Locus 6035

Sequence ID 3L_DroMel_CAF1
Location 16,078,923 – 16,079,233
Length 310
Max. P 0.994545
window9660 window9661 window9662 window9663

overview

Window 0

Location 16,078,923 – 16,079,043
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.07
Mean single sequence MFE -40.92
Consensus MFE -31.48
Energy contribution -30.96
Covariance contribution -0.52
Combinations/Pair 1.22
Mean z-score -3.27
Structure conservation index 0.77
SVM decision value 2.49
SVM RNA-class probability 0.994545
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16078923 120 - 23771897
UGGACGUUGCCAGAUAGCGUGCGAAAAACACGUAACCAACGAUCUGGCAAUGCCGCUCGUUUAUGCGGGUGGCGAGUGCGCAAUAUUCGUGAAUGCACUAAAUUUAAAAAAAAGUUCAAC
(((((((((((((((.(((((.......)))))........))))))))))(((((((((....))))))))).((((((..((....))...))))))..............))))).. ( -43.60)
>DroSec_CAF1 822 119 - 1
UGGACGUUGCCAGAUAGCGUGCGAAAAACACGUAACCAACGAUCUGGCAAUGCCGCGCGUUUAUGCGGGUGGCGAGUGUGCAAUAUUCGUGAAUGCACUAAAUUUAAA-AAAAGUUCAAC
(((((((((((((((.(((((.......)))))........))))))))))(((((.(((....))).)))))....(((((...........)))))..........-....))))).. ( -41.10)
>DroSim_CAF1 445 119 - 1
UGGACGUUGCCAGAUAGCGAGCGAAAAACACGUAACCAACGAUCUGGCAAUGCCGCGCGUUUAUGCGGGUGGCGACUGUGCAAUAUUUGUGAAUGCACUAAAUUUAAA-AAAAGUUCAAC
(((((((((((((((.(....)........(((.....)))))))))))))(((((.(((....))).)))))....(((((...........)))))..........-....))))).. ( -38.20)
>DroEre_CAF1 1225 119 - 1
CGGGCGUUGCCAGAUACCGUGCGAAAAACACGUAACCAAC-AUCUGGCAAUGCUGCGCGUUUAUGCGGGAGGCGAGUGCGCAAUCUUCGUGAAUGCACCAAGUUUAAAAAUAUGUUCAAC
.((((((((((((((....((((.......))))......-))))))))))))...(((((((((.(((..(((....)))..))).))))))))).))..................... ( -41.80)
>DroYak_CAF1 417 120 - 1
CGAGCGUUGCCAGAUAUCUUGCGAAAAACACGUAACCAACGACCUGGCAAUGCUGCGCAUUUAUGCGGGUGGAGAGUGCUCGAUCUUCAUGAAUGCACCAAGUUUAAAAAAUAGUUGAAA
..(((((((((((.....(((((.......)))))........)))))))))))..(((((((((.((((.(((....))).)))).)))))))))........................ ( -39.92)
>consensus
UGGACGUUGCCAGAUAGCGUGCGAAAAACACGUAACCAACGAUCUGGCAAUGCCGCGCGUUUAUGCGGGUGGCGAGUGCGCAAUAUUCGUGAAUGCACUAAAUUUAAAAAAAAGUUCAAC
(((.(((((((((((....((((.......)))).......)))))))))))))).(((((((((...((.(((....))).))...)))))))))........................ (-31.48 = -30.96 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,078,963 – 16,079,083
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.08
Mean single sequence MFE -41.34
Consensus MFE -32.78
Energy contribution -33.30
Covariance contribution 0.52
Combinations/Pair 1.06
Mean z-score -1.57
Structure conservation index 0.79
SVM decision value 0.32
SVM RNA-class probability 0.685097
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16078963 120 - 23771897
AUUUUCACGAAUGCGCGUGCAAAGCGAAAAUCGAGGCUGGUGGACGUUGCCAGAUAGCGUGCGAAAAACACGUAACCAACGAUCUGGCAAUGCCGCUCGUUUAUGCGGGUGGCGAGUGCG
............((((((.((.(((..........)))..)).))((((((((((.(((((.......)))))........))))))))))(((((((((....)))))))))..)))). ( -45.90)
>DroSec_CAF1 861 120 - 1
AUUUUCACGAAUGCGCGUGUAAAGCGAAAAUCGAGGGUGGUGGACGUUGCCAGAUAGCGUGCGAAAAACACGUAACCAACGAUCUGGCAAUGCCGCGCGUUUAUGCGGGUGGCGAGUGUG
.....(((...(((.(((((((((((.....).......((((.(((((((((((.(((((.......)))))........))))))))))))))))).)))))))).)))....))).. ( -41.80)
>DroSim_CAF1 484 120 - 1
AUUUUCACGAAUGCGCGUGUAAAGCGAAAAUCGAGGGUGGUGGACGUUGCCAGAUAGCGAGCGAAAAACACGUAACCAACGAUCUGGCAAUGCCGCGCGUUUAUGCGGGUGGCGACUGUG
.......((...((.(((((((((((.....).......((((.(((((((((((.(....)........(((.....)))))))))))))))))))).)))))))).))..))...... ( -37.50)
>DroEre_CAF1 1265 119 - 1
AUUUUCACGAAUGCGCGUGCAAAGCGAAAAUCGAGGGAGGCGGGCGUUGCCAGAUACCGUGCGAAAAACACGUAACCAAC-AUCUGGCAAUGCUGCGCGUUUAUGCGGGAGGCGAGUGCG
.....(((((((((((.(((....((.....))......)))(((((((((((((....((((.......))))......-))))))))))))))))))))).(((.....))).))).. ( -41.80)
>DroYak_CAF1 457 120 - 1
AUUUUCACGAAUGCGCGUGCAAAGCGAAAAUCGAGAGAGGCGAGCGUUGCCAGAUAUCUUGCGAAAAACACGUAACCAACGACCUGGCAAUGCUGCGCAUUUAUGCGGGUGGAGAGUGCU
.....(((...(.(((.((((.........((....)).((((((((((((((.....(((((.......)))))........))))))))))).))).....)))).))).)..))).. ( -39.72)
>consensus
AUUUUCACGAAUGCGCGUGCAAAGCGAAAAUCGAGGGUGGUGGACGUUGCCAGAUAGCGUGCGAAAAACACGUAACCAACGAUCUGGCAAUGCCGCGCGUUUAUGCGGGUGGCGAGUGCG
.....(((..((.((((((.....((.....))......((((.(((((((((((....((((.......)))).......))))))))))))))).....)))))).)).....))).. (-32.78 = -33.30 +   0.52)

alignment

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secondary structure

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Window 2

Location 16,079,003 – 16,079,120
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.20
Mean single sequence MFE -36.30
Consensus MFE -24.91
Energy contribution -25.43
Covariance contribution 0.53
Combinations/Pair 1.04
Mean z-score -2.08
Structure conservation index 0.69
SVM decision value 0.47
SVM RNA-class probability 0.750338
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16079003 117 - 23771897
ACAAAAAAUUUGGCAGCGACGGU---GCCAGAACGCCGCCAUUUUCACGAAUGCGCGUGCAAAGCGAAAAUCGAGGCUGGUGGACGUUGCCAGAUAGCGUGCGAAAAACACGUAACCAAC
.......(((((((((((.((((---(......)))))(((((.((.(((...(((.......)))....))).))..))))).))))))))))).(((((.......)))))....... ( -39.50)
>DroPse_CAF1 4189 108 - 1
ACAAAAAAUUUGGCAGCGACAGUAGUUCGACAACGCCGCCAUUUUCACGAAUGCGCGUGCAAAA---UAAUCGUCUGGAGC-GGCGUUGCCAGA-AGCUGGCGGAAAAUUGUU-------
((((....((((.(((((((....))).(.(((((((((.(((((((((......)))).))))---)..((.....))))-))))))).)...-.)))).))))...)))).------- ( -32.80)
>DroSim_CAF1 524 117 - 1
ACAAAAAAUUUGGCAGCGACGGU---GCCAGAACGCCGCCAUUUUCACGAAUGCGCGUGUAAAGCGAAAAUCGAGGGUGGUGGACGUUGCCAGAUAGCGAGCGAAAAACACGUAACCAAC
.......(((((((((((...((---......)).(((((((((((.......(((.......)))......))))))))))).))))))))))).....(((.......)))....... ( -36.62)
>DroEre_CAF1 1304 117 - 1
ACAAAAAAUUUGGCAGCGACGGU---GCCAGAACGCCGCCAUUUUCACGAAUGCGCGUGCAAAGCGAAAAUCGAGGGAGGCGGGCGUUGCCAGAUACCGUGCGAAAAACACGUAACCAAC
.......((((((((((...(((---(......))))(((.((..(.(((...(((.......)))....))).)..))...)))))))))))))..((((.......))))........ ( -38.40)
>DroYak_CAF1 497 117 - 1
ACAAAAAAUUUGGCAGCGACGGU---GCCAGAACGCCGCCAUUUUCACGAAUGCGCGUGCAAAGCGAAAAUCGAGAGAGGCGAGCGUUGCCAGAUAUCUUGCGAAAAACACGUAACCAAC
.......(((((((((((.((((---(......))))(((..((((.(((...(((.......)))....))).)))))))..))))))))))))...(((((.......)))))..... ( -37.70)
>DroPer_CAF1 3114 108 - 1
ACAAAAAAUUUGGCAGCGACAGUAGUUCGACAACGCCGCCAUUUUCACGAAUGCGCGUGCAAAA---UAAUCGUCUGGAGC-GGCGUUGCCAGA-AGCUGGCGGAAAAUUGUU-------
((((....((((.(((((((....))).(.(((((((((.(((((((((......)))).))))---)..((.....))))-))))))).)...-.)))).))))...)))).------- ( -32.80)
>consensus
ACAAAAAAUUUGGCAGCGACGGU___GCCAGAACGCCGCCAUUUUCACGAAUGCGCGUGCAAAGCGAAAAUCGAGGGAGGCGGGCGUUGCCAGAUAGCGUGCGAAAAACACGUAACCAAC
.......(((((((((((..((.....)).....((((((((((....))))).))).))........................)))))))))))......................... (-24.91 = -25.43 +   0.53)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,079,120 – 16,079,233
Length 113
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 95.18
Mean single sequence MFE -31.30
Consensus MFE -24.56
Energy contribution -25.00
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.68
Structure conservation index 0.78
SVM decision value 0.05
SVM RNA-class probability 0.560730
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16079120 113 + 23771897
ACAUCAAAAUAAUCAAAAUAAAGCAUUCUUCCAGUGCUCAACAAUCAGUCCGUGCGAGCACGCGCGAGUGUGUGUGUGCGCAGGAAAACCCGCCGAUCGGGA-AAAGUGUAGA-A
......................(((((.....)))))((.(((.....((((((((.((((((....))))))...))))).)))...((((.....)))).-....))).))-. ( -32.20)
>DroSec_CAF1 1018 112 + 1
ACAUCAAAAUAAUCAAAAUAAAGCAUUCUUCCAGUGCUCAAAAAUCAGUCCGUGCGAGCACGCGCGUGUGUGUGUGUGCGCAGGA-AACCCGCCGAUCGGGA-AAAGUGUAGA-A
((((.................((((((.....))))))..........(((.((((.((((((((....)))))))).)))))))-..((((.....)))).-...))))...-. ( -31.70)
>DroSim_CAF1 641 113 + 1
ACAUCAAAAUAAUCAAAAUAAAGCAUUCUUCCAGUGCUCAACAAUCAGUCCGUGCGAGCACGCGCGUGUGUGUGUGUGCGCAGGAAAACCCGCCGAUCGGGA-AAAGUGUAGA-A
......................(((((.....)))))((.(((.....(((.((((.((((((((....)))))))).)))))))...((((.....)))).-....))).))-. ( -32.20)
>DroEre_CAF1 1421 114 + 1
ACAUCAAAAUAAUCAAAAUAAAGCAUUCUUCCAGUGCUCAACAAUCAGUCCGUGCGAGCACGCGGGUGUGUGUGUGUGCGCAGGAAAAGCCGCCGAUCGGGA-AAAGUGUAGAAA
......................(((((.((((.((((((.((.........))..))))))((((.(.(.((((....)))).)...).))))......)))-).)))))..... ( -31.40)
>DroYak_CAF1 614 112 + 1
ACAUCAAAAUAAUCAAAAUAAAGCAUUCUUCCAGUGCUCAACAAUCAGUCCGUUCGAGCACGCGGGUGUGU--GUGUGCGCAGGAAAA-CCGCCGAUCGGAAAAAAGUGUAAAAA
......................(((((.((((.(((((((((.........))).))))))((((.(.(((--(....)))).)....-)))).....))))...)))))..... ( -29.00)
>consensus
ACAUCAAAAUAAUCAAAAUAAAGCAUUCUUCCAGUGCUCAACAAUCAGUCCGUGCGAGCACGCGCGUGUGUGUGUGUGCGCAGGAAAACCCGCCGAUCGGGA_AAAGUGUAGA_A
((((.................((((((.....))))))..........((((..((.(((((((((....)))))))))((.((.....))))))..)))).....))))..... (-24.56 = -25.00 +   0.44)

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 12:07:33 2006