Locus 4833

Sequence ID	3R_DroMel_CAF1
Location	12,645,435 – 12,645,529
Length	94
Max. P	0.998360

overview

Window 1

Location	12,645,435 – 12,645,529
Length	94
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	96.07
Mean single sequence MFE	-42.50
Consensus MFE	-39.12
Energy contribution	-38.96
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.11
Structure conservation index	0.92
SVM decision value	3.08
SVM RNA-class probability	0.998360
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12645435 94 + 27905053
AAGUGGGUGGGGGGUGCUGAGGGAUCUUAACCCCAGUGCGGGAUCAACGAUUAUCUGCCAGA-GGCGGAUCUUCGCGCCCCCAGAAUC-----CCCUGCC
.....((..(((((..(((.(((.......))))))..)(((.....(((..(((((((...-)))))))..)))....))).....)-----)))..)) ( -43.60)
>DroSec_CAF1 21917 94 + 1
AAGUGGGUGGGGGGUGCUGAGGGAUCUUAACCCCAGUGCGGGAUCAACGAUUAUCUGCGAGA-GGCGGAUCUUCGCGCCCCCAGAAUC-----CCCUGCC
.....((..(((((..(((.(((.......))))))..)(((.....(((..((((((....-.))))))..)))....))).....)-----)))..)) ( -42.00)
>DroSim_CAF1 19880 94 + 1
AAGUGGGUGGGGGGUGCUGAGGGAUCUUAACCCCAGUGCGGGAUCAACGAUUAUCUGCGAGA-GGCGGAUCUUCGCGCCCCCAGAAUC-----CCCUGCC
.....((..(((((..(((.(((.......))))))..)(((.....(((..((((((....-.))))))..)))....))).....)-----)))..)) ( -42.00)
>DroEre_CAF1 25203 95 + 1
AAGUGGGUGGGGGGUGCUGAGGGAUCUUAACCCCAGUGCGGGAUCAACGAUUAUCUGCGAGAUGGCGGAUCUUCGCGCCCCCAGAAUC-----CCCUGCC
.....((..(((((..(((.(((.......))))))..)(((.....(((..((((((......))))))..)))....))).....)-----)))..)) ( -42.20)
>DroYak_CAF1 13714 100 + 1
AAGUGGGUGGGGGGUGCUGAGGGAUCUUAACCCCGGUGCGGGAUCAACGAUUAUCUGCGAGAUGGCGGAUCUUCGCGCCCCCAGAAUGACGCGCCCUGCC
....(((((((((((((.((((((((((.((....))..)))))).......((((((......)))))))))))))))))).(.....).))))).... ( -42.70)
>consensus
AAGUGGGUGGGGGGUGCUGAGGGAUCUUAACCCCAGUGCGGGAUCAACGAUUAUCUGCGAGA_GGCGGAUCUUCGCGCCCCCAGAAUC_____CCCUGCC
.....((..(((.(..(((.(((.......))))))..)(((.....(((..((((((......))))))..)))....)))...........)))..)) (-39.12 = -38.96 +  -0.16)

alignment

secondary structure

dotplot

Window 2

Location	12,645,435 – 12,645,529
Length	94
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	96.07
Mean single sequence MFE	-37.08
Consensus MFE	-31.55
Energy contribution	-31.55
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.75
Structure conservation index	0.85
SVM decision value	1.12
SVM RNA-class probability	0.917756
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12645435 94 - 27905053
GGCAGGG-----GAUUCUGGGGGCGCGAAGAUCCGCC-UCUGGCAGAUAAUCGUUGAUCCCGCACUGGGGUUAAGAUCCCUCAGCACCCCCCACCCACUU
((..(((-----(...(((((((.((((..(((.(((-...))).)))..))))(((((((.....)))))))....)))))))...))))..))..... ( -38.70)
>DroSec_CAF1 21917 94 - 1
GGCAGGG-----GAUUCUGGGGGCGCGAAGAUCCGCC-UCUCGCAGAUAAUCGUUGAUCCCGCACUGGGGUUAAGAUCCCUCAGCACCCCCCACCCACUU
((..(((-----(...(((((((.((((.((......-)))))).....(((.((((((((.....))))))))))))))))))...))))..))..... ( -37.00)
>DroSim_CAF1 19880 94 - 1
GGCAGGG-----GAUUCUGGGGGCGCGAAGAUCCGCC-UCUCGCAGAUAAUCGUUGAUCCCGCACUGGGGUUAAGAUCCCUCAGCACCCCCCACCCACUU
((..(((-----(...(((((((.((((.((......-)))))).....(((.((((((((.....))))))))))))))))))...))))..))..... ( -37.00)
>DroEre_CAF1 25203 95 - 1
GGCAGGG-----GAUUCUGGGGGCGCGAAGAUCCGCCAUCUCGCAGAUAAUCGUUGAUCCCGCACUGGGGUUAAGAUCCCUCAGCACCCCCCACCCACUU
((..(((-----(...(((((((.((((.(((.....))))))).....(((.((((((((.....))))))))))))))))))...))))..))..... ( -37.70)
>DroYak_CAF1 13714 100 - 1
GGCAGGGCGCGUCAUUCUGGGGGCGCGAAGAUCCGCCAUCUCGCAGAUAAUCGUUGAUCCCGCACCGGGGUUAAGAUCCCUCAGCACCCCCCACCCACUU
((..(((.(.((....(((((((.((((.(((.....))))))).....(((.(((((((((...))))))))))))))))))).)).))))..)).... ( -35.00)
>consensus
GGCAGGG_____GAUUCUGGGGGCGCGAAGAUCCGCC_UCUCGCAGAUAAUCGUUGAUCCCGCACUGGGGUUAAGAUCCCUCAGCACCCCCCACCCACUU
....(((.........(((((((.((((..(((.((......)).)))..))))(((((((.....)))))))....))))))).........))).... (-31.55 = -31.55 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:59 2006