Locus 2761

Sequence ID X_DroMel_CAF1
Location 7,443,233 – 7,443,329
Length 96
Max. P 0.983173
window4508 window4509

overview

Window 8

Location 7,443,233 – 7,443,329
Length 96
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 79.11
Mean single sequence MFE -20.92
Consensus MFE -11.93
Energy contribution -12.18
Covariance contribution 0.25
Combinations/Pair 1.33
Mean z-score -3.20
Structure conservation index 0.57
SVM decision value 1.94
SVM RNA-class probability 0.983173
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7443233 96 + 22224390
CCUGCAUCGAAUACCUUCA---GCACGCACUUGUUGCCCUUCUUCGCAUAUCGAUGCGUGCAUCUAAUGCACUUUCUC---CCCCCAUUUCUCGUU-CCCUCU
..(((((.(((....))).---(((((((.(((.(((........)))...)))))))))).....))))).......---...............-...... ( -20.40)
>DroSec_CAF1 191306 96 + 1
CCUGCAUCGAAUACCUUCA---GCACGCACUUGUUGCCCUCCUUCGCAUAUCGAUGCGUGCAUCUAAUGCACUUUCUC---CCCCCAUUUCUCGUU-CCCUCU
..(((((.(((....))).---(((((((.(((.(((........)))...)))))))))).....))))).......---...............-...... ( -20.40)
>DroSim_CAF1 186565 96 + 1
CCUGCAUCGAAUACCUUCA---GCACGCACUUGUUGCCCUCCUUCGCAUAUCGAUGCGUGCAUCUAAUGCACUUUCUC---CCCCCAUUUCUCGUU-CCCUCU
..(((((.(((....))).---(((((((.(((.(((........)))...)))))))))).....))))).......---...............-...... ( -20.40)
>DroEre_CAF1 206564 100 + 1
CCUGCGUCGAAUUCCUUUAGCAACACGCACUUGUUGCCCUCCUUCGCAUAUCGAUGCGUGCAUCUAAUGCACUUUCUC---CACCCAUUUCCCCUUUCCCUAU
...(((((((.........((((((......)))))).............)))))))((((((...))))))......---...................... ( -20.75)
>DroYak_CAF1 235983 97 + 1
CCCGCGUCGAAUACCUUAA---CCACGCACUUGUUGCCCUGCUUCGCAUAUCGAUGCGUGCAUCUAAUGCACUUUCUC---CGCCCAUUUCUCCUACGCCCAU
...(((((((.........---....(((.....)))..(((...)))..)))))))((((((...))))))......---...................... ( -18.80)
>DroPer_CAF1 275167 93 + 1
GCUCAAACGGAGCCUAUUU---CCACGCACUUGUUGCCC------GGGUAUCGGUGCGUGUAUCUAGCCUGAUUUACCUACCUCCCUGGUCUCCUC-CUCCGC
.......(((((.(((..(---.((((((((...(((..------..)))..)))))))).)..)))............(((.....)))......-))))). ( -24.80)
>consensus
CCUGCAUCGAAUACCUUCA___GCACGCACUUGUUGCCCUCCUUCGCAUAUCGAUGCGUGCAUCUAAUGCACUUUCUC___CCCCCAUUUCUCCUU_CCCUCU
...(((((((................((....))(((........)))..)))))))((((((...))))))............................... (-11.93 = -12.18 +   0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,443,233 – 7,443,329
Length 96
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 79.11
Mean single sequence MFE -25.03
Consensus MFE -14.20
Energy contribution -15.03
Covariance contribution 0.84
Combinations/Pair 1.32
Mean z-score -1.72
Structure conservation index 0.57
SVM decision value 0.10
SVM RNA-class probability 0.585785
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7443233 96 - 22224390
AGAGGG-AACGAGAAAUGGGGG---GAGAAAGUGCAUUAGAUGCACGCAUCGAUAUGCGAAGAAGGGCAACAAGUGCGUGC---UGAAGGUAUUCGAUGCAGG
......-..(.(....).)...---......((((((...))))))(((((((.((((..((..(.((.....)).)...)---)....)))))))))))... ( -23.20)
>DroSec_CAF1 191306 96 - 1
AGAGGG-AACGAGAAAUGGGGG---GAGAAAGUGCAUUAGAUGCACGCAUCGAUAUGCGAAGGAGGGCAACAAGUGCGUGC---UGAAGGUAUUCGAUGCAGG
......-..(.(....).)...---......((((((...))))))(((((((.((((...((.(.(((.....))).).)---)....)))))))))))... ( -24.30)
>DroSim_CAF1 186565 96 - 1
AGAGGG-AACGAGAAAUGGGGG---GAGAAAGUGCAUUAGAUGCACGCAUCGAUAUGCGAAGGAGGGCAACAAGUGCGUGC---UGAAGGUAUUCGAUGCAGG
......-..(.(....).)...---......((((((...))))))(((((((.((((...((.(.(((.....))).).)---)....)))))))))))... ( -24.30)
>DroEre_CAF1 206564 100 - 1
AUAGGGAAAGGGGAAAUGGGUG---GAGAAAGUGCAUUAGAUGCACGCAUCGAUAUGCGAAGGAGGGCAACAAGUGCGUGUUGCUAAAGGAAUUCGACGCAGG
...................(((---..(((..(((((..((((....))))...)))))......(((((((......))))))).......)))..)))... ( -24.60)
>DroYak_CAF1 235983 97 - 1
AUGGGCGUAGGAGAAAUGGGCG---GAGAAAGUGCAUUAGAUGCACGCAUCGAUAUGCGAAGCAGGGCAACAAGUGCGUGG---UUAAGGUAUUCGACGCGGG
....((((.(((..((((.((.---......)).))))..((((((((.(((.....))).))..(....)..))))))..---........))).))))... ( -26.00)
>DroPer_CAF1 275167 93 - 1
GCGGAG-GAGGAGACCAGGGAGGUAGGUAAAUCAGGCUAGAUACACGCACCGAUACCC------GGGCAACAAGUGCGUGG---AAAUAGGCUCCGUUUGAGC
((((((-...((.(((.........)))...))...(((....(((((((((.....)------)(....)..))))))).---...))).))))))...... ( -27.80)
>consensus
AGAGGG_AACGAGAAAUGGGGG___GAGAAAGUGCAUUAGAUGCACGCAUCGAUAUGCGAAGGAGGGCAACAAGUGCGUGC___UGAAGGUAUUCGAUGCAGG
................................(((((..(((((((((((.....(((........)))....))))))))..........)))..))))).. (-14.20 = -15.03 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:34 2006