Locus 1973

Sequence ID	3L_DroMel_CAF1
Location	5,449,734 – 5,449,907
Length	173
Max. P	0.963413

overview

Window 2

Location	5,449,734 – 5,449,853
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.66
Mean single sequence MFE	-40.72
Consensus MFE	-35.41
Energy contribution	-35.48
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-2.05
Structure conservation index	0.87
SVM decision value	0.47
SVM RNA-class probability	0.750583
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5449734 119 + 23771897
CCUCCUGGGGCAGCACUUUCGCUGGGUUUUGUUCCGCACUGCUUACGAGCUAACAACAAUCAUCAGCACACUGUGCCC-CCGGGCCAAGGAAUGCACAUCCGACACCGUGUAUCCUGGCC
....((((((..((((....(((((...(((((.......(((....)))....)))))...))))).....))))))-))))((((.(((.(((((..........)))))))))))). ( -41.30)
>DroSec_CAF1 11187 120 + 1
CCUCCUGGGGCAGCACUUUCGCUGGGUUUUGUUCCGCACUGCUUACGAGCUAACAACAAUCAUCAGCACACAGUGCCCCCCGGGCCAAGGAAUGCACAUCCGACACCGUGUAUCCUGGCC
....((((((..(((((...(((((...(((((.......(((....)))....)))))...)))))....))))).))))))((((.(((.(((((..........)))))))))))). ( -42.80)
>DroSim_CAF1 11285 120 + 1
CCUCCUGGGGCAGCACUUUCGCUGGGUUUUGUUCCGCACUGCUUACGAGCUAACAACAAUCAUCAGCACACAGUGCCCUCCGGGCCAAGGAAUGCACAUCCGACACCGUGUAUCCUGGCC
....((((((..(((((...(((((...(((((.......(((....)))....)))))...)))))....))))).))))))((((.(((.(((((..........)))))))))))). ( -39.80)
>DroEre_CAF1 10924 118 + 1
CCUCCUGGGGCAGCACUUUCGUUGGGU-UUGUUUCGCACUGCUUACCAGCUAACAACAAUCAUCAGCACACUGUGGCC-CCGGGCCAAGGAAUGCACAUCCGACACCGUGUAUCCUGGCC
....(((((((.(((.....(((((..-(((((.....(((.....))).....)))))...)))))....))).)))-))))((((.(((.(((((..........)))))))))))). ( -39.00)
>consensus
CCUCCUGGGGCAGCACUUUCGCUGGGUUUUGUUCCGCACUGCUUACGAGCUAACAACAAUCAUCAGCACACAGUGCCC_CCGGGCCAAGGAAUGCACAUCCGACACCGUGUAUCCUGGCC
....((((((..((((....(((((...(((((.......(((....)))....)))))...))))).....)))))).))))((((.(((.(((((..........)))))))))))). (-35.41 = -35.48 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	5,449,813 – 5,449,907
Length	94
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.98
Mean single sequence MFE	-29.10
Consensus MFE	-17.17
Energy contribution	-17.89
Covariance contribution	0.72
Combinations/Pair	1.10
Mean z-score	-2.09
Structure conservation index	0.59
SVM decision value	1.55
SVM RNA-class probability	0.963413
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5449813 94 + 23771897
CGGGCCAAGGAAUGCACAUCCGACACCGUGUAUCCUGGCCACUUUCCCCGCCCAU----------UUCCCAGGCCCACC--------------CA--UCCUGUCAGCAUGCAACAAAUGC
.(((((.((((.(((((..........)))))))))(((..........)))...----------......)))))...--------------..--........((((.......)))) ( -25.20)
>DroSec_CAF1 11267 94 + 1
CGGGCCAAGGAAUGCACAUCCGACACCGUGUAUCCUGGCCACUUUCCCCGCCCAU----------UUCCCAGGACCACC--------------CA--UCCUGUCAGCAUGCAACAAAUGC
..(((((.(((.(((((..........)))))))))))))...............----------....(((((.....--------------..--)))))...((((.......)))) ( -25.20)
>DroSim_CAF1 11365 94 + 1
CGGGCCAAGGAAUGCACAUCCGACACCGUGUAUCCUGGCCACUUUCCCCGCCCAU----------UUCCCAGGACCACC--------------CA--UCCUGUCAGCAUGCAACAAAUGC
..(((((.(((.(((((..........)))))))))))))...............----------....(((((.....--------------..--)))))...((((.......)))) ( -25.20)
>DroEre_CAF1 11002 108 + 1
CGGGCCAAGGAAUGCACAUCCGACACCGUGUAUCCUGGCCACUUUCCCCGCCCAU----------UUUCCAGGACCUCCCAUCCCCCAUCCCCCA--UCCUGUCAGCAUGCAACAAAUGC
..(((((.(((.(((((..........)))))))))))))...............----------....(((((.....................--)))))...((((.......)))) ( -23.80)
>DroMoj_CAF1 2166 111 + 1
C-GGGCAAGGAAUGCACAGGCGACACGAGGUG--CUGCCAGCACCAACAGCUGCAGCUGCAGCUCCACCCAGCACCAGC-----UGCGUGCUGCGUGCUCUGU-UGCAUGCAACAAAUGC
.-..(((.....((((((((.(.((((.((((--(.....)))))..((((((((((((..(((......)))..))))-----)))).))))))))))))).-)))))))......... ( -46.10)
>consensus
CGGGCCAAGGAAUGCACAUCCGACACCGUGUAUCCUGGCCACUUUCCCCGCCCAU__________UUCCCAGGACCACC______________CA__UCCUGUCAGCAUGCAACAAAUGC
..(((((.(((.(((((..........))))))))))))).............................((((.........................))))...((((.......)))) (-17.17 = -17.89 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:32 2006