Locus 5994

Sequence ID 2R_DroMel_CAF1
Location 18,842,616 – 18,842,710
Length 94
Max. P 0.916702
window9611 window9612

overview

Window 1

Location 18,842,616 – 18,842,710
Length 94
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 78.18
Mean single sequence MFE -19.20
Consensus MFE -11.84
Energy contribution -11.90
Covariance contribution 0.06
Combinations/Pair 1.10
Mean z-score -1.41
Structure conservation index 0.62
SVM decision value 0.08
SVM RNA-class probability 0.573367
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18842616 94 + 20766785
UGCGAUUCUUUCGCCCUCACUUCG-UC--C-UUUUUUAUGCAUUCGCCUUAAUUGCAUCAACUUGGG-AAUUGUUUGACCAGCGAAUUGACCAAAUAAA
.((((.....))))..........-((--(-(..((.(((((...........))))).))...)))-).(((((((..(((....)))..))))))). ( -16.30)
>DroSec_CAF1 16645 81 + 1
UGCGAUUCUUUCGC-----------------UUUUUUAUGCAUUUGCCUUAAUUGCAUCAACUUGGG-AAUUGUUUGACCAGCGAAUUGGCCAAAUAAA
.((((.....))))-----------------......(((((...........))))).........-..(((((((.((((....)))).))))))). ( -15.80)
>DroSim_CAF1 16768 81 + 1
GGCGAUUCUUUCGC-----------------UUUUUUAUGCAUUUGCCUUAAUUGCAUCAACUUGGG-AAUUGUUUGACCAGCGAAUUGGCCAAAUAAA
(((.(....(((((-----------------(...(((.(((.((.((................)).-)).))).)))..)))))).).)))....... ( -17.79)
>DroEre_CAF1 20528 79 + 1
----------------UCACUUCG-UC--CUUUUUUUAUGCAUUUCCCUUAAUUGCAUCAACUUGGG-AAUUGUUUGACCAGCGAAUUGGCCAAAUAAA
----------------........-((--((......(((((...........)))))......)))-).(((((((.((((....)))).))))))). ( -16.00)
>DroYak_CAF1 17008 97 + 1
UGCGAUUCUUUCGCUCUCACUUCG-UACCAUUUUUUUAUGCAUUUGCCUUAAUUGCAUCAACUUGGG-AAUUGUUUGACCAGCGAAUUGGCCAAAUAAA
.((((.....))))..........-..(((.......(((((...........))))).....))).-..(((((((.((((....)))).))))))). ( -18.80)
>DroPer_CAF1 22698 97 + 1
UUCUUAUUUUUGGGGGACGGUGCCCCC--CAUUUUUUAUGCAUUUCCCUUAAUUGCAUCAAACUGGGCGAUUGUUUGGCCAGGGAAUUGGCCAAAUAAA
..........((((((.......))))--))..(((.(((((...........))))).)))........((((((((((((....)))))))))))). ( -30.50)
>consensus
UGCGAUUCUUUCGC__UCACUUCG_UC__C_UUUUUUAUGCAUUUGCCUUAAUUGCAUCAACUUGGG_AAUUGUUUGACCAGCGAAUUGGCCAAAUAAA
.((((.....)))).......................(((((...........)))))............(((((((.((((....)))).))))))). (-11.84 = -11.90 +   0.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,842,616 – 18,842,710
Length 94
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 78.18
Mean single sequence MFE -20.40
Consensus MFE -13.39
Energy contribution -13.53
Covariance contribution 0.14
Combinations/Pair 1.17
Mean z-score -1.92
Structure conservation index 0.66
SVM decision value 1.11
SVM RNA-class probability 0.916702
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18842616 94 - 20766785
UUUAUUUGGUCAAUUCGCUGGUCAAACAAUU-CCCAAGUUGAUGCAAUUAAGGCGAAUGCAUAAAAAA-G--GA-CGAAGUGAGGGCGAAAGAAUCGCA
(((((((.(((.(((((((.......((((.-.....))))..........)))))))..........-.--))-).))))))).((((.....)))). ( -19.83)
>DroSec_CAF1 16645 81 - 1
UUUAUUUGGCCAAUUCGCUGGUCAAACAAUU-CCCAAGUUGAUGCAAUUAAGGCAAAUGCAUAAAAAA-----------------GCGAAAGAAUCGCA
....((((((((......))))))))((((.-.....))))(((((.((.....)).)))))......-----------------((((.....)))). ( -17.90)
>DroSim_CAF1 16768 81 - 1
UUUAUUUGGCCAAUUCGCUGGUCAAACAAUU-CCCAAGUUGAUGCAAUUAAGGCAAAUGCAUAAAAAA-----------------GCGAAAGAAUCGCC
....((((((((......))))))))((((.-.....))))(((((.((.....)).)))))......-----------------((((.....)))). ( -17.00)
>DroEre_CAF1 20528 79 - 1
UUUAUUUGGCCAAUUCGCUGGUCAAACAAUU-CCCAAGUUGAUGCAAUUAAGGGAAAUGCAUAAAAAAAG--GA-CGAAGUGA----------------
....((((((((......))))))))((.((-(((.(((((...)))))..))))).))...........--..-........---------------- ( -16.00)
>DroYak_CAF1 17008 97 - 1
UUUAUUUGGCCAAUUCGCUGGUCAAACAAUU-CCCAAGUUGAUGCAAUUAAGGCAAAUGCAUAAAAAAAUGGUA-CGAAGUGAGAGCGAAAGAAUCGCA
....((((((((......)))))))).....-.(((..((.(((((.((.....)).)))))...))..)))..-....((((...(....)..)))). ( -22.10)
>DroPer_CAF1 22698 97 - 1
UUUAUUUGGCCAAUUCCCUGGCCAAACAAUCGCCCAGUUUGAUGCAAUUAAGGGAAAUGCAUAAAAAAUG--GGGGGCACCGUCCCCCAAAAAUAAGAA
....((((((((......))))))))...((.....((((.(((((.((.....)).)))))...))))(--((((((...)))))))........)). ( -29.60)
>consensus
UUUAUUUGGCCAAUUCGCUGGUCAAACAAUU_CCCAAGUUGAUGCAAUUAAGGCAAAUGCAUAAAAAA_G__GA_CGAAGUGA__GCGAAAGAAUCGCA
....((((((((......))))))))(((((.....)))))(((((.((.....)).))))).......................((((.....)))). (-13.39 = -13.53 +   0.14)

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 11:59:53 2006