Locus 179

Sequence ID 4_DroMel_CAF1
Location 1,103,179 – 1,103,379
Length 200
Max. P 0.999385
window285 window286 window287 window288 window289

overview

Window 5

Location 1,103,179 – 1,103,299
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.00
Mean single sequence MFE -39.66
Consensus MFE -32.02
Energy contribution -32.14
Covariance contribution 0.12
Combinations/Pair 1.18
Mean z-score -2.20
Structure conservation index 0.81
SVM decision value 1.72
SVM RNA-class probability 0.973786
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1103179 120 + 1281640
CGCAUUGCAGCGGGUUGUGGAAAUGACUUCCGGGAGCCAAGGCUGUUGCAGCAGUUUAAGUUAAAGCAGCAACAGCACUUUACAACCACAACGCAGCAUCCUUGGCGACAGCAGAUGCAU
.(((((((..(((((..(....)..))..)))(..(((((((.((((((....((((......)))).((....))................)))))).)))))))..).))).)))).. ( -42.60)
>DroSec_CAF1 16940 120 + 1
CGCAUUGCAGCGGAUUGUGGAAACGACUUCCGGGAGCCAAGGCUGUUGCAGCAGUUUAAGUUAAAGCAGCAACAGCACUUUACAACCACAACGCAGCAUCCCUGGCGACAGCAGAUGCAU
.((.(((....(((...((....))...)))((..(..(((((((((((.((.............)).)))))))).)))..)..)).))).)).(((((.(((....)))..))))).. ( -41.52)
>DroSim_CAF1 7573 120 + 1
CGCAUUGCAGCAGAUUGUGGAAACGACUUCCGGGAGCCAAGGUUGUUGCAGCAGUUUAAGUUAAAGCAGCAACAGCACUUUACAACCACAACGCAGCAUCCCUGGCGACAGCAGAUGCAU
.(((((((......((.(((((.....))))).))((((.((.((((((....((((......)))).((....))................)))))).)).))))....))).)))).. ( -35.90)
>DroEre_CAF1 16494 120 + 1
CGCAUUACAGCAGGCUGUGAAAAUAACUUCCGUGAGCCAAGGCUGUUGCAGCAGUUAAAGCUAUAGCAGCAGCAGCACUUUACAACCACAACGCAGCAGCCCUGGCGACAGCAGAUGCAU
.........(((.((((((((......))).....((((.((((((((((((.......)))...((....))...................))))))))).)))).)))))...))).. ( -40.50)
>DroYak_CAF1 8476 120 + 1
CGCAUUACAGCAGGCUGUGGAAAUGACUUUCGGGAUCCCAGGCUGUUGCAACAGUUUAAGCUAUAGCAGCAGCAGCACUUUACAACCACAACGCAGCAUCCCUGGCGACAGCAAAUGCAU
.(((((.(((...((((((((((....))))((....))..((((((((...(((....)))...))))))))..................))))))....)))((....)).))))).. ( -37.80)
>consensus
CGCAUUGCAGCAGGUUGUGGAAAUGACUUCCGGGAGCCAAGGCUGUUGCAGCAGUUUAAGUUAAAGCAGCAACAGCACUUUACAACCACAACGCAGCAUCCCUGGCGACAGCAGAUGCAU
.(((((.(((...(((((((((.....))))((.....(((((((((((.((.............)).)))))))).))).....)).....)))))....)))((....)).))))).. (-32.02 = -32.14 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,103,179 – 1,103,299
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.00
Mean single sequence MFE -42.45
Consensus MFE -35.96
Energy contribution -36.20
Covariance contribution 0.24
Combinations/Pair 1.15
Mean z-score -1.95
Structure conservation index 0.85
SVM decision value 1.84
SVM RNA-class probability 0.979648
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1103179 120 - 1281640
AUGCAUCUGCUGUCGCCAAGGAUGCUGCGUUGUGGUUGUAAAGUGCUGUUGCUGCUUUAACUUAAACUGCUGCAACAGCCUUGGCUCCCGGAAGUCAUUUCCACAACCCGCUGCAAUGCG
..((((((((....))...)))))).(((((((((((((.(((.((((((((.((.............)).))))))))))).......(((((...)))))))))))....))))))). ( -44.12)
>DroSec_CAF1 16940 120 - 1
AUGCAUCUGCUGUCGCCAGGGAUGCUGCGUUGUGGUUGUAAAGUGCUGUUGCUGCUUUAACUUAAACUGCUGCAACAGCCUUGGCUCCCGGAAGUCGUUUCCACAAUCCGCUGCAAUGCG
..((((((.(((....))))))))).((((((..((.((.(((.((((((((.((.............)).))))))))))).))....(((((...))))).......))..)))))). ( -44.62)
>DroSim_CAF1 7573 120 - 1
AUGCAUCUGCUGUCGCCAGGGAUGCUGCGUUGUGGUUGUAAAGUGCUGUUGCUGCUUUAACUUAAACUGCUGCAACAACCUUGGCUCCCGGAAGUCGUUUCCACAAUCUGCUGCAAUGCG
..((((.(((.((.(((((((.((.((((..(..(((.((((((((....)).)))))).....)))..))))).)).)))))))....(((((...))))).......)).))))))). ( -40.40)
>DroEre_CAF1 16494 120 - 1
AUGCAUCUGCUGUCGCCAGGGCUGCUGCGUUGUGGUUGUAAAGUGCUGCUGCUGCUAUAGCUUUAACUGCUGCAACAGCCUUGGCUCACGGAAGUUAUUUUCACAGCCUGCUGUAAUGCG
.((((.(.(((((.((((((((((.((((..(..((..((((((...((....))....))))))))..))))).))))))))))..((....)).......)))))..).))))..... ( -45.70)
>DroYak_CAF1 8476 120 - 1
AUGCAUUUGCUGUCGCCAGGGAUGCUGCGUUGUGGUUGUAAAGUGCUGCUGCUGCUAUAGCUUAAACUGUUGCAACAGCCUGGGAUCCCGAAAGUCAUUUCCACAGCCUGCUGUAAUGCG
..((((((.(((....))))))))).((((((..((.....((.(((((((.(((.((((......)))).))).)))).(((((...(....)....))))).)))))))..)))))). ( -37.40)
>consensus
AUGCAUCUGCUGUCGCCAGGGAUGCUGCGUUGUGGUUGUAAAGUGCUGUUGCUGCUUUAACUUAAACUGCUGCAACAGCCUUGGCUCCCGGAAGUCAUUUCCACAACCUGCUGCAAUGCG
..((((((.(((....))))))))).(((((((((((((.(((.((((((((.((.............)).))))))))))).......(((((...)))))))))))....))))))). (-35.96 = -36.20 +   0.24)

alignment

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secondary structure

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Window 7

Location 1,103,219 – 1,103,339
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.17
Mean single sequence MFE -34.51
Consensus MFE -29.36
Energy contribution -29.48
Covariance contribution 0.12
Combinations/Pair 1.16
Mean z-score -1.64
Structure conservation index 0.85
SVM decision value 1.11
SVM RNA-class probability 0.917186
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1103219 120 + 1281640
GGCUGUUGCAGCAGUUUAAGUUAAAGCAGCAACAGCACUUUACAACCACAACGCAGCAUCCUUGGCGACAGCAGAUGCAUUGACAAUUAAAGAAACACCUGCUGCCUUUGAAUGGCGCCC
.((((((((.((.............)).))))))))...............(((.(((((.(((....)))..))))).....((.((((((.............)))))).)))))... ( -30.74)
>DroSec_CAF1 16980 120 + 1
GGCUGUUGCAGCAGUUUAAGUUAAAGCAGCAACAGCACUUUACAACCACAACGCAGCAUCCCUGGCGACAGCAGAUGCAUUGACAAUUAAAGAAGCAUCUGCUGCCUUUGAAUGACGCCU
.((((((((.((.............)).))))))))................((.(((((.(((....)))..))))).....((.((((((.(((....)))..)))))).))..)).. ( -36.52)
>DroSim_CAF1 7613 120 + 1
GGUUGUUGCAGCAGUUUAAGUUAAAGCAGCAACAGCACUUUACAACCACAACGCAGCAUCCCUGGCGACAGCAGAUGCAUUGACAAUUAAAGAAGCAUCUGCUGCCUUUGAAUGACGCCU
((.((((((....((((......)))).((....))................)))))).))..((((.((((((((((.((..........)).)))))))))).(.......).)))). ( -34.40)
>DroEre_CAF1 16534 120 + 1
GGCUGUUGCAGCAGUUAAAGCUAUAGCAGCAGCAGCACUUUACAACCACAACGCAGCAGCCCUGGCGACAGCAGAUGCAUUGGCAAUUAAAGAAGCACCUGUUGUUUUUGAAUGGCGCCU
((((((((((((.......)))...((....))...................)))))))))..(((((((((((.(((.((..........)).))).)))))))..........)))). ( -35.90)
>DroYak_CAF1 8516 120 + 1
GGCUGUUGCAACAGUUUAAGCUAUAGCAGCAGCAGCACUUUACAACCACAACGCAGCAUCCCUGGCGACAGCAAAUGCAUUGGCAAUUAAAGAAGCACUUGUAGCCUUUGAUUGGCGCCU
.((((((((...(((....)))...))))))))...................((.((((..(((....)))...))))...(.(((((((((..((.......))))))))))).))).. ( -35.00)
>consensus
GGCUGUUGCAGCAGUUUAAGUUAAAGCAGCAACAGCACUUUACAACCACAACGCAGCAUCCCUGGCGACAGCAGAUGCAUUGACAAUUAAAGAAGCACCUGCUGCCUUUGAAUGGCGCCU
.((((((((.((.............)).))))))))................((.(((((.(((....)))..)))))...(.((.((((((.(((....)))..)))))).)).))).. (-29.36 = -29.48 +   0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,103,219 – 1,103,339
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.17
Mean single sequence MFE -41.52
Consensus MFE -37.29
Energy contribution -36.97
Covariance contribution -0.32
Combinations/Pair 1.21
Mean z-score -2.37
Structure conservation index 0.90
SVM decision value 3.56
SVM RNA-class probability 0.999385
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1103219 120 - 1281640
GGGCGCCAUUCAAAGGCAGCAGGUGUUUCUUUAAUUGUCAAUGCAUCUGCUGUCGCCAAGGAUGCUGCGUUGUGGUUGUAAAGUGCUGUUGCUGCUUUAACUUAAACUGCUGCAACAGCC
.((((((((((...((((((((((((................)))))))))))).....)))))..))))).............((((((((.((.............)).)))))))). ( -42.71)
>DroSec_CAF1 16980 120 - 1
AGGCGUCAUUCAAAGGCAGCAGAUGCUUCUUUAAUUGUCAAUGCAUCUGCUGUCGCCAGGGAUGCUGCGUUGUGGUUGUAAAGUGCUGUUGCUGCUUUAACUUAAACUGCUGCAACAGCC
..(((.(((((...((((((((((((................)))))))))))).....))))).)))................((((((((.((.............)).)))))))). ( -45.31)
>DroSim_CAF1 7613 120 - 1
AGGCGUCAUUCAAAGGCAGCAGAUGCUUCUUUAAUUGUCAAUGCAUCUGCUGUCGCCAGGGAUGCUGCGUUGUGGUUGUAAAGUGCUGUUGCUGCUUUAACUUAAACUGCUGCAACAACC
..(((.(((((...((((((((((((................)))))))))))).....))))).)))((((..((..((((((((....)).)))))).........))..)))).... ( -44.09)
>DroEre_CAF1 16534 120 - 1
AGGCGCCAUUCAAAAACAACAGGUGCUUCUUUAAUUGCCAAUGCAUCUGCUGUCGCCAGGGCUGCUGCGUUGUGGUUGUAAAGUGCUGCUGCUGCUAUAGCUUUAACUGCUGCAACAGCC
.(((((....(((..(((((((((((................))))))((.((.((....)).)).)))))))..)))....)))))((((.(((..(((......)))..))).)))). ( -39.09)
>DroYak_CAF1 8516 120 - 1
AGGCGCCAAUCAAAGGCUACAAGUGCUUCUUUAAUUGCCAAUGCAUUUGCUGUCGCCAGGGAUGCUGCGUUGUGGUUGUAAAGUGCUGCUGCUGCUAUAGCUUAAACUGUUGCAACAGCC
....(((.......)))....((..(((...((((..(.((((((.((.(((....))).))...)))))))..))))..)))..))((((.(((.((((......)))).))).)))). ( -36.40)
>consensus
AGGCGCCAUUCAAAGGCAGCAGGUGCUUCUUUAAUUGUCAAUGCAUCUGCUGUCGCCAGGGAUGCUGCGUUGUGGUUGUAAAGUGCUGUUGCUGCUUUAACUUAAACUGCUGCAACAGCC
..(((.(((((...((((((((((((................)))))))))))).....))))).)))((((..(..((.((((...((....))....))))..))..)..)))).... (-37.29 = -36.97 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,103,259 – 1,103,379
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.16
Mean single sequence MFE -38.64
Consensus MFE -35.75
Energy contribution -35.95
Covariance contribution 0.20
Combinations/Pair 1.19
Mean z-score -1.99
Structure conservation index 0.93
SVM decision value 3.01
SVM RNA-class probability 0.998099
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1103259 120 - 1281640
AAGAUGCGAUUUGCCUUCGAUUCUAAUCAUUCGCAAUCGGGGGCGCCAUUCAAAGGCAGCAGGUGUUUCUUUAAUUGUCAAUGCAUCUGCUGUCGCCAAGGAUGCUGCGUUGUGGUUGUA
..((((((....(((((((((((.........).))))))))))((.((((...((((((((((((................)))))))))))).....))))))))))))......... ( -40.09)
>DroSec_CAF1 17020 120 - 1
AAGAUGCGAUUUGCCUUCGAUUCUAAUCAUUCGCAAUCGGAGGCGUCAUUCAAAGGCAGCAGAUGCUUCUUUAAUUGUCAAUGCAUCUGCUGUCGCCAGGGAUGCUGCGUUGUGGUUGUA
..((((((....(((((((((((.........).))))))))))(.(((((...((((((((((((................)))))))))))).....))))))))))))......... ( -44.69)
>DroSim_CAF1 7653 120 - 1
AAGAUGCGAUUUGCCUUCGAUUCUAAUCAUUCGCAAUCGGAGGCGUCAUUCAAAGGCAGCAGAUGCUUCUUUAAUUGUCAAUGCAUCUGCUGUCGCCAGGGAUGCUGCGUUGUGGUUGUA
..((((((....(((((((((((.........).))))))))))(.(((((...((((((((((((................)))))))))))).....))))))))))))......... ( -44.69)
>DroEre_CAF1 16574 119 - 1
-AUAUGCGAUUUGCCUUUGAUUCUAAUCAUUCGCAACCGGAGGCGCCAUUCAAAAACAACAGGUGCUUCUUUAAUUGCCAAUGCAUCUGCUGUCGCCAGGGCUGCUGCGUUGUGGUUGUA
-................((((....))))...(((((((((((((((..............)))))))))........(((((((...((.(((.....))).))))))))).)))))). ( -33.04)
>DroYak_CAF1 8556 119 - 1
-AUAUGCGAUUUGCCUUUGAUUCUAAUUAUUCGCAAUCCGAGGCGCCAAUCAAAGGCUACAAGUGCUUCUUUAAUUGCCAAUGCAUUUGCUGUCGCCAGGGAUGCUGCGUUGUGGUUGUA
-....(((....((((((((((.......((((.....)))).....))))))))))......))).....((((..(.((((((.((.(((....))).))...)))))))..)))).. ( -30.70)
>consensus
AAGAUGCGAUUUGCCUUCGAUUCUAAUCAUUCGCAAUCGGAGGCGCCAUUCAAAGGCAGCAGGUGCUUCUUUAAUUGUCAAUGCAUCUGCUGUCGCCAGGGAUGCUGCGUUGUGGUUGUA
....(((((((.(((((((((((.........).))))))))))(((((((...((((((((((((................)))))))))))).....)))))..)).....))))))) (-35.75 = -35.95 +   0.20)

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 09:38:23 2006