Locus 7842

Sequence ID	3L_DroMel_CAF1
Location	20,992,370 – 20,992,551
Length	181
Max. P	0.949157

overview

Window 6

Location	20,992,370 – 20,992,480
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	86.20
Mean single sequence MFE	-19.04
Consensus MFE	-15.90
Energy contribution	-15.74
Covariance contribution	-0.16
Combinations/Pair	1.14
Mean z-score	-2.06
Structure conservation index	0.84
SVM decision value	1.39
SVM RNA-class probability	0.949157
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20992370 110 - 23771897
UGUUACUUUGAAUACUCGGGGCACUAAGCUGUUAUUUUCCACUUGAUCUGAUUUCAAAGAUCAAAAUUUUGAAAUAACAUGCAUACAGAAAACUCUAUCCCUUAACCACU
.................((((......(((((((((((....(((((((........)))))))......))))))))).))....(((....))).))))......... ( -21.40)
>DroSec_CAF1 10034 97 - 1
UUUUACUUUGAAUACUCGGGGCACUAAGCUGUUAUUUUCCACUUGAUCUGAUUUCAAAGAUCAAAAUUUUAAAAUAACAUGCAUA-------------CCCUUAACCACU
.................((((...((.(((((((((((....(((((((........)))))))......))))))))).)).))-------------))))........ ( -19.00)
>DroSim_CAF1 17445 90 - 1
UGUUACUUUGAAUACUCGGGGCACUAAGCUGUUAUUUUCCACUUGAUCUGAUUUCAAAGAUCAAAAUUUUAAAAUAAU--------------------CCCUUAACCACU
.....((((((....))))))...((((..((((((((....(((((((........)))))))......))))))))--------------------..))))...... ( -15.10)
>DroEre_CAF1 18517 110 - 1
UGUUAUUUCGAAUACUCGGGGUACUAAGCUGUUAUUUUCCACUUGAUCUGAUUUCAAAGAUCAAAAUUUUAAAAUAUCAUGCAUACAGAAAACUUGAUCCCUUGACCACU
.((((....((....))(((((.....((((.((((((....(((((((........)))))))......)))))).)).))...(((.....)))))))).)))).... ( -18.20)
>DroYak_CAF1 16196 110 - 1
UGUUAUUUUGAAUACUCGGGGUACUAAGCUGUUAUUUUCCACUUGAUCUGAUUUCAAAGAUCAAAAUUUUAAAAUAACAUGCAUACAGAAAACUUGUUCCCUUGACCACU
...............((((((......(((((((((((....(((((((........)))))))......))))))))).))..((((.....))))..))))))..... ( -21.50)
>consensus
UGUUACUUUGAAUACUCGGGGCACUAAGCUGUUAUUUUCCACUUGAUCUGAUUUCAAAGAUCAAAAUUUUAAAAUAACAUGCAUACAGAAAACU___UCCCUUAACCACU
.................(((((.....))(((((((((....(((((((........)))))))......)))))))))...................)))......... (-15.90 = -15.74 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	20,992,410 – 20,992,518
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	98.15
Mean single sequence MFE	-20.92
Consensus MFE	-19.90
Energy contribution	-19.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.28
Structure conservation index	0.95
SVM decision value	0.43
SVM RNA-class probability	0.732157
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20992410 108 + 23771897
AAAAUUUUGAUCUUUGAAAUCAGAUCAAGUGGAAAAUAACAGCUUAGUGCCCCGAGUAUUCAAAGUAACAACAAUAUUAGCCAGUGUUUUAAGUGGCCCACAAACUUG
......(((((((........)))))))((((.........(((((((((.....)))))..)))).............((((.(......).))))))))....... ( -21.60)
>DroSec_CAF1 10061 108 + 1
AAAAUUUUGAUCUUUGAAAUCAGAUCAAGUGGAAAAUAACAGCUUAGUGCCCCGAGUAUUCAAAGUAAAAACAAUAUUAGCCAGUGUUUUAAGUGGCCCACAAACUUG
......(((((((........)))))))((((.........(((((((((.....)))))..)))).............((((.(......).))))))))....... ( -21.60)
>DroSim_CAF1 17465 108 + 1
AAAAUUUUGAUCUUUGAAAUCAGAUCAAGUGGAAAAUAACAGCUUAGUGCCCCGAGUAUUCAAAGUAACAACAAUAUUAGCCAGUGUUUUAAGUGGCCCACAAACUUG
......(((((((........)))))))((((.........(((((((((.....)))))..)))).............((((.(......).))))))))....... ( -21.60)
>DroEre_CAF1 18557 108 + 1
AAAAUUUUGAUCUUUGAAAUCAGAUCAAGUGGAAAAUAACAGCUUAGUACCCCGAGUAUUCGAAAUAACAACAAUAUUAGCCAGUGUUUUAAGUGGCCCACAAACUUG
......(((((((........)))))))((((.........(((..(....)..)))......................((((.(......).))))))))....... ( -19.90)
>DroYak_CAF1 16236 108 + 1
AAAAUUUUGAUCUUUGAAAUCAGAUCAAGUGGAAAAUAACAGCUUAGUACCCCGAGUAUUCAAAAUAACAACAAUAUUAGCCAGUGUUUUAAGUGGCCCACAAACUUG
......(((((((........)))))))((((.........(((..(....)..)))......................((((.(......).))))))))....... ( -19.90)
>consensus
AAAAUUUUGAUCUUUGAAAUCAGAUCAAGUGGAAAAUAACAGCUUAGUGCCCCGAGUAUUCAAAGUAACAACAAUAUUAGCCAGUGUUUUAAGUGGCCCACAAACUUG
......(((((((........)))))))((((.........(((..(....)..)))......................((((.(......).))))))))....... (-19.90 = -19.90 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	20,992,442 – 20,992,551
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	96.15
Mean single sequence MFE	-19.38
Consensus MFE	-16.98
Energy contribution	-16.74
Covariance contribution	-0.24
Combinations/Pair	1.05
Mean z-score	-1.63
Structure conservation index	0.88
SVM decision value	1.15
SVM RNA-class probability	0.923137
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20992442 109 + 23771897
AAAAUAACAGCUUAGUGCCCCGAGUAUUCAAAGUAACAACAAUAUUAGCCAGUGUUUUAAGUGGCCCACAAACUUGGCCAGUAGGCAAUAACAAAUACGAAUACAAACU
.........(((((.((..((((((.......((....)).......((((.(......).))))......)))))).)).)))))....................... ( -20.70)
>DroSec_CAF1 10093 109 + 1
AAAAUAACAGCUUAGUGCCCCGAGUAUUCAAAGUAAAAACAAUAUUAGCCAGUGUUUUAAGUGGCCCACAAACUUGGCCAGUAGGCAAUAACAAAUACGAAUACAAACU
.........(((((.((..((((((.......((....)).......((((.(......).))))......)))))).)).)))))....................... ( -20.70)
>DroSim_CAF1 17497 109 + 1
AAAAUAACAGCUUAGUGCCCCGAGUAUUCAAAGUAACAACAAUAUUAGCCAGUGUUUUAAGUGGCCCACAAACUUGGCCAGUAGGCAAUAACAAAUACGAAUACAAACU
.........(((((.((..((((((.......((....)).......((((.(......).))))......)))))).)).)))))....................... ( -20.70)
>DroEre_CAF1 18589 109 + 1
AAAAUAACAGCUUAGUACCCCGAGUAUUCGAAAUAACAACAAUAUUAGCCAGUGUUUUAAGUGGCCCACAAACUUGGCCAAUAGGCAAUAACAAAUACAAGUGCAAACU
.........(((((.....((((((......((((.......)))).((((.(......).))))......))))))....)))))....................... ( -17.40)
>DroYak_CAF1 16268 109 + 1
AAAAUAACAGCUUAGUACCCCGAGUAUUCAAAAUAACAACAAUAUUAGCCAGUGUUUUAAGUGGCCCACAAACUUGGCCAAUAGGCAAUAACAAAUACAAAUGCAAACU
.........(((((.....((((((......((((.......)))).((((.(......).))))......))))))....)))))....................... ( -17.40)
>consensus
AAAAUAACAGCUUAGUGCCCCGAGUAUUCAAAGUAACAACAAUAUUAGCCAGUGUUUUAAGUGGCCCACAAACUUGGCCAGUAGGCAAUAACAAAUACGAAUACAAACU
.........(((((.....((((((......((((.......)))).((((.(......).))))......))))))....)))))....................... (-16.98 = -16.74 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:25 2006