Locus 4948

Sequence ID	2R_DroMel_CAF1
Location	16,126,251 – 16,126,394
Length	143
Max. P	0.833929

overview

Window 7

Location	16,126,251 – 16,126,357
Length	106
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	82.73
Mean single sequence MFE	-36.70
Consensus MFE	-26.52
Energy contribution	-26.76
Covariance contribution	0.24
Combinations/Pair	1.19
Mean z-score	-1.97
Structure conservation index	0.72
SVM decision value	0.73
SVM RNA-class probability	0.833929
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16126251 106 - 20766785
AUCCAAAGUUGGUUUAU-ACUUUGCUGCUGCUGCAUUGAACGCGAGUGUGUCAUGACCAGUGCAGCGGCGCAGACGCGGCCAAGACAAUGGAUC-CACCAGCGUCACA
........((((((...-..(((((.((((((((((((.((....))..((....)))))))))))))))))))...))))))(((..(((...-..)))..)))... ( -38.70)
>DroSec_CAF1 15490 107 - 1
AUCAAAUGUUAGUUUUUCACUUUGGUGCUGCUACAUUGAACGCGACUGUGUCAUGGCCAGUGCAGCGGCACAGACGCGGCCAAGACAAUGGAAC-CACCAGCGUCACA
........................((((((((.(((((..((.(((...))).))..))))).)))))))).((((((((((......)))...-..)).)))))... ( -34.00)
>DroSim_CAF1 15583 107 - 1
AUCAAAUGUUAGUUUUUCACUUUGGUACUGCUGCAUUGAACGCGUCUGUGUCAUGGCCAGUGCAGUGGCACAGACGCGGCCAAGACAAUGGAAC-CACCAGCGUCACA
.....((((((((.....))).((((.((..((..(((..((((((((((((((.((....)).))))))))))))))..)))..))..)).))-))..))))).... ( -39.60)
>DroEre_CAF1 16038 106 - 1
GUCAAAUGUUAGGUUAU-AUUUCGGUGCUGCUACGCUGAACGCGACUGUGUCAUGGCCAGUGCAGCGGCACAGACACGGCCAAGACAAUGGAUC-CACCAGCGUCACA
(((((((((......))-))))..((((((((.(((((..((.(((...))).))..))))).)))))))).)))........(((..(((...-..)))..)))... ( -35.90)
>DroYak_CAF1 15906 89 - 1
-------------------UGGUGGUGCUGCUACGCUGAACGCGACUGUGUCAUGGCCAGUGCAGCGGCACAGGCACGGCCAAGACAAUGGAUCCCACCAACGUCACA
-------------------(((((((((((((.(((((..((.(((...))).))..))))).)))))))).(((...)))..............)))))........ ( -35.30)
>consensus
AUCAAAUGUUAGUUUAU_ACUUUGGUGCUGCUACAUUGAACGCGACUGUGUCAUGGCCAGUGCAGCGGCACAGACGCGGCCAAGACAAUGGAUC_CACCAGCGUCACA
........................((((((((.(((((..((.((.....)).))..))))).)))))))).((((((((((......)))......)).)))))... (-26.52 = -26.76 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	16,126,283 – 16,126,394
Length	111
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	79.06
Mean single sequence MFE	-28.76
Consensus MFE	-21.62
Energy contribution	-22.12
Covariance contribution	0.50
Combinations/Pair	1.22
Mean z-score	-1.46
Structure conservation index	0.75
SVM decision value	0.01
SVM RNA-class probability	0.537503
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16126283 111 - 20766785
UUCAUAUCAAUCGGUUCACUAUGUA---CCUACCUAUUCAAUCCAAAGUUGGUUUAU-ACUUUGCUGCUGCUGCAUUGAACGCGAGUGUGUCAUGACCAGUGCAGCGGCGCAGAC
......................(((---...(((.(((........))).)))...)-))(((((.((((((((((((.((....))..((....))))))))))))))))))). ( -30.40)
>DroSec_CAF1 15522 115 - 1
UUCAUAUCAAUUAGUUCACUACAUACUACAUACCUAUUAAAUCAAAUGUUAGUUUUUCACUUUGGUGCUGCUACAUUGAACGCGACUGUGUCAUGGCCAGUGCAGCGGCACAGAC
.......(((.......(((((((.....................))).))))........)))((((((((.(((((..((.(((...))).))..))))).)))))))).... ( -24.16)
>DroSim_CAF1 15615 108 - 1
UUCAUAUCAAUCAGUUCACUAU-------GUACCUAUUAAAUCAAAUGUUAGUUUUUCACUUUGGUACUGCUGCAUUGAACGCGUCUGUGUCAUGGCCAGUGCAGUGGCACAGAC
......(((((((((.......-------(((((.........((((....))))........))))).)))).)))))....(((((((((((.((....)).))))))))))) ( -30.03)
>DroEre_CAF1 16070 104 - 1
UUCGAA--AAU-----UACGAU---CCUGGUACCUCUUAAGUCAAAUGUUAGGUUAU-AUUUCGGUGCUGCUACGCUGAACGCGACUGUGUCAUGGCCAGUGCAGCGGCACAGAC
..((((--(..-----((..(.---(((..((..............))..))))..)-))))))((((((((.(((((..((.(((...))).))..))))).)))))))).... ( -30.44)
>consensus
UUCAUAUCAAUCAGUUCACUAU______CGUACCUAUUAAAUCAAAUGUUAGUUUAU_ACUUUGGUGCUGCUACAUUGAACGCGACUGUGUCAUGGCCAGUGCAGCGGCACAGAC
................................................................((((((((((((((..((.((.....)).))..)))))))))))))).... (-21.62 = -22.12 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:57 2006