Multiple sequence alignment - TraesCS3A01G156100
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 | TraesCS3A01G156100 | chr3A | 100.000 | 8464 | 0 | 0 | 1 | 8464 | 150710395 | 150718858 | 0.000000e+00 | 15631 |
1 | TraesCS3A01G156100 | chr3A | 90.090 | 111 | 11 | 0 | 5489 | 5599 | 130843939 | 130843829 | 2.460000e-30 | 145 |
2 | TraesCS3A01G156100 | chr3B | 98.015 | 5038 | 62 | 14 | 2805 | 7821 | 193609008 | 193614028 | 0.000000e+00 | 8715 |
3 | TraesCS3A01G156100 | chr3B | 97.110 | 1903 | 53 | 1 | 914 | 2814 | 193605389 | 193607291 | 0.000000e+00 | 3208 |
4 | TraesCS3A01G156100 | chr3B | 95.686 | 649 | 11 | 7 | 7824 | 8464 | 193614335 | 193614974 | 0.000000e+00 | 1027 |
5 | TraesCS3A01G156100 | chr3B | 92.079 | 101 | 6 | 2 | 5493 | 5593 | 609305093 | 609304995 | 3.190000e-29 | 141 |
6 | TraesCS3A01G156100 | chr3D | 98.116 | 4141 | 48 | 14 | 3699 | 7826 | 135374738 | 135378861 | 0.000000e+00 | 7188 |
7 | TraesCS3A01G156100 | chr3D | 98.296 | 2230 | 35 | 2 | 1472 | 3700 | 135372349 | 135374576 | 0.000000e+00 | 3904 |
8 | TraesCS3A01G156100 | chr3D | 95.327 | 642 | 17 | 5 | 7824 | 8464 | 135379155 | 135379784 | 0.000000e+00 | 1007 |
9 | TraesCS3A01G156100 | chr3D | 85.284 | 897 | 104 | 16 | 3 | 884 | 135369069 | 135369952 | 0.000000e+00 | 900 |
10 | TraesCS3A01G156100 | chr3D | 95.564 | 541 | 18 | 4 | 877 | 1416 | 135371711 | 135372246 | 0.000000e+00 | 861 |
11 | TraesCS3A01G156100 | chr3D | 88.000 | 100 | 12 | 0 | 5497 | 5596 | 336537981 | 336537882 | 1.490000e-22 | 119 |
12 | TraesCS3A01G156100 | chr5B | 87.387 | 111 | 13 | 1 | 5484 | 5594 | 575975748 | 575975639 | 8.920000e-25 | 126 |
13 | TraesCS3A01G156100 | chr1A | 84.956 | 113 | 15 | 2 | 5489 | 5599 | 64714438 | 64714326 | 6.940000e-21 | 113 |
14 | TraesCS3A01G156100 | chr5D | 85.981 | 107 | 12 | 2 | 5487 | 5593 | 11305366 | 11305263 | 2.500000e-20 | 111 |
15 | TraesCS3A01G156100 | chr6A | 86.139 | 101 | 13 | 1 | 5493 | 5593 | 34179545 | 34179644 | 3.230000e-19 | 108 |
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 | TraesCS3A01G156100 | chr3A | 150710395 | 150718858 | 8463 | False | 15631.000000 | 15631 | 100.0000 | 1 | 8464 | 1 | chr3A.!!$F1 | 8463 |
1 | TraesCS3A01G156100 | chr3B | 193605389 | 193614974 | 9585 | False | 4316.666667 | 8715 | 96.9370 | 914 | 8464 | 3 | chr3B.!!$F1 | 7550 |
2 | TraesCS3A01G156100 | chr3D | 135369069 | 135379784 | 10715 | False | 2772.000000 | 7188 | 94.5174 | 3 | 8464 | 5 | chr3D.!!$F1 | 8461 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
535 | 537 | 0.179240 | GTTCGTGTTGAGCGATGCAG | 60.179 | 55.000 | 0.00 | 0.0 | 38.21 | 4.41 | F |
680 | 682 | 0.391228 | TTACGTGAGAGCAAGGCACA | 59.609 | 50.000 | 0.00 | 0.0 | 32.96 | 4.57 | F |
964 | 2744 | 0.464452 | CGCTCTAAAACCCCCGAGAT | 59.536 | 55.000 | 0.00 | 0.0 | 0.00 | 2.75 | F |
1812 | 3645 | 1.203125 | CCCCAACTGGTTGTAATGGGT | 60.203 | 52.381 | 11.73 | 0.0 | 42.50 | 4.51 | F |
2054 | 3887 | 1.210931 | CGCAAGGACACAATGCCAG | 59.789 | 57.895 | 0.00 | 0.0 | 36.75 | 4.85 | F |
2132 | 3965 | 6.280643 | AGCAGCAACATTATCGTGTTATCTA | 58.719 | 36.000 | 0.00 | 0.0 | 40.17 | 1.98 | F |
3712 | 7434 | 6.312918 | CGTTTCCTTACTAGCACATATGTTGT | 59.687 | 38.462 | 5.37 | 5.8 | 39.91 | 3.32 | F |
5047 | 8771 | 2.645838 | TCTAAGGCATCTCCAATGGC | 57.354 | 50.000 | 0.00 | 3.6 | 43.88 | 4.40 | F |
5288 | 9012 | 6.635030 | AAGACAACCTTCGCTCTTTTATTT | 57.365 | 33.333 | 0.00 | 0.0 | 0.00 | 1.40 | F |
6870 | 10596 | 2.100749 | CCGTGCTGATACATGAGGTACA | 59.899 | 50.000 | 0.00 | 0.0 | 34.07 | 2.90 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1411 | 3194 | 0.035056 | AAGCCCCACACATCTACTGC | 60.035 | 55.000 | 0.00 | 0.00 | 0.00 | 4.40 | R |
2051 | 3884 | 3.119173 | TGGTTGAAGCTTGAAAACACTGG | 60.119 | 43.478 | 2.10 | 0.00 | 0.00 | 4.00 | R |
2054 | 3887 | 4.110036 | AGTGGTTGAAGCTTGAAAACAC | 57.890 | 40.909 | 23.19 | 23.19 | 40.94 | 3.32 | R |
3657 | 7216 | 4.217118 | GCCTGTGAAAGTTCATGTTGAGAT | 59.783 | 41.667 | 0.00 | 0.00 | 39.73 | 2.75 | R |
3809 | 7531 | 6.293626 | GGATGAACCTATGAATGAAATGTCCG | 60.294 | 42.308 | 0.00 | 0.00 | 35.41 | 4.79 | R |
4024 | 7746 | 8.078060 | TCATCCAGTTCTGATAATCAACAGTA | 57.922 | 34.615 | 1.00 | 0.00 | 35.84 | 2.74 | R |
5288 | 9012 | 3.306917 | TTGCGTGAGTTCGAGGATAAA | 57.693 | 42.857 | 0.00 | 0.00 | 0.00 | 1.40 | R |
5972 | 9698 | 1.178534 | CCTTTGGGCGCTTTCTCCAA | 61.179 | 55.000 | 7.64 | 9.39 | 38.62 | 3.53 | R |
7096 | 10822 | 1.539827 | GCAACATGGTCACAACCTACC | 59.460 | 52.381 | 0.00 | 0.00 | 46.60 | 3.18 | R |
7923 | 11972 | 0.546267 | ACCACAGCCAGGAGAGATGT | 60.546 | 55.000 | 0.00 | 0.00 | 0.00 | 3.06 | 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 | 6.326323 | ACCTAAAATTCATGTTTTCTGGTGGT | 59.674 | 34.615 | 13.46 | 7.30 | 37.02 | 4.16 |
36 | 37 | 4.605640 | AATTCATGTTTTCTGGTGGTGG | 57.394 | 40.909 | 0.00 | 0.00 | 0.00 | 4.61 |
38 | 39 | 0.318120 | CATGTTTTCTGGTGGTGGGC | 59.682 | 55.000 | 0.00 | 0.00 | 0.00 | 5.36 |
51 | 52 | 2.436542 | GTGGTGGGCCCTTAAAAACTTT | 59.563 | 45.455 | 25.70 | 0.00 | 0.00 | 2.66 |
65 | 66 | 0.463654 | AACTTTCTGCCAGCACACGA | 60.464 | 50.000 | 0.00 | 0.00 | 0.00 | 4.35 |
71 | 72 | 0.461516 | CTGCCAGCACACGATGAGAT | 60.462 | 55.000 | 0.00 | 0.00 | 0.00 | 2.75 |
72 | 73 | 0.741927 | TGCCAGCACACGATGAGATG | 60.742 | 55.000 | 0.00 | 0.00 | 0.00 | 2.90 |
79 | 80 | 3.055591 | GCACACGATGAGATGATTCGAT | 58.944 | 45.455 | 0.00 | 0.00 | 36.73 | 3.59 |
88 | 89 | 6.143598 | CGATGAGATGATTCGATGCCATATAC | 59.856 | 42.308 | 0.00 | 0.00 | 34.92 | 1.47 |
91 | 92 | 5.724328 | AGATGATTCGATGCCATATACGTT | 58.276 | 37.500 | 0.00 | 0.00 | 0.00 | 3.99 |
100 | 101 | 5.291858 | CGATGCCATATACGTTAAGATGCAT | 59.708 | 40.000 | 0.00 | 0.00 | 0.00 | 3.96 |
103 | 104 | 7.270757 | TGCCATATACGTTAAGATGCATTTT | 57.729 | 32.000 | 7.70 | 7.70 | 0.00 | 1.82 |
129 | 130 | 4.436451 | CCGATGTGTGATTGTGACAATGAG | 60.436 | 45.833 | 16.52 | 0.00 | 0.00 | 2.90 |
130 | 131 | 4.152938 | CGATGTGTGATTGTGACAATGAGT | 59.847 | 41.667 | 16.52 | 0.00 | 0.00 | 3.41 |
152 | 153 | 4.272018 | GTCATAAGTTCTGGTATGCAGCTG | 59.728 | 45.833 | 10.11 | 10.11 | 0.00 | 4.24 |
154 | 155 | 3.641434 | AAGTTCTGGTATGCAGCTGAT | 57.359 | 42.857 | 20.43 | 10.74 | 31.31 | 2.90 |
155 | 156 | 2.915349 | AGTTCTGGTATGCAGCTGATG | 58.085 | 47.619 | 20.43 | 0.00 | 31.31 | 3.07 |
189 | 190 | 3.058293 | GTCAAACTTTCACGGATGCATCA | 60.058 | 43.478 | 27.25 | 4.61 | 0.00 | 3.07 |
201 | 202 | 3.306989 | CGGATGCATCATAGTACATGGGT | 60.307 | 47.826 | 27.25 | 0.00 | 0.00 | 4.51 |
206 | 207 | 3.557898 | GCATCATAGTACATGGGTGAGGG | 60.558 | 52.174 | 0.00 | 0.00 | 0.00 | 4.30 |
207 | 208 | 3.699025 | TCATAGTACATGGGTGAGGGA | 57.301 | 47.619 | 0.00 | 0.00 | 0.00 | 4.20 |
208 | 209 | 4.213531 | TCATAGTACATGGGTGAGGGAT | 57.786 | 45.455 | 0.00 | 0.00 | 0.00 | 3.85 |
209 | 210 | 5.348259 | TCATAGTACATGGGTGAGGGATA | 57.652 | 43.478 | 0.00 | 0.00 | 0.00 | 2.59 |
211 | 212 | 6.331032 | TCATAGTACATGGGTGAGGGATATT | 58.669 | 40.000 | 0.00 | 0.00 | 0.00 | 1.28 |
212 | 213 | 7.483881 | TCATAGTACATGGGTGAGGGATATTA | 58.516 | 38.462 | 0.00 | 0.00 | 0.00 | 0.98 |
213 | 214 | 7.959152 | TCATAGTACATGGGTGAGGGATATTAA | 59.041 | 37.037 | 0.00 | 0.00 | 0.00 | 1.40 |
218 | 219 | 5.612688 | ACATGGGTGAGGGATATTAATGACT | 59.387 | 40.000 | 0.00 | 0.00 | 0.00 | 3.41 |
227 | 228 | 7.500227 | TGAGGGATATTAATGACTCAAGCTTTG | 59.500 | 37.037 | 0.00 | 0.00 | 32.60 | 2.77 |
228 | 229 | 7.349598 | AGGGATATTAATGACTCAAGCTTTGT | 58.650 | 34.615 | 0.00 | 0.00 | 0.00 | 2.83 |
240 | 241 | 2.928757 | CAAGCTTTGTGAGGAGAGATCG | 59.071 | 50.000 | 0.00 | 0.00 | 0.00 | 3.69 |
245 | 246 | 1.387539 | TGTGAGGAGAGATCGAGCAG | 58.612 | 55.000 | 2.38 | 0.00 | 0.00 | 4.24 |
249 | 250 | 2.224744 | TGAGGAGAGATCGAGCAGCTAT | 60.225 | 50.000 | 2.38 | 0.00 | 0.00 | 2.97 |
254 | 255 | 5.101628 | GGAGAGATCGAGCAGCTATTATTG | 58.898 | 45.833 | 2.38 | 0.00 | 0.00 | 1.90 |
267 | 268 | 6.866770 | GCAGCTATTATTGTCTCGGTTATGTA | 59.133 | 38.462 | 0.00 | 0.00 | 0.00 | 2.29 |
269 | 270 | 8.297426 | CAGCTATTATTGTCTCGGTTATGTAGA | 58.703 | 37.037 | 0.00 | 0.00 | 0.00 | 2.59 |
277 | 278 | 5.163550 | TGTCTCGGTTATGTAGACAATCTGG | 60.164 | 44.000 | 2.09 | 0.00 | 44.89 | 3.86 |
285 | 286 | 2.418976 | TGTAGACAATCTGGACGAGTCG | 59.581 | 50.000 | 11.85 | 11.85 | 34.56 | 4.18 |
289 | 290 | 3.695060 | AGACAATCTGGACGAGTCGTAAT | 59.305 | 43.478 | 19.93 | 7.30 | 41.37 | 1.89 |
297 | 298 | 8.789825 | ATCTGGACGAGTCGTAATAAGTATAT | 57.210 | 34.615 | 19.93 | 1.51 | 41.37 | 0.86 |
299 | 300 | 7.658982 | TCTGGACGAGTCGTAATAAGTATATGT | 59.341 | 37.037 | 19.93 | 0.00 | 41.37 | 2.29 |
329 | 331 | 2.817901 | ACATTACCAACCGCTACGATC | 58.182 | 47.619 | 0.00 | 0.00 | 0.00 | 3.69 |
336 | 338 | 2.351835 | CCAACCGCTACGATCTATGGAG | 60.352 | 54.545 | 0.00 | 0.00 | 0.00 | 3.86 |
337 | 339 | 2.273538 | ACCGCTACGATCTATGGAGT | 57.726 | 50.000 | 0.00 | 0.00 | 0.00 | 3.85 |
358 | 360 | 6.408548 | GGAGTTGATAAGGGAGTTCATCATGA | 60.409 | 42.308 | 0.00 | 0.00 | 0.00 | 3.07 |
418 | 420 | 1.202510 | TGAAGCATGTTTGGCAACCAC | 60.203 | 47.619 | 0.00 | 0.00 | 30.78 | 4.16 |
421 | 423 | 2.037053 | CATGTTTGGCAACCACCGA | 58.963 | 52.632 | 0.00 | 0.00 | 30.78 | 4.69 |
424 | 426 | 0.180642 | TGTTTGGCAACCACCGACTA | 59.819 | 50.000 | 0.00 | 0.00 | 30.78 | 2.59 |
430 | 432 | 1.408266 | GGCAACCACCGACTATTGGAT | 60.408 | 52.381 | 0.00 | 0.00 | 36.28 | 3.41 |
432 | 434 | 2.679639 | GCAACCACCGACTATTGGATGA | 60.680 | 50.000 | 2.35 | 0.00 | 37.77 | 2.92 |
458 | 460 | 8.897752 | ACTCAAACTAAATATTGATGGAGCTTC | 58.102 | 33.333 | 0.00 | 0.00 | 35.20 | 3.86 |
477 | 479 | 1.697432 | TCAGAATTTGAGACGGGGTGT | 59.303 | 47.619 | 0.00 | 0.00 | 0.00 | 4.16 |
481 | 483 | 2.762535 | ATTTGAGACGGGGTGTACAG | 57.237 | 50.000 | 0.00 | 0.00 | 0.00 | 2.74 |
482 | 484 | 1.707106 | TTTGAGACGGGGTGTACAGA | 58.293 | 50.000 | 0.00 | 0.00 | 0.00 | 3.41 |
497 | 499 | 3.135712 | TGTACAGAAACATGAGTGGTGGT | 59.864 | 43.478 | 0.00 | 0.00 | 0.00 | 4.16 |
520 | 522 | 2.234908 | AGAGACCATGAGGGAAAGTTCG | 59.765 | 50.000 | 0.00 | 0.00 | 41.15 | 3.95 |
523 | 525 | 1.420138 | ACCATGAGGGAAAGTTCGTGT | 59.580 | 47.619 | 0.00 | 0.00 | 41.15 | 4.49 |
525 | 527 | 2.226437 | CCATGAGGGAAAGTTCGTGTTG | 59.774 | 50.000 | 0.00 | 0.00 | 40.01 | 3.33 |
526 | 528 | 2.992124 | TGAGGGAAAGTTCGTGTTGA | 57.008 | 45.000 | 0.00 | 0.00 | 0.00 | 3.18 |
528 | 530 | 1.531578 | GAGGGAAAGTTCGTGTTGAGC | 59.468 | 52.381 | 0.00 | 0.00 | 0.00 | 4.26 |
529 | 531 | 0.234884 | GGGAAAGTTCGTGTTGAGCG | 59.765 | 55.000 | 0.00 | 0.00 | 32.25 | 5.03 |
531 | 533 | 1.798813 | GGAAAGTTCGTGTTGAGCGAT | 59.201 | 47.619 | 0.00 | 0.00 | 38.21 | 4.58 |
532 | 534 | 2.411547 | GGAAAGTTCGTGTTGAGCGATG | 60.412 | 50.000 | 0.00 | 0.00 | 38.21 | 3.84 |
533 | 535 | 0.512952 | AAGTTCGTGTTGAGCGATGC | 59.487 | 50.000 | 0.00 | 0.00 | 38.21 | 3.91 |
534 | 536 | 0.599991 | AGTTCGTGTTGAGCGATGCA | 60.600 | 50.000 | 0.00 | 0.00 | 38.21 | 3.96 |
535 | 537 | 0.179240 | GTTCGTGTTGAGCGATGCAG | 60.179 | 55.000 | 0.00 | 0.00 | 38.21 | 4.41 |
537 | 539 | 1.737735 | CGTGTTGAGCGATGCAGGA | 60.738 | 57.895 | 0.00 | 0.00 | 0.00 | 3.86 |
550 | 552 | 5.816258 | AGCGATGCAGGAAATATATGATCAG | 59.184 | 40.000 | 0.09 | 0.00 | 0.00 | 2.90 |
567 | 569 | 2.846193 | TCAGCTACGAGCCTTTTGTTT | 58.154 | 42.857 | 0.00 | 0.00 | 43.77 | 2.83 |
579 | 581 | 6.074356 | CGAGCCTTTTGTTTTGGAACTTAATG | 60.074 | 38.462 | 0.00 | 0.00 | 36.70 | 1.90 |
582 | 584 | 5.522097 | CCTTTTGTTTTGGAACTTAATGCGT | 59.478 | 36.000 | 0.00 | 0.00 | 36.70 | 5.24 |
583 | 585 | 5.957910 | TTTGTTTTGGAACTTAATGCGTG | 57.042 | 34.783 | 0.00 | 0.00 | 36.70 | 5.34 |
596 | 598 | 2.223537 | ATGCGTGTCGAGATGCAATA | 57.776 | 45.000 | 30.12 | 10.42 | 41.22 | 1.90 |
603 | 605 | 5.034797 | CGTGTCGAGATGCAATAGTTCTTA | 58.965 | 41.667 | 0.00 | 0.00 | 0.00 | 2.10 |
606 | 608 | 7.194278 | GTGTCGAGATGCAATAGTTCTTACTA | 58.806 | 38.462 | 0.00 | 0.00 | 40.96 | 1.82 |
609 | 611 | 7.327275 | GTCGAGATGCAATAGTTCTTACTATGG | 59.673 | 40.741 | 0.00 | 0.00 | 44.85 | 2.74 |
618 | 620 | 7.863901 | ATAGTTCTTACTATGGAGAATGGCT | 57.136 | 36.000 | 0.00 | 0.00 | 44.12 | 4.75 |
624 | 626 | 6.382859 | TCTTACTATGGAGAATGGCTACACAA | 59.617 | 38.462 | 0.00 | 0.00 | 41.23 | 3.33 |
625 | 627 | 5.028549 | ACTATGGAGAATGGCTACACAAG | 57.971 | 43.478 | 0.00 | 0.00 | 41.23 | 3.16 |
662 | 664 | 7.903995 | AACAAATTGTCAAACTGTTGTCATT | 57.096 | 28.000 | 12.46 | 0.00 | 33.66 | 2.57 |
663 | 665 | 8.994429 | AACAAATTGTCAAACTGTTGTCATTA | 57.006 | 26.923 | 12.46 | 0.00 | 33.66 | 1.90 |
668 | 670 | 4.870991 | TGTCAAACTGTTGTCATTACGTGA | 59.129 | 37.500 | 0.00 | 0.00 | 36.07 | 4.35 |
674 | 676 | 3.723260 | TGTTGTCATTACGTGAGAGCAA | 58.277 | 40.909 | 0.00 | 0.00 | 38.17 | 3.91 |
680 | 682 | 0.391228 | TTACGTGAGAGCAAGGCACA | 59.609 | 50.000 | 0.00 | 0.00 | 32.96 | 4.57 |
681 | 683 | 0.391228 | TACGTGAGAGCAAGGCACAA | 59.609 | 50.000 | 0.00 | 0.00 | 32.96 | 3.33 |
697 | 699 | 2.799917 | GCACAAATCGCTCGATAGGAGT | 60.800 | 50.000 | 5.12 | 0.14 | 45.03 | 3.85 |
705 | 707 | 2.748605 | GCTCGATAGGAGTCCACATTG | 58.251 | 52.381 | 12.86 | 8.20 | 45.03 | 2.82 |
717 | 719 | 3.256631 | AGTCCACATTGTTTTGGAGATGC | 59.743 | 43.478 | 0.00 | 0.00 | 42.75 | 3.91 |
718 | 720 | 3.005684 | GTCCACATTGTTTTGGAGATGCA | 59.994 | 43.478 | 0.00 | 0.00 | 42.75 | 3.96 |
731 | 733 | 3.827008 | GAGATGCACACCTATCTCCAA | 57.173 | 47.619 | 1.95 | 0.00 | 42.10 | 3.53 |
738 | 740 | 3.821033 | GCACACCTATCTCCAACACTTTT | 59.179 | 43.478 | 0.00 | 0.00 | 0.00 | 2.27 |
741 | 743 | 6.464222 | CACACCTATCTCCAACACTTTTAGA | 58.536 | 40.000 | 0.00 | 0.00 | 0.00 | 2.10 |
742 | 744 | 6.591834 | CACACCTATCTCCAACACTTTTAGAG | 59.408 | 42.308 | 0.00 | 0.00 | 0.00 | 2.43 |
743 | 745 | 6.497259 | ACACCTATCTCCAACACTTTTAGAGA | 59.503 | 38.462 | 0.00 | 0.00 | 37.94 | 3.10 |
745 | 747 | 8.696374 | CACCTATCTCCAACACTTTTAGAGATA | 58.304 | 37.037 | 7.57 | 7.57 | 42.68 | 1.98 |
746 | 748 | 9.268282 | ACCTATCTCCAACACTTTTAGAGATAA | 57.732 | 33.333 | 8.81 | 0.00 | 42.80 | 1.75 |
749 | 751 | 7.884816 | TCTCCAACACTTTTAGAGATAAACG | 57.115 | 36.000 | 0.00 | 0.00 | 0.00 | 3.60 |
750 | 752 | 6.872020 | TCTCCAACACTTTTAGAGATAAACGG | 59.128 | 38.462 | 0.00 | 0.00 | 0.00 | 4.44 |
751 | 753 | 5.935789 | TCCAACACTTTTAGAGATAAACGGG | 59.064 | 40.000 | 0.00 | 0.00 | 0.00 | 5.28 |
774 | 788 | 4.787598 | ACGAGAAGTTAATTTTGCTGCTG | 58.212 | 39.130 | 0.00 | 0.00 | 0.00 | 4.41 |
823 | 837 | 8.410141 | AGTTTTAGAGATATCAACCTCTCTTCG | 58.590 | 37.037 | 5.32 | 0.00 | 44.51 | 3.79 |
849 | 863 | 7.729124 | AATCCCTGATTTTCTGATTGACATT | 57.271 | 32.000 | 0.00 | 0.00 | 0.00 | 2.71 |
964 | 2744 | 0.464452 | CGCTCTAAAACCCCCGAGAT | 59.536 | 55.000 | 0.00 | 0.00 | 0.00 | 2.75 |
1160 | 2943 | 3.151710 | CATCCGCCCCCTCGTGTA | 61.152 | 66.667 | 0.00 | 0.00 | 0.00 | 2.90 |
1161 | 2944 | 2.122989 | ATCCGCCCCCTCGTGTAT | 60.123 | 61.111 | 0.00 | 0.00 | 0.00 | 2.29 |
1165 | 2948 | 3.537874 | GCCCCCTCGTGTATCGCT | 61.538 | 66.667 | 0.00 | 0.00 | 39.67 | 4.93 |
1239 | 3022 | 2.844839 | GAGGGGATGGCTAGCGGT | 60.845 | 66.667 | 9.00 | 0.00 | 0.00 | 5.68 |
1377 | 3160 | 2.448749 | AACCTCCTACGTGCAGGTT | 58.551 | 52.632 | 18.35 | 17.46 | 44.29 | 3.50 |
1411 | 3194 | 5.055642 | TGCCTTATATACTTCGACGGATG | 57.944 | 43.478 | 0.00 | 0.00 | 0.00 | 3.51 |
1447 | 3230 | 1.398390 | GCTTGTTTCGCCTCGATTCAT | 59.602 | 47.619 | 0.00 | 0.00 | 35.23 | 2.57 |
1451 | 3234 | 2.094234 | TGTTTCGCCTCGATTCATCTCA | 60.094 | 45.455 | 0.00 | 0.00 | 35.23 | 3.27 |
1464 | 3247 | 5.910166 | CGATTCATCTCAGTTTAGGTAGACG | 59.090 | 44.000 | 0.00 | 0.00 | 0.00 | 4.18 |
1506 | 3336 | 1.291132 | GCATTCTGCCTAAGACGTCC | 58.709 | 55.000 | 13.01 | 0.00 | 37.42 | 4.79 |
1664 | 3494 | 6.593382 | AGTGCTCAACTGAGATCACTAATTTC | 59.407 | 38.462 | 14.61 | 0.00 | 44.74 | 2.17 |
1667 | 3497 | 6.037786 | TCAACTGAGATCACTAATTTCGGT | 57.962 | 37.500 | 0.00 | 0.00 | 39.22 | 4.69 |
1812 | 3645 | 1.203125 | CCCCAACTGGTTGTAATGGGT | 60.203 | 52.381 | 11.73 | 0.00 | 42.50 | 4.51 |
2054 | 3887 | 1.210931 | CGCAAGGACACAATGCCAG | 59.789 | 57.895 | 0.00 | 0.00 | 36.75 | 4.85 |
2132 | 3965 | 6.280643 | AGCAGCAACATTATCGTGTTATCTA | 58.719 | 36.000 | 0.00 | 0.00 | 40.17 | 1.98 |
2467 | 4300 | 6.851222 | ATCCTTCATCGCTAAAATGTAGTG | 57.149 | 37.500 | 0.00 | 0.00 | 0.00 | 2.74 |
2912 | 6471 | 9.751542 | GTAACATGCTATATTCTGTACTTCACT | 57.248 | 33.333 | 0.00 | 0.00 | 0.00 | 3.41 |
3712 | 7434 | 6.312918 | CGTTTCCTTACTAGCACATATGTTGT | 59.687 | 38.462 | 5.37 | 5.80 | 39.91 | 3.32 |
4024 | 7746 | 4.647564 | AGGTCCATCTTCTGTGACAAAT | 57.352 | 40.909 | 0.00 | 0.00 | 30.81 | 2.32 |
4121 | 7843 | 8.628882 | AGTTTCAGTTTCATTTACCTTTTTCG | 57.371 | 30.769 | 0.00 | 0.00 | 0.00 | 3.46 |
4202 | 7924 | 9.010029 | GTTTGAACTTTATTGATCCCACTAGAA | 57.990 | 33.333 | 0.00 | 0.00 | 0.00 | 2.10 |
4871 | 8595 | 5.476945 | ACCAGAGGTTGAATGTTGAAATACC | 59.523 | 40.000 | 0.00 | 0.00 | 27.29 | 2.73 |
4890 | 8614 | 9.232473 | GAAATACCTCCTTCTTGTTAACAGAAT | 57.768 | 33.333 | 8.56 | 3.17 | 0.00 | 2.40 |
4893 | 8617 | 5.310857 | ACCTCCTTCTTGTTAACAGAATCCT | 59.689 | 40.000 | 8.56 | 0.00 | 0.00 | 3.24 |
5047 | 8771 | 2.645838 | TCTAAGGCATCTCCAATGGC | 57.354 | 50.000 | 0.00 | 3.60 | 43.88 | 4.40 |
5288 | 9012 | 6.635030 | AAGACAACCTTCGCTCTTTTATTT | 57.365 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
5304 | 9029 | 9.974750 | CTCTTTTATTTTTATCCTCGAACTCAC | 57.025 | 33.333 | 0.00 | 0.00 | 0.00 | 3.51 |
5926 | 9652 | 8.992349 | TCTTCCTGATATTTTAGATGAACAGGA | 58.008 | 33.333 | 0.00 | 0.00 | 46.78 | 3.86 |
5972 | 9698 | 6.640518 | TGACAGTAGTTTGAGAGAAAGTGTT | 58.359 | 36.000 | 0.00 | 0.00 | 0.00 | 3.32 |
6870 | 10596 | 2.100749 | CCGTGCTGATACATGAGGTACA | 59.899 | 50.000 | 0.00 | 0.00 | 34.07 | 2.90 |
6967 | 10693 | 3.169512 | TGACCTCTGTCCATAGTGTCA | 57.830 | 47.619 | 0.00 | 0.00 | 41.01 | 3.58 |
7094 | 10820 | 4.513198 | TTTTAGCATGCTAAAAGGCGTT | 57.487 | 36.364 | 41.60 | 15.82 | 46.92 | 4.84 |
7095 | 10821 | 5.630661 | TTTTAGCATGCTAAAAGGCGTTA | 57.369 | 34.783 | 41.60 | 27.98 | 46.92 | 3.18 |
7096 | 10822 | 4.875544 | TTAGCATGCTAAAAGGCGTTAG | 57.124 | 40.909 | 32.70 | 6.63 | 35.80 | 2.34 |
7097 | 10823 | 2.017049 | AGCATGCTAAAAGGCGTTAGG | 58.983 | 47.619 | 21.21 | 0.00 | 32.62 | 2.69 |
7310 | 11036 | 0.613853 | TCCCGGTCTTTGACGAGGAT | 60.614 | 55.000 | 0.00 | 0.00 | 34.56 | 3.24 |
7376 | 11102 | 2.822255 | GCCGATTTGCCCGTGCTA | 60.822 | 61.111 | 0.00 | 0.00 | 38.71 | 3.49 |
7480 | 11206 | 4.262808 | GGTGTAGCGAGGGAGATAGTAGTA | 60.263 | 50.000 | 0.00 | 0.00 | 0.00 | 1.82 |
7481 | 11207 | 4.931002 | GTGTAGCGAGGGAGATAGTAGTAG | 59.069 | 50.000 | 0.00 | 0.00 | 0.00 | 2.57 |
7482 | 11208 | 4.592351 | TGTAGCGAGGGAGATAGTAGTAGT | 59.408 | 45.833 | 0.00 | 0.00 | 0.00 | 2.73 |
7623 | 11350 | 8.091449 | GGGGTCAGATAGAATAGAATACAGTTG | 58.909 | 40.741 | 0.00 | 0.00 | 0.00 | 3.16 |
7630 | 11357 | 6.567602 | AGAATAGAATACAGTTGGGCTCTT | 57.432 | 37.500 | 0.00 | 0.00 | 0.00 | 2.85 |
7756 | 11501 | 7.742089 | CAGAGTTAATTTCGTTTCTGACATGAC | 59.258 | 37.037 | 0.00 | 0.00 | 35.28 | 3.06 |
7761 | 11506 | 5.666969 | TTTCGTTTCTGACATGACGATTT | 57.333 | 34.783 | 0.00 | 0.00 | 43.09 | 2.17 |
7762 | 11507 | 5.666969 | TTCGTTTCTGACATGACGATTTT | 57.333 | 34.783 | 0.00 | 0.00 | 43.09 | 1.82 |
7763 | 11508 | 5.264060 | TCGTTTCTGACATGACGATTTTC | 57.736 | 39.130 | 0.00 | 0.00 | 39.33 | 2.29 |
7822 | 11567 | 8.424918 | AGAATTGGAGTAGACTGGTTATATGTG | 58.575 | 37.037 | 0.00 | 0.00 | 0.00 | 3.21 |
7860 | 11909 | 0.766674 | TGTTGCCCCTGTCCTACTGT | 60.767 | 55.000 | 0.00 | 0.00 | 0.00 | 3.55 |
7907 | 11956 | 7.360575 | ACCACGTGATATACTGAAACTTTTC | 57.639 | 36.000 | 19.30 | 0.00 | 37.69 | 2.29 |
7942 | 11991 | 0.546267 | ACATCTCTCCTGGCTGTGGT | 60.546 | 55.000 | 0.00 | 0.00 | 0.00 | 4.16 |
7943 | 11992 | 0.107800 | CATCTCTCCTGGCTGTGGTG | 60.108 | 60.000 | 0.00 | 0.00 | 0.00 | 4.17 |
7944 | 11993 | 0.546267 | ATCTCTCCTGGCTGTGGTGT | 60.546 | 55.000 | 0.00 | 0.00 | 0.00 | 4.16 |
7946 | 11995 | 2.033141 | CTCCTGGCTGTGGTGTGG | 59.967 | 66.667 | 0.00 | 0.00 | 0.00 | 4.17 |
7947 | 11996 | 4.269523 | TCCTGGCTGTGGTGTGGC | 62.270 | 66.667 | 0.00 | 0.00 | 0.00 | 5.01 |
7950 | 12005 | 4.584518 | TGGCTGTGGTGTGGCTGG | 62.585 | 66.667 | 0.00 | 0.00 | 0.00 | 4.85 |
7952 | 12007 | 3.289834 | GCTGTGGTGTGGCTGGTG | 61.290 | 66.667 | 0.00 | 0.00 | 0.00 | 4.17 |
8006 | 12061 | 3.192001 | GGTTAAAGCCTTAAAACTCCCCG | 59.808 | 47.826 | 3.49 | 0.00 | 0.00 | 5.73 |
8007 | 12062 | 2.963599 | AAAGCCTTAAAACTCCCCGA | 57.036 | 45.000 | 0.00 | 0.00 | 0.00 | 5.14 |
8008 | 12063 | 2.195741 | AAGCCTTAAAACTCCCCGAC | 57.804 | 50.000 | 0.00 | 0.00 | 0.00 | 4.79 |
8009 | 12064 | 0.327259 | AGCCTTAAAACTCCCCGACC | 59.673 | 55.000 | 0.00 | 0.00 | 0.00 | 4.79 |
8010 | 12065 | 0.327259 | GCCTTAAAACTCCCCGACCT | 59.673 | 55.000 | 0.00 | 0.00 | 0.00 | 3.85 |
8206 | 12266 | 2.522193 | CGGTAGCCTCCCTCCCTC | 60.522 | 72.222 | 0.00 | 0.00 | 0.00 | 4.30 |
8207 | 12267 | 2.122769 | GGTAGCCTCCCTCCCTCC | 60.123 | 72.222 | 0.00 | 0.00 | 0.00 | 4.30 |
8208 | 12268 | 2.696893 | GTAGCCTCCCTCCCTCCA | 59.303 | 66.667 | 0.00 | 0.00 | 0.00 | 3.86 |
8209 | 12269 | 1.762858 | GTAGCCTCCCTCCCTCCAC | 60.763 | 68.421 | 0.00 | 0.00 | 0.00 | 4.02 |
8210 | 12270 | 1.941820 | TAGCCTCCCTCCCTCCACT | 60.942 | 63.158 | 0.00 | 0.00 | 0.00 | 4.00 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
3 | 4 | 7.384932 | CAGAAAACATGAATTTTAGGTTGGACC | 59.615 | 37.037 | 0.00 | 0.00 | 33.38 | 4.46 |
4 | 5 | 7.384932 | CCAGAAAACATGAATTTTAGGTTGGAC | 59.615 | 37.037 | 0.00 | 0.00 | 31.90 | 4.02 |
6 | 7 | 7.171337 | CACCAGAAAACATGAATTTTAGGTTGG | 59.829 | 37.037 | 0.00 | 6.12 | 37.68 | 3.77 |
7 | 8 | 7.171337 | CCACCAGAAAACATGAATTTTAGGTTG | 59.829 | 37.037 | 0.00 | 5.32 | 37.68 | 3.77 |
20 | 21 | 0.831711 | GGCCCACCACCAGAAAACAT | 60.832 | 55.000 | 0.00 | 0.00 | 35.26 | 2.71 |
34 | 35 | 2.367241 | GCAGAAAGTTTTTAAGGGCCCA | 59.633 | 45.455 | 27.56 | 0.00 | 0.00 | 5.36 |
36 | 37 | 2.367241 | TGGCAGAAAGTTTTTAAGGGCC | 59.633 | 45.455 | 0.00 | 0.00 | 39.29 | 5.80 |
38 | 39 | 3.069443 | TGCTGGCAGAAAGTTTTTAAGGG | 59.931 | 43.478 | 20.86 | 0.00 | 0.00 | 3.95 |
51 | 52 | 1.079612 | CTCATCGTGTGCTGGCAGA | 60.080 | 57.895 | 20.86 | 0.00 | 0.00 | 4.26 |
65 | 66 | 5.981915 | CGTATATGGCATCGAATCATCTCAT | 59.018 | 40.000 | 1.65 | 0.00 | 0.00 | 2.90 |
71 | 72 | 6.683715 | TCTTAACGTATATGGCATCGAATCA | 58.316 | 36.000 | 13.17 | 0.00 | 0.00 | 2.57 |
72 | 73 | 7.613146 | CATCTTAACGTATATGGCATCGAATC | 58.387 | 38.462 | 13.17 | 0.00 | 0.00 | 2.52 |
79 | 80 | 6.875948 | AAATGCATCTTAACGTATATGGCA | 57.124 | 33.333 | 0.00 | 0.00 | 0.00 | 4.92 |
100 | 101 | 1.959985 | ACAATCACACATCGGGCAAAA | 59.040 | 42.857 | 0.00 | 0.00 | 0.00 | 2.44 |
103 | 104 | 0.036022 | TCACAATCACACATCGGGCA | 59.964 | 50.000 | 0.00 | 0.00 | 0.00 | 5.36 |
129 | 130 | 4.272018 | CAGCTGCATACCAGAACTTATGAC | 59.728 | 45.833 | 0.00 | 0.00 | 44.64 | 3.06 |
130 | 131 | 4.162131 | TCAGCTGCATACCAGAACTTATGA | 59.838 | 41.667 | 9.47 | 0.00 | 44.64 | 2.15 |
131 | 132 | 4.445453 | TCAGCTGCATACCAGAACTTATG | 58.555 | 43.478 | 9.47 | 0.00 | 44.64 | 1.90 |
132 | 133 | 4.760530 | TCAGCTGCATACCAGAACTTAT | 57.239 | 40.909 | 9.47 | 0.00 | 44.64 | 1.73 |
164 | 165 | 3.058293 | TGCATCCGTGAAAGTTTGACATC | 60.058 | 43.478 | 6.03 | 0.00 | 0.00 | 3.06 |
179 | 180 | 3.264947 | CCCATGTACTATGATGCATCCG | 58.735 | 50.000 | 23.67 | 14.06 | 0.00 | 4.18 |
189 | 190 | 8.772250 | CATTAATATCCCTCACCCATGTACTAT | 58.228 | 37.037 | 0.00 | 0.00 | 0.00 | 2.12 |
201 | 202 | 6.753913 | AGCTTGAGTCATTAATATCCCTCA | 57.246 | 37.500 | 0.00 | 0.00 | 0.00 | 3.86 |
206 | 207 | 8.341173 | CCTCACAAAGCTTGAGTCATTAATATC | 58.659 | 37.037 | 11.91 | 0.00 | 39.15 | 1.63 |
207 | 208 | 8.049117 | TCCTCACAAAGCTTGAGTCATTAATAT | 58.951 | 33.333 | 11.91 | 0.00 | 39.15 | 1.28 |
208 | 209 | 7.394016 | TCCTCACAAAGCTTGAGTCATTAATA | 58.606 | 34.615 | 11.91 | 0.00 | 39.15 | 0.98 |
209 | 210 | 6.240894 | TCCTCACAAAGCTTGAGTCATTAAT | 58.759 | 36.000 | 11.91 | 0.00 | 39.15 | 1.40 |
211 | 212 | 5.012046 | TCTCCTCACAAAGCTTGAGTCATTA | 59.988 | 40.000 | 11.91 | 0.00 | 39.15 | 1.90 |
212 | 213 | 4.070716 | CTCCTCACAAAGCTTGAGTCATT | 58.929 | 43.478 | 11.91 | 0.00 | 39.15 | 2.57 |
213 | 214 | 3.326006 | TCTCCTCACAAAGCTTGAGTCAT | 59.674 | 43.478 | 11.91 | 0.00 | 39.15 | 3.06 |
218 | 219 | 3.367806 | CGATCTCTCCTCACAAAGCTTGA | 60.368 | 47.826 | 0.00 | 0.00 | 0.00 | 3.02 |
227 | 228 | 0.030638 | GCTGCTCGATCTCTCCTCAC | 59.969 | 60.000 | 0.00 | 0.00 | 0.00 | 3.51 |
228 | 229 | 0.106769 | AGCTGCTCGATCTCTCCTCA | 60.107 | 55.000 | 0.00 | 0.00 | 0.00 | 3.86 |
240 | 241 | 3.983741 | ACCGAGACAATAATAGCTGCTC | 58.016 | 45.455 | 4.91 | 0.00 | 0.00 | 4.26 |
245 | 246 | 8.080417 | TGTCTACATAACCGAGACAATAATAGC | 58.920 | 37.037 | 1.59 | 0.00 | 44.97 | 2.97 |
254 | 255 | 5.067413 | TCCAGATTGTCTACATAACCGAGAC | 59.933 | 44.000 | 0.00 | 0.00 | 40.07 | 3.36 |
267 | 268 | 1.535833 | ACGACTCGTCCAGATTGTCT | 58.464 | 50.000 | 0.00 | 0.00 | 33.69 | 3.41 |
269 | 270 | 5.125097 | ACTTATTACGACTCGTCCAGATTGT | 59.875 | 40.000 | 7.52 | 0.00 | 41.54 | 2.71 |
277 | 278 | 9.208169 | GCATACATATACTTATTACGACTCGTC | 57.792 | 37.037 | 7.52 | 0.00 | 41.54 | 4.20 |
297 | 298 | 4.871557 | GGTTGGTAATGTACTTCGCATACA | 59.128 | 41.667 | 0.00 | 0.00 | 36.98 | 2.29 |
299 | 300 | 4.114073 | CGGTTGGTAATGTACTTCGCATA | 58.886 | 43.478 | 0.00 | 0.00 | 0.00 | 3.14 |
312 | 314 | 3.005050 | CCATAGATCGTAGCGGTTGGTAA | 59.995 | 47.826 | 0.00 | 0.00 | 0.00 | 2.85 |
329 | 331 | 6.485830 | TGAACTCCCTTATCAACTCCATAG | 57.514 | 41.667 | 0.00 | 0.00 | 0.00 | 2.23 |
336 | 338 | 6.352516 | AGTCATGATGAACTCCCTTATCAAC | 58.647 | 40.000 | 0.00 | 0.00 | 33.71 | 3.18 |
337 | 339 | 6.566079 | AGTCATGATGAACTCCCTTATCAA | 57.434 | 37.500 | 0.00 | 0.00 | 33.71 | 2.57 |
358 | 360 | 7.438564 | TGCCGTTGTACATGTATATTCATAGT | 58.561 | 34.615 | 9.18 | 0.01 | 0.00 | 2.12 |
418 | 420 | 4.759782 | AGTTTGAGTCATCCAATAGTCGG | 58.240 | 43.478 | 0.00 | 0.00 | 0.00 | 4.79 |
430 | 432 | 8.049117 | AGCTCCATCAATATTTAGTTTGAGTCA | 58.951 | 33.333 | 0.00 | 0.00 | 35.47 | 3.41 |
432 | 434 | 8.814038 | AAGCTCCATCAATATTTAGTTTGAGT | 57.186 | 30.769 | 0.00 | 0.00 | 35.47 | 3.41 |
446 | 448 | 5.413833 | GTCTCAAATTCTGAAGCTCCATCAA | 59.586 | 40.000 | 0.00 | 0.00 | 32.17 | 2.57 |
458 | 460 | 2.185004 | ACACCCCGTCTCAAATTCTG | 57.815 | 50.000 | 0.00 | 0.00 | 0.00 | 3.02 |
477 | 479 | 5.305902 | TCTTACCACCACTCATGTTTCTGTA | 59.694 | 40.000 | 0.00 | 0.00 | 0.00 | 2.74 |
481 | 483 | 4.691216 | GTCTCTTACCACCACTCATGTTTC | 59.309 | 45.833 | 0.00 | 0.00 | 0.00 | 2.78 |
482 | 484 | 4.642429 | GTCTCTTACCACCACTCATGTTT | 58.358 | 43.478 | 0.00 | 0.00 | 0.00 | 2.83 |
497 | 499 | 4.081642 | CGAACTTTCCCTCATGGTCTCTTA | 60.082 | 45.833 | 0.00 | 0.00 | 34.77 | 2.10 |
511 | 513 | 1.214367 | TCGCTCAACACGAACTTTCC | 58.786 | 50.000 | 0.00 | 0.00 | 36.44 | 3.13 |
520 | 522 | 0.874390 | TTTCCTGCATCGCTCAACAC | 59.126 | 50.000 | 0.00 | 0.00 | 0.00 | 3.32 |
523 | 525 | 5.550290 | TCATATATTTCCTGCATCGCTCAA | 58.450 | 37.500 | 0.00 | 0.00 | 0.00 | 3.02 |
525 | 527 | 5.814188 | TGATCATATATTTCCTGCATCGCTC | 59.186 | 40.000 | 0.00 | 0.00 | 0.00 | 5.03 |
526 | 528 | 5.737860 | TGATCATATATTTCCTGCATCGCT | 58.262 | 37.500 | 0.00 | 0.00 | 0.00 | 4.93 |
528 | 530 | 5.816258 | AGCTGATCATATATTTCCTGCATCG | 59.184 | 40.000 | 0.00 | 0.00 | 0.00 | 3.84 |
529 | 531 | 7.042858 | CGTAGCTGATCATATATTTCCTGCATC | 60.043 | 40.741 | 0.00 | 0.00 | 0.00 | 3.91 |
531 | 533 | 6.071391 | TCGTAGCTGATCATATATTTCCTGCA | 60.071 | 38.462 | 0.00 | 0.00 | 0.00 | 4.41 |
532 | 534 | 6.333416 | TCGTAGCTGATCATATATTTCCTGC | 58.667 | 40.000 | 0.00 | 0.00 | 0.00 | 4.85 |
533 | 535 | 6.475076 | GCTCGTAGCTGATCATATATTTCCTG | 59.525 | 42.308 | 0.00 | 0.00 | 38.45 | 3.86 |
534 | 536 | 6.406400 | GGCTCGTAGCTGATCATATATTTCCT | 60.406 | 42.308 | 0.00 | 0.00 | 41.99 | 3.36 |
535 | 537 | 5.751028 | GGCTCGTAGCTGATCATATATTTCC | 59.249 | 44.000 | 0.00 | 0.00 | 41.99 | 3.13 |
537 | 539 | 6.537453 | AGGCTCGTAGCTGATCATATATTT | 57.463 | 37.500 | 0.00 | 0.00 | 41.99 | 1.40 |
550 | 552 | 2.292292 | TCCAAAACAAAAGGCTCGTAGC | 59.708 | 45.455 | 0.00 | 0.00 | 41.46 | 3.58 |
567 | 569 | 2.734606 | CTCGACACGCATTAAGTTCCAA | 59.265 | 45.455 | 0.00 | 0.00 | 0.00 | 3.53 |
579 | 581 | 1.560923 | ACTATTGCATCTCGACACGC | 58.439 | 50.000 | 0.00 | 0.00 | 0.00 | 5.34 |
582 | 584 | 6.208988 | AGTAAGAACTATTGCATCTCGACA | 57.791 | 37.500 | 0.00 | 0.00 | 32.84 | 4.35 |
583 | 585 | 7.327275 | CCATAGTAAGAACTATTGCATCTCGAC | 59.673 | 40.741 | 0.00 | 0.00 | 44.88 | 4.20 |
596 | 598 | 6.611642 | TGTAGCCATTCTCCATAGTAAGAACT | 59.388 | 38.462 | 0.00 | 0.00 | 39.91 | 3.01 |
603 | 605 | 4.684485 | GCTTGTGTAGCCATTCTCCATAGT | 60.684 | 45.833 | 0.00 | 0.00 | 44.48 | 2.12 |
606 | 608 | 2.648059 | GCTTGTGTAGCCATTCTCCAT | 58.352 | 47.619 | 0.00 | 0.00 | 44.48 | 3.41 |
632 | 634 | 9.086336 | ACAACAGTTTGACAATTTGTTTCTATG | 57.914 | 29.630 | 12.55 | 3.95 | 36.48 | 2.23 |
633 | 635 | 9.301153 | GACAACAGTTTGACAATTTGTTTCTAT | 57.699 | 29.630 | 12.55 | 3.22 | 36.48 | 1.98 |
634 | 636 | 8.300286 | TGACAACAGTTTGACAATTTGTTTCTA | 58.700 | 29.630 | 12.55 | 3.32 | 34.96 | 2.10 |
644 | 646 | 5.351740 | TCACGTAATGACAACAGTTTGACAA | 59.648 | 36.000 | 0.00 | 0.00 | 40.13 | 3.18 |
651 | 653 | 3.243737 | TGCTCTCACGTAATGACAACAGT | 60.244 | 43.478 | 0.00 | 0.00 | 32.37 | 3.55 |
662 | 664 | 0.391228 | TTGTGCCTTGCTCTCACGTA | 59.609 | 50.000 | 0.00 | 0.00 | 33.69 | 3.57 |
663 | 665 | 0.463654 | TTTGTGCCTTGCTCTCACGT | 60.464 | 50.000 | 0.00 | 0.00 | 33.69 | 4.49 |
668 | 670 | 0.607489 | AGCGATTTGTGCCTTGCTCT | 60.607 | 50.000 | 0.00 | 0.00 | 0.00 | 4.09 |
674 | 676 | 1.539065 | CCTATCGAGCGATTTGTGCCT | 60.539 | 52.381 | 10.89 | 0.00 | 36.17 | 4.75 |
680 | 682 | 2.034812 | GTGGACTCCTATCGAGCGATTT | 59.965 | 50.000 | 10.89 | 0.00 | 43.01 | 2.17 |
681 | 683 | 1.609555 | GTGGACTCCTATCGAGCGATT | 59.390 | 52.381 | 10.89 | 0.00 | 43.01 | 3.34 |
697 | 699 | 3.005684 | GTGCATCTCCAAAACAATGTGGA | 59.994 | 43.478 | 0.00 | 0.00 | 41.72 | 4.02 |
705 | 707 | 4.265073 | AGATAGGTGTGCATCTCCAAAAC | 58.735 | 43.478 | 0.00 | 0.00 | 32.63 | 2.43 |
717 | 719 | 6.464222 | TCTAAAAGTGTTGGAGATAGGTGTG | 58.536 | 40.000 | 0.00 | 0.00 | 0.00 | 3.82 |
718 | 720 | 6.497259 | TCTCTAAAAGTGTTGGAGATAGGTGT | 59.503 | 38.462 | 5.05 | 0.00 | 0.00 | 4.16 |
730 | 732 | 5.636543 | CGTCCCGTTTATCTCTAAAAGTGTT | 59.363 | 40.000 | 0.00 | 0.00 | 0.00 | 3.32 |
731 | 733 | 5.047802 | TCGTCCCGTTTATCTCTAAAAGTGT | 60.048 | 40.000 | 0.00 | 0.00 | 0.00 | 3.55 |
738 | 740 | 4.521146 | ACTTCTCGTCCCGTTTATCTCTA | 58.479 | 43.478 | 0.00 | 0.00 | 0.00 | 2.43 |
741 | 743 | 5.649782 | TTAACTTCTCGTCCCGTTTATCT | 57.350 | 39.130 | 0.00 | 0.00 | 0.00 | 1.98 |
742 | 744 | 6.898912 | AATTAACTTCTCGTCCCGTTTATC | 57.101 | 37.500 | 0.00 | 0.00 | 0.00 | 1.75 |
743 | 745 | 7.524065 | CAAAATTAACTTCTCGTCCCGTTTAT | 58.476 | 34.615 | 0.00 | 0.00 | 0.00 | 1.40 |
745 | 747 | 5.754778 | CAAAATTAACTTCTCGTCCCGTTT | 58.245 | 37.500 | 0.00 | 0.00 | 0.00 | 3.60 |
746 | 748 | 4.319984 | GCAAAATTAACTTCTCGTCCCGTT | 60.320 | 41.667 | 0.00 | 0.00 | 0.00 | 4.44 |
747 | 749 | 3.187842 | GCAAAATTAACTTCTCGTCCCGT | 59.812 | 43.478 | 0.00 | 0.00 | 0.00 | 5.28 |
748 | 750 | 3.435671 | AGCAAAATTAACTTCTCGTCCCG | 59.564 | 43.478 | 0.00 | 0.00 | 0.00 | 5.14 |
749 | 751 | 4.723248 | CAGCAAAATTAACTTCTCGTCCC | 58.277 | 43.478 | 0.00 | 0.00 | 0.00 | 4.46 |
750 | 752 | 4.083271 | AGCAGCAAAATTAACTTCTCGTCC | 60.083 | 41.667 | 0.00 | 0.00 | 0.00 | 4.79 |
751 | 753 | 4.848299 | CAGCAGCAAAATTAACTTCTCGTC | 59.152 | 41.667 | 0.00 | 0.00 | 0.00 | 4.20 |
759 | 773 | 6.671402 | GCACATGAATCAGCAGCAAAATTAAC | 60.671 | 38.462 | 0.00 | 0.00 | 0.00 | 2.01 |
760 | 774 | 5.349270 | GCACATGAATCAGCAGCAAAATTAA | 59.651 | 36.000 | 0.00 | 0.00 | 0.00 | 1.40 |
769 | 783 | 5.556355 | TCTTTTAGCACATGAATCAGCAG | 57.444 | 39.130 | 0.00 | 0.00 | 0.00 | 4.24 |
770 | 784 | 5.556355 | CTCTTTTAGCACATGAATCAGCA | 57.444 | 39.130 | 0.00 | 0.00 | 0.00 | 4.41 |
804 | 818 | 7.309920 | GGATTACGAAGAGAGGTTGATATCTC | 58.690 | 42.308 | 3.98 | 0.00 | 41.90 | 2.75 |
806 | 820 | 6.209788 | AGGGATTACGAAGAGAGGTTGATATC | 59.790 | 42.308 | 0.00 | 0.00 | 0.00 | 1.63 |
807 | 821 | 6.015010 | CAGGGATTACGAAGAGAGGTTGATAT | 60.015 | 42.308 | 0.00 | 0.00 | 0.00 | 1.63 |
812 | 826 | 3.709587 | TCAGGGATTACGAAGAGAGGTT | 58.290 | 45.455 | 0.00 | 0.00 | 0.00 | 3.50 |
813 | 827 | 3.383698 | TCAGGGATTACGAAGAGAGGT | 57.616 | 47.619 | 0.00 | 0.00 | 0.00 | 3.85 |
814 | 828 | 4.946478 | AATCAGGGATTACGAAGAGAGG | 57.054 | 45.455 | 0.00 | 0.00 | 29.72 | 3.69 |
815 | 829 | 6.478344 | CAGAAAATCAGGGATTACGAAGAGAG | 59.522 | 42.308 | 0.00 | 0.00 | 31.46 | 3.20 |
816 | 830 | 6.154534 | TCAGAAAATCAGGGATTACGAAGAGA | 59.845 | 38.462 | 0.00 | 0.00 | 31.46 | 3.10 |
817 | 831 | 6.341316 | TCAGAAAATCAGGGATTACGAAGAG | 58.659 | 40.000 | 0.00 | 0.00 | 31.46 | 2.85 |
818 | 832 | 6.294361 | TCAGAAAATCAGGGATTACGAAGA | 57.706 | 37.500 | 0.00 | 0.00 | 31.46 | 2.87 |
823 | 837 | 7.630242 | TGTCAATCAGAAAATCAGGGATTAC | 57.370 | 36.000 | 0.00 | 0.00 | 31.46 | 1.89 |
866 | 880 | 9.950496 | TTTAGGCATTTTATTAATTTTGGCAGA | 57.050 | 25.926 | 0.00 | 0.00 | 32.64 | 4.26 |
900 | 2680 | 5.476945 | GGGGTGCTCATCTTTTTCTTTTAGA | 59.523 | 40.000 | 0.00 | 0.00 | 0.00 | 2.10 |
901 | 2681 | 5.619981 | CGGGGTGCTCATCTTTTTCTTTTAG | 60.620 | 44.000 | 0.00 | 0.00 | 0.00 | 1.85 |
902 | 2682 | 4.217550 | CGGGGTGCTCATCTTTTTCTTTTA | 59.782 | 41.667 | 0.00 | 0.00 | 0.00 | 1.52 |
907 | 2687 | 0.811281 | CCGGGGTGCTCATCTTTTTC | 59.189 | 55.000 | 0.00 | 0.00 | 0.00 | 2.29 |
1033 | 2813 | 0.845102 | GTTTGGGAGAGGGGGAGGAA | 60.845 | 60.000 | 0.00 | 0.00 | 0.00 | 3.36 |
1041 | 2821 | 0.833949 | GAGCTAGGGTTTGGGAGAGG | 59.166 | 60.000 | 0.00 | 0.00 | 0.00 | 3.69 |
1194 | 2977 | 4.641645 | CTGGCCGTGCTGTTCCCA | 62.642 | 66.667 | 0.00 | 0.00 | 0.00 | 4.37 |
1411 | 3194 | 0.035056 | AAGCCCCACACATCTACTGC | 60.035 | 55.000 | 0.00 | 0.00 | 0.00 | 4.40 |
1440 | 3223 | 5.910166 | CGTCTACCTAAACTGAGATGAATCG | 59.090 | 44.000 | 0.00 | 0.00 | 0.00 | 3.34 |
1447 | 3230 | 4.660168 | AGGAACGTCTACCTAAACTGAGA | 58.340 | 43.478 | 7.05 | 0.00 | 34.47 | 3.27 |
1451 | 3234 | 3.095332 | GGGAGGAACGTCTACCTAAACT | 58.905 | 50.000 | 8.51 | 0.00 | 34.87 | 2.66 |
1464 | 3247 | 4.029809 | CACCACCGGGGGAGGAAC | 62.030 | 72.222 | 34.83 | 0.00 | 41.63 | 3.62 |
1502 | 3332 | 5.428496 | AATGTGCATTATTCATCTGGACG | 57.572 | 39.130 | 0.00 | 0.00 | 34.38 | 4.79 |
1506 | 3336 | 9.338291 | GCTACAATAATGTGCATTATTCATCTG | 57.662 | 33.333 | 20.83 | 15.07 | 45.72 | 2.90 |
1545 | 3375 | 3.837213 | ATGCTACACAGTGCATGAAAC | 57.163 | 42.857 | 0.00 | 0.00 | 46.58 | 2.78 |
2051 | 3884 | 3.119173 | TGGTTGAAGCTTGAAAACACTGG | 60.119 | 43.478 | 2.10 | 0.00 | 0.00 | 4.00 |
2054 | 3887 | 4.110036 | AGTGGTTGAAGCTTGAAAACAC | 57.890 | 40.909 | 23.19 | 23.19 | 40.94 | 3.32 |
2354 | 4187 | 5.570320 | ACATACACCTTTGTTAAGCCTCAT | 58.430 | 37.500 | 0.00 | 0.00 | 37.15 | 2.90 |
2909 | 6468 | 7.173907 | AGTGAAAAAGATGTGGTCAATCTAGTG | 59.826 | 37.037 | 0.00 | 0.00 | 0.00 | 2.74 |
2912 | 6471 | 6.368791 | CGAGTGAAAAAGATGTGGTCAATCTA | 59.631 | 38.462 | 0.00 | 0.00 | 32.62 | 1.98 |
3657 | 7216 | 4.217118 | GCCTGTGAAAGTTCATGTTGAGAT | 59.783 | 41.667 | 0.00 | 0.00 | 39.73 | 2.75 |
3809 | 7531 | 6.293626 | GGATGAACCTATGAATGAAATGTCCG | 60.294 | 42.308 | 0.00 | 0.00 | 35.41 | 4.79 |
4024 | 7746 | 8.078060 | TCATCCAGTTCTGATAATCAACAGTA | 57.922 | 34.615 | 1.00 | 0.00 | 35.84 | 2.74 |
4121 | 7843 | 8.243426 | TGCATGAGAACAAATTAAACCATAGAC | 58.757 | 33.333 | 0.00 | 0.00 | 0.00 | 2.59 |
4494 | 8218 | 6.419710 | TGAGTTAATGACACTAAACGTCACAG | 59.580 | 38.462 | 0.00 | 0.00 | 45.64 | 3.66 |
4871 | 8595 | 7.371126 | GAAGGATTCTGTTAACAAGAAGGAG | 57.629 | 40.000 | 10.03 | 0.00 | 43.23 | 3.69 |
4890 | 8614 | 6.688073 | ACTCTGAAAGGACAATAAGAAGGA | 57.312 | 37.500 | 0.00 | 0.00 | 0.00 | 3.36 |
4893 | 8617 | 8.647796 | TGAAGTACTCTGAAAGGACAATAAGAA | 58.352 | 33.333 | 0.00 | 0.00 | 41.87 | 2.52 |
5288 | 9012 | 3.306917 | TTGCGTGAGTTCGAGGATAAA | 57.693 | 42.857 | 0.00 | 0.00 | 0.00 | 1.40 |
5304 | 9029 | 3.945285 | AGGTACCACATAGGATTTTTGCG | 59.055 | 43.478 | 15.94 | 0.00 | 41.22 | 4.85 |
5568 | 9293 | 6.652205 | ACTCCCTCCAATCCAAATTAAGTA | 57.348 | 37.500 | 0.00 | 0.00 | 0.00 | 2.24 |
5926 | 9652 | 7.663081 | TGTCATCTTGAAACTTAGCTGAATTCT | 59.337 | 33.333 | 7.05 | 0.00 | 0.00 | 2.40 |
5972 | 9698 | 1.178534 | CCTTTGGGCGCTTTCTCCAA | 61.179 | 55.000 | 7.64 | 9.39 | 38.62 | 3.53 |
6967 | 10693 | 7.754924 | CACATTAATTAAACGTGAAGAATGCCT | 59.245 | 33.333 | 19.20 | 0.00 | 0.00 | 4.75 |
7094 | 10820 | 3.558321 | GCAACATGGTCACAACCTACCTA | 60.558 | 47.826 | 0.00 | 0.00 | 46.60 | 3.08 |
7095 | 10821 | 2.814097 | GCAACATGGTCACAACCTACCT | 60.814 | 50.000 | 0.00 | 0.00 | 46.60 | 3.08 |
7096 | 10822 | 1.539827 | GCAACATGGTCACAACCTACC | 59.460 | 52.381 | 0.00 | 0.00 | 46.60 | 3.18 |
7097 | 10823 | 1.539827 | GGCAACATGGTCACAACCTAC | 59.460 | 52.381 | 0.00 | 0.00 | 46.60 | 3.18 |
7310 | 11036 | 0.179023 | TGCAGGTCTTGTGCATGTCA | 60.179 | 50.000 | 0.00 | 0.00 | 45.96 | 3.58 |
7480 | 11206 | 5.112220 | CAATGTGCATTGTTGTGTCTACT | 57.888 | 39.130 | 14.75 | 0.00 | 42.32 | 2.57 |
7598 | 11325 | 8.091449 | CCAACTGTATTCTATTCTATCTGACCC | 58.909 | 40.741 | 0.00 | 0.00 | 0.00 | 4.46 |
7623 | 11350 | 0.543749 | AGGTATGACAGCAAGAGCCC | 59.456 | 55.000 | 0.00 | 0.00 | 43.56 | 5.19 |
7666 | 11401 | 4.729227 | TGCAGTACTTCGGATGACAATA | 57.271 | 40.909 | 0.00 | 0.00 | 0.00 | 1.90 |
7667 | 11402 | 3.610040 | TGCAGTACTTCGGATGACAAT | 57.390 | 42.857 | 0.00 | 0.00 | 0.00 | 2.71 |
7668 | 11403 | 3.394674 | TTGCAGTACTTCGGATGACAA | 57.605 | 42.857 | 0.00 | 0.00 | 0.00 | 3.18 |
7738 | 11483 | 5.862924 | AATCGTCATGTCAGAAACGAAAT | 57.137 | 34.783 | 8.83 | 0.15 | 45.93 | 2.17 |
7746 | 11491 | 8.777865 | ATAAAGAAGAAAATCGTCATGTCAGA | 57.222 | 30.769 | 0.00 | 0.00 | 0.00 | 3.27 |
7783 | 11528 | 6.155475 | ACTCCAATTCTAGCTCATACTCAC | 57.845 | 41.667 | 0.00 | 0.00 | 0.00 | 3.51 |
7860 | 11909 | 2.554462 | GAGATGAGATGCTACACCGCTA | 59.446 | 50.000 | 0.00 | 0.00 | 0.00 | 4.26 |
7913 | 11962 | 3.431486 | CCAGGAGAGATGTAGTGGAAAGC | 60.431 | 52.174 | 0.00 | 0.00 | 0.00 | 3.51 |
7923 | 11972 | 0.546267 | ACCACAGCCAGGAGAGATGT | 60.546 | 55.000 | 0.00 | 0.00 | 0.00 | 3.06 |
7942 | 11991 | 2.431683 | GAGGAAGCACCAGCCACA | 59.568 | 61.111 | 2.96 | 0.00 | 43.56 | 4.17 |
7943 | 11992 | 2.360475 | GGAGGAAGCACCAGCCAC | 60.360 | 66.667 | 2.96 | 0.00 | 43.56 | 5.01 |
7944 | 11993 | 3.650950 | GGGAGGAAGCACCAGCCA | 61.651 | 66.667 | 11.57 | 0.00 | 43.56 | 4.75 |
7950 | 12005 | 4.373116 | TGTCGCGGGAGGAAGCAC | 62.373 | 66.667 | 6.13 | 0.00 | 0.00 | 4.40 |
7952 | 12007 | 3.708220 | CTCTGTCGCGGGAGGAAGC | 62.708 | 68.421 | 6.13 | 0.00 | 0.00 | 3.86 |
8006 | 12061 | 4.083862 | GGCGGGTCAGGTCAGGTC | 62.084 | 72.222 | 0.00 | 0.00 | 0.00 | 3.85 |
8007 | 12062 | 4.954118 | TGGCGGGTCAGGTCAGGT | 62.954 | 66.667 | 0.00 | 0.00 | 0.00 | 4.00 |
8008 | 12063 | 4.394712 | GTGGCGGGTCAGGTCAGG | 62.395 | 72.222 | 0.00 | 0.00 | 0.00 | 3.86 |
8009 | 12064 | 3.302347 | GAGTGGCGGGTCAGGTCAG | 62.302 | 68.421 | 0.00 | 0.00 | 0.00 | 3.51 |
8010 | 12065 | 3.311110 | GAGTGGCGGGTCAGGTCA | 61.311 | 66.667 | 0.00 | 0.00 | 0.00 | 4.02 |
8150 | 12209 | 1.152943 | CGGGGAGGTCGAGATCTGA | 60.153 | 63.158 | 0.00 | 0.00 | 0.00 | 3.27 |
8206 | 12266 | 3.995809 | TAAGGGAGGGCGGGAGTGG | 62.996 | 68.421 | 0.00 | 0.00 | 0.00 | 4.00 |
8207 | 12267 | 2.365105 | TAAGGGAGGGCGGGAGTG | 60.365 | 66.667 | 0.00 | 0.00 | 0.00 | 3.51 |
8208 | 12268 | 2.041819 | CTAAGGGAGGGCGGGAGT | 60.042 | 66.667 | 0.00 | 0.00 | 0.00 | 3.85 |
8209 | 12269 | 2.844839 | CCTAAGGGAGGGCGGGAG | 60.845 | 72.222 | 0.00 | 0.00 | 42.39 | 4.30 |
8336 | 12396 | 3.820467 | CAGATCTCCTCGAGCTTGTAGAT | 59.180 | 47.826 | 6.99 | 9.20 | 35.90 | 1.98 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.