Locus 2944

Sequence ID X_DroMel_CAF1
Location 7,888,331 – 7,888,470
Length 139
Max. P 0.944383
window4829 window4830 window4831 window4832

overview

Window 9

Location 7,888,331 – 7,888,430
Length 99
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.77
Mean single sequence MFE -42.18
Consensus MFE -27.97
Energy contribution -28.50
Covariance contribution 0.53
Combinations/Pair 1.14
Mean z-score -1.61
Structure conservation index 0.66
SVM decision value 0.77
SVM RNA-class probability 0.846016
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7888331 99 + 22224390
CUG------CAUCAAGAAAUUGUCCGUCAGCCC---------CGAUUUGCCCGUAGAACC------GGCGCUGAACUCCAGCGAGGCCAGCGACUGCUCUACGGGAUCAUCAAAUUGUGG
(((------(..(((....)))...).))).((---------(((((((((((((((..(------(((((((..(((....)))..))))).))).)))))))).....))))))).)) ( -37.60)
>DroPse_CAF1 1972 111 + 1
CUGCUGGGCCAUCAAAAAGUUAUCGGUUAGGCC---------CGACUUGCCCGUGGAGGCCGCCGCCGCGCUGAACUCCAGGGAGGCCAGCGACUGCUCAACGGGGUCGUCGAACUGCGG
((((.((((((((...........)))..))))---------)(((...(((((.(((((....))).(((((..(((....)))..))))).....)).)))))...))).....)))) ( -43.70)
>DroSec_CAF1 2219 100 + 1
CUG------CAUUAAGAAGUUGUCCGUUAACCC--------UCGAUUUGCCCGUAGAACC------GGCGCUGAACUCCAGUGAGGCCAGCGACUGCUCUACGGGAUCAUCAAAUUGUGG
...------.........((((.....))))((--------.(((((((((((((((..(------(((((((..(((....)))..))))).))).)))))))).....))))))).)) ( -35.80)
>DroEre_CAF1 2244 99 + 1
CUG------CAUCAAGAAGUUGUCCGUCAGCCC---------CGAUUUGCCCGUAGAGCC------UGCGCUGAACUCCAACGAGGCCAGCGAUUGCUCUACGGGAUCAUCAAAUUGUGG
...------.........((((.....))))((---------(((((((((((((((((.------..(((((..(((....)))..)))))...)))))))))).....))))))).)) ( -41.10)
>DroAna_CAF1 2107 114 + 1
CUG------CAUCAGAAAACUAUCCGUCAGCGAGGCGGCGGAAGACUUGCCCGUGGAGCCGGUGCCGGCGCUGAAUUCCAGCGAGGCCAGCGACUGCUCCACGGGAUCAUCAAACUGCGG
(((------((...........((((((.((...)))))))).((....((((((((((((.((((..(((((.....))))).)).)).))...))))))))))....))....))))) ( -51.20)
>DroPer_CAF1 7123 111 + 1
CUGCUGGGCCAUCAAAAAGUUAUCGGUUAGGCC---------CGACUUGCCCGUGGAGGCCGCCGCCGCGCUGAACUCCAGGGAGGCCAGCGACUGCUCAACGGGGUCGUCGAACUGCGG
((((.((((((((...........)))..))))---------)(((...(((((.(((((....))).(((((..(((....)))..))))).....)).)))))...))).....)))) ( -43.70)
>consensus
CUG______CAUCAAAAAGUUAUCCGUCAGCCC_________CGACUUGCCCGUAGAGCC______GGCGCUGAACUCCAGCGAGGCCAGCGACUGCUCUACGGGAUCAUCAAACUGCGG
...........................................(((...((((((((((.........(((((..(((....)))..)))))...))))))))))...)))......... (-27.97 = -28.50 +   0.53)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,888,331 – 7,888,430
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.77
Mean single sequence MFE -44.27
Consensus MFE -30.03
Energy contribution -30.00
Covariance contribution -0.03
Combinations/Pair 1.19
Mean z-score -1.98
Structure conservation index 0.68
SVM decision value 1.34
SVM RNA-class probability 0.944383
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7888331 99 - 22224390
CCACAAUUUGAUGAUCCCGUAGAGCAGUCGCUGGCCUCGCUGGAGUUCAGCGCC------GGUUCUACGGGCAAAUCG---------GGGCUGACGGACAAUUUCUUGAUG------CAG
......((((((...((((((((((.(.(((((..(((....)))..))))).)------.))))))))))...))))---------))((....(((.....)))....)------).. ( -38.10)
>DroPse_CAF1 1972 111 - 1
CCGCAGUUCGACGACCCCGUUGAGCAGUCGCUGGCCUCCCUGGAGUUCAGCGCGGCGGCGGCCUCCACGGGCAAGUCG---------GGCCUAACCGAUAACUUUUUGAUGGCCCAGCAG
((((.((((((((....)))))))).(.(((((..(((....)))..)))))).))))..((((....))))..((.(---------((((....(((.......)))..))))).)).. ( -49.20)
>DroSec_CAF1 2219 100 - 1
CCACAAUUUGAUGAUCCCGUAGAGCAGUCGCUGGCCUCACUGGAGUUCAGCGCC------GGUUCUACGGGCAAAUCGA--------GGGUUAACGGACAACUUCUUAAUG------CAG
.......(((((...((((((((((.(.(((((..(((....)))..))))).)------.))))))))))...)))))--------(.(((((.(((....)))))))).------).. ( -39.30)
>DroEre_CAF1 2244 99 - 1
CCACAAUUUGAUGAUCCCGUAGAGCAAUCGCUGGCCUCGUUGGAGUUCAGCGCA------GGCUCUACGGGCAAAUCG---------GGGCUGACGGACAACUUCUUGAUG------CAG
......((((((...((((((((((...(((((..(((....)))..)))))..------.))))))))))...))))---------))((....(((.....)))....)------).. ( -40.40)
>DroAna_CAF1 2107 114 - 1
CCGCAGUUUGAUGAUCCCGUGGAGCAGUCGCUGGCCUCGCUGGAAUUCAGCGCCGGCACCGGCUCCACGGGCAAGUCUUCCGCCGCCUCGCUGACGGAUAGUUUUCUGAUG------CAG
..(((....(((...((((((((((.(..((((((...((((.....))))))))))..).))))))))))...))).(((((.((...)).).))))...........))------).. ( -49.40)
>DroPer_CAF1 7123 111 - 1
CCGCAGUUCGACGACCCCGUUGAGCAGUCGCUGGCCUCCCUGGAGUUCAGCGCGGCGGCGGCCUCCACGGGCAAGUCG---------GGCCUAACCGAUAACUUUUUGAUGGCCCAGCAG
((((.((((((((....)))))))).(.(((((..(((....)))..)))))).))))..((((....))))..((.(---------((((....(((.......)))..))))).)).. ( -49.20)
>consensus
CCACAAUUUGAUGAUCCCGUAGAGCAGUCGCUGGCCUCGCUGGAGUUCAGCGCC______GGCUCCACGGGCAAAUCG_________GGGCUAACGGACAACUUCUUGAUG______CAG
.........(((...((((((((((...(((((..(((....)))..))))).........))))))))))...)))........................................... (-30.03 = -30.00 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,888,358 – 7,888,470
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.17
Mean single sequence MFE -44.62
Consensus MFE -32.36
Energy contribution -33.14
Covariance contribution 0.78
Combinations/Pair 1.15
Mean z-score -1.80
Structure conservation index 0.73
SVM decision value 0.60
SVM RNA-class probability 0.796290
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7888358 112 + 22224390
--CGAUUUGCCCGUAGAACC------GGCGCUGAACUCCAGCGAGGCCAGCGACUGCUCUACGGGAUCAUCAAAUUGUGGUAUCUGUUUGAGGCCUGAGGCCAGCGAGGCCAGUGAGGCA
--.(((...((((((((..(------(((((((..(((....)))..))))).))).))))))))))).((((((.(......).)))))).((((.(((((.....))))..).)))). ( -46.30)
>DroSec_CAF1 2246 105 + 1
-UCGAUUUGCCCGUAGAACC------GGCGCUGAACUCCAGUGAGGCCAGCGACUGCUCUACGGGAUCAUCAAAUUGUGGUAUCUGUUUGAGGCCCGAGGCCAGC--------CGAGGCA
-..(((...((((((((..(------(((((((..(((....)))..))))).))).))))))))...)))...(((.(((.((.....)).)))))).(((...--------...))). ( -41.70)
>DroEre_CAF1 2271 103 + 1
--CGAUUUGCCCGUAGAGCC------UGCGCUGAACUCCAACGAGGCCAGCGAUUGCUCUACGGGAUCAUCAAAUUGUGGUAUCUGUUUGAGGCCCGAGGCCAG---------UGAGGCA
--.(((...((((((((((.------..(((((..(((....)))..)))))...))))))))))...)))...(((.(((.((.....)).)))))).(((..---------...))). ( -46.10)
>DroYak_CAF1 2311 103 + 1
--CGAUUUGCCCGUAGAGCC------GGCGCUGAACUCCAACGAGGCAAGCGACUGCUCUACGGGAUCAUCAAAUUGUGGUAUCUGUUUGAGGCCCGAGGCCAG---------CGAGGCA
--.(((...((((((((((.------((((((...(((....)))...)))).))))))))))))...)))...(((.(((.((.....)).)))))).(((..---------...))). ( -42.90)
>DroAna_CAF1 2141 109 + 1
GAAGACUUGCCCGUGGAGCCGGUGCCGGCGCUGAAUUCCAGCGAGGCCAGCGACUGCUCCACGGGAUCAUCAAACUGCGGAAUCUGUUUCAGGCCGGCGGCCAG---------CGAAU--
((.((....((((((((((((.((((..(((((.....))))).)).)).))...)))))))))).)).))....(((((((....)))).((((...)))).)---------))...-- ( -47.10)
>DroPer_CAF1 7156 109 + 1
--CGACUUGCCCGUGGAGGCCGCCGCCGCGCUGAACUCCAGGGAGGCCAGCGACUGCUCAACGGGGUCGUCGAACUGCGGGAUUUGCUUCAGACCCGAUGACAG---------CGAGGCA
--...(((((((((.(((((....))).(((((..(((....)))..))))).....)).)))).(((((((..(((.((......)).)))...))))))).)---------))))... ( -43.60)
>consensus
__CGAUUUGCCCGUAGAGCC______GGCGCUGAACUCCAGCGAGGCCAGCGACUGCUCUACGGGAUCAUCAAAUUGUGGUAUCUGUUUGAGGCCCGAGGCCAG_________CGAGGCA
...(((...((((((((((.......(((((((..(((....)))..))))).))))))))))))...)))....................(((.....))).................. (-32.36 = -33.14 +   0.78)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,888,358 – 7,888,470
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.17
Mean single sequence MFE -44.05
Consensus MFE -33.72
Energy contribution -33.75
Covariance contribution 0.03
Combinations/Pair 1.16
Mean z-score -2.15
Structure conservation index 0.77
SVM decision value 0.97
SVM RNA-class probability 0.892737
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7888358 112 - 22224390
UGCCUCACUGGCCUCGCUGGCCUCAGGCCUCAAACAGAUACCACAAUUUGAUGAUCCCGUAGAGCAGUCGCUGGCCUCGCUGGAGUUCAGCGCC------GGUUCUACGGGCAAAUCG--
.((((....((((.....))))..)))).....................(((...((((((((((.(.(((((..(((....)))..))))).)------.))))))))))...))).-- ( -47.90)
>DroSec_CAF1 2246 105 - 1
UGCCUCG--------GCUGGCCUCGGGCCUCAAACAGAUACCACAAUUUGAUGAUCCCGUAGAGCAGUCGCUGGCCUCACUGGAGUUCAGCGCC------GGUUCUACGGGCAAAUCGA-
.((....--------)).((((...))))..................(((((...((((((((((.(.(((((..(((....)))..))))).)------.))))))))))...)))))- ( -42.80)
>DroEre_CAF1 2271 103 - 1
UGCCUCA---------CUGGCCUCGGGCCUCAAACAGAUACCACAAUUUGAUGAUCCCGUAGAGCAAUCGCUGGCCUCGUUGGAGUUCAGCGCA------GGCUCUACGGGCAAAUCG--
.(((...---------..)))....((..((.....))..)).......(((...((((((((((...(((((..(((....)))..)))))..------.))))))))))...))).-- ( -42.80)
>DroYak_CAF1 2311 103 - 1
UGCCUCG---------CUGGCCUCGGGCCUCAAACAGAUACCACAAUUUGAUGAUCCCGUAGAGCAGUCGCUUGCCUCGUUGGAGUUCAGCGCC------GGCUCUACGGGCAAAUCG--
.(((...---------..)))....((..((.....))..)).......(((...((((((((((.(.((((...(((....)))...)))).)------.))))))))))...))).-- ( -36.60)
>DroAna_CAF1 2141 109 - 1
--AUUCG---------CUGGCCGCCGGCCUGAAACAGAUUCCGCAGUUUGAUGAUCCCGUGGAGCAGUCGCUGGCCUCGCUGGAAUUCAGCGCCGGCACCGGCUCCACGGGCAAGUCUUC
--....(---------(.((((...)))).(((.....))).)).....(((...((((((((((.(..((((((...((((.....))))))))))..).))))))))))...)))... ( -47.20)
>DroPer_CAF1 7156 109 - 1
UGCCUCG---------CUGUCAUCGGGUCUGAAGCAAAUCCCGCAGUUCGACGACCCCGUUGAGCAGUCGCUGGCCUCCCUGGAGUUCAGCGCGGCGGCGGCCUCCACGGGCAAGUCG--
.....((---------(((((...(((..(......)..)))((.((((((((....))))))))....((((..(((....)))..)))))))))))))((((....))))......-- ( -47.00)
>consensus
UGCCUCG_________CUGGCCUCGGGCCUCAAACAGAUACCACAAUUUGAUGAUCCCGUAGAGCAGUCGCUGGCCUCGCUGGAGUUCAGCGCC______GGCUCUACGGGCAAAUCG__
..................(((.....)))....................(((...((((((((((...((((((.(((....))).)))))).........))))))))))...)))... (-33.72 = -33.75 +   0.03)

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 10:47:22 2006