Locus 6463

Sequence ID 3L_DroMel_CAF1
Location 17,237,643 – 17,237,953
Length 310
Max. P 0.999812
window10399 window10400 window10401 window10402 window10403

overview

Window 9

Location 17,237,643 – 17,237,761
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.42
Mean single sequence MFE -29.95
Consensus MFE -19.66
Energy contribution -20.42
Covariance contribution 0.76
Combinations/Pair 1.05
Mean z-score -1.70
Structure conservation index 0.66
SVM decision value 0.31
SVM RNA-class probability 0.681438
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17237643 118 + 23771897
CAAUGAAAUUAUAUUUAUUGAAAAUGGAU-GAACACUUUUGGCCAGC-AUCGACUGCUUUUCUCGCAGUGUACUUGUGGGCCACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAA
..(((..(((((.((((((.......)))-)))......(((((.((-(...(((((.......))))).....))).))))).)))))..)))(((((((........))))))).... ( -31.30)
>DroSec_CAF1 121640 117 + 1
AAAAGAUAUU--CUUCAUCGAAAAUAUAAGGAAAAGUAUUGGCCCGC-AUCGUUUGCUUUUCUCGCAGUGUACUUGUGGGCAACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAA
....((((((--.(((..............))).)))))).((((((-(....((((.......))))......))))))).............(((((((........))))))).... ( -27.74)
>DroSim_CAF1 115519 116 + 1
AACAGACAUU--CUUCAUCGAAAAUAUAU-GAAAAGUAUUGGCCAGC-AUCGCUUGCUUUUCUCGCAGUGUACUUGUGGGCCACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAA
..........--..............(((-(.....((((((((.((-(.((((.((.......))))))....))).))))).)))....))))((((((........))))))..... ( -28.50)
>DroEre_CAF1 124884 106 + 1
------------CUUUAUUGCAAUUUUCU-GCAAUCGAUUGGCCAGC-GCCGACUGCUUUUCCCACAGUGUACUUGUGGGCCACGUAAUGGCGUAGUUGCCUCUGCCCCGGCAACUUAAA
------------....((((((......)-)))))..........((-((((..(((....(((((((.....)))))))....))).))))))(((((((........))))))).... ( -33.40)
>DroYak_CAF1 128082 106 + 1
------------UUUUAAUGAAGUUAUCU-UC-AUCUAUUGGCAAGCCAUCGACUGCUUUUGCCGCAGUGUACUUGUGGGCCACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAA
------------.....((((((....))-))-))....(.(((((....(.(((((.......))))))..))))).)((((.....))))..(((((((........))))))).... ( -28.80)
>consensus
_A__GA_AUU__CUUUAUUGAAAAUAUAU_GAAAACUAUUGGCCAGC_AUCGACUGCUUUUCUCGCAGUGUACUUGUGGGCCACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAA
.......................................(((((.((.....(((((.......)))))......)).)))))...........(((((((........))))))).... (-19.66 = -20.42 +   0.76)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,237,682 – 17,237,801
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.39
Mean single sequence MFE -37.05
Consensus MFE -29.36
Energy contribution -29.16
Covariance contribution -0.20
Combinations/Pair 1.11
Mean z-score -1.98
Structure conservation index 0.79
SVM decision value 0.85
SVM RNA-class probability 0.866827
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17237682 119 + 23771897
GGCCAGC-AUCGACUGCUUUUCUCGCAGUGUACUUGUGGGCCACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAAUAAAUGUUUUCUAUAAUCAAAUGGUAAUGCAGUCAGGGCC
((((...-...((((((..((..((...((...((((((((((.....))))..(((((((........)))))))..............)))))).))..))..)).))))))..)))) ( -33.80)
>DroSec_CAF1 121678 119 + 1
GGCCCGC-AUCGUUUGCUUUUCUCGCAGUGUACUUGUGGGCAACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAAUAAAUGUUUUCUAUAAUCAAAUGGUAAUGCAGUCAGGGCC
(((((((-(.....))).......(((...((((((((((.(((((........(((((((........))))))).......))))).)))))).......)))).))).....))))) ( -35.97)
>DroSim_CAF1 115556 119 + 1
GGCCAGC-AUCGCUUGCUUUUCUCGCAGUGUACUUGUGGGCCACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAAUAAAUGUUUUCUAUAAUCAAAUGGUAAUGCAGUCAGGGCC
(((((((-(.....))))......(((...((((..(((((((.....))))..(((((((........)))))))....................)))...)))).)))......)))) ( -33.60)
>DroEre_CAF1 124911 119 + 1
GGCCAGC-GCCGACUGCUUUUCCCACAGUGUACUUGUGGGCCACGUAAUGGCGUAGUUGCCUCUGCCCCGGCAACUUAAAUAAAUGUUUUCUAUAAUCAAAUGGUAAUGCAGUCAGGGCC
((((.((-((((..(((....(((((((.....)))))))....))).))))))(((((((........)))))))........(((...((((......))))....))).....)))) ( -38.10)
>DroYak_CAF1 128108 120 + 1
GGCAAGCCAUCGACUGCUUUUGCCGCAGUGUACUUGUGGGCCACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAAUAAAUGUUUUCUAUAAUCAAAUGGUAAUGCAGUCGGGGCC
.....(((.((((((((..((((((...((...((((((((((.....))))..(((((((........)))))))..............)))))).))..)))))).))))))))))). ( -43.80)
>consensus
GGCCAGC_AUCGACUGCUUUUCUCGCAGUGUACUUGUGGGCCACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAAUAAAUGUUUUCUAUAAUCAAAUGGUAAUGCAGUCAGGGCC
((((.......((((((..((.(((...((...(((((((..((((........(((((((........))))))).......))))..))))))).))..))).)).))))))..)))) (-29.36 = -29.16 +  -0.20)

alignment

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secondary structure

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Window 1

Location 17,237,721 – 17,237,841
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.50
Mean single sequence MFE -32.36
Consensus MFE -29.02
Energy contribution -30.30
Covariance contribution 1.28
Combinations/Pair 1.03
Mean z-score -2.70
Structure conservation index 0.90
SVM decision value 4.14
SVM RNA-class probability 0.999812
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17237721 120 + 23771897
CCACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAAUAAAUGUUUUCUAUAAUCAAAUGGUAAUGCAGUCAGGGCCACAGCCUCUGAACACUGCCCGAAAACCUAGCCAAGCGUUC
........((((..(((((((........))))))).........((((((....(((....)))...(((((((((((....))).))))...))))..))))))...))))....... ( -33.80)
>DroSec_CAF1 121717 120 + 1
CAACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAAUAAAUGUUUUCUAUAAUCAAAUGGUAAUGCAGUCAGGGCCACAGCCUCUGCACACUGCCCGAAAACCUAGCCAAGCGUUC
........((((..(((((((........))))))).........((((((....(((....)))...(((((((((((....))).)))...)))))..))))))...))))....... ( -33.60)
>DroSim_CAF1 115595 120 + 1
CCACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAAUAAAUGUUUUCUAUAAUCAAAUGGUAAUGCAGUCAGGGCCACAGCCUCUGCACACUGCCCGAAAACCUAGCCAAGCGUUC
........((((..(((((((........))))))).........((((((....(((....)))...(((((((((((....))).)))...)))))..))))))...))))....... ( -33.60)
>DroEre_CAF1 124950 109 + 1
CCACGUAAUGGCGUAGUUGCCUCUGCCCCGGCAACUUAAAUAAAUGUUUUCUAUAAUCAAAUGGUAAUGCAGUCAGGGCCGCAGCCUC-----------CGAAAACCUAGCCAAGCGUUC
..((((..((((..(((((((........))))))).........((((((....(((....)))..(((.((....)).))).....-----------.))))))...)))).)))).. ( -27.70)
>DroYak_CAF1 128148 120 + 1
CCACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAAUAAAUGUUUUCUAUAAUCAAAUGGUAAUGCAGUCGGGGCCGCAGCCUCUGAACACUGCCCGAAAACCCAGCCAAGCGUUC
........((((..(((((((........))))))).........((((((....(((....)))...(((((((((((....))).))))...))))..))))))...))))....... ( -33.10)
>consensus
CCACAUAAUGGCAUAGUUGCCUCUCCCCCGGCAACUUAAAUAAAUGUUUUCUAUAAUCAAAUGGUAAUGCAGUCAGGGCCACAGCCUCUGAACACUGCCCGAAAACCUAGCCAAGCGUUC
........((((..(((((((........))))))).........((((((....(((....)))...(((((((((((....))).)))...)))))..))))))...))))....... (-29.02 = -30.30 +   1.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,237,801 – 17,237,921
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.58
Mean single sequence MFE -41.62
Consensus MFE -32.74
Energy contribution -33.26
Covariance contribution 0.52
Combinations/Pair 1.11
Mean z-score -1.92
Structure conservation index 0.79
SVM decision value 0.91
SVM RNA-class probability 0.880245
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17237801 120 - 23771897
GGGUUUUAGGGUUUUGGAUUUCCGAAGCCUUCGGUUCAGUCGCAAUUCAGUUUAGAACGAACUGGCUAAAAGUCUGCCCUGAACGCUUGGCUAGGUUUUCGGGCAGUGUUCAGAGGCUGU
((.((((((((((((((....)))))))).(((((((..((.............))..))))))))))))).)).((((((((((((.(.((........)).)))))))))).)))... ( -44.82)
>DroSec_CAF1 121797 120 - 1
GGGCUUUAGGGUUUUGGAUUUCCGAAGCCUUCGGUUCAGUCGAAGUUCAGUUUAGAACGAACUGGCUAAAAGUCUGCCCUGAACGCUUGGCUAGGUUUUCGGGCAGUGUGCAGAGGCUGU
(((((((((((((((((....)))))))))).(((.((((....((((......))))..))))))).)))))))((((((.(((((.(.((........)).)))))).))).)))... ( -42.50)
>DroSim_CAF1 115675 120 - 1
GGGCUUUAGGGUUUUGGAUUUCCGAAGCCUUCGGUUCAGUCGUAGUUCAGUUUAGAACGAACUGGCUAAAAGUCUGCCCUGAACGCUUGGCUAGGUUUUCGGGCAGUGUGCAGAGGCUGU
(((((..((((((((((....)))))))))).)))))((((.((((.((((((.....)))))))))).....((((((.(((.(((......))).)))))))))........)))).. ( -43.30)
>DroEre_CAF1 125030 108 - 1
GGGUUUUAGGGU-UUGGAUUUCUGAAGCCUUUGGUUCACUCGGAGUUCAGUUUAGAACGAACUAGCUAAAAGUCUGCCCUGAACGCUUGGCUAGGUUUUCG-----------GAGGCUGC
(..((..(((.(-(..(....)..)).)))..))..).(((.((((((......))))...((((((((..(((......).))..))))))))....)).-----------)))..... ( -32.20)
>DroYak_CAF1 128228 120 - 1
GGGCUUUAGGGUUUUGGAUUUCUGAAGCCUUCGGUUCAGUCGGAGUUCAGUUUAGAACGAACUAGCUAAAAGUCUGCCCUGAACGCUUGGCUGGGUUUUCGGGCAGUGUUCAGAGGCUGC
((((((((((((((..(....)..))))))).((((.(((....((((......))))..))))))).)))))))((((((((((((.(.((((....)))).)))))))))).)))... ( -45.30)
>consensus
GGGCUUUAGGGUUUUGGAUUUCCGAAGCCUUCGGUUCAGUCGGAGUUCAGUUUAGAACGAACUGGCUAAAAGUCUGCCCUGAACGCUUGGCUAGGUUUUCGGGCAGUGUGCAGAGGCUGU
.((((((((((((((((....))))))))))((((((..((.............))..)))))).........((((((.(((.((((....)))).)))))))))......)))))).. (-32.74 = -33.26 +   0.52)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,237,841 – 17,237,953
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.14
Mean single sequence MFE -37.62
Consensus MFE -31.38
Energy contribution -31.02
Covariance contribution -0.36
Combinations/Pair 1.12
Mean z-score -1.35
Structure conservation index 0.83
SVM decision value 0.21
SVM RNA-class probability 0.634395
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17237841 112 - 23771897
AUGAGGCUGACCUCCCUCG-UU-------CCUGGGUUCUUGGGUUUUAGGGUUUUGGAUUUCCGAAGCCUUCGGUUCAGUCGCAAUUCAGUUUAGAACGAACUGGCUAAAAGUCUGCCCU
((((((........)))))-).-------...((((....((.((((((((((((((....)))))))).(((((((..((.............))..))))))))))))).)).)))). ( -36.32)
>DroSec_CAF1 121837 113 - 1
AUGAGGCUGACCUCCCUCGGUU-------CCUGGGUUCUUGGGCUUUAGGGUUUUGGAUUUCCGAAGCCUUCGGUUCAGUCGAAGUUCAGUUUAGAACGAACUGGCUAAAAGUCUGCCCU
...(((..((((......))))-------)))((((....(((((((((((((((((....)))))))))).(((.((((....((((......))))..))))))).))))))))))). ( -37.60)
>DroSim_CAF1 115715 113 - 1
AUGAGGCUGACCUCCCUCGGUU-------CCUGGGUUCUUGGGCUUUAGGGUUUUGGAUUUCCGAAGCCUUCGGUUCAGUCGUAGUUCAGUUUAGAACGAACUGGCUAAAAGUCUGCCCU
...(((..((((......))))-------)))((((....(((((((((((((((((....)))))))))).(((.((((....((((......))))..))))))).))))))))))). ( -37.60)
>DroEre_CAF1 125059 112 - 1
ACGAGGCUGACCUCCCCCGGUU-------CCUGGGUCCUUGGGUUUUAGGGU-UUGGAUUUCUGAAGCCUUUGGUUCACUCGGAGUUCAGUUUAGAACGAACUAGCUAAAAGUCUGCCCU
....(((.(((.....(..(((-------(((((((((..(((((((((((.-......)))))))))))..))...)))))).((((......))))))))..)......))).))).. ( -36.80)
>DroYak_CAF1 128268 120 - 1
ACGAGGCUGACCUCCCUCGGUUUCUGGGUCCUGGGUCCUUGGGCUUUAGGGUUUUGGAUUUCUGAAGCCUUCGGUUCAGUCGGAGUUCAGUUUAGAACGAACUAGCUAAAAGUCUGCCCU
..((((((((......)))))))).((((.(((((.((..(((((((((((........)))))))))))..)))))))....((((.(((((.....)))))))))........)))). ( -39.80)
>consensus
AUGAGGCUGACCUCCCUCGGUU_______CCUGGGUUCUUGGGCUUUAGGGUUUUGGAUUUCCGAAGCCUUCGGUUCAGUCGGAGUUCAGUUUAGAACGAACUGGCUAAAAGUCUGCCCU
.(((((........))))).............((((....(((((((((((((((((....))))))))))((((((..((.............))..))))))....))))))))))). (-31.38 = -31.02 +  -0.36)

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 12:19:56 2006