Locus 4034

Sequence ID	3L_DroMel_CAF1
Location	11,775,404 – 11,775,513
Length	109
Max. P	0.947760

overview

Window 2

Location	11,775,404 – 11,775,513
Length	109
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	79.43
Mean single sequence MFE	-25.93
Consensus MFE	-23.98
Energy contribution	-23.98
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.92
SVM decision value	1.38
SVM RNA-class probability	0.947760
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11775404 109 + 23771897
-U---AGGAAAGAUG------CAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUCUAACAAUUCUUUGUCCAAAUAA
-.---.(((((((((------..(((((((((((((.......)))))....((((((.....))))))...................))))))))....))..))))..)))...... ( -28.40)
>DroVir_CAF1 11245 116 + 1
AUCGAAAAAAGAAUAUUACCGACAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCGCUCGUA---UCUUGCCUGAAUUU
.(((....((((....(((.((..((((((((((((.......)))))....((((((.....))))))...................)))))))..)))))---))))...))).... ( -27.50)
>DroGri_CAF1 11330 113 + 1
---GUAAAAAGUAAAUGAACAACAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUCACAUU---UUUCGCCCGAAUUC
---(..((((((...(((......((((((((((((.......)))))....((((((.....))))))...................)))))))))).)))---)))..)........ ( -25.00)
>DroEre_CAF1 11264 104 + 1
-U---A-----GAUG------UUAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUCUAAAAUUUUUUUGUCCAAAUAG
-.---.-----....------..(((((((((((((.......)))))....((((((.....))))))...................))))))))....................... ( -24.40)
>DroYak_CAF1 11338 109 + 1
-U---AGAGAAGAUA------UUAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUCUAAAAAUACACCGUCAAAAUAG
-.---..........------..(((((((((((((.......)))))....((((((.....))))))...................))))))))....................... ( -24.40)
>DroAna_CAF1 10765 106 + 1
-----ACGU--AAUU------UAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUCUUAAAUUUCCUCUUCCGAAUUA
-----..(.--((((------(((((((((((((((.......)))))....((((((.....))))))...................))))))))..)))))).)............. ( -25.90)
>consensus
_U___AAAAA_GAUA______UAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUCUAAAA_UUCUUCGUCCAAAUAA
........................((((((((((((.......)))))....((((((.....))))))...................)))))))........................ (-23.98 = -23.98 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	11,775,404 – 11,775,513
Length	109
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	79.43
Mean single sequence MFE	-27.99
Consensus MFE	-24.00
Energy contribution	-24.17
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.24
Structure conservation index	0.86
SVM decision value	0.42
SVM RNA-class probability	0.727558
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11775404 109 - 23771897
UUAUUUGGACAAAGAAUUGUUAGAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUUG------CAUCUUUCCU---A-
......(((..((((..(((..(((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))))------))))))))).---.- ( -31.10)
>DroVir_CAF1 11245 116 - 1
AAAUUCAGGCAAGA---UACGAGCGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUGUCGGUAAUAUUCUUUUUUCGAU
....(((((.((((---..(((..(((((((.(((((........)))))(((((.......)))))....(((((.......))))))))))))..))).......)))).))).)). ( -27.00)
>DroGri_CAF1 11330 113 - 1
GAAUUCGGGCGAAA---AAUGUGAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUGUUGUUCAUUUACUUUUUAC---
(((((((((((...---....((((((((...(((((........)))))..)))))))).......)).)))))))))...........((((.....)))).............--- ( -29.14)
>DroEre_CAF1 11264 104 - 1
CUAUUUGGACAAAAAAAUUUUAGAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAA------CAUC-----U---A-
.......................((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))..------....-----.---.- ( -24.90)
>DroYak_CAF1 11338 109 - 1
CUAUUUUGACGGUGUAUUUUUAGAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAA------UAUCUUCUCU---A-
.......((.(((((........((((((((.(((((........)))))(((((.......)))))....(((((.......))))))))))))).)------)))).))...---.- ( -26.40)
>DroAna_CAF1 10765 106 - 1
UAAUUCGGAAGAGGAAAUUUAAGAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUUA------AAUU--ACGU-----
...(((....)))(.((((((..((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))))------))))--.)..----- ( -29.40)
>consensus
CAAUUCGGACAAAAAA_UUUUAGAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAA______UAUC_UUUCU___A_
.......................((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))....................... (-24.00 = -24.17 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:54 2006