Locus 2169

Sequence ID 2L_DroMel_CAF1
Location 5,863,117 – 5,863,236
Length 119
Max. P 0.985244
window3501 window3502

overview

Window 1

Location 5,863,117 – 5,863,212
Length 95
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 78.02
Mean single sequence MFE -22.12
Consensus MFE -14.49
Energy contribution -15.18
Covariance contribution 0.69
Combinations/Pair 1.05
Mean z-score -2.38
Structure conservation index 0.66
SVM decision value 2.00
SVM RNA-class probability 0.985244
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5863117 95 + 22407834
AUAAGGUUGCAUAAAAAA-------------------GAGCGAAU-UGAGGGUCAGUGAAAAGCACUUUGCUGUCUCCAAUUGCAA-AUCAACCAAUUCCGAUCCCCAAAAAAAAA
....((((((........-------------------).((.(((-((.(((.(((..((......))..))).))))))))))..-..)))))...................... ( -20.00)
>DroSec_CAF1 53093 91 + 1
AUAAGGUUGCAUAAAAAA--------------------AGCGAAUUUGAGGGUCAGUGAAAAGCACUUUGCUGUCUCCAAUUGCAAAAUCAACCAAUUCCGAGCCUCAAAA-----
......((((........--------------------.)))).(((((((.((.(((.....)))(((((...........))))).............)).))))))).----- ( -19.30)
>DroSim_CAF1 53854 93 + 1
AUAAAGUUGCAUAAAAAAA------------------CAGCGAAG-UGAGGGUCAGUGAAAAGCACUUUGCUGUCUCCAAUUGCAAAAUCAACCAAUUCCGACCCUCAAAAA----
.....((((..........------------------))))....-((((((((.(((.....)))(((((...........))))).............))))))))....---- ( -21.90)
>DroEre_CAF1 77318 113 + 1
AAAAAGUUGUACAAA-AAUCCUGGCAUCCAGGGCAUUGAGCGAAU-UGAGGGUCAGUGAAAAACACUUUGCUGUUUCCAAUUGCAA-AUCAACCAAUUCCAAGCACCAAAAAAAAA
.....((((..(((.-..((((((...))))))..))).((.(((-((.(((.(((..((......))..))).))))))))))..-..))))....................... ( -22.90)
>DroYak_CAF1 78267 114 + 1
AUAAGGUUGAACAAAAAAUCCUGGCAUUCAGAACGAUGAGCGAAU-UGAGGGUCAGUGAAAAGCACUUUGCUGUCUCCAAUUGCAA-AUCAACCAAUUUCCCCCACCAAAAAAAAA
....((((((..........(((.....)))........((.(((-((.(((.(((..((......))..))).))))))))))..-.))))))...................... ( -26.50)
>consensus
AUAAGGUUGCAUAAAAAA___________________GAGCGAAU_UGAGGGUCAGUGAAAAGCACUUUGCUGUCUCCAAUUGCAA_AUCAACCAAUUCCGACCCCCAAAAAAAAA
....(((((...........(((.....)))........((((...((.(((.(((..((......))..))).))))).)))).....)))))...................... (-14.49 = -15.18 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 5,863,138 – 5,863,236
Length 98
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 86.78
Mean single sequence MFE -15.45
Consensus MFE -10.14
Energy contribution -9.98
Covariance contribution -0.16
Combinations/Pair 1.09
Mean z-score -2.34
Structure conservation index 0.66
SVM decision value 0.37
SVM RNA-class probability 0.709491
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5863138 98 + 22407834
CGAAU-UGAGGGUCAGUGAAAAGCACUUUGCUGUCUCCAAUUGCAA-AUCAACCAAUUCCGAUCCCCAAAAAAAAAAAAAAUCCGAAAAUAAUAAAAACA
..(((-((.(((.(((..((......))..))).))))))))....-.........(((.(((.................))).)))............. ( -13.63)
>DroSec_CAF1 53113 93 + 1
CGAAUUUGAGGGUCAGUGAAAAGCACUUUGCUGUCUCCAAUUGCAAAAUCAACCAAUUCCGAGCCUCAAAA-------AAAUCAGAAAAUAAUAAAAACA
....(((((((.((.(((.....)))(((((...........))))).............)).))))))).-------...................... ( -17.60)
>DroSim_CAF1 53876 95 + 1
CGAAG-UGAGGGUCAGUGAAAAGCACUUUGCUGUCUCCAAUUGCAAAAUCAACCAAUUCCGACCCUCAAAAA----AAAAAUCAGAAAAUAAUAAAAACA
.....-((((((((.(((.....)))(((((...........))))).............))))))))....----........................ ( -20.20)
>DroEre_CAF1 77357 92 + 1
CGAAU-UGAGGGUCAGUGAAAAACACUUUGCUGUUUCCAAUUGCAA-AUCAACCAAUUCCAAGCACCAAAAAAAAAA------AGAAAAUAAUAAAAACA
.((((-((.(((.(((..((......))..)))..)))..(((...-..))).))))))..................------................. ( -12.30)
>DroYak_CAF1 78307 96 + 1
CGAAU-UGAGGGUCAGUGAAAAGCACUUUGCUGUCUCCAAUUGCAA-AUCAACCAAUUUCCCCCACCAAAAAAAAAU--AGCCAGAAAAUAAUAAAAACA
..(((-((.(((.(((..((......))..))).))))))))....-..............................--..................... ( -13.50)
>consensus
CGAAU_UGAGGGUCAGUGAAAAGCACUUUGCUGUCUCCAAUUGCAA_AUCAACCAAUUCCGACCCCCAAAAAAAAAA_AAAUCAGAAAAUAAUAAAAACA
.(....((.(((.(((..((......))..))).)))))....)........................................................ (-10.14 =  -9.98 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:19 2006