Locus 7507

Sequence ID	3L_DroMel_CAF1
Location	20,172,785 – 20,172,908
Length	123
Max. P	0.864053

overview

Window 8

Location	20,172,785 – 20,172,884
Length	99
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	77.46
Mean single sequence MFE	-30.89
Consensus MFE	-18.75
Energy contribution	-18.45
Covariance contribution	-0.30
Combinations/Pair	1.39
Mean z-score	-1.83
Structure conservation index	0.61
SVM decision value	0.84
SVM RNA-class probability	0.864053
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20172785 99 + 23771897
GCCACCACCACCG---GCGUCCACUGAGGAUGCCUCACUGGCAAAAUCGAGCUGCCGAUGUUCCUGUUUCACCUGCAGCUGCAGCACGUUCUUAAUGUCCUC--
((((........(---((((((.....)))))))....))))......(((((((...(((..((((.......))))..)))))).))))...........-- ( -28.50)
>DroPse_CAF1 5368 102 + 1
GCCGGCAUCGCCUCCCGCUGUUGCCGCCGCAGCCUCACUGGCAUAGUCUAAGUGCUGCUGCUCCUGUUUCACUUGCAGCUGCAGCACAUUUUUAAUGUCCUC--
(((((((..((.....))...)))))..)).(((.....)))(((....(((((.((((((..((((.......))))..)))))))))))....)))....-- ( -33.10)
>DroSim_CAF1 6031 99 + 1
GCCACCACCACCG---GCGUCCACUGAGGAUGCCUCACUGGCAAAAUCGAGCUGCCGCUGUUCUUGUUUCACCUGCAGAUGCAGCACGUUCUUAAUGUCCUC--
((((........(---((((((.....)))))))....)))).....((.(((((..((((.............))))..))))).))..............-- ( -29.62)
>DroYak_CAF1 5071 99 + 1
GCCACCACCGCCA---GCGUCCACUGAGGAUGCCUCACUGGCAUAUUCAAGCUGUCGCUGUUCCUGUUUUACUUGCAGCUGCAGCACGUUCUUAAUGUCCUC--
.........((((---((((((.....)))))).....))))........(((((.(((((.............))))).))))).................-- ( -29.12)
>DroAna_CAF1 5819 98 + 1
UCCGCCACUCUC------CACCGCAGCGGAUGGCUCGCUGGCAUAGUCCAGCUGGCGCUGUUCCUGCUUCACCUGCAGCUGAAGGACAUUCUUAAUGUCCUCUC
(((((..(....------....)..)))))..(((.(((((......))))).)))(((((.............)))))...(((((((.....)))))))... ( -31.92)
>DroPer_CAF1 5361 102 + 1
GCCGGCAUCGCCUCCCGCUGUUGCCGCCGCAGCCUCACUGGCAUAGUCUAAGUGCUGCUGCUCCUGUUUCACUUGCAGCUGCAGCACAUUUUUAAUGUCCUC--
(((((((..((.....))...)))))..)).(((.....)))(((....(((((.((((((..((((.......))))..)))))))))))....)))....-- ( -33.10)
>consensus
GCCACCACCGCCG___GCGUCCACUGAGGAUGCCUCACUGGCAUAGUCGAGCUGCCGCUGUUCCUGUUUCACCUGCAGCUGCAGCACAUUCUUAAUGUCCUC__
................((((((.....))))))......((((.........))))(((((..((((.......))))..)))))((((.....))))...... (-18.75 = -18.45 +  -0.30)

alignment

secondary structure

dotplot

Window 9

Location	20,172,809 – 20,172,908
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	78.11
Mean single sequence MFE	-24.67
Consensus MFE	-15.47
Energy contribution	-15.22
Covariance contribution	-0.25
Combinations/Pair	1.33
Mean z-score	-1.47
Structure conservation index	0.63
SVM decision value	0.26
SVM RNA-class probability	0.659201
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20172809 99 + 23771897
GGAUGCCUCACUGGCAAAAUCGAGCUGCCGAUGUUCCUGUUUCACCUGCAGCUGCAGCACGUUCUUAAUGUCCUCCUGCCCCGCUCCAUUGUCCUCCAG
(((((((.....))).....((((((((.(.((.........)).).))))))((((.((((.....))))....))))..)).......))))..... ( -22.10)
>DroVir_CAF1 10872 90 + 1
AGCUGCAUCAUUGGCAUAGUCCAGCUGCCGAUGCUCUUGCUUGACGUGCAACUGCAACACACUUUUAAUCUCCUCCUGCCC---------AUCCUCUGG
.(.((((.((((((((.........))))))))...((((.......)))).)))).).....................((---------(.....))) ( -16.10)
>DroPse_CAF1 5395 99 + 1
CGCAGCCUCACUGGCAUAGUCUAAGUGCUGCUGCUCCUGUUUCACUUGCAGCUGCAGCACAUUUUUAAUGUCCUCCUGGCCGCCUGUUCCCUCUUCCAA
.((.(((.....(((((.....(((((.((((((..((((.......))))..)))))))))))...))))).....))).))................ ( -30.00)
>DroSim_CAF1 6055 99 + 1
GGAUGCCUCACUGGCAAAAUCGAGCUGCCGCUGUUCUUGUUUCACCUGCAGAUGCAGCACGUUCUUAAUGUCCUCCUGCCCCGCUCCAUCGUCAUCCAG
(((((((.....)))......((((.((.(((((..((((.......))))..)))))((((.....))))......))...)))).......)))).. ( -25.10)
>DroYak_CAF1 5095 99 + 1
GGAUGCCUCACUGGCAUAUUCAAGCUGUCGCUGUUCCUGUUUUACUUGCAGCUGCAGCACGUUCUUAAUGUCCUCCUGCCCCGCUCCAUCGUCCUCCAG
(((((.......((((.......(((((.(((((.............))))).)))))((((.....)))).....)))).........)))))..... ( -24.71)
>DroPer_CAF1 5388 99 + 1
CGCAGCCUCACUGGCAUAGUCUAAGUGCUGCUGCUCCUGUUUCACUUGCAGCUGCAGCACAUUUUUAAUGUCCUCCUGGCCGCCUGUUCCCUCUUCCAA
.((.(((.....(((((.....(((((.((((((..((((.......))))..)))))))))))...))))).....))).))................ ( -30.00)
>consensus
GGAUGCCUCACUGGCAUAGUCGAGCUGCCGCUGCUCCUGUUUCACUUGCAGCUGCAGCACAUUCUUAAUGUCCUCCUGCCCCGCUCCAUCGUCCUCCAG
....(((.....)))..............(((((..((((.......))))..)))))......................................... (-15.47 = -15.22 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:01 2006