Locus 105

Sequence ID	X_DroMel_CAF1
Location	427,229 – 427,324
Length	95
Max. P	0.998952

overview

Window 8

Location	427,229 – 427,324
Length	95
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	76.59
Mean single sequence MFE	-29.80
Consensus MFE	-19.30
Energy contribution	-19.90
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.92
Structure conservation index	0.65
SVM decision value	3.30
SVM RNA-class probability	0.998952
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 427229 95 + 22224390
GGGAGUGGGGAUCCUGA-------CAGAGUGUGUGCCACUCGGCACAUAAUUGUUUGAAACAAAUGUUGUGCACACACUCACAGCGGCAGCA---GCACACACUC
....((.((....)).)-------).((((((((((......(((((((.((((.....)))).)).)))))...........((....)).---)))))))))) ( -31.50)
>DroPse_CAF1 42949 79 + 1
--------------UGU-------GUGAGUGUGUGCCACUCGGCACAUAAUUGUUUGAAACAAAUGUAGUGCACACACACACUCCAACAAUC---GUACACA--C
--------------(((-------(((((((((((.......(((((((.((((.....)))).))).))))...)))))))))..((....---)))))))--. ( -24.40)
>DroSec_CAF1 29668 98 + 1
GGGAGUGGGGAUCCUUA-------CAGAGUGUGUGCCACUCGGCACAUAAUUGUUUGAAACAAAUGUAGUGCACACACUCACAGCGGCAGCAGUAGCACACACUC
....(((((....))))-------).((((((((((.(((..(((((((.((((.....)))).))).))))...........((....))))).)))))))))) ( -34.70)
>DroYak_CAF1 26986 101 + 1
GUGAGUGGGGAUACAGAGAUCCAGCAGAGUGUGUGCCACUCGGCACAUAAUUGUUUGAAACAAAUGUAGUGCACACACUCACAGCGGCAGCA----CACACACUC
(((.(((.((((......))))....((((((((((.(((....((((..((((.....)))))))))))))))))))))...((....)).----))).))).. ( -34.00)
>DroPer_CAF1 46515 79 + 1
--------------UGU-------GUGAGUGUGUGCCACUCGGCACAUAAUUGUUUGAAACAAAUGUAGUGCACACACACACUCCAACAAUC---GUACACA--C
--------------(((-------(((((((((((.......(((((((.((((.....)))).))).))))...)))))))))..((....---)))))))--. ( -24.40)
>consensus
G_GAGUGGGGAU_CUGA_______CAGAGUGUGUGCCACUCGGCACAUAAUUGUUUGAAACAAAUGUAGUGCACACACUCACAGCGGCAGCA___GCACACACUC
..........................((((((((((.(((....((((..((((.....)))))))))))))))))))))......................... (-19.30 = -19.90 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	427,229 – 427,324
Length	95
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	76.59
Mean single sequence MFE	-31.64
Consensus MFE	-18.88
Energy contribution	-19.48
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.76
Structure conservation index	0.60
SVM decision value	2.94
SVM RNA-class probability	0.997838
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 427229 95 - 22224390
GAGUGUGUGC---UGCUGCCGCUGUGAGUGUGUGCACAACAUUUGUUUCAAACAAUUAUGUGCCGAGUGGCACACACUCUG-------UCAGGAUCCCCACUCCC
((((((((((---..(((((((.....))).))(((((....((((.....))))...)))))..))..))))))))))..-------...((....))...... ( -35.10)
>DroPse_CAF1 42949 79 - 1
G--UGUGUAC---GAUUGUUGGAGUGUGUGUGUGCACUACAUUUGUUUCAAACAAUUAUGUGCCGAGUGGCACACACUCAC-------ACA--------------
(--((((...---(((((((.(((((((((....))).))))))......))))))).((((((....))))))....)))-------)).-------------- ( -26.10)
>DroSec_CAF1 29668 98 - 1
GAGUGUGUGCUACUGCUGCCGCUGUGAGUGUGUGCACUACAUUUGUUUCAAACAAUUAUGUGCCGAGUGGCACACACUCUG-------UAAGGAUCCCCACUCCC
((((((((((((((...(((((.....))).))((((.....((((.....))))....))))..))))))))))))))..-------...((....))...... ( -35.10)
>DroYak_CAF1 26986 101 - 1
GAGUGUGUG----UGCUGCCGCUGUGAGUGUGUGCACUACAUUUGUUUCAAACAAUUAUGUGCCGAGUGGCACACACUCUGCUGGAUCUCUGUAUCCCCACUCAC
(((((.(..----(((..((((...(((((((((((((((((((((.....))))..))))....))).)))))))))).)).))......)))..).))))).. ( -35.80)
>DroPer_CAF1 46515 79 - 1
G--UGUGUAC---GAUUGUUGGAGUGUGUGUGUGCACUACAUUUGUUUCAAACAAUUAUGUGCCGAGUGGCACACACUCAC-------ACA--------------
(--((((...---(((((((.(((((((((....))).))))))......))))))).((((((....))))))....)))-------)).-------------- ( -26.10)
>consensus
GAGUGUGUGC___UGCUGCCGCUGUGAGUGUGUGCACUACAUUUGUUUCAAACAAUUAUGUGCCGAGUGGCACACACUCUG_______UCAG_AUCCCCACUC_C
.........................(((((((((((((((((((((.....))))..))))....))).)))))))))).......................... (-18.88 = -19.48 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:27 2006