Locus 1765

Sequence ID 3L_DroMel_CAF1
Location 5,057,162 – 5,057,399
Length 237
Max. P 0.980488
window2727 window2728 window2729

overview

Window 7

Location 5,057,162 – 5,057,280
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.97
Mean single sequence MFE -24.16
Consensus MFE -18.88
Energy contribution -19.86
Covariance contribution 0.98
Combinations/Pair 1.03
Mean z-score -1.48
Structure conservation index 0.78
SVM decision value 0.08
SVM RNA-class probability 0.571998
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5057162 118 - 23771897
UUGCUAAGCAAUUAAAAAAUAUAGAAAAAAAAAAUGGCAUUGAUUGCAGCUGCCACCGCACACCGACCAUGUGGCAC--AUAGUUCUAUAGUUCCAAAGCCGCACGUGUGCUUUUUUAUC
((((...)))).........((((((((......((((((((....))).)))))..((((((......((((((..--...................)))))).)))))))))))))). ( -25.60)
>DroSec_CAF1 263639 94 - 1
UUGCUAAGCAAUUAAAAAAUAUAGAAAAAA---ACUG---------------------CACACCGACCAUGUGGCAC--AUAGUUCUAUAGUUCCAAAGCCGCACGUGUGCUUUUUUAUC
((((...))))............((.((((---(..(---------------------(((((......((((((..--...................)))))).)))))).))))).)) ( -16.70)
>DroSim_CAF1 284952 115 - 1
UUGCUAAGCAAUUAAAAAAUAUAGAAAAAA---ACUGCAUUGAUUGCAGCUGCCACCGCACACCGACCAUGUGGCAC--AUAGUUCUAUAGUUCCAAAGCCGCACGUGUGCUUUUUUAUC
((((...)))).........((((((((..---.(((((.....)))))........((((((......((((((..--...................)))))).)))))))))))))). ( -24.50)
>DroEre_CAF1 270412 115 - 1
UUGCUAAGCAAUUAAAAAAUAUAGAAAAAA---ACUGCAUUGAUUGCAGCUGCCACCGCACACCUACCAUGUGGCAC--AUAGUUCUAUAGUUCCAAAGCCGCACGUGUGCUUUUUUAUC
((((...)))).........((((((((..---.(((((.....)))))........((((((......((((((..--...................)))))).)))))))))))))). ( -24.50)
>DroYak_CAF1 274048 120 - 1
UUGCUAAGCAAUUAAAAAAUAUAGAAAAAAAAAGCUGCAUUGAUUGCAGCUGCCACCGCACACCGACCAUGUGGCACACACAGUUCUAUAGUUCCAAAGCCGCACGUGUGCUUUUUUAUC
((((...)))).........((((((((....(((((((.....)))))))......((((((......((((((.......................)))))).)))))))))))))). ( -29.50)
>consensus
UUGCUAAGCAAUUAAAAAAUAUAGAAAAAA___ACUGCAUUGAUUGCAGCUGCCACCGCACACCGACCAUGUGGCAC__AUAGUUCUAUAGUUCCAAAGCCGCACGUGUGCUUUUUUAUC
((((...)))).........((((((((......(((((.....)))))........((((((......((((((.......................)))))).)))))))))))))). (-18.88 = -19.86 +   0.98)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,057,240 – 5,057,360
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.62
Mean single sequence MFE -31.26
Consensus MFE -26.82
Energy contribution -27.50
Covariance contribution 0.68
Combinations/Pair 1.06
Mean z-score -1.90
Structure conservation index 0.86
SVM decision value 1.86
SVM RNA-class probability 0.980488
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5057240 120 - 23771897
AUUCAGUUCGGAACCGAUAGCGGAUGCAGUUGGCAAAGGAAGCCUUGACCAUCCGCUCCAAUUGUUCCGACGCGCUUCCUUUGCUAAGCAAUUAAAAAAUAUAGAAAAAAAAAAUGGCAU
.(((.(((((((((.(((((((((((.....(((.......))).....))))))))...)))))))))).))((((........))))..............))).............. ( -31.90)
>DroSec_CAF1 263699 114 - 1
AUUCAGUUCGGAACCGAUAGCGGAUGCAGCUGGCAAAGGAAGCCCUGACCAUCCGCUCCAAUUGUUCCGACGCGCUUCCUUUGCUAAGCAAUUAAAAAAUAUAGAAAAAA---ACUG---
.(((.(((((((((.((((((((((((((..(((.......))))))..))))))))...)))))))))).))((((........))))..............)))....---....--- ( -32.30)
>DroSim_CAF1 285030 117 - 1
AUUCAGUUCGGAACCGAUAGCGGAUGCAGCUGGCAAAGGAAGCCCUGACCAUCCGCUCCAAUUGUUCCGACGCGCUUCCUUUGCUAAGCAAUUAAAAAAUAUAGAAAAAA---ACUGCAU
.(((.(((((((((.((((((((((((((..(((.......))))))..))))))))...)))))))))).))((((........))))..............)))....---....... ( -32.30)
>DroEre_CAF1 270490 117 - 1
GCUCAGUUCGGAGCCGAUAGCGGAUGCAGCUGCCAAAGGAAGCCCUGACCAUCCGCUCCAAUUGUUCCGACGCGCUUCCUUUGCUAAGCAAUUAAAAAAUAUAGAAAAAA---ACUGCAU
((...(((((((((.((((((((((((((..((........)).)))..))))))))...)))))))))).))((((........)))).....................---...)).. ( -29.90)
>DroYak_CAF1 274128 120 - 1
AUUCAGUUCGCCACCGAUAGCGGAUGCAGCUGCCAAAGGAAGCCCUGACCAUCCGCUCCAAUUGUUCCGACGCGCUUCCUUUGCUAAGCAAUUAAAAAAUAUAGAAAAAAAAAGCUGCAU
.....((((((........))))))((((((((.(((((((((...(......)((((..........)).)))))))))))))(((....)))..................)))))).. ( -29.90)
>consensus
AUUCAGUUCGGAACCGAUAGCGGAUGCAGCUGGCAAAGGAAGCCCUGACCAUCCGCUCCAAUUGUUCCGACGCGCUUCCUUUGCUAAGCAAUUAAAAAAUAUAGAAAAAA___ACUGCAU
.(((.(((((((((.((((((((((((((..(((.......))))))..))))))))...)))))))))).))((((........))))..............))).............. (-26.82 = -27.50 +   0.68)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,057,280 – 5,057,399
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.15
Mean single sequence MFE -41.21
Consensus MFE -35.56
Energy contribution -35.72
Covariance contribution 0.16
Combinations/Pair 1.09
Mean z-score -1.42
Structure conservation index 0.86
SVM decision value 0.40
SVM RNA-class probability 0.723214
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5057280 119 + 23771897
AGGAAGCGCGUCGGAACAAUUGGAGCGGAUGGUCAAGGCUUCCUUUGCCAACUGCAUCCGCUAUCGGUUCCGAACUGAAUUGAAUAGCGACCAAAGACGCCGUAAUUGACGUUGAUCCA-
.(((...(((((.........(((((((.((((.((((...)))).)))).)))).)))(((((((((((......)))))).))))).......)))))(((.....)))....))).- ( -41.70)
>DroSec_CAF1 263733 119 + 1
AGGAAGCGCGUCGGAACAAUUGGAGCGGAUGGUCAGGGCUUCCUUUGCCAGCUGCAUCCGCUAUCGGUUCCGAACUGAAUUGAAAAGCGACCAAAGACGCCGUAAUUGACGUUGAUCCA-
.(((...((((((((((......((((((((..((((((.......)))..)))))))))))....)))))......(((((....(((........)))..))))))))))...))).- ( -41.00)
>DroSim_CAF1 285067 119 + 1
AGGAAGCGCGUCGGAACAAUUGGAGCGGAUGGUCAGGGCUUCCUUUGCCAGCUGCAUCCGCUAUCGGUUCCGAACUGAAUUGAAAAGCGACCAAAGACGCCGUAAUUGACGUUGAUCCA-
.(((...((((((((((......((((((((..((((((.......)))..)))))))))))....)))))......(((((....(((........)))..))))))))))...))).- ( -41.00)
>DroEre_CAF1 270527 120 + 1
AGGAAGCGCGUCGGAACAAUUGGAGCGGAUGGUCAGGGCUUCCUUUGGCAGCUGCAUCCGCUAUCGGCUCCGAACUGAGCUGAAAUGCGACCAAAGACGCCGUAAUUGACGUUGAUCCAG
.(((((((((.(((.....((((((((((((..(((.(((......)))..))))))))))).(((((((......))))))).......)))).....)))....)).))))..))).. ( -43.30)
>DroYak_CAF1 274168 119 + 1
AGGAAGCGCGUCGGAACAAUUGGAGCGGAUGGUCAGGGCUUCCUUUGGCAGCUGCAUCCGCUAUCGGUGGCGAACUGAAUUGAAAAGCGACCAAAGACGCCGUAAUUGACGUUGAUCCA-
.(((...(((((.........((((((((((..(((.(((......)))..))))))))))).))(((.((...............)).)))...)))))(((.....)))....))).- ( -39.06)
>consensus
AGGAAGCGCGUCGGAACAAUUGGAGCGGAUGGUCAGGGCUUCCUUUGCCAGCUGCAUCCGCUAUCGGUUCCGAACUGAAUUGAAAAGCGACCAAAGACGCCGUAAUUGACGUUGAUCCA_
.(((...(((((.........(((((((.((((.((((...)))).)))).)))).)))((..(((((((......)))))))...)).......)))))(((.....)))....))).. (-35.56 = -35.72 +   0.16)

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 10:15:43 2006