Locus 1303

Sequence ID 3R_DroMel_CAF1
Location 3,826,404 – 3,826,555
Length 151
Max. P 0.994922
window2134 window2135 window2136

overview

Window 4

Location 3,826,404 – 3,826,518
Length 114
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 87.37
Mean single sequence MFE -33.45
Consensus MFE -31.26
Energy contribution -30.50
Covariance contribution -0.76
Combinations/Pair 1.21
Mean z-score -2.12
Structure conservation index 0.93
SVM decision value 2.52
SVM RNA-class probability 0.994922
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3826404 114 - 27905053
UGGUGCUGUUCAGCCAAUAUUUAUGCAGCACGUGAUAUGUGUGCUGCAGACACUCAAUUGAGGGGGAUUGACUCUGGAAAAAAGGAGCUUAAUCAUUAAAUACAU----ACGUUUACA
..(((((((...............)))))))((((.(((((((.........(((....)))...((((((((((........)))).))))))........)))----)))))))). ( -30.46)
>DroSec_CAF1 54117 114 - 1
UGGUGCUGUUCAGCCAAUAUUUAUGCAGCACGCGAUAUGUGUGCUGCAGACACUCGAUUGAGGGGGAUUGACUCUGGAAAAAAGGAGCUUAAUCAUUAAAUACAU----ACGUUUACA
((((........)))).((((((((((((((((.....))))))))))....(((......))).((((((((((........)))).))))))..))))))...----......... ( -32.70)
>DroSim_CAF1 58888 118 - 1
UGGUGCUGUUCAGCCAAUAUUUAUGCAGCACGCGAUAUGUGUGCUGCAGACACUCGAUUGAGGGGGAUUGACACUGGAAAAAAAGAGCUUAAUCAUUAAAUACAUAUGUACGUUUACA
..((((.......((........((((((((((.....))))))))))....(((....))))).(((((((.((........)).).)))))).............))))....... ( -29.40)
>DroEre_CAF1 45508 113 - 1
UGGUGCUGUUCAGCCAAUAUUUAUGCAGCACGCGAUAUGCGUGCUGCAGGCACUCAAUUGAGGGGGAUUGACUCUGGAGAUAAGGAAUUUAAUCAUUAGAUA-----GUACUUAUAAA
.(((((((((..(((........((((((((((.....))))))))))))).(((....)))...((((((.(((........)))..))))))....))))-----)))))...... ( -37.30)
>DroYak_CAF1 60795 118 - 1
UGGUGCUGUUCAGCCAAUAUCUAUGCAGCACGCCACAUGCGUGCAGCAUGCACUCAAAUGGGGGAGAUUGACUCUGGAAAUAAAGAGUUUAAUCAUUGGAUAAAUAUGUACGUCUACA
..((((((((...(((((.(((((((.((((((.....)))))).))))...(((....))))))((((((((((........)))).)))))))))))...)))).))))....... ( -37.40)
>consensus
UGGUGCUGUUCAGCCAAUAUUUAUGCAGCACGCGAUAUGUGUGCUGCAGACACUCAAUUGAGGGGGAUUGACUCUGGAAAAAAGGAGCUUAAUCAUUAAAUACAU__GUACGUUUACA
((((........)))).((((((((((((((((.....))))))))))....(((....)))...((((((((((........)))).))))))..))))))................ (-31.26 = -30.50 +  -0.76)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,826,440 – 3,826,555
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 82.86
Mean single sequence MFE -28.72
Consensus MFE -19.04
Energy contribution -20.34
Covariance contribution 1.30
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.66
SVM decision value -0.01
SVM RNA-class probability 0.530795
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3826440 115 + 27905053
UCCAGAGUCAAUCCCCCUCAAUUGAGUGUCUGCAGCACACAUAUCACGUGCUGCAUAAAUAUUGGCUGAACAGCACCAAAGACCGGUCAGAAGAGUCCUACAGCAAGGACAAGCA
.....(((((((....(((....)))....((((((((.........)))))))).....))))))).....(((((.......))).......(((((......)))))..)). ( -30.90)
>DroSec_CAF1 54153 115 + 1
UCCAGAGUCAAUCCCCCUCAAUCGAGUGUCUGCAGCACACAUAUCGCGUGCUGCAUAAAUAUUGGCUGAACAGCACCAAAGACCGAUCAGAAGAGUCCUACAGCAAGGACAAGCA
.....(((((((....(((....)))....((((((((.(.....).)))))))).....))))))).....((............((....))(((((......)))))..)). ( -29.70)
>DroSim_CAF1 58928 115 + 1
UCCAGUGUCAAUCCCCCUCAAUCGAGUGUCUGCAGCACACAUAUCGCGUGCUGCAUAAAUAUUGGCUGAACAGCACCAAAGACCGAUCAGAAGAGUCCUACAGCAAGGACAAACA
.(((((((........(((....)))....((((((((.(.....).))))))))...)))))))((((.(.((......).).).))))....(((((......)))))..... ( -29.90)
>DroEre_CAF1 45543 97 + 1
UCCAGAGUCAAUCCCCCUCAAUUGAGUGCCUGCAGCACGCAUAUCGCGUGCUGCAUAAAUAUUGGCUGAACAGCACCAAAGACCGAUCAGAACAGUC------------------
....(((.........)))..(((.((((.((((((((((.....)))))))))).......((......)))))))))..................------------------ ( -27.10)
>DroYak_CAF1 60835 95 + 1
UCCAGAGUCAAUCUCCCCCAUUUGAGUGCAUGCUGCACGCAUGUGGCGUGCUGCAUAGAUAUUGGCUGAACAGCACCAAAGACCGAUCAGAGCAA--------------------
....(((.....))).....((((.((((((((.((((((.....)))))).))))......((......))))))))))...............-------------------- ( -26.00)
>consensus
UCCAGAGUCAAUCCCCCUCAAUUGAGUGUCUGCAGCACACAUAUCGCGUGCUGCAUAAAUAUUGGCUGAACAGCACCAAAGACCGAUCAGAAGAGUCCUACAGCAAGGACAA_CA
....(.(((.....................((((((((.........))))))))......((((.((.....)))))).))))..........(((((......)))))..... (-19.04 = -20.34 +   1.30)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,826,440 – 3,826,555
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 82.86
Mean single sequence MFE -35.90
Consensus MFE -29.22
Energy contribution -28.50
Covariance contribution -0.72
Combinations/Pair 1.26
Mean z-score -1.56
Structure conservation index 0.81
SVM decision value 0.16
SVM RNA-class probability 0.612941
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3826440 115 - 27905053
UGCUUGUCCUUGCUGUAGGACUCUUCUGACCGGUCUUUGGUGCUGUUCAGCCAAUAUUUAUGCAGCACGUGAUAUGUGUGCUGCAGACACUCAAUUGAGGGGGAUUGACUCUGGA
.....(((((......)))))........((((...(..((.((.(((((..........(((((((((.......))))))))).........))))).)).))..)..)))). ( -35.51)
>DroSec_CAF1 54153 115 - 1
UGCUUGUCCUUGCUGUAGGACUCUUCUGAUCGGUCUUUGGUGCUGUUCAGCCAAUAUUUAUGCAGCACGCGAUAUGUGUGCUGCAGACACUCGAUUGAGGGGGAUUGACUCUGGA
......(((......(((..((((((.((((((((.(((((........)))))......((((((((((.....)))))))))))))...)))))))))))..))).....))) ( -39.50)
>DroSim_CAF1 58928 115 - 1
UGUUUGUCCUUGCUGUAGGACUCUUCUGAUCGGUCUUUGGUGCUGUUCAGCCAAUAUUUAUGCAGCACGCGAUAUGUGUGCUGCAGACACUCGAUUGAGGGGGAUUGACACUGGA
((((.(((((......)))))((((((((((((((.(((((........)))))......((((((((((.....)))))))))))))...))))).))))))...))))..... ( -39.80)
>DroEre_CAF1 45543 97 - 1
------------------GACUGUUCUGAUCGGUCUUUGGUGCUGUUCAGCCAAUAUUUAUGCAGCACGCGAUAUGCGUGCUGCAGGCACUCAAUUGAGGGGGAUUGACUCUGGA
------------------(((((.......)))))((..(.((.((((.(((........((((((((((.....))))))))))))).(((....)))..)))).).).)..)) ( -34.00)
>DroYak_CAF1 60835 95 - 1
--------------------UUGCUCUGAUCGGUCUUUGGUGCUGUUCAGCCAAUAUCUAUGCAGCACGCCACAUGCGUGCAGCAUGCACUCAAAUGGGGGAGAUUGACUCUGGA
--------------------....((((((((((((((.(((((((..((.......))..))))))).(((..((.((((.....)))).))..))).))))))))).)).))) ( -30.70)
>consensus
UG_UUGUCCUUGCUGUAGGACUCUUCUGAUCGGUCUUUGGUGCUGUUCAGCCAAUAUUUAUGCAGCACGCGAUAUGUGUGCUGCAGACACUCAAUUGAGGGGGAUUGACUCUGGA
....................(((((((((...(((.(((((........)))))......((((((((((.....)))))))))))))..)))...))))))............. (-29.22 = -28.50 +  -0.72)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:16 2006