Locus 943

Sequence ID 2R_DroMel_CAF1
Location 4,074,801 – 4,075,158
Length 357
Max. P 0.992176
window1681 window1682 window1683 window1684

overview

Window 1

Location 4,074,801 – 4,074,919
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.38
Mean single sequence MFE -24.70
Consensus MFE -22.36
Energy contribution -22.96
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.27
Structure conservation index 0.91
SVM decision value 0.35
SVM RNA-class probability 0.699098
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4074801 118 + 20766785
UGACCUUUCGGCCACAAUAUGCGCUCGUUAGUCAAUGUUUAGCAAUUUGUUAUCAAUCAAUAAUAAAAGUAAAUAACAUAAUAAUGAGAACACAGCCGAUGGA--CCCACUCCCCCGAAG
...((..(((((.......((..(((((((....(((((......((((((((......)))))))).......)))))..)))))))..))..))))).)).--............... ( -21.82)
>DroSec_CAF1 57486 118 + 1
UGACCUUUCGGCCACAAUAUGCGCUCGUUAGUCAAUGUUUAGCAAUUUGUUAUCAAUCAAUAAUAAAUGUAAAUAACAUAAUAAUGAGAACACAGGCGAUGGA--CCCACUCCCCCGAAG
......(((((........((..(((((((....(((((.....(((((((((......)))))))))......)))))..)))))))..))..((.((((..--..)).))))))))). ( -24.20)
>DroSim_CAF1 65690 120 + 1
UGACCUUUCGGCCACAAUAUGCGCUCGUUAGUCAAUGUUUAGCAAUUUGUUAUCAAUCAAUAAUAAAUGUAAAUAACAUAAUAAUGAGAACACAGGCGAUGGACACCCACUCCCCCGAAG
......(((((........((..(((((((....(((((.....(((((((((......)))))))))......)))))..)))))))..))..((.(((((....))).))))))))). ( -26.10)
>DroEre_CAF1 58942 118 + 1
UGACCUUUCGGCCACAAUAUGCGCUCGUUAGUCAAUGUUCAGCAAUUUGUUAUCAAUCAAUAAUAAAUGUAAAUAACAUAAUAAUGAGAGCACAGGCGCUGGG--GCCACUCCCCCGAAG
......(((((((......(((.(((((((....(((((.....(((((((((......)))))))))......)))))..))))))).)))..)))...(((--(.....)))))))). ( -30.30)
>DroYak_CAF1 61867 118 + 1
UGACCUUUCGGCCACAAUAUGCGCUCGUUAGUCAAUGCUUAGCAAUUUGUUAUCAAUCAAUAAUAAAUGUAAAUAACAUAAUAAUGAGAACACAGGCGUUGGA--CCCACUCCCCCGAAG
......(((((........((..(((((((....(((.(((...(((((((((......))))))))).....))))))..)))))))..))..((.((.(..--..))).)).))))). ( -21.10)
>consensus
UGACCUUUCGGCCACAAUAUGCGCUCGUUAGUCAAUGUUUAGCAAUUUGUUAUCAAUCAAUAAUAAAUGUAAAUAACAUAAUAAUGAGAACACAGGCGAUGGA__CCCACUCCCCCGAAG
......(((((........((..(((((((....(((((.....(((((((((......)))))))))......)))))..)))))))..))..((.(.(((....)))).)).))))). (-22.36 = -22.96 +   0.60)

alignment

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secondary structure

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Window 2

Location 4,074,919 – 4,075,039
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.75
Mean single sequence MFE -35.01
Consensus MFE -29.50
Energy contribution -30.14
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.21
Structure conservation index 0.84
SVM decision value 2.31
SVM RNA-class probability 0.992176
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4074919 120 + 20766785
AUGAUGAGGCAUCAGGGCAUUGGCUCAAAUUGUCUGUGGGAAAAAUAGGAAUUUGGCCUAAAUGAGUUAUGGCCCGCAUAAACAAAAAAGGAAGUGCGAAAGCGCCCACGGAGGCAUGCG
.(((((...)))))((((..(((((((.........((((..((((....))))..))))..)))))))..))))((((................((....))(((......))))))). ( -35.40)
>DroSec_CAF1 57604 120 + 1
AUGAUGAGGCAGCAGGGCAUUGGCUCAAAUUGUCUGUGGGAAAAAUAGGAAUUUGGCCUAAAUGAGUUAUGGCCCGCAUAAACAAAAAAGGAAGUGCGAAAGCGCCCACGGAGGCAUGCG
........(((((.((((....))))......((((((((..............((((............))))(((((...(......)...)))))......)))))))).)).))). ( -36.00)
>DroSim_CAF1 65810 112 + 1
AUGAUGAGG--------CAUUGGCUCAAAUUGUCUGUGGGAAAAAUAGGAAUUUGGCCUAAAUGAGUUAUGGCCCGCAUAAACAAAAAAGGAAGUGCGAAAGCGCCCACGGAGGCAUGCG
........(--------(((.(.(((...((((.((((.(..((((....))))((((............))))).)))).))))....((..((((....))))))...))).))))). ( -31.10)
>DroEre_CAF1 59060 118 + 1
AUGAUGAGGCAUCAGGACAUUGGCUCAAAUUGUCUGUGGA-AGAAAAGGAAUUUGGCCUAAAUGAGUUAUGGCCCGCAUGAACAAAAA-GGAAGUGCGAAAGCGCCCACGGAGGCAUGCG
.......(((.......(((((((.((((((.(((.....-.....))))))))))))..)))).......)))((((((........-((..((((....)))))).......)))))) ( -31.30)
>DroYak_CAF1 61985 120 + 1
AUGAUGAGGCAUCAGGGCAUGGGCUCAAAUGGCCUGUGGAAAGAAAAGGAAUUUGGCCUAAAUGAGUUAUUGCCCGCAUAAACAAAAACGGAAGUGCGAAAGCGCCCACGGAGGCAUGCG
.(((((...)))))(((((..((((((...((((....................))))....))))))..)))))((((........((....))((....))(((......))))))). ( -41.25)
>consensus
AUGAUGAGGCAUCAGGGCAUUGGCUCAAAUUGUCUGUGGGAAAAAUAGGAAUUUGGCCUAAAUGAGUUAUGGCCCGCAUAAACAAAAAAGGAAGUGCGAAAGCGCCCACGGAGGCAUGCG
.......(((.......(((.(((.((((((.(((((.......))))))))))))))...))).......)))(((((................((....))(((......)))))))) (-29.50 = -30.14 +   0.64)

alignment

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secondary structure

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Window 3

Location 4,075,039 – 4,075,158
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.50
Mean single sequence MFE -26.82
Consensus MFE -23.44
Energy contribution -24.08
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -1.56
Structure conservation index 0.87
SVM decision value 1.03
SVM RNA-class probability 0.903110
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4075039 119 + 20766785
AUAUUGUAUUU-UUCCGCCCCAUCACGGCAGCUGUUUUCCGAAUGGACAACGCCACCAAUUGAGCGAAUCAAUGGCCAUCCAGUCAGUCUUGAAAACACAAAGAUACAAAAACACAGACG
...((((((((-((..(((.......))).(.(((((((.((.((((....((((....((((.....))))))))..)))).....))..))))))))))))))))))........... ( -26.80)
>DroSec_CAF1 57724 120 + 1
AUAUUGUAUUUUUUCCGCCCCAUCACGGCAGCUGUUUUCCGAAUAGACAACGCCGCCAAUUGAGCGAAUCAAUGGCCAUCCAGUCAGUCUUGAAAACACAAAGAUACAAAAACACAGACU
...((((((((((...(((.......))).(.(((((((.((...(((......((((.((((.....))))))))......)))..))..))))))))))))))))))........... ( -27.80)
>DroSim_CAF1 65922 120 + 1
AUAUUGUAUUUUUUCCGCCCCAUCACGGCAGCUGUUUUCCGAAUAGACAACGCCGCCAAUUGAGCGAAUCAAUGGCCAUCCAGUCAGUCUUGAAAACACAAAGAUACAAAAACACAGACG
...((((((((((...(((.......))).(.(((((((.((...(((......((((.((((.....))))))))......)))..))..))))))))))))))))))........... ( -27.80)
>DroEre_CAF1 59178 120 + 1
AUAUUGUAUUUUUUCCGCCCCAUCACGGCAGCUGUUUUCCGAAUAGACAACGCCGCCAAUUGAGCGAAUCAAUGACCAGCCAGUCAGUCUUGAAAACAAAAAGAUACAAAAACACGGACG
...(((((((((((..(((.......)))...(((((((.....((((.....((((....).)))......((((......)))))))).))))))))))))))))))........... ( -27.40)
>DroYak_CAF1 62105 120 + 1
AUAUUAUAUUUUUUCCGCCCCAUCACGGCAGCUGUUUUCCGAAUAGACAACUCCGCCAAUUGAGCGAAUCAAUGGCCGUCCAGUCAGUCUUGAAAAUACAAAGAUACAAAAACACGGAGG
............(((((((.......))).(.((((((.......(((....(.((((.((((.....)))))))).)....))).(((((.........)))))...))))))))))). ( -24.30)
>consensus
AUAUUGUAUUUUUUCCGCCCCAUCACGGCAGCUGUUUUCCGAAUAGACAACGCCGCCAAUUGAGCGAAUCAAUGGCCAUCCAGUCAGUCUUGAAAACACAAAGAUACAAAAACACAGACG
...((((((((((...(((.......)))...(((((((.((...(((......((((.((((.....))))))))......)))..))..))))))).))))))))))........... (-23.44 = -24.08 +   0.64)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,075,039 – 4,075,158
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.50
Mean single sequence MFE -35.12
Consensus MFE -30.08
Energy contribution -29.84
Covariance contribution -0.24
Combinations/Pair 1.12
Mean z-score -1.30
Structure conservation index 0.86
SVM decision value 0.07
SVM RNA-class probability 0.569043
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4075039 119 - 20766785
CGUCUGUGUUUUUGUAUCUUUGUGUUUUCAAGACUGACUGGAUGGCCAUUGAUUCGCUCAAUUGGUGGCGUUGUCCAUUCGGAAAACAGCUGCCGUGAUGGGGCGGAA-AAAUACAAUAU
....(((((((((.........(((((((.....(((.(((((.(((((..(((.....)))..)))))...))))).)))))))))).(((((.......)))))))-))))))).... ( -36.80)
>DroSec_CAF1 57724 120 - 1
AGUCUGUGUUUUUGUAUCUUUGUGUUUUCAAGACUGACUGGAUGGCCAUUGAUUCGCUCAAUUGGCGGCGUUGUCUAUUCGGAAAACAGCUGCCGUGAUGGGGCGGAAAAAAUACAAUAU
....(((((((((...((..((.((..((.((.....)).))..))))..))(((((((...((((((((((.(((....))).))).))))))).....)))))))))))))))).... ( -36.40)
>DroSim_CAF1 65922 120 - 1
CGUCUGUGUUUUUGUAUCUUUGUGUUUUCAAGACUGACUGGAUGGCCAUUGAUUCGCUCAAUUGGCGGCGUUGUCUAUUCGGAAAACAGCUGCCGUGAUGGGGCGGAAAAAAUACAAUAU
....(((((((((...((..((.((..((.((.....)).))..))))..))(((((((...((((((((((.(((....))).))).))))))).....)))))))))))))))).... ( -36.40)
>DroEre_CAF1 59178 120 - 1
CGUCCGUGUUUUUGUAUCUUUUUGUUUUCAAGACUGACUGGCUGGUCAUUGAUUCGCUCAAUUGGCGGCGUUGUCUAUUCGGAAAACAGCUGCCGUGAUGGGGCGGAAAAAAUACAAUAU
.....((((((((..............((((((((........)))).))))(((((((...((((((((((.(((....))).))).))))))).....)))))))))))))))..... ( -36.70)
>DroYak_CAF1 62105 120 - 1
CCUCCGUGUUUUUGUAUCUUUGUAUUUUCAAGACUGACUGGACGGCCAUUGAUUCGCUCAAUUGGCGGAGUUGUCUAUUCGGAAAACAGCUGCCGUGAUGGGGCGGAAAAAAUAUAAUAU
...................(((((((((.....((((.((((((((......((((((.....)))))))))))))).)))).......(((((.......)))))..)))))))))... ( -29.30)
>consensus
CGUCUGUGUUUUUGUAUCUUUGUGUUUUCAAGACUGACUGGAUGGCCAUUGAUUCGCUCAAUUGGCGGCGUUGUCUAUUCGGAAAACAGCUGCCGUGAUGGGGCGGAAAAAAUACAAUAU
.....((((((((.........(((((((..((..(((....(.((((((((.....)))).)))).)....)))..))..))))))).(((((.......))))).))))))))..... (-30.08 = -29.84 +  -0.24)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:21 2006