Locus 7317

Sequence ID	3L_DroMel_CAF1
Location	19,607,428 – 19,607,561
Length	133
Max. P	0.996996

overview

Window 8

Location	19,607,428 – 19,607,531
Length	103
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	76.29
Mean single sequence MFE	-23.76
Consensus MFE	-8.00
Energy contribution	-8.52
Covariance contribution	0.52
Combinations/Pair	1.30
Mean z-score	-2.13
Structure conservation index	0.34
SVM decision value	1.10
SVM RNA-class probability	0.915607
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19607428 103 + 23771897
UCAUAAUUCAUAAUUCCUUCUAGUAUUGCUUUGAAAUGCUUUUAGGAAGUCCUUCAAA-UUUGAUUUCGUACAUAU--GUAUAUGUACAUAUGCGUGUGU-----AUGCGC--------
(((..........(((((...((((((.......))))))...)))))..........-..)))...(((((((((--((((((....))))))))))))-----)))...-------- ( -27.15)
>DroSec_CAF1 22444 103 + 1
UCAUAAUUCAUAAUUCCUUCUAGUAUUGCUUUGAAAUGCUUUCAGGAAGUCCUUCAAA-UUUGAUUUAGUACAUAU--GUAUAUGUACAUAUACGAGUGU-----AUGUGC--------
(((..........(((((...((((((.......))))))...)))))..........-..)))....((((((.(--((((((....))))))).))))-----))....-------- ( -20.95)
>DroSim_CAF1 22289 103 + 1
UCAUAAUUCAUAAUUCCUUCUAGUAUUGCUUUGAAAUGCUUUCAGGAAGUCCUUCAAA-UUUGAUUGAGUACAUAU--GUAUAUGUACAUAUACGUGUGU-----AUGUGC--------
.............(((((...((((((.......))))))...))))).((..(((..-..)))..))((((((((--((((((....))))))))))))-----))....-------- ( -26.10)
>DroEre_CAF1 22676 116 + 1
ACAUAA-UCACAAUUGCAUCUAGAAUGGCUUUGAAAUGGUUUUAGGAAGUCCUUCAAAAUGAUAUUCCAUACACAU--GUAUAUGUACUUAUGCUCGUAUAGUGCAUGUAUAUUAAAUA
......-...............(((.((((((.(((....)))..)))))).)))...................((--(((((((((((.(((....))))))))))))))))...... ( -21.00)
>DroYak_CAF1 22172 111 + 1
GCAUAA-UCACAAUUGCAUCUAGAAUUGCUUUGAAAUAGUUUAAGGAAGUCCUUCAAAAUCAGAUUCCAUACACAAGUGUAUAUUUAUGUGUGCAC-------GCAUGUGUAUUAUACA
(.((((-(((((..(((.....(((((..(((((.........(((....))))))))....))))).........((((((((....))))))))-------))))))).))))).). ( -23.60)
>consensus
UCAUAAUUCAUAAUUCCUUCUAGUAUUGCUUUGAAAUGCUUUCAGGAAGUCCUUCAAA_UUUGAUUCCGUACAUAU__GUAUAUGUACAUAUGCGCGUGU_____AUGUGC________
........((((..........((((((.((((((..(((((...)))))..))))))........))))))......((((((....))))))............))))......... ( -8.00 =  -8.52 +   0.52)

alignment

secondary structure

dotplot

Window 9

Location	19,607,467 – 19,607,561
Length	94
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	72.64
Mean single sequence MFE	-27.90
Consensus MFE	-11.73
Energy contribution	-11.79
Covariance contribution	0.06
Combinations/Pair	1.23
Mean z-score	-2.80
Structure conservation index	0.42
SVM decision value	1.38
SVM RNA-class probability	0.948134
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19607467 94 + 23771897
UUUUAGGAAGUCCUUCAAA-UUUGAUUUCGUACAUAU--GUAUAUGUACAUAUGCGUGUGU--AUGCGC------------------UCUAGGAAUAGUGCAAGUGUAUCCUAAAGC
((((((((.(..(((....-........(((((((((--((((((....))))))))))))--))).((------------------.(((....))).)))))..).)))))))). ( -29.90)
>DroSec_CAF1 22483 95 + 1
UUUCAGGAAGUCCUUCAAA-UUUGAUUUAGUACAUAU--GUAUAUGUACAUAUACGAGUGU--AUGUGC-----------------GUCUAGGAGUAGUGCAAGUGAAUCCUAGAAC
.(((((((..(((((((..-..)))....((((((.(--.((.(((((((((((....)))--))))))-----------------)).)).).)).)))).)).)).)))).))). ( -22.20)
>DroSim_CAF1 22328 95 + 1
UUUCAGGAAGUCCUUCAAA-UUUGAUUGAGUACAUAU--GUAUAUGUACAUAUACGUGUGU--AUGUGC-----------------CUCUAGGACUAGUGCAAGUGAUUCCUAGAAC
.(((((((((((((((((.-.....))))((((((((--((((((....))))))))))))--))....-----------------....))))))............)))).))). ( -26.90)
>DroYak_CAF1 22210 113 + 1
UUUAAGGAAGUCCUUCAAAAUCAGAUUCCAUACACAAGUGUAUAUUUAUGUGUGCAC----GCAUGUGUAUUAUACACAUGCAUUGCUCUAGGAUUAGUGCAAUUGCAUCCGGCAGC
.....(((((((((.(((...................((((((((....))))))))----(((((((((...))))))))).)))....))))))..(((....))))))...... ( -32.60)
>consensus
UUUCAGGAAGUCCUUCAAA_UUUGAUUUAGUACAUAU__GUAUAUGUACAUAUACGUGUGU__AUGUGC_________________CUCUAGGAAUAGUGCAAGUGAAUCCUAGAAC
....(((....)))...............((((((....((((((....))))))........))))))..................(((((((..............))))))).. (-11.73 = -11.79 +   0.06)

alignment

secondary structure

dotplot

Window 0

Location	19,607,467 – 19,607,561
Length	94
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	72.64
Mean single sequence MFE	-23.82
Consensus MFE	-11.83
Energy contribution	-12.14
Covariance contribution	0.31
Combinations/Pair	1.18
Mean z-score	-2.89
Structure conservation index	0.50
SVM decision value	2.78
SVM RNA-class probability	0.996996
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19607467 94 - 23771897
GCUUUAGGAUACACUUGCACUAUUCCUAGA------------------GCGCAU--ACACACGCAUAUGUACAUAUAC--AUAUGUACGAAAUCAAA-UUUGAAGGACUUCCUAAAA
(((((((((..............)))))))------------------))....--......(((((((((....)))--)))))).((((......-)))).(((....))).... ( -23.64)
>DroSec_CAF1 22483 95 - 1
GUUCUAGGAUUCACUUGCACUACUCCUAGAC-----------------GCACAU--ACACUCGUAUAUGUACAUAUAC--AUAUGUACUAAAUCAAA-UUUGAAGGACUUCCUGAAA
(((((((((..............))))))).-----------------))..((--((....))))..(((((((...--.))))))).........-.....(((....))).... ( -17.54)
>DroSim_CAF1 22328 95 - 1
GUUCUAGGAAUCACUUGCACUAGUCCUAGAG-----------------GCACAU--ACACACGUAUAUGUACAUAUAC--AUAUGUACUCAAUCAAA-UUUGAAGGACUUCCUGAAA
.(((.((((............((((((.(((-----------------..((((--(.....((((((....))))))--.))))).)))..(((..-..)))))))))))))))). ( -21.20)
>DroYak_CAF1 22210 113 - 1
GCUGCCGGAUGCAAUUGCACUAAUCCUAGAGCAAUGCAUGUGUAUAAUACACAUGC----GUGCACACAUAAAUAUACACUUGUGUAUGGAAUCUGAUUUUGAAGGACUUCCUUAAA
.....(((((((((((((.(((....))).)))))(((((((((...)))))))))----.))).........((((((....))))))..)))))......((((....))))... ( -32.90)
>consensus
GCUCUAGGAUUCACUUGCACUAAUCCUAGAG_________________GCACAU__ACACACGCAUAUGUACAUAUAC__AUAUGUACGAAAUCAAA_UUUGAAGGACUUCCUGAAA
..(((((((..............)))))))......................................(((((((......)))))))...............(((....))).... (-11.83 = -12.14 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:52 2006