Locus 1663

Sequence ID	3R_DroMel_CAF1
Location	4,792,823 – 4,792,989
Length	166
Max. P	0.999032

overview

Window 3

Location	4,792,823 – 4,792,925
Length	102
Sequences	3
Columns	102
Reading direction	forward
Mean pairwise identity	98.69
Mean single sequence MFE	-20.23
Consensus MFE	-20.23
Energy contribution	-20.23
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.22
Structure conservation index	1.00
SVM decision value	2.31
SVM RNA-class probability	0.992083
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4792823 102 + 27905053
CAACCACAACCGAACAAACAACAAAAAACAAACAACAGACAAUGCAAAAUGCAAUUGAGAUGCAAAUGCAAAUUGCAUUUGCCACAUGUUGCAAAUGCCGUG
...........................................(((...((((((......((((((((.....)))))))).....))))))..))).... ( -19.50)
>DroSec_CAF1 28244 102 + 1
CAACCACAACCGAACAAACAACACAAAACAAACAACAGACAAUGCAAAAUGCAAUUGAGAUGCAAAUGCAAAUUGCAUUUGCCACAUGUUGCAGAUGCCGUG
...........................................(((...((((((......((((((((.....)))))))).....))))))..))).... ( -20.60)
>DroSim_CAF1 23651 102 + 1
CAACCACAACCGAACAAACAACACAAAACAAACAACAGACAAUGCAAAAUGCAAUUGAGAUGCAAAUGCAAAUUGCAUUUGCCACAUGUUGCAGAUGCCGUG
...........................................(((...((((((......((((((((.....)))))))).....))))))..))).... ( -20.60)
>consensus
CAACCACAACCGAACAAACAACACAAAACAAACAACAGACAAUGCAAAAUGCAAUUGAGAUGCAAAUGCAAAUUGCAUUUGCCACAUGUUGCAGAUGCCGUG
...........................................(((...((((((......((((((((.....)))))))).....))))))..))).... (-20.23 = -20.23 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	4,792,823 – 4,792,925
Length	102
Sequences	3
Columns	102
Reading direction	reverse
Mean pairwise identity	98.69
Mean single sequence MFE	-29.57
Consensus MFE	-29.40
Energy contribution	-29.73
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.23
Structure conservation index	0.99
SVM decision value	2.26
SVM RNA-class probability	0.991290
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4792823 102 - 27905053
CACGGCAUUUGCAACAUGUGGCAAAUGCAAUUUGCAUUUGCAUCUCAAUUGCAUUUUGCAUUGUCUGUUGUUUGUUUUUUGUUGUUUGUUCGGUUGUGGUUG
((((((....((((((.(..((((((((((..((((.(((.....))).))))..)))))))...)))..)........)))))).......)))))).... ( -28.50)
>DroSec_CAF1 28244 102 - 1
CACGGCAUCUGCAACAUGUGGCAAAUGCAAUUUGCAUUUGCAUCUCAAUUGCAUUUUGCAUUGUCUGUUGUUUGUUUUGUGUUGUUUGUUCGGUUGUGGUUG
((((((....((((((((..((((((((((..((((.(((.....))).))))..))))))..........))))..)))))))).......)))))).... ( -30.10)
>DroSim_CAF1 23651 102 - 1
CACGGCAUCUGCAACAUGUGGCAAAUGCAAUUUGCAUUUGCAUCUCAAUUGCAUUUUGCAUUGUCUGUUGUUUGUUUUGUGUUGUUUGUUCGGUUGUGGUUG
((((((....((((((((..((((((((((..((((.(((.....))).))))..))))))..........))))..)))))))).......)))))).... ( -30.10)
>consensus
CACGGCAUCUGCAACAUGUGGCAAAUGCAAUUUGCAUUUGCAUCUCAAUUGCAUUUUGCAUUGUCUGUUGUUUGUUUUGUGUUGUUUGUUCGGUUGUGGUUG
((((((....((((((((..((((((((((..((((.(((.....))).))))..))))))..........))))..)))))))).......)))))).... (-29.40 = -29.73 +   0.33)

alignment

secondary structure

dotplot

Window 5

Location	4,792,859 – 4,792,949
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	97.78
Mean single sequence MFE	-26.42
Consensus MFE	-26.14
Energy contribution	-25.98
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.89
Structure conservation index	0.99
SVM decision value	2.80
SVM RNA-class probability	0.997108
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4792859 90 + 27905053
AGACAAUGCAAAAUGCAAUUGAGAUGCAAAUGCAAAUUGCAUUUGCCACAUGUUGCAAAUGCCGUGUGCUGUUCCAUGCUGUGUGUGCCA
.......(((...((((((......((((((((.....)))))))).....)))))).((((.(((((......))))).)))).))).. ( -24.40)
>DroSec_CAF1 28280 90 + 1
AGACAAUGCAAAAUGCAAUUGAGAUGCAAAUGCAAAUUGCAUUUGCCACAUGUUGCAGAUGCCGUGUGCUGUUCCAUACUGUGUGUGCCA
.((((.(((.....)))........((((((((.....))))))))....))))(((.((((.(((((......))))).)))).))).. ( -27.20)
>DroSim_CAF1 23687 90 + 1
AGACAAUGCAAAAUGCAAUUGAGAUGCAAAUGCAAAUUGCAUUUGCCACAUGUUGCAGAUGCCGUGUGCUGUUCCAUGCUGUGUGUGCCA
.((((.(((.....)))........((((((((.....))))))))....))))(((.((((.(((((......))))).)))).))).. ( -26.20)
>DroEre_CAF1 28567 90 + 1
AGACAAUGCAAAAUGCAAUUGAGAUGCAAAUGCAAAUUGCAUUUGCCACAUGUUGCAGAUGCCGUGUGCUGUUCCAUGCUGUGUGUGCCA
.((((.(((.....)))........((((((((.....))))))))....))))(((.((((.(((((......))))).)))).))).. ( -26.20)
>DroYak_CAF1 28921 90 + 1
AGACAAUGCAAAAUGCAAUUGAGAUGCAAAUGCAAAUUGCAUUUGCCACAUGUUGCAGAUGCCGUGUGCUGCGCCAUGCCGUGUGUGCCA
(((((..(((...((((((......((((((((.....)))))))).....))))))..)))..))).))(((((((...))).)))).. ( -28.10)
>consensus
AGACAAUGCAAAAUGCAAUUGAGAUGCAAAUGCAAAUUGCAUUUGCCACAUGUUGCAGAUGCCGUGUGCUGUUCCAUGCUGUGUGUGCCA
.((((.(((.....)))........((((((((.....))))))))....))))(((.((((.(((((......))))).)))).))).. (-26.14 = -25.98 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	4,792,859 – 4,792,949
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	97.78
Mean single sequence MFE	-25.00
Consensus MFE	-24.08
Energy contribution	-23.92
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.19
Structure conservation index	0.96
SVM decision value	3.34
SVM RNA-class probability	0.999032
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4792859 90 - 27905053
UGGCACACACAGCAUGGAACAGCACACGGCAUUUGCAACAUGUGGCAAAUGCAAUUUGCAUUUGCAUCUCAAUUGCAUUUUGCAUUGUCU
.((((......((........)).....(((..(((((..((..((((((((.....))))))))....)).)))))...)))..)))). ( -24.90)
>DroSec_CAF1 28280 90 - 1
UGGCACACACAGUAUGGAACAGCACACGGCAUCUGCAACAUGUGGCAAAUGCAAUUUGCAUUUGCAUCUCAAUUGCAUUUUGCAUUGUCU
.((((......((.((......)).)).(((..(((((..((..((((((((.....))))))))....)).)))))...)))..)))). ( -23.50)
>DroSim_CAF1 23687 90 - 1
UGGCACACACAGCAUGGAACAGCACACGGCAUCUGCAACAUGUGGCAAAUGCAAUUUGCAUUUGCAUCUCAAUUGCAUUUUGCAUUGUCU
.((((......((........)).....(((..(((((..((..((((((((.....))))))))....)).)))))...)))..)))). ( -24.20)
>DroEre_CAF1 28567 90 - 1
UGGCACACACAGCAUGGAACAGCACACGGCAUCUGCAACAUGUGGCAAAUGCAAUUUGCAUUUGCAUCUCAAUUGCAUUUUGCAUUGUCU
.((((......((........)).....(((..(((((..((..((((((((.....))))))))....)).)))))...)))..)))). ( -24.20)
>DroYak_CAF1 28921 90 - 1
UGGCACACACGGCAUGGCGCAGCACACGGCAUCUGCAACAUGUGGCAAAUGCAAUUUGCAUUUGCAUCUCAAUUGCAUUUUGCAUUGUCU
.(((.....(.(((((..((((..........))))..))))).)..(((((((..((((.(((.....))).))))..)))))))))). ( -28.20)
>consensus
UGGCACACACAGCAUGGAACAGCACACGGCAUCUGCAACAUGUGGCAAAUGCAAUUUGCAUUUGCAUCUCAAUUGCAUUUUGCAUUGUCU
.((((......((........)).....(((..(((((..((..((((((((.....))))))))....)).)))))...)))..)))). (-24.08 = -23.92 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	4,792,899 – 4,792,989
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	97.78
Mean single sequence MFE	-22.79
Consensus MFE	-23.08
Energy contribution	-22.76
Covariance contribution	-0.32
Combinations/Pair	1.08
Mean z-score	-1.20
Structure conservation index	1.01
SVM decision value	0.55
SVM RNA-class probability	0.778417
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4792899 90 - 27905053
UGUUAAUGGUGUGCAUUAUUUUCAUGUUUAUUUAUGUUGCUGGCACACACAGCAUGGAACAGCACACGGCAUUUGCAACAUGUGGCAAAU
((((((((((((((........((((......)))).(((((.......))))).......)))))).((....))..))).)))))... ( -23.30)
>DroSec_CAF1 28320 90 - 1
UGUUAAUGGUGUGCAUUAUUUUCAUGUUUAUUUAUGUUGCUGGCACACACAGUAUGGAACAGCACACGGCAUCUGCAACAUGUGGCAAAU
((((((((((((((........((((......)))).(((((.......))))).......)))))).((....))..))).)))))... ( -21.30)
>DroSim_CAF1 23727 90 - 1
UGUUAAUGGUGUGCAUUAUUUUCAUGUUUAUUUAUGUUGCUGGCACACACAGCAUGGAACAGCACACGGCAUCUGCAACAUGUGGCAAAU
((((((((((((((........((((......)))).(((((.......))))).......)))))).((....))..))).)))))... ( -23.30)
>DroEre_CAF1 28607 90 - 1
UGUUAAUGGUGUGCAUUAUUUUCAUGUUUAUUUAUGUUGCUGGCACACACAGCAUGGAACAGCACACGGCAUCUGCAACAUGUGGCAAAU
((((((((((((((........((((......)))).(((((.......))))).......)))))).((....))..))).)))))... ( -23.30)
>DroYak_CAF1 28961 90 - 1
UGUUAAUGGUGUGCAUUAUUUUCAUGUUUAUUUAUGUUGCUGGCACACACGGCAUGGCGCAGCACACGGCAUCUGCAACAUGUGGCAAAU
........((((((........((((......))))......)))))).(.(((((..((((..........))))..))))).)..... ( -22.74)
>consensus
UGUUAAUGGUGUGCAUUAUUUUCAUGUUUAUUUAUGUUGCUGGCACACACAGCAUGGAACAGCACACGGCAUCUGCAACAUGUGGCAAAU
((((((((((((((........((((......)))).(((((.......))))).......)))))).((....))..))).)))))... (-23.08 = -22.76 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:17 2006