Locus 3576

Sequence ID 3L_DroMel_CAF1
Location 10,518,801 – 10,518,895
Length 94
Max. P 0.985473
window5574 window5575

overview

Window 4

Location 10,518,801 – 10,518,895
Length 94
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 84.76
Mean single sequence MFE -31.78
Consensus MFE -22.25
Energy contribution -23.17
Covariance contribution 0.92
Combinations/Pair 1.11
Mean z-score -2.19
Structure conservation index 0.70
SVM decision value 0.79
SVM RNA-class probability 0.851595
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10518801 94 + 23771897
AGAUAGA-----------GAAAGCAUG-AGAGACAG----GGAUAGGGACAACAGAUGUGGCUGUUGCAUUUGACUGAGCCAAAAUGACUUGGCCAUGUUUCUGUUGUCG
.((((((-----------((((.((((-.....(((----...((((..((((((......))))))..)))).))).(((((......)))))))))))))).))))). ( -27.70)
>DroSec_CAF1 398261 101 + 1
AGAAGGAGAUGGC-----GAAAGCAUGGAGAGACAG----GGACAGGGACAACAGAUGUGUCUGUUGCAUUUGACUGAGCCAAACUGACUUGGCCAUGUUCCUGUUGUCG
.......(((.((-----....)).......(((((----(((((..(.(((((((....)))))))).......((.(((((......)))))))))))))))))))). ( -35.50)
>DroSim_CAF1 406636 106 + 1
AGAAGGAGAUGGAAGAAGGAAAGCAUGGAGAGACAG----GGACAGGGACAACAGAUGUGUCUGUUGCAUUUGACUGAGCCAAACUGACUUGGCCAUGUUCCUGUUGUCG
.......((..(....((((..(((((......(((----...((((..(((((((....)))))))..)))).))).(((((......)))))))))))))).)..)). ( -32.50)
>DroEre_CAF1 405215 100 + 1
GGAAAGAGUUGGC-----GAAAGCCUG-AGAGACAG----GGAUAGGUACAACAGAUGUGGCUGUUGCAUUUCACUGAGCCAAACUGACUUGGCCAUGUUCCUGAUGUCG
..........(((-----....)))..-.((.((((----(((((....((((((......))))))........((.(((((......))))))))))))))).).)). ( -32.10)
>DroYak_CAF1 407006 104 + 1
GGACAGAGAUGGU-----GAAAGCAUA-AGAGACAGUAGAGGAGAGGUGGAACAGAUGUGGCUGUUGCAUUUGGCUGAGCCAAACUGUCUUGGCCAUGUUCCUGAUGUCU
(((((.....((.-----....((...-.((((((((.........(((.(((((......))))).)))(((((...))))))))))))).))......))...))))) ( -31.10)
>consensus
AGAAAGAGAUGGC_____GAAAGCAUG_AGAGACAG____GGACAGGGACAACAGAUGUGGCUGUUGCAUUUGACUGAGCCAAACUGACUUGGCCAUGUUCCUGUUGUCG
...............................((((.......(((((((((.(((((((.......)))))))..((.(((((......)))))))))))))))))))). (-22.25 = -23.17 +   0.92)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,518,801 – 10,518,895
Length 94
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 84.76
Mean single sequence MFE -24.84
Consensus MFE -18.86
Energy contribution -19.10
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.74
Structure conservation index 0.76
SVM decision value 2.01
SVM RNA-class probability 0.985473
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10518801 94 - 23771897
CGACAACAGAAACAUGGCCAAGUCAUUUUGGCUCAGUCAAAUGCAACAGCCACAUCUGUUGUCCCUAUCC----CUGUCUCU-CAUGCUUUC-----------UCUAUCU
.(((((((((....((((((((....)))))).)).......((....))....))))))))).......----........-.........-----------....... ( -21.60)
>DroSec_CAF1 398261 101 - 1
CGACAACAGGAACAUGGCCAAGUCAGUUUGGCUCAGUCAAAUGCAACAGACACAUCUGUUGUCCCUGUCC----CUGUCUCUCCAUGCUUUC-----GCCAUCUCCUUCU
.(((((((((....((((..((((.....))))..))))...((((((((....)))))))).)))))..----.)))).............-----............. ( -26.60)
>DroSim_CAF1 406636 106 - 1
CGACAACAGGAACAUGGCCAAGUCAGUUUGGCUCAGUCAAAUGCAACAGACACAUCUGUUGUCCCUGUCC----CUGUCUCUCCAUGCUUUCCUUCUUCCAUCUCCUUCU
.(((((((((....((((..((((.....))))..))))...((((((((....)))))))).)))))..----.))))............................... ( -26.60)
>DroEre_CAF1 405215 100 - 1
CGACAUCAGGAACAUGGCCAAGUCAGUUUGGCUCAGUGAAAUGCAACAGCCACAUCUGUUGUACCUAUCC----CUGUCUCU-CAGGCUUUC-----GCCAACUCUUUCC
.((((...(((.((((((((((....)))))))..)))...((((((((......))))))))....)))----.))))...-..(((....-----))).......... ( -27.70)
>DroYak_CAF1 407006 104 - 1
AGACAUCAGGAACAUGGCCAAGACAGUUUGGCUCAGCCAAAUGCAACAGCCACAUCUGUUCCACCUCUCCUCUACUGUCUCU-UAUGCUUUC-----ACCAUCUCUGUCC
.((((...((.....(((..((((((((((((...))))).((.(((((......))))).))..........)))))))..-...)))...-----.)).....)))). ( -21.70)
>consensus
CGACAACAGGAACAUGGCCAAGUCAGUUUGGCUCAGUCAAAUGCAACAGCCACAUCUGUUGUCCCUAUCC____CUGUCUCU_CAUGCUUUC_____GCCAUCUCUUUCU
.((((...(((...((((((((....)))))).)).......(((((((......))))))).....))).....))))............................... (-18.86 = -19.10 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:21 2006