Locus 8511

Sequence ID	3L_DroMel_CAF1
Location	22,301,954 – 22,302,154
Length	200
Max. P	0.994988

overview

Window 0

Location	22,301,954 – 22,302,074
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.32
Mean single sequence MFE	-29.91
Consensus MFE	-23.97
Energy contribution	-24.01
Covariance contribution	0.04
Combinations/Pair	1.11
Mean z-score	-1.52
Structure conservation index	0.80
SVM decision value	0.22
SVM RNA-class probability	0.641560
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22301954 120 + 23771897
UCAUAUUAGUGGGAAAUGUAAUUUAACAUUGACAGAAGAACUUAUUAAUGUCAGCUCCCCCCUCUGUUUUACAAUAAAAGCGCACACAGAGUGCGCCAUUUUUUACGACACUUGGCUGCU
......(((.(((.(((((......)))))((((..............)))).......))).)))............(((((((.....))))((((..............)))).))) ( -24.18)
>DroSec_CAF1 60581 118 + 1
UCAUAUUAGUGGGAAAUGUCAUUUAGCAUUGAGAGAAGAACUUAUUAAUGCCAGCUCCCGCC--UGUUUUACAAUAAAAGCGCACACUGAGUGCGCCAUUUUUUAUGACACUUGGCUGCU
(((((...((((((..((.......((((((((((.....))).)))))))))..)))))).--...............((((((.....)))))).......)))))............ ( -28.51)
>DroSim_CAF1 42646 118 + 1
UCAUAUUAGUGGGAAAUGUCAUUUAGCAUUGAGAGAAGAACUUAUUAAUGCCAGCUCCCGCC--UGUUUUACAAUAAAAGCGCACACUGAGUGCGCCAUUUUUUACGACACUUGGCUGCU
........((((((..((.......((((((((((.....))).)))))))))..)))))).--..............(((((((.....))))((((..............)))).))) ( -28.05)
>DroEre_CAF1 59015 119 + 1
UCAUAUUGGGGGGAGAUGUCAUUUAGCACUGACAGAAGAACUUAUUAAUGUCAGCUCCC-CCUAUAUUUUACAAUAAAAGCGCACACUGAGUGCGCCAUUUUUUACGACACUUGGCUGCU
......(((((((((.(((......)))((((((..............)))))))))))-))))..............(((((((.....))))((((..............)))).))) ( -36.08)
>DroYak_CAF1 36258 120 + 1
UCAUAUUAGGGGGAAAUGUCAUUUAGCAUUGACAGAAGAACUUAUUAAUGUCAGCUCCCCCCUCUGUUUAACAAUAAAAGCGCACGCUGAGUGCGCCAUUUUUUACGACACUUGGCUGCU
........(((((((((((......)))))((((..............))))...))))))....((((........))))(((.((..((((((..........)).))))..))))). ( -32.74)
>consensus
UCAUAUUAGUGGGAAAUGUCAUUUAGCAUUGACAGAAGAACUUAUUAAUGUCAGCUCCCCCCU_UGUUUUACAAUAAAAGCGCACACUGAGUGCGCCAUUUUUUACGACACUUGGCUGCU
........((((((..((.......(((((((.((......)).)))))))))..)))))).................(((((((.....))))((((..............)))).))) (-23.97 = -24.01 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	22,301,954 – 22,302,074
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.32
Mean single sequence MFE	-31.00
Consensus MFE	-24.38
Energy contribution	-24.46
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.51
Structure conservation index	0.79
SVM decision value	0.04
SVM RNA-class probability	0.551280
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22301954 120 - 23771897
AGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCUGUGUGCGCUUUUAUUGUAAAACAGAGGGGGGAGCUGACAUUAAUAAGUUCUUCUGUCAAUGUUAAAUUACAUUUCCCACUAAUAUGA
..((....((((...........(((((((.....))))))).....(((((((((((.(((((((((..........))))))))).))..))))...))))).....))))....)). ( -31.30)
>DroSec_CAF1 60581 118 - 1
AGCAGCCAAGUGUCAUAAAAAAUGGCGCACUCAGUGUGCGCUUUUAUUGUAAAACA--GGCGGGAGCUGGCAUUAAUAAGUUCUUCUCUCAAUGCUAAAUGACAUUUCCCACUAAUAUGA
....(..(((((((((.......(((((((.....)))))))......(((....(--((..((((((..........))))))..)))...)))...)))))))))..).......... ( -28.60)
>DroSim_CAF1 42646 118 - 1
AGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCAGUGUGCGCUUUUAUUGUAAAACA--GGCGGGAGCUGGCAUUAAUAAGUUCUUCUCUCAAUGCUAAAUGACAUUUCCCACUAAUAUGA
(((((((...(((..((......(((((((.....))))))).......))..)))--)))(((((..(((........)))...)))))..))))........................ ( -28.32)
>DroEre_CAF1 59015 119 - 1
AGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCAGUGUGCGCUUUUAUUGUAAAAUAUAGG-GGGAGCUGACAUUAAUAAGUUCUUCUGUCAGUGCUAAAUGACAUCUCCCCCCAAUAUGA
............(((((......(((((((.....)))))))................((-(((((.((.((((....(((.((......)).))).)))).)).)))))))...))))) ( -32.60)
>DroYak_CAF1 36258 120 - 1
AGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCAGCGUGCGCUUUUAUUGUUAAACAGAGGGGGGAGCUGACAUUAAUAAGUUCUUCUGUCAAUGCUAAAUGACAUUUCCCCCUAAUAUGA
.(((((..((((.(((........)))))))..)).)))...............((.(((((((((((..........)))))...(((((........)))))...))))))....)). ( -34.20)
>consensus
AGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCAGUGUGCGCUUUUAUUGUAAAACA_AGGCGGGAGCUGACAUUAAUAAGUUCUUCUGUCAAUGCUAAAUGACAUUUCCCACUAAUAUGA
.......(((((((((.......(((((((.....)))))))..(((((.........((.(((((((..........)))))))))..)))))....)))))))))............. (-24.38 = -24.46 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	22,301,994 – 22,302,114
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.66
Mean single sequence MFE	-28.81
Consensus MFE	-26.38
Energy contribution	-26.18
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-1.26
Structure conservation index	0.92
SVM decision value	0.52
SVM RNA-class probability	0.767434
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22301994 120 - 23771897
CACUUUGAAGCAGCAGAGACAUAAAAAUGAUAUUAGUUUGAGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCUGUGUGCGCUUUUAUUGUAAAACAGAGGGGGGAGCUGACAUUAAUAAG
..(((((......)))))............(((((((.(.(((..((..(((((((.....))))))).((((((.((((.......))))..))))))..))..))).).))))))).. ( -30.60)
>DroSec_CAF1 60621 118 - 1
CACUUUGAAGCAGCAGAGACAUAAAAAUUAUAUUAGUUUGAGCAGCCAAGUGUCAUAAAAAAUGGCGCACUCAGUGUGCGCUUUUAUUGUAAAACA--GGCGGGAGCUGGCAUUAAUAAG
..(((((......)))))............(((((((.(.(((.(((..((...((((.(((.(((((((.....)))))))))).))))...)).--)))....))).).))))))).. ( -29.20)
>DroSim_CAF1 42686 118 - 1
CACUUUGAAGCAGCAGAGACAUAAAAAUUAUAUUAGUUUGAGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCAGUGUGCGCUUUUAUUGUAAAACA--GGCGGGAGCUGGCAUUAAUAAG
..(((((......)))))............(((((((.(.(((.(((...(((..((......(((((((.....))))))).......))..)))--)))....))).).))))))).. ( -29.42)
>DroEre_CAF1 59055 119 - 1
CACUUUGAAGCAGCAGAGACAUAAAAAUUAUAUUAGUUUGAGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCAGUGUGCGCUUUUAUUGUAAAAUAUAGG-GGGAGCUGACAUUAAUAAG
..(((((......)))))............(((((((.(.(((..((..((((..((......(((((((.....))))))).......))..))))...-))..))).).))))))).. ( -28.52)
>DroYak_CAF1 36298 120 - 1
CACUUUGAAGCAGCAGAGACAUAAAAAUUAUAUUAGUUUGAGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCAGCGUGCGCUUUUAUUGUUAAACAGAGGGGGGAGCUGACAUUAAUAAG
..(((((......)))))............(((((((.(.(((..((...(.((.(((.....(((((((.....))))))).......)))....)).).))..))).).))))))).. ( -26.30)
>consensus
CACUUUGAAGCAGCAGAGACAUAAAAAUUAUAUUAGUUUGAGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCAGUGUGCGCUUUUAUUGUAAAACA_AGGCGGGAGCUGACAUUAAUAAG
..(((((......)))))............(((((((.(.(((..((...(((..((......(((((((.....))))))).......))..))).....))..))).).))))))).. (-26.38 = -26.18 +  -0.20)

alignment

secondary structure

dotplot

Window 3

Location	22,302,034 – 22,302,154
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-32.50
Consensus MFE	-32.48
Energy contribution	-32.36
Covariance contribution	-0.12
Combinations/Pair	1.05
Mean z-score	-1.84
Structure conservation index	1.00
SVM decision value	2.53
SVM RNA-class probability	0.994988
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22302034 120 + 23771897
CGCACACAGAGUGCGCCAUUUUUUACGACACUUGGCUGCUCAAACUAAUAUCAUUUUUAUGUCUCUGCUGCUUCAAAGUGUCAAUAAAAGUGCUGCGCCAAAAGUGGGACACAUUCCGGC
.((.(((...(((((.(((((((...((((((((((.((....(((((........))).))....)).)))...)))))))...))))))).))))).....)))(((.....))).)) ( -30.10)
>DroSec_CAF1 60659 120 + 1
CGCACACUGAGUGCGCCAUUUUUUAUGACACUUGGCUGCUCAAACUAAUAUAAUUUUUAUGUCUCUGCUGCUUCAAAGUGUCAAUAAAAGUGCUGCGCCAAAAGUGGGACACAUUCCGGC
.((.((((..(((((.(((((((..(((((((((((.((....(((((........))).))....)).)))...))))))))..))))))).)))))....))))(((.....))).)) ( -34.10)
>DroSim_CAF1 42724 120 + 1
CGCACACUGAGUGCGCCAUUUUUUACGACACUUGGCUGCUCAAACUAAUAUAAUUUUUAUGUCUCUGCUGCUUCAAAGUGUCAAUAAAAGUGCUGCGCCAAAAGUGGGACACAUUCCGGC
.((.((((..(((((.(((((((...((((((((((.((....(((((........))).))....)).)))...)))))))...))))))).)))))....))))(((.....))).)) ( -32.90)
>DroEre_CAF1 59094 120 + 1
CGCACACUGAGUGCGCCAUUUUUUACGACACUUGGCUGCUCAAACUAAUAUAAUUUUUAUGUCUCUGCUGCUUCAAAGUGUCAAUAAAAGUGCUGCGCCAAAAGUGGGACACAUUCCGGC
.((.((((..(((((.(((((((...((((((((((.((....(((((........))).))....)).)))...)))))))...))))))).)))))....))))(((.....))).)) ( -32.90)
>DroYak_CAF1 36338 120 + 1
CGCACGCUGAGUGCGCCAUUUUUUACGACACUUGGCUGCUCAAACUAAUAUAAUUUUUAUGUCUCUGCUGCUUCAAAGUGUCAAUAAAAAUGCUGCGCCAAAAGUGGGACACAUUCCGGC
.((.((((..(((((.(((((((...((((((((((.((....(((((........))).))....)).)))...)))))))...))))))).)))))....))))(((.....))).)) ( -32.50)
>consensus
CGCACACUGAGUGCGCCAUUUUUUACGACACUUGGCUGCUCAAACUAAUAUAAUUUUUAUGUCUCUGCUGCUUCAAAGUGUCAAUAAAAGUGCUGCGCCAAAAGUGGGACACAUUCCGGC
.((.((((..(((((.(((((((...((((((((((.((....(((((........))).))....)).)))...)))))))...))))))).)))))....))))(((.....))).)) (-32.48 = -32.36 +  -0.12)

alignment

secondary structure

dotplot

Window 4

Location	22,302,034 – 22,302,154
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-33.44
Consensus MFE	-33.02
Energy contribution	-32.86
Covariance contribution	-0.16
Combinations/Pair	1.02
Mean z-score	-1.26
Structure conservation index	0.99
SVM decision value	0.52
SVM RNA-class probability	0.766612
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22302034 120 - 23771897
GCCGGAAUGUGUCCCACUUUUGGCGCAGCACUUUUAUUGACACUUUGAAGCAGCAGAGACAUAAAAAUGAUAUUAGUUUGAGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCUGUGUGCG
(((((((.(((...))))))))))((.....((((((.(((((((....((.((..((((.(((........)))))))..)).)).)))))))))))))....))((((.....)))). ( -32.90)
>DroSec_CAF1 60659 120 - 1
GCCGGAAUGUGUCCCACUUUUGGCGCAGCACUUUUAUUGACACUUUGAAGCAGCAGAGACAUAAAAAUUAUAUUAGUUUGAGCAGCCAAGUGUCAUAAAAAAUGGCGCACUCAGUGUGCG
(((((((.(((...))))))))))((.....((((((.(((((((....((.((..((((.(((........)))))))..)).)).)))))))))))))....))((((.....)))). ( -33.30)
>DroSim_CAF1 42724 120 - 1
GCCGGAAUGUGUCCCACUUUUGGCGCAGCACUUUUAUUGACACUUUGAAGCAGCAGAGACAUAAAAAUUAUAUUAGUUUGAGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCAGUGUGCG
(((((((.(((...))))))))))((.....((((((.(((((((....((.((..((((.(((........)))))))..)).)).)))))))))))))....))((((.....)))). ( -32.90)
>DroEre_CAF1 59094 120 - 1
GCCGGAAUGUGUCCCACUUUUGGCGCAGCACUUUUAUUGACACUUUGAAGCAGCAGAGACAUAAAAAUUAUAUUAGUUUGAGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCAGUGUGCG
(((((((.(((...))))))))))((.....((((((.(((((((....((.((..((((.(((........)))))))..)).)).)))))))))))))....))((((.....)))). ( -32.90)
>DroYak_CAF1 36338 120 - 1
GCCGGAAUGUGUCCCACUUUUGGCGCAGCAUUUUUAUUGACACUUUGAAGCAGCAGAGACAUAAAAAUUAUAUUAGUUUGAGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCAGCGUGCG
(((((((.(((...))))))))))((..(((((((..((((((((....((.((..((((.(((........)))))))..)).)).))))))))..)))))))((((.....)))))). ( -35.20)
>consensus
GCCGGAAUGUGUCCCACUUUUGGCGCAGCACUUUUAUUGACACUUUGAAGCAGCAGAGACAUAAAAAUUAUAUUAGUUUGAGCAGCCAAGUGUCGUAAAAAAUGGCGCACUCAGUGUGCG
(((((((.(((...))))))))))((.....((((((.(((((((....((.((..((((.(((........)))))))..)).)).)))))))))))))....))((((.....)))). (-33.02 = -32.86 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:33 2006