Locus 8335

Sequence ID	3R_DroMel_CAF1
Location	22,247,436 – 22,247,597
Length	161
Max. P	0.744644

overview

Window 7

Location	22,247,436 – 22,247,527
Length	91
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	82.85
Mean single sequence MFE	-28.31
Consensus MFE	-19.20
Energy contribution	-19.50
Covariance contribution	0.30
Combinations/Pair	1.32
Mean z-score	-1.60
Structure conservation index	0.68
SVM decision value	-0.03
SVM RNA-class probability	0.516081
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22247436 91 + 27905053
UCAGGUGCUGGAAAGUGCAGCGCUUCAAUAUUCAUCUG-------------GCGAAUAUUUGCGUCGCGUAGUUGGCAA-AUUUUACCGCUGCGCU-UAUUCGUCU
..((((((((.......))))))))............(-------------(((((((...((((.(((.((((....)-)))....))).)))).-)))))))). ( -29.30)
>DroSec_CAF1 19747 91 + 1
UCAGGUGCUGGAAAGUGCUGCGCUUCAAUAUUCAUCCG-------------GCGAAUAUUUGCGUCGCGUAGUUGGCAA-AUUUUACCGCUGCGCU-UAUUCGUCU
...((..((....))..))..................(-------------(((((((...((((.(((.((((....)-)))....))).)))).-)))))))). ( -26.90)
>DroSim_CAF1 19827 91 + 1
UCAGGUGCUGGAAAGUGCUGCGCUUCAAUAUUCAUCCG-------------GCGAAUAUUUGCGUCGCGCAGUUGGCAA-AUUUUACCGCUGCGCU-UAUUCGUCU
...((..((....))..))((((...(((((((.....-------------..))))))).)))).(((((((.((...-......))))))))).-......... ( -28.60)
>DroEre_CAF1 26833 91 + 1
UCAGGUGCUGGGAAGUGCAGCGCUUCAAAAUUCAUCUG-------------GCGAAUAUUUGCGUCGCGUAGUUGGCAA-AUUUUACCGCUGCGCU-UAUUCGGCU
......((((((((((((((((....((((((((.(((-------------((((.........)))).))).)))...-)))))..)))))))))-).)))))). ( -29.90)
>DroYak_CAF1 24711 82 + 1
UCAGGU----------GCAGCGCUUCAAUAUUCAUCUG-------------GCGAGUAUUUGCGUCGCGUAGUUGGCAA-AUUUCACCGCUGCGCUUUACUCGUCU
.(((((----------(...............))))))-------------(((((((...((((.(((.((((....)-)))....))).))))..))))))).. ( -23.86)
>DroAna_CAF1 20987 105 + 1
UCAGGUGCUGCAAAGUAUAGUGCUUCAAUAUUCAUCGGAUGCUGGAAGCAAGCGGACAUUUUCGUGGCAUAGUUGGCAAAAUUUUGCCGCGAUGCU-UAUUGGUCU
..(((..(((.......)))..)))(((((..(((((..(((((....).))))..)......((((((.((((.....)))).))))))))))..-))))).... ( -31.30)
>consensus
UCAGGUGCUGGAAAGUGCAGCGCUUCAAUAUUCAUCUG_____________GCGAAUAUUUGCGUCGCGUAGUUGGCAA_AUUUUACCGCUGCGCU_UAUUCGUCU
....(((((....))))).((((...(((((((....................))))))).)))).(((((((.((..........)))))))))........... (-19.20 = -19.50 +   0.30)

alignment

secondary structure

dotplot

Window 8

Location	22,247,489 – 22,247,597
Length	108
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	91.74
Mean single sequence MFE	-27.47
Consensus MFE	-24.74
Energy contribution	-24.22
Covariance contribution	-0.53
Combinations/Pair	1.17
Mean z-score	-1.34
Structure conservation index	0.90
SVM decision value	0.46
SVM RNA-class probability	0.744644
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22247489 108 + 27905053
GCGUAGUUGGCAA-AUUUUACCGCUGCGCU-UAUUCGUCUGGCUGUUCUUGUUGGCUAACAAAACU-UUGGCCCACAAAACCGCACACUCGUACGUAUGCACUCACACAAA
(((((((.((...-......))))))))).-....((..((((.(((.((((.((((((.......-)))))).))))))).)).))..)).................... ( -26.90)
>DroSec_CAF1 19800 108 + 1
GCGUAGUUGGCAA-AUUUUACCGCUGCGCU-UAUUCGUCUGGCUGUUCUUGUUGGCUAACAAAACU-UUGGCCCACAAAACCGCACACUCGUACGUAUGCACUCACACAAA
(((((((.((...-......))))))))).-....((..((((.(((.((((.((((((.......-)))))).))))))).)).))..)).................... ( -26.90)
>DroSim_CAF1 19880 108 + 1
GCGCAGUUGGCAA-AUUUUACCGCUGCGCU-UAUUCGUCUGGCUGUUCUUGUUGGCUAACAAAACU-UUGGCCCACAAAACCGCACACUCGUACGUAUGCACUCACACAAA
(((((((.((...-......))))))))).-....((..((((.(((.((((.((((((.......-)))))).))))))).)).))..)).................... ( -28.90)
>DroEre_CAF1 26886 108 + 1
GCGUAGUUGGCAA-AUUUUACCGCUGCGCU-UAUUCGGCUGGCUGUUCUUGUUGGCUAACAAAACU-UUGGCCCACAAAACCGCACACUAGUACAUAUGCACUCGCACAAG
(((((((.((...-......))))))))).-((((.((.((((.(((.((((.((((((.......-)))))).))))))).)).))))))))....(((....))).... ( -27.50)
>DroYak_CAF1 24754 109 + 1
GCGUAGUUGGCAA-AUUUCACCGCUGCGCUUUACUCGUCUGGCUGUUCUUGUUGGCUAACAAAACU-UUGGCCCACAAAACCGCACACUCGUACAUAUGCACUCACACAAG
(((((((.((...-......)))))))))......((..((((.(((.((((.((((((.......-)))))).))))))).)).))..)).................... ( -26.90)
>DroAna_CAF1 21053 108 + 1
GCAUAGUUGGCAAAAUUUUGCCGCGAUGCU-UAUUGGUCUUGUUGUUCUUGUUGGCUAACAAAACUUUUGGCCCACAAAACCGCACACUCGCACACA--CACGCGUACAAA
((((.((.(((((....))))))).)))).-..(((....(((.(((.((((.((((((........)))))).))))))).)))....(((.....--...)))..))). ( -27.70)
>consensus
GCGUAGUUGGCAA_AUUUUACCGCUGCGCU_UAUUCGUCUGGCUGUUCUUGUUGGCUAACAAAACU_UUGGCCCACAAAACCGCACACUCGUACAUAUGCACUCACACAAA
(((((((.((..........)))))))))............((.(((.((((.((((((........)))))).))))))).))........................... (-24.74 = -24.22 +  -0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:08 2006