Locus 6567

Sequence ID 2L_DroMel_CAF1
Location 18,468,157 – 18,468,365
Length 208
Max. P 0.999021
window10477 window10478 window10479 window10480

overview

Window 7

Location 18,468,157 – 18,468,250
Length 93
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 81.73
Mean single sequence MFE -25.80
Consensus MFE -17.27
Energy contribution -17.83
Covariance contribution 0.56
Combinations/Pair 1.27
Mean z-score -1.88
Structure conservation index 0.67
SVM decision value 0.38
SVM RNA-class probability 0.712144
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18468157 93 + 22407834
--UGUUCUGAGCCAAACUAUUGUUAAAUAUCAUUACGAAUGCCA-----AA---GUAUGUAAAUGCAA---CCGGGCAUAUGUAAAUAUUGGCAUUGGUGACAUGU
--(((((..((((((..((((....))))...(((((.(((((.-----..---((((....))))..---...))))).)))))...))))).)..).))))... ( -23.00)
>DroSec_CAF1 27168 96 + 1
--UGUUCCGAGCCAGACUAUUGUUAAAUUUCAUUACGAAUGCCU-----AAUGCCUAUGUAAAUGCAA---CCGGGCAUAUGUAAAUAUUGGCAUUGGUGACAUGU
--(((((((((((((((....)))........(((((.((((((-----..(((..........))).---..)))))).)))))....)))).)))).))))... ( -25.60)
>DroSim_CAF1 22987 93 + 1
--UGUUCCGAGCCAGACUAUUGUUAAAUUUCAUUACGAAUGCCU-----AA---GUAUGUAAAUGCAA---CCGGGCGUAUGUAAAUAUUGGCAUUGGUGACAUGU
--(((((((((((((((....)))........(((((.((((((-----..---((((....))))..---..)))))).)))))....)))).)))).))))... ( -25.80)
>DroEre_CAF1 22469 94 + 1
--UGCUCUGAGCCGGACUCUCGUUCAUUUUCAUUACAAAUGCCU----UAA---GUAUGUAAAUGCAA---CCGGGCAUAUGUAAAUAUUGGCAUUGGUGACAUGU
--........(((((((....)))).......(((((.((((((----...---((((....))))..---..)))))).))))).....)))..((....))... ( -25.10)
>DroYak_CAF1 22391 94 + 1
--UGUUCCGAGCCGGACUUUUGUUCAAUUUCAUUACGAAUGCCU----UAA---GUAUGUAAAUGCAA---CCGGGCAUAUGUAAAUAUUGGCAUUGGUGACAUGU
--(((((((((((((((....)))).......(((((.((((((----...---((((....))))..---..)))))).))))).....))).)))).))))... ( -28.60)
>DroAna_CAF1 18448 100 + 1
GCUGUUGAGAACCAAACUC-CGUCCAGCUCGAU--CGAGAGCCGACAUUCG---CCAAGCAAAUGCAUCCGCCGGGCGCAUGUAAAUAUUGGUAUUGGUGACAUGU
((((((....(((((....-.(((..((((...--...)))).)))....(---((((.....(((((.(((...))).)))))....))))).))))))))).)) ( -26.70)
>consensus
__UGUUCCGAGCCAGACUAUUGUUAAAUUUCAUUACGAAUGCCU_____AA___GUAUGUAAAUGCAA___CCGGGCAUAUGUAAAUAUUGGCAUUGGUGACAUGU
..(((((((((((((((....)))........(((((.((((((..........((((....)))).......)))))).)))))....)))).)))).))))... (-17.27 = -17.83 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,468,213 – 18,468,330
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.71
Mean single sequence MFE -33.23
Consensus MFE -26.27
Energy contribution -27.17
Covariance contribution 0.89
Combinations/Pair 1.11
Mean z-score -2.47
Structure conservation index 0.79
SVM decision value 0.11
SVM RNA-class probability 0.589452
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18468213 117 + 22407834
AA---CCGGGCAUAUGUAAAUAUUGGCAUUGGUGACAUGUGCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUA
.(---((((((.((((((((((((.((((((....)).)))).)))))))))))))))........((((.(..(((((((((..((.......))..)))))))))..).)))))))). ( -37.00)
>DroGri_CAF1 27577 114 + 1
A------CUGCAUAUUUACACAUUGGUAUUAGUGACAUGUGCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUA
.------...(((((....(((((.((((.........)))).)))))..)))))........((.((((.(..(((((((((..((.......))..)))))))))..).)))).)).. ( -24.90)
>DroSec_CAF1 27227 117 + 1
AA---CCGGGCAUAUGUAAAUAUUGGCAUUGGUGACAUGUGCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUA
.(---((((((.((((((((((((.((((((....)).)))).)))))))))))))))........((((.(..(((((((((..((.......))..)))))))))..).)))))))). ( -37.00)
>DroSim_CAF1 23043 117 + 1
AA---CCGGGCGUAUGUAAAUAUUGGCAUUGGUGACAUGUGCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUA
.(---((((((.((((((((((((.((((((....)).)))).)))))))))))))))........((((.(..(((((((((..((.......))..)))))))))..).)))))))). ( -37.00)
>DroWil_CAF1 28887 117 + 1
UA---CAGUUCAAAUAAUAUUAUUGGUAUUAGUGACAUGUGCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUA
..---(((((((..((((((.....)))))).)))...((((((....)))))).))))....((.((((.(..(((((((((..((.......))..)))))))))..).)))).)).. ( -25.90)
>DroAna_CAF1 18508 120 + 1
AUCCGCCGGGCGCAUGUAAAUAUUGGUAUUGGUGACAUGUGCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUA
....(((((((.((((((((((((.((((((....)).)))).)))))))))))))))........((((.(..(((((((((..((.......))..)))))))))..).)))))))). ( -37.60)
>consensus
AA___CCGGGCAUAUGUAAAUAUUGGCAUUGGUGACAUGUGCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUA
........(((.((((((((((((.((((.........)))).))))))))))))))).....((.((((.(..(((((((((..((.......))..)))))))))..).)))).)).. (-26.27 = -27.17 +   0.89)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,468,250 – 18,468,365
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 96.41
Mean single sequence MFE -28.72
Consensus MFE -28.20
Energy contribution -28.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.98
SVM decision value 3.33
SVM RNA-class probability 0.999016
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18468250 115 + 22407834
GCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGGACGCAAACUUGCUGAUGUUAGUAAA----AAA-UAA
((((..((((((....(..((..((.((((.(..(((((((((..((.......))..)))))))))..).)))).)).))..)..)))))))))).............----...-... ( -28.20)
>DroGri_CAF1 27611 115 + 1
GCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGGACGCAAACUUGCUGAUGUUAGUAAA----AAA-AAA
((((..((((((....(..((..((.((((.(..(((((((((..((.......))..)))))))))..).)))).)).))..)..)))))))))).............----...-... ( -28.20)
>DroSec_CAF1 27264 116 + 1
GCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGGACGCAAACUUGCUGAUGUUAGUAAA---AAAA-UAA
((((..((((((....(..((..((.((((.(..(((((((((..((.......))..)))))))))..).)))).)).))..)..)))))))))).............---....-... ( -28.20)
>DroWil_CAF1 28924 116 + 1
GCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGGACGCAAACUUGCUGAUGUUGGCAAA----AAGCUAA
((....((((((....(..((..((.((((.(..(((((((((..((.......))..)))))))))..).)))).)).))..)..))))))(((((......))))).----..))... ( -31.20)
>DroYak_CAF1 22485 115 + 1
GCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGGACGCAAACUUGCUGAUGUUAGUAAA----AAA-UAA
((((..((((((....(..((..((.((((.(..(((((((((..((.......))..)))))))))..).)))).)).))..)..)))))))))).............----...-... ( -28.20)
>DroAna_CAF1 18548 119 + 1
GCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGGACGCAAACUUGCUGAUGUUAAUACAAAAAAGA-UAA
((((..((((((....(..((..((.((((.(..(((((((((..((.......))..)))))))))..).)))).)).))..)..))))))))))...(((....))).......-... ( -28.30)
>consensus
GCAAAUGUUUGUAUGGCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGGACGCAAACUUGCUGAUGUUAGUAAA____AAA_UAA
((((..((((((....(..((..((.((((.(..(((((((((..((.......))..)))))))))..).)))).)).))..)..))))))))))........................ (-28.20 = -28.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,468,250 – 18,468,365
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.41
Mean single sequence MFE -27.28
Consensus MFE -26.70
Energy contribution -26.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.98
SVM decision value 3.33
SVM RNA-class probability 0.999021
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18468250 115 - 22407834
UUA-UUU----UUUACUAACAUCAGCAAGUUUGCGUCCAAUACCGGAGAUCAAAACUUGUGAAACUGGUAUUAAAAGUCACAAGUUAGGGUCUCAGGGAAUCAGCCAUACAAACAUUUGC
...-...----.............(((((((((.((......((.((((((..(((((((((..((.........)))))))))))..)))))).))......))....)))))..)))) ( -26.70)
>DroGri_CAF1 27611 115 - 1
UUU-UUU----UUUACUAACAUCAGCAAGUUUGCGUCCAAUACCGGAGAUCAAAACUUGUGAAACUGGUAUUAAAAGUCACAAGUUAGGGUCUCAGGGAAUCAGCCAUACAAACAUUUGC
...-...----.............(((((((((.((......((.((((((..(((((((((..((.........)))))))))))..)))))).))......))....)))))..)))) ( -26.70)
>DroSec_CAF1 27264 116 - 1
UUA-UUUU---UUUACUAACAUCAGCAAGUUUGCGUCCAAUACCGGAGAUCAAAACUUGUGAAACUGGUAUUAAAAGUCACAAGUUAGGGUCUCAGGGAAUCAGCCAUACAAACAUUUGC
...-....---.............(((((((((.((......((.((((((..(((((((((..((.........)))))))))))..)))))).))......))....)))))..)))) ( -26.70)
>DroWil_CAF1 28924 116 - 1
UUAGCUU----UUUGCCAACAUCAGCAAGUUUGCGUCCAAUACCGGAGAUCAAAACUUGUGAAACUGGUAUUAAAAGUCACAAGUUAGGGUCUCAGGGAAUCAGCCAUACAAACAUUUGC
...(((.----.((.((.......(((....)))...........((((((..(((((((((..((.........)))))))))))..)))))).)).))..)))............... ( -28.60)
>DroYak_CAF1 22485 115 - 1
UUA-UUU----UUUACUAACAUCAGCAAGUUUGCGUCCAAUACCGGAGAUCAAAACUUGUGAAACUGGUAUUAAAAGUCACAAGUUAGGGUCUCAGGGAAUCAGCCAUACAAACAUUUGC
...-...----.............(((((((((.((......((.((((((..(((((((((..((.........)))))))))))..)))))).))......))....)))))..)))) ( -26.70)
>DroAna_CAF1 18548 119 - 1
UUA-UCUUUUUUGUAUUAACAUCAGCAAGUUUGCGUCCAAUACCGGAGAUCAAAACUUGUGAAACUGGUAUUAAAAGUCACAAGUUAGGGUCUCAGGGAAUCAGCCAUACAAACAUUUGC
...-.....(((((((........(((....)))........((.((((((..(((((((((..((.........)))))))))))..)))))).)).........)))))))....... ( -28.30)
>consensus
UUA_UUU____UUUACUAACAUCAGCAAGUUUGCGUCCAAUACCGGAGAUCAAAACUUGUGAAACUGGUAUUAAAAGUCACAAGUUAGGGUCUCAGGGAAUCAGCCAUACAAACAUUUGC
........................(((((((((.((......((.((((((..(((((((((..((.........)))))))))))..)))))).))......))....)))))..)))) (-26.70 = -26.70 +  -0.00)

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 12:14:25 2006