Locus 2456

Sequence ID X_DroMel_CAF1
Location 6,569,622 – 6,569,858
Length 236
Max. P 0.999262
window4005 window4006 window4007 window4008 window4009

overview

Window 5

Location 6,569,622 – 6,569,738
Length 116
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 93.56
Mean single sequence MFE -18.55
Consensus MFE -16.80
Energy contribution -16.43
Covariance contribution -0.37
Combinations/Pair 1.08
Mean z-score -1.41
Structure conservation index 0.91
SVM decision value 0.10
SVM RNA-class probability 0.581951
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6569622 116 - 22224390
CCAAUUGCGUUAAAUUAACCCACUUUUCUCCCCCAUGUCGAAACAAUCGAUCGAUAGAACGAUCGAUCUGUGGUUAGCAAAUCGAUAACACUCGCCAUCUCCUUCCUUCUCUCAUU
....((((((((...))))((((............(((....)))((((((((......))))))))..))))...))))..(((......)))...................... ( -18.20)
>DroSec_CAF1 14551 111 - 1
CCAAUUGCGUUAAAUUAACCCACUUUUCUCU-CCAUGUCGAAACAAUCGAUCGAUAGAACGAUCGAUCUGUGGUUAGCCAAUCGAUAACACUCGCCAUCUCC----UUCUCUCAUU
......((((((...))))............-...((((((.(((((((((((......)))))))).)))((....))..))))))......)).......----.......... ( -20.50)
>DroSim_CAF1 25106 111 - 1
CCAAUUGCGUUAAAUUAACCCACUUUUCUCU-CCAUGUCAAAACAAUCGAUCGAUAGAACGAUCGAUCUGUGGUUAGCCAAUCGAUAACACUCGCCAUCUCC----UUCUCUCAUU
.(.((((.(((((......((((........-...(((....)))((((((((......))))))))..))))))))))))).)..................----.......... ( -17.80)
>DroEre_CAF1 14246 110 - 1
CCAAUUGCGUUAAAUUAACCCACUUUCCUC--CCAUGUCGAAGCAAUCGAUCGAUAGAACGAUCGAUCUGUGGUUAACAAAUCGAUAACACUCGCCAUCCC----UUUCUCUCAUU
......((((((...))))...........--...((((((.(((((((((((......)))))))).)))(.....)...))))))......))......----........... ( -17.70)
>consensus
CCAAUUGCGUUAAAUUAACCCACUUUUCUCU_CCAUGUCGAAACAAUCGAUCGAUAGAACGAUCGAUCUGUGGUUAGCAAAUCGAUAACACUCGCCAUCUCC____UUCUCUCAUU
......(((((((......((((............(((....)))((((((((......))))))))..))))))))).....((......))))..................... (-16.80 = -16.43 +  -0.37)

alignment

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secondary structure

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Window 6

Location 6,569,659 – 6,569,778
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.60
Mean single sequence MFE -34.46
Consensus MFE -27.72
Energy contribution -27.40
Covariance contribution -0.32
Combinations/Pair 1.12
Mean z-score -1.71
Structure conservation index 0.80
SVM decision value 0.65
SVM RNA-class probability 0.810115
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6569659 119 + 22224390
UGC-UAACCACAGAUCGAUCGUUCUAUCGAUCGAUUGUUUCGACAUGGGGGAGAAAAGUGGGUUAAUUUAACGCAAUUGGGCGGCAAUUGAGCAGAAUGAAUGAACGAUCUGUUCGUCGC
(((-...((((.(((((((((......))))))))).((((..(.....)..)))).))))((((...))))))).....(((((....(((((((.((......)).)))))))))))) ( -37.30)
>DroSec_CAF1 14584 118 + 1
GGC-UAACCACAGAUCGAUCGUUCUAUCGAUCGAUUGUUUCGACAUGG-AGAGAAAAGUGGGUUAAUUUAACGCAAUUGGGAGGCAAUUGAGCAGAAUGAAUGAACGAUCUGUUCGUCGC
(((-.....((((((((.((((((..((..(((((((((((..((...-.........((.((((...)))).))..)).)))))))))))...))..)))))).))))))))..))).. ( -35.84)
>DroSim_CAF1 25139 118 + 1
GGC-UAACCACAGAUCGAUCGUUCUAUCGAUCGAUUGUUUUGACAUGG-AGAGAAAAGUGGGUUAAUUUAACGCAAUUGGGAGGCAAUUGAGCAGAAUGAAUGAACGAUCUGUUCGUCGC
(((-.....((((((((.((((((..((..(((((((((((..((...-.........((.((((...)))).))..)).)))))))))))...))..)))))).))))))))..))).. ( -33.94)
>DroEre_CAF1 14279 117 + 1
UGU-UAACCACAGAUCGAUCGUUCUAUCGAUCGAUUGCUUCGACAUGG--GAGGAAAGUGGGUUAAUUUAACGCAAUUGGGCGGCAAUUGAGCAGAAUGAAUGAACGAUCUAUUCAUCGC
...-...((((.(((((((((......))))))))).((((......)--)))....)))).((((((...(((......)))..))))))((.((.((((((.......)))))))))) ( -31.00)
>DroYak_CAF1 24175 117 + 1
UGUUUAAUCAGAGAUCGAUCGUUGUAUCGAUCGAUU-UUUCGACAUGG--GAGGAAAGUGGGUUAAUUUAACGCAAUUGGUCGGCAAUUGAGCAGAAUGAAUGAACGAUCUGUUCGUCGC
.........((((((((((((......)))))))))-)))((((....--.......((.(..(((((......)))))..).))....(((((((.((......)).))))))))))). ( -34.20)
>consensus
UGC_UAACCACAGAUCGAUCGUUCUAUCGAUCGAUUGUUUCGACAUGG__GAGAAAAGUGGGUUAAUUUAACGCAAUUGGGCGGCAAUUGAGCAGAAUGAAUGAACGAUCUGUUCGUCGC
.......((((.(((((((((......))))))))).((((.........))))...))))...........(((((((.....)))))(((((((.((......)).)))))))...)) (-27.72 = -27.40 +  -0.32)

alignment

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secondary structure

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Window 7

Location 6,569,659 – 6,569,778
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.60
Mean single sequence MFE -26.58
Consensus MFE -23.26
Energy contribution -23.18
Covariance contribution -0.08
Combinations/Pair 1.10
Mean z-score -1.73
Structure conservation index 0.88
SVM decision value 1.68
SVM RNA-class probability 0.971651
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6569659 119 - 22224390
GCGACGAACAGAUCGUUCAUUCAUUCUGCUCAAUUGCCGCCCAAUUGCGUUAAAUUAACCCACUUUUCUCCCCCAUGUCGAAACAAUCGAUCGAUAGAACGAUCGAUCUGUGGUUA-GCA
(((((..((((((((.((.((((((..((.((((((.....)))))).))..)))....................((((((.........))))))))).)).)))))))).))).-)). ( -29.40)
>DroSec_CAF1 14584 118 - 1
GCGACGAACAGAUCGUUCAUUCAUUCUGCUCAAUUGCCUCCCAAUUGCGUUAAAUUAACCCACUUUUCUCU-CCAUGUCGAAACAAUCGAUCGAUAGAACGAUCGAUCUGUGGUUA-GCC
(((((..((((((((.((.((((((..((.((((((.....)))))).))..)))................-...((((((.........))))))))).)).)))))))).))).-)). ( -28.50)
>DroSim_CAF1 25139 118 - 1
GCGACGAACAGAUCGUUCAUUCAUUCUGCUCAAUUGCCUCCCAAUUGCGUUAAAUUAACCCACUUUUCUCU-CCAUGUCAAAACAAUCGAUCGAUAGAACGAUCGAUCUGUGGUUA-GCC
(((((((((.....))))....(((..((.((((((.....)))))).))..)))................-....)))...(((((((((((......)))))))).))).....-)). ( -25.50)
>DroEre_CAF1 14279 117 - 1
GCGAUGAAUAGAUCGUUCAUUCAUUCUGCUCAAUUGCCGCCCAAUUGCGUUAAAUUAACCCACUUUCCUC--CCAUGUCGAAGCAAUCGAUCGAUAGAACGAUCGAUCUGUGGUUA-ACA
..(((((((.((....)))))))))..((.((((((.....)))))).))....((((((....(((..(--....)..)))(((((((((((......)))))))).))))))))-).. ( -25.80)
>DroYak_CAF1 24175 117 - 1
GCGACGAACAGAUCGUUCAUUCAUUCUGCUCAAUUGCCGACCAAUUGCGUUAAAUUAACCCACUUUCCUC--CCAUGUCGAAA-AAUCGAUCGAUACAACGAUCGAUCUCUGAUUAAACA
.((((((((.....))))....(((..((.((((((.....)))))).))..)))...............--....))))...-.((((((((......))))))))............. ( -23.70)
>consensus
GCGACGAACAGAUCGUUCAUUCAUUCUGCUCAAUUGCCGCCCAAUUGCGUUAAAUUAACCCACUUUUCUC__CCAUGUCGAAACAAUCGAUCGAUAGAACGAUCGAUCUGUGGUUA_GCA
.((((((((.....))))....(((..((.((((((.....)))))).))..))).....................))))..(((((((((((......)))))))).)))......... (-23.26 = -23.18 +  -0.08)

alignment

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secondary structure

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Window 8

Location 6,569,738 – 6,569,858
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.50
Mean single sequence MFE -35.28
Consensus MFE -31.30
Energy contribution -31.70
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.62
Structure conservation index 0.89
SVM decision value 3.36
SVM RNA-class probability 0.999081
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6569738 120 + 22224390
GCGGCAAUUGAGCAGAAUGAAUGAACGAUCUGUUCGUCGCGCCCAAGCGACAUCGUAAUUGAUUAAUAAAAAAUUAUGCCCGAAAUAGUCGCGGGCACUGAAAUUAACCGUAAGUGCCGA
(((((....(((((((.((......)).)))))))(((((......)))))..(((((((...........))))))).........))))).((((((.............)))))).. ( -38.52)
>DroSec_CAF1 14662 120 + 1
GAGGCAAUUGAGCAGAAUGAAUGAACGAUCUGUUCGUCGCGCACAAGCGACAUCGUAAUUGAUUAAUAAAAAAUUAUGCCCGAAAUAGUCGCGGGCACUGAAAUUAACCGUAAGUGCCGA
..((((...(((((((.((......)).)))))))(((((......))))).((((((((...........))))))(((((.........)))))...)).............)))).. ( -34.60)
>DroSim_CAF1 25217 120 + 1
GAGGCAAUUGAGCAGAAUGAAUGAACGAUCUGUUCGUCGCGCCCAGGCGACAUUGUAAUUGAUUAAUAAAAAAUUAUGCCCGAAAUAGUCGCGGGCACUGAAAUUAACCGUAAGUGCCGA
..((((...(((((((.((......)).)))))))(((((......))))).........................((((((.........)))))).................)))).. ( -33.70)
>DroEre_CAF1 14356 118 + 1
GCGGCAAUUGAGCAGAAUGAAUGAACGAUCUAUUCAUCGCGCCCAAGCGACAUCGUAAUUGAUUAAUAAAAAAUUAUGCCCGAAAUAGUC--GGGCACUGAAAUUAACCGUAAGUGCCGA
.(((((.((((.((((((.(((..(((((.......((((......)))).))))).))).)))............(((((((.....))--))))))))...)))).(....)))))). ( -32.20)
>DroYak_CAF1 24252 120 + 1
UCGGCAAUUGAGCAGAAUGAAUGAACGAUCUGUUCGUCGCGCCCAAGCGACAACGUAAUUGAUUAAUAAAAAAUUAUGCCCGAAAUAGUCGCGGGCACUGAAAUUAACCGUAAGUGCCGA
((((((...(((((((.((......)).)))))))(((((......))))).((((((((...........)))))((((((.........))))))...........)))...)))))) ( -37.40)
>consensus
GCGGCAAUUGAGCAGAAUGAAUGAACGAUCUGUUCGUCGCGCCCAAGCGACAUCGUAAUUGAUUAAUAAAAAAUUAUGCCCGAAAUAGUCGCGGGCACUGAAAUUAACCGUAAGUGCCGA
..((((...(((((((.((......)).)))))))(((((......))))).........................)))).............((((((.............)))))).. (-31.30 = -31.70 +   0.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,569,738 – 6,569,858
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.50
Mean single sequence MFE -34.20
Consensus MFE -30.92
Energy contribution -30.80
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -2.49
Structure conservation index 0.90
SVM decision value 3.47
SVM RNA-class probability 0.999262
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6569738 120 - 22224390
UCGGCACUUACGGUUAAUUUCAGUGCCCGCGACUAUUUCGGGCAUAAUUUUUUAUUAAUCAAUUACGAUGUCGCUUGGGCGCGACGAACAGAUCGUUCAUUCAUUCUGCUCAAUUGCCGC
.(((((.....(((((((....(((((((.........)))))))........))))))).........(((((......)))))((.((((..(......)..)))).))...))))). ( -33.40)
>DroSec_CAF1 14662 120 - 1
UCGGCACUUACGGUUAAUUUCAGUGCCCGCGACUAUUUCGGGCAUAAUUUUUUAUUAAUCAAUUACGAUGUCGCUUGUGCGCGACGAACAGAUCGUUCAUUCAUUCUGCUCAAUUGCCUC
..((((.....(((((((....(((((((.........)))))))........))))))).........(((((......)))))((.((((..(......)..)))).))...)))).. ( -32.00)
>DroSim_CAF1 25217 120 - 1
UCGGCACUUACGGUUAAUUUCAGUGCCCGCGACUAUUUCGGGCAUAAUUUUUUAUUAAUCAAUUACAAUGUCGCCUGGGCGCGACGAACAGAUCGUUCAUUCAUUCUGCUCAAUUGCCUC
..((((.....(((((((....(((((((.........)))))))........))))))).........(((((......)))))((.((((..(......)..)))).))...)))).. ( -31.50)
>DroEre_CAF1 14356 118 - 1
UCGGCACUUACGGUUAAUUUCAGUGCCC--GACUAUUUCGGGCAUAAUUUUUUAUUAAUCAAUUACGAUGUCGCUUGGGCGCGAUGAAUAGAUCGUUCAUUCAUUCUGCUCAAUUGCCGC
.(((((.....(((((((....((((((--((.....))))))))........)))))))..............(((((((.(((((((.((....))))))))).))))))).))))). ( -38.90)
>DroYak_CAF1 24252 120 - 1
UCGGCACUUACGGUUAAUUUCAGUGCCCGCGACUAUUUCGGGCAUAAUUUUUUAUUAAUCAAUUACGUUGUCGCUUGGGCGCGACGAACAGAUCGUUCAUUCAUUCUGCUCAAUUGCCGA
((((((.....(((((((....(((((((.........)))))))........)))))))......((((.(((....)))))))((.((((..(......)..)))).))...)))))) ( -35.20)
>consensus
UCGGCACUUACGGUUAAUUUCAGUGCCCGCGACUAUUUCGGGCAUAAUUUUUUAUUAAUCAAUUACGAUGUCGCUUGGGCGCGACGAACAGAUCGUUCAUUCAUUCUGCUCAAUUGCCGC
..((((.....(((((((....(((((((.........)))))))........))))))).........(((((......)))))((.((((..(......)..)))).))...)))).. (-30.92 = -30.80 +  -0.12)

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 10:35:09 2006