Locus 3954

Sequence ID 2L_DroMel_CAF1
Location 11,521,990 – 11,522,118
Length 128
Max. P 0.988575
window6234 window6235 window6236 window6237

overview

Window 4

Location 11,521,990 – 11,522,097
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.14
Mean single sequence MFE -48.72
Consensus MFE -32.24
Energy contribution -33.24
Covariance contribution 1.00
Combinations/Pair 1.13
Mean z-score -2.35
Structure conservation index 0.66
SVM decision value 2.13
SVM RNA-class probability 0.988575
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11521990 107 + 22407834
-UAUAGAGAGCUGGAAAUUUGUUUUCUGGGAGGC------------UUGUAUGCCGGCGGUCUUUCGCGAAUGUUCGUGGGUGCUCCACCCACGGUAUCAUGAGCUGAGUAAGCCGGCGG
-..((((((((.........))))))))......------------.....(((((((...(((..((..(((.(((((((((...)))))))))...)))..)).)))...))))))). ( -43.20)
>DroSec_CAF1 3928 119 + 1
-UACAGAGAUCCGGAAUUUGGUUUUCUGUGUGGCUGGUCGCGGGUAUUGUAUGCCGGCGGCCUCUCGCGAAUGUUUGUGGGUGCUCCACCCACGGUAUCAUGCGCUGAGUACGCCGGCGG
-((((((((.(((.....))).))))))))((((.((((((.(((((...))))).)))))).((((((.(((.(((((((((...)))))))))...))).))).)))...)))).... ( -53.90)
>DroSim_CAF1 3581 119 + 1
-UACAGAGAUCCGGAAUUCGGUUUUCUGUGUGGCUUGUCGCGGGGCUUGUAUGCCGGCGGCCUCUCGCGAAUGUUUGUGGGUGCUCCACCCACGGUAUCAUGCGCUGAGUACGCCGGCGG
-((((((((.(((.....))).))))))))..((..(((....)))..)).((((((((..(((..(((.(((.(((((((((...)))))))))...))).))).)))..)))))))). ( -56.70)
>DroEre_CAF1 2959 119 + 1
-UAUAGAGAGCUGGAACUUUGCUUACUGGAUGGCUUGUUCAGUGGUGUGUAGGCCGGCGGUCUCUCGCGAAUGUUCGUGGGAGCUCCACCCACGGUAUCAUGAGCUGAGUACGCCGGCGG
-((((.(..((((.(((...(((........)))..)))))))..).)))).(((((((..(((..((..(((.(((((((.......)))))))...)))..)).)))..))))))).. ( -48.60)
>DroYak_CAF1 3639 105 + 1
AUAUAGGGAGCU---------------GGAUGCCUUUUUUUGGGGCUCGUAGGCCGGCGGAGUUUCGCGAAUGUUCGUGCGAGCUCCACUUACAGUAUCAUGAGCUGAGUACGCCGGCGG
..........((---------------(((.(((((.....))))))).)))((((((((((((((((((....))))).))))))).....((((.......)))).....)))))).. ( -41.20)
>consensus
_UAUAGAGAGCUGGAAUUUGGUUUUCUGGGUGGCUUGUCGCGGGGCUUGUAUGCCGGCGGCCUCUCGCGAAUGUUCGUGGGUGCUCCACCCACGGUAUCAUGAGCUGAGUACGCCGGCGG
..........((((((.......)))))).......................(((((((....(((((..(((.(((((((((...)))))))))...)))..)).)))..))))))).. (-32.24 = -33.24 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,521,990 – 11,522,097
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.14
Mean single sequence MFE -37.38
Consensus MFE -24.88
Energy contribution -26.80
Covariance contribution 1.92
Combinations/Pair 1.04
Mean z-score -2.26
Structure conservation index 0.67
SVM decision value 1.92
SVM RNA-class probability 0.982768
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11521990 107 - 22407834
CCGCCGGCUUACUCAGCUCAUGAUACCGUGGGUGGAGCACCCACGAACAUUCGCGAAAGACCGCCGGCAUACAA------------GCCUCCCAGAAAACAAAUUUCCAGCUCUCUAUA-
..((((((...((..((..(((....((((((((...))))))))..)))..))...))...))))))......------------.................................- ( -29.40)
>DroSec_CAF1 3928 119 - 1
CCGCCGGCGUACUCAGCGCAUGAUACCGUGGGUGGAGCACCCACAAACAUUCGCGAGAGGCCGCCGGCAUACAAUACCCGCGACCAGCCACACAGAAAACCAAAUUCCGGAUCUCUGUA-
..(((((((..(((.(((.(((.....(((((((...)))))))...))).)))..)))..)))))))...........((.....))...(((((...((.......))...))))).- ( -45.20)
>DroSim_CAF1 3581 119 - 1
CCGCCGGCGUACUCAGCGCAUGAUACCGUGGGUGGAGCACCCACAAACAUUCGCGAGAGGCCGCCGGCAUACAAGCCCCGCGACAAGCCACACAGAAAACCGAAUUCCGGAUCUCUGUA-
..(((((((..(((.(((.(((.....(((((((...)))))))...))).)))..)))..)))))))...........((.....))...(((((...(((.....)))...))))).- ( -47.90)
>DroEre_CAF1 2959 119 - 1
CCGCCGGCGUACUCAGCUCAUGAUACCGUGGGUGGAGCUCCCACGAACAUUCGCGAGAGACCGCCGGCCUACACACCACUGAACAAGCCAUCCAGUAAGCAAAGUUCCAGCUCUCUAUA-
..(((((((..(((.((..(((....((((((.......))))))..)))..))..)))..))))))).........................((..(((.........)))..))...- ( -34.90)
>DroYak_CAF1 3639 105 - 1
CCGCCGGCGUACUCAGCUCAUGAUACUGUAAGUGGAGCUCGCACGAACAUUCGCGAAACUCCGCCGGCCUACGAGCCCCAAAAAAAGGCAUCC---------------AGCUCCCUAUAU
..(((((((((.(((.....)))))).......((((.((((..........))))..))))))))))....((((((........)).....---------------.))))....... ( -29.50)
>consensus
CCGCCGGCGUACUCAGCUCAUGAUACCGUGGGUGGAGCACCCACGAACAUUCGCGAGAGACCGCCGGCAUACAAGCCCCGCAACAAGCCACCCAGAAAACAAAAUUCCAGCUCUCUAUA_
..(((((((..(((.((..(((....((((((((...))))))))..)))..))..)))..))))))).................................................... (-24.88 = -26.80 +   1.92)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,522,023 – 11,522,118
Length 95
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 80.48
Mean single sequence MFE -44.84
Consensus MFE -35.12
Energy contribution -35.44
Covariance contribution 0.32
Combinations/Pair 1.13
Mean z-score -1.98
Structure conservation index 0.78
SVM decision value 1.16
SVM RNA-class probability 0.924019
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11522023 95 + 22407834
------UUGUAUGCCGGCGGUCUUUCGCGAAUGUUCGUGGGUGCUCCACCCACGGUAUCAUGAGCUGAGUAAGCCGGCGGAGGUCCUUUGGGCAAAU---------------UGUG
------.....(((((((...(((..((..(((.(((((((((...)))))))))...)))..)).)))...)))))))...((((...))))....---------------.... ( -39.80)
>DroSec_CAF1 3967 101 + 1
CGGGUAUUGUAUGCCGGCGGCCUCUCGCGAAUGUUUGUGGGUGCUCCACCCACGGUAUCAUGCGCUGAGUACGCCGGCGGAGGACCUUUGGGCAAAU---------------UGUG
.((((......((((((((..(((..(((.(((.(((((((((...)))))))))...))).))).)))..))))))))....))))..........---------------.... ( -45.30)
>DroSim_CAF1 3620 101 + 1
CGGGGCUUGUAUGCCGGCGGCCUCUCGCGAAUGUUUGUGGGUGCUCCACCCACGGUAUCAUGCGCUGAGUACGCCGGCGGAGGACCUUUGGGCAAAU---------------UGUG
.(((((((...((((((((..(((..(((.(((.(((((((((...)))))))))...))).))).)))..)))))))).))).)))).........---------------.... ( -45.60)
>DroEre_CAF1 2998 116 + 1
AGUGGUGUGUAGGCCGGCGGUCUCUCGCGAAUGUUCGUGGGAGCUCCACCCACGGUAUCAUGAGCUGAGUACGCCGGCGGAGGUCCUUUGGGCAAGUUAGAUCCACCUCCAGUGCG
........(((.(((((((..(((..((..(((.(((((((.......)))))))...)))..)).)))..)))))))((((((.....((((......).)))))))))..))). ( -48.50)
>DroYak_CAF1 3664 101 + 1
UGGGGCUCGUAGGCCGGCGGAGUUUCGCGAAUGUUCGUGCGAGCUCCACUUACAGUAUCAUGAGCUGAGUACGCCGGCGGAGGUCCUUUGGGCGAA--------------AG-UCU
.(((.(((....((((((((((((((((((....))))).))))))).....((((.......)))).....)))))).))).)))...((((...--------------.)-))) ( -45.00)
>consensus
CGGGGCUUGUAUGCCGGCGGCCUCUCGCGAAUGUUCGUGGGUGCUCCACCCACGGUAUCAUGAGCUGAGUACGCCGGCGGAGGUCCUUUGGGCAAAU_______________UGUG
......((((..(((((((....(((((..(((.(((((((((...)))))))))...)))..)).)))..)))))))((....)).....))))..................... (-35.12 = -35.44 +   0.32)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,522,023 – 11,522,118
Length 95
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 80.48
Mean single sequence MFE -36.70
Consensus MFE -27.32
Energy contribution -27.68
Covariance contribution 0.36
Combinations/Pair 1.09
Mean z-score -2.04
Structure conservation index 0.74
SVM decision value 1.17
SVM RNA-class probability 0.925052
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11522023 95 - 22407834
CACA---------------AUUUGCCCAAAGGACCUCCGCCGGCUUACUCAGCUCAUGAUACCGUGGGUGGAGCACCCACGAACAUUCGCGAAAGACCGCCGGCAUACAA------
....---------------...........((....))((((((...((..((..(((....((((((((...))))))))..)))..))...))...))))))......------ ( -31.10)
>DroSec_CAF1 3967 101 - 1
CACA---------------AUUUGCCCAAAGGUCCUCCGCCGGCGUACUCAGCGCAUGAUACCGUGGGUGGAGCACCCACAAACAUUCGCGAGAGGCCGCCGGCAUACAAUACCCG
....---------------...........((....))(((((((..(((.(((.(((.....(((((((...)))))))...))).)))..)))..)))))))............ ( -39.70)
>DroSim_CAF1 3620 101 - 1
CACA---------------AUUUGCCCAAAGGUCCUCCGCCGGCGUACUCAGCGCAUGAUACCGUGGGUGGAGCACCCACAAACAUUCGCGAGAGGCCGCCGGCAUACAAGCCCCG
....---------------....((.....((....))(((((((..(((.(((.(((.....(((((((...)))))))...))).)))..)))..)))))))......)).... ( -40.30)
>DroEre_CAF1 2998 116 - 1
CGCACUGGAGGUGGAUCUAACUUGCCCAAAGGACCUCCGCCGGCGUACUCAGCUCAUGAUACCGUGGGUGGAGCUCCCACGAACAUUCGCGAGAGACCGCCGGCCUACACACCACU
......((.(((((.(((..(((((.....(((.(((((((.(((...(((.....)))...))).))))))).)))...((....)))))))))))))))..))........... ( -41.80)
>DroYak_CAF1 3664 101 - 1
AGA-CU--------------UUCGCCCAAAGGACCUCCGCCGGCGUACUCAGCUCAUGAUACUGUAAGUGGAGCUCGCACGAACAUUCGCGAAACUCCGCCGGCCUACGAGCCCCA
...-..--------------..........((..(((.(((((((((.(((.....)))))).......((((.((((..........))))..))))))))))....)))..)). ( -30.60)
>consensus
CACA_______________AUUUGCCCAAAGGACCUCCGCCGGCGUACUCAGCUCAUGAUACCGUGGGUGGAGCACCCACGAACAUUCGCGAGAGACCGCCGGCAUACAAGCCCCG
.......................(((....(((.(((((((.(((...(((.....)))...))).))))))).)))...........(((......))).)))............ (-27.32 = -27.68 +   0.36)

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 11:05:41 2006