Locus 10205

Sequence ID	3R_DroMel_CAF1
Location	27,376,532 – 27,376,698
Length	166
Max. P	0.975066

overview

Window 8

Location	27,376,532 – 27,376,631
Length	99
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	87.43
Mean single sequence MFE	-33.50
Consensus MFE	-24.48
Energy contribution	-26.28
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-1.92
Structure conservation index	0.73
SVM decision value	0.46
SVM RNA-class probability	0.743437
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27376532 99 + 27905053
CUGCAGACAGUCUGCGGCGGCAGCGUUUGUCU----GCCAGAUUCUUCAGCUCUCUGCAGCUC--------UGCAGCUUGGCUUUUUGCUGCCUUCCUGUCUUGGCCAAUU
..((((((((...(((((((((((....).))----))).........((((..(((((....--------)))))...))))....)))))....))))))..))..... ( -34.30)
>DroSec_CAF1 121912 107 + 1
CUGCAGACAGUCUGCGGCGGCAGCGUUUGUCU----GCCAGAUUCUUCAGCUCUCUGCAGCUCAGCAGCUUUGCAGCUUGGCUUUUUGCUGCCUUCCUGUCUUGGCCAAUU
..((((((((...(((((((((((....).))----))).........((((..((((((((....)))..)))))...))))....)))))....))))))..))..... ( -35.40)
>DroSim_CAF1 86134 107 + 1
CUGCAGACAGUCUGCGGCGGCAGCGUUUGUCU----GCCAGAUUCUUCAGCUCUCUGCAGCUCAGCAGCUUUGCAGCUUGGCUUUUUGCUGCCUUCCUGUCUUGGCCAAUU
..((((((((...(((((((((((....).))----))).........((((..((((((((....)))..)))))...))))....)))))....))))))..))..... ( -35.40)
>DroEre_CAF1 89703 95 + 1
CUGCAGACAGUCUGCGGCGGCAGCGUUUGUCUGCCUGCCAGAUUCUUCAGCGCUCU----------------GCAGCUUGGCUUUUUACUGCCUUCCUGUCUUGGCCAAUU
..((((((((...((.((((.((((((.(((((.....))))).....))))))))----------------)).))..(((........)))...))))))..))..... ( -31.50)
>DroYak_CAF1 79770 95 + 1
CUGCAGACAGUCUGCGGCGGCAGCGUUUGUCUGCCUGCCAGAUUCUUCAGCGCUCU----------------GCAGCUUAGCUUUUUGCUGCCUUCCUGUCUUGGCCAAUU
..((((((((...(((((((((((....).))))).))).((....)).)).....----------------(((((..........)))))....))))))..))..... ( -30.90)
>consensus
CUGCAGACAGUCUGCGGCGGCAGCGUUUGUCU____GCCAGAUUCUUCAGCUCUCUGCAGCUC________UGCAGCUUGGCUUUUUGCUGCCUUCCUGUCUUGGCCAAUU
..((((.....))))((((((((((((((.(.....).))))).....((((..((((((..........))))))...))))....))))))...(......)))).... (-24.48 = -26.28 +   1.80)

alignment

secondary structure

dotplot

Window 9

Location	27,376,532 – 27,376,631
Length	99
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	87.43
Mean single sequence MFE	-35.04
Consensus MFE	-25.02
Energy contribution	-25.76
Covariance contribution	0.74
Combinations/Pair	1.04
Mean z-score	-2.64
Structure conservation index	0.71
SVM decision value	1.20
SVM RNA-class probability	0.930222
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27376532 99 - 27905053
AAUUGGCCAAGACAGGAAGGCAGCAAAAAGCCAAGCUGCA--------GAGCUGCAGAGAGCUGAAGAAUCUGGC----AGACAAACGCUGCCGCCGCAGACUGUCUGCAG
.....((..((((((....((.((....(((....(((((--------....)))))...))).........(((----((.(....)))))))).))...)))))))).. ( -33.80)
>DroSec_CAF1 121912 107 - 1
AAUUGGCCAAGACAGGAAGGCAGCAAAAAGCCAAGCUGCAAAGCUGCUGAGCUGCAGAGAGCUGAAGAAUCUGGC----AGACAAACGCUGCCGCCGCAGACUGUCUGCAG
....(((..((.(((....(((((..........)))))....)))))..)))(((((.(((((.......((((----((.(....)))))))...))).)).))))).. ( -37.40)
>DroSim_CAF1 86134 107 - 1
AAUUGGCCAAGACAGGAAGGCAGCAAAAAGCCAAGCUGCAAAGCUGCUGAGCUGCAGAGAGCUGAAGAAUCUGGC----AGACAAACGCUGCCGCCGCAGACUGUCUGCAG
....(((..((.(((....(((((..........)))))....)))))..)))(((((.(((((.......((((----((.(....)))))))...))).)).))))).. ( -37.40)
>DroEre_CAF1 89703 95 - 1
AAUUGGCCAAGACAGGAAGGCAGUAAAAAGCCAAGCUGC----------------AGAGCGCUGAAGAAUCUGGCAGGCAGACAAACGCUGCCGCCGCAGACUGUCUGCAG
.....((..((((((...(((........)))...((((----------------(((...(....)..)))(((.(((((.(....))))))))))))).)))))))).. ( -34.40)
>DroYak_CAF1 79770 95 - 1
AAUUGGCCAAGACAGGAAGGCAGCAAAAAGCUAAGCUGC----------------AGAGCGCUGAAGAAUCUGGCAGGCAGACAAACGCUGCCGCCGCAGACUGUCUGCAG
.....((((.((((((...(((((..........)))))----------------....).))).....))))))..(((((((....((((....))))..))))))).. ( -32.20)
>consensus
AAUUGGCCAAGACAGGAAGGCAGCAAAAAGCCAAGCUGCA________GAGCUGCAGAGAGCUGAAGAAUCUGGC____AGACAAACGCUGCCGCCGCAGACUGUCUGCAG
....((((......)...((((((....(((....(((((............)))))...)))......(((.......))).....)))))))))((((.....)))).. (-25.02 = -25.76 +   0.74)

alignment

secondary structure

dotplot

Window 0

Location	27,376,591 – 27,376,698
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	97.75
Mean single sequence MFE	-34.92
Consensus MFE	-33.86
Energy contribution	-34.10
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.59
Structure conservation index	0.97
SVM decision value	1.74
SVM RNA-class probability	0.975066
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27376591 107 - 27905053
GGCUUUGCAAGCCUUAUGAUUUCGCCUUUGCCGACGUUGCGCUAAUUUGUUGGCAUCCAUCGAGUGGAAUUGGCCAAGACAGGAAGGCAGCAAAAAGCCAAGCUGCA
((((((((..(((((.((.(((.(((..((((((((...........))))))))(((((...)))))...))).))).))..))))).)))..)))))........ ( -36.70)
>DroSec_CAF1 121979 107 - 1
GGCUUUGCAAGCCUUAUGAUUUCGCCUUUGCCGACGUUGCGCUAAAUUGUUGGCAUCCAUCGAGUGGAAUUGGCCAAGACAGGAAGGCAGCAAAAAGCCAAGCUGCA
((((((((..(((((.((.(((.(((..((((((((...........))))))))(((((...)))))...))).))).))..))))).)))..)))))........ ( -36.70)
>DroSim_CAF1 86201 107 - 1
GGCUUUGCAAGCCUUAUGAUUUCGCCUUUGCCGACGUUGCGCUAAUUUGUUGGCAUCCAUCGAGUGGAAUUGGCCAAGACAGGAAGGCAGCAAAAAGCCAAGCUGCA
((((((((..(((((.((.(((.(((..((((((((...........))))))))(((((...)))))...))).))).))..))))).)))..)))))........ ( -36.70)
>DroEre_CAF1 89759 106 - 1
UGCUUUGCAAGCCUUAUGAUUUCGCCUUUGCCGACGUUGCGCUAAUUUGUUGGCAUCCAUCGAGUGGAAUUGGCCAAGACAGGAAGGCAGUAAAAAGCCAAGCUGC-
.(((((....(((((.((.(((.(((..((((((((...........))))))))(((((...)))))...))).))).))..))))).....)))))........- ( -31.60)
>DroYak_CAF1 79826 106 - 1
UGCUUUGCAAGCCUUAUGAUUUCGCCUUUGCCGACGUUGCGCUAAUUUGUUGGCAUCCAUCGAGUGGAAUUGGCCAAGACAGGAAGGCAGCAAAAAGCUAAGCUGC-
.(((((((..(((((.((.(((.(((..((((((((...........))))))))(((((...)))))...))).))).))..))))).)))..))))........- ( -32.90)
>consensus
GGCUUUGCAAGCCUUAUGAUUUCGCCUUUGCCGACGUUGCGCUAAUUUGUUGGCAUCCAUCGAGUGGAAUUGGCCAAGACAGGAAGGCAGCAAAAAGCCAAGCUGCA
((((((((..(((((.((.(((.(((..((((((((...........))))))))(((((...)))))...))).))).))..))))).)))..)))))........ (-33.86 = -34.10 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:51:21 2006