Locus 3493

Sequence ID	3R_DroMel_CAF1
Location	9,438,007 – 9,438,109
Length	102
Max. P	0.999248

overview

Window 3

Location	9,438,007 – 9,438,109
Length	102
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	89.00
Mean single sequence MFE	-41.73
Consensus MFE	-34.37
Energy contribution	-35.28
Covariance contribution	0.92
Combinations/Pair	1.12
Mean z-score	-3.47
Structure conservation index	0.82
SVM decision value	1.83
SVM RNA-class probability	0.979027
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9438007 102 + 27905053
AGAAGUUGCGCCGCCACAGGAUCAUAUGUGGCUGCUGA---UGAGCCGGCGACCAGGAGAAUGGUCGCCAGGGCAAGGCAAACAAAUGUGCGCAUUUUCGAGGAA
.((((.((((((((((((........))))))((((..---((..((((((((((......)))))))).)).)).)))).......).))))).))))...... ( -45.60)
>DroSec_CAF1 67635 102 + 1
AGAAGUUGCGCCGCCACAGGAUCAUAUGUGGCUGCUGA---UGAGCCGGCGACUAGGAGAAUGGUCGCCAGGGCAAGGCAAACAAAUGUGCGCAUUUUCGAGGAA
.((((.((((((((((((........))))))((((..---((..((((((((((......)))))))).)).)).)))).......).))))).))))...... ( -43.30)
>DroSim_CAF1 55792 102 + 1
AGAAGUUGCGCCGCCACAGGAUCAUAUGUGGCUGCUGA---UGAGCCGGCGACCAGGAGAAUGGUCGCCAGGGCAAGGCAAACAAAUGUGCGCAUUUUCGAGGAA
.((((.((((((((((((........))))))((((..---((..((((((((((......)))))))).)).)).)))).......).))))).))))...... ( -45.60)
>DroEre_CAF1 75929 102 + 1
AGAAGUUGCGCCGCCACAGGAUCAUAUGUGGCAGCUGA---GGAGCCGGCGACCAGGAGGAUGGUCGCCAAGACAAGGCAAACAAAUGUGCGCAUAUUCGUGAAA
.(((..((((((((((((........)))))).(((..---(.....((((((((......))))))))....)..)))........).)))))..)))...... ( -40.90)
>DroYak_CAF1 69913 102 + 1
AGAAGUUGCGCCGCCACAGGAUCAUAUGUGGCUGCUGA---GGAGCCGGCGACCAGGAGGAUGGUCGCCAGGGCGAGGCAAACAAAUGUGCGCAUAUUCGAGAAA
.(((..((((((((((((........))))))((((..---...(((((((((((......))))))))..)))..)))).......).)))))..)))...... ( -45.50)
>DroAna_CAF1 63964 101 + 1
AGGAGUUGAGCGGCC---GGAUCGAAUGUAGCCGCCGAAGUUGAGCUGGCGACCAGGAGGACGGCCGCCAGGGCAAGACAAACGAAUGUGCGCAU-UUCAGGAAA
.(((((((.((((((---(..((...((..(((((((....)).)).)))...)).))...)))))))))(.(((...(....)....))).)))-)))...... ( -29.50)
>consensus
AGAAGUUGCGCCGCCACAGGAUCAUAUGUGGCUGCUGA___UGAGCCGGCGACCAGGAGAAUGGUCGCCAGGGCAAGGCAAACAAAUGUGCGCAUUUUCGAGAAA
.(((..(((((.((((((........))))))............(((((((((((......))))))))..)))...............)))))..)))...... (-34.37 = -35.28 +   0.92)

alignment

secondary structure

dotplot

Window 4

Location	9,438,007 – 9,438,109
Length	102
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	89.00
Mean single sequence MFE	-38.89
Consensus MFE	-34.92
Energy contribution	-35.37
Covariance contribution	0.45
Combinations/Pair	1.23
Mean z-score	-4.07
Structure conservation index	0.90
SVM decision value	3.46
SVM RNA-class probability	0.999248
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9438007 102 - 27905053
UUCCUCGAAAAUGCGCACAUUUGUUUGCCUUGCCCUGGCGACCAUUCUCCUGGUCGCCGGCUCA---UCAGCAGCCACAUAUGAUCCUGUGGCGGCGCAACUUCU
......(((..(((((.........(((..((..((((((((((......))))))))))..))---...)))((((((........)))))).)))))..))). ( -42.60)
>DroSec_CAF1 67635 102 - 1
UUCCUCGAAAAUGCGCACAUUUGUUUGCCUUGCCCUGGCGACCAUUCUCCUAGUCGCCGGCUCA---UCAGCAGCCACAUAUGAUCCUGUGGCGGCGCAACUUCU
......(((..(((((.........(((..((..((((((((..........))))))))..))---...)))((((((........)))))).)))))..))). ( -36.80)
>DroSim_CAF1 55792 102 - 1
UUCCUCGAAAAUGCGCACAUUUGUUUGCCUUGCCCUGGCGACCAUUCUCCUGGUCGCCGGCUCA---UCAGCAGCCACAUAUGAUCCUGUGGCGGCGCAACUUCU
......(((..(((((.........(((..((..((((((((((......))))))))))..))---...)))((((((........)))))).)))))..))). ( -42.60)
>DroEre_CAF1 75929 102 - 1
UUUCACGAAUAUGCGCACAUUUGUUUGCCUUGUCUUGGCGACCAUCCUCCUGGUCGCCGGCUCC---UCAGCUGCCACAUAUGAUCCUGUGGCGGCGCAACUUCU
......(((..(((.......((...(((.......((((((((......)))))))))))...---.))(((((((((........))))))))))))..))). ( -38.61)
>DroYak_CAF1 69913 102 - 1
UUUCUCGAAUAUGCGCACAUUUGUUUGCCUCGCCCUGGCGACCAUCCUCCUGGUCGCCGGCUCC---UCAGCAGCCACAUAUGAUCCUGUGGCGGCGCAACUUCU
......(((..(((((.........(((......((((((((((......))))))))))....---...)))((((((........)))))).)))))..))). ( -40.02)
>DroAna_CAF1 63964 101 - 1
UUUCCUGAA-AUGCGCACAUUCGUUUGUCUUGCCCUGGCGGCCGUCCUCCUGGUCGCCAGCUCAACUUCGGCGGCUACAUUCGAUCC---GGCCGCUCAACUCCU
.........-..((((....(((..(((...(((((((((((((......)))))))))).....(....).))).)))..)))...---.).)))......... ( -32.70)
>consensus
UUCCUCGAAAAUGCGCACAUUUGUUUGCCUUGCCCUGGCGACCAUCCUCCUGGUCGCCGGCUCA___UCAGCAGCCACAUAUGAUCCUGUGGCGGCGCAACUUCU
......(((..(((((.....((((.....((..((((((((((......))))))))))..)).....))))((((((........)))))).)))))..))). (-34.92 = -35.37 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:30 2006