Locus 3147

Sequence ID	X_DroMel_CAF1
Location	8,367,010 – 8,367,202
Length	192
Max. P	0.999979

overview

Window 0

Location	8,367,010 – 8,367,123
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.44
Mean single sequence MFE	-38.82
Consensus MFE	-34.16
Energy contribution	-34.08
Covariance contribution	-0.08
Combinations/Pair	1.09
Mean z-score	-2.24
Structure conservation index	0.88
SVM decision value	3.00
SVM RNA-class probability	0.998070
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8367010 113 + 22224390
UGUUAGUUUCGCUUGUUUUAUCAGCCGUUUUUGCGGCUGCUCUAGGUGCCAGUACCGCUGCUCUGCCGGCGUCUAAAAGUGCAUUGCACUUUUAAGUGUUUUCGGCCUGGG-------AA
..........((.........(((((((....))))))).....((((....))))))..(((.(((((((..(((((((((...)))))))))..)))...))))..)))-------.. ( -38.40)
>DroSec_CAF1 32177 113 + 1
UGUUAGUUUCGCUUGUUUUAUCAGCCGUUUUUGCGGCUGCUCUAGGUGCCAGUACCGCUGCUCUGCCGGCGUCUAAAAGUGCAUUGCACUUUUAAGUGUUUUCGGCCUGGU-------AA
..........((.........(((((((....))))))).....((((....))))))((((..(((((((..(((((((((...)))))))))..)))...))))..)))-------). ( -39.00)
>DroSim_CAF1 35366 113 + 1
UGUUAGUUUCGCUUGUUUUAUCAGCCGUUUUUGCGGCUGCUCUAGGUGCCAGUACCGCUGCUCUGCCGGCGUCUAAAAGUGCAUUGCACUUUUAAGUGUUUUCGGCCUGGG-------AA
..........((.........(((((((....))))))).....((((....))))))..(((.(((((((..(((((((((...)))))))))..)))...))))..)))-------.. ( -38.40)
>DroEre_CAF1 28882 113 + 1
GCUUGGUUUCGCUUGUUUUAUCAGCCGUUUUUGCGGCUUGUUUAGGUGCUAGUACCGCUGCUCUGCCGGCGUCAAAAAGUGCAUUGCACUUUUAAGUGUUUUCGGGCUGGG-------AA
((((((...(((((.........(((((....))(((..((...((((....))))...))...))))))....((((((((...)))))))))))))...))))))....-------.. ( -36.30)
>DroYak_CAF1 31111 120 + 1
UGUUAGUUUCGCCUGUUUUAUCAGCCGUUUUUGCGGCUGCUCUAGGUGCCAGUACCGCUGCUCUGCCGGCGUCUGAAAGUGCAUUGCACUUUUAAGUGUUUUCGGCCUGGGAAAUGGGAA
...........((((((((..(((((((....)))))))..(((((.((.((.....)))).).(((((((..(((((((((...)))))))))..)))...)))))))))))))))).. ( -42.00)
>consensus
UGUUAGUUUCGCUUGUUUUAUCAGCCGUUUUUGCGGCUGCUCUAGGUGCCAGUACCGCUGCUCUGCCGGCGUCUAAAAGUGCAUUGCACUUUUAAGUGUUUUCGGCCUGGG_______AA
.........((((((......(((((((....)))))))...))))))((((..((((((......)))))..(((((((((...))))))))).........)..)))).......... (-34.16 = -34.08 +  -0.08)

alignment

secondary structure

dotplot

Window 1

Location	8,367,010 – 8,367,123
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.44
Mean single sequence MFE	-30.26
Consensus MFE	-27.26
Energy contribution	-28.26
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.90
SVM decision value	2.69
SVM RNA-class probability	0.996358
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8367010 113 - 22224390
UU-------CCCAGGCCGAAAACACUUAAAAGUGCAAUGCACUUUUAGACGCCGGCAGAGCAGCGGUACUGGCACCUAGAGCAGCCGCAAAAACGGCUGAUAAAACAAGCGAAACUAACA
((-------(((((((((.......((((((((((...))))))))))..(((....).))..)))).)))).........((((((......))))))...........)))....... ( -31.80)
>DroSec_CAF1 32177 113 - 1
UU-------ACCAGGCCGAAAACACUUAAAAGUGCAAUGCACUUUUAGACGCCGGCAGAGCAGCGGUACUGGCACCUAGAGCAGCCGCAAAAACGGCUGAUAAAACAAGCGAAACUAACA
..-------.((((((((.......((((((((((...))))))))))..(((....).))..)))).)))).........((((((......))))))..................... ( -31.90)
>DroSim_CAF1 35366 113 - 1
UU-------CCCAGGCCGAAAACACUUAAAAGUGCAAUGCACUUUUAGACGCCGGCAGAGCAGCGGUACUGGCACCUAGAGCAGCCGCAAAAACGGCUGAUAAAACAAGCGAAACUAACA
((-------(((((((((.......((((((((((...))))))))))..(((....).))..)))).)))).........((((((......))))))...........)))....... ( -31.80)
>DroEre_CAF1 28882 113 - 1
UU-------CCCAGCCCGAAAACACUUAAAAGUGCAAUGCACUUUUUGACGCCGGCAGAGCAGCGGUACUAGCACCUAAACAAGCCGCAAAAACGGCUGAUAAAACAAGCGAAACCAAGC
..-------..(((((...........((((((((...))))))))....(((....).)).(((((................)))))......))))).........((........)) ( -23.69)
>DroYak_CAF1 31111 120 - 1
UUCCCAUUUCCCAGGCCGAAAACACUUAAAAGUGCAAUGCACUUUCAGACGCCGGCAGAGCAGCGGUACUGGCACCUAGAGCAGCCGCAAAAACGGCUGAUAAAACAGGCGAAACUAACA
(((((.....((((((((..........(((((((...))))))).....(((....).))..)))).)))).........((((((......))))))........)).)))....... ( -32.10)
>consensus
UU_______CCCAGGCCGAAAACACUUAAAAGUGCAAUGCACUUUUAGACGCCGGCAGAGCAGCGGUACUGGCACCUAGAGCAGCCGCAAAAACGGCUGAUAAAACAAGCGAAACUAACA
..........((((((((.......((((((((((...))))))))))..(((....).))..)))).)))).........((((((......))))))..................... (-27.26 = -28.26 +   1.00)

alignment

secondary structure

dotplot

Window 2

Location	8,367,050 – 8,367,162
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.59
Mean single sequence MFE	-44.46
Consensus MFE	-42.40
Energy contribution	-42.88
Covariance contribution	0.48
Combinations/Pair	1.05
Mean z-score	-2.82
Structure conservation index	0.95
SVM decision value	5.20
SVM RNA-class probability	0.999979
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8367050 112 + 22224390
UCUAGGUGCCAGUACCGCUGCUCUGCCGGCGUCUAAAAGUGCAUUGCACUUUUAAGUGUUUUCGGCCUGGG-------AAAUCGGAUGGAAAGCGG-GAAAAGACGCCAGAGAAAAGCCC
....((((....))))(((.((((...(((((((((((((((...)))))))))..(((((((.(.((((.-------...)))).).))))))).-.....))))))))))...))).. ( -41.00)
>DroSec_CAF1 32217 113 + 1
UCUAGGUGCCAGUACCGCUGCUCUGCCGGCGUCUAAAAGUGCAUUGCACUUUUAAGUGUUUUCGGCCUGGU-------AAAUCGGGUGGGAAGCGGGGAAAAGACCCCAGAGAAAAGCCU
....((((....))))(((.((((((..(((..(((((((((...)))))))))..)))((((.((((((.-------...)))))).))))))((((......))))))))...))).. ( -43.80)
>DroSim_CAF1 35406 113 + 1
UCUAGGUGCCAGUACCGCUGCUCUGCCGGCGUCUAAAAGUGCAUUGCACUUUUAAGUGUUUUCGGCCUGGG-------AAAUCGGGUGGAAAGCGGGGAAAAGACGCCAGAGAAAAGCCC
....((((....))))(((.((((...(((((((((((((((...)))))))))..(((((((.((((((.-------...)))))).))))))).......))))))))))...))).. ( -47.90)
>DroEre_CAF1 28922 112 + 1
UUUAGGUGCUAGUACCGCUGCUCUGCCGGCGUCAAAAAGUGCAUUGCACUUUUAAGUGUUUUCGGGCUGGG-------AAAUCGGGUGGAAAGCGG-GAAAAGACGCCAGAGAAAAGCCC
....((((....))))(((.((((...((((((.((((((((...))))))))...(((((((.(.((((.-------...)))).).))))))).-.....))))))))))...))).. ( -42.40)
>DroYak_CAF1 31151 119 + 1
UCUAGGUGCCAGUACCGCUGCUCUGCCGGCGUCUGAAAGUGCAUUGCACUUUUAAGUGUUUUCGGCCUGGGAAAUGGGAAAUCGGGUGGAAAGCGG-GAAAAGACGCCAGAGAAAAGCCC
....((((....))))(((.((((...(((((((((((((((...))))))))...(((((((.((((((...........)))))).))))))).-....)))))))))))...))).. ( -47.20)
>consensus
UCUAGGUGCCAGUACCGCUGCUCUGCCGGCGUCUAAAAGUGCAUUGCACUUUUAAGUGUUUUCGGCCUGGG_______AAAUCGGGUGGAAAGCGG_GAAAAGACGCCAGAGAAAAGCCC
....((((....))))(((.((((...(((((((((((((((...)))))))))..(((((((.((((((...........)))))).))))))).......))))))))))...))).. (-42.40 = -42.88 +   0.48)

alignment

secondary structure

dotplot

Window 3

Location	8,367,050 – 8,367,162
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.59
Mean single sequence MFE	-34.02
Consensus MFE	-31.05
Energy contribution	-31.85
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	0.91
SVM decision value	1.22
SVM RNA-class probability	0.932475
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8367050 112 - 22224390
GGGCUUUUCUCUGGCGUCUUUUC-CCGCUUUCCAUCCGAUUU-------CCCAGGCCGAAAACACUUAAAAGUGCAAUGCACUUUUAGACGCCGGCAGAGCAGCGGUACUGGCACCUAGA
..(((.(((((((((((((((((-..((((............-------...)))).)))))....(((((((((...))))))))))))))))).)))).)))(((......))).... ( -35.66)
>DroSec_CAF1 32217 113 - 1
AGGCUUUUCUCUGGGGUCUUUUCCCCGCUUCCCACCCGAUUU-------ACCAGGCCGAAAACACUUAAAAGUGCAAUGCACUUUUAGACGCCGGCAGAGCAGCGGUACUGGCACCUAGA
..(((.((((((((.((((((((...((((............-------...)))).)))))....(((((((((...)))))))))))).)))).)))).)))(((......))).... ( -31.36)
>DroSim_CAF1 35406 113 - 1
GGGCUUUUCUCUGGCGUCUUUUCCCCGCUUUCCACCCGAUUU-------CCCAGGCCGAAAACACUUAAAAGUGCAAUGCACUUUUAGACGCCGGCAGAGCAGCGGUACUGGCACCUAGA
..(((.((((((((((((........(.((((..((.(....-------..).))..)))).)...(((((((((...))))))))))))))))).)))).)))(((......))).... ( -36.50)
>DroEre_CAF1 28922 112 - 1
GGGCUUUUCUCUGGCGUCUUUUC-CCGCUUUCCACCCGAUUU-------CCCAGCCCGAAAACACUUAAAAGUGCAAUGCACUUUUUGACGCCGGCAGAGCAGCGGUACUAGCACCUAAA
..(((.(((((((((((((((((-..(((.............-------...)))..))))).....((((((((...)))))))).)))))))).)))).)))(((......))).... ( -33.59)
>DroYak_CAF1 31151 119 - 1
GGGCUUUUCUCUGGCGUCUUUUC-CCGCUUUCCACCCGAUUUCCCAUUUCCCAGGCCGAAAACACUUAAAAGUGCAAUGCACUUUCAGACGCCGGCAGAGCAGCGGUACUGGCACCUAGA
..(((.(((((((((((((....-.............(.((((((........))..)))).).....(((((((...))))))).))))))))).)))).)))(((......))).... ( -33.00)
>consensus
GGGCUUUUCUCUGGCGUCUUUUC_CCGCUUUCCACCCGAUUU_______CCCAGGCCGAAAACACUUAAAAGUGCAAUGCACUUUUAGACGCCGGCAGAGCAGCGGUACUGGCACCUAGA
..(((.(((((((((((((((((...((((......................)))).)))))....(((((((((...))))))))))))))))).)))).)))(((......))).... (-31.05 = -31.85 +   0.80)

alignment

secondary structure

dotplot

Window 4

Location	8,367,090 – 8,367,202
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.15
Mean single sequence MFE	-29.05
Consensus MFE	-24.24
Energy contribution	-24.68
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.51
Structure conservation index	0.83
SVM decision value	0.34
SVM RNA-class probability	0.694741
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8367090 112 + 22224390
GCAUUGCACUUUUAAGUGUUUUCGGCCUGGG-------AAAUCGGAUGGAAAGCGG-GAAAAGACGCCAGAGAAAAGCCCCAUGUGGCACAGUUGCAAAUAGACGAAAAAAAGAAGUAGA
...((((((((((...(((((((.(.((((.-------...)))).).))))))).-.)))))..((((.(...........).)))).....)))))...................... ( -23.10)
>DroSec_CAF1 32257 110 + 1
GCAUUGCACUUUUAAGUGUUUUCGGCCUGGU-------AAAUCGGGUGGGAAGCGGGGAAAAGACCCCAGAGAAAAGCCUCAUGUGGCACAGUUGCAAAUAGACGAAAA-A--AUGUAGA
...(((((((((.....((((((.((((((.-------...)))))).))))))((((......))))))))....(((......))).....)))))...........-.--....... ( -33.40)
>DroSim_CAF1 35446 111 + 1
GCAUUGCACUUUUAAGUGUUUUCGGCCUGGG-------AAAUCGGGUGGAAAGCGGGGAAAAGACGCCAGAGAAAAGCCCCAUGUGGCACAGUUGCAAAUAGACGAAAAAA--AAGUAGA
...((((((((((...(((((((.((((((.-------...)))))).)))))))...)))))..((((.(...........).)))).....))))).............--....... ( -30.30)
>DroEre_CAF1 28962 108 + 1
GCAUUGCACUUUUAAGUGUUUUCGGGCUGGG-------AAAUCGGGUGGAAAGCGG-GAAAAGACGCCAGAGAAAAGCCCCAUGUGGCACAGUUGCACAUACACGAAAA----AGGUAAA
...((((.(((((..((((....(((((...-------...((.((((........-.......)))).))....))))).(((((.((....)))))))))))..)))----)))))). ( -29.46)
>DroYak_CAF1 31191 105 + 1
GCAUUGCACUUUUAAGUGUUUUCGGCCUGGGAAAUGGGAAAUCGGGUGGAAAGCGG-GAAAAGACGCCAGAGAAAAGCCCCAUGUGGCACAGUUGCA----------AA----AAGUAGA
...((((((((((...(((((((.((((((...........)))))).))))))).-.)))))..((((.(...........).)))).....))))----------).----....... ( -29.00)
>consensus
GCAUUGCACUUUUAAGUGUUUUCGGCCUGGG_______AAAUCGGGUGGAAAGCGG_GAAAAGACGCCAGAGAAAAGCCCCAUGUGGCACAGUUGCAAAUAGACGAAAA_A__AAGUAGA
((((((..(((((...(((((((.((((((...........)))))).)))))))...)))))..((((.(...........).)))).))).)))........................ (-24.24 = -24.68 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:11 2006