Locus 1034

Sequence ID 3L_DroMel_CAF1
Location 3,065,283 – 3,065,394
Length 111
Max. P 0.930771
window1597 window1598

overview

Window 7

Location 3,065,283 – 3,065,375
Length 92
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 80.55
Mean single sequence MFE -30.17
Consensus MFE -16.91
Energy contribution -16.80
Covariance contribution -0.11
Combinations/Pair 1.26
Mean z-score -2.89
Structure conservation index 0.56
SVM decision value 1.18
SVM RNA-class probability 0.927077
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3065283 92 - 23771897
GCA----GGCCAAACAAUAACAAA--AACCGCGCUGUUACGUCACGUUAAGUGAAUAUGUAGAUGUGGCAGAGCGGU----CUUAAGGCCUACCAUUUACCG
..(----((((.............--.(((((.((((((((((((((.........)))).)))))))))).)))))----.....)))))........... ( -30.41)
>DroPse_CAF1 32024 88 - 1
GCAGGUAAACCAAACAAUAACAAA--AAGCCCGCUGUUACGUCACGUAA----AAUGCGUUGAUGUGGCAGCACGGGCAACA-CGUCG-------UUUACCG
...(((((((..............--......(((((((((((((((..----...))).))))))))))))((((....).-))).)-------)))))). ( -33.80)
>DroSec_CAF1 26048 94 - 1
GCA----GGCCAAACAAUAACAAA--AACCCCGCUGUUACGUCACGUUUAGUGAAUAUGUAGAUGUGGCAGAGCGGU--ACGUUACGGCCUACCAUUUACCG
..(----((((......((((...--.(((.(.((((((((((((((.........)))).)))))))))).).)))--..)))).)))))........... ( -26.30)
>DroSim_CAF1 26019 94 - 1
GCA----GGCCAAACAAUAACAAA--AACCGCGCUGUUACGUCACGUUUAGUGAAUAUGUAGAUGUGGCAGAGCGGU--ACGUUACGGCCUACCAUUUACCG
..(----((((......((((...--.(((((.((((((((((((((.........)))).)))))))))).)))))--..)))).)))))........... ( -32.60)
>DroYak_CAF1 26241 95 - 1
GCA----GGCCAAACAAUAACAAAAAAACCGCGCUGUUACGUCACGUUAAGUGAAUAUGUAGAUGUGGCAGAGCGGU--ACG-GAUGGUCUACCAUUUACCG
...----((..................(((((.((((((((((((((.........)))).)))))))))).)))))--..(-(((((....)))))).)). ( -31.80)
>DroAna_CAF1 27991 94 - 1
GCA----GGCUAAACAAUAACAAA--AAGUACGCUGUUACGUCACGU-AAGUUCAUAUGUAGAUGUGGCAGAGCGGGUGUCG-CUUAGUUUACCAUUUACCG
...----((.(((((.........--.......((((((((((((((-(......))))).))))))))))((((.....))-))..)))))))........ ( -26.10)
>consensus
GCA____GGCCAAACAAUAACAAA__AACCGCGCUGUUACGUCACGUUAAGUGAAUAUGUAGAUGUGGCAGAGCGGU__ACG_UAUGGCCUACCAUUUACCG
.......((((......................((((((((((((((.........)))).))))))))))...(.....).....))))............ (-16.91 = -16.80 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,065,304 – 3,065,394
Length 90
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 79.37
Mean single sequence MFE -28.45
Consensus MFE -15.66
Energy contribution -16.08
Covariance contribution 0.42
Combinations/Pair 1.17
Mean z-score -2.59
Structure conservation index 0.55
SVM decision value 1.21
SVM RNA-class probability 0.930771
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3065304 90 - 23771897
--A--------UAGUCACACGUU----UGGGGAGCA----GGCCAAACAAUAACAAA--AACCGCGCUGUUACGUCACGUUAAGUGAAUAUGUAGAUGUGGCAGAGCGGU
--.--------.........(((----(((......----..)))))).........--.(((((.((((((((((((((.........)))).)))))))))).))))) ( -31.70)
>DroPse_CAF1 32041 87 - 1
--A--------UGCUGGCAC-------UGAGAGGCAGGUAAACCAAACAAUAACAAA--AAGCCCGCUGUUACGUCACGUAA----AAUGCGUUGAUGUGGCAGCACGGG
--.--------....(((.(-------(....))..((....)).............--..))).(((((((((((((((..----...))).))))))))))))..... ( -28.30)
>DroSec_CAF1 26071 92 - 1
AGA--------UAGUCACACGUU----UGGGGAGCA----GGCCAAACAAUAACAAA--AACCCCGCUGUUACGUCACGUUUAGUGAAUAUGUAGAUGUGGCAGAGCGGU
...--------.........(((----(((......----..)))))).........--.(((.(.((((((((((((((.........)))).)))))))))).).))) ( -25.40)
>DroSim_CAF1 26042 92 - 1
AGA--------UAGUCACACGUU----UGGGGAGCA----GGCCAAACAAUAACAAA--AACCGCGCUGUUACGUCACGUUUAGUGAAUAUGUAGAUGUGGCAGAGCGGU
...--------.........(((----(((......----..)))))).........--.(((((.((((((((((((((.........)))).)))))))))).))))) ( -31.70)
>DroYak_CAF1 26263 102 - 1
AGAUAGUCAGAUAGUCACACGUU----UGGGGAGCA----GGCCAAACAAUAACAAAAAAACCGCGCUGUUACGUCACGUUAAGUGAAUAUGUAGAUGUGGCAGAGCGGU
....................(((----(((......----..))))))............(((((.((((((((((((((.........)))).)))))))))).))))) ( -31.70)
>DroAna_CAF1 28015 91 - 1
-----------UACU-ACAUAUUGUGGGGGGGAGCA----GGCUAAACAAUAACAAA--AAGUACGCUGUUACGUCACGU-AAGUUCAUAUGUAGAUGUGGCAGAGCGGG
-----------....-...((((((..((.......----..))..)))))).....--.....((((((((((((((((-(......))))).))))))))..)))).. ( -21.90)
>consensus
__A________UAGUCACACGUU____UGGGGAGCA____GGCCAAACAAUAACAAA__AACCGCGCUGUUACGUCACGUUAAGUGAAUAUGUAGAUGUGGCAGAGCGGU
............................................................(((.(.((((((((((((((.........)))).)))))))))).).))) (-15.66 = -16.08 +   0.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:21 2006