Locus 5829

Sequence ID	2R_DroMel_CAF1
Location	18,465,814 – 18,465,937
Length	123
Max. P	0.988469

overview

Window 6

Location	18,465,814 – 18,465,913
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	85.56
Mean single sequence MFE	-30.88
Consensus MFE	-22.84
Energy contribution	-23.38
Covariance contribution	0.54
Combinations/Pair	1.04
Mean z-score	-1.74
Structure conservation index	0.74
SVM decision value	0.28
SVM RNA-class probability	0.666083
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18465814 99 + 20766785
GGCUGACGCUGCAUGCAGCAGUGAAUUAUUUAUGCCAACUUGACAUUUACUUGGCCAGUAGCCUCUCUAAGCCCUGAGCUCAGUGCUCUCAGCCCAGAG
(((((.((((((.....))))))..........(((((............)))))...))))).((((..((...((((.....))))...))..)))) ( -31.10)
>DroSec_CAF1 27954 77 + 1
GGCUGA----------------------GUUAUGCCAACUUGACAUUUACUUGGCCAGGAGCCUCUCUAAGCCCUGAGCUCUGUGCUCUCAGCCCUGAG
((((((----------------------((((........))))...(((..(((((((.((........)))))).)))..)))...))))))..... ( -25.10)
>DroSim_CAF1 28182 99 + 1
GGCUGACGCUGCAUGCAGCAGUGAAUUAUUUAUGCCAACUUGACAUUUACUUGGCCAGGAGCCUCUCUAAGCCCUGAGCUCUGUGCUCUCAGCCCUGAG
((((((((((((.....))))))........................(((..(((((((.((........)))))).)))..)))...))))))..... ( -31.90)
>DroEre_CAF1 27953 99 + 1
GGCUGGCGCUGCAUGCAGCUGUGAAUUAUUUAUGCCAACUUGACAUUUACUUGGCCAGGAGCCUCUCUAAGCCCUGAGCUUUGUGCUCUCAGCUCUGAG
(((((((((((....)))).((((.....)))))))..((((.((......))..)))))))).(((..(((...((((.....))))...)))..))) ( -32.20)
>DroYak_CAF1 28701 99 + 1
GGCUGAGGCUGCAUGCAGCAGUGAAUUAUUUAUGCCAACUUGGCAUUUACUUGGCCAGGAGCCUCUCUAAGCCCCGAGCUUUGAGCUCUCAGUACUGAG
(((..(((((((.....))))).........(((((.....)))))...))..))).(((((.((...((((.....)))).))))))).......... ( -34.10)
>consensus
GGCUGACGCUGCAUGCAGCAGUGAAUUAUUUAUGCCAACUUGACAUUUACUUGGCCAGGAGCCUCUCUAAGCCCUGAGCUCUGUGCUCUCAGCCCUGAG
((((..((((((.....))))))..........(((((............)))))....)))).(((...((...((((.....))))...))...))) (-22.84 = -23.38 +   0.54)

alignment

secondary structure

dotplot

Window 7

Location	18,465,814 – 18,465,913
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	85.56
Mean single sequence MFE	-33.34
Consensus MFE	-28.36
Energy contribution	-28.84
Covariance contribution	0.48
Combinations/Pair	1.04
Mean z-score	-2.39
Structure conservation index	0.85
SVM decision value	2.12
SVM RNA-class probability	0.988469
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18465814 99 - 20766785
CUCUGGGCUGAGAGCACUGAGCUCAGGGCUUAGAGAGGCUACUGGCCAAGUAAAUGUCAAGUUGGCAUAAAUAAUUCACUGCUGCAUGCAGCGUCAGCC
(((((((((..((((.....))))..))))))))).((((((..(((((.(........).)))))..............((((....)))))).)))) ( -37.60)
>DroSec_CAF1 27954 77 - 1
CUCAGGGCUGAGAGCACAGAGCUCAGGGCUUAGAGAGGCUCCUGGCCAAGUAAAUGUCAAGUUGGCAUAAC----------------------UCAGCC
.....((((((((((.....)))((((((((....)))).))))(((((.(........).)))))....)----------------------)))))) ( -29.60)
>DroSim_CAF1 28182 99 - 1
CUCAGGGCUGAGAGCACAGAGCUCAGGGCUUAGAGAGGCUCCUGGCCAAGUAAAUGUCAAGUUGGCAUAAAUAAUUCACUGCUGCAUGCAGCGUCAGCC
.....((((((((((.....))))(((((((....)))).))).(((((.(........).)))))..............((((....)))).)))))) ( -33.40)
>DroEre_CAF1 27953 99 - 1
CUCAGAGCUGAGAGCACAAAGCUCAGGGCUUAGAGAGGCUCCUGGCCAAGUAAAUGUCAAGUUGGCAUAAAUAAUUCACAGCUGCAUGCAGCGCCAGCC
(((.(((((..((((.....))))..))))).))).((((...(((.......(((((.....)))))............((((....))))))))))) ( -34.50)
>DroYak_CAF1 28701 99 - 1
CUCAGUACUGAGAGCUCAAAGCUCGGGGCUUAGAGAGGCUCCUGGCCAAGUAAAUGCCAAGUUGGCAUAAAUAAUUCACUGCUGCAUGCAGCCUCAGCC
.......(((((.(((....(((.(((((((....))))))).)))..)))..(((((.....)))))............((((....))))))))).. ( -31.60)
>consensus
CUCAGGGCUGAGAGCACAGAGCUCAGGGCUUAGAGAGGCUCCUGGCCAAGUAAAUGUCAAGUUGGCAUAAAUAAUUCACUGCUGCAUGCAGCGUCAGCC
(((.(((((..((((.....))))..))))).))).((((....(((((.(........).)))))..............((((....))))...)))) (-28.36 = -28.84 +   0.48)

alignment

secondary structure

dotplot

Window 8

Location	18,465,837 – 18,465,937
Length	100
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	81.48
Mean single sequence MFE	-28.95
Consensus MFE	-20.75
Energy contribution	-22.02
Covariance contribution	1.26
Combinations/Pair	1.12
Mean z-score	-2.48
Structure conservation index	0.72
SVM decision value	1.00
SVM RNA-class probability	0.898000
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18465837 100 - 20766785
A--AGU--------AGGCAAGGCAAAGGACAAGGCUCUGGGCUGAGAGCACUGAGCUCAGGGCUUAGAGAGGCUACUGGCCAAGUAAAUGUCAAGUUGGCAUAAAUAAUU
.--...--------......(.(((..((((((((((((((((.((....)).)))))))))))).....(((.....))).......))))...))).).......... ( -35.20)
>DroSec_CAF1 27960 95 - 1
A--AGU--------AGGCAAGGCAAAGGACAAGGCUCAGGGCUGAGAGCACAGAGCUCAGGGCUUAGAGAGGCUCCUGGCCAAGUAAAUGUCAAGUUGGCAUAAC-----
.--...--------......(((..(((((....(((..((((..((((.....))))..))))..)))..).)))).)))......(((((.....)))))...----- ( -29.70)
>DroSim_CAF1 28205 100 - 1
A--AGU--------AGGCAAGGCAAAGGACAAGGCUCAGGGCUGAGAGCACAGAGCUCAGGGCUUAGAGAGGCUCCUGGCCAAGUAAAUGUCAAGUUGGCAUAAAUAAUU
.--...--------......(((..(((((....(((..((((..((((.....))))..))))..)))..).)))).)))......(((((.....)))))........ ( -29.70)
>DroEre_CAF1 27976 100 - 1
A--AGU--------AGGCAAGGCAAAGGACAAGGCUCAGAGCUGAGAGCACAAAGCUCAGGGCUUAGAGAGGCUCCUGGCCAAGUAAAUGUCAAGUUGGCAUAAAUAAUU
.--...--------......(((..(((((....(((.(((((..((((.....))))..))))).)))..).)))).)))......(((((.....)))))........ ( -30.10)
>DroYak_CAF1 28724 108 - 1
A--AGUAGGCAAGUAGGCAAGGCAAAGGACAAGGCUCAGUACUGAGAGCUCAAAGCUCGGGGCUUAGAGAGGCUCCUGGCCAAGUAAAUGCCAAGUUGGCAUAAAUAAUU
.--....(.(((.(.((((..((.........(((((........)))))....(((.(((((((....))))))).)))...))...)))).).))).).......... ( -31.50)
>DroAna_CAF1 26165 81 - 1
AGUAAU--------GGGCAAGGCAAAGGACAAGGCUCACAGCU--------------CGA-------GAAGACUGCCGGCCAAGUAAAUGUCAAGCUGGCAUAAAUAAUU
.((...--------.(((..((((....((..((((..(((.(--------------(..-------...)))))..))))..))...))))..))).)).......... ( -17.50)
>consensus
A__AGU________AGGCAAGGCAAAGGACAAGGCUCAGGGCUGAGAGCACAGAGCUCAGGGCUUAGAGAGGCUCCUGGCCAAGUAAAUGUCAAGUUGGCAUAAAUAAUU
....................(((...((...((.(((.(((((..((((.....))))..)))))...))).)).)).)))......(((((.....)))))........ (-20.75 = -22.02 +   1.26)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:30 2006