Locus 1117

Sequence ID 2R_DroMel_CAF1
Location 4,465,950 – 4,466,110
Length 160
Max. P 0.911449
window1972 window1973

overview

Window 2

Location 4,465,950 – 4,466,070
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.90
Mean single sequence MFE -30.73
Consensus MFE -24.95
Energy contribution -25.73
Covariance contribution 0.78
Combinations/Pair 1.12
Mean z-score -1.54
Structure conservation index 0.81
SVM decision value 0.09
SVM RNA-class probability 0.576144
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4465950 120 - 20766785
ACCAUGCCCCCGGGGCACCUGGCCGGGCACACGCUCGCCCAGACAGUCACAUAGACAUCCAUAGCCACUACCAUAUCCACAUCUACCGCCACCGACACCGCCGAGAGCGUGAUGAAACAA
..(((((.(.((((((..((((.(((((....))))).))))...(((.....)))...............................)))..((....))))).).)))))......... ( -32.70)
>DroSec_CAF1 13963 119 - 1
ACCAUGCC-CCGGGGCACCUGGCCGGGCACACGCUCGCCCAGACAGUCACAUAGACAUCCACAGCCACAUCCAUAUCCACAUCUACCGCCACCGCCACCGCCGAGAGCGUGAUGAAACAA
..((((((-.((((((..((((.(((((....))))).))))...(((.....))).......))).....................((....)).....))).).)))))......... ( -33.20)
>DroSim_CAF1 14016 120 - 1
ACCAUGCCCCCGGGGCACCUGGCCGGGCACACGCUCGCCCAGACAGUCACAUAGACAUCCACAGCCACAUCCAUAUCCACAUCUACCGCCACCGACACCGCCGAGAGCGUGAUGAAACAA
..(((((.(.((((((..((((.(((((....))))).))))...(((.....)))...............................)))..((....))))).).)))))......... ( -32.70)
>DroEre_CAF1 14125 108 - 1
ACCAUGCCCCCGGGGCACCUGGCCGGGCACACGCUCGCCCAGACAGUCACAUAGACAUCCAC------------AUCCACAUCUACCGCCACCGACACCGCCGAGAGCGUGAUGAAACAA
..(((((.(.((((((..((((.(((((....))))).))))...(((.....)))......------------.............)))..((....))))).).)))))......... ( -32.70)
>DroYak_CAF1 13886 108 - 1
ACCAUGCCCCCGAGGCACCUGGCCGGGCACACGCUCGCCCAGACAGUCACAUAGACAUCCAC------------AUCCACUUCUACCGCCAUCGACACCGCCGAGAGCGUGAUGAAACAA
..........((((((..((((.(((((....))))).))))...(((.....)))......------------.............))).))).((.((((....).))).))...... ( -29.40)
>DroAna_CAF1 12961 96 - 1
ACCAUACCCACGGGGCACCUGGCCGGGCACACGCUUACCCAGACAGCCACAGACACAUCCAU------------AAAG------------GCAGACUUUGCCGAAAGCGUGAUGAAACAA
........((((.(((..((((..((((....))))..))))...)))..............------------...(------------((((...))))).....))))......... ( -23.70)
>consensus
ACCAUGCCCCCGGGGCACCUGGCCGGGCACACGCUCGCCCAGACAGUCACAUAGACAUCCAC____________AUCCACAUCUACCGCCACCGACACCGCCGAGAGCGUGAUGAAACAA
..........((((((..((((.(((((....))))).))))...(((.....)))...............................))).))).((.((((....).))).))...... (-24.95 = -25.73 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 4,465,990 – 4,466,110
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.98
Mean single sequence MFE -34.38
Consensus MFE -28.56
Energy contribution -29.45
Covariance contribution 0.89
Combinations/Pair 1.07
Mean z-score -2.55
Structure conservation index 0.83
SVM decision value 1.08
SVM RNA-class probability 0.911449
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4465990 120 - 20766785
CUGAUUGGCAUCUCCUGACCACAAAUUGGGAUUUGCCAUAACCAUGCCCCCGGGGCACCUGGCCGGGCACACGCUCGCCCAGACAGUCACAUAGACAUCCAUAGCCACUACCAUAUCCAC
.....(((((..(((..(.......)..)))..)))))......(((((...))))).((((.(((((....))))).))))...(((.....)))........................ ( -36.10)
>DroSec_CAF1 14003 119 - 1
CUGAUUGGCAUCUCCUGACCACAAAUUGGGAUUUGCCAUAACCAUGCC-CCGGGGCACCUGGCCGGGCACACGCUCGCCCAGACAGUCACAUAGACAUCCACAGCCACAUCCAUAUCCAC
(((..(((((..(((..(.......)..)))..)))))......((((-....)))).((((.(((((....))))).))))...(((.....))).....)))................ ( -36.60)
>DroSim_CAF1 14056 120 - 1
CUGAUUGGCAUCUCCUGACCACAAAUUGGGAUUUGCCAUAACCAUGCCCCCGGGGCACCUGGCCGGGCACACGCUCGCCCAGACAGUCACAUAGACAUCCACAGCCACAUCCAUAUCCAC
(((..(((((..(((..(.......)..)))..)))))......(((((...))))).((((.(((((....))))).))))...(((.....))).....)))................ ( -36.90)
>DroEre_CAF1 14165 108 - 1
CUGAUUGGCAUCUCCUGACCACAAAUUCGGAUUUGCCAUAACCAUGCCCCCGGGGCACCUGGCCGGGCACACGCUCGCCCAGACAGUCACAUAGACAUCCAC------------AUCCAC
.....(((((..(((.((........)))))..)))))......(((((...))))).((((.(((((....))))).))))...(((.....)))......------------...... ( -34.00)
>DroYak_CAF1 13926 108 - 1
CUGAUUGGCAUCUCCUGACCACAAAUUGGGAUUUGCCAUAACCAUGCCCCCGAGGCACCUGGCCGGGCACACGCUCGCCCAGACAGUCACAUAGACAUCCAC------------AUCCAC
.....(((((..(((..(.......)..)))..)))))......((((.....)))).((((.(((((....))))).))))...(((.....)))......------------...... ( -33.90)
>DroAna_CAF1 12991 96 - 1
CUGAUUGGUAUCUCCU---------UUGGG-GCUGGCAUAACCAUACCCACGGGGCACCUGGCCGGGCACACGCUUACCCAGACAGCCACAGACACAUCCAU------------AAAG--
(((..((((...((((---------.((((-..(((.....)))..)))).))))...((((..((((....))))..))))...)))))))..........------------....-- ( -28.80)
>consensus
CUGAUUGGCAUCUCCUGACCACAAAUUGGGAUUUGCCAUAACCAUGCCCCCGGGGCACCUGGCCGGGCACACGCUCGCCCAGACAGUCACAUAGACAUCCAC____________AUCCAC
(((..(((((..((((((.......))))))..)))))......((((.....)))).((((.(((((....))))).)))).))).................................. (-28.56 = -29.45 +   0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:57 2006