Locus 5088

Sequence ID	3R_DroMel_CAF1
Location	13,417,989 – 13,418,144
Length	155
Max. P	0.913506

overview

Window 2

Location	13,417,989 – 13,418,086
Length	97
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	80.69
Mean single sequence MFE	-21.49
Consensus MFE	-11.11
Energy contribution	-11.17
Covariance contribution	0.06
Combinations/Pair	1.08
Mean z-score	-2.62
Structure conservation index	0.52
SVM decision value	0.65
SVM RNA-class probability	0.811188
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13417989 97 + 27905053
UUGCCUUACCACCUGCACAU-UACAACAAACAAUACUACUUUAUUGUU------GUACU-------UUUUUACACAUUUCGCAGCGGUUGGCAAAUUAAAACGAAAUAACU
(((((..(((..((((....-.......(((((((......)))))))------(((..-------....))).......)))).))).)))))................. ( -20.10)
>DroSec_CAF1 43534 102 + 1
UUGCCUUACCACCUGCACAU-UGCAACAAACAAUGCUAUAUUAUUGUU------GUACUUCU--UUUUUUUACACAUUUCGCAGCGGUUGGCAAAUUAAAACGAAAUAACU
(((((..(((..((((.(((-((.......))))).........(((.------(((.....--......))))))....)))).))).)))))................. ( -18.60)
>DroSim_CAF1 46041 102 + 1
UUGCCUUACCACCUGCACAU-UACAACAAACAAUGCUAUAUUAUUGUU------GUACUUCU--UUUUUUUAAACAUUUCGCAGCGGUUGGCAAAUUAAAACGAAAUAACU
(((((..(((..((((....-((((((((..............)))))------))).....--(((....)))......)))).))).)))))................. ( -18.84)
>DroEre_CAF1 44213 91 + 1
UUGCCUUGCCACCUGCGCAU-UACAGCAAACAGUGCUAUUU-----UU------GUACU--------UUUUACACAUUUCGCAGCGGUUGGCAAAUUAAAACGAAAUAACU
(((((..(((..((((((..-....))(((.(((((.....-----..------)))))--------.))).........)))).))).)))))................. ( -22.60)
>DroYak_CAF1 48256 96 + 1
UUGCCUUACCACCUGCGCAU-UACAGCAAACAGUGCUAUUUUAUUCUU------GUACU--------UUUUAAACAUUUCGCAGCGGUUGGCAAAUUAAAACGAAAUAACU
(((((..(((..((((((..-....))(((.(((((............------)))))--------.))).........)))).))).)))))................. ( -21.50)
>DroAna_CAF1 40360 108 + 1
UUGCCGAACCACCUGCAUAUGUACA---UAUAUAUGUACAUAAGAAUUACAAAGGGGCUUGUGGGUUUUUGGAACAUUUCGCAGCGGCUGGCAAAUUAAAAUGCAAUAACU
((((((..((..((((.((((((((---(....))))))))).(((......(((((((....))))))).......))))))).)).))))))................. ( -27.32)
>consensus
UUGCCUUACCACCUGCACAU_UACAACAAACAAUGCUAUAUUAUUGUU______GUACU_______UUUUUAAACAUUUCGCAGCGGUUGGCAAAUUAAAACGAAAUAACU
(((((..(((..((((................................................................)))).))).)))))................. (-11.11 = -11.17 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	13,417,989 – 13,418,086
Length	97
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	80.69
Mean single sequence MFE	-23.73
Consensus MFE	-13.79
Energy contribution	-13.85
Covariance contribution	0.06
Combinations/Pair	1.24
Mean z-score	-1.87
Structure conservation index	0.58
SVM decision value	0.13
SVM RNA-class probability	0.599412
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13417989 97 - 27905053
AGUUAUUUCGUUUUAAUUUGCCAACCGCUGCGAAAUGUGUAAAAA-------AGUAC------AACAAUAAAGUAGUAUUGUUUGUUGUA-AUGUGCAGGUGGUAAGGCAA
.................(((((.(((((((((.....))).....-------.((((------(((((((((.........)))))))).-.))))).))))))..))))) ( -21.70)
>DroSec_CAF1 43534 102 - 1
AGUUAUUUCGUUUUAAUUUGCCAACCGCUGCGAAAUGUGUAAAAAAA--AGAAGUAC------AACAAUAAUAUAGCAUUGUUUGUUGCA-AUGUGCAGGUGGUAAGGCAA
.................(((((.((((((((....((((((......--.....)))------.)))........(((((((.....)))-))))))).)))))..))))) ( -23.80)
>DroSim_CAF1 46041 102 - 1
AGUUAUUUCGUUUUAAUUUGCCAACCGCUGCGAAAUGUUUAAAAAAA--AGAAGUAC------AACAAUAAUAUAGCAUUGUUUGUUGUA-AUGUGCAGGUGGUAAGGCAA
.................(((((.(((((((((...............--.....(((------(((((((((.....)))).))))))))-...)))).)))))..))))) ( -22.20)
>DroEre_CAF1 44213 91 - 1
AGUUAUUUCGUUUUAAUUUGCCAACCGCUGCGAAAUGUGUAAAA--------AGUAC------AA-----AAAUAGCACUGUUUGCUGUA-AUGCGCAGGUGGCAAGGCAA
.................(((((..((((((((.....((((...--------..)))------).-----..((((((.....)))))).-...)))).))))...))))) ( -23.10)
>DroYak_CAF1 48256 96 - 1
AGUUAUUUCGUUUUAAUUUGCCAACCGCUGCGAAAUGUUUAAAA--------AGUAC------AAGAAUAAAAUAGCACUGUUUGCUGUA-AUGCGCAGGUGGUAAGGCAA
.................(((((.(((((((((...(((......--------...))------)........((((((.....)))))).-...)))).)))))..))))) ( -22.90)
>DroAna_CAF1 40360 108 - 1
AGUUAUUGCAUUUUAAUUUGCCAGCCGCUGCGAAAUGUUCCAAAAACCCACAAGCCCCUUUGUAAUUCUUAUGUACAUAUAUA---UGUACAUAUGCAGGUGGUUCGGCAA
.................(((((((((((((((.................(((((....)))))......(((((((((....)---)))))))))))).)))))).))))) ( -28.70)
>consensus
AGUUAUUUCGUUUUAAUUUGCCAACCGCUGCGAAAUGUGUAAAAA_______AGUAC______AACAAUAAAAUAGCAUUGUUUGUUGUA_AUGUGCAGGUGGUAAGGCAA
.................(((((.(((((((((...(......).............................((((((.....)))))).....)))).)))))..))))) (-13.79 = -13.85 +   0.06)

alignment

secondary structure

dotplot

Window 4

Location	13,418,046 – 13,418,144
Length	98
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	79.86
Mean single sequence MFE	-20.80
Consensus MFE	-7.20
Energy contribution	-8.60
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-2.54
Structure conservation index	0.35
SVM decision value	1.09
SVM RNA-class probability	0.913506
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13418046 98 + 27905053
ACACAUUUCGCAGCGGUUGGCAAAUUAAAACGAAAUAACUCUUCAUCAGGAGGGGCC-------UUCCCCUCGC-------CAAACAAAAAAACCAAAAAA-----C--CAUGCACACA
.........(((..(((((((..........(((.......))).....((((((..-------..))))))))-------)).................)-----)--).)))..... ( -22.22)
>DroSec_CAF1 43596 89 + 1
ACACAUUUCGCAGCGGUUGGCAAAUUAAAACGAAAUAACUCUUCAUCAGGAGGGGCC-------UUCCCCUCGC-------CAAACAAAA---------AA-----G--CAUGCACACA
.........(((((..(((((..........(((.......))).....((((((..-------..))))))))-------)))......---------..-----)--).)))..... ( -23.20)
>DroSim_CAF1 46103 89 + 1
AAACAUUUCGCAGCGGUUGGCAAAUUAAAACGAAAUAACUCUUCAUCAGGAGGGGCC-------UUCCCCUCGC-------CAAACAAAA---------AA-----G--CAUGCACACA
.........(((((..(((((..........(((.......))).....((((((..-------..))))))))-------)))......---------..-----)--).)))..... ( -23.20)
>DroEre_CAF1 44264 101 + 1
ACACAUUUCGCAGCGGUUGGCAAAUUAAAACGAAAUAACUCUUCAUCAGG---GGCC-------GUCCCCUCGCACAAAAGCAAACAAAAA--------AAUAUAUACAUAUGCAUAUA
.........((.((..(((((..........(((.......)))...(((---((..-------..))))).)).)))..)).........--------.((((....))))))..... ( -16.70)
>DroYak_CAF1 48312 92 + 1
AAACAUUUCGCAGCGGUUGGCAAAUUAAAACGAAAUAACUCUUCAUCAGG---GUCCGCGGCAGGUCCCCUCGC-----------CAAAAA--------AA-----GCAUAUACACUCA
.........((.....(((((..........(((.......)))....((---(.((......)).)))...))-----------)))...--------..-----))........... ( -18.70)
>consensus
ACACAUUUCGCAGCGGUUGGCAAAUUAAAACGAAAUAACUCUUCAUCAGGAGGGGCC_______UUCCCCUCGC_______CAAACAAAAA________AA_____G__CAUGCACACA
....((((((....((((....))))....)))))).............((((((...........))))))............................................... ( -7.20 =  -8.60 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:52 2006