Locus 5129

Sequence ID 3R_DroMel_CAF1
Location 13,500,986 – 13,501,106
Length 120
Max. P 0.951192
window8370 window8371

overview

Window 0

Location 13,500,986 – 13,501,106
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.35
Mean single sequence MFE -43.25
Consensus MFE -31.80
Energy contribution -32.80
Covariance contribution 1.00
Combinations/Pair 1.14
Mean z-score -1.84
Structure conservation index 0.74
SVM decision value 1.41
SVM RNA-class probability 0.951192
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13500986 120 + 27905053
CUGCUGCUCUGCUUCUCGGACUUCUCCGCGUCGAGCUUCUGCCGCAGCUUAUCCUGUUGCUGCUUGACAUGGGUGGCCAGGACCUGUUCCAGCCACUGGUCAAAGGAUGCUUGCAGGGCA
.....(((((((..(.((((....)))).)..((((.(((((.(((((.......))))).))(((((...((((((..(((.....))).)))))).))))).))).))))))))))). ( -48.80)
>DroPse_CAF1 1792 99 + 1
CUA---UUCUGAGCC------GC------------CUUCCUCUCCAGCACCUGCUGCUGCUGCUUGAUGUGUGUGGCCAGGACCUGCUCCAGCCACUGAUCAAAGGAAGCCUGCAGUGCG
...---....(((..------..------------....)))....((((.(((.(((.((..(((((....(((((..(((.....))).)))))..))))).)).)))..))))))). ( -30.00)
>DroSec_CAF1 1674 120 + 1
CUGCUGCUCUGCUUCUCGGACUUCUCCGCAUCGAGCUUCUGCCGCAGCUUAUCCUGCUGCUGCUUGACAUGGGUGGCCAGGACCUGUUCCAGCCACUGGUCAAAGGAUGCUUGCAGGGCA
.....(((((((.....(((....)))(((((........((.(((((.......))))).))(((((...((((((..(((.....))).)))))).)))))..)))))..))))))). ( -51.10)
>DroSim_CAF1 1789 120 + 1
CUGCUGCUCUGCUUCUCGGACUUCUCCGCAUCAAGCUUCUGCCGCAGCUUAUCCUGCUGCUGCUUGACAUGGGUGGCCAGGACCUGUUCCAGCCACUGGUCAAAGGAUGCUUGCAGGGCA
.....(((((((.....(((....)))(((((........((.(((((.......))))).))(((((...((((((..(((.....))).)))))).)))))..)))))..))))))). ( -51.10)
>DroYak_CAF1 1671 117 + 1
CU---GCUCUGCUUCUCGGACAGCUCCGUAUCGAACUUCUGCCGCAGCUUAUCCUGCUGCAGCUUGACAUGGGUGGUAAGGACCUGUUCCAGCCACUGGUCAAAGGAUGCUUGCAGGGCA
..---(((((((.....(((....)))(((((........((.(((((.......))))).))(((((...((((((..(((.....))).)))))).)))))..)))))..))))))). ( -47.10)
>DroPer_CAF1 1795 99 + 1
CUA---UUCUGAGCC------GC------------CUUCCUCUCCAGCUCCAGCUGCUGCUGCUUGAUGUGUGUGGCCAGGACCUGCUCCAGCCACUGAUCAAAGGAAGCCUGCAGGGCG
...---........(------((------------(........((((....))))((((.((((..(.((.(((((..(((.....))).)))))....)).)..))))..)))))))) ( -31.40)
>consensus
CUG__GCUCUGCUUCUCGGACUUCUCCGCAUCGAGCUUCUGCCGCAGCUUAUCCUGCUGCUGCUUGACAUGGGUGGCCAGGACCUGUUCCAGCCACUGGUCAAAGGAUGCUUGCAGGGCA
.....(((((((....((((....)))).........(((((.(((((.......))))).))(((((...((((((..(((.....))).)))))).))))).))).....))))))). (-31.80 = -32.80 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

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Window 1

Location 13,500,986 – 13,501,106
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.35
Mean single sequence MFE -41.85
Consensus MFE -25.83
Energy contribution -28.47
Covariance contribution 2.64
Combinations/Pair 1.06
Mean z-score -1.36
Structure conservation index 0.62
SVM decision value 0.06
SVM RNA-class probability 0.561709
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13500986 120 - 27905053
UGCCCUGCAAGCAUCCUUUGACCAGUGGCUGGAACAGGUCCUGGCCACCCAUGUCAAGCAGCAACAGGAUAAGCUGCGGCAGAAGCUCGACGCGGAGAAGUCCGAGAAGCAGAGCAGCAG
(((.((((.........(((((..(((((((((.....))).))))))....)))))(((((..........))))).))))..((((..(.((((....))))....)..)))).))). ( -44.20)
>DroPse_CAF1 1792 99 - 1
CGCACUGCAGGCUUCCUUUGAUCAGUGGCUGGAGCAGGUCCUGGCCACACACAUCAAGCAGCAGCAGCAGGUGCUGGAGAGGAAG------------GC------GGCUCAGAA---UAG
......((.(.((((((((.....(((((..(........)..)))))..........(((((.(....).))))).))))))))------------.)------.))......---... ( -36.10)
>DroSec_CAF1 1674 120 - 1
UGCCCUGCAAGCAUCCUUUGACCAGUGGCUGGAACAGGUCCUGGCCACCCAUGUCAAGCAGCAGCAGGAUAAGCUGCGGCAGAAGCUCGAUGCGGAGAAGUCCGAGAAGCAGAGCAGCAG
(((.((((..(((((..(((((..(((((((((.....))).))))))....)))))((.(((((.......))))).))........)))))(((....))).....)))).))).... ( -47.80)
>DroSim_CAF1 1789 120 - 1
UGCCCUGCAAGCAUCCUUUGACCAGUGGCUGGAACAGGUCCUGGCCACCCAUGUCAAGCAGCAGCAGGAUAAGCUGCGGCAGAAGCUUGAUGCGGAGAAGUCCGAGAAGCAGAGCAGCAG
(((.((((..(((((..(((((..(((((((((.....))).))))))....)))))((.(((((.......))))).))........)))))(((....))).....)))).))).... ( -47.50)
>DroYak_CAF1 1671 117 - 1
UGCCCUGCAAGCAUCCUUUGACCAGUGGCUGGAACAGGUCCUUACCACCCAUGUCAAGCUGCAGCAGGAUAAGCUGCGGCAGAAGUUCGAUACGGAGCUGUCCGAGAAGCAGAGC---AG
(((.((((.(((.((..(((((..((((..(((.....)))...))))....)))))((((((((.......)))))))).)).))).....((((....))))....)))).))---). ( -42.30)
>DroPer_CAF1 1795 99 - 1
CGCCCUGCAGGCUUCCUUUGAUCAGUGGCUGGAGCAGGUCCUGGCCACACACAUCAAGCAGCAGCAGCUGGAGCUGGAGAGGAAG------------GC------GGCUCAGAA---UAG
......((.(.((((((((.....(((((..(........)..)))))................((((....)))).))))))))------------.)------.))......---... ( -33.20)
>consensus
UGCCCUGCAAGCAUCCUUUGACCAGUGGCUGGAACAGGUCCUGGCCACCCAUGUCAAGCAGCAGCAGGAUAAGCUGCGGCAGAAGCUCGAUGCGGAGAAGUCCGAGAAGCAGAGC__CAG
.((.((((.(((.((..(((((..((((((((........))))))))....)))))((.(((((.......))))).)).)).))).....((((....))))....)))).))..... (-25.83 = -28.47 +   2.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:03 2006