Locus 3266

Sequence ID 2R_DroMel_CAF1
Location 11,171,922 – 11,172,039
Length 117
Max. P 0.982806
window5357 window5358 window5359 window5360

overview

Window 7

Location 11,171,922 – 11,172,019
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.41
Mean single sequence MFE -38.12
Consensus MFE -35.12
Energy contribution -35.12
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.94
Structure conservation index 0.92
SVM decision value 1.93
SVM RNA-class probability 0.982806
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11171922 97 + 20766785
-------------------ACCAUGGUA-AUGGUACGGUGCGACCGGAUGAUGGUUCACAACGACCGUGU---CAUUUAAACGGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUG
-------------------(((((....-)))))..(((((((.(((((((.(((((.((.(((((.(((---.......)))))))).))))))).))))))).))))...)))..... ( -38.10)
>DroVir_CAF1 137006 92 + 1
--------------------------UU-AUGGUACGGUGCGACCGGAUGAUGGUUCACAACGACCGUGCAU-ACUUUUAACUGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUG
--------------------------..-(((((....(((((.(((((((.(((((.((.(((((((....-.......)).))))).))))))).))))))).)))))..)))))... ( -35.70)
>DroGri_CAF1 137694 93 + 1
--------------------------CUGAUGGUACGGUGCGACCGGAUGACGGUUCACAACGACCGUGCUU-AUUUUUAACUGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUG
--------------------------..((((((....(((((.(((((((.(((((.((.((((((.(.((-(....)))))))))).))))))).))))))).)))))..)))))).. ( -37.20)
>DroWil_CAF1 129231 116 + 1
AAAUAAGGGGAGAUCCCCCAUAAUGGUA-AUGGUACGGUGCGACCGGAUGACGGUUCACAACGACCGUGU---CAAUUUUACUGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUG
......((((.....))))........(-(((((....(((((.(((((((.(((((.((.((((((((.---......))).))))).))))))).))))))).)))))..)))))).. ( -45.70)
>DroMoj_CAF1 144537 93 + 1
--------------------------UU-AUGGUACGGUGCGACCGGAUGAUGGUUCACAACGACCGUACAGUUUUUUCAACGGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUG
--------------------------..-(((((....(((((.(((((((.(((((.((.(((((.....(((.....))).))))).))))))).))))))).)))))..)))))... ( -34.80)
>DroAna_CAF1 94925 96 + 1
--------------------UAACGGUA-AUGGUACGGUGCGACCGGAUGAUGGUUCACAACGACCGUGU---CCUUCGAACGGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUG
--------------------.......(-(((((....(((((.(((((((.(((((.((.(((((.(((---.......)))))))).))))))).))))))).)))))..)))))).. ( -37.20)
>consensus
__________________________UA_AUGGUACGGUGCGACCGGAUGAUGGUUCACAACGACCGUGC___CAUUUUAACGGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUG
.............................(((((....(((((.(((((((.(((((.((.(((((((............)).))))).))))))).))))))).)))))..)))))... (-35.12 = -35.12 +   0.00)

alignment

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secondary structure

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Window 8

Location 11,171,922 – 11,172,019
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.41
Mean single sequence MFE -29.37
Consensus MFE -24.54
Energy contribution -24.32
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.21
Structure conservation index 0.84
SVM decision value 1.15
SVM RNA-class probability 0.922107
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11171922 97 - 20766785
CAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCCGUUUAAAUG---ACACGGUCGUUGUGAACCAUCAUCCGGUCGCACCGUACCAU-UACCAUGGU-------------------
...((((..((((((..((((....))))...(((((.(((.....)---))..))))))))))).))))....(((.....))).(((((-....)))))------------------- ( -29.50)
>DroVir_CAF1 137006 92 - 1
CAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCAGUUAAAAGU-AUGCACGGUCGUUGUGAACCAUCAUCCGGUCGCACCGUACCAU-AA--------------------------
...((((..((((((..((((....))))...(((((.((.......-..))..))))))))))).))))....(((.....)))......-..-------------------------- ( -24.80)
>DroGri_CAF1 137694 93 - 1
CAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCAGUUAAAAAU-AAGCACGGUCGUUGUGAACCGUCAUCCGGUCGCACCGUACCAUCAG--------------------------
...((((((((((((..((((....))))...(((((.(((......-.)))..)))))))))))..)))))).(((.....))).........-------------------------- ( -27.80)
>DroWil_CAF1 129231 116 - 1
CAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCAGUAAAAUUG---ACACGGUCGUUGUGAACCGUCAUCCGGUCGCACCGUACCAU-UACCAUUAUGGGGGAUCUCCCCUUAUUU
..(((((.((((.....((((....)))).((......)).....))---))..(((((.(((((.(((.....)))))))).)).)))..-..)))))..(((((....)))))..... ( -36.80)
>DroMoj_CAF1 144537 93 - 1
CAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCCGUUGAAAAAACUGUACGGUCGUUGUGAACCAUCAUCCGGUCGCACCGUACCAU-AA--------------------------
..(((((.(((......((((....))))....)))))))).........(((((((....((((.((.......)))))))))))))...-..-------------------------- ( -27.70)
>DroAna_CAF1 94925 96 - 1
CAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCCGUUCGAAGG---ACACGGUCGUUGUGAACCAUCAUCCGGUCGCACCGUACCAU-UACCGUUA--------------------
..(((((..((((((..((((....))))...(((((.((((....)---).))))))))))))).........(((.....)))..))))-).......-------------------- ( -29.60)
>consensus
CAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCAGUUAAAAAG___ACACGGUCGUUGUGAACCAUCAUCCGGUCGCACCGUACCAU_AA__________________________
...((((..((((((..((((....))))...(((((.((............))))))))))))).))))....(((.....)))................................... (-24.54 = -24.32 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,171,942 – 11,172,039
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.56
Mean single sequence MFE -32.08
Consensus MFE -27.67
Energy contribution -27.45
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.52
Structure conservation index 0.86
SVM decision value 0.62
SVM RNA-class probability 0.802167
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11171942 97 + 20766785
CGACCGGAUGAUGGUUCACAACGACCGUGU---CAUUUAAACGGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAACGAUUUAUC---A----------------GUGUCC-
(((.(((((((.(((((.((.(((((.(((---.......)))))))).))))))).))))))).)))..((((.((..(((...)))..)).---.----------------))))..- ( -29.00)
>DroPse_CAF1 86108 113 + 1
CGACCGGACGAUGGUUCACAACGACCGUGU---CUCUUAAACUGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAGCGAUUUAUC---AUCAUCGUCGCGCCCCAGUGCUC-
.((((((((((.(((((.((.((((((.((---.......)))))))).))))))).))))))).......(((.........))).......---......)))((((....))))..- ( -37.70)
>DroGri_CAF1 137708 98 + 1
CGACCGGAUGACGGUUCACAACGACCGUGCUU-AUUUUUAACUGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAGCGAUUUAUC---A----------------A-AUCA-
(((.(((((((.(((((.((.((((((.(.((-(....)))))))))).))))))).))))))).)))...(((.........))).......---.----------------.-....- ( -29.50)
>DroWil_CAF1 129270 98 + 1
CGACCGGAUGACGGUUCACAACGACCGUGU---CAAUUUUACUGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAACGAUUUAUC---A----------------UAAUCUC
(((.(((((((.(((((.((.((((((((.---......))).))))).))))))).))))))).))).................((((....---.----------------.)))).. ( -30.00)
>DroMoj_CAF1 144550 102 + 1
CGACCGGAUGAUGGUUCACAACGACCGUACAGUUUUUUCAACGGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAACGAUUUAUCAGCA----------------A-AUCA-
(((.(((((((.(((((.((.(((((.....(((.....))).))))).))))))).))))))).))).................(((((......)----------------)-))).- ( -28.60)
>DroPer_CAF1 85824 113 + 1
CGACCGGACGAUGGUUCACAACGACCGUGU---CUCUUAAACUGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAGCGAUUUAUC---AUCAUCGUCGCGCCCCAGUGCUC-
.((((((((((.(((((.((.((((((.((---.......)))))))).))))))).))))))).......(((.........))).......---......)))((((....))))..- ( -37.70)
>consensus
CGACCGGAUGAUGGUUCACAACGACCGUGU___CUUUUAAACUGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAACGAUUUAUC___A________________GUAUCC_
(((.(((((((.(((((.((.(((((((............)).))))).))))))).))))))).))).................................................... (-27.67 = -27.45 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,171,942 – 11,172,039
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.56
Mean single sequence MFE -32.07
Consensus MFE -24.14
Energy contribution -23.92
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.74
Structure conservation index 0.75
SVM decision value 0.73
SVM RNA-class probability 0.835726
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11171942 97 - 20766785
-GGACAC----------------U---GAUAAAUCGUUGACAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCCGUUUAAAUG---ACACGGUCGUUGUGAACCAUCAUCCGGUCG
-(((((.----------------(---((....))).))....((((..((((((..((((....))))...(((((.(((.....)---))..))))))))))).))))..)))..... ( -27.30)
>DroPse_CAF1 86108 113 - 1
-GAGCACUGGGGCGCGACGAUGAU---GAUAAAUCGCUGACAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCAGUUUAAGAG---ACACGGUCGUUGUGAACCAUCGUCCGGUCG
-........((.((.(((((((..---.......((((.......))))((((((..((((....))))...(((((.(((.....)---))..)))))))))))..))))))))).)). ( -38.90)
>DroGri_CAF1 137708 98 - 1
-UGAU-U----------------U---GAUAAAUCGCUGACAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCAGUUAAAAAU-AAGCACGGUCGUUGUGAACCGUCAUCCGGUCG
-.(((-(----------------.---....))))...(((..((((((((((((..((((....))))...(((((.(((......-.)))..)))))))))))..))))))...))). ( -30.20)
>DroWil_CAF1 129270 98 - 1
GAGAUUA----------------U---GAUAAAUCGUUGACAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCAGUAAAAUUG---ACACGGUCGUUGUGAACCGUCAUCCGGUCG
..((((.----------------.---....))))...(((..((((((((((((..((((....))))...(((((.((.......---..)))))))))))))..))))))...))). ( -30.00)
>DroMoj_CAF1 144550 102 - 1
-UGAU-U----------------UGCUGAUAAAUCGUUGACAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCCGUUGAAAAAACUGUACGGUCGUUGUGAACCAUCAUCCGGUCG
-.(((-(----------------((....))))))...(((..((((..((((((..((((....))))...(((((.((............))))))))))))).))))......))). ( -27.10)
>DroPer_CAF1 85824 113 - 1
-GAGCACUGGGGCGCGACGAUGAU---GAUAAAUCGCUGACAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCAGUUUAAGAG---ACACGGUCGUUGUGAACCAUCGUCCGGUCG
-........((.((.(((((((..---.......((((.......))))((((((..((((....))))...(((((.(((.....)---))..)))))))))))..))))))))).)). ( -38.90)
>consensus
_GGACAC________________U___GAUAAAUCGCUGACAAAUGGCGUUACAAACGGACGAAAGUCCCACCGACCAGUUUAAAAG___ACACGGUCGUUGUGAACCAUCAUCCGGUCG
......................................(((..((((..((((((..((((....))))...(((((.((............))))))))))))).))))......))). (-24.14 = -23.92 +  -0.22)

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 10:51:28 2006