Locus 6197

Sequence ID 3R_DroMel_CAF1
Location 16,190,735 – 16,190,910
Length 175
Max. P 0.998391
window10099 window10100 window10101 window10102 window10103

overview

Window 9

Location 16,190,735 – 16,190,855
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.58
Mean single sequence MFE -32.75
Consensus MFE -31.44
Energy contribution -31.28
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -2.23
Structure conservation index 0.96
SVM decision value 3.09
SVM RNA-class probability 0.998391
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16190735 120 - 27905053
UUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAUUAGCACACUUUUCACAUUUUCUCUUUGAGUGUCUGGCGCUGGCGAUUGCAGUUUUUAAUCCAUUUUCGCUCCCUUUCUGG
...((((.(((((..(.(((((((.((.(((((.(((((..................)))))..))))).))...))))))).)...))))).............))))........... ( -31.51)
>DroSec_CAF1 19935 120 - 1
UUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAUUAGCACACUUUUCACAUUUCCUCUUUGAGUGUCUGGCGCUGGCGAUUGCAGUUUUUAAUCCAUUUUCGCUCCCUUUCUGG
...((((.(((((..(.(((((((.((.(((((.((((((...............))))))...))))).))...))))))).)...))))).............))))........... ( -33.80)
>DroSim_CAF1 13497 120 - 1
UUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAUUAGCACACUUUUCACAUUUUCUCUUUGAGCGUCUGGCGCUGGCGAUUGCAGUUUUUAAUCCAUUUUCGCUCCCUUUCUGG
...((((.(((((..(.(((((((.((.(((((.(((((..................)))))..))))).))...))))))).)...))))).............))))........... ( -31.21)
>DroEre_CAF1 19291 120 - 1
UUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAUUAGCACACUUUUCACAUUUUCUCUUUGAGUGUCUGGCGCUGGCGAUUGCAGUUUUUAAUCCAUUUUCGCUCCCUUUUUGG
...((((.(((((..(.(((((((.((.(((((.(((((..................)))))..))))).))...))))))).)...))))).............))))........... ( -31.51)
>DroYak_CAF1 20653 120 - 1
UUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAUUAGCACACUUUUCACAUUUUCUCUUUGAGAGUCUGGCGCUGGCGAUUGCAGUUUUUAAUCCAUUUUCGCUCCCUUUUUGG
...((((.(((((..(.(((((((.((((((((.(((((..................)))))..))))))))...))))))).)...))))).............))))........... ( -35.71)
>consensus
UUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAUUAGCACACUUUUCACAUUUUCUCUUUGAGUGUCUGGCGCUGGCGAUUGCAGUUUUUAAUCCAUUUUCGCUCCCUUUCUGG
...((((.(((((..(.(((((((.((.(((((.((((((...............))))))...))))).))...))))))).)...))))).............))))........... (-31.44 = -31.28 +  -0.16)

alignment

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secondary structure

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Window 0

Location 16,190,775 – 16,190,895
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.42
Mean single sequence MFE -33.02
Consensus MFE -29.98
Energy contribution -30.98
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.91
SVM decision value 2.86
SVM RNA-class probability 0.997452
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16190775 120 + 27905053
AGCGCCAGACACUCAAAGAGAAAAUGUGAAAAGUGUGCUAAUUUCCAUUGAGAGCUGCACUGGAGCAGCAGCAUCACAAAGGCAGUGCAUAAAAAGUGUUUAAUUCAAAUUGUGCACAGC
.(((((...(((.............)))....(((((((..((((....))))(((((......))))))))).)))...))).((((((((....((.......))..)))))))).)) ( -34.62)
>DroSec_CAF1 19975 120 + 1
AGCGCCAGACACUCAAAGAGGAAAUGUGAAAAGUGUGCUAAUUUCCAUUGAGAGCUGCACUGGAGCAGCAGCAUCACAAAGGCAGUGCAUAAAAAGUGUUUAAUUCAAAUAGUGCACUGC
.((........(((((...((((((...............)))))).))))).(((((......))))).)).........(((((((((......((.......))....))))))))) ( -33.06)
>DroSim_CAF1 13537 120 + 1
AGCGCCAGACGCUCAAAGAGAAAAUGUGAAAAGUGUGCUAAUUUCCAUUGAGAGCUGCACUGGAGCAGCAGCAUCACAAAGGCAGUGCAUAAAAAGUGUUUAAUUCAAAUAGUGCACUGC
((((.....))))...................(((((((..((((....))))(((((......))))))))).)))....(((((((((......((.......))....))))))))) ( -32.90)
>DroEre_CAF1 19331 120 + 1
AGCGCCAGACACUCAAAGAGAAAAUGUGAAAAGUGUGCUAAUUUCCAUUGAGAGCUGCACUGGAGCAGCAGCAUCACAAAGGCAGCGCAUAAAAAGUGUUUAAUUCAAAGUGUGCACUGC
.(((((...(((.............)))....(((((((..((((....))))(((((......))))))))).)))...))).((((((....(((.....)))....))))))...)) ( -31.82)
>DroYak_CAF1 20693 120 + 1
AGCGCCAGACUCUCAAAGAGAAAAUGUGAAAAGUGUGCUAAUUUCCAUUGAGAGCUGCACUGGAGCAGCAGCAUCACAAAGGCAGCGCAUAAAAAGUGUUUAAUUCAAAUUGUGCACUGC
.(((((...(((.....)))............(((((((..((((....))))(((((......))))))))).)))...))).))........(((((.((((....)))).))))).. ( -32.70)
>consensus
AGCGCCAGACACUCAAAGAGAAAAUGUGAAAAGUGUGCUAAUUUCCAUUGAGAGCUGCACUGGAGCAGCAGCAUCACAAAGGCAGUGCAUAAAAAGUGUUUAAUUCAAAUUGUGCACUGC
.(((((.....(((...)))............(((((((..((((....))))(((((......))))))))).)))...)))((((((((.....((.......))...)))))))))) (-29.98 = -30.98 +   1.00)

alignment

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secondary structure

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Window 1

Location 16,190,775 – 16,190,895
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.42
Mean single sequence MFE -30.64
Consensus MFE -27.96
Energy contribution -28.00
Covariance contribution 0.04
Combinations/Pair 1.06
Mean z-score -1.74
Structure conservation index 0.91
SVM decision value 1.68
SVM RNA-class probability 0.971506
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16190775 120 - 27905053
GCUGUGCACAAUUUGAAUUAAACACUUUUUAUGCACUGCCUUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAUUAGCACACUUUUCACAUUUUCUCUUUGAGUGUCUGGCGCU
((.(((((.((.................)).))))).(((...(((.(((((((((......)))))....(((....)))))))))).....((((((.......))))))..))))). ( -29.03)
>DroSec_CAF1 19975 120 - 1
GCAGUGCACUAUUUGAAUUAAACACUUUUUAUGCACUGCCUUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAUUAGCACACUUUUCACAUUUCCUCUUUGAGUGUCUGGCGCU
((((((((.((...(((........))).)))))))))).........((((((((......))))).(((((.((((((...............))))))...))))).....)))... ( -30.76)
>DroSim_CAF1 13537 120 - 1
GCAGUGCACUAUUUGAAUUAAACACUUUUUAUGCACUGCCUUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAUUAGCACACUUUUCACAUUUUCUCUUUGAGCGUCUGGCGCU
((((((((.((...(((........))).))))))))))....(((.(((((((((......)))))....(((....))))))))))...................((((.....)))) ( -31.30)
>DroEre_CAF1 19331 120 - 1
GCAGUGCACACUUUGAAUUAAACACUUUUUAUGCGCUGCCUUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAUUAGCACACUUUUCACAUUUUCUCUUUGAGUGUCUGGCGCU
((((((((.....((((..........))))))))))(((...(((.(((((((((......)))))....(((....)))))))))).....((((((.......))))))..))))). ( -30.10)
>DroYak_CAF1 20693 120 - 1
GCAGUGCACAAUUUGAAUUAAACACUUUUUAUGCGCUGCCUUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAUUAGCACACUUUUCACAUUUUCUCUUUGAGAGUCUGGCGCU
((((((((.((.................)).))))))))...((.((.((....))))))((((.((((((((.(((((..................)))))..))))))))...)))). ( -32.00)
>consensus
GCAGUGCACAAUUUGAAUUAAACACUUUUUAUGCACUGCCUUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAUUAGCACACUUUUCACAUUUUCUCUUUGAGUGUCUGGCGCU
((((((((.....((((..........))))))))))))....(((.(((((((((......)))))....(((....))))))))))...................((((.....)))) (-27.96 = -28.00 +   0.04)

alignment

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secondary structure

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Window 2

Location 16,190,815 – 16,190,910
Length 95
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.39
Mean single sequence MFE -30.88
Consensus MFE -22.62
Energy contribution -23.66
Covariance contribution 1.04
Combinations/Pair 1.04
Mean z-score -2.27
Structure conservation index 0.73
SVM decision value 1.93
SVM RNA-class probability 0.982848
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16190815 95 + 27905053
AUUUCCAUUGAGAGCUGCACUGGAGCAGCAGCAUCACAAAGGCAGUGCAUAAAAAGUGUUUAAUUCAAAUUGUGCACAGCGCGAAAAGGGGGCAG-------------------------
.(..((.(((.(((((((.........))))).)).)))..((.((((((((....((.......))..)))))))).)).......))..)...------------------------- ( -25.90)
>DroSec_CAF1 20015 119 + 1
AUUUCCAUUGAGAGCUGCACUGGAGCAGCAGCAUCACAAAGGCAGUGCAUAAAAAGUGUUUAAUUCAAAUAGUGCACUGCGAGAAAAGG-GGCAGUCCUAGAGCAAAGAUUGGUUUUAAA
....(((......(((((......))))).((.((......(((((((((......((.......))....)))))))))......(((-(....)))).))))......)))....... ( -30.60)
>DroSim_CAF1 13577 101 + 1
AUUUCCAUUGAGAGCUGCACUGGAGCAGCAGCAUCACAAAGGCAGUGCAUAAAAAGUGUUUAAUUCAAAUAGUGCACUGCGAGAAAAGGGGGCAGUCCUAC-------------------
.(..((.(((.(((((((.........))))).)).)))..(((((((((......((.......))....))))))))).......))..).........------------------- ( -28.80)
>DroEre_CAF1 19371 120 + 1
AUUUCCAUUGAGAGCUGCACUGGAGCAGCAGCAUCACAAAGGCAGCGCAUAAAAAGUGUUUAAUUCAAAGUGUGCACUGCUAGAAAAUGCGUCCGUCUUAGGGCAAAGUGUGGCUUGAAA
...........((((..((((.........((((......(((((.(((((.....((.......))...))))).))))).....))))((((......))))..))))..)))).... ( -37.30)
>DroYak_CAF1 20733 100 + 1
AUUUCCAUUGAGAGCUGCACUGGAGCAGCAGCAUCACAAAGGCAGCGCAUAAAAAGUGUUUAAUUCAAAUUGUGCACUGCCAGGA--------------------AAGUAUGGUUUGAAA
.(((((.(((.(((((((.........))))).)).))).(((((.((((((....((.......))..)))))).))))).)))--------------------))............. ( -31.80)
>consensus
AUUUCCAUUGAGAGCUGCACUGGAGCAGCAGCAUCACAAAGGCAGUGCAUAAAAAGUGUUUAAUUCAAAUUGUGCACUGCGAGAAAAGG_GGCAGUC_UA_____AAG__UGG_UU_AAA
.((((..(((.(((((((.........))))).)).)))..((((((((((.....((.......))...))))))))))..)))).................................. (-22.62 = -23.66 +   1.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,190,815 – 16,190,910
Length 95
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.39
Mean single sequence MFE -26.47
Consensus MFE -23.14
Energy contribution -23.34
Covariance contribution 0.20
Combinations/Pair 1.07
Mean z-score -1.86
Structure conservation index 0.87
SVM decision value 1.52
SVM RNA-class probability 0.961306
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16190815 95 - 27905053
-------------------------CUGCCCCCUUUUCGCGCUGUGCACAAUUUGAAUUAAACACUUUUUAUGCACUGCCUUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAU
-------------------------........((((((.((.(((((.((.................)).))))).))..(((.((.(((((.((....))))))))).))))))))). ( -20.53)
>DroSec_CAF1 20015 119 - 1
UUUAAAACCAAUCUUUGCUCUAGGACUGCC-CCUUUUCUCGCAGUGCACUAUUUGAAUUAAACACUUUUUAUGCACUGCCUUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAU
.......(((...........(((......-)))......((((((((.((...(((........))).))))))))))..(((.((.(((((.((....))))))))).)))))).... ( -26.70)
>DroSim_CAF1 13577 101 - 1
-------------------GUAGGACUGCCCCCUUUUCUCGCAGUGCACUAUUUGAAUUAAACACUUUUUAUGCACUGCCUUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAU
-------------------..(((.......)))(((((.((((((((.((...(((........))).))))))))))..(((.((.(((((.((....))))))))).))).))))). ( -25.40)
>DroEre_CAF1 19371 120 - 1
UUUCAAGCCACACUUUGCCCUAAGACGGACGCAUUUUCUAGCAGUGCACACUUUGAAUUAAACACUUUUUAUGCGCUGCCUUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAU
((((((((((((...(((((......))..))).......((((((((.....((((..........))))))))))))...))))..)))(((((......)))))......))))).. ( -29.20)
>DroYak_CAF1 20733 100 - 1
UUUCAAACCAUACUU--------------------UCCUGGCAGUGCACAAUUUGAAUUAAACACUUUUUAUGCGCUGCCUUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAU
.............((--------------------(((.(((((((((.((.................)).))))))))).(((.((.(((((.((....))))))))).))).))))). ( -30.53)
>consensus
UUU_AA_CCA__CUU_____UA_GACUGCC_CCUUUUCUCGCAGUGCACAAUUUGAAUUAAACACUUUUUAUGCACUGCCUUUGUGAUGCUGCUGCUCCAGUGCAGCUCUCAAUGGAAAU
.................................(((((..((((((((.....((((..........))))))))))))..(((.((.(((((.((....))))))))).))).))))). (-23.14 = -23.34 +   0.20)

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 12:15:13 2006