Locus 3083

Sequence ID 2L_DroMel_CAF1
Location 8,788,469 – 8,788,750
Length 281
Max. P 0.994249
window4908 window4909 window4910 window4911 window4912

overview

Window 8

Location 8,788,469 – 8,788,589
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 93.58
Mean single sequence MFE -41.57
Consensus MFE -37.38
Energy contribution -37.13
Covariance contribution -0.25
Combinations/Pair 1.09
Mean z-score -1.30
Structure conservation index 0.90
SVM decision value 0.46
SVM RNA-class probability 0.744469
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8788469 120 - 22407834
GACAUCGGCGGGAACGUCAUCGUUGAGGCACAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACAGCGCAGCGGCAGACAGCAGCAUCCUGGCUGAAGGCUGCCUUC
((((((.(((.(((((((((((..((((..(..........)..))))))))))))))).....))).).)))))..........(((((....((((......))))....)))))... ( -43.20)
>DroSec_CAF1 91225 120 - 1
GACAUCGACGGGAACGUCAUCGUUGAGGCACAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACAGCGCAGCGGCAGACAGCAGCAUCCUGGCUGAAGGCUGCCUUC
((((((.(((.(((((((((((..((((..(..........)..))))))))))))))).....))).).)))))..........(((((....((((......))))....)))))... ( -42.90)
>DroSim_CAF1 94785 120 - 1
GACAUCGGCGGGAACGUCAUCGCUGAGGCACAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACAGCGCAGCGGCAGACAGCAGCAUCCUGGCUGAAGGCUGCCUUC
((((((.(((.((((((((((((....))............((....)))))))))))).....))).).)))))..........(((((....((((......))))....)))))... ( -43.40)
>DroEre_CAF1 97706 120 - 1
GACAUCGGCGGGAACGUCAUCGUUGAGGCACAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACGGCGCAGCGGCAGACAGCAGCAUCCUGGCUGAAGGCCGCCUUU
.......(((.(((((((((((..((((..(..........)..))))))))))))))).....(((((....))))).))).(((((...((((((....)).))))...))))).... ( -43.20)
>DroYak_CAF1 96497 112 - 1
GACUUCGGCGGGAACGUCAUCGUUGAGGCACAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACAGCGCAGCGGCAGACAGCAGCAUCCUGGCUGAAGG--------
..(((((((.((((((((((((..((((..(..........)..))))))))))))))...((((...((.((((...((......)).)))))).)))).)).))))))).-------- ( -40.90)
>DroAna_CAF1 113518 108 - 1
GACAUCGGCG-GAACGUCAUCGUUGAGGCAUAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACAGCGCAGCGGCAGACAGCAGCAUCCUGGCUGA-----------
((((((.(((-(((((((((((..(((((.............).))))))))))))))).....))).).))))).((((.(((..((........))...))))))).----------- ( -35.82)
>consensus
GACAUCGGCGGGAACGUCAUCGUUGAGGCACAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACAGCGCAGCGGCAGACAGCAGCAUCCUGGCUGAAGGCUGCCUUC
((((((.(((.(((((((((((..((((..(..........)..))))))))))))))).....))).).))))).((((.(((..((........))...)))))))............ (-37.38 = -37.13 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,788,509 – 8,788,615
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 93.37
Mean single sequence MFE -35.52
Consensus MFE -32.49
Energy contribution -32.68
Covariance contribution 0.19
Combinations/Pair 1.03
Mean z-score -1.13
Structure conservation index 0.91
SVM decision value 0.28
SVM RNA-class probability 0.667435
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8788509 106 - 22407834
UC--------------CUGGCAUCGCCUGUCAGUCAGUUAGACAUCGGCGGGAACGUCAUCGUUGAGGCACAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACAGC
..--------------.((((((.(((.....(((.....)))....(((.(((((((((((..((((..(..........)..)))))))))))))))...)))..))))))))).... ( -34.90)
>DroSec_CAF1 91265 106 - 1
UC--------------CUGGCAUCGCCUGUCAGUCAGUUAGACAUCGACGGGAACGUCAUCGUUGAGGCACAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACAGC
..--------------...((((..((((((.(((.....)))...))))))((((((((((..((((..(..........)..))))))))))))))...))))((((....))))... ( -33.40)
>DroSim_CAF1 94825 106 - 1
UC--------------CUGGCAUCGCCUGUCAGUCAGUUAGACAUCGGCGGGAACGUCAUCGCUGAGGCACAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACAGC
..--------------.((((((.(((.....(((.....)))....(((.((((((((((((....))............((....))))))))))))...)))..))))))))).... ( -35.10)
>DroEre_CAF1 97746 106 - 1
UC--------------CUGGCAUCGCCUGUCAGUCAGUUAGACAUCGGCGGGAACGUCAUCGUUGAGGCACAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACGGC
.(--------------(((((((.(((.....(((.....)))....(((.(((((((((((..((((..(..........)..)))))))))))))))...)))..))))))))).)). ( -36.90)
>DroYak_CAF1 96529 106 - 1
UC--------------CUGGCAUCGCCUGUCAGUCAGUUAGACUUCGGCGGGAACGUCAUCGUUGAGGCACAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACAGC
..--------------.((((((.(((....((((.....))))...(((.(((((((((((..((((..(..........)..)))))))))))))))...)))..))))))))).... ( -35.00)
>DroAna_CAF1 113547 119 - 1
UCUCCACUCACGCGUUCUGCCAUCGCCUGUCAGUCAGCUAGACAUCGGCG-GAACGUCAUCGUUGAGGCAUAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACAGC
.(((.((....((((((((((......((((((....)).))))..))))-))))))....)).)))((((..((((....((....))(....)))))..))))((((....))))... ( -37.80)
>consensus
UC______________CUGGCAUCGCCUGUCAGUCAGUUAGACAUCGGCGGGAACGUCAUCGUUGAGGCACAAGAACAAAAGGACUUCCGGUGACGUUUAAAUGCGUGGCAUGUCACAGC
.................((((((.(((.....(((.....)))....(((.(((((((((((..((((..(..........)..)))))))))))))))...)))..))))))))).... (-32.49 = -32.68 +   0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,788,589 – 8,788,690
Length 101
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 93.90
Mean single sequence MFE -31.36
Consensus MFE -29.88
Energy contribution -30.36
Covariance contribution 0.48
Combinations/Pair 1.04
Mean z-score -1.69
Structure conservation index 0.95
SVM decision value 2.46
SVM RNA-class probability 0.994249
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8788589 101 + 22407834
UAACUGACUGACAGGCGAUGCCAGGAGGUCCUUCUCCUGCCCCACAAAA-ACC----CCCUGCCCAACUCAAUGGGCGCUCAACUGCCAGCAGAGUUCAAGUGUAA
...(((.(((.(((..((.(((((((((....)))))))..........-...----....(((((......)))))))))..))).))))))............. ( -32.30)
>DroSec_CAF1 91345 101 + 1
UAACUGACUGACAGGCGAUGCCAGGAGGUCCUUCUCCUGCCCCACAAAA-CCC----CCCUGCCCAGCUCAAUGGCCGCUCAACUGCCAGCAGAGUUCAAGUGUAA
...(((.(((.(((..((.(((((((((....)))))))..........-...----....(.(((......))).)))))..))).))))))............. ( -26.00)
>DroSim_CAF1 94905 101 + 1
UAACUGACUGACAGGCGAUGCCAGGAGGUCCUUCUCCUGCCCCACAAAA-ACC----CCCUGCCCAGCUCAAUGGGCGCUCAACUGCCAGCAGAGUUCAAGUGUAA
...(((.(((.(((..((.(((((((((....)))))))..........-...----....(((((......)))))))))..))).))))))............. ( -33.10)
>DroEre_CAF1 97826 105 + 1
UAACUGACUGACAGGCGAUGCCAGGAGGUCCU-CUCCUGCCCCACAGAAAGCCCCACCCCUGCCCAGCUCAAUGGGCGCCCAACUGCCAGCAGAGUUCAAGUGUAA
...(((.(((.(((.....((((((((.....-))))))......................(((((......)))))))....))).))))))............. ( -29.30)
>DroYak_CAF1 96609 102 + 1
UAACUGACUGACAGGCGAUGCCAGGAGGUCCUCCUCCUGCCCCACACAAAACC----CCCUGCCCAGCUCGUUGGGCGCUCAACUGCCAGCAGAGUUCAAGUGUAA
...(((.(((.(((..((.(((((((((....)))))))..............----....((((((....))))))))))..))).))))))............. ( -36.10)
>consensus
UAACUGACUGACAGGCGAUGCCAGGAGGUCCUUCUCCUGCCCCACAAAA_ACC____CCCUGCCCAGCUCAAUGGGCGCUCAACUGCCAGCAGAGUUCAAGUGUAA
...(((.(((.(((..((.(((((((((....)))))))......................(((((......)))))))))..))).))))))............. (-29.88 = -30.36 +   0.48)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,788,589 – 8,788,690
Length 101
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 93.90
Mean single sequence MFE -40.22
Consensus MFE -35.72
Energy contribution -35.76
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.45
Structure conservation index 0.89
SVM decision value 1.01
SVM RNA-class probability 0.899011
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8788589 101 - 22407834
UUACACUUGAACUCUGCUGGCAGUUGAGCGCCCAUUGAGUUGGGCAGGG----GGU-UUUUGUGGGGCAGGAGAAGGACCUCCUGGCAUCGCCUGUCAGUCAGUUA
.........((((..((((((((.((((((((((......)))))((((----(((-((((.(........).))))))))))).)).))).)))))))).)))). ( -42.10)
>DroSec_CAF1 91345 101 - 1
UUACACUUGAACUCUGCUGGCAGUUGAGCGGCCAUUGAGCUGGGCAGGG----GGG-UUUUGUGGGGCAGGAGAAGGACCUCCUGGCAUCGCCUGUCAGUCAGUUA
.........((((..((((((((.(((.((((......))))(.(((((----((.-((((.((...)).))))....))))))).).))).)))))))).)))). ( -36.10)
>DroSim_CAF1 94905 101 - 1
UUACACUUGAACUCUGCUGGCAGUUGAGCGCCCAUUGAGCUGGGCAGGG----GGU-UUUUGUGGGGCAGGAGAAGGACCUCCUGGCAUCGCCUGUCAGUCAGUUA
.........((((..((((((((.((((((((((......)))))((((----(((-((((.(........).))))))))))).)).))).)))))))).)))). ( -41.30)
>DroEre_CAF1 97826 105 - 1
UUACACUUGAACUCUGCUGGCAGUUGGGCGCCCAUUGAGCUGGGCAGGGGUGGGGCUUUCUGUGGGGCAGGAG-AGGACCUCCUGGCAUCGCCUGUCAGUCAGUUA
.........((((..((((((((.(((((.(((((.(((((..((....))..)))))...))))).((((((-.....)))))))).))).)))))))).)))). ( -41.60)
>DroYak_CAF1 96609 102 - 1
UUACACUUGAACUCUGCUGGCAGUUGAGCGCCCAACGAGCUGGGCAGGG----GGUUUUGUGUGGGGCAGGAGGAGGACCUCCUGGCAUCGCCUGUCAGUCAGUUA
.........((((..((((((((.((((((((((......)))))....----..............(((((((....))))))))).))).)))))))).)))). ( -40.00)
>consensus
UUACACUUGAACUCUGCUGGCAGUUGAGCGCCCAUUGAGCUGGGCAGGG____GGU_UUUUGUGGGGCAGGAGAAGGACCUCCUGGCAUCGCCUGUCAGUCAGUUA
.........((((..((((((((.((((((((((......)))))......................((((((......)))))))).))).)))))))).)))). (-35.72 = -35.76 +   0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,788,650 – 8,788,750
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.31
Mean single sequence MFE -20.22
Consensus MFE -14.96
Energy contribution -14.85
Covariance contribution -0.11
Combinations/Pair 1.26
Mean z-score -1.55
Structure conservation index 0.74
SVM decision value 0.19
SVM RNA-class probability 0.626085
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8788650 100 - 22407834
--UACAUUUCUUUUU--UCACGCUCAUCUGUACA----------------UUUACUUUAUUUUAAAUAUAAAUUUCGCAUUUACACUUGAACUCUGCUGGCAGUUGAGCGCCCAUUGAGU
--.......(((...--...((((((.((((..(----------------((((........))))).........(((((((....))))...)))..)))).))))))......))). ( -15.40)
>DroSec_CAF1 91406 100 - 1
--UACAUUUCUUUUU--UCACGCUCAGCUGUACA----------------UUUACUUUAUUUUAAAUAUAAAUUUCGCAUUUACACUUGAACUCUGCUGGCAGUUGAGCGGCCAUUGAGC
--.......(((...--...(((((((((((..(----------------((((........))))).........(((((((....))))...)))..)))))))))))......))). ( -20.40)
>DroSim_CAF1 94966 100 - 1
--UACAUUUCUGUUG--UCACGCUCAGCUGUACA----------------UUUACUUUAUUUUAAAUAUAAAUUUCGCAUUUACACUUGAACUCUGCUGGCAGUUGAGCGCCCAUUGAGC
--.....(((...((--...(((((((((((..(----------------((((........))))).........(((((((....))))...)))..)))))))))))..))..))). ( -19.50)
>DroEre_CAF1 97891 100 - 1
--UGCAAAUCUUUUU--UCACGCUCAGCUGUACA----------------UUUACUUUAUUUUAAAUAUAAAUUUCGCAUUUACACUUGAACUCUGCUGGCAGUUGGGCGCCCAUUGAGC
--.......(((...--...(((((((((((..(----------------((((........))))).........(((((((....))))...)))..)))))))))))......))). ( -18.40)
>DroYak_CAF1 96671 100 - 1
--UACAAAUCUUUUU--UCACGCUCAGCUGUACA----------------UUUACUUUAUUUGAAAUAUAAAUUUCGCAUUUACACUUGAACUCUGCUGGCAGUUGAGCGCCCAACGAGC
--.............--...(((((((((((...----------------............(((((....)))))(((((((....))))...)))..))))))))))).......... ( -21.60)
>DroAna_CAF1 113681 120 - 1
CCGACCUUUAAUUUUUCUCAUUUGUGGCUGUACAAUGUCCUUAGAAUAUUUUUCCUUUAUUUUAUAGAGAAGUUUUACAUUUACACUUGAACCCUGCUGGCAGUUGAACGCUUAGCGGGC
.................(((..(((((.((((.(((.(((((((((((.........))))))).)).)).))).)))).)))))..)))..(((((((((........)).))))))). ( -26.00)
>consensus
__UACAUUUCUUUUU__UCACGCUCAGCUGUACA________________UUUACUUUAUUUUAAAUAUAAAUUUCGCAUUUACACUUGAACUCUGCUGGCAGUUGAGCGCCCAUUGAGC
....................(((((((((((........................(((((.......)))))....(((((((....))))...)))..))))))))))).......... (-14.96 = -14.85 +  -0.11)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:01 2006