Locus 1769

Sequence ID	2R_DroMel_CAF1
Location	6,612,263 – 6,612,399
Length	136
Max. P	0.961463

overview

Window 5

Location	6,612,263 – 6,612,370
Length	107
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	78.93
Mean single sequence MFE	-27.32
Consensus MFE	-19.84
Energy contribution	-20.32
Covariance contribution	0.48
Combinations/Pair	1.05
Mean z-score	-2.12
Structure conservation index	0.73
SVM decision value	1.53
SVM RNA-class probability	0.961463
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6612263 107 + 20766785
------------CAGAUACAAGUACGUAUAUGGGAAUGCUGGAAUACAGCUCCCAGAUGCGUAUGUAAAUUCAUAAAUAAUACAUAUGCAGAUGCGGAAUGGUGUUGUUUGCUUUUGCC
------------.........((((((((.(((((..((((.....))))))))).))))))))(((((....((((((((((...(((....))).....))))))))))..))))). ( -35.20)
>DroSec_CAF1 164537 105 + 1
--------------GAUACAAAUACGGACACUGGAAUACUGGGAUACAGCUCCCAGAUGCGUAUGUAAAUUCAUAAAUAAUACAUAUGCAGAUGCGGAAUGGUGUUGUUUGCUUUUGCC
--------------....((((..(((((.(..(....)..)(((((...(((((..((((((((((.............))))))))))..)).)))...))))))))))..)))).. ( -29.72)
>DroSim_CAF1 151387 107 + 1
------------CAGAUACAAAUACGGACACUGGAAUACUGGGAUACAGCUCCCAGAUGCGUAUGUAAAUUCAUAAAUAAUACAUAUGCAGAUGCGGAAUGGUGNNNNNNNNNNNNNNN
------------................((((......((((((......)))))).((((((((((.............))))))))))..........))))............... ( -22.82)
>DroEre_CAF1 163494 119 + 1
CAGAAACCGAAACAGAUACAAAUACGAAUACUGAGAUACUGAGAUACAGCUCCCAGAUGCGCAUGUAAAUUCAUAAAUAAUACAUAUGCAGAUGCGGAUUGGUGUUGUUUGCUUUUGCC
............((((..((((((...((((..(....(((.....))).(((((..((((.(((((.............))))).))))..)).))))..))))))))))..)))).. ( -23.52)
>DroYak_CAF1 171416 93 + 1
UAG------------AUACAA--------------GUACUGGGAUACAGCUCCCAGAUGCGUAUGUAAAUUCAUAAAUAAUACAUAUGCAGAUGCGGAUUGGUGUUGUUUGCUUUUGCC
...------------......--------------(((((((((......)))))).)))(((((((.............)))))))(((((.((((((.......)))))).))))). ( -25.32)
>consensus
____________CAGAUACAAAUACGGACACUGGAAUACUGGGAUACAGCUCCCAGAUGCGUAUGUAAAUUCAUAAAUAAUACAUAUGCAGAUGCGGAAUGGUGUUGUUUGCUUUUGCC
..........................................(((((...(((((..((((((((((.............))))))))))..)).)))...)))))............. (-19.84 = -20.32 +   0.48)

alignment

secondary structure

dotplot

Window 6

Location	6,612,290 – 6,612,399
Length	109
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	84.72
Mean single sequence MFE	-31.28
Consensus MFE	-19.20
Energy contribution	-19.80
Covariance contribution	0.60
Combinations/Pair	1.14
Mean z-score	-2.24
Structure conservation index	0.61
SVM decision value	0.31
SVM RNA-class probability	0.681881
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6612290 109 + 20766785
UGGAAUACAGCUCCCAGAUGCGUAUGUAAAUUCAUAAAUAAUACAUAUGCAGAUGCGGAAUGGUGUUGUUUGCUUUUGCCACUGCCAUCAGCGGA---GCAAUUGUGA-UCCA
.(((.((((((((((...((((((((((.............))))))))))(((((((..(((((..(....)...)))))))).)))).).)))---))...)))).-))). ( -35.62)
>DroSec_CAF1 164562 109 + 1
UGGGAUACAGCUCCCAGAUGCGUAUGUAAAUUCAUAAAUAAUACAUAUGCAGAUGCGGAAUGGUGUUGUUUGCUUUUGCCACUGCCAUCAGCGGA---GCAAUUGUGA-UCCA
..(((((((((((((...((((((((((.............))))))))))(((((((..(((((..(....)...)))))))).)))).).)))---))...))).)-))). ( -34.92)
>DroEre_CAF1 163533 109 + 1
UGAGAUACAGCUCCCAGAUGCGCAUGUAAAUUCAUAAAUAAUACAUAUGCAGAUGCGGAUUGGUGUUGUUUGCUUUUGCCACUGCCAUCAGCGAA---GCAAUUGGGA-UCCA
...........(((((((((.(((.(((((....((((((((((...(((....))).....))))))))))..)))))...))))))).((...---))...)))))-.... ( -27.40)
>DroYak_CAF1 171429 109 + 1
UGGGAUACAGCUCCCAGAUGCGUAUGUAAAUUCAUAAAUAAUACAUAUGCAGAUGCGGAUUGGUGUUGUUUGCUUUUGCCACUGCCAUCAGCGGA---GCAAUUGGGA-UCCA
..((((.((((((((...((((((((((.............))))))))))(((((((..(((((..(....)...)))))))).)))).).)))---))...))..)-))). ( -34.02)
>DroAna_CAF1 178504 99 + 1
-----------CCACAAAUACGUAUGUAAAUUCAUAAAUAAUACAUAUGCAGAUGCCGCAUCGUG---UUUGUUUUUGCCACUGCCACUGAGGCACCCACCAUUGUGGCCCCA
-----------..(((((((((((((((.............)))))))...((((...)))))))---)))))....(((((((((.....)))).........))))).... ( -24.42)
>consensus
UGGGAUACAGCUCCCAGAUGCGUAUGUAAAUUCAUAAAUAAUACAUAUGCAGAUGCGGAAUGGUGUUGUUUGCUUUUGCCACUGCCAUCAGCGGA___GCAAUUGUGA_UCCA
...........((((((.((((((((((.............))))))))))(((((((..(((((...........)))))))).)))).............))))))..... (-19.20 = -19.80 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:45 2006