Locus 1077

Sequence ID 3L_DroMel_CAF1
Location 3,150,394 – 3,150,527
Length 133
Max. P 0.982819
window1662 window1663 window1664

overview

Window 2

Location 3,150,394 – 3,150,494
Length 100
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 82.41
Mean single sequence MFE -31.24
Consensus MFE -25.35
Energy contribution -25.47
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.54
Structure conservation index 0.81
SVM decision value 0.21
SVM RNA-class probability 0.636893
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3150394 100 + 23771897
AUCUGAUGUACAUAGCUGUGCU----UCCGCCAAGUGCAGCUGGUUUCAGCC----GUUGGCGUUCUGGCCAAGACCAAGACAUCUGGUUAUCUGACUUGGCCAUAUC
...(((...((.((((((..((----(.....)))..)))))))).)))(((----...)))....((((((((((((.(....))))).......)))))))).... ( -33.41)
>DroSec_CAF1 14175 108 + 1
AUCUGAUGUGAAUAGCUUUGCUUAUUUCCGCCAAGUGCAGCUGGUUUCAGCCGAUCGUUGGCGUUCUGGCCAAGACCAAGACAUCUGGUUAUCUGACUUGGUCAUAUC
....(((((((..(((...)))........((((((.(((.(((((...(((((...))))).....))))).(((((.(....))))))..)))))))))))))))) ( -30.00)
>DroEre_CAF1 14305 95 + 1
AUCUG---UGGA----------UAUUUCCGCCAAGUGCAGCAGGUUUUAGCCGUUCGUUGGCGUUCUGGCCAAGACCAACACAUCUGGUUAUCUGACUUGGCCAUAUC
.....---.(((----------....)))(((((((.(((..((((...((((.....)))).....))))..(((((.......)))))..))))))))))...... ( -30.30)
>consensus
AUCUGAUGUGAAUAGCU_UGCUUAUUUCCGCCAAGUGCAGCUGGUUUCAGCCG_UCGUUGGCGUUCUGGCCAAGACCAAGACAUCUGGUUAUCUGACUUGGCCAUAUC
.............................(((((((.(((..((((...((((.....)))).....))))..(((((.......)))))..))))))))))...... (-25.35 = -25.47 +   0.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,150,394 – 3,150,494
Length 100
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 82.41
Mean single sequence MFE -33.50
Consensus MFE -27.53
Energy contribution -29.20
Covariance contribution 1.67
Combinations/Pair 1.00
Mean z-score -2.69
Structure conservation index 0.82
SVM decision value 1.93
SVM RNA-class probability 0.982819
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3150394 100 - 23771897
GAUAUGGCCAAGUCAGAUAACCAGAUGUCUUGGUCUUGGCCAGAACGCCAAC----GGCUGAAACCAGCUGCACUUGGCGGA----AGCACAGCUAUGUACAUCAGAU
....(((((((((((((((......)))).))).))))))))...(((((((----(((((....))))))...))))))((----.(.(((....))).).)).... ( -37.00)
>DroSec_CAF1 14175 108 - 1
GAUAUGACCAAGUCAGAUAACCAGAUGUCUUGGUCUUGGCCAGAACGCCAACGAUCGGCUGAAACCAGCUGCACUUGGCGGAAAUAAGCAAAGCUAUUCACAUCAGAU
(((..(((((((.((..........)).))))))).......(((((((((....((((((....))))))...))))))......(((...))).)))..))).... ( -31.40)
>DroEre_CAF1 14305 95 - 1
GAUAUGGCCAAGUCAGAUAACCAGAUGUGUUGGUCUUGGCCAGAACGCCAACGAACGGCUAAAACCUGCUGCACUUGGCGGAAAUA----------UCCA---CAGAU
((((((((((((((((...((.....)).)))).)))))))....((((((.(..((((........))))..)))))))...)))----------))..---..... ( -32.10)
>consensus
GAUAUGGCCAAGUCAGAUAACCAGAUGUCUUGGUCUUGGCCAGAACGCCAACGA_CGGCUGAAACCAGCUGCACUUGGCGGAAAUAAGCA_AGCUAUCCACAUCAGAU
....(((((((((((((((......)))).))).))))))))...((((((....((((((....))))))...))))))............................ (-27.53 = -29.20 +   1.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,150,430 – 3,150,527
Length 97
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 80.52
Mean single sequence MFE -30.68
Consensus MFE -20.25
Energy contribution -20.44
Covariance contribution 0.19
Combinations/Pair 1.19
Mean z-score -1.59
Structure conservation index 0.66
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3150430 97 - 23771897
CU-----GAAGCGCAUAGCUGCAGGCCAGGCGGAAGUAGAUAUGGCCAAGUCAGAUAACCAGAUGUCUUGGUCUUGGCCAGAACGCCAAC----GGCUGAAACCAG
((-----(.(((.....))).)))(((.((((..........(((((((((((((((......)))).))).))))))))...))))...----)))......... ( -34.02)
>DroSec_CAF1 14215 101 - 1
CU-----GAAGCACAUAGCUGCAGGCCAGGCGGAAGUAGAUAUGACCAAGUCAGAUAACCAGAUGUCUUGGUCUUGGCCAGAACGCCAACGAUCGGCUGAAACCAG
((-----(.(((.....))).)))(((..((....)).(((..(((((((.((..........)).)))))))(((((......)))))..))))))......... ( -32.10)
>DroEre_CAF1 14332 101 - 1
CU-----GAAGCACAUAGCUGCAGGCCAGGCGGAAGUAGAUAUGGCCAAGUCAGAUAACCAGAUGUGUUGGUCUUGGCCAGAACGCCAACGAACGGCUAAAACCUG
((-----((.(((......))).(((((.((....)).....)))))...)))).....(((..((.(((((....))))).))(((.......)))......))) ( -30.60)
>DroAna_CAF1 13578 89 - 1
CCACAUGGAAACUCAAAGUUGCA-----GGCGGAAGUAGAUAUGGCCGAG------AACCAGAUGU------CUUGGCCAGAACGCCAACAGUUGGCUGAAAGCUG
......(....)........((.-----((((..........((((((((------(........)------))))))))...))))..(((....)))...)).. ( -26.02)
>consensus
CU_____GAAGCACAUAGCUGCAGGCCAGGCGGAAGUAGAUAUGGCCAAGUCAGAUAACCAGAUGUCUUGGUCUUGGCCAGAACGCCAACGAUCGGCUGAAACCAG
...............((((((.......((((..........((((((((.(.....((.....))....).))))))))...))))......))))))....... (-20.25 = -20.44 +   0.19)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:24 2006