Locus 3993

Sequence ID	3R_DroMel_CAF1
Location	10,856,681 – 10,856,820
Length	139
Max. P	0.878101

overview

Window 4

Location	10,856,681 – 10,856,784
Length	103
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	82.13
Mean single sequence MFE	-28.76
Consensus MFE	-22.96
Energy contribution	-23.85
Covariance contribution	0.89
Combinations/Pair	1.08
Mean z-score	-2.18
Structure conservation index	0.80
SVM decision value	0.90
SVM RNA-class probability	0.878101
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10856681 103 - 27905053
UUUUCAGUAAAUUUAACAUUAGCUCCUUUUGUUGGGCCAUAAAAAAUUCGCCAUCCAGAAGGAGCUAGGCGAUGGUUACACUGAGCA--CUAUUUGGGA-------------AACCAA
..((((((.((((.....(((((((((((((...(((.(........).)))...))))))))))))).....))))..))))))..--....((((..-------------..)))) ( -34.80)
>DroSec_CAF1 126034 103 - 1
UUUUCAGUAAAUUUAACAUUAGCUCCUUUUGUUGGGCCAUAAAAAAUUCGCCAGCCAGAAGGAGCUAGGCGAUGGUUACACUGAGCA--CUAAUUGGGG-------------AACUAA
..((((((.((((.....(((((((((((((...(((.(........).)))...))))))))))))).....))))..))))))..--....((((..-------------..)))) ( -31.10)
>DroSim_CAF1 132557 103 - 1
UUUUCAGUAAAUUUAACAUUAGCUCCUUUUGUUGGGCCAUAAAAAAUUCGCCAGCCAGAAGGAGCUAGGCGAUGGUUACACUGAGCA--CUAAUUGGGG-------------AACUAA
..((((((.((((.....(((((((((((((...(((.(........).)))...))))))))))))).....))))..))))))..--....((((..-------------..)))) ( -31.10)
>DroEre_CAF1 128851 115 - 1
UUUUCAGUAAAUUUAACAUUAGCUCCUAUUGUUGGGCCAUAAAAAAUCCGCCAGCCAGAAGGAGGUAGAUGAUGGUUACACUGAGCA--CUAAGUUGGGCAGCUCCUUAAA-GACUUA
..((((((.....(((((.(((...))).)))))((((((.....(((..((..((....)).))..))).))))))..))))))..--.(((((((((.....)))....-)))))) ( -24.50)
>DroYak_CAF1 137369 116 - 1
UUUUCAGUAAAUUUAACAUUAGCUCCUAUUGUUGGGCCAUAAAAAAUCCGCCAGCCCGAAGGAGGUAGACGGUGGUUACACUGAGCA--CUAAAUUGGGCAGCUCUUUAAUCAACUUA
....................((((((((...((((((((........(((((.((((....).)))....)))))......)).)).--))))..)))).)))).............. ( -25.44)
>DroPer_CAF1 163989 105 - 1
UUUUCAGUAAAUUUAACAUUAGCUCCUUUUGUGCGGCCAUAAAAAAUCUACUAGGCAGAAGGAGCUAGACCAAAGCUGCACUGAGAAAACAAAAUAAGG-------------GACCAU
((((((((..........((((((((((((((..((..............))..))))))))))))))...........))))))))............-------------...... ( -25.64)
>consensus
UUUUCAGUAAAUUUAACAUUAGCUCCUUUUGUUGGGCCAUAAAAAAUCCGCCAGCCAGAAGGAGCUAGACGAUGGUUACACUGAGCA__CUAAUUGGGG_____________AACUAA
..((((((.((((.....(((((((((((((...(((............)))...))))))))))))).....))))..))))))................................. (-22.96 = -23.85 +   0.89)

alignment

secondary structure

dotplot

Window 5

Location	10,856,705 – 10,856,820
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.61
Mean single sequence MFE	-25.29
Consensus MFE	-16.72
Energy contribution	-17.91
Covariance contribution	1.19
Combinations/Pair	1.04
Mean z-score	-2.24
Structure conservation index	0.66
SVM decision value	0.65
SVM RNA-class probability	0.812612
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10856705 115 - 27905053
GAGAAGA----AAAUAAUAAUAAAGCACUUGAAACAAACGUUUUCAGUAAAUUUAACAUUAGCUCCUUUUGUUGG-GCCAUAAAAAAUUCGCCAUCCAGAAGGAGCUAGGCGAUGGUUAC
.......----......((((...(((((.(((((....))))).)))..........(((((((((((((...(-((.(........).)))...)))))))))))))))....)))). ( -30.50)
>DroPse_CAF1 162827 119 - 1
GAGAAGAAGAAAAAUAAUAAUAAAGCACUUGAAACAAACGUUUUCAGUAAAUUUAACAUUAGCUCCUUUUGUGCG-GCCAUAAAAAAUCUACUAGGCAGAAGGAGCUAGACCAAAGCUGC
.......................((((((.(((((....))))).)))..........((((((((((((((..(-(..............))..))))))))))))))......))).. ( -27.14)
>DroWil_CAF1 141527 107 - 1
GUGUAAA----AAAUAAUCAUAAAGCACUUGAAACAAACGUUUUCAGUAAAUUUAACAUUAGCUUCUUUUGUUUG-CCUAUAAUAAAAACUUCAACCAGCGGCAGCG--------UUGAG
.((((..----((((((.....(((((((.(((((....))))).))).(((.....))).))))...)))))).-..)))).........(((((..((....)))--------)))). ( -13.00)
>DroYak_CAF1 137406 115 - 1
GAGAAGA----AAAUAAUAAUAAAGCACUUGAAACAAACGUUUUCAGUAAAUUUAACAUUAGCUCCUAUUGUUGG-GCCAUAAAAAAUCCGCCAGCCCGAAGGAGGUAGACGGUGGUUAC
.......----......((((...(((((.(((((....))))).)))..........(((.(((((....((((-((................))))))))))).)))...)).)))). ( -21.39)
>DroAna_CAF1 130284 109 - 1
GAGAAGA----AAAUAAUAAUAAAGCACUUGAAACAAACGUUUUCAGUAAAUUUAACAUUAGCUCCUUUUGUUGUGGCUAU-AAAAAUCUGCCAGGCAGAAGGAGCUAGGC------CAC
.......----.............(((((.(((((....))))).)))..........(((((((((((((((.((((...-........)))))))))))))))))))))------... ( -32.60)
>DroPer_CAF1 164015 119 - 1
GAGAAGAAGAAAAAUAAUAAUAAAGCACUUGAAACAAACGUUUUCAGUAAAUUUAACAUUAGCUCCUUUUGUGCG-GCCAUAAAAAAUCUACUAGGCAGAAGGAGCUAGACCAAAGCUGC
.......................((((((.(((((....))))).)))..........((((((((((((((..(-(..............))..))))))))))))))......))).. ( -27.14)
>consensus
GAGAAGA____AAAUAAUAAUAAAGCACUUGAAACAAACGUUUUCAGUAAAUUUAACAUUAGCUCCUUUUGUUGG_GCCAUAAAAAAUCCGCCAGCCAGAAGGAGCUAGAC_A__GUUAC
....................((((..(((.(((((....))))).)))...))))...(((((((((((((.........................)))))))))))))........... (-16.72 = -17.91 +   1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:27 2006