Locus 7229

Sequence ID	3R_DroMel_CAF1
Location	19,044,175 – 19,044,307
Length	132
Max. P	0.901611

overview

Window 2

Location	19,044,175 – 19,044,267
Length	92
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	66.55
Mean single sequence MFE	-33.98
Consensus MFE	-18.82
Energy contribution	-19.52
Covariance contribution	0.70
Combinations/Pair	1.17
Mean z-score	-1.47
Structure conservation index	0.55
SVM decision value	0.64
SVM RNA-class probability	0.809469
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19044175 92 + 27905053
GACCACCCGAGGUGGGUGCA-CCACCA----G-UACCAACCACCAUUG-UACCGCCAG---UGGCGGCA---GCACUAGUGCUCUGCACAUCCUGCAGAGCUGCC
..(((((...)))))(((((-(.....----)-).....((.((((((-......)))---))).))..---))))....((((((((.....)))))))).... ( -34.40)
>DroPse_CAF1 57341 86 + 1
UUCCACCCGCCGAUGGUGCG-CCC------------GAUCCGACAUUGGAAUUUCCAU---UCGCCCCU---CCCCCGCCGCUCUGGAGAUCCUGGAGGGCUGCU
........((.(((((....-.((------------(((.....))))).....))))---).))....---.....(((.(((..(.....)..)))))).... ( -23.30)
>DroSec_CAF1 56781 92 + 1
GACCACCAGCGGUGGGUGCA-CCACCA----G-UACCAACCCCCAUUG-AACCGCCAG---UGGCUGCA---GCACUAGUGCUCUGCACAUCCUGCAGAGCUGCC
......(((((((.(((((.-......----)-)))).)))..(((((-......)))---))))))..---(((.....((((((((.....))))))))))). ( -33.60)
>DroEre_CAF1 59747 92 + 1
GACCACCAGACGUGGGUGCA-CCACCG----G-UAGCAACCACCAUUG-AGCCGCCAG---UGGCUCCA---GCACUGGUGCUCUGCACAUCCUGCAGAGCUGCC
....(((((..((((.((((-((...)----)-).))).))))....(-(((((....---))))))..---...)))))((((((((.....)))))))).... ( -41.10)
>DroYak_CAF1 60239 80 + 1
GACCACCAGACGUGGGUGCA-CCUCC-----------------UAUUG-CACCGCCAG---UGGCUCCA---GCACUGGUGCUCUGCACAUCCUGCAGAGCUGCC
...(((.....)))((((((-.....-----------------...))-))))(((((---((.(....---))))))))((((((((.....)))))))).... ( -34.50)
>DroMoj_CAF1 61001 95 + 1
CACCGCCUGAAGUGUUCGCUGCCACCGAGCUGCUGCUC---------G-AGCUGCCGGAGUUGGCGCCGUUGCCGCCAGAGCUCUGCAGGUCCUGCAGGGCCGCC
...........(((..(.((((....((((....))))---------(-(.((((.((((((((((.......)))))..))))))))).))..)))))..))). ( -37.00)
>consensus
GACCACCAGACGUGGGUGCA_CCACC_____G_UACCAACC_CCAUUG_AACCGCCAG___UGGCUCCA___GCACUAGUGCUCUGCACAUCCUGCAGAGCUGCC
..((((.....))))..((..................................((((....))))...............((((((((.....)))))))).)). (-18.82 = -19.52 +   0.70)

alignment

secondary structure

dotplot

Window 3

Location	19,044,175 – 19,044,267
Length	92
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	66.55
Mean single sequence MFE	-39.83
Consensus MFE	-17.65
Energy contribution	-19.32
Covariance contribution	1.67
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.44
SVM decision value	0.10
SVM RNA-class probability	0.583477
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19044175 92 - 27905053
GGCAGCUCUGCAGGAUGUGCAGAGCACUAGUGC---UGCCGCCA---CUGGCGGUA-CAAUGGUGGUUGGUA-C----UGGUGG-UGCACCCACCUCGGGUGGUC
.(((((((((((.....))))))))((((((((---((((((((---.((......-)).)))))).)))))-)----))))..-)))..(((((...))))).. ( -47.40)
>DroPse_CAF1 57341 86 - 1
AGCAGCCCUCCAGGAUCUCCAGAGCGGCGGGGG---AGGGGCGA---AUGGAAAUUCCAAUGUCGGAUC------------GGG-CGCACCAUCGGCGGGUGGAA
.((.((((....((....)).((.(((((..((---((...(..---...)...))))..)))))..))------------)))-))).(((((....))))).. ( -30.90)
>DroSec_CAF1 56781 92 - 1
GGCAGCUCUGCAGGAUGUGCAGAGCACUAGUGC---UGCAGCCA---CUGGCGGUU-CAAUGGGGGUUGGUA-C----UGGUGG-UGCACCCACCGCUGGUGGUC
((((((((((((.....)))))))).....)))---)...((((---(..(((((.-.....(((....(((-(----.....)-))).))))))))..))))). ( -43.50)
>DroEre_CAF1 59747 92 - 1
GGCAGCUCUGCAGGAUGUGCAGAGCACCAGUGC---UGGAGCCA---CUGGCGGCU-CAAUGGUGGUUGCUA-C----CGGUGG-UGCACCCACGUCUGGUGGUC
(((.((((((((.....))))))))(((((((.---(((.((((---((((..((.-...........))..-)----))))))-)....))))).))))).))) ( -43.60)
>DroYak_CAF1 60239 80 - 1
GGCAGCUCUGCAGGAUGUGCAGAGCACCAGUGC---UGGAGCCA---CUGGCGGUG-CAAUA-----------------GGAGG-UGCACCCACGUCUGGUGGUC
(((.((((((((.....))))))))(((((.((---..(.....---)..))((((-((...-----------------.....-)))))).....))))).))) ( -35.20)
>DroMoj_CAF1 61001 95 - 1
GGCGGCCCUGCAGGACCUGCAGAGCUCUGGCGGCAACGGCGCCAACUCCGGCAGCU-C---------GAGCAGCAGCUCGGUGGCAGCGAACACUUCAGGCGGUG
.((.(((((((...(((....(((((..(.((....)).)(((......)))))))-)---------((((....))))))).)))).((.....)).))).)). ( -38.40)
>consensus
GGCAGCUCUGCAGGAUGUGCAGAGCACCAGUGC___UGGAGCCA___CUGGCGGUU_CAAUGG_GGUUGGUA_C_____GGUGG_UGCACCCACGUCUGGUGGUC
.((.((((((((.....))))))))...............(((......)))..................................))..((((.....)))).. (-17.65 = -19.32 +   1.67)

alignment

secondary structure

dotplot

Window 4

Location	19,044,201 – 19,044,307
Length	106
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	75.09
Mean single sequence MFE	-40.88
Consensus MFE	-24.10
Energy contribution	-24.38
Covariance contribution	0.28
Combinations/Pair	1.19
Mean z-score	-1.80
Structure conservation index	0.59
SVM decision value	1.02
SVM RNA-class probability	0.901611
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19044201 106 + 27905053
-G-UACCAACCACCAUUG-UACCGCCAG---UGGCGGCA---GCACUAGUGCUCUGCACAUCCUGCAGAGCUGCCGUCUGGACACUGCUAUUCCCGGUGGUGUUGUGGAGAUUCA
-.-.........((((..-(((((((..---.(((((((---((....))((((((((.....))))))))))))))).(((.........))).)))))))..))))....... ( -43.00)
>DroPse_CAF1 57364 103 + 1
------GAUCCGACAUUGGAAUUUCCAU---UCGCCCCU---CCCCCGCCGCUCUGGAGAUCCUGGAGGGCUGCUGUCUGGACGCUGCUGUUGCCGGUCGUAUUGUGGAGAUUCA
------............((((((((((---..((....---.....(((.(((..(.....)..))))))....(.((((..((....))..)))).)))...)))))))))). ( -31.90)
>DroSec_CAF1 56807 106 + 1
-G-UACCAACCCCCAUUG-AACCGCCAG---UGGCUGCA---GCACUAGUGCUCUGCACAUCCUGCAGAGCUGCCGUCUGGACACUGCUAUUCCCGGUGGUGUUGUGCAGAUUCA
-(-(((............-.....((((---((((.((.---(((....)))((((((.....)))))))).)))).))))((((..((......))..)))).))))....... ( -37.30)
>DroEre_CAF1 59773 106 + 1
-G-UAGCAACCACCAUUG-AGCCGCCAG---UGGCUCCA---GCACUGGUGCUCUGCACAUCCUGCAGAGCUGCCGUCUGGACGCUGCUAUUCCCGGUGGUGUUGUGCAGAUUCA
-.-..(((..((((((((-.(.....((---..((((((---(.((.(((((((((((.....)))))))).)))))))))).))..))....)))))))))...)))....... ( -47.50)
>DroYak_CAF1 60264 95 + 1
-------------UAUUG-CACCGCCAG---UGGCUCCA---GCACUGGUGCUCUGCACAUCCUGCAGAGCUGCCGUCUGGACACUGCUAUUCCCGGUGGUGUUGUGCAGAUUCA
-------------(((.(-(((((((((---((((((((---(.((.(((((((((((.....)))))))).))))))))))....))))))...)))))))).)))........ ( -43.60)
>DroMoj_CAF1 61031 105 + 1
UGCUGCUC---------G-AGCUGCCGGAGUUGGCGCCGUUGCCGCCAGAGCUCUGCAGGUCCUGCAGGGCCGCCGUCUGCACGCUGCUGUUGCCCGUCGUAUUGUGCAGAUUCA
..((((..---------(-(.((((.((((((((((.......)))))..))))))))).))..)))).......(((((((((.(((...........))).)))))))))... ( -42.00)
>consensus
_G_UACCAACC_CCAUUG_AACCGCCAG___UGGCUCCA___GCACUAGUGCUCUGCACAUCCUGCAGAGCUGCCGUCUGGACACUGCUAUUCCCGGUGGUGUUGUGCAGAUUCA
.......................((((....))))...............((((((((.....))))))))....(((((.(((.((((((.....)))))).))).)))))... (-24.10 = -24.38 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:48 2006