Locus 5658

Sequence ID 3R_DroMel_CAF1
Location 14,849,969 – 14,850,249
Length 280
Max. P 0.999868
window9245 window9246 window9247 window9248 window9249

overview

Window 5

Location 14,849,969 – 14,850,089
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.08
Mean single sequence MFE -38.85
Consensus MFE -34.12
Energy contribution -33.80
Covariance contribution -0.32
Combinations/Pair 1.18
Mean z-score -1.23
Structure conservation index 0.88
SVM decision value 0.22
SVM RNA-class probability 0.639841
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14849969 120 - 27905053
ACCUUUAUGUUCUUGGCAGUAUCUUCGGCCACUUUUUGCGCCAGUUUUCCGCUGUCGAGAGCAGUUUGCAACUGCUGCACACACCAGCAGAGCUCCACUUCGAACUGGGUGACAAGGUCG
(((((..(((((((((((((.....((((((.....)).))).)......)))))))))))))...((((.....))))(((.((((..(((......)))...)))))))..))))).. ( -37.30)
>DroSec_CAF1 3206 120 - 1
ACCUUUAUGUUCUUGGCGGUAUCUUCGGCCACUUUCUGGGCCAAUUUUCCGCUGUCGAGAGCAGUUUGCAACUGCUGCACACACCAGCAGAGUUCCACUUCGAACUGGGUGACGAGAUCG
.......(((((((((((((......((((.(.....)))))........)))))))))))))...((.((((.((((........)))))))).))...(((.((.(....).)).))) ( -39.54)
>DroSim_CAF1 4018 120 - 1
ACCUUUAUGUUCUUGGCGGUAUCUUCGGCCACUUUCUGGGCCAGUUUUCCGCUGUCGAGAGCAGUUUGCAACUGCUGCACACACCAGCAGAGUUCCACUUCGAGCUGGGUGACGAGAUCG
.......(((((((((((((.....(((((.(.....))))).)......)))))))))))))...((((.....))))(((.(((((.(((......)))..))))))))......... ( -40.30)
>DroEre_CAF1 3377 120 - 1
ACCUUUAUGUUCUUGGCGGUAUCUUCGGCCACUUUCUGGGCCAGUUUUCCGCUUUCAAGGGCGGUUUGCAACUGCUGCACACACCAGCAGAGCUCCACUUCAAACUGGGUGACGAGGUCC
..........(((((((((((.....((((.(.....))))).((...((((((....))))))...))...)))))).(((.((((..(((......)))...))))))).)))))... ( -37.60)
>DroYak_CAF1 3814 120 - 1
ACCUUUAUGUUCUUGGCGGUAUCUUCGGCCACUUUCUGGGCCAGCUUUCCGCUUUCAAGAGCGGUUUUCAACUGCUGCACACACCAGCAGAGCUCCACUUCGAACUGGGUGACAAGGUUU
(((((...((((..((.((.......((((.(.....)))))((((..((((((....)))))).......((((((.......)))))))))))).))..))))..(....)))))).. ( -39.50)
>consensus
ACCUUUAUGUUCUUGGCGGUAUCUUCGGCCACUUUCUGGGCCAGUUUUCCGCUGUCGAGAGCAGUUUGCAACUGCUGCACACACCAGCAGAGCUCCACUUCGAACUGGGUGACGAGGUCG
((((....((((((((((((......((((........))))........))))))))))))((((((...((((((.......))))))((.....)).)))))))))).......... (-34.12 = -33.80 +  -0.32)

alignment

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secondary structure

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Window 6

Location 14,850,009 – 14,850,129
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.67
Mean single sequence MFE -37.92
Consensus MFE -31.48
Energy contribution -31.92
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.40
Structure conservation index 0.83
SVM decision value 0.24
SVM RNA-class probability 0.647014
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14850009 120 + 27905053
GUGCAGCAGUUGCAAACUGCUCUCGACAGCGGAAAACUGGCGCAAAAAGUGGCCGAAGAUACUGCCAAGAACAUAAAGGUACUAACCAGUUCAACAGCGCCGCUCAUCAGGAAGCGGCAG
..((.(((((..(...(((((......))))).....((((.((.....))))))..)..)))))...((((.....(((....))).))))....))((((((........)))))).. ( -33.90)
>DroSec_CAF1 3246 120 + 1
GUGCAGCAGUUGCAAACUGCUCUCGACAGCGGAAAAUUGGCCCAGAAAGUGGCCGAAGAUACCGCCAAGAACAUAAAGGUGCUGACCAGCUCAACAGCGCCGCUCAUCAGGAAGCGGCAG
(.((((((((.....)))))).....((((((....(((((((.....).)))))).....))(((...........)))))))....)).)......((((((........)))))).. ( -37.70)
>DroSim_CAF1 4058 120 + 1
GUGCAGCAGUUGCAAACUGCUCUCGACAGCGGAAAACUGGCCCAGAAAGUGGCCGAAGAUACCGCCAAGAACAUAAAGGUGCUGACCAGCUCAACAGCGCCGCUCGUCAGAAAGCGGCAG
.(((.(((((.....)))))(((.(((.((((.....((((((.....).)))))......))))............(((((((..........)))))))....)))))).....))). ( -38.60)
>DroEre_CAF1 3417 120 + 1
GUGCAGCAGUUGCAAACCGCCCUUGAAAGCGGAAAACUGGCCCAGAAAGUGGCCGAAGAUACCGCCAAGAACAUAAAGGUCCUGACCAGCUCAACGGCGCCGCUCAUCAGGAAGCGGCAG
.(((((...)))))....(((.((((..((((.....((((((.....).)))))......))))............(((....)))...)))).)))((((((........)))))).. ( -38.60)
>DroYak_CAF1 3854 120 + 1
GUGCAGCAGUUGAAAACCGCUCUUGAAAGCGGAAAGCUGGCCCAGAAAGUGGCCGAAGAUACCGCCAAGAACAUAAAGGUCCUGACCAGCUCAACAGCGCCGCUCAUCAGAAAGCGGCAG
.....((.(((((...(((((......)))))...(((((..(((....((((.(......).)))).((.(.....).))))).)))))))))).))((((((........)))))).. ( -40.80)
>consensus
GUGCAGCAGUUGCAAACUGCUCUCGACAGCGGAAAACUGGCCCAGAAAGUGGCCGAAGAUACCGCCAAGAACAUAAAGGUCCUGACCAGCUCAACAGCGCCGCUCAUCAGGAAGCGGCAG
..((.(((((.....)))))....((..((((.....(((((........)))))......))))............(((....)))...))....))((((((........)))))).. (-31.48 = -31.92 +   0.44)

alignment

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secondary structure

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Window 7

Location 14,850,009 – 14,850,129
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.67
Mean single sequence MFE -46.59
Consensus MFE -42.94
Energy contribution -42.58
Covariance contribution -0.36
Combinations/Pair 1.14
Mean z-score -2.55
Structure conservation index 0.92
SVM decision value 4.31
SVM RNA-class probability 0.999868
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14850009 120 - 27905053
CUGCCGCUUCCUGAUGAGCGGCGCUGUUGAACUGGUUAGUACCUUUAUGUUCUUGGCAGUAUCUUCGGCCACUUUUUGCGCCAGUUUUCCGCUGUCGAGAGCAGUUUGCAACUGCUGCAC
..(((((((......)))))))((.((((.((((((....))).....((((((((((((.....((((((.....)).))).)......)))))))))))))))...)))).))..... ( -42.80)
>DroSec_CAF1 3246 120 - 1
CUGCCGCUUCCUGAUGAGCGGCGCUGUUGAGCUGGUCAGCACCUUUAUGUUCUUGGCGGUAUCUUCGGCCACUUUCUGGGCCAAUUUUCCGCUGUCGAGAGCAGUUUGCAACUGCUGCAC
..(((((((......)))))))((.((((.(((....))).......(((((((((((((......((((.(.....)))))........))))))))))))).....)))).))..... ( -45.94)
>DroSim_CAF1 4058 120 - 1
CUGCCGCUUUCUGACGAGCGGCGCUGUUGAGCUGGUCAGCACCUUUAUGUUCUUGGCGGUAUCUUCGGCCACUUUCUGGGCCAGUUUUCCGCUGUCGAGAGCAGUUUGCAACUGCUGCAC
..(((((((......)))))))((.((((.(((....))).......(((((((((((((.....(((((.(.....))))).)......))))))))))))).....)))).))..... ( -46.10)
>DroEre_CAF1 3417 120 - 1
CUGCCGCUUCCUGAUGAGCGGCGCCGUUGAGCUGGUCAGGACCUUUAUGUUCUUGGCGGUAUCUUCGGCCACUUUCUGGGCCAGUUUUCCGCUUUCAAGGGCGGUUUGCAACUGCUGCAC
..(((((((......)))))))((.(((((((((((((((((......)))))((((.(......).)))).......))))))))..((((((....))))))....)))).))..... ( -46.60)
>DroYak_CAF1 3854 120 - 1
CUGCCGCUUUCUGAUGAGCGGCGCUGUUGAGCUGGUCAGGACCUUUAUGUUCUUGGCGGUAUCUUCGGCCACUUUCUGGGCCAGCUUUCCGCUUUCAAGAGCGGUUUUCAACUGCUGCAC
..(((((((......)))))))((.(((((((((((((((((......)))))((((.(......).)))).......)))))))...((((((....))))))...))))).))..... ( -51.50)
>consensus
CUGCCGCUUCCUGAUGAGCGGCGCUGUUGAGCUGGUCAGCACCUUUAUGUUCUUGGCGGUAUCUUCGGCCACUUUCUGGGCCAGUUUUCCGCUGUCGAGAGCAGUUUGCAACUGCUGCAC
..(((((((......)))))))((.((((.((((((....))).....((((((((((((......((((........))))........)))))))))))))))...)))).))..... (-42.94 = -42.58 +  -0.36)

alignment

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secondary structure

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Window 8

Location 14,850,089 – 14,850,209
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.17
Mean single sequence MFE -41.20
Consensus MFE -35.38
Energy contribution -35.42
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.24
Structure conservation index 0.86
SVM decision value 0.04
SVM RNA-class probability 0.551985
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14850089 120 + 27905053
ACUAACCAGUUCAACAGCGCCGCUCAUCAGGAAGCGGCAGGUGAUGAAGCUAGCCCUGGGCGACUACCGAGCGAAGAUGCAGCAGGAGGAGCAGAAGUUGCUACUAGCCUCCAGGCAAAU
.......((((((.((.(((((((........)))))).).)).)).)))).(((.((((.(.(((...(((((...(((..........)))....)))))..)))).))))))).... ( -36.10)
>DroSec_CAF1 3326 120 + 1
GCUGACCAGCUCAACAGCGCCGCUCAUCAGGAAGCGGCAGGUGAUGAAGCUAGCCCUGGGCGACUACCGAGCGAAGAUGCAGCAGGAGGAGCAGAAAUUGCUACUAGCCUCCAAGCAAAU
((((....((((......((((((........)))))).((((.....(((.......)))...)))))))).......)))).((((((((((...))))).....)))))........ ( -40.10)
>DroSim_CAF1 4138 120 + 1
GCUGACCAGCUCAACAGCGCCGCUCGUCAGAAAGCGGCAGGUGAUGAAGCUAGCUCUGGGCGACUACCGAGCGAAGAUGCAGCAGGAGGAGCAGAAGUUGCUACUAGCCUCCAAACAAAU
((((...((((((.((.(((((((........)))))).).)).)).)))).((((.((.......)))))).......)))).((((((((((...))))).....)))))........ ( -43.30)
>DroEre_CAF1 3497 120 + 1
CCUGACCAGCUCAACGGCGCCGCUCAUCAGGAAGCGGCAGGUGAUGAAGCUAGCCCUGGGCGACUACCGAGCGAAGAUGCAGCAGGAGGAGCAGAAAAUGCUUCUAGCCUCCCGGCAAAU
((((....(((((..(((((((((........)))))).(((......))).))).))))).........((......))..))))(((((((.....))))))).(((....))).... ( -43.00)
>DroYak_CAF1 3934 120 + 1
CCUGACCAGCUCAACAGCGCCGCUCAUCAGAAAGCGGCAGGUGAUGAAGCUAGCCCUUGGCGACUACCGAGCGAAGAUGCAGCAGGAGGAGCAGAAAAUGCUUCUAGCCUCCAGGCAAAU
((((...((((((.((.(((((((........)))))).).)).)).)))).((.(((.((.........)).)))..))..))))(((((((.....))))))).(((....))).... ( -43.50)
>consensus
CCUGACCAGCUCAACAGCGCCGCUCAUCAGGAAGCGGCAGGUGAUGAAGCUAGCCCUGGGCGACUACCGAGCGAAGAUGCAGCAGGAGGAGCAGAAAUUGCUACUAGCCUCCAGGCAAAU
........((((......((((((........)))))).((((.....(((.......)))...)))))))).....(((....(((((((((.....)))).....)))))..)))... (-35.38 = -35.42 +   0.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,850,129 – 14,850,249
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -38.28
Consensus MFE -32.76
Energy contribution -32.88
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -1.32
Structure conservation index 0.86
SVM decision value 0.17
SVM RNA-class probability 0.617917
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14850129 120 - 27905053
GCUAGACUUUUUGGAUGAUUCAGCCGUAGGUGUGAAUUUGAUUUGCCUGGAGGCUAGUAGCAACUUCUGCUCCUCCUGCUGCAUCUUCGCUCGGUAGUCGCCCAGGGCUAGCUUCAUCAC
(((((.((..((((.(((((..((((.....(((((..((....((..(((((..(((((......)))))))))).))..))..))))).))))))))).)))))))))))........ ( -39.90)
>DroSec_CAF1 3366 120 - 1
GCUAGACUUUUUGGAUGAUUCAGCCGUUGGUGUGAAUUUGAUUUGCUUGGAGGCUAGUAGCAAUUUCUGCUCCUCCUGCUGCAUCUUCGCUCGGUAGUCGCCCAGGGCUAGCUUCAUCAC
(((((.((..((((.(((((..((((.....(((((..((....((..(((((..(((((......)))))))))).))..))..))))).))))))))).)))))))))))........ ( -40.00)
>DroSim_CAF1 4178 120 - 1
GCUAGACUUUUUGGAUGAUUCAGCCGUUGGUGUGAAUUUGAUUUGUUUGGAGGCUAGUAGCAACUUCUGCUCCUCCUGCUGCAUCUUCGCUCGGUAGUCGCCCAGAGCUAGCUUCAUCAC
(((((.(((..(((.(((((..((((.....(((((..((....((..(((((..(((((......)))))))))).))..))..))))).))))))))).)))))))))))........ ( -39.00)
>DroEre_CAF1 3537 120 - 1
GCUAGACUUUUUGGAUGCUUCAGCCGUAGGUGUGAAUUUGAUUUGCCGGGAGGCUAGAAGCAUUUUCUGCUCCUCCUGCUGCAUCUUCGCUCGGUAGUCGCCCAGGGCUAGCUUCAUCAC
(((((.((..((((..((..(.((((.....(((((..((....((.((((((.((((((...))))))..))))))))..))..))))).)))).)..)))))))))))))........ ( -37.40)
>DroYak_CAF1 3974 120 - 1
GCUAGACUUUUUGGAUGCUUCAGUCGUAGGUGUAAAUUUGAUUUGCCUGGAGGCUAGAAGCAUUUUCUGCUCCUCCUGCUGCAUCUUCGCUCGGUAGUCGCCAAGGGCUAGCUUCAUCAC
(((((.(((((.((..(((((((.((.(((((((..........((..(((((.((((((...))))))..))))).))))))))).)))).)).)))..))))))))))))........ ( -35.10)
>consensus
GCUAGACUUUUUGGAUGAUUCAGCCGUAGGUGUGAAUUUGAUUUGCCUGGAGGCUAGUAGCAAUUUCUGCUCCUCCUGCUGCAUCUUCGCUCGGUAGUCGCCCAGGGCUAGCUUCAUCAC
(((((.((((..((.(((((..((((.....(((((..((....((..(((((.....((((.....))))))))).))..))..))))).))))))))))).)))))))))........ (-32.76 = -32.88 +   0.12)

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 12:00:59 2006