Locus 3249

Sequence ID	2L_DroMel_CAF1
Location	9,354,927 – 9,355,086
Length	159
Max. P	0.976586

overview

Window 8

Location	9,354,927 – 9,355,017
Length	90
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	77.99
Mean single sequence MFE	-33.45
Consensus MFE	-20.80
Energy contribution	-21.90
Covariance contribution	1.10
Combinations/Pair	1.13
Mean z-score	-2.31
Structure conservation index	0.62
SVM decision value	1.50
SVM RNA-class probability	0.959496
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9354927 90 + 22407834
AGGGCGUGGCCAAGGUGUUUACCUUCCCGCCCACUUUG-GUCCUG-----------------CCAGAGACAUUUAAUAAGCAGUUGUUGAGCGAAGGCUCAACUCCGA
.(((((.((..(((((....)))))))))))).(((((-(.....-----------------))))))..............(..(((((((....)))))))..).. ( -37.90)
>DroSec_CAF1 23873 90 + 1
AGGGCGUGGCCAAGGUGUUUACCUUCCCGCCCACUUUG-GUCCUG-----------------CCAGAGACAUUUAAUAAGCAGUUGUUGAGCGAAGGCUCAACUCCGA
.(((((.((..(((((....)))))))))))).(((((-(.....-----------------))))))..............(..(((((((....)))))))..).. ( -37.90)
>DroSim_CAF1 23963 90 + 1
UGGGCGUGGCCAAGGUGUUUACCUUCCCGCCCACUUUC-GUCCUG-----------------CCAGAGACAUUUAAUAAGCAGUUGUUGAGCGAAGGCUCAACUCCGA
((((((.((..(((((....)))))))))))))...((-(..(((-----------------(................))))..(((((((....)))))))..))) ( -33.19)
>DroEre_CAF1 24358 72 + 1
GGGGCGUGGCCGAGGUGUUUACCUUGCCGCCCACUUUC-GUCCUG-----------------CCAGAGACAUUUAAUAAGCAGUUGUUG------------------A
.((((..(((.(((((....))))))))))))......-((((..-----------------...).)))..(((((((....))))))------------------) ( -19.70)
>DroYak_CAF1 26372 90 + 1
AGGGCGUGGCCAAGGUGUUUACCUUUCCGCCCACUUUG-GUCCUG-----------------CCAGAGACAUUUAAUAAGCAGUUGCUGAGCGCAGGCUCAACACCGA
.(((((.((..(((((....)))))))))))).(((((-(.....-----------------))))))..........(((....)))((((....))))........ ( -30.00)
>DroAna_CAF1 36335 106 + 1
AGGGCGUGGCUGAGGUGCUUACCCGCCUGCCCACCUACCUUCCUGUCCAACUGGCAGGACGGGCAAGGACAUUUAAUAAGCAGC--CUAAGCGAAGGCUCAACACCCG
.(((.((((((((((((......))))).........(((((((((((........))))))).))))............))))--)..(((....)))..)).))). ( -42.00)
>consensus
AGGGCGUGGCCAAGGUGUUUACCUUCCCGCCCACUUUC_GUCCUG_________________CCAGAGACAUUUAAUAAGCAGUUGUUGAGCGAAGGCUCAACUCCGA
.(((((.((..(((((....)))))))))))).......((((((..................))).))).................(((((....)))))....... (-20.80 = -21.90 +   1.10)

alignment

secondary structure

dotplot

Window 9

Location	9,354,927 – 9,355,017
Length	90
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	77.99
Mean single sequence MFE	-34.53
Consensus MFE	-21.89
Energy contribution	-22.69
Covariance contribution	0.80
Combinations/Pair	1.20
Mean z-score	-2.54
Structure conservation index	0.63
SVM decision value	1.77
SVM RNA-class probability	0.976586
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9354927 90 - 22407834
UCGGAGUUGAGCCUUCGCUCAACAACUGCUUAUUAAAUGUCUCUGG-----------------CAGGAC-CAAAGUGGGCGGGAAGGUAAACACCUUGGCCACGCCCU
..((.(((((((....)))))))..(((((..............))-----------------)))..)-).....(((((((.((((....))))...)).))))). ( -34.44)
>DroSec_CAF1 23873 90 - 1
UCGGAGUUGAGCCUUCGCUCAACAACUGCUUAUUAAAUGUCUCUGG-----------------CAGGAC-CAAAGUGGGCGGGAAGGUAAACACCUUGGCCACGCCCU
..((.(((((((....)))))))..(((((..............))-----------------)))..)-).....(((((((.((((....))))...)).))))). ( -34.44)
>DroSim_CAF1 23963 90 - 1
UCGGAGUUGAGCCUUCGCUCAACAACUGCUUAUUAAAUGUCUCUGG-----------------CAGGAC-GAAAGUGGGCGGGAAGGUAAACACCUUGGCCACGCCCA
.....(((((((....)))))))..(((((..............))-----------------))).((-....))(((((((.((((....))))...)).))))). ( -35.04)
>DroEre_CAF1 24358 72 - 1
U------------------CAACAACUGCUUAUUAAAUGUCUCUGG-----------------CAGGAC-GAAAGUGGGCGGCAAGGUAAACACCUCGGCCACGCCCC
.------------------......(((((..............))-----------------))).((-....))(((((((.((((....))))..)))..)))). ( -22.44)
>DroYak_CAF1 26372 90 - 1
UCGGUGUUGAGCCUGCGCUCAGCAACUGCUUAUUAAAUGUCUCUGG-----------------CAGGAC-CAAAGUGGGCGGAAAGGUAAACACCUUGGCCACGCCCU
..((((((((((....)))))))..(((((..............))-----------------))).))-).....(((((..(((((....))))).....))))). ( -33.64)
>DroAna_CAF1 36335 106 - 1
CGGGUGUUGAGCCUUCGCUUAG--GCUGCUUAUUAAAUGUCCUUGCCCGUCCUGCCAGUUGGACAGGAAGGUAGGUGGGCAGGCGGGUAAGCACCUCAGCCACGCCCU
.(((((((((((....)))))(--((((..........((.((((((((.((((((......((......)).....)))))))))))))).))..))))))))))). ( -47.20)
>consensus
UCGGAGUUGAGCCUUCGCUCAACAACUGCUUAUUAAAUGUCUCUGG_________________CAGGAC_CAAAGUGGGCGGGAAGGUAAACACCUUGGCCACGCCCU
.....(((((((....)))))))..(((((((((....(((.(((..................))))))....))))))))).(((((....)))))(((...))).. (-21.89 = -22.69 +   0.80)

alignment

secondary structure

dotplot

Window 0

Location	9,354,989 – 9,355,086
Length	97
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	78.52
Mean single sequence MFE	-25.32
Consensus MFE	-13.87
Energy contribution	-14.17
Covariance contribution	0.30
Combinations/Pair	1.37
Mean z-score	-1.86
Structure conservation index	0.55
SVM decision value	0.28
SVM RNA-class probability	0.667470
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9354989 97 + 22407834
CAGUUGUUGAGCGAAGGCUCAACUCCGAAACUCUCACCAGGAAUUUC------GAAGCUGCUCU-UGUGGUCUUUAAAUAUUUCAAAACUCAAUAGCCACUUAU
((((((((((((....)))))))..(((((.(((.....))).))))------).)))))....-.(((((..((................))..))))).... ( -26.09)
>DroSec_CAF1 23935 97 + 1
CAGUUGUUGAGCGAAGGCUCAACUCCGAAACUCUCGCCAGGAACUUC------GAAGCUGCUCU-UGUGGUCUUUAAAUAUUUCAAAACUCAAUGGCCACUUAU
((((((((((((....)))))))..((((..(((.....)))..)))------).)))))....-.((((((......................)))))).... ( -27.55)
>DroSim_CAF1 24025 97 + 1
CAGUUGUUGAGCGAAGGCUCAACUCCGAAACUCUCGCCAGGAACUUC------GAAGCUGCUCU-UGUGGUCUUUAAAUAUUUCAAAACUCAAUGGCCACUUAU
((((((((((((....)))))))..((((..(((.....)))..)))------).)))))....-.((((((......................)))))).... ( -27.55)
>DroEre_CAF1 24420 79 + 1
CAGUUGUUG------------------AAACUCCCGCCAGGAACUUC------GAAGCUGCUCU-UGUGGUCUUUAAAUAUUUCACAACUCAAUGGCCUCUUGU
.((((((.(------------------(((.(((.....))).....------(((((..(...-.)..).)))).....)))))))))).............. ( -14.30)
>DroYak_CAF1 26434 97 + 1
CAGUUGCUGAGCGCAGGCUCAACACCGAAACUUCGGCCAGGAACUUC------GAGGCUGCUCU-UGUGGUCUUUAAAUAUUUCAAAACUCAAUGGCCACUUAU
........(((.((((.(((....((((....))))....(.....)------))).)))).))-)((((((......................)))))).... ( -24.75)
>DroAna_CAF1 36415 102 + 1
CAGC--CUAAGCGAAGGCUCAACACCCGGUUUCUGGGGAAAACUUUCCUCGCAGAAGCUGCACUUUGUGGCCUGUGCAUAUUUCAUAGCUCAACGGCUACUUAC
....--....(((.((((((((....((((((((((((((....)))).).)))))))))....))).))))).)))........(((((....)))))..... ( -31.70)
>consensus
CAGUUGUUGAGCGAAGGCUCAACUCCGAAACUCUCGCCAGGAACUUC______GAAGCUGCUCU_UGUGGUCUUUAAAUAUUUCAAAACUCAAUGGCCACUUAU
(((((..(((((....)))))..........(((.....))).............)))))......((((((......................)))))).... (-13.87 = -14.17 +   0.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:57 2006