Locus 5589

Sequence ID	3R_DroMel_CAF1
Location	14,771,599 – 14,771,752
Length	153
Max. P	0.581265

overview

Window 0

Location	14,771,599 – 14,771,712
Length	113
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	80.75
Mean single sequence MFE	-27.76
Consensus MFE	-17.87
Energy contribution	-18.20
Covariance contribution	0.34
Combinations/Pair	1.17
Mean z-score	-1.50
Structure conservation index	0.64
SVM decision value	0.08
SVM RNA-class probability	0.575116
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14771599 113 - 27905053
CCAACAACCAACCAUCUAACAGCAACGCCCACACGUAGCACAGAGCCAUAAAGUGCUCGUAAUCAACGUGAAACUGCGAUGCACGCACACACAUCUAUUGCUGAAUGGGUGAU
.........................((((((....(((((.(((........(((((((((.((.....))...))))).)))).........)))..)))))..)))))).. ( -27.03)
>DroPse_CAF1 28909 100 - 1
AGGGCAA----------AGCAACGACGCCCACACGUAGCAGAGGGCCAUAAAAGGCUCGUAAUCAACGUGAAACUGCGACGCACACGCACCCAUCUACGACUCCUUUCGU---
.((((..----------.........)))).(((((......(((((......))))).......)))))....((((.......)))).......((((......))))--- ( -25.52)
>DroSim_CAF1 32093 113 - 1
CCAACAACCAACCAUCUAACAGCAACGCCCACACGUAGCACGGAGCCAUAAAGUGCUCGUAAUCAACGUGAAACUGCGAUGCACGCACACACAUCUAUUGCUGAAUGGGUGAU
............((((((.((((((.......(((.(((((...........)))))))).......(((....((((.....))))..))).....))))))..)))))).. ( -27.70)
>DroEre_CAF1 30738 109 - 1
CCAACAA----CCAUCCAACAGCAACGCCCACACGUCGCACGGAGCCAUAAAGUGCUCGUAAUCAACGUGAAACUGCGAUGCACGCACACACGUCUAUUGCUGAAUGGGUGUU
.......----.((((((...((.(((......))).))...(((((.....).))))(((((..(((((....((((.....))))..)))))..)))))....)))))).. ( -30.00)
>DroYak_CAF1 39655 109 - 1
CCAACAA----CCGUCUAACAGCAACGCCCACACGUAGCACGGAGCCAUAAAGUGCUCGUAAUCAACGUGAAACUGCGAUGCACGCACACACGUCUAUUGCUGAAUGGGUGUU
.......----............((((((((...(.(((((...........))))))(((((..(((((....((((.....))))..)))))..)))))....)))))))) ( -30.80)
>DroPer_CAF1 28965 100 - 1
AGGGCAA----------AGCAACGACGCCCACACGUAGCAGAGGGCCAUAAAAGGCUCGUAAUCAACGUGAAACUGCGACGCACACGCACCCAUCUACGACUCCUUUCGU---
.((((..----------.........)))).(((((......(((((......))))).......)))))....((((.......)))).......((((......))))--- ( -25.52)
>consensus
CCAACAA____CCAUCUAACAGCAACGCCCACACGUAGCACAGAGCCAUAAAGUGCUCGUAAUCAACGUGAAACUGCGAUGCACGCACACACAUCUAUUGCUGAAUGGGUG_U
.....................(((.(((...(((((......((((........)))).......))))).....))).))).........((((((((....)))))))).. (-17.87 = -18.20 +   0.34)

alignment

secondary structure

dotplot

Window 1

Location	14,771,632 – 14,771,752
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.60
Mean single sequence MFE	-27.96
Consensus MFE	-18.73
Energy contribution	-19.20
Covariance contribution	0.47
Combinations/Pair	1.11
Mean z-score	-1.17
Structure conservation index	0.67
SVM decision value	0.10
SVM RNA-class probability	0.581265
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14771632 120 - 27905053
GCAUAGACAUCAUGUCUAUGGUCAUACUACUCGGCCAGAUCCAACAACCAACCAUCUAACAGCAACGCCCACACGUAGCACAGAGCCAUAAAGUGCUCGUAAUCAACGUGAAACUGCGAU
((((((((.....))))))((((.........)))).........................))..(((...(((((......(((((.....).)))).......))))).....))).. ( -25.72)
>DroPse_CAF1 28939 104 - 1
GCAUAGACAUUAGGUCCAAGGUA------GUCAGCAAGGCAGGGCAA----------AGCAACGACGCCCACACGUAGCAGAGGGCCAUAAAAGGCUCGUAAUCAACGUGAAACUGCGAC
.....(((.....)))....(((------((..........((((..----------.........)))).(((((......(((((......))))).......)))))..)))))... ( -27.02)
>DroEre_CAF1 30771 116 - 1
GCAUAGACAUCAUGUCUAUGGCCGUACUACUCGGCCAGAUCCAACAA----CCAUCCAACAGCAACGCCCACACGUCGCACGGAGCCAUAAAGUGCUCGUAAUCAACGUGAAACUGCGAU
((((((((.....))))))(((((.......)))))...........----..........))..(((...(((((.(.(((.((((.....).))))))...).))))).....))).. ( -30.50)
>DroYak_CAF1 39688 116 - 1
GCAUAGACAUCAUGUCUAUGGUCUUACUACUCGGCCAGAUCCAACAA----CCGUCUAACAGCAACGCCCACACGUAGCACGGAGCCAUAAAGUGCUCGUAAUCAACGUGAAACUGCGAU
((((((((.....))))))((((.........))))...........----..........))..........((((((((((((((.....).))))(....)..))))...))))).. ( -25.40)
>DroAna_CAF1 32857 99 - 1
GCAUAGGCAUCAUGUCUUUGGCAGU------C-GCCAGGACAGGC--------------GAGCAACGCCCACACGUAGCACUGAGCCAUAAAGUGCUCGUAAUCAACGUGAAACUGCGAC
((..((((.....))))...)).((------(-((.((....(((--------------(.....))))..(((((((((((.........))))))........)))))...))))))) ( -31.70)
>DroPer_CAF1 28995 104 - 1
GCAUAGACAUUAUGUCCAAGGUA------GUCAGCAAGGCAGGGCAA----------AGCAACGACGCCCACACGUAGCAGAGGGCCAUAAAAGGCUCGUAAUCAACGUGAAACUGCGAC
.....(((.....)))....(((------((..........((((..----------.........)))).(((((......(((((......))))).......)))))..)))))... ( -27.42)
>consensus
GCAUAGACAUCAUGUCUAUGGUA_U____CUCGGCCAGAUCCAACAA__________AACAGCAACGCCCACACGUAGCACAGAGCCAUAAAGUGCUCGUAAUCAACGUGAAACUGCGAC
.(((((((.....))))))).............................................(((...(((((......((((........)))).......))))).....))).. (-18.73 = -19.20 +   0.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:50 2006