Locus 5301

Sequence ID	3R_DroMel_CAF1
Location	13,835,780 – 13,835,884
Length	104
Max. P	0.904942

overview

Window 9

Location	13,835,780 – 13,835,884
Length	104
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	84.96
Mean single sequence MFE	-33.33
Consensus MFE	-25.25
Energy contribution	-26.03
Covariance contribution	0.78
Combinations/Pair	1.07
Mean z-score	-1.91
Structure conservation index	0.76
SVM decision value	0.03
SVM RNA-class probability	0.551126
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13835780 104 + 27905053
CGCUAGUGCAUCCGGCCCUGCAUCCGCAGGUGCCAGUGCGCUCCUAUCUCUGACUAAAUACAGACAAAGUAAUGGAGCAGCCGAUGCAUCAAGUAAGUGGAACG-----------
.(((.(((((((.((((((((....))))).))).(.(((((((...((.((.((......)).)).))....))))).))))))))))..)))..........----------- ( -37.50)
>DroVir_CAF1 136465 115 + 1
CACUCGUGCAUCCGGCACUGCAUCCGCAGGUGCCCGUCCGCUCCUAUCUCUGACUAAAUACAGACAAAGUAAUGGAGCAGCCUAUGCAUCAAGUGAGUACAGAAGAGCAGCUAAA
((((.((((((..((((((((....))).))))).....(((((...((.((.((......)).)).))....))))).....))))))..)))).................... ( -31.50)
>DroGri_CAF1 135825 114 + 1
CACUCGUGCAUCCGGCACUGCAUCCGCAGGUGCCCGUUCGCUCCUAUCUCUGACUAAAUACAGACAAAGUAAUGGAGCAGCCUAUGCAUCAAGUGAGUACAGCA-AGCAACGCAA
((((.((((((..((((((((....))).))))).(((.(((((...((.((.((......)).)).))....))))))))..))))))..))))......((.-......)).. ( -32.90)
>DroSim_CAF1 110400 106 + 1
CGCUAGUGCAUCCGGCCCUGCAUCCGCAGGUGCCAGUGCGCUCCUAUCUCUGACUAAAUACAGACAAAGUAAUGGAA-AACCGAUGCAUCAAGUAAGUGUCACU--------AUU
(((((((((((..((((((((....))))).))).)))))))......((((........))))....(((.(((..-..))).)))........)))).....--------... ( -31.40)
>DroWil_CAF1 101541 109 + 1
CACUUGUACAUCCGGCACUGCAUCCGCAGGUGCCAGUACGCUCCUAUCUCUGACUAAAUACAGACAAAGUAAUGGAGCAGCCUAUGCAUCAAGUAAGUAGAGUA------AUAAA
.((((.(((....((((((((....))).)))))..((((((((...((.((.((......)).)).))....))))).((....)).....))).))))))).------..... ( -28.80)
>DroMoj_CAF1 159578 113 + 1
CACUCGUGCAUCCGGCACUGCAUCCGCAGGUGCCCGUACGCUCCUAUCUCUGACUAAAUACAGACAAAGUAAUGGAGCAGCCUAUGCAUCAAGUGAGUAAAG--GCGCAGCGCCA
.....((((....((((((((....))).))))).((..(((((...((.((.((......)).)).))....))))).((((.(((.((....))))).))--)))).)))).. ( -37.90)
>consensus
CACUCGUGCAUCCGGCACUGCAUCCGCAGGUGCCAGUACGCUCCUAUCUCUGACUAAAUACAGACAAAGUAAUGGAGCAGCCUAUGCAUCAAGUAAGUACAGCA______C_AAA
.((((((((((..((((((((....))).))))).....(((((...((.((.((......)).)).))....))))).....)))))).....))))................. (-25.25 = -26.03 +   0.78)

alignment

secondary structure

dotplot

Window 0

Location	13,835,780 – 13,835,884
Length	104
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	84.96
Mean single sequence MFE	-41.68
Consensus MFE	-34.18
Energy contribution	-34.73
Covariance contribution	0.56
Combinations/Pair	1.12
Mean z-score	-2.63
Structure conservation index	0.82
SVM decision value	1.04
SVM RNA-class probability	0.904942
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13835780 104 - 27905053
-----------CGUUCCACUUACUUGAUGCAUCGGCUGCUCCAUUACUUUGUCUGUAUUUAGUCAGAGAUAGGAGCGCACUGGCACCUGCGGAUGCAGGGCCGGAUGCACUAGCG
-----------.((..((......))..))....((((((((....(((((.(((....))).)))))...)))))((((((((.(((((....)))))))))).)))...))). ( -41.00)
>DroVir_CAF1 136465 115 - 1
UUUAGCUGCUCUUCUGUACUCACUUGAUGCAUAGGCUGCUCCAUUACUUUGUCUGUAUUUAGUCAGAGAUAGGAGCGGACGGGCACCUGCGGAUGCAGUGCCGGAUGCACGAGUG
...((.(((......)))))((((((.(((((...(((((((....(((((.(((....))).)))))...))))))).(.(((((.(((....)))))))).)))))))))))) ( -44.70)
>DroGri_CAF1 135825 114 - 1
UUGCGUUGCU-UGCUGUACUCACUUGAUGCAUAGGCUGCUCCAUUACUUUGUCUGUAUUUAGUCAGAGAUAGGAGCGAACGGGCACCUGCGGAUGCAGUGCCGGAUGCACGAGUG
..(((.....-)))......((((((.(((((.(..((((((....(((((.(((....))).)))))...))))))..).(((((.(((....))))))))..))))))))))) ( -43.00)
>DroSim_CAF1 110400 106 - 1
AAU--------AGUGACACUUACUUGAUGCAUCGGUU-UUCCAUUACUUUGUCUGUAUUUAGUCAGAGAUAGGAGCGCACUGGCACCUGCGGAUGCAGGGCCGGAUGCACUAGCG
..(--------((((.((.........(((.((((..-..))....(((((.(((....))).)))))....))..)))(((((.(((((....)))))))))).)))))))... ( -35.50)
>DroWil_CAF1 101541 109 - 1
UUUAU------UACUCUACUUACUUGAUGCAUAGGCUGCUCCAUUACUUUGUCUGUAUUUAGUCAGAGAUAGGAGCGUACUGGCACCUGCGGAUGCAGUGCCGGAUGUACAAGUG
.....------.........((((((.(((((.....(((((....(((((.(((....))).)))))...)))))...(((((((.(((....))))))))))))))))))))) ( -40.10)
>DroMoj_CAF1 159578 113 - 1
UGGCGCUGCGC--CUUUACUCACUUGAUGCAUAGGCUGCUCCAUUACUUUGUCUGUAUUUAGUCAGAGAUAGGAGCGUACGGGCACCUGCGGAUGCAGUGCCGGAUGCACGAGUG
.((((...)))--)......((((((.(((((.....(((((....(((((.(((....))).)))))...)))))...(.(((((.(((....)))))))).)))))))))))) ( -45.80)
>consensus
UUU_G______UGCUCUACUCACUUGAUGCAUAGGCUGCUCCAUUACUUUGUCUGUAUUUAGUCAGAGAUAGGAGCGCACGGGCACCUGCGGAUGCAGUGCCGGAUGCACGAGUG
....................((((((.(((((.(..((((((....(((((.(((....))).)))))...))))))..).(((((.(((....))))))))..))))))))))) (-34.18 = -34.73 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:30 2006