Locus 1748

Sequence ID X_DroMel_CAF1
Location 4,863,081 – 4,863,229
Length 148
Max. P 0.996225
window2862 window2863 window2864

overview

Window 2

Location 4,863,081 – 4,863,199
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 95.85
Mean single sequence MFE -32.68
Consensus MFE -27.43
Energy contribution -27.71
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.37
Structure conservation index 0.84
SVM decision value 0.02
SVM RNA-class probability 0.545317
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4863081 118 + 22224390
GGCCCGGUUGGUUGCUGCUCCAAUUGGCCAACUGAUGCUAACGGCCAACUGUUCGAUCGCUGCACAAAUUAUAAUUUGCCAAGUAUUCGCAUUUUAGCGGCAACUUUGUCGCCAGAAU
(((......((((((((((.((.((((((.............)))))).))..(((..(((...(((((....)))))...)))..)))......)))))))))).....)))..... ( -35.52)
>DroSec_CAF1 14859 114 + 1
GGCCCGGU----UGCUGCUCCAAUUGGCCAACUGAUGCUAACGGCCAACUGUUCGAUCGCUGCACAAAUUAUAAUUUGCCAAGUAUUCGCAUUUUAGCGGCAACUUUGUCGCCAGAAU
(((..(((----(((((((.((.((((((.............)))))).))..(((..(((...(((((....)))))...)))..)))......)))))))))).....)))..... ( -34.22)
>DroSim_CAF1 14845 114 + 1
GGCCCGGU----UGCUGCUCCAAUUGGCCAACUGAUGCUAACGGCCAACUGUUCGAUCGCUGCACAAAUUAUAAUUUGCCAAGUAUUCGCAUUUUAGCGGCAACUUUGUCGCCAGAAU
(((..(((----(((((((.((.((((((.............)))))).))..(((..(((...(((((....)))))...)))..)))......)))))))))).....)))..... ( -34.22)
>DroEre_CAF1 17889 113 + 1
GGUCCGU-----UGCUGCUCCAAUUGGCCAACUGAUGCUAACGGCCAACUGUUCGAUCGCCGCACAAAUUAUAAUAUGCCAAGUAUUCGCAUUUUAGCGGCAACUUUGUCGCCAGAAU
(((..((-----((((((.....((((((.............)))))).(((.((.....)).))).....(((.((((.........)))).)))))))))))......)))..... ( -26.72)
>DroYak_CAF1 15062 114 + 1
GGCCCGUU----UGCUGCUCCAAUUGGCCAACUGAUGCUAACGGCCAACUGUUUGAUGGCCGCACAAAUUAUAAUUUGCCAAGUAUUCGCAUUUUAGCGGCAACUUUGUCGCCAGAAU
((((...(----((......)))..))))..(((((((...((((((.(.....).))))))..(((((....)))))..........))))....((((((....)))))))))... ( -32.70)
>consensus
GGCCCGGU____UGCUGCUCCAAUUGGCCAACUGAUGCUAACGGCCAACUGUUCGAUCGCUGCACAAAUUAUAAUUUGCCAAGUAUUCGCAUUUUAGCGGCAACUUUGUCGCCAGAAU
(((.........(((((((.((.((((((.............)))))).))..(((..(((...(((((....)))))...)))..)))......)))))))........)))..... (-27.43 = -27.71 +   0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,863,081 – 4,863,199
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 95.85
Mean single sequence MFE -34.68
Consensus MFE -32.18
Energy contribution -32.58
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.35
Structure conservation index 0.93
SVM decision value 0.93
SVM RNA-class probability 0.884178
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4863081 118 - 22224390
AUUCUGGCGACAAAGUUGCCGCUAAAAUGCGAAUACUUGGCAAAUUAUAAUUUGUGCAGCGAUCGAACAGUUGGCCGUUAGCAUCAGUUGGCCAAUUGGAGCAGCAACCAACCGGGCC
((((.((((((...))))))((......)))))).((((((((((....)))))(((.((.......((((((((((...........))))))))))..)).))).....))))).. ( -34.70)
>DroSec_CAF1 14859 114 - 1
AUUCUGGCGACAAAGUUGCCGCUAAAAUGCGAAUACUUGGCAAAUUAUAAUUUGUGCAGCGAUCGAACAGUUGGCCGUUAGCAUCAGUUGGCCAAUUGGAGCAGCA----ACCGGGCC
((((.((((((...))))))((......)))))).((((((((((....)))))(((.((.......((((((((((...........))))))))))..)).)))----.))))).. ( -34.70)
>DroSim_CAF1 14845 114 - 1
AUUCUGGCGACAAAGUUGCCGCUAAAAUGCGAAUACUUGGCAAAUUAUAAUUUGUGCAGCGAUCGAACAGUUGGCCGUUAGCAUCAGUUGGCCAAUUGGAGCAGCA----ACCGGGCC
((((.((((((...))))))((......)))))).((((((((((....)))))(((.((.......((((((((((...........))))))))))..)).)))----.))))).. ( -34.70)
>DroEre_CAF1 17889 113 - 1
AUUCUGGCGACAAAGUUGCCGCUAAAAUGCGAAUACUUGGCAUAUUAUAAUUUGUGCGGCGAUCGAACAGUUGGCCGUUAGCAUCAGUUGGCCAAUUGGAGCAGCA-----ACGGACC
..((((((..(...((((((((......)).........(((((........)))))))))))....((((((((((...........))))))))))..)..)).-----.)))).. ( -34.40)
>DroYak_CAF1 15062 114 - 1
AUUCUGGCGACAAAGUUGCCGCUAAAAUGCGAAUACUUGGCAAAUUAUAAUUUGUGCGGCCAUCAAACAGUUGGCCGUUAGCAUCAGUUGGCCAAUUGGAGCAGCA----AACGGGCC
.....((((((...))))))(((....(((.........((((((....))))))(((((((.(.....).)))))))..((..(((((....)))))..)).)))----....))). ( -34.90)
>consensus
AUUCUGGCGACAAAGUUGCCGCUAAAAUGCGAAUACUUGGCAAAUUAUAAUUUGUGCAGCGAUCGAACAGUUGGCCGUUAGCAUCAGUUGGCCAAUUGGAGCAGCA____ACCGGGCC
((((.((((((...))))))((......)))))).((((((((((....))))))((.((.......((((((((((...........))))))))))..)).)).......)))).. (-32.18 = -32.58 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,863,121 – 4,863,229
Length 108
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 92.84
Mean single sequence MFE -33.68
Consensus MFE -27.56
Energy contribution -28.12
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.74
Structure conservation index 0.82
SVM decision value 2.67
SVM RNA-class probability 0.996225
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4863121 108 + 22224390
ACGGCCAACUGUUCGAUCGCUGCACAAAUUAUAAUUUGCCAAGUAUUCGCAUUUUAGCGGCAACUUUGUCGCCAGAAUGCG-GAUUGGAAUUACCACAA-----CCAGCGGUUU
((((....))))..((((((((..(((((....)))))(((...(((((((((((.((((((....)))))).))))))))-))))))...........-----.)))))))). ( -35.30)
>DroSec_CAF1 14895 113 + 1
ACGGCCAACUGUUCGAUCGCUGCACAAAUUAUAAUUUGCCAAGUAUUCGCAUUUUAGCGGCAACUUUGUCGCCAGAAUGCG-GAUUGGAAUUACCACAACACAACCAGCAGUUU
.((..(....)..))...(((((.(((((....)))))(((...(((((((((((.((((((....)))))).))))))))-))))))...................))))).. ( -33.30)
>DroSim_CAF1 14881 114 + 1
ACGGCCAACUGUUCGAUCGCUGCACAAAUUAUAAUUUGCCAAGUAUUCGCAUUUUAGCGGCAACUUUGUCGCCAGAAUGCGGGAUUGGAAUUACCACAACACAGCCAGCAGUUU
......(((((((.....((((..(((((....)))))((((...((((((((((.((((((....)))))).)))))))))).)))).............)))).))))))). ( -34.00)
>DroEre_CAF1 17924 107 + 1
ACGGCCAACUGUUCGAUCGCCGCACAAAUUAUAAUAUGCCAAGUAUUCGCAUUUUAGCGGCAACUUUGUCGCCAGAAUGCG-GAUUGGAAUUACCACAA-----CUAGGAGU-U
.((((.............))))................((.((((((((((((((.((((((....)))))).))))))))-)))(((.....)))..)-----)).))...-. ( -29.92)
>DroYak_CAF1 15098 107 + 1
ACGGCCAACUGUUUGAUGGCCGCACAAAUUAUAAUUUGCCAAGUAUUCGCAUUUUAGCGGCAACUUUGUCGCCAGAAUGCG-GAUUGGAAUUGCCACAA-----CUAGCUGU-U
..(((((.(.....).)))))((((((((....)))))(((...(((((((((((.((((((....)))))).))))))))-))))))...))).....-----........-. ( -35.90)
>consensus
ACGGCCAACUGUUCGAUCGCUGCACAAAUUAUAAUUUGCCAAGUAUUCGCAUUUUAGCGGCAACUUUGUCGCCAGAAUGCG_GAUUGGAAUUACCACAA_____CCAGCAGUUU
.((..(....)..))...(((((.(((((....)))))((((.....((((((((.((((((....)))))).))))))))...))))...................))))).. (-27.56 = -28.12 +   0.56)

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 10:18:03 2006