Locus 665

Sequence ID 2L_DroMel_CAF1
Location 1,965,407 – 1,965,527
Length 120
Max. P 0.970535
window1088 window1089 window1090

overview

Window 8

Location 1,965,407 – 1,965,499
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.80
Mean single sequence MFE -35.18
Consensus MFE -28.62
Energy contribution -28.62
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.81
SVM decision value 0.66
SVM RNA-class probability 0.815921
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1965407 92 + 22407834
-----------------AGCAACGGAUUCUCGUUGGACCCUUUAGCGCAUUGGAUAGCGCGUUGGACUUCUAAUCCAAAGGUGGCGGGUUCGAUUCCCGCAAGGGUUGA-----------
-----------------..((((((....))))))(((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))..----------- ( -34.20)
>DroSec_CAF1 7870 92 + 1
-----------------AGCAGCGGAUUCUCGUUGGACCCUUUAGCGCAUUGGAUAGCGCGUUGGACUUCUAAUCCAAAGGUGGCGGGUUCGAUUCCCGCAAGGGUUGA-----------
-----------------..((((((....))))))(((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))..----------- ( -34.20)
>DroSim_CAF1 12009 92 + 1
-----------------AGCAGCGGAUUCUCGUUGGACCCUUUAGCGCAUUGGAUAGCGCGUUGGACUUCUAAUCCAAAGGUGGCGGGUUCGAUUCCCGCAAGGGUUGA-----------
-----------------..((((((....))))))(((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))..----------- ( -34.20)
>DroEre_CAF1 17042 103 + 1
-----------------AUCCGGCGAAUCUCGUAGGACCCUUUAGCGCAUUGGAUAGCGCGUUGGACUUCUAAUCCAAAGGUGGCGGGUUCGAUUCCCGCAAGGGUUGAUUGCCAUUAGC
-----------------....(((.((((.....((((((....((((........)))).(((((.......))))).......))))))....(((....)))..)))))))...... ( -35.70)
>DroYak_CAF1 14896 103 + 1
-----------------AUGCGGCGAUUCGCGUAGGACCCUUUAGCGCAUUGGAUAGCGCGUUGGACUUCUAAUCCAAAGGUGGCGGGUUCGAUUCCCGCAAGGGUUGAUUGCCACUAGA
-----------------....(((((((.((...((((((....((((........)))).(((((.......))))).......)))))).....((....)))).)))))))...... ( -37.00)
>DroAna_CAF1 38382 119 + 1
AUAUGAAUGAGCAAAAAGUCGGGCGGAAGUUGUAAGACCCUUUGGCGCAGCGGAUAGCGCGUUGGACUUCUAAUCCAAAGGUCGCGGGUUCGAUCCCCGCAAGGGUUGAAA-ACACAAAC
..........((.....(((.(((....)))....)))((((((((((........))))(((((....))))).))))))..))(..(((((..(((....)))))))).-.)...... ( -35.80)
>consensus
_________________AGCAGCCGAUUCUCGUAGGACCCUUUAGCGCAUUGGAUAGCGCGUUGGACUUCUAAUCCAAAGGUGGCGGGUUCGAUUCCCGCAAGGGUUGA___________
...................................(((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))............. (-28.62 = -28.62 +  -0.00)

alignment

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secondary structure

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Window 9

Location 1,965,407 – 1,965,499
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.80
Mean single sequence MFE -31.93
Consensus MFE -28.30
Energy contribution -28.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.89
SVM decision value 1.33
SVM RNA-class probability 0.943428
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1965407 92 - 22407834
-----------UCAACCCUUGCGGGAAUCGAACCCGCCACCUUUGGAUUAGAAGUCCAACGCGCUAUCCAAUGCGCUAAAGGGUCCAACGAGAAUCCGUUGCU-----------------
-----------...(((((((((((.......))))).....((((((.....)))))).((((........))))..)))))).(((((......)))))..----------------- ( -32.40)
>DroSec_CAF1 7870 92 - 1
-----------UCAACCCUUGCGGGAAUCGAACCCGCCACCUUUGGAUUAGAAGUCCAACGCGCUAUCCAAUGCGCUAAAGGGUCCAACGAGAAUCCGCUGCU-----------------
-----------.........(((((..(((.((((.......((((((.....)))))).((((........))))....))))....)))...)))))....----------------- ( -28.50)
>DroSim_CAF1 12009 92 - 1
-----------UCAACCCUUGCGGGAAUCGAACCCGCCACCUUUGGAUUAGAAGUCCAACGCGCUAUCCAAUGCGCUAAAGGGUCCAACGAGAAUCCGCUGCU-----------------
-----------.........(((((..(((.((((.......((((((.....)))))).((((........))))....))))....)))...)))))....----------------- ( -28.50)
>DroEre_CAF1 17042 103 - 1
GCUAAUGGCAAUCAACCCUUGCGGGAAUCGAACCCGCCACCUUUGGAUUAGAAGUCCAACGCGCUAUCCAAUGCGCUAAAGGGUCCUACGAGAUUCGCCGGAU-----------------
.....((((((((..((((((((((.......))))).....((((((.....)))))).((((........))))..)))))((....)))))).))))...----------------- ( -33.90)
>DroYak_CAF1 14896 103 - 1
UCUAGUGGCAAUCAACCCUUGCGGGAAUCGAACCCGCCACCUUUGGAUUAGAAGUCCAACGCGCUAUCCAAUGCGCUAAAGGGUCCUACGCGAAUCGCCGCAU-----------------
....(((((......((((((((((.......))))).....((((((.....)))))).((((........))))..)))))((......))...)))))..----------------- ( -35.30)
>DroAna_CAF1 38382 119 - 1
GUUUGUGU-UUUCAACCCUUGCGGGGAUCGAACCCGCGACCUUUGGAUUAGAAGUCCAACGCGCUAUCCGCUGCGCCAAAGGGUCUUACAACUUCCGCCCGACUUUUUGCUCAUUCAUAU
(..((.((-.(((((...(((((((.......)))))))...)))))..(((((((....((((........))))....((((............))))))))))).)).))..).... ( -33.00)
>consensus
___________UCAACCCUUGCGGGAAUCGAACCCGCCACCUUUGGAUUAGAAGUCCAACGCGCUAUCCAAUGCGCUAAAGGGUCCAACGAGAAUCCCCUGAU_________________
..............(((((((((((.......))))).....((((((.....)))))).((((........))))..)))))).................................... (-28.30 = -28.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,965,430 – 1,965,527
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.76
Mean single sequence MFE -26.97
Consensus MFE -21.10
Energy contribution -21.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.78
SVM decision value 1.66
SVM RNA-class probability 0.970535
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1965430 97 - 22407834
CU--UUA-GCAU-----GUACA----AAAAAAGGAGUACU-----------UCAACCCUUGCGGGAAUCGAACCCGCCACCUUUGGAUUAGAAGUCCAACGCGCUAUCCAAUGCGCUAAA
..--...-....-----.....----....((((.((...-----------...))))))(((((.......))))).....((((((.....)))))).((((........)))).... ( -24.40)
>DroSec_CAF1 7893 91 - 1
CC--UAA------------ACA----AAAAAAGGAGUACU-----------UCAACCCUUGCGGGAAUCGAACCCGCCACCUUUGGAUUAGAAGUCCAACGCGCUAUCCAAUGCGCUAAA
..--...------------...----....((((.((...-----------...))))))(((((.......))))).....((((((.....)))))).((((........)))).... ( -24.40)
>DroSim_CAF1 12032 98 - 1
CC--CUAAGCAU-----GUACA----AAAAAAGGAGUACU-----------UCAACCCUUGCGGGAAUCGAACCCGCCACCUUUGGAUUAGAAGUCCAACGCGCUAUCCAAUGCGCUAAA
..--........-----.....----....((((.((...-----------...))))))(((((.......))))).....((((((.....)))))).((((........)))).... ( -24.40)
>DroEre_CAF1 17065 103 - 1
AC--C-----------UUUGCC----AAAAAAGUAGCACAGCUAAUGGCAAUCAACCCUUGCGGGAAUCGAACCCGCCACCUUUGGAUUAGAAGUCCAACGCGCUAUCCAAUGCGCUAAA
..--.-----------.(((((----(......((((...)))).)))))).........(((((.......))))).....((((((.....)))))).((((........)))).... ( -29.00)
>DroYak_CAF1 14919 118 - 1
GC--CAAAGCAUUUUAUUUGCCAGGCAAAAAAGUAGUACAUCUAGUGGCAAUCAACCCUUGCGGGAAUCGAACCCGCCACCUUUGGAUUAGAAGUCCAACGCGCUAUCCAAUGCGCUAAA
((--(...(((.......)))..))).......(((..(((...(((((...........(((((.......))))).....((((((.....))))))...)))))...)))..))).. ( -31.40)
>DroAna_CAF1 38422 104 - 1
ACAUC-----------UUUUAA----AUAUAAGUAACACAGUUUGUGU-UUUCAACCCUUGCGGGGAUCGAACCCGCGACCUUUGGAUUAGAAGUCCAACGCGCUAUCCGCUGCGCCAAA
....(-----------((((((----........(((((.....))))-)(((((...(((((((.......)))))))...))))))))))))......((((........)))).... ( -28.20)
>consensus
CC__C_A__________UUACA____AAAAAAGGAGUACA___________UCAACCCUUGCGGGAAUCGAACCCGCCACCUUUGGAUUAGAAGUCCAACGCGCUAUCCAAUGCGCUAAA
............................................................(((((.......))))).....((((((.....)))))).((((........)))).... (-21.10 = -21.10 +  -0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:22 2006