Locus 6133

Sequence ID 3R_DroMel_CAF1
Location 16,061,199 – 16,061,337
Length 138
Max. P 0.994721
window9996 window9997 window9998 window9999

overview

Window 6

Location 16,061,199 – 16,061,298
Length 99
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 91.75
Mean single sequence MFE -32.58
Consensus MFE -29.14
Energy contribution -29.45
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.21
Structure conservation index 0.89
SVM decision value 1.64
SVM RNA-class probability 0.969138
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16061199 99 + 27905053
ACGGCUGAAAUUCAGCAAUAAAUUGCCGUGAGUUAGUCAGA-GUGGAGCAUGCUUCAUUAAUGCGACAAGCGUGAGAGGCGAACCUCUCACCCCAA-------UCCC
..((((((....(.((((....)))).)....))))))..(-((((((....)))))))...((.....))((((((((....)))))))).....-------.... ( -31.20)
>DroSec_CAF1 21559 98 + 1
ACGGCUGAAAUUCAGCAA-AAAUUGCCGUGAGUGAGUCAGA-GUGGAGCAUGCUUCCUUAAUGCGACAAGCGUGAGAGGCUAACCUCUCACCCCAC-------ACCC
..((((((.((((((((.-....)))..)))))...)))).-((((.((((.........)))).......((((((((....)))))))).))))-------.)). ( -33.10)
>DroSim_CAF1 19986 99 + 1
ACGGCUGAAAUUCAGCAAUAAAUUGCCGUGAGUGAGUCAGA-GUGGAGCAUGCUUCAUUAAUGCGACAAGCGUGAGAGGCUAACCUCUCACCCCAC-------ACCC
..((((((.(((((((((....))))..)))))...)))).-((((.((((.........)))).......((((((((....)))))))).))))-------.)). ( -34.00)
>DroYak_CAF1 27606 107 + 1
ACAGCUGAAAUUCAGCAAUAAAUUGCCGUGAGUGAGUCAGAGGUGGAGCAUGCUUCAUUAAUGCGACAAGCGUGAGGGGCUAACCUCGCACCCCACACCACACACCC
...((((.....))))...........(((.(((.(((...(((((((....))))))).....)))....((((((......))))))......))))))...... ( -32.00)
>consensus
ACGGCUGAAAUUCAGCAAUAAAUUGCCGUGAGUGAGUCAGA_GUGGAGCAUGCUUCAUUAAUGCGACAAGCGUGAGAGGCUAACCUCUCACCCCAC_______ACCC
....((((.(((((((((....))))..)))))...))))..((((.((((.........)))).......((((((((....)))))))).))))........... (-29.14 = -29.45 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 16,061,199 – 16,061,298
Length 99
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 91.75
Mean single sequence MFE -34.65
Consensus MFE -29.08
Energy contribution -30.14
Covariance contribution 1.06
Combinations/Pair 1.03
Mean z-score -1.84
Structure conservation index 0.84
SVM decision value 0.69
SVM RNA-class probability 0.824960
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16061199 99 - 27905053
GGGA-------UUGGGGUGAGAGGUUCGCCUCUCACGCUUGUCGCAUUAAUGAAGCAUGCUCCAC-UCUGACUAACUCACGGCAAUUUAUUGCUGAAUUUCAGCCGU
.(((-------.((((((((((((....))))))))((.(((..((....))..))).)))))).-))).........(((((((((((....))))))...))))) ( -33.20)
>DroSec_CAF1 21559 98 - 1
GGGU-------GUGGGGUGAGAGGUUAGCCUCUCACGCUUGUCGCAUUAAGGAAGCAUGCUCCAC-UCUGACUCACUCACGGCAAUUU-UUGCUGAAUUUCAGCCGU
((((-------(.(((((((((((....))))))))((((.((.......))))))...))))))-))..........((((((((((-.....)))))...))))) ( -34.50)
>DroSim_CAF1 19986 99 - 1
GGGU-------GUGGGGUGAGAGGUUAGCCUCUCACGCUUGUCGCAUUAAUGAAGCAUGCUCCAC-UCUGACUCACUCACGGCAAUUUAUUGCUGAAUUUCAGCCGU
.(((-------(((((((((((((....))))))))((.(((..((....))..))).)).....-.....)))))...((((((....)))))).......))).. ( -35.70)
>DroYak_CAF1 27606 107 - 1
GGGUGUGUGGUGUGGGGUGCGAGGUUAGCCCCUCACGCUUGUCGCAUUAAUGAAGCAUGCUCCACCUCUGACUCACUCACGGCAAUUUAUUGCUGAAUUUCAGCUGU
(((((.((((((..(.((((((((......))))..((.....)).........)))).)..))))....)).))))).((((((....))))))............ ( -35.20)
>consensus
GGGU_______GUGGGGUGAGAGGUUAGCCUCUCACGCUUGUCGCAUUAAUGAAGCAUGCUCCAC_UCUGACUCACUCACGGCAAUUUAUUGCUGAAUUUCAGCCGU
((((.......(((((((((((((....))))))))((.(((..(......)..))).))))))).........))))(((((((((((....))))))...))))) (-29.08 = -30.14 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 16,061,239 – 16,061,337
Length 98
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 86.44
Mean single sequence MFE -29.05
Consensus MFE -24.26
Energy contribution -24.57
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -3.11
Structure conservation index 0.84
SVM decision value 2.50
SVM RNA-class probability 0.994721
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16061239 98 + 27905053
A-GUGGAGCAUGCUUCAUUAAUGCGACAAGCGUGAGAGGCGAACCUCUCACCCCAA-------UCCCCUUAACCCUAAAGCGGCCCACCCUUAACCCCCUACCAGC
.-((((.((.(((((.......((.....))((((((((....)))))))).....-------..............))))))))))).................. ( -27.80)
>DroSec_CAF1 21598 98 + 1
A-GUGGAGCAUGCUUCCUUAAUGCGACAAGCGUGAGAGGCUAACCUCUCACCCCAC-------ACCCCUUAACCCUAAAGCGGGCCACCCUUAACCGCCUGCCAGC
.-((((.((((.........)))).......((((((((....)))))))).))))-------................((((((...........)))))).... ( -31.90)
>DroSim_CAF1 20026 98 + 1
A-GUGGAGCAUGCUUCAUUAAUGCGACAAGCGUGAGAGGCUAACCUCUCACCCCAC-------ACCCCUUAACCCUAAAGCGGCCCACCCUUAACCCCCUGCCAGC
.-((((.((.(((((.......((.....))((((((((....)))))))).....-------..............))))))))))).................. ( -27.80)
>DroYak_CAF1 27646 99 + 1
AGGUGGAGCAUGCUUCAUUAAUGCGACAAGCGUGAGGGGCUAACCUCGCACCCCACACCACACACCCCUAAACCCUAAAGCGGCCCACCCUUUACUCCU-------
.(((((.((.(((((.......((.....))(((.(((((.......)).)))))).....................))))))))))))..........------- ( -28.70)
>consensus
A_GUGGAGCAUGCUUCAUUAAUGCGACAAGCGUGAGAGGCUAACCUCUCACCCCAC_______ACCCCUUAACCCUAAAGCGGCCCACCCUUAACCCCCUGCCAGC
..((((.((.(((((.......((.....))((((((((....))))))))..........................))))))))))).................. (-24.26 = -24.57 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 16,061,239 – 16,061,337
Length 98
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 86.44
Mean single sequence MFE -38.17
Consensus MFE -26.11
Energy contribution -26.93
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -2.01
Structure conservation index 0.68
SVM decision value 0.50
SVM RNA-class probability 0.761459
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16061239 98 - 27905053
GCUGGUAGGGGGUUAAGGGUGGGCCGCUUUAGGGUUAAGGGGA-------UUGGGGUGAGAGGUUCGCCUCUCACGCUUGUCGCAUUAAUGAAGCAUGCUCCAC-U
.................(((((((.(((((...(((((.(.((-------(.((.((((((((....)))))))).)).))).).))))))))))..)).))))-) ( -38.00)
>DroSec_CAF1 21598 98 - 1
GCUGGCAGGCGGUUAAGGGUGGCCCGCUUUAGGGUUAAGGGGU-------GUGGGGUGAGAGGUUAGCCUCUCACGCUUGUCGCAUUAAGGAAGCAUGCUCCAC-U
((.(((((((.........((((((......))))))......-------.....((((((((....))))))))))))))))).....(((.(....))))..-. ( -38.80)
>DroSim_CAF1 20026 98 - 1
GCUGGCAGGGGGUUAAGGGUGGGCCGCUUUAGGGUUAAGGGGU-------GUGGGGUGAGAGGUUAGCCUCUCACGCUUGUCGCAUUAAUGAAGCAUGCUCCAC-U
..((((.....))))..(((((((.(((((...(((((...((-------(.((.((((((((....)))))))).))...))).))))))))))..)).))))-) ( -36.20)
>DroYak_CAF1 27646 99 - 1
-------AGGAGUAAAGGGUGGGCCGCUUUAGGGUUUAGGGGUGUGUGGUGUGGGGUGCGAGGUUAGCCCCUCACGCUUGUCGCAUUAAUGAAGCAUGCUCCACCU
-------.........((((((((.((((((.........((((((.(((((((((.((.......)).)))))))))...))))))..))))))..)).)))))) ( -39.70)
>consensus
GCUGGCAGGGGGUUAAGGGUGGGCCGCUUUAGGGUUAAGGGGU_______GUGGGGUGAGAGGUUAGCCUCUCACGCUUGUCGCAUUAAUGAAGCAUGCUCCAC_U
........(((((...((.....))((((((........................((((((((....))))))))((.....)).....))))))..))))).... (-26.11 = -26.93 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:31 2006