Locus 7359

Sequence ID 2L_DroMel_CAF1
Location 20,504,976 – 20,505,172
Length 196
Max. P 0.977028
window11813 window11814 window11815

overview

Window 3

Location 20,504,976 – 20,505,079
Length 103
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 80.52
Mean single sequence MFE -36.87
Consensus MFE -25.97
Energy contribution -27.25
Covariance contribution 1.28
Combinations/Pair 1.21
Mean z-score -2.32
Structure conservation index 0.70
SVM decision value 1.11
SVM RNA-class probability 0.916857
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20504976 103 + 22407834
UACCGCUAACUGCGCAUACAAUGGCUGCGGAA-AUUCCCCAGCAAGCCAA------------UGCCAAAAAUUGGCAUCUGUGUUUGCG--AGUGGAAGGGGCACAGGUGCUGCUAAC
..(((((...((((.(((((.(((((((((..-.....)).)).)))))(------------(((((.....)))))).))))).))))--))))).((.((((....)))).))... ( -38.10)
>DroSec_CAF1 22061 103 + 1
UACCGCUAACUGCGCAUACAAUGGCUGUGGAA-AUUCCCCGGCAAGCCAA------------UGCCAAAAAUUGGCAUCUGUGUUUGCG--AGUGGAAGGGGCACAGGUGCUGCGAAC
..(((((...((((.(((((...((((.((..-...)).))))..(((((------------(.......))))))...))))).))))--)))))..(.((((....)))).).... ( -36.20)
>DroSim_CAF1 27128 103 + 1
UACCGCUAACUGCGCAUACAAUGGCUGUGGAA-AUUCCCCAGCAAGCCAA------------UGCCAAAAAUUGGCAUCUGUGUUUGCG--AGUGGUAGGGGCACAGGUGCUGCGAAC
(((((((...((((.(((((...((((.((..-...)).))))..(((((------------(.......))))))...))))).))))--)))))))(.((((....)))).).... ( -39.10)
>DroEre_CAF1 20945 101 + 1
UACCGCUAACUGCGCAUACAAUGGCUGUGGAAAAUUCCCCAGCCAGCCAG------------CGCCAAAAAUUGGCAUCUGUGUUUGCGGGAGUGGAAGGGGCACAGGUGCAG-----
..(((((..(((((.(((((.((((((.(((....))).)))))).....------------.((((.....))))...))))).))))).))))).....(((....)))..----- ( -39.60)
>DroYak_CAF1 20880 104 + 1
UACCGCUAACUGCGCUUACAAUGGCUGUGGAAAAUGGCCCAGCAAGCCAA------------UGCCAAAAAUUGGCAUCUGCGUUUGCG--AGUGGAAGGGACACAGGUGCUGCAAAU
....((.....((((((.....((((((.....))))))..(((((((((------------(((((.....)))))).)).)))))).--.(((.......))))))))).)).... ( -34.30)
>DroAna_CAF1 13453 109 + 1
UACCGCUAACUGCAAUAGCAAUAGCUGCGAAAAAUUCGGUAGUAAGCCACUGGCACUGCCACUGUCGAAAAUUGGCAUCAGCAAUGGCG--AGAGG-------ACAGGUGCCGUAAAU
(((.(((.(((((..((((....))))(((.....)))))))).)))....((((((....((.(((...((((.......))))..))--).)).-------...)))))))))... ( -33.90)
>consensus
UACCGCUAACUGCGCAUACAAUGGCUGUGGAA_AUUCCCCAGCAAGCCAA____________UGCCAAAAAUUGGCAUCUGUGUUUGCG__AGUGGAAGGGGCACAGGUGCUGCAAAC
..(((((...((((.(((((.(((((((((........)).)).)))))..............(((((...)))))...))))).))))..)))))..(.((((....)))).).... (-25.97 = -27.25 +   1.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,505,015 – 20,505,119
Length 104
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 74.54
Mean single sequence MFE -31.67
Consensus MFE -15.50
Energy contribution -16.10
Covariance contribution 0.60
Combinations/Pair 1.26
Mean z-score -2.40
Structure conservation index 0.49
SVM decision value 1.78
SVM RNA-class probability 0.977028
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20505015 104 + 22407834
AGCAAGCCAA------------UGCCAAAAAUUGGCAUCUGUGUUUGCG--AGUGGAAGGGGCACAGGUGCUGCUAACGGCAGUGGUAAUGGAAACAGGAGUAAAACCCAAAAUGGGA
.((..((((.------------((((.......(((((((((((((.(.--.......))))))))))))))......)))).))))..((....))...))....(((.....))). ( -35.52)
>DroSec_CAF1 22100 104 + 1
GGCAAGCCAA------------UGCCAAAAAUUGGCAUCUGUGUUUGCG--AGUGGAAGGGGCACAGGUGCUGCGAACGGCAGUGGUGAUGGAAACAGGAGUAAAACCCAAAAUGGCU
.(((((((((------------(((((.....)))))).)).)))))).--.......(((.(((.(.(((((....))))).).))).((....)).........)))......... ( -34.20)
>DroSim_CAF1 27167 104 + 1
AGCAAGCCAA------------UGCCAAAAAUUGGCAUCUGUGUUUGCG--AGUGGUAGGGGCACAGGUGCUGCGAACGGCAGUGGUAAUGGAAACAGGAGUAAAACCCAAAAUGGGA
.((..((((.------------((((.......(((((((((((((((.--....))))..)))))))))))......)))).))))..((....))...))....(((.....))). ( -36.52)
>DroEre_CAF1 20985 82 + 1
AGCCAGCCAG------------CGCCAAAAAUUGGCAUCUGUGUUUGCGGGAGUGGAAGGGGCACAGGUGCAG-------------CAAUGGAAC-AGGAGUAUA-CCC---------
..((..(((.------------.((((.....))(((((((((((..(....)..).....)))))))))).)-------------)..)))...-.))......-...--------- ( -23.30)
>DroYak_CAF1 20920 104 + 1
AGCAAGCCAA------------UGCCAAAAAUUGGCAUCUGCGUUUGCG--AGUGGAAGGGACACAGGUGCUGCAAAUGGGAGUGGCAAUGGAACGAGGAGUAAAACCCAAAAUGGGU
.(((((((((------------(((((.....)))))).)).)))))).--.(((.......)))...(((..(........)..))).................((((.....)))) ( -30.60)
>DroAna_CAF1 13493 109 + 1
AGUAAGCCACUGGCACUGCCACUGUCGAAAAUUGGCAUCAGCAAUGGCG--AGAGG-------ACAGGUGCCGUAAAUGCGAAUGGUAACGGAAACGCGAGUAGUAACCAAAAUGGGU
.....(((...((((((....((.(((...((((.......))))..))--).)).-------...))))))...........((((.((....((....)).)).)))).....))) ( -29.90)
>consensus
AGCAAGCCAA____________UGCCAAAAAUUGGCAUCUGUGUUUGCG__AGUGGAAGGGGCACAGGUGCUGCAAACGGCAGUGGUAAUGGAAACAGGAGUAAAACCCAAAAUGGGU
......(((..............(((((...)))))(((((((((..(....)..).....))))))))(((((........)))))..))).......................... (-15.50 = -16.10 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,505,079 – 20,505,172
Length 93
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 85.62
Mean single sequence MFE -30.86
Consensus MFE -20.47
Energy contribution -21.43
Covariance contribution 0.96
Combinations/Pair 1.15
Mean z-score -1.83
Structure conservation index 0.66
SVM decision value 0.04
SVM RNA-class probability 0.553969
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20505079 93 + 22407834
GGCAGUGGUAAUGGAAACAGGAGUAAAACCCAAAAUGGGACCAGUACCAGGACAUC-CAACGGCACCCACUGGUGGCCACUGUCACCAUGGUCG
(((((((((..((....)).........(((.....)))((((((....((....)-)...((...)))))))).))))))))).......... ( -32.20)
>DroSec_CAF1 22164 94 + 1
GGCAGUGGUGAUGGAAACAGGAGUAAAACCCAAAAUGGCUCCAGUACCAGGACUUCCCAACGGCACCCACUGGUGGCCACUGUCACCAUGGUCG
(((.((((((((((.....((........))....((((((((((....((.....))...((...))))))).))))))))))))))).))). ( -34.60)
>DroSim_CAF1 27231 94 + 1
GGCAGUGGUAAUGGAAACAGGAGUAAAACCCAAAAUGGGACCAGUACCAGGACUUCCCAACGGCACCCACUGGUGGCCACUGUCACCAUGGUCG
(((((((((..((....)).........(((.....)))((((((....((.....))...((...)))))))).))))))))).......... ( -31.60)
>DroYak_CAF1 20984 94 + 1
GGGAGUGGCAAUGGAACGAGGAGUAAAACCCAAAAUGGGUCCAGUACCAGGACUUUCAAACAGCAUCCACUGGUGGCCACUGUCACCAUGGUCG
((.((((((..((((((.....))....(((.....))))))).((((((...................)))))))))))).)).......... ( -27.71)
>DroAna_CAF1 13562 93 + 1
GCGAAUGGUAACGGAAACGCGAGUAGUAACCAAAAUGGGUGCAGUAACGGGAGUUG-GAAUGGCAGCCACUGGUGGCCACUGUCACCACGAAAG
.((..((((.((....((....)).)).)))).....(((((((((((....))))-...((((.(((...))).))))))).)))).)).... ( -28.20)
>consensus
GGCAGUGGUAAUGGAAACAGGAGUAAAACCCAAAAUGGGUCCAGUACCAGGACUUCCCAACGGCACCCACUGGUGGCCACUGUCACCAUGGUCG
(((((((((..((....)).........(((.....))).....((((((...................))))))))))))))).......... (-20.47 = -21.43 +   0.96)

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 12:34:43 2006