Locus 3963

Sequence ID	3L_DroMel_CAF1
Location	11,506,526 – 11,506,708
Length	182
Max. P	0.906377

overview

Window 3

Location	11,506,526 – 11,506,642
Length	116
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	79.43
Mean single sequence MFE	-31.08
Consensus MFE	-15.84
Energy contribution	-16.04
Covariance contribution	0.20
Combinations/Pair	1.11
Mean z-score	-1.93
Structure conservation index	0.51
SVM decision value	0.12
SVM RNA-class probability	0.595374
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11506526 116 - 23771897
AUACACUUACAGAUGCUAUUGCAUCUUUGAGAGAUGGAAAUGGCAAAUUGGCGCUGAGAUUGUCAAUCUCGGAUGCAGUG--AAAUCUG-CCUAUGGCAAAUCUAGCUCUUGAUUCAGA
..........((((((....))))))(..((((.((((..((.((........(((((((.....)))))))..((((..--....)))-)...)).))..)))).))))..)...... ( -33.10)
>DroSec_CAF1 12550 113 - 1
AUACACUUUCAGAUGCUAUUGCAUC--UGAGAGAUGGCAUUGGCAAAUUGGCGCUGAGAUUGUCAAUCUUG-AUGCAGUG--AAAUCCC-CCUAGGGCACAUCAAGCUAUUGAUUCAGA
...(((((((((((((....)))))--)))))).)).((.((((......(((..(((((.....))))).-.))).(((--....(((-....)))))).....)))).))....... ( -36.00)
>DroSim_CAF1 10915 94 - 1
AUACACUUUCAGAUGCUAUUGCAUC--UGAGAGAUGGCAAUGGCAAAUUGGCGCUGAGAUUGUCAAUCUUG-AUGCA----------------------AAUCAACAUUUUAAUUCAGA
.....(((((((((((....)))))--))))))..(.((((.....)))).).(((((.(((..(((.(((-((...----------------------.))))).))).)))))))). ( -28.70)
>DroEre_CAF1 6809 114 - 1
AUACAUUUCCCGAUGCUAUUGCAUC--UCAGAGAUGGCAAUGGCAAAUUGGCGCCGAGAUUGUCAAUCUUG-AUACAGUA--AAGUCCCCCUUAAGGCAAAUCAAACUGUUGGUCCGGA
.........(((.((((((((((((--.....))).)))))))))....(((..((((((.....))))))-..(((((.--.......((....))........)))))..)))))). ( -28.89)
>DroYak_CAF1 10910 116 - 1
AUACAUUUACAGAUGCUGCUGCAUC--UGAGUGAUGGCAAUGGCAAAUUGGCGCCGAGAUUGUCAAUCUUG-AUACAGUACAAAUCCCCCCCUAAGGCAAAUCGAGCUGUUGUUCCAGA
...((((..(((((((....)))))--)))))).((((((((((........)))...))))))).(((.(-(.(((((........((......))........)))))...)).))) ( -28.69)
>consensus
AUACACUUACAGAUGCUAUUGCAUC__UGAGAGAUGGCAAUGGCAAAUUGGCGCUGAGAUUGUCAAUCUUG_AUGCAGUA__AAAUCCC_CCUAAGGCAAAUCAAGCUGUUGAUUCAGA
...........(((((....))))).....((((((((((((((........)))...)))))).)))))................................................. (-15.84 = -16.04 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	11,506,603 – 11,506,708
Length	105
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	88.13
Mean single sequence MFE	-29.56
Consensus MFE	-19.46
Energy contribution	-19.42
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-2.37
Structure conservation index	0.66
SVM decision value	0.18
SVM RNA-class probability	0.619808
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11506603 105 + 23771897
UUCCAUCUCUCAAAGAUGCAAUAGCAUCUGUAAGUGUAUCUGCAUCUGGAAACCGGUUGGAACCGUUCACCCGCCAGAUAUU------CAUACAGAAUGCAU------AAUAGCGAA
...(((((.....))))).....(((((((((.(.(((((((.....(....)(((.((((....)))).))).))))))).------).))))).))))..------......... ( -27.60)
>DroSec_CAF1 12626 115 + 1
UGCCAUCUCUCA--GAUGCAAUAGCAUCUGAAAGUGUAUCUGCAUCUGAAAACCGGUUGGAACCGUUCACCCGCCAGAUAUUCAUAUUCAUACAGAAUGCAUAAUCAUAAUAGCGGA
(((...((.(((--(((((....)))))))).)).)))((((((((((.....(((.((((....)))).))).))))).....(((((.....))))).............))))) ( -29.90)
>DroSim_CAF1 10972 109 + 1
UGCCAUCUCUCA--GAUGCAAUAGCAUCUGAAAGUGUAUCUGCAUCUGAAAACCGGUUGGAACCGUUCACCCGCCAGAUAUUCAUAUUCAUACAGAAUGCAU------AAUAGCGGA
(((...((.(((--(((((....)))))))).)).)))((((((((((.....(((.((((....)))).))).))))).....(((((.....)))))...------....))))) ( -29.90)
>DroEre_CAF1 6886 102 + 1
UGCCAUCUCUGA--GAUGCAAUAGCAUCGGGAAAUGUAUCUGCAUCUGG-AACCGGUUGGAACCGUUCACCCGCCAGAU------AUUCAUACAGAAUGCAU------AAUAGCGGA
...(((.(((..--(((((....))))).))).)))..(((((((((((-...(((.((((....)))).)))))))))------((((.....))))....------....))))) ( -29.80)
>DroYak_CAF1 10989 104 + 1
UGCCAUCACUCA--GAUGCAGCAGCAUCUGUAAAUGUAUCUGCAUCUGA-AACCGGUUGGAACCGUUCACCCGCCAGAUA----UAUUCAUACAGAAUGCAU------AAUAGCGGA
.........(((--(((((((..((((......))))..))))))))))-...((((....)))).....((((...((.----(((((.....))))).))------....)))). ( -30.60)
>consensus
UGCCAUCUCUCA__GAUGCAAUAGCAUCUGAAAGUGUAUCUGCAUCUGAAAACCGGUUGGAACCGUUCACCCGCCAGAUAUU__UAUUCAUACAGAAUGCAU______AAUAGCGGA
..((..........(((((....))))).....(((((((((.(((((.....(((.((((....)))).))).))))).............))).))))))............)). (-19.46 = -19.42 +  -0.04)

alignment

secondary structure

dotplot

Window 5

Location	11,506,603 – 11,506,708
Length	105
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	88.13
Mean single sequence MFE	-35.94
Consensus MFE	-24.45
Energy contribution	-24.61
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-3.03
Structure conservation index	0.68
SVM decision value	1.05
SVM RNA-class probability	0.906377
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11506603 105 - 23771897
UUCGCUAUU------AUGCAUUCUGUAUG------AAUAUCUGGCGGGUGAACGGUUCCAACCGGUUUCCAGAUGCAGAUACACUUACAGAUGCUAUUGCAUCUUUGAGAGAUGGAA
....(((((------.(((((.(((...(------((...((((..((.........))..)))).)))))))))))......((((.((((((....)))))).)))).))))).. ( -30.60)
>DroSec_CAF1 12626 115 - 1
UCCGCUAUUAUGAUUAUGCAUUCUGUAUGAAUAUGAAUAUCUGGCGGGUGAACGGUUCCAACCGGUUUUCAGAUGCAGAUACACUUUCAGAUGCUAUUGCAUC--UGAGAGAUGGCA
...(((((((((.((((((.....)))))).))))).((((((.((..((((((((....))))...))))..))))))))..(((((((((((....)))))--)))))).)))). ( -41.70)
>DroSim_CAF1 10972 109 - 1
UCCGCUAUU------AUGCAUUCUGUAUGAAUAUGAAUAUCUGGCGGGUGAACGGUUCCAACCGGUUUUCAGAUGCAGAUACACUUUCAGAUGCUAUUGCAUC--UGAGAGAUGGCA
...(((((.------......(((((((.....((((...((((..((.........))..))))..)))).)))))))....(((((((((((....)))))--))))))))))). ( -39.50)
>DroEre_CAF1 6886 102 - 1
UCCGCUAUU------AUGCAUUCUGUAUGAAU------AUCUGGCGGGUGAACGGUUCCAACCGGUU-CCAGAUGCAGAUACAUUUCCCGAUGCUAUUGCAUC--UCAGAGAUGGCA
...((..((------((((.....)))))).(------(((((.((.(.(((((((....))).)))-))...))))))))((((((..(((((....)))))--...)))))))). ( -30.60)
>DroYak_CAF1 10989 104 - 1
UCCGCUAUU------AUGCAUUCUGUAUGAAUA----UAUCUGGCGGGUGAACGGUUCCAACCGGUU-UCAGAUGCAGAUACAUUUACAGAUGCUGCUGCAUC--UGAGUGAUGGCA
...((((((------((..........(((((.----((((((.((..(((.((((....))))...-)))..)))))))).)))))(((((((....)))))--)).)))))))). ( -37.30)
>consensus
UCCGCUAUU______AUGCAUUCUGUAUGAAUA__AAUAUCUGGCGGGUGAACGGUUCCAACCGGUUUUCAGAUGCAGAUACACUUACAGAUGCUAUUGCAUC__UGAGAGAUGGCA
...((((((.......(((((.(((...............((((..((.........))..))))....))))))))......(((...(((((....)))))...))).)))))). (-24.45 = -24.61 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:10 2006