Locus 5467

Sequence ID	2L_DroMel_CAF1
Location	15,593,430 – 15,593,546
Length	116
Max. P	0.999878

overview

Window 6

Location	15,593,430 – 15,593,533
Length	103
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	94.76
Mean single sequence MFE	-34.38
Consensus MFE	-29.90
Energy contribution	-30.18
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-2.57
Structure conservation index	0.87
SVM decision value	3.31
SVM RNA-class probability	0.998968
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15593430 103 + 22407834
CCGAACAUCUGUAUUAAUUUACGGAUUUGGAUUUCAAUUGCUUAUUGGCUUGGGUCAGAGAGCAAUGCGGACCAAAUCGGACAGCUGACAGGUCAGCCGGUCA
.(((...((((((......))))))(((((..(((.(((((((.(((((....))))).)))))))..)))))))))))(((.(((((....)))))..))). ( -36.30)
>DroSec_CAF1 100054 103 + 1
CCGAACAUCUGUAUUAAUUUACGGAUUUGGAUUUAAAUUGCUUAUUGGCUUGGGUCAGAGAGCAAUGCGGACCAAAUCGGACAGCUGACAGGUCAGCCGGUCA
.(((...((((((......))))))(((((.(((..(((((((.(((((....))))).)))))))..)))))))))))(((.(((((....)))))..))). ( -36.70)
>DroSim_CAF1 92147 103 + 1
CCGAACAUCUGUAUUAAUUUACGGAUUUGGAUUUCAAUUGCUUAUUGGCUUGGGUCAGAGAGCAAUGCGGACCAAAUCGGACAGCUGACAGGUCAGCCGGUCA
.(((...((((((......))))))(((((..(((.(((((((.(((((....))))).)))))))..)))))))))))(((.(((((....)))))..))). ( -36.30)
>DroEre_CAF1 94223 103 + 1
CCCAAUUUCUGUAUUAAUUUACGGAUUUGGAUUUCAAUUGCUUAUUGGCUUGGGUCAGAGAGCAAUGCGGAUCAAAACGGACAGCUGACAGGUCAACCGGUCG
(((((..((((((......)))))).)))(((((..(((((((.(((((....))))).)))))))..))))).....))......(((.((....)).))). ( -29.80)
>DroYak_CAF1 97850 103 + 1
CCCAACAUCUGUAUUAAUUUACGGACUUGGAUUUCAAUUGCUUAUUGGCCUGGGUCAGAGAGCAAUGCGGACCAAAUCAGACAGCUGACAGGUCAACCGGUUG
..((((.((((((......))))))..(((......(((((((.(((((....))))).)))))))...((((...((((....))))..))))..))))))) ( -32.80)
>consensus
CCGAACAUCUGUAUUAAUUUACGGAUUUGGAUUUCAAUUGCUUAUUGGCUUGGGUCAGAGAGCAAUGCGGACCAAAUCGGACAGCUGACAGGUCAGCCGGUCA
.......((((((......))))))(((((.(((..(((((((.(((((....))))).)))))))..))))))))...(((.(((((....)))))..))). (-29.90 = -30.18 +   0.28)

alignment

secondary structure

dotplot

Window 7

Location	15,593,453 – 15,593,546
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	95.70
Mean single sequence MFE	-30.26
Consensus MFE	-28.26
Energy contribution	-28.74
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-2.61
Structure conservation index	0.93
SVM decision value	4.35
SVM RNA-class probability	0.999878
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15593453 93 + 22407834
GAUUUGGAUUUCAAUUGCUUAUUGGCUUGGGUCAGAGAGCAAUGCGGACCAAAUCGGACAGCUGACAGGUCAGCCGGUCAUUAAUCUCAAUUA
(((((((..(((.(((((((.(((((....))))).)))))))..)))))))))).(((.(((((....)))))..))).............. ( -33.20)
>DroSec_CAF1 100077 93 + 1
GAUUUGGAUUUAAAUUGCUUAUUGGCUUGGGUCAGAGAGCAAUGCGGACCAAAUCGGACAGCUGACAGGUCAGCCGGUCAUUAAUCUCAAUUA
(((((((.(((..(((((((.(((((....))))).)))))))..)))))))))).(((.(((((....)))))..))).............. ( -33.60)
>DroSim_CAF1 92170 93 + 1
GAUUUGGAUUUCAAUUGCUUAUUGGCUUGGGUCAGAGAGCAAUGCGGACCAAAUCGGACAGCUGACAGGUCAGCCGGUCAUUAAUCUCAAUUA
(((((((..(((.(((((((.(((((....))))).)))))))..)))))))))).(((.(((((....)))))..))).............. ( -33.20)
>DroEre_CAF1 94246 93 + 1
GAUUUGGAUUUCAAUUGCUUAUUGGCUUGGGUCAGAGAGCAAUGCGGAUCAAAACGGACAGCUGACAGGUCAACCGGUCGUUAAUCUCAAUUA
((((..(((((..(((((((.(((((....))))).)))))))..)))))..((((..(.(.(((....))).).)..))))))))....... ( -23.60)
>DroYak_CAF1 97873 93 + 1
GACUUGGAUUUCAAUUGCUUAUUGGCCUGGGUCAGAGAGCAAUGCGGACCAAAUCAGACAGCUGACAGGUCAACCGGUUGUUAAUCUCAAUUA
((.((((..(((.(((((((.(((((....))))).)))))))..))))))).)).((((((((..........))))))))........... ( -27.70)
>consensus
GAUUUGGAUUUCAAUUGCUUAUUGGCUUGGGUCAGAGAGCAAUGCGGACCAAAUCGGACAGCUGACAGGUCAGCCGGUCAUUAAUCUCAAUUA
(((((((.(((..(((((((.(((((....))))).)))))))..)))))))))).(((.(((((....)))))..))).............. (-28.26 = -28.74 +   0.48)

alignment

secondary structure

dotplot

Window 8

Location	15,593,453 – 15,593,546
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	95.70
Mean single sequence MFE	-22.64
Consensus MFE	-20.64
Energy contribution	-20.32
Covariance contribution	-0.32
Combinations/Pair	1.13
Mean z-score	-1.56
Structure conservation index	0.91
SVM decision value	1.48
SVM RNA-class probability	0.957596
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15593453 93 - 22407834
UAAUUGAGAUUAAUGACCGGCUGACCUGUCAGCUGUCCGAUUUGGUCCGCAUUGCUCUCUGACCCAAGCCAAUAAGCAAUUGAAAUCCAAAUC
..............(..(((((((....)))))))..)(((((((....(((((((...((........))...))))).))....))))))) ( -24.10)
>DroSec_CAF1 100077 93 - 1
UAAUUGAGAUUAAUGACCGGCUGACCUGUCAGCUGUCCGAUUUGGUCCGCAUUGCUCUCUGACCCAAGCCAAUAAGCAAUUUAAAUCCAAAUC
..............(..(((((((....)))))))..)(((((((.....((((((...((........))...))))))......))))))) ( -23.20)
>DroSim_CAF1 92170 93 - 1
UAAUUGAGAUUAAUGACCGGCUGACCUGUCAGCUGUCCGAUUUGGUCCGCAUUGCUCUCUGACCCAAGCCAAUAAGCAAUUGAAAUCCAAAUC
..............(..(((((((....)))))))..)(((((((....(((((((...((........))...))))).))....))))))) ( -24.10)
>DroEre_CAF1 94246 93 - 1
UAAUUGAGAUUAACGACCGGUUGACCUGUCAGCUGUCCGUUUUGAUCCGCAUUGCUCUCUGACCCAAGCCAAUAAGCAAUUGAAAUCCAAAUC
...(((.((((((((..(((((((....)))))))..))))......((.((((((...((........))...)))))))).)))))))... ( -20.20)
>DroYak_CAF1 97873 93 - 1
UAAUUGAGAUUAACAACCGGUUGACCUGUCAGCUGUCUGAUUUGGUCCGCAUUGCUCUCUGACCCAGGCCAAUAAGCAAUUGAAAUCCAAGUC
.................(((((((....)))))))...(((((((....(((((((...((.(....).))...))))).))....))))))) ( -21.60)
>consensus
UAAUUGAGAUUAAUGACCGGCUGACCUGUCAGCUGUCCGAUUUGGUCCGCAUUGCUCUCUGACCCAAGCCAAUAAGCAAUUGAAAUCCAAAUC
..............(..(((((((....)))))))..)(((((((.....((((((...((........))...))))))......))))))) (-20.64 = -20.32 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:53 2006