Locus 7285

Sequence ID	3L_DroMel_CAF1
Location	19,497,850 – 19,498,043
Length	193
Max. P	0.769201

overview

Window 2

Location	19,497,850 – 19,497,949
Length	99
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	76.94
Mean single sequence MFE	-26.07
Consensus MFE	-15.59
Energy contribution	-15.45
Covariance contribution	-0.14
Combinations/Pair	1.08
Mean z-score	-1.65
Structure conservation index	0.60
SVM decision value	0.52
SVM RNA-class probability	0.769201
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19497850 99 - 23771897
GCUCGCACGCAUGCGCAGCAGCCACGCACCAGUUUGGCGACAAAGCGACAAAAAAAAA----GUGUAACUAUGUGUUUGGCUGAGAUCGAAUCGAAGCGGUCG
(((((((....)))).)))(((((.((((.((((..((......)).(((........----.)))))))..)))).)))))..(((((........))))). ( -28.10)
>DroPse_CAF1 6692 80 - 1
GCUCGCACGCAUGCGCGGCAGCCACGCACCAGUUUGGCGACAAAGCGAAAAAAAAACA-------C-ACUAUAUUUAUAGCAGAAAAC---------------
..((((.(((....)))(..((((.((....)).))))..)...))))..........-------.-.((((....))))........--------------- ( -17.30)
>DroSec_CAF1 8510 103 - 1
GCUCGCACGCAUGCGCAGCAGCCACGCACCAGUUUGGCGACAAAGCGACAAAAAAAAAUAGAGUGUAACUAUGUGUUUGGCUGAGAUCGAAUCGAAACGGCCG
(((((((....)))).))).((((.((....)).)))).(((.((..(((.............)))..)).)))....(((((...(((...)))..))))). ( -25.92)
>DroSim_CAF1 8732 83 - 1
GCUCGCACGCAUGCGCAGCAGCCACGCACCAGUUUGGCGACAAAGCGACAAAAAAAAAAA--------------------UUGAGAUCGAAUCGAAACGGUCG
(((((((....)))).))).((((.((....)).))))......................--------------------....(((((........))))). ( -20.70)
>DroEre_CAF1 9012 95 - 1
GCUCGCACGCAUGCGCAGCAGCCACGCACCAGUUUGGCGACAAAGCGACAAAAAA-------GUGUAACUG-GUGUAUGGCAGAGAUCGAAUCGAAAAUUGAA
(((((((....)))).))).((((..((((((((..((......)).(((.....-------.))))))))-)))..)))).....((((........)))). ( -32.40)
>DroYak_CAF1 8709 88 - 1
GCUCGCACGCAUGCGCAGCAGCCACGCACCAGUUUGGCGACAAAGCGACAAAAAA-------GUGUAACUG-GUGUAUGGCAGAGAUCGAACCGAA-------
(((((((....)))).))).((((..((((((((..((......)).(((.....-------.))))))))-)))..))))...............------- ( -32.00)
>consensus
GCUCGCACGCAUGCGCAGCAGCCACGCACCAGUUUGGCGACAAAGCGACAAAAAAAAA____GUGUAACUA_GUGUAUGGCAGAGAUCGAAUCGAAACGG_CG
(((((((....)))).))).((((.((....)).))))................................................................. (-15.59 = -15.45 +  -0.14)

alignment

secondary structure

dotplot

Window 3

Location	19,497,949 – 19,498,043
Length	94
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	87.10
Mean single sequence MFE	-34.48
Consensus MFE	-29.45
Energy contribution	-30.95
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.85
SVM decision value	0.34
SVM RNA-class probability	0.694342
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19497949 94 - 23771897
GCAGAGCCACGCGGCCGACUGGACUGGACUGUUGGCCAG-CCCGGCCCUAUAAUCGCUUAUAUACGUUCGGUCAGUUGGCCAACAGUCGC---GAAAA
((.(.(((....))))..........(((((((((((((-((((..(.((((........)))).)..)))...))))))))))))))))---..... ( -38.70)
>DroPse_CAF1 6772 97 - 1
GCAAGGCAGCGCGGCCGACUGGACUGGACUGUUGGCCAG-CCCGGCCCUAUAAUCGCUUAUAUACGUUCGGUCAGUUGGCCAACACUCGCACAGAAAA
((.((((...))(((((((((.(((((((....((((..-...)))).(((((....)))))...))))))))))))))))....)).))........ ( -36.20)
>DroSim_CAF1 8815 94 - 1
GCAGAGCUACGCGGCCGACUGGACUGGACUGUUGGCCAG-CCCGGCCCUAUAAUCGCUUAUAUACGUUCGGUCAGUUGGCCAACAGUCGC---GAAAA
((.........(((((....)).)))(((((((((((((-((((..(.((((........)))).)..)))...))))))))))))))))---..... ( -38.10)
>DroEre_CAF1 9107 93 - 1
GCAGAGCCACGCGGCCGACUGGACUGGACUGUUGGCCAG-CCCGGCCCUAUAAUCGCUUAUAUACGUUCGGUCAGUUGGCCAACAC-CGC---GAAAA
((...((...))(((((((((.(((((((....((((..-...)))).(((((....)))))...)))))))))))))))).....-.))---..... ( -35.60)
>DroWil_CAF1 5735 75 - 1
GCA-----ACGCGG----------UGGACUGAUGGCCAGGCCCGGCCCUAUAAUCGCUUAUAUACGUUCGGUCAGUUGGCCAA--GUCGG---GU---
...-----....((----------(.(((((((((((......)))).(((((....)))))........))))))).)))..--.....---..--- ( -22.10)
>DroPer_CAF1 6605 97 - 1
GCAAGGCAGCGCGGCCGACUGGACUGGACUGUUGGCCAG-CCCGGCCCUAUAAUCGCUUAUAUACGUUCGGUCAGUUGGCCAACACUCGCACAGAAAA
((.((((...))(((((((((.(((((((....((((..-...)))).(((((....)))))...))))))))))))))))....)).))........ ( -36.20)
>consensus
GCAGAGCAACGCGGCCGACUGGACUGGACUGUUGGCCAG_CCCGGCCCUAUAAUCGCUUAUAUACGUUCGGUCAGUUGGCCAACACUCGC___GAAAA
((........))(((((((((.(((((((....((((......)))).(((((....)))))...))))))))))))))))................. (-29.45 = -30.95 +   1.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:07 2006