Locus 2392

Sequence ID	3L_DroMel_CAF1
Location	6,730,662 – 6,730,802
Length	140
Max. P	0.996236

overview

Window 8

Location	6,730,662 – 6,730,775
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	69.85
Mean single sequence MFE	-39.87
Consensus MFE	-23.10
Energy contribution	-22.55
Covariance contribution	-0.55
Combinations/Pair	1.30
Mean z-score	-2.57
Structure conservation index	0.58
SVM decision value	2.67
SVM RNA-class probability	0.996236
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6730662 113 - 23771897
GCAACUUUGUGGUUGUGUCUGGUGAAGAACUCAAUUCGCCGCAGGAUUCGAAUCGA---GCC--UGGGCGCCAAACACAAUUGCAUAGCGGCGG--CGGCGAAAUGGCAUCGAAAAAAUG
((..((.((..(((((((.(((((((........)))(((.((((.((((...)))---)))--))))))))).)))))))..)).))..))..--..((......))............ ( -41.30)
>DroPse_CAF1 3026 85 - 1
GCCGUUUUGCGGUUGUGUCUGGCGGUUG-----UGCUGCCUCUGGUAUCGCGGC-A---G-C--CGGCUGCCAAACACAAUUGCAGUGCAGCGG-----UGA------------------
((((((((((((((((((.(((((((((-----.((((((.(.......).)))-)---)-)--))))))))).))))))))))))...)))))-----)..------------------ ( -50.50)
>DroSec_CAF1 3607 113 - 1
GCAACUUUGUUGUUGUGUCUGGUGAAGAUCAAAAUUCGCCGCAGGAUUCGAAUCGA---GCC--UGGGCGCCAAACACAAUUGCAUAGCGGCGG--CGGCGAAAUGGCAUCGAAAAAAUG
((..((.(((.(((((((.(((((((........)))(((.((((.((((...)))---)))--))))))))).))))))).))).))..))..--..((......))............ ( -38.20)
>DroSim_CAF1 1819 113 - 1
GCAACUUUGUUGUUGUGUCUGGUGAAGAACAAAAUUCGCCGCAGGAUUCGAAUCGA---GCC--UGGGCGCCAAACACAAUUGCAUAGCGGCGG--CGGCGAAAUGGCAUCGAAAAAAUG
((..((.(((.(((((((.(((((((........)))(((.((((.((((...)))---)))--))))))))).))))))).))).))..))..--..((......))............ ( -38.20)
>DroYak_CAF1 3632 100 - 1
GCAACUUUGUUGUUGUGUCUGGCGAAGAACUCAAUUCGCCGCAGGAUUCGAAG--------C--UGGGCGCCAAACACAAUUGCACAGCGGCGG--CGGCGAAAUGGAAUCG--------
((..((.(((.(((((((.(((((((........)))(((.(((.........--------)--))))))))).))))))).))).))..))..--................-------- ( -32.70)
>DroAna_CAF1 3586 107 - 1
GCAACUUUGUUUUUGUGUUUGGCGA---------UUUGCAGAGAGCCUCGAGUUUAUCGGCCGGCGAGCGCCAAACACAACUGCACUGCGGCGGAUUGGCAGAAAGG-AUUG---AAAUG
.(((((((((..((((((((((((.---------(((((...(.(((..((.....)))))).)))))))))))))))))..)).((((.(.....).)))).))))-.)))---..... ( -38.30)
>consensus
GCAACUUUGUUGUUGUGUCUGGCGAAGAAC__AAUUCGCCGCAGGAUUCGAAUCGA___GCC__UGGGCGCCAAACACAAUUGCAUAGCGGCGG__CGGCGAAAUGGCAUCG___AAAUG
((..((.(((..((((((.(((((((........)))(((..........................))))))).))))))..))).))..))............................ (-23.10 = -22.55 +  -0.55)

alignment

secondary structure

dotplot

Window 9

Location	6,730,700 – 6,730,802
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	67.98
Mean single sequence MFE	-36.12
Consensus MFE	-14.86
Energy contribution	-15.20
Covariance contribution	0.34
Combinations/Pair	1.47
Mean z-score	-2.36
Structure conservation index	0.41
SVM decision value	2.00
SVM RNA-class probability	0.985211
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6730700 102 - 23771897
ACUCCUGCUAUUAAAUCA--------AGGUU-----GGCUGCAACUUUGUGGUUGUGUCUGGUGAAGAACUCAAUUCGCCGCAGGAUUCGAAUCGA---GCC--UGGGCGCCAAACACAA
................((--------(((((-----(....))))))))...((((((.(((((((........)))(((.((((.((((...)))---)))--))))))))).)))))) ( -33.30)
>DroPse_CAF1 3043 103 - 1
AUAACCGCUAUGAUGG-ACAUGAUCGAACAU---G-CACCGCCGUUUUGCGGUUGUGUCUGGCGGUUG-----UGCUGCCUCUGGUAUCGCGGC-A---G-C--CGGCUGCCAAACACAA
..((((((...(((((-.((((......)))---)-.....)))))..))))))((((.(((((((((-----.((((((.(.......).)))-)---)-)--))))))))).)))).. ( -49.00)
>DroSec_CAF1 3645 102 - 1
ACACCUGCUAUUAAAUCA--------AGGUU-----GGCUGCAACUUUGUUGUUGUGUCUGGUGAAGAUCAAAAUUCGCCGCAGGAUUCGAAUCGA---GCC--UGGGCGCCAAACACAA
................((--------(((((-----(....))))))))...((((((.(((((((........)))(((.((((.((((...)))---)))--))))))))).)))))) ( -33.30)
>DroSim_CAF1 1857 102 - 1
ACACCUGCUAUUAAAUCA--------AGGUU-----GGCUGCAACUUUGUUGUUGUGUCUGGUGAAGAACAAAAUUCGCCGCAGGAUUCGAAUCGA---GCC--UGGGCGCCAAACACAA
................((--------(((((-----(....))))))))...((((((.(((((((........)))(((.((((.((((...)))---)))--))))))))).)))))) ( -33.30)
>DroYak_CAF1 3662 97 - 1
ACACCUGCUAUGAAAUCG--------UGGUU-----GGCUGCAACUUUGUUGUUGUGUCUGGCGAAGAACUCAAUUCGCCGCAGGAUUCGAAG--------C--UGGGCGCCAAACACAA
...((.((((((....))--------)))).-----))..(((((...)))))(((((.(((((((........)))(((.(((.........--------)--))))))))).))))). ( -31.60)
>DroAna_CAF1 3622 109 - 1
--UGCCGCUAUAAAAUCGCAGCAUCGAGGAUAAUGCGCCCGCAACUUUGUUUUUGUGUUUGGCGA---------UUUGCAGAGAGCCUCGAGUUUAUCGGCCGGCGAGCGCCAAACACAA
--(((.((.........)).)))..(((((((((((....)))...))))))))((((((((((.---------(((((...(.(((..((.....)))))).))))))))))))))).. ( -36.20)
>consensus
ACACCUGCUAUUAAAUCA________AGGUU_____GGCUGCAACUUUGUUGUUGUGUCUGGCGAAGAAC__AAUUCGCCGCAGGAUUCGAAUCGA___GCC__UGGGCGCCAAACACAA
...(((((............................(((.(((((......)))))))).((((((........)))))))))))................................... (-14.86 = -15.20 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:11 2006