Locus 5721

Sequence ID	2R_DroMel_CAF1
Location	18,124,185 – 18,124,295
Length	110
Max. P	0.996019

overview

Window 1

Location	18,124,185 – 18,124,295
Length	110
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	86.49
Mean single sequence MFE	-23.56
Consensus MFE	-15.44
Energy contribution	-15.52
Covariance contribution	0.08
Combinations/Pair	1.22
Mean z-score	-3.10
Structure conservation index	0.66
SVM decision value	1.19
SVM RNA-class probability	0.927879
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18124185 110 + 20766785
UCCCCCAACUCUUCACUGCACUCCUUUCAUCAGCGACCUUCCCCACAUCUUCUGU-UCCCAGCAUACCUGUGGAAAAUCUCGCCGAAAUUGGAGUCAAGUGUUUUCCCUUA
.............((((..(((((.....((.((((..((..(((((....(((.-...)))......)))))..))..)))).))....)))))..)))).......... ( -24.10)
>DroSec_CAF1 8023 110 + 1
UCCCCCAUCCCUUCCCAACCAUUCCUUCAUCAGCGACCUUCCCCACAUCUUCUGU-UCCCAGCAUAGCUGUGGAAAAUCUCGCCGAAAUUGGAGUCAAGUGUUUUCCCUUA
...............((...(((((....((.((((..((..(((((.((.(((.-...)))...)).)))))..))..)))).))....)))))....)).......... ( -20.50)
>DroSim_CAF1 8065 110 + 1
UCCUCCAUCCCUUCCCUGCACUCCUUUCAUCAGCGACCUUCCCCACAUCUUCUGU-UCCCAGCAUAGCUGUGGAAAAUCUCGCCGAAAUUGGAGUCAAGUGUUUUCCCUUA
................((.(((((.....((.((((..((..(((((.((.(((.-...)))...)).)))))..))..)))).))....))))))).............. ( -23.30)
>DroEre_CAF1 8735 96 + 1
UCACCC-------------GCUCCUUUCAUCAGCGAGUUUCCUC-CAUCCUCUGC-UCCCAGCAUAGCUGUGGAAAAUCUCGCCGAAAUUGGAGUCAAGUGUUUUCCCUUA
.(((..-------------(((((.....((.(((((.....((-(((.((.(((-.....))).))..)))))....))))).))....)))))...))).......... ( -27.00)
>DroYak_CAF1 8236 110 + 1
UCCCCCCUCCCCAUCCUGCACUCCUUUCAUCAGCGAUCUUCCUC-CAUCCUCUGCAUCCCAGCAUAGCUGUGGAAAAUCUCGCCGAAAUUGGAGUCAAGUGUUUUCCCUUA
...........(((..((.(((((.....((.((((..((..((-(((.((.(((......))).))..))))).))..)))).))....))))))).))).......... ( -22.90)
>consensus
UCCCCCAUCCCUUCCCUGCACUCCUUUCAUCAGCGACCUUCCCCACAUCUUCUGU_UCCCAGCAUAGCUGUGGAAAAUCUCGCCGAAAUUGGAGUCAAGUGUUUUCCCUUA
...................(((((.....((.((((..((..(((((..((.(((......))).)).)))))..))..)))).))....)))))................ (-15.44 = -15.52 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	18,124,185 – 18,124,295
Length	110
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	86.49
Mean single sequence MFE	-37.82
Consensus MFE	-26.76
Energy contribution	-28.32
Covariance contribution	1.56
Combinations/Pair	1.03
Mean z-score	-4.46
Structure conservation index	0.71
SVM decision value	2.64
SVM RNA-class probability	0.996019
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18124185 110 - 20766785
UAAGGGAAAACACUUGACUCCAAUUUCGGCGAGAUUUUCCACAGGUAUGCUGGGA-ACAGAAGAUGUGGGGAAGGUCGCUGAUGAAAGGAGUGCAGUGAAGAGUUGGGGGA
..........((((..(((((....(((((((..((..(((((......(((...-.)))....)))))..))..))))))).....)))))..))))............. ( -40.30)
>DroSec_CAF1 8023 110 - 1
UAAGGGAAAACACUUGACUCCAAUUUCGGCGAGAUUUUCCACAGCUAUGCUGGGA-ACAGAAGAUGUGGGGAAGGUCGCUGAUGAAGGAAUGGUUGGGAAGGGAUGGGGGA
............((..(((((....(((((((..((..(((((.((...(((...-.))).)).)))))..))..)))))))....)))...))..))............. ( -37.10)
>DroSim_CAF1 8065 110 - 1
UAAGGGAAAACACUUGACUCCAAUUUCGGCGAGAUUUUCCACAGCUAUGCUGGGA-ACAGAAGAUGUGGGGAAGGUCGCUGAUGAAAGGAGUGCAGGGAAGGGAUGGAGGA
............(((((((((....(((((((..((..(((((.((...(((...-.))).)).)))))..))..))))))).....))))).)))).............. ( -40.90)
>DroEre_CAF1 8735 96 - 1
UAAGGGAAAACACUUGACUCCAAUUUCGGCGAGAUUUUCCACAGCUAUGCUGGGA-GCAGAGGAUG-GAGGAAACUCGCUGAUGAAAGGAGC-------------GGGUGA
..........((((((.((((....((((((((.(((((..((.((.(((.....-))).))..))-..))))))))))))).....)))))-------------))))). ( -36.80)
>DroYak_CAF1 8236 110 - 1
UAAGGGAAAACACUUGACUCCAAUUUCGGCGAGAUUUUCCACAGCUAUGCUGGGAUGCAGAGGAUG-GAGGAAGAUCGCUGAUGAAAGGAGUGCAGGAUGGGGAGGGGGGA
..........(((((((((((....(((((((..(((((((...((.(((......))).))..))-)))))...))))))).....))))).)))).))........... ( -34.00)
>consensus
UAAGGGAAAACACUUGACUCCAAUUUCGGCGAGAUUUUCCACAGCUAUGCUGGGA_ACAGAAGAUGUGGGGAAGGUCGCUGAUGAAAGGAGUGCAGGGAAGGGAUGGGGGA
((((........))))(((((....(((((((..(((((((((.((...(((.....))).)).)))))))))..))))))).....)))))................... (-26.76 = -28.32 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:41 2006