Locus 263

Sequence ID	3L_DroMel_CAF1
Location	739,351 – 739,476
Length	125
Max. P	0.955544

overview

Window 2

Location	739,351 – 739,442
Length	91
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	78.55
Mean single sequence MFE	-23.25
Consensus MFE	-16.56
Energy contribution	-16.53
Covariance contribution	-0.03
Combinations/Pair	1.11
Mean z-score	-2.13
Structure conservation index	0.71
SVM decision value	1.42
SVM RNA-class probability	0.951956
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 739351 91 + 23771897
-------------CAAUCAACAGCGCCGACGACUUUGGCGAGGUGCGCAUAAAAAUCGCAUUUAAUUGUGAUUUUCACACGAAAUACAAUGCGCAUGAGCA--------ACU--
-------------.........(((((((.....)))))...((((((((...(((((((......)))))))(((....))).....))))))))..)).--------...-- ( -26.70)
>DroGri_CAF1 126180 81 + 1
-----------------------CGACGUCGACUUUGU--AGGUGCGCAUAAAAAUUGCAUUUAAUUGCGAUUUUCACACGAAAUACAAAGCGCAUGAGCA--------ACUGU
-----------------------...(((((.((((((--(....((....(((((((((......)))))))))....))...))))))))).)))....--------..... ( -20.40)
>DroEre_CAF1 99614 79 + 1
-------------CAAUCAA------------CUUUGGCGAGGUGCGCAUAAAAAUCGCAUUUAAUUGUGAUUUUCACACGAAAUACAAUGCGCAUGAGCA--------ACU--
-------------.......------------.....((...((((((((...(((((((......)))))))(((....))).....))))))))..)).--------...-- ( -20.70)
>DroWil_CAF1 92817 80 + 1
-------------CAAUC---------GACGACUUUGU--AGGUGCGCAUAAAAAUCGCAUUUAAUUGUGAUUUUCACACGAAAUACAAUGCGCAUGAGCA--------ACU--
-------------.....---------.......((((--..((((((((...(((((((......)))))))(((....))).....))))))))..)))--------)..-- ( -21.10)
>DroMoj_CAF1 109634 99 + 1
GCAGCCGAAGCGACAGCCAA---CGACGACGUCUUUGU--AGGUGCGCAUAAAAAUUGCAUUUAAUUGUGAUUUUCACACGAAACACAAAGCGCAUGAGCA--------ACU--
((.......(((...(((.(---(((.(....).))))--.))).)))...(((((..((......))..)))))...............))((....)).--------...-- ( -20.60)
>DroAna_CAF1 101853 99 + 1
-------------CAAUCAACAUCGCCGACGACUUUGGCGAGGUGCGCAUAAAAAUCGCAUUUAAUUGUGAUUUUCACACGAAAUACAAUGCGCAUGAGCAGCGCUGGCACU--
-------------.........(((((((.....)))))))(((((.((..(((((((((......)))))))))...............((((.......)))))))))))-- ( -30.00)
>consensus
_____________CAAUCAA___CG_CGACGACUUUGG__AGGUGCGCAUAAAAAUCGCAUUUAAUUGUGAUUUUCACACGAAAUACAAUGCGCAUGAGCA________ACU__
..........................................((((((((...(((((((......)))))))(((....))).....)))))))).................. (-16.56 = -16.53 +  -0.03)

alignment

secondary structure

dotplot

Window 3

Location	739,351 – 739,442
Length	91
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	78.55
Mean single sequence MFE	-23.35
Consensus MFE	-17.03
Energy contribution	-16.87
Covariance contribution	-0.16
Combinations/Pair	1.17
Mean z-score	-1.55
Structure conservation index	0.73
SVM decision value	0.84
SVM RNA-class probability	0.864452
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 739351 91 - 23771897
--AGU--------UGCUCAUGCGCAUUGUAUUUCGUGUGAAAAUCACAAUUAAAUGCGAUUUUUAUGCGCACCUCGCCAAAGUCGUCGGCGCUGUUGAUUG-------------
--...--------.((...((((((((((((((..((((.....))))...))))))))......))))))....(((.........))))).........------------- ( -23.00)
>DroGri_CAF1 126180 81 - 1
ACAGU--------UGCUCAUGCGCUUUGUAUUUCGUGUGAAAAUCGCAAUUAAAUGCAAUUUUUAUGCGCACCU--ACAAAGUCGACGUCG-----------------------
...((--------(((....))((((((((...(((((((((((.(((......))).)))))))))))....)--))))))).)))....----------------------- ( -22.70)
>DroEre_CAF1 99614 79 - 1
--AGU--------UGCUCAUGCGCAUUGUAUUUCGUGUGAAAAUCACAAUUAAAUGCGAUUUUUAUGCGCACCUCGCCAAAG------------UUGAUUG-------------
--...--------.((...((((((((((((((..((((.....))))...))))))))......))))))....)).....------------.......------------- ( -18.20)
>DroWil_CAF1 92817 80 - 1
--AGU--------UGCUCAUGCGCAUUGUAUUUCGUGUGAAAAUCACAAUUAAAUGCGAUUUUUAUGCGCACCU--ACAAAGUCGUC---------GAUUG-------------
--(((--------((.....((((.(((((...((((((((((((.((......)).))))))))))))....)--)))).).))))---------)))).------------- ( -18.80)
>DroMoj_CAF1 109634 99 - 1
--AGU--------UGCUCAUGCGCUUUGUGUUUCGUGUGAAAAUCACAAUUAAAUGCAAUUUUUAUGCGCACCU--ACAAAGACGUCGUCG---UUGGCUGUCGCUUCGGCUGC
--((.--------(((.((((....((((((((..((((.....))))...))))))))....)))).))).))--.....(((((((...---.)))).)))((....))... ( -26.70)
>DroAna_CAF1 101853 99 - 1
--AGUGCCAGCGCUGCUCAUGCGCAUUGUAUUUCGUGUGAAAAUCACAAUUAAAUGCGAUUUUUAUGCGCACCUCGCCAAAGUCGUCGGCGAUGUUGAUUG-------------
--.((((((((((.......))))(((((((((..((((.....))))...))))))))).....)).)))).(((((.........))))).........------------- ( -30.70)
>consensus
__AGU________UGCUCAUGCGCAUUGUAUUUCGUGUGAAAAUCACAAUUAAAUGCGAUUUUUAUGCGCACCU__ACAAAGUCGUCG_CG___UUGAUUG_____________
...................((((((((((((((..((((.....))))...))))))))......))))))........................................... (-17.03 = -16.87 +  -0.16)

alignment

secondary structure

dotplot

Window 4

Location	739,374 – 739,476
Length	102
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	78.83
Mean single sequence MFE	-30.32
Consensus MFE	-18.64
Energy contribution	-19.34
Covariance contribution	0.70
Combinations/Pair	1.04
Mean z-score	-1.81
Structure conservation index	0.61
SVM decision value	0.63
SVM RNA-class probability	0.805141
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 739374 102 + 23771897
GGCGAG--GUGCGCAUAAAAAUCGCAUUUAAUUGUGAUUUUCACACGAAAUACAAUGCGCAUGAGCA--------ACUGGCGCCGC----UGGUUAAAAUGCUUAAAUCGAAGGGG
..(((.--((((((((...(((((((......)))))))(((....))).....))))))))(((((--------((..((...))----..)).....)))))...)))...... ( -28.60)
>DroPse_CAF1 104440 93 + 1
GGCGAGGGGUGCGCAUAAAAAUCGCAUUUAAUUGUGAUUUUCACACGAAAUACAAUGCGCAUGAGCA--------ACUGGCGCCGC----UGCUUGACA----------GAGGG-G
((((..((((((((((...(((((((......)))))))(((....))).....)))))))).....--------.))..)))).(----(.(((....----------))).)-) ( -27.30)
>DroWil_CAF1 92831 94 + 1
GU--AG--GUGCGCAUAAAAAUCGCAUUUAAUUGUGAUUUUCACACGAAAUACAAUGCGCAUGAGCA--------ACUGGCGCCCC----GGGG------GGUUAACCAGACAUGG
((--..--((((((((...(((((((......)))))))(((....))).....))))))))..)).--------.((((.((((.----...)------)))...))))...... ( -31.70)
>DroMoj_CAF1 109667 92 + 1
GU--AG--GUGCGCAUAAAAAUUGCAUUUAAUUGUGAUUUUCACACGAAACACAAAGCGCAUGAGCA--------ACUGGCGCCAGUUGCUGGUUGCC------------GAGCCG
..--.(--(((((((.......)))......(((((..((((....))))))))).))((((.((((--------((((....)))))))).).))).------------..))). ( -30.20)
>DroAna_CAF1 101876 99 + 1
GGCGAG--GUGCGCAUAAAAAUCGCAUUUAAUUGUGAUUUUCACACGAAAUACAAUGCGCAUGAGCAGCGCUGGCACUGGCGCCGC----UGCUUAGCA-----------GAGGCG
.((.((--((((((((...(((((((......)))))))(((....))).....)))))))).....((....)).)).))(((.(----(((...)))-----------).))). ( -35.50)
>DroPer_CAF1 109885 94 + 1
GGCGAGGGGUGCGCAUAAAAAUCGCAUUUAAUUGUGAUUUUCACACGAAAUACAAUGCGCAUGAGCA--------ACUGGCGCCGC----UGCUUGACA----------GAGGGGG
((((..((((((((((...(((((((......)))))))(((....))).....)))))))).....--------.))..)))).(----(.(((....----------))).)). ( -28.60)
>consensus
GGCGAG__GUGCGCAUAAAAAUCGCAUUUAAUUGUGAUUUUCACACGAAAUACAAUGCGCAUGAGCA________ACUGGCGCCGC____UGCUUGACA__________GAAGGGG
(((.....((((((((...(((((((......)))))))(((....))).....))))))))..((.............)))))................................ (-18.64 = -19.34 +   0.70)

alignment

secondary structure

dotplot

Window 5

Location	739,374 – 739,476
Length	102
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	78.83
Mean single sequence MFE	-28.55
Consensus MFE	-18.74
Energy contribution	-18.63
Covariance contribution	-0.11
Combinations/Pair	1.11
Mean z-score	-2.37
Structure conservation index	0.66
SVM decision value	1.46
SVM RNA-class probability	0.955544
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 739374 102 - 23771897
CCCCUUCGAUUUAAGCAUUUUAACCA----GCGGCGCCAGU--------UGCUCAUGCGCAUUGUAUUUCGUGUGAAAAUCACAAUUAAAUGCGAUUUUUAUGCGCAC--CUCGCC
..............((.........(----(((((....))--------))))..((((((((((((((..((((.....))))...))))))))......)))))).--...)). ( -25.90)
>DroPse_CAF1 104440 93 - 1
C-CCCUC----------UGUCAAGCA----GCGGCGCCAGU--------UGCUCAUGCGCAUUGUAUUUCGUGUGAAAAUCACAAUUAAAUGCGAUUUUUAUGCGCACCCCUCGCC
.-.....----------......(((----(((((....))--------))))..((((((((((((((..((((.....))))...))))))))......))))))......)). ( -25.90)
>DroWil_CAF1 92831 94 - 1
CCAUGUCUGGUUAACC------CCCC----GGGGCGCCAGU--------UGCUCAUGCGCAUUGUAUUUCGUGUGAAAAUCACAAUUAAAUGCGAUUUUUAUGCGCAC--CU--AC
.((...(((((...((------(...----.))).))))).--------))....((((((((((((((..((((.....))))...))))))))......)))))).--..--.. ( -29.00)
>DroMoj_CAF1 109667 92 - 1
CGGCUC------------GGCAACCAGCAACUGGCGCCAGU--------UGCUCAUGCGCUUUGUGUUUCGUGUGAAAAUCACAAUUAAAUGCAAUUUUUAUGCGCAC--CU--AC
......------------((.....((((((((....))))--------))))..(((((.((((((((..((((.....))))...)))))))).......))))))--).--.. ( -28.90)
>DroAna_CAF1 101876 99 - 1
CGCCUC-----------UGCUAAGCA----GCGGCGCCAGUGCCAGCGCUGCUCAUGCGCAUUGUAUUUCGUGUGAAAAUCACAAUUAAAUGCGAUUUUUAUGCGCAC--CUCGCC
.(((.(-----------(((...)))----).)))((..((((((((((.......))))(((((((((..((((.....))))...))))))))).....)).))))--...)). ( -35.70)
>DroPer_CAF1 109885 94 - 1
CCCCCUC----------UGUCAAGCA----GCGGCGCCAGU--------UGCUCAUGCGCAUUGUAUUUCGUGUGAAAAUCACAAUUAAAUGCGAUUUUUAUGCGCACCCCUCGCC
.......----------......(((----(((((....))--------))))..((((((((((((((..((((.....))))...))))))))......))))))......)). ( -25.90)
>consensus
CCCCUUC__________UGUCAACCA____GCGGCGCCAGU________UGCUCAUGCGCAUUGUAUUUCGUGUGAAAAUCACAAUUAAAUGCGAUUUUUAUGCGCAC__CUCGCC
.................................((((.............((....))..(((((((((..((((.....))))...)))))))))......)))).......... (-18.74 = -18.63 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:47 2006