Locus 2628

Sequence ID X_DroMel_CAF1
Location 7,007,875 – 7,008,261
Length 386
Max. P 0.998335
window4305 window4306 window4307 window4308 window4309 window4310

overview

Window 5

Location 7,007,875 – 7,007,995
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.54
Mean single sequence MFE -37.05
Consensus MFE -30.83
Energy contribution -31.70
Covariance contribution 0.87
Combinations/Pair 1.19
Mean z-score -2.79
Structure conservation index 0.83
SVM decision value 2.45
SVM RNA-class probability 0.994046
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7007875 120 + 22224390
UAUAUUCCGAGUUUUAAAAAGUUAGAAUACUUCCUUUUCAAUUGACCACCAAACGCCACCUGUUGGCCGGGGCAGUUUCAGCCGUUGGCCCAUAGAUGGCGACAGUAUGCUUAUUGGACA
.....((((((((...(((((..((....))..))))).....))).......(((((.((((.(((((((((.......))).)))))).)))).)))))............))))).. ( -35.10)
>DroSec_CAF1 9081 119 + 1
-AUAUUCCGAGUUUUAAGAAGUUAGAACACUUCCUUAUCAAAUGACCACCAAACGCCACCUGUUGGCCGGGGCAGUUUCAGCCGUUGGCCCACAGAUGGCGACAGUAUGCUUAUUGGACA
-....((((((((((((....))))))).........................(((((.((((.(((((((((.......))).)))))).)))).)))))............))))).. ( -37.80)
>DroEre_CAF1 14938 104 + 1
-AUAUUCCGAGUUUUGAAGCCUUAA---------------AAUGACCACCAAACGCCACCUGUUGGCCAGGCCAGUUUCAGCCGUUGGCCAACAGAUGGCGACAGUAUGCUUAUUGGACA
-....((((((((((((....))))---------------)))..........(((((.(((((((((((((........)))..)))))))))).)))))............))))).. ( -38.40)
>DroYak_CAF1 23419 119 + 1
-AUAUUCAACAUUUUGAAGACUUUAAAUACAUUCUUAGCAAAUGACCACCAAACGCCACCUGUUGGCCGGGCCUGUUUCAGCCGUUGGCCAACAGAUGGCGACAGCAUGCUUAUUGGACA
-........(((((..((((............))))...)))))....((((.(((((.(((((((((((((........)))..)))))))))).)))))..((....))..))))... ( -36.90)
>consensus
_AUAUUCCGAGUUUUAAAAACUUAAAAUACUUCCUUAUCAAAUGACCACCAAACGCCACCUGUUGGCCGGGCCAGUUUCAGCCGUUGGCCAACAGAUGGCGACAGUAUGCUUAUUGGACA
..........(((((((....)))))))....................((((.(((((.((((((((((((((.......))).))))))))))).)))))..((....))..))))... (-30.83 = -31.70 +   0.87)

alignment

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secondary structure

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Window 6

Location 7,007,875 – 7,007,995
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.54
Mean single sequence MFE -42.95
Consensus MFE -32.90
Energy contribution -34.15
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -3.72
Structure conservation index 0.77
SVM decision value 3.07
SVM RNA-class probability 0.998335
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7007875 120 - 22224390
UGUCCAAUAAGCAUACUGUCGCCAUCUAUGGGCCAACGGCUGAAACUGCCCCGGCCAACAGGUGGCGUUUGGUGGUCAAUUGAAAAGGAAGUAUUCUAACUUUUUAAAACUCGGAAUAUA
..(((.....((.(((((.((((((((...((((...(((.......)))..))))...))))))))..)))))))...((((((((..((....))..)))))))).....)))..... ( -38.90)
>DroSec_CAF1 9081 119 - 1
UGUCCAAUAAGCAUACUGUCGCCAUCUGUGGGCCAACGGCUGAAACUGCCCCGGCCAACAGGUGGCGUUUGGUGGUCAUUUGAUAAGGAAGUGUUCUAACUUCUUAAAACUCGGAAUAU-
..(((........(((((.((((((((((.((((...(((.......)))..)))).))))))))))..)))))(((....))).(((((((......))))))).......)))....- ( -44.10)
>DroEre_CAF1 14938 104 - 1
UGUCCAAUAAGCAUACUGUCGCCAUCUGUUGGCCAACGGCUGAAACUGGCCUGGCCAACAGGUGGCGUUUGGUGGUCAUU---------------UUAAGGCUUCAAAACUCGGAAUAU-
..(((...............(((((((((((((((..((((......)))))))))))))))))))((((...((((...---------------....))))...))))..)))....- ( -45.20)
>DroYak_CAF1 23419 119 - 1
UGUCCAAUAAGCAUGCUGUCGCCAUCUGUUGGCCAACGGCUGAAACAGGCCCGGCCAACAGGUGGCGUUUGGUGGUCAUUUGCUAAGAAUGUAUUUAAAGUCUUCAAAAUGUUGAAUAU-
.........(((((..((.(((((((((((((((...((((......)))).)))))))))))))))(((((..(....)..))))).................))..)))))......- ( -43.60)
>consensus
UGUCCAAUAAGCAUACUGUCGCCAUCUGUGGGCCAACGGCUGAAACUGCCCCGGCCAACAGGUGGCGUUUGGUGGUCAUUUGAUAAGGAAGUAUUCUAACUCUUCAAAACUCGGAAUAU_
((.(((.(((((........((((((((((((((...((((......)))).))))))))))))))))))).))).)).......................................... (-32.90 = -34.15 +   1.25)

alignment

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secondary structure

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Window 7

Location 7,007,915 – 7,008,035
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.39
Mean single sequence MFE -42.97
Consensus MFE -40.47
Energy contribution -41.10
Covariance contribution 0.63
Combinations/Pair 1.05
Mean z-score -2.28
Structure conservation index 0.94
SVM decision value 1.42
SVM RNA-class probability 0.952404
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7007915 120 + 22224390
AUUGACCACCAAACGCCACCUGUUGGCCGGGGCAGUUUCAGCCGUUGGCCCAUAGAUGGCGACAGUAUGCUUAUUGGACACGCGCAAACGUAAAUGCCAAUUGGAAGCCUCGAAUUGGUU
.......(((((.(((((.((((.(((((((((.......))).)))))).)))).))))).......(((((((((.((.(((....)))...)))))))...))))......))))). ( -40.40)
>DroSec_CAF1 9120 120 + 1
AAUGACCACCAAACGCCACCUGUUGGCCGGGGCAGUUUCAGCCGUUGGCCCACAGAUGGCGACAGUAUGCUUAUUGGACACGCGCAAACGUAAAUGCCAAUUGGAAGCCUCGAAUUGGUU
.......(((((.(((((.((((.(((((((((.......))).)))))).)))).))))).......(((((((((.((.(((....)))...)))))))...))))......))))). ( -42.30)
>DroEre_CAF1 14962 120 + 1
AAUGACCACCAAACGCCACCUGUUGGCCAGGCCAGUUUCAGCCGUUGGCCAACAGAUGGCGACAGUAUGCUUAUUGGACACGCGCAAACGUAAAUGCCAAUUGGAAGCCUCGAACUGGUU
...(((((.....(((((.(((((((((((((........)))..)))))))))).))))).......(((((((((.((.(((....)))...)))))))...)))).......))))) ( -44.50)
>DroYak_CAF1 23458 120 + 1
AAUGACCACCAAACGCCACCUGUUGGCCGGGCCUGUUUCAGCCGUUGGCCAACAGAUGGCGACAGCAUGCUUAUUGGACACGCGCAAACGUAAAUGCCAAUUGGAAGCCUCGAAUUGGUU
.......(((((.(((((.(((((((((((((........)))..)))))))))).)))))...((...((.(((((.((.(((....)))...))))))).))..))......))))). ( -44.70)
>consensus
AAUGACCACCAAACGCCACCUGUUGGCCGGGCCAGUUUCAGCCGUUGGCCAACAGAUGGCGACAGUAUGCUUAUUGGACACGCGCAAACGUAAAUGCCAAUUGGAAGCCUCGAAUUGGUU
...(((((.....(((((.((((((((((((((.......))).))))))))))).))))).......(((((((((.((.(((....)))...)))))))...)))).......))))) (-40.47 = -41.10 +   0.63)

alignment

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secondary structure

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Window 8

Location 7,007,915 – 7,008,035
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.39
Mean single sequence MFE -48.30
Consensus MFE -44.46
Energy contribution -45.52
Covariance contribution 1.06
Combinations/Pair 1.03
Mean z-score -3.19
Structure conservation index 0.92
SVM decision value 1.79
SVM RNA-class probability 0.977509
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7007915 120 - 22224390
AACCAAUUCGAGGCUUCCAAUUGGCAUUUACGUUUGCGCGUGUCCAAUAAGCAUACUGUCGCCAUCUAUGGGCCAACGGCUGAAACUGCCCCGGCCAACAGGUGGCGUUUGGUGGUCAAU
...........((((.((((((((....(((((....))))).)))))...........((((((((...((((...(((.......)))..))))...))))))))..))).))))... ( -41.20)
>DroSec_CAF1 9120 120 - 1
AACCAAUUCGAGGCUUCCAAUUGGCAUUUACGUUUGCGCGUGUCCAAUAAGCAUACUGUCGCCAUCUGUGGGCCAACGGCUGAAACUGCCCCGGCCAACAGGUGGCGUUUGGUGGUCAUU
...........((((.((((((((....(((((....))))).)))))...........((((((((((.((((...(((.......)))..)))).))))))))))..))).))))... ( -46.00)
>DroEre_CAF1 14962 120 - 1
AACCAGUUCGAGGCUUCCAAUUGGCAUUUACGUUUGCGCGUGUCCAAUAAGCAUACUGUCGCCAUCUGUUGGCCAACGGCUGAAACUGGCCUGGCCAACAGGUGGCGUUUGGUGGUCAUU
...........((((.((((((((....(((((....))))).)))))...........((((((((((((((((..((((......))))))))))))))))))))..))).))))... ( -52.50)
>DroYak_CAF1 23458 120 - 1
AACCAAUUCGAGGCUUCCAAUUGGCAUUUACGUUUGCGCGUGUCCAAUAAGCAUGCUGUCGCCAUCUGUUGGCCAACGGCUGAAACAGGCCCGGCCAACAGGUGGCGUUUGGUGGUCAUU
...........((((.((((...(((........)))((((((.......))))))...(((((((((((((((...((((......)))).))))))))))))))).)))).))))... ( -53.50)
>consensus
AACCAAUUCGAGGCUUCCAAUUGGCAUUUACGUUUGCGCGUGUCCAAUAAGCAUACUGUCGCCAUCUGUGGGCCAACGGCUGAAACUGCCCCGGCCAACAGGUGGCGUUUGGUGGUCAUU
.(((((......((((...(((((....(((((....))))).))))))))).......(((((((((((((((...((((......)))).))))))))))))))).)))))....... (-44.46 = -45.52 +   1.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,008,035 – 7,008,150
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.21
Mean single sequence MFE -37.38
Consensus MFE -31.60
Energy contribution -32.10
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.23
Structure conservation index 0.85
SVM decision value 1.34
SVM RNA-class probability 0.943555
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7008035 115 - 22224390
CCACUAUGGUGUAUGUAUAUCCAGAUUUGCAUAUGUGUA----AGCCCCGUAUGUGUGUGAGUGUGCCACUCACAUGUGUGCACUGGUGUGCGUUUGUCCAUAAAACCACCCCA-AUGGC
....(((((...(((((((.((((.((((((....))))----))....(((((..((((((((...))))))))..))))).)))))))))))....)))))...(((.....-.))). ( -39.40)
>DroSec_CAF1 9240 115 - 1
CCAGUAUGGUGUAUGUAUAUCCAAAUUUGCAUAUGUGUA----AGCCCCGUAUGUGUGUGAGUGUGCCACUCACAUGUGUGCACUGGUGUGCGUUUGUCCAUAAAACCACCCCA-AUGGC
(((((..(((.((..(((((.((....)).)))))..))----.)))..(((((..((((((((...))))))))..)))))))))).(((.((((.......)))))))....-..... ( -37.00)
>DroEre_CAF1 15082 114 - 1
CUAGU--AUGGUAUGUAUAUCCAGAUUUGCAUAUGUGUA----AGCCUAGUAUGUGUGUGAGUGUGCCACUCACAUGUGUGAACUGGUGUGCGUUUGUCCAUAAAACCACCCCAAAUGGC
....(--((((.(((((((.((((.((((((....))))----)).....((((..((((((((...))))))))..))))..)))))))))))....)))))...(((.......))). ( -34.40)
>DroYak_CAF1 23578 119 - 1
CCAGUAUAUGGUAUGUAUAUCCUGAUUUGCAUAUGUGUACAUAUGCCCUGUAUGUGUGUGAGUGUGCCACUCACAUGUGUGCACUGGUGUGCGAUUGUCCAUAAAACCACCCCA-AUGGC
......(((((..((((((((.......(((((((....)))))))..((((((..((((((((...))))))))..))))))..)))))))).....)))))...(((.....-.))). ( -38.70)
>consensus
CCAGUAUAGGGUAUGUAUAUCCAGAUUUGCAUAUGUGUA____AGCCCCGUAUGUGUGUGAGUGUGCCACUCACAUGUGUGCACUGGUGUGCGUUUGUCCAUAAAACCACCCCA_AUGGC
..........(((((((.((....)).)))))))..........(((..(((((..((((((((...))))))))..)))))..(((.(((.((((.......))))))).)))...))) (-31.60 = -32.10 +   0.50)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,008,150 – 7,008,261
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.71
Mean single sequence MFE -19.60
Consensus MFE -16.86
Energy contribution -16.42
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -1.83
Structure conservation index 0.86
SVM decision value 0.17
SVM RNA-class probability 0.615031
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7008150 111 - 22224390
UCU---GUGACAAUUGACCCCUUGGAUCCUAUCAAAUUUCCACUUUUCCGAACGACUUACAAGGAAAUCGGGUUCCUUGACCAAUUCUCGACCCUUUUUCCU------UGCAUUUUCCCU
...---...............(((((....................)))))........((((((((..(((((....((.....))..)))))..))))))------)).......... ( -19.25)
>DroSec_CAF1 9355 110 - 1
CCU---GUGACAAUUGACCCCUUGGAUCCUAUCAAAUGUCCACUUUUCCGAACGACUUCCAAGGAAAUCGGGUUCCUUGACCAAUUCUCGACCCUU-UUCCU------UGCAUUUUCCCU
..(---(.((((.((((((....))......)))).)))))).................((((((((..(((((....((.....))..))))).)-)))))------)).......... ( -20.60)
>DroYak_CAF1 23697 119 - 1
UCUGCUGCGACAAUUGACCCCUCGGAUCAUAUCAAAUUUCCACUUUUCCGAACAACUUCCAAGGAAAUCGGGUUCCUUGACCAAUUCUCGACCCUU-UUCUUUUUUCCUGCAUUUUCCCU
.......(((.(((((.....(((((....................)))))........(((((((......)))))))..))))).)))......-....................... ( -18.95)
>consensus
UCU___GUGACAAUUGACCCCUUGGAUCCUAUCAAAUUUCCACUUUUCCGAACGACUUCCAAGGAAAUCGGGUUCCUUGACCAAUUCUCGACCCUU_UUCCU______UGCAUUUUCCCU
.......(((.(((((.....(((((....................)))))........(((((((......)))))))..))))).))).............................. (-16.86 = -16.42 +  -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 10:39:38 2006