Locus 3093

Sequence ID	2L_DroMel_CAF1
Location	8,803,066 – 8,803,202
Length	136
Max. P	0.633108

overview

Window 5

Location	8,803,066 – 8,803,162
Length	96
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	79.45
Mean single sequence MFE	-20.28
Consensus MFE	-16.30
Energy contribution	-17.02
Covariance contribution	0.72
Combinations/Pair	1.17
Mean z-score	-1.23
Structure conservation index	0.80
SVM decision value	-0.05
SVM RNA-class probability	0.509235
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8803066 96 - 22407834
CCAGCCGAACCGA-----AAUACUCGCCCAUCCAUCCAGGCGAACCUUCCGUCCUUCUGC--------CCGGCCAUUCAAGUCAUCCAUCUCGGCUUUGGCAGCUUUCG
...((((((((((-----.....(((((..........))))).....(((..(....).--------.)))..................)))).))))))........ ( -23.50)
>DroSec_CAF1 11130 96 - 1
CCAGCCGAACCGA-----AAUACUCGCCCAUCCAUCCAGGCGAACCUUCUGUCCUUCUGC--------CCGGCCAUUCAAGUCAUCCAUCUCGGCUUUGGCAGCUUUCG
...((((((((((-----.....(((((..........))))).................--------..(((.......))).......)))).))))))........ ( -22.00)
>DroSim_CAF1 10946 96 - 1
CCAGCCGAACCGA-----AAUACUCGCCCAUCCAUCCAGGCGAACCUUCUGUCCUUCUGC--------CCGGCCAUUCAAGUCAUCCAUCUCGGCUUUGGCAGCUUUCG
...((((((((((-----.....(((((..........))))).................--------..(((.......))).......)))).))))))........ ( -22.00)
>DroEre_CAF1 12699 109 - 1
CCAGCCGAACCGAAAUACUAUACUCGCCCAUCCAUCCAGGCGAACCUUCUGUCCUUCUGUCCUCCUGCCCGGCCAUCCAAGUCAUCCAUCUCGGCUUUGGCAGCUUUCG
...((((((((((..........(((((..........)))))...........................(((.......))).......)))).))))))........ ( -22.00)
>DroAna_CAF1 13292 78 - 1
CCAGCCAGGCCAA-----AA-CCUAAACCAUCCAUCCAUCCAAAU-------------------------GUCCAUCCAAGCCAUCCAUCUCGGAUUUGGCAGCUCUUG
..(((.(((....-----..-))).....................-------------------------..........(((((((.....)))..)))).))).... ( -11.90)
>consensus
CCAGCCGAACCGA_____AAUACUCGCCCAUCCAUCCAGGCGAACCUUCUGUCCUUCUGC________CCGGCCAUUCAAGUCAUCCAUCUCGGCUUUGGCAGCUUUCG
...((((((((((..........(((((..........)))))...........................(((.......))).......)))).))))))........ (-16.30 = -17.02 +   0.72)

alignment

secondary structure

dotplot

Window 6

Location	8,803,105 – 8,803,202
Length	97
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	91.63
Mean single sequence MFE	-31.90
Consensus MFE	-25.42
Energy contribution	-25.43
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.80
SVM decision value	0.20
SVM RNA-class probability	0.633108
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8803105 97 + 22407834
GG--------GCAGAAGGACGGAAGGUUCGCCUGGAUGGAUGGGCGAGUAUU-----UCGGUUCGGCUGGAUGGGUUGUCAGUCGGUGGGCCAGCUCAUAUGAAAUUUUA
((--------((((..((((.((((..(((((((......)))))))...))-----)).))))..))...(((.(..((....))..).)))))))............. ( -32.50)
>DroSec_CAF1 11169 97 + 1
GG--------GCAGAAGGACAGAAGGUUCGCCUGGAUGGAUGGGCGAGUAUU-----UCGGUUCGGCUGGAUGGGUUGUCAGUUGGUGGGCCAGCUCAUAUGAAAUUUUA
((--------((((..((((.((((..(((((((......)))))))...))-----)).))))..))...(((.(..((....))..).)))))))............. ( -31.00)
>DroSim_CAF1 10985 97 + 1
GG--------GCAGAAGGACAGAAGGUUCGCCUGGAUGGAUGGGCGAGUAUU-----UCGGUUCGGCUGGAUGGGUUGUCAGUUGGUGGGCCAGCUCAUAUGAAAUUUUA
((--------((((..((((.((((..(((((((......)))))))...))-----)).))))..))...(((.(..((....))..).)))))))............. ( -31.00)
>DroEre_CAF1 12738 110 + 1
GGGCAGGAGGACAGAAGGACAGAAGGUUCGCCUGGAUGGAUGGGCGAGUAUAGUAUUUCGGUUCGGCUGGAUGGGUUGUCAGUCGGUGGGCCAGCUCAUAUGAAAUUUUA
((((....(..(....)..)....((((((((.((((.((...((.......))...)).))))((((((........)))))))))))))).))))............. ( -33.10)
>consensus
GG________GCAGAAGGACAGAAGGUUCGCCUGGAUGGAUGGGCGAGUAUU_____UCGGUUCGGCUGGAUGGGUUGUCAGUCGGUGGGCCAGCUCAUAUGAAAUUUUA
...........(((..((((.(((..((((((((......))))))))..)......)).))))..))).((((((((((........)).))))))))........... (-25.42 = -25.43 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:14 2006