Locus 3723

Sequence ID 3R_DroMel_CAF1
Location 10,113,137 – 10,113,289
Length 152
Max. P 0.998646
window5965 window5966 window5967 window5968

overview

Window 5

Location 10,113,137 – 10,113,250
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.54
Mean single sequence MFE -30.76
Consensus MFE -27.46
Energy contribution -28.18
Covariance contribution 0.72
Combinations/Pair 1.06
Mean z-score -1.97
Structure conservation index 0.89
SVM decision value 2.46
SVM RNA-class probability 0.994212
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10113137 113 + 27905053
ACUUGUCAGCUGC------GUCCACUUCGCAUUUGGUUCUUUGCCAAAGUUAUUAACCAAUUUUUUGGGAAGACACCCAAAGGCUUUAUGCAUUCGCAAGGCGCGAUGUAAACAAAUAG-
..((((..(((((------(((......((.((((((.....))))))..............(((((((......)))))))))....(((....))).))))))..))..))))....- ( -26.90)
>DroSec_CAF1 22574 113 + 1
ACUUGUCAGCUGC------GUCCACUUCGCGUUUGGUUCUUUGCCAAAGUUAUUAACCAAAUUUUUGGGAAGACACCCAAAGGCUUUAUGCAUUCGCAAGGCGCGAAGUACACAAAUCG-
.............------((..(((((((((((((((....((....))....))))))))(((((((......)))))))((((..(((....))))))))))))))..))......- ( -31.00)
>DroSim_CAF1 18774 113 + 1
ACUUGUCAGCUGC------GUCCACUUCGCAUUUGGUUCUUUGCCAAAGUUAUUAACUAAAUUUUUGGGAAGACACCCAAAGGCUUUAUGCAUUCGCAAGGCGCGAAGUAAACAAAUCG-
.............------((..(((((((.((((((.....))))))..............(((((((......)))))))((((..(((....))))))))))))))..))......- ( -30.50)
>DroEre_CAF1 22750 113 + 1
ACCUGUCAGCUGC------GCUUACUUCGCAUUUGAUUCUUUGCCAAAGUUAUUAACCAAACUUUUGGGAAGACACCCAAAGGCUUUAUGCAUUCGCAAGGCGCGAAGUAAACAAAUAC-
.............------(.(((((((((....((....))(((................((((((((......)))))))).....(((....))).)))))))))))).)......- ( -28.60)
>DroYak_CAF1 22805 120 + 1
ACUUGUCAGCUGCUCAUUCGUUCACUUCGCAUUUGGUUCUUUGCGAAAGUCAUUAACCAAAUUUUUGGGAAGACACCCAAAGGCUUUAUGCAUUCGCAAGGCGCGAAGUAAACAAACACA
...................(((.(((((((((((((((..(.((....)).)..))))))))(((((((......)))))))((((..(((....)))))))))))))).)))....... ( -36.80)
>consensus
ACUUGUCAGCUGC______GUCCACUUCGCAUUUGGUUCUUUGCCAAAGUUAUUAACCAAAUUUUUGGGAAGACACCCAAAGGCUUUAUGCAUUCGCAAGGCGCGAAGUAAACAAAUAG_
...................((..(((((((((((((((..(.((....)).)..))))))))(((((((......)))))))((((..(((....))))))))))))))..))....... (-27.46 = -28.18 +   0.72)

alignment

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secondary structure

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Window 6

Location 10,113,137 – 10,113,250
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.54
Mean single sequence MFE -31.48
Consensus MFE -27.74
Energy contribution -27.82
Covariance contribution 0.08
Combinations/Pair 1.18
Mean z-score -1.44
Structure conservation index 0.88
SVM decision value 0.81
SVM RNA-class probability 0.857161
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10113137 113 - 27905053
-CUAUUUGUUUACAUCGCGCCUUGCGAAUGCAUAAAGCCUUUGGGUGUCUUCCCAAAAAAUUGGUUAAUAACUUUGGCAAAGAACCAAAUGCGAAGUGGAC------GCAGCUGACAAGU
-......((((((.((((((..(((....)))....)).((((((......))))))...((((((.....(....).....))))))..)))).))))))------...(((....))) ( -26.50)
>DroSec_CAF1 22574 113 - 1
-CGAUUUGUGUACUUCGCGCCUUGCGAAUGCAUAAAGCCUUUGGGUGUCUUCCCAAAAAUUUGGUUAAUAACUUUGGCAAAGAACCAAACGCGAAGUGGAC------GCAGCUGACAAGU
-......((.(((((((((...(((....))).......((((((......))))))..(((((((.....(....).....)))))))))))))))).))------...(((....))) ( -30.20)
>DroSim_CAF1 18774 113 - 1
-CGAUUUGUUUACUUCGCGCCUUGCGAAUGCAUAAAGCCUUUGGGUGUCUUCCCAAAAAUUUAGUUAAUAACUUUGGCAAAGAACCAAAUGCGAAGUGGAC------GCAGCUGACAAGU
-......((((((((((((...(((....)))....(((((((((......)))))).....(((.....)))..)))...........))))))))))))------...(((....))) ( -29.70)
>DroEre_CAF1 22750 113 - 1
-GUAUUUGUUUACUUCGCGCCUUGCGAAUGCAUAAAGCCUUUGGGUGUCUUCCCAAAAGUUUGGUUAAUAACUUUGGCAAAGAAUCAAAUGCGAAGUAAGC------GCAGCUGACAGGU
-......((((((((((((...(((....)))....(((..((((......))))((((((........)))))))))...........))))))))))))------............. ( -32.00)
>DroYak_CAF1 22805 120 - 1
UGUGUUUGUUUACUUCGCGCCUUGCGAAUGCAUAAAGCCUUUGGGUGUCUUCCCAAAAAUUUGGUUAAUGACUUUCGCAAAGAACCAAAUGCGAAGUGAACGAAUGAGCAGCUGACAAGU
((((((((((((((((((((.(((((((..(((..((((((((((......)))))).....)))).)))...))))))).).......))))))))))))))))..)))(((....))) ( -39.01)
>consensus
_CUAUUUGUUUACUUCGCGCCUUGCGAAUGCAUAAAGCCUUUGGGUGUCUUCCCAAAAAUUUGGUUAAUAACUUUGGCAAAGAACCAAAUGCGAAGUGGAC______GCAGCUGACAAGU
.......(((((((((((((..(((....)))....)).((((((......)))))).((((((((.....(....).....))))))))))))))))))).........(((....))) (-27.74 = -27.82 +   0.08)

alignment

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secondary structure

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Window 7

Location 10,113,171 – 10,113,289
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.60
Mean single sequence MFE -28.86
Consensus MFE -24.96
Energy contribution -25.28
Covariance contribution 0.32
Combinations/Pair 1.09
Mean z-score -1.27
Structure conservation index 0.86
SVM decision value 0.20
SVM RNA-class probability 0.632321
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10113171 118 + 27905053
UUGCCAAAGUUAUUAACCAAUUUUUUGGGAAGACACCCAAAGGCUUUAUGCAUUCGCAAGGCGCGAUGUAAACAAAUAG--AUUUUGGUCAACGAAUCGAACGUGUCCGCUCAAUUAGCA
(((((((((((..........((((((((......)))))))).....(((((.(((.....))))))))........)--))))))).)))................(((.....))). ( -26.00)
>DroSec_CAF1 22608 118 + 1
UUGCCAAAGUUAUUAACCAAAUUUUUGGGAAGACACCCAAAGGCUUUAUGCAUUCGCAAGGCGCGAAGUACACAAAUCG--AUUUUGGUCAACGGAUCGAACGUGUCUGCCCAAUUAGCA
.(((.((((((........))))))((((.((((((......((((..(((...(....))))..)))).......(((--((((........)))))))..)))))).))))....))) ( -29.50)
>DroSim_CAF1 18808 118 + 1
UUGCCAAAGUUAUUAACUAAAUUUUUGGGAAGACACCCAAAGGCUUUAUGCAUUCGCAAGGCGCGAAGUAAACAAAUCG--AUUUUGGUCAACGGAUCGAACGUGUCUGCCCAAUUAGCA
.(((...(((.....)))......(((((.((((((......((((..(((...(....))))..)))).......(((--((((........)))))))..)))))).)))))...))) ( -30.20)
>DroEre_CAF1 22784 118 + 1
UUGCCAAAGUUAUUAACCAAACUUUUGGGAAGACACCCAAAGGCUUUAUGCAUUCGCAAGGCGCGAAGUAAACAAAUAC--UUUUUGGUCAACGGAUCGAACGUGUCUGCCCAAUUAGCA
.(((.((((((........))))))((((.((((((......((((..(((...(....))))..))))..........--..(((((((....))))))).)))))).))))....))) ( -31.50)
>DroYak_CAF1 22845 120 + 1
UUGCGAAAGUCAUUAACCAAAUUUUUGGGAAGACACCCAAAGGCUUUAUGCAUUCGCAAGGCGCGAAGUAAACAAACACAAUUUUUGGUCAACGAAUCGAACGUGUCUGUCCAAUUAGCA
.((((((...............(((((((......)))))))((.....)).))))))(((((((..((......))......((((((......)))))))))))))............ ( -27.10)
>consensus
UUGCCAAAGUUAUUAACCAAAUUUUUGGGAAGACACCCAAAGGCUUUAUGCAUUCGCAAGGCGCGAAGUAAACAAAUAG__AUUUUGGUCAACGGAUCGAACGUGUCUGCCCAAUUAGCA
.(((.((((((........))))))((((.((((((((((((((.....)).(((((.....)))))...............))))))((........))..)))))).))))....))) (-24.96 = -25.28 +   0.32)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,113,171 – 10,113,289
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.60
Mean single sequence MFE -35.32
Consensus MFE -30.08
Energy contribution -30.56
Covariance contribution 0.48
Combinations/Pair 1.05
Mean z-score -2.64
Structure conservation index 0.85
SVM decision value 3.17
SVM RNA-class probability 0.998646
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10113171 118 - 27905053
UGCUAAUUGAGCGGACACGUUCGAUUCGUUGACCAAAAU--CUAUUUGUUUACAUCGCGCCUUGCGAAUGCAUAAAGCCUUUGGGUGUCUUCCCAAAAAAUUGGUUAAUAACUUUGGCAA
(((((((((((((....)))))))...(((((((((...--...(((((...((((((.....))).))).)))))...((((((......))))))...)))))))))....)))))). ( -34.40)
>DroSec_CAF1 22608 118 - 1
UGCUAAUUGGGCAGACACGUUCGAUCCGUUGACCAAAAU--CGAUUUGUGUACUUCGCGCCUUGCGAAUGCAUAAAGCCUUUGGGUGUCUUCCCAAAAAUUUGGUUAAUAACUUUGGCAA
((((((((((((......))))))...((((((((((..--...((((((((.(((((.....)))))))))))))...((((((......))))))..))))))))))....)))))). ( -39.00)
>DroSim_CAF1 18808 118 - 1
UGCUAAUUGGGCAGACACGUUCGAUCCGUUGACCAAAAU--CGAUUUGUUUACUUCGCGCCUUGCGAAUGCAUAAAGCCUUUGGGUGUCUUCCCAAAAAUUUAGUUAAUAACUUUGGCAA
(((((((((((.((((((..((((....))))(((((..--(....(((....(((((.....))))).)))....)..))))))))))).)))))......(((.....))))))))). ( -33.00)
>DroEre_CAF1 22784 118 - 1
UGCUAAUUGGGCAGACACGUUCGAUCCGUUGACCAAAAA--GUAUUUGUUUACUUCGCGCCUUGCGAAUGCAUAAAGCCUUUGGGUGUCUUCCCAAAAGUUUGGUUAAUAACUUUGGCAA
(((((.(((((.((((((..((((....))))(((((((--(((......))))).((....(((....)))....)).))))))))))).)))))(((((........)))))))))). ( -34.70)
>DroYak_CAF1 22845 120 - 1
UGCUAAUUGGACAGACACGUUCGAUUCGUUGACCAAAAAUUGUGUUUGUUUACUUCGCGCCUUGCGAAUGCAUAAAGCCUUUGGGUGUCUUCCCAAAAAUUUGGUUAAUGACUUUCGCAA
(((..(((((((......)))))))((((((((((((..((((((........(((((.....))))).))))))....((((((......))))))..)))))))))))).....))). ( -35.50)
>consensus
UGCUAAUUGGGCAGACACGUUCGAUCCGUUGACCAAAAU__CUAUUUGUUUACUUCGCGCCUUGCGAAUGCAUAAAGCCUUUGGGUGUCUUCCCAAAAAUUUGGUUAAUAACUUUGGCAA
((((((((((((......))))))...((((((((((.......(((((.((.(((((.....))))))).)))))...((((((......))))))..))))))))))....)))))). (-30.08 = -30.56 +   0.48)

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 11:08:28 2006