Locus 4096

Sequence ID	2L_DroMel_CAF1
Location	11,784,079 – 11,784,266
Length	187
Max. P	0.995310

overview

Window 4

Location	11,784,079 – 11,784,190
Length	111
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	88.85
Mean single sequence MFE	-30.36
Consensus MFE	-22.28
Energy contribution	-22.12
Covariance contribution	-0.16
Combinations/Pair	1.13
Mean z-score	-5.12
Structure conservation index	0.73
SVM decision value	2.56
SVM RNA-class probability	0.995310
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11784079 111 + 22407834
AAAACAGCAACAAUAAUGUGUUAAUGUGUGCAAACACACACAAAUGCAUC----UGCAUACAUG----UAGAGUAUAGGGCAACCGCAGAAAAUGCAAAACACAUGCCAAGGAGAAAUU
...............(((((((..((((((......))))))..((((((----(((((((...----....)))).((....)))))))...)))).))))))).............. ( -30.60)
>DroSec_CAF1 41846 112 + 1
AAAACAGCAACAAUAAUGUGUUAAUGUGUGCAAACACACACAAAUGCAUC----UGCAUACAUACA--UAGAGUA-AGGGCAACCGCAGAAAAUGCAAAACACAUGCCAACGAGAAAUU
...............(((((((..((((((......))))))..((((((----(((.....(((.--....)))-.((....)))))))...)))).))))))).............. ( -29.90)
>DroSim_CAF1 40950 112 + 1
AAAACAGCAACAAUAAUGUGUUAAUGUGUGCAAACACACACAAAUGCAUC----UGCAUACAUACA--UAGAGUA-AGGGCAACCGCAGAAAAUGCAAAACACAUGCCAAGGAGAAAUU
...............(((((((..((((((......))))))..((((((----(((.....(((.--....)))-.((....)))))))...)))).))))))).............. ( -29.90)
>DroEre_CAF1 52215 118 + 1
AAAACAGCAACAAUAAUGUGUUAAUGUGUGCAAACACACACAAAUGUAUGUAUGUAUAUACAUACAUGCGAAGUA-AGGGCAACCGCAGAAAAUGCAAAACACAUGCCAAGAAGAAAUU
...............(((((((..((((((......))))))..(((((((((((....))))))))))).....-.((....))(((.....)))..))))))).............. ( -33.20)
>DroYak_CAF1 43808 115 + 1
AAAACAGCAAAAAUAAUGUGUUAAUGUGUGCAAACACACACAC---UGUGUAUGUAUAGACAUACAUGUAAAGUA-AGGGCAACCGCAGAAAAUGCAAAACACAUGCCAAGGAGAUAUU
...............(((((((..((((((......)))))).---.((((((((....))))))))........-.((....))(((.....)))..))))))).............. ( -28.20)
>consensus
AAAACAGCAACAAUAAUGUGUUAAUGUGUGCAAACACACACAAAUGCAUC____UGCAUACAUACA__UAGAGUA_AGGGCAACCGCAGAAAAUGCAAAACACAUGCCAAGGAGAAAUU
...............(((((((..((((((......)))))).(((((......)))))..................((....))(((.....)))..))))))).............. (-22.28 = -22.12 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	11,784,079 – 11,784,190
Length	111
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	88.85
Mean single sequence MFE	-27.35
Consensus MFE	-18.15
Energy contribution	-18.03
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-2.84
Structure conservation index	0.66
SVM decision value	0.49
SVM RNA-class probability	0.755113
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11784079 111 - 22407834
AAUUUCUCCUUGGCAUGUGUUUUGCAUUUUCUGCGGUUGCCCUAUACUCUA----CAUGUAUGCA----GAUGCAUUUGUGUGUGUUUGCACACAUUAACACAUUAUUGUUGCUGUUUU
...........((((((((((.((((...(((((((....)).((((....----...)))))))----))))))..(((((((....)))))))..)))))).......))))..... ( -27.81)
>DroSec_CAF1 41846 112 - 1
AAUUUCUCGUUGGCAUGUGUUUUGCAUUUUCUGCGGUUGCCCU-UACUCUA--UGUAUGUAUGCA----GAUGCAUUUGUGUGUGUUUGCACACAUUAACACAUUAUUGUUGCUGUUUU
...........((((((((((.((((...((((((..(((...-(((....--.))).)))))))----))))))..(((((((....)))))))..)))))).......))))..... ( -27.71)
>DroSim_CAF1 40950 112 - 1
AAUUUCUCCUUGGCAUGUGUUUUGCAUUUUCUGCGGUUGCCCU-UACUCUA--UGUAUGUAUGCA----GAUGCAUUUGUGUGUGUUUGCACACAUUAACACAUUAUUGUUGCUGUUUU
...........((((((((((.((((...((((((..(((...-(((....--.))).)))))))----))))))..(((((((....)))))))..)))))).......))))..... ( -27.71)
>DroEre_CAF1 52215 118 - 1
AAUUUCUUCUUGGCAUGUGUUUUGCAUUUUCUGCGGUUGCCCU-UACUUCGCAUGUAUGUAUAUACAUACAUACAUUUGUGUGUGUUUGCACACAUUAACACAUUAUUGUUGCUGUUUU
...........((((((((((...........((((.......-....))))((((((((((....)))))))))).(((((((....)))))))..)))))).......))))..... ( -27.91)
>DroYak_CAF1 43808 115 - 1
AAUAUCUCCUUGGCAUGUGUUUUGCAUUUUCUGCGGUUGCCCU-UACUUUACAUGUAUGUCUAUACAUACACA---GUGUGUGUGUUUGCACACAUUAACACAUUAUUUUUGCUGUUUU
...........(((((((((((((((.....))))).......-.........(((((((....))))))).(---((((((((....))))))))))))))).......))))..... ( -25.61)
>consensus
AAUUUCUCCUUGGCAUGUGUUUUGCAUUUUCUGCGGUUGCCCU_UACUCUA__UGUAUGUAUGCA____GAUGCAUUUGUGUGUGUUUGCACACAUUAACACAUUAUUGUUGCUGUUUU
...........((((((((((.(((((....((.(((........))).)).....)))))................(((((((....)))))))..)))))).......))))..... (-18.15 = -18.03 +  -0.12)

alignment

secondary structure

dotplot

Window 6

Location	11,784,118 – 11,784,226
Length	108
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	88.56
Mean single sequence MFE	-28.92
Consensus MFE	-18.88
Energy contribution	-20.56
Covariance contribution	1.68
Combinations/Pair	1.16
Mean z-score	-3.29
Structure conservation index	0.65
SVM decision value	0.78
SVM RNA-class probability	0.847670
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11784118 108 + 22407834
ACAAAUGCAUC----UGCAUACAUG----UAGAGUAUAGGGCAACCGCAGAAAAUGCAAAACACAUGCCAAGGAGAAAUUCGCUCCAUUGAAGAGAGUAGGAUGUGGAAAAGGACA
.....((((((----(((((((...----....)))).((....)))))))...))))...(((((.((..(((....)))(((((......).)))).))))))).......... ( -30.40)
>DroSec_CAF1 41885 109 + 1
ACAAAUGCAUC----UGCAUACAUACA--UAGAGUA-AGGGCAACCGCAGAAAAUGCAAAACACAUGCCAACGAGAAAUUCGCUCCAUUGAAGAGAGUAGGAUGUGGAAAAGGACA
.....((((((----(((.....(((.--....)))-.((....)))))))...))))...(((((.((...(((...)))(((((......).)))).))))))).......... ( -26.30)
>DroSim_CAF1 40989 109 + 1
ACAAAUGCAUC----UGCAUACAUACA--UAGAGUA-AGGGCAACCGCAGAAAAUGCAAAACACAUGCCAAGGAGAAAUUCGCUCCAUUGAAGAGAGUAGGAUGUGGAAAAGGACA
.....((((((----(((.....(((.--....)))-.((....)))))))...))))...(((((.((..(((....)))(((((......).)))).))))))).......... ( -29.70)
>DroEre_CAF1 52254 114 + 1
ACAAAUGUAUGUAUGUAUAUACAUACAUGCGAAGUA-AGGGCAACCGCAGAAAAUGCAAAACACAUGCCAAGAAGAAAUUCGCUCCAUUGAAGAGAGUA-GAUGUGGAAAAGGACA
.....(((((((((((....))))))))))).....-.((....))(((.....)))....(((((.....(((....)))(((((......).)))).-.))))).......... ( -31.10)
>DroYak_CAF1 43847 112 + 1
ACAC---UGUGUAUGUAUAGACAUACAUGUAAAGUA-AGGGCAACCGCAGAAAAUGCAAAACACAUGCCAAGGAGAUAUUCGCUCCAUUGAAGAGAGUAGGAUGUGGAAAAGGACA
....---.((((((((....))))))))........-.((....))(((.....)))....(((((.((..(((....)))(((((......).)))).))))))).......... ( -27.10)
>consensus
ACAAAUGCAUC____UGCAUACAUACA__UAGAGUA_AGGGCAACCGCAGAAAAUGCAAAACACAUGCCAAGGAGAAAUUCGCUCCAUUGAAGAGAGUAGGAUGUGGAAAAGGACA
....(((((......)))))..................((....))(((.....)))....(((((.((..(((....)))(((((......).)))).))))))).......... (-18.88 = -20.56 +   1.68)

alignment

secondary structure

dotplot

Window 7

Location	11,784,150 – 11,784,266
Length	116
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	98.28
Mean single sequence MFE	-31.48
Consensus MFE	-28.62
Energy contribution	-30.46
Covariance contribution	1.84
Combinations/Pair	1.03
Mean z-score	-1.94
Structure conservation index	0.91
SVM decision value	1.90
SVM RNA-class probability	0.982077
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11784150 116 + 22407834
GCAACCGCAGAAAAUGCAAAACACAUGCCAAGGAGAAAUUCGCUCCAUUGAAGAGAGUAGGAUGUGGAAAAGGACACACCGGAUGUGGCACUGCAUCCGAAGGAUGAUGAUGCAAG
(((.(((((.....)))....(((((.((..(((....)))(((((......).)))).))))))).....))......(((((((......)))))))...........)))... ( -32.70)
>DroSec_CAF1 41918 116 + 1
GCAACCGCAGAAAAUGCAAAACACAUGCCAACGAGAAAUUCGCUCCAUUGAAGAGAGUAGGAUGUGGAAAAGGACACACCGGAUGUGGCACUGCAUCCGAAGGAUGAUGAUGCAAG
((....(((.....)))....(((((.((............(((((......).)))).((.((((........)))))))))))))))..(((((((....).....)))))).. ( -29.70)
>DroSim_CAF1 41022 116 + 1
GCAACCGCAGAAAAUGCAAAACACAUGCCAAGGAGAAAUUCGCUCCAUUGAAGAGAGUAGGAUGUGGAAAAGGACACACCGGAUGUGGCACUGCAUCCGAAGGAUGAUGAUGCAAG
(((.(((((.....)))....(((((.((..(((....)))(((((......).)))).))))))).....))......(((((((......)))))))...........)))... ( -32.70)
>DroEre_CAF1 52293 115 + 1
GCAACCGCAGAAAAUGCAAAACACAUGCCAAGAAGAAAUUCGCUCCAUUGAAGAGAGUA-GAUGUGGAAAAGGACACAGCGGAUGUGGCACUGCAUCCGAAGGAUGAUGAUGCAAG
(((.(((((.....)))....(((((.....(((....)))(((((......).)))).-.))))).....)).(((..(((((((......)))))))...).))....)))... ( -30.60)
>DroYak_CAF1 43883 116 + 1
GCAACCGCAGAAAAUGCAAAACACAUGCCAAGGAGAUAUUCGCUCCAUUGAAGAGAGUAGGAUGUGGAAAAGGACACACCGGAUGUGGCACUGCAUCCGAAGGAUGAUGAUGCAAG
((....(((.....)))....(((((.((..((((.......)))).............((.((((........)))))))))))))))..(((((((....).....)))))).. ( -31.70)
>consensus
GCAACCGCAGAAAAUGCAAAACACAUGCCAAGGAGAAAUUCGCUCCAUUGAAGAGAGUAGGAUGUGGAAAAGGACACACCGGAUGUGGCACUGCAUCCGAAGGAUGAUGAUGCAAG
(((.(((((.....)))....(((((.((..(((....)))(((((......).)))).))))))).....))......(((((((......)))))))...........)))... (-28.62 = -30.46 +   1.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:17 2006