Locus 4786

Sequence ID	2R_DroMel_CAF1
Location	15,740,477 – 15,740,621
Length	144
Max. P	0.919919

overview

Window 8

Location	15,740,477 – 15,740,586
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	94.31
Mean single sequence MFE	-29.60
Consensus MFE	-26.66
Energy contribution	-26.70
Covariance contribution	0.04
Combinations/Pair	1.10
Mean z-score	-1.28
Structure conservation index	0.90
SVM decision value	0.54
SVM RNA-class probability	0.776315
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15740477 109 - 20766785
AUUUCGUGACAGGAUGUUGGUCCUUGGACAUCCUGUGGGCGGCCCCAAUAGGACAUGCGACAUUUAAUUGCAUACUCGGAUAAACAAAUAUUCAAUUCUUUGGCUUCUU
...((((.((((((((((.(....).)))))))))).).)))..((((.((((.((((((.......))))))....(((((......)))))..))))))))...... ( -28.70)
>DroSec_CAF1 616278 109 - 1
AUUUCGUGACAGGAUGUUGGUCCUUGGACAUCCUGUGGGCGGCCCCAAUAGGACAUGCGACAUUUAAUUGCAUACUCGGAUAAGCAAAUAUUCAAUUCUUUGGCUCCCU
........((((((((((.(....).))))))))))(((.((((.....((((.((((((.......))))))....(((((......)))))..))))..))))))). ( -32.60)
>DroSim_CAF1 523822 107 - 1
AUUUCGUGACAGGAUGUUGGUCCUUGGACAUCCUGUGGGCGGCCCCAAUAGGACAUGCGACAUUUAAUUGCAUACUCGGAUAAGCAAAUAUUCAAUUCUU--GCUCCUU
.....(..(..(((((((((((....))).(((((((((....))).))))))....))))))))..)..)......(((...((((...........))--))))).. ( -28.10)
>DroEre_CAF1 520855 108 - 1
AUUUCGUGACAGGAUGUUGGUCCUUGGACAUCCUGUGGGUGGCCCCAAUAGGACAUGCGACAUUUAAUUGCAUACUCCGAUAAACAAAUAUUCCAUUCUUUGGCC-CUU
........((((((((((.(....).))))))))))(((.((((......(((.((((((.......))))))..)))((((......)))).........))))-))) ( -29.20)
>DroYak_CAF1 539669 107 - 1
AUUUCGUGACAGGAUGUUGGUCCUUGGACAUCCUGUGGGUGGCCCCAAUAGGACAUGCGACAUUUAAUUGCAUACUCGGAUAAAUAAAUGUUCAAUUCGUUGGCC--UU
......(.((((((((((.(....).)))))))))).)..((((......((..((((((.......))))))..))(((((......)))))........))))--.. ( -29.40)
>consensus
AUUUCGUGACAGGAUGUUGGUCCUUGGACAUCCUGUGGGCGGCCCCAAUAGGACAUGCGACAUUUAAUUGCAUACUCGGAUAAACAAAUAUUCAAUUCUUUGGCU_CUU
........((((((((((.(....).))))))))))(((.((((((....))..((((((.......))))))....(((((......)))))........)))).))) (-26.66 = -26.70 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	15,740,509 – 15,740,621
Length	112
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	98.04
Mean single sequence MFE	-34.04
Consensus MFE	-32.62
Energy contribution	-33.22
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.96
SVM decision value	1.13
SVM RNA-class probability	0.919919
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15740509 112 + 20766785
GAGUAUGCAAUUAAAUGUCGCAUGUCCUAUUGGGGCCGCCCACAGGAUGUCCAAGGACCAACAUCCUGUCACGAAAUGUCAGUCAUGACCUGCUGCACCAUUGGGAACCACA
...(((((.((.....)).)))))(((((.(((.((.((..(((((((((..........)))))))))........((((....))))..)).)).))).)))))...... ( -33.20)
>DroSec_CAF1 616310 112 + 1
GAGUAUGCAAUUAAAUGUCGCAUGUCCUAUUGGGGCCGCCCACAGGAUGUCCAAGGACCAACAUCCUGUCACGAAAUGUCAGUCGUGACCUGCUGCACCAUUGGGAACCACA
...(((((.((.....)).)))))(((((.(((.((.((....(((((((..........)))))))(((((((........)))))))..)).)).))).)))))...... ( -35.70)
>DroSim_CAF1 523852 112 + 1
GAGUAUGCAAUUAAAUGUCGCAUGUCCUAUUGGGGCCGCCCACAGGAUGUCCAAGGACCAACAUCCUGUCACGAAAUGUCAGUCGUGACCUGCUGCACCAUUGGGAACCACG
...(((((.((.....)).)))))(((((.(((.((.((....(((((((..........)))))))(((((((........)))))))..)).)).))).)))))...... ( -35.70)
>DroEre_CAF1 520886 112 + 1
GAGUAUGCAAUUAAAUGUCGCAUGUCCUAUUGGGGCCACCCACAGGAUGUCCAAGGACCAACAUCCUGUCACGAAAUGUCAGUCGUGACCUGCUGCACCAUUGGGAACCACA
...(((((.((.....)).)))))(((((.(((.((.......(((((((..........)))))))(((((((........))))))).....)).))).)))))...... ( -32.70)
>DroYak_CAF1 539699 112 + 1
GAGUAUGCAAUUAAAUGUCGCAUGUCCUAUUGGGGCCACCCACAGGAUGUCCAAGGACCAACAUCCUGUCACGAAAUGUCACUCGUGACCAGCUGCACCAUUGGGAACCACA
...(((((.((.....)).)))))(((((.(((.((.......(((((((..........)))))))(((((((........))))))).....)).))).)))))...... ( -32.90)
>consensus
GAGUAUGCAAUUAAAUGUCGCAUGUCCUAUUGGGGCCGCCCACAGGAUGUCCAAGGACCAACAUCCUGUCACGAAAUGUCAGUCGUGACCUGCUGCACCAUUGGGAACCACA
...(((((.((.....)).)))))(((((.(((.((.((....(((((((..........)))))))(((((((........)))))))..)).)).))).)))))...... (-32.62 = -33.22 +   0.60)

alignment

secondary structure

dotplot

Window 0

Location	15,740,509 – 15,740,621
Length	112
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	98.04
Mean single sequence MFE	-37.64
Consensus MFE	-37.34
Energy contribution	-37.18
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.24
Structure conservation index	0.99
SVM decision value	0.54
SVM RNA-class probability	0.773953
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15740509 112 - 20766785
UGUGGUUCCCAAUGGUGCAGCAGGUCAUGACUGACAUUUCGUGACAGGAUGUUGGUCCUUGGACAUCCUGUGGGCGGCCCCAAUAGGACAUGCGACAUUUAAUUGCAUACUC
..(((...)))...((((((...(((((((........))))))).(((((((((((....))).(((((((((....))).))))))....))))))))..)))))).... ( -35.70)
>DroSec_CAF1 616310 112 - 1
UGUGGUUCCCAAUGGUGCAGCAGGUCACGACUGACAUUUCGUGACAGGAUGUUGGUCCUUGGACAUCCUGUGGGCGGCCCCAAUAGGACAUGCGACAUUUAAUUGCAUACUC
..(((...)))...((((((...(((((((........))))))).(((((((((((....))).(((((((((....))).))))))....))))))))..)))))).... ( -37.50)
>DroSim_CAF1 523852 112 - 1
CGUGGUUCCCAAUGGUGCAGCAGGUCACGACUGACAUUUCGUGACAGGAUGUUGGUCCUUGGACAUCCUGUGGGCGGCCCCAAUAGGACAUGCGACAUUUAAUUGCAUACUC
.(((((.((....)).)).(((((((((((........))))))).(((((((((((....))).(((((((((....))).))))))....))))))))..)))).))).. ( -37.70)
>DroEre_CAF1 520886 112 - 1
UGUGGUUCCCAAUGGUGCAGCAGGUCACGACUGACAUUUCGUGACAGGAUGUUGGUCCUUGGACAUCCUGUGGGUGGCCCCAAUAGGACAUGCGACAUUUAAUUGCAUACUC
..(((...)))...((((((...(((((((........))))))).(((((((((((....))).(((((((((....))).))))))....))))))))..)))))).... ( -37.80)
>DroYak_CAF1 539699 112 - 1
UGUGGUUCCCAAUGGUGCAGCUGGUCACGAGUGACAUUUCGUGACAGGAUGUUGGUCCUUGGACAUCCUGUGGGUGGCCCCAAUAGGACAUGCGACAUUUAAUUGCAUACUC
..(((...)))...((((((...((((((((......)))))))).(((((((((((....))).(((((((((....))).))))))....))))))))..)))))).... ( -39.50)
>consensus
UGUGGUUCCCAAUGGUGCAGCAGGUCACGACUGACAUUUCGUGACAGGAUGUUGGUCCUUGGACAUCCUGUGGGCGGCCCCAAUAGGACAUGCGACAUUUAAUUGCAUACUC
..(((...)))...((((((...(((((((........))))))).(((((((((((....))).(((((((((....))).))))))....))))))))..)))))).... (-37.34 = -37.18 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:11 2006