Locus 5504

Sequence ID X_DroMel_CAF1
Location 14,271,311 – 14,271,511
Length 200
Max. P 0.999248
window8929 window8930 window8931

overview

Window 9

Location 14,271,311 – 14,271,414
Length 103
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 94.29
Mean single sequence MFE -16.58
Consensus MFE -15.18
Energy contribution -15.38
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.20
Structure conservation index 0.92
SVM decision value 3.46
SVM RNA-class probability 0.999248
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14271311 103 + 22224390
AACACCCAACACCCUGUCGUCCUUGCAAAAGUUUUAAUCUUAAAUCAACCAAACGACGACAAAUGUUCACAAGCAAUUUCUUGUGCUUAGCAAAUAUUUACCC
..............(((((((.((......((((.......))))......)).)))))))..((((((((((......))))))...))))........... ( -15.60)
>DroSec_CAF1 11912 101 + 1
--CACCCAUCACUCUGUCGUCCUUGCAAAAGUUUUAAUCUUAAAUCAACCAAACGACGACAAAUGUUCACAAGCAAUUUCUUGUGCUUAGCAAAUAUUUACCC
--............(((((((.((......((((.......))))......)).)))))))..((((((((((......))))))...))))........... ( -15.60)
>DroSim_CAF1 15938 101 + 1
--CACCCAGCACACUGUCGUCCUUGCAAAAGUUUUAAUCUUAAAUCAACCAAACGACGACAAAUGUUCACAAGCAAUUUCUUGUGCUUAGCAAAUAUUUACCC
--......((....(((((((.((......((((.......))))......)).)))))))..((..((((((......))))))..))))............ ( -16.90)
>DroEre_CAF1 14357 99 + 1
----CACGGCAAACUGUCGUCAUGGCAAAAGUUUUAAUCUUAAAUCAACCAAACGACGACAAAUGUUCACAAGCAAUUUCUUGUGCUUAGCAAAUAUUUACCC
----....((....(((((((.(((.....((((.......))))...)))...)))))))..((..((((((......))))))..))))............ ( -17.90)
>DroYak_CAF1 15004 99 + 1
----CACAGCACACUGUCGUCAUUGCAAAAGUUUUAAUCUUAAAUCAACCAAACGACGACAAAUGUUCACAAGCAAUUUCUUGUGCUUAGCAAAUAUUUACCC
----....((....(((((((.((......((((.......))))......)).)))))))..((..((((((......))))))..))))............ ( -16.90)
>consensus
__CACCCAGCACACUGUCGUCCUUGCAAAAGUUUUAAUCUUAAAUCAACCAAACGACGACAAAUGUUCACAAGCAAUUUCUUGUGCUUAGCAAAUAUUUACCC
..............(((((((.((......((((.......))))......)).)))))))..((((((((((......))))))...))))........... (-15.18 = -15.38 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,271,311 – 14,271,414
Length 103
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 94.29
Mean single sequence MFE -24.68
Consensus MFE -20.22
Energy contribution -20.42
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.49
Structure conservation index 0.82
SVM decision value 0.29
SVM RNA-class probability 0.669663
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14271311 103 - 22224390
GGGUAAAUAUUUGCUAAGCACAAGAAAUUGCUUGUGAACAUUUGUCGUCGUUUGGUUGAUUUAAGAUUAAAACUUUUGCAAGGACGACAGGGUGUUGGGUGUU
.(((((....)))))...((((((......))))))(((((((((((((.(((((((.......))))))).(((....)))))))))).))))))....... ( -24.40)
>DroSec_CAF1 11912 101 - 1
GGGUAAAUAUUUGCUAAGCACAAGAAAUUGCUUGUGAACAUUUGUCGUCGUUUGGUUGAUUUAAGAUUAAAACUUUUGCAAGGACGACAGAGUGAUGGGUG--
.(((((....)))))...((((((......)))))).((.(((((((((.(((((((.......))))))).(((....))))))))))))))........-- ( -22.80)
>DroSim_CAF1 15938 101 - 1
GGGUAAAUAUUUGCUAAGCACAAGAAAUUGCUUGUGAACAUUUGUCGUCGUUUGGUUGAUUUAAGAUUAAAACUUUUGCAAGGACGACAGUGUGCUGGGUG--
............(((.((((((((......)))))..(((((.((((((.(((((((.......))))))).(((....))))))))))))))))).))).-- ( -24.10)
>DroEre_CAF1 14357 99 - 1
GGGUAAAUAUUUGCUAAGCACAAGAAAUUGCUUGUGAACAUUUGUCGUCGUUUGGUUGAUUUAAGAUUAAAACUUUUGCCAUGACGACAGUUUGCCGUG----
.(((((((..........((((((......))))))......((((((((..((((.(.((((....)))).)....)))))))))))))))))))...---- ( -28.00)
>DroYak_CAF1 15004 99 - 1
GGGUAAAUAUUUGCUAAGCACAAGAAAUUGCUUGUGAACAUUUGUCGUCGUUUGGUUGAUUUAAGAUUAAAACUUUUGCAAUGACGACAGUGUGCUGUG----
.(((((....))))).((((((((......)))))..(((((.(((((((((.((((.............)))).....)))))))))))))))))...---- ( -24.12)
>consensus
GGGUAAAUAUUUGCUAAGCACAAGAAAUUGCUUGUGAACAUUUGUCGUCGUUUGGUUGAUUUAAGAUUAAAACUUUUGCAAGGACGACAGUGUGCUGGGUG__
.(((((....)))))...((((((......))))))..(((((((((((((..((((.............))))...))...)))))))).)))......... (-20.22 = -20.42 +   0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,271,414 – 14,271,511
Length 97
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 82.18
Mean single sequence MFE -16.54
Consensus MFE -14.52
Energy contribution -14.96
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -1.61
Structure conservation index 0.88
SVM decision value 0.45
SVM RNA-class probability 0.741440
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14271414 97 - 22224390
GUUGGCACUCCACACCCAACCC--ACACUCUUCGCCCCCGCUGCCAACGCCCAUUUAAGCUAAAAAGUAAACCAAUUGUUAGUUUUAAUGGAAUUUAUU
(((((((...............--.................)))))))..(((((.(((((((.((.........)).))))))).)))))........ ( -17.35)
>DroSec_CAF1 12013 93 - 1
GUUGGCACUCCAC--CC-ACCCCCG--CUCUUCGCC-CCGCUGCCAACGACCAUUUAAGCUAAAAAGUAAACCAAUUGUUAGUUUUAAUGGAAUUUAUU
(((((((......--..-.......--.........-....)))))))..(((((.(((((((.((.........)).))))))).)))))........ ( -17.69)
>DroSim_CAF1 16039 96 - 1
GUUGGCACCCCAC--CC-AUCCCCACACUCCUCGCCCCCGCUGCCAACGACCAUUUAAGCUAAAAAGUAAACCAAUUGUUAGUUUUAAUGGAAUUUAUU
(((((((......--..-.......................)))))))..(((((.(((((((.((.........)).))))))).)))))........ ( -17.58)
>DroEre_CAF1 14456 77 - 1
GUUGCC--UCCAC--A-----------------CGC-CCCCUGCUCACGCCCAUUUAAGCUAAAAAGUAAACCAAUUGUUAGUUUUAAUGGAAUUUAUU
......--.....--.-----------------.((-.....))......(((((.(((((((.((.........)).))))))).)))))........ (  -9.30)
>DroYak_CAF1 15103 95 - 1
GUUGGCACUCCAC--AG-CCCGGCACACUUUUCUGC-UCCCUGCCAACGCCCAUUUAAGCUAAAAAGUAAACCAAUUGUUAGUUUUAAUGGAAUUUAUU
(((((((.....(--((-...((....))...))).-....)))))))..(((((.(((((((.((.........)).))))))).)))))........ ( -20.80)
>consensus
GUUGGCACUCCAC__CC_ACCC_CACACUCUUCGCC_CCGCUGCCAACGCCCAUUUAAGCUAAAAAGUAAACCAAUUGUUAGUUUUAAUGGAAUUUAUU
(((((((..................................)))))))..(((((.(((((((.((.........)).))))))).)))))........ (-14.52 = -14.96 +   0.44)

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 11:49:33 2006