Locus 1067

Sequence ID 3R_DroMel_CAF1
Location 3,289,751 – 3,289,870
Length 119
Max. P 0.726633
window1725 window1726

overview

Window 5

Location 3,289,751 – 3,289,846
Length 95
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.45
Mean single sequence MFE -20.14
Consensus MFE -13.53
Energy contribution -13.92
Covariance contribution 0.39
Combinations/Pair 1.10
Mean z-score -1.61
Structure conservation index 0.67
SVM decision value 0.03
SVM RNA-class probability 0.546287
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3289751 95 + 27905053
-------AAAUCUGAAUGUCAAAUGCAGCAG----CUCAGAGAUCUGAUCAGAUAUGA--------CAAGAUGACAAAUUAGAA------AAUUUGUCAAAGAAGUUAUCGCGAUCUUUG
-------...(((((.(((........))).----.))))).....((((.((((...--------.....(((((((((....------))))))))).......))))..)))).... ( -21.36)
>DroSec_CAF1 42676 95 + 1
-------AAAUCUGAAUGUCAAAUGCAGCCG----CUCAGAGAUCUGAUCAGAUAUGA--------CAAGAUGACAAAUUAGAA------AAUUUGUCAAAGAAGUUAUCGCGAUCUUUG
-------..((((..(((((....((....)----)((((....))))...)))))..--------..))))((((((((....------))))))))(((((.((....))..))))). ( -20.00)
>DroSim_CAF1 43853 95 + 1
-------AAAUCUGAAUGUCAAAUGCAGCCG----CUCAGAGAUCUGAUCAGAUAUGA--------CAAGAUGACAAAUUAGAA------AAUUUGUCAAAGAAGUUAUCGCGAUCUUUG
-------..((((..(((((....((....)----)((((....))))...)))))..--------..))))((((((((....------))))))))(((((.((....))..))))). ( -20.00)
>DroEre_CAF1 44359 95 + 1
-------AAAUCUGAAUGUCAAAUGCAGCAG----CUCAGAGAUCUGAUCAGAUAUGA--------CAAGAUGACAAAUUAGAA------AAUUUGUCAAAGAACUUAUCGCGAUCUUUG
-------...(((((.(((........))).----.))))).....((((.((((...--------.....(((((((((....------))))))))).......))))..)))).... ( -21.36)
>DroWil_CAF1 153605 120 + 1
UUGUUUGAAAUGUAAAAGUCAAGUGCAGAAAUACCAUAAGAGAUCAUAUCAUAUAUGUUCUGGAAAAAUAUUGACAAAUUACAAAUUUCAAAUUUGUCAUAGACAUUAUCAAGAUCUCAG
..(((((((((((((..(((((.(.(((((.....(((.((.......)).)))...))))).)......)))))...)))))..)))))))).((((...))))............... ( -17.80)
>DroYak_CAF1 62057 95 + 1
-------AAAUCUGUAUGUCAAAUGCAGCAG----CUCAGAGGACUGAUCAGAUAUGA--------CAAGAUGACAAAUUAGAA------AAUUUGUCAAAGAAGUUAUCGCGAUCUUUG
-------..((((.((((((....((....)----)((((....))))...)))))).--------..))))((((((((....------))))))))(((((.((....))..))))). ( -20.30)
>consensus
_______AAAUCUGAAUGUCAAAUGCAGCAG____CUCAGAGAUCUGAUCAGAUAUGA________CAAGAUGACAAAUUAGAA______AAUUUGUCAAAGAAGUUAUCGCGAUCUUUG
.....................................((((((((...(((....))).............(((((((((..........))))))))).............)))))))) (-13.53 = -13.92 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 3,289,780 – 3,289,870
Length 90
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.78
Mean single sequence MFE -23.12
Consensus MFE -10.65
Energy contribution -10.93
Covariance contribution 0.28
Combinations/Pair 1.14
Mean z-score -2.01
Structure conservation index 0.46
SVM decision value 0.41
SVM RNA-class probability 0.726633
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3289780 90 - 27905053
---CGGAAGUGGAAU------CCCAACCAGG-------CCCAAAGAUCGCGAUAACUUCUUUGACAAAUU------UUCUAAUUUGUCAUCUUG--------UCAUAUCUGAUCAGAUCU
---.((...(((...------.))).))...-------......(((((.((((((.....(((((((((------....)))))))))....)--------)..)))))))))...... ( -20.60)
>DroSec_CAF1 42705 97 - 1
---CGGAAGUGGAAU------CCCAACCAGGCCGGCAGCCCAAAGAUCGCGAUAACUUCUUUGACAAAUU------UUCUAAUUUGUCAUCUUG--------UCAUAUCUGAUCAGAUCU
---.((...(((...------.))).)).(((.....)))....(((((.((((((.....(((((((((------....)))))))))....)--------)..)))))))))...... ( -23.70)
>DroSim_CAF1 43882 97 - 1
---CGGAAGUGGAAU------CCCAAGCAGGCCAGCAGCCCAAAGAUCGCGAUAACUUCUUUGACAAAUU------UUCUAAUUUGUCAUCUUG--------UCAUAUCUGAUCAGAUCU
---..(...(((...------.)))..).(((.....)))....(((((.((((((.....(((((((((------....)))))))))....)--------)..)))))))))...... ( -21.60)
>DroEre_CAF1 44388 97 - 1
---CGGAAGUGGAAU------CCCAUCCAACCCGCCAAGCCAAAGAUCGCGAUAAGUUCUUUGACAAAUU------UUCUAAUUUGUCAUCUUG--------UCAUAUCUGAUCAGAUCU
---(((...((((..------....))))..)))..........(((((.((((((.....(((((((((------....))))))))).))))--------)).....)))))...... ( -23.70)
>DroWil_CAF1 153645 112 - 1
AAUUGUAAAAUAUAU------GCCACAAAG--AUGCUGCUCUGAGAUCUUGAUAAUGUCUAUGACAAAUUUGAAAUUUGUAAUUUGUCAAUAUUUUUCCAGAACAUAUAUGAUAUGAUCU
.((..((..((((((------(...((.((--......)).))...(((.((.(((((...(((((((((..........))))))))))))))..)).))).)))))))..))..)).. ( -18.20)
>DroYak_CAF1 62086 103 - 1
---CGGAUGUGGAGUCCCGGUCCCAUCCAACCCGGCAAUCCAAAGAUCGCGAUAACUUCUUUGACAAAUU------UUCUAAUUUGUCAUCUUG--------UCAUAUCUGAUCAGUCCU
---.((((.((((...((((...........))))...))))..(((((.((((((.....(((((((((------....)))))))))....)--------)..))))))))).)))). ( -30.90)
>consensus
___CGGAAGUGGAAU______CCCAACCAGGCCGGCAGCCCAAAGAUCGCGAUAACUUCUUUGACAAAUU______UUCUAAUUUGUCAUCUUG________UCAUAUCUGAUCAGAUCU
...((((.((((.............................(((((...........)))))((((((((..........))))))))..............)))).))))......... (-10.65 = -10.93 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:43 2006