Locus 3059

Sequence ID	3R_DroMel_CAF1
Location	8,097,559 – 8,097,792
Length	233
Max. P	0.972622

overview

Window 9

Location	8,097,559 – 8,097,672
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.34
Mean single sequence MFE	-22.26
Consensus MFE	-19.42
Energy contribution	-19.02
Covariance contribution	-0.40
Combinations/Pair	1.08
Mean z-score	-1.33
Structure conservation index	0.87
SVM decision value	0.36
SVM RNA-class probability	0.704367
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8097559 113 + 27905053
UUCUGCAAUGCUGCAGCCAUUAAUCAAGUUAACAAUUAGGCAUUUAGCAG-------UCAGCUAAUCAAAUUUGCAGCAUAUGCGUUAAAUACCACAUAAAGUUUUAUUGGACCAUCGCA
....((((((((((((((....................)))..(((((..-------...))))).......)))))))).)))........(((.((((....)))))))......... ( -25.35)
>DroSec_CAF1 49221 113 + 1
UUCUGCAAAGCUGCAGCCAUUAAUCAAGUUAACAAUUAGACAUUUAGCAG-------UCAGCUAAUCAAAUUUGCAGCAUAUGCGUUAAACGCCACAUAAAGUUUUAUUGGACCAUCGCA
.........(((((((...........(((........)))..(((((..-------...)))))......)))))))...((((.......(((.((((....))))))).....)))) ( -21.70)
>DroSim_CAF1 21310 113 + 1
UUCUGCAAAGCUGCAGCCAUUAAUCAAGUUAACAAUUAGGCAUUUAGCAG-------UCAGCUAAUCAAAUUUGCAGCAUAUGCGUUAAAUACCACAUAAAGUUUUAUUGGACCAUCGCA
....((...(((((((((....................)))..(((((..-------...))))).......))))))..(((.(((.((((..((.....))..)))).)))))).)). ( -23.35)
>DroEre_CAF1 24302 113 + 1
UUCUGCAAAGCUGCAACCAUUAAUCAAGUUAACAAUUAGGCAUUUAGCAG-------UCAGCUAAUCAAAUUUGCAGCAUAUGCGUUAAAUACCACAUAAAGUUUUAUUGGACCAUCGCA
....((...(((((((...........(((........)))..(((((..-------...)))))......)))))))..(((.(((.((((..((.....))..)))).)))))).)). ( -20.90)
>DroYak_CAF1 17669 120 + 1
UUCUGCAAAGCUGCAACCAUUAAUCAAGUUAACAAUUAGGCAUUUAGCAGUCAGCAGUCAGCUAAUCAAAUUUGCAGCAUAUGCGUUAAAUACCACAUAAAGUUUUAUUGGACCAUCGCC
....((...(((((((......................(((........)))(((.....)))........)))))))..(((.(((.((((..((.....))..)))).)))))).)). ( -20.00)
>consensus
UUCUGCAAAGCUGCAGCCAUUAAUCAAGUUAACAAUUAGGCAUUUAGCAG_______UCAGCUAAUCAAAUUUGCAGCAUAUGCGUUAAAUACCACAUAAAGUUUUAUUGGACCAUCGCA
.........(((((((...........(((........)))..(((((............)))))......)))))))....(((.......(((.((((....))))))).....))). (-19.42 = -19.02 +  -0.40)

alignment

secondary structure

dotplot

Window 0

Location	8,097,559 – 8,097,672
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.34
Mean single sequence MFE	-28.15
Consensus MFE	-26.40
Energy contribution	-26.00
Covariance contribution	-0.40
Combinations/Pair	1.07
Mean z-score	-1.53
Structure conservation index	0.94
SVM decision value	1.70
SVM RNA-class probability	0.972622
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8097559 113 - 27905053
UGCGAUGGUCCAAUAAAACUUUAUGUGGUAUUUAACGCAUAUGCUGCAAAUUUGAUUAGCUGA-------CUGCUAAAUGCCUAAUUGUUAACUUGAUUAAUGGCUGCAGCAUUGCAGAA
((((((...............((((((........)))))).((((((.......(((((...-------..)))))..(((((((((......))))))..)))))))))))))))... ( -30.90)
>DroSec_CAF1 49221 113 - 1
UGCGAUGGUCCAAUAAAACUUUAUGUGGCGUUUAACGCAUAUGCUGCAAAUUUGAUUAGCUGA-------CUGCUAAAUGUCUAAUUGUUAACUUGAUUAAUGGCUGCAGCUUUGCAGAA
(((((................((((((........)))))).((((((.......(((((...-------..)))))..(((((((((......))))))..))))))))).)))))... ( -26.40)
>DroSim_CAF1 21310 113 - 1
UGCGAUGGUCCAAUAAAACUUUAUGUGGUAUUUAACGCAUAUGCUGCAAAUUUGAUUAGCUGA-------CUGCUAAAUGCCUAAUUGUUAACUUGAUUAAUGGCUGCAGCUUUGCAGAA
(((((................((((((........)))))).((((((.......(((((...-------..)))))..(((((((((......))))))..))))))))).)))))... ( -29.10)
>DroEre_CAF1 24302 113 - 1
UGCGAUGGUCCAAUAAAACUUUAUGUGGUAUUUAACGCAUAUGCUGCAAAUUUGAUUAGCUGA-------CUGCUAAAUGCCUAAUUGUUAACUUGAUUAAUGGUUGCAGCUUUGCAGAA
(((((................((((((........)))))).(((((((..((((((((.(((-------(.((.....))......)))).).)))))))...))))))).)))))... ( -27.10)
>DroYak_CAF1 17669 120 - 1
GGCGAUGGUCCAAUAAAACUUUAUGUGGUAUUUAACGCAUAUGCUGCAAAUUUGAUUAGCUGACUGCUGACUGCUAAAUGCCUAAUUGUUAACUUGAUUAAUGGUUGCAGCUUUGCAGAA
.((((................((((((........)))))).(((((((..((((((((.((((........((.....))......)))).).)))))))...))))))).)))).... ( -27.24)
>consensus
UGCGAUGGUCCAAUAAAACUUUAUGUGGUAUUUAACGCAUAUGCUGCAAAUUUGAUUAGCUGA_______CUGCUAAAUGCCUAAUUGUUAACUUGAUUAAUGGCUGCAGCUUUGCAGAA
.((((................((((((........)))))).((((((.......(((((............)))))..(((((((((......))))))..))))))))).)))).... (-26.40 = -26.00 +  -0.40)

alignment

secondary structure

dotplot

Window 1

Location	8,097,632 – 8,097,752
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.67
Mean single sequence MFE	-31.08
Consensus MFE	-29.48
Energy contribution	-29.04
Covariance contribution	-0.44
Combinations/Pair	1.11
Mean z-score	-1.19
Structure conservation index	0.95
SVM decision value	0.37
SVM RNA-class probability	0.708640
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8097632 120 - 27905053
GCCGCAAAUUGAUAUGCACAAGUGAGCGGAGGAUAAUUUCCGUGGCUUUCAUGUUGAUUAGAAGGGGAUUAGUACAUCAUUGCGAUGGUCCAAUAAAACUUUAUGUGGUAUUUAACGCAU
(((((((((..(((((...((((..(((((((....))))))).)))).)))))..)))......((((((...((....))...))))))............))))))........... ( -31.00)
>DroSec_CAF1 49294 120 - 1
GCCGCAAAUUGAUAUGCACAAGUGAGCGGAGGAUAAUUUCCGUGGCUUUCAUGUUGAUUAGAAGGGGAUUAGUACAUUAUUGCGAUGGUCCAAUAAAACUUUAUGUGGCGUUUAACGCAU
(((((((((..(((((...((((..(((((((....))))))).)))).)))))..)))......((((((...((....))...))))))............))))))........... ( -33.40)
>DroSim_CAF1 21383 120 - 1
GCCGCAAAUUGAUAUGCACAAGUGAGCGGAGGAUAAUUUCCGUGGCUUUCAUGUUGAUUACAAGGGGAUUAGUACAUCAUUGCGAUGGUCCAAUAAAACUUUAUGUGGUAUUUAACGCAU
(((((((((..(((((...((((..(((((((....))))))).)))).)))))..)))......((((((...((....))...))))))............))))))........... ( -31.00)
>DroEre_CAF1 24375 120 - 1
GCCGCAAAUUGAUAUGCACAAGUGAGCGGAGGAUAAUUUCCGUGGCUUUCAUGUUGAUUAGAAGGGGAUUAGUACAUCAUUGCGAUGGUCCAAUAAAACUUUAUGUGGUAUUUAACGCAU
(((((((((..(((((...((((..(((((((....))))))).)))).)))))..)))......((((((...((....))...))))))............))))))........... ( -31.00)
>DroYak_CAF1 17749 120 - 1
GCCACAAAUUAAUAUGCACAAGUGAGCGAAGGAUAAUUUGCGUGGCUUUCAUGUUGAUUAGACGGGGAUUAGUACAUCAUGGCGAUGGUCCAAUAAAACUUUAUGUGGUAUUUAACGCAU
((((((((((((((((...((((.((((((......))))).).)))).))))))))))......((((.....((((.....))))))))............))))))........... ( -29.00)
>consensus
GCCGCAAAUUGAUAUGCACAAGUGAGCGGAGGAUAAUUUCCGUGGCUUUCAUGUUGAUUAGAAGGGGAUUAGUACAUCAUUGCGAUGGUCCAAUAAAACUUUAUGUGGUAUUUAACGCAU
((((((((((((((((...((((..(((((((....))))))).)))).))))))))))......((((.....((((.....))))))))............))))))........... (-29.48 = -29.04 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	8,097,672 – 8,097,792
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.17
Mean single sequence MFE	-34.36
Consensus MFE	-30.62
Energy contribution	-30.54
Covariance contribution	-0.08
Combinations/Pair	1.09
Mean z-score	-1.57
Structure conservation index	0.89
SVM decision value	1.32
SVM RNA-class probability	0.941409
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8097672 120 - 27905053
AACCCCUCGAACCUUUGAUUGGAAUCUAUUGGUGGUUUUGGCCGCAAAUUGAUAUGCACAAGUGAGCGGAGGAUAAUUUCCGUGGCUUUCAUGUUGAUUAGAAGGGGAUUAGUACAUCAU
..(((((....((.......))..(((....(((((....))))).(((..(((((...((((..(((((((....))))))).)))).)))))..)))))))))))............. ( -33.90)
>DroSec_CAF1 49334 120 - 1
AACCCCUCGAACCUUCGAUAAGAAUCUUUUGGUGGUUUUGGCCGCAAAUUGAUAUGCACAAGUGAGCGGAGGAUAAUUUCCGUGGCUUUCAUGUUGAUUAGAAGGGGAUUAGUACAUUAU
..((((((((....))))......(((....(((((....))))).(((..(((((...((((..(((((((....))))))).)))).)))))..)))))).))))............. ( -33.80)
>DroSim_CAF1 21423 120 - 1
AACCCCUCGAACCUUCGAUAAGAAUCUUUUGGUGGUUUUGGCCGCAAAUUGAUAUGCACAAGUGAGCGGAGGAUAAUUUCCGUGGCUUUCAUGUUGAUUACAAGGGGAUUAGUACAUCAU
..((((((((....))))..........((((((((....))))).(((..(((((...((((..(((((((....))))))).)))).)))))..))).)))))))............. ( -34.20)
>DroEre_CAF1 24415 120 - 1
AGCCCCUCGAACCAUCGAUAAGAAUCUAUUGGUGGGUUUGGCCGCAAAUUGAUAUGCACAAGUGAGCGGAGGAUAAUUUCCGUGGCUUUCAUGUUGAUUAGAAGGGGAUUAGUACAUCAU
..((((((((((((((((((......))))))).))))))......(((..(((((...((((..(((((((....))))))).)))).)))))..)))...)))))............. ( -37.20)
>DroYak_CAF1 17789 120 - 1
AACCCCUCGAACCUUCGAUAAGAAUCUAUUGGUGGUUUUGGCCACAAAUUAAUAUGCACAAGUGAGCGAAGGAUAAUUUGCGUGGCUUUCAUGUUGAUUAGACGGGGAUUAGUACAUCAU
..((((((((....))))......(((....(((((....))))).((((((((((...((((.((((((......))))).).)))).))))))))))))).))))............. ( -32.70)
>consensus
AACCCCUCGAACCUUCGAUAAGAAUCUAUUGGUGGUUUUGGCCGCAAAUUGAUAUGCACAAGUGAGCGGAGGAUAAUUUCCGUGGCUUUCAUGUUGAUUAGAAGGGGAUUAGUACAUCAU
..((((((((....)))).............(((((....))))).((((((((((...((((..(((((((....))))))).)))).))))))))))....))))............. (-30.62 = -30.54 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:50 2006