Locus 4852

Sequence ID	2R_DroMel_CAF1
Location	15,908,883 – 15,909,027
Length	144
Max. P	0.706590

overview

Window 1

Location	15,908,883 – 15,908,975
Length	92
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	81.75
Mean single sequence MFE	-20.93
Consensus MFE	-13.49
Energy contribution	-14.94
Covariance contribution	1.45
Combinations/Pair	1.24
Mean z-score	-1.59
Structure conservation index	0.64
SVM decision value	0.02
SVM RNA-class probability	0.542931
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15908883 92 + 20766785
U----GAUGCC--GUGCAGAUGGGAUCUUAAUUCG---CCAAUCUCAGUUGUCCAUUCGCAUUUUCGGCCAAUUACAUUUGGCCACUUCUUUGUUGCAACA
.----..(((.--((((..((((((.......)).---.((((....)))).))))..))))....((((((......))))))...........)))... ( -22.70)
>DroSec_CAF1 36741 92 + 1
U----GAUGCC--GUGCAAAUGGGAUCUCAAUUCG---CCAAUCUCAGUUGUCCAUUCGCAUUUUCGGCCAAUUACAUUUGGCCACUUCUUUGUUGCAAGA
.----..(((.--((((.((((((....(((((..---........))))))))))).))))....((((((......))))))...........)))... ( -22.10)
>DroSim_CAF1 34180 92 + 1
U----GAUGCC--GUGCAGAUGGGAUCUUAAUUCG---CCAAUCUCAGUUGUCCAUUCGCAUUUUCGGCCAAUUACAUUUGGCCACUUCUUUGUUGCAACA
.----..(((.--((((..((((((.......)).---.((((....)))).))))..))))....((((((......))))))...........)))... ( -22.70)
>DroEre_CAF1 34785 79 + 1
-------------------AUGGGAUCUCAAUUCG---CCAAUCUCAGUUGUCCGUUCGCAUUUUCGGCCAAUUACAUUUGGCCACUUCUUUGUUGCAACC
-------------------.((((((.........---...))))))(((((..............((((((......))))))((......)).))))). ( -16.60)
>DroYak_CAF1 37850 91 + 1
U----GAUGCC--GUGCAGAUGGGAUCUUAAUUCG---CCAAUCUCAGUUGUCCACUCGCAUUUUCGGCCAAUUACAUUUGGCCACUUCUUUGUUGCAGC-
.----(((((.--((((((.((((((.........---...)))))).)))..)))..)))))...((((((......))))))................- ( -21.70)
>DroAna_CAF1 29978 101 + 1
UUUAAGGUCCGGAAUUCCAAUUUGAUCUUCAUUUACACCCCAUCACAGUUGGCCAAUCAUAUCGUUGGCCAAUUACAUUUGCCCUCUUCUUUGUUGCACCA
.....(((.(((....))............................(((((((((((......))))))))))).....................).))). ( -19.80)
>consensus
U____GAUGCC__GUGCAGAUGGGAUCUUAAUUCG___CCAAUCUCAGUUGUCCAUUCGCAUUUUCGGCCAAUUACAUUUGGCCACUUCUUUGUUGCAACA
.....(((((.....((((.((((((...............)))))).))))......)))))...((((((......))))))................. (-13.49 = -14.94 +   1.45)

alignment

secondary structure

dotplot

Window 2

Location	15,908,935 – 15,909,027
Length	92
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	77.09
Mean single sequence MFE	-28.61
Consensus MFE	-16.96
Energy contribution	-17.35
Covariance contribution	0.39
Combinations/Pair	1.11
Mean z-score	-1.60
Structure conservation index	0.59
SVM decision value	0.36
SVM RNA-class probability	0.706590
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15908935 92 + 20766785
UUUUCGGCCAAUUACAUUUGGCCACUUCUUUGUUGCAACAGCAAGGGCGUUGCAGGGGCACAGA----GCCA-AACAGGUGGCAGUUGGAUGGCGGU
....(.((((....((....(((((((.(((.(((((((.((....))))))))).(((.....----))))-)).)))))))...))..)))).). ( -32.40)
>DroSec_CAF1 36793 78 + 1
UUUUCGGCCAAUUACAUUUGGCCACUUCUUUGUUGCAAGAGCAAGGGCGCUGCAGGGGCACAAA----GCCA-AACAUGUGGC--------------
.....((((((......))))))...((((((((.....)))))))).((..(((.(((.....----))).-..).))..))-------------- ( -26.90)
>DroSim_CAF1 34232 78 + 1
UUUUCGGCCAAUUACAUUUGGCCACUUCUUUGUUGCAACAGCAAGGGCGCUGCAGGGGCACAAA----GCCA-AACAUGUGGC--------------
.....((((((......))))))...(((((((((...))))))))).((..(((.(((.....----))).-..).))..))-------------- ( -28.20)
>DroEre_CAF1 34824 88 + 1
UUUUCGGCCAAUUACAUUUGGCCACUUCUUUGUUGCAACC-----GGCGCUGCAGGGACGCAAA----GCCAAAACAGGUGGCAGUUGGAUGGCGGC
.....((((((......))))))........(((((..((-----(((..(((......)))..----((((.......)))).)))))...))))) ( -29.40)
>DroYak_CAF1 37902 85 + 1
UUUUCGGCCAAUUACAUUUGGCCACUUCUUUGUUGCAGC-------GCGCUGCAGGGGCACAAC----UCCA-AACAGGUGGCAGUUGGAUGGCGGC
....(.((((....((....(((((((.(((..(((((.-------...)))))((((.....)----))))-)).)))))))...))..)))).). ( -29.60)
>DroAna_CAF1 30039 84 + 1
UCGUUGGCCAAUUACAUUUGCCCUCUUCUUUGUUGCACCA---GGGGCUCUGCAGGGGCACAGGUGCCCCCA-AACAAGUGGCACU---------AU
......((((.........(((((................---)))))......((((((....))))))..-......))))...---------.. ( -25.19)
>consensus
UUUUCGGCCAAUUACAUUUGGCCACUUCUUUGUUGCAACA___AGGGCGCUGCAGGGGCACAAA____GCCA_AACAGGUGGCAGU_________G_
.....((((((......))))))...(((((((.((............)).)))))))..........((((.......)))).............. (-16.96 = -17.35 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:48 2006