Locus 2391

Sequence ID	3L_DroMel_CAF1
Location	6,729,430 – 6,729,655
Length	225
Max. P	0.865307

overview

Window 5

Location	6,729,430 – 6,729,538
Length	108
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	70.85
Mean single sequence MFE	-45.73
Consensus MFE	-15.88
Energy contribution	-17.93
Covariance contribution	2.06
Combinations/Pair	1.30
Mean z-score	-1.88
Structure conservation index	0.35
SVM decision value	0.05
SVM RNA-class probability	0.561032
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6729430 108 - 23771897
AGGUGGU---------GGCGGCGGAGGAGGUGGAGCUCCAGCUGGUGCAUAUGCUCUACCCCAUCCCGUGCAGGCACCGCCGCCGUUUGCCUACAAUAUACCGCCCAAUCAGCCGCC
.((((((---------((((((((.((.((((((((....((....))....))))))))))...((.....))..))))))))((......)).....))))))............ ( -49.30)
>DroSec_CAF1 2365 117 - 1
AGGUAGUGGUGGCGGCGGCGGCGGAGGAGGUGGAGCUCCAGCUGGAGCAUAUGCUCUACCCCAUCCCGUGCAGGCACCGCCGCCGUUCGCCUACAACAUACCGCCCAAUCAGCCGCC
.((((((.((((((((((((((((.((.((((((((....((....))....))))))))))...((.....))..))))))))).))))).)).)).))))............... ( -58.50)
>DroEre_CAF1 2182 105 - 1
CGGC------------GGUGGCGGAGGCGGAGGAGCUCCUGCUGGGGCAUACGCCGUGCCCCAUCCCGUGCAGCCACCGCCGCCGUUCGCCUACAAUAUUCCGCCCAAUCAGCCGGC
((((------------((((((((.(((((((...))))(((((((((((.....))))))))......)))))).))))))))((......)).................)))).. ( -50.70)
>DroWil_CAF1 2045 84 - 1
AGGUG------------------GAGGAGGUGGGGCAGCCGC------------CAUG---AAUCCCAUGCAGCCGCCACCGCCGUUUGCCUACAAUAUACCGCCCAAUCAGCCGCC
.((((------------------(..((((((((((.((.((------------.(((---.....))))).)).))).)))))((......))..............))..))))) ( -31.40)
>DroYak_CAF1 2397 105 - 1
AGGU------------GGCGGCGGAGGAGGUGGAGCCCCAGCUGGCGCAUAUGCUGUGCCGCAUCCCGUGCAGCCACCGCCGCCCUUUGCCUACAAUAUACCACCCAAUCAGCCGGC
.(((------------((.((((((((.((((((((....)))(((((((((((......))))...)))).))).)))))..)))))))).........)))))............ ( -42.40)
>DroAna_CAF1 2167 90 - 1
GGGUGCU---------GGAGGUGGAGGUGGUGCC------GCUU--------GCGCUGCACCACC----ACAAGCGCCGCCACCAUUUGCCUACAAUAUUCCGCCCAACCAGCCGCC
.((((((---------((.(((((((((((((.(------((((--------(.(.((...)).)----.)))))).)))))))..(((....)))...))))))...)))).)))) ( -42.10)
>consensus
AGGUG___________GGCGGCGGAGGAGGUGGAGCUCCAGCUGG_GCAUAUGCUCUGCCCCAUCCCGUGCAGCCACCGCCGCCGUUUGCCUACAAUAUACCGCCCAAUCAGCCGCC
.(((............((((((((.((.((((((((....)))...((....))...................))))).)).))).)))))...........)))............ (-15.88 = -17.93 +   2.06)

alignment

secondary structure

dotplot

Window 6

Location	6,729,538 – 6,729,655
Length	117
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	78.30
Mean single sequence MFE	-48.87
Consensus MFE	-24.33
Energy contribution	-24.58
Covariance contribution	0.25
Combinations/Pair	1.24
Mean z-score	-2.18
Structure conservation index	0.50
SVM decision value	0.54
SVM RNA-class probability	0.774809
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6729538 117 + 23771897
CCACCGAAGGGUGGGUAAUUGAAGGGCUUUGCGCUCGGUGGCAUCGGCAUGUCGGGCAGUGCUGGCAUAGCCGGAUAGCCAAUGAAGCCCAUUUGUGGCGGCGCAGCACCACCGCCG
(((((....))))).........(((((((..(((....)))...(((.((((.(((.(((....))).))).)))))))...)))))))......(((((.(......).))))). ( -53.50)
>DroGri_CAF1 2351 112 + 1
CCACCGAAAUGUGGAUAAUUAAAUGGCUUGCUACUGGGUGGCGCUGGCAUUUCCGGCAAUUGUGGCAUUGCCGGAUAUCCAAUGAAACCCAUUUGAGGUGGAUGAGGCACAC-----
((((......)))).........((.(((((((((((((..((.(((.((.(((((((((......))))))))).))))).))..))))......))))).)))).))...----- ( -38.90)
>DroSec_CAF1 2482 117 + 1
CCACCGAAGGGUGGGUAAUUGAAGGGCUUUGCGCUCGGUGGCAUCGGCAUGUCGGGCAGUGCUGGCAUGGCCGGAUAGCCAAUGAAGCCCAUUUGGGGCGGUGCAGCCCCACCGCCG
(((((....)))))....(..(((((((((..(((....)))...(((.((((.(((.(((....))).))).)))))))...))))))).))..)(((((((......))))))). ( -58.20)
>DroWil_CAF1 2129 113 + 1
CCACCAAAGGGUGGAUAGUUGAAUGGUUUGCUGGUCGGGGGCUCUGGCAUGGAGGGCAAUGGCGGAACUGCCGGAUAACCAAUGAAACCCAUCUGUGGUGGAGGUGCUCCACC----
(((((....)))))((((.((...(((((..(((((((.((.((((.(((........))).)))).)).)))....))))...))))))).))))(((((((...)))))))---- ( -42.30)
>DroYak_CAF1 2502 117 + 1
CCACCGAAGGGUGGGUAAUUGAAGGGCUUGGCGCUCGGUGGCAUUGGCAUAUCGGGCAGUGCUGGCAUAGCCGGAUAACCAACAAAGCCCAUUUGUGGCGGUGCAGGACCACCUCCG
(((((....))))).........(((((((((((((((((((....)).)))))))).(((....))).)))((....))....))))))......((.((((......)))).)). ( -49.50)
>DroMoj_CAF1 1967 112 + 1
CCACCGAAGGGUGGAUAAUUGAAUGGCUUGCUGCUGGGAGGCGCUGGCAUGUCUGGCAGCUGUGGCAUUGGCGGAUAGCCAAUGAAGCCCAUUUGAGGUGGUGCAGGGGCAC-----
(((((....)))))....(..(((((((((((((..((..((....))...))..))))).....(((((((.....)))))))))).)))))..)....((((....))))----- ( -50.80)
>consensus
CCACCGAAGGGUGGAUAAUUGAAGGGCUUGCCGCUCGGUGGCACUGGCAUGUCGGGCAGUGCUGGCAUUGCCGGAUAGCCAAUGAAGCCCAUUUGUGGCGGUGCAGCACCACC____
(((((....)))))..........((((....((((((..((....))...)))))).....((((...))))...))))......((((....).))).................. (-24.33 = -24.58 +   0.25)

alignment

secondary structure

dotplot

Window 7

Location	6,729,538 – 6,729,655
Length	117
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	78.30
Mean single sequence MFE	-40.03
Consensus MFE	-24.28
Energy contribution	-24.62
Covariance contribution	0.34
Combinations/Pair	1.36
Mean z-score	-1.92
Structure conservation index	0.61
SVM decision value	0.85
SVM RNA-class probability	0.865307
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6729538 117 - 23771897
CGGCGGUGGUGCUGCGCCGCCACAAAUGGGCUUCAUUGGCUAUCCGGCUAUGCCAGCACUGCCCGACAUGCCGAUGCCACCGAGCGCAAAGCCCUUCAAUUACCCACCCUUCGGUGG
.(((((((......)))))))......(((((((((((((..((.(((..((....))..))).))...)))))))............)))))).........(((((....))))) ( -46.40)
>DroGri_CAF1 2351 112 - 1
-----GUGUGCCUCAUCCACCUCAAAUGGGUUUCAUUGGAUAUCCGGCAAUGCCACAAUUGCCGGAAAUGCCAGCGCCACCCAGUAGCAAGCCAUUUAAUUAUCCACAUUUCGGUGG
-----...........(((((.....(((((..(.((((((.(((((((((......))))))))).)).)))).)..)))))((.....))....................))))) ( -33.70)
>DroSec_CAF1 2482 117 - 1
CGGCGGUGGGGCUGCACCGCCCCAAAUGGGCUUCAUUGGCUAUCCGGCCAUGCCAGCACUGCCCGACAUGCCGAUGCCACCGAGCGCAAAGCCCUUCAAUUACCCACCCUUCGGUGG
.(((..((((((......))))))..((.(((((((((((..((.(((..((....))..))).))...))))))).....)))).))..)))..........(((((....))))) ( -46.30)
>DroWil_CAF1 2129 113 - 1
----GGUGGAGCACCUCCACCACAGAUGGGUUUCAUUGGUUAUCCGGCAGUUCCGCCAUUGCCCUCCAUGCCAGAGCCCCCGACCAGCAAACCAUUCAACUAUCCACCCUUUGGUGG
----(((((((...)))))))...((..(((((..((((((....((((((......))))))(((.......))).....)))))).)))))..))......(((((....))))) ( -36.00)
>DroYak_CAF1 2502 117 - 1
CGGAGGUGGUCCUGCACCGCCACAAAUGGGCUUUGUUGGUUAUCCGGCUAUGCCAGCACUGCCCGAUAUGCCAAUGCCACCGAGCGCCAAGCCCUUCAAUUACCCACCCUUCGGUGG
.(((((((((.....))))))......((((((.((((((((((.(((..((....))..))).)))).))))))((......))...)))))))))......(((((....))))) ( -42.90)
>DroMoj_CAF1 1967 112 - 1
-----GUGCCCCUGCACCACCUCAAAUGGGCUUCAUUGGCUAUCCGCCAAUGCCACAGCUGCCAGACAUGCCAGCGCCUCCCAGCAGCAAGCCAUUCAAUUAUCCACCCUUCGGUGG
-----((((....))))...........((((((((((((.....))))))).....(((((..((..((....))..))...))))))))))..........(((((....))))) ( -34.90)
>consensus
____GGUGGGCCUGCACCACCACAAAUGGGCUUCAUUGGCUAUCCGGCAAUGCCACCACUGCCCGACAUGCCAAUGCCACCGAGCACCAAGCCAUUCAAUUACCCACCCUUCGGUGG
....((((((.....)))))).......(((((..(((((..((.(((............))).))...))))).((......))...)))))..........(((((....))))) (-24.28 = -24.62 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:09 2006