Locus 546

Sequence ID 2L_DroMel_CAF1
Location 1,687,821 – 1,687,966
Length 145
Max. P 0.922036
window883 window884 window885

overview

Window 3

Location 1,687,821 – 1,687,926
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.47
Mean single sequence MFE -31.73
Consensus MFE -22.71
Energy contribution -23.40
Covariance contribution 0.69
Combinations/Pair 1.10
Mean z-score -2.45
Structure conservation index 0.72
SVM decision value 1.15
SVM RNA-class probability 0.922036
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1687821 105 + 22407834
GAGGUUUC-AUAAUAUGCGUCAUUUGCCGGAAUUAAUUGCCAUUCAAAGCGGACAAGAUGGUCGAAAAUAGACGCG--------------UACAUAAAGAUACAAAUGUAUCUGUAUGUU
........-....((((((((...(((..((((........))))...)))(((......))).......))))))--------------))((((.((((((....)))))).)))).. ( -26.60)
>DroSec_CAF1 6797 119 + 1
GAGGUUUC-AUAAUAUGCGUCAUUUGCCGGAAUUAAUUGCCAUUCAAAGCGGACAAGUUGGUCGAAAAUAGACGCGUAGUUGUAUCCACGUACAUAAAGAUACAAAUGUAUCUGUGUGUU
..((...(-(...((((((((...(((..((((........))))...)))(((......))).......))))))))..))...))....(((((.((((((....)))))).))))). ( -32.00)
>DroSim_CAF1 7761 117 + 1
--GGUUUC-AUAAUAUGCGUCAUUUGCCGGAAUUAAUUGCCAUUCAAAGCAGACAAGUUGGUCGAAAAUAGACGCGUAGUUGUAUCCACGUACAUAAAGAUACAAAUGUAUCUGUGUGUU
--((...(-(...((((((((...(((..((((........))))...)))(((......))).......))))))))..))...))....(((((.((((((....)))))).))))). ( -32.70)
>DroYak_CAF1 7750 120 + 1
GUGGUUUCUAUAAUAUGCGUCAUUUGCCGGAAUUAAUUGCCAUUCGAAGCGAAUAAGACUGUCGAAAAUAGACGCGUAGUUGUAGCCACACACAUAAAGAUACAAAAGUAUAUGUGUGCG
((((...((((((((((((((.((((.(((..(((.((((........)))).)))..))).))))....))))))).))))))))))).((((((...((((....)))).)))))).. ( -35.60)
>consensus
GAGGUUUC_AUAAUAUGCGUCAUUUGCCGGAAUUAAUUGCCAUUCAAAGCGGACAAGAUGGUCGAAAAUAGACGCGUAGUUGUAUCCACGUACAUAAAGAUACAAAUGUAUCUGUGUGUU
.............((((((((...(((..((((........))))...)))(((......))).......)))))))).............(((((.((((((....)))))).))))). (-22.71 = -23.40 +   0.69)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,687,821 – 1,687,926
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.47
Mean single sequence MFE -25.57
Consensus MFE -19.41
Energy contribution -19.98
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -1.96
Structure conservation index 0.76
SVM decision value 0.76
SVM RNA-class probability 0.842785
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1687821 105 - 22407834
AACAUACAGAUACAUUUGUAUCUUUAUGUA--------------CGCGUCUAUUUUCGACCAUCUUGUCCGCUUUGAAUGGCAAUUAAUUCCGGCAAAUGACGCAUAUUAU-GAAACCUC
.(((((.((((((....)))))).))))).--------------.(((((.......(((......))).(((..((((........)))).)))....))))).......-........ ( -25.60)
>DroSec_CAF1 6797 119 - 1
AACACACAGAUACAUUUGUAUCUUUAUGUACGUGGAUACAACUACGCGUCUAUUUUCGACCAACUUGUCCGCUUUGAAUGGCAAUUAAUUCCGGCAAAUGACGCAUAUUAU-GAAACCUC
.(((.(.((((((....)))))).).)))..((((......))))(((((.......(((......))).(((..((((........)))).)))....))))).......-........ ( -24.50)
>DroSim_CAF1 7761 117 - 1
AACACACAGAUACAUUUGUAUCUUUAUGUACGUGGAUACAACUACGCGUCUAUUUUCGACCAACUUGUCUGCUUUGAAUGGCAAUUAAUUCCGGCAAAUGACGCAUAUUAU-GAAACC--
.(((.(.((((((....)))))).).)))..((((......))))(((((.......(((......)))((((..((((........)))).))))...))))).......-......-- ( -25.40)
>DroYak_CAF1 7750 120 - 1
CGCACACAUAUACUUUUGUAUCUUUAUGUGUGUGGCUACAACUACGCGUCUAUUUUCGACAGUCUUAUUCGCUUCGAAUGGCAAUUAAUUCCGGCAAAUGACGCAUAUUAUAGAAACCAC
(((((((((((((....)))....))))))))))...........(((((....(((((.(((.......))))))))..((...........))....)))))................ ( -26.80)
>consensus
AACACACAGAUACAUUUGUAUCUUUAUGUACGUGGAUACAACUACGCGUCUAUUUUCGACCAACUUGUCCGCUUUGAAUGGCAAUUAAUUCCGGCAAAUGACGCAUAUUAU_GAAACCUC
.(((.(.((((((....)))))).).)))..((((......))))(((((.......(((......))).(((..((((........)))).)))....)))))................ (-19.41 = -19.98 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,687,860 – 1,687,966
Length 106
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.67
Mean single sequence MFE -30.42
Consensus MFE -23.45
Energy contribution -23.89
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.40
Structure conservation index 0.77
SVM decision value -0.01
SVM RNA-class probability 0.527720
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1687860 106 + 22407834
CAUUCAAAGCGGACAAGAUGGUCGAAAAUAGACGCG--------------UACAUAAAGAUACAAAUGUAUCUGUAUGUUGGCAGCUGGCCACUUGAGAUAUGCUGCACUCAACGCACAA
........(((..((((.(((((......((..((.--------------.(((((.((((((....)))))).)))))..))..)))))))))))((.....))........))).... ( -26.30)
>DroSec_CAF1 6836 120 + 1
CAUUCAAAGCGGACAAGUUGGUCGAAAAUAGACGCGUAGUUGUAUCCACGUACAUAAAGAUACAAAUGUAUCUGUGUGUUGGCAGCUGGCCACUUGAGAUAUGCUGCACUCAGCGCACAA
........((...(((((.((((.......)))((.((((((...(((...(((((.((((((....)))))).))))))))))))))))))))))......((((....)))))).... ( -33.10)
>DroSim_CAF1 7798 120 + 1
CAUUCAAAGCAGACAAGUUGGUCGAAAAUAGACGCGUAGUUGUAUCCACGUACAUAAAGAUACAAAUGUAUCUGUGUGUUGGCAGCUGGCCACUUGAGAUAUGCUGCACUCAGCGCACAA
........((...(((((.((((.......)))((.((((((...(((...(((((.((((((....)))))).))))))))))))))))))))))......((((....)))))).... ( -33.10)
>DroYak_CAF1 7790 120 + 1
CAUUCGAAGCGAAUAAGACUGUCGAAAAUAGACGCGUAGUUGUAGCCACACACAUAAAGAUACAAAAGUAUAUGUGUGCGCGCAGCUGACCACUUGAGAUAUGCUGCACUCAACGCACAA
..((((((((......).)).))))).......((((.......((..((((((((....(((....))))))))))).))(((((................))))).....)))).... ( -29.19)
>consensus
CAUUCAAAGCGGACAAGAUGGUCGAAAAUAGACGCGUAGUUGUAUCCACGUACAUAAAGAUACAAAUGUAUCUGUGUGUUGGCAGCUGGCCACUUGAGAUAUGCUGCACUCAACGCACAA
....................(((.......)))((((..............(((((.((((((....)))))).)))))..(((((................))))).....)))).... (-23.45 = -23.89 +   0.44)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:02 2006