Locus 3368

Sequence ID	3R_DroMel_CAF1
Location	9,099,360 – 9,099,498
Length	138
Max. P	0.595185

overview

Window 7

Location	9,099,360 – 9,099,458
Length	98
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.65
Mean single sequence MFE	-31.03
Consensus MFE	-20.01
Energy contribution	-21.38
Covariance contribution	1.38
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	0.64
SVM decision value	-0.01
SVM RNA-class probability	0.530408
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9099360 98 + 27905053
---CCCUCCAUCCAACGAAAAGCUCACGAAAACGGUCGAAAUGCGAACGAGUUUUGGCCGCUUAUCAA--------UAGCUUUUGCCUUUGGCCUGAGAACUCGUUU-----------GA
---.......((.(((((....((((.(....((((((((((.(....).))))))))))....((((--------..((....))..))))).))))...))))).-----------)) ( -24.50)
>DroSec_CAF1 9066 104 + 1
---CCCUCCAUCCAACGAAAAGCUCACGAAAACGGUCGAAAUGCGAACGAGUUUUGGCCGCUUAUCAAUAGCAA--UAGCUUUUGCCUUUGGCCUGAGAACUCGUUU-----------GA
---.......................(((......))).....(((((((((((((((((.....(((.(((..--..))).)))....)))))..)))))))))))-----------). ( -27.70)
>DroSim_CAF1 10228 104 + 1
---CCCUCCAUCCAACGAAAAGCUCACGAAAACGGUCGAAAUGCGAACGAGUUUUGGCCGCUUAUCAAUAGCAA--UAGCUUUUGCCUUUGGCCUGAGAACUCGUUU-----------GA
---.......................(((......))).....(((((((((((((((((.....(((.(((..--..))).)))....)))))..)))))))))))-----------). ( -27.70)
>DroEre_CAF1 9992 107 + 1
----CCGCCA-CCAACGAAAAGCUCACGAAAACGGUCGAAAUGCGAACGAGUUUUGGCCGCUUAUCAAUAGCUU--UUG------ACUUUGGCCUGAGAACUCGUUUGCUUUGCGCCUGA
----......-.....................(((.((....((((((((((((((((((....((((......--)))------)...)))))..)))))))))))))....)).))). ( -32.80)
>DroYak_CAF1 9323 114 + 1
---CCCGCCA-CCAACGAAAAGCUCACGAAAACGGUCGAAAUGCGAACGAGUUUUGGCCGCUUAUCAAUAGCUU--UUGCUAUUGCUUUUGGCCUGAGAACUCGUUUGCUUUGCGCCUGA
---.......-.....................(((.((....((((((((((((((((((.....(((((((..--..)))))))....)))))..)))))))))))))....)).))). ( -39.50)
>DroAna_CAF1 12569 115 + 1
UGGCUCUACAUCCCCC----ACCUCGUGC-AACGGUCCAAAUCCGAACGAGUUUUGGCCGCUUAUCAAUAGCGAUAUAGCCGUUGCCUUUGGCCCGAGAACUCGUUUGCUUGGCGGCUGA
.((((.((......((----(.(((((..-..(((.......))).)))))...))).((((.......)))).)).))))((((((...(((.(((....)))...))).))))))... ( -34.00)
>consensus
___CCCUCCAUCCAACGAAAAGCUCACGAAAACGGUCGAAAUGCGAACGAGUUUUGGCCGCUUAUCAAUAGCAA__UAGCUUUUGCCUUUGGCCUGAGAACUCGUUU___________GA
.....................((...(((......)))....))((((((((((((((((((.......)))......((....))....))))..)))))))))))............. (-20.01 = -21.38 +   1.38)

alignment

secondary structure

dotplot

Window 8

Location	9,099,397 – 9,099,498
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	86.15
Mean single sequence MFE	-34.92
Consensus MFE	-26.39
Energy contribution	-27.27
Covariance contribution	0.88
Combinations/Pair	1.00
Mean z-score	-2.38
Structure conservation index	0.76
SVM decision value	0.12
SVM RNA-class probability	0.595185
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9099397 101 + 27905053
AUGCGAACGAGUUUUGGCCGCUUAUCAA--------UAGCUUUUGCCUUUGGCCUGAGAACUCGUUU-----------GACUUUGGGCCCUGUUACAAUUUGCGUUUGCCUGCUUAGCAU
((((((((((((((((((((.....(((--------......)))....)))))..)))))))))))-----------......((((..(((........)))...)))).....)))) ( -28.70)
>DroSec_CAF1 9103 107 + 1
AUGCGAACGAGUUUUGGCCGCUUAUCAAUAGCAA--UAGCUUUUGCCUUUGGCCUGAGAACUCGUUU-----------GACUUUGGGCCCUGUUACAAUUUGCGUUUGCCUGCUUAGCAU
((((((((((((((((((((.....(((.(((..--..))).)))....)))))..)))))))))))-----------......((((..(((........)))...)))).....)))) ( -32.90)
>DroSim_CAF1 10265 107 + 1
AUGCGAACGAGUUUUGGCCGCUUAUCAAUAGCAA--UAGCUUUUGCCUUUGGCCUGAGAACUCGUUU-----------GACUUUGGGCCCUGUUACAAUUUGCGUUUGCCUGCUUAGCAU
((((((((((((((((((((.....(((.(((..--..))).)))....)))))..)))))))))))-----------......((((..(((........)))...)))).....)))) ( -32.90)
>DroEre_CAF1 10027 112 + 1
AUGCGAACGAGUUUUGGCCGCUUAUCAAUAGCUU--UUG------ACUUUGGCCUGAGAACUCGUUUGCUUUGCGCCUGACUUUGGGCCCUGUUACAAUUUGCCUUUGCCUGCUUAGCAU
..((((((((((((((((((....((((......--)))------)...)))))..)))))))))))))..(((((((......)))).............((........))...))). ( -35.50)
>DroYak_CAF1 9359 118 + 1
AUGCGAACGAGUUUUGGCCGCUUAUCAAUAGCUU--UUGCUAUUGCUUUUGGCCUGAGAACUCGUUUGCUUUGCGCCUGACUUUGGGCCCUGUUACAAUUUGCCUUUGCCUGCUUAGCAU
..((((((((((((((((((.....(((((((..--..)))))))....)))))..)))))))))))))..(((((((......)))).............((........))...))). ( -42.20)
>DroAna_CAF1 12604 120 + 1
AUCCGAACGAGUUUUGGCCGCUUAUCAAUAGCGAUAUAGCCGUUGCCUUUGGCCCGAGAACUCGUUUGCUUGGCGGCUGACUUUGGGCCCUGUUACAAUUUGCUUUUGCCUGCUUUGCAU
....((((((((((((((((.....(((..((......))..)))....)))))..)))))))))))((..(((((((.......))))............((....))..)))..)).. ( -37.30)
>consensus
AUGCGAACGAGUUUUGGCCGCUUAUCAAUAGCAA__UAGCUUUUGCCUUUGGCCUGAGAACUCGUUU___________GACUUUGGGCCCUGUUACAAUUUGCGUUUGCCUGCUUAGCAU
((((((((((((((((((((((.......)))......((....))....))))..))))))))))).................((((...((........))....)))).....)))) (-26.39 = -27.27 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:23 2006