Locus 8052

Sequence ID	3R_DroMel_CAF1
Location	21,631,046 – 21,631,188
Length	142
Max. P	0.845517

overview

Window 9

Location	21,631,046 – 21,631,151
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	92.53
Mean single sequence MFE	-32.61
Consensus MFE	-25.56
Energy contribution	-26.04
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-1.89
Structure conservation index	0.78
SVM decision value	0.77
SVM RNA-class probability	0.845517
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21631046 105 + 27905053
UAGUAUUUUUUCGGGUGAUAAUUGCAUACGGCGACGUGCACUCGACAACAGCAACAACGAGUGCACUACAAGUUGGAUGUUGCUGCUGGUGUUGCUGUUGCACUU
..........(((((((....((((.....))))....)))))))(((((((((((.(.((((((..(((.......)))))).))).))))))))))))..... ( -35.90)
>DroSec_CAF1 120468 105 + 1
UAGUAUUUUUUCGGGUGAUAAUUGCAUACGGCGACGUGCACUCGACAACAGCAACAACGAGUGCACUACAAGUUGGAUGUUGCUGCUGGUGUUGCUGUUGCACUU
..........(((((((....((((.....))))....)))))))(((((((((((.(.((((((..(((.......)))))).))).))))))))))))..... ( -35.90)
>DroSim_CAF1 117021 105 + 1
UAGUAUUUUUUCGGGUGAUAAUUGCAUACGGCGACGUGCACUCGACAACAGCAACAACGAGUGCACUACAAGUUGGAUGUUGCUGCUGGUGUUGCCGUUGCACUU
......................((((.(((((((((((((((((.............))))))))).((.(((........)))....))))))))))))))... ( -33.52)
>DroEre_CAF1 112738 99 + 1
UAGUAUUUUUUCGGGUGAUAAUUGCAUACGGCGACGUGCACUCGACAACAGCAACAACGAGUGCACUACAAGUUGGAUGUUGCUGCUGGU------GUUGCACUU
............(((((......((((.((((((((((((((((.............)))))))))..(.....)...)))))))...))------))..))))) ( -28.82)
>DroYak_CAF1 117396 93 + 1
UAGUAUUUUUUUGGGUGAUAAUUGCAUACGGCGACGUGCACUCGACAACAGCAGCAACGAGGGCACUACAAGUUGCAUGUUGCU------------GUUGCACUU
..........(((((((....((((.....))))....)))))))...(((((((((((...(((........))).)))))))------------))))..... ( -28.90)
>consensus
UAGUAUUUUUUCGGGUGAUAAUUGCAUACGGCGACGUGCACUCGACAACAGCAACAACGAGUGCACUACAAGUUGGAUGUUGCUGCUGGUGUUGC_GUUGCACUU
..(((.....(((((((....((((.....))))....)))))))((.((((((((.(((.(........).)))..)))))))).))..........))).... (-25.56 = -26.04 +   0.48)

alignment

secondary structure

dotplot

Window 0

Location	21,631,046 – 21,631,151
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	92.53
Mean single sequence MFE	-26.22
Consensus MFE	-20.28
Energy contribution	-21.92
Covariance contribution	1.64
Combinations/Pair	1.05
Mean z-score	-1.55
Structure conservation index	0.77
SVM decision value	0.04
SVM RNA-class probability	0.551527
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21631046 105 - 27905053
AAGUGCAACAGCAACACCAGCAGCAACAUCCAACUUGUAGUGCACUCGUUGUUGCUGUUGUCGAGUGCACGUCGCCGUAUGCAAUUAUCACCCGAAAAAAUACUA
..(((((....(.(((.((((((((((.....((.....))......)))))))))).))).)..)))))...((.....))....................... ( -26.50)
>DroSec_CAF1 120468 105 - 1
AAGUGCAACAGCAACACCAGCAGCAACAUCCAACUUGUAGUGCACUCGUUGUUGCUGUUGUCGAGUGCACGUCGCCGUAUGCAAUUAUCACCCGAAAAAAUACUA
..(((((....(.(((.((((((((((.....((.....))......)))))))))).))).)..)))))...((.....))....................... ( -26.50)
>DroSim_CAF1 117021 105 - 1
AAGUGCAACGGCAACACCAGCAGCAACAUCCAACUUGUAGUGCACUCGUUGUUGCUGUUGUCGAGUGCACGUCGCCGUAUGCAAUUAUCACCCGAAAAAAUACUA
...(((((((((.((.......((((........)))).(((((((((.............))))))))))).))))).))))...................... ( -31.12)
>DroEre_CAF1 112738 99 - 1
AAGUGCAAC------ACCAGCAGCAACAUCCAACUUGUAGUGCACUCGUUGUUGCUGUUGUCGAGUGCACGUCGCCGUAUGCAAUUAUCACCCGAAAAAAUACUA
..(((((((------(.((((((((((.....((.....))......)))))))))).)))....)))))...((.....))....................... ( -24.50)
>DroYak_CAF1 117396 93 - 1
AAGUGCAAC------------AGCAACAUGCAACUUGUAGUGCCCUCGUUGCUGCUGUUGUCGAGUGCACGUCGCCGUAUGCAAUUAUCACCCAAAAAAAUACUA
...((((((------------.((.((.(((.....)))((((.((((..((....))...)))).)))))).)).)).))))...................... ( -22.50)
>consensus
AAGUGCAAC_GCAACACCAGCAGCAACAUCCAACUUGUAGUGCACUCGUUGUUGCUGUUGUCGAGUGCACGUCGCCGUAUGCAAUUAUCACCCGAAAAAAUACUA
..(((((......(((.((((((((((.....((.....))......)))))))))).)))....)))))...((.....))....................... (-20.28 = -21.92 +   1.64)

alignment

secondary structure

dotplot

Window 1

Location	21,631,086 – 21,631,188
Length	102
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	91.62
Mean single sequence MFE	-31.40
Consensus MFE	-23.10
Energy contribution	-23.80
Covariance contribution	0.70
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.74
SVM decision value	0.32
SVM RNA-class probability	0.686377
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21631086 102 - 27905053
GAAGUUGUUAGUUGCUCGCAACAUGAGAAACAGCA---GCAAGUGCAACAGCAACACCAGCAGCAACAUCCAACUUGUAGUGCACUCGUUGUUGCUGUUGUCGAG
...((((((.(((.((((.....)))).)))))))---))....(((((((((((((.((..((((((.......)))..))).)).).)))))))))))).... ( -31.80)
>DroSec_CAF1 120508 102 - 1
GAAGUUGUUAGUUGCUCGCAACAUGAGAAACAGCA---GCAAGUGCAACAGCAACACCAGCAGCAACAUCCAACUUGUAGUGCACUCGUUGUUGCUGUUGUCGAG
...((((((.(((.((((.....)))).)))))))---))....(((((((((((((.((..((((((.......)))..))).)).).)))))))))))).... ( -31.80)
>DroSim_CAF1 117061 102 - 1
GAAGUUGUUAGUUGCUCGCAACAUGAGAAACAGCA---GCAAGUGCAACGGCAACACCAGCAGCAACAUCCAACUUGUAGUGCACUCGUUGUUGCUGUUGUCGAG
...((((((.(((.((((.....)))).)))))))---))........((((((((...((((((((.....((.....))......)))))))))))))))).. ( -31.90)
>DroEre_CAF1 112778 96 - 1
GAAGUUGUUAGUUGCUCGCAACAUGAGAAACAGCA---GCAAGUGCAAC------ACCAGCAGCAACAUCCAACUUGUAGUGCACUCGUUGUUGCUGUUGUCGAG
...(((((.((...)).))))).(((..(((((((---(((((((((..------((.((.............)).))..))))))...)))))))))).))).. ( -28.12)
>DroYak_CAF1 117436 93 - 1
GAAGUUGUUAGUUGCUCGCAACAUGAGAAACAGCAGCAGCAAGUGCAAC------------AGCAACAUGCAACUUGUAGUGCCCUCGUUGCUGCUGUUGUCGAG
...(((((.((...)).))))).(((..((((((((((((.((.(((..------------.((((........))))..))).)).)))))))))))).))).. ( -33.40)
>consensus
GAAGUUGUUAGUUGCUCGCAACAUGAGAAACAGCA___GCAAGUGCAAC_GCAACACCAGCAGCAACAUCCAACUUGUAGUGCACUCGUUGUUGCUGUUGUCGAG
...(((((.((...)).))))).(((..(((((((...((.((((((...((.......)).((((........))))..)))))).))...))))))).))).. (-23.10 = -23.80 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:01:22 2006