Locus 4791

Sequence ID	X_DroMel_CAF1
Location	12,452,280 – 12,452,409
Length	129
Max. P	0.855449

overview

Window 0

Location	12,452,280 – 12,452,376
Length	96
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	70.17
Mean single sequence MFE	-23.27
Consensus MFE	-12.24
Energy contribution	-11.80
Covariance contribution	-0.44
Combinations/Pair	1.32
Mean z-score	-1.53
Structure conservation index	0.53
SVM decision value	0.36
SVM RNA-class probability	0.705185
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12452280 96 - 22224390
AUUUGCGGCACAAUUGCCAUUUAAUAGGCACUUGAACUGUGAGACACACAUCUGA----AGAUUGAAGACA--GGCGAAAGCCGGUGACUUGUCGUAUUGG----A
.((..(((..(((.((((........)))).)))..)))..))((.((.(((...----.)))))..((((--(((....)))(....).)))))).....----. ( -28.00)
>DroPse_CAF1 7087 90 - 1
AUUUGCGGCACAAUUGCCAUUUAAUAGGCACUUGAAGUGCGA--CAGACAUAUACUAUAUGUACGUACGUAAAGGCAAAAGU----------ACGAUUCAA----U
.(((((((((....))))............(((...(((((.--...((((((...)))))).)))))...))))))))...----------.........----. ( -21.50)
>DroSec_CAF1 5345 96 - 1
AUUUGCGGCACAAUUGCCAUUUAAUAGGCACUUGAACUGUGAGACACACAUCUGA----AGAAUGAAGACU--GGCGAAAGCCGGCGACUUGUCGAAUCGA----A
..(..(((..(((.((((........)))).)))..)))..)((((..((((...----.).)))..(.((--(((....))))))....)))).......----. ( -27.70)
>DroEre_CAF1 5815 81 - 1
AUUUGCGGCACAAUUGCCAUUUAAUAGGCACUUGAACUGUGAGACACACAUCUAGAAA-GGAACGCAGUCA--------------------GGCGAAUUGG----A
((((((....(((.((((........)))).))).((((((.(.....).(((.....-))).))))))..--------------------.))))))...----. ( -17.00)
>DroYak_CAF1 5951 105 - 1
AUUUGCGGCACAAUUGCCAUUUAAUAGGCACUUGAACUGUGAGACACACAUCUAGAAC-AGUACGAAGACACCGGCAAAAGUCGUAGAAUUGUCGAAUUGAGAAAG
.((((((((.(((.((((........)))).))).(((((.(((......)))...))-)))..................)))))))).................. ( -23.70)
>DroPer_CAF1 7095 90 - 1
AUUUGUGGCACAAUUGCCAUUUAAUAGGCACUUGAAGUGCGA--CAGACAUAUACUAUAUGUACGUACGUAAAGGGAAAAGU----------ACGAUUCAA----U
..((((.((((((.((((........)))).))...)))).)--)))((((((...)))))).(((((............))----------)))......----. ( -21.70)
>consensus
AUUUGCGGCACAAUUGCCAUUUAAUAGGCACUUGAACUGUGAGACACACAUCUAA_A__AGAACGAAGACA__GGCAAAAGU_________GUCGAAUCGA____A
.(((((((..(((.((((........)))).)))..)))))))....................(((........((....))..........)))........... (-12.24 = -11.80 +  -0.44)

alignment

secondary structure

dotplot

Window 1

Location	12,452,312 – 12,452,409
Length	97
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	84.18
Mean single sequence MFE	-23.18
Consensus MFE	-19.74
Energy contribution	-19.60
Covariance contribution	-0.14
Combinations/Pair	1.06
Mean z-score	-2.04
Structure conservation index	0.85
SVM decision value	0.81
SVM RNA-class probability	0.855449
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12452312 97 - 22224390
CUUUC-AUUUUUCUCGAAAAGUCACGUCGUAUCAAUUUGCGGCACAAUUGCCAUUUAAUAGGCACUUGAACUGUGAGACACACAUCUGA----AGAUUGAAG
..(((-(.(((((........((((((((((......)))))).(((.((((........)))).)))....))))((......)).))----))).)))). ( -24.50)
>DroVir_CAF1 8201 86 - 1
CUUUUAUUUUUCGAUGAAAAGUCACGUCGUAUCAAUUUGCGGCACAAUUGCCAUUUAAUAGGCACUUGAACUGUGAGAUAUGAAUA----------------
.(((((((....)))))))..((((((((((......)))))).(((.((((........)))).)))....))))..........---------------- ( -20.90)
>DroSec_CAF1 5377 97 - 1
CUUUC-AUUUUCCUCGAAAAGUCACGUCGUAUCAAUUUGCGGCACAAUUGCCAUUUAAUAGGCACUUGAACUGUGAGACACACAUCUGA----AGAAUGAAG
..(((-(((((.((((...(((...((((((......)))))).(((.((((........)))).))).))).)))).((......)).----)))))))). ( -23.80)
>DroEre_CAF1 5829 100 - 1
CUUUC-UUUUUCCUCGAAAAGUCACGUCGUAUCAAUUUGCGGCACAAUUGCCAUUUAAUAGGCACUUGAACUGUGAGACACACAUCUAGAAA-GGAACGCAG
(((((-((((((...))))).((((((((((......)))))).(((.((((........)))).)))....))))...........)))))-)........ ( -24.30)
>DroWil_CAF1 29717 96 - 1
CUUUC-UUUUGC--UGAAAAGUCACGUCGUAUCAAUUUGCGACACAAUUGCCAUUUAAUAGGCACUUGAACUGUGAGAUAUAUAUAUAU---AUAUACGAAC
.((((-......--.))))..((((((((((......)))))).(((.((((........)))).)))....)))).((((((....))---))))...... ( -22.20)
>DroYak_CAF1 5989 100 - 1
CUUUC-UUUUUCCUCGAAAAGUCACGUCGUAUCAAUUUGCGGCACAAUUGCCAUUUAAUAGGCACUUGAACUGUGAGACACACAUCUAGAAC-AGUACGAAG
.....-.......(((.........((((((......)))))).(((.((((........)))).))).(((((.(((......)))...))-))).))).. ( -23.40)
>consensus
CUUUC_UUUUUCCUCGAAAAGUCACGUCGUAUCAAUUUGCGGCACAAUUGCCAUUUAAUAGGCACUUGAACUGUGAGACACACAUCUAA____AGAACGAAG
.....................((((((((((......)))))).(((.((((........)))).)))....)))).......................... (-19.74 = -19.60 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:14 2006