Locus 6684

Sequence ID 3R_DroMel_CAF1
Location 17,576,478 – 17,576,605
Length 127
Max. P 0.998725
window10867 window10868 window10869

overview

Window 7

Location 17,576,478 – 17,576,574
Length 96
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 82.57
Mean single sequence MFE -26.86
Consensus MFE -18.76
Energy contribution -19.84
Covariance contribution 1.08
Combinations/Pair 1.10
Mean z-score -4.03
Structure conservation index 0.70
SVM decision value 3.20
SVM RNA-class probability 0.998725
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17576478 96 + 27905053
UUAAAAUCUUUAUAAUUAUUAAAGUAUGCCACUUUGUCUUUCUCGCCAUAAUUUAAUGACAAAGAUACGGUGUAAUCAGUGCUU-UACAAGCACAAU
.......(((((.......)))))((((((.(((((((...................)))))))....))))))....(((((.-....)))))... ( -18.31)
>DroSec_CAF1 11722 96 + 1
UUAAAAUCUUUAUAAUUAUAAAAGUAUGCCACUGUGUCUUUGUCGUCAUAAUUGUAUGACAAAGAUACGGUGUUAUCAGUGCUU-UACAAUCACAAG
....................(((((((..(((((((((((((((((((....)).)))))))))))))))))......))))))-)........... ( -29.80)
>DroSim_CAF1 10929 96 + 1
UUAAAAUCUUUAUAAUUAUAAAAGUAUGCCACUGUGUCUUUGUCGUCAUAAUUUUAUGACAAAGAUACGGUGUUAUCAGUGCUU-UACAAGCACAAG
.......................(.(((.(((((((((((((((((.(.....).))))))))))))))))).)))).(((((.-....)))))... ( -29.90)
>DroEre_CAF1 11035 85 + 1
UUAAAAUGUUUAUACUCAUUAAAGUAUGCCACCGUGUCUUUGUCGUCAUGGGUUUAUGACGAAGAUACGGUGAUAUCA------------GCACAAG
......((((((((((......)))))).(((((((((((((((((.(.....).))))))))))))))))).....)------------))).... ( -28.80)
>DroYak_CAF1 13723 97 + 1
UUAAAAUGUUUAUAACCACUUAAGUAUGUCACUGCCUCUUUGUCGUCAUGGGUUUAUGACAAAGAUACGGCGAUAUCAGUGGUUCUACAAGCACAAC
......(((((..(((((((...(.(((((.(((..((((((((((.(.....).))))))))))..))).)))))))))))))....))))).... ( -27.50)
>consensus
UUAAAAUCUUUAUAAUUAUUAAAGUAUGCCACUGUGUCUUUGUCGUCAUAAUUUUAUGACAAAGAUACGGUGUUAUCAGUGCUU_UACAAGCACAAG
.......................(.(((.(((((((((((((((((.........))))))))))))))))).)))).................... (-18.76 = -19.84 +   1.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,576,478 – 17,576,574
Length 96
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 82.57
Mean single sequence MFE -22.05
Consensus MFE -12.02
Energy contribution -11.58
Covariance contribution -0.44
Combinations/Pair 1.27
Mean z-score -2.60
Structure conservation index 0.55
SVM decision value 0.88
SVM RNA-class probability 0.873168
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17576478 96 - 27905053
AUUGUGCUUGUA-AAGCACUGAUUACACCGUAUCUUUGUCAUUAAAUUAUGGCGAGAAAGACAAAGUGGCAUACUUUAAUAAUUAUAAAGAUUUUAA
...(((((....-.)))))......(((..(.((((((((((......)))))))...))).)..))).....(((((.......)))))....... ( -16.20)
>DroSec_CAF1 11722 96 - 1
CUUGUGAUUGUA-AAGCACUGAUAACACCGUAUCUUUGUCAUACAAUUAUGACGACAAAGACACAGUGGCAUACUUUUAUAAUUAUAAAGAUUUUAA
.(((((((((((-(((...((....(((.((.((((((((.............)))))))).)).))).))...))))))))))))))......... ( -23.82)
>DroSim_CAF1 10929 96 - 1
CUUGUGCUUGUA-AAGCACUGAUAACACCGUAUCUUUGUCAUAAAAUUAUGACGACAAAGACACAGUGGCAUACUUUUAUAAUUAUAAAGAUUUUAA
.(((((.(((((-(((...((....(((.((.((((((((.............)))))))).)).))).))...)))))))).)))))......... ( -19.72)
>DroEre_CAF1 11035 85 - 1
CUUGUGC------------UGAUAUCACCGUAUCUUCGUCAUAAACCCAUGACGACAAAGACACGGUGGCAUACUUUAAUGAGUAUAAACAUUUUAA
.((((((------------(....(((((((.((((((((((......)))))))...))).)))))))(((......))))))))))......... ( -25.00)
>DroYak_CAF1 13723 97 - 1
GUUGUGCUUGUAGAACCACUGAUAUCGCCGUAUCUUUGUCAUAAACCCAUGACGACAAAGAGGCAGUGACAUACUUAAGUGGUUAUAAACAUUUUAA
...(((.(((((..((((((.((.((((.((.((((((((.............)))))))).)).)))).)).....))))))))))).)))..... ( -25.52)
>consensus
CUUGUGCUUGUA_AAGCACUGAUAACACCGUAUCUUUGUCAUAAAAUUAUGACGACAAAGACACAGUGGCAUACUUUAAUAAUUAUAAAGAUUUUAA
.........................(((.((.((((((((((......)))))))...))).)).)))............................. (-12.02 = -11.58 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,576,509 – 17,576,605
Length 96
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 81.74
Mean single sequence MFE -24.18
Consensus MFE -14.98
Energy contribution -15.66
Covariance contribution 0.68
Combinations/Pair 1.13
Mean z-score -2.19
Structure conservation index 0.62
SVM decision value 0.79
SVM RNA-class probability 0.852338
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17576509 96 + 27905053
CUUUGUCUUUCUCGCCAUAAUUUAAUGACAAAGAUACGGUGUAAUCAGUGCUU-UACAAGCACAAUGUCUUUAAUGGAUGCAUAAAUUAAUUGUUAU
(((((((...................))))))).....((((.....(((((.-....)))))...((((.....)))))))).............. ( -16.81)
>DroSec_CAF1 11753 96 + 1
CUGUGUCUUUGUCGUCAUAAUUGUAUGACAAAGAUACGGUGUUAUCAGUGCUU-UACAAUCACAAGGUCUUUAGUGGAUGCAUAAAUGAAUUGUUAU
(((((((((((((((((....)).)))))))))))))))..((((..((((((-(((................))))).))))..))))........ ( -26.99)
>DroSim_CAF1 10960 96 + 1
CUGUGUCUUUGUCGUCAUAAUUUUAUGACAAAGAUACGGUGUUAUCAGUGCUU-UACAAGCACAAGGUCUUUAGUGGAUGCAUAAAUGAAUUGUUAU
(((((((((((((((.(.....).))))))))))))))).....((((((((.-....)))))...((((.....)))).......)))........ ( -27.50)
>DroEre_CAF1 11066 85 + 1
CCGUGUCUUUGUCGUCAUGGGUUUAUGACGAAGAUACGGUGAUAUCA------------GCACAAGCGCUUGAAUGGAUGCAUAAAUUAAUUGUUAU
(((((((((((((((.(.....).)))))))))))))))((((((((------------((......)).)))(((....)))........))))). ( -23.30)
>DroYak_CAF1 13754 97 + 1
CUGCCUCUUUGUCGUCAUGGGUUUAUGACAAAGAUACGGCGAUAUCAGUGGUUCUACAAGCACAACCGCUUGAAUGAAUGCAUAAUUUAAUUGCCAU
.....((((((((((.(.....).))))))))))...((((((....(((((((..(((((......)))))...)))).)))......)))))).. ( -26.30)
>consensus
CUGUGUCUUUGUCGUCAUAAUUUUAUGACAAAGAUACGGUGUUAUCAGUGCUU_UACAAGCACAAGGUCUUUAAUGGAUGCAUAAAUUAAUUGUUAU
(((((((((((((((.........))))))))))))))).......................................................... (-14.98 = -15.66 +   0.68)

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 12:27:32 2006