Locus 1334

Sequence ID	2L_DroMel_CAF1
Location	3,528,963 – 3,529,063
Length	100
Max. P	0.999994

overview

Window 0

Location	3,528,963 – 3,529,063
Length	100
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	94.87
Mean single sequence MFE	-40.73
Consensus MFE	-41.03
Energy contribution	-40.62
Covariance contribution	-0.41
Combinations/Pair	1.07
Mean z-score	-2.82
Structure conservation index	1.01
SVM decision value	5.79
SVM RNA-class probability	0.999994
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3528963 100 + 22407834
UGGUCAGCAAGAACAGGCCGUAGCUGGUGAGGCUCAGCAACUUAUUGCCGAGCGAUGCCAGCGCGGUGUCGACCAAGAGGGGCAACUCAUACUUGCAGAA
......(((((.....(((((.(((((((..((((.((((....)))).))))..))))))))))))...........(((....)))...))))).... ( -40.80)
>DroSec_CAF1 37976 100 + 1
UGGUCAGCAAGAACAGGCCGUAGCUGGUGAGGCUCAGCAACUUAUUGCCGAGCGAUGCCAGCGCGGUGUCGAGCAAGAGGGGCAACUCAUACUUGCAGAA
......(((((.....(((((.(((((((..((((.((((....)))).))))..))))))))))))...........(((....)))...))))).... ( -40.80)
>DroSim_CAF1 39641 100 + 1
UGGUCAGCAAGAACAGGCCGUAGCUGGUGAGGCUCAGCAACUUAUUGCCGAGCGAUGCCAGCGCGGUGUCGACCAAGAGGGGCAACUCAUACUUGCAGAA
......(((((.....(((((.(((((((..((((.((((....)))).))))..))))))))))))...........(((....)))...))))).... ( -40.80)
>DroEre_CAF1 39084 100 + 1
UGGUCAGCAAGAACAGGCCGUAGCUGGUGAGGCUUAGCAACUUAUUGCCAAGCGAUGCCAGCGCGGUGUCGACCAAGAGGGGCAACUCAUACUUGCAGAA
......(((((.....(((((.(((((((..((((.((((....)))).))))..))))))))))))...........(((....)))...))))).... ( -38.60)
>DroYak_CAF1 37533 100 + 1
UGGUCAGCAAGAACAGGCCGUAGCUGGUGAGGCUCAGCAACUUAUUGCCGAGCGAUGCCAGCGCGGUGUCGACCAAUAGGGGCAACUCAUACUUGCAGAA
......(((((.....(((((.(((((((..((((.((((....)))).))))..))))))))))))...........(((....)))...))))).... ( -40.80)
>DroAna_CAF1 34192 100 + 1
UGGCCAGCAAGAACAGGCCGUAGCUGGUGAAGCUCAGCAGGGUAUUGCCGAGCGAUGCCAGCGCGGUGUCGAUGCGUUGGGGCAACUCAUACUUGCAAAA
......(((((.....(((((.(((((((..((((.((((....)))).))))..))))))))))))..........((((....))))..))))).... ( -42.60)
>consensus
UGGUCAGCAAGAACAGGCCGUAGCUGGUGAGGCUCAGCAACUUAUUGCCGAGCGAUGCCAGCGCGGUGUCGACCAAGAGGGGCAACUCAUACUUGCAGAA
......(((((.....(((((.(((((((..((((.((((....)))).))))..))))))))))))...........(((....)))...))))).... (-41.03 = -40.62 +  -0.41)

alignment

secondary structure

dotplot

Window 1

Location	3,528,963 – 3,529,063
Length	100
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	94.87
Mean single sequence MFE	-36.62
Consensus MFE	-34.62
Energy contribution	-34.73
Covariance contribution	0.11
Combinations/Pair	1.09
Mean z-score	-2.56
Structure conservation index	0.95
SVM decision value	4.16
SVM RNA-class probability	0.999821
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3528963 100 - 22407834
UUCUGCAAGUAUGAGUUGCCCCUCUUGGUCGACACCGCGCUGGCAUCGCUCGGCAAUAAGUUGCUGAGCCUCACCAGCUACGGCCUGUUCUUGCUGACCA
.((.(((((.((..((((((......)).)))).(((.(((((....(((((((((....)))))))))....)))))..)))...)).))))).))... ( -37.40)
>DroSec_CAF1 37976 100 - 1
UUCUGCAAGUAUGAGUUGCCCCUCUUGCUCGACACCGCGCUGGCAUCGCUCGGCAAUAAGUUGCUGAGCCUCACCAGCUACGGCCUGUUCUUGCUGACCA
.((.(((((...((((..........))))(((((((.(((((....(((((((((....)))))))))....)))))..)))..))))))))).))... ( -36.60)
>DroSim_CAF1 39641 100 - 1
UUCUGCAAGUAUGAGUUGCCCCUCUUGGUCGACACCGCGCUGGCAUCGCUCGGCAAUAAGUUGCUGAGCCUCACCAGCUACGGCCUGUUCUUGCUGACCA
.((.(((((.((..((((((......)).)))).(((.(((((....(((((((((....)))))))))....)))))..)))...)).))))).))... ( -37.40)
>DroEre_CAF1 39084 100 - 1
UUCUGCAAGUAUGAGUUGCCCCUCUUGGUCGACACCGCGCUGGCAUCGCUUGGCAAUAAGUUGCUAAGCCUCACCAGCUACGGCCUGUUCUUGCUGACCA
.((.(((((.((..((((((......)).)))).(((.(((((....(((((((((....)))))))))....)))))..)))...)).))))).))... ( -35.50)
>DroYak_CAF1 37533 100 - 1
UUCUGCAAGUAUGAGUUGCCCCUAUUGGUCGACACCGCGCUGGCAUCGCUCGGCAAUAAGUUGCUGAGCCUCACCAGCUACGGCCUGUUCUUGCUGACCA
.((.(((((.((..((((((......)).)))).(((.(((((....(((((((((....)))))))))....)))))..)))...)).))))).))... ( -37.40)
>DroAna_CAF1 34192 100 - 1
UUUUGCAAGUAUGAGUUGCCCCAACGCAUCGACACCGCGCUGGCAUCGCUCGGCAAUACCCUGCUGAGCUUCACCAGCUACGGCCUGUUCUUGCUGGCCA
....((..(((((.((((...)))).)))..))...))(((((....((((((((......))))))))....)))))...((((.((....)).)))). ( -35.40)
>consensus
UUCUGCAAGUAUGAGUUGCCCCUCUUGGUCGACACCGCGCUGGCAUCGCUCGGCAAUAAGUUGCUGAGCCUCACCAGCUACGGCCUGUUCUUGCUGACCA
.((.(((((.((..((((.((.....)).)))).(((.(((((....(((((((((....)))))))))....)))))..)))...)).))))).))... (-34.62 = -34.73 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:56 2006