Locus 2105

Sequence ID	3L_DroMel_CAF1
Location	5,768,828 – 5,769,062
Length	234
Max. P	0.968796

overview

Window 5

Location	5,768,828 – 5,768,942
Length	114
Sequences	3
Columns	114
Reading direction	reverse
Mean pairwise identity	98.25
Mean single sequence MFE	-38.27
Consensus MFE	-38.15
Energy contribution	-37.93
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.39
Structure conservation index	1.00
SVM decision value	1.63
SVM RNA-class probability	0.968796
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5768828 114 - 23771897
ACCAACGAGGCCUUUGAGCGAAGGAUCUCGGAGACGAAGCACGUGAAACAGUGUUUGGAGAACAAGCACAAGGACACCAUGGAUCACAUCCAUCAGGUGCAGCGCAACAUGACC
.....((((((((((....))))).)))))..(.((..((((.(((....(((((((.....)))))))..........(((((...)))))))).))))..)))......... ( -37.00)
>DroSec_CAF1 11427 114 - 1
ACCAACGAGGCCUUCGAGCGAAGGAUCUCGGAGACGAAGCACGUGAAGCAGUGUUUGGAGAACAAGCACAAGGACACCAUGGACCACAUCCAUCAGGUGCAGCGCAACAUGACC
.....((((((((((....))))).)))))...........((((..((.(((((((.....)))))))...(.(((((((((.....)))))..)))))...))..))))... ( -38.90)
>DroSim_CAF1 11298 114 - 1
ACCAACGAGGCCUUCGAGCGAAGGAUCUCGGAGACGAAGCACGUGAAGCAGUGUUUGGAGAACAAGCACAAGGACACCAUGGACCACAUCCAUCAGGUGCAGCGCAACAUGACC
.....((((((((((....))))).)))))...........((((..((.(((((((.....)))))))...(.(((((((((.....)))))..)))))...))..))))... ( -38.90)
>consensus
ACCAACGAGGCCUUCGAGCGAAGGAUCUCGGAGACGAAGCACGUGAAGCAGUGUUUGGAGAACAAGCACAAGGACACCAUGGACCACAUCCAUCAGGUGCAGCGCAACAUGACC
.....((((((((((....))))).)))))..(.((..((((.(((....(((((((.....)))))))..........((((.....))))))).))))..)))......... (-38.15 = -37.93 +  -0.22)

alignment

secondary structure

dotplot

Window 6

Location	5,768,942 – 5,769,062
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.06
Mean single sequence MFE	-46.50
Consensus MFE	-43.91
Energy contribution	-44.47
Covariance contribution	0.56
Combinations/Pair	1.02
Mean z-score	-1.53
Structure conservation index	0.94
SVM decision value	-0.04
SVM RNA-class probability	0.514490
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5768942 120 + 23771897
CCUGUCCGUCUGGUUCUGCAUAUCCUCGCACACCUGCUUCAGCAGCAAAUCGAUGUAGGCCCGCAGCUGCCCGGCGGACACCAGCGCCUUGGCGUUGGCCUCCAGAUUCUCGUACGUCUG
..((((((((.(((.((((....(((((.....((((....)))).....)))....))...))))..))).))))))))(((((((....)))))))....(((((........))))) ( -45.20)
>DroSec_CAF1 11541 120 + 1
CCUGUCCGUCUGGUUCUGCAUGUCCUCGCACACCUGCUUCAGCAGCAGAUCGAUGUAGGCCCGCAGCUGGCCGGCGGACACCAGCGCCUUGGCGUUGGCCUCCAGAUUCUCGUACGUCUG
..((((((.((((((((((..(.(((.((((..(((((.....)))))...).)))))))..))))..))))))))))))(((((((....)))))))....(((((........))))) ( -46.90)
>DroSim_CAF1 11412 120 + 1
CCUGUCCGUCUGGUUCUGCAUGUCCUCGCACACCUGCUUCAGCAGCAGAUCGAUGUAGGCCCGCAGCUGACCGGCGGACACCAGCGCCUUGGCGUUGGCCUCCAGAUUCUCGUACGUCUG
..((((((.((((((((((..(.(((.((((..(((((.....)))))...).)))))))..))))..))))))))))))(((((((....)))))))....(((((........))))) ( -47.40)
>consensus
CCUGUCCGUCUGGUUCUGCAUGUCCUCGCACACCUGCUUCAGCAGCAGAUCGAUGUAGGCCCGCAGCUGACCGGCGGACACCAGCGCCUUGGCGUUGGCCUCCAGAUUCUCGUACGUCUG
..((((((.((((((((((....(((.((((..(((((.....)))))...).))))))...))))..))))))))))))(((((((....)))))))....(((((........))))) (-43.91 = -44.47 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:29 2006