Locus 2620

Sequence ID	3L_DroMel_CAF1
Location	7,231,762 – 7,232,011
Length	249
Max. P	0.828956

overview

Window 3

Location	7,231,762 – 7,231,871
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.15
Mean single sequence MFE	-30.52
Consensus MFE	-15.18
Energy contribution	-17.82
Covariance contribution	2.64
Combinations/Pair	1.12
Mean z-score	-2.56
Structure conservation index	0.50
SVM decision value	0.71
SVM RNA-class probability	0.828956
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7231762 109 + 23771897
UGCCCG-------CCUUUCCUUUCCACCAACACAAUCCGCAUCAAUAUGUGGUGGAGGGCACACUUAGCCAUUCGCACUUCAUUAGCCCACAUUUCCAAUAUGGUCAUGUGGGUGC----
(((((.-------.........(((((((.((...............))))))))))))))......((.....)).........((((((((..((.....))..))))))))..---- ( -31.86)
>DroSec_CAF1 13416 108 + 1
UGCCCG-------CCUUUCA-UUCCACCAACAUAUUCCGCAUCAAUAUGUGGUGGAGUUCACACUUGGCCAUUCGCACUUCAUUAGCCCACUUUUCCAAUAUGUUCAUGUGGGUGC----
(((..(-------((....(-((((((((.((((((.......)))))))))))))))........))).....)))........((((((.................))))))..---- ( -29.13)
>DroSim_CAF1 13343 108 + 1
UGCCCG-------CCUUUCA-UUCCACCAACAUAUUCCGCAUCAAUAUGUGGUGGAGUUCACACUUGGCCAUUCGCACUUCAUUAGCCCACAUUUCCAAUAUGGUCAUGUGGGUGC----
(((..(-------((....(-((((((((.((((((.......)))))))))))))))........))).....)))........((((((((..((.....))..))))))))..---- ( -35.80)
>DroEre_CAF1 13773 116 + 1
UAGAAGUAAUAGCACUUUCA-UCACACCAACGCAUUUCGAAUCGAUAUGCG---GAGGGCGCACUUAGCCAUUCGCACUUCAUUAGCACACUUUUCCAAUAUGGUUAUGUGGGCGCCCGC
..(((((......)))))..-.........(((((.(((...))).)))))---..((((((.....((.....))............(((....((.....))....))).)))))).. ( -29.80)
>DroYak_CAF1 14745 109 + 1
UUCACG-------CCUUUCA-UUACCCCAACAUAUUCGGAAUCAAUAUGUG---GAGGGCACACUUAGCCAUUCGCACUUCAUUAGCACACUUUUCCAAUAUGGUUAUGUGGGCGCCCGC
....((-------(((..((-(.(((.....(((((.((((......((((---((.(((.......))).))))))((.....)).......)))))))))))).))).)))))..... ( -26.00)
>consensus
UGCCCG_______CCUUUCA_UUCCACCAACAUAUUCCGCAUCAAUAUGUGGUGGAGGGCACACUUAGCCAUUCGCACUUCAUUAGCCCACUUUUCCAAUAUGGUCAUGUGGGUGC____
.....................((((((((.((((((.......))))))))))))))..........((.....)).........((((((....((.....))....))))))...... (-15.18 = -17.82 +   2.64)

alignment

secondary structure

dotplot

Window 4

Location	7,231,795 – 7,231,902
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.97
Mean single sequence MFE	-36.52
Consensus MFE	-25.25
Energy contribution	-26.45
Covariance contribution	1.20
Combinations/Pair	1.15
Mean z-score	-1.92
Structure conservation index	0.69
SVM decision value	0.34
SVM RNA-class probability	0.697349
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7231795 107 + 23771897
AUCAAUAUGUGGUGGAGGGCACACUUAGCCAUUCGCACUUCAUUAGCCCACAUUUCCAAUAUGGUCAUGUGGGUGC-------------CUAGCUUCUGGGCUAAUGGUGUCGUCUUCCG
.............(((((((((((...((.....))....(((((((((((((..((.....))..))))))))((-------------((((...))))))))))))))).))))))). ( -41.60)
>DroSec_CAF1 13448 107 + 1
AUCAAUAUGUGGUGGAGUUCACACUUGGCCAUUCGCACUUCAUUAGCCCACUUUUCCAAUAUGUUCAUGUGGGUGC-------------CUGGCUUCUGGGCUAAUGGUGUCGUCUUCCG
........(((((.((((....)))).))))).((.((.(((((((((((.....(((...((..(....)..)).-------------.)))....))))))))))).))))....... ( -30.60)
>DroSim_CAF1 13375 107 + 1
AUCAAUAUGUGGUGGAGUUCACACUUGGCCAUUCGCACUUCAUUAGCCCACAUUUCCAAUAUGGUCAUGUGGGUGC-------------CUGGCUUCGGGGCUAAUGGUGUCGUCUUCCG
........(((((.((((....)))).))))).((.((.((((((((((((((..((.....))..))))))))((-------------((.(...).)))))))))).))))....... ( -35.90)
>DroEre_CAF1 13812 117 + 1
AUCGAUAUGCG---GAGGGCGCACUUAGCCAUUCGCACUUCAUUAGCACACUUUUCCAAUAUGGUUAUGUGGGCGCCCGCUGUUUUCCCCUGGCUUCUGGCUUAAUGGUGUCGUCUUCCG
.........((---(((((((((((.(((((...((........(((.(((....((.....))....)))(((....))))))........))...)))))....)))).))))))))) ( -37.19)
>DroYak_CAF1 14777 117 + 1
AUCAAUAUGUG---GAGGGCACACUUAGCCAUUCGCACUUCAUUAGCACACUUUUCCAAUAUGGUUAUGUGGGCGCCCGCUGUUUUCCCCCGGCUUCUGGGCUAAUGGUGUCGUCUUCCG
..........(---(((((((((((..(((....((.........)).(((....((.....))....))))))((((((((........))))....))))....))))).))))))). ( -37.30)
>consensus
AUCAAUAUGUGGUGGAGGGCACACUUAGCCAUUCGCACUUCAUUAGCCCACUUUUCCAAUAUGGUCAUGUGGGUGC_____________CUGGCUUCUGGGCUAAUGGUGUCGUCUUCCG
.............(((((((((((((((((...............((((((....((.....))....))))))((................)).....)))))..))))).))))))). (-25.25 = -26.45 +   1.20)

alignment

secondary structure

dotplot

Window 5

Location	7,231,835 – 7,231,938
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.04
Mean single sequence MFE	-32.97
Consensus MFE	-18.55
Energy contribution	-18.99
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.89
Structure conservation index	0.56
SVM decision value	0.30
SVM RNA-class probability	0.679709
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7231835 103 + 23771897
CAUUAGCCCACAUUUCCAAUAUGGUCAUGUGGGUGC-------------CUAGCUUCUGGGCUAAUGGUGUCGUCUUCCGGCAUAAUUGCACUCCAGUGGCAUAGGUUGCCUUCCC----
.....((((((((..((.....))..))))))))((-------------((((((.((((((.(((.((((((.....)))))).)))))...)))).))).))))).........---- ( -38.80)
>DroSec_CAF1 13488 97 + 1
CAUUAGCCCACUUUUCCAAUAUGUUCAUGUGGGUGC-------------CUGGCUUCUGGGCUAAUGGUGUCGUCUUCCGGCAUUAUUGGACUCC------CUAGGUUGCCUUCCC----
.....((((((.................))))))..-------------..(((.((((((((((((((((((.....))))))))))))....)------)))))..))).....---- ( -33.03)
>DroSim_CAF1 13415 97 + 1
CAUUAGCCCACAUUUCCAAUAUGGUCAUGUGGGUGC-------------CUGGCUUCGGGGCUAAUGGUGUCGUCUUCCGGCAUAAUUGCACUCC------AUAGGUUGCCUUCCC----
.....((((((((..((.....))..))))))))((-------------(((.....(((((.(((.((((((.....)))))).))))).))).------.))))).........---- ( -31.30)
>DroEre_CAF1 13849 111 + 1
CAUUAGCACACUUUUCCAAUAUGGUUAUGUGGGCGCCCGCUGUUUUCCCCUGGCUUCUGGCUUAAUGGUGUCGUCUUCCGGCAUAAUUGCACUCCAGUGGAAUAG-----CUACUC----
.....((.(((....((.....))....))).))....(((((..(((.((((......((......((((((.....))))))....))...)))).)))))))-----).....---- ( -29.60)
>DroYak_CAF1 14814 115 + 1
CAUUAGCACACUUUUCCAAUAUGGUUAUGUGGGCGCCCGCUGUUUUCCCCCGGCUUCUGGGCUAAUGGUGUCGUCUUCCGGCAUAAUUGCACUCCAGUGGAAUAG-----CGUCUCUCUA
....((.((.((.(((((...(((....(((...((((((((........))))....))))((((.((((((.....)))))).))))))).))).))))).))-----.))))..... ( -32.10)
>consensus
CAUUAGCCCACUUUUCCAAUAUGGUCAUGUGGGUGC_____________CUGGCUUCUGGGCUAAUGGUGUCGUCUUCCGGCAUAAUUGCACUCCAGUGG_AUAGGUUGCCUUCCC____
(((((((((.....((((.(((....))))))).((................))....)))))))))((((((.....)))))).................................... (-18.55 = -18.99 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	7,231,902 – 7,232,011
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.46
Mean single sequence MFE	-26.40
Consensus MFE	-16.50
Energy contribution	-17.66
Covariance contribution	1.16
Combinations/Pair	1.04
Mean z-score	-1.62
Structure conservation index	0.63
SVM decision value	-0.04
SVM RNA-class probability	0.510767
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7231902 109 - 23771897
UGUUACCAAUC-GAACGACACCCUUGUUUGCACUCAAGCCAAAGUGAAAAUCAAUUUACUUAUGCCAUAUGGCA----------GGGAAGGCAACCUAUGCCACUGGAGUGCAAUUAUGC
...........-((((((.....))))))((((((.((((.(((((((......))))))).((((....))))----------))...((((.....)))).)).))))))........ ( -30.30)
>DroSec_CAF1 13555 103 - 1
UGUUGUCAAUC-GAACGACACCCUUGUUUGCACUCAAGCCAAAGUGAAUAUCAAUUUACUUACGCCAUAUGGCA----------GGGAAGGCAACCUAG------GGAGUCCAAUAAUGC
(((((((....-))..(((.((((.(.((((.(((......((((((((....))))))))..(((....))).----------)))...)))).).))------)).)))))))).... ( -28.10)
>DroSim_CAF1 13482 103 - 1
UGUUGCCAAUC-GAACGACACCCUUGUUUGCACUCAAGCCAAAGUGAAAAUCAAUUUACUUAUGCCAUAUGGCA----------GGGAAGGCAACCUAU------GGAGUGCAAUUAUGC
(((((......-...))))).......((((((((..(((.(((((((......))))))).((((....))))----------.....)))..(....------)))))))))...... ( -26.60)
>DroEre_CAF1 13929 101 - 1
C---UGCAAUC-GAACGACACCCUGGUCUGCACUCAAGCCAAAGUGAAAAUCAAUUUACCCACACCAUAUGGCG----------GAGUAG-----CUAUUCCACUGGAGUGCAAUUAUGC
.---.(((...-....(((......)))(((((((..((((..(((................)))....))))(----------((((..-----..)))))....)))))))....))) ( -25.39)
>DroYak_CAF1 14894 112 - 1
C---UCCAAUCCAAACGACACCCUAGUCUGCACUCGAGCCAAAGUGAAAAUCAAUUUACCCAUACCAUAUGGCAGCUAUAUAGAGAGACG-----CUAUUCCACUGGAGUGCAAUUAUGC
.---............(((......)))(((((((.((.....(((((......))))).........(((((..((........))..)-----))))....)).)))))))....... ( -21.60)
>consensus
UGUUGCCAAUC_GAACGACACCCUUGUUUGCACUCAAGCCAAAGUGAAAAUCAAUUUACUUAUGCCAUAUGGCA__________GGGAAGGCAACCUAU_CCACUGGAGUGCAAUUAUGC
................(((......)))(((((((..(((((((((((......)))))))........))))...........((........))..........)))))))....... (-16.50 = -17.66 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:43 2006