Locus 4952

Sequence ID	3L_DroMel_CAF1
Location	13,705,730 – 13,705,959
Length	229
Max. P	0.999176

overview

Window 8

Location	13,705,730 – 13,705,822
Length	92
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	74.70
Mean single sequence MFE	-29.28
Consensus MFE	-13.56
Energy contribution	-15.20
Covariance contribution	1.64
Combinations/Pair	1.16
Mean z-score	-2.18
Structure conservation index	0.46
SVM decision value	1.48
SVM RNA-class probability	0.957512
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13705730 92 + 23771897
AAAAUCACAAGGCCCUGUCGUCGCUGCAUCU---GC---U---------------GCUGCUGUGUGGCAUGCAACUCAAUGCACAUGCAACAGCCCACUGUCCACCCCAUCCA
..........((..((((.((.((.((....---))---.---------------)).))((((((((((........)))).)))))))))).))................. ( -20.00)
>DroSec_CAF1 112952 92 + 1
AAAAUCACAAGGCCCUGUCGUCGCUGCAUCU---GC---U---------------GCUGCUGUGUGGCAUGCAACUCAAUGCACGUGCAGCAGCCCACUGACCACCCCAUCCA
..........((....((.(((((.......---))---.---------------(((((((..((((((........)))).))..))))))).....))).)).....)). ( -28.90)
>DroSim_CAF1 123840 92 + 1
AAAAUCACAAGGCCCUGUCGUCGCUGCAUCU---GC---U---------------GCUGCUGUGUGGCAUGCAACUCAAUGCACAUGCAGCAGCCCACUGGCCACCCCAUCCA
..........((((..((....((.......---))---.---------------(((((((((((((((........)))).)))))))))))..)).)))).......... ( -32.70)
>DroAna_CAF1 170368 84 + 1
AAAAUCACAGGGCCUUGUCGUCGCUGCAGCU------------------------GCAGCUGUGUGGCACGCCACUCUUGACUCUUGCACCG-CCCGGC-GCCACCC---CCA
.........((((..(((.((((((((....------------------------))))).(.((((....)))).)..)))....)))..)-)))((.-.......---)). ( -27.30)
>DroPer_CAF1 105127 112 + 1
AAAAUCACCAGGCCUUGUCAUCGGUGCAGCAACAGCAUCAGCAUCAGCAGCAGCUGCUGAUGUGCGGCAUGCAACUCAAUGCACAUGCAUCGACCACCCGCCCA-CACAUCCA
..........(((...((..((((((((......((....((((((((((...))))))))))...)).((((......))))..))))))))..))..)))..-........ ( -37.50)
>consensus
AAAAUCACAAGGCCCUGUCGUCGCUGCAUCU___GC___U_______________GCUGCUGUGUGGCAUGCAACUCAAUGCACAUGCAGCAGCCCACUGGCCACCCCAUCCA
...........((..((....))..))............................(((((((((((((((........)))).)))))))))))................... (-13.56 = -15.20 +   1.64)

alignment

secondary structure

dotplot

Window 9

Location	13,705,764 – 13,705,854
Length	90
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	74.19
Mean single sequence MFE	-24.45
Consensus MFE	-13.67
Energy contribution	-15.59
Covariance contribution	1.92
Combinations/Pair	1.21
Mean z-score	-2.82
Structure conservation index	0.56
SVM decision value	3.42
SVM RNA-class probability	0.999176
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13705764 90 + 23771897
---------------GCUGCUGUGUGGCAUGCAACUCAAUGCACAUGCAACAGCCCACUGUCCACCCCAUCCAAGCC-------AACUCACAUAUUCGGCUAUCAAAUAUCA-
---------------((((.((((((((((........)))).)))))).))))...................((((-------.............))))...........- ( -21.02)
>DroSec_CAF1 112986 90 + 1
---------------GCUGCUGUGUGGCAUGCAACUCAAUGCACGUGCAGCAGCCCACUGACCACCCCAUCCAAGCC-------AACUCACAUAUUCGGCUAUCAAAUAUCA-
---------------(((((((..((((((........)))).))..)))))))...................((((-------.............))))...........- ( -26.82)
>DroSim_CAF1 123874 90 + 1
---------------GCUGCUGUGUGGCAUGCAACUCAAUGCACAUGCAGCAGCCCACUGGCCACCCCAUCCAAGCC-------AACUCACAUAUUCGGCUAUCAAAUAUCA-
---------------(((((((((((((((........)))).)))))))))))....(((.....)))....((((-------.............))))...........- ( -28.32)
>DroAna_CAF1 170399 93 + 1
---------------GCAGCUGUGUGGCACGCCACUCUUGACUCUUGCACCG-CCCGGC-GCCACCC---CCAGGCCUCGUAUUCACUCACAUUUUCGGCUAUCGAAUAACAG
---------------..(((((.((((....))))...(((....(((...(-((.((.-.......---)).)))...))).....)))......)))))............ ( -18.50)
>DroPer_CAF1 105167 102 + 1
GCAUCAGCAGCAGCUGCUGAUGUGCGGCAUGCAACUCAAUGCACAUGCAUCGACCACCCGCCCA-CACAUCCA--CC-------CACCUACAUAUUCGGGUAUCAAAUAUCA-
((((((((((...))))))))))((((..((....((.((((....)))).)).)).))))...-.......(--((-------(............))))...........- ( -27.60)
>consensus
_______________GCUGCUGUGUGGCAUGCAACUCAAUGCACAUGCAGCAGCCCACUGGCCACCCCAUCCAAGCC_______AACUCACAUAUUCGGCUAUCAAAUAUCA_
...............(((((((((((((((........)))).)))))))))))...................((((....................))))............ (-13.67 = -15.59 +   1.92)

alignment

secondary structure

dotplot

Window 0

Location	13,705,854 – 13,705,959
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	88.62
Mean single sequence MFE	-33.37
Consensus MFE	-25.78
Energy contribution	-26.90
Covariance contribution	1.12
Combinations/Pair	1.18
Mean z-score	-1.76
Structure conservation index	0.77
SVM decision value	0.50
SVM RNA-class probability	0.760042
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13705854 105 + 23771897
GCACACGUCCAGGCGUGUCCUGUUCUCCUUUUCAAGCGGCAAUGAUGGCAAGCCCGAGUCACAGUGACUUCUUCACUUCUUUACUGUGACUAUUUAUGGGGUGAU
...(((.(((((((.(((((((((..........))))).......)))).)))..(((((((((((.............))))))))))).....))))))).. ( -29.23)
>DroSec_CAF1 113076 96 + 1
GCACACGUCCAGGCGUGUCCUGUUCUCCUUUUCAAGCGGCAAUGAUGGCAAGUCCGAGUCACAGUGACU-C--------UUCACUGUGACUGUUUAAGGAGUGAU
(.((((((....)))))).)....((((((...(((((.((....)).).......(((((((((((..-.--------.))))))))))))))))))))).... ( -34.00)
>DroSim_CAF1 123964 97 + 1
GCACACGUCCAGGCGUGUCCUGUUCUCCUUUUCAAGCGGCAAUGAUGGCAAGUCCGAGUCACAGUGACUUC--------UUCACUGUGACUGUUUGAGGGAUGAU
(.((((((....)))))).)...((((((..(((((((.((....)).).......(((((((((((....--------.))))))))))))))))))))).)). ( -36.20)
>DroEre_CAF1 119347 97 + 1
GCACACGUCCAGGCGUGUCCUGUUCUCCUUUUCAAGCGGCAAUGAUGGCAAGCCCGAGUCACGGUGACUAU--------UUCACUGUGACUGCUUAAGUGGUGAU
(.((((((....)))))).)...((.((.(((.(((((((...........)))..(((((((((((....--------.)))))))))))))))))).)).)). ( -34.40)
>DroYak_CAF1 122917 96 + 1
GCACACGUCCAGGCGUGUCCUGUUCUCCUUUUCAAGCGGCAAGGAUGCCAAGCCCGAGUCACCGUGACUGU--------UUCACUGUGACUG-UUCGGUGCUGAU
((((((((....)))))).......(((((.((....)).))))).))..((((((((((((.((((....--------.)))).)))))..-.)))).)))... ( -33.00)
>consensus
GCACACGUCCAGGCGUGUCCUGUUCUCCUUUUCAAGCGGCAAUGAUGGCAAGCCCGAGUCACAGUGACUUC________UUCACUGUGACUGUUUAAGGGGUGAU
(.((((((....)))))).)...((.((((((.(((((((...........)))..(((((((((((.............))))))))))))))))))))).)). (-25.78 = -26.90 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:50 2006