Locus 1065

Sequence ID	2R_DroMel_CAF1
Location	4,338,411 – 4,338,511
Length	100
Max. P	0.618045

overview

Window 9

Location	4,338,411 – 4,338,511
Length	100
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	78.85
Mean single sequence MFE	-37.00
Consensus MFE	-16.71
Energy contribution	-18.04
Covariance contribution	1.34
Combinations/Pair	1.28
Mean z-score	-2.26
Structure conservation index	0.45
SVM decision value	0.17
SVM RNA-class probability	0.618045
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4338411 100 + 20766785
GUAAAGGAGCGCAAGAAGGCGGCCAAGGCCAAGCCGAAGAAG----AUCCUGGGCGGCCUGCUUAUGGUGAAUCA--------CAUGAAGAUGUGGCACCAGCACCGUGAGC
.....((..(((......))).)).(((((..(((..((...----...)).))))))))((((((((((..(((--------(((....))))))......)))))))))) ( -37.70)
>DroSec_CAF1 8878 100 + 1
GUAAAGGAGCGCAAGAAGGCGGCCAAGGCCAAGCCGAAGAAG----GUCCUGGGUGGCCUGCUAAUGGUGAAUCA--------UAUGAAGAUGUGGCACCAGCACCGUGAGC
.....((.((...((.((((.(((.(((....(((......)----))))).))).)))).))..(((((...((--------(((....))))).))))))).))...... ( -34.80)
>DroSim_CAF1 8905 100 + 1
GUUAAGGAGCGUAAGAAGGCGGCCAAGGCCAAGCCGAAAAAG----GUCCUGGGUGGCCUGCUAAUGGUGAAUCA--------UAUGAAGAUGUGGCACCAGCACCGUGAGC
(((..((.((...((.((((.(((.(((....(((......)----))))).))).)))).))..(((((...((--------(((....))))).))))))).))...))) ( -35.20)
>DroEre_CAF1 6448 100 + 1
GUGAAGGAGCGCAGGAAGGCGGCCAGGGCCAAGCCGAAGAAG----AUCCUGGGCGGCCUCCUGAUGCUGAACCA--------CAUGAAGAUGUGGCACCAGCAUCGGGAGC
.....((.((.(((((.((((((....)))..))).......----.))))).))..))(((((((((((..(((--------(((....))))))...))))))))))).. ( -48.60)
>DroYak_CAF1 7074 100 + 1
GUGAAGGAGCGCAAGAAGGCUGCCAGGGCCAAGCCGAAGAAG----AUCCUGGGCGGCCUCCUGAUGGUAAAUCA--------CUUGAAGAUGUGGCAUCAGCAUCGUGAGC
........((.((.(((((((((((((..(...........)----..))).)))))))).((((((.((.(((.--------......))).)).))))))..)).)).)) ( -32.10)
>DroAna_CAF1 15784 100 + 1
GUGAAGGAGCGGAAGAAGGCUGCCAAGAC---GGCAAAAAUGUCGAUUCCUGGGA---------AUGCUCAGUCCUUAAUGCGCCACAAAAUGUGGCUGCAACACCGCGAAC
........((((...(((((((......(---((((....)))))((((....))---------))...))).))))..((((((((.....))))).)))...)))).... ( -33.60)
>consensus
GUGAAGGAGCGCAAGAAGGCGGCCAAGGCCAAGCCGAAGAAG____AUCCUGGGCGGCCUGCUAAUGGUGAAUCA________CAUGAAGAUGUGGCACCAGCACCGUGAGC
.....((.((...((.((((.(((.(((......(......)......))).))).)))).))..(((((.(((...............)))....))))))).))...... (-16.71 = -18.04 +   1.34)

alignment

secondary structure

dotplot

Window 0

Location	4,338,411 – 4,338,511
Length	100
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	78.85
Mean single sequence MFE	-33.93
Consensus MFE	-13.44
Energy contribution	-14.34
Covariance contribution	0.91
Combinations/Pair	1.26
Mean z-score	-2.39
Structure conservation index	0.40
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4338411 100 - 20766785
GCUCACGGUGCUGGUGCCACAUCUUCAUG--------UGAUUCACCAUAAGCAGGCCGCCCAGGAU----CUUCUUCGGCUUGGCCUUGGCCGCCUUCUUGCGCUCCUUUAC
......((.(((((((.(((((....)))--------))...)))))((((.((((.(((.(((..----...))).)))..(((....))))))).)))).)).))..... ( -35.10)
>DroSec_CAF1 8878 100 - 1
GCUCACGGUGCUGGUGCCACAUCUUCAUA--------UGAUUCACCAUUAGCAGGCCACCCAGGAC----CUUCUUCGGCUUGGCCUUGGCCGCCUUCUUGCGCUCCUUUAC
((....((((((((((....(((......--------.)))....))))))).(((((.(((((.(----(......)))))))...)))))))).....)).......... ( -31.00)
>DroSim_CAF1 8905 100 - 1
GCUCACGGUGCUGGUGCCACAUCUUCAUA--------UGAUUCACCAUUAGCAGGCCACCCAGGAC----CUUUUUCGGCUUGGCCUUGGCCGCCUUCUUACGCUCCUUAAC
......((.(((((((...(((......)--------))...)))))...((.(((((.(((((.(----(......)))))))...)))))))........)).))..... ( -29.80)
>DroEre_CAF1 6448 100 - 1
GCUCCCGAUGCUGGUGCCACAUCUUCAUG--------UGGUUCAGCAUCAGGAGGCCGCCCAGGAU----CUUCUUCGGCUUGGCCCUGGCCGCCUUCCUGCGCUCCUUCAC
((....((((((((.(((((((....)))--------))))))))))))((((((.((.(((((..----(..(....)...)..))))).)).)))))))).......... ( -45.50)
>DroYak_CAF1 7074 100 - 1
GCUCACGAUGCUGAUGCCACAUCUUCAAG--------UGAUUUACCAUCAGGAGGCCGCCCAGGAU----CUUCUUCGGCUUGGCCCUGGCAGCCUUCUUGCGCUCCUUCAC
((.((.((((.(((...(((........)--------))..))).))))(((((((.(((.(((..----(..(....)...)..)))))).))))))))).))........ ( -31.80)
>DroAna_CAF1 15784 100 - 1
GUUCGCGGUGUUGCAGCCACAUUUUGUGGCGCAUUAAGGACUGAGCAU---------UCCCAGGAAUCGACAUUUUUGCC---GUCUUGGCAGCCUUCUUCCGCUCCUUCAC
....((((...(((.(((((.....))))))))..((((.(((.....---------..((((((..((.((....)).)---))))))))))))))...))))........ ( -30.41)
>consensus
GCUCACGGUGCUGGUGCCACAUCUUCAUG________UGAUUCACCAUCAGCAGGCCGCCCAGGAU____CUUCUUCGGCUUGGCCUUGGCCGCCUUCUUGCGCUCCUUCAC
((.((.((....(((((((.(((...............)))............(((((((.((((.......)))).))..))))).)))).))).)).)).))........ (-13.44 = -14.34 +   0.91)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:30 2006