Locus 6170

Sequence ID	3R_DroMel_CAF1
Location	16,162,799 – 16,162,902
Length	103
Max. P	0.840649

overview

Window 8

Location	16,162,799 – 16,162,902
Length	103
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	96.62
Mean single sequence MFE	-38.97
Consensus MFE	-34.79
Energy contribution	-35.10
Covariance contribution	0.31
Combinations/Pair	1.03
Mean z-score	-2.10
Structure conservation index	0.89
SVM decision value	0.75
SVM RNA-class probability	0.840649
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16162799 103 + 27905053
CCGUAAACCUUUUCGGUUCUUGGCCAUAUGUUGCCGCUGUGUUGGCCACUCC-UGCAGCUUGUGGGCCACAUUGCGGUCGGUUUGCUGGUCAGCAAGCCCGCCU
..(((((((.....)))...((((((((.(((((.(..(((.....)))..)-.))))).))).)))))..))))(((.((((((((....)))))))).))). ( -39.80)
>DroSec_CAF1 32398 103 + 1
CCGUAAACCUUUUCGGUUCUUGGCCAUAUGUUGCCGCUGUGUUGGCCACUCC-UGCAGCUUGUGGGCCACAUUGCGGUCGGUUUGCUGGUCAGCAAGCCCGCCU
..(((((((.....)))...((((((((.(((((.(..(((.....)))..)-.))))).))).)))))..))))(((.((((((((....)))))))).))). ( -39.80)
>DroSim_CAF1 34534 103 + 1
CCGUAAACCUUUUCGGUUCUUGGCCAUAUGUUGCCGCUGUGUUGGCCACUCC-UGCAGCUUGUGGGCCACAUUGCGGUCGGUUUGCUGGUCAGCAAGCCCGCCU
..(((((((.....)))...((((((((.(((((.(..(((.....)))..)-.))))).))).)))))..))))(((.((((((((....)))))))).))). ( -39.80)
>DroEre_CAF1 32320 104 + 1
CCGUAAACCUUUUCGGCUCUUGGCCAUAUGUUGCCGCUGUGUUGGCCACUCCACACAGCUUGUGGGCCACAUUGUGGUCGCUUUGCUGGUCAGCAAGCCCCCCU
..............(((....((((((((((.((((((((((.((.....))))))))).....))).))).)))))))...(((((....))))))))..... ( -36.50)
>consensus
CCGUAAACCUUUUCGGUUCUUGGCCAUAUGUUGCCGCUGUGUUGGCCACUCC_UGCAGCUUGUGGGCCACAUUGCGGUCGGUUUGCUGGUCAGCAAGCCCGCCU
(((..((((.....))))..))).........(((((.((((.((((((............)).)))))))).))))).((((((((....))))))))..... (-34.79 = -35.10 +   0.31)

alignment

secondary structure

dotplot

Window 9

Location	16,162,799 – 16,162,902
Length	103
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	96.62
Mean single sequence MFE	-36.68
Consensus MFE	-31.51
Energy contribution	-31.20
Covariance contribution	-0.31
Combinations/Pair	1.11
Mean z-score	-1.89
Structure conservation index	0.86
SVM decision value	0.19
SVM RNA-class probability	0.626908
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16162799 103 - 27905053
AGGCGGGCUUGCUGACCAGCAAACCGACCGCAAUGUGGCCCACAAGCUGCA-GGAGUGGCCAACACAGCGGCAACAUAUGGCCAAGAACCGAAAAGGUUUACGG
.(((.((.(((((....))))).))(.((((..((..((......))..))-...(((.....))).)))))........)))..(((((.....))))).... ( -35.60)
>DroSec_CAF1 32398 103 - 1
AGGCGGGCUUGCUGACCAGCAAACCGACCGCAAUGUGGCCCACAAGCUGCA-GGAGUGGCCAACACAGCGGCAACAUAUGGCCAAGAACCGAAAAGGUUUACGG
.(((.((.(((((....))))).))(.((((..((..((......))..))-...(((.....))).)))))........)))..(((((.....))))).... ( -35.60)
>DroSim_CAF1 34534 103 - 1
AGGCGGGCUUGCUGACCAGCAAACCGACCGCAAUGUGGCCCACAAGCUGCA-GGAGUGGCCAACACAGCGGCAACAUAUGGCCAAGAACCGAAAAGGUUUACGG
.(((.((.(((((....))))).))(.((((..((..((......))..))-...(((.....))).)))))........)))..(((((.....))))).... ( -35.60)
>DroEre_CAF1 32320 104 - 1
AGGGGGGCUUGCUGACCAGCAAAGCGACCACAAUGUGGCCCACAAGCUGUGUGGAGUGGCCAACACAGCGGCAACAUAUGGCCAAGAGCCGAAAAGGUUUACGG
..((..(((((((....))).))))..))......(((((.....(((((((((.....)).)))))))(....)....))))).(((((.....))))).... ( -39.90)
>consensus
AGGCGGGCUUGCUGACCAGCAAACCGACCGCAAUGUGGCCCACAAGCUGCA_GGAGUGGCCAACACAGCGGCAACAUAUGGCCAAGAACCGAAAAGGUUUACGG
.((((((((((((....)))))......(((...)))))))....(((((.....(((.....))).)))))........)))..(((((.....))))).... (-31.51 = -31.20 +  -0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:29 2006