Locus 7439

Sequence ID	2L_DroMel_CAF1
Location	20,647,383 – 20,647,520
Length	137
Max. P	0.888548

overview

Window 7

Location	20,647,383 – 20,647,489
Length	106
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	79.12
Mean single sequence MFE	-37.40
Consensus MFE	-24.22
Energy contribution	-24.62
Covariance contribution	0.39
Combinations/Pair	1.29
Mean z-score	-1.26
Structure conservation index	0.65
SVM decision value	-0.04
SVM RNA-class probability	0.512081
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20647383 106 + 22407834
UCGCCCAGUAUGCGAAACGAAUUCUGUGUGGUGGCGGUGCUGGAGCUAAGUGGGAAGUUUACCUCCGACAGCGACGAGCUGUCCAGACUGGCGCUGGGCA-----GACUCU
((((.......)))).......(((((.(((((.((((.(((((.....((.(((.(....).))).))(((.....))).))))))))).))))).)))-----)).... ( -39.60)
>DroGri_CAF1 131 99 + 1
UCGCCAAGUAUGCGAAAUGAGUUUUGCGU------------CGAAUUAAACGGAAAAUUUAUCUCCGACAGGGAUGAGCUGUCCAGACUGGCAUUGGGUGUCAGCGAUACG
..((((.((((((((((....))))))))------------..........(((...((((((.((....))))))))...)))..)))))).....(((((...))))). ( -27.00)
>DroSec_CAF1 179 100 + 1
UCGCCCAGUAUGCGAAACGAAUUCUGUG------CGGUGCUGGAGUUAAGUGGAAAGUUUACCUCCGACAGCGACGAGCUGUCCAGGCUAGCGCUGGGCA-----GACUCU
((((.......)))).......(((((.------(((((((((((.(((((....).)))).))))((((((.....))))))......))))))).)))-----)).... ( -38.40)
>DroSim_CAF1 179 100 + 1
UCGCCCAGUAUGCGAAACGAAUUCUGUG------CGGUGCUGGAGUUAAGUGGAAAGUUUACCUCCGACAGCGACGAGCUGUCCAGGCUAGCGCUGGGCA-----GACUCU
((((.......)))).......(((((.------(((((((((((.(((((....).)))).))))((((((.....))))))......))))))).)))-----)).... ( -38.40)
>DroYak_CAF1 399 103 + 1
UCGCCCAGUAUCCGAAAGGAAUUCUGUGU---GACGGUGCUGGAGCUAAGUGGAAAGUUCACCUCCGACAGCGACGAGCUGUCCAGGCUAGGGCUGGGCA-----GACUCU
((((.(((..(((....)))...))).))---))((.((.(((((....(((((...)))))))))).)).))..(((((((((((.(...).)))))))-----).))). ( -43.20)
>DroAna_CAF1 173 106 + 1
UCGCCGAGUAUCCGAAACGAGUUCUGGGUGGCCUCAUUCGUCGACUUGAGCGGGAAGUUCACCUCCGACAGCGAGGAGCUGUCCAGACUGGCAUUGGGCA-----GGCUCU
.....((((.(((((..(.(((.(((((..(((((.((.((((...(((((.....)))))....)))))).)))..))..)))))))).)..)))))..-----.)))). ( -37.80)
>consensus
UCGCCCAGUAUGCGAAACGAAUUCUGUGU_____CGGUGCUGGAGUUAAGUGGAAAGUUUACCUCCGACAGCGACGAGCUGUCCAGACUAGCGCUGGGCA_____GACUCU
..(((((((..((............................((((.(((((.....))))).))))((((((.....)))))).......)))))))))............ (-24.22 = -24.62 +   0.39)

alignment

secondary structure

dotplot

Window 8

Location	20,647,423 – 20,647,520
Length	97
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	87.01
Mean single sequence MFE	-39.55
Consensus MFE	-32.51
Energy contribution	-31.68
Covariance contribution	-0.83
Combinations/Pair	1.22
Mean z-score	-1.76
Structure conservation index	0.82
SVM decision value	0.08
SVM RNA-class probability	0.571832
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20647423 97 + 22407834
UGGAGCUAAGUGGGAAGUUUACCUCCGACAGCGACGAGCUGUCCAGACUGGCGCUGGGCAGACUCUUGCUGACCAGCUUCGCCUGCUGUUGCUGCUG
.((((((..((.(((.(....).))).))(((((.(((((((((((.......)))))))).))))))))....))))))((..((....)).)).. ( -39.60)
>DroSec_CAF1 213 97 + 1
UGGAGUUAAGUGGAAAGUUUACCUCCGACAGCGACGAGCUGUCCAGGCUAGCGCUGGGCAGACUCUUGCUGGCCAACUUCGCCUGCUGUUGCUGCUG
.((((.(((((....).)))).))))(.(((((((((((((((((((....).)))))))).)))..((.(((.......))).)).)))))))).. ( -40.30)
>DroSim_CAF1 213 97 + 1
UGGAGUUAAGUGGAAAGUUUACCUCCGACAGCGACGAGCUGUCCAGGCUAGCGCUGGGCAGACUCUUGCUGGCCAGCUUCGCCUGCUGUUGCUGCUG
.((((.(((((....).)))).))))(.(((((((((((((((((((....).)))))))).)))..((.(((.......))).)).)))))))).. ( -40.30)
>DroEre_CAF1 216 89 + 1
UGGAGCUCAGUGGAAAGUUGACCUCCGACAGCGACGAGCUGUCUAGGCUAGCGCUUGGCAGACUCUUGCUGGCCAGCUUCGCCUGCUGC--------
.((((.(((((....).)))).))))..((((((.((((((.((((((....))))))))).)))))))))..((((.......)))).-------- ( -36.10)
>DroYak_CAF1 436 97 + 1
UGGAGCUAAGUGGAAAGUUCACCUCCGACAGCGACGAGCUGUCCAGGCUAGGGCUGGGCAGACUCUUGCUGGCCAGCUUCGCCUGCUGUUGUUGCUG
.((((....(((((...)))))))))..(((((((.(((....(((((..(((((((.(((.(....)))).))))))).)))))..)))))))))) ( -42.30)
>DroAna_CAF1 213 97 + 1
UCGACUUGAGCGGGAAGUUCACCUCCGACAGCGAGGAGCUGUCCAGACUGGCAUUGGGCAGGCUCUUGCUGGCCAGCUUGUCCUUCUGGAUCUGCUG
(((...(((((.....)))))....)))(((((((.((((((((((.......))))))).))))))))))..((((..((((....))))..)))) ( -38.70)
>consensus
UGGAGCUAAGUGGAAAGUUUACCUCCGACAGCGACGAGCUGUCCAGGCUAGCGCUGGGCAGACUCUUGCUGGCCAGCUUCGCCUGCUGUUGCUGCUG
.((((((...((((.........)))).((((((.(((((((((((.......)))))))).)))))))))...))))))................. (-32.51 = -31.68 +  -0.83)

alignment

secondary structure

dotplot

Window 9

Location	20,647,423 – 20,647,520
Length	97
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	87.01
Mean single sequence MFE	-36.11
Consensus MFE	-31.58
Energy contribution	-31.72
Covariance contribution	0.14
Combinations/Pair	1.22
Mean z-score	-1.99
Structure conservation index	0.87
SVM decision value	0.95
SVM RNA-class probability	0.888548
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20647423 97 - 22407834
CAGCAGCAACAGCAGGCGAAGCUGGUCAGCAAGAGUCUGCCCAGCGCCAGUCUGGACAGCUCGUCGCUGUCGGAGGUAAACUUCCCACUUAGCUCCA
..(.(((.....(((((...(((((.((((....).))).)))))....)))))((((((.....))))))(((((....)))))......))).). ( -38.10)
>DroSec_CAF1 213 97 - 1
CAGCAGCAACAGCAGGCGAAGUUGGCCAGCAAGAGUCUGCCCAGCGCUAGCCUGGACAGCUCGUCGCUGUCGGAGGUAAACUUUCCACUUAACUCCA
............(((((...(((((.((((....).))).)))))....)))))((((((.....))))))((((.................)))). ( -34.53)
>DroSim_CAF1 213 97 - 1
CAGCAGCAACAGCAGGCGAAGCUGGCCAGCAAGAGUCUGCCCAGCGCUAGCCUGGACAGCUCGUCGCUGUCGGAGGUAAACUUUCCACUUAACUCCA
............(((((...(((((.((((....).))).)))))....)))))((((((.....))))))((((.................)))). ( -36.93)
>DroEre_CAF1 216 89 - 1
--------GCAGCAGGCGAAGCUGGCCAGCAAGAGUCUGCCAAGCGCUAGCCUAGACAGCUCGUCGCUGUCGGAGGUCAACUUUCCACUGAGCUCCA
--------.....((((...((((((..((....))..))).)))....)))).((((((.....))))))((((.(((.........))).)))). ( -35.40)
>DroYak_CAF1 436 97 - 1
CAGCAACAACAGCAGGCGAAGCUGGCCAGCAAGAGUCUGCCCAGCCCUAGCCUGGACAGCUCGUCGCUGUCGGAGGUGAACUUUCCACUUAGCUCCA
............(((((...(((((.((((....).))).)))))....)))))((((((.....))))))((((.(((.........))).)))). ( -37.90)
>DroAna_CAF1 213 97 - 1
CAGCAGAUCCAGAAGGACAAGCUGGCCAGCAAGAGCCUGCCCAAUGCCAGUCUGGACAGCUCCUCGCUGUCGGAGGUGAACUUCCCGCUCAAGUCGA
.(((...(((....)))((..(((((..(((......))).....)))))..))((((((.....))))))(((((....))))).)))........ ( -33.80)
>consensus
CAGCAGCAACAGCAGGCGAAGCUGGCCAGCAAGAGUCUGCCCAGCGCUAGCCUGGACAGCUCGUCGCUGUCGGAGGUAAACUUUCCACUUAACUCCA
............(((((...(((((.((((....).))).)))))....)))))((((((.....))))))((((.(((.........))).)))). (-31.58 = -31.72 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:53 2006