Locus 3540

Sequence ID X_DroMel_CAF1
Location 9,488,240 – 9,488,330
Length 90
Max. P 0.858010
window5796 window5797

overview

Window 6

Location 9,488,240 – 9,488,330
Length 90
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 68.19
Mean single sequence MFE -14.26
Consensus MFE -6.00
Energy contribution -6.52
Covariance contribution 0.52
Combinations/Pair 1.25
Mean z-score -1.75
Structure conservation index 0.42
SVM decision value 0.24
SVM RNA-class probability 0.650109
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9488240 90 + 22224390
AACCACGGAUAGUUGGAUGCGCGUAUACUGAUUCACAGAUACGACAA-AA-UGGCAAAACCAAAA--AAAAAAAACAUAAAUGCGCAUAUGGCA
...........((((.((((((((((.(((.....))))))).....-..-(((.....)))...--...............)))))).)))). ( -18.80)
>DroGri_CAF1 41902 73 + 1
------------UUAAAUGCACA---AUAGAUG--CAUAUGCGAUAAGAAGCAAUU-ACA-GACA--CAGACACACACACAUGCACAUAUAGCA
------------.....(((...---(((..((--(((.(((........)))...-...-....--..(.....)....)))))..))).))) (  -7.70)
>DroSim_CAF1 31307 87 + 1
AACCACGGAUAGUUGGAUGCGCGUAUACUGAUUCACAGAUACGACAAAAA-UGGCAGAAAAAAACAAAAA------AAAAAUCCGCAUAUGGCA
..((((((((.((.....))((((((.(((.....)))))))).).....-...................------....)))))....))).. ( -13.80)
>DroEre_CAF1 31465 80 + 1
AACCACGGAUUGUUGGAUGCGCGUAUACUGAUUCACAGAUACGACAAAAG------------AAA--AAAAAAAACAUAAAUGCGCAUAUGGCA
..........(((((.((((((((((.(((.....)))))))..(....)------------...--...............)))))).))))) ( -14.70)
>DroYak_CAF1 31677 89 + 1
AACCACGGAUAGUUGGAUGCGCGUAUACUGAUUCACAGAUACGAUAAAAAACAGCA-AAA--AAA--ACAAAAAACAUAUAUGCGCAUAUGGCA
...........((((.((((((((((((((.....)))....(........)....-...--...--..........))))))))))).)))). ( -16.30)
>consensus
AACCACGGAUAGUUGGAUGCGCGUAUACUGAUUCACAGAUACGACAAAAA_CAGCA_AAA__AAA__AAAAAAAACAUAAAUGCGCAUAUGGCA
...........((((.((((((((........................................................)))))))).)))). ( -6.00 =  -6.52 +   0.52)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 9,488,240 – 9,488,330
Length 90
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 68.19
Mean single sequence MFE -17.87
Consensus MFE -6.02
Energy contribution -7.66
Covariance contribution 1.64
Combinations/Pair 1.25
Mean z-score -2.02
Structure conservation index 0.34
SVM decision value 0.82
SVM RNA-class probability 0.858010
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9488240 90 - 22224390
UGCCAUAUGCGCAUUUAUGUUUUUUUU--UUUUGGUUUUGCCA-UU-UUGUCGUAUCUGUGAAUCAGUAUACGCGCAUCCAACUAUCCGUGGUU
.(((((((((((...............--...(((.....)))-..-.....(((((((.....))).))))))))))..........))))). ( -20.60)
>DroGri_CAF1 41902 73 - 1
UGCUAUAUGUGCAUGUGUGUGUGUCUG--UGUC-UGU-AAUUGCUUCUUAUCGCAUAUG--CAUCUAU---UGUGCAUUUAA------------
(((.(((.(((((((((((.......(--((..-...-...))).......))))))))--))).)))---...))).....------------ ( -19.04)
>DroSim_CAF1 31307 87 - 1
UGCCAUAUGCGGAUUUUU------UUUUUGUUUUUUUCUGCCA-UUUUUGUCGUAUCUGUGAAUCAGUAUACGCGCAUCCAACUAUCCGUGGUU
.(((((..(((((.....------............)))))..-....(((((((((((.....))).))))).)))...........))))). ( -17.43)
>DroEre_CAF1 31465 80 - 1
UGCCAUAUGCGCAUUUAUGUUUUUUUU--UUU------------CUUUUGUCGUAUCUGUGAAUCAGUAUACGCGCAUCCAACAAUCCGUGGUU
.(((((((((((...............--...------------(....)..(((((((.....))).))))))))))..........))))). ( -15.40)
>DroYak_CAF1 31677 89 - 1
UGCCAUAUGCGCAUAUAUGUUUUUUGU--UUU--UUU-UGCUGUUUUUUAUCGUAUCUGUGAAUCAGUAUACGCGCAUCCAACUAUCCGUGGUU
.(((((((((((.............((--...--...-.))...........(((((((.....))).))))))))))..........))))). ( -16.90)
>consensus
UGCCAUAUGCGCAUUUAUGUUUUUUUU__UUU__UUU_UGCCA_UUUUUGUCGUAUCUGUGAAUCAGUAUACGCGCAUCCAACUAUCCGUGGUU
.(((((((((((.............................((.....))..(((((((.....))).))))))))))..........))))). ( -6.02 =  -7.66 +   1.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:58 2006