Locus 57

Sequence ID	3R_DroMel_CAF1
Location	330,492 – 330,591
Length	99
Max. P	0.990863

overview

Window 4

Location	330,492 – 330,591
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	72.30
Mean single sequence MFE	-36.20
Consensus MFE	-14.65
Energy contribution	-16.80
Covariance contribution	2.15
Combinations/Pair	1.44
Mean z-score	-2.63
Structure conservation index	0.40
SVM decision value	2.24
SVM RNA-class probability	0.990863
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 330492 99 + 27905053
UUACCCAGUAUAGCCAUGAAGCCGCAAUGCUUUCUGGCUUCUCUGGGGCAAGGGCAUUUGUCCACACUGGCACAGGCAACUCUGGCAUUGAAAUCUUGC
...(((((...(((((.(((((......))))).)))))...)))))((((((((....)))).((.((.((.((....)).)).)).)).....)))) ( -39.20)
>DroGri_CAF1 18022 98 + 1
-GGCACACCUGAUUCAUAAGGGCGCAAUCGUGGCGAGCAGCCGCUGGGCAUGGACACUUGUCAAUGCCCGCACUUGCAAUUAGUGCAUCGAAUUGCUGC
-.(((..(((........)))..(((((((((((.....))))).((((((.(((....))).))))))(((((.......)))))...).)))))))) ( -38.60)
>DroSec_CAF1 12967 99 + 1
UUACCCAGACUAGCCAUGAAGCCGCAAUGCUUUCUGGCUUCUCUUGGGCAAGGACAUUUGUCCACACUGGCACCGGCAACUCUGGCAUUGAAAUCUUGC
...((.(((..(((((.(((((......))))).)))))..))).))((((((((....)))).((.((.((..(....)..)).)).)).....)))) ( -33.20)
>DroSim_CAF1 7986 99 + 1
UUACCCAGACUAGCCAUGAAGCCGCAAUGCUUUCUGGCUUCUCUUGGGCAAGGACAUUUGUCCACACUGGCACCGGCAACUCUGGCAUUGAAAUCUUGC
...((.(((..(((((.(((((......))))).)))))..))).))((((((((....)))).((.((.((..(....)..)).)).)).....)))) ( -33.20)
>DroEre_CAF1 10808 99 + 1
GUACCCAGUUCAGCCAUGAAGCUGCAGUGCUUCCUGGCUUCUCUGGGGCAAGGACAUUUGUCCACACUGGCACCGAGAACUCGGGCAUUGAAAUCCUGC
...(((((...(((((.(((((......))))).)))))...)))))(((.((((....)))).((...((.((((....))))))..))......))) ( -41.50)
>DroPer_CAF1 8228 96 + 1
---CCCUUCUGAGCCAUAAAGUGGCAAUUUCGGCGAGCCGCCUCCGGACACGGACACUUGUCCAGGCUGGCAUUGUCUAGCCGAGCCUUGAACUGCUGC
---....((((.(((((...)))))......((((...))))..))))...((((....))))((((((((........))).)))))........... ( -31.50)
>consensus
UUACCCAGAUUAGCCAUGAAGCCGCAAUGCUUUCUGGCUUCUCUUGGGCAAGGACAUUUGUCCACACUGGCACCGGCAACUCGGGCAUUGAAAUCCUGC
...((.((...(((((.(((((......))))).)))))...)).))(((.((((....))))......((.((((....))))))..........))) (-14.65 = -16.80 +   2.15)

alignment

secondary structure

dotplot

Window 5

Location	330,492 – 330,591
Length	99
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	72.30
Mean single sequence MFE	-35.03
Consensus MFE	-15.86
Energy contribution	-17.62
Covariance contribution	1.76
Combinations/Pair	1.41
Mean z-score	-1.68
Structure conservation index	0.45
SVM decision value	-0.02
SVM RNA-class probability	0.523579
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 330492 99 - 27905053
GCAAGAUUUCAAUGCCAGAGUUGCCUGUGCCAGUGUGGACAAAUGCCCUUGCCCCAGAGAAGCCAGAAAGCAUUGCGGCUUCAUGGCUAUACUGGGUAA
(((((.........(((.(.(.((....)).).).))).........)))))(((((...(((((..((((......))))..)))))...)))))... ( -32.17)
>DroGri_CAF1 18022 98 - 1
GCAGCAAUUCGAUGCACUAAUUGCAAGUGCGGGCAUUGACAAGUGUCCAUGCCCAGCGGCUGCUCGCCACGAUUGCGCCCUUAUGAAUCAGGUGUGCC-
(((((........(((((.......)))))((((((.(((....))).))))))....)))))...........(((((((........))).)))).- ( -37.80)
>DroSec_CAF1 12967 99 - 1
GCAAGAUUUCAAUGCCAGAGUUGCCGGUGCCAGUGUGGACAAAUGUCCUUGCCCAAGAGAAGCCAGAAAGCAUUGCGGCUUCAUGGCUAGUCUGGGUAA
..............(((((.(.(((((.((......((((....))))..))))....((((((............))))))..))).).))))).... ( -32.00)
>DroSim_CAF1 7986 99 - 1
GCAAGAUUUCAAUGCCAGAGUUGCCGGUGCCAGUGUGGACAAAUGUCCUUGCCCAAGAGAAGCCAGAAAGCAUUGCGGCUUCAUGGCUAGUCUGGGUAA
..............(((((.(.(((((.((......((((....))))..))))....((((((............))))))..))).).))))).... ( -32.00)
>DroEre_CAF1 10808 99 - 1
GCAGGAUUUCAAUGCCCGAGUUCUCGGUGCCAGUGUGGACAAAUGUCCUUGCCCCAGAGAAGCCAGGAAGCACUGCAGCUUCAUGGCUGAACUGGGUAC
((((.....((..((((((....)))).))...)).((((....))))))))(((((...(((((.(((((......))))).)))))...)))))... ( -40.30)
>DroPer_CAF1 8228 96 - 1
GCAGCAGUUCAAGGCUCGGCUAGACAAUGCCAGCCUGGACAAGUGUCCGUGUCCGGAGGCGGCUCGCCGAAAUUGCCACUUUAUGGCUCAGAAGGG---
(.(((.(((((.((((.(((........))))))))))))..((.((((....)))).)).)))).((......((((.....))))......)).--- ( -35.90)
>consensus
GCAAGAUUUCAAUGCCAGAGUUGCCGGUGCCAGUGUGGACAAAUGUCCUUGCCCAAGAGAAGCCAGAAAGCAUUGCGGCUUCAUGGCUAAACUGGGUAA
(((......((((......))))....)))......((((....)))).(((((.((...(((((..((((......))))..)))))...))))))). (-15.86 = -17.62 +   1.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:38 2006