Locus 6956

Sequence ID	2L_DroMel_CAF1
Location	19,322,587 – 19,322,807
Length	220
Max. P	0.808015

overview

Window 3

Location	19,322,587 – 19,322,694
Length	107
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	91.74
Mean single sequence MFE	-25.38
Consensus MFE	-22.24
Energy contribution	-22.68
Covariance contribution	0.44
Combinations/Pair	1.08
Mean z-score	-1.57
Structure conservation index	0.88
SVM decision value	0.42
SVM RNA-class probability	0.728154
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19322587 107 + 22407834
---AUAAGUAUUU-CAGUGUAAAACUGCGAAUGCAACUUUCUGCAUUUUGAUGCGGCAGUUAUUCGACUUUAUCGUGUGUGCUGACACGAAAUAUUUUAGCAUUCUAUUUA
---.((((((...-((((.....)))).((((((((((..((((((....)))))).))))...........((((((......)))))).........)))))))))))) ( -27.20)
>DroSec_CAF1 15075 111 + 1
AUGAUAAUUAUUUCCAGUGUAAAGCUGCGAAUGCAACUUUUUGCAUUUUGAUGCGGCAGUUAUUCGACUUUAUCGUGUGUGCUGACACGAAAUAUUUUAGCAUUCUAUUUA
(((..((.((((((..((((...(((((((((((((....))))))))....)))))((((((.(((.....))).))).))).)))))))))).))...)))........ ( -24.50)
>DroSim_CAF1 16903 111 + 1
AUGAUAAUUAUUUCCAGUGGAAAACUGCGAAUGCAACUUUCUGCAUUUUGAUGCGGCAGUUAUUCGACUUUAUCUUGUGUGCUGACACGAAAUAUUUUAGCAUUCUAUUUA
(((..((.((((((.(((.((((((((((((((((......))))))).......)))))).))).))).......((((....)))))))))).))...)))........ ( -24.91)
>DroEre_CAF1 14104 111 + 1
AUUUUCAGUGUUUUCAGUGUAAGCCUGCGAAUGCAAGUUUCUGCAUUUUUAUGCGGCAGUUAUUCGACUUUAUCGUGUGUGCUGACACGAAGUAUUUUAGCAUUCUAUUUA
.....(((.((((.......))))))).((((((......((((((....))))))..........(((...((((((......)))))))))......))))))...... ( -24.90)
>consensus
AUGAUAAGUAUUUCCAGUGUAAAACUGCGAAUGCAACUUUCUGCAUUUUGAUGCGGCAGUUAUUCGACUUUAUCGUGUGUGCUGACACGAAAUAUUUUAGCAUUCUAUUUA
..............((((.....)))).((((((((((..((((((....)))))).))))...........((((((......)))))).........))))))...... (-22.24 = -22.68 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	19,322,587 – 19,322,694
Length	107
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	91.74
Mean single sequence MFE	-20.90
Consensus MFE	-17.83
Energy contribution	-18.07
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.85
SVM decision value	0.54
SVM RNA-class probability	0.775250
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19322587 107 - 22407834
UAAAUAGAAUGCUAAAAUAUUUCGUGUCAGCACACACGAUAAAGUCGAAUAACUGCCGCAUCAAAAUGCAGAAAGUUGCAUUCGCAGUUUUACACUG-AAAUACUUAU---
......((((((.........((((((......))))))...........((((..(((((....)))).)..)))))))))).((((.....))))-..........--- ( -21.50)
>DroSec_CAF1 15075 111 - 1
UAAAUAGAAUGCUAAAAUAUUUCGUGUCAGCACACACGAUAAAGUCGAAUAACUGCCGCAUCAAAAUGCAAAAAGUUGCAUUCGCAGCUUUACACUGGAAAUAAUUAUCAU
......((.............((((((......))))))................((((((....))))..((((((((....)))))))).....)).........)).. ( -20.40)
>DroSim_CAF1 16903 111 - 1
UAAAUAGAAUGCUAAAAUAUUUCGUGUCAGCACACAAGAUAAAGUCGAAUAACUGCCGCAUCAAAAUGCAGAAAGUUGCAUUCGCAGUUUUCCACUGGAAAUAAUUAUCAU
.................((((((((((....)))).......(((.(((.((((((.((((....)))).(((.......)))))))))))).))).))))))........ ( -21.40)
>DroEre_CAF1 14104 111 - 1
UAAAUAGAAUGCUAAAAUACUUCGUGUCAGCACACACGAUAAAGUCGAAUAACUGCCGCAUAAAAAUGCAGAAACUUGCAUUCGCAGGCUUACACUGAAAACACUGAAAAU
....................(((((((.(((.....((((...)))).....((((.((((....)))).(((.......)))))))))).)))).)))............ ( -20.30)
>consensus
UAAAUAGAAUGCUAAAAUAUUUCGUGUCAGCACACACGAUAAAGUCGAAUAACUGCCGCAUCAAAAUGCAGAAAGUUGCAUUCGCAGUUUUACACUGGAAAUAAUUAUCAU
......((((((.........((((((......))))))..................((((....))))........)))))).(((.......))).............. (-17.83 = -18.07 +   0.25)

alignment

secondary structure

dotplot

Window 5

Location	19,322,616 – 19,322,734
Length	118
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	94.07
Mean single sequence MFE	-28.32
Consensus MFE	-23.98
Energy contribution	-24.97
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.95
Structure conservation index	0.85
SVM decision value	0.64
SVM RNA-class probability	0.808015
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19322616 118 - 22407834
UUUCGGGGAAACCCACCGUGGAAUCGCUUUAAAUGUGCAUUAAAUAGAAUGCUAAAAUAUUUCGUGUCAGCACACACGAUAAAGUCGAAUAACUGCCGCAUCAAAAUGCAGAAAGUUG
(((((((....)))...((((..((((((((.....(((((......))))).........((((((......))))))))))).))).......))))...........)))).... ( -30.70)
>DroSec_CAF1 15108 118 - 1
UUUCGGGGAAACCCCCCGUGGAACCGCUUUAAAUGUGCAUUAAAUAGAAUGCUAAAAUAUUUCGUGUCAGCACACACGAUAAAGUCGAAUAACUGCCGCAUCAAAAUGCAAAAAGUUG
...(((((.....)))))......(((((((.....(((((......))))).........((((((......))))))))))).))..(((((...((((....))))....))))) ( -28.60)
>DroSim_CAF1 16936 118 - 1
UUUCGGGGAAACCCACCGUGGAAUCGCUUUAAAUGUGCAUUAAAUAGAAUGCUAAAAUAUUUCGUGUCAGCACACAAGAUAAAGUCGAAUAACUGCCGCAUCAAAAUGCAGAAAGUUG
(((((((....)))...((((..((((((((..((((((((......)))))...........(((....))))))...))))).))).......))))...........)))).... ( -27.80)
>DroEre_CAF1 14137 117 - 1
UUUCGGGGAAACC-AUCACCGAGUCGCUUUAAACGUGCAUUAAAUAGAAUGCUAAAAUACUUCGUGUCAGCACACACGAUAAAGUCGAAUAACUGCCGCAUAAAAAUGCAGAAACUUG
.....((....))-.....((((((((((((.....(((((......))))).........((((((......))))))))))).))).........((((....)))).....)))) ( -26.20)
>consensus
UUUCGGGGAAACCCACCGUGGAAUCGCUUUAAAUGUGCAUUAAAUAGAAUGCUAAAAUAUUUCGUGUCAGCACACACGAUAAAGUCGAAUAACUGCCGCAUCAAAAUGCAGAAAGUUG
....(((....))).........((((((((.....(((((......))))).........((((((......))))))))))).))).(((((...((((....))))....))))) (-23.98 = -24.97 +   1.00)

alignment

secondary structure

dotplot

Window 6

Location	19,322,694 – 19,322,807
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.28
Mean single sequence MFE	-40.80
Consensus MFE	-29.21
Energy contribution	-29.09
Covariance contribution	-0.12
Combinations/Pair	1.09
Mean z-score	-1.54
Structure conservation index	0.72
SVM decision value	0.11
SVM RNA-class probability	0.590254
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19322694 113 - 22407834
ACACUCGGCUUUGCGGUUAGCAGCUGGAGGCUGCCAUCUCCUCCAGGAAUGCAUCUUGGGAUCACGCACAGU-------CUUUCGGGGAAACCCACCGUGGAAUCGCUUUAAAUGUGCAU
.(((..((((.((((....(((((.....))))).......(((((((.....)))))))....)))).)))-------)....(((....)))...))).....((.........)).. ( -38.70)
>DroSec_CAF1 15186 120 - 1
ACACUCGGCUUUGCGGUUAGCAGCUGGAGGCUGCCAUCUCCUCCAGGAGUGCAUCUUGGGAUCACGCACAGUCGCACAUCUUUCGGGGAAACCCCCCGUGGAACCGCUUUAAAUGUGCAU
......((((.((((....(((((.....))))).......(((((((.....)))))))....)))).))))((((((.....((((.....))))(((....))).....)))))).. ( -46.30)
>DroSim_CAF1 17014 120 - 1
ACACUCGGCUUUGCGGUUAGCAGCUGGAGGCUGCCAUCUCCUCCAGGAGUGCAUCUCGGGAUCACGCACAGUCGCACAUCUUUCGGGGAAACCCACCGUGGAAUCGCUUUAAAUGUGCAU
......((((.((((........((.((((.(((...((((....)))).))))))).))....)))).))))((((((.....(((....)))...(((....))).....)))))).. ( -43.50)
>DroEre_CAF1 14215 108 - 1
GCACUCGACUUUGCGGUUAGCAGCUGGAGGCUGUCUGCUCCUCCAGGAAUGCAUCUC-----------CAGUCGAACAUCUUUCGGGGAAACC-AUCACCGAGUCGCUUUAAACGUGCAU
((((((((((....((...(((.(((((((..(....).)))))))...)))....)-----------)))))))......(((((.((....-.)).)))))...........)))).. ( -34.70)
>consensus
ACACUCGGCUUUGCGGUUAGCAGCUGGAGGCUGCCAUCUCCUCCAGGAAUGCAUCUCGGGAUCACGCACAGUCGCACAUCUUUCGGGGAAACCCACCGUGGAAUCGCUUUAAAUGUGCAU
.(((........((((((.(((.(((((((.........)))))))...)))................................(((....))).......)))))).......)))... (-29.21 = -29.09 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:55 2006