Locus 8053

Sequence ID 3R_DroMel_CAF1
Location 21,632,963 – 21,633,119
Length 156
Max. P 0.994311
window12962 window12963 window12964

overview

Window 2

Location 21,632,963 – 21,633,079
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 96.31
Mean single sequence MFE -32.18
Consensus MFE -28.66
Energy contribution -29.02
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -2.11
Structure conservation index 0.89
SVM decision value 2.04
SVM RNA-class probability 0.986305
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21632963 116 + 27905053
GCAUGCAUUUCACAUGAGCCGGCAGUUGCCGCUUUCCAUUUGGUUUAUUGCGAAUUUUAUUGUUUUACGGUAGUUUAUGGCAAAUGCCAUACAACGAGCCGUGUAAAUAUUUG----UUC
(((......(((.((((((.(((....))))))...))).))).....)))((((..((((....((((((.(((((((((....)))))).)))..))))))..))))...)----))) ( -33.10)
>DroSec_CAF1 122420 116 + 1
GCAUGCAUUUCACAUGAGCCGGCAGUUGCCGCUUUCCAUUUGGUUUAUUGCGAAUUUUAUUGUUUUACGGUAGUUUAUGGCAAAUGCCAUACAACGAGCCGUGUAAAUAUUUG----UUC
(((......(((.((((((.(((....))))))...))).))).....)))((((..((((....((((((.(((((((((....)))))).)))..))))))..))))...)----))) ( -33.10)
>DroSim_CAF1 118964 116 + 1
GCCUGCAUUUCACAUGAGCCGGCAGUUGCCGCUUUCCAUUUGGUUUAUUGCGAAUUUUAUUGUUUUACGGUAGUUUAUGGCAAAUGCCAUACAACGAGCCGUGUAAAUAUUUG----UUC
....(((..(((.((((((.(((....))))))...))).))).....)))((((..((((....((((((.(((((((((....)))))).)))..))))))..))))...)----))) ( -32.50)
>DroEre_CAF1 114650 116 + 1
GCAUGCAUUUCACAUGAGCCGGCAGUUGCCGCUUUCCAUUUGGUUUAUUGCGAAUUUUAUUGUUUUACGGUAGUUUAUGGCAAAUGCCAUACAACGAGCCGUGUAAAUAUUUG----UUC
(((......(((.((((((.(((....))))))...))).))).....)))((((..((((....((((((.(((((((((....)))))).)))..))))))..))))...)----))) ( -33.10)
>DroYak_CAF1 119341 116 + 1
GCAUGCAUUUCACAUGAGCCGGCAGUUGCCGCUUUCCAUUUGGUUUAUUGCGAAUUUUAUUGUUUUACGGUAGUUUAUGGCAAAUGCCAUACAACGAGCCGUGUAAAUAUUUG----UUC
(((......(((.((((((.(((....))))))...))).))).....)))((((..((((....((((((.(((((((((....)))))).)))..))))))..))))...)----))) ( -33.10)
>DroAna_CAF1 101533 120 + 1
GCAUGCAUUUCACAUGAGACGGCAGUUUCCGCUUUCCAUUUGGUUUAUUGCGAAUUUUAUUGUUUAAUGGUAGUUUAUGGCAAUCGCCAUACACCAAGCCGUGUAAAUAUUUGUCUGUUC
.((((.......))))((((((((((..(((.........)))...))))).........(((((((((((.((.((((((....)))))).))...))))).))))))..))))).... ( -28.20)
>consensus
GCAUGCAUUUCACAUGAGCCGGCAGUUGCCGCUUUCCAUUUGGUUUAUUGCGAAUUUUAUUGUUUUACGGUAGUUUAUGGCAAAUGCCAUACAACGAGCCGUGUAAAUAUUUG____UUC
...((((..(((.(((((.((((....))))))...))).))).....))))........(((((((((((.(((((((((....)))))).)))..)))))).)))))........... (-28.66 = -29.02 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,632,963 – 21,633,079
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.31
Mean single sequence MFE -27.57
Consensus MFE -24.85
Energy contribution -25.35
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.90
SVM decision value 2.32
SVM RNA-class probability 0.992366
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21632963 116 - 27905053
GAA----CAAAUAUUUACACGGCUCGUUGUAUGGCAUUUGCCAUAAACUACCGUAAAACAAUAAAAUUCGCAAUAAACCAAAUGGAAAGCGGCAACUGCCGGCUCAUGUGAAAUGCAUGC
...----...........((((...(((.((((((....)))))))))..))))............((((((.....((....))..((((((....))).)))..))))))........ ( -27.60)
>DroSec_CAF1 122420 116 - 1
GAA----CAAAUAUUUACACGGCUCGUUGUAUGGCAUUUGCCAUAAACUACCGUAAAACAAUAAAAUUCGCAAUAAACCAAAUGGAAAGCGGCAACUGCCGGCUCAUGUGAAAUGCAUGC
...----...........((((...(((.((((((....)))))))))..))))............((((((.....((....))..((((((....))).)))..))))))........ ( -27.60)
>DroSim_CAF1 118964 116 - 1
GAA----CAAAUAUUUACACGGCUCGUUGUAUGGCAUUUGCCAUAAACUACCGUAAAACAAUAAAAUUCGCAAUAAACCAAAUGGAAAGCGGCAACUGCCGGCUCAUGUGAAAUGCAGGC
...----...........((((...(((.((((((....)))))))))..))))............((((((.....((....))..((((((....))).)))..))))))........ ( -27.60)
>DroEre_CAF1 114650 116 - 1
GAA----CAAAUAUUUACACGGCUCGUUGUAUGGCAUUUGCCAUAAACUACCGUAAAACAAUAAAAUUCGCAAUAAACCAAAUGGAAAGCGGCAACUGCCGGCUCAUGUGAAAUGCAUGC
...----...........((((...(((.((((((....)))))))))..))))............((((((.....((....))..((((((....))).)))..))))))........ ( -27.60)
>DroYak_CAF1 119341 116 - 1
GAA----CAAAUAUUUACACGGCUCGUUGUAUGGCAUUUGCCAUAAACUACCGUAAAACAAUAAAAUUCGCAAUAAACCAAAUGGAAAGCGGCAACUGCCGGCUCAUGUGAAAUGCAUGC
...----...........((((...(((.((((((....)))))))))..))))............((((((.....((....))..((((((....))).)))..))))))........ ( -27.60)
>DroAna_CAF1 101533 120 - 1
GAACAGACAAAUAUUUACACGGCUUGGUGUAUGGCGAUUGCCAUAAACUACCAUUAAACAAUAAAAUUCGCAAUAAACCAAAUGGAAAGCGGAAACUGCCGUCUCAUGUGAAAUGCAUGC
..................(((((.(((((((((((....))))))...))))).............(((((......((....))...)))))....)))))..(((((.....))))). ( -27.40)
>consensus
GAA____CAAAUAUUUACACGGCUCGUUGUAUGGCAUUUGCCAUAAACUACCGUAAAACAAUAAAAUUCGCAAUAAACCAAAUGGAAAGCGGCAACUGCCGGCUCAUGUGAAAUGCAUGC
..................((((...(((.((((((....)))))))))..))))............((((((.....((....))..((((((....)))).))..))))))........ (-24.85 = -25.35 +   0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,633,003 – 21,633,119
Length 116
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 98.62
Mean single sequence MFE -30.72
Consensus MFE -29.48
Energy contribution -29.68
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.96
SVM decision value 2.47
SVM RNA-class probability 0.994311
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21633003 116 + 27905053
UGGUUUAUUGCGAAUUUUAUUGUUUUACGGUAGUUUAUGGCAAAUGCCAUACAACGAGCCGUGUAAAUAUUUGUUCUAGGCCGUGUCCCCCACAAUUCCCUUUGCAUUUUGCCCAG
.(((..(.(((((((..((((....((((((.(((((((((....)))))).)))..))))))..))))...))))......(((.....)))..........))).)..)))... ( -30.40)
>DroSec_CAF1 122460 116 + 1
UGGUUUAUUGCGAAUUUUAUUGUUUUACGGUAGUUUAUGGCAAAUGCCAUACAACGAGCCGUGUAAAUAUUUGUUCUAGGCCGUGUCCCCCACAAUUCCCUUUGCAUUUUGCCCAG
.(((..(.(((((((..((((....((((((.(((((((((....)))))).)))..))))))..))))...))))......(((.....)))..........))).)..)))... ( -30.40)
>DroSim_CAF1 119004 116 + 1
UGGUUUAUUGCGAAUUUUAUUGUUUUACGGUAGUUUAUGGCAAAUGCCAUACAACGAGCCGUGUAAAUAUUUGUUCUAGGCCGUGUCCCCCACAAUUCCCUUUGCAUUUUGCCCAG
.(((..(.(((((((..((((....((((((.(((((((((....)))))).)))..))))))..))))...))))......(((.....)))..........))).)..)))... ( -30.40)
>DroEre_CAF1 114690 116 + 1
UGGUUUAUUGCGAAUUUUAUUGUUUUACGGUAGUUUAUGGCAAAUGCCAUACAACGAGCCGUGUAAAUAUUUGUUCUAGGCCGUGUCCCCCACAAUUCCCUUUGCAGUUUGCCCAG
.(((..(((((((((..((((....((((((.(((((((((....)))))).)))..))))))..))))...))))......(((.....)))..........)))))..)))... ( -33.60)
>DroYak_CAF1 119381 116 + 1
UGGUUUAUUGCGAAUUUUAUUGUUUUACGGUAGUUUAUGGCAAAUGCCAUACAACGAGCCGUGUAAAUAUUUGUUCUAGGCCGUGUCCCCCUCAAUUCCCUUUGCAUUUCGCCCGG
.((((((..(((((...((((....((((((.(((((((((....)))))).)))..))))))..)))))))))..))))))(((.......(((......))).....))).... ( -28.80)
>consensus
UGGUUUAUUGCGAAUUUUAUUGUUUUACGGUAGUUUAUGGCAAAUGCCAUACAACGAGCCGUGUAAAUAUUUGUUCUAGGCCGUGUCCCCCACAAUUCCCUUUGCAUUUUGCCCAG
.(((..(.(((((((..((((....((((((.(((((((((....)))))).)))..))))))..))))...)))).(((...(((.....)))....)))..))).)..)))... (-29.48 = -29.68 +   0.20)

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 13:01:25 2006