Locus 4348

Sequence ID X_DroMel_CAF1
Location 11,448,285 – 11,448,397
Length 112
Max. P 0.904690
window7143 window7144

overview

Window 3

Location 11,448,285 – 11,448,384
Length 99
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 67.73
Mean single sequence MFE -32.83
Consensus MFE -16.33
Energy contribution -17.77
Covariance contribution 1.44
Combinations/Pair 1.33
Mean z-score -1.54
Structure conservation index 0.50
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11448285 99 - 22224390
AACAAGGUUCCAUUGGUGAACAGAGUGCCGGCGUGGGACAAAACAUUAUUGAGGGCGACUUGCUGGUGUUAAAUGCCAAUUCCACAAACGUGGAUCUU---------------------U
...((((....((((((......((..((((((((........))).....(((....))))))))..))....))))))(((((....)))))))))---------------------. ( -25.60)
>DroSec_CAF1 1968 99 - 1
GAAAAGGUUCCAUCGGUAAACAGAGUGCCGGCAUAGGACGCAACAUUAUUGACGGCGACCUGCCGGUGUCCAAUGCCAAUGCCACAAACGCGAAUCUU---------------------U
..(((((((((...((((.......))))(((((.((((((..((....)).((((.....)))))))))).)))))............).)))))))---------------------) ( -35.30)
>DroSim_CAF1 1911 93 - 1
GAAAAGGUUCCAUCGGUAAACAGAGUGCCGGCAUAGGACGCAACAUUAUUUACGGCGACCUGCCGGUGUCCAAUGACACUGCA------UUGAAUCUU---------------------U
..((((((((.((((((.........(((((((..((.(((.............))).)))))))))(((....))))))).)------).)))))))---------------------) ( -28.62)
>DroYak_CAF1 5371 120 - 1
GAAAGGGUUCCGUUGGUGGAGAGAGUGCCAGAGUAGGACCAAGCAAUGUACGCGACCGCCUGCUGGUGCACAAUGACAAUUCCGCGUUCGGGAAUCUUAGUGUCAUCGAUGGCUCUCUUU
.((((((..((((((((((.(((((((((..((((((.....((.......)).....)))))).).))))........(((((....))))).))))....))))))))))..)))))) ( -41.80)
>consensus
GAAAAGGUUCCAUCGGUAAACAGAGUGCCGGCAUAGGACGAAACAUUAUUGACGGCGACCUGCCGGUGUCCAAUGACAAUGCCACAAACGUGAAUCUU_____________________U
...(((((((((((((((......(..(((((..(((.(((.............))).))))))))..)....))))))))..........)))))))...................... (-16.33 = -17.77 +   1.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,448,304 – 11,448,397
Length 93
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 68.80
Mean single sequence MFE -34.67
Consensus MFE -18.40
Energy contribution -18.52
Covariance contribution 0.12
Combinations/Pair 1.41
Mean z-score -1.83
Structure conservation index 0.53
SVM decision value 1.04
SVM RNA-class probability 0.904690
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11448304 93 - 22224390
---------------------------GGUGCUAUAGAUGAACAAGGUUCCAUUGGUGAACAGAGUGCCGGCGUGGGACAAAACAUUAUUGAGGGCGACUUGCUGGUGUUAAAUGCCAAU
---------------------------((..((......((((...))))..(((.....)))))..))(((((..((((...((....))(((....))).....))))..)))))... ( -21.80)
>DroSec_CAF1 1987 113 - 1
-------UAGAUGGAAAAGGUGCUUUAGGUGCUAUAGAUGGAAAAGGUUCCAUCGGUAAACAGAGUGCCGGCAUAGGACGCAACAUUAUUGACGGCGACCUGCCGGUGUCCAAUGCCAAU
-------...........((..((((...((((...(((((((....)))))))))))...))))..))(((((.((((((..((....)).((((.....)))))))))).)))))... ( -45.90)
>DroSim_CAF1 1924 120 - 1
GGUGCUAUAGAUGGAAAAGGUGCUAUAGGUGCUAUAGAUGGAAAAGGUUCCAUCGGUAAACAGAGUGCCGGCAUAGGACGCAACAUUAUUUACGGCGACCUGCCGGUGUCCAAUGACACU
(((((..(((((((.....(((((....(((((...(((((((....)))))))((((.......))))))))).)).)))....)))))))..)).)))....((((((....)))))) ( -37.50)
>DroYak_CAF1 5411 100 - 1
--------------------UGGUCGUCGUGCUACAGAUGGAAAGGGUUCCGUUGGUGGAGAGAGUGCCAGAGUAGGACCAAGCAAUGUACGCGACCGCCUGCUGGUGCACAAUGACAAU
--------------------..(((((.((.((((.(((((((....))))))).)))).....(..(((..(((((.....((.......)).....))))))))..))).)))))... ( -33.50)
>consensus
____________________UGCU_UAGGUGCUAUAGAUGGAAAAGGUUCCAUCGGUAAACAGAGUGCCGGCAUAGGACGAAACAUUAUUGACGGCGACCUGCCGGUGUCCAAUGACAAU
................................(((.(((((((....))))))).)))......(..(((((..(((.(((.............))).))))))))..)........... (-18.40 = -18.52 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:46 2006