Locus 2377

Sequence ID X_DroMel_CAF1
Location 6,345,302 – 6,345,440
Length 138
Max. P 0.935377
window3865 window3866 window3867 window3868

overview

Window 5

Location 6,345,302 – 6,345,401
Length 99
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 93.37
Mean single sequence MFE -37.72
Consensus MFE -35.50
Energy contribution -36.25
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.94
SVM decision value 1.24
SVM RNA-class probability 0.935377
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6345302 99 + 22224390
UUUUGAAUGAGUCUCCACGGAAUAAGCGCGUUCGCAUCGCUGACUAUCUGAGCAGCGGCAGAGCUCCAACCGGAGCUCCAAUUGGAGGUCAGUGGUGG--------C
....(((((.((.((....))....)).))))).(((((((((((.((..(((....)).(((((((....)))))))...)..))))))))))))).--------. ( -39.10)
>DroSec_CAF1 29684 99 + 1
UUUUGAAUGAGUCUCCACGGAAUAAGCGCGUCCGCAUCGCUGACUAUCUGAGCAGCGGCAGAGCUCCAAGUGGAGCUCCAAUUGGAGGUCAGUGGUGG--------C
..........(((.((((.......((((....))..(((((.((.....))))))))).((.((((((.(((....))).)))))).)).)))).))--------) ( -38.00)
>DroEre_CAF1 27572 99 + 1
UUUUGAAUGAGUCUCCACGGAAUAAGCGCGUUCGCAUCGCUGACUAUCUGAGCAGCGGCAGAGCUCCAAUUGGAGCUCCAAUUGCAGGUCAGUGGUGG--------C
....(((((.((.((....))....)).))))).(((((((((((......((....)).(((((((....)))))))........))))))))))).--------. ( -36.60)
>DroYak_CAF1 26305 107 + 1
UUUUGAAUGAGUCUCCACGGAAUAAGCGCGUUCGCAUCGCUGACUAUCUGAGCAGCGGCAGAGCUCCAACUGGAGCUCCAAUUGGAGGUCAGUGCUGGCAAUUUGGC
..(..(((..(((..(((.......((((....))..(((((.((.....))))))))).((.((((((.(((....))).)))))).)).)))..))).)))..). ( -37.20)
>consensus
UUUUGAAUGAGUCUCCACGGAAUAAGCGCGUUCGCAUCGCUGACUAUCUGAGCAGCGGCAGAGCUCCAACUGGAGCUCCAAUUGGAGGUCAGUGGUGG________C
....(((((.((.((....))....)).))))).(((((((((((.(((((((....)).(((((((....)))))))...)))))))))))))))).......... (-35.50 = -36.25 +   0.75)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,345,302 – 6,345,401
Length 99
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 93.37
Mean single sequence MFE -32.65
Consensus MFE -30.51
Energy contribution -30.70
Covariance contribution 0.19
Combinations/Pair 1.07
Mean z-score -1.47
Structure conservation index 0.93
SVM decision value 0.36
SVM RNA-class probability 0.706475
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6345302 99 - 22224390
G--------CCACCACUGACCUCCAAUUGGAGCUCCGGUUGGAGCUCUGCCGCUGCUCAGAUAGUCAGCGAUGCGAACGCGCUUAUUCCGUGGAGACUCAUUCAAAA
.--------...((((.((.((((((((((....)))))))))).)).(((((((((.....)).)))))..((....)))).......)))).............. ( -32.60)
>DroSec_CAF1 29684 99 - 1
G--------CCACCACUGACCUCCAAUUGGAGCUCCACUUGGAGCUCUGCCGCUGCUCAGAUAGUCAGCGAUGCGGACGCGCUUAUUCCGUGGAGACUCAUUCAAAA
.--------.......(((.((((....((((((((....))))))))..(((((((.....)).)))))..(((((.........)))))))))..)))....... ( -32.90)
>DroEre_CAF1 27572 99 - 1
G--------CCACCACUGACCUGCAAUUGGAGCUCCAAUUGGAGCUCUGCCGCUGCUCAGAUAGUCAGCGAUGCGAACGCGCUUAUUCCGUGGAGACUCAUUCAAAA
.--------...((((.((...((....((((((((....))))))))..(((((((.....)).)))))..((....))))....)).)))).............. ( -32.30)
>DroYak_CAF1 26305 107 - 1
GCCAAAUUGCCAGCACUGACCUCCAAUUGGAGCUCCAGUUGGAGCUCUGCCGCUGCUCAGAUAGUCAGCGAUGCGAACGCGCUUAUUCCGUGGAGACUCAUUCAAAA
................(((.((((((((((....))))))))))(((..((((((((.....)).)))))..(((....))).......)..)))......)))... ( -32.80)
>consensus
G________CCACCACUGACCUCCAAUUGGAGCUCCAGUUGGAGCUCUGCCGCUGCUCAGAUAGUCAGCGAUGCGAACGCGCUUAUUCCGUGGAGACUCAUUCAAAA
................(((.((((((((((....))))))))))(((..((((((((.....)).)))))..(((....))).......)..)))......)))... (-30.51 = -30.70 +   0.19)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,345,341 – 6,345,440
Length 99
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 87.68
Mean single sequence MFE -32.23
Consensus MFE -24.56
Energy contribution -24.25
Covariance contribution -0.31
Combinations/Pair 1.10
Mean z-score -2.34
Structure conservation index 0.76
SVM decision value 1.17
SVM RNA-class probability 0.925449
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6345341 99 + 22224390
CUGACUAUCUGAGCAGCGGCAGAGCUCCAACCGGAGCUCCAAUUGGAGGUCAGUGGUGG--------CAAUUGGAUAAUGUUUACUAUAUUGG-CGUAGCUAAAAAAU
((((((.((..(((....)).(((((((....)))))))...)..))))))))...(((--------(...((..((((((.....)))))).-))..))))...... ( -29.00)
>DroSec_CAF1 29723 98 + 1
CUGACUAUCUGAGCAGCGGCAGAGCUCCAAGUGGAGCUCCAAUUGGAGGUCAGUGGUGG--------CAAUUGGAUAAUGU-UGCUAUAUUGG-CUUAGCUAAAAAAU
((((((.((..(((....)).(((((((....)))))))...)..))))))))..((((--------((((........))-)))))).((((-(...)))))..... ( -34.60)
>DroEre_CAF1 27611 98 + 1
CUGACUAUCUGAGCAGCGGCAGAGCUCCAAUUGGAGCUCCAAUUGCAGGUCAGUGGUGG--------CAAUUGGAUAAUGU-AACUAUAUUGCAAGUAGCCAAA-AAU
...((((.((((.(.((((..(((((((....)))))))...)))).).))))))))((--------(.(((.(.((((((-....))))))).))).)))...-... ( -32.20)
>DroYak_CAF1 26344 105 + 1
CUGACUAUCUGAGCAGCGGCAGAGCUCCAACUGGAGCUCCAAUUGGAGGUCAGUGCUGGCAAUUUGGCAAUUGGAUAAUGU-UACCGCAUUGG-AGUAGCUAAA-AAU
((((((.((..(((....)).(((((((....)))))))...)..)))))))).........((((((.(((...((((((-....)))))).-))).))))))-... ( -33.10)
>consensus
CUGACUAUCUGAGCAGCGGCAGAGCUCCAACUGGAGCUCCAAUUGGAGGUCAGUGGUGG________CAAUUGGAUAAUGU_UACUAUAUUGG_AGUAGCUAAA_AAU
((((((.(((((((....)).(((((((....)))))))...))))))))))).................((((.((((((.....)))))).......))))..... (-24.56 = -24.25 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,345,341 – 6,345,440
Length 99
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 87.68
Mean single sequence MFE -26.52
Consensus MFE -20.86
Energy contribution -20.93
Covariance contribution 0.06
Combinations/Pair 1.17
Mean z-score -2.13
Structure conservation index 0.79
SVM decision value 1.04
SVM RNA-class probability 0.904682
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6345341 99 - 22224390
AUUUUUUAGCUACG-CCAAUAUAGUAAACAUUAUCCAAUUG--------CCACCACUGACCUCCAAUUGGAGCUCCGGUUGGAGCUCUGCCGCUGCUCAGAUAGUCAG
........((((..-......))))................--------......(((((((((((((((....)))))))))).((((........))))..))))) ( -22.90)
>DroSec_CAF1 29723 98 - 1
AUUUUUUAGCUAAG-CCAAUAUAGCA-ACAUUAUCCAAUUG--------CCACCACUGACCUCCAAUUGGAGCUCCACUUGGAGCUCUGCCGCUGCUCAGAUAGUCAG
........((((..-......)))).-..............--------......(((((........((((((((....))))))))((....)).......))))) ( -23.30)
>DroEre_CAF1 27611 98 - 1
AUU-UUUGGCUACUUGCAAUAUAGUU-ACAUUAUCCAAUUG--------CCACCACUGACCUGCAAUUGGAGCUCCAAUUGGAGCUCUGCCGCUGCUCAGAUAGUCAG
...-..((((((((.(((........-......((((((((--------(............)))))))))(((((....)))))........)))..)).)))))). ( -29.00)
>DroYak_CAF1 26344 105 - 1
AUU-UUUAGCUACU-CCAAUGCGGUA-ACAUUAUCCAAUUGCCAAAUUGCCAGCACUGACCUCCAAUUGGAGCUCCAGUUGGAGCUCUGCCGCUGCUCAGAUAGUCAG
...-....((((((-.....((((((-........(((((....)))))........((.((((((((((....)))))))))).)))))))).....)).))))... ( -30.90)
>consensus
AUU_UUUAGCUACG_CCAAUAUAGUA_ACAUUAUCCAAUUG________CCACCACUGACCUCCAAUUGGAGCUCCAGUUGGAGCUCUGCCGCUGCUCAGAUAGUCAG
........((((.........))))..............................(((((((((((((((....)))))))))).((((........))))..))))) (-20.86 = -20.93 +   0.06)

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 10:33:03 2006