Locus 5524

Sequence ID 2R_DroMel_CAF1
Location 17,664,611 – 17,664,869
Length 258
Max. P 0.980636
window8850 window8851 window8852 window8853 window8854

overview

Window 0

Location 17,664,611 – 17,664,709
Length 98
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.07
Mean single sequence MFE -33.26
Consensus MFE -23.61
Energy contribution -25.43
Covariance contribution 1.81
Combinations/Pair 1.04
Mean z-score -2.78
Structure conservation index 0.71
SVM decision value 1.87
SVM RNA-class probability 0.980636
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17664611 98 + 20766785
AUGUAAAUUGUGCCAAAUCAAUGCCUGGCUCAUAGCCUUGCUGCCGAAUGUGGUAAUUAAAAUCGCUGGGCAGCCAAAG----------------------GAGCGGGCAGUGGGCAUUA
.........(((((.......((((((.(((........((((((.(..(((((.......)))))).)))))).....----------------------)))))))))...))))).. ( -33.62)
>DroSec_CAF1 18047 98 + 1
AUGUAAAUUGUGCCAAAUCAAUGCCUGGCUCUUAGGCUUGCUGCCGAAUGUGGUAAUUAAAAUCGCUGGGCAGCAAAAG----------------------GAGCGGGCAGCGGGCAUUA
.........(((((.......((((((.(((((....((((((((.(..(((((.......)))))).)))))))).))----------------------)))))))))...))))).. ( -37.80)
>DroEre_CAF1 18406 97 + 1
AUGUAAAUUGUGGCAAAUCAAUGCCUGGCUCAUAGCCUUGCAGCCGAAUGUGGUAAUUAAAAUCGCUGGGCGGCAAAAA----------------------GAGCAGGCAGCG-GCAUUA
........(((.((.......((((((.(((...((...)).((((...(((((.......)))))....)))).....----------------------))))))))))).-)))... ( -29.71)
>DroYak_CAF1 30110 119 + 1
AUGUAAAUUGUGCCAAAUCAAUGCCUGGCUCAUAGCCUUGCUGCCGAAUGUGGUAAUUAAAAUCGCUGGGCAGCAAAAAAAAAAAACAAAACAAAACGAGCGAGCGAUCAGCG-GCAUUA
.........(((((.......((((.(((.....)))((((((((.(..(((((.......)))))).)))))))).....................).))).((.....)))-)))).. ( -31.90)
>consensus
AUGUAAAUUGUGCCAAAUCAAUGCCUGGCUCAUAGCCUUGCUGCCGAAUGUGGUAAUUAAAAUCGCUGGGCAGCAAAAA______________________GAGCGGGCAGCG_GCAUUA
.........(((((.......((((((((.....)))((((((((.(..(((((.......)))))).)))))))).............................)))))...))))).. (-23.61 = -25.43 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 17,664,611 – 17,664,709
Length 98
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.07
Mean single sequence MFE -26.84
Consensus MFE -17.38
Energy contribution -18.62
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.65
SVM decision value 0.15
SVM RNA-class probability 0.609181
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17664611 98 - 20766785
UAAUGCCCACUGCCCGCUC----------------------CUUUGGCUGCCCAGCGAUUUUAAUUACCACAUUCGGCAGCAAGGCUAUGAGCCAGGCAUUGAUUUGGCACAAUUUACAU
...((((((.((((.((((----------------------(((((.(((((.......................))))))))))....))))..)))).))....)))).......... ( -26.50)
>DroSec_CAF1 18047 98 - 1
UAAUGCCCGCUGCCCGCUC----------------------CUUUUGCUGCCCAGCGAUUUUAAUUACCACAUUCGGCAGCAAGCCUAAGAGCCAGGCAUUGAUUUGGCACAAUUUACAU
...((((((.((((.((((----------------------..(((((((((.......................))))))))).....))))..)))).))....)))).......... ( -26.70)
>DroEre_CAF1 18406 97 - 1
UAAUGC-CGCUGCCUGCUC----------------------UUUUUGCCGCCCAGCGAUUUUAAUUACCACAUUCGGCUGCAAGGCUAUGAGCCAGGCAUUGAUUUGCCACAAUUUACAU
......-((.(((((((((----------------------.....(((...((((((...............)).))))...)))...))).)))))).)).................. ( -24.86)
>DroYak_CAF1 30110 119 - 1
UAAUGC-CGCUGAUCGCUCGCUCGUUUUGUUUUGUUUUUUUUUUUUGCUGCCCAGCGAUUUUAAUUACCACAUUCGGCAGCAAGGCUAUGAGCCAGGCAUUGAUUUGGCACAAUUUACAU
((((((-(((.....))..((((((...((((((((........(((((....))))).........((......)).)))))))).))))))..))))))).................. ( -29.30)
>consensus
UAAUGC_CGCUGCCCGCUC______________________CUUUUGCUGCCCAGCGAUUUUAAUUACCACAUUCGGCAGCAAGGCUAUGAGCCAGGCAUUGAUUUGGCACAAUUUACAU
(((((((.....................................((((((((.......................))))))))(((.....))).))))))).................. (-17.38 = -18.62 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 17,664,690 – 17,664,789
Length 99
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.35
Mean single sequence MFE -32.83
Consensus MFE -28.31
Energy contribution -28.62
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -1.33
Structure conservation index 0.86
SVM decision value -0.05
SVM RNA-class probability 0.510493
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17664690 99 + 20766785
---------------------GAGCGGGCAGUGGGCAUUAGUAUGCAACUCUCACUCGGCGACAGCGGCCGCAACUGUUGGCCAUAUAAGCGGACUGAAAAGAAAGGCCAACGCUCAGUG
---------------------(((((((((((..((((....)))).))).(((.((.((......((((((....).)))))......)).)).)))........)))..))))).... ( -32.90)
>DroSec_CAF1 18126 99 + 1
---------------------GAGCGGGCAGCGGGCAUUAGUAUGCAACUCUCACUCGGCGACAGCGGCCGCAACUGUUGGCCAUAUAAGCGGACUGAAAAGAAAGGCCAACGCUCAGUG
---------------------((((((.((((((((((....))))..........((((.......))))...)))))).))........((.((........)).))...)))).... ( -31.90)
>DroEre_CAF1 18485 98 + 1
---------------------GAGCAGGCAGCG-GCAUUAGUAUGCAACUCUCACUCGGAGACAGCGGCCGCAACUGUUGGCCAUAUAAGCGGACUGAAAAGAAAGGCCAACGCUCAGUG
---------------------((((.(((.((.-((((....))))...((((.....))))..)).)))......(((((((......................))))))))))).... ( -33.25)
>DroYak_CAF1 30190 119 + 1
AAAAAACAAAACAAAACGAGCGAGCGAUCAGCG-GCAUUAGUAUGCAACUCUCACUCGGAGACAGCGGCCGCAACUGUUGGCCAUAUAAGCGGACUGAAAAGAAAGGCCAACGCUCAGUG
.................((((..(((..(.((.-((((....))))...((((.....))))..)))..)))....(((((((......................))))))))))).... ( -33.25)
>consensus
_____________________GAGCGGGCAGCG_GCAUUAGUAUGCAACUCUCACUCGGAGACAGCGGCCGCAACUGUUGGCCAUAUAAGCGGACUGAAAAGAAAGGCCAACGCUCAGUG
.....................((((.(((.((..((((....))))...........(....).)).)))......(((((((......................))))))))))).... (-28.31 = -28.62 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 17,664,749 – 17,664,869
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -34.06
Consensus MFE -32.96
Energy contribution -32.96
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.68
Structure conservation index 0.97
SVM decision value 0.80
SVM RNA-class probability 0.854448
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17664749 120 + 20766785
GCCAUAUAAGCGGACUGAAAAGAAAGGCCAACGCUCAGUGCUCAACAAAACAAUUUACCAAGUUUGGCCUAAACGGCCAGUGACAGUCCGGCGACAACAACAAUUGCAACUGUUACGGCA
(((......((.(.((....))..(((((((.(((..(((...............)))..))))))))))...).))..((((((((...((((.........)))).))))))))))). ( -34.06)
>DroSec_CAF1 18185 120 + 1
GCCAUAUAAGCGGACUGAAAAGAAAGGCCAACGCUCAGUGCUCAACAAAACAAUUUACCAAGUUUGGCCUAAACGGCCAGUGACAGUCCGGCGACAACAACAAUUGCAACUGUUACGGCA
(((......((.(.((....))..(((((((.(((..(((...............)))..))))))))))...).))..((((((((...((((.........)))).))))))))))). ( -34.06)
>DroEre_CAF1 18543 120 + 1
GCCAUAUAAGCGGACUGAAAAGAAAGGCCAACGCUCAGUGCUCAACAAAACAAUUUACCAAGUUUGGCCUAAACGGCCAGUGACAGUCCGGCGACAACAACAAUUGCAACUGUUACGGCA
(((......((.(.((....))..(((((((.(((..(((...............)))..))))))))))...).))..((((((((...((((.........)))).))))))))))). ( -34.06)
>DroYak_CAF1 30269 120 + 1
GCCAUAUAAGCGGACUGAAAAGAAAGGCCAACGCUCAGUGCUCAACAAAACAAUUUACCAAGUUUGGCCUAAACGGCCAGUGACAGUCCGGCGACAACAACAAUUGCAACUGUUACGGCA
(((......((.(.((....))..(((((((.(((..(((...............)))..))))))))))...).))..((((((((...((((.........)))).))))))))))). ( -34.06)
>consensus
GCCAUAUAAGCGGACUGAAAAGAAAGGCCAACGCUCAGUGCUCAACAAAACAAUUUACCAAGUUUGGCCUAAACGGCCAGUGACAGUCCGGCGACAACAACAAUUGCAACUGUUACGGCA
(((........((.(((.......(((((((.(((..(((...............)))..))))))))))...))))).((((((((...((((.........)))).))))))))))). (-32.96 = -32.96 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 17,664,749 – 17,664,869
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -39.62
Consensus MFE -39.62
Energy contribution -39.62
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.23
Structure conservation index 1.00
SVM decision value 0.57
SVM RNA-class probability 0.785168
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17664749 120 - 20766785
UGCCGUAACAGUUGCAAUUGUUGUUGUCGCCGGACUGUCACUGGCCGUUUAGGCCAAACUUGGUAAAUUGUUUUGUUGAGCACUGAGCGUUGGCCUUUCUUUUCAGUCCGCUUAUAUGGC
.((((((...((.(((((....))))).))(((((((.....((((((((((((((....))))....(((((....)))))))))))...))))........)))))))....)))))) ( -39.62)
>DroSec_CAF1 18185 120 - 1
UGCCGUAACAGUUGCAAUUGUUGUUGUCGCCGGACUGUCACUGGCCGUUUAGGCCAAACUUGGUAAAUUGUUUUGUUGAGCACUGAGCGUUGGCCUUUCUUUUCAGUCCGCUUAUAUGGC
.((((((...((.(((((....))))).))(((((((.....((((((((((((((....))))....(((((....)))))))))))...))))........)))))))....)))))) ( -39.62)
>DroEre_CAF1 18543 120 - 1
UGCCGUAACAGUUGCAAUUGUUGUUGUCGCCGGACUGUCACUGGCCGUUUAGGCCAAACUUGGUAAAUUGUUUUGUUGAGCACUGAGCGUUGGCCUUUCUUUUCAGUCCGCUUAUAUGGC
.((((((...((.(((((....))))).))(((((((.....((((((((((((((....))))....(((((....)))))))))))...))))........)))))))....)))))) ( -39.62)
>DroYak_CAF1 30269 120 - 1
UGCCGUAACAGUUGCAAUUGUUGUUGUCGCCGGACUGUCACUGGCCGUUUAGGCCAAACUUGGUAAAUUGUUUUGUUGAGCACUGAGCGUUGGCCUUUCUUUUCAGUCCGCUUAUAUGGC
.((((((...((.(((((....))))).))(((((((.....((((((((((((((....))))....(((((....)))))))))))...))))........)))))))....)))))) ( -39.62)
>consensus
UGCCGUAACAGUUGCAAUUGUUGUUGUCGCCGGACUGUCACUGGCCGUUUAGGCCAAACUUGGUAAAUUGUUUUGUUGAGCACUGAGCGUUGGCCUUUCUUUUCAGUCCGCUUAUAUGGC
.((((((...((.(((((....))))).))(((((((.....((((((((((((((....))))....(((((....)))))))))))...))))........)))))))....)))))) (-39.62 = -39.62 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:43 2006