Locus 1276

Sequence ID 3L_DroMel_CAF1
Location 3,688,897 – 3,688,987
Length 90
Max. P 0.808828
window1992 window1993

overview

Window 2

Location 3,688,897 – 3,688,987
Length 90
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 95.74
Mean single sequence MFE -20.13
Consensus MFE -15.64
Energy contribution -16.20
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.81
Structure conservation index 0.78
SVM decision value 0.05
SVM RNA-class probability 0.556493
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3688897 90 + 23771897
GUUUAUCAGUCGCUGCCGGGCUGGGAAAUAUUCCC-CUU-UUGGAUUUU-CCAGCAUUUUCCUCCCUGAUUUUCCCCUUCCACUGUCAGCAAA
...........((((.((((((((((((...(((.-...-..)))))))-)))))....((......)).............))).))))... ( -22.10)
>DroSec_CAF1 84275 90 + 1
GUUUAUCAGUCGCUGCCGGGCUGGGAAGUAUUCCC-CUU-UUGGAUUUU-CCAGCAUUUUCCUCCCUGAUUUUCCCCUUCCACUGUCAACAAA
....(((((..........(((((((((...(((.-...-..)))))))-)))))..........)))))....................... ( -17.45)
>DroSim_CAF1 79257 90 + 1
GUUUAUCAGUCGCUGCCGGGCUGGGAAGUAUUCCC-CUU-UUGGAUUUU-CCAGCAUUUUCCUCCCUGAUUUUCCCCUUCCACUGUCAGCAAA
...........((((.((((((((((((...(((.-...-..)))))))-)))))....((......)).............))).))))... ( -21.80)
>DroEre_CAF1 78838 91 + 1
GUUUAUCAGUCGCUGCCGGGCUGGGAAAUAUUCCCCCUU-UUGGUUUUU-CCAGCAUUUUUCUCCCUGAUUUUCCCCUUCCACUGUCAGCAAA
...........((((.((((((((((((....((.....-..)).))))-))))).....((.....)).............))).))))... ( -21.80)
>DroYak_CAF1 66347 93 + 1
GUUUAUCAGUCGCCGCCGGGCUGGGAAAUAUUCCCACUUUUUGGUUUUUACCAGCAUUUUCCUCCCUGAUUUUCCCCUUCCACUGUCAGCAAA
(((...((((.(((....)))(((((.....)))))....(((((....)))))...........................))))..)))... ( -17.50)
>consensus
GUUUAUCAGUCGCUGCCGGGCUGGGAAAUAUUCCC_CUU_UUGGAUUUU_CCAGCAUUUUCCUCCCUGAUUUUCCCCUUCCACUGUCAGCAAA
...........((((.((((((((.(((...(((........))).))).)))))............((.........))..))).))))... (-15.64 = -16.20 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 3,688,897 – 3,688,987
Length 90
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 95.74
Mean single sequence MFE -22.38
Consensus MFE -19.54
Energy contribution -19.22
Covariance contribution -0.32
Combinations/Pair 1.10
Mean z-score -1.44
Structure conservation index 0.87
SVM decision value 0.64
SVM RNA-class probability 0.808828
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3688897 90 - 23771897
UUUGCUGACAGUGGAAGGGGAAAAUCAGGGAGGAAAAUGCUGG-AAAAUCCAA-AAG-GGGAAUAUUUCCCAGCCCGGCAGCGACUGAUAAAC
.((((((...(.((...((((((.((((.(.......).))))-....(((..-...-.)))...))))))..)))..))))))......... ( -23.40)
>DroSec_CAF1 84275 90 - 1
UUUGUUGACAGUGGAAGGGGAAAAUCAGGGAGGAAAAUGCUGG-AAAAUCCAA-AAG-GGGAAUACUUCCCAGCCCGGCAGCGACUGAUAAAC
.((((((...(.((...(((((..((((.(.......).))))-....(((..-...-.)))....)))))..)))..))))))......... ( -19.90)
>DroSim_CAF1 79257 90 - 1
UUUGCUGACAGUGGAAGGGGAAAAUCAGGGAGGAAAAUGCUGG-AAAAUCCAA-AAG-GGGAAUACUUCCCAGCCCGGCAGCGACUGAUAAAC
.((((((...(.((...(((((..((((.(.......).))))-....(((..-...-.)))....)))))..)))..))))))......... ( -22.30)
>DroEre_CAF1 78838 91 - 1
UUUGCUGACAGUGGAAGGGGAAAAUCAGGGAGAAAAAUGCUGG-AAAAACCAA-AAGGGGGAAUAUUUCCCAGCCCGGCAGCGACUGAUAAAC
((..(.....)..))........(((((...(.....((((((-.....((..-..))((((.....))))...)))))).)..))))).... ( -22.70)
>DroYak_CAF1 66347 93 - 1
UUUGCUGACAGUGGAAGGGGAAAAUCAGGGAGGAAAAUGCUGGUAAAAACCAAAAAGUGGGAAUAUUUCCCAGCCCGGCGGCGACUGAUAAAC
.((((((...(.((...(((((((((((.(.......).))))).....(((.....))).....))))))..)))..))))))......... ( -23.60)
>consensus
UUUGCUGACAGUGGAAGGGGAAAAUCAGGGAGGAAAAUGCUGG_AAAAUCCAA_AAG_GGGAAUAUUUCCCAGCCCGGCAGCGACUGAUAAAC
.((((((...(.((...(((((..((((.(.......).))))......((........)).....)))))..)))..))))))......... (-19.54 = -19.22 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:36 2006