Locus 6024

Sequence ID	3R_DroMel_CAF1
Location	15,881,424 – 15,881,558
Length	134
Max. P	0.802201

overview

Window 6

Location	15,881,424 – 15,881,519
Length	95
Sequences	3
Columns	112
Reading direction	forward
Mean pairwise identity	80.95
Mean single sequence MFE	-30.43
Consensus MFE	-23.01
Energy contribution	-23.77
Covariance contribution	0.75
Combinations/Pair	1.06
Mean z-score	-1.80
Structure conservation index	0.76
SVM decision value	0.62
SVM RNA-class probability	0.802201
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15881424 95 + 27905053
AUGGGCCAUAUGGCUAAGGGCUUACCAUGGG------------GC-UUUGUUGUGUGCCAACUGCCAUUAAAUGGCUAAUUAAGAU----UUCAGUCCGCUGGCAGUCGUCC
...(((((((((((...((.....)).(((.------------((-........)).)))...)))))...))))))......(((----(((((....)))).)))).... ( -28.90)
>DroPse_CAF1 9224 112 + 1
AUUGGCCAUAUGGCUGAGCGCUUACCUCGGUAGCCAGCUACCAGCUAUUGUUGUCUGCCAACUGCCAUUAAAUGCCUAAUUAAGAUCUAUCUCACUUUACUGGCAGUUGUCC
.(..(((....)))..)..((..((..(((((((.........)))))))..))..))(((((((((.((((((........(((....))))).)))).)))))))))... ( -31.20)
>DroPer_CAF1 9221 112 + 1
AUUGGCCAUAUGGCUGAGCGCUUACCUCGGUAGCCAGCUACCAGCUAUUGUUGUCUGCCAACUGCCAUUAAAUGCCUAAUUAAGAUCUAUCUCACUUUACUGGCAGUUGUCC
.(..(((....)))..)..((..((..(((((((.........)))))))..))..))(((((((((.((((((........(((....))))).)))).)))))))))... ( -31.20)
>consensus
AUUGGCCAUAUGGCUGAGCGCUUACCUCGGUAGCCAGCUACCAGCUAUUGUUGUCUGCCAACUGCCAUUAAAUGCCUAAUUAAGAUCUAUCUCACUUUACUGGCAGUUGUCC
.((((((....))))))..((..((..(((((((.........)))))))..))..))(((((((((((((........))))((......)).......)))))))))... (-23.01 = -23.77 +   0.75)

alignment

secondary structure

dotplot

Window 7

Location	15,881,424 – 15,881,519
Length	95
Sequences	3
Columns	112
Reading direction	reverse
Mean pairwise identity	80.95
Mean single sequence MFE	-31.10
Consensus MFE	-23.81
Energy contribution	-25.04
Covariance contribution	1.23
Combinations/Pair	1.07
Mean z-score	-1.75
Structure conservation index	0.77
SVM decision value	0.56
SVM RNA-class probability	0.781240
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15881424 95 - 27905053
GGACGACUGCCAGCGGACUGAA----AUCUUAAUUAGCCAUUUAAUGGCAGUUGGCACACAACAAA-GC------------CCCAUGGUAAGCCCUUAGCCAUAUGGCCCAU
((.(((((((((..((.((((.----.......))))))......)))))))))............-((------------(..(((((.........)))))..))))).. ( -28.30)
>DroPse_CAF1 9224 112 - 1
GGACAACUGCCAGUAAAGUGAGAUAGAUCUUAAUUAGGCAUUUAAUGGCAGUUGGCAGACAACAAUAGCUGGUAGCUGGCUACCGAGGUAAGCGCUCAGCCAUAUGGCCAAU
((.(((((((((.((((.(((((....)))))........)))).)))))))((((..............(((((....)))))((((....).))).))))..)).))... ( -32.50)
>DroPer_CAF1 9221 112 - 1
GGACAACUGCCAGUAAAGUGAGAUAGAUCUUAAUUAGGCAUUUAAUGGCAGUUGGCAGACAACAAUAGCUGGUAGCUGGCUACCGAGGUAAGCGCUCAGCCAUAUGGCCAAU
((.(((((((((.((((.(((((....)))))........)))).)))))))((((..............(((((....)))))((((....).))).))))..)).))... ( -32.50)
>consensus
GGACAACUGCCAGUAAAGUGAGAUAGAUCUUAAUUAGGCAUUUAAUGGCAGUUGGCAGACAACAAUAGCUGGUAGCUGGCUACCGAGGUAAGCGCUCAGCCAUAUGGCCAAU
...(((((((((...(((((..................)))))..)))))))))((..((.....(((((((...))))))).....))..)).....(((....))).... (-23.81 = -25.04 +   1.23)

alignment

secondary structure

dotplot

Window 8

Location	15,881,455 – 15,881,558
Length	103
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	82.22
Mean single sequence MFE	-34.63
Consensus MFE	-24.01
Energy contribution	-24.90
Covariance contribution	0.89
Combinations/Pair	1.08
Mean z-score	-1.99
Structure conservation index	0.69
SVM decision value	0.50
SVM RNA-class probability	0.760422
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15881455 103 - 27905053
AAGGGAU-UUGAAAAGGCGUGAGAUUUGCGGCCAGCUGCUGGACGACUGCCAGCGGACUGAA----AUCUUAAUUAGCCAUUUAAUGGCAGUUGGCACACAACAAA-GC-----------
..(((((-((.....(.((..(...)..)).)((((((((((.......))))))).)))))----))))).....(((((...))))).((((.....))))...-..----------- ( -32.10)
>DroPse_CAF1 9256 120 - 1
AAGGGAUAUUUAAAAGGCGUGAGUUUUGCGUCCCACUGCUGGACAACUGCCAGUAAAGUGAGAUAGAUCUUAAUUAGGCAUUUAAUGGCAGUUGGCAGACAACAAUAGCUGGUAGCUGGC
..(((((......(((((....)))))..))))).((((....(((((((((.((((.(((((....)))))........)))).))))))))))))).......((((.....)))).. ( -37.10)
>DroPer_CAF1 9253 120 - 1
AAGGGAUAUUUAAAAGGCGUGAGUUUUGCAGCCCACUGCUGGACAACUGCCAGUAAAGUGAGAUAGAUCUUAAUUAGGCAUUUAAUGGCAGUUGGCAGACAACAAUAGCUGGUAGCUGGC
..(((........(((((....)))))....))).((((....(((((((((.((((.(((((....)))))........)))).))))))))))))).......((((.....)))).. ( -34.70)
>consensus
AAGGGAUAUUUAAAAGGCGUGAGUUUUGCGGCCCACUGCUGGACAACUGCCAGUAAAGUGAGAUAGAUCUUAAUUAGGCAUUUAAUGGCAGUUGGCAGACAACAAUAGCUGGUAGCUGGC
..(((........(((((....)))))....))).((((....(((((((((...(((((..................)))))..)))))))))))))...................... (-24.01 = -24.90 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:42 2006