Locus 6502

Sequence ID	3L_DroMel_CAF1
Location	17,262,836 – 17,262,995
Length	159
Max. P	0.999196

overview

Window 7

Location	17,262,836 – 17,262,955
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.31
Mean single sequence MFE	-45.34
Consensus MFE	-42.10
Energy contribution	-42.34
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.15
Structure conservation index	0.93
SVM decision value	3.43
SVM RNA-class probability	0.999196
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17262836 119 + 23771897
UCAUCCAGUUGGGUCGACUUGGCGGACUUGGCAUUUCAGCUCUUCUAUUUAGCUGAUUGUCGUCUGGCGGAGGCAGGAGCCUCCACUUCGUACCACUCCU-UUCGAGUCCUGGCUGCGUG
.(((.((((..((((((...(.(((((..((((..((((((.........)))))).))))))))).)((((((....))))))................-.))))..))..)))).))) ( -46.10)
>DroSec_CAF1 146400 119 + 1
UCAUCCAGUUGGGUCGACUUGGCGGACUUGGCAUUUCAGCUCUUCUAUUUAGCUGAUUGUCGUCUGGCGGAGGCAGGAGCCUCCACUUCGUACCACUCCU-UUCGAGUCCUGGCUGCGUG
.(((.((((..((((((...(.(((((..((((..((((((.........)))))).))))))))).)((((((....))))))................-.))))..))..)))).))) ( -46.10)
>DroSim_CAF1 141411 119 + 1
UCAUCCAGUUGGGUCGACUUGGCGGACUUGGCAUUUCAGCUCUUCUAUUUAGCUGAUUGUCGUCUGGCGGAGGCAGGAGCCUCCACUUCGUACCACUCCU-UUCGAGUCCUGGCUGCGUG
.(((.((((..((((((...(.(((((..((((..((((((.........)))))).))))))))).)((((((....))))))................-.))))..))..)))).))) ( -46.10)
>DroEre_CAF1 149493 119 + 1
UCAUCCAGUUGGGCCGACUUGGCGGACUUGGCAUUUCAGCUCUCCUAUUUAGCUGAUUGUCGUCUGGCGGAGGCAGGAGCCUCCAUUUCGUGCCACUCCU-UUCGAGUCCUGGCUGCGUG
.(((.((((..((...((((((.(((..((((((.((((((.........))))))..(((....)))((((((....)))))).....)))))).))).-.))))))))..)))).))) ( -46.60)
>DroYak_CAF1 153850 120 + 1
UCAUCCAGUUGGCUCGACUUGGCGGACUUGGCAUUCCAGCUCUCCUAUUUAGCUGAUUGUCGUCUGGCGGAGGCAGAAUCCUCCAUUGCGUACCACUCGUAGUCAAGUCCUGGCUGCGUG
.(((.((((..(...((((((((((((..((((...(((((.........)))))..))))))))...(((((......)))))..((((.......)))))))))))))..)))).))) ( -41.80)
>consensus
UCAUCCAGUUGGGUCGACUUGGCGGACUUGGCAUUUCAGCUCUUCUAUUUAGCUGAUUGUCGUCUGGCGGAGGCAGGAGCCUCCACUUCGUACCACUCCU_UUCGAGUCCUGGCUGCGUG
.(((.((((..(...((((((((((((..((((..((((((.........)))))).)))))))))..((((((....))))))..................))))))))..)))).))) (-42.10 = -42.34 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	17,262,836 – 17,262,955
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.31
Mean single sequence MFE	-41.00
Consensus MFE	-38.36
Energy contribution	-38.52
Covariance contribution	0.16
Combinations/Pair	1.12
Mean z-score	-2.03
Structure conservation index	0.94
SVM decision value	3.20
SVM RNA-class probability	0.998729
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17262836 119 - 23771897
CACGCAGCCAGGACUCGAA-AGGAGUGGUACGAAGUGGAGGCUCCUGCCUCCGCCAGACGACAAUCAGCUAAAUAGAAGAGCUGAAAUGCCAAGUCCGCCAAGUCGACCCAACUGGAUGA
....((.((((...((((.-.(((.(((((....((((((((....))))))))..........((((((.........))))))..)))))..)))......)))).....)))).)). ( -42.00)
>DroSec_CAF1 146400 119 - 1
CACGCAGCCAGGACUCGAA-AGGAGUGGUACGAAGUGGAGGCUCCUGCCUCCGCCAGACGACAAUCAGCUAAAUAGAAGAGCUGAAAUGCCAAGUCCGCCAAGUCGACCCAACUGGAUGA
....((.((((...((((.-.(((.(((((....((((((((....))))))))..........((((((.........))))))..)))))..)))......)))).....)))).)). ( -42.00)
>DroSim_CAF1 141411 119 - 1
CACGCAGCCAGGACUCGAA-AGGAGUGGUACGAAGUGGAGGCUCCUGCCUCCGCCAGACGACAAUCAGCUAAAUAGAAGAGCUGAAAUGCCAAGUCCGCCAAGUCGACCCAACUGGAUGA
....((.((((...((((.-.(((.(((((....((((((((....))))))))..........((((((.........))))))..)))))..)))......)))).....)))).)). ( -42.00)
>DroEre_CAF1 149493 119 - 1
CACGCAGCCAGGACUCGAA-AGGAGUGGCACGAAAUGGAGGCUCCUGCCUCCGCCAGACGACAAUCAGCUAAAUAGGAGAGCUGAAAUGCCAAGUCCGCCAAGUCGGCCCAACUGGAUGA
....((.((((........-.(((.(((((......((((((....))))))............((((((.........))))))..)))))..)))(((.....)))....)))).)). ( -42.10)
>DroYak_CAF1 153850 120 - 1
CACGCAGCCAGGACUUGACUACGAGUGGUACGCAAUGGAGGAUUCUGCCUCCGCCAGACGACAAUCAGCUAAAUAGGAGAGCUGGAAUGCCAAGUCCGCCAAGUCGAGCCAACUGGAUGA
....((.((((..(((((((..(.((((.(((((..(((((......)))))............((((((.........))))))..)))...))))))).)))))))....)))).)). ( -36.90)
>consensus
CACGCAGCCAGGACUCGAA_AGGAGUGGUACGAAGUGGAGGCUCCUGCCUCCGCCAGACGACAAUCAGCUAAAUAGAAGAGCUGAAAUGCCAAGUCCGCCAAGUCGACCCAACUGGAUGA
....((.((((...((((...(((.(((((((..((((((((....))))))))....))....((((((.........))))))..)))))..)))......)))).....)))).)). (-38.36 = -38.52 +   0.16)

alignment

secondary structure

dotplot

Window 9

Location	17,262,876 – 17,262,995
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.98
Mean single sequence MFE	-34.56
Consensus MFE	-32.68
Energy contribution	-32.92
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.37
Structure conservation index	0.95
SVM decision value	1.14
SVM RNA-class probability	0.921071
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17262876 119 + 23771897
UCUUCUAUUUAGCUGAUUGUCGUCUGGCGGAGGCAGGAGCCUCCACUUCGUACCACUCCU-UUCGAGUCCUGGCUGCGUGUGCUUAGCAUUUUUGUUGACAUAUUCAUUGGCAAACUCAA
...........((..((.((.(((.((.((((((....))))))..........((((..-...)))))).))).))(((((.((((((....)))))))))))..))..))........ ( -32.60)
>DroSec_CAF1 146440 119 + 1
UCUUCUAUUUAGCUGAUUGUCGUCUGGCGGAGGCAGGAGCCUCCACUUCGUACCACUCCU-UUCGAGUCCUGGCUGCGUGUGCUCAGCAUUUUUGUUGACAUAUUCAUUGGCAAACUCAA
...........((..((.((.(((.((.((((((....))))))..........((((..-...)))))).))).))(((((.((((((....)))))))))))..))..))........ ( -34.80)
>DroSim_CAF1 141451 119 + 1
UCUUCUAUUUAGCUGAUUGUCGUCUGGCGGAGGCAGGAGCCUCCACUUCGUACCACUCCU-UUCGAGUCCUGGCUGCGUGUGCUCAGCAUUUUUGUUGACAUAUUCAUUGGCAAACUCAA
...........((..((.((.(((.((.((((((....))))))..........((((..-...)))))).))).))(((((.((((((....)))))))))))..))..))........ ( -34.80)
>DroEre_CAF1 149533 119 + 1
UCUCCUAUUUAGCUGAUUGUCGUCUGGCGGAGGCAGGAGCCUCCAUUUCGUGCCACUCCU-UUCGAGUCCUGGCUGCGUGUGCUCAGCAUUUUUGUUGACAUAUUCAUUGGCAAACUCAA
...........((..((.........((((((((....)))))).......(((((((..-...))))...))).))(((((.((((((....)))))))))))..))..))........ ( -35.40)
>DroYak_CAF1 153890 120 + 1
UCUCCUAUUUAGCUGAUUGUCGUCUGGCGGAGGCAGAAUCCUCCAUUGCGUACCACUCGUAGUCAAGUCCUGGCUGCGUGUGCUCAGCAUUUUUGUUGACAUAUUCAUUGGCAAACUCAA
...........((((((....))).)))(((((......))))).((((....(((.((((((((.....)))))))).))).((((((....))))))...........))))...... ( -35.20)
>consensus
UCUUCUAUUUAGCUGAUUGUCGUCUGGCGGAGGCAGGAGCCUCCACUUCGUACCACUCCU_UUCGAGUCCUGGCUGCGUGUGCUCAGCAUUUUUGUUGACAUAUUCAUUGGCAAACUCAA
...........((..((.((.(((.((.((((((....))))))..........((((......)))))).))).))(((((.((((((....)))))))))))..))..))........ (-32.68 = -32.92 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:38 2006