Locus 5818

Sequence ID	2R_DroMel_CAF1
Location	18,427,840 – 18,427,980
Length	140
Max. P	0.986582

overview

Window 8

Location	18,427,840 – 18,427,951
Length	111
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	76.66
Mean single sequence MFE	-33.32
Consensus MFE	-19.45
Energy contribution	-20.31
Covariance contribution	0.86
Combinations/Pair	1.15
Mean z-score	-2.61
Structure conservation index	0.58
SVM decision value	2.05
SVM RNA-class probability	0.986582
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18427840 111 - 20766785
GGCAGUGCGUUCUCCUUCUCAAACGCAUUUAGCACCCUAAGUGCGGGAG---GUGCUGCAGCUCCAACUACCAGCGCUUCAGCUCCCUUAGCUGCCAAAAGCCCAACCGCUACA
(((((((((((..........))))).....((((.....))))(((((---.((..((.(((.........)))))..)).)))))...))))))...(((......)))... ( -38.00)
>DroVir_CAF1 2866 96 - 1
GGCAGCAAGUUUUCCUUCUCGAAUGCGUUCAGCAGCCUCAACACGGCAGGCAGCAGCACACC---------CAGCG------GCUCACUAACUGCCACCAGCAGUGCC---ACA
((((((..............((.(((.....)))...)).....(((((..(((.((.....---------..)).------)))......)))))....))..))))---... ( -24.50)
>DroSec_CAF1 1745 111 - 1
GGCAGCGCGUUCUCCUUCUCAAACGCAUUUAGCACUUUAAGUGCGGGAG---GUGCUGUAGCUCCAACUACCACCGCUCCACCUCCCUUGACUGCCAACAGCCCCACCUCUACA
(((((((((((..........))))).....((((.....))))(((((---(((....(((.............))).))))))))..).))))).................. ( -35.52)
>DroSim_CAF1 1083 111 - 1
GGCAGCGCGUUCUCCUUCUCAAACGCAUUUAGCACUCUAAGUGCGGGAG---GUGCUGUAGCUCCAACUACCACCGCUCCACCUCCCUUAACUGCCAACAGCCCCACCUCUACA
(((((.(((((..........))))).....((((.....))))(((((---(((....(((.............))).))))))))....))))).................. ( -35.12)
>DroEre_CAF1 1098 108 - 1
GGCAGCGCGUUCUCCUUCUCAAACGCAUUUAGCACCCUAAGUGCGGGAG---GUGCUGCAUCUCCAACUACCAUCGCUUCUGCUCCCUUAGCUGCCAGCAGCUCUACA---GCA
((((((..(((............(((((((((....)))))))))((((---(((...)))))))))).......((....)).......))))))....(((....)---)). ( -36.30)
>DroYak_CAF1 1104 108 - 1
GGCAGCGCGUUCUCCUUCUCCAAUGCAUUCAGCAAUUUAAGUGCGGGAG---GUGCUGCAGCUCCAACUACCACCGCGCCUGCUCCCUUAGCUGCCAACAGCUCCACC---ACA
(((((((((((..........)))))....((((......((((((..(---(((.((......))..)))).)))))).))))......))))))............---... ( -30.50)
>consensus
GGCAGCGCGUUCUCCUUCUCAAACGCAUUUAGCACCCUAAGUGCGGGAG___GUGCUGCAGCUCCAACUACCACCGCUCCAGCUCCCUUAACUGCCAACAGCCCCACC___ACA
(((((...................((((((((....))))))))(((((.....((...................)).....)))))....))))).................. (-19.45 = -20.31 +   0.86)

alignment

secondary structure

dotplot

Window 9

Location	18,427,877 – 18,427,980
Length	103
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	78.81
Mean single sequence MFE	-33.22
Consensus MFE	-21.99
Energy contribution	-22.33
Covariance contribution	0.34
Combinations/Pair	1.37
Mean z-score	-1.94
Structure conservation index	0.66
SVM decision value	1.04
SVM RNA-class probability	0.905452
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18427877 103 - 20766785
CAACGGUAA---CAUCUAGC---ACUGCUGUUCCCGGCAGUGCGUUCUCCUUCUCAAACGCAUUUAGCACCCUAAGUGCGGGAG---GUGCUGCAGCUCCAACUACCAGCGC
....((((.---......((---(((((((....)))))))))(((............(((((((((....)))))))))((((---.((...)).)))))))))))..... ( -38.60)
>DroVir_CAF1 2895 100 - 1
--GCAGUCAGCACAACGAACGCAGCUUCUGCGCCAGGCAGCAAGUUUUCCUUCUCGAAUGCGUUCAGCAGCCUCAACACGGCAGGCAGCAGCACACC---------CAGCG-
--((.(((........(((((((((((((((.....)))).)))).(((......))))))))))....(((.......))).))).)).((.....---------..)).- ( -28.40)
>DroSec_CAF1 1782 103 - 1
CAACGGUAA---CAUCUAGC---ACUGCUGUUCCUGGCAGCGCGUUCUCCUUCUCAAACGCAUUUAGCACUUUAAGUGCGGGAG---GUGCUGUAGCUCCAACUACCACCGC
...((((..---.....(((---((.(((((.....)))))...........(((...(((((((((....))))))))).)))---)))))((((......)))).)))). ( -33.10)
>DroSim_CAF1 1120 103 - 1
CAACGGUAA---CAUCUAUC---GCUGCUGUUCCUGGCAGCGCGUUCUCCUUCUCAAACGCAUUUAGCACUCUAAGUGCGGGAG---GUGCUGUAGCUCCAACUACCACCGC
...((((..---.......(---((((((......))))))).((...(((((.....(((((((((....)))))))))))))---).)).((((......)))).)))). ( -33.00)
>DroEre_CAF1 1132 103 - 1
CAGCGGUAA---CAUCCAGC---ACUGCUGUUCCUGGCAGCGCGUUCUCCUUCUCAAACGCAUUUAGCACCCUAAGUGCGGGAG---GUGCUGCAUCUCCAACUACCAUCGC
..((((((.---..(((.((---.(((((......))))).))...............(((((((((....)))))))))))).---.)))))).................. ( -35.40)
>DroYak_CAF1 1138 103 - 1
CAACGGUAA---CAUCCAGC---ACUGCUGUUCCGGGCAGCGCGUUCUCCUUCUCCAAUGCAUUCAGCAAUUUAAGUGCGGGAG---GUGCUGCAGCUCCAACUACCACCGC
...((((..---..(((.((---((((((((.....)))))(((((..........))))).............))))).)))(---(.((....)).)).......)))). ( -30.80)
>consensus
CAACGGUAA___CAUCUAGC___ACUGCUGUUCCUGGCAGCGCGUUCUCCUUCUCAAACGCAUUUAGCACCCUAAGUGCGGGAG___GUGCUGCAGCUCCAACUACCACCGC
.(((((((.................)))))))....(((((((...((((........(((((((((....)))))))))))))...))))))).................. (-21.99 = -22.33 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:12 2006