Locus 3079

Sequence ID 2L_DroMel_CAF1
Location 8,785,354 – 8,785,514
Length 160
Max. P 0.988561
window4898 window4899 window4900 window4901 window4902

overview

Window 8

Location 8,785,354 – 8,785,461
Length 107
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.56
Mean single sequence MFE -28.37
Consensus MFE -24.67
Energy contribution -24.83
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.47
Structure conservation index 0.87
SVM decision value 2.08
SVM RNA-class probability 0.987452
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8785354 107 + 22407834
---U--UUUCUGUCACCUGUUUCAACACUUGAAAU--------GUGACGGCAGCCGCCAAACAACCUAAUUAGUAUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC
---.--.....(((((..((((((.....))))))--------)))))(((....)))...........(((((.((.....)).)))))((((((((.......))))))))....... ( -27.70)
>DroSec_CAF1 88067 108 + 1
U--U--UUUCUGUCACCUGUUUCAACACUUGAAAU--------GUGACGGCAGCCGCCAAACAACCUAAUUAGUGUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC
.--.--.....(((((..((((((.....))))))--------)))))(((....)))...........((((((((.....))))))))((((((((.......))))))))....... ( -33.70)
>DroSim_CAF1 91582 110 + 1
UUUU--UUUCUGUCACCUGUUUCAACACUUGAAAU--------GUGACGGCAGCCGCCAAACAACCUAAUUAGUAUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC
....--.....(((((..((((((.....))))))--------)))))(((....)))...........(((((.((.....)).)))))((((((((.......))))))))....... ( -27.70)
>DroEre_CAF1 94587 112 + 1
UUUUUAUUUCUGUCACCUGUUUCAACACUUGAAAU--------GUGACGGCAGCCGCCAAACAACCUAAUUAGUAUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC
...........(((((..((((((.....))))))--------)))))(((....)))...........(((((.((.....)).)))))((((((((.......))))))))....... ( -27.70)
>DroYak_CAF1 93200 107 + 1
UU-----UUCUGUCACCUGUUUCAACACUUGAAAU--------GUGACGGCAGCCGCCAAACAACCUAAUUAGUAUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC
..-----....(((((..((((((.....))))))--------)))))(((....)))...........(((((.((.....)).)))))((((((((.......))))))))....... ( -27.70)
>DroAna_CAF1 110226 116 + 1
U--U--UUUCUGUCACCUGUUCCAACACUUGAAAUGUGAAAAUGUGACGGCAGCCGCCAAACAACCUAAUUAGUAUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC
.--.--.....(((((...(((((..........)).)))...)))))(((....)))...........(((((.((.....)).)))))((((((((.......))))))))....... ( -25.70)
>consensus
U__U__UUUCUGUCACCUGUUUCAACACUUGAAAU________GUGACGGCAGCCGCCAAACAACCUAAUUAGUAUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC
...........(((((..((((((.....))))))........)))))(((....)))...........(((((.((.....)).)))))((((((((.......))))))))....... (-24.67 = -24.83 +   0.17)

alignment

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secondary structure

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Window 9

Location 8,785,354 – 8,785,461
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.56
Mean single sequence MFE -35.42
Consensus MFE -31.09
Energy contribution -30.82
Covariance contribution -0.28
Combinations/Pair 1.06
Mean z-score -2.36
Structure conservation index 0.88
SVM decision value 2.13
SVM RNA-class probability 0.988561
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8785354 107 - 22407834
GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCAUACUAAUUAGGUUGUUUGGCGGCUGCCGUCAC--------AUUUCAAGUGUUGAAACAGGUGACAGAAA--A---
....((((((....)))))).((((((((..((((.((.((........)).)).))))..))))))))...(((((--------.(((((.....)))))...))))).....--.--- ( -34.80)
>DroSec_CAF1 88067 108 - 1
GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCACACUAAUUAGGUUGUUUGGCGGCUGCCGUCAC--------AUUUCAAGUGUUGAAACAGGUGACAGAAA--A--A
....((((((....)))))).((((((((..(((((((.....))).((....))))))..))))))))...(((((--------.(((((.....)))))...))))).....--.--. ( -36.40)
>DroSim_CAF1 91582 110 - 1
GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCAUACUAAUUAGGUUGUUUGGCGGCUGCCGUCAC--------AUUUCAAGUGUUGAAACAGGUGACAGAAA--AAAA
....((((((....)))))).((((((((..((((.((.((........)).)).))))..))))))))...(((((--------.(((((.....)))))...))))).....--.... ( -34.80)
>DroEre_CAF1 94587 112 - 1
GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCAUACUAAUUAGGUUGUUUGGCGGCUGCCGUCAC--------AUUUCAAGUGUUGAAACAGGUGACAGAAAUAAAAA
....((((((....)))))).((((((((..((((.((.((........)).)).))))..))))))))...(((((--------.(((((.....)))))...)))))........... ( -34.80)
>DroYak_CAF1 93200 107 - 1
GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCAUACUAAUUAGGUUGUUUGGCGGCUGCCGUCAC--------AUUUCAAGUGUUGAAACAGGUGACAGAA-----AA
....((((((....)))))).((((((((..((((.((.((........)).)).))))..))))))))...(((((--------.(((((.....)))))...)))))....-----.. ( -34.80)
>DroAna_CAF1 110226 116 - 1
GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCAUACUAAUUAGGUUGUUUGGCGGCUGCCGUCACAUUUUCACAUUUCAAGUGUUGGAACAGGUGACAGAAA--A--A
....((((((....)))))).((((((((..((((.((.((........)).)).))))..))))))))...(((((..((((((((.....))).)))))...))))).....--.--. ( -36.90)
>consensus
GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCAUACUAAUUAGGUUGUUUGGCGGCUGCCGUCAC________AUUUCAAGUGUUGAAACAGGUGACAGAAA__A__A
....((((((....)))))).((((((((((((((((((.....))))..))))))).....)))))))...(((((.........(((((.....)))))...)))))........... (-31.09 = -30.82 +  -0.28)

alignment

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secondary structure

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Window 0

Location 8,785,384 – 8,785,483
Length 99
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.68
Mean single sequence MFE -24.73
Consensus MFE -21.39
Energy contribution -22.08
Covariance contribution 0.69
Combinations/Pair 1.05
Mean z-score -2.07
Structure conservation index 0.86
SVM decision value 0.91
SVM RNA-class probability 0.879904
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8785384 99 + 22407834
---GUGACGGCAGCCGCCAAACAACCUAAUUAGUAUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC-------AGUACUCAUGGCACAAAAAAAA-----------
---(((..(((....)))......((...(((((.((.....)).)))))((((((((.......))))))))(((((..-------.)))))...)))))........----------- ( -23.10)
>DroSec_CAF1 88098 95 + 1
---GUGACGGCAGCCGCCAAACAACCUAAUUAGUGUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC-------AGUACUCAUGGCAAAAAA---------------
---.....(((.(((((............((((((((.....))))))))))))).))).......((((((.(((((..-------.)))))..))))))....--------------- ( -28.70)
>DroSim_CAF1 91615 99 + 1
---GUGACGGCAGCCGCCAAACAACCUAAUUAGUAUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC-------AGUACUCAUGGCAAAAAAAAAA-----------
---.....(((.(((((............(((((.((.....)).)))))))))).))).......((((((.(((((..-------.)))))..))))))........----------- ( -22.70)
>DroEre_CAF1 94622 110 + 1
---GUGACGGCAGCCGCCAAACAACCUAAUUAGUAUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC-------AGUACUCAUGGAAAAAGAAAACGAGAAUGGCAA
---.....(((....))).................(((............((((((((.......))))))))(((((..-------.))))).......................))). ( -22.50)
>DroYak_CAF1 93230 111 + 1
---GUGACGGCAGCCGCCAAACAACCUAAUUAGUAUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUCAGUACUCAGUACUCAUGGCAAAAAAAAAACAGAA------
---.....(((.(((((............(((((.((.....)).)))))))))).))).......((((((.((((((........))))))..)))))).............------ ( -25.00)
>DroAna_CAF1 110262 95 + 1
AAUGUGACGGCAGCCGCCAAACAACCUAAUUAGUAUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC-------GU---UCACAGCAUGCAG---------------
..(((...(((....)))..))).........((((((............((((((((.......)))))))).((....-------..---..)).))))))..--------------- ( -26.40)
>consensus
___GUGACGGCAGCCGCCAAACAACCUAAUUAGUAUGCAAAACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUC_______AGUACUCAUGGCAAAAAAAAAA___________
........(((....))).................(((............((((((((.......))))))))((((((........))))))....))).................... (-21.39 = -22.08 +   0.69)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,785,384 – 8,785,483
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.68
Mean single sequence MFE -29.07
Consensus MFE -25.91
Energy contribution -25.77
Covariance contribution -0.14
Combinations/Pair 1.04
Mean z-score -1.31
Structure conservation index 0.89
SVM decision value -0.05
SVM RNA-class probability 0.509643
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8785384 99 - 22407834
-----------UUUUUUUUGUGCCAUGAGUACU-------GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCAUACUAAUUAGGUUGUUUGGCGGCUGCCGUCAC---
-----------........((((.....))))(-------((..((((((....)))))).((((((((..((((.((.((........)).)).))))..))))))))....))).--- ( -28.00)
>DroSec_CAF1 88098 95 - 1
---------------UUUUUUGCCAUGAGUACU-------GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCACACUAAUUAGGUUGUUUGGCGGCUGCCGUCAC---
---------------....(((((...(((((.-------..)))))..)))))....(..((((((((..(((((((.....))).((....))))))..))))))))..).....--- ( -27.60)
>DroSim_CAF1 91615 99 - 1
-----------UUUUUUUUUUGCCAUGAGUACU-------GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCAUACUAAUUAGGUUGUUUGGCGGCUGCCGUCAC---
-----------..........((((..(((((.-------..)))))..((((((.(((((((.((((((.....)))....)))..))))))).))))))))))(((....)))..--- ( -26.40)
>DroEre_CAF1 94622 110 - 1
UUGCCAUUCUCGUUUUCUUUUUCCAUGAGUACU-------GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCAUACUAAUUAGGUUGUUUGGCGGCUGCCGUCAC---
..((((..(((((.(((.........))).)).-------))).((((((....)))))))))).((.(((((((((((.....))))..))))))).)).((((((...)))))).--- ( -29.40)
>DroYak_CAF1 93230 111 - 1
------UUCUGUUUUUUUUUUGCCAUGAGUACUGAGUACUGAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCAUACUAAUUAGGUUGUUUGGCGGCUGCCGUCAC---
------...............((((..((((((.(....).))))))..((((((.(((((((.((((((.....)))....)))..))))))).))))))))))(((....)))..--- ( -30.20)
>DroAna_CAF1 110262 95 - 1
---------------CUGCAUGCUGUGA---AC-------GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCAUACUAAUUAGGUUGUUUGGCGGCUGCCGUCACAUU
---------------........(((((---.(-------(.((((((((....)))))).((((((((..((((.((.((........)).)).))))..))))))))))))))))).. ( -32.80)
>consensus
___________UUUUUUUUUUGCCAUGAGUACU_______GAGUACUGCGGCAACGUAGUUGGCUGCCACUUAAUGUGUUUUGCAUACUAAUUAGGUUGUUUGGCGGCUGCCGUCAC___
.........................(((................((((((....)))))).((((((((((((((((((.....))))..))))))).....)))))))....))).... (-25.91 = -25.77 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,785,421 – 8,785,514
Length 93
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 75.04
Mean single sequence MFE -21.95
Consensus MFE -14.68
Energy contribution -14.80
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -1.45
Structure conservation index 0.67
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8785421 93 + 22407834
AACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUCAGUACUCAUGGCACAAAAAAAAA----AAAAAAACGAGAAAAGCGGACGCGGAUUGG
..(((.....)))....(((((..((((((((.(((((...)))))..))))...........----.......((.......))))))..).)))) ( -18.20)
>DroSec_CAF1 88135 90 + 1
AACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUCAGUACUCAUGGCAAAAAA-------ACGAGAAAAGCAAAAAUGCGGACGCGGAGUGG
....((((..(((....((..((.((((((((.(((((...)))))..))))).....-------)))))....(((....))))).)))..)))). ( -22.00)
>DroSim_CAF1 91652 97 + 1
AACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUCAGUACUCAUGGCAAAAAAAAAAAGUACGAGAAAAGCAAAAAUGCGGACGCGGAGUGG
..(((.....((((((((.......)))))))).((.(((.(((((................))))))))....(((....)))....))...))). ( -24.19)
>DroAna_CAF1 110302 77 + 1
AACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUCGU---UCACAGCAUGCAG-----------------CUCGGAGUGGGCCAAUGAGUGG
..........((((((((.......))))))))..(((((((---(((((((.....)-----------------))....))))))....))))). ( -23.40)
>consensus
AACACAUUAAGUGGCAGCCAACUACGUUGCCGCAGUACUCAGUACUCAUGGCAAAAAA_________GAGAAAAGCAAAAAUGCGGACGCGGAGUGG
..(((.....((((((((.......)))))))).................................................((....))...))). (-14.68 = -14.80 +   0.12)

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 10:43:52 2006