Locus 4178

Sequence ID	2R_DroMel_CAF1
Location	13,744,858 – 13,744,961
Length	103
Max. P	0.747751

overview

Window 7

Location	13,744,858 – 13,744,961
Length	103
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	77.72
Mean single sequence MFE	-14.83
Consensus MFE	-9.00
Energy contribution	-9.17
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.56
Structure conservation index	0.61
SVM decision value	0.32
SVM RNA-class probability	0.687709
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13744858 103 + 20766785
CGACUCUG------UCCUCAGGCCCGAGUAGAAAUUCUCUAAGCACGCUGUCAAGUUAUGUCUACAUUCCUUGAUCAUAUUUUUUCCAA--CU-GUUUUCAUACCUCCU------AUU-
......((------....(((((..(..((((.....))))..)..)).((((((..(((....)))..))))))..............--))-)....))........------...- ( -15.00)
>DroVir_CAF1 51724 92 + 1
CG-CUCUG------UCCUC------GAGUAAAAAUUCUCUAAACAUGCUGUCAAGUUAUGUCUACAUUCCUUGAUCAUAUUUUUUCCAA--CU-UUUUAU--ACCCU--------GUG-
.(-(((..------.....------))))(((((......(((.(((..((((((..(((....)))..))))))..))).))).....--.)-))))..--.....--------...- ( -12.00)
>DroGri_CAF1 49978 88 + 1
CG-CUCUG------UCCUC------GAGUAAAAAUUCUCUAAACAUGCUGUCAAGUUAUGUCUACAUUCCUUGAUCAUAUUUUUUCCAA--CU-UUUUUC--CCUC-------------
.(-(..((------(....------(((........)))...))).)).((((((..(((....)))..))))))..............--..-......--....------------- ( -11.90)
>DroWil_CAF1 48348 97 + 1
UGCCUCUG------UCCUC------GAGUAAAAAUUCUCUAAACAUGCUGUCAAGUUAUGUCUACAUUCCUUGAUCAUAUUUUUUCCAG--GUUGGUUUUAC-UCUCCU------CUC-
........------.....------((((((((..(((..(((.(((..((((((..(((....)))..))))))..))).)))...))--)....))))))-))....------...- ( -18.60)
>DroMoj_CAF1 57520 101 + 1
CG-CUCUG------UCCUC------GAGUAAAAAUUCUCUAAACAUGCUGUCAAGUUAUGUCUACAUUCCUUGAUCAUAUUUUUUCCAA--CC-UUUUUU--CCCCCACACUAACGUGG
.(-(..((------(....------(((........)))...))).)).((((((..(((....)))..))))))..............--..-......--...((((......)))) ( -15.90)
>DroAna_CAF1 48622 108 + 1
CGAUUCUGUCCGUGUCCUCGGGCCCAAGUAAAAAUUCUCUAAACACGCUGUCAAGUUAUGUCUACAUUCCUUGAUCAUAUUUUUUCCGUUUCU-GUUCUC---UCUACU------ACU-
.((..(.(((((......)))))..........................((((((..(((....)))..))))))............)..)).-......---......------...- ( -15.60)
>consensus
CG_CUCUG______UCCUC______GAGUAAAAAUUCUCUAAACAUGCUGUCAAGUUAUGUCUACAUUCCUUGAUCAUAUUUUUUCCAA__CU_GUUUUC___CCCCCU______AUG_
.........................(((........)))..........((((((..(((....)))..))))))............................................ ( -9.00 =  -9.17 +   0.17)

alignment

secondary structure

dotplot

Window 8

Location	13,744,858 – 13,744,961
Length	103
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	77.72
Mean single sequence MFE	-19.08
Consensus MFE	-13.69
Energy contribution	-13.63
Covariance contribution	-0.05
Combinations/Pair	1.16
Mean z-score	-1.23
Structure conservation index	0.72
SVM decision value	0.47
SVM RNA-class probability	0.747751
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13744858 103 - 20766785
-AAU------AGGAGGUAUGAAAAC-AG--UUGGAAAAAAUAUGAUCAAGGAAUGUAGACAUAACUUGACAGCGUGCUUAGAGAAUUUCUACUCGGGCCUGAGGA------CAGAGUCG
-...------...(((((((.....-.(--((......))).((.(((((..(((....)))..))))))).))))))).(((........))).((((((....------))).))). ( -19.90)
>DroVir_CAF1 51724 92 - 1
-CAC--------AGGGU--AUAAAA-AG--UUGGAAAAAAUAUGAUCAAGGAAUGUAGACAUAACUUGACAGCAUGUUUAGAGAAUUUUUACUC------GAGGA------CAGAG-CG
-...--------.((((--(...((-((--((.....(((((((.(((((..(((....)))..)))))...)))))))....)))))))))))------.....------.....-.. ( -17.20)
>DroGri_CAF1 49978 88 - 1
-------------GAGG--GAAAAA-AG--UUGGAAAAAAUAUGAUCAAGGAAUGUAGACAUAACUUGACAGCAUGUUUAGAGAAUUUUUACUC------GAGGA------CAGAG-CG
-------------(((.--...(((-((--((.....(((((((.(((((..(((....)))..)))))...)))))))....))))))).)))------.....------.....-.. ( -16.60)
>DroWil_CAF1 48348 97 - 1
-GAG------AGGAGA-GUAAAACCAAC--CUGGAAAAAAUAUGAUCAAGGAAUGUAGACAUAACUUGACAGCAUGUUUAGAGAAUUUUUACUC------GAGGA------CAGAGGCA
-...------....((-((((((((...--..))...(((((((.(((((..(((....)))..)))))...))))))).......))))))))------.....------........ ( -21.80)
>DroMoj_CAF1 57520 101 - 1
CCACGUUAGUGUGGGGG--AAAAAA-GG--UUGGAAAAAAUAUGAUCAAGGAAUGUAGACAUAACUUGACAGCAUGUUUAGAGAAUUUUUACUC------GAGGA------CAGAG-CG
(((((....)))))...--......-..--............((.(((((..(((....)))..)))))))((.(((((.(((........)))------..)))------))..)-). ( -20.90)
>DroAna_CAF1 48622 108 - 1
-AGU------AGUAGA---GAGAAC-AGAAACGGAAAAAAUAUGAUCAAGGAAUGUAGACAUAACUUGACAGCGUGUUUAGAGAAUUUUUACUUGGGCCCGAGGACACGGACAGAAUCG
-.((------((((((---((...(-......)....(((((((.(((((..(((....)))..)))))...)))))))......)))))))).....(((......)))))....... ( -18.10)
>consensus
_AAC______AGGAGG___AAAAAA_AG__UUGGAAAAAAUAUGAUCAAGGAAUGUAGACAUAACUUGACAGCAUGUUUAGAGAAUUUUUACUC______GAGGA______CAGAG_CG
.....................................(((((((.(((((..(((....)))..)))))...)))))))............((((....))))................ (-13.69 = -13.63 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:37 2006