Locus 9757

Sequence ID 3R_DroMel_CAF1
Location 25,847,471 – 25,847,814
Length 343
Max. P 0.993196
window15584 window15585 window15586 window15587 window15588

overview

Window 4

Location 25,847,471 – 25,847,589
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.76
Mean single sequence MFE -41.26
Consensus MFE -35.44
Energy contribution -35.25
Covariance contribution -0.19
Combinations/Pair 1.14
Mean z-score -1.79
Structure conservation index 0.86
SVM decision value 0.78
SVM RNA-class probability 0.848649
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25847471 118 - 27905053
AGUGACGGAUUCGAUUCCCCGGGGAAUCCU-ACCAAUUAGUGCAAAUUCCGA-AAUGCACGGAAAAGCGAACGAAAGCUGCGAAUUCGUUACACUGCUGCACUUGGACUUUUCGGGGCGC
.(((((((((((((((((....))))))..-..........((...(((((.-......))))).(((........))))))))))))))))...((.((.((((((...)))))))))) ( -39.20)
>DroSec_CAF1 1914 118 - 1
AGUGACGGACUCGAUUCCCCGGGGAAUCCC-CCCAAUUUGUGCAUAAUCCGA-AAUGCGCGGAAAAGCGAACGAAAGCUGCGAAUUCGUUACACUGCUGCACUUGGACUUUUCGGGGCGC
.((((((((.(((.((((..((((.....)-))).....((((((.......-.)))))))))).(((........))).))).))))))))...((.((.((((((...)))))))))) ( -40.30)
>DroSim_CAF1 1896 119 - 1
AGUGACGGAUUCGAUUCCCCGGGGAAUCCCCCCCAAUUAGUGCAUAAUUCGA-AAUGCGCGGAAAAGCGAACGAAAGCUGCGAAUUCGUUACACUGCUGCACUUGGACUUUUCGGGGCGC
.((((((((((((.((((..((((......)))).....((((((.......-.)))))))))).(((........))).))))))))))))...((.((.((((((...)))))))))) ( -44.40)
>DroYak_CAF1 100 116 - 1
AGUGACGAAUUCGAUUCCCCGGGGAAUCCC-CCCAAGUGGUGUAUAUUCCGAAAAUGCGCGGUAAAGCGGACGAAAGCUGCGAAUUCGUUAC---GCUGCAUUUGAACUUUUGGGGGCGC
.(((((((((((..((..((((((.....)-))).....((((((.........))))))))..))((((.(....))))))))))))))))---(((.(.............).))).. ( -41.12)
>consensus
AGUGACGGAUUCGAUUCCCCGGGGAAUCCC_CCCAAUUAGUGCAUAAUCCGA_AAUGCGCGGAAAAGCGAACGAAAGCUGCGAAUUCGUUACACUGCUGCACUUGGACUUUUCGGGGCGC
.(((((((((((((((((....))))))...........((((((.........))))))......(((..(....).))))))))))))))...((.((.((((((...)))))))))) (-35.44 = -35.25 +  -0.19)

alignment

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secondary structure

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Window 5

Location 25,847,589 – 25,847,694
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.33
Mean single sequence MFE -28.75
Consensus MFE -20.49
Energy contribution -23.55
Covariance contribution 3.06
Combinations/Pair 1.03
Mean z-score -1.77
Structure conservation index 0.71
SVM decision value 0.16
SVM RNA-class probability 0.611995
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25847589 105 + 27905053
UUUAAUCCUGUUUGCUGUUCUUUUCGCACU------------CGCUUUUGUUUUUGCAAUGCAG---GCUCCUGCACUUGCGGUACACACACAUACCAGCAGCUGCUACGGCCGCCGCUG
........(((.((((((.......(((..------------.((....))...)))..(((((---....)))))...)))))).))).......((((.((.((....)).)).)))) ( -30.30)
>DroSec_CAF1 2032 105 + 1
UUUAGUCCUGUUUGCUGUUCUUUUCGCACU------------CGCUUUUGUUUUUGCAAUGCAG---GCUCCUGCACUUGCGGUACACACACAUACCAGCAGCUGCUACGGCCGCCGCUG
........(((.((((((.......(((..------------.((....))...)))..(((((---....)))))...)))))).))).......((((.((.((....)).)).)))) ( -30.30)
>DroSim_CAF1 2015 105 + 1
UUUAGUCCUGUUUGCUGUUCUUUUCGCACU------------CGCUUUUGUUUUUGCAAUGCAG---GCUCCUGCACUUGCGGUACACACACAUACCAGCAGCUGCUACGGCCGCCGCUG
........(((.((((((.......(((..------------.((....))...)))..(((((---....)))))...)))))).))).......((((.((.((....)).)).)))) ( -30.30)
>DroYak_CAF1 216 120 + 1
UUUAGUCCUGUUUCUUGUUUGUUUCGCACUUUACGCACUUUUCACUUUUGUUUUUGCAAUGCAAAAUGCUCCUGCACUUGCGAUACACACACAUACCAACAGCUGCUACGGCCGCCGCUG
..((((.(((((...(((.(((.(((((.......................((((((...))))))(((....)))..)))))...))).)))....)))))..))))((((....)))) ( -24.10)
>consensus
UUUAGUCCUGUUUGCUGUUCUUUUCGCACU____________CGCUUUUGUUUUUGCAAUGCAG___GCUCCUGCACUUGCGGUACACACACAUACCAGCAGCUGCUACGGCCGCCGCUG
........(((.((.(((.....(((((...................((((....))))(((((.......)))))..))))).))))).)))...((((.((.((....)).)).)))) (-20.49 = -23.55 +   3.06)

alignment

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secondary structure

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Window 6

Location 25,847,589 – 25,847,694
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.33
Mean single sequence MFE -33.85
Consensus MFE -27.62
Energy contribution -27.12
Covariance contribution -0.50
Combinations/Pair 1.13
Mean z-score -2.43
Structure conservation index 0.82
SVM decision value 1.49
SVM RNA-class probability 0.958124
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25847589 105 - 27905053
CAGCGGCGGCCGUAGCAGCUGCUGGUAUGUGUGUGUACCGCAAGUGCAGGAGC---CUGCAUUGCAAAAACAAAAGCG------------AGUGCGAAAAGAACAGCAAACAGGAUUAAA
(((((((.((....)).)))))))((.(((((.((((((((.(((((((....---)))))))(......)....)))------------.)))))......))).)).))......... ( -33.90)
>DroSec_CAF1 2032 105 - 1
CAGCGGCGGCCGUAGCAGCUGCUGGUAUGUGUGUGUACCGCAAGUGCAGGAGC---CUGCAUUGCAAAAACAAAAGCG------------AGUGCGAAAAGAACAGCAAACAGGACUAAA
(((((((.((....)).)))))))((.(((((.((((((((.(((((((....---)))))))(......)....)))------------.)))))......))).)).))......... ( -33.90)
>DroSim_CAF1 2015 105 - 1
CAGCGGCGGCCGUAGCAGCUGCUGGUAUGUGUGUGUACCGCAAGUGCAGGAGC---CUGCAUUGCAAAAACAAAAGCG------------AGUGCGAAAAGAACAGCAAACAGGACUAAA
(((((((.((....)).)))))))((.(((((.((((((((.(((((((....---)))))))(......)....)))------------.)))))......))).)).))......... ( -33.90)
>DroYak_CAF1 216 120 - 1
CAGCGGCGGCCGUAGCAGCUGUUGGUAUGUGUGUGUAUCGCAAGUGCAGGAGCAUUUUGCAUUGCAAAAACAAAAGUGAAAAGUGCGUAAAGUGCGAAACAAACAAGAAACAGGACUAAA
(((((((.((....)).)))))))((...(((.(((.(((((..(((....(((((((.((((...........)))).))))))))))...))))).))).)))....))......... ( -33.70)
>consensus
CAGCGGCGGCCGUAGCAGCUGCUGGUAUGUGUGUGUACCGCAAGUGCAGGAGC___CUGCAUUGCAAAAACAAAAGCG____________AGUGCGAAAAGAACAGCAAACAGGACUAAA
(((((((.((....)).)))))))((.(((.(((....(((((((((((.......)))))))((..........))...............))))......)))))).))......... (-27.62 = -27.12 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 25,847,654 – 25,847,774
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -55.21
Consensus MFE -52.75
Energy contribution -53.19
Covariance contribution 0.44
Combinations/Pair 1.07
Mean z-score -2.87
Structure conservation index 0.96
SVM decision value 2.38
SVM RNA-class probability 0.993196
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25847654 120 - 27905053
AAUGCGCGCGGCAGUGGGUUGAAGCGAGACGGGUAGAGCUAGAGAGAUGCCCGUUUGCCCGCUGUGCGUGUGUGUGUGUGCAGCGGCGGCCGUAGCAGCUGCUGGUAUGUGUGUGUACCG
.((((((((((((((((((.......(((((((((...((....)).)))))))))))))))))).)))))))))....(((((.((.......)).))))).(((((......))))). ( -55.31)
>DroSec_CAF1 2097 120 - 1
AAUGCGCGCGGCAGUGGGUUGAAGCGAGACGGGUAGAGCUAGAGCGAUGCCCGUUUGCCCGCUGUGCGUGUGUGUGUGUGCAGCGGCGGCCGUAGCAGCUGCUGGUAUGUGUGUGUACCG
.((((((((((((((((((.......(((((((((..((....))..)))))))))))))))))).)))))))))....(((((.((.......)).))))).(((((......))))). ( -59.11)
>DroSim_CAF1 2080 120 - 1
AAUGCGCGCGGCAGUGGGUUGAAGCGAGACGGGUAGAGCUAGAGCGAUGCCCGUUUGCCCGCUGUGCGUGUGUGUGUGUGCAGCGGCGGCCGUAGCAGCUGCUGGUAUGUGUGUGUACCG
.((((((((((((((((((.......(((((((((..((....))..)))))))))))))))))).)))))))))....(((((.((.......)).))))).(((((......))))). ( -59.11)
>DroYak_CAF1 296 114 - 1
AAUGCGCACGGCAGUGGGUUGAAGCGAGACGGGAAUA------GCGAUGCCCGUUUGCCCGCUGUGCGUGUGUGUGUGUGCAGCGGCGGCCGUAGCAGCUGUUGGUAUGUGUGUGUAUCG
.((((((((((((((((((.......(((((((.((.------...)).)))))))))))))))).)))))))))(..(((((((((.((....)).)))))).)))..).......... ( -47.31)
>consensus
AAUGCGCGCGGCAGUGGGUUGAAGCGAGACGGGUAGAGCUAGAGCGAUGCCCGUUUGCCCGCUGUGCGUGUGUGUGUGUGCAGCGGCGGCCGUAGCAGCUGCUGGUAUGUGUGUGUACCG
.((((((((((((((((((.......(((((((((..((....))..)))))))))))))))))).)))))))))....(((((.((.......)).))))).(((((......))))). (-52.75 = -53.19 +   0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 25,847,694 – 25,847,814
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.92
Mean single sequence MFE -43.04
Consensus MFE -38.77
Energy contribution -39.59
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -2.89
Structure conservation index 0.90
SVM decision value 2.28
SVM RNA-class probability 0.991593
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25847694 120 - 27905053
AUAAAUCAAGCGAAGUAGCAACAAAUGCGGGAAAUGUGAAAAUGCGCGCGGCAGUGGGUUGAAGCGAGACGGGUAGAGCUAGAGAGAUGCCCGUUUGCCCGCUGUGCGUGUGUGUGUGUG
.....(((.........(((.....)))........)))..((((((((((((((((((.......(((((((((...((....)).)))))))))))))))))).)))))))))..... ( -41.84)
>DroSec_CAF1 2137 120 - 1
AUAAAUCCAGCGAAGUAGCAACAAAAGCGGGAAAUGUGAAAAUGCGCGCGGCAGUGGGUUGAAGCGAGACGGGUAGAGCUAGAGCGAUGCCCGUUUGCCCGCUGUGCGUGUGUGUGUGUG
.....(((.((...((....))....)).))).........((((((((((((((((((.......(((((((((..((....))..)))))))))))))))))).)))))))))..... ( -47.21)
>DroSim_CAF1 2120 120 - 1
AUAAAUCAAGCGAAGUAGCAACAAAAGCGGGAAAUGUGAAAAUGCGCGCGGCAGUGGGUUGAAGCGAGACGGGUAGAGCUAGAGCGAUGCCCGUUUGCCCGCUGUGCGUGUGUGUGUGUG
.....((..((...((....))....))..)).........((((((((((((((((((.......(((((((((..((....))..)))))))))))))))))).)))))))))..... ( -45.01)
>DroYak_CAF1 336 114 - 1
GUGAAUCAAGCGGAGUGACAACAAAAGCGGGAAAUGUGAAAAUGCGCACGGCAGUGGGUUGAAGCGAGACGGGAAUA------GCGAUGCCCGUUUGCCCGCUGUGCGUGUGUGUGUGUG
.....((..((...((....))....))..)).........((((((((((((((((((.......(((((((.((.------...)).)))))))))))))))).)))))))))..... ( -38.11)
>consensus
AUAAAUCAAGCGAAGUAGCAACAAAAGCGGGAAAUGUGAAAAUGCGCGCGGCAGUGGGUUGAAGCGAGACGGGUAGAGCUAGAGCGAUGCCCGUUUGCCCGCUGUGCGUGUGUGUGUGUG
.....((..((...((....))....))..)).........((((((((((((((((((.......(((((((((..((....))..)))))))))))))))))).)))))))))..... (-38.77 = -39.59 +   0.81)

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 13:41:31 2006