Locus 7423

Sequence ID	3L_DroMel_CAF1
Location	19,976,069 – 19,976,178
Length	109
Max. P	0.769548

overview

Window 2

Location	19,976,069 – 19,976,178
Length	109
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	71.31
Mean single sequence MFE	-26.10
Consensus MFE	-5.82
Energy contribution	-6.46
Covariance contribution	0.64
Combinations/Pair	1.38
Mean z-score	-1.81
Structure conservation index	0.22
SVM decision value	0.53
SVM RNA-class probability	0.769548
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19976069 109 + 23771897
AUUUCACACUCUUCUUCGGGCUGAUUAGCCCGAGGACUUUAAGCC---AGCCGGGGAUUUCCUGAUUUGU--CGUUUACUCCGAAUUUAAAUUUAAAUUUAAAGUGGGAGUUCA
............((((((((((....)))))))))).........---...((((.....))))......--.(...(((((.(.(((((((....))))))).).))))).). ( -30.60)
>DroSec_CAF1 66448 111 + 1
AUUUCACACUCUUUUUCGGGCUGAUUAGCCCGAGGACUUUAAGCC---AGGCGGGGAUUUCCUGAUUUGUCUCGUUUACCACGAAUUUAAAUUUAAAUUUAAGGUGGGUGUUGA
...((((((((.((((((((((....))))))))))....((((.---((((((((....)))....))))).))))(((..(((((((....)))))))..)))))))).))) ( -33.90)
>DroEre_CAF1 17303 83 + 1
---UCACACUCUU---CG--------------AGGACUUUAAGCC---AGCCGGGGAUUUCCCGAUUUCU--CGUUUACCCAGAAUUUAAAUAUAAAUUUGAA------GUUGA
---...((..(((---(.--------------.((....(((((.---((.((((.....))))....))--.))))).)).(((((((....))))))))))------).)). ( -14.50)
>DroYak_CAF1 17749 100 + 1
AUUUCACACUCUU---CGAGCUGAUUAGCCCGAGGACUUUAAGCC---AGCCGGGGAUUUCCUGAUUUGU--CGCUUACCCAGAAUUUAAAUAUAAAUUUGAA------GUUCA
.........((((---((.(((....))).))))))...((((((---((.((((.....))))..))).--.)))))....((((((((((....))))).)------)))). ( -20.50)
>DroAna_CAF1 17840 104 + 1
-UUUUACACUU-AAACCGGCUUGAUUAGCCCAAGGACUUGAAGUCCUUGGUUGGGUAUUUCUUGUUUCGU--UGUUU----UGAAUAAAAAUUUAAAAUAGAAGUGUG--CUUA
-...(((((((-..(((((((.....))))(((((((.....)))))))....))).............(--(((((----(((((....))))))))))))))))))--.... ( -31.00)
>consensus
AUUUCACACUCUU___CGGGCUGAUUAGCCCGAGGACUUUAAGCC___AGCCGGGGAUUUCCUGAUUUGU__CGUUUACCCAGAAUUUAAAUUUAAAUUUGAAGUG_G_GUUCA
..(((...........((((((....))))))...................((((.....))))..................)))............................. ( -5.82 =  -6.46 +   0.64)

alignment

secondary structure

dotplot

Window 3

Location	19,976,069 – 19,976,178
Length	109
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	71.31
Mean single sequence MFE	-22.96
Consensus MFE	-6.36
Energy contribution	-7.72
Covariance contribution	1.36
Combinations/Pair	1.28
Mean z-score	-1.74
Structure conservation index	0.28
SVM decision value	0.22
SVM RNA-class probability	0.640824
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19976069 109 - 23771897
UGAACUCCCACUUUAAAUUUAAAUUUAAAUUCGGAGUAAACG--ACAAAUCAGGAAAUCCCCGGCU---GGCUUAAAGUCCUCGGGCUAAUCAGCCCGAAGAAGAGUGUGAAAU
...(((((...(((((((....)))))))...))))).....--.....(((((......))....---.((((....((.(((((((....))))))).)).)))).)))... ( -26.60)
>DroSec_CAF1 66448 111 - 1
UCAACACCCACCUUAAAUUUAAAUUUAAAUUCGUGGUAAACGAGACAAAUCAGGAAAUCCCCGCCU---GGCUUAAAGUCCUCGGGCUAAUCAGCCCGAAAAAGAGUGUGAAAU
(((.(((.((((...((((((....))))))...)))......(((((..((((.........)))---)..))...))).(((((((....)))))))....).))))))... ( -25.90)
>DroEre_CAF1 17303 83 - 1
UCAAC------UUCAAAUUUAUAUUUAAAUUCUGGGUAAACG--AGAAAUCGGGAAAUCCCCGGCU---GGCUUAAAGUCCU--------------CG---AAGAGUGUGA---
...((------((..((((((....))))))..))))...((--((...(((((.....)))))..---(((.....)))))--------------))---..........--- ( -16.80)
>DroYak_CAF1 17749 100 - 1
UGAAC------UUCAAAUUUAUAUUUAAAUUCUGGGUAAGCG--ACAAAUCAGGAAAUCCCCGGCU---GGCUUAAAGUCCUCGGGCUAAUCAGCUCG---AAGAGUGUGAAAU
.....------......(((((((((......(((((.((((--(....)).((......)).)))---.)))))......(((((((....))))))---).))))))))).. ( -22.00)
>DroAna_CAF1 17840 104 - 1
UAAG--CACACUUCUAUUUUAAAUUUUUAUUCA----AAACA--ACGAAACAAGAAAUACCCAACCAAGGACUUCAAGUCCUUGGGCUAAUCAAGCCGGUUU-AAGUGUAAAA-
....--.((((((.........((((((.(((.----.....--..)))...))))))(((....(((((((.....)))))))((((.....)))))))..-))))))....- ( -23.50)
>consensus
UCAAC_C_CACUUCAAAUUUAAAUUUAAAUUCGGGGUAAACG__ACAAAUCAGGAAAUCCCCGGCU___GGCUUAAAGUCCUCGGGCUAAUCAGCCCG___AAGAGUGUGAAAU
.......................((((.((((.....................................(((.....))).(((((((....)))))))....)))).)))).. ( -6.36 =  -7.72 +   1.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:43 2006