Locus 5590

Sequence ID 2R_DroMel_CAF1
Location 17,861,479 – 17,861,706
Length 227
Max. P 0.869037
window8951 window8952 window8953

overview

Window 1

Location 17,861,479 – 17,861,587
Length 108
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 81.17
Mean single sequence MFE -27.47
Consensus MFE -19.07
Energy contribution -20.17
Covariance contribution 1.09
Combinations/Pair 1.19
Mean z-score -2.09
Structure conservation index 0.69
SVM decision value 0.85
SVM RNA-class probability 0.866633
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17861479 108 + 20766785
AUAUGUCAGAAGUAAGCCUAUUUCGUUUACGAAAUGGUUUCUGCAUUUUCUCUCUGUGCAGGUAAAUAUGAUUUUCGUGUCUGGCAGCAAUUACUGAUGUUGUCAUUA
...(((((((...(((((.((((((....)))))))))))((((((.........)))))).....((((.....)))))))))))(((((.......)))))..... ( -27.50)
>DroSec_CAF1 26803 108 + 1
AUAUGUCAGAAGUAAGCCUAUUUUGCUUACGAAAUGGUUUCUGCAUUUUCUCUCUGUGCAGGUAAAUAUGACUGUCGUGUCUGGCAACAAUUACUGGUGUUGUCAUUA
(((((.(((..((((((.......)))))).........(((((((.........))))))).........))).))))).((((((((........))))))))... ( -29.00)
>DroEre_CAF1 29424 93 + 1
UCAUAGCAGAAG-------------CUUAUGAAUUGGCUUCUGCAUUUUCUCUCUGUGCAGUUAAG--UGCCUGUCGUGUCUGGCAACAAUUACUGGUGUUGUCAUUA
.(((.(((((((-------------((........))))))))).............((((.....--...)))).)))..((((((((........))))))))... ( -25.90)
>consensus
AUAUGUCAGAAGUAAGCCUAUUU_GCUUACGAAAUGGUUUCUGCAUUUUCUCUCUGUGCAGGUAAAUAUGACUGUCGUGUCUGGCAACAAUUACUGGUGUUGUCAUUA
.((((.(((..((((((.......))))))..........((((((.........))))))..........))).))))..((((((((........))))))))... (-19.07 = -20.17 +   1.09)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,861,551 – 17,861,666
Length 115
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 95.97
Mean single sequence MFE -29.17
Consensus MFE -26.14
Energy contribution -25.70
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -2.40
Structure conservation index 0.90
SVM decision value 0.86
SVM RNA-class probability 0.869037
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17861551 115 - 20766785
UAAUCAAAGUGUUUGCACGCAUUUUUAAACCGAUUUGCGCCUGUGCAAAUCUUUAUUAAUUUCCGAGUG-GUGUUCUUACUAAUGACAACAUCAGUAAUUGCUGCCAGACACGAAA
........(((((((((.(((..........((((((((....))))))))..............(.((-(((((.(((....))).))))))).)...))))).))))))).... ( -29.50)
>DroSec_CAF1 26875 115 - 1
UAAUCAAAGUGUUUGCACGCAUUUUUAAACCGAUUUGCGCCUGUGCAAAUCUUUAUUAAUUUCCGAGUG-GUGUUCUUACUAAUGACAACACCAGUAAUUGUUGCCAGACACGACA
........(((((((((.(((..........((((((((....))))))))..............(.((-(((((.(((....))).))))))).)...))))).))))))).... ( -29.70)
>DroEre_CAF1 29481 116 - 1
UUAUCAAAGUGUUUGCACGCAUUUUUAAACCGAUUUGCGCCUGUGCAAAUCCUUACUAAUUUCCGAGUGGGUGUUCUUACUAAUGACAACACCAGUAAUUGUUGCCAGACACGACA
........(((((((((.(((..........((((((((....))))))))..((((........))))((((((.(((....))).))))))......))))).))))))).... ( -28.30)
>consensus
UAAUCAAAGUGUUUGCACGCAUUUUUAAACCGAUUUGCGCCUGUGCAAAUCUUUAUUAAUUUCCGAGUG_GUGUUCUUACUAAUGACAACACCAGUAAUUGUUGCCAGACACGACA
........(((((((((.(((..........((((((((....))))))))..............(.((.(((((.(((....))).))))))).)...))))).))))))).... (-26.14 = -25.70 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,861,587 – 17,861,706
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.66
Mean single sequence MFE -33.43
Consensus MFE -30.60
Energy contribution -30.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.92
SVM decision value 0.57
SVM RNA-class probability 0.784105
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17861587 119 - 20766785
UCAUUUGGGAAUUUCGGGCCGCUUGGGUUUUGUGAAUGAAUAAUCAAAGUGUUUGCACGCAUUUUUAAACCGAUUUGCGCCUGUGCAAAUCUUUAUUAAUUUCCGAGUG-GUGUUCUUAC
.....(((((((.....(((((((((((((...(((((..........(((....))).)))))..)))))((((((((....))))))))............))))))-))))))))). ( -34.20)
>DroSec_CAF1 26911 119 - 1
UCAUUUGGGAAUUUCGGGCCGCUUGGGUUUUGUGAAUGAAUAAUCAAAGUGUUUGCACGCAUUUUUAAACCGAUUUGCGCCUGUGCAAAUCUUUAUUAAUUUCCGAGUG-GUGUUCUUAC
.....(((((((.....(((((((((((((...(((((..........(((....))).)))))..)))))((((((((....))))))))............))))))-))))))))). ( -34.20)
>DroEre_CAF1 29517 120 - 1
UCAUUUGGGAAUUUCUGGCCGCCUGGGUUUUGUGAAUGAAUUAUCAAAGUGUUUGCACGCAUUUUUAAACCGAUUUGCGCCUGUGCAAAUCCUUACUAAUUUCCGAGUGGGUGUUCUUAC
(((((((((((((...((.......(((((...(((((..........(((....))).)))))..)))))((((((((....))))))))))....))))))))))))).......... ( -31.90)
>consensus
UCAUUUGGGAAUUUCGGGCCGCUUGGGUUUUGUGAAUGAAUAAUCAAAGUGUUUGCACGCAUUUUUAAACCGAUUUGCGCCUGUGCAAAUCUUUAUUAAUUUCCGAGUG_GUGUUCUUAC
.((((((((((((............(((((...(((((..........(((....))).)))))..)))))((((((((....))))))))......))))))))))))........... (-30.60 = -30.60 +  -0.00)

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 11:49:20 2006