Locus 8171

Sequence ID 3R_DroMel_CAF1
Location 21,976,270 – 21,976,410
Length 140
Max. P 0.999779
window13137 window13138 window13139 window13140

overview

Window 7

Location 21,976,270 – 21,976,388
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 91.86
Mean single sequence MFE -37.70
Consensus MFE -28.74
Energy contribution -28.98
Covariance contribution 0.24
Combinations/Pair 1.19
Mean z-score -1.69
Structure conservation index 0.76
SVM decision value 0.20
SVM RNA-class probability 0.631774
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21976270 118 + 27905053
UGUCCGUCACGUAUUGAAAUAUAUGACCGGAGACAAGGCCUCGGAAUUACAGCUGCUGGCCAUCAAGUGGGCCAGAUGCCAGAAGUCCAUCUGGCACAUUGCCAUUAUUAAUGACGCA
....((((((((((......)))))...(....)..(((................((((((........)))))).(((((((......)))))))....)))........))))).. ( -35.80)
>DroSec_CAF1 15751 118 + 1
UGUCCGUCACGUAUUGAAAUAUAUGACCGGAGACAAGGUCUCGGAAUUACAGCUGCUGGCCAUCAAGUGGGCCAGAUGCCAGAAGUCCAUCUGGCACAUUGCCAUUAUUAAUGACGCA
..(((((((..(((....)))..))))..(((((...))))))))......((..((((((........)))))).(((((((......)))))))(((((.......)))))..)). ( -38.20)
>DroEre_CAF1 15640 118 + 1
UGUCCGUCACGUAUUGAAAUAUAUGACCGGAGACAAGGCCUUGGAAUUACAGCUGCUGGCCAUCAAGUGGGCCAGAUGCCAGAAGUCCAUCUGGCACAUUGCCAUUAUUAAUGACGCA
....((((((((((......)))))...(....)..(((..((............((((((........)))))).(((((((......)))))))))..)))........))))).. ( -37.90)
>DroYak_CAF1 16479 118 + 1
UGUCCGUCACGUAUUGAAAUAUAUGACCGGAGACAAGGCCUCGGAAUUACAGCUGCUGGCCAUCAAGUGGGCCAGAUGCCAGAAGUCCAUCUGGCACAUUGCCAUUAUUAAUGACGCA
....((((((((((......)))))...(....)..(((................((((((........)))))).(((((((......)))))))....)))........))))).. ( -35.80)
>DroAna_CAF1 23242 117 + 1
UGUCCGGCACGUAUUGUAAUAUAUGAGCGGACACGAGGCCUCGGAAUGCCAGAUGCUGGCCAUCAAGUGGAACUGG-GCCAUCUGGGUAUCUGGCGCACUGCCAUUAUUAAUGAUGCA
((((((.(.(((((......))))).)))))))...(((...((..(((((((((((((((....((.....)).)-))).....)))))))))))..)))))............... ( -40.80)
>consensus
UGUCCGUCACGUAUUGAAAUAUAUGACCGGAGACAAGGCCUCGGAAUUACAGCUGCUGGCCAUCAAGUGGGCCAGAUGCCAGAAGUCCAUCUGGCACAUUGCCAUUAUUAAUGACGCA
....((((((((((......)))))...((......((((.(((........)))..))))....((((.((((((((.........)))))))).)))).))........))))).. (-28.74 = -28.98 +   0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,976,270 – 21,976,388
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 91.86
Mean single sequence MFE -38.28
Consensus MFE -32.36
Energy contribution -33.68
Covariance contribution 1.32
Combinations/Pair 1.08
Mean z-score -1.94
Structure conservation index 0.85
SVM decision value 1.78
SVM RNA-class probability 0.976877
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21976270 118 - 27905053
UGCGUCAUUAAUAAUGGCAAUGUGCCAGAUGGACUUCUGGCAUCUGGCCCACUUGAUGGCCAGCAGCUGUAAUUCCGAGGCCUUGUCUCCGGUCAUAUAUUUCAAUACGUGACGGACA
(((((((((((....(((...((((((((......))))))))...)))...))))))))..)))........((((((((...)))))..((((..(((....)))..))))))).. ( -40.20)
>DroSec_CAF1 15751 118 - 1
UGCGUCAUUAAUAAUGGCAAUGUGCCAGAUGGACUUCUGGCAUCUGGCCCACUUGAUGGCCAGCAGCUGUAAUUCCGAGACCUUGUCUCCGGUCAUAUAUUUCAAUACGUGACGGACA
(((((((((((....(((...((((((((......))))))))...)))...))))))))..)))........((((((((...)))))..((((..(((....)))..))))))).. ( -40.80)
>DroEre_CAF1 15640 118 - 1
UGCGUCAUUAAUAAUGGCAAUGUGCCAGAUGGACUUCUGGCAUCUGGCCCACUUGAUGGCCAGCAGCUGUAAUUCCAAGGCCUUGUCUCCGGUCAUAUAUUUCAAUACGUGACGGACA
..((((((.....(((((...((((((((......))))))))((((((........))))))..)))))........((((........))))..............)))))).... ( -38.90)
>DroYak_CAF1 16479 118 - 1
UGCGUCAUUAAUAAUGGCAAUGUGCCAGAUGGACUUCUGGCAUCUGGCCCACUUGAUGGCCAGCAGCUGUAAUUCCGAGGCCUUGUCUCCGGUCAUAUAUUUCAAUACGUGACGGACA
(((((((((((....(((...((((((((......))))))))...)))...))))))))..)))........((((((((...)))))..((((..(((....)))..))))))).. ( -40.20)
>DroAna_CAF1 23242 117 - 1
UGCAUCAUUAAUAAUGGCAGUGCGCCAGAUACCCAGAUGGC-CCAGUUCCACUUGAUGGCCAGCAUCUGGCAUUCCGAGGCCUCGUGUCCGCUCAUAUAUUACAAUACGUGCCGGACA
...............(((..((.(((((((.......((((-((((......)))..)))))..)))))))....))..)))...((((((..((..(((....)))..)).)))))) ( -31.30)
>consensus
UGCGUCAUUAAUAAUGGCAAUGUGCCAGAUGGACUUCUGGCAUCUGGCCCACUUGAUGGCCAGCAGCUGUAAUUCCGAGGCCUUGUCUCCGGUCAUAUAUUUCAAUACGUGACGGACA
(((((((((((....(((...((((((((......))))))))...)))...))))))))..)))........((((((((...)))))..((((..(((....)))..))))))).. (-32.36 = -33.68 +   1.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,976,310 – 21,976,410
Length 100
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 90.80
Mean single sequence MFE -37.22
Consensus MFE -30.48
Energy contribution -31.60
Covariance contribution 1.12
Combinations/Pair 1.09
Mean z-score -3.17
Structure conservation index 0.82
SVM decision value 3.23
SVM RNA-class probability 0.998788
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21976310 100 + 27905053
UCGGAAUUACAGCUGCUGGCCAUCAAGUGGGCCAGAUGCCAGAAGUCCAUCUGGCACAUUGCCAUUAUUAAUGACGCAAUUGACAUGGCCAGCAUGCAGU
...........((((((((((((......(((.(..(((((((......)))))))..).)))....(((((......))))).)))))))))).))... ( -38.70)
>DroSec_CAF1 15791 100 + 1
UCGGAAUUACAGCUGCUGGCCAUCAAGUGGGCCAGAUGCCAGAAGUCCAUCUGGCACAUUGCCAUUAUUAAUGACGCAAUUGACAUGGCCAGCAUGCAGU
...........((((((((((((......(((.(..(((((((......)))))))..).)))....(((((......))))).)))))))))).))... ( -38.70)
>DroEre_CAF1 15680 100 + 1
UUGGAAUUACAGCUGCUGGCCAUCAAGUGGGCCAGAUGCCAGAAGUCCAUCUGGCACAUUGCCAUUAUUAAUGACGCAAUUGACAUGGCCAGCAUGCAGG
...........((((((((((((......(((.(..(((((((......)))))))..).)))....(((((......))))).)))))))))).))... ( -38.70)
>DroYak_CAF1 16519 100 + 1
UCGGAAUUACAGCUGCUGGCCAUCAAGUGGGCCAGAUGCCAGAAGUCCAUCUGGCACAUUGCCAUUAUUAAUGACGCAAUUGACAUGGCCAGCAUGCAGU
...........((((((((((((......(((.(..(((((((......)))))))..).)))....(((((......))))).)))))))))).))... ( -38.70)
>DroAna_CAF1 23282 99 + 1
UCGGAAUGCCAGAUGCUGGCCAUCAAGUGGAACUGG-GCCAUCUGGGUAUCUGGCGCACUGCCAUUAUUAAUGAUGCAAUUGACAUGCCCUGCAUGGACU
.(((..(((((((((((((((....((.....)).)-))).....)))))))))))..))).(((((....))))).......(((((...))))).... ( -31.30)
>consensus
UCGGAAUUACAGCUGCUGGCCAUCAAGUGGGCCAGAUGCCAGAAGUCCAUCUGGCACAUUGCCAUUAUUAAUGACGCAAUUGACAUGGCCAGCAUGCAGU
...........((((((((((((((((((.((((((((.........)))))))).)))((((((.....)))..))).))))..))))))))).))... (-30.48 = -31.60 +   1.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,976,310 – 21,976,410
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 90.80
Mean single sequence MFE -38.00
Consensus MFE -32.36
Energy contribution -33.28
Covariance contribution 0.92
Combinations/Pair 1.06
Mean z-score -3.47
Structure conservation index 0.85
SVM decision value 4.06
SVM RNA-class probability 0.999779
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21976310 100 - 27905053
ACUGCAUGCUGGCCAUGUCAAUUGCGUCAUUAAUAAUGGCAAUGUGCCAGAUGGACUUCUGGCAUCUGGCCCACUUGAUGGCCAGCAGCUGUAAUUCCGA
((.((.(((((((((..((((....(((((.....)))))..((.((((((((..(....).)))))))).)).))))))))))))))).))........ ( -40.60)
>DroSec_CAF1 15791 100 - 1
ACUGCAUGCUGGCCAUGUCAAUUGCGUCAUUAAUAAUGGCAAUGUGCCAGAUGGACUUCUGGCAUCUGGCCCACUUGAUGGCCAGCAGCUGUAAUUCCGA
((.((.(((((((((..((((....(((((.....)))))..((.((((((((..(....).)))))))).)).))))))))))))))).))........ ( -40.60)
>DroEre_CAF1 15680 100 - 1
CCUGCAUGCUGGCCAUGUCAAUUGCGUCAUUAAUAAUGGCAAUGUGCCAGAUGGACUUCUGGCAUCUGGCCCACUUGAUGGCCAGCAGCUGUAAUUCCAA
...((.(((((((((..((((....(((((.....)))))..((.((((((((..(....).)))))))).)).)))))))))))))))........... ( -39.80)
>DroYak_CAF1 16519 100 - 1
ACUGCAUGCUGGCCAUGUCAAUUGCGUCAUUAAUAAUGGCAAUGUGCCAGAUGGACUUCUGGCAUCUGGCCCACUUGAUGGCCAGCAGCUGUAAUUCCGA
((.((.(((((((((..((((....(((((.....)))))..((.((((((((..(....).)))))))).)).))))))))))))))).))........ ( -40.60)
>DroAna_CAF1 23282 99 - 1
AGUCCAUGCAGGGCAUGUCAAUUGCAUCAUUAAUAAUGGCAGUGCGCCAGAUACCCAGAUGGC-CCAGUUCCACUUGAUGGCCAGCAUCUGGCAUUCCGA
.((((.....))))((((((..(((.(((((((...(((.(.((.((((..........))))-.)).).))).)))))))...)))..))))))..... ( -28.40)
>consensus
ACUGCAUGCUGGCCAUGUCAAUUGCGUCAUUAAUAAUGGCAAUGUGCCAGAUGGACUUCUGGCAUCUGGCCCACUUGAUGGCCAGCAGCUGUAAUUCCGA
..(((((((((((((..((((.((.(((((.....)))))...((((((((......))))))))......)).)))))))))))))..))))....... (-32.36 = -33.28 +   0.92)

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 13:04:14 2006