Locus 5050

Sequence ID	3L_DroMel_CAF1
Location	13,833,430 – 13,833,614
Length	184
Max. P	0.836720

overview

Window 8

Location	13,833,430 – 13,833,538
Length	108
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.76
Mean single sequence MFE	-24.85
Consensus MFE	-21.17
Energy contribution	-21.42
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.07
Structure conservation index	0.85
SVM decision value	0.74
SVM RNA-class probability	0.836720
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13833430 108 + 23771897
CUCU--------AUAUAUGUAGUAUAUCUAGGUAUAGUACAAGUUCGUGUUGAAUUGUAUGUGU-U---AUAGUGUCUAUAUAGCAGAUACAGAUAUAUAACCAUUUCUUGUUAUGUACU
....--------.....((((.(((((....))))).)))).............((((((.(((-(---(((.......))))))).)))))).((((((((........)))))))).. ( -24.90)
>DroSec_CAF1 8366 109 + 1
CUCU--------AUAUAUGUAGUAUAUCUAGGUAUAGUACAAGUUCGUGUUGAAUUGUAUGUGUUU---AUAGUGUCUAUAUAGCAGAUACAGAUAUAUAACCAUUUCUUGUUAUGUACU
....--------.....((((.(((((....))))).)))).............((((((.(((((---((((...))))).)))).)))))).((((((((........)))))))).. ( -23.20)
>DroSim_CAF1 7637 109 + 1
CUCU--------AUAUAUGUAGUAUAUCUAGGUAUAGUACAAGUUCGUGUUGAAUUGUAUGUGUUU---AUAGUGUCUAUAUAGCAGAUACAGAUAUAUAACCAUUUCUUGUUAUGUACU
....--------.....((((.(((((....))))).)))).............((((((.(((((---((((...))))).)))).)))))).((((((((........)))))))).. ( -23.20)
>DroYak_CAF1 8015 120 + 1
CUCUCUAUACAUAUAUAUGUAGUAUAUCUAGGUAUAGUACAAGUUCGUGUUGAAUUGUAUGUGUUUAGUAUAGUGUCUAUAUAGCAGAUACAGAUAUAUAACCAUUUCUUGUUAUGUACU
....(((.((((((((.((((.(((((....))))).))))(((((.....))))))))))))).)))....((((((.......))))))...((((((((........)))))))).. ( -28.10)
>consensus
CUCU________AUAUAUGUAGUAUAUCUAGGUAUAGUACAAGUUCGUGUUGAAUUGUAUGUGUUU___AUAGUGUCUAUAUAGCAGAUACAGAUAUAUAACCAUUUCUUGUUAUGUACU
.................((((.(((((....))))).)))).............((((((.((((....((((...))))..)))).)))))).((((((((........)))))))).. (-21.17 = -21.42 +   0.25)

alignment

secondary structure

dotplot

Window 9

Location	13,833,462 – 13,833,578
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.36
Mean single sequence MFE	-11.68
Consensus MFE	-10.10
Energy contribution	-10.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.87
SVM decision value	0.25
SVM RNA-class probability	0.652281
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13833462 116 - 23771897
AACCAACAACCAACUACAACAAAAACAAACUGUGCCACCUAGUACAUAACAAGAAAUGGUUAUAUAUCUGUAUCUGCUAUAUAGACACUAU---A-ACACAUACAAUUCAACACGAACUU
..............................(((((......)))))......((((((((((((..(((((((.....)))))))...)))---)-)).)))....)))........... ( -13.70)
>DroSec_CAF1 8398 110 - 1
AA-------CCAACUACAACAAAAACAAACUGUGCCACCUAGUACAUAACAAGAAAUGGUUAUAUAUCUGUAUCUGCUAUAUAGACACUAU---AAACACAUACAAUUCAACACGAACUU
..-------.....................((((.....((((..(((((.(....).)))))...(((((((.....))))))).)))).---...))))................... ( -10.90)
>DroSim_CAF1 7669 117 - 1
AACCAACAACCAACUACAACAAAAACAAACUGUGCCACCUAGUACAUAACAAGAAAUGGUUAUAUAUCUGUAUCUGCUAUAUAGACACUAU---AAACACAUACAAUUCAACACGAACUU
..............................((((.....((((..(((((.(....).)))))...(((((((.....))))))).)))).---...))))................... ( -10.90)
>DroYak_CAF1 8055 120 - 1
AACCAACAACCAACUACAACAAAAACAAACUGUGCCACCUAGUACAUAACAAGAAAUGGUUAUAUAUCUGUAUCUGCUAUAUAGACACUAUACUAAACACAUACAAUUCAACACGAACUU
..............................((((.....(((((.(((((.(....).)))))...(((((((.....))))))).....)))))..))))................... ( -11.20)
>consensus
AACCAACAACCAACUACAACAAAAACAAACUGUGCCACCUAGUACAUAACAAGAAAUGGUUAUAUAUCUGUAUCUGCUAUAUAGACACUAU___AAACACAUACAAUUCAACACGAACUU
..............................((((.....((((..(((((.(....).)))))...(((((((.....))))))).)))).......))))................... (-10.10 = -10.10 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	13,833,498 – 13,833,614
Length	116
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	95.69
Mean single sequence MFE	-11.50
Consensus MFE	-11.50
Energy contribution	-11.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.36
Structure conservation index	1.00
SVM decision value	0.06
SVM RNA-class probability	0.564036
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13833498 116 - 23771897
AAAACCUUUAAUGAAUUCAGACCAGACCACAAAAACAACCAACAACCAACUACAACAAAAACAAACUGUGCCACCUAGUACAUAACAAGAAAUGGUUAUAUAUCUGUAUCUGCUAU
.................((((.((((.........................................((((......))))(((((.(....).)))))...))))..)))).... ( -11.50)
>DroSec_CAF1 8435 109 - 1
AAAACCUUUAAUGAAUUCAGACCAGACCACAAAAACAA-------CCAACUACAACAAAAACAAACUGUGCCACCUAGUACAUAACAAGAAAUGGUUAUAUAUCUGUAUCUGCUAU
.................((((.((((............-------......................((((......))))(((((.(....).)))))...))))..)))).... ( -11.50)
>DroSim_CAF1 7706 116 - 1
AAAACCUUUAAUGAAUUCAGACCAGACCACAAAAACAACCAACAACCAACUACAACAAAAACAAACUGUGCCACCUAGUACAUAACAAGAAAUGGUUAUAUAUCUGUAUCUGCUAU
.................((((.((((.........................................((((......))))(((((.(....).)))))...))))..)))).... ( -11.50)
>DroYak_CAF1 8095 116 - 1
AAAUCCUUUAAUCAAUUCAGACCAGACCACAAGAACAACCAACAACCAACUACAACAAAAACAAACUGUGCCACCUAGUACAUAACAAGAAAUGGUUAUAUAUCUGUAUCUGCUAU
.................((((.((((.........................................((((......))))(((((.(....).)))))...))))..)))).... ( -11.50)
>consensus
AAAACCUUUAAUGAAUUCAGACCAGACCACAAAAACAACCAACAACCAACUACAACAAAAACAAACUGUGCCACCUAGUACAUAACAAGAAAUGGUUAUAUAUCUGUAUCUGCUAU
.................((((.((((.........................................((((......))))(((((.(....).)))))...))))..)))).... (-11.50 = -11.50 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:50 2006