Locus 7372

Sequence ID X_DroMel_CAF1
Location 18,368,174 – 18,368,341
Length 167
Max. P 0.982508
window12081 window12082 window12083 window12084 window12085

overview

Window 1

Location 18,368,174 – 18,368,285
Length 111
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 84.24
Mean single sequence MFE -39.60
Consensus MFE -29.03
Energy contribution -28.92
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -2.78
Structure conservation index 0.73
SVM decision value 1.31
SVM RNA-class probability 0.940905
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18368174 111 + 22224390
GCUGGCUGGUGGGUGAUAUAAUGUACAAAUCGCCAGAAUGGGGCC--------GAAAUGGCUGAAUGUCACAAGAAGGAAGAGGAAACUAUCCGGCUUGCGGCAGCGAAGCUCCACCUA
.(((((.(((..(((........)))..))))))))..((((((.--------....(.(((....(((.((((..(((..((....)).)))..)))).)))))).).)))))).... ( -36.50)
>DroSec_CAF1 12770 111 + 1
GCGGUCUGGUGGGUGAUACAAUGUACAAAUCGCCAGAAUGGAGCC--------GAAAUGGCUGAAUGUCACAAGAAGGAAGAGGAAACUAUCCGGCUUGCGGCAGCGAAGCUCCACCUA
..((((((((((....(((...)))....)))))))).((((((.--------....(.(((....(((.((((..(((..((....)).)))..)))).)))))).).)))))))).. ( -38.10)
>DroYak_CAF1 11850 110 + 1
GCUGGCUGGUGGGUGAUA-------CAAAUCGGCAGAAUGGGGCCGAAAUGGCCAAAUGGCCAAAUGUCACCA--AGGAAAAGGAAACUAUCCGACUUGCGGCAGCGAAGCUCCACCUA
(((.((((.(((((((((-------....(((((........)))))..(((((....)))))..))))))).--.(((..((....)).)))......)).))))..)))........ ( -44.20)
>consensus
GCUGGCUGGUGGGUGAUA_AAUGUACAAAUCGCCAGAAUGGGGCC________GAAAUGGCUGAAUGUCACAAGAAGGAAGAGGAAACUAUCCGGCUUGCGGCAGCGAAGCUCCACCUA
.......(((((((((((...........((....))....((((.............))))...)))))).....(((..((....)).)))(((((((....)).)))))))))).. (-29.03 = -28.92 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,368,214 – 18,368,315
Length 101
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 87.46
Mean single sequence MFE -35.34
Consensus MFE -29.45
Energy contribution -30.95
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.83
SVM decision value 0.84
SVM RNA-class probability 0.864075
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18368214 101 + 22224390
GGGCC--------GAAAUGGCUGAAUGUCACAAGAAGGAA-GAGGAAACUAUCCGGCUUGCGGCAGCGAAGCUCCACCUACAAAGGGGCACAGGUGCGCCUACGCAGGUG
.((((--------.....))))...((((.((((..(((.-.((....)).)))..)))).)))).........(((((.(..(((.(((....))).)))..).))))) ( -37.10)
>DroSec_CAF1 12810 100 + 1
GAGCC--------GAAAUGGCUGAAUGUCACAAGAAGGAA-GAGGAAACUAUCCGGCUUGCGGCAGCGAAGCUCCACCUACA-AGGGGCACAGGUGCGCCUACGCAGGUG
.((((--------.....))))...((((.((((..(((.-.((....)).)))..)))).))))(((..(((((.......-.)))))..(((....))).)))..... ( -37.40)
>DroEre_CAF1 12027 95 + 1
------------CGAAAUGGACGAAUGUCACAA--AGGAAAAAGGAAACUAUCCGGCUUGCGGCAGCGAAGCUCCACCUACA-AGGGGCACAGGUGCGCCUACGCAGGUG
------------.....(((((....))).)).--.(((...((....)).))).((((((((((.(...(((((.......-.)))))...).))).....))))))). ( -29.20)
>DroYak_CAF1 11883 106 + 1
GGGCCGAAAUGGCCAAAUGGCCAAAUGUCACCA--AGGAA-AAGGAAACUAUCCGACUUGCGGCAGCGAAGCUCCACCUACA-AGGGGCACAGGUGCGCCUACGCAGGUG
((.......(((((....))))).......)).--.(((.-.((....)).))).((((((((((.(...(((((.......-.)))))...).))).....))))))). ( -37.64)
>consensus
GGGCC________GAAAUGGCCGAAUGUCACAA__AGGAA_AAGGAAACUAUCCGGCUUGCGGCAGCGAAGCUCCACCUACA_AGGGGCACAGGUGCGCCUACGCAGGUG
..................((((...((((.((((..(((...((....)).)))..)))).))))....)))).(((((....(((.(((....))).)))....))))) (-29.45 = -30.95 +   1.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,368,214 – 18,368,315
Length 101
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 87.46
Mean single sequence MFE -36.00
Consensus MFE -29.14
Energy contribution -28.95
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.16
Structure conservation index 0.81
SVM decision value 1.20
SVM RNA-class probability 0.929283
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18368214 101 - 22224390
CACCUGCGUAGGCGCACCUGUGCCCCUUUGUAGGUGGAGCUUCGCUGCCGCAAGCCGGAUAGUUUCCUC-UUCCUUCUUGUGACAUUCAGCCAUUUC--------GGCCC
((((((((.(((.(((....))).))).))))))))..((......))((((((..(((.((......)-))))..)))))).......(((.....--------))).. ( -35.30)
>DroSec_CAF1 12810 100 - 1
CACCUGCGUAGGCGCACCUGUGCCCCU-UGUAGGUGGAGCUUCGCUGCCGCAAGCCGGAUAGUUUCCUC-UUCCUUCUUGUGACAUUCAGCCAUUUC--------GGCUC
((((((((..(((((....)))))...-))))))))(((((..((((.((((((..(((.((......)-))))..)))))).....))))......--------))))) ( -37.80)
>DroEre_CAF1 12027 95 - 1
CACCUGCGUAGGCGCACCUGUGCCCCU-UGUAGGUGGAGCUUCGCUGCCGCAAGCCGGAUAGUUUCCUUUUUCCU--UUGUGACAUUCGUCCAUUUCG------------
((((((((..(((((....)))))...-))))))))(((((...(((.(....).)))..)))))..........--.((.(((....))))).....------------ ( -30.80)
>DroYak_CAF1 11883 106 - 1
CACCUGCGUAGGCGCACCUGUGCCCCU-UGUAGGUGGAGCUUCGCUGCCGCAAGUCGGAUAGUUUCCUU-UUCCU--UGGUGACAUUUGGCCAUUUGGCCAUUUCGGCCC
((((((((..(((((....)))))...-))))))))(.((......)))....((((((..(((.((..-.....--.)).)))...(((((....))))).)))))).. ( -40.10)
>consensus
CACCUGCGUAGGCGCACCUGUGCCCCU_UGUAGGUGGAGCUUCGCUGCCGCAAGCCGGAUAGUUUCCUC_UUCCU__UUGUGACAUUCAGCCAUUUC________GGCCC
((((((((.(((.(((....))).))).))))))))(((..((((.(.(....).)(((.....)))............))))..)))...................... (-29.14 = -28.95 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,368,246 – 18,368,341
Length 95
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 97.19
Mean single sequence MFE -38.78
Consensus MFE -38.71
Energy contribution -38.78
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.64
Structure conservation index 1.00
SVM decision value 1.92
SVM RNA-class probability 0.982508
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18368246 95 + 22224390
-GAGGAAACUAUCCGGCUUGCGGCAGCGAAGCUCCACCUACAAAGGGGCACAGGUGCGCCUACGCAGGUGGGCCGCAUGCUAAUAACAGUGCCUUA
-((((..(((....(((.(((((((((...)))((((((.(..(((.(((....))).)))..).)))))))))))).)))......))).)))). ( -39.00)
>DroSec_CAF1 12842 94 + 1
-GAGGAAACUAUCCGGCUUGCGGCAGCGAAGCUCCACCUACA-AGGGGCACAGGUGCGCCUACGCAGGUGGGCCGCAUGCUAAUAACAGCGCCUUA
-.((....))....(((.(((((((((...)))((((((.(.-(((.(((....))).)))..).)))))))))))).(((......))))))... ( -40.20)
>DroEre_CAF1 12053 95 + 1
AAAGGAAACUAUCCGGCUUGCGGCAGCGAAGCUCCACCUACA-AGGGGCACAGGUGCGCCUACGCAGGUGGGCCGCAUGCUAAUAACAGCGCCUUA
..((....))....(((.(((((((((...)))((((((.(.-(((.(((....))).)))..).)))))))))))).(((......))))))... ( -40.10)
>DroYak_CAF1 11921 94 + 1
-AAGGAAACUAUCCGACUUGCGGCAGCGAAGCUCCACCUACA-AGGGGCACAGGUGCGCCUACGCAGGUGGGCCGCAUGCUAAUAACAGCGCCUUA
-((((.............(((((((((...)))((((((.(.-(((.(((....))).)))..).)))))))))))).(((......))).)))). ( -35.80)
>consensus
_AAGGAAACUAUCCGGCUUGCGGCAGCGAAGCUCCACCUACA_AGGGGCACAGGUGCGCCUACGCAGGUGGGCCGCAUGCUAAUAACAGCGCCUUA
..((....))....(((.(((((((((...)))((((((....(((.(((....))).)))....)))))))))))).(((......))))))... (-38.71 = -38.78 +   0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,368,246 – 18,368,341
Length 95
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 97.19
Mean single sequence MFE -46.75
Consensus MFE -46.09
Energy contribution -46.15
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -4.42
Structure conservation index 0.99
SVM decision value 1.51
SVM RNA-class probability 0.960321
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18368246 95 - 22224390
UAAGGCACUGUUAUUAGCAUGCGGCCCACCUGCGUAGGCGCACCUGUGCCCCUUUGUAGGUGGAGCUUCGCUGCCGCAAGCCGGAUAGUUUCCUC-
..(((.((((((....((.(((((((((((((((.(((.(((....))).))).)))))))))(((...))))))))).))..))))))..))).- ( -45.10)
>DroSec_CAF1 12842 94 - 1
UAAGGCGCUGUUAUUAGCAUGCGGCCCACCUGCGUAGGCGCACCUGUGCCCCU-UGUAGGUGGAGCUUCGCUGCCGCAAGCCGGAUAGUUUCCUC-
...(((((((....)))).(((((((((((((((..(((((....)))))...-)))))))))(((...))))))))).)))(((.....)))..- ( -48.20)
>DroEre_CAF1 12053 95 - 1
UAAGGCGCUGUUAUUAGCAUGCGGCCCACCUGCGUAGGCGCACCUGUGCCCCU-UGUAGGUGGAGCUUCGCUGCCGCAAGCCGGAUAGUUUCCUUU
...(((((((....)))).(((((((((((((((..(((((....)))))...-)))))))))(((...))))))))).)))(((.....)))... ( -48.20)
>DroYak_CAF1 11921 94 - 1
UAAGGCGCUGUUAUUAGCAUGCGGCCCACCUGCGUAGGCGCACCUGUGCCCCU-UGUAGGUGGAGCUUCGCUGCCGCAAGUCGGAUAGUUUCCUU-
...(((((((....)))).(((((((((((((((..(((((....)))))...-)))))))))(((...))))))))).)))(((.....)))..- ( -45.50)
>consensus
UAAGGCGCUGUUAUUAGCAUGCGGCCCACCUGCGUAGGCGCACCUGUGCCCCU_UGUAGGUGGAGCUUCGCUGCCGCAAGCCGGAUAGUUUCCUC_
...(((((((....)))).(((((((((((((((.(((.(((....))).))).)))))))))(((...))))))))).)))(((.....)))... (-46.09 = -46.15 +   0.06)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:18 2006