Locus 5504

Sequence ID	2L_DroMel_CAF1
Location	15,751,524 – 15,751,660
Length	136
Max. P	0.990757

overview

Window 2

Location	15,751,524 – 15,751,640
Length	116
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	80.17
Mean single sequence MFE	-25.28
Consensus MFE	-16.71
Energy contribution	-17.48
Covariance contribution	0.77
Combinations/Pair	1.24
Mean z-score	-2.73
Structure conservation index	0.66
SVM decision value	2.23
SVM RNA-class probability	0.990757
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15751524 116 + 22407834
UUUAAGGCCUAACUUCCACUUCCGUUCCAAUCGUAUUUUAUUGAAAUCGGAUUUGUUCUUUAGAUCCAUUAAGCUAUUUUCUAGCUUGAUGUUUGGUUAUAGAUUUAGUUUUGAAA
((((((((........((..((((((.((((........)))).)).))))..)).(((...((((((((((((((.....))))))))))...))))..)))....)))))))). ( -23.60)
>DroSec_CAF1 3230 110 + 1
UUUAAGGCCUAACUUCCACUUCCAUUCCAAUCGUAUUUUAUUGGAAUCGGAUUUGUUUCUUAGAUCCAUUAAGUUAUUUCCUAGCUUGAUGUUUGGUCAUAGAUUUAGUU------
((((.((((.(((..........((((((((........)))))))).(((((((.....)))))))(((((((((.....)))))))))))).)))).)))).......------ ( -27.00)
>DroSim_CAF1 3229 116 + 1
UUUAAGGCCUAACUUCCACUUCCAUUCCAAUCGUAUUUUAUUGGAAUCGGAUUUGUUUCUUAGAUCCAUUAAGCUAUUUCCUAGCUUGAUGUUUGGUCAUAGAUUUAGUUUUGAAA
((((((((........((..(((((((((((........)))))))).)))..))..(((..((((((((((((((.....))))))))))...))))..)))....)))))))). ( -30.90)
>DroEre_CAF1 3297 96 + 1
UUUAAGGC--------------CAUUCCAAUCGUAUUUUAUUGGAAG-AAAGUUGUUUCUAAGAUCCAUUGAGCUGUUUCCUAGCUUGAA-----GUUAUAGACUUAGCUAUAAAA
........--------------..(((((((........))))))).-..(((((..((((.(((...(..(((((.....)))))..).-----))).))))..)))))...... ( -19.90)
>DroYak_CAF1 3220 116 + 1
UUUAAGGCCCAACUACCACUUCCAUUCCAAUCGUAUUUUAUUGGAAUUGAAGUUGUUUCUAAUAUCCAUUGAGCUGUUUCCCAGCUUCAUCUUUGAUUGUAGAUUUACUUAUGAGA
..((((........((.(((((.((((((((........)))))))).))))).)).((((..(((...(((((((.....)))).))).....)))..))))....))))..... ( -25.00)
>consensus
UUUAAGGCCUAACUUCCACUUCCAUUCCAAUCGUAUUUUAUUGGAAUCGGAUUUGUUUCUUAGAUCCAUUAAGCUAUUUCCUAGCUUGAUGUUUGGUUAUAGAUUUAGUUAUGAAA
((((.((((..........(((.((((((((........)))))))).)))...............((((((((((.....))))))))))...)))).))))............. (-16.71 = -17.48 +   0.77)

alignment

secondary structure

dotplot

Window 3

Location	15,751,524 – 15,751,640
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	80.17
Mean single sequence MFE	-23.60
Consensus MFE	-14.28
Energy contribution	-16.24
Covariance contribution	1.96
Combinations/Pair	1.27
Mean z-score	-2.77
Structure conservation index	0.61
SVM decision value	2.12
SVM RNA-class probability	0.988532
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15751524 116 - 22407834
UUUCAAAACUAAAUCUAUAACCAAACAUCAAGCUAGAAAAUAGCUUAAUGGAUCUAAAGAACAAAUCCGAUUUCAAUAAAAUACGAUUGGAACGGAAGUGGAAGUUAGGCCUUAAA
.........................(((.((((((.....)))))).)))(..((((....((..((((.(((((((........)))))))))))..))....))))..)..... ( -24.80)
>DroSec_CAF1 3230 110 - 1
------AACUAAAUCUAUGACCAAACAUCAAGCUAGGAAAUAACUUAAUGGAUCUAAGAAACAAAUCCGAUUCCAAUAAAAUACGAUUGGAAUGGAAGUGGAAGUUAGGCCUUAAA
------..(((..(..(((......)))..)..)))........((((.((.(((((....((..(((.((((((((........)))))))))))..))....))))))))))). ( -19.80)
>DroSim_CAF1 3229 116 - 1
UUUCAAAACUAAAUCUAUGACCAAACAUCAAGCUAGGAAAUAGCUUAAUGGAUCUAAGAAACAAAUCCGAUUCCAAUAAAAUACGAUUGGAAUGGAAGUGGAAGUUAGGCCUUAAA
........((((.(((((.......(((.((((((.....)))))).)))...............(((.((((((((........))))))))))).)))))..))))........ ( -25.80)
>DroEre_CAF1 3297 96 - 1
UUUUAUAGCUAAGUCUAUAAC-----UUCAAGCUAGGAAACAGCUCAAUGGAUCUUAGAAACAACUUU-CUUCCAAUAAAAUACGAUUGGAAUG--------------GCCUUAAA
.((((..((((..((((....-----((((((((.(....)))))...))))...)))).........-.(((((((........)))))))))--------------))..)))) ( -19.70)
>DroYak_CAF1 3220 116 - 1
UCUCAUAAGUAAAUCUACAAUCAAAGAUGAAGCUGGGAAACAGCUCAAUGGAUAUUAGAAACAACUUCAAUUCCAAUAAAAUACGAUUGGAAUGGAAGUGGUAGUUGGGCCUUAAA
.((((........((((..(((...(.(((.((((.....))))))).).)))..)))).((.(((((.((((((((........)))))))).))))).))...))))....... ( -27.90)
>consensus
UUUCAAAACUAAAUCUAUAACCAAACAUCAAGCUAGGAAAUAGCUUAAUGGAUCUAAGAAACAAAUCCGAUUCCAAUAAAAUACGAUUGGAAUGGAAGUGGAAGUUAGGCCUUAAA
.............................((((((.....))))))...((.(((((....((..((((.(((((((........)))))))))))..))....)))))))..... (-14.28 = -16.24 +   1.96)

alignment

secondary structure

dotplot

Window 4

Location	15,751,564 – 15,751,660
Length	96
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	70.60
Mean single sequence MFE	-19.57
Consensus MFE	-13.79
Energy contribution	-16.23
Covariance contribution	2.44
Combinations/Pair	1.30
Mean z-score	-1.38
Structure conservation index	0.70
SVM decision value	0.77
SVM RNA-class probability	0.845709
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15751564 96 + 22407834
UUGAAAUCGGAUUUGUUCUUUAGAUCCAUUAAGCUAUUUUCUAGCUUGAUGUUUGGUUAUAGAUUUAGUUUUGAAACACAAACACGAAUAACUCU--------------------G
.......((((.((((((.........(((((((((.....)))))))))((((((((.((((......)))).))).)))))..)))))).)))--------------------) ( -23.50)
>DroSim_CAF1 3269 96 + 1
UUGGAAUCGGAUUUGUUUCUUAGAUCCAUUAAGCUAUUUCCUAGCUUGAUGUUUGGUCAUAGAUUUAGUUUUGAAACUCAAAAACGCAUAACUCU--------------------G
...((((((((((((.....)))))))(((((((((.....)))))))))...........))))).(((((........)))))..........--------------------. ( -21.80)
>DroEre_CAF1 3323 110 + 1
UUGGAAG-AAAGUUGUUUCUAAGAUCCAUUGAGCUGUUUCCUAGCUUGAA-----GUUAUAGACUUAGCUAUAAAAAACAAAAACGAAUAGAUUUCUGAUAAUAGAUAAUAUAAAA
(((..((-(((.((((((..........(..(((((.....)))))..).-----.((((((......))))))...........)))))).)))))..))).............. ( -16.50)
>DroYak_CAF1 3260 96 + 1
UUGGAAUUGAAGUUGUUUCUAAUAUCCAUUGAGCUGUUUCCCAGCUUCAUCUUUGAUUGUAGAUUUACUUAUGAGAAACAAAAACGAAUAACUUU--------------------A
......(((...((((((((.(((......((((((.....)))))).((((........)))).....))).))))))))...)))........--------------------. ( -16.50)
>consensus
UUGGAAUCGAAGUUGUUUCUAAGAUCCAUUAAGCUAUUUCCUAGCUUGAUGUUUGGUUAUAGAUUUAGUUAUGAAAAACAAAAACGAAUAACUCU____________________A
(((...(((((((((..((((.((((((((((((((.....))))))))))...)))).))))..)))))))))....)))................................... (-13.79 = -16.23 +   2.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:46 2006