Locus 7590

Sequence ID 3L_DroMel_CAF1
Location 20,401,451 – 20,401,570
Length 119
Max. P 0.843438
window12331 window12332

overview

Window 1

Location 20,401,451 – 20,401,570
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 77.53
Mean single sequence MFE -28.70
Consensus MFE -19.59
Energy contribution -20.15
Covariance contribution 0.56
Combinations/Pair 1.14
Mean z-score -1.79
Structure conservation index 0.68
SVM decision value 0.68
SVM RNA-class probability 0.820917
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20401451 119 + 23771897
UCAAAAUGCUGGCCCGUUAAGUGUGAAGCCUGAAAGAAUGCUACAAUAUGUAUUGUAGAUUCACUUUCAAUAAAAUCUGAGUGCAACAAUCGUUUUGAUUUCUUUCAGGUGGCUUGGGC
...........(((((...(((.....(((((((((((..(((((((....)))))))...(((((............)))))................))))))))))).)))))))) ( -31.00)
>DroSec_CAF1 15733 102 + 1
ACAAAAUGCUGUCCCGUGAAGUUUGAAGCCUGAAAGAAUGCUACAAUAUGUAUUGUAGAUUCACUUUCAAUAAAAUC-----------------UUGAUUUCUUUCAGGGGGCUUGGGC
.......((((((((.....((.....))(((((((((..(((((((....)))))))........((((.......-----------------)))).))))))))))))))...))) ( -25.10)
>DroSim_CAF1 20013 102 + 1
ACAAAAUGCAGGCCCGUGAAGUUUGAAGCCUGAAAGAAUGCUACAAUAUGUAUUGUAGAUUCACUUUCAAUAAAAUC-----------------UUGAUUUCUUUCAGGUGGCUUGGGC
........((((((((.......))..(((((((((((..(((((((....)))))))........((((.......-----------------)))).)))))))))))))))))... ( -29.00)
>DroYak_CAF1 34328 102 + 1
CCAAAAUGUUGGCCCGAAAACUGUGGAGCCUGAAAGAAUGCUAUGAUAUAUAUGGCGCAGUGAGAUUAACAGAGCUU-----------------CUCAUUUUUUUCAGGUGGCUUGGGC
...........((((((.....((...(((((((((((.((((((.....))))))...((((((...........)-----------------)))))))))))))))).)))))))) ( -29.70)
>consensus
ACAAAAUGCUGGCCCGUGAAGUGUGAAGCCUGAAAGAAUGCUACAAUAUGUAUUGUAGAUUCACUUUCAAUAAAAUC_________________UUGAUUUCUUUCAGGUGGCUUGGGC
...........(((((...(((.....(((((((((((..(((((((....)))))))..(((................................))).))))))))))).)))))))) (-19.59 = -20.15 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 20,401,451 – 20,401,570
Length 119
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 77.53
Mean single sequence MFE -23.94
Consensus MFE -16.24
Energy contribution -17.92
Covariance contribution 1.69
Combinations/Pair 1.07
Mean z-score -1.83
Structure conservation index 0.68
SVM decision value 0.76
SVM RNA-class probability 0.843438
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20401451 119 - 23771897
GCCCAAGCCACCUGAAAGAAAUCAAAACGAUUGUUGCACUCAGAUUUUAUUGAAAGUGAAUCUACAAUACAUAUUGUAGCAUUCUUUCAGGCUUCACACUUAACGGGCCAGCAUUUUGA
(((((((((..((((..(.((((.....))))....)..)))).......((((((.....(((((((....)))))))....)))))))))))..........))))........... ( -28.30)
>DroSec_CAF1 15733 102 - 1
GCCCAAGCCCCCUGAAAGAAAUCAA-----------------GAUUUUAUUGAAAGUGAAUCUACAAUACAUAUUGUAGCAUUCUUUCAGGCUUCAAACUUCACGGGACAGCAUUUUGU
((.....(((((((((((((.((((-----------------.......))))........(((((((....)))))))..)))))))))).............)))...))....... ( -23.71)
>DroSim_CAF1 20013 102 - 1
GCCCAAGCCACCUGAAAGAAAUCAA-----------------GAUUUUAUUGAAAGUGAAUCUACAAUACAUAUUGUAGCAUUCUUUCAGGCUUCAAACUUCACGGGCCUGCAUUUUGU
(((((((((...((((((((.((((-----------------.......))))........(((((((....)))))))..)))))))))))))..........))))........... ( -25.40)
>DroYak_CAF1 34328 102 - 1
GCCCAAGCCACCUGAAAAAAAUGAG-----------------AAGCUCUGUUAAUCUCACUGCGCCAUAUAUAUCAUAGCAUUCUUUCAGGCUCCACAGUUUUCGGGCCAACAUUUUGG
((((......(((((((....((((-----------------(...........))))).(((...............)))...))))))).......(....)))))........... ( -18.36)
>consensus
GCCCAAGCCACCUGAAAGAAAUCAA_________________GAUUUUAUUGAAAGUGAAUCUACAAUACAUAUUGUAGCAUUCUUUCAGGCUUCAAACUUCACGGGCCAGCAUUUUGU
(((((((((...((((((((.......................(((((....)))))....(((((((....)))))))..)))))))))))))..........))))........... (-16.24 = -17.92 +   1.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:01 2006