Locus 5347

Sequence ID	X_DroMel_CAF1
Location	13,932,646 – 13,932,797
Length	151
Max. P	0.632758

overview

Window 3

Location	13,932,646 – 13,932,757
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.11
Mean single sequence MFE	-28.96
Consensus MFE	-24.20
Energy contribution	-24.60
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.35
Structure conservation index	0.84
SVM decision value	0.19
SVM RNA-class probability	0.627945
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13932646 111 - 22224390
GUAUCUUAUGUGAUGAAAUUUAUGCUUAAUUAAAAGCGACACAAGGCGUCACAAGCAACGCACAACGCGUUCGCCCAGAUAAGAUGCGAA---------AGAACCAAGCGGGCCAUCGGC
(((((((((((((((.......(((((......)))))........))))))..(((((((.....))))).))....)))))))))...---------....((....))(((...))) ( -30.66)
>DroSec_CAF1 12601 111 - 1
GUAUCUUAUGUGAUGAAAUUUAUGCUUAAUUAAAAGCGACACAAGGCGUCACAAGCAACGCACAACGCGUUCGCUCAGAUAAGACGCGAA---------AUAACCAAGCGGGCCAUCGGC
(..((((((((((((.......(((((......)))))........)))))).((((((((.....))))).)))...))))))..)...---------....((....))(((...))) ( -28.36)
>DroSim_CAF1 16165 111 - 1
GUAUCUUAUGUGAUGAAAUUUAUGCUUAAUUAAAAGCGACACAAGGCGUCACAAGCAACGCACAACGCGUUCGCCCAGAUAAGACGCGAA---------AUAACCGAGCGGGCCAUCGGC
(..((((((((((((.......(((((......)))))........))))))..(((((((.....))))).))....))))))..)...---------....((((........)))). ( -29.86)
>DroEre_CAF1 14169 120 - 1
GUAUCUUAUGUGAUGAAAUUUAUGCUUAAUUAAAAGCGACACAAGGCGUCACAAGCAACGCACAACGCAUUCGCCCAGAUAAGAACCGAAGGCACCAAAGGAACCAAGUUGGCCAUCGGC
...((((((((((((.......(((((......)))))........))))))..((((.((.....)).)).))....)))))).((((.(((......(....)......))).)))). ( -27.56)
>DroYak_CAF1 14788 111 - 1
GUAUCUUAUGUGAUGAAAUUUAUGCUUAAUUAAAAGCGACACAAGGCGUCACAAGCAACGCACAACGCGUUCGCUCAGAUAAGACGCGAA---------AGAACCAAGCGGGCCAUCGGC
(..((((((((((((.......(((((......)))))........)))))).((((((((.....))))).)))...))))))..)...---------....((....))(((...))) ( -28.36)
>consensus
GUAUCUUAUGUGAUGAAAUUUAUGCUUAAUUAAAAGCGACACAAGGCGUCACAAGCAACGCACAACGCGUUCGCCCAGAUAAGACGCGAA_________AGAACCAAGCGGGCCAUCGGC
((.((((((((((((.......(((((......)))))........))))))..(((((((.....))))).))....)))))).))........................(((...))) (-24.20 = -24.60 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	13,932,677 – 13,932,797
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-34.72
Consensus MFE	-30.86
Energy contribution	-30.62
Covariance contribution	-0.24
Combinations/Pair	1.15
Mean z-score	-1.22
Structure conservation index	0.89
SVM decision value	0.20
SVM RNA-class probability	0.632758
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13932677 120 + 22224390
AUCUGGGCGAACGCGUUGUGCGUUGCUUGUGACGCCUUGUGUCGCUUUUAAUUAAGCAUAAAUUUCAUCACAUAAGAUACGAGAUGCAGUUAAAAGGGGCACGCAGUGGUGCCUUAUUUU
....(((((.((((.....((((((....))))))...(((((.(((((((((..((((...((..(((......)))..)).))))))))))))).))))))).))..)))))...... ( -35.60)
>DroSec_CAF1 12632 120 + 1
AUCUGAGCGAACGCGUUGUGCGUUGCUUGUGACGCCUUGUGUCGCUUUUAAUUAAGCAUAAAUUUCAUCACAUAAGAUACGAGAUGCAGUUAAAAAGGGCACGCAGCGGUGCCUUAUUUU
....((((.(((((.....)))))))))(((((((...)))))))((((((((..((((...((..(((......)))..)).))))))))))))(((((((......)))))))..... ( -35.00)
>DroSim_CAF1 16196 120 + 1
AUCUGGGCGAACGCGUUGUGCGUUGCUUGUGACGCCUUGUGUCGCUUUUAAUUAAGCAUAAAUUUCAUCACAUAAGAUACGAGAUGCAGUUAAAAAGGGCACGCAGCGGUGCCUUAUUUU
....(((((..(((....(((((.(((((((((((...)))))))((((((((..((((...((..(((......)))..)).)))))))))))).)))))))))))).)))))...... ( -34.20)
>DroEre_CAF1 14209 119 + 1
AUCUGGGCGAAUGCGUUGUGCGUUGCUUGUGACGCCUUGUGUCGCUUUUAAUUAAGCAUAAAUUUCAUCACAUAAGAUACGAGCUGCAGUUAAGAGGGGCACGCAGCGCUGUUUGAGUU-
.......(((((((((((((.(((.(((.((((((((((((((((((......))))....((........))..))))))))..)).)))).))).))).)))))))).)))))....- ( -37.60)
>DroYak_CAF1 14819 120 + 1
AUCUGAGCGAACGCGUUGUGCGUUGCUUGUGACGCCUUGUGUCGCUUUUAAUUAAGCAUAAAUUUCAUCACAUAAGAUACGAGAUGCAGUUAAAAUGGGCACGCAGUGGUGCUUUAGUUU
....((((....(((..((((((.(((((((((((...)))))))((((((((..((((...((..(((......)))..)).)))))))))))).))))))))).)..)))....)))) ( -31.20)
>consensus
AUCUGGGCGAACGCGUUGUGCGUUGCUUGUGACGCCUUGUGUCGCUUUUAAUUAAGCAUAAAUUUCAUCACAUAAGAUACGAGAUGCAGUUAAAAAGGGCACGCAGCGGUGCCUUAUUUU
....((((.(((((.....)))))))))(((((((...)))))))((((((((..((((...((..(((......)))..)).))))))))))))(((((((......)))))))..... (-30.86 = -30.62 +  -0.24)

alignment

secondary structure

dotplot

Window 5

Location	13,932,677 – 13,932,797
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-27.77
Consensus MFE	-23.90
Energy contribution	-24.90
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.29
Structure conservation index	0.86
SVM decision value	0.14
SVM RNA-class probability	0.603341
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13932677 120 - 22224390
AAAAUAAGGCACCACUGCGUGCCCCUUUUAACUGCAUCUCGUAUCUUAUGUGAUGAAAUUUAUGCUUAAUUAAAAGCGACACAAGGCGUCACAAGCAACGCACAACGCGUUCGCCCAGAU
.......(((((......)))))........(((..............(((((((.......(((((......)))))........))))))).(((((((.....))))).)).))).. ( -28.96)
>DroSec_CAF1 12632 120 - 1
AAAAUAAGGCACCGCUGCGUGCCCUUUUUAACUGCAUCUCGUAUCUUAUGUGAUGAAAUUUAUGCUUAAUUAAAAGCGACACAAGGCGUCACAAGCAACGCACAACGCGUUCGCUCAGAU
.......(((((......)))))........(((..............(((((((.......(((((......)))))........)))))))((((((((.....))))).)))))).. ( -29.76)
>DroSim_CAF1 16196 120 - 1
AAAAUAAGGCACCGCUGCGUGCCCUUUUUAACUGCAUCUCGUAUCUUAUGUGAUGAAAUUUAUGCUUAAUUAAAAGCGACACAAGGCGUCACAAGCAACGCACAACGCGUUCGCCCAGAU
.......(((...(((..((((((((........((((.((((...)))).)))).......(((((......)))))....)))).).))).)))(((((.....))))).)))..... ( -29.50)
>DroEre_CAF1 14209 119 - 1
-AACUCAAACAGCGCUGCGUGCCCCUCUUAACUGCAGCUCGUAUCUUAUGUGAUGAAAUUUAUGCUUAAUUAAAAGCGACACAAGGCGUCACAAGCAACGCACAACGCAUUCGCCCAGAU
-..........(((((((((..........)).)))))..........(((((((.......(((((......)))))........))))))).))...((.....))............ ( -24.16)
>DroYak_CAF1 14819 120 - 1
AAACUAAAGCACCACUGCGUGCCCAUUUUAACUGCAUCUCGUAUCUUAUGUGAUGAAAUUUAUGCUUAAUUAAAAGCGACACAAGGCGUCACAAGCAACGCACAACGCGUUCGCUCAGAU
........((((......)))).........(((..............(((((((.......(((((......)))))........)))))))((((((((.....))))).)))))).. ( -26.46)
>consensus
AAAAUAAGGCACCGCUGCGUGCCCCUUUUAACUGCAUCUCGUAUCUUAUGUGAUGAAAUUUAUGCUUAAUUAAAAGCGACACAAGGCGUCACAAGCAACGCACAACGCGUUCGCCCAGAU
.......(((((......)))))........(((..............(((((((.......(((((......)))))........))))))).(((((((.....))))).)).))).. (-23.90 = -24.90 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:44 2006