Multiple sequence alignment - TraesCS5A01G276600
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 | TraesCS5A01G276600 | chr5A | 100.000 | 5427 | 0 | 0 | 1 | 5427 | 485823317 | 485828743 | 0.000000e+00 | 10022 |
1 | TraesCS5A01G276600 | chr5D | 91.154 | 5200 | 271 | 76 | 1 | 5121 | 384848193 | 384853282 | 0.000000e+00 | 6879 |
2 | TraesCS5A01G276600 | chr5D | 93.103 | 290 | 13 | 2 | 5138 | 5427 | 384853275 | 384853557 | 8.410000e-113 | 418 |
3 | TraesCS5A01G276600 | chr5B | 94.555 | 1102 | 49 | 5 | 1914 | 3005 | 462145812 | 462144712 | 0.000000e+00 | 1692 |
4 | TraesCS5A01G276600 | chr5B | 89.332 | 1378 | 87 | 28 | 440 | 1804 | 462147827 | 462146497 | 0.000000e+00 | 1676 |
5 | TraesCS5A01G276600 | chr5B | 95.881 | 704 | 29 | 0 | 3114 | 3817 | 462144715 | 462144012 | 0.000000e+00 | 1140 |
6 | TraesCS5A01G276600 | chr5B | 94.624 | 558 | 21 | 5 | 3822 | 4370 | 462143889 | 462143332 | 0.000000e+00 | 856 |
7 | TraesCS5A01G276600 | chr5B | 92.537 | 268 | 14 | 3 | 4973 | 5238 | 462143064 | 462142801 | 3.970000e-101 | 379 |
8 | TraesCS5A01G276600 | chr5B | 93.243 | 222 | 14 | 1 | 5207 | 5427 | 462142792 | 462142571 | 5.240000e-85 | 326 |
9 | TraesCS5A01G276600 | chr5B | 87.442 | 215 | 14 | 8 | 4376 | 4585 | 462143289 | 462143083 | 9.090000e-58 | 235 |
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 | TraesCS5A01G276600 | chr5A | 485823317 | 485828743 | 5426 | False | 10022.000000 | 10022 | 100.000000 | 1 | 5427 | 1 | chr5A.!!$F1 | 5426 |
1 | TraesCS5A01G276600 | chr5D | 384848193 | 384853557 | 5364 | False | 3648.500000 | 6879 | 92.128500 | 1 | 5427 | 2 | chr5D.!!$F1 | 5426 |
2 | TraesCS5A01G276600 | chr5B | 462142571 | 462147827 | 5256 | True | 900.571429 | 1692 | 92.516286 | 440 | 5427 | 7 | chr5B.!!$R1 | 4987 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
428 | 430 | 0.444260 | GTGCTTCGCTTAGAGTTGGC | 59.556 | 55.0 | 0.00 | 0.0 | 0.00 | 4.52 | F |
900 | 934 | 0.613853 | ACCCACTTTCTCCGGATCGA | 60.614 | 55.0 | 3.57 | 0.0 | 0.00 | 3.59 | F |
1444 | 1496 | 0.240945 | CTGCATCGTTTGGTTGGTCC | 59.759 | 55.0 | 0.00 | 0.0 | 0.00 | 4.46 | F |
1880 | 2538 | 0.109272 | CTGCGACTACGAGCTTTCCA | 60.109 | 55.0 | 0.00 | 0.0 | 42.66 | 3.53 | F |
2093 | 2751 | 0.545309 | CCCTGTCTCCCAGTCCTTGA | 60.545 | 60.0 | 0.00 | 0.0 | 39.74 | 3.02 | F |
3471 | 4140 | 0.886490 | CTGGGCTCAAACTGAACGCT | 60.886 | 55.0 | 0.00 | 0.0 | 0.00 | 5.07 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1442 | 1494 | 0.106469 | AGCGCTCTATGGAGTCTGGA | 60.106 | 55.000 | 2.64 | 0.00 | 41.38 | 3.86 | R |
1861 | 2519 | 0.109272 | TGGAAAGCTCGTAGTCGCAG | 60.109 | 55.000 | 0.00 | 0.00 | 36.96 | 5.18 | R |
3260 | 3929 | 0.324943 | GGCTGGCTTCTTAGTGGTCA | 59.675 | 55.000 | 0.00 | 0.00 | 0.00 | 4.02 | R |
3851 | 4638 | 0.829990 | TCTCAGCCGGCATTATGTCA | 59.170 | 50.000 | 31.54 | 6.10 | 0.00 | 3.58 | R |
4008 | 4795 | 2.191641 | GATCTGGGTCAGGCCTGC | 59.808 | 66.667 | 28.91 | 21.69 | 37.43 | 4.85 | R |
4810 | 5653 | 0.251474 | ACTGATTGCTGGTGCCATGT | 60.251 | 50.000 | 0.00 | 0.00 | 38.71 | 3.21 | 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 |
---|---|---|---|---|---|---|---|---|---|
31 | 32 | 2.430248 | TGCTCATGAATGATGGCACT | 57.570 | 45.000 | 0.00 | 0.00 | 34.93 | 4.40 |
40 | 41 | 3.064324 | GATGGCACTGGCACACCC | 61.064 | 66.667 | 7.57 | 0.00 | 41.84 | 4.61 |
83 | 84 | 6.002082 | ACCCTCTTAATGGTAGTTTCACAAC | 58.998 | 40.000 | 0.00 | 0.00 | 31.61 | 3.32 |
131 | 132 | 3.780850 | CCTCCAAGGTAATCCTACAAGGT | 59.219 | 47.826 | 0.00 | 0.00 | 44.35 | 3.50 |
195 | 197 | 6.237313 | AGTGCGTTTAAATCTACAAGGTTC | 57.763 | 37.500 | 0.00 | 0.00 | 0.00 | 3.62 |
197 | 199 | 4.152759 | TGCGTTTAAATCTACAAGGTTCGG | 59.847 | 41.667 | 0.00 | 0.00 | 0.00 | 4.30 |
212 | 214 | 4.470602 | AGGTTCGGAAAAAGGTCAAAGAT | 58.529 | 39.130 | 0.00 | 0.00 | 0.00 | 2.40 |
312 | 314 | 5.446143 | AGCCAAATAAAATGTTCGACACA | 57.554 | 34.783 | 3.49 | 3.49 | 40.71 | 3.72 |
374 | 376 | 3.192633 | GCCCAAGGAACGAAACATGTATT | 59.807 | 43.478 | 0.00 | 0.00 | 0.00 | 1.89 |
384 | 386 | 6.668541 | ACGAAACATGTATTGAATGAGAGG | 57.331 | 37.500 | 0.00 | 0.00 | 0.00 | 3.69 |
385 | 387 | 6.406370 | ACGAAACATGTATTGAATGAGAGGA | 58.594 | 36.000 | 0.00 | 0.00 | 0.00 | 3.71 |
386 | 388 | 7.050377 | ACGAAACATGTATTGAATGAGAGGAT | 58.950 | 34.615 | 0.00 | 0.00 | 0.00 | 3.24 |
387 | 389 | 7.225538 | ACGAAACATGTATTGAATGAGAGGATC | 59.774 | 37.037 | 0.00 | 0.00 | 0.00 | 3.36 |
428 | 430 | 0.444260 | GTGCTTCGCTTAGAGTTGGC | 59.556 | 55.000 | 0.00 | 0.00 | 0.00 | 4.52 |
437 | 439 | 2.810400 | GCTTAGAGTTGGCCAGAACACA | 60.810 | 50.000 | 5.11 | 0.00 | 0.00 | 3.72 |
464 | 466 | 8.559536 | CGTCCAATTATTGTTATAGACATGCTT | 58.440 | 33.333 | 4.15 | 0.00 | 38.26 | 3.91 |
546 | 548 | 7.483375 | TCTCGACAAAACAAACATAAACAAGTG | 59.517 | 33.333 | 0.00 | 0.00 | 0.00 | 3.16 |
547 | 549 | 6.034044 | TCGACAAAACAAACATAAACAAGTGC | 59.966 | 34.615 | 0.00 | 0.00 | 0.00 | 4.40 |
549 | 551 | 5.864474 | ACAAAACAAACATAAACAAGTGCGA | 59.136 | 32.000 | 0.00 | 0.00 | 0.00 | 5.10 |
553 | 555 | 5.646606 | ACAAACATAAACAAGTGCGACTTT | 58.353 | 33.333 | 0.00 | 0.00 | 36.03 | 2.66 |
563 | 565 | 3.455619 | AGTGCGACTTTAGCAATTTCG | 57.544 | 42.857 | 0.00 | 0.00 | 46.97 | 3.46 |
569 | 571 | 3.543494 | CGACTTTAGCAATTTCGCAATGG | 59.457 | 43.478 | 0.00 | 0.00 | 0.00 | 3.16 |
571 | 573 | 5.132897 | ACTTTAGCAATTTCGCAATGGAA | 57.867 | 34.783 | 0.00 | 0.00 | 0.00 | 3.53 |
577 | 579 | 6.064846 | AGCAATTTCGCAATGGAACTATAG | 57.935 | 37.500 | 0.00 | 0.00 | 0.00 | 1.31 |
604 | 606 | 7.828712 | AGTATCCCATAAATAAGAGTCTACGC | 58.171 | 38.462 | 0.00 | 0.00 | 0.00 | 4.42 |
624 | 626 | 2.033151 | GCGGCGTAATTTATCCTCACAC | 60.033 | 50.000 | 9.37 | 0.00 | 0.00 | 3.82 |
629 | 631 | 5.057149 | GCGTAATTTATCCTCACACCTCAT | 58.943 | 41.667 | 0.00 | 0.00 | 0.00 | 2.90 |
630 | 632 | 5.527582 | GCGTAATTTATCCTCACACCTCATT | 59.472 | 40.000 | 0.00 | 0.00 | 0.00 | 2.57 |
634 | 636 | 7.781324 | AATTTATCCTCACACCTCATTGTTT | 57.219 | 32.000 | 0.00 | 0.00 | 0.00 | 2.83 |
637 | 639 | 4.437682 | TCCTCACACCTCATTGTTTCTT | 57.562 | 40.909 | 0.00 | 0.00 | 0.00 | 2.52 |
667 | 669 | 4.142773 | CCGAAAAAGCCGTAGCAGAAAATA | 60.143 | 41.667 | 0.00 | 0.00 | 43.56 | 1.40 |
671 | 673 | 3.199880 | AGCCGTAGCAGAAAATAGCAT | 57.800 | 42.857 | 0.00 | 0.00 | 43.56 | 3.79 |
679 | 681 | 7.360946 | CCGTAGCAGAAAATAGCATATAAACCC | 60.361 | 40.741 | 0.00 | 0.00 | 0.00 | 4.11 |
684 | 686 | 5.768164 | AGAAAATAGCATATAAACCCACCGG | 59.232 | 40.000 | 0.00 | 0.00 | 0.00 | 5.28 |
778 | 808 | 5.846164 | AGAAAATGGACCCCTCAAAGAAAAT | 59.154 | 36.000 | 0.00 | 0.00 | 0.00 | 1.82 |
779 | 809 | 5.488262 | AAATGGACCCCTCAAAGAAAATG | 57.512 | 39.130 | 0.00 | 0.00 | 0.00 | 2.32 |
782 | 813 | 3.116939 | TGGACCCCTCAAAGAAAATGGAA | 60.117 | 43.478 | 0.00 | 0.00 | 0.00 | 3.53 |
797 | 828 | 2.488204 | TGGAAAATGGAGCACGATGA | 57.512 | 45.000 | 0.00 | 0.00 | 0.00 | 2.92 |
817 | 848 | 1.615392 | AGAAGCACAATTGGCAGGTTC | 59.385 | 47.619 | 21.70 | 21.70 | 38.41 | 3.62 |
864 | 898 | 1.694696 | CCACTAGGCCACTAATCTCCC | 59.305 | 57.143 | 5.01 | 0.00 | 0.00 | 4.30 |
900 | 934 | 0.613853 | ACCCACTTTCTCCGGATCGA | 60.614 | 55.000 | 3.57 | 0.00 | 0.00 | 3.59 |
914 | 948 | 1.536284 | GGATCGAGGCTTAACAGGACG | 60.536 | 57.143 | 0.00 | 0.00 | 0.00 | 4.79 |
1014 | 1061 | 0.829333 | CCATCTCCAGTCCAGTCCAG | 59.171 | 60.000 | 0.00 | 0.00 | 0.00 | 3.86 |
1022 | 1069 | 4.316823 | TCCAGTCCAGACGCCCCT | 62.317 | 66.667 | 0.00 | 0.00 | 36.20 | 4.79 |
1100 | 1147 | 4.056125 | CTCGCCTGTCGGTGCTCA | 62.056 | 66.667 | 0.00 | 0.00 | 40.70 | 4.26 |
1346 | 1397 | 2.887152 | CAGGGGTGTTCTTTTTCTGGAG | 59.113 | 50.000 | 0.00 | 0.00 | 0.00 | 3.86 |
1442 | 1494 | 1.686355 | TTCTGCATCGTTTGGTTGGT | 58.314 | 45.000 | 0.00 | 0.00 | 0.00 | 3.67 |
1444 | 1496 | 0.240945 | CTGCATCGTTTGGTTGGTCC | 59.759 | 55.000 | 0.00 | 0.00 | 0.00 | 4.46 |
1453 | 1505 | 3.180449 | TGGTTGGTCCAGACTCCAT | 57.820 | 52.632 | 0.00 | 0.00 | 41.93 | 3.41 |
1491 | 1543 | 1.620822 | GGTGATTTTGCCTCTGTGGT | 58.379 | 50.000 | 0.00 | 0.00 | 38.35 | 4.16 |
1586 | 1638 | 0.882484 | TCAACGGATTTGCTGTCGCA | 60.882 | 50.000 | 0.00 | 0.00 | 46.24 | 5.10 |
1687 | 1750 | 5.059833 | GTGATTTGTGGATCTAAGCTAGGG | 58.940 | 45.833 | 0.00 | 0.00 | 0.00 | 3.53 |
1723 | 1786 | 1.337071 | TCGAGAGTTGTGTGTCAGACC | 59.663 | 52.381 | 0.00 | 0.00 | 0.00 | 3.85 |
1842 | 2500 | 3.135712 | TCAGAAGCTTGGTTTCTGTGGTA | 59.864 | 43.478 | 18.43 | 2.91 | 46.12 | 3.25 |
1845 | 2503 | 5.010012 | CAGAAGCTTGGTTTCTGTGGTAATT | 59.990 | 40.000 | 2.10 | 0.00 | 42.87 | 1.40 |
1864 | 2522 | 9.528489 | TGGTAATTAATAAATTATCCCTCCTGC | 57.472 | 33.333 | 0.00 | 0.00 | 37.72 | 4.85 |
1865 | 2523 | 8.674607 | GGTAATTAATAAATTATCCCTCCTGCG | 58.325 | 37.037 | 0.00 | 0.00 | 39.23 | 5.18 |
1866 | 2524 | 9.444600 | GTAATTAATAAATTATCCCTCCTGCGA | 57.555 | 33.333 | 0.00 | 0.00 | 39.23 | 5.10 |
1878 | 2536 | 0.170561 | TCCTGCGACTACGAGCTTTC | 59.829 | 55.000 | 0.00 | 0.00 | 42.66 | 2.62 |
1880 | 2538 | 0.109272 | CTGCGACTACGAGCTTTCCA | 60.109 | 55.000 | 0.00 | 0.00 | 42.66 | 3.53 |
1907 | 2565 | 0.773644 | AGCAGAGTTTGTGGGGACAT | 59.226 | 50.000 | 0.00 | 0.00 | 46.14 | 3.06 |
1908 | 2566 | 1.985159 | AGCAGAGTTTGTGGGGACATA | 59.015 | 47.619 | 0.00 | 0.00 | 46.14 | 2.29 |
1913 | 2571 | 4.991056 | CAGAGTTTGTGGGGACATATATCG | 59.009 | 45.833 | 0.00 | 0.00 | 46.14 | 2.92 |
1921 | 2579 | 4.755123 | GTGGGGACATATATCGGTCAAAAG | 59.245 | 45.833 | 8.45 | 0.00 | 46.14 | 2.27 |
1935 | 2593 | 4.150451 | CGGTCAAAAGAAACCATCAATTGC | 59.850 | 41.667 | 0.00 | 0.00 | 35.13 | 3.56 |
1960 | 2618 | 6.535963 | AAGATAAAAATGCAGAAGGGGAAG | 57.464 | 37.500 | 0.00 | 0.00 | 0.00 | 3.46 |
2038 | 2696 | 2.057922 | AGACAGTGAGGGTTGTCCATT | 58.942 | 47.619 | 0.00 | 0.00 | 43.64 | 3.16 |
2055 | 2713 | 8.461222 | GTTGTCCATTTCATGAATCACTATCAA | 58.539 | 33.333 | 9.40 | 6.88 | 0.00 | 2.57 |
2069 | 2727 | 6.106648 | TCACTATCAATCCTCCAGCTTATG | 57.893 | 41.667 | 0.00 | 0.00 | 0.00 | 1.90 |
2093 | 2751 | 0.545309 | CCCTGTCTCCCAGTCCTTGA | 60.545 | 60.000 | 0.00 | 0.00 | 39.74 | 3.02 |
2106 | 2764 | 4.384056 | CAGTCCTTGACTTGTTCAGATGT | 58.616 | 43.478 | 0.00 | 0.00 | 41.37 | 3.06 |
2152 | 2810 | 9.696917 | ACTGCTATTTTTAACTGATGGAAAAAG | 57.303 | 29.630 | 0.00 | 0.00 | 35.98 | 2.27 |
2225 | 2884 | 3.357079 | CAACAGCTGGCCGTGGAC | 61.357 | 66.667 | 19.93 | 0.00 | 0.00 | 4.02 |
2321 | 2986 | 2.288518 | GGCTACTGAGGAGATTAAGCCG | 60.289 | 54.545 | 0.00 | 0.00 | 38.74 | 5.52 |
2415 | 3080 | 8.833231 | ATTACCGATTAATCTGGTTACTCATG | 57.167 | 34.615 | 26.10 | 4.97 | 36.01 | 3.07 |
2422 | 3087 | 3.057969 | TCTGGTTACTCATGCTTGTGG | 57.942 | 47.619 | 6.61 | 1.39 | 0.00 | 4.17 |
2481 | 3147 | 3.624777 | CTTGTCATTGACTATTGGCCCT | 58.375 | 45.455 | 17.26 | 0.00 | 33.15 | 5.19 |
2503 | 3169 | 4.450976 | TGAATACCATGCATCACAGGTAC | 58.549 | 43.478 | 14.11 | 5.53 | 35.92 | 3.34 |
2574 | 3240 | 7.981225 | AGAAAATCAGCTTATGTTTGTGTGTTT | 59.019 | 29.630 | 0.00 | 0.00 | 0.00 | 2.83 |
2592 | 3258 | 1.422531 | TTGCCCTTTGGTTGCAGATT | 58.577 | 45.000 | 0.00 | 0.00 | 36.21 | 2.40 |
2689 | 3355 | 6.436532 | AGGAAAGAGTCGGTATGTTTCTAGAA | 59.563 | 38.462 | 0.00 | 0.00 | 0.00 | 2.10 |
2692 | 3358 | 9.152595 | GAAAGAGTCGGTATGTTTCTAGAAAAT | 57.847 | 33.333 | 19.30 | 15.84 | 31.33 | 1.82 |
2738 | 3405 | 2.709934 | AGATATGGCTTCCTGCAGACAT | 59.290 | 45.455 | 17.39 | 6.23 | 45.23 | 3.06 |
2780 | 3447 | 4.824479 | TTCACCACATGAGCATCTAGAA | 57.176 | 40.909 | 0.00 | 0.00 | 38.99 | 2.10 |
2838 | 3505 | 5.604758 | TTTCCCACAAATGAACATCAACA | 57.395 | 34.783 | 0.00 | 0.00 | 0.00 | 3.33 |
2866 | 3533 | 5.598830 | TCTTAAGACAACTCTGGTGACTCTT | 59.401 | 40.000 | 0.00 | 0.00 | 0.00 | 2.85 |
2931 | 3598 | 9.104965 | TGTGTACTTAGTATGGATAAACAATGC | 57.895 | 33.333 | 0.00 | 0.00 | 0.00 | 3.56 |
2967 | 3634 | 4.342378 | TGTCATATCTCTACTGTTCTGCCC | 59.658 | 45.833 | 0.00 | 0.00 | 0.00 | 5.36 |
2981 | 3650 | 7.906327 | ACTGTTCTGCCCAAATAAATACATTT | 58.094 | 30.769 | 0.00 | 0.00 | 0.00 | 2.32 |
3079 | 3748 | 6.486253 | TCACTGTGCTTTCATTTCATAGAC | 57.514 | 37.500 | 2.12 | 0.00 | 0.00 | 2.59 |
3080 | 3749 | 6.233434 | TCACTGTGCTTTCATTTCATAGACT | 58.767 | 36.000 | 2.12 | 0.00 | 0.00 | 3.24 |
3083 | 3752 | 4.631377 | TGTGCTTTCATTTCATAGACTCCG | 59.369 | 41.667 | 0.00 | 0.00 | 0.00 | 4.63 |
3086 | 3755 | 5.525012 | TGCTTTCATTTCATAGACTCCGATG | 59.475 | 40.000 | 0.00 | 0.00 | 0.00 | 3.84 |
3099 | 3768 | 6.037786 | AGACTCCGATGATTGTTACTTTGA | 57.962 | 37.500 | 0.00 | 0.00 | 0.00 | 2.69 |
3207 | 3876 | 7.214467 | AGACATGTACGATGTGGAAAAATTT | 57.786 | 32.000 | 13.42 | 0.00 | 31.52 | 1.82 |
3260 | 3929 | 8.763601 | AGTAGTAGATAAACTTCCTGCTGAATT | 58.236 | 33.333 | 0.00 | 0.00 | 31.06 | 2.17 |
3298 | 3967 | 5.172934 | CAGCCGTTATTAGAGTACCAAACA | 58.827 | 41.667 | 0.00 | 0.00 | 0.00 | 2.83 |
3356 | 4025 | 2.100749 | CCGCCTTCCAAAAGAACAGTTT | 59.899 | 45.455 | 0.00 | 0.00 | 34.14 | 2.66 |
3471 | 4140 | 0.886490 | CTGGGCTCAAACTGAACGCT | 60.886 | 55.000 | 0.00 | 0.00 | 0.00 | 5.07 |
3544 | 4213 | 1.728490 | GAAATCGGATGGCAGGGTGC | 61.728 | 60.000 | 0.00 | 0.00 | 44.08 | 5.01 |
3789 | 4458 | 9.614792 | AACTCATCCAGTACCATTTAATTAGTC | 57.385 | 33.333 | 0.00 | 0.00 | 32.30 | 2.59 |
3793 | 4462 | 4.210537 | CCAGTACCATTTAATTAGTCCGCG | 59.789 | 45.833 | 0.00 | 0.00 | 0.00 | 6.46 |
3851 | 4638 | 3.759581 | ACAATCTGTCTTTGTGCAGGAT | 58.240 | 40.909 | 0.00 | 0.00 | 36.02 | 3.24 |
3914 | 4701 | 1.137086 | GGCGATTCAGACCTAGCAAGA | 59.863 | 52.381 | 0.00 | 0.00 | 0.00 | 3.02 |
3930 | 4717 | 3.151022 | GAGCCCTGGACCTCGAGG | 61.151 | 72.222 | 30.11 | 30.11 | 40.98 | 4.63 |
3950 | 4737 | 3.898627 | CTGCTCGCAGACCGACGTT | 62.899 | 63.158 | 13.43 | 0.00 | 46.30 | 3.99 |
4008 | 4795 | 2.335369 | CCGGTAAGAGGATCGCGG | 59.665 | 66.667 | 6.13 | 0.00 | 42.67 | 6.46 |
4129 | 4919 | 3.551863 | GCCTACTCATGCTACTGCTAGTG | 60.552 | 52.174 | 0.00 | 0.00 | 40.48 | 2.74 |
4130 | 4920 | 2.593346 | ACTCATGCTACTGCTAGTGC | 57.407 | 50.000 | 0.00 | 0.00 | 40.48 | 4.40 |
4131 | 4921 | 2.106566 | ACTCATGCTACTGCTAGTGCT | 58.893 | 47.619 | 0.00 | 0.00 | 40.48 | 4.40 |
4216 | 5016 | 4.568072 | TGGGTAGATATGCAAGTGTTGT | 57.432 | 40.909 | 0.00 | 0.00 | 0.00 | 3.32 |
4223 | 5023 | 6.875948 | AGATATGCAAGTGTTGTTGTTGTA | 57.124 | 33.333 | 0.00 | 0.00 | 0.00 | 2.41 |
4224 | 5024 | 6.668323 | AGATATGCAAGTGTTGTTGTTGTAC | 58.332 | 36.000 | 0.00 | 0.00 | 0.00 | 2.90 |
4329 | 5129 | 0.388649 | GTGTGCTACAGAGTGGACCG | 60.389 | 60.000 | 0.00 | 0.00 | 0.00 | 4.79 |
4389 | 5227 | 4.700213 | GTGCCTCATGTACCAAGTTGTATT | 59.300 | 41.667 | 1.45 | 0.00 | 0.00 | 1.89 |
4390 | 5228 | 4.699735 | TGCCTCATGTACCAAGTTGTATTG | 59.300 | 41.667 | 1.45 | 0.00 | 0.00 | 1.90 |
4391 | 5229 | 4.438744 | GCCTCATGTACCAAGTTGTATTGC | 60.439 | 45.833 | 1.45 | 0.00 | 0.00 | 3.56 |
4392 | 5230 | 4.943705 | CCTCATGTACCAAGTTGTATTGCT | 59.056 | 41.667 | 1.45 | 0.00 | 0.00 | 3.91 |
4393 | 5231 | 5.415701 | CCTCATGTACCAAGTTGTATTGCTT | 59.584 | 40.000 | 1.45 | 0.00 | 0.00 | 3.91 |
4394 | 5232 | 6.597672 | CCTCATGTACCAAGTTGTATTGCTTA | 59.402 | 38.462 | 1.45 | 0.00 | 0.00 | 3.09 |
4449 | 5287 | 6.215845 | GCAGAAATTGGCTCTGAAGTTTTTA | 58.784 | 36.000 | 9.37 | 0.00 | 42.51 | 1.52 |
4480 | 5318 | 7.856145 | ATGGAAGATGTGATTTCTGTCTAAC | 57.144 | 36.000 | 0.00 | 0.00 | 0.00 | 2.34 |
4482 | 5320 | 7.223584 | TGGAAGATGTGATTTCTGTCTAACAA | 58.776 | 34.615 | 0.00 | 0.00 | 0.00 | 2.83 |
4513 | 5353 | 9.282247 | GCAAGTTTATCTATTGATGACACTTTG | 57.718 | 33.333 | 0.00 | 2.32 | 34.32 | 2.77 |
4521 | 5361 | 5.633830 | ATTGATGACACTTTGTGGTCATC | 57.366 | 39.130 | 21.61 | 21.61 | 43.15 | 2.92 |
4530 | 5370 | 4.153655 | CACTTTGTGGTCATCATCACTCTG | 59.846 | 45.833 | 0.00 | 0.00 | 35.15 | 3.35 |
4552 | 5395 | 9.424319 | CTCTGTTGCAGTTTCTCTACTTAAATA | 57.576 | 33.333 | 0.00 | 0.00 | 32.61 | 1.40 |
4594 | 5437 | 7.307930 | GCAAGAAAAACTAACCCAATTCAATGG | 60.308 | 37.037 | 0.00 | 0.00 | 40.35 | 3.16 |
4600 | 5443 | 1.648116 | ACCCAATTCAATGGCTTGCT | 58.352 | 45.000 | 0.00 | 0.00 | 39.26 | 3.91 |
4612 | 5455 | 2.105124 | GCTTGCTGCCTTCATCTCC | 58.895 | 57.895 | 0.00 | 0.00 | 35.15 | 3.71 |
4626 | 5469 | 1.265635 | CATCTCCGTCTCCGTCTCATC | 59.734 | 57.143 | 0.00 | 0.00 | 0.00 | 2.92 |
4641 | 5484 | 1.227497 | CATCTTCTCCTCGCCTGCC | 60.227 | 63.158 | 0.00 | 0.00 | 0.00 | 4.85 |
4683 | 5526 | 3.503363 | GCCACTCATCAGCGGTGC | 61.503 | 66.667 | 10.38 | 0.00 | 0.00 | 5.01 |
4718 | 5561 | 0.180171 | ATGCGCACTGGGCTACATTA | 59.820 | 50.000 | 14.90 | 0.00 | 42.10 | 1.90 |
4753 | 5596 | 5.256474 | AGCTTAATGACAATAGTTGCTGGT | 58.744 | 37.500 | 0.00 | 0.00 | 0.00 | 4.00 |
4755 | 5598 | 6.316390 | AGCTTAATGACAATAGTTGCTGGTAC | 59.684 | 38.462 | 0.00 | 0.00 | 0.00 | 3.34 |
4792 | 5635 | 3.831911 | TCCAACAGAATAAGCAAAAGGGG | 59.168 | 43.478 | 0.00 | 0.00 | 0.00 | 4.79 |
4794 | 5637 | 2.179427 | ACAGAATAAGCAAAAGGGGCC | 58.821 | 47.619 | 0.00 | 0.00 | 0.00 | 5.80 |
4795 | 5638 | 2.225369 | ACAGAATAAGCAAAAGGGGCCT | 60.225 | 45.455 | 0.84 | 0.00 | 0.00 | 5.19 |
4825 | 5668 | 1.466856 | CTACACATGGCACCAGCAAT | 58.533 | 50.000 | 0.00 | 0.00 | 44.61 | 3.56 |
4837 | 5680 | 2.030540 | CACCAGCAATCAGTGGAAACAG | 60.031 | 50.000 | 0.00 | 0.00 | 44.46 | 3.16 |
4841 | 5684 | 1.668047 | GCAATCAGTGGAAACAGCTGC | 60.668 | 52.381 | 15.27 | 0.00 | 44.46 | 5.25 |
4862 | 5705 | 3.192466 | CAACTTGCAGCAAAAGAAAGCT | 58.808 | 40.909 | 9.65 | 0.00 | 42.94 | 3.74 |
4871 | 5714 | 5.938438 | AGCAAAAGAAAGCTGTTCTCTAG | 57.062 | 39.130 | 10.34 | 6.03 | 40.13 | 2.43 |
4873 | 5716 | 4.023707 | GCAAAAGAAAGCTGTTCTCTAGCA | 60.024 | 41.667 | 10.34 | 0.00 | 43.53 | 3.49 |
4874 | 5717 | 5.687828 | CAAAAGAAAGCTGTTCTCTAGCAG | 58.312 | 41.667 | 10.34 | 0.00 | 43.53 | 4.24 |
4883 | 5727 | 2.872245 | TGTTCTCTAGCAGCACAACAAC | 59.128 | 45.455 | 0.00 | 0.00 | 0.00 | 3.32 |
4943 | 5787 | 2.952310 | CCTAACCCCGTACAGTACTACC | 59.048 | 54.545 | 9.10 | 0.00 | 0.00 | 3.18 |
4944 | 5788 | 1.463674 | AACCCCGTACAGTACTACCG | 58.536 | 55.000 | 9.10 | 0.00 | 0.00 | 4.02 |
4947 | 5791 | 1.940613 | CCCCGTACAGTACTACCGTAC | 59.059 | 57.143 | 9.10 | 10.52 | 45.04 | 3.67 |
4964 | 5808 | 9.454859 | ACTACCGTACTTATTTTGTAGACTACT | 57.545 | 33.333 | 13.67 | 0.00 | 32.19 | 2.57 |
5051 | 5896 | 3.172339 | CCTCTCTCTCATTCCCTATGGG | 58.828 | 54.545 | 0.00 | 0.00 | 46.11 | 4.00 |
5077 | 5922 | 1.823899 | GCGCCCAATTCTACAGGGG | 60.824 | 63.158 | 0.00 | 0.00 | 43.04 | 4.79 |
5108 | 5953 | 0.823460 | CCCTCTCTGAAGCTCCAGTC | 59.177 | 60.000 | 0.00 | 0.00 | 35.71 | 3.51 |
5153 | 5999 | 2.481104 | CCGTTTGCAGCTTCTCCAAAAA | 60.481 | 45.455 | 0.00 | 0.00 | 31.11 | 1.94 |
5229 | 6075 | 1.897133 | AGCACACAATGGAATGCATGT | 59.103 | 42.857 | 0.00 | 0.00 | 40.63 | 3.21 |
5235 | 6081 | 2.244510 | ACAATGGAATGCATGTAGGGGA | 59.755 | 45.455 | 0.00 | 0.00 | 0.00 | 4.81 |
5243 | 6130 | 5.013183 | GGAATGCATGTAGGGGATAGTTACT | 59.987 | 44.000 | 0.00 | 0.00 | 0.00 | 2.24 |
5273 | 6160 | 3.862845 | CGTTGGGTGAAAACAAAAGGAAG | 59.137 | 43.478 | 0.00 | 0.00 | 0.00 | 3.46 |
5288 | 6175 | 1.074405 | AGGAAGCACAAGGATCAGCAA | 59.926 | 47.619 | 0.00 | 0.00 | 0.00 | 3.91 |
5341 | 6228 | 2.938354 | CCTTCTCCAGGCACAACAG | 58.062 | 57.895 | 0.00 | 0.00 | 35.13 | 3.16 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
9 | 10 | 3.119245 | AGTGCCATCATTCATGAGCAAAC | 60.119 | 43.478 | 6.63 | 0.00 | 39.17 | 2.93 |
10 | 11 | 3.093814 | AGTGCCATCATTCATGAGCAAA | 58.906 | 40.909 | 6.63 | 0.00 | 39.17 | 3.68 |
31 | 32 | 1.932156 | AAAGTGTGAGGGGTGTGCCA | 61.932 | 55.000 | 0.00 | 0.00 | 36.17 | 4.92 |
40 | 41 | 3.066760 | GGGTTGACAAAGAAAGTGTGAGG | 59.933 | 47.826 | 0.00 | 0.00 | 0.00 | 3.86 |
157 | 159 | 4.287766 | ACGCACTAAGGAAGGAGAAAAT | 57.712 | 40.909 | 0.00 | 0.00 | 0.00 | 1.82 |
195 | 197 | 4.275936 | ACTCACATCTTTGACCTTTTTCCG | 59.724 | 41.667 | 0.00 | 0.00 | 0.00 | 4.30 |
197 | 199 | 8.479313 | AAAAACTCACATCTTTGACCTTTTTC | 57.521 | 30.769 | 0.00 | 0.00 | 0.00 | 2.29 |
264 | 266 | 8.255111 | TCTATAGCTCATGGATTCAGAAGAAA | 57.745 | 34.615 | 0.00 | 0.00 | 37.29 | 2.52 |
267 | 269 | 6.591062 | GCTTCTATAGCTCATGGATTCAGAAG | 59.409 | 42.308 | 14.32 | 14.32 | 46.77 | 2.85 |
269 | 271 | 6.035368 | GCTTCTATAGCTCATGGATTCAGA | 57.965 | 41.667 | 0.00 | 0.00 | 46.77 | 3.27 |
286 | 288 | 7.041030 | TGTGTCGAACATTTTATTTGGCTTCTA | 60.041 | 33.333 | 0.00 | 0.00 | 32.36 | 2.10 |
306 | 308 | 5.861787 | TGTCATACACTTGATAACTGTGTCG | 59.138 | 40.000 | 0.00 | 0.00 | 42.91 | 4.35 |
374 | 376 | 3.181482 | GCTTCTCACGATCCTCTCATTCA | 60.181 | 47.826 | 0.00 | 0.00 | 0.00 | 2.57 |
384 | 386 | 3.762779 | CCAAAATTGGCTTCTCACGATC | 58.237 | 45.455 | 0.00 | 0.00 | 42.21 | 3.69 |
385 | 387 | 3.855689 | CCAAAATTGGCTTCTCACGAT | 57.144 | 42.857 | 0.00 | 0.00 | 42.21 | 3.73 |
428 | 430 | 4.215399 | ACAATAATTGGACGTGTGTTCTGG | 59.785 | 41.667 | 0.00 | 0.00 | 34.12 | 3.86 |
437 | 439 | 7.715249 | AGCATGTCTATAACAATAATTGGACGT | 59.285 | 33.333 | 0.00 | 0.00 | 42.37 | 4.34 |
464 | 466 | 6.606069 | ACAGCTATAAGTGGTAGAGATGAGA | 58.394 | 40.000 | 0.74 | 0.00 | 39.32 | 3.27 |
546 | 548 | 2.241259 | TGCGAAATTGCTAAAGTCGC | 57.759 | 45.000 | 10.64 | 10.64 | 45.80 | 5.19 |
547 | 549 | 3.543494 | CCATTGCGAAATTGCTAAAGTCG | 59.457 | 43.478 | 0.00 | 0.00 | 35.36 | 4.18 |
549 | 551 | 4.782019 | TCCATTGCGAAATTGCTAAAGT | 57.218 | 36.364 | 0.00 | 0.00 | 35.36 | 2.66 |
553 | 555 | 6.989759 | TCTATAGTTCCATTGCGAAATTGCTA | 59.010 | 34.615 | 0.00 | 0.00 | 35.36 | 3.49 |
563 | 565 | 6.769512 | TGGGATACTTCTATAGTTCCATTGC | 58.230 | 40.000 | 0.00 | 0.00 | 38.33 | 3.56 |
577 | 579 | 9.843334 | CGTAGACTCTTATTTATGGGATACTTC | 57.157 | 37.037 | 0.00 | 0.00 | 0.00 | 3.01 |
599 | 601 | 2.660236 | GAGGATAAATTACGCCGCGTAG | 59.340 | 50.000 | 23.56 | 0.00 | 43.21 | 3.51 |
600 | 602 | 2.034432 | TGAGGATAAATTACGCCGCGTA | 59.966 | 45.455 | 21.35 | 21.35 | 41.54 | 4.42 |
601 | 603 | 1.202440 | TGAGGATAAATTACGCCGCGT | 60.202 | 47.619 | 23.72 | 23.72 | 44.35 | 6.01 |
604 | 606 | 2.542595 | GGTGTGAGGATAAATTACGCCG | 59.457 | 50.000 | 0.00 | 0.00 | 0.00 | 6.46 |
624 | 626 | 2.160417 | GGCGAGTCAAGAAACAATGAGG | 59.840 | 50.000 | 0.00 | 0.00 | 0.00 | 3.86 |
629 | 631 | 1.942677 | TTCGGCGAGTCAAGAAACAA | 58.057 | 45.000 | 10.46 | 0.00 | 0.00 | 2.83 |
630 | 632 | 1.942677 | TTTCGGCGAGTCAAGAAACA | 58.057 | 45.000 | 10.46 | 0.00 | 0.00 | 2.83 |
634 | 636 | 0.865769 | GCTTTTTCGGCGAGTCAAGA | 59.134 | 50.000 | 21.73 | 6.06 | 0.00 | 3.02 |
637 | 639 | 3.650369 | GGCTTTTTCGGCGAGTCA | 58.350 | 55.556 | 10.46 | 0.00 | 0.00 | 3.41 |
667 | 669 | 2.240160 | TGTTCCGGTGGGTTTATATGCT | 59.760 | 45.455 | 0.00 | 0.00 | 33.83 | 3.79 |
671 | 673 | 5.773680 | TCAATTTTGTTCCGGTGGGTTTATA | 59.226 | 36.000 | 0.00 | 0.00 | 33.83 | 0.98 |
679 | 681 | 2.665519 | CGAGCTCAATTTTGTTCCGGTG | 60.666 | 50.000 | 15.40 | 0.00 | 0.00 | 4.94 |
684 | 686 | 2.287547 | TGGTGCGAGCTCAATTTTGTTC | 60.288 | 45.455 | 15.40 | 0.00 | 0.00 | 3.18 |
778 | 808 | 2.027285 | TCTCATCGTGCTCCATTTTCCA | 60.027 | 45.455 | 0.00 | 0.00 | 0.00 | 3.53 |
779 | 809 | 2.632377 | TCTCATCGTGCTCCATTTTCC | 58.368 | 47.619 | 0.00 | 0.00 | 0.00 | 3.13 |
782 | 813 | 2.012673 | GCTTCTCATCGTGCTCCATTT | 58.987 | 47.619 | 0.00 | 0.00 | 0.00 | 2.32 |
797 | 828 | 1.615392 | GAACCTGCCAATTGTGCTTCT | 59.385 | 47.619 | 16.52 | 3.18 | 0.00 | 2.85 |
817 | 848 | 6.103997 | TCGGCTGTTTTAGTAAACTCCATAG | 58.896 | 40.000 | 0.00 | 0.00 | 43.25 | 2.23 |
864 | 898 | 3.185797 | GTGGGTTTAGTACGCTTGACAAG | 59.814 | 47.826 | 11.02 | 11.02 | 40.20 | 3.16 |
900 | 934 | 4.772886 | ATTTATCCGTCCTGTTAAGCCT | 57.227 | 40.909 | 0.00 | 0.00 | 0.00 | 4.58 |
914 | 948 | 4.082949 | GCCCGGCACTTGTATAATTTATCC | 60.083 | 45.833 | 3.91 | 0.00 | 0.00 | 2.59 |
1100 | 1147 | 2.443016 | AGCGGAGAGGAAGCGGAT | 60.443 | 61.111 | 0.00 | 0.00 | 35.78 | 4.18 |
1284 | 1331 | 0.466124 | GGGGAAACGAGAGCAGCTAT | 59.534 | 55.000 | 0.00 | 0.00 | 0.00 | 2.97 |
1442 | 1494 | 0.106469 | AGCGCTCTATGGAGTCTGGA | 60.106 | 55.000 | 2.64 | 0.00 | 41.38 | 3.86 |
1444 | 1496 | 2.499197 | TCTAGCGCTCTATGGAGTCTG | 58.501 | 52.381 | 16.34 | 0.00 | 41.38 | 3.51 |
1446 | 1498 | 2.415357 | GCATCTAGCGCTCTATGGAGTC | 60.415 | 54.545 | 24.99 | 10.91 | 41.38 | 3.36 |
1447 | 1499 | 1.543802 | GCATCTAGCGCTCTATGGAGT | 59.456 | 52.381 | 24.99 | 0.18 | 41.38 | 3.85 |
1448 | 1500 | 2.276472 | GCATCTAGCGCTCTATGGAG | 57.724 | 55.000 | 24.99 | 13.61 | 42.18 | 3.86 |
1470 | 1522 | 0.890683 | CACAGAGGCAAAATCACCCC | 59.109 | 55.000 | 0.00 | 0.00 | 0.00 | 4.95 |
1473 | 1525 | 3.733443 | AAACCACAGAGGCAAAATCAC | 57.267 | 42.857 | 0.00 | 0.00 | 43.14 | 3.06 |
1491 | 1543 | 2.363306 | ACTGCACAGATGGGTCAAAA | 57.637 | 45.000 | 4.31 | 0.00 | 0.00 | 2.44 |
1586 | 1638 | 9.125026 | ACTTTTATCTGAGTTTTTCATGTGACT | 57.875 | 29.630 | 0.00 | 0.00 | 34.68 | 3.41 |
1687 | 1750 | 1.018148 | TCGAGAGTCGAGATGCCTTC | 58.982 | 55.000 | 0.00 | 0.00 | 44.82 | 3.46 |
1826 | 2484 | 9.869757 | ATTTATTAATTACCACAGAAACCAAGC | 57.130 | 29.630 | 0.00 | 0.00 | 0.00 | 4.01 |
1842 | 2500 | 8.164070 | AGTCGCAGGAGGGATAATTTATTAATT | 58.836 | 33.333 | 0.00 | 0.00 | 39.07 | 1.40 |
1845 | 2503 | 6.681729 | AGTCGCAGGAGGGATAATTTATTA | 57.318 | 37.500 | 0.00 | 0.00 | 39.07 | 0.98 |
1856 | 2514 | 3.111939 | CTCGTAGTCGCAGGAGGG | 58.888 | 66.667 | 0.00 | 0.00 | 36.96 | 4.30 |
1857 | 2515 | 1.658686 | AAGCTCGTAGTCGCAGGAGG | 61.659 | 60.000 | 0.00 | 0.00 | 36.96 | 4.30 |
1861 | 2519 | 0.109272 | TGGAAAGCTCGTAGTCGCAG | 60.109 | 55.000 | 0.00 | 0.00 | 36.96 | 5.18 |
1862 | 2520 | 0.530744 | ATGGAAAGCTCGTAGTCGCA | 59.469 | 50.000 | 0.00 | 0.00 | 36.96 | 5.10 |
1863 | 2521 | 2.033049 | TCTATGGAAAGCTCGTAGTCGC | 59.967 | 50.000 | 0.00 | 0.00 | 36.96 | 5.19 |
1864 | 2522 | 3.965292 | TCTATGGAAAGCTCGTAGTCG | 57.035 | 47.619 | 0.00 | 0.00 | 38.55 | 4.18 |
1865 | 2523 | 6.963049 | TTTTTCTATGGAAAGCTCGTAGTC | 57.037 | 37.500 | 4.33 | 0.00 | 41.66 | 2.59 |
1866 | 2524 | 6.969828 | CTTTTTCTATGGAAAGCTCGTAGT | 57.030 | 37.500 | 4.33 | 0.00 | 41.66 | 2.73 |
1878 | 2536 | 5.464168 | CCACAAACTCTGCTTTTTCTATGG | 58.536 | 41.667 | 0.00 | 0.00 | 0.00 | 2.74 |
1880 | 2538 | 4.524328 | CCCCACAAACTCTGCTTTTTCTAT | 59.476 | 41.667 | 0.00 | 0.00 | 0.00 | 1.98 |
1892 | 2550 | 4.202326 | ACCGATATATGTCCCCACAAACTC | 60.202 | 45.833 | 0.00 | 0.00 | 35.64 | 3.01 |
1907 | 2565 | 8.746052 | ATTGATGGTTTCTTTTGACCGATATA | 57.254 | 30.769 | 0.00 | 0.00 | 38.81 | 0.86 |
1908 | 2566 | 7.645058 | ATTGATGGTTTCTTTTGACCGATAT | 57.355 | 32.000 | 0.00 | 0.00 | 38.81 | 1.63 |
1913 | 2571 | 5.055812 | TGCAATTGATGGTTTCTTTTGACC | 58.944 | 37.500 | 10.34 | 0.00 | 36.45 | 4.02 |
1935 | 2593 | 6.284891 | TCCCCTTCTGCATTTTTATCTTTG | 57.715 | 37.500 | 0.00 | 0.00 | 0.00 | 2.77 |
1951 | 2609 | 1.963515 | TCTTTGCTTTGCTTCCCCTTC | 59.036 | 47.619 | 0.00 | 0.00 | 0.00 | 3.46 |
2003 | 2661 | 6.017440 | CCTCACTGTCTAGCTCATACTCTAAC | 60.017 | 46.154 | 0.00 | 0.00 | 0.00 | 2.34 |
2038 | 2696 | 7.140522 | TGGAGGATTGATAGTGATTCATGAA | 57.859 | 36.000 | 11.26 | 11.26 | 0.00 | 2.57 |
2069 | 2727 | 3.627690 | CTGGGAGACAGGGAGAGC | 58.372 | 66.667 | 0.00 | 0.00 | 43.70 | 4.09 |
2106 | 2764 | 3.380004 | AGTTGATTTGTTTGTCGGCAGAA | 59.620 | 39.130 | 0.00 | 0.00 | 0.00 | 3.02 |
2152 | 2810 | 6.089954 | GCCACATCAGTTAAAAGCAGAATTTC | 59.910 | 38.462 | 0.00 | 0.00 | 0.00 | 2.17 |
2157 | 2816 | 2.819608 | GGCCACATCAGTTAAAAGCAGA | 59.180 | 45.455 | 0.00 | 0.00 | 0.00 | 4.26 |
2249 | 2908 | 5.664457 | TCAGTATTGTCTGCGATCTTCATT | 58.336 | 37.500 | 0.00 | 0.00 | 35.63 | 2.57 |
2321 | 2986 | 1.363807 | GCTTGGTTTGGTCCAGCAC | 59.636 | 57.895 | 0.00 | 0.00 | 38.80 | 4.40 |
2374 | 3039 | 5.765176 | TCGGTAATAGTTATGGATGTGACG | 58.235 | 41.667 | 0.00 | 0.00 | 0.00 | 4.35 |
2415 | 3080 | 0.595095 | CCTCTGCAGAAACCACAAGC | 59.405 | 55.000 | 18.85 | 0.00 | 0.00 | 4.01 |
2422 | 3087 | 3.870419 | GACTGATCATCCTCTGCAGAAAC | 59.130 | 47.826 | 18.85 | 1.64 | 0.00 | 2.78 |
2481 | 3147 | 3.650281 | ACCTGTGATGCATGGTATTCA | 57.350 | 42.857 | 2.46 | 0.00 | 30.47 | 2.57 |
2503 | 3169 | 0.515564 | CAAGTTCCAAGTTACGGGCG | 59.484 | 55.000 | 0.00 | 0.00 | 0.00 | 6.13 |
2574 | 3240 | 0.680618 | CAATCTGCAACCAAAGGGCA | 59.319 | 50.000 | 0.00 | 0.00 | 37.90 | 5.36 |
2592 | 3258 | 2.011947 | GCAATCACTACAGCATCAGCA | 58.988 | 47.619 | 0.00 | 0.00 | 45.49 | 4.41 |
2780 | 3447 | 9.846248 | GTGCTCATATAGTGAACAAGAAAATTT | 57.154 | 29.630 | 0.00 | 0.00 | 34.89 | 1.82 |
2798 | 3465 | 6.321181 | GTGGGAAATAAATCAAGGTGCTCATA | 59.679 | 38.462 | 0.00 | 0.00 | 0.00 | 2.15 |
2866 | 3533 | 8.918202 | ATAGAACTAACCACTCATTGACAAAA | 57.082 | 30.769 | 0.00 | 0.00 | 0.00 | 2.44 |
2967 | 3634 | 9.206870 | AGTTGCAGAACCAAATGTATTTATTTG | 57.793 | 29.630 | 0.00 | 0.00 | 44.01 | 2.32 |
2981 | 3650 | 6.647334 | TCATTATTTTGAGTTGCAGAACCA | 57.353 | 33.333 | 0.00 | 0.00 | 31.81 | 3.67 |
3039 | 3708 | 6.506147 | CACAGTGATTTTGTGGAATTCAGAA | 58.494 | 36.000 | 7.93 | 0.00 | 41.66 | 3.02 |
3079 | 3748 | 6.968131 | TCTTCAAAGTAACAATCATCGGAG | 57.032 | 37.500 | 0.00 | 0.00 | 0.00 | 4.63 |
3080 | 3749 | 6.708502 | TGTTCTTCAAAGTAACAATCATCGGA | 59.291 | 34.615 | 0.00 | 0.00 | 30.54 | 4.55 |
3207 | 3876 | 5.630121 | ACAACACCATCCAAGTTCATCTTA | 58.370 | 37.500 | 0.00 | 0.00 | 34.66 | 2.10 |
3260 | 3929 | 0.324943 | GGCTGGCTTCTTAGTGGTCA | 59.675 | 55.000 | 0.00 | 0.00 | 0.00 | 4.02 |
3298 | 3967 | 2.569404 | GGATGAAGTCTTCTGTCACCCT | 59.431 | 50.000 | 13.67 | 0.00 | 0.00 | 4.34 |
3356 | 4025 | 7.103641 | AGAGAAAATAATTGCAAGTCGTAGGA | 58.896 | 34.615 | 1.02 | 0.00 | 0.00 | 2.94 |
3544 | 4213 | 2.734723 | CCGCATATCGACCGCCAG | 60.735 | 66.667 | 0.00 | 0.00 | 41.67 | 4.85 |
3552 | 4221 | 1.548973 | GCAAGTCGGTCCGCATATCG | 61.549 | 60.000 | 6.34 | 0.00 | 38.08 | 2.92 |
3789 | 4458 | 3.865745 | AGAGAAAACAGAATATGACGCGG | 59.134 | 43.478 | 12.47 | 0.00 | 0.00 | 6.46 |
3793 | 4462 | 7.604164 | TCTGGTCAAGAGAAAACAGAATATGAC | 59.396 | 37.037 | 0.00 | 0.00 | 32.09 | 3.06 |
3851 | 4638 | 0.829990 | TCTCAGCCGGCATTATGTCA | 59.170 | 50.000 | 31.54 | 6.10 | 0.00 | 3.58 |
4008 | 4795 | 2.191641 | GATCTGGGTCAGGCCTGC | 59.808 | 66.667 | 28.91 | 21.69 | 37.43 | 4.85 |
4129 | 4919 | 1.521681 | AAACGATCTAGGCGGCAGC | 60.522 | 57.895 | 13.08 | 0.00 | 44.18 | 5.25 |
4130 | 4920 | 0.460284 | ACAAACGATCTAGGCGGCAG | 60.460 | 55.000 | 13.08 | 6.93 | 0.00 | 4.85 |
4131 | 4921 | 0.036765 | AACAAACGATCTAGGCGGCA | 60.037 | 50.000 | 13.08 | 0.00 | 0.00 | 5.69 |
4329 | 5129 | 1.840737 | TGCCTAGAGACAGACCTCAC | 58.159 | 55.000 | 0.00 | 0.00 | 35.68 | 3.51 |
4389 | 5227 | 9.205513 | TGAGCTGATATAGGATGATTATAAGCA | 57.794 | 33.333 | 5.78 | 5.78 | 0.00 | 3.91 |
4390 | 5228 | 9.474920 | GTGAGCTGATATAGGATGATTATAAGC | 57.525 | 37.037 | 0.00 | 0.00 | 0.00 | 3.09 |
4391 | 5229 | 9.979578 | GGTGAGCTGATATAGGATGATTATAAG | 57.020 | 37.037 | 0.00 | 0.00 | 0.00 | 1.73 |
4392 | 5230 | 9.492730 | TGGTGAGCTGATATAGGATGATTATAA | 57.507 | 33.333 | 0.00 | 0.00 | 0.00 | 0.98 |
4393 | 5231 | 9.140874 | CTGGTGAGCTGATATAGGATGATTATA | 57.859 | 37.037 | 0.00 | 0.00 | 0.00 | 0.98 |
4394 | 5232 | 7.622878 | ACTGGTGAGCTGATATAGGATGATTAT | 59.377 | 37.037 | 0.00 | 0.00 | 0.00 | 1.28 |
4449 | 5287 | 7.614583 | ACAGAAATCACATCTTCCATTGAGAAT | 59.385 | 33.333 | 0.00 | 0.00 | 0.00 | 2.40 |
4480 | 5318 | 8.453320 | TCATCAATAGATAAACTTGCACAGTTG | 58.547 | 33.333 | 12.87 | 2.52 | 37.88 | 3.16 |
4482 | 5320 | 7.607607 | TGTCATCAATAGATAAACTTGCACAGT | 59.392 | 33.333 | 0.00 | 0.00 | 32.33 | 3.55 |
4495 | 5334 | 6.475504 | TGACCACAAAGTGTCATCAATAGAT | 58.524 | 36.000 | 0.00 | 0.00 | 33.87 | 1.98 |
4502 | 5342 | 4.696877 | TGATGATGACCACAAAGTGTCATC | 59.303 | 41.667 | 20.23 | 20.23 | 43.15 | 2.92 |
4513 | 5353 | 2.417933 | GCAACAGAGTGATGATGACCAC | 59.582 | 50.000 | 0.00 | 0.00 | 0.00 | 4.16 |
4521 | 5361 | 4.063689 | AGAGAAACTGCAACAGAGTGATG | 58.936 | 43.478 | 0.78 | 0.00 | 35.18 | 3.07 |
4568 | 5411 | 7.307930 | CCATTGAATTGGGTTAGTTTTTCTTGC | 60.308 | 37.037 | 0.00 | 0.00 | 32.80 | 4.01 |
4594 | 5437 | 1.712977 | CGGAGATGAAGGCAGCAAGC | 61.713 | 60.000 | 0.00 | 0.00 | 44.65 | 4.01 |
4600 | 5443 | 2.202866 | GGAGACGGAGATGAAGGCA | 58.797 | 57.895 | 0.00 | 0.00 | 0.00 | 4.75 |
4626 | 5469 | 4.521062 | CCGGCAGGCGAGGAGAAG | 62.521 | 72.222 | 19.71 | 0.00 | 0.00 | 2.85 |
4718 | 5561 | 4.020218 | TGTCATTAAGCTACTGCAAGGTCT | 60.020 | 41.667 | 0.00 | 0.00 | 42.74 | 3.85 |
4753 | 5596 | 5.626142 | TGTTGGATTTAACAGCTCCAAGTA | 58.374 | 37.500 | 3.59 | 0.00 | 46.74 | 2.24 |
4774 | 5617 | 2.179427 | GGCCCCTTTTGCTTATTCTGT | 58.821 | 47.619 | 0.00 | 0.00 | 0.00 | 3.41 |
4781 | 5624 | 2.924635 | GCCAGGCCCCTTTTGCTT | 60.925 | 61.111 | 0.00 | 0.00 | 0.00 | 3.91 |
4782 | 5625 | 2.970744 | AAAGCCAGGCCCCTTTTGCT | 62.971 | 55.000 | 8.22 | 0.00 | 0.00 | 3.91 |
4806 | 5649 | 1.402968 | GATTGCTGGTGCCATGTGTAG | 59.597 | 52.381 | 0.00 | 0.00 | 38.71 | 2.74 |
4810 | 5653 | 0.251474 | ACTGATTGCTGGTGCCATGT | 60.251 | 50.000 | 0.00 | 0.00 | 38.71 | 3.21 |
4820 | 5663 | 1.884579 | CAGCTGTTTCCACTGATTGCT | 59.115 | 47.619 | 5.25 | 0.00 | 33.10 | 3.91 |
4825 | 5668 | 1.024271 | GTTGCAGCTGTTTCCACTGA | 58.976 | 50.000 | 16.64 | 0.00 | 33.10 | 3.41 |
4841 | 5684 | 3.192466 | AGCTTTCTTTTGCTGCAAGTTG | 58.808 | 40.909 | 15.39 | 9.60 | 38.21 | 3.16 |
4850 | 5693 | 4.023707 | TGCTAGAGAACAGCTTTCTTTTGC | 60.024 | 41.667 | 18.43 | 18.43 | 39.83 | 3.68 |
4862 | 5705 | 2.872245 | GTTGTTGTGCTGCTAGAGAACA | 59.128 | 45.455 | 0.00 | 0.00 | 38.64 | 3.18 |
4863 | 5706 | 3.134458 | AGTTGTTGTGCTGCTAGAGAAC | 58.866 | 45.455 | 0.00 | 1.84 | 0.00 | 3.01 |
4865 | 5708 | 3.133691 | CAAGTTGTTGTGCTGCTAGAGA | 58.866 | 45.455 | 0.00 | 0.00 | 0.00 | 3.10 |
4866 | 5709 | 2.874701 | ACAAGTTGTTGTGCTGCTAGAG | 59.125 | 45.455 | 1.64 | 0.00 | 45.58 | 2.43 |
4870 | 5713 | 1.134946 | GGAACAAGTTGTTGTGCTGCT | 59.865 | 47.619 | 25.46 | 0.00 | 46.68 | 4.24 |
4871 | 5714 | 1.135141 | TGGAACAAGTTGTTGTGCTGC | 60.135 | 47.619 | 25.46 | 9.82 | 46.68 | 5.25 |
4873 | 5716 | 3.951775 | TTTGGAACAAGTTGTTGTGCT | 57.048 | 38.095 | 25.46 | 0.86 | 46.68 | 4.40 |
4874 | 5717 | 4.629200 | TGAATTTGGAACAAGTTGTTGTGC | 59.371 | 37.500 | 25.46 | 11.23 | 46.68 | 4.57 |
4875 | 5718 | 5.636965 | TGTGAATTTGGAACAAGTTGTTGTG | 59.363 | 36.000 | 25.46 | 0.00 | 46.68 | 3.33 |
4912 | 5756 | 1.630369 | ACGGGGTTAGGGTTAAACTCC | 59.370 | 52.381 | 0.00 | 0.00 | 43.01 | 3.85 |
4916 | 5760 | 3.247162 | ACTGTACGGGGTTAGGGTTAAA | 58.753 | 45.455 | 6.65 | 0.00 | 0.00 | 1.52 |
4954 | 5798 | 7.674120 | TCACTCAGTTGTAGTAGTAGTCTACA | 58.326 | 38.462 | 12.54 | 2.29 | 46.30 | 2.74 |
4955 | 5799 | 8.721019 | ATCACTCAGTTGTAGTAGTAGTCTAC | 57.279 | 38.462 | 1.39 | 1.39 | 44.79 | 2.59 |
4957 | 5801 | 9.550406 | GATATCACTCAGTTGTAGTAGTAGTCT | 57.450 | 37.037 | 0.00 | 0.00 | 0.00 | 3.24 |
4958 | 5802 | 9.550406 | AGATATCACTCAGTTGTAGTAGTAGTC | 57.450 | 37.037 | 5.32 | 0.00 | 0.00 | 2.59 |
4961 | 5805 | 9.775854 | GGTAGATATCACTCAGTTGTAGTAGTA | 57.224 | 37.037 | 5.32 | 0.00 | 0.00 | 1.82 |
4962 | 5806 | 8.272889 | TGGTAGATATCACTCAGTTGTAGTAGT | 58.727 | 37.037 | 5.32 | 0.00 | 0.00 | 2.73 |
4963 | 5807 | 8.678593 | TGGTAGATATCACTCAGTTGTAGTAG | 57.321 | 38.462 | 5.32 | 0.00 | 0.00 | 2.57 |
4964 | 5808 | 8.272889 | ACTGGTAGATATCACTCAGTTGTAGTA | 58.727 | 37.037 | 14.82 | 0.00 | 32.34 | 1.82 |
5066 | 5911 | 1.589414 | AAGAGCAGCCCCTGTAGAAT | 58.411 | 50.000 | 0.00 | 0.00 | 33.43 | 2.40 |
5108 | 5953 | 4.025015 | CCAAAATTCAGGCTTCATCTCG | 57.975 | 45.455 | 0.00 | 0.00 | 0.00 | 4.04 |
5130 | 5976 | 2.335712 | GGAGAAGCTGCAAACGGGG | 61.336 | 63.158 | 1.02 | 0.00 | 0.00 | 5.73 |
5153 | 5999 | 1.403687 | GCCCGAGGACTAGGAGCAAT | 61.404 | 60.000 | 0.00 | 0.00 | 0.00 | 3.56 |
5229 | 6075 | 7.025520 | ACGAGCTTATAGTAACTATCCCCTA | 57.974 | 40.000 | 0.00 | 0.00 | 0.00 | 3.53 |
5235 | 6081 | 6.548622 | TCACCCAACGAGCTTATAGTAACTAT | 59.451 | 38.462 | 0.00 | 0.00 | 0.00 | 2.12 |
5243 | 6130 | 4.643463 | TGTTTTCACCCAACGAGCTTATA | 58.357 | 39.130 | 0.00 | 0.00 | 0.00 | 0.98 |
5273 | 6160 | 1.068748 | CACAGTTGCTGATCCTTGTGC | 60.069 | 52.381 | 2.91 | 0.00 | 35.18 | 4.57 |
5288 | 6175 | 4.270008 | GGTAATTTCCCTGCATACACAGT | 58.730 | 43.478 | 0.00 | 0.00 | 35.83 | 3.55 |
5341 | 6228 | 4.156739 | CCTTTCCAGGATTACTTGAAGCAC | 59.843 | 45.833 | 0.00 | 0.00 | 44.19 | 4.40 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.