Multiple sequence alignment - TraesCS4D01G192800
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 | TraesCS4D01G192800 | chr4D | 100.000 | 3459 | 0 | 0 | 1 | 3459 | 335900043 | 335896585 | 0.000000e+00 | 6388.0 |
1 | TraesCS4D01G192800 | chr4D | 85.636 | 550 | 64 | 11 | 59 | 600 | 192974289 | 192974831 | 6.480000e-157 | 564.0 |
2 | TraesCS4D01G192800 | chr4D | 83.546 | 626 | 73 | 16 | 59 | 659 | 180028971 | 180029591 | 3.020000e-155 | 558.0 |
3 | TraesCS4D01G192800 | chr4D | 93.651 | 126 | 8 | 0 | 75 | 200 | 492280557 | 492280432 | 4.560000e-44 | 189.0 |
4 | TraesCS4D01G192800 | chr4D | 91.071 | 112 | 10 | 0 | 501 | 612 | 124711708 | 124711819 | 5.980000e-33 | 152.0 |
5 | TraesCS4D01G192800 | chr4A | 91.919 | 2809 | 132 | 24 | 689 | 3459 | 137164064 | 137166815 | 0.000000e+00 | 3842.0 |
6 | TraesCS4D01G192800 | chr4B | 92.448 | 2410 | 82 | 31 | 689 | 3022 | 413876317 | 413873932 | 0.000000e+00 | 3350.0 |
7 | TraesCS4D01G192800 | chr4B | 90.000 | 60 | 6 | 0 | 1 | 60 | 285844759 | 285844700 | 1.030000e-10 | 78.7 |
8 | TraesCS4D01G192800 | chr1D | 83.360 | 625 | 69 | 20 | 59 | 656 | 90299114 | 90299730 | 2.350000e-151 | 545.0 |
9 | TraesCS4D01G192800 | chr1D | 91.071 | 112 | 10 | 0 | 504 | 615 | 198418529 | 198418418 | 5.980000e-33 | 152.0 |
10 | TraesCS4D01G192800 | chr3D | 89.329 | 328 | 32 | 3 | 180 | 504 | 490460320 | 490460647 | 3.210000e-110 | 409.0 |
11 | TraesCS4D01G192800 | chr3D | 89.058 | 329 | 32 | 4 | 180 | 504 | 557958377 | 557958049 | 4.160000e-109 | 405.0 |
12 | TraesCS4D01G192800 | chr3D | 81.395 | 172 | 19 | 2 | 501 | 659 | 183958964 | 183959135 | 1.010000e-25 | 128.0 |
13 | TraesCS4D01G192800 | chr3D | 93.548 | 62 | 4 | 0 | 1 | 62 | 11797575 | 11797514 | 3.680000e-15 | 93.5 |
14 | TraesCS4D01G192800 | chr3D | 93.333 | 60 | 4 | 0 | 1 | 60 | 48441019 | 48440960 | 4.750000e-14 | 89.8 |
15 | TraesCS4D01G192800 | chr5A | 89.024 | 328 | 33 | 3 | 179 | 503 | 85352409 | 85352736 | 1.500000e-108 | 403.0 |
16 | TraesCS4D01G192800 | chr1B | 88.393 | 336 | 33 | 6 | 175 | 506 | 640026967 | 640027300 | 1.930000e-107 | 399.0 |
17 | TraesCS4D01G192800 | chr1B | 96.522 | 115 | 4 | 0 | 70 | 184 | 685229532 | 685229418 | 1.270000e-44 | 191.0 |
18 | TraesCS4D01G192800 | chr1B | 91.803 | 61 | 5 | 0 | 1 | 61 | 277427088 | 277427148 | 6.150000e-13 | 86.1 |
19 | TraesCS4D01G192800 | chr6D | 87.683 | 341 | 38 | 4 | 175 | 511 | 57182120 | 57181780 | 9.000000e-106 | 394.0 |
20 | TraesCS4D01G192800 | chr6D | 88.462 | 156 | 18 | 0 | 504 | 659 | 22968359 | 22968204 | 4.560000e-44 | 189.0 |
21 | TraesCS4D01G192800 | chr2D | 84.264 | 394 | 55 | 5 | 179 | 568 | 155618153 | 155617763 | 9.060000e-101 | 377.0 |
22 | TraesCS4D01G192800 | chr2D | 92.593 | 54 | 4 | 0 | 1 | 54 | 51726232 | 51726179 | 1.030000e-10 | 78.7 |
23 | TraesCS4D01G192800 | chr2D | 87.719 | 57 | 6 | 1 | 606 | 661 | 170608111 | 170608167 | 8.010000e-07 | 65.8 |
24 | TraesCS4D01G192800 | chr2B | 95.161 | 124 | 5 | 1 | 61 | 184 | 481660150 | 481660028 | 9.800000e-46 | 195.0 |
25 | TraesCS4D01G192800 | chr2B | 83.019 | 159 | 23 | 4 | 501 | 659 | 177780344 | 177780498 | 1.290000e-29 | 141.0 |
26 | TraesCS4D01G192800 | chr2B | 92.308 | 52 | 4 | 0 | 606 | 657 | 651862468 | 651862417 | 1.330000e-09 | 75.0 |
27 | TraesCS4D01G192800 | chr5B | 96.522 | 115 | 4 | 0 | 70 | 184 | 577366067 | 577365953 | 1.270000e-44 | 191.0 |
28 | TraesCS4D01G192800 | chr1A | 96.491 | 114 | 4 | 0 | 71 | 184 | 252325440 | 252325327 | 4.560000e-44 | 189.0 |
29 | TraesCS4D01G192800 | chrUn | 95.690 | 116 | 4 | 1 | 66 | 181 | 47459746 | 47459860 | 5.900000e-43 | 185.0 |
30 | TraesCS4D01G192800 | chr6B | 84.118 | 170 | 13 | 4 | 501 | 657 | 720771509 | 720771677 | 5.980000e-33 | 152.0 |
31 | TraesCS4D01G192800 | chr6A | 93.443 | 61 | 4 | 0 | 1 | 61 | 234195087 | 234195147 | 1.320000e-14 | 91.6 |
32 | TraesCS4D01G192800 | chr7B | 77.241 | 145 | 29 | 4 | 1468 | 1610 | 92063163 | 92063021 | 7.960000e-12 | 82.4 |
33 | TraesCS4D01G192800 | chr7B | 90.741 | 54 | 5 | 0 | 606 | 659 | 269800919 | 269800866 | 4.790000e-09 | 73.1 |
34 | TraesCS4D01G192800 | chr3B | 92.308 | 52 | 4 | 0 | 606 | 657 | 36545493 | 36545442 | 1.330000e-09 | 75.0 |
35 | TraesCS4D01G192800 | chr3B | 90.741 | 54 | 5 | 0 | 1 | 54 | 331070838 | 331070891 | 4.790000e-09 | 73.1 |
36 | TraesCS4D01G192800 | chr3B | 92.157 | 51 | 4 | 0 | 606 | 656 | 703297984 | 703297934 | 4.790000e-09 | 73.1 |
37 | TraesCS4D01G192800 | chr3B | 88.889 | 54 | 6 | 0 | 606 | 659 | 719722334 | 719722387 | 2.230000e-07 | 67.6 |
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 | TraesCS4D01G192800 | chr4D | 335896585 | 335900043 | 3458 | True | 6388 | 6388 | 100.000 | 1 | 3459 | 1 | chr4D.!!$R1 | 3458 |
1 | TraesCS4D01G192800 | chr4D | 192974289 | 192974831 | 542 | False | 564 | 564 | 85.636 | 59 | 600 | 1 | chr4D.!!$F3 | 541 |
2 | TraesCS4D01G192800 | chr4D | 180028971 | 180029591 | 620 | False | 558 | 558 | 83.546 | 59 | 659 | 1 | chr4D.!!$F2 | 600 |
3 | TraesCS4D01G192800 | chr4A | 137164064 | 137166815 | 2751 | False | 3842 | 3842 | 91.919 | 689 | 3459 | 1 | chr4A.!!$F1 | 2770 |
4 | TraesCS4D01G192800 | chr4B | 413873932 | 413876317 | 2385 | True | 3350 | 3350 | 92.448 | 689 | 3022 | 1 | chr4B.!!$R2 | 2333 |
5 | TraesCS4D01G192800 | chr1D | 90299114 | 90299730 | 616 | False | 545 | 545 | 83.360 | 59 | 656 | 1 | chr1D.!!$F1 | 597 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
668 | 699 | 0.035439 | ACCAGCCTAACCATCCAACG | 60.035 | 55.0 | 0.0 | 0.0 | 0.0 | 4.1 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2519 | 2609 | 0.094216 | CTCGTCGAAGCAATGCACAG | 59.906 | 55.0 | 8.35 | 0.0 | 0.0 | 3.66 | 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 |
---|---|---|---|---|---|---|---|---|---|
34 | 35 | 7.875316 | GGAAACCTAAAATTTTGAGAGAAGC | 57.125 | 36.000 | 13.76 | 0.00 | 0.00 | 3.86 |
35 | 36 | 6.868864 | GGAAACCTAAAATTTTGAGAGAAGCC | 59.131 | 38.462 | 13.76 | 2.48 | 0.00 | 4.35 |
36 | 37 | 5.984695 | ACCTAAAATTTTGAGAGAAGCCC | 57.015 | 39.130 | 13.76 | 0.00 | 0.00 | 5.19 |
37 | 38 | 5.645201 | ACCTAAAATTTTGAGAGAAGCCCT | 58.355 | 37.500 | 13.76 | 0.00 | 0.00 | 5.19 |
38 | 39 | 6.790319 | ACCTAAAATTTTGAGAGAAGCCCTA | 58.210 | 36.000 | 13.76 | 0.00 | 0.00 | 3.53 |
39 | 40 | 7.414266 | ACCTAAAATTTTGAGAGAAGCCCTAT | 58.586 | 34.615 | 13.76 | 0.00 | 0.00 | 2.57 |
40 | 41 | 8.557450 | ACCTAAAATTTTGAGAGAAGCCCTATA | 58.443 | 33.333 | 13.76 | 0.00 | 0.00 | 1.31 |
41 | 42 | 9.408648 | CCTAAAATTTTGAGAGAAGCCCTATAA | 57.591 | 33.333 | 13.76 | 0.00 | 0.00 | 0.98 |
44 | 45 | 7.646548 | AATTTTGAGAGAAGCCCTATAAACC | 57.353 | 36.000 | 0.00 | 0.00 | 0.00 | 3.27 |
45 | 46 | 4.402056 | TTGAGAGAAGCCCTATAAACCG | 57.598 | 45.455 | 0.00 | 0.00 | 0.00 | 4.44 |
46 | 47 | 3.638860 | TGAGAGAAGCCCTATAAACCGA | 58.361 | 45.455 | 0.00 | 0.00 | 0.00 | 4.69 |
47 | 48 | 4.028131 | TGAGAGAAGCCCTATAAACCGAA | 58.972 | 43.478 | 0.00 | 0.00 | 0.00 | 4.30 |
48 | 49 | 4.468510 | TGAGAGAAGCCCTATAAACCGAAA | 59.531 | 41.667 | 0.00 | 0.00 | 0.00 | 3.46 |
49 | 50 | 5.046159 | TGAGAGAAGCCCTATAAACCGAAAA | 60.046 | 40.000 | 0.00 | 0.00 | 0.00 | 2.29 |
50 | 51 | 5.429130 | AGAGAAGCCCTATAAACCGAAAAG | 58.571 | 41.667 | 0.00 | 0.00 | 0.00 | 2.27 |
52 | 53 | 4.226620 | AGAAGCCCTATAAACCGAAAAGGA | 59.773 | 41.667 | 0.00 | 0.00 | 45.00 | 3.36 |
53 | 54 | 4.152284 | AGCCCTATAAACCGAAAAGGAG | 57.848 | 45.455 | 0.00 | 0.00 | 45.00 | 3.69 |
54 | 55 | 3.778629 | AGCCCTATAAACCGAAAAGGAGA | 59.221 | 43.478 | 0.00 | 0.00 | 45.00 | 3.71 |
55 | 56 | 4.226620 | AGCCCTATAAACCGAAAAGGAGAA | 59.773 | 41.667 | 0.00 | 0.00 | 45.00 | 2.87 |
56 | 57 | 4.945543 | GCCCTATAAACCGAAAAGGAGAAA | 59.054 | 41.667 | 0.00 | 0.00 | 45.00 | 2.52 |
57 | 58 | 5.066117 | GCCCTATAAACCGAAAAGGAGAAAG | 59.934 | 44.000 | 0.00 | 0.00 | 45.00 | 2.62 |
64 | 65 | 6.954487 | AACCGAAAAGGAGAAAGTATTGTT | 57.046 | 33.333 | 0.00 | 0.00 | 45.00 | 2.83 |
68 | 70 | 7.041303 | ACCGAAAAGGAGAAAGTATTGTTCTTC | 60.041 | 37.037 | 0.00 | 0.00 | 45.00 | 2.87 |
69 | 71 | 7.173390 | CCGAAAAGGAGAAAGTATTGTTCTTCT | 59.827 | 37.037 | 0.00 | 0.00 | 41.84 | 2.85 |
70 | 72 | 8.224437 | CGAAAAGGAGAAAGTATTGTTCTTCTC | 58.776 | 37.037 | 2.71 | 2.71 | 39.59 | 2.87 |
75 | 77 | 8.536175 | AGGAGAAAGTATTGTTCTTCTCCTAAG | 58.464 | 37.037 | 24.06 | 0.00 | 36.38 | 2.18 |
101 | 103 | 4.899457 | TGGTCATAGTGGGAGTAACATAGG | 59.101 | 45.833 | 0.00 | 0.00 | 0.00 | 2.57 |
112 | 114 | 9.086758 | GTGGGAGTAACATAGGTAGTAACATAT | 57.913 | 37.037 | 0.00 | 0.00 | 32.96 | 1.78 |
130 | 132 | 9.743057 | GTAACATATATGCCACATAAGCAAAAA | 57.257 | 29.630 | 12.79 | 0.00 | 44.83 | 1.94 |
144 | 149 | 2.633967 | AGCAAAAATGATGAGGTGGCAA | 59.366 | 40.909 | 0.00 | 0.00 | 0.00 | 4.52 |
164 | 169 | 5.047188 | GCAAGTAGTTAATGAGGAGAGAGC | 58.953 | 45.833 | 0.00 | 0.00 | 0.00 | 4.09 |
181 | 186 | 7.014808 | AGGAGAGAGCCAAATAGAGTAACATAC | 59.985 | 40.741 | 0.00 | 0.00 | 0.00 | 2.39 |
194 | 202 | 7.098074 | AGAGTAACATACTACCTCCTTTTCG | 57.902 | 40.000 | 0.00 | 0.00 | 39.59 | 3.46 |
204 | 212 | 5.960202 | ACTACCTCCTTTTCGGTTTATAGGA | 59.040 | 40.000 | 0.00 | 0.00 | 34.76 | 2.94 |
207 | 215 | 5.250082 | ACCTCCTTTTCGGTTTATAGGACTT | 59.750 | 40.000 | 0.00 | 0.00 | 31.92 | 3.01 |
227 | 235 | 9.093458 | AGGACTTAATTCAAAAATCTCACCAAT | 57.907 | 29.630 | 0.00 | 0.00 | 0.00 | 3.16 |
237 | 245 | 9.690913 | TCAAAAATCTCACCAATCAAGATAGAT | 57.309 | 29.630 | 0.00 | 0.00 | 0.00 | 1.98 |
239 | 247 | 9.690913 | AAAAATCTCACCAATCAAGATAGATGA | 57.309 | 29.630 | 0.00 | 0.00 | 0.00 | 2.92 |
246 | 254 | 5.996513 | ACCAATCAAGATAGATGATGAGTGC | 59.003 | 40.000 | 0.00 | 0.00 | 37.58 | 4.40 |
255 | 263 | 3.987547 | AGATGATGAGTGCTGGAATACG | 58.012 | 45.455 | 0.00 | 0.00 | 0.00 | 3.06 |
263 | 271 | 4.688879 | TGAGTGCTGGAATACGTTTTGTAG | 59.311 | 41.667 | 0.00 | 0.00 | 36.25 | 2.74 |
301 | 314 | 8.351495 | TCAATTAATGTGCTTGTTTTCTTCAC | 57.649 | 30.769 | 0.00 | 0.00 | 0.00 | 3.18 |
305 | 318 | 8.539770 | TTAATGTGCTTGTTTTCTTCACAAAA | 57.460 | 26.923 | 0.00 | 0.00 | 40.46 | 2.44 |
320 | 334 | 8.309163 | TCTTCACAAAATTATGTTTCCAATGC | 57.691 | 30.769 | 0.00 | 0.00 | 0.00 | 3.56 |
380 | 394 | 8.378421 | GCATTGTTCAATTTTCTCTTAATGCTC | 58.622 | 33.333 | 0.00 | 0.00 | 42.52 | 4.26 |
381 | 395 | 9.414295 | CATTGTTCAATTTTCTCTTAATGCTCA | 57.586 | 29.630 | 0.00 | 0.00 | 0.00 | 4.26 |
416 | 430 | 9.897744 | GATTTGATACACTTTGAAATCTGAACA | 57.102 | 29.630 | 0.00 | 0.00 | 32.59 | 3.18 |
426 | 440 | 6.897706 | TTGAAATCTGAACATGTGATGGAA | 57.102 | 33.333 | 0.00 | 0.00 | 33.60 | 3.53 |
428 | 442 | 6.680810 | TGAAATCTGAACATGTGATGGAAAC | 58.319 | 36.000 | 0.00 | 0.00 | 33.60 | 2.78 |
451 | 466 | 8.707938 | AACAATCAAATTGAGCCTTATAAAGC | 57.292 | 30.769 | 1.10 | 0.00 | 42.83 | 3.51 |
454 | 469 | 4.338118 | TCAAATTGAGCCTTATAAAGCGGG | 59.662 | 41.667 | 0.44 | 0.00 | 0.00 | 6.13 |
458 | 473 | 3.275999 | TGAGCCTTATAAAGCGGGAAAC | 58.724 | 45.455 | 0.44 | 0.00 | 0.00 | 2.78 |
503 | 519 | 2.265526 | ACCGGAAAGGAGGGAGTATT | 57.734 | 50.000 | 9.46 | 0.00 | 45.00 | 1.89 |
504 | 520 | 3.409804 | ACCGGAAAGGAGGGAGTATTA | 57.590 | 47.619 | 9.46 | 0.00 | 45.00 | 0.98 |
505 | 521 | 3.937751 | ACCGGAAAGGAGGGAGTATTAT | 58.062 | 45.455 | 9.46 | 0.00 | 45.00 | 1.28 |
516 | 532 | 7.025620 | AGGAGGGAGTATTATGTTACCATCAT | 58.974 | 38.462 | 0.00 | 0.00 | 32.29 | 2.45 |
526 | 542 | 7.827819 | TTATGTTACCATCATATAGCGCTTC | 57.172 | 36.000 | 18.68 | 0.00 | 32.29 | 3.86 |
532 | 548 | 3.376234 | CCATCATATAGCGCTTCCCAATG | 59.624 | 47.826 | 18.68 | 14.38 | 0.00 | 2.82 |
545 | 561 | 4.491676 | CTTCCCAATGCAAAATGAGTCTG | 58.508 | 43.478 | 0.00 | 0.00 | 0.00 | 3.51 |
546 | 562 | 3.499338 | TCCCAATGCAAAATGAGTCTGT | 58.501 | 40.909 | 0.00 | 0.00 | 0.00 | 3.41 |
549 | 565 | 5.538053 | TCCCAATGCAAAATGAGTCTGTAAA | 59.462 | 36.000 | 0.00 | 0.00 | 0.00 | 2.01 |
551 | 567 | 6.449698 | CCAATGCAAAATGAGTCTGTAAAGT | 58.550 | 36.000 | 0.00 | 0.00 | 0.00 | 2.66 |
600 | 616 | 8.753133 | ACCATACATATGACACTATCCACTATG | 58.247 | 37.037 | 10.38 | 2.57 | 35.75 | 2.23 |
659 | 690 | 2.565834 | TCTCCACTGTAACCAGCCTAAC | 59.434 | 50.000 | 0.00 | 0.00 | 42.81 | 2.34 |
660 | 691 | 1.626825 | TCCACTGTAACCAGCCTAACC | 59.373 | 52.381 | 0.00 | 0.00 | 42.81 | 2.85 |
661 | 692 | 1.349688 | CCACTGTAACCAGCCTAACCA | 59.650 | 52.381 | 0.00 | 0.00 | 42.81 | 3.67 |
662 | 693 | 2.026262 | CCACTGTAACCAGCCTAACCAT | 60.026 | 50.000 | 0.00 | 0.00 | 42.81 | 3.55 |
663 | 694 | 3.270877 | CACTGTAACCAGCCTAACCATC | 58.729 | 50.000 | 0.00 | 0.00 | 42.81 | 3.51 |
664 | 695 | 2.238898 | ACTGTAACCAGCCTAACCATCC | 59.761 | 50.000 | 0.00 | 0.00 | 42.81 | 3.51 |
665 | 696 | 2.238646 | CTGTAACCAGCCTAACCATCCA | 59.761 | 50.000 | 0.00 | 0.00 | 0.00 | 3.41 |
666 | 697 | 2.645297 | TGTAACCAGCCTAACCATCCAA | 59.355 | 45.455 | 0.00 | 0.00 | 0.00 | 3.53 |
667 | 698 | 2.215942 | AACCAGCCTAACCATCCAAC | 57.784 | 50.000 | 0.00 | 0.00 | 0.00 | 3.77 |
668 | 699 | 0.035439 | ACCAGCCTAACCATCCAACG | 60.035 | 55.000 | 0.00 | 0.00 | 0.00 | 4.10 |
669 | 700 | 0.748005 | CCAGCCTAACCATCCAACGG | 60.748 | 60.000 | 0.00 | 0.00 | 0.00 | 4.44 |
670 | 701 | 0.748005 | CAGCCTAACCATCCAACGGG | 60.748 | 60.000 | 0.00 | 0.00 | 0.00 | 5.28 |
671 | 702 | 1.205460 | AGCCTAACCATCCAACGGGT | 61.205 | 55.000 | 0.00 | 0.00 | 39.65 | 5.28 |
673 | 704 | 1.459450 | CCTAACCATCCAACGGGTTG | 58.541 | 55.000 | 6.33 | 4.58 | 46.44 | 3.77 |
681 | 712 | 4.676586 | CAACGGGTTGGTTCGCGC | 62.677 | 66.667 | 0.00 | 0.00 | 45.24 | 6.86 |
682 | 713 | 4.922026 | AACGGGTTGGTTCGCGCT | 62.922 | 61.111 | 5.56 | 0.00 | 45.24 | 5.92 |
683 | 714 | 4.922026 | ACGGGTTGGTTCGCGCTT | 62.922 | 61.111 | 5.56 | 0.00 | 45.24 | 4.68 |
684 | 715 | 4.383602 | CGGGTTGGTTCGCGCTTG | 62.384 | 66.667 | 5.56 | 0.00 | 37.01 | 4.01 |
685 | 716 | 4.700365 | GGGTTGGTTCGCGCTTGC | 62.700 | 66.667 | 5.56 | 0.00 | 0.00 | 4.01 |
686 | 717 | 3.959975 | GGTTGGTTCGCGCTTGCA | 61.960 | 61.111 | 5.56 | 0.00 | 39.07 | 4.08 |
687 | 718 | 2.725815 | GTTGGTTCGCGCTTGCAC | 60.726 | 61.111 | 5.56 | 0.00 | 39.07 | 4.57 |
692 | 723 | 3.345808 | TTCGCGCTTGCACTGGAC | 61.346 | 61.111 | 5.56 | 0.00 | 39.07 | 4.02 |
713 | 744 | 2.484889 | GTGTTCTCTTCGTTCTTGGCT | 58.515 | 47.619 | 0.00 | 0.00 | 0.00 | 4.75 |
739 | 770 | 0.704076 | CCTCCATTTCCTCCCCACAA | 59.296 | 55.000 | 0.00 | 0.00 | 0.00 | 3.33 |
748 | 779 | 0.392998 | CCTCCCCACAACAAGGATCG | 60.393 | 60.000 | 0.00 | 0.00 | 0.00 | 3.69 |
761 | 792 | 2.124695 | GATCGGTCCTGCCCCAAC | 60.125 | 66.667 | 0.00 | 0.00 | 0.00 | 3.77 |
769 | 800 | 4.785453 | CTGCCCCAACCGCTCTCC | 62.785 | 72.222 | 0.00 | 0.00 | 0.00 | 3.71 |
776 | 807 | 1.374947 | CAACCGCTCTCCCTCCAAA | 59.625 | 57.895 | 0.00 | 0.00 | 0.00 | 3.28 |
777 | 808 | 0.955919 | CAACCGCTCTCCCTCCAAAC | 60.956 | 60.000 | 0.00 | 0.00 | 0.00 | 2.93 |
815 | 846 | 3.383620 | TTTGCTGTGCCCAATTAAGTG | 57.616 | 42.857 | 0.00 | 0.00 | 0.00 | 3.16 |
852 | 884 | 3.397618 | TGTTCCATCCTCCCTTCTCAAAA | 59.602 | 43.478 | 0.00 | 0.00 | 0.00 | 2.44 |
920 | 956 | 2.745102 | GCCGTCTCAAGAAGTATAGGC | 58.255 | 52.381 | 0.00 | 0.00 | 35.00 | 3.93 |
921 | 957 | 2.362717 | GCCGTCTCAAGAAGTATAGGCT | 59.637 | 50.000 | 0.00 | 0.00 | 39.01 | 4.58 |
1077 | 1114 | 1.363807 | CCATGCATGCTGCCATCAG | 59.636 | 57.895 | 21.69 | 0.10 | 44.23 | 2.90 |
1085 | 1122 | 4.206958 | CTGCCATCAGCTACGCAA | 57.793 | 55.556 | 0.00 | 0.00 | 44.23 | 4.85 |
1426 | 1463 | 3.627218 | GACGCGCTGCCGGTATTC | 61.627 | 66.667 | 5.73 | 0.00 | 34.32 | 1.75 |
1744 | 1781 | 0.322816 | GCCTGGTCATGGAGCAAGAA | 60.323 | 55.000 | 0.00 | 0.00 | 39.59 | 2.52 |
2035 | 2114 | 4.400961 | AGGAAGGACAGCAGCGCC | 62.401 | 66.667 | 2.29 | 0.00 | 0.00 | 6.53 |
2353 | 2435 | 0.251077 | AGTTCTTTGCTCCCCTGCTG | 60.251 | 55.000 | 0.00 | 0.00 | 0.00 | 4.41 |
2403 | 2493 | 5.278022 | GGTTTGCTCTTTTTCTGTTCGATCT | 60.278 | 40.000 | 0.00 | 0.00 | 0.00 | 2.75 |
2519 | 2609 | 6.040962 | TCACTATCGTCTATCGTGTGTTAC | 57.959 | 41.667 | 0.00 | 0.00 | 40.80 | 2.50 |
2543 | 2633 | 1.725931 | GCATTGCTTCGACGAGGTTTG | 60.726 | 52.381 | 8.86 | 5.43 | 0.00 | 2.93 |
2560 | 2672 | 1.775039 | TTGCTCTGAATATGCCGCGC | 61.775 | 55.000 | 0.00 | 0.00 | 0.00 | 6.86 |
2565 | 2677 | 1.272212 | TCTGAATATGCCGCGCTATGA | 59.728 | 47.619 | 5.56 | 0.00 | 0.00 | 2.15 |
2566 | 2678 | 2.068519 | CTGAATATGCCGCGCTATGAA | 58.931 | 47.619 | 5.56 | 0.00 | 0.00 | 2.57 |
2567 | 2679 | 2.674852 | CTGAATATGCCGCGCTATGAAT | 59.325 | 45.455 | 5.56 | 0.00 | 0.00 | 2.57 |
2568 | 2680 | 3.073678 | TGAATATGCCGCGCTATGAATT | 58.926 | 40.909 | 5.56 | 0.00 | 0.00 | 2.17 |
2569 | 2681 | 3.501828 | TGAATATGCCGCGCTATGAATTT | 59.498 | 39.130 | 5.56 | 0.00 | 0.00 | 1.82 |
2570 | 2682 | 3.747099 | ATATGCCGCGCTATGAATTTC | 57.253 | 42.857 | 5.56 | 0.00 | 0.00 | 2.17 |
2654 | 2783 | 2.024176 | TTCGTATTCAGCTCCTTGGC | 57.976 | 50.000 | 0.00 | 0.00 | 0.00 | 4.52 |
2675 | 2804 | 1.187974 | TTTCATTCATGGCTGGGCTG | 58.812 | 50.000 | 0.00 | 0.00 | 0.00 | 4.85 |
2676 | 2805 | 0.685131 | TTCATTCATGGCTGGGCTGG | 60.685 | 55.000 | 0.00 | 0.00 | 0.00 | 4.85 |
2677 | 2806 | 2.131709 | CATTCATGGCTGGGCTGGG | 61.132 | 63.158 | 0.00 | 0.00 | 0.00 | 4.45 |
2678 | 2807 | 4.764771 | TTCATGGCTGGGCTGGGC | 62.765 | 66.667 | 0.00 | 0.00 | 0.00 | 5.36 |
2724 | 2853 | 2.228822 | GAGCTGCCGGATTTTGAAAAGA | 59.771 | 45.455 | 5.05 | 0.00 | 0.00 | 2.52 |
2779 | 2915 | 0.679002 | CCACTTGTGCTGCTGGCTAT | 60.679 | 55.000 | 0.00 | 0.00 | 42.39 | 2.97 |
2824 | 2960 | 1.684386 | ATCCTCCTCGCCTGCTTCAG | 61.684 | 60.000 | 0.00 | 0.00 | 0.00 | 3.02 |
2922 | 3060 | 4.585955 | TTAATGTCTCGTCCTCCATAGC | 57.414 | 45.455 | 0.00 | 0.00 | 0.00 | 2.97 |
2934 | 3072 | 4.985409 | GTCCTCCATAGCAATAACTTCTCG | 59.015 | 45.833 | 0.00 | 0.00 | 0.00 | 4.04 |
2955 | 3093 | 5.410067 | TCGAACCCGAAACGAGTAAATATT | 58.590 | 37.500 | 0.00 | 0.00 | 42.51 | 1.28 |
3064 | 3203 | 4.051237 | AGTTTTTCAGCCGATTTTTCTGC | 58.949 | 39.130 | 0.00 | 0.00 | 0.00 | 4.26 |
3080 | 3219 | 3.648339 | TCTGCATTTTCAGCTGGTTTC | 57.352 | 42.857 | 15.13 | 0.00 | 34.19 | 2.78 |
3090 | 3229 | 6.584185 | TTTCAGCTGGTTTCTTATTAACCC | 57.416 | 37.500 | 15.13 | 0.00 | 43.55 | 4.11 |
3180 | 3320 | 9.511272 | GATCTTTTAAACAACTCCCCTAGTTTA | 57.489 | 33.333 | 0.00 | 0.00 | 46.61 | 2.01 |
3235 | 3375 | 9.912634 | ATGAATTTTATAAATATGCGGGAAGTG | 57.087 | 29.630 | 0.00 | 0.00 | 0.00 | 3.16 |
3237 | 3377 | 9.744468 | GAATTTTATAAATATGCGGGAAGTGTT | 57.256 | 29.630 | 0.00 | 0.00 | 0.00 | 3.32 |
3238 | 3378 | 9.744468 | AATTTTATAAATATGCGGGAAGTGTTC | 57.256 | 29.630 | 0.00 | 0.00 | 0.00 | 3.18 |
3241 | 3381 | 4.637483 | AAATATGCGGGAAGTGTTCATG | 57.363 | 40.909 | 0.00 | 0.00 | 0.00 | 3.07 |
3242 | 3382 | 3.558931 | ATATGCGGGAAGTGTTCATGA | 57.441 | 42.857 | 0.00 | 0.00 | 0.00 | 3.07 |
3244 | 3384 | 2.198827 | TGCGGGAAGTGTTCATGAAT | 57.801 | 45.000 | 12.12 | 0.00 | 0.00 | 2.57 |
3246 | 3386 | 2.890311 | TGCGGGAAGTGTTCATGAATTT | 59.110 | 40.909 | 12.12 | 6.94 | 0.00 | 1.82 |
3248 | 3388 | 3.674753 | GCGGGAAGTGTTCATGAATTTTG | 59.325 | 43.478 | 12.12 | 3.51 | 0.00 | 2.44 |
3249 | 3389 | 4.558496 | GCGGGAAGTGTTCATGAATTTTGA | 60.558 | 41.667 | 12.12 | 0.00 | 0.00 | 2.69 |
3250 | 3390 | 5.527951 | CGGGAAGTGTTCATGAATTTTGAA | 58.472 | 37.500 | 12.12 | 1.77 | 0.00 | 2.69 |
3251 | 3391 | 5.630680 | CGGGAAGTGTTCATGAATTTTGAAG | 59.369 | 40.000 | 12.12 | 0.00 | 33.95 | 3.02 |
3342 | 3483 | 9.832445 | AAAAGAGAAAAAGGGAAAGAAAATACC | 57.168 | 29.630 | 0.00 | 0.00 | 0.00 | 2.73 |
3361 | 3502 | 7.637709 | AATACCGAAAAGAAAAGAAACATGC | 57.362 | 32.000 | 0.00 | 0.00 | 0.00 | 4.06 |
3393 | 3534 | 2.235891 | GAATCTTCCCAAAACCGGTGT | 58.764 | 47.619 | 8.52 | 0.00 | 0.00 | 4.16 |
3399 | 3540 | 2.048601 | TCCCAAAACCGGTGTAAGAGA | 58.951 | 47.619 | 8.52 | 0.00 | 0.00 | 3.10 |
3407 | 3548 | 3.080319 | ACCGGTGTAAGAGAGACTACAC | 58.920 | 50.000 | 6.12 | 4.20 | 41.30 | 2.90 |
3431 | 3572 | 2.029290 | GCTCGTTGAGGAGTCCAACTTA | 60.029 | 50.000 | 12.86 | 0.00 | 41.11 | 2.24 |
3435 | 3576 | 3.674997 | GTTGAGGAGTCCAACTTATGCA | 58.325 | 45.455 | 12.86 | 0.00 | 40.37 | 3.96 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
2 | 3 | 9.483916 | CTCAAAATTTTAGGTTTCCCGTTTTAT | 57.516 | 29.630 | 2.44 | 0.00 | 35.12 | 1.40 |
3 | 4 | 8.693625 | TCTCAAAATTTTAGGTTTCCCGTTTTA | 58.306 | 29.630 | 2.44 | 0.00 | 35.12 | 1.52 |
4 | 5 | 7.557724 | TCTCAAAATTTTAGGTTTCCCGTTTT | 58.442 | 30.769 | 2.44 | 0.00 | 35.12 | 2.43 |
5 | 6 | 7.068962 | TCTCTCAAAATTTTAGGTTTCCCGTTT | 59.931 | 33.333 | 2.44 | 0.00 | 35.12 | 3.60 |
6 | 7 | 6.548251 | TCTCTCAAAATTTTAGGTTTCCCGTT | 59.452 | 34.615 | 2.44 | 0.00 | 35.12 | 4.44 |
7 | 8 | 6.066032 | TCTCTCAAAATTTTAGGTTTCCCGT | 58.934 | 36.000 | 2.44 | 0.00 | 35.12 | 5.28 |
8 | 9 | 6.569179 | TCTCTCAAAATTTTAGGTTTCCCG | 57.431 | 37.500 | 2.44 | 0.00 | 35.12 | 5.14 |
9 | 10 | 6.868864 | GCTTCTCTCAAAATTTTAGGTTTCCC | 59.131 | 38.462 | 2.44 | 0.00 | 0.00 | 3.97 |
10 | 11 | 6.868864 | GGCTTCTCTCAAAATTTTAGGTTTCC | 59.131 | 38.462 | 2.44 | 0.00 | 0.00 | 3.13 |
11 | 12 | 6.868864 | GGGCTTCTCTCAAAATTTTAGGTTTC | 59.131 | 38.462 | 2.44 | 0.00 | 0.00 | 2.78 |
12 | 13 | 6.554982 | AGGGCTTCTCTCAAAATTTTAGGTTT | 59.445 | 34.615 | 2.44 | 0.00 | 0.00 | 3.27 |
13 | 14 | 6.077993 | AGGGCTTCTCTCAAAATTTTAGGTT | 58.922 | 36.000 | 2.44 | 0.00 | 0.00 | 3.50 |
14 | 15 | 5.645201 | AGGGCTTCTCTCAAAATTTTAGGT | 58.355 | 37.500 | 2.44 | 0.00 | 0.00 | 3.08 |
15 | 16 | 7.888250 | ATAGGGCTTCTCTCAAAATTTTAGG | 57.112 | 36.000 | 2.44 | 0.00 | 0.00 | 2.69 |
18 | 19 | 8.531982 | GGTTTATAGGGCTTCTCTCAAAATTTT | 58.468 | 33.333 | 0.00 | 0.00 | 0.00 | 1.82 |
19 | 20 | 7.148069 | CGGTTTATAGGGCTTCTCTCAAAATTT | 60.148 | 37.037 | 0.00 | 0.00 | 0.00 | 1.82 |
20 | 21 | 6.318900 | CGGTTTATAGGGCTTCTCTCAAAATT | 59.681 | 38.462 | 0.00 | 0.00 | 0.00 | 1.82 |
21 | 22 | 5.823045 | CGGTTTATAGGGCTTCTCTCAAAAT | 59.177 | 40.000 | 0.00 | 0.00 | 0.00 | 1.82 |
22 | 23 | 5.046159 | TCGGTTTATAGGGCTTCTCTCAAAA | 60.046 | 40.000 | 0.00 | 0.00 | 0.00 | 2.44 |
23 | 24 | 4.468510 | TCGGTTTATAGGGCTTCTCTCAAA | 59.531 | 41.667 | 0.00 | 0.00 | 0.00 | 2.69 |
24 | 25 | 4.028131 | TCGGTTTATAGGGCTTCTCTCAA | 58.972 | 43.478 | 0.00 | 0.00 | 0.00 | 3.02 |
25 | 26 | 3.638860 | TCGGTTTATAGGGCTTCTCTCA | 58.361 | 45.455 | 0.00 | 0.00 | 0.00 | 3.27 |
26 | 27 | 4.667519 | TTCGGTTTATAGGGCTTCTCTC | 57.332 | 45.455 | 0.00 | 0.00 | 0.00 | 3.20 |
27 | 28 | 5.429130 | CTTTTCGGTTTATAGGGCTTCTCT | 58.571 | 41.667 | 0.00 | 0.00 | 0.00 | 3.10 |
28 | 29 | 4.575236 | CCTTTTCGGTTTATAGGGCTTCTC | 59.425 | 45.833 | 0.00 | 0.00 | 0.00 | 2.87 |
29 | 30 | 4.226620 | TCCTTTTCGGTTTATAGGGCTTCT | 59.773 | 41.667 | 0.00 | 0.00 | 0.00 | 2.85 |
30 | 31 | 4.520179 | TCCTTTTCGGTTTATAGGGCTTC | 58.480 | 43.478 | 0.00 | 0.00 | 0.00 | 3.86 |
31 | 32 | 4.226620 | TCTCCTTTTCGGTTTATAGGGCTT | 59.773 | 41.667 | 0.00 | 0.00 | 0.00 | 4.35 |
32 | 33 | 3.778629 | TCTCCTTTTCGGTTTATAGGGCT | 59.221 | 43.478 | 0.00 | 0.00 | 0.00 | 5.19 |
33 | 34 | 4.146745 | TCTCCTTTTCGGTTTATAGGGC | 57.853 | 45.455 | 0.00 | 0.00 | 0.00 | 5.19 |
34 | 35 | 6.178324 | ACTTTCTCCTTTTCGGTTTATAGGG | 58.822 | 40.000 | 0.00 | 0.00 | 0.00 | 3.53 |
35 | 36 | 8.959705 | ATACTTTCTCCTTTTCGGTTTATAGG | 57.040 | 34.615 | 0.00 | 0.00 | 0.00 | 2.57 |
37 | 38 | 9.729281 | ACAATACTTTCTCCTTTTCGGTTTATA | 57.271 | 29.630 | 0.00 | 0.00 | 0.00 | 0.98 |
38 | 39 | 8.631480 | ACAATACTTTCTCCTTTTCGGTTTAT | 57.369 | 30.769 | 0.00 | 0.00 | 0.00 | 1.40 |
39 | 40 | 8.454570 | AACAATACTTTCTCCTTTTCGGTTTA | 57.545 | 30.769 | 0.00 | 0.00 | 0.00 | 2.01 |
40 | 41 | 6.954487 | ACAATACTTTCTCCTTTTCGGTTT | 57.046 | 33.333 | 0.00 | 0.00 | 0.00 | 3.27 |
41 | 42 | 6.771267 | AGAACAATACTTTCTCCTTTTCGGTT | 59.229 | 34.615 | 0.00 | 0.00 | 0.00 | 4.44 |
42 | 43 | 6.296803 | AGAACAATACTTTCTCCTTTTCGGT | 58.703 | 36.000 | 0.00 | 0.00 | 0.00 | 4.69 |
43 | 44 | 6.803154 | AGAACAATACTTTCTCCTTTTCGG | 57.197 | 37.500 | 0.00 | 0.00 | 0.00 | 4.30 |
44 | 45 | 8.089115 | AGAAGAACAATACTTTCTCCTTTTCG | 57.911 | 34.615 | 0.00 | 0.00 | 31.87 | 3.46 |
45 | 46 | 8.508062 | GGAGAAGAACAATACTTTCTCCTTTTC | 58.492 | 37.037 | 19.65 | 0.00 | 37.91 | 2.29 |
46 | 47 | 8.221251 | AGGAGAAGAACAATACTTTCTCCTTTT | 58.779 | 33.333 | 22.49 | 7.42 | 42.26 | 2.27 |
47 | 48 | 7.750655 | AGGAGAAGAACAATACTTTCTCCTTT | 58.249 | 34.615 | 22.49 | 7.99 | 42.26 | 3.11 |
48 | 49 | 7.323052 | AGGAGAAGAACAATACTTTCTCCTT | 57.677 | 36.000 | 22.49 | 11.38 | 42.26 | 3.36 |
49 | 50 | 6.943899 | AGGAGAAGAACAATACTTTCTCCT | 57.056 | 37.500 | 22.49 | 22.49 | 41.39 | 3.69 |
50 | 51 | 7.766738 | CCTTAGGAGAAGAACAATACTTTCTCC | 59.233 | 40.741 | 19.42 | 19.42 | 39.29 | 3.71 |
51 | 52 | 7.279090 | GCCTTAGGAGAAGAACAATACTTTCTC | 59.721 | 40.741 | 0.69 | 4.87 | 31.87 | 2.87 |
52 | 53 | 7.037945 | AGCCTTAGGAGAAGAACAATACTTTCT | 60.038 | 37.037 | 0.69 | 0.00 | 34.66 | 2.52 |
53 | 54 | 7.065204 | CAGCCTTAGGAGAAGAACAATACTTTC | 59.935 | 40.741 | 0.69 | 0.00 | 0.00 | 2.62 |
54 | 55 | 6.881602 | CAGCCTTAGGAGAAGAACAATACTTT | 59.118 | 38.462 | 0.69 | 0.00 | 0.00 | 2.66 |
55 | 56 | 6.410540 | CAGCCTTAGGAGAAGAACAATACTT | 58.589 | 40.000 | 0.69 | 0.00 | 0.00 | 2.24 |
56 | 57 | 5.104735 | CCAGCCTTAGGAGAAGAACAATACT | 60.105 | 44.000 | 0.69 | 0.00 | 0.00 | 2.12 |
57 | 58 | 5.119694 | CCAGCCTTAGGAGAAGAACAATAC | 58.880 | 45.833 | 0.69 | 0.00 | 0.00 | 1.89 |
64 | 65 | 2.623418 | TGACCAGCCTTAGGAGAAGA | 57.377 | 50.000 | 0.69 | 0.00 | 0.00 | 2.87 |
68 | 70 | 2.366916 | CCACTATGACCAGCCTTAGGAG | 59.633 | 54.545 | 0.69 | 0.00 | 0.00 | 3.69 |
69 | 71 | 2.398588 | CCACTATGACCAGCCTTAGGA | 58.601 | 52.381 | 0.69 | 0.00 | 0.00 | 2.94 |
70 | 72 | 1.417890 | CCCACTATGACCAGCCTTAGG | 59.582 | 57.143 | 0.00 | 0.00 | 0.00 | 2.69 |
75 | 77 | 1.789523 | TACTCCCACTATGACCAGCC | 58.210 | 55.000 | 0.00 | 0.00 | 0.00 | 4.85 |
101 | 103 | 8.771920 | TGCTTATGTGGCATATATGTTACTAC | 57.228 | 34.615 | 14.14 | 6.50 | 34.56 | 2.73 |
112 | 114 | 7.110043 | TCATCATTTTTGCTTATGTGGCATA | 57.890 | 32.000 | 0.00 | 0.00 | 39.54 | 3.14 |
130 | 132 | 5.435686 | TTAACTACTTGCCACCTCATCAT | 57.564 | 39.130 | 0.00 | 0.00 | 0.00 | 2.45 |
144 | 149 | 4.873010 | TGGCTCTCTCCTCATTAACTACT | 58.127 | 43.478 | 0.00 | 0.00 | 0.00 | 2.57 |
164 | 169 | 8.480133 | AGGAGGTAGTATGTTACTCTATTTGG | 57.520 | 38.462 | 0.00 | 0.00 | 40.14 | 3.28 |
181 | 186 | 6.097981 | AGTCCTATAAACCGAAAAGGAGGTAG | 59.902 | 42.308 | 0.00 | 0.00 | 45.00 | 3.18 |
223 | 231 | 6.147985 | CAGCACTCATCATCTATCTTGATTGG | 59.852 | 42.308 | 0.00 | 0.00 | 31.50 | 3.16 |
224 | 232 | 6.147985 | CCAGCACTCATCATCTATCTTGATTG | 59.852 | 42.308 | 0.00 | 0.00 | 31.50 | 2.67 |
227 | 235 | 4.897670 | TCCAGCACTCATCATCTATCTTGA | 59.102 | 41.667 | 0.00 | 0.00 | 0.00 | 3.02 |
232 | 240 | 5.244851 | ACGTATTCCAGCACTCATCATCTAT | 59.755 | 40.000 | 0.00 | 0.00 | 0.00 | 1.98 |
237 | 245 | 3.610040 | AACGTATTCCAGCACTCATCA | 57.390 | 42.857 | 0.00 | 0.00 | 0.00 | 3.07 |
239 | 247 | 4.072131 | ACAAAACGTATTCCAGCACTCAT | 58.928 | 39.130 | 0.00 | 0.00 | 0.00 | 2.90 |
246 | 254 | 5.753744 | TGCAAACTACAAAACGTATTCCAG | 58.246 | 37.500 | 0.00 | 0.00 | 0.00 | 3.86 |
275 | 283 | 8.816144 | GTGAAGAAAACAAGCACATTAATTGAA | 58.184 | 29.630 | 0.00 | 0.00 | 0.00 | 2.69 |
276 | 284 | 7.978414 | TGTGAAGAAAACAAGCACATTAATTGA | 59.022 | 29.630 | 0.00 | 0.00 | 34.85 | 2.57 |
286 | 299 | 8.715191 | ACATAATTTTGTGAAGAAAACAAGCA | 57.285 | 26.923 | 0.33 | 0.00 | 38.67 | 3.91 |
287 | 300 | 9.986833 | AAACATAATTTTGTGAAGAAAACAAGC | 57.013 | 25.926 | 2.10 | 0.00 | 38.67 | 4.01 |
297 | 310 | 8.618702 | ATGCATTGGAAACATAATTTTGTGAA | 57.381 | 26.923 | 2.10 | 0.00 | 42.32 | 3.18 |
360 | 374 | 7.543172 | GCATGTGAGCATTAAGAGAAAATTGAA | 59.457 | 33.333 | 0.00 | 0.00 | 31.99 | 2.69 |
377 | 391 | 5.457799 | GTGTATCAAATCATTGCATGTGAGC | 59.542 | 40.000 | 8.11 | 0.00 | 36.45 | 4.26 |
380 | 394 | 7.542824 | TCAAAGTGTATCAAATCATTGCATGTG | 59.457 | 33.333 | 0.00 | 0.00 | 36.45 | 3.21 |
381 | 395 | 7.604549 | TCAAAGTGTATCAAATCATTGCATGT | 58.395 | 30.769 | 0.00 | 0.00 | 36.45 | 3.21 |
395 | 409 | 8.506437 | TCACATGTTCAGATTTCAAAGTGTATC | 58.494 | 33.333 | 0.00 | 0.00 | 0.00 | 2.24 |
398 | 412 | 6.698008 | TCACATGTTCAGATTTCAAAGTGT | 57.302 | 33.333 | 0.00 | 0.00 | 0.00 | 3.55 |
402 | 416 | 6.897706 | TCCATCACATGTTCAGATTTCAAA | 57.102 | 33.333 | 0.00 | 0.00 | 0.00 | 2.69 |
406 | 420 | 6.653526 | TGTTTCCATCACATGTTCAGATTT | 57.346 | 33.333 | 0.00 | 0.00 | 0.00 | 2.17 |
416 | 430 | 6.592607 | GCTCAATTTGATTGTTTCCATCACAT | 59.407 | 34.615 | 0.00 | 0.00 | 41.02 | 3.21 |
426 | 440 | 7.489113 | CGCTTTATAAGGCTCAATTTGATTGTT | 59.511 | 33.333 | 16.50 | 0.00 | 41.02 | 2.83 |
428 | 442 | 6.418819 | CCGCTTTATAAGGCTCAATTTGATTG | 59.581 | 38.462 | 16.50 | 0.00 | 41.57 | 2.67 |
429 | 443 | 6.461509 | CCCGCTTTATAAGGCTCAATTTGATT | 60.462 | 38.462 | 16.50 | 0.00 | 0.00 | 2.57 |
431 | 445 | 4.338118 | CCCGCTTTATAAGGCTCAATTTGA | 59.662 | 41.667 | 16.50 | 0.00 | 0.00 | 2.69 |
435 | 450 | 3.857157 | TCCCGCTTTATAAGGCTCAAT | 57.143 | 42.857 | 16.50 | 0.00 | 0.00 | 2.57 |
450 | 465 | 5.128992 | TCTCAAAATTTTAGGTTTCCCGC | 57.871 | 39.130 | 2.44 | 0.00 | 35.12 | 6.13 |
451 | 466 | 6.156519 | CCTTCTCAAAATTTTAGGTTTCCCG | 58.843 | 40.000 | 2.44 | 0.00 | 35.12 | 5.14 |
454 | 469 | 5.932303 | GGGCCTTCTCAAAATTTTAGGTTTC | 59.068 | 40.000 | 15.62 | 8.29 | 0.00 | 2.78 |
458 | 473 | 8.533569 | TTATAGGGCCTTCTCAAAATTTTAGG | 57.466 | 34.615 | 13.45 | 11.60 | 0.00 | 2.69 |
463 | 478 | 5.359860 | CGGTTTATAGGGCCTTCTCAAAATT | 59.640 | 40.000 | 13.45 | 0.00 | 0.00 | 1.82 |
473 | 488 | 1.493446 | CCTTTCCGGTTTATAGGGCCT | 59.507 | 52.381 | 12.58 | 12.58 | 0.00 | 5.19 |
474 | 489 | 1.491754 | TCCTTTCCGGTTTATAGGGCC | 59.508 | 52.381 | 0.00 | 0.00 | 0.00 | 5.80 |
516 | 532 | 2.340210 | TTGCATTGGGAAGCGCTATA | 57.660 | 45.000 | 12.05 | 0.00 | 0.00 | 1.31 |
526 | 542 | 3.947910 | ACAGACTCATTTTGCATTGGG | 57.052 | 42.857 | 0.00 | 0.00 | 0.00 | 4.12 |
633 | 662 | 3.197983 | GGCTGGTTACAGTGGAGAGTAAT | 59.802 | 47.826 | 0.00 | 0.00 | 46.62 | 1.89 |
646 | 677 | 3.014623 | GTTGGATGGTTAGGCTGGTTAC | 58.985 | 50.000 | 0.00 | 0.00 | 0.00 | 2.50 |
648 | 679 | 1.613255 | CGTTGGATGGTTAGGCTGGTT | 60.613 | 52.381 | 0.00 | 0.00 | 0.00 | 3.67 |
664 | 695 | 4.676586 | GCGCGAACCAACCCGTTG | 62.677 | 66.667 | 12.10 | 0.39 | 40.13 | 4.10 |
665 | 696 | 4.922026 | AGCGCGAACCAACCCGTT | 62.922 | 61.111 | 12.10 | 0.00 | 0.00 | 4.44 |
666 | 697 | 4.922026 | AAGCGCGAACCAACCCGT | 62.922 | 61.111 | 12.10 | 0.00 | 0.00 | 5.28 |
667 | 698 | 4.383602 | CAAGCGCGAACCAACCCG | 62.384 | 66.667 | 12.10 | 0.00 | 0.00 | 5.28 |
668 | 699 | 4.700365 | GCAAGCGCGAACCAACCC | 62.700 | 66.667 | 12.10 | 0.00 | 0.00 | 4.11 |
669 | 700 | 3.959975 | TGCAAGCGCGAACCAACC | 61.960 | 61.111 | 12.10 | 0.00 | 42.97 | 3.77 |
670 | 701 | 2.725815 | GTGCAAGCGCGAACCAAC | 60.726 | 61.111 | 12.10 | 0.00 | 42.97 | 3.77 |
671 | 702 | 2.899838 | AGTGCAAGCGCGAACCAA | 60.900 | 55.556 | 12.10 | 0.00 | 42.97 | 3.67 |
672 | 703 | 3.648982 | CAGTGCAAGCGCGAACCA | 61.649 | 61.111 | 12.10 | 0.00 | 42.97 | 3.67 |
673 | 704 | 4.389576 | CCAGTGCAAGCGCGAACC | 62.390 | 66.667 | 12.10 | 0.00 | 42.97 | 3.62 |
674 | 705 | 3.345808 | TCCAGTGCAAGCGCGAAC | 61.346 | 61.111 | 12.10 | 0.00 | 42.97 | 3.95 |
675 | 706 | 3.345808 | GTCCAGTGCAAGCGCGAA | 61.346 | 61.111 | 12.10 | 0.00 | 42.97 | 4.70 |
678 | 709 | 4.374702 | CACGTCCAGTGCAAGCGC | 62.375 | 66.667 | 0.00 | 0.00 | 44.72 | 5.92 |
686 | 717 | 1.030457 | ACGAAGAGAACACGTCCAGT | 58.970 | 50.000 | 0.00 | 0.00 | 35.33 | 4.00 |
687 | 718 | 2.052157 | GAACGAAGAGAACACGTCCAG | 58.948 | 52.381 | 0.00 | 0.00 | 39.31 | 3.86 |
692 | 723 | 1.192534 | GCCAAGAACGAAGAGAACACG | 59.807 | 52.381 | 0.00 | 0.00 | 0.00 | 4.49 |
761 | 792 | 1.376037 | GTGTTTGGAGGGAGAGCGG | 60.376 | 63.158 | 0.00 | 0.00 | 0.00 | 5.52 |
769 | 800 | 2.158813 | AGTAGGTGTGTGTGTTTGGAGG | 60.159 | 50.000 | 0.00 | 0.00 | 0.00 | 4.30 |
776 | 807 | 2.973694 | AAACGAGTAGGTGTGTGTGT | 57.026 | 45.000 | 0.00 | 0.00 | 0.00 | 3.72 |
777 | 808 | 3.787476 | GCAAAAACGAGTAGGTGTGTGTG | 60.787 | 47.826 | 0.00 | 0.00 | 0.00 | 3.82 |
815 | 846 | 2.037772 | TGGAACAGAGAAACAGAGGAGC | 59.962 | 50.000 | 0.00 | 0.00 | 0.00 | 4.70 |
852 | 884 | 6.959639 | TGTCCTAAGCTTTTGTTTGAATCT | 57.040 | 33.333 | 3.20 | 0.00 | 0.00 | 2.40 |
920 | 956 | 1.870901 | GTGGCTTCGCGTACCGTAG | 60.871 | 63.158 | 5.77 | 6.18 | 37.40 | 3.51 |
921 | 957 | 1.936436 | ATGTGGCTTCGCGTACCGTA | 61.936 | 55.000 | 5.77 | 0.00 | 38.35 | 4.02 |
929 | 965 | 4.539152 | CACAACATGTGGCTTCGC | 57.461 | 55.556 | 0.00 | 0.00 | 44.27 | 4.70 |
1172 | 1209 | 3.100862 | GAAAGCCTGCATCGACGGC | 62.101 | 63.158 | 5.80 | 5.80 | 44.09 | 5.68 |
1744 | 1781 | 3.862642 | GCGTCTGACTTTCACATCCTTCT | 60.863 | 47.826 | 6.21 | 0.00 | 0.00 | 2.85 |
2293 | 2372 | 3.731547 | TGGCCTCTGATCCACAGG | 58.268 | 61.111 | 3.32 | 0.00 | 45.76 | 4.00 |
2403 | 2493 | 3.982701 | CGCAAAATGCTTCAAATCTCACA | 59.017 | 39.130 | 0.43 | 0.00 | 42.25 | 3.58 |
2519 | 2609 | 0.094216 | CTCGTCGAAGCAATGCACAG | 59.906 | 55.000 | 8.35 | 0.00 | 0.00 | 3.66 |
2543 | 2633 | 0.667487 | TAGCGCGGCATATTCAGAGC | 60.667 | 55.000 | 8.83 | 0.00 | 0.00 | 4.09 |
2565 | 2677 | 9.550406 | TGCTCTCTGAATTTTGAAATTGAAATT | 57.450 | 25.926 | 6.44 | 6.98 | 38.64 | 1.82 |
2566 | 2678 | 9.550406 | TTGCTCTCTGAATTTTGAAATTGAAAT | 57.450 | 25.926 | 6.44 | 0.00 | 38.64 | 2.17 |
2567 | 2679 | 8.945481 | TTGCTCTCTGAATTTTGAAATTGAAA | 57.055 | 26.923 | 6.44 | 0.00 | 38.64 | 2.69 |
2568 | 2680 | 8.819974 | GTTTGCTCTCTGAATTTTGAAATTGAA | 58.180 | 29.630 | 6.44 | 0.00 | 38.64 | 2.69 |
2569 | 2681 | 8.199449 | AGTTTGCTCTCTGAATTTTGAAATTGA | 58.801 | 29.630 | 6.44 | 0.00 | 38.64 | 2.57 |
2570 | 2682 | 8.273557 | CAGTTTGCTCTCTGAATTTTGAAATTG | 58.726 | 33.333 | 6.44 | 0.00 | 38.64 | 2.32 |
2654 | 2783 | 1.829222 | AGCCCAGCCATGAATGAAAAG | 59.171 | 47.619 | 0.00 | 0.00 | 0.00 | 2.27 |
2676 | 2805 | 2.210711 | CCGGATCCAGGGTAGAGCC | 61.211 | 68.421 | 13.41 | 0.00 | 36.43 | 4.70 |
2677 | 2806 | 1.152525 | TCCGGATCCAGGGTAGAGC | 60.153 | 63.158 | 13.41 | 0.00 | 0.00 | 4.09 |
2678 | 2807 | 1.173444 | CGTCCGGATCCAGGGTAGAG | 61.173 | 65.000 | 7.81 | 0.00 | 0.00 | 2.43 |
2679 | 2808 | 1.152819 | CGTCCGGATCCAGGGTAGA | 60.153 | 63.158 | 7.81 | 0.00 | 0.00 | 2.59 |
2724 | 2853 | 9.097257 | CCCACGCATTATTATGAAAGAAATTTT | 57.903 | 29.630 | 0.00 | 0.00 | 33.37 | 1.82 |
2779 | 2915 | 4.901197 | TGTGATGCAGGAAAGTAGGTAA | 57.099 | 40.909 | 0.00 | 0.00 | 0.00 | 2.85 |
2824 | 2960 | 1.355971 | TTATGCGAGTGTTCTTCGGC | 58.644 | 50.000 | 0.00 | 0.00 | 0.00 | 5.54 |
2864 | 3000 | 2.958578 | AAGTCCACCAGCCAACCGTG | 62.959 | 60.000 | 0.00 | 0.00 | 0.00 | 4.94 |
2894 | 3030 | 4.344448 | GAGGACGAGACATTAAAGTCGAG | 58.656 | 47.826 | 5.26 | 6.21 | 43.24 | 4.04 |
2922 | 3060 | 4.433805 | CGTTTCGGGTTCGAGAAGTTATTG | 60.434 | 45.833 | 0.00 | 0.00 | 46.75 | 1.90 |
2934 | 3072 | 6.834876 | ACAAATATTTACTCGTTTCGGGTTC | 58.165 | 36.000 | 0.00 | 0.00 | 37.20 | 3.62 |
2955 | 3093 | 4.837093 | ATGAGACTCCCCGAAAATACAA | 57.163 | 40.909 | 0.00 | 0.00 | 0.00 | 2.41 |
2964 | 3102 | 1.227089 | CGCTGAATGAGACTCCCCG | 60.227 | 63.158 | 0.00 | 0.00 | 0.00 | 5.73 |
3023 | 3162 | 2.694760 | GGTCGTACGAAGCGAGGGT | 61.695 | 63.158 | 21.39 | 0.00 | 39.14 | 4.34 |
3029 | 3168 | 2.540931 | TGAAAAACTGGTCGTACGAAGC | 59.459 | 45.455 | 21.39 | 13.95 | 0.00 | 3.86 |
3064 | 3203 | 7.545615 | GGGTTAATAAGAAACCAGCTGAAAATG | 59.454 | 37.037 | 17.39 | 0.00 | 46.85 | 2.32 |
3210 | 3350 | 8.908903 | ACACTTCCCGCATATTTATAAAATTCA | 58.091 | 29.630 | 1.21 | 0.00 | 0.00 | 2.57 |
3211 | 3351 | 9.744468 | AACACTTCCCGCATATTTATAAAATTC | 57.256 | 29.630 | 1.21 | 0.00 | 0.00 | 2.17 |
3218 | 3358 | 6.061441 | TCATGAACACTTCCCGCATATTTAT | 58.939 | 36.000 | 0.00 | 0.00 | 0.00 | 1.40 |
3219 | 3359 | 5.432645 | TCATGAACACTTCCCGCATATTTA | 58.567 | 37.500 | 0.00 | 0.00 | 0.00 | 1.40 |
3228 | 3368 | 6.748132 | TCTTCAAAATTCATGAACACTTCCC | 58.252 | 36.000 | 11.07 | 0.00 | 33.47 | 3.97 |
3316 | 3457 | 9.832445 | GGTATTTTCTTTCCCTTTTTCTCTTTT | 57.168 | 29.630 | 0.00 | 0.00 | 0.00 | 2.27 |
3320 | 3461 | 7.210718 | TCGGTATTTTCTTTCCCTTTTTCTC | 57.789 | 36.000 | 0.00 | 0.00 | 0.00 | 2.87 |
3321 | 3462 | 7.591421 | TTCGGTATTTTCTTTCCCTTTTTCT | 57.409 | 32.000 | 0.00 | 0.00 | 0.00 | 2.52 |
3322 | 3463 | 8.651391 | TTTTCGGTATTTTCTTTCCCTTTTTC | 57.349 | 30.769 | 0.00 | 0.00 | 0.00 | 2.29 |
3323 | 3464 | 8.479689 | TCTTTTCGGTATTTTCTTTCCCTTTTT | 58.520 | 29.630 | 0.00 | 0.00 | 0.00 | 1.94 |
3329 | 3470 | 9.524106 | TTCTTTTCTTTTCGGTATTTTCTTTCC | 57.476 | 29.630 | 0.00 | 0.00 | 0.00 | 3.13 |
3341 | 3482 | 4.367450 | TGGCATGTTTCTTTTCTTTTCGG | 58.633 | 39.130 | 0.00 | 0.00 | 0.00 | 4.30 |
3342 | 3483 | 6.183360 | GCTATGGCATGTTTCTTTTCTTTTCG | 60.183 | 38.462 | 10.98 | 0.00 | 38.54 | 3.46 |
3359 | 3500 | 3.701040 | GGAAGATTCCAAAAGCTATGGCA | 59.299 | 43.478 | 12.56 | 3.71 | 46.76 | 4.92 |
3393 | 3534 | 2.641305 | GAGCCCGTGTAGTCTCTCTTA | 58.359 | 52.381 | 0.00 | 0.00 | 0.00 | 2.10 |
3407 | 3548 | 2.182030 | GACTCCTCAACGAGCCCG | 59.818 | 66.667 | 0.00 | 0.00 | 42.50 | 6.13 |
3419 | 3560 | 5.841957 | AAATGATGCATAAGTTGGACTCC | 57.158 | 39.130 | 0.00 | 0.00 | 0.00 | 3.85 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.