Locus 4201

Sequence ID 3R_DroMel_CAF1
Location 11,350,266 – 11,350,408
Length 142
Max. P 0.999908
window6774 window6775 window6776 window6777

overview

Window 4

Location 11,350,266 – 11,350,386
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.91
Mean single sequence MFE -26.02
Consensus MFE -20.66
Energy contribution -20.70
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.84
Structure conservation index 0.79
SVM decision value 0.81
SVM RNA-class probability 0.856789
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11350266 120 + 27905053
GCUUGAUUUAAUUAAUUUCAAUUUUAAAUCAGCUAAAAUCCCCCUGAAAGCCAACUCAAAACCCGACUCGAAGUCCCAAUUCGGGGAAUAUCAGGCCAAAAGUUUAAGUCCUUCAGGAGU
(((.(((((((............)))))))))).........((((((.((.((((.....((.((.......((((......))))...)).)).....))))...))..))))))... ( -22.50)
>DroSec_CAF1 92502 120 + 1
GCUUGAUUUAAUUAAUUUCAAUUUUAAAUCAGCUAAACUCCCCCUGAAAGCUAACUCCAAACCCGACUCAACGUCCCAAUUCGGGGAAUAUCAGGGCAAAAGUUUAAGUCCUUCAGGAGU
(((.(((((((............))))))))))...((((((((((((((....))........(((.....)))....)))))))......(((((..........)))))...))))) ( -27.20)
>DroSim_CAF1 87691 120 + 1
GCUUGAUUUAAUUAAUUUCAAUUUUAAAUCAGCUAAAUUCCCCCUGAAAGCCAACUCAAAACCCGACUCGACGUCCCAAUUCGGGGAAUAUCAGGGCAAAAGUUUAAGUCCUUCAGGAGU
(((.(((((((............)))))))))).........((((((.....................((..((((......))))...)).((((..........))))))))))... ( -25.40)
>DroEre_CAF1 85481 119 + 1
GCGUGAUUUAAUUAAUUUCAAUUUUAAAUCAGCAAAAGUGCCCCUGAAAGCCAACUG-AAACCCGACUUGAAGUCCCAAUUCGGGGAAUAUCAGGCCAAAAGUUUAACUCCUUCAGGAGU
((.((((((((............))))))))))......((.((((((.(((.....-...(((((.(((......))).)))))........)))....((.....))..)))))).)) ( -28.79)
>DroYak_CAF1 87780 119 + 1
GCUUGAUUUAAUUAAUUUCAAUUUUAAAUCACCAAAAUUCCCCUUGAAAGCCAACUG-AAACCCGACUUGAAGUCCCAAUUCAGGGAAUAUCAGGCCAAAAGUUGAACUCCUUCAGGAGU
(((((((((((............)))))))..(((........))).))))(((((.-......(.(((((..((((......))))...))))))....))))).(((((....))))) ( -26.20)
>consensus
GCUUGAUUUAAUUAAUUUCAAUUUUAAAUCAGCUAAAUUCCCCCUGAAAGCCAACUC_AAACCCGACUCGAAGUCCCAAUUCGGGGAAUAUCAGGCCAAAAGUUUAAGUCCUUCAGGAGU
((.((((((((............)))))))))).........((((((.(..((((.....((.((.......((((......))))...)).)).....)))).....).))))))... (-20.66 = -20.70 +   0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,350,266 – 11,350,386
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.91
Mean single sequence MFE -36.64
Consensus MFE -33.06
Energy contribution -34.26
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.88
Structure conservation index 0.90
SVM decision value 4.49
SVM RNA-class probability 0.999908
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11350266 120 - 27905053
ACUCCUGAAGGACUUAAACUUUUGGCCUGAUAUUCCCCGAAUUGGGACUUCGAGUCGGGUUUUGAGUUGGCUUUCAGGGGGAUUUUAGCUGAUUUAAAAUUGAAAUUAAUUAAAUCAAGC
.((((((((((.((..(((((..((((((((..((((......))))......))))))))..))))))))))))))))).......((((((((((............))))))).))) ( -39.60)
>DroSec_CAF1 92502 120 - 1
ACUCCUGAAGGACUUAAACUUUUGCCCUGAUAUUCCCCGAAUUGGGACGUUGAGUCGGGUUUGGAGUUAGCUUUCAGGGGGAGUUUAGCUGAUUUAAAAUUGAAAUUAAUUAAAUCAAGC
.((((((((((.((..((((((.((((.(((..((((......))))......)))))))..)))))))))))))))))).......((((((((((............))))))).))) ( -36.40)
>DroSim_CAF1 87691 120 - 1
ACUCCUGAAGGACUUAAACUUUUGCCCUGAUAUUCCCCGAAUUGGGACGUCGAGUCGGGUUUUGAGUUGGCUUUCAGGGGGAAUUUAGCUGAUUUAAAAUUGAAAUUAAUUAAAUCAAGC
.((((((((((.((..(((((..((((((((..((((......)))).))))....))))...))))))))))))))))).......((((((((((............))))))).))) ( -37.00)
>DroEre_CAF1 85481 119 - 1
ACUCCUGAAGGAGUUAAACUUUUGGCCUGAUAUUCCCCGAAUUGGGACUUCAAGUCGGGUUU-CAGUUGGCUUUCAGGGGCACUUUUGCUGAUUUAAAAUUGAAAUUAAUUAAAUCACGC
.((((((((((.....((((...((((((((..((((......))))......)))))))).-.))))..)))))))))).......((((((((((............)))))))).)) ( -35.20)
>DroYak_CAF1 87780 119 - 1
ACUCCUGAAGGAGUUCAACUUUUGGCCUGAUAUUCCCUGAAUUGGGACUUCAAGUCGGGUUU-CAGUUGGCUUUCAAGGGGAAUUUUGGUGAUUUAAAAUUGAAAUUAAUUAAAUCAAGC
.((((((((((...((((((...((((((((..((((......))))......)))))))).-.))))))))))).)))))(((((..((........))..)))))............. ( -35.00)
>consensus
ACUCCUGAAGGACUUAAACUUUUGGCCUGAUAUUCCCCGAAUUGGGACUUCGAGUCGGGUUU_GAGUUGGCUUUCAGGGGGAAUUUAGCUGAUUUAAAAUUGAAAUUAAUUAAAUCAAGC
.((((((((((.....(((((..((((((((..((((......))))......))))))))..)))))..)))))))))).......((((((((((............)))))))).)) (-33.06 = -34.26 +   1.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,350,306 – 11,350,408
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.79
Mean single sequence MFE -29.09
Consensus MFE -19.40
Energy contribution -20.16
Covariance contribution 0.76
Combinations/Pair 1.04
Mean z-score -1.92
Structure conservation index 0.67
SVM decision value 0.14
SVM RNA-class probability 0.602999
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11350306 102 + 27905053
CCCCUGAAAGCCAACUCAAAACCCGACUCGAAGUCCCAAUUCGGGGAAUAUCAGGCCAAAAGUUUAAGUCCUUCAGGAGUUGCGCGAUUCGCAUUCAGGCAA------------------
..((((((.((.(((((.......((((.((..((((......))))...))((((.....)))).))))......)))))))(((...))).))))))...------------------ ( -26.92)
>DroSec_CAF1 92542 102 + 1
CCCCUGAAAGCUAACUCCAAACCCGACUCAACGUCCCAAUUCGGGGAAUAUCAGGGCAAAAGUUUAAGUCCUUCAGGAGUUGCACGAUUCGCAUUCAGGCAA------------------
..((((((.(((((((((...(((((..............))))).......(((((..........)))))...)))))))........)).))))))...------------------ ( -28.64)
>DroSim_CAF1 87731 120 + 1
CCCCUGAAAGCCAACUCAAAACCCGACUCGACGUCCCAAUUCGGGGAAUAUCAGGGCAAAAGUUUAAGUCCUUCAGGAGUUGCACGAUUCGCAUUCAGGCAAGCCAUGGCGAAUUUCCCU
.((((((................((......))((((......))))...)))))).....((.(((.(((....))).))).))(((((((.....((....))...)))))))..... ( -30.20)
>DroEre_CAF1 85521 101 + 1
CCCCUGAAAGCCAACUG-AAACCCGACUUGAAGUCCCAAUUCGGGGAAUAUCAGGCCAAAAGUUUAACUCCUUCAGGAGUUGCGCGAUUCGCAUUCAGACAA------------------
...(((((.((...(((-(..(((((.(((......))).))))).....)))).......((.(((((((....))))))).)).....)).)))))....------------------ ( -32.30)
>DroYak_CAF1 87820 97 + 1
CCCUUGAAAGCCAACUG-AAACCCGACUUGAAGUCCCAAUUCAGGGAAUAUCAGGCCAAAAGUUGAACUCCUUCAGGAGUUGCGCGAUUCGCAUUC----AA------------------
....((((.(((((((.-......(.(((((..((((......))))...))))))....)))))((((((....))))))))(((...))).)))----).------------------ ( -27.40)
>consensus
CCCCUGAAAGCCAACUC_AAACCCGACUCGAAGUCCCAAUUCGGGGAAUAUCAGGCCAAAAGUUUAAGUCCUUCAGGAGUUGCGCGAUUCGCAUUCAGGCAA__________________
..((((((.((..........((.((.......((((......))))...)).))......((.(((.(((....))).))).)).....)).))))))..................... (-19.40 = -20.16 +   0.76)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,350,306 – 11,350,408
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.79
Mean single sequence MFE -35.46
Consensus MFE -31.86
Energy contribution -32.62
Covariance contribution 0.76
Combinations/Pair 1.03
Mean z-score -1.82
Structure conservation index 0.90
SVM decision value 1.16
SVM RNA-class probability 0.923562
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11350306 102 - 27905053
------------------UUGCCUGAAUGCGAAUCGCGCAACUCCUGAAGGACUUAAACUUUUGGCCUGAUAUUCCCCGAAUUGGGACUUCGAGUCGGGUUUUGAGUUGGCUUUCAGGGG
------------------.........((((.....)))).((((((((((.((..(((((..((((((((..((((......))))......))))))))..))))))))))))))))) ( -37.40)
>DroSec_CAF1 92542 102 - 1
------------------UUGCCUGAAUGCGAAUCGUGCAACUCCUGAAGGACUUAAACUUUUGCCCUGAUAUUCCCCGAAUUGGGACGUUGAGUCGGGUUUGGAGUUAGCUUUCAGGGG
------------------((((.(((.......))).))))((((((((((.((..((((((.((((.(((..((((......))))......)))))))..)))))))))))))))))) ( -33.50)
>DroSim_CAF1 87731 120 - 1
AGGGAAAUUCGCCAUGGCUUGCCUGAAUGCGAAUCGUGCAACUCCUGAAGGACUUAAACUUUUGCCCUGAUAUUCCCCGAAUUGGGACGUCGAGUCGGGUUUUGAGUUGGCUUUCAGGGG
.(.(..((((((...((....)).....))))))..).)..((((((((((.((..(((((..((((((((..((((......)))).))))....))))...))))))))))))))))) ( -40.10)
>DroEre_CAF1 85521 101 - 1
------------------UUGUCUGAAUGCGAAUCGCGCAACUCCUGAAGGAGUUAAACUUUUGGCCUGAUAUUCCCCGAAUUGGGACUUCAAGUCGGGUUU-CAGUUGGCUUUCAGGGG
------------------.........((((.....)))).((((((((((.....((((...((((((((..((((......))))......)))))))).-.))))..)))))))))) ( -34.10)
>DroYak_CAF1 87820 97 - 1
------------------UU----GAAUGCGAAUCGCGCAACUCCUGAAGGAGUUCAACUUUUGGCCUGAUAUUCCCUGAAUUGGGACUUCAAGUCGGGUUU-CAGUUGGCUUUCAAGGG
------------------((----(((.(((...)))((((((((....))))))(((((...((((((((..((((......))))......)))))))).-.))))))).)))))... ( -32.20)
>consensus
__________________UUGCCUGAAUGCGAAUCGCGCAACUCCUGAAGGACUUAAACUUUUGGCCUGAUAUUCCCCGAAUUGGGACUUCGAGUCGGGUUU_GAGUUGGCUUUCAGGGG
...........................((((.....)))).((((((((((.....(((((..((((((((..((((......))))......))))))))..)))))..)))))))))) (-31.86 = -32.62 +   0.76)

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 11:21:30 2006