Locus 3654

Sequence ID X_DroMel_CAF1
Location 9,793,135 – 9,793,415
Length 280
Max. P 0.989219
window5975 window5976 window5977 window5978 window5979 window5980 window5981

overview

Window 5

Location 9,793,135 – 9,793,255
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 84.40
Mean single sequence MFE -30.40
Consensus MFE -19.64
Energy contribution -19.09
Covariance contribution -0.55
Combinations/Pair 1.13
Mean z-score -2.96
Structure conservation index 0.65
SVM decision value 1.00
SVM RNA-class probability 0.897622
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9793135 120 - 22224390
AUGGUGAAGAACUAGAACAAAAAAGGGCUUCAAGCUGGGAGCGAUUUAGUUUGAAUACUCAUAGAGAUUUCAGACUAAAUCAAUAGAUCAAGAUCUAUAGUUAGCCCUACUGUUUGAUUU
.((((.....))))(((((....((((((...(((((.....(((((((((((((..(((...)))..)))))))))))))..(((((....))))))))))))))))..)))))..... ( -36.40)
>DroSec_CAF1 7876 114 - 1
AUGGUGAAGAACUAGAACAAGAAAGGGCUUCAAG-----UCUGAUUUGGUGUGAAUACUCAUUGAAAACUCAGACUAAAAAAUAAGAUACAAGUCUGUAGUUAGCCUUACUUUUUGAAU-
.((((.....))))...((((((((((((.(.((-----(((((((..(((........)))..))...)))))))........((((....))))...)..))))))..))))))...- ( -26.20)
>DroSim_CAF1 9014 119 - 1
AUGGUGAAGAACUAGAACAAGAAAGGGCUUCAAGCUGGGUCUGAUUUGGUGUGAAUACUCAUUGAAAACUCAGACUAAAAAAUAAGAUACAAAUCUGUAGUUAGCCUUACUUUUUGAAU-
.((((.....))))...((((((((((((...((((((((((((((..(((........)))..))...)))))))........((((....)))).)))))))))))..))))))...- ( -28.60)
>consensus
AUGGUGAAGAACUAGAACAAGAAAGGGCUUCAAGCUGGGUCUGAUUUGGUGUGAAUACUCAUUGAAAACUCAGACUAAAAAAUAAGAUACAAAUCUGUAGUUAGCCUUACUUUUUGAAU_
.((((.....))))...((((((((((((.(.............((((((.(((...............))).)))))).....((((....))))...)..))))))..)))))).... (-19.64 = -19.09 +  -0.55)

alignment

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secondary structure

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Window 6

Location 9,793,215 – 9,793,335
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -36.13
Consensus MFE -33.80
Energy contribution -33.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -4.39
Structure conservation index 0.94
SVM decision value 1.73
SVM RNA-class probability 0.974238
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9793215 120 + 22224390
UCCCAGCUUGAAGCCCUUUUUUGUUCUAGUUCUUCACCAUAGGGGCAUUUAGCUGCUCCGAUGGCCAAAAAUACCUGCCCAUUUUUGGGCAUUUCACCAUUUUCCAUGGCCAUUGCCCAA
...(((((.((.((((((...((...........))....)))))).)).)))))...((((((((((((((...((((((....)))))).......)))))...)))))))))..... ( -37.30)
>DroSec_CAF1 7955 115 + 1
A-----CUUGAAGCCCUUUCUUGUUCUAGUUCUUCACCAUAGGGGCAUUUAGCUGCUCCGAUGGCCAAAAAUACCUGCCCAUUUUUGGGCAUUUCACCAUUUUCCAUGGCCAUUGCCCAA
.-----..(((((..((..........))..))))).....((((((......))))))(((((((((((((...((((((....)))))).......)))))...))))))))...... ( -33.80)
>DroSim_CAF1 9093 120 + 1
ACCCAGCUUGAAGCCCUUUCUUGUUCUAGUUCUUCACCAUAGGGGCAUUUAGCUGCUCCGAUGGCCAAAAAUACCUGCCCAUUUUUGGGCAUUUCACCAUUUUCCAUGGCCAUUGCCCAA
...(((((.((.((((((...((...........))....)))))).)).)))))...((((((((((((((...((((((....)))))).......)))))...)))))))))..... ( -37.30)
>consensus
ACCCAGCUUGAAGCCCUUUCUUGUUCUAGUUCUUCACCAUAGGGGCAUUUAGCUGCUCCGAUGGCCAAAAAUACCUGCCCAUUUUUGGGCAUUUCACCAUUUUCCAUGGCCAUUGCCCAA
........(((((..((..........))..))))).....((((((......))))))(((((((((((((...((((((....)))))).......)))))...))))))))...... (-33.80 = -33.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,793,215 – 9,793,335
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -37.71
Consensus MFE -36.00
Energy contribution -36.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.92
Structure conservation index 0.95
SVM decision value 1.94
SVM RNA-class probability 0.983149
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9793215 120 - 22224390
UUGGGCAAUGGCCAUGGAAAAUGGUGAAAUGCCCAAAAAUGGGCAGGUAUUUUUGGCCAUCGGAGCAGCUAAAUGCCCCUAUGGUGAAGAACUAGAACAAAAAAGGGCUUCAAGCUGGGA
(((((((.(.(((((.....))))).)..)))))))..((((.((((....)))).)))).....(((((....((((...((((.....))))..........))))....)))))... ( -38.52)
>DroSec_CAF1 7955 115 - 1
UUGGGCAAUGGCCAUGGAAAAUGGUGAAAUGCCCAAAAAUGGGCAGGUAUUUUUGGCCAUCGGAGCAGCUAAAUGCCCCUAUGGUGAAGAACUAGAACAAGAAAGGGCUUCAAG-----U
(((((((.(.(((((.....))))).)..)))))))...((..(.(((..((((.(((((.((.(((......))).)).))))).))))))).)..)).(((.....)))...-----. ( -36.10)
>DroSim_CAF1 9093 120 - 1
UUGGGCAAUGGCCAUGGAAAAUGGUGAAAUGCCCAAAAAUGGGCAGGUAUUUUUGGCCAUCGGAGCAGCUAAAUGCCCCUAUGGUGAAGAACUAGAACAAGAAAGGGCUUCAAGCUGGGU
(((((((.(.(((((.....))))).)..)))))))..((((.((((....)))).)))).....(((((....((((...((((.....))))..........))))....)))))... ( -38.52)
>consensus
UUGGGCAAUGGCCAUGGAAAAUGGUGAAAUGCCCAAAAAUGGGCAGGUAUUUUUGGCCAUCGGAGCAGCUAAAUGCCCCUAUGGUGAAGAACUAGAACAAGAAAGGGCUUCAAGCUGGGU
(((((((.(.(((((.....))))).)..)))))))...((..(.(((..((((.(((((.((.(((......))).)).))))).))))))).)..))..................... (-36.00 = -36.00 +   0.00)

alignment

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secondary structure

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Window 8

Location 9,793,255 – 9,793,375
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -39.70
Consensus MFE -38.89
Energy contribution -38.67
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -3.62
Structure conservation index 0.98
SVM decision value 2.15
SVM RNA-class probability 0.989219
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9793255 120 + 22224390
AGGGGCAUUUAGCUGCUCCGAUGGCCAAAAAUACCUGCCCAUUUUUGGGCAUUUCACCAUUUUCCAUGGCCAUUGCCCAAAACUGUAUUUAACGCCGAACAAAGGCCGCAUUAAGUGUCC
..((((((((((.(((..((((((((((((((...((((((....)))))).......)))))...)))))))))..................(((.......))).))))))))))))) ( -40.40)
>DroSec_CAF1 7990 120 + 1
AGGGGCAUUUAGCUGCUCCGAUGGCCAAAAAUACCUGCCCAUUUUUGGGCAUUUCACCAUUUUCCAUGGCCAUUGCCCAAAACUGUGUUUAACGCUGAACAAAGGCCGCAUUAAGUGUCC
..((((((((((.(((..((((((((((((((...((((((....)))))).......)))))...))))))))).......((.((((((....)))))).))...))))))))))))) ( -40.90)
>DroSim_CAF1 9133 120 + 1
AGGGGCAUUUAGCUGCUCCGAUGGCCAAAAAUACCUGCCCAUUUUUGGGCAUUUCACCAUUUUCCAUGGCCAUUGCCCAAAACUGUAUUUAACGCUGAACAAAGGCCGCAUUAAGUGUCC
..((((((((((.(((..((((((((((((((...((((((....)))))).......)))))...)))))))))..................(((.......))).))))))))))))) ( -37.80)
>consensus
AGGGGCAUUUAGCUGCUCCGAUGGCCAAAAAUACCUGCCCAUUUUUGGGCAUUUCACCAUUUUCCAUGGCCAUUGCCCAAAACUGUAUUUAACGCUGAACAAAGGCCGCAUUAAGUGUCC
..((((((((((.(((..((((((((((((((...((((((....)))))).......)))))...)))))))))..................(((.......))).))))))))))))) (-38.89 = -38.67 +  -0.22)

alignment

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secondary structure

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Window 9

Location 9,793,255 – 9,793,375
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -39.03
Consensus MFE -39.25
Energy contribution -39.03
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.98
Structure conservation index 1.01
SVM decision value 1.07
SVM RNA-class probability 0.911062
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9793255 120 - 22224390
GGACACUUAAUGCGGCCUUUGUUCGGCGUUAAAUACAGUUUUGGGCAAUGGCCAUGGAAAAUGGUGAAAUGCCCAAAAAUGGGCAGGUAUUUUUGGCCAUCGGAGCAGCUAAAUGCCCCU
((.((.(((.(((((((.((((((((..((......))..)))))))).))))((((..((..(((...((((((....))))))..)))..))..))))....)))..))).))))... ( -38.50)
>DroSec_CAF1 7990 120 - 1
GGACACUUAAUGCGGCCUUUGUUCAGCGUUAAACACAGUUUUGGGCAAUGGCCAUGGAAAAUGGUGAAAUGCCCAAAAAUGGGCAGGUAUUUUUGGCCAUCGGAGCAGCUAAAUGCCCCU
((.((.(((.(((((((.((((((((..((......))..)))))))).))))((((..((..(((...((((((....))))))..)))..))..))))....)))..))).))))... ( -39.30)
>DroSim_CAF1 9133 120 - 1
GGACACUUAAUGCGGCCUUUGUUCAGCGUUAAAUACAGUUUUGGGCAAUGGCCAUGGAAAAUGGUGAAAUGCCCAAAAAUGGGCAGGUAUUUUUGGCCAUCGGAGCAGCUAAAUGCCCCU
((.((.(((.(((((((.((((((((..((......))..)))))))).))))((((..((..(((...((((((....))))))..)))..))..))))....)))..))).))))... ( -39.30)
>consensus
GGACACUUAAUGCGGCCUUUGUUCAGCGUUAAAUACAGUUUUGGGCAAUGGCCAUGGAAAAUGGUGAAAUGCCCAAAAAUGGGCAGGUAUUUUUGGCCAUCGGAGCAGCUAAAUGCCCCU
((.((.(((.(((((((.((((((((..((......))..)))))))).))))((((..((..(((...((((((....))))))..)))..))..))))....)))..))).))))... (-39.25 = -39.03 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,793,295 – 9,793,415
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -37.65
Consensus MFE -35.72
Energy contribution -36.05
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.82
Structure conservation index 0.95
SVM decision value 0.43
SVM RNA-class probability 0.733518
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9793295 120 + 22224390
AUUUUUGGGCAUUUCACCAUUUUCCAUGGCCAUUGCCCAAAACUGUAUUUAACGCCGAACAAAGGCCGCAUUAAGUGUCCUAGCAGCCGCAGGCAGGAUGAAGGAUAAAGGAGUCCUGCU
..(((((((((.....((((.....))))....)))))))))((((.......(((.......)))(((.....)))...........))))(((((((.............))))))). ( -34.32)
>DroSec_CAF1 8030 120 + 1
AUUUUUGGGCAUUUCACCAUUUUCCAUGGCCAUUGCCCAAAACUGUGUUUAACGCUGAACAAAGGCCGCAUUAAGUGUCCUGGCAGCCGCAGGCAGGAUGAAGGAUAAAGGAGUCCUGCU
..(((((((((.....((((.....))))....)))))))))(((((......((((.....(((.(((.....))).)))..)))))))))(((((((.............))))))). ( -40.82)
>DroSim_CAF1 9173 120 + 1
AUUUUUGGGCAUUUCACCAUUUUCCAUGGCCAUUGCCCAAAACUGUAUUUAACGCUGAACAAAGGCCGCAUUAAGUGUCCUGGCAGCCGCAGGCAGGAUGAAGGAUAAAGGAGUCCUGCU
..(((((((((.....((((.....))))....)))))))))((((.......((((.....(((.(((.....))).)))..)))).))))(((((((.............))))))). ( -37.82)
>consensus
AUUUUUGGGCAUUUCACCAUUUUCCAUGGCCAUUGCCCAAAACUGUAUUUAACGCUGAACAAAGGCCGCAUUAAGUGUCCUGGCAGCCGCAGGCAGGAUGAAGGAUAAAGGAGUCCUGCU
..(((((((((.....((((.....))))....)))))))))((((.......((((.....(((.(((.....))).)))..)))).))))(((((((.............))))))). (-35.72 = -36.05 +   0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,793,295 – 9,793,415
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -37.09
Consensus MFE -36.98
Energy contribution -36.76
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.72
Structure conservation index 1.00
SVM decision value 0.61
SVM RNA-class probability 0.799020
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9793295 120 - 22224390
AGCAGGACUCCUUUAUCCUUCAUCCUGCCUGCGGCUGCUAGGACACUUAAUGCGGCCUUUGUUCGGCGUUAAAUACAGUUUUGGGCAAUGGCCAUGGAAAAUGGUGAAAUGCCCAAAAAU
.((((((...............))))))....((((((.((....))....)))))).....................(((((((((.(.(((((.....))))).)..))))))))).. ( -37.56)
>DroSec_CAF1 8030 120 - 1
AGCAGGACUCCUUUAUCCUUCAUCCUGCCUGCGGCUGCCAGGACACUUAAUGCGGCCUUUGUUCAGCGUUAAACACAGUUUUGGGCAAUGGCCAUGGAAAAUGGUGAAAUGCCCAAAAAU
.((((((...............))))))(((.((((((.((....))....))))))..((((........)))))))(((((((((.(.(((((.....))))).)..))))))))).. ( -37.56)
>DroSim_CAF1 9173 120 - 1
AGCAGGACUCCUUUAUCCUUCAUCCUGCCUGCGGCUGCCAGGACACUUAAUGCGGCCUUUGUUCAGCGUUAAAUACAGUUUUGGGCAAUGGCCAUGGAAAAUGGUGAAAUGCCCAAAAAU
.((((((...............))))))....((((((.((....))....)))))).....................(((((((((.(.(((((.....))))).)..))))))))).. ( -36.16)
>consensus
AGCAGGACUCCUUUAUCCUUCAUCCUGCCUGCGGCUGCCAGGACACUUAAUGCGGCCUUUGUUCAGCGUUAAAUACAGUUUUGGGCAAUGGCCAUGGAAAAUGGUGAAAUGCCCAAAAAU
.((((((...............))))))(((.((((((.((....))....))))))..((((........)))))))(((((((((.(.(((((.....))))).)..))))))))).. (-36.98 = -36.76 +  -0.22)

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 11:04:46 2006