Locus 5813

Sequence ID	2R_DroMel_CAF1
Location	18,410,529 – 18,410,693
Length	164
Max. P	0.993393

overview

Window 8

Location	18,410,529 – 18,410,621
Length	92
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	97.46
Mean single sequence MFE	-26.66
Consensus MFE	-25.36
Energy contribution	-25.36
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.18
Structure conservation index	0.95
SVM decision value	0.21
SVM RNA-class probability	0.637038
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18410529 92 - 20766785
GCCUCGUUUGGUUUUGAUUAC------UCUAGACCAAGCGAACCUGGCCAACAACUGUCUGGCAUUGAGAGCAGCGGCACAAUGGUAACAACAUCAGC
((((((((((((((.((....------)).))))))))))).....((((((....)).))))............)))....((((......)))).. ( -26.50)
>DroSec_CAF1 13519 92 - 1
GCCUCGUUUGGUUUUGAUUAC------UCUAGACCAAGCGAACCUGGCCAACAACUGUCUGGCAUUGAGAGCAGCGGCACAAUGGUAACAACAUCAGC
((((((((((((((.((....------)).))))))))))).....((((((....)).))))............)))....((((......)))).. ( -26.50)
>DroSim_CAF1 13615 92 - 1
GCCUCGUUUGGUUUUGAUUAC------UCUAGACCAAGCGAACCUGGCCAACAACUGUCUGGCAUUGAGAGCAGCGGCACAAUGGUAACAACAUCAGC
((((((((((((((.((....------)).))))))))))).....((((((....)).))))............)))....((((......)))).. ( -26.50)
>DroEre_CAF1 13579 92 - 1
GCCUCGUUUGGUUUUGAUUAC------UCUAGACCAAGCGAACCUGGCCAACAACUGUCUGGCAUUGAGAGCAGCGGCACAAUGGUAACAACAUCAGC
((((((((((((((.((....------)).))))))))))).....((((((....)).))))............)))....((((......)))).. ( -26.50)
>DroYak_CAF1 13740 98 - 1
GCCUCGUUUGGUUUUGAUUACUCGUACUCUAGACCAAGCGAACCUGGCCAACAACUGUCUGGCAUUGAGAGCAGCGGCACAAUGGUAACAACAUCAGC
((((((((((((((.((.((....)).)).))))))))))).....((((((....)).))))............)))....((((......)))).. ( -27.30)
>consensus
GCCUCGUUUGGUUUUGAUUAC______UCUAGACCAAGCGAACCUGGCCAACAACUGUCUGGCAUUGAGAGCAGCGGCACAAUGGUAACAACAUCAGC
((((((((((((((.((..........)).))))))))))).....((((((....)).))))............)))....((((......)))).. (-25.36 = -25.36 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	18,410,553 – 18,410,658
Length	105
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	96.28
Mean single sequence MFE	-37.68
Consensus MFE	-34.78
Energy contribution	-35.18
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.31
Structure conservation index	0.92
SVM decision value	0.68
SVM RNA-class probability	0.821226
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18410553 105 - 20766785
ACGACUUCCGAGGCGGCAGCUGACGCUUUGGGUGACCGCCUCGUUUGGUUUUGAUUAC------UCUAGACCAAGCGAACCUGGCCAACAACUGUCUGGCAUUGAGAGCAG
..(.((..((((((((((.(..(....)..).)).)))))))(((((((((.((....------)).))))))))).......((((((....)).))))...)..))).. ( -38.60)
>DroSec_CAF1 13543 105 - 1
ACGACUUCCGAGGCGGCAGCUGACGCUUUGGGUGACCGCCUCGUUUGGUUUUGAUUAC------UCUAGACCAAGCGAACCUGGCCAACAACUGUCUGGCAUUGAGAGCAG
..(.((..((((((((((.(..(....)..).)).)))))))(((((((((.((....------)).))))))))).......((((((....)).))))...)..))).. ( -38.60)
>DroSim_CAF1 13639 105 - 1
ACGACUUCCGAGGCGGCAGCUGACGCUUUGGGUGACCGCCUCGUUUGGUUUUGAUUAC------UCUAGACCAAGCGAACCUGGCCAACAACUGUCUGGCAUUGAGAGCAG
..(.((..((((((((((.(..(....)..).)).)))))))(((((((((.((....------)).))))))))).......((((((....)).))))...)..))).. ( -38.60)
>DroEre_CAF1 13603 102 - 1
--GACUUCCGACGC-GCAGCUGACGCUUUGGGUGACCGCCUCGUUUGGUUUUGAUUAC------UCUAGACCAAGCGAACCUGGCCAACAACUGUCUGGCAUUGAGAGCAG
--(.((..(((.((-((((.((.......((....))((((((((((((((.((....------)).)))))))))))....)))...)).))))...)).)))..))).. ( -33.20)
>DroYak_CAF1 13764 111 - 1
ACGACUUCCGAGGCGGCAGCUGACGCUUUGGGUGACCGCCUCGUUUGGUUUUGAUUACUCGUACUCUAGACCAAGCGAACCUGGCCAACAACUGUCUGGCAUUGAGAGCAG
..(.((..((((((((((.(..(....)..).)).)))))))(((((((((.((.((....)).)).))))))))).......((((((....)).))))...)..))).. ( -39.40)
>consensus
ACGACUUCCGAGGCGGCAGCUGACGCUUUGGGUGACCGCCUCGUUUGGUUUUGAUUAC______UCUAGACCAAGCGAACCUGGCCAACAACUGUCUGGCAUUGAGAGCAG
..(.((..((((((((((.(..(....)..).)).)))))))(((((((((.((..........)).))))))))).......((((((....)).))))...)..))).. (-34.78 = -35.18 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	18,410,587 – 18,410,693
Length	106
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	93.48
Mean single sequence MFE	-32.21
Consensus MFE	-25.77
Energy contribution	-26.57
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.57
Structure conservation index	0.80
SVM decision value	0.32
SVM RNA-class probability	0.685784
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18410587 106 + 20766785
CGCUUGGUCUAGA------GUAAUCAAAACCAAACGAGGCGGUCACCCAAAGCGUCAGCUGCCGCCUCGGAAGUCGUUGCCGCACCGUUAUGGCUUAUAAAAAUGUUUAUAU-----
...(((((...((------....))...))))).(((((((((.......(((....)))))))))))).(((((((.((......)).)))))))................----- ( -32.41)
>DroSec_CAF1 13577 106 + 1
CGCUUGGUCUAGA------GUAAUCAAAACCAAACGAGGCGGUCACCCAAAGCGUCAGCUGCCGCCUCGGAAGUCGUUGCGGCACCGUUAUGGCUUAUAAAAAUGUUUAUAU-----
...(((((...((------....))...))))).(((((((((.......(((....)))))))))))).(((((((.(((....))).)))))))................----- ( -36.61)
>DroSim_CAF1 13673 106 + 1
CGCUUGGUCUAGA------GUAAUCAAAACCAAACGAGGCGGUCACCCAAAGCGUCAGCUGCCGCCUCGGAAGUCGUUGCCGCACCGUUAUGGCUUAUAAAAAUGUUUAUAU-----
...(((((...((------....))...))))).(((((((((.......(((....)))))))))))).(((((((.((......)).)))))))................----- ( -32.41)
>DroEre_CAF1 13637 101 + 1
CGCUUGGUCUAGA------GUAAUCAAAACCAAACGAGGCGGUCACCCAAAGCGUCAGCUGC-GCGUCGGAAGUC---GCCGCACCGUUAUGGCUUAUAAAAAUGUUUAUA------
.(((((((...((------....))...))))((((..(((((.((((...((((.....))-))...))..)).---)))))..))))..))).................------ ( -28.40)
>DroYak_CAF1 13798 117 + 1
CGCUUGGUCUAGAGUACGAGUAAUCAAAACCAAACGAGGCGGUCACCCAAAGCGUCAGCUGCCGCCUCGGAAGUCGUUGCCGCACCGUUAUGGCUUAUAAAAAUGUUUAUAUAUAUA
.(((((..........))))).....((((....(((((((((.......(((....)))))))))))).(((((((.((......)).)))))))........))))......... ( -31.21)
>consensus
CGCUUGGUCUAGA______GUAAUCAAAACCAAACGAGGCGGUCACCCAAAGCGUCAGCUGCCGCCUCGGAAGUCGUUGCCGCACCGUUAUGGCUUAUAAAAAUGUUUAUAU_____
...(((((...((..........))...))))).(((((((((.......(((....)))))))))))).(((((((.((......)).)))))))..................... (-25.77 = -26.57 +   0.80)

alignment

secondary structure

dotplot

Window 1

Location	18,410,587 – 18,410,693
Length	106
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	93.48
Mean single sequence MFE	-35.84
Consensus MFE	-30.56
Energy contribution	-31.36
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.17
Structure conservation index	0.85
SVM decision value	2.39
SVM RNA-class probability	0.993393
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18410587 106 - 20766785
-----AUAUAAACAUUUUUAUAAGCCAUAACGGUGCGGCAACGACUUCCGAGGCGGCAGCUGACGCUUUGGGUGACCGCCUCGUUUGGUUUUGAUUAC------UCUAGACCAAGCG
-----.((((((....)))))).........((..((....))....))(((((((((.(..(....)..).)).)))))))(((((((((.((....------)).))))))))). ( -37.70)
>DroSec_CAF1 13577 106 - 1
-----AUAUAAACAUUUUUAUAAGCCAUAACGGUGCCGCAACGACUUCCGAGGCGGCAGCUGACGCUUUGGGUGACCGCCUCGUUUGGUUUUGAUUAC------UCUAGACCAAGCG
-----.((((((....)))))).((.....(((((((((..((.....))..)))))).))).......((....))))..((((((((((.((....------)).)))))))))) ( -34.80)
>DroSim_CAF1 13673 106 - 1
-----AUAUAAACAUUUUUAUAAGCCAUAACGGUGCGGCAACGACUUCCGAGGCGGCAGCUGACGCUUUGGGUGACCGCCUCGUUUGGUUUUGAUUAC------UCUAGACCAAGCG
-----.((((((....)))))).........((..((....))....))(((((((((.(..(....)..).)).)))))))(((((((((.((....------)).))))))))). ( -37.70)
>DroEre_CAF1 13637 101 - 1
------UAUAAACAUUUUUAUAAGCCAUAACGGUGCGGC---GACUUCCGACGC-GCAGCUGACGCUUUGGGUGACCGCCUCGUUUGGUUUUGAUUAC------UCUAGACCAAGCG
------((((((....)))))).(((.....)))..(((---(...(((((.((-((....).))).)))))....)))).((((((((((.((....------)).)))))))))) ( -30.50)
>DroYak_CAF1 13798 117 - 1
UAUAUAUAUAAACAUUUUUAUAAGCCAUAACGGUGCGGCAACGACUUCCGAGGCGGCAGCUGACGCUUUGGGUGACCGCCUCGUUUGGUUUUGAUUACUCGUACUCUAGACCAAGCG
......((((((....)))))).........((..((....))....))(((((((((.(..(....)..).)).)))))))(((((((((.((.((....)).)).))))))))). ( -38.50)
>consensus
_____AUAUAAACAUUUUUAUAAGCCAUAACGGUGCGGCAACGACUUCCGAGGCGGCAGCUGACGCUUUGGGUGACCGCCUCGUUUGGUUUUGAUUAC______UCUAGACCAAGCG
......((((((....)))))).........((..((....))....))(((((((((.(..(....)..).)).)))))))(((((((((.((..........)).))))))))). (-30.56 = -31.36 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:04 2006