Locus 4317

Sequence ID	3R_DroMel_CAF1
Location	11,440,271 – 11,440,423
Length	152
Max. P	0.995352

overview

Window 3

Location	11,440,271 – 11,440,391
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.45
Mean single sequence MFE	-31.93
Consensus MFE	-29.90
Energy contribution	-29.30
Covariance contribution	-0.60
Combinations/Pair	1.17
Mean z-score	-1.67
Structure conservation index	0.94
SVM decision value	1.24
SVM RNA-class probability	0.934947
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11440271 120 + 27905053
GUGAUUCACCAGAUCCUUCCCCCCCCCCCCCUGUAGCAUUAUCGCUUUUAUUGCGUUUUAAUUUGGCUUGUCCUUUUCAGCGAGGCAUGCAAGGACAUGCAUCCAGGAUGUGGUCAAUAU
...(((.((((.(((((....................((((.(((.......)))...))))...((.(((((((..((((...)).)).))))))).))....))))).)))).))).. ( -28.30)
>DroSec_CAF1 180257 112 + 1
GUGACUCACCAGAUCCUUUCC--------CCUGUAGCAUUAUCGCUUUUAUUGCGUUUUAAUUUGGCUUGUCCUUGUCAGCGAGGCAUGCAAGGACAUGCAUCCAGGAUGUGGUCAAUAU
.......((((.(((((....--------........((((.(((.......)))...))))...((.(((((((((..((...))..))))))))).))....))))).))))...... ( -32.20)
>DroSim_CAF1 174445 114 + 1
GAUACUCACCAGAUCCUUUCC------CCCCUGUAGCAUUAUCGCUUUUAUUGCGUUUUAAUUUGGCUUGUCCUUGUCAGCGAGGCAUGCAAGGACAUGCAUCCAGGAUGUGGUCAAUAU
.......((((.(((((....------..........((((.(((.......)))...))))...((.(((((((((..((...))..))))))))).))....))))).))))...... ( -32.20)
>DroEre_CAF1 169728 109 + 1
GUGACUCGCCAGAUUCCUUCC--------CCU---GCAUUAUCGCCUUUAUUGCGUUUUAAUUUGGCUUGUCCUUGUCUGUGAGGCAUGCAAGGACAUGCAUCCAGGAUGUGGCCAAUAU
.......((((.((.(((...--------..(---(((.....(((...((((.....))))..))).(((((((((.((.....)).)))))))))))))...))))).))))...... ( -33.20)
>DroYak_CAF1 173132 102 + 1
GUGACCCGCCAGAUCCCUGCC--------CC----------UCGCUUUUAUUGCGUUUUAAUUUGGCUUGUCCUUGUCUGUGAGGCAUGCAAGGACAUGCAUCCAGGAUGUGGUCAAUAU
.(((((.(((((((.......--------..----------.(((.......))).....))))))).(((((((((.((.....)).))))))))).(((((...)))))))))).... ( -33.76)
>consensus
GUGACUCACCAGAUCCUUUCC________CCUGUAGCAUUAUCGCUUUUAUUGCGUUUUAAUUUGGCUUGUCCUUGUCAGCGAGGCAUGCAAGGACAUGCAUCCAGGAUGUGGUCAAUAU
.......((((.((((..........................(((.......)))..........((.(((((((((..((...))..))))))))).)).....)))).))))...... (-29.90 = -29.30 +  -0.60)

alignment

secondary structure

dotplot

Window 4

Location	11,440,271 – 11,440,391
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.45
Mean single sequence MFE	-33.29
Consensus MFE	-26.84
Energy contribution	-26.64
Covariance contribution	-0.20
Combinations/Pair	1.15
Mean z-score	-2.19
Structure conservation index	0.81
SVM decision value	1.52
SVM RNA-class probability	0.961148
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11440271 120 - 27905053
AUAUUGACCACAUCCUGGAUGCAUGUCCUUGCAUGCCUCGCUGAAAAGGACAAGCCAAAUUAAAACGCAAUAAAAGCGAUAAUGCUACAGGGGGGGGGGGGGAAGGAUCUGGUGAAUCAC
..(((.((((.(((((..(((((......))))).((((.(((....((.....)).........(((.......))).........))).))))........))))).)))).)))... ( -33.10)
>DroSec_CAF1 180257 112 - 1
AUAUUGACCACAUCCUGGAUGCAUGUCCUUGCAUGCCUCGCUGACAAGGACAAGCCAAAUUAAAACGCAAUAAAAGCGAUAAUGCUACAGG--------GGAAAGGAUCUGGUGAGUCAC
....(((((((..((((...(((((((((((((.((...)))).)))))))..............(((.......)))...))))..))))--------(((.....))).))).)))). ( -33.90)
>DroSim_CAF1 174445 114 - 1
AUAUUGACCACAUCCUGGAUGCAUGUCCUUGCAUGCCUCGCUGACAAGGACAAGCCAAAUUAAAACGCAAUAAAAGCGAUAAUGCUACAGGGG------GGAAAGGAUCUGGUGAGUAUC
(((((.((((.(((((..(((((......))))).((((.(((....((.....)).........(((.......))).........))).))------))..))))).)))).))))). ( -35.10)
>DroEre_CAF1 169728 109 - 1
AUAUUGGCCACAUCCUGGAUGCAUGUCCUUGCAUGCCUCACAGACAAGGACAAGCCAAAUUAAAACGCAAUAAAGGCGAUAAUGC---AGG--------GGAAGGAAUCUGGCGAGUCAC
..(((.((((..((((...((((((((((((..((.....))..)))))))..(((..................)))....))))---)..--------...))))...)))).)))... ( -32.47)
>DroYak_CAF1 173132 102 - 1
AUAUUGACCACAUCCUGGAUGCAUGUCCUUGCAUGCCUCACAGACAAGGACAAGCCAAAUUAAAACGCAAUAAAAGCGA----------GG--------GGCAGGGAUCUGGCGGGUCAC
....(((((....(((....((.((((((((..((.....))..)))))))).))..........(((.......))))----------))--------(.(((....))).).))))). ( -31.90)
>consensus
AUAUUGACCACAUCCUGGAUGCAUGUCCUUGCAUGCCUCGCUGACAAGGACAAGCCAAAUUAAAACGCAAUAAAAGCGAUAAUGCUACAGG________GGAAAGGAUCUGGUGAGUCAC
..(((.((((.(((((....((.((((((((...(.....)...)))))))).))..........(((.......))).........................))))).)))).)))... (-26.84 = -26.64 +  -0.20)

alignment

secondary structure

dotplot

Window 5

Location	11,440,311 – 11,440,423
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.06
Mean single sequence MFE	-26.64
Consensus MFE	-23.04
Energy contribution	-23.08
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-2.15
Structure conservation index	0.86
SVM decision value	2.57
SVM RNA-class probability	0.995352
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11440311 112 - 27905053
AACAUGCUACAUUUCGGGCCCAACACCCCC--------GUAUAUUGACCACAUCCUGGAUGCAUGUCCUUGCAUGCCUCGCUGAAAAGGACAAGCCAAAUUAAAACGCAAUAAAAGCGAU
....((((......((((.........)))--------)..(((((.(((.....)))..((.(((((((....((...))....))))))).))............)))))..)))).. ( -24.30)
>DroSec_CAF1 180289 112 - 1
AACAUGCUACAUUUCGGGCCCAUCACCCCC--------GUAUAUUGACCACAUCCUGGAUGCAUGUCCUUGCAUGCCUCGCUGACAAGGACAAGCCAAAUUAAAACGCAAUAAAAGCGAU
....((((......((((.........)))--------)..(((((.(((.....)))..((.((((((((((.((...)))).)))))))).))............)))))..)))).. ( -27.60)
>DroSim_CAF1 174479 112 - 1
AACAUGCUACAUUUCGGGCCCAACACCCAC--------GUAUAUUGACCACAUCCUGGAUGCAUGUCCUUGCAUGCCUCGCUGACAAGGACAAGCCAAAUUAAAACGCAAUAAAAGCGAU
....((((.......(((.......)))..--------...(((((.(((.....)))..((.((((((((((.((...)))).)))))))).))............)))))..)))).. ( -27.40)
>DroEre_CAF1 169757 110 - 1
AACAUGCUACAUUUCGGGCCCAACACCC----------CUAUAUUGGCCACAUCCUGGAUGCAUGUCCUUGCAUGCCUCACAGACAAGGACAAGCCAAAUUAAAACGCAAUAAAGGCGAU
....((((.......(((........))----------)....(((((..((((...))))..((((((((..((.....))..)))))))).)))))................)))).. ( -26.80)
>DroYak_CAF1 173155 119 - 1
AACAUGCUACAUUUCGGGCCCAACACCCACCCACCUAUGUAUAUUGACCACAUCCUGGAUGCAUGUCCUUGCAUGCCUCACAGACAAGGACAAGCCAAAUUAAAACGCAAUAAAAGCGA-
....((((((((...(((...........)))....)))).(((((.(((.....)))..((.((((((((..((.....))..)))))))).))............)))))..)))).- ( -27.10)
>consensus
AACAUGCUACAUUUCGGGCCCAACACCCAC________GUAUAUUGACCACAUCCUGGAUGCAUGUCCUUGCAUGCCUCGCUGACAAGGACAAGCCAAAUUAAAACGCAAUAAAAGCGAU
....((((.......(((.......))).............(((((.(((.....)))..((.((((((((...(.....)...)))))))).))............)))))..)))).. (-23.04 = -23.08 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:53 2006