Locus 8668

Sequence ID 3R_DroMel_CAF1
Location 23,156,833 – 23,156,970
Length 137
Max. P 0.832293
window13919 window13920 window13921

overview

Window 9

Location 23,156,833 – 23,156,935
Length 102
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.34
Mean single sequence MFE -33.55
Consensus MFE -27.06
Energy contribution -29.38
Covariance contribution 2.31
Combinations/Pair 1.03
Mean z-score -1.92
Structure conservation index 0.81
SVM decision value 0.72
SVM RNA-class probability 0.832293
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23156833 102 + 27905053
GGCUAGGAAAUAAAGGACUCGUUUAAUUUCUAUUUCCUUGGGCACAAUUAGCGAUAAUCAGCUGGCAAUGGCAGCC-----------GUUGGUCCUUCGCUUUUCCCAUUC------GC-
.((.(((((((..((((..........)))))))))))((((.......(((((..((((((.(((.......)))-----------))))))...)))))...))))...------))- ( -26.40)
>DroSec_CAF1 7476 114 + 1
GGCUAGGAAAUAAAGGACUCGUUUAAUUUCUAUUUCCUUGGGCACAAUUAGCGAUAAUCAGCUGGCAAUGGCAGCCAGCAUUUUGUCGCUGGUCCUUCGCUUUUCCCAUUC------GCA
.((..(((((..((((((..((((((...........)))))).....(((((((((...((((((.......))))))...)))))))))))))))....))))).....------)). ( -36.80)
>DroSim_CAF1 12029 120 + 1
GGCUAGGAAAUAAAGGACUCGUUUAAUUUCUAUUUCCUUGGGCACAAUUAGCGAUAAUCAGCUGGCAAUGGCAGCCAGCAUUUUGUCGCUGGUCCUUCGCUUUUCCCAUUCGCAUUCGCA
.....(((((..((((((..((((((...........)))))).....(((((((((...((((((.......))))))...)))))))))))))))....))))).....((....)). ( -37.70)
>DroYak_CAF1 12032 120 + 1
GGCUAGGAAAUAAAGGACUCGUUUAAUUUCUAUUUCCUUGGGCACAAUUAGCGAUAAUCAGCUGGCAAUGGCAAGCAGCAUUUUGUCGCUGGUCCUUCGCUUUUCCCAUUCGCAUUCGCA
.((.(((((((..((((..........)))))))))))((((.......(((((..((((((.(((((..((.....))...)))))))))))...)))))...))))...))....... ( -33.30)
>consensus
GGCUAGGAAAUAAAGGACUCGUUUAAUUUCUAUUUCCUUGGGCACAAUUAGCGAUAAUCAGCUGGCAAUGGCAGCCAGCAUUUUGUCGCUGGUCCUUCGCUUUUCCCAUUC______GCA
.....(((((..((((((..((((((...........)))))).....(((((((((...((((((.......))))))...)))))))))))))))....))))).............. (-27.06 = -29.38 +   2.31)

alignment

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secondary structure

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dotplot

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Window 0

Location 23,156,833 – 23,156,935
Length 102
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.34
Mean single sequence MFE -31.12
Consensus MFE -26.74
Energy contribution -27.80
Covariance contribution 1.06
Combinations/Pair 1.00
Mean z-score -1.33
Structure conservation index 0.86
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23156833 102 - 27905053
-GC------GAAUGGGAAAAGCGAAGGACCAAC-----------GGCUGCCAUUGCCAGCUGAUUAUCGCUAAUUGUGCCCAAGGAAAUAGAAAUUAAACGAGUCCUUUAUUUCCUAGCC
-((------...((((.(((((((........(-----------(((((.......))))))....)))))..))...))))((((((((((.(((.....)))..)))))))))).)). ( -25.70)
>DroSec_CAF1 7476 114 - 1
UGC------GAAUGGGAAAAGCGAAGGACCAGCGACAAAAUGCUGGCUGCCAUUGCCAGCUGAUUAUCGCUAAUUGUGCCCAAGGAAAUAGAAAUUAAACGAGUCCUUUAUUUCCUAGCC
...------...(((((((...(((((((((((((......((((((.......))))))......)))))..((((..(....)..)))).........).))))))).)))))))... ( -34.80)
>DroSim_CAF1 12029 120 - 1
UGCGAAUGCGAAUGGGAAAAGCGAAGGACCAGCGACAAAAUGCUGGCUGCCAUUGCCAGCUGAUUAUCGCUAAUUGUGCCCAAGGAAAUAGAAAUUAAACGAGUCCUUUAUUUCCUAGCC
.((....))...(((((((...(((((((((((((......((((((.......))))))......)))))..((((..(....)..)))).........).))))))).)))))))... ( -35.40)
>DroYak_CAF1 12032 120 - 1
UGCGAAUGCGAAUGGGAAAAGCGAAGGACCAGCGACAAAAUGCUGCUUGCCAUUGCCAGCUGAUUAUCGCUAAUUGUGCCCAAGGAAAUAGAAAUUAAACGAGUCCUUUAUUUCCUAGCC
.((....))...(((((((...(((((((((((((......(((((........).))))......)))))..((((..(....)..)))).........).))))))).)))))))... ( -28.60)
>consensus
UGC______GAAUGGGAAAAGCGAAGGACCAGCGACAAAAUGCUGGCUGCCAUUGCCAGCUGAUUAUCGCUAAUUGUGCCCAAGGAAAUAGAAAUUAAACGAGUCCUUUAUUUCCUAGCC
.((.........((((....((((.((.((((((......))))))...)).)))).(((........))).......))))((((((((((.(((.....)))..)))))))))).)). (-26.74 = -27.80 +   1.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 23,156,873 – 23,156,970
Length 97
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.99
Mean single sequence MFE -26.28
Consensus MFE -19.62
Energy contribution -20.43
Covariance contribution 0.81
Combinations/Pair 1.05
Mean z-score -1.89
Structure conservation index 0.75
SVM decision value 0.63
SVM RNA-class probability 0.805518
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23156873 97 + 27905053
GGCACAAUUAGCGAUAAUCAGCUGGCAAUGGCAGCC-----------GUUGGUCCUUCGCUUUUCCCAUUC------GC------AUUCCCAUUUCCAGCACAACUCUCCUCCCAUUUCG
.((.......))........(((((.(((((..((.-----------..(((.............)))...------))------....))))).))))).................... ( -17.82)
>DroSec_CAF1 7516 114 + 1
GGCACAAUUAGCGAUAAUCAGCUGGCAAUGGCAGCCAGCAUUUUGUCGCUGGUCCUUCGCUUUUCCCAUUC------GCAUUGCCAUUCCCAUUUCCAGCACAACUCCCCACCCAAUUCG
((((..(((((((((((...((((((.......))))))...))))))))))).....((...........------))..))))................................... ( -30.60)
>DroSim_CAF1 12069 120 + 1
GGCACAAUUAGCGAUAAUCAGCUGGCAAUGGCAGCCAGCAUUUUGUCGCUGGUCCUUCGCUUUUCCCAUUCGCAUUCGCAUUGCCAUUCCCAUUUCCAGCACAACUCCCCACCCAUUUCG
((((..(((((((((((...((((((.......))))))...)))))))))))..................((....))..))))................................... ( -31.70)
>DroYak_CAF1 12072 120 + 1
GGCACAAUUAGCGAUAAUCAGCUGGCAAUGGCAAGCAGCAUUUUGUCGCUGGUCCUUCGCUUUUCCCAUUCGCAUUCGCAUUCACAUUCCCAUUCCCAGCACAACUCCCCACCCAUUUCG
.((......(((((..((((((.(((((..((.....))...)))))))))))...)))))..........((....))...................)).................... ( -25.00)
>consensus
GGCACAAUUAGCGAUAAUCAGCUGGCAAUGGCAGCCAGCAUUUUGUCGCUGGUCCUUCGCUUUUCCCAUUC______GCAUUGCCAUUCCCAUUUCCAGCACAACUCCCCACCCAUUUCG
.((.......))........(((((.(((((..((((((........)))))).....((.................))..........))))).))))).................... (-19.62 = -20.43 +   0.81)

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 13:16:47 2006