Locus 7019

Sequence ID	2L_DroMel_CAF1
Location	19,569,644 – 19,569,796
Length	152
Max. P	0.955535

overview

Window 9

Location	19,569,644 – 19,569,764
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	81.94
Mean single sequence MFE	-29.63
Consensus MFE	-22.04
Energy contribution	-22.60
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.30
Structure conservation index	0.74
SVM decision value	1.21
SVM RNA-class probability	0.931470
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19569644 120 - 22407834
UCCUCGAAAAACAUCGAUGUUUGUGAUUUUUUGAAAAAAUCGACGACAUCGACGUUGGCAUUUCAGUAAAGGAAUUCCAAAAUCUCAUUUACCUGUGAAAACCGCGCCCCAAAUGUUUUA
.......((((((((((((((..(((((((.....)))))))..))))))))....(((......((((((..(((....)))..).)))))..(((.....)))))).....)))))). ( -26.00)
>DroSec_CAF1 8965 108 - 1
UCCUCAAAAAACAUCGAUGUUUGUGAUUUUCCGAAAACAUCGAUGACAUCGAUGUUGCGAUUGCAACGAAGGAAUUCCAAAAUCUGAUUUGCCUGUAACAACGGCGCG------------
(((((......(((((((((((.((......)).)))))))))))........(((((....)))))).)))).................((((((....)))).)).------------ ( -30.10)
>DroSim_CAF1 9556 120 - 1
UCCUCAAAAAACAUCGAUGUUUGUGAUUUUGCGAAAACAUCGAUGACAUCGAUGUUGCUAUUGCAACGAAGGAAUUCCAAAAUAUGAUUUGCCUGUGACAACGGCGCCCCAAAUGUUAUA
(((((......(((((((((((.((......)).)))))))))))........(((((....)))))).)))).......(((((.....((((((....)))).)).....)))))... ( -32.80)
>consensus
UCCUCAAAAAACAUCGAUGUUUGUGAUUUUCCGAAAACAUCGAUGACAUCGAUGUUGCCAUUGCAACGAAGGAAUUCCAAAAUCUGAUUUGCCUGUGACAACGGCGCCCCAAAUGUU_UA
((((.....((((((((((((..((((.((.....)).))))..))))))))))))((....)).....)))).................((((((....)))).))............. (-22.04 = -22.60 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	19,569,684 – 19,569,796
Length	112
Sequences	3
Columns	115
Reading direction	forward
Mean pairwise identity	87.72
Mean single sequence MFE	-31.90
Consensus MFE	-24.74
Energy contribution	-25.97
Covariance contribution	1.23
Combinations/Pair	1.06
Mean z-score	-3.26
Structure conservation index	0.78
SVM decision value	1.26
SVM RNA-class probability	0.937846
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19569684 112 + 22407834
UUGGAAUUCCUUUACUGAAAUGCCAACGUCGAUGUCGUCGAUUUUUUCAAAAAAUCACAAACAUCGAUGUUUUUCGAGGAAUCAUCGAUGUUUCUCCACCUCUAAUAAGGC---G
..((....))...........((((((((((((((.((.((((((.....))))))))..)))))))))))....(((((((.......)))))))............)))---. ( -28.20)
>DroSec_CAF1 8993 115 + 1
UUGGAAUUCCUUCGUUGCAAUCGCAACAUCGAUGUCAUCGAUGUUUUCGGAAAAUCACAAACAUCGAUGUUUUUUGAGGAAUCAUCGAUCUUUCUCCGCCUCUAAUGUGGCCUCU
..((((((((...(((((....))))).((((...(((((((((((...(.....)..)))))))))))....)))))))))....((....)))))(((.(....).))).... ( -33.90)
>DroSim_CAF1 9596 112 + 1
UUGGAAUUCCUUCGUUGCAAUAGCAACAUCGAUGUCAUCGAUGUUUUCGCAAAAUCACAAACAUCGAUGUUUUUUGAGGAAUCAUCGAUCUUUCUCCGCCUCUAAUGUGGC---G
..((((((((...(((((....))))).((((...(((((((((((............)))))))))))....)))))))))....((....)))))(((.(....).)))---. ( -33.60)
>consensus
UUGGAAUUCCUUCGUUGCAAUAGCAACAUCGAUGUCAUCGAUGUUUUCGAAAAAUCACAAACAUCGAUGUUUUUUGAGGAAUCAUCGAUCUUUCUCCGCCUCUAAUGUGGC___G
..((((((((...(((((....))))).((((...(((((((((((............)))))))))))....)))))))))....((....)))))(((........))).... (-24.74 = -25.97 +   1.23)

alignment

secondary structure

dotplot

Window 1

Location	19,569,684 – 19,569,796
Length	112
Sequences	3
Columns	115
Reading direction	reverse
Mean pairwise identity	87.72
Mean single sequence MFE	-33.53
Consensus MFE	-27.86
Energy contribution	-27.53
Covariance contribution	-0.32
Combinations/Pair	1.15
Mean z-score	-3.09
Structure conservation index	0.83
SVM decision value	1.46
SVM RNA-class probability	0.955535
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19569684 112 - 22407834
C---GCCUUAUUAGAGGUGGAGAAACAUCGAUGAUUCCUCGAAAAACAUCGAUGUUUGUGAUUUUUUGAAAAAAUCGACGACAUCGACGUUGGCAUUUCAGUAAAGGAAUUCCAA
(---(((((....))))))........((((.......))))..(((.((((((((..(((((((.....)))))))..)))))))).)))((.(((((......))))).)).. ( -30.00)
>DroSec_CAF1 8993 115 - 1
AGAGGCCACAUUAGAGGCGGAGAAAGAUCGAUGAUUCCUCAAAAAACAUCGAUGUUUGUGAUUUUCCGAAAACAUCGAUGACAUCGAUGUUGCGAUUGCAACGAAGGAAUUCCAA
....(((........)))((((....(((((((.((......))..(((((((((((.((......)).))))))))))).)))))))(((((....))))).......)))).. ( -34.80)
>DroSim_CAF1 9596 112 - 1
C---GCCACAUUAGAGGCGGAGAAAGAUCGAUGAUUCCUCAAAAAACAUCGAUGUUUGUGAUUUUGCGAAAACAUCGAUGACAUCGAUGUUGCUAUUGCAACGAAGGAAUUCCAA
.---(((........)))((((....(((((((.((......))..(((((((((((.((......)).))))))))))).)))))))(((((....))))).......)))).. ( -35.80)
>consensus
C___GCCACAUUAGAGGCGGAGAAAGAUCGAUGAUUCCUCAAAAAACAUCGAUGUUUGUGAUUUUCCGAAAACAUCGAUGACAUCGAUGUUGCCAUUGCAACGAAGGAAUUCCAA
....(((........)))((((....(((((((.((.....))...(((((((((((.((......)).))))))))))).)))))))(((((....))))).......)))).. (-27.86 = -27.53 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:27 2006