Locus 5876

Sequence ID 2R_DroMel_CAF1
Location 18,573,876 – 18,574,036
Length 160
Max. P 0.999612
window9433 window9434 window9435

overview

Window 3

Location 18,573,876 – 18,573,996
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.08
Mean single sequence MFE -51.02
Consensus MFE -47.96
Energy contribution -48.20
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -2.22
Structure conservation index 0.94
SVM decision value 3.78
SVM RNA-class probability 0.999612
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18573876 120 + 20766785
AGCCAGGGUCAGGUCAACAGGCUGACCACCUUCUGGCAGGAGUCCGAUGUGGACAUGUCCCGUGGCCUUGAUUUUGUGCCGCGCGGCCAUGUCCUCGCUCGGUUCACCCAUCUGCAGCAC
.((((((((..(((((......))))))))..)))))..(((.((((((.(((((((.(((((((((........).)))))).)).))))))).)).)))))))............... ( -52.60)
>DroSec_CAF1 53590 120 + 1
AGCCAGGGUCAGGUUAACAAGCUGACCACCUUCUGGCAGGAGUCCGAUGUGGACAUGUCCCGUGGCAUUGACUUCGUGCCGCGCGGCCAUGUCCUCGCUCGGUUCACCCAUCUGCAGCAC
.(((((((((((.(.....).)))))).....)))))..(((.((((((.(((((((.((((((((((.......)))))))).)).))))))).)).)))))))............... ( -53.70)
>DroSim_CAF1 49532 120 + 1
AGCCAGGGUCAGGUGAACAAGCUGACCACCUUCUGGCAGGAGUCCGAUGUGGACAUGUCCCGUGGCCUUGACUUCGUGCCGCGCGGCCAUGUCCUCGCUCGGUUCACUCAUCUGCAGCAC
.(((((((((((.(.....).)))))).....)))))..((((((((((.(((((((.((((((((..((....)).)))))).)).))))))).)).))))...))))........... ( -54.20)
>DroEre_CAF1 55697 120 + 1
AGCCAGGGUCAGGUCAACAGGCUGACCACCUUCUGGCAGGAGUCCGAUGUGGACAUGUCCCGCGGCCUUGAUUUUGUGCCACGCGGCCAUGUCCUCGCUCGGUUCACCCAUCUGCAGCAC
.((((((((..(((((......))))))))..)))))..(((.((((((.(((((((.((((.((((........).))).)).)).))))))).)).)))))))............... ( -49.10)
>DroYak_CAF1 55425 120 + 1
AGCCAGGGUAAGAUCAACAGGCUGACCACAUUCUGGCAGGAGUCCGAUGUGGACAUGUCCCGCGGCCUUGAUUUCGUGCCGCGCGGCCACGUCCUCGCUCGGUUCACCCAUCUGCAGCAC
.((((((((..(.(((......))).)..))))))))..(((.((((((.((((.((.((((((((..((....)).)))))).)).)).)))).)).)))))))............... ( -45.50)
>consensus
AGCCAGGGUCAGGUCAACAGGCUGACCACCUUCUGGCAGGAGUCCGAUGUGGACAUGUCCCGUGGCCUUGAUUUCGUGCCGCGCGGCCAUGUCCUCGCUCGGUUCACCCAUCUGCAGCAC
.(((((((((((.(.....).)))))).....)))))..(((.((((((.(((((((.((((((((...........)))))).)).))))))).)).)))))))............... (-47.96 = -48.20 +   0.24)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,573,876 – 18,573,996
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.08
Mean single sequence MFE -48.86
Consensus MFE -43.76
Energy contribution -43.88
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -1.19
Structure conservation index 0.90
SVM decision value 0.13
SVM RNA-class probability 0.600427
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18573876 120 - 20766785
GUGCUGCAGAUGGGUGAACCGAGCGAGGACAUGGCCGCGCGGCACAAAAUCAAGGCCACGGGACAUGUCCACAUCGGACUCCUGCCAGAAGGUGGUCAGCCUGUUGACCUGACCCUGGCU
...........(((....((((..(.(((((((.((.((.(((.(........)))).)))).))))))).).))))...)))(((((..(((((((((....))))))..)))))))). ( -48.60)
>DroSec_CAF1 53590 120 - 1
GUGCUGCAGAUGGGUGAACCGAGCGAGGACAUGGCCGCGCGGCACGAAGUCAAUGCCACGGGACAUGUCCACAUCGGACUCCUGCCAGAAGGUGGUCAGCUUGUUAACCUGACCCUGGCU
..(((((((..((((...((((..(.(((((((.((.((.((((.........)))).)))).))))))).).)))))))))))).....((.((((((.........))))))))))). ( -45.90)
>DroSim_CAF1 49532 120 - 1
GUGCUGCAGAUGAGUGAACCGAGCGAGGACAUGGCCGCGCGGCACGAAGUCAAGGCCACGGGACAUGUCCACAUCGGACUCCUGCCAGAAGGUGGUCAGCUUGUUCACCUGACCCUGGCU
..(((((((..((((...((((..(.(((((((.((.((.(((.(........)))).)))).))))))).).)))))))))))).....((.((((((.........))))))))))). ( -47.10)
>DroEre_CAF1 55697 120 - 1
GUGCUGCAGAUGGGUGAACCGAGCGAGGACAUGGCCGCGUGGCACAAAAUCAAGGCCGCGGGACAUGUCCACAUCGGACUCCUGCCAGAAGGUGGUCAGCCUGUUGACCUGACCCUGGCU
...........(((....((((..(.(((((((.((.((((((.(........))))))))).))))))).).))))...)))(((((..(((((((((....))))))..)))))))). ( -52.10)
>DroYak_CAF1 55425 120 - 1
GUGCUGCAGAUGGGUGAACCGAGCGAGGACGUGGCCGCGCGGCACGAAAUCAAGGCCGCGGGACAUGUCCACAUCGGACUCCUGCCAGAAUGUGGUCAGCCUGUUGAUCUUACCCUGGCU
...........(((....((((..(.(((((((.((.((((((.(........))))))))).))))))).).))))...)))(((((..((.((((((....)))))).))..))))). ( -50.60)
>consensus
GUGCUGCAGAUGGGUGAACCGAGCGAGGACAUGGCCGCGCGGCACGAAAUCAAGGCCACGGGACAUGUCCACAUCGGACUCCUGCCAGAAGGUGGUCAGCCUGUUGACCUGACCCUGGCU
...........((((...((((..(.(((((((.((.((.(((...........))).)))).))))))).).))))))))..(((((..(((((((((....))))))..)))))))). (-43.76 = -43.88 +   0.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,573,916 – 18,574,036
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.00
Mean single sequence MFE -48.00
Consensus MFE -44.44
Energy contribution -44.48
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.18
Structure conservation index 0.93
SVM decision value 0.27
SVM RNA-class probability 0.663459
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18573916 120 - 20766785
CGCUGGAGUUCUCCACCUUGAUGGUGUAGCUGAAUUCGUGGUGCUGCAGAUGGGUGAACCGAGCGAGGACAUGGCCGCGCGGCACAAAAUCAAGGCCACGGGACAUGUCCACAUCGGACU
((((.(.((((.(((((.....)))(((((............))))).....)).))))).)))).(((((((.((.((.(((.(........)))).)))).))))))).......... ( -46.50)
>DroSec_CAF1 53630 120 - 1
CGCUGGAGUUCUCCACCUUGAUGGUGUAGCUGAAUGCGUGGUGCUGCAGAUGGGUGAACCGAGCGAGGACAUGGCCGCGCGGCACGAAGUCAAUGCCACGGGACAUGUCCACAUCGGACU
((((.(.((((.(((((.....)))(((((............))))).....)).))))).)))).(((((((.((.((.((((.........)))).)))).))))))).......... ( -46.90)
>DroSim_CAF1 49572 120 - 1
CGCUGGAGUUCUCCACCUUGAUGGUGUAGCUGAAUGCGUGGUGCUGCAGAUGAGUGAACCGAGCGAGGACAUGGCCGCGCGGCACGAAGUCAAGGCCACGGGACAUGUCCACAUCGGACU
((((.(.((((..((((.....))))..(((.(.((((......))))..).)))))))).)))).(((((((.((.((.(((.(........)))).)))).))))))).......... ( -44.40)
>DroEre_CAF1 55737 120 - 1
CGCUGGAGUUCUCCACCUCGAUGGUGUAGCUGAAUGGGUGGUGCUGCAGAUGGGUGAACCGAGCGAGGACAUGGCCGCGUGGCACAAAAUCAAGGCCGCGGGACAUGUCCACAUCGGACU
((((.(.((((.(((((.....)))(((((............))))).....)).))))).)))).(((((((.((.((((((.(........))))))))).))))))).......... ( -50.00)
>DroYak_CAF1 55465 120 - 1
CGCUGGAGUUCUCCACCUUGAUGGUGUAGCUGAAUGGGUGGUGCUGCAGAUGGGUGAACCGAGCGAGGACGUGGCCGCGCGGCACGAAAUCAAGGCCGCGGGACAUGUCCACAUCGGACU
((((.(.((((.(((((.....)))(((((............))))).....)).))))).)))).(((((((.((.((((((.(........))))))))).))))))).......... ( -52.20)
>consensus
CGCUGGAGUUCUCCACCUUGAUGGUGUAGCUGAAUGCGUGGUGCUGCAGAUGGGUGAACCGAGCGAGGACAUGGCCGCGCGGCACGAAAUCAAGGCCACGGGACAUGUCCACAUCGGACU
((((.(.((((.(((((.....)))(((((............))))).....)).))))).)))).(((((((.((.((.(((...........))).)))).))))))).......... (-44.44 = -44.48 +   0.04)

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 11:57:03 2006