Locus 1008

Sequence ID	3L_DroMel_CAF1
Location	2,989,010 – 2,989,150
Length	140
Max. P	0.942555

overview

Window 8

Location	2,989,010 – 2,989,110
Length	100
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	76.58
Mean single sequence MFE	-25.15
Consensus MFE	-20.08
Energy contribution	-19.62
Covariance contribution	-0.47
Combinations/Pair	1.40
Mean z-score	-1.55
Structure conservation index	0.80
SVM decision value	1.33
SVM RNA-class probability	0.942555
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2989010 100 + 23771897
CUU--UUUUUUUUUUUUGUAGGAGCUCAAGGGUUUAAAGUUU-------------UUUCGGAUGGCUGGCAUGUAGAUUUCAGUCAGCUUUCAGUGGUUAAGCCGCGUAAUCCGA
...--................(((((....))))).......-------------..(((((((((((((.((.......)))))))))....((((.....))))...)))))) ( -25.60)
>DroSec_CAF1 23411 92 + 1
-----U-----UUUUUUAAAGGAGCUCAAGGGUUUAAAGUUU-------------UUUCGGAUGGCUGGCAUGUAGAUUUCAGUCAGCUUUCAGUGGUUAAGCCGCGUAAUCCGA
-----.-----..........(((((....))))).......-------------..(((((((((((((.((.......)))))))))....((((.....))))...)))))) ( -25.60)
>DroSim_CAF1 23900 97 + 1
-----UUUUUUUUUUUUGAAGGAGCUUAAGGGUUUAAAGUUU-------------UUUCGGAUGGCUGGCAUGUAGAUUUCAGUCAGCUUUCAGUGGUUAAGCCGCGUAAUCCGA
-----............((((((((((.........))))))-------------))))(((((((((((.((.......)))))))))....((((.....))))...)))).. ( -27.50)
>DroEre_CAF1 25771 89 + 1
-------------UUUUUAAGGAGCUUAAGGGUUUAAAGUUU-------------UGUCGGAUGGCUGGCAUGUAGAUUUCAGUCAGCUUUCAGUGGCUAAGCCGCGUAAUCCGA
-------------.......(((((((.........))))))-------------).(((((((((((((.((.......)))))))))....(((((...)))))...)))))) ( -26.00)
>DroYak_CAF1 23463 102 + 1
GUUAUUUUUUUUUUUUUGAGGCAGCUUAAGGGUUUAAAGUUU-------------UUUCGGAUGGCUGGCAUGUAGAUUUCAGUCAGCUUUCAGUGGUUAAGCCGCGUAAUCCGA
...(((((....((((((((....))))))))...)))))..-------------..(((((((((((((.((.......)))))))))....((((.....))))...)))))) ( -26.00)
>DroAna_CAF1 22034 103 + 1
------UUUUUU--UUU--GUGAGUUUAAAGGCUUAAAAUUGUUUUCCCCUUUUUUUGCGGCU--UUGUUCUGUGGAUCUGAAAAGGCUUUUGGCAGUUGAGCUGUGUAAUCCAA
------......--...--.((..((....((((((..((((((....(((((((...(.((.--.......)).)....))))))).....))))))))))))....))..)). ( -20.20)
>consensus
_____UUUUUUUUUUUUGAAGGAGCUUAAGGGUUUAAAGUUU_____________UUUCGGAUGGCUGGCAUGUAGAUUUCAGUCAGCUUUCAGUGGUUAAGCCGCGUAAUCCGA
.....................(((((....)))))......................(((((((((((((.((.......)))))))))....(((((...)))))...)))))) (-20.08 = -19.62 +  -0.47)

alignment

secondary structure

dotplot

Window 9

Location	2,989,048 – 2,989,150
Length	102
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	81.35
Mean single sequence MFE	-31.20
Consensus MFE	-17.84
Energy contribution	-19.95
Covariance contribution	2.11
Combinations/Pair	1.12
Mean z-score	-2.00
Structure conservation index	0.57
SVM decision value	0.08
SVM RNA-class probability	0.573763
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2989048 102 + 23771897
UUUUUCGGAUGGCUGGCAUGUAGA---UUUCAGUCAGCUUUCAG--UGGUUAAGCCGCGUAAUCCGAGCUGUAUUUAUGGUUCUUUCAGCCAUUCAGAAAGCUGUAA
....(((((((((((((.((....---...)))))))))....(--(((.....))))...))))))(((......((((((.....))))))......)))..... ( -31.90)
>DroSec_CAF1 23441 102 + 1
UUUUUCGGAUGGCUGGCAUGUAGA---UUUCAGUCAGCUUUCAG--UGGUUAAGCCGCGUAAUCCGAGCUGUAUUUAUGGUUCUUUCAGCCAUUCAGAAAGCUGUAA
....(((((((((((((.((....---...)))))))))....(--(((.....))))...))))))(((......((((((.....))))))......)))..... ( -31.90)
>DroSim_CAF1 23935 102 + 1
UUUUUCGGAUGGCUGGCAUGUAGA---UUUCAGUCAGCUUUCAG--UGGUUAAGCCGCGUAAUCCGAGCUGUAUUUAUGGUUCUUUCAGCCAUUCAGAAAGCUGUAA
....(((((((((((((.((....---...)))))))))....(--(((.....))))...))))))(((......((((((.....))))))......)))..... ( -31.90)
>DroEre_CAF1 25798 102 + 1
UUUGUCGGAUGGCUGGCAUGUAGA---UUUCAGUCAGCUUUCAG--UGGCUAAGCCGCGUAAUCCGAGCUGUAUUUAUGGUUCUUUCAGCCAUUCAGCAUGCUUUAA
....(((((((((((((.((....---...)))))))))....(--((((...)))))...))))))((((.....((((((.....)))))).))))......... ( -34.60)
>DroYak_CAF1 23503 102 + 1
UUUUUCGGAUGGCUGGCAUGUAGA---UUUCAGUCAGCUUUCAG--UGGUUAAGCCGCGUAAUCCGAGCUGUGUUUAUGGUUGUUUCAGCCAUUCAGAAGGCUGUAA
....(((((((((((((.((....---...)))))))))....(--(((.....))))...))))))(((......(((((((...)))))))......)))..... ( -33.80)
>DroPer_CAF1 24713 97 + 1
UGUUUUUGGUGUUGGUGGUGUUGAAGCCCUCGAUA--UUUUCGAACAUUUUGAGCCGUUUAAGCCGCGCUGUGUUAAUGGA-----CACCCAGUCG-AGAGCACU--
(((((((((((((((..(((((((.....))))))--)..)).(((((...(.((.((....)).)).).)))))....))-----)))).....)-))))))..-- ( -23.10)
>consensus
UUUUUCGGAUGGCUGGCAUGUAGA___UUUCAGUCAGCUUUCAG__UGGUUAAGCCGCGUAAUCCGAGCUGUAUUUAUGGUUCUUUCAGCCAUUCAGAAAGCUGUAA
....(((((((((((((.((..........)))))))))........((.....)).....))))))(((......((((((.....))))))......)))..... (-17.84 = -19.95 +   2.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:44 2006