Locus 5288

Sequence ID 3R_DroMel_CAF1
Location 13,811,265 – 13,811,395
Length 130
Max. P 0.647343
window8626 window8627 window8628

overview

Window 6

Location 13,811,265 – 13,811,366
Length 101
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 77.60
Mean single sequence MFE -30.36
Consensus MFE -13.09
Energy contribution -15.62
Covariance contribution 2.53
Combinations/Pair 1.14
Mean z-score -2.18
Structure conservation index 0.43
SVM decision value 0.17
SVM RNA-class probability 0.616331
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13811265 101 + 27905053
CAAAUCAUCAGCUCACAAUUGAGCGGAAGUGAGCUGCAAAAAAGUAGCAGUU------GUUGCAACAACAGCUGCAGCAGCAACACGG--CUC-GAUUGGGAGUCGCCCU
..........((((.(((((((((....(((.(((((......))))).(((------((((((........)))))))))..))).)--)))-))))).))))...... ( -40.00)
>DroSec_CAF1 83210 101 + 1
CAAAUCAUCAGCUCACAAUUGAGCGGAAGUGAACUGCAAAAAAGAAGCAGUU------GUUGCAACUACAGCUGCAGCAGCAACACGA--CUC-GAUUGGGAGUCGCCCU
..........(((((....)))))((..(((...(((.........)))(((------((((((.(....).)))))))))..)))((--(((-......)))))..)). ( -32.40)
>DroSim_CAF1 85141 101 + 1
CACAUCAUCAGCUCACAACUGAGCGGAAGUGAGCUGCAAAAAAGAAGCAGUU------GUUGCAACUACAGCUGCAACAGCAACACGG--CUC-GAUUGGGAGUCGCCCU
........((((((((..((....))..))))))))..........((.(((------((((((.(....).))))))))).....((--(((-......)))))))... ( -35.40)
>DroEre_CAF1 81216 101 + 1
CAAAUCAUCAGCUCACAAUUGGGCGGAAGUGAGCUGCAAAAAACAGGCAAAU------GUUGCAACUACUGCUGCGGCAGCAACUCGA--CUC-GAUUGGGAGUCACCCU
..........((((.((((((((((..(((..(((((....((((......)------)))(((.(....).))).))))).))))).--)))-))))).))))...... ( -30.10)
>DroYak_CAF1 90175 92 + 1
CAAAUCAUCAGCUCACAAUUGGGCGGAAGUGAGCUGCAAAAAAGAAACAAGU------GUUGCAACUACAACUGC---------ACGA--CUC-GAUUGGGAGUCGCCCU
..........((((.((((((((((..(((.((.(((((.............------.))))).))...)))..---------.)).--)))-))))).))))...... ( -23.44)
>DroAna_CAF1 82933 107 + 1
UAUAGCGCUAAAAUACAAUUGAGCGGAAGUGAACUCUAACUAAGAGGCAGCAACGACAUUAGCCACUGCAAUUGC--CAGUAGAACGUAUCUUGGAUUGU-UGGCACCCU
....((((..............((....))...((((.....)))))).))..........((((..(((((..(--((..(((.....)))))))))))-))))..... ( -20.80)
>consensus
CAAAUCAUCAGCUCACAAUUGAGCGGAAGUGAGCUGCAAAAAAGAAGCAGUU______GUUGCAACUACAGCUGCAGCAGCAACACGA__CUC_GAUUGGGAGUCGCCCU
..((((..((((((((............))))))))......................((((((........))))))................))))(((.....))). (-13.09 = -15.62 +   2.53)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,811,265 – 13,811,366
Length 101
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 77.60
Mean single sequence MFE -31.87
Consensus MFE -16.62
Energy contribution -16.77
Covariance contribution 0.14
Combinations/Pair 1.35
Mean z-score -1.86
Structure conservation index 0.52
SVM decision value 0.24
SVM RNA-class probability 0.647343
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13811265 101 - 27905053
AGGGCGACUCCCAAUC-GAG--CCGUGUUGCUGCUGCAGCUGUUGUUGCAAC------AACUGCUACUUUUUUGCAGCUCACUUCCGCUCAAUUGUGAGCUGAUGAUUUG
.(((.....)))((((-(((--(..((((((.((.((....)).)).)))))------)...))).........((((((((............)))))))).))))).. ( -32.00)
>DroSec_CAF1 83210 101 - 1
AGGGCGACUCCCAAUC-GAG--UCGUGUUGCUGCUGCAGCUGUAGUUGCAAC------AACUGCUUCUUUUUUGCAGUUCACUUCCGCUCAAUUGUGAGCUGAUGAUUUG
.(((((((((......-)))--))))(((((.(((((....))))).)))))------((((((.........)))))).....))(((((....))))).......... ( -37.60)
>DroSim_CAF1 85141 101 - 1
AGGGCGACUCCCAAUC-GAG--CCGUGUUGCUGUUGCAGCUGUAGUUGCAAC------AACUGCUUCUUUUUUGCAGCUCACUUCCGCUCAGUUGUGAGCUGAUGAUGUG
.(((.....))).(((-(((--(.((.....(((((((((....))))))))------))).))))........((((((((............))))))))..)))... ( -33.00)
>DroEre_CAF1 81216 101 - 1
AGGGUGACUCCCAAUC-GAG--UCGAGUUGCUGCCGCAGCAGUAGUUGCAAC------AUUUGCCUGUUUUUUGCAGCUCACUUCCGCCCAAUUGUGAGCUGAUGAUUUG
.(((((((((......-)))--))..(((((.((..(....)..)).)))))------....))))........((((((((............))))))))........ ( -33.20)
>DroYak_CAF1 90175 92 - 1
AGGGCGACUCCCAAUC-GAG--UCGU---------GCAGUUGUAGUUGCAAC------ACUUGUUUCUUUUUUGCAGCUCACUUCCGCCCAAUUGUGAGCUGAUGAUUUG
.(.(((((((......-)))--))))---------.).(((((....)))))------................((((((((............))))))))........ ( -29.90)
>DroAna_CAF1 82933 107 - 1
AGGGUGCCA-ACAAUCCAAGAUACGUUCUACUG--GCAAUUGCAGUGGCUAAUGUCGUUGCUGCCUCUUAGUUAGAGUUCACUUCCGCUCAAUUGUAUUUUAGCGCUAUA
.((((....-...))))((((((((..(((..(--(((...((((((((....))))))))))))...)))...((((........))))...))))))))......... ( -25.50)
>consensus
AGGGCGACUCCCAAUC_GAG__UCGUGUUGCUGCUGCAGCUGUAGUUGCAAC______AACUGCUUCUUUUUUGCAGCUCACUUCCGCUCAAUUGUGAGCUGAUGAUUUG
.((((..(((.......)))...............(((((....))))).............))))........((((((((............))))))))........ (-16.62 = -16.77 +   0.14)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,811,305 – 13,811,395
Length 90
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 76.32
Mean single sequence MFE -29.22
Consensus MFE -14.77
Energy contribution -15.97
Covariance contribution 1.20
Combinations/Pair 1.35
Mean z-score -1.72
Structure conservation index 0.51
SVM decision value -0.04
SVM RNA-class probability 0.514588
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13811305 90 - 27905053
GGCCAGUUUGCGGCAGAACCGUUCUC-AAAAGGGCGACUCCCAAUC-GAG--CCGUGUUGCUGCUGCAGCUGUUGUUGCAAC------AACUGCUACUUU
(((.((((.(((((((.((.((((..-....(((.....)))....-)))--).)).)))))))((((((....))))))..------)))))))..... ( -29.80)
>DroSec_CAF1 83250 90 - 1
GGCCAGUUUGCGGCAGAAUCGUUCUU-AAAAGGGCGACUCCCAAUC-GAG--UCGUGUUGCUGCUGCAGCUGUAGUUGCAAC------AACUGCUUCUUU
....((((.(((((((...((((((.-...)))))(((((......-)))--))..)...)))))))))))(((((((...)------))))))...... ( -31.60)
>DroSim_CAF1 85181 90 - 1
GGCCAGUUUGCGGCAGAAUCGUUCUU-AAAAGGGCGACUCCCAAUC-GAG--CCGUGUUGCUGUUGCAGCUGUAGUUGCAAC------AACUGCUUCUUU
(((..(.(((.((.((..(((((((.-...)))))))))))))).)-..)--))..((.(.(((((((((....))))))))------).).))...... ( -30.00)
>DroEre_CAF1 81256 90 - 1
GGCCAGUUUGCGGCAGAAUCGUUCUU-GAAAGGGUGACUCCCAAUC-GAG--UCGAGUUGCUGCCGCAGCAGUAGUUGCAAC------AUUUGCCUGUUU
(((.(((.((((((((..(((..(((-((..(((.....)))..))-)))--.)))....))))))))((((...))))...------))).)))..... ( -35.00)
>DroYak_CAF1 90215 81 - 1
GGCUAGUUUGCUGCAGAAUCGUUCUU-GAAAGGGCGACUCCCAAUC-GAG--UCGU---------GCAGUUGUAGUUGCAAC------ACUUGUUUCUUU
(((((....((((((.....(((((.-...)))))(((((......-)))--)).)---------)))))..))))).....------............ ( -20.90)
>DroAna_CAF1 82973 97 - 1
GGCUACUUCACAGCAGAACCUAUCUGCAAAAGGGUGCCA-ACAAUCCAAGAUACGUUCUACUG--GCAAUUGCAGUGGCUAAUGUCGUUGCUGCCUCUUA
(((.......(((.(((((.(((((......((((....-...)))).))))).))))).)))--......((((((((....)))))))).)))..... ( -28.00)
>consensus
GGCCAGUUUGCGGCAGAAUCGUUCUU_AAAAGGGCGACUCCCAAUC_GAG__UCGUGUUGCUGCUGCAGCUGUAGUUGCAAC______AACUGCUUCUUU
(((......(((((((...((..(((.....(((.....))).....)))...))..))))))).(((((....))))).............)))..... (-14.77 = -15.97 +   1.20)

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 11:51:09 2006