Multiple sequence alignment - TraesCS6D01G193000
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 | TraesCS6D01G193000 | chr6D | 100.000 | 3413 | 0 | 0 | 1 | 3413 | 267199556 | 267202968 | 0.000000e+00 | 6303.0 |
1 | TraesCS6D01G193000 | chr6A | 94.965 | 2820 | 66 | 23 | 535 | 3302 | 380109803 | 380112598 | 0.000000e+00 | 4351.0 |
2 | TraesCS6D01G193000 | chr6A | 92.537 | 201 | 12 | 1 | 2 | 202 | 380109364 | 380109561 | 5.570000e-73 | 285.0 |
3 | TraesCS6D01G193000 | chr6A | 84.912 | 285 | 17 | 3 | 231 | 514 | 380109559 | 380109818 | 7.260000e-67 | 265.0 |
4 | TraesCS6D01G193000 | chr6B | 96.899 | 2096 | 37 | 7 | 651 | 2744 | 415729624 | 415731693 | 0.000000e+00 | 3485.0 |
5 | TraesCS6D01G193000 | chr6B | 93.569 | 311 | 15 | 2 | 3106 | 3413 | 415732431 | 415732739 | 3.100000e-125 | 459.0 |
6 | TraesCS6D01G193000 | chr6B | 93.578 | 218 | 10 | 2 | 2925 | 3138 | 415732212 | 415732429 | 4.250000e-84 | 322.0 |
7 | TraesCS6D01G193000 | chr6B | 95.604 | 91 | 4 | 0 | 2786 | 2876 | 415731901 | 415731991 | 2.740000e-31 | 147.0 |
8 | TraesCS6D01G193000 | chr6B | 100.000 | 37 | 0 | 0 | 535 | 571 | 415729511 | 415729547 | 6.110000e-08 | 69.4 |
9 | TraesCS6D01G193000 | chr5D | 93.506 | 77 | 5 | 0 | 1211 | 1287 | 552784603 | 552784527 | 7.740000e-22 | 115.0 |
10 | TraesCS6D01G193000 | chr5B | 93.506 | 77 | 5 | 0 | 1211 | 1287 | 697679891 | 697679967 | 7.740000e-22 | 115.0 |
11 | TraesCS6D01G193000 | chr5B | 90.909 | 77 | 7 | 0 | 1211 | 1287 | 697778088 | 697778164 | 1.680000e-18 | 104.0 |
12 | TraesCS6D01G193000 | chr4A | 92.208 | 77 | 6 | 0 | 1211 | 1287 | 615212962 | 615213038 | 3.600000e-20 | 110.0 |
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 | TraesCS6D01G193000 | chr6D | 267199556 | 267202968 | 3412 | False | 6303.000000 | 6303 | 100.000000 | 1 | 3413 | 1 | chr6D.!!$F1 | 3412 |
1 | TraesCS6D01G193000 | chr6A | 380109364 | 380112598 | 3234 | False | 1633.666667 | 4351 | 90.804667 | 2 | 3302 | 3 | chr6A.!!$F1 | 3300 |
2 | TraesCS6D01G193000 | chr6B | 415729511 | 415732739 | 3228 | False | 896.480000 | 3485 | 95.930000 | 535 | 3413 | 5 | chr6B.!!$F1 | 2878 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
933 | 995 | 0.796255 | CCCTCTCCCTATCCATCCCT | 59.204 | 60.000 | 0.0 | 0.0 | 0.0 | 4.20 | F |
934 | 996 | 1.153132 | CCCTCTCCCTATCCATCCCTT | 59.847 | 57.143 | 0.0 | 0.0 | 0.0 | 3.95 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2271 | 2333 | 1.304381 | ACCCGGCATGCACATCTTT | 60.304 | 52.632 | 21.36 | 0.0 | 0.0 | 2.52 | R |
2613 | 2675 | 4.060205 | CAAGAGGAAAACAAAATGGCCAG | 58.940 | 43.478 | 13.05 | 0.0 | 0.0 | 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 |
---|---|---|---|---|---|---|---|---|---|
40 | 41 | 3.742369 | GTGCCCAAAGAATGTTGTGAATG | 59.258 | 43.478 | 0.00 | 0.00 | 0.00 | 2.67 |
43 | 44 | 4.813027 | CCCAAAGAATGTTGTGAATGGAG | 58.187 | 43.478 | 0.00 | 0.00 | 0.00 | 3.86 |
65 | 66 | 6.321435 | GGAGCATAGCAAATAGGTTAGGTTTT | 59.679 | 38.462 | 0.00 | 0.00 | 0.00 | 2.43 |
112 | 113 | 8.677300 | TGCAGATTCAAGTCCTAAATTTATCAC | 58.323 | 33.333 | 0.00 | 0.00 | 0.00 | 3.06 |
135 | 136 | 4.498009 | CGAATGCTCGCCTTTTATTGGATT | 60.498 | 41.667 | 0.00 | 0.00 | 38.45 | 3.01 |
136 | 137 | 5.343307 | AATGCTCGCCTTTTATTGGATTT | 57.657 | 34.783 | 0.00 | 0.00 | 0.00 | 2.17 |
137 | 138 | 6.463995 | AATGCTCGCCTTTTATTGGATTTA | 57.536 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
168 | 169 | 1.879380 | CCTTTTGGTGATGTTCGCTCA | 59.121 | 47.619 | 0.00 | 0.00 | 34.07 | 4.26 |
178 | 179 | 3.006217 | TGATGTTCGCTCATAGGAGATGG | 59.994 | 47.826 | 8.95 | 0.00 | 44.26 | 3.51 |
181 | 182 | 1.735920 | CGCTCATAGGAGATGGCGC | 60.736 | 63.158 | 8.95 | 0.00 | 44.26 | 6.53 |
206 | 207 | 6.296365 | CATGTTGACTACAAGATGCCTATG | 57.704 | 41.667 | 7.04 | 0.00 | 45.67 | 2.23 |
207 | 208 | 5.675684 | TGTTGACTACAAGATGCCTATGA | 57.324 | 39.130 | 0.00 | 0.00 | 36.64 | 2.15 |
208 | 209 | 6.239217 | TGTTGACTACAAGATGCCTATGAT | 57.761 | 37.500 | 0.00 | 0.00 | 36.64 | 2.45 |
209 | 210 | 6.051074 | TGTTGACTACAAGATGCCTATGATG | 58.949 | 40.000 | 0.00 | 0.00 | 36.64 | 3.07 |
210 | 211 | 6.127083 | TGTTGACTACAAGATGCCTATGATGA | 60.127 | 38.462 | 0.00 | 0.00 | 36.64 | 2.92 |
211 | 212 | 6.676990 | TGACTACAAGATGCCTATGATGAT | 57.323 | 37.500 | 0.00 | 0.00 | 0.00 | 2.45 |
212 | 213 | 7.071069 | TGACTACAAGATGCCTATGATGATT | 57.929 | 36.000 | 0.00 | 0.00 | 0.00 | 2.57 |
213 | 214 | 7.157347 | TGACTACAAGATGCCTATGATGATTC | 58.843 | 38.462 | 0.00 | 0.00 | 0.00 | 2.52 |
214 | 215 | 7.015974 | TGACTACAAGATGCCTATGATGATTCT | 59.984 | 37.037 | 0.00 | 0.00 | 0.00 | 2.40 |
215 | 216 | 8.427902 | ACTACAAGATGCCTATGATGATTCTA | 57.572 | 34.615 | 0.00 | 0.00 | 0.00 | 2.10 |
216 | 217 | 9.044646 | ACTACAAGATGCCTATGATGATTCTAT | 57.955 | 33.333 | 0.00 | 0.00 | 0.00 | 1.98 |
217 | 218 | 9.531942 | CTACAAGATGCCTATGATGATTCTATC | 57.468 | 37.037 | 0.00 | 0.00 | 0.00 | 2.08 |
218 | 219 | 7.914859 | ACAAGATGCCTATGATGATTCTATCA | 58.085 | 34.615 | 0.00 | 0.00 | 44.55 | 2.15 |
219 | 220 | 8.380867 | ACAAGATGCCTATGATGATTCTATCAA | 58.619 | 33.333 | 0.00 | 0.00 | 43.50 | 2.57 |
220 | 221 | 9.397280 | CAAGATGCCTATGATGATTCTATCAAT | 57.603 | 33.333 | 0.00 | 0.00 | 43.50 | 2.57 |
221 | 222 | 9.616156 | AAGATGCCTATGATGATTCTATCAATC | 57.384 | 33.333 | 0.00 | 0.00 | 43.50 | 2.67 |
222 | 223 | 8.212312 | AGATGCCTATGATGATTCTATCAATCC | 58.788 | 37.037 | 0.00 | 0.00 | 43.50 | 3.01 |
223 | 224 | 6.656902 | TGCCTATGATGATTCTATCAATCCC | 58.343 | 40.000 | 0.00 | 0.00 | 43.50 | 3.85 |
224 | 225 | 6.216046 | TGCCTATGATGATTCTATCAATCCCA | 59.784 | 38.462 | 0.00 | 0.00 | 43.50 | 4.37 |
225 | 226 | 7.092128 | TGCCTATGATGATTCTATCAATCCCAT | 60.092 | 37.037 | 0.00 | 0.00 | 43.50 | 4.00 |
226 | 227 | 7.228906 | GCCTATGATGATTCTATCAATCCCATG | 59.771 | 40.741 | 0.00 | 0.00 | 43.50 | 3.66 |
227 | 228 | 7.720074 | CCTATGATGATTCTATCAATCCCATGG | 59.280 | 40.741 | 4.14 | 4.14 | 43.50 | 3.66 |
228 | 229 | 6.458630 | TGATGATTCTATCAATCCCATGGT | 57.541 | 37.500 | 11.73 | 0.00 | 43.50 | 3.55 |
229 | 230 | 6.855667 | TGATGATTCTATCAATCCCATGGTT | 58.144 | 36.000 | 11.73 | 0.00 | 43.50 | 3.67 |
230 | 231 | 7.299896 | TGATGATTCTATCAATCCCATGGTTT | 58.700 | 34.615 | 11.73 | 0.74 | 43.50 | 3.27 |
231 | 232 | 6.964807 | TGATTCTATCAATCCCATGGTTTG | 57.035 | 37.500 | 11.73 | 13.92 | 36.11 | 2.93 |
232 | 233 | 5.302568 | TGATTCTATCAATCCCATGGTTTGC | 59.697 | 40.000 | 11.73 | 1.05 | 36.11 | 3.68 |
233 | 234 | 4.524802 | TCTATCAATCCCATGGTTTGCT | 57.475 | 40.909 | 11.73 | 8.41 | 33.73 | 3.91 |
234 | 235 | 4.209538 | TCTATCAATCCCATGGTTTGCTG | 58.790 | 43.478 | 11.73 | 7.70 | 33.73 | 4.41 |
235 | 236 | 1.559368 | TCAATCCCATGGTTTGCTGG | 58.441 | 50.000 | 11.73 | 0.00 | 33.73 | 4.85 |
325 | 327 | 4.985538 | AAATGTCCGTGTTGGTGTAAAA | 57.014 | 36.364 | 0.00 | 0.00 | 39.52 | 1.52 |
387 | 389 | 7.201145 | GCTAGACTAATCCTACGAATGTCAAA | 58.799 | 38.462 | 0.00 | 0.00 | 0.00 | 2.69 |
398 | 400 | 3.689649 | ACGAATGTCAAAGATACCTTGGC | 59.310 | 43.478 | 0.00 | 0.00 | 31.91 | 4.52 |
407 | 409 | 6.016276 | GTCAAAGATACCTTGGCTTTTTGAGA | 60.016 | 38.462 | 8.01 | 0.00 | 34.78 | 3.27 |
415 | 417 | 2.985896 | TGGCTTTTTGAGAGATACCCG | 58.014 | 47.619 | 0.00 | 0.00 | 0.00 | 5.28 |
438 | 440 | 5.523552 | CGTGAAATACCATGATGAGTAAGCA | 59.476 | 40.000 | 0.00 | 0.00 | 0.00 | 3.91 |
460 | 462 | 5.487433 | CACCTGTGTCTGTACCATAATTCA | 58.513 | 41.667 | 0.00 | 0.00 | 0.00 | 2.57 |
492 | 494 | 2.508891 | CGAAGACACCGCGAGATGC | 61.509 | 63.158 | 8.23 | 0.00 | 41.47 | 3.91 |
498 | 500 | 3.147595 | ACCGCGAGATGCTGCCTA | 61.148 | 61.111 | 8.23 | 0.00 | 43.27 | 3.93 |
499 | 501 | 2.106938 | CCGCGAGATGCTGCCTAA | 59.893 | 61.111 | 8.23 | 0.00 | 43.27 | 2.69 |
500 | 502 | 1.521457 | CCGCGAGATGCTGCCTAAA | 60.521 | 57.895 | 8.23 | 0.00 | 43.27 | 1.85 |
501 | 503 | 1.638467 | CGCGAGATGCTGCCTAAAC | 59.362 | 57.895 | 0.00 | 0.00 | 43.27 | 2.01 |
502 | 504 | 1.638467 | GCGAGATGCTGCCTAAACG | 59.362 | 57.895 | 0.00 | 0.00 | 41.73 | 3.60 |
503 | 505 | 1.084370 | GCGAGATGCTGCCTAAACGT | 61.084 | 55.000 | 0.00 | 0.00 | 41.73 | 3.99 |
504 | 506 | 1.801395 | GCGAGATGCTGCCTAAACGTA | 60.801 | 52.381 | 0.00 | 0.00 | 41.73 | 3.57 |
505 | 507 | 2.536365 | CGAGATGCTGCCTAAACGTAA | 58.464 | 47.619 | 0.00 | 0.00 | 0.00 | 3.18 |
506 | 508 | 2.927477 | CGAGATGCTGCCTAAACGTAAA | 59.073 | 45.455 | 0.00 | 0.00 | 0.00 | 2.01 |
507 | 509 | 3.241995 | CGAGATGCTGCCTAAACGTAAAC | 60.242 | 47.826 | 0.00 | 0.00 | 0.00 | 2.01 |
508 | 510 | 3.670625 | AGATGCTGCCTAAACGTAAACA | 58.329 | 40.909 | 0.00 | 0.00 | 0.00 | 2.83 |
509 | 511 | 3.684788 | AGATGCTGCCTAAACGTAAACAG | 59.315 | 43.478 | 0.00 | 0.00 | 0.00 | 3.16 |
510 | 512 | 2.841215 | TGCTGCCTAAACGTAAACAGT | 58.159 | 42.857 | 0.00 | 0.00 | 0.00 | 3.55 |
511 | 513 | 2.803956 | TGCTGCCTAAACGTAAACAGTC | 59.196 | 45.455 | 0.00 | 0.00 | 0.00 | 3.51 |
512 | 514 | 2.803956 | GCTGCCTAAACGTAAACAGTCA | 59.196 | 45.455 | 0.00 | 0.00 | 0.00 | 3.41 |
513 | 515 | 3.363673 | GCTGCCTAAACGTAAACAGTCAC | 60.364 | 47.826 | 0.00 | 0.00 | 0.00 | 3.67 |
514 | 516 | 4.056050 | CTGCCTAAACGTAAACAGTCACT | 58.944 | 43.478 | 0.00 | 0.00 | 0.00 | 3.41 |
515 | 517 | 4.444536 | TGCCTAAACGTAAACAGTCACTT | 58.555 | 39.130 | 0.00 | 0.00 | 0.00 | 3.16 |
516 | 518 | 5.599732 | TGCCTAAACGTAAACAGTCACTTA | 58.400 | 37.500 | 0.00 | 0.00 | 0.00 | 2.24 |
517 | 519 | 5.463061 | TGCCTAAACGTAAACAGTCACTTAC | 59.537 | 40.000 | 0.00 | 0.00 | 0.00 | 2.34 |
518 | 520 | 5.693555 | GCCTAAACGTAAACAGTCACTTACT | 59.306 | 40.000 | 0.00 | 0.00 | 39.81 | 2.24 |
519 | 521 | 6.128982 | GCCTAAACGTAAACAGTCACTTACTC | 60.129 | 42.308 | 0.00 | 0.00 | 35.76 | 2.59 |
520 | 522 | 6.919662 | CCTAAACGTAAACAGTCACTTACTCA | 59.080 | 38.462 | 0.00 | 0.00 | 35.76 | 3.41 |
521 | 523 | 6.579491 | AAACGTAAACAGTCACTTACTCAC | 57.421 | 37.500 | 0.00 | 0.00 | 35.76 | 3.51 |
522 | 524 | 5.511234 | ACGTAAACAGTCACTTACTCACT | 57.489 | 39.130 | 0.00 | 0.00 | 35.76 | 3.41 |
523 | 525 | 5.899299 | ACGTAAACAGTCACTTACTCACTT | 58.101 | 37.500 | 0.00 | 0.00 | 35.76 | 3.16 |
524 | 526 | 5.975939 | ACGTAAACAGTCACTTACTCACTTC | 59.024 | 40.000 | 0.00 | 0.00 | 35.76 | 3.01 |
525 | 527 | 5.401674 | CGTAAACAGTCACTTACTCACTTCC | 59.598 | 44.000 | 0.00 | 0.00 | 35.76 | 3.46 |
526 | 528 | 5.615925 | AAACAGTCACTTACTCACTTCCT | 57.384 | 39.130 | 0.00 | 0.00 | 35.76 | 3.36 |
527 | 529 | 5.615925 | AACAGTCACTTACTCACTTCCTT | 57.384 | 39.130 | 0.00 | 0.00 | 35.76 | 3.36 |
528 | 530 | 6.726490 | AACAGTCACTTACTCACTTCCTTA | 57.274 | 37.500 | 0.00 | 0.00 | 35.76 | 2.69 |
529 | 531 | 6.726490 | ACAGTCACTTACTCACTTCCTTAA | 57.274 | 37.500 | 0.00 | 0.00 | 35.76 | 1.85 |
530 | 532 | 7.120923 | ACAGTCACTTACTCACTTCCTTAAA | 57.879 | 36.000 | 0.00 | 0.00 | 35.76 | 1.52 |
531 | 533 | 7.210873 | ACAGTCACTTACTCACTTCCTTAAAG | 58.789 | 38.462 | 0.00 | 0.00 | 35.76 | 1.85 |
532 | 534 | 7.069578 | ACAGTCACTTACTCACTTCCTTAAAGA | 59.930 | 37.037 | 0.00 | 0.00 | 35.76 | 2.52 |
533 | 535 | 7.926555 | CAGTCACTTACTCACTTCCTTAAAGAA | 59.073 | 37.037 | 0.00 | 0.00 | 35.76 | 2.52 |
577 | 579 | 4.202264 | ACTCCTCTAGAAAATATGCACCCG | 60.202 | 45.833 | 0.00 | 0.00 | 0.00 | 5.28 |
933 | 995 | 0.796255 | CCCTCTCCCTATCCATCCCT | 59.204 | 60.000 | 0.00 | 0.00 | 0.00 | 4.20 |
934 | 996 | 1.153132 | CCCTCTCCCTATCCATCCCTT | 59.847 | 57.143 | 0.00 | 0.00 | 0.00 | 3.95 |
935 | 997 | 2.545810 | CCTCTCCCTATCCATCCCTTC | 58.454 | 57.143 | 0.00 | 0.00 | 0.00 | 3.46 |
936 | 998 | 2.545810 | CTCTCCCTATCCATCCCTTCC | 58.454 | 57.143 | 0.00 | 0.00 | 0.00 | 3.46 |
1950 | 2012 | 2.567049 | GACCCAGTCGACCTCGTG | 59.433 | 66.667 | 13.01 | 3.52 | 40.80 | 4.35 |
1977 | 2039 | 3.134127 | GAGACCCGCAATGCCACC | 61.134 | 66.667 | 0.00 | 0.00 | 0.00 | 4.61 |
2271 | 2333 | 0.904865 | ACGACAAGGATGAGGAGGCA | 60.905 | 55.000 | 0.00 | 0.00 | 0.00 | 4.75 |
2613 | 2675 | 2.668457 | CTGTCGTTATGTCCTTGACTGC | 59.332 | 50.000 | 0.00 | 0.00 | 33.15 | 4.40 |
2668 | 2730 | 8.963725 | TGCTTGAAGATGATTCATTATTCTTGT | 58.036 | 29.630 | 18.61 | 0.00 | 0.00 | 3.16 |
2721 | 2783 | 6.824305 | TGGAGGTATACGGTTATAGCTTAC | 57.176 | 41.667 | 0.00 | 4.58 | 45.20 | 2.34 |
2740 | 2802 | 6.148480 | AGCTTACTTGTTTACTGCTTCAGATG | 59.852 | 38.462 | 0.29 | 0.00 | 35.18 | 2.90 |
2843 | 3071 | 1.268625 | CTGCAGCAATCATGTGTGTGT | 59.731 | 47.619 | 0.00 | 0.00 | 0.00 | 3.72 |
2910 | 3152 | 5.631096 | CGTGCTCATCATCGTAGTTCATATT | 59.369 | 40.000 | 0.00 | 0.00 | 0.00 | 1.28 |
2912 | 3154 | 5.928264 | TGCTCATCATCGTAGTTCATATTGG | 59.072 | 40.000 | 0.00 | 0.00 | 0.00 | 3.16 |
2970 | 3373 | 1.078848 | GCGTCTGCTCATCTGGGTT | 60.079 | 57.895 | 0.00 | 0.00 | 38.39 | 4.11 |
3080 | 3487 | 4.383552 | GGTCATCTCAACCTATGCACTTCT | 60.384 | 45.833 | 0.00 | 0.00 | 33.78 | 2.85 |
3112 | 3519 | 0.998226 | CTGTTGCGTGCATGTTTCCG | 60.998 | 55.000 | 7.93 | 0.00 | 0.00 | 4.30 |
3113 | 3520 | 1.729131 | GTTGCGTGCATGTTTCCGG | 60.729 | 57.895 | 7.93 | 0.00 | 0.00 | 5.14 |
3172 | 3616 | 2.290367 | TGTGTTCCAAAATGCAGACTCG | 59.710 | 45.455 | 0.00 | 0.00 | 0.00 | 4.18 |
3266 | 3726 | 4.649267 | TGAACTCCATTAACATCACCCA | 57.351 | 40.909 | 0.00 | 0.00 | 0.00 | 4.51 |
3336 | 3796 | 6.919721 | GGTCTAGCATTATAGAGAAGACCAG | 58.080 | 44.000 | 12.51 | 0.00 | 46.94 | 4.00 |
3342 | 3802 | 5.295950 | CATTATAGAGAAGACCAGCCACAG | 58.704 | 45.833 | 0.00 | 0.00 | 0.00 | 3.66 |
3362 | 3822 | 2.503356 | AGGTTCATGAAGCAGGGAGTAG | 59.497 | 50.000 | 32.68 | 0.00 | 40.96 | 2.57 |
3374 | 3834 | 1.268283 | GGGAGTAGCAGCTGGGAACT | 61.268 | 60.000 | 17.12 | 6.32 | 0.00 | 3.01 |
3375 | 3835 | 1.486211 | GGAGTAGCAGCTGGGAACTA | 58.514 | 55.000 | 17.12 | 5.24 | 0.00 | 2.24 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
0 | 1 | 2.030185 | GCACAAGAGGACGAACTCACTA | 60.030 | 50.000 | 12.26 | 0.00 | 39.97 | 2.74 |
7 | 8 | 0.181587 | TTTGGGCACAAGAGGACGAA | 59.818 | 50.000 | 0.00 | 0.00 | 37.97 | 3.85 |
9 | 10 | 0.250295 | TCTTTGGGCACAAGAGGACG | 60.250 | 55.000 | 0.00 | 0.00 | 37.97 | 4.79 |
40 | 41 | 4.974399 | ACCTAACCTATTTGCTATGCTCC | 58.026 | 43.478 | 0.00 | 0.00 | 0.00 | 4.70 |
65 | 66 | 4.996122 | GCATGGATTGGTTTCATCACAAAA | 59.004 | 37.500 | 0.00 | 0.00 | 0.00 | 2.44 |
87 | 88 | 7.852945 | CGTGATAAATTTAGGACTTGAATCTGC | 59.147 | 37.037 | 3.94 | 0.00 | 0.00 | 4.26 |
137 | 138 | 9.178758 | GAACATCACCAAAAGGTCTAGAATAAT | 57.821 | 33.333 | 0.00 | 0.00 | 0.00 | 1.28 |
146 | 147 | 1.880027 | AGCGAACATCACCAAAAGGTC | 59.120 | 47.619 | 0.00 | 0.00 | 0.00 | 3.85 |
168 | 169 | 1.346062 | ACATGAGCGCCATCTCCTAT | 58.654 | 50.000 | 2.29 | 0.00 | 31.94 | 2.57 |
178 | 179 | 2.337583 | TCTTGTAGTCAACATGAGCGC | 58.662 | 47.619 | 0.00 | 0.00 | 37.35 | 5.92 |
181 | 182 | 4.511527 | AGGCATCTTGTAGTCAACATGAG | 58.488 | 43.478 | 0.00 | 0.00 | 43.29 | 2.90 |
202 | 203 | 8.272889 | ACCATGGGATTGATAGAATCATCATAG | 58.727 | 37.037 | 18.09 | 0.00 | 39.39 | 2.23 |
203 | 204 | 8.166479 | ACCATGGGATTGATAGAATCATCATA | 57.834 | 34.615 | 18.09 | 0.00 | 39.39 | 2.15 |
205 | 206 | 6.458630 | ACCATGGGATTGATAGAATCATCA | 57.541 | 37.500 | 18.09 | 0.00 | 39.39 | 3.07 |
206 | 207 | 7.600065 | CAAACCATGGGATTGATAGAATCATC | 58.400 | 38.462 | 21.74 | 0.00 | 37.62 | 2.92 |
207 | 208 | 6.014840 | GCAAACCATGGGATTGATAGAATCAT | 60.015 | 38.462 | 27.43 | 0.00 | 37.62 | 2.45 |
208 | 209 | 5.302568 | GCAAACCATGGGATTGATAGAATCA | 59.697 | 40.000 | 27.43 | 0.00 | 37.62 | 2.57 |
209 | 210 | 5.537674 | AGCAAACCATGGGATTGATAGAATC | 59.462 | 40.000 | 27.43 | 13.25 | 37.62 | 2.52 |
210 | 211 | 5.303589 | CAGCAAACCATGGGATTGATAGAAT | 59.696 | 40.000 | 27.43 | 9.44 | 37.62 | 2.40 |
211 | 212 | 4.646040 | CAGCAAACCATGGGATTGATAGAA | 59.354 | 41.667 | 27.43 | 0.00 | 37.62 | 2.10 |
212 | 213 | 4.209538 | CAGCAAACCATGGGATTGATAGA | 58.790 | 43.478 | 27.43 | 0.00 | 37.62 | 1.98 |
213 | 214 | 3.319972 | CCAGCAAACCATGGGATTGATAG | 59.680 | 47.826 | 27.43 | 15.93 | 37.62 | 2.08 |
214 | 215 | 3.298619 | CCAGCAAACCATGGGATTGATA | 58.701 | 45.455 | 27.43 | 0.00 | 37.62 | 2.15 |
215 | 216 | 2.112998 | CCAGCAAACCATGGGATTGAT | 58.887 | 47.619 | 27.43 | 21.70 | 37.62 | 2.57 |
216 | 217 | 1.203162 | ACCAGCAAACCATGGGATTGA | 60.203 | 47.619 | 27.43 | 0.00 | 37.62 | 2.57 |
217 | 218 | 1.269012 | ACCAGCAAACCATGGGATTG | 58.731 | 50.000 | 21.87 | 21.87 | 41.13 | 2.67 |
218 | 219 | 2.028561 | AACCAGCAAACCATGGGATT | 57.971 | 45.000 | 18.09 | 8.02 | 41.13 | 3.01 |
219 | 220 | 1.624813 | CAAACCAGCAAACCATGGGAT | 59.375 | 47.619 | 18.09 | 0.78 | 41.13 | 3.85 |
220 | 221 | 1.047002 | CAAACCAGCAAACCATGGGA | 58.953 | 50.000 | 18.09 | 0.00 | 41.13 | 4.37 |
221 | 222 | 0.035176 | CCAAACCAGCAAACCATGGG | 59.965 | 55.000 | 18.09 | 0.00 | 41.13 | 4.00 |
222 | 223 | 0.758123 | ACCAAACCAGCAAACCATGG | 59.242 | 50.000 | 11.19 | 11.19 | 42.60 | 3.66 |
223 | 224 | 1.688197 | AGACCAAACCAGCAAACCATG | 59.312 | 47.619 | 0.00 | 0.00 | 0.00 | 3.66 |
224 | 225 | 2.086610 | AGACCAAACCAGCAAACCAT | 57.913 | 45.000 | 0.00 | 0.00 | 0.00 | 3.55 |
225 | 226 | 1.859302 | AAGACCAAACCAGCAAACCA | 58.141 | 45.000 | 0.00 | 0.00 | 0.00 | 3.67 |
226 | 227 | 2.798145 | CGAAAGACCAAACCAGCAAACC | 60.798 | 50.000 | 0.00 | 0.00 | 0.00 | 3.27 |
227 | 228 | 2.098443 | TCGAAAGACCAAACCAGCAAAC | 59.902 | 45.455 | 0.00 | 0.00 | 33.31 | 2.93 |
228 | 229 | 2.370349 | TCGAAAGACCAAACCAGCAAA | 58.630 | 42.857 | 0.00 | 0.00 | 33.31 | 3.68 |
229 | 230 | 2.045561 | TCGAAAGACCAAACCAGCAA | 57.954 | 45.000 | 0.00 | 0.00 | 33.31 | 3.91 |
230 | 231 | 2.045561 | TTCGAAAGACCAAACCAGCA | 57.954 | 45.000 | 0.00 | 0.00 | 41.84 | 4.41 |
231 | 232 | 3.430333 | TTTTCGAAAGACCAAACCAGC | 57.570 | 42.857 | 10.98 | 0.00 | 41.84 | 4.85 |
232 | 233 | 3.735746 | GCATTTTCGAAAGACCAAACCAG | 59.264 | 43.478 | 10.98 | 0.00 | 41.84 | 4.00 |
233 | 234 | 3.383185 | AGCATTTTCGAAAGACCAAACCA | 59.617 | 39.130 | 10.98 | 0.00 | 41.84 | 3.67 |
234 | 235 | 3.977427 | AGCATTTTCGAAAGACCAAACC | 58.023 | 40.909 | 10.98 | 0.00 | 41.84 | 3.27 |
235 | 236 | 4.803613 | ACAAGCATTTTCGAAAGACCAAAC | 59.196 | 37.500 | 10.98 | 0.00 | 41.84 | 2.93 |
339 | 341 | 8.392372 | AGCGAAATACAGTATAGACATAGACA | 57.608 | 34.615 | 0.00 | 0.00 | 0.00 | 3.41 |
340 | 342 | 9.976255 | CTAGCGAAATACAGTATAGACATAGAC | 57.024 | 37.037 | 0.00 | 0.00 | 0.00 | 2.59 |
341 | 343 | 9.939802 | TCTAGCGAAATACAGTATAGACATAGA | 57.060 | 33.333 | 0.00 | 0.00 | 0.00 | 1.98 |
342 | 344 | 9.976255 | GTCTAGCGAAATACAGTATAGACATAG | 57.024 | 37.037 | 11.65 | 5.43 | 38.22 | 2.23 |
343 | 345 | 9.722184 | AGTCTAGCGAAATACAGTATAGACATA | 57.278 | 33.333 | 16.29 | 0.57 | 39.90 | 2.29 |
344 | 346 | 8.624367 | AGTCTAGCGAAATACAGTATAGACAT | 57.376 | 34.615 | 16.29 | 4.54 | 39.90 | 3.06 |
345 | 347 | 9.551734 | TTAGTCTAGCGAAATACAGTATAGACA | 57.448 | 33.333 | 16.29 | 5.15 | 39.90 | 3.41 |
348 | 350 | 9.991388 | GGATTAGTCTAGCGAAATACAGTATAG | 57.009 | 37.037 | 0.00 | 0.00 | 0.00 | 1.31 |
349 | 351 | 9.736414 | AGGATTAGTCTAGCGAAATACAGTATA | 57.264 | 33.333 | 0.00 | 0.00 | 0.00 | 1.47 |
350 | 352 | 8.638629 | AGGATTAGTCTAGCGAAATACAGTAT | 57.361 | 34.615 | 0.00 | 0.00 | 0.00 | 2.12 |
351 | 353 | 8.997323 | GTAGGATTAGTCTAGCGAAATACAGTA | 58.003 | 37.037 | 0.00 | 0.00 | 0.00 | 2.74 |
352 | 354 | 6.963083 | AGGATTAGTCTAGCGAAATACAGT | 57.037 | 37.500 | 0.00 | 0.00 | 0.00 | 3.55 |
353 | 355 | 7.016466 | CGTAGGATTAGTCTAGCGAAATACAG | 58.984 | 42.308 | 0.00 | 0.00 | 0.00 | 2.74 |
354 | 356 | 6.707608 | TCGTAGGATTAGTCTAGCGAAATACA | 59.292 | 38.462 | 0.00 | 0.00 | 0.00 | 2.29 |
355 | 357 | 7.126726 | TCGTAGGATTAGTCTAGCGAAATAC | 57.873 | 40.000 | 0.00 | 0.00 | 0.00 | 1.89 |
356 | 358 | 7.734924 | TTCGTAGGATTAGTCTAGCGAAATA | 57.265 | 36.000 | 0.00 | 0.00 | 32.80 | 1.40 |
357 | 359 | 6.630444 | TTCGTAGGATTAGTCTAGCGAAAT | 57.370 | 37.500 | 0.00 | 0.00 | 32.80 | 2.17 |
358 | 360 | 6.039047 | ACATTCGTAGGATTAGTCTAGCGAAA | 59.961 | 38.462 | 12.13 | 2.16 | 35.80 | 3.46 |
359 | 361 | 5.530171 | ACATTCGTAGGATTAGTCTAGCGAA | 59.470 | 40.000 | 11.13 | 11.13 | 36.17 | 4.70 |
360 | 362 | 5.061853 | ACATTCGTAGGATTAGTCTAGCGA | 58.938 | 41.667 | 0.00 | 0.00 | 0.00 | 4.93 |
361 | 363 | 5.049612 | TGACATTCGTAGGATTAGTCTAGCG | 60.050 | 44.000 | 11.26 | 0.00 | 0.00 | 4.26 |
362 | 364 | 6.315091 | TGACATTCGTAGGATTAGTCTAGC | 57.685 | 41.667 | 11.26 | 0.00 | 0.00 | 3.42 |
387 | 389 | 5.505181 | TCTCTCAAAAAGCCAAGGTATCT | 57.495 | 39.130 | 0.00 | 0.00 | 0.00 | 1.98 |
398 | 400 | 6.743575 | ATTTCACGGGTATCTCTCAAAAAG | 57.256 | 37.500 | 0.00 | 0.00 | 0.00 | 2.27 |
407 | 409 | 5.306937 | TCATCATGGTATTTCACGGGTATCT | 59.693 | 40.000 | 0.00 | 0.00 | 0.00 | 1.98 |
415 | 417 | 6.238484 | GGTGCTTACTCATCATGGTATTTCAC | 60.238 | 42.308 | 0.00 | 0.00 | 0.00 | 3.18 |
460 | 462 | 5.519722 | GGTGTCTTCGACAATTGATTTTGT | 58.480 | 37.500 | 13.59 | 0.00 | 44.49 | 2.83 |
492 | 494 | 4.056050 | AGTGACTGTTTACGTTTAGGCAG | 58.944 | 43.478 | 0.00 | 0.00 | 0.00 | 4.85 |
496 | 498 | 7.646922 | AGTGAGTAAGTGACTGTTTACGTTTAG | 59.353 | 37.037 | 0.00 | 0.00 | 39.06 | 1.85 |
498 | 500 | 6.335777 | AGTGAGTAAGTGACTGTTTACGTTT | 58.664 | 36.000 | 0.00 | 0.00 | 39.06 | 3.60 |
499 | 501 | 5.899299 | AGTGAGTAAGTGACTGTTTACGTT | 58.101 | 37.500 | 0.00 | 0.00 | 39.06 | 3.99 |
500 | 502 | 5.511234 | AGTGAGTAAGTGACTGTTTACGT | 57.489 | 39.130 | 0.00 | 0.00 | 39.06 | 3.57 |
501 | 503 | 5.401674 | GGAAGTGAGTAAGTGACTGTTTACG | 59.598 | 44.000 | 0.00 | 0.00 | 39.06 | 3.18 |
502 | 504 | 6.514063 | AGGAAGTGAGTAAGTGACTGTTTAC | 58.486 | 40.000 | 0.00 | 0.00 | 39.06 | 2.01 |
503 | 505 | 6.726490 | AGGAAGTGAGTAAGTGACTGTTTA | 57.274 | 37.500 | 0.00 | 0.00 | 39.06 | 2.01 |
504 | 506 | 5.615925 | AGGAAGTGAGTAAGTGACTGTTT | 57.384 | 39.130 | 0.00 | 0.00 | 39.06 | 2.83 |
505 | 507 | 5.615925 | AAGGAAGTGAGTAAGTGACTGTT | 57.384 | 39.130 | 0.00 | 0.00 | 39.06 | 3.16 |
506 | 508 | 6.726490 | TTAAGGAAGTGAGTAAGTGACTGT | 57.274 | 37.500 | 0.00 | 0.00 | 39.06 | 3.55 |
507 | 509 | 7.434492 | TCTTTAAGGAAGTGAGTAAGTGACTG | 58.566 | 38.462 | 0.00 | 0.00 | 36.15 | 3.51 |
508 | 510 | 7.598759 | TCTTTAAGGAAGTGAGTAAGTGACT | 57.401 | 36.000 | 0.00 | 0.00 | 37.61 | 3.41 |
509 | 511 | 8.658499 | TTTCTTTAAGGAAGTGAGTAAGTGAC | 57.342 | 34.615 | 0.00 | 0.00 | 36.70 | 3.67 |
510 | 512 | 9.326413 | CTTTTCTTTAAGGAAGTGAGTAAGTGA | 57.674 | 33.333 | 0.00 | 0.00 | 36.70 | 3.41 |
511 | 513 | 9.110502 | ACTTTTCTTTAAGGAAGTGAGTAAGTG | 57.889 | 33.333 | 10.36 | 0.00 | 36.70 | 3.16 |
520 | 522 | 6.930731 | TGTTTGCACTTTTCTTTAAGGAAGT | 58.069 | 32.000 | 0.00 | 8.19 | 36.70 | 3.01 |
521 | 523 | 7.035612 | ACTGTTTGCACTTTTCTTTAAGGAAG | 58.964 | 34.615 | 0.00 | 7.21 | 36.67 | 3.46 |
522 | 524 | 6.930731 | ACTGTTTGCACTTTTCTTTAAGGAA | 58.069 | 32.000 | 0.00 | 0.00 | 0.00 | 3.36 |
523 | 525 | 6.151985 | TGACTGTTTGCACTTTTCTTTAAGGA | 59.848 | 34.615 | 0.00 | 0.00 | 0.00 | 3.36 |
524 | 526 | 6.253512 | GTGACTGTTTGCACTTTTCTTTAAGG | 59.746 | 38.462 | 0.00 | 0.00 | 32.44 | 2.69 |
525 | 527 | 6.021468 | CGTGACTGTTTGCACTTTTCTTTAAG | 60.021 | 38.462 | 0.00 | 0.00 | 32.98 | 1.85 |
526 | 528 | 5.797934 | CGTGACTGTTTGCACTTTTCTTTAA | 59.202 | 36.000 | 0.00 | 0.00 | 32.98 | 1.52 |
527 | 529 | 5.328691 | CGTGACTGTTTGCACTTTTCTTTA | 58.671 | 37.500 | 0.00 | 0.00 | 32.98 | 1.85 |
528 | 530 | 4.165779 | CGTGACTGTTTGCACTTTTCTTT | 58.834 | 39.130 | 0.00 | 0.00 | 32.98 | 2.52 |
529 | 531 | 3.427503 | CCGTGACTGTTTGCACTTTTCTT | 60.428 | 43.478 | 0.00 | 0.00 | 32.98 | 2.52 |
530 | 532 | 2.097466 | CCGTGACTGTTTGCACTTTTCT | 59.903 | 45.455 | 0.00 | 0.00 | 32.98 | 2.52 |
531 | 533 | 2.159435 | ACCGTGACTGTTTGCACTTTTC | 60.159 | 45.455 | 0.00 | 0.00 | 32.98 | 2.29 |
532 | 534 | 1.816224 | ACCGTGACTGTTTGCACTTTT | 59.184 | 42.857 | 0.00 | 0.00 | 32.98 | 2.27 |
533 | 535 | 1.400494 | GACCGTGACTGTTTGCACTTT | 59.600 | 47.619 | 0.00 | 0.00 | 32.98 | 2.66 |
577 | 579 | 1.784283 | CATTTCACGGGAAAACGCAAC | 59.216 | 47.619 | 18.20 | 0.00 | 45.52 | 4.17 |
633 | 681 | 3.764466 | CCGGCTCCACGCTCTCTT | 61.764 | 66.667 | 0.00 | 0.00 | 39.13 | 2.85 |
649 | 697 | 1.581447 | CTTGCCTTTCTGCCGTTCC | 59.419 | 57.895 | 0.00 | 0.00 | 0.00 | 3.62 |
933 | 995 | 1.382695 | GTCGGGGGAGAGGATGGAA | 60.383 | 63.158 | 0.00 | 0.00 | 0.00 | 3.53 |
934 | 996 | 2.282446 | GTCGGGGGAGAGGATGGA | 59.718 | 66.667 | 0.00 | 0.00 | 0.00 | 3.41 |
935 | 997 | 2.844839 | GGTCGGGGGAGAGGATGG | 60.845 | 72.222 | 0.00 | 0.00 | 0.00 | 3.51 |
936 | 998 | 2.844839 | GGGTCGGGGGAGAGGATG | 60.845 | 72.222 | 0.00 | 0.00 | 0.00 | 3.51 |
985 | 1047 | 2.586245 | CATGGAGGCGGCTTCTGA | 59.414 | 61.111 | 19.35 | 0.00 | 0.00 | 3.27 |
986 | 1048 | 2.515523 | CCATGGAGGCGGCTTCTG | 60.516 | 66.667 | 19.35 | 13.37 | 0.00 | 3.02 |
1359 | 1421 | 1.286501 | CGGTGTTGATGGTGATACCG | 58.713 | 55.000 | 0.00 | 0.00 | 42.58 | 4.02 |
1950 | 2012 | 3.866582 | CGGGTCTCCCTGATGCCC | 61.867 | 72.222 | 3.25 | 0.00 | 42.67 | 5.36 |
1977 | 2039 | 2.154854 | ACATCTCAACACCAGTGACG | 57.845 | 50.000 | 4.48 | 0.00 | 0.00 | 4.35 |
2271 | 2333 | 1.304381 | ACCCGGCATGCACATCTTT | 60.304 | 52.632 | 21.36 | 0.00 | 0.00 | 2.52 |
2613 | 2675 | 4.060205 | CAAGAGGAAAACAAAATGGCCAG | 58.940 | 43.478 | 13.05 | 0.00 | 0.00 | 4.85 |
2721 | 2783 | 6.093219 | AGCATACATCTGAAGCAGTAAACAAG | 59.907 | 38.462 | 0.00 | 0.00 | 32.61 | 3.16 |
2740 | 2802 | 7.256756 | AGATAAATCTGTCAAGCAAGCATAC | 57.743 | 36.000 | 0.00 | 0.00 | 35.42 | 2.39 |
2780 | 2854 | 9.294030 | GCTGAAAATCAATATGAACTACCAAAG | 57.706 | 33.333 | 0.00 | 0.00 | 0.00 | 2.77 |
2843 | 3071 | 8.266392 | ACTGTTTTTGCATTGAAAAAGATGAA | 57.734 | 26.923 | 12.33 | 0.00 | 35.89 | 2.57 |
2896 | 3138 | 6.823689 | AGCAGAAAACCAATATGAACTACGAT | 59.176 | 34.615 | 0.00 | 0.00 | 0.00 | 3.73 |
2897 | 3139 | 6.092122 | CAGCAGAAAACCAATATGAACTACGA | 59.908 | 38.462 | 0.00 | 0.00 | 0.00 | 3.43 |
2898 | 3140 | 6.250819 | CAGCAGAAAACCAATATGAACTACG | 58.749 | 40.000 | 0.00 | 0.00 | 0.00 | 3.51 |
3080 | 3487 | 5.123027 | TGCACGCAACAGATTGTTATGATTA | 59.877 | 36.000 | 0.00 | 0.00 | 38.77 | 1.75 |
3172 | 3616 | 5.049405 | CACCACAAGACAGGTACAAAAGATC | 60.049 | 44.000 | 0.00 | 0.00 | 36.07 | 2.75 |
3266 | 3726 | 7.334421 | CAGCATGTTACTCCACTATAAAACACT | 59.666 | 37.037 | 0.00 | 0.00 | 30.40 | 3.55 |
3321 | 3781 | 3.706594 | CCTGTGGCTGGTCTTCTCTATAA | 59.293 | 47.826 | 0.00 | 0.00 | 0.00 | 0.98 |
3336 | 3796 | 0.524862 | CTGCTTCATGAACCTGTGGC | 59.475 | 55.000 | 3.38 | 6.11 | 0.00 | 5.01 |
3342 | 3802 | 2.911484 | CTACTCCCTGCTTCATGAACC | 58.089 | 52.381 | 3.38 | 0.00 | 0.00 | 3.62 |
3362 | 3822 | 1.079503 | CGACTTTAGTTCCCAGCTGC | 58.920 | 55.000 | 8.66 | 0.00 | 0.00 | 5.25 |
3374 | 3834 | 6.147164 | CACCTTACAATTCTTGAGCGACTTTA | 59.853 | 38.462 | 0.00 | 0.00 | 0.00 | 1.85 |
3375 | 3835 | 5.049405 | CACCTTACAATTCTTGAGCGACTTT | 60.049 | 40.000 | 0.00 | 0.00 | 0.00 | 2.66 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.