Locus 3906

Sequence ID	3L_DroMel_CAF1
Location	11,318,424 – 11,318,608
Length	184
Max. P	0.967473

overview

Window 1

Location	11,318,424 – 11,318,533
Length	109
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	78.39
Mean single sequence MFE	-25.42
Consensus MFE	-9.88
Energy contribution	-10.36
Covariance contribution	0.48
Combinations/Pair	1.05
Mean z-score	-2.37
Structure conservation index	0.39
SVM decision value	1.19
SVM RNA-class probability	0.928989
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11318424 109 + 23771897
UUAUAGAACUUUCUAGUUUCACUAGCAAACUAAAAGAUACAUGUUUUGUAUCUUGAGG-------UAAGCA-ACCGUGAGUACUUCCAGGUACAUCUACCUAGAAACUGCUCAUCUC
.....(((((....))))).....((..(((..((((((((.....))))))))..))-------)..)).-...(((((((.(((.(((((....))))).)))..)))))))... ( -28.50)
>DroSec_CAF1 39226 109 + 1
UUAUAGAACUUUCUAAUUUAACUAGCAAACUAAAAGAUACAUUUUUUGUAUCUUAAGG-------UAAGCA-GCUGUGAGUACUUUCAGGUACAUCUACCUAGAUACUGCUCAUCUC
...((((....)))).........((..(((..((((((((.....))))))))..))-------)..)).-...(((((((...(((((((....))))).))...)))))))... ( -26.30)
>DroSim_CAF1 46269 109 + 1
UUAUAGAACUUUCUCGUUUGACUAGCAAACUAGAAGAUACAUUUUUUAUAUCUUAAGG-------UAAGCA-GCUGUGAGUACUUCCAGGUACAUCUACCUAGAUACUGCUCAUCUC
.........(((((.(((((.....))))).)))))...................(((-------(.((((-(......(((((....)))))((((....)))).))))).)))). ( -22.00)
>DroEre_CAF1 43094 105 + 1
UUGUAGAACUUUCUAGAUACGCAGUUAAACU-----------ACGAUGUAUCUUAAGGCUCUAAGCAAGCA-ACUGAGCGUACUUUCAGGUACAUCUACCUAGAUACUGCUCAUCUC
(((((((.((((..(((((((..((......-----------))..))))))).)))).)))..))))...-..((((((((((....)))))((((....))))...))))).... ( -26.60)
>DroYak_CAF1 31030 117 + 1
UUAUGGAACUUUCCAGUUCUGCAGUCAAACUAAAAGAGGAAUAUGAUGUAUCUCAAGGCACUAAGUAAGCAAACUGAGCGUACUUCCAGGUACAUCUACCUAGAUACCGCUCAUCUC
...((((....))))(((.(((.............((((.((.....)).))))...((.....))..))))))((((((....((.(((((....))))).))...)))))).... ( -23.70)
>consensus
UUAUAGAACUUUCUAGUUUCACUAGCAAACUAAAAGAUACAUAUUUUGUAUCUUAAGG_______UAAGCA_ACUGUGAGUACUUCCAGGUACAUCUACCUAGAUACUGCUCAUCUC
...((((....))))................................((((((..(((.........((....))....(((((....))))).....))))))))).......... ( -9.88 = -10.36 +   0.48)

alignment

secondary structure

dotplot

Window 2

Location	11,318,424 – 11,318,533
Length	109
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	78.39
Mean single sequence MFE	-29.48
Consensus MFE	-16.42
Energy contribution	-17.34
Covariance contribution	0.92
Combinations/Pair	1.17
Mean z-score	-2.39
Structure conservation index	0.56
SVM decision value	1.61
SVM RNA-class probability	0.967473
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11318424 109 - 23771897
GAGAUGAGCAGUUUCUAGGUAGAUGUACCUGGAAGUACUCACGGU-UGCUUA-------CCUCAAGAUACAAAACAUGUAUCUUUUAGUUUGCUAGUGAAACUAGAAAGUUCUAUAA
(((.(((((((.(((((((((....)))))))))((....))..)-))))))-------.)))((((((((.....)))))))).(((..(.((((.....))))...)..)))... ( -31.50)
>DroSec_CAF1 39226 109 - 1
GAGAUGAGCAGUAUCUAGGUAGAUGUACCUGAAAGUACUCACAGC-UGCUUA-------CCUUAAGAUACAAAAAAUGUAUCUUUUAGUUUGCUAGUUAAAUUAGAAAGUUCUAUAA
(((.((((((((...((((((....))))))...((....)).))-))))))-------.)))..((((((.....))))))((((((((((.....)))))))))).......... ( -25.70)
>DroSim_CAF1 46269 109 - 1
GAGAUGAGCAGUAUCUAGGUAGAUGUACCUGGAAGUACUCACAGC-UGCUUA-------CCUUAAGAUAUAAAAAAUGUAUCUUCUAGUUUGCUAGUCAAACGAGAAAGUUCUAUAA
(((.((((((((.((((((((....)))))))).((....)).))-))))))-------.)))..((((((.....))))))((((.(((((.....))))).)))).......... ( -30.30)
>DroEre_CAF1 43094 105 - 1
GAGAUGAGCAGUAUCUAGGUAGAUGUACCUGAAAGUACGCUCAGU-UGCUUGCUUAGAGCCUUAAGAUACAUCGU-----------AGUUUAACUGCGUAUCUAGAAAGUUCUACAA
(((.(((((.((((.((((((....))))))...)))))))))..-..)))...((((((.((.((((((...((-----------((.....))))))))))..)).))))))... ( -29.30)
>DroYak_CAF1 31030 117 - 1
GAGAUGAGCGGUAUCUAGGUAGAUGUACCUGGAAGUACGCUCAGUUUGCUUACUUAGUGCCUUGAGAUACAUCAUAUUCCUCUUUUAGUUUGACUGCAGAACUGGAAAGUUCCAUAA
...(((.(((((.((((((((....)))))))).(((..(((((..((((.....))))..))))).)))......................))))).(((((....)))))))).. ( -30.60)
>consensus
GAGAUGAGCAGUAUCUAGGUAGAUGUACCUGGAAGUACUCACAGU_UGCUUA_______CCUUAAGAUACAAAAAAUGUAUCUUUUAGUUUGCUAGUGAAACUAGAAAGUUCUAUAA
.....((((.(((((((((((....)))))..(((((.........))))).............))))))............(((((((((.......))))))))).))))..... (-16.42 = -17.34 +   0.92)

alignment

secondary structure

dotplot

Window 3

Location	11,318,496 – 11,318,608
Length	112
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	94.09
Mean single sequence MFE	-33.14
Consensus MFE	-28.52
Energy contribution	-28.92
Covariance contribution	0.40
Combinations/Pair	1.06
Mean z-score	-1.49
Structure conservation index	0.86
SVM decision value	0.81
SVM RNA-class probability	0.856582
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11318496 112 - 23771897
ACUCACAGCCUCUGCCUGGCAUUGUUGUCAUAAAUUACACUUCAAUUGUUGCCCAGGUCGAAGCACUUGCCAUCGGAGAUGAGCAGUUUCUAGGUAGAUGUACCUGGAAGUA
.......((.((.((((((((..((((...............))))...)).)))))).)).))..((((((((...)))).))))((((((((((....)))))))))).. ( -33.66)
>DroSec_CAF1 39298 112 - 1
ACUCACAGCCUCUGCCUGGCAUUGUUGUCAUAAAUUACACUUCAAUUGUUGCCCAGGUGGAAGCACUUGCCAUCGGAGAUGAGCAGUAUCUAGGUAGAUGUACCUGAAAGUA
.......((.((..(((((((..((((...............))))...)).)))))..)).))((((((((((...)))).))......((((((....)))))).)))). ( -31.16)
>DroSim_CAF1 46341 112 - 1
ACUCACAGCCUCUGCCUGGCAUUGUUGUCAUAAAUUACACUUCAAUUGUUGCCCAGGUCGAAGCACUUGCCAUCGGAGAUGAGCAGUAUCUAGGUAGAUGUACCUGGAAGUA
.......((.((.((((((((..((((...............))))...)).)))))).)).))(((.((((((...)))).))))).((((((((....)))))))).... ( -32.66)
>DroEre_CAF1 43162 108 - 1
ACU----GCCUCUGCCUGGCAUUGUUGUCAUAAAUUACACUUCAAUUGUGGCCCAGGUCGGGGCACUUGCCAUCAGAGAUGAGCAGUAUCUAGGUAGAUGUACCUGAAAGUA
..(----(((((.((((((.......(((((((............))))))))))))).)))))).((((((((...)))).))))....((((((....))))))...... ( -33.71)
>DroYak_CAF1 31110 108 - 1
ACU----GCCUCUGCCUGGCAUUGUUGUCAUAAAUUACACUUCAAUUGUUGCCCAGGUCGGGCCACUUGCCAUCGGAGAUGAGCGGUAUCUAGGUAGAUGUACCUGGAAGUA
(((----(((((((..((((((((.(((........)))...)))..((.((((.....)))).)).))))).)))))....))))).((((((((....)))))))).... ( -34.50)
>consensus
ACUCACAGCCUCUGCCUGGCAUUGUUGUCAUAAAUUACACUUCAAUUGUUGCCCAGGUCGAAGCACUUGCCAUCGGAGAUGAGCAGUAUCUAGGUAGAUGUACCUGGAAGUA
.......((.((..(((((((..((((...............))))...)).)))))..)).))(((.((((((...)))).))))).((((((((....)))))))).... (-28.52 = -28.92 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:42 2006