Locus 5104

Sequence ID	3R_DroMel_CAF1
Location	13,445,853 – 13,445,969
Length	116
Max. P	0.795833

overview

Window 3

Location	13,445,853 – 13,445,969
Length	116
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	78.16
Mean single sequence MFE	-30.15
Consensus MFE	-22.75
Energy contribution	-22.92
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.12
Structure conservation index	0.75
SVM decision value	0.38
SVM RNA-class probability	0.711744
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13445853 116 + 27905053
AUUA--UUAUC-AAUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUCAGAAACUGUUGUGUCAAAGUACCAAAAU
....--.....-....((((.(((((((.......))))))).))))((((.(((.....)))((((........)))).....................))))............... ( -26.50)
>DroGri_CAF1 2334 111 + 1
UGUA--CU-----UUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCAUUGAAACUGUUGUUAUCCAUUGAGCGU-UU
.(((--..-----...((((.(((((((.......))))))).))))....))).....((((((((.........(((.(((((......))...))).))).......))))))-)) ( -27.79)
>DroSec_CAF1 923 112 + 1
AACA--UCC-----UUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGACGCAAAUACCUGUGUCAAAAUACCUAAAU
....--...-----..((((.(((((((.......))))))).)))).....(((.....)))((((........)))).........((((((......))))))............. ( -31.40)
>DroYak_CAF1 1802 110 + 1
AGUAGGUUACC-GACUGGAGAUGCUGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUUGCAGAAAGUUGUGUC--------UAAAU
..(((...(((-((((((((.(((.(((.......))).))).))))....(((.....((..((((........))))....))......)))...))))).)))--------))... ( -22.20)
>DroMoj_CAF1 2091 116 + 1
UUUA--AUCCCAAUUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUUGACCAAGUUGGGAACAGCUGAGCAU-UU
....--.(((((((((((((.(((((((.......))))))).)))((((..(((.....)))((((........)))).........).))).))))))))))............-.. ( -38.00)
>DroAna_CAF1 1911 115 + 1
AUAA--AUACA-ACUUGGAGAUGCGGGGUAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAUGUACAUGGUUGUACCAAAUGCCCUA-CU
....--.((((-((..((((.(((((((.......))))))).))))..((((..........((((........))))((((((...))))))))))))))))............-.. ( -35.00)
>consensus
AUUA__UUACC_AAUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUUGAAAAUGGUUGUAUCAAAUGACCUA_AU
................((((.(((((((.......))))))).)))).....(((.....)))((((........))))........................................ (-22.75 = -22.92 +   0.17)

alignment

secondary structure

dotplot

Window 4

Location	13,445,853 – 13,445,969
Length	116
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	78.16
Mean single sequence MFE	-36.42
Consensus MFE	-31.88
Energy contribution	-32.05
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.21
Structure conservation index	0.88
SVM decision value	0.60
SVM RNA-class probability	0.795833
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13445853 116 - 27905053
AUUUUGGUACUUUGACACAACAGUUUCUGACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAUU-GAUAA--UAAU
......((.....(((......)))....))((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))....-.....--.... ( -34.10)
>DroGri_CAF1 2334 111 - 1
AA-ACGCUCAAUGGAUAACAACAGUUUCAAUGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAA-----AG--UACA
..-..(((.....((.(((....)))))..(((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))))..-----))--)... ( -34.40)
>DroSec_CAF1 923 112 - 1
AUUUAGGUAUUUUGACACAGGUAUUUGCGUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAA-----GGA--UGUU
.......(((((((((.(((....))).)))((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))).)-----)))--)).. ( -37.60)
>DroYak_CAF1 1802 110 - 1
AUUUA--------GACACAACUUUCUGCAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCAGCAUCUCCAGUC-GGUAACCUACU
.....--------(((.((......))....((((((((..((((.(((.(.((((....))))).))).))))......(((........))).)))))))).)))-........... ( -32.10)
>DroMoj_CAF1 2091 116 - 1
AA-AUGCUCAGCUGUUCCCAACUUGGUCAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAAUUGGGAU--UAAA
..-............((((((...(.....)((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))...)))))).--.... ( -39.60)
>DroAna_CAF1 1911 115 - 1
AG-UAGGGCAUUUGGUACAACCAUGUACAUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUACCCCGCAUCUCCAAGU-UGUAU--UUAU
((-((.(((.....(((((....)))))...((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))..))-).)))--)... ( -40.70)
>consensus
AU_UAGGUCAUUUGACACAACCAUUUGCAACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAAU_GGUAA__UAAU
...............................((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))................ (-31.88 = -32.05 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:20 2006