Locus 7057

Sequence ID	3R_DroMel_CAF1
Location	18,643,952 – 18,644,067
Length	115
Max. P	0.670744

overview

Window 7

Location	18,643,952 – 18,644,055
Length	103
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	79.25
Mean single sequence MFE	-34.68
Consensus MFE	-18.81
Energy contribution	-20.03
Covariance contribution	1.22
Combinations/Pair	1.09
Mean z-score	-1.97
Structure conservation index	0.54
SVM decision value	0.29
SVM RNA-class probability	0.670744
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18643952 103 + 27905053
UGACUC------------GGGGUCGAC-GGUCAUCGUUGCAUGCGAAUUUAAUCAAGUCAUGCAAUAGAAUUUACGGUUCCAUUGCCU-UUCGGCCGUCGAUGCCGAUGGUCGUUCC
.(((((------------((.((((((-((((.(((((((((((............).)))))))).))......(((......))).-...)))))))))).))))..)))..... ( -41.50)
>DroSim_CAF1 70351 103 + 1
UGGCUC------------GGGGUCGAG-GGUCAUCGUUGCAUGCGAAUUUAAUCAAGUCAUGCAAUAGAAUUUACGGUUCCAUUGCCU-UUCGGCCGUCGAUGCCGAUGGUCGUUCG
.(((((------------((.(((((.-((((.(((((((((((............).)))))))).))......(((......))).-...)))).))))).))))..)))..... ( -37.30)
>DroEre_CAF1 71599 102 + 1
UGGCUC------------GGGGUCGAC-GGUCAUCGUUGCAUGCGAAUUUAAUCAAGUCAUGCAAUAGAAUUUACGGUUCCAUUGCCU-UUCGGCCGUCGAUGCCGAUGCUCGU-CG
.(((((------------((.((((((-((((.(((((((((((............).)))))))).))......(((......))).-...)))))))))).)))).)))...-.. ( -42.10)
>DroWil_CAF1 71200 90 + 1
----UU------------GAAGGCGACGGGUCAACGUUGCAUGCGAAUUUAAUCAAGUCAUGCAAUAAAAUUUACGGUUCCUUUGCCUCUUUUGCCUACGAUGCCA-----------
----((------------(.((((((.(((.....(((((((((............).)))))))).........(((......)))))).)))))).))).....----------- ( -22.10)
>DroYak_CAF1 72650 114 + 1
UGGGUCGGAGUCGGAGUCGGGGUCGAG-GGUCAUCGUUGCAUGCGAAUUUAAUCAAGUCAUGCAAUAGAAUUUACGGUUCCAUUGCCU-UUCGGCCGUCGAUGCCGAUGCUCGU-CG
.........(.(((.(((((.(((((.-((((.(((((((((((............).)))))))).))......(((......))).-...)))).))))).)))))..))).-). ( -40.70)
>DroAna_CAF1 70009 95 + 1
-GGUCC------------UGGGUCGCCAGGUCAUCGUUGCAUGCGAAUUUAAUCAAGUCAUGCAAUAGAAUUUACGGUUCCACUGCCC-AUCCACAGAUUUGGCCGAAG--------
-.(.((------------(((....))))).).(((((((((((............).)))))))).)).....(((((...(((...-.....)))....)))))...-------- ( -24.40)
>consensus
UGGCUC____________GGGGUCGAC_GGUCAUCGUUGCAUGCGAAUUUAAUCAAGUCAUGCAAUAGAAUUUACGGUUCCAUUGCCU_UUCGGCCGUCGAUGCCGAUG_UCGU_CG
..................((.((((...((((...(((((((((............).)))))))).........(((......))).....))))..)))).))............ (-18.81 = -20.03 +   1.22)

alignment

secondary structure

dotplot

Window 8

Location	18,643,976 – 18,644,067
Length	91
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.58
Mean single sequence MFE	-23.12
Consensus MFE	-14.98
Energy contribution	-15.07
Covariance contribution	0.09
Combinations/Pair	1.14
Mean z-score	-1.30
Structure conservation index	0.65
SVM decision value	0.28
SVM RNA-class probability	0.664316
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18643976 91 - 27905053
ACAA--------------ACGAG--------------GACGGAACGACCAUCGGCAUCGACGGCCGAA-AGGCAAUGGAACCGUAAAUUCUAUUGCAUGACUUGAUUAAAUUCGCAUGCA
....--------------..(((--------------.((((..((.....))...((.(..(((...-.)))..).)).))))...)))...((((((....((......)).)))))) ( -24.10)
>DroSec_CAF1 73346 91 - 1
ACAA--------------GCGAG--------------GACCGAACGACCAUCGGCAUCGACGGCCGAA-AGGCAAUGGAACCGUAAAUUCUAUUGCAUGACUUGAUUAAAUUCGCAUGCA
....--------------((((.--------------(.((((.......))))).))).).(((...-.)))(((((((.......)))))))(((((....((......)).))))). ( -24.70)
>DroSim_CAF1 70375 91 - 1
ACAA--------------GCGAG--------------GACCGAACGACCAUCGGCAUCGACGGCCGAA-AGGCAAUGGAACCGUAAAUUCUAUUGCAUGACUUGAUUAAAUUCGCAUGCA
....--------------((((.--------------(.((((.......))))).))).).(((...-.)))(((((((.......)))))))(((((....((......)).))))). ( -24.70)
>DroEre_CAF1 71623 100 - 1
ACA----AUAACCGGCAACCGAC--------------AACCG-ACGAGCAUCGGCAUCGACGGCCGAA-AGGCAAUGGAACCGUAAAUUCUAUUGCAUGACUUGAUUAAAUUCGCAUGCA
...----.......(((..(((.--------------.....-.(((((((((((.......))))).-..(((((((((.......))))))))).)).)))).......)))..))). ( -25.64)
>DroWil_CAF1 71221 71 - 1
AC-------------------------------------------------UGGCAUCGUAGGCAAAAGAGGCAAAGGAACCGUAAAUUUUAUUGCAUGACUUGAUUAAAUUCGCAUGCA
..-------------------------------------------------..(((((((..((((.((((.....(....).....)))).))))...))..((......))).)))). ( -10.50)
>DroYak_CAF1 72686 118 - 1
GCAACCAACAACCAACAAACGACAAAGGACAAGCGACAACCG-ACGAGCAUCGGCAUCGACGGCCGAA-AGGCAAUGGAACCGUAAAUUCUAUUGCAUGACUUGAUUAAAUUCGCAUGCA
(((........((.............))....((((......-.(((((((((((.......))))).-..(((((((((.......))))))))).)).)))).......)))).))). ( -29.06)
>consensus
ACAA______________ACGAG______________GACCG_ACGACCAUCGGCAUCGACGGCCGAA_AGGCAAUGGAACCGUAAAUUCUAUUGCAUGACUUGAUUAAAUUCGCAUGCA
..................................................(((((.......)))))....(((((((((.......)))))))))........................ (-14.98 = -15.07 +   0.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:29 2006