Locus 2406

Sequence ID	3R_DroMel_CAF1
Location	6,754,234 – 6,754,423
Length	189
Max. P	0.999306

overview

Window 5

Location	6,754,234 – 6,754,343
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.29
Mean single sequence MFE	-44.68
Consensus MFE	-37.88
Energy contribution	-37.96
Covariance contribution	0.08
Combinations/Pair	1.04
Mean z-score	-2.90
Structure conservation index	0.85
SVM decision value	3.50
SVM RNA-class probability	0.999306
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6754234 109 + 27905053
CGACAUUCUAUAAAUUAAUCAGACGGAGUGCUCUUAGCUCCGCCAGGAGCCAGAAGCCCGGAGCAGG-----------CAGCGAGGAGCACUUCCUGGCCAGCCUCCCGCUGGCAACUCA
...................(((..(((((((((((.((((((((.((.((.....)))).).)).))-----------.))).))))))))))))))((((((.....))))))...... ( -42.90)
>DroSec_CAF1 18399 109 + 1
CGACAUUCUAUAAAUUAAUCAGACGGAGUGCUCUUAGCUCCGCCAGGAGCCAGAAGCCCGGAGCAGC-----------CAGCGAGGAGCACUUCCUGGCCAGCCUCCCGCUGGCAACUCA
...................(((..(((((((((((.(((((....))))).....((..((.....)-----------).)).))))))))))))))((((((.....))))))...... ( -41.30)
>DroSim_CAF1 22800 109 + 1
CGACAUUCUAUAAAUUAAUCAGACGGAGUGCUCUUAGCUCCGCCAGGAGCCAGAAGCCCGGAGCAGC-----------CAGCGAGGAGCACUUCCUGGCCAGCCUCCCGCUGGCAACUCA
...................(((..(((((((((((.(((((....))))).....((..((.....)-----------).)).))))))))))))))((((((.....))))))...... ( -41.30)
>DroEre_CAF1 2787 120 + 1
CGACAUUCUAUAAAUUAAUCAGACGGAGUGCUCUUAGCUCCGCUAGGAGCCAGAAGCCCGGAGAAGCCAGCGAGGAACCAGCGAGGAGCACUUCCUGGCCAGCCUCCCGCUGGCAACUCA
.......................(((.(((((((((((...))))))))).....)))))(((..((((((((((..((((.((((....))))))))....))))..))))))..))). ( -47.40)
>DroYak_CAF1 14723 120 + 1
CGACAUUCUAUAAAUUAAUCAGACGGAGUGCUCUUAGCUCCGCCAGGAGCAAGAAGCCCGGAGUAUCCAGCGAGGAGCCAGCGAGGAGCACUUCCUGGCCAGCCUCCCGCUGGCAACUCA
.......................(((.((..((((.(((((....))))))))).)))))((((..((((((.(((((..((.(((((...))))).))..).))))))))))..)))). ( -50.50)
>consensus
CGACAUUCUAUAAAUUAAUCAGACGGAGUGCUCUUAGCUCCGCCAGGAGCCAGAAGCCCGGAGCAGC___________CAGCGAGGAGCACUUCCUGGCCAGCCUCCCGCUGGCAACUCA
...................(((..(((((((((((.(((((....))))).....((.....))...................))))))))))))))((((((.....))))))...... (-37.88 = -37.96 +   0.08)

alignment

secondary structure

dotplot

Window 6

Location	6,754,234 – 6,754,343
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.29
Mean single sequence MFE	-49.76
Consensus MFE	-36.86
Energy contribution	-37.06
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.53
Structure conservation index	0.74
SVM decision value	0.90
SVM RNA-class probability	0.878339
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6754234 109 - 27905053
UGAGUUGCCAGCGGGAGGCUGGCCAGGAAGUGCUCCUCGCUG-----------CCUGCUCCGGGCUUCUGGCUCCUGGCGGAGCUAAGAGCACUCCGUCUGAUUAAUUUAUAGAAUGUCG
((((((((((((.....))))))((((.(((((((......(-----------((((...)))))...(((((((....))))))).)))))))...))))...)))))).......... ( -43.20)
>DroSec_CAF1 18399 109 - 1
UGAGUUGCCAGCGGGAGGCUGGCCAGGAAGUGCUCCUCGCUG-----------GCUGCUCCGGGCUUCUGGCUCCUGGCGGAGCUAAGAGCACUCCGUCUGAUUAAUUUAUAGAAUGUCG
.((((.((((((((((((((........))).)))).)))))-----------)).))))((((((..(((((((....)))))))..)))...)))....................... ( -48.00)
>DroSim_CAF1 22800 109 - 1
UGAGUUGCCAGCGGGAGGCUGGCCAGGAAGUGCUCCUCGCUG-----------GCUGCUCCGGGCUUCUGGCUCCUGGCGGAGCUAAGAGCACUCCGUCUGAUUAAUUUAUAGAAUGUCG
.((((.((((((((((((((........))).)))).)))))-----------)).))))((((((..(((((((....)))))))..)))...)))....................... ( -48.00)
>DroEre_CAF1 2787 120 - 1
UGAGUUGCCAGCGGGAGGCUGGCCAGGAAGUGCUCCUCGCUGGUUCCUCGCUGGCUUCUCCGGGCUUCUGGCUCCUAGCGGAGCUAAGAGCACUCCGUCUGAUUAAUUUAUAGAAUGUCG
.(((..(((((((((..((..((.((((.....)))).))..))..)))))))))..)))((((((..(((((((....)))))))..)))...)))....................... ( -56.90)
>DroYak_CAF1 14723 120 - 1
UGAGUUGCCAGCGGGAGGCUGGCCAGGAAGUGCUCCUCGCUGGCUCCUCGCUGGAUACUCCGGGCUUCUUGCUCCUGGCGGAGCUAAGAGCACUCCGUCUGAUUAAUUUAUAGAAUGUCG
.((((..((((((((..((..((.((((.....)))).))..))..))))))))..))))((((((.((((((((....))))).))))))...)))....................... ( -52.70)
>consensus
UGAGUUGCCAGCGGGAGGCUGGCCAGGAAGUGCUCCUCGCUG___________GCUGCUCCGGGCUUCUGGCUCCUGGCGGAGCUAAGAGCACUCCGUCUGAUUAAUUUAUAGAAUGUCG
((((((((((((.....))))))((((.(((((((((((..(...............)..))))....(((((((....))))))).)))))))...))))...)))))).......... (-36.86 = -37.06 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	6,754,303 – 6,754,423
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.50
Mean single sequence MFE	-35.36
Consensus MFE	-34.88
Energy contribution	-34.64
Covariance contribution	-0.24
Combinations/Pair	1.02
Mean z-score	-1.83
Structure conservation index	0.99
SVM decision value	1.94
SVM RNA-class probability	0.983175
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6754303 120 + 27905053
GCGAGGAGCACUUCCUGGCCAGCCUCCCGCUGGCAACUCAAUCGCGAUAAAGCCCCAGGUGAAUUAUAGUUAUUUGAUUUUGUUUUGGUGAUUUGUUUGCUUGAGUUUCAGUUCUUUAAA
..(((((((........((((((.....))))))(((((((..((((((((.(.(((((.((((((........))))))...))))).).)))).)))))))))))...)))))))... ( -35.60)
>DroSec_CAF1 18468 120 + 1
GCGAGGAGCACUUCCUGGCCAGCCUCCCGCUGGCAACUCAAUCGCGAUAAAGCCCCAGGUGAAUUAUAGUUAUUUGAUUUUGUUUUGGUGAUUUGUUUGCUUGAGUUUCAGUUCUUUAAA
..(((((((........((((((.....))))))(((((((..((((((((.(.(((((.((((((........))))))...))))).).)))).)))))))))))...)))))))... ( -35.60)
>DroSim_CAF1 22869 120 + 1
GCGAGGAGCACUUCCUGGCCAGCCUCCCGCUGGCAACUCAAUCGCGAUAAAGCCUCAGGUGAAUUAUAGUUAUUUGAUUUUGUUUUGGUGAUUUGUUUGCUUGAGUUUCAGUUCUUUAAA
..(((((((........((((((.....)))))).........((......))((((((..(((...((((((..((......))..)))))).)))..)))))).....)))))))... ( -35.00)
>DroEre_CAF1 2867 120 + 1
GCGAGGAGCACUUCCUGGCCAGCCUCCCGCUGGCAACUCAAUCGCGAUAAAGCCCCAGGUGAAUUAUAGUUAUUUGAUUUUGUUUUGGUGAUUUGUUUGCUUGAGUUUCAGUUCUUUAAA
..(((((((........((((((.....))))))(((((((..((((((((.(.(((((.((((((........))))))...))))).).)))).)))))))))))...)))))))... ( -35.60)
>DroYak_CAF1 14803 120 + 1
GCGAGGAGCACUUCCUGGCCAGCCUCCCGCUGGCAACUCAAUCGCGAUAAAGCCUCAGGUGAAUUAUAGUUAUUUGAUUUUGUUUUGGUGAUUUGUUUGCUUGAGUUUCAGUUCUUUAAA
..(((((((........((((((.....)))))).........((......))((((((..(((...((((((..((......))..)))))).)))..)))))).....)))))))... ( -35.00)
>consensus
GCGAGGAGCACUUCCUGGCCAGCCUCCCGCUGGCAACUCAAUCGCGAUAAAGCCCCAGGUGAAUUAUAGUUAUUUGAUUUUGUUUUGGUGAUUUGUUUGCUUGAGUUUCAGUUCUUUAAA
..(((((((........((((((.....))))))(((((((..((((((((.(.(((((.((((((........))))))...))))).).)))).)))))))))))...)))))))... (-34.88 = -34.64 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:56 2006