Locus 4867

Sequence ID 2R_DroMel_CAF1
Location 15,931,124 – 15,931,215
Length 91
Max. P 0.827145
window7812 window7813

overview

Window 2

Location 15,931,124 – 15,931,215
Length 91
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.96
Mean single sequence MFE -28.05
Consensus MFE -17.59
Energy contribution -17.92
Covariance contribution 0.34
Combinations/Pair 1.21
Mean z-score -2.67
Structure conservation index 0.63
SVM decision value 0.42
SVM RNA-class probability 0.729558
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15931124 91 + 20766785
GAGUGUUUGCGGAAAUGUGAUGAUUAUUGGUUGAGCAAAUAAAA-------------------------AGACGGA-AACGUCUAUAUUUUAUUUGCACAACCUGCGGG---CGGUAUUC
.(.((((((((..((((.......))))(((((.((((((((((-------------------------(((((..-..)))))...)))))))))).)))))))))))---)).).... ( -33.00)
>DroSec_CAF1 58596 91 + 1
GAGUGUUUGCGGAAAUGUGAUGAUUAUUGGUUGAGCAAAUAGAA-------------------------AGACGGA-AAUGUCUAUAUUUUAUUUGCACAACCUGCGGG---CGGCAUUU
..(((((((((..((((.......))))(((((.((((((((((-------------------------(((((..-..)))))...)))))))))).)))))))))))---).)).... ( -27.20)
>DroSim_CAF1 57479 91 + 1
GAGUGUUUGCGGAAAUGUGAUGAUUAUUGGUUGAGCAAAUAGAA-------------------------AGACGGA-AAUGUCUAUAUUUUAUUUGCACAACCUGCGGG---CGGCAUUU
..(((((((((..((((.......))))(((((.((((((((((-------------------------(((((..-..)))))...)))))))))).)))))))))))---).)).... ( -27.20)
>DroEre_CAF1 58264 91 + 1
GAGUGUUUGCGGAAAUGUGAUGAUUAUUGGUUGAGCAAAUAGAA-------------------------AGACGGA-AACGGCUAUAUUUUAUUUGCACAACCUGGGGG---CGGCAUUU
(((((((.((...((((.......))))(((((.((((((((((-------------------------((.((..-..)).))...)))))))))).))))).....)---)))))))) ( -26.20)
>DroYak_CAF1 60670 95 + 1
GAGUGUUUGCGGAAAUGUGAUGAUUAUUGGUUGUGCAAAUAGAA-------------------------AGACGGAAAACGGCUAUAUUUUAUUUGCACAACCUGCGGGCUGCGGCAUUU
(((((((.((((...((((.........((((((((((((((((-------------------------((.((.....)).))...))))))))))))))))))))..))))))))))) ( -31.90)
>DroAna_CAF1 53051 117 + 1
GAGUGUUUGCGGAAAUGUGAUGAUUAUUGGUUGAACAAAUAGAUGUGCUGCGGGACCCGGGCUAUAUUUAAACAGAUAUUUUCUUUCUUUUAUUUGCCCAACCUGCCGG---CGAAAUAC
..((((((((((.((((.......))))(((((..((((((((((((((.(((...)))))).)))))))...(((.....)))........))))..)))))..)).)---).)))))) ( -22.80)
>consensus
GAGUGUUUGCGGAAAUGUGAUGAUUAUUGGUUGAGCAAAUAGAA_________________________AGACGGA_AACGUCUAUAUUUUAUUUGCACAACCUGCGGG___CGGCAUUU
(((((((..((....))..)........(((((.((((((((((.........................(((((.....)))))...)))))))))).)))))...........)))))) (-17.59 = -17.92 +   0.34)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,931,124 – 15,931,215
Length 91
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.96
Mean single sequence MFE -20.32
Consensus MFE -12.30
Energy contribution -12.16
Covariance contribution -0.14
Combinations/Pair 1.08
Mean z-score -3.21
Structure conservation index 0.61
SVM decision value 0.70
SVM RNA-class probability 0.827145
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15931124 91 - 20766785
GAAUACCG---CCCGCAGGUUGUGCAAAUAAAAUAUAGACGUU-UCCGUCU-------------------------UUUUAUUUGCUCAACCAAUAAUCAUCACAUUUCCGCAAACACUC
........---......(((((.((((((((((...(((((..-..)))))-------------------------)))))))))).)))))............................ ( -23.40)
>DroSec_CAF1 58596 91 - 1
AAAUGCCG---CCCGCAGGUUGUGCAAAUAAAAUAUAGACAUU-UCCGUCU-------------------------UUCUAUUUGCUCAACCAAUAAUCAUCACAUUUCCGCAAACACUC
...(((..---...)))(((((.(((((((......((((...-...))))-------------------------...))))))).)))))............................ ( -20.00)
>DroSim_CAF1 57479 91 - 1
AAAUGCCG---CCCGCAGGUUGUGCAAAUAAAAUAUAGACAUU-UCCGUCU-------------------------UUCUAUUUGCUCAACCAAUAAUCAUCACAUUUCCGCAAACACUC
...(((..---...)))(((((.(((((((......((((...-...))))-------------------------...))))))).)))))............................ ( -20.00)
>DroEre_CAF1 58264 91 - 1
AAAUGCCG---CCCCCAGGUUGUGCAAAUAAAAUAUAGCCGUU-UCCGUCU-------------------------UUCUAUUUGCUCAACCAAUAAUCAUCACAUUUCCGCAAACACUC
........---......(((((.(((((((......((.((..-..)).))-------------------------...))))))).)))))............................ ( -15.30)
>DroYak_CAF1 60670 95 - 1
AAAUGCCGCAGCCCGCAGGUUGUGCAAAUAAAAUAUAGCCGUUUUCCGUCU-------------------------UUCUAUUUGCACAACCAAUAAUCAUCACAUUUCCGCAAACACUC
...(((.((.....)).(((((((((((((......((.((.....)).))-------------------------...)))))))))))))..................)))....... ( -23.20)
>DroAna_CAF1 53051 117 - 1
GUAUUUCG---CCGGCAGGUUGGGCAAAUAAAAGAAAGAAAAUAUCUGUUUAAAUAUAGCCCGGGUCCCGCAGCACAUCUAUUUGUUCAACCAAUAAUCAUCACAUUUCCGCAAACACUC
........---......(((((((((((((..(((.(((.....))).))).......((.(((...)))..)).....)))))))))))))............................ ( -20.00)
>consensus
AAAUGCCG___CCCGCAGGUUGUGCAAAUAAAAUAUAGACAUU_UCCGUCU_________________________UUCUAUUUGCUCAACCAAUAAUCAUCACAUUUCCGCAAACACUC
.................(((((.(((((((.................................................))))))).)))))............................ (-12.30 = -12.16 +  -0.14)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:08 2006