Locus 2515

Sequence ID 3L_DroMel_CAF1
Location 7,068,848 – 7,068,979
Length 131
Max. P 0.990791
window3900 window3901 window3902 window3903

overview

Window 0

Location 7,068,848 – 7,068,957
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.19
Mean single sequence MFE -37.80
Consensus MFE -31.18
Energy contribution -32.34
Covariance contribution 1.16
Combinations/Pair 1.15
Mean z-score -1.76
Structure conservation index 0.82
SVM decision value 0.94
SVM RNA-class probability 0.886968
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7068848 109 + 23771897
CGUGGUGUUUAGUGU----------UGUUUCGCGUUGUUUUCAGUUGUUUUGAGCCGAGAACUCUCCGCUCAGCGGCGACUGCGAAUGCAAAUGCAAAGUGCAUGUGCAGCCAACAGCU-
.............((----------((((..((...((((.((((((((((((((.(((....))).)))))).)))))))).))))(((.((((.....)))).))).)).)))))).- ( -38.70)
>DroSec_CAF1 81427 110 + 1
CGUGGUGUUUAGUGU----------UGUUUCGCGCUGUUUUCAGUUGUUUUGAGCCGAGAACUCUCCGCUCAGCGGCGACUGCGAAUGCAAAUGCAAAGUGCAUGUGCAGCCAUCAGCUA
.(((((...((((((----------......))))))(((.((((((((((((((.(((....))).)))))).)))))))).)))((((.((((.....)))).)))))))))...... ( -39.90)
>DroSim_CAF1 114159 110 + 1
CGUGGUGUUUAGUGU----------UGUUUCGCGCUGUUUUCAGUUGUUUUGAGCCGAGAACUCUCCGCUCAGCGGCGACUGCGAAUGCAAAUGCAAAGUGCAUGUGCAGCCAUCAGCUA
.(((((...((((((----------......))))))(((.((((((((((((((.(((....))).)))))).)))))))).)))((((.((((.....)))).)))))))))...... ( -39.90)
>DroEre_CAF1 97699 108 + 1
CGUGGUGUUUAGUGU----------UGUUUCGCGUUGUUUUCAGUUGCUUUGAGCCGCGAACU--CCGCUCAGCGGCAAUUGCAAAUGCAAAUGCAAAGUGCAUGUGCAGCCACAAGCUA
.((((((((.((((.----------.(((.((((..((..((((.....))))))))))))).--.)))).))).(((..((((..(((....)))...))))..))).)))))...... ( -35.10)
>DroYak_CAF1 95970 113 + 1
CGUGGUGUUUAGUGUUGUUCGGUGUUGUUUCGCGUUGUUUUCAGUUGCUUUGAGCCGAGAACU--CCGCUCAGCGGCAA-----AUUGCAAAUGCAAAGUGCAUGUGCAGCCAUCACCUA
.((((((...............(((((((..(((..((((((.(((......))).)))))).--.)))..))))))).-----.(((((.((((.....)))).))))).))))))... ( -35.40)
>consensus
CGUGGUGUUUAGUGU__________UGUUUCGCGUUGUUUUCAGUUGUUUUGAGCCGAGAACUCUCCGCUCAGCGGCGACUGCGAAUGCAAAUGCAAAGUGCAUGUGCAGCCAUCAGCUA
.(((((..............................((((.((((((((((((((.(((....))).)))))).)))))))).))))(((.((((.....)))).))).)))))...... (-31.18 = -32.34 +   1.16)

alignment

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secondary structure

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Window 1

Location 7,068,848 – 7,068,957
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.19
Mean single sequence MFE -32.10
Consensus MFE -24.44
Energy contribution -25.12
Covariance contribution 0.68
Combinations/Pair 1.04
Mean z-score -1.93
Structure conservation index 0.76
SVM decision value 0.68
SVM RNA-class probability 0.821340
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7068848 109 - 23771897
-AGCUGUUGGCUGCACAUGCACUUUGCAUUUGCAUUCGCAGUCGCCGCUGAGCGGAGAGUUCUCGGCUCAAAACAACUGAAAACAACGCGAAACA----------ACACUAAACACCACG
-((.(((((..((((.((((.....)))).))))((((((((....)))((((.(((....))).))))..................))))).))----------))))).......... ( -32.80)
>DroSec_CAF1 81427 110 - 1
UAGCUGAUGGCUGCACAUGCACUUUGCAUUUGCAUUCGCAGUCGCCGCUGAGCGGAGAGUUCUCGGCUCAAAACAACUGAAAACAGCGCGAAACA----------ACACUAAACACCACG
..((((.((..((((.((((.....)))).))))..))))))...((((((((.(((....))).)))))......(((....))).))).....----------............... ( -32.80)
>DroSim_CAF1 114159 110 - 1
UAGCUGAUGGCUGCACAUGCACUUUGCAUUUGCAUUCGCAGUCGCCGCUGAGCGGAGAGUUCUCGGCUCAAAACAACUGAAAACAGCGCGAAACA----------ACACUAAACACCACG
..((((.((..((((.((((.....)))).))))..))))))...((((((((.(((....))).)))))......(((....))).))).....----------............... ( -32.80)
>DroEre_CAF1 97699 108 - 1
UAGCUUGUGGCUGCACAUGCACUUUGCAUUUGCAUUUGCAAUUGCCGCUGAGCGG--AGUUCGCGGCUCAAAGCAACUGAAAACAACGCGAAACA----------ACACUAAACACCACG
......((((.((((.((((.....)))).))))(((((....(((((.((((..--.)))))))))(((.......))).......)))))...----------..........)))). ( -31.10)
>DroYak_CAF1 95970 113 - 1
UAGGUGAUGGCUGCACAUGCACUUUGCAUUUGCAAU-----UUGCCGCUGAGCGG--AGUUCUCGGCUCAAAGCAACUGAAAACAACGCGAAACAACACCGAACAACACUAAACACCACG
..((((..(((((((.((((.....)))).))))..-----..)))(((((((.(--(....)).))))..)))......................)))).................... ( -31.00)
>consensus
UAGCUGAUGGCUGCACAUGCACUUUGCAUUUGCAUUCGCAGUCGCCGCUGAGCGGAGAGUUCUCGGCUCAAAACAACUGAAAACAACGCGAAACA__________ACACUAAACACCACG
.......(((.((((.((((.....)))).))))(((((....((((..((((.....)))).))))(((.......))).......))))).......................))).. (-24.44 = -25.12 +   0.68)

alignment

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secondary structure

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Window 2

Location 7,068,878 – 7,068,979
Length 101
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 87.43
Mean single sequence MFE -31.64
Consensus MFE -27.40
Energy contribution -28.40
Covariance contribution 1.00
Combinations/Pair 1.10
Mean z-score -2.26
Structure conservation index 0.87
SVM decision value 2.23
SVM RNA-class probability 0.990791
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7068878 101 + 23771897
UCAGUUGUUUUGAGCCGAGAACUCUCCGCUCAGCGGCGACUGCGAAUGCAAAUGCAAAGUGCAUGUGCAGCCAACAGCU-UUAUUUUGUUUUGGUUUUUGAU---------
.((((((((((((((.(((....))).)))))).))))))))((((((((.((((.....)))).))))(((((.(((.-.......)))))))).))))..--------- ( -35.70)
>DroSec_CAF1 81457 102 + 1
UCAGUUGUUUUGAGCCGAGAACUCUCCGCUCAGCGGCGACUGCGAAUGCAAAUGCAAAGUGCAUGUGCAGCCAUCAGCUAUUAUUUUGUUUUGGUUUUUGAU---------
.((((((((((((((.(((....))).)))))).))))))))((((((((.((((.....)))).))))((((..(((.........))).)))).))))..--------- ( -33.70)
>DroSim_CAF1 114189 102 + 1
UCAGUUGUUUUGAGCCGAGAACUCUCCGCUCAGCGGCGACUGCGAAUGCAAAUGCAAAGUGCAUGUGCAGCCAUCAGCUAUUAUUUUGUUUUGGUUUUUGAU---------
.((((((((((((((.(((....))).)))))).))))))))((((((((.((((.....)))).))))((((..(((.........))).)))).))))..--------- ( -33.70)
>DroEre_CAF1 97729 104 + 1
UCAGUUGCUUUGAGCCGCGAACU--CCGCUCAGCGGCAAUUGCAAAUGCAAAUGCAAAGUGCAUGUGCAGCCACAAGCUAUUAUUUUGUUUUGGUUUUUCGUUUUG-----
.((((((((((((((.(......--).)))))).))))))))....((((.((((.....)))).))))((((.((((.........))))))))...........----- ( -28.90)
>DroYak_CAF1 96010 104 + 1
UCAGUUGCUUUGAGCCGAGAACU--CCGCUCAGCGGCAA-----AUUGCAAAUGCAAAGUGCAUGUGCAGCCAUCACCUAAUAUUUUGUUUUGGUUUUUGAUUUUUGUAUU
(((((((((((((((.((....)--).)))))).)))))-----..((((.((((.....)))).))))((((..((..........))..))))..)))).......... ( -26.20)
>consensus
UCAGUUGUUUUGAGCCGAGAACUCUCCGCUCAGCGGCGACUGCGAAUGCAAAUGCAAAGUGCAUGUGCAGCCAUCAGCUAUUAUUUUGUUUUGGUUUUUGAU_________
.((((((((((((((.(((....))).)))))).))))))))....((((.((((.....)))).))))((((...((.........))..))))................ (-27.40 = -28.40 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,068,878 – 7,068,979
Length 101
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 87.43
Mean single sequence MFE -28.62
Consensus MFE -21.16
Energy contribution -21.96
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.65
Structure conservation index 0.74
SVM decision value 1.51
SVM RNA-class probability 0.960237
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7068878 101 - 23771897
---------AUCAAAAACCAAAACAAAAUAA-AGCUGUUGGCUGCACAUGCACUUUGCAUUUGCAUUCGCAGUCGCCGCUGAGCGGAGAGUUCUCGGCUCAAAACAACUGA
---------.(((..................-(((.((.((((((..(((((.........)))))..)))))))).)))((((.(((....))).))))........))) ( -29.50)
>DroSec_CAF1 81457 102 - 1
---------AUCAAAAACCAAAACAAAAUAAUAGCUGAUGGCUGCACAUGCACUUUGCAUUUGCAUUCGCAGUCGCCGCUGAGCGGAGAGUUCUCGGCUCAAAACAACUGA
---------.(((...................(((.(.(((((((..(((((.........)))))..)))))))).)))((((.(((....))).))))........))) ( -29.40)
>DroSim_CAF1 114189 102 - 1
---------AUCAAAAACCAAAACAAAAUAAUAGCUGAUGGCUGCACAUGCACUUUGCAUUUGCAUUCGCAGUCGCCGCUGAGCGGAGAGUUCUCGGCUCAAAACAACUGA
---------.(((...................(((.(.(((((((..(((((.........)))))..)))))))).)))((((.(((....))).))))........))) ( -29.40)
>DroEre_CAF1 97729 104 - 1
-----CAAAACGAAAAACCAAAACAAAAUAAUAGCUUGUGGCUGCACAUGCACUUUGCAUUUGCAUUUGCAAUUGCCGCUGAGCGG--AGUUCGCGGCUCAAAGCAACUGA
-----............................(((((..(.((((.((((.....)))).)))).)..)....(((((.((((..--.)))))))))...))))...... ( -28.90)
>DroYak_CAF1 96010 104 - 1
AAUACAAAAAUCAAAAACCAAAACAAAAUAUUAGGUGAUGGCUGCACAUGCACUUUGCAUUUGCAAU-----UUGCCGCUGAGCGG--AGUUCUCGGCUCAAAGCAACUGA
..............................((((.....(((((((.((((.....)))).))))..-----..)))(((((((.(--(....)).))))..)))..)))) ( -25.90)
>consensus
_________AUCAAAAACCAAAACAAAAUAAUAGCUGAUGGCUGCACAUGCACUUUGCAUUUGCAUUCGCAGUCGCCGCUGAGCGGAGAGUUCUCGGCUCAAAACAACUGA
.......................................(((((((.((((.....)))).)))).........)))..(((((.(((....))).))))).......... (-21.16 = -21.96 +   0.80)

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 10:34:34 2006