Locus 6176

Sequence ID	2L_DroMel_CAF1
Location	17,226,639 – 17,226,737
Length	98
Max. P	0.971211

overview

Window 2

Location	17,226,639 – 17,226,737
Length	98
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	80.49
Mean single sequence MFE	-31.30
Consensus MFE	-14.33
Energy contribution	-15.83
Covariance contribution	1.50
Combinations/Pair	1.13
Mean z-score	-3.42
Structure conservation index	0.46
SVM decision value	1.29
SVM RNA-class probability	0.938724
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17226639 98 + 22407834
CG------------AGUGUGUGUGUGUGU-UUUUUCAUAAAUCUCCAAAUUGAGAUUUAUGUUAGUUUUGCAUAUUUUAGCCAUGUCCGU-GAGCGGUU-AGCAGCGCCCGCA
..------------.(((.((((((((((-.((..((((((((((......))))))))))..))....))))))....((.....(((.-...)))..-.)).)))).))). ( -27.50)
>DroVir_CAF1 166582 100 + 1
UGU--G----UGUGUGUGUGUGCAU---U-UUUUUCAUAAAUCUCUAAAUUGAGAUUUAUGUUAGUUUUGCAUAUUUUAGCCAUGUCCGAAAAGCGGUU-UGG--CGGCAGCA
...--.----(((.((((((((((.---.-.((..((((((((((......))))))))))..))...)))))))....((((...(((.....)))..-)))--).)))))) ( -32.60)
>DroGri_CAF1 196983 107 + 1
UUU--GCUGUGCUGUGUGUGCGUGUGUGU-UUUUUCAUAAAUCUCUAAAUUGAGAUUUAUGAUAGUUUUGCAUAUUUUAGCCAUGUCCGAGAAGCGGUU-UGG--CGGCAACA
.((--((((..(.....)..)(((((((.-....(((((((((((......)))))))))))......)))))))....((((...(((.....)))..-)))--)))))).. ( -35.90)
>DroEre_CAF1 69520 103 + 1
CGUACG----UGUGUGUGUG----UGUGUGUUUUUCAUAAAUCUCCAAAUUGAGAUUUAUGUUAGUUUUGCAUAUUUUAGCCAUGUCCGA-GAGCGGUU-GGCAUCGCCGGCA
((.(((----((.((..(((----((((...((..((((((((((......))))))))))..))...)))))))....))))))).)).-.....(((-(((...)))))). ( -32.10)
>DroWil_CAF1 84959 89 + 1
U--------------GUGUG----UGCGAGUUUUUCAUAAAUCUCUAAAUUGAGAUUUAUGUUAGUUUUGCAUAUUUUAGCCAUGUCCAA-AAGCGGUU-UGG--CGGCC--A
.--------------..(((----((((((.((..((((((((((......))))))))))..)).)))))))))....((((...((..-....))..-)))--)....--. ( -30.40)
>DroMoj_CAF1 145507 104 + 1
CGU--G----UAUGUGUGUGUGUAUGUAU-UUUUUCAUAAAUCUCUAAAUUGAGAUUUAUGUUAGUUUUGCAUAUUUUAGCCAUGUCCAAAAAGCGGUUUUGG--CGGCAUCA
.(.--.----((((.((....(((((((.-.((..((((((((((......))))))))))..))...)))))))....))))))..).....((.((....)--).)).... ( -29.30)
>consensus
CGU__G____U_UGUGUGUGUGU_UGUGU_UUUUUCAUAAAUCUCUAAAUUGAGAUUUAUGUUAGUUUUGCAUAUUUUAGCCAUGUCCGA_AAGCGGUU_UGG__CGGCAGCA
.......................(((((...((..((((((((((......))))))))))..))...))))).......(((...(((.....)))...))).......... (-14.33 = -15.83 +   1.50)

alignment

secondary structure

dotplot

Window 3

Location	17,226,639 – 17,226,737
Length	98
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	80.49
Mean single sequence MFE	-22.54
Consensus MFE	-15.49
Energy contribution	-15.27
Covariance contribution	-0.22
Combinations/Pair	1.07
Mean z-score	-3.62
Structure conservation index	0.69
SVM decision value	1.67
SVM RNA-class probability	0.971211
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17226639 98 - 22407834
UGCGGGCGCUGCU-AACCGCUC-ACGGACAUGGCUAAAAUAUGCAAAACUAACAUAAAUCUCAAUUUGGAGAUUUAUGAAAAA-ACACACACACACACU------------CG
((((......(((-(.(((...-.)))...)))).......)))).......((((((((((......)))))))))).....-...............------------.. ( -21.22)
>DroVir_CAF1 166582 100 - 1
UGCUGCCG--CCA-AACCGCUUUUCGGACAUGGCUAAAAUAUGCAAAACUAACAUAAAUCUCAAUUUAGAGAUUUAUGAAAAA-A---AUGCACACACACACA----C--ACA
.......(--(((-..(((.....)))...)))).......((((.......((((((((((......)))))))))).....-.---.))))..........----.--... ( -22.64)
>DroGri_CAF1 196983 107 - 1
UGUUGCCG--CCA-AACCGCUUCUCGGACAUGGCUAAAAUAUGCAAAACUAUCAUAAAUCUCAAUUUAGAGAUUUAUGAAAAA-ACACACACGCACACACAGCACAGC--AAA
((((...(--(((-..(((.....)))...))))...))))(((.......(((((((((((......)))))))))))....-........((.......))...))--).. ( -26.00)
>DroEre_CAF1 69520 103 - 1
UGCCGGCGAUGCC-AACCGCUC-UCGGACAUGGCUAAAAUAUGCAAAACUAACAUAAAUCUCAAUUUGGAGAUUUAUGAAAAACACACA----CACACACACA----CGUACG
.((((((...)))-..(((...-.)))....)))..................((((((((((......))))))))))...........----..........----...... ( -22.10)
>DroWil_CAF1 84959 89 - 1
U--GGCCG--CCA-AACCGCUU-UUGGACAUGGCUAAAAUAUGCAAAACUAACAUAAAUCUCAAUUUAGAGAUUUAUGAAAAACUCGCA----CACAC--------------A
(--((((.--(((-((.....)-))))....))))).....(((........((((((((((......))))))))))........)))----.....--------------. ( -22.89)
>DroMoj_CAF1 145507 104 - 1
UGAUGCCG--CCAAAACCGCUUUUUGGACAUGGCUAAAAUAUGCAAAACUAACAUAAAUCUCAAUUUAGAGAUUUAUGAAAAA-AUACAUACACACACACAUA----C--ACG
....(((.--((((((.....))))))....)))..................((((((((((......)))))))))).....-...................----.--... ( -20.40)
>consensus
UGCUGCCG__CCA_AACCGCUU_UCGGACAUGGCUAAAAUAUGCAAAACUAACAUAAAUCUCAAUUUAGAGAUUUAUGAAAAA_ACACA_ACACACACACA_A____C__ACA
................(((.....))).....((........))........((((((((((......))))))))))................................... (-15.49 = -15.27 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:28 2006