Locus 1305

Sequence ID	2R_DroMel_CAF1
Location	5,065,851 – 5,065,977
Length	126
Max. P	0.999726

overview

Window 9

Location	5,065,851 – 5,065,944
Length	93
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	71.17
Mean single sequence MFE	-34.92
Consensus MFE	-9.04
Energy contribution	-9.84
Covariance contribution	0.80
Combinations/Pair	1.26
Mean z-score	-3.11
Structure conservation index	0.26
SVM decision value	3.59
SVM RNA-class probability	0.999422
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5065851 93 + 20766785
ACACAACCACUCCAACC--------AUCCACGAAUAAUC--------AAACGCACACAAACUUUUUGUAUGU---GUGCGCGCAAAGCUAACGGGUGGGAGGGAGA-GG-UUGC------
...(((((.((((..((--------((((..........--------....(((((((.((.....)).)))---))))((.....))....))))))...)))).-))-))).------ ( -40.20)
>DroSec_CAF1 8677 92 + 1
-CACAACCACUCCAACC--------AUCCACGAAUAAUC--------ACACGUACACAAACUUUUUGGAUGU---GUGCGCGCAAAGCUAACGGGUGGGAGGGAGA-GG-UUGC------
-..(((((.((((..((--------((((..........--------....(((((((..(.....)..)))---))))((.....))....))))))...)))).-))-))).------ ( -37.60)
>DroSim_CAF1 8822 92 + 1
-CACAACCACUCCAACC--------AUCCACGAAUAAUC--------ACACGCACACAAACUUUUUGGAUGU---GUGCGCGCAAAGCUAACGGGUGGGAGGGAGA-GG-UUGC------
-..(((((.((((..((--------((((..........--------....(((((((..(.....)..)))---))))((.....))....))))))...)))).-))-))).------ ( -39.60)
>DroEre_CAF1 8892 93 + 1
ACACAAGCACACCAACC--------AUCCUCGAAUAAUC--------AUACGCACACAAAGUU-UUGGAUGU---AUGCGCGCAAAGCUAACGGGUGGGAGGGAAA-GGGGCGC------
......((.(.((..((--------((((.........(--------(((((..((.......-.))..)))---))).((.....))....))))))..))....-.).))..------ ( -22.10)
>DroAna_CAF1 8258 116 + 1
ACACAUACACUUUGACCCAAGGCUCCCCCUCGAUGGGUUUUUGUUGUUCUCGCACGCAAAGUUAGUGGGGGUAGUGUGG---GAGUGCGAGUGGGAGGGAGGGAGGUAG-UUGGGGUGGU
.......(((((..((((....(((((.((((.....((..(..((..(((((((.....))..)))))..))..)..)---)....)))).)))))....)).....)-)..))))).. ( -35.10)
>consensus
ACACAACCACUCCAACC________AUCCACGAAUAAUC________ACACGCACACAAACUUUUUGGAUGU___GUGCGCGCAAAGCUAACGGGUGGGAGGGAGA_GG_UUGC______
.........((((..((........((((......................(((((((...........)))...))))((.....))....))))))...))))............... ( -9.04 =  -9.84 +   0.80)

alignment

secondary structure

dotplot

Window 0

Location	5,065,851 – 5,065,944
Length	93
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	71.17
Mean single sequence MFE	-35.17
Consensus MFE	-8.81
Energy contribution	-11.53
Covariance contribution	2.72
Combinations/Pair	1.10
Mean z-score	-3.49
Structure conservation index	0.25
SVM decision value	3.95
SVM RNA-class probability	0.999726
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5065851 93 - 20766785
------GCAA-CC-UCUCCCUCCCACCCGUUAGCUUUGCGCGCAC---ACAUACAAAAAGUUUGUGUGCGUUU--------GAUUAUUCGUGGAU--------GGUUGGAGUGGUUGUGU
------((((-((-.((((...(((((((......(((.((((((---(((.((.....)).))))))))).)--------)).....)).)).)--------))..)))).)))))).. ( -38.50)
>DroSec_CAF1 8677 92 - 1
------GCAA-CC-UCUCCCUCCCACCCGUUAGCUUUGCGCGCAC---ACAUCCAAAAAGUUUGUGUACGUGU--------GAUUAUUCGUGGAU--------GGUUGGAGUGGUUGUG-
------((((-((-.((((...(((((((......(..((((.((---(((..(.....)..))))).)))).--------.).....)).)).)--------))..)))).)))))).- ( -37.40)
>DroSim_CAF1 8822 92 - 1
------GCAA-CC-UCUCCCUCCCACCCGUUAGCUUUGCGCGCAC---ACAUCCAAAAAGUUUGUGUGCGUGU--------GAUUAUUCGUGGAU--------GGUUGGAGUGGUUGUG-
------((((-((-.((((...(((((((......(..(((((((---(((..(.....)..)))))))))).--------.).....)).)).)--------))..)))).)))))).- ( -44.00)
>DroEre_CAF1 8892 93 - 1
------GCGCCCC-UUUCCCUCCCACCCGUUAGCUUUGCGCGCAU---ACAUCCAA-AACUUUGUGUGCGUAU--------GAUUAUUCGAGGAU--------GGUUGGUGUGCUUGUGU
------((((.((-...((.((((........((...))((((((---(((.....-.....)))))))))..--------........).))).--------))..)).))))...... ( -27.00)
>DroAna_CAF1 8258 116 - 1
ACCACCCCAA-CUACCUCCCUCCCUCCCACUCGCACUC---CCACACUACCCCCACUAACUUUGCGUGCGAGAACAACAAAAACCCAUCGAGGGGGAGCCUUGGGUCAAAGUGUAUGUGU
..(((....(-((....(((...(((((.(((((((..---........................)))))))............((.....)))))))....)))....)))....))). ( -28.97)
>consensus
______GCAA_CC_UCUCCCUCCCACCCGUUAGCUUUGCGCGCAC___ACAUCCAAAAAGUUUGUGUGCGUGU________GAUUAUUCGUGGAU________GGUUGGAGUGGUUGUGU
.................((((((.(((.........(((((((((..................))))))))).........((....))..............))).)))).))...... ( -8.81 = -11.53 +   2.72)

alignment

secondary structure

dotplot

Window 1

Location	5,065,882 – 5,065,977
Length	95
Sequences	4
Columns	96
Reading direction	reverse
Mean pairwise identity	93.89
Mean single sequence MFE	-26.35
Consensus MFE	-23.85
Energy contribution	-24.42
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.40
Structure conservation index	0.91
SVM decision value	0.05
SVM RNA-class probability	0.557026
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5065882 95 - 20766785
CAACAAGCACGCGCUGUCGUAACGGUUCUUGGCGCAA-CCUCUCCCUCCCACCCGUUAGCUUUGCGCGCACACAUACAAAAAGUUUGUGUGCGUUU
....((((..((((.....((((((.....((.(...-.....)))......)))))).....))))(((((((.((.....)).))))))))))) ( -28.00)
>DroSec_CAF1 8707 95 - 1
CAACAAGCACGCGCUGUCGUAACGGUUCUUGGCGCAA-CCUCUCCCUCCCACCCGUUAGCUUUGCGCGCACACAUCCAAAAAGUUUGUGUACGUGU
......((((((((.....((((((.....((.(...-.....)))......)))))).....))))(.(((((..(.....)..))))).))))) ( -23.70)
>DroSim_CAF1 8852 95 - 1
CAACAAGCACGCGCUGUCGUAACGGUUCUUGGCGCAA-CCUCUCCCUCCCACCCGUUAGCUUUGCGCGCACACAUCCAAAAAGUUUGUGUGCGUGU
......((((((((.....((((((.....((.(...-.....)))......)))))).....))))(((((((..(.....)..))))))))))) ( -30.30)
>DroEre_CAF1 8923 95 - 1
CAACAAGCACGCGCUGUCGUAACGGUUCUUGGUGCGCCCCUUUCCCUCCCACCCGUUAGCUUUGCGCGCAUACAUCCAA-AACUUUGUGUGCGUAU
......((..((((.....((((((....(((................))).)))))).....))))(((((((.....-.....))))))))).. ( -23.39)
>consensus
CAACAAGCACGCGCUGUCGUAACGGUUCUUGGCGCAA_CCUCUCCCUCCCACCCGUUAGCUUUGCGCGCACACAUCCAAAAAGUUUGUGUGCGUGU
......((((((((.....((((((....(((................))).)))))).....))))(((((((...........))))))))))) (-23.85 = -24.42 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:49 2006