Locus 9959

Sequence ID	3R_DroMel_CAF1
Location	26,682,513 – 26,682,815
Length	302
Max. P	0.959609

overview

Window 9

Location	26,682,513 – 26,682,618
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.34
Mean single sequence MFE	-25.94
Consensus MFE	-23.88
Energy contribution	-23.92
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.13
Structure conservation index	0.92
SVM decision value	0.12
SVM RNA-class probability	0.591606
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26682513 105 - 27905053
--------------AACCAGGCUUAGUUGGCAGCGCA-UAAGCCACAGAAACAAUUAUAUACCCGCUUAUCUGAGCGGCAGAUAUAGAAAAUUGAUCUGGCGAUAAAUCGAGCUACUCAA
--------------.....((((..(((....((((.-...))..((((..(((((((((..((((((....))))))...)))))....)))).))))))....)))..))))...... ( -26.00)
>DroSec_CAF1 273191 105 - 1
--------------UACCAGGCUUAGUUGGCAGCGCA-UAAGCCACAGAAACAAUUAUAUACCCGCUUAUCUGGGCGGCAGAUAUAGAAAAUUGAUCUGGCGAUAAAUCGAGCUACUCAA
--------------.....((((..(((....((((.-...))..((((..(((((((((..((((((....))))))...)))))....)))).))))))....)))..))))...... ( -25.20)
>DroSim_CAF1 269931 105 - 1
--------------AACCAGGCUUAGUUGGCAGCGCA-UAAGCCACAGAAACAAUUAUAUACCCGCUUAUCUGGGCGGCAGAUAUAGAAAAUUGAUCUGGCGAUAAAUCGAGCUACUCAA
--------------.....((((..(((....((((.-...))..((((..(((((((((..((((((....))))))...)))))....)))).))))))....)))..))))...... ( -25.20)
>DroEre_CAF1 289098 105 - 1
--------------AACCAGGCUUAGUCGGCAGCGCA-UAAGCCACAGUAACAAUUAUAUACCCGCUUAUCUGGGCGGCAGAUAUAGAAAAUUGAUCUGGCGAUAAAUCGAGCUACUCAA
--------------.....((((((..((....))..-))))))..........((((((..((((((....))))))...))))))....((((..((((..........)))).)))) ( -24.10)
>DroYak_CAF1 278089 120 - 1
GAAAAGCAGAAAAGCAGCAGGCUUAGUUGGCAGCGCAGUAAGCCACAGUAACAAUUAUAUACCCGCUUAUCUGGGCGGCAGAUAUAGAAAAUUGAUCUGGCGAUAAAUCGAGCUACUCAA
((..(((.((......((.((((((.(((......))))))))).(((...(((((((((..((((((....))))))...)))))....))))..)))))......))..)))..)).. ( -29.20)
>consensus
______________AACCAGGCUUAGUUGGCAGCGCA_UAAGCCACAGAAACAAUUAUAUACCCGCUUAUCUGGGCGGCAGAUAUAGAAAAUUGAUCUGGCGAUAAAUCGAGCUACUCAA
...................((((..(((....((((.....))..(((...(((((((((..((((((....))))))...)))))....))))..)))))....)))..))))...... (-23.88 = -23.92 +   0.04)

alignment

secondary structure

dotplot

Window 0

Location	26,682,553 – 26,682,655
Length	102
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	95.92
Mean single sequence MFE	-27.12
Consensus MFE	-25.62
Energy contribution	-25.25
Covariance contribution	-0.38
Combinations/Pair	1.10
Mean z-score	-1.45
Structure conservation index	0.94
SVM decision value	0.05
SVM RNA-class probability	0.557877
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26682553 102 - 27905053
GGCUCAGGGCAAGAAGCGAAACGAAAACCAAGACCAAAACCAGGCUUAGUUGGCAGCGCAUAAGCCACAGAAACAAUUAUAUACCCGCUUAUCUGAGCGGCA
.(((((((.....(((((.......(((.(((.((.......))))).)))(((.........)))...................))))).))))))).... ( -25.20)
>DroSec_CAF1 273231 102 - 1
GGCUCAGAGCAAGAAGCGAAACGGAAACCAGGACCAAUACCAGGCUUAGUUGGCAGCGCAUAAGCCACAGAAACAAUUAUAUACCCGCUUAUCUGGGCGGCA
.(((((((.....(((((....(....)..............((((((....((...)).))))))...................))))).))))))).... ( -27.40)
>DroSim_CAF1 269971 102 - 1
GGCUCAGAGCAAGAAGCGAAACGGAAACCAGGACCAAAACCAGGCUUAGUUGGCAGCGCAUAAGCCACAGAAACAAUUAUAUACCCGCUUAUCUGGGCGGCA
.(((((((.....(((((....(....)..............((((((....((...)).))))))...................))))).))))))).... ( -27.40)
>DroEre_CAF1 289138 102 - 1
GGCUCAGAGCAAGAAGCGAAGCGAAAACCAGGACCAAAACCAGGCUUAGUCGGCAGCGCAUAAGCCACAGUAACAAUUAUAUACCCGCUUAUCUGGGCGGCA
.(((((((((.....)).(((((.......((.......)).((((((..((....))..))))))...................))))).))))))).... ( -28.50)
>consensus
GGCUCAGAGCAAGAAGCGAAACGAAAACCAGGACCAAAACCAGGCUUAGUUGGCAGCGCAUAAGCCACAGAAACAAUUAUAUACCCGCUUAUCUGGGCGGCA
.(((((((.....(((((....(....)..............((((((....((...)).))))))...................))))).))))))).... (-25.62 = -25.25 +  -0.38)

alignment

secondary structure

dotplot

Window 1

Location	26,682,618 – 26,682,735
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.16
Mean single sequence MFE	-30.35
Consensus MFE	-26.98
Energy contribution	-26.58
Covariance contribution	-0.40
Combinations/Pair	1.17
Mean z-score	-1.61
Structure conservation index	0.89
SVM decision value	1.50
SVM RNA-class probability	0.959609
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26682618 117 + 27905053
---UUGGUCUUGGUUUUCGUUUCGCUUCUUGCCCUGAGCCUUACUUAGUAGCUUAAGUUCUGCUUAACUUACUUUAGUGGGCAAAUGGCAAAUUUUAGGCGGAAAAUUCUACGAAAUUCU
---........(..(((((((((((((.(((((.(..((((.(((.(((((.(((((.....))))).)))))..)))))))..).))))).....))))))).......))))))..). ( -31.71)
>DroSec_CAF1 273296 117 + 1
---UUGGUCCUGGUUUCCGUUUCGCUUCUUGCUCUGAGCCUUACUUAGUACCUUAAGUUCUGCUUAACUUACUUUAGUGGGCAAAUGGCAAAUUUUCGGCGGAAAAUUCUACGAAGUUCU
---((.((.....((((((((.......(((((.(..((((.(((.((((..(((((.....)))))..))))..)))))))..).)))))......)))))))).....)).))..... ( -28.42)
>DroSim_CAF1 270036 117 + 1
---UUGGUCCUGGUUUCCGUUUCGCUUCUUGCUCUGAGCCUUACUUAGUACCUUAAGUUCUGCUUAACUUACUUUAGUGGGCAAAUGGCAAAUUUUCGGCGGAAAAUUCUACGAAGUUCU
---((.((.....((((((((.......(((((.(..((((.(((.((((..(((((.....)))))..))))..)))))))..).)))))......)))))))).....)).))..... ( -28.42)
>DroEre_CAF1 289203 117 + 1
---UUGGUCCUGGUUUUCGCUUCGCUUCUUGCUCUGAGCCUUACUUAGUUCCUUAAGUUCUGCUUAACUUACUUUAGUGGGCAAAUGGCAAAUUUGAGGCGGAAAAUUCUACGAAGUUCU
---((.((.....(((((((((((....(((((.(..((((.(((.(((...(((((.....)))))...)))..)))))))..).)))))...))))))))))).....)).))..... ( -31.20)
>DroYak_CAF1 278209 120 + 1
UGGUUGCUCCUGGUUUUCGUUUCGCUUCUUGUUCUGAGCCUUACUUAGUGCCUUAAGUUCUGCUUAACUUACUUUAGUGGGCAAAUGGCAAAUUUGAGGCGGAGAAUUCUACGAAGUUCU
.((.....)).(..((((((....((((.....(((((.....))))).((((((((((.((((...(((((....))))).....))))))))))))))))))......))))))..). ( -32.00)
>consensus
___UUGGUCCUGGUUUUCGUUUCGCUUCUUGCUCUGAGCCUUACUUAGUACCUUAAGUUCUGCUUAACUUACUUUAGUGGGCAAAUGGCAAAUUUUAGGCGGAAAAUUCUACGAAGUUCU
.......((.((((((((((((......(((((.(..((((.(((.((((..(((((.....)))))..))))..)))))))..).))))).....)))))))))...))).))...... (-26.98 = -26.58 +  -0.40)

alignment

secondary structure

dotplot

Window 2

Location	26,682,695 – 26,682,815
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.83
Mean single sequence MFE	-34.20
Consensus MFE	-28.08
Energy contribution	-28.08
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.82
SVM decision value	0.10
SVM RNA-class probability	0.584504
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26682695 120 + 27905053
GCAAAUGGCAAAUUUUAGGCGGAAAAUUCUACGAAAUUCUUUGUAUUUGCAUACACAUCCGUGGCGGCAUUGUCUUUGACGCUUAGUCGCAUAAUUUGCCAGACAAAACGGUCAUAGGAC
(((((((.((((.(((..(..((....))..).)))...))))))))))).......((((((((.(..((((((..(((.....)))(((.....))).))))))..).))))).))). ( -29.80)
>DroSec_CAF1 273373 120 + 1
GCAAAUGGCAAAUUUUCGGCGGAAAAUUCUACGAAGUUCUUUGUAUUUGCAUACACAUCCGUGGCGGCAUUGUCUUUGACGCUUAGUCGCAUAAUUUGCCAGACAAAACAGUCAUAGGAC
(((((((.((((.(((((..(((....))).)))))...))))))))))).......((((((((....((((((..(((.....)))(((.....))).))))))....))))).))). ( -33.60)
>DroSim_CAF1 270113 120 + 1
GCAAAUGGCAAAUUUUCGGCGGAAAAUUCUACGAAGUUCUUUGUAUUUGCAUACACAUCCGUGGCGGCAUUGUCUUUGACGCUUAGUCGCAUAAUUUGCCAGACAAAACGGUCAUAGGAC
(((((((.((((.(((((..(((....))).)))))...))))))))))).......((((((((.(..((((((..(((.....)))(((.....))).))))))..).))))).))). ( -35.00)
>DroEre_CAF1 289280 120 + 1
GCAAAUGGCAAAUUUGAGGCGGAAAAUUCUACGAAGUUCUUUGUAUUUGCAUACACAUCCGUGGCGGCAUUGUCUUUGACGCUUAGUCGCAUAAUUUGCCAGACAAAACGGUCAGCGGAG
((...(((((((((.(((((((.......((((((....))))))..(((...(((....)))...)))))))))).(((.....)))....)))))))))(((......))).)).... ( -32.50)
>DroYak_CAF1 278289 120 + 1
GCAAAUGGCAAAUUUGAGGCGGAGAAUUCUACGAAGUUCUUUGUAUUUGCAUACACAGCCGUGGCGGCAUUGUCUUUGCCGCUUAGUCGCAUAAUUUGCCAGACAAAACGGUCAGCGGAG
((...(((((((((....((((((((((......))))))))))...(((...(((....)))((((((.......))))))......))).)))))))))(((......))).)).... ( -40.10)
>consensus
GCAAAUGGCAAAUUUUAGGCGGAAAAUUCUACGAAGUUCUUUGUAUUUGCAUACACAUCCGUGGCGGCAUUGUCUUUGACGCUUAGUCGCAUAAUUUGCCAGACAAAACGGUCAUAGGAC
.....(((((((((....((((.......((((((....))))))..(((...(((....)))...))).................))))..)))))))))(((......)))....... (-28.08 = -28.08 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:45:44 2006