Locus 160

Sequence ID	X_DroMel_CAF1
Location	574,480 – 574,602
Length	122
Max. P	0.996487

overview

Window 4

Location	574,480 – 574,574
Length	94
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	74.96
Mean single sequence MFE	-15.30
Consensus MFE	-8.40
Energy contribution	-9.03
Covariance contribution	0.63
Combinations/Pair	1.23
Mean z-score	-2.77
Structure conservation index	0.55
SVM decision value	2.70
SVM RNA-class probability	0.996487
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 574480 94 + 22224390
CAUCCACUUUCAAA------------------------GAAAUAAGCUCAUCAUAUCUUAUCAGUU-UUCCAAUUUUAUGUUCAUAUAUUCCACUCCGGGAAUACAUAUAUAAAAUUUA
..............------------------------............................-....((((((((((.....((((((......))))))...)))))))))).. ( -10.40)
>DroSec_CAF1 38272 94 + 1
CUUUCACUUUCAAA------------------------GAAAGAAGCUCAUCAAAUCUUAGUAUUU-UUCCAAUUUUAUGUAUAUAUAUUCCCCUCCGGGAAUACAUAUAUAAAAAAUA
..............------------------------((((((.(((...........))).)))-)))..(((((.(((((((.(((((((....))))))).))))))).))))). ( -19.10)
>DroSim_CAF1 37805 94 + 1
CUUUCACUUUCAAA------------------------GAAAGAAGCUCAUCAAAUCUUAGUAUUU-UCCCAAUUUUAUGUAUAUAUAUUCCACUCCGGGAAUACAUAUAUAAAAAAUA
(((((.........------------------------))))).......................-.....(((((.(((((((.((((((......)))))).))))))).))))). ( -15.60)
>DroEre_CAF1 38579 118 + 1
CUUCCACUUUCAAAAGGAAAAUUUGGAAUGAAUACAAAAAAAUAAGCGCAACAAAUCUUAGUAUUGUUUUCAAUUUCAUAUUCAUAUACUCCACUCCGGGAAUAUACAAGUAUA-AAUA
.(((((.((((.....))))...)))))((((.((((.(...((((..........)))).).)))).))))((((.(((((..((((.(((......))).))))..))))))-))). ( -16.10)
>consensus
CUUCCACUUUCAAA________________________GAAAGAAGCUCAUCAAAUCUUAGUAUUU_UUCCAAUUUUAUGUACAUAUAUUCCACUCCGGGAAUACAUAUAUAAAAAAUA
..............................................................................(((((((.((((((......)))))).)))))))....... ( -8.40 =  -9.03 +   0.63)

alignment

secondary structure

dotplot

Window 5

Location	574,495 – 574,602
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	72.84
Mean single sequence MFE	-14.20
Consensus MFE	-4.47
Energy contribution	-4.47
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.24
Structure conservation index	0.31
SVM decision value	1.85
SVM RNA-class probability	0.979894
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 574495 107 + 22224390
AAAUAAGCUCAUCAUAUCUUAUCAGUU-UUCCAAUUUUAUGUUCAUAUAUUCCACUCCGGGAAUACAUAUAUAAAAUUUACGUCUGUAUAUACC------------CGUUCUUUCCCACA
...................((((((..-....((((((((((.....((((((......))))))...)))))))))).....))).)))....------------.............. ( -12.90)
>DroSec_CAF1 38287 111 + 1
AAAGAAGCUCAUCAAAUCUUAGUAUUU-UUCCAAUUUUAUGUAUAUAUAUUCCCCUCCGGGAAUACAUAUAUAAAAAAUACCUCUGUAUAUAUC--------CUCUCGUUCUUUCCCACA
((((((.....................-......((((((((((...(((((((....))))))).)))))))))).((((....)))).....--------......))))))...... ( -17.00)
>DroSim_CAF1 37820 111 + 1
AAAGAAGCUCAUCAAAUCUUAGUAUUU-UCCCAAUUUUAUGUAUAUAUAUUCCACUCCGGGAAUACAUAUAUAAAAAAUACCUCUGUAUAUAUC--------CUCUCGUUCUUUCCCACA
((((((.....................-......((((((((((...((((((......)))))).)))))))))).((((....)))).....--------......))))))...... ( -14.40)
>DroEre_CAF1 38618 109 + 1
AAAUAAGCGCAACAAAUCUUAGUAUUGUUUUCAAUUUCAUAUUCAUAUACUCCACUCCGGGAAUAUACAAGUAUA-AAUAACACUGUGUAC--C--------CUCUCGCUUCUUCCCACA
....(((((..........((((.((((((........(((((..((((.(((......))).))))..))))))-))))).)))).....--.--------....)))))......... ( -14.35)
>DroYak_CAF1 41916 102 + 1
UAAUA----------AUCCAAGUAUGG-UUCCAAUUUCAUUUUCAUACACUCCACUCCGGGAAUAU------AUA-AAUAACACUGUAUGCAACCUCUCGUUCUCUCGCCCAUUCCCACA
.....----------......((((((-..............))))))..........((((((((------(((-........))))).........((......))...))))))... ( -12.34)
>consensus
AAAUAAGCUCAUCAAAUCUUAGUAUUU_UUCCAAUUUUAUGUUCAUAUAUUCCACUCCGGGAAUACAUAUAUAAAAAAUACCUCUGUAUAUAUC________CUCUCGUUCUUUCCCACA
..........................................................(((((.................................................)))))... ( -4.47 =  -4.47 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	574,495 – 574,602
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	72.84
Mean single sequence MFE	-23.38
Consensus MFE	-9.44
Energy contribution	-9.76
Covariance contribution	0.32
Combinations/Pair	1.50
Mean z-score	-1.80
Structure conservation index	0.40
SVM decision value	0.31
SVM RNA-class probability	0.681856
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 574495 107 - 22224390
UGUGGGAAAGAACG------------GGUAUAUACAGACGUAAAUUUUAUAUAUGUAUUCCCGGAGUGGAAUAUAUGAACAUAAAAUUGGAA-AACUGAUAAGAUAUGAUGAGCUUAUUU
.......(((..((------------..(((((.(((.....((((((((.((((((((((......))))))))))...))))))))....-..))).....))))).))..))).... ( -17.20)
>DroSec_CAF1 38287 111 - 1
UGUGGGAAAGAACGAGAG--------GAUAUAUACAGAGGUAUUUUUUAUAUAUGUAUUCCCGGAGGGGAAUAUAUAUACAUAAAAUUGGAA-AAAUACUAAGAUUUGAUGAGCUUCUUU
.............(((((--------(...(((.((((((((((((((.(((((((((((((....)))))))))))))((......)))))-)))))))....)))))))..)))))). ( -29.60)
>DroSim_CAF1 37820 111 - 1
UGUGGGAAAGAACGAGAG--------GAUAUAUACAGAGGUAUUUUUUAUAUAUGUAUUCCCGGAGUGGAAUAUAUAUACAUAAAAUUGGGA-AAAUACUAAGAUUUGAUGAGCUUCUUU
.............(((((--------(...(((.((((((((((((((.((((((((((((......))))))))))))((......)))))-)))))))....)))))))..)))))). ( -25.30)
>DroEre_CAF1 38618 109 - 1
UGUGGGAAGAAGCGAGAG--------G--GUACACAGUGUUAUU-UAUACUUGUAUAUUCCCGGAGUGGAGUAUAUGAAUAUGAAAUUGAAAACAAUACUAAGAUUUGUUGCGCUUAUUU
.........(((((...(--------(--((....((((((.((-((((.(..((((((((......))))))))..).))))))..(....).))))))...))))....))))).... ( -22.40)
>DroYak_CAF1 41916 102 - 1
UGUGGGAAUGGGCGAGAGAACGAGAGGUUGCAUACAGUGUUAUU-UAU------AUAUUCCCGGAGUGGAGUGUAUGAAAAUGAAAUUGGAA-CCAUACUUGGAU----------UAUUA
...(((.((((((((.....(....).))))...((((.(((((-(((------(((((((......)))))))))))..)))).))))...-)))).)))....----------..... ( -22.40)
>consensus
UGUGGGAAAGAACGAGAG________GAUAUAUACAGAGGUAUUUUUUAUAUAUGUAUUCCCGGAGUGGAAUAUAUGAACAUAAAAUUGGAA_AAAUACUAAGAUUUGAUGAGCUUAUUU
.................................................((((((((((((......))))))))))))......................................... ( -9.44 =  -9.76 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:36 2006