Locus 2719

Sequence ID X_DroMel_CAF1
Location 7,297,562 – 7,297,690
Length 128
Max. P 0.966983
window4451 window4452

overview

Window 1

Location 7,297,562 – 7,297,659
Length 97
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 67.46
Mean single sequence MFE -28.50
Consensus MFE -13.24
Energy contribution -13.88
Covariance contribution 0.64
Combinations/Pair 1.25
Mean z-score -1.46
Structure conservation index 0.46
SVM decision value -0.04
SVM RNA-class probability 0.515719
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7297562 97 - 22224390
GGUGUUCCACUUGGUGGUGGACCACAUCCAGGCCCCUGGGGAUAGGCCACCUAU--GUAGAUGGCAGUUAUGUAUGUAUAAGUCACAAAUUAAUCAC-UA-
.(((.((((((....)))))).))).(((((....)))))(((..((((.((..--..)).))))..(((((....)))))))).............-..- ( -26.50)
>DroSec_CAF1 47410 87 - 1
GGGGUUCCACUUGGUGGUGGACCACAUCCAGGCCCCUGGGGAUAUGCCACCUAU--------AGCAGUUCC----AUAUAAGUCACAAAUUAAUCAC-UA-
..(((.(((((....))))))))....((((....))))(((..(((.......--------.)))..)))----......................-..- ( -23.00)
>DroSim_CAF1 46376 93 - 1
GGGGUUCCACUUGGUGGUGGACCACAUCCAGGCCCCUGGGGAUAAGCCACCUAU--AAGGAUAGCAGUUAC----GCAUAAGUCACAAAUAAAUCAC-UA-
...(((...((((..(((((......(((((....)))))......)))))..)--)))...))).((.((----......)).))...........-..- ( -22.80)
>DroEre_CAF1 57818 95 - 1
GGGGUUCCACUUGGCGGAGGACCGCAUCCAGGUCCCUGGGGAUGGGCCAGCUAA--GUGGAGAGCAGUUGA----UUAGAAGUCAGCAAUGCAUCCAAGGG
.((((((((((((((...((.(((..(((((....)))))..))).)).)))))--)))))..((((((((----(.....))))))..)))))))..... ( -42.30)
>DroYak_CAF1 74186 86 - 1
GGGGUGCCACUUGGUGGGGGGCCACAUCCAGGGCCCUGGGGAUAGGCCACCUAGUUAUGGACAGCAGUU--------AGA------GAAUGCAUCGCAUA-
(.(((((..(((..((((.((((...(((((....)))))....)))).))))......(((....)))--------.))------)...))))).)...- ( -29.30)
>DroPer_CAF1 107565 75 - 1
GGCGGGCCACUUGGUGGCGGUCCGCAGGGACCACCCUGGGGAUAAGCGCUCUUA--AAG--------------------AAAACAAAAAU--AUGAA-AA-
((((.(((((...))))).((((.(((((....))))).))))...))))....--...--------------------...........--.....-..- ( -27.10)
>consensus
GGGGUUCCACUUGGUGGUGGACCACAUCCAGGCCCCUGGGGAUAGGCCACCUAU__AUGGA_AGCAGUU_______UAUAAGUCACAAAUGAAUCAC_UA_
((((((((.....((((....))))..((((....)))))))...))).)).................................................. (-13.24 = -13.88 +   0.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,297,597 – 7,297,690
Length 93
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 74.50
Mean single sequence MFE -37.15
Consensus MFE -21.42
Energy contribution -22.83
Covariance contribution 1.42
Combinations/Pair 1.18
Mean z-score -2.09
Structure conservation index 0.58
SVM decision value 1.60
SVM RNA-class probability 0.966983
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7297597 93 + 22224390
CCAUCUAC--AUAGGUGGCCUAUCCCCAGGGGCCUGGAUGUGGUCCACCACCAAGUGGAACACCUCCGUCGGGACCGCGACCAUCGGGUCCACCA---------
........--...((((((((........))))).(((.(((.(((((......))))).))).)))....(((((.((.....)))))))))).--------- ( -37.60)
>DroSec_CAF1 47441 87 + 1
CU--------AUAGGUGGCAUAUCCCCAGGGGCCUGGAUGUGGUCCACCACCAAGUGGAACCCCUGCGCCGGGCCCGCGACCAUCGGGUCCACCA---------
..--------...((((............((((((((.((((((((((......)))).)))...)))))))))))..((((....)))))))).--------- ( -39.30)
>DroSim_CAF1 46407 93 + 1
CUAUCCUU--AUAGGUGGCUUAUCCCCAGGGGCCUGGAUGUGGUCCACCACCAAGUGGAACCCCUCCGCCGGGCCCGCGACCAUCGGGUCCACCA---------
........--...((((............((((((((..(.(((((((......)))).))).)....))))))))..((((....)))))))).--------- ( -38.70)
>DroEre_CAF1 57851 93 + 1
CUCUCCAC--UUAGCUGGCCCAUCCCCAGGGACCUGGAUGCGGUCCUCCGCCAAGUGGAACCCCUCCGUCGGGCCCUCGACCAUCUGGUCCUCCA---------
...(((((--((.((.(((((((((..((....))))))).)).))...)).)))))))..(((......))).....((((....)))).....--------- ( -32.90)
>DroYak_CAF1 74208 95 + 1
CUGUCCAUAACUAGGUGGCCUAUCCCCAGGGCCCUGGAUGUGGCCCCCCACCAAGUGGCACCCCUCCCCCGGGCCCACGACCAUCUGGUCCUCCA---------
....(((((.(((((.(.(((......))).)))))).)))))...........((((...(((......))).))))((((....)))).....--------- ( -32.20)
>DroPer_CAF1 107583 97 + 1
-----CUU--UAAGAGCGCUUAUCCCCAGGGUGGUCCCUGCGGACCGCCACCAAGUGGCCCGCCGCCAUCUGGACCUCCGCCAUCGGGACGCCCGCCAGGCGGA
-----...--((((....))))...((((((((((((....)))))))).....(((((.....)))))))))...((((((..((((...))))...)))))) ( -42.20)
>consensus
CU_UCCAU__AUAGGUGGCCUAUCCCCAGGGGCCUGGAUGUGGUCCACCACCAAGUGGAACCCCUCCGCCGGGCCCGCGACCAUCGGGUCCACCA_________
.............((((...........(((.(((((....((....((((...))))....))....))))))))..((((....)))))))).......... (-21.42 = -22.83 +   1.42)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:43 2006