Locus 4634

Sequence ID	3R_DroMel_CAF1
Location	12,188,406 – 12,188,651
Length	245
Max. P	0.990382

overview

Window 9

Location	12,188,406 – 12,188,526
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.71
Mean single sequence MFE	-33.22
Consensus MFE	-31.93
Energy contribution	-32.02
Covariance contribution	0.09
Combinations/Pair	1.05
Mean z-score	-1.59
Structure conservation index	0.96
SVM decision value	2.21
SVM RNA-class probability	0.990382
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12188406 120 + 27905053
UUGAGAGAUCCAUGAUUUCAUAGAUUGUUCGGAAUGCUGGGAAAAUAUUUUUCACGGACUGAGCGGAAGCUUCUGCACAUGUACAUACAUAGGUGUAGAUCCAGUGGCAGAUUUCGAUAA
....((((((...)))))).........(((((((.((((((((....)))))....(((((((....)))(((((((((((....))))..)))))))..))))..))))))))))... ( -33.10)
>DroSec_CAF1 2210 116 + 1
UUGAGAGAUCCAUGAUUUCAUAGAUUGUUCGGAAUGCUGGGAAAAUGUUUUUCACGGACUGGGCGGAAGCUUCUGCACACGUA----CAUAGGUGUAGAUCCAGUGGCAGAUUUCGAUAA
....((((((...)))))).........(((((((.((((((((....)))))....(((((((....)).(((((((.(...----....)))))))).)))))..))))))))))... ( -34.30)
>DroSim_CAF1 2209 116 + 1
UUGAGAGAUCCAUGAUUUCAUAGAUUGUUCGGAAUGCUGGGAAAAUAUUUUUCACGGACUGGGCGGAAGCUUCUGCACAUGUA----CAUAGGUGUAGAUCCAGUGGCAGAUUUCGAUAA
....((((((...)))))).........(((((((.((((((((....)))))....(((((((....)).(((((((.....----.....))))))).)))))..))))))))))... ( -33.40)
>DroEre_CAF1 2459 112 + 1
GUCAGAGAUUCAUGAUUUCAUAGAUUGUUCGGAAUGCUGGGAAAAUAUUUUUCACGGACUGGGCGGAAGCUUCUGCACAUG--------UACGUGUAGAUCCAGUGGCAGAUUUCGAUAA
......(((..(((....)))..)))..(((((((.((((((((....)))))....(((((((....)).(((((((...--------...))))))).)))))..))))))))))... ( -33.20)
>DroYak_CAF1 2153 116 + 1
GUCAGAGAUUCAUGAUUUCAUAGAUUGUUCGGAAUGCUGGGAAAAUAUUUUUCACGGACUGGGCGGAAGCUUCUGCACAUGUA----UGUACGUGUAGAUCCAGUGGCAGAUUUCGAUAA
......(((..(((....)))..)))..(((((((.((((((((....)))))....(((((((....)).(((((((.....----.....))))))).)))))..))))))))))... ( -32.10)
>consensus
UUGAGAGAUCCAUGAUUUCAUAGAUUGUUCGGAAUGCUGGGAAAAUAUUUUUCACGGACUGGGCGGAAGCUUCUGCACAUGUA____CAUAGGUGUAGAUCCAGUGGCAGAUUUCGAUAA
....((((((...)))))).........(((((((.((((((((....)))))....(((((((....)).(((((((.(((......))).))))))).)))))..))))))))))... (-31.93 = -32.02 +   0.09)

alignment

secondary structure

dotplot

Window 0

Location	12,188,446 – 12,188,546
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	94.26
Mean single sequence MFE	-26.34
Consensus MFE	-24.89
Energy contribution	-24.86
Covariance contribution	-0.03
Combinations/Pair	1.07
Mean z-score	-1.30
Structure conservation index	0.94
SVM decision value	0.99
SVM RNA-class probability	0.896407
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12188446 100 + 27905053
GAAAAUAUUUUUCACGGACUGAGCGGAAGCUUCUGCACAUGUACAUACAUAGGUGUAGAUCCAGUGGCAGAUUUCGAUAAGUCAUUGGGCUAUAAUUUGC
............((((((...(((....)))(((((((((((....))))..)))))))))).)))(((((((......((((....))))..))))))) ( -26.70)
>DroSec_CAF1 2250 96 + 1
GAAAAUGUUUUUCACGGACUGGGCGGAAGCUUCUGCACACGUA----CAUAGGUGUAGAUCCAGUGGCAGAUUUCGAUAAGUCAUUGGGCUAUAAUUUGC
((((.....))))....(((((((....)).(((((((.(...----....)))))))).))))).(((((((......((((....))))..))))))) ( -26.60)
>DroSim_CAF1 2249 96 + 1
GAAAAUAUUUUUCACGGACUGGGCGGAAGCUUCUGCACAUGUA----CAUAGGUGUAGAUCCAGUGGCAGAUUUCGAUAAGUCAUUGGGCUAUAAUUUGC
((((.....))))....(((((((....)).(((((((.....----.....))))))).))))).(((((((......((((....))))..))))))) ( -25.70)
>DroEre_CAF1 2499 92 + 1
GAAAAUAUUUUUCACGGACUGGGCGGAAGCUUCUGCACAUG--------UACGUGUAGAUCCAGUGGCAGAUUUCGAUAAGUCAUUGGGCUAUAAUUUGC
((((.....))))....(((((((....)).(((((((...--------...))))))).))))).(((((((......((((....))))..))))))) ( -26.90)
>DroYak_CAF1 2193 96 + 1
GAAAAUAUUUUUCACGGACUGGGCGGAAGCUUCUGCACAUGUA----UGUACGUGUAGAUCCAGUGGCAGAUUUCGAUAAGUCAUUGGGCUAUAAUUUGC
((((.....))))....(((((((....)).(((((((.....----.....))))))).))))).(((((((......((((....))))..))))))) ( -25.80)
>consensus
GAAAAUAUUUUUCACGGACUGGGCGGAAGCUUCUGCACAUGUA____CAUAGGUGUAGAUCCAGUGGCAGAUUUCGAUAAGUCAUUGGGCUAUAAUUUGC
............((((((...(((....)))(((((((.(((......))).)))))))))).)))(((((((......((((....))))..))))))) (-24.89 = -24.86 +  -0.03)

alignment

secondary structure

dotplot

Window 1

Location	12,188,546 – 12,188,651
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	95.05
Mean single sequence MFE	-15.30
Consensus MFE	-12.25
Energy contribution	-13.05
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.54
Structure conservation index	0.80
SVM decision value	0.06
SVM RNA-class probability	0.561542
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12188546 105 + 27905053
UACUGUCGACGAGAAAUUUUUUCAUUAUAAUUAGACACAUCACAGGGAAACAACAACAAUUUCCACAAAAACCGACUAAAAAUAAAGUUGACAUUUCACACAGCA
...(((((((((((.....)))).((((..((((...........(((((.........)))))...........))))..)))).)))))))............ ( -14.45)
>DroSec_CAF1 2346 105 + 1
UACUGUCGACGUGAAAUUUUUUCAUUAUACUUAGACACAUCACAGGGAAACAACAACAAUUUCCACAAAAACCGACUACAAAUAAAGUUGACAUUUCACACAGCA
..((((....(((((((............................(((((.........)))))........(((((........)))))..))))))))))).. ( -14.30)
>DroSim_CAF1 2345 105 + 1
UACUGUCGACGUGAAAUUUUUUCAUUAUAAUUAGACACAUCAGAGGGAAACAACAACAAUUUCCACAAAAACCGACUAAAAAUAAAGUUGACAUUUCACACAGCA
..((((....(((((((.((..(.((((..((((...........(((((.........)))))...........))))..)))).)..)).))))))))))).. ( -14.75)
>DroEre_CAF1 2591 105 + 1
UACUGUCGACGUGAAAUUUUUUCAUUAUAAUUAGGCACAUCAUAGGGAAACAGCAACAGCUUCCACAAAAACCGACUAAAAAUAAAGUUGACAUUUCACACAGCG
..((((....(((((((.((..(.((((..((((...........(((...(((....))))))...........))))..)))).)..)).))))))))))).. ( -17.55)
>DroYak_CAF1 2289 105 + 1
UACUGUCGACGUGAAAUUUUUUCAUUAUAAUUAGGCACAUCAUAGAGAAACAACAACAGUUUCCACAAAAACCGACUAAACAUAAAGUUGACAUUUCACACAGCA
..((((....(((((((.((..(.((((..((((............(((((.......)))))............))))..)))).)..)).))))))))))).. ( -15.45)
>consensus
UACUGUCGACGUGAAAUUUUUUCAUUAUAAUUAGACACAUCACAGGGAAACAACAACAAUUUCCACAAAAACCGACUAAAAAUAAAGUUGACAUUUCACACAGCA
..((((....(((((((.((..(.((((..((((...........(((((.........)))))...........))))..)))).)..)).))))))))))).. (-12.25 = -13.05 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:15 2006