Locus 3868

Sequence ID	3R_DroMel_CAF1
Location	10,526,165 – 10,526,301
Length	136
Max. P	0.858482

overview

Window 6

Location	10,526,165 – 10,526,261
Length	96
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	77.12
Mean single sequence MFE	-39.20
Consensus MFE	-26.40
Energy contribution	-26.43
Covariance contribution	0.03
Combinations/Pair	1.25
Mean z-score	-1.54
Structure conservation index	0.67
SVM decision value	0.82
SVM RNA-class probability	0.858482
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10526165 96 - 27905053
CUGGACAUUCCCUCCACCAGCGCAGCUGCAGCGGCAGCGGCCGUUGCCGCCAGCAAUGCACCAAACC---------CUGGCAACAACCGGGAGGAGUCGUCGGAU
...((((((((..((....(((..((((..((((((((....))))))))))))..)))........---------.((....))...))..))))).))).... ( -40.10)
>DroPse_CAF1 1367 105 - 1
CUGGACAUUCCCUCCACGAGUGCCGCCGCAGCAGCAGCCGCCGUUGCGGCCAGCAACUCUUCGACCAGCAGCAGCACCAACAACAACAGGGAGGAGUCUUCGGAU
(((((.(((((..((..((((((.((((((((.((....)).))))))))..)).))))........((....)).............))..))))).))))).. ( -41.00)
>DroSec_CAF1 1507 96 - 1
CUGGACAUUCCCUCCACCAGCGCAGCUGCAGCGGCAGCGGCCGUCGCCGCAAGCAAUGCACCAAACC---------CUGGCAACAAUCGGGAGGAGUCGUCGGAU
...((((((((..((......(((..(((.(((((.((....)).)))))..))).)))........---------.((....))...))..))))).))).... ( -35.10)
>DroEre_CAF1 1292 96 - 1
CUGGACAUUCCCUCCACCAGCGCAGCUGCGGCGGCAGCGGCCGUUGCCGCCAGCAAUGCUCCAAGCA---------GUGGCAACAACCGGGAGGAGUCGUCGGAU
...((((((((..((......(((..((((((((((((....))))))))).))).)))........---------.((....))...))..))))).))).... ( -42.80)
>DroAna_CAF1 2802 93 - 1
CUGGACCUGCCCUCCACCAGUGCCGCAGCAGCUGCUGUCGCCGUGGCUGCCAGUAGCUCCGCGAGCA------------ACAGCAUUCGGGAGGAAUCUUCGGAC
(((((..(..(((((.(.(((((.(((((....))))).(((((((..((.....)).))))).)).------------...))))).)))))).)..))))).. ( -35.20)
>DroPer_CAF1 3031 105 - 1
CUGGACAUUCCCUCCACGAGUGCCGCCGCAGCAGCAGCCGCCGUUGCGGCCAGCAACUCUUCGACGAGCAGCAGCACCAACAACAACAGGGAGGAGUCUUCGGAU
(((((.(((((..((..((((((.((((((((.((....)).))))))))..)).))))........((....)).............))..))))).))))).. ( -41.00)
>consensus
CUGGACAUUCCCUCCACCAGCGCAGCUGCAGCGGCAGCCGCCGUUGCCGCCAGCAACGCUCCAAACA_________CUGACAACAACCGGGAGGAGUCGUCGGAU
((((..(((((..((....(.((.(((((....))))).)))(((((.....)))))...............................))..)))))..)))).. (-26.40 = -26.43 +   0.03)

alignment

secondary structure

dotplot

Window 7

Location	10,526,196 – 10,526,301
Length	105
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	79.50
Mean single sequence MFE	-35.83
Consensus MFE	-18.40
Energy contribution	-18.79
Covariance contribution	0.39
Combinations/Pair	1.23
Mean z-score	-2.04
Structure conservation index	0.51
SVM decision value	0.13
SVM RNA-class probability	0.597304
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10526196 105 - 27905053
CAACGUGCUGAGCUCCAAAUUCAUUCCGAGCUUUGAGUCUCUGGACAUUCCCUCCACCAGCGCAGCUGCAGCGGCAGCGGCCGUUGCCGCCAGCAAUGCA---CCAAA
....(((((((((((............)))))....(((....)))...........)))))).((((..((((((((....))))))))))))......---..... ( -38.00)
>DroPse_CAF1 1407 105 - 1
CAAUGUCCUCAGUUCGAAAUUCAUUCCCAGCUUCGAGUCGCUGGACAUUCCCUCCACGAGUGCCGCCGCAGCAGCAGCCGCCGUUGCGGCCAGCAACUCU---UCGAC
.(((((((.(..((((((.............))))))..)..)))))))........((((((.((((((((.((....)).))))))))..)).)))).---..... ( -37.12)
>DroEre_CAF1 1323 105 - 1
CAACGUGCUGAGCUCCAAAUUCAUUCCCAGCUUUGAGUCUCUGGACAUUCCCUCCACCAGCGCAGCUGCGGCGGCAGCGGCCGUUGCCGCCAGCAAUGCU---CCAAG
....((((((((((..............))))....(((....)))...........))))))(((((((((((((((....))))))))).)))..)))---..... ( -37.44)
>DroWil_CAF1 2425 108 - 1
CAAUGUGCUUAGCUCCAAGUUCAUGCCGAGCUUCGAGUCGCUUGACAUUCCUUCCACAAGCGCAGCAGCUGCUGCCGCUGCUGUUGCGGCAAAUAACACAAACGCAAU
...((((.(((((((.((((((.....)))))).)))).(((((............)))))((((((((.((....)).))))))))......)))))))........ ( -35.30)
>DroAna_CAF1 2830 105 - 1
CAACGUGCUCAGCUCCAAGUUCAUUCCCACCUUUGAAUCCCUGGACCUGCCCUCCACCAGUGCCGCAGCAGCUGCUGUCGCCGUGGCUGCCAGUAGCUCC---GCGAG
....(..(((((.((((.(((((..........)))))...)))).))).........))..)(((.(.((((((((.(((....)).).))))))))).---))).. ( -30.60)
>DroPer_CAF1 3071 105 - 1
CAAUGUUCUCAGUUCGAAAUUCAUUCCCAGCUUCGAGUCGCUGGACAUUCCCUCCACGAGUGCCGCCGCAGCAGCAGCCGCCGUUGCGGCCAGCAACUCU---UCGAC
.............(((((........(((((........))))).............((((((.((((((((.((....)).))))))))..)).)))))---)))). ( -36.50)
>consensus
CAACGUGCUCAGCUCCAAAUUCAUUCCCAGCUUCGAGUCGCUGGACAUUCCCUCCACCAGCGCAGCAGCAGCAGCAGCCGCCGUUGCGGCCAGCAACUCU___CCAAC
....((((((((((..............))))....(((....)))...........)))))).((.(((((.((....)).))))).)).................. (-18.40 = -18.79 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:04 2006