Locus 3588

Sequence ID	2R_DroMel_CAF1
Location	11,941,142 – 11,941,242
Length	100
Max. P	0.973631

overview

Window 8

Location	11,941,142 – 11,941,242
Length	100
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	89.81
Mean single sequence MFE	-30.18
Consensus MFE	-24.88
Energy contribution	-24.56
Covariance contribution	-0.32
Combinations/Pair	1.09
Mean z-score	-2.10
Structure conservation index	0.82
SVM decision value	1.71
SVM RNA-class probability	0.973631
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11941142 100 + 20766785
AUUUAACUCGAA-AUAUGGAAACUCGAUUUGUUUUUUCUCUCAGUGCACAGCAUCCUGGGCUGGCUGUGUGCUGUCAGUUGUUCUGGCAGCGAAAAAUGUU
...(((.((((.-....(....))))).))).((((((.......(((((((..(....)...)))))))((((((((.....)))))))))))))).... ( -30.50)
>DroSec_CAF1 42633 99 + 1
AUUUAGCUCGAC-AUGUUAAAACUUCAUUUGUUU-UUCUCUCAGUGCACAGCAUCCUGGGCUGGCUGUGUGCUGUCAGUUGUUCUGGCAGCGAAAAAUGUU
.((((((.....-..)))))).........((((-(((.......(((((((..(....)...)))))))((((((((.....)))))))))))))))... ( -31.90)
>DroSim_CAF1 40493 100 + 1
AUUUAGCUCGAA-AUGUUGAAACUCCAUUUGUUUUUUCUCUCAGUGCACAGCAUCCUGGGCUGGCUGUGUGCUGUCAGUUGUUCUGGCAGCGAAAAAUGUU
.((((((.....-..))))))...........((((((.......(((((((..(....)...)))))))((((((((.....)))))))))))))).... ( -30.50)
>DroEre_CAF1 40080 99 + 1
ACUUAGCUCGCA-AUGUUGAAAUCCCAUUUGUUU-UUCUCUCAGUGCACAGCAUCCUGGGCUGGCUGUGUGCUGUCAGUUGUUCUGGCAGCGAAAAAUGUU
..(((((.....-..)))))..........((((-(((.......(((((((..(....)...)))))))((((((((.....)))))))))))))))... ( -30.90)
>DroYak_CAF1 41671 94 + 1
A------ACGCAGAUGUUAAAGUUCCAUUGGUUU-UUCUCUCAGUGCACAGCAUCCUGGGCUGGCUGUGUGCUGUUGGUUGUUCUGGCAGCGAAAAAUGUU
.------.......................((((-(((...(((..((((((..(....)...))))))..)))...(((((....))))))))))))... ( -27.10)
>consensus
AUUUAGCUCGAA_AUGUUGAAACUCCAUUUGUUU_UUCUCUCAGUGCACAGCAUCCUGGGCUGGCUGUGUGCUGUCAGUUGUUCUGGCAGCGAAAAAUGUU
..............................((((.(((.......(((((((..(....)...)))))))((((((((.....)))))))))))))))... (-24.88 = -24.56 +  -0.32)

alignment

secondary structure

dotplot

Window 9

Location	11,941,142 – 11,941,242
Length	100
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	89.81
Mean single sequence MFE	-22.30
Consensus MFE	-20.32
Energy contribution	-20.72
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.36
Structure conservation index	0.91
SVM decision value	0.53
SVM RNA-class probability	0.771048
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11941142 100 - 20766785
AACAUUUUUCGCUGCCAGAACAACUGACAGCACACAGCCAGCCCAGGAUGCUGUGCACUGAGAGAAAAAACAAAUCGAGUUUCCAUAU-UUCGAGUUAAAU
(((.((((((((((.(((.....))).)))).((((((...(....)..))))))......)))))).......(((((.........-)))))))).... ( -25.50)
>DroSec_CAF1 42633 99 - 1
AACAUUUUUCGCUGCCAGAACAACUGACAGCACACAGCCAGCCCAGGAUGCUGUGCACUGAGAGAA-AAACAAAUGAAGUUUUAACAU-GUCGAGCUAAAU
....((((((((((.(((.....))).)))).((((((...(....)..))))))....))))))(-((((.......))))).....-............ ( -22.70)
>DroSim_CAF1 40493 100 - 1
AACAUUUUUCGCUGCCAGAACAACUGACAGCACACAGCCAGCCCAGGAUGCUGUGCACUGAGAGAAAAAACAAAUGGAGUUUCAACAU-UUCGAGCUAAAU
....((((((((((.(((.....))).)))).((((((...(....)..))))))......)))))).......((((((......))-))))........ ( -23.30)
>DroEre_CAF1 40080 99 - 1
AACAUUUUUCGCUGCCAGAACAACUGACAGCACACAGCCAGCCCAGGAUGCUGUGCACUGAGAGAA-AAACAAAUGGGAUUUCAACAU-UGCGAGCUAAGU
....((((((((((.(((.....))).)))).((((((...(....)..))))))......)))))-)....((((.........)))-)........... ( -22.40)
>DroYak_CAF1 41671 94 - 1
AACAUUUUUCGCUGCCAGAACAACCAACAGCACACAGCCAGCCCAGGAUGCUGUGCACUGAGAGAA-AAACCAAUGGAACUUUAACAUCUGCGU------U
....((((((((((.............)))).((((((...(....)..))))))......)))))-)((((((((.........))).)).))------) ( -17.62)
>consensus
AACAUUUUUCGCUGCCAGAACAACUGACAGCACACAGCCAGCCCAGGAUGCUGUGCACUGAGAGAA_AAACAAAUGGAGUUUCAACAU_UUCGAGCUAAAU
....((((((((((.(((.....))).)))).((((((...(....)..))))))....)))))).................................... (-20.32 = -20.72 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:20 2006