Locus 6633

Sequence ID	3R_DroMel_CAF1
Location	17,440,967 – 17,441,114
Length	147
Max. P	0.981924

overview

Window 8

Location	17,440,967 – 17,441,086
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	95.11
Mean single sequence MFE	-33.34
Consensus MFE	-31.76
Energy contribution	-31.80
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.34
Structure conservation index	0.95
SVM decision value	1.17
SVM RNA-class probability	0.926081
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17440967 119 - 27905053
ACCCAGCCGCAACAGCCAUGGCAAUAACAAUAGUGCUGGCGACAGCGGGAACAAAAGUAACGCAUGGAGCCAGCCCCUCCACGCGCACACUUGGAGCCAACAACACAUGACAUGGUCGA
............(.((((((.((...........((((((..(((((...((....))..))).))..))))))..(((((.(......).)))))...........)).)))))).). ( -33.70)
>DroSec_CAF1 42438 119 - 1
AACCAGCCGCAACAGCCAUGGCAAUAACACUAGUGCUGGCGACAGCGGGAACAAAAGUAACGCAUGGAGCCAGCCCCUCCACGCGCACACUUGGAGCCAACAACACAUGACAUGGUCGA
............(.((((((.((...........((((((..(((((...((....))..))).))..))))))..(((((.(......).)))))...........)).)))))).). ( -33.70)
>DroSim_CAF1 39560 118 - 1
AACCAGCCGCAACAGCCAUGGCAAUAACAAUAGUGCUGGCGACAGCGGGAACAA-AGUAACGCAUGGAGCCAGCCCCUCCACGCGCACACUUGGAGCCAACAACACAUGACAUGGUCGA
............(.((((((.((...........((((((..(((((..(....-..)..))).))..))))))..(((((.(......).)))))...........)).)))))).). ( -33.30)
>DroEre_CAF1 41916 115 - 1
ACCCAGGCGCAACAGCCAUGGCAAUAACAAUAGUGCUGGCGACAGCAGGAACAAAAGUAACGCAUGGAG----CCCCUCCACGCGCGCACUUGGAGCCAACAACACAUGACAUGGUCGG
..((((((......))).((((...........(((((....))))).......((((..(((.(((((----...))))).)))...))))...)))).............))).... ( -34.50)
>DroYak_CAF1 42365 115 - 1
ACCCAGCCGCAACAGCCAUGGCAAUAACAAUAGUGCUGGCGACAGCGGGAACAAAAGUAACGCAUGGAG----CCCCUCCACGCGCACACUUGGAACCAACAACACAUGACAUGGUCGA
............(.((((((.((...........((((....))))((...(((..((..(((.(((((----...))))).))).))..)))...)).........)).)))))).). ( -31.50)
>consensus
ACCCAGCCGCAACAGCCAUGGCAAUAACAAUAGUGCUGGCGACAGCGGGAACAAAAGUAACGCAUGGAGCCAGCCCCUCCACGCGCACACUUGGAGCCAACAACACAUGACAUGGUCGA
............(.((((((.((..........(((((....)))))((.....((((..(((.(((((.......))))).)))...))))....)).........)).)))))).). (-31.76 = -31.80 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	17,441,006 – 17,441,114
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	95.35
Mean single sequence MFE	-35.08
Consensus MFE	-30.54
Energy contribution	-32.42
Covariance contribution	1.88
Combinations/Pair	1.06
Mean z-score	-1.90
Structure conservation index	0.87
SVM decision value	1.90
SVM RNA-class probability	0.981924
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17441006 108 + 27905053
GGAGGGGCUGGCUCCAUGCGUUACUUUUGUUCCCGCUGUCGCCAGCACUAUUGUUAUUGCCAUGGCUGUUGCGGCUGGGUAUUAUUUGCUUGGACCUUAGACCCUCUU
((((((((((((..((.(((..((....))...)))))..)))))).(((..((.((.((....)).)).))(((..((((.....))))..).)).))).)))))). ( -41.50)
>DroSec_CAF1 42477 108 + 1
GGAGGGGCUGGCUCCAUGCGUUACUUUUGUUCCCGCUGUCGCCAGCACUAGUGUUAUUGCCAUGGCUGUUGCGGCUGGUUAUUAUUUACUUGGACCUUAGACCCUCUU
((((((((((((..((.(((..((....))...)))))..))))))((((((((.((.((....)).)).)).))))))......................)))))). ( -37.50)
>DroSim_CAF1 39599 107 + 1
GGAGGGGCUGGCUCCAUGCGUUACU-UUGUUCCCGCUGUCGCCAGCACUAUUGUUAUUGCCAUGGCUGUUGCGGCUGGUUAUUAUUUACUUGGACCUUAGACCCUCUU
((((((((((((..((.(((.....-.......)))))..)))))).(((..(((...(((((.((....)).).)))).............)))..))).)))))). ( -34.49)
>DroEre_CAF1 41955 104 + 1
GGAGGGG----CUCCAUGCGUUACUUUUGUUCCUGCUGUCGCCAGCACUAUUGUUAUUGCCAUGGCUGUUGCGCCUGGGUAUUAUUUACUUGGACCUUAGACCCUCUU
((((((.----......((((.((.........(((((....)))))...........((....)).)).))))(..((((.....))))..)........)))))). ( -29.30)
>DroYak_CAF1 42404 104 + 1
GGAGGGG----CUCCAUGCGUUACUUUUGUUCCCGCUGUCGCCAGCACUAUUGUUAUUGCCAUGGCUGUUGCGGCUGGGUAUUAUUUACUUGGACCUUAGACCCUCUU
(((((((----(..((.(((..((....))...)))....(((((((.((....)).)))..))))))..))(((..((((.....))))..).)).....)))))). ( -32.60)
>consensus
GGAGGGGCUGGCUCCAUGCGUUACUUUUGUUCCCGCUGUCGCCAGCACUAUUGUUAUUGCCAUGGCUGUUGCGGCUGGGUAUUAUUUACUUGGACCUUAGACCCUCUU
((((((((((((..((.(((..((....))...)))))..)))))).(((..((.((.((....)).)).))(((..((((.....))))..).)).))).)))))). (-30.54 = -32.42 +   1.88)

alignment

secondary structure

dotplot

Window 0

Location	17,441,006 – 17,441,114
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	95.35
Mean single sequence MFE	-32.64
Consensus MFE	-25.88
Energy contribution	-26.16
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-2.67
Structure conservation index	0.79
SVM decision value	1.64
SVM RNA-class probability	0.969336
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17441006 108 - 27905053
AAGAGGGUCUAAGGUCCAAGCAAAUAAUACCCAGCCGCAACAGCCAUGGCAAUAACAAUAGUGCUGGCGACAGCGGGAACAAAAGUAACGCAUGGAGCCAGCCCCUCC
..(((((.((..((((((.((........(((.(((((....))...)))............((((....))))))).((....))...)).)))).)))).))))). ( -36.20)
>DroSec_CAF1 42477 108 - 1
AAGAGGGUCUAAGGUCCAAGUAAAUAAUAACCAGCCGCAACAGCCAUGGCAAUAACACUAGUGCUGGCGACAGCGGGAACAAAAGUAACGCAUGGAGCCAGCCCCUCC
..(((((.(((.(((..............))).(((((....))...)))........))).((((((..(((((...((....))..))).))..))))))))))). ( -32.94)
>DroSim_CAF1 39599 107 - 1
AAGAGGGUCUAAGGUCCAAGUAAAUAAUAACCAGCCGCAACAGCCAUGGCAAUAACAAUAGUGCUGGCGACAGCGGGAACAA-AGUAACGCAUGGAGCCAGCCCCUCC
..(((((.(((.(((..............))).(((((....))...)))........))).((((((..(((((..(....-..)..))).))..))))))))))). ( -32.74)
>DroEre_CAF1 41955 104 - 1
AAGAGGGUCUAAGGUCCAAGUAAAUAAUACCCAGGCGCAACAGCCAUGGCAAUAACAAUAGUGCUGGCGACAGCAGGAACAAAAGUAACGCAUGGAG----CCCCUCC
..(((((.....(.((((.((.........((((((......))).)))............(((((....)))))..............)).)))).----)))))). ( -30.60)
>DroYak_CAF1 42404 104 - 1
AAGAGGGUCUAAGGUCCAAGUAAAUAAUACCCAGCCGCAACAGCCAUGGCAAUAACAAUAGUGCUGGCGACAGCGGGAACAAAAGUAACGCAUGGAG----CCCCUCC
..(((((.....(.((((.((........(((.(((((....))...)))............((((....))))))).((....))...)).)))).----)))))). ( -30.70)
>consensus
AAGAGGGUCUAAGGUCCAAGUAAAUAAUACCCAGCCGCAACAGCCAUGGCAAUAACAAUAGUGCUGGCGACAGCGGGAACAAAAGUAACGCAUGGAGCCAGCCCCUCC
..(((((.....(.((((.((.........((.(((((....))...)))...........(((((....))))))).((....))...)).)))).)....))))). (-25.88 = -26.16 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:26 2006