Locus 210

Sequence ID 3R_DroMel_CAF1
Location 870,520 – 870,753
Length 233
Max. P 0.994585
window371 window372 window373 window374 window375

overview

Window 1

Location 870,520 – 870,638
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.01
Mean single sequence MFE -36.52
Consensus MFE -27.01
Energy contribution -30.57
Covariance contribution 3.56
Combinations/Pair 1.09
Mean z-score -2.78
Structure conservation index 0.74
SVM decision value 1.85
SVM RNA-class probability 0.980127
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 870520 118 + 27905053
AAACCACCGCAUCGCAAAAUGUGGAGCGAAUAACCAAAGAGAAUCGGAUAAAAAGCCGACAGAGCG--AGCAGCUCAUAGAGCAGUUAUGAGCUGGUCGGCUAAGCGAUUCAACUGGGUU
.((((..(((..(((.....)))..)))............((((((.......(((((((......--..((((((((((.....)))))))))))))))))...)))))).....)))) ( -40.00)
>DroSec_CAF1 45515 106 + 1
AAACCGCCGCAUCGCAAAAUGUGGAGCGAAUAACCGAAGAGAAUCGGAUAAAAAGCCGACAGAUCG--AG------------CAGUUAUGAGCUGGUCGGCUAAGCGAUUCAACUGGGUU
.((((.((((((......)))))).((......((((......))))......(((((((((.(((--..------------......))).)).)))))))..))..........)))) ( -30.60)
>DroSim_CAF1 44737 118 + 1
AAACCGCCGCAUCGCAAAAUGUGGAGCGAAUAACCGAAGAGAAUCGGAUAAAAAGCCGACAGAUCG--AGCAGCUUAUAGAGCAGUUAUGAGCUGGUCGGCUAAGCGAUUCAACUGGGUU
.((((.((((((......)))))).((......((((......))))......(((((((......--..((((((((((.....)))))))))))))))))..))..........)))) ( -38.30)
>DroEre_CAF1 44739 120 + 1
AAGCCAUCGCAUCGCAAAAUGUGGAGCGAAUAACUGAGGAGAAUAGGCUAAAAAGCCAACUGAAAGCUGCACGCUCAUGGAGCAGUUAUGAGCUGGUCGGCUAAUAGAUUCAAUUGGGUG
..(((.((((..(((.....)))..))))...........((((.((((....))))..(((..((((((..((((((((.....))))))))..).)))))..))))))).....))). ( -37.20)
>consensus
AAACCACCGCAUCGCAAAAUGUGGAGCGAAUAACCGAAGAGAAUCGGAUAAAAAGCCGACAGAUCG__AGCAGCUCAUAGAGCAGUUAUGAGCUGGUCGGCUAAGCGAUUCAACUGGGUU
.((((..(((..(((.....)))..)))............((((((.......(((((((..........((((((((((.....)))))))))))))))))...)))))).....)))) (-27.01 = -30.57 +   3.56) 

alignment

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secondary structure

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Window 2

Location 870,520 – 870,638
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.01
Mean single sequence MFE -32.07
Consensus MFE -21.99
Energy contribution -25.55
Covariance contribution 3.56
Combinations/Pair 1.03
Mean z-score -2.18
Structure conservation index 0.69
SVM decision value 0.83
SVM RNA-class probability 0.860587
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 870520 118 - 27905053
AACCCAGUUGAAUCGCUUAGCCGACCAGCUCAUAACUGCUCUAUGAGCUGCU--CGCUCUGUCGGCUUUUUAUCCGAUUCUCUUUGGUUAUUCGCUCCACAUUUUGCGAUGCGGUGGUUU
.((((((..((((((...((((((((((((((((.......)))))))))..--......))))))).......))))))...)))((...((((..........)))).)))))..... ( -37.40)
>DroSec_CAF1 45515 106 - 1
AACCCAGUUGAAUCGCUUAGCCGACCAGCUCAUAACUG------------CU--CGAUCUGUCGGCUUUUUAUCCGAUUCUCUUCGGUUAUUCGCUCCACAUUUUGCGAUGCGGCGGUUU
((((..((((.(((((..(((((((.((.((.......------------..--.)).)))))))))......((((......))))..................))))).)))))))). ( -29.20)
>DroSim_CAF1 44737 118 - 1
AACCCAGUUGAAUCGCUUAGCCGACCAGCUCAUAACUGCUCUAUAAGCUGCU--CGAUCUGUCGGCUUUUUAUCCGAUUCUCUUCGGUUAUUCGCUCCACAUUUUGCGAUGCGGCGGUUU
((((..((((.(((((..((((((((((((.(((.......))).)))))..--......)))))))......((((......))))..................))))).)))))))). ( -32.80)
>DroEre_CAF1 44739 120 - 1
CACCCAAUUGAAUCUAUUAGCCGACCAGCUCAUAACUGCUCCAUGAGCGUGCAGCUUUCAGUUGGCUUUUUAGCCUAUUCUCCUCAGUUAUUCGCUCCACAUUUUGCGAUGCGAUGGCUU
.........(((((((..(((((((.(((((((....((((...))))))).))))....)))))))...)))...)))).....((((((.(((((((.....)).)).))))))))). ( -28.90)
>consensus
AACCCAGUUGAAUCGCUUAGCCGACCAGCUCAUAACUGCUCUAUGAGCUGCU__CGAUCUGUCGGCUUUUUAUCCGAUUCUCUUCGGUUAUUCGCUCCACAUUUUGCGAUGCGGCGGUUU
...((....((((((...((((((((((((((((.......)))))))))..........))))))).......))))))......((...((((..........)))).))...))... (-21.99 = -25.55 +   3.56) 

alignment

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secondary structure

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dotplot

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Window 3

Location 870,560 – 870,676
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.95
Mean single sequence MFE -37.92
Consensus MFE -23.01
Energy contribution -27.07
Covariance contribution 4.06
Combinations/Pair 1.10
Mean z-score -2.86
Structure conservation index 0.61
SVM decision value 2.49
SVM RNA-class probability 0.994585
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 870560 116 + 27905053
GAAUCGGAUAAAAAGCCGACAGAGCG--AGCAGCUCAUAGAGCAGUUAUGAGCUGGUCGGCUAAGCGAUUCAACUGGGUU--ACAAUAAUUAGCAGGAGCCCCGGCUCCGAAACCAAUGU
((((((.......(((((((......--..((((((((((.....)))))))))))))))))...))))))...((((((--(.......)))).(((((....)))))....))).... ( -42.50)
>DroSec_CAF1 45555 104 + 1
GAAUCGGAUAAAAAGCCGACAGAUCG--AG------------CAGUUAUGAGCUGGUCGGCUAAGCGAUUCAACUGGGUU--ACAAUAAUUAGCCGGAGCCCCGGCUCCAAAAGCAAUUU
((((((.......(((((((((.(((--..------------......))).)).)))))))...)))))).....((((--(.......)))))(((((....)))))........... ( -33.00)
>DroSim_CAF1 44777 116 + 1
GAAUCGGAUAAAAAGCCGACAGAUCG--AGCAGCUUAUAGAGCAGUUAUGAGCUGGUCGGCUAAGCGAUUCAACUGGGUU--ACAAUAAUUAGCCGGAGCCCCGGCUCCAAAAGCAAUUU
((((((.......(((((((......--..((((((((((.....)))))))))))))))))...)))))).....((((--(.......)))))(((((....)))))........... ( -40.70)
>DroEre_CAF1 44779 114 + 1
GAAUAGGCUAAAAAGCCAACUGAAAGCUGCACGCUCAUGGAGCAGUUAUGAGCUGGUCGGCUAAUAGAUUCAAUUGGGUGAUUCGAUGUUUAACCAGAGGACCGGCUCC------AGUUU
.....((((....))))(((((..((((((.(.(....)).))))))..(((((((((..((..(((((((((((....)))).)).)))))...))..))))))))))------)))). ( -35.50)
>consensus
GAAUCGGAUAAAAAGCCGACAGAUCG__AGCAGCUCAUAGAGCAGUUAUGAGCUGGUCGGCUAAGCGAUUCAACUGGGUU__ACAAUAAUUAGCCGGAGCCCCGGCUCCAAAAGCAAUUU
((((((.......(((((((..........((((((((((.....)))))))))))))))))...)))))).....(((.............)))(((((....)))))........... (-23.01 = -27.07 +   4.06) 

alignment

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secondary structure

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dotplot

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Window 4

Location 870,560 – 870,676
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.95
Mean single sequence MFE -34.09
Consensus MFE -22.46
Energy contribution -25.90
Covariance contribution 3.44
Combinations/Pair 1.11
Mean z-score -2.31
Structure conservation index 0.66
SVM decision value 1.68
SVM RNA-class probability 0.971542
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 870560 116 - 27905053
ACAUUGGUUUCGGAGCCGGGGCUCCUGCUAAUUAUUGU--AACCCAGUUGAAUCGCUUAGCCGACCAGCUCAUAACUGCUCUAUGAGCUGCU--CGCUCUGUCGGCUUUUUAUCCGAUUC
..(((((....(((((....)))))(((........))--)..))))).((((((...((((((((((((((((.......)))))))))..--......))))))).......)))))) ( -40.90)
>DroSec_CAF1 45555 104 - 1
AAAUUGCUUUUGGAGCCGGGGCUCCGGCUAAUUAUUGU--AACCCAGUUGAAUCGCUUAGCCGACCAGCUCAUAACUG------------CU--CGAUCUGUCGGCUUUUUAUCCGAUUC
...((((......((((((....)))))).......))--)).......((((((...(((((((.((.((.......------------..--.)).))))))))).......)))))) ( -29.82)
>DroSim_CAF1 44777 116 - 1
AAAUUGCUUUUGGAGCCGGGGCUCCGGCUAAUUAUUGU--AACCCAGUUGAAUCGCUUAGCCGACCAGCUCAUAACUGCUCUAUAAGCUGCU--CGAUCUGUCGGCUUUUUAUCCGAUUC
...((((......((((((....)))))).......))--)).......((((((...((((((((((((.(((.......))).)))))..--......))))))).......)))))) ( -33.42)
>DroEre_CAF1 44779 114 - 1
AAACU------GGAGCCGGUCCUCUGGUUAAACAUCGAAUCACCCAAUUGAAUCUAUUAGCCGACCAGCUCAUAACUGCUCCAUGAGCGUGCAGCUUUCAGUUGGCUUUUUAGCCUAUUC
.((((------(((((.((((....((((((.....((.(((......))).))..)))))))))).))))......(((.(((....))).)))...)))))((((....))))..... ( -32.20)
>consensus
AAAUUGCUUUUGGAGCCGGGGCUCCGGCUAAUUAUUGU__AACCCAGUUGAAUCGCUUAGCCGACCAGCUCAUAACUGCUCUAUGAGCUGCU__CGAUCUGUCGGCUUUUUAUCCGAUUC
.............((((((....))))))....................((((((...((((((((((((((((.......)))))))))..........))))))).......)))))) (-22.46 = -25.90 +   3.44) 

alignment

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secondary structure

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dotplot

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Window 5

Location 870,638 – 870,753
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.53
Mean single sequence MFE -38.25
Consensus MFE -28.50
Energy contribution -28.00
Covariance contribution -0.50
Combinations/Pair 1.17
Mean z-score -1.70
Structure conservation index 0.75
SVM decision value 0.38
SVM RNA-class probability 0.712565
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 870638 115 + 27905053
--ACAAUAAUUAGCAGGAGCCCCGGCUCCGAAACCAAUGUUCGGGCGUGAAUGCAACUGCAUGUGGCUCUUGUUGCCUCUUCGGCCCGAUGUGG---CGACCCCGAACAAUGUAAUUCCA
--.............(((((....)))))(((..((.((((((((.((.(((((....)))).).))....((((((.(.(((...))).).))---)))))))))))).))...))).. ( -39.90)
>DroSec_CAF1 45621 115 + 1
--ACAAUAAUUAGCCGGAGCCCCGGCUCCAAAAGCAAUUUUCGGGCGUGGAUGCAACUGCAUGUGGCUCUCGUUGCCUCUUCGGCCCGAUGUGG---CGACCCCAAACAAUGUAAUUCCA
--..........((((((((....)))))....(((....((((((..(((.(((((.((.....))....))))).)))...)))))))))))---)...................... ( -37.80)
>DroSim_CAF1 44855 115 + 1
--ACAAUAAUUAGCCGGAGCCCCGGCUCCAAAAGCAAUUUUCGGGCGUGGAUGCAACUGCAUGUGGCUCUCGUUGCCUCUUCGGCCCGAUGUGG---CGACCCCAAACAAUGUAAUUCCA
--..........((((((((....)))))....(((....((((((..(((.(((((.((.....))....))))).)))...)))))))))))---)...................... ( -37.80)
>DroEre_CAF1 44859 111 + 1
AUUCGAUGUUUAACCAGAGGACCGGCUCC------AGUUUUCGGGCCCGAAUGCAACUGCAUGCGGCUCUU-UUGCC--UUCGGCCCGAUGGGGUUUCGACCCCAAACAAUGUAAUUCCA
..................(((...((...------.....(((((((.((((((....))))..(((....-..)))--.)))))))))((((((....))))))......))...))). ( -37.50)
>consensus
__ACAAUAAUUAGCCGGAGCCCCGGCUCCAAAAGCAAUUUUCGGGCGUGAAUGCAACUGCAUGUGGCUCUCGUUGCCUCUUCGGCCCGAUGUGG___CGACCCCAAACAAUGUAAUUCCA
..(((..........(((((....)))))...........((((((.(((((((....))))..(((.......)))...))))))))))))............................ (-28.50 = -28.00 +  -0.50) 

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 09:37:38 2006