Locus 1669

Sequence ID	2L_DroMel_CAF1
Location	4,521,818 – 4,521,978
Length	160
Max. P	0.826431

overview

Window 2

Location	4,521,818 – 4,521,938
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.39
Mean single sequence MFE	-43.40
Consensus MFE	-28.95
Energy contribution	-27.57
Covariance contribution	-1.38
Combinations/Pair	1.48
Mean z-score	-1.79
Structure conservation index	0.67
SVM decision value	0.58
SVM RNA-class probability	0.787846
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4521818 120 - 22407834
GCUGCCAGGAUCCCUGUCCGGGAUCGUGUGGCUUUAAUGCUUUCUGUAGUGUUGUAAACCACUCGCCCAUCUGCACCUGCGACUCUGGUUACACAGGUGACCCAUUCGCCGGCUGUAACC
((......((((((.....))))))(.((((.(((((((((......))))))).)).)))).))).....((((((.((((....((((((....))))))...)))).)).))))... ( -39.20)
>DroPse_CAF1 37844 120 - 1
GCUGCACAGAUCCUUGUCCGGGGUCAUGCGGCUUCAAUGCCUACUGCAGUGUCGUUGGCCACUCGCCUAUCUGCUCGUGCGACAAUGGCUUCACUGGCGAUCCAUUCGCUGGCUGCAAUC
((((((..((((((.....)))))).))))))............(((((.(((((((.((((..((......))..))).).)))))))....(..((((.....))))..))))))... ( -42.80)
>DroGri_CAF1 38109 120 - 1
GUUGCAAGGAUCCAUGUCCCGGCUCCUGUGGCUUUAAUGCCUACUGCAACGUAGUGAAUCAUUCACCAGUUUGCACCUGCGAAACCGGCUAUUCUGGCGAUCCAUUUGCUGGCUGCAAUC
((((((((((.((.......)).))))(((((......))).))))))))...((((.....))))....(((((((.(((((..((.(......).)).....))))).)).))))).. ( -35.50)
>DroEre_CAF1 37089 120 - 1
GCUGCCAGGAUCCCUGUCCGGGAUCCUGUGGCUUUAAUGCUUACUGCAGUGUGGUAAACCACUCGCCCAUUUGCACCUGCGACACUGGGUACACAGGUGACCCCUUCGCCGGCUGUAACC
((..(.((((((((.....)))))))))..))............((((((((((....))))..(((((.((((....))))...))))).....(((((.....))))).))))))... ( -48.30)
>DroAna_CAF1 37357 120 - 1
GCUGCCAGGAUCCUUGUCCGGGAUCCUGUGGCUUCAAUGCCUACUGCAGCGUGGUGAACCACUCGCCCGUCUGCUCUUGCGACAAUGGCUUCACUGGUGAUCCGUUCUCCGGAUGCAAUC
((((((((((((((.....))))))))).(((......)))....)))))((((....))))..(((.(((.((....)))))...)))....((((.((.....)).))))........ ( -49.60)
>DroPer_CAF1 39492 120 - 1
GCUGCACAGACCCUUGUCCGGGGUCAUGCGGCUUCAAUGCCUACUGCAGUGUCGUUGGCCACUCGCCCAUCUGUUCGUGCGACAAUGGCUUCACUGGCGAUCCAUUCGCUGGCUGCAAUC
((((((..((((((.....)))))).))))))......(((.....(((((.....(((((.((((.(........).))))...))))).)))))((((.....)))).)))....... ( -45.00)
>consensus
GCUGCAAGGAUCCUUGUCCGGGAUCCUGUGGCUUCAAUGCCUACUGCAGUGUCGUAAACCACUCGCCCAUCUGCACCUGCGACAAUGGCUACACUGGCGAUCCAUUCGCCGGCUGCAAUC
(((((...((((((.....))))))....(((......)))....)))))........((....(((....(((....))).....)))......(((((.....)))))))........ (-28.95 = -27.57 +  -1.38)

alignment

secondary structure

dotplot

Window 3

Location	4,521,858 – 4,521,978
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.00
Mean single sequence MFE	-43.08
Consensus MFE	-32.46
Energy contribution	-31.30
Covariance contribution	-1.16
Combinations/Pair	1.44
Mean z-score	-2.05
Structure conservation index	0.75
SVM decision value	0.70
SVM RNA-class probability	0.826431
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4521858 120 - 22407834
AACACAGAGUGUCCUGCCAACCUGGCGUGCAUCAAUGAGCGCUGCCAGGAUCCCUGUCCGGGAUCGUGUGGCUUUAAUGCUUUCUGUAGUGUUGUAAACCACUCGCCCAUCUGCACCUGC
......(((((....((((..(((((((((........)))).)))))((((((.....))))))...))))..(((((((......))))))).....)))))((......))...... ( -41.30)
>DroPse_CAF1 37884 120 - 1
AAUUCCGAGUGUCCUGCCAAUCUGGCGUGCAUCAAUGAGCGCUGCACAGAUCCUUGUCCGGGGUCAUGCGGCUUCAAUGCCUACUGCAGUGUCGUUGGCCACUCGCCUAUCUGCUCGUGC
.....(((((.....(((.....)))(((..(((((((.(((((((..((((((.....))))))....(((......)))...)))))))))))))).)))..........)))))... ( -42.60)
>DroGri_CAF1 38149 120 - 1
AACUCAGAAUGCCCGGCUAAUUUGGCCUGCAUUAACGAACGUUGCAAGGAUCCAUGUCCCGGCUCCUGUGGCUUUAAUGCCUACUGCAACGUAGUGAAUCAUUCACCAGUUUGCACCUGC
....((((((((..((((.....)))).)))))..(((((((((((((((.((.......)).))))(((((......))).))))))))...((((.....))))..)))))...))). ( -37.10)
>DroEre_CAF1 37129 120 - 1
AACACCGAGUGUCCUGCAAACCUGGCCUGCAUCAAUGAGCGCUGCCAGGAUCCCUGUCCGGGAUCCUGUGGCUUUAAUGCUUACUGCAGUGUGGUAAACCACUCGCCCAUUUGCACCUGC
.((((...))))..((((((...((((((((....(((((((..(.((((((((.....)))))))))..))......))))).))))).((((....))))..)))..))))))..... ( -44.60)
>DroAna_CAF1 37397 120 - 1
AACACUGAGUGUCCUGCCACUCUGGCCUGCAUUAAUGAGCGCUGCCAGGAUCCUUGUCCGGGAUCCUGUGGCUUCAAUGCCUACUGCAGCGUGGUGAACCACUCGCCCGUCUGCUCUUGC
.......(((((...(((.....)))..)))))...((((((((((((((((((.....))))))))).(((......)))....)))))((((....))))..........)))).... ( -48.10)
>DroPer_CAF1 39532 120 - 1
AAUUCCGAGUGUCCUGCCAAUCUGGCGUGCAUCAAUGAGCGCUGCACAGACCCUUGUCCGGGGUCAUGCGGCUUCAAUGCCUACUGCAGUGUCGUUGGCCACUCGCCCAUCUGUUCGUGC
.....((((((....(((.....))).....(((((((.(((((((..((((((.....))))))....(((......)))...)))))))))))))).))))))............... ( -44.80)
>consensus
AACACCGAGUGUCCUGCCAAUCUGGCCUGCAUCAAUGAGCGCUGCAAGGAUCCUUGUCCGGGAUCCUGUGGCUUCAAUGCCUACUGCAGUGUCGUAAACCACUCGCCCAUCUGCACCUGC
......(((((...((((.....))))...........(((((((...((((((.....))))))....(((......)))....))))))).......)))))................ (-32.46 = -31.30 +  -1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:02 2006