Locus 4862

Sequence ID	3L_DroMel_CAF1
Location	13,600,635 – 13,600,770
Length	135
Max. P	0.997038

overview

Window 2

Location	13,600,635 – 13,600,730
Length	95
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	85.77
Mean single sequence MFE	-30.02
Consensus MFE	-26.54
Energy contribution	-26.82
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-2.58
Structure conservation index	0.88
SVM decision value	2.79
SVM RNA-class probability	0.997038
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13600635 95 - 23771897
AUGUUGUAUAACAGCAGCGGCAACAAGCCGUCCUGCUG---GUGGGCGUGGCACACACGCACUCACACUCAUACGCGCACAAUAACACAUCGACAUAC
((((((.....((((((((((.....))))..))))))---(((((((((.....))))).).)))........................)))))).. ( -32.10)
>DroSec_CAF1 7446 94 - 1
AUGUUGUAUAACAGCAGCGGAAACAAGCCGUCCUGCU----GUGGGCGUGGCACAAUCGCACUCACACUCAUACGCGCACAAUAACACAUCGACAUAC
((((((......((((((((.......)))..)))))----(((.(((((((......))...........))))).)))..........)))))).. ( -23.60)
>DroSim_CAF1 16807 98 - 1
AUGUUGUAUAACAGCAGCGGCAACAAGCCGUCCUGCUGCCUGUGGGCGUGGCCCACUCGCACUCACACUCAUACGCGCACAAUAACACAUCGACACAC
.((((((....((((((((((.....))))..))))))..((((.(((((.....................))))).))))))))))........... ( -29.80)
>DroEre_CAF1 10336 89 - 1
AUGUUGCAUAACAGCAGCGGCAACAAGCCGUCCUGCUG---GUGGGCGUGGCAGAC------GCACACGCACACGCACACAAUCACACUUCGACAUAC
.((((((....((((((((((.....))))..))))))---(((.(((((((....------)).))))).)))))).)))................. ( -35.20)
>DroYak_CAF1 13692 83 - 1
AUGUUGUAUAACAGCGGCGGCAACAAGCCGGCCUGCUG---GUGGGCGUGGC------------ACACUCAUACGCACACAAUAACACAUCGACAUGC
((((((.....((((((((((.....))).))).))))---(((.(((((..------------.......))))).)))..........)))))).. ( -29.40)
>consensus
AUGUUGUAUAACAGCAGCGGCAACAAGCCGUCCUGCUG___GUGGGCGUGGCACAC_CGCACUCACACUCAUACGCGCACAAUAACACAUCGACAUAC
((((((.....((((((((((.....))))..))))))...(((.(((((.....................))))).)))..........)))))).. (-26.54 = -26.82 +   0.28)

alignment

secondary structure

dotplot

Window 3

Location	13,600,675 – 13,600,770
Length	95
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	84.81
Mean single sequence MFE	-28.87
Consensus MFE	-22.91
Energy contribution	-23.60
Covariance contribution	0.69
Combinations/Pair	1.03
Mean z-score	-2.12
Structure conservation index	0.79
SVM decision value	0.42
SVM RNA-class probability	0.730999
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13600675 95 - 23771897
AUAAAAUGUCACUUAAUUGCAAUUUAGUAAAUUGUUUUCCAUGUUGU-----AUAACAGCAGCGGCAACAAGCCGUCCUGCUG--------------------GUGGGCGUGGCACACAC
......((((((......((((((.....))))))..........((-----....((((((((((.....))))..))))))--------------------....))))))))..... ( -27.00)
>DroSec_CAF1 7486 94 - 1
AUAAAAUGUCACUUAAUUGCAAUUUAGUAAAUUGUUUUCCAUGUUGU-----AUAACAGCAGCGGAAACAAGCCGUCCUGCU---------------------GUGGGCGUGGCACAAUC
......((((((....((((......)))).((((((((..(((((.-----....)))))..))))))))...((((....---------------------..))))))))))..... ( -26.20)
>DroSim_CAF1 16847 98 - 1
AUAAAAUGUCACUUAAUUGCAAUUUAGUAAAUUGUUUUCCAUGUUGU-----AUAACAGCAGCGGCAACAAGCCGUCCUGCUGCCU-----------------GUGGGCGUGGCCCACUC
.....(((..((......((((((.....)))))).......))..)-----))..((((((((((.....))))..))))))...-----------------((((((...)))))).. ( -27.82)
>DroEre_CAF1 10372 93 - 1
AUAAAAUGUCACUUAAUUGCAAUUUAGUAAAUUGUUUUCCAUGUUGC-----AUAACAGCAGCGGCAACAAGCCGUCCUGCUG--------------------GUGGGCGUGGCAGAC--
......((((((......((((((.....))))))..........((-----....((((((((((.....))))..))))))--------------------....))))))))...-- ( -28.90)
>DroYak_CAF1 13726 89 - 1
AUAAAAUGUCACUUAAUUGCAAUUUAGUAAAUUGUUUUCCAUGUUGU-----AUAACAGCGGCGGCAACAAGCCGGCCUGCUG--------------------GUGGGCGUGGC------
.......(((((....((((......)))).(((((..((.(((((.-----....)))))..)).)))))(((.(((....)--------------------)).))))))))------ ( -26.20)
>DroAna_CAF1 43324 116 - 1
AUAAAAUGUCACUUAAUUGCAAUUUAGUAAAUUGUUUUCCAUGUCGUACAAUAUAACAACAGCGGCAACAAGCCGCCCUGCUGCCCGGCUGCCCCCUUUGGUCGGGGGCGUGGCAC----
......((((((......((....(((((..(((((.....((.....))....)))))..(((((.....)))))..)))))....)).((((((.......)))))))))))).---- ( -37.10)
>consensus
AUAAAAUGUCACUUAAUUGCAAUUUAGUAAAUUGUUUUCCAUGUUGU_____AUAACAGCAGCGGCAACAAGCCGUCCUGCUG____________________GUGGGCGUGGCACAC__
.......(((((......((((((.....))))))..((((((((((.....)))))(((((((((.....))))..))))).....................))))).)))))...... (-22.91 = -23.60 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:29 2006