Locus 8164

Sequence ID 3L_DroMel_CAF1
Location 21,511,418 – 21,511,738
Length 320
Max. P 0.992552
window13337 window13338 window13339 window13340 window13341 window13342 window13343 window13344 window13345

overview

Window 7

Location 21,511,418 – 21,511,538
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -51.57
Consensus MFE -50.45
Energy contribution -50.23
Covariance contribution -0.22
Combinations/Pair 1.02
Mean z-score -2.47
Structure conservation index 0.98
SVM decision value 1.54
SVM RNA-class probability 0.962130
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21511418 120 + 23771897
ACGGACCACCCCGAAAUUGACUGGAGUGCGAUGCGUGCCGAGUGGUUGCAGUUCGAAUUUGUAAUUACAAUUCGUGGCGCCUUGCCGGGGAAGUUCUGCUGGGGGAGCCCCCAGCACUGG
..((((..(((((......((....))((((.((((..(((((((((((((.......))))))))))...)))..)))).)))))))))..))))((((((((....)))))))).... ( -52.00)
>DroSec_CAF1 16488 120 + 1
ACGGACCACCCCGAAAUUGACUGGAGUGCGAUGCGUGCCAAGUGGUUGCAGUUCGAAUUUGUAAUUACAAUUCGUGGCGCCUUGCCGGGGAAGUUCUGCUGGGGGAACCCCCAGCACUGG
..((((..(((((......((....))((((.(.((((((.((((((((((.......))))))))))......))))))))))))))))..))))((((((((....)))))))).... ( -50.70)
>DroSim_CAF1 16115 120 + 1
ACGGACCACCCCGAAAUUGACUGGAGUGCGAUGCGUGCCGAGUGGUUGCAGUUCGAAUUUGUAAUUACAAUUCGUGGCGCCUUGCCGGGGAAGUUCUGCUGGGGGAACCCCCAGCACUGG
..((((..(((((......((....))((((.((((..(((((((((((((.......))))))))))...)))..)))).)))))))))..))))((((((((....)))))))).... ( -52.00)
>consensus
ACGGACCACCCCGAAAUUGACUGGAGUGCGAUGCGUGCCGAGUGGUUGCAGUUCGAAUUUGUAAUUACAAUUCGUGGCGCCUUGCCGGGGAAGUUCUGCUGGGGGAACCCCCAGCACUGG
..((((..(((((......((....))((((.(.((((((.((((((((((.......))))))))))......))))))))))))))))..))))((((((((....)))))))).... (-50.45 = -50.23 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 21,511,418 – 21,511,538
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -41.00
Consensus MFE -40.80
Energy contribution -40.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 1.00
SVM decision value 0.18
SVM RNA-class probability 0.622964
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21511418 120 - 23771897
CCAGUGCUGGGGGCUCCCCCAGCAGAACUUCCCCGGCAAGGCGCCACGAAUUGUAAUUACAAAUUCGAACUGCAACCACUCGGCACGCAUCGCACUCCAGUCAAUUUCGGGGUGGUCCGU
....((((((((....))))))))(.(((.((((((...((((((.((((((((....)).))))))...((....))...)))..((...))......)))....)))))).))).).. ( -40.90)
>DroSec_CAF1 16488 120 - 1
CCAGUGCUGGGGGUUCCCCCAGCAGAACUUCCCCGGCAAGGCGCCACGAAUUGUAAUUACAAAUUCGAACUGCAACCACUUGGCACGCAUCGCACUCCAGUCAAUUUCGGGGUGGUCCGU
....((((((((....))))))))(.(((.((((((...(((((((((((((((....)).))))))...((....))..))))..((...))......)))....)))))).))).).. ( -41.20)
>DroSim_CAF1 16115 120 - 1
CCAGUGCUGGGGGUUCCCCCAGCAGAACUUCCCCGGCAAGGCGCCACGAAUUGUAAUUACAAAUUCGAACUGCAACCACUCGGCACGCAUCGCACUCCAGUCAAUUUCGGGGUGGUCCGU
....((((((((....))))))))(.(((.((((((...((((((.((((((((....)).))))))...((....))...)))..((...))......)))....)))))).))).).. ( -40.90)
>consensus
CCAGUGCUGGGGGUUCCCCCAGCAGAACUUCCCCGGCAAGGCGCCACGAAUUGUAAUUACAAAUUCGAACUGCAACCACUCGGCACGCAUCGCACUCCAGUCAAUUUCGGGGUGGUCCGU
....((((((((....))))))))(.(((.((((((...((((((.((((((((....)).))))))...((....))...)))..((...))......)))....)))))).))).).. (-40.80 = -40.80 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 21,511,458 – 21,511,578
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -54.23
Consensus MFE -54.45
Energy contribution -54.23
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -4.48
Structure conservation index 1.00
SVM decision value 1.99
SVM RNA-class probability 0.984925
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21511458 120 + 23771897
AGUGGUUGCAGUUCGAAUUUGUAAUUACAAUUCGUGGCGCCUUGCCGGGGAAGUUCUGCUGGGGGAGCCCCCAGCACUGGCUGAAAACAAUUUUCUCCAGGUUUUCUCCGUGGUAAGGGC
.((((((((((.......))))))))))........((.((((((((.(((.....((((((((....))))))))((((..((((.....)))).))))......))).)))))))))) ( -52.90)
>DroSec_CAF1 16528 120 + 1
AGUGGUUGCAGUUCGAAUUUGUAAUUACAAUUCGUGGCGCCUUGCCGGGGAAGUUCUGCUGGGGGAACCCCCAGCACUGGCUGAAAACAAUUUUCUCCAGGUUUUCUCCGUGGCAAGGGC
.((((((((((.......))))))))))........((.((((((((.(((.....((((((((....))))))))((((..((((.....)))).))))......))).)))))))))) ( -54.90)
>DroSim_CAF1 16155 120 + 1
AGUGGUUGCAGUUCGAAUUUGUAAUUACAAUUCGUGGCGCCUUGCCGGGGAAGUUCUGCUGGGGGAACCCCCAGCACUGGCUGAAAACAAUUUUCUCCAGGUUUUCUCCGUGGCAAGGGC
.((((((((((.......))))))))))........((.((((((((.(((.....((((((((....))))))))((((..((((.....)))).))))......))).)))))))))) ( -54.90)
>consensus
AGUGGUUGCAGUUCGAAUUUGUAAUUACAAUUCGUGGCGCCUUGCCGGGGAAGUUCUGCUGGGGGAACCCCCAGCACUGGCUGAAAACAAUUUUCUCCAGGUUUUCUCCGUGGCAAGGGC
.((((((((((.......))))))))))........((.((((((((.(((.....((((((((....))))))))((((..((((.....)))).))))......))).)))))))))) (-54.45 = -54.23 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 21,511,458 – 21,511,578
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -44.20
Consensus MFE -44.23
Energy contribution -44.57
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.65
Structure conservation index 1.00
SVM decision value 2.34
SVM RNA-class probability 0.992552
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21511458 120 - 23771897
GCCCUUACCACGGAGAAAACCUGGAGAAAAUUGUUUUCAGCCAGUGCUGGGGGCUCCCCCAGCAGAACUUCCCCGGCAAGGCGCCACGAAUUGUAAUUACAAAUUCGAACUGCAACCACU
((((((.((..((((.....((((.((((.....))))..))))((((((((....))))))))....))))..)).)))).))..((((((((....)).))))))............. ( -39.80)
>DroSec_CAF1 16528 120 - 1
GCCCUUGCCACGGAGAAAACCUGGAGAAAAUUGUUUUCAGCCAGUGCUGGGGGUUCCCCCAGCAGAACUUCCCCGGCAAGGCGCCACGAAUUGUAAUUACAAAUUCGAACUGCAACCACU
(((((((((..((((.....((((.((((.....))))..))))((((((((....))))))))....))))..))))))).))..((((((((....)).))))))............. ( -46.40)
>DroSim_CAF1 16155 120 - 1
GCCCUUGCCACGGAGAAAACCUGGAGAAAAUUGUUUUCAGCCAGUGCUGGGGGUUCCCCCAGCAGAACUUCCCCGGCAAGGCGCCACGAAUUGUAAUUACAAAUUCGAACUGCAACCACU
(((((((((..((((.....((((.((((.....))))..))))((((((((....))))))))....))))..))))))).))..((((((((....)).))))))............. ( -46.40)
>consensus
GCCCUUGCCACGGAGAAAACCUGGAGAAAAUUGUUUUCAGCCAGUGCUGGGGGUUCCCCCAGCAGAACUUCCCCGGCAAGGCGCCACGAAUUGUAAUUACAAAUUCGAACUGCAACCACU
(((((((((..((((.....((((.((((.....))))..))))((((((((....))))))))....))))..))))))).))..((((((((....)).))))))............. (-44.23 = -44.57 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 21,511,498 – 21,511,618
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -47.47
Consensus MFE -46.94
Energy contribution -46.50
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -2.64
Structure conservation index 0.99
SVM decision value 1.84
SVM RNA-class probability 0.979633
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21511498 120 + 23771897
CUUGCCGGGGAAGUUCUGCUGGGGGAGCCCCCAGCACUGGCUGAAAACAAUUUUCUCCAGGUUUUCUCCGUGGUAAGGGCGGCGAGGGCUACGUGACAAUUUGCCAAUACCCAAAUUUCU
.((((((.(((.....((((((((....))))))))((((..((((.....)))).))))......))).))))))(((.((((((..(.....)....))))))....)))........ ( -45.80)
>DroSec_CAF1 16568 120 + 1
CUUGCCGGGGAAGUUCUGCUGGGGGAACCCCCAGCACUGGCUGAAAACAAUUUUCUCCAGGUUUUCUCCGUGGCAAGGGCGGCGAGGGUUACGUGACAAUUUGCCAAUACCCAAAUUUCU
.((((((.(((.....((((((((....))))))))((((..((((.....)))).))))......))).))))))(((.((((((.(((....)))..))))))....)))........ ( -48.80)
>DroSim_CAF1 16195 120 + 1
CUUGCCGGGGAAGUUCUGCUGGGGGAACCCCCAGCACUGGCUGAAAACAAUUUUCUCCAGGUUUUCUCCGUGGCAAGGGCGGCGAGGGCUACGUGACAAUUUGCCAAUACCCAAAUUUCU
.((((((.(((.....((((((((....))))))))((((..((((.....)))).))))......))).))))))(((.((((((..(.....)....))))))....)))........ ( -47.80)
>consensus
CUUGCCGGGGAAGUUCUGCUGGGGGAACCCCCAGCACUGGCUGAAAACAAUUUUCUCCAGGUUUUCUCCGUGGCAAGGGCGGCGAGGGCUACGUGACAAUUUGCCAAUACCCAAAUUUCU
.((((((.(((.....((((((((....))))))))((((..((((.....)))).))))......))).))))))(((.((((((..(.....)....))))))....)))........ (-46.94 = -46.50 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 21,511,498 – 21,511,618
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -41.70
Consensus MFE -41.15
Energy contribution -41.27
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.69
Structure conservation index 0.99
SVM decision value 0.50
SVM RNA-class probability 0.761692
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21511498 120 - 23771897
AGAAAUUUGGGUAUUGGCAAAUUGUCACGUAGCCCUCGCCGCCCUUACCACGGAGAAAACCUGGAGAAAAUUGUUUUCAGCCAGUGCUGGGGGCUCCCCCAGCAGAACUUCCCCGGCAAG
........((((..((((.....))))....))))..((((..........((.(((...((((.((((.....))))..))))((((((((....))))))))....)))))))))... ( -38.90)
>DroSec_CAF1 16568 120 - 1
AGAAAUUUGGGUAUUGGCAAAUUGUCACGUAACCCUCGCCGCCCUUGCCACGGAGAAAACCUGGAGAAAAUUGUUUUCAGCCAGUGCUGGGGGUUCCCCCAGCAGAACUUCCCCGGCAAG
........((((((((((.....)))).)).))))........((((((..((((.....((((.((((.....))))..))))((((((((....))))))))....))))..)))))) ( -43.00)
>DroSim_CAF1 16195 120 - 1
AGAAAUUUGGGUAUUGGCAAAUUGUCACGUAGCCCUCGCCGCCCUUGCCACGGAGAAAACCUGGAGAAAAUUGUUUUCAGCCAGUGCUGGGGGUUCCCCCAGCAGAACUUCCCCGGCAAG
........((((..((((.....))))....))))........((((((..((((.....((((.((((.....))))..))))((((((((....))))))))....))))..)))))) ( -43.20)
>consensus
AGAAAUUUGGGUAUUGGCAAAUUGUCACGUAGCCCUCGCCGCCCUUGCCACGGAGAAAACCUGGAGAAAAUUGUUUUCAGCCAGUGCUGGGGGUUCCCCCAGCAGAACUUCCCCGGCAAG
........((((..((((.....))))....))))........((((((..((((.....((((.((((.....))))..))))((((((((....))))))))....))))..)))))) (-41.15 = -41.27 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 21,511,578 – 21,511,698
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -44.23
Consensus MFE -43.11
Energy contribution -43.00
Covariance contribution -0.11
Combinations/Pair 1.05
Mean z-score -2.42
Structure conservation index 0.97
SVM decision value 1.47
SVM RNA-class probability 0.956736
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21511578 120 + 23771897
GGCGAGGGCUACGUGACAAUUUGCCAAUACCCAAAUUUCUCCGUGGACCAGGAACGCCUUCUCCGAUGGCGUAAAAAACGAAUAGCCCGUGGGCUUGUUUUUUACCCACGAGGCGAGCCA
(((..((.(((((.((.((((((........))))))..))))))).)).....(((((....((.(((.((((((((((...((((....)))))))))))))))))))))))).))). ( -45.60)
>DroSec_CAF1 16648 120 + 1
GGCGAGGGUUACGUGACAAUUUGCCAAUACCCAAAUUUCUCCGUGGACCAGGAACGCCUCCUCCGAUGGCGUAAAAAACGAAUAGCCCGUGGGCUUGUUUUUUACCCACGAGGCGAGCCA
(((...(((((((.((.((((((........))))))..))))).)))).....((((((....(.(((.((((((((((...((((....)))))))))))))))))))))))).))). ( -43.90)
>DroSim_CAF1 16275 120 + 1
GGCGAGGGCUACGUGACAAUUUGCCAAUACCCAAAUUUCUCCGUGGACCAGGAACGCCUCCUCCGAUGGCGUAAAAAACGAAUAGCCCGUGGGCUUGUUUUUUACCGACGAGGCGAGCCA
(((..((.(((((.((.((((((........))))))..))))))).)).....((((((.((.....(.((((((((((...((((....))))))))))))))))).)))))).))). ( -43.20)
>consensus
GGCGAGGGCUACGUGACAAUUUGCCAAUACCCAAAUUUCUCCGUGGACCAGGAACGCCUCCUCCGAUGGCGUAAAAAACGAAUAGCCCGUGGGCUUGUUUUUUACCCACGAGGCGAGCCA
(((..((.(((((.((.((((((........))))))..))))))).)).....((((((....(.(((.((((((((((...((((....)))))))))))))))))))))))).))). (-43.11 = -43.00 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 21,511,618 – 21,511,738
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -39.87
Consensus MFE -38.55
Energy contribution -38.67
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.57
Structure conservation index 0.97
SVM decision value 0.18
SVM RNA-class probability 0.620663
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21511618 120 + 23771897
CCGUGGACCAGGAACGCCUUCUCCGAUGGCGUAAAAAACGAAUAGCCCGUGGGCUUGUUUUUUACCCACGAGGCGAGCCAACAUGUGGUAACCCAUAAUUUACGCCUAGGGAUGUUAUGA
((.(((....((..(((((....((.(((.((((((((((...((((....))))))))))))))))))))))))..))....(((((....)))))........))).))......... ( -40.50)
>DroSec_CAF1 16688 120 + 1
CCGUGGACCAGGAACGCCUCCUCCGAUGGCGUAAAAAACGAAUAGCCCGUGGGCUUGUUUUUUACCCACGAGGCGAGCCAACAUGUGGUAACCCAUAAUUUACGCCUAGGGAUGUUAUGA
((.(((....((..((((((....(.(((.((((((((((...((((....))))))))))))))))))))))))..))....(((((....)))))........))).))......... ( -41.00)
>DroSim_CAF1 16315 120 + 1
CCGUGGACCAGGAACGCCUCCUCCGAUGGCGUAAAAAACGAAUAGCCCGUGGGCUUGUUUUUUACCGACGAGGCGAGCCAACAUGUGGUAACCCAUAAUUUACGCCUAGGGAUGUUAUGA
((.(((....((..((((((.((.....(.((((((((((...((((....))))))))))))))))).))))))..))....(((((....)))))........))).))......... ( -38.10)
>consensus
CCGUGGACCAGGAACGCCUCCUCCGAUGGCGUAAAAAACGAAUAGCCCGUGGGCUUGUUUUUUACCCACGAGGCGAGCCAACAUGUGGUAACCCAUAAUUUACGCCUAGGGAUGUUAUGA
((.(((....((..((((((....(.(((.((((((((((...((((....))))))))))))))))))))))))..))....(((((....)))))........))).))......... (-38.55 = -38.67 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 21,511,618 – 21,511,738
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -40.70
Consensus MFE -40.50
Energy contribution -40.83
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 1.00
SVM decision value 0.65
SVM RNA-class probability 0.811192
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21511618 120 - 23771897
UCAUAACAUCCCUAGGCGUAAAUUAUGGGUUACCACAUGUUGGCUCGCCUCGUGGGUAAAAAACAAGCCCACGGGCUAUUCGUUUUUUACGCCAUCGGAGAAGGCGUUCCUGGUCCACGG
..........((..((((((((..((((((..(((.....)))...(((.(((((((.........)))))))))).))))))..))))))))...(((..(((....)))..)))..)) ( -42.90)
>DroSec_CAF1 16688 120 - 1
UCAUAACAUCCCUAGGCGUAAAUUAUGGGUUACCACAUGUUGGCUCGCCUCGUGGGUAAAAAACAAGCCCACGGGCUAUUCGUUUUUUACGCCAUCGGAGGAGGCGUUCCUGGUCCACGG
..........((..((((((((..((((((..(((.....)))...(((.(((((((.........)))))))))).))))))..))))))))...(((..(((....)))..)))..)) ( -42.50)
>DroSim_CAF1 16315 120 - 1
UCAUAACAUCCCUAGGCGUAAAUUAUGGGUUACCACAUGUUGGCUCGCCUCGUCGGUAAAAAACAAGCCCACGGGCUAUUCGUUUUUUACGCCAUCGGAGGAGGCGUUCCUGGUCCACGG
..........((..((((((((..((((((((((..(((..((....)).))).)))))......((((....)))).)))))..))))))))...(((..(((....)))..)))..)) ( -36.70)
>consensus
UCAUAACAUCCCUAGGCGUAAAUUAUGGGUUACCACAUGUUGGCUCGCCUCGUGGGUAAAAAACAAGCCCACGGGCUAUUCGUUUUUUACGCCAUCGGAGGAGGCGUUCCUGGUCCACGG
..........((..((((((((..((((((..(((.....)))...(((.(((((((.........)))))))))).))))))..))))))))...(((..(((....)))..)))..)) (-40.50 = -40.83 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:07 2006