Locus 2322

Sequence ID	3R_DroMel_CAF1
Location	6,611,991 – 6,612,102
Length	111
Max. P	0.929830

overview

Window 7

Location	6,611,991 – 6,612,102
Length	111
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	89.17
Mean single sequence MFE	-28.24
Consensus MFE	-22.00
Energy contribution	-21.76
Covariance contribution	-0.24
Combinations/Pair	1.12
Mean z-score	-2.13
Structure conservation index	0.78
SVM decision value	1.20
SVM RNA-class probability	0.929830
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6611991 111 + 27905053
UAAGCAGUGUCGCA-UCAAAGAACAAGCCGGCCAAGGCCGUAUUUUCUGUAGGAAUUCCUAUGUCGAUUGCGAUCCAAGUAAAUUUACUUCAGAUGACAAUAUAAAUCUUUC
......(..(((((-((..((((.((..((((....))))..))))))(((((....)))))...)).)))))..)(((((....))))).((((..........))))... ( -25.90)
>DroSec_CAF1 5290 111 + 1
UAAGCAGUGUCGCA-UCAAAGAACAAGCCGGCCAAGGCCGCAUUUUCUGUAGGAAUUCCUAUGUCGAUUGCUAUCCAAGUAAAUUUACUUAAGAUGACAAUAUAAAUCUUUC
.......(((((((-((..((((...((.(((....)))))...))))(((((....)))))...)).))).(((.(((((....)))))..)))))))............. ( -24.60)
>DroSim_CAF1 5293 110 + 1
UAAGCAGUGUCGCA-UCAAAGAACAAGC-GGCCAUGGCCGCAUUUUCUGUAGGAAUUCCUAUGUCGAUUGCGAUCCAAGUAAAUUUACUUCAGAUGACAAUAUAAAUCUUUC
......(..(((((-((..((((...((-(((....)))))...))))(((((....)))))...)).)))))..)(((((....))))).((((..........))))... ( -29.30)
>DroEre_CAF1 5310 112 + 1
UAAGCAGUGUCGCAAUCGAAAAACAAGGUGGCUUAGGCCGACUUAUUAAUAGGAUGUCCUAUGUUGAUUGCGAUGUAAGUAAAUUUACUUCAGAUGACAAUAUAAAUCUUUC
.......((((((((((((.....(((.((((....)))).)))....(((((....))))).))))))))((.(((((....))))).))....))))............. ( -29.30)
>DroYak_CAF1 5342 112 + 1
UAAGCAGUGUCGCAAUCGAAGAAGAAGCUGGCUUAGGCCGACUUUUAUAUAGGAUGUCCUAUGUUGAUUGCGAUGUAAGUAAAUUUACUUCAGAUGACAAUAUAAAUCUUUC
.......((((((((((((...(((((.((((....)))).))))).((((((....))))))))))))))((.(((((....))))).))....))))............. ( -32.10)
>consensus
UAAGCAGUGUCGCA_UCAAAGAACAAGCCGGCCAAGGCCGAAUUUUCUGUAGGAAUUCCUAUGUCGAUUGCGAUCCAAGUAAAUUUACUUCAGAUGACAAUAUAAAUCUUUC
......(..(((((.((...........((((....))))........(((((....)))))...)).)))))..)(((((....))))).((((..........))))... (-22.00 = -21.76 +  -0.24)

alignment

secondary structure

dotplot

Window 8

Location	6,611,991 – 6,612,102
Length	111
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	89.17
Mean single sequence MFE	-28.46
Consensus MFE	-20.32
Energy contribution	-20.48
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-2.39
Structure conservation index	0.71
SVM decision value	0.72
SVM RNA-class probability	0.833315
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6611991 111 - 27905053
GAAAGAUUUAUAUUGUCAUCUGAAGUAAAUUUACUUGGAUCGCAAUCGACAUAGGAAUUCCUACAGAAAAUACGGCCUUGGCCGGCUUGUUCUUUGA-UGCGACACUGCUUA
.............((((((((.(((((....))))))))).(((.((((..((((....)))).((((....((((....)))).....))))))))-)))))))....... ( -27.50)
>DroSec_CAF1 5290 111 - 1
GAAAGAUUUAUAUUGUCAUCUUAAGUAAAUUUACUUGGAUAGCAAUCGACAUAGGAAUUCCUACAGAAAAUGCGGCCUUGGCCGGCUUGUUCUUUGA-UGCGACACUGCUUA
.............((((((((.(((((....))))))))).(((.((((..((((....)))).((((...(((((....))).))...))))))))-)))))))....... ( -28.10)
>DroSim_CAF1 5293 110 - 1
GAAAGAUUUAUAUUGUCAUCUGAAGUAAAUUUACUUGGAUCGCAAUCGACAUAGGAAUUCCUACAGAAAAUGCGGCCAUGGCC-GCUUGUUCUUUGA-UGCGACACUGCUUA
.............((((((((.(((((....))))))))).(((.((((..((((....)))).((((...(((((....)))-))...))))))))-)))))))....... ( -31.40)
>DroEre_CAF1 5310 112 - 1
GAAAGAUUUAUAUUGUCAUCUGAAGUAAAUUUACUUACAUCGCAAUCAACAUAGGACAUCCUAUUAAUAAGUCGGCCUAAGCCACCUUGUUUUUCGAUUGCGACACUGCUUA
.............((((....((.((((......)))).))((((((...(((((....))))).((((((..(((....)))..))))))....))))))))))....... ( -28.00)
>DroYak_CAF1 5342 112 - 1
GAAAGAUUUAUAUUGUCAUCUGAAGUAAAUUUACUUACAUCGCAAUCAACAUAGGACAUCCUAUAUAAAAGUCGGCCUAAGCCAGCUUCUUCUUCGAUUGCGACACUGCUUA
.............((((....((.((((......)))).))((((((...(((((....)))))....((((.(((....))).)))).......))))))))))....... ( -27.30)
>consensus
GAAAGAUUUAUAUUGUCAUCUGAAGUAAAUUUACUUGGAUCGCAAUCGACAUAGGAAUUCCUACAGAAAAUGCGGCCUUGGCCAGCUUGUUCUUUGA_UGCGACACUGCUUA
.............((((((((.(((((....))))))))).(((.((....((((....))))..........(((....)))............)).)))))))....... (-20.32 = -20.48 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:36 2006