Locus 1734

Sequence ID 3R_DroMel_CAF1
Location 4,982,853 – 4,983,031
Length 178
Max. P 0.966272
window2851 window2852 window2853

overview

Window 1

Location 4,982,853 – 4,982,970
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.92
Mean single sequence MFE -40.78
Consensus MFE -34.53
Energy contribution -32.57
Covariance contribution -1.96
Combinations/Pair 1.50
Mean z-score -1.98
Structure conservation index 0.85
SVM decision value 0.62
SVM RNA-class probability 0.802789
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4982853 117 - 27905053
AAACUGCCAGCGCCCUUUUGGGCGGCCCGUAUGCCCAGGGCGCUCCCGCCCUGAAAAUGGUGCAGAAACGCUACAUUGGAUUACAUCACUGGCUGGGACCAAUCCG---CUCCAAGGAGC
...(.((((((((((....)))))....(((..(((((((((....)))))))..((((..((......))..))))))..)))....))))).)(((....)))(---(((....)))) ( -46.50)
>DroVir_CAF1 116151 114 - 1
AAACCGCCAGCGCCCUUCUGGGCGGGCCCUACGCCCAGGGCGCCCCCGCCCUGAAAAUGGUGCAAAAACGUUACAUUGGAUUACAUCAAUGGCUGGGACCAAUACG------CAAGGAGC
......((((((((((((.(((((((((((......)))))....)))))).)))...)).))..........((((((......)))))))))))........(.------...).... ( -41.30)
>DroGri_CAF1 110633 114 - 1
AAACCGCUAGCGCUUUACUGGGCGGCCCCUACGCCCAGGGCGCCCCUGCCCUGAAAAUGGUGCAAAAACGGUAUAUUGGAUUACACCAGUGGCUGGGACCCAUACG------CAAAGAGC
.....((..(((((...(((((((.......))))))))))))(((.((((((......((......)).(((........)))..))).))).)))........)------)....... ( -39.40)
>DroWil_CAF1 98359 120 - 1
AAACUGCCAACGCUCUAUUGGGCGGCCCAUAUGCCCAAGGUGCACCCGCCUUAAAAAUGGUACAAAAACGUUAUAUUGGAUUACAUCAAUGGUUGGGACCAAUACGAACCACCAAAGAGC
...........(((((.(((((((.......)))))))((((.....(((........)))........(((.((((((.(..((........))..)))))))..)))))))..))))) ( -31.20)
>DroMoj_CAF1 106745 114 - 1
AAACUGCCAGCGCCCUACUGGGCGGGCCAUACGCCCAGGGCGCACCCGCCCUGAAAAUGGUGCAAAAACGCUACAUUGGAUUACAUCAAUGGCUGGGACCAAUACG------CAAAGAGC
....(((..(((((((...(((((.......)))))))))))).(((((((.......)).))......((..((((((......)))))))).)))........)------))...... ( -41.20)
>DroAna_CAF1 85029 117 - 1
AAACUUCCAGUGCCCUUCUGGGCGGACCAUACGCCCAGGGCGCUCCCGCCUUGAAAAUGGUGCAGAAACGCUACAUUGGAUUACAUCAGUGGCUGGGACCAAUUCG---CACCAAGGAGC
....((((((((((((...(((((.......))))))))))))).............((((((.(((..(((((..((.....))...)))))((....)).))))---))))).)))). ( -45.10)
>consensus
AAACUGCCAGCGCCCUACUGGGCGGCCCAUACGCCCAGGGCGCACCCGCCCUGAAAAUGGUGCAAAAACGCUACAUUGGAUUACAUCAAUGGCUGGGACCAAUACG______CAAAGAGC
......(((((((((....(((((.......)))))((((((....))))))......)).))..........((((((......)))))))))))........................ (-34.53 = -32.57 +  -1.96)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,982,890 – 4,983,004
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.60
Mean single sequence MFE -41.70
Consensus MFE -36.23
Energy contribution -35.23
Covariance contribution -0.99
Combinations/Pair 1.43
Mean z-score -2.17
Structure conservation index 0.87
SVM decision value 1.21
SVM RNA-class probability 0.930803
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4982890 114 - 27905053
GCAGAUCCGGGCGCU---AGC---AAAAUGGUGGUUUUAGAAACUGCCAGCGCCCUUUUGGGCGGCCCGUAUGCCCAGGGCGCUCCCGCCCUGAAAAUGGUGCAGAAACGCUACAUUGGA
(((....(((((...---...---....(((..(((.....)))..))).(((((....))))))))))..))).(((((((....)))))))..((((..((......))..))))... ( -48.40)
>DroVir_CAF1 116185 117 - 1
GGCACCACAAGCGAUUACAAC---AAAAUGGUGGUUUUAGAAACCGCCAGCGCCCUUCUGGGCGGGCCCUACGCCCAGGGCGCCCCCGCCCUGAAAAUGGUGCAAAAACGUUACAUUGGA
.((((((...(((........---....((((((((.....)))))))).(((((....))))).......))).(((((((....)))))))....))))))................. ( -48.70)
>DroGri_CAF1 110667 117 - 1
GGCACAACAAGCGAUUACAAC---AAAAUGGUGGUUCUGGAAACCGCUAGCGCUUUACUGGGCGGCCCCUACGCCCAGGGCGCCCCUGCCCUGAAAAUGGUGCAAAAACGGUAUAUUGGA
.((((...(((((........---....((((((((.....)))))))).)))))....(((((.......)))))((((((....)))))).......))))................. ( -37.72)
>DroWil_CAF1 98399 113 - 1
ACAGAAACA-ACAGU---AGC---AAAAUGGUGGUUUUAGAAACUGCCAACGCUCUAUUGGGCGGCCCAUAUGCCCAAGGUGCACCCGCCUUAAAAAUGGUACAAAAACGUUAUAUUGGA
.......((-(..((---(((---....(((..(((.....)))..)))..(..((((((((((.......)))))((((((....))))))...)))))..)......))))).))).. ( -29.30)
>DroMoj_CAF1 106779 117 - 1
GGGACCGCAAGCGAUUUCAAC---AAAAUGGUGGUUUUAGAAACUGCCAGCGCCCUACUGGGCGGGCCAUACGCCCAGGGCGCACCCGCCCUGAAAAUGGUGCAAAAACGCUACAUUGGA
....(((..((((........---....(((..(((.....)))..)))(((((.....(((((.......)))))((((((....))))))......))))).....))))....))). ( -44.40)
>DroPer_CAF1 134665 117 - 1
ACAAGCCCAAGCGAU---AGCCACAAAAUGGUGGUUCUAGAGACUGCCAGCGCCCUGCUGGGCGGCCCAUAUGCCCAGGGCGCGCCCGCCUUGAAAAUGGUACAAAAACGCUACAUUGGA
......(((((((..---.((.......(((..(((.....)))..)))(((((((...(((((.......))))))))))))))..(((........))).......))))....))). ( -41.70)
>consensus
GCAACCACAAGCGAU___AAC___AAAAUGGUGGUUUUAGAAACUGCCAGCGCCCUACUGGGCGGCCCAUACGCCCAGGGCGCACCCGCCCUGAAAAUGGUGCAAAAACGCUACAUUGGA
.........((((...............((((((((.....))))))))(((((.....(((((.......)))))((((((....))))))......))))).....))))........ (-36.23 = -35.23 +  -0.99)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,982,930 – 4,983,031
Length 101
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 75.02
Mean single sequence MFE -31.67
Consensus MFE -21.83
Energy contribution -20.94
Covariance contribution -0.89
Combinations/Pair 1.33
Mean z-score -1.81
Structure conservation index 0.69
SVM decision value 1.59
SVM RNA-class probability 0.966272
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4982930 101 - 27905053
AAGCAUCAACUAUCAACAGCAACUAUCGCAGAUCCGGGCGCU---AGC---AAAAUGGUGGUUUUAGAAACUGCCAGCGCCCUUUUGGGCGGCCCGUAUGCCCAGGG
..((((............((.......)).....(((((...---...---....(((..(((.....)))..))).(((((....)))))))))).))))...... ( -32.60)
>DroPse_CAF1 128207 97 - 1
----AACAACA---CACAACAGCUAUCACAGGCCGAAGCGAU---AGCCACAAAAUGGUGGUUCUAGAGACUGCCAGCGCCCUGCUGGGCGGCCCAUAUGCCCAGGG
----.......---..............((((.((..((...---.)).......(((..(((.....)))..))).)).))))(((((((.......))))))).. ( -28.70)
>DroYak_CAF1 91634 95 - 1
------CAACUAGCAACAGCAACUAUCGCUGAUCCGGGCGCU---AGC---AAAAUGGUGGUUUUAGAAACUACCACCGCCCUUUUGGGCGGCCCCUAUGCCCAAGG
------..........((((.......))))....(((((.(---((.---....((((((((.....))))))))((((((....))))))...)))))))).... ( -37.10)
>DroMoj_CAF1 106819 99 - 1
----AACAACA-AAAACUAAAAUAAUCGGGACCGCAAGCGAUUUCAAC---AAAAUGGUGGUUUUAGAAACUGCCAGCGCCCUACUGGGCGGGCCAUACGCCCAGGG
----.......-...............(((..(((....(....)...---....(((..(((.....)))..)))))))))..(((((((.......))))))).. ( -30.00)
>DroAna_CAF1 85106 94 - 1
---CUGCAGCU----AUAACUUCGUUUGCAGACCCGGGCGAU---AGC---AAAAUGGUGGUUUUAGAAACUUCCAGUGCCCUUCUGGGCGGACCAUACGCCCAGGG
---(((((((.----........).)))))).((((((((..---...---....(((.((((.....)))).))).(((((....))))).......))))).))) ( -33.30)
>DroPer_CAF1 134705 97 - 1
----AACAACA---CACAACAGCUAUCACAAGCCCAAGCGAU---AGCCACAAAAUGGUGGUUCUAGAGACUGCCAGCGCCCUGCUGGGCGGCCCAUAUGCCCAGGG
----.......---.......((((((.(........).)))---))).......(((..(((.....)))..))).(((((....))))).(((.........))) ( -28.30)
>consensus
____AACAACA___AACAACAACUAUCGCAGACCCAAGCGAU___AGC___AAAAUGGUGGUUUUAGAAACUGCCAGCGCCCUUCUGGGCGGCCCAUAUGCCCAGGG
.....................................(((...............((((((((.....)))))))).)))....(((((((.......))))))).. (-21.83 = -20.94 +  -0.89)

alignment

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secondary structure

Postscript

dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:01 2006