Locus 4987

Sequence ID 3R_DroMel_CAF1
Location 13,130,596 – 13,130,716
Length 120
Max. P 0.997477
window8154 window8155

overview

Window 4

Location 13,130,596 – 13,130,689
Length 93
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 82.93
Mean single sequence MFE -19.62
Consensus MFE -15.24
Energy contribution -14.84
Covariance contribution -0.40
Combinations/Pair 1.17
Mean z-score -3.21
Structure conservation index 0.78
SVM decision value 2.87
SVM RNA-class probability 0.997477
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13130596 93 - 27905053
CGAAAUA--UGUUAGUGUAAUUC---UUCAAGCACUGCCAUAUUUCUCGGCGGGACCGUUGACCUGCCACCCCCAUCGAGCAUCUACCACCCACACCU
.((((((--((.((((((.....---.....)))))).))))))))..((((((........)))))).............................. ( -25.10)
>DroSec_CAF1 159992 93 - 1
AAAAAUA--CUUUAGUGUAAUUC---UUCAAGCACUGCCAUAUUUCUCGGCGGGACCGUUGACCUGCCACCCCCAUCGACCAUAUACCACCCACACCA
..(((((--...((((((.....---.....))))))...)))))...((((((........)))))).............................. ( -15.60)
>DroSim_CAF1 145013 92 - 1
A-AAAUA--UUUUAGUGUAAUUC---UUCAAGCACUGCCAUAUUUCUCGGCGGGACCGUUGACCUGCCACCCCCAUCGACCAUCUACCACCCACACCA
.-(((((--(..((((((.....---.....))))))..))))))...((((((........)))))).............................. ( -17.60)
>DroEre_CAF1 150295 97 - 1
GAUAUUAUUUUUUGGUGUAAUUUUUUUUCAAGCACUGCCAUAUUUCUCGGCAGGACCUUUGACCUGCCACCCACACCUACCACCCACCACCC-CACCA
.............(((((.............((...))..........((((((........))))))....)))))...............-..... ( -17.30)
>DroYak_CAF1 158341 79 - 1
AGAAAUA--UUUUAGUGUAAUUC---UUCAAGCACUGCCAUAUUUCUCGGCAGGACCUUUGACCUGCCACCCCCAC-----------CA--U-CACCA
(((((((--(..((((((.....---.....))))))..)))))))).((((((........))))))........-----------..--.-..... ( -22.50)
>consensus
AAAAAUA__UUUUAGUGUAAUUC___UUCAAGCACUGCCAUAUUUCUCGGCGGGACCGUUGACCUGCCACCCCCAUCGACCAUCUACCACCCACACCA
............((((((.............))))))...........((((((........)))))).............................. (-15.24 = -14.84 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,130,619 – 13,130,716
Length 97
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 66.73
Mean single sequence MFE -22.89
Consensus MFE -11.60
Energy contribution -11.84
Covariance contribution 0.24
Combinations/Pair 1.25
Mean z-score -2.04
Structure conservation index 0.51
SVM decision value 1.61
SVM RNA-class probability 0.967473
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13130619 97 - 27905053
UGUUUUAA-----AAAAUAA--------AGUAAAAUUUCACGAAAUA--UGUUAGUGUAAUUC---UUCAAGCACUGCCAUAUUUCUCGGCGGGACCGUUGACCUGCCACCCCCA
........-----.......--------.............((((((--((.((((((.....---.....)))))).))))))))..((((((........))))))....... ( -25.10)
>DroSec_CAF1 160015 96 - 1
A----UAG--AAUGGCAUAA--------AGUAAAGUUUUAAAAAAUA--CUUUAGUGUAAUUC---UUCAAGCACUGCCAUAUUUCUCGGCGGGACCGUUGACCUGCCACCCCCA
.----...--.(((((((((--------((((.............))--)))))((((.....---.....)))))))))).......((((((........))))))....... ( -24.12)
>DroEre_CAF1 150317 106 - 1
CGC----A-----GAAAUAACUACCCAAGGUAGAUUUUUUGAUAUUAUUUUUUGGUGUAAUUUUUUUUCAAGCACUGCCAUAUUUCUCGGCAGGACCUUUGACCUGCCACCCACA
.(.----(-----((((((.(((((...)))))....................(((((.............)))))....))))))))((((((........))))))....... ( -24.82)
>DroYak_CAF1 158350 96 - 1
UGUUUUAA-----GAUGUGA---------GUAAAUUUUUAAGAAAUA--UUUUAGUGUAAUUC---UUCAAGCACUGCCAUAUUUCUCGGCAGGACCUUUGACCUGCCACCCCCA
........-----.......---------...........(((((((--(..((((((.....---.....))))))..)))))))).((((((........))))))....... ( -22.80)
>DroAna_CAF1 148903 89 - 1
UAUCUGUGAAUGUGGCUUAA--------UGUAUUUUUUCAA------------AGUGUCUUUC---GUCGUGGGCUGCCAUAUUUCUCAACAGGACCAUUGACCUGCCCACG---
.....(((((((((((....--------((........)).------------...((((...---.....)))).))))))))......((((........))))..))).--- ( -17.60)
>consensus
UGU_UUAA_____GAAAUAA________AGUAAAUUUUUAAAAAAUA__UUUUAGUGUAAUUC___UUCAAGCACUGCCAUAUUUCUCGGCAGGACCGUUGACCUGCCACCCCCA
....................................................((((((.............))))))...........((((((........))))))....... (-11.60 = -11.84 +   0.24)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:39 2006