Locus 2886

Sequence ID	3L_DroMel_CAF1
Location	8,245,344 – 8,245,445
Length	101
Max. P	0.925705

overview

Window 8

Location	8,245,344 – 8,245,445
Length	101
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	79.10
Mean single sequence MFE	-20.38
Consensus MFE	-16.06
Energy contribution	-16.08
Covariance contribution	0.03
Combinations/Pair	1.09
Mean z-score	-1.82
Structure conservation index	0.79
SVM decision value	1.13
SVM RNA-class probability	0.920203
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8245344 101 + 23771897
UUUUUUCUUGCUUC-AAAA-----------UGGCAAAAAACAAAAAAAAUGAAUCAAAUAAAAGAUGGCCAAACGCUGCCCAUAAAUCGCAGGCAGCGUGCCUACAACAAUGG
.......(((((..-....-----------.)))))..............................(((...((((((((...........)))))))))))........... ( -21.30)
>DroSec_CAF1 67787 96 + 1
UUUUUUCUUGUUUC-AAAA-----------UGGCGAAAA-----AAAAAUGAAUCAAAUAAAAGAUGGCCAAACGCUGCCCAUAAAUCGCAGGCAGCGUGCCUACAACAAUGG
((((((.(((((..-....-----------.))))).))-----))))..................(((...((((((((...........)))))))))))........... ( -21.20)
>DroSim_CAF1 65885 99 + 1
UUUUUUCUUGUUUC-AAAA-----------UGGCAAAAAA--AAAAAAAUAAAUCAAAUAAAAGAUGGCCAAACGCUGCCCAUAAAUCGCAGGCAGCGUGCCUACAACAAUGG
((((((.(((((..-....-----------.))))).)))--))).....................(((...((((((((...........)))))))))))........... ( -21.50)
>DroEre_CAF1 72321 95 + 1
UUUUUUCUUGCCUC-AAAA-----------UGAUGGAAAA------AAACGAAUAAUAUAAAAGAUGGCCAAACGCUGCCCAUAAAUCGCAGGCAGCGUGCCUACAACAAUGG
((((((((....((-....-----------.)).))))))------))..................(((...((((((((...........)))))))))))........... ( -21.40)
>DroYak_CAF1 71619 94 + 1
UUUUUUCCUGCUUC-AAAA-----------UGGUAAAAAA------AAACAAA-AAUAUAAAAGAUGGCCAAACGCUGCCUAUAAAUCGCAGACAGCGUGCCUACAACAAUGG
((((((..((((..-....-----------.))))..)))------)))....-............(((...((((((.((.........)).)))))))))........... ( -14.80)
>DroAna_CAF1 70797 102 + 1
-UUUCUACUAUUUUUACAACAACUUUCCACCGGCAUGC----------ACUCUUUGGGUCGAAGAUGGCCAAACGUUGCCCAUAAAUCGCCGGCAGCGUGCCUACAACAAUGG
-..............................(((((((----------........((((......))))......((((...........)))))))))))........... ( -22.10)
>consensus
UUUUUUCUUGCUUC_AAAA___________UGGCAAAAAA______AAACGAAUCAAAUAAAAGAUGGCCAAACGCUGCCCAUAAAUCGCAGGCAGCGUGCCUACAACAAUGG
..................................................................(((...((((((((...........)))))))))))........... (-16.06 = -16.08 +   0.03)

alignment

secondary structure

dotplot

Window 9

Location	8,245,344 – 8,245,445
Length	101
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	79.10
Mean single sequence MFE	-25.46
Consensus MFE	-18.26
Energy contribution	-18.35
Covariance contribution	0.09
Combinations/Pair	1.15
Mean z-score	-1.97
Structure conservation index	0.72
SVM decision value	1.17
SVM RNA-class probability	0.925705
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8245344 101 - 23771897
CCAUUGUUGUAGGCACGCUGCCUGCGAUUUAUGGGCAGCGUUUGGCCAUCUUUUAUUUGAUUCAUUUUUUUUGUUUUUUGCCA-----------UUUU-GAAGCAAGAAAAAA
...........((((((((((((.........)))))))))...))).................(((((((((((((......-----------....-))))))))))))). ( -28.90)
>DroSec_CAF1 67787 96 - 1
CCAUUGUUGUAGGCACGCUGCCUGCGAUUUAUGGGCAGCGUUUGGCCAUCUUUUAUUUGAUUCAUUUUU-----UUUUCGCCA-----------UUUU-GAAACAAGAAAAAA
...........((((((((((((.........)))))))))...)))...((((.((((.((((.....-----.........-----------...)-))).)))).)))). ( -23.53)
>DroSim_CAF1 65885 99 - 1
CCAUUGUUGUAGGCACGCUGCCUGCGAUUUAUGGGCAGCGUUUGGCCAUCUUUUAUUUGAUUUAUUUUUUU--UUUUUUGCCA-----------UUUU-GAAACAAGAAAAAA
...........((((((((((((.........)))))))))...))).....................(((--(((((((...-----------....-....)))))))))) ( -23.80)
>DroEre_CAF1 72321 95 - 1
CCAUUGUUGUAGGCACGCUGCCUGCGAUUUAUGGGCAGCGUUUGGCCAUCUUUUAUAUUAUUCGUUU------UUUUCCAUCA-----------UUUU-GAGGCAAGAAAAAA
...........((((((((((((.........)))))))))...))).................(((------((((((.((.-----------....-)))).))))))).. ( -25.00)
>DroYak_CAF1 71619 94 - 1
CCAUUGUUGUAGGCACGCUGUCUGCGAUUUAUAGGCAGCGUUUGGCCAUCUUUUAUAUU-UUUGUUU------UUUUUUACCA-----------UUUU-GAAGCAGGAAAAAA
...........(((((((((((((.......))))))))))...)))..........((-(((((((------(.........-----------....-)))))))))).... ( -23.72)
>DroAna_CAF1 70797 102 - 1
CCAUUGUUGUAGGCACGCUGCCGGCGAUUUAUGGGCAACGUUUGGCCAUCUUCGACCCAAAGAGU----------GCAUGCCGGUGGAAAGUUGUUGUAAAAAUAGUAGAAA-
((((((..(((.((((.((...(((((...((((.((.....)).))))..))).))...)).))----------)).))))))))).........................- ( -27.80)
>consensus
CCAUUGUUGUAGGCACGCUGCCUGCGAUUUAUGGGCAGCGUUUGGCCAUCUUUUAUUUGAUUCAUUU______UUUUUUGCCA___________UUUU_GAAACAAGAAAAAA
...........(((((((((((((.......))))))))))...))).................................................................. (-18.26 = -18.35 +   0.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:13 2006