Locus 2019

Sequence ID	3R_DroMel_CAF1
Location	5,732,094 – 5,732,195
Length	101
Max. P	0.983461

overview

Window 8

Location	5,732,094 – 5,732,195
Length	101
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	92.35
Mean single sequence MFE	-30.94
Consensus MFE	-26.92
Energy contribution	-26.88
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.58
Structure conservation index	0.87
SVM decision value	1.18
SVM RNA-class probability	0.926683
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5732094 101 + 27905053
GAUAGACAGAGACGGGUUGUGGCCAGAGGGAGACGGAGCAUCGCUGUCUC---GGGGCUGUUGCAUAAAUAGAAAAUUUAUUUAUUGAUUACGCCGUCUGA----AUU
.........((((((((.(..(((.((((.((.((......)))).))))---..)))..).))(((((((((...)))))))))........))))))..----... ( -30.30)
>DroSec_CAF1 23631 108 + 1
GAUAGACAGAGACGGGGCGUGGCCAGAGGGAGACGGAGCAUCGCUGUCUCGACGGGGCUGUUGCAUAAAUAGAAAACUUAUUUAUUGAUUACGCCGUCUGAAUGAAUU
......((.((((((.(((..(((...(.(((((((.......)))))))..)..)))..).))((((((((.....))))))))........))))))...)).... ( -31.60)
>DroSim_CAF1 24247 108 + 1
GAUAGACAGAGACGGGGCGUGGCCAGAGGGAGACGGAGCAUCGCUGUCUCGGCGGGGCUGUUGCAUAAAUAGAAAAUUUAUUUAUUGAUUACGCCGUCUGAAUGAAUU
..(((((.(((((((.(.(((.((....(....)))..)))).)))))))((((..((....))(((((((((...)))))))))......)))))))))........ ( -33.80)
>DroEre_CAF1 19191 101 + 1
GAUAGACAAAGAUGGGGAGCGGCCAGAGGGAGACGGAGCAUCGCUGUCUC---GGGGAUGUUGCAUAAAUAGAAAACUUAUUUAUUGAUUACGCCGUCUGA----AUU
.........((((((.(.(((((......(((((((.......)))))))---......)))))((((((((.....))))))))......).))))))..----... ( -26.80)
>DroYak_CAF1 6890 101 + 1
GAUAGACAGAGAUGGGGAGCGGCCAGAGGGAGACGGAGCAUCGCUGUCUC---GGGGCUGUUGCAUAAAUAGAAAAUUUAUUUAUUGAUUACGCCGUCUGA----AUU
.........(((((((.(((((((.((((.((.((......)))).))))---..))))))).)(((((((((...)))))))))........))))))..----... ( -32.20)
>consensus
GAUAGACAGAGACGGGGAGUGGCCAGAGGGAGACGGAGCAUCGCUGUCUC___GGGGCUGUUGCAUAAAUAGAAAAUUUAUUUAUUGAUUACGCCGUCUGA____AUU
.........((((((.....((((.....(((((((.......))))))).....))))((..(((((((((.....))))))).))...)).))))))......... (-26.92 = -26.88 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	5,732,094 – 5,732,195
Length	101
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	92.35
Mean single sequence MFE	-22.89
Consensus MFE	-19.76
Energy contribution	-19.32
Covariance contribution	-0.44
Combinations/Pair	1.12
Mean z-score	-1.90
Structure conservation index	0.86
SVM decision value	1.94
SVM RNA-class probability	0.983461
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5732094 101 - 27905053
AAU----UCAGACGGCGUAAUCAAUAAAUAAAUUUUCUAUUUAUGCAACAGCCCC---GAGACAGCGAUGCUCCGUCUCCCUCUGGCCACAACCCGUCUCUGUCUAUC
...----..((((((.((.....(((((((.......)))))))......(((..---((((((((...)))..))))).....)))....))))))))......... ( -21.20)
>DroSec_CAF1 23631 108 - 1
AAUUCAUUCAGACGGCGUAAUCAAUAAAUAAGUUUUCUAUUUAUGCAACAGCCCCGUCGAGACAGCGAUGCUCCGUCUCCCUCUGGCCACGCCCCGUCUCUGUCUAUC
..........(((((.((.....(((((((.......)))))))......)).))))).((((((.((((...(((..((....))..)))...)))).))))))... ( -27.90)
>DroSim_CAF1 24247 108 - 1
AAUUCAUUCAGACGGCGUAAUCAAUAAAUAAAUUUUCUAUUUAUGCAACAGCCCCGCCGAGACAGCGAUGCUCCGUCUCCCUCUGGCCACGCCCCGUCUCUGUCUAUC
............(((((......(((((((.......)))))))((....))..)))))((((((.((((...(((..((....))..)))...)))).))))))... ( -27.10)
>DroEre_CAF1 19191 101 - 1
AAU----UCAGACGGCGUAAUCAAUAAAUAAGUUUUCUAUUUAUGCAACAUCCCC---GAGACAGCGAUGCUCCGUCUCCCUCUGGCCGCUCCCCAUCUUUGUCUAUC
...----.....(((.(......(((((((.......))))))).......).))---)((((((.((((....((..((....))..))....)))).))))))... ( -17.12)
>DroYak_CAF1 6890 101 - 1
AAU----UCAGACGGCGUAAUCAAUAAAUAAAUUUUCUAUUUAUGCAACAGCCCC---GAGACAGCGAUGCUCCGUCUCCCUCUGGCCGCUCCCCAUCUCUGUCUAUC
...----......(((.......(((((((.......)))))))......)))..---.((((((.((((....((..((....))..))....)))).))))))... ( -21.12)
>consensus
AAU____UCAGACGGCGUAAUCAAUAAAUAAAUUUUCUAUUUAUGCAACAGCCCC___GAGACAGCGAUGCUCCGUCUCCCUCUGGCCACGCCCCGUCUCUGUCUAUC
.............(((.......(((((((.......)))))))......)))......((((((.((((....((..((....))..))....)))).))))))... (-19.76 = -19.32 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:22 2006