Multiple sequence alignment - TraesCS5D01G443400
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 | TraesCS5D01G443400 | chr5D | 100.000 | 5700 | 0 | 0 | 1 | 5700 | 494809546 | 494815245 | 0.000000e+00 | 10527.0 |
1 | TraesCS5D01G443400 | chr5B | 92.962 | 4234 | 177 | 51 | 1 | 4164 | 611380380 | 611384562 | 0.000000e+00 | 6056.0 |
2 | TraesCS5D01G443400 | chr5B | 92.041 | 1068 | 62 | 7 | 4167 | 5231 | 611384690 | 611385737 | 0.000000e+00 | 1480.0 |
3 | TraesCS5D01G443400 | chr5B | 85.944 | 498 | 37 | 19 | 5231 | 5700 | 611385844 | 611386336 | 8.530000e-138 | 501.0 |
4 | TraesCS5D01G443400 | chr5A | 90.076 | 3295 | 205 | 56 | 427 | 3656 | 618960799 | 618964036 | 0.000000e+00 | 4161.0 |
5 | TraesCS5D01G443400 | chr5A | 93.144 | 846 | 46 | 6 | 4380 | 5215 | 618964034 | 618964877 | 0.000000e+00 | 1230.0 |
6 | TraesCS5D01G443400 | chr5A | 93.662 | 284 | 11 | 3 | 5416 | 5698 | 618965096 | 618965373 | 8.830000e-113 | 418.0 |
7 | TraesCS5D01G443400 | chr5A | 86.250 | 80 | 9 | 2 | 5291 | 5370 | 536709658 | 536709581 | 1.020000e-12 | 86.1 |
8 | TraesCS5D01G443400 | chr6A | 87.013 | 77 | 10 | 0 | 5295 | 5371 | 108179057 | 108178981 | 2.830000e-13 | 87.9 |
9 | TraesCS5D01G443400 | chr6A | 85.714 | 70 | 10 | 0 | 5299 | 5368 | 596741216 | 596741285 | 2.200000e-09 | 75.0 |
10 | TraesCS5D01G443400 | chr6D | 87.671 | 73 | 9 | 0 | 5299 | 5371 | 358361381 | 358361309 | 1.020000e-12 | 86.1 |
11 | TraesCS5D01G443400 | chr2B | 81.132 | 106 | 16 | 4 | 301 | 406 | 791140506 | 791140607 | 1.320000e-11 | 82.4 |
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 | TraesCS5D01G443400 | chr5D | 494809546 | 494815245 | 5699 | False | 10527.000000 | 10527 | 100.000000 | 1 | 5700 | 1 | chr5D.!!$F1 | 5699 |
1 | TraesCS5D01G443400 | chr5B | 611380380 | 611386336 | 5956 | False | 2679.000000 | 6056 | 90.315667 | 1 | 5700 | 3 | chr5B.!!$F1 | 5699 |
2 | TraesCS5D01G443400 | chr5A | 618960799 | 618965373 | 4574 | False | 1936.333333 | 4161 | 92.294000 | 427 | 5698 | 3 | chr5A.!!$F1 | 5271 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
296 | 313 | 0.608640 | CCCGCCCCTGTATCTGTATC | 59.391 | 60.000 | 0.00 | 0.00 | 0.00 | 2.24 | F |
1035 | 1055 | 0.238289 | CAAAAGTGTGCGCTAGTGGG | 59.762 | 55.000 | 9.73 | 0.00 | 0.00 | 4.61 | F |
1206 | 1226 | 0.825840 | GCCCAACCCACTTGTAAGCA | 60.826 | 55.000 | 0.00 | 0.00 | 0.00 | 3.91 | F |
2618 | 2678 | 1.227674 | GCCCGCTTACCTCTCCATG | 60.228 | 63.158 | 0.00 | 0.00 | 0.00 | 3.66 | F |
3171 | 3284 | 0.603975 | GTCTTCCAGGTGCCTGTGAC | 60.604 | 60.000 | 16.15 | 15.52 | 42.15 | 3.67 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1271 | 1292 | 0.991920 | CCAGGAGGGAGGTTTTAGCA | 59.008 | 55.000 | 0.00 | 0.00 | 40.01 | 3.49 | R |
2713 | 2807 | 0.740737 | GTCAGCCAAGCAACTTGTGT | 59.259 | 50.000 | 6.58 | 0.00 | 39.58 | 3.72 | R |
2716 | 2810 | 2.498167 | AGTAGTCAGCCAAGCAACTTG | 58.502 | 47.619 | 0.24 | 0.24 | 40.75 | 3.16 | R |
3631 | 3756 | 0.252467 | CCCTCCAAGACCTCCTCTGT | 60.252 | 60.000 | 0.00 | 0.00 | 0.00 | 3.41 | R |
5060 | 5318 | 0.034186 | TCATGCTCTCCCCGCAAAAT | 60.034 | 50.000 | 0.00 | 0.00 | 41.26 | 1.82 | 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 |
---|---|---|---|---|---|---|---|---|---|
32 | 33 | 2.246874 | TCCTCCTCCTCTTCCCCGT | 61.247 | 63.158 | 0.00 | 0.00 | 0.00 | 5.28 |
42 | 43 | 1.677966 | CTTCCCCGTCTCGACCAGA | 60.678 | 63.158 | 0.00 | 0.00 | 0.00 | 3.86 |
124 | 129 | 1.220749 | CGCCCTTGGATTCTTCCGA | 59.779 | 57.895 | 0.00 | 0.00 | 45.89 | 4.55 |
161 | 166 | 2.574006 | ATCTGCTCTGCTTTGACCAA | 57.426 | 45.000 | 0.00 | 0.00 | 0.00 | 3.67 |
173 | 182 | 7.541162 | TCTGCTTTGACCAATCTATTTCATTG | 58.459 | 34.615 | 0.00 | 0.00 | 0.00 | 2.82 |
233 | 242 | 8.576442 | AGAACCATACAAGTTTATTTTCCAGTG | 58.424 | 33.333 | 0.00 | 0.00 | 0.00 | 3.66 |
280 | 289 | 3.124921 | CACAGTTAAGGCCGCCCG | 61.125 | 66.667 | 5.55 | 0.00 | 35.76 | 6.13 |
296 | 313 | 0.608640 | CCCGCCCCTGTATCTGTATC | 59.391 | 60.000 | 0.00 | 0.00 | 0.00 | 2.24 |
391 | 408 | 2.988684 | GCACCCCCAAACATGCGA | 60.989 | 61.111 | 0.00 | 0.00 | 0.00 | 5.10 |
396 | 413 | 1.283613 | ACCCCCAAACATGCGATTCTA | 59.716 | 47.619 | 0.00 | 0.00 | 0.00 | 2.10 |
399 | 416 | 2.643551 | CCCAAACATGCGATTCTAGGT | 58.356 | 47.619 | 0.00 | 0.00 | 0.00 | 3.08 |
509 | 526 | 7.011389 | CCATATGTTTGCTAGAATGAGTTTCGA | 59.989 | 37.037 | 1.24 | 0.00 | 39.46 | 3.71 |
510 | 527 | 6.992063 | ATGTTTGCTAGAATGAGTTTCGAT | 57.008 | 33.333 | 0.00 | 0.00 | 39.46 | 3.59 |
511 | 528 | 6.801539 | TGTTTGCTAGAATGAGTTTCGATT | 57.198 | 33.333 | 0.00 | 0.00 | 39.46 | 3.34 |
512 | 529 | 6.831769 | TGTTTGCTAGAATGAGTTTCGATTC | 58.168 | 36.000 | 0.00 | 0.00 | 39.46 | 2.52 |
513 | 530 | 6.426633 | TGTTTGCTAGAATGAGTTTCGATTCA | 59.573 | 34.615 | 0.00 | 0.00 | 39.46 | 2.57 |
598 | 618 | 1.663911 | TGCTTCCTTACAGGCCCTTA | 58.336 | 50.000 | 0.00 | 0.00 | 34.61 | 2.69 |
617 | 637 | 6.493802 | GCCCTTAGCCTTAATTAAGCCTTTAT | 59.506 | 38.462 | 18.18 | 4.19 | 34.35 | 1.40 |
618 | 638 | 7.668469 | GCCCTTAGCCTTAATTAAGCCTTTATA | 59.332 | 37.037 | 18.18 | 0.00 | 34.35 | 0.98 |
635 | 655 | 6.659776 | CCTTTATAACTAGCAAATTCTCCGC | 58.340 | 40.000 | 0.00 | 0.00 | 0.00 | 5.54 |
647 | 667 | 2.768253 | TTCTCCGCAAGACATCATGT | 57.232 | 45.000 | 0.00 | 0.00 | 43.02 | 3.21 |
662 | 682 | 3.077519 | ATGTCGGGCGTAGGAGCAC | 62.078 | 63.158 | 0.00 | 0.00 | 39.27 | 4.40 |
669 | 689 | 1.741770 | GCGTAGGAGCACACTTGGG | 60.742 | 63.158 | 0.00 | 0.00 | 37.05 | 4.12 |
670 | 690 | 1.741770 | CGTAGGAGCACACTTGGGC | 60.742 | 63.158 | 0.00 | 0.00 | 46.94 | 5.36 |
711 | 731 | 2.224549 | TGGAACAGATTTTGTAACGCGG | 59.775 | 45.455 | 12.47 | 0.00 | 39.73 | 6.46 |
737 | 757 | 2.802719 | TGTCTGTTTGATTAAGGGGCC | 58.197 | 47.619 | 0.00 | 0.00 | 0.00 | 5.80 |
738 | 758 | 2.100197 | GTCTGTTTGATTAAGGGGCCC | 58.900 | 52.381 | 17.12 | 17.12 | 0.00 | 5.80 |
739 | 759 | 1.102978 | CTGTTTGATTAAGGGGCCCG | 58.897 | 55.000 | 18.95 | 0.00 | 0.00 | 6.13 |
740 | 760 | 0.968393 | TGTTTGATTAAGGGGCCCGC | 60.968 | 55.000 | 18.95 | 9.16 | 0.00 | 6.13 |
755 | 775 | 1.267186 | GCCCGCGTGTCTAAATAAACG | 60.267 | 52.381 | 4.92 | 0.00 | 39.00 | 3.60 |
833 | 853 | 5.547465 | TGTCACTTTGTTATACTGACCAGG | 58.453 | 41.667 | 1.82 | 0.00 | 31.94 | 4.45 |
845 | 865 | 1.827344 | CTGACCAGGCTGATGTCAGTA | 59.173 | 52.381 | 30.15 | 11.67 | 46.85 | 2.74 |
929 | 949 | 6.265196 | AGAAGAGTAGCACAGATCAAGGATAG | 59.735 | 42.308 | 0.00 | 0.00 | 0.00 | 2.08 |
967 | 987 | 2.707902 | GCACCTAGCAGGGCAATAC | 58.292 | 57.895 | 7.06 | 0.00 | 44.79 | 1.89 |
1035 | 1055 | 0.238289 | CAAAAGTGTGCGCTAGTGGG | 59.762 | 55.000 | 9.73 | 0.00 | 0.00 | 4.61 |
1206 | 1226 | 0.825840 | GCCCAACCCACTTGTAAGCA | 60.826 | 55.000 | 0.00 | 0.00 | 0.00 | 3.91 |
1217 | 1237 | 2.939353 | GTAAGCACCCCACCCCCT | 60.939 | 66.667 | 0.00 | 0.00 | 0.00 | 4.79 |
1218 | 1238 | 2.612746 | TAAGCACCCCACCCCCTC | 60.613 | 66.667 | 0.00 | 0.00 | 0.00 | 4.30 |
1262 | 1283 | 7.489113 | GGCCATGTATTCTGTTTGACAAAATAG | 59.511 | 37.037 | 1.27 | 4.81 | 36.22 | 1.73 |
1271 | 1292 | 7.715657 | TCTGTTTGACAAAATAGCATCAAAGT | 58.284 | 30.769 | 1.27 | 0.00 | 40.67 | 2.66 |
1283 | 1304 | 3.838120 | GCATCAAAGTGCTAAAACCTCC | 58.162 | 45.455 | 0.00 | 0.00 | 41.82 | 4.30 |
1750 | 1783 | 1.726853 | GAACACTACGCTGGCTTGAT | 58.273 | 50.000 | 0.00 | 0.00 | 0.00 | 2.57 |
1896 | 1952 | 4.471904 | TGGATGCCTAACTGACACTTAG | 57.528 | 45.455 | 0.00 | 0.00 | 0.00 | 2.18 |
1903 | 1959 | 9.162764 | GATGCCTAACTGACACTTAGAAATAAA | 57.837 | 33.333 | 4.06 | 0.00 | 0.00 | 1.40 |
1904 | 1960 | 8.911918 | TGCCTAACTGACACTTAGAAATAAAA | 57.088 | 30.769 | 4.06 | 0.00 | 0.00 | 1.52 |
1952 | 2008 | 5.163447 | TGACACTTGACTGCACTACTAGTTT | 60.163 | 40.000 | 0.00 | 0.00 | 0.00 | 2.66 |
1953 | 2009 | 5.671493 | ACACTTGACTGCACTACTAGTTTT | 58.329 | 37.500 | 0.00 | 0.00 | 0.00 | 2.43 |
1954 | 2010 | 6.812998 | ACACTTGACTGCACTACTAGTTTTA | 58.187 | 36.000 | 0.00 | 0.00 | 0.00 | 1.52 |
1956 | 2012 | 7.931948 | ACACTTGACTGCACTACTAGTTTTATT | 59.068 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
1958 | 2014 | 9.991906 | ACTTGACTGCACTACTAGTTTTATTTA | 57.008 | 29.630 | 0.00 | 0.00 | 0.00 | 1.40 |
1977 | 2033 | 5.512753 | TTTATTGCAAGCTTCACAACAGA | 57.487 | 34.783 | 12.42 | 0.00 | 0.00 | 3.41 |
1998 | 2054 | 7.257006 | CAGAAAAACTGCGAAATTAGATGTG | 57.743 | 36.000 | 0.00 | 0.00 | 39.86 | 3.21 |
2132 | 2188 | 1.283029 | TGATTTCAGGCTTCTGGGAGG | 59.717 | 52.381 | 0.00 | 0.00 | 38.96 | 4.30 |
2159 | 2215 | 2.419457 | TAGGTGTAGTTGTTGGGGGA | 57.581 | 50.000 | 0.00 | 0.00 | 0.00 | 4.81 |
2303 | 2360 | 4.782156 | CCCTTAGATGAGGATGAAGCCTAT | 59.218 | 45.833 | 0.00 | 0.00 | 38.73 | 2.57 |
2564 | 2624 | 7.823745 | ATGCCCTTATGTAATTAGTGAAAGG | 57.176 | 36.000 | 8.08 | 8.08 | 33.37 | 3.11 |
2566 | 2626 | 6.635030 | CCCTTATGTAATTAGTGAAAGGGC | 57.365 | 41.667 | 16.28 | 0.00 | 43.72 | 5.19 |
2567 | 2627 | 6.126409 | CCCTTATGTAATTAGTGAAAGGGCA | 58.874 | 40.000 | 16.28 | 0.00 | 43.72 | 5.36 |
2568 | 2628 | 6.777580 | CCCTTATGTAATTAGTGAAAGGGCAT | 59.222 | 38.462 | 16.28 | 4.22 | 43.72 | 4.40 |
2569 | 2629 | 7.040409 | CCCTTATGTAATTAGTGAAAGGGCATC | 60.040 | 40.741 | 16.28 | 0.00 | 43.72 | 3.91 |
2570 | 2630 | 7.502226 | CCTTATGTAATTAGTGAAAGGGCATCA | 59.498 | 37.037 | 7.48 | 0.00 | 0.00 | 3.07 |
2571 | 2631 | 8.815565 | TTATGTAATTAGTGAAAGGGCATCAA | 57.184 | 30.769 | 0.00 | 0.00 | 0.00 | 2.57 |
2572 | 2632 | 6.509418 | TGTAATTAGTGAAAGGGCATCAAC | 57.491 | 37.500 | 0.00 | 0.00 | 0.00 | 3.18 |
2573 | 2633 | 6.245408 | TGTAATTAGTGAAAGGGCATCAACT | 58.755 | 36.000 | 0.00 | 0.00 | 0.00 | 3.16 |
2574 | 2634 | 5.649782 | AATTAGTGAAAGGGCATCAACTG | 57.350 | 39.130 | 0.00 | 0.00 | 0.00 | 3.16 |
2575 | 2635 | 2.664402 | AGTGAAAGGGCATCAACTGT | 57.336 | 45.000 | 0.00 | 0.00 | 0.00 | 3.55 |
2576 | 2636 | 3.788227 | AGTGAAAGGGCATCAACTGTA | 57.212 | 42.857 | 0.00 | 0.00 | 0.00 | 2.74 |
2577 | 2637 | 3.679389 | AGTGAAAGGGCATCAACTGTAG | 58.321 | 45.455 | 0.00 | 0.00 | 0.00 | 2.74 |
2578 | 2638 | 3.327757 | AGTGAAAGGGCATCAACTGTAGA | 59.672 | 43.478 | 0.00 | 0.00 | 0.00 | 2.59 |
2579 | 2639 | 4.018960 | AGTGAAAGGGCATCAACTGTAGAT | 60.019 | 41.667 | 0.00 | 0.00 | 0.00 | 1.98 |
2580 | 2640 | 4.095483 | GTGAAAGGGCATCAACTGTAGATG | 59.905 | 45.833 | 0.00 | 0.00 | 44.38 | 2.90 |
2581 | 2641 | 4.019411 | TGAAAGGGCATCAACTGTAGATGA | 60.019 | 41.667 | 7.31 | 0.00 | 44.34 | 2.92 |
2582 | 2642 | 4.785346 | AAGGGCATCAACTGTAGATGAT | 57.215 | 40.909 | 7.31 | 0.00 | 44.34 | 2.45 |
2583 | 2643 | 4.348863 | AGGGCATCAACTGTAGATGATC | 57.651 | 45.455 | 7.31 | 0.00 | 44.34 | 2.92 |
2584 | 2644 | 3.972638 | AGGGCATCAACTGTAGATGATCT | 59.027 | 43.478 | 0.00 | 0.00 | 44.34 | 2.75 |
2585 | 2645 | 4.411540 | AGGGCATCAACTGTAGATGATCTT | 59.588 | 41.667 | 0.00 | 0.00 | 44.34 | 2.40 |
2586 | 2646 | 5.104193 | AGGGCATCAACTGTAGATGATCTTT | 60.104 | 40.000 | 0.00 | 0.00 | 44.34 | 2.52 |
2587 | 2647 | 5.008415 | GGGCATCAACTGTAGATGATCTTTG | 59.992 | 44.000 | 0.00 | 0.00 | 44.34 | 2.77 |
2588 | 2648 | 5.587844 | GGCATCAACTGTAGATGATCTTTGT | 59.412 | 40.000 | 0.00 | 0.00 | 44.34 | 2.83 |
2589 | 2649 | 6.457934 | GGCATCAACTGTAGATGATCTTTGTG | 60.458 | 42.308 | 0.00 | 2.42 | 44.34 | 3.33 |
2590 | 2650 | 6.484540 | CATCAACTGTAGATGATCTTTGTGC | 58.515 | 40.000 | 0.00 | 0.00 | 44.34 | 4.57 |
2591 | 2651 | 5.550290 | TCAACTGTAGATGATCTTTGTGCA | 58.450 | 37.500 | 0.00 | 0.00 | 0.00 | 4.57 |
2592 | 2652 | 5.997129 | TCAACTGTAGATGATCTTTGTGCAA | 59.003 | 36.000 | 0.00 | 0.00 | 0.00 | 4.08 |
2616 | 2676 | 2.284331 | TGCCCGCTTACCTCTCCA | 60.284 | 61.111 | 0.00 | 0.00 | 0.00 | 3.86 |
2617 | 2677 | 1.689233 | TGCCCGCTTACCTCTCCAT | 60.689 | 57.895 | 0.00 | 0.00 | 0.00 | 3.41 |
2618 | 2678 | 1.227674 | GCCCGCTTACCTCTCCATG | 60.228 | 63.158 | 0.00 | 0.00 | 0.00 | 3.66 |
2660 | 2747 | 7.856145 | AACATGTTTAAAATGAAAACCTGCA | 57.144 | 28.000 | 4.92 | 0.00 | 36.50 | 4.41 |
2661 | 2748 | 7.856145 | ACATGTTTAAAATGAAAACCTGCAA | 57.144 | 28.000 | 1.64 | 0.00 | 36.50 | 4.08 |
2662 | 2749 | 8.273780 | ACATGTTTAAAATGAAAACCTGCAAA | 57.726 | 26.923 | 1.64 | 0.00 | 36.50 | 3.68 |
2663 | 2750 | 8.734386 | ACATGTTTAAAATGAAAACCTGCAAAA | 58.266 | 25.926 | 1.64 | 0.00 | 36.50 | 2.44 |
2664 | 2751 | 9.008289 | CATGTTTAAAATGAAAACCTGCAAAAC | 57.992 | 29.630 | 0.00 | 0.00 | 36.26 | 2.43 |
2665 | 2752 | 8.329203 | TGTTTAAAATGAAAACCTGCAAAACT | 57.671 | 26.923 | 0.00 | 0.00 | 36.26 | 2.66 |
2666 | 2753 | 8.233190 | TGTTTAAAATGAAAACCTGCAAAACTG | 58.767 | 29.630 | 0.00 | 0.00 | 36.26 | 3.16 |
2716 | 2810 | 6.774354 | AATGCATTTCAAATCTGTCAACAC | 57.226 | 33.333 | 5.99 | 0.00 | 0.00 | 3.32 |
2734 | 2828 | 2.221169 | CACAAGTTGCTTGGCTGACTA | 58.779 | 47.619 | 12.66 | 0.00 | 44.81 | 2.59 |
2735 | 2829 | 2.031682 | CACAAGTTGCTTGGCTGACTAC | 60.032 | 50.000 | 12.66 | 0.00 | 44.81 | 2.73 |
2836 | 2948 | 9.638176 | ATCAGGCTATTTTATGAGTTCTGATTT | 57.362 | 29.630 | 0.00 | 0.00 | 34.88 | 2.17 |
2837 | 2949 | 9.466497 | TCAGGCTATTTTATGAGTTCTGATTTT | 57.534 | 29.630 | 0.00 | 0.00 | 0.00 | 1.82 |
2884 | 2997 | 2.586425 | ACTTTCATGTGGGGACAGTTG | 58.414 | 47.619 | 0.00 | 0.00 | 44.46 | 3.16 |
2910 | 3023 | 8.405531 | GCATCAACCTGTATTGTGTTATAATGT | 58.594 | 33.333 | 0.00 | 0.00 | 0.00 | 2.71 |
2935 | 3048 | 2.744202 | AGCACCATGAAGACTTAAAGCG | 59.256 | 45.455 | 0.00 | 0.00 | 0.00 | 4.68 |
2981 | 3094 | 2.607750 | TCCTGTGGCCCACCTCTC | 60.608 | 66.667 | 12.25 | 0.00 | 36.63 | 3.20 |
3171 | 3284 | 0.603975 | GTCTTCCAGGTGCCTGTGAC | 60.604 | 60.000 | 16.15 | 15.52 | 42.15 | 3.67 |
3297 | 3412 | 1.270518 | TGTCTTCTCTGCTCAACTGGC | 60.271 | 52.381 | 0.00 | 0.00 | 0.00 | 4.85 |
3405 | 3522 | 4.781775 | AAGCTAGAGACTAGAGCTGGTA | 57.218 | 45.455 | 10.56 | 0.00 | 45.74 | 3.25 |
3553 | 3677 | 3.243535 | CCAGCCCTTTCTGAGTTTTGTTC | 60.244 | 47.826 | 0.00 | 0.00 | 36.19 | 3.18 |
3557 | 3681 | 4.215613 | GCCCTTTCTGAGTTTTGTTCGTAT | 59.784 | 41.667 | 0.00 | 0.00 | 0.00 | 3.06 |
3558 | 3682 | 5.278315 | GCCCTTTCTGAGTTTTGTTCGTATT | 60.278 | 40.000 | 0.00 | 0.00 | 0.00 | 1.89 |
3559 | 3683 | 6.142817 | CCCTTTCTGAGTTTTGTTCGTATTG | 58.857 | 40.000 | 0.00 | 0.00 | 0.00 | 1.90 |
3560 | 3684 | 6.017440 | CCCTTTCTGAGTTTTGTTCGTATTGA | 60.017 | 38.462 | 0.00 | 0.00 | 0.00 | 2.57 |
3561 | 3685 | 7.414436 | CCTTTCTGAGTTTTGTTCGTATTGAA | 58.586 | 34.615 | 0.00 | 0.00 | 0.00 | 2.69 |
3562 | 3686 | 7.913297 | CCTTTCTGAGTTTTGTTCGTATTGAAA | 59.087 | 33.333 | 0.00 | 0.00 | 38.60 | 2.69 |
3563 | 3687 | 8.835467 | TTTCTGAGTTTTGTTCGTATTGAAAG | 57.165 | 30.769 | 0.00 | 0.00 | 38.60 | 2.62 |
3564 | 3688 | 7.548196 | TCTGAGTTTTGTTCGTATTGAAAGT | 57.452 | 32.000 | 0.00 | 0.00 | 38.60 | 2.66 |
3590 | 3715 | 6.960468 | TGAAACACTATTGTTGCATCGTTTA | 58.040 | 32.000 | 2.55 | 0.00 | 45.10 | 2.01 |
3630 | 3755 | 8.635328 | TGACAGTTTCAGTACTTTGTATGTCTA | 58.365 | 33.333 | 19.84 | 9.87 | 0.00 | 2.59 |
3631 | 3756 | 9.472361 | GACAGTTTCAGTACTTTGTATGTCTAA | 57.528 | 33.333 | 15.20 | 0.00 | 0.00 | 2.10 |
3675 | 3800 | 1.541588 | GCTTCTGGCATCGACCTTTTT | 59.458 | 47.619 | 0.00 | 0.00 | 41.35 | 1.94 |
3690 | 3815 | 2.811431 | CCTTTTTGACTCCACGTATGCA | 59.189 | 45.455 | 0.00 | 0.00 | 0.00 | 3.96 |
3704 | 3829 | 5.030295 | CACGTATGCAAATTCATCTTGTCC | 58.970 | 41.667 | 0.00 | 0.00 | 0.00 | 4.02 |
3709 | 3834 | 5.885230 | TGCAAATTCATCTTGTCCTGTAG | 57.115 | 39.130 | 0.00 | 0.00 | 0.00 | 2.74 |
3710 | 3835 | 4.156556 | TGCAAATTCATCTTGTCCTGTAGC | 59.843 | 41.667 | 0.00 | 0.00 | 0.00 | 3.58 |
3715 | 3840 | 8.461222 | CAAATTCATCTTGTCCTGTAGCATTTA | 58.539 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
3725 | 3850 | 7.217200 | TGTCCTGTAGCATTTATAGTTCCATC | 58.783 | 38.462 | 0.00 | 0.00 | 0.00 | 3.51 |
3735 | 3860 | 7.415541 | GCATTTATAGTTCCATCAGCTTGTTGA | 60.416 | 37.037 | 0.00 | 0.00 | 0.00 | 3.18 |
3736 | 3861 | 8.627403 | CATTTATAGTTCCATCAGCTTGTTGAT | 58.373 | 33.333 | 0.00 | 0.00 | 38.30 | 2.57 |
3738 | 3863 | 3.005554 | AGTTCCATCAGCTTGTTGATCG | 58.994 | 45.455 | 0.00 | 0.00 | 35.67 | 3.69 |
3739 | 3864 | 2.028420 | TCCATCAGCTTGTTGATCGG | 57.972 | 50.000 | 0.00 | 4.08 | 35.67 | 4.18 |
3844 | 3969 | 4.008330 | ACATGGTTGAAAGAGAGATGCAG | 58.992 | 43.478 | 0.00 | 0.00 | 0.00 | 4.41 |
3852 | 3977 | 3.996921 | AAGAGAGATGCAGAATGGTGT | 57.003 | 42.857 | 0.00 | 0.00 | 35.86 | 4.16 |
3856 | 3981 | 5.609423 | AGAGAGATGCAGAATGGTGTATTC | 58.391 | 41.667 | 0.00 | 0.00 | 44.52 | 1.75 |
3903 | 4028 | 2.031157 | AGATTAACCTGCGTGCAACAAC | 60.031 | 45.455 | 0.00 | 0.00 | 35.74 | 3.32 |
3934 | 4059 | 4.579869 | AGGTACCTGTTGTGCTGAAATAG | 58.420 | 43.478 | 15.42 | 0.00 | 0.00 | 1.73 |
4035 | 4160 | 7.267857 | TCATGGATGTTGACTAATGACTACTG | 58.732 | 38.462 | 0.00 | 0.00 | 0.00 | 2.74 |
4042 | 4167 | 6.888088 | TGTTGACTAATGACTACTGTAGCCTA | 59.112 | 38.462 | 14.55 | 2.14 | 0.00 | 3.93 |
4044 | 4169 | 6.420638 | TGACTAATGACTACTGTAGCCTACA | 58.579 | 40.000 | 14.55 | 4.20 | 37.13 | 2.74 |
4128 | 4253 | 3.003793 | GCTCAGACAAGGTTCAGAAAACC | 59.996 | 47.826 | 0.00 | 0.00 | 40.58 | 3.27 |
4260 | 4511 | 2.629617 | GCAGGGGTATTGATCCCAATTG | 59.370 | 50.000 | 0.00 | 0.00 | 46.26 | 2.32 |
4267 | 4518 | 6.782494 | GGGGTATTGATCCCAATTGTAATTCT | 59.218 | 38.462 | 4.43 | 0.00 | 46.26 | 2.40 |
4287 | 4538 | 2.483106 | CTCAGTGCTTCACAGATGTTGG | 59.517 | 50.000 | 0.00 | 0.00 | 36.74 | 3.77 |
4289 | 4540 | 3.079578 | CAGTGCTTCACAGATGTTGGAT | 58.920 | 45.455 | 0.00 | 0.00 | 36.74 | 3.41 |
4290 | 4541 | 4.020307 | TCAGTGCTTCACAGATGTTGGATA | 60.020 | 41.667 | 0.00 | 0.00 | 36.74 | 2.59 |
4291 | 4542 | 4.696877 | CAGTGCTTCACAGATGTTGGATAA | 59.303 | 41.667 | 0.00 | 0.00 | 36.74 | 1.75 |
4292 | 4543 | 5.181811 | CAGTGCTTCACAGATGTTGGATAAA | 59.818 | 40.000 | 0.00 | 0.00 | 36.74 | 1.40 |
4293 | 4544 | 5.182001 | AGTGCTTCACAGATGTTGGATAAAC | 59.818 | 40.000 | 0.00 | 0.00 | 36.74 | 2.01 |
4294 | 4545 | 5.182001 | GTGCTTCACAGATGTTGGATAAACT | 59.818 | 40.000 | 0.00 | 0.00 | 35.64 | 2.66 |
4295 | 4546 | 5.769662 | TGCTTCACAGATGTTGGATAAACTT | 59.230 | 36.000 | 0.00 | 0.00 | 39.70 | 2.66 |
4302 | 4553 | 7.117812 | CACAGATGTTGGATAAACTTTACGTCT | 59.882 | 37.037 | 0.00 | 0.00 | 39.70 | 4.18 |
4431 | 4682 | 0.036388 | ATCACACCCGTGCTTACCTG | 60.036 | 55.000 | 0.00 | 0.00 | 43.28 | 4.00 |
4497 | 4748 | 2.034812 | GGAGATGTAAGCCGAGTCGAAT | 59.965 | 50.000 | 15.64 | 1.87 | 0.00 | 3.34 |
4502 | 4753 | 1.134907 | GTAAGCCGAGTCGAATCCCAA | 60.135 | 52.381 | 15.64 | 0.00 | 0.00 | 4.12 |
4509 | 4760 | 2.804572 | CGAGTCGAATCCCAATCATGCT | 60.805 | 50.000 | 6.73 | 0.00 | 0.00 | 3.79 |
4514 | 4765 | 4.096984 | GTCGAATCCCAATCATGCTTTTCT | 59.903 | 41.667 | 0.00 | 0.00 | 0.00 | 2.52 |
4516 | 4767 | 4.142315 | CGAATCCCAATCATGCTTTTCTGT | 60.142 | 41.667 | 0.00 | 0.00 | 0.00 | 3.41 |
4529 | 4780 | 6.974932 | TGCTTTTCTGTAGAGCAATAAGAG | 57.025 | 37.500 | 0.00 | 0.00 | 42.89 | 2.85 |
4530 | 4781 | 5.352569 | TGCTTTTCTGTAGAGCAATAAGAGC | 59.647 | 40.000 | 0.00 | 0.00 | 42.89 | 4.09 |
4531 | 4782 | 5.501574 | GCTTTTCTGTAGAGCAATAAGAGCG | 60.502 | 44.000 | 0.00 | 0.00 | 36.45 | 5.03 |
4636 | 4888 | 0.108138 | CGATCAAGGCCGGAGAGTTT | 60.108 | 55.000 | 5.05 | 0.00 | 0.00 | 2.66 |
4725 | 4977 | 2.027653 | TGTCCGTGCAAGATATGTCCAA | 60.028 | 45.455 | 0.00 | 0.00 | 0.00 | 3.53 |
4726 | 4978 | 3.206150 | GTCCGTGCAAGATATGTCCAAT | 58.794 | 45.455 | 0.00 | 0.00 | 0.00 | 3.16 |
4913 | 5165 | 6.073058 | ACAGTTGTTAGTTCACTGTATGCATG | 60.073 | 38.462 | 10.16 | 0.00 | 39.53 | 4.06 |
5048 | 5306 | 2.280079 | GATGGGCTGGAAAGGGGG | 59.720 | 66.667 | 0.00 | 0.00 | 0.00 | 5.40 |
5060 | 5318 | 3.311327 | TGGAAAGGGGGTGATCTCTGATA | 60.311 | 47.826 | 0.00 | 0.00 | 0.00 | 2.15 |
5065 | 5323 | 5.316158 | AGGGGGTGATCTCTGATATTTTG | 57.684 | 43.478 | 0.00 | 0.00 | 0.00 | 2.44 |
5066 | 5324 | 3.823304 | GGGGGTGATCTCTGATATTTTGC | 59.177 | 47.826 | 0.00 | 0.00 | 0.00 | 3.68 |
5091 | 5349 | 4.536316 | GCATGAGGCTCTGGAGTG | 57.464 | 61.111 | 16.72 | 7.86 | 40.25 | 3.51 |
5118 | 5376 | 5.532557 | AGCATTTGTTCTTTGCCTTTCTAC | 58.467 | 37.500 | 0.00 | 0.00 | 37.07 | 2.59 |
5171 | 5429 | 3.076916 | GTGGAAAGGGCATGGGGC | 61.077 | 66.667 | 0.00 | 0.00 | 43.74 | 5.80 |
5251 | 5618 | 3.096852 | GGCTACTTTTGGGGCTTTATGT | 58.903 | 45.455 | 0.00 | 0.00 | 0.00 | 2.29 |
5257 | 5624 | 6.487299 | ACTTTTGGGGCTTTATGTAAAACA | 57.513 | 33.333 | 0.00 | 0.00 | 0.00 | 2.83 |
5264 | 5631 | 6.106003 | GGGGCTTTATGTAAAACAAGGAATG | 58.894 | 40.000 | 0.00 | 0.00 | 0.00 | 2.67 |
5265 | 5632 | 6.295632 | GGGGCTTTATGTAAAACAAGGAATGT | 60.296 | 38.462 | 0.00 | 0.00 | 46.82 | 2.71 |
5293 | 5665 | 4.766891 | TGTTTTCAGGATAGAAGGCCTTTG | 59.233 | 41.667 | 21.54 | 12.95 | 30.41 | 2.77 |
5337 | 5719 | 0.673985 | CGTTCGCTGGATAGGATGGA | 59.326 | 55.000 | 0.00 | 0.00 | 0.00 | 3.41 |
5341 | 5723 | 3.407424 | TCGCTGGATAGGATGGAATTG | 57.593 | 47.619 | 0.00 | 0.00 | 0.00 | 2.32 |
5350 | 5732 | 1.029947 | GGATGGAATTGGCGAACGGT | 61.030 | 55.000 | 0.00 | 0.00 | 0.00 | 4.83 |
5371 | 5753 | 1.577328 | CGGCTGGCAGGTTTAGTGTG | 61.577 | 60.000 | 17.64 | 0.00 | 0.00 | 3.82 |
5379 | 5761 | 2.751816 | GCAGGTTTAGTGTGTTTCCCCT | 60.752 | 50.000 | 0.00 | 0.00 | 0.00 | 4.79 |
5386 | 5768 | 1.493022 | AGTGTGTTTCCCCTGCTGTAA | 59.507 | 47.619 | 0.00 | 0.00 | 0.00 | 2.41 |
5387 | 5769 | 2.108250 | AGTGTGTTTCCCCTGCTGTAAT | 59.892 | 45.455 | 0.00 | 0.00 | 0.00 | 1.89 |
5388 | 5770 | 3.329520 | AGTGTGTTTCCCCTGCTGTAATA | 59.670 | 43.478 | 0.00 | 0.00 | 0.00 | 0.98 |
5423 | 5810 | 1.213182 | TGTTTCAGTGCTGGGTGGTTA | 59.787 | 47.619 | 0.00 | 0.00 | 0.00 | 2.85 |
5494 | 5887 | 1.040339 | TTTGGGCCAAAGTTCGCACT | 61.040 | 50.000 | 27.28 | 0.00 | 33.11 | 4.40 |
5546 | 5939 | 5.106515 | GGATAAGGTTCTGCTTTTCTGTCAC | 60.107 | 44.000 | 0.00 | 0.00 | 0.00 | 3.67 |
5603 | 5997 | 1.964552 | CAAGGTTGGCATGGCAAAAA | 58.035 | 45.000 | 33.36 | 12.26 | 0.00 | 1.94 |
5622 | 6016 | 3.853355 | AATTTGCCAACCATCCAAACA | 57.147 | 38.095 | 0.00 | 0.00 | 32.02 | 2.83 |
5623 | 6017 | 3.853355 | ATTTGCCAACCATCCAAACAA | 57.147 | 38.095 | 0.00 | 0.00 | 32.02 | 2.83 |
5624 | 6018 | 2.906691 | TTGCCAACCATCCAAACAAG | 57.093 | 45.000 | 0.00 | 0.00 | 0.00 | 3.16 |
5625 | 6019 | 1.047002 | TGCCAACCATCCAAACAAGG | 58.953 | 50.000 | 0.00 | 0.00 | 0.00 | 3.61 |
5688 | 6083 | 9.549078 | TTCCCATACAAAATGGAACTTTTAAAC | 57.451 | 29.630 | 5.59 | 0.00 | 41.64 | 2.01 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
32 | 33 | 4.710167 | TCGCCGGTCTGGTCGAGA | 62.710 | 66.667 | 1.90 | 0.00 | 39.98 | 4.04 |
124 | 129 | 6.538263 | AGCAGATAACAGGAAAAAGAAGTCT | 58.462 | 36.000 | 0.00 | 0.00 | 0.00 | 3.24 |
161 | 166 | 8.814038 | AGAAACTAGGCAACAATGAAATAGAT | 57.186 | 30.769 | 0.00 | 0.00 | 41.41 | 1.98 |
173 | 182 | 0.389426 | TCCGCGAGAAACTAGGCAAC | 60.389 | 55.000 | 8.23 | 0.00 | 0.00 | 4.17 |
233 | 242 | 2.511659 | GGTTTAGTTGAACCCAGACCC | 58.488 | 52.381 | 0.00 | 0.00 | 42.63 | 4.46 |
244 | 253 | 2.560981 | GTGTGGAATGGGGGTTTAGTTG | 59.439 | 50.000 | 0.00 | 0.00 | 0.00 | 3.16 |
322 | 339 | 9.342308 | TCACCATAATCTCCTCAACAAATAATC | 57.658 | 33.333 | 0.00 | 0.00 | 0.00 | 1.75 |
365 | 382 | 0.618968 | TTTGGGGGTGCCACAGTTTT | 60.619 | 50.000 | 0.00 | 0.00 | 38.60 | 2.43 |
366 | 383 | 1.002274 | TTTGGGGGTGCCACAGTTT | 59.998 | 52.632 | 0.00 | 0.00 | 38.60 | 2.66 |
391 | 408 | 0.824759 | GACAGTGGCGGACCTAGAAT | 59.175 | 55.000 | 0.00 | 0.00 | 36.63 | 2.40 |
396 | 413 | 4.008933 | GCAGACAGTGGCGGACCT | 62.009 | 66.667 | 0.00 | 0.00 | 36.63 | 3.85 |
399 | 416 | 2.031012 | CTTGCAGACAGTGGCGGA | 59.969 | 61.111 | 0.00 | 0.00 | 0.00 | 5.54 |
509 | 526 | 5.988310 | TCTCATCATTTGCTTGGTTGAAT | 57.012 | 34.783 | 0.00 | 0.00 | 0.00 | 2.57 |
510 | 527 | 5.775686 | CTTCTCATCATTTGCTTGGTTGAA | 58.224 | 37.500 | 0.00 | 0.00 | 0.00 | 2.69 |
511 | 528 | 4.321452 | GCTTCTCATCATTTGCTTGGTTGA | 60.321 | 41.667 | 0.00 | 0.00 | 0.00 | 3.18 |
512 | 529 | 3.924686 | GCTTCTCATCATTTGCTTGGTTG | 59.075 | 43.478 | 0.00 | 0.00 | 0.00 | 3.77 |
513 | 530 | 3.830755 | AGCTTCTCATCATTTGCTTGGTT | 59.169 | 39.130 | 0.00 | 0.00 | 0.00 | 3.67 |
551 | 568 | 5.357878 | TGTGCAAGAGAGACTTTCAAAACAT | 59.642 | 36.000 | 0.00 | 0.00 | 34.04 | 2.71 |
617 | 637 | 4.630069 | GTCTTGCGGAGAATTTGCTAGTTA | 59.370 | 41.667 | 0.00 | 0.00 | 35.79 | 2.24 |
618 | 638 | 3.437049 | GTCTTGCGGAGAATTTGCTAGTT | 59.563 | 43.478 | 0.00 | 0.00 | 35.79 | 2.24 |
635 | 655 | 0.740868 | ACGCCCGACATGATGTCTTG | 60.741 | 55.000 | 21.83 | 13.84 | 44.85 | 3.02 |
647 | 667 | 3.755628 | GTGTGCTCCTACGCCCGA | 61.756 | 66.667 | 0.00 | 0.00 | 0.00 | 5.14 |
648 | 668 | 3.296709 | AAGTGTGCTCCTACGCCCG | 62.297 | 63.158 | 0.00 | 0.00 | 0.00 | 6.13 |
711 | 731 | 6.447162 | CCCCTTAATCAAACAGACAACTTTC | 58.553 | 40.000 | 0.00 | 0.00 | 0.00 | 2.62 |
737 | 757 | 1.994779 | ACCGTTTATTTAGACACGCGG | 59.005 | 47.619 | 12.47 | 1.27 | 43.05 | 6.46 |
738 | 758 | 2.662637 | TCACCGTTTATTTAGACACGCG | 59.337 | 45.455 | 3.53 | 3.53 | 0.00 | 6.01 |
739 | 759 | 4.852609 | ATCACCGTTTATTTAGACACGC | 57.147 | 40.909 | 0.00 | 0.00 | 0.00 | 5.34 |
740 | 760 | 7.274033 | TGACTTATCACCGTTTATTTAGACACG | 59.726 | 37.037 | 0.00 | 0.00 | 0.00 | 4.49 |
967 | 987 | 2.238942 | TCACTACACAACCTGCAGTG | 57.761 | 50.000 | 13.81 | 7.93 | 41.40 | 3.66 |
1206 | 1226 | 4.932605 | AAACGGAGGGGGTGGGGT | 62.933 | 66.667 | 0.00 | 0.00 | 0.00 | 4.95 |
1217 | 1237 | 1.946768 | CCAGCACAGAAAAGAAACGGA | 59.053 | 47.619 | 0.00 | 0.00 | 0.00 | 4.69 |
1218 | 1238 | 1.600413 | GCCAGCACAGAAAAGAAACGG | 60.600 | 52.381 | 0.00 | 0.00 | 0.00 | 4.44 |
1219 | 1239 | 1.600413 | GGCCAGCACAGAAAAGAAACG | 60.600 | 52.381 | 0.00 | 0.00 | 0.00 | 3.60 |
1262 | 1283 | 3.367395 | GGGAGGTTTTAGCACTTTGATGC | 60.367 | 47.826 | 0.00 | 0.00 | 46.50 | 3.91 |
1271 | 1292 | 0.991920 | CCAGGAGGGAGGTTTTAGCA | 59.008 | 55.000 | 0.00 | 0.00 | 40.01 | 3.49 |
1571 | 1604 | 6.872628 | ATGAATTCAGATGCACGTATCAAT | 57.127 | 33.333 | 14.54 | 0.00 | 0.00 | 2.57 |
1615 | 1648 | 8.547481 | TCAACTCCATATAGTCTGATGGTTTA | 57.453 | 34.615 | 12.87 | 0.00 | 42.82 | 2.01 |
1808 | 1841 | 9.727627 | GAAACATATAAGCAAAATTCTGGAGAG | 57.272 | 33.333 | 0.00 | 0.00 | 0.00 | 3.20 |
1844 | 1900 | 7.435068 | TTTACCTGTGCTCTAAAGAATTCAC | 57.565 | 36.000 | 8.44 | 0.00 | 0.00 | 3.18 |
1952 | 2008 | 7.656412 | TCTGTTGTGAAGCTTGCAATAAATAA | 58.344 | 30.769 | 2.10 | 0.00 | 0.00 | 1.40 |
1953 | 2009 | 7.213216 | TCTGTTGTGAAGCTTGCAATAAATA | 57.787 | 32.000 | 2.10 | 0.00 | 0.00 | 1.40 |
1954 | 2010 | 6.088016 | TCTGTTGTGAAGCTTGCAATAAAT | 57.912 | 33.333 | 2.10 | 0.00 | 0.00 | 1.40 |
1956 | 2012 | 5.512753 | TTCTGTTGTGAAGCTTGCAATAA | 57.487 | 34.783 | 2.10 | 3.25 | 0.00 | 1.40 |
1958 | 2014 | 4.389890 | TTTCTGTTGTGAAGCTTGCAAT | 57.610 | 36.364 | 2.10 | 0.00 | 0.00 | 3.56 |
1977 | 2033 | 8.816640 | AAATCACATCTAATTTCGCAGTTTTT | 57.183 | 26.923 | 0.00 | 0.00 | 0.00 | 1.94 |
2017 | 2073 | 2.375174 | AGCAACACATGGGTCCTAAAGA | 59.625 | 45.455 | 0.00 | 0.00 | 0.00 | 2.52 |
2102 | 2158 | 3.350833 | AGCCTGAAATCATGAGGAACAC | 58.649 | 45.455 | 0.09 | 0.00 | 0.00 | 3.32 |
2132 | 2188 | 5.469084 | CCCAACAACTACACCTAAAGAGTTC | 59.531 | 44.000 | 0.00 | 0.00 | 29.73 | 3.01 |
2159 | 2215 | 9.355215 | CACAGTTTTCGTTGTTCTATACTAGAT | 57.645 | 33.333 | 0.00 | 0.00 | 34.22 | 1.98 |
2263 | 2320 | 8.997323 | CATCTAAGGGAATGAGTAAATAAGCAG | 58.003 | 37.037 | 0.00 | 0.00 | 0.00 | 4.24 |
2556 | 2616 | 2.664402 | ACAGTTGATGCCCTTTCACT | 57.336 | 45.000 | 0.00 | 0.00 | 0.00 | 3.41 |
2560 | 2620 | 4.574674 | TCATCTACAGTTGATGCCCTTT | 57.425 | 40.909 | 17.43 | 0.00 | 40.59 | 3.11 |
2563 | 2623 | 4.348863 | AGATCATCTACAGTTGATGCCC | 57.651 | 45.455 | 17.43 | 12.05 | 40.59 | 5.36 |
2564 | 2624 | 5.587844 | ACAAAGATCATCTACAGTTGATGCC | 59.412 | 40.000 | 17.43 | 12.32 | 40.59 | 4.40 |
2565 | 2625 | 6.484540 | CACAAAGATCATCTACAGTTGATGC | 58.515 | 40.000 | 17.43 | 7.16 | 40.59 | 3.91 |
2566 | 2626 | 6.093082 | TGCACAAAGATCATCTACAGTTGATG | 59.907 | 38.462 | 16.43 | 16.43 | 41.75 | 3.07 |
2567 | 2627 | 6.175471 | TGCACAAAGATCATCTACAGTTGAT | 58.825 | 36.000 | 4.16 | 3.06 | 37.23 | 2.57 |
2568 | 2628 | 5.550290 | TGCACAAAGATCATCTACAGTTGA | 58.450 | 37.500 | 4.16 | 0.00 | 0.00 | 3.18 |
2569 | 2629 | 5.868043 | TGCACAAAGATCATCTACAGTTG | 57.132 | 39.130 | 0.00 | 0.00 | 0.00 | 3.16 |
2570 | 2630 | 6.882610 | TTTGCACAAAGATCATCTACAGTT | 57.117 | 33.333 | 0.00 | 0.00 | 0.00 | 3.16 |
2645 | 2732 | 6.878389 | TCTTCAGTTTTGCAGGTTTTCATTTT | 59.122 | 30.769 | 0.00 | 0.00 | 0.00 | 1.82 |
2713 | 2807 | 0.740737 | GTCAGCCAAGCAACTTGTGT | 59.259 | 50.000 | 6.58 | 0.00 | 39.58 | 3.72 |
2716 | 2810 | 2.498167 | AGTAGTCAGCCAAGCAACTTG | 58.502 | 47.619 | 0.24 | 0.24 | 40.75 | 3.16 |
2884 | 2997 | 8.405531 | ACATTATAACACAATACAGGTTGATGC | 58.594 | 33.333 | 0.00 | 0.00 | 33.37 | 3.91 |
2910 | 3023 | 6.257849 | CGCTTTAAGTCTTCATGGTGCTATAA | 59.742 | 38.462 | 0.00 | 0.00 | 0.00 | 0.98 |
2930 | 3043 | 4.875536 | ACCAAATTCTTGCTTTTTCGCTTT | 59.124 | 33.333 | 0.00 | 0.00 | 0.00 | 3.51 |
2935 | 3048 | 6.512297 | TCCTACACCAAATTCTTGCTTTTTC | 58.488 | 36.000 | 0.00 | 0.00 | 0.00 | 2.29 |
2981 | 3094 | 4.517832 | GGTAACCACAACCAAAGGTTAGAG | 59.482 | 45.833 | 0.40 | 0.00 | 45.01 | 2.43 |
3297 | 3412 | 4.843220 | AAAGCAGAACTTTCAGACATGG | 57.157 | 40.909 | 0.00 | 0.00 | 45.78 | 3.66 |
3359 | 3475 | 6.613755 | TGAATTGTGATGCTGTCATGATAG | 57.386 | 37.500 | 14.69 | 14.69 | 39.48 | 2.08 |
3525 | 3649 | 2.919602 | ACTCAGAAAGGGCTGGGATAAA | 59.080 | 45.455 | 0.00 | 0.00 | 38.70 | 1.40 |
3532 | 3656 | 3.548818 | CGAACAAAACTCAGAAAGGGCTG | 60.549 | 47.826 | 0.00 | 0.00 | 37.24 | 4.85 |
3553 | 3677 | 9.445786 | ACAATAGTGTTTCAAACTTTCAATACG | 57.554 | 29.630 | 1.10 | 0.00 | 32.58 | 3.06 |
3557 | 3681 | 7.600375 | TGCAACAATAGTGTTTCAAACTTTCAA | 59.400 | 29.630 | 5.68 | 0.00 | 46.01 | 2.69 |
3558 | 3682 | 7.093354 | TGCAACAATAGTGTTTCAAACTTTCA | 58.907 | 30.769 | 5.68 | 0.00 | 46.01 | 2.69 |
3559 | 3683 | 7.518731 | TGCAACAATAGTGTTTCAAACTTTC | 57.481 | 32.000 | 5.68 | 0.00 | 46.01 | 2.62 |
3560 | 3684 | 7.043458 | CGATGCAACAATAGTGTTTCAAACTTT | 60.043 | 33.333 | 12.09 | 0.00 | 46.01 | 2.66 |
3561 | 3685 | 6.417635 | CGATGCAACAATAGTGTTTCAAACTT | 59.582 | 34.615 | 12.09 | 0.00 | 46.01 | 2.66 |
3562 | 3686 | 5.914635 | CGATGCAACAATAGTGTTTCAAACT | 59.085 | 36.000 | 12.09 | 0.00 | 46.01 | 2.66 |
3563 | 3687 | 5.685511 | ACGATGCAACAATAGTGTTTCAAAC | 59.314 | 36.000 | 12.09 | 8.71 | 46.01 | 2.93 |
3564 | 3688 | 5.826586 | ACGATGCAACAATAGTGTTTCAAA | 58.173 | 33.333 | 12.09 | 0.00 | 46.01 | 2.69 |
3590 | 3715 | 7.336931 | ACTGAAACTGTCAAACTTGTTACAGAT | 59.663 | 33.333 | 17.93 | 7.88 | 41.47 | 2.90 |
3630 | 3755 | 1.650528 | CCTCCAAGACCTCCTCTGTT | 58.349 | 55.000 | 0.00 | 0.00 | 0.00 | 3.16 |
3631 | 3756 | 0.252467 | CCCTCCAAGACCTCCTCTGT | 60.252 | 60.000 | 0.00 | 0.00 | 0.00 | 3.41 |
3675 | 3800 | 3.669536 | TGAATTTGCATACGTGGAGTCA | 58.330 | 40.909 | 0.00 | 0.00 | 0.00 | 3.41 |
3690 | 3815 | 7.472334 | AAATGCTACAGGACAAGATGAATTT | 57.528 | 32.000 | 0.00 | 0.00 | 0.00 | 1.82 |
3704 | 3829 | 6.933521 | AGCTGATGGAACTATAAATGCTACAG | 59.066 | 38.462 | 0.00 | 0.00 | 0.00 | 2.74 |
3709 | 3834 | 6.382869 | ACAAGCTGATGGAACTATAAATGC | 57.617 | 37.500 | 0.00 | 0.00 | 0.00 | 3.56 |
3710 | 3835 | 7.988737 | TCAACAAGCTGATGGAACTATAAATG | 58.011 | 34.615 | 0.00 | 0.00 | 0.00 | 2.32 |
3715 | 3840 | 4.813161 | CGATCAACAAGCTGATGGAACTAT | 59.187 | 41.667 | 0.00 | 0.00 | 36.15 | 2.12 |
3725 | 3850 | 3.837213 | AAACATCCGATCAACAAGCTG | 57.163 | 42.857 | 0.00 | 0.00 | 0.00 | 4.24 |
3748 | 3873 | 7.453393 | ACCTGTCATTTCAGAAGTATGAGAAA | 58.547 | 34.615 | 0.00 | 0.00 | 37.61 | 2.52 |
3751 | 3876 | 7.323420 | TGTACCTGTCATTTCAGAAGTATGAG | 58.677 | 38.462 | 0.00 | 0.00 | 37.61 | 2.90 |
3844 | 3969 | 4.267928 | GCACTACTGTCGAATACACCATTC | 59.732 | 45.833 | 0.00 | 0.00 | 39.84 | 2.67 |
3852 | 3977 | 3.617284 | TCTCCAGCACTACTGTCGAATA | 58.383 | 45.455 | 0.00 | 0.00 | 45.68 | 1.75 |
3856 | 3981 | 2.425312 | AGAATCTCCAGCACTACTGTCG | 59.575 | 50.000 | 0.00 | 0.00 | 45.68 | 4.35 |
3934 | 4059 | 3.788333 | AATGACCATAACATGCTGTGC | 57.212 | 42.857 | 0.00 | 0.00 | 0.00 | 4.57 |
3948 | 4073 | 9.816354 | AGGTGCACAAAATATAATTAAATGACC | 57.184 | 29.630 | 20.43 | 0.00 | 0.00 | 4.02 |
3955 | 4080 | 9.853555 | CAAGTGAAGGTGCACAAAATATAATTA | 57.146 | 29.630 | 20.43 | 0.00 | 41.19 | 1.40 |
4100 | 4225 | 4.774726 | TCTGAACCTTGTCTGAGCTTCTAT | 59.225 | 41.667 | 0.00 | 0.00 | 0.00 | 1.98 |
4128 | 4253 | 4.196626 | TGTGTAATAGGAGAAACCGGTG | 57.803 | 45.455 | 8.52 | 0.00 | 44.74 | 4.94 |
4202 | 4452 | 3.056607 | AGGGCACATCAATAGTTGTTTGC | 60.057 | 43.478 | 0.00 | 0.00 | 33.27 | 3.68 |
4203 | 4453 | 4.218200 | TCAGGGCACATCAATAGTTGTTTG | 59.782 | 41.667 | 0.00 | 0.00 | 0.00 | 2.93 |
4208 | 4458 | 4.012374 | CACTTCAGGGCACATCAATAGTT | 58.988 | 43.478 | 0.00 | 0.00 | 0.00 | 2.24 |
4260 | 4511 | 5.641209 | ACATCTGTGAAGCACTGAGAATTAC | 59.359 | 40.000 | 11.70 | 0.00 | 43.37 | 1.89 |
4267 | 4518 | 2.104622 | TCCAACATCTGTGAAGCACTGA | 59.895 | 45.455 | 9.10 | 9.10 | 44.01 | 3.41 |
4290 | 4541 | 9.878599 | CAGATTTTACATTCAGACGTAAAGTTT | 57.121 | 29.630 | 0.00 | 0.00 | 38.45 | 2.66 |
4291 | 4542 | 9.052759 | ACAGATTTTACATTCAGACGTAAAGTT | 57.947 | 29.630 | 0.00 | 0.00 | 38.45 | 2.66 |
4292 | 4543 | 8.603242 | ACAGATTTTACATTCAGACGTAAAGT | 57.397 | 30.769 | 0.00 | 3.22 | 38.45 | 2.66 |
4293 | 4544 | 9.318041 | CAACAGATTTTACATTCAGACGTAAAG | 57.682 | 33.333 | 0.00 | 0.00 | 38.45 | 1.85 |
4294 | 4545 | 9.047371 | TCAACAGATTTTACATTCAGACGTAAA | 57.953 | 29.630 | 0.00 | 1.67 | 36.16 | 2.01 |
4295 | 4546 | 8.596271 | TCAACAGATTTTACATTCAGACGTAA | 57.404 | 30.769 | 0.00 | 0.00 | 0.00 | 3.18 |
4302 | 4553 | 8.408043 | ACAAGGATCAACAGATTTTACATTCA | 57.592 | 30.769 | 0.00 | 0.00 | 0.00 | 2.57 |
4370 | 4621 | 0.384309 | GCCATCGACTATCCGTGACA | 59.616 | 55.000 | 0.00 | 0.00 | 0.00 | 3.58 |
4431 | 4682 | 5.052481 | TCATGGACGTTGATCAGATGATTC | 58.948 | 41.667 | 0.00 | 0.00 | 34.37 | 2.52 |
4497 | 4748 | 5.178096 | TCTACAGAAAAGCATGATTGGGA | 57.822 | 39.130 | 0.00 | 0.00 | 0.00 | 4.37 |
4502 | 4753 | 7.772292 | TCTTATTGCTCTACAGAAAAGCATGAT | 59.228 | 33.333 | 0.00 | 0.00 | 44.84 | 2.45 |
4509 | 4760 | 5.479306 | ACGCTCTTATTGCTCTACAGAAAA | 58.521 | 37.500 | 0.00 | 0.00 | 0.00 | 2.29 |
4514 | 4765 | 2.681344 | TCGACGCTCTTATTGCTCTACA | 59.319 | 45.455 | 0.00 | 0.00 | 0.00 | 2.74 |
4516 | 4767 | 2.943690 | ACTCGACGCTCTTATTGCTCTA | 59.056 | 45.455 | 0.00 | 0.00 | 0.00 | 2.43 |
4524 | 4775 | 2.486592 | TGTCATTCACTCGACGCTCTTA | 59.513 | 45.455 | 0.00 | 0.00 | 34.78 | 2.10 |
4529 | 4780 | 1.585668 | CAGATGTCATTCACTCGACGC | 59.414 | 52.381 | 0.00 | 0.00 | 34.78 | 5.19 |
4530 | 4781 | 2.868662 | ACAGATGTCATTCACTCGACG | 58.131 | 47.619 | 0.00 | 0.00 | 34.78 | 5.12 |
4531 | 4782 | 5.597813 | AAAACAGATGTCATTCACTCGAC | 57.402 | 39.130 | 0.00 | 0.00 | 0.00 | 4.20 |
4573 | 4825 | 2.483714 | CCGGAGATAGTGATGGGTGTTG | 60.484 | 54.545 | 0.00 | 0.00 | 0.00 | 3.33 |
4603 | 4855 | 0.608308 | TGATCGCCTCCCGTATCGAT | 60.608 | 55.000 | 2.16 | 2.16 | 43.33 | 3.59 |
4636 | 4888 | 3.777106 | AACTGCTTCCAGAAGATGTCA | 57.223 | 42.857 | 11.57 | 0.00 | 41.77 | 3.58 |
4725 | 4977 | 8.041323 | ACGTGGAGAGTATTTCTTATCACAAAT | 58.959 | 33.333 | 0.00 | 0.00 | 35.87 | 2.32 |
4726 | 4978 | 7.330946 | CACGTGGAGAGTATTTCTTATCACAAA | 59.669 | 37.037 | 7.95 | 0.00 | 35.87 | 2.83 |
4790 | 5042 | 3.313012 | TCAGGTTCTACCACATTGTCG | 57.687 | 47.619 | 0.00 | 0.00 | 41.95 | 4.35 |
4913 | 5165 | 4.545610 | CTTAATCCTGAGACTGATCGAGC | 58.454 | 47.826 | 0.00 | 0.00 | 0.00 | 5.03 |
4963 | 5215 | 5.056553 | AGCCAACAGAAAACCTTAACCTA | 57.943 | 39.130 | 0.00 | 0.00 | 0.00 | 3.08 |
5048 | 5306 | 3.499918 | CCCCGCAAAATATCAGAGATCAC | 59.500 | 47.826 | 0.00 | 0.00 | 0.00 | 3.06 |
5060 | 5318 | 0.034186 | TCATGCTCTCCCCGCAAAAT | 60.034 | 50.000 | 0.00 | 0.00 | 41.26 | 1.82 |
5065 | 5323 | 4.925861 | GCCTCATGCTCTCCCCGC | 62.926 | 72.222 | 0.00 | 0.00 | 36.87 | 6.13 |
5086 | 5344 | 5.693814 | CAAAGAACAAATGCTCTACACTCC | 58.306 | 41.667 | 0.00 | 0.00 | 0.00 | 3.85 |
5091 | 5349 | 4.773323 | AGGCAAAGAACAAATGCTCTAC | 57.227 | 40.909 | 0.00 | 0.00 | 39.94 | 2.59 |
5118 | 5376 | 3.507233 | ACACTCCACACATATTTTGCCAG | 59.493 | 43.478 | 0.00 | 0.00 | 0.00 | 4.85 |
5287 | 5659 | 0.463620 | TTGCAGTCCCAAACAAAGGC | 59.536 | 50.000 | 0.00 | 0.00 | 0.00 | 4.35 |
5293 | 5665 | 1.474077 | CTGGCTATTGCAGTCCCAAAC | 59.526 | 52.381 | 0.66 | 0.00 | 41.91 | 2.93 |
5328 | 5710 | 2.494059 | CGTTCGCCAATTCCATCCTAT | 58.506 | 47.619 | 0.00 | 0.00 | 0.00 | 2.57 |
5337 | 5719 | 3.732892 | CCGCACCGTTCGCCAATT | 61.733 | 61.111 | 0.00 | 0.00 | 0.00 | 2.32 |
5357 | 5739 | 1.611977 | GGGAAACACACTAAACCTGCC | 59.388 | 52.381 | 0.00 | 0.00 | 0.00 | 4.85 |
5360 | 5742 | 2.751816 | GCAGGGGAAACACACTAAACCT | 60.752 | 50.000 | 0.00 | 0.00 | 34.58 | 3.50 |
5362 | 5744 | 2.293399 | CAGCAGGGGAAACACACTAAAC | 59.707 | 50.000 | 0.00 | 0.00 | 34.58 | 2.01 |
5367 | 5749 | 1.975660 | TTACAGCAGGGGAAACACAC | 58.024 | 50.000 | 0.00 | 0.00 | 34.58 | 3.82 |
5371 | 5753 | 4.781934 | ACTCATATTACAGCAGGGGAAAC | 58.218 | 43.478 | 0.00 | 0.00 | 0.00 | 2.78 |
5388 | 5770 | 8.850156 | AGCACTGAAACAAAACTTATTACTCAT | 58.150 | 29.630 | 0.00 | 0.00 | 0.00 | 2.90 |
5408 | 5793 | 0.687354 | AGAGTAACCACCCAGCACTG | 59.313 | 55.000 | 0.00 | 0.00 | 0.00 | 3.66 |
5409 | 5794 | 1.072331 | CAAGAGTAACCACCCAGCACT | 59.928 | 52.381 | 0.00 | 0.00 | 0.00 | 4.40 |
5411 | 5796 | 1.136828 | ACAAGAGTAACCACCCAGCA | 58.863 | 50.000 | 0.00 | 0.00 | 0.00 | 4.41 |
5412 | 5797 | 2.614734 | GGTACAAGAGTAACCACCCAGC | 60.615 | 54.545 | 0.00 | 0.00 | 31.53 | 4.85 |
5413 | 5798 | 2.904434 | AGGTACAAGAGTAACCACCCAG | 59.096 | 50.000 | 0.00 | 0.00 | 38.76 | 4.45 |
5423 | 5810 | 1.958288 | ATCAGGCCAGGTACAAGAGT | 58.042 | 50.000 | 5.01 | 0.00 | 0.00 | 3.24 |
5467 | 5860 | 3.092851 | TTTGGCCCAAAGCAAAAGC | 57.907 | 47.368 | 4.38 | 0.00 | 39.59 | 3.51 |
5479 | 5872 | 0.887387 | TGGTAGTGCGAACTTTGGCC | 60.887 | 55.000 | 0.00 | 0.00 | 0.00 | 5.36 |
5494 | 5887 | 1.493022 | AGGCCAGCCGAATATTTGGTA | 59.507 | 47.619 | 20.81 | 0.00 | 41.95 | 3.25 |
5546 | 5939 | 2.110967 | CCTGCAGACATTGGCCGAG | 61.111 | 63.158 | 17.39 | 0.00 | 0.00 | 4.63 |
5603 | 5997 | 3.496515 | CCTTGTTTGGATGGTTGGCAAAT | 60.497 | 43.478 | 0.00 | 0.00 | 0.00 | 2.32 |
5622 | 6016 | 8.655901 | TGGTTTATAGCCAAAATTTTCTTCCTT | 58.344 | 29.630 | 0.00 | 0.00 | 32.29 | 3.36 |
5623 | 6017 | 8.201242 | TGGTTTATAGCCAAAATTTTCTTCCT | 57.799 | 30.769 | 0.00 | 0.00 | 32.29 | 3.36 |
5624 | 6018 | 8.840833 | TTGGTTTATAGCCAAAATTTTCTTCC | 57.159 | 30.769 | 0.00 | 0.00 | 42.39 | 3.46 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.