Locus 8532

Sequence ID	3L_DroMel_CAF1
Location	22,315,380 – 22,315,496
Length	116
Max. P	0.986221

overview

Window 1

Location	22,315,380 – 22,315,496
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.34
Mean single sequence MFE	-31.50
Consensus MFE	-27.85
Energy contribution	-27.72
Covariance contribution	-0.13
Combinations/Pair	1.07
Mean z-score	-1.85
Structure conservation index	0.88
SVM decision value	0.57
SVM RNA-class probability	0.786765
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22315380 116 + 23771897
GACGACAACAAUAUUAAAUUGUCAUGCCGAGCUUCAGCUGC----UUCCUCAGCUUCUUGCUCAGCCACAGGUCAUUAGACCCACGGGCAUCUAAAUUGCAUUAUCAACGCCAAUAACGG
...(((((..........)))))((((.((((...(((((.----.....)))))....)))).(((...((((....))))....))).........)))).................. ( -28.70)
>DroSec_CAF1 74069 116 + 1
GACGACAACAAUAUUAAAUUGUCAUGCCGAGCUUCAGCUGC----UUCCUCAGCUUCUGGCUCGGCCACAGGUCAUUAGACCCACGGGCAUCUAAAUUGCAUUAUCAACGCCAAUAACGG
((((((((..........)))))..((((((((..(((((.----.....)))))...)))))))).....))).(((((((....))..)))))......................... ( -32.90)
>DroEre_CAF1 72421 120 + 1
GACGACAGCAAUAUUAAAUUGUCAUGCCGAGCUUCAGCUGCUGGCUGCCUCAGCUUCUUGCUCGGCCACAGGUCAUUAGACCCACGGGCAUCUAAAUUGCAUUAUCAACGUUAAUAACGG
.......(((((.(((...((((..(((((((...(((((..((...)).)))))....)))))))....((((....))))....))))..))))))))........(((.....))). ( -35.70)
>DroYak_CAF1 52531 116 + 1
GACGACAACAAUAUUAAAUUGUCAUGCCGAGCUUCAGCUGC----UUCCUCAGCUUCUUGUUCGGCCACAGGUCAUUAGACCCACGGGCAUCUAAAUUGCAUUAUCAACGCCAAUAACGG
((((((((..........)))))..(((((((...(((((.----.....)))))....))))))).....))).(((((((....))..)))))......................... ( -28.70)
>consensus
GACGACAACAAUAUUAAAUUGUCAUGCCGAGCUUCAGCUGC____UUCCUCAGCUUCUUGCUCGGCCACAGGUCAUUAGACCCACGGGCAUCUAAAUUGCAUUAUCAACGCCAAUAACGG
((((((((..........)))))..(((((((...(((((..........)))))....))))))).....))).(((((((....))..)))))......................... (-27.85 = -27.72 +  -0.13)

alignment

secondary structure

dotplot

Window 2

Location	22,315,380 – 22,315,496
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.34
Mean single sequence MFE	-41.90
Consensus MFE	-38.74
Energy contribution	-39.05
Covariance contribution	0.31
Combinations/Pair	1.03
Mean z-score	-2.87
Structure conservation index	0.92
SVM decision value	2.03
SVM RNA-class probability	0.986221
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22315380 116 - 23771897
CCGUUAUUGGCGUUGAUAAUGCAAUUUAGAUGCCCGUGGGUCUAAUGACCUGUGGCUGAGCAAGAAGCUGAGGAA----GCAGCUGAAGCUCGGCAUGACAAUUUAAUAUUGUUGUCGUC
........((((((..(((......)))))))))((..((((....))))..))(((((((....(((((.....----.)))))...)))))))((((((((........)))))))). ( -42.80)
>DroSec_CAF1 74069 116 - 1
CCGUUAUUGGCGUUGAUAAUGCAAUUUAGAUGCCCGUGGGUCUAAUGACCUGUGGCCGAGCCAGAAGCUGAGGAA----GCAGCUGAAGCUCGGCAUGACAAUUUAAUAUUGUUGUCGUC
........((((((..(((......)))))))))((..((((....))))..))(((((((....(((((.....----.)))))...)))))))((((((((........)))))))). ( -45.00)
>DroEre_CAF1 72421 120 - 1
CCGUUAUUAACGUUGAUAAUGCAAUUUAGAUGCCCGUGGGUCUAAUGACCUGUGGCCGAGCAAGAAGCUGAGGCAGCCAGCAGCUGAAGCUCGGCAUGACAAUUUAAUAUUGCUGUCGUC
..(((((((....)))))))(((((((((((...((..((((....))))..))(((((((....(((((..(....)..)))))...)))))))......)))))).)))))....... ( -41.40)
>DroYak_CAF1 52531 116 - 1
CCGUUAUUGGCGUUGAUAAUGCAAUUUAGAUGCCCGUGGGUCUAAUGACCUGUGGCCGAACAAGAAGCUGAGGAA----GCAGCUGAAGCUCGGCAUGACAAUUUAAUAUUGUUGUCGUC
........((((((..(((......)))))))))((..((((....))))..))(((((.(....(((((.....----.)))))...).)))))((((((((........)))))))). ( -38.40)
>consensus
CCGUUAUUGGCGUUGAUAAUGCAAUUUAGAUGCCCGUGGGUCUAAUGACCUGUGGCCGAGCAAGAAGCUGAGGAA____GCAGCUGAAGCUCGGCAUGACAAUUUAAUAUUGUUGUCGUC
.(((((((......))))))).............((..((((....))))..))(((((((....(((((..........)))))...)))))))((((((((........)))))))). (-38.74 = -39.05 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:18:18 2006