Locus 3595

Sequence ID	X_DroMel_CAF1
Location	9,637,132 – 9,637,308
Length	176
Max. P	0.913496

overview

Window 7

Location	9,637,132 – 9,637,230
Length	98
Sequences	3
Columns	99
Reading direction	forward
Mean pairwise identity	82.25
Mean single sequence MFE	-24.37
Consensus MFE	-16.23
Energy contribution	-17.57
Covariance contribution	1.34
Combinations/Pair	1.17
Mean z-score	-2.15
Structure conservation index	0.67
SVM decision value	0.59
SVM RNA-class probability	0.793823
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9637132 98 + 22224390
UACUGGGUAUUACUGAGCUUCACUUGGAA-CCCAAAAAAAAGAUCAAAUGCAAUUUUUUGCUACCCAGCUUCAUAACGCUUCCAAUAUGUGGGGCUGGG
...(((((....(..((.....))..).)-))))...............((((....))))..((((((((((((............)))))))))))) ( -28.40)
>DroSec_CAF1 12653 95 + 1
UACAGGGUAUUUGUGAGCUCCACUUGAGA-CCCAAAAAA---AUCAAAUGCAAUUUUUUGCUACCCAGUUUCAUAACGCUCUCAAUAUGUGGAGCUGGG
....((((....(((.....))).....)-)))......---.......((((....))))..((((((((((((............)))))))))))) ( -27.50)
>DroYak_CAF1 14577 92 + 1
UACAGGGUAUUACUGGGCUCCAUUUGGCAUCCCCAA--A---AUCAAAUGCAAUUUUUCGCUACCCAGUUUCAUAACUCCCUCAAUAUGUGG--CUGUA
(((((((....((((((.....(((((.....))))--)---.......((........))..)))))).)).......((.(.....).))--))))) ( -17.20)
>consensus
UACAGGGUAUUACUGAGCUCCACUUGGAA_CCCAAAAAA___AUCAAAUGCAAUUUUUUGCUACCCAGUUUCAUAACGCUCUCAAUAUGUGG_GCUGGG
....(((.....(((((.....)))))...)))................((((....))))..((((((((((((............)))))))))))) (-16.23 = -17.57 +   1.34)

alignment

secondary structure

dotplot

Window 8

Location	9,637,151 – 9,637,269
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	78.17
Mean single sequence MFE	-29.05
Consensus MFE	-16.46
Energy contribution	-20.27
Covariance contribution	3.81
Combinations/Pair	1.15
Mean z-score	-2.32
Structure conservation index	0.57
SVM decision value	1.09
SVM RNA-class probability	0.913496
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9637151 118 + 22224390
UCACUUGGAA-CCCAAAAAAAAGAUCAAAUGCAAUUUUUUGCUACCCAGCUUCAUAACGCUUCCAAUAUGUGGGGCUGGGU-GCUCCGAAAGUCGCCGCAUGGCAGACCAUGUACAGACA
....(((((.-...................((((....))))((((((((((((((............)))))))))))))-).)))))..(((...((((((....))))))...))). ( -38.90)
>DroSec_CAF1 12672 115 + 1
CCACUUGAGA-CCCAAAAAA---AUCAAAUGCAAUUUUUUGCUACCCAGUUUCAUAACGCUCUCAAUAUGUGGAGCUGGGU-GCUCCGAAAGUCGCCACAUGGCAGACCAUGUACAGACA
......(((.-.........---.......((((....))))((((((((((((((............)))))))))))))-)))).....(((...((((((....))))))...))). ( -34.40)
>DroEre_CAF1 14129 92 + 1
CCAUGUGAGA-CCCAAA--A---AUCAAAAGCGAUUUUUUGCUACCCACUUUCAUAACUCGCUCAAUAUGUGG----------------------CCGCCUGGCAGACCAUGUACAGACA
....(((((.-......--.---......(((((....)))))..............)))))((..(((((((----------------------(.((...)).).)))))))..)).. ( -15.79)
>DroYak_CAF1 14596 113 + 1
CCAUUUGGCAUCCCCAA--A---AUCAAAUGCAAUUUUUCGCUACCCAGUUUCAUAACUCCCUCAAUAUGUGG--CUGUAUGGCUCCAAAAGUCGCCGCAUGGCAGACCAUGUACAGACA
...((((((((......--.---.....))))........((((..((((..((((..........))))..)--)))..))))..)))).(((...((((((....))))))...))). ( -27.10)
>consensus
CCACUUGAGA_CCCAAA__A___AUCAAAUGCAAUUUUUUGCUACCCAGUUUCAUAACGCUCUCAAUAUGUGG__CUGGGU_GCUCCGAAAGUCGCCGCAUGGCAGACCAUGUACAGACA
..............................((((....)))).(((((((((((((............)))))))))))))..........(((...((((((....))))))...))). (-16.46 = -20.27 +   3.81)

alignment

secondary structure

dotplot

Window 9

Location	9,637,190 – 9,637,308
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.32
Mean single sequence MFE	-36.23
Consensus MFE	-24.44
Energy contribution	-27.88
Covariance contribution	3.44
Combinations/Pair	1.10
Mean z-score	-1.66
Structure conservation index	0.67
SVM decision value	0.14
SVM RNA-class probability	0.603858
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9637190 118 + 22224390
GCUACCCAGCUUCAUAACGCUUCCAAUAUGUGGGGCUGGGU-GCUCCGAAAGUCGCCGCAUGGCAGACCAUGUACAGACAUCUGUCGGUUGGUUGGCCAUUUCCCA-GCCCCUCGUGUUU
(((....)))..............((((((.(((((((((.-((..(....)..))...(((((.(((((...((((....))))....))))).)))))..))))-))))).)))))). ( -48.60)
>DroSec_CAF1 12708 118 + 1
GCUACCCAGUUUCAUAACGCUCUCAAUAUGUGGAGCUGGGU-GCUCCGAAAGUCGCCACAUGGCAGACCAUGUACAGACAUCUGUCGGUUGGUUGGCCAUUUCCCU-GCCCCUCGUGCUU
((.(((((((((((((............)))))))))))))-((..(....)..))...(((((.(((((...((((....))))....))))).)))))......-.........)).. ( -38.90)
>DroEre_CAF1 14163 97 + 1
GCUACCCACUUUCAUAACUCGCUCAAUAUGUGG----------------------CCGCCUGGCAGACCAUGUACAGACAUCUGUCCGUUGGUUGGCCAUUUCCCA-GAGCCGCUUGUUU
....................((((.....((((----------------------(((.(..((.(((.((((....))))..))).))..).)))))))......-))))......... ( -27.30)
>DroYak_CAF1 14631 118 + 1
GCUACCCAGUUUCAUAACUCCCUCAAUAUGUGG--CUGUAUGGCUCCAAAAGUCGCCGCAUGGCAGACCAUGUACAGACAUCUGUCGGUUGGUUGGUCAUUUCCCAAGCCCCACUUGCUU
((((..((((..((((..........))))..)--)))..)))).......(((...((((((....))))))...)))....((.(((.((((((.......))))..)).))).)).. ( -30.10)
>consensus
GCUACCCAGUUUCAUAACGCUCUCAAUAUGUGG__CUGGGU_GCUCCGAAAGUCGCCGCAUGGCAGACCAUGUACAGACAUCUGUCGGUUGGUUGGCCAUUUCCCA_GCCCCUCGUGCUU
((.(((((((((((((............))))))))))))).))...............(((((.(((((...((((....))))....))))).))))).................... (-24.44 = -27.88 +   3.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:22 2006