Locus 10296

Sequence ID	3R_DroMel_CAF1
Location	27,601,598 – 27,601,769
Length	171
Max. P	0.776316

overview

Window 3

Location	27,601,598 – 27,601,697
Length	99
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	72.31
Mean single sequence MFE	-22.70
Consensus MFE	-12.54
Energy contribution	-12.48
Covariance contribution	-0.05
Combinations/Pair	1.14
Mean z-score	-1.53
Structure conservation index	0.55
SVM decision value	0.35
SVM RNA-class probability	0.702217
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27601598 99 - 27905053
CA-GCCACCCAAGGCUCCAGGUGUUCACAAUAGUCA----CUUUAAUGUUCAAU------UUCCAGGCAAACCAUCGUGCUGGUUUUCUACUUUCUGUGCCUGGUGAACA
.(-(((......))))..(((((...........))----)))...((((((..------..((((((((((((......))))))...((.....)))))))))))))) ( -26.50)
>DroPse_CAF1 4967 99 - 1
CAAUCUGUA-AAAGCUAU--------A-UACAAACAUUCUAUAU-AUGUACCCUUUCAUCGUGCAGGCAAACUAUUGUGCUGGUAUUUUACUUUCUGUGUCUGGUGACAA
.....(((.-...((((.--------(-((((.((((.......-))))...........((((.((((........)))).)))).........))))).)))).))). ( -15.40)
>DroSec_CAF1 3344 99 - 1
C-----ACCCAAGGCUCUAGGUGUUCACAAUAGUCAUUCAAUUUAAUGUUCAAU------UUCCAGGCAAACCAUCGUGCUGGUUUUCUACUUUCUGUGCCUGGUGAACA
.-----......((((....((....))...))))...........((((((..------..((((((((((((......))))))...((.....)))))))))))))) ( -23.40)
>DroSim_CAF1 3332 99 - 1
C-----ACCCAAGGCUCUAGGUGUUCACUAUAGUCAUUCAAUUUAAUGUUCAAU------UUCCAGGCAAACCAUCGUGCUGGUUUUCUACUUUCUGUGCCUGGUGAACA
.-----......((((.(((.......))).))))...........((((((..------..((((((((((((......))))))...((.....)))))))))))))) ( -26.10)
>DroEre_CAF1 3394 99 - 1
CU-CCUGCCCAAGACUCCAGUUCUUCAUAGAACUAA----UUUUAAUGUUGGUU------UCCCAGGCAAACCAUUGUGCUGGUUUUCUACUUUCUGUGUCUGGUGAACA
..-...............((((((....))))))..----...........(((------..((((((((((((......))))))...((.....))))))))..))). ( -22.90)
>DroYak_CAF1 3414 99 - 1
CU-UCCGUCCAAGCUUCCAGUUCUUCGUAGAACUAA----UUUUGUUGUGUGUU------UCCCAGGCAAACCAUUGUGCUGGUUUUCUACUUUCUGUGUCUGGUAAACA
..-...............((((((....))))))..----..........((((------(.((((((((((((......))))))...((.....)))))))).))))) ( -21.90)
>consensus
C___C_ACCCAAGGCUCCAGGUGUUCACAAUAGUCA____AUUUAAUGUUCAAU______UUCCAGGCAAACCAUCGUGCUGGUUUUCUACUUUCUGUGCCUGGUGAACA
..............................................................((((((((((((......))))))...((.....))))))))...... (-12.54 = -12.48 +  -0.05)

alignment

secondary structure

dotplot

Window 4

Location	27,601,667 – 27,601,769
Length	102
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	81.88
Mean single sequence MFE	-33.80
Consensus MFE	-27.56
Energy contribution	-26.98
Covariance contribution	-0.58
Combinations/Pair	1.41
Mean z-score	-1.69
Structure conservation index	0.82
SVM decision value	0.54
SVM RNA-class probability	0.776316
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27601667 102 + 27905053
AUUGUGAACACCUGGAGCCUUGGGUGGCUGGGUCUUACAAUGGGUAAACUGCCUCCUGGGUGCAGUAGACUCGUGCCUCAUAAUUGGGGCUGGGGUUGUAAA
(((((((..((((..((((......)))))))).)))))))((((..(((((((....)).)))))..))))..((((((....))))))............ ( -36.70)
>DroSec_CAF1 3417 98 + 1
AUUGUGAACACCUAGAGCCUUGGGU----GGGUCUUACAAUGGGUAAACUGCCUCCUGGGUGCAGUAGACUCGUGCCUCAUAAUUGGGGCUGGGGUUGUAGA
.....((.(((((((....))))))----)..))(((((((((((..(((((((....)).)))))..))))..((((((....))))))....))))))). ( -35.90)
>DroSim_CAF1 3405 98 + 1
AUAGUGAACACCUAGAGCCUUGGGU----GGGUCUUACAAUGGGUAAACUGCCUCCUGGGUGCAGUAGACUCGUGCCUCAUAAUUGGGGCUGGGGUUGUAGA
.....((.(((((((....))))))----)..))(((((((((((..(((((((....)).)))))..))))..((((((....))))))....))))))). ( -35.90)
>DroEre_CAF1 3463 102 + 1
UCUAUGAAGAACUGGAGUCUUGGGCAGGAGGGUCUUACAAUGGGUAAACUGCCUCCUGGGUGCAGUAGACUCGUGCCUCGUAAUUGGGGCUGGGAUUGUAGA
((((..(...((((.(.((..((((((...(.((.......)).)...))))))...)).).))))...((((.((((((....)))))))))).)..)))) ( -33.90)
>DroYak_CAF1 3483 102 + 1
UCUACGAAGAACUGGAAGCUUGGACGGAAGGGUCUUACAAUGGGUAAACUGCCUCCUGGGUGCAGUAGACUCGUGCCUCAUAAUUUGGGCUGGGAUUGUAGA
(((((((....((...((((..((..(..((((......((((((..(((((((....)).)))))..))))))))))..)..))..))))))..))))))) ( -30.40)
>DroAna_CAF1 3590 98 + 1
ACAAUGCCAAAUGAGGUGUUUAGAG----GGAACAUACAGUGGAUAAACUGCUUCCUGUGUGCAGUAGACCCUUGUCUCGUAGUUGGGACUGGGAUUGUAAA
(((((.(((...((((.(((((..(----....(((((((.(((........)))))))))))..)))))))))((((((....))))))))).)))))... ( -30.00)
>consensus
ACUAUGAACAACUAGAGCCUUGGGU____GGGUCUUACAAUGGGUAAACUGCCUCCUGGGUGCAGUAGACUCGUGCCUCAUAAUUGGGGCUGGGAUUGUAGA
...........(((.(((((((.................((((((..(((((((....)).)))))..))))))((((((....))))))))))))).))). (-27.56 = -26.98 +  -0.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:53:30 2006