Locus 2331

Sequence ID	2R_DroMel_CAF1
Location	8,541,386 – 8,541,525
Length	139
Max. P	0.611450

overview

Window 5

Location	8,541,386 – 8,541,485
Length	99
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	82.14
Mean single sequence MFE	-22.70
Consensus MFE	-16.06
Energy contribution	-17.12
Covariance contribution	1.06
Combinations/Pair	1.04
Mean z-score	-1.52
Structure conservation index	0.71
SVM decision value	-0.00
SVM RNA-class probability	0.533099
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8541386 99 - 20766785
UAUCAGGCGGCAAUCAAUAAAACGCAAUAAUGCGAAUUGCAUUUGUGGAGCGGAGCGUUCCGAAUGCCCCAUAAAACUGAAACGGUUGGCAAGAGAAA----A
..((.((.((((.((........((((..((((.....))))))))((((((...)))))))).))))))....(((((...))))).....))....----. ( -24.80)
>DroSec_CAF1 17021 103 - 1
UAUCAGGCGGCAAUCAAUAAAACGCAAUAAUGCGAAUUGCAUUUGUGGAGCGGAGCGGGCCGAACGCCCCAUAAAACUGAAACGGUUGGCAAGAAAAAAAAAA
........(.(((((.......((((....)))).......(((((((.(((...((...))..))).)))))))........))))).)............. ( -23.90)
>DroSim_CAF1 20593 103 - 1
UAUCAGGCGGCAAUCAAUAAAACGCAAUAAUGCGAAUUGCAUUUGUGGAGCGGAGCGGGCCAAACGCCCCAUAAAACUGAAACGGUUGGCAAAAAGAAAAAAA
........(.(((((.......((((....)))).......(((((((.(((............))).)))))))........))))).)............. ( -23.00)
>DroEre_CAF1 6476 78 - 1
UAUCAGGCGGCAAUCAAUAAUACGCAAUAAUGCGAAUUGCAUUUGUGGAGCGGAGCGGGCCGAACGGUCCAUAAA-------------------------AAA
..((...(.((((....((((.((((....)))).))))...)))).)....))..(((((....))))).....-------------------------... ( -19.10)
>consensus
UAUCAGGCGGCAAUCAAUAAAACGCAAUAAUGCGAAUUGCAUUUGUGGAGCGGAGCGGGCCGAACGCCCCAUAAAACUGAAACGGUUGGCAAGAAAAA__AAA
..((((...(((((........((((....)))).))))).(((((((.(((............))).))))))).))))....................... (-16.06 = -17.12 +   1.06)

alignment

secondary structure

dotplot

Window 6

Location	8,541,405 – 8,541,525
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.36
Mean single sequence MFE	-29.52
Consensus MFE	-22.14
Energy contribution	-22.50
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-1.64
Structure conservation index	0.75
SVM decision value	0.16
SVM RNA-class probability	0.611450
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8541405 120 + 20766785
UCAGUUUUAUGGGGCAUUCGGAACGCUCCGCUCCACAAAUGCAAUUCGCAUUAUUGCGUUUUAUUGAUUGCCGCCUGAUAAUUUCCACAAUCACAAUCGGCAGUCUGUUGACACUCUGAU
((((.....((((((....(((....))))))))).(((((((((.......)))))))))....((((((((..((((..........))))....))))))))..........)))). ( -31.70)
>DroSec_CAF1 17044 120 + 1
UCAGUUUUAUGGGGCGUUCGGCCCGCUCCGCUCCACAAAUGCAAUUCGCAUUAUUGCGUUUUAUUGAUUGCCGCCUGAUAUUUUCCACAAUCACAAUCGGCAGUCUGUUGACACUCUGAU
((((......((((((.......))))))(.((.(((((((((((.......)))))))))....((((((((..((((..........))))....)))))))).)).)))...)))). ( -32.90)
>DroSim_CAF1 20616 120 + 1
UCAGUUUUAUGGGGCGUUUGGCCCGCUCCGCUCCACAAAUGCAAUUCGCAUUAUUGCGUUUUAUUGAUUGCCGCCUGAUAAUUUCCACAAUCACAAUCGGCAGUCUGUUGACACUCUGAU
((((......((((((.......))))))(.((.(((((((((((.......)))))))))....((((((((..((((..........))))....)))))))).)).)))...)))). ( -32.90)
>DroEre_CAF1 6479 109 + 1
-----UUUAUGGACCGUUCGGCCCGCUCCGCUCCACAAAUGCAAUUCGCAUUAUUGCGUAUUAUUGAUUGCCGCCUGAUAAUUUCCAC------AAUCGGCAGUCUGUUGACACUCUGAU
-----.....((.((....)).)).....(.((.(((.(((((((.......)))))))......((((((((..((..........)------)..))))))))))).)))........ ( -23.50)
>DroYak_CAF1 20246 105 + 1
UCAGUUUUAUGGACCGUU---------UCGCUCCACAAAUGCAAUUCGCAUUAUUGGGUAUUAUUGAUUGCCGACUGAUAAUUUCCAC------AAUCGGCAGUCUGUUGACACUCUGAU
.........((((.((..---------.)).))))..(((((.....)))))...((((.(((..(((((((((.((..........)------).)))))))))...))).)))).... ( -26.60)
>consensus
UCAGUUUUAUGGGGCGUUCGGCCCGCUCCGCUCCACAAAUGCAAUUCGCAUUAUUGCGUUUUAUUGAUUGCCGCCUGAUAAUUUCCACAAUCACAAUCGGCAGUCUGUUGACACUCUGAU
.........(((((((............)))))))..(((((.....))))).....((.(((..((((((((........................))))))))...))).))...... (-22.14 = -22.50 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:09 2006