Locus 5512

Sequence ID 2L_DroMel_CAF1
Location 15,774,552 – 15,774,686
Length 134
Max. P 0.976131
window8748 window8749 window8750 window8751

overview

Window 8

Location 15,774,552 – 15,774,646
Length 94
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 86.37
Mean single sequence MFE -20.75
Consensus MFE -17.23
Energy contribution -17.23
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.83
SVM decision value 0.92
SVM RNA-class probability 0.882673
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15774552 94 + 22407834
GAAA-AAAUCUUUUUAGUUGCGUCGCACUCCCUGGGAAAACUCAACCAAGGAACUCCCAAGGUAGUCGACAUUUUCCGCCCACAGGAC---CUCCCCC
....-................((((.(((((.(((((...((......))....))))).)).)))))))....(((.......))).---....... ( -20.60)
>DroSec_CAF1 25866 96 + 1
GAAA-AAAUCUUUUUAGUUGCGUCGCACUCCCUGGGAAAACUUAACCAAGAAACUCCCAAGGUAGUCGACAUUUUCCACCCGCAGGACA-CCUCCCCC
....-................((((.(((((.(((((...(((....)))....))))).)).)))))))....(((.......)))..-........ ( -19.60)
>DroSim_CAF1 26230 98 + 1
GAAAAAAAUCUUUUUAGUUGCGUCGCACUCCCUGGGAAAACUCAACCAAGAAACUCCCAAGGUAGUCGACAUUUUCCACCCGCAGGACAAACUACCCC
..............(((((..((((.(((((.(((((....((......))...))))).)).)))))))....(((.......)))..))))).... ( -22.30)
>DroEre_CAF1 27881 86 + 1
GGAA-AAAUCUUUUUAGUUGCGUCGCACUCCCUGGGAAAACCCAACCGAGAAACUCCCAAGGUAGUCGACAUUUCCAACCCGCAGCC-----------
((((-(...((....))....((((.(((((.(((((.................))))).)).))))))).)))))...........----------- ( -20.43)
>DroYak_CAF1 27334 86 + 1
GAAA-AAAUCUUUUUAGUUGCGUCGCACUCCCUGGGAAAACUCAACCAAGAAACUCCCAAGGUAGUCGACAUUUCUACCCCGCAGCC-----------
....-...........(((((((((.(((((.(((((....((......))...))))).)).)))))))...........))))).----------- ( -20.80)
>consensus
GAAA_AAAUCUUUUUAGUUGCGUCGCACUCCCUGGGAAAACUCAACCAAGAAACUCCCAAGGUAGUCGACAUUUUCCACCCGCAGGAC___CU_CCCC
.....................((((.(((((.(((((.................))))).)).)))))))............................ (-17.23 = -17.23 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,774,552 – 15,774,646
Length 94
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 86.37
Mean single sequence MFE -29.44
Consensus MFE -25.08
Energy contribution -24.60
Covariance contribution -0.48
Combinations/Pair 1.16
Mean z-score -1.52
Structure conservation index 0.85
SVM decision value 0.25
SVM RNA-class probability 0.655188
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15774552 94 - 22407834
GGGGGAG---GUCCUGUGGGCGGAAAAUGUCGACUACCUUGGGAGUUCCUUGGUUGAGUUUUCCCAGGGAGUGCGACGCAACUAAAAAGAUUU-UUUC
.(..(((---((((((....))).....(((((((.(((((((((...(((....)))..)))))))))))).))))...........)))))-)..) ( -31.70)
>DroSec_CAF1 25866 96 - 1
GGGGGAGG-UGUCCUGCGGGUGGAAAAUGUCGACUACCUUGGGAGUUUCUUGGUUAAGUUUUCCCAGGGAGUGCGACGCAACUAAAAAGAUUU-UUUC
.(..((((-(.(((.......)))....(((((((.(((((((((...(((....)))..)))))))))))).))))............))))-)..) ( -29.50)
>DroSim_CAF1 26230 98 - 1
GGGGUAGUUUGUCCUGCGGGUGGAAAAUGUCGACUACCUUGGGAGUUUCUUGGUUGAGUUUUCCCAGGGAGUGCGACGCAACUAAAAAGAUUUUUUUC
(..((..((..(((...)))..))....(((((((.(((((((((.(((......)))..)))))))))))).))))))..)................ ( -29.40)
>DroEre_CAF1 27881 86 - 1
-----------GGCUGCGGGUUGGAAAUGUCGACUACCUUGGGAGUUUCUCGGUUGGGUUUUCCCAGGGAGUGCGACGCAACUAAAAAGAUUU-UUCC
-----------..((...(((((....((((((((.(((((((((...(((....)))..)))))))))))).))))))))))....))....-.... ( -29.80)
>DroYak_CAF1 27334 86 - 1
-----------GGCUGCGGGGUAGAAAUGUCGACUACCUUGGGAGUUUCUUGGUUGAGUUUUCCCAGGGAGUGCGACGCAACUAAAAAGAUUU-UUUC
-----------((.(((.....(....)(((((((.(((((((((.(((......)))..)))))))))))).))))))).))..........-.... ( -26.80)
>consensus
GGGG_AG___GUCCUGCGGGUGGAAAAUGUCGACUACCUUGGGAGUUUCUUGGUUGAGUUUUCCCAGGGAGUGCGACGCAACUAAAAAGAUUU_UUUC
............................(((((((.(((((((((...(((....)))..)))))))))))).))))..................... (-25.08 = -24.60 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,774,569 – 15,774,686
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.27
Mean single sequence MFE -19.78
Consensus MFE -17.23
Energy contribution -17.23
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.87
SVM decision value 1.76
SVM RNA-class probability 0.976131
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15774569 117 + 22407834
UGCGUCGCACUCCCUGGGAAAACUCAACCAAGGAACUCCCAAGGUAGUCGACAUUUUCCGCCCACAGGAC---CUCCCCCCCUCCGAAUCCCCCCUCCCCCGCUGAAUCCCCACCUUCCA
.((((((.(((((.(((((...((......))....))))).)).)))))))....(((.......))).---............................))................. ( -22.60)
>DroSec_CAF1 25883 104 + 1
UGCGUCGCACUCCCUGGGAAAACUUAACCAAGAAACUCCCAAGGUAGUCGACAUUUUCCACCCGCAGGACA-CCUCCCCCCC---------------ACCACCCGAAUCACCUCCUUCCC
...((((.(((((.(((((...(((....)))....))))).)).)))))))....(((.......)))..-..........---------------....................... ( -19.60)
>DroSim_CAF1 26248 105 + 1
UGCGUCGCACUCCCUGGGAAAACUCAACCAAGAAACUCCCAAGGUAGUCGACAUUUUCCACCCGCAGGACAAACUACCCCCC---------------ACCACCCGAAUCCCCUCCUUUCC
...((((.(((((.(((((....((......))...))))).)).)))))))....(((.......))).............---------------....................... ( -19.70)
>DroEre_CAF1 27898 89 + 1
UGCGUCGCACUCCCUGGGAAAACCCAACCGAGAAACUCCCAAGGUAGUCGACAUUUCCAACCCGCAGCC-----------------------------CCACACGAAUCC--ACAUUCCA
...((((.(((((.(((((.................))))).)).))))))).................-----------------------------............--........ ( -17.23)
>consensus
UGCGUCGCACUCCCUGGGAAAACUCAACCAAGAAACUCCCAAGGUAGUCGACAUUUUCCACCCGCAGGAC___CUCCCCCCC_______________ACCACCCGAAUCCCCACCUUCCA
...((((.(((((.(((((.................))))).)).))))))).................................................................... (-17.23 = -17.23 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,774,569 – 15,774,686
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.27
Mean single sequence MFE -35.67
Consensus MFE -25.11
Energy contribution -24.55
Covariance contribution -0.56
Combinations/Pair 1.16
Mean z-score -1.75
Structure conservation index 0.70
SVM decision value 0.85
SVM RNA-class probability 0.866136
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15774569 117 - 22407834
UGGAAGGUGGGGAUUCAGCGGGGGAGGGGGGAUUCGGAGGGGGGGAG---GUCCUGUGGGCGGAAAAUGUCGACUACCUUGGGAGUUCCUUGGUUGAGUUUUCCCAGGGAGUGCGACGCA
.....((.(..((((((((.((((((......(((.((((..(((..---..)))((.((((.....)))).))..)))).))).)))))).))))))))..))).....(((...))). ( -39.40)
>DroSec_CAF1 25883 104 - 1
GGGAAGGAGGUGAUUCGGGUGGU---------------GGGGGGGAGG-UGUCCUGCGGGUGGAAAAUGUCGACUACCUUGGGAGUUUCUUGGUUAAGUUUUCCCAGGGAGUGCGACGCA
.........((..(((.(.(.(.---------------.(((.(....-).)))..).).).)))...(((((((.(((((((((...(((....)))..)))))))))))).)))))). ( -34.60)
>DroSim_CAF1 26248 105 - 1
GGAAAGGAGGGGAUUCGGGUGGU---------------GGGGGGUAGUUUGUCCUGCGGGUGGAAAAUGUCGACUACCUUGGGAGUUUCUUGGUUGAGUUUUCCCAGGGAGUGCGACGCA
.............(((.(.(.(.---------------.(((.(.....).)))..).).).)))...(((((((.(((((((((.(((......)))..)))))))))))).))))... ( -36.20)
>DroEre_CAF1 27898 89 - 1
UGGAAUGU--GGAUUCGUGUGG-----------------------------GGCUGCGGGUUGGAAAUGUCGACUACCUUGGGAGUUUCUCGGUUGGGUUUUCCCAGGGAGUGCGACGCA
..((((..--..))))((((.(-----------------------------.(((...((((((.....)))))).(((((((((...(((....)))..)))))))))))).).)))). ( -32.50)
>consensus
GGGAAGGAGGGGAUUCGGGUGGU_______________GGGGGGGAG___GUCCUGCGGGUGGAAAAUGUCGACUACCUUGGGAGUUUCUUGGUUGAGUUUUCCCAGGGAGUGCGACGCA
....................................................................(((((((.(((((((((...(((....)))..)))))))))))).))))... (-25.11 = -24.55 +  -0.56)

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 11:46:02 2006