Locus 5559

Sequence ID 3L_DroMel_CAF1
Location 15,249,334 – 15,249,540
Length 206
Max. P 0.999988
window8790 window8791 window8792 window8793 window8794

overview

Window 0

Location 15,249,334 – 15,249,442
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.43
Mean single sequence MFE -24.89
Consensus MFE -22.05
Energy contribution -23.05
Covariance contribution 1.00
Combinations/Pair 1.10
Mean z-score -1.57
Structure conservation index 0.89
SVM decision value 1.11
SVM RNA-class probability 0.917361
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15249334 108 - 23771897
UUGACUCUGAUUUUGAUUCCGAUUCC------------GAAUCGGAUUCGGAUUCGGAUUCUGGCACAUCACAUCUUAAGCUUCAAUUAUCACCGCCGUAUUAUUGCAUUUUCACAUGGU
..((.(((((.(((((.((((((...------------..)))))).))))).))))).)).(((.............................)))(((....)))............. ( -22.95)
>DroSec_CAF1 138516 102 - 1
UUGACUCUGAUUUUGAUUCCGAUUCC------------GAAUCGGAU------UCGUAUUCUGGCACAUCACAUCUUAAGCUUCAAUUAUCACCGCCGUCUUAUUGCAUUUGCACAUGAU
..(((...((...(((.((((((...------------..)))))).------)))...)).(((.............................))))))(((((((....))).)))). ( -17.85)
>DroSim_CAF1 146261 108 - 1
UUGACUCUGAUUUUGAUUCCGAUUCC------------GAAUCGGAUUCAGAUUCGGAUUCUGGCACAUCACAUCUUAAGCUUCAAUUAUCACCGCCGUCUUAUUGCAUUUGCACAUGAU
..((((((((.(((((.((((((...------------..)))))).))))).)))))....(((.............................))))))(((((((....))).)))). ( -26.15)
>DroEre_CAF1 138854 120 - 1
UUGACUCUGAUUUUGAUUCCGAUUCCGAUUCCGCUGCCGAAUCGGAUUCGUAUUCGGAUUCAGGCACAUCACAUCUUAAGCUUCAAUUAUCACCGCCGUCUUGUUGCAUUUGCACAUGGU
((((..((((.(((((...(((.((((((((.......)))))))).)))...))))).))))((..............)).))))........((((...(((.((....))))))))) ( -29.24)
>DroYak_CAF1 144789 108 - 1
UUGACUCUGAUUUUGAUUCCGAUUCC------------GAAUCGGAUUCGGAUUCGGAUUCAGGCACAUCACAUCUUAAGCUUCAAUUAUCACCGCCGUCUUGUUGCAUUUGCACAUGGU
((((..((((.(((((.(((((.(((------------(...)))).))))).))))).))))((..............)).))))........((((...(((.((....))))))))) ( -28.24)
>consensus
UUGACUCUGAUUUUGAUUCCGAUUCC____________GAAUCGGAUUCGGAUUCGGAUUCUGGCACAUCACAUCUUAAGCUUCAAUUAUCACCGCCGUCUUAUUGCAUUUGCACAUGGU
..((.(((((.(((((.((((((((.............)))))))).))))).))))).)).(((.............................)))...(((((((....))).)))). (-22.05 = -23.05 +   1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,249,374 – 15,249,482
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.20
Mean single sequence MFE -30.62
Consensus MFE -25.72
Energy contribution -26.32
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.15
Structure conservation index 0.84
SVM decision value 2.16
SVM RNA-class probability 0.989388
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15249374 108 + 23771897
CUUAAGAUGUGAUGUGCCAGAAUCCGAAUCCGAAUCCGAUUC------------GGAAUCGGAAUCAAAAUCAGAGUCAAAGCUAUUUGCCGCCAUUUGUGUCUCCAGACACUGCACAUA
......((((((((.((..((.(((((.(((((((...))))------------))).))))).)).........(.((((....)))).))))))..(((((....)))))..))))). ( -32.20)
>DroSec_CAF1 138556 102 + 1
CUUAAGAUGUGAUGUGCCAGAAUACGA------AUCCGAUUC------------GGAAUCGGAAUCAAAAUCAGAGUCAAAGCUAUUUGCCGCCAUUUGUGUCUCCAGACACUGCACAUA
......(((((..(((.((((....((------.((((((..------------...)))))).))........(((....))).)))).))).....(((((....)))))..))))). ( -24.10)
>DroSim_CAF1 146301 108 + 1
CUUAAGAUGUGAUGUGCCAGAAUCCGAAUCUGAAUCCGAUUC------------GGAAUCGGAAUCAAAAUCAGAGUCAAAGCUAUUUGCCGCCAUUUGUGUCUCCAGACACUGCACAUA
......((((((((.((..((.(((((.(((((((...))))------------))).))))).)).........(.((((....)))).))))))..(((((....)))))..))))). ( -30.00)
>DroEre_CAF1 138894 120 + 1
CUUAAGAUGUGAUGUGCCUGAAUCCGAAUACGAAUCCGAUUCGGCAGCGGAAUCGGAAUCGGAAUCAAAAUCAGAGUCAAAGCUAUUUGCCGCCAUUUGUGUCUCCAGACACUGCACAUA
......((((((((.((((((....((...(((.((((((((.......)))))))).)))...))....)))).(.((((....)))).))))))..(((((....)))))..))))). ( -34.00)
>DroYak_CAF1 144829 108 + 1
CUUAAGAUGUGAUGUGCCUGAAUCCGAAUCCGAAUCCGAUUC------------GGAAUCGGAAUCAAAAUCAGAGUCAAAGCUAUUUGCCGCCAUUUGUGUCUCCAGACACUGCACAUA
......((((((((.((.(((.(((((.(((((((...))))------------))).))))).)))........(.((((....)))).))))))..(((((....)))))..))))). ( -32.80)
>consensus
CUUAAGAUGUGAUGUGCCAGAAUCCGAAUCCGAAUCCGAUUC____________GGAAUCGGAAUCAAAAUCAGAGUCAAAGCUAUUUGCCGCCAUUUGUGUCUCCAGACACUGCACAUA
......((((((((.((..((.((.((....((.((((((((.............)))))))).))....)).)).))...((.....)).)))))..(((((....)))))..))))). (-25.72 = -26.32 +   0.60)

alignment

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secondary structure

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Window 2

Location 15,249,374 – 15,249,482
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.20
Mean single sequence MFE -35.76
Consensus MFE -35.12
Energy contribution -36.40
Covariance contribution 1.28
Combinations/Pair 1.03
Mean z-score -2.79
Structure conservation index 0.98
SVM decision value 5.48
SVM RNA-class probability 0.999988
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15249374 108 - 23771897
UAUGUGCAGUGUCUGGAGACACAAAUGGCGGCAAAUAGCUUUGACUCUGAUUUUGAUUCCGAUUCC------------GAAUCGGAUUCGGAUUCGGAUUCUGGCACAUCACAUCUUAAG
.((((((.(((((....)))))....(((........)))..((.(((((.(((((.((((((...------------..)))))).))))).))))).))..))))))........... ( -35.90)
>DroSec_CAF1 138556 102 - 1
UAUGUGCAGUGUCUGGAGACACAAAUGGCGGCAAAUAGCUUUGACUCUGAUUUUGAUUCCGAUUCC------------GAAUCGGAU------UCGUAUUCUGGCACAUCACAUCUUAAG
.((((((.(((((....))))).....(((((.....)))..((.((((((((.((.......)).------------)))))))).------))))......))))))........... ( -27.00)
>DroSim_CAF1 146301 108 - 1
UAUGUGCAGUGUCUGGAGACACAAAUGGCGGCAAAUAGCUUUGACUCUGAUUUUGAUUCCGAUUCC------------GAAUCGGAUUCAGAUUCGGAUUCUGGCACAUCACAUCUUAAG
.((((((.(((((....)))))....(((........)))..((.(((((.(((((.((((((...------------..)))))).))))).))))).))..))))))........... ( -36.70)
>DroEre_CAF1 138894 120 - 1
UAUGUGCAGUGUCUGGAGACACAAAUGGCGGCAAAUAGCUUUGACUCUGAUUUUGAUUCCGAUUCCGAUUCCGCUGCCGAAUCGGAUUCGUAUUCGGAUUCAGGCACAUCACAUCUUAAG
.((((((.(((((....)))))....(((........)))......((((.(((((...(((.((((((((.......)))))))).)))...))))).))))))))))........... ( -40.10)
>DroYak_CAF1 144829 108 - 1
UAUGUGCAGUGUCUGGAGACACAAAUGGCGGCAAAUAGCUUUGACUCUGAUUUUGAUUCCGAUUCC------------GAAUCGGAUUCGGAUUCGGAUUCAGGCACAUCACAUCUUAAG
.((((((.(((((....)))))....(((........)))......((((.(((((.(((((.(((------------(...)))).))))).))))).))))))))))........... ( -39.10)
>consensus
UAUGUGCAGUGUCUGGAGACACAAAUGGCGGCAAAUAGCUUUGACUCUGAUUUUGAUUCCGAUUCC____________GAAUCGGAUUCGGAUUCGGAUUCUGGCACAUCACAUCUUAAG
.((((((.(((((....)))))....(((........)))..((.(((((.(((((.((((((((.............)))))))).))))).))))).))..))))))........... (-35.12 = -36.40 +   1.28)

alignment

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secondary structure

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Window 3

Location 15,249,442 – 15,249,540
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.46
Mean single sequence MFE -37.10
Consensus MFE -24.73
Energy contribution -25.90
Covariance contribution 1.17
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.67
SVM decision value 0.50
SVM RNA-class probability 0.761883
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15249442 98 + 23771897
AGCUAUUUGCCGCCAUUUGUGUCUCCAGACACUGCACAUAUGACAUUGUGCAUCACCGGCAGGACAAAGGCCAAGAAGAGUGGGCGGCAA----------------------GUGGGCGG
..(((((((((((((((((((((....)))))((((((........)))))).....(((.........))).....)))).))))))))----------------------)))).... ( -40.00)
>DroSec_CAF1 138618 98 + 1
AGCUAUUUGCCGCCAUUUGUGUCUCCAGACACUGCACAUAUGACAUUGUGCAUCACCGGCAGGACAAAGGCCAAGCAGAGUGGGCGGCAA----------------------GUGGGCGG
..((((((((((((....(((((....)))))((((((........)))))).((((.((.((.......))..)).).)))))))))))----------------------)))).... ( -40.40)
>DroSim_CAF1 146369 98 + 1
AGCUAUUUGCCGCCAUUUGUGUCUCCAGACACUGCACAUAUGACAUUGUGCAUCACUGGCAGGACAAAGGCCAAGCAGAGUGGGCGGCAA----------------------GUGGGCGG
..((((((((((((....(((((....)))))((((((........)))))).((((.((.((.......))..))..))))))))))))----------------------)))).... ( -41.80)
>DroEre_CAF1 138974 96 + 1
AGCUAUUUGCCGCCAUUUGUGUCUCCAGACACUGCACAUAUGACAUUGUGCAUCAGCGGCAGGACAAAGGCCAAGAAGAGUGGGCG-----------------------GCAGUGGGCG-
.(((..(((((((((((((((((....)))))((((((........)))))).....(((.........))).....)))).))))-----------------------))))..))).- ( -38.10)
>DroYak_CAF1 144897 119 + 1
AGCUAUUUGCCGCCAUUUGUGUCUCCAGACACUGCACAUAUGACAUUGUGCAUCAGCGGCAGGACAAAGGCCAAGAAGAGUGGGCGCAAAGUGGGCGUGGAGUGUGCGGGGAGUGGGCA-
..((((((.((((((((((((((....)))))((((((........))))))...(((.(........(.(((.......))).)........).))).))))).)))).))))))...- ( -40.89)
>DroAna_CAF1 131119 84 + 1
AGCUAUUUGCCACCAUUUCUGUCUCCAGACACAGCACAUAUGACAAUGUGCAUCAGCGGCAGGACAAAGGCCAGGAAAAGCGGA------------------------------------
.(((...((((........((((....))))..((((((......))))))......))))((.......))......)))...------------------------------------ ( -21.40)
>consensus
AGCUAUUUGCCGCCAUUUGUGUCUCCAGACACUGCACAUAUGACAUUGUGCAUCACCGGCAGGACAAAGGCCAAGAAGAGUGGGCGGCAA______________________GUGGGCG_
.(((.(((((((((....(((((....))))).(((((........)))))......))).)).))))(.(((.......))).)..............................))).. (-24.73 = -25.90 +   1.17)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,249,442 – 15,249,540
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.46
Mean single sequence MFE -33.37
Consensus MFE -23.79
Energy contribution -23.85
Covariance contribution 0.06
Combinations/Pair 1.08
Mean z-score -2.09
Structure conservation index 0.71
SVM decision value 0.51
SVM RNA-class probability 0.763673
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15249442 98 - 23771897
CCGCCCAC----------------------UUGCCGCCCACUCUUCUUGGCCUUUGUCCUGCCGGUGAUGCACAAUGUCAUAUGUGCAGUGUCUGGAGACACAAAUGGCGGCAAAUAGCU
..((....----------------------((((((((((((......(((.........))))))).((((((........))))))(((((....)))))....))))))))...)). ( -34.20)
>DroSec_CAF1 138618 98 - 1
CCGCCCAC----------------------UUGCCGCCCACUCUGCUUGGCCUUUGUCCUGCCGGUGAUGCACAAUGUCAUAUGUGCAGUGUCUGGAGACACAAAUGGCGGCAAAUAGCU
..((....----------------------((((((((((((..((..(((....)))..)).)))).((((((........))))))(((((....)))))....))))))))...)). ( -37.10)
>DroSim_CAF1 146369 98 - 1
CCGCCCAC----------------------UUGCCGCCCACUCUGCUUGGCCUUUGUCCUGCCAGUGAUGCACAAUGUCAUAUGUGCAGUGUCUGGAGACACAAAUGGCGGCAAAUAGCU
..((....----------------------((((((((((((..((..(((....)))..)).)))).((((((........))))))(((((....)))))....))))))))...)). ( -37.10)
>DroEre_CAF1 138974 96 - 1
-CGCCCACUGC-----------------------CGCCCACUCUUCUUGGCCUUUGUCCUGCCGCUGAUGCACAAUGUCAUAUGUGCAGUGUCUGGAGACACAAAUGGCGGCAAAUAGCU
-.((....(((-----------------------((((......((.((((.........))))..))((((((........))))))(((((....)))))....)))))))....)). ( -32.80)
>DroYak_CAF1 144897 119 - 1
-UGCCCACUCCCCGCACACUCCACGCCCACUUUGCGCCCACUCUUCUUGGCCUUUGUCCUGCCGCUGAUGCACAAUGUCAUAUGUGCAGUGUCUGGAGACACAAAUGGCGGCAAAUAGCU
-............(((((......((.......))(((..........)))...)))..(((((((..((((((........))))))(((((....)))))....)))))))....)). ( -31.40)
>DroAna_CAF1 131119 84 - 1
------------------------------------UCCGCUUUUCCUGGCCUUUGUCCUGCCGCUGAUGCACAUUGUCAUAUGUGCUGUGUCUGGAGACAGAAAUGGUGGCAAAUAGCU
------------------------------------...(((......(((....))).(((((((...((((((......))))))....((((....))))...)))))))...))). ( -27.60)
>consensus
_CGCCCAC______________________UUGCCGCCCACUCUUCUUGGCCUUUGUCCUGCCGCUGAUGCACAAUGUCAUAUGUGCAGUGUCUGGAGACACAAAUGGCGGCAAAUAGCU
................................................(((.((((.((.((((....((((((........))))))(((((....)))))...))))))))))..))) (-23.79 = -23.85 +   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 11:53:24 2006