Locus 3825

Sequence ID X_DroMel_CAF1
Location 10,163,553 – 10,163,682
Length 129
Max. P 0.984742
window6289 window6290 window6291 window6292

overview

Window 9

Location 10,163,553 – 10,163,647
Length 94
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 75.37
Mean single sequence MFE -28.18
Consensus MFE -19.20
Energy contribution -20.64
Covariance contribution 1.44
Combinations/Pair 1.05
Mean z-score -1.60
Structure conservation index 0.68
SVM decision value 0.76
SVM RNA-class probability 0.842286
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10163553 94 + 22224390
CCUGCAAAAUUAGCGAGCGACCACUGU--CCACGUAUCGGCUGGCAGUAAAGUAGCCAACGGAUGCUGCAGCUGCAUCUGCAGUCACCUGCAGCAG
.((((.......((.(((....((((.--(((.((....)))))))))...(((((........))))).)))))...(((((....))))))))) ( -30.90)
>DroSec_CAF1 9591 96 + 1
CGUGCAAAAUUAGCGAGCAACCACUGUCCCCACGUAUCGGCUGGCAGUAAAGUAGCCAACGGAUGCUGCAGCUGCAUCUGCAGUCACCUGCAGCAG
(((((.......))(.((.((.((((((.((.......))..))))))...)).))).)))..((((((((((((....))))....)))))))). ( -30.30)
>DroSim_CAF1 11996 96 + 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGUAAAGUAGCCAACGGAUGCUGCAGCUGCAUCUGCAGUCACCUGCAGCAG
...............................................................((((((((((((....))))....)))))))). ( -18.10)
>DroEre_CAF1 31350 94 + 1
CCUUUGAAAUUAGCGAGCGACCACUGU--CCACGUAUCGGCUGGCUGUAAAGUAGCCAACGGAUGCUGCAACUGCAUCUGCAGUCACCUGCAGCAG
............(((.(.(((....))--)).)))(((.(.((((((.....)))))).).)))(((((((((((....)))))....)))))).. ( -31.40)
>DroYak_CAF1 12511 94 + 1
CCUUAAAAAUUAGCGAACGACCACUGU--CCAAAUAUCGGUGGGCUGUAACGUAGCCAACGGAUGCUGCAGCUGCAUCUGCAGUCACCUGCAGCAG
((...................(((((.--........)))))(((((.....)))))...)).((((((((((((....))))....)))))))). ( -30.20)
>consensus
CCUGCAAAAUUAGCGAGCGACCACUGU__CCACGUAUCGGCUGGCAGUAAAGUAGCCAACGGAUGCUGCAGCUGCAUCUGCAGUCACCUGCAGCAG
....................................((.(.((((.........)))).).))((((((((((((....)))))....))))))). (-19.20 = -20.64 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 10,163,553 – 10,163,647
Length 94
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 75.37
Mean single sequence MFE -31.40
Consensus MFE -22.27
Energy contribution -24.24
Covariance contribution 1.97
Combinations/Pair 1.08
Mean z-score -1.62
Structure conservation index 0.71
SVM decision value 1.02
SVM RNA-class probability 0.900713
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10163553 94 - 22224390
CUGCUGCAGGUGACUGCAGAUGCAGCUGCAGCAUCCGUUGGCUACUUUACUGCCAGCCGAUACGUGG--ACAGUGGUCGCUCGCUAAUUUUGCAGG
...((((((....)))))).(((((..((((((((.((((((.........)))))).))).....(--((....)))))).)).....))))).. ( -35.80)
>DroSec_CAF1 9591 96 - 1
CUGCUGCAGGUGACUGCAGAUGCAGCUGCAGCAUCCGUUGGCUACUUUACUGCCAGCCGAUACGUGGGGACAGUGGUUGCUCGCUAAUUUUGCACG
...((((((....))))))..(((((..(.(.(((.((((((.........)))))).))).).((....)))..)))))..((.......))... ( -39.70)
>DroSim_CAF1 11996 96 - 1
CUGCUGCAGGUGACUGCAGAUGCAGCUGCAGCAUCCGUUGGCUACUUUACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
.((((((((....((((....))))))))))))............................................................... ( -17.70)
>DroEre_CAF1 31350 94 - 1
CUGCUGCAGGUGACUGCAGAUGCAGUUGCAGCAUCCGUUGGCUACUUUACAGCCAGCCGAUACGUGG--ACAGUGGUCGCUCGCUAAUUUCAAAGG
...((((((....)))))).((.((((((((((((.(((((((.......))))))).))).....(--((....)))))).)).)))).)).... ( -34.40)
>DroYak_CAF1 12511 94 - 1
CUGCUGCAGGUGACUGCAGAUGCAGCUGCAGCAUCCGUUGGCUACGUUACAGCCCACCGAUAUUUGG--ACAGUGGUCGUUCGCUAAUUUUUAAGG
.((((((((....((((....))))))))))))...((((((.(((((((.(.(((........)))--.).)))).)))..))))))........ ( -29.40)
>consensus
CUGCUGCAGGUGACUGCAGAUGCAGCUGCAGCAUCCGUUGGCUACUUUACAGCCAGCCGAUACGUGG__ACAGUGGUCGCUCGCUAAUUUUGAAGG
..(((((((....((((....)))))))))))(((.((((((.........)))))).)))..........(((((....)))))........... (-22.27 = -24.24 +   1.97)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 10,163,590 – 10,163,682
Length 92
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 91.28
Mean single sequence MFE -30.92
Consensus MFE -24.60
Energy contribution -25.60
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.49
Structure conservation index 0.80
SVM decision value 1.98
SVM RNA-class probability 0.984742
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10163590 92 + 22224390
GCUGGCAGUAAAGUAGCCAACGGAUGCUGCAGCUGCAUCUGCAGUCACCUGCAGCAGGUGUAGCCUUGAACACAA-ACACAAACG---GCCAAAUA-
..((((.((...(((((........))))).(((((((((((.((.....)).)))))))))))...........-......)).---))))....- ( -31.40)
>DroSec_CAF1 9630 92 + 1
GCUGGCAGUAAAGUAGCCAACGGAUGCUGCAGCUGCAUCUGCAGUCACCUGCAGCAGGUGUAGCCUUGAACACAA-ACACGAACG---GCCAAACA-
..((((.((...(((((........))))).(((((((((((.((.....)).)))))))))))...........-......)).---))))....- ( -31.40)
>DroSim_CAF1 12035 92 + 1
NNNNNNNGUAAAGUAGCCAACGGAUGCUGCAGCUGCAUCUGCAGUCACCUGCAGCAGGUGUAGCCUUGAACACAA-ACACGAACG---GCCAAACA-
...............(((......((((((((((((....))))....)))))))).((((........))))..-........)---))......- ( -26.30)
>DroEre_CAF1 31387 96 + 1
GCUGGCUGUAAAGUAGCCAACGGAUGCUGCAACUGCAUCUGCAGUCACCUGCAGCAGGUGUAGCCUUGAACACAA-ACACGAACGGCGGCCAAACAG
..(((((((...((..........((((((((((((....)))))....))))))).((((........))))..-......)).)))))))..... ( -32.40)
>DroYak_CAF1 12548 93 + 1
GUGGGCUGUAACGUAGCCAACGGAUGCUGCAGCUGCAUCUGCAGUCACCUGCAGCAGGUGUAGCCUUGAACACAAAACACGAAUG---UCCAAACA-
((.(((((.....))))).))((((((((((.((((...(((((....))))))))).)))))).(((....))).........)---))).....- ( -33.10)
>consensus
GCUGGCAGUAAAGUAGCCAACGGAUGCUGCAGCUGCAUCUGCAGUCACCUGCAGCAGGUGUAGCCUUGAACACAA_ACACGAACG___GCCAAACA_
...(((......(((((........))))).(((((((((((.((.....)).)))))))))))........................)))...... (-24.60 = -25.60 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 10,163,590 – 10,163,682
Length 92
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 91.28
Mean single sequence MFE -31.40
Consensus MFE -24.36
Energy contribution -25.48
Covariance contribution 1.12
Combinations/Pair 1.07
Mean z-score -1.54
Structure conservation index 0.78
SVM decision value 0.13
SVM RNA-class probability 0.600292
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10163590 92 - 22224390
-UAUUUGGC---CGUUUGUGU-UUGUGUUCAAGGCUACACCUGCUGCAGGUGACUGCAGAUGCAGCUGCAGCAUCCGUUGGCUACUUUACUGCCAGC
-....((((---(.....((.-.......)).)))))....((((((((....((((....))))))))))))...((((((.........)))))) ( -31.00)
>DroSec_CAF1 9630 92 - 1
-UGUUUGGC---CGUUCGUGU-UUGUGUUCAAGGCUACACCUGCUGCAGGUGACUGCAGAUGCAGCUGCAGCAUCCGUUGGCUACUUUACUGCCAGC
-.((.((((---(.....((.-.......)).))))).)).((((((((....((((....))))))))))))...((((((.........)))))) ( -32.10)
>DroSim_CAF1 12035 92 - 1
-UGUUUGGC---CGUUCGUGU-UUGUGUUCAAGGCUACACCUGCUGCAGGUGACUGCAGAUGCAGCUGCAGCAUCCGUUGGCUACUUUACNNNNNNN
-....((((---((..((.(.-..(((((...((((.((....((((((....)))))).)).))))..)))))))).))))))............. ( -28.90)
>DroEre_CAF1 31387 96 - 1
CUGUUUGGCCGCCGUUCGUGU-UUGUGUUCAAGGCUACACCUGCUGCAGGUGACUGCAGAUGCAGUUGCAGCAUCCGUUGGCUACUUUACAGCCAGC
...((((..(((.........-..)))..))))(((.((.(((((((((....)))))...)))).)).)))....(((((((.......))))))) ( -32.90)
>DroYak_CAF1 12548 93 - 1
-UGUUUGGA---CAUUCGUGUUUUGUGUUCAAGGCUACACCUGCUGCAGGUGACUGCAGAUGCAGCUGCAGCAUCCGUUGGCUACGUUACAGCCCAC
-..((((((---(((.........)))))))))(((.((.(((((((((....)))))...)))).)).)))....((.((((.......)))).)) ( -32.10)
>consensus
_UGUUUGGC___CGUUCGUGU_UUGUGUUCAAGGCUACACCUGCUGCAGGUGACUGCAGAUGCAGCUGCAGCAUCCGUUGGCUACUUUACAGCCAGC
......((.........((((.(((....)))....)))).((((((((....((((....)))))))))))).))((((((.........)))))) (-24.36 = -25.48 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:37 2006