Locus 3467

Sequence ID	3R_DroMel_CAF1
Location	9,367,055 – 9,367,148
Length	93
Max. P	0.998437

overview

Window 2

Location	9,367,055 – 9,367,148
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	89.87
Mean single sequence MFE	-20.55
Consensus MFE	-16.92
Energy contribution	-17.24
Covariance contribution	0.32
Combinations/Pair	1.12
Mean z-score	-1.96
Structure conservation index	0.82
SVM decision value	1.43
SVM RNA-class probability	0.953493
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9367055 93 + 27905053
UUUUGGGCUUUUUUUUUUGUUGUUGUCCGGUUGGUUGCAUUUUGUGCAUGUCAAGCCAAGGUUCAUUAAGCUGAAUUUUUCAGCAAUUUGGAA
....((((................))))((((...(((((...))))).....))))....((((....(((((.....)))))....)))). ( -20.09)
>DroSec_CAF1 136398 91 + 1
UUUUGGGCUUUUUUUUU--UUGUUGUCCGGCUGGCUGCAUUUUGUGCAUGUCAAGCCAAGGUUCAUUAAGCUGAAUUUUUCAGCAAUUUGCAA
....((((.........--.....))))((((((((((((...))))).))).))))............(((((.....)))))......... ( -24.94)
>DroSim_CAF1 145502 90 + 1
UUUUGGGCUUUUU-UUU--UUGUUGUCCGGCUGGCUGCAUUUUGUGCAUGUCAAGCCAAGGUUCAUUAAGCUGAAUUUUUCAGCAAUUUGCAA
....((((.....-...--.....))))((((((((((((...))))).))).))))............(((((.....)))))......... ( -25.02)
>DroEre_CAF1 137089 93 + 1
UUUAAGUUUUUUUUUCUUUUUGUUGCUCGGCUGACUGCAUUUUGUGCAUGUCAAGCCAAGGUUCAUUAAGCUAAAUUUUUCAGCAAUUUGCAA
.....................((((((.((((((((((((...))))).))).))))..((((.....)))).........))))))...... ( -20.10)
>DroYak_CAF1 137556 90 + 1
UUUUGUUUU--UUUUUUUUUUGUU-UUCAGCUGGCUGCAUUUUGUGCAUGUCAAGCCAAGGUUCAUUAAGCUAAAUUUUUCAGCAAUUUGCAA
.........--.............-...((((((((((((...))))).))).(((....))).....))))..........((.....)).. ( -12.60)
>consensus
UUUUGGGCUUUUUUUUUU_UUGUUGUCCGGCUGGCUGCAUUUUGUGCAUGUCAAGCCAAGGUUCAUUAAGCUGAAUUUUUCAGCAAUUUGCAA
...................((((((...((((((((((((...))))).))).))))((((((((......)))))))).))))))....... (-16.92 = -17.24 +   0.32)

alignment

secondary structure

dotplot

Window 3

Location	9,367,055 – 9,367,148
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	89.87
Mean single sequence MFE	-17.72
Consensus MFE	-14.46
Energy contribution	-13.86
Covariance contribution	-0.60
Combinations/Pair	1.25
Mean z-score	-3.09
Structure conservation index	0.82
SVM decision value	3.10
SVM RNA-class probability	0.998437
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9367055 93 - 27905053
UUCCAAAUUGCUGAAAAAUUCAGCUUAAUGAACCUUGGCUUGACAUGCACAAAAUGCAACCAACCGGACAACAACAAAAAAAAAAGCCCAAAA
.........(((((.....)))))............(((((....((((.....)))).((....))................)))))..... ( -15.80)
>DroSec_CAF1 136398 91 - 1
UUGCAAAUUGCUGAAAAAUUCAGCUUAAUGAACCUUGGCUUGACAUGCACAAAAUGCAGCCAGCCGGACAACAA--AAAAAAAAAGCCCAAAA
..((.....(((((.....)))))..........((((((.(...((((.....)))).).)))))).......--.........))...... ( -18.30)
>DroSim_CAF1 145502 90 - 1
UUGCAAAUUGCUGAAAAAUUCAGCUUAAUGAACCUUGGCUUGACAUGCACAAAAUGCAGCCAGCCGGACAACAA--AAA-AAAAAGCCCAAAA
..((.....(((((.....)))))..........((((((.(...((((.....)))).).)))))).......--...-.....))...... ( -18.30)
>DroEre_CAF1 137089 93 - 1
UUGCAAAUUGCUGAAAAAUUUAGCUUAAUGAACCUUGGCUUGACAUGCACAAAAUGCAGUCAGCCGAGCAACAAAAAGAAAAAAAAACUUAAA
((((.....(((((.....)))))..........((((((.(((.((((.....)))))))))))))))))...................... ( -22.60)
>DroYak_CAF1 137556 90 - 1
UUGCAAAUUGCUGAAAAAUUUAGCUUAAUGAACCUUGGCUUGACAUGCACAAAAUGCAGCCAGCUGAA-AACAAAAAAAAAA--AAAACAAAA
..((.....(((((.....)))))...........(((((.(.(((.......)))))))))))....-.............--......... ( -13.60)
>consensus
UUGCAAAUUGCUGAAAAAUUCAGCUUAAUGAACCUUGGCUUGACAUGCACAAAAUGCAGCCAGCCGGACAACAA_AAAAAAAAAAGCCCAAAA
.........(((((.....)))))..........((((((.(...((((.....)))).).)))))).......................... (-14.46 = -13.86 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:43 2006