Locus 807

Sequence ID	3L_DroMel_CAF1
Location	2,426,364 – 2,426,512
Length	148
Max. P	0.966951

overview

Window 1

Location	2,426,364 – 2,426,456
Length	92
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	92.71
Mean single sequence MFE	-33.13
Consensus MFE	-30.93
Energy contribution	-30.82
Covariance contribution	-0.11
Combinations/Pair	1.08
Mean z-score	-1.21
Structure conservation index	0.93
SVM decision value	0.75
SVM RNA-class probability	0.840856
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2426364 92 + 23771897
UGCGCCUCCGCAGGCCAUUGCCAGUCCGCUCCUGAGCGGCGGCAGCUGCUCCU---------CCUCGAC---CACCUCGCCCCAAUCCUCGCCAGCGGUUCGCA
.(((...((((.((((((((((.(.(((((....))))))))))).)).....---------...(((.---....)))...........))).))))..))). ( -31.80)
>DroSec_CAF1 59401 92 + 1
UGCGCCUCCGCAGGCCAUUGCCAGUCCGCUCAUGAGCGGCGGCAGCUGCUCCU---------CCUCGAC---CACCUCGCCCCAAUCCUCGCCAGCGGUUCGCA
.(((...((((.((((((((((.(.(((((....))))))))))).)).....---------...(((.---....)))...........))).))))..))). ( -31.80)
>DroSim_CAF1 53400 92 + 1
UGCGCCUCCGCAGGCCAUUGCCAGUCCGCUCCUGAGCGGCGGCAGCUGCUCCU---------CCUCGAC---CACCUCGCCCCAAUCCUCGCCAGCGGUUCGCA
.(((...((((.((((((((((.(.(((((....))))))))))).)).....---------...(((.---....)))...........))).))))..))). ( -31.80)
>DroEre_CAF1 53264 92 + 1
UGCGCCUCCGCAGGCCAUUGCCAGUCCGCUCCUGAGCGGCGGCAGCUGCUCCU---------CCUCGAC---CACCUCGCCCCAAUCCUCGCCAGCGGUUCGCA
.(((...((((.((((((((((.(.(((((....))))))))))).)).....---------...(((.---....)))...........))).))))..))). ( -31.80)
>DroYak_CAF1 54613 92 + 1
UGCGCCUCCGCAGGCCAUUGCCAGUCCGCUGCUGAGCGGCGGCAGCUGCUCCU---------CCUCGAC---CACCUCGCCCCAAUCCUCGCCAGCGGUUCGCA
.(((...((((.(((....((((((.....)))).))((.(((((.((.((..---------....)).---)).)).))))).......))).))))..))). ( -32.50)
>DroAna_CAF1 46581 104 + 1
UGCGCCUCCGCAGGCCACUGCCAGUCCUCUCCUGAGCGGCGGUAGCUGCACCUCGAACUCCGCCGCGACCUCCACCUCGCCCCAGUCCUCGCCAGCGGUGCGCA
.((((..((((.(((.((((.(((.......))).(((((((.((...(.....)..)))))))))................))))....))).)))).)))). ( -39.10)
>consensus
UGCGCCUCCGCAGGCCAUUGCCAGUCCGCUCCUGAGCGGCGGCAGCUGCUCCU_________CCUCGAC___CACCUCGCCCCAAUCCUCGCCAGCGGUUCGCA
.(((...((((.((((((((((.(.(((((....))))))))))).)).................(((........)))...........))).))))..))). (-30.93 = -30.82 +  -0.11)

alignment

secondary structure

dotplot

Window 2

Location	2,426,422 – 2,426,512
Length	90
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	72.45
Mean single sequence MFE	-28.64
Consensus MFE	-22.69
Energy contribution	-23.47
Covariance contribution	0.78
Combinations/Pair	1.05
Mean z-score	-1.33
Structure conservation index	0.79
SVM decision value	1.60
SVM RNA-class probability	0.966951
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2426422 90 + 23771897
AC---CACCUCGCCCCAAUCCUCGCCAGCGGUUCGCACCACCAAGGCGAGUCGUCUGCGCGCCGCCGCGCUUGGUGAGUCUCC--UCCUCCUCCU------------------
..---...((((((......((((((.(.(((....))).)...))))))......(((((....)))))..)))))).....--..........------------------ ( -28.90)
>DroGri_CAF1 56262 93 + 1
-------CCUCGCCCCAAUCCUCGCCAGCGGUGCGCACAACCAAAGCCAGUCGAUUGCGUGCCGCAGCGCUUGGUGAGUCAGCCAUAAGU----------CACUUCAUAC---
-------.((((((........(((..((((..(((((.((........)).)..))))..)))).)))...))))))............----------..........--- ( -26.30)
>DroEre_CAF1 53322 92 + 1
AC---CACCUCGCCCCAAUCCUCGCCAGCGGUUCGCACCACCAAGGCGAGUCGUCUGCGCGCCGCCGCGCUUGGUGAGUCUCC--UCCUCCUCCUCC----------------
..---...((((((......((((((.(.(((....))).)...))))))......(((((....)))))..)))))).....--............---------------- ( -28.90)
>DroYak_CAF1 54671 106 + 1
AC---CACCUCGCCCCAAUCCUCGCCAGCGGUUCGCACCACCAAGGCGAGUCGUCUGCGCGCUGCCGCGCUUGGUGAGUCUCC--UCCUCCUACUCCC--CUUUCUCCUCAAC
..---...((((((.........((..(((..((((.(......)))))..)))..))((((....))))..)))))).....--.............--............. ( -29.40)
>DroMoj_CAF1 61009 94 + 1
-------CCUCGCCCCAAUCCUCGCCAGCGGUGCGCACAACCAAAGCCAGUCGUCUGCGUGCCGCAGCGCUCGGUGAGUUAUUCAU---U---CA---AUCAUUUGAUAC---
-------.............((((((((((.(((((((.......((.((....))))))).)))).)))).))))))........---(---((---(....))))...--- ( -27.91)
>DroAna_CAF1 46648 95 + 1
ACCUCCACCUCGCCCCAGUCCUCGCCAGCGGUGCGCACCACCAAGGCGAGUCGACUACGCGCGGCCGCUCUCGGUGAGUGCCCCUUUAUCCUCCU------------------
.......((.(((...((((((((((...((((.....))))..))))))..))))..))).)).(((((.....)))))...............------------------ ( -30.40)
>consensus
AC___CACCUCGCCCCAAUCCUCGCCAGCGGUGCGCACCACCAAGGCGAGUCGUCUGCGCGCCGCCGCGCUUGGUGAGUCUCC__UCCUCCUCCU__________________
........((((((......((((((...(((.......)))..))))))......((((......))))..))))))................................... (-22.69 = -23.47 +   0.78)

alignment

secondary structure

dotplot

Window 3

Location	2,426,422 – 2,426,512
Length	90
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	72.45
Mean single sequence MFE	-35.77
Consensus MFE	-27.23
Energy contribution	-28.37
Covariance contribution	1.14
Combinations/Pair	1.09
Mean z-score	-0.71
Structure conservation index	0.76
SVM decision value	0.37
SVM RNA-class probability	0.710009
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2426422 90 - 23771897
------------------AGGAGGAGGA--GGAGACUCACCAAGCGCGGCGGCGCGCAGACGACUCGCCUUGGUGGUGCGAACCGCUGGCGAGGAUUGGGGCGAGGUG---GU
------------------........((--(....))).(((((((((....)))))......((((((..((((((....))))))))))))..)))).........---.. ( -38.80)
>DroGri_CAF1 56262 93 - 1
---GUAUGAAGUG----------ACUUAUGGCUGACUCACCAAGCGCUGCGGCACGCAAUCGACUGGCUUUGGUUGUGCGCACCGCUGGCGAGGAUUGGGGCGAGG-------
---..........----------............(((.((((.((((((((..((((..(((((......)))))))))..)))).))))....))))...))).------- ( -29.70)
>DroEre_CAF1 53322 92 - 1
----------------GGAGGAGGAGGA--GGAGACUCACCAAGCGCGGCGGCGCGCAGACGACUCGCCUUGGUGGUGCGAACCGCUGGCGAGGAUUGGGGCGAGGUG---GU
----------------..........((--(....))).(((((((((....)))))......((((((..((((((....))))))))))))..)))).........---.. ( -38.80)
>DroYak_CAF1 54671 106 - 1
GUUGAGGAGAAAG--GGGAGUAGGAGGA--GGAGACUCACCAAGCGCGGCAGCGCGCAGACGACUCGCCUUGGUGGUGCGAACCGCUGGCGAGGAUUGGGGCGAGGUG---GU
(((..........--...........((--(....))).(((((((((....)))))......((((((..((((((....))))))))))))..)))))))......---.. ( -39.50)
>DroMoj_CAF1 61009 94 - 1
---GUAUCAAAUGAU---UG---A---AUGAAUAACUCACCGAGCGCUGCGGCACGCAGACGACUGGCUUUGGUUGUGCGCACCGCUGGCGAGGAUUGGGGCGAGG-------
---...((((....)---))---)---........(((.((((.((((((((..(((..((((((......)))))))))..)))).))))....))))...))).------- ( -30.20)
>DroAna_CAF1 46648 95 - 1
------------------AGGAGGAUAAAGGGGCACUCACCGAGAGCGGCCGCGCGUAGUCGACUCGCCUUGGUGGUGCGCACCGCUGGCGAGGACUGGGGCGAGGUGGAGGU
------------------..(((............)))(((.....(.(((.(((.(((((..((((((..((((((....)))))))))))))))).).))).))).).))) ( -37.60)
>consensus
__________________AGGAGGAGGA__GGAGACUCACCAAGCGCGGCGGCGCGCAGACGACUCGCCUUGGUGGUGCGAACCGCUGGCGAGGAUUGGGGCGAGGUG___GU
...................................(((.((..(((((....)))))......((((((..((((((....))))))))))))......)).)))........ (-27.23 = -28.37 +   1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:42 2006