Locus 3659

Sequence ID	X_DroMel_CAF1
Location	9,795,819 – 9,796,046
Length	227
Max. P	0.770148

overview

Window 4

Location	9,795,819 – 9,795,936
Length	117
Sequences	3
Columns	119
Reading direction	forward
Mean pairwise identity	95.51
Mean single sequence MFE	-34.27
Consensus MFE	-31.36
Energy contribution	-31.37
Covariance contribution	0.01
Combinations/Pair	1.10
Mean z-score	-1.61
Structure conservation index	0.92
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9795819 117 + 22224390
AAUCCCAUCUGCCGGGCAUAUAUACGAAUGUGCAC--ACGUGUAUGUGGCAGAAUGGGAUGGAGAUAGAUGGAUGACCGGCAUUAGAGAGAGAUGGCGACAAAGAGUGGGCAUUACACA
.((((((((((((....(((((((((..((....)--))))))))))))))).))))))).................((.((((.......)))).)).......(((.......))). ( -33.80)
>DroSec_CAF1 10505 118 + 1
AAUCCCAUCUGCCAGG-AUAUAUACGAAUGUGCACACACGCGUGUGUGGCAGAGUGGGAGGGAGAUAGAUGGAUGACCGGCAUUAGAGAGAGAUGGCGACAAAGAGUGGGCAUUACACA
..((((((((((((..-...((((((..(((....)))..))))))))))))).)))))..................((.((((.......)))).)).......(((.......))). ( -34.50)
>DroSim_CAF1 11638 118 + 1
AAUCCCAUCUGCCAGG-AUAUAUACGAAUGUGCACACACGCGUGUGUGGCAGAGUGGGAGGGAGAUAGAUGGAUGACCGGCAUUAGAGAGAGAUGGCGACAAAGAGUGGGCAUUACACA
..((((((((((((..-...((((((..(((....)))..))))))))))))).)))))..................((.((((.......)))).)).......(((.......))). ( -34.50)
>consensus
AAUCCCAUCUGCCAGG_AUAUAUACGAAUGUGCACACACGCGUGUGUGGCAGAGUGGGAGGGAGAUAGAUGGAUGACCGGCAUUAGAGAGAGAUGGCGACAAAGAGUGGGCAUUACACA
..((((((((((((......((((((..(((....)))..))))))))))))).)))))..................((.((((.......)))).)).......(((.......))). (-31.36 = -31.37 +   0.01)

alignment

secondary structure

dotplot

Window 5

Location	9,795,897 – 9,796,006
Length	109
Sequences	3
Columns	109
Reading direction	forward
Mean pairwise identity	99.39
Mean single sequence MFE	-31.17
Consensus MFE	-31.39
Energy contribution	-31.17
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.64
Structure conservation index	1.01
SVM decision value	0.53
SVM RNA-class probability	0.770148
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9795897 109 + 22224390
CAUUAGAGAGAGAUGGCGACAAAGAGUGGGCAUUACACAAAGGCCUUUUUGGCCGAUAAUGGAGCUUAUCUUGGCGGGGAUAAUGCCAGCAUAAAGCCGUAGGCAAAUA
(((((....(.((((.(.((.....)).).)))).).....((((.....))))..)))))..((((((..(((((.......)))))((.....)).))))))..... ( -29.50)
>DroSec_CAF1 10584 109 + 1
CAUUAGAGAGAGAUGGCGACAAAGAGUGGGCAUUACACAAAGGCCUUUUUGGCCGAUAAUGGAGCUUAUCUUGGCGGGGAUAACGCCAGCAUAAAGCCGUAGGCAAAUA
(((((....(.((((.(.((.....)).).)))).).....((((.....))))..)))))..((((((..(((((.......)))))((.....)).))))))..... ( -32.00)
>DroSim_CAF1 11717 109 + 1
CAUUAGAGAGAGAUGGCGACAAAGAGUGGGCAUUACACAAAGGCCUUUUUGGCCGAUAAUGGAGCUUAUCUUGGCGGGGAUAACGCCAGCAUAAAGCCGUAGGCAAAUA
(((((....(.((((.(.((.....)).).)))).).....((((.....))))..)))))..((((((..(((((.......)))))((.....)).))))))..... ( -32.00)
>consensus
CAUUAGAGAGAGAUGGCGACAAAGAGUGGGCAUUACACAAAGGCCUUUUUGGCCGAUAAUGGAGCUUAUCUUGGCGGGGAUAACGCCAGCAUAAAGCCGUAGGCAAAUA
(((((....(.((((.(.((.....)).).)))).).....((((.....))))..)))))..((((((..(((((.......)))))((.....)).))))))..... (-31.39 = -31.17 +  -0.22)

alignment

secondary structure

dotplot

Window 6

Location	9,795,897 – 9,796,006
Length	109
Sequences	3
Columns	109
Reading direction	reverse
Mean pairwise identity	99.39
Mean single sequence MFE	-25.57
Consensus MFE	-24.63
Energy contribution	-24.97
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.96
SVM decision value	0.17
SVM RNA-class probability	0.619141
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9795897 109 - 22224390
UAUUUGCCUACGGCUUUAUGCUGGCAUUAUCCCCGCCAAGAUAAGCUCCAUUAUCGGCCAAAAAGGCCUUUGUGUAAUGCCCACUCUUUGUCGCCAUCUCUCUCUAAUG
..........((((.....(..(((((((..(.......(((((......)))))((((.....))))...)..)))))))..).....))))................ ( -24.50)
>DroSec_CAF1 10584 109 - 1
UAUUUGCCUACGGCUUUAUGCUGGCGUUAUCCCCGCCAAGAUAAGCUCCAUUAUCGGCCAAAAAGGCCUUUGUGUAAUGCCCACUCUUUGUCGCCAUCUCUCUCUAAUG
...........(((.(((((((((((.......))))).(((((......)))))((((.....))))...)))))).)))............................ ( -26.10)
>DroSim_CAF1 11717 109 - 1
UAUUUGCCUACGGCUUUAUGCUGGCGUUAUCCCCGCCAAGAUAAGCUCCAUUAUCGGCCAAAAAGGCCUUUGUGUAAUGCCCACUCUUUGUCGCCAUCUCUCUCUAAUG
...........(((.(((((((((((.......))))).(((((......)))))((((.....))))...)))))).)))............................ ( -26.10)
>consensus
UAUUUGCCUACGGCUUUAUGCUGGCGUUAUCCCCGCCAAGAUAAGCUCCAUUAUCGGCCAAAAAGGCCUUUGUGUAAUGCCCACUCUUUGUCGCCAUCUCUCUCUAAUG
...........(((.(((((((((((.......))))).(((((......)))))((((.....))))...)))))).)))............................ (-24.63 = -24.97 +   0.33)

alignment

secondary structure

dotplot

Window 7

Location	9,795,936 – 9,796,046
Length	110
Sequences	3
Columns	110
Reading direction	reverse
Mean pairwise identity	99.39
Mean single sequence MFE	-28.87
Consensus MFE	-28.15
Energy contribution	-27.93
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.39
Structure conservation index	0.98
SVM decision value	-0.05
SVM RNA-class probability	0.508608
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9795936 110 - 22224390
AUAAAUAUGCGUGCUUGUUUGUUUCGGCCACCAAAUUGUGUAUUUGCCUACGGCUUUAUGCUGGCAUUAUCCCCGCCAAGAUAAGCUCCAUUAUCGGCCAAAAAGGCCUU
......(((.(.((((((((.....((((((......)))....((((...(((.....)))))))........))).)))))))).))))....((((.....)))).. ( -28.40)
>DroSec_CAF1 10623 110 - 1
AUAAAUAUGCGUGCUUGUUUGUUUCGGCCACCAAAUUGUGUAUUUGCCUACGGCUUUAUGCUGGCGUUAUCCCCGCCAAGAUAAGCUCCAUUAUCGGCCAAAAAGGCCUU
......(((.(.((((((((((...((((..(((((.....))))).....))))....))(((((.......))))))))))))).))))....((((.....)))).. ( -29.10)
>DroSim_CAF1 11756 110 - 1
AUAAAUAUGCGUGCUUGUUUGUUUCGGCCACCAAAUUGUGUAUUUGCCUACGGCUUUAUGCUGGCGUUAUCCCCGCCAAGAUAAGCUCCAUUAUCGGCCAAAAAGGCCUU
......(((.(.((((((((((...((((..(((((.....))))).....))))....))(((((.......))))))))))))).))))....((((.....)))).. ( -29.10)
>consensus
AUAAAUAUGCGUGCUUGUUUGUUUCGGCCACCAAAUUGUGUAUUUGCCUACGGCUUUAUGCUGGCGUUAUCCCCGCCAAGAUAAGCUCCAUUAUCGGCCAAAAAGGCCUU
......(((.(.((((((((.....((((((......)))....((((...(((.....)))))))........))).)))))))).))))....((((.....)))).. (-28.15 = -27.93 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:00 2006