Locus 199

Sequence ID 2L_DroMel_CAF1
Location 595,416 – 595,563
Length 147
Max. P 0.914638
window296 window297 window298

overview

Window 6

Location 595,416 – 595,526
Length 110
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.58
Mean single sequence MFE -29.47
Consensus MFE -18.10
Energy contribution -18.43
Covariance contribution 0.33
Combinations/Pair 1.05
Mean z-score -2.32
Structure conservation index 0.61
SVM decision value 1.10
SVM RNA-class probability 0.914638
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 595416 110 - 22407834
AAAGGGAGAA---------AGAGCAAG-AGCAGCGCUUCUCCGUGGGCGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGCCAGAAACAUAAAAGCAUUAAUUUAGUCAUUAUCUUCUUAA
..(((((((.---------...((...-.)).((((((.((((....))))..))))))....((((((((.((((((......)))))).))))))))............))))))).. ( -34.80)
>DroVir_CAF1 33154 97 - 1
----------------------GCUGG-AGGAGCGUGCGCCCGAGCGAGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGCCAAAAACAUAAAAGCAUUAAUUUAGUCAUUAUCUUCUUAA
----------------------...((-((((..((((((.(((.......))).))))))..((((((((.((((((......)))))).))))))))............))))))... ( -28.20)
>DroGri_CAF1 32486 101 - 1
---GAGAGAA---------ACUGCUGA-AGAAGCGAGCC------CGAGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGCCAAAAACAUAAAAGCAUUAAUUUAGUCAUUAUCUUCUUAA
---(((((((---------(..(((((-(...(((..(.------........)..)))....((((((((.((((((......)))))).)))))))).))))))..)).)).)))).. ( -21.70)
>DroYak_CAF1 27025 120 - 1
AAAGGCAGAAAGAGCAGAAAGAGCAAGAAGCAGCGCUUCUCCGUGGGCGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGCCAGAAACAUAAAAGCAUUAAUUUAGUCAUUAUCUUCUUAA
.............((.......))((((((..((((((.((((....))))..))))))....((((((((.((((((......)))))).)))))))).............)))))).. ( -33.20)
>DroMoj_CAF1 31149 97 - 1
----------------------GUUGG-AGGAGCGUGCGCCCGAGCGAGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGCCAAAAACAUAAAAGCAUUAAUUUAGUCAUUAUCUUCUUAA
----------------------...((-((((..((((((.(((.......))).))))))..((((((((.((((((......)))))).))))))))............))))))... ( -28.20)
>DroAna_CAF1 27377 109 - 1
GAAGGGCUGU---------GGAGAGGG-AAGAGCGCAUC-CCGUGGGCGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGCCAAAAACAUAAAAGCAUUAAUUUAGUCAUUAUCUUCUUAA
(((((...((---------((..(((.-....((((.((-(((....)))...))))))....((((((((.((((((......)))))).)))))))).)))..))))..))))).... ( -30.70)
>consensus
___GGGAGAA_________AGAGCUGG_AGGAGCGCGCC_CCGUGCGAGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGCCAAAAACAUAAAAGCAUUAAUUUAGUCAUUAUCUUCUUAA
................................((((....((......)).....))))....((((((((.((((((......)))))).))))))))..................... (-18.10 = -18.43 +   0.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 595,456 – 595,563
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.71
Mean single sequence MFE -19.61
Consensus MFE -16.40
Energy contribution -16.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.42
Structure conservation index 0.84
SVM decision value 0.18
SVM RNA-class probability 0.619782
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 595456 107 + 22407834
GCAACACAUAAACAUCAUUAUGCGCUCAAUCCGCCCACGGAGAAGCGCUGCU-CUUGCUCU---------UUCUCCCUUUCUGAGCUUUAUCUUUAUCAU---CAUUCUUGCAGACGUUG
((((.................(((((...((((....))))..)))))....-...((((.---------............))))..............---.....))))........ ( -21.42)
>DroSec_CAF1 26778 110 + 1
GCAACACAUAAACAUCAUUAUGCGCUCAAUCCGCCCACGGAGAAGCGCUGCU-CUUGCUCU---------UUCUCCCUUUUCCAGCUUUAUCUUUAUCAUCUCCAUUCUUGCAGACGUUG
.((((..((((((........(((((...((((....))))..))))).((.-...))...---------..............).)))))........(((.((....)).))).)))) ( -18.40)
>DroSim_CAF1 25346 110 + 1
GCAACACAUAAACAUCAUUAUGCGCUCAAUCCGCCCACGGAGAAGCGCUGCU-CUUGCUCU---------UUCUCCCUUUGCCAGCUUUAUCUUUAUCAUCUCCAUUCUUGCAGACGUUG
.((((................(((((...((((....))))..))))).(((-...((...---------..........)).))).............(((.((....)).))).)))) ( -19.12)
>DroEre_CAF1 27123 111 + 1
GCAACACAUAAACAUCAUUAUGCGCUCAAUCCGCCCACGGAGAAGCGCUGCUUCUUGCUCU---------UUCUGCCUUUUCCAGCUUUAUCUUUAUCAUCUCCAUUCUUGCAGAUGUUA
..........((((((....((((((...((((....))))..)))((((......((...---------....))......))))........................))))))))). ( -22.10)
>DroYak_CAF1 27065 109 + 1
GCAACACAUAAACAUCAUUAUGCGCUCAAUCCGCCCACGGAGAAGCGCUGCUUCUUGCUCUUUCUGCUCUUUCUGCCUUUUCCAGCUUUAUCUUUAUCAUCUCCGUUCU-----------
(((..................(((((...((((....))))..))))).((.....))......)))..........................................----------- ( -17.00)
>consensus
GCAACACAUAAACAUCAUUAUGCGCUCAAUCCGCCCACGGAGAAGCGCUGCU_CUUGCUCU_________UUCUCCCUUUUCCAGCUUUAUCUUUAUCAUCUCCAUUCUUGCAGACGUUG
((...................(((((...((((....))))..))))).((.....))..........................)).................................. (-16.40 = -16.40 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 595,456 – 595,563
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.71
Mean single sequence MFE -28.44
Consensus MFE -21.44
Energy contribution -23.12
Covariance contribution 1.68
Combinations/Pair 1.03
Mean z-score -1.77
Structure conservation index 0.75
SVM decision value 0.38
SVM RNA-class probability 0.713937
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 595456 107 - 22407834
CAACGUCUGCAAGAAUG---AUGAUAAAGAUAAAGCUCAGAAAGGGAGAA---------AGAGCAAG-AGCAGCGCUUCUCCGUGGGCGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGC
...((((..(.......---........((......))......((((((---------.(.((...-....)).))))))))..)))).....(((((((((......))))))))).. ( -28.10)
>DroSec_CAF1 26778 110 - 1
CAACGUCUGCAAGAAUGGAGAUGAUAAAGAUAAAGCUGGAAAAGGGAGAA---------AGAGCAAG-AGCAGCGCUUCUCCGUGGGCGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGC
...((((..(.........................((.....))((((((---------.(.((...-....)).))))))))..)))).....(((((((((......))))))))).. ( -28.30)
>DroSim_CAF1 25346 110 - 1
CAACGUCUGCAAGAAUGGAGAUGAUAAAGAUAAAGCUGGCAAAGGGAGAA---------AGAGCAAG-AGCAGCGCUUCUCCGUGGGCGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGC
...(((((.((....)).))))).....(((...(((.((....((((((---------.(.((...-....)).))))))))).)))..))).(((((((((......))))))))).. ( -30.80)
>DroEre_CAF1 27123 111 - 1
UAACAUCUGCAAGAAUGGAGAUGAUAAAGAUAAAGCUGGAAAAGGCAGAA---------AGAGCAAGAAGCAGCGCUUCUCCGUGGGCGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGC
....((((((....(((((((.(...........((((......((....---------...))......)))).).)))))))..))))))..(((((((((......))))))))).. ( -30.90)
>DroYak_CAF1 27065 109 - 1
-----------AGAACGGAGAUGAUAAAGAUAAAGCUGGAAAAGGCAGAAAGAGCAGAAAGAGCAAGAAGCAGCGCUUCUCCGUGGGCGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGC
-----------.(.(((((((.............(((......))).............((.((........)).)))))))))...)......(((((((((......))))))))).. ( -24.10)
>consensus
CAACGUCUGCAAGAAUGGAGAUGAUAAAGAUAAAGCUGGAAAAGGGAGAA_________AGAGCAAG_AGCAGCGCUUCUCCGUGGGCGGAUUGAGCGCAUAAUGAUGUUUAUGUGUUGC
...(((((.((....)).)))))...........(((........................))).....(((((((((.((((....))))..))))((((((......))))))))))) (-21.44 = -23.12 +   1.68)

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 09:29:04 2006