Locus 5418

Sequence ID 3R_DroMel_CAF1
Location 14,276,804 – 14,276,941
Length 137
Max. P 0.981537
window8816 window8817 window8818

overview

Window 6

Location 14,276,804 – 14,276,915
Length 111
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 85.20
Mean single sequence MFE -26.46
Consensus MFE -22.65
Energy contribution -23.53
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -1.50
Structure conservation index 0.86
SVM decision value 0.21
SVM RNA-class probability 0.634809
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14276804 111 - 27905053
GGAUUGCAAUUUGAGCAAUUGGAACUGCAAGUGCCUGGCUACUGGUACGA-UGCCAUACGGCACUUACAUACUAACUUACACACCCGACUCAGCCAAUCCGAUCCUAACUCA
((((((....(((((...((((........(((((........)))))..-((((....)))).....................))))))))).))))))............ ( -26.10)
>DroSec_CAF1 56104 100 - 1
GGAUUGCAAUUUGAGCAAUUGGAACUGCAAGUGCCUGGCUACUGGUACGAGUGCCAUACGGCACUU------------ACACACCCGACUCGGCCAAUCCGAUCCUAACUCA
((((((....(((.((..((((...((.(((((((((((.(((......)))))))...)))))))------------.))...))))....)))))..))))))....... ( -32.30)
>DroSim_CAF1 47809 100 - 1
GGAUUGCAAUUUAAGCAAUUGGAACUGCAAGUGCCUUGCUACUGGUACGAGUGCCAUACGGCACUU------------ACACACCCGACUCAGCCAAUCCGAUCCUAACUCA
(((((((.......))))(((((...((..(((((........)))))(((((((....)))))))------------..............))...))))))))....... ( -30.00)
>DroYak_CAF1 52964 89 - 1
GGACUGCAAUUUGAGCAAUUUGAACUGGAAGUGCCUGGCUACUGGUUCGA-U----------ACUU------------ACACACCAGACUCAGCCAAUCCGAUCCUAACUCA
(((..(((.(((.((.........)).))).))).(((((.(((((....-.----------....------------....)))))....))))).)))............ ( -17.42)
>consensus
GGAUUGCAAUUUGAGCAAUUGGAACUGCAAGUGCCUGGCUACUGGUACGA_UGCCAUACGGCACUU____________ACACACCCGACUCAGCCAAUCCGAUCCUAACUCA
((((((....(((((...((((........(((((........)))))(((((((....)))))))..................))))))))).))))))............ (-22.65 = -23.53 +   0.88)

alignment

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secondary structure

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Window 7

Location 14,276,843 – 14,276,941
Length 98
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 81.52
Mean single sequence MFE -27.66
Consensus MFE -15.16
Energy contribution -15.08
Covariance contribution -0.08
Combinations/Pair 1.15
Mean z-score -1.98
Structure conservation index 0.55
SVM decision value 0.09
SVM RNA-class probability 0.580936
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14276843 98 + 27905053
AGUAUGUAAGUGCCGUAUGGCA-UCGUACCAGU-------AGCCAGGCACUUGCAGUUCCAAUUGCUCAAAUUGCAAUCCACAUUUGCGGUUGAUGCCUUUUUGAG
....((((((((((...((((.-.(......).-------.))))))))))))))..........((((((..((((.......))))(((....)))..)))))) ( -30.70)
>DroSec_CAF1 56138 92 + 1
-------AAGUGCCGUAUGGCACUCGUACCAGU-------AGCCAGGCACUUGCAGUUCCAAUUGCUCAAAUUGCAAUCCGCAUUUGCGGCUGAUGCCUUUUUGAG
-------(((((((...(((((((......)))-------.)))))))))))(((((....)))))(((((..(((..((((....))))....)))...))))). ( -31.50)
>DroSim_CAF1 47843 92 + 1
-------AAGUGCCGUAUGGCACUCGUACCAGU-------AGCAAGGCACUUGCAGUUCCAAUUGCUUAAAUUGCAAUCCGCAUUUGCGGUUGAUGCCUUUUUGAG
-------.((((((....))))))........(-------((.((((((...(((((....)))))........(((.((((....))))))).)))))).))).. ( -27.80)
>DroEre_CAF1 58264 87 + 1
-------G-GC----------A-UCGAACCAGUAGCCAGUAGCCAGGCACUUGCAGUUCAAACUGCUCAAAUUGCAAUCAGCAUUUGCGGUUGAUGCCUUUUUGAG
-------(-((----------(-((.(((((((.(((........)))))).(((((....))))).......((((.......))))))))))))))........ ( -29.30)
>DroYak_CAF1 52998 81 + 1
-------AAGU----------A-UCGAACCAGU-------AGCCAGGCACUUCCAGUUCAAAUUGCUCAAAUUGCAGUCCGCAUUUGCGGUUGAUGCCUUUUUGAG
-------....----------.-..((((.(((-------.((...)))))....))))......((((((..(((..((((....))))....)))...)))))) ( -19.00)
>consensus
_______AAGUGCCGUAUGGCA_UCGUACCAGU_______AGCCAGGCACUUGCAGUUCCAAUUGCUCAAAUUGCAAUCCGCAUUUGCGGUUGAUGCCUUUUUGAG
............................................(((((...(((((....)))))((((.((((((.......)))))))))))))))....... (-15.16 = -15.08 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,276,843 – 14,276,941
Length 98
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 81.52
Mean single sequence MFE -30.28
Consensus MFE -16.92
Energy contribution -17.70
Covariance contribution 0.78
Combinations/Pair 1.09
Mean z-score -2.99
Structure conservation index 0.56
SVM decision value 1.89
SVM RNA-class probability 0.981537
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14276843 98 - 27905053
CUCAAAAAGGCAUCAACCGCAAAUGUGGAUUGCAAUUUGAGCAAUUGGAACUGCAAGUGCCUGGCU-------ACUGGUACGA-UGCCAUACGGCACUUACAUACU
........((((((..((((....)))).(((((.((..(....)..))..)))))(((((.....-------...)))))))-)))).................. ( -30.10)
>DroSec_CAF1 56138 92 - 1
CUCAAAAAGGCAUCAGCCGCAAAUGCGGAUUGCAAUUUGAGCAAUUGGAACUGCAAGUGCCUGGCU-------ACUGGUACGAGUGCCAUACGGCACUU-------
.(((((...(((....((((....))))..)))..)))))(((........)))..(((((.....-------...)))))(((((((....)))))))------- ( -33.40)
>DroSim_CAF1 47843 92 - 1
CUCAAAAAGGCAUCAACCGCAAAUGCGGAUUGCAAUUUAAGCAAUUGGAACUGCAAGUGCCUUGCU-------ACUGGUACGAGUGCCAUACGGCACUU-------
......(((((((...((((....)))).(((((.(((((....)))))..))))))))))))...-------........(((((((....)))))))------- ( -32.10)
>DroEre_CAF1 58264 87 - 1
CUCAAAAAGGCAUCAACCGCAAAUGCUGAUUGCAAUUUGAGCAGUUUGAACUGCAAGUGCCUGGCUACUGGCUACUGGUUCGA-U----------GC-C-------
........((((((((((.(((((((.....)).))))).(((((....))))).((((((........))).))))))).))-)----------))-)------- ( -30.90)
>DroYak_CAF1 52998 81 - 1
CUCAAAAAGGCAUCAACCGCAAAUGCGGACUGCAAUUUGAGCAAUUUGAACUGGAAGUGCCUGGCU-------ACUGGUUCGA-U----------ACUU-------
((((((...(((....((((....))))..)))..))))))....((((((..(.(((.....)))-------.)..))))))-.----------....------- ( -24.90)
>consensus
CUCAAAAAGGCAUCAACCGCAAAUGCGGAUUGCAAUUUGAGCAAUUGGAACUGCAAGUGCCUGGCU_______ACUGGUACGA_UGCCAUACGGCACUU_______
((((((...(((....((((....))))..)))..))))))...............(((((...............)))))...((((....)))).......... (-16.92 = -17.70 +   0.78)

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 11:54:12 2006