Locus 1104

Sequence ID	3R_DroMel_CAF1
Location	3,343,884 – 3,344,072
Length	188
Max. P	0.993355

overview

Window 6

Location	3,343,884 – 3,343,996
Length	112
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	74.15
Mean single sequence MFE	-28.03
Consensus MFE	-20.17
Energy contribution	-20.73
Covariance contribution	0.56
Combinations/Pair	1.07
Mean z-score	-1.20
Structure conservation index	0.72
SVM decision value	0.18
SVM RNA-class probability	0.623492
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3343884 112 + 27905053
AUCG-------GCAGCAGACUUUUAUUAUCGUGUAUAUAUGAAAGUAUGUUAUUAUCCUUCGCAGACGCUACUGGUACGCUUCGUCACUACGUGGACUACCUG-ACGUCCAAAGUGAUGA
...(-------((((((.((((((((............)))))))).))))...........(((......)))....)))((((((((...(((((......-..))))).)))))))) ( -28.30)
>DroSec_CAF1 37327 97 + 1
AUGGUUAAAUAACAGCAGACUUUUAUUAUCGUGUGUAUAUGGAAGUAUGUUAUUAGCCUU----------------------CGUCACUACGUGGAAUGCCUG-CCGUCCACAGUGAUGA
..((((((.(((((....(((((((((((.....))).)))))))).))))))))))).(----------------------(((((((..(((((..(....-)..))))))))))))) ( -29.80)
>DroSim_CAF1 31511 112 + 1
UUUG--------GAGCAGACUUUUAUUAUCGUGUAUAUAUGAAAGUAUGUUAUUAGCCUUCGCAGACGCUACUGGUGCGCUUCGUCACUACGUGGACUGACUGACUGUCCACACUGAUGA
...(--------((((.(((...((((.(((((....))))).)))).)))....(((...((....))....)))..)))))((((....((((((.........))))))..)))).. ( -26.00)
>consensus
AUCG________CAGCAGACUUUUAUUAUCGUGUAUAUAUGAAAGUAUGUUAUUAGCCUUCGCAGACGCUACUGGU_CGCUUCGUCACUACGUGGACUGCCUG_CCGUCCACAGUGAUGA
.............((((.(((((((((((.....))).)))))))).))))...............................(((((((..((((((.........))))))))))))). (-20.17 = -20.73 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	3,343,917 – 3,344,033
Length	116
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	75.00
Mean single sequence MFE	-30.83
Consensus MFE	-18.27
Energy contribution	-19.17
Covariance contribution	0.89
Combinations/Pair	1.07
Mean z-score	-1.76
Structure conservation index	0.59
SVM decision value	0.51
SVM RNA-class probability	0.762428
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3343917 116 + 27905053
GAAAGUAUGUUAUUAUCCUUCGCAGACGCUACUGGUACGCUUCGUCACUACGUGGACUACCUG-ACGUCCAAAGUGAUGAAUGUGGUCAAUAUUUGAUAGCUUAUGCGUAUAUGUGU---
....................((((.((((....(((.((((((((((((...(((((......-..))))).))))))))).)))((((.....)))).)))...))))...)))).--- ( -34.20)
>DroSec_CAF1 37367 90 + 1
GGAAGUAUGUUAUUAGCCUU----------------------CGUCACUACGUGGAAUGCCUG-CCGUCCACAGUGAUGAAUGUGGUCAAUAUUUAUUGGCUUAUGCUAAUAU-------
..........(((((((.((----------------------(((((((..(((((..(....-)..))))))))))))))...(((((((....)))))))...))))))).------- ( -28.30)
>DroSim_CAF1 31543 120 + 1
GAAAGUAUGUUAUUAGCCUUCGCAGACGCUACUGGUGCGCUUCGUCACUACGUGGACUGACUGACUGUCCACACUGAUGAAUGUGGUCAAUAUUUAAUAGCUUAUGCUAAUAUGUGUAUG
....(((..((((((((.(..((...(((.....)))((((((((((....((((((.........))))))..))))))).)))..............))..).))))))).)..))). ( -30.00)
>consensus
GAAAGUAUGUUAUUAGCCUUCGCAGACGCUACUGGU_CGCUUCGUCACUACGUGGACUGCCUG_CCGUCCACAGUGAUGAAUGUGGUCAAUAUUUAAUAGCUUAUGCUAAUAUGUGU___
....(((((((((((...........................(((((((..((((((.........)))))))))))))(((((.....))))))))))))..))))............. (-18.27 = -19.17 +   0.89)

alignment

secondary structure

dotplot

Window 8

Location	3,343,957 – 3,344,072
Length	115
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	77.46
Mean single sequence MFE	-29.73
Consensus MFE	-20.99
Energy contribution	-22.44
Covariance contribution	1.45
Combinations/Pair	1.10
Mean z-score	-2.33
Structure conservation index	0.71
SVM decision value	2.39
SVM RNA-class probability	0.993355
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3343957 115 + 27905053
UUCGUCACUACGUGGACUACCUG-ACGUCCAAAGUGAUGAAUGUGGUCAAUAUUUGAUAGCUUAUGCGUAUAUGUGU----AACUGUAUUAGGUAAAUAUGAUUGCUAUAAUUACCAAUA
(((((((((...(((((......-..))))).))))))))).(..((((.(((((((((..(((((((....)))))----))...)))))))))....))))..).............. ( -30.80)
>DroSec_CAF1 37387 99 + 1
--CGUCACUACGUGGAAUGCCUG-CCGUCCACAGUGAUGAAUGUGGUCAAUAUUUAUUGGCUUAUGCUAAUAU------------------GGUGAAUAUGAUUGCUACACUUACCUUUA
--(((((((..(((((..(....-)..))))))))))))...(..((((.(((((((((((....))))....------------------.)))))))))))..).............. ( -27.60)
>DroSim_CAF1 31583 120 + 1
UUCGUCACUACGUGGACUGACUGACUGUCCACACUGAUGAAUGUGGUCAAUAUUUAAUAGCUUAUGCUAAUAUGUGUAUGUAAAAGCAUUAGGUGAAUAUGAUUGCUAUAGUUACCUAUA
(((((((....((((((.........))))))..))))))).(..((((.((((((....((.(((((..(((......)))..))))).)).))))))))))..)(((((....))))) ( -30.80)
>consensus
UUCGUCACUACGUGGACUGCCUG_CCGUCCACAGUGAUGAAUGUGGUCAAUAUUUAAUAGCUUAUGCUAAUAUGUGU____AA__G_AUUAGGUGAAUAUGAUUGCUAUAAUUACCUAUA
.((((((((..((((((.........))))))))))))))..(..((((.((((((.((((....))))........................))))))))))..).............. (-20.99 = -22.44 +   1.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:00 2006