Locus 4709

Sequence ID 2L_DroMel_CAF1
Location 13,513,617 – 13,513,791
Length 174
Max. P 0.988801
window7450 window7451 window7452 window7453

overview

Window 0

Location 13,513,617 – 13,513,721
Length 104
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 75.94
Mean single sequence MFE -26.18
Consensus MFE -11.48
Energy contribution -12.24
Covariance contribution 0.76
Combinations/Pair 1.20
Mean z-score -2.48
Structure conservation index 0.44
SVM decision value 2.14
SVM RNA-class probability 0.988801
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13513617 104 - 22407834
AGUCUAAUAAUAAGGCAAAAAUAUUUGCCAAACAAAAUUGAGCAGCUCGGCAAAUAUUAUU-------UUGCCGAUAAUUGUGAGAGUGUGCAGCUGUCAGAUUGAGGCCA
.((((........((((((....))))))......((((..(((((((((((((......)-------)))))))....(((........))))))))..)))).)))).. ( -31.20)
>DroSec_CAF1 5004 104 - 1
AGUCUAAUAAUAAGGCAAAAAUAUUUGCCAAACAAAAUUGAGCAGCUCGGUAAAUAUUAUU-------UAGCCGAUAAUUGUGAGAGUGUGCAGCUGUCAGAUUGAGGCCA
.((((........((((((....))))))......((((..((((((((((.((......)-------).)))))....(((........))))))))..)))).)))).. ( -25.60)
>DroEre_CAF1 4906 111 - 1
UGUCUAAUAAUAAGGUAAAAAUAUUUGCCAAACAAAAUCGAGCAGCUCGGUAAAUAUUAUUCAUAUGAUAGCCGAUAAUUGUGAGAGUGUGCAGCUGUCAGAUUGAGGCCA
.((((........((((((....))))))......((((..((((((((((...((((((....)))))))))))....(((........))))))))..)))).)))).. ( -27.10)
>DroYak_CAF1 5169 111 - 1
AAUGUAAUAAUAAGGUAAAAAUAUUUGCCAAACUAAAUCGAGCAGCUUGGUAAAUAUUAUUCAUAUGAUAGCCAAUAAUUGUGAGAGUGUGCAGCUGUCAGAUUGAGGCCA
.............(((...((((((((((((.((.........)).)))))))))))).((((..(((((((..(((.((....)).)))...)))))))...))))))). ( -26.60)
>DroAna_CAF1 3670 83 - 1
AAUG-GAUACGCAAAUAAAAAUAUUGCACUAACGAUAUCGGACA--------------------------GCCGAUAAAUGUGAGAGUGCCCAGGUGUCGGCUUAAGCUC-
....-(((((...((((....))))(((((.(((.((((((...--------------------------.))))))..)))...)))))....)))))(((....))).- ( -20.40)
>consensus
AGUCUAAUAAUAAGGUAAAAAUAUUUGCCAAACAAAAUCGAGCAGCUCGGUAAAUAUUAUU_______UAGCCGAUAAUUGUGAGAGUGUGCAGCUGUCAGAUUGAGGCCA
.............((((((....)))))).........................................(((..(((((.(((.(((.....))).)))))))).))).. (-11.48 = -12.24 +   0.76)

alignment

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secondary structure

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Window 1

Location 13,513,648 – 13,513,754
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.65
Mean single sequence MFE -23.42
Consensus MFE -5.80
Energy contribution -7.36
Covariance contribution 1.56
Combinations/Pair 1.21
Mean z-score -2.02
Structure conservation index 0.25
SVM decision value 1.25
SVM RNA-class probability 0.935609
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13513648 106 + 22407834
AAUUAUCGGCAA-------AAUAAUAUUUGCCGAGCUGCUCAAUUUUGUUUGGCAAAUAUUUUUGCCUUAUUAUUAGACUACCUACUUAUUUAUUGAGUGU-------GGUUUGGGCAUA
.......(((((-------((..(((((((((((((...........))))))))))))))))))))......(((((((((..(((((.....)))))))-------)))))))..... ( -34.80)
>DroSec_CAF1 5035 106 + 1
AAUUAUCGGCUA-------AAUAAUAUUUACCGAGCUGCUCAAUUUUGUUUGGCAAAUAUUUUUGCCUUAUUAUUAGACUACCUACUUAUUUAUUGAGUGU-------GGUUUGGGCAUU
.....((((.((-------(((...)))))))))..(((((..........((((((....))))))........(((((((..(((((.....)))))))-------)))))))))).. ( -27.40)
>DroEre_CAF1 4937 113 + 1
AAUUAUCGGCUAUCAUAUGAAUAAUAUUUACCGAGCUGCUCGAUUUUGUUUGGCAAAUAUUUUUACCUUAUUAUUAGACAACCUACUUAUUUAUUGAGUGU-------GGUUUGGGCACA
.....((((.((..((((.....)))).))))))(.(((((((...(((((((..((((.........)))).)))))))(((((((((.....)))))).-------))))))))))). ( -21.70)
>DroYak_CAF1 5200 113 + 1
AAUUAUUGGCUAUCAUAUGAAUAAUAUUUACCAAGCUGCUCGAUUUAGUUUGGCAAAUAUUUUUACCUUAUUAUUACAUUACCUACAUAUUUAUGGAGUGU-------GGUUUGGGCAUA
........((.......((((.(((((((.((((((((.......)))))))).)))))))))))((.....((((((((.((...........)))))))-------)))..))))... ( -22.80)
>DroAna_CAF1 3700 93 + 1
AUUUAUCGGC--------------------------UGUCCGAUAUCGUUAGUGCAAUAUUUUUAUUUGCGUAUC-CAUUACCCAAUUAGUUAUCGAUUUUUUAUAGAGCUUUAGUAAUU
...((((((.--------------------------...))))))(((.(((.((((.........))))(((..-...)))........))).)))....................... ( -10.40)
>consensus
AAUUAUCGGCUA_______AAUAAUAUUUACCGAGCUGCUCGAUUUUGUUUGGCAAAUAUUUUUACCUUAUUAUUAGACUACCUACUUAUUUAUUGAGUGU_______GGUUUGGGCAUA
..............................((((((((((.(((...))).))).............................((((((.....))))))........)))))))..... ( -5.80 =  -7.36 +   1.56)

alignment

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secondary structure

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Window 2

Location 13,513,648 – 13,513,754
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.65
Mean single sequence MFE -19.05
Consensus MFE -6.22
Energy contribution -7.98
Covariance contribution 1.76
Combinations/Pair 1.20
Mean z-score -2.01
Structure conservation index 0.33
SVM decision value 1.12
SVM RNA-class probability 0.918538
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13513648 106 - 22407834
UAUGCCCAAACC-------ACACUCAAUAAAUAAGUAGGUAGUCUAAUAAUAAGGCAAAAAUAUUUGCCAAACAAAAUUGAGCAGCUCGGCAAAUAUUAUU-------UUGCCGAUAAUU
..(((.((((((-------((.............)).))).............((((((....))))))........))).)))..((((((((......)-------)))))))..... ( -24.52)
>DroSec_CAF1 5035 106 - 1
AAUGCCCAAACC-------ACACUCAAUAAAUAAGUAGGUAGUCUAAUAAUAAGGCAAAAAUAUUUGCCAAACAAAAUUGAGCAGCUCGGUAAAUAUUAUU-------UAGCCGAUAAUU
..(((.((((((-------((.............)).))).............((((((....))))))........))).)))..(((((.((......)-------).)))))..... ( -18.92)
>DroEre_CAF1 4937 113 - 1
UGUGCCCAAACC-------ACACUCAAUAAAUAAGUAGGUUGUCUAAUAAUAAGGUAAAAAUAUUUGCCAAACAAAAUCGAGCAGCUCGGUAAAUAUUAUUCAUAUGAUAGCCGAUAAUU
((((.......)-------)))...............(((((((.(((((((.((((((....)))))).......((((((...))))))...))))))).....)))))))....... ( -22.70)
>DroYak_CAF1 5200 113 - 1
UAUGCCCAAACC-------ACACUCCAUAAAUAUGUAGGUAAUGUAAUAAUAAGGUAAAAAUAUUUGCCAAACUAAAUCGAGCAGCUUGGUAAAUAUUAUUCAUAUGAUAGCCAAUAAUU
..(((.(..(((-------(((...........))).))).............((((((....))))))..........).)))..(((((...((((((....)))))))))))..... ( -16.30)
>DroAna_CAF1 3700 93 - 1
AAUUACUAAAGCUCUAUAAAAAAUCGAUAACUAAUUGGGUAAUG-GAUACGCAAAUAAAAAUAUUGCACUAACGAUAUCGGACA--------------------------GCCGAUAAAU
......................(((.((.(((.....))).)).-)))..((((.........))))........((((((...--------------------------.))))))... ( -12.80)
>consensus
UAUGCCCAAACC_______ACACUCAAUAAAUAAGUAGGUAGUCUAAUAAUAAGGUAAAAAUAUUUGCCAAACAAAAUCGAGCAGCUCGGUAAAUAUUAUU_______UAGCCGAUAAUU
.....................................(((.............((((((....)))))).......((((((...))))))...................)))....... ( -6.22 =  -7.98 +   1.76)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,513,681 – 13,513,791
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.82
Mean single sequence MFE -21.53
Consensus MFE -9.02
Energy contribution -11.46
Covariance contribution 2.44
Combinations/Pair 1.31
Mean z-score -1.90
Structure conservation index 0.42
SVM decision value 0.51
SVM RNA-class probability 0.763076
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13513681 110 - 22407834
--UGGGGGUGACACAACUCCCCGAUAUAAGGUACU-CUACUAUGCCCAAACC-------ACACUCAAUAAAUAAGUAGGUAGUCUAAUAAUAAGGCAAAAAUAUUUGCCAAACAAAAUUG
--.((((((......)).))))..(((.((((((.-(((((...........-------..............)))))))).))).)))....((((((....))))))........... ( -22.71)
>DroSec_CAF1 5068 110 - 1
--UGGGAGUGACACACCUCCCCGAUAUUAGGUACC-CUACAAUGCCCAAACC-------ACACUCAAUAAAUAAGUAGGUAGUCUAAUAAUAAGGCAAAAAUAUUUGCCAAACAAAAUUG
--.(((((........)))))...(((((((((((-.(((............-------...............))))))).)))))))....((((((....))))))........... ( -23.43)
>DroEre_CAF1 4977 110 - 1
--UGGGAGUGAUACAGCUCCCUGAUAUUGGGUACC-CUACUGUGCCCAAACC-------ACACUCAAUAAAUAAGUAGGUUGUCUAAUAAUAAGGUAAAAAUAUUUGCCAAACAAAAUCG
--.((((((......)))))).((((((((((((.-.....))))))))(((-------((.............)).))))))).........((((((....))))))........... ( -29.02)
>DroYak_CAF1 5240 111 - 1
--UGGCAGUGACACACCUCCCCAAUAUUGGGUACCCCUACUAUGCCCAAACC-------ACACUCCAUAAAUAUGUAGGUAAUGUAAUAAUAAGGUAAAAAUAUUUGCCAAACUAAAUCG
--((((((......((((........(((((((.........)))))))(((-------(((...........))).)))............))))........)))))).......... ( -19.64)
>DroAna_CAF1 3714 112 - 1
AAUGACAGUAUAGGAAUUCCUC------UAGUACC-CCACAAUUACUAAAGCUCUAUAAAAAAUCGAUAACUAAUUGGGUAAUG-GAUACGCAAAUAAAAAUAUUGCACUAACGAUAUCG
..((.((((((.((....))((------((.((((-(...(((((..........................)))))))))).))-)).............))))))))............ ( -12.87)
>consensus
__UGGGAGUGACACAACUCCCCGAUAUUAGGUACC_CUACUAUGCCCAAACC_______ACACUCAAUAAAUAAGUAGGUAGUCUAAUAAUAAGGUAAAAAUAUUUGCCAAACAAAAUCG
...((((((......))))))...(((((((((((..(((..................................))))))).)))))))....((((((....))))))........... ( -9.02 = -11.46 +   2.44)

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 11:25:17 2006