Locus 113

Sequence ID	3L_DroMel_CAF1
Location	380,692 – 380,818
Length	126
Max. P	0.637449

overview

Window 0

Location	380,692 – 380,792
Length	100
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	77.53
Mean single sequence MFE	-18.39
Consensus MFE	-11.29
Energy contribution	-12.60
Covariance contribution	1.31
Combinations/Pair	1.24
Mean z-score	-1.33
Structure conservation index	0.61
SVM decision value	-0.05
SVM RNA-class probability	0.509609
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 380692 100 - 23771897
-----GUUUUACUUGUUCUCACAGUUGUGAUUACAUAAUACGAUAAAACAGGGCAAACGCCCCUUUCCCAAUCUA-UACAUUCGAAAAAGGAACUGCCUAAAACAG
-----((((((...(((((....((((((....))))))...........((((....)))).............-.............)))))....)))))).. ( -17.80)
>DroSec_CAF1 34789 105 - 1
AUAAUGUUUUACUUGUUCUCACAGUUGUGAUUGCAUAACUCGAUAAAACAGGCCAAACGCCCCUAUCCCAAUCUA-UACAUUCGAAAAAGGAACUGCCUAAAACAG
....(((((((...(((((...(((((((....))))))).((((.....(((.....)))..))))........-.............)))))....))))))). ( -17.90)
>DroSim_CAF1 35534 105 - 1
AUAAUGUUUUACUUGUUCUCACAGUUGUGAUUACAUAACUCGAUAAAACAGGGCAAACGCCCCUAUCCCAAUCUA-CACAUUCGAAAAAGGAACUGCCUAAAACAG
....(((((((...(((((...(((((((....))))))).((((.....((((....)))).))))........-.............)))))....))))))). ( -21.30)
>DroEre_CAF1 36207 105 - 1
AUAAUGUUCUCCUUGUUCUCACAGUUGUGAUUACAUAAUACGAUAAAACCGGGCAAACGCCCCUAUCCCAAUCUA-CCCAUUUACAAAAGGAACUGUCUAGAGCAG
....((((((...(((..((((....))))..)))......((((.....((((....))))...(((.......-.............)))..)))).)))))). ( -20.55)
>DroYak_CAF1 36658 100 - 1
UUAAUGUUUUCCUUGUUCUCACAGUUGUGA-----UAAUACGAUAAAACCGGGCAAACGCCCCUAUCCCUAUCUA-UAGAUUUACAAAAGGAACUGUCUUCAACAG
........(((((((((.((((....))))-----.)))..((((.....((((....)))).......))))..-...........))))))((((.....)))) ( -18.90)
>DroAna_CAF1 31175 99 - 1
AGAAUC--CCGAUACUUCUCACAGUUGCGAUUACACAAUAUGAUAAAACAGAGCAAACGCCCCAUCAACGGUCAAACGCA-----UAAGGGAAAAGUCAGAGAAAC
......--.......(((((...((((.(....).)))).((((........((....))(((.....((......))..-----...)))....))))))))).. ( -13.90)
>consensus
AUAAUGUUUUACUUGUUCUCACAGUUGUGAUUACAUAAUACGAUAAAACAGGGCAAACGCCCCUAUCCCAAUCUA_CACAUUCGAAAAAGGAACUGCCUAAAACAG
....((((((....(((((....((((((....))))))...........((((....))))...........................))))).....)))))). (-11.29 = -12.60 +   1.31)

alignment

secondary structure

dotplot

Window 1

Location	380,719 – 380,818
Length	99
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	71.06
Mean single sequence MFE	-21.11
Consensus MFE	-8.80
Energy contribution	-9.36
Covariance contribution	0.56
Combinations/Pair	1.21
Mean z-score	-1.75
Structure conservation index	0.42
SVM decision value	0.21
SVM RNA-class probability	0.637449
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 380719 99 - 23771897
-------ACAGCGUUUGUAAUGUUAUGGUUAUG------------GUUUUACUUGUUCUCACAGUUGUGAUUACAUAAUACGAUAAAACAGGGCAAACGCCCCUUUCCCAAUCUA-UAC
-------...((((((((..((((....((((.------------((.(((..(((..((((....))))..)))))).)).))))))))..))))))))...............-... ( -24.50)
>DroSec_CAF1 34816 109 - 1
-------AC--GGUUUGUAAUUUUAUGGUUAUGAAAAACCAUAAUGUUUUACUUGUUCUCACAGUUGUGAUUGCAUAACUCGAUAAAACAGGCCAAACGCCCCUAUCCCAAUCUA-UAC
-------..--(((((((....((((((((......))))))))((((.....(((..((((....))))..)))......))))..))))))).....................-... ( -22.70)
>DroSim_CAF1 35561 109 - 1
-------AC--GGUUUGUAAUGUUAUGGUUAUGGAAAACCAUAAUGUUUUACUUGUUCUCACAGUUGUGAUUACAUAACUCGAUAAAACAGGGCAAACGCCCCUAUCCCAAUCUA-CAC
-------..--.((((((((((((((((((......))))))))))))...((((((.....(((((((....)))))))......)))))))))))).................-... ( -26.80)
>DroEre_CAF1 36234 118 - 1
AUAAAAAACAACAUUUGUUAGGUCAUGGUUAAGGAAACCCAUAAUGUUCUCCUUGUUCUCACAGUUGUGAUUACAUAAUACGAUAAAACCGGGCAAACGCCCCUAUCCCAAUCUA-CCC
......((((.....)))).(((...((((((((((((.......))).)))))((..((((....))))..))............))))((((....))))............)-)). ( -22.50)
>DroAna_CAF1 31197 113 - 1
CAAAAAAAUAACCUUCCC----ACAUAUUUAUCCUUACCCAGAAUC--CCGAUACUUCUCACAGUUGCGAUUACACAAUAUGAUAAAACAGAGCAAACGCCCCAUCAACGGUCAAACGC
..........(((.....----.....((((((.........((((--.((((..........)))).)))).........)))))).....((....)).........)))....... (  -9.07)
>consensus
_______ACA_CGUUUGUAAUGUUAUGGUUAUGGAAAACCAUAAUGUUUUACUUGUUCUCACAGUUGUGAUUACAUAAUACGAUAAAACAGGGCAAACGCCCCUAUCCCAAUCUA_CAC
.........................(((.........................(((..((((....))))..)))...............((((....)))).....)))......... ( -8.80 =  -9.36 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:48 2006