Locus 201

Sequence ID 3L_DroMel_CAF1
Location 568,545 – 568,853
Length 308
Max. P 0.995623
window289 window290 window291 window292 window293 window294 window295 window296

overview

Window 9

Location 568,545 – 568,665
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.27
Mean single sequence MFE -48.42
Consensus MFE -46.34
Energy contribution -46.77
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -2.35
Structure conservation index 0.96
SVM decision value 2.04
SVM RNA-class probability 0.986466
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 568545 120 + 23771897
CACCUGUGCGUUUGUCUAUGACGUGCUAGGUUGGAGGAUGUGGAGUAUUUCUUUCCGCACUCGGGACAGAUGUGCUCGUCCUCCAGCAACGAAGUGCUGUUGAGGAUUUCGCCCUGCUCC
.(((((..((((.......))))..).))))((((((((...((((((.((((((((....))))).))).))))))))))))))(((.((((((.((....)).))))))...)))... ( -47.40)
>DroSec_CAF1 1 115 + 1
-----GUGCGUUUGUCUAUGACGUGCUAGGUUGGAGGAUGUGGAGUACUUCUUUCCGCACUCGGGACAGAUGUGCUCGUCCUCCAGCAGCGAAGUGCUGUUGAGGAUCUCGCCCUGCUCC
-----(..((((.......))))..)(((((((((((((...((((((.((((((((....))))).))).)))))))))))))))).((((..(.((....)).)..)))).))).... ( -46.50)
>DroSim_CAF1 1 120 + 1
CACCUGUGCGUUUGUCUAUGACGUGCUAGGUUGGAGGAUGUGGAGUACUUCUUUCCGCACUCGGGACAGAUGUGCUCGUCCUCCAGCAGCGAAGUGCUGUUGAGGAUUUCGCCCUGCUCC
.(((((..((((.......))))..).))))((((((((...((((((.((((((((....))))).))).))))))))))))))((((((((((.((....)).)))))))..)))... ( -52.30)
>DroEre_CAF1 1 115 + 1
-----GUGCGUUUGUCUAUGACGUGCCAGGUUGGAGGAUGUGGAGUACUUCUUUCCGCACUCGGGACAGAUGUGCUCGUCCUCCAGCAGCGAGCUGCUGUUGAGGAUUUCGCCCGGCUCC
-----..(((((.......)))))(((..((((((((((...((((((.((((((((....))))).))).)))))))))))))))).(((((.(.((....)).).)))))..)))... ( -47.50)
>consensus
_____GUGCGUUUGUCUAUGACGUGCUAGGUUGGAGGAUGUGGAGUACUUCUUUCCGCACUCGGGACAGAUGUGCUCGUCCUCCAGCAGCGAAGUGCUGUUGAGGAUUUCGCCCUGCUCC
.....(..((((.......))))..)...((((((((((...((((((.((((((((....))))).))).)))))))))))))))).(((((((.((....)).)))))))........ (-46.34 = -46.77 +   0.44) 

alignment

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secondary structure

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Window 0

Location 568,585 – 568,705
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.42
Mean single sequence MFE -46.80
Consensus MFE -41.41
Energy contribution -41.98
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.63
Structure conservation index 0.88
SVM decision value 0.20
SVM RNA-class probability 0.632143
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 568585 120 - 23771897
UGGGACUCCAGGGGCACUCAUCGGUGCACCACCAUCAUGGGGAGCAGGGCGAAAUCCUCAACAGCACUUCGUUGCUGGAGGACGAGCACAUCUGUCCCGAGUGCGGAAAGAAAUACUCCA
(((....)))...((((((...((((...))))......((((.((((((....(((((..(((((......))))))))))...))...))))))))))))))(((.........))). ( -42.40)
>DroSec_CAF1 36 120 - 1
UGGGACUCCAGGGGCACUCAUCGGUGCACCACCAUCAUGGGGAGCAGGGCGAGAUCCUCAACAGCACUUCGCUGCUGGAGGACGAGCACAUCUGUCCCGAGUGCGGAAAGAAGUACUCCA
.((((((((.((.(((((....))))).)).((.....))))))((((((..(.(((((..((((.....))))...))))))..))...))))))))((((((........)))))).. ( -48.20)
>DroSim_CAF1 41 120 - 1
UGGGACUCCAGGGGCACUCAUCGGUGCACCACCAUCAUGGGGAGCAGGGCGAAAUCCUCAACAGCACUUCGCUGCUGGAGGACGAGCACAUCUGUCCCGAGUGCGGAAAGAAGUACUCCA
.((((((((.((.(((((....))))).)).((.....))))))((((((....(((((..((((.....))))...)))))...))...))))))))((((((........)))))).. ( -46.80)
>DroEre_CAF1 36 120 - 1
UGGGACUCCAGGGGCAUUCGUCGGCGCACCACCACCAUGCGGAGCCGGGCGAAAUCCUCAACAGCAGCUCGCUGCUGGAGGACGAGCACAUCUGUCCCGAGUGCGGAAAGAAGUACUCCA
.(((((...(((.((.((((((.(.((.((.(......).)).))).)))))).(((((..((((((....)))))))))))...))...))))))))((((((........)))))).. ( -49.80)
>consensus
UGGGACUCCAGGGGCACUCAUCGGUGCACCACCAUCAUGGGGAGCAGGGCGAAAUCCUCAACAGCACUUCGCUGCUGGAGGACGAGCACAUCUGUCCCGAGUGCGGAAAGAAGUACUCCA
.((((((((.((.(((((....))))).)).((.....))))).....((....(((((..(((((......))))))))))...))......)))))((((((........)))))).. (-41.41 = -41.98 +   0.56) 

alignment

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secondary structure

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dotplot

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Window 1

Location 568,625 – 568,739
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.03
Mean single sequence MFE -52.83
Consensus MFE -42.33
Energy contribution -43.70
Covariance contribution 1.37
Combinations/Pair 1.03
Mean z-score -1.54
Structure conservation index 0.80
SVM decision value 0.11
SVM RNA-class probability 0.587851
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 568625 114 + 23771897
CUCCAGCAACGAAGUGCUGUUGAGGAUUUCGCCCUGCUCCCCAUGAUGGUGGUGCACCGAUGAGUGCCCCUGGAGUCCCAGGUGGUCCUCCGAGGAUUGACGGCUGGAG------GUGGA
(((((((..((((((.((....)).))))))...(((.((((.....)).)).)))((...(((..(((((((....))))).))..)))...)).......)))))))------..... ( -48.30)
>DroSec_CAF1 76 114 + 1
CUCCAGCAGCGAAGUGCUGUUGAGGAUCUCGCCCUGCUCCCCAUGAUGGUGGUGCACCGAUGAGUGCCCCUGGAGUCCCAGGUGGUCCUCCGAAGAUUGACGGCUGGAG------GUGGA
(((((((.((((..(.((....)).)..))))..(((.((((.....)).)).))).((..(((..(((((((....))))).))..)))))..........)))))))------..... ( -45.70)
>DroSim_CAF1 81 114 + 1
CUCCAGCAGCGAAGUGCUGUUGAGGAUUUCGCCCUGCUCCCCAUGAUGGUGGUGCACCGAUGAGUGCCCCUGGAGUCCCAGGUGGUCCUCCGGGGAUUGACGGCUGGAG------GUGGA
(((((((.(((((((.((....)).))))))).....(((((....(((((...)))))..(((..(((((((....))))).))..))).)))))......)))))))------..... ( -54.60)
>DroEre_CAF1 76 120 + 1
CUCCAGCAGCGAGCUGCUGUUGAGGAUUUCGCCCGGCUCCGCAUGGUGGUGGUGCGCCGACGAAUGCCCCUGGAGUCCCAGGUGGUCCUCCGAGGACUGUCGGCUGGAGCUGGAGCUGGA
.((((((.(((((.(.((....)).).)))))((((((((((((.......))))((((((.......(((((....))))).(((((.....))))))))))).)))))))).)))))) ( -62.70)
>consensus
CUCCAGCAGCGAAGUGCUGUUGAGGAUUUCGCCCUGCUCCCCAUGAUGGUGGUGCACCGAUGAGUGCCCCUGGAGUCCCAGGUGGUCCUCCGAGGAUUGACGGCUGGAG______GUGGA
(((((((.(((((((.((....)).)))))))...((.((((.....)).)).)).((...(((.((((((((....))))).))).)))...)).......)))))))........... (-42.33 = -43.70 +   1.37) 

alignment

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secondary structure

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Window 2

Location 568,625 – 568,739
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.03
Mean single sequence MFE -49.75
Consensus MFE -42.99
Energy contribution -43.05
Covariance contribution 0.06
Combinations/Pair 1.12
Mean z-score -2.70
Structure conservation index 0.86
SVM decision value 2.01
SVM RNA-class probability 0.985449
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 568625 114 - 23771897
UCCAC------CUCCAGCCGUCAAUCCUCGGAGGACCACCUGGGACUCCAGGGGCACUCAUCGGUGCACCACCAUCAUGGGGAGCAGGGCGAAAUCCUCAACAGCACUUCGUUGCUGGAG
.....------(((((((((((..(((((((((..((....))..)))).((.(((((....))))).))........)))))....))))...........(((.....)))))))))) ( -45.10)
>DroSec_CAF1 76 114 - 1
UCCAC------CUCCAGCCGUCAAUCUUCGGAGGACCACCUGGGACUCCAGGGGCACUCAUCGGUGCACCACCAUCAUGGGGAGCAGGGCGAGAUCCUCAACAGCACUUCGCUGCUGGAG
.....------(((((((((((..(((((((((..((....))..)))).((.(((((....))))).))........)))))....))))...........(((.....)))))))))) ( -44.70)
>DroSim_CAF1 81 114 - 1
UCCAC------CUCCAGCCGUCAAUCCCCGGAGGACCACCUGGGACUCCAGGGGCACUCAUCGGUGCACCACCAUCAUGGGGAGCAGGGCGAAAUCCUCAACAGCACUUCGCUGCUGGAG
.....------(((((((((((..(((((((((..((....))..)))).((.(((((....))))).))........)))))....))))...........(((.....)))))))))) ( -50.50)
>DroEre_CAF1 76 120 - 1
UCCAGCUCCAGCUCCAGCCGACAGUCCUCGGAGGACCACCUGGGACUCCAGGGGCAUUCGUCGGCGCACCACCACCAUGCGGAGCCGGGCGAAAUCCUCAACAGCAGCUCGCUGCUGGAG
....((.((.(((((.((((((.((((..((((..((....))..))))..))))....))))))(((.........)))))))).))))......(((..((((((....))))))))) ( -58.70)
>consensus
UCCAC______CUCCAGCCGUCAAUCCUCGGAGGACCACCUGGGACUCCAGGGGCACUCAUCGGUGCACCACCAUCAUGGGGAGCAGGGCGAAAUCCUCAACAGCACUUCGCUGCUGGAG
...........(((((((((((..(((((((((..((....))..)))).((.(((((....))))).))........)))))....))))...........(((.....)))))))))) (-42.99 = -43.05 +   0.06) 

alignment

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secondary structure

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dotplot

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Window 3

Location 568,665 – 568,773
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.91
Mean single sequence MFE -38.55
Consensus MFE -33.96
Energy contribution -33.65
Covariance contribution -0.31
Combinations/Pair 1.10
Mean z-score -1.78
Structure conservation index 0.88
SVM decision value 0.89
SVM RNA-class probability 0.874454
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 568665 108 - 23771897
CGACUCGAAUUCCUGCGCC------AGCAGCAGUUCCAGUUCCAC------CUCCAGCCGUCAAUCCUCGGAGGACCACCUGGGACUCCAGGGGCACUCAUCGGUGCACCACCAUCAUGG
.((((.(((((.((((...------.)))).))))).))))....------......((((....((..((((..((....))..))))..))(((((....))))).........)))) ( -36.10)
>DroSec_CAF1 116 108 - 1
CGACUCGAAUUCCUGCGCC------AGCAGCAGUUCCAGUUCCAC------CUCCAGCCGUCAAUCUUCGGAGGACCACCUGGGACUCCAGGGGCACUCAUCGGUGCACCACCAUCAUGG
.((((.(((((.((((...------.)))).))))).))))....------..(((((((((..((....)).)))..(((((....)))))))).......((((...))))....))) ( -36.90)
>DroSim_CAF1 121 108 - 1
CGACUCGAAUUCCUGCGCC------AGCAGCAGUUCCAGUUCCAC------CUCCAGCCGUCAAUCCCCGGAGGACCACCUGGGACUCCAGGGGCACUCAUCGGUGCACCACCAUCAUGG
.((((.(((((.((((...------.)))).))))).))))....------......((((....(((.((((..((....))..)))).)))(((((....))))).........)))) ( -37.90)
>DroEre_CAF1 116 120 - 1
CGACUCGAAUUCCUGCACCAGCACCAGCAGCAGUUCCAGUUCCAGCUCCAGCUCCAGCCGACAGUCCUCGGAGGACCACCUGGGACUCCAGGGGCAUUCGUCGGCGCACCACCACCAUGC
.((((.(((((.((((..........)))).))))).))))..(((....)))...((((((.((((..((((..((....))..))))..))))....))))))............... ( -43.30)
>consensus
CGACUCGAAUUCCUGCGCC______AGCAGCAGUUCCAGUUCCAC______CUCCAGCCGUCAAUCCUCGGAGGACCACCUGGGACUCCAGGGGCACUCAUCGGUGCACCACCAUCAUGG
.((((.(((((.((((..........)))).))))).))))(((............((((.....((((((((..((....))..)))).)))).......))))............))) (-33.96 = -33.65 +  -0.31) 

alignment

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secondary structure

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Window 4

Location 568,705 – 568,813
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.77
Mean single sequence MFE -40.64
Consensus MFE -35.69
Energy contribution -36.00
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -3.31
Structure conservation index 0.88
SVM decision value 2.60
SVM RNA-class probability 0.995623
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 568705 108 - 23771897
AGGUCUUCGAUCGCAGGAAACUGCGUCGUUGCACAAUCUCCGACUCGAAUUCCUGCGCC------AGCAGCAGUUCCAGUUCCAC------CUCCAGCCGUCAAUCCUCGGAGGACCACC
.(((((((((.(((((....)))))))((((..........((((.(((((.((((...------.)))).))))).))))....------...))))............)))))))... ( -38.53)
>DroSec_CAF1 156 108 - 1
AGGUCUUCGACCGCAGGAAACUGCGUCGAUGCACAAUCUCCGACUCGAAUUCCUGCGCC------AGCAGCAGUUCCAGUUCCAC------CUCCAGCCGUCAAUCUUCGGAGGACCACC
.((((((((((.((((....)))))))(((((.........((((.(((((.((((...------.)))).))))).))))....------.....).))))........)))))))... ( -40.47)
>DroSim_CAF1 161 108 - 1
AGGUCUUCGACCGCAGGAAACUGCGUCGAUGCACAAUCUCCGACUCGAAUUCCUGCGCC------AGCAGCAGUUCCAGUUCCAC------CUCCAGCCGUCAAUCCCCGGAGGACCACC
.((((((((((.((((....)))))))(((((.........((((.(((((.((((...------.)))).))))).))))....------.....).))))........)))))))... ( -40.47)
>DroEre_CAF1 156 120 - 1
AGGUGUUUGAUCGCAGGAAACUGCGUCGAUGCACCAUCUCCGACUCGAAUUCCUGCACCAGCACCAGCAGCAGUUCCAGUUCCAGCUCCAGCUCCAGCCGACAGUCCUCGGAGGACCACC
.(((((((((.(((((....))))))))).))))).(((((((...(((((.((((..........)))).)))))..(((..(((....)))..))).........)))))))...... ( -43.10)
>consensus
AGGUCUUCGACCGCAGGAAACUGCGUCGAUGCACAAUCUCCGACUCGAAUUCCUGCGCC______AGCAGCAGUUCCAGUUCCAC______CUCCAGCCGUCAAUCCUCGGAGGACCACC
.((((.((((.(((((....)))))))))........((((((((.(((((.((((..........)))).))))).))))..................(........)))))))))... (-35.69 = -36.00 +   0.31) 

alignment

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secondary structure

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dotplot

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Window 5

Location 568,739 – 568,853
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.30
Mean single sequence MFE -46.07
Consensus MFE -39.21
Energy contribution -39.78
Covariance contribution 0.56
Combinations/Pair 1.02
Mean z-score -1.98
Structure conservation index 0.85
SVM decision value 0.69
SVM RNA-class probability 0.823144
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 568739 114 + 23771897
ACUGGAACUGCUGCU------GGCGCAGGAAUUCGAGUCGGAGAUUGUGCAACGACGCAGUUUCCUGCGAUCGAAGACCUUGUGGCUGUAGUAGUUGGAGUCGUCGUCCGAGGAGGCGUA
(((..(((((((((.------(.((((((..(((((((.((((((((((......)))))))))).))..)))))...)))))).).)))))))))..)))((((.((....)))))).. ( -47.80)
>DroSec_CAF1 190 114 + 1
ACUGGAACUGCUGCU------GGCGCAGGAAUUCGAGUCGGAGAUUGUGCAUCGACGCAGUUUCCUGCGGUCGAAGACCUUGUGGCUGUAGUAGUUGGAGUCGUCGUCCGAGGAGGCGUA
(((..(((((((((.------(.((((((..(((((((.((((((((((......)))))))))).))..)))))...)))))).).)))))))))..)))((((.((....)))))).. ( -47.80)
>DroSim_CAF1 195 114 + 1
ACUGGAACUGCUGCU------GGCGCAGGAAUUCGAGUCGGAGAUUGUGCAUCGACGCAGUUUCCUGCGGUCGAAGACCUUGUGGCUGUAGUAGUUGGAGUCGUCGUCCGAGGAGGCGUA
(((..(((((((((.------(.((((((..(((((((.((((((((((......)))))))))).))..)))))...)))))).).)))))))))..)))((((.((....)))))).. ( -47.80)
>DroEre_CAF1 196 120 + 1
ACUGGAACUGCUGCUGGUGCUGGUGCAGGAAUUCGAGUCGGAGAUGGUGCAUCGACGCAGUUUCCUGCGAUCAAACACCUUGUGGCUGUAAUAGUUGGAGUCGUCGUCCGAGGAGGCGUA
((((..((.((..(.((((.(((((((((((.....((((..(......)..)))).....))))))).))))..))))..)..)).))..))))......((((.((....)))))).. ( -40.90)
>consensus
ACUGGAACUGCUGCU______GGCGCAGGAAUUCGAGUCGGAGAUUGUGCAUCGACGCAGUUUCCUGCGAUCGAAGACCUUGUGGCUGUAGUAGUUGGAGUCGUCGUCCGAGGAGGCGUA
(((..(((((((((.......(.((((((..(((((((.((((((((((......)))))))))).))..)))))...)))))).).)))))))))..)))((((.((....)))))).. (-39.21 = -39.78 +   0.56) 

alignment

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secondary structure

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dotplot

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Window 6

Location 568,739 – 568,853
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.30
Mean single sequence MFE -35.38
Consensus MFE -32.49
Energy contribution -32.55
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.32
Structure conservation index 0.92
SVM decision value 1.70
SVM RNA-class probability 0.972878
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 568739 114 - 23771897
UACGCCUCCUCGGACGACGACUCCAACUACUACAGCCACAAGGUCUUCGAUCGCAGGAAACUGCGUCGUUGCACAAUCUCCGACUCGAAUUCCUGCGCC------AGCAGCAGUUCCAGU
.........((((((((((((.............(((....)))........((((....))))))))))).......)))))((.(((((.((((...------.)))).))))).)). ( -35.81)
>DroSec_CAF1 190 114 - 1
UACGCCUCCUCGGACGACGACUCCAACUACUACAGCCACAAGGUCUUCGACCGCAGGAAACUGCGUCGAUGCACAAUCUCCGACUCGAAUUCCUGCGCC------AGCAGCAGUUCCAGU
.........(((((.(((.......................((((...))))((((....)))))))(((.....))))))))((.(((((.((((...------.)))).))))).)). ( -34.90)
>DroSim_CAF1 195 114 - 1
UACGCCUCCUCGGACGACGACUCCAACUACUACAGCCACAAGGUCUUCGACCGCAGGAAACUGCGUCGAUGCACAAUCUCCGACUCGAAUUCCUGCGCC------AGCAGCAGUUCCAGU
.........(((((.(((.......................((((...))))((((....)))))))(((.....))))))))((.(((((.((((...------.)))).))))).)). ( -34.90)
>DroEre_CAF1 196 120 - 1
UACGCCUCCUCGGACGACGACUCCAACUAUUACAGCCACAAGGUGUUUGAUCGCAGGAAACUGCGUCGAUGCACCAUCUCCGACUCGAAUUCCUGCACCAGCACCAGCAGCAGUUCCAGU
.........(((((.((.(....).................(((((((((.(((((....))))))))).))))).)))))))((.(((((.((((..........)))).))))).)). ( -35.90)
>consensus
UACGCCUCCUCGGACGACGACUCCAACUACUACAGCCACAAGGUCUUCGACCGCAGGAAACUGCGUCGAUGCACAAUCUCCGACUCGAAUUCCUGCGCC______AGCAGCAGUUCCAGU
.........(((((.((.................(((....)))..((((.(((((....))))))))).......)))))))((.(((((.((((..........)))).))))).)). (-32.49 = -32.55 +   0.06) 

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 09:35:48 2006