Locus 3063

Sequence ID 3R_DroMel_CAF1
Location 8,099,732 – 8,099,979
Length 247
Max. P 0.982828
window4960 window4961 window4962 window4963

overview

Window 0

Location 8,099,732 – 8,099,849
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.70
Mean single sequence MFE -32.84
Consensus MFE -28.52
Energy contribution -28.92
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.87
SVM decision value 1.19
SVM RNA-class probability 0.928240
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8099732 117 + 27905053
AUAUGGUUAACAACUCUUGACCAAGCAACGGUUAAAAAGGUUCAACGAGCCAUCGUCUUAGGCAGCGAAUGAGGCCCAAGACUUUUGGCUCUGCCAACUGACAAAGCGACUGACCAC---
...((((((.......((((((.......))))))...(((.....((((((..(((((.(((..(....)..))).)))))...)))))).)))...............)))))).--- ( -34.80)
>DroSec_CAF1 51377 117 + 1
AUAUGGUUAACAACUCUUGACCAAGCAACGGUUAAAAAGGUUCAACGAGCCAUCGUCUUAGCCAGCGAAUGAGGCCCCAGACUUUUGGCUCUGCCAACUGACAAAGCGACUGACCAC---
...((((((.......((((((.......))))))...(((.....((((((..((((..(((.........)))...))))...)))))).)))...............)))))).--- ( -30.90)
>DroSim_CAF1 23448 117 + 1
AUAUGGUUAACAACUCUUGACCAAGCAACGGUUAAAAAGGUUCAACGAGCCAUCGUCUUAGCCAGCGAAUGAGGCCCAAGACUUUUGGCUCUGCCAACUGACAAAGCGACUGACCAC---
...((((((.......((((((.......))))))...(((.....((((((..(((((.(((.........)))..)))))...)))))).)))...............)))))).--- ( -32.30)
>DroEre_CAF1 26442 120 + 1
AUAUGGUUAACAACUCUUGACCAAGCAACGGUUAAAAAGGUUCAACGAGCCAUCGUCUUCGCCAGCGAAUGAGGCCCAAGACUUUUGGCUCUGGCAACUGACAAAGUGACUGACCACCAC
...((((((...(((.((((((.......))))))...(((((...((((((..(((((.(((.........)))..)))))...))))))..).)))).....)))...)))))).... ( -32.40)
>DroYak_CAF1 19804 117 + 1
AUAUGGUUAACAACUCUUGACCAAGCAACGGUUAAAAAGGUUCAACGAGCCAUCGUCUUUGCCAGCGAAUGAGGCCCAAGACUUUUGGCUCUGGCAACUGACAAAGUGACUGACCAC---
...(((((((......)))))))......(((((....(((((...)))))...(((.(((((((.(...(((........)))....).)))))))..)))........)))))..--- ( -33.80)
>consensus
AUAUGGUUAACAACUCUUGACCAAGCAACGGUUAAAAAGGUUCAACGAGCCAUCGUCUUAGCCAGCGAAUGAGGCCCAAGACUUUUGGCUCUGCCAACUGACAAAGCGACUGACCAC___
...((((((.......((((((.......))))))...((((....((((((..(((((.(((.........)))..)))))...))))))....))))...........)))))).... (-28.52 = -28.92 +   0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,099,732 – 8,099,849
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.70
Mean single sequence MFE -37.79
Consensus MFE -32.54
Energy contribution -33.10
Covariance contribution 0.56
Combinations/Pair 1.02
Mean z-score -1.53
Structure conservation index 0.86
SVM decision value 0.56
SVM RNA-class probability 0.782570
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8099732 117 - 27905053
---GUGGUCAGUCGCUUUGUCAGUUGGCAGAGCCAAAAGUCUUGGGCCUCAUUCGCUGCCUAAGACGAUGGCUCGUUGAACCUUUUUAACCGUUGCUUGGUCAAGAGUUGUUAACCAUAU
---(((((.((..(((((.......((((((((((...(((((((((..(....)..)))))))))..))))))((((((....))))))...))))......)))))..)).))))).. ( -41.32)
>DroSec_CAF1 51377 117 - 1
---GUGGUCAGUCGCUUUGUCAGUUGGCAGAGCCAAAAGUCUGGGGCCUCAUUCGCUGGCUAAGACGAUGGCUCGUUGAACCUUUUUAACCGUUGCUUGGUCAAGAGUUGUUAACCAUAU
---(((((.((..(((((.......((((((((((...((((..((((.........)))).))))..))))))((((((....))))))...))))......)))))..)).))))).. ( -38.42)
>DroSim_CAF1 23448 117 - 1
---GUGGUCAGUCGCUUUGUCAGUUGGCAGAGCCAAAAGUCUUGGGCCUCAUUCGCUGGCUAAGACGAUGGCUCGUUGAACCUUUUUAACCGUUGCUUGGUCAAGAGUUGUUAACCAUAU
---(((((.((..(((((.......((((((((((...(((((((.((.........)))))))))..))))))((((((....))))))...))))......)))))..)).))))).. ( -38.42)
>DroEre_CAF1 26442 120 - 1
GUGGUGGUCAGUCACUUUGUCAGUUGCCAGAGCCAAAAGUCUUGGGCCUCAUUCGCUGGCGAAGACGAUGGCUCGUUGAACCUUUUUAACCGUUGCUUGGUCAAGAGUUGUUAACCAUAU
(((((...(((.(.(((..(((((.((..((((((...(((((.(.((.........))).)))))..))))))((((((....)))))).)).)).)))..))).))))...))))).. ( -35.10)
>DroYak_CAF1 19804 117 - 1
---GUGGUCAGUCACUUUGUCAGUUGCCAGAGCCAAAAGUCUUGGGCCUCAUUCGCUGGCAAAGACGAUGGCUCGUUGAACCUUUUUAACCGUUGCUUGGUCAAGAGUUGUUAACCAUAU
---(((((.((..(((((((((((.((..((((((...(((((..(((.........))).)))))..))))))((((((....)))))).)).)).))).).)))))..)).))))).. ( -35.70)
>consensus
___GUGGUCAGUCGCUUUGUCAGUUGGCAGAGCCAAAAGUCUUGGGCCUCAUUCGCUGGCUAAGACGAUGGCUCGUUGAACCUUUUUAACCGUUGCUUGGUCAAGAGUUGUUAACCAUAU
...(((((.((..((((((((((.(..(.((((((...(((((((.((.........)))))))))..))))))((((((....)))))).)..).)))).).)))))..)).))))).. (-32.54 = -33.10 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,099,812 – 8,099,907
Length 95
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.19
Mean single sequence MFE -38.90
Consensus MFE -26.01
Energy contribution -26.17
Covariance contribution 0.16
Combinations/Pair 1.15
Mean z-score -2.30
Structure conservation index 0.67
SVM decision value 0.82
SVM RNA-class probability 0.859764
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8099812 95 + 27905053
ACUUUUGGCUCUGCCAACUGACAAAGCGACUGACCAC---------------AAGUCAAAUUGGUGAACGGAGG-------GGCGCUGCGGUUGCCGAGGCAGCCGCC---GCCAAGAAA
.((((((..((.(((((((.....)).((((......---------------.))))...))))))).))))))-------((((..((((((((....)))))))))---)))...... ( -36.80)
>DroSec_CAF1 51457 95 + 1
ACUUUUGGCUCUGCCAACUGACAAAGCGACUGACCAC---------------AAGCCAAAUUGGUGGACAGAGG-------AGCGCUGCGGUUGCCGGGGCAGCCGCC---GCCAAGAAA
..(((((((...............((((.(((.((((---------------((......)).)))).)))...-------..))))((((((((....)))))))).---))))))).. ( -36.10)
>DroSim_CAF1 23528 95 + 1
ACUUUUGGCUCUGCCAACUGACAAAGCGACUGACCAC---------------AAGCCAAAUUGAUGGACAGAGG-------GGAGCUGCGGUUGCCGAGGCAGCCGCC---GCCAAGAAA
..(((((((.((.((..(((.((.......)).((((---------------((......))).))).)))..)-------).))..((((((((....)))))))).---))))))).. ( -35.20)
>DroEre_CAF1 26522 120 + 1
ACUUUUGGCUCUGGCAACUGACAAAGUGACUGACCACCACCACAAGCCAGCCAAGCCGAAUUGGUGGACCGAGGACUGGUGGACUCUGCGGUUACCGAGGCAGCCGCCGUCGCCAAGAAA
..(((((((..((((..(((.....(((((((.((((((((.(...(((.((((......)))))))...).))..))))))......))))))).....)))..))))..))))))).. ( -43.70)
>DroYak_CAF1 19884 95 + 1
ACUUUUGGCUCUGGCAACUGACAAAGUGACUGACCAC---------------AAGCCAAAUCGGUGGACCGAGG-------GGCUCUGCGGUUGCCGAGGCAGCCGCC---GCCAAGAAA
..(((((((..(((((((((.((..(((......)))---------------.((((...((((....))))..-------)))).))))))))))).(((....)))---))))))).. ( -42.70)
>consensus
ACUUUUGGCUCUGCCAACUGACAAAGCGACUGACCAC_______________AAGCCAAAUUGGUGGACAGAGG_______GGCGCUGCGGUUGCCGAGGCAGCCGCC___GCCAAGAAA
..(((((((((((...(((((....((...........................))....)))))...))))...............((((((((....))))))))....))))))).. (-26.01 = -26.17 +   0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,099,871 – 8,099,979
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.00
Mean single sequence MFE -39.34
Consensus MFE -33.78
Energy contribution -34.02
Covariance contribution 0.24
Combinations/Pair 1.09
Mean z-score -2.00
Structure conservation index 0.86
SVM decision value 1.93
SVM RNA-class probability 0.982828
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8099871 108 + 27905053
-GGCGCUGCGGUUGCCGAGGCAGCCGCC---GCCAAGAAAAAUAGCCAAGCUUGGAAAAUGCGUUGGAGUAAUAGCCGGUAACG----AACCCGAGUUGGUGGAUGGA----UUUCCAUA
-((((..((((((((....)))))))))---)))..........(((((.(((((......(((((..(.......)..)))))----...))))))))))..((((.----...)))). ( -40.90)
>DroSec_CAF1 51516 112 + 1
-AGCGCUGCGGUUGCCGGGGCAGCCGCC---GCCAAGAAAAAUAGCCAAGCUUGGAAAAUGCGUUGGAGUAAUAGUCGGUAACGAACGAACCCGAGCUGGUGGAUGGA----UUUCCAUA
-.(.((.((((((((....)))))))).---)))..........((((.((((((....(((......)))....(((....)))......))))))))))..((((.----...)))). ( -41.00)
>DroSim_CAF1 23587 112 + 1
-GGAGCUGCGGUUGCCGAGGCAGCCGCC---GCCAAGAAAAAUAGUCAAGCUUGGAAAAUGCGUUGGAGUAAUAGUCGGUAACGAACGAACCCGAGCUGGUGGAUGGA----UUUCCAUA
-.(.((.((((((((....)))))))).---)))..............(((((((....(((......)))....(((....)))......))))))).(((((....----..))))). ( -38.60)
>DroEre_CAF1 26602 112 + 1
GGACUCUGCGGUUACCGAGGCAGCCGCCGUCGCCAAGAAAAAUGGCCAAGUUUGGAAAAUGCGUUGGAGUAAUAGUCGGUAACG----AGCCCGAGCUUGUGGAUGGA----UUUCCAUA
(((....((((((.(....).))))))((((((((.......))))(((((((((....(((......)))....(((....))----)..)))))))))..))))..----..)))... ( -35.30)
>DroYak_CAF1 19943 112 + 1
-GGCUCUGCGGUUGCCGAGGCAGCCGCC---GCCAAGAAAAAUAGCCAAGUUUGGAAAAUGCGUUGGAGUAAUAGUCGGUAACG----AACCCGAGCUUGUGGAUGGAUGCAUUUCCAUA
-(((...((((((((....)))))))).---)))...........((((((((((....(((......)))....(((....))----)..))))))))).).(((((......))))). ( -40.90)
>consensus
_GGCGCUGCGGUUGCCGAGGCAGCCGCC___GCCAAGAAAAAUAGCCAAGCUUGGAAAAUGCGUUGGAGUAAUAGUCGGUAACG____AACCCGAGCUGGUGGAUGGA____UUUCCAUA
.(((...((((((((....))))))))....)))...........((((((((((......(((((..(.......)..))))).......)))))))..)))(((((......))))). (-33.78 = -34.02 +   0.24)

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 10:52:01 2006