Locus 9493

Sequence ID	3R_DroMel_CAF1
Location	25,105,008 – 25,105,129
Length	121
Max. P	0.975474

overview

Window 8

Location	25,105,008 – 25,105,106
Length	98
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	76.50
Mean single sequence MFE	-35.58
Consensus MFE	-23.41
Energy contribution	-24.48
Covariance contribution	1.08
Combinations/Pair	1.35
Mean z-score	-1.13
Structure conservation index	0.66
SVM decision value	0.01
SVM RNA-class probability	0.537702
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25105008 98 - 27905053
GU--------CCCAGAUUCCGAGUUCUGGGCUCUGGUGUCUGGAGUUC-GUGUAGCUUCAAGUGCCAA--CAGGCUGGAGAGAAGAUGCUGUCGCUGCUUGGGGUACAA
..--------.((((((.((((((.....)))).)).)))))).....-.((((.(((((((((((..--..)))..((.((......)).))...)))))))))))). ( -33.80)
>DroSec_CAF1 33941 98 - 1
GU--------UCCAGAUUCCCAGUUCUGGGCUUUGGUGUCUGGAGUUC-GCGGAGCUCCAAGUGCCCA--CAGGCUGGAGAGGAGAUGCUGUCGCUGCUUGGGGUACAA
..--------.(((((..((((....)))).)))))....((((((((-...)))))))).((((((.--(((((.(((.((......)).)).).))))))))))).. ( -41.30)
>DroSim_CAF1 34902 98 - 1
GU--------UCCAGAUUCCCAGUUCUGGGCUCUGGUGUCUGGAGUUC-GCGGAGCUCCAAGGGCCAA--CAGGCUGGAGAGGAGAUGCUGUCGCUGCUUGGGGUACAA
..--------.(((((........)))))((((((((.(.((((((((-...)))))))).).)))).--(((((.(((.((......)).)).).))))))))).... ( -36.80)
>DroEre_CAF1 34344 100 - 1
GU--------UCCAGACUCCGAGUUCUGGGCUCUGGUAUCUGUAGUUCCAAGGAGCUCCAAGUGGCGGA-GGGGCUGGGGAGCAGCUGCUGUCGCUGCUUGGGGUACAA
..--------..((((..(((.....)))..))))(((((...(((((....)))))(((((..(((((-(.(((((.....))))).)).))))..)))))))))).. ( -44.70)
>DroYak_CAF1 35155 107 - 1
GUUCUGUGGCUCCAGAUUCCGAGUUCUGGGCUCUGGUGUCUGAAGUUCCAUGAAGCUUCAAGUGCCGG--GAGGCUGGAGAGAAGAUGCUGUCGCUGCUUGGGGUACAA
.(((((..(((.(((((.((((((.....)))).)).))))).)))..)).)))((((((((((((..--..)))..((.((......)).))...))))))))).... ( -38.40)
>DroAna_CAF1 39014 79 - 1
-------------------------UUGGAUUCUGGUGUCUGGAGUUCUCUGGAGAUUCGAGUACUGGAUGAUGCUG-----AGGAUGUUGUCGCUGCUUGGGGUACAA
-------------------------(..(((((..((.((..((....))..)).))..)))).)..).((((.(..-----((.(.((....))).))..).)).)). ( -18.50)
>consensus
GU________UCCAGAUUCCGAGUUCUGGGCUCUGGUGUCUGGAGUUC_GUGGAGCUCCAAGUGCCGA__CAGGCUGGAGAGAAGAUGCUGUCGCUGCUUGGGGUACAA
...........(((((........)))))(((((((((..((((((((....))))))))..)))).....((((.(((.((......)).)).).))))))))).... (-23.41 = -24.48 +   1.08)

alignment

secondary structure

dotplot

Window 9

Location	25,105,039 – 25,105,129
Length	90
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	75.99
Mean single sequence MFE	-35.73
Consensus MFE	-22.92
Energy contribution	-24.87
Covariance contribution	1.95
Combinations/Pair	1.33
Mean z-score	-2.15
Structure conservation index	0.64
SVM decision value	1.75
SVM RNA-class probability	0.975474
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25105039 90 - 27905053
CAGCUGGUUUCUGGGUUUCUGCGGU--------CCCAGAUUCCGAGUUCUGGGCUCUGGUGUCUGGAGUUC-GUGUAGCUUCAAGUGCCAA--CAGGCUGG
(((((((..((((((..........--------))))))..))((((.....))))(((((..(((((((.-....)))))))..))))).--..))))). ( -35.50)
>DroSec_CAF1 33972 90 - 1
CAGCUGGUUUCUGGUACUCUGCGGU--------UCCAGAUUCCCAGUUCUGGGCUUUGGUGUCUGGAGUUC-GCGGAGCUCCAAGUGCCCA--CAGGCUGG
((((((((...(((..(((((((((--------(((((((.((((....)))).......)))))))).))-))))))..)))...)))..--..))))). ( -38.70)
>DroSim_CAF1 34933 90 - 1
CAGCUGGUUUCUGGGAUUCUGCGGU--------UCCAGAUUCCCAGUUCUGGGCUCUGGUGUCUGGAGUUC-GCGGAGCUCCAAGGGCCAA--CAGGCUGG
(((((((((..(((..(((((((((--------(((((((..((((.........)))).)))))))).))-))))))..)))..))))..--..))))). ( -42.80)
>DroEre_CAF1 34375 92 - 1
CAGCUGGUUUCUGGGAUUCUGGGGU--------UCCAGACUCCGAGUUCUGGGCUCUGGUAUCUGUAGUUCCAAGGAGCUCCAAGUGGCGGA-GGGGCUGG
(((((....((..((((((.(((((--------(...))))))))))))..))(((((.((..((.(((((....))))).))..)).))))-).))))). ( -40.10)
>DroYak_CAF1 35186 99 - 1
CAGCUGGUUUCUGGGAUUCUGCGGUUCUGUGGCUCCAGAUUCCGAGUUCUGGGCUCUGGUGUCUGAAGUUCCAUGAAGCUUCAAGUGCCGG--GAGGCUGG
(((((...((((((.(((.((.((((..((((((.(((((.((((((.....)))).)).))))).))..))))..)))).))))).))))--))))))). ( -37.70)
>DroAna_CAF1 39041 73 - 1
CAGCUGGUUUCUGGGAUUCUG---------------------------UUGGAUUCUGGUGUCUGGAGUUCUCUGGAGAUUCGAGUACUGGAUGAUGCUG-
((.(..((..((.((((((((---------------------------..((((((..(...)..))))))..)))).)))).)).))..).))......- ( -19.60)
>consensus
CAGCUGGUUUCUGGGAUUCUGCGGU________UCCAGAUUCCGAGUUCUGGGCUCUGGUGUCUGGAGUUC_GUGGAGCUCCAAGUGCCGA__CAGGCUGG
(((((((..((((((..................))))))..))............((((((..((((((((....))))))))..))))))....))))). (-22.92 = -24.87 +   1.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:35:52 2006