Locus 179

Sequence ID 3L_DroMel_CAF1
Location 532,427 – 532,604
Length 177
Max. P 0.901735
window257 window258 window259

overview

Window 7

Location 532,427 – 532,531
Length 104
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.20
Mean single sequence MFE -20.15
Consensus MFE -15.87
Energy contribution -16.32
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -1.72
Structure conservation index 0.79
SVM decision value 1.02
SVM RNA-class probability 0.901735
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 532427 104 + 23771897
--GUCCCCCGCACCCC-UGUUCCCCGAGCUCAUUGAAAAUUCCAGCGGACGCAAUUACCACCCCAAUUGUCUCCCAAUCUAAGUUUUCGCUUUUGAGCGGC------UCC-------GCC
--.......((....(-(((((...((((.....(((((((..((.(((.((((((........)))))).)))....)).)))))))))))..)))))).------...-------)). ( -19.90)
>DroSec_CAF1 6598 98 + 1
--GUCCC------CCC-UUUUCCCCGAGCUCAUUGAAAAUUCCAGCGGACGCAAUUACCACCCCACUUGUCUCCCAAUCUAAGUUUUCGCUUUUGAGCUGC------UCC-------GCC
--.....------...-.........((((((.((((((((..((.(((.((((............)))).)))....)).))))))))....))))))..------...-------... ( -15.90)
>DroSim_CAF1 7475 98 + 1
--GUCGC------CCC-UUUUCCCCGAGCUCAUUGAAAAUUCCAGCGGACGCAAUUACCACCCCAAUUGUCUCCCAAUCUAAGUUUUCGCUUUUGAGCUGC------UCC-------GCC
--.....------...-.........((((((.((((((((..((.(((.((((((........)))))).)))....)).))))))))....))))))..------...-------... ( -19.00)
>DroEre_CAF1 6824 96 + 1
--------------CC-UUUUCCCCGAGCUCAUUGAAAAUUCCAGCGGACGCAAUUACCACCCCAAUUGUCUCCCAAUCUAAGUUUUUGCUUUUGAGCGGCACCAAC---------CGCC
--------------..-..........(((((............(.(((.((((((........)))))).)))).....((((....)))).)))))(((......---------.))) ( -18.30)
>DroYak_CAF1 7027 105 + 1
--------------CC-UUUUCCCCGAGCUCAUUGAAAAUUCCAGCGGACGCAAUUACCACCCCAAUUGUCUCCCAAUCUAAGUUUUCGCUUUUGAGCGAAAAGAGCUCUGCCUCUUUCC
--------------..-........((((((.............(.(((.((((((........)))))).))))........((((((((....))))))))))))))........... ( -27.20)
>DroAna_CAF1 9947 110 + 1
GCGCCUUUCCCAAGCCAAUUCCCCGGCGCUCAUUGAAAAUUCCAACGGACGCAAUUACCACCCCAAUUGUCUCCCAAUCUAAGUUCCUCUGUUUGAGCUUCUCC---UCC-------GCC
(((..........(((........)))((((((((.......))).(((.((((((........)))))).)))...................)))))......---..)-------)). ( -20.60)
>consensus
__GUC_C______CCC_UUUUCCCCGAGCUCAUUGAAAAUUCCAGCGGACGCAAUUACCACCCCAAUUGUCUCCCAAUCUAAGUUUUCGCUUUUGAGCGGC______UCC_______GCC
...........................(((((.((((((((.....(((.((((((........)))))).))).......))))))))....)))))...................... (-15.87 = -16.32 +   0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 532,504 – 532,604
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.53
Mean single sequence MFE -17.73
Consensus MFE -11.38
Energy contribution -11.80
Covariance contribution 0.42
Combinations/Pair 1.15
Mean z-score -1.84
Structure conservation index 0.64
SVM decision value 0.05
SVM RNA-class probability 0.561098
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 532504 100 + 23771897
AAGUUUUCGCUUUUGAGCGGC------UCC-------GCCUCUUUGCUCGACUGUAUUUUCAGUGUUUCCUUCGCU-UUAUUUAUUUUUCGCUUAUUGCGACUUAUAAAAAUAU------
........((...((((((((------...-------))).....)))))((((......)))).........)).-...(((((...((((.....))))...))))).....------ ( -18.40)
>DroSec_CAF1 6669 100 + 1
AAGUUUUCGCUUUUGAGCUGC------UCC-------GCCUCUUUGCUCGACUGUAUUUUCAGUGUUUCCUUCGCU-UUAUUUAUUUUUCGCUUAUUGCGACUUAUAAAAAUAU------
........((...(((((...------...-------........)))))((((......)))).........)).-...(((((...((((.....))))...))))).....------ ( -16.54)
>DroSim_CAF1 7546 100 + 1
AAGUUUUCGCUUUUGAGCUGC------UCC-------GCCUCUUUGCUCGACUGUAUUUCCAGUGUUUCCUUCGCU-UUAUUUAUUUUUCGCUUAUUGCGACUUAUAAAAAUAU------
........((...(((((...------...-------........)))))((((......)))).........)).-...(((((...((((.....))))...))))).....------ ( -16.04)
>DroEre_CAF1 6889 104 + 1
AAGUUUUUGCUUUUGAGCGGCACCAAC---------CGCCUCUUCGCUCGACUGUAUUUUCAGCAUUUCCUUCGCU-UUAUGUAUUUUUCGCUUAUUGCGACUUAUAAAAAUAU------
..((((((((..(((((((((......---------.))).....))))))(((......)))..........)).-...........((((.....)))).....))))))..------ ( -17.90)
>DroYak_CAF1 7092 113 + 1
AAGUUUUCGCUUUUGAGCGAAAAGAGCUCUGCCUCUUUCCUCUUUGCUCGACUGUAUUUUCAGUAUUUCCUUCGCU-UUAUUUAUUUUUCGCUUAUUGCGACUUAUAAAAAUAU------
......((((...((((((((((((((..................)))).((((......))))............-........))))))))))..)))).............------ ( -25.77)
>DroAna_CAF1 10027 108 + 1
AAGUUCCUCUGUUUGAGCUUCUCC---UCC-------GCCUCUUUGCUC--UCGUACUUUUCGUAUUUCUUUCGCUUUUAUUUAUUUUUCGCUUAUUGCGACUUAUAAAAAUACCAUAUA
((((..........((((......---...-------........))))--..((((.....)))).......))))...(((((...((((.....))))...)))))........... ( -11.73)
>consensus
AAGUUUUCGCUUUUGAGCGGC______UCC_______GCCUCUUUGCUCGACUGUAUUUUCAGUAUUUCCUUCGCU_UUAUUUAUUUUUCGCUUAUUGCGACUUAUAAAAAUAU______
........((..((((((...........................))))))(((......)))..........)).....(((((...((((.....))))...)))))........... (-11.38 = -11.80 +   0.42)

alignment

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secondary structure

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dotplot

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Window 9

Location 532,504 – 532,604
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.53
Mean single sequence MFE -18.98
Consensus MFE -11.56
Energy contribution -11.31
Covariance contribution -0.25
Combinations/Pair 1.18
Mean z-score -1.95
Structure conservation index 0.61
SVM decision value -0.03
SVM RNA-class probability 0.518375
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 532504 100 - 23771897
------AUAUUUUUAUAAGUCGCAAUAAGCGAAAAAUAAAUAA-AGCGAAGGAAACACUGAAAAUACAGUCGAGCAAAGAGGC-------GGA------GCCGCUCAAAAGCGAAAACUU
------.....(((((...((((.....))))...)))))...-.((...(....)((((......)))).((((.....(((-------...------)))))))....))........ ( -19.10)
>DroSec_CAF1 6669 100 - 1
------AUAUUUUUAUAAGUCGCAAUAAGCGAAAAAUAAAUAA-AGCGAAGGAAACACUGAAAAUACAGUCGAGCAAAGAGGC-------GGA------GCAGCUCAAAAGCGAAAACUU
------.....(((((...((((.....))))...)))))...-.((...(....)((((......)))).((((........-------...------...))))....))........ ( -16.74)
>DroSim_CAF1 7546 100 - 1
------AUAUUUUUAUAAGUCGCAAUAAGCGAAAAAUAAAUAA-AGCGAAGGAAACACUGGAAAUACAGUCGAGCAAAGAGGC-------GGA------GCAGCUCAAAAGCGAAAACUU
------.....(((((...((((.....))))...)))))...-.((...(....)((((......)))).((((........-------...------...))))....))........ ( -18.04)
>DroEre_CAF1 6889 104 - 1
------AUAUUUUUAUAAGUCGCAAUAAGCGAAAAAUACAUAA-AGCGAAGGAAAUGCUGAAAAUACAGUCGAGCGAAGAGGCG---------GUUGGUGCCGCUCAAAAGCAAAAACUU
------.(((((((.....((((.....))))...........-((((.......))))))))))).......((.....((((---------((....)))))).....))........ ( -20.50)
>DroYak_CAF1 7092 113 - 1
------AUAUUUUUAUAAGUCGCAAUAAGCGAAAAAUAAAUAA-AGCGAAGGAAAUACUGAAAAUACAGUCGAGCAAAGAGGAAAGAGGCAGAGCUCUUUUCGCUCAAAAGCGAAAACUU
------.....(((((...((((.....))))...)))))...-.((.........((((......)))).((((.....((((((((......))))))))))))....))........ ( -23.90)
>DroAna_CAF1 10027 108 - 1
UAUAUGGUAUUUUUAUAAGUCGCAAUAAGCGAAAAAUAAAUAAAAGCGAAAGAAAUACGAAAAGUACGA--GAGCAAAGAGGC-------GGA---GGAGAAGCUCAAACAGAGGAACUU
......((((((((.....((((.....))))..............(....).......))))))))..--((((........-------...---......)))).............. ( -15.63)
>consensus
______AUAUUUUUAUAAGUCGCAAUAAGCGAAAAAUAAAUAA_AGCGAAGGAAACACUGAAAAUACAGUCGAGCAAAGAGGC_______GGA______GCAGCUCAAAAGCGAAAACUU
.......((((((((....((((.....))))..............(....)......)))))))).....((((...........................)))).............. (-11.56 = -11.31 +  -0.25)

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 09:35:04 2006