Locus 4695

Sequence ID 3R_DroMel_CAF1
Location 12,345,691 – 12,345,870
Length 179
Max. P 0.981153
window7716 window7717 window7718

overview

Window 6

Location 12,345,691 – 12,345,799
Length 108
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 86.02
Mean single sequence MFE -34.56
Consensus MFE -28.40
Energy contribution -28.84
Covariance contribution 0.44
Combinations/Pair 1.07
Mean z-score -2.36
Structure conservation index 0.82
SVM decision value 1.88
SVM RNA-class probability 0.981153
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12345691 108 + 27905053
GAUACAGUUACA------GAUACAGAUACAGAUGCUUGUGUAU--AGAUACUACUGCCGAAAUAUAGGUUGUAUUUGUAUGGCUUUGCAGCUGCGACCGGAUCGGCAAGUGUCUGC
..........((------(((((..(((((.(....).)))))--.........((((((......(((((((.(((((......))))).)))))))...)))))).))))))). ( -35.00)
>DroSec_CAF1 14485 114 + 1
GAUACAGUUACAGAUACAGAUACAGAUACAGAUGCUUCUGUAU--AGAUACUACUGCCGAAAUAUAGGUUGUAUUUGUAUGGCUUUGCAGCUGCGACCGGAUCGGCAAGUGUCUGC
................(((((((..(((((((....)))))))--.........((((((......(((((((.(((((......))))).)))))))...)))))).))))))). ( -39.10)
>DroSim_CAF1 13615 114 + 1
GAUACAGUUACAGUUACAGAUACAGAUACAGAUGCUUGUGUAU--AGAUACCACUGCCGAAAUAUAGGUUGUAUUUGUAUGGCUUUGCAGCUGCGACCGGAUCGGCAAGUGUCUGC
................(((((((..(((((.(....).)))))--.........((((((......(((((((.(((((......))))).)))))))...)))))).))))))). ( -35.00)
>DroEre_CAF1 14412 91 + 1
GAUACAGAUUCA------AAUAGGGAUACAGAUGC-------------------UGCCGAAAUAUAGGUUGUAUUUGUAUGGCUUUGCUGCUGCGACCGGAUCGGCAAGUGUCUGC
.......((((.------.....)))).(((((((-------------------((((((......(((((((...(((......)))...)))))))...))))).)))))))). ( -28.90)
>DroYak_CAF1 10421 110 + 1
GAUACGGAUACA------GAUACGGAUACAGAUGCUUGUGUGUAGAGAUACUACUGCCGAAAUAUAGGUGGUAUUUGUAUGGCUUUGCAGCUGCGACCGGAUCGGCAAGUGUCUGC
..........((------(((((..((((((....))))))((((.....))))((((((......(((.(((.(((((......))))).))).)))...)))))).))))))). ( -34.80)
>consensus
GAUACAGUUACA______GAUACAGAUACAGAUGCUUGUGUAU__AGAUACUACUGCCGAAAUAUAGGUUGUAUUUGUAUGGCUUUGCAGCUGCGACCGGAUCGGCAAGUGUCUGC
......................(((((((..........((((....))))...((((((......(((((((.(((((......))))).)))))))...)))))).))))))). (-28.40 = -28.84 +   0.44)

alignment

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secondary structure

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Window 7

Location 12,345,725 – 12,345,830
Length 105
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 89.55
Mean single sequence MFE -33.04
Consensus MFE -25.92
Energy contribution -28.40
Covariance contribution 2.48
Combinations/Pair 1.06
Mean z-score -1.57
Structure conservation index 0.78
SVM decision value 0.27
SVM RNA-class probability 0.663581
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12345725 105 + 27905053
UAU--AGAUACUACUGCCGAAAUAUAGGUUGUAUUUGUAUGGCUUUGCAGCUGCGACCGGAUCGGCAAGUGUCUGCAUUGCUUUUUUGGCUCGACU---------UUGACUUCGUU
..(--(((((((..((((((......(((((((.(((((......))))).)))))))...))))))))))))))....(((.....))).(((..---------......))).. ( -32.70)
>DroSec_CAF1 14525 114 + 1
UAU--AGAUACUACUGCCGAAAUAUAGGUUGUAUUUGUAUGGCUUUGCAGCUGCGACCGGAUCGGCAAGUGUCUGCAUUGCUUUUUUGGCCCGACUCCAUUCGGUUUGACUUCGUU
..(--(((((((..((((((......(((((((.(((((......))))).)))))))...))))))))))))))....(((.....)))((((......))))............ ( -36.00)
>DroSim_CAF1 13655 114 + 1
UAU--AGAUACCACUGCCGAAAUAUAGGUUGUAUUUGUAUGGCUUUGCAGCUGCGACCGGAUCGGCAAGUGUCUGCAUUGCUUUUUUGGCCCGACUCCAUUCGGUUUGACUUCGUU
...--.((...((..((((((.....(((((((.(((((......))))).)))))))(((((((..((((....))))(((.....))))))).))).)))))).))...))... ( -34.80)
>DroEre_CAF1 14441 102 + 1
--------------UGCCGAAAUAUAGGUUGUAUUUGUAUGGCUUUGCUGCUGCGACCGGAUCGGCAAGUGUCUGCAUUGCUUUUUUGGCUCGACUCCAUUCGGUUUGACUGCGUU
--------------.((((((.....(((((((...(((......)))...)))))))(((((((((......)))...(((.....))).))).))).))))))........... ( -28.90)
>DroYak_CAF1 10455 116 + 1
UGUAGAGAUACUACUGCCGAAAUAUAGGUGGUAUUUGUAUGGCUUUGCAGCUGCGACCGGAUCGGCAAGUGUCUGCAUUGCUUUUUUAGCUCGACUCCAUUCGGUUUGACUUCGUU
(((..(((((((..((((((......(((.(((.(((((......))))).))).)))...))))))))))))))))..(((.....)))((((..((....)).))))....... ( -32.80)
>consensus
UAU__AGAUACUACUGCCGAAAUAUAGGUUGUAUUUGUAUGGCUUUGCAGCUGCGACCGGAUCGGCAAGUGUCUGCAUUGCUUUUUUGGCUCGACUCCAUUCGGUUUGACUUCGUU
.....(((((((..((((((......(((((((.(((((......))))).)))))))...))))))))))))).....(((.....)))((((......))))............ (-25.92 = -28.40 +   2.48)

alignment

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secondary structure

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Window 8

Location 12,345,763 – 12,345,870
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.61
Mean single sequence MFE -29.63
Consensus MFE -20.64
Energy contribution -21.75
Covariance contribution 1.11
Combinations/Pair 1.12
Mean z-score -1.29
Structure conservation index 0.70
SVM decision value -0.04
SVM RNA-class probability 0.510770
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12345763 107 - 27905053
GCAAGGAAAAUUGUAGCAUAUGCGGCUGGCUAAUAAACCAAACGAAGUCAA---------AGUCGAGCCAAAAAAGCAAUGCAGACACUUGCC--GAUCCGGUCGCAGCUGCAAA--GCC
....((....(((((((...(((((((((..............(....)..---------.((((.((.......))...((((....)))))--))))))))))))))))))).--.)) ( -27.40)
>DroSec_CAF1 14563 116 - 1
GCAAGGAAAAUUGUAGCAUAUGCGGCUGGCUAAUAAACCAAACGAAGUCAAACCGAAUGGAGUCGGGCCAAAAAAGCAAUGCAGACACUUGCC--GAUCCGGUCGCAGCUGCAAA--GCC
....((....(((((((...(((((((((........(((..((.........))..))).((((.((.......))...((((....)))))--))))))))))))))))))).--.)) ( -31.30)
>DroSim_CAF1 13693 116 - 1
GCAAGGAAAAUUGUAGCAUAUGCGGCUGGCUAAUAAACCAAACGAAGUCAAACCGAAUGGAGUCGGGCCAAAAAAGCAAUGCAGACACUUGCC--GAUCCGGUCGCAGCUGCAAA--GCC
....((....(((((((...(((((((((........(((..((.........))..))).((((.((.......))...((((....)))))--))))))))))))))))))).--.)) ( -31.30)
>DroEre_CAF1 14467 116 - 1
GCAAGGAAAAUCGUAGCAUAUGCGGCUGGCUAAUAAACCAAACGCAGUCAAACCGAAUGGAGUCGAGCCAAAAAAGCAAUGCAGACACUUGCC--GAUCCGGUCGCAGCAGCAAA--GCC
............((.((...((((..(((........)))..)))).......(((.((((.(((.((.......))...((((....)))))--)))))).)))..)).))...--... ( -25.50)
>DroYak_CAF1 10495 116 - 1
GCAAGGAAAAUUGUAGCAUAUGCGGCUGGCUAAUAAACCAAACGAAGUCAAACCGAAUGGAGUCGAGCUAAAAAAGCAAUGCAGACACUUGCC--GAUCCGGUCGCAGCUGCAAA--GCC
....((....(((((((...(((((((((........(((..((.........))..))).((((.(((.....)))...((((....)))))--))))))))))))))))))).--.)) ( -33.20)
>DroPer_CAF1 11540 91 - 1
GGAGAGAAAAUCGCAGCAUAUG----UGGCUAAUAAACCAGACCAAA--------------GCCCAG-----------GCCCAGGCACUUGCAGGGAGCCGGCCACAGCUGCAGUCAGCG
............(((((...((----(((((.........(......--------------...).(-----------((((..((....))..)).)))))))))))))))........ ( -29.10)
>consensus
GCAAGGAAAAUUGUAGCAUAUGCGGCUGGCUAAUAAACCAAACGAAGUCAAACCGAAUGGAGUCGAGCCAAAAAAGCAAUGCAGACACUUGCC__GAUCCGGUCGCAGCUGCAAA__GCC
....((....(((((((...(((((((((.......................((....)).(((..((............)).)))............))))))))))))))))....)) (-20.64 = -21.75 +   1.11)

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 11:36:47 2006