Locus 2595

Sequence ID X_DroMel_CAF1
Location 6,938,347 – 6,938,520
Length 173
Max. P 0.839707
window4237 window4238 window4239

overview

Window 7

Location 6,938,347 – 6,938,450
Length 103
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.89
Mean single sequence MFE -37.71
Consensus MFE -32.58
Energy contribution -31.89
Covariance contribution -0.69
Combinations/Pair 1.10
Mean z-score -1.64
Structure conservation index 0.86
SVM decision value 0.53
SVM RNA-class probability 0.772565
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6938347 103 + 22224390
AGGCAGAUGUUCCGCAUUCUCGGAAGCUGGAUGCCGGCAAGGUGAUAGUUCUAUUUU-----UUUGGGCCGGGUGGGUGGAAAACGCCGAAAGGUGGAACGUGGCAAG------------
..((..(((((((((...(((((..(((((...)))))...........((((....-----..)))))))))..((((.....)))).....))))))))).))...------------ ( -35.40)
>DroSec_CAF1 23399 102 + 1
AGGCAGAUGUUCCGCAUUCUCGGAAGCUGGAUGCCGGCAAGGUGAUAGUUUUAUUU------UUUGGGCCGGGUGGGUGGAAAACGCCGAAAGGUGGAACGUGGCAAG------------
..((..(((((((((...(((((..(((((...)))))(((((((.....))))))------).....)))))..((((.....)))).....))))))))).))...------------ ( -36.00)
>DroEre_CAF1 31962 106 + 1
AGGCAGAUGUUCCGCAUUCUCGGAAGCUGGAUGCCGGCAAGGUGAUAGCCCUAUUU------UUUGGGCCG-UUGGGUGGAAAACGCCGAAAGGUGGAACGUGGCAAGCUGC-------A
..((((.(((..(((((((.((...(((((...))))).........((((.....------...))))))-..))))).....((((....))))...))..)))..))))-------. ( -38.70)
>DroYak_CAF1 24579 119 + 1
AGGCAGAUGUUCCGCAUUCUCGGAAGCUGGAUGCCGGCAAGGUGAUAGCCCUACUUUUUAUUUUUGGGCCG-UUGGGUGGAAAACGCCGAAAGGUGGAACGUGGCAAGCUGCAAACUGCA
..((((..(((((((.(((......(((((...))))).....((..((((..............))))..-)).((((.....)))))))..)))))))(..(....)..)...)))). ( -40.74)
>consensus
AGGCAGAUGUUCCGCAUUCUCGGAAGCUGGAUGCCGGCAAGGUGAUAGCCCUAUUU______UUUGGGCCG_GUGGGUGGAAAACGCCGAAAGGUGGAACGUGGCAAG____________
..((..(((((((((.(((.((...(((((...))))).........((((..............))))))....((((.....)))))))..))))))))).))............... (-32.58 = -31.89 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,938,387 – 6,938,481
Length 94
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.74
Mean single sequence MFE -33.88
Consensus MFE -21.08
Energy contribution -20.64
Covariance contribution -0.44
Combinations/Pair 1.13
Mean z-score -2.16
Structure conservation index 0.62
SVM decision value 0.75
SVM RNA-class probability 0.839707
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6938387 94 + 22224390
GGUGAUAGUUCUAUUUU-----UUUGGGCCGGGUGGGUGGAAAACGCCGAAAGGUGGAACGUGGCAAG---------------------CUGCAUGUUAAUUACUUGGAAGCAAGCUGCA
.......((((....((-----(((.(.((....)).).)))))((((....))))))))(..((..(---------------------((.((.((.....)).))..)))..))..). ( -27.80)
>DroSec_CAF1 23439 93 + 1
GGUGAUAGUUUUAUUU------UUUGGGCCGGGUGGGUGGAAAACGCCGAAAGGUGGAACGUGGCAAG---------------------CUGCAAGUUAAUUACUUGGAAGCAAGCUGCA
.......(((((((((------((((((((.....)))(.....).))))))))))))))(..((..(---------------------((.(((((.....)))))..)))..))..). ( -30.80)
>DroEre_CAF1 32002 106 + 1
GGUGAUAGCCCUAUUU------UUUGGGCCG-UUGGGUGGAAAACGCCGAAAGGUGGAACGUGGCAAGCUGC-------AACCGGCAAGCUGCAAGUUAAUUACUUGGAAGCAAGCUGCA
...((..((((.....------...))))..-))..........((((....))))....(..((..((((.-------...))))..(((.(((((.....)))))..)))..))..). ( -36.50)
>DroYak_CAF1 24619 119 + 1
GGUGAUAGCCCUACUUUUUAUUUUUGGGCCG-UUGGGUGGAAAACGCCGAAAGGUGGAACGUGGCAAGCUGCAAACUGCAAGCGGCAAGCUGCAAGUUAAUUACUUGGAAGCAAGCUGCA
(((..((((.((((.((((((((((.(((.(-((........)))))).)))))))))).))))...))))...)))....(((((..(((.(((((.....)))))..)))..))))). ( -40.40)
>consensus
GGUGAUAGCCCUAUUU______UUUGGGCCG_GUGGGUGGAAAACGCCGAAAGGUGGAACGUGGCAAG_____________________CUGCAAGUUAAUUACUUGGAAGCAAGCUGCA
.......((((..............)))).......(..(....((((....)))).(((...(((.(((.................))))))..))).....((((....)))))..). (-21.08 = -20.64 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,938,422 – 6,938,520
Length 98
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.79
Mean single sequence MFE -28.60
Consensus MFE -21.10
Energy contribution -21.10
Covariance contribution -0.00
Combinations/Pair 1.05
Mean z-score -1.52
Structure conservation index 0.74
SVM decision value 0.05
SVM RNA-class probability 0.557782
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6938422 98 + 22224390
AAAACGCCGAAAGGUGGAACGUGGCAAG---------------------CUGCAUGUUAAUUACUUGGAAGCAAGCUGCAUUUUGUAUUGCUACCCGAUUUAAAUUCUG-UGAACAUCUU
....((((....))))....((((((((---------------------(...((((......((((....))))..))))...)).))))))).............((-....)).... ( -22.60)
>DroSec_CAF1 23473 98 + 1
AAAACGCCGAAAGGUGGAACGUGGCAAG---------------------CUGCAAGUUAAUUACUUGGAAGCAAGCUGCAUUUUGUAUUGCUACCCGACUUAAAUUCUG-UGAACAUGUU
....((((....)))).(((((((((((---------------------((.(((((.....)))))..)))....(((.....)))))))))).............((-....)).))) ( -25.80)
>DroEre_CAF1 32035 113 + 1
AAAACGCCGAAAGGUGGAACGUGGCAAGCUGC-------AACCGGCAAGCUGCAAGUUAAUUACUUGGAAGCAAGCUGCAUUUUGUAUCGCUACCCGACUUAAUUUCCGUUGAAUAUGUU
..((((((....)))((((.(..((..((((.-------...))))..(((.(((((.....)))))..)))..))..)...(((..(((.....)))..))).)))))))......... ( -30.80)
>DroYak_CAF1 24658 111 + 1
AAAACGCCGAAAGGUGGAACGUGGCAAGCUGCAAACUGCAAGCGGCAAGCUGCAAGUUAAUUACUUGGAAGCAAGCUGCAUUUUGUAUCGCUACCCGACUUAA---------AAAUUCUU
....((((....))))....(((((....(((.....))).(((((..(((.(((((.....)))))..)))..)))))..........))))).........---------........ ( -35.20)
>consensus
AAAACGCCGAAAGGUGGAACGUGGCAAG_____________________CUGCAAGUUAAUUACUUGGAAGCAAGCUGCAUUUUGUAUCGCUACCCGACUUAAAUUCUG_UGAACAUCUU
....((((....))))....(((((...........................(((((.....)))))((.(((((......))))).))))))).......................... (-21.10 = -21.10 +  -0.00)

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 10:38:35 2006