Locus 4491

Sequence ID 3L_DroMel_CAF1
Location 12,978,536 – 12,978,696
Length 160
Max. P 0.971555
window7012 window7013 window7014

overview

Window 2

Location 12,978,536 – 12,978,656
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.56
Mean single sequence MFE -30.90
Consensus MFE -22.95
Energy contribution -24.89
Covariance contribution 1.94
Combinations/Pair 1.09
Mean z-score -2.01
Structure conservation index 0.74
SVM decision value 1.11
SVM RNA-class probability 0.916996
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12978536 120 - 23771897
AUACGGUGCGUAUGAGCGAUCCCUGCGAACAAUUAGUUGACGCAAUUUCUCAUAUGCUAACACCUCUCGUUGUCGCCGCAAUGCAAGCGAAGCCCCGGCGAUAUAAGUUGUAGCUCAAAA
.(((((((((((((((.(((...(((((((.....)))..))))))).)))))))))....)))......((((((((....((.......))..))))))))......)))........ ( -32.60)
>DroSim_CAF1 105547 120 - 1
AUACGGUGCGUAUGAGCGAUCCCUGUCAACAAUCAGUUGACGCAAUUUCUCAUAUGCUAACACCUCUCGUUGUCGCCGCAAAGCAAGCGAAACCCCGGCGAUAUAAGUUGUAGCUCAAAA
.(((((((((((((((.(((...(((((((.....)))))))..))).)))))))))....)))......(((((((((.......))(......))))))))......)))........ ( -34.70)
>DroEre_CAF1 101687 93 - 1
AUACGGUGCGUAUGAGCGAUCCCUGUCAACUAUCCGUUGACGCAAUUUCUCAUAUACCAACACCUCUCGU---------------------------ACGAUAUAAACUGUAGCUAAAAA
.((((((.((((((((.(......((((((.....))))))(........)............).)))))---------------------------)))......))))))........ ( -20.80)
>DroYak_CAF1 99956 120 - 1
AUACGGUGCGUAUGAGCGAUCCCUGUCAACUAUCAGUUGACGUAAUUUAUCAUAUGCCAACACCUCUCGUUGUUGCCGCAAAGCAACCAAGAGCCAGGCGAUAUAAACUGUAGCUCAAAA
.((((((((((((((..(((..(.((((((.....)))))))..)))..))))))))...(.((((((...(((((......)))))...)))..))).)......))))))........ ( -35.50)
>consensus
AUACGGUGCGUAUGAGCGAUCCCUGUCAACAAUCAGUUGACGCAAUUUCUCAUAUGCCAACACCUCUCGUUGUCGCCGCAAAGCAAGCGAAACCCCGGCGAUAUAAACUGUAGCUCAAAA
.(((((((((((((((.(((...(((((((.....)))))))..))).))))))))).............(((((((...................)))))))...))))))........ (-22.95 = -24.89 +   1.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 12,978,576 – 12,978,696
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.13
Mean single sequence MFE -37.82
Consensus MFE -29.72
Energy contribution -30.68
Covariance contribution 0.96
Combinations/Pair 1.15
Mean z-score -1.47
Structure conservation index 0.79
SVM decision value -0.04
SVM RNA-class probability 0.513182
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12978576 120 + 23771897
UGCGGCGACAACGAGAGGUGUUAGCAUAUGAGAAAUUGCGUCAACUAAUUGUUCGCAGGGAUCGCUCAUACGCACCGUAUUCCGGUACCAGUACCGGUUACGCUGCCGAACGUCAAAGUG
..((((((((.(....).)))).((.((((((...(((((.(((....)))..)))))......)))))).))..((((..((((((....)))))).))))..))))............ ( -39.30)
>DroSec_CAF1 95933 103 + 1
-----------------GUGUUAGCAUAUGAGAAAUUGCGUCAACUGAUUGUUGACAGGGAUCGCUCAUACGCACCGUAUUCCGGUACCAGUACCGGUGACGCUGCCGAACGUCAAAGUG
-----------------((((((((.((((((..(((.(((((((.....)))))).).)))..)))))).))........((((((....))))))))))))................. ( -35.70)
>DroSim_CAF1 105587 120 + 1
UGCGGCGACAACGAGAGGUGUUAGCAUAUGAGAAAUUGCGUCAACUGAUUGUUGACAGGGAUCGCUCAUACGCACCGUAUUCCGGUACUAGUACCGGUGACGCUGCCGAACGUCAAAGUG
(((((.((((.(....).)))).((.((((((..(((.(((((((.....)))))).).)))..)))))).)).)))))..((((((....))))))(((((........)))))..... ( -44.50)
>DroEre_CAF1 101710 110 + 1
----------ACGAGAGGUGUUGGUAUAUGAGAAAUUGCGUCAACGGAUAGUUGACAGGGAUCGCUCAUACGCACCGUAUUCCGGUACCUGUACCUGUAAAGCUGCCGAACGUCAAAGUG
----------....((.((.((((((((((((..(((.(((((((.....)))))).).)))..)))))).((....(((...((((....)))).)))..)))))))))).))...... ( -32.10)
>DroYak_CAF1 99996 120 + 1
UGCGGCAACAACGAGAGGUGUUGGCAUAUGAUAAAUUACGUCAACUGAUAGUUGACAGGGAUCGCUCAUACGCACCGUAUUCCGGUAGCUGUACCUGCGACGCUGCCGAACGUCAAAGUG
((((((((((.(....).)))))((.(((((...((..(((((((.....)))))).)..))...))))).)).)))))...((((((((((....)))..)))))))............ ( -37.50)
>consensus
UGCGGC_ACAACGAGAGGUGUUAGCAUAUGAGAAAUUGCGUCAACUGAUUGUUGACAGGGAUCGCUCAUACGCACCGUAUUCCGGUACCAGUACCGGUGACGCUGCCGAACGUCAAAGUG
...........((...(((((((((.((((((..(((.(((((((.....)))))).).)))..)))))).))........((((((....)))))))))))))..))............ (-29.72 = -30.68 +   0.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,978,576 – 12,978,696
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.13
Mean single sequence MFE -38.64
Consensus MFE -29.40
Energy contribution -30.92
Covariance contribution 1.52
Combinations/Pair 1.06
Mean z-score -2.55
Structure conservation index 0.76
SVM decision value 1.68
SVM RNA-class probability 0.971555
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12978576 120 - 23771897
CACUUUGACGUUCGGCAGCGUAACCGGUACUGGUACCGGAAUACGGUGCGUAUGAGCGAUCCCUGCGAACAAUUAGUUGACGCAAUUUCUCAUAUGCUAACACCUCUCGUUGUCGCCGCA
.....((.((..((((((((...((((((....)))))).....((((((((((((.(((...(((((((.....)))..))))))).)))))))))....)))...)))))))).)))) ( -40.50)
>DroSec_CAF1 95933 103 - 1
CACUUUGACGUUCGGCAGCGUCACCGGUACUGGUACCGGAAUACGGUGCGUAUGAGCGAUCCCUGUCAACAAUCAGUUGACGCAAUUUCUCAUAUGCUAACAC-----------------
.....((((((......))))))((((((....)))))).....(..(((((((((.(((...(((((((.....)))))))..))).)))))))))...)..----------------- ( -38.40)
>DroSim_CAF1 105587 120 - 1
CACUUUGACGUUCGGCAGCGUCACCGGUACUAGUACCGGAAUACGGUGCGUAUGAGCGAUCCCUGUCAACAAUCAGUUGACGCAAUUUCUCAUAUGCUAACACCUCUCGUUGUCGCCGCA
.....((.((..((((((((...((((((....)))))).....((((((((((((.(((...(((((((.....)))))))..))).)))))))))....)))...)))))))).)))) ( -44.50)
>DroEre_CAF1 101710 110 - 1
CACUUUGACGUUCGGCAGCUUUACAGGUACAGGUACCGGAAUACGGUGCGUAUGAGCGAUCCCUGUCAACUAUCCGUUGACGCAAUUUCUCAUAUACCAACACCUCUCGU----------
........................((((....((((((.....))))))(((((((.(((...(((((((.....)))))))..))).)))))))......)))).....---------- ( -28.80)
>DroYak_CAF1 99996 120 - 1
CACUUUGACGUUCGGCAGCGUCGCAGGUACAGCUACCGGAAUACGGUGCGUAUGAGCGAUCCCUGUCAACUAUCAGUUGACGUAAUUUAUCAUAUGCCAACACCUCUCGUUGUUGCCGCA
............((((((((.((.((((......((((.....))))((((((((..(((..(.((((((.....)))))))..)))..))))))))....))))..)).)))))))).. ( -41.00)
>consensus
CACUUUGACGUUCGGCAGCGUCACCGGUACUGGUACCGGAAUACGGUGCGUAUGAGCGAUCCCUGUCAACAAUCAGUUGACGCAAUUUCUCAUAUGCUAACACCUCUCGUUGU_GCCGCA
.....((((((......))))))((((((....)))))).....((((((((((((.(((...(((((((.....)))))))..))).)))))))))....)))................ (-29.40 = -30.92 +   1.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:49 2006