Locus 3946

Sequence ID	3R_DroMel_CAF1
Location	10,676,692 – 10,676,840
Length	148
Max. P	0.958880

overview

Window 5

Location	10,676,692 – 10,676,809
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.08
Mean single sequence MFE	-35.10
Consensus MFE	-28.20
Energy contribution	-29.00
Covariance contribution	0.80
Combinations/Pair	1.07
Mean z-score	-2.11
Structure conservation index	0.80
SVM decision value	1.49
SVM RNA-class probability	0.958880
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10676692 117 + 27905053
CCCCCCCAAAAGGUGGCCCAAAGUCAGAGUUGAUGGAAAAUCUCCAAUUACCUCGUGCAGCGGCCAGGGUUCACAGCUCCCUGGUCAAUGCACCG---CAACUUAUCUGGAAAACUGUCA
.....(((..((((.((.........(((.(((((((.....))).)))).)))(((((..((((((((.........))))))))..))))).)---).))))...))).......... ( -37.40)
>DroSec_CAF1 18061 116 + 1
CAC-CCCAAAAGGUGGCCCAAAGUCAGAGUUUAUGGAAAAUCUGCAAUUACUUCGUGCAGCGGCCAGGGUUCACAGCUCCCUGGUCAAUGCACCC---CAACUUAUCUGGAAAACUGUCA
(((-(......))))..(((..(.((((.(((....))).))))).........(((((..((((((((.........))))))))..)))))..---.........))).......... ( -33.30)
>DroSim_CAF1 20105 116 + 1
CAC-CCCAAAAGGUGGCCCAAAAUCAGAGUUGAUGGAAAAUCUCCAAUUACUUCGUGCAGCGGCCAGGGUUCACAGCUCCCUGGUCAAUGCACCC---CAACUUAUCUGGAAAACUGUCA
(((-(......))))........(((((((((.((((.....))))........(((((..((((((((.........))))))))..)))))..---))))...))))).......... ( -37.80)
>DroEre_CAF1 15287 114 + 1
C---CCCUAAAGGUGGGCCAAAGUCAGAACUGAUGGAAAAUCUCCAAUUACCUCGUGCGUCGGCCAGGGUUCACAGCUCCAUGGUCAAUGCACCC---CAACUUAUCUGGAAAACUGUCA
.---.((..(((.((((.........((..(((((((.....))).))))..))((((((.(((((((((.....)).)).))))).))))))))---)).)))....)).......... ( -31.20)
>DroYak_CAF1 10153 117 + 1
C---CCCCAAAGGUGGCCCAAAGUCAGAGUUGAUGGAAAAUCUCCAAUUACCUCGUGCGUCGGCCAGAGUUCACAGCUCCAUGGUCAAUGCACCCAGGCAACUUAUCUGGAAAACUGUCA
.---..(((.((((.(((........(((.(((((((.....))).)))).)))((((((.(((((((((.....))))..))))).))))))...))).))))...))).......... ( -35.80)
>consensus
C_C_CCCAAAAGGUGGCCCAAAGUCAGAGUUGAUGGAAAAUCUCCAAUUACCUCGUGCAGCGGCCAGGGUUCACAGCUCCCUGGUCAAUGCACCC___CAACUUAUCUGGAAAACUGUCA
...........((..(.(((......(((.(((((((.....))).)))).)))(((((..((((((((.........))))))))..)))))..............)))....)..)). (-28.20 = -29.00 +   0.80)

alignment

secondary structure

dotplot

Window 6

Location	10,676,732 – 10,676,840
Length	108
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	92.12
Mean single sequence MFE	-25.91
Consensus MFE	-20.52
Energy contribution	-20.48
Covariance contribution	-0.04
Combinations/Pair	1.15
Mean z-score	-2.14
Structure conservation index	0.79
SVM decision value	1.34
SVM RNA-class probability	0.944538
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10676732 108 + 27905053
UCUCCAAUUACCUCGUGCAGCGGCCAGGGUUCACAGCUCCCUGGUCAAUGCACCG---CAACUUAUCUGGAAAACUGUCAAGCUCCUUAUCCACAAUUCCACGGCAUACAC
...((.........(((((..((((((((.........))))))))..)))))..---.........(((((...(((..............))).))))).))....... ( -26.44)
>DroSec_CAF1 18100 108 + 1
UCUGCAAUUACUUCGUGCAGCGGCCAGGGUUCACAGCUCCCUGGUCAAUGCACCC---CAACUUAUCUGGAAAACUGUCAAGCUCCAAAUCCCCAAUUCCACGGCAUACAC
..(((.........(((((..((((((((.........))))))))..)))))..---.........((((...((....)).))))................)))..... ( -28.50)
>DroSim_CAF1 20144 108 + 1
UCUCCAAUUACUUCGUGCAGCGGCCAGGGUUCACAGCUCCCUGGUCAAUGCACCC---CAACUUAUCUGGAAAACUGUCAAGCUCCAAAUCCCCAAUUCCACGGCAUACAC
...((.........(((((..((((((((.........))))))))..)))))..---.........((((...((....)).))))...............))....... ( -26.90)
>DroEre_CAF1 15324 108 + 1
UCUCCAAUUACCUCGUGCGUCGGCCAGGGUUCACAGCUCCAUGGUCAAUGCACCC---CAACUUAUCUGGAAAACUGUCAAGCUCCUUAUCCCCAAUCCCAUGGCAUACAC
..((((..((....((((((.(((((((((.....)).)).))))).))))))..---.....))..))))....(((((.....................)))))..... ( -22.00)
>DroYak_CAF1 10190 111 + 1
UCUCCAAUUACCUCGUGCGUCGGCCAGAGUUCACAGCUCCAUGGUCAAUGCACCCAGGCAACUUAUCUGGAAAACUGUCAAGCUUCUUAUCCCCAAUCCGCCGGCAUACAC
..((((........((((((.(((((((((.....))))..))))).))))))..((....))....))))....((((..((................)).))))..... ( -25.69)
>consensus
UCUCCAAUUACCUCGUGCAGCGGCCAGGGUUCACAGCUCCCUGGUCAAUGCACCC___CAACUUAUCUGGAAAACUGUCAAGCUCCUUAUCCCCAAUUCCACGGCAUACAC
..........((..(((((..((((((((.........))))))))..)))))...............(((...((....)).)))................))....... (-20.52 = -20.48 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:10 2006