Locus 5022

Sequence ID 3L_DroMel_CAF1
Location 13,773,790 – 13,774,021
Length 231
Max. P 0.999939
window7943 window7944 window7945 window7946 window7947

overview

Window 3

Location 13,773,790 – 13,773,906
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.26
Mean single sequence MFE -38.49
Consensus MFE -34.44
Energy contribution -34.64
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -3.26
Structure conservation index 0.89
SVM decision value 4.69
SVM RNA-class probability 0.999939
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13773790 116 + 23771897
AUGGCAGGGGUCCCCUUCUCAGCCUUCAGAGGCCAUAAUAUCUUUGCCCCGCCAGAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGCCCCCCU----C
.((((.(((((..........((((....))))............)))))))))((.(((..(((.(((((((............))))))).)))..)))))............----. ( -38.15)
>DroSec_CAF1 20442 114 + 1
AUGGCAGGGGGCCCAUUCUCAGCCUUCAGAGGCCAUAAUAUCUUCGCC-CGCCAGAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCACCACAAGACCCCCC-----
.(((..((((((.......((((((((.(.(((.(........).)))-)....))).))))).(.(((((((............))))))).))))))).)))...........----- ( -37.60)
>DroSim_CAF1 15787 115 + 1
AUGGCAGGGGGCCCAUUCUCAGCCUUCAGAGGCCAUAAUAUCUUCGCCCCGCCAGAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGACCCCCC-----
.((((..(((((.........((((....))))............)))))))))((.(((..(((.(((((((............))))))).)))..)))))............----- ( -37.90)
>DroEre_CAF1 19912 120 + 1
AUGGCAGGGGGCCCAUUCUCAGCCUUCAGAGGCCAUAAUAUCUUUGCCCCGCCAGAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGUCCCCCCACUUU
.(((..(((((((((((((..((...((((((........))))))....)).)))))))..(((.(((((((............))))))).)))...........))))))))).... ( -39.70)
>DroYak_CAF1 18569 120 + 1
AUGGCAGGGGGCCCAUUCCCAGCCUUCGGAGGCCAUAAUAUCUUCGCCCCGCCAGAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGUCCACCCCCCUC
......((((((.......((((((((((.(((.(........).)))...)).))).))))).(.(((((((............))))))).))))))).................... ( -39.10)
>consensus
AUGGCAGGGGGCCCAUUCUCAGCCUUCAGAGGCCAUAAUAUCUUCGCCCCGCCAGAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGACCCCCC_____
......((((((.......((((((((.(.(((.(........).))).)....))).))))).(.(((((((............))))))).))))))).................... (-34.44 = -34.64 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,773,790 – 13,773,906
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.26
Mean single sequence MFE -46.28
Consensus MFE -40.76
Energy contribution -41.00
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -2.73
Structure conservation index 0.88
SVM decision value 3.89
SVM RNA-class probability 0.999688
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13773790 116 - 23771897
G----AGGGGGGCUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUCUGGCGGGGCAAAGAUAUUAUGGCCUCUGAAGGCUGAGAAGGGGACCCCUGCCAU
.----((((((.((((((((((..(((.(((((((............))))))).)))..)))))...))))).)...........(((((....)))))..........)))))..... ( -42.70)
>DroSec_CAF1 20442 114 - 1
-----GGGGGGUCUUGUGGUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUCUGGCG-GGCGAAGAUAUUAUGGCCUCUGAAGGCUGAGAAUGGGCCCCCUGCCAU
-----(((((((((..((((((((((..(((((((............))))))).(((.(((.....))).-.)))...........))))))....)))).....)))))))))..... ( -47.10)
>DroSim_CAF1 15787 115 - 1
-----GGGGGGUCUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUCUGGCGGGGCGAAGAUAUUAUGGCCUCUGAAGGCUGAGAAUGGGCCCCCUGCCAU
-----(((((((((((((((((..(((.(((((((............))))))).)))..)))))...))))))).....((((..(((((....)))))...))))..)))))...... ( -46.70)
>DroEre_CAF1 19912 120 - 1
AAAGUGGGGGGACUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUCUGGCGGGGCAAAGAUAUUAUGGCCUCUGAAGGCUGAGAAUGGGCCCCCUGCCAU
...(..((....))..)(((((..(((.(((((((............))))))).)))..))))).(((((((((.....((((..(((((....)))))...)))).)))))..)))). ( -48.50)
>DroYak_CAF1 18569 120 - 1
GAGGGGGGUGGACUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUCUGGCGGGGCGAAGAUAUUAUGGCCUCCGAAGGCUGGGAAUGGGCCCCCUGCCAU
.((((((.(.(.((.((..(((((((..(((((((............))))))).(((.(((.....)))...)))...........)))))))...)).))...).).))))))..... ( -46.40)
>consensus
_____GGGGGGACUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUCUGGCGGGGCGAAGAUAUUAUGGCCUCUGAAGGCUGAGAAUGGGCCCCCUGCCAU
.................(((((..(((.(((((((............))))))).)))..))))).((((((((......((((..(((((....)))))...))))....)))))))). (-40.76 = -41.00 +   0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,773,830 – 13,773,946
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.59
Mean single sequence MFE -29.69
Consensus MFE -25.20
Energy contribution -25.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.68
Structure conservation index 0.85
SVM decision value 3.10
SVM RNA-class probability 0.998424
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13773830 116 + 23771897
UCUUUGCCCCGCCAGAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGCCCCCCU----CCCCACCAUCUUUCAAGUGCCCUGGGUUGACACUCGCACAU
..........((.((.((((..(((.(((((((............))))))).)))..))))....(((((....----...(((..........)))....)))))....)).)).... ( -26.80)
>DroSec_CAF1 20482 109 + 1
UCUUCGCC-CGCCAGAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCACCACAAGACCCCCC----------CUACUUUCAAGUGCCCUGGGUUGACACUCGCACAU
........-.((.((..(((..(((.(((((((............))))))).)))..)))......(((((...----------.((((....))))....)))))....)).)).... ( -28.80)
>DroSim_CAF1 15827 109 + 1
UCUUCGCCCCGCCAGAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGACCCCCC-----------CACUUUCAAGUGCCCUGGGUUGACACUCGCACAU
..........((.((.((((..(((.(((((((............))))))).)))..)))).....(((((...-----------((((....))))....)))))....)).)).... ( -30.90)
>DroEre_CAF1 19952 118 + 1
UCUUUGCCCCGCCAGAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGUCCCCCCACUUUCCCCC--ACUUUCAAGUGCCCUGGGUUGACACUCGCACAA
..........((.((.((((..(((.(((((((............))))))).)))..)))).....(((..((((........(--(((....))))...))))..))).)).)).... ( -30.70)
>DroYak_CAF1 18609 120 + 1
UCUUCGCCCCGCCAGAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGUCCACCCCCCUCCCCCCACACUUUCAAGUGCCCUGGGUUGACACUCGCACAA
..........((.((.((((..(((.(((((((............))))))).)))..)))).....(((.((((...........((((....))))....)))).))).)).)).... ( -31.26)
>consensus
UCUUCGCCCCGCCAGAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGACCCCCC_____CCC_C_CACUUUCAAGUGCCCUGGGUUGACACUCGCACAU
..........(((.....))).(((.(((((((............))))))).))).......................................((((...((((....)))))))).. (-25.20 = -25.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,773,830 – 13,773,946
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.59
Mean single sequence MFE -38.72
Consensus MFE -35.00
Energy contribution -34.80
Covariance contribution -0.20
Combinations/Pair 1.06
Mean z-score -2.04
Structure conservation index 0.90
SVM decision value 2.48
SVM RNA-class probability 0.994499
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13773830 116 - 23771897
AUGUGCGAGUGUCAACCCAGGGCACUUGAAAGAUGGUGGGG----AGGGGGGCUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUCUGGCGGGGCAAAGA
.(((((((((.((..(((....((((........)))))))----...)).))))))(((((..(((.(((((((............))))))).)))..)))))........))).... ( -37.40)
>DroSec_CAF1 20482 109 - 1
AUGUGCGAGUGUCAACCCAGGGCACUUGAAAGUAG----------GGGGGGUCUUGUGGUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUCUGGCG-GGCGAAGA
.....((..((((((((((((((.((((....)))----------)....)))))).)))((..(((.(((((((............))))))).)))..))....)))))-..)).... ( -36.70)
>DroSim_CAF1 15827 109 - 1
AUGUGCGAGUGUCAACCCAGGGCACUUGAAAGUG-----------GGGGGGUCUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUCUGGCGGGGCGAAGA
.....((((((((.......))))))))......-----------.....((((((((((((..(((.(((((((............))))))).)))..)))))...)))))))..... ( -38.80)
>DroEre_CAF1 19952 118 - 1
UUGUGCGAGUGUCAACCCAGGGCACUUGAAAGU--GGGGGAAAGUGGGGGGACUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUCUGGCGGGGCAAAGA
((((.((((((((.......))))))))...((--.((.....(..((....))..)(((((..(((.(((((((............))))))).)))..))))))).))...))))... ( -41.00)
>DroYak_CAF1 18609 120 - 1
UUGUGCGAGUGUCAACCCAGGGCACUUGAAAGUGUGGGGGGAGGGGGGUGGACUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUCUGGCGGGGCGAAGA
((((.(.(.(.((..(((...(((((....)))))...)))..)).).).).((((((((((..(((.(((((((............))))))).)))..)))))...)))))))))... ( -39.70)
>consensus
AUGUGCGAGUGUCAACCCAGGGCACUUGAAAGUG_G_GGG_____GGGGGGACUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUCUGGCGGGGCGAAGA
.(((.((((((((.......))))))))........................((((((((((..(((.(((((((............))))))).)))..)))))...)))))))).... (-35.00 = -34.80 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,773,906 – 13,774,021
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 94.49
Mean single sequence MFE -24.41
Consensus MFE -22.10
Energy contribution -22.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.35
Structure conservation index 0.91
SVM decision value 0.81
SVM RNA-class probability 0.856485
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13773906 115 - 23771897
AUAAAUAAAAUAAAUGUAGGUGAAAAUAUACAUAAAUAAUGGGCACAAGCGCGGCUUUUUUUAUGAAGUGUUUGAAUGUGCGAGUGUCAACCCAGGGCACUUGAAAGAUGGUGGG
.............(((((.((....)).)))))........(((((..((((((((((......))))).......)))))..)))))..((((...((.((....)))).)))) ( -22.91)
>DroSec_CAF1 20556 110 - 1
AUAAAUAAAAUAAAUGUAGGUGAAAAUAUACAUAAAUAAUGGGCACAAGCGCGGCUUUUUUUAUGAAGUGUUUGAAUGUGCGAGUGUCAACCCAGGGCACUUGAAAGUAG-----
.............(((((.((....)).))))).........(((((..((..(((((......)))))...))..)))))(((((((.......)))))))........----- ( -22.60)
>DroSim_CAF1 15902 109 - 1
AUAAAUAAAAUAAAUGUAGGUGAAAAUAUACAUAAAUAAUGGGCACAAGCGCGGCUUUUUUUAUGAAGUGUUUGAAUGUGCGAGUGUCAACCCAGGGCACUUGAAAGUG------
.............(((((.((....)).))))).........(((((..((..(((((......)))))...))..)))))(((((((.......))))))).......------ ( -22.60)
>DroEre_CAF1 20032 112 - 1
AUAAAUAAAAUAAAUGUAGGUGAAAAUAUACAUAAAUAAUGGGCACAAGCGCGGCUUU-UUUAUGAAGUGUUUGAUUGUGCGAGUGUCAACCCAGGGCACUUGAAAGU--GGGGG
.............(((((.((....)).)))))........(((((..((((((((((-.....))))).......)))))..)))))..(((....((((....)))--).))) ( -25.01)
>DroYak_CAF1 18689 115 - 1
AUAAAUAAAAUAAAUGUAGGUGAAAAUAUACAUAAAUAAUGGGCACAAGCGCGGCUUUUUUUAUGAAGUGUUUGAUUGUGCGAGUGUCAACCCAGGGCACUUGAAAGUGUGGGGG
.............(((((.((....)).)))))........(((((..((((((((((......))))).......)))))..)))))..(((...(((((....))))).))). ( -28.91)
>consensus
AUAAAUAAAAUAAAUGUAGGUGAAAAUAUACAUAAAUAAUGGGCACAAGCGCGGCUUUUUUUAUGAAGUGUUUGAAUGUGCGAGUGUCAACCCAGGGCACUUGAAAGUG_G_GGG
.............(((((.((....)).))))).........((((((((((..(.........)..)))))))..))).((((((((.......))))))))............ (-22.10 = -22.10 +  -0.00)

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 11:39:51 2006