Locus 694

Sequence ID	2L_DroMel_CAF1
Location	2,013,149 – 2,013,279
Length	130
Max. P	0.977381

overview

Window 6

Location	2,013,149 – 2,013,254
Length	105
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	80.53
Mean single sequence MFE	-26.47
Consensus MFE	-25.40
Energy contribution	-25.57
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.39
Structure conservation index	0.96
SVM decision value	1.79
SVM RNA-class probability	0.977381
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2013149 105 + 22407834
AACAA----AAACAAA------A---AAAAAAGGAAUUCCUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCGCGC
.....----.......------.---.....(((....)))..((((((((((((.......))))).....((.((((((....)))))).)).............))))))).... ( -28.70)
>DroGri_CAF1 279087 99 + 1
UACAA----AAAUAAU-CGGUAUAAA--------------UCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCCCGG
.....----.......-(((......--------------...((((((((((((.......))))).....((.((((((....)))))).)).............)))))))))). ( -27.30)
>DroSec_CAF1 30703 99 + 1
---------AUAUAAA------A---AA-AAUUGAUUCUCUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCGCGC
---------.......------.---..-..............((((((((((((.......))))).....((.((((((....)))))).)).............))))))).... ( -26.90)
>DroEre_CAF1 27864 110 + 1
AAUAA----AAACAAA-AACGAA---AAAAGAUAACUUCUUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCGCGC
.....----.......-......---..((((.....))))..((((((((((((.......))))).....((.((((((....)))))).)).............))))))).... ( -27.70)
>DroYak_CAF1 32230 115 + 1
AAUAAAUAAAAACAGACAAAAAA---AAAAGACAACUUUCUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUAGAACCGCGG
.......................---.................(((((..(((((.......))))).....((.((((((....)))))).))...............))))).... ( -22.20)
>DroPer_CAF1 34911 99 + 1
--UAA----AAAUAAA------A----AAAGAUAAC--GUUAAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACC-CAC
--...----.......------.----.........--.....((((((((((((.......))))).....((.((((((....)))))).)).............)))))))-... ( -26.00)
>consensus
AAUAA____AAACAAA______A___AAAAGAUAACUUCCUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCGCGC
...........................................((((((((((((.......))))).....((.((((((....)))))).)).............))))))).... (-25.40 = -25.57 +   0.17)

alignment

secondary structure

dotplot

Window 7

Location	2,013,149 – 2,013,254
Length	105
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	80.53
Mean single sequence MFE	-27.58
Consensus MFE	-25.35
Energy contribution	-25.22
Covariance contribution	-0.14
Combinations/Pair	1.05
Mean z-score	-1.08
Structure conservation index	0.92
SVM decision value	-0.03
SVM RNA-class probability	0.515872
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2013149 105 - 22407834
GCGCGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUGAGGAAUUCCUUUUUU---U------UUUGUUU----UUGUU
....(((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))).((((....))))....---.------.......----..... ( -28.70)
>DroGri_CAF1 279087 99 - 1
CCGGGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUGA--------------UUUAUACCG-AUUAUUU----UUGUA
...((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))..--------------.........-.......----..... ( -26.90)
>DroSec_CAF1 30703 99 - 1
GCGCGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUGAGAGAAUCAAUU-UU---U------UUUAUAU---------
....(((((((.(((((........)))))(((((.......)))))....(((((.......))))))))))))((((((((.....)-))---)------))))...--------- ( -28.40)
>DroEre_CAF1 27864 110 - 1
GCGCGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUGAAGAAGUUAUCUUUU---UUCGUU-UUUGUUU----UUAUU
(((.(((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))).(((((((....)))))---))))).-.......----..... ( -28.90)
>DroYak_CAF1 32230 115 - 1
CCGCGGUUCUAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUGAGAAAGUUGUCUUUU---UUUUUUGUCUGUUUUUAUUUAUU
....(((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))).(((((((....)))))---))..................... ( -26.20)
>DroPer_CAF1 34911 99 - 1
GUG-GGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUUAAC--GUUAUCUUU----U------UUUAUUU----UUA--
(((-(((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))..))--.........----.------.......----...-- ( -26.40)
>consensus
GCGCGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUGAGAAAGUUAUCUUUU___U______UUUAUUU____UUAUU
....(((((((.(((((........)))))(((((.......)))))....(((((.......))))))))))))........................................... (-25.35 = -25.22 +  -0.14)

alignment

secondary structure

dotplot

Window 8

Location	2,013,174 – 2,013,279
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.03
Mean single sequence MFE	-30.52
Consensus MFE	-25.32
Energy contribution	-25.48
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.36
Structure conservation index	0.83
SVM decision value	1.21
SVM RNA-class probability	0.931365
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2013174 105 + 22407834
CCUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCGCGCUGAUCA----CCCGUCGCCAAA---UC--------GUUCA
.....((((((((((((.......))))).....((.((((((....)))))).)).............)))))))(((.((....----..)).)))....---..--------..... ( -30.20)
>DroVir_CAF1 22133 116 + 1
GCUCAGGUUCCACCGAGACUUGAACUCGGAUCGCAGGAUUCAGAGUCCUAAGUGCUAACCAUUACACCAUGGAACCUGUUAGAUAA----GCGACCACAAACAAACAAAAAUUUUGCCGU
(((((((((((((((((.......)))))..((((((((.....)))))..)))...............))))))))).......)----))............................ ( -28.51)
>DroPse_CAF1 36096 104 + 1
GUUAAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACC-CACUGGGCG----AGGGCCAUCAAA---GA--------GCUCU
.....(((((..(((((.......))))).((((((.((((((....)))))).))..........((((((...)-)).))))))----))))))......---..--------..... ( -31.30)
>DroGri_CAF1 279108 118 + 1
--UCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCCCGGUGAUCAAGAAUCGACAGCAAACAAGCAAAAUUUUAUUACU
--...((((((((((((.......))))).....((.((((((....)))))).)).............))))))).((((........))))...((......)).............. ( -29.90)
>DroMoj_CAF1 21196 115 + 1
CC-UAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCCAACUGAUCA----GUGAUCGCCGAGAAACAAAACUUGAAUUCU
..-..((((((((((((.......))))).....((.((((((....)))))).)).............))))))).....((((.----..))))..((((........))))...... ( -29.60)
>DroAna_CAF1 28086 105 + 1
UCCAAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCGCUAUGGUCG----GUCACUGCCAGA---UC--------GUUCC
.....((((((((((((.......))))).....((.((((((....)))))).)).............)))))))...(((((((----((....))).))---))--------))... ( -33.60)
>consensus
CCUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCCCACUGAUCA____GCGACCGCCAAA___CA________GUUCU
.....((((((((((((.......))))).....((.((((((....)))))).)).............)))))))............................................ (-25.32 = -25.48 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:08 2006