Locus 4406

Sequence ID 3L_DroMel_CAF1
Location 12,899,625 – 12,899,808
Length 183
Max. P 0.954008
window6829 window6830 window6831

overview

Window 9

Location 12,899,625 – 12,899,729
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.84
Mean single sequence MFE -21.24
Consensus MFE -12.81
Energy contribution -13.28
Covariance contribution 0.47
Combinations/Pair 1.12
Mean z-score -1.71
Structure conservation index 0.60
SVM decision value 0.07
SVM RNA-class probability 0.566467
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12899625 104 - 23771897
UCC------------ACUUUUCCCCAGCCACCCAAUCUUGCCCAGCUUAUUCUCCAACGCACAUUGUCGCAAAAUAUGACAGUUGGU----UGGGAUGGCAAAGCGUAUAUCACAAUCGC
...------------...........(((((((((((.......((............))..(((((((.......))))))).)))----)))).))))...(((...........))) ( -23.30)
>DroSec_CAF1 20605 104 - 1
UCC------------ACUUUUCCCCAGCCACCCAAUCUUGCCCAGCUUAUUCUCCAACGCACAUUGUGGCAAAAUAUGACAGUUCGU----UGGGAUGGCAAAGCGUAUAUCACAAUCCC
...------------...........((((((((((.(((((((((............))....)).))))).....((....))))----)))).)))).................... ( -19.80)
>DroSim_CAF1 18438 108 - 1
UCC------------ACUUUUCCCCAGCCACCCAAUCUUGCCCAGCUUAUUCUCCAACGCACAUUGUCGCAAAAUAUGACAGUUCGUUGGUUGGGAUGGCAAAGCGUAUAUCACAAUCGC
...------------...........(((((((((....((...)).......((((((...(((((((.......))))))).))))))))))).))))...(((...........))) ( -26.70)
>DroEre_CAF1 25869 100 - 1
UCC------------ACUUUUCCCCAGCCACCCAAUCUUGCCCAGCUUCUUCUCCAAGGCACAUUGUCGCAAAAUAUGACAGU--------UGGGAUGGCACAGCGUAUAUCACAAUCGC
...------------...........((((((((((..((((...............))))...(((((.......)))))))--------)))).))))...(((...........))) ( -22.16)
>DroYak_CAF1 22887 112 - 1
UCCACUUCCACAUCCACUUUUCCCCAGCCACCCAAUCUUGCCCAGCUUAUACUCCAACGCACAUUGUCGCAAAAUAUGACAGU--------UGGGAUGGCAAAGCGUAUAUCACCAUCAC
..........................((((((((((........((............))....(((((.......)))))))--------)))).)))).................... ( -18.20)
>DroPer_CAF1 24042 83 - 1
U-C------------ACGUUACCCCACCCCACUA------------UUAUACCCCG----ACAUUGUCACAAAAGAUGACAGU--------UGGGCUGGCAAAACGUAUAUCACAAUGUC
.-.------------(((((...(((.((((...------------..........----..((((((((....).)))))))--------)))).)))...)))))............. ( -17.26)
>consensus
UCC____________ACUUUUCCCCAGCCACCCAAUCUUGCCCAGCUUAUUCUCCAACGCACAUUGUCGCAAAAUAUGACAGU________UGGGAUGGCAAAGCGUAUAUCACAAUCGC
..........................((((((((..........((............))..(((((((.......)))))))........)))).)))).................... (-12.81 = -13.28 +   0.47)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,899,661 – 12,899,768
Length 107
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 94.28
Mean single sequence MFE -19.84
Consensus MFE -18.67
Energy contribution -18.67
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.94
SVM decision value 1.44
SVM RNA-class probability 0.954008
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12899661 107 - 23771897
UGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCACUUCC------------ACUUUUCCCCAGCCACCCAAUCUUGCCCAGCUUAUUCUCCAACGCACAUUGUCGCAAAAUAUGAC
.(((((((...)))))))((.(((.....)))..........------------.................((((..(((.................))).))))..)).......... ( -18.33)
>DroSec_CAF1 20641 107 - 1
UGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCACUUCC------------ACUUUUCCCCAGCCACCCAAUCUUGCCCAGCUUAUUCUCCAACGCACAUUGUGGCAAAAUAUGAC
.(((((((...)))))))...(((.....)))..........------------...........(((((.......(((.................)))....))))).......... ( -22.33)
>DroSim_CAF1 18478 107 - 1
UGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCACUUCC------------ACUUUUCCCCAGCCACCCAAUCUUGCCCAGCUUAUUCUCCAACGCACAUUGUCGCAAAAUAUGAC
.(((((((...)))))))((.(((.....)))..........------------.................((((..(((.................))).))))..)).......... ( -18.33)
>DroEre_CAF1 25901 107 - 1
UGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCACUUCC------------ACUUUUCCCCAGCCACCCAAUCUUGCCCAGCUUCUUCUCCAAGGCACAUUGUCGCAAAAUAUGAC
.(((((((...)))))))((.(((.....)))..........------------.................((((..((((...............)))).))))..)).......... ( -21.86)
>DroYak_CAF1 22919 119 - 1
UGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCACUUCCACUUCCACAUCCACUUUUCCCCAGCCACCCAAUCUUGCCCAGCUUAUACUCCAACGCACAUUGUCGCAAAAUAUGAC
.(((((((...)))))))((.(((.....))).......................................((((..(((.................))).))))..)).......... ( -18.33)
>consensus
UGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCACUUCC____________ACUUUUCCCCAGCCACCCAAUCUUGCCCAGCUUAUUCUCCAACGCACAUUGUCGCAAAAUAUGAC
.(((((((...)))))))((.(((.....))).......................................((((..(((.................))).))))..)).......... (-18.67 = -18.67 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,899,701 – 12,899,808
Length 107
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 90.24
Mean single sequence MFE -22.23
Consensus MFE -19.48
Energy contribution -19.90
Covariance contribution 0.42
Combinations/Pair 1.09
Mean z-score -1.77
Structure conservation index 0.88
SVM decision value 0.80
SVM RNA-class probability 0.853264
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12899701 107 - 23771897
CCACCACAACAUCCAGCUAAUCCAGACGAUCCAAGUGAGCUGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCACUUCC------------ACUUUUCCCCAGCCACCCAAUCUUG
...............(((.(((.....)))..(((((.((.(((((((...))))))))).(((.....)))...)))))..------------..........)))............ ( -22.20)
>DroSec_CAF1 20681 107 - 1
CCACCACAACAUCCAGCUAAUCCAGACGAUCCAAGUGAGCUGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCACUUCC------------ACUUUUCCCCAGCCACCCAAUCUUG
...............(((.(((.....)))..(((((.((.(((((((...))))))))).(((.....)))...)))))..------------..........)))............ ( -22.20)
>DroSim_CAF1 18518 107 - 1
CCACCACAACAUCCAGCUAAUCCAGACGAUCCAAGUGAGCUGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCACUUCC------------ACUUUUCCCCAGCCACCCAAUCUUG
...............(((.(((.....)))..(((((.((.(((((((...))))))))).(((.....)))...)))))..------------..........)))............ ( -22.20)
>DroEre_CAF1 25941 107 - 1
CCACCACAACAGCCAGCUAAUCCAGACGAUCCAAGUGAGCUGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCACUUCC------------ACUUUUCCCCAGCCACCCAAUCUUG
...............(((.(((.....)))..(((((.((.(((((((...))))))))).(((.....)))...)))))..------------..........)))............ ( -22.20)
>DroYak_CAF1 22959 119 - 1
CCACCACAACAUCCAGCUAAUCCAGACGAUCCUAGUGAGCUGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCACUUCCACUUCCACAUCCACUUUUCCCCAGCCACCCAAUCUUG
...........................(((....(((.((((((((((...)))))))...(((.....)))................................))))))...)))... ( -21.70)
>DroAna_CAF1 48022 107 - 1
CCACCACAACAUCCAGCUAAUCCAGACGAUCUGAGUGAGCUGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCCCAUCCCUAU--------ACCUUUCUCCUGUUUC----UUUUU
.......((((...((((.(..(((.....)))..).))))(((((((...)))))))...(((.....)))..............--------..........))))..----..... ( -22.90)
>consensus
CCACCACAACAUCCAGCUAAUCCAGACGAUCCAAGUGAGCUGGCACUUUCCGAGUGCCGCAGCCUCUUUGGCAUCCACUUCC____________ACUUUUCCCCAGCCACCCAAUCUUG
...............(((.(((.....)))..(((((.((.(((((((...))))))))).(((.....)))...)))))........................)))............ (-19.48 = -19.90 +   0.42)

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 11:21:51 2006