Locus 3051

Sequence ID 3R_DroMel_CAF1
Location 8,093,184 – 8,093,384
Length 200
Max. P 0.999901
window4936 window4937 window4938 window4939 window4940

overview

Window 6

Location 8,093,184 – 8,093,304
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.47
Mean single sequence MFE -33.46
Consensus MFE -32.96
Energy contribution -32.92
Covariance contribution -0.04
Combinations/Pair 1.03
Mean z-score -1.92
Structure conservation index 0.99
SVM decision value 2.96
SVM RNA-class probability 0.997902
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8093184 120 + 27905053
CAUAUAUAUGCAAUCUCAUAUGCAUUACUUUGCAUGUCUGGCGAGUUAAGGAACUCAAGCGUAAAGGUCAAAAGAUCAACGCUUGAGGGGCAAAAAUGGCAGGGAGGGAGGUUUUUCUAA
...........(((((((((((((......)))))))(((.((..((...(..(((((((((...((((....)))).)))))))))...).))..)).))).....))))))....... ( -33.50)
>DroSec_CAF1 44928 118 + 1
CAUA--UAUGCAAUCUCAUAUGCAUUACUUUGCAUGUCUGGCGAGUUAAGGAACUCAAGCGUAAAGGUCAAAAGAUCAACGCUUGAGGGGCAGAAAUGGCAGGGAGGGAGGUUUUUCUAA
....--.....(((((((((((((......)))))))(((.((..((...(..(((((((((...((((....)))).)))))))))...).))..)).))).....))))))....... ( -33.90)
>DroSim_CAF1 16962 118 + 1
CAUA--UAUGCAAUCUCAUAUGCAUUACUUUGCAUGUCUGGCGAGUUAAGGAACUCAAGCGUAAAGGUCAAAAGAUCAACGCUUGAGGGGCAGAAAUGGCAGGGAGGGAGGUUUUUCUAA
....--.....(((((((((((((......)))))))(((.((..((...(..(((((((((...((((....)))).)))))))))...).))..)).))).....))))))....... ( -33.90)
>DroEre_CAF1 19992 118 + 1
CAUA--CAUGCAAUCUCAUAUGCAUUACUUUGCAUGUCUGGCGAGUUAAGGAACUCAAGCGUAAAGGUCAAAAGAUCAACGCUAGAGGGGCAAAAAUGGCAGGGAGGGAGGUUUUUCUAA
....--...((..((((...(((.....(((((.(.(((((((((((....))))).........((((....))))...)))))).).)))))....)))..))))...))........ ( -32.40)
>DroYak_CAF1 13441 118 + 1
CAUA--UAUGCAAUCUCAUAUGCAUUACUUUGCAUGUCUGGCGAGUUAAGGAACUCAAGCGUAAAGGUCAAAAGAUCAACGCUUGAGGGACAGAAAUGGCAGGGAGGGAGGUUUUUCUAU
....--.....((((((.((((((......))))))(((.((...........(((((((((...((((....)))).)))))))))...((....))))..)))..))))))....... ( -33.60)
>consensus
CAUA__UAUGCAAUCUCAUAUGCAUUACUUUGCAUGUCUGGCGAGUUAAGGAACUCAAGCGUAAAGGUCAAAAGAUCAACGCUUGAGGGGCAGAAAUGGCAGGGAGGGAGGUUUUUCUAA
...........(((((((((((((......)))))))(((.((..((...(..(((((((((...((((....)))).)))))))))...).))..)).))).....))))))....... (-32.96 = -32.92 +  -0.04)

alignment

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secondary structure

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Window 7

Location 8,093,224 – 8,093,344
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.17
Mean single sequence MFE -41.24
Consensus MFE -39.54
Energy contribution -40.14
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -3.41
Structure conservation index 0.96
SVM decision value 4.45
SVM RNA-class probability 0.999901
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8093224 120 + 27905053
GCGAGUUAAGGAACUCAAGCGUAAAGGUCAAAAGAUCAACGCUUGAGGGGCAAAAAUGGCAGGGAGGGAGGUUUUUCUAAAGAAUUUCCCUACUUUUCCUGUGUUAAUGCUCUGAUUUCG
..((((((.....(((((((((...((((....)))).)))))))))(((((......(((((((((((((((((.....))))))))))).....)))))).....))))))))))).. ( -41.90)
>DroSec_CAF1 44966 120 + 1
GCGAGUUAAGGAACUCAAGCGUAAAGGUCAAAAGAUCAACGCUUGAGGGGCAGAAAUGGCAGGGAGGGAGGUUUUUCUAAAGAAUUUCCCUACUUUUCCUGUGUUAAUGCUCUGAUUUCG
..((((((.....(((((((((...((((....)))).)))))))))(((((..((((.((((((((((((((((.....))))))))))).....)))))))))..))))))))))).. ( -43.10)
>DroSim_CAF1 17000 120 + 1
GCGAGUUAAGGAACUCAAGCGUAAAGGUCAAAAGAUCAACGCUUGAGGGGCAGAAAUGGCAGGGAGGGAGGUUUUUCUAAAGAAUUUCCCUACUUUUCCUGUGUUAAUGCUCUGAUUUCG
..((((((.....(((((((((...((((....)))).)))))))))(((((..((((.((((((((((((((((.....))))))))))).....)))))))))..))))))))))).. ( -43.10)
>DroEre_CAF1 20030 120 + 1
GCGAGUUAAGGAACUCAAGCGUAAAGGUCAAAAGAUCAACGCUAGAGGGGCAAAAAUGGCAGGGAGGGAGGUUUUUCUAAAGAAUUUCCCUACUUUUCCCGUGUUAAUGCUCUGAUUUCG
..(((((....))))).(((((...((((....)))).)))))...((((((....(((((((((((((((((((.....))))))))))......)))).))))).))))))....... ( -37.50)
>DroYak_CAF1 13479 120 + 1
GCGAGUUAAGGAACUCAAGCGUAAAGGUCAAAAGAUCAACGCUUGAGGGACAGAAAUGGCAGGGAGGGAGGUUUUUCUAUAGAAUUUCCCUACUUUUCCUGUGUUAAUGCUCUGAUUUCG
..((((.......(((((((((...((((....)))).)))))))))...((....))(((((((((((((((((.....))))))))))).....))))))......))))........ ( -40.60)
>consensus
GCGAGUUAAGGAACUCAAGCGUAAAGGUCAAAAGAUCAACGCUUGAGGGGCAGAAAUGGCAGGGAGGGAGGUUUUUCUAAAGAAUUUCCCUACUUUUCCUGUGUUAAUGCUCUGAUUUCG
..((((((.....(((((((((...((((....)))).)))))))))(((((..((((.((((((((((((((((.....))))))))))).....)))))))))..))))))))))).. (-39.54 = -40.14 +   0.60)

alignment

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secondary structure

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Window 8

Location 8,093,224 – 8,093,344
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.17
Mean single sequence MFE -30.20
Consensus MFE -30.08
Energy contribution -29.88
Covariance contribution -0.20
Combinations/Pair 1.07
Mean z-score -2.55
Structure conservation index 1.00
SVM decision value 4.18
SVM RNA-class probability 0.999825
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8093224 120 - 27905053
CGAAAUCAGAGCAUUAACACAGGAAAAGUAGGGAAAUUCUUUAGAAAAACCUCCCUCCCUGCCAUUUUUGCCCCUCAAGCGUUGAUCUUUUGACCUUUACGCUUGAGUUCCUUAACUCGC
........(((........((((((..(((((((.....................)))))))..))))))...(((((((((.(.((....)).)...)))))))))........))).. ( -29.10)
>DroSec_CAF1 44966 120 - 1
CGAAAUCAGAGCAUUAACACAGGAAAAGUAGGGAAAUUCUUUAGAAAAACCUCCCUCCCUGCCAUUUCUGCCCCUCAAGCGUUGAUCUUUUGACCUUUACGCUUGAGUUCCUUAACUCGC
........(((........((((((..(((((((.....................)))))))..))))))...(((((((((.(.((....)).)...)))))))))........))).. ( -31.60)
>DroSim_CAF1 17000 120 - 1
CGAAAUCAGAGCAUUAACACAGGAAAAGUAGGGAAAUUCUUUAGAAAAACCUCCCUCCCUGCCAUUUCUGCCCCUCAAGCGUUGAUCUUUUGACCUUUACGCUUGAGUUCCUUAACUCGC
........(((........((((((..(((((((.....................)))))))..))))))...(((((((((.(.((....)).)...)))))))))........))).. ( -31.60)
>DroEre_CAF1 20030 120 - 1
CGAAAUCAGAGCAUUAACACGGGAAAAGUAGGGAAAUUCUUUAGAAAAACCUCCCUCCCUGCCAUUUUUGCCCCUCUAGCGUUGAUCUUUUGACCUUUACGCUUGAGUUCCUUAACUCGC
........(((.........((((((((((((((.....................)))))))...)))).)))(((.(((((.(.((....)).)...))))).)))........))).. ( -25.90)
>DroYak_CAF1 13479 120 - 1
CGAAAUCAGAGCAUUAACACAGGAAAAGUAGGGAAAUUCUAUAGAAAAACCUCCCUCCCUGCCAUUUCUGUCCCUCAAGCGUUGAUCUUUUGACCUUUACGCUUGAGUUCCUUAACUCGC
........(((.......(((((((..(((((((.....................)))))))..)))))))..(((((((((.(.((....)).)...)))))))))........))).. ( -32.80)
>consensus
CGAAAUCAGAGCAUUAACACAGGAAAAGUAGGGAAAUUCUUUAGAAAAACCUCCCUCCCUGCCAUUUCUGCCCCUCAAGCGUUGAUCUUUUGACCUUUACGCUUGAGUUCCUUAACUCGC
........(((........((((((..(((((((.....................)))))))..))))))...(((((((((.(.((....)).)...)))))))))........))).. (-30.08 = -29.88 +  -0.20)

alignment

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secondary structure

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Window 9

Location 8,093,264 – 8,093,384
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.00
Mean single sequence MFE -37.24
Consensus MFE -35.62
Energy contribution -35.54
Covariance contribution -0.08
Combinations/Pair 1.05
Mean z-score -2.31
Structure conservation index 0.96
SVM decision value 3.79
SVM RNA-class probability 0.999615
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8093264 120 + 27905053
GCUUGAGGGGCAAAAAUGGCAGGGAGGGAGGUUUUUCUAAAGAAUUUCCCUACUUUUCCUGUGUUAAUGCUCUGAUUUCGUUUCCAAAAAUGUACGCAGCAUUUGCAUUUGCCCAUUGUC
.......(((((((....(((((((((((((((((.....))))))))))).....))))))((.((((((.((....(((((....)))))..)).)))))).)).)))))))...... ( -38.50)
>DroSec_CAF1 45006 120 + 1
GCUUGAGGGGCAGAAAUGGCAGGGAGGGAGGUUUUUCUAAAGAAUUUCCCUACUUUUCCUGUGUUAAUGCUCUGAUUUCGUUUCGAAAAAUGUACGCAGCAUUUGCAUUUGCCCAUUGUC
.......(((((((....(((((((((((((((((.....))))))))))).....))))))((.((((((.((....(((((....)))))..)).)))))).)).)))))))...... ( -38.60)
>DroSim_CAF1 17040 120 + 1
GCUUGAGGGGCAGAAAUGGCAGGGAGGGAGGUUUUUCUAAAGAAUUUCCCUACUUUUCCUGUGUUAAUGCUCUGAUUUCGUUUCGAAAAAUGUACGCAGCAUUUGCAUUUGCCCAUUGUC
.......(((((((....(((((((((((((((((.....))))))))))).....))))))((.((((((.((....(((((....)))))..)).)))))).)).)))))))...... ( -38.60)
>DroEre_CAF1 20070 120 + 1
GCUAGAGGGGCAAAAAUGGCAGGGAGGGAGGUUUUUCUAAAGAAUUUCCCUACUUUUCCCGUGUUAAUGCUCUGAUUUCGUUUUGAAAAAUGUAUGCAGCAUUUGCAUUUGCCCAUUGUC
.......(((((((.((((.(((((((((((((((.....))))))))))).))))..))))((.((((((.......(((((....))))).....)))))).)).)))))))...... ( -36.10)
>DroYak_CAF1 13519 120 + 1
GCUUGAGGGACAGAAAUGGCAGGGAGGGAGGUUUUUCUAUAGAAUUUCCCUACUUUUCCUGUGUUAAUGCUCUGAUUUCGUUUCGAAAAAUGUAUGCAGCAUUUGCAUUUGCCCAUUGUC
......(((.((((....(((((((((((((((((.....))))))))))).....))))))((.((((((.......(((((....))))).....)))))).)).)))))))...... ( -34.40)
>consensus
GCUUGAGGGGCAGAAAUGGCAGGGAGGGAGGUUUUUCUAAAGAAUUUCCCUACUUUUCCUGUGUUAAUGCUCUGAUUUCGUUUCGAAAAAUGUACGCAGCAUUUGCAUUUGCCCAUUGUC
.......(((((((....(((((((((((((((((.....))))))))))).....))))))((.((((((.((....(((((....)))))..)).)))))).)).)))))))...... (-35.62 = -35.54 +  -0.08)

alignment

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secondary structure

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Window 0

Location 8,093,264 – 8,093,384
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.00
Mean single sequence MFE -26.68
Consensus MFE -23.52
Energy contribution -23.16
Covariance contribution -0.36
Combinations/Pair 1.10
Mean z-score -1.44
Structure conservation index 0.88
SVM decision value 0.52
SVM RNA-class probability 0.767337
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8093264 120 - 27905053
GACAAUGGGCAAAUGCAAAUGCUGCGUACAUUUUUGGAAACGAAAUCAGAGCAUUAACACAGGAAAAGUAGGGAAAUUCUUUAGAAAAACCUCCCUCCCUGCCAUUUUUGCCCCUCAAGC
......(((((((....((((((.(......(((((....)))))...)))))))....((((...((..(((...(((....)))...)))..)).)))).....)))))))....... ( -29.40)
>DroSec_CAF1 45006 120 - 1
GACAAUGGGCAAAUGCAAAUGCUGCGUACAUUUUUCGAAACGAAAUCAGAGCAUUAACACAGGAAAAGUAGGGAAAUUCUUUAGAAAAACCUCCCUCCCUGCCAUUUCUGCCCCUCAAGC
......((((.......((((((.(.......(((((...)))))...))))))).....(((((..(((((((.....................)))))))..)))))))))....... ( -26.30)
>DroSim_CAF1 17040 120 - 1
GACAAUGGGCAAAUGCAAAUGCUGCGUACAUUUUUCGAAACGAAAUCAGAGCAUUAACACAGGAAAAGUAGGGAAAUUCUUUAGAAAAACCUCCCUCCCUGCCAUUUCUGCCCCUCAAGC
......((((.......((((((.(.......(((((...)))))...))))))).....(((((..(((((((.....................)))))))..)))))))))....... ( -26.30)
>DroEre_CAF1 20070 120 - 1
GACAAUGGGCAAAUGCAAAUGCUGCAUACAUUUUUCAAAACGAAAUCAGAGCAUUAACACGGGAAAAGUAGGGAAAUUCUUUAGAAAAACCUCCCUCCCUGCCAUUUUUGCCCCUCUAGC
......(((((((.(((((((((.(.......((((.....))))...))))))).....((((......((((..(((....))).....)))))))))))....)))))))....... ( -25.90)
>DroYak_CAF1 13519 120 - 1
GACAAUGGGCAAAUGCAAAUGCUGCAUACAUUUUUCGAAACGAAAUCAGAGCAUUAACACAGGAAAAGUAGGGAAAUUCUAUAGAAAAACCUCCCUCCCUGCCAUUUCUGUCCCUCAAGC
......(((..((((((((((.......)))))((((...))))......)))))...(((((((..(((((((.....................)))))))..))))))))))...... ( -25.50)
>consensus
GACAAUGGGCAAAUGCAAAUGCUGCGUACAUUUUUCGAAACGAAAUCAGAGCAUUAACACAGGAAAAGUAGGGAAAUUCUUUAGAAAAACCUCCCUCCCUGCCAUUUCUGCCCCUCAAGC
......((((.((((((((((.......)))))(((.....)))......))))).....(((((..(((((((.....................)))))))..)))))))))....... (-23.52 = -23.16 +  -0.36)

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 10:51:38 2006