Locus 5540

Sequence ID	2R_DroMel_CAF1
Location	17,691,458 – 17,691,698
Length	240
Max. P	0.745012

overview

Window 9

Location	17,691,458 – 17,691,578
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.83
Mean single sequence MFE	-45.58
Consensus MFE	-43.04
Energy contribution	-43.04
Covariance contribution	-0.00
Combinations/Pair	1.10
Mean z-score	-1.17
Structure conservation index	0.94
SVM decision value	0.46
SVM RNA-class probability	0.745012
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17691458 120 - 20766785
CACCAACUGUUGCUGCCAGCCACAGCUGAAAGCGAUAUUAAGGGCUCCCGAUGGACUUGGCGUCAUGCUGCAGUGUUCGAUGAAGCUGCGCGAUAUGCCGAUGCUGUGGAGCGCGGGUGU
((((...(((((((..((((....))))..)))))))....(.(((((..((((..(((((((..(((.(((((.(((...)))))))))))..)))))))..))))))))).).)))). ( -48.60)
>DroSec_CAF1 1080 120 - 1
CACCAACUGUUGCUGCCAGCCGCAGCUGAAAGCGAUACUAAGGGCUCCCGAUGGACUUGGCGUCAUGCUGCAGUGUUCAAUGAAGCUGCGCGAUAUGCCGAUGCUGUGGAGCGCAGGUGU
((((...(((((((..((((....))))..)))))))....(.(((((..((((..(((((((..(((.(((((.(((...)))))))))))..)))))))..))))))))).).)))). ( -48.70)
>DroSim_CAF1 277 120 - 1
CACCAACUGUUGCUGCCAGCCACAGCUGAAAGCGAUACUAAGGGCUCCCGAUGGACUUGGCGUCAUGCUGCAGUGUUCGAUGAAGCUGCGCGAUAUGCCGAUGCUGUGGAGCGCAGGUGU
((((...(((((((..((((....))))..)))))))....(.(((((..((((..(((((((..(((.(((((.(((...)))))))))))..)))))))..))))))))).).)))). ( -48.70)
>DroEre_CAF1 898 120 - 1
CACUAACUGUUGCUGCCAGCCGCAGCUGAAUGCGAUACUGAGGGCUCCUGUUGGACUUGGCAUCAUACUGCAGUGUUCGAUGAAGCUGCGCGAAAUGCCAAUGCUGUGGAGCGUGGGUGU
((((.((((((((...((((....))))...))))))......(((((...(((..(((((((.....((((((.(((...)))))))))....)))))))..))).))))))).)))). ( -40.50)
>DroYak_CAF1 777 120 - 1
CACUAAUUGUUGCUGCCAGCCACAGCUGAAAGCGAUAUUGAGGGCUCCUGUUGGACUUGGCGUCAAGCUGCAGUGUUCGAUGAAGCUGCGCGAAAUCCCGAUGCUGUGGAGCGUGGGUGU
((((...(((((((..((((....))))..)))))))......(((((.((.(((.((.((((..((((.((........)).)))))))).)).)))....))...)))))...)))). ( -41.40)
>consensus
CACCAACUGUUGCUGCCAGCCACAGCUGAAAGCGAUACUAAGGGCUCCCGAUGGACUUGGCGUCAUGCUGCAGUGUUCGAUGAAGCUGCGCGAUAUGCCGAUGCUGUGGAGCGCGGGUGU
((((...(((((((..((((....))))..)))))))....(.(((((...(((..(((((((..(((.(((((.(((...)))))))))))..)))))))..))).))))).).)))). (-43.04 = -43.04 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	17,691,578 – 17,691,698
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-41.84
Consensus MFE	-37.90
Energy contribution	-37.98
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-1.20
Structure conservation index	0.91
SVM decision value	0.28
SVM RNA-class probability	0.667287
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17691578 120 + 20766785
CAAUGCUUUAAGGUCUCGCUUUCAUUGGAGGGCGAACUGGGUCUGGAGCAGCACUUGGCCAUCAAAUCCGAGUCCCAGACCAGCAUAUUUCUGGGUCCUCUUGACGGGAGGCGGAUCAGU
...........((((.(((((((...(((((((...(((((.(((((...((.....)).......))).)).))))).((((.......))))))))))).....)))))))))))... ( -45.00)
>DroSec_CAF1 1200 120 + 1
CAAUGCUUUAAGGUCUCGCUUUCGUUGGAGGGAGAACUGGGUCUGGAGCAGCACUUGGCCAUCAAAUCUGAGUCCCAGACCAGCAUAUUUCUGGGUCCUCUUGACGGAAGGCGGAUCAGU
...........((((.(((((((((..(..(((...(((((.(((((...((.....)).......))).)).))))).((((.......)))).)))..)..)).)))))))))))... ( -40.50)
>DroSim_CAF1 397 120 + 1
CAAUGCUUUAAGGUCUCGCUUUCGUUGGAGGGCGAACUGGGUCUGGAGCAGCACUUGGCCAUCAAAUCCGAGUCCCAGACCAGCAUAUUUCUGGGUCCUCUUGACGGAAGGCGGAUCAGU
...........((((.(((((((((((((((((...(((((.(((((...((.....)).......))).)).))))).((((.......)))))))))).)))).)))))))))))... ( -45.70)
>DroEre_CAF1 1018 120 + 1
CAAUGCUUUAAGGUCUCGCUUUCUUUGGAGGGCGAACUGGGUCUGGACCAGCACUUGGCCAUCAAAUCCGAGUCCCAGACCAGCAUAUUCCUAGGUCCCCUUGACGGAAGACGGAUCAGC
..(((((....(((.((((((((....))))))))))).(((((((....(.((((((.........))))))))))))))))))).......(((((.(((.....)))..)))))... ( -39.30)
>DroYak_CAF1 897 120 + 1
CAAUGCUUUAAGGUCUCGCUUUCUUUGGAGGGCGAACUGGGUCUGGAGCAGCACUUGGCCAUCAAAUCCGAGUCCCAGACCAGCAUAUUCUUAGGACCUCUUGACGGGAGACGGAUCAGU
..........(((((((((((((....))))))))....(((((((.(....((((((.........)))))))))))))).............))))).(((((.(....).).)))). ( -38.70)
>consensus
CAAUGCUUUAAGGUCUCGCUUUCGUUGGAGGGCGAACUGGGUCUGGAGCAGCACUUGGCCAUCAAAUCCGAGUCCCAGACCAGCAUAUUUCUGGGUCCUCUUGACGGAAGGCGGAUCAGU
..(((((....(((.((((((((....))))))))))).(((((((....(.((((((.........))))))))))))))))))).......(((((((((.....)))).)))))... (-37.90 = -37.98 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:18 2006