Locus 7223

Sequence ID 3R_DroMel_CAF1
Location 19,026,099 – 19,026,295
Length 196
Max. P 0.789551
window11687 window11688 window11689

overview

Window 7

Location 19,026,099 – 19,026,189
Length 90
Sequences 6
Columns 90
Reading direction forward
Mean pairwise identity 92.59
Mean single sequence MFE -22.60
Consensus MFE -17.78
Energy contribution -18.33
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.63
Structure conservation index 0.79
SVM decision value 0.21
SVM RNA-class probability 0.633224
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19026099 90 + 27905053
UGGCCAAACACUUUGACAAUUAUGUAACGUUUUGACAGCCAAAAUGUUGCAGAAUCAACAAUGGCGUGCCGACUAAAAGCAGCCAAAGCA
..((........((((......((((((((((((.....))))))))))))...))))...((((.(((.........)))))))..)). ( -22.90)
>DroSec_CAF1 38908 90 + 1
UGGCCAAACACUUUGACAAUUAUGUAACGUUUUGACAGCCAAAAUGUUGCAGAAUCAACAAUGGCGUGCCGACUAAAAGCAGCCAAAGCA
..((........((((......((((((((((((.....))))))))))))...))))...((((.(((.........)))))))..)). ( -22.90)
>DroSim_CAF1 40566 90 + 1
UGGCCAAACACUUUGACAAUUAUGUAACGUUUUGACAGCCAAAAUGUUGCAGAAUCAACAAUGGCGUGCCGACUAAAAGCAGCCAAAGCA
..((........((((......((((((((((((.....))))))))))))...))))...((((.(((.........)))))))..)). ( -22.90)
>DroEre_CAF1 41391 90 + 1
UGGGCAAACACUUUGACAAUUAUGUAACGUUUUGACAGCCAAAAUGUUGCAGAAUCAACAAUGGCGUGCCGACUAAAAGCAGCCAAAGCA
...((.......((((......((((((((((((.....))))))))))))...))))...((((.(((.........)))))))..)). ( -23.80)
>DroYak_CAF1 41681 90 + 1
UGGCCAAACACUUUGACAAUUAUGUAACGUUUUGACAGCCAAAAUGUUGCAGAAUCAACAAUGGCGUGCCGACUAAAAGCAGCCAAAGCA
..((........((((......((((((((((((.....))))))))))))...))))...((((.(((.........)))))))..)). ( -22.90)
>DroAna_CAF1 39522 85 + 1
UGGCCAAACACUUUGACAAUUAUGUAACGUUUUGACAGCCAAAAUGUUGCAGAAUCAACAAUGGCAACACCAUCGACAUCGACAU-----
..((((......((((......((((((((((((.....))))))))))))...))))...)))).......(((....)))...----- ( -20.20)
>consensus
UGGCCAAACACUUUGACAAUUAUGUAACGUUUUGACAGCCAAAAUGUUGCAGAAUCAACAAUGGCGUGCCGACUAAAAGCAGCCAAAGCA
............((((......((((((((((((.....))))))))))))...))))...((((.(((.........)))))))..... (-17.78 = -18.33 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 19,026,099 – 19,026,189
Length 90
Sequences 6
Columns 90
Reading direction reverse
Mean pairwise identity 92.59
Mean single sequence MFE -23.27
Consensus MFE -20.40
Energy contribution -20.27
Covariance contribution -0.13
Combinations/Pair 1.14
Mean z-score -1.57
Structure conservation index 0.88
SVM decision value 0.58
SVM RNA-class probability 0.789551
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19026099 90 - 27905053
UGCUUUGGCUGCUUUUAGUCGGCACGCCAUUGUUGAUUCUGCAACAUUUUGGCUGUCAAAACGUUACAUAAUUGUCAAAGUGUUUGGCCA
.....(((((((....((((((((......))))))))..))(((((((((((....................))))))))))).))))) ( -23.95)
>DroSec_CAF1 38908 90 - 1
UGCUUUGGCUGCUUUUAGUCGGCACGCCAUUGUUGAUUCUGCAACAUUUUGGCUGUCAAAACGUUACAUAAUUGUCAAAGUGUUUGGCCA
.....(((((((....((((((((......))))))))..))(((((((((((....................))))))))))).))))) ( -23.95)
>DroSim_CAF1 40566 90 - 1
UGCUUUGGCUGCUUUUAGUCGGCACGCCAUUGUUGAUUCUGCAACAUUUUGGCUGUCAAAACGUUACAUAAUUGUCAAAGUGUUUGGCCA
.....(((((((....((((((((......))))))))..))(((((((((((....................))))))))))).))))) ( -23.95)
>DroEre_CAF1 41391 90 - 1
UGCUUUGGCUGCUUUUAGUCGGCACGCCAUUGUUGAUUCUGCAACAUUUUGGCUGUCAAAACGUUACAUAAUUGUCAAAGUGUUUGCCCA
.((((((((.((.....)).((((.((((.(((((......)))))...))))))))................))))))))......... ( -23.60)
>DroYak_CAF1 41681 90 - 1
UGCUUUGGCUGCUUUUAGUCGGCACGCCAUUGUUGAUUCUGCAACAUUUUGGCUGUCAAAACGUUACAUAAUUGUCAAAGUGUUUGGCCA
.....(((((((....((((((((......))))))))..))(((((((((((....................))))))))))).))))) ( -23.95)
>DroAna_CAF1 39522 85 - 1
-----AUGUCGAUGUCGAUGGUGUUGCCAUUGUUGAUUCUGCAACAUUUUGGCUGUCAAAACGUUACAUAAUUGUCAAAGUGUUUGGCCA
-----..(((((.(((((..(((....)))..)))))))...(((((((((((....................))))))))))).))).. ( -20.25)
>consensus
UGCUUUGGCUGCUUUUAGUCGGCACGCCAUUGUUGAUUCUGCAACAUUUUGGCUGUCAAAACGUUACAUAAUUGUCAAAGUGUUUGGCCA
((((..(((((....))))))))).((((.(((((......)))))...)))).((((((((...(((....)))....)).)))))).. (-20.40 = -20.27 +  -0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 19,026,189 – 19,026,295
Length 106
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 81.66
Mean single sequence MFE -20.75
Consensus MFE -11.84
Energy contribution -11.53
Covariance contribution -0.30
Combinations/Pair 1.29
Mean z-score -1.95
Structure conservation index 0.57
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19026189 106 - 27905053
CGA-AUUGUGCAAAGCCCAAAAAAAAAAAAUCAAAAAUAAAGACAACACAAUACAAA-----GUCUGUCUGCAACGGAAACGGCA---AUAUCGAAGUUGCGAUUGGAUUGCUUU
...-.....((((...((((....................(((((..((........-----)).)))))....((....))(((---((......)))))..)))).))))... ( -18.40)
>DroSec_CAF1 38998 101 - 1
CGA-AUUGUGCAAAGCACAAA-----AAAAUCAAAAAUAAAGACAACACAAUACAAA-----GACUGUCUGCAACGGAAACGGCA---AUAUCGAAGUUGCGAUUGGAUUGCUUU
...-.((((((...)))))).-----............((((.(((..((((.(...-----............((....))(((---((......))))))))))..))))))) ( -20.60)
>DroSim_CAF1 40656 101 - 1
CGA-AUUGUGCAAAGCACAAA-----AAAAUCAAAAAUAAAGACAACACAAUACAAA-----GGCUGUCUGCAACGGAAACGGCA---AUAUCGAAGUUGCGAUUGGAUUGCUUU
...-.((((((...)))))).-----............((((.(((..((((.(...-----.((.....))..((....))(((---((......))))))))))..))))))) ( -21.70)
>DroEre_CAF1 41481 106 - 1
CGA-AUUGUGCAAAGCACAAACAAAAAAAAUCAAAAAUAAAGACAACACAAUACAAC-----GUCUGUCUGCAACGGAAACGGCA---AUAUCGAAGUUGCGAUUGGAUUGCUUU
...-.((((((...))))))..................((((.(((..((((.((((-----.((.((.(((..((....)))))---..)).)).))))..))))..))))))) ( -21.60)
>DroYak_CAF1 41771 103 - 1
CGA-AUUGUGCAAAGCUCAA---AAAAAAAUCAAAAAUAAAGACAACACAAUACAAA-----GUCUGUCUGCAACGGAAACGGCA---AUAUCGAAGUUGUGAUUGGAUUGCUUU
...-.(((.((...)).)))---...............((((.(((..((((((((.-----.((.((.(((..((....)))))---..)).))..)))).))))..))))))) ( -18.30)
>DroPer_CAF1 35259 100 - 1
CGAAAUUGUGUAA----------AGAAAAAUAAAAGUU--GGACAACAAAAAGCUAACGUCUGUCUGUCUGCAGCGGAAACAGCAGACAGAUCGGUG---GAGGAGGACUGUGUG
......(((.(((----------.............))--).)))(((.....((..(..(.((((((((((...(....).)))))))))).)..)---..)).....)))... ( -23.92)
>consensus
CGA_AUUGUGCAAAGCACAAA__AAAAAAAUCAAAAAUAAAGACAACACAAUACAAA_____GUCUGUCUGCAACGGAAACGGCA___AUAUCGAAGUUGCGAUUGGAUUGCUUU
(((.....(((.............................(((((....................)))))....((....)))))......))).....((((.....))))... (-11.84 = -11.53 +  -0.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:34 2006