Locus 4629

Sequence ID	2R_DroMel_CAF1
Location	15,142,083 – 15,142,213
Length	130
Max. P	0.831119

overview

Window 1

Location	15,142,083 – 15,142,187
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	91.73
Mean single sequence MFE	-29.44
Consensus MFE	-24.84
Energy contribution	-25.08
Covariance contribution	0.24
Combinations/Pair	1.18
Mean z-score	-1.52
Structure conservation index	0.84
SVM decision value	0.72
SVM RNA-class probability	0.831119
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15142083 104 - 20766785
UUGCAAUAUGUCGAGUAAAUUUGUGUUUACAGCUACGUUGGAGUUUGCGUUGCAAUUAGCUUGCAGCUUUCCCUGGCCGCCGGCAACCAUUGUAAUUUUCCACA
(((((((.(((((.((((((....)))))).((((.(..((((((.(((..((.....)).)))))))))..)))))...)))))...)))))))......... ( -26.20)
>DroSec_CAF1 114124 104 - 1
UUGCAAUAUGCCGAGUAAAUUUGUGUUUACAGCUACGUUGGAGCUUGCGUUGCAAUUAGCUUGCAGCUUUUCCUGGCCGCCGGCAACCAUUGUAAUUUUCCACA
(((((((.(((((.((((((....)))))).((((.(..((((((.(((..((.....)).)))))))))..)))))...)))))...)))))))......... ( -31.90)
>DroSim_CAF1 99081 104 - 1
UUGCAAUAUGCCGAGUAAAUUUGUGUUUGCAGCUACGUUGGAGCUUGCGUUGCAAUUAGCUUGCAGCUUUUCCUGGCCGCCGGCAACCAUUGUAAUUUUCCACA
(((((((.(((((.((((((....)))))).((((.(..((((((.(((..((.....)).)))))))))..)))))...)))))...)))))))......... ( -31.90)
>DroEre_CAF1 117888 104 - 1
UUGCAAUAUGUAGAGGGAAUUCGUGUUUACAGCAGUGUUGCAGCUUGCACUGCAACUAGCCUGCAGCUUUCCCUGGCCGCCGGCAACCAUUGUAAUUUUCCACA
(((((((.((((((.((....).).))))))(((((((........))))))).....(((.((.(((......))).)).)))....)))))))......... ( -31.00)
>DroYak_CAF1 119959 103 - 1
CUGCAAUAUGUCG-GUAAAUUUGUGUUUAAAGCAGCGUUGGAGCUUGCAUUGCAAUUAGCUUGCAGCUUUCCCUGGCCGCCGGCAACCAUUGUAAUUUUCCACA
.((((((.(((((-((.......(((.....)))(.((..(((((.(((..((.....)).)))))))....)..))))))))))...)))))).......... ( -26.20)
>consensus
UUGCAAUAUGUCGAGUAAAUUUGUGUUUACAGCUACGUUGGAGCUUGCGUUGCAAUUAGCUUGCAGCUUUCCCUGGCCGCCGGCAACCAUUGUAAUUUUCCACA
(((((((.(((((.((((((....)))))).((((.(..((((((.(((..((.....)).)))))))))..)))))...)))))...)))))))......... (-24.84 = -25.08 +   0.24)

alignment

secondary structure

dotplot

Window 2

Location	15,142,123 – 15,142,213
Length	90
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	76.59
Mean single sequence MFE	-18.97
Consensus MFE	-6.73
Energy contribution	-7.49
Covariance contribution	0.76
Combinations/Pair	1.33
Mean z-score	-1.85
Structure conservation index	0.35
SVM decision value	0.15
SVM RNA-class probability	0.605814
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15142123 90 + 20766785
GCAAGCUAAUUGCAACGCAAACUCCAACGUAGCUGUAAACACAAAUUUACUCGACAUAUUGCAAU--AAUCGAGUAUGCAUUUGUAAACCAU------------
(((.((((.((((...)))).........)))))))....((((((.(((((((..(((....))--).)))))))...)))))).......------------ ( -15.40)
>DroSec_CAF1 114164 92 + 1
GCAAGCUAAUUGCAACGCAAGCUCCAACGUAGCUGUAAACACAAAUUUACUCGGCAUAUUGCAAUAUAAUCGAGUAUGCAUUUGUAAACCCU------------
(((.((((.(((...(....)...)))..)))))))....((((((.(((((((.((((....))))..)))))))...)))))).......------------ ( -18.00)
>DroSim_CAF1 99121 92 + 1
GCAAGCUAAUUGCAACGCAAGCUCCAACGUAGCUGCAAACACAAAUUUACUCGGCAUAUUGCAAUAUAAUCGAGUAUGCAUUUGUAAACCCU------------
(((.((((.(((...(....)...)))..)))))))....((((((.(((((((.((((....))))..)))))))...)))))).......------------ ( -20.40)
>DroEre_CAF1 117928 89 + 1
GCAGGCUAGUUGCAGUGCAAGCUGCAACACUGCUGUAAACACGAAUUCCCUCUACAUAUUGCAAU--A------------CUUGUAG-CCCAUCAAUAUAGGAU
...(((((((((((((....))))))))..(((.(((.....((......))....))).)))..--.------------....)))-)).............. ( -20.80)
>DroYak_CAF1 119999 88 + 1
GCAAGCUAAUUGCAAUGCAAGCUCCAACGCUGCUUUAAACACAAAUUUAC-CGACAUAUUGCAGC--AAUCGAGUAUGCAGUUAUAG-CCCA------------
((((.....))))..((((.((((....(((((.................-.........)))))--....)))).)))).......-....------------ ( -20.27)
>consensus
GCAAGCUAAUUGCAACGCAAGCUCCAACGUAGCUGUAAACACAAAUUUACUCGACAUAUUGCAAU__AAUCGAGUAUGCAUUUGUAAACCCU____________
((((.....))))...(((.((((....((.((...........................)).))......)))).)))......................... ( -6.73 =  -7.49 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:02 2006