Locus 3952

Sequence ID	3L_DroMel_CAF1
Location	11,488,885 – 11,488,994
Length	109
Max. P	0.956676

overview

Window 1

Location	11,488,885 – 11,488,994
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.25
Mean single sequence MFE	-32.86
Consensus MFE	-22.86
Energy contribution	-22.78
Covariance contribution	-0.08
Combinations/Pair	1.07
Mean z-score	-1.93
Structure conservation index	0.70
SVM decision value	1.47
SVM RNA-class probability	0.956676
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11488885 109 + 23771897
ACCUCCAUCGAUGGCUUCUUCAAUCGGAAACGGGGGCGUCCGCCAAAGAAUCGCUUUGUGGAGGUCUACAAGAGCGUGAGUAUUUUUCGA-----------AAUAUGUUAGGAUGCAUUU
..((((...(((..........)))(....)))))((((((..........((((((((((....)))).))))))...((((((....)-----------)))))....)))))).... ( -30.60)
>DroPse_CAF1 10572 84 + 1
ACCUCCAUCGAUGGGUUCUUCAAUCGGAAACGGGGCCGUCCGCCCAAGAACCGUUUUGUGGAGGUAUACAAGAGCGUAAGUAGA------------------------------------
((((((((.((..(((((((....((....))((((.....)))))))))))..)).))))))))........((....))...------------------------------------ ( -34.20)
>DroSec_CAF1 3865 120 + 1
ACCUCCAUCGAUGGCUUCUUCAAUCGGAAACGGGGGCGUCCGCCAAAGAAUCGCUUUGUGGAGGUCUACAAGAGCGUGAGUAUUUUUCGAAAAUAUUUUGAAAUAUAUUAGGAUGUAUUU
(((((((.(((.((((((((...(((....))).(((....))).)))))..)))))))))))))........((((.(((((.(((((((.....))))))).)))))...)))).... ( -34.00)
>DroPer_CAF1 871 84 + 1
ACCUCCAUCGAUGGGUUCUUCAAUCGGAAACGGGGCCGUCCGCCCAAGAACCGUUUUGUGGAGGUCUACAAGAGCGUAAGUAGA------------------------------------
.(((((((.((..(((((((....((....))((((.....)))))))))))..)).)))))))(((((..........)))))------------------------------------ ( -34.00)
>DroYak_CAF1 97 104 + 1
ACCUCCAUCGAUGGCUUCUUCAAUCGGAAACGGGGGCGGCCGCCAAAGAAUCGCUUUGUGGAGGUCUACAAGAGCGUGAGUAUACUUAGA-----------A-----UUGGGAUGCACUU
.....((((...((((.((((...((....)))))).)))).((((.....((((((((((....)))).))))))((((....))))..-----------.-----))))))))..... ( -31.50)
>consensus
ACCUCCAUCGAUGGCUUCUUCAAUCGGAAACGGGGGCGUCCGCCAAAGAAUCGCUUUGUGGAGGUCUACAAGAGCGUGAGUAUA_UU_GA___________A_____UU_GGAUG_A_UU
((((((((.(((((.(((((...(((....))).(((....))).)))))))).)).)))))))).(((......))).......................................... (-22.86 = -22.78 +  -0.08)

alignment

secondary structure

dotplot

Window 2

Location	11,488,885 – 11,488,994
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	76.25
Mean single sequence MFE	-26.24
Consensus MFE	-20.74
Energy contribution	-20.70
Covariance contribution	-0.04
Combinations/Pair	1.05
Mean z-score	-1.09
Structure conservation index	0.79
SVM decision value	0.40
SVM RNA-class probability	0.722049
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11488885 109 - 23771897
AAAUGCAUCCUAACAUAUU-----------UCGAAAAAUACUCACGCUCUUGUAGACCUCCACAAAGCGAUUCUUUGGCGGACGCCCCCGUUUCCGAUUGAAGAAGCCAUCGAUGGAGGU
....((.(((.........-----------((((..........((((.((((.(....).)))))))).(((((..(((((.((....)).)))).)..)))))....)))).))).)) ( -25.10)
>DroPse_CAF1 10572 84 - 1
------------------------------------UCUACUUACGCUCUUGUAUACCUCCACAAAACGGUUCUUGGGCGGACGGCCCCGUUUCCGAUUGAAGAACCCAUCGAUGGAGGU
------------------------------------...................(((((((......(((((((.((((((((....))..)))).)).)))))))......))))))) ( -27.60)
>DroSec_CAF1 3865 120 - 1
AAAUACAUCCUAAUAUAUUUCAAAAUAUUUUCGAAAAAUACUCACGCUCUUGUAGACCUCCACAAAGCGAUUCUUUGGCGGACGCCCCCGUUUCCGAUUGAAGAAGCCAUCGAUGGAGGU
....((.(((.(((((........))))).((((..........((((.((((.(....).)))))))).(((((..(((((.((....)).)))).)..)))))....)))).))).)) ( -25.60)
>DroPer_CAF1 871 84 - 1
------------------------------------UCUACUUACGCUCUUGUAGACCUCCACAAAACGGUUCUUGGGCGGACGGCCCCGUUUCCGAUUGAAGAACCCAUCGAUGGAGGU
------------------------------------(((((..........)))))((((((......(((((((.((((((((....))..)))).)).)))))))......)))))). ( -30.30)
>DroYak_CAF1 97 104 - 1
AAGUGCAUCCCAA-----U-----------UCUAAGUAUACUCACGCUCUUGUAGACCUCCACAAAGCGAUUCUUUGGCGGCCGCCCCCGUUUCCGAUUGAAGAAGCCAUCGAUGGAGGU
(((.((.......-----.-----------...............)).)))....(((((((.....((((((((..((((..((....))..))).)..))))....)))).))))))) ( -22.60)
>consensus
AA_U_CAUCC_AA_____U___________UC_AA_UAUACUCACGCUCUUGUAGACCUCCACAAAGCGAUUCUUUGGCGGACGCCCCCGUUUCCGAUUGAAGAAGCCAUCGAUGGAGGU
.......................................................(((((((.....((((((((..(((((((....))..)))).)..))))....)))).))))))) (-20.74 = -20.70 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:48 2006