Locus 4289

Sequence ID 2L_DroMel_CAF1
Location 12,268,480 – 12,268,604
Length 124
Max. P 0.626378
window6761 window6762

overview

Window 1

Location 12,268,480 – 12,268,573
Length 93
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 77.93
Mean single sequence MFE -29.35
Consensus MFE -18.77
Energy contribution -19.25
Covariance contribution 0.48
Combinations/Pair 1.17
Mean z-score -1.28
Structure conservation index 0.64
SVM decision value 0.03
SVM RNA-class probability 0.551131
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12268480 93 - 22407834
UGAAGGCCCACUUGGGACAGCUGGCUGAGAUGCCGUGCAAAGUUGUGGGUAGGUGUUUGGGGAAAAUCAUCUUCGACGGCGUCGACAUGGGUC
....((((((..((.(((.((((((......)))).))...(((((.((.((((((((.....))).))))))).))))))))..)))))))) ( -32.30)
>DroSec_CAF1 91555 82 - 1
UGAAGGCCCACUUGGGACAGCUGGCUGAGAUGCCGUAGA-----------AGGUGUAUGGGGAAAAUCAUCUUCGACGGCGUCGACAUGGGUC
....((((((.......(((....))).((((((((.((-----------(((((.((.......))))))))).))))))))....)))))) ( -34.10)
>DroSim_CAF1 95660 82 - 1
UGAAGGCCCACUUGGGACAGCUGGCUGAGAUGCCGUAGA-----------AGGUGUGUGGGGAAAAUCAUCUUCGACGGCGUCGACAUGGGUC
....((((((.......(((....))).((((((((.((-----------(((((............))))))).))))))))....)))))) ( -33.70)
>DroEre_CAF1 89413 88 - 1
UGAAGGCCCACUUGGGACAGUCGGCUGAGAUGCCGAC-----UUGGGGAAAAGUGUGCGGGGAAAAUCAUCUUCGACGGCGUCGACAUGGGUC
....((((((..((.((((((((((......))))))-----).........((((.((((((......)))))))).)))))..)))))))) ( -31.30)
>DroYak_CAF1 95369 87 - 1
UGAAGGCCCACUUGGGACAGCCGACUGAGAUGCCGAG-----UUAGGGA-AAGUGUGCGGGGAAAAUCAUCUUCGACGGCGUCGACAUGGGUC
....((((((..((.(((.(((((((....(.((...-----...)).)-.)))...((((((......)))))).)))))))..)))))))) ( -27.20)
>DroPer_CAF1 148648 74 - 1
UGAAGGCACACUGGGGACAGCUAACAGAGAGAGAGAG-------------------AUAGGGCGACCCUUCUAUGGCGGCGUCGACAUGGGUC
....(((.((.((..(((.(((..((.........((-------------------(..((....))..))).))..))))))..)))).))) ( -17.50)
>consensus
UGAAGGCCCACUUGGGACAGCUGGCUGAGAUGCCGAG_____________AGGUGUGUGGGGAAAAUCAUCUUCGACGGCGUCGACAUGGGUC
....((((((..((.(((.((((((......))).......................((((((......))))))..))))))..)))))))) (-18.77 = -19.25 +   0.48)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,268,512 – 12,268,604
Length 92
Sequences 6
Columns 92
Reading direction forward
Mean pairwise identity 79.95
Mean single sequence MFE -17.10
Consensus MFE -10.62
Energy contribution -11.07
Covariance contribution 0.45
Combinations/Pair 1.18
Mean z-score -1.60
Structure conservation index 0.62
SVM decision value 0.19
SVM RNA-class probability 0.626378
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12268512 92 + 22407834
CCCAAACACCUACCCACAACUUUGCACGGCAUCUCAGCCAGCUGUCCCAAGUGGGCCUUCAUUUUGAGGCUAAAAAACUUUUAUAAUAGAUU
.........(((.((((......((..(((......))).))........))))(((((......)))))................)))... ( -16.44)
>DroSec_CAF1 91587 81 + 1
CCCAUACACCU-----------UCUACGGCAUCUCAGCCAGCUGUCCCAAGUGGGCCUUCAUUUUGAGGCUAAAAAACUUUUAUAAUAGAUU
...........-----------((((.(((......))).........((((.((((((......)))))).....))))......)))).. ( -15.30)
>DroSim_CAF1 95692 81 + 1
CCCACACACCU-----------UCUACGGCAUCUCAGCCAGCUGUCCCAAGUGGGCCUUCAUUUUGAGGCUAAAAAACUUUUAUAAUAGAUU
...........-----------((((.(((......))).........((((.((((((......)))))).....))))......)))).. ( -15.30)
>DroEre_CAF1 89445 87 + 1
CCCGCACACUUUUCCCCAA-----GUCGGCAUCUCAGCCGACUGUCCCAAGUGGGCCUUCAUUUUGAGGCUAAAAAACUUUUAUAAUAGAUU
......(((((.......(-----((((((......))))))).....)))))((((((......))))))..................... ( -24.40)
>DroYak_CAF1 95401 86 + 1
CCCGCACACUU-UCCCUAA-----CUCGGCAUCUCAGUCGGCUGUCCCAAGUGGGCCUUCAUUUUGAGGCUAAAAAACUUUUAUAAUAGAUU
......(((((-.......-----.(((((......))))).......)))))((((((......))))))..................... ( -15.66)
>DroPer_CAF1 148680 73 + 1
CCUAU-------------------CUCUCUCUCUCUGUUAGCUGUCCCCAGUGUGCCUUCAUUUUGGGGGUAAAAAACUUUUAUAAUAGAUU
.....-------------------.........(((((((((((....)))).(((((((.....)))))))...........))))))).. ( -15.50)
>consensus
CCCACACACCU_____________CACGGCAUCUCAGCCAGCUGUCCCAAGUGGGCCUUCAUUUUGAGGCUAAAAAACUUUUAUAAUAGAUU
...........................(((......)))..((((...((((.((((((......)))))).....)))).....))))... (-10.62 = -11.07 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:15 2006