Locus 881

Sequence ID X_DroMel_CAF1
Location 2,493,086 – 2,493,253
Length 167
Max. P 0.553166
window1431 window1432

overview

Window 1

Location 2,493,086 – 2,493,200
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.57
Mean single sequence MFE -40.64
Consensus MFE -29.80
Energy contribution -30.84
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -1.61
Structure conservation index 0.73
SVM decision value 0.02
SVM RNA-class probability 0.542455
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2493086 114 + 22224390
GGAGGCGACAGGGCUGACAUCAUUUUGCAGUCGGUAAUCGAUUGCAGUGGGA--AUUUGACAUUUGA----CAGUGUUGUAAAGCGGCGAGGCAGCAGCACUAGUUGCGUCGCGUCUCAG
.(((((.((((.((((.((((...(((((((((.....)))))))))...))--..........)).----)))).))))......((((.(((((.......))))).))))))))).. ( -42.80)
>DroSec_CAF1 11815 114 + 1
GGAGGCGGCAGGGCUGACAUCAUUUUGCAGUCGGUAAUCGAUUGCAGUGGGA--AUUUGACAUUUGA----CAGUGUUGUAAAGCGGCAGGGCAGCAGCACUAGUUGCGUCGCGUCUCAG
.(((((.((((.((((.((((...(((((((((.....)))))))))...))--..........)).----)))).))))...(((((...(((((.......))))))))))))))).. ( -40.70)
>DroSim_CAF1 8968 114 + 1
GGAGGCGACAGGGCUGACAUCAUUUUGCAGUCGUUAAUCGAUUGCAGUGGGA--AUUUGACAUUUGA----CAGUGUUGUAAAGCGGCGGGGCAGCAGCACUAGUUGCGUCGCGUCUCAG
.(((((.((((.((((.((((...(((((((((.....)))))))))...))--..........)).----)))).))))......((((.(((((.......))))).))))))))).. ( -42.20)
>DroEre_CAF1 11996 116 + 1
GGUGG---AAGGGCUGACAUCAUUUUGCAGUCGGCUAUCGAUUGCAGUGGCAGUUUUUGGC-UUUGACAAGCAGUGUUGCAAAGCGGUGGGGGAGCAGCACUAGUUGCGUAGCGUCUCAG
....(---(.(.((((.((((....((((((((.....))))))))(..(((.(.((((..-.....)))).).)))..).....)))).....(((((....))))).)))).).)).. ( -36.10)
>DroYak_CAF1 11642 114 + 1
GGAGG---CAGGGCUGACAUAAUUUUGCAGUCGGUUAUCGAUUGCAGUGGGA--UUGUGGC-UUUGACAGGCAGUGUUGUAAAGCGGCGUGGCAGCAGCACUAGUUGCGUAGCGUCUCAG
.((((---(...(((..((((((((((((((((.....)))))))))...))--)))))((-((((.(((......))))))))))))((.((.(((((....))))))).))))))).. ( -41.40)
>consensus
GGAGGCG_CAGGGCUGACAUCAUUUUGCAGUCGGUAAUCGAUUGCAGUGGGA__AUUUGACAUUUGA____CAGUGUUGUAAAGCGGCGGGGCAGCAGCACUAGUUGCGUCGCGUCUCAG
.((((((...(.((.(((......(((((((((.....))))))))).........................((((((((...((......)).)))))))).))))).)..)))))).. (-29.80 = -30.84 +   1.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 2,493,160 – 2,493,253
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.06
Mean single sequence MFE -40.63
Consensus MFE -18.46
Energy contribution -20.13
Covariance contribution 1.67
Combinations/Pair 1.20
Mean z-score -1.91
Structure conservation index 0.45
SVM decision value 0.04
SVM RNA-class probability 0.553166
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2493160 93 + 22224390
AAAGCGGCGAGGCAGCAGCACUAGUUGCGUCGCGUCUCAGUCGCUGCGCUGUCG------------ACUGCGACGUCCUUGCUGCGCUCCUGUAACGGCUCUCUC---------------
...(((((((((..(((((....)))))...(((((.(((((((......).))------------)))).))))))))))))))(((........)))......--------------- ( -40.90)
>DroSec_CAF1 11889 93 + 1
AAAGCGGCAGGGCAGCAGCACUAGUUGCGUCGCGUCUCAGUCGCUGCGCUGUCG------------ACGGCGACGUCCUUGCUGAGCUCCUGUAACGGCUCUCUC---------------
.....((((((((.(((((....)))))((((((((.((((......))))..)------------)).)))))).)))))))(((((........)))))....--------------- ( -38.50)
>DroSim_CAF1 9042 93 + 1
AAAGCGGCGGGGCAGCAGCACUAGUUGCGUCGCGUCUCAGUCGCUGCGCUGUCG------------ACGGCGACGUCCUUGCUGAGCUCCUGUAACGGCUCUCUC---------------
..(((((((.(((.(((((....)))))))).))))...(((((((((....))------------.)))))))......)))(((((........)))))....--------------- ( -38.20)
>DroEre_CAF1 12072 108 + 1
AAAGCGGUGGGGGAGCAGCACUAGUUGCGUAGCGUCUCAGUCGCUGCGCCGUCG------------ACGGCGACGUCCUUGCUGCGCUCCUGUAACUGCUCUCUCUCCGUCUCUCGCUCU
...((((.((((((((((...(((..((((((((.....(((((((((....))------------.))))))).....))))))))..)))...)))))))))).)))).......... ( -53.60)
>DroYak_CAF1 11716 111 + 1
AAAGCGGCGUGGCAGCAGCACUAGUUGCGUAGCGUCUCAGUCGCUGCGCGGUCGACUUCGCCUGCGACGGCGACGUCCUUGCUGCGCUCCUGUAACUGCUCUCUCUCUGUA---------
...((((.(.((.(((((...(((..((((((((.....((((((((((((.((....)).))))).))))))).....))))))))..)))...))))).)).).)))).--------- ( -52.70)
>DroAna_CAF1 11515 78 + 1
AAAGCGUCGG----ACAGCACUAGUUGCGUCG-----CAGUCGCGUCUCAGUUA------------G---CAGCGUCCU-GUACACCUCCUGUU--CGCUCUCUC---------------
..((((..((----((.((.(((..((.(.((-----(....))).).))..))------------)---..)))))).-..(((.....))).--)))).....--------------- ( -19.90)
>consensus
AAAGCGGCGGGGCAGCAGCACUAGUUGCGUCGCGUCUCAGUCGCUGCGCUGUCG____________ACGGCGACGUCCUUGCUGAGCUCCUGUAACGGCUCUCUC_______________
....((((((((..(((((....)))))...........(((((((.....................)))))))..)))))))).................................... (-18.46 = -20.13 +   1.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:11 2006