Locus 6885

Sequence ID	3L_DroMel_CAF1
Location	18,558,448 – 18,558,568
Length	120
Max. P	0.959682

overview

Window 3

Location	18,558,448 – 18,558,568
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.11
Mean single sequence MFE	-48.49
Consensus MFE	-48.93
Energy contribution	-48.49
Covariance contribution	-0.44
Combinations/Pair	1.05
Mean z-score	-2.13
Structure conservation index	1.01
SVM decision value	1.50
SVM RNA-class probability	0.959682
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18558448 120 + 23771897
GAGCCGCUCUGAAAGAUCAACACCUGGUCCAUGGCGUUCACGUAGCAGGCCAGAUUGAACUCCACGGCCACGGUGUUGUUCUGGAACAUCCAGCGGAGAAGCUCGGGGAUUCCCCUCGCA
((((..(((((..(((.((((((((((.((.(((.(((((...............))))).))).))))).))))))).)))((.....))..)))))..))))((((...))))..... ( -49.36)
>DroSec_CAF1 182231 120 + 1
GAGCCGCUCUGGAAGAUCAGCACCUGGUCCAUGGCGUUCACGUAACAGGCCAGAUUGAACUCCACGGCCACGGUGUUGUUCUGGAACAUCCAGCGGAGAAGCUCGGGGAUUCCCCUCGCA
((((..(((((..(((.((((((((((.((.(((.(((((...............))))).))).))))).))))))).)))((.....))..)))))..))))((((...))))..... ( -49.56)
>DroEre_CAF1 178495 120 + 1
GAGCCGCUCUGGAAGAUCAGCACCUGGUCCAUGGCGUUCACAUAGCAGGCCAGAUUGAACUCCACGGCCACGGUGUUGUUCUGGAACAUCCAGCGGAGAAGCUCGGGGAUCCCUCUUGCA
((((..(((((..(((.((((((((((.((.(((.(((((...............))))).))).))))).))))))).)))((.....))..)))))..))))((((...))))..... ( -46.56)
>consensus
GAGCCGCUCUGGAAGAUCAGCACCUGGUCCAUGGCGUUCACGUAGCAGGCCAGAUUGAACUCCACGGCCACGGUGUUGUUCUGGAACAUCCAGCGGAGAAGCUCGGGGAUUCCCCUCGCA
((((..(((((..(((.((((((((((.((.(((.(((((...............))))).))).))))).))))))).)))((.....))..)))))..))))((((...))))..... (-48.93 = -48.49 +  -0.44)

alignment

secondary structure

dotplot

Window 4

Location	18,558,448 – 18,558,568
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.11
Mean single sequence MFE	-50.97
Consensus MFE	-48.35
Energy contribution	-48.47
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.38
Structure conservation index	0.95
SVM decision value	1.32
SVM RNA-class probability	0.941630
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18558448 120 - 23771897
UGCGAGGGGAAUCCCCGAGCUUCUCCGCUGGAUGUUCCAGAACAACACCGUGGCCGUGGAGUUCAAUCUGGCCUGCUACGUGAACGCCAUGGACCAGGUGUUGAUCUUUCAGAGCGGCUC
.....((((...))))(((((.(((..((((.....))))..(((((((.(((((((((.(((((...(((....)))..))))).)))))).))))))))))........))).))))) ( -55.70)
>DroSec_CAF1 182231 120 - 1
UGCGAGGGGAAUCCCCGAGCUUCUCCGCUGGAUGUUCCAGAACAACACCGUGGCCGUGGAGUUCAAUCUGGCCUGUUACGUGAACGCCAUGGACCAGGUGCUGAUCUUCCAGAGCGGCUC
.....((((...))))(((((.(((..((((.....))))..((.((((.(((((((((.(((((...(((....)))..))))).)))))).))))))).))........))).))))) ( -49.00)
>DroEre_CAF1 178495 120 - 1
UGCAAGAGGGAUCCCCGAGCUUCUCCGCUGGAUGUUCCAGAACAACACCGUGGCCGUGGAGUUCAAUCUGGCCUGCUAUGUGAACGCCAUGGACCAGGUGCUGAUCUUCCAGAGCGGCUC
.......(((...)))(((((.(((..((((.....))))..((.((((.(((((((((.(((((...(((....)))..))))).)))))).))))))).))........))).))))) ( -48.20)
>consensus
UGCGAGGGGAAUCCCCGAGCUUCUCCGCUGGAUGUUCCAGAACAACACCGUGGCCGUGGAGUUCAAUCUGGCCUGCUACGUGAACGCCAUGGACCAGGUGCUGAUCUUCCAGAGCGGCUC
.....((((...))))(((((.(((..((((.....))))..((.((((.(((((((((.(((((...(((....)))..))))).)))))).))))))).))........))).))))) (-48.35 = -48.47 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:09 2006