Locus 5534

Sequence ID	3L_DroMel_CAF1
Location	15,192,265 – 15,192,392
Length	127
Max. P	0.992845

overview

Window 4

Location	15,192,265 – 15,192,373
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.28
Mean single sequence MFE	-38.80
Consensus MFE	-23.42
Energy contribution	-23.20
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-3.06
Structure conservation index	0.60
SVM decision value	2.33
SVM RNA-class probability	0.992497
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15192265 108 + 23771897
----UGUUGCCCCAUGCCUUGACACAGAUUUGUUGGCCAAAGUUGGCGACAACGUCGUCGCCUUUUUUGGCCCAGGCGUCUAAGCC----GG----GACUUGUAAAAGGAUCCUCGGCUC
----.........((((((.((((......))))((((((((..((((((......))))))..)))))))).))))))...((((----((----(((((.....))).))).))))). ( -45.80)
>DroVir_CAF1 71150 91 + 1
----UGUUGC-CCAUGGCUUGACACAGAUUUGUUGGCCAAAGUUGGCGACAACGUCGUCGCCUUUUUAGGCCCAGGCGUCUAAGUU----GCAGGCAACU--------------------
----.(((((-(..(((((((((((......)).((((.(((..((((((......))))))..))).)))).....))).)))))----)..)))))).-------------------- ( -36.80)
>DroPse_CAF1 70841 110 + 1
----UGUUGCCCCAUGCCUUGACACAGAUUUGUUGGCCAAAGUUGGCGACAACGUCGUCGCCUUUUUUGGUCCAGGCGUCUAAGCCAGCAGA----CUCUUAUAAAAGGAUCCACU--CU
----............((((.....(((((((((((((((((..((((((......))))))..))))))))..(((......)))))))))----.))).....)))).......--.. ( -37.30)
>DroGri_CAF1 77502 99 + 1
UUGCUGUUGC-CCAUGGCUUGACACAGAUUUGUUGGCCAAAGUUGGCGACAGCGUCGUCGCCUUUUUAGGCCCAGGCGUCUAAGUU----GCAGGCAACU----------------GCUU
..((((((((-(..(((((.((((......))))))))).....)))))))))(.((((((((....))))...)))).)......----((((....))----------------)).. ( -41.20)
>DroMoj_CAF1 76009 91 + 1
----UGUUGC-CCAUGGCUUGACACAGAUUUGUUGGCCAAAGUUGGCGACAACGUCGUCGCCUUUUUAGGCCCAGGCGUCUAUUUC----GCAGCCAACU--------------------
----......-...((((((((.(.((((.(.(.((((.(((..((((((......))))))..))).)))).).).)))).).))----).)))))...-------------------- ( -33.00)
>DroPer_CAF1 70982 110 + 1
----UGUUGCCCCAUGCCUUGACACAGAUUUGUUGGCCAAAGUUGGCGACAACGUCGUCGCCUUUUUUGGUCCAGGCGUCUAAGCCAGCCGA----GUCUUAUAAAAGGAUCCACU--CU
----............((((.....(((((((.(((((((((..((((((......))))))..)))))).)))(((......)))...)))----)))).....)))).......--.. ( -38.70)
>consensus
____UGUUGC_CCAUGCCUUGACACAGAUUUGUUGGCCAAAGUUGGCGACAACGUCGUCGCCUUUUUAGGCCCAGGCGUCUAAGCC____GC____AACU___________________U
.........................((((.(.(.((((.(((..((((((......))))))..))).)))).).).))))....................................... (-23.42 = -23.20 +  -0.22)

alignment

secondary structure

dotplot

Window 5

Location	15,192,265 – 15,192,373
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.28
Mean single sequence MFE	-38.12
Consensus MFE	-20.77
Energy contribution	-21.35
Covariance contribution	0.58
Combinations/Pair	1.06
Mean z-score	-3.09
Structure conservation index	0.54
SVM decision value	2.36
SVM RNA-class probability	0.992845
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15192265 108 - 23771897
GAGCCGAGGAUCCUUUUACAAGUC----CC----GGCUUAGACGCCUGGGCCAAAAAAGGCGACGACGUUGUCGCCAACUUUGGCCAACAAAUCUGUGUCAAGGCAUGGGGCAACA----
((((((.((((..........)))----))----)))))....(((..(((((((...(((((((....)))))))...))))))).......((((((....)))))))))....---- ( -46.30)
>DroVir_CAF1 71150 91 - 1
--------------------AGUUGCCUGC----AACUUAGACGCCUGGGCCUAAAAAGGCGACGACGUUGUCGCCAACUUUGGCCAACAAAUCUGUGUCAAGCCAUGG-GCAACA----
--------------------.((((((((.----..(((.(((((...((((......(((((((....)))))))......)))).........))))))))...)))-))))).---- ( -35.90)
>DroPse_CAF1 70841 110 - 1
AG--AGUGGAUCCUUUUAUAAGAG----UCUGCUGGCUUAGACGCCUGGACCAAAAAAGGCGACGACGUUGUCGCCAACUUUGGCCAACAAAUCUGUGUCAAGGCAUGGGGCAACA----
..--((..((..(((....)))..----))..)).........((((((.(((((...(((((((....)))))))...))))))))......((((((....)))))))))....---- ( -38.60)
>DroGri_CAF1 77502 99 - 1
AAGC----------------AGUUGCCUGC----AACUUAGACGCCUGGGCCUAAAAAGGCGACGACGCUGUCGCCAACUUUGGCCAACAAAUCUGUGUCAAGCCAUGG-GCAACAGCAA
..((----------------.((((((((.----..(((.(((((...((((......(((((((....)))))))......)))).........))))))))...)))-))))).)).. ( -38.40)
>DroMoj_CAF1 76009 91 - 1
--------------------AGUUGGCUGC----GAAAUAGACGCCUGGGCCUAAAAAGGCGACGACGUUGUCGCCAACUUUGGCCAACAAAUCUGUGUCAAGCCAUGG-GCAACA----
--------------------...(((((..----((.(((((......((((......(((((((....)))))))......))))......))))).)).)))))..(-....).---- ( -33.90)
>DroPer_CAF1 70982 110 - 1
AG--AGUGGAUCCUUUUAUAAGAC----UCGGCUGGCUUAGACGCCUGGACCAAAAAAGGCGACGACGUUGUCGCCAACUUUGGCCAACAAAUCUGUGUCAAGGCAUGGGGCAACA----
..--(((.((..(((....)))..----)).))).........((((((.(((((...(((((((....)))))))...))))))))......((((((....)))))))))....---- ( -35.60)
>consensus
A___________________AGUU____GC____GACUUAGACGCCUGGGCCAAAAAAGGCGACGACGUUGUCGCCAACUUUGGCCAACAAAUCUGUGUCAAGCCAUGG_GCAACA____
..................................(((.((((......((((......(((((((....)))))))......))))......)))).))).................... (-20.77 = -21.35 +   0.58)

alignment

secondary structure

dotplot

Window 6

Location	15,192,301 – 15,192,392
Length	91
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	83.38
Mean single sequence MFE	-36.08
Consensus MFE	-21.95
Energy contribution	-23.82
Covariance contribution	1.86
Combinations/Pair	1.08
Mean z-score	-2.50
Structure conservation index	0.61
SVM decision value	0.09
SVM RNA-class probability	0.577791
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15192301 91 + 23771897
AGUUGGCGACAACGUCGUCGCCUUUUUUGGCCCAGGCGUCUAAGCC----GGGACUUGUAAAAGGAUCCUCGGCUCGGCUCGGCUCCUGCGCCUU
....((((((......))))))......(((.((((.(((..((((----(((((((.....))).))).)))))..)....)).)))).))).. ( -38.70)
>DroPse_CAF1 70877 89 + 1
AGUUGGCGACAACGUCGUCGCCUUUUUUGGUCCAGGCGUCUAAGCCAGCAGACUCUUAUAAAAGGAUCCACU--CUGGCCUGGCUCCUUCU----
.((((((....(((((...(((......)))...)))))....))))))............(((((.(((..--......))).)))))..---- ( -28.80)
>DroSec_CAF1 81835 91 + 1
AGUUGGCGACAACGUCGUCGCCUUUUUUGGCCCAGGCGUCUAAGCC----GGGACUUGUAAAAGGAUCCUCGGCUUGGUUCGGCUCCUGCGCCUU
....((((((......))))))......(((.((((.(((((((((----(((((((.....))).))).))))))))....)).)))).))).. ( -41.60)
>DroEre_CAF1 81832 84 + 1
AGUUGGCGACAACGCCGUCGCCUUUUUUGGCCCAGGCGUCUAAGCC----GGGCCUUGUAAAAGGAUGCUCGGC------CGGCUCCUGCGCCU-
.((((....))))((((.((((((((..(((((.(((......)))----)))))....)))))).))..))))------.(((......))).- ( -39.80)
>DroYak_CAF1 85139 90 + 1
AGUUGGCGACAACGUCGUCGCCUUUUUUGGCCCAGGCGUCUUAGCC----GGGACUUGUAAAAGGAUCCUCGGCUCGGAUCGGCUCCUGCGCCU-
....((((((......))))))......(((.(((((((((.((((----(((((((.....))).))).))))).))).))...)))).))).- ( -39.60)
>DroPer_CAF1 71018 89 + 1
AGUUGGCGACAACGUCGUCGCCUUUUUUGGUCCAGGCGUCUAAGCCAGCCGAGUCUUAUAAAAGGAUCCACU--CUGGCCUGGCUCCUUCU----
....((((((......))))))...((((((...(((......))).))))))........(((((.(((..--......))).)))))..---- ( -28.00)
>consensus
AGUUGGCGACAACGUCGUCGCCUUUUUUGGCCCAGGCGUCUAAGCC____GGGACUUGUAAAAGGAUCCUCGGCUUGGCUCGGCUCCUGCGCCU_
....((((((......))))))......(((.((((.(((...(((....((..(((....)))..))........)))..))).)))).))).. (-21.95 = -23.82 +   1.86)

alignment

secondary structure

dotplot

Window 7

Location	15,192,301 – 15,192,392
Length	91
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	83.38
Mean single sequence MFE	-36.22
Consensus MFE	-23.52
Energy contribution	-24.18
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.78
Structure conservation index	0.65
SVM decision value	0.43
SVM RNA-class probability	0.734383
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15192301 91 - 23771897
AAGGCGCAGGAGCCGAGCCGAGCCGAGGAUCCUUUUACAAGUCCC----GGCUUAGACGCCUGGGCCAAAAAAGGCGACGACGUUGUCGCCAACU
..(((.((((.......(..(((((.((((..........)))))----))))..)...)))).)))......(((((((....))))))).... ( -39.60)
>DroPse_CAF1 70877 89 - 1
----AGAAGGAGCCAGGCCAG--AGUGGAUCCUUUUAUAAGAGUCUGCUGGCUUAGACGCCUGGACCAAAAAAGGCGACGACGUUGUCGCCAACU
----....((..((((((...--((..((..(((....)))..))..))(.......))))))).))......(((((((....))))))).... ( -32.50)
>DroSec_CAF1 81835 91 - 1
AAGGCGCAGGAGCCGAACCAAGCCGAGGAUCCUUUUACAAGUCCC----GGCUUAGACGCCUGGGCCAAAAAAGGCGACGACGUUGUCGCCAACU
..(((.((((.(.(.....((((((.((((..........)))))----))))).).).)))).)))......(((((((....))))))).... ( -38.00)
>DroEre_CAF1 81832 84 - 1
-AGGCGCAGGAGCCG------GCCGAGCAUCCUUUUACAAGGCCC----GGCUUAGACGCCUGGGCCAAAAAAGGCGACGGCGUUGUCGCCAACU
-.(((((((..((((------..((.....((((((....(((((----(((......))).)))))..)))))))).)))).))).)))).... ( -37.60)
>DroYak_CAF1 85139 90 - 1
-AGGCGCAGGAGCCGAUCCGAGCCGAGGAUCCUUUUACAAGUCCC----GGCUAAGACGCCUGGGCCAAAAAAGGCGACGACGUUGUCGCCAACU
-.(((.((((...((.((..(((((.((((..........)))))----))))..)))))))).)))......(((((((....))))))).... ( -40.10)
>DroPer_CAF1 71018 89 - 1
----AGAAGGAGCCAGGCCAG--AGUGGAUCCUUUUAUAAGACUCGGCUGGCUUAGACGCCUGGACCAAAAAAGGCGACGACGUUGUCGCCAACU
----....((..((((((...--(((.((..(((....)))..)).)))(.......))))))).))......(((((((....))))))).... ( -29.50)
>consensus
_AGGCGCAGGAGCCGAGCCAAGCCGAGGAUCCUUUUACAAGUCCC____GGCUUAGACGCCUGGGCCAAAAAAGGCGACGACGUUGUCGCCAACU
.......((((.((............)).))))................(((((((....)))))))......(((((((....))))))).... (-23.52 = -24.18 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:39 2006