41 |
1431 | 1471 | 1.839424 | AAATTACAGGCAGGCAGGAC | 58.161 | 50.000 | 0.00 | 0.00 | 0.00 | 3.85 |
1485 | 1525 | 3.505680 | TCTGCATTCCGTATTTTTGCTGT | 59.494 | 39.130 | 0.00 | 0.00 | 34.89 | 4.40 |
1560 | 1600 | 3.536158 | TTTGGAGAACGCTTTTGATCG | 57.464 | 42.857 | 0.00 | 0.00 | 0.00 | 3.69 |
1685 | 1726 | 5.698832 | TCCATTTCATGCAGTTTACTTTCG | 58.301 | 37.500 | 0.00 | 0.00 | 0.00 | 3.46 |
1831 | 1877 | 1.739466 | GATGCTCGAATTGAAGTGGCA | 59.261 | 47.619 | 0.00 | 0.00 | 0.00 | 4.92 |
1839 | 1885 | 3.361644 | CGAATTGAAGTGGCATTTGTTCG | 59.638 | 43.478 | 14.94 | 14.94 | 0.00 | 3.95 |
1880 | 1926 | 4.546570 | TCAACATACACGAGAACAGAGTG | 58.453 | 43.478 | 0.00 | 0.00 | 41.28 | 3.51 |
1903 | 1949 | 3.008375 | TCATACTTGAAGTGAGCAAGGCT | 59.992 | 43.478 | 8.33 | 0.00 | 45.31 | 4.58 |
1905 | 1951 | 2.225467 | ACTTGAAGTGAGCAAGGCTTC | 58.775 | 47.619 | 0.00 | 0.00 | 45.31 | 3.86 |
1948 | 1994 | 3.589988 | CCTGAACTAGTGAACGCTGAAT | 58.410 | 45.455 | 0.00 | 0.00 | 0.00 | 2.57 |
1992 | 2038 | 2.807108 | GCGAGGTGTTCTTTTCTCCAGT | 60.807 | 50.000 | 0.00 | 0.00 | 0.00 | 4.00 |
2052 | 2154 | 2.030805 | AGCAAAACCGTCTCTGCATTTC | 60.031 | 45.455 | 0.00 | 0.00 | 37.26 | 2.17 |
2078 | 2183 | 0.944311 | CTCACGTGTGCGCTAAAGGT | 60.944 | 55.000 | 16.51 | 2.88 | 42.83 | 3.50 |
2093 | 2350 | 8.732531 | TGCGCTAAAGGTATAGTAATTTTGTTT | 58.267 | 29.630 | 9.73 | 0.00 | 0.00 | 2.83 |
2094 | 2351 | 9.218359 | GCGCTAAAGGTATAGTAATTTTGTTTC | 57.782 | 33.333 | 0.00 | 0.00 | 0.00 | 2.78 |
2143 | 3004 | 4.260620 | CCAGTCGACTGAAATTTCGTTTGT | 60.261 | 41.667 | 40.21 | 9.15 | 46.59 | 2.83 |
2147 | 3008 | 2.719046 | GACTGAAATTTCGTTTGTGCCG | 59.281 | 45.455 | 13.34 | 0.00 | 0.00 | 5.69 |
2201 | 3207 | 6.737301 | CGAACGACTAAGATCGATACTTATGG | 59.263 | 42.308 | 13.91 | 8.74 | 45.13 | 2.74 |
2203 | 3209 | 5.415077 | ACGACTAAGATCGATACTTATGGGG | 59.585 | 44.000 | 13.91 | 8.03 | 45.13 | 4.96 |
2221 | 3793 | 0.379669 | GGCCGAACGACTAAGATCGA | 59.620 | 55.000 | 1.63 | 0.00 | 45.13 | 3.59 |
2241 | 3844 | 3.707793 | GATACTAGTGAGCCCAAACGAG | 58.292 | 50.000 | 5.39 | 0.00 | 0.00 | 4.18 |
2261 | 3864 | 3.438183 | AGTAAGATCGGTACTTGTGGGT | 58.562 | 45.455 | 6.36 | 0.00 | 0.00 | 4.51 |
2262 | 3865 | 3.446516 | AGTAAGATCGGTACTTGTGGGTC | 59.553 | 47.826 | 6.36 | 0.00 | 0.00 | 4.46 |
2264 | 3867 | 0.899720 | GATCGGTACTTGTGGGTCCA | 59.100 | 55.000 | 0.00 | 0.00 | 0.00 | 4.02 |
2266 | 3869 | 0.393820 | TCGGTACTTGTGGGTCCAAC | 59.606 | 55.000 | 0.00 | 0.00 | 0.00 | 3.77 |
2270 | 3927 | 2.490168 | GGTACTTGTGGGTCCAACCAAT | 60.490 | 50.000 | 0.00 | 0.00 | 43.34 | 3.16 |
2281 | 3938 | 5.131308 | TGGGTCCAACCAATTAAGATCGATA | 59.869 | 40.000 | 0.00 | 0.00 | 41.02 | 2.92 |
2282 | 3939 | 6.059484 | GGGTCCAACCAATTAAGATCGATAA | 58.941 | 40.000 | 0.00 | 0.00 | 41.02 | 1.75 |
2296 | 3953 | 2.096248 | TCGATAATTGTGGGCCCAAAC | 58.904 | 47.619 | 30.64 | 16.86 | 0.00 | 2.93 |
2304 | 3961 | 0.035739 | GTGGGCCCAAACGACTAAGA | 59.964 | 55.000 | 30.64 | 0.00 | 0.00 | 2.10 |
2306 | 3963 | 1.353022 | TGGGCCCAAACGACTAAGATT | 59.647 | 47.619 | 26.33 | 0.00 | 0.00 | 2.40 |
2312 | 4348 | 4.828829 | CCCAAACGACTAAGATTGGTACT | 58.171 | 43.478 | 0.00 | 0.00 | 40.94 | 2.73 |
2315 | 4351 | 5.390567 | CCAAACGACTAAGATTGGTACTTGC | 60.391 | 44.000 | 0.00 | 0.00 | 38.68 | 4.01 |
2319 | 4355 | 2.835764 | ACTAAGATTGGTACTTGCGGGA | 59.164 | 45.455 | 0.00 | 0.00 | 0.00 | 5.14 |
2325 | 4361 | 0.402504 | TGGTACTTGCGGGACCAAAT | 59.597 | 50.000 | 10.67 | 0.00 | 40.29 | 2.32 |
2346 | 4382 | 5.916661 | ATGACTAAGATCCGTACTTGTGT | 57.083 | 39.130 | 0.00 | 0.00 | 0.00 | 3.72 |
2395 | 4431 | 2.358267 | CTGAGCGAATAAGACCGGTACT | 59.642 | 50.000 | 7.34 | 3.50 | 36.60 | 2.73 |
2484 | 4524 | 4.677673 | AAGTAAGAACGGTACTTGTGGT | 57.322 | 40.909 | 0.00 | 0.00 | 39.70 | 4.16 |
2518 | 4558 | 0.469917 | ATCGATACTTGTGGGCCTGG | 59.530 | 55.000 | 4.53 | 0.00 | 0.00 | 4.45 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
1 | 2 | 9.930158 | AGGGGCAATAAAATAGAAGTATTTACA | 57.070 | 29.630 | 0.00 | 0.00 | 37.79 | 2.41 |
8 | 9 | 9.930158 | TTAACATAGGGGCAATAAAATAGAAGT | 57.070 | 29.630 | 0.00 | 0.00 | 0.00 | 3.01 |
14 | 15 | 8.141268 | CGTTCATTAACATAGGGGCAATAAAAT | 58.859 | 33.333 | 0.00 | 0.00 | 35.16 | 1.82 |
15 | 16 | 7.339721 | TCGTTCATTAACATAGGGGCAATAAAA | 59.660 | 33.333 | 0.00 | 0.00 | 35.16 | 1.52 |
16 | 17 | 6.829298 | TCGTTCATTAACATAGGGGCAATAAA | 59.171 | 34.615 | 0.00 | 0.00 | 35.16 | 1.40 |
17 | 18 | 6.358178 | TCGTTCATTAACATAGGGGCAATAA | 58.642 | 36.000 | 0.00 | 0.00 | 35.16 | 1.40 |
18 | 19 | 5.931294 | TCGTTCATTAACATAGGGGCAATA | 58.069 | 37.500 | 0.00 | 0.00 | 35.16 | 1.90 |
19 | 20 | 4.787551 | TCGTTCATTAACATAGGGGCAAT | 58.212 | 39.130 | 0.00 | 0.00 | 35.16 | 3.56 |
20 | 21 | 4.223556 | TCGTTCATTAACATAGGGGCAA | 57.776 | 40.909 | 0.00 | 0.00 | 35.16 | 4.52 |
21 | 22 | 3.916359 | TCGTTCATTAACATAGGGGCA | 57.084 | 42.857 | 0.00 | 0.00 | 35.16 | 5.36 |
22 | 23 | 4.819630 | TGATTCGTTCATTAACATAGGGGC | 59.180 | 41.667 | 0.00 | 0.00 | 35.16 | 5.80 |
23 | 24 | 6.935741 | TTGATTCGTTCATTAACATAGGGG | 57.064 | 37.500 | 0.00 | 0.00 | 35.16 | 4.79 |
29 | 30 | 9.554724 | GAGCTTTTATTGATTCGTTCATTAACA | 57.445 | 29.630 | 0.00 | 0.00 | 35.16 | 2.41 |
30 | 31 | 9.010366 | GGAGCTTTTATTGATTCGTTCATTAAC | 57.990 | 33.333 | 0.00 | 0.00 | 32.59 | 2.01 |
31 | 32 | 8.956426 | AGGAGCTTTTATTGATTCGTTCATTAA | 58.044 | 29.630 | 0.00 | 0.00 | 33.34 | 1.40 |
32 | 33 | 8.506168 | AGGAGCTTTTATTGATTCGTTCATTA | 57.494 | 30.769 | 0.00 | 0.00 | 33.34 | 1.90 |
33 | 34 | 7.396540 | AGGAGCTTTTATTGATTCGTTCATT | 57.603 | 32.000 | 0.00 | 0.00 | 33.34 | 2.57 |
34 | 35 | 8.682936 | ATAGGAGCTTTTATTGATTCGTTCAT | 57.317 | 30.769 | 0.00 | 0.00 | 33.34 | 2.57 |
35 | 36 | 8.506168 | AATAGGAGCTTTTATTGATTCGTTCA | 57.494 | 30.769 | 0.00 | 0.00 | 0.00 | 3.18 |
36 | 37 | 9.439537 | GAAATAGGAGCTTTTATTGATTCGTTC | 57.560 | 33.333 | 0.00 | 0.00 | 0.00 | 3.95 |
37 | 38 | 8.956426 | TGAAATAGGAGCTTTTATTGATTCGTT | 58.044 | 29.630 | 0.00 | 0.00 | 0.00 | 3.85 |
38 | 39 | 8.506168 | TGAAATAGGAGCTTTTATTGATTCGT | 57.494 | 30.769 | 0.00 | 0.00 | 0.00 | 3.85 |
39 | 40 | 8.830580 | TCTGAAATAGGAGCTTTTATTGATTCG | 58.169 | 33.333 | 0.00 | 0.00 | 0.00 | 3.34 |
41 | 42 | 9.129532 | CCTCTGAAATAGGAGCTTTTATTGATT | 57.870 | 33.333 | 0.00 | 0.00 | 36.08 | 2.57 |
42 | 43 | 8.497745 | TCCTCTGAAATAGGAGCTTTTATTGAT | 58.502 | 33.333 | 0.00 | 0.00 | 38.24 | 2.57 |
43 | 44 | 7.861629 | TCCTCTGAAATAGGAGCTTTTATTGA | 58.138 | 34.615 | 0.00 | 0.00 | 38.24 | 2.57 |
44 | 45 | 8.511604 | TTCCTCTGAAATAGGAGCTTTTATTG | 57.488 | 34.615 | 0.00 | 0.00 | 43.90 | 1.90 |
45 | 46 | 9.533831 | TTTTCCTCTGAAATAGGAGCTTTTATT | 57.466 | 29.630 | 0.00 | 0.00 | 43.90 | 1.40 |
46 | 47 | 9.533831 | TTTTTCCTCTGAAATAGGAGCTTTTAT | 57.466 | 29.630 | 0.00 | 0.00 | 43.90 | 1.40 |
47 | 48 | 8.934023 | TTTTTCCTCTGAAATAGGAGCTTTTA | 57.066 | 30.769 | 0.00 | 0.00 | 43.90 | 1.52 |
48 | 49 | 7.839680 | TTTTTCCTCTGAAATAGGAGCTTTT | 57.160 | 32.000 | 0.00 | 0.00 | 43.90 | 2.27 |
70 | 71 | 7.595502 | TCGTAAATTCGCCATAAACATGTTTTT | 59.404 | 29.630 | 27.66 | 17.84 | 34.23 | 1.94 |
71 | 72 | 7.085116 | TCGTAAATTCGCCATAAACATGTTTT | 58.915 | 30.769 | 27.66 | 13.43 | 34.23 | 2.43 |
72 | 73 | 6.613233 | TCGTAAATTCGCCATAAACATGTTT | 58.387 | 32.000 | 25.99 | 25.99 | 36.63 | 2.83 |
73 | 74 | 6.184580 | TCGTAAATTCGCCATAAACATGTT | 57.815 | 33.333 | 4.92 | 4.92 | 0.00 | 2.71 |
74 | 75 | 5.729454 | GCTCGTAAATTCGCCATAAACATGT | 60.729 | 40.000 | 0.00 | 0.00 | 0.00 | 3.21 |
75 | 76 | 4.670621 | GCTCGTAAATTCGCCATAAACATG | 59.329 | 41.667 | 0.00 | 0.00 | 0.00 | 3.21 |
76 | 77 | 4.261031 | GGCTCGTAAATTCGCCATAAACAT | 60.261 | 41.667 | 0.00 | 0.00 | 42.06 | 2.71 |
77 | 78 | 3.064271 | GGCTCGTAAATTCGCCATAAACA | 59.936 | 43.478 | 0.00 | 0.00 | 42.06 | 2.83 |
78 | 79 | 3.614588 | GGCTCGTAAATTCGCCATAAAC | 58.385 | 45.455 | 0.00 | 0.00 | 42.06 | 2.01 |
79 | 80 | 2.285756 | CGGCTCGTAAATTCGCCATAAA | 59.714 | 45.455 | 0.00 | 0.00 | 42.59 | 1.40 |
80 | 81 | 1.862201 | CGGCTCGTAAATTCGCCATAA | 59.138 | 47.619 | 0.00 | 0.00 | 42.59 | 1.90 |
81 | 82 | 1.202440 | ACGGCTCGTAAATTCGCCATA | 60.202 | 47.619 | 0.00 | 0.00 | 42.59 | 2.74 |
82 | 83 | 0.461339 | ACGGCTCGTAAATTCGCCAT | 60.461 | 50.000 | 0.00 | 0.00 | 42.59 | 4.40 |
95 | 96 | 0.539986 | TTAAGGTGGATGGACGGCTC | 59.460 | 55.000 | 0.00 | 0.00 | 0.00 | 4.70 |
118 | 119 | 7.461918 | GTCGTAACTTCTATTTTTCCACCATC | 58.538 | 38.462 | 0.00 | 0.00 | 0.00 | 3.51 |
120 | 121 | 5.406175 | CGTCGTAACTTCTATTTTTCCACCA | 59.594 | 40.000 | 0.00 | 0.00 | 0.00 | 4.17 |
126 | 127 | 8.801715 | TGTAACTCGTCGTAACTTCTATTTTT | 57.198 | 30.769 | 0.00 | 0.00 | 0.00 | 1.94 |
127 | 128 | 8.801715 | TTGTAACTCGTCGTAACTTCTATTTT | 57.198 | 30.769 | 0.00 | 0.00 | 0.00 | 1.82 |
142 | 145 | 6.091713 | CCCGTAATTCTCATTTTGTAACTCGT | 59.908 | 38.462 | 0.00 | 0.00 | 0.00 | 4.18 |
166 | 169 | 6.204108 | CGGTCCCACTGTTATATGTAATTTCC | 59.796 | 42.308 | 0.00 | 0.00 | 0.00 | 3.13 |
182 | 185 | 1.061546 | AAACATGTACCGGTCCCACT | 58.938 | 50.000 | 12.40 | 0.00 | 0.00 | 4.00 |
197 | 200 | 2.649531 | AACTGGTCCCATCGAAAACA | 57.350 | 45.000 | 0.00 | 0.00 | 0.00 | 2.83 |
203 | 206 | 3.064820 | CGGAAAAATAACTGGTCCCATCG | 59.935 | 47.826 | 0.00 | 0.00 | 0.00 | 3.84 |
223 | 226 | 1.067212 | CAAGACGGATCTACCCTTCGG | 59.933 | 57.143 | 0.00 | 0.00 | 33.57 | 4.30 |
226 | 229 | 2.544844 | TCCAAGACGGATCTACCCTT | 57.455 | 50.000 | 0.00 | 0.00 | 39.64 | 3.95 |
290 | 293 | 1.301716 | CCGGATTATCTGCGTGGGG | 60.302 | 63.158 | 0.00 | 0.00 | 36.91 | 4.96 |
347 | 350 | 3.204827 | CCTTGATTGAGGCCGCCG | 61.205 | 66.667 | 3.22 | 0.00 | 0.00 | 6.46 |
361 | 364 | 2.115266 | CCGGTGGTTGCTTCCCTT | 59.885 | 61.111 | 0.00 | 0.00 | 0.00 | 3.95 |
382 | 385 | 2.107953 | GAGCGAGACCAGGGATGC | 59.892 | 66.667 | 0.00 | 0.00 | 0.00 | 3.91 |
384 | 387 | 1.760086 | CAGGAGCGAGACCAGGGAT | 60.760 | 63.158 | 0.00 | 0.00 | 0.00 | 3.85 |
505 | 516 | 4.988598 | CTTGCTGGGCGTCACCGT | 62.989 | 66.667 | 0.00 | 0.00 | 40.62 | 4.83 |
549 | 560 | 0.179056 | GCTACACCCATGTATGCCGT | 60.179 | 55.000 | 0.00 | 0.00 | 40.57 | 5.68 |
551 | 562 | 1.134098 | ACTGCTACACCCATGTATGCC | 60.134 | 52.381 | 0.00 | 0.00 | 40.57 | 4.40 |
609 | 620 | 1.371558 | GGAGGAGTTGAACCGTGCT | 59.628 | 57.895 | 0.00 | 0.00 | 0.00 | 4.40 |
620 | 631 | 1.083141 | GGAAGGGAAGGGGAGGAGT | 59.917 | 63.158 | 0.00 | 0.00 | 0.00 | 3.85 |
686 | 699 | 9.765795 | AGAAACAATGAACTACTATAGGCATAC | 57.234 | 33.333 | 4.43 | 0.00 | 0.00 | 2.39 |
812 | 829 | 9.435688 | TCACAATAGAACAAATATGGGATATCG | 57.564 | 33.333 | 0.00 | 0.00 | 0.00 | 2.92 |
1029 | 1059 | 0.106015 | AGAAAGCACACCAAAGGGCT | 60.106 | 50.000 | 0.00 | 0.00 | 37.90 | 5.19 |
1040 | 1070 | 3.214328 | TCAGTTCCAGGAAAGAAAGCAC | 58.786 | 45.455 | 2.45 | 0.00 | 0.00 | 4.40 |
1084 | 1114 | 3.511146 | TGCCAACCAATCTCTTTCCATTC | 59.489 | 43.478 | 0.00 | 0.00 | 0.00 | 2.67 |
1098 | 1128 | 0.467290 | GGTCTGTTCCTTGCCAACCA | 60.467 | 55.000 | 0.00 | 0.00 | 0.00 | 3.67 |
1205 | 1235 | 9.069082 | TCCTAGTTTAGCTACAGAATACTGATC | 57.931 | 37.037 | 0.00 | 0.00 | 46.03 | 2.92 |
1283 | 1313 | 9.411801 | GAAGAATAACAAATTTTCCAAGGAGAC | 57.588 | 33.333 | 0.00 | 0.00 | 0.00 | 3.36 |
1396 | 1433 | 9.181805 | GCCTGTAATTTACTTCTTCAAAAAGAC | 57.818 | 33.333 | 7.99 | 0.00 | 41.23 | 3.01 |
1431 | 1471 | 1.691196 | TGGAAGAAGCAGTTGTTGGG | 58.309 | 50.000 | 0.00 | 0.00 | 0.00 | 4.12 |
1485 | 1525 | 6.636454 | AACTGGGAACTGATGGATAGTTAA | 57.364 | 37.500 | 0.00 | 0.00 | 38.42 | 2.01 |
1560 | 1600 | 1.008079 | GTGCTGCAAGTTGCCACTC | 60.008 | 57.895 | 24.59 | 13.28 | 44.23 | 3.51 |
1685 | 1726 | 8.503196 | TGTACATGACATATGTTCACAAGAAAC | 58.497 | 33.333 | 10.30 | 5.90 | 31.62 | 2.78 |
1722 | 1766 | 4.515028 | TCCTAGATTTCTGTCCGGACTA | 57.485 | 45.455 | 33.39 | 19.81 | 0.00 | 2.59 |
1807 | 1852 | 2.417586 | CACTTCAATTCGAGCATCAGCA | 59.582 | 45.455 | 0.00 | 0.00 | 45.49 | 4.41 |
1831 | 1877 | 5.122396 | GCATTAGTCTGAAGTCCGAACAAAT | 59.878 | 40.000 | 0.00 | 0.00 | 0.00 | 2.32 |
1839 | 1885 | 6.341316 | TGTTGATAGCATTAGTCTGAAGTCC | 58.659 | 40.000 | 0.00 | 0.00 | 0.00 | 3.85 |
1880 | 1926 | 3.126000 | GCCTTGCTCACTTCAAGTATGAC | 59.874 | 47.826 | 0.00 | 0.00 | 39.30 | 3.06 |
1903 | 1949 | 2.079421 | AGGGGATATACCTCGGAGGAA | 58.921 | 52.381 | 30.13 | 14.89 | 45.50 | 3.36 |
1905 | 1951 | 1.358103 | TCAGGGGATATACCTCGGAGG | 59.642 | 57.143 | 22.40 | 22.40 | 45.50 | 4.30 |
1948 | 1994 | 2.280797 | GGCACGTGTCTTCAGGCA | 60.281 | 61.111 | 18.38 | 0.00 | 33.37 | 4.75 |
2052 | 2154 | 2.639286 | GCACACGTGAGCCCAAAG | 59.361 | 61.111 | 25.07 | 4.56 | 0.00 | 2.77 |
2093 | 2350 | 5.395657 | CCTCGCCATTGCCTATATTATGAGA | 60.396 | 44.000 | 0.00 | 0.00 | 0.00 | 3.27 |
2094 | 2351 | 4.813161 | CCTCGCCATTGCCTATATTATGAG | 59.187 | 45.833 | 0.00 | 0.00 | 0.00 | 2.90 |
2095 | 2352 | 4.469586 | TCCTCGCCATTGCCTATATTATGA | 59.530 | 41.667 | 0.00 | 0.00 | 0.00 | 2.15 |
2121 | 2458 | 4.666176 | CACAAACGAAATTTCAGTCGACTG | 59.334 | 41.667 | 34.76 | 34.76 | 45.08 | 3.51 |
2147 | 3008 | 3.919223 | AGTATCGATCTTAGCCGTTCC | 57.081 | 47.619 | 0.00 | 0.00 | 0.00 | 3.62 |
2153 | 3014 | 4.434520 | GGCCCATAAGTATCGATCTTAGC | 58.565 | 47.826 | 0.00 | 9.29 | 32.13 | 3.09 |
2201 | 3207 | 0.594284 | CGATCTTAGTCGTTCGGCCC | 60.594 | 60.000 | 0.00 | 0.00 | 36.88 | 5.80 |
2203 | 3209 | 2.402640 | ATCGATCTTAGTCGTTCGGC | 57.597 | 50.000 | 0.00 | 0.00 | 42.07 | 5.54 |
2221 | 3793 | 3.097614 | ACTCGTTTGGGCTCACTAGTAT | 58.902 | 45.455 | 0.00 | 0.00 | 0.00 | 2.12 |
2241 | 3844 | 3.429960 | GGACCCACAAGTACCGATCTTAC | 60.430 | 52.174 | 0.00 | 0.00 | 0.00 | 2.34 |
2249 | 3852 | 0.475044 | TGGTTGGACCCACAAGTACC | 59.525 | 55.000 | 0.00 | 0.95 | 37.50 | 3.34 |
2261 | 3864 | 8.620416 | CACAATTATCGATCTTAATTGGTTGGA | 58.380 | 33.333 | 25.13 | 3.15 | 45.17 | 3.53 |
2262 | 3865 | 7.862372 | CCACAATTATCGATCTTAATTGGTTGG | 59.138 | 37.037 | 25.13 | 21.46 | 45.17 | 3.77 |
2264 | 3867 | 7.470009 | GCCCACAATTATCGATCTTAATTGGTT | 60.470 | 37.037 | 25.13 | 11.01 | 45.17 | 3.67 |
2266 | 3869 | 6.381801 | GCCCACAATTATCGATCTTAATTGG | 58.618 | 40.000 | 25.13 | 17.50 | 45.17 | 3.16 |
2270 | 3927 | 4.141367 | TGGGCCCACAATTATCGATCTTAA | 60.141 | 41.667 | 24.45 | 0.00 | 0.00 | 1.85 |
2281 | 3938 | 0.469144 | AGTCGTTTGGGCCCACAATT | 60.469 | 50.000 | 28.70 | 5.29 | 0.00 | 2.32 |
2282 | 3939 | 0.402504 | TAGTCGTTTGGGCCCACAAT | 59.597 | 50.000 | 28.70 | 10.82 | 0.00 | 2.71 |
2296 | 3953 | 2.858344 | CCGCAAGTACCAATCTTAGTCG | 59.142 | 50.000 | 0.00 | 0.00 | 0.00 | 4.18 |
2304 | 3961 | 2.071502 | TGGTCCCGCAAGTACCAAT | 58.928 | 52.632 | 0.00 | 0.00 | 45.22 | 3.16 |
2306 | 3963 | 0.402504 | ATTTGGTCCCGCAAGTACCA | 59.597 | 50.000 | 0.00 | 0.00 | 46.13 | 3.25 |
2312 | 4348 | 2.039216 | TCTTAGTCATTTGGTCCCGCAA | 59.961 | 45.455 | 0.00 | 0.00 | 0.00 | 4.85 |
2315 | 4351 | 3.467803 | GGATCTTAGTCATTTGGTCCCG | 58.532 | 50.000 | 0.00 | 0.00 | 0.00 | 5.14 |
2319 | 4355 | 5.934402 | AGTACGGATCTTAGTCATTTGGT | 57.066 | 39.130 | 0.00 | 0.00 | 0.00 | 3.67 |
2325 | 4361 | 4.617530 | GCACACAAGTACGGATCTTAGTCA | 60.618 | 45.833 | 0.00 | 0.00 | 0.00 | 3.41 |
2346 | 4382 | 4.025061 | GCTACTATCTTAGTCGTTCGAGCA | 60.025 | 45.833 | 0.00 | 0.00 | 40.14 | 4.26 |
2395 | 4431 | 2.435069 | TCTTAGTTGTTCGGACCCACAA | 59.565 | 45.455 | 0.00 | 0.53 | 0.00 | 3.33 |
2457 | 4493 | 7.144000 | CACAAGTACCGTTCTTACTTACTCTT | 58.856 | 38.462 | 0.00 | 0.00 | 37.62 | 2.85 |
2461 | 4497 | 5.532557 | ACCACAAGTACCGTTCTTACTTAC | 58.467 | 41.667 | 0.00 | 0.00 | 37.62 | 2.34 |
2463 | 4499 | 4.677673 | ACCACAAGTACCGTTCTTACTT | 57.322 | 40.909 | 0.00 | 0.00 | 39.83 | 2.24 |
2484 | 4524 | 7.285629 | ACAAGTATCGATCTTAGTCATCCAGAA | 59.714 | 37.037 | 0.00 | 0.00 | 0.00 | 3.02 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.