Locus 5963

Sequence ID	X_DroMel_CAF1
Location	15,367,931 – 15,368,171
Length	240
Max. P	0.984428

overview

Window 0

Location	15,367,931 – 15,368,051
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.28
Mean single sequence MFE	-31.08
Consensus MFE	-24.89
Energy contribution	-24.82
Covariance contribution	-0.06
Combinations/Pair	1.08
Mean z-score	-1.54
Structure conservation index	0.80
SVM decision value	0.16
SVM RNA-class probability	0.611731
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15367931 120 + 22224390
CAUUUUUGCCUAUCACAGCAUAUAUGAAAUUAAUAACCUUUGCCAACUUUCUGGCCAAAGUGUGCUUUUCUCGGCAAAGUGUGCCAUCAGCUUUGCUGUCACACCUGGCGUAUGCGUAUU
....((((((......(((((((((.......)))..((((((((......))).)))))))))))......))))))(((((....((((...)))).)))))...(((....)))... ( -29.90)
>DroSec_CAF1 745 120 + 1
CAUUUUUGGCUAUCACCGCAUAUACGAAAUCAAUAACCUUUGCCAACUUUUUGGCCAAAGUGUGCUUUUCUCGGCGAAGUGUGCCAUCAGCUUUGCUGUCACACCUGGCGUAUGCGUAUU
................(((((((.(((........(((((((((((....)))).))))).)).......)))((.(.(((((....((((...)))).))))).).))))))))).... ( -32.46)
>DroSim_CAF1 3250 120 + 1
CAUUUUUGGCUAUCACCGCAUAUACGAAAUUAAUAACCUUUGCCAACUUUUUGGCCAAAGUGUGCUUUUCUCGGCGAAGUGUGCCAUCAGCUUUGCUGUCACACCUGGCGUAUGCGUAUU
................(((((((.(((........(((((((((((....)))).))))).)).......)))((.(.(((((....((((...)))).))))).).))))))))).... ( -32.46)
>DroEre_CAF1 7885 120 + 1
CCUGGUUGAGUAUGACAGCAUACAUGAAAUUAAAAACCACUUCAAACUUUCCGGCCAAAGUGUGCGUUUCUCGGCCAAUUGUGCCAUCAGCUCUGCUGUCACACCUGGCGUAUGCGUAUU
..((((((.(((((....))))).((((............)))).......))))))....((((((....((.(((..((((....((((...)))).))))..)))))...)))))). ( -29.50)
>consensus
CAUUUUUGGCUAUCACAGCAUAUACGAAAUUAAUAACCUUUGCCAACUUUCUGGCCAAAGUGUGCUUUUCUCGGCGAAGUGUGCCAUCAGCUUUGCUGUCACACCUGGCGUAUGCGUAUU
.................((((((.......................(.....)((((..(((((........((((.....))))..((((...)))).))))).))))))))))..... (-24.89 = -24.82 +  -0.06)

alignment

secondary structure

dotplot

Window 1

Location	15,367,931 – 15,368,051
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.28
Mean single sequence MFE	-34.61
Consensus MFE	-26.09
Energy contribution	-26.47
Covariance contribution	0.38
Combinations/Pair	1.09
Mean z-score	-1.94
Structure conservation index	0.75
SVM decision value	0.45
SVM RNA-class probability	0.740346
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15367931 120 - 22224390
AAUACGCAUACGCCAGGUGUGACAGCAAAGCUGAUGGCACACUUUGCCGAGAAAAGCACACUUUGGCCAGAAAGUUGGCAAAGGUUAUUAAUUUCAUAUAUGCUGUGAUAGGCAAAAAUG
...........(((...(((.((((((..(((..(((((.....))))).....)))..(((((.(((((....))))).)))))...............)))))).))))))....... ( -32.60)
>DroSec_CAF1 745 120 - 1
AAUACGCAUACGCCAGGUGUGACAGCAAAGCUGAUGGCACACUUCGCCGAGAAAAGCACACUUUGGCCAAAAAGUUGGCAAAGGUUAUUGAUUUCGUAUAUGCGGUGAUAGCCAAAAAUG
.....(((((.((.(((((((.((((...))))....))))))).))(((((.......(((((.(((((....))))).)))))......)))))..)))))(((....)))....... ( -35.02)
>DroSim_CAF1 3250 120 - 1
AAUACGCAUACGCCAGGUGUGACAGCAAAGCUGAUGGCACACUUCGCCGAGAAAAGCACACUUUGGCCAAAAAGUUGGCAAAGGUUAUUAAUUUCGUAUAUGCGGUGAUAGCCAAAAAUG
.....(((((.((.(((((((.((((...))))....))))))).))(((((.......(((((.(((((....))))).)))))......)))))..)))))(((....)))....... ( -35.02)
>DroEre_CAF1 7885 120 - 1
AAUACGCAUACGCCAGGUGUGACAGCAGAGCUGAUGGCACAAUUGGCCGAGAAACGCACACUUUGGCCGGAAAGUUUGAAGUGGUUUUUAAUUUCAUGUAUGCUGUCAUACUCAACCAGG
.....((....))..(((((((((((((((((..((((.(((.((((........)).))..)))))))...)))))(((((........))))).....))))))))))))........ ( -35.80)
>consensus
AAUACGCAUACGCCAGGUGUGACAGCAAAGCUGAUGGCACACUUCGCCGAGAAAAGCACACUUUGGCCAAAAAGUUGGCAAAGGUUAUUAAUUUCAUAUAUGCGGUGAUAGCCAAAAAUG
.....(((((.((.(((((((.((((...))))....))))))).)).((((.......(((((.(((((....))))).)))))......))))...)))))................. (-26.09 = -26.47 +   0.38)

alignment

secondary structure

dotplot

Window 2

Location	15,367,971 – 15,368,091
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.31
Mean single sequence MFE	-39.58
Consensus MFE	-33.44
Energy contribution	-34.75
Covariance contribution	1.31
Combinations/Pair	1.08
Mean z-score	-2.77
Structure conservation index	0.84
SVM decision value	1.36
SVM RNA-class probability	0.945770
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15367971 120 + 22224390
UGCCAACUUUCUGGCCAAAGUGUGCUUUUCUCGGCAAAGUGUGCCAUCAGCUUUGCUGUCACACCUGGCGUAUGCGUAUUUAUUUGCUAUAUGUGCGCAUUUUAAUAGGCCACUUUGCGU
.((((......))))(((((((.((((......((...(((((....((((...)))).)))))...))..((((((((.(((.....))).))))))))......)))))))))))... ( -38.20)
>DroSec_CAF1 785 120 + 1
UGCCAACUUUUUGGCCAAAGUGUGCUUUUCUCGGCGAAGUGUGCCAUCAGCUUUGCUGUCACACCUGGCGUAUGCGUAUUUAUUUGCCAUAUGUGCGCAUUUUAACAGGGCACUUUGCGU
.(((((....)))))((((((((........(((((((((.........))))))))).....((((....((((((((.(((.....))).)))))))).....))))))))))))... ( -41.40)
>DroSim_CAF1 3290 120 + 1
UGCCAACUUUUUGGCCAAAGUGUGCUUUUCUCGGCGAAGUGUGCCAUCAGCUUUGCUGUCACACCUGGCGUAUGCGUAUUUAUUUGCCAUAUGUGCGCAUUUUAACAGGGCACUUUGCGU
.(((((....)))))((((((((........(((((((((.........))))))))).....((((....((((((((.(((.....))).)))))))).....))))))))))))... ( -41.40)
>DroEre_CAF1 7925 120 + 1
UUCAAACUUUCCGGCCAAAGUGUGCGUUUCUCGGCCAAUUGUGCCAUCAGCUCUGCUGUCACACCUGGCGUAUGCGUAUUUAUUUGCCAUAUGUGCGCAUUUUGACAGGACACUUUGCGU
..((((.(.(((.(.(((((((((((.......((((..((((....((((...)))).))))..))))(((((.(((......)))))))).))))))))))).).))).).))))... ( -37.30)
>consensus
UGCCAACUUUCUGGCCAAAGUGUGCUUUUCUCGGCGAAGUGUGCCAUCAGCUUUGCUGUCACACCUGGCGUAUGCGUAUUUAUUUGCCAUAUGUGCGCAUUUUAACAGGGCACUUUGCGU
.((((......))))((((((((........(((((((((.........))))))))).....((((....((((((((.(((.....))).)))))))).....))))))))))))... (-33.44 = -34.75 +   1.31)

alignment

secondary structure

dotplot

Window 3

Location	15,367,971 – 15,368,091
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.31
Mean single sequence MFE	-35.77
Consensus MFE	-31.20
Energy contribution	-31.77
Covariance contribution	0.56
Combinations/Pair	1.06
Mean z-score	-2.55
Structure conservation index	0.87
SVM decision value	1.52
SVM RNA-class probability	0.960817
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15367971 120 - 22224390
ACGCAAAGUGGCCUAUUAAAAUGCGCACAUAUAGCAAAUAAAUACGCAUACGCCAGGUGUGACAGCAAAGCUGAUGGCACACUUUGCCGAGAAAAGCACACUUUGGCCAGAAAGUUGGCA
...(((((((((........(((((....(((.....)))....)))))..((.(((((((.((((...))))....))))))).))........)).)))))))(((((....))))). ( -35.10)
>DroSec_CAF1 785 120 - 1
ACGCAAAGUGCCCUGUUAAAAUGCGCACAUAUGGCAAAUAAAUACGCAUACGCCAGGUGUGACAGCAAAGCUGAUGGCACACUUCGCCGAGAAAAGCACACUUUGGCCAAAAAGUUGGCA
...(((((((...........(((.(((((.((((................)))).)))))...)))..(((..((((.......)))).....))).)))))))(((((....))))). ( -36.29)
>DroSim_CAF1 3290 120 - 1
ACGCAAAGUGCCCUGUUAAAAUGCGCACAUAUGGCAAAUAAAUACGCAUACGCCAGGUGUGACAGCAAAGCUGAUGGCACACUUCGCCGAGAAAAGCACACUUUGGCCAAAAAGUUGGCA
...(((((((...........(((.(((((.((((................)))).)))))...)))..(((..((((.......)))).....))).)))))))(((((....))))). ( -36.29)
>DroEre_CAF1 7925 120 - 1
ACGCAAAGUGUCCUGUCAAAAUGCGCACAUAUGGCAAAUAAAUACGCAUACGCCAGGUGUGACAGCAGAGCUGAUGGCACAAUUGGCCGAGAAACGCACACUUUGGCCGGAAAGUUUGAA
...((((.(.(((.((((((.(((((((((.((((................)))).))))).((((...)))).((((.(....))))).....))))...)))))).))).).)))).. ( -35.39)
>consensus
ACGCAAAGUGCCCUGUUAAAAUGCGCACAUAUGGCAAAUAAAUACGCAUACGCCAGGUGUGACAGCAAAGCUGAUGGCACACUUCGCCGAGAAAAGCACACUUUGGCCAAAAAGUUGGCA
...(((((((...........(((.(((((.((((................)))).)))))...)))..(((..((((.......)))).....))).)))))))(((((....))))). (-31.20 = -31.77 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	15,368,011 – 15,368,131
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-38.87
Consensus MFE	-35.29
Energy contribution	-35.91
Covariance contribution	0.62
Combinations/Pair	1.09
Mean z-score	-2.50
Structure conservation index	0.91
SVM decision value	1.97
SVM RNA-class probability	0.984428
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15368011 120 - 22224390
CUUCCAGCGACAAGUGGAAAAGCUUCGCAGUGGAAGAGACACGCAAAGUGGCCUAUUAAAAUGCGCACAUAUAGCAAAUAAAUACGCAUACGCCAGGUGUGACAGCAAAGCUGAUGGCAC
((((((((((..(((......)))))))..))))))...(((.....)))(((.((((...(((.(((((...((................))...)))))...)))....))))))).. ( -30.79)
>DroSec_CAF1 825 120 - 1
CUUCCAGCGACAAGUGGUAAAGCUUCUCAGUGGCAGAGGCACGCAAAGUGCCCUGUUAAAAUGCGCACAUAUGGCAAAUAAAUACGCAUACGCCAGGUGUGACAGCAAAGCUGAUGGCAC
((..((((((.((((......)))).))..((((((.(((((.....)))))))))))...(((.(((((.((((................)))).)))))...)))..))))..))... ( -40.39)
>DroSim_CAF1 3330 120 - 1
CUUCCAGCGACAAGUGGAAAAGCUUCGCAGUGGCAGAGGAACGCAAAGUGCCCUGUUAAAAUGCGCACAUAUGGCAAAUAAAUACGCAUACGCCAGGUGUGACAGCAAAGCUGAUGGCAC
.(((((.(.....))))))..(((...(((((((((.((.((.....)).)))))))....(((.(((((.((((................)))).)))))...)))..))))..))).. ( -35.99)
>DroEre_CAF1 7965 120 - 1
CUUCCUGCGACAAGUGGAAGCGCCACGCAGUGGCAGAGACACGCAAAGUGUCCUGUCAAAAUGCGCACAUAUGGCAAAUAAAUACGCAUACGCCAGGUGUGACAGCAGAGCUGAUGGCAC
(((((.((.....))))))).((((((((.((((((.(((((.....)))))))))))...))))(((((.((((................)))).))))).((((...)))).)))).. ( -48.29)
>consensus
CUUCCAGCGACAAGUGGAAAAGCUUCGCAGUGGCAGAGACACGCAAAGUGCCCUGUUAAAAUGCGCACAUAUGGCAAAUAAAUACGCAUACGCCAGGUGUGACAGCAAAGCUGAUGGCAC
.((((.((.....))))))..(((...(((((((((.(((((.....))))))))))....(((.(((((.((((................)))).)))))...)))..))))..))).. (-35.29 = -35.91 +   0.62)

alignment

secondary structure

dotplot

Window 5

Location	15,368,051 – 15,368,171
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-32.65
Consensus MFE	-28.67
Energy contribution	-29.30
Covariance contribution	0.63
Combinations/Pair	1.10
Mean z-score	-1.57
Structure conservation index	0.88
SVM decision value	0.30
SVM RNA-class probability	0.680419
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15368051 120 - 22224390
GUCCUUUUGGCGACAAUUAAGCCCCAUAAUGAGCUAUAAACUUCCAGCGACAAGUGGAAAAGCUUCGCAGUGGAAGAGACACGCAAAGUGGCCUAUUAAAAUGCGCACAUAUAGCAAAUA
........(((.........))).........((((((..((((((((((..(((......)))))))..))))))...........(((((..........)).))).))))))..... ( -27.30)
>DroSec_CAF1 865 120 - 1
GUCCUUUUGGCGACAAUUAAGCCCCAUAAUGAGCUAUAAACUUCCAGCGACAAGUGGUAAAGCUUCUCAGUGGCAGAGGCACGCAAAGUGCCCUGUUAAAAUGCGCACAUAUGGCAAAUA
(.((...(((((.((...((((.((((.....(((..........))).....))))....)))).....((((((.(((((.....)))))))))))...))))).))...)))..... ( -31.10)
>DroSim_CAF1 3370 120 - 1
GUCCUUUUGGCGACAAUUAAGCCCCAUAAUGAGCUAUAAACUUCCAGCGACAAGUGGAAAAGCUUCGCAGUGGCAGAGGAACGCAAAGUGCCCUGUUAAAAUGCGCACAUAUGGCAAAUA
........(((.........)))(((((.((.((.......(((((.(.....)))))).......(((.((((((.((.((.....)).))))))))...))))).)))))))...... ( -29.50)
>DroEre_CAF1 8005 120 - 1
GGCCUUUUGGCGACAAUUAAGCCCCAUAAUGAGCUAUAAACUUCCUGCGACAAGUGGAAGCGCCACGCAGUGGCAGAGACACGCAAAGUGUCCUGUCAAAAUGCGCACAUAUGGCAAAUA
.(((...(((((.......(((.(......).))).....(((((.((.....))))))))))))((((.((((((.(((((.....)))))))))))...)))).......)))..... ( -42.70)
>consensus
GUCCUUUUGGCGACAAUUAAGCCCCAUAAUGAGCUAUAAACUUCCAGCGACAAGUGGAAAAGCUUCGCAGUGGCAGAGACACGCAAAGUGCCCUGUUAAAAUGCGCACAUAUGGCAAAUA
........(((.........))).........((((((...((((.((.....))))))......((((.((((((.(((((.....)))))))))))...))))....))))))..... (-28.67 = -29.30 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:44 2006