Locus 7561

Sequence ID X_DroMel_CAF1
Location 18,832,297 – 18,832,542
Length 245
Max. P 0.999989
window12410 window12411 window12412 window12413 window12414 window12415

overview

Window 0

Location 18,832,297 – 18,832,393
Length 96
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 92.78
Mean single sequence MFE -30.84
Consensus MFE -29.54
Energy contribution -29.22
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -2.27
Structure conservation index 0.96
SVM decision value 4.20
SVM RNA-class probability 0.999834
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18832297 96 + 22224390
---UUUUUUUUUGGCUCAUCUCUGGCAUGCAAAUCCCGAGCCCCACACCAUCGCCCAGCAUCUUGGGCUUACUUUAUUGGCUUUUGGCUGGUGUGGGGG
---................(((.((.((....)))).)))(((((((((...((((((....))))))..........(((.....)))))))))))). ( -34.70)
>DroSec_CAF1 69150 93 + 1
------UUGUUUGGCUCAUUUCUGGCAUGCAAAUCCUGAGCCCCACACCAUCGCCCAGCAUCUUGGGCUUACUUUAUUGGCUUUUGGCUUGUGUGGGGG
------((((.((.(........).)).))))........((((((((....((((((....))))))..........(((.....))).)))))))). ( -31.20)
>DroSim_CAF1 49367 96 + 1
---UUUUUUUUUGGCUCAUCUCUGGCAUGCAAAUCCUGAGCCCCACACCAUCGCCCAGCAUCUUGGGCUUACUUUAUUGGCUUUUGGCUUGUGUGGGGG
---................(((.((.((....)))).)))((((((((....((((((....))))))..........(((.....))).)))))))). ( -29.90)
>DroEre_CAF1 66883 92 + 1
-------UUUUUGGCUCUGCUCUGGCAUGCAAAUCCUGAGCCUCACACCAUCGCCCAGCAUCUUGGGCUUACUUUAUUGGCUUUUGGCUUGUGUGGGGA
-------......((..(((....))).))..........((((((((....((((((....))))))..........(((.....))).)))))))). ( -27.60)
>DroYak_CAF1 66001 99 + 1
UUUUUUUUUUUUGGCUCAUCUCUGGCAUGCAAAUCCUGAGCCCCACACCAUCGCCCAGGAUCUUGGGCUUACUUUAUUGGCUUUUGGCUUGUGUGGGGG
...................(((.((.((....)))).)))((((((((....((((((....))))))..........(((.....))).)))))))). ( -30.80)
>consensus
___UUUUUUUUUGGCUCAUCUCUGGCAUGCAAAUCCUGAGCCCCACACCAUCGCCCAGCAUCUUGGGCUUACUUUAUUGGCUUUUGGCUUGUGUGGGGG
...................(((.((.((....)))).)))((((((((....((((((....))))))..........(((.....))).)))))))). (-29.54 = -29.22 +  -0.32)

alignment

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secondary structure

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Window 1

Location 18,832,297 – 18,832,393
Length 96
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 92.78
Mean single sequence MFE -31.36
Consensus MFE -29.56
Energy contribution -29.84
Covariance contribution 0.28
Combinations/Pair 1.04
Mean z-score -3.35
Structure conservation index 0.94
SVM decision value 5.53
SVM RNA-class probability 0.999989
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18832297 96 - 22224390
CCCCCACACCAGCCAAAAGCCAAUAAAGUAAGCCCAAGAUGCUGGGCGAUGGUGUGGGGCUCGGGAUUUGCAUGCCAGAGAUGAGCCAAAAAAAAA---
...((((((((((.....))...........(((((......)))))..))))))))((((((...((((.....))))..)))))).........--- ( -35.70)
>DroSec_CAF1 69150 93 - 1
CCCCCACACAAGCCAAAAGCCAAUAAAGUAAGCCCAAGAUGCUGGGCGAUGGUGUGGGGCUCAGGAUUUGCAUGCCAGAAAUGAGCCAAACAA------
...((((((..((.....))...........(((((......)))))....))))))((((((...((((.....))))..))))))......------ ( -31.00)
>DroSim_CAF1 49367 96 - 1
CCCCCACACAAGCCAAAAGCCAAUAAAGUAAGCCCAAGAUGCUGGGCGAUGGUGUGGGGCUCAGGAUUUGCAUGCCAGAGAUGAGCCAAAAAAAAA---
...((((((..((.....))...........(((((......)))))....))))))((((((...((((.....))))..)))))).........--- ( -32.10)
>DroEre_CAF1 66883 92 - 1
UCCCCACACAAGCCAAAAGCCAAUAAAGUAAGCCCAAGAUGCUGGGCGAUGGUGUGAGGCUCAGGAUUUGCAUGCCAGAGCAGAGCCAAAAA-------
....(((((..((.....))...........(((((......)))))....))))).(((((....((((.....))))...))))).....------- ( -25.90)
>DroYak_CAF1 66001 99 - 1
CCCCCACACAAGCCAAAAGCCAAUAAAGUAAGCCCAAGAUCCUGGGCGAUGGUGUGGGGCUCAGGAUUUGCAUGCCAGAGAUGAGCCAAAAAAAAAAAA
...((((((..((.....))...........(((((......)))))....))))))((((((...((((.....))))..))))))............ ( -32.10)
>consensus
CCCCCACACAAGCCAAAAGCCAAUAAAGUAAGCCCAAGAUGCUGGGCGAUGGUGUGGGGCUCAGGAUUUGCAUGCCAGAGAUGAGCCAAAAAAAAA___
...((((((..((.....))...........(((((......)))))....))))))((((((...((((.....))))..))))))............ (-29.56 = -29.84 +   0.28)

alignment

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secondary structure

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Window 2

Location 18,832,393 – 18,832,485
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.43
Mean single sequence MFE -30.20
Consensus MFE -17.88
Energy contribution -19.35
Covariance contribution 1.48
Combinations/Pair 1.15
Mean z-score -2.81
Structure conservation index 0.59
SVM decision value 1.24
SVM RNA-class probability 0.934674
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18832393 92 + 22224390
AAAAGUUUU--GCAAAUUAAUUACAUUUUAUUGGGCUCGAC-----UUGAGUUG----------GAAUGAACUCAA----------GCGGGGCGGCAAACUUUAUUUGCGGCCC-CGCAC
..(((((..--((..(.(((.......))).)..))..)))-----))(((((.----------.....)))))..----------(((((((.(((((.....))))).))))-))).. ( -34.20)
>DroPse_CAF1 93542 100 + 1
AAAAGUUUUUGGCAAAUUAAUUACAUUUUAUUGGGCUCGACU---CUCGAGUUGCUCGACCCAAGAAUGAACUCC------------CGAGGCACCCGUC----UUCCAUGCCC-CGCAU
..........((((.........(((((..(((((.(((((.---........).))))))))))))))......------------.(((((....)))----))...)))).-..... ( -21.20)
>DroSec_CAF1 69243 92 + 1
AAAAGUUUU--GCAAAUUAAUUACAUUUUAUUGGGCUCGAC-----UUGAGUUG----------GAAUGAACUCAA----------GCGGGGCGGCAAACUUUAUUUGCGGCCC-CGCAC
..(((((..--((..(.(((.......))).)..))..)))-----))(((((.----------.....)))))..----------(((((((.(((((.....))))).))))-))).. ( -34.20)
>DroSim_CAF1 49463 92 + 1
AAAAGUUUU--GCAAAUUAAUUACAUUUUAUUGGGCUCGAC-----UUGAGUUG----------GAAUGAACUCAA----------GCGGGGCGGCAAACUUUAUUUGCGGCCC-CGCAC
..(((((..--((..(.(((.......))).)..))..)))-----))(((((.----------.....)))))..----------(((((((.(((((.....))))).))))-))).. ( -34.20)
>DroEre_CAF1 66975 92 + 1
AAAAGUUUU--GCAAAUUAAUUACAUUUUAUUGGGCUCGAC-----UUGAGCUG----------GAAUGAACUCGA----------GCGGGGCGGCAAACUUUAUUUGCGACCC-CGCUC
.........--............((((((....(((((...-----..))))))----------))))).....((----------((((((..(((((.....)))))..)))-))))) ( -29.80)
>DroYak_CAF1 66100 108 + 1
AAAAGUUUU--GCAAAUUAAUUACAUUUUAUUGGGCUCGACUUGACUUGAGUUG----------GAAUGAACUCGAAGUGGGGGGAGGGGGAGGAUAAACUUUAUUUGCGAGCCGGGCAC
........(--((..........((......))(((((..(((.(((((((((.----------.....))))).)))).)))(.(((..(((......)))..))).))))))..))). ( -27.60)
>consensus
AAAAGUUUU__GCAAAUUAAUUACAUUUUAUUGGGCUCGAC_____UUGAGUUG__________GAAUGAACUCAA__________GCGGGGCGGCAAACUUUAUUUGCGGCCC_CGCAC
...(((((....(..........((......))(((((((......)))))))...........)...))))).............(((((((.(((((.....))))).)))).))).. (-17.88 = -19.35 +   1.48)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,832,393 – 18,832,485
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.43
Mean single sequence MFE -29.65
Consensus MFE -12.45
Energy contribution -13.34
Covariance contribution 0.89
Combinations/Pair 1.24
Mean z-score -3.66
Structure conservation index 0.42
SVM decision value 1.34
SVM RNA-class probability 0.943563
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18832393 92 - 22224390
GUGCG-GGGCCGCAAAUAAAGUUUGCCGCCCCGC----------UUGAGUUCAUUC----------CAACUCAA-----GUCGAGCCCAAUAAAAUGUAAUUAAUUUGC--AAAACUUUU
(.(((-((((.((((((...)))))).)))))((----------(((((((.....----------.)))))))-----))...)).).......(((((.....))))--)........ ( -31.70)
>DroPse_CAF1 93542 100 - 1
AUGCG-GGGCAUGGAA----GACGGGUGCCUCG------------GGAGUUCAUUCUUGGGUCGAGCAACUCGAG---AGUCGAGCCCAAUAAAAUGUAAUUAAUUUGCCAAAAACUUUU
...((-((((((....----.....))))))))------------((.((((((((((((((......)))))))---))).))))))........((((.....))))........... ( -30.40)
>DroSec_CAF1 69243 92 - 1
GUGCG-GGGCCGCAAAUAAAGUUUGCCGCCCCGC----------UUGAGUUCAUUC----------CAACUCAA-----GUCGAGCCCAAUAAAAUGUAAUUAAUUUGC--AAAACUUUU
(.(((-((((.((((((...)))))).)))))((----------(((((((.....----------.)))))))-----))...)).).......(((((.....))))--)........ ( -31.70)
>DroSim_CAF1 49463 92 - 1
GUGCG-GGGCCGCAAAUAAAGUUUGCCGCCCCGC----------UUGAGUUCAUUC----------CAACUCAA-----GUCGAGCCCAAUAAAAUGUAAUUAAUUUGC--AAAACUUUU
(.(((-((((.((((((...)))))).)))))((----------(((((((.....----------.)))))))-----))...)).).......(((((.....))))--)........ ( -31.70)
>DroEre_CAF1 66975 92 - 1
GAGCG-GGGUCGCAAAUAAAGUUUGCCGCCCCGC----------UCGAGUUCAUUC----------CAGCUCAA-----GUCGAGCCCAAUAAAAUGUAAUUAAUUUGC--AAAACUUUU
(((((-((((.((((((...)))))).)))))))----------))(((((.....----------..((((..-----...)))).........(((((.....))))--).))))).. ( -34.90)
>DroYak_CAF1 66100 108 - 1
GUGCCCGGCUCGCAAAUAAAGUUUAUCCUCCCCCUCCCCCCACUUCGAGUUCAUUC----------CAACUCAAGUCAAGUCGAGCCCAAUAAAAUGUAAUUAAUUUGC--AAAACUUUU
......(((((((......((......))............((((.(((((.....----------.)))))))))...).))))))........(((((.....))))--)........ ( -17.50)
>consensus
GUGCG_GGGCCGCAAAUAAAGUUUGCCGCCCCGC__________UUGAGUUCAUUC__________CAACUCAA_____GUCGAGCCCAAUAAAAUGUAAUUAAUUUGC__AAAACUUUU
..(((.((((.(((((.....))))).)))))))............(((((................)))))........................((((.....))))........... (-12.45 = -13.34 +   0.89)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,832,452 – 18,832,542
Length 90
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 77.24
Mean single sequence MFE -30.12
Consensus MFE -18.20
Energy contribution -19.92
Covariance contribution 1.72
Combinations/Pair 1.12
Mean z-score -3.03
Structure conservation index 0.60
SVM decision value 3.31
SVM RNA-class probability 0.998971
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18832452 90 + 22224390
GCGGGGCGGCAAACUUUAUUUGCGGCCCCGCACAAUAAGCAAGGGUUUAA-AGUUCG---AGC--------------ACUUGGCCCAGUAUUAUUAUUA--AUAAUAAGC
(((((((.(((((.....))))).))))))).......((..((((...(-(((...---...--------------)))).))))..((((((.....--)))))).)) ( -33.70)
>DroPse_CAF1 93614 103 + 1
-CGAGGCACCCGUC----UUCCAUGCCCCGCAUAAC--UCAAGGGUUUAAAAGUUCACAGAGCGAGGGGGAGGCGAUAGAGGGGGGAGUAUUAAUAAUACUAUAAUACAU
-.......(((.((----(.((.(.((((.(..(((--(....)))).....((((...))))).)))).)))....))).)))...((((((.........)))))).. ( -26.00)
>DroSec_CAF1 69302 90 + 1
GCGGGGCGGCAAACUUUAUUUGCGGCCCCGCACAAUAAGCAAGGGUUUAA-AGUUCA---AGC--------------ACUUGGCCCAGUAUUAUUAAUA--AUAAUAAGC
(((((((.(((((.....))))).))))))).......((..((((...(-(((...---...--------------)))).))))..((((((.....--)))))).)) ( -33.70)
>DroSim_CAF1 49522 90 + 1
GCGGGGCGGCAAACUUUAUUUGCGGCCCCGCACAAUAAGCAAGGGUUUAA-AGUUCA---AGC--------------ACUUGGCCUAGUAUUAUUAAUA--AUAAUAAGC
(((((((.(((((.....))))).))))))).......((..((((...(-(((...---...--------------)))).))))..((((((.....--)))))).)) ( -31.10)
>DroEre_CAF1 67034 90 + 1
GCGGGGCGGCAAACUUUAUUUGCGACCCCGCUCAAUAAGCAAGGGUUUAA-AGAUCA---AGC--------------ACUUGGCCCAGUAUUAUUAAUA--AUAAUAAGC
((((((..(((((.....)))))..)))))).......((..((((...(-((....---...--------------.))).))))..((((((.....--)))))).)) ( -26.10)
>consensus
GCGGGGCGGCAAACUUUAUUUGCGGCCCCGCACAAUAAGCAAGGGUUUAA_AGUUCA___AGC______________ACUUGGCCCAGUAUUAUUAAUA__AUAAUAAGC
(((((((.(((((.....))))).)))))))...........(((((..................................)))))........................ (-18.20 = -19.92 +   1.72)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,832,452 – 18,832,542
Length 90
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 77.24
Mean single sequence MFE -27.36
Consensus MFE -17.62
Energy contribution -18.14
Covariance contribution 0.52
Combinations/Pair 1.25
Mean z-score -2.62
Structure conservation index 0.64
SVM decision value 2.62
SVM RNA-class probability 0.995832
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18832452 90 - 22224390
GCUUAUUAU--UAAUAAUAAUACUGGGCCAAGU--------------GCU---CGAACU-UUAAACCCUUGCUUAUUGUGCGGGGCCGCAAAUAAAGUUUGCCGCCCCGC
.........--..(((((((....(((..((((--------------...---...)))-)....)))....)))))))(((((((.((((((...)))))).))))))) ( -30.10)
>DroPse_CAF1 93614 103 - 1
AUGUAUUAUAGUAUUAUUAAUACUCCCCCCUCUAUCGCCUCCCCCUCGCUCUGUGAACUUUUAAACCCUUGA--GUUAUGCGGGGCAUGGAA----GACGGGUGCCUCG-
..((((((.........))))))...(((.(((....((....((((((......(((((..........))--)))..))))))...)).)----)).))).......- ( -22.30)
>DroSec_CAF1 69302 90 - 1
GCUUAUUAU--UAUUAAUAAUACUGGGCCAAGU--------------GCU---UGAACU-UUAAACCCUUGCUUAUUGUGCGGGGCCGCAAAUAAAGUUUGCCGCCCCGC
((((((((.--...))))))....(((..((((--------------...---...)))-)....)))..)).......(((((((.((((((...)))))).))))))) ( -28.90)
>DroSim_CAF1 49522 90 - 1
GCUUAUUAU--UAUUAAUAAUACUAGGCCAAGU--------------GCU---UGAACU-UUAAACCCUUGCUUAUUGUGCGGGGCCGCAAAUAAAGUUUGCCGCCCCGC
(((((.(((--((....))))).)))))(((..--------------((.---.(....-.......)..))...))).(((((((.((((((...)))))).))))))) ( -28.40)
>DroEre_CAF1 67034 90 - 1
GCUUAUUAU--UAUUAAUAAUACUGGGCCAAGU--------------GCU---UGAUCU-UUAAACCCUUGCUUAUUGAGCGGGGUCGCAAAUAAAGUUUGCCGCCCCGC
(((((.(((--((....))))).)))))(((..--------------((.---.(....-.......)..))...))).(((((((.((((((...)))))).))))))) ( -27.10)
>consensus
GCUUAUUAU__UAUUAAUAAUACUGGGCCAAGU______________GCU___UGAACU_UUAAACCCUUGCUUAUUGUGCGGGGCCGCAAAUAAAGUUUGCCGCCCCGC
(((((.(((..........))).)))))...................................................(((((((.(((((.....))))).))))))) (-17.62 = -18.14 +   0.52)

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 12:42:08 2006