Locus 8079

Sequence ID 3L_DroMel_CAF1
Location 21,269,785 – 21,270,145
Length 360
Max. P 0.906951
window13200 window13201 window13202 window13203 window13204 window13205

overview

Window 0

Location 21,269,785 – 21,269,905
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -42.16
Consensus MFE -40.01
Energy contribution -39.38
Covariance contribution -0.62
Combinations/Pair 1.09
Mean z-score -1.65
Structure conservation index 0.95
SVM decision value 0.56
SVM RNA-class probability 0.782852
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21269785 120 + 23771897
CAGGGAAUACCCACUCCGGUAGUAGCCCUCAUGGAUCUGGAGUCAAUCAAUCCCAAGCGUCGUCCUGCUGCCAAGCAGGCGGCUCAGAAGGUCAUAUCUAAGCUGUUGCCCGAGGAGAAG
..(((....))).(((((((((((((.......((((((((.........)))...(.((((.((((((....)))))))))).)...)))))........)))))))))...))))... ( -41.66)
>DroSec_CAF1 28062 120 + 1
CAGGGAAUACCCACUCCGGUGGUAGCCCUCAUGGAUCUGGAGUCAAUCAAUCCCAAGCGGCGUCCUGCUACCAAGCAGGCGGCUCAGAAGAUCAUAUCCAAGCUGUUACCCGAGGAGAAG
..(((....))).(((((((..((((.......(((((.(((((........((....)).(.((((((....))))))))))))...)))))........))))..)))...))))... ( -43.16)
>DroSim_CAF1 30318 120 + 1
CAGGGAAUACCCACUCCGGUGGUAGCCCUCAUGGAUCUGGAGUCAAUCAAUCCCAAGCGGCGUCCUGCUACCAAGCAGGCGGCUCAGAAGAUCAUAUCCAAGCUGUUACCCGAGGAGAAG
..(((....))).(((((((..((((.......(((((.(((((........((....)).(.((((((....))))))))))))...)))))........))))..)))...))))... ( -43.16)
>DroEre_CAF1 29237 120 + 1
CAGGGAAUACCCACUCCGGUGGUAGCCCUCAUGGAUCUGGAGUCAAUCAAUCCCAAGCGUCGUUCUGCUGCCAAGCAGGCGGCUCAAAAGAUCAUCUCAAAGCUGUUGCCCGAGGAGAAG
..(((....))).(((((((..((((.......(((((.(((((...........((((......))))(((.....))))))))...)))))........))))..)))...))))... ( -40.66)
>consensus
CAGGGAAUACCCACUCCGGUGGUAGCCCUCAUGGAUCUGGAGUCAAUCAAUCCCAAGCGGCGUCCUGCUACCAAGCAGGCGGCUCAGAAGAUCAUAUCCAAGCUGUUACCCGAGGAGAAG
..(((....))).(((((((..((((.......(((((.(((((.........(....)..(.((((((....))))))))))))...)))))........))))..)))...))))... (-40.01 = -39.38 +  -0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 21,269,825 – 21,269,945
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.75
Mean single sequence MFE -40.45
Consensus MFE -37.38
Energy contribution -37.38
Covariance contribution 0.00
Combinations/Pair 1.15
Mean z-score -1.64
Structure conservation index 0.92
SVM decision value 0.65
SVM RNA-class probability 0.812404
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21269825 120 - 23771897
UAACAUUCAAGGCCUCGCUAGCGGUGUCCAAUUGCAUGAUCUUCUCCUCGGGCAACAGCUUAGAUAUGACCUUCUGAGCCGCCUGCUUGGCAGCAGGACGACGCUUGGGAUUGAUUGACU
...((.((((..(((....((((.(((((..((((..((.....))..((((((.(.(((((((........))))))).)..))))))))))..))))).)))).))).)))).))... ( -39.30)
>DroSec_CAF1 28102 120 - 1
UCACAUUCAAGCCUUCGCUAGCGGUGUCCAAUUGCAUGAUCUUCUCCUCGGGUAACAGCUUGGAUAUGAUCUUCUGAGCCGCCUGCUUGGUAGCAGGACGCCGCUUGGGAUUGAUUGACU
...((.((((.(((.....((((((((((........((((...(((...(((....))).)))...))))......((..((.....))..)).)))))))))).))).)))).))... ( -43.00)
>DroSim_CAF1 30358 120 - 1
UCACAUUCAAGCCUUCGCUAGCGGUGUCCAAUUGCAUGAUCUUCUCCUCGGGUAACAGCUUGGAUAUGAUCUUCUGAGCCGCCUGCUUGGUAGCAGGACGCCGCUUGGGAUUGAUUGACU
...((.((((.(((.....((((((((((........((((...(((...(((....))).)))...))))......((..((.....))..)).)))))))))).))).)))).))... ( -43.00)
>DroEre_CAF1 29277 120 - 1
UCACAUUUAAACCCUCGCUAGCGGUGUCCAAUUGCAUGAUCUUCUCCUCGGGCAACAGCUUUGAGAUGAUCUUUUGAGCCGCCUGCUUGGCAGCAGAACGACGCUUGGGAUUGAUUGACU
...((.((((.(((..((..(((((...(((......((((.((((...((((....)))).)))).))))..))).)))))(((((....)))))......))..))).)))).))... ( -36.50)
>consensus
UCACAUUCAAGCCCUCGCUAGCGGUGUCCAAUUGCAUGAUCUUCUCCUCGGGCAACAGCUUGGAUAUGAUCUUCUGAGCCGCCUGCUUGGCAGCAGGACGACGCUUGGGAUUGAUUGACU
...((.((((.(((.....((((((((((..((((..((.....))..((((((.(.(((((((........))))))).)..))))))))))..)))))))))).))).)))).))... (-37.38 = -37.38 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 21,269,945 – 21,270,065
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.61
Mean single sequence MFE -43.44
Consensus MFE -38.67
Energy contribution -38.11
Covariance contribution -0.56
Combinations/Pair 1.13
Mean z-score -1.73
Structure conservation index 0.89
SVM decision value 0.65
SVM RNA-class probability 0.812319
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21269945 120 + 23771897
UGCGGCGCAUUGGAGGCCAGAAGAAGCGCAUCCUCCAUAACGUCGCCAAUCGGCCACAUCUCUUUGGAGAUGUGGUAGAGUUUAAACCGGGCUCAGAUCCCAGCGACGAUCUGGGCACAC
.((((((...((((((...(......)....))))))...))))))...((.((((((((((....)))))))))).))...........(((((((((........))))))))).... ( -50.90)
>DroSec_CAF1 28222 120 + 1
UGCGACGCAUUGGCGGCCAGAAGAAGCGCAUCCUCCAUAACGUCGCCAAUCGGCCACAUCUCUUUGGCGAUGUGGUAGAGUUCAAACUGGGUUCAGAUUCCAGCGACGAUCUGGGCACCC
(((..(((....))).(((((.((......))........((((((.((((.((((((((.(....).)))))))).(((..(.....)..))).))))...)))))).))))))))... ( -41.10)
>DroSim_CAF1 30478 120 + 1
UGCGACGCAUUGGUGGCCAGAAGAAGCGCAUCCUCCAUAACGUCGCCAAUCGGCCACAUCUCUUUGGCGAUGUGGUAGAGUUCAAACCGGGUUCAGAUCCCAGCGACGAUCUGGGCACCC
...........((((.(((((.....(((...(((.((.((((((((((..((......))..)))))))))).)).)))........(((.......))).)))....))))).)))). ( -44.20)
>DroEre_CAF1 29397 120 + 1
UGCGACGAAUUGGCGGCCAAAAGAAGCGCAUCCUCCAUAACGUCGCCAAUCGGCCACAUCUCUUUGGCGAUGUGGUAGAGUUUAAACCAAGCUCAAAUCCCAGCGACGAUCUGGGUACCC
.((((((...(((.((...............)).)))...))))))......((((((((.(....).)))))))).((((((.....))))))....(((((.......)))))..... ( -37.56)
>consensus
UGCGACGCAUUGGCGGCCAGAAGAAGCGCAUCCUCCAUAACGUCGCCAAUCGGCCACAUCUCUUUGGCGAUGUGGUAGAGUUCAAACCGGGCUCAGAUCCCAGCGACGAUCUGGGCACCC
.((((((...(((.((...............)).)))...))))))...((.((((((((.(....).)))))))).))...........(((((((((........))))))))).... (-38.67 = -38.11 +  -0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 21,269,985 – 21,270,105
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.89
Mean single sequence MFE -41.38
Consensus MFE -36.65
Energy contribution -35.65
Covariance contribution -1.00
Combinations/Pair 1.17
Mean z-score -2.00
Structure conservation index 0.89
SVM decision value 1.05
SVM RNA-class probability 0.906951
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21269985 120 + 23771897
CGUCGCCAAUCGGCCACAUCUCUUUGGAGAUGUGGUAGAGUUUAAACCGGGCUCAGAUCCCAGCGACGAUCUGGGCACACUAGAAGUUACUGGUUUCUUACGUGGACAGUCUCUUAACGU
.(((.....((.((((((((((....)))))))))).))((..((((((((((((((((........)))))))))..((.....))..)))))))...))...)))............. ( -43.40)
>DroSec_CAF1 28262 120 + 1
CGUCGCCAAUCGGCCACAUCUCUUUGGCGAUGUGGUAGAGUUCAAACUGGGUUCAGAUUCCAGCGACGAUCUGGGCACCCUAGAAGUUACUGGUUUCUUACGUGGACAGUCUCUAAACGU
(((((((((..((......))..)))))))))...(((((......(((.((..(((..((((..((..((((((...)))))).))..))))..))).)).))).....)))))..... ( -39.70)
>DroSim_CAF1 30518 120 + 1
CGUCGCCAAUCGGCCACAUCUCUUUGGCGAUGUGGUAGAGUUCAAACCGGGUUCAGAUCCCAGCGACGAUCUGGGCACCCUAGAAGUUACUGGUUUCUUACGUGGACAGUCUCUAAACGU
(((((((((..((......))..)))))))))...(((((......(((.((..(((..((((..((..((((((...)))))).))..))))..))).)).))).....)))))..... ( -42.80)
>DroEre_CAF1 29437 120 + 1
CGUCGCCAAUCGGCCACAUCUCUUUGGCGAUGUGGUAGAGUUUAAACCAAGCUCAAAUCCCAGCGACGAUCUGGGUACCCUAGAAGUCACUGGAUUCUUACGCGGACAGUCUCUAAACGU
.(((((......((((((((.(....).)))))))).((((((.....)))))).....((((.(((..((((((...)))))).))).))))........)).)))............. ( -39.60)
>consensus
CGUCGCCAAUCGGCCACAUCUCUUUGGCGAUGUGGUAGAGUUCAAACCGGGCUCAGAUCCCAGCGACGAUCUGGGCACCCUAGAAGUUACUGGUUUCUUACGUGGACAGUCUCUAAACGU
.(((((......((((((((.(....).)))))))).((((((.....))))))(((..((((.(((..(((((.....))))).))).))))..)))...)).)))............. (-36.65 = -35.65 +  -1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 21,270,025 – 21,270,145
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.47
Mean single sequence MFE -40.83
Consensus MFE -34.16
Energy contribution -34.85
Covariance contribution 0.69
Combinations/Pair 1.09
Mean z-score -2.08
Structure conservation index 0.84
SVM decision value 0.83
SVM RNA-class probability 0.861488
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21270025 120 + 23771897
UUUAAACCGGGCUCAGAUCCCAGCGACGAUCUGGGCACACUAGAAGUUACUGGUUUCUUACGUGGACAGUCUCUUAACGUGAAUGGUUUGGUCCACAUUCCCGGCUUGGGUGAUUUCCAG
......(((((...(((..((((..((..(((((.....))))).))..))))..)))...((((((...((.((......)).))....))))))...)))))..((((.....)))). ( -39.60)
>DroSec_CAF1 28302 120 + 1
UUCAAACUGGGUUCAGAUUCCAGCGACGAUCUGGGCACCCUAGAAGUUACUGGUUUCUUACGUGGACAGUCUCUAAACGUGAAUGGUUUGGUCCACAUUCCCGGUUUGGGUGAUUUCCAG
..(((((((((...(((..((((..((..((((((...)))))).))..))))..)))...((((((.....(((........)))....))))))...)))))))))((......)).. ( -44.10)
>DroSim_CAF1 30558 120 + 1
UUCAAACCGGGUUCAGAUCCCAGCGACGAUCUGGGCACCCUAGAAGUUACUGGUUUCUUACGUGGACAGUCUCUAAACGUGAAUGGUUUGGUCCACAUUCCCGGCUUGGGUGAUUUCCAG
..(((.(((((...(((..((((..((..((((((...)))))).))..))))..)))...((((((.....(((........)))....))))))...))))).)))((......)).. ( -42.30)
>DroEre_CAF1 29477 120 + 1
UUUAAACCAAGCUCAAAUCCCAGCGACGAUCUGGGUACCCUAGAAGUCACUGGAUUCUUACGCGGACAGUCUCUAAACGUGAAUGGUUUGGUUCACAUUCCCGGCUUGGGUGAUUUCCAG
......((((((.......((((.(((..((((((...)))))).))).)))).......((.(((..((..((((((.......))))))...))..)))))))))))........... ( -37.30)
>consensus
UUCAAACCGGGCUCAGAUCCCAGCGACGAUCUGGGCACCCUAGAAGUUACUGGUUUCUUACGUGGACAGUCUCUAAACGUGAAUGGUUUGGUCCACAUUCCCGGCUUGGGUGAUUUCCAG
......(((((...(((..((((.(((..(((((.....))))).))).))))..)))...((((((.....(((........)))....))))))...)))))..((((.....)))). (-34.16 = -34.85 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 21,270,025 – 21,270,145
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.47
Mean single sequence MFE -37.45
Consensus MFE -32.66
Energy contribution -32.48
Covariance contribution -0.19
Combinations/Pair 1.15
Mean z-score -1.84
Structure conservation index 0.87
SVM decision value 0.75
SVM RNA-class probability 0.841665
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21270025 120 - 23771897
CUGGAAAUCACCCAAGCCGGGAAUGUGGACCAAACCAUUCACGUUAAGAGACUGUCCACGUAAGAAACCAGUAACUUCUAGUGUGCCCAGAUCGUCGCUGGGAUCUGAGCCCGGUUUAAA
..((.......))((((((((.((((((((.......................)))))))).(((..((((..((.(((.(.....).)))..))..))))..)))...))))))))... ( -35.40)
>DroSec_CAF1 28302 120 - 1
CUGGAAAUCACCCAAACCGGGAAUGUGGACCAAACCAUUCACGUUUAGAGACUGUCCACGUAAGAAACCAGUAACUUCUAGGGUGCCCAGAUCGUCGCUGGAAUCUGAACCCAGUUUGAA
............(((((.(((.((((((((.......................)))))))).(((..((((..((.(((.((....)))))..))..))))..)))...))).))))).. ( -34.60)
>DroSim_CAF1 30558 120 - 1
CUGGAAAUCACCCAAGCCGGGAAUGUGGACCAAACCAUUCACGUUUAGAGACUGUCCACGUAAGAAACCAGUAACUUCUAGGGUGCCCAGAUCGUCGCUGGGAUCUGAACCCGGUUUGAA
............(((((((((.((((((((.......................)))))))).(((..((((..((.(((.((....)))))..))..))))..)))...))))))))).. ( -42.70)
>DroEre_CAF1 29477 120 - 1
CUGGAAAUCACCCAAGCCGGGAAUGUGAACCAAACCAUUCACGUUUAGAGACUGUCCGCGUAAGAAUCCAGUGACUUCUAGGGUACCCAGAUCGUCGCUGGGAUUUGAGCUUGGUUUAAA
..(((..((.(((.....)))((((((((........))))))))....))...)))((...(((.(((((((((.(((.((....)))))..))))))))).)))..)).......... ( -37.10)
>consensus
CUGGAAAUCACCCAAGCCGGGAAUGUGGACCAAACCAUUCACGUUUAGAGACUGUCCACGUAAGAAACCAGUAACUUCUAGGGUGCCCAGAUCGUCGCUGGGAUCUGAACCCGGUUUAAA
..((.......))((((((((.((((((((.......................)))))))).(((..(((((.((.(((.((....)))))..)).)))))..)))...))))))))... (-32.66 = -32.48 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:05:43 2006