Locus 2414

Sequence ID	2R_DroMel_CAF1
Location	8,687,221 – 8,687,404
Length	183
Max. P	0.689088

overview

Window 6

Location	8,687,221 – 8,687,314
Length	93
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	82.44
Mean single sequence MFE	-31.14
Consensus MFE	-20.05
Energy contribution	-20.33
Covariance contribution	0.28
Combinations/Pair	1.22
Mean z-score	-2.05
Structure conservation index	0.64
SVM decision value	0.24
SVM RNA-class probability	0.647458
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8687221 93 + 20766785
AGGCAAAGCUGCAAAAACAGCUGAU-----CGCAAGCGAAAGCUUUCCGUGCG------CAGCGGAGCUUUUGAGUUGGCCGGCA-GCUGAUAAAUGAGCACAGU----
......((((((.....(((((.(.-----.((((((....))))(((((...------..)))))))...).)))))....)))-)))................---- ( -31.20)
>DroSec_CAF1 2582 93 + 1
AGGCAAAGCUACAAAAACAGCUGAU-----CGCCAGCGAAAGCUUUCCGUGCG------CAGCGGAGCUUUUGAGUUGGCCGGCA-GCUGAUAAAUGAGCACAGU----
.......(((.......((((((..-----.((((((((((((..(((((...------..)))))))))))..))))))...))-)))).......))).....---- ( -35.54)
>DroSim_CAF1 4979 93 + 1
AGGCAAAGCUGCAAAAACAGCUGAU-----CGCAAGCGAAAGCUUUCCGUGCG------CAACGGAGCUUUUGAGUUGGCCGGCA-GCUGAUAAAUGAGCACAGU----
......((((((.....(((((.(.-----.((((((....))))(((((...------..)))))))...).)))))....)))-)))................---- ( -31.50)
>DroEre_CAF1 2499 93 + 1
AGGCAAAGCUGCAAAAACAGCUGAU-----UGCUCGCGAAAGCUUUCCGUUCG------CCGCGGAGCUUUUGAGUUGGCCCGCA-GCUGAUAAAUGAGCACAGU----
......(((((......)))))...-----(((((((....)).....(((.(------(.((((.(((........))))))).-)).)))....)))))....---- ( -32.10)
>DroYak_CAF1 4924 93 + 1
AGGCAAAGCUACAAAAACAGCUGAU-----CGCAGGCGAAAGCUUUCCGUUCG------CCGCGCAGCUUUUGAGUUGGCCUGCA-GCUGAUAAAUGAGCACAGU----
((((..((((.((((...(((((..-----(((.((((((.(.....).))))------)))))))))))))))))).))))...-(((........))).....---- ( -30.20)
>DroPer_CAF1 3113 108 + 1
AAGAAAACUUGGGAUAACAGCUGUUUUGGACGCUA-CAAAAGCUCGUCGAGCGAGAAAGAAGCAAAGCUUUUGUGUGGGCUUGCAGGCUGAUAAAAAAGCACAGUACAG
....................((((.(((...(((.-(.....((((.....))))...).)))...((((((.(((.((((....)))).))).)))))).))).)))) ( -26.30)
>consensus
AGGCAAAGCUGCAAAAACAGCUGAU_____CGCAAGCGAAAGCUUUCCGUGCG______CAGCGGAGCUUUUGAGUUGGCCGGCA_GCUGAUAAAUGAGCACAGU____
.(((..(((((......)))))..............((((((((..((((...........)))))))))))).....))).....(((........)))......... (-20.05 = -20.33 +   0.28)

alignment

secondary structure

dotplot

Window 7

Location	8,687,314 – 8,687,404
Length	90
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	80.85
Mean single sequence MFE	-30.18
Consensus MFE	-19.14
Energy contribution	-19.38
Covariance contribution	0.24
Combinations/Pair	1.16
Mean z-score	-1.83
Structure conservation index	0.63
SVM decision value	0.32
SVM RNA-class probability	0.689088
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8687314 90 - 20766785
AGAGGUGUCUCGGUUGA----ACGGUGGGAACUGAAGAAGGCGGCGUUGGCGAAGACGCUGCUGAUUUGUUUGCCUGUUGACCGACGAGCGACA
....((...((((((.(----((((.(.((((.(((...(((((((((......)))))))))..))))))).))))))))))))...)).... ( -34.20)
>DroSec_CAF1 2675 86 - 1
AGAGGUGUCUCGGUUGA----ACGGGGGGAACUGAAGAAGGCGGCGGUGGCGAAGACGCUGCUGAU----UUGCCUGUUGACCGACGAGCGACA
....((...((((((.(----(((((.(((.((.....)).((((((((.......)))))))).)----)).))))))))))))...)).... ( -31.20)
>DroSim_CAF1 5072 86 - 1
AGAGGUGUCUCGGUUGA----ACGGUGGGAACUGAAGAAGGCGGCGGUGGCGAAGACGCUGCUGGU----UUGCCUGUUGACCGACGAGCGACA
....((...(((((..(----.((((....))))....(((((((((..(((....)))..)))..----)))))).)..)))))...)).... ( -31.20)
>DroEre_CAF1 2592 79 - 1
AG--------CGGUUGACAAGACAGGAGGAACUGAAGAAGGCGGCGGC---GAAGGCGCUGCUGGU----UUGCCUGUUGACCGACGAGCGACA
.(--------(.((((....((((((..(((((......(((((((.(---....)))))))))))----)).))))))...))))..)).... ( -30.50)
>DroYak_CAF1 5017 76 - 1
AG--------CGGUUGACAAUACAGGAGGAACUGAAAAAGGUGGCGUU------GGAGCUGCUGGU----UUGCCUGUUGACCGACGAGCGACA
.(--------((((..(((...(((......)))(((..((..((...------...))..))..)----))...)))..)))).)........ ( -23.80)
>consensus
AGAGGUGUCUCGGUUGA____ACGGGGGGAACUGAAGAAGGCGGCGGUGGCGAAGACGCUGCUGGU____UUGCCUGUUGACCGACGAGCGACA
..........((((..(.....(((......)))....(((((((((((.......))))))).........)))).)..)))).......... (-19.14 = -19.38 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:34 2006