Locus 3130

Sequence ID 2R_DroMel_CAF1
Location 10,684,823 – 10,684,937
Length 114
Max. P 0.924942
window5162 window5163 window5164

overview

Window 2

Location 10,684,823 – 10,684,917
Length 94
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 79.35
Mean single sequence MFE -25.47
Consensus MFE -19.67
Energy contribution -20.39
Covariance contribution 0.72
Combinations/Pair 1.09
Mean z-score -1.92
Structure conservation index 0.77
SVM decision value 1.16
SVM RNA-class probability 0.924206
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10684823 94 + 20766785
-------------CCA--C----GUC--CGUCAGACAUCCAGUCGAGCAUGCAUUUCCUUCCUCUUCUGCGCUGCAGCGCAGAAUUUCCAUUCCAAUGCACUCUGAUUGAAAGUC
-------------...--.----(((--.....)))...((((((((..((((((.........((((((((....))))))))..........))))))))).)))))...... ( -27.01)
>DroEre_CAF1 22005 94 + 1
-------------CCA--C----GUC--CGUCAGACAUCCAGUCGAGCAUGUAUUUCCUUCCUCUUCCACGCUGCAGCGCAGAAUUUCCAUUCCAAUGCACUCUGAUUGAAAGUC
-------------...--.----(((--.....)))...((((((((..((((((.........(((..(((....)))..)))..........))))))))).)))))...... ( -16.41)
>DroWil_CAF1 31302 109 + 1
UUACUCACUCAGUCACUGA----GGC--AUUCAGUCAGCCAGUCGAGCAUGUGUUUCCUUCCUUUUCUGCGCUGCAGCGCAGAAUUUCCGUUUCAAUGCCCUCUGAUUGAAAGAC
....((..(((((((..(.----(((--(((.((..(((((........)).)))..)).....((((((((....))))))))..........)))))))..)))))))..)). ( -30.70)
>DroMoj_CAF1 37437 104 + 1
--------UCAGUCAUUCACUCAUUC--UGUCAGCCAUUCCCUCGAGCAUGUAUUUCCUUCCU-UUCUGCGCUGCAGCGCAGAAUUUCCGUUUCAAUGCACUCUGAUUGAAAGUC
--------(((((((...........--.....(((........).)).((((((........-((((((((....))))))))..........))))))...)))))))..... ( -23.47)
>DroAna_CAF1 21487 99 + 1
----------AGUCCU--C----CUCCUCGGCGGAAAACCAGUCGAGCUUGUAUUUCCUUCCUCUUCUGCGCUGCAGCGCAGAAUUUCCGUUUCAAUGCACUCUGAUUGAAAGUC
----------..(((.--(----(.....)).)))....((((((((..((((((.........((((((((....))))))))..........))))))))).)))))...... ( -28.31)
>DroPer_CAF1 24883 100 + 1
--------UUAGUCCUUCA----GUA--CGUCAGUCCGCCAGUGGAGCAUGUAUUUCCUGCCU-UUCUGCGCUGCAGCGCAGAAUUUCCGUUUCAAUGCACUCUGAUUGAAAGUC
--------.......((((----...--.(((((...((...((((((..(((.....)))..-((((((((....)))))))).....))))))..))...))))))))).... ( -26.90)
>consensus
__________AGUCCU__A____GUC__CGUCAGACAUCCAGUCGAGCAUGUAUUUCCUUCCUCUUCUGCGCUGCAGCGCAGAAUUUCCGUUUCAAUGCACUCUGAUUGAAAGUC
.......................................((((((((..((((((.........((((((((....))))))))..........))))))))).)))))...... (-19.67 = -20.39 +   0.72)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,684,839 – 10,684,937
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.79
Mean single sequence MFE -29.10
Consensus MFE -21.20
Energy contribution -22.37
Covariance contribution 1.17
Combinations/Pair 1.17
Mean z-score -2.11
Structure conservation index 0.73
SVM decision value 1.17
SVM RNA-class probability 0.924942
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10684839 98 + 20766785
--UCCAGUCGAGCAUGCAUUUCCUUCCUCUUCUGCGCUGCAGCGCAGAAUUUCCAUUCCAAUGCACUCUGAUUGAAAGUCUUACGUGCUG--------------------UGUGGGUCCU
--..((((((((..((((((.........((((((((....))))))))..........))))))))).)))))...(.((((((.....--------------------)))))).).. ( -28.71)
>DroVir_CAF1 36272 97 + 1
--UUCCCUCGAGCAUGUAUUUCCUUCCU--UCUGCGCUGCAGCGCAGAAUUUCCGUUUCAAUGCACCCUGAUUGAAAGUCUUACGUACUUA-------------------UGUGGCCCUU
--..(((..(((.(((((.........(--(((((((....))))))))......(((((((........)))))))....))))).))).-------------------.).))..... ( -23.30)
>DroGri_CAF1 27554 100 + 1
AGUUCACACGUGCAUGUAUUUCCUUCCU-UUCUGCGCUGCAGCGCAGAAUUUCCGUUUCGGUGCACUCUGAUUGAAAGUCUUACGUACUUA-------------------UGUGGCCCUU
.(..((((.((((...............-((((((((....))))))))((((....((((......))))..)))).......))))...-------------------))))..)... ( -25.50)
>DroWil_CAF1 31333 116 + 1
--GCCAGUCGAGCAUGUGUUUCCUUCCUUUUCUGCGCUGCAGCGCAGAAUUUCCGUUUCAAUGCCCUCUGAUUGAAAGACUUACGUGCUCAAGGACCUCCAACCCUGCAGUGUUGGCC--
--(((((.((((((((((..((.......((((((((....))))))))......(((((((........)))))))))..)))))))))..((....))...........)))))).-- ( -40.10)
>DroAna_CAF1 21508 98 + 1
--ACCAGUCGAGCUUGUAUUUCCUUCCUCUUCUGCGCUGCAGCGCAGAAUUUCCGUUUCAAUGCACUCUGAUUGAAAGUCUUACGUGCUU--------------------UUUGGUUAUU
--(((((..((((.((((...........((((((((....))))))))......(((((((........)))))))....)))).))))--------------------.))))).... ( -27.80)
>DroPer_CAF1 24906 98 + 1
--GCCAGUGGAGCAUGUAUUUCCUGCCU-UUCUGCGCUGCAGCGCAGAAUUUCCGUUUCAAUGCACUCUGAUUGAAAGUCUUACGUGGUG------C-------------UCUGUGUCUG
--(((((.(.(.((((((..........-((((((((....))))))))......(((((((........)))))))....)))))).).------)-------------.))).))... ( -29.20)
>consensus
__UCCAGUCGAGCAUGUAUUUCCUUCCU_UUCUGCGCUGCAGCGCAGAAUUUCCGUUUCAAUGCACUCUGAUUGAAAGUCUUACGUGCUU____________________UGUGGGCCUU
.........(((((((((...........((((((((....))))))))......(((((((........)))))))....))))))))).............................. (-21.20 = -22.37 +   1.17)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,684,839 – 10,684,937
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.79
Mean single sequence MFE -28.98
Consensus MFE -19.82
Energy contribution -20.18
Covariance contribution 0.36
Combinations/Pair 1.17
Mean z-score -1.88
Structure conservation index 0.68
SVM decision value 0.85
SVM RNA-class probability 0.867201
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10684839 98 - 20766785
AGGACCCACA--------------------CAGCACGUAAGACUUUCAAUCAGAGUGCAUUGGAAUGGAAAUUCUGCGCUGCAGCGCAGAAGAGGAAGGAAAUGCAUGCUCGACUGGA--
.....(((..--------------------((((.(....).............(((((((..........((((((((....)))))))).........)))))))))).)..))).-- ( -26.91)
>DroVir_CAF1 36272 97 - 1
AAGGGCCACA-------------------UAAGUACGUAAGACUUUCAAUCAGGGUGCAUUGAAACGGAAAUUCUGCGCUGCAGCGCAGA--AGGAAGGAAAUACAUGCUCGAGGGAA--
.....((...-------------------..((((.(((...(((((..((((......))))........((((((((....)))))))--))))))....))).))))....))..-- ( -25.50)
>DroGri_CAF1 27554 100 - 1
AAGGGCCACA-------------------UAAGUACGUAAGACUUUCAAUCAGAGUGCACCGAAACGGAAAUUCUGCGCUGCAGCGCAGAA-AGGAAGGAAAUACAUGCACGUGUGAACU
..((..((((-------------------(((((.(....))))).........((((((((...)))...((((((((....))))))))-..............))))))))))..)) ( -31.00)
>DroWil_CAF1 31333 116 - 1
--GGCCAACACUGCAGGGUUGGAGGUCCUUGAGCACGUAAGUCUUUCAAUCAGAGGGCAUUGAAACGGAAAUUCUGCGCUGCAGCGCAGAAAAGGAAGGAAACACAUGCUCGACUGGC--
--..(((((........))))).((((...(((((.((...((((((..((((......))))........((((((((....))))))))...))))))...)).)))))))))...-- ( -37.40)
>DroAna_CAF1 21508 98 - 1
AAUAACCAAA--------------------AAGCACGUAAGACUUUCAAUCAGAGUGCAUUGAAACGGAAAUUCUGCGCUGCAGCGCAGAAGAGGAAGGAAAUACAAGCUCGACUGGU--
....((((..--------------------.(((..(((...(((((..((...((........)).))..((((((((....))))))))..)))))....)))..)))....))))-- ( -25.40)
>DroPer_CAF1 24906 98 - 1
CAGACACAGA-------------G------CACCACGUAAGACUUUCAAUCAGAGUGCAUUGAAACGGAAAUUCUGCGCUGCAGCGCAGAA-AGGCAGGAAAUACAUGCUCCACUGGC--
(((...(((.-------------(------(((..(....)....((.....)))))).)))....(((..((((((((....))))))))-..((((......).)))))).)))..-- ( -27.70)
>consensus
AAGACCCACA____________________AAGCACGUAAGACUUUCAAUCAGAGUGCAUUGAAACGGAAAUUCUGCGCUGCAGCGCAGAA_AGGAAGGAAAUACAUGCUCGACUGGA__
................................(((.(((...(((((..((((......))))........((((((((....))))))))..)))))....))).)))........... (-19.82 = -20.18 +   0.36)

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 10:48:16 2006