Locus 3524

Sequence ID 3L_DroMel_CAF1
Location 10,339,164 – 10,339,270
Length 106
Max. P 0.999350
window5500 window5501

overview

Window 0

Location 10,339,164 – 10,339,270
Length 106
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 87.77
Mean single sequence MFE -37.94
Consensus MFE -37.53
Energy contribution -37.69
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -5.32
Structure conservation index 0.99
SVM decision value 3.53
SVM RNA-class probability 0.999350
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10339164 106 + 23771897
AU------A-UUUUUUACCUGGUUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCA--UUAUAAACUCGUAGGAACUUCAUACCGUGCUCUUGGAAGACCAAAAAACAACCA---
..------.-.........((((((...(((..((((.(((((..((((((((((....--.........))))))))))..))))).))))..))).))))))...........--- ( -38.62)
>DroPse_CAF1 231841 115 + 1
AUGUGUGUAUUUUUUUACCUGGUUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAUAUUAUAAACUCGUAGGAACUUCAUACCGUGCUCUUGGAAGACCAAAAGACAACGA---
.(((.((((......))).((((((...(((..((((.(((((..((((((((((...............))))))))))..))))).))))..))).))))))..).)))....--- ( -39.66)
>DroGri_CAF1 232740 106 + 1
A---------UAUGCUACCUGGUUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUAAAUUUAAAUACUCAUAGGAACUUCAUACCGUGCUCUUGGAAGACCAAAACACAACAA---
.---------.........((((((...(((..((((.(((((..((((((((.(...............).))))))))..))))).))))..))).))))))...........--- ( -32.76)
>DroWil_CAF1 331562 109 + 1
A---------UAUGCUACCUGGUUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAUUUAAUAAACUCGUAGGAACUUCAUACCGUGCUCUUGGAAGACCAAAAAACAACGUUAC
.---------.........((((((...(((..((((.(((((..((((((((((...............))))))))))..))))).))))..))).)))))).............. ( -38.46)
>DroMoj_CAF1 283097 106 + 1
G---------UAUGCUACCUGGUUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAAUUUAAAUACUCGUAGGAACUUCAUACCGUGCUCUUGGAAGACCAAAACACAACUC---
.---------.........((((((...(((..((((.(((((..((((((((((...............))))))))))..))))).))))..))).))))))...........--- ( -38.46)
>DroPer_CAF1 226831 115 + 1
AUGUGUGUAUUUUUUUACCUGGUUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAUAUUAUAAACUCGUAGGAACUUCAUACCGUGCUCUUGGAAGACCAAAAGACAACGA---
.(((.((((......))).((((((...(((..((((.(((((..((((((((((...............))))))))))..))))).))))..))).))))))..).)))....--- ( -39.66)
>consensus
A_________UAUGCUACCUGGUUUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAUUUUAUAAACUCGUAGGAACUUCAUACCGUGCUCUUGGAAGACCAAAAAACAACGA___
...................((((((...(((..((((.(((((..((((((((((...............))))))))))..))))).))))..))).)))))).............. (-37.53 = -37.69 +   0.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,339,164 – 10,339,270
Length 106
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 87.77
Mean single sequence MFE -36.04
Consensus MFE -32.20
Energy contribution -32.06
Covariance contribution -0.14
Combinations/Pair 1.04
Mean z-score -4.09
Structure conservation index 0.89
SVM decision value 3.11
SVM RNA-class probability 0.998479
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10339164 106 - 23771897
---UGGUUGUUUUUUGGUCUUCCAAGAGCACGGUAUGAAGUUCCUACGAGUUUAUAA--UGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAACCAGGUAAAAAA-U------AU
---((((((((((((((....))))))).))((((((.((((((((((.........--....)))))))))).))))))..((.....))...))))).........-.------.. ( -33.92)
>DroPse_CAF1 231841 115 - 1
---UCGUUGUCUUUUGGUCUUCCAAGAGCACGGUAUGAAGUUCCUACGAGUUUAUAAUAUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAACCAGGUAAAAAAAUACACACAU
---..((..((.(((((....)))))(((..((((((.(((((((((..((((((...))))))))))))))).))))))..)))))..)).........(((......)))...... ( -35.00)
>DroGri_CAF1 232740 106 - 1
---UUGUUGUGUUUUGGUCUUCCAAGAGCACGGUAUGAAGUUCCUAUGAGUAUUUAAAUUUAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAACCAGGUAGCAUA---------U
---.....(((((((((....)).)))))))((((((.((((((((((..((........)).)))))))))).))))))..((((.(((......)))..))))...---------. ( -36.40)
>DroWil_CAF1 331562 109 - 1
GUAACGUUGUUUUUUGGUCUUCCAAGAGCACGGUAUGAAGUUCCUACGAGUUUAUUAAAUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAACCAGGUAGCAUA---------U
.......((((.((((((...(((..(((..((((((.(((((((((..((((((...))))))))))))))).))))))..)))..))).....)))))).))))..---------. ( -36.80)
>DroMoj_CAF1 283097 106 - 1
---GAGUUGUGUUUUGGUCUUCCAAGAGCACGGUAUGAAGUUCCUACGAGUAUUUAAAUUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAACCAGGUAGCAUA---------C
---.....(((((((((....)).)))))))((((((.((((((((((..((.......))..)))))))))).))))))..((((.(((......)))..))))...---------. ( -39.10)
>DroPer_CAF1 226831 115 - 1
---UCGUUGUCUUUUGGUCUUCCAAGAGCACGGUAUGAAGUUCCUACGAGUUUAUAAUAUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAACCAGGUAAAAAAAUACACACAU
---..((..((.(((((....)))))(((..((((((.(((((((((..((((((...))))))))))))))).))))))..)))))..)).........(((......)))...... ( -35.00)
>consensus
___UCGUUGUCUUUUGGUCUUCCAAGAGCACGGUAUGAAGUUCCUACGAGUUUAUAAAAUGAACGUAGGAACUCUAUACCUCGCUGAUGGCAAAAACCAGGUAAAAAA_________U
............((((((...(((..(((..((((((.((((((((((...............)))))))))).))))))..)))..))).....))))))................. (-32.20 = -32.06 +  -0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:12 2006