Locus 8293

Sequence ID 3R_DroMel_CAF1
Location 22,149,766 – 22,149,925
Length 159
Max. P 0.995425
window13373 window13374 window13375 window13376

overview

Window 3

Location 22,149,766 – 22,149,885
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.39
Mean single sequence MFE -35.20
Consensus MFE -31.06
Energy contribution -31.00
Covariance contribution -0.06
Combinations/Pair 1.09
Mean z-score -1.60
Structure conservation index 0.88
SVM decision value 0.53
SVM RNA-class probability 0.770049
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22149766 119 + 27905053
UGUCGGGGUUGCACAGAUUUGUUCUAGA-CCCCUCCGCAUUUUACCCUACGGCUGUGUGUUGCGUUUGUCGCACAAAUAACAGCAACACUUUGUGUGCAACUGCAUCUGCAGUUGCAUCU
....((((((....(((.....))).))-))))..................(((((.(((.(((.....))))))....)))))..........((((((((((....)))))))))).. ( -40.30)
>DroSec_CAF1 80215 120 + 1
UGUCGGUGUCGCACAGAUUUGUUCUAGCUCCCCUCCGCAUUUUACCCUACGGCUGUGUGUUGCGUUUGUCGCACAAAUAACAGCAACACUUUGUGUGCAGCUGCAUCUGCAGUUGCAUCU
....(((...(((((((..((((...((........)).............(((((.(((.(((.....))))))....))))))))).)))))))((((((((....))))))))))). ( -36.90)
>DroSim_CAF1 74690 114 + 1
UGUCGGUGUCGCACAGAUUUGUUCUAGCUCCCCUUCGCAUUUUACCCUACGGCUGUGUGUUGCGUUUGUCGCACAAAUAACAGCAACACUUUGUGUGCAGCU------GCAGUUGCAUCU
(((.(.((.((((((((..((((...((........)).............(((((.(((.(((.....))))))....))))))))).)))))))))).).------)))......... ( -29.90)
>DroYak_CAF1 73136 119 + 1
UGUCGGUGUCACACAGAUUUGUUCUAGACUCCCUGCGCAUUU-CCCCUACGGCUGUGUGUUGCGUUUGCCGUACAUAUAACAGCAACACUUUGUGUGCAGCUGCAUCUGCAGUUGCAUCU
.(((((((...))).((..(((..(((.....))).)))..)-).....))))...((((((((((............))).))))))).....((((((((((....)))))))))).. ( -33.70)
>consensus
UGUCGGUGUCGCACAGAUUUGUUCUAGAUCCCCUCCGCAUUUUACCCUACGGCUGUGUGUUGCGUUUGUCGCACAAAUAACAGCAACACUUUGUGUGCAGCUGCAUCUGCAGUUGCAUCU
..........(((((((..((((............((............))(((((.(((.(((.....))))))....))))))))).)))))))((((((((....)))))))).... (-31.06 = -31.00 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,149,766 – 22,149,885
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.39
Mean single sequence MFE -35.34
Consensus MFE -26.24
Energy contribution -27.55
Covariance contribution 1.31
Combinations/Pair 1.03
Mean z-score -1.73
Structure conservation index 0.74
SVM decision value 0.02
SVM RNA-class probability 0.544967
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22149766 119 - 27905053
AGAUGCAACUGCAGAUGCAGUUGCACACAAAGUGUUGCUGUUAUUUGUGCGACAAACGCAACACACAGCCGUAGGGUAAAAUGCGGAGGGG-UCUAGAACAAAUCUGUGCAACCCCGACA
...(((((((((....)))))))))......(((((((((((........))))...)))))))....(((((........))))).((((-(.....(((....)))...))))).... ( -41.80)
>DroSec_CAF1 80215 120 - 1
AGAUGCAACUGCAGAUGCAGCUGCACACAAAGUGUUGCUGUUAUUUGUGCGACAAACGCAACACACAGCCGUAGGGUAAAAUGCGGAGGGGAGCUAGAACAAAUCUGUGCGACACCGACA
...((((.((((....)))).))))......(((((((((((........))))...)))))))....(((((........))))).(((..((((((.....)))).))..).)).... ( -36.30)
>DroSim_CAF1 74690 114 - 1
AGAUGCAACUGC------AGCUGCACACAAAGUGUUGCUGUUAUUUGUGCGACAAACGCAACACACAGCCGUAGGGUAAAAUGCGAAGGGGAGCUAGAACAAAUCUGUGCGACACCGACA
.(.((((...((------(((.((((.....)))).)))))......)))).)...((((.......(((....)))....))))..(((..((((((.....)))).))..).)).... ( -30.00)
>DroYak_CAF1 73136 119 - 1
AGAUGCAACUGCAGAUGCAGCUGCACACAAAGUGUUGCUGUUAUAUGUACGGCAAACGCAACACACAGCCGUAGGGG-AAAUGCGCAGGGAGUCUAGAACAAAUCUGUGUGACACCGACA
...((((.((((....)))).)))).......(((((.((((...(.((((((..............)))))).)..-....(((((((..((.....))...))))))))))).))))) ( -33.24)
>consensus
AGAUGCAACUGCAGAUGCAGCUGCACACAAAGUGUUGCUGUUAUUUGUGCGACAAACGCAACACACAGCCGUAGGGUAAAAUGCGGAGGGGAGCUAGAACAAAUCUGUGCGACACCGACA
...((((.((((....)))).))))......(((((((((((........))))...)))))))....(((((........))))).(((..((((((.....)))).))..).)).... (-26.24 = -27.55 +   1.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 22,149,805 – 22,149,925
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -39.40
Consensus MFE -38.06
Energy contribution -38.62
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -3.23
Structure conservation index 0.97
SVM decision value 2.57
SVM RNA-class probability 0.995425
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22149805 120 + 27905053
UUUACCCUACGGCUGUGUGUUGCGUUUGUCGCACAAAUAACAGCAACACUUUGUGUGCAACUGCAUCUGCAGUUGCAUCUGGCAUGUUAUUUGCUGUCUGAUGAUACCUAAACCCAGCCC
..........(((((.((...(.(((..((((((((((((((((.((((...))))((((((((....)))))))).....)).))))))))).)))..))..).)))...)).))))). ( -41.90)
>DroSec_CAF1 80255 120 + 1
UUUACCCUACGGCUGUGUGUUGCGUUUGUCGCACAAAUAACAGCAACACUUUGUGUGCAGCUGCAUCUGCAGUUGCAUCUGGCAUGUUAUUUGCUGUCUGAUGAUACCUAAACCCAGCCC
..........(((((.((...(.(((..((((((((((((((((.((((...))))((((((((....)))))))).....)).))))))))).)))..))..).)))...)).))))). ( -41.90)
>DroSim_CAF1 74730 114 + 1
UUUACCCUACGGCUGUGUGUUGCGUUUGUCGCACAAAUAACAGCAACACUUUGUGUGCAGCU------GCAGUUGCAUCUGGCAUGUUAUUUGCUGUCUGAUGAUACCUAAACCCAGCCC
..........(((((.((...(.(((..((((((((((((((((..(((.....)))(((.(------((....))).))))).))))))))).)))..))..).)))...)).))))). ( -34.40)
>DroYak_CAF1 73176 119 + 1
UU-CCCCUACGGCUGUGUGUUGCGUUUGCCGUACAUAUAACAGCAACACUUUGUGUGCAGCUGCAUCUGCAGUUGCAUCUGGCAUGUUAUUUGCUGUCUGAUGAUACCUAAACCCAGCCC
..-.......(((((.((((((((((............))).)))))))...((((((((((((....))))))))(((.((((.((.....)))))).))).)))).......))))). ( -39.40)
>consensus
UUUACCCUACGGCUGUGUGUUGCGUUUGUCGCACAAAUAACAGCAACACUUUGUGUGCAGCUGCAUCUGCAGUUGCAUCUGGCAUGUUAUUUGCUGUCUGAUGAUACCUAAACCCAGCCC
..........(((((.((((((((((((.....)))))....)))))))...((((((((((((....))))))))(((.((((.((.....)))))).))).)))).......))))). (-38.06 = -38.62 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 22,149,805 – 22,149,925
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -36.60
Consensus MFE -32.40
Energy contribution -33.15
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.89
SVM decision value 1.03
SVM RNA-class probability 0.902963
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22149805 120 - 27905053
GGGCUGGGUUUAGGUAUCAUCAGACAGCAAAUAACAUGCCAGAUGCAACUGCAGAUGCAGUUGCACACAAAGUGUUGCUGUUAUUUGUGCGACAAACGCAACACACAGCCGUAGGGUAAA
.(((((.(((................((((((((((.((.....((((((((....))))))))((((...)))).))))))))))))(((.....))))))...))))).......... ( -40.70)
>DroSec_CAF1 80255 120 - 1
GGGCUGGGUUUAGGUAUCAUCAGACAGCAAAUAACAUGCCAGAUGCAACUGCAGAUGCAGCUGCACACAAAGUGUUGCUGUUAUUUGUGCGACAAACGCAACACACAGCCGUAGGGUAAA
.(((((.(((................((((((((((.((.....(((.((((....)))).)))((((...)))).))))))))))))(((.....))))))...))))).......... ( -36.50)
>DroSim_CAF1 74730 114 - 1
GGGCUGGGUUUAGGUAUCAUCAGACAGCAAAUAACAUGCCAGAUGCAACUGC------AGCUGCACACAAAGUGUUGCUGUUAUUUGUGCGACAAACGCAACACACAGCCGUAGGGUAAA
.(((((.(((................((((((((((.(((((.(((....))------).)))(((.....)))..))))))))))))(((.....))))))...))))).......... ( -32.40)
>DroYak_CAF1 73176 119 - 1
GGGCUGGGUUUAGGUAUCAUCAGACAGCAAAUAACAUGCCAGAUGCAACUGCAGAUGCAGCUGCACACAAAGUGUUGCUGUUAUAUGUACGGCAAACGCAACACACAGCCGUAGGGG-AA
.(((((.(((...(((.(((..(((((((....((((......((((.((((....)))).))))......)))))))))))..)))))).((....)))))...))))).......-.. ( -36.80)
>consensus
GGGCUGGGUUUAGGUAUCAUCAGACAGCAAAUAACAUGCCAGAUGCAACUGCAGAUGCAGCUGCACACAAAGUGUUGCUGUUAUUUGUGCGACAAACGCAACACACAGCCGUAGGGUAAA
.(((((................(((((((....((((......((((.((((....)))).))))......)))))))))))...((((((.....))).)))..))))).......... (-32.40 = -33.15 +   0.75)

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 13:08:08 2006