Locus 3767

Sequence ID 2L_DroMel_CAF1
Location 10,979,894 – 10,980,090
Length 196
Max. P 0.974323
window5932 window5933 window5934 window5935

overview

Window 2

Location 10,979,894 – 10,980,010
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.55
Mean single sequence MFE -26.70
Consensus MFE -22.24
Energy contribution -22.64
Covariance contribution 0.40
Combinations/Pair 1.07
Mean z-score -2.06
Structure conservation index 0.83
SVM decision value 1.73
SVM RNA-class probability 0.974323
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10979894 116 + 22407834
UGGUCAUGCAAAGUGCAGAUUUAUUAUCUCAAAACACUGUAAACUAGUCACCUU----CUAACUUGCAAUUUUAAUGUAAUGUGUGUGCACAUUAUAUUUACAAUGCAUCUUGCAUUUUG
.....((((((..((((....................(((((..(((.......----)))..))))).....(((((((((((....))))))))))).....))))..)))))).... ( -26.80)
>DroSec_CAF1 8087 120 + 1
UGGUCAUGCAAAGUGCAGAUUAAUUAUCUCAAAACACUGUAAACUAGUCACCUUCUUUCUAACUUGCAAUUUGAAUGUAAUGUGUGUGCACAUUAUGUUUACGAUGCAUCUGGCAUUUUG
........((((((((((((....((((.........(((((..(((...........)))..)))))...(((((((((((((....))))))))))))).)))).)))).)))))))) ( -27.10)
>DroSim_CAF1 7359 120 + 1
UGGUCAUGCAAAGUGCAGAAUUAUUAUCUCAAAACACUGUAAACUAGUCACCUUCUUUCUAACUUGCACUUUGAAUGUAAUGUGUGUGCACAUUAUGUUUACGAUGCAUCUGGCAUUUUG
........(((((((((((................((((.....))))................((((.(.(((((((((((((....))))))))))))).).))))))).)))))))) ( -26.80)
>DroEre_CAF1 8077 119 + 1
-GGUCAUGCAAAGUGCAGAUUUAUUAUCUCAAAACACUGUAAACUAGUCAACUUCUUUCUACCUUGCAAUAUUUUUGUAAUGUGUGUGCACAUUAUGAUUACAAUGCAUUUUGCAUUUUG
-....((((((((((((....................(((((..(((...........)))..)))))......(..(((((((....)))))))..)......)))))))))))).... ( -28.00)
>DroYak_CAF1 7405 115 + 1
-GGUCAUGCAAAGUGCAGAUUUUUUAUCUCAAAACACUGUUAACUAUUCACCU----UCUACCUUGCAAUAUUUAUGUAAUGUGUGUGCACAUUAUGGUUAUAAUGCAGUUUGCAUUUUG
-.......((((((((((((.........((......))..............----.......((((.(((...(((((((((....)))))))))...))).)))))))))))))))) ( -24.80)
>consensus
UGGUCAUGCAAAGUGCAGAUUUAUUAUCUCAAAACACUGUAAACUAGUCACCUUCUUUCUAACUUGCAAUUUUAAUGUAAUGUGUGUGCACAUUAUGUUUACAAUGCAUCUUGCAUUUUG
........((((((((((((.....))))...................................((((.....(((((((((((....))))))))))).....))))....)))))))) (-22.24 = -22.64 +   0.40)

alignment

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secondary structure

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Window 3

Location 10,979,894 – 10,980,010
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.55
Mean single sequence MFE -26.26
Consensus MFE -20.68
Energy contribution -22.28
Covariance contribution 1.60
Combinations/Pair 1.06
Mean z-score -2.28
Structure conservation index 0.79
SVM decision value 1.54
SVM RNA-class probability 0.962781
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10979894 116 - 22407834
CAAAAUGCAAGAUGCAUUGUAAAUAUAAUGUGCACACACAUUACAUUAAAAUUGCAAGUUAG----AAGGUGACUAGUUUACAGUGUUUUGAGAUAAUAAAUCUGCACUUUGCAUGACCA
....(((((((.((((((((((((.(((((((....)))))))...................----.((....)).)))))))))......((((.....))))))).)))))))..... ( -27.80)
>DroSec_CAF1 8087 120 - 1
CAAAAUGCCAGAUGCAUCGUAAACAUAAUGUGCACACACAUUACAUUCAAAUUGCAAGUUAGAAAGAAGGUGACUAGUUUACAGUGUUUUGAGAUAAUUAAUCUGCACUUUGCAUGACCA
((((.(((((((.((((.((((((.(((((((....)))))))........................((....)).)))))).))))))))((((.....))))))).))))........ ( -25.20)
>DroSim_CAF1 7359 120 - 1
CAAAAUGCCAGAUGCAUCGUAAACAUAAUGUGCACACACAUUACAUUCAAAGUGCAAGUUAGAAAGAAGGUGACUAGUUUACAGUGUUUUGAGAUAAUAAUUCUGCACUUUGCAUGACCA
....((((.....))))........(((((((....)))))))(((.((((((((((((((......((....)).((((.(((....)))))))..))))).))))))))).))).... ( -27.00)
>DroEre_CAF1 8077 119 - 1
CAAAAUGCAAAAUGCAUUGUAAUCAUAAUGUGCACACACAUUACAAAAAUAUUGCAAGGUAGAAAGAAGUUGACUAGUUUACAGUGUUUUGAGAUAAUAAAUCUGCACUUUGCAUGACC-
....(((((((.((((((((.(((.(((((((....)))))))..(((((((((.(((.(((...........))).))).)))))))))..))).))))...)))).)))))))....- ( -29.00)
>DroYak_CAF1 7405 115 - 1
CAAAAUGCAAACUGCAUUAUAACCAUAAUGUGCACACACAUUACAUAAAUAUUGCAAGGUAGA----AGGUGAAUAGUUAACAGUGUUUUGAGAUAAAAAAUCUGCACUUUGCAUGACC-
....(((((((.(((..........(((((((....)))))))((.((((((((..((.((..----.......)).))..))))))))))((((.....))))))).)))))))....- ( -22.30)
>consensus
CAAAAUGCAAGAUGCAUUGUAAACAUAAUGUGCACACACAUUACAUUAAAAUUGCAAGUUAGAAAGAAGGUGACUAGUUUACAGUGUUUUGAGAUAAUAAAUCUGCACUUUGCAUGACCA
....(((((((.((((((((((((.(((((((....)))))))........................((....)).)))))))))......((((.....))))))).)))))))..... (-20.68 = -22.28 +   1.60)

alignment

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secondary structure

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Window 4

Location 10,979,934 – 10,980,050
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.06
Mean single sequence MFE -21.24
Consensus MFE -16.96
Energy contribution -17.16
Covariance contribution 0.20
Combinations/Pair 1.16
Mean z-score -1.58
Structure conservation index 0.80
SVM decision value 0.37
SVM RNA-class probability 0.709652
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10979934 116 + 22407834
AAACUAGUCACCUU----CUAACUUGCAAUUUUAAUGUAAUGUGUGUGCACAUUAUAUUUACAAUGCAUCUUGCAUUUUGCAUAAUACUUUAAUUCAUUUCAUACUCGCGAUUCGUGAUU
.....((((((..(----(.....((((.....(((((((((((....))))))))))).....))))...(((.....)))...........................))...)))))) ( -22.80)
>DroSec_CAF1 8127 120 + 1
AAACUAGUCACCUUCUUUCUAACUUGCAAUUUGAAUGUAAUGUGUGUGCACAUUAUGUUUACGAUGCAUCUGGCAUUUUGCAUAAUACUUUAAUUCAUUUCAUACUCGCGAUUCGUGAUU
.....((((((..((.........(((((..(((((((((((((....))))))))))))).(((((.....))))))))))(((....))).................))...)))))) ( -24.00)
>DroSim_CAF1 7399 120 + 1
AAACUAGUCACCUUCUUUCUAACUUGCACUUUGAAUGUAAUGUGUGUGCACAUUAUGUUUACGAUGCAUCUGGCAUUUUGCAUAAUACUUUAAUUCAUUUCAUACUCGCGAUUCGUGAUU
.....((((((..((.........((((.(.(((((((((((((....))))))))))))).).))))....((.....))............................))...)))))) ( -23.20)
>DroEre_CAF1 8116 120 + 1
AAACUAGUCAACUUCUUUCUACCUUGCAAUAUUUUUGUAAUGUGUGUGCACAUUAUGAUUACAAUGCAUUUUGCAUUUUGCAUUAUACUUAAAUUCAUUUCAUACACGCGAUUCAUGAUU
.....(((((.............((((((.....))))))((((((((......((((.......(.((..(((.....)))..)).)......))))....)))))))).....))))) ( -18.42)
>DroYak_CAF1 7444 116 + 1
UAACUAUUCACCU----UCUACCUUGCAAUAUUUAUGUAAUGUGUGUGCACAUUAUGGUUAUAAUGCAGUUUGCAUUUUGCAUAAUACUUAAAUUCAUUUCAUACUCGCGAUUCACGAUU
.............----......((((..(((...(((((((((....)))))))))...)))((((((........))))))........................))))......... ( -17.80)
>consensus
AAACUAGUCACCUUCUUUCUAACUUGCAAUUUUAAUGUAAUGUGUGUGCACAUUAUGUUUACAAUGCAUCUUGCAUUUUGCAUAAUACUUUAAUUCAUUUCAUACUCGCGAUUCGUGAUU
........................(((((.....((((((((((....))))))))))....(((((.....)))))))))).......................(((((...))))).. (-16.96 = -17.16 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,979,970 – 10,980,090
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.25
Mean single sequence MFE -21.41
Consensus MFE -18.42
Energy contribution -19.10
Covariance contribution 0.68
Combinations/Pair 1.04
Mean z-score -1.31
Structure conservation index 0.86
SVM decision value 0.28
SVM RNA-class probability 0.664664
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10979970 120 - 22407834
AACAGAAAGAUAGGAGGAUCCUAAACAAAAACUGCGGCUCAAUCACGAAUCGCGAGUAUGAAAUGAAUUAAAGUAUUAUGCAAAAUGCAAGAUGCAUUGUAAAUAUAAUGUGCACACACA
..........((((.....)))).((((..((((((..((......))..))).)))...............(((((.(((.....))).))))).))))........((((....)))) ( -23.20)
>DroSec_CAF1 8167 120 - 1
AACAGAAAGAUAGGAGGAUCCUAAAGAAAAACUGCGGCUCAAUCACGAAUCGCGAGUAUGAAAUGAAUUAAAGUAUUAUGCAAAAUGCCAGAUGCAUCGUAAACAUAAUGUGCACACACA
.((.......((((.....))))..((...((((((..((......))..))).)))...............(((((..((.....))..))))).))))........((((....)))) ( -18.80)
>DroSim_CAF1 7439 120 - 1
AACAGAAAGAUAGGAGGAUCCUAAACAAAAACUGCGGCUCAAUCACGAAUCGCGAGUAUGAAAUGAAUUAAAGUAUUAUGCAAAAUGCCAGAUGCAUCGUAAACAUAAUGUGCACACACA
..........((((.....)))).((....((((((..((......))..))).)))...............(((((..((.....))..)))))...))........((((....)))) ( -18.50)
>DroEre_CAF1 8156 120 - 1
AACAGAAAGAUAGGAGGAUCCUAAACAAAAACUGCGGCUCAAUCAUGAAUCGCGUGUAUGAAAUGAAUUUAAGUAUAAUGCAAAAUGCAAAAUGCAUUGUAAUCAUAAUGUGCACACACA
..........((((.....))))..........(((..(((....)))..)))(((((((..((((.......(((((((((..........))))))))).))))..)))))))..... ( -26.50)
>DroYak_CAF1 7480 120 - 1
AACAGAAAGAUAGGAGGAUCCUAAACAAAAACUGCGGAUCAAUCGUGAAUCGCGAGUAUGAAAUGAAUUUAAGUAUUAUGCAAAAUGCAAACUGCAUUAUAACCAUAAUGUGCACACACA
............((..(((((..............)))))..(((((...)))))((((((.((........)).))))))..(((((.....)))))....))....((((....)))) ( -20.04)
>consensus
AACAGAAAGAUAGGAGGAUCCUAAACAAAAACUGCGGCUCAAUCACGAAUCGCGAGUAUGAAAUGAAUUAAAGUAUUAUGCAAAAUGCAAGAUGCAUUGUAAACAUAAUGUGCACACACA
..........((((.....)))).......((((((..((......))..)))).))...............(((((.(((.....))).))))).............((((....)))) (-18.42 = -19.10 +   0.68)

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 11:00:37 2006