Locus 1850

Sequence ID 2R_DroMel_CAF1
Location 6,961,811 – 6,961,940
Length 129
Max. P 0.994585
window3072 window3073 window3074

overview

Window 2

Location 6,961,811 – 6,961,911
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 94.16
Mean single sequence MFE -27.31
Consensus MFE -25.40
Energy contribution -25.52
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -1.29
Structure conservation index 0.93
SVM decision value 0.83
SVM RNA-class probability 0.861362
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6961811 100 - 20766785
UUGAUCCCUUAGCCUGUUCCGAUUCCGCAUUCCCCCGAGCAAGCACAACUGUACCUGUCAUUGAGUUAUCAGCUGACUUUUGGGUAAGUUUGAGGAGAAA
....(((((((((.(((((.((........))....))))).))..((((.(((((((((((((....)))).))))....)))))))))))))).)).. ( -24.40)
>DroSec_CAF1 5940 99 - 1
UUGAUCCCUCAGCUUGUUCCGAUCCCGCAUUCUCCCGAGCAAUCACAACUGUACCUGUCAUUGAGUUAUCAGCUGACUU-UGGGUAAGUUUUAGGAGAAA
..((((...(.....)....)))).....((((((.((....))..((((.(((((((((((((....)))).))))..-.)))))))))...)))))). ( -22.70)
>DroSim_CAF1 13349 99 - 1
UUGAUCCCUCAGCUUGUUUCGAUCCCGCAUUCUCCCGAGCAAGCACAACUGUACCUGUCAUUGAGUUAUCAGCUGACUU-UGGGUAAGUUUGAGGAGAAA
....((((((((((((((.((..............)))))))))..((((.(((((((((((((....)))).))))..-.)))))))))))))).)).. ( -29.74)
>DroEre_CAF1 12744 99 - 1
UUGAUCCCUCAGCUUGUUCCGAUUCCGCAUUUCCCCGAGCAAGCACAACUGUACCUGUCAUUGAGUUAUCAGCUGACUU-UGGGUAAGUUUGAGGGGAAA
....(((((((((((((((.((.........))...))))))))..((((.(((((((((((((....)))).))))..-.))))))))))))))))... ( -33.80)
>DroYak_CAF1 6078 99 - 1
UUGAUCCCGCAGCUUGUUUCGAUUCCGCAUUCCCUCGAGCAAGCACAACUGUACCUGUCAUUGAGUUAUCGGCUGACUU-UGGGUAAGUUUGAGGAGAAA
....((((.(((((((((.(((............))))))))))..((((.(((((((((((((....)))).))))..-.))))))))))).)).)).. ( -25.90)
>consensus
UUGAUCCCUCAGCUUGUUCCGAUUCCGCAUUCCCCCGAGCAAGCACAACUGUACCUGUCAUUGAGUUAUCAGCUGACUU_UGGGUAAGUUUGAGGAGAAA
....(((((((((((((((.((........))....))))))))..((((.(((((((((((((....)))).))))....)))))))))))))).)).. (-25.40 = -25.52 +   0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,961,838 – 6,961,940
Length 102
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 76.27
Mean single sequence MFE -33.66
Consensus MFE -20.44
Energy contribution -21.11
Covariance contribution 0.67
Combinations/Pair 1.14
Mean z-score -2.39
Structure conservation index 0.61
SVM decision value 1.91
SVM RNA-class probability 0.982411
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6961838 102 + 20766785
GCUGAUAACUCAAUGACAGGUACAGUUGUGC---UUGCUCGGGGGAAUGCGGAAUCGGAACAGGCUAAGGGAUCAACUGUACCUGGCACGGGGCAUAGUCUGGUG
................((((((((((((.((---(((.((.((...........)).)).)))))........)))))))))))).(((.((((...)))).))) ( -33.00)
>DroSec_CAF1 5966 89 + 1
GCUGAUAACUCAAUGACAGGUACAGUUGUGA---UUGCUCGGGAGAAUGCGGGAUCGGAACAAGCUGAGGGAUCAACUGUACCUG-------------UCUGGUG
.......(((....((((((((((((..(((---((.(((((.....(.((....)).).....))))).)))))))))))))))-------------)).))). ( -33.60)
>DroSim_CAF1 13375 89 + 1
GCUGAUAACUCAAUGACAGGUACAGUUGUGC---UUGCUCGGGAGAAUGCGGGAUCGAAACAAGCUGAGGGAUCAACUGUACCUG-------------UCUGGUG
.......(((....((((((((((((((...---((.(((((.......((....)).......))))).)).))))))))))))-------------)).))). ( -32.54)
>DroEre_CAF1 12770 102 + 1
GCUGAUAACUCAAUGACAGGUACAGUUGUGC---UUGCUCGGGGAAAUGCGGAAUCGGAACAAGCUGAGGGAUCAACUGUACCUGGCACGGGGCAUAGUCUGGUG
................((((((((((((...---((.(((((.....(.((....)).).....))))).)).)))))))))))).(((.((((...)))).))) ( -33.70)
>DroYak_CAF1 6104 102 + 1
GCCGAUAACUCAAUGACAGGUACAGUUGUGC---UUGCUCGAGGGAAUGCGGAAUCGAAACAAGCUGCGGGAUCAACUGUACCUGGCACGGGGCAUAGUCUGGUG
((((((..(((..((.((((((((((((.((---(((.((((............))))..)))))........)))))))))))).))..)))....))).))). ( -34.80)
>DroAna_CAF1 15720 83 + 1
GCCGAGAUCCCAAUGCCGGGUACAGUUGGGUACAUCGCUAAGG--AA------------------UGAAGGAUCAACUGUACCUGGCAUUCGGU-UAUUA-AGAG
(((((.......(((((((((((((((((...(.(((......--..------------------))).)..))))))))))))))))))))))-.....-.... ( -34.31)
>consensus
GCUGAUAACUCAAUGACAGGUACAGUUGUGC___UUGCUCGGGGGAAUGCGGAAUCGGAACAAGCUGAGGGAUCAACUGUACCUGGCACGGGGC_UAGUCUGGUG
................((((((((((((......((.(((((.......((....)).......))))).)).)))))))))))).................... (-20.44 = -21.11 +   0.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,961,838 – 6,961,940
Length 102
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 76.27
Mean single sequence MFE -30.08
Consensus MFE -19.82
Energy contribution -20.72
Covariance contribution 0.91
Combinations/Pair 1.13
Mean z-score -3.45
Structure conservation index 0.66
SVM decision value 2.49
SVM RNA-class probability 0.994585
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6961838 102 - 20766785
CACCAGACUAUGCCCCGUGCCAGGUACAGUUGAUCCCUUAGCCUGUUCCGAUUCCGCAUUCCCCCGAGCAA---GCACAACUGUACCUGUCAUUGAGUUAUCAGC
.....((....((.(.(((.(((((((((((((.....).((.(((((.((........))....))))).---)).)))))))))))).))).).))..))... ( -26.90)
>DroSec_CAF1 5966 89 - 1
CACCAGA-------------CAGGUACAGUUGAUCCCUCAGCUUGUUCCGAUCCCGCAUUCUCCCGAGCAA---UCACAACUGUACCUGUCAUUGAGUUAUCAGC
.....((-------------((((((((((((........(((((....((........))...)))))..---...)))))))))))))).((((....)))). ( -29.12)
>DroSim_CAF1 13375 89 - 1
CACCAGA-------------CAGGUACAGUUGAUCCCUCAGCUUGUUUCGAUCCCGCAUUCUCCCGAGCAA---GCACAACUGUACCUGUCAUUGAGUUAUCAGC
.....((-------------((((((((((((........(((((((.((..............)))))))---)).)))))))))))))).((((....)))). ( -31.84)
>DroEre_CAF1 12770 102 - 1
CACCAGACUAUGCCCCGUGCCAGGUACAGUUGAUCCCUCAGCUUGUUCCGAUUCCGCAUUUCCCCGAGCAA---GCACAACUGUACCUGUCAUUGAGUUAUCAGC
.....((....((.(.(((.((((((((((((........((((((((.((.........))...))))))---)).)))))))))))).))).).))..))... ( -30.40)
>DroYak_CAF1 6104 102 - 1
CACCAGACUAUGCCCCGUGCCAGGUACAGUUGAUCCCGCAGCUUGUUUCGAUUCCGCAUUCCCUCGAGCAA---GCACAACUGUACCUGUCAUUGAGUUAUCGGC
...........(((..(((.((((((((((((........(((((((.(((............))))))))---)).)))))))))))).))).((....))))) ( -31.60)
>DroAna_CAF1 15720 83 - 1
CUCU-UAAUA-ACCGAAUGCCAGGUACAGUUGAUCCUUCA------------------UU--CCUUAGCGAUGUACCCAACUGUACCCGGCAUUGGGAUCUCGGC
....-.....-.((.((((((.((((((((((......((------------------((--.......))))....)))))))))).)))))).))........ ( -30.60)
>consensus
CACCAGACUA_GCCCCGUGCCAGGUACAGUUGAUCCCUCAGCUUGUUCCGAUUCCGCAUUCCCCCGAGCAA___GCACAACUGUACCUGUCAUUGAGUUAUCAGC
....................((((((((((((........(((((....((........))...)))))........))))))))))))...((((....)))). (-19.82 = -20.72 +   0.91)

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 10:14:46 2006