Locus 2848

Sequence ID	3R_DroMel_CAF1
Location	7,654,436 – 7,654,563
Length	127
Max. P	0.999812

overview

Window 1

Location	7,654,436 – 7,654,539
Length	103
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	82.68
Mean single sequence MFE	-29.05
Consensus MFE	-19.27
Energy contribution	-19.00
Covariance contribution	-0.27
Combinations/Pair	1.18
Mean z-score	-2.71
Structure conservation index	0.66
SVM decision value	0.66
SVM RNA-class probability	0.814338
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7654436 103 + 27905053
ACUCCGGCAACAGUUCCAACUGCAGAUCCUAGACCAACUCCUGGUCCAUUGCCAGUAGCCAAAAAUGGCCAACUAACUGUUCUUGGGCUGGCAAUAAAUUUCC
.....((...((((....)))).....))..(((((.....))))).(((((((((.((((....))))...((((......)))))))))))))........ ( -27.60)
>DroSec_CAF1 9465 103 + 1
ACUCCGGCAACAGUUCCAGCUGCAGAUCCUAGUCCAACUCCUGGACCAUUGCCAGUAGCCAAAAAUGGCCAACUAACUGUUCUUGGGCUGGCAAUAAAUUUCC
.((.((((..........)))).))......(((((.....))))).(((((((((.((((....))))...((((......)))))))))))))........ ( -29.50)
>DroSim_CAF1 9116 103 + 1
ACUCCGGCAACAGUUCCAGCUGCAGAUCCUAGUCCAACUCCUGGACCAUUGCCAGUAGCCAAAAAUGGGCAACUAACUGUUCUUGGGCUGGCAAUAAAUUUCC
.((.((((..........)))).))......(((((.....))))).(((((((((..((((.(((((........))))).)))))))))))))........ ( -30.60)
>DroEre_CAF1 9264 102 + 1
ACUCCGGCUACAGUUCCAGCUGUGUAUCCAAGUCCCACUCCUGGUCCAUUGCCAGUAGCCAAAAAUGGCCAACUAACUGUUCUUGGGCUGGCAAUAAAUUU-C
...(((((((((((....))))))...(((((..(.....(((((.....)))))..((((....)))).........)..))))))))))..........-. ( -28.90)
>DroYak_CAF1 9063 102 + 1
ACUCCGGCUACAGUUCCAGUUGCAGAUCCUUGUGCAACUUCUGGUCCAUUGCCAGUAGCCAAAAAUGGCCAACUAACUGUUCUUGGGCUGGCAAUAAAUUU-C
.....((...(((....(((((((.(....).))))))).)))..))(((((((((.((((....))))...((((......)))))))))))))......-. ( -32.80)
>DroAna_CAF1 14044 79 + 1
ACUCCAGCACGAGUUGCAACUU----------------------GCAAGUGCCAGCAGCCAAAAAUGGCUAGCUAACUGUUCUUUGGCUGGCCAUAAAUA--A
......((((...((((.....----------------------))))))))............((((((((((((.......)))))))))))).....--. ( -24.90)
>consensus
ACUCCGGCAACAGUUCCAGCUGCAGAUCCUAGUCCAACUCCUGGUCCAUUGCCAGUAGCCAAAAAUGGCCAACUAACUGUUCUUGGGCUGGCAAUAAAUUU_C
..........((((....)))).........................(((((((((..((((.(((((........))))).)))))))))))))........ (-19.27 = -19.00 +  -0.27)

alignment

secondary structure

dotplot

Window 2

Location	7,654,464 – 7,654,563
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	94.54
Mean single sequence MFE	-33.50
Consensus MFE	-30.04
Energy contribution	-30.64
Covariance contribution	0.60
Combinations/Pair	1.06
Mean z-score	-2.77
Structure conservation index	0.90
SVM decision value	4.14
SVM RNA-class probability	0.999812
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7654464 99 + 27905053
CUAGACCAACUCCUGGUCCAUUGCCAGUAGCCAAAAAUGGCCAACUAACUGUUCUUGGGCUGGCAAUAAAUUUCCAGCGGGUUGCCUGGGGUUUUUAAG
((((..((((((((((...(((((((((.((((....))))...((((......)))))))))))))......)))).)))))).)))).......... ( -34.80)
>DroSec_CAF1 9493 99 + 1
CUAGUCCAACUCCUGGACCAUUGCCAGUAGCCAAAAAUGGCCAACUAACUGUUCUUGGGCUGGCAAUAAAUUUCCAGCGAGUUGCCUGGGGUUUUUAAG
((((..(((((((((((..(((((((((.((((....))))...((((......))))))))))))).....))))).)))))).)))).......... ( -37.20)
>DroSim_CAF1 9144 99 + 1
CUAGUCCAACUCCUGGACCAUUGCCAGUAGCCAAAAAUGGGCAACUAACUGUUCUUGGGCUGGCAAUAAAUUUCCAGCGAGUUGCCUGGGGUUUUUAAG
((((..(((((((((((..(((((((((..((((.(((((........))))).))))))))))))).....))))).)))))).)))).......... ( -38.30)
>DroEre_CAF1 9292 98 + 1
CAAGUCCCACUCCUGGUCCAUUGCCAGUAGCCAAAAAUGGCCAACUAACUGUUCUUGGGCUGGCAAUAAAUUU-CAGCGGGUUGCCUAGAGUUUUUAAG
........((((((((...(((((((((.((((....))))...((((......))))))))))))).....)-))).))))................. ( -25.50)
>DroYak_CAF1 9091 98 + 1
CUUGUGCAACUUCUGGUCCAUUGCCAGUAGCCAAAAAUGGCCAACUAACUGUUCUUGGGCUGGCAAUAAAUUU-CAGCGGGUUGCCUGGGGUUUUUAAG
((((.(((((((((((...(((((((((.((((....))))...((((......))))))))))))).....)-))).))))))).))))......... ( -31.70)
>consensus
CUAGUCCAACUCCUGGUCCAUUGCCAGUAGCCAAAAAUGGCCAACUAACUGUUCUUGGGCUGGCAAUAAAUUUCCAGCGGGUUGCCUGGGGUUUUUAAG
((((..((((((((((...(((((((((..((((.(((((........))))).)))))))))))))......)))).)))))).)))).......... (-30.04 = -30.64 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	7,654,464 – 7,654,563
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	94.54
Mean single sequence MFE	-32.54
Consensus MFE	-24.42
Energy contribution	-25.82
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-2.72
Structure conservation index	0.75
SVM decision value	0.88
SVM RNA-class probability	0.874158
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7654464 99 - 27905053
CUUAAAAACCCCAGGCAACCCGCUGGAAAUUUAUUGCCAGCCCAAGAACAGUUAGUUGGCCAUUUUUGGCUACUGGCAAUGGACCAGGAGUUGGUCUAG
............(((((((.(.((((...(((((((((((......(((.....)))(((((....))))).)))))))))))))))).))).)))).. ( -31.50)
>DroSec_CAF1 9493 99 - 1
CUUAAAAACCCCAGGCAACUCGCUGGAAAUUUAUUGCCAGCCCAAGAACAGUUAGUUGGCCAUUUUUGGCUACUGGCAAUGGUCCAGGAGUUGGACUAG
............((.((((((.(((((....(((((((((......(((.....)))(((((....))))).))))))))).)))))))))))..)).. ( -36.00)
>DroSim_CAF1 9144 99 - 1
CUUAAAAACCCCAGGCAACUCGCUGGAAAUUUAUUGCCAGCCCAAGAACAGUUAGUUGCCCAUUUUUGGCUACUGGCAAUGGUCCAGGAGUUGGACUAG
............((.((((((.(((((....(((((((((.(((((((..((.....))...)))))))...))))))))).)))))))))))..)).. ( -34.40)
>DroEre_CAF1 9292 98 - 1
CUUAAAAACUCUAGGCAACCCGCUG-AAAUUUAUUGCCAGCCCAAGAACAGUUAGUUGGCCAUUUUUGGCUACUGGCAAUGGACCAGGAGUGGGACUUG
..................((((((.-...(((((((((((......(((.....)))(((((....))))).))))))))))).....))))))..... ( -30.40)
>DroYak_CAF1 9091 98 - 1
CUUAAAAACCCCAGGCAACCCGCUG-AAAUUUAUUGCCAGCCCAAGAACAGUUAGUUGGCCAUUUUUGGCUACUGGCAAUGGACCAGAAGUUGCACAAG
..............(((((...(((-...(((((((((((......(((.....)))(((((....))))).))))))))))).)))..)))))..... ( -30.40)
>consensus
CUUAAAAACCCCAGGCAACCCGCUGGAAAUUUAUUGCCAGCCCAAGAACAGUUAGUUGGCCAUUUUUGGCUACUGGCAAUGGACCAGGAGUUGGACUAG
...............((((.(.((((...(((((((((((.(((((((..(((....)))..)))))))...)))))))))))))))).))))...... (-24.42 = -25.82 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:09 2006