Locus 227

Sequence ID	3R_DroMel_CAF1
Location	910,718 – 910,811
Length	93
Max. P	0.979143

overview

Window 8

Location	910,718 – 910,811
Length	93
Sequences	3
Columns	108
Reading direction	forward
Mean pairwise identity	82.52
Mean single sequence MFE	-54.13
Consensus MFE	-45.24
Energy contribution	-45.13
Covariance contribution	-0.11
Combinations/Pair	1.07
Mean z-score	-2.58
Structure conservation index	0.84
SVM decision value	1.83
SVM RNA-class probability	0.979143
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 910718 93 + 27905053
AG---CCAGUUGAUCCCACUGGCCGGCGGCUGCGGCGGCUAUCGAGGCCUGGGCCGCAGCUGCCGCCGCUGAGUUGGCUGCAUGGCUCUGG------------CUCUG
((---((((...........((((((((((((((((((((.....))))...))))))))))))((.(((.....))).))..))))))))------------))... ( -51.40)
>DroSim_CAF1 4907 87 + 1
AG---CCAGCUGAUCCCACUGGCCGGCGGCUGCGGCGGCUAUCGAGGCCUGUGCCGCAGCUGCUGCCGCUGAGUGGGCUGCAUGGCUCC------------------G
((---(((((....((((((((((((((((((((((((((.....))))...)))))))))))))..))).))))))..)).)))))..------------------. ( -53.80)
>DroYak_CAF1 12751 108 + 1
AGCCGCCAGCUGAUCCCACUGGCCGGCGGCUGCGGCGGCUAUCGAGGCCUGGGCCGCAGCAGCCGCCGCUGAGUUGGCUGCAUGGCUCUGGCUCUGACUCUGGCUCUG
(((((((.(((.........))).)))))))(((((((((.....(((....))).....))))))))).((((..(...((.(((....))).))...)..)))).. ( -57.20)
>consensus
AG___CCAGCUGAUCCCACUGGCCGGCGGCUGCGGCGGCUAUCGAGGCCUGGGCCGCAGCUGCCGCCGCUGAGUUGGCUGCAUGGCUCUGG____________CUCUG
......((((..((..((.((((.((((((((((((((((.....))))...)))))))))))))))).)).))..))))............................ (-45.24 = -45.13 +  -0.11)

alignment

secondary structure

dotplot

Window 9

Location	910,718 – 910,811
Length	93
Sequences	3
Columns	108
Reading direction	reverse
Mean pairwise identity	82.52
Mean single sequence MFE	-48.47
Consensus MFE	-37.65
Energy contribution	-37.77
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-2.15
Structure conservation index	0.78
SVM decision value	0.97
SVM RNA-class probability	0.892280
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 910718 93 - 27905053
CAGAG------------CCAGAGCCAUGCAGCCAACUCAGCGGCGGCAGCUGCGGCCCAGGCCUCGAUAGCCGCCGCAGCCGCCGGCCAGUGGGAUCAACUGG---CU
...((------------((((.((......))...((((..((((((.((((((((...(((.......))))))))))).))).)))..)))).....))))---)) ( -45.80)
>DroSim_CAF1 4907 87 - 1
C------------------GGAGCCAUGCAGCCCACUCAGCGGCAGCAGCUGCGGCACAGGCCUCGAUAGCCGCCGCAGCCGCCGGCCAGUGGGAUCAGCUGG---CU
.------------------..(((((.((..((((((....(((.((.((((((((...(((.......))))))))))).))..)))))))))....)))))---)) ( -46.30)
>DroYak_CAF1 12751 108 - 1
CAGAGCCAGAGUCAGAGCCAGAGCCAUGCAGCCAACUCAGCGGCGGCUGCUGCGGCCCAGGCCUCGAUAGCCGCCGCAGCCGCCGGCCAGUGGGAUCAGCUGGCGGCU
...((((.((((..(...((......))...)..))))..((((((((((.(((((.............))))).))))))))))((((((.......)))))))))) ( -53.32)
>consensus
CAGAG____________CCAGAGCCAUGCAGCCAACUCAGCGGCGGCAGCUGCGGCCCAGGCCUCGAUAGCCGCCGCAGCCGCCGGCCAGUGGGAUCAGCUGG___CU
......................(((.....(((........)))(((.((((((((...(((.......))))))))))).))))))((((.......))))...... (-37.65 = -37.77 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:11 2006