Locus 5622

Sequence ID 3R_DroMel_CAF1
Location 14,817,683 – 14,817,860
Length 177
Max. P 0.999935
window9160 window9161 window9162 window9163

overview

Window 0

Location 14,817,683 – 14,817,788
Length 105
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 94.00
Mean single sequence MFE -25.50
Consensus MFE -22.22
Energy contribution -22.66
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.58
Structure conservation index 0.87
SVM decision value 1.20
SVM RNA-class probability 0.929131
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14817683 105 + 27905053
GUAAUACUUGGCACGAGGCAUUGGUCUAAAUAUAUUGUUUAUGGGCACACAUAUUGAUUUCAAAUAUGCGCUAAGGGAAUUCUCAAUAAUUCCAUAGGCAUUUAU
...(((.((((..(((....)))..)))).)))..(((((((((((...((((((.......)))))).))...(((....))).......)))))))))..... ( -19.60)
>DroSec_CAF1 10210 104 + 1
GUAAUACUUGGCACGAGGCAUUGGUCUAAAUAUAUGGU-UAUAGGCACACAUAUUGAUUUCAAGUGUGCGCUAAGGGAAUUUUCAAUAAUUCCAUAGGCAUUUAU
((....((((((...((((....))))...........-.....((((((...(((....)))))))))))))))((((((......))))))....))...... ( -26.60)
>DroSim_CAF1 10699 105 + 1
GUAAUACUUGGCACGAGGCAUUGGUCUAAAUAUAUUGUAUAUGGGCACACAUAUUGAUUUCAAGUGUGCGCUAAGGGAAUUUUCAAUAAUUCCAUAGGCAUUUAU
((....((((((...((((....)))).................((((((...(((....)))))))))))))))((((((......))))))....))...... ( -26.60)
>DroEre_CAF1 11993 105 + 1
GAAAUACUUGGCACGAGGCAUUGGUCUAAAUAUAUUGUUUAUGGGCACAGAUAUUGAUUUCAUGUGUGCGCUAAGGGAAUUUUCAAUAAUUCCAUAGGCACUUAU
......((((((...((((....))))...............(.(((((((........)).))))).)))))))((((((......))))))............ ( -24.70)
>DroYak_CAF1 10985 105 + 1
GUAAUACUUGGCGCGAGGCAUUGGUCCAAAUAUAUUGUUUAUGGGCACAGAUAUUGAUUUCAAGUGUGCGCCAAGGGAAUUUUCAAUAAUUCCAUAGGCACUAAU
((....(((((((((..((.((((((((.............))))).)))...(((....))))).)))))))))((((((......))))))....))...... ( -30.02)
>consensus
GUAAUACUUGGCACGAGGCAUUGGUCUAAAUAUAUUGUUUAUGGGCACACAUAUUGAUUUCAAGUGUGCGCUAAGGGAAUUUUCAAUAAUUCCAUAGGCAUUUAU
......((((((...((((....)))).................(((((....(((....))).)))))))))))((((((......))))))............ (-22.22 = -22.66 +   0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,817,715 – 14,817,822
Length 107
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 89.40
Mean single sequence MFE -30.10
Consensus MFE -27.42
Energy contribution -27.10
Covariance contribution -0.32
Combinations/Pair 1.21
Mean z-score -3.08
Structure conservation index 0.91
SVM decision value 4.55
SVM RNA-class probability 0.999918
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14817715 107 + 27905053
UAUUGUUUAUGGGCACACAUAUUGAUUUCAAAUAUGCGCUAAGGGAAUUCUCAAUAAUUCCAUAGGCAUUUAUCAGCUUUUGGAUAUUGUGUGCCCUGUA-UUUAGUA-----
(((((..((((((((((((((((((.(((...............)))...))))))..((((.((((........)))).))))...))))))))).)))-..)))))----- ( -31.26)
>DroSec_CAF1 10242 107 + 1
UAUGGU-UAUAGGCACACAUAUUGAUUUCAAGUGUGCGCUAAGGGAAUUUUCAAUAAUUCCAUAGGCAUUUAUCAGCUUUUGGAUAUUGUGUGCCUUGUUUUUAAGUA-----
..(((.-.(((((((((((((((((.(((.(((....)))....)))...))))))..((((.((((........)))).))))...)))))))).)))..)))....----- ( -30.00)
>DroSim_CAF1 10731 107 + 1
UAUUGUAUAUGGGCACACAUAUUGAUUUCAAGUGUGCGCUAAGGGAAUUUUCAAUAAUUCCAUAGGCAUUUAUCAGCCUUUGGAUAUUCUGUGCCUUGUU-UUAAGUA-----
..(((.....(((((((..((((((.(((.(((....)))....)))...))))))..((((.((((........)))).)))).....)))))))....-.)))...----- ( -28.30)
>DroEre_CAF1 12025 107 + 1
UAUUGUUUAUGGGCACAGAUAUUGAUUUCAUGUGUGCGCUAAGGGAAUUUUCAAUAAUUCCAUAGGCACUUAUCAGCUUUAGGAUUUUCUGUGCCUUGUU-UUCAGUA-----
(((((.....(((((((((..((((....(((.((((.(((..((((((......)))))).))))))).))).....)))).....)))))))))....-..)))))----- ( -31.40)
>DroYak_CAF1 11017 112 + 1
UAUUGUUUAUGGGCACAGAUAUUGAUUUCAAGUGUGCGCCAAGGGAAUUUUCAAUAAUUCCAUAGGCACUAAUCAGCUCUAGGAUUUUCUGUGCCUUGUU-UUAAGUAGAUUG
((((......(((((((((....((((..((((..(.(((...((((((......))))))...))).)......))).)..)))).)))))))))....-...))))..... ( -29.52)
>consensus
UAUUGUUUAUGGGCACACAUAUUGAUUUCAAGUGUGCGCUAAGGGAAUUUUCAAUAAUUCCAUAGGCAUUUAUCAGCUUUUGGAUAUUCUGUGCCUUGUU_UUAAGUA_____
..........(((((((((((((((.(((...((.....))...)))...))))))..((((.((((........)))).))))...)))))))))................. (-27.42 = -27.10 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,817,715 – 14,817,822
Length 107
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 89.40
Mean single sequence MFE -27.90
Consensus MFE -25.48
Energy contribution -25.40
Covariance contribution -0.08
Combinations/Pair 1.16
Mean z-score -4.65
Structure conservation index 0.91
SVM decision value 4.66
SVM RNA-class probability 0.999935
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14817715 107 - 27905053
-----UACUAAA-UACAGGGCACACAAUAUCCAAAAGCUGAUAAAUGCCUAUGGAAUUAUUGAGAAUUCCCUUAGCGCAUAUUUGAAAUCAAUAUGUGUGCCCAUAAACAAUA
-----.......-....(((((((((.((((........)))).(((((((.((((((......))))))..))).))))..............))))))))).......... ( -30.90)
>DroSec_CAF1 10242 107 - 1
-----UACUUAAAAACAAGGCACACAAUAUCCAAAAGCUGAUAAAUGCCUAUGGAAUUAUUGAAAAUUCCCUUAGCGCACACUUGAAAUCAAUAUGUGUGCCUAUA-ACCAUA
-----............(((((((((.((((........))))..((((((.((((((......))))))..))).)))...............)))))))))...-...... ( -26.90)
>DroSim_CAF1 10731 107 - 1
-----UACUUAA-AACAAGGCACAGAAUAUCCAAAGGCUGAUAAAUGCCUAUGGAAUUAUUGAAAAUUCCCUUAGCGCACACUUGAAAUCAAUAUGUGUGCCCAUAUACAAUA
-----.......-.....((((((.(...((((.((((........)))).))))..((((((...(((....((......)).))).))))))).))))))........... ( -24.20)
>DroEre_CAF1 12025 107 - 1
-----UACUGAA-AACAAGGCACAGAAAAUCCUAAAGCUGAUAAGUGCCUAUGGAAUUAUUGAAAAUUCCCUUAGCGCACACAUGAAAUCAAUAUCUGUGCCCAUAAACAAUA
-----.......-.....((((((((..(((........)))..(((((((.((((((......))))))..))).))))..............))))))))........... ( -27.90)
>DroYak_CAF1 11017 112 - 1
CAAUCUACUUAA-AACAAGGCACAGAAAAUCCUAGAGCUGAUUAGUGCCUAUGGAAUUAUUGAAAAUUCCCUUGGCGCACACUUGAAAUCAAUAUCUGUGCCCAUAAACAAUA
............-.....((((((((.((((........)))).(((((...((((((......))))))...)))))................))))))))........... ( -29.60)
>consensus
_____UACUUAA_AACAAGGCACAGAAUAUCCAAAAGCUGAUAAAUGCCUAUGGAAUUAUUGAAAAUUCCCUUAGCGCACACUUGAAAUCAAUAUGUGUGCCCAUAAACAAUA
..................((((((((.((((........)))).(((((((.((((((......))))))..))).))))..............))))))))........... (-25.48 = -25.40 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,817,752 – 14,817,860
Length 108
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 82.82
Mean single sequence MFE -25.70
Consensus MFE -15.96
Energy contribution -16.08
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -2.12
Structure conservation index 0.62
SVM decision value 0.51
SVM RNA-class probability 0.764309
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14817752 108 + 27905053
GCUAAGGGAAUUCUCAAUAAUUCCAUAGGCAUUUAUCAGCUUUUGGAUAUUGUGUGCCCUGUA-UUUAGUA-------UUGGAUUUCCCACUUACAUAAGUGCUUAUCAGCUAAGA
(((.((((....(.(((((..((((.((((........)))).))))))))).)..))))(((-(((((((-------.(((.....)))..))).))))))).....)))..... ( -30.00)
>DroSec_CAF1 10278 109 + 1
GCUAAGGGAAUUUUCAAUAAUUCCAUAGGCAUUUAUCAGCUUUUGGAUAUUGUGUGCCUUGUUUUUAAGUA-------UUGGAUUUCCCACUUACAUAAGUACUUAUCAGCGAAGA
(((..(((((..(((((((.......((((((.((((........))))....))))))..........))-------))))).)))))((((....)))).......)))..... ( -26.43)
>DroSim_CAF1 10768 108 + 1
GCUAAGGGAAUUUUCAAUAAUUCCAUAGGCAUUUAUCAGCCUUUGGAUAUUCUGUGCCUUGUU-UUAAGUA-------UUGGAUUUUCCAAUUACAUAUGUACUUAUCAGCGAAGA
((((((((((..(((((((.......((((((.((((........))))....))))))....-.....))-------)))))..))))...(((....))))))...)))..... ( -24.99)
>DroEre_CAF1 12062 103 + 1
GCUAAGGGAAUUUUCAAUAAUUCCAUAGGCACUUAUCAGCUUUAGGAUUUUCUGUGCCUUGUU-UUCAGUA------------UUAUACACUUAUGUAUGUACUUAUAAGCAAAGA
......((((((......))))))...(((((..(((........))).....)))))(((((-(..((((------------(.(((((....))))))))))...))))))... ( -24.20)
>DroYak_CAF1 11054 111 + 1
GCCAAGGGAAUUUUCAAUAAUUCCAUAGGCACUAAUCAGCUCUAGGAUUUUCUGUGCCUUGUU-UUAAGUAGAUUGUUUUAGAUUUUCCACUCA----UGUACUUAUUAGAAAAGU
(((...((((((......))))))...))).(((((.((.((((((((..((((...((((..-.))))))))..))))))))......((...----.)).)).)))))...... ( -22.90)
>consensus
GCUAAGGGAAUUUUCAAUAAUUCCAUAGGCAUUUAUCAGCUUUUGGAUAUUCUGUGCCUUGUU_UUAAGUA_______UUGGAUUUUCCACUUACAUAUGUACUUAUCAGCAAAGA
((((((((((((......))))))...(((((.((((........))))....)))))............................................)))...)))..... (-15.96 = -16.08 +   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 11:59:39 2006