Locus 7494

Sequence ID	3R_DroMel_CAF1
Location	20,012,926 – 20,013,080
Length	154
Max. P	0.953828

overview

Window 6

Location	20,012,926 – 20,013,040
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.72
Mean single sequence MFE	-32.77
Consensus MFE	-22.87
Energy contribution	-22.37
Covariance contribution	-0.49
Combinations/Pair	1.54
Mean z-score	-1.77
Structure conservation index	0.70
SVM decision value	1.16
SVM RNA-class probability	0.924820
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20012926 114 - 27905053
CUGACUGUAAUCGUAUUUUUUAGCAUAAAUGGCCAUCACCACAUUGGUGGCCGUCUGGUGCCAGUCGUAGCGACAUUGCACAACCUUUUUGUCGUCGUUCUAUAAUAGG------GGAGU
.....((((((...........((((..((((((((((......))))))))))...))))..((((...))))))))))...((((.((((.(.....).)))).)))------).... ( -30.60)
>DroEre_CAF1 8809 113 - 1
CUGACUGUAAUCAUAUUUUUUGGCAUAAAUGGCCACAACCACAUUGGUGGCCGUCUGGUGCCAGUCGUAGCGGCACUGCACAACCUUUUUGUCAUCAUUCUAAA-AAGG------AGAGU
..(((((....)).......((((((..((((((((..........))))))))...)))))))))((((.....))))....((((((((.........))))-))))------..... ( -32.10)
>DroWil_CAF1 6997 117 - 1
CUGGGCAUAGUGAUAUUUUUUGGCAUAGAUAGUGACCACCACAUUGGUAGCGGUCUGAUGCCAAUCAUGGCGGCAUUGAACAACCUUUUUAUCCUCGUUCUGAA-AUUCGUAA--UGAGU
..((((...(((((......((((((((((.((.((((......)))).)).)))).))))))))))).))(........)..))........((((((.((..-...)).))--)))). ( -28.80)
>DroYak_CAF1 8800 112 - 1
CUGACUGUAAUCAUACUUUUUGGCAUAAAUGGCCACUACCACAUUGGUGGCCGUCUGGUGCCAGUCGUAGCGGCACUGCACAACCUUUUUGUCGUCGUUCUGA--AAGU------AGAGU
..........((.(((((.(((((((..((((((((((......))))))))))...)))))))(((.((((((((..............)).)))))).)))--))))------))).. ( -36.44)
>DroMoj_CAF1 6622 119 - 1
UUCCGCGUAAUGAUAUUUUUUGGCAUAGACGGCGACAACAACAUUUGUAGCUGUCUGAUGCCAAUCAUAUCGGCAUUGAAUAACCUUUUUGUCAUCAUCCUGCA-AAACAUUAAGAGAUU
....(((..(((((.....((((((((((((((.((((......)))).))))))).))))))).......((((..((......))..)))))))))..))).-............... ( -34.30)
>DroAna_CAF1 6983 109 - 1
CUGAGCGUAAUGGUAUUUUUUGGCAUAAAUGGCCACCACAACGUUUGUGGCGGUCUGGUGCCAAUCGUAGCGACACUGCACAACCUUUUUGUCCUCAUUCUGAA-AAA----------GU
.((((..(((.(((.....(((((((....((((.(((((.....))))).))))..)))))))..((((.....))))...)))...)))..)))).......-...----------.. ( -34.40)
>consensus
CUGACCGUAAUCAUAUUUUUUGGCAUAAAUGGCCACCACCACAUUGGUGGCCGUCUGGUGCCAAUCGUAGCGGCACUGCACAACCUUUUUGUCAUCAUUCUGAA_AAGC______AGAGU
.((((........(((...(((((((..((((((((((......))))))))))...)))))))..)))..((((..............))))))))....................... (-22.87 = -22.37 +  -0.49)

alignment

secondary structure

dotplot

Window 7

Location	20,012,960 – 20,013,080
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.89
Mean single sequence MFE	-34.40
Consensus MFE	-20.22
Energy contribution	-20.95
Covariance contribution	0.73
Combinations/Pair	1.45
Mean z-score	-1.47
Structure conservation index	0.59
SVM decision value	-0.03
SVM RNA-class probability	0.520519
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20012960 120 + 27905053
UGCAAUGUCGCUACGACUGGCACCAGACGGCCACCAAUGUGGUGAUGGCCAUUUAUGCUAAAAAAUACGAUUACAGUCAGAGCGUGAUAGAGCUGAACCCCAUCAGGCUGCACGUCAACC
(((...((((...))))..)))...((((((((((.....))))..((((...(((........))).(((.....((((..(......)..)))).....))).)))))).)))).... ( -31.80)
>DroPse_CAF1 8989 120 + 1
UGCAGUGCCGAUAUGAUUGGCAUCAAACGGCCACAAAUGUGGUGGUGGCCAUUUACGCCAAGAAGUAUCAUUAUGCCCAGAGUGUGAUAGAAAUAAAUCCUAUCCGUCUGCAUGUUAAGC
(((((.((.((((.(((((((.....((.(((((....))))).)).)))..((((((......((((....)))).....))))))........)))).)))).)))))))........ ( -33.60)
>DroGri_CAF1 10747 120 + 1
UCACAUGCCGCUACGAUUGGCAUCAGACGGCCACAAAUGUGGUUGUCGCAGUCUAUGCCAAAAAAUAUCAUUACGCCCAAAGCGUGCUGGAAGUGAAUCCGAUUCGUCUGCACAUAAUGC
.........((.(((((((((((..(((((((((....))))))))).......))))))).....(((..(((((.....)))))..(((......))))))))))..))......... ( -35.40)
>DroWil_CAF1 7034 120 + 1
UUCAAUGCCGCCAUGAUUGGCAUCAGACCGCUACCAAUGUGGUGGUCACUAUCUAUGCCAAAAAAUAUCACUAUGCCCAGAGUAUAGUGGAGGUGAAUCCCAUAAGGCUCCAUGUUAAUC
....(((..(((....(((((((..(((((((((....))))))))).......)))))))......(((((((((.....))))))))).((......))....)))..)))....... ( -36.90)
>DroAna_CAF1 7012 120 + 1
UGCAGUGUCGCUACGAUUGGCACCAGACCGCCACAAACGUUGUGGUGGCCAUUUAUGCCAAAAAAUACCAUUACGCUCAGAGUCUGGUGGAAAUAAAUCCUAUUCGGCUGCAUGUCAAUU
((((((...((((....))))((((((((((((((.....))))))(((.......)))....................).)))))))(((......)))......))))))........ ( -35.10)
>DroPer_CAF1 9215 120 + 1
UGCAGUGCCGAUAUGAUUGGCAUCAAACGGCCACAAAUGUGGUGGUGGCCAUUUACGCCAAGAAGUAUCAUUAUGCCCAGAGUGUGAUAGAAAUAAAUCCUAUCCGUCUGCAUGUUAAGC
(((((.((.((((.(((((((.....((.(((((....))))).)).)))..((((((......((((....)))).....))))))........)))).)))).)))))))........ ( -33.60)
>consensus
UGCAAUGCCGCUACGAUUGGCAUCAGACGGCCACAAAUGUGGUGGUGGCCAUUUAUGCCAAAAAAUAUCAUUACGCCCAGAGUGUGAUAGAAAUAAAUCCUAUCCGGCUGCAUGUUAAGC
....((((.(((....(((((((.(((..(((((..........)))))..))))))))))........(((((((.....))))))).................))).))))....... (-20.22 = -20.95 +   0.73)

alignment

secondary structure

dotplot

Window 8

Location	20,012,960 – 20,013,080
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.89
Mean single sequence MFE	-39.73
Consensus MFE	-20.64
Energy contribution	-20.12
Covariance contribution	-0.52
Combinations/Pair	1.47
Mean z-score	-2.55
Structure conservation index	0.52
SVM decision value	1.44
SVM RNA-class probability	0.953828
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20012960 120 - 27905053
GGUUGACGUGCAGCCUGAUGGGGUUCAGCUCUAUCACGCUCUGACUGUAAUCGUAUUUUUUAGCAUAAAUGGCCAUCACCACAUUGGUGGCCGUCUGGUGCCAGUCGUAGCGACAUUGCA
(((((.....)))))((((((((.....))))))))((((.(((((((((.........)))((((..((((((((((......))))))))))...)))))))))).))))........ ( -46.10)
>DroPse_CAF1 8989 120 - 1
GCUUAACAUGCAGACGGAUAGGAUUUAUUUCUAUCACACUCUGGGCAUAAUGAUACUUCUUGGCGUAAAUGGCCACCACCACAUUUGUGGCCGUUUGAUGCCAAUCAUAUCGGCACUGCA
..........((((..(((((((.....)))))))....)))).(((...(((((....(((((((((((((((((..........)))))))))).)))))))...)))))....))). ( -40.20)
>DroGri_CAF1 10747 120 - 1
GCAUUAUGUGCAGACGAAUCGGAUUCACUUCCAGCACGCUUUGGGCGUAAUGAUAUUUUUUGGCAUAGACUGCGACAACCACAUUUGUGGCCGUCUGAUGCCAAUCGUAGCGGCAUGUGA
...((((((((..((((((((((......)))...((((.....))))...))).....(((((((((((.((.((((......)))).)).)))).)))))))))))....)))))))) ( -42.20)
>DroWil_CAF1 7034 120 - 1
GAUUAACAUGGAGCCUUAUGGGAUUCACCUCCACUAUACUCUGGGCAUAGUGAUAUUUUUUGGCAUAGAUAGUGACCACCACAUUGGUAGCGGUCUGAUGCCAAUCAUGGCGGCAUUGAA
............(((((((((..........((((((.(.....).)))))).......(((((((((((.((.((((......)))).)).)))).))))))))))))).)))...... ( -33.10)
>DroAna_CAF1 7012 120 - 1
AAUUGACAUGCAGCCGAAUAGGAUUUAUUUCCACCAGACUCUGAGCGUAAUGGUAUUUUUUGGCAUAAAUGGCCACCACAACGUUUGUGGCGGUCUGGUGCCAAUCGUAGCGACACUGCA
........(((((.......(((......)))............((((.(((((......((((((....((((.(((((.....))))).))))..))))))))))).))).).))))) ( -36.60)
>DroPer_CAF1 9215 120 - 1
GCUUAACAUGCAGACGGAUAGGAUUUAUUUCUAUCACACUCUGGGCAUAAUGAUACUUCUUGGCGUAAAUGGCCACCACCACAUUUGUGGCCGUUUGAUGCCAAUCAUAUCGGCACUGCA
..........((((..(((((((.....)))))))....)))).(((...(((((....(((((((((((((((((..........)))))))))).)))))))...)))))....))). ( -40.20)
>consensus
GCUUAACAUGCAGACGGAUAGGAUUCAUUUCCAUCACACUCUGGGCAUAAUGAUAUUUUUUGGCAUAAAUGGCCACCACCACAUUUGUGGCCGUCUGAUGCCAAUCAUAGCGGCACUGCA
........(((((.......(((......)))............((...((((......(((((((((((.(((((..........))))).)))).)))))))))))....)).))))) (-20.64 = -20.12 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:21 2006