Locus 879

Sequence ID	3R_DroMel_CAF1
Location	2,972,962 – 2,973,052
Length	90
Max. P	0.780986

overview

Window 7

Location	2,972,962 – 2,973,052
Length	90
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	72.93
Mean single sequence MFE	-16.36
Consensus MFE	-2.34
Energy contribution	-2.30
Covariance contribution	-0.04
Combinations/Pair	1.17
Mean z-score	-1.70
Structure conservation index	0.14
SVM decision value	0.56
SVM RNA-class probability	0.780986
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2972962 90 + 27905053
UGUAUUCAGUGUGUAU-----------UCUAUCGCAAAAAUUCUGUCAAAGAAUUUCUGGGCUUUUUAAGAAAUAUUUUUAAAUACUGAAUAAUAACAAAC
..((((((((((....-----------.....(.((.(((((((.....))))))).)).)....((((((.....))))))))))))))))......... ( -17.80)
>DroSec_CAF1 19566 76 + 1
U------------UAG-----------UCUAUCGCAA-AAUUCUGUUCAAGAAUUUCUGGGCUUUUUAAGAAAUAUU-UAAAAUACUAAAUGAUAACUGAC
(------------(((-----------(.((((((((-((((((.....))))))).))((..(((((((.....))-)))))..))...)))))))))). ( -12.00)
>DroSim_CAF1 17494 77 + 1
U------------CAG-----------UCUAUCGCAAAAAUUCUGUCAAAGAAUUUCUGGGCUUUUUAAGAAAUAUU-UAAAAUACUGAAUAAUAACAAAC
(------------(((-----------(....(.((.(((((((.....))))))).)).)..(((((((.....))-))))).)))))............ ( -11.00)
>DroEre_CAF1 18209 97 + 1
UAUAUUCAGUGUGUAUGCGUAAGUGUGGGUAUCCGAAAAAUUCUGUCAAAAGUUUUCUGGGCUUUUUAAGAAAUAUU-UAAAAUACUGAAUAAUA---AAC
..((((((((((.(((((....))))).............((((...(((((((.....)))))))..)))).....-....))))))))))...---... ( -20.90)
>DroYak_CAF1 15581 96 + 1
UAUAUUCAGUGUGUAUGCCU-AGUGUGUGUAUCAGGAAAAUUCUCUCAAAAGUUUUCUGGGCUUUUUAAGAAAAUUU-UAAAAUACUGAAUAAUA---AAC
..((((((((((.....(((-.(((....))).)))((((((.(((.(((((((.....)))))))..))).)))))-)...))))))))))...---... ( -20.10)
>consensus
U_UAUUCAGUGUGUAU___________UCUAUCGCAAAAAUUCUGUCAAAGAAUUUCUGGGCUUUUUAAGAAAUAUU_UAAAAUACUGAAUAAUAAC_AAC
....................................................((((((..........))))))........................... ( -2.34 =  -2.30 +  -0.04)

alignment

secondary structure

dotplot

Window 8

Location	2,972,962 – 2,973,052
Length	90
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	72.93
Mean single sequence MFE	-14.38
Consensus MFE	-2.32
Energy contribution	-3.68
Covariance contribution	1.36
Combinations/Pair	1.09
Mean z-score	-1.63
Structure conservation index	0.16
SVM decision value	0.35
SVM RNA-class probability	0.701315
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2972962 90 - 27905053
GUUUGUUAUUAUUCAGUAUUUAAAAAUAUUUCUUAAAAAGCCCAGAAAUUCUUUGACAGAAUUUUUGCGAUAGA-----------AUACACACUGAAUACA
.........((((((((.(((((.........)))))....(((((((((((.....)))))))))).).....-----------......)))))))).. ( -14.60)
>DroSec_CAF1 19566 76 - 1
GUCAGUUAUCAUUUAGUAUUUUA-AAUAUUUCUUAAAAAGCCCAGAAAUUCUUGAACAGAAUU-UUGCGAUAGA-----------CUA------------A
(((...((((((((((....)))-)))............((...((((((((.....))))))-))))))))))-----------)..------------. ( -10.80)
>DroSim_CAF1 17494 77 - 1
GUUUGUUAUUAUUCAGUAUUUUA-AAUAUUUCUUAAAAAGCCCAGAAAUUCUUUGACAGAAUUUUUGCGAUAGA-----------CUG------------A
(((((((........((.(((((-(.......)))))).)).((((((((((.....)))))))))).))))))-----------)..------------. ( -13.70)
>DroEre_CAF1 18209 97 - 1
GUU---UAUUAUUCAGUAUUUUA-AAUAUUUCUUAAAAAGCCCAGAAAACUUUUGACAGAAUUUUUCGGAUACCCACACUUACGCAUACACACUGAAUAUA
...---...((((((((.(((((-(.......)))))).((...(((((.(((.....))).)))))((....))........))......)))))))).. ( -13.90)
>DroYak_CAF1 15581 96 - 1
GUU---UAUUAUUCAGUAUUUUA-AAAUUUUCUUAAAAAGCCCAGAAAACUUUUGAGAGAAUUUUCCUGAUACACACACU-AGGCAUACACACUGAAUAUA
...---...((((((((.....(-((((((((((((((............)))))))))))))))((((..........)-))).......)))))))).. ( -18.90)
>consensus
GUU_GUUAUUAUUCAGUAUUUUA_AAUAUUUCUUAAAAAGCCCAGAAAUUCUUUGACAGAAUUUUUGCGAUAGA___________AUACACACUGAAUA_A
........................................(.((((((((((.....)))))))))).)................................ ( -2.32 =  -3.68 +   1.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:27 2006