Locus 2118

Sequence ID 3R_DroMel_CAF1
Location 6,048,533 – 6,048,794
Length 261
Max. P 0.645231
window3460 window3461 window3462

overview

Window 0

Location 6,048,533 – 6,048,632
Length 99
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 78.59
Mean single sequence MFE -31.92
Consensus MFE -16.58
Energy contribution -16.98
Covariance contribution 0.39
Combinations/Pair 1.38
Mean z-score -1.90
Structure conservation index 0.52
SVM decision value 0.12
SVM RNA-class probability 0.595347
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6048533 99 - 27905053
CUCCUCGCUGGAGUUCGAUGCAGCCCUAUUAUCCGUAUCAAGAUCGUAAGAUUGUAGCUGAUAGCUGGCUGCAUUGGCGAGAUGUAGGGAACAGAUCAA
((((.....)))).(((((((((((...(((((.((.....((((....))))...)).)))))..))))))))))).((..(((.....)))..)).. ( -34.30)
>DroSec_CAF1 54461 99 - 1
CUCUCCGCUGGAGUUCGAUGCAGCCCCAUUAUCCGCAUCAAGAUCGUAAGAUUGUAGCUGAUAGCUGGCUGCAUGGGCAAGAUCUAGGGAACAGAUCAA
..((((...)))).((.((((((((...(((((.((.....((((....))))...)).)))))..)))))))).))...(((((.(....)))))).. ( -35.40)
>DroSim_CAF1 55712 99 - 1
CUGCUCGCUGGAGUUCGAUGCAGCCCCAUUAUCCGCAUUAAGAUCGUAAGAUUGUAGCUGAAUGCUGGCUGCAUACGCAAAAUCUAGGGAACAGAUCAA
(((.((.(((((...((((((((((.((((....((.....((((....))))...))..))))..)))))))).)).....))))).)).)))..... ( -34.70)
>DroEre_CAF1 55010 99 - 1
CUCCUCGCUAGAGUUCGAUACAGCCGCGUUAUCCGUAUCCAGAUCGUAGGAUUGCAGCUGAUAACUGGCUGCAUUUGCGAGAUCUAGGUAACAGAUAAA
.......(((((.((((...((((((.((((((.((((((........))))....)).))))))))))))......)))).)))))............ ( -29.00)
>DroYak_CAF1 56941 99 - 1
CUCCUCGCUGGAGUUCGAUACAGCUCCAUUAUCCGUAUCCAGGUCGUAGGAUUGCAGCUGAUAGCUGGCUGCAUUUGCGAGAUCUAGGUACCAGAUCAA
....(((((((((((......)))))))........((((........))))(((((((.......)))))))...))))(((((.(....)))))).. ( -31.00)
>DroPer_CAF1 53471 99 - 1
GCCUUCGGUGCUGUUUCCUGACACUUCAUUAUCCAUAUCCAAGUCGUAUAUCUGCAGCUGUCUGCUGGCUGCUUCGCCCAGACCGAGGAAGCAGACUAG
......(((.(((((((((......................(((.(((....))).)))(((((..(((......))))))))..)))))))))))).. ( -27.10)
>consensus
CUCCUCGCUGGAGUUCGAUGCAGCCCCAUUAUCCGUAUCAAGAUCGUAAGAUUGCAGCUGAUAGCUGGCUGCAUUGGCGAGAUCUAGGGAACAGAUCAA
............(((((((((.............))))).(((((.......(((((((.......))))))).......)))))...))))....... (-16.58 = -16.98 +   0.39)

alignment

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secondary structure

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Window 1

Location 6,048,598 – 6,048,695
Length 97
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 76.87
Mean single sequence MFE -32.22
Consensus MFE -18.39
Energy contribution -20.25
Covariance contribution 1.86
Combinations/Pair 1.12
Mean z-score -1.62
Structure conservation index 0.57
SVM decision value 0.23
SVM RNA-class probability 0.645231
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6048598 97 - 27905053
GCUGUUGGCAUUCCGCAGCCAAGAAAGAGGUCUUUCCAGGGACGUGACUCCGC------CAUUGAACACCUCCUCGCUGGAGUUCGAUGCAGCCCUAUUAUCC
(((((.(((....(((..((..(((((....)))))...))..))).....))------)(((((((.((........)).)))))))))))).......... ( -29.00)
>DroPse_CAF1 53340 100 - 1
GCUCUGGACCUGCCGCAGCCAGCUCAGAGGUCUCUCCAUC---GUCAGCCCAGAACUGGGAUUGUACUGGCCUUCGGUGCUGUUUCCUGACACUUCAUUAUCC
.(((((..(..((....))..)..)))))...........---(((((((((....))))...((((((.....))))))......)))))............ ( -27.80)
>DroSec_CAF1 54526 97 - 1
GCUGUUGGCAUUUCGUAGCCAAGAAAGAGGUCUUUCCAGAGAUGUUACUUCGC------CAUUGAACUCCUCUCCGCUGGAGUUCGAUGCAGCCCCAUUAUCC
(((((((((........)))))(((.((.(((((....))))).))..)))..------(((((((((((........))))))))))))))).......... ( -32.00)
>DroSim_CAF1 55777 97 - 1
GCUGUUGGCAUUCCGUAGCCAAGAAAGAGGUCUUUCCAGAGAUGUCACUUCGC------CAUUGAACUCCUGCUCGCUGGAGUUCGAUGCAGCCCCAUUAUCC
(((((((((........)))))(((.((.(((((....))))).))..)))..------(((((((((((........))))))))))))))).......... ( -33.80)
>DroEre_CAF1 55075 103 - 1
GCUGUUGGCGUUCCGUAGCCAGGAAAGAGGUCUUUCCAGGGCGGUGACUCCUGCACUUGCAUUGAACUCCUCCUCGCUAGAGUUCGAUACAGCCGCGUUAUCC
(((((.((.(((((((..((.((((((....)))))).)))))).))).)).((....))(((((((((..........)))))))))))))).......... ( -34.40)
>DroYak_CAF1 57006 97 - 1
GCUGUUGGCGUUCCGUAGCCAAGAAAGAGGUCUUUCCAGGGAGGUAACUCCUG------CAUUGAACUCCUCCUCGCUGGAGUUCGAUACAGCUCCAUUAUCC
(((((((((........)))).(((((....)))))..(((((....))))).------.((((((((((........))))))))))))))).......... ( -36.30)
>consensus
GCUGUUGGCAUUCCGUAGCCAAGAAAGAGGUCUUUCCAGGGAGGUCACUCCGC______CAUUGAACUCCUCCUCGCUGGAGUUCGAUGCAGCCCCAUUAUCC
(((((((((........)))).(((((....)))))........................((((((((((........))))))))))))))).......... (-18.39 = -20.25 +   1.86)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,048,695 – 6,048,794
Length 99
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 82.68
Mean single sequence MFE -38.98
Consensus MFE -28.90
Energy contribution -28.10
Covariance contribution -0.80
Combinations/Pair 1.29
Mean z-score -1.49
Structure conservation index 0.74
SVM decision value 0.07
SVM RNA-class probability 0.570607
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6048695 99 + 27905053
GUGUUCGGCAGUCCCGCUGGUCAUGUGGUCAUCCAGGUGGCCAAGGAGCUGUUACAUCGAUCAGCCGGAAACAGUCAAGUGGGUUAA---------GGAUACA--UUACC
(((((((((((..((..(((((((.(((....))).))))))).))..)))))..(((.((..((.(....).))...)).)))...---------)))))).--..... ( -36.00)
>DroSec_CAF1 54623 108 + 1
AUGUUCGGCAGUCCCGCUGGUCAUGUGGUCAUCCAGGUGGCCAAGGAGCUGCUACAUCGAUCAGCCGGAAACAGUCAAGUGGGUUAAGGAUAUCAAGGAUACU--UUCCC
(((((((((((..((..(((((((.(((....))).))))))).))..)))))..(((.((..((.(....).))...)).)))...))))))...(((....--.))). ( -37.50)
>DroSim_CAF1 55874 108 + 1
AUGUUCGGCAGUCCCGCUGGUCAUGUGGUCAUCCAGGUGGCCAAGGAGCUGCUACAUCGAUCAGCCGGAAACAGUCAAGUGGGUUAAAGAUAUCAAGGAUACU--UUCCC
.((((((((((..((..(((((((.(((....))).))))))).))..)))))..(((....(((((....)...(....)))))...))).....)))))..--..... ( -36.10)
>DroEre_CAF1 55178 103 + 1
AUGUUCGGCAGUCCCGCUGGUCAUGUGGUCAUCCAGGUGGCCAAGGAGCUGCUGCAUCGCUCAGCCGGAAACAGUCAGGUGGGCUAAGGACAUCAAGGCUGGA-------
.....((((((..((..(((((((.(((....))).))))))).))..))))))......(((((((....).(((.((....))...))).....)))))).------- ( -44.90)
>DroYak_CAF1 57103 108 + 1
AUGUUCGGCAGUCCCGCUGGUCAUGUGGUCAUCCAGGUGGCCAAGGAGCUGCUGCAUCGCUCAGCCGGGAACAGUCAAGUGGGUUGAGAAUAUCAAGGCUACA--UUCCC
((((.((((((..((..(((((((.(((....))).))))))).))..)))))).....(((((((....((......)).)))))))............)))--).... ( -40.00)
>DroMoj_CAF1 69440 101 + 1
AUGUUCGCCAGCCCGGCGGGGCAUGUGGUCGUCCAGGUGGCCAAGGAGCUGCUGCAUCGCUCCGCGGGCAAUAGUCAAGUGCGUGCG------CAGU-UUGCAUAUUA--
..........(((((.((((((((((((....)).((..((......))..)))))).)))))))))))((((((.((.(((....)------)).)-).)).)))).-- ( -39.40)
>consensus
AUGUUCGGCAGUCCCGCUGGUCAUGUGGUCAUCCAGGUGGCCAAGGAGCUGCUACAUCGAUCAGCCGGAAACAGUCAAGUGGGUUAAGGAUAUCAAGGAUACA__UUCCC
((((..((((((.((..(((((((.(((....))).))))))).)).)))))))))).....((((....((......)).))))......................... (-28.90 = -28.10 +  -0.80)

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 10:27:51 2006