Locus 9191

Sequence ID	3R_DroMel_CAF1
Location	24,511,164 – 24,511,320
Length	156
Max. P	0.983302

overview

Window 1

Location	24,511,164 – 24,511,269
Length	105
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	81.40
Mean single sequence MFE	-30.60
Consensus MFE	-21.43
Energy contribution	-22.15
Covariance contribution	0.72
Combinations/Pair	1.10
Mean z-score	-2.27
Structure conservation index	0.70
SVM decision value	0.85
SVM RNA-class probability	0.865763
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24511164 105 + 27905053
CUUUCCGCUGCACCGGAAA--CUCACGGAGCU--UCACCAUUGCAUGCUAGCUACUUUUGACCUUGGCAAUAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAU
......(((((.(((....--....))).)).--......(((((((((.((((..........))))..........((....)).....)))))))))....))).. ( -28.50)
>DroPse_CAF1 11397 99 + 1
CUUUCCGUUGCAUCGGAAAGGCCCCCGGAAAGCCAUUGCAUUGCAUGCCA-CCACGACUGACCUUGUC---------ACGGCAACGCACUCGGCAUGCAAACUACAGAU
(((((((......)))))))((....((....))...)).(((((((((.-....(((.......)))---------.((....)).....)))))))))......... ( -32.50)
>DroSim_CAF1 9857 105 + 1
CUUUCCGCUGCACCGGAAA--CUCACGGAGCU--UCACCAUUGCAUGCCAGCUACUUUUGACCUUGGCAAUAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAU
......(((((.(((....--....))).)).--......(((((((((.((((..........))))..........((....)).....)))))))))....))).. ( -31.20)
>DroEre_CAF1 9766 105 + 1
CUUUCCGCUGCACCGGAAA--CUCACGGAGCA--UCACCAUUGCAUGCCAGCUACUUUUGACCUUGGCAAUAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAU
......(((((.(((....--....))).)).--......(((((((((.((((..........))))..........((....)).....)))))))))....))).. ( -31.70)
>DroYak_CAF1 9892 105 + 1
CUUUCCGCUGCACCGGAAA--CUCACGGAGCU--ACACCAUUGCAUGCCAGCUACUUUUGACCUUGGCAAUAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAU
......(((((.(((....--....))).)).--......(((((((((.((((..........))))..........((....)).....)))))))))....))).. ( -31.20)
>DroAna_CAF1 10375 88 + 1
UUUUCCGCUGCUCGGGAAA--GCACCGGAAAG-----ACAUUGCAUGCCAGCUUCUAUUGACCUUGGC--------------AACGCACUCGGCAUGCAAACUAAGCAU
(((((((.((((......)--))).)))))))-----...(((((((((....((....))....(..--------------..)......)))))))))......... ( -28.50)
>consensus
CUUUCCGCUGCACCGGAAA__CUCACGGAGCU__UCACCAUUGCAUGCCAGCUACUUUUGACCUUGGCAAUAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAU
.((((((......)))))).....................(((((((((.((((..........))))..........((....)).....)))))))))......... (-21.43 = -22.15 +   0.72)

alignment

secondary structure

dotplot

Window 2

Location	24,511,199 – 24,511,295
Length	96
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	78.21
Mean single sequence MFE	-27.17
Consensus MFE	-18.76
Energy contribution	-18.79
Covariance contribution	0.03
Combinations/Pair	1.20
Mean z-score	-2.88
Structure conservation index	0.69
SVM decision value	1.94
SVM RNA-class probability	0.983302
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24511199 96 + 27905053
AUUGCAUGCUAGCUACUUUUGACCUUGGCAAUAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAUCAGCGAAUAGCAAAUG--------------AUUGCUAAGA
.(((((((((.((((..........))))..........((....)).....))))))))).((.(((((((((.....))...))--------------).)))).)). ( -26.10)
>DroPse_CAF1 11436 100 + 1
AUUGCAUGCCA-CCACGACUGACCUUGUC---------ACGGCAACGCACUCGGCAUGCAAACUACAGAUCAGCAAAACCUCAACGAUCCGUAGUAGCGUUUUGCUAAGA
.(((((((((.-....(((.......)))---------.((....)).....)))))))))..........(((((((((((.(((...))).).)).)))))))).... ( -32.70)
>DroSec_CAF1 9848 96 + 1
AUUGCAUGCCAGCUACUUUUGACCUUGGCAAUAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAUCAGCGAAUAGCAGAUG--------------AUUGCUAAGA
.(((((((((.((((..........))))..........((....)).....))))))))).((.(((((((((.....))...))--------------).)))).)). ( -28.80)
>DroEre_CAF1 9801 96 + 1
AUUGCAUGCCAGCUACUUUUGACCUUGGCAAUAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAUCAGCAAAUAGCAAAUG--------------AUUGCUAAGA
.(((((((((.((((..........))))..........((....)).....))))))))).((.(((((((((.....))...))--------------).)))).)). ( -28.10)
>DroYak_CAF1 9927 96 + 1
AUUGCAUGCCAGCUACUUUUGACCUUGGCAAUAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAUCAGCGAAUAGCAAAUG--------------AUUGCUAAGA
.(((((((((.((((..........))))..........((....)).....))))))))).((.(((((((((.....))...))--------------).)))).)). ( -28.80)
>DroAna_CAF1 10407 75 + 1
AUUGCAUGCCAGCUUCUAUUGACCUUGGC--------------AACGCACUCGGCAUGCAAACUAAGCAUCAACAAUCAG---------------------UUGUUAAGA
.(((((((((....((....))....(..--------------..)......))))))))).((.((((.(........)---------------------.)))).)). ( -18.50)
>consensus
AUUGCAUGCCAGCUACUUUUGACCUUGGCAAUAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAUCAGCAAAUAGCAAAUG______________AUUGCUAAGA
.(((((((((.((((..........))))..........((....)).....)))))))))..........(((((.........................))))).... (-18.76 = -18.79 +   0.03)

alignment

secondary structure

dotplot

Window 3

Location	24,511,199 – 24,511,295
Length	96
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	78.21
Mean single sequence MFE	-26.98
Consensus MFE	-17.59
Energy contribution	-18.01
Covariance contribution	0.42
Combinations/Pair	1.10
Mean z-score	-1.61
Structure conservation index	0.65
SVM decision value	0.65
SVM RNA-class probability	0.811145
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24511199 96 - 27905053
UCUUAGCAAU--------------CAUUUGCUAUUCGCUGAUGCCUAGUUUGCAUGCCGAGUGCGUUGCCGUUUUUCUAUUGCCAAGGUCAAAAGUAGCUAGCAUGCAAU
...((((((.--------------...))))))...((....)).....((((((((..(((...(((((................)).))).....))).)))))))). ( -22.69)
>DroPse_CAF1 11436 100 - 1
UCUUAGCAAAACGCUACUACGGAUCGUUGAGGUUUUGCUGAUCUGUAGUUUGCAUGCCGAGUGCGUUGCCGU---------GACAAGGUCAGUCGUGG-UGGCAUGCAAU
...((((.....))))(((((((((((.........)).))))))))).((((((((((..(((((((((..---------.....)).))).)))).-)))))))))). ( -37.50)
>DroSec_CAF1 9848 96 - 1
UCUUAGCAAU--------------CAUCUGCUAUUCGCUGAUGCCUAGUUUGCAUGCCGAGUGCGUUGCCGUUUUUCUAUUGCCAAGGUCAAAAGUAGCUGGCAUGCAAU
..((((....--------------((((.((.....)).)))).)))).((((((((((..(((.(((((................)).)))..)))..)))))))))). ( -25.59)
>DroEre_CAF1 9801 96 - 1
UCUUAGCAAU--------------CAUUUGCUAUUUGCUGAUGCCUAGUUUGCAUGCCGAGUGCGUUGCCGUUUUUCUAUUGCCAAGGUCAAAAGUAGCUGGCAUGCAAU
...((((((.--------------...))))))...((....)).....((((((((((..(((.(((((................)).)))..)))..)))))))))). ( -26.49)
>DroYak_CAF1 9927 96 - 1
UCUUAGCAAU--------------CAUUUGCUAUUCGCUGAUGCCUAGUUUGCAUGCCGAGUGCGUUGCCGUUUUUCUAUUGCCAAGGUCAAAAGUAGCUGGCAUGCAAU
...((((((.--------------...))))))...((....)).....((((((((((..(((.(((((................)).)))..)))..)))))))))). ( -26.79)
>DroAna_CAF1 10407 75 - 1
UCUUAACAA---------------------CUGAUUGUUGAUGCUUAGUUUGCAUGCCGAGUGCGUU--------------GCCAAGGUCAAUAGAAGCUGGCAUGCAAU
......(((---------------------(.....)))).........(((((((((.(((..(((--------------((....).))))....)))))))))))). ( -22.80)
>consensus
UCUUAGCAAU______________CAUUUGCUAUUCGCUGAUGCCUAGUUUGCAUGCCGAGUGCGUUGCCGUUUUUCUAUUGCCAAGGUCAAAAGUAGCUGGCAUGCAAU
..(((((.............................)))))........((((((((((..(((...(((................))).....)))..)))))))))). (-17.59 = -18.01 +   0.42)

alignment

secondary structure

dotplot

Window 4

Location	24,511,230 – 24,511,320
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	98.67
Mean single sequence MFE	-21.00
Consensus MFE	-20.38
Energy contribution	-20.22
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.15
Structure conservation index	0.97
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24511230 90 + 27905053
UAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAUCAGCGAAUAGCAAAUGAUUGCUAAGAACUCGCCUGUUGUUUUCAAAGCUGA
........((....))...(((((.((.(((((((((.........((((((....)))))).(....))))))..)))).))..))))) ( -20.70)
>DroSec_CAF1 9879 90 + 1
UAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAUCAGCGAAUAGCAGAUGAUUGCUAAGAACUCGCCUGUUGUUUUCAAAGCUGA
........((....))...(((((((((.......))))..(.(((((((((.(((.(.......).))).))))))))).)...))))) ( -20.00)
>DroSim_CAF1 9923 90 + 1
UAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAUCAGCGAAUAGCAAAUGAUUGCUAAGAACUCGCCUGUUGUUUUCAAAGCUGA
........((....))...(((((.((.(((((((((.........((((((....)))))).(....))))))..)))).))..))))) ( -20.70)
>DroEre_CAF1 9832 90 + 1
UAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAUCAGCAAAUAGCAAAUGAUUGCUAAGAACUCGCCUGUUGUUUUCAAAGCUGA
........((....))...(((((.((.(((((((((.........((((((....)))))).(....))))))..)))).))..))))) ( -20.70)
>DroYak_CAF1 9958 90 + 1
UAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAUCAGCGAAUAGCAAAUGAUUGCUAAGAACUUGCCUGUUGUUUUCAAAGCUGA
........((....))...(((((.((.((((((((((....(...((((((....)))))).)....))))))..)))).))..))))) ( -22.90)
>consensus
UAGAAAAACGGCAACGCACUCGGCAUGCAAACUAGGCAUCAGCGAAUAGCAAAUGAUUGCUAAGAACUCGCCUGUUGUUUUCAAAGCUGA
........((....))...(((((.((.(((((((((.....(...((((((....)))))).).....)))))..)))).))..))))) (-20.38 = -20.22 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:28:37 2006