Locus 6200

Sequence ID 2R_DroMel_CAF1
Location 19,517,653 – 19,517,749
Length 96
Max. P 0.993921
window9927 window9928

overview

Window 7

Location 19,517,653 – 19,517,749
Length 96
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 75.81
Mean single sequence MFE -36.32
Consensus MFE -18.14
Energy contribution -17.97
Covariance contribution -0.17
Combinations/Pair 1.26
Mean z-score -2.20
Structure conservation index 0.50
SVM decision value 1.16
SVM RNA-class probability 0.924837
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19517653 96 + 20766785
U---------GGAGACGGACUUGGAGGAC------------UGCUGCUUCUUGUACAGCUCUAUGGCCUCCUGCUCUAGCUUUAGCAGCUCCUGCUGCUCGUGCUGAAGUCGCUCCU
.---------((((...((((((((((..------------.((((.........)))).......))))).....((((...((((((....))))))...))))))))).)))). ( -37.30)
>DroPse_CAF1 14518 117 + 1
UAUGCUUUUCGGCAGUUGUCUUUGAAGAAUAUUGCCGGUCGUGCUGUUUCUUGUACAGCUCGAUGGACUCCUGCUCAAGCUUCAGCAGUUCCUGCUGCUCGAGCUGCAGCCGCUCUU
...((....(((((((..(((....)))..)))))))((((.(((((.......))))).))))((....((((...(((((.((((((....)))))).))))))))))))).... ( -44.10)
>DroEre_CAF1 14401 96 + 1
U---------GGAGACGGACUUGGAAGAC------------UGCUGCUUCUUGUACAGCUCAAUGGCCUCCUGCUCCAGCUUUAGCAGCUCCUGCUGCUCGUGCUGAAGGCGCUCCU
.---------((((.(((.((..((.(.(------------((.(((.....)))))))))...))))....(((.((((...((((((....))))))...))))..)))))))). ( -33.30)
>DroYak_CAF1 14361 96 + 1
A---------GGAGAUGGACUUGGAAGAC------------UGCUGCUUCUUGUACAGCUCAAUGGCCUCCUGCUCUAGCUUCAGCAGCUCCUGCUGCUCGUGCUGAAGCCGCUCCU
(---------((((..((.((..((.(.(------------((.(((.....)))))))))...))))....(((.((((...((((((....))))))...)))).)))..))))) ( -32.50)
>DroAna_CAF1 15113 91 + 1
--------------ACGGAUUUCGAGGAC------------UGCUGCUUCUUGUACAGCUCUAUGGCUUCCUGUUCGAGCCUCAGCAGUUCCUGCUGUUCAAGCUGAAGGCGCUCUU
--------------..(((..(((.((((------------((.(((.....)))))).))).)))..))).....((((..((((((...)))))).....((.....)))))).. ( -26.60)
>DroPer_CAF1 14620 117 + 1
UAUGCUUUUCGGCAGUUGUCUUUGAAGAAUAUUGCCGGUCGUGCUGUUUCUUGUACAGCUCGAUGGACUCCUGCUCAAGCUUCAGCAGUUCCUGCUGCUCGAGCUGCAGCCGCUCUU
...((....(((((((..(((....)))..)))))))((((.(((((.......))))).))))((....((((...(((((.((((((....)))))).))))))))))))).... ( -44.10)
>consensus
U_________GGAGACGGACUUGGAAGAC____________UGCUGCUUCUUGUACAGCUCAAUGGCCUCCUGCUCAAGCUUCAGCAGCUCCUGCUGCUCGAGCUGAAGCCGCUCCU
..........................................((.(((((......(((.............)))..(((...((((((....))))))...)))))))).)).... (-18.14 = -17.97 +  -0.17)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,517,653 – 19,517,749
Length 96
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 75.81
Mean single sequence MFE -37.02
Consensus MFE -19.91
Energy contribution -20.38
Covariance contribution 0.48
Combinations/Pair 1.19
Mean z-score -2.85
Structure conservation index 0.54
SVM decision value 2.44
SVM RNA-class probability 0.993921
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19517653 96 - 20766785
AGGAGCGACUUCAGCACGAGCAGCAGGAGCUGCUAAAGCUAGAGCAGGAGGCCAUAGAGCUGUACAAGAAGCAGCA------------GUCCUCCAAGUCCGUCUCC---------A
.((((((.((..(((...((((((....))))))...)))..))..(((((.(.....(((((.......))))).------------).))))).....)).))))---------. ( -37.70)
>DroPse_CAF1 14518 117 - 1
AAGAGCGGCUGCAGCUCGAGCAGCAGGAACUGCUGAAGCUUGAGCAGGAGUCCAUCGAGCUGUACAAGAAACAGCACGACCGGCAAUAUUCUUCAAAGACAACUGCCGAAAAGCAUA
....((((((.(.(((((((((((((...)))))...)))))))).).))))..(((.(((((.......))))).))).(((((....(((....)))....)))))....))... ( -42.90)
>DroEre_CAF1 14401 96 - 1
AGGAGCGCCUUCAGCACGAGCAGCAGGAGCUGCUAAAGCUGGAGCAGGAGGCCAUUGAGCUGUACAAGAAGCAGCA------------GUCUUCCAAGUCCGUCUCC---------A
.((((((.(((((((...((((((....))))))...)))))))..(((((.(.....(((((.......))))).------------).))))).....)).))))---------. ( -39.00)
>DroYak_CAF1 14361 96 - 1
AGGAGCGGCUUCAGCACGAGCAGCAGGAGCUGCUGAAGCUAGAGCAGGAGGCCAUUGAGCUGUACAAGAAGCAGCA------------GUCUUCCAAGUCCAUCUCC---------U
(((((..(((..(((...((((((....))))))...)))..))).(((((.(.....(((((.......))))).------------).)))))........))))---------) ( -34.90)
>DroAna_CAF1 15113 91 - 1
AAGAGCGCCUUCAGCUUGAACAGCAGGAACUGCUGAGGCUCGAACAGGAAGCCAUAGAGCUGUACAAGAAGCAGCA------------GUCCUCGAAAUCCGU--------------
....(((..(((.(((.....)))((((.(((((..(((((......).)))).....(((........)))))))------------))))).)))...)))-------------- ( -24.70)
>DroPer_CAF1 14620 117 - 1
AAGAGCGGCUGCAGCUCGAGCAGCAGGAACUGCUGAAGCUUGAGCAGGAGUCCAUCGAGCUGUACAAGAAACAGCACGACCGGCAAUAUUCUUCAAAGACAACUGCCGAAAAGCAUA
....((((((.(.(((((((((((((...)))))...)))))))).).))))..(((.(((((.......))))).))).(((((....(((....)))....)))))....))... ( -42.90)
>consensus
AAGAGCGGCUUCAGCACGAGCAGCAGGAACUGCUGAAGCUAGAGCAGGAGGCCAUAGAGCUGUACAAGAAGCAGCA____________GUCUUCCAAGUCCAUCUCC_________A
(((((.((((((.((.(.((((((((...)))))...))).).)).))))))).....(((((.......)))))..............))))........................ (-19.91 = -20.38 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:19 2006