Locus 5904

Sequence ID	2L_DroMel_CAF1
Location	16,685,056 – 16,685,238
Length	182
Max. P	0.958139

overview

Window 7

Location	16,685,056 – 16,685,169
Length	113
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	83.28
Mean single sequence MFE	-23.60
Consensus MFE	-15.16
Energy contribution	-15.72
Covariance contribution	0.56
Combinations/Pair	1.11
Mean z-score	-2.54
Structure conservation index	0.64
SVM decision value	0.29
SVM RNA-class probability	0.672184
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16685056 113 + 22407834
AUUUCCCUUUGCCUACGUUUCCUCCACUCUUUCCAUUAGGCUGGCCAUCACAUUUGAGGUUUUAUCCUUGGGCUGUCAACACGUGCUU--UGACACGCCCCCUUUAGAAUCCUCC
.....((...(((((.....................))))).))...........(((((((((.....((((((((((........)--))))).))))....))))).)))). ( -26.50)
>DroSec_CAF1 139915 113 + 1
AUUUCCCUUUGCCUACGUUUCCUCCUCUCUUCCCAUUAGACUGGCCAUCACUUUUGAGGUUUUAUCCUUGGGCUGUCAACACGUGAUU--UGACACGCCCCCUUUAGAAUCCUCC
..........(((...((((.................)))).)))..........(((((((((.....((((((((((........)--))))).))))....))))).)))). ( -23.33)
>DroSim_CAF1 139838 113 + 1
AUUUCCCUUUGCCUACGUUUCCUCCUCUCUUCCCAUUAGGCUGGCCAUCACUUUUGAGGUUUUAUCCUUGGGCUGUCAACACGUGCUU--UGACACGCCCCCUUUAGAAUCCUCC
.....((...(((((.....................))))).))...........(((((((((.....((((((((((........)--))))).))))....))))).)))). ( -26.50)
>DroEre_CAF1 140457 113 + 1
AUUUCCCAUCGCCUACGUUUCCUCCUCUCUUCCCAUUAGGCUGCCCAUCACUUUUGAGGUUUUAUCCUUGGGCUGUCAACACGUGCUU--UGACACGCCCCCUUUAGCGUCCUCC
..........(((((.....................)))))..............((((..........((((((((((........)--))))).))))..........)))). ( -23.15)
>DroYak_CAF1 139720 113 + 1
AUUUUCCUUUGCCUACGUUUCCUCCUCUCCUUCCAUUAGGCUGCCCAUCACUUUUGAGGUUUUAUCCUUGGGCUGUCAACACGUGCUU--UGACACGCCCCUUUAAGCGUCCUUC
..........(((((.....................))))).((...........((((......))))((((((((((........)--))))).))))......))....... ( -22.30)
>DroPer_CAF1 157032 91 + 1
AC-UCCCCCA------------GCCUCCCUUUUCAUU-------CCAUCACUUUUGAGGUUUUGGCUUUAGGCUGUCGACACGUGCUGUGUGACACGCCCCGUU----GUCCCCC
..-......(------------(((..((((......-------...........))))....))))...(((((((.((((.....)))))))).))).....----....... ( -19.83)
>consensus
AUUUCCCUUUGCCUACGUUUCCUCCUCUCUUCCCAUUAGGCUGGCCAUCACUUUUGAGGUUUUAUCCUUGGGCUGUCAACACGUGCUU__UGACACGCCCCCUUUAGAAUCCUCC
..........(((((.....................)))))..............((((..........(((((((((............))))).))))..........)))). (-15.16 = -15.72 +   0.56)

alignment

secondary structure

dotplot

Window 8

Location	16,685,056 – 16,685,169
Length	113
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	83.28
Mean single sequence MFE	-28.28
Consensus MFE	-19.44
Energy contribution	-19.93
Covariance contribution	0.49
Combinations/Pair	1.14
Mean z-score	-1.88
Structure conservation index	0.69
SVM decision value	0.09
SVM RNA-class probability	0.577042
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16685056 113 - 22407834
GGAGGAUUCUAAAGGGGGCGUGUCA--AAGCACGUGUUGACAGCCCAAGGAUAAAACCUCAAAUGUGAUGGCCAGCCUAAUGGAAAGAGUGGAGGAAACGUAGGCAAAGGGAAAU
.(((((((((.....((((.(((((--(........)))))))))).)))))....))))..........(((..((....))..........(....)...))).......... ( -28.90)
>DroSec_CAF1 139915 113 - 1
GGAGGAUUCUAAAGGGGGCGUGUCA--AAUCACGUGUUGACAGCCCAAGGAUAAAACCUCAAAAGUGAUGGCCAGUCUAAUGGGAAGAGAGGAGGAAACGUAGGCAAAGGGAAAU
.(((((((((.....((((.(((((--(........)))))))))).)))))....))))..........(((..(((....)))........(....)...))).......... ( -27.90)
>DroSim_CAF1 139838 113 - 1
GGAGGAUUCUAAAGGGGGCGUGUCA--AAGCACGUGUUGACAGCCCAAGGAUAAAACCUCAAAAGUGAUGGCCAGCCUAAUGGGAAGAGAGGAGGAAACGUAGGCAAAGGGAAAU
.(((((((((.....((((.(((((--(........)))))))))).)))))....))))..........(((..((....))..........(....)...))).......... ( -29.10)
>DroEre_CAF1 140457 113 - 1
GGAGGACGCUAAAGGGGGCGUGUCA--AAGCACGUGUUGACAGCCCAAGGAUAAAACCUCAAAAGUGAUGGGCAGCCUAAUGGGAAGAGAGGAGGAAACGUAGGCGAUGGGAAAU
......((((.....((((.(((((--(........))))))(((((.((......))(((....)))))))).))))...............(....)...))))......... ( -28.50)
>DroYak_CAF1 139720 113 - 1
GAAGGACGCUUAAAGGGGCGUGUCA--AAGCACGUGUUGACAGCCCAAGGAUAAAACCUCAAAAGUGAUGGGCAGCCUAAUGGAAGGAGAGGAGGAAACGUAGGCAAAGGAAAAU
.......(((((...((((.(((((--(........))))))))))..........((((....((.....))..(((......))).)))).(....).))))).......... ( -28.60)
>DroPer_CAF1 157032 91 - 1
GGGGGAC----AACGGGGCGUGUCACACAGCACGUGUCGACAGCCUAAAGCCAAAACCUCAAAAGUGAUGG-------AAUGAAAAGGGAGGC------------UGGGGGA-GU
.(....)----..(((.((((((......)))))).))).((((((....((....(((((....))).))-------..(....))).))))------------)).....-.. ( -26.70)
>consensus
GGAGGACUCUAAAGGGGGCGUGUCA__AAGCACGUGUUGACAGCCCAAGGAUAAAACCUCAAAAGUGAUGGCCAGCCUAAUGGAAAGAGAGGAGGAAACGUAGGCAAAGGGAAAU
.((((..........((((.(((((....((....)))))))))))..........))))..............(((((..............(....).))))).......... (-19.44 = -19.93 +   0.49)

alignment

secondary structure

dotplot

Window 9

Location	16,685,096 – 16,685,203
Length	107
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	79.17
Mean single sequence MFE	-25.99
Consensus MFE	-17.69
Energy contribution	-17.17
Covariance contribution	-0.53
Combinations/Pair	1.37
Mean z-score	-1.23
Structure conservation index	0.68
SVM decision value	0.12
SVM RNA-class probability	0.592154
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16685096 107 + 22407834
CUGGCCAUCACAUUUGAGGUUU----UAUCCUUGGGCUGUCAACACGUGCUUUGACACGCCCCCUUUAGAAUCCUCCGGGUAUUUUUUGUACCAGUUUUCAGUUAGGAAGU
(((((..........(((((((----((.....((((((((((........)))))).))))....))))).))))..(((((.....)))))........)))))..... ( -29.70)
>DroSec_CAF1 139955 107 + 1
CUGGCCAUCACUUUUGAGGUUU----UAUCCUUGGGCUGUCAACACGUGAUUUGACACGCCCCCUUUAGAAUCCUCCGGGUAUUUUUUGUACCACUUUUCAGUUAGGAUGU
(((((..........(((((((----((.....((((((((((........)))))).))))....))))).))))..(((((.....)))))........)))))..... ( -29.70)
>DroSim_CAF1 139878 107 + 1
CUGGCCAUCACUUUUGAGGUUU----UAUCCUUGGGCUGUCAACACGUGCUUUGACACGCCCCCUUUAGAAUCCUCCGGGUAUUUUUUGUACCACUUUUCAGUUAGGAUGU
(((((..........(((((((----((.....((((((((((........)))))).))))....))))).))))..(((((.....)))))........)))))..... ( -29.70)
>DroEre_CAF1 140497 107 + 1
CUGCCCAUCACUUUUGAGGUUU----UAUCCUUGGGCUGUCAACACGUGCUUUGACACGCCCCCUUUAGCGUCCUCCCGGUGUUUGUUGUACCACUUUUCAGUUAGGAAGU
.(((.((.((((...((((...----.......((((((((((........)))))).))))..........))))..))))..))..)))..((((((......)))))) ( -24.35)
>DroYak_CAF1 139760 103 + 1
CUGCCCAUCACUUUUGAGGUUU----UAUCCUUGGGCUGUCAACACGUGCUUUGACACGCCCCUUUAAGCGUCCUUCUGGUAUUU-UUGUACUACUUUUUAGUC---AAAU
.((((..........((((...----...))))((((((((((........)))))).))))................))))..(-(((.((((.....)))))---))). ( -22.80)
>DroAna_CAF1 79756 94 + 1
-----------UUUUGAGGUUUUUUUUGUCUCUCGGCUGUCGACACGUGCUUUGACACGCCCCCUUUUGGACAGCCCGC-CCCCCGUUGGAGGAAGUUUAA-----AUAGU
-----------.((((((.(((((((........(((((((....((((......))))....(....))))))))...-........))))))).)))))-----).... ( -19.71)
>consensus
CUGGCCAUCACUUUUGAGGUUU____UAUCCUUGGGCUGUCAACACGUGCUUUGACACGCCCCCUUUAGAAUCCUCCGGGUAUUUUUUGUACCACUUUUCAGUUAGGAAGU
...............((((..........))))((((((((((........)))))).))))................(((((.....))))).................. (-17.69 = -17.17 +  -0.53)

alignment

secondary structure

dotplot

Window 0

Location	16,685,096 – 16,685,203
Length	107
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	79.17
Mean single sequence MFE	-28.08
Consensus MFE	-14.77
Energy contribution	-15.38
Covariance contribution	0.61
Combinations/Pair	1.21
Mean z-score	-1.99
Structure conservation index	0.53
SVM decision value	0.22
SVM RNA-class probability	0.642096
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16685096 107 - 22407834
ACUUCCUAACUGAAAACUGGUACAAAAAAUACCCGGAGGAUUCUAAAGGGGGCGUGUCAAAGCACGUGUUGACAGCCCAAGGAUA----AAACCUCAAAUGUGAUGGCCAG
................(((((.......(((....(((((((((.....((((.((((((........)))))))))).))))).----...))))...)))....))))) ( -26.10)
>DroSec_CAF1 139955 107 - 1
ACAUCCUAACUGAAAAGUGGUACAAAAAAUACCCGGAGGAUUCUAAAGGGGGCGUGUCAAAUCACGUGUUGACAGCCCAAGGAUA----AAACCUCAAAAGUGAUGGCCAG
.((((((.(((....)))((((.......))))..(((((((((.....((((.((((((........)))))))))).))))).----...))))...)).))))..... ( -28.90)
>DroSim_CAF1 139878 107 - 1
ACAUCCUAACUGAAAAGUGGUACAAAAAAUACCCGGAGGAUUCUAAAGGGGGCGUGUCAAAGCACGUGUUGACAGCCCAAGGAUA----AAACCUCAAAAGUGAUGGCCAG
.((((((.(((....)))((((.......))))..(((((((((.....((((.((((((........)))))))))).))))).----...))))...)).))))..... ( -28.90)
>DroEre_CAF1 140497 107 - 1
ACUUCCUAACUGAAAAGUGGUACAACAAACACCGGGAGGACGCUAAAGGGGGCGUGUCAAAGCACGUGUUGACAGCCCAAGGAUA----AAACCUCAAAAGUGAUGGGCAG
.((((((.(((....)))(((.........)))))))))(((((......)))))(((((........))))).(((((.((...----...))(((....)))))))).. ( -30.90)
>DroYak_CAF1 139760 103 - 1
AUUU---GACUAAAAAGUAGUACAA-AAAUACCAGAAGGACGCUUAAAGGGGCGUGUCAAAGCACGUGUUGACAGCCCAAGGAUA----AAACCUCAAAAGUGAUGGGCAG
.(((---(((((.....)))).)))-)....((....))..(((((...((((.((((((........)))))))))).(((...----...))).........))))).. ( -24.60)
>DroAna_CAF1 79756 94 - 1
ACUAU-----UUAAACUUCCUCCAACGGGGG-GCGGGCUGUCCAAAAGGGGGCGUGUCAAAGCACGUGUCGACAGCCGAGAGACAAAAAAAACCUCAAAA-----------
.....-----.....(.((((((...)))))-).)((((((((....)((.((((((....)))))).)))))))))..(((...........)))....----------- ( -29.10)
>consensus
ACUUCCUAACUGAAAAGUGGUACAAAAAAUACCCGGAGGAUUCUAAAGGGGGCGUGUCAAAGCACGUGUUGACAGCCCAAGGAUA____AAACCUCAAAAGUGAUGGCCAG
..................((((.......))))..((((...(.....)((((.((((((........))))))))))..............))))............... (-14.77 = -15.38 +   0.61)

alignment

secondary structure

dotplot

Window 1

Location	16,685,131 – 16,685,238
Length	107
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	75.98
Mean single sequence MFE	-27.93
Consensus MFE	-16.32
Energy contribution	-17.85
Covariance contribution	1.53
Combinations/Pair	1.27
Mean z-score	-2.13
Structure conservation index	0.58
SVM decision value	1.49
SVM RNA-class probability	0.958139
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16685131 107 - 22407834
GUGAGGAAUGGAAGACAUAAGACAACAUGUGUUACACUUCCUAACUGAAAACUGGUACAAAAAAUACCCGGAGGAUUCUAAAGGGGGCGUGUCAAAGCACGUGUUGA
.......(((.....)))....(((((((((((((((.((((....(((..((((((.......))))...))..))).....)))).))))...))))))))))). ( -28.50)
>DroSec_CAF1 139990 107 - 1
GUGAGGAAUGGAAGACAUAAGACAACAUGUGUUACACAUCCUAACUGAAAAGUGGUACAAAAAAUACCCGGAGGAUUCUAAAGGGGGCGUGUCAAAUCACGUGUUGA
.......(((.....)))....(((((((((..((((..(((.(((....)))((((.......))))...............)))..)))).....))))))))). ( -25.20)
>DroSim_CAF1 139913 100 - 1
GU-------GGAAGACAUAAAAGAACAUGUGUUACACAUCCUAACUGAAAAGUGGUACAAAAAAUACCCGGAGGAUUCUAAAGGGGGCGUGUCAAAGCACGUGUUGA
((-------(.....))).....((((((((((((((..(((.(((....)))((((.......))))...............)))..))))...)))))))))).. ( -24.70)
>DroEre_CAF1 140532 107 - 1
GUAAGGAAUGGAAGACAGAAUUUAACAUGUGUUACACUUCCUAACUGAAAAGUGGUACAACAAACACCGGGAGGACGCUAAAGGGGGCGUGUCAAAGCACGUGUUGA
.....................((((((((((((...((((((.(((....)))(((.........)))))))))(((((......))))).....)))))))))))) ( -30.40)
>DroYak_CAF1 139795 103 - 1
GUACGAAAGGAAAGACAUGAUUUAACAUGUGUUACAUUU---GACUAAAAAGUAGUACAA-AAAUACCAGAAGGACGCUUAAAGGGGCGUGUCAAAGCACGUGUUGA
...(....)............(((((((((((....(((---(((...............-.....((....))((((((....))))))))))))))))))))))) ( -25.70)
>DroAna_CAF1 79784 99 - 1
UCCGAGCCUG--AGAAACAGGAUAACAUGUGUUGCACUAU-----UUAAACUUCCUCCAACGGGGG-GCGGGCUGUCCAAAAGGGGGCGUGUCAAAGCACGUGUCGA
..(((.((((--.....))))....((((((((((((...-----.....((.(((((....))))-).))...((((......))))))))...))))))))))). ( -33.10)
>consensus
GUAAGGAAUGGAAGACAUAAGAUAACAUGUGUUACACUUCCUAACUGAAAAGUGGUACAAAAAAUACCCGGAGGAUUCUAAAGGGGGCGUGUCAAAGCACGUGUUGA
......................(((((((((((((((.((((.(((....)))((((.......))))...............)))).))))...))))))))))). (-16.32 = -17.85 +   1.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:58 2006