Locus 8187

Sequence ID	3L_DroMel_CAF1
Location	21,536,588 – 21,536,695
Length	107
Max. P	0.998447

overview

Window 7

Location	21,536,588 – 21,536,695
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	76.76
Mean single sequence MFE	-41.44
Consensus MFE	-25.02
Energy contribution	-25.90
Covariance contribution	0.88
Combinations/Pair	1.14
Mean z-score	-2.40
Structure conservation index	0.60
SVM decision value	2.11
SVM RNA-class probability	0.988146
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21536588 107 + 23771897
ACUUCAUUAAGGGCUCCUCCGCUCUUCCGCGCAUUUGAGGGCCAAGGAGCUGGAGCUGGAGCUCGAGCCGAAGGAAGAGACUGAGGAUCCAGCCGAGCUCCAGCUCU
...........(((((((..((((((..........))))))..)))))))((((((((((((((.((....(((............))).)))))))))))))))) ( -49.00)
>DroSec_CAF1 7953 90 + 1
ACUUCAUUAAGGGCUCCUCCGCUCCUCCGCGC-----------AAGGAGCUGAAGCUGG------AGCCGGAGCAAGAGGCUGAGGAUCCAGCCGAGCUUCAGCUCU
.(((((......((((((.(((......))).-----------.)))))))))))..((------(((.(((((....(((((......)))))..))))).))))) ( -38.30)
>DroSim_CAF1 7011 90 + 1
ACUUCAUUAAGGGCUCCUCCGCUCCUCCGCGC-----------AAGGAGCUGAAGCUGG------AGCCGGAGCAAGAGGCUGAGGAUCCAGCCGAGCUUCAGCUCU
.(((((......((((((.(((......))).-----------.)))))))))))..((------(((.(((((....(((((......)))))..))))).))))) ( -38.30)
>DroEre_CAF1 25907 85 + 1
ACUUCAUUAAGGGC----CCGCUCCUCCGCGCACUCGGGGGCCAAGGAGCUGG------------AGCCGGAGGAAGAGGAU------CCAGCCGAACUCCAGCUCC
...........(((----((......(((......))))))))..((((((((------------((.(((.(((......)------))..)))..)))))))))) ( -36.70)
>DroYak_CAF1 26281 103 + 1
ACUUCAUUAAGGGC----CCGCUCCUUCGCGCAUUUGGGGGCCAAGGAGCUGGAGCUGUAGCUGGAGCCAGAGGAAGAGGAUGAGGAGCCAGCCGAGCUUCAGCUCC
...........(((----((.(..............).)))))..((((((((((((...(((((..((...............))..)))))..)))))))))))) ( -44.90)
>consensus
ACUUCAUUAAGGGCUCCUCCGCUCCUCCGCGCA_U_G_GGGCCAAGGAGCUGGAGCUGG______AGCCGGAGGAAGAGGCUGAGGAUCCAGCCGAGCUUCAGCUCU
..........((((......)))).....................((((((((((((...........(.......).(((((......))))).)))))))))))) (-25.02 = -25.90 +   0.88)

alignment

secondary structure

dotplot

Window 8

Location	21,536,588 – 21,536,695
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	76.76
Mean single sequence MFE	-43.12
Consensus MFE	-26.74
Energy contribution	-27.54
Covariance contribution	0.80
Combinations/Pair	1.15
Mean z-score	-2.85
Structure conservation index	0.62
SVM decision value	3.10
SVM RNA-class probability	0.998447
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21536588 107 - 23771897
AGAGCUGGAGCUCGGCUGGAUCCUCAGUCUCUUCCUUCGGCUCGAGCUCCAGCUCCAGCUCCUUGGCCCUCAAAUGCGCGGAAGAGCGGAGGAGCCCUUAAUGAAGU
.(((((((((((((((((((...............)))))).)))))))))))))..(((((((.(((.((.........)).).)).)))))))............ ( -49.56)
>DroSec_CAF1 7953 90 - 1
AGAGCUGAAGCUCGGCUGGAUCCUCAGCCUCUUGCUCCGGCU------CCAGCUUCAGCUCCUU-----------GCGCGGAGGAGCGGAGGAGCCCUUAAUGAAGU
.((((((.(((..((((((....))))))....))).)))))------)..(((((((((((((-----------.(((......))))))))))......)))))) ( -41.60)
>DroSim_CAF1 7011 90 - 1
AGAGCUGAAGCUCGGCUGGAUCCUCAGCCUCUUGCUCCGGCU------CCAGCUUCAGCUCCUU-----------GCGCGGAGGAGCGGAGGAGCCCUUAAUGAAGU
.((((((.(((..((((((....))))))....))).)))))------)..(((((((((((((-----------.(((......))))))))))......)))))) ( -41.60)
>DroEre_CAF1 25907 85 - 1
GGAGCUGGAGUUCGGCUGG------AUCCUCUUCCUCCGGCU------------CCAGCUCCUUGGCCCCCGAGUGCGCGGAGGAGCGG----GCCCUUAAUGAAGU
(((((((((((.(((..((------(......))).))))))------------))))))))..((((((((......)))......))----)))........... ( -41.50)
>DroYak_CAF1 26281 103 - 1
GGAGCUGAAGCUCGGCUGGCUCCUCAUCCUCUUCCUCUGGCUCCAGCUACAGCUCCAGCUCCUUGGCCCCCAAAUGCGCGAAGGAGCGG----GCCCUUAAUGAAGU
(((((((.((((.((((((..((...............))..))))))..)))).)))))))..(((((......((.(....).))))----)))........... ( -41.36)
>consensus
AGAGCUGAAGCUCGGCUGGAUCCUCAGCCUCUUCCUCCGGCU______CCAGCUCCAGCUCCUUGGCCC_C_A_UGCGCGGAGGAGCGGAGGAGCCCUUAAUGAAGU
.(((((((((((.(((((((...............)))))))........)))))))))))...............((..((((.((......))))))..)).... (-26.74 = -27.54 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:57 2006