Locus 41

Sequence ID	2R_DroMel_CAF1
Location	1,258,617 – 1,258,776
Length	159
Max. P	0.897915

overview

Window 5

Location	1,258,617 – 1,258,736
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	95.80
Mean single sequence MFE	-39.12
Consensus MFE	-34.70
Energy contribution	-35.18
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-1.42
Structure conservation index	0.89
SVM decision value	0.73
SVM RNA-class probability	0.834228
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1258617 119 + 20766785
GGUAGCUGCUCCGUCGUUCGGUGGCCAUUAUGUUGCAGCUCCUUGGGGAUGCGGCGAAAACAGCAACAUAAAAACACAGGGAACCUCAGCGUCAGCAACGUCAAUGGACGAAUGACGAU
...........(((((((((....((((((((((((.(((((((((..(((..((.......))..))).....).))))))......))....))))))).))))).))))))))).. ( -39.80)
>DroSec_CAF1 10170 119 + 1
GGUAGCUGCUCCGUCGUUCGGUGGCCAUUAUGUUGCAGCUCCUUGGGGAUGCGGCGAAAACAGCAACAUAAAAACACAGGGAACCUCAGCGUCAGCAACGUCAAUGGACGAAUGACGAU
...........(((((((((....((((((((((((.(((((((((..(((..((.......))..))).....).))))))......))....))))))).))))).))))))))).. ( -39.80)
>DroSim_CAF1 16082 119 + 1
GGUAGCUGCUCCGUCGUUCGGUGGCCAUUAUGUUGCAGCUCCUUGGGGAUGCGGCGAAAACAGCAACAUAAAAACACAGGGAACCUCAGCGUCAGCAACGUCAAUGGACGAAUGACGAU
...........(((((((((....((((((((((((.(((((((((..(((..((.......))..))).....).))))))......))....))))))).))))).))))))))).. ( -39.80)
>DroEre_CAF1 14852 119 + 1
GGUAGCUGGUCUGUCGUUCGGUGGCCAUUAUGUUGCAGCUCCUUGGGGAUGCGGCGAAAGCAGCAACAUAAAAACACAGGGAACCUUAGCGUCAGCCACUUCAAUGGACGAAUGACGAU
........(((.(((((((((((((..(((((((((.(((((....))).)).((....)).)))))))))..((.((((....))).).))..))))).((....))))))))))))) ( -42.50)
>DroYak_CAF1 13308 119 + 1
GGUAGCUGGUUCUUCGUUCGGUGGCCAUUAUGUUGCAGCUUCUUAGGGAUGCUGCGAAAACAGCAACAUAAAAACACAGGGAACCUCAGCAUCAGCAACGUCAAUGGACGAAUGACGAU
..........((.(((((((....((((((((((((..((....)).((((((((.......))..............(((...))))))))).))))))).))))).))))))).)). ( -33.70)
>consensus
GGUAGCUGCUCCGUCGUUCGGUGGCCAUUAUGUUGCAGCUCCUUGGGGAUGCGGCGAAAACAGCAACAUAAAAACACAGGGAACCUCAGCGUCAGCAACGUCAAUGGACGAAUGACGAU
...........(((((((((....((((((((((((.((((((((.(.(((..((.......))..))).....).))))))......))....))))))).))))).))))))))).. (-34.70 = -35.18 +   0.48)

alignment

secondary structure

dotplot

Window 6

Location	1,258,657 – 1,258,776
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	96.97
Mean single sequence MFE	-29.88
Consensus MFE	-26.42
Energy contribution	-26.50
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.59
Structure conservation index	0.88
SVM decision value	1.00
SVM RNA-class probability	0.897915
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1258657 119 + 20766785
CCUUGGGGAUGCGGCGAAAACAGCAACAUAAAAACACAGGGAACCUCAGCGUCAGCAACGUCAAUGGACGAAUGACGAUGGUUGUUGCUCAGGUAGAUAAAUUCGUAAUACAACCAAAA
((((((..(((..((.......))..))).....).)))))........(((((....((((....))))..))))).(((((((....(..((......))..)....)))))))... ( -29.40)
>DroSec_CAF1 10210 119 + 1
CCUUGGGGAUGCGGCGAAAACAGCAACAUAAAAACACAGGGAACCUCAGCGUCAGCAACGUCAAUGGACGAAUGACGAUGGUUGUUGCUCAGGUAGAUAAAUUCGUAAUACAACCAAAA
((((((..(((..((.......))..))).....).)))))........(((((....((((....))))..))))).(((((((....(..((......))..)....)))))))... ( -29.40)
>DroSim_CAF1 16122 119 + 1
CCUUGGGGAUGCGGCGAAAACAGCAACAUAAAAACACAGGGAACCUCAGCGUCAGCAACGUCAAUGGACGAAUGACGAUGGUUGUUGCUCAGGUAGAUAAAUUCGUAAUACAACCAAAA
((((((..(((..((.......))..))).....).)))))........(((((....((((....))))..))))).(((((((....(..((......))..)....)))))))... ( -29.40)
>DroEre_CAF1 14892 119 + 1
CCUUGGGGAUGCGGCGAAAGCAGCAACAUAAAAACACAGGGAACCUUAGCGUCAGCCACUUCAAUGGACGAAUGACGAUGGUUGUUGCUCAGGUAGAUAAAUUCGUAAUACAACCAAAA
(((((..(.(((.((....)).))).).........))))).((((.((((.(((((((.(((.........))).).)))))).)))).))))......................... ( -31.30)
>DroYak_CAF1 13348 119 + 1
UCUUAGGGAUGCUGCGAAAACAGCAACAUAAAAACACAGGGAACCUCAGCAUCAGCAACGUCAAUGGACGAAUGACGAUGGUUGUUGCUCAGGUAGAUAAAUUCUUAAUACAACCAAAA
..((((((((((((......))))..................((((.((((.((((..(((((.........)))))...)))).)))).))))......))))))))........... ( -29.90)
>consensus
CCUUGGGGAUGCGGCGAAAACAGCAACAUAAAAACACAGGGAACCUCAGCGUCAGCAACGUCAAUGGACGAAUGACGAUGGUUGUUGCUCAGGUAGAUAAAUUCGUAAUACAACCAAAA
(((((.(.(((..((.......))..))).....).))))).((((.((((.((((..(((((.........)))))...)))).)))).))))......................... (-26.42 = -26.50 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:24:28 2006