Locus 28

Sequence ID	4_DroMel_CAF1
Location	259,925 – 260,032
Length	107
Max. P	0.954810

overview

Window 7

Location	259,925 – 260,032
Length	107
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	80.45
Mean single sequence MFE	-23.20
Consensus MFE	-10.68
Energy contribution	-10.84
Covariance contribution	0.16
Combinations/Pair	1.18
Mean z-score	-2.73
Structure conservation index	0.46
SVM decision value	1.45
SVM RNA-class probability	0.954810
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 259925 107 + 1281640
CAGUGUAUAUACAAGUUAUAUAU------------ACAAUCGCUCUUUGACGCACAUGCCCAAAGAGAUUCUAUAUUUAGCAAUUUCAUGAACUUUUCGAACACGUUCACAUUGCGCUC
..(((((((((.....)))))))------------)).....(((((((..((....)).)))))))............(((((....(((((...........))))).))))).... ( -23.50)
>DroSec_CAF1 2207 100 + 1
CAGUGUAUAUACAAUAUA----U------------AUAUACGCUCUUUGACGCACAUGCCCAAAGAGAUUCUAUAUUUAACA-UUUUAUGAACUUUUCGAA--CGUUCACAUUGCGCGC
..(((((((((.....))----)------------)))))).(((((((..((....)).)))))))...............-.....(((((........--.))))).......... ( -19.20)
>DroSim_CAF1 2157 104 + 1
CAGUGUAUAUACAAUAUAUGUAU------------AUAUACGCUCUUUGACGCACAUGCCCAAAGAGAUUCUAUAUUUAGCA-UUUUAUGAACUUUUCGAA--CGUUCACAUUGCGCGC
..(((((((((((.....)))))------------)))))).(((((((..((....)).)))))))............(((-.....(((((........--.)))))...))).... ( -26.80)
>DroEre_CAF1 1494 111 + 1
CAUUGUACAUACAAAUUAUAUAUAUGUAUGUACAUAUAAACGCUCUUUGAGGCACAUGCCCAAAGAGAUUCUAUAUUUAGCAUUUUC------AUUUCGAG--CGCUCACAUUACGCUU
...((((((((((.((.....)).))))))))))((((....(((((((.(((....))))))))))....))))............------.....(((--((.........))))) ( -30.30)
>DroYak_CAF1 1703 105 + 1
CAGUGUACAUACAAAGUAUAUAU------------AAAAACGCUCUUUGAAGCACAUACCCAAUGAGAUUCUAUAUUUAGAAGUUUCAUGAACAUUUCGGA--CGCUCACAUUACGCUC
.((((((....(((((.......------------.........))))).(((.........(((((((((((....))).))))))))((.....))...--.))).....)))))). ( -16.19)
>consensus
CAGUGUAUAUACAAAAUAUAUAU____________AUAAACGCUCUUUGACGCACAUGCCCAAAGAGAUUCUAUAUUUAGCA_UUUCAUGAACUUUUCGAA__CGUUCACAUUGCGCUC
..(((((...................................(((((((..((....)).)))))))...............................(((....)))....))))).. (-10.68 = -10.84 +   0.16)

alignment

secondary structure

dotplot

Window 8

Location	259,925 – 260,032
Length	107
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	80.45
Mean single sequence MFE	-26.86
Consensus MFE	-14.30
Energy contribution	-15.38
Covariance contribution	1.08
Combinations/Pair	1.23
Mean z-score	-2.35
Structure conservation index	0.53
SVM decision value	0.95
SVM RNA-class probability	0.887398
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 259925 107 - 1281640
GAGCGCAAUGUGAACGUGUUCGAAAAGUUCAUGAAAUUGCUAAAUAUAGAAUCUCUUUGGGCAUGUGCGUCAAAGAGCGAUUGU------------AUAUAUAACUUGUAUAUACACUG
..(((((((((((((...........))))))...))))).............(((((((((....)).)))))))))...(((------------((((((.....)))))))))... ( -27.10)
>DroSec_CAF1 2207 100 - 1
GCGCGCAAUGUGAACG--UUCGAAAAGUUCAUAAAA-UGUUAAAUAUAGAAUCUCUUUGGGCAUGUGCGUCAAAGAGCGUAUAU------------A----UAUAUUGUAUAUACACUG
((((((..(((((((.--........)))))))..(-((((......((.....))...))))))))))).....((.((((((------------(----(.....)))))))).)). ( -24.80)
>DroSim_CAF1 2157 104 - 1
GCGCGCAAUGUGAACG--UUCGAAAAGUUCAUAAAA-UGCUAAAUAUAGAAUCUCUUUGGGCAUGUGCGUCAAAGAGCGUAUAU------------AUACAUAUAUUGUAUAUACACUG
(((((((.(((((((.--........)))))))...-))).............(((((((((....)).))))))))))).(((------------(((((.....))))))))..... ( -28.90)
>DroEre_CAF1 1494 111 - 1
AAGCGUAAUGUGAGCG--CUCGAAAU------GAAAAUGCUAAAUAUAGAAUCUCUUUGGGCAUGUGCCUCAAAGAGCGUUUAUAUGUACAUACAUAUAUAUAAUUUGUAUGUACAAUG
.(((((.......)))--))......------...........(((((((..((((((((((....))).)))))))..)))))))(((((((((...........))))))))).... ( -34.00)
>DroYak_CAF1 1703 105 - 1
GAGCGUAAUGUGAGCG--UCCGAAAUGUUCAUGAAACUUCUAAAUAUAGAAUCUCAUUGGGUAUGUGCUUCAAAGAGCGUUUUU------------AUAUAUACUUUGUAUGUACACUG
..((.(((((((((((--(.....)))))))......(((((....)))))...))))).)).(((((..(((((.(..(....------------..)..).)))))...)))))... ( -19.50)
>consensus
GAGCGCAAUGUGAACG__UUCGAAAAGUUCAUGAAA_UGCUAAAUAUAGAAUCUCUUUGGGCAUGUGCGUCAAAGAGCGUUUAU____________AUAUAUAAAUUGUAUAUACACUG
((((((..(((((((...........)))))))....................(((((((((....)).)))))))))))))..................................... (-14.30 = -15.38 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:54 2006