Locus 6728

Sequence ID 2L_DroMel_CAF1
Location 18,800,918 – 18,801,115
Length 197
Max. P 0.999570
window10742 window10743 window10744 window10745 window10746

overview

Window 2

Location 18,800,918 – 18,801,009
Length 91
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 80.92
Mean single sequence MFE -19.48
Consensus MFE -12.17
Energy contribution -12.37
Covariance contribution 0.20
Combinations/Pair 1.22
Mean z-score -2.05
Structure conservation index 0.62
SVM decision value 0.53
SVM RNA-class probability 0.772390
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18800918 91 - 22407834
UCGUGCUCCUC-------GGCAAUGUCUUCUGGCCA----CGCUGGCCAAUUUAAAAUUCAAUUUAAUUUCAAUUGAUAUUGGAAAAUCUUUUGAGCACCUG
..((((((...-------..(((((((...(((((.----....)))))..(((((......)))))........)))))))(.....)....))))))... ( -22.10)
>DroPse_CAF1 78839 91 - 1
CC--ACUCCCC---------CAAUGUCUCCUGGUCGCUGUCGCUGGCCAAUUUAAAAUUCAAUUUAAUUUCAAUUGAUAUUGGAAAAUCUUUUCAGCGCCAC
..--......(---------(((((((...(((((((....)).)))))..(((((......)))))........))))))))................... ( -17.00)
>DroEre_CAF1 64214 91 - 1
CCGUGCUCCUC-------GGCAAUGUCUUCUGGCCA----CGCUGGCCAAUUUAAAAUUCAAUUUAAUUUCAAUUGAUAUUGGAAAAUCUUUUGAGAAGCUC
....(((.(((-------(((((((((...(((((.----....)))))..(((((......)))))........)))))))(.....)..))))).))).. ( -20.20)
>DroYak_CAF1 64003 98 - 1
UCGUACUCCUCGAAGUACGGCAAUGUCUUCUGGCCA----CGCUGGCCAAUUUAAAAUUCAAUUUGAUUUCAAUUGAUAUUGGAAAAUCUUUUGAGCACCUC
.((((((......))))))((.........(((((.----....))))).........((((...(((((((((....))))))..)))..))))))..... ( -23.60)
>DroAna_CAF1 58820 92 - 1
CCUUACACCUC------CGGACAUACCCUCUGGCCA----CGGUGGCCAAUUUAGAAAUCAAUUUAAUUUCAAUUGUCAAUGAAAAAUCUUUUUACACUCUC
...........------..((((.......(((((.----....))))).....(((((.......)))))...))))........................ ( -14.30)
>DroPer_CAF1 78173 91 - 1
CC--ACUCCCC---------CAAUGUCUUCUGGCCGCUGUCGCUGGCCAAUUUAAAAUUCAAUUUAAUUUCAAUUGAUAUUGGAAAAUCUUUUCAGCGCCAC
..--......(---------(((((((...(((((((....)).)))))..(((((......)))))........))))))))................... ( -19.70)
>consensus
CCGUACUCCUC_______GGCAAUGUCUUCUGGCCA____CGCUGGCCAAUUUAAAAUUCAAUUUAAUUUCAAUUGAUAUUGGAAAAUCUUUUGAGCACCUC
....................(((((((...((((((.......))))))..(((((......)))))........))))))).................... (-12.17 = -12.37 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 18,800,940 – 18,801,048
Length 108
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 82.75
Mean single sequence MFE -21.95
Consensus MFE -14.38
Energy contribution -14.52
Covariance contribution 0.14
Combinations/Pair 1.11
Mean z-score -1.80
Structure conservation index 0.65
SVM decision value 0.03
SVM RNA-class probability 0.551044
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18800940 108 - 22407834
ACACACGCCCACUUUCGCCACAUUUUCCAGGGGUUUCCUUCGUGCUCCUC-------GGCAAUGUCUUCUGGCCA----CGCUGGCCAAUUUAAAAUUCAAUUUAAUUUCAAUUGAUAU
...................(((((.((.((((((.........)))))).-------)).)))))....(((((.----....))))).........((((((.......))))))... ( -21.40)
>DroSec_CAF1 63448 108 - 1
ACACACGCCCACUUUCGCCACAUUUUCCAGGGGUUUCCUUCUUGCUCCUC-------GGCAAUGUCUUCUGGCCA----CGCUGGCCAAUUUAAAAUUCAAUUUAAUUUCAAUUGAUUU
...................(((((.((.((((((.........)))))).-------)).)))))....(((((.----....))))).........((((((.......))))))... ( -21.40)
>DroSim_CAF1 64075 108 - 1
ACACACGCCCACUUUGGCCACAUUUUCCAGGGGUUUCCUUCUUGCUCCUC-------GGCAAUGUCUUCUGGCCA----CGCUGGCCAAUUUAAAAUUCAAUUUAAUUUCAAUUGAUAU
......(((.....((((((((((.((.((((((.........)))))).-------)).))))).....)))))----....)))...........((((((.......))))))... ( -24.60)
>DroEre_CAF1 64236 108 - 1
ACACACGCCCAUGUUUUCCACAUUUUCCAGGGGUUUCCUCCGUGCUCCUC-------GGCAAUGUCUUCUGGCCA----CGCUGGCCAAUUUAAAAUUCAAUUUAAUUUCAAUUGAUAU
......(((.((((.....)))).....((((((.........)))))).-------))).........(((((.----....))))).........((((((.......))))))... ( -21.40)
>DroYak_CAF1 64025 115 - 1
ACACACGCCCAUUAUCCCGACAUUUUCCAGGGGUUUCCUUCGUACUCCUCGAAGUACGGCAAUGUCUUCUGGCCA----CGCUGGCCAAUUUAAAAUUCAAUUUGAUUUCAAUUGAUAU
......(((....(((((...........))))).......(((((......)))))))).........(((((.----....))))).........((((((.(....)))))))... ( -25.90)
>DroPer_CAF1 78195 88 - 1
--------------------CAGAAGCCAAGUGUUACCCCC--ACUCCCC---------CAAUGUCUUCUGGCCGCUGUCGCUGGCCAAUUUAAAAUUCAAUUUAAUUUCAAUUGAUAU
--------------------.(((((.((((((.......)--)))....---------...)).)))))((((((....)).))))..........((((((.......))))))... ( -17.01)
>consensus
ACACACGCCCACUUUCGCCACAUUUUCCAGGGGUUUCCUUCGUGCUCCUC_______GGCAAUGUCUUCUGGCCA____CGCUGGCCAAUUUAAAAUUCAAUUUAAUUUCAAUUGAUAU
............................((((((.........))))))....................((((((.......)))))).........((((((.......))))))... (-14.38 = -14.52 +   0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 18,800,980 – 18,801,087
Length 107
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 92.17
Mean single sequence MFE -29.14
Consensus MFE -22.75
Energy contribution -22.99
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.64
Structure conservation index 0.78
SVM decision value 0.31
SVM RNA-class probability 0.683913
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18800980 107 - 22407834
ACAAGUGUGGCCAACUUCGGGCCACGCCCAUAUUAGCCCACACACGCCCACUUUCGCCACAUUUUCCAGGGGUUUCCUUCGUGCUCCUC-------GGCAAUGUCUUCUGGCCA
....((((((........((((...))))........))))))............((((((((.((.((((((.........)))))).-------)).))))).....))).. ( -29.29)
>DroSec_CAF1 63488 107 - 1
ACAAGUGUGGCCAACUUCGAGCCACGCCCAUAUUAGCCCACACACGCCCACUUUCGCCACAUUUUCCAGGGGUUUCCUUCUUGCUCCUC-------GGCAAUGUCUUCUGGCCA
....((((((((......).)))))))........(((.......((........)).(((((.((.((((((.........)))))).-------)).))))).....))).. ( -26.00)
>DroSim_CAF1 64115 107 - 1
ACAAGUGUGGCCAACUUCGAGCCACGCCCAUAUUAGCCCACACACGCCCACUUUGGCCACAUUUUCCAGGGGUUUCCUUCUUGCUCCUC-------GGCAAUGUCUUCUGGCCA
....((((((((......).)))))))..........................((((((((((.((.((((((.........)))))).-------)).))))).....))))) ( -29.70)
>DroEre_CAF1 64276 107 - 1
ACAAGUGUGGCCAACUUCGGGCCACGCCCAUAUCAGCCCACACACGCCCAUGUUUUCCACAUUUUCCAGGGGUUUCCUCCGUGCUCCUC-------GGCAAUGUCUUCUGGCCA
....((((((((.......))))))))........(((...(((.(((.((((.....)))).....((((((.........)))))).-------)))..))).....))).. ( -28.40)
>DroYak_CAF1 64065 114 - 1
ACAAGUGUGGCCAACUUCGGGCCACGCCCAUAUCAGCCCACACACGCCCAUUAUCCCGACAUUUUCCAGGGGUUUCCUUCGUACUCCUCGAAGUACGGCAAUGUCUUCUGGCCA
....((((((((.......))))))))........(((...(((.(((....(((((...........))))).......(((((......))))))))..))).....))).. ( -32.30)
>consensus
ACAAGUGUGGCCAACUUCGGGCCACGCCCAUAUUAGCCCACACACGCCCACUUUCGCCACAUUUUCCAGGGGUUUCCUUCGUGCUCCUC_______GGCAAUGUCUUCUGGCCA
....((((((((.......))))))))........(((...(((.(((...................((((((.........))))))........)))..))).....))).. (-22.75 = -22.99 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 18,801,009 – 18,801,115
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 95.47
Mean single sequence MFE -36.52
Consensus MFE -33.46
Energy contribution -32.74
Covariance contribution -0.72
Combinations/Pair 1.11
Mean z-score -1.90
Structure conservation index 0.92
SVM decision value 2.59
SVM RNA-class probability 0.995587
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18801009 106 + 22407834
AGGAAACCCCUGGAAAAUGUGGCGAAAGUGGGCGUGUGUGGGCUAAUAUGGGCGUGGCCCGAAGUUGGCCACACUUGUUUGUGACAGCCCAAGAGGGCAAUAAAGA
.(....)((((..........((....))((((..((((((.(((((.(((((...)))))..))))))))))).((((...))))))))...))))......... ( -37.70)
>DroSec_CAF1 63517 106 + 1
AGGAAACCCCUGGAAAAUGUGGCGAAAGUGGGCGUGUGUGGGCUAAUAUGGGCGUGGCUCGAAGUUGGCCACACUUGUUUGUGACAGCCCAAGAGGGCAAUAAAGC
.(....)((((..........((....))((((..((((((.(((((.(((((...)))))..))))))))))).((((...))))))))...))))......... ( -34.70)
>DroSim_CAF1 64144 106 + 1
AGGAAACCCCUGGAAAAUGUGGCCAAAGUGGGCGUGUGUGGGCUAAUAUGGGCGUGGCUCGAAGUUGGCCACACUUGUUUGUGACAGCCCAAGAGGGCAAUAAAGC
(((.....)))......(((.(((....(((((..((((((.(((((.(((((...)))))..))))))))))).((((...)))))))))....))).))).... ( -35.50)
>DroEre_CAF1 64305 106 + 1
AGGAAACCCCUGGAAAAUGUGGAAAACAUGGGCGUGUGUGGGCUGAUAUGGGCGUGGCCCGAAGUUGGCCACACUUGUUUGUGACAGCCCAAGAGGGCAAUAAAGC
(((.....)))...............(((..(((.((((((.(..((.(((((...)))))..))..))))))).)))..)))...((((....))))........ ( -37.00)
>DroYak_CAF1 64101 106 + 1
AGGAAACCCCUGGAAAAUGUCGGGAUAAUGGGCGUGUGUGGGCUGAUAUGGGCGUGGCCCGAAGUUGGCCACACUUGUUUGUGACAGCCCAAGAGGGCAAUAAAGC
.(....).(((((......)))))...((..(((.((((((.(..((.(((((...)))))..))..))))))).)))..))....((((....))))........ ( -37.70)
>consensus
AGGAAACCCCUGGAAAAUGUGGCGAAAGUGGGCGUGUGUGGGCUAAUAUGGGCGUGGCCCGAAGUUGGCCACACUUGUUUGUGACAGCCCAAGAGGGCAAUAAAGC
(((.....)))................(..((((.((((((.(((((.(((((...)))))..))))))))))).))))..)....((((....))))........ (-33.46 = -32.74 +  -0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 18,801,009 – 18,801,115
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 95.47
Mean single sequence MFE -30.23
Consensus MFE -27.33
Energy contribution -27.89
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.51
Structure conservation index 0.90
SVM decision value 3.73
SVM RNA-class probability 0.999570
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18801009 106 - 22407834
UCUUUAUUGCCCUCUUGGGCUGUCACAAACAAGUGUGGCCAACUUCGGGCCACGCCCAUAUUAGCCCACACACGCCCACUUUCGCCACAUUUUCCAGGGGUUUCCU
........(((((..(((((((..........((((((((.......))))))))......))))))).....((........))...........)))))..... ( -30.19)
>DroSec_CAF1 63517 106 - 1
GCUUUAUUGCCCUCUUGGGCUGUCACAAACAAGUGUGGCCAACUUCGAGCCACGCCCAUAUUAGCCCACACACGCCCACUUUCGCCACAUUUUCCAGGGGUUUCCU
........(((((..(((((((..........((((((((......).)))))))......))))))).....((........))...........)))))..... ( -26.99)
>DroSim_CAF1 64144 106 - 1
GCUUUAUUGCCCUCUUGGGCUGUCACAAACAAGUGUGGCCAACUUCGAGCCACGCCCAUAUUAGCCCACACACGCCCACUUUGGCCACAUUUUCCAGGGGUUUCCU
........(((((..(((((((..........((((((((......).)))))))......))))))).....(((......)))...........)))))..... ( -30.39)
>DroEre_CAF1 64305 106 - 1
GCUUUAUUGCCCUCUUGGGCUGUCACAAACAAGUGUGGCCAACUUCGGGCCACGCCCAUAUCAGCCCACACACGCCCAUGUUUUCCACAUUUUCCAGGGGUUUCCU
........(((((..(((((((..........((((((((.......))))))))......))))))).........((((.....))))......)))))..... ( -31.99)
>DroYak_CAF1 64101 106 - 1
GCUUUAUUGCCCUCUUGGGCUGUCACAAACAAGUGUGGCCAACUUCGGGCCACGCCCAUAUCAGCCCACACACGCCCAUUAUCCCGACAUUUUCCAGGGGUUUCCU
((......)).....(((((((..........((((((((.......))))))))......)))))))............(((((...........)))))..... ( -31.59)
>consensus
GCUUUAUUGCCCUCUUGGGCUGUCACAAACAAGUGUGGCCAACUUCGGGCCACGCCCAUAUUAGCCCACACACGCCCACUUUCGCCACAUUUUCCAGGGGUUUCCU
........(((((..(((((((..........((((((((.......))))))))......))))))).....((........))...........)))))..... (-27.33 = -27.89 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:35 2006