Locus 2364

Sequence ID	3L_DroMel_CAF1
Location	6,624,883 – 6,625,033
Length	150
Max. P	0.962468

overview

Window 5

Location	6,624,883 – 6,624,993
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.72
Mean single sequence MFE	-35.88
Consensus MFE	-19.94
Energy contribution	-20.54
Covariance contribution	0.60
Combinations/Pair	1.22
Mean z-score	-2.50
Structure conservation index	0.56
SVM decision value	1.54
SVM RNA-class probability	0.962468
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6624883 110 + 23771897
UAGGGAUAUCUC--ACAUGGGUAUGUGUGCUUAUGUGUAUGU--------GCGCCCAUUCAGUAUACUCGACAUUUGGGUCUGCUUUAAAGCGUUAAUUCGCUUUCGAGGGUGUGUAUAA
...........(--(((((((((....))))))))))((((.--------.(((((....((((.((((((...)))))).))))..((((((......))))))...)))))..)))). ( -37.20)
>DroSec_CAF1 1919 110 + 1
UAGGGAUAUCUC--ACAUGGGUAUGUGUGCCUAUGUGUGUGU--------GCGCCCAUUCAGUAUACUCGACAUUUGGGUCUGCUUUAAAGCGUUAAUUCGCUUUCGAGGGUGUGUAUAA
...........(--(((((((((....))))))))))((((.--------.(((((....((((.((((((...)))))).))))..((((((......))))))...)))))..)))). ( -40.00)
>DroSim_CAF1 10060 110 + 1
UAGGGAUAUCUC--ACAUGGGUAUGUGUGCCUAUGUGUGUGU--------GCGCCCAUUCAGUAUACUCGACAUUUGGGUCUGCUUUAAAGCGUUAAUUCGCUUUCGAGGGUGUGUAUAA
...........(--(((((((((....))))))))))((((.--------.(((((....((((.((((((...)))))).))))..((((((......))))))...)))))..)))). ( -40.00)
>DroYak_CAF1 3955 94 + 1
UAGGGAU-UCUC--ACAUGGAUAUGUGCGCUUAUGUGUGGG-----------------------UACUCGACAUUUGGGUCUGCUUUAAAGCGUUAAUUCGGUUUCGAGGGUGUGUAUAA
((.(.((-((((--..((.((.....((((((....(..(.-----------------------.((((((...)))))))..)....))))))....)).))...)))))).).))... ( -21.40)
>DroAna_CAF1 2156 117 + 1
UGGGGUGAGCACAUACUUGGGCAAGGAUACCCGUGUGUGUAUAGGAUGUGGUGGGCAUCCA-CACUCCCGACAU-UGGGUCAG-UUUAAAGCGUUAAUUCGCUUUUGAGGGUGUGUAUAA
........((((((((..(((........)))))))))))...((((((.....))))))(-(((.((((((..-...)))..-((.((((((......)))))).))))).)))).... ( -40.80)
>consensus
UAGGGAUAUCUC__ACAUGGGUAUGUGUGCCUAUGUGUGUGU________GCGCCCAUUCAGUAUACUCGACAUUUGGGUCUGCUUUAAAGCGUUAAUUCGCUUUCGAGGGUGUGUAUAA
..............(((((((((....)))))))))..........................((((((((((......)))...((.((((((......)))))).)))))))))..... (-19.94 = -20.54 +   0.60)

alignment

secondary structure

dotplot

Window 6

Location	6,624,921 – 6,625,033
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.05
Mean single sequence MFE	-26.65
Consensus MFE	-17.84
Energy contribution	-20.44
Covariance contribution	2.60
Combinations/Pair	1.10
Mean z-score	-3.02
Structure conservation index	0.67
SVM decision value	1.13
SVM RNA-class probability	0.919839
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6624921 112 - 23771897
AAUAAUCAAUUCGGUAGUCACUCAAUUAUUGAGCCCUUCAUUAUACACACCCUCGAAAGCGAAUUAACGCUUUAAAGCAGACCCAAAUGUCGAGUAUACUGAAUGGGCGC--------AC
..........((((((((......))))))))((((((((.(((((.....((..((((((......))))))..))..(((......)))..))))).)))).))))..--------.. ( -30.20)
>DroSec_CAF1 1957 112 - 1
AAUAAUCAAUUCGGUAGUCACUCAAUUAUUGAGCCCUUCAUUAUACACACCCUCGAAAGCGAAUUAACGCUUUAAAGCAGACCCAAAUGUCGAGUAUACUGAAUGGGCGC--------AC
..........((((((((......))))))))((((((((.(((((.....((..((((((......))))))..))..(((......)))..))))).)))).))))..--------.. ( -30.20)
>DroSim_CAF1 10098 112 - 1
AAUAAUCAAUUCGGUAGUCACUCAAUUAUUGAGCCCUUCAUUAUACACACCCUCGAAAGCGAAUUAACGCUUUAAAGCAGACCCAAAUGUCGAGUAUACUGAAUGGGCGC--------AC
..........((((((((......))))))))((((((((.(((((.....((..((((((......))))))..))..(((......)))..))))).)))).))))..--------.. ( -30.20)
>DroYak_CAF1 3992 97 - 1
AAUAAUCAAUUCGGUAGUCACUCAAUUAUUGAGCCCUUCAUUAUACACACCCUCGAAACCGAAUUAACGCUUUAAAGCAGACCCAAAUGUCGAGUA-----------------------C
.......((((((((.....((((.....))))...(((...............)))))))))))...(((....))).(((......))).....-----------------------. ( -14.16)
>DroAna_CAF1 2196 117 - 1
AAUAAUCAAUUCGGUAUUCACUCAAUUAUUGAGCCCUUCAUUAUACACACCCUCAAAAGCGAAUUAACGCUUUAAA-CUGACCCA-AUGUCGGGAGUG-UGGAUGCCCACCACAUCCUAU
............(((((((.((((.....))))...........((((.(((...((((((......))))))...-..(((...-..)))))).)))-))))))))............. ( -28.50)
>consensus
AAUAAUCAAUUCGGUAGUCACUCAAUUAUUGAGCCCUUCAUUAUACACACCCUCGAAAGCGAAUUAACGCUUUAAAGCAGACCCAAAUGUCGAGUAUACUGAAUGGGCGC________AC
..........((((((((......))))))))((((((((.(((((.........((((((......))))))......(((......)))..))))).)))).))))............ (-17.84 = -20.44 +   2.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:30 2006