Locus 5644

Sequence ID	2R_DroMel_CAF1
Location	17,946,126 – 17,946,260
Length	134
Max. P	0.985526

overview

Window 8

Location	17,946,126 – 17,946,220
Length	94
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	65.32
Mean single sequence MFE	-39.78
Consensus MFE	-13.36
Energy contribution	-15.84
Covariance contribution	2.48
Combinations/Pair	1.24
Mean z-score	-2.72
Structure conservation index	0.34
SVM decision value	2.01
SVM RNA-class probability	0.985526
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17946126 94 + 20766785
UCCAGGGUGUUGCAGCUGCAAUUUCAGUUGCAUUUG------CAGUG------GCACUGGCAGUUGC--AGCUGCGGUGGGGGCU-UGCCC-----------CACCAAGUAUUUGCUCAG
....((((...((((((((((((((((((((....)------))...------..))))).))))))--))))))(((((((...-..)))-----------))))........)))).. ( -46.50)
>DroVir_CAF1 4671 81 + 1
--CGAGUUGUUGGCGCUGCAAGUGCCGCAGGUGCUGCAG--------------------GUGGUUAAGGUGGUGCUGUCGGUGCAUUGGU-----------------CGUGUUUGUUCAG
--(((.(.....((((((..((..((((....((((...--------------------.))))....))))..))..))))))...).)-----------------))........... ( -25.70)
>DroSec_CAF1 3477 94 + 1
UCCAGGGUGUUGCAGCUGCAAUUUCAGUUGCAGUUG------CAGUG------GCACUGGCAGUUGC--AGCUGCGGUGGGUGCU-UGCCC-----------CACCAAGUAUUUGCUCAG
....((((...((((((((((((((((((((....)------))...------..))))).))))))--))))))((((((.(..-..)))-----------))))........)))).. ( -43.70)
>DroEre_CAF1 8255 100 + 1
--UAGGGUGUUGCAGCUGCAAUUGCAGUUGCAGUUGCAGUUUCAGUGGCAGUGGCAGUGGCAGUGGC--AGUUGCGGUGGGUGCU-CC---------------ACCAAGUAUUUGCUCAG
--..((((...((((((((.(((((..((((..((((..........))))..))))..))))).))--))))))(((((.....-))---------------)))........)))).. ( -42.90)
>DroYak_CAF1 8253 111 + 1
UCCAGGGUGUUGCAGCUGCAAUUUCAAUUGCAGUUGCAGUUGCAGUG------GCAGUGGCAGUUGC--AGUAGCGAUGGGUGCU-UCCCCUCCCCCCACCGCAUCAGGUAUUUGCUCAG
....(((.(((((.(((((((((.(.(((((..((((....))))..------))))).).))))))--))).)))))(((....-..)))....)))(((......))).......... ( -40.10)
>consensus
UCCAGGGUGUUGCAGCUGCAAUUUCAGUUGCAGUUGCAG___CAGUG______GCACUGGCAGUUGC__AGCUGCGGUGGGUGCU_UGCCC___________CACCAAGUAUUUGCUCAG
....((((..((((((((((((....)))))))))))).....................(((((......))))).......................................)))).. (-13.36 = -15.84 +   2.48)

alignment

secondary structure

dotplot

Window 9

Location	17,946,162 – 17,946,260
Length	98
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	71.36
Mean single sequence MFE	-30.12
Consensus MFE	-7.48
Energy contribution	-8.36
Covariance contribution	0.88
Combinations/Pair	1.06
Mean z-score	-1.65
Structure conservation index	0.25
SVM decision value	-0.02
SVM RNA-class probability	0.523674
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17946162 98 - 20766785
AACGCAAUUAGGUCGCUGACUGCAGUUAAUUGAUGAUCAACUGAGCAAAUACUUGGUG-----------GGGCA-AGCCCCCACCGCAGCU--GCAACUGCCAGUGC------CACUG--
..........((.(((((...((((((..(((.....)))....(((....(((((((-----------(((..-...)))))))).)).)--))))))))))))))------)....-- ( -33.10)
>DroVir_CAF1 4708 83 - 1
AACACAAUUAGGUCGGC-CCUGCAGUUAAUUGACAUGCAGCUGAACAAACACG-----------------ACCAAUGCACCGACAGCACCACCUUAACCAC-------------------
..........(((((..-.((((((((....))).))))).((......))))-----------------)))..(((.......))).............------------------- ( -15.80)
>DroSec_CAF1 3513 98 - 1
AACGCAAUUAGGUCGCUGACUGCAGUUAAUUGAUGUUCAGCUGAGCAAAUACUUGGUG-----------GGGCA-AGCACCCACCGCAGCU--GCAACUGCCAGUGC------CACUG--
..........((.(((((.((((((((......(((((....))))).......((((-----------((...-....))))))..))))--)))...).))))))------)....-- ( -34.30)
>DroEre_CAF1 8293 102 - 1
AACGCAAUUAGGUCGCUGACUGCAGUUAAUUGAUGUUCAGCUGAGCAAAUACUUGGU---------------GG-AGCACCCACCGCAACU--GCCACUGCCACUGCCACUGCCACUGAA
...(((....(((.((.....((((((......(((((....))))).......(((---------------((-.....)))))..))))--))....)).))).....)))....... ( -27.30)
>DroYak_CAF1 8293 111 - 1
AACGCAAUUAGGUCGCUGACUGCAGUUAAUUGAUGUUCAGCUGAGCAAAUACCUGAUGCGGUGGGGGGAGGGGA-AGCACCCAUCGCUACU--GCAACUGCCACUGC------CACUGCA
...((((((((((.((((....)))).......(((((....)))))...)))))))(((((((.(((((((..-....))).))((....--))..)).)))))))------...))). ( -40.10)
>consensus
AACGCAAUUAGGUCGCUGACUGCAGUUAAUUGAUGUUCAGCUGAGCAAAUACUUGGUG___________GGGCA_AGCACCCACCGCAACU__GCAACUGCCACUGC______CACUG__
....(((((((.(.((.....))).))))))).(((((....))))).............................((.......))................................. ( -7.48 =  -8.36 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:52 2006