Locus 5696

Sequence ID	2R_DroMel_CAF1
Location	18,042,264 – 18,042,377
Length	113
Max. P	0.823395

overview

Window 1

Location	18,042,264 – 18,042,377
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.04
Mean single sequence MFE	-31.20
Consensus MFE	-23.30
Energy contribution	-23.17
Covariance contribution	-0.14
Combinations/Pair	1.20
Mean z-score	-1.46
Structure conservation index	0.75
SVM decision value	0.69
SVM RNA-class probability	0.823395
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18042264 113 + 20766785
--ACACUCAA-AGUUAAGUGAAACCAAUUGAAAUUUAUUGACGCGAAUUGGGUUUCACUUGAACCU-GCUAACCCCGGGGCGCUGGCUUGGCGUUUCGCAUUACCAGAAUAC---AGAAG
--....((..-..((((((((((((......(((((........))))).))))))))))))..((-(.(((...((..(((((.....)))))..))..))).))).....---.)).. ( -30.70)
>DroGri_CAF1 75558 108 + 1
CAGCUCAGAAAUGUUAAGUGAAACCAAUUGAAGUUUAUUGGCGCGAAUUGGGUUUCACUUGAACCUCGGUCACCUCGAAGCGCUUAAAAUGAGUUUCAAAUUACAAAA------------
.((((((......((((((((((((((((...(((....)))...)))).))))))))))))...((((.....))))...........)))))).............------------ ( -24.60)
>DroSec_CAF1 52828 113 + 1
--ACACUUAU-AGUUAAGUGAAACCAAUUGAAAUUUAUUGACGCGAAUUGGGUUUCACUUGAACCU-GCUAACCCCGGGGCGCUGGCUUGACGUUUCGCAUUACCAGAAUAC---CGAAG
--........-..((((((((((((......(((((........))))).))))))))))))..((-(.(((...((..((((......).)))..))..))).))).....---..... ( -26.20)
>DroYak_CAF1 53574 116 + 1
--ACACUCAA-AGUUAAGUGAAACCAAUUGAAAUUUAUUGACGCGAAUUGGGUUUCACUUGAACCU-GCUAACCCCGGGGCGCUGGCUUGGCGUUUCGCAUUACCAGAAUGGAGACGGAA
--...(((..-..((((((((((((......(((((........))))).))))))))))))..((-(.(((...((..(((((.....)))))..))..))).)))....)))...... ( -33.80)
>DroMoj_CAF1 70473 110 + 1
CUGGGCGUAC-GGUUAAGUGAAACCAAUUGAAGUUUAUUGACGCGAAUUGGGUUUCACUUGAACCG--GGCACCUCGAGACGCUUAAAAUGCGUUUCACAUUACCAAA-UGC---AG---
(((((.(..(-((((((((((((((((((...(((....)))...)))).))))))))))).))))--..).))..(((((((.......)))))))...........-..)---))--- ( -40.00)
>DroAna_CAF1 47728 111 + 1
--ACACUCAG-AGUUAAGUGAAACCAAUUGAAAUUUAUUGACGCGAAUUGGGUUUCACUUGAACCC-GCUAACCCCGGGGCGCUGGCGGAGCGUUUCGCAUUACCAGAAG-----CAAAA
--........-..((((((((((((......(((((........))))).)))))))))))).(((-(.......))))((.((((..(.(((...))).)..))))..)-----).... ( -31.90)
>consensus
__ACACUCAA_AGUUAAGUGAAACCAAUUGAAAUUUAUUGACGCGAAUUGGGUUUCACUUGAACCU_GCUAACCCCGGGGCGCUGGCUUGGCGUUUCGCAUUACCAGAAU_C___CGAA_
.............((((((((((((......(((((........))))).))))))))))))..............((((((((.....))))))))....................... (-23.30 = -23.17 +  -0.14)

alignment

secondary structure

dotplot

Window 2

Location	18,042,264 – 18,042,377
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.04
Mean single sequence MFE	-29.98
Consensus MFE	-19.33
Energy contribution	-19.06
Covariance contribution	-0.27
Combinations/Pair	1.28
Mean z-score	-1.30
Structure conservation index	0.64
SVM decision value	0.02
SVM RNA-class probability	0.543223
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18042264 113 - 20766785
CUUCU---GUAUUCUGGUAAUGCGAAACGCCAAGCCAGCGCCCCGGGGUUAGC-AGGUUCAAGUGAAACCCAAUUCGCGUCAAUAAAUUUCAAUUGGUUUCACUUAACU-UUGAGUGU--
...((---((...(((((...(((...)))...))))).(((....)))..))-))(((.((((((((((.((((................))))))))))))))))).-........-- ( -27.99)
>DroGri_CAF1 75558 108 - 1
------------UUUUGUAAUUUGAAACUCAUUUUAAGCGCUUCGAGGUGACCGAGGUUCAAGUGAAACCCAAUUCGCGCCAAUAAACUUCAAUUGGUUUCACUUAACAUUUCUGAGCUG
------------...............((((......(.((((((.(....))))))).)((((((((((.((((................))))))))))))))........))))... ( -24.99)
>DroSec_CAF1 52828 113 - 1
CUUCG---GUAUUCUGGUAAUGCGAAACGUCAAGCCAGCGCCCCGGGGUUAGC-AGGUUCAAGUGAAACCCAAUUCGCGUCAAUAAAUUUCAAUUGGUUUCACUUAACU-AUAAGUGU--
(((((---(..(.(((((...(((...)))...))))).)..)))))).....-.((((.((((((((((.((((................))))))))))))))))))-........-- ( -28.99)
>DroYak_CAF1 53574 116 - 1
UUCCGUCUCCAUUCUGGUAAUGCGAAACGCCAAGCCAGCGCCCCGGGGUUAGC-AGGUUCAAGUGAAACCCAAUUCGCGUCAAUAAAUUUCAAUUGGUUUCACUUAACU-UUGAGUGU--
((((((..((.....))..))).)))(((((((((.(((.(....).))).))-.((((.((((((((((.((((................))))))))))))))))))-))).))))-- ( -29.19)
>DroMoj_CAF1 70473 110 - 1
---CU---GCA-UUUGGUAAUGUGAAACGCAUUUUAAGCGUCUCGAGGUGCC--CGGUUCAAGUGAAACCCAAUUCGCGUCAAUAAACUUCAAUUGGUUUCACUUAACC-GUACGCCCAG
---..---(((-((....)))))((.((((.......)))).))(.((((..--(((((.((((((((((.((((...((......))...))))))))))))))))))-)..))))).. ( -35.70)
>DroAna_CAF1 47728 111 - 1
UUUUG-----CUUCUGGUAAUGCGAAACGCUCCGCCAGCGCCCCGGGGUUAGC-GGGUUCAAGUGAAACCCAAUUCGCGUCAAUAAAUUUCAAUUGGUUUCACUUAACU-CUGAGUGU--
.((((-----(..........)))))((((((.((.(((.(....).))).))-(((((.((((((((((.((((................))))))))))))))))))-).))))))-- ( -32.99)
>consensus
_UUCG___G_AUUCUGGUAAUGCGAAACGCCAAGCCAGCGCCCCGGGGUUAGC_AGGUUCAAGUGAAACCCAAUUCGCGUCAAUAAAUUUCAAUUGGUUUCACUUAACU_UUGAGUGU__
.............(((((...(((...)))...))))).(((....)))......((((.((((((((((.((((................))))))))))))))))))........... (-19.33 = -19.06 +  -0.27)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:03 2006