Locus 5026

Sequence ID 3L_DroMel_CAF1
Location 13,789,423 – 13,789,579
Length 156
Max. P 0.999388
window7956 window7957 window7958

overview

Window 6

Location 13,789,423 – 13,789,539
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.39
Mean single sequence MFE -31.42
Consensus MFE -28.60
Energy contribution -29.60
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.29
Structure conservation index 0.91
SVM decision value 3.56
SVM RNA-class probability 0.999388
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13789423 116 + 23771897
AGAGUCGCGCGUCCUUCUAGGCCAUAUAUUUUAGCUAAUCCCUGAGAUAUGCAGCCAAAAGCUCUUAAAAGUGCGGAGUACUUUUUAGAGCUUCUAGACUUUUCAAGGCUUA----CAUC
.(((((.........(((((((..((((((((((.......))))))))))..)))..(((((((.((((((((...)))))))).))))))).))))........))))).----.... ( -34.73)
>DroSec_CAF1 26454 116 + 1
AGAGUCGCGCGUCCUUCUAGGCCAUAUAUUUUAGCUAAUCCCUGAGAUAUGCAGCCAAAAGCUCUUAAAAGUUCGGACUACUUUUUAGAGCUCUUAGACUUUUCAAGGCUUA----CAUC
.(((((.........(((((((..((((((((((.......))))))))))..)))...((((((.((((((.......)))))).))))))..))))........))))).----.... ( -31.03)
>DroSim_CAF1 22586 116 + 1
AGAGUCGCGCGUCCUUCUAUGCCAUAUAUUUUACCUAAUCUCUGAGAUAUGCAGCCCAAAGCUCUUAAAAGUGCGGAGUACUUUUUACAGCUCUUAGACUUUUCAAGGCUUA----CAUC
((((((((((((......))))..(((((((((.........)))))))))..))....((((...((((((((...))))))))...))))....))))))..........----.... ( -21.60)
>DroEre_CAF1 25908 116 + 1
AGAGUCGCGCGUCCUUCUAGGCCAUAUAUUUUAGCUAAUCCCUGAGAUAUGCAGCCAAAAGCUCUUAAAAGUGCGGAGUACUUUUUAGAGCUCUUAGACUUUUCAAGGCUUA----CAUC
.(((((.........(((((((..((((((((((.......))))))))))..)))...((((((.((((((((...)))))))).))))))..))))........))))).----.... ( -33.93)
>DroYak_CAF1 24803 120 + 1
AGAGUCGCGCUUCCUUGUAGGCCAUAUAUUUUAGCUAAUCCCUGAGAUAUGCAGCCAAAAGCUCUUAAAAGUGCGGAGUACUUUUUAGAGCUCCUAGACUUUUCAGGGCUUACAUACAUC
...............(((((((..((((((((((.......))))))))))..)))..(((((((.((((((..(((((.((....)).)))))...)))))).)))))))...)))).. ( -35.80)
>consensus
AGAGUCGCGCGUCCUUCUAGGCCAUAUAUUUUAGCUAAUCCCUGAGAUAUGCAGCCAAAAGCUCUUAAAAGUGCGGAGUACUUUUUAGAGCUCUUAGACUUUUCAAGGCUUA____CAUC
((((((.............(((..((((((((((.......))))))))))..)))...((((((.((((((((...)))))))).))))))....)))))).................. (-28.60 = -29.60 +   1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,789,463 – 13,789,579
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.73
Mean single sequence MFE -31.78
Consensus MFE -27.34
Energy contribution -27.78
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.35
Structure conservation index 0.86
SVM decision value 0.35
SVM RNA-class probability 0.699999
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13789463 116 + 23771897
CCUGAGAUAUGCAGCCAAAAGCUCUUAAAAGUGCGGAGUACUUUUUAGAGCUUCUAGACUUUUCAAGGCUUA----CAUCUGCUGUGGAUGGGUUCCGCUUAAUUAUCCCGUCGUCGCUA
............(((...(((((((.((((((((...)))))))).)))))))...(((....((.(((...----.....))).))((((((..............)))))))))))). ( -33.64)
>DroSec_CAF1 26494 116 + 1
CCUGAGAUAUGCAGCCAAAAGCUCUUAAAAGUUCGGACUACUUUUUAGAGCUCUUAGACUUUUCAAGGCUUA----CAUCUGCUGUGGAUGGGUUCCGCUUAAUUAUCCCGUCGUCGCUA
............(((....((((((.((((((.......)))))).))))))....(((....((.(((...----.....))).))((((((..............)))))))))))). ( -29.84)
>DroSim_CAF1 22626 116 + 1
UCUGAGAUAUGCAGCCCAAAGCUCUUAAAAGUGCGGAGUACUUUUUACAGCUCUUAGACUUUUCAAGGCUUA----CAUCUGCUGUGGAUAGGUUCCGCUUAAUUAUCCCGUCUUCGCUA
...(((((..((((....((((.(((((((((..(((((..........)))))...)))))).))))))).----...)))).(((((.....)))))...........)))))..... ( -27.80)
>DroEre_CAF1 25948 116 + 1
CCUGAGAUAUGCAGCCAAAAGCUCUUAAAAGUGCGGAGUACUUUUUAGAGCUCUUAGACUUUUCAAGGCUUA----CAUCUGCUGUGGAUGGGUUCCGCUUAAUUAUCCCGUCGUCGCUA
............(((....((((((.((((((((...)))))))).))))))....(((....((.(((...----.....))).))((((((..............)))))))))))). ( -32.74)
>DroYak_CAF1 24843 120 + 1
CCUGAGAUAUGCAGCCAAAAGCUCUUAAAAGUGCGGAGUACUUUUUAGAGCUCCUAGACUUUUCAGGGCUUACAUACAUCUGCUGUGGAUGGGCUCCGCUUAAUUAUCCCGUCGUCGCUA
...(.((((.((((((..(((((((.((((((..(((((.((....)).)))))...)))))).))))))).....(((((.....)))))))))..)).....)))).).......... ( -34.90)
>consensus
CCUGAGAUAUGCAGCCAAAAGCUCUUAAAAGUGCGGAGUACUUUUUAGAGCUCUUAGACUUUUCAAGGCUUA____CAUCUGCUGUGGAUGGGUUCCGCUUAAUUAUCCCGUCGUCGCUA
.....(((..(((((....((((((.((((((((...)))))))).))))))(((.((....)).))).............))))).((((((..............))))))))).... (-27.34 = -27.78 +   0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,789,463 – 13,789,579
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.73
Mean single sequence MFE -31.86
Consensus MFE -31.04
Energy contribution -30.88
Covariance contribution -0.16
Combinations/Pair 1.09
Mean z-score -1.52
Structure conservation index 0.97
SVM decision value 2.05
SVM RNA-class probability 0.986755
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13789463 116 - 23771897
UAGCGACGACGGGAUAAUUAAGCGGAACCCAUCCACAGCAGAUG----UAAGCCUUGAAAAGUCUAGAAGCUCUAAAAAGUACUCCGCACUUUUAAGAGCUUUUGGCUGCAUAUCUCAGG
..........((((((.(((((((((.....)))(((.....))----)..).)))))..((.(((((((((((.((((((.......)))))).)))))))))))))...))))))... ( -31.80)
>DroSec_CAF1 26494 116 - 1
UAGCGACGACGGGAUAAUUAAGCGGAACCCAUCCACAGCAGAUG----UAAGCCUUGAAAAGUCUAAGAGCUCUAAAAAGUAGUCCGAACUUUUAAGAGCUUUUGGCUGCAUAUCUCAGG
..........((((((.(((((((((.....)))(((.....))----)..).)))))..((.(((((((((((.((((((.......)))))).)))))))))))))...))))))... ( -32.00)
>DroSim_CAF1 22626 116 - 1
UAGCGAAGACGGGAUAAUUAAGCGGAACCUAUCCACAGCAGAUG----UAAGCCUUGAAAAGUCUAAGAGCUGUAAAAAGUACUCCGCACUUUUAAGAGCUUUGGGCUGCAUAUCUCAGA
..........((((((.....(.(((.....))).).((((...----.(((((((((((.(((..((.(((......))).))..).))))))))).))))....)))).))))))... ( -29.50)
>DroEre_CAF1 25948 116 - 1
UAGCGACGACGGGAUAAUUAAGCGGAACCCAUCCACAGCAGAUG----UAAGCCUUGAAAAGUCUAAGAGCUCUAAAAAGUACUCCGCACUUUUAAGAGCUUUUGGCUGCAUAUCUCAGG
..........((((((.(((((((((.....)))(((.....))----)..).)))))..((.(((((((((((.((((((.......)))))).)))))))))))))...))))))... ( -31.80)
>DroYak_CAF1 24843 120 - 1
UAGCGACGACGGGAUAAUUAAGCGGAGCCCAUCCACAGCAGAUGUAUGUAAGCCCUGAAAAGUCUAGGAGCUCUAAAAAGUACUCCGCACUUUUAAGAGCUUUUGGCUGCAUAUCUCAGG
..((...((.(((....((.....)).))).))....)).((.(((((((.(((((....))...(((((((((.((((((.......)))))).))))))))))))))))))).))... ( -34.20)
>consensus
UAGCGACGACGGGAUAAUUAAGCGGAACCCAUCCACAGCAGAUG____UAAGCCUUGAAAAGUCUAAGAGCUCUAAAAAGUACUCCGCACUUUUAAGAGCUUUUGGCUGCAUAUCUCAGG
..........((((((.....(.(((.....))).).((((.............((....)).(((((((((((.((((((.......)))))).))))))))))))))).))))))... (-31.04 = -30.88 +  -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 11:40:01 2006