Locus 7657

Sequence ID	3L_DroMel_CAF1
Location	20,569,136 – 20,569,279
Length	143
Max. P	0.858317

overview

Window 5

Location	20,569,136 – 20,569,251
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.92
Mean single sequence MFE	-34.64
Consensus MFE	-25.60
Energy contribution	-25.96
Covariance contribution	0.36
Combinations/Pair	1.10
Mean z-score	-1.87
Structure conservation index	0.74
SVM decision value	0.46
SVM RNA-class probability	0.743917
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20569136 115 + 23771897
CGCCUCAACUCUUGACCCAGCUGCAUAAGCAAUUAUGAUCUUUAUGA---UCCCCGGCGAUCUUGACUGUUGAUGAUC-UUCAUCA-UGAUCAAUGUCCGAGAUCAUCUAGAGCGAGGGA
..((((..((((.((....((((.((((....))))((((.....))---))..))))(((((((((.((((((.((.-......)-).)))))))).))))))).)).)))).)))).. ( -34.10)
>DroSec_CAF1 13912 115 + 1
CGCCUCAACUCUUGACCCAGCUGCAUAAGCAAUUAUGAUCUUGAUGA---UCCCCGGCGAUCUUGACUGCUGAUGAUC-UUCAUCA-UGAUCAAUGUCUGAGAUCAUCUGGAGCGAGGGA
((((...............(((.....)))......((((.....))---))...)))).(((((.((.(.(((((((-((...((-(.....)))...))))))))).).))))))).. ( -34.50)
>DroAna_CAF1 34937 108 + 1
CGCCACGACUCUUGACCCAGCUGCAUAAGCAAUUAUGAUCUUGAUGACCAUCCCC------------CCCAGAUGACCCAUCACCAGUGACCAAUGUCCGAGAUCAACUGGAGCGAGGGA
........((((((..((((.(((....)))....(((((((((((..((((...------------....))))...))))....(.(((....))))))))))).))))..)))))). ( -30.60)
>DroSim_CAF1 7574 115 + 1
CGCCUCAACUCUUGACCCAGCUGCAUAAGCAAUUAUGAUCUUGAUGA---UCCCCGGCGAUCUUGACUGCUGAUGAUC-UUCAUCA-UGAUCAAUGUCCGAGAUCAUCUGGAGCGAGGGA
........((((((..((((.(((....)))...(((((((((....---....(((((........))))).(((((-.......-.))))).....)))))))))))))..)))))). ( -35.50)
>DroEre_CAF1 7435 114 + 1
CGCCUCCACUCUUGACCCAGCUGCACAAGCAAUUAUGAGCUUGCUGA---UCC-CGGCUAGCUUGACUGCUGAUGGUC-UUCAUCA-UGAUCAAUGUCCGAGAUCAUCUGGAGCGAGGGA
........((((((..((((((((....))).....(((((.((((.---...-)))).)))))....)))(((((((-((...((-(.....)))...))))))))).))..)))))). ( -38.50)
>consensus
CGCCUCAACUCUUGACCCAGCUGCAUAAGCAAUUAUGAUCUUGAUGA___UCCCCGGCGAUCUUGACUGCUGAUGAUC_UUCAUCA_UGAUCAAUGUCCGAGAUCAUCUGGAGCGAGGGA
........((((((..((((.(((....)))....((((((((............................(((((....)))))...(((....))))))))))).))))..)))))). (-25.60 = -25.96 +   0.36)

alignment

secondary structure

dotplot

Window 6

Location	20,569,136 – 20,569,251
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.92
Mean single sequence MFE	-40.68
Consensus MFE	-27.02
Energy contribution	-29.86
Covariance contribution	2.84
Combinations/Pair	1.03
Mean z-score	-2.56
Structure conservation index	0.66
SVM decision value	0.64
SVM RNA-class probability	0.809654
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20569136 115 - 23771897
UCCCUCGCUCUAGAUGAUCUCGGACAUUGAUCA-UGAUGAA-GAUCAUCAACAGUCAAGAUCGCCGGGGA---UCAUAAAGAUCAUAAUUGCUUAUGCAGCUGGGUCAAGAGUUGAGGCG
..(((((((((..((((((((((...(((((..-(((((..-...)))))...))))).....)).))))---))))...((((....((((....))))...)))).)))).))))).. ( -39.20)
>DroSec_CAF1 13912 115 - 1
UCCCUCGCUCCAGAUGAUCUCAGACAUUGAUCA-UGAUGAA-GAUCAUCAGCAGUCAAGAUCGCCGGGGA---UCAUCAAGAUCAUAAUUGCUUAUGCAGCUGGGUCAAGAGUUGAGGCG
..((((((((..(((((((((.((..(((((..-(((((..-...)))))...)))))..))....))))---)))))..((((....((((....))))...))))..))).))))).. ( -42.30)
>DroAna_CAF1 34937 108 - 1
UCCCUCGCUCCAGUUGAUCUCGGACAUUGGUCACUGGUGAUGGGUCAUCUGGG------------GGGGAUGGUCAUCAAGAUCAUAAUUGCUUAUGCAGCUGGGUCAAGAGUCGUGGCG
((((((...((((.(((((.((..(((..(...)..))).))))))).)))))------------)))))(((((.....)))))....(((....)))((((.(.(....).).)))). ( -34.60)
>DroSim_CAF1 7574 115 - 1
UCCCUCGCUCCAGAUGAUCUCGGACAUUGAUCA-UGAUGAA-GAUCAUCAGCAGUCAAGAUCGCCGGGGA---UCAUCAAGAUCAUAAUUGCUUAUGCAGCUGGGUCAAGAGUUGAGGCG
..((((((((..(((((((((((...(((((..-(((((..-...)))))...))))).....)).))))---)))))..((((....((((....))))...))))..))).))))).. ( -42.40)
>DroEre_CAF1 7435 114 - 1
UCCCUCGCUCCAGAUGAUCUCGGACAUUGAUCA-UGAUGAA-GACCAUCAGCAGUCAAGCUAGCCG-GGA---UCAGCAAGCUCAUAAUUGCUUGUGCAGCUGGGUCAAGAGUGGAGGCG
((((((..(((((.(((((((((...(((((..-(((((..-...)))))...))))).....)))-)))---)))((((((........))))))....)))))....))).))).... ( -44.90)
>consensus
UCCCUCGCUCCAGAUGAUCUCGGACAUUGAUCA_UGAUGAA_GAUCAUCAGCAGUCAAGAUCGCCGGGGA___UCAUCAAGAUCAUAAUUGCUUAUGCAGCUGGGUCAAGAGUUGAGGCG
..((((((((..(((((((((((...(((((...(((((......)))))...))))).....))))))....)))))..((((....((((....))))...))))..)))).)))).. (-27.02 = -29.86 +   2.84)

alignment

secondary structure

dotplot

Window 7

Location	20,569,176 – 20,569,279
Length	103
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	94.17
Mean single sequence MFE	-37.58
Consensus MFE	-34.64
Energy contribution	-34.83
Covariance contribution	0.19
Combinations/Pair	1.06
Mean z-score	-1.75
Structure conservation index	0.92
SVM decision value	0.82
SVM RNA-class probability	0.858317
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20569176 103 + 23771897
UUUAUGAUCCCCGGCGAUCUUGACUGUUGAUGAUCUUCAUCAUGAUCAAUGUCCGAGAUCAUCUAGAGCGAGGGAGCUGUGGCUGGGAUCUUGGGGGACUUCG
.....((((((((((..(((((.((.(.(((((((((...(((.....)))...))))))))).).)))))))..)))).....))))))..((....))... ( -37.70)
>DroSec_CAF1 13952 103 + 1
UUGAUGAUCCCCGGCGAUCUUGACUGCUGAUGAUCUUCAUCAUGAUCAAUGUCUGAGAUCAUCUGGAGCGAGGGAGCUGUGGCUGGGAUCUUGGGGGACUUCG
.....((((((((((..(((((.((.(.(((((((((...(((.....)))...))))))))).).)))))))..)))).....))))))..((....))... ( -39.00)
>DroSim_CAF1 7614 102 + 1
UUGAUGAUCCCCGGCGAUCUUGACUGCUGAUGAUCUUCAUCAUGAUCAAUGUCCGAGAUCAUCUGGAGCGAGGGAGCUGUGGCUGGGAUCU-GGGGGACUUCG
.....((((((((((..(((((.((.(.(((((((((...(((.....)))...))))))))).).)))))))..)))).....)))))).-((....))... ( -39.00)
>DroEre_CAF1 7475 102 + 1
UUGCUGAUCC-CGGCUAGCUUGACUGCUGAUGGUCUUCAUCAUGAUCAAUGUCCGAGAUCAUCUGGAGCGAGGGAGCUGCGGCUGGUAUCUUGGGGGACUUCG
.....(((.(-((((((((((..((((((((((((((...(((.....)))...)))))))))...))).)).)))))..)))))).)))..((....))... ( -34.60)
>consensus
UUGAUGAUCCCCGGCGAUCUUGACUGCUGAUGAUCUUCAUCAUGAUCAAUGUCCGAGAUCAUCUGGAGCGAGGGAGCUGUGGCUGGGAUCUUGGGGGACUUCG
.....((((((((((..(((((.((.(.(((((((((...(((.....)))...))))))))).).)))))))..)))).....))))))..((....))... (-34.64 = -34.83 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:52:59 2006