Locus 1702

Sequence ID 3L_DroMel_CAF1
Location 4,965,948 – 4,966,041
Length 93
Max. P 0.975900
window2627 window2628

overview

Window 7

Location 4,965,948 – 4,966,041
Length 93
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 85.34
Mean single sequence MFE -27.28
Consensus MFE -19.93
Energy contribution -20.12
Covariance contribution 0.19
Combinations/Pair 1.10
Mean z-score -1.57
Structure conservation index 0.73
SVM decision value 0.18
SVM RNA-class probability 0.620831
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4965948 93 + 23771897
CACAAAC--------AAACACACAAACGCCCACCAAAAAGGAUACCCAUCAAUGAGU-GUUUUGUGUGUGUUGUGUGU-------UGUUUGUUG-------UUCGUUAUUUGUUGU
.((((((--------((.(((((((.(((.(((.....(((((((.((....)).))-)))))))).)))))))))))-------)))))))..-------............... ( -26.30)
>DroSec_CAF1 186677 100 + 1
CACAAAC--------AAACACACAAACGCCCACCAAAAAGGAUACCCAUCAAUGAGU-GUUUUGUGUGUGUUGUGUGUUGUGCGUUGUUUGUUG-------CUCGUUAUUUGUUGU
.((((((--------((.(.(((((((((.(((((...(((((((.((....)).))-))))).)).)))..)))).))))).)))))))))..-------............... ( -25.80)
>DroSim_CAF1 205894 100 + 1
CACAAAC--------AAACACACAAACGCCCACCAAAAAGGAUACCCAUCAAUGAGU-GUUUUGUGUGUGUUGUGUGUUGUGCGUUGUUUGUUG-------UUCGUUAUUUGUUGU
.((((((--------((.(.(((((((((.(((((...(((((((.((....)).))-))))).)).)))..)))).))))).)))))))))..-------............... ( -25.80)
>DroYak_CAF1 193484 116 + 1
CACAAACACAAAUACAAACACACGGCCGCCCACCAAAAAGGAUACCCAUCAAUGAGUGGUAUUGUGUGCGUUGUGUGGUGUGUGUUGUUUGUUGUUCGUUGUACGUUAUUUGUUGU
.((((..((((..((((.((((((.(((((.((((...(.(((((((........).)))))).).)).)).).))))))))))))))...))))...)))).............. ( -31.20)
>consensus
CACAAAC________AAACACACAAACGCCCACCAAAAAGGAUACCCAUCAAUGAGU_GUUUUGUGUGUGUUGUGUGUUGUGCGUUGUUUGUUG_______UUCGUUAUUUGUUGU
.((((((.........(((((((((.(((.(((.((((.....((.((....)).))..))))))).)))))))))))).......))))))........................ (-19.93 = -20.12 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 4,965,948 – 4,966,041
Length 93
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 85.34
Mean single sequence MFE -26.83
Consensus MFE -19.91
Energy contribution -19.85
Covariance contribution -0.06
Combinations/Pair 1.08
Mean z-score -2.73
Structure conservation index 0.74
SVM decision value 1.76
SVM RNA-class probability 0.975900
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4965948 93 - 23771897
ACAACAAAUAACGAA-------CAACAAACA-------ACACACAACACACACAAAAC-ACUCAUUGAUGGGUAUCCUUUUUGGUGGGCGUUUGUGUGUUU--------GUUUGUG
...............-------..(((((((-------(........(((((((((.(-.(((((..(.(((...)))..)..))))).))))))))))))--------)))))). ( -26.60)
>DroSec_CAF1 186677 100 - 1
ACAACAAAUAACGAG-------CAACAAACAACGCACAACACACAACACACACAAAAC-ACUCAUUGAUGGGUAUCCUUUUUGGUGGGCGUUUGUGUGUUU--------GUUUGUG
..............(-------(..........))...(((.((((.(((((((((.(-.(((((..(.(((...)))..)..))))).))))))))))))--------)).))). ( -26.20)
>DroSim_CAF1 205894 100 - 1
ACAACAAAUAACGAA-------CAACAAACAACGCACAACACACAACACACACAAAAC-ACUCAUUGAUGGGUAUCCUUUUUGGUGGGCGUUUGUGUGUUU--------GUUUGUG
...............-------............(((((.(((.((((((((...(((-.(((((..(.(((...)))..)..))))).))))))))))))--------))))))) ( -26.10)
>DroYak_CAF1 193484 116 - 1
ACAACAAAUAACGUACAACGAACAACAAACAACACACACCACACAACGCACACAAUACCACUCAUUGAUGGGUAUCCUUUUUGGUGGGCGGCCGUGUGUUUGUAUUUGUGUUUGUG
...........((.....))........((((.(((((....((((.((((((....((.(((((..(.(((...)))..)..))))).))..))))))))))...))))))))). ( -28.40)
>consensus
ACAACAAAUAACGAA_______CAACAAACAACGCACAACACACAACACACACAAAAC_ACUCAUUGAUGGGUAUCCUUUUUGGUGGGCGUUUGUGUGUUU________GUUUGUG
.......................................((((.((((((((((((....(((((..(.(((...)))..)..)))))..)))))))))..........))))))) (-19.91 = -19.85 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:04 2006