Locus 1880

Sequence ID	X_DroMel_CAF1
Location	5,207,669 – 5,207,759
Length	90
Max. P	0.765214

overview

Window 2

Location	5,207,669 – 5,207,759
Length	90
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	82.72
Mean single sequence MFE	-23.96
Consensus MFE	-17.57
Energy contribution	-17.41
Covariance contribution	-0.16
Combinations/Pair	1.23
Mean z-score	-1.83
Structure conservation index	0.73
SVM decision value	0.51
SVM RNA-class probability	0.765214
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5207669 90 + 22224390
CGUUUUGAAUUUCUCCAAGGCUCGAGUGUUUCCUUAUAAUUCCGCA----UGCGGAAUUAAAGGCUUAAAGAU-UUGCUGGAAUAAUGAAGAAGC
.(((((..(((..((((..((..((((.(((((((.((((((((..----..))))))))))))...))).))-))))))))..)))...))))) ( -23.20)
>DroSec_CAF1 28105 90 + 1
CGCUUUGAAUUUCUCCAAGACUCGAGUGAUUCCUUAUAAUUCCGCA----UGCGGAAUUAAAGGCUUAAAGAU-UUGCUGGAAUAAUGAAGAAGC
.(((((..(((..((((.((.((...(((..((((.((((((((..----..)))))))))))).)))..)).-))..))))..)))...))))) ( -25.40)
>DroSim_CAF1 21800 90 + 1
CGCUUUGAAUUUCUCCAAGACUCGAGUGAUUCCUUAUGAUUCCGCA----UGCGGAAUUAAAGGCUUAAAGAU-UUGCUGGAAUAAUGAAGAAGC
.(((((..(((..((((.((.((...(((..((((.((((((((..----..)))))))))))).)))..)).-))..))))..)))...))))) ( -25.50)
>DroEre_CAF1 31309 91 + 1
GGUUUUGAAUUUCUGCAGGGCUCUAGCGAUGCCUUAUGAUGCCGUA----UACGGAAUUAAAGGCUUUAAGACUUCGCUGGCAUAAUGAAGGAGU
........((((((.((.....(((((((.(((((.((((.(((..----..))).))))))))).........))))))).....)).)))))) ( -25.30)
>DroYak_CAF1 28711 86 + 1
CGUUUUCAAUUUCUCC--------AUCGCUGCCUUAUGAUUUCGCAUGCGUACGGAAUUAAAGGCUUAAAGAU-UUGCUGGAAUAAUGAAGGUGU
((..((((.((..(((--------(((...(((((.((((((((........))))))))))))).....)).-....))))..))))))..)). ( -20.40)
>consensus
CGUUUUGAAUUUCUCCAAGACUCGAGUGAUUCCUUAUGAUUCCGCA____UGCGGAAUUAAAGGCUUAAAGAU_UUGCUGGAAUAAUGAAGAAGC
.(((((..(((..((((..............((((.((((((((((....))))))))))))))..............))))..)))...))))) (-17.57 = -17.41 +  -0.16)

alignment

secondary structure

dotplot

Window 3

Location	5,207,669 – 5,207,759
Length	90
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	82.72
Mean single sequence MFE	-19.05
Consensus MFE	-14.67
Energy contribution	-15.35
Covariance contribution	0.68
Combinations/Pair	1.17
Mean z-score	-1.55
Structure conservation index	0.77
SVM decision value	0.09
SVM RNA-class probability	0.577420
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5207669 90 - 22224390
GCUUCUUCAUUAUUCCAGCAA-AUCUUUAAGCCUUUAAUUCCGCA----UGCGGAAUUAUAAGGAAACACUCGAGCCUUGGAGAAAUUCAAAACG
(((.............)))..-.((((((((.(((((((((((..----..))))))))...(....)....))).))))))))........... ( -20.82)
>DroSec_CAF1 28105 90 - 1
GCUUCUUCAUUAUUCCAGCAA-AUCUUUAAGCCUUUAAUUCCGCA----UGCGGAAUUAUAAGGAAUCACUCGAGUCUUGGAGAAAUUCAAAGCG
(((((((((..((((.((...-.((((((......((((((((..----..))))))))))))))....)).))))..)))))).......))). ( -23.01)
>DroSim_CAF1 21800 90 - 1
GCUUCUUCAUUAUUCCAGCAA-AUCUUUAAGCCUUUAAUUCCGCA----UGCGGAAUCAUAAGGAAUCACUCGAGUCUUGGAGAAAUUCAAAGCG
(((((((((..((((.((...-.........((((..((((((..----..))))))...)))).....)).))))..)))))).......))). ( -20.24)
>DroEre_CAF1 31309 91 - 1
ACUCCUUCAUUAUGCCAGCGAAGUCUUAAAGCCUUUAAUUCCGUA----UACGGCAUCAUAAGGCAUCGCUAGAGCCCUGCAGAAAUUCAAAACC
.............((((((((.((((((..(((............----...)))....)))))).))))).).))................... ( -16.96)
>DroYak_CAF1 28711 86 - 1
ACACCUUCAUUAUUCCAGCAA-AUCUUUAAGCCUUUAAUUCCGUACGCAUGCGAAAUCAUAAGGCAGCGAU--------GGAGAAAUUGAAAACG
.....((((...(((((((((-....))..(((((..(((.((((....)))).)))...))))).))..)--------))))....)))).... ( -14.20)
>consensus
GCUUCUUCAUUAUUCCAGCAA_AUCUUUAAGCCUUUAAUUCCGCA____UGCGGAAUCAUAAGGAAUCACUCGAGCCUUGGAGAAAUUCAAAACG
............((((((.............((((..((((((((....))))))))...)))).............))))))............ (-14.67 = -15.35 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:52 2006