Locus 8548

Sequence ID 3L_DroMel_CAF1
Location 22,330,048 – 22,330,194
Length 146
Max. P 0.987883
window14009 window14010 window14011 window14012

overview

Window 9

Location 22,330,048 – 22,330,167
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.89
Mean single sequence MFE -33.88
Consensus MFE -26.66
Energy contribution -26.72
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.10
Structure conservation index 0.79
SVM decision value 0.99
SVM RNA-class probability 0.896314
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22330048 119 + 23771897
CAAGCCAAUCGGAAUUGCCCUUACUGCGGUCGGCU-UUGAGUUGGUUGGCAUGUAAUGCAGAUGUUUCCAGCCAGAUUGCAUCUUUAAGAUGCAUUUUCUCACGCGGCUUUUCGGGUUAA
......((((.(((..(((....((((((((((((-.......)))))))......))))).........((.(((.((((((.....))))))...)))...)))))..))).)))).. ( -34.10)
>DroSec_CAF1 9413 119 + 1
GAAGCCAAUCUGAAUUGCCCUUGCUGCGGUCGGCUUUUGAGUUGGUUAGCAUGUAAUGCAGAUGUUU-CAGCCAGAUUGCAUCUUUAAGAUGCAUUUUCUCACGCGGCUUUUCGGGUUAA
((((((.(((((.(((((...(((((...((((((....)))))).))))).))))).)))))....-..((.(((.((((((.....))))))...)))...))))))))......... ( -36.20)
>DroEre_CAF1 7349 104 + 1
UAAGCCAAUCUGAAUUGCCCUUACUGCGGUCG----------------GCAUGUAAUGCAUAUGUUUCCAGCCAGAUUGCAUCUUUAAGAUGCAUUUUCUCACGCGGCUUUUCGGGUUAA
......((((((((..(((........((..(----------------((((((.....))))))).)).((.(((.((((((.....))))))...)))...)))))..)))))))).. ( -31.20)
>DroYak_CAF1 6840 104 + 1
UAAGCCAAUCUGAAUUGCCCUUACUGCGGUUG----------------GCAUGUAAUGCAUAUGUUUCCAGCCAGAUUGCAUCUUUAAGAUGCAUUUUCUCACGCGGCUUUUCGGGUUAA
......((((((((..(((........(((((----------------((((((.....)))))...))))))(((.((((((.....))))))...))).....)))..)))))))).. ( -34.00)
>consensus
UAAGCCAAUCUGAAUUGCCCUUACUGCGGUCG________________GCAUGUAAUGCAGAUGUUUCCAGCCAGAUUGCAUCUUUAAGAUGCAUUUUCUCACGCGGCUUUUCGGGUUAA
......((((((((..(((.(((((((.....................))).))))..............((.(((.((((((.....))))))...)))...)))))..)))))))).. (-26.66 = -26.72 +   0.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,330,048 – 22,330,167
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.89
Mean single sequence MFE -29.95
Consensus MFE -25.25
Energy contribution -25.75
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.84
SVM decision value 1.08
SVM RNA-class probability 0.911430
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22330048 119 - 23771897
UUAACCCGAAAAGCCGCGUGAGAAAAUGCAUCUUAAAGAUGCAAUCUGGCUGGAAACAUCUGCAUUACAUGCCAACCAACUCAA-AGCCGACCGCAGUAAGGGCAAUUCCGAUUGGCUUG
..........((((((((.((((...((((((.....)))))).)))(((((....)....((((...))))............-))))..)))).....(((....)))....))))). ( -30.20)
>DroSec_CAF1 9413 119 - 1
UUAACCCGAAAAGCCGCGUGAGAAAAUGCAUCUUAAAGAUGCAAUCUGGCUG-AAACAUCUGCAUUACAUGCUAACCAACUCAAAAGCCGACCGCAGCAAGGGCAAUUCAGAUUGGCUUC
..........(((((((((((((...((((((.....)))))).))).((.(-(....)).))....)))))..............(((............)))..........))))). ( -27.00)
>DroEre_CAF1 7349 104 - 1
UUAACCCGAAAAGCCGCGUGAGAAAAUGCAUCUUAAAGAUGCAAUCUGGCUGGAAACAUAUGCAUUACAUGC----------------CGACCGCAGUAAGGGCAAUUCAGAUUGGCUUA
..........(((((.(....).....(((((.....)))))(((((((.((....))..(((.((((.(((----------------.....)))))))..)))..)))))))))))). ( -31.30)
>DroYak_CAF1 6840 104 - 1
UUAACCCGAAAAGCCGCGUGAGAAAAUGCAUCUUAAAGAUGCAAUCUGGCUGGAAACAUAUGCAUUACAUGC----------------CAACCGCAGUAAGGGCAAUUCAGAUUGGCUUA
..........(((((.(....).....(((((.....)))))(((((((.((....))..(((.((((.(((----------------.....)))))))..)))..)))))))))))). ( -31.30)
>consensus
UUAACCCGAAAAGCCGCGUGAGAAAAUGCAUCUUAAAGAUGCAAUCUGGCUGGAAACAUAUGCAUUACAUGC________________CGACCGCAGUAAGGGCAAUUCAGAUUGGCUUA
..........(((((.(....).....(((((.....)))))(((((((.((....))..(((.((((.(((.....................)))))))..)))..)))))))))))). (-25.25 = -25.75 +   0.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 22,330,087 – 22,330,194
Length 107
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 92.74
Mean single sequence MFE -29.62
Consensus MFE -26.05
Energy contribution -26.05
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.68
Structure conservation index 0.88
SVM decision value 0.57
SVM RNA-class probability 0.785969
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22330087 107 + 23771897
GUUGGUUGGCAUGUAAUGCAGAUGUUUCCAGCCAGAUUGCAUCUUUAAGAUGCAUUUUCUCACGCGGCUUUUCGGGUUAACCGCAUGGCAGCCACGAAACUGAAACC
..((((((.(((((...............(((((((.((((((.....))))))...))).....))))....((.....))))))).))))))............. ( -31.90)
>DroSec_CAF1 9453 106 + 1
GUUGGUUAGCAUGUAAUGCAGAUGUUU-CAGCCAGAUUGCAUCUUUAAGAUGCAUUUUCUCACGCGGCUUUUCGGGUUAACCGCAUGGCAGCCACGAAACUGAAACC
....(((.((((...)))).)))((((-(((..(((.((((((.....))))))...)))..((.((((...(((.....)))......)))).))...))))))). ( -30.30)
>DroEre_CAF1 7381 99 + 1
--------GCAUGUAAUGCAUAUGUUUCCAGCCAGAUUGCAUCUUUAAGAUGCAUUUUCUCACGCGGCUUUUCGGGUUAACCGCACGGCAGCCACGAAACUGAAACC
--------((((...))))....(((((.(((((((.((((((.....))))))...))).....))))(((((((((..((....)).)))).)))))..))))). ( -28.00)
>DroYak_CAF1 6872 99 + 1
--------GCAUGUAAUGCAUAUGUUUCCAGCCAGAUUGCAUCUUUAAGAUGCAUUUUCUCACGCGGCUUUUCGGGUUAACCGCAUUGCAGCCACGAAACUGAAACC
--------((.((((((((..........(((((((.((((((.....))))))...))).....))))....((.....))))))))))))............... ( -28.30)
>consensus
________GCAUGUAAUGCAGAUGUUUCCAGCCAGAUUGCAUCUUUAAGAUGCAUUUUCUCACGCGGCUUUUCGGGUUAACCGCAUGGCAGCCACGAAACUGAAACC
........((((...))))....((((.(((..(((.((((((.....))))))...)))..((.((((...(((.....)))......)))).))...))))))). (-26.05 = -26.05 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 22,330,087 – 22,330,194
Length 107
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 92.74
Mean single sequence MFE -33.38
Consensus MFE -30.30
Energy contribution -30.55
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.55
Structure conservation index 0.91
SVM decision value 2.10
SVM RNA-class probability 0.987883
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22330087 107 - 23771897
GGUUUCAGUUUCGUGGCUGCCAUGCGGUUAACCCGAAAAGCCGCGUGAGAAAAUGCAUCUUAAAGAUGCAAUCUGGCUGGAAACAUCUGCAUUACAUGCCAACCAAC
((((...(((((((((((......(((.....)))...))))))((.(((...((((((.....)))))).))).))..)))))....((((...)))).))))... ( -35.40)
>DroSec_CAF1 9453 106 - 1
GGUUUCAGUUUCGUGGCUGCCAUGCGGUUAACCCGAAAAGCCGCGUGAGAAAAUGCAUCUUAAAGAUGCAAUCUGGCUG-AAACAUCUGCAUUACAUGCUAACCAAC
((((...(((((((((((......(((.....)))...))))))((.(((...((((((.....)))))).))).)).)-))))....((((...)))).))))... ( -35.70)
>DroEre_CAF1 7381 99 - 1
GGUUUCAGUUUCGUGGCUGCCGUGCGGUUAACCCGAAAAGCCGCGUGAGAAAAUGCAUCUUAAAGAUGCAAUCUGGCUGGAAACAUAUGCAUUACAUGC--------
.......(((((((((((......(((.....)))...))))))((.(((...((((((.....)))))).))).))..)))))....((((...))))-------- ( -31.20)
>DroYak_CAF1 6872 99 - 1
GGUUUCAGUUUCGUGGCUGCAAUGCGGUUAACCCGAAAAGCCGCGUGAGAAAAUGCAUCUUAAAGAUGCAAUCUGGCUGGAAACAUAUGCAUUACAUGC--------
.......(((((((((((......(((.....)))...))))))((.(((...((((((.....)))))).))).))..)))))....((((...))))-------- ( -31.20)
>consensus
GGUUUCAGUUUCGUGGCUGCCAUGCGGUUAACCCGAAAAGCCGCGUGAGAAAAUGCAUCUUAAAGAUGCAAUCUGGCUGGAAACAUAUGCAUUACAUGC________
.......(((((((((((......(((.....)))...))))))((.(((...((((((.....)))))).))).))..)))))....((((...))))........ (-30.30 = -30.55 +   0.25)

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 13:18:47 2006