Locus 1108

Sequence ID	2R_DroMel_CAF1
Location	4,436,208 – 4,436,304
Length	96
Max. P	0.712761

overview

Window 8

Location	4,436,208 – 4,436,304
Length	96
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.91
Mean single sequence MFE	-37.60
Consensus MFE	-18.94
Energy contribution	-18.22
Covariance contribution	-0.72
Combinations/Pair	1.25
Mean z-score	-1.82
Structure conservation index	0.50
SVM decision value	0.38
SVM RNA-class probability	0.712761
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4436208 96 + 20766785
CUGCCGCAGG------------CCAGGCAGCUGCAACAAAUCUUAUGCAAACGAACCAGAGCAUUCUCAGUGGGAUGCCGCUCUUUGGAG------------CUGUUCCGCAACAGCAGC
.((((.....------------...))))(((((........................(((....))).(((((((...((((....)))------------).)))))))....))))) ( -29.60)
>DroPse_CAF1 6878 120 + 1
CUGCAGGCGGAAGCUUGCCCGUGCAAGGAUCUGGAUCGAAUCUGAUGCAGACAAAUCAAAGCAUUCUUAGUGGGAUGCCCCUGUUUGGGGCACACCCACAAGCGGUUCCACAGCAGCAGC
..((((((....))))))((((((...((((((.((((....)))).))))....))...)).......(((((.((((((.....))))))..)))))..))))............... ( -48.10)
>DroSec_CAF1 6059 96 + 1
CUGCCGCAGG------------CCAGGCAGUUGCAACGAAUCUUAUGCAAACAAACCAGAGCAUCCUCAGUGGGAUGCCGCUCUUUGGAG------------CUGUUCCACAACAGCAGC
(((((.....------------...)))))(((((..........))))).....((((((((((((....))))))).....))))).(------------(((((....))))))... ( -31.20)
>DroSim_CAF1 6573 96 + 1
CUGCCGCAGG------------CCAGGCAGCUGCAACGAAUCUUAUGCAAACGAACCAGAGCAUCCUCAGUGGGAUGCCGCUCUUUGGAG------------CUGUUCCACAACAGCAGC
.((((.....------------...))))(((((........................(((....))).(((((((...((((....)))------------).)))))))....))))) ( -30.20)
>DroPer_CAF1 6893 120 + 1
CUGCAGGCGGAACCUUGCCCGUGCAAGGAUCUGGAUCGAAUCUGAUGCAGACAAAUCAAAGCAUUCUUAGUGGGAUGCCCCUGUUUGGGGCACACCCACAAGCGGUUCCACAGCAGCAGC
((((..(.((((((.(((((......)).((((.((((....)))).)))).........)))......(((((.((((((.....))))))..)))))....)))))).).)))).... ( -48.90)
>consensus
CUGCCGCAGG____________CCAGGCAGCUGCAACGAAUCUUAUGCAAACAAACCAGAGCAUUCUCAGUGGGAUGCCGCUCUUUGGAG____________CUGUUCCACAACAGCAGC
((((.....................(((..(((((..........)))))..........(((((((....))))))).)))...(((((...............))))).....)))). (-18.94 = -18.22 +  -0.72)

alignment

secondary structure

dotplot

Window 9

Location	4,436,208 – 4,436,304
Length	96
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.91
Mean single sequence MFE	-40.58
Consensus MFE	-13.14
Energy contribution	-14.34
Covariance contribution	1.20
Combinations/Pair	1.08
Mean z-score	-1.72
Structure conservation index	0.32
SVM decision value	0.02
SVM RNA-class probability	0.543998
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4436208 96 - 20766785
GCUGCUGUUGCGGAACAG------------CUCCAAAGAGCGGCAUCCCACUGAGAAUGCUCUGGUUCGUUUGCAUAAGAUUUGUUGCAGCUGCCUGG------------CCUGCGGCAG
....(((((((((..(((------------(((....))))((((..(((..(((....)))))).....(((((..........))))).)))))).------------.))))))))) ( -31.70)
>DroPse_CAF1 6878 120 - 1
GCUGCUGCUGUGGAACCGCUUGUGGGUGUGCCCCAAACAGGGGCAUCCCACUAAGAAUGCUUUGAUUUGUCUGCAUCAGAUUCGAUCCAGAUCCUUGCACGGGCAAGCUUCCGCCUGCAG
....((((.((((((..(((((((((.(((((((.....)))))))))))).......((((((....(((((.(((......))).))))).....)).))))))))))))))..)))) ( -49.10)
>DroSec_CAF1 6059 96 - 1
GCUGCUGUUGUGGAACAG------------CUCCAAAGAGCGGCAUCCCACUGAGGAUGCUCUGGUUUGUUUGCAUAAGAUUCGUUGCAACUGCCUGG------------CCUGCGGCAG
....((((((..(..(((------------(((....))))(((((((......)))))))..(((..(((.(((..........)))))).))))).------------.)..)))))) ( -33.10)
>DroSim_CAF1 6573 96 - 1
GCUGCUGUUGUGGAACAG------------CUCCAAAGAGCGGCAUCCCACUGAGGAUGCUCUGGUUCGUUUGCAUAAGAUUCGUUGCAGCUGCCUGG------------CCUGCGGCAG
.(((((((.((.(..(((------------(......(((((((((((......)))))))...))))...((((..........))))))))..).)------------)..))))))) ( -33.70)
>DroPer_CAF1 6893 120 - 1
GCUGCUGCUGUGGAACCGCUUGUGGGUGUGCCCCAAACAGGGGCAUCCCACUAAGAAUGCUUUGAUUUGUCUGCAUCAGAUUCGAUCCAGAUCCUUGCACGGGCAAGGUUCCGCCUGCAG
....((((.((((((((.((((((((.(((((((.....)))))))))))).)))..(((((((....(((((.(((......))).))))).....)).))))).))))))))..)))) ( -55.30)
>consensus
GCUGCUGUUGUGGAACAG____________CUCCAAAGAGCGGCAUCCCACUGAGAAUGCUCUGGUUUGUUUGCAUAAGAUUCGUUGCAGCUGCCUGG____________CCUGCGGCAG
.(((((((...((....................((((..(..((((.(......).))))..)..)))).(((((..........)))))....................)).))))))) (-13.14 = -14.34 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:44 2006