Locus 8324

Sequence ID	X_DroMel_CAF1
Location	20,671,943 – 20,672,080
Length	137
Max. P	0.924579

overview

Window 3

Location	20,671,943 – 20,672,046
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.51
Mean single sequence MFE	-31.44
Consensus MFE	-25.29
Energy contribution	-27.57
Covariance contribution	2.28
Combinations/Pair	1.04
Mean z-score	-2.08
Structure conservation index	0.80
SVM decision value	1.16
SVM RNA-class probability	0.924579
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20671943 103 + 22224390
UGGUUCCACA--AAA----------AGGGGCGAUGGAUGUUGGGUGACCAACAAAUUGAAACGAAUUCUCGUAUUGGAGUUCGAAUUGCAAUUGAGAUUGGUUGCACUGCAUAGU-----
..(((((...--...----------.))))).(((..((((((....))))))........((((((((......))))))))...(((((((......)))))))...)))...----- ( -30.70)
>DroSec_CAF1 73833 103 + 1
UGGUUCCACA--AAA----------AGGGGCGAUGGAUGUUGGGUGACCAACAAAUUGAAACGAAUUCUCGUAUUGGAGUUCGAAUUGCAAUUGAGAUUGGUUGCACUGCACAGU-----
..(((((...--...----------.)))))......((((((....)))))).((((...((((((((......))))))))...(((((((......))))))).....))))----- ( -31.30)
>DroEre_CAF1 68322 107 + 1
UGGUGCCACACAAAA----------AGGGGCGGUGGAUGUUGGGUGACCAACAAAUUGAAACGAAUUCUCGUAUUGGAGUUCGAAUUGCAAUUGAGAUUGGUUGCACUGCAUAGCAG---
.(((((.((.(((..----------((..(((((...((((((....))))))........((((((((......)))))))).)))))..))....))))).))))).........--- ( -33.30)
>DroYak_CAF1 69908 120 + 1
UGGUUCCGCCAAAGAGAGGGGGGGGGGGGGCGUUGGAUGUUGGGUGACCAACAAAUUGAAACGAAUUCUCGUAUUGGAGUUCGAAUUGCAAUUGAGAUUGGUUGCACUGCAUAGUGGGCU
..(((((.((.............)).)))))......((((((....))))))........((((((((......))))))))...(((((((......)))))))(..(...)..)... ( -34.92)
>DroAna_CAF1 38781 91 + 1
UGGUUUCA-----------------GGAGGCCAUGGAUGUUGGGUCACCAACAAAUUGAAACGAAUUCUCGUAUUGGAGUUCGAAUUGCAAUUGAAAUUGGUUGCACA------------
((((((..-----------------..))))))....((((((....))))))........((((((((......))))))))...(((((((......)))))))..------------ ( -27.00)
>consensus
UGGUUCCACA__AAA__________AGGGGCGAUGGAUGUUGGGUGACCAACAAAUUGAAACGAAUUCUCGUAUUGGAGUUCGAAUUGCAAUUGAGAUUGGUUGCACUGCAUAGU_____
..(((((...................)))))......((((((....))))))........((((((((......))))))))...(((((((......))))))).............. (-25.29 = -27.57 +   2.28)

alignment

secondary structure

dotplot

Window 4

Location	20,671,971 – 20,672,080
Length	109
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.74
Mean single sequence MFE	-34.27
Consensus MFE	-24.29
Energy contribution	-24.85
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.44
Structure conservation index	0.71
SVM decision value	0.75
SVM RNA-class probability	0.840969
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20671971 109 + 22224390
UGGGUGACCAACAAAUUGAAACGAAUUCUCGUAUUGGAGUUCGAAUUGCAAUUGAGAUUGGUUGCACUGCAUAGU------GGGCUAUG---UGCACUGAACAAAAUACAUUUC--GAUG
(((....)))....(((((((((((((((......))))))))...(((((((......)))))))..((((((.------...)))))---).................))))--))). ( -29.70)
>DroSec_CAF1 73861 112 + 1
UGGGUGACCAACAAAUUGAAACGAAUUCUCGUAUUGGAGUUCGAAUUGCAAUUGAGAUUGGUUGCACUGCACAGU------GGGCUAUGCGGUGCACUGCAGAAAAUGCAUUUC--GAUA
(((....)))...........((((((((......)))))))).......((((((((.(((.((((((((.((.------...)).)))))))))))(((.....))))))))--))). ( -38.30)
>DroEre_CAF1 68352 112 + 1
UGGGUGACCAACAAAUUGAAACGAAUUCUCGUAUUGGAGUUCGAAUUGCAAUUGAGAUUGGUUGCACUGCAUAGCAG---UGGGCUAGA---UGCACUGCACAAAAUUCAGUUC--AAUG
(((....)))...........((((((((......)))))))).((((.(((((((.((...((((.((((((((..---...))))..---)))).))))..)).))))))))--))). ( -34.00)
>DroYak_CAF1 69948 117 + 1
UGGGUGACCAACAAAUUGAAACGAAUUCUCGUAUUGGAGUUCGAAUUGCAAUUGAGAUUGGUUGCACUGCAUAGUGGGCUAGGGCUAUG---UGCACUGCACAAAAUACAGUGCCAAAAG
..(((((((((..(((((...((((((((......)))))))).....)))))....))))))(((.((((((...(((....))).))---)))).)))............)))..... ( -35.10)
>consensus
UGGGUGACCAACAAAUUGAAACGAAUUCUCGUAUUGGAGUUCGAAUUGCAAUUGAGAUUGGUUGCACUGCAUAGU______GGGCUAUG___UGCACUGCACAAAAUACAGUUC__AAUG
..(((((((((..(((((...((((((((......)))))))).....)))))....))))))(((...((((((........))))))...))))))...................... (-24.29 = -24.85 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	20,671,971 – 20,672,080
Length	109
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.74
Mean single sequence MFE	-26.82
Consensus MFE	-18.49
Energy contribution	-18.55
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-2.18
Structure conservation index	0.69
SVM decision value	0.41
SVM RNA-class probability	0.726203
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20671971 109 - 22224390
CAUC--GAAAUGUAUUUUGUUCAGUGCA---CAUAGCCC------ACUAUGCAGUGCAACCAAUCUCAAUUGCAAUUCGAACUCCAAUACGAGAAUUCGUUUCAAUUUGUUGGUCACCCA
..((--(((.((((..(((.....((((---(((((...------.))))...)))))........))).)))).)))))...((((((...(((.....)))....))))))....... ( -20.62)
>DroSec_CAF1 73861 112 - 1
UAUC--GAAAUGCAUUUUCUGCAGUGCACCGCAUAGCCC------ACUGUGCAGUGCAACCAAUCUCAAUUGCAAUUCGAACUCCAAUACGAGAAUUCGUUUCAAUUUGUUGGUCACCCA
..((--(((.((((..........(((((.((((((...------.)))))).)))))............)))).)))))...((((((...(((.....)))....))))))....... ( -30.35)
>DroEre_CAF1 68352 112 - 1
CAUU--GAACUGAAUUUUGUGCAGUGCA---UCUAGCCCA---CUGCUAUGCAGUGCAACCAAUCUCAAUUGCAAUUCGAACUCCAAUACGAGAAUUCGUUUCAAUUUGUUGGUCACCCA
....--.............((((.((((---..((((...---..)))))))).))))((((((...(((((.((..(((((((......)))..)))).))))))).))))))...... ( -24.90)
>DroYak_CAF1 69948 117 - 1
CUUUUGGCACUGUAUUUUGUGCAGUGCA---CAUAGCCCUAGCCCACUAUGCAGUGCAACCAAUCUCAAUUGCAAUUCGAACUCCAAUACGAGAAUUCGUUUCAAUUUGUUGGUCACCCA
......(((((((((..((.((((.((.---....)).)).)).))..))))))))).((((((...(((((.((..(((((((......)))..)))).))))))).))))))...... ( -31.40)
>consensus
CAUC__GAAAUGUAUUUUGUGCAGUGCA___CAUAGCCC______ACUAUGCAGUGCAACCAAUCUCAAUUGCAAUUCGAACUCCAAUACGAGAAUUCGUUUCAAUUUGUUGGUCACCCA
...................((((.((((.....(((..........))))))).))))((((((...(((((.((..(((((((......)))..)))).))))))).))))))...... (-18.49 = -18.55 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:01:15 2006