Locus 7489

Sequence ID	3L_DroMel_CAF1
Location	20,102,715 – 20,102,898
Length	183
Max. P	0.881698

overview

Window 6

Location	20,102,715 – 20,102,821
Length	106
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	90.04
Mean single sequence MFE	-44.50
Consensus MFE	-34.74
Energy contribution	-34.58
Covariance contribution	-0.16
Combinations/Pair	1.13
Mean z-score	-1.95
Structure conservation index	0.78
SVM decision value	0.92
SVM RNA-class probability	0.881698
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20102715 106 + 23771897
UACUCCUGCAACUGACGAGUAGAAGGAGCCCGUACUCCUCCCCAGCUUCGCAACCGAGGUGGCUCCGGCCACAAGGAGCAAGGUGCUC------GGGUCGAGUACGUAAAUG
..(((((.(.(((....))).).)))))..(((((((..(((.(((.((....((...(((((....)))))..)).....)).))).------)))..)))))))...... ( -41.60)
>DroSec_CAF1 17067 106 + 1
UGCUCCUGCACCUGACGAGGAGAAGGAGCCCGUACUCCUGCCCAGCUCCGCAACCGUGGUUGCUCCGGCCACAAGGAGCAAGGUGCUC------GGGUCGAGUACGUAAAUG
.((((((.(.(((....))).).)))))).(((((((..(((((((.((((....))))(((((((........)))))))...))).------)))).)))))))...... ( -48.20)
>DroSim_CAF1 17465 106 + 1
UGCUCCUGCACCUGACGAGGAGAAGGAGCCCGUACUCCUGCCCAGCUCCGCAACCGUGGUGGCUCCGGCCACAAGGAGCAAGGUGCUC------GGGUCGAGUACGUAAAUG
.((((((.(.(((....))).).)))))).(((((((..(((((((.((....((...(((((....)))))..)).....)).))).------)))).)))))))...... ( -48.70)
>DroEre_CAF1 16779 106 + 1
UGUUUCUGCACCUGACGAGGAGAAGGAGCCCGCACUCCUCUCCAGCACGGCAACCCAGGUGGCUCCUGCCACAAGGAGCAAGGUGCUC------GGGUCGAGUACGUAAAUG
........((((((....(((((.((((......))))))))).....(....).))))))((((((......))))))...((((((------(...)))))))....... ( -44.00)
>DroYak_CAF1 17273 112 + 1
UGUUUCUGCACCUGACGAGGAGAAGGAGCCCGUACUCCUCCCCAGGACCGCGACCGAGGUGACUCCUGCCACAAGGAGCAAGGUGCUCGAGUACGGGUCGAGUACGUAAAUG
(((((((...((((..((((((..((...))...))))))..))))...(((...(((....))).)))....)))))))..((((((((.......))))))))....... ( -40.00)
>consensus
UGCUCCUGCACCUGACGAGGAGAAGGAGCCCGUACUCCUCCCCAGCUCCGCAACCGAGGUGGCUCCGGCCACAAGGAGCAAGGUGCUC______GGGUCGAGUACGUAAAUG
.((((((.(.(((....))).).)))))).(((((((...(((..........((...(((((....)))))..))(((.....))).......)))..)))))))...... (-34.74 = -34.58 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	20,102,715 – 20,102,821
Length	106
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	90.04
Mean single sequence MFE	-45.24
Consensus MFE	-34.83
Energy contribution	-36.31
Covariance contribution	1.48
Combinations/Pair	1.06
Mean z-score	-1.85
Structure conservation index	0.77
SVM decision value	0.64
SVM RNA-class probability	0.807907
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20102715 106 - 23771897
CAUUUACGUACUCGACCC------GAGCACCUUGCUCCUUGUGGCCGGAGCCACCUCGGUUGCGAAGCUGGGGAGGAGUACGGGCUCCUUCUACUCGUCAGUUGCAGGAGUA
......(((((((..(((------.(((...((((.((..(((((....)))))...))..)))).))).)))..))))))).((((((.(.(((....))).).)))))). ( -44.90)
>DroSec_CAF1 17067 106 - 1
CAUUUACGUACUCGACCC------GAGCACCUUGCUCCUUGUGGCCGGAGCAACCACGGUUGCGGAGCUGGGCAGGAGUACGGGCUCCUUCUCCUCGUCAGGUGCAGGAGCA
......(((((((.....------((((.....))))....((.((((.(((((....)))))....)))).)).))))))).((((((.(.(((....))).).)))))). ( -47.10)
>DroSim_CAF1 17465 106 - 1
CAUUUACGUACUCGACCC------GAGCACCUUGCUCCUUGUGGCCGGAGCCACCACGGUUGCGGAGCUGGGCAGGAGUACGGGCUCCUUCUCCUCGUCAGGUGCAGGAGCA
......(((((((..(((------((((.....))))...((..(((.((((.....)))).))).)).)))...))))))).((((((.(.(((....))).).)))))). ( -46.60)
>DroEre_CAF1 16779 106 - 1
CAUUUACGUACUCGACCC------GAGCACCUUGCUCCUUGUGGCAGGAGCCACCUGGGUUGCCGUGCUGGAGAGGAGUGCGGGCUCCUUCUCCUCGUCAGGUGCAGAAACA
.......((((..(((..------.(((((...((.(((.(((((....)))))..)))..)).)))))((((((((((....))))).)))))..)))..))))....... ( -44.70)
>DroYak_CAF1 17273 112 - 1
CAUUUACGUACUCGACCCGUACUCGAGCACCUUGCUCCUUGUGGCAGGAGUCACCUCGGUCGCGGUCCUGGGGAGGAGUACGGGCUCCUUCUCCUCGUCAGGUGCAGAAACA
.......((((..((((((.((.((((.((((((((......)))))).))...)))))))).))))((((.((((((...((....)).)))))).))))))))....... ( -42.90)
>consensus
CAUUUACGUACUCGACCC______GAGCACCUUGCUCCUUGUGGCCGGAGCCACCUCGGUUGCGGAGCUGGGGAGGAGUACGGGCUCCUUCUCCUCGUCAGGUGCAGGAGCA
.......(((((.(((........((((.((.(((((((((((((....)))))((((((......)))))))))))))).)))))).........))).)))))....... (-34.83 = -36.31 +   1.48)

alignment

secondary structure

dotplot

Window 8

Location	20,102,791 – 20,102,898
Length	107
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	78.15
Mean single sequence MFE	-27.90
Consensus MFE	-17.64
Energy contribution	-17.53
Covariance contribution	-0.11
Combinations/Pair	1.12
Mean z-score	-1.38
Structure conservation index	0.63
SVM decision value	0.15
SVM RNA-class probability	0.608661
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20102791 107 - 23771897
ACUCGAAUCCAGAUGAUAUAUUGCACCGAUGCCUCUCGUGCAGGCGCAUUAAGUUCGCUUAUUGCCGGCAAUAAACUCAUUUACGUACUCGACCC----------GAGCACCUUGCU
.((((.....((((((..((((((......(((((....).))))(((.((((....)))).)))..))))))...)))))).((....))...)----------)))......... ( -26.50)
>DroPse_CAF1 16134 115 - 1
UUUCAAAUCCAAAUGAAAUAUUGCACCGAAGUCUCUCGUGAAGGGGCAUUAAGGGGGUUUAUUGCCAGCAAUAAACUCAUUUGCGUACCCC--CCAAAUCCAGGGGAGACUCUUGUC
(((((........)))))........(((((((((((.((..((((.((((((.((((((((((....)))))))))).)))).)).))))--.......)).)))))))).))).. ( -32.90)
>DroSim_CAF1 17541 107 - 1
ACUCGAAUCCAGAUGAUAUAUUGCACCGAUGCCUCUCGUGCAGGCGCAUUAAGUUCGCUUACUGCCGGCAAUAAACUCAUUUACGUACUCGACCC----------GAGCACCUUGCU
.((((.....((((((..((((((......(((((....).))))(((.((((....)))).)))..))))))...)))))).((....))...)----------)))......... ( -26.00)
>DroYak_CAF1 17349 113 - 1
ACUCGAAUCCAGAUGAUAUAUUGCAACGAUGCCUCUCGUGCAGGCGCAUUAAGUUCGCUUAUUGCCGGCAAUAAACUCAUUUACGUACUCGACCCGUACUC----GAGCACCUUGCU
.(((((....((((((..((((((......(((((....).))))(((.((((....)))).)))..))))))...))))))..((((.......))))))----)))......... ( -30.70)
>DroAna_CAF1 15921 95 - 1
ACUCGAAUCCAGAUGAUAUAUUGCAUCGAUGCCUCUCGUGCAGGCGCAUUAACUCUGCUUAUUGCCGGCAAUAAACUCAUUUACGUAG----------------------CUUUCAU
..........((((((..((((((..(((((((((....).))))(((.......)))..))))...))))))...))))))......----------------------....... ( -18.40)
>DroPer_CAF1 15999 115 - 1
UUUCAAAUCCAAAUGAAAUAUUGCACCGAAGUCUCUCGUGAAGGGGCAUUAAGGGGGUUUAUUGCCAGCAAUAAACUCAUUUGCGUACCCC--CCAAAUCCAGGGGAGACUCUUGUC
(((((........)))))........(((((((((((.((..((((.((((((.((((((((((....)))))))))).)))).)).))))--.......)).)))))))).))).. ( -32.90)
>consensus
ACUCGAAUCCAGAUGAUAUAUUGCACCGAUGCCUCUCGUGCAGGCGCAUUAAGUUCGCUUAUUGCCGGCAAUAAACUCAUUUACGUACUCG__CC__________GAGCACCUUGCU
..........((((((..((((((......(((((....).))))(((.((((....)))).)))..))))))...))))))................................... (-17.64 = -17.53 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:31 2006