Locus 40

Sequence ID	2R_DroMel_CAF1
Location	1,256,666 – 1,256,813
Length	147
Max. P	0.945589

overview

Window 2

Location	1,256,666 – 1,256,781
Length	115
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	96.00
Mean single sequence MFE	-37.83
Consensus MFE	-34.34
Energy contribution	-34.82
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-1.42
Structure conservation index	0.91
SVM decision value	0.93
SVM RNA-class probability	0.883927
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1256666 115 + 20766785
UUCCUUGUGAAGGAGAGUGGGGCUCAGAGUGGAGCAAAGUUUGUGCUGGUAUAUGUUUCGCAUACGUACCACUCGCCGUGGAUUGCGUGGUGGGGCAAACAAUGCGGCAAACAAU
(((((.....)))))......((((......))))...((((((((..((...(((..(((.((((((((((.....))))..)))))))))..))).))...)).))))))... ( -37.60)
>DroSec_CAF1 8356 115 + 1
UUCCUUGUGAAGGAGAGUGGGGCUCGGAGUGGAGCAAAGUUUGAGCUGGUAUAUGUUUCGCAUACGUACCACUCGCCGUGGAUUGCGUGGUGGGGCAAACAAUGCGGCAAACAAU
.((((.....))))((((((((((((((.(.......).)))))))).(..((((.....))))..).))))))(((((.(.((((........)))).)...)))))....... ( -38.10)
>DroSim_CAF1 14167 115 + 1
UUCCUUGUGAAGGAGAGUGGGGCUCGGAGUGGAGCAAAGUUUGAGCUGGUAUAUGUUUCGCAUACGUACCACUCGCCGUGGAUUGCGUGGUGGGGCAAACAAUGCGGCAAACAAU
.((((.....))))((((((((((((((.(.......).)))))))).(..((((.....))))..).))))))(((((.(.((((........)))).)...)))))....... ( -38.10)
>DroEre_CAF1 12495 115 + 1
UUCCUUAUGAAGGAGAGUGGGGCUUGGAGUGGACCAAAGUUUGAGCUGGUAUAUGUUUCGUAUACGUACCACUCGCCGUGGAUUGCGUGGUGGGGCAAACAAUGCGGCAAACAAU
.((((.....))))((((((((((..((.(.......).))..)))).(((((((...)))))))...))))))(((((.(.((((........)))).)...)))))....... ( -39.80)
>DroYak_CAF1 11848 115 + 1
UUCCUUAUAAAGGAGAGUGGGGCUCGCAGUGGACCAAAGAUUGAACUGGUAUAUGUUUCGUAUACGUACCACUCGCCGUGGAUUGCGUGGUGGGGCAAACAAUGCGGCAAACAAU
.((((.....))))((((((..(...((((..............))))(((((((...))))))))..))))))(((((.(.((((........)))).)...)))))....... ( -35.54)
>consensus
UUCCUUGUGAAGGAGAGUGGGGCUCGGAGUGGAGCAAAGUUUGAGCUGGUAUAUGUUUCGCAUACGUACCACUCGCCGUGGAUUGCGUGGUGGGGCAAACAAUGCGGCAAACAAU
.((((.....))))((((((((((((((.(.......).))))))))....(((((.......)))))))))))(((((.(.((((........)))).)...)))))....... (-34.34 = -34.82 +   0.48)

alignment

secondary structure

dotplot

Window 3

Location	1,256,666 – 1,256,781
Length	115
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	96.00
Mean single sequence MFE	-27.92
Consensus MFE	-24.75
Energy contribution	-24.75
Covariance contribution	-0.00
Combinations/Pair	1.07
Mean z-score	-1.64
Structure conservation index	0.89
SVM decision value	1.35
SVM RNA-class probability	0.945589
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1256666 115 - 20766785
AUUGUUUGCCGCAUUGUUUGCCCCACCACGCAAUCCACGGCGAGUGGUACGUAUGCGAAACAUAUACCAGCACAAACUUUGCUCCACUCUGAGCCCCACUCUCCUUCACAAGGAA
.......((((.(((((.((......)).)))))...))))((((((...(((((.....)))))...............((((......)))).))))))((((.....)))). ( -28.50)
>DroSec_CAF1 8356 115 - 1
AUUGUUUGCCGCAUUGUUUGCCCCACCACGCAAUCCACGGCGAGUGGUACGUAUGCGAAACAUAUACCAGCUCAAACUUUGCUCCACUCCGAGCCCCACUCUCCUUCACAAGGAA
.......((((.(((((.((......)).)))))...))))((((((...(((((.....)))))...............((((......)))).))))))((((.....)))). ( -28.60)
>DroSim_CAF1 14167 115 - 1
AUUGUUUGCCGCAUUGUUUGCCCCACCACGCAAUCCACGGCGAGUGGUACGUAUGCGAAACAUAUACCAGCUCAAACUUUGCUCCACUCCGAGCCCCACUCUCCUUCACAAGGAA
.......((((.(((((.((......)).)))))...))))((((((...(((((.....)))))...............((((......)))).))))))((((.....)))). ( -28.60)
>DroEre_CAF1 12495 115 - 1
AUUGUUUGCCGCAUUGUUUGCCCCACCACGCAAUCCACGGCGAGUGGUACGUAUACGAAACAUAUACCAGCUCAAACUUUGGUCCACUCCAAGCCCCACUCUCCUUCAUAAGGAA
.......((((.(((((.((......)).)))))...))))((((((..((((((.......)))))...........((((......)))))..))))))((((.....)))). ( -27.60)
>DroYak_CAF1 11848 115 - 1
AUUGUUUGCCGCAUUGUUUGCCCCACCACGCAAUCCACGGCGAGUGGUACGUAUACGAAACAUAUACCAGUUCAAUCUUUGGUCCACUGCGAGCCCCACUCUCCUUUAUAAGGAA
.......((((.(((((.((......)).)))))...))))((((((..((....))........(((((........)))))............))))))((((.....)))). ( -26.30)
>consensus
AUUGUUUGCCGCAUUGUUUGCCCCACCACGCAAUCCACGGCGAGUGGUACGUAUGCGAAACAUAUACCAGCUCAAACUUUGCUCCACUCCGAGCCCCACUCUCCUUCACAAGGAA
.......((((.(((((.((......)).)))))...))))((((((...(((((.......)))))..((((.................)))).))))))((((.....)))). (-24.75 = -24.75 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	1,256,706 – 1,256,813
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	97.76
Mean single sequence MFE	-36.92
Consensus MFE	-34.86
Energy contribution	-35.02
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-1.28
Structure conservation index	0.94
SVM decision value	0.44
SVM RNA-class probability	0.738722
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1256706 107 + 20766785
UUGUGCUGGUAUAUGUUUCGCAUACGUACCACUCGCCGUGGAUUGCGUGGUGGGGCAAACAAUGCGGCAAACAAUGGUUGCCGCUGAUGCCACUGCAGAUGACUUUG
((((..((((((.(((..(((.((((((((((.....))))..)))))))))..)))......(((((((.......)))))))..))))))..))))......... ( -40.80)
>DroSec_CAF1 8396 107 + 1
UUGAGCUGGUAUAUGUUUCGCAUACGUACCACUCGCCGUGGAUUGCGUGGUGGGGCAAACAAUGCGGCAAACAAUGGUCGCCGCUGAUGCCACUGCAGAUGACUUUG
(((((.((((((.(((..(((.((((((((((.....))))..)))))))))..)))......(((((...........)))))..)))))))).)))......... ( -36.80)
>DroSim_CAF1 14207 107 + 1
UUGAGCUGGUAUAUGUUUCGCAUACGUACCACUCGCCGUGGAUUGCGUGGUGGGGCAAACAAUGCGGCAAACAAUGGUCGCCGCUGAUGCCACUGCAGAUGACUUUG
(((((.((((((.(((..(((.((((((((((.....))))..)))))))))..)))......(((((...........)))))..)))))))).)))......... ( -36.80)
>DroEre_CAF1 12535 107 + 1
UUGAGCUGGUAUAUGUUUCGUAUACGUACCACUCGCCGUGGAUUGCGUGGUGGGGCAAACAAUGCGGCAAACAAUGGUUGCCGCUGAUGCCACUGCAGAUGACUCUG
...((.((((((.(((..(...((((((((((.....))))..))))))..)..)))......(((((((.......)))))))..)))))))).((((....)))) ( -35.70)
>DroYak_CAF1 11888 107 + 1
UUGAACUGGUAUAUGUUUCGUAUACGUACCACUCGCCGUGGAUUGCGUGGUGGGGCAAACAAUGCGGCAAACAAUGGUUGCCGCUGAUGCCACUGCAGAUGACUUUG
(((...((((((.(((..(...((((((((((.....))))..))))))..)..)))......(((((((.......)))))))..))))))...)))......... ( -34.50)
>consensus
UUGAGCUGGUAUAUGUUUCGCAUACGUACCACUCGCCGUGGAUUGCGUGGUGGGGCAAACAAUGCGGCAAACAAUGGUUGCCGCUGAUGCCACUGCAGAUGACUUUG
(((...((((((.(((..(((.((((((((((.....))))..)))))))))..)))......(((((((.......)))))))..))))))...)))......... (-34.86 = -35.02 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:24:26 2006