Locus 6508

Sequence ID 3R_DroMel_CAF1
Location 17,161,402 – 17,161,530
Length 128
Max. P 0.999953
window10586 window10587 window10588 window10589

overview

Window 6

Location 17,161,402 – 17,161,510
Length 108
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 91.41
Mean single sequence MFE -28.93
Consensus MFE -25.83
Energy contribution -26.31
Covariance contribution 0.48
Combinations/Pair 1.05
Mean z-score -1.83
Structure conservation index 0.89
SVM decision value 2.08
SVM RNA-class probability 0.987398
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17161402 108 + 27905053
CGACAAAAACUUGUACAGAGCAAAAUGAA-----UGGA-AGCCGGAGGAGAGGGCGUGGCAAAAAACGGAUUAAAUAUGUAUACAAUACCCGCCCUCGCCUCCAGCAGCACAGC
..........((((.....))))......-----....-.((.(((((.(((((((.((......(((.........)))........))))))))).))))).))........ ( -30.14)
>DroSec_CAF1 70614 108 + 1
CGACAAAAACUUGUACAGAGCAAAAUGAA-----UGGA-GGCCGGAGGAGAGGGCGUGGCAAAAAACGAAUUAAAUAUGUAUACAAUACCCGCCCUCGCCUCCAGCAGCACAGC
..........((((.....))))......-----(((.-.((.(((((.(((((((.((.............................))))))))).))))).))..).)).. ( -31.05)
>DroSim_CAF1 61919 108 + 1
CGACAAAAACUUGUACAGAGCAAAAUGAA-----UGGA-GGCCGGAGGAGAGGGCGUGGCAAAAAACGAAUUAAAUAUGUAUACAAUACCCGCCCUCGCCUCCAGCAGCACAGC
..........((((.....))))......-----(((.-.((.(((((.(((((((.((.............................))))))))).))))).))..).)).. ( -31.05)
>DroEre_CAF1 61797 111 + 1
CGACAAAAACUUGUACAGAGCAAAAUGAACUGAAUGGA-AGCCGAAGGAGAGGGCGUGGCAAA-AAUGAAUUAAAUAUGAAUACAGUCCC-GCCCUCGCCUCCAGCAGCACAGC
..........((((.....))))..((..(((..((((-.(((....).(((((((.(((...-.....................))).)-)))))))).)))).)))..)).. ( -26.86)
>DroYak_CAF1 89364 113 + 1
CGACAAAAACUUGUACAGAGCAAAAUGAACGGAAUGGAGAGCCAGAGGAGAGGGCGUGGCAAA-AAUGAAUUAAAUAUGAAUAUAACCCCUGCCCUCGCCUCCAGCAGCACAGC
..((((....)))).....((.............(((....)))((((.(((((((.((....-.....((.....)).........)).))))))).))))..))........ ( -25.57)
>consensus
CGACAAAAACUUGUACAGAGCAAAAUGAA_____UGGA_AGCCGGAGGAGAGGGCGUGGCAAAAAACGAAUUAAAUAUGUAUACAAUACCCGCCCUCGCCUCCAGCAGCACAGC
..((((....)))).....((..............((....))(((((.(((((((.((.............................))))))))).))))).))........ (-25.83 = -26.31 +   0.48)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,161,402 – 17,161,510
Length 108
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 91.41
Mean single sequence MFE -36.55
Consensus MFE -32.30
Energy contribution -32.62
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -3.08
Structure conservation index 0.88
SVM decision value 4.36
SVM RNA-class probability 0.999879
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17161402 108 - 27905053
GCUGUGCUGCUGGAGGCGAGGGCGGGUAUUGUAUACAUAUUUAAUCCGUUUUUUGCCACGCCCUCUCCUCCGGCU-UCCA-----UUCAUUUUGCUCUGUACAAGUUUUUGUCG
..(((((.((((((((.(((((((((((.........................)))).))))))).)))))))).-..((-----.......))....)))))........... ( -38.81)
>DroSec_CAF1 70614 108 - 1
GCUGUGCUGCUGGAGGCGAGGGCGGGUAUUGUAUACAUAUUUAAUUCGUUUUUUGCCACGCCCUCUCCUCCGGCC-UCCA-----UUCAUUUUGCUCUGUACAAGUUUUUGUCG
..(((((.((((((((.(((((((((((.........................)))).))))))).)))))))).-..((-----.......))....)))))........... ( -38.41)
>DroSim_CAF1 61919 108 - 1
GCUGUGCUGCUGGAGGCGAGGGCGGGUAUUGUAUACAUAUUUAAUUCGUUUUUUGCCACGCCCUCUCCUCCGGCC-UCCA-----UUCAUUUUGCUCUGUACAAGUUUUUGUCG
..(((((.((((((((.(((((((((((.........................)))).))))))).)))))))).-..((-----.......))....)))))........... ( -38.41)
>DroEre_CAF1 61797 111 - 1
GCUGUGCUGCUGGAGGCGAGGGC-GGGACUGUAUUCAUAUUUAAUUCAUU-UUUGCCACGCCCUCUCCUUCGGCU-UCCAUUCAGUUCAUUUUGCUCUGUACAAGUUUUUGUCG
..(((((.((((((((.((((((-(((.(.....................-...))).))))))).)))))))).-.......(((.......)))..)))))........... ( -34.36)
>DroYak_CAF1 89364 113 - 1
GCUGUGCUGCUGGAGGCGAGGGCAGGGGUUAUAUUCAUAUUUAAUUCAUU-UUUGCCACGCCCUCUCCUCUGGCUCUCCAUUCCGUUCAUUUUGCUCUGUACAAGUUUUUGUCG
..(((((.((..((((.((((((...(((.....................-...)))..)))))).))))..))..........((.......))...)))))........... ( -32.76)
>consensus
GCUGUGCUGCUGGAGGCGAGGGCGGGUAUUGUAUACAUAUUUAAUUCGUUUUUUGCCACGCCCUCUCCUCCGGCU_UCCA_____UUCAUUUUGCUCUGUACAAGUUUUUGUCG
..(((((.((((((((.(((((((((((.........................)))).))))))).))))))))........................)))))........... (-32.30 = -32.62 +   0.32)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,161,435 – 17,161,530
Length 95
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 93.18
Mean single sequence MFE -32.15
Consensus MFE -28.15
Energy contribution -28.63
Covariance contribution 0.48
Combinations/Pair 1.05
Mean z-score -4.29
Structure conservation index 0.88
SVM decision value 4.34
SVM RNA-class probability 0.999874
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17161435 95 + 27905053
-AGCCGGAGGAGAGGGCGUGGCAAAAAACGGAUUAAAUAUGUAUACAAUACCCGCCCUCGCCUCCAGCAGCACAGCAAAAAGGCCAAUACUAUUUA
-.((((((((.(((((((.((......(((.........)))........))))))))).))))).((......)).....)))............ ( -32.84)
>DroSec_CAF1 70647 95 + 1
-GGCCGGAGGAGAGGGCGUGGCAAAAAACGAAUUAAAUAUGUAUACAAUACCCGCCCUCGCCUCCAGCAGCACAGCAAAAAGGCCAAUACUAUUUA
-(((((((((.(((((((.((.............................))))))))).))))).((......)).....))))........... ( -36.75)
>DroSim_CAF1 61952 95 + 1
-GGCCGGAGGAGAGGGCGUGGCAAAAAACGAAUUAAAUAUGUAUACAAUACCCGCCCUCGCCUCCAGCAGCACAGCAAAAAGGCCAAUACUAUUUA
-(((((((((.(((((((.((.............................))))))))).))))).((......)).....))))........... ( -36.75)
>DroEre_CAF1 61835 93 + 1
-AGCCGAAGGAGAGGGCGUGGCAAA-AAUGAAUUAAAUAUGAAUACAGUCCC-GCCCUCGCCUCCAGCAGCACAGCAAAAAGGCCAAUACUAUUUA
-.((((.(((.(((((((.(((...-.....................))).)-)))))).))).).((......)).....)))............ ( -27.26)
>DroYak_CAF1 89402 95 + 1
GAGCCAGAGGAGAGGGCGUGGCAAA-AAUGAAUUAAAUAUGAAUAUAACCCCUGCCCUCGCCUCCAGCAGCACAGCAAAAAGGCCAAUACUAUUUA
(.(((.((((.(((((((.((....-.....((.....)).........)).))))))).))))..((......)).....))))........... ( -27.17)
>consensus
_AGCCGGAGGAGAGGGCGUGGCAAAAAACGAAUUAAAUAUGUAUACAAUACCCGCCCUCGCCUCCAGCAGCACAGCAAAAAGGCCAAUACUAUUUA
..((((((((.(((((((.((.............................))))))))).))))).((......)).....)))............ (-28.15 = -28.63 +   0.48)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,161,435 – 17,161,530
Length 95
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 93.18
Mean single sequence MFE -37.49
Consensus MFE -34.71
Energy contribution -35.03
Covariance contribution 0.32
Combinations/Pair 1.11
Mean z-score -4.57
Structure conservation index 0.93
SVM decision value 4.82
SVM RNA-class probability 0.999953
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17161435 95 - 27905053
UAAAUAGUAUUGGCCUUUUUGCUGUGCUGCUGGAGGCGAGGGCGGGUAUUGUAUACAUAUUUAAUCCGUUUUUUGCCACGCCCUCUCCUCCGGCU-
.....(((((.(((......))))))))((((((((.(((((((((((.........................)))).))))))).)))))))).- ( -40.21)
>DroSec_CAF1 70647 95 - 1
UAAAUAGUAUUGGCCUUUUUGCUGUGCUGCUGGAGGCGAGGGCGGGUAUUGUAUACAUAUUUAAUUCGUUUUUUGCCACGCCCUCUCCUCCGGCC-
.....(((((.(((......))))))))((((((((.(((((((((((.........................)))).))))))).)))))))).- ( -39.81)
>DroSim_CAF1 61952 95 - 1
UAAAUAGUAUUGGCCUUUUUGCUGUGCUGCUGGAGGCGAGGGCGGGUAUUGUAUACAUAUUUAAUUCGUUUUUUGCCACGCCCUCUCCUCCGGCC-
.....(((((.(((......))))))))((((((((.(((((((((((.........................)))).))))))).)))))))).- ( -39.81)
>DroEre_CAF1 61835 93 - 1
UAAAUAGUAUUGGCCUUUUUGCUGUGCUGCUGGAGGCGAGGGC-GGGACUGUAUUCAUAUUUAAUUCAUU-UUUGCCACGCCCUCUCCUUCGGCU-
.....(((((.(((......))))))))((((((((.((((((-(((.(.....................-...))).))))))).)))))))).- ( -34.36)
>DroYak_CAF1 89402 95 - 1
UAAAUAGUAUUGGCCUUUUUGCUGUGCUGCUGGAGGCGAGGGCAGGGGUUAUAUUCAUAUUUAAUUCAUU-UUUGCCACGCCCUCUCCUCUGGCUC
.....(((((.(((......))))))))((..((((.((((((...(((.....................-...)))..)))))).))))..)).. ( -33.26)
>consensus
UAAAUAGUAUUGGCCUUUUUGCUGUGCUGCUGGAGGCGAGGGCGGGUAUUGUAUACAUAUUUAAUUCGUUUUUUGCCACGCCCUCUCCUCCGGCU_
.....(((((.(((......))))))))((((((((.(((((((((((.........................)))).))))))).)))))))).. (-34.71 = -35.03 +   0.32)

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 12:23:05 2006