Locus 4493

Sequence ID X_DroMel_CAF1
Location 11,880,493 – 11,880,687
Length 194
Max. P 0.989161
window7387 window7388 window7389 window7390

overview

Window 7

Location 11,880,493 – 11,880,589
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 96.46
Mean single sequence MFE -23.32
Consensus MFE -20.82
Energy contribution -20.70
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.52
Structure conservation index 0.89
SVM decision value 1.00
SVM RNA-class probability 0.897504
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11880493 96 - 22224390
UGCACACACAUUCAGACGCAUAUGUAUGGAUCAGUGUGCAUUUGUGUGUGUGCUUCUGGCGACGCAUUAUUUUGUAUUUUAAUAAUUCAAAUAUCA
.(((((((((..((((.((((((..........)))))).)))))))))))))..........(((......)))..................... ( -23.60)
>DroSec_CAF1 12484 96 - 1
UGCACACACAUUCAGUCGCAUAUGUAUGGAUCAGUGUGCAUUUGUGUGUGUGCUUCUGGCGACGCAUUAUUUUGUAUUUUAAUAAUUCAAAUAUCA
.((((((((((..(((.((((((..........))))))))).))))))))))..........(((......)))..................... ( -22.50)
>DroSim_CAF1 14821 96 - 1
UGCACACACAUUCAGUCGCAUAUGUAUGGAUCAGUGUGCAUUUGUGUGUGUGCUUCUGGCGACGCAUUAUUUUGUAUUUUAAUAAUUCAAAUAUCA
.((((((((((..(((.((((((..........))))))))).))))))))))..........(((......)))..................... ( -22.50)
>DroEre_CAF1 14620 96 - 1
UGCACACACAUUCAGUCGCCAGUGUGUGGAUCAGCGUGCAUUUGUGUGUGUGCUUCUGGCGACGCAUUAUUUUGUAUUUUAAUAAUUCAAAUAUCA
..............((((((((..........((((..(((....)))..)))).))))))))(((......)))..................... ( -24.10)
>DroYak_CAF1 16135 96 - 1
UGCACACACGUUCAGUCGCAUGUGUAUGGAUCAGUGUGCAUUUGUGUGUGCGCUUCUGGCGACGCAUUAUUUUGUAUUUUAAUAAUUCAAAUAUCA
(((((((..(((((...((....)).)))))..)))))))...((((((.(((.....)))))))))...((((.(((.....))).))))..... ( -23.90)
>consensus
UGCACACACAUUCAGUCGCAUAUGUAUGGAUCAGUGUGCAUUUGUGUGUGUGCUUCUGGCGACGCAUUAUUUUGUAUUUUAAUAAUUCAAAUAUCA
(((((((..(((((...((....)).)))))..)))))))...((((((.(((.....)))))))))...((((.(((.....))).))))..... (-20.82 = -20.70 +  -0.12)

alignment

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secondary structure

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Window 8

Location 11,880,533 – 11,880,626
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 94.73
Mean single sequence MFE -19.22
Consensus MFE -17.22
Energy contribution -17.46
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -1.82
Structure conservation index 0.90
SVM decision value 2.15
SVM RNA-class probability 0.989161
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11880533 93 + 22224390
GAAGCACACACACAAAUGCACACUGAUCCAUACAUAUGCGUCUGAAUGUGUGUGCAUAUUUAUUUUUAUCCAACACAAUACAGUGCGUACCGU
...(((((((((((.(((((...((.......))..))))).))..)))))))))..................(((......)))........ ( -20.60)
>DroSec_CAF1 12524 93 + 1
GAAGCACACACACAAAUGCACACUGAUCCAUACAUAUGCGACUGAAUGUGUGUGCAUAUUUAUUUUUAUCCAACACAAUACAGUGCGUAUCUU
...(((((((((((..((((...((.......))..))))..))..)))))))))..................(((......)))........ ( -18.30)
>DroSim_CAF1 14861 93 + 1
GAAGCACACACACAAAUGCACACUGAUCCAUACAUAUGCGACUGAAUGUGUGUGCAUAUUUAUUUUUAUCCAACACAAUACAGUGCGUAUCUA
...(((((((((((..((((...((.......))..))))..))..)))))))))..................(((......)))........ ( -18.30)
>DroEre_CAF1 14660 93 + 1
GAAGCACACACACAAAUGCACGCUGAUCCACACACUGGCGACUGAAUGUGUGUGCAUAUUUAUUUUUAUCCAACACAAUACAGUGCGUAUCAU
((.(((((((((((..(((.((.((.......)).)))))..))..)))))))))..................(((......)))....)).. ( -19.20)
>DroYak_CAF1 16175 93 + 1
GAAGCGCACACACAAAUGCACACUGAUCCAUACACAUGCGACUGAACGUGUGUGCAUAUUUAUUUUUAUCCAACACAAUACAGUGCGUAUCUU
((.((((((......((((((((((.......))...(((......))))))))))).........(((........)))..)))))).)).. ( -19.70)
>consensus
GAAGCACACACACAAAUGCACACUGAUCCAUACAUAUGCGACUGAAUGUGUGUGCAUAUUUAUUUUUAUCCAACACAAUACAGUGCGUAUCUU
...(((((((((((..((((...((.......))..))))..))..)))))))))..................(((......)))........ (-17.22 = -17.46 +   0.24)

alignment

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secondary structure

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Window 9

Location 11,880,533 – 11,880,626
Length 93
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 94.73
Mean single sequence MFE -25.80
Consensus MFE -21.94
Energy contribution -21.98
Covariance contribution 0.04
Combinations/Pair 1.14
Mean z-score -2.03
Structure conservation index 0.85
SVM decision value 1.96
SVM RNA-class probability 0.983842
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11880533 93 - 22224390
ACGGUACGCACUGUAUUGUGUUGGAUAAAAAUAAAUAUGCACACACAUUCAGACGCAUAUGUAUGGAUCAGUGUGCAUUUGUGUGUGUGCUUC
..(((((((.(((...(((((((.(((........))).)).)))))..)))(((((.((((((........)))))).)))))))))))).. ( -29.30)
>DroSec_CAF1 12524 93 - 1
AAGAUACGCACUGUAUUGUGUUGGAUAAAAAUAAAUAUGCACACACAUUCAGUCGCAUAUGUAUGGAUCAGUGUGCAUUUGUGUGUGUGCUUC
.......((((......)))).................((((((((((..(((.((((((..........))))))))).))))))))))... ( -25.00)
>DroSim_CAF1 14861 93 - 1
UAGAUACGCACUGUAUUGUGUUGGAUAAAAAUAAAUAUGCACACACAUUCAGUCGCAUAUGUAUGGAUCAGUGUGCAUUUGUGUGUGUGCUUC
.......((((......)))).................((((((((((..(((.((((((..........))))))))).))))))))))... ( -25.00)
>DroEre_CAF1 14660 93 - 1
AUGAUACGCACUGUAUUGUGUUGGAUAAAAAUAAAUAUGCACACACAUUCAGUCGCCAGUGUGUGGAUCAGCGUGCAUUUGUGUGUGUGCUUC
.((((((((((((...(((((((.(((........))).)).))))).........))))))))..))))(((..(((....)))..)))... ( -25.60)
>DroYak_CAF1 16175 93 - 1
AAGAUACGCACUGUAUUGUGUUGGAUAAAAAUAAAUAUGCACACACGUUCAGUCGCAUGUGUAUGGAUCAGUGUGCAUUUGUGUGUGCGCUUC
...((((((((((...(((((((.(((........))).)).)))))..)))).....)))))).....((((..(((....)))..)))).. ( -24.10)
>consensus
AAGAUACGCACUGUAUUGUGUUGGAUAAAAAUAAAUAUGCACACACAUUCAGUCGCAUAUGUAUGGAUCAGUGUGCAUUUGUGUGUGUGCUUC
.......((((......)))).................(((((((((..(((..((((((..........))))))..))))))))))))... (-21.94 = -21.98 +   0.04)

alignment

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secondary structure

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Window 0

Location 11,880,589 – 11,880,687
Length 98
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 74.04
Mean single sequence MFE -19.45
Consensus MFE -10.36
Energy contribution -10.56
Covariance contribution 0.20
Combinations/Pair 1.16
Mean z-score -1.70
Structure conservation index 0.53
SVM decision value 0.18
SVM RNA-class probability 0.621887
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11880589 98 - 22224390
UUU--CCUA-U-------------UUGUCUUUUAUCA---AGCUCCUAAUUAGGUUCCCCCAUUAAAUGGCAUAACACUUACGGUACGCACUGUAUUGUGUUGGAUAAAAAUAAAUA
...--..((-(-------------((((.(((((((.---.(((..((((..((...))..))))...))).((((((.((((((....))))))..)))))))))))))))))))) ( -21.50)
>DroSec_CAF1 12580 85 - 1
----------------------------GUUUUAUCC---AGCUCCUAAUUAGGUUGC-CCAUUAAAUGGCAUAACACUUAAGAUACGCACUGUAUUGUGUUGGAUAAAAAUAAAUA
----------------------------.((((((((---(((......(((((((((-(........))))....))))))(((((.....)))))..)))))))))))....... ( -22.10)
>DroSim_CAF1 14917 85 - 1
----------------------------GUUUUAUCA---AGCUCCUAAUUAGGUUGC-CCAUUAAAUGGCAUAACACUUUAGAUACGCACUGUAUUGUGUUGGAUAAAAAUAAAUA
----------------------------.(((((((.---....(((....))).(((-(........))))((((((....(((((.....))))))))))))))))))....... ( -16.30)
>DroEre_CAF1 14716 116 - 1
AUUACCCCAGCAUGAAAUAAUACCUCAUACCUCAUCGCAUAGCUCCUAAUUAGGUUCC-CCAUCAAAUGGCCCAAUGCUUAUGAUACGCACUGUAUUGUGUUGGAUAAAAAUAAAUA
......(((((((.....(((((........((((.((((....(((....)))....-((((...))))....))))..))))........))))))))))))............. ( -17.29)
>DroYak_CAF1 16231 108 - 1
AUAUUCCCAGCCUGUAA-----CUGCAUAUCUCAUCG---AGAUCCUAAUUAGGUUGC-CCAUCAAAUGGCCCAAUACUUAAGAUACGCACUGUAUUGUGUUGGAUAAAAAUAAAUA
.......(((((((...-----......(((((...)---))))......))))))).-((((...)))).(((((((....(((((.....))))))))))))............. ( -20.06)
>consensus
_U___CC_A__________________UAUUUUAUCA___AGCUCCUAAUUAGGUUGC_CCAUUAAAUGGCAUAACACUUAAGAUACGCACUGUAUUGUGUUGGAUAAAAAUAAAUA
.............................(((((((........(((....))).....((((...))))..((((((....(((((.....))))))))))))))))))....... (-10.36 = -10.56 +   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 11:26:30 2006