Locus 4522

Sequence ID 2L_DroMel_CAF1
Location 12,963,913 – 12,964,048
Length 135
Max. P 0.985768
window7112 window7113 window7114 window7115

overview

Window 2

Location 12,963,913 – 12,964,008
Length 95
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.79
Mean single sequence MFE -34.92
Consensus MFE -16.34
Energy contribution -16.45
Covariance contribution 0.11
Combinations/Pair 1.20
Mean z-score -2.31
Structure conservation index 0.47
SVM decision value 0.95
SVM RNA-class probability 0.889003
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12963913 95 + 22407834
GCGAACCUUU--UUUGAUUAUGAUUGGGACACAUGGU-GAAAUG---ACUG-----------------CUGGUCAACUCAAUAUGGCUAAAAGCCAA--GCGAGAUGGCCAGCAGGUCCU
..........--.............(((((.(((...-...)))---.(((-----------------(((((((.(((....((((.....)))).--..))).))))))))))))))) ( -35.50)
>DroPse_CAF1 43482 120 + 1
GCGGACCUUUUUUUUGAUUAUGAUUCGAACACAUGGGCGACACAGGGUUUGGGGGGUAGGGGAGGGGAGGGGCUGACUCAAUAAGGCUAAAAGCCAGCGACGAGGACGCCACGAGGUCCU
..(((((((((((((..((((..(((((((...(((....).))..)))))))..))))..)))))))..(((...(((.....(((.....)))......)))...)))...)))))). ( -35.50)
>DroSec_CAF1 8706 95 + 1
GCGAACCUUU--UUUGAUUAUGAUUGGGACACAUGGU-GAAAUG---ACUG-----------------CUGGUCAACUCAAUAUGGCUAAAAGCCAA--GCGAGUUGGCCAGCAGGUCCU
..........--.............(((((.(((...-...)))---.(((-----------------(((((((((((....((((.....)))).--..))))))))))))))))))) ( -39.70)
>DroSim_CAF1 9522 95 + 1
GCGAACCUUU--UUUGAUUAUGAUUGGGACACAUGGU-GAAAUG---ACUG-----------------CUGGUCAACUCAAUAUGGCUAAAAGCCAA--GCGAGAUGGCCAGCAGGUCCU
..........--.............(((((.(((...-...)))---.(((-----------------(((((((.(((....((((.....)))).--..))).))))))))))))))) ( -35.50)
>DroYak_CAF1 10206 95 + 1
GCGAACCUUU--UUUGAUUAUGAUUGGGACACAUGGC-GAAAUG---ACUG-----------------CUGGUCAACUCAAUAUGGCUAAAAGCCAA--GCGAGAAAGCCAGCAGGUCCU
..........--.............(((((.(((...-...)))---.(((-----------------(((((...(((....((((.....)))).--..)))...))))))))))))) ( -30.30)
>DroPer_CAF1 41830 120 + 1
GCGGACCUUUUUUUUGAUUAUGAUUGGAACACAUGGGCGACACAGGGUUUGGGGGGUAGGGGAGGGGAGGGGCUGACUCAAUAAGGCUAAAAGCCAGCGACGAGGACGCCACGAGGUCCU
..(((((((((((((..((((..((.((((...(((....).))..)))).))..))))..)))))))..(((...(((.....(((.....)))......)))...)))...)))))). ( -33.00)
>consensus
GCGAACCUUU__UUUGAUUAUGAUUGGGACACAUGGU_GAAAUG___ACUG_________________CUGGUCAACUCAAUAUGGCUAAAAGCCAA__GCGAGAAGGCCAGCAGGUCCU
..........................((((....((((........))))..................(((((...(((....((((.....)))).....)))...)))))...)))). (-16.34 = -16.45 +   0.11)

alignment

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secondary structure

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Window 3

Location 12,963,913 – 12,964,008
Length 95
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.79
Mean single sequence MFE -29.35
Consensus MFE -21.08
Energy contribution -21.08
Covariance contribution 0.00
Combinations/Pair 1.09
Mean z-score -2.48
Structure conservation index 0.72
SVM decision value 2.00
SVM RNA-class probability 0.985326
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12963913 95 - 22407834
AGGACCUGCUGGCCAUCUCGC--UUGGCUUUUAGCCAUAUUGAGUUGACCAG-----------------CAGU---CAUUUC-ACCAUGUGUCCCAAUCAUAAUCAAA--AAAGGUUCGC
.(((((((((((.((.((((.--.((((.....))))...)))).)).))))-----------------)...---......-....((((.......))))......--..)))))).. ( -30.00)
>DroPse_CAF1 43482 120 - 1
AGGACCUCGUGGCGUCCUCGUCGCUGGCUUUUAGCCUUAUUGAGUCAGCCCCUCCCCUCCCCUACCCCCCAAACCCUGUGUCGCCCAUGUGUUCGAAUCAUAAUCAAAAAAAAGGUCCGC
.((((((...((((....))))((((((((...........))))))))...........................(((((((..(....)..)))..))))..........)))))).. ( -27.00)
>DroSec_CAF1 8706 95 - 1
AGGACCUGCUGGCCAACUCGC--UUGGCUUUUAGCCAUAUUGAGUUGACCAG-----------------CAGU---CAUUUC-ACCAUGUGUCCCAAUCAUAAUCAAA--AAAGGUUCGC
.(((((((((((.(((((((.--.((((.....))))...))))))).))))-----------------)...---......-....((((.......))))......--..)))))).. ( -34.10)
>DroSim_CAF1 9522 95 - 1
AGGACCUGCUGGCCAUCUCGC--UUGGCUUUUAGCCAUAUUGAGUUGACCAG-----------------CAGU---CAUUUC-ACCAUGUGUCCCAAUCAUAAUCAAA--AAAGGUUCGC
.(((((((((((.((.((((.--.((((.....))))...)))).)).))))-----------------)...---......-....((((.......))))......--..)))))).. ( -30.00)
>DroYak_CAF1 10206 95 - 1
AGGACCUGCUGGCUUUCUCGC--UUGGCUUUUAGCCAUAUUGAGUUGACCAG-----------------CAGU---CAUUUC-GCCAUGUGUCCCAAUCAUAAUCAAA--AAAGGUUCGC
.((((((((((((...((((.--.((((.....))))...))))..).))))-----------------)...---......-....((((.......))))......--..)))))).. ( -28.00)
>DroPer_CAF1 41830 120 - 1
AGGACCUCGUGGCGUCCUCGUCGCUGGCUUUUAGCCUUAUUGAGUCAGCCCCUCCCCUCCCCUACCCCCCAAACCCUGUGUCGCCCAUGUGUUCCAAUCAUAAUCAAAAAAAAGGUCCGC
.((((((.(.((((.(...(..((((((((...........))))))))..).................((.....)).).))))).((((.......))))..........)))))).. ( -27.00)
>consensus
AGGACCUGCUGGCCAUCUCGC__UUGGCUUUUAGCCAUAUUGAGUUGACCAG_________________CAGU___CAUUUC_ACCAUGUGUCCCAAUCAUAAUCAAA__AAAGGUUCGC
.((((((.((((....((((....((((.....))))...))))....))))...................................((((.......))))..........)))))).. (-21.08 = -21.08 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,963,950 – 12,964,048
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.18
Mean single sequence MFE -34.53
Consensus MFE -20.27
Energy contribution -20.67
Covariance contribution 0.39
Combinations/Pair 1.17
Mean z-score -2.94
Structure conservation index 0.59
SVM decision value 2.02
SVM RNA-class probability 0.985768
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12963950 98 + 22407834
AAUG---ACUG-----------------CUGGUCAACUCAAUAUGGCUAAAAGCCAA--GCGAGAUGGCCAGCAGGUCCUUGGGUAUUAGGCUAAUUGCUGAACCAACCUGAAAAGAUAU
....---.(((-----------------(((((((.(((....((((.....)))).--..))).))))))))))(((.(..(((....(((.....)))......)))..)...))).. ( -36.00)
>DroPse_CAF1 43522 120 + 1
CACAGGGUUUGGGGGGUAGGGGAGGGGAGGGGCUGACUCAAUAAGGCUAAAAGCCAGCGACGAGGACGCCACGAGGUCCUUGGGUAUUAGGCUAAUUGUCGGACCAAGCUGAAAAGAUAU
.....(((((((......(((..((.......))..))).....(((....((((.((..(((((((........))))))).))....))))....)))...))))))).......... ( -32.10)
>DroSec_CAF1 8743 98 + 1
AAUG---ACUG-----------------CUGGUCAACUCAAUAUGGCUAAAAGCCAA--GCGAGUUGGCCAGCAGGUCCUUGGGUAUUAGGCUAAUUGCUGAACCAACCUGAAAAGAUAU
....---.(((-----------------(((((((((((....((((.....)))).--..))))))))))))))(((.(..(((....(((.....)))......)))..)...))).. ( -40.20)
>DroSim_CAF1 9559 98 + 1
AAUG---ACUG-----------------CUGGUCAACUCAAUAUGGCUAAAAGCCAA--GCGAGAUGGCCAGCAGGUCCUUGGGUAUUAGGCUAAUUGCUGAACCAACCUGAAAAGAUAU
....---.(((-----------------(((((((.(((....((((.....)))).--..))).))))))))))(((.(..(((....(((.....)))......)))..)...))).. ( -36.00)
>DroYak_CAF1 10243 98 + 1
AAUG---ACUG-----------------CUGGUCAACUCAAUAUGGCUAAAAGCCAA--GCGAGAAAGCCAGCAGGUCCUUGGGUAUUAGGCUAAUUCCUGAACCAACCUGAAAAGAUAU
....---.(((-----------------(((((...(((....((((.....)))).--..)))...))))))))(((.(..(((.(((((......)))))....)))..)...))).. ( -30.80)
>DroPer_CAF1 41870 120 + 1
CACAGGGUUUGGGGGGUAGGGGAGGGGAGGGGCUGACUCAAUAAGGCUAAAAGCCAGCGACGAGGACGCCACGAGGUCCUUGGGUAUUAGGCUAAUUGUCGGACCAAGCUGAAAAGAUAU
.....(((((((......(((..((.......))..))).....(((....((((.((..(((((((........))))))).))....))))....)))...))))))).......... ( -32.10)
>consensus
AAUG___ACUG_________________CUGGUCAACUCAAUAUGGCUAAAAGCCAA__GCGAGAAGGCCAGCAGGUCCUUGGGUAUUAGGCUAAUUGCUGAACCAACCUGAAAAGAUAU
............................(((((...(((....((((.....)))).....)))...)))))(((((.....(((....(((.....)))..))).)))))......... (-20.27 = -20.67 +   0.39)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,963,950 – 12,964,048
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.18
Mean single sequence MFE -30.43
Consensus MFE -16.65
Energy contribution -16.32
Covariance contribution -0.33
Combinations/Pair 1.12
Mean z-score -2.95
Structure conservation index 0.55
SVM decision value 1.96
SVM RNA-class probability 0.984096
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12963950 98 - 22407834
AUAUCUUUUCAGGUUGGUUCAGCAAUUAGCCUAAUACCCAAGGACCUGCUGGCCAUCUCGC--UUGGCUUUUAGCCAUAUUGAGUUGACCAG-----------------CAGU---CAUU
..........(((((((((....)))))))))..........(((.((((((.((.((((.--.((((.....))))...)))).)).))))-----------------))))---)... ( -33.40)
>DroPse_CAF1 43522 120 - 1
AUAUCUUUUCAGCUUGGUCCGACAAUUAGCCUAAUACCCAAGGACCUCGUGGCGUCCUCGUCGCUGGCUUUUAGCCUUAUUGAGUCAGCCCCUCCCCUCCCCUACCCCCCAAACCCUGUG
...........((..(((((.....................)))))..))((((....))))((((((((...........))))))))............................... ( -22.90)
>DroSec_CAF1 8743 98 - 1
AUAUCUUUUCAGGUUGGUUCAGCAAUUAGCCUAAUACCCAAGGACCUGCUGGCCAACUCGC--UUGGCUUUUAGCCAUAUUGAGUUGACCAG-----------------CAGU---CAUU
..........(((((((((....)))))))))..........(((.((((((.(((((((.--.((((.....))))...))))))).))))-----------------))))---)... ( -37.50)
>DroSim_CAF1 9559 98 - 1
AUAUCUUUUCAGGUUGGUUCAGCAAUUAGCCUAAUACCCAAGGACCUGCUGGCCAUCUCGC--UUGGCUUUUAGCCAUAUUGAGUUGACCAG-----------------CAGU---CAUU
..........(((((((((....)))))))))..........(((.((((((.((.((((.--.((((.....))))...)))).)).))))-----------------))))---)... ( -33.40)
>DroYak_CAF1 10243 98 - 1
AUAUCUUUUCAGGUUGGUUCAGGAAUUAGCCUAAUACCCAAGGACCUGCUGGCUUUCUCGC--UUGGCUUUUAGCCAUAUUGAGUUGACCAG-----------------CAGU---CAUU
..........(((((((((....)))))))))..........(((.(((((((...((((.--.((((.....))))...))))..).))))-----------------))))---)... ( -32.50)
>DroPer_CAF1 41870 120 - 1
AUAUCUUUUCAGCUUGGUCCGACAAUUAGCCUAAUACCCAAGGACCUCGUGGCGUCCUCGUCGCUGGCUUUUAGCCUUAUUGAGUCAGCCCCUCCCCUCCCCUACCCCCCAAACCCUGUG
...........((..(((((.....................)))))..))((((....))))((((((((...........))))))))............................... ( -22.90)
>consensus
AUAUCUUUUCAGGUUGGUUCAGCAAUUAGCCUAAUACCCAAGGACCUGCUGGCCAUCUCGC__UUGGCUUUUAGCCAUAUUGAGUUGACCAG_________________CAGU___CAUU
...........((..(((((.....................)))))..))((....((((....((((.....))))...))))....)).............................. (-16.65 = -16.32 +  -0.33)

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 11:19:53 2006