Locus 5000

Sequence ID 3L_DroMel_CAF1
Location 13,756,404 – 13,756,566
Length 162
Max. P 0.988253
window7902 window7903 window7904

overview

Window 2

Location 13,756,404 – 13,756,494
Length 90
Sequences 3
Columns 99
Reading direction forward
Mean pairwise identity 88.89
Mean single sequence MFE -33.07
Consensus MFE -26.47
Energy contribution -26.47
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.95
Structure conservation index 0.80
SVM decision value 1.06
SVM RNA-class probability 0.908950
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13756404 90 + 23771897
GGCUGAAGGAGCAGAUAGGAUGGGAUUGAAUGGACCAGCCUAUCUAUUCUUCUAUCUCAAAAAGCGGG---GAGCCGAGGA------UGUCCUCCAGUU
((((((((((..(((((((.(((..(.....)..))).))))))).))))))..((((.......)))---)))))((((.------...))))..... ( -33.40)
>DroSim_CAF1 175391 90 + 1
GGCUGAAGGAGCAGAUAGGAUGGGAUUGAAUGGACCAGCCUAUCUAUUCUUCUAUCUCAAAAAUCGGG---GGACCGAGGA------UGUCCUCCAGUU
((..((((((..(((((((.(((..(.....)..))).))))))).))))))..)).........(((---((((......------.))))))).... ( -32.50)
>DroYak_CAF1 174366 99 + 1
GGCUGAAGGAGCAGAUAGGAUGGGAUUGAAUGGACCAGCCUAUCUAUUCUUCUAUCUCAAAAAGUGGGCGAGGAGUGAGGAGGAGUGAGUCCUCCAGUU
.(((.....)))(((((((.(((..(.....)..))).)))))))(((((((...((((.....)))).)))))))..((((((.....)))))).... ( -33.30)
>consensus
GGCUGAAGGAGCAGAUAGGAUGGGAUUGAAUGGACCAGCCUAUCUAUUCUUCUAUCUCAAAAAGCGGG___GGACCGAGGA______UGUCCUCCAGUU
((..((((((..(((((((.(((..(.....)..))).))))))).))))))..))....................(((((........)))))..... (-26.47 = -26.47 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,756,404 – 13,756,494
Length 90
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 88.89
Mean single sequence MFE -26.87
Consensus MFE -24.83
Energy contribution -24.94
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -3.12
Structure conservation index 0.92
SVM decision value 2.11
SVM RNA-class probability 0.988253
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13756404 90 - 23771897
AACUGGAGGACA------UCCUCGGCUC---CCCGCUUUUUGAGAUAGAAGAAUAGAUAGGCUGGUCCAUUCAAUCCCAUCCUAUCUGCUCCUUCAGCC
..((((((((..------..((((((..---...)))....))).........((((((((.(((...........))).)))))))).)))))))).. ( -26.60)
>DroSim_CAF1 175391 90 - 1
AACUGGAGGACA------UCCUCGGUCC---CCCGAUUUUUGAGAUAGAAGAAUAGAUAGGCUGGUCCAUUCAAUCCCAUCCUAUCUGCUCCUUCAGCC
..((((((((((------...((((...---.))))....))...........((((((((.(((...........))).)))))))).)))))))).. ( -27.30)
>DroYak_CAF1 174366 99 - 1
AACUGGAGGACUCACUCCUCCUCACUCCUCGCCCACUUUUUGAGAUAGAAGAAUAGAUAGGCUGGUCCAUUCAAUCCCAUCCUAUCUGCUCCUUCAGCC
....((((((.....))))))......((((.........))))...((((..((((((((.(((...........))).))))))))...)))).... ( -26.70)
>consensus
AACUGGAGGACA______UCCUCGGUCC___CCCGCUUUUUGAGAUAGAAGAAUAGAUAGGCUGGUCCAUUCAAUCCCAUCCUAUCUGCUCCUUCAGCC
..((((((((..........(((((..............))))).........((((((((.(((...........))).)))))))).)))))))).. (-24.83 = -24.94 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,756,465 – 13,756,566
Length 101
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 89.47
Mean single sequence MFE -27.70
Consensus MFE -21.69
Energy contribution -21.80
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.17
Structure conservation index 0.78
SVM decision value 0.18
SVM RNA-class probability 0.621003
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13756465 101 - 23771897
AAACUAAACACAAGUCGGCAAGA-ACAGUUUAUUGAAUAUGCAAAAUGUUGUGAACUGCAGCACAGUUGUGCAAACUGGAGGACA------UCCUCGGCUC---CCCGCUU
...........(((.(((.....-.((((((((..(((((.....))))))))))))).(((.(((((.....)))))((((...------.)))).))).---.)))))) ( -25.90)
>DroSim_CAF1 175452 101 - 1
AAACUAAACACAAGUCGGCAAGA-ACAGUUUAUUGAAUAUGCAAAAUGUUGUGAACUGCAGCACAGUUGUGCAAACUGGAGGACA------UCCUCGGUCC---CCCGAUU
............((((((.....-.((((((((..(((((.....)))))))))))))..((((....))))..((((.(((...------.)))))))..---.)))))) ( -25.80)
>DroYak_CAF1 174427 111 - 1
AAACUAAACACAAGUCGGCAAGAAACAGUUUAUUGAAUAUGCAAAAUGUUGUGAACUGCAGCACAGUUGUGCAAACUGGAGGACUCACUCCUCCUCACUCCUCGCCCACUU
...........((((.(((.((...((((((((..(((((.....)))))))))))))..((((....)))).....((((((.....))))))......)).))).)))) ( -31.40)
>consensus
AAACUAAACACAAGUCGGCAAGA_ACAGUUUAUUGAAUAUGCAAAAUGUUGUGAACUGCAGCACAGUUGUGCAAACUGGAGGACA______UCCUCGGUCC___CCCGCUU
...........((((.((.......((((((((..(((((.....)))))))))))))..((((....))))......(((((........)))))........)).)))) (-21.69 = -21.80 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:10 2006