Locus 3660

Sequence ID 2R_DroMel_CAF1
Location 12,144,450 – 12,144,585
Length 135
Max. P 0.652790
window5955 window5956

overview

Window 5

Location 12,144,450 – 12,144,545
Length 95
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 83.84
Mean single sequence MFE -39.80
Consensus MFE -29.75
Energy contribution -29.50
Covariance contribution -0.25
Combinations/Pair 1.23
Mean z-score -1.55
Structure conservation index 0.75
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12144450 95 - 20766785
UUUGGCGGUGCCGGAUUAUCUGGUACCUUUGCCACCCGGCGGCAGCAA---------CAAUCCAUCGAUGGCCAGUGGUUCG---GGCUACGUGCCAGAAUUGCAAC
..((((((((((((.....)))))))).(((((.......)))))...---------.............))))(..((((.---(((.....))).))))..)... ( -38.60)
>DroSec_CAF1 516 95 - 1
UUUGGCGGUGCCGGAUUACCUGGUACCUUUGCCACCCGGUGGCAGCAA---------CAAUCCAUCAGUGGCCAGUGGUUCG---GGCUACGUGCCAGAAUUGCAAC
..((((((((((((.....)))))))).(((((((...)))))))...---------.............))))(..((((.---(((.....))).))))..)... ( -41.00)
>DroSim_CAF1 516 95 - 1
UUUGGCGGUGCCGGAUUACCUGGUACCUUUGCCACCCGGCGGCAGUAA---------CAAUCCAUCAGUGGCCAGUGGUUCG---GGCUACGUGCCAGAAUUGCAAC
..((((((((((((.....)))))))).(((((.......)))))...---------.............))))(..((((.---(((.....))).))))..)... ( -38.10)
>DroEre_CAF1 6115 95 - 1
UUUGGCGGUGCCGGACUACCUGGUACCUUUGCCACCCGGCGGCAGCAA---------CAAUCCAUCGGUGGCCAGUGGUUCG---GGCUACGUCCCGGAAUCGCAAC
..((((((((((((.....)))))))).....((((.(..((......---------....))..)))))))))((((((((---((......))).)))))))... ( -37.60)
>DroYak_CAF1 6128 95 - 1
CUUGGCGGUACCUGACUACCUGGUACCUUUGCCACCCGGCGGCAGCAA---------CAAUCCAUCGGUGGCCAGCGGAUCG---GGCUACGUCCCAGAAUUGCAAC
..((((((((((.........)))))).....((((.(..((......---------....))..)))))))))((((.(((---((......))).)).))))... ( -29.70)
>DroAna_CAF1 540 107 - 1
UCUGGCGGUGCCGGACUACUUGGUGCCCCUGCCCCCGGGUGGCAGCAGUGGCCUCGGCACCCCACAAAUGGCCAGUGGCUCCGGUGGCUACGGUGCGGAAUCGCAGC
..(((.((((((((.(((((.(.((((((((....)))).)))).)))))).).))))))))))....((((((.((....)).)))))).(.((((....)))).) ( -53.80)
>consensus
UUUGGCGGUGCCGGACUACCUGGUACCUUUGCCACCCGGCGGCAGCAA_________CAAUCCAUCAGUGGCCAGUGGUUCG___GGCUACGUGCCAGAAUUGCAAC
..((((((((((((.....)))))))).(((((.......))))).........................))))(((((((....((.......)).)))))))... (-29.75 = -29.50 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 12,144,478 – 12,144,585
Length 107
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 80.12
Mean single sequence MFE -44.12
Consensus MFE -30.85
Energy contribution -31.47
Covariance contribution 0.62
Combinations/Pair 1.28
Mean z-score -1.35
Structure conservation index 0.70
SVM decision value 0.25
SVM RNA-class probability 0.652790
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12144478 107 - 20766785
ACGACACAGUCAUCCGGCCGCCCAAUGGCGAGGAGUUCUGUUUGGCGGUGCCGGAUUAUCUGGUACCUUUGCCACCCGGCGGCAGCAA---------CAAUCCAUCGAUGGCCAGU
..(((...)))....(((((((....)))(((((((((((((....((((((((.....))))))))...(((....)))))))).))---------)..))).))...))))... ( -41.30)
>DroSec_CAF1 544 107 - 1
ACGACACAGUCAUCCGGCCGCCCAAUGGCGAAGAGUUCUGUUUGGCGGUGCCGGAUUACCUGGUACCUUUGCCACCCGGUGGCAGCAA---------CAAUCCAUCAGUGGCCAGU
..(((...)))....((((((...((((((((.(....).))))((((((((((.....))))))))..((((((...))))))))..---------....))))..))))))... ( -40.80)
>DroEre_CAF1 6143 107 - 1
ACGACACAGUCAUCCGGCCGCCCAAUGGCGAGGAGUUCUGUUUGGCGGUGCCGGACUACCUGGUACCUUUGCCACCCGGCGGCAGCAA---------CAAUCCAUCGGUGGCCAGU
..(((...)))....(((((((..((((...(..((((((((((((((((((((.....))))))))...))))...))))).)))..---------)...)))).)))))))... ( -43.20)
>DroYak_CAF1 6156 107 - 1
ACGACACAGUCAUCCGGCCGCCCAAUGGAGAGGAGUUCUGCUUGGCGGUACCUGACUACCUGGUACCUUUGCCACCCGGCGGCAGCAA---------CAAUCCAUCGGUGGCCAGC
..(((...)))....(((((((..(((((..(..((((((((((((((((((.........))))))...))))...))))).)))..---------)..))))).)))))))... ( -45.50)
>DroMoj_CAF1 688 101 - 1
ACGAGACGGUCAUCCGGCCGCCCAAUGGCGAAGAGUUUUGUCUAGCCGUGCCGGACUAUCUGGUGCCGCUGCCUGGCAACGGC---------------GCGCCCCAUGCGCCCGGA
(((((((((((....))))(((....))).....))))))).((((.(..((((.....))))..).))))((.(....)(((---------------(((.....)))))).)). ( -41.40)
>DroAna_CAF1 571 116 - 1
AUGACACCGUCAUCCGGCCGCCCAACGGCGAGGAGUUCUGUCUGGCGGUGCCGGACUACUUGGUGCCCCUGCCCCCGGGUGGCAGCAGUGGCCUCGGCACCCCACAAAUGGCCAGU
(((((...)))))..(((((((....))).............(((.((((((((.(((((.(.((((((((....)))).)))).)))))).).)))))))))).....))))... ( -52.50)
>consensus
ACGACACAGUCAUCCGGCCGCCCAAUGGCGAGGAGUUCUGUUUGGCGGUGCCGGACUACCUGGUACCUUUGCCACCCGGCGGCAGCAA_________CAAUCCAUCGGUGGCCAGU
.....((((...(((...((((....)))).)))...))))(((((((((((((.....)))))))).(((((.......))))).........................))))). (-30.85 = -31.47 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:09 2006