Multiple sequence alignment - TraesCS5B01G443200
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 | TraesCS5B01G443200 | chr5B | 100.000 | 2498 | 0 | 0 | 1 | 2498 | 616222411 | 616224908 | 0.000000e+00 | 4614 |
1 | TraesCS5B01G443200 | chr5B | 99.041 | 1877 | 14 | 1 | 626 | 2498 | 616310222 | 616312098 | 0.000000e+00 | 3363 |
2 | TraesCS5B01G443200 | chr5B | 99.041 | 1877 | 14 | 1 | 626 | 2498 | 616321858 | 616323734 | 0.000000e+00 | 3363 |
3 | TraesCS5B01G443200 | chr5B | 98.934 | 1877 | 16 | 1 | 626 | 2498 | 616265373 | 616267249 | 0.000000e+00 | 3352 |
4 | TraesCS5B01G443200 | chr5B | 98.828 | 1877 | 18 | 1 | 626 | 2498 | 616276294 | 616278170 | 0.000000e+00 | 3341 |
5 | TraesCS5B01G443200 | chr5B | 98.775 | 1877 | 18 | 2 | 626 | 2498 | 616245609 | 616247484 | 0.000000e+00 | 3334 |
6 | TraesCS5B01G443200 | chr5B | 98.615 | 1877 | 21 | 2 | 626 | 2498 | 616299290 | 616301165 | 0.000000e+00 | 3317 |
7 | TraesCS5B01G443200 | chr5B | 97.619 | 504 | 9 | 3 | 1 | 502 | 616332089 | 616332591 | 0.000000e+00 | 861 |
8 | TraesCS5B01G443200 | chr5B | 97.416 | 503 | 12 | 1 | 1 | 502 | 616264872 | 616265374 | 0.000000e+00 | 856 |
9 | TraesCS5B01G443200 | chr5B | 97.416 | 503 | 12 | 1 | 1 | 502 | 616275793 | 616276295 | 0.000000e+00 | 856 |
10 | TraesCS5B01G443200 | chr5B | 97.416 | 503 | 12 | 1 | 1 | 502 | 616309721 | 616310223 | 0.000000e+00 | 856 |
11 | TraesCS5B01G443200 | chr5B | 97.416 | 503 | 12 | 1 | 1 | 502 | 616321357 | 616321859 | 0.000000e+00 | 856 |
12 | TraesCS5B01G443200 | chr5B | 96.620 | 503 | 15 | 2 | 1 | 502 | 616245109 | 616245610 | 0.000000e+00 | 833 |
13 | TraesCS5B01G443200 | chr5B | 96.421 | 503 | 15 | 3 | 1 | 502 | 616298791 | 616299291 | 0.000000e+00 | 826 |
14 | TraesCS5B01G443200 | chr5B | 91.540 | 461 | 30 | 5 | 697 | 1154 | 616103971 | 616104425 | 5.870000e-176 | 627 |
15 | TraesCS5B01G443200 | chr5B | 91.264 | 435 | 29 | 5 | 697 | 1128 | 615965239 | 615964811 | 3.580000e-163 | 584 |
16 | TraesCS5B01G443200 | chr5B | 96.970 | 66 | 2 | 0 | 626 | 691 | 616159604 | 616159669 | 7.300000e-21 | 111 |
17 | TraesCS5B01G443200 | chr5D | 91.540 | 1915 | 115 | 17 | 626 | 2498 | 497103588 | 497105497 | 0.000000e+00 | 2595 |
18 | TraesCS5B01G443200 | chrUn | 91.880 | 1835 | 112 | 14 | 696 | 2498 | 68274357 | 68272528 | 0.000000e+00 | 2529 |
19 | TraesCS5B01G443200 | chrUn | 91.880 | 1835 | 112 | 14 | 696 | 2498 | 302517263 | 302519092 | 0.000000e+00 | 2529 |
20 | TraesCS5B01G443200 | chrUn | 94.024 | 502 | 28 | 1 | 1 | 502 | 335556619 | 335556120 | 0.000000e+00 | 760 |
21 | TraesCS5B01G443200 | chrUn | 94.024 | 502 | 28 | 1 | 1 | 502 | 417158058 | 417158557 | 0.000000e+00 | 760 |
22 | TraesCS5B01G443200 | chr7B | 95.522 | 134 | 6 | 0 | 494 | 627 | 705539826 | 705539959 | 5.410000e-52 | 215 |
23 | TraesCS5B01G443200 | chr7B | 96.094 | 128 | 5 | 0 | 501 | 628 | 728671957 | 728671830 | 2.520000e-50 | 209 |
24 | TraesCS5B01G443200 | chr7B | 95.385 | 130 | 6 | 0 | 498 | 627 | 642706337 | 642706208 | 9.060000e-50 | 207 |
25 | TraesCS5B01G443200 | chr4B | 95.420 | 131 | 6 | 0 | 501 | 631 | 116479399 | 116479269 | 2.520000e-50 | 209 |
26 | TraesCS5B01G443200 | chr3A | 95.385 | 130 | 6 | 0 | 499 | 628 | 78187592 | 78187721 | 9.060000e-50 | 207 |
27 | TraesCS5B01G443200 | chr3A | 93.431 | 137 | 7 | 2 | 492 | 627 | 31653016 | 31653151 | 4.210000e-48 | 202 |
28 | TraesCS5B01G443200 | chr2B | 95.385 | 130 | 6 | 0 | 498 | 627 | 712620227 | 712620356 | 9.060000e-50 | 207 |
29 | TraesCS5B01G443200 | chr2D | 93.431 | 137 | 8 | 1 | 493 | 628 | 138806853 | 138806989 | 4.210000e-48 | 202 |
30 | TraesCS5B01G443200 | chr1B | 91.608 | 143 | 11 | 1 | 486 | 627 | 688707692 | 688707834 | 1.960000e-46 | 196 |
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 | TraesCS5B01G443200 | chr5B | 616222411 | 616224908 | 2497 | False | 4614.0 | 4614 | 100.0000 | 1 | 2498 | 1 | chr5B.!!$F3 | 2497 |
1 | TraesCS5B01G443200 | chr5B | 616309721 | 616312098 | 2377 | False | 2109.5 | 3363 | 98.2285 | 1 | 2498 | 2 | chr5B.!!$F9 | 2497 |
2 | TraesCS5B01G443200 | chr5B | 616321357 | 616323734 | 2377 | False | 2109.5 | 3363 | 98.2285 | 1 | 2498 | 2 | chr5B.!!$F10 | 2497 |
3 | TraesCS5B01G443200 | chr5B | 616264872 | 616267249 | 2377 | False | 2104.0 | 3352 | 98.1750 | 1 | 2498 | 2 | chr5B.!!$F6 | 2497 |
4 | TraesCS5B01G443200 | chr5B | 616275793 | 616278170 | 2377 | False | 2098.5 | 3341 | 98.1220 | 1 | 2498 | 2 | chr5B.!!$F7 | 2497 |
5 | TraesCS5B01G443200 | chr5B | 616245109 | 616247484 | 2375 | False | 2083.5 | 3334 | 97.6975 | 1 | 2498 | 2 | chr5B.!!$F5 | 2497 |
6 | TraesCS5B01G443200 | chr5B | 616298791 | 616301165 | 2374 | False | 2071.5 | 3317 | 97.5180 | 1 | 2498 | 2 | chr5B.!!$F8 | 2497 |
7 | TraesCS5B01G443200 | chr5B | 616332089 | 616332591 | 502 | False | 861.0 | 861 | 97.6190 | 1 | 502 | 1 | chr5B.!!$F4 | 501 |
8 | TraesCS5B01G443200 | chr5D | 497103588 | 497105497 | 1909 | False | 2595.0 | 2595 | 91.5400 | 626 | 2498 | 1 | chr5D.!!$F1 | 1872 |
9 | TraesCS5B01G443200 | chrUn | 68272528 | 68274357 | 1829 | True | 2529.0 | 2529 | 91.8800 | 696 | 2498 | 1 | chrUn.!!$R1 | 1802 |
10 | TraesCS5B01G443200 | chrUn | 302517263 | 302519092 | 1829 | False | 2529.0 | 2529 | 91.8800 | 696 | 2498 | 1 | chrUn.!!$F1 | 1802 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
517 | 520 | 0.038744 | ACTACTCCCTCCGTTCCGAA | 59.961 | 55.0 | 0.0 | 0.0 | 0.0 | 4.3 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2454 | 2499 | 1.078214 | CTCTGCCGAAATGCCCTGA | 60.078 | 57.895 | 0.0 | 0.0 | 0.0 | 3.86 | 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 |
---|---|---|---|---|---|---|---|---|---|
236 | 238 | 1.129811 | GGGGATGTTACGAAAGTTGCG | 59.870 | 52.381 | 0.38 | 0.38 | 46.40 | 4.85 |
282 | 284 | 6.128472 | GGCATGACAAAGCAAAATAAAAGAGG | 60.128 | 38.462 | 0.00 | 0.00 | 0.00 | 3.69 |
325 | 328 | 9.974980 | ATATTATCGCCAACGGAAAAATAAATT | 57.025 | 25.926 | 0.00 | 0.00 | 40.63 | 1.82 |
495 | 498 | 2.500098 | CCACTAGCACCTAGTTGGCTAA | 59.500 | 50.000 | 2.31 | 0.00 | 43.82 | 3.09 |
500 | 503 | 3.442076 | AGCACCTAGTTGGCTAACTACT | 58.558 | 45.455 | 17.78 | 11.00 | 45.07 | 2.57 |
501 | 504 | 4.607239 | AGCACCTAGTTGGCTAACTACTA | 58.393 | 43.478 | 17.78 | 1.27 | 45.07 | 1.82 |
502 | 505 | 4.401837 | AGCACCTAGTTGGCTAACTACTAC | 59.598 | 45.833 | 17.78 | 8.53 | 45.07 | 2.73 |
503 | 506 | 4.401837 | GCACCTAGTTGGCTAACTACTACT | 59.598 | 45.833 | 17.78 | 0.00 | 45.07 | 2.57 |
504 | 507 | 5.450274 | GCACCTAGTTGGCTAACTACTACTC | 60.450 | 48.000 | 17.78 | 4.22 | 45.07 | 2.59 |
505 | 508 | 5.067544 | CACCTAGTTGGCTAACTACTACTCC | 59.932 | 48.000 | 17.78 | 0.00 | 45.07 | 3.85 |
506 | 509 | 4.583907 | CCTAGTTGGCTAACTACTACTCCC | 59.416 | 50.000 | 17.78 | 0.00 | 45.07 | 4.30 |
507 | 510 | 4.334208 | AGTTGGCTAACTACTACTCCCT | 57.666 | 45.455 | 14.53 | 0.00 | 45.07 | 4.20 |
508 | 511 | 4.279982 | AGTTGGCTAACTACTACTCCCTC | 58.720 | 47.826 | 14.53 | 0.00 | 45.07 | 4.30 |
509 | 512 | 3.309600 | TGGCTAACTACTACTCCCTCC | 57.690 | 52.381 | 0.00 | 0.00 | 0.00 | 4.30 |
510 | 513 | 2.228925 | GGCTAACTACTACTCCCTCCG | 58.771 | 57.143 | 0.00 | 0.00 | 0.00 | 4.63 |
511 | 514 | 2.422661 | GGCTAACTACTACTCCCTCCGT | 60.423 | 54.545 | 0.00 | 0.00 | 0.00 | 4.69 |
512 | 515 | 3.286353 | GCTAACTACTACTCCCTCCGTT | 58.714 | 50.000 | 0.00 | 0.00 | 0.00 | 4.44 |
513 | 516 | 3.314913 | GCTAACTACTACTCCCTCCGTTC | 59.685 | 52.174 | 0.00 | 0.00 | 0.00 | 3.95 |
514 | 517 | 2.433662 | ACTACTACTCCCTCCGTTCC | 57.566 | 55.000 | 0.00 | 0.00 | 0.00 | 3.62 |
515 | 518 | 1.307097 | CTACTACTCCCTCCGTTCCG | 58.693 | 60.000 | 0.00 | 0.00 | 0.00 | 4.30 |
516 | 519 | 0.911769 | TACTACTCCCTCCGTTCCGA | 59.088 | 55.000 | 0.00 | 0.00 | 0.00 | 4.55 |
517 | 520 | 0.038744 | ACTACTCCCTCCGTTCCGAA | 59.961 | 55.000 | 0.00 | 0.00 | 0.00 | 4.30 |
518 | 521 | 1.341778 | ACTACTCCCTCCGTTCCGAAT | 60.342 | 52.381 | 0.00 | 0.00 | 0.00 | 3.34 |
519 | 522 | 1.755380 | CTACTCCCTCCGTTCCGAATT | 59.245 | 52.381 | 0.00 | 0.00 | 0.00 | 2.17 |
520 | 523 | 1.856629 | ACTCCCTCCGTTCCGAATTA | 58.143 | 50.000 | 0.00 | 0.00 | 0.00 | 1.40 |
521 | 524 | 1.479730 | ACTCCCTCCGTTCCGAATTAC | 59.520 | 52.381 | 0.00 | 0.00 | 0.00 | 1.89 |
522 | 525 | 1.755380 | CTCCCTCCGTTCCGAATTACT | 59.245 | 52.381 | 0.00 | 0.00 | 0.00 | 2.24 |
523 | 526 | 2.167900 | CTCCCTCCGTTCCGAATTACTT | 59.832 | 50.000 | 0.00 | 0.00 | 0.00 | 2.24 |
524 | 527 | 2.093869 | TCCCTCCGTTCCGAATTACTTG | 60.094 | 50.000 | 0.00 | 0.00 | 0.00 | 3.16 |
525 | 528 | 2.354403 | CCCTCCGTTCCGAATTACTTGT | 60.354 | 50.000 | 0.00 | 0.00 | 0.00 | 3.16 |
526 | 529 | 2.928116 | CCTCCGTTCCGAATTACTTGTC | 59.072 | 50.000 | 0.00 | 0.00 | 0.00 | 3.18 |
527 | 530 | 3.368116 | CCTCCGTTCCGAATTACTTGTCT | 60.368 | 47.826 | 0.00 | 0.00 | 0.00 | 3.41 |
528 | 531 | 4.243270 | CTCCGTTCCGAATTACTTGTCTT | 58.757 | 43.478 | 0.00 | 0.00 | 0.00 | 3.01 |
529 | 532 | 3.991773 | TCCGTTCCGAATTACTTGTCTTG | 59.008 | 43.478 | 0.00 | 0.00 | 0.00 | 3.02 |
530 | 533 | 3.124636 | CCGTTCCGAATTACTTGTCTTGG | 59.875 | 47.826 | 0.00 | 0.00 | 0.00 | 3.61 |
531 | 534 | 3.991773 | CGTTCCGAATTACTTGTCTTGGA | 59.008 | 43.478 | 0.00 | 0.00 | 0.00 | 3.53 |
532 | 535 | 4.630069 | CGTTCCGAATTACTTGTCTTGGAT | 59.370 | 41.667 | 0.00 | 0.00 | 0.00 | 3.41 |
533 | 536 | 5.121768 | CGTTCCGAATTACTTGTCTTGGATT | 59.878 | 40.000 | 0.00 | 0.00 | 0.00 | 3.01 |
534 | 537 | 6.348213 | CGTTCCGAATTACTTGTCTTGGATTT | 60.348 | 38.462 | 0.00 | 0.00 | 0.00 | 2.17 |
535 | 538 | 6.494893 | TCCGAATTACTTGTCTTGGATTTG | 57.505 | 37.500 | 0.00 | 0.00 | 0.00 | 2.32 |
536 | 539 | 6.001460 | TCCGAATTACTTGTCTTGGATTTGT | 58.999 | 36.000 | 0.00 | 0.00 | 0.00 | 2.83 |
537 | 540 | 6.148811 | TCCGAATTACTTGTCTTGGATTTGTC | 59.851 | 38.462 | 0.00 | 0.00 | 0.00 | 3.18 |
538 | 541 | 6.149474 | CCGAATTACTTGTCTTGGATTTGTCT | 59.851 | 38.462 | 0.00 | 0.00 | 0.00 | 3.41 |
539 | 542 | 7.333423 | CCGAATTACTTGTCTTGGATTTGTCTA | 59.667 | 37.037 | 0.00 | 0.00 | 0.00 | 2.59 |
540 | 543 | 8.383619 | CGAATTACTTGTCTTGGATTTGTCTAG | 58.616 | 37.037 | 0.00 | 0.00 | 0.00 | 2.43 |
541 | 544 | 9.436957 | GAATTACTTGTCTTGGATTTGTCTAGA | 57.563 | 33.333 | 0.00 | 0.00 | 0.00 | 2.43 |
542 | 545 | 9.965902 | AATTACTTGTCTTGGATTTGTCTAGAT | 57.034 | 29.630 | 0.00 | 0.00 | 0.00 | 1.98 |
544 | 547 | 9.871238 | TTACTTGTCTTGGATTTGTCTAGATAC | 57.129 | 33.333 | 0.00 | 0.00 | 0.00 | 2.24 |
545 | 548 | 7.907389 | ACTTGTCTTGGATTTGTCTAGATACA | 58.093 | 34.615 | 0.00 | 0.00 | 0.00 | 2.29 |
546 | 549 | 8.037758 | ACTTGTCTTGGATTTGTCTAGATACAG | 58.962 | 37.037 | 0.00 | 0.00 | 0.00 | 2.74 |
547 | 550 | 7.718334 | TGTCTTGGATTTGTCTAGATACAGA | 57.282 | 36.000 | 0.00 | 0.00 | 0.00 | 3.41 |
548 | 551 | 8.311395 | TGTCTTGGATTTGTCTAGATACAGAT | 57.689 | 34.615 | 0.00 | 0.00 | 0.00 | 2.90 |
549 | 552 | 8.200120 | TGTCTTGGATTTGTCTAGATACAGATG | 58.800 | 37.037 | 0.00 | 0.00 | 0.00 | 2.90 |
550 | 553 | 8.200792 | GTCTTGGATTTGTCTAGATACAGATGT | 58.799 | 37.037 | 0.00 | 0.00 | 0.00 | 3.06 |
551 | 554 | 9.421399 | TCTTGGATTTGTCTAGATACAGATGTA | 57.579 | 33.333 | 0.00 | 0.00 | 34.67 | 2.29 |
570 | 573 | 9.190858 | CAGATGTATCTAGACTCACTTTAATGC | 57.809 | 37.037 | 0.00 | 0.00 | 34.85 | 3.56 |
571 | 574 | 9.142014 | AGATGTATCTAGACTCACTTTAATGCT | 57.858 | 33.333 | 0.00 | 0.00 | 34.85 | 3.79 |
574 | 577 | 9.185680 | TGTATCTAGACTCACTTTAATGCTACA | 57.814 | 33.333 | 0.00 | 0.00 | 0.00 | 2.74 |
578 | 581 | 9.185680 | TCTAGACTCACTTTAATGCTACATACA | 57.814 | 33.333 | 0.00 | 0.00 | 0.00 | 2.29 |
579 | 582 | 9.973450 | CTAGACTCACTTTAATGCTACATACAT | 57.027 | 33.333 | 0.00 | 0.00 | 0.00 | 2.29 |
580 | 583 | 8.879342 | AGACTCACTTTAATGCTACATACATC | 57.121 | 34.615 | 0.00 | 0.00 | 0.00 | 3.06 |
581 | 584 | 7.928706 | AGACTCACTTTAATGCTACATACATCC | 59.071 | 37.037 | 0.00 | 0.00 | 0.00 | 3.51 |
582 | 585 | 6.701841 | ACTCACTTTAATGCTACATACATCCG | 59.298 | 38.462 | 0.00 | 0.00 | 0.00 | 4.18 |
583 | 586 | 6.578944 | TCACTTTAATGCTACATACATCCGT | 58.421 | 36.000 | 0.00 | 0.00 | 0.00 | 4.69 |
584 | 587 | 7.718525 | TCACTTTAATGCTACATACATCCGTA | 58.281 | 34.615 | 0.00 | 0.00 | 0.00 | 4.02 |
585 | 588 | 8.364894 | TCACTTTAATGCTACATACATCCGTAT | 58.635 | 33.333 | 0.00 | 0.00 | 38.96 | 3.06 |
586 | 589 | 8.988934 | CACTTTAATGCTACATACATCCGTATT | 58.011 | 33.333 | 0.00 | 0.00 | 36.11 | 1.89 |
587 | 590 | 9.555727 | ACTTTAATGCTACATACATCCGTATTT | 57.444 | 29.630 | 0.00 | 0.00 | 36.11 | 1.40 |
591 | 594 | 8.758633 | AATGCTACATACATCCGTATTTAGAC | 57.241 | 34.615 | 9.06 | 3.32 | 39.32 | 2.59 |
592 | 595 | 7.279750 | TGCTACATACATCCGTATTTAGACA | 57.720 | 36.000 | 9.06 | 5.16 | 39.32 | 3.41 |
593 | 596 | 7.718525 | TGCTACATACATCCGTATTTAGACAA | 58.281 | 34.615 | 9.06 | 0.00 | 39.32 | 3.18 |
594 | 597 | 8.198778 | TGCTACATACATCCGTATTTAGACAAA | 58.801 | 33.333 | 9.06 | 0.00 | 39.32 | 2.83 |
595 | 598 | 9.204570 | GCTACATACATCCGTATTTAGACAAAT | 57.795 | 33.333 | 9.06 | 0.00 | 39.32 | 2.32 |
602 | 605 | 9.530633 | ACATCCGTATTTAGACAAATCTAAGAC | 57.469 | 33.333 | 0.00 | 0.83 | 45.93 | 3.01 |
603 | 606 | 9.529325 | CATCCGTATTTAGACAAATCTAAGACA | 57.471 | 33.333 | 9.81 | 0.00 | 45.93 | 3.41 |
605 | 608 | 9.932207 | TCCGTATTTAGACAAATCTAAGACAAA | 57.068 | 29.630 | 9.81 | 0.00 | 45.93 | 2.83 |
618 | 621 | 9.855021 | AAATCTAAGACAAATAATTTGGAACGG | 57.145 | 29.630 | 0.00 | 0.00 | 44.81 | 4.44 |
619 | 622 | 8.801882 | ATCTAAGACAAATAATTTGGAACGGA | 57.198 | 30.769 | 0.00 | 0.00 | 44.81 | 4.69 |
620 | 623 | 8.263940 | TCTAAGACAAATAATTTGGAACGGAG | 57.736 | 34.615 | 0.00 | 0.00 | 44.81 | 4.63 |
621 | 624 | 5.897377 | AGACAAATAATTTGGAACGGAGG | 57.103 | 39.130 | 0.00 | 0.00 | 44.81 | 4.30 |
622 | 625 | 4.705023 | AGACAAATAATTTGGAACGGAGGG | 59.295 | 41.667 | 0.00 | 0.00 | 44.81 | 4.30 |
623 | 626 | 4.668636 | ACAAATAATTTGGAACGGAGGGA | 58.331 | 39.130 | 0.00 | 0.00 | 44.81 | 4.20 |
624 | 627 | 4.705023 | ACAAATAATTTGGAACGGAGGGAG | 59.295 | 41.667 | 0.00 | 0.00 | 44.81 | 4.30 |
1667 | 1698 | 4.171005 | CCGGCTGTATATATGTACCGTTG | 58.829 | 47.826 | 7.12 | 0.00 | 37.51 | 4.10 |
1835 | 1871 | 3.111853 | TGTCATCTCGCACTTGTTCTT | 57.888 | 42.857 | 0.00 | 0.00 | 0.00 | 2.52 |
1975 | 2016 | 1.270305 | CGTGACAGTCACCCAATCTGT | 60.270 | 52.381 | 25.11 | 0.00 | 44.20 | 3.41 |
2075 | 2116 | 1.407979 | CTAGCGGTCCATCGTAGGTTT | 59.592 | 52.381 | 0.00 | 0.00 | 0.00 | 3.27 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
236 | 238 | 4.201990 | GCCTCTGTCATTTTCATGTGGATC | 60.202 | 45.833 | 0.00 | 0.00 | 0.00 | 3.36 |
325 | 328 | 2.301583 | TGTGTGCTGGTTGCTACATAGA | 59.698 | 45.455 | 0.00 | 0.00 | 43.37 | 1.98 |
339 | 342 | 7.744087 | TTGAGTTGTTCTAATATTGTGTGCT | 57.256 | 32.000 | 0.00 | 0.00 | 0.00 | 4.40 |
378 | 381 | 0.672342 | ACTCGCACACGTAAGAACCT | 59.328 | 50.000 | 0.00 | 0.00 | 41.18 | 3.50 |
495 | 498 | 2.433662 | GGAACGGAGGGAGTAGTAGT | 57.566 | 55.000 | 0.00 | 0.00 | 0.00 | 2.73 |
510 | 513 | 6.496338 | AATCCAAGACAAGTAATTCGGAAC | 57.504 | 37.500 | 0.00 | 0.00 | 0.00 | 3.62 |
511 | 514 | 6.488683 | ACAAATCCAAGACAAGTAATTCGGAA | 59.511 | 34.615 | 0.00 | 0.00 | 0.00 | 4.30 |
512 | 515 | 6.001460 | ACAAATCCAAGACAAGTAATTCGGA | 58.999 | 36.000 | 0.00 | 0.00 | 0.00 | 4.55 |
513 | 516 | 6.149474 | AGACAAATCCAAGACAAGTAATTCGG | 59.851 | 38.462 | 0.00 | 0.00 | 0.00 | 4.30 |
514 | 517 | 7.133891 | AGACAAATCCAAGACAAGTAATTCG | 57.866 | 36.000 | 0.00 | 0.00 | 0.00 | 3.34 |
515 | 518 | 9.436957 | TCTAGACAAATCCAAGACAAGTAATTC | 57.563 | 33.333 | 0.00 | 0.00 | 0.00 | 2.17 |
516 | 519 | 9.965902 | ATCTAGACAAATCCAAGACAAGTAATT | 57.034 | 29.630 | 0.00 | 0.00 | 0.00 | 1.40 |
518 | 521 | 9.871238 | GTATCTAGACAAATCCAAGACAAGTAA | 57.129 | 33.333 | 0.00 | 0.00 | 0.00 | 2.24 |
519 | 522 | 9.031537 | TGTATCTAGACAAATCCAAGACAAGTA | 57.968 | 33.333 | 0.00 | 0.00 | 0.00 | 2.24 |
520 | 523 | 7.907389 | TGTATCTAGACAAATCCAAGACAAGT | 58.093 | 34.615 | 0.00 | 0.00 | 0.00 | 3.16 |
521 | 524 | 8.253810 | TCTGTATCTAGACAAATCCAAGACAAG | 58.746 | 37.037 | 0.00 | 0.00 | 0.00 | 3.16 |
522 | 525 | 8.134202 | TCTGTATCTAGACAAATCCAAGACAA | 57.866 | 34.615 | 0.00 | 0.00 | 0.00 | 3.18 |
523 | 526 | 7.718334 | TCTGTATCTAGACAAATCCAAGACA | 57.282 | 36.000 | 0.00 | 0.00 | 0.00 | 3.41 |
524 | 527 | 8.200792 | ACATCTGTATCTAGACAAATCCAAGAC | 58.799 | 37.037 | 0.00 | 0.00 | 0.00 | 3.01 |
525 | 528 | 8.311395 | ACATCTGTATCTAGACAAATCCAAGA | 57.689 | 34.615 | 0.00 | 0.00 | 0.00 | 3.02 |
544 | 547 | 9.190858 | GCATTAAAGTGAGTCTAGATACATCTG | 57.809 | 37.037 | 0.00 | 0.00 | 37.76 | 2.90 |
545 | 548 | 9.142014 | AGCATTAAAGTGAGTCTAGATACATCT | 57.858 | 33.333 | 0.00 | 0.00 | 40.86 | 2.90 |
548 | 551 | 9.185680 | TGTAGCATTAAAGTGAGTCTAGATACA | 57.814 | 33.333 | 0.00 | 0.00 | 0.00 | 2.29 |
552 | 555 | 9.185680 | TGTATGTAGCATTAAAGTGAGTCTAGA | 57.814 | 33.333 | 0.00 | 0.00 | 0.00 | 2.43 |
553 | 556 | 9.973450 | ATGTATGTAGCATTAAAGTGAGTCTAG | 57.027 | 33.333 | 0.00 | 0.00 | 0.00 | 2.43 |
554 | 557 | 9.967346 | GATGTATGTAGCATTAAAGTGAGTCTA | 57.033 | 33.333 | 0.00 | 0.00 | 0.00 | 2.59 |
555 | 558 | 7.928706 | GGATGTATGTAGCATTAAAGTGAGTCT | 59.071 | 37.037 | 0.00 | 0.00 | 0.00 | 3.24 |
556 | 559 | 7.096023 | CGGATGTATGTAGCATTAAAGTGAGTC | 60.096 | 40.741 | 0.00 | 0.00 | 0.00 | 3.36 |
557 | 560 | 6.701841 | CGGATGTATGTAGCATTAAAGTGAGT | 59.298 | 38.462 | 0.00 | 0.00 | 0.00 | 3.41 |
558 | 561 | 6.701841 | ACGGATGTATGTAGCATTAAAGTGAG | 59.298 | 38.462 | 0.00 | 0.00 | 0.00 | 3.51 |
559 | 562 | 6.578944 | ACGGATGTATGTAGCATTAAAGTGA | 58.421 | 36.000 | 0.00 | 0.00 | 0.00 | 3.41 |
560 | 563 | 6.844696 | ACGGATGTATGTAGCATTAAAGTG | 57.155 | 37.500 | 0.00 | 0.00 | 0.00 | 3.16 |
561 | 564 | 9.555727 | AAATACGGATGTATGTAGCATTAAAGT | 57.444 | 29.630 | 0.00 | 0.00 | 40.42 | 2.66 |
565 | 568 | 9.850628 | GTCTAAATACGGATGTATGTAGCATTA | 57.149 | 33.333 | 7.48 | 0.00 | 43.95 | 1.90 |
566 | 569 | 8.364894 | TGTCTAAATACGGATGTATGTAGCATT | 58.635 | 33.333 | 7.48 | 0.00 | 43.95 | 3.56 |
567 | 570 | 7.892609 | TGTCTAAATACGGATGTATGTAGCAT | 58.107 | 34.615 | 7.48 | 0.00 | 43.95 | 3.79 |
568 | 571 | 7.279750 | TGTCTAAATACGGATGTATGTAGCA | 57.720 | 36.000 | 7.48 | 6.68 | 43.95 | 3.49 |
569 | 572 | 8.583810 | TTTGTCTAAATACGGATGTATGTAGC | 57.416 | 34.615 | 7.48 | 4.82 | 43.95 | 3.58 |
576 | 579 | 9.530633 | GTCTTAGATTTGTCTAAATACGGATGT | 57.469 | 33.333 | 0.26 | 0.00 | 36.66 | 3.06 |
577 | 580 | 9.529325 | TGTCTTAGATTTGTCTAAATACGGATG | 57.471 | 33.333 | 0.26 | 0.00 | 36.66 | 3.51 |
579 | 582 | 9.932207 | TTTGTCTTAGATTTGTCTAAATACGGA | 57.068 | 29.630 | 0.26 | 0.00 | 36.66 | 4.69 |
592 | 595 | 9.855021 | CCGTTCCAAATTATTTGTCTTAGATTT | 57.145 | 29.630 | 15.40 | 0.00 | 38.98 | 2.17 |
593 | 596 | 9.238368 | TCCGTTCCAAATTATTTGTCTTAGATT | 57.762 | 29.630 | 15.40 | 0.00 | 38.98 | 2.40 |
594 | 597 | 8.801882 | TCCGTTCCAAATTATTTGTCTTAGAT | 57.198 | 30.769 | 15.40 | 0.00 | 38.98 | 1.98 |
595 | 598 | 7.335924 | CCTCCGTTCCAAATTATTTGTCTTAGA | 59.664 | 37.037 | 15.40 | 3.73 | 38.98 | 2.10 |
596 | 599 | 7.415206 | CCCTCCGTTCCAAATTATTTGTCTTAG | 60.415 | 40.741 | 15.40 | 6.14 | 38.98 | 2.18 |
597 | 600 | 6.376018 | CCCTCCGTTCCAAATTATTTGTCTTA | 59.624 | 38.462 | 15.40 | 0.00 | 38.98 | 2.10 |
598 | 601 | 5.185056 | CCCTCCGTTCCAAATTATTTGTCTT | 59.815 | 40.000 | 15.40 | 0.00 | 38.98 | 3.01 |
599 | 602 | 4.705023 | CCCTCCGTTCCAAATTATTTGTCT | 59.295 | 41.667 | 15.40 | 0.00 | 38.98 | 3.41 |
600 | 603 | 4.703093 | TCCCTCCGTTCCAAATTATTTGTC | 59.297 | 41.667 | 15.40 | 5.99 | 38.98 | 3.18 |
601 | 604 | 4.668636 | TCCCTCCGTTCCAAATTATTTGT | 58.331 | 39.130 | 15.40 | 0.00 | 38.98 | 2.83 |
602 | 605 | 4.705023 | ACTCCCTCCGTTCCAAATTATTTG | 59.295 | 41.667 | 10.46 | 10.46 | 40.32 | 2.32 |
603 | 606 | 4.930696 | ACTCCCTCCGTTCCAAATTATTT | 58.069 | 39.130 | 0.00 | 0.00 | 0.00 | 1.40 |
604 | 607 | 4.586306 | ACTCCCTCCGTTCCAAATTATT | 57.414 | 40.909 | 0.00 | 0.00 | 0.00 | 1.40 |
605 | 608 | 4.102681 | CCTACTCCCTCCGTTCCAAATTAT | 59.897 | 45.833 | 0.00 | 0.00 | 0.00 | 1.28 |
606 | 609 | 3.453353 | CCTACTCCCTCCGTTCCAAATTA | 59.547 | 47.826 | 0.00 | 0.00 | 0.00 | 1.40 |
607 | 610 | 2.238898 | CCTACTCCCTCCGTTCCAAATT | 59.761 | 50.000 | 0.00 | 0.00 | 0.00 | 1.82 |
608 | 611 | 1.838077 | CCTACTCCCTCCGTTCCAAAT | 59.162 | 52.381 | 0.00 | 0.00 | 0.00 | 2.32 |
609 | 612 | 1.272807 | CCTACTCCCTCCGTTCCAAA | 58.727 | 55.000 | 0.00 | 0.00 | 0.00 | 3.28 |
610 | 613 | 0.115745 | ACCTACTCCCTCCGTTCCAA | 59.884 | 55.000 | 0.00 | 0.00 | 0.00 | 3.53 |
611 | 614 | 1.002069 | TACCTACTCCCTCCGTTCCA | 58.998 | 55.000 | 0.00 | 0.00 | 0.00 | 3.53 |
612 | 615 | 1.397672 | GTACCTACTCCCTCCGTTCC | 58.602 | 60.000 | 0.00 | 0.00 | 0.00 | 3.62 |
613 | 616 | 1.020437 | CGTACCTACTCCCTCCGTTC | 58.980 | 60.000 | 0.00 | 0.00 | 0.00 | 3.95 |
614 | 617 | 0.329596 | ACGTACCTACTCCCTCCGTT | 59.670 | 55.000 | 0.00 | 0.00 | 0.00 | 4.44 |
615 | 618 | 0.393537 | CACGTACCTACTCCCTCCGT | 60.394 | 60.000 | 0.00 | 0.00 | 0.00 | 4.69 |
616 | 619 | 0.393537 | ACACGTACCTACTCCCTCCG | 60.394 | 60.000 | 0.00 | 0.00 | 0.00 | 4.63 |
617 | 620 | 1.101331 | CACACGTACCTACTCCCTCC | 58.899 | 60.000 | 0.00 | 0.00 | 0.00 | 4.30 |
618 | 621 | 1.742268 | GACACACGTACCTACTCCCTC | 59.258 | 57.143 | 0.00 | 0.00 | 0.00 | 4.30 |
619 | 622 | 1.615384 | GGACACACGTACCTACTCCCT | 60.615 | 57.143 | 0.00 | 0.00 | 0.00 | 4.20 |
620 | 623 | 0.813821 | GGACACACGTACCTACTCCC | 59.186 | 60.000 | 0.00 | 0.00 | 0.00 | 4.30 |
621 | 624 | 0.813821 | GGGACACACGTACCTACTCC | 59.186 | 60.000 | 0.00 | 0.00 | 43.75 | 3.85 |
622 | 625 | 0.449388 | CGGGACACACGTACCTACTC | 59.551 | 60.000 | 0.00 | 0.00 | 45.14 | 2.59 |
623 | 626 | 0.036732 | TCGGGACACACGTACCTACT | 59.963 | 55.000 | 0.00 | 0.00 | 45.14 | 2.57 |
624 | 627 | 0.169009 | GTCGGGACACACGTACCTAC | 59.831 | 60.000 | 0.00 | 0.00 | 45.14 | 3.18 |
1975 | 2016 | 2.134354 | TGGATGGGTGAGCCATAATGA | 58.866 | 47.619 | 17.19 | 0.00 | 34.19 | 2.57 |
2454 | 2499 | 1.078214 | CTCTGCCGAAATGCCCTGA | 60.078 | 57.895 | 0.00 | 0.00 | 0.00 | 3.86 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.