Locus 8539

Sequence ID	X_DroMel_CAF1
Location	21,155,879 – 21,156,063
Length	184
Max. P	0.951305

overview

Window 2

Location	21,155,879 – 21,155,984
Length	105
Sequences	3
Columns	105
Reading direction	forward
Mean pairwise identity	84.13
Mean single sequence MFE	-32.13
Consensus MFE	-26.59
Energy contribution	-26.60
Covariance contribution	0.01
Combinations/Pair	1.18
Mean z-score	-1.61
Structure conservation index	0.83
SVM decision value	0.20
SVM RNA-class probability	0.628909
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21155879 105 + 22224390
ACAUUAUUGUUAGUUCGCUGCUAUUAUAUUGGCCUCAGCUGUAUCUGCGGUUAGCGAGUGCACCCACCGCAGUUAGCACGUGCCAGCACCUUAUUUGGCGAAUUC
...........((((((((((((......))))....((((...(((((((..((....))....))))))).))))..(((....))).......)))))))). ( -30.70)
>DroSec_CAF1 20058 105 + 1
ACAUUUUAGUUAGUUCGCUGCUAUUAUUUUGGCCCCAGCUGUAGCUGCGGUUAGCGAGUGCACCCACCGCAGUUAGCACGUGCCAGCACCGCAUUUGGCGAACUC
...........((((((((..........(((((.((((....)))).)))))(((.((((...(((.((.....))..)))...)))))))....)))))))). ( -36.40)
>DroYak_CAF1 20778 104 + 1
UCAUUUUUGCUAUUUCGCUGCUAUUAUUUUGGCCUUAGCGGUACCCAC-GUUAGCGAGUGCACACACCGCAGUAAGCGAGUGUCCGCACCACAUUUGGCCAGUUC
........((((..((((.((((......))))..(((((.......)-))))))))((((..(((((((.....))).))))..))))......))))...... ( -29.30)
>consensus
ACAUUUUUGUUAGUUCGCUGCUAUUAUUUUGGCCUCAGCUGUACCUGCGGUUAGCGAGUGCACCCACCGCAGUUAGCACGUGCCAGCACCACAUUUGGCGAAUUC
...........((((((((((((......))))....(((((((.(((.....(((.(((....)))))).....))).))).)))).........)))))))). (-26.59 = -26.60 +   0.01)

alignment

secondary structure

dotplot

Window 3

Location	21,155,879 – 21,155,984
Length	105
Sequences	3
Columns	105
Reading direction	reverse
Mean pairwise identity	84.13
Mean single sequence MFE	-37.10
Consensus MFE	-21.64
Energy contribution	-22.53
Covariance contribution	0.89
Combinations/Pair	1.08
Mean z-score	-2.86
Structure conservation index	0.58
SVM decision value	0.34
SVM RNA-class probability	0.693907
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21155879 105 - 22224390
GAAUUCGCCAAAUAAGGUGCUGGCACGUGCUAACUGCGGUGGGUGCACUCGCUAACCGCAGAUACAGCUGAGGCCAAUAUAAUAGCAGCGAACUAACAAUAAUGU
...(((((....((..(((.((((....(((..(((((((.((((....)))).)))))))....)))....)))).)))..))...)))))............. ( -32.20)
>DroSec_CAF1 20058 105 - 1
GAGUUCGCCAAAUGCGGUGCUGGCACGUGCUAACUGCGGUGGGUGCACUCGCUAACCGCAGCUACAGCUGGGGCCAAAAUAAUAGCAGCGAACUAACUAAAAUGU
.(((((((....(((.((..((((....(((..(((((((.((((....)))).)))))))....)))....))))..))....))))))))))........... ( -38.20)
>DroYak_CAF1 20778 104 - 1
GAACUGGCCAAAUGUGGUGCGGACACUCGCUUACUGCGGUGUGUGCACUCGCUAAC-GUGGGUACCGCUAAGGCCAAAAUAAUAGCAGCGAAAUAGCAAAAAUGA
....(((((....((((((((.((((.(((.....))))))).)))((((((....-)))))))))))...)))))...........((......))........ ( -40.90)
>consensus
GAAUUCGCCAAAUGAGGUGCUGGCACGUGCUAACUGCGGUGGGUGCACUCGCUAACCGCAGAUACAGCUGAGGCCAAAAUAAUAGCAGCGAACUAACAAAAAUGU
....((((........(((....)))..((((.(((((((.((((....)))).))))))).....((....))........)))).)))).............. (-21.64 = -22.53 +   0.89)

alignment

secondary structure

dotplot

Window 4

Location	21,155,904 – 21,156,024
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	82.22
Mean single sequence MFE	-49.03
Consensus MFE	-33.18
Energy contribution	-33.63
Covariance contribution	0.46
Combinations/Pair	1.18
Mean z-score	-2.67
Structure conservation index	0.68
SVM decision value	1.41
SVM RNA-class probability	0.951305
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21155904 120 - 22224390
CGAUAGCGCCUGCCAUCGACAUAUCGAUACACAUGGUGGCGAAUUCGCCAAAUAAGGUGCUGGCACGUGCUAACUGCGGUGGGUGCACUCGCUAACCGCAGAUACAGCUGAGGCCAAUAU
....(((((((((((((((....))))......))))((((....)))).....)))))))(((....(((..(((((((.((((....)))).)))))))....)))....)))..... ( -47.40)
>DroSec_CAF1 20083 120 - 1
CGAUAGCGCCUGCCAUCGACGUAUCGAUACACUUGGUGGCGAGUUCGCCAAAUGCGGUGCUGGCACGUGCUAACUGCGGUGGGUGCACUCGCUAACCGCAGCUACAGCUGGGGCCAAAAU
...((((....((((((((.((........))))))))))((((.((((...((((((..((((....))))))))))...)))).)))))))).((.((((....)))).))....... ( -49.40)
>DroYak_CAF1 20803 118 - 1
CGAUAACGCCUGCGA-CGGCUUAUCGGUAUACGAUGUGGUGAACUGGCCAAAUGUGGUGCGGACACUCGCUUACUGCGGUGUGUGCACUCGCUAAC-GUGGGUACCGCUAAGGCCAAAAU
((((((.(((.....-.)))))))))((.(((......))).))(((((....((((((((.((((.(((.....))))))).)))((((((....-)))))))))))...))))).... ( -50.30)
>consensus
CGAUAGCGCCUGCCAUCGACAUAUCGAUACACAUGGUGGCGAAUUCGCCAAAUGAGGUGCUGGCACGUGCUAACUGCGGUGGGUGCACUCGCUAACCGCAGAUACAGCUGAGGCCAAAAU
.......((((((((((((....)))))........(((((....))))).....)))((((((....))...(((((((.((((....)))).)))))))...))))..))))...... (-33.18 = -33.63 +   0.46)

alignment

secondary structure

dotplot

Window 5

Location	21,155,944 – 21,156,063
Length	119
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	81.89
Mean single sequence MFE	-43.53
Consensus MFE	-31.99
Energy contribution	-33.33
Covariance contribution	1.35
Combinations/Pair	1.19
Mean z-score	-1.76
Structure conservation index	0.73
SVM decision value	0.34
SVM RNA-class probability	0.695325
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21155944 119 + 22224390
ACCGCAGUUAGCACGUGCCAGCACCUUAUUUGGCGAAUUCGCCACCAUGUGUAUCGAUAUGUCGAUGGCAGGCGCUAUCGAUUUUGAUGGAUGUUC-UCAAAGCGUGUUCGGCGCGGUCA
(((((.....))..(((((((((((((...(((((....)))))..((((.((((((...(((((((((....))))))))).)))))).))))..-...))).))))).)))))))).. ( -47.80)
>DroSec_CAF1 20123 119 + 1
ACCGCAGUUAGCACGUGCCAGCACCGCAUUUGGCGAACUCGCCACCAAGUGUAUCGAUACGUCGAUGGCAGGCGCUAUCGAUUUUGAUGGAUGUUC-UCAAAGCGUGCUCGGGGUGGUCA
(((((....(((((((...((((((((((((((((....)))))...)))))(((((...(((((((((....))))))))).))))))).)))).-.....)))))))....))))).. ( -47.50)
>DroYak_CAF1 20842 119 + 1
ACCGCAGUAAGCGAGUGUCCGCACCACAUUUGGCCAGUUCACCACAUCGUAUACCGAUAAGCCG-UCGCAGGCGUUAUCGAUUUUUAUGGACGGUAUUGAUAGCGUGUUCGGCGUGGUCA
(((((......(((((((.......)))))))(((.(..(((...((((.((((((....(((.-.....)))....((.((....)).))))))))))))...)))..))))))))).. ( -35.30)
>consensus
ACCGCAGUUAGCACGUGCCAGCACCACAUUUGGCGAAUUCGCCACCAAGUGUAUCGAUAAGUCGAUGGCAGGCGCUAUCGAUUUUGAUGGAUGUUC_UCAAAGCGUGUUCGGCGUGGUCA
(((((....(((((((..............(((((....)))))..((((.((((((...(((((((((....))))))))).)))))).))))........)))))))....))))).. (-31.99 = -33.33 +   1.35)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:06:51 2006