Locus 8761

Sequence ID 3R_DroMel_CAF1
Location 23,384,841 – 23,384,971
Length 130
Max. P 0.991888
window14069 window14070 window14071 window14072

overview

Window 9

Location 23,384,841 – 23,384,949
Length 108
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 84.72
Mean single sequence MFE -33.84
Consensus MFE -29.58
Energy contribution -29.96
Covariance contribution 0.38
Combinations/Pair 1.12
Mean z-score -2.00
Structure conservation index 0.87
SVM decision value 1.22
SVM RNA-class probability 0.932048
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23384841 108 + 27905053
GUUCAUCGUUCGACUCGGUGUGACCGUUCGCAGAACAGUGCUAAUAAACUGCGGAGUUACACACUCGCCUUCUGGCAGUGCGGUCACACCAAUUCGAUGUUUUCAACA
(((......((((...(((((((((((((((((...............)))))))......((((.(((....)))))))))))))))))...)))).......))). ( -39.88)
>DroSec_CAF1 10442 108 + 1
GUUCAUCGUUCGACUCGGUGUGACCGUUCGCAGAACAGUGCUAAUAAACUGCGGAGUUACACACUCGCUUUAUGGCAGUGCGUUCACACCAUUUCUAUGUAUUCAACA
................(((((((.(((((((((...............)))))))......((((.(((....))))))))).))))))).................. ( -27.56)
>DroSim_CAF1 10664 108 + 1
GUUCAUCGUUCGACUCGGUGUGACCGUUCGCAGGAUAGUGCCAAUAAACUGCGGAGUUACACACUCGCCUUCUGGCAGUGCGGUCACACCAUUUCUAUGUUUUCAACA
................(((((((((((((((((..((.......))..)))))))......((((.(((....))))))))))))))))).................. ( -38.80)
>DroYak_CAF1 10594 106 + 1
GUUCAUCGUUCGACUCAGUGUGACCGUUCAGAGGGCAGUGU-GUUUAGCCGUGGAGUUUACCACUUGCG-UCUAACAGUGCGGUCACACUCAUUCUAUGUUUUCAGUA
...........((.(.(((((((((...(....)(((.(((-.....((.((((......))))..)).-....))).)))))))))))).).))............. ( -29.10)
>consensus
GUUCAUCGUUCGACUCGGUGUGACCGUUCGCAGAACAGUGCUAAUAAACUGCGGAGUUACACACUCGCCUUCUGGCAGUGCGGUCACACCAAUUCUAUGUUUUCAACA
................(((((((((((((((((...............)))))))......((((.(((....))))))))))))))))).................. (-29.58 = -29.96 +   0.38)

alignment

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secondary structure

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dotplot

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Window 0

Location 23,384,841 – 23,384,949
Length 108
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 84.72
Mean single sequence MFE -36.60
Consensus MFE -30.17
Energy contribution -30.43
Covariance contribution 0.25
Combinations/Pair 1.19
Mean z-score -2.79
Structure conservation index 0.82
SVM decision value 2.29
SVM RNA-class probability 0.991888
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23384841 108 - 27905053
UGUUGAAAACAUCGAAUUGGUGUGACCGCACUGCCAGAAGGCGAGUGUGUAACUCCGCAGUUUAUUAGCACUGUUCUGCGAACGGUCACACCGAGUCGAACGAUGAAC
...........((((.(((((((((((((((((((....))).))))).......(((((..((.......))..)))))...))))))))))).))))......... ( -43.10)
>DroSec_CAF1 10442 108 - 1
UGUUGAAUACAUAGAAAUGGUGUGAACGCACUGCCAUAAAGCGAGUGUGUAACUCCGCAGUUUAUUAGCACUGUUCUGCGAACGGUCACACCGAGUCGAACGAUGAAC
.........(((.((..(((((((((((((((((......)).))))))).....(((((..((.......))..))))).....))))))))..)).....)))... ( -31.90)
>DroSim_CAF1 10664 108 - 1
UGUUGAAAACAUAGAAAUGGUGUGACCGCACUGCCAGAAGGCGAGUGUGUAACUCCGCAGUUUAUUGGCACUAUCCUGCGAACGGUCACACCGAGUCGAACGAUGAAC
.........(((.((..((((((((((((((((((....))).))))).......(((((..((.......))..)))))...))))))))))..)).....)))... ( -39.40)
>DroYak_CAF1 10594 106 - 1
UACUGAAAACAUAGAAUGAGUGUGACCGCACUGUUAGA-CGCAAGUGGUAAACUCCACGGCUAAAC-ACACUGCCCUCUGAACGGUCACACUGAGUCGAACGAUGAAC
.........(((.((.(.((((((((((.....(((((-.....((((......))))(((.....-.....))).))))).)))))))))).).)).....)))... ( -32.00)
>consensus
UGUUGAAAACAUAGAAAUGGUGUGACCGCACUGCCAGAAGGCGAGUGUGUAACUCCGCAGUUUAUUAGCACUGUCCUGCGAACGGUCACACCGAGUCGAACGAUGAAC
.............((.((((((((((((((((((......)).))))........(((((..((.......))..)))))..)))))))))))).))........... (-30.17 = -30.43 +   0.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 23,384,869 – 23,384,971
Length 102
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 82.19
Mean single sequence MFE -29.94
Consensus MFE -21.95
Energy contribution -22.63
Covariance contribution 0.69
Combinations/Pair 1.21
Mean z-score -2.52
Structure conservation index 0.73
SVM decision value 1.91
SVM RNA-class probability 0.982169
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23384869 102 + 27905053
CGCAGAACAGUGCUAAUAAACUGCGGAGUUACACACUCGCCUUCUGGCAGUGCGGUCACACCAAUUCGAUGUUUUCAACAUUCAUAGAAAUGGUUGAUAACA
(((((...............)))))..(((.(.((((.(((....))))))).)((((.((((.((((((((.....)))))....))).))))))))))). ( -26.36)
>DroSec_CAF1 10470 102 + 1
CGCAGAACAGUGCUAAUAAACUGCGGAGUUACACACUCGCUUUAUGGCAGUGCGUUCACACCAUUUCUAUGUAUUCAACAUUCAUAGAAAUGGUUCAUAGCU
.((.((((.(..((...........((((.....))))(((....)))))..)))))..((((((((((((...........)))))))))))).....)). ( -31.00)
>DroSim_CAF1 10692 102 + 1
CGCAGGAUAGUGCCAAUAAACUGCGGAGUUACACACUCGCCUUCUGGCAGUGCGGUCACACCAUUUCUAUGUUUUCAACAUUCAUAGAAAUGGUUCAUAGCU
(((((..((.......))..))))).((((((.((((.(((....))))))).).....((((((((((((...........))))))))))))...))))) ( -34.10)
>DroYak_CAF1 10622 100 + 1
CAGAGGGCAGUGU-GUUUAGCCGUGGAGUUUACCACUUGCG-UCUAACAGUGCGGUCACACUCAUUCUAUGUUUUCAGUAUUCAUAGAAAUGGUUGAUGGCU
......(((.(((-.....((.((((......))))..)).-....))).)))(((((((..(((((((((..(.....)..))))).))))..)).))))) ( -28.30)
>consensus
CGCAGAACAGUGCUAAUAAACUGCGGAGUUACACACUCGCCUUCUGGCAGUGCGGUCACACCAAUUCUAUGUUUUCAACAUUCAUAGAAAUGGUUCAUAGCU
.........(((.......((((((((((.....))))(((....)))..)))))))))((((((((((((...........))))))))))))........ (-21.95 = -22.63 +   0.69)

alignment

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secondary structure

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dotplot

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Window 2

Location 23,384,869 – 23,384,971
Length 102
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 82.19
Mean single sequence MFE -29.32
Consensus MFE -21.65
Energy contribution -23.02
Covariance contribution 1.38
Combinations/Pair 1.14
Mean z-score -2.17
Structure conservation index 0.74
SVM decision value 1.28
SVM RNA-class probability 0.939622
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23384869 102 - 27905053
UGUUAUCAACCAUUUCUAUGAAUGUUGAAAACAUCGAAUUGGUGUGACCGCACUGCCAGAAGGCGAGUGUGUAACUCCGCAGUUUAUUAGCACUGUUCUGCG
((((.(((((.((((....))))))))).)))).......((.((...(((((((((....))).))))))..)).))((((..((.......))..)))). ( -29.00)
>DroSec_CAF1 10470 102 - 1
AGCUAUGAACCAUUUCUAUGAAUGUUGAAUACAUAGAAAUGGUGUGAACGCACUGCCAUAAAGCGAGUGUGUAACUCCGCAGUUUAUUAGCACUGUUCUGCG
.(((((((((((((((((((.((.....)).))))))))))(((.(((((((((((......)).)))))))...))))).))))).))))........... ( -32.30)
>DroSim_CAF1 10692 102 - 1
AGCUAUGAACCAUUUCUAUGAAUGUUGAAAACAUAGAAAUGGUGUGACCGCACUGCCAGAAGGCGAGUGUGUAACUCCGCAGUUUAUUGGCACUAUCCUGCG
........((((((((((((...........))))))))))))((...(((((((((....))).))))))..))..(((((..((.......))..))))) ( -33.40)
>DroYak_CAF1 10622 100 - 1
AGCCAUCAACCAUUUCUAUGAAUACUGAAAACAUAGAAUGAGUGUGACCGCACUGUUAGA-CGCAAGUGGUAAACUCCACGGCUAAAC-ACACUGCCCUCUG
((((.........(((((((...........))))))).((((...(((((..(((....-.))).)))))..))))...))))....-............. ( -22.60)
>consensus
AGCUAUCAACCAUUUCUAUGAAUGUUGAAAACAUAGAAAUGGUGUGACCGCACUGCCAGAAGGCGAGUGUGUAACUCCGCAGUUUAUUAGCACUGUCCUGCG
........((((((((((((...........))))))))))))((...((((((((......)).))))))..))..(((((..((.......))..))))) (-21.65 = -23.02 +   1.38)

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 13:19:06 2006