Locus 4134

Sequence ID	3L_DroMel_CAF1
Location	12,087,991 – 12,088,126
Length	135
Max. P	0.978686

overview

Window 3

Location	12,087,991 – 12,088,100
Length	109
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	91.34
Mean single sequence MFE	-33.30
Consensus MFE	-22.70
Energy contribution	-23.10
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.74
Structure conservation index	0.68
SVM decision value	0.14
SVM RNA-class probability	0.604899
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12087991 109 + 23771897
UUUUCUGCCCAUCAAUUGC--UAGCAACAAAGCGCGUAGGCCAGCAACAACGACCAUCGACCAACUGGCAACAUGCGGC--AUGCUGCAUGGAGCAUGCAGCAUGCAACAGAC
...((((............--...........(((((..(((((......((.....)).....)))))...)))))((--((((((((((...))))))))))))..)))). ( -39.00)
>DroSec_CAF1 45322 111 + 1
UUUUCUGCCCAUCAAUUGCAAUAGCAACAAAGCGCGUAGGCCAGCAACAACGACCAUCGACCAACUGGCAACAUGCGGC--AUGCAACUUGCAGCAUGCAGCAUGCAACAGAC
...((((........(((((...((.......(((((..(((((......((.....)).....)))))...)))))((--((((........)))))).)).))))))))). ( -32.00)
>DroSim_CAF1 47579 111 + 1
UUUUCUGCCCAUCAAUUGCAAUAGCAACAAAGCGCGUAGGCCAGCAACAACGACCAUCGACCAACUGGCAACAUGCGGC--AUGCAACUUGCAGCAUGCAGCAUGCAACAGAC
...((((........(((((...((.......(((((..(((((......((.....)).....)))))...)))))((--((((........)))))).)).))))))))). ( -32.00)
>DroEre_CAF1 48028 106 + 1
UUUUCUGGCCAUCAAUUGC--CAGCAACAAAACGCGUAGGCCAGCAACAACGA---GCGACCAACUGGCAACUUGCAGC--AUGCAACUUGCAGCAUGCAGCAUGCAACAGAC
...((((........((((--((((........))((.((...((........---))..)).))))))))..(((.((--((((........)))))).))).....)))). ( -29.80)
>DroYak_CAF1 46730 108 + 1
UUUGCUGGCCAUCAAUUGG--CAGCAACAAAACGCGUAGGCCAGCAACAACGA---GCGACCAACUGGCAACAUGCAGCACAUGCAACUUGCAGCAUGCAGCAUGCAACAGAC
.(((((((((.((....))--..((........))...)))))))))......---........(((....(((((.(((..(((.....)))...))).)))))...))).. ( -33.70)
>consensus
UUUUCUGCCCAUCAAUUGC__UAGCAACAAAGCGCGUAGGCCAGCAACAACGACCAUCGACCAACUGGCAACAUGCGGC__AUGCAACUUGCAGCAUGCAGCAUGCAACAGAC
...((((........((((....))))......((((..(((((......((.....)).....))))).....((.((..((((........)))))).))))))..)))). (-22.70 = -23.10 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	12,087,991 – 12,088,100
Length	109
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	91.34
Mean single sequence MFE	-40.58
Consensus MFE	-29.20
Energy contribution	-30.00
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.19
Structure conservation index	0.72
SVM decision value	0.31
SVM RNA-class probability	0.684980
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12087991 109 - 23771897
GUCUGUUGCAUGCUGCAUGCUCCAUGCAGCAU--GCCGCAUGUUGCCAGUUGGUCGAUGGUCGUUGUUGCUGGCCUACGCGCUUUGUUGCUA--GCAAUUGAUGGGCAGAAAA
...(((.((((((((((((...))))))))))--)).)))..(((((.((..((((((....)))).(((((((..(((.....))).))))--)))))..)).))))).... ( -43.90)
>DroSec_CAF1 45322 111 - 1
GUCUGUUGCAUGCUGCAUGCUGCAAGUUGCAU--GCCGCAUGUUGCCAGUUGGUCGAUGGUCGUUGUUGCUGGCCUACGCGCUUUGUUGCUAUUGCAAUUGAUGGGCAGAAAA
.((((((((((((.((((((........))))--)).)))))).((((((....((((....))))..)))))).....((.((.(((((....))))).))))))))))... ( -40.70)
>DroSim_CAF1 47579 111 - 1
GUCUGUUGCAUGCUGCAUGCUGCAAGUUGCAU--GCCGCAUGUUGCCAGUUGGUCGAUGGUCGUUGUUGCUGGCCUACGCGCUUUGUUGCUAUUGCAAUUGAUGGGCAGAAAA
.((((((((((((.((((((........))))--)).)))))).((((((....((((....))))..)))))).....((.((.(((((....))))).))))))))))... ( -40.70)
>DroEre_CAF1 48028 106 - 1
GUCUGUUGCAUGCUGCAUGCUGCAAGUUGCAU--GCUGCAAGUUGCCAGUUGGUCGC---UCGUUGUUGCUGGCCUACGCGUUUUGUUGCUG--GCAAUUGAUGGCCAGAAAA
.((((..((.(((.((((((........))))--)).)))((((((((((.((((((---........)).)))).))(((......)))))--))))))....))))))... ( -39.80)
>DroYak_CAF1 46730 108 - 1
GUCUGUUGCAUGCUGCAUGCUGCAAGUUGCAUGUGCUGCAUGUUGCCAGUUGGUCGC---UCGUUGUUGCUGGCCUACGCGUUUUGUUGCUG--CCAAUUGAUGGCCAGCAAA
....((.((((((.(((((.(((.....)))))))).)))))).))..((.((((((---........)).)))).))........((((((--(((.....))).)))))). ( -37.80)
>consensus
GUCUGUUGCAUGCUGCAUGCUGCAAGUUGCAU__GCCGCAUGUUGCCAGUUGGUCGAUGGUCGUUGUUGCUGGCCUACGCGCUUUGUUGCUA__GCAAUUGAUGGGCAGAAAA
(((((((((((((.((((((........))))..)).))))((.((((((....((.....)).....))))))..)))).....(((((....))))).)))))))...... (-29.20 = -30.00 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	12,088,022 – 12,088,126
Length	104
Sequences	3
Columns	104
Reading direction	forward
Mean pairwise identity	88.46
Mean single sequence MFE	-29.87
Consensus MFE	-27.77
Energy contribution	-28.10
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.59
Structure conservation index	0.93
SVM decision value	1.82
SVM RNA-class probability	0.978686
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12088022 104 + 23771897
GCGUAGGCCAGCAACAACGACCAUCGACCAACUGGCAACAUGCGGCAUGCUGCAUGGAGCAUGCAGCAUGCAACAGACAACGGACAACAUUCAACAAUGCGACA
((((.((((((......((.....)).....)))))....((..((((((((((((...))))))))))))..))...................).)))).... ( -35.10)
>DroSec_CAF1 45355 104 + 1
GCGUAGGCCAGCAACAACGACCAUCGACCAACUGGCAACAUGCGGCAUGCAACUUGCAGCAUGCAGCAUGCAACAGACAACGGACAACAUUCGACAAUGCGACA
((((.((((((......((.....)).....)))))..(((((.((((((........)))))).)))))..........((((.....)))).).)))).... ( -30.50)
>DroEre_CAF1 48059 94 + 1
GCGUAGGCCAGCAACAACGA---GCGACCAACUGGCAACUUGCAGCAUGCAACUUGCAGCAUGCAGCAUGCAACAGAC-------AACAUUCAACAAUGCGACA
((((.((...((........---))..))..(((((((.((((.....)))).)))).(((((...)))))..)))..-------...........)))).... ( -24.00)
>consensus
GCGUAGGCCAGCAACAACGACCAUCGACCAACUGGCAACAUGCGGCAUGCAACUUGCAGCAUGCAGCAUGCAACAGACAACGGACAACAUUCAACAAUGCGACA
((((.((((((......((.....)).....)))))..(((((.((((((........)))))).)))))........................).)))).... (-27.77 = -28.10 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:14 2006