Locus 8604

Sequence ID	3R_DroMel_CAF1
Location	22,998,410 – 22,998,526
Length	116
Max. P	0.995418

overview

Window 4

Location	22,998,410 – 22,998,526
Length	116
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	88.79
Mean single sequence MFE	-34.03
Consensus MFE	-30.07
Energy contribution	-31.01
Covariance contribution	0.94
Combinations/Pair	1.09
Mean z-score	-4.30
Structure conservation index	0.88
SVM decision value	2.57
SVM RNA-class probability	0.995418
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22998410 116 + 27905053
UAGUAUUAAGAUAAGAUCAGGUAUACAAAUAAAUUUGCCCAACCCGUGGCCAUAACAUGCUUGAUUAACUAGCUAAUUUAUUUGUGUACCUCAUCUUUGUCUGAGAGACCUGGAUU
..((....(((((((((.(((((((((((((((((.((.........(((........)))..........)).))))))))))))))))).))).)))))).....))....... ( -31.91)
>DroSec_CAF1 1013 116 + 1
UAGUAUUAAGAUAAGAUCAGGUAUACAAAUAAAUUGGCCCAACCCGUGGCCAUGAAACGCUUGAUUAACUAGCCAAUUUAUUUGUGUACCUCAUUUUUGUCUGAGAGACCUGGAUU
..((....((((((((..((((((((((((((((((((.........(((........)))..........))))))))))))))))))))...)))))))).....))....... ( -37.31)
>DroEre_CAF1 4666 116 + 1
UAGUAUUAAGAUAAGAUCAGGUAUACAAAUACAUUGGCCCAACCUGUGGCCUCGAAAAGCUUGAUUAACACGCUUAUUUAUUUGUGUACCUCAUCUUACCAUAAACGACCUGGAUU
..((.(((.(.((((((.(((((((((((((....(((((.....).)))).....((((.((.....)).))))...))))))))))))).)))))).).))))).......... ( -33.00)
>DroYak_CAF1 4767 116 + 1
UAGUAUUAAGAUAAGAUCAGGUAUACAAAUAAAUUGGCCCAACCCGUGGCCUCGAAAAGCUUGAUUAACUAGCCAAUUUAUUUGUGUACCCCAUCUUACACUAACAGACCUGCAUU
...........((((((..((((((((((((((((((((((.....)))..((((.....)))).......)))))))))))))))))))..)))))).................. ( -33.90)
>consensus
UAGUAUUAAGAUAAGAUCAGGUAUACAAAUAAAUUGGCCCAACCCGUGGCCACGAAAAGCUUGAUUAACUAGCCAAUUUAUUUGUGUACCUCAUCUUACUCUAAGAGACCUGGAUU
..((.(((...((((((.((((((((((((((((((((.........(((........)))..........)))))))))))))))))))).))))))...)))...))....... (-30.07 = -31.01 +   0.94)

alignment

secondary structure

dotplot

Window 5

Location	22,998,410 – 22,998,526
Length	116
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	88.79
Mean single sequence MFE	-36.00
Consensus MFE	-29.29
Energy contribution	-30.60
Covariance contribution	1.31
Combinations/Pair	1.03
Mean z-score	-4.05
Structure conservation index	0.81
SVM decision value	2.12
SVM RNA-class probability	0.988506
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22998410 116 - 27905053
AAUCCAGGUCUCUCAGACAAAGAUGAGGUACACAAAUAAAUUAGCUAGUUAAUCAAGCAUGUUAUGGCCACGGGUUGGGCAAAUUUAUUUGUAUACCUGAUCUUAUCUUAAUACUA
.......(((.....))).(((((.(((((.(((((((((((.(((.(.....).)))......((.(((.....))).))))))))))))).))))).)))))............ ( -32.20)
>DroSec_CAF1 1013 116 - 1
AAUCCAGGUCUCUCAGACAAAAAUGAGGUACACAAAUAAAUUGGCUAGUUAAUCAAGCGUUUCAUGGCCACGGGUUGGGCCAAUUUAUUUGUAUACCUGAUCUUAUCUUAAUACUA
.......(((.....)))....((.(((((.(((((((((((((((...(((((..((........))....)))))))))))))))))))).))))).))............... ( -32.30)
>DroEre_CAF1 4666 116 - 1
AAUCCAGGUCGUUUAUGGUAAGAUGAGGUACACAAAUAAAUAAGCGUGUUAAUCAAGCUUUUCGAGGCCACAGGUUGGGCCAAUGUAUUUGUAUACCUGAUCUUAUCUUAAUACUA
......(((.(((...((((((((.(((((.(((((((...((((.((.....)).)))).....((((........))))....))))))).))))).))))))))..)))))). ( -36.20)
>DroYak_CAF1 4767 116 - 1
AAUGCAGGUCUGUUAGUGUAAGAUGGGGUACACAAAUAAAUUGGCUAGUUAAUCAAGCUUUUCGAGGCCACGGGUUGGGCCAAUUUAUUUGUAUACCUGAUCUUAUCUUAAUACUA
..........((((((.(((((((.(((((.(((((((((((((((...(((((..((((....))))....)))))))))))))))))))).))))).))))))).))))))... ( -43.30)
>consensus
AAUCCAGGUCUCUCAGACAAAGAUGAGGUACACAAAUAAAUUAGCUAGUUAAUCAAGCUUUUCAAGGCCACGGGUUGGGCCAAUUUAUUUGUAUACCUGAUCUUAUCUUAAUACUA
...................(((((.(((((.(((((((((((((((...(((((..((........))....)))))))))))))))))))).))))).)))))............ (-29.29 = -30.60 +   1.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:15:23 2006