Locus 7543

Sequence ID	3R_DroMel_CAF1
Location	20,205,390 – 20,205,492
Length	102
Max. P	0.978051

overview

Window 3

Location	20,205,390 – 20,205,492
Length	102
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	94.15
Mean single sequence MFE	-25.48
Consensus MFE	-19.54
Energy contribution	-20.74
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-3.33
Structure conservation index	0.77
SVM decision value	1.81
SVM RNA-class probability	0.978051
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20205390 102 + 27905053
CUGUACAGCUGUUGGAUUCA-GCAUUUUAAUUAUGUCAAAUUUACUCAGCUUUACGCUGCUCUUCUGGCUACCAUUUCAGUAGCAGCUCUUUC--UCUGUAAUUU
..(((.(((((.((((((..-((((.......))))..))))))..))))).)))((((((...((((........)))).))))))......--.......... ( -26.80)
>DroSec_CAF1 16832 101 + 1
-UGUACAGCUGUUGGAUUCA-GCAUUUUAAUUAUGUCAAAUUUACUCAGCUUUACGCUGCUCUUCUGGCUGCCAUUUCAGUAGCAGCUCUUUC--UCUGUAAUUU
-.(((.(((((.((((((..-((((.......))))..))))))..))))).)))((((((...((((........)))).))))))......--.......... ( -26.80)
>DroSim_CAF1 16700 101 + 1
-UGUACAGCUGUUGGAUUCA-GCAUUUUAAUUAUGUCAAAUUUACUCAGCUUUACGCUGCUCUUCUGGCUGCCAUUUCAGUAGCAGCUCUUUC--UCUGUAAUUU
-.(((.(((((.((((((..-((((.......))))..))))))..))))).)))((((((...((((........)))).))))))......--.......... ( -26.80)
>DroEre_CAF1 16818 101 + 1
-UAUACAGCUGUUGGAUUCA-GCAUUUUAAUUAUGUCAAAUUUACUCAGAUUUACGCUGCUGUUCUGGCUGACAUUUCAGCAGCAGCUCUUUC--UCUGUAAUUU
-..((((((((.((((((..-((((.......))))..))))))..)))......((((((......(((((....)))))))))))......--.))))).... ( -25.40)
>DroYak_CAF1 17076 102 + 1
-UAUUCAGCU--UGGAUUCAGGCAUUUUAAUUAUGUCAAAUUUACUCAGCUUUACGCUGCCGUUCUGGCUGCCAUUUCAGUAGCAGCUCUUUCUCUCUGUAAUUU
-....(((..--(((.....(((((.......))))).........((((.....)))))))..)))(((((.((....)).))))).................. ( -21.60)
>consensus
_UGUACAGCUGUUGGAUUCA_GCAUUUUAAUUAUGUCAAAUUUACUCAGCUUUACGCUGCUCUUCUGGCUGCCAUUUCAGUAGCAGCUCUUUC__UCUGUAAUUU
..(((.(((((.((((((...((((.......))))..))))))..))))).)))((((((...((((........)))).)))))).................. (-19.54 = -20.74 +   1.20)

alignment

secondary structure

dotplot

Window 4

Location	20,205,390 – 20,205,492
Length	102
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	94.15
Mean single sequence MFE	-23.18
Consensus MFE	-17.08
Energy contribution	-17.36
Covariance contribution	0.28
Combinations/Pair	1.10
Mean z-score	-2.38
Structure conservation index	0.74
SVM decision value	0.34
SVM RNA-class probability	0.694265
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20205390 102 - 27905053
AAAUUACAGA--GAAAGAGCUGCUACUGAAAUGGUAGCCAGAAGAGCAGCGUAAAGCUGAGUAAAUUUGACAUAAUUAAAAUGC-UGAAUCCAACAGCUGUACAG
..........--......((((((.((....(((...)))..))))))))(((.(((((.....((((..(((.......))).-.))))....))))).))).. ( -23.90)
>DroSec_CAF1 16832 101 - 1
AAAUUACAGA--GAAAGAGCUGCUACUGAAAUGGCAGCCAGAAGAGCAGCGUAAAGCUGAGUAAAUUUGACAUAAUUAAAAUGC-UGAAUCCAACAGCUGUACA-
..........--......((((((.((....(((...)))..))))))))(((.(((((.....((((..(((.......))).-.))))....))))).))).- ( -23.90)
>DroSim_CAF1 16700 101 - 1
AAAUUACAGA--GAAAGAGCUGCUACUGAAAUGGCAGCCAGAAGAGCAGCGUAAAGCUGAGUAAAUUUGACAUAAUUAAAAUGC-UGAAUCCAACAGCUGUACA-
..........--......((((((.((....(((...)))..))))))))(((.(((((.....((((..(((.......))).-.))))....))))).))).- ( -23.90)
>DroEre_CAF1 16818 101 - 1
AAAUUACAGA--GAAAGAGCUGCUGCUGAAAUGUCAGCCAGAACAGCAGCGUAAAUCUGAGUAAAUUUGACAUAAUUAAAAUGC-UGAAUCCAACAGCUGUAUA-
......((((--......(((((((((((....)))))......)))))).....)))).......................((-((.......))))......- ( -23.50)
>DroYak_CAF1 17076 102 - 1
AAAUUACAGAGAGAAAGAGCUGCUACUGAAAUGGCAGCCAGAACGGCAGCGUAAAGCUGAGUAAAUUUGACAUAAUUAAAAUGCCUGAAUCCA--AGCUGAAUA-
......(((.((...((.(((((((......)))))))((((((..((((.....)))).))...))))...............))...))..--..)))....- ( -20.70)
>consensus
AAAUUACAGA__GAAAGAGCUGCUACUGAAAUGGCAGCCAGAAGAGCAGCGUAAAGCUGAGUAAAUUUGACAUAAUUAAAAUGC_UGAAUCCAACAGCUGUACA_
....(((((.........(((((((......)))))))((((....((((.....))))......))))............................)))))... (-17.08 = -17.36 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:26 2006