Locus 1010

Sequence ID 2R_DroMel_CAF1
Location 4,212,857 – 4,213,094
Length 237
Max. P 0.998239
window1786 window1787 window1788

overview

Window 6

Location 4,212,857 – 4,212,977
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.58
Mean single sequence MFE -44.88
Consensus MFE -33.70
Energy contribution -34.74
Covariance contribution 1.04
Combinations/Pair 1.08
Mean z-score -2.22
Structure conservation index 0.75
SVM decision value 0.98
SVM RNA-class probability 0.893530
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4212857 120 + 20766785
CGAGUAAUCAAUCCUCGCCCCGCGUCCAGAUGGUCCACAACCUGGGCGGCAUAGACCUCCAGGCUGGCCGUAUAGAUCACCAGGUCGUACCACUUGGACACAAAGUCCAGGAACUCGUCU
(((((......((((.((...))((((((.((((..((.(((((((((((.(((.((....))))))))))........)))))).)))))).)))))).........)))))))))... ( -42.70)
>DroSec_CAF1 24515 120 + 1
CGAGUAAUCAAUCCUCGCCCCGCGUCCAAUUGGUCCACAACCUGGGCGGCAUAAGCCUCCAGGCUGGCCGUGUAGAUCACCAGGUCGUACCACUUGGACACGAAGUCCAGGAACUCGUCA
(((((......((((.((..((.((((((.((((..((.(((((((((((...((((....)))).)))))(.....).)))))).)))))).)))))).))..).).)))))))))... ( -50.20)
>DroSim_CAF1 56458 120 + 1
CGAGUAAUCAAUCCUCGCCCCGCGUCCAGUUGGUCCACAACCUGGGCGGCAUAAGCCUCCAGGCUGGCCGUGUAGAUCACCAGGUCGUACCACUUGGACACGAAGUCCAGGAACUCGUCG
(((((......((((.((..((.((((((.((((..((.(((((((((((...((((....)))).)))))(.....).)))))).)))))).)))))).))..).).)))))))))... ( -49.90)
>DroEre_CAF1 26376 120 + 1
CGAGACAUCCUUCCCUGUCCCGCGUCCAGGAGGUCCACCACCUGGGCAGCAUAGACCUCCAGACUGGCCGUGUAGACCACCAGGUCGUACCACUUGGACACGAAGUGCAGGAACUCAUCG
.(((...((((.(.((....((.(((((((.(((..((.((((((.(.(((..(.((........)))..))).)....)))))).))))).))))))).)).)).).)))).))).... ( -41.60)
>DroYak_CAF1 27195 120 + 1
CGAGACAUUCUUCCUUGUCCCGCGUCCAGAAGGUCCACCACCUGGGUGGCAUAGACCUCCAGGCUGGCCGUGUAGAUCACCAGGUCGUACCACUUGGACACGCAGUCCAGGAACUCAUCG
.(((((..............((((.((((..((....)).((((((.((......)))))))))))).))))..((((....))))))....(((((((.....)))))))..))).... ( -40.00)
>consensus
CGAGUAAUCAAUCCUCGCCCCGCGUCCAGAUGGUCCACAACCUGGGCGGCAUAGACCUCCAGGCUGGCCGUGUAGAUCACCAGGUCGUACCACUUGGACACGAAGUCCAGGAACUCGUCG
.((((......((((.....((.((((((.((((..((.(((((((((((...(.((....)).).)))))........)))))).)))))).)))))).))......)))))))).... (-33.70 = -34.74 +   1.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,212,857 – 4,212,977
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.58
Mean single sequence MFE -54.66
Consensus MFE -45.86
Energy contribution -46.66
Covariance contribution 0.80
Combinations/Pair 1.17
Mean z-score -2.74
Structure conservation index 0.84
SVM decision value 3.04
SVM RNA-class probability 0.998239
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4212857 120 - 20766785
AGACGAGUUCCUGGACUUUGUGUCCAAGUGGUACGACCUGGUGAUCUAUACGGCCAGCCUGGAGGUCUAUGCCGCCCAGGUUGUGGACCAUCUGGACGCGGGGCGAGGAUUGAUUACUCG
...(((((((((.(.(((((((((((..(((((((((((((.(...((((.((((........))))))))...))))))))))..))))..)))))))))))).))))......))))) ( -55.30)
>DroSec_CAF1 24515 120 - 1
UGACGAGUUCCUGGACUUCGUGUCCAAGUGGUACGACCUGGUGAUCUACACGGCCAGCCUGGAGGCUUAUGCCGCCCAGGUUGUGGACCAAUUGGACGCGGGGCGAGGAUUGAUUACUCG
...(((((((((.(.((((((((((((.(((((((((((((((.....))((((.((((....))))...)))).)))))))))..)))).))))))))))))).))))......))))) ( -59.50)
>DroSim_CAF1 56458 120 - 1
CGACGAGUUCCUGGACUUCGUGUCCAAGUGGUACGACCUGGUGAUCUACACGGCCAGCCUGGAGGCUUAUGCCGCCCAGGUUGUGGACCAACUGGACGCGGGGCGAGGAUUGAUUACUCG
...(((((((((.(.(((((((((((..(((((((((((((((.....))((((.((((....))))...)))).)))))))))..))))..)))))))))))).))))......))))) ( -58.90)
>DroEre_CAF1 26376 120 - 1
CGAUGAGUUCCUGCACUUCGUGUCCAAGUGGUACGACCUGGUGGUCUACACGGCCAGUCUGGAGGUCUAUGCUGCCCAGGUGGUGGACCUCCUGGACGCGGGACAGGGAAGGAUGUCUCG
....(((.((((...(((((((((((........(((.((((.((....)).))))))).((((((((..((..(....)..)))))))))))))))))))...))...))))...))). ( -52.40)
>DroYak_CAF1 27195 120 - 1
CGAUGAGUUCCUGGACUGCGUGUCCAAGUGGUACGACCUGGUGAUCUACACGGCCAGCCUGGAGGUCUAUGCCACCCAGGUGGUGGACCUUCUGGACGCGGGACAAGGAAGAAUGUCUCG
.((((..((((((..((((((((((....)).))...(((((..........)))))((.((((((((..(((((....))))))))))))).))))))))..).)))))...))))... ( -47.20)
>consensus
CGACGAGUUCCUGGACUUCGUGUCCAAGUGGUACGACCUGGUGAUCUACACGGCCAGCCUGGAGGUCUAUGCCGCCCAGGUUGUGGACCAACUGGACGCGGGGCGAGGAUUGAUUACUCG
...(((((((((.(.(((((((((((.(((((.(.(((((((..........)))))(((((.(((....)))..)))))..)).)))))).)))))))))))).))))......))))) (-45.86 = -46.66 +   0.80)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,212,977 – 4,213,094
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.57
Mean single sequence MFE -46.89
Consensus MFE -34.72
Energy contribution -35.20
Covariance contribution 0.48
Combinations/Pair 1.14
Mean z-score -2.10
Structure conservation index 0.74
SVM decision value 0.78
SVM RNA-class probability 0.849176
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4212977 117 + 20766785
ACAUGCGGCCGCUUGAAGACCCGGAAAACGAUAGGUUC---CAUCCCGUCGAUGGAAAUAUUGAGCACAUAGUCCGGUUGUGCGUGUUCGGGCAACUGGCUACAUCCCACGUUGUCGUGG
..(((..((((.(((....((((((...(((((..(((---((((.....))))))).))))).(((((.........)))))...))))))))).))))..))).(((((....))))) ( -43.10)
>DroSec_CAF1 24635 117 + 1
ACAUGCGGCCGCUUGAAGACCCGGAAAACGAUAGGUUC---CGUCCCGUCGAUGGAAAUAUUGAGCACAUAGUCCGGUCGUGCGUUUUCGGGCAACUGGCUGCAUCCCACGUUAUCGUGG
..(((((((((.(((....((((((((.(((((..(((---((((.....))))))).))))).((((...........)))).))))))))))).))))))))).(((((....))))) ( -47.90)
>DroSim_CAF1 56578 117 + 1
ACAUGCGGCCGCUUGAAGACCCGGAAAACGAUAGGUUC---CAUCCCGUCGAUGGAAAUAUUGAGCACAUAGUCCGGUCGUGCGUUUUCGGGCAACUGGCUGCAUCCCACGUUAUCGUGG
..(((((((((.(((....((((((((.(((((..(((---((((.....))))))).))))).((((...........)))).))))))))))).))))))))).(((((....))))) ( -48.30)
>DroEre_CAF1 26496 120 + 1
ACAUGCGGCCGCUUGAAGACCCGAAACACGAUCGGUUCGGACAUGGGUUCGAUGGAAACGUUGAGCACAUAAUCCGGUUGCGCGUGAUCGGGCAGCUGGCUGCAACCCACGUUGUCAUGG
...((((((((((....(.(((((..((((......(((((.(((.((((((((....)))))))).)))..))))).....)))).))))))))).)))))))..(((.(....).))) ( -48.70)
>DroYak_CAF1 27315 120 + 1
ACAUGCGGCCGCUUGAAGACCCGAAACACGAUCGGCUCGACCAUCGGAUCGAUGGACACGUUGAGUACAUAGUCCGGCUGGGCGUGAUCGGGCAACUGGCUGCAACCCACGUUGUCAUGG
...((((((((.(((....(((((..((((..(((((.(((.......((((((....)))))).......))).)))))..)))).)))))))).))))))))..(((.(....).))) ( -46.44)
>consensus
ACAUGCGGCCGCUUGAAGACCCGGAAAACGAUAGGUUC___CAUCCCGUCGAUGGAAAUAUUGAGCACAUAGUCCGGUUGUGCGUGUUCGGGCAACUGGCUGCAUCCCACGUUGUCGUGG
...((((((((.(((....((((.(((((...................((((((....))))))((((...........)))))))))))))))).))))))))..(((((....))))) (-34.72 = -35.20 +   0.48)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:02 2006