Locus 2806

Sequence ID	3R_DroMel_CAF1
Location	7,510,186 – 7,510,358
Length	172
Max. P	0.824512

overview

Window 6

Location	7,510,186 – 7,510,278
Length	92
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	86.84
Mean single sequence MFE	-23.48
Consensus MFE	-16.06
Energy contribution	-16.18
Covariance contribution	0.12
Combinations/Pair	1.28
Mean z-score	-2.18
Structure conservation index	0.68
SVM decision value	0.45
SVM RNA-class probability	0.739857
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7510186 92 + 27905053
UUAUAACUAAUCGUUAAGAGCGAUAGCCGUGAACUUAAGUCUAUCAAUACCAUAAGAAUAAUUGGGUUGAU-AGGUGUAACUAGCAGCUGGUG
.....(((.(((((.....)))))(((.((....(((..(((((((((.(((..........)))))))))-)))..)))...)).)))))). ( -21.30)
>DroSec_CAF1 5905 93 + 1
UUAUAACUAAUCGUUAAGUGCGAUAGCCGUGAACUUAAGUCUAUCAAUACGAUUCGAAUGAUUGGGUUGAUUAGGUUUAACUAGCAGCUGGUG
.....(((.(((((.....)))))(((.((....((((..(((((((..(((((.....)))))..)))).)))..))))...)).)))))). ( -21.00)
>DroSim_CAF1 6247 93 + 1
UUAUAACUAAUCGUUAAGAGCGAUAGCAGUGAACUUAAGUCUAUCAAUACGAUAAGAAUGAUUGGGUUGAUUAGAUUUAACUAGCAGCUGGUG
.....(((.(((((.....)))))(((.((....(((((((((((((..((((.......))))..)))).)))))))))...)).)))))). ( -21.40)
>DroEre_CAF1 5954 92 + 1
UUAUAACUAAACGCUUAGAGCGAUACCAGUGAACUUAAGUCUAUCAAUGUGAUAAGAAUGACUAGGUUGAU-AGGCUUAACCAGCAACUGGUC
...........(((.....)))..((((((....((((((((((((((.((...........)).))))))-))))))))......)))))). ( -27.20)
>DroYak_CAF1 5976 92 + 1
UUAUAACCAAUCGUUAAGUGCGAUACCAGUGAACCUAGGCCUAUCAAUGCAAUAAGAAUGAUUAGGUUGAU-AGGUUUAACUAUCAGCUGGUU
.........(((((.....)))))((((((((...(((((((((((((..(((.......)))..))))))-)))))))....))).))))). ( -26.50)
>consensus
UUAUAACUAAUCGUUAAGAGCGAUAGCAGUGAACUUAAGUCUAUCAAUACGAUAAGAAUGAUUGGGUUGAU_AGGUUUAACUAGCAGCUGGUG
.....(((((((((.....)))))....((....((((((((((((((.((((.......)))).)))))).))))))))...))...)))). (-16.06 = -16.18 +   0.12)

alignment

secondary structure

dotplot

Window 7

Location	7,510,199 – 7,510,318
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.79
Mean single sequence MFE	-31.58
Consensus MFE	-20.26
Energy contribution	-21.22
Covariance contribution	0.96
Combinations/Pair	1.21
Mean z-score	-2.22
Structure conservation index	0.64
SVM decision value	0.12
SVM RNA-class probability	0.595447
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7510199 119 + 27905053
UUAAGAGCGAUAGCCGUGAACUUAAGUCUAUCAAUACCAUAAGAAUAAUUGGGUUGAU-AGGUGUAACUAGCAGCUGGUGGUCUUUAUCAGUUUCUCUCUUCUUGAUUAGAAGAAUUGAU
..((((.((.((((.((....(((..(((((((((.(((..........)))))))))-)))..)))...)).)))).)).)))).((((((.....((((((.....)))))))))))) ( -30.70)
>DroSec_CAF1 5918 120 + 1
UUAAGUGCGAUAGCCGUGAACUUAAGUCUAUCAAUACGAUUCGAAUGAUUGGGUUGAUUAGGUUUAACUAGCAGCUGGUGUUCUUUAUCAGUUACUGUCUUCUUGAUUAGAAGAAUUGAG
(((((((((.....)))..))))))...........((((((...((((..((..(((.(((((.....)))((((((((.....)))))))).)))))..))..))))...)))))).. ( -28.20)
>DroSim_CAF1 6260 120 + 1
UUAAGAGCGAUAGCAGUGAACUUAAGUCUAUCAAUACGAUAAGAAUGAUUGGGUUGAUUAGAUUUAACUAGCAGCUGGUGUUCUUUAUCAGUUACUGUCUUCUUGAUUAGAAGAAUUGAG
..(((((((.((((.((....(((((((((((((..((((.......))))..)))).)))))))))...)).)))).)))))))..(((((.....((((((.....))))))))))). ( -32.70)
>DroEre_CAF1 5967 118 + 1
CUUAGAGCGAUACCAGUGAACUUAAGUCUAUCAAUGUGAUAAGAAUGACUAGGUUGAU-AGGCUUAACCAGCAACUGGUC-UUUUUAUCAGUUUCUGUGUUCUUGAUUAGAAGAAUUGCU
.....((((((.(((((....((((((((((((((.((...........)).))))))-))))))))......)))))((-((((.(((((...........))))).)))))))))))) ( -33.80)
>DroYak_CAF1 5989 118 + 1
UUAAGUGCGAUACCAGUGAACCUAGGCCUAUCAAUGCAAUAAGAAUGAUUAGGUUGAU-AGGUUUAACUAUCAGCUGGUU-UCUUUAUCAGUUUCUGUGUUCUUCAUUAGAAGAAUUGCU
......((((.((((((((...(((((((((((((..(((.......)))..))))))-)))))))....))).))))).-))...............(((((((....))))))).)). ( -32.50)
>consensus
UUAAGAGCGAUAGCAGUGAACUUAAGUCUAUCAAUACGAUAAGAAUGAUUGGGUUGAU_AGGUUUAACUAGCAGCUGGUG_UCUUUAUCAGUUUCUGUCUUCUUGAUUAGAAGAAUUGAU
.......((((..........((((((((((((((.((((.......)))).)))))).)))))))).(((.((((((((.....)))))))).)))((((((.....)))))))))).. (-20.26 = -21.22 +   0.96)

alignment

secondary structure

dotplot

Window 8

Location	7,510,239 – 7,510,358
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.53
Mean single sequence MFE	-30.65
Consensus MFE	-17.14
Energy contribution	-18.26
Covariance contribution	1.12
Combinations/Pair	1.19
Mean z-score	-2.42
Structure conservation index	0.56
SVM decision value	0.69
SVM RNA-class probability	0.824512
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7510239 119 + 27905053
AAGAAUAAUUGGGUUGAU-AGGUGUAACUAGCAGCUGGUGGUCUUUAUCAGUUUCUCUCUUCUUGAUUAGAAGAAUUGAUUGUUGCCAUCAGCCGGAAAUUUAUCUUUUUGUCCAAUCUA
.......((((((..((.-(((((.........(((((((((....((((((.....((((((.....))))))))))))....)))))))))........))))).))..))))))... ( -32.83)
>DroSec_CAF1 5958 120 + 1
UCGAAUGAUUGGGUUGAUUAGGUUUAACUAGCAGCUGGUGUUCUUUAUCAGUUACUGUCUUCUUGAUUAGAAGAAUUGAGUGUAACCACCAGUCUGAAGUGUAUCUUUUUGUCUAAUCUA
......(((((((..((..((((...(((..(((((((((.......(((((.....((((((.....))))))))))).......)))))).))).)))..)))).))..))))))).. ( -32.24)
>DroSim_CAF1 6300 120 + 1
AAGAAUGAUUGGGUUGAUUAGAUUUAACUAGCAGCUGGUGUUCUUUAUCAGUUACUGUCUUCUUGAUUAGAAGAAUUGAGUUUAACCACCAGUCUGAAGAGUAUCUUUUUGUUUAAUCUA
.(((..((((((..((.((((((((((.(((.((((((((.....)))))))).)))((((((.....)))))).)))))))))).)))))))).((((((...))))))......))). ( -30.10)
>DroEre_CAF1 6007 117 + 1
AAGAAUGACUAGGUUGAU-AGGCUUAACCAGCAACUGGUC-UUUUUAUCAGUUUCUGUGUUCUUGAUUAGAAGAAUUGCUGGUUACCAUCAGUUUGACAUGCAUAUUUCUGUUU-UUCUA
.((((.(((.(((.((((-.((..((((((((((....((-((((.(((((...........))))).)))))).))))))))))))))))((.......)).....)))))).-)))). ( -29.10)
>DroYak_CAF1 6029 118 + 1
AAGAAUGAUUAGGUUGAU-AGGUUUAACUAUCAGCUGGUU-UCUUUAUCAGUUUCUGUGUUCUUCAUUAGAAGAAUUGCUGGUUACCUCUAGUCUGACACGUAUCUUUAUCUUUAAUCUA
......((((((((((((-((......)))))))).(((.-.....((((((......(((((((....))))))).)))))).))).)))))).......................... ( -29.00)
>consensus
AAGAAUGAUUGGGUUGAU_AGGUUUAACUAGCAGCUGGUG_UCUUUAUCAGUUUCUGUCUUCUUGAUUAGAAGAAUUGAUUGUUACCACCAGUCUGAAAUGUAUCUUUUUGUUUAAUCUA
......(((((((((((......))))))..(((((((((.......(((((.....((((((.....))))))))))).......)))))).))).................))))).. (-17.14 = -18.26 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:07 2006