Locus 7409

Sequence ID 3L_DroMel_CAF1
Location 19,933,810 – 19,933,940
Length 130
Max. P 0.996573
window12033 window12034 window12035 window12036

overview

Window 3

Location 19,933,810 – 19,933,920
Length 110
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 80.92
Mean single sequence MFE -32.72
Consensus MFE -22.93
Energy contribution -23.77
Covariance contribution 0.84
Combinations/Pair 1.19
Mean z-score -1.77
Structure conservation index 0.70
SVM decision value 0.57
SVM RNA-class probability 0.783845
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19933810 110 + 23771897
GAUUUGGGGCCAGGUAUCGAUUUGGUUUUCACUACAGGCUCCUUGGGCUCAACGUUGGUGGAGUACCUCUUGGUACUCAGCCUAUAUAGACCUA----CAAGGAUACCCAAUCA
((((.((((((..(((..((........))..))).)))((((((((.((......(((.(((((((....))))))).)))......))))..----))))))..))))))). ( -38.70)
>DroVir_CAF1 3352 107 + 1
GAUUUUGGUCCAGGUAUUGUCUUUGUACGCACAAUUGGUUCCUUGGGCUCCCAAUUUGUAGAAUAAGCUUUCAUAC------AAUUUACACCUAAAAUUAACAUUAGCCAGUC-
((((((((((((((.((((...((((....)))).)))).)).))))).......((((((((......))).)))------))........)))))))..............- ( -16.10)
>DroSec_CAF1 1715 110 + 1
GAUUUGGGGCCAGGUAUCGAUUUGGUUUUCACCACAGGCUCCUUGGGCUCAACGUUGGUGGAGUACCUCUUGGUACUCAGCCUAUAAAGACCUA----UAAGGAUACCCAGUCA
((((.((((((((((....))))))).............((((((((.((......(((.(((((((....))))))).)))......))))))----..))))..))))))). ( -37.60)
>DroSim_CAF1 1700 110 + 1
GAUUUGGGGCCAGGUAUCGAUUUGGUUUUCACCACAGGCUCCUUGGGCUCAACGUUGGUGGAGUACCUCUUGGUACUCAGCCUAUAUAGACCUA----UAAGGAUAGCCAGUCA
((((((..(((((((....)))))).)..)).....(((((((((((.((......(((.(((((((....))))))).)))......))))))----..))))..))))))). ( -37.90)
>DroEre_CAF1 1698 114 + 1
GAUUUGGGGCCAGGUAUUGAUUUAGUUUUCACCACAGGUUCCUUGGGCUCAAUGCUGGUGGAGUACCUCUUGGUACUCAACCUAUAUAGACCUACAUAUAACGAUACCCUUUCA
.....((((((..((..(((........)))..)).)))))).((((.((.(((..(((.(((((((....))))))).)))..))).)))))).................... ( -32.20)
>DroYak_CAF1 1702 114 + 1
GACUUGGGGCCAGGUAUUGAUUUAGUUUUCACCACAGGUUCCUUGGGCUCAAUGUUGGUGGAGUACCUCUUGGUACUCAACCUAUAUAGACCUACAUAUAACGAAACCCCAUCA
....(((((((..((..(((........)))..)).)).....((((.((.((((.(((.(((((((....))))))).))).)))).))))))............)))))... ( -33.80)
>consensus
GAUUUGGGGCCAGGUAUCGAUUUGGUUUUCACCACAGGCUCCUUGGGCUCAACGUUGGUGGAGUACCUCUUGGUACUCAGCCUAUAUAGACCUA____UAACGAUACCCAGUCA
.....((((((.(((...((........)))))...)))))).((((.((......(((.(((((((....))))))).)))......)))))).................... (-22.93 = -23.77 +   0.84)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,933,810 – 19,933,920
Length 110
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 80.92
Mean single sequence MFE -32.67
Consensus MFE -22.12
Energy contribution -22.48
Covariance contribution 0.36
Combinations/Pair 1.27
Mean z-score -2.06
Structure conservation index 0.68
SVM decision value 0.75
SVM RNA-class probability 0.839534
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19933810 110 - 23771897
UGAUUGGGUAUCCUUG----UAGGUCUAUAUAGGCUGAGUACCAAGAGGUACUCCACCAACGUUGAGCCCAAGGAGCCUGUAGUGAAAACCAAAUCGAUACCUGGCCCCAAAUC
...(((((..((((((----..((..((....((..(((((((....)))))))..)).....))..))))))))(((.(((.(((........))).)))..))))))))... ( -35.90)
>DroVir_CAF1 3352 107 - 1
-GACUGGCUAAUGUUAAUUUUAGGUGUAAAUU------GUAUGAAAGCUUAUUCUACAAAUUGGGAGCCCAAGGAACCAAUUGUGCGUACAAAGACAAUACCUGGACCAAAAUC
-...((((....))))..(((((((((...((------(((((...........(((((.((((...((...))..)))))))))))))))).....)))))))))........ ( -20.20)
>DroSec_CAF1 1715 110 - 1
UGACUGGGUAUCCUUA----UAGGUCUUUAUAGGCUGAGUACCAAGAGGUACUCCACCAACGUUGAGCCCAAGGAGCCUGUGGUGAAAACCAAAUCGAUACCUGGCCCCAAAUC
...(..((((((...(----(((((((((...(((((((((((....)))))))...((....)))))).))))).)))))(((....))).....))))))..)......... ( -38.80)
>DroSim_CAF1 1700 110 - 1
UGACUGGCUAUCCUUA----UAGGUCUAUAUAGGCUGAGUACCAAGAGGUACUCCACCAACGUUGAGCCCAAGGAGCCUGUGGUGAAAACCAAAUCGAUACCUGGCCCCAAAUC
.....((((.......----.((((....((((((((((((((....)))))))......(.(((....))).))))))))(((....)))........))))))))....... ( -32.60)
>DroEre_CAF1 1698 114 - 1
UGAAAGGGUAUCGUUAUAUGUAGGUCUAUAUAGGUUGAGUACCAAGAGGUACUCCACCAGCAUUGAGCCCAAGGAACCUGUGGUGAAAACUAAAUCAAUACCUGGCCCCAAAUC
.....(((....(((.((((((....))))))(((.(((((((....))))))).)))))).....(((..(((......((((....))))........)))))))))..... ( -32.74)
>DroYak_CAF1 1702 114 - 1
UGAUGGGGUUUCGUUAUAUGUAGGUCUAUAUAGGUUGAGUACCAAGAGGUACUCCACCAACAUUGAGCCCAAGGAACCUGUGGUGAAAACUAAAUCAAUACCUGGCCCCAAGUC
...(((((((..(((.((((((....))))))(((.(((((((....))))))).))))))(((((.....((....)).((((....))))..)))))....))))))).... ( -35.80)
>consensus
UGACUGGGUAUCCUUA____UAGGUCUAUAUAGGCUGAGUACCAAGAGGUACUCCACCAACGUUGAGCCCAAGGAACCUGUGGUGAAAACCAAAUCAAUACCUGGCCCCAAAUC
.....((((...........(((((....((((((((((((((....)))))))......(.(((....))).))))))))(((....)))........)))))))))...... (-22.12 = -22.48 +   0.36)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,933,850 – 19,933,940
Length 90
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 71.99
Mean single sequence MFE -27.63
Consensus MFE -15.08
Energy contribution -15.42
Covariance contribution 0.33
Combinations/Pair 1.25
Mean z-score -2.65
Structure conservation index 0.55
SVM decision value 2.72
SVM RNA-class probability 0.996573
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19933850 90 + 23771897
CCUUGGGCUCAACGUUGGUGGAGUACCUCUUGGUACUCAGCCUAUAUAGACCUA----CAAGGAUACCCAAUCAGUUCC-----------AGAUUCGCUGGAGC-U--------
(((((((.((......(((.(((((((....))))))).)))......))))..----)))))..........((((((-----------((.....)))))))-)-------- ( -34.00)
>DroSec_CAF1 1755 91 + 1
CCUUGGGCUCAACGUUGGUGGAGUACCUCUUGGUACUCAGCCUAUAAAGACCUA----UAAGGAUACCCAGUCAGUUCC-----------AGAUUCGCUGGAGCCU--------
..(((((.........(((.(((((((....))))))).)))........((..----...))...)))))...(((((-----------((.....)))))))..-------- ( -32.30)
>DroSim_CAF1 1740 91 + 1
CCUUGGGCUCAACGUUGGUGGAGUACCUCUUGGUACUCAGCCUAUAUAGACCUA----UAAGGAUAGCCAGUCAGUUCC-----------AGAUUCGCUGGAGCCU--------
....((((((......(((.(((((((....))))))).)))........((..----...)).((((.((((......-----------.)))).))))))))))-------- ( -32.50)
>DroEre_CAF1 1738 95 + 1
CCUUGGGCUCAAUGCUGGUGGAGUACCUCUUGGUACUCAACCUAUAUAGACCUACAUAUAACGAUACCCUUUCAGUCUC-----------AGAUUCGCUGAAACCU--------
...((((.((.(((..(((.(((((((....))))))).)))..))).))))))...............(((((((...-----------......)))))))...-------- ( -26.50)
>DroYak_CAF1 1742 95 + 1
CCUUGGGCUCAAUGUUGGUGGAGUACCUCUUGGUACUCAACCUAUAUAGACCUACAUAUAACGAAACCCCAUCAUUCUC-----------AGAUUCGCUAAUACCU--------
...((((.((.((((.(((.(((((((....))))))).))).)))).)))))).........................-----------................-------- ( -23.00)
>DroPer_CAF1 2140 107 + 1
CCUUGGGCUCUUGGAGAGUUGAGUAUCUAUUACAGCCCAAUCGAUACACAUCUA----AAAACAAA---AAUUUGUUUUAAUUAAUUUUAACAAACUGUGAUACAUAUCUGCAU
..(((((((.....(((........))).....)))))))..((((...(((..----(((((((.---...)))))))...........((.....)))))...))))..... ( -17.50)
>consensus
CCUUGGGCUCAACGUUGGUGGAGUACCUCUUGGUACUCAACCUAUAUAGACCUA____UAAGGAUACCCAAUCAGUUCC___________AGAUUCGCUGAAACCU________
...((((.((......(((.(((((((....))))))).)))......))))))............................................................ (-15.08 = -15.42 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,933,850 – 19,933,940
Length 90
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 71.99
Mean single sequence MFE -29.60
Consensus MFE -13.07
Energy contribution -13.27
Covariance contribution 0.20
Combinations/Pair 1.41
Mean z-score -2.38
Structure conservation index 0.44
SVM decision value 1.92
SVM RNA-class probability 0.982565
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19933850 90 - 23771897
--------A-GCUCCAGCGAAUCU-----------GGAACUGAUUGGGUAUCCUUG----UAGGUCUAUAUAGGCUGAGUACCAAGAGGUACUCCACCAACGUUGAGCCCAAGG
--------(-(.(((((.....))-----------))).))..((((((.((..((----(.(((((....)))))(((((((....))))))).....)))..)))))))).. ( -30.20)
>DroSec_CAF1 1755 91 - 1
--------AGGCUCCAGCGAAUCU-----------GGAACUGACUGGGUAUCCUUA----UAGGUCUUUAUAGGCUGAGUACCAAGAGGUACUCCACCAACGUUGAGCCCAAGG
--------.(((((.((((.....-----------......((((..(((....))----).))))......((..(((((((....)))))))..))..)))))))))..... ( -30.60)
>DroSim_CAF1 1740 91 - 1
--------AGGCUCCAGCGAAUCU-----------GGAACUGACUGGCUAUCCUUA----UAGGUCUAUAUAGGCUGAGUACCAAGAGGUACUCCACCAACGUUGAGCCCAAGG
--------.(((((.((((....(-----------(((.(((...((....))...----))).))))....((..(((((((....)))))))..))..)))))))))..... ( -30.30)
>DroEre_CAF1 1738 95 - 1
--------AGGUUUCAGCGAAUCU-----------GAGACUGAAAGGGUAUCGUUAUAUGUAGGUCUAUAUAGGUUGAGUACCAAGAGGUACUCCACCAGCAUUGAGCCCAAGG
--------.((((((((.....))-----------))))))....((((.(((...((((((....))))))(((.(((((((....))))))).))).....))))))).... ( -33.50)
>DroYak_CAF1 1742 95 - 1
--------AGGUAUUAGCGAAUCU-----------GAGAAUGAUGGGGUUUCGUUAUAUGUAGGUCUAUAUAGGUUGAGUACCAAGAGGUACUCCACCAACAUUGAGCCCAAGG
--------.(((..((((((((((-----------.(......).))).)))))))((((((....))))))(((.(((((((....))))))).)))........)))..... ( -28.00)
>DroPer_CAF1 2140 107 - 1
AUGCAGAUAUGUAUCACAGUUUGUUAAAAUUAAUUAAAACAAAUU---UUUGUUUU----UAGAUGUGUAUCGAUUGGGCUGUAAUAGAUACUCAACUCUCCAAGAGCCCAAGG
.....((((..((((..(((((....)))))....(((((((...---.)))))))----..))))..))))..(((((((.(...(((........)))...).))))))).. ( -25.00)
>consensus
________AGGCUCCAGCGAAUCU___________GAAACUGAUUGGGUAUCCUUA____UAGGUCUAUAUAGGCUGAGUACCAAGAGGUACUCCACCAACGUUGAGCCCAAGG
.........(((((................................................(((((....)))))(((((((....)))))))..........)))))..... (-13.07 = -13.27 +   0.20)

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 12:46:16 2006