Locus 4385

Sequence ID	3L_DroMel_CAF1
Location	12,858,164 – 12,858,296
Length	132
Max. P	0.999176

overview

Window 2

Location	12,858,164 – 12,858,270
Length	106
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	94.91
Mean single sequence MFE	-32.66
Consensus MFE	-26.68
Energy contribution	-26.84
Covariance contribution	0.16
Combinations/Pair	1.09
Mean z-score	-1.75
Structure conservation index	0.82
SVM decision value	0.75
SVM RNA-class probability	0.841801
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12858164 106 + 23771897
GGCUGACCACUCGAUGUUGGCCAUGAGUUGACCCAACAUUUAUUUGAUUUGGUCAGUAUGAAUGCUUCCGUUCUUGGUCUGCCGUUGAUGCUGAUUGAGUGCAUUU
(((..((........))..)))....((((...)))).......(((((..((((((((.(((((..(((....)))...).)))).))))))))..))).))... ( -32.20)
>DroSec_CAF1 96602 106 + 1
GGCUGACCACUCGGUAGUGGCCAUCAGUUGACCCAACAUUUAUUUGAUUUGGUCAGUAUGAAUGCUUCCGUUCUUGGUCUGCCGUUGAUGCUGAUUGAGUGCAUUU
(((.(((((..(((.((((..(((...((((((.((((......)).)).)))))).)))..)))).)))....))))).)))...(((((.........))))). ( -32.30)
>DroSim_CAF1 97993 106 + 1
GGCUGACCACUCGGCAGUGGCCAUCAGUUGACCCAACAUUUAUUUGAUUUGGUCAGUAUGAAUGCUUCCGUUCUUGGUCUGCCGUUGAUGCUGAUUGAGUGCAUUU
(((.(((((..(((.((((..(((...((((((.((((......)).)).)))))).)))..)))).)))....))))).)))...(((((.........))))). ( -32.30)
>DroEre_CAF1 101871 106 + 1
CCCUGACCACUCGGUAGUGGCCAUCAGUUGACCCAACAUUUAUUUGAUUUGGUCAGUAUGAAUGUUUCUGGGCUUGGUCUGCCGUUGAUGCUGAUUGAGUGCAUUU
.......((((((((...(((.(((((....(((((((((((((((((...))))).))))))))...))))...((....)).)))))))).))))))))..... ( -30.00)
>DroYak_CAF1 107993 106 + 1
GGCUGACCACUCGGUAGUGGCCAUCAGUUGACCCAACAUUUAUUUGAUUUGGUCAGUAUGAAUGUUGCUGGUCUUGGUCUGCCGUUGAUGCUGAUUGAGUGCAUUU
(((.(((((...(((....))).......(((((((((((((((((((...))))).))))))))))..)))).))))).)))...(((((.........))))). ( -36.50)
>consensus
GGCUGACCACUCGGUAGUGGCCAUCAGUUGACCCAACAUUUAUUUGAUUUGGUCAGUAUGAAUGCUUCCGUUCUUGGUCUGCCGUUGAUGCUGAUUGAGUGCAUUU
(((((((((((....)))))...))))))...............(((((..((((((((.(((((..(((....)))...).)))).))))))))..))).))... (-26.68 = -26.84 +   0.16)

alignment

secondary structure

dotplot

Window 3

Location	12,858,164 – 12,858,270
Length	106
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	94.91
Mean single sequence MFE	-26.60
Consensus MFE	-21.76
Energy contribution	-22.32
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.04
Structure conservation index	0.82
SVM decision value	1.36
SVM RNA-class probability	0.946322
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12858164 106 - 23771897
AAAUGCACUCAAUCAGCAUCAACGGCAGACCAAGAACGGAAGCAUUCAUACUGACCAAAUCAAAUAAAUGUUGGGUCAACUCAUGGCCAACAUCGAGUGGUCAGCC
..((((.........))))....(((.((((..((((....)..)))....(((((....((......))...)))))(((((((.....))).)))))))).))) ( -25.60)
>DroSec_CAF1 96602 106 - 1
AAAUGCACUCAAUCAGCAUCAACGGCAGACCAAGAACGGAAGCAUUCAUACUGACCAAAUCAAAUAAAUGUUGGGUCAACUGAUGGCCACUACCGAGUGGUCAGCC
..((((.........))))....(((.(((((....(((.((...((((..(((((....((......))...)))))....))))...)).)))..))))).))) ( -26.40)
>DroSim_CAF1 97993 106 - 1
AAAUGCACUCAAUCAGCAUCAACGGCAGACCAAGAACGGAAGCAUUCAUACUGACCAAAUCAAAUAAAUGUUGGGUCAACUGAUGGCCACUGCCGAGUGGUCAGCC
..((((.........))))....(((.(((((....(((..((..(((...(((((....((......))...)))))..)))..)).....)))..))))).))) ( -26.50)
>DroEre_CAF1 101871 106 - 1
AAAUGCACUCAAUCAGCAUCAACGGCAGACCAAGCCCAGAAACAUUCAUACUGACCAAAUCAAAUAAAUGUUGGGUCAACUGAUGGCCACUACCGAGUGGUCAGGG
.......(((.(((((.......(((.......)))...............(((((....((......))...))))).)))))(((((((....))))))).))) ( -26.20)
>DroYak_CAF1 107993 106 - 1
AAAUGCACUCAAUCAGCAUCAACGGCAGACCAAGACCAGCAACAUUCAUACUGACCAAAUCAAAUAAAUGUUGGGUCAACUGAUGGCCACUACCGAGUGGUCAGCC
..((((.........))))....(((.......((((..(((((((.((..(((.....))).)).)))))))))))......((((((((....))))))))))) ( -28.30)
>consensus
AAAUGCACUCAAUCAGCAUCAACGGCAGACCAAGAACGGAAGCAUUCAUACUGACCAAAUCAAAUAAAUGUUGGGUCAACUGAUGGCCACUACCGAGUGGUCAGCC
..((((.........))))....(((.((((.........((((((.((..(((.....))).)).)))))).))))......((((((((....))))))))))) (-21.76 = -22.32 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	12,858,190 – 12,858,296
Length	106
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	95.99
Mean single sequence MFE	-27.78
Consensus MFE	-25.76
Energy contribution	-25.28
Covariance contribution	-0.48
Combinations/Pair	1.07
Mean z-score	-2.21
Structure conservation index	0.93
SVM decision value	3.42
SVM RNA-class probability	0.999176
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12858190 106 + 23771897
GUUGACCCAACAUUUAUUUGAUUUGGUCAGUAUGAAUGCUUCCGUUCUUGGUCUGCCGUUGAUGCUGAUUGAGUGCAUUUUAGCUUUCAAUAACAAAAAUGUUGCU
.......((((((((..((((((..((((((((.(((((..(((....)))...).)))).))))))))..)))((......)).........))))))))))).. ( -28.90)
>DroSec_CAF1 96628 104 + 1
GUUGACCCAACAUUUAUUUGAUUUGGUCAGUAUGAAUGCUUCCGUUCUUGGUCUGCCGUUGAUGCUGAUUGAGUGCAUUUUAGCUUUCAAUAACA--AAUGUUGCU
.......((((((((..((((((..((((((((.(((((..(((....)))...).)))).))))))))..)))((......))...)))....)--))))))).. ( -28.60)
>DroSim_CAF1 98019 104 + 1
GUUGACCCAACAUUUAUUUGAUUUGGUCAGUAUGAAUGCUUCCGUUCUUGGUCUGCCGUUGAUGCUGAUUGAGUGCAUUUUAGCUUUCAAUAACA--AAUGUUGCU
.......((((((((..((((((..((((((((.(((((..(((....)))...).)))).))))))))..)))((......))...)))....)--))))))).. ( -28.60)
>DroEre_CAF1 101897 104 + 1
GUUGACCCAACAUUUAUUUGAUUUGGUCAGUAUGAAUGUUUCUGGGCUUGGUCUGCCGUUGAUGCUGAUUGAGUGCAUUUAAGCUUUCAAUAACA--AAUGUUGCU
.......((((((((..((((((..((((((((.(((.......(((.......)))))).))))))))..)))((......))...)))....)--))))))).. ( -26.01)
>DroYak_CAF1 108019 104 + 1
GUUGACCCAACAUUUAUUUGAUUUGGUCAGUAUGAAUGUUGCUGGUCUUGGUCUGCCGUUGAUGCUGAUUGAGUGCAUUUUAGCUUUCAAUAACA--AAUGUUGUU
((((((((((((((((((((((...))))).))))))))))..))))..((....))(((((.(((((.((....))..)))))..)))))))).--......... ( -26.80)
>consensus
GUUGACCCAACAUUUAUUUGAUUUGGUCAGUAUGAAUGCUUCCGUUCUUGGUCUGCCGUUGAUGCUGAUUGAGUGCAUUUUAGCUUUCAAUAACA__AAUGUUGCU
.......(((((((....(((((..((((((((.(((((..(((....)))...).)))).))))))))..)))((......)).........))..))))))).. (-25.76 = -25.28 +  -0.48)

alignment

secondary structure

dotplot

Window 5

Location	12,858,190 – 12,858,296
Length	106
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	95.99
Mean single sequence MFE	-20.39
Consensus MFE	-16.37
Energy contribution	-16.37
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.02
Structure conservation index	0.80
SVM decision value	0.82
SVM RNA-class probability	0.859343
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12858190 106 - 23771897
AGCAACAUUUUUGUUAUUGAAAGCUAAAAUGCACUCAAUCAGCAUCAACGGCAGACCAAGAACGGAAGCAUUCAUACUGACCAAAUCAAAUAAAUGUUGGGUCAAC
..((((((((.(((((((((..((......))..))))).)))).....(((((........(....)........))).)).........))))))))....... ( -20.19)
>DroSec_CAF1 96628 104 - 1
AGCAACAUU--UGUUAUUGAAAGCUAAAAUGCACUCAAUCAGCAUCAACGGCAGACCAAGAACGGAAGCAUUCAUACUGACCAAAUCAAAUAAAUGUUGGGUCAAC
..(((((((--(((((((((..((......))..)))))..........(((((........(....)........))).))......)))))))))))....... ( -20.99)
>DroSim_CAF1 98019 104 - 1
AGCAACAUU--UGUUAUUGAAAGCUAAAAUGCACUCAAUCAGCAUCAACGGCAGACCAAGAACGGAAGCAUUCAUACUGACCAAAUCAAAUAAAUGUUGGGUCAAC
..(((((((--(((((((((..((......))..)))))..........(((((........(....)........))).))......)))))))))))....... ( -20.99)
>DroEre_CAF1 101897 104 - 1
AGCAACAUU--UGUUAUUGAAAGCUUAAAUGCACUCAAUCAGCAUCAACGGCAGACCAAGCCCAGAAACAUUCAUACUGACCAAAUCAAAUAAAUGUUGGGUCAAC
..(((((((--((((.((((..((......))..))))((((.......(((.......)))..((.....))...))))........)))))))))))....... ( -20.40)
>DroYak_CAF1 108019 104 - 1
AACAACAUU--UGUUAUUGAAAGCUAAAAUGCACUCAAUCAGCAUCAACGGCAGACCAAGACCAGCAACAUUCAUACUGACCAAAUCAAAUAAAUGUUGGGUCAAC
.........--(((((((((..((......))..))))).)))).....((....))..((((..(((((((.((..(((.....))).)).)))))))))))... ( -19.40)
>consensus
AGCAACAUU__UGUUAUUGAAAGCUAAAAUGCACUCAAUCAGCAUCAACGGCAGACCAAGAACGGAAGCAUUCAUACUGACCAAAUCAAAUAAAUGUUGGGUCAAC
..(((((((..(((((((((..((......))..))))).)))).....(((((......................))).))..........)))))))....... (-16.37 = -16.37 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:16 2006