Locus 8974

Sequence ID	3R_DroMel_CAF1
Location	24,075,162 – 24,075,309
Length	147
Max. P	0.842283

overview

Window 3

Location	24,075,162 – 24,075,275
Length	113
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	92.67
Mean single sequence MFE	-29.08
Consensus MFE	-22.27
Energy contribution	-22.78
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.39
Structure conservation index	0.77
SVM decision value	0.57
SVM RNA-class probability	0.783745
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24075162 113 + 27905053
UUGC------UUCUGCUUCUGCUGGCGCUGUCAUAAUGCUGCAAUUGUUCAUUAUCCACUAAUGAACAAAAAGUGUGUGAAAAUCGCACAGACAAAAACCUAAAUGAAGAAAAUGCCGC
..((------.....((((....((...((((.....(((....((((((((((.....))))))))))..)))(((((.....))))).))))....)).....)))).....))... ( -28.00)
>DroPse_CAF1 285438 113 + 1
CUGC------UCAUGCCGCUGCUGCCGCUGUCAUAAUGCUGCAAUUGUUCAUUAUCCACUAAUGAACAAAAAGUGUGUGAAAAUCUCACUGACAAAAACCUAAAUGAAGAAAAUGCCGC
....------((((((.((....)).))(((((..(((((....((((((((((.....))))))))))..)))))((((.....))))))))).........))))............ ( -25.00)
>DroEre_CAF1 277312 113 + 1
CUGA------UUCUGCCUCUGCUGGCGCUGUCAUAAUGCUGCAAUUGUUCAUUAUCCACUAAUGAACAAAAAGUGUGUGAAAAUCGCACAGACAAAAACCUAAAUGAAGAAAAUGCCGC
.(((------(..((((......))))..))))....((.(((.((((((((((.....))))))))))....((((((.....)))))).......................))).)) ( -30.20)
>DroYak_CAF1 276970 119 + 1
GUGACUCUGCUUUUGCUUCUGCUGGCGCUGUCAUAAUGCUGCAAUUGUUCAUUAUCCACUAAUGAACAAAAAGUGUGUGAAAAUCGCACAGACAAAAACCUAAAUGAAGAAAAUGCCGC
(((((..((((...((....)).))))..)))))...((.(((.((((((((((.....))))))))))....((((((.....)))))).......................))).)) ( -33.10)
>consensus
CUGA______UUCUGCCUCUGCUGGCGCUGUCAUAAUGCUGCAAUUGUUCAUUAUCCACUAAUGAACAAAAAGUGUGUGAAAAUCGCACAGACAAAAACCUAAAUGAAGAAAAUGCCGC
..............((....)).((((.((((.....(((....((((((((((.....))))))))))..)))(((((.....))))).)))).....((......))....)))).. (-22.27 = -22.78 +   0.50)

alignment

secondary structure

dotplot

Window 4

Location	24,075,196 – 24,075,309
Length	113
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	95.28
Mean single sequence MFE	-27.25
Consensus MFE	-22.10
Energy contribution	-23.35
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-2.96
Structure conservation index	0.81
SVM decision value	0.76
SVM RNA-class probability	0.842283
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24075196 113 + 27905053
GCAAUUGUUCAUUAUCCACUAAUGAACAAAAAGUGUGUGAAAAUCGCACAGACAAAAACCUAAAUGAAGAAAAUGCCGCACAGCACUCGCUGAGCGAUGAAAAAGGAGCAUCG
(((.((((((((((.....))))))))))....((((((.....)))))).......................))).((.((((....)))).))((((.........)))). ( -29.80)
>DroPse_CAF1 285472 111 + 1
GCAAUUGUUCAUUAUCCACUAAUGAACAAAAAGUGUGUGAAAAUCUCACUGACAAAAACCUAAAUGAAGAAAAUGCCGCACAGAGCACACGGA--GAUGAAAAAGGAGCAACG
((..((((((((((.....))))))))))...((((((((.....))))............................((.....))))))...--............)).... ( -20.00)
>DroEre_CAF1 277346 113 + 1
GCAAUUGUUCAUUAUCCACUAAUGAACAAAAAGUGUGUGAAAAUCGCACAGACAAAAACCUAAAUGAAGAAAAUGCCGCACAGCACUCGCUGAGCGAUGAAAAAGGAGCAGCG
((..((((((((((.....))))))))))....((((((.....))))))........(((...............(((.((((....)))).))).(....)))).)).... ( -29.60)
>DroYak_CAF1 277010 113 + 1
GCAAUUGUUCAUUAUCCACUAAUGAACAAAAAGUGUGUGAAAAUCGCACAGACAAAAACCUAAAUGAAGAAAAUGCCGCACAGCACUCGCUGAGCGAUGAAAAAGGAGCAGCG
((..((((((((((.....))))))))))....((((((.....))))))........(((...............(((.((((....)))).))).(....)))).)).... ( -29.60)
>consensus
GCAAUUGUUCAUUAUCCACUAAUGAACAAAAAGUGUGUGAAAAUCGCACAGACAAAAACCUAAAUGAAGAAAAUGCCGCACAGCACUCGCUGAGCGAUGAAAAAGGAGCAGCG
(((.((((((((((.....))))))))))...((.((((.......)))).))....................)))(((.((((....)))).)))................. (-22.10 = -23.35 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:23:57 2006