Locus 77

Sequence ID 2R_DroMel_CAF1
Location 1,330,414 – 1,330,567
Length 153
Max. P 0.902480
window153 window154 window155 window156

overview

Window 3

Location 1,330,414 – 1,330,534
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.53
Mean single sequence MFE -40.20
Consensus MFE -30.57
Energy contribution -32.81
Covariance contribution 2.25
Combinations/Pair 1.14
Mean z-score -2.16
Structure conservation index 0.76
SVM decision value 1.02
SVM RNA-class probability 0.902480
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1330414 120 + 20766785
GAAUGCAAAUGGGGGCUCGAGCCCGGCAUGCGUUAUCCAUCGCCGUGCAAUUGAAUUAUUGCAUGCCGCGGCUAAUUCCGCAUGUUUGCUCGUCCUGUAAUUAGCCGAGCGCGCAUUAAU
.(((((......((((....))))((((((((..((...((((((((((((......))))))))..))))...))..)))))))).(((((..(((....))).)))))..)))))... ( -45.60)
>DroSec_CAF1 48939 120 + 1
GAAUGCAAAUGGGCGACCGAGCCCGGCAUGCGUUAUCCAUCGCCGUGCAAUUGAAUUAUUGCAUGCCGCGACUAAUUCCGCAUGUUUGCUCGUCCUGUAAUUAGCCGAGCGCACAUUAAU
...(((....((((......))))((((((((..((...((((((((((((......))))))))..))))...))..)))))))).(((((..(((....))).))))))))....... ( -44.90)
>DroEre_CAF1 29942 119 + 1
GAAUGCAAAUGUGAGCCCGGGUCCGGCGUGCGUU-UCCAUCGCCGUGCAAUUGAAUUAUUGCAUGCCGCGACUAAUUCCGCAUGCUUGCUCGUCCUGUAAUUAGCCGAGCGCACAUUAAU
.......((((((.((.(((....((((((((..-....((((((((((((......))))))))..)))).......))))))))(((.......))).....))).)).))))))... ( -40.12)
>DroYak_CAF1 15918 101 + 1
GAAUGCAAAUGUGGGCCCGAGUCCGGCAUGCGUUAUCCAUCGCAGUGCAAUUGAAUUAUUGCA-------------------UGCUUGCUCGUCCUGUAAUUAGCCGAGCGCACAUUAAU
.......((((((.((.(((((..(((.((((........))))(((((((......))))))-------------------)))).)))))..(((....)))....)).))))))... ( -30.20)
>consensus
GAAUGCAAAUGGGGGCCCGAGCCCGGCAUGCGUUAUCCAUCGCCGUGCAAUUGAAUUAUUGCAUGCCGCGACUAAUUCCGCAUGCUUGCUCGUCCUGUAAUUAGCCGAGCGCACAUUAAU
...(((......((((....))))((((((((.......((((((((((((......))))))))..)))).......)))))))).(((((..(((....))).))))))))....... (-30.57 = -32.81 +   2.25) 

alignment

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secondary structure

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dotplot

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Window 4

Location 1,330,414 – 1,330,534
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.53
Mean single sequence MFE -39.62
Consensus MFE -27.21
Energy contribution -30.03
Covariance contribution 2.81
Combinations/Pair 1.08
Mean z-score -2.16
Structure conservation index 0.69
SVM decision value 0.67
SVM RNA-class probability 0.817301
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1330414 120 - 20766785
AUUAAUGCGCGCUCGGCUAAUUACAGGACGAGCAAACAUGCGGAAUUAGCCGCGGCAUGCAAUAAUUCAAUUGCACGGCGAUGGAUAACGCAUGCCGGGCUCGAGCCCCCAUUUGCAUUC
...(((((..(((((.((.......)).)))))......((((......))))(((((((....(((((.((((...)))))))))...)))))))((((....))))......))))). ( -43.80)
>DroSec_CAF1 48939 120 - 1
AUUAAUGUGCGCUCGGCUAAUUACAGGACGAGCAAACAUGCGGAAUUAGUCGCGGCAUGCAAUAAUUCAAUUGCACGGCGAUGGAUAACGCAUGCCGGGCUCGGUCGCCCAUUUGCAUUC
......(((((((((.((.......)).)))))...((((((..(((.(((((.(..((((((......))))))).))))).)))..))))))..((((......))))....)))).. ( -45.00)
>DroEre_CAF1 29942 119 - 1
AUUAAUGUGCGCUCGGCUAAUUACAGGACGAGCAAGCAUGCGGAAUUAGUCGCGGCAUGCAAUAAUUCAAUUGCACGGCGAUGGA-AACGCACGCCGGACCCGGGCUCACAUUUGCAUUC
...((((((.((((((...................((.(((((......))))))).((((((......))))))(((((.((..-..))..)))))...)))))).))))))....... ( -40.40)
>DroYak_CAF1 15918 101 - 1
AUUAAUGUGCGCUCGGCUAAUUACAGGACGAGCAAGCA-------------------UGCAAUAAUUCAAUUGCACUGCGAUGGAUAACGCAUGCCGGACUCGGGCCCACAUUUGCAUUC
...((((((.((((((((..((....))..)))..(((-------------------(((....(((((.((((...)))))))))...))))))......))))).))))))....... ( -29.30)
>consensus
AUUAAUGUGCGCUCGGCUAAUUACAGGACGAGCAAACAUGCGGAAUUAGUCGCGGCAUGCAAUAAUUCAAUUGCACGGCGAUGGAUAACGCAUGCCGGACUCGGGCCCACAUUUGCAUUC
...((((((.((((((((..((....))..)))...............(((.((((((((....(((((.((((...)))))))))...))))))))))).))))).))))))....... (-27.21 = -30.03 +   2.81) 

alignment

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secondary structure

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dotplot

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Window 5

Location 1,330,454 – 1,330,567
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.27
Mean single sequence MFE -36.23
Consensus MFE -29.25
Energy contribution -29.50
Covariance contribution 0.25
Combinations/Pair 1.06
Mean z-score -1.48
Structure conservation index 0.81
SVM decision value 0.11
SVM RNA-class probability 0.589732
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1330454 113 + 20766785
CGCCGUGCAAUUGAAUUAUUGCAUGCCGCGGCUAAUUCCGCAUGUUUGCUCGUCCUGUAAUUAGCCGAGCGCGCAUUAAUUG-------AAGUGCCUGCGACUGUCAUGGGCAGUCCGAC
.((.(.(((.((.(((((.(((.(((..((((((((((.(.(((......))).).).))))))))).))).))).))))).-------)).)))).))((((((.....)))))).... ( -40.10)
>DroSec_CAF1 48979 113 + 1
CGCCGUGCAAUUGAAUUAUUGCAUGCCGCGACUAAUUCCGCAUGUUUGCUCGUCCUGUAAUUAGCCGAGCGCACAUUAAUUG-------AAGUGCCCGCGACUGUCAUGGGCAGUCCGAC
.(.((((((((......)))))))).)(((........)))......(((((..(((....))).)))))((((.((....)-------).)))).((.((((((.....)))))))).. ( -36.40)
>DroEre_CAF1 29981 120 + 1
CGCCGUGCAAUUGAAUUAUUGCAUGCCGCGACUAAUUCCGCAUGCUUGCUCGUCCUGUAAUUAGCCGAGCGCACAUUAAUUGCGCCUGAAAGUGCCUGCGACUGUCAUGGGCAGUCCGAC
(((((((((((......))))))))..))).........(((.((..(((((..(((....))).)))))((.((.....)).))........)).)))((((((.....)))))).... ( -38.00)
>DroYak_CAF1 15958 94 + 1
CGCAGUGCAAUUGAAUUAUUGCA-------------------UGCUUGCUCGUCCUGUAAUUAGCCGAGCGCACAUUAAUUG-------AAGUGCCUACGACUGUCAUGGGCAGUCCGAC
.(((.((((((......))))))-------------------)))..(((((..(((....))).)))))((((.((....)-------).))))....((((((.....)))))).... ( -30.40)
>consensus
CGCCGUGCAAUUGAAUUAUUGCAUGCCGCGACUAAUUCCGCAUGCUUGCUCGUCCUGUAAUUAGCCGAGCGCACAUUAAUUG_______AAGUGCCUGCGACUGUCAUGGGCAGUCCGAC
.((((((((((......))))))))..(((........)))..))..(((((..(((....))).)))))((((.................))))....((((((.....)))))).... (-29.25 = -29.50 +   0.25) 

alignment

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secondary structure

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dotplot

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Window 6

Location 1,330,454 – 1,330,567
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.27
Mean single sequence MFE -36.73
Consensus MFE -28.66
Energy contribution -29.53
Covariance contribution 0.87
Combinations/Pair 1.06
Mean z-score -1.65
Structure conservation index 0.78
SVM decision value 0.36
SVM RNA-class probability 0.702393
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1330454 113 - 20766785
GUCGGACUGCCCAUGACAGUCGCAGGCACUU-------CAAUUAAUGCGCGCUCGGCUAAUUACAGGACGAGCAAACAUGCGGAAUUAGCCGCGGCAUGCAAUAAUUCAAUUGCACGGCG
(((((((((.......)))))....(((.((-------.(((((.((((.((((((((((((.........(((....)))..))))))))).))).)))).))))).)).))).)))). ( -38.70)
>DroSec_CAF1 48979 113 - 1
GUCGGACUGCCCAUGACAGUCGCGGGCACUU-------CAAUUAAUGUGCGCUCGGCUAAUUACAGGACGAGCAAACAUGCGGAAUUAGUCGCGGCAUGCAAUAAUUCAAUUGCACGGCG
((((...((((..((((..(((((.((((..-------........))))(((((.((.......)).))))).....))))).....)))).))))((((((......)))))))))). ( -37.20)
>DroEre_CAF1 29981 120 - 1
GUCGGACUGCCCAUGACAGUCGCAGGCACUUUCAGGCGCAAUUAAUGUGCGCUCGGCUAAUUACAGGACGAGCAAGCAUGCGGAAUUAGUCGCGGCAUGCAAUAAUUCAAUUGCACGGCG
((((...((((..((((..(((((.((........(((((.....)))))(((((.((.......)).)))))..)).))))).....)))).))))((((((......)))))))))). ( -42.40)
>DroYak_CAF1 15958 94 - 1
GUCGGACUGCCCAUGACAGUCGUAGGCACUU-------CAAUUAAUGUGCGCUCGGCUAAUUACAGGACGAGCAAGCA-------------------UGCAAUAAUUCAAUUGCACUGCG
....(((((.......)))))....((((..-------........))))(((((.((.......)).)))))..(((-------------------((((((......)))))).))). ( -28.60)
>consensus
GUCGGACUGCCCAUGACAGUCGCAGGCACUU_______CAAUUAAUGUGCGCUCGGCUAAUUACAGGACGAGCAAACAUGCGGAAUUAGUCGCGGCAUGCAAUAAUUCAAUUGCACGGCG
(((((((((.......)))))((((((((.................))))(((((.((.......)).)))))..((((((.(.........).))))))..........)))).)))). (-28.66 = -29.53 +   0.87) 

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 09:26:00 2006