Locus 6753

Sequence ID X_DroMel_CAF1
Location 16,771,084 – 16,771,274
Length 190
Max. P 0.998437
window11053 window11054 window11055 window11056 window11057

overview

Window 3

Location 16,771,084 – 16,771,194
Length 110
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 93.30
Mean single sequence MFE -25.17
Consensus MFE -19.80
Energy contribution -19.96
Covariance contribution 0.16
Combinations/Pair 1.10
Mean z-score -1.52
Structure conservation index 0.79
SVM decision value 0.07
SVM RNA-class probability 0.566249
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16771084 110 + 22224390
CCUUUGUGUGUUAGUCUAGGUGUAAGCACACUCGUACUCGGUUGAAACGGACUUCCUGUUUUCAAAUAUAAAUCAAUCGAGACCUAUCGAAAAA-AUCGAUAUAAUCGAUC
.....(((((((...(.....)..)))))))(((..((((((((((((((.....)))))............)))))))))...((((((....-.))))))....))).. ( -25.80)
>DroSec_CAF1 8097 110 + 1
CCUUUGUGUGUUAGUCUAGGUGUAAGCACACUCGUACUCGGUUGAAACGGACUUCCUGUUUUCAAAUAUAAAUCAAUCGAGACCUAUCGAAAAA-UUCGAUAUAAUCGAUC
.....(((((((...(.....)..)))))))(((..((((((((((((((.....)))))............)))))))))...((((((....-.))))))....))).. ( -25.80)
>DroSim_CAF1 8027 110 + 1
CCUUUGUGUGUUAGUCUAGGUGUAAGCACACUCGUACUCGGUUGAAACGGACUUCCUGUUUUCAAAUAUAAAUCAAUCGAGACCUAUCGAAAAA-AUCGAUAUAAUCGAUC
.....(((((((...(.....)..)))))))(((..((((((((((((((.....)))))............)))))))))...((((((....-.))))))....))).. ( -25.80)
>DroEre_CAF1 10778 110 + 1
CCUUUGUGUGUUAGUCUAGGUGUAAGCACACUCGUGCCUAGUUGAUACGGACUUCCUGUUUUCAAAUAUAAAUUAAUCGACACCUAUCGAAAAC-AUCGAUAUAAUCGAUC
..((((.(((((((.(((((((..((....))..))))))))))))))((....))......)))).........(((((....((((((....-.))))))...))))). ( -26.50)
>DroYak_CAF1 8018 111 + 1
CCUUUGUGUGUUAGUCUAGGUGUAAGCACACUUGUACUUGGUUGAUACGGACUUCCUGCUUUCAAAUAUAAAUUAAUCGACGCUUAUCGAAAUCGAUCGAUAUAAUCCAUC
.......(((((((.(((((((((((....))))))))))))))))))(((......((......................)).((((((......))))))...)))... ( -21.95)
>consensus
CCUUUGUGUGUUAGUCUAGGUGUAAGCACACUCGUACUCGGUUGAAACGGACUUCCUGUUUUCAAAUAUAAAUCAAUCGAGACCUAUCGAAAAA_AUCGAUAUAAUCGAUC
.....(((((((...(.....)..)))))))..((.(((((((((...((....))((....))........))))))))))).((((((......))))))......... (-19.80 = -19.96 +   0.16)

alignment

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secondary structure

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Window 4

Location 16,771,116 – 16,771,234
Length 118
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 91.55
Mean single sequence MFE -25.40
Consensus MFE -21.62
Energy contribution -21.38
Covariance contribution -0.24
Combinations/Pair 1.18
Mean z-score -1.58
Structure conservation index 0.85
SVM decision value 0.94
SVM RNA-class probability 0.886527
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16771116 118 + 22224390
CGUACUCGGUUGAAACGGACUUCCUGUUUUCAAAUAUAAAUCAAUCGAGACCUAUCGAAAAA-AUCGAUAUAAUCGAUCGACUUAAAUUCGCAAGUGUUUUUUAUUUGCUGAAUGCAAG
.((.((((((((((((((.....)))))............)))))))))))...((((....-.(((((...)))))))))(((..(((((((((((.....))))))).))))..))) ( -27.80)
>DroSec_CAF1 8129 118 + 1
CGUACUCGGUUGAAACGGACUUCCUGUUUUCAAAUAUAAAUCAAUCGAGACCUAUCGAAAAA-UUCGAUAUAAUCGAUCGACUUAAAAUCGCAAGUGUUUUUUAUUUGCUGAAUGAAAG
.((.((((((((((((((.....)))))............))))))))))).((((((....-.))))))...(((.((((.......))(((((((.....))))))).)).)))... ( -25.20)
>DroSim_CAF1 8059 118 + 1
CGUACUCGGUUGAAACGGACUUCCUGUUUUCAAAUAUAAAUCAAUCGAGACCUAUCGAAAAA-AUCGAUAUAAUCGAUCGACUUAAAAUCGCAAGUGUUUUUUAUUUGCUGAAUGAAAG
.((.((((((((((((((.....)))))............))))))))))).((((((....-.))))))...(((.((((.......))(((((((.....))))))).)).)))... ( -25.20)
>DroEre_CAF1 10810 118 + 1
CGUGCCUAGUUGAUACGGACUUCCUGUUUUCAAAUAUAAAUUAAUCGACACCUAUCGAAAAC-AUCGAUAUAAUCGAUCGACUUGAAAUCGCAAAUGUUUUUUAUUUGCUGAAUGCAAG
.........((((.((((.....))))..)))).......(..(((((....((((((....-.))))))...)))))..)((((...(((((((((.....))))))).))...)))) ( -24.00)
>DroYak_CAF1 8050 119 + 1
UGUACUUGGUUGAUACGGACUUCCUGCUUUCAAAUAUAAAUUAAUCGACGCUUAUCGAAAUCGAUCGAUAUAAUCCAUCGACUUGAAAUCGCAAAUGUUUUUUAUUUGCCGAAUGCAAG
((((.(((((.((((.((((....(((((((((...........((((......))))..(((((.(((...))).))))).))))))..)))...))))..)))).))))).)))).. ( -24.80)
>consensus
CGUACUCGGUUGAAACGGACUUCCUGUUUUCAAAUAUAAAUCAAUCGAGACCUAUCGAAAAA_AUCGAUAUAAUCGAUCGACUUAAAAUCGCAAGUGUUUUUUAUUUGCUGAAUGCAAG
.(((.(((.(((((((((.....))).))))))...(((.((.(((((....((((((......))))))...))))).)).))).....(((((((.....)))))))))).)))... (-21.62 = -21.38 +  -0.24)

alignment

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secondary structure

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Window 5

Location 16,771,116 – 16,771,234
Length 118
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 91.55
Mean single sequence MFE -29.80
Consensus MFE -23.10
Energy contribution -23.90
Covariance contribution 0.80
Combinations/Pair 1.11
Mean z-score -2.65
Structure conservation index 0.78
SVM decision value 1.79
SVM RNA-class probability 0.977482
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16771116 118 - 22224390
CUUGCAUUCAGCAAAUAAAAAACACUUGCGAAUUUAAGUCGAUCGAUUAUAUCGAU-UUUUUCGAUAGGUCUCGAUUGAUUUAUAUUUGAAAACAGGAAGUCCGUUUCAACCGAGUACG
.((((.....)))).........(((((.((((.((((((((((((...((((((.-....))))))....)))))))))))).))))((((...((....)).))))...)))))... ( -32.80)
>DroSec_CAF1 8129 118 - 1
CUUUCAUUCAGCAAAUAAAAAACACUUGCGAUUUUAAGUCGAUCGAUUAUAUCGAA-UUUUUCGAUAGGUCUCGAUUGAUUUAUAUUUGAAAACAGGAAGUCCGUUUCAACCGAGUACG
.....((((.((((...........)))).....((((((((((((...((((((.-....))))))....))))))))))))...((((((...((....)).))))))..))))... ( -29.30)
>DroSim_CAF1 8059 118 - 1
CUUUCAUUCAGCAAAUAAAAAACACUUGCGAUUUUAAGUCGAUCGAUUAUAUCGAU-UUUUUCGAUAGGUCUCGAUUGAUUUAUAUUUGAAAACAGGAAGUCCGUUUCAACCGAGUACG
.....((((.((((...........)))).....((((((((((((...((((((.-....))))))....))))))))))))...((((((...((....)).))))))..))))... ( -30.10)
>DroEre_CAF1 10810 118 - 1
CUUGCAUUCAGCAAAUAAAAAACAUUUGCGAUUUCAAGUCGAUCGAUUAUAUCGAU-GUUUUCGAUAGGUGUCGAUUAAUUUAUAUUUGAAAACAGGAAGUCCGUAUCAACUAGGCACG
..(((.....((((((.......))))))((((((((((..((((((..((((((.-....))))))...))))))..))))....(((....)))))))))............))).. ( -28.90)
>DroYak_CAF1 8050 119 - 1
CUUGCAUUCGGCAAAUAAAAAACAUUUGCGAUUUCAAGUCGAUGGAUUAUAUCGAUCGAUUUCGAUAAGCGUCGAUUAAUUUAUAUUUGAAAGCAGGAAGUCCGUAUCAACCAAGUACA
(((((.((((((((((.......)))))).......((((((((.....((((((......))))))..))))))))..........)))).)))))......((((.......)))). ( -27.90)
>consensus
CUUGCAUUCAGCAAAUAAAAAACACUUGCGAUUUUAAGUCGAUCGAUUAUAUCGAU_UUUUUCGAUAGGUCUCGAUUGAUUUAUAUUUGAAAACAGGAAGUCCGUUUCAACCGAGUACG
.((((.....)))).........(((((.(.....(((((((((((...((((((......))))))....)))))))))))....((((((...((....)).))))))))))))... (-23.10 = -23.90 +   0.80)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,771,155 – 16,771,274
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.95
Mean single sequence MFE -26.42
Consensus MFE -21.62
Energy contribution -21.18
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -3.05
Structure conservation index 0.82
SVM decision value 3.10
SVM RNA-class probability 0.998437
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16771155 119 + 22224390
AUCAAUCGAGACCUAUCGAAAAA-AUCGAUAUAAUCGAUCGACUUAAAUUCGCAAGUGUUUUUUAUUUGCUGAAUGCAAGUCAAACAAAUAGUUUCUGAAAUAUGCAUUUCGAAAUUCAA
....(((((....((((((....-.))))))...))))).(((((..(((((((((((.....))))))).))))..)))))........((((((.(((((....)))))))))))... ( -29.90)
>DroSec_CAF1 8168 119 + 1
AUCAAUCGAGACCUAUCGAAAAA-UUCGAUAUAAUCGAUCGACUUAAAAUCGCAAGUGUUUUUUAUUUGCUGAAUGAAAGUCAAACAAACAGUUUCUGAAAUAUGCAUUUUGAUAUUCAA
(((((((((....((((((....-.))))))...))))..(((((..(.(((((((((.....))))))).)).)..)))))...........................)))))...... ( -23.40)
>DroSim_CAF1 8098 119 + 1
AUCAAUCGAGACCUAUCGAAAAA-AUCGAUAUAAUCGAUCGACUUAAAAUCGCAAGUGUUUUUUAUUUGCUGAAUGAAAGUCAAACAAACAGUUUCUGAAAUAUGCAUUUUGAUAUUCAA
(((((((((....((((((....-.))))))...))))..(((((..(.(((((((((.....))))))).)).)..)))))...........................)))))...... ( -23.40)
>DroEre_CAF1 10849 119 + 1
AUUAAUCGACACCUAUCGAAAAC-AUCGAUAUAAUCGAUCGACUUGAAAUCGCAAAUGUUUUUUAUUUGCUGAAUGCAAGUCAAACAUACAAUUUCUGAGAUAUGCAUUUCGAAAUUCAA
....(((((....((((((....-.))))))...))))).((((((...(((((((((.....))))))).))...))))))........((((((.(((((....)))))))))))... ( -29.20)
>DroYak_CAF1 8089 115 + 1
AUUAAUCGACGCUUAUCGAAAUCGAUCGAUAUAAUCCAUCGACUUGAAAUCGCAAAUGUUUUUUAUUUGCCGAAUGCAAGUCAAACAUACAAUUUCUGAAAUAUGCAUUUCGAUA-----
....(((((.((.((((((......)))))).........((((((...(((((((((.....)))))).)))...))))))......................))...))))).----- ( -26.20)
>consensus
AUCAAUCGAGACCUAUCGAAAAA_AUCGAUAUAAUCGAUCGACUUAAAAUCGCAAGUGUUUUUUAUUUGCUGAAUGCAAGUCAAACAAACAGUUUCUGAAAUAUGCAUUUCGAUAUUCAA
....(((((....((((((......))))))...))))).(((((..(.(((((((((.....))))))).)).)..)))))...............(((((....)))))......... (-21.62 = -21.18 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,771,155 – 16,771,274
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.95
Mean single sequence MFE -28.07
Consensus MFE -20.64
Energy contribution -21.04
Covariance contribution 0.40
Combinations/Pair 1.12
Mean z-score -2.54
Structure conservation index 0.74
SVM decision value 1.11
SVM RNA-class probability 0.916448
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16771155 119 - 22224390
UUGAAUUUCGAAAUGCAUAUUUCAGAAACUAUUUGUUUGACUUGCAUUCAGCAAAUAAAAAACACUUGCGAAUUUAAGUCGAUCGAUUAUAUCGAU-UUUUUCGAUAGGUCUCGAUUGAU
((((((((.(((.((((..((.((((.....))))...))..))))))).((((...........))))))))))))(((((((((...((((((.-....))))))....))))))))) ( -28.70)
>DroSec_CAF1 8168 119 - 1
UUGAAUAUCAAAAUGCAUAUUUCAGAAACUGUUUGUUUGACUUUCAUUCAGCAAAUAAAAAACACUUGCGAUUUUAAGUCGAUCGAUUAUAUCGAA-UUUUUCGAUAGGUCUCGAUUGAU
.((((..(((((..(((............)))...)))))..))))....((((...........))))........(((((((((...((((((.-....))))))....))))))))) ( -25.00)
>DroSim_CAF1 8098 119 - 1
UUGAAUAUCAAAAUGCAUAUUUCAGAAACUGUUUGUUUGACUUUCAUUCAGCAAAUAAAAAACACUUGCGAUUUUAAGUCGAUCGAUUAUAUCGAU-UUUUUCGAUAGGUCUCGAUUGAU
.((((..(((((..(((............)))...)))))..))))....((((...........))))........(((((((((...((((((.-....))))))....))))))))) ( -25.80)
>DroEre_CAF1 10849 119 - 1
UUGAAUUUCGAAAUGCAUAUCUCAGAAAUUGUAUGUUUGACUUGCAUUCAGCAAAUAAAAAACAUUUGCGAUUUCAAGUCGAUCGAUUAUAUCGAU-GUUUUCGAUAGGUGUCGAUUAAU
...((((((...............))))))........((((((...((.((((((.......))))))))...))))))(((((((..((((((.-....))))))...)))))))... ( -29.96)
>DroYak_CAF1 8089 115 - 1
-----UAUCGAAAUGCAUAUUUCAGAAAUUGUAUGUUUGACUUGCAUUCGGCAAAUAAAAAACAUUUGCGAUUUCAAGUCGAUGGAUUAUAUCGAUCGAUUUCGAUAAGCGUCGAUUAAU
-----.(((((...((.((((...((((((((((((((.(.((((.....)))).)...))))))..))))))))((((((((.(((...))).)))))))).)))).)).))))).... ( -30.90)
>consensus
UUGAAUAUCGAAAUGCAUAUUUCAGAAACUGUUUGUUUGACUUGCAUUCAGCAAAUAAAAAACACUUGCGAUUUUAAGUCGAUCGAUUAUAUCGAU_UUUUUCGAUAGGUCUCGAUUGAU
.........((((((((............((((((((.((.......)))))))))).........))).)))))..(((((((((...((((((......))))))....))))))))) (-20.64 = -21.04 +   0.40)

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 12:22:06 2006