Locus 4563

Sequence ID	3R_DroMel_CAF1
Location	12,066,707 – 12,066,986
Length	279
Max. P	0.989642

overview

Window 1

Location	12,066,707 – 12,066,826
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.46
Mean single sequence MFE	-25.51
Consensus MFE	-21.70
Energy contribution	-22.70
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.85
SVM decision value	0.18
SVM RNA-class probability	0.619536
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12066707 119 + 27905053
UUAUUUCAUUUCAUUUGGCGACUUUUUGGGCCAAAAGAGAUAAGCUGGGCGAAAAGCAGGGAAAAAAA-CGAAAAACAAAAAAUGUUUCAAGGCGAAAUUCGCACAGCAAUCUUGGCAAU
.......(((((.((((((..(.....).)))))).)))))..((((.(((((..((...((((....-................))))...))....))))).))))............ ( -27.45)
>DroSec_CAF1 3324 117 + 1
UUAUUUCAUUUCAUUUGGCGACUUUUUGGGCCAAAAGAGAUAAGCUGGGCGAAAAGCAGGGAAA-AAA-CGAAAAACAAAAAAUGU-UCAAGGCGAAAUUCGCACAGCAAUCUUGGCAAU
.......(((((.((((((..(.....).)))))).)))))..((((.(((((..((...(((.-...-................)-))...))....))))).))))............ ( -26.55)
>DroSim_CAF1 3755 118 + 1
UUAUUUCAUUUCAUUUGGCGACUUUUUGGGCCAAAAGAGAUAAGCUGCGCGAAAAGCAGGGAAA-AAA-CGAAAAACAAAAAAUGUUUCAAGGCGAAAUUCGCACAGCAAUCUUGGCAAU
.......(((((.((((((..(.....).)))))).)))))..((((.(((((..((...((((-...-................))))...))....))))).))))............ ( -28.31)
>DroEre_CAF1 5295 118 + 1
UUAUUUCAUUUAAUUUAGCGACUUUUUGGGCCAAAAGAGAUAAGCUGGGCGAAAAGCAAGGAAA-AAAGCGAAAAACAA-AAAUGUUUCAAGGCGAAAUUCGCACAGCAAUCUUGGCAAU
.............................((((....((((..((((.(((((..((...((((-..............-.....))))...))....))))).)))).))))))))... ( -22.91)
>DroYak_CAF1 5374 118 + 1
UUUUUUCAUUUCAUUUAGCGACUUUUUGGCCCAAAAGAGAUAAGCUGGGCGAAAAGCAGGGAAA-AAA-CGAAAAACAAAAAAUGUUUCAAGGCGAAAUUCGCACAGCAAUCUUGGCAAU
.................((..((((((......))))))....((((.(((((..((...((((-...-................))))...))....))))).)))).......))... ( -22.31)
>consensus
UUAUUUCAUUUCAUUUGGCGACUUUUUGGGCCAAAAGAGAUAAGCUGGGCGAAAAGCAGGGAAA_AAA_CGAAAAACAAAAAAUGUUUCAAGGCGAAAUUCGCACAGCAAUCUUGGCAAU
.......(((((.((((((..........)))))).)))))..((((.(((((..((...((((.....................))))...))....))))).))))............ (-21.70 = -22.70 +   1.00)

alignment

secondary structure

dotplot

Window 2

Location	12,066,786 – 12,066,906
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.17
Mean single sequence MFE	-32.90
Consensus MFE	-32.40
Energy contribution	-32.60
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.82
Structure conservation index	0.98
SVM decision value	2.04
SVM RNA-class probability	0.986405
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12066786 120 + 27905053
AAAUGUUUCAAGGCGAAAUUCGCACAGCAAUCUUGGCAAUAGCGCAUAAAAUAGCACAGAGCGCACACGAAGCGGGCAAAAAGUACCUGGCAGAUACAGAUACGACUGCCAGUGUGCGGA
...((((((...(((.....)))...((..(((.(((....))((........)).))))..))....))))))........(((((((((((............))))))).))))... ( -32.90)
>DroSec_CAF1 3402 119 + 1
AAAUGU-UCAAGGCGAAAUUCGCACAGCAAUCUUGGCAAUAGCGCAUAAAAUAGCACAGAGCGCACACGAAGCGGGCAAAAAGUACCUGGCAGAUACAGAUACGACUGCCAGUGUGCGGA
....((-((...(((.....)))...((.((.(((((......)).))).)).))...))))((((((......((((....(((.(((.......))).)))...)))).))))))... ( -32.90)
>DroSim_CAF1 3833 120 + 1
AAAUGUUUCAAGGCGAAAUUCGCACAGCAAUCUUGGCAAUAGCGCAUAAAAUAGCACAGAGCGCACACGAAGCGGGCAAAAAGUACCUGGCAGAUACAGAUACGACUGCCAGUGUGCGGA
...((((((...(((.....)))...((..(((.(((....))((........)).))))..))....))))))........(((((((((((............))))))).))))... ( -32.90)
>DroEre_CAF1 5373 120 + 1
AAAUGUUUCAAGGCGAAAUUCGCACAGCAAUCUUGGCAAUAGCGCAUAAAAUAGCACAGAGCGCACACGAAGCGGGCAAAAAGUACCUGGCAGAUACAGAUACGACUGCCAGUGUGCGAA
...((((((...(((.....)))...((..(((.(((....))((........)).))))..))....))))))........(((((((((((............))))))).))))... ( -32.90)
>DroYak_CAF1 5452 120 + 1
AAAUGUUUCAAGGCGAAAUUCGCACAGCAAUCUUGGCAAUAGCGCAUAAAAUAGCACAGAGCGCACACGAAGCGGGCAAAAAGUACCUGGCAGAUACAGAUACGACUGCCAGUGUGCGAA
...((((((...(((.....)))...((..(((.(((....))((........)).))))..))....))))))........(((((((((((............))))))).))))... ( -32.90)
>consensus
AAAUGUUUCAAGGCGAAAUUCGCACAGCAAUCUUGGCAAUAGCGCAUAAAAUAGCACAGAGCGCACACGAAGCGGGCAAAAAGUACCUGGCAGAUACAGAUACGACUGCCAGUGUGCGGA
...((((((...(((.....)))...((..(((.(((....))((........)).))))..))....))))))........(((((((((((............))))))).))))... (-32.40 = -32.60 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	12,066,786 – 12,066,906
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.17
Mean single sequence MFE	-35.10
Consensus MFE	-34.22
Energy contribution	-34.22
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.89
Structure conservation index	0.97
SVM decision value	2.17
SVM RNA-class probability	0.989642
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12066786 120 - 27905053
UCCGCACACUGGCAGUCGUAUCUGUAUCUGCCAGGUACUUUUUGCCCGCUUCGUGUGCGCUCUGUGCUAUUUUAUGCGCUAUUGCCAAGAUUGCUGUGCGAAUUUCGCCUUGAAACAUUU
..((((((..(((((..(((((((.......)))))))...))))).((.((.((.(((....((((........))))...))))).))..)))))))).................... ( -34.30)
>DroSec_CAF1 3402 119 - 1
UCCGCACACUGGCAGUCGUAUCUGUAUCUGCCAGGUACUUUUUGCCCGCUUCGUGUGCGCUCUGUGCUAUUUUAUGCGCUAUUGCCAAGAUUGCUGUGCGAAUUUCGCCUUGA-ACAUUU
..((((((..(((((..(((((((.......)))))))...))))).((.((.((.(((....((((........))))...))))).))..)))))))).............-...... ( -34.30)
>DroSim_CAF1 3833 120 - 1
UCCGCACACUGGCAGUCGUAUCUGUAUCUGCCAGGUACUUUUUGCCCGCUUCGUGUGCGCUCUGUGCUAUUUUAUGCGCUAUUGCCAAGAUUGCUGUGCGAAUUUCGCCUUGAAACAUUU
..((((((..(((((..(((((((.......)))))))...))))).((.((.((.(((....((((........))))...))))).))..)))))))).................... ( -34.30)
>DroEre_CAF1 5373 120 - 1
UUCGCACACUGGCAGUCGUAUCUGUAUCUGCCAGGUACUUUUUGCCCGCUUCGUGUGCGCUCUGUGCUAUUUUAUGCGCUAUUGCCAAGAUUGCUGUGCGAAUUUCGCCUUGAAACAUUU
((((((((..(((((..(((((((.......)))))))...))))).((.((.((.(((....((((........))))...))))).))..)))))))))).................. ( -36.30)
>DroYak_CAF1 5452 120 - 1
UUCGCACACUGGCAGUCGUAUCUGUAUCUGCCAGGUACUUUUUGCCCGCUUCGUGUGCGCUCUGUGCUAUUUUAUGCGCUAUUGCCAAGAUUGCUGUGCGAAUUUCGCCUUGAAACAUUU
((((((((..(((((..(((((((.......)))))))...))))).((.((.((.(((....((((........))))...))))).))..)))))))))).................. ( -36.30)
>consensus
UCCGCACACUGGCAGUCGUAUCUGUAUCUGCCAGGUACUUUUUGCCCGCUUCGUGUGCGCUCUGUGCUAUUUUAUGCGCUAUUGCCAAGAUUGCUGUGCGAAUUUCGCCUUGAAACAUUU
..((((((..(((((..(((((((.......)))))))...))))).((.((.((.(((....((((........))))...))))).))..)))))))).................... (-34.22 = -34.22 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	12,066,866 – 12,066,986
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.50
Mean single sequence MFE	-33.38
Consensus MFE	-30.50
Energy contribution	-30.66
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-1.19
Structure conservation index	0.91
SVM decision value	0.13
SVM RNA-class probability	0.598940
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12066866 120 - 27905053
ACCCCUCUUUGUUAAAACAUUUUUGUUUAUUUCAGCGGCGCGGUCGUAUCUGUAUCUCAGAUGUUGGCUGACUGGUUCGCUCCGCACACUGGCAGUCGUAUCUGUAUCUGCCAGGUACUU
..............(((((....)))))......((((.((((...((((((.....))))))...(((....))))))).))))((.(((((((............))))))))).... ( -32.80)
>DroSec_CAF1 3481 120 - 1
ACCCCUCUUUGUUAAAACAUUUUUGUUUAUUUCAGCGGCGCGGUCGUAUCUGUAUCUCAGAUGUUGGCUGACUGGUUCGCUCCGCACACUGGCAGUCGUAUCUGUAUCUGCCAGGUACUU
..............(((((....)))))......((((.((((...((((((.....))))))...(((....))))))).))))((.(((((((............))))))))).... ( -32.80)
>DroSim_CAF1 3913 118 - 1
ACCCCUCUUUGUUA-AACAUUUUUGU-UAUUUCAGCGGCGCGGUCGUAUCUGUAUCUCAGAUGUUGGCUGACUGGUUCGCUCCGCACACUGGCAGUCGUAUCUGUAUCUGCCAGGUACUU
..............-((((....)))-)......((((.((((...((((((.....))))))...(((....))))))).))))((.(((((((............))))))))).... ( -31.90)
>DroEre_CAF1 5453 120 - 1
CCCCCUCUUUGAGGAAACAUUUUUGUUUAUUUCAGCGGCGCGCUCGUAUCUGUAUCUCAGAUGUUGGCUGACUGGUUCGCUUCGCACACUGGCAGUCGUAUCUGUAUCUGCCAGGUACUU
...((((...))))(((((....)))))......((((.(((((..((((((.....))))))..))).((.....)))).))))((.(((((((............))))))))).... ( -36.00)
>DroYak_CAF1 5532 120 - 1
CCCCCUCUUUGUGGAAACAUUUUUGUUUAUUUCAGCGGCGCGCUCGUAUCUGUAUCUCAGAUGUUGGCUGACUGGUUCGCUUCGCACACUGGCAGUCGUAUCUGUAUCUGCCAGGUACUU
..........(((....)))..............((((.(((((..((((((.....))))))..))).((.....)))).))))((.(((((((............))))))))).... ( -33.40)
>consensus
ACCCCUCUUUGUUAAAACAUUUUUGUUUAUUUCAGCGGCGCGGUCGUAUCUGUAUCUCAGAUGUUGGCUGACUGGUUCGCUCCGCACACUGGCAGUCGUAUCUGUAUCUGCCAGGUACUU
..............(((((....)))))......((((.(((....((((((.....))))))..((((....))))))).))))((.(((((((............))))))))).... (-30.50 = -30.66 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:37 2006