Locus 6126

Sequence ID 3R_DroMel_CAF1
Location 16,053,617 – 16,053,864
Length 247
Max. P 0.887291
window9986 window9987 window9988

overview

Window 6

Location 16,053,617 – 16,053,724
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.05
Mean single sequence MFE -46.75
Consensus MFE -27.88
Energy contribution -30.02
Covariance contribution 2.14
Combinations/Pair 1.11
Mean z-score -1.62
Structure conservation index 0.60
SVM decision value 0.03
SVM RNA-class probability 0.547624
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16053617 107 - 27905053
----CACCAGUACCGGCCAUGCCAGGA------CCCAC---UGCGGUGCUGGUGAGCAGGACAUUGCCGCGACUAUCCACUAGGGCGGUGCCGCCGCCCGACAUAUUCAAGGCGGUCGUG
----(((((((((((((...)))((..------....)---)..)))))))))).((((....))))(((((((..((....((((((.....))))))((.....))..)).))))))) ( -48.40)
>DroPse_CAF1 10477 109 - 1
-----ACCGGCCCCGCCCAUGCCCGGGUGUCCCCCCACGGGUGCCACGCUGGUGAGCAGCACAUUGCCACGGCUAUCCACCAGGGCAGUGCCACCACCAGCCAGAUUUAAGGC------G
-----.((((((((((((......))))((......))))).)))..(((((((.(..((((..((((..((.......))..))))))))..)))))))).........)).------. ( -43.90)
>DroSec_CAF1 11935 107 - 1
----CACCAGUACCGGCCAUGGCAGGA------CCCAC---UGCGGUGCUGGUGAGCAGGACAUUGCCGCGACUAUCUACCAGCGCGGUGCCGCCGCCCGACAUAUUCAAGGCGGCUGUG
----(((((((((((((....))((..------....)---).))))))))))).(((((.....((((((.((.......)))))))).))((((((.((.....))..))))))))). ( -47.80)
>DroSim_CAF1 12061 107 - 1
----CACCAGUACCGCCCAUGCCAGGA------CCCAC---UGCGGUGCUGGUGAGCAGGACAUUGCCGCGACUAUCCACCAGGGCGGUGCCGCCGCCCGACAUAUUCAAGGCGGCUGUG
----((((((((((((((......)).------.....---.)))))))))))).......(((.(((((............((((((.....))))))((.....))...))))).))) ( -48.21)
>DroYak_CAF1 19972 111 - 1
CCUGCACCAGCACCGCCCAUUCCAGGA------CCCAC---UGCGGUGCUGGUGAGCAGGACAUUGCCGCGACUAUCCACUAGGGCGGUUCCGCCUCCCGACAUAUUCAAGGCGGCCGUG
((((((((((((((((((......)).------.....---.)))))))))))..))))).(((.(((((..(((.....)))((((....))))................))))).))) ( -50.01)
>DroPer_CAF1 10400 109 - 1
-----ACCGGCCCCGCCCAUGCCCGGGUGUCCCCCCACGGGUGCCACGCUGGUGAGCAGCACAUUGCCACGGCUAUCCACUAGGGCAGUGCCGCCACCCGCCAGAUUUAAGGC------G
-----...((((((((((......))))((......))))).))).....((((.((.((((..((((..((.......))..)))))))).))))))((((........)))------) ( -42.20)
>consensus
____CACCAGCACCGCCCAUGCCAGGA______CCCAC___UGCGGUGCUGGUGAGCAGGACAUUGCCGCGACUAUCCACCAGGGCGGUGCCGCCGCCCGACAUAUUCAAGGCGGC_GUG
....((((((((((((........((........))......)))))))))))).......(((((((.(............))))))))(((((...............)))))..... (-27.88 = -30.02 +   2.14)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,053,657 – 16,053,751
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.41
Mean single sequence MFE -38.14
Consensus MFE -22.73
Energy contribution -24.92
Covariance contribution 2.20
Combinations/Pair 1.08
Mean z-score -1.62
Structure conservation index 0.60
SVM decision value 0.50
SVM RNA-class probability 0.761691
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16053657 94 - 27905053
-----CGCCGCCACC------AGAGGAUCCUCCUCCAG------CACCAGUACCGGCCAUGCCAGGA------CCCAC---UGCGGUGCUGGUGAGCAGGACAUUGCCGCGACUAUCCAC
-----(((.((((((------.((((.....)))).((------((((.(((..((((......)).------))...---))))))))))))).)).((......)))))......... ( -34.40)
>DroPse_CAF1 10511 103 - 1
-----CGCCACCUCCACCGGCCGAGGAGCCGCC------------ACCGGCCCCGCCCAUGCCCGGGUGUCCCCCCACGGGUGCCACGCUGGUGAGCAGCACAUUGCCACGGCUAUCCAC
-----.(((.((((........)))).((.(((------------((((((..(((((.((...(((....))).)).)))))....))))))).)).))..........)))....... ( -40.40)
>DroSec_CAF1 11975 94 - 1
-----CGCCGCCACC------AGAGGAUCCUCCUCCAG------CACCAGUACCGGCCAUGGCAGGA------CCCAC---UGCGGUGCUGGUGAGCAGGACAUUGCCGCGACUAUCUAC
-----(((.((..((------.((((.....))))...------(((((((((((((....))((..------....)---).)))))))))))....)).....)).)))......... ( -35.50)
>DroSim_CAF1 12101 94 - 1
-----CGCCGCCACC------AGAGGAUCCUCCUCCAG------CACCAGUACCGCCCAUGCCAGGA------CCCAC---UGCGGUGCUGGUGAGCAGGACAUUGCCGCGACUAUCCAC
-----(((.((..((------.((((.....))))...------((((((((((((((......)).------.....---.))))))))))))....)).....)).)))......... ( -34.81)
>DroYak_CAF1 20012 105 - 1
ACCGCCGCCGCCACC------AGAGGAUCCUCCUCCAGCUCCUGCACCAGCACCGCCCAUUCCAGGA------CCCAC---UGCGGUGCUGGUGAGCAGGACAUUGCCGCGACUAUCCAC
.....(((.((....------.((((.....))))..(.(((((((((((((((((((......)).------.....---.)))))))))))..)))))))...)).)))......... ( -43.31)
>DroPer_CAF1 10434 103 - 1
-----CGCCACCUCCACCGCCCGAGGAGCCGCC------------ACCGGCCCCGCCCAUGCCCGGGUGUCCCCCCACGGGUGCCACGCUGGUGAGCAGCACAUUGCCACGGCUAUCCAC
-----.(((.((((........)))).((.(((------------((((((..(((((.((...(((....))).)).)))))....))))))).)).))..........)))....... ( -40.40)
>consensus
_____CGCCGCCACC______AGAGGAUCCUCCUCCAG______CACCAGCACCGCCCAUGCCAGGA______CCCAC___UGCGGUGCUGGUGAGCAGGACAUUGCCGCGACUAUCCAC
.....(((..............((((.....)))).........((((((((((((........((........))......)))))))))))).((((....)))).)))......... (-22.73 = -24.92 +   2.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,053,751 – 16,053,864
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.77
Mean single sequence MFE -36.35
Consensus MFE -31.85
Energy contribution -32.18
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.88
SVM decision value 0.95
SVM RNA-class probability 0.887291
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16053751 113 - 27905053
UACUCUCAUUUUUAUUUUCAUUUGCCAUUUCUGGCACUCACCUGUAGUGGGAUUGUGUCGUCCUGCGGCCGCCAGACCAAGAUUGCGUGGCAGGGUCAUGCAAUCUCCGCCUC-------
.......................((....((((((.(((((.....)))))...(.((((.....)))))))))))...((((((((((((...))))))))))))..))...------- ( -35.80)
>DroPse_CAF1 10614 104 - 1
UAAAG------UUAUUUG---UUGUUGAUUUCGGCACUCACCUGUCGUGGGAUUGUGUCGUCCUGCGGCCGCCAGACUGAGAUUGCGUGGCAGAGUCAUGCAAUCACCGCCGC-------
..(((------(((....---....))))))((((........((((..((((......))))..))))...........(((((((((((...)))))))))))...)))).------- ( -36.00)
>DroSec_CAF1 12069 113 - 1
UACUAUCAUUUUUAUUUUCAUUUGGCAUUUCUGGCACUCACCUGUCGUGGGAUUGUGUCGUCCUGCGGCCGCCAGACCAAGAUUGCGUGGCAGGGUCAUGCAAUCUCCGCCUC-------
.......................(((...((((((........((((..((((......))))..)))).))))))...((((((((((((...))))))))))))..)))..------- ( -41.10)
>DroSim_CAF1 12195 113 - 1
UACUCUCAUUUUUAUUUUCAUUUGGCAUUUCUGGCACUCACCUGUCGUGGGAUUGUGUCGUCCUGCGGCCGCCAGACCAAGAUUGCGUGGCAGGGUCAUACAAUCUCCGCCUC-------
.......................(((...((((((........((((..((((......))))..)))).))))))...((((((..((((...))))..))))))..)))..------- ( -35.40)
>DroYak_CAF1 20117 113 - 1
UACCCUCAUUUUUAUUU--AUU-----UUUCUGGCACUCACCUGUCGUGGGAUUGUGUCGUCCUGCGGCCGCUAAACUAAGAUUGCGUGGCAGGGUCAUGCAAUCUCCGCCUCCACCUCC
.................--...-----.....(((........((((..((((......))))..))))..........((((((((((((...))))))))))))..)))......... ( -33.80)
>DroPer_CAF1 10537 104 - 1
UAAAG------UUAUUUG---UUGUUGAUUUCGGCACUCACCUGUCGUGGGAUUGUGUCGUCCUGCGGCCGCCAGACUGAGAUUGCGUGGCAGAGUCAUGCAAUCACCGCCGC-------
..(((------(((....---....))))))((((........((((..((((......))))..))))...........(((((((((((...)))))))))))...)))).------- ( -36.00)
>consensus
UACUCUCAUUUUUAUUUU_AUUUGGCAUUUCUGGCACUCACCUGUCGUGGGAUUGUGUCGUCCUGCGGCCGCCAGACCAAGAUUGCGUGGCAGGGUCAUGCAAUCUCCGCCUC_______
................................(((........((((..((((......))))..))))...........(((((((((((...)))))))))))...)))......... (-31.85 = -32.18 +   0.33)

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 12:13:21 2006