Locus 3849

Sequence ID	3R_DroMel_CAF1
Location	10,494,037 – 10,494,140
Length	103
Max. P	0.853906

overview

Window 4

Location	10,494,037 – 10,494,140
Length	103
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	80.53
Mean single sequence MFE	-32.53
Consensus MFE	-22.42
Energy contribution	-22.65
Covariance contribution	0.23
Combinations/Pair	1.25
Mean z-score	-1.21
Structure conservation index	0.69
SVM decision value	-0.03
SVM RNA-class probability	0.520314
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10494037 103 + 27905053
UAUUUCACUGUAGUUAAUUGUGCUGGU-UUAGUUUUU---GGCACACCUCGCGGGGUCGCUCUGUAUGAACUGGGCGCCCUCGGUGAGUGCCAGUGGGUUUGUGGUG
.....(((..(((.....(((((..(.-.......).---.))))).(((((((((.(((((.((....)).))))).))))(((....))).))))).)))..))) ( -37.00)
>DroSec_CAF1 40134 101 + 1
UAUUUCACUGUAGUUAAUUU--GUGGU-UUAGUAUUU---GGCGCACCUCGCGGGGUCGCUCUGUAUGAACUGGGCACCCUCGGUGAGUGCCAGUGGGUUUGUGGUG
...(((((((..(((((.((--(....-.)))...))---)))((((.(((((((((.((((.((....)).)))))))))..)))))))))))))))......... ( -31.30)
>DroEre_CAF1 40892 101 + 1
UUUUUCACUGUAGUUAAUUG--GUGGU-UUAGUGUUU---GGCGCACCUCGCGGGGUCGCUCUGUAUGAACUGGGCGCCCUCGGUGAGUGCCAGUGGAUUUGUGGUG
.....(((..(((...((((--((...-...(((...---..)))..(((((((((.(((((.((....)).))))).)))).))))).))))))....)))..))) ( -35.40)
>DroWil_CAF1 38015 99 + 1
UUUCU---UGCAAAUAUUC---GAU-A-UUAGGGUUUGGGGGCGCACCUCGCGGGGUCGCUUUGUAUGUAUUGGGCGCCCUCGGUUAGGGCUAGAGGAUUUGUUGUU
.....---.((((((.(((---...-.-.........((((((((((((....)))).((.......)).....))))))))(((....))).))).)))))).... ( -26.90)
>DroYak_CAF1 40636 102 + 1
UUUUUCACUGUAGUUAAUUG--GUGGUUUUAGUAUUU---GGCGCACCUCGCGGGGUCGCUCUGUAUGAACUGGGCGCCCUCGGUGAGUGCCAGUGGAUUUGUGGUG
...(((((((..(((((.((--.((....)).)).))---)))((((.((((((((.(((((.((....)).))))).)))).)))))))))))))))......... ( -34.90)
>DroPer_CAF1 35945 85 + 1
UUU---------------UU--GUG-A-UUAGUAUUU---GGCGCACCUCGCGGGGUCGCUCUGUAUGUACGUGGCGCCUUCGGUGAGGGCCAGAGGAUUCGUGGUU
...---------------(.--.((-(-......(((---(((...((((((((((.((((.(((....))).)))).)))).))))))))))))....)))..).. ( -29.70)
>consensus
UUUUUCACUGUAGUUAAUUG__GUGGU_UUAGUAUUU___GGCGCACCUCGCGGGGUCGCUCUGUAUGAACUGGGCGCCCUCGGUGAGUGCCAGUGGAUUUGUGGUG
........................................(((((.(.(((.((((.(((((.((....)).)))))))))))).).)))))............... (-22.42 = -22.65 +   0.23)

alignment

secondary structure

dotplot

Window 5

Location	10,494,037 – 10,494,140
Length	103
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	80.53
Mean single sequence MFE	-23.32
Consensus MFE	-13.99
Energy contribution	-14.72
Covariance contribution	0.72
Combinations/Pair	1.12
Mean z-score	-2.33
Structure conservation index	0.60
SVM decision value	0.80
SVM RNA-class probability	0.853906
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10494037 103 - 27905053
CACCACAAACCCACUGGCACUCACCGAGGGCGCCCAGUUCAUACAGAGCGACCCCGCGAGGUGUGCC---AAAAACUAA-ACCAGCACAAUUAACUACAGUGAAAUA
...........(((((...(((..((.((((((.(.((....)).).))).))))).))).(((((.---.........-....)))))........)))))..... ( -25.54)
>DroSec_CAF1 40134 101 - 1
CACCACAAACCCACUGGCACUCACCGAGGGUGCCCAGUUCAUACAGAGCGACCCCGCGAGGUGCGCC---AAAUACUAA-ACCAC--AAAUUAACUACAGUGAAAUA
...(((......((((((((((.....))))).))))).......(.(((.(.((....)).)))))---.........-.....--............)))..... ( -24.70)
>DroEre_CAF1 40892 101 - 1
CACCACAAAUCCACUGGCACUCACCGAGGGCGCCCAGUUCAUACAGAGCGACCCCGCGAGGUGCGCC---AAACACUAA-ACCAC--CAAUUAACUACAGUGAAAAA
...........(((((...(((...)))(((((((.((....))...(((....)))..)).)))))---.........-.....--..........)))))..... ( -24.90)
>DroWil_CAF1 38015 99 - 1
AACAACAAAUCCUCUAGCCCUAACCGAGGGCGCCCAAUACAUACAAAGCGACCCCGCGAGGUGCGCCCCCAAACCCUAA-U-AUC---GAAUAUUUGCA---AGAAA
.....(((((..((..(((((.....)))))................(((.(.((....)).)))).............-.-...---))..)))))..---..... ( -20.20)
>DroYak_CAF1 40636 102 - 1
CACCACAAAUCCACUGGCACUCACCGAGGGCGCCCAGUUCAUACAGAGCGACCCCGCGAGGUGCGCC---AAAUACUAAAACCAC--CAAUUAACUACAGUGAAAAA
...........(((((...(((...)))(((((((.((....))...(((....)))..)).)))))---...............--..........)))))..... ( -24.90)
>DroPer_CAF1 35945 85 - 1
AACCACGAAUCCUCUGGCCCUCACCGAAGGCGCCACGUACAUACAGAGCGACCCCGCGAGGUGCGCC---AAAUACUAA-U-CAC--AA---------------AAA
.....((...(((((((((((......))).))))............(((....)))))))..))..---.........-.-...--..---------------... ( -19.70)
>consensus
CACCACAAAUCCACUGGCACUCACCGAGGGCGCCCAGUUCAUACAGAGCGACCCCGCGAGGUGCGCC___AAAUACUAA_ACCAC__CAAUUAACUACAGUGAAAAA
................(((((...((.((((((.(.((....)).).))).)))))...)))))........................................... (-13.99 = -14.72 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:34 2006