Locus 1654

Sequence ID	3R_DroMel_CAF1
Location	4,784,825 – 4,785,077
Length	252
Max. P	0.998324

overview

Window 7

Location	4,784,825 – 4,784,937
Length	112
Sequences	3
Columns	112
Reading direction	reverse
Mean pairwise identity	79.38
Mean single sequence MFE	-30.05
Consensus MFE	-22.69
Energy contribution	-22.69
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.33
Structure conservation index	0.76
SVM decision value	-0.01
SVM RNA-class probability	0.526182
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4784825 112 - 27905053
CUUUCCCGCAAACAGUCUCGGUCAUAAAAGUAUCGCCCAAAUCGGGCCAGGCUAUGGCGAGCCGAGUCAAGCCAAGCCUUCCUGCUGGCCUUUCAGGCCGGCCUUAUCGCCA
...................(((.((((.......((((.....)))).(((((.((((............)))))))))....(((((((.....))))))).)))).))). ( -37.80)
>DroSec_CAF1 20047 84 - 1
------------CAGCCUCGGUCAUAAAAGUAUCGC-CAAGUCGGA---------------CCGAGCCAAGCCAAGCCUUCCUGCUGGCCUUUCAGGCCGGCCUUAUCGCCA
------------..(.(((((((......(.....)-.......))---------------))))).).......((......(((((((.....)))))))......)).. ( -25.42)
>DroSim_CAF1 15509 96 - 1
CUUUCUCGCAUACAGCCUCGGUCAUAAAAGUAUCGC-CAAGUCGGA---------------CCGAGCCAAGCCAAGCCUUCCUGCUGGCCUUUCAGGCCGGCCUUAUCGCCA
.......((.....(.(((((((......(.....)-.......))---------------))))).)..(((.(((......)))((((.....)))))))......)).. ( -26.92)
>consensus
CUUUC_CGCA_ACAGCCUCGGUCAUAAAAGUAUCGC_CAAGUCGGA_______________CCGAGCCAAGCCAAGCCUUCCUGCUGGCCUUUCAGGCCGGCCUUAUCGCCA
...................(((.((((.......((.....((((................)))).....))...........(((((((.....))))))).)))).))). (-22.69 = -22.69 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	4,784,937 – 4,785,037
Length	100
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	93.27
Mean single sequence MFE	-37.04
Consensus MFE	-33.58
Energy contribution	-33.86
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-2.09
Structure conservation index	0.91
SVM decision value	3.07
SVM RNA-class probability	0.998324
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4784937 100 - 27905053
CAAAAAUUUGCAUAGUUGUUGCUGGGCCUCCAGGGAGUGGAUUUGGAUCCGCUGCGUGGAGGGUCCACU--ACCCGUGCAGAGUGCCA--GUUCCAGUACAUCU
......(((((((....((.(.((((((((((.(.(((((((....))))))).).)))).))))))).--))..)))))))((((..--......)))).... ( -38.80)
>DroSec_CAF1 20131 97 - 1
CAAAAAUUUGCAUAGUUGUUGCUGGGCCUCCAGGGAGUGGAUUUGGAUCCGCUGCGUGGAGGGUCCACU--ACCCAUGAAGAGUGCCAGAGUUCCAGUA-----
...............(((..(((.(((((((((((((((((((....(((((...))))).))))))))--.))).))..))).)))..)))..)))..----- ( -33.80)
>DroSim_CAF1 15605 102 - 1
CAAAAAUUUGCAUAGUUGUUGCUGGGCCUCCAGGGAGUGGAUUUGGAUCCGCUGCGUGGAGGGUCCACU--ACCCAUGAAGAGUGCCAGAGUUCCAGUACAUCU
.............((.(((.((((((((((((.(.(((((((....))))))).).))))))...((((--..........)))).......))))))))).)) ( -35.00)
>DroEre_CAF1 20409 99 - 1
CAAAAAUUUGCAUAGUUGUUGCUGGGCCUCCAGGGAGUGGAUUUGGAUUCGCUGCGUGGAGGGUCCACUG---CCAUGCAGAGUGCCA--GUUCCAGUACAUCU
......(((((((.((....(.((((((((((.(.(((((((....))))))).).)))).))))))).)---).)))))))((((..--......)))).... ( -37.00)
>DroYak_CAF1 20742 102 - 1
CAAAAAUUUGCAUAGUUGUUGCUGGGCCUCCAGGGAGUGGAUUUGGAUCCGCUGCGUGGAGGGUCCACUCUACCAAUGCAGAGUGCCA--GUUCCAGUACAUCU
...............(((..(((((.((((((.(.(((((((....))))))).).))))))...((((((........)))))))))--))..)))....... ( -40.60)
>consensus
CAAAAAUUUGCAUAGUUGUUGCUGGGCCUCCAGGGAGUGGAUUUGGAUCCGCUGCGUGGAGGGUCCACU__ACCCAUGCAGAGUGCCA__GUUCCAGUACAUCU
......((((((((((....)))(((((((((.(.(((((((....))))))).).)))).))))).........)))))))((((..........)))).... (-33.58 = -33.86 +   0.28)

alignment

secondary structure

dotplot

Window 9

Location	4,784,973 – 4,785,077
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	86.77
Mean single sequence MFE	-26.25
Consensus MFE	-19.78
Energy contribution	-21.50
Covariance contribution	1.72
Combinations/Pair	1.06
Mean z-score	-2.46
Structure conservation index	0.75
SVM decision value	0.05
SVM RNA-class probability	0.559339
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4784973 104 + 27905053
ACCCUCCACGCAGCGGAUCCAAAUCCACUCCCUGGAGGCC----------------CAGCAACAACUAUGCAAAUUUUUGUGUAGUUUUUAUGAUGCUUAACAAUUUUUAGUCGCCGCUU
..((((((.(.((.((((....)))).)).).))))))..----------------.((((.(((((((((((....))))))))).....)).))))...................... ( -26.00)
>DroSec_CAF1 20164 104 + 1
ACCCUCCACGCAGCGGAUCCAAAUCCACUCCCUGGAGGCC----------------CAGCAACAACUAUGCAAAUUUUUGUGUAGUUUUUAUGAUGCUUAACUAUUUUUAGUCGCCGCUU
..((((((.(.((.((((....)))).)).).))))))..----------------.(((...((((((((((....))))))))))........((...((((....)))).)).))). ( -28.00)
>DroSim_CAF1 15643 104 + 1
ACCCUCCACGCAGCGGAUCCAAAUCCACUCCCUGGAGGCC----------------CAGCAACAACUAUGCAAAUUUUUGUGUAGUUUUUAUGAUGCUUAACUAUUUUUAGUCGCCGCUU
..((((((.(.((.((((....)))).)).).))))))..----------------.(((...((((((((((....))))))))))........((...((((....)))).)).))). ( -28.00)
>DroEre_CAF1 20444 104 + 1
ACCCUCCACGCAGCGAAUCCAAAUCCACUCCCUGGAGGCC----------------CAGCAACAACUAUGCAAAUUUUUGUGUAGUUUUUAUGAUGCUUAACUAUUUUUAGUCGCUGCUU
.........(((((((...........(((....)))...----------------.((((.(((((((((((....))))))))).....)).)))).............))))))).. ( -27.20)
>DroYak_CAF1 20780 104 + 1
ACCCUCCACGCAGCGGAUCCAAAUCCACUCCCUGGAGGCC----------------CAGCAACAACUAUGCAAAUUUUUGUGUAGUUUUUAUGACGCUUAACUAUUUUUAGUCGCCGCUC
..((((((.(.((.((((....)))).)).).))))))..----------------.(((...((((((((((....))))))))))........((...((((....)))).)).))). ( -28.30)
>DroAna_CAF1 20095 110 + 1
ACCCUCCACGCUG---------AUACACUCCCUAGAGGCCGCUGCCUAGUGGACCCAGGCAACAACUAUGCAAAUUUGUGUAUUUUUUUUAUGAUGCUUAACUAUUUUUAGUCAGU-UUU
.........((((---------((..........(.(((((((....))))).)))(((((.((...(((((......)))))........)).)))))...........))))))-... ( -20.00)
>consensus
ACCCUCCACGCAGCGGAUCCAAAUCCACUCCCUGGAGGCC________________CAGCAACAACUAUGCAAAUUUUUGUGUAGUUUUUAUGAUGCUUAACUAUUUUUAGUCGCCGCUU
..((((((.(.((.((((....)))).)).).))))))...................((((.(((((((((((....))))))))).....)).))))..((((....))))........ (-19.78 = -21.50 +   1.72)

alignment

secondary structure

dotplot

Window 0

Location	4,784,973 – 4,785,077
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	86.77
Mean single sequence MFE	-36.30
Consensus MFE	-29.93
Energy contribution	-30.85
Covariance contribution	0.92
Combinations/Pair	1.17
Mean z-score	-3.72
Structure conservation index	0.82
SVM decision value	1.86
SVM RNA-class probability	0.980481
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4784973 104 - 27905053
AAGCGGCGACUAAAAAUUGUUAAGCAUCAUAAAAACUACACAAAAAUUUGCAUAGUUGUUGCUG----------------GGCCUCCAGGGAGUGGAUUUGGAUCCGCUGCGUGGAGGGU
.(((((((((((.(((((..........................)))))...))))))))))).----------------..((((((.(.(((((((....))))))).).)))))).. ( -37.77)
>DroSec_CAF1 20164 104 - 1
AAGCGGCGACUAAAAAUAGUUAAGCAUCAUAAAAACUACACAAAAAUUUGCAUAGUUGUUGCUG----------------GGCCUCCAGGGAGUGGAUUUGGAUCCGCUGCGUGGAGGGU
.(((((((((((....(((((............)))))..(((....)))..))))))))))).----------------..((((((.(.(((((((....))))))).).)))))).. ( -38.30)
>DroSim_CAF1 15643 104 - 1
AAGCGGCGACUAAAAAUAGUUAAGCAUCAUAAAAACUACACAAAAAUUUGCAUAGUUGUUGCUG----------------GGCCUCCAGGGAGUGGAUUUGGAUCCGCUGCGUGGAGGGU
.(((((((((((....(((((............)))))..(((....)))..))))))))))).----------------..((((((.(.(((((((....))))))).).)))))).. ( -38.30)
>DroEre_CAF1 20444 104 - 1
AAGCAGCGACUAAAAAUAGUUAAGCAUCAUAAAAACUACACAAAAAUUUGCAUAGUUGUUGCUG----------------GGCCUCCAGGGAGUGGAUUUGGAUUCGCUGCGUGGAGGGU
.(((((((((((....(((((............)))))..(((....)))..))))))))))).----------------..((((((.(.(((((((....))))))).).)))))).. ( -36.20)
>DroYak_CAF1 20780 104 - 1
GAGCGGCGACUAAAAAUAGUUAAGCGUCAUAAAAACUACACAAAAAUUUGCAUAGUUGUUGCUG----------------GGCCUCCAGGGAGUGGAUUUGGAUCCGCUGCGUGGAGGGU
.(((((((((((....(((((............)))))..(((....)))..))))))))))).----------------..((((((.(.(((((((....))))))).).)))))).. ( -38.40)
>DroAna_CAF1 20095 110 - 1
AAA-ACUGACUAAAAAUAGUUAAGCAUCAUAAAAAAAAUACACAAAUUUGCAUAGUUGUUGCCUGGGUCCACUAGGCAGCGGCCUCUAGGGAGUGUAU---------CAGCGUGGAGGGU
...-..((((((....))))))..................(((.....((((..((((((((((((.....))))))))))))(((....))))))).---------....)))...... ( -28.80)
>consensus
AAGCGGCGACUAAAAAUAGUUAAGCAUCAUAAAAACUACACAAAAAUUUGCAUAGUUGUUGCUG________________GGCCUCCAGGGAGUGGAUUUGGAUCCGCUGCGUGGAGGGU
.(((((((((((.((....))..(((......................))).)))))))))))...................((((((.(.(((((((....))))))).).)))))).. (-29.93 = -30.85 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:01 2006