Locus 5792

Sequence ID	2L_DroMel_CAF1
Location	16,406,262 – 16,406,431
Length	169
Max. P	0.999886

overview

Window 3

Location	16,406,262 – 16,406,357
Length	95
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	88.91
Mean single sequence MFE	-27.37
Consensus MFE	-23.47
Energy contribution	-24.50
Covariance contribution	1.03
Combinations/Pair	1.22
Mean z-score	-2.36
Structure conservation index	0.86
SVM decision value	1.29
SVM RNA-class probability	0.938384
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16406262 95 + 22407834
AAGUUUUCCGUUUGAAGGCGGACAGUGAAUUUCAUCUGGAUUGUUGUUGUCCCGGGUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUU
......((((((....))))))..((((((.((((((((((.......)).)))))))).))))))..(((((......)))))........... ( -29.90)
>DroSec_CAF1 30669 95 + 1
AAGUUUUCCGUUUGAAGGCGGACAGUGAAUUUCAUCUGGAUUGUUGUUGUCCCGGGUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUU
......((((((....))))))..((((((.((((((((((.......)).)))))))).))))))..(((((......)))))........... ( -29.90)
>DroSim_CAF1 30218 95 + 1
AAGUUUUCCGUUUGAAGGCGGACAGUGAAUUUCAUCUGGAUUGUUGUUGUCCCGGGUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUU
......((((((....))))))..((((((.((((((((((.......)).)))))))).))))))..(((((......)))))........... ( -29.90)
>DroEre_CAF1 26265 95 + 1
AAGUUUUCCGUUUGAAGGCGGACAGUGAGUUUCAUCUGGAUUGUUGUCGUCCCUGGCGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUU
......((((((....))))))..((((((......((((..(((((((....)))))))..)).)).(((((......)))))))))))..... ( -24.30)
>DroYak_CAF1 31505 95 + 1
AAGUUCUCCGUUUGAAGGCGGGCAGUGAAUUUCAUCUGGAUUGUUGUUGUCCCGGGUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUU
..((((.((.......)).)))).((((((.((((((((((.......)).)))))))).))))))..(((((......)))))........... ( -29.60)
>DroPer_CAF1 4717 80 + 1
A---GCCCCCCUCGA-----GACUGUGGACU----UUGGAC---UGUUGUCCCGGGUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUU
.---.........((-----(..(((((((.----((((((---....)))).....)).))))))).(((((......))))).)))....... ( -20.60)
>consensus
AAGUUUUCCGUUUGAAGGCGGACAGUGAAUUUCAUCUGGAUUGUUGUUGUCCCGGGUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUU
......((((((....))))))..((((((.((((((((((.......)).)))))))).))))))..(((((......)))))........... (-23.47 = -24.50 +   1.03)

alignment

secondary structure

dotplot

Window 4

Location	16,406,281 – 16,406,394
Length	113
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	86.10
Mean single sequence MFE	-32.95
Consensus MFE	-21.87
Energy contribution	-24.40
Covariance contribution	2.53
Combinations/Pair	1.15
Mean z-score	-3.69
Structure conservation index	0.66
SVM decision value	0.37
SVM RNA-class probability	0.707457
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16406281 113 + 22407834
GGAC----AGUGAAUUUCAUCUGGAUUGUUGUUGUCCCGGGUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGUAUGAAAUUAAUGCCGC-
((.(----(((((((.((((((((((.......)).)))))))).))))))..(((((......))))).....(((((((((((((((......))))))))))))))).))))..- ( -39.20)
>DroPse_CAF1 4777 99 + 1
-GAC----UGUGG-----------AC---UGUUGUCCCGGGUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGCAUGAAAUGAAUGCCCCC
-...----.(.((-----------((---....)))))(((.(..((((....(((((......))))).......(((((((.(((((......))))).)))))))))))..)))) ( -25.30)
>DroEre_CAF1 26284 113 + 1
GGAC----AGUGAGUUUCAUCUGGAUUGUUGUCGUCCCUGGCGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGUAUGAAAUUAAUGCCGC-
((.(----(((((((......((((..(((((((....)))))))..)).)).(((((......)))))))))))((((((((((((((......))))))))))))))..))))..- ( -32.50)
>DroYak_CAF1 31524 113 + 1
GGGC----AGUGAAUUUCAUCUGGAUUGUUGUUGUCCCGGGUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGUAUGAAAUUAAGGCCGC-
.(((----.((((((.((((((((((.......)).)))))))).))))))..(((((......))))).....(((((((((((((((......)))))))))))))))..)))..- ( -42.00)
>DroAna_CAF1 26004 117 + 1
GAGCUAGUAGACAAUUUUGUCUGGUUUGUUGUUGUCCCGGGUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGUAUGAAAUUAAUGCCGC-
(((.....(((((....)))))((..(((((..((.((..(((.....)))..)).))..)))))..)).))).(((((((((((((((......))))))))))))))).......- ( -33.60)
>DroPer_CAF1 4729 105 + 1
-GAC----UGUGGACU----UUGGAC---UGUUGUCCCGGGUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGCAUGAAAUGAAUGCCCC-
-...----.(((((((----..((((---....))))..))(((.((((.....)))).)))....))))).(((.(((((((.(((((......))))).)))))))..)))....- ( -25.10)
>consensus
GGAC____AGUGAAUUUCAUCUGGAUUGUUGUUGUCCCGGGUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGUAUGAAAUUAAUGCCGC_
.........((((((.((.(((((............))))).)).))))))..(((((......))))).....(((((((((((((((......)))))))))))))))........ (-21.87 = -24.40 +   2.53)

alignment

secondary structure

dotplot

Window 5

Location	16,406,317 – 16,406,431
Length	114
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	96.37
Mean single sequence MFE	-32.82
Consensus MFE	-29.72
Energy contribution	-30.08
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-3.74
Structure conservation index	0.91
SVM decision value	4.39
SVM RNA-class probability	0.999886
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16406317 114 + 22407834
GUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGUAUGAAAUUAAUGCCGCUGGCUUUGAGGCCGAGUCAUCUGCACAGAGAAAAAUG
(((.....)))..(((((......))))).(((.(((((((((((((((......))))))))))))))).(((.(.((((((.......)))))).).)))..)))....... ( -32.50)
>DroSec_CAF1 30724 114 + 1
GUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGUAUGAAAUUAAUGCCGCUGGCUUUGAGGCCGAGUCUUCUGCACAGAGAAAAAUG
(((.....)))..(((((......))))).(((.(((((((((((((((......))))))))))))))).(((.(((((((....)))).))).....)))..)))....... ( -32.30)
>DroSim_CAF1 30273 114 + 1
GUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGUAUGAAAUUAAUGCCGCUGGCUUUGAGGCCGAGUCAUCUGCACAGAGAAAAAUG
(((.....)))..(((((......))))).(((.(((((((((((((((......))))))))))))))).(((.(.((((((.......)))))).).)))..)))....... ( -32.50)
>DroEre_CAF1 26320 114 + 1
GCGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGUAUGAAAUUAAUGCCGCUGGCUUUGAGGCCGAGUCAUCUGCACAGCGAAAAAUG
((((((.......(((((......)))))((((.(((((((((((((((......)))))))))))))))........((((....)))))))))))).))............. ( -33.50)
>DroYak_CAF1 31560 114 + 1
GUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGUAUGAAAUUAAGGCCGCUGGCUUUGAGGCCGAGUCAUCUGCACAGAGAAAAACG
((((((.......(((((......)))))((((.(((((((((((((((......))))))))))))))).((((.(.......).)))))))))))).))............. ( -34.20)
>DroAna_CAF1 26044 114 + 1
GUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGUAUGAAAUUAAUGCCGCUGGCUUUGAGACAGACUCUUCUGCACAGAACAAAAAA
....(((((....(((((......))))).(((((((((((((((((((......)))))))))))))))..(((...)))..)))).((((....))))....)))))..... ( -31.90)
>consensus
GUGAUGUUCACAAGGAAUUUCAAUGUUCCACUCAUAAUUUCAUAUAAUUUCCAUUAAUUGUAUGAAAUUAAUGCCGCUGGCUUUGAGGCCGAGUCAUCUGCACAGAGAAAAAUG
(((((((((....(((((......))))).(((((((((((((((((((......)))))))))))))))..(((...)))..))))...))).)))).))............. (-29.72 = -30.08 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:01 2006