Locus 4633

Sequence ID 3R_DroMel_CAF1
Location 12,184,992 – 12,185,114
Length 122
Max. P 0.982825
window7615 window7616 window7617 window7618

overview

Window 5

Location 12,184,992 – 12,185,090
Length 98
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 92.97
Mean single sequence MFE -28.52
Consensus MFE -24.12
Energy contribution -23.88
Covariance contribution -0.24
Combinations/Pair 1.04
Mean z-score -1.71
Structure conservation index 0.85
SVM decision value 1.26
SVM RNA-class probability 0.936884
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12184992 98 + 27905053
GUUGAUUU-G-UUUUUAUUGAACGAUGUGUCAAAAGUUG-GAAGACACUAACGCGUUAGAUGCGCACAGGC-ACUAACGCGUGGUAAUCGAUGGGCAGCACU
.......(-(-((((((((((.....(((((........-...)))))..(((((((((.(((......))-)))))))))).....)))))))).)))).. ( -29.60)
>DroSec_CAF1 9530 98 + 1
GUUGAUUU-G-UUUUUAUUGAACGAUGUGUCAAAAGUUG-AAUGACACUAACGCGUUAGAUGCGCAAAGGC-ACUAACGCGUGGUAAUCGAUGGGCAGCACU
.......(-(-((((((((((.....((((((.......-..))))))..(((((((((.(((......))-)))))))))).....)))))))).)))).. ( -30.70)
>DroSim_CAF1 10247 101 + 1
GUUGAUUUUGUUUUUUAUUGAACGAUGUGUCAAACGUUGGAAUGACACUAACGCGUUAGAUGCGCACAGGCAACUAACGCGUGGUAAUCGAUGGGCAGC-CU
.........(((.((((((((.((((((.....)))))).......((((.((((((((.(((......))).))))))))))))..)))))))).)))-.. ( -31.20)
>DroEre_CAF1 8975 98 + 1
GUUGAUUU-G-UUUUUAUUGAACGAUGUGUCAAAUGUUG-AAAGGCACUAACGCGUUAGAUACGCAAAAGC-ACUAACGCGUGGUAAUCGAUGGGCAGCACU
......((-(-(((.....)))))).((((....(((((-(...((....(((((((((....((....))-.))))))))).))..))))))....)))). ( -25.20)
>DroYak_CAF1 9537 98 + 1
GUUGAUUU-G-UUUUUAUUGAGCGAUGUGUCAAAAGUUG-AAAGGCACUAACGCGUUAGAUACGCAAACGC-ACUAACGCGUGUUAAUCGAUGGGCAGCACU
.......(-(-((((((((((..((((((((........-...)))))..(((((((((....((....))-.))))))))))))..)))))))).)))).. ( -25.90)
>consensus
GUUGAUUU_G_UUUUUAUUGAACGAUGUGUCAAAAGUUG_AAAGACACUAACGCGUUAGAUGCGCAAAGGC_ACUAACGCGUGGUAAUCGAUGGGCAGCACU
((((.........((((((((.....(((((............)))))..(((((((((....((....))..))))))))).....))))))))))))... (-24.12 = -23.88 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,184,992 – 12,185,090
Length 98
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 92.97
Mean single sequence MFE -23.89
Consensus MFE -19.48
Energy contribution -19.88
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.27
Structure conservation index 0.82
SVM decision value 1.93
SVM RNA-class probability 0.982825
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12184992 98 - 27905053
AGUGCUGCCCAUCGAUUACCACGCGUUAGU-GCCUGUGCGCAUCUAACGCGUUAGUGUCUUC-CAACUUUUGACACAUCGUUCAAUAAAAA-C-AAAUCAAC
.((.........((((....((((((((((-((......))).)))))))))..(((((...-........)))))))))..........)-)-........ ( -25.11)
>DroSec_CAF1 9530 98 - 1
AGUGCUGCCCAUCGAUUACCACGCGUUAGU-GCCUUUGCGCAUCUAACGCGUUAGUGUCAUU-CAACUUUUGACACAUCGUUCAAUAAAAA-C-AAAUCAAC
.((.........((((....((((((((((-((......))).)))))))))..((((((..-.......))))))))))..........)-)-........ ( -26.51)
>DroSim_CAF1 10247 101 - 1
AG-GCUGCCCAUCGAUUACCACGCGUUAGUUGCCUGUGCGCAUCUAACGCGUUAGUGUCAUUCCAACGUUUGACACAUCGUUCAAUAAAAAACAAAAUCAAC
.(-(....))...((((...(((((((((.(((......))).)))))))))..((((((..(....)..))))))...................))))... ( -27.60)
>DroEre_CAF1 8975 98 - 1
AGUGCUGCCCAUCGAUUACCACGCGUUAGU-GCUUUUGCGUAUCUAACGCGUUAGUGCCUUU-CAACAUUUGACACAUCGUUCAAUAAAAA-C-AAAUCAAC
.((.........((((....((((((((((-((......))).)))))))))..(((....(-((.....))))))))))..........)-)-........ ( -18.71)
>DroYak_CAF1 9537 98 - 1
AGUGCUGCCCAUCGAUUAACACGCGUUAGU-GCGUUUGCGUAUCUAACGCGUUAGUGCCUUU-CAACUUUUGACACAUCGCUCAAUAAAAA-C-AAAUCAAC
.(.((...............((((((((((-(((....)))).)))))))))..(((....(-((.....))))))...)).)........-.-........ ( -21.50)
>consensus
AGUGCUGCCCAUCGAUUACCACGCGUUAGU_GCCUUUGCGCAUCUAACGCGUUAGUGUCUUU_CAACUUUUGACACAUCGUUCAAUAAAAA_C_AAAUCAAC
.............((((...(((((((((..((....))....)))))))))..(((((............)))))...................))))... (-19.48 = -19.88 +   0.40)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,185,013 – 12,185,114
Length 101
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 91.55
Mean single sequence MFE -32.24
Consensus MFE -24.96
Energy contribution -24.72
Covariance contribution -0.24
Combinations/Pair 1.12
Mean z-score -2.34
Structure conservation index 0.77
SVM decision value 1.37
SVM RNA-class probability 0.947478
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12185013 101 + 27905053
GAUGUGUCAAAAGUUG-GAAGACACUAACGCGUUAGAUGCGCACAGGC-ACUAACGCGUGGUAAUCGAUGGGCAGCACUGGUGUGCUCAAAAUGAGCACAGCU
...((((.....((((-(...((....(((((((((.(((......))-)))))))))).))..))))).....)))).(.(((((((.....))))))).). ( -38.30)
>DroSec_CAF1 9551 101 + 1
GAUGUGUCAAAAGUUG-AAUGACACUAACGCGUUAGAUGCGCAAAGGC-ACUAACGCGUGGUAAUCGAUGGGCAGCACUGGUGUGCUCAAAAUGAGCAGAACU
...((((.....((((-(...((....(((((((((.(((......))-)))))))))).))..))))).....)))).(((.(((((.....)))))..))) ( -34.40)
>DroSim_CAF1 10270 102 + 1
GAUGUGUCAAACGUUGGAAUGACACUAACGCGUUAGAUGCGCACAGGCAACUAACGCGUGGUAAUCGAUGGGCAGC-CUGGUGUGGUCAAAAUGAGCAGAACU
...........((((...((.(((((((((((((((.(((......))).)))))))))(((..((....))..))-))))))).))...))))......... ( -30.20)
>DroEre_CAF1 8996 101 + 1
GAUGUGUCAAAUGUUG-AAAGGCACUAACGCGUUAGAUACGCAAAAGC-ACUAACGCGUGGUAAUCGAUGGGCAGCACUGGUGAGCUCAAAAUGAGCAGAGUU
...((((....(((((-(...((....(((((((((....((....))-.))))))))).))..))))))....))))......((((.....))))...... ( -28.60)
>DroYak_CAF1 9558 101 + 1
GAUGUGUCAAAAGUUG-AAAGGCACUAACGCGUUAGAUACGCAAACGC-ACUAACGCGUGUUAAUCGAUGGGCAGCACUGGUGAGCUCAAAAUGAGCUGAGCU
...((((.....((((-(..(((((....(((((((....((....))-.))))))))))))..))))).....)))).(.(.(((((.....))))).).). ( -29.70)
>consensus
GAUGUGUCAAAAGUUG_AAAGACACUAACGCGUUAGAUGCGCAAAGGC_ACUAACGCGUGGUAAUCGAUGGGCAGCACUGGUGUGCUCAAAAUGAGCAGAGCU
((((((((............)))))..(((((((((....((....))..)))))))))....))).............(.(.(((((.....))))).).). (-24.96 = -24.72 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,185,013 – 12,185,114
Length 101
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 91.55
Mean single sequence MFE -28.06
Consensus MFE -21.66
Energy contribution -22.22
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.40
Structure conservation index 0.77
SVM decision value 1.42
SVM RNA-class probability 0.951865
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12185013 101 - 27905053
AGCUGUGCUCAUUUUGAGCACACCAGUGCUGCCCAUCGAUUACCACGCGUUAGU-GCCUGUGCGCAUCUAACGCGUUAGUGUCUUC-CAACUUUUGACACAUC
((((((((((.....))))))).....)))..............((((((((((-((......))).)))))))))..(((((...-........)))))... ( -34.10)
>DroSec_CAF1 9551 101 - 1
AGUUCUGCUCAUUUUGAGCACACCAGUGCUGCCCAUCGAUUACCACGCGUUAGU-GCCUUUGCGCAUCUAACGCGUUAGUGUCAUU-CAACUUUUGACACAUC
.....(((((.....)))))........................((((((((((-((......))).)))))))))..((((((..-.......))))))... ( -30.10)
>DroSim_CAF1 10270 102 - 1
AGUUCUGCUCAUUUUGACCACACCAG-GCUGCCCAUCGAUUACCACGCGUUAGUUGCCUGUGCGCAUCUAACGCGUUAGUGUCAUUCCAACGUUUGACACAUC
.....((..((.((((.......)))-).))..)).........(((((((((.(((......))).)))))))))..((((((..(....)..))))))... ( -25.50)
>DroEre_CAF1 8996 101 - 1
AACUCUGCUCAUUUUGAGCUCACCAGUGCUGCCCAUCGAUUACCACGCGUUAGU-GCUUUUGCGUAUCUAACGCGUUAGUGCCUUU-CAACAUUUGACACAUC
......((((.....))))......(..(((.............((((((((((-((......))).))))))))))))..)....-................ ( -22.91)
>DroYak_CAF1 9558 101 - 1
AGCUCAGCUCAUUUUGAGCUCACCAGUGCUGCCCAUCGAUUAACACGCGUUAGU-GCGUUUGCGUAUCUAACGCGUUAGUGCCUUU-CAACUUUUGACACAUC
(((((((......))))))).....(..(((.............((((((((((-(((....)))).))))))))))))..)....-................ ( -27.71)
>consensus
AGCUCUGCUCAUUUUGAGCACACCAGUGCUGCCCAUCGAUUACCACGCGUUAGU_GCCUUUGCGCAUCUAACGCGUUAGUGUCUUU_CAACUUUUGACACAUC
.....(((((.....)))))........................(((((((((..((....))....)))))))))..(((((............)))))... (-21.66 = -22.22 +   0.56)

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 11:35:12 2006