Locus 9684

Sequence ID	3R_DroMel_CAF1
Location	25,616,159 – 25,616,255
Length	96
Max. P	0.701775

overview

Window 4

Location	25,616,159 – 25,616,255
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	86.46
Mean single sequence MFE	-29.02
Consensus MFE	-19.32
Energy contribution	-19.80
Covariance contribution	0.48
Combinations/Pair	1.19
Mean z-score	-2.10
Structure conservation index	0.67
SVM decision value	0.25
SVM RNA-class probability	0.654731
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25616159 96 + 27905053
GCCUACGCUGCCAGCAGCGGCAGUCACAACAGCAACAAUGCGGCUGCCAUGGCCGCCGUCUGCCAAAUGCAGAAUUUUUUCAACCAGCAACAGCAG
((....((((...(((..(((((.(......(((....)))(((.((....)).)))).)))))...))).(((....)))...))))....)).. ( -32.80)
>DroSec_CAF1 42788 90 + 1
GCCUACGCUGCCAGCAGCGGCAGUCACAACAGCAACAAUGCGGCUGCCAUGGCCGCCGUCUGCCAAAUGCAGAAUUUUUUCAACCAAC------AG
((....((((....))))(((((.(......(((....)))(((.((....)).)))).)))))....)).(((....))).......------.. ( -30.50)
>DroSim_CAF1 43718 84 + 1
GCCUACGCUGCCAGC------AGUCACAACAGCAACAAUGCGGCUGCCAUGGCCGCCGUCUGCCAAAUGCAGAAUUUUUUCAACCAGC------AG
((....((.((((((------((((.((..........)).))))))..)))).))..(((((.....))))).............))------.. ( -24.70)
>DroEre_CAF1 43999 78 + 1
GCCUACGCUGCAAGUGGCGG------------CAACAAUGCGGCUGCCAUGGCCGCCGUCUGCCAAAUGCACAAUUUUUUCAACCAGC------AG
......(.((((..((((((------------.......(((((.((....)).)))))))))))..)))))................------.. ( -25.61)
>DroYak_CAF1 46250 90 + 1
GCCUACGCUGGAAGUAGCGGCAGUCACAACAGCAACAAUGCGGCUGCCAUGGCCGCCGUCUGUCAAAUGCAGAAUUUUUUCAACCAGC------AG
......(((((..(((..(((((.(......(((....)))(((.((....)).)))).)))))...))).(((....)))..)))))------.. ( -31.50)
>consensus
GCCUACGCUGCCAGCAGCGGCAGUCACAACAGCAACAAUGCGGCUGCCAUGGCCGCCGUCUGCCAAAUGCAGAAUUUUUUCAACCAGC______AG
.....(((((....)))))....................((((((.....))))))..(((((.....)))))....................... (-19.32 = -19.80 +   0.48)

alignment

secondary structure

dotplot

Window 5

Location	25,616,159 – 25,616,255
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	86.46
Mean single sequence MFE	-36.12
Consensus MFE	-22.90
Energy contribution	-25.74
Covariance contribution	2.84
Combinations/Pair	1.04
Mean z-score	-2.47
Structure conservation index	0.63
SVM decision value	0.35
SVM RNA-class probability	0.701775
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25616159 96 - 27905053
CUGCUGUUGCUGGUUGAAAAAAUUCUGCAUUUGGCAGACGGCGGCCAUGGCAGCCGCAUUGUUGCUGUUGUGACUGCCGCUGCUGGCAGCGUAGGC
((((.(((((..((.(.......(((((.....)))))((((((.((..(((((.((...)).)))))..)).))))))).))..))))))))).. ( -45.90)
>DroSec_CAF1 42788 90 - 1
CU------GUUGGUUGAAAAAAUUCUGCAUUUGGCAGACGGCGGCCAUGGCAGCCGCAUUGUUGCUGUUGUGACUGCCGCUGCUGGCAGCGUAGGC
..------((((((.(((....))).))..(..((((.((((((.((..(((((.((...)).)))))..)).))))))))))..)))))...... ( -38.40)
>DroSim_CAF1 43718 84 - 1
CU------GCUGGUUGAAAAAAUUCUGCAUUUGGCAGACGGCGGCCAUGGCAGCCGCAUUGUUGCUGUUGUGACU------GCUGGCAGCGUAGGC
..------((((...........(((((.....)))))((((((.((..(((((.((...)).)))))..)).))------)))).))))...... ( -34.40)
>DroEre_CAF1 43999 78 - 1
CU------GCUGGUUGAAAAAAUUGUGCAUUUGGCAGACGGCGGCCAUGGCAGCCGCAUUGUUG------------CCGCCACUUGCAGCGUAGGC
((------((.((((.....)))).((((..((((....(((.((....)).)))(((....))------------).))))..))))..)))).. ( -26.80)
>DroYak_CAF1 46250 90 - 1
CU------GCUGGUUGAAAAAAUUCUGCAUUUGACAGACGGCGGCCAUGGCAGCCGCAUUGUUGCUGUUGUGACUGCCGCUACUUCCAGCGUAGGC
..------(((((..(.......(((((....).))))((((((.((..(((((.((...)).)))))..)).))))))...)..)))))...... ( -35.10)
>consensus
CU______GCUGGUUGAAAAAAUUCUGCAUUUGGCAGACGGCGGCCAUGGCAGCCGCAUUGUUGCUGUUGUGACUGCCGCUGCUGGCAGCGUAGGC
........((((...........(((((.....)))))((((((.((..(((((.((...)).)))))..)).)))))).......))))...... (-22.90 = -25.74 +   2.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:39:50 2006