Locus 770

Sequence ID 2R_DroMel_CAF1
Location 3,725,781 – 3,725,981
Length 200
Max. P 0.858746
window1343 window1344 window1345

overview

Window 3

Location 3,725,781 – 3,725,901
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.28
Mean single sequence MFE -45.32
Consensus MFE -26.50
Energy contribution -25.84
Covariance contribution -0.66
Combinations/Pair 1.37
Mean z-score -1.92
Structure conservation index 0.58
SVM decision value 0.10
SVM RNA-class probability 0.581101
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3725781 120 + 20766785
AUAACACUCCGGAGGGAUAUAUCUGCUCCUGUCCAGACCAUCUAUACCUGCAGCCAAACGGAAAGCGCUGCAGCAUGCAGCACGCCUGCGAUCACUGGGAUACGUGUUCACAGGUGUGCG
.......((.(((((((.........)))).))).))..........((((((((.........).)))))))......(((((((((.((.(((........))).)).))))))))). ( -39.70)
>DroVir_CAF1 3646 120 + 1
ACAAUACGCCCGAGGGUUACAUCUGUUCAUGCCCGCCACAUUUGUAUUUGCAGCCGAAUGGCAAACGCUGCAGCAUGCAGCACGCUUGUGAGCAUUGGGACACCUGCUCACAGGUGUGCG
.............((((.((....))....))))........((((((((((((............))))))).)))))(((((((((((((((..((....))))))))))))))))). ( -48.10)
>DroGri_CAF1 3974 120 + 1
ACAACACGCCCGAGGGUUACAUCUGCUCGUGUCCCCCACAUUUGUAUUUGCAGCCAAAUGGCAAGCGUUGCAGCAUGCAGCACGCCUGCGAGCACUGGGACACGUGUGCCCAGGUCUGUG
...(((.(((...((((.......((.((((((((.......((((..(((.(((....)))..))).))))((.(((((.....))))).))...)))))))).)))))).))).))). ( -43.61)
>DroWil_CAF1 3259 120 + 1
AUAAUACCCCAGAGGGUUAUAUAUGCUCGUGCCCGGCUCACUUGUUCCUGCAACCGAAUGGCAAGCGUUGUAGUAUGCAACAUGCCUGUGAUAAUUGGGAUACAUGCUCACAGGUGUGUG
.....((((....))))((((.(((((..(((((((.....((((....)))))))...))))))))))))).......((((((((((((....((.....))...)))))))))))). ( -35.40)
>DroMoj_CAF1 4455 120 + 1
ACAAUACGCCCGAGGGCUACAUCUGCUCCUGCCCGCCCCACCUGUAUCUGCAGCCCAAUGGCAAGCGCUGCAGCAUGCAGCACGCCUGCGAGCACUGGGACACCUGCUCGCAGGUGUGCG
.............((((.............))))........((((((((((((.(........).))))))).)))))(((((((((((((((..((....))))))))))))))))). ( -57.02)
>DroAna_CAF1 3249 120 + 1
ACAAUACACCGGAGGGUUACAUCUGCUCCUGCCCGGAUCACUUGUACCUGCAGCCGAACGGGAAGCGGUGCAGCAUGCAGCAUGCCUGCGAUCACUGGGACAGCUGUUCCCAGGUGUGUG
...(((((((...(((..(((.(((.(((((....((((...((((((.((..((.....))..))))))))(((.((.....)).)))))))..)))))))).))).))).))))))). ( -48.10)
>consensus
ACAAUACGCCCGAGGGUUACAUCUGCUCCUGCCCGCCACACUUGUACCUGCAGCCGAAUGGCAAGCGCUGCAGCAUGCAGCACGCCUGCGAGCACUGGGACACCUGCUCACAGGUGUGCG
.............((((.............))))........(((..(((((((............)))))))...)))(((((((((.((.((..........)).)).))))))))). (-26.50 = -25.84 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,725,821 – 3,725,941
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.17
Mean single sequence MFE -48.68
Consensus MFE -29.64
Energy contribution -28.23
Covariance contribution -1.41
Combinations/Pair 1.52
Mean z-score -2.02
Structure conservation index 0.61
SVM decision value 0.82
SVM RNA-class probability 0.858746
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3725821 120 + 20766785
UCUAUACCUGCAGCCAAACGGAAAGCGCUGCAGCAUGCAGCACGCCUGCGAUCACUGGGAUACGUGUUCACAGGUGUGCGAAAGUAGCGGUAAGGGUUAUGACUGCCGUUGCUUGGAUGG
.......((((((((.........).)))))))(((.(.(((((((((.((.(((........))).)).)))))))))..(((((((((((.(........))))))))))))).))). ( -50.60)
>DroVir_CAF1 3686 120 + 1
UUUGUAUUUGCAGCCGAAUGGCAAACGCUGCAGCAUGCAGCACGCUUGUGAGCAUUGGGACACCUGCUCACAGGUGUGCGAAAACAACGGCAAAGGCUAUGCCUGUCAGUGCCUCGAAGG
.((((.(((((.(((....)))....(((((.....)))))(((((((((((((..((....)))))))))))))))))))).)))).((((.((((...)))).....))))....... ( -53.40)
>DroGri_CAF1 4014 120 + 1
UUUGUAUUUGCAGCCAAAUGGCAAGCGUUGCAGCAUGCAGCACGCCUGCGAGCACUGGGACACGUGUGCCCAGGUCUGUGAGAACAAUGGCAAGAGCUACGCCUGCCAGUGCCUCGAGGG
.........((.(((....)))..))(((((.....)))))...(((.((((((((((.(..((((.((.(..((((((....)))..)))..).))))))..).)))))).))))))). ( -43.10)
>DroWil_CAF1 3299 120 + 1
CUUGUUCCUGCAACCGAAUGGCAAGCGUUGUAGUAUGCAACAUGCCUGUGAUAAUUGGGAUACAUGCUCACAGGUGUGUGAAACAAAGGGCAAAGGUUAUCAGUGUCGUUGCCUGGAGGG
....((((.(((((.((.((..((.(.((((....((..((((((((((((....((.....))...))))))))))))....))....)))).).))..))...)))))))..)))).. ( -36.70)
>DroMoj_CAF1 4495 120 + 1
CCUGUAUCUGCAGCCCAAUGGCAAGCGCUGCAGCAUGCAGCACGCCUGCGAGCACUGGGACACCUGCUCGCAGGUGUGCGAGAGCAGCGGCAAGGGCUAUGCCUGCCAGUGCCUGGAGGG
((((((((((((((.(........).))))))).)))).(((((((((((((((..((....))))))))))))))))).........((((..(((.......)))..))))...))). ( -64.70)
>DroAna_CAF1 3289 120 + 1
CUUGUACCUGCAGCCGAACGGGAAGCGGUGCAGCAUGCAGCAUGCCUGCGAUCACUGGGACAGCUGUUCCCAGGUGUGUGAGACCAGCGGCAAGGGGUACGAGUGUCGCUGCUUGGAGGG
(((((((((...((((...((((.((((.(((((.....)).)))))))..)).(((((((....).))))))..........))..))))...)))))))))................. ( -43.60)
>consensus
CUUGUACCUGCAGCCGAAUGGCAAGCGCUGCAGCAUGCAGCACGCCUGCGAGCACUGGGACACCUGCUCACAGGUGUGCGAAAACAACGGCAAGGGCUAUGACUGCCAGUGCCUGGAGGG
.((((..(((((((............)))))))......(((((((((.((.((..........)).)).)))))))))....)))).((((..(((.......)))..))))....... (-29.64 = -28.23 +  -1.41)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,725,861 – 3,725,981
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.33
Mean single sequence MFE -45.29
Consensus MFE -24.73
Energy contribution -24.48
Covariance contribution -0.24
Combinations/Pair 1.45
Mean z-score -1.79
Structure conservation index 0.55
SVM decision value 0.18
SVM RNA-class probability 0.621102
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3725861 120 + 20766785
CACGCCUGCGAUCACUGGGAUACGUGUUCACAGGUGUGCGAAAGUAGCGGUAAGGGUUAUGACUGCCGUUGCUUGGAUGGAUUCGACUUGGGCUUCGAUCGGUUCACAUGCAAAAGCACC
((((((((.((.(((........))).)).))))))))...(((((((((((.(........))))))))))))((((.(((.(((........)))))).))))...(((....))).. ( -42.50)
>DroVir_CAF1 3726 120 + 1
CACGCUUGUGAGCAUUGGGACACCUGCUCACAGGUGUGCGAAAACAACGGCAAAGGCUAUGCCUGUCAGUGCCUCGAAGGCUACGAUCUAGCCUACGACAAAUUUACGUGCAAGAGCACA
((((((((((((((..((....))))))))))))))))..........((((.((((...)))).....))))(((.((((((.....)))))).))).........((((....)))). ( -50.90)
>DroWil_CAF1 3339 120 + 1
CAUGCCUGUGAUAAUUGGGAUACAUGCUCACAGGUGUGUGAAACAAAGGGCAAAGGUUAUCAGUGUCGUUGCCUGGAGGGUUAUGACUUGGCCUAUGAUAAAUUUACAUGUAAAAGUACC
...((((((((....((.....))...))))))))(((((((........((.((((((.....(((((.(((.....))).))))).)))))).)).....)))))))........... ( -32.22)
>DroMoj_CAF1 4535 120 + 1
CACGCCUGCGAGCACUGGGACACCUGCUCGCAGGUGUGCGAGAGCAGCGGCAAGGGCUAUGCCUGCCAGUGCCUGGAGGGCUAUGACCUGGCCUACGACAAGUUCACGUGCAAGAGCACC
((((((((((((((..((....))))))))))))))))...((((...((((..(((.......)))..))))..(.((((((.....)))))).).....))))..((((....)))). ( -58.60)
>DroAna_CAF1 3329 120 + 1
CAUGCCUGCGAUCACUGGGACAGCUGUUCCCAGGUGUGUGAGACCAGCGGCAAGGGGUACGAGUGUCGCUGCUUGGAGGGCUUCGACUUGGCCUACGACAAGUUCACCUGCAAGAGCACU
...(((((.((.(((((...))).)).)).)))))((((.....((((((((.(.....)...))))))))((((.(((.....((((((........))))))..))).)))).)))). ( -41.50)
>DroPer_CAF1 2960 120 + 1
CAUGCCUGCGACCACUGGGACACCUGCUCGCAGGUGUGCCAGACCAGCGGCAAGGGCUACGACUGUCGCUGUUUGGAGGGAUUCGACCUCGCCUACGACAAAUUCACGUGCAAGAGCACC
.......(((((((((((.(((((((....))))))).))))..((((((((.(........)))))))))..))).((.......))))))...............((((....)))). ( -46.00)
>consensus
CACGCCUGCGAUCACUGGGACACCUGCUCACAGGUGUGCGAAACCAGCGGCAAGGGCUAUGACUGUCGCUGCCUGGAGGGCUACGACCUGGCCUACGACAAAUUCACGUGCAAGAGCACC
(((((((((((.((..((....)))).)))))))))))..........((((..(((.......)))..))))..(.(((((.......))))).)............(((....))).. (-24.73 = -24.48 +  -0.24)

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 09:46:48 2006