Locus 3934

Sequence ID	2L_DroMel_CAF1
Location	11,479,247 – 11,479,337
Length	90
Max. P	0.974859

overview

Window 2

Location	11,479,247 – 11,479,337
Length	90
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	74.87
Mean single sequence MFE	-19.07
Consensus MFE	-14.90
Energy contribution	-14.90
Covariance contribution	0.00
Combinations/Pair	1.21
Mean z-score	-1.22
Structure conservation index	0.78
SVM decision value	0.92
SVM RNA-class probability	0.881173
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11479247 90 + 22407834
GGCUUGGUAACAUUUUUUUUUACCAGUUUCCUCAUUAUACCCUUGCAGAGGGUAUAUUGCUAAUAGCCAGAUGUUUGAAA---------UAAAGAUAUU
((((((((((.........)))))).......((.(((((((((...))))))))).)).....)))).(((((((....---------...))))))) ( -22.90)
>DroSec_CAF1 43044 98 + 1
GGCUUGGUAACAUUUU-UUUCACCAGUUUCCUCAUUAUACCCUUACAAAGGGUAUAUUGCUAAUAGCCAGAUGUUUGAAACGCAGUGAAUAUAGAUAUU
...........((((.-.(((((..(((((..(((((((((((.....)))))))...((.....))..))))...)))))...)))))...))))... ( -21.50)
>DroSim_CAF1 46774 90 + 1
GGCUUGGUAACAUUUUUUUUCACCAGUUUCCUCAUUAUACCAUUACAAAGGGUAUAUUGCUAAUAGCCAGUUGUUUGAAAC--------UAUAGCUAU-
((((((((.............)))).......((.((((((.........)))))).)).....))))((((((.......--------.))))))..- ( -16.22)
>DroEre_CAF1 49075 78 + 1
GGCUUGGUAACAAUUUUUUCUACCAGUUUCCUC-UUCUACCCUUGCUGAGGGUAUGUCGAUUUCAGUCAGAAUAUUGCA--------------------
(((((((((...........)))))).......-...(((((((...))))))).)))(((....)))...........-------------------- ( -14.20)
>DroYak_CAF1 48862 98 + 1
GGCUUGGUAACCAUUUUUUUCACCAGUUUCCUCAUUCUGCCCUUGCUGAGGGUAUAAUGACUUUAGUCAGCAGUUUGCAACGCAGUGAAU-UACAUAUU
((((((((.............))))......(((((.(((((((...))))))).)))))....)))).(.((((..(......)..)))-).)..... ( -20.52)
>consensus
GGCUUGGUAACAUUUUUUUUCACCAGUUUCCUCAUUAUACCCUUGCAGAGGGUAUAUUGCUAAUAGCCAGAUGUUUGAAAC________UAUAGAUAUU
((((((((.............)))).......((.(((((((((...))))))))).)).....))))............................... (-14.90 = -14.90 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	11,479,247 – 11,479,337
Length	90
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	74.87
Mean single sequence MFE	-19.80
Consensus MFE	-13.96
Energy contribution	-15.16
Covariance contribution	1.20
Combinations/Pair	1.10
Mean z-score	-1.92
Structure conservation index	0.71
SVM decision value	1.74
SVM RNA-class probability	0.974859
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11479247 90 - 22407834
AAUAUCUUUA---------UUUCAAACAUCUGGCUAUUAGCAAUAUACCCUCUGCAAGGGUAUAAUGAGGAAACUGGUAAAAAAAAAUGUUACCAAGCC
..........---------............((((..(((((.((((((((.....))))))))((.((....)).)).........)))))...)))) ( -21.60)
>DroSec_CAF1 43044 98 - 1
AAUAUCUAUAUUCACUGCGUUUCAAACAUCUGGCUAUUAGCAAUAUACCCUUUGUAAGGGUAUAAUGAGGAAACUGGUGAAA-AAAAUGUUACCAAGCC
..........(((((((.(((((...(((...((.....))..((((((((.....)))))))))))..)))))))))))).-................ ( -23.10)
>DroSim_CAF1 46774 90 - 1
-AUAGCUAUA--------GUUUCAAACAACUGGCUAUUAGCAAUAUACCCUUUGUAAUGGUAUAAUGAGGAAACUGGUGAAAAAAAAUGUUACCAAGCC
-...(((..(--------(((((...((....(((((((.(((........))))))))))....))..))))))(((((.........))))).))). ( -18.80)
>DroEre_CAF1 49075 78 - 1
--------------------UGCAAUAUUCUGACUGAAAUCGACAUACCCUCAGCAAGGGUAGAA-GAGGAAACUGGUAGAAAAAAUUGUUACCAAGCC
--------------------.(((((.(((((.((..........((((((.....))))))...-.((....)))))))))...)))))......... ( -15.20)
>DroYak_CAF1 48862 98 - 1
AAUAUGUA-AUUCACUGCGUUGCAAACUGCUGACUAAAGUCAUUAUACCCUCAGCAAGGGCAGAAUGAGGAAACUGGUGAAAAAAAUGGUUACCAAGCC
........-.((((((..........((((((((....))))......(((.....)))))))....((....))))))))......((((....)))) ( -20.30)
>consensus
AAUAUCUAUA________GUUUCAAACAUCUGGCUAUUAGCAAUAUACCCUCUGCAAGGGUAUAAUGAGGAAACUGGUGAAAAAAAAUGUUACCAAGCC
...............................((((.....((.((((((((.....)))))))).))((....))(((((.........))))).)))) (-13.96 = -15.16 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:08 2006