Locus 3546

Sequence ID 2L_DroMel_CAF1
Location 10,341,977 – 10,342,088
Length 111
Max. P 0.825806
window5598 window5599

overview

Window 8

Location 10,341,977 – 10,342,088
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 79.95
Mean single sequence MFE -24.32
Consensus MFE -13.24
Energy contribution -14.92
Covariance contribution 1.68
Combinations/Pair 1.18
Mean z-score -2.15
Structure conservation index 0.54
SVM decision value 0.70
SVM RNA-class probability 0.825806
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10341977 111 + 22407834
GUUUCGUCAGUUACUGGUUUCAUAUAUUAGUGUACAUAUAUACACGUCUGCACCACCUUCAUUUGUUUAGUCAUAGUCUCAAGCUAAACAAAUGAACCAGGUGUGCACCUA
...............(((...........(((((......)))))....((((.(((((((((((((((((...........)))))))))))))...))))))))))).. ( -30.50)
>DroSec_CAF1 3579 111 + 1
GUUUCGUCAGUUACUGGUUUCAUAUAUUUGUGCACAUAUACACACGUCUGCUCCACCUACAUUUGUUUUGUCAUAGUCUCAAGCAAAACAAAUGAACCAGGUGUGCACCCA
......((((...))))...........((((........)))).(..(((..(((((.((((((((((((...........))))))))))))....))))).)))..). ( -23.50)
>DroSim_CAF1 1860 111 + 1
GUUUCGUCAGUUACUGGUUUCAUAUAUUUGUGCACAUAUAUACACGUCUGCUCCACCUACAUUUGUUUAGUCAUAGUCUCAAGCAAAACAAAUGAACCAGGUGUGCACCCA
......((((...)))).....(((((.((....)).)))))...(..(((..(((((.(((((((((.((...........)).)))))))))....))))).)))..). ( -19.30)
>DroEre_CAF1 3665 88 + 1
------------AAUGG-UUAAUAUAUAUGUGUACAUAUAUACACGACUACACCUCUUUCGUUUGUUUAGUCAUAGUCUU----------AAUUAACCAGGUGUGCCCGUA
------------..(((-((((((((((((....)))))))....(((((.((...........)).)))))........----------.))))))))((....)).... ( -18.60)
>DroYak_CAF1 2469 108 + 1
---UCGUCAGUUACUGUUUUCAUGUAUAUGUACACAUAUAUACACGACUGCACCUCCUACGUUUGUUUAGUCAUAGUCUUUGGCUACACAAAUGAACCAGGUGUGCCCUUA
---..(((......((....))(((((((((....))))))))).))).((((((....(((((((.((((((.......)))))).)))))))....))))))....... ( -29.70)
>consensus
GUUUCGUCAGUUACUGGUUUCAUAUAUUUGUGCACAUAUAUACACGUCUGCACCACCUACAUUUGUUUAGUCAUAGUCUCAAGCAAAACAAAUGAACCAGGUGUGCACCUA
.............................((((((((........((.......))...((((((((((((...........))))))))))))......))))))))... (-13.24 = -14.92 +   1.68)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,341,977 – 10,342,088
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 79.95
Mean single sequence MFE -27.44
Consensus MFE -14.10
Energy contribution -15.86
Covariance contribution 1.76
Combinations/Pair 1.26
Mean z-score -2.18
Structure conservation index 0.51
SVM decision value 0.62
SVM RNA-class probability 0.803191
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10341977 111 - 22407834
UAGGUGCACACCUGGUUCAUUUGUUUAGCUUGAGACUAUGACUAAACAAAUGAAGGUGGUGCAGACGUGUAUAUAUGUACACUAAUAUAUGAAACCAGUAACUGACGAAAC
..(((((((((((...(((((((((((((..........).)))))))))))))))).))))....((((((....))))))...........)))............... ( -32.00)
>DroSec_CAF1 3579 111 - 1
UGGGUGCACACCUGGUUCAUUUGUUUUGCUUGAGACUAUGACAAAACAAAUGUAGGUGGAGCAGACGUGUGUAUAUGUGCACAAAUAUAUGAAACCAGUAACUGACGAAAC
(((.(((.((((((...((((((((((((..........).)))))))))))))))))..)))....((((((....))))))...........))).............. ( -29.70)
>DroSim_CAF1 1860 111 - 1
UGGGUGCACACCUGGUUCAUUUGUUUUGCUUGAGACUAUGACUAAACAAAUGUAGGUGGAGCAGACGUGUAUAUAUGUGCACAAAUAUAUGAAACCAGUAACUGACGAAAC
(((.(((.((((((...(((((((((..(..........)...)))))))))))))))..)))...((((((....))))))............))).............. ( -26.60)
>DroEre_CAF1 3665 88 - 1
UACGGGCACACCUGGUUAAUU----------AAGACUAUGACUAAACAAACGAAAGAGGUGUAGUCGUGUAUAUAUGUACACAUAUAUAUUAA-CCAUU------------
...((.....))(((((((..----------.....((((((((.((...(....)..)).))))))))((((((((....))))))))))))-)))..------------ ( -25.10)
>DroYak_CAF1 2469 108 - 1
UAAGGGCACACCUGGUUCAUUUGUGUAGCCAAAGACUAUGACUAAACAAACGUAGGAGGUGCAGUCGUGUAUAUAUGUGUACAUAUACAUGAAAACAGUAACUGACGA---
.....((((..((((((((....)).)))))....(((((..........))))))..))))..((((((((((........))))))))))...(((...)))....--- ( -23.80)
>consensus
UAGGUGCACACCUGGUUCAUUUGUUUAGCUUGAGACUAUGACUAAACAAAUGUAGGUGGUGCAGACGUGUAUAUAUGUGCACAAAUAUAUGAAACCAGUAACUGACGAAAC
.....((((..((....(((((((((((.............)))))))))))..))..))))....((((((....))))))............................. (-14.10 = -15.86 +   1.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:07 2006