Locus 8485

Sequence ID dm3.chr3L
Location 23,565,072 – 23,565,179
Length 107
Max. P 0.999875
window11654 window11655

overview

Window 4

Location 23,565,072 – 23,565,179
Length 107
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 68.64
Shannon entropy 0.45477
G+C content 0.34161
Mean single sequence MFE -35.33
Consensus MFE -23.90
Energy contribution -25.58
Covariance contribution 1.68
Combinations/Pair 1.27
Mean z-score -5.47
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.62
SVM RNA-class probability 0.999863
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23565072 107 + 24543557
UUCUGUUCGCCUGGUACUUGAAAUCGAAAAAUCACUCA-UUUGACCGCUAAAAUG-ACAU---------AACUUAGUCAAUUUAUUGUUUUUGUGUACCAGGUUUAAAUAAUCUGUAG
........(((((((((.(((((.(((....(((....-..)))....((((.((-((..---------......)))).))))))).))))).)))))))))............... ( -22.10, z-score =  -2.32, R)
>droEre2.scaffold_4820 291585 117 + 10470090
UCCUGUUCGCCUGGUAAUUUAAAACGAAAAAUUUCACAAUUUUGCCUACAAAAUGUAAAUUAUUAUGGCGAAU-UGUAGAUUUUUCGGAUUGAAUUACCAGGCGAUCAUAAUCAGCAG
...((.((((((((((((((((..((((((((((.(((((((.(((.....(((....))).....)))))))-)))))))))))))..)))))))))))))))).)).......... ( -46.80, z-score =  -8.86, R)
>droSec1.super_141 1621 118 + 69287
UCCAGUUCGCCUGGUAGUUUAAACCGAAAAAUCUCUCAAUUUGGCAUACAAAAUGCACAUUUUUGUGCAAAAUCUUUGGAUCUUUCGAUUUUAGAUACCAGGCGAUGAUAAUCAGUAG
......((((((((((.((((((.(((((.((((.....((((.....)))).((((((....))))))........)))).)))))..))))))))))))))))............. ( -37.10, z-score =  -5.22, R)
>consensus
UCCUGUUCGCCUGGUAAUUUAAAACGAAAAAUCUCUCAAUUUGGCCUACAAAAUG_ACAUU_UU_UG__AAAU_UGUAGAUUUUUCGAUUUUAAAUACCAGGCGAUAAUAAUCAGUAG
......(((((((((((((((((.(((((((((.............................................))))))))).)))))))))))))))))............. (-23.90 = -25.58 +   1.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 23,565,072 – 23,565,179
Length 107
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 68.64
Shannon entropy 0.45477
G+C content 0.34161
Mean single sequence MFE -34.20
Consensus MFE -17.10
Energy contribution -19.21
Covariance contribution 2.12
Combinations/Pair 1.13
Mean z-score -4.83
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.67
SVM RNA-class probability 0.999875
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23565072 107 - 24543557
CUACAGAUUAUUUAAACCUGGUACACAAAAACAAUAAAUUGACUAAGUU---------AUGU-CAUUUUAGCGGUCAAA-UGAGUGAUUUUUCGAUUUCAAGUACCAGGCGAACAGAA
................((((((((..............((((((..(((---------(...-.....)))))))))).-(((.(((....)))...))).))))))))......... ( -23.00, z-score =  -2.22, R)
>droEre2.scaffold_4820 291585 117 - 10470090
CUGCUGAUUAUGAUCGCCUGGUAAUUCAAUCCGAAAAAUCUACA-AUUCGCCAUAAUAAUUUACAUUUUGUAGGCAAAAUUGUGAAAUUUUUCGUUUUAAAUUACCAGGCGAACAGGA
..........((.(((((((((((((.((..((((((((.((((-(((.(((((((...........)))).)))..)))))))..))))))))..)).))))))))))))).))... ( -40.00, z-score =  -6.61, R)
>droSec1.super_141 1621 118 - 69287
CUACUGAUUAUCAUCGCCUGGUAUCUAAAAUCGAAAGAUCCAAAGAUUUUGCACAAAAAUGUGCAUUUUGUAUGCCAAAUUGAGAGAUUUUUCGGUUUAAACUACCAGGCGAACUGGA
.............((((((((((....(((((((((((((....(((((.(((..(((((....)))))...))).)))))....)))))))))))))....))))))))))...... ( -39.60, z-score =  -5.65, R)
>consensus
CUACUGAUUAUCAUCGCCUGGUAAAUAAAAACGAAAAAUCCACA_AUUU__CA_AA_AAUGU_CAUUUUGUAGGCCAAAUUGAGAGAUUUUUCGAUUUAAACUACCAGGCGAACAGGA
.............(((((((((((...(((.(((((((((.............................................))))))))).)))...)))))))))))...... (-17.10 = -19.21 +   2.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:46:30 2011