Locus 9502

Sequence ID 3R_DroMel_CAF1
Location 25,117,404 – 25,117,587
Length 183
Max. P 0.901755
window15210 window15211 window15212

overview

Window 0

Location 25,117,404 – 25,117,494
Length 90
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 82.85
Mean single sequence MFE -22.23
Consensus MFE -11.78
Energy contribution -13.22
Covariance contribution 1.44
Combinations/Pair 1.12
Mean z-score -2.78
Structure conservation index 0.53
SVM decision value 0.49
SVM RNA-class probability 0.755819
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25117404 90 + 27905053
UCCAUUUCAGUUGGCAAUUUAUGCAGACUU--AUCGUAUAUGCCACAAC-GUACGAGUAUGCAUAUAUCUGCAU------ACAUAUGUCAUAUGUUCGC
.......((..(((((((.((((((((..(--((.((((((........-......)))))))))..)))))))------).)).)))))..))..... ( -20.34)
>DroSim_CAF1 48529 90 + 1
UCCAUUCCAGUCGGCAAUUUAUGCAGACUU--AUCGCAUAUGCCACAUC-GUACGAGUAUGCAUAUAUCUGCAU------ACAUAUGUCAUAUGUUCGC
........((((.(((.....))).)))).--...(((((((.((..((-....))(((((((......)))))------))...)).))))))).... ( -22.30)
>DroEre_CAF1 48776 99 + 1
UCCAUUCCAGUCGACAAUUUAUGCAGACUUAUAUCGCAUAUGGCAUGUGGAUAUGCAUAUGCAUAUAUCUGCAUACUCGUACAUAUGUCAUAAGUUCGC
.........(((((.....((((((((..(((((.(((((((.((((....)))))))))))))))))))))))).))).))................. ( -25.50)
>DroYak_CAF1 47893 92 + 1
UCCAUUCCAGUCGACAAUUUAUGCAGACUUAUAUCGCAUAUGCCAUAUC-AUAU------GCAUACAUCUGCAUACUCGUACAUAUGUCAUAUGUUCGC
...................((((((((..(((...(((((((......)-))))------)))))..))))))))..((.((((((...)))))).)). ( -20.80)
>consensus
UCCAUUCCAGUCGACAAUUUAUGCAGACUU__AUCGCAUAUGCCACAUC_AUACGAGUAUGCAUAUAUCUGCAU______ACAUAUGUCAUAUGUUCGC
........((((.(((.....))).))))......(((((((.(((((..........(((((......)))))........))))).))))))).... (-11.78 = -13.22 +   1.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 25,117,404 – 25,117,494
Length 90
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 82.85
Mean single sequence MFE -24.53
Consensus MFE -15.90
Energy contribution -16.90
Covariance contribution 1.00
Combinations/Pair 1.11
Mean z-score -2.30
Structure conservation index 0.65
SVM decision value 1.02
SVM RNA-class probability 0.901755
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25117404 90 - 27905053
GCGAACAUAUGACAUAUGU------AUGCAGAUAUAUGCAUACUCGUAC-GUUGUGGCAUAUACGAU--AAGUCUGCAUAAAUUGCCAACUGAAAUGGA
((((((((((...))))))------((((((((((((((.(((......-...))))))))).....--..))))))))...))))............. ( -20.51)
>DroSim_CAF1 48529 90 - 1
GCGAACAUAUGACAUAUGU------AUGCAGAUAUAUGCAUACUCGUAC-GAUGUGGCAUAUGCGAU--AAGUCUGCAUAAAUUGCCGACUGGAAUGGA
.....((((((.(((((((------(((((......)))))))......-.))))).))))))....--.((((.(((.....))).))))........ ( -24.41)
>DroEre_CAF1 48776 99 - 1
GCGAACUUAUGACAUAUGUACGAGUAUGCAGAUAUAUGCAUAUGCAUAUCCACAUGCCAUAUGCGAUAUAAGUCUGCAUAAAUUGUCGACUGGAAUGGA
......((((..((..((.((((.(((((((((((((((((((((((......))).))))))).))))..)))))))))..))))))..))..)))). ( -27.30)
>DroYak_CAF1 47893 92 - 1
GCGAACAUAUGACAUAUGUACGAGUAUGCAGAUGUAUGC------AUAU-GAUAUGGCAUAUGCGAUAUAAGUCUGCAUAAAUUGUCGACUGGAAUGGA
.((.((((((...)))))).))..(((((((((((((((------((((-(......))))))).))))..)))))))))................... ( -25.90)
>consensus
GCGAACAUAUGACAUAUGU______AUGCAGAUAUAUGCAUACUCAUAC_GAUAUGGCAUAUGCGAU__AAGUCUGCAUAAAUUGCCGACUGGAAUGGA
.....((((((.(((((((......(((((......)))))......))..))))).))))))(.((...((((.(((.....))).))))...)).). (-15.90 = -16.90 +   1.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 25,117,494 – 25,117,587
Length 93
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 76.34
Mean single sequence MFE -13.93
Consensus MFE -8.94
Energy contribution -9.50
Covariance contribution 0.56
Combinations/Pair 1.12
Mean z-score -1.42
Structure conservation index 0.64
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25117494 93 - 27905053
ACAUAAUUCGCUUCAUUCACAAACCAAAGCACGCGCCGGGCUUAGUAAAUAUUGAAAGAAGCUGAAAAUCAAAUAAAAUA-----AAAUGAACUGGUC
......((((((((.((((.......((((.((...)).)))).........)))).))))).)))..............-----............. ( -12.89)
>DroVir_CAF1 60716 83 - 1
GCAUAAUUUGCUUCAUUCAAAA-UCCAAGCACGCGCCGUGCUUAGUAAAUAUUGAAAAGAGU--------AAAUAAAAUCAAAUAAA------UGUAC
.....((((((((..(((((..-.(.(((((((...))))))).)......)))))..))))--------)))).............------..... ( -16.70)
>DroMoj_CAF1 56700 83 - 1
GCAUAAUUUGCUUCAUUGAAAA-CCAAAGCACGCGCCGUGCUUAGUAAAUAUUGAAAAGAGU--------AAAUAAAAUCAAAUAAA------UGUAC
.....((((((((((......(-(..(((((((...))))))).))......)))....)))--------)))).............------..... ( -12.20)
>consensus
GCAUAAUUUGCUUCAUUCAAAA_CCAAAGCACGCGCCGUGCUUAGUAAAUAUUGAAAAGAGU________AAAUAAAAUCAAAUAAA______UGUAC
.........((((..(((((....(.(((((((...))))))).)......)))))..)))).................................... ( -8.94 =  -9.50 +   0.56)

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 13:36:03 2006