Locus 6338

Sequence ID	2L_DroMel_CAF1
Location	17,695,302 – 17,695,439
Length	137
Max. P	0.899984

overview

Window 2

Location	17,695,302 – 17,695,405
Length	103
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	98.54
Mean single sequence MFE	-27.23
Consensus MFE	-27.60
Energy contribution	-27.22
Covariance contribution	-0.38
Combinations/Pair	1.03
Mean z-score	-2.17
Structure conservation index	1.01
SVM decision value	1.01
SVM RNA-class probability	0.899984
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17695302 103 + 22407834
AUAUUUGUUGCUGACCUAGAUUUGUUGGCUGCAAAUUUACUACAUGUGAAGUGAAAUUUUUGUGGCCCAAAAUCAGACUAUGCAACCAAGUUGGGUUAUUUAA
...........((((((.(((((...(((..((((((((((.(....).))))))...))))..)))..))))).((((.((....))))))))))))..... ( -25.00)
>DroSec_CAF1 86107 103 + 1
AUAUUUGUUGCUGACCUAGAUUUGUUGGCUGCAAAUGUACUACAUGUGAAGUGCAAUUUUUGUGGCCCAAAAUCAGACUAUGCAACCAAGUUGGGUUAUUUAA
...........((((((.(((((...(((..((((((((((.(....).))))))...))))..)))..))))).((((.((....))))))))))))..... ( -27.40)
>DroSim_CAF1 68667 103 + 1
AUAUUUGUUGCUGACCUAGAUUUGUUGGCUGCAAAUGUACUACAUGUGAAGUGCAAUUUUUGUGGCCCAAAAUCAGACUAUGCAACCAAGUUGGGUUAUUUAA
...........((((((.(((((...(((..((((((((((.(....).))))))...))))..)))..))))).((((.((....))))))))))))..... ( -27.40)
>DroYak_CAF1 89898 103 + 1
AUAUUUGUUGCUGACCUAGAUUUGUUGGCUGCAAAUGUACUACAUGUGAAGUGCAAUUUUUGUGGCCCAAAAUCAGACUAUGCAAGCAAGUUGGGUUAUUUAA
...........((((((.(((((...(((..((((((((((.(....).))))))...))))..)))..))))).((((.((....))))))))))))..... ( -29.10)
>consensus
AUAUUUGUUGCUGACCUAGAUUUGUUGGCUGCAAAUGUACUACAUGUGAAGUGCAAUUUUUGUGGCCCAAAAUCAGACUAUGCAACCAAGUUGGGUUAUUUAA
...........((((((.(((((...(((..((((((((((.(....).))))))...))))..)))..))))).((((.((....))))))))))))..... (-27.60 = -27.22 +  -0.38)

alignment

secondary structure

dotplot

Window 3

Location	17,695,302 – 17,695,405
Length	103
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	98.54
Mean single sequence MFE	-19.93
Consensus MFE	-18.42
Energy contribution	-18.92
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.92
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17695302 103 - 22407834
UUAAAUAACCCAACUUGGUUGCAUAGUCUGAUUUUGGGCCACAAAAAUUUCACUUCACAUGUAGUAAAUUUGCAGCCAACAAAUCUAGGUCAGCAACAAAUAU
.................(((((.(..((((((((..(((.....((((((.(((........)))))))))...)))...))))).)))..))))))...... ( -19.10)
>DroSec_CAF1 86107 103 - 1
UUAAAUAACCCAACUUGGUUGCAUAGUCUGAUUUUGGGCCACAAAAAUUGCACUUCACAUGUAGUACAUUUGCAGCCAACAAAUCUAGGUCAGCAACAAAUAU
.................(((((.(..((((((((..(((..((((.((((((.......))))))...))))..)))...))))).)))..))))))...... ( -20.90)
>DroSim_CAF1 68667 103 - 1
UUAAAUAACCCAACUUGGUUGCAUAGUCUGAUUUUGGGCCACAAAAAUUGCACUUCACAUGUAGUACAUUUGCAGCCAACAAAUCUAGGUCAGCAACAAAUAU
.................(((((.(..((((((((..(((..((((.((((((.......))))))...))))..)))...))))).)))..))))))...... ( -20.90)
>DroYak_CAF1 89898 103 - 1
UUAAAUAACCCAACUUGCUUGCAUAGUCUGAUUUUGGGCCACAAAAAUUGCACUUCACAUGUAGUACAUUUGCAGCCAACAAAUCUAGGUCAGCAACAAAUAU
..............(((.((((.(..((((((((..(((..((((.((((((.......))))))...))))..)))...))))).)))..)))))))).... ( -18.80)
>consensus
UUAAAUAACCCAACUUGGUUGCAUAGUCUGAUUUUGGGCCACAAAAAUUGCACUUCACAUGUAGUACAUUUGCAGCCAACAAAUCUAGGUCAGCAACAAAUAU
.................(((((.(..((((((((..(((..((((.((((((.......))))))...))))..)))...))))).)))..))))))...... (-18.42 = -18.92 +   0.50)

alignment

secondary structure

dotplot

Window 4

Location	17,695,325 – 17,695,439
Length	114
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	96.05
Mean single sequence MFE	-32.37
Consensus MFE	-27.99
Energy contribution	-28.68
Covariance contribution	0.69
Combinations/Pair	1.06
Mean z-score	-2.00
Structure conservation index	0.86
SVM decision value	0.51
SVM RNA-class probability	0.764837
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17695325 114 + 22407834
GUUGGCUGCAAAUUUACUACAUGUGAAGUGAAAUUUUUGUGGCCCAAAAUCAGACUAUGCAACCAAGUUGGGUUAUUUAAAUCGCAAACAUGUGUACGGGUAACCGCUCGCCCA
...(((.((.....(((.((((((...((((..(((..(((((((((....................)))))))))..)))))))..))))))))).((....))))..))).. ( -29.75)
>DroSec_CAF1 86130 114 + 1
GUUGGCUGCAAAUGUACUACAUGUGAAGUGCAAUUUUUGUGGCCCAAAAUCAGACUAUGCAACCAAGUUGGGUUAUUUAAAUCGCAAACAAGUGUACGGGUAACCGCUCGACAA
((((((.......((((.((.(((....(((.((((..(((((((((....................)))))))))..)))).))).))).))))))((....)))).)))).. ( -31.35)
>DroSim_CAF1 68690 114 + 1
GUUGGCUGCAAAUGUACUACAUGUGAAGUGCAAUUUUUGUGGCCCAAAAUCAGACUAUGCAACCAAGUUGGGUUAUUUAAAUCGCAAACAUGUGUACGGGUAACCGCUCGCCCA
...(((.((....((((.((((((....(((.((((..(((((((((....................)))))))))..)))).))).))))))))))((....))))..))).. ( -35.85)
>DroYak_CAF1 89921 114 + 1
GUUGGCUGCAAAUGUACUACAUGUGAAGUGCAAUUUUUGUGGCCCAAAAUCAGACUAUGCAAGCAAGUUGGGUUAUUUAAAUCGCAAACAUGUGUAUGGCUAACCACUCGCCCA
(((((((......((((.((((((....(((.((((..((((((((.......(((.((....)))))))))))))..)))).))).))))))))))))))))).......... ( -32.51)
>consensus
GUUGGCUGCAAAUGUACUACAUGUGAAGUGCAAUUUUUGUGGCCCAAAAUCAGACUAUGCAACCAAGUUGGGUUAUUUAAAUCGCAAACAUGUGUACGGGUAACCGCUCGCCCA
..(((.(((...(((((.((((((....(((.((((..(((((((((....................)))))))))..)))).))).))))))))))).))).)))........ (-27.99 = -28.68 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:43 2006