Locus 5988

Sequence ID 2R_DroMel_CAF1
Location 18,823,907 – 18,824,049
Length 142
Max. P 0.868614
window9602 window9603 window9604

overview

Window 2

Location 18,823,907 – 18,824,014
Length 107
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 82.24
Mean single sequence MFE -29.14
Consensus MFE -20.16
Energy contribution -20.44
Covariance contribution 0.28
Combinations/Pair 1.10
Mean z-score -1.73
Structure conservation index 0.69
SVM decision value 0.24
SVM RNA-class probability 0.649978
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18823907 107 - 20766785
CAGACUCGCAGUUGCAACACCUGCUACUUCCAGCGGAAAGCCAGCAUCGGUGCCAGCCGCUUGGCACUUUUCUAGCUGAAUGUGGUUUCAAUACAAGAUAUUCCAUU
.((((.((((((.(((.....))).))...((((((((((((((...((((....)))).)))))...))))).))))..))))))))................... ( -27.00)
>DroSec_CAF1 15833 107 - 1
CAGACUCGCAGUUGCAACACCUGCGACUUUCAGCGAAAAGCCAGCAUCGGUGCCAGCCGCUUGGCACUUUUCUAGCUGAAUGUGGUUUCAAUAAAAGAUAUUCCAUA
.((((.((((((((((.....)))))).((((((((((((((((...((((....)))).)))))..)))))..))))))))))))))................... ( -31.80)
>DroSim_CAF1 15374 107 - 1
CAGACUCGCAGUUGCAACACCUGCGACUUCCAGCGAAAAGGCAGCAUCGGUGCCAGCCGCUUGGCACUUUUCUAGCUGAAUGUGGUUUCAAUAAAAGAUAUUCCAUA
.((((.((((((((((.....))))))...((((((((((((.....((((....))))....)).))))))..))))..))))))))................... ( -30.10)
>DroEre_CAF1 14090 100 - 1
CAGACUCGCAGUUGCAACACCUGCGACUUCCAGCGAA-ACCCACCAUCGGUGCCAUCCGCUUGGCACUUUUCUAGCCAAAUGCGA------UAGAAGCCAUUUGGAU
.(((.(((((((((((.....)))))))....)))).-..........(((((((......)))))))..)))..((((((((..------.....).))))))).. ( -30.90)
>DroYak_CAF1 15574 93 - 1
CAGACUCGCAGUUGCAACACCUGCGACUUGCAGCGAAAAGCCACCAACGGAGCCAUCCGCUUGGCAUAUUUCUAGCCAAAUCUGA------UAGAU--------AAU
((((.(((((((((((.....)))))))....))))...((((....((((....))))..))))...............)))).------.....--------... ( -25.90)
>consensus
CAGACUCGCAGUUGCAACACCUGCGACUUCCAGCGAAAAGCCAGCAUCGGUGCCAGCCGCUUGGCACUUUUCUAGCUGAAUGUGGUUUCAAUAAAAGAUAUUCCAUU
.(((.(((((((((((.....)))))))....))))............(((((((......)))))))..))).................................. (-20.16 = -20.44 +   0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,823,946 – 18,824,049
Length 103
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 81.73
Mean single sequence MFE -39.68
Consensus MFE -28.77
Energy contribution -30.97
Covariance contribution 2.20
Combinations/Pair 1.21
Mean z-score -1.44
Structure conservation index 0.72
SVM decision value 0.16
SVM RNA-class probability 0.614155
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18823946 103 + 20766785
AGUGCCAAGCGGCUGGCACCGAUGCUGGCUUUCCGCUGGAAGUAGCAGGUGUUGCAACUGCGAGUCUGCGGUGUGGCUGCCACACCUGCAAUUUGAGUCGCUU---
......((((((((((((((..(((((.(((((....)))))))))))))))).......(((((.((((((((((...))))))).))))))))))))))))--- ( -43.40)
>DroSec_CAF1 15872 103 + 1
AGUGCCAAGCGGCUGGCACCGAUGCUGGCUUUUCGCUGAAAGUCGCAGGUGUUGCAACUGCGAGUCUGCGGUGUGGCUGCCACACCUGCAAUUUGAGUCGCUU---
......((((((((((((((..(((.(((((((....)))))))))))))))).......(((((.((((((((((...))))))).))))))))))))))))--- ( -42.80)
>DroSim_CAF1 15413 103 + 1
AGUGCCAAGCGGCUGGCACCGAUGCUGCCUUUUCGCUGGAAGUCGCAGGUGUUGCAACUGCGAGUCUGCGGUGUGGCUGCCACACCUGCAAUUUGAGUCGCUU---
.((((((......))))))(((((((((..((((....))))..))).)))))).....((((.((((((((((((...))))))).)))....)).))))..--- ( -40.50)
>DroEre_CAF1 14123 102 + 1
AGUGCCAAGCGGAUGGCACCGAUGGUGGGU-UUCGCUGGAAGUCGCAGGUGUUGCAACUGCGAGUCUGCGGUGUGGCUGCCACACCUGCAAUUUGAGUCGCUC---
(((((((.(((((...((((...))))...-))))))))((((.((((((((.(((((((((....)))))).....))).)))))))).))))....)))).--- ( -39.60)
>DroYak_CAF1 15599 103 + 1
UAUGCCAAGCGGAUGGCUCCGUUGGUGGCUUUUCGCUGCAAGUCGCAGGUGUUGCAACUGCGAGUCUGCGGUGUGGCUGCCAUACCUGCAAUUUGAGUCGCUU---
...((.(..(((((.((.....(((..(((...((((((((.((((((.........)))))).).))))))).)))..))).....)).)))))..).))..--- ( -40.90)
>DroAna_CAF1 10844 86 + 1
-------------UGACAGCACUGCUGAAUGUUC-------AUCGCAGGUGCUGCAGAUGGUUGUCGGCGUUGCGGUUGCCACACCUGCAAUUCGAGUUGCUUGGC
-------------.(((.(((.((((((....((-------(((((((...)))).)))))...)))))).))).)))((((.....(((((....))))).)))) ( -30.90)
>consensus
AGUGCCAAGCGGCUGGCACCGAUGCUGGCUUUUCGCUGGAAGUCGCAGGUGUUGCAACUGCGAGUCUGCGGUGUGGCUGCCACACCUGCAAUUUGAGUCGCUU___
.((((((......))))))((((...((((((......))))))((((((((.(((((((((....)))))).....))).)))))))).......))))...... (-28.77 = -30.97 +   2.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,823,946 – 18,824,049
Length 103
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 81.73
Mean single sequence MFE -36.13
Consensus MFE -26.15
Energy contribution -28.73
Covariance contribution 2.59
Combinations/Pair 1.07
Mean z-score -2.32
Structure conservation index 0.72
SVM decision value 0.86
SVM RNA-class probability 0.868614
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18823946 103 - 20766785
---AAGCGACUCAAAUUGCAGGUGUGGCAGCCACACCGCAGACUCGCAGUUGCAACACCUGCUACUUCCAGCGGAAAGCCAGCAUCGGUGCCAGCCGCUUGGCACU
---..((((.((....(((.(((((((...)))))))))))).)))).((((......(((((......))))).....))))...((((((((....)))))))) ( -38.40)
>DroSec_CAF1 15872 103 - 1
---AAGCGACUCAAAUUGCAGGUGUGGCAGCCACACCGCAGACUCGCAGUUGCAACACCUGCGACUUUCAGCGAAAAGCCAGCAUCGGUGCCAGCCGCUUGGCACU
---..((........((((.(((((((...)))))))))))..(((((((((((.....)))))))....)))).......))...((((((((....)))))))) ( -39.50)
>DroSim_CAF1 15413 103 - 1
---AAGCGACUCAAAUUGCAGGUGUGGCAGCCACACCGCAGACUCGCAGUUGCAACACCUGCGACUUCCAGCGAAAAGGCAGCAUCGGUGCCAGCCGCUUGGCACU
---..((..((....((((.(((((((...)))))))))))..(((((((((((.....)))))))....))))...))..))...((((((((....)))))))) ( -40.00)
>DroEre_CAF1 14123 102 - 1
---GAGCGACUCAAAUUGCAGGUGUGGCAGCCACACCGCAGACUCGCAGUUGCAACACCUGCGACUUCCAGCGAA-ACCCACCAUCGGUGCCAUCCGCUUGGCACU
---...(((......((((.(((((((...)))))))))))..(((((((((((.....)))))))....)))).-........)))((((((......)))))). ( -38.70)
>DroYak_CAF1 15599 103 - 1
---AAGCGACUCAAAUUGCAGGUAUGGCAGCCACACCGCAGACUCGCAGUUGCAACACCUGCGACUUGCAGCGAAAAGCCACCAACGGAGCCAUCCGCUUGGCAUA
---...((.(((((.((((((((...(((((......((......)).)))))...)))))))).))).))))....((((....((((....))))..))))... ( -33.50)
>DroAna_CAF1 10844 86 - 1
GCCAAGCAACUCGAAUUGCAGGUGUGGCAACCGCAACGCCGACAACCAUCUGCAGCACCUGCGAU-------GAACAUUCAGCAGUGCUGUCA-------------
.....((((......)))).(((((.((....)).)))))...........(((((((.(((((.-------......)).))))))))))..------------- ( -26.70)
>consensus
___AAGCGACUCAAAUUGCAGGUGUGGCAGCCACACCGCAGACUCGCAGUUGCAACACCUGCGACUUCCAGCGAAAAGCCAGCAUCGGUGCCAGCCGCUUGGCACU
.....((((.((....(((.(((((((...)))))))))))).))))(((((((.....))))))).....................((((((......)))))). (-26.15 = -28.73 +   2.59)

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 11:59:45 2006