Locus 1199

Sequence ID	3L_DroMel_CAF1
Location	3,383,505 – 3,383,689
Length	184
Max. P	0.999986

overview

Window 4

Location	3,383,505 – 3,383,611
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.97
Mean single sequence MFE	-37.66
Consensus MFE	-36.08
Energy contribution	-36.48
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.98
Structure conservation index	0.96
SVM decision value	5.42
SVM RNA-class probability	0.999986
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3383505 106 + 23771897
ACUGUUUGUAAUUCGCGUUGAGCGCGCGAAUUAUGAUUGAAUAAUGAAAUGCCCCAAUGGGCAAU--------------GGGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAAC
....((((((((((((((.....)))))))))((((((((.........(((((....)))))..--------------.......(((((((.....)))))))))))))))))))).. ( -37.50)
>DroSec_CAF1 50969 106 + 1
ACUGUUUGUAAUUCGCGUUGAGCGCGCGAAUUAUGAUUGAAUAAUGAAAUGCCCCAAUGGGCAAU--------------GGGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAAC
....((((((((((((((.....)))))))))((((((((.........(((((....)))))..--------------.......(((((((.....)))))))))))))))))))).. ( -37.50)
>DroSim_CAF1 49129 106 + 1
ACUGUUUGUAAUUCGCGUUGAGCGCGCGAAUUAUGAUUGAAUAAUGAAAUGCCCCAAUGGGCAAU--------------GGGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAAC
....((((((((((((((.....)))))))))((((((((.........(((((....)))))..--------------.......(((((((.....)))))))))))))))))))).. ( -37.50)
>DroEre_CAF1 49932 113 + 1
ACUGCUUGUAAUUCGCGUUGAGCGCGCGAAUUAUGAUUGAAUAAUGAAAUGCCCCAAUGGGC-------AAUGGGUAAUGGGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAAC
..(((..(((((((((((.....)))))))))))((((((.........(((((....))))-------)................(((((((.....)))))))))))))..))).... ( -37.90)
>DroYak_CAF1 49902 120 + 1
ACUGUUUGUAAUUCGCGUUGAGCGCGCGAAUUAUGAUUGAAUAAUGAAAUGCCCCAAUGGGCAAUGGGCAAUGGGUAAUGGGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAAC
....((((((((((((((.....)))))))))((((((((.........(((((....)))))....((.((.....))..))...(((((((.....)))))))))))))))))))).. ( -37.90)
>consensus
ACUGUUUGUAAUUCGCGUUGAGCGCGCGAAUUAUGAUUGAAUAAUGAAAUGCCCCAAUGGGCAAU______________GGGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAAC
....((((((((((((((.....)))))))))((((((((.........(((((....))))).......................(((((((.....)))))))))))))))))))).. (-36.08 = -36.48 +   0.40)

alignment

secondary structure

dotplot

Window 5

Location	3,383,505 – 3,383,611
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.97
Mean single sequence MFE	-30.52
Consensus MFE	-29.46
Energy contribution	-29.30
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-2.28
Structure conservation index	0.97
SVM decision value	4.23
SVM RNA-class probability	0.999842
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3383505 106 - 23771897
GUUUUGCAUAAUUGAAGGCAGCGACUGACUGCCCAUUGCCC--------------AUUGCCCAUUGGGGCAUUUCAUUAUUCAAUCAUAAUUCGCGCGCUCAACGCGAAUUACAAACAGU
((((((.(((((.((((((((.......)))))........--------------..(((((....))))).)))))))).))....(((((((((.......))))))))).))))... ( -30.00)
>DroSec_CAF1 50969 106 - 1
GUUUUGCAUAAUUGAAGGCAGCGACUGACUGCCCAUUGCCC--------------AUUGCCCAUUGGGGCAUUUCAUUAUUCAAUCAUAAUUCGCGCGCUCAACGCGAAUUACAAACAGU
((((((.(((((.((((((((.......)))))........--------------..(((((....))))).)))))))).))....(((((((((.......))))))))).))))... ( -30.00)
>DroSim_CAF1 49129 106 - 1
GUUUUGCAUAAUUGAAGGCAGCGACUGACUGCCCAUUGCCC--------------AUUGCCCAUUGGGGCAUUUCAUUAUUCAAUCAUAAUUCGCGCGCUCAACGCGAAUUACAAACAGU
((((((.(((((.((((((((.......)))))........--------------..(((((....))))).)))))))).))....(((((((((.......))))))))).))))... ( -30.00)
>DroEre_CAF1 49932 113 - 1
GUUUUGCAUAAUUGAAGGCAGCGACUGACUGCCCAUUGCCCAUUACCCAUU-------GCCCAUUGGGGCAUUUCAUUAUUCAAUCAUAAUUCGCGCGCUCAACGCGAAUUACAAGCAGU
...((((...(((((((((((.......))))).................(-------((((....)))))........))))))..(((((((((.......)))))))))...)))). ( -32.60)
>DroYak_CAF1 49902 120 - 1
GUUUUGCAUAAUUGAAGGCAGCGACUGACUGCCCAUUGCCCAUUACCCAUUGCCCAUUGCCCAUUGGGGCAUUUCAUUAUUCAAUCAUAAUUCGCGCGCUCAACGCGAAUUACAAACAGU
((((((.(((((.((((((((.......)))))........................(((((....))))).)))))))).))....(((((((((.......))))))))).))))... ( -30.00)
>consensus
GUUUUGCAUAAUUGAAGGCAGCGACUGACUGCCCAUUGCCC______________AUUGCCCAUUGGGGCAUUUCAUUAUUCAAUCAUAAUUCGCGCGCUCAACGCGAAUUACAAACAGU
((((((.(((((.((((((((.......))))).........................((((....))))..)))))))).))....(((((((((.......))))))))).))))... (-29.46 = -29.30 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	3,383,545 – 3,383,651
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.32
Mean single sequence MFE	-28.10
Consensus MFE	-26.30
Energy contribution	-26.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	0.94
SVM decision value	1.36
SVM RNA-class probability	0.946320
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3383545 106 + 23771897
AUAAUGAAAUGCCCCAAUGGGCAAU--------------GGGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAACGGUUACUGCACUUUGCAUUAAUUAACAAACGGGCAAACAA
.........(((((....))))).(--------------(.((...(((((((.....)))))))..(((((((((((...((....))..)))))).))))).........))...)). ( -27.60)
>DroSec_CAF1 51009 106 + 1
AUAAUGAAAUGCCCCAAUGGGCAAU--------------GGGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAACGGUUACUGCACUUUGCAUUAAUUAACAAACGGGCAAACAA
.........(((((....))))).(--------------(.((...(((((((.....)))))))..(((((((((((...((....))..)))))).))))).........))...)). ( -27.60)
>DroSim_CAF1 49169 106 + 1
AUAAUGAAAUGCCCCAAUGGGCAAU--------------GGGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAACGGUUACUGCACUUUGCAUUAAUUAACAAACGGGCAAACAA
.........(((((....))))).(--------------(.((...(((((((.....)))))))..(((((((((((...((....))..)))))).))))).........))...)). ( -27.60)
>DroEre_CAF1 49972 113 + 1
AUAAUGAAAUGCCCCAAUGGGC-------AAUGGGUAAUGGGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAACGGUUACUGCACUUUGCAUUAAUUAACAAACGGGCAAACAA
.........(((((...((...-------..((.(((((.......(((((((.....)))))))...))))).))....(((((.(((.....))).)))))..))...)))))..... ( -28.20)
>DroYak_CAF1 49942 120 + 1
AUAAUGAAAUGCCCCAAUGGGCAAUGGGCAAUGGGUAAUGGGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAACGGUUACUGCACUUUGCAUUAAUUAACAAACGGGCAAACAA
.........(((((....))))).((.((..((.(((((.......(((((((.....)))))))...))))).))....(((((.(((.....))).))))).........))...)). ( -29.50)
>consensus
AUAAUGAAAUGCCCCAAUGGGCAAU______________GGGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAACGGUUACUGCACUUUGCAUUAAUUAACAAACGGGCAAACAA
.........(((((...((...........................(((((((.....)))))))..(((((((((((...((....))..)))))).)))))..))...)))))..... (-26.30 = -26.30 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	3,383,571 – 3,383,689
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.65
Mean single sequence MFE	-34.25
Consensus MFE	-32.73
Energy contribution	-33.13
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.96
SVM decision value	2.57
SVM RNA-class probability	0.995387
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3383571 118 + 23771897
GGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAACGGUUACUGCACUUUGCAUUAAUUAACAAACGGGCAAACAAAGCGAAAUUCGCGCAGCUGACACAAUUUUGCACGUGCU--
((((..(((((((.....))))))).......(((((((..((((((((..(((((................)))))....(((.....))))))).))))....)))))))..))))-- ( -34.69)
>DroSec_CAF1 51035 118 + 1
GGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAACGGUUACUGCACUUUGCAUUAAUUAACAAACGGGCAAACAAAGCGAAAUUCGCGCAGCUGACACAAUUUUGCACGUGCU--
((((..(((((((.....))))))).......(((((((..((((((((..(((((................)))))....(((.....))))))).))))....)))))))..))))-- ( -34.69)
>DroSim_CAF1 49195 118 + 1
GGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAACGGUUACUGCACUUUGCAUUAAUUAACAAACGGGCAAACAAAGCGAAAUUCGCGCAGCUGACACAAUUUUGCACGUGCU--
((((..(((((((.....))))))).......(((((((..((((((((..(((((................)))))....(((.....))))))).))))....)))))))..))))-- ( -34.69)
>DroEre_CAF1 50005 118 + 1
GGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAACGGUUACUGCACUUUGCAUUAAUUAACAAACGGGCAAACAAAGCGAAAUUGCCGCAGCUGACACAAUUUUGCACGUGCU--
((((..(((((((.....))))))).......(((((((..((((((((..((((..........))))..(((((...........))))))))).))))....)))))))..))))-- ( -32.40)
>DroYak_CAF1 49982 120 + 1
GGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAACGGUUACUGCACUUUGCAUUAAUUAACAAACGGGCAAACAAAGCGAAAUUCGCGCAGCUGACACAAUUUUGCACGUGCUUA
((((..(((((((.....))))))).......(((((((..((((((((..(((((................)))))....(((.....))))))).))))....)))))))..)))).. ( -34.79)
>consensus
GGCAAUGGGCAGUCAGUCGCUGCCUUCAAUUAUGCAAAACGGUUACUGCACUUUGCAUUAAUUAACAAACGGGCAAACAAAGCGAAAUUCGCGCAGCUGACACAAUUUUGCACGUGCU__
((((..(((((((.....))))))).......(((((((..((((((((..(((((................)))))....(((.....))))))).))))....)))))))..)))).. (-32.73 = -33.13 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	3,383,571 – 3,383,689
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.65
Mean single sequence MFE	-34.42
Consensus MFE	-33.12
Energy contribution	-33.32
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.31
Structure conservation index	0.96
SVM decision value	0.44
SVM RNA-class probability	0.736946
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3383571 118 - 23771897
--AGCACGUGCAAAAUUGUGUCAGCUGCGCGAAUUUCGCUUUGUUUGCCCGUUUGUUAAUUAAUGCAAAGUGCAGUAACCGUUUUGCAUAAUUGAAGGCAGCGACUGACUGCCCAUUGCC
--.(((.(((((((((.((....(((((((.......((.......))...(((((........)))))))))))).)).))))))))).......(((((.......)))))...))). ( -34.30)
>DroSec_CAF1 51035 118 - 1
--AGCACGUGCAAAAUUGUGUCAGCUGCGCGAAUUUCGCUUUGUUUGCCCGUUUGUUAAUUAAUGCAAAGUGCAGUAACCGUUUUGCAUAAUUGAAGGCAGCGACUGACUGCCCAUUGCC
--.(((.(((((((((.((....(((((((.......((.......))...(((((........)))))))))))).)).))))))))).......(((((.......)))))...))). ( -34.30)
>DroSim_CAF1 49195 118 - 1
--AGCACGUGCAAAAUUGUGUCAGCUGCGCGAAUUUCGCUUUGUUUGCCCGUUUGUUAAUUAAUGCAAAGUGCAGUAACCGUUUUGCAUAAUUGAAGGCAGCGACUGACUGCCCAUUGCC
--.(((.(((((((((.((....(((((((.......((.......))...(((((........)))))))))))).)).))))))))).......(((((.......)))))...))). ( -34.30)
>DroEre_CAF1 50005 118 - 1
--AGCACGUGCAAAAUUGUGUCAGCUGCGGCAAUUUCGCUUUGUUUGCCCGUUUGUUAAUUAAUGCAAAGUGCAGUAACCGUUUUGCAUAAUUGAAGGCAGCGACUGACUGCCCAUUGCC
--.(((.(((((((((.((....((((((((((...........)))))..(((((........)))))..))))).)).))))))))).......(((((.......)))))...))). ( -34.90)
>DroYak_CAF1 49982 120 - 1
UAAGCACGUGCAAAAUUGUGUCAGCUGCGCGAAUUUCGCUUUGUUUGCCCGUUUGUUAAUUAAUGCAAAGUGCAGUAACCGUUUUGCAUAAUUGAAGGCAGCGACUGACUGCCCAUUGCC
...(((.(((((((((.((....(((((((.......((.......))...(((((........)))))))))))).)).))))))))).......(((((.......)))))...))). ( -34.30)
>consensus
__AGCACGUGCAAAAUUGUGUCAGCUGCGCGAAUUUCGCUUUGUUUGCCCGUUUGUUAAUUAAUGCAAAGUGCAGUAACCGUUUUGCAUAAUUGAAGGCAGCGACUGACUGCCCAUUGCC
...(((.(((((((((.((....(((((((.......((.......))...(((((........)))))))))))).)).))))))))).......(((((.......)))))...))). (-33.12 = -33.32 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:59 2006