Locus 4035

Sequence ID X_DroMel_CAF1
Location 10,670,543 – 10,670,650
Length 107
Max. P 0.999735
window6633 window6634

overview

Window 3

Location 10,670,543 – 10,670,650
Length 107
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 76.44
Mean single sequence MFE -40.17
Consensus MFE -29.11
Energy contribution -29.33
Covariance contribution 0.23
Combinations/Pair 1.08
Mean z-score -2.86
Structure conservation index 0.72
SVM decision value 3.97
SVM RNA-class probability 0.999735
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10670543 107 + 22224390
CCCCCAGCGGCAACUGCGACGCAUUUUUGUGUGUGCGUCCUGUGCGUUGCCAUGCUGCGAUUU-----------UCCAUUUCGAUUUGGGAUGGUUGGGAUCGCAUU--GGCUUGGAUUC
..((.(((((((((.(((((((((........)))))))....))))))))....((((((((-----------.((((..(.....)..))))...))))))))..--.))).)).... ( -43.80)
>DroEre_CAF1 835 89 + 1
CCC-CUGAGGCAACUGCGACGCAUUUUUGUGUGUGCGUCCUGUGCGUUGCCAUGCUGCGAUUUCC------------AUUUCGAUUCGGGAUGGAUGGGUUC------------------
.((-(...((((((.(((((((((........)))))))....))))))))...........(((------------((..((...))..))))).)))...------------------ ( -34.80)
>DroYak_CAF1 1854 119 + 1
CCC-CUGAGGCAACUGCGACGCACUUUUGUGUGUGCGUCCUGUGCGUUGCCAUGCUGCGAUUUCCAUUUCCAUUUCCAUUUCGAUUUGGGAUGGCUGGGAUCGUAUUCUCGCUUAGAUUC
...-((((((((((.(((((((((........)))))))....))))))))....(((((((.(((...(((((.(((........)))))))).)))))))))).......)))).... ( -41.90)
>consensus
CCC_CUGAGGCAACUGCGACGCAUUUUUGUGUGUGCGUCCUGUGCGUUGCCAUGCUGCGAUUUCC_________UCCAUUUCGAUUUGGGAUGGAUGGGAUCG_AUU___GCUU_GAUUC
(((.....((((((.(((((((((........)))))))....))))))))........................((((..((...))..))))..)))..................... (-29.11 = -29.33 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 10,670,543 – 10,670,650
Length 107
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 76.44
Mean single sequence MFE -32.40
Consensus MFE -21.67
Energy contribution -22.33
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.67
SVM decision value 2.67
SVM RNA-class probability 0.996250
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10670543 107 - 22224390
GAAUCCAAGCC--AAUGCGAUCCCAACCAUCCCAAAUCGAAAUGGA-----------AAAUCGCAGCAUGGCAACGCACAGGACGCACACACAAAAAUGCGUCGCAGUUGCCGCUGGGGG
...(((.(((.--..((((((.....((((..(.....)..)))).-----------..))))))....((((((((....((((((..........)))))))).))))))))).))). ( -33.40)
>DroEre_CAF1 835 89 - 1
------------------GAACCCAUCCAUCCCGAAUCGAAAU------------GGAAAUCGCAGCAUGGCAACGCACAGGACGCACACACAAAAAUGCGUCGCAGUUGCCUCAG-GGG
------------------...(((.(((((..((...))..))------------)))...........((((((((....((((((..........)))))))).))))))...)-)). ( -28.10)
>DroYak_CAF1 1854 119 - 1
GAAUCUAAGCGAGAAUACGAUCCCAGCCAUCCCAAAUCGAAAUGGAAAUGGAAAUGGAAAUCGCAGCAUGGCAACGCACAGGACGCACACACAAAAGUGCGUCGCAGUUGCCUCAG-GGG
...(((..((((((......))(((.((((.(((........)))..))))...)))...)))).....((((((((....(((((((........))))))))).))))))..))-).. ( -35.70)
>consensus
GAAUC_AAGC___AAU_CGAUCCCAACCAUCCCAAAUCGAAAUGGA_________GGAAAUCGCAGCAUGGCAACGCACAGGACGCACACACAAAAAUGCGUCGCAGUUGCCUCAG_GGG
.....................(((..((((..(.....)..))))........................((((((((....((((((..........)))))))).)))))).....))) (-21.67 = -22.33 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:48 2006