Locus 6116

Sequence ID 2L_DroMel_CAF1
Location 17,116,960 – 17,117,152
Length 192
Max. P 0.999958
window9742 window9743 window9744 window9745

overview

Window 2

Location 17,116,960 – 17,117,080
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.92
Mean single sequence MFE -37.38
Consensus MFE -36.63
Energy contribution -36.67
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.17
Structure conservation index 0.98
SVM decision value 3.75
SVM RNA-class probability 0.999584
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17116960 120 + 22407834
GCGCAAGGGAAAUGCUCCAAAAAUACCUAAAUGCGUUAAUUGAGCGCGACAUUUGCUGAAACUACAGCAUUAUAUAAUGCAAAGCAGAAACGCCAAUGGCGGAUGCGUUGGCAGCGGAUG
((((..((..(((((.................)))))..))..))))..(((((((((.(((....(((((....)))))...(((....((((...))))..))))))..))))))))) ( -37.83)
>DroSec_CAF1 80763 120 + 1
GUGCAAGGGAAAUGCUCCAAAAAUACCUAACUGCGUUAAUUGAGCGCGACAUUUGCUGAAACUACAGCAUUAUAUAAUGCAAAGCAGGAACGCCAGUGGCGGAUGCGUUGGCAGCGGAUG
((((..((..(((((.................)))))..))..))))..(((((((((.(((....(((((....)))))...(((....((((...))))..))))))..))))))))) ( -35.93)
>DroSim_CAF1 96433 120 + 1
GCGCAAGGGAAAUGCUCCAAAAAUACCUAACUGCGUUAAUUGAGCGCGACAUUUGCUGAAACUACAGCAUUAUAUAAUGCAAAGCAGGAACGCCAGUGGCGGAUGCGUUGGCAGCGGAUG
((((..((..(((((.................)))))..))..))))..(((((((((.(((....(((((....)))))...(((....((((...))))..))))))..))))))))) ( -37.83)
>DroEre_CAF1 82859 120 + 1
GCGCAGGGGAAAUGCUCCAAAAAUACCUAACUGCGUUAAUUGAGCGCGACAUUUGCUGAAACUAGAGCAUUAUAUAAUGCAAAGCAGGAACGCCAGGGGCGGAUGCGUUGGCAGCGGAUG
((((.((((.....)))).........((((...)))).....))))..(((((((((.(((....(((((....)))))...(((....((((...))))..))))))..))))))))) ( -38.70)
>DroYak_CAF1 82710 120 + 1
GCGCAGGGGAAAUGCUCCAAAAAUACCUAACUGCGUUAAUUGAGCGCGACAUUUGCUGAAACUACAGCAUUAUAUAAUGCAAAGCAGGAACGCCAGAGGCGGAUGCGUUGGCAGCGGAUA
((((.((((.....)))).........((((...)))).....))))...((((((((.(((....(((((....)))))...(((....((((...))))..))))))..)))))))). ( -36.60)
>consensus
GCGCAAGGGAAAUGCUCCAAAAAUACCUAACUGCGUUAAUUGAGCGCGACAUUUGCUGAAACUACAGCAUUAUAUAAUGCAAAGCAGGAACGCCAGUGGCGGAUGCGUUGGCAGCGGAUG
((((..((..(((((.................)))))..))..))))..(((((((((.(((....(((((....)))))...(((....((((...))))..))))))..))))))))) (-36.63 = -36.67 +   0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,117,000 – 17,117,112
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.27
Mean single sequence MFE -39.76
Consensus MFE -36.90
Energy contribution -37.10
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.90
Structure conservation index 0.93
SVM decision value 4.87
SVM RNA-class probability 0.999958
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17117000 112 + 22407834
UGAGCGCGACAUUUGCUGAAACUACAGCAUUAUAUAAUGCAAAGCAGAAACGCCAAUGGCGGAUGCGUUGGCAGCGGAUGUAGAGCA--------GCGGAAAUUGGCUUAUAGAUGCCGG
...((((.((((((((((.(((....(((((....)))))...(((....((((...))))..))))))..))))))))))...)).--------))......((((........)))). ( -39.70)
>DroSec_CAF1 80803 112 + 1
UGAGCGCGACAUUUGCUGAAACUACAGCAUUAUAUAAUGCAAAGCAGGAACGCCAGUGGCGGAUGCGUUGGCAGCGGAUGUAGAGCA--------GCGGAAAUUGGCUUAUAGAUGCCGG
...((((.((((((((((.(((....(((((....)))))...(((....((((...))))..))))))..))))))))))...)).--------))......((((........)))). ( -39.70)
>DroSim_CAF1 96473 112 + 1
UGAGCGCGACAUUUGCUGAAACUACAGCAUUAUAUAAUGCAAAGCAGGAACGCCAGUGGCGGAUGCGUUGGCAGCGGAUGUAGAGCA--------UCGGAAAUUGGCUUAUAGAUGCCGG
.((((...((((((((((.(((....(((((....)))))...(((....((((...))))..))))))..))))))))))...)).--------))......((((........)))). ( -38.90)
>DroEre_CAF1 82899 120 + 1
UGAGCGCGACAUUUGCUGAAACUAGAGCAUUAUAUAAUGCAAAGCAGGAACGCCAGGGGCGGAUGCGUUGGCAGCGGAUGUAGCGCAGAAAUAGCGCGGAAAUUGGCUUAUAGAUGCCGG
...((((.((((((((((.(((....(((((....)))))...(((....((((...))))..))))))..)))))))))).)))).................((((........)))). ( -43.60)
>DroYak_CAF1 82750 112 + 1
UGAGCGCGACAUUUGCUGAAACUACAGCAUUAUAUAAUGCAAAGCAGGAACGCCAGAGGCGGAUGCGUUGGCAGCGGAUAUAGUGCA--------GCGGAAAUUGGCUUAUAGAUGCCGG
...((((...((((((((.(((....(((((....)))))...(((....((((...))))..))))))..))))))))...)))).--------........((((........)))). ( -36.90)
>consensus
UGAGCGCGACAUUUGCUGAAACUACAGCAUUAUAUAAUGCAAAGCAGGAACGCCAGUGGCGGAUGCGUUGGCAGCGGAUGUAGAGCA________GCGGAAAUUGGCUUAUAGAUGCCGG
...((...((((((((((.(((....(((((....)))))...(((....((((...))))..))))))..))))))))))...)).................((((........)))). (-36.90 = -37.10 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,117,000 – 17,117,112
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.27
Mean single sequence MFE -28.82
Consensus MFE -26.68
Energy contribution -26.52
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.85
Structure conservation index 0.93
SVM decision value 2.67
SVM RNA-class probability 0.996205
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17117000 112 - 22407834
CCGGCAUCUAUAAGCCAAUUUCCGC--------UGCUCUACAUCCGCUGCCAACGCAUCCGCCAUUGGCGUUUCUGCUUUGCAUUAUAUAAUGCUGUAGUUUCAGCAAAUGUCGCGCUCA
..(((........))).........--------.((.(.((((..((((((((.((....))..)))))(...((((...(((((....))))).))))...))))..)))).).))... ( -28.80)
>DroSec_CAF1 80803 112 - 1
CCGGCAUCUAUAAGCCAAUUUCCGC--------UGCUCUACAUCCGCUGCCAACGCAUCCGCCACUGGCGUUCCUGCUUUGCAUUAUAUAAUGCUGUAGUUUCAGCAAAUGUCGCGCUCA
..(((........))).........--------.((.(.((((..(((((((..((....))...))))....((((...(((((....))))).))))....)))..)))).).))... ( -27.40)
>DroSim_CAF1 96473 112 - 1
CCGGCAUCUAUAAGCCAAUUUCCGA--------UGCUCUACAUCCGCUGCCAACGCAUCCGCCACUGGCGUUCCUGCUUUGCAUUAUAUAAUGCUGUAGUUUCAGCAAAUGUCGCGCUCA
..(((........))).......((--------.((.(.((((..(((((((..((....))...))))....((((...(((((....))))).))))....)))..)))).).)))). ( -28.90)
>DroEre_CAF1 82899 120 - 1
CCGGCAUCUAUAAGCCAAUUUCCGCGCUAUUUCUGCGCUACAUCCGCUGCCAACGCAUCCGCCCCUGGCGUUCCUGCUUUGCAUUAUAUAAUGCUCUAGUUUCAGCAAAUGUCGCGCUCA
..(((........)))..................((((.((((..((((..((((((..((((...))))....)))...(((((....)))))....))).))))..)))).))))... ( -32.70)
>DroYak_CAF1 82750 112 - 1
CCGGCAUCUAUAAGCCAAUUUCCGC--------UGCACUAUAUCCGCUGCCAACGCAUCCGCCUCUGGCGUUCCUGCUUUGCAUUAUAUAAUGCUGUAGUUUCAGCAAAUGUCGCGCUCA
..(((........)))......(((--------.(((.(((((....(((.((.(((..((((...))))....))).)))))..))))).(((((......)))))..))).))).... ( -26.30)
>consensus
CCGGCAUCUAUAAGCCAAUUUCCGC________UGCUCUACAUCCGCUGCCAACGCAUCCGCCACUGGCGUUCCUGCUUUGCAUUAUAUAAUGCUGUAGUUUCAGCAAAUGUCGCGCUCA
..(((........)))..................((.(.((((..((((..((((((..((((...))))....)))...(((((....)))))....))).))))..)))).).))... (-26.68 = -26.52 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,117,040 – 17,117,152
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.19
Mean single sequence MFE -34.18
Consensus MFE -28.00
Energy contribution -28.68
Covariance contribution 0.68
Combinations/Pair 1.04
Mean z-score -1.39
Structure conservation index 0.82
SVM decision value 0.17
SVM RNA-class probability 0.617706
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17117040 112 - 22407834
UGGAACGGAAGGCGGGGCUAAAUAGCUACAUAUCUAUGGCCCGGCAUCUAUAAGCCAAUUUCCGC--------UGCUCUACAUCCGCUGCCAACGCAUCCGCCAUUGGCGUUUCUGCUUU
.((((((((.(((((((((..((((........)))))))))(((........)))......)))--------)..))).........(((((.((....))..))))))))))...... ( -34.00)
>DroSec_CAF1 80843 112 - 1
UGGAACGGAAGGCGGGGCUAAAUAGCUACAUAUCUAUGGCCCGGCAUCUAUAAGCCAAUUUCCGC--------UGCUCUACAUCCGCUGCCAACGCAUCCGCCACUGGCGUUCCUGCUUU
.((((((((.(((((((((..((((........)))))))))(((........)))......)))--------)..))).........((((..((....))...)))))))))...... ( -36.00)
>DroSim_CAF1 96513 112 - 1
UGGAACGGAAGGCGGGGCUAAAUAGCUACAUAUCUAUGGCCCGGCAUCUAUAAGCCAAUUUCCGA--------UGCUCUACAUCCGCUGCCAACGCAUCCGCCACUGGCGUUCCUGCUUU
.((((((((.(((((((((..((((........)))))))))(((........))).......((--------((.....))))))))((....)).)))(((...))))))))...... ( -35.70)
>DroEre_CAF1 82939 117 - 1
UCGAACGGAAGACGG--CU-AAUAGCUGCAUAUCUAUGGCCCGGCAUCUAUAAGCCAAUUUCCGCGCUAUUUCUGCGCUACAUCCGCUGCCAACGCAUCCGCCCCUGGCGUUCCUGCUUU
..(((((((((..((--((-.((((.(((....(....)....))).)))).))))..)))))((((.......))))..........((((..((....))...))))))))....... ( -35.00)
>DroYak_CAF1 82790 112 - 1
UGAAACGGAAGGCGGGGCUAAAUAGCUACAUAUCUAUGGCCCGGCAUCUAUAAGCCAAUUUCCGC--------UGCACUAUAUCCGCUGCCAACGCAUCCGCCUCUGGCGUUCCUGCUUU
......(((((((((((((..((((........)))))))))(((........)))......)))--------)..............((((..((....))...)))).))))...... ( -30.20)
>consensus
UGGAACGGAAGGCGGGGCUAAAUAGCUACAUAUCUAUGGCCCGGCAUCUAUAAGCCAAUUUCCGC________UGCUCUACAUCCGCUGCCAACGCAUCCGCCACUGGCGUUCCUGCUUU
.((((((((((...(((((..((((........)))))))))(((........)))..))))).........................((((..((....))...)))))))))...... (-28.00 = -28.68 +   0.68)

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 12:02:20 2006