Locus 6896

Sequence ID	3R_DroMel_CAF1
Location	18,222,500 – 18,222,603
Length	103
Max. P	0.815882

overview

Window 7

Location	18,222,500 – 18,222,603
Length	103
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	84.26
Mean single sequence MFE	-29.75
Consensus MFE	-28.32
Energy contribution	-28.18
Covariance contribution	-0.14
Combinations/Pair	1.04
Mean z-score	-1.49
Structure conservation index	0.95
SVM decision value	0.66
SVM RNA-class probability	0.815882
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18222500 103 + 27905053
UAAAAAGAAAAAAA--GACAACCGACGAGGAUGGGAUUCGAAC-CCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCU-UAACCUCUCGGCCACCUCGUCU------------
..............--.......(((((((.((((.......)-))).((((((...)))).((((((.....)))))).))..-..............))))))).------------ ( -28.80)
>DroPse_CAF1 20528 101 + 1
UAAA----AAAAAGGACUCUCCCGACGAGGAUGGGAUUCGAAC-CCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCU-UAACCUCUCGGCCACCUCGUCA------------
....----.....((......))(((((((.((((.......)-))).((((((...)))).((((((.....)))))).))..-..............))))))).------------ ( -30.60)
>DroSec_CAF1 24799 107 + 1
UAGAAAGAAAAAAUAGUUCAACCGACGAGGAUGGGAUUCGAACCCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUUAACCUCUCGGCCACCUCGUUC------------
.....................((((.((((.((((........)))).((((((...)))).((((((.....)))))).))......))))))))...........------------ ( -28.30)
>DroEre_CAF1 24580 96 + 1
UAA-----AAAAGG----AUUUCGACGAGGAUGGGAUUCGAAC-CCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCU-UAACCUCUCGGCCACCUCGUCA------------
...-----......----.....(((((((.((((.......)-))).((((((...)))).((((((.....)))))).))..-..............))))))).------------ ( -29.30)
>DroWil_CAF1 23689 113 + 1
UAGGAAAAAAAAAA----UCCUCGACGAGGAUGGGAUUCGAAC-CCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCU-UAACCUCUCGGCCACCUCGUCGUUGUGUGCCGGC
.((((.........----))))....((((.((((.......)-))).((((((...)))).((((((.....)))))).))..-...))))((((((((.........))).))))). ( -32.20)
>DroYak_CAF1 20046 98 + 1
AAA-----AAAAUUAA--CUCUCGACGAGGAUGGGAUUCGAAC-CCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCU-UAACCUCUCGGCCACCUCGUCA------------
...-----........--.....(((((((.((((.......)-))).((((((...)))).((((((.....)))))).))..-..............))))))).------------ ( -29.30)
>consensus
UAAA____AAAAAA____CUCCCGACGAGGAUGGGAUUCGAAC_CCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCU_UAACCUCUCGGCCACCUCGUCA____________
.......................(((((((.(((..............((((((...)))).((((((.....)))))).))......((....))))))))))))............. (-28.32 = -28.18 +  -0.14)

alignment

secondary structure

dotplot

Window 8

Location	18,222,500 – 18,222,603
Length	103
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	84.26
Mean single sequence MFE	-36.43
Consensus MFE	-29.88
Energy contribution	-30.05
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.82
SVM decision value	0.28
SVM RNA-class probability	0.666061
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18222500 103 - 27905053
------------AGACGAGGUGGCCGAGAGGUUA-AGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGG-GUUCGAAUCCCAUCCUCGUCGGUUGUC--UUUUUUUCUUUUUA
------------....((((..(((((((((...-..((((((((.......))))))((((...))))))((((-(.......))))))))).)))))..))--))............ ( -36.70)
>DroPse_CAF1 20528 101 - 1
------------UGACGAGGUGGCCGAGAGGUUA-AGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGG-GUUCGAAUCCCAUCCUCGUCGGGAGAGUCCUUUUU----UUUA
------------.((((((((((((....)))))-..((((((((.......))))))((((...))))))((((-(.......))))))))))))(((.....)))....----.... ( -37.00)
>DroSec_CAF1 24799 107 - 1
------------GAACGAGGUGGCCGAGAGGUUAAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGGUUCGAAUCCCAUCCUCGUCGGUUGAACUAUUUUUUCUUUCUA
------------((.((((((((((....)))))...((((((((.......))))))((((...))))))(((((((....))))))))))))))((..(((.......)))..)).. ( -33.90)
>DroEre_CAF1 24580 96 - 1
------------UGACGAGGUGGCCGAGAGGUUA-AGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGG-GUUCGAAUCCCAUCCUCGUCGAAAU----CCUUUU-----UUA
------------.((((((((((((....)))))-..((((((((.......))))))((((...))))))((((-(.......)))))))))))).....----......-----... ( -35.20)
>DroWil_CAF1 23689 113 - 1
GCCGGCACACAACGACGAGGUGGCCGAGAGGUUA-AGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGG-GUUCGAAUCCCAUCCUCGUCGAGGA----UUUUUUUUUUCCUA
............(((((((((((((....)))))-..((((((((.......))))))((((...))))))((((-(.......)))))))))))))((((----.........)))). ( -40.60)
>DroYak_CAF1 20046 98 - 1
------------UGACGAGGUGGCCGAGAGGUUA-AGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGG-GUUCGAAUCCCAUCCUCGUCGAGAG--UUAAUUUU-----UUU
------------.((((((((((((....)))))-..((((((((.......))))))((((...))))))((((-(.......)))))))))))).....--........-----... ( -35.20)
>consensus
____________UGACGAGGUGGCCGAGAGGUUA_AGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGG_GUUCGAAUCCCAUCCUCGUCGAGAG____AUUUUU____UUUA
.............((((((((((((....)))))...((((((((.......))))))((((...))))))((((.(.......))))))))))))....................... (-29.88 = -30.05 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:47 2006