Locus 9440

Sequence ID	3R_DroMel_CAF1
Location	25,007,025 – 25,007,164
Length	139
Max. P	0.850991

overview

Window 8

Location	25,007,025 – 25,007,127
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	97.06
Mean single sequence MFE	-34.90
Consensus MFE	-28.66
Energy contribution	-29.06
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.82
SVM decision value	0.64
SVM RNA-class probability	0.809205
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25007025 102 + 27905053
CCAUUCCGCACCCAUCAUUCUCCGCCGGCUGCGGCCCUGCUUCAUCGGAAGUCGCAGGCCAAGGCUCUUCCGCUGAUGCCCCACGUUGGGCGCCAUUAAUAU
.......((.((((.(.......((((....))))...((.(((.((((((.....(((....))))))))).))).)).....).)))).))......... ( -31.90)
>DroSec_CAF1 29476 102 + 1
CCAUUCCGCACCCAACAUCCUCCGCCGGCUGCGGCCCUGCUUCAUCGGAAGUCGCAGGCCAAGGCUCUUCCGCUGAUGCCCCACGUUGGGCGCCAUUAAUAU
.......((.((((((.......((((....))))...((.(((.((((((.....(((....))))))))).))).)).....)))))).))......... ( -36.00)
>DroSim_CAF1 23575 102 + 1
CCAUUCCGCACCCAACAUCCUCCGCCGGCUGCGGCCCUGCUUCAUCGGAAGUCGCAGGCCAAGGCUCUUCCGCUGAUGCCCCACGUUGGGCGCCAUUAAUAU
.......((.((((((.......((((....))))...((.(((.((((((.....(((....))))))))).))).)).....)))))).))......... ( -36.00)
>DroEre_CAF1 31297 102 + 1
CCAUUCCGCGCCCAUCAUUCUCCGCCGGCUGCCGCCCUGCUUCAUCGGAAGUCGCAGGCCAAGGCUCUUCCGCUGAUGCCCCACGUUGGGCGCCAUUAAUAU
.......(((((((.(..........(((....)))..((.(((.((((((.....(((....))))))))).))).)).....).)))))))......... ( -34.90)
>DroYak_CAF1 23079 102 + 1
CCACUCCGCGCCCAUCAUCCUCCGCCGGCUGCGACCCUGCUUCAUCGGAAGUCGCAGGCCAAGGCUCUUCCGCUGAUGCCCCACGUUGGGCGCCAUUAAUAU
.......(((((((.(..........(((((((((.(((......)))..)))))).)))..(((((.......)).)))....).)))))))......... ( -35.70)
>consensus
CCAUUCCGCACCCAUCAUCCUCCGCCGGCUGCGGCCCUGCUUCAUCGGAAGUCGCAGGCCAAGGCUCUUCCGCUGAUGCCCCACGUUGGGCGCCAUUAAUAU
.......((.((((.(.......((((....))))...((.(((.((((((.....(((....))))))))).))).)).....).)))).))......... (-28.66 = -29.06 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	25,007,053 – 25,007,164
Length	111
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	98.02
Mean single sequence MFE	-38.34
Consensus MFE	-36.98
Energy contribution	-37.02
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.35
Structure conservation index	0.96
SVM decision value	0.79
SVM RNA-class probability	0.850991
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25007053 111 - 27905053
AAAAACAACCGGCGGCAGAGGCAAUACCAGGCAUACCAUAUUAAUGGCGCCCAACGUGGGGCAUCAGCGGAAGAGCCUUGGCCUGCGACUUCCGAUGAAGCAGGGCCGCAG
...........(((((.(((((..(.((..((...((((....)))).((((......))))....)))).)..)))))..(((((..(.......)..)))))))))).. ( -40.20)
>DroSec_CAF1 29504 111 - 1
AAAAACAACCGGCGGCAGAGGCAAUAACAGGCAUACCAUAUUAAUGGCGCCCAACGUGGGGCAUCAGCGGAAGAGCCUUGGCCUGCGACUUCCGAUGAAGCAGGGCCGCAG
...........(((((.(((((.............((((....)))).((((......)))).....(....).)))))..(((((..(.......)..)))))))))).. ( -38.70)
>DroSim_CAF1 23603 111 - 1
AAAAACAACCGGCGGCAGAGGCAAUACCAGGCAUACCAUAUUAAUGGCGCCCAACGUGGGGCAUCAGCGGAAGAGCCUUGGCCUGCGACUUCCGAUGAAGCAGGGCCGCAG
...........(((((.(((((..(.((..((...((((....)))).((((......))))....)))).)..)))))..(((((..(.......)..)))))))))).. ( -40.20)
>DroEre_CAF1 31325 111 - 1
AAAAACAACUGGCGGCAGAGGCAAUAGCAGGCAUACCAUAUUAAUGGCGCCCAACGUGGGGCAUCAGCGGAAGAGCCUUGGCCUGCGACUUCCGAUGAAGCAGGGCGGCAG
.........(((..((....((....))..))...)))......((.(((((..((..((.((...((......))..)).))..)).((((....))))..))))).)). ( -36.10)
>DroYak_CAF1 23107 111 - 1
AAAAACAACUGGCGGCAGAGGCAAUAGCAGGCAUACCAUAUUAAUGGCGCCCAACGUGGGGCAUCAGCGGAAGAGCCUUGGCCUGCGACUUCCGAUGAAGCAGGGUCGCAG
...........(((((.(((((....((.......((((....)))).((((......))))....))......)))))..(((((..(.......)..)))))))))).. ( -36.50)
>consensus
AAAAACAACCGGCGGCAGAGGCAAUACCAGGCAUACCAUAUUAAUGGCGCCCAACGUGGGGCAUCAGCGGAAGAGCCUUGGCCUGCGACUUCCGAUGAAGCAGGGCCGCAG
...........(((((.(((((.............((((....)))).((((......)))).....(....).)))))..(((((..(.......)..)))))))))).. (-36.98 = -37.02 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:34:42 2006