Locus 2517

Sequence ID	2L_DroMel_CAF1
Location	6,956,534 – 6,956,666
Length	132
Max. P	0.999623

overview

Window 7

Location	6,956,534 – 6,956,626
Length	92
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	70.60
Mean single sequence MFE	-20.46
Consensus MFE	-6.68
Energy contribution	-7.76
Covariance contribution	1.08
Combinations/Pair	1.22
Mean z-score	-1.86
Structure conservation index	0.33
SVM decision value	0.55
SVM RNA-class probability	0.778396
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6956534 92 + 22407834
GAUUUCACAUAAGGUACACUUCUUGC--ACA-------------GUACAUAUGCAUGUACAU----AGGUAUGUAUGCACAUCUAUAUGCUAUCCCACUUACGUGCAGAUU
......................((((--((.-------------((((((....))))))..----.((((((((........))))))))...........))))))... ( -19.30)
>DroSec_CAF1 5984 102 + 1
GGUUUUACAUACGGUACACUUCUUGC--ACA-------GAUUGAGUACAUAUGCAUGUACAUAUGUAGGUAUGUAUGCUCAUCUAUAUGAUAUCCCACUUACGUGCAGAUU
......................((((--(((-------(((.(((((.((((((...(((....))).)))))).)))))))))...((......)).....))))))... ( -21.80)
>DroSim_CAF1 5988 102 + 1
GAUUUUACAUACGGUACACUUCUUGC--ACA-------GAUUGAGUACAUAUGCAUGUACAUAUGUAGGUAUGUAUGCUCAUCUAUAUGAUAUCCCACUUACGUGCAGAUU
......................((((--(((-------(((.(((((.((((((...(((....))).)))))).)))))))))...((......)).....))))))... ( -21.80)
>DroEre_CAF1 6057 81 + 1
GACCUCAC-UGAGGUACACUUUUUGC--ACA-------GCUUGUGUACAUACAUAUGUACAU--------------------AUAUGUACUAUUUCACUUACAUGAAGAUU
.(((((..-.)))))...........--(((-------...(((((((((....))))))))--------------------)..)))....(((((......)))))... ( -17.40)
>DroYak_CAF1 6018 96 + 1
AACCUCACAUAAGGUACACCUUCUGUGUACAUAUGUAUGCCUAUGUAC-UAUGUAUGUACAU-------UAUGUA-------CUAUGUACUAUUCCACUUACAUGAAGAUU
......(((.((((....)))).)))(((((((.(((((...((((((-.......))))))-------..))))-------))))))))..................... ( -22.00)
>consensus
GAUUUCACAUAAGGUACACUUCUUGC__ACA_______GAUUGAGUACAUAUGCAUGUACAU____AGGUAUGUAUGC_CAUCUAUAUGCUAUCCCACUUACGUGCAGAUU
.............((((...........................))))...((((((((..........((((((........))))))..........)))))))).... ( -6.68 =  -7.76 +   1.08)

alignment

secondary structure

dotplot

Window 8

Location	6,956,534 – 6,956,626
Length	92
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	70.60
Mean single sequence MFE	-25.60
Consensus MFE	-8.05
Energy contribution	-8.98
Covariance contribution	0.93
Combinations/Pair	1.18
Mean z-score	-3.15
Structure conservation index	0.31
SVM decision value	3.80
SVM RNA-class probability	0.999623
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6956534 92 - 22407834
AAUCUGCACGUAAGUGGGAUAGCAUAUAGAUGUGCAUACAUACCU----AUGUACAUGCAUAUGUAC-------------UGU--GCAAGAAGUGUACCUUAUGUGAAAUC
......((((((((.......((((((..(((((((((......)----))))))))..))))))..-------------.((--(((.....)))))))))))))..... ( -27.00)
>DroSec_CAF1 5984 102 - 1
AAUCUGCACGUAAGUGGGAUAUCAUAUAGAUGAGCAUACAUACCUACAUAUGUACAUGCAUAUGUACUCAAUC-------UGU--GCAAGAAGUGUACCGUAUGUAAAACC
.((((.(((....))))))).((((....))))...(((((((.(((((((((....))))))))).......-------.((--(((.....))))).)))))))..... ( -27.20)
>DroSim_CAF1 5988 102 - 1
AAUCUGCACGUAAGUGGGAUAUCAUAUAGAUGAGCAUACAUACCUACAUAUGUACAUGCAUAUGUACUCAAUC-------UGU--GCAAGAAGUGUACCGUAUGUAAAAUC
.((((.(((....))))))).((((....))))...(((((((.(((((((((....))))))))).......-------.((--(((.....))))).)))))))..... ( -27.20)
>DroEre_CAF1 6057 81 - 1
AAUCUUCAUGUAAGUGAAAUAGUACAUAU--------------------AUGUACAUAUGUAUGUACACAAGC-------UGU--GCAAAAAGUGUACCUCA-GUGAGGUC
...((((((...(((......((((((((--------------------(((....)))))))))))....))-------)((--(((.....)))))....-)))))).. ( -19.90)
>DroYak_CAF1 6018 96 - 1
AAUCUUCAUGUAAGUGGAAUAGUACAUAG-------UACAUA-------AUGUACAUACAUA-GUACAUAGGCAUACAUAUGUACACAGAAGGUGUACCUUAUGUGAGGUU
...(((((((((((.......((((((.(-------(((...-------..)))).......-(((((((........))))))).......))))))))))))))))).. ( -26.71)
>consensus
AAUCUGCACGUAAGUGGGAUAGCAUAUAGAUG_GCAUACAUACCU____AUGUACAUGCAUAUGUACACAAGC_______UGU__GCAAGAAGUGUACCUUAUGUGAAAUC
.((((.(((....)))))))................((((((.........((((((....))))))..................(((.....)))....))))))..... ( -8.05 =  -8.98 +   0.93)

alignment

secondary structure

dotplot

Window 9

Location	6,956,563 – 6,956,666
Length	103
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	80.88
Mean single sequence MFE	-26.30
Consensus MFE	-17.50
Energy contribution	-17.90
Covariance contribution	0.40
Combinations/Pair	1.08
Mean z-score	-2.22
Structure conservation index	0.67
SVM decision value	1.18
SVM RNA-class probability	0.927182
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6956563 103 - 22407834
CAUCGGUUCGCCACAGCACCCCACAGCCCAGCUAGAAUUGAAUCUGCACGUAAGUGGGAUAGCAUAUAGAUGUGCAUACAUACCU----AUGUACAUGCAUAUGUAC----
..(((((((((....)).......(((...))).)))))))((((.(((....))))))).((((((..(((((((((......)----))))))))..))))))..---- ( -29.40)
>DroSec_CAF1 6015 111 - 1
CAUCGGUUCGCCACAGCACCCCACAGCCCAGCUGGAAUUGAAUCUGCACGUAAGUGGGAUAUCAUAUAGAUGAGCAUACAUACCUACAUAUGUACAUGCAUAUGUACUCAA
..(((((((((....))......((((...)))))))))))((((.(((....)))))))..........((((..........(((((((((....))))))))))))). ( -28.30)
>DroSim_CAF1 6019 111 - 1
CAUCGGUUCGCCACAGCACCCCACAGCCCAGCUGGAAUUGAAUCUGCACGUAAGUGGGAUAUCAUAUAGAUGAGCAUACAUACCUACAUAUGUACAUGCAUAUGUACUCAA
..(((((((((....))......((((...)))))))))))((((.(((....)))))))..........((((..........(((((((((....))))))))))))). ( -28.30)
>DroEre_CAF1 6087 91 - 1
CAUCGGUUCGCCACAGCACCCCACAGCACAGCUGGAAUUGAAUCUUCAUGUAAGUGAAAUAGUACAUAU--------------------AUGUACAUAUGUAUGUACACAA
..(((((((((....))......((((...)))))))))))...(((((....)))))...((((((((--------------------(((....))))))))))).... ( -24.90)
>DroYak_CAF1 6058 96 - 1
CAUCGGUUCGCCACAGCACCCCACAGCACAGCUGGAAUUGAAUCUUCAUGUAAGUGGAAUAGUACAUAG-------UACAUA-------AUGUACAUACAUA-GUACAUAG
..(((((((((....))......((((...)))))))))))......(((((.(((........)))..-------))))).-------((((((.......-)))))).. ( -20.60)
>consensus
CAUCGGUUCGCCACAGCACCCCACAGCCCAGCUGGAAUUGAAUCUGCACGUAAGUGGGAUAGCAUAUAGAUG_GCAUACAUACCU____AUGUACAUGCAUAUGUACACAA
..(((((((((....))......((((...)))))))))))((((.(((....)))))))...............................((((((....)))))).... (-17.50 = -17.90 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:47 2006