Locus 1549

Sequence ID	3L_DroMel_CAF1
Location	4,522,829 – 4,522,948
Length	119
Max. P	0.593494

overview

Window 6

Location	4,522,829 – 4,522,948
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.75
Mean single sequence MFE	-26.28
Consensus MFE	-17.31
Energy contribution	-18.38
Covariance contribution	1.06
Combinations/Pair	1.11
Mean z-score	-1.73
Structure conservation index	0.66
SVM decision value	0.08
SVM RNA-class probability	0.575170
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4522829 119 + 23771897
ACUAACAACAACGCCUCUGUUAAAUAUAACAGUGAAUUUCGCCGCUUUAACAGCAACUGAGAGCGGCUAACAGUGCGAGAGAAAUUCGAACGGGGCAGCAACAAA-AAAGAAGAAAAAGA
............((((((((((....))))).((((((((((((((((..(((...)))))))))))...(.....)...))))))))...))))).........-.............. ( -29.30)
>DroSec_CAF1 100473 116 + 1
---AACUACAACGCCUCUGUUAAAUAUAACAGUGAGUUUCGCCGCCUUAACAGCAACUGAGAGCGGGUAACAGCGCGAGAGAAAUUCGAACG-GGCAGCAACAAAAAAAGAAGAAAAAGA
---.........((((((((((....))))))((((((((.((((((((........)))).)))).......(....).))))))))...)-)))........................ ( -27.70)
>DroEre_CAF1 106606 118 + 1
AAAAAUACCAUCGCCUCUGUGAAACUUAACAGUGAAUUUCGCCGUCUUAACAGCAAUUGAGAGCGGGUAACAGUGCGAGAGAAA-CCGAACGAGCCAGCAACAAA-AAAGAAGAAGAAUA
.......(..((((..((((((((.(((....))).)))).(((((((((......)))))).)))...)))).))))..)...-....................-.............. ( -19.40)
>DroYak_CAF1 102821 119 + 1
UAUGACACCGCCGCCUCUGUAAAAUAUAACAGUGAAUUUCGCCGCAUUAACAGCAAUUGAGAGCGGCUAACAGUGCGAGAGAAAUUCGAACGGGGCAGUAACAAA-AAAGAAGAAAAAGA
..((..((.(((.((.((((........))))((((((((.(((((((...(((...(....)..)))...)))))).).))))))))...))))).))..))..-.............. ( -28.70)
>consensus
AAUAACAACAACGCCUCUGUUAAAUAUAACAGUGAAUUUCGCCGCCUUAACAGCAACUGAGAGCGGCUAACAGUGCGAGAGAAAUUCGAACGGGGCAGCAACAAA_AAAGAAGAAAAAGA
............((((((((((....))))).((((((((.((((.(((...((........))...)))....))).).))))))))...)))))........................ (-17.31 = -18.38 +   1.06)

alignment

secondary structure

dotplot

Window 7

Location	4,522,829 – 4,522,948
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.75
Mean single sequence MFE	-28.23
Consensus MFE	-19.38
Energy contribution	-20.50
Covariance contribution	1.12
Combinations/Pair	1.15
Mean z-score	-1.63
Structure conservation index	0.69
SVM decision value	0.12
SVM RNA-class probability	0.593494
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4522829 119 - 23771897
UCUUUUUCUUCUUU-UUUGUUGCUGCCCCGUUCGAAUUUCUCUCGCACUGUUAGCCGCUCUCAGUUGCUGUUAAAGCGGCGAAAUUCACUGUUAUAUUUAACAGAGGCGUUGUUGUUAGU
..............-.........(((......(((((((.(.(((....(((((.((........)).))))).)))).))))))).((((((....)))))).)))............ ( -28.20)
>DroSec_CAF1 100473 116 - 1
UCUUUUUCUUCUUUUUUUGUUGCUGCC-CGUUCGAAUUUCUCUCGCGCUGUUACCCGCUCUCAGUUGCUGUUAAGGCGGCGAAACUCACUGUUAUAUUUAACAGAGGCGUUGUAGUU---
.....................(((((.-((((.((.((((....(((........))).....((((((.....)))))))))).)).((((((....)))))).))))..))))).--- ( -25.30)
>DroEre_CAF1 106606 118 - 1
UAUUCUUCUUCUUU-UUUGUUGCUGGCUCGUUCGG-UUUCUCUCGCACUGUUACCCGCUCUCAAUUGCUGUUAAGACGGCGAAAUUCACUGUUAAGUUUCACAGAGGCGAUGGUAUUUUU
..............-...(..(((((.....))))-)..)...........(((((((.(((....(((((....)))))((((((........))))))...))))))..))))..... ( -22.90)
>DroYak_CAF1 102821 119 - 1
UCUUUUUCUUCUUU-UUUGUUACUGCCCCGUUCGAAUUUCUCUCGCACUGUUAGCCGCUCUCAAUUGCUGUUAAUGCGGCGAAAUUCACUGUUAUAUUUUACAGAGGCGGCGGUGUCAUA
..............-..((.(((((((((....(((((((.(.((((...(((((.((........)).)))))))))).))))))).((((........)))).)).))))))).)).. ( -36.50)
>consensus
UCUUUUUCUUCUUU_UUUGUUGCUGCCCCGUUCGAAUUUCUCUCGCACUGUUACCCGCUCUCAAUUGCUGUUAAGGCGGCGAAAUUCACUGUUAUAUUUAACAGAGGCGUUGGUGUUAUU
..................((((((.........(((((((....((..........))........(((((....)))))))))))).((((((....)))))).))))))......... (-19.38 = -20.50 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:24 2006