Locus 1618

Sequence ID 3L_DroMel_CAF1
Location 4,746,064 – 4,746,163
Length 99
Max. P 0.950757
window2500 window2501

overview

Window 0

Location 4,746,064 – 4,746,163
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.28
Mean single sequence MFE -44.16
Consensus MFE -28.24
Energy contribution -29.72
Covariance contribution 1.48
Combinations/Pair 1.26
Mean z-score -2.09
Structure conservation index 0.64
SVM decision value 1.40
SVM RNA-class probability 0.950757
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4746064 99 + 23771897
ACGGAACUGUUCGUGGUAUCCCGGCCCGCCCAUCCUACGGAUAUCA---------------UCCACAUGCUGCUGCCAUUUUCGCAGCA-ACGGAGGGAGUGCCGGGAACCA-----CAG
............(((((.(((((((.(.(((.(((...((((...)---------------)))....(.((((((.......))))))-.))))))).).)))))))))))-----).. ( -45.40)
>DroPse_CAF1 19363 120 + 1
AUGGCACUGUGCGGGGCAUACCGGCGCGGCCCUCCUACGGCUACCAUCACCAUCACCAGCAUCCCCAUGCGGCGGCCAUCUUUGCCACGGACGGGGGCGGCGACUCGCCCCUGAGGGGGG
......((((((.((.....)).))))))(((((((...................((.((((....))))(((((......)))))..)).(((((((((....)))))))))))))))) ( -52.60)
>DroSec_CAF1 6299 99 + 1
ACGGCACUGUUCGUGGUAUCCCGGCCCGCCCAUCCUACGGAUAUCA---------------UCCACAUGCUGCUGCCAUUUUCGCAGCG-ACAGAGGGAGUGCCGGGAACCA-----CAG
............(((((.(((((((.(.(((.......((((...)---------------)))...((.((((((.......))))))-.))..))).).)))))))))))-----).. ( -42.10)
>DroSim_CAF1 6861 99 + 1
ACGGCACUGUUCGUGGUAUCCCGGCCCGCCCAUCCUACGGGUAUCA---------------UCCACAUGCUGCUGCCAUUUUCGCAGCG-ACUGAGGGAGUGCCGGGAACCA-----CAG
............(((((.(((((((.(.(((..((....)).....---------------....((.(.((((((.......))))))-.))).))).).)))))))))))-----).. ( -41.50)
>DroYak_CAF1 5112 99 + 1
AUGGAACGGUGCGUGGCAUCCCGGCUCGCCCAUCCUACGGAUAUCA---------------UCCACAUGCUGCUGCCAUUUUCGCGGCA-ACGGAGGGAGUGCCGGGCACAA-----CAG
........((((.(((((((((((....))..(((...((((...)---------------)))....(.((((((.......))))))-.)))))))).))))).))))..-----... ( -39.20)
>consensus
ACGGCACUGUUCGUGGUAUCCCGGCCCGCCCAUCCUACGGAUAUCA_______________UCCACAUGCUGCUGCCAUUUUCGCAGCG_ACGGAGGGAGUGCCGGGAACCA_____CAG
......(((....((((.(((((((.(.(((((((...))))...................(((...((((((..........))))))...)))))).).))))))))))).....))) (-28.24 = -29.72 +   1.48)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,746,064 – 4,746,163
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.28
Mean single sequence MFE -45.74
Consensus MFE -26.95
Energy contribution -28.19
Covariance contribution 1.24
Combinations/Pair 1.21
Mean z-score -1.69
Structure conservation index 0.59
SVM decision value 0.11
SVM RNA-class probability 0.588601
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4746064 99 - 23771897
CUG-----UGGUUCCCGGCACUCCCUCCGU-UGCUGCGAAAAUGGCAGCAGCAUGUGGA---------------UGAUAUCCGUAGGAUGGGCGGGCCGGGAUACCACGAACAGUUCCGU
.((-----(((((((((((.(.((((((((-((((((.......))))))))....(((---------------(...))))...))).))).).))))))).))))))........... ( -50.50)
>DroPse_CAF1 19363 120 - 1
CCCCCCUCAGGGGCGAGUCGCCGCCCCCGUCCGUGGCAAAGAUGGCCGCCGCAUGGGGAUGCUGGUGAUGGUGAUGGUAGCCGUAGGAGGGCCGCGCCGGUAUGCCCCGCACAGUGCCAU
.........((((((.(((((((((((((((.(((((.......))))).).))))))..)).))))))((((.((((..((......))))))))))....))))))((.....))... ( -52.60)
>DroSec_CAF1 6299 99 - 1
CUG-----UGGUUCCCGGCACUCCCUCUGU-CGCUGCGAAAAUGGCAGCAGCAUGUGGA---------------UGAUAUCCGUAGGAUGGGCGGGCCGGGAUACCACGAACAGUGCCGU
.((-----(((((((((((.(.((((((((-.(((((.......))))).))....(((---------------(...))))...))).))).).))))))).))))))........... ( -43.80)
>DroSim_CAF1 6861 99 - 1
CUG-----UGGUUCCCGGCACUCCCUCAGU-CGCUGCGAAAAUGGCAGCAGCAUGUGGA---------------UGAUACCCGUAGGAUGGGCGGGCCGGGAUACCACGAACAGUGCCGU
.((-----(((((((((((.(.(((((.((-.(((((.......))))).))(((.((.---------------.....)))))..)).))).).))))))).))))))........... ( -42.60)
>DroYak_CAF1 5112 99 - 1
CUG-----UUGUGCCCGGCACUCCCUCCGU-UGCCGCGAAAAUGGCAGCAGCAUGUGGA---------------UGAUAUCCGUAGGAUGGGCGAGCCGGGAUGCCACGCACCGUUCCAU
..(-----(.(((((((((.(.((((((((-(((((......))))))).......(((---------------(...))))...))).))).).)))))).))).))............ ( -39.20)
>consensus
CUG_____UGGUUCCCGGCACUCCCUCCGU_CGCUGCGAAAAUGGCAGCAGCAUGUGGA_______________UGAUAUCCGUAGGAUGGGCGGGCCGGGAUACCACGAACAGUGCCGU
.........((((((((((.(.((((((....(((((..........)))))....((......................))...))).))).).))))))).))).............. (-26.95 = -28.19 +   1.24)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:00 2006