Locus 5049

Sequence ID 2R_DroMel_CAF1
Location 16,408,984 – 16,409,123
Length 139
Max. P 0.849150
window8067 window8068

overview

Window 7

Location 16,408,984 – 16,409,088
Length 104
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 87.33
Mean single sequence MFE -22.60
Consensus MFE -17.52
Energy contribution -17.08
Covariance contribution -0.44
Combinations/Pair 1.28
Mean z-score -1.81
Structure conservation index 0.78
SVM decision value 0.58
SVM RNA-class probability 0.788144
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16408984 104 - 20766785
UUAAUAAUUCCGAAUA------CACAUAUGUACA--UAUGUAUGUGCGUGUGUGCAGGUGAAUAAAUUAUUUUUACCACACUGUUGAUCAACGAUUCAAGCACUUUCAAUUU
...........((((.------((((((((((((--(....)))))))))))))..((((((.........))))))....((((....))))))))............... ( -24.10)
>DroSec_CAF1 78751 106 - 1
UUAAUAAAUCCGAAUA------CUCAUAUGUACGUGUAUGUAAGUGCGUGUGUGCAGGUGAAUAAAUUAUUUUUACCACACUGUUGAUCAACGAUUCAAGCACUUUCAAUUU
...........(((..------...((((((((..........))))))))((((.((((((.........))))))......((((........)))))))).)))..... ( -21.00)
>DroSim_CAF1 80627 106 - 1
UUAAUAAAUCCGAAUA------CACAUAUGUACGUGUAUGUAUGUGCGUGUGUGCAGGUGAAUAAAUUAUUUUUACCACACUGUUGAUCAACGAUUCAAGCACUUUCAAUUU
...........((((.------((((((((((((((....))))))))))))))..((((((.........))))))....((((....))))))))............... ( -24.60)
>DroEre_CAF1 84370 110 - 1
UUAAUAAAUCCGAGUACACGCACUCAUACAUAUG--UGCAUAUGUACGUGUGUGCGGGCGAAUAAAUUAUUUUUACCACACUGUUGAUCAACGGUUCAAGCACUUUCAAUUU
.........((((((......)))).((((((((--(((....))))))))))).))((...((((.....))))....((((((....))))))....))........... ( -24.00)
>DroYak_CAF1 84501 99 - 1
UUAAUAAAUC-----------AUACAUACAUACG--UAUGUAUGUACGUGUGUGCAGAUGAAUAAAUUAUUUUUACCACACUGUUGAUCAACGAUUCAAGCACUUUCAAUUU
((((((...(-----------((((((((....)--))))))))...(((((((.((((((.....)))))).)).)))))))))))......................... ( -19.30)
>consensus
UUAAUAAAUCCGAAUA______CACAUAUGUACG__UAUGUAUGUGCGUGUGUGCAGGUGAAUAAAUUAUUUUUACCACACUGUUGAUCAACGAUUCAAGCACUUUCAAUUU
......................(((.((((((((....)))))))).))).((((.((((((.........))))))......((((........))))))))......... (-17.52 = -17.08 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,409,024 – 16,409,123
Length 99
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 87.10
Mean single sequence MFE -21.92
Consensus MFE -15.88
Energy contribution -14.88
Covariance contribution -1.00
Combinations/Pair 1.35
Mean z-score -2.19
Structure conservation index 0.72
SVM decision value 0.78
SVM RNA-class probability 0.849150
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16409024 99 - 20766785
UUAUCAAACUGUACUUGUGUCCUCAUAUUAAUAUAUUAAUAAUUCCGAAUA------CACAUAUGUACA--UAUGUAUGUGCGUGUGUGCAGGUGAAUAAAUUAUUU
...(((..((((((..((((..((.((((((....)))))).....))..)------)))(((((((((--(....)))))))))))))))).)))........... ( -22.40)
>DroSec_CAF1 78791 101 - 1
UUAUCAAACUGUACUUGUGUCCUCAUAUUAAUAUAUUAAUAAAUCCGAAUA------CUCAUAUGUACGUGUAUGUAAGUGCGUGUGUGCAGGUGAAUAAAUUAUUU
...(((..((((((..(((((....((((((....)))))).....).)))------)..((((((((..........)))))))))))))).)))........... ( -17.20)
>DroSim_CAF1 80667 101 - 1
UUAUCAAACUGUACUUGUGUCCUCAUAUUAAUAUAUUAAUAAAUCCGAAUA------CACAUAUGUACGUGUAUGUAUGUGCGUGUGUGCAGGUGAAUAAAUUAUUU
...(((..((((((..((((..((.((((((....)))))).....))..)------)))(((((((((((....))))))))))))))))).)))........... ( -22.90)
>DroEre_CAF1 84410 105 - 1
UUAUCAAACUGUACUUGUGUCCUCAUAUUAAUAUAUUAAUAAAUCCGAGUACACGCACUCAUACAUAUG--UGCAUAUGUACGUGUGUGCGGGCGAAUAAAUUAUUU
.........((((((((.(......((((((....))))))...)))))))))(((.((..((((((((--(((....))))))))))).)))))............ ( -26.20)
>DroYak_CAF1 84541 94 - 1
UUAUCAAACUGUACUUGUGUCCUCAUAUUAAUAUAUUAAUAAAUC-----------AUACAUACAUACG--UAUGUAUGUACGUGUGUGCAGAUGAAUAAAUUAUUU
...(((..((((((.((((......((((((....))))))...(-----------((((((((....)--))))))))))))...)))))).)))........... ( -20.90)
>consensus
UUAUCAAACUGUACUUGUGUCCUCAUAUUAAUAUAUUAAUAAAUCCGAAUA______CACAUAUGUACG__UAUGUAUGUGCGUGUGUGCAGGUGAAUAAAUUAUUU
........((((((...........((((((....))))))................(((.((((((((....)))))))).))).))))))............... (-15.88 = -14.88 +  -1.00)

alignment

Postscript

secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:10 2006