Locus 6985

Sequence ID	2L_DroMel_CAF1
Location	19,414,591 – 19,414,751
Length	160
Max. P	0.935690

overview

Window 2

Location	19,414,591 – 19,414,711
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.67
Mean single sequence MFE	-37.47
Consensus MFE	-31.68
Energy contribution	-30.72
Covariance contribution	-0.96
Combinations/Pair	1.26
Mean z-score	-1.72
Structure conservation index	0.85
SVM decision value	1.25
SVM RNA-class probability	0.935690
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19414591 120 + 22407834
AUCGCUCCGAGCACUGGACCUCCGGCAAUGAUUUGGGCAAAACCGGCACCCACUACUGGUUCUCUAAUGCACAACUCGUGACCAUUAAGCGUUGGGCGCCCAAACAACCAGACAAUGCUG
.........((((((((....))))...((.(((((((..((((((.........)))))).((((((((..................)))))))).))))))))).........)))). ( -31.17)
>DroSec_CAF1 17550 120 + 1
AUCGCUCCGAGCACUGGACCUCCGGCAAUGACUUGGGCAAAACCGGCACCCACUACUGGUUCUCCAACGCCCAACUCGUGACCAUCAAGCGUUGGGCGCCCAAGCAACCAGACAAUGCUG
...((.(((((((((((....))))...)).))))))).....(((((.......((((((((....((((((((.(.((.....)).).))))))))....)).))))))....))))) ( -42.20)
>DroSim_CAF1 17803 120 + 1
AUCGCUCCGAGCACUGGACCUCCGGCAAUGACUUGGGCAAAACCGGCACCCACUACUGGUUCUCCAAUGCCCAACUCGUGACCAUCAAGCGUUGGGCGCCCAAGCAACCAGACAAUGCUG
.........((((((((....))))...((.(((((((..((((((.........)))))).......(((((((.(.((.....)).).)))))))))))))))).........)))). ( -41.80)
>DroEre_CAF1 17137 120 + 1
AUCGCUCCGAGCACUGGACUUCCGGCAAUGACUUGGGCCAAACCGGCACCCACAAUUGGUUCUCCAAUGCCCAACUCGUGACCAUCAAGCGUUGGGCGCCCAACCAACCAGACAACUCUG
...((.(((((((((((....))))...)).)))))))......(((.......(((((....)))))(((((((.(.((.....)).).))))))))))........((((....)))) ( -38.30)
>DroYak_CAF1 17850 120 + 1
AUCGCUCUGAGCACUGGACUUCUGGCAAUGACUUGGCCCGAACCGGAGACUACUAUUGGUUCUCCAAUGUCCAACUCGUGACCAUUAAGCGUUGGGCGCCCAACCAACCAGACAACUCUG
...(((.((..(((((((((((.(((.........))).)))..((((((((....))).)))))...)))))....)))..))...)))(((((....)))))....((((....)))) ( -33.90)
>consensus
AUCGCUCCGAGCACUGGACCUCCGGCAAUGACUUGGGCAAAACCGGCACCCACUACUGGUUCUCCAAUGCCCAACUCGUGACCAUCAAGCGUUGGGCGCCCAACCAACCAGACAAUGCUG
...((.(((((((((((....))))...)).))))))).....(((((.......((((((......((((((((.(.((.....)).).)))))))).......))))))....))))) (-31.68 = -30.72 +  -0.96)

alignment

secondary structure

dotplot

Window 3

Location	19,414,631 – 19,414,751
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.67
Mean single sequence MFE	-37.63
Consensus MFE	-32.78
Energy contribution	-31.94
Covariance contribution	-0.84
Combinations/Pair	1.17
Mean z-score	-1.59
Structure conservation index	0.87
SVM decision value	1.07
SVM RNA-class probability	0.909529
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19414631 120 + 22407834
AACCGGCACCCACUACUGGUUCUCUAAUGCACAACUCGUGACCAUUAAGCGUUGGGCGCCCAAACAACCAGACAAUGCUGGCGGUAGGGAGCAUUGCAUACACUUGGGCUACAUCUACGG
..(((((..(((....)))....(((((((..................)))))))))((((((.......(.(((((((..(....)..))))))))......))))))........))) ( -29.79)
>DroSec_CAF1 17590 120 + 1
AACCGGCACCCACUACUGGUUCUCCAACGCCCAACUCGUGACCAUCAAGCGUUGGGCGCCCAAGCAACCAGACAAUGCUGGCGGCAGGGAGCAUUGCAUACACCUGGGCUACAUCUACAA
....(...((((...((((((((....((((((((.(.((.....)).).))))))))....)).)))))).(((((((..(....)..)))))))........))))...)........ ( -38.40)
>DroSim_CAF1 17843 120 + 1
AACCGGCACCCACUACUGGUUCUCCAAUGCCCAACUCGUGACCAUCAAGCGUUGGGCGCCCAAGCAACCAGACAAUGCUGGCGGCAGGGAGCAUUGCAUACACCUGGGCUACAUCUACAA
((((((.........)))))).......(((((((.(.((.....)).).)))))))((((..((..((((......))))..))(((..............)))))))........... ( -38.04)
>DroEre_CAF1 17177 120 + 1
AACCGGCACCCACAAUUGGUUCUCCAAUGCCCAACUCGUGACCAUCAAGCGUUGGGCGCCCAACCAACCAGACAACUCUGGGGGCAAGGAGCAUUGCAUUCACUUGGGCUACAUCUACGG
..(((.........(((((....)))))(((((((.(.((.....)).).)))))))((((((((..(((((....)))))))((((......))))......))))))........))) ( -41.80)
>DroYak_CAF1 17890 120 + 1
AACCGGAGACUACUAUUGGUUCUCCAAUGUCCAACUCGUGACCAUUAAGCGUUGGGCGCCCAACCAACCAGACAACUCUGGGGGCAAUGAGCAUUGCAUACACAUGGGCUACAUCUACGG
..((((((((((....))).)))))...(((((((.(...........).)))))))(((((.((..(((((....)))))))(((((....))))).......))))).........)) ( -40.10)
>consensus
AACCGGCACCCACUACUGGUUCUCCAAUGCCCAACUCGUGACCAUCAAGCGUUGGGCGCCCAACCAACCAGACAAUGCUGGCGGCAGGGAGCAUUGCAUACACCUGGGCUACAUCUACGG
((((((.........)))))).......(((((((.(.((.....)).).)))))))(((((.....((((......))))..((((......)))).......)))))........... (-32.78 = -31.94 +  -0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:36 2006