Locus 791

Sequence ID	3R_DroMel_CAF1
Location	2,709,717 – 2,709,917
Length	200
Max. P	0.799138

overview

Window 1

Location	2,709,717 – 2,709,837
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.42
Mean single sequence MFE	-31.46
Consensus MFE	-23.06
Energy contribution	-23.06
Covariance contribution	0.00
Combinations/Pair	1.18
Mean z-score	-1.82
Structure conservation index	0.73
SVM decision value	0.25
SVM RNA-class probability	0.651000
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2709717 120 - 27905053
CCCGUCACUUGAAGCCGUUCUUCGGCACAUCAUUUAUCAGAGCCUUCUAUUUAUAGGCUCUCGAUCCGGCAACACUCGGCGAAACCAAGCUGAGACAGACCAAAAAAAAAAAGAGAACUU
...(((.......(((((.(....).)).......((((((((((.........))))))).)))..)))....((((((........))))))...))).................... ( -32.30)
>DroSec_CAF1 20064 117 - 1
CCCGUCACUUGAAGCCGUUCUUCGGCACAUCAUUUAUCAGAGCCUUCUAUUUAUAGGAUCUCGAUCCGGCUACACUCGGCGAAACCAAGCUGACACGGCC-A--AGAAAAAGGAGAACUU
................((((((((((...((........)))))((((.......((((....))))((((....(((((........)))))...))))-.--))))...))))))).. ( -30.60)
>DroSim_CAF1 21147 117 - 1
CCCGUCACUUGAAGCUGUUCUUCGGCACAUCAUUUAUCAGAGCCUUCUAUUUAUAGGAUCUCGAUCCGGCUACACUCGGCGAAACCAAGCUGACACGGCC-A--AGAAAAAGGAGAACUU
................((((((((((...((........)))))((((.......((((....))))((((....(((((........)))))...))))-.--))))...))))))).. ( -30.30)
>DroEre_CAF1 21040 115 - 1
CCCGUCACUCGAAGCCGUUCUUCGGCACAUCAUUUAUCAGGGCCUUCUAUUUAUAGGCUCUCGAUCCGGCUGCACUGCACCAAACCGAGCUGGCACAGCC-C--AGAA--GGGAGAACUU
...((((((((..((((.....)))).........((((((((((.........))))))).)))..((.(((...)))))....)))).))))....((-(--....--)))....... ( -34.50)
>DroYak_CAF1 20902 116 - 1
CCCGUCACUCGAAGCCGUUCUUCGGCACAUCAUUUAUCAGAGCCUUCUAUUUAUAGGCUCUCGAUCCCGCUACACUUGGCGAAACCAAGCUGGCACUGCC-A--ACAA-AAUUAGAACUU
....((....((((.....))))((((........((((((((((.........))))))).)))...((((..(((((.....))))).))))..))))-.--....-.....)).... ( -29.60)
>consensus
CCCGUCACUUGAAGCCGUUCUUCGGCACAUCAUUUAUCAGAGCCUUCUAUUUAUAGGCUCUCGAUCCGGCUACACUCGGCGAAACCAAGCUGACACAGCC_A__AGAAAAAGGAGAACUU
...((((((((..((((.....)))).........((((((((((.........))))))).)))....................)))).)))).......................... (-23.06 = -23.06 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	2,709,797 – 2,709,917
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	98.17
Mean single sequence MFE	-33.12
Consensus MFE	-32.17
Energy contribution	-32.08
Covariance contribution	-0.08
Combinations/Pair	1.10
Mean z-score	-0.89
Structure conservation index	0.97
SVM decision value	0.61
SVM RNA-class probability	0.799138
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2709797 120 - 27905053
AGCAGGCGUUAGCGUUUAGCGUUAACGUUAACUCAAUCGACCUGUCAUUUGGGCCUCAGCUGGCUCCUCGCGUAAUUGCCCCCGUCACUUGAAGCCGUUCUUCGGCACAUCAUUUAUCAG
....((((((((((.....))))))))))...((((..(((.........(((((......)))))...(((....)))....)))..)))).((((.....)))).............. ( -33.20)
>DroSec_CAF1 20141 120 - 1
AGCAGGCGUUAGCGUUUAGCGUUAACGUUAACUCAAUCGACCUGUCAUUUGGGCCUCAGCUGGCUCCUCGCAUAAUUGCCCCCGUCACUUGAAGCCGUUCUUCGGCACAUCAUUUAUCAG
....((((((((((.....))))))))))...((((..(((.........(((((......)))))...(((....)))....)))..)))).((((.....)))).............. ( -33.90)
>DroSim_CAF1 21224 120 - 1
AGCAGGCGUUAGCGUUUAGCGUUAACGUUAACUCAAUCGACCUGUCAUUUGGGCCUCAGCUGGCUCCUCGCAUAAUUGCCCCCGUCACUUGAAGCUGUUCUUCGGCACAUCAUUUAUCAG
(((.((((((((((.....))))))))))...((((..(((.........(((((......)))))...(((....)))....)))..)))).)))((.(....).))............ ( -32.00)
>DroEre_CAF1 21115 120 - 1
AGCAGGCGUUAGCGUUUAGCGUUAACGUUAACUCAAUCGACCUGUCAUUUGGGCCUCAGCUGGCUCCUCGCAUAAUUGCCCCCGUCACUCGAAGCCGUUCUUCGGCACAUCAUUUAUCAG
....((((((((((.....)))))))))).......((((..((.(....(((((......)))))...(((....)))....).)).)))).((((.....)))).............. ( -33.10)
>DroYak_CAF1 20978 120 - 1
GGCAGGCGUUAGCGUUUAGCGUUAACGUUAACUCAAUCGACCUGUCAUUUGGGCCUCAGCUGGCUCCUCGUAUAAUUGCCCCCGUCACUCGAAGCCGUUCUUCGGCACAUCAUUUAUCAG
((((((((((((((.....)))))))).....((....))))))))....(((((......)))))...(.((((.((....((.....))..((((.....))))....)).))))).. ( -32.60)
>DroAna_CAF1 19361 120 - 1
AGCAGGCGUUAGCGUUUAGCGUUAACGUUAACUCAAUCGACCUGUCAUUUGGGCCUCAGUUGGCUCCUCGCAUAAUUGCCCCCGUCACUUGAAGCCGUUCUUCGGCACAUCAUUUAUCAG
....((((((((((.....))))))))))...((((..(((.........(((((......)))))...(((....)))....)))..)))).((((.....)))).............. ( -33.90)
>consensus
AGCAGGCGUUAGCGUUUAGCGUUAACGUUAACUCAAUCGACCUGUCAUUUGGGCCUCAGCUGGCUCCUCGCAUAAUUGCCCCCGUCACUUGAAGCCGUUCUUCGGCACAUCAUUUAUCAG
....((((((((((.....))))))))))...((((..(((.........(((((......)))))...(((....)))....)))..)))).((((.....)))).............. (-32.17 = -32.08 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:14 2006