Locus 5901

Sequence ID	3L_DroMel_CAF1
Location	15,853,444 – 15,853,641
Length	197
Max. P	0.969896

overview

Window 7

Location	15,853,444 – 15,853,542
Length	98
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	86.97
Mean single sequence MFE	-38.16
Consensus MFE	-27.28
Energy contribution	-29.48
Covariance contribution	2.20
Combinations/Pair	1.08
Mean z-score	-1.85
Structure conservation index	0.71
SVM decision value	0.27
SVM RNA-class probability	0.661331
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15853444 98 + 23771897
--------CAAGUUUUCUUUUCUCUGUACCCAAAUCCUUUGGGUAGUGGGUGGUGGUGGUGCGUUCGUAGGCUUGGCCACCACGCCGCACCGGAUGUCCUGGCAUU
--------..................(((((((.....)))))))((((((((((((.(.((.(....).)).).)))))))).)))).((((.....)))).... ( -37.10)
>DroSec_CAF1 60658 106 + 1
CAAUUUUAAAAGAUUUCUUUUCUCUGUACCCAAAUCCUUUGGGUAGUGGGUGGUGGUGGUGCGUUCGUAGGCUUGGCCACCGCGCCGCACCGGAUGUCCUGGCAUU
.......(((((....))))).....(((((((.....)))))))((((((((((((.(.((.(....).)).).)))))))).)))).((((.....)))).... ( -37.80)
>DroSim_CAF1 62226 106 + 1
CAAUUUUAAAAGAUUUCUUUUCUCUGUACCCAAAUCCUUUGGGUAGUGGGUGGUGGUGGUGCGUUCGUAGGCUUGGCCACCGCGCCGCACCGGAUGUCCUGGCAUU
.......(((((....))))).....(((((((.....)))))))((((((((((((.(.((.(....).)).).)))))))).)))).((((.....)))).... ( -37.80)
>DroEre_CAF1 60476 100 + 1
CAACGUUAGAGGAUUUGUUUUCUGUGCACCCAAAUCCUUGGGGGAGU------UGGUGGUGCGGUCGUAGGCUUGGCCACCGCACCGCACCGGAUGUCCUGGCAUU
(((((((((((((....))))))).)).(((((....)))))...))------)).(((((((((((..(((...)))..)).)))))))))(((((....))))) ( -39.30)
>DroYak_CAF1 102054 104 + 1
CAAUAUUAGAAGAUUUUUUUUCUCUGUACCCAAAUCCUUGGGGGGGUGGG-GGUGGUGGUGCG-UUGAAGGCUUGGCCACCGCACCGCACCGGAUGUCCUGGCAUU
...(((.((((((....))))))..)))(((((....)))))..((((.(-(((((((((((.-......))...)))))))).)).)))).(((((....))))) ( -38.80)
>consensus
CAAUUUUAAAAGAUUUCUUUUCUCUGUACCCAAAUCCUUUGGGUAGUGGGUGGUGGUGGUGCGUUCGUAGGCUUGGCCACCGCGCCGCACCGGAUGUCCUGGCAUU
..........................(((((((.....)))))))((((((((((((.(.((........)).).)))))))).)))).((((.....)))).... (-27.28 = -29.48 +   2.20)

alignment

secondary structure

dotplot

Window 8

Location	15,853,542 – 15,853,641
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	98.18
Mean single sequence MFE	-27.40
Consensus MFE	-23.20
Energy contribution	-23.80
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.33
Structure conservation index	0.85
SVM decision value	1.61
SVM RNA-class probability	0.967103
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15853542 99 + 23771897
UCCGCCAUGCUAAUACAGAGUCGCUAUGAGUCAGCCAUUGUUGGGCCAUGUUUGCCUUCGAAUGGCUCGUGCUUUUCUUAGUUUUCAUUAGCAUUUUCU
......((((((((...(((..((((.((((((((((((...((((.......))))...))))))).).))))....)))).)))))))))))..... ( -26.40)
>DroSec_CAF1 60764 99 + 1
UCCGCCAUGCUAAUACAGACUCGCUAUGAGUCAGCCAUUGUUGGGCCAUGUUUGCCUUCGAAUGGCUCGUGCUUUUCUUAGUUUUCAUUAGCAUUUUCU
......((((((((...(((((.....)))))(((((((...((((.......))))...)))))))...................))))))))..... ( -28.10)
>DroSim_CAF1 62332 99 + 1
UCCGCCAUGCUAAUACAGAGUCGCUAUGAGUCAGCCAUUGUUGGGCCAUGUUUGCCUUCGAAUGGCUCGUGCUUUUCUUAGUUUUCAUUAGCAUUUUCU
......((((((((...(((..((((.((((((((((((...((((.......))))...))))))).).))))....)))).)))))))))))..... ( -26.40)
>DroEre_CAF1 60576 99 + 1
UCCGCCAUGCUAAUACAGAGUCGCAAUGAGUCAGCCAUUGUUGGGCCAUGUUUGGCUUUGAAUGGCUCGUGCUUUUCUUAGUUUUCAUUAGCAUUUUCU
......((((((((((((((..(((.(((((((..((..((..(((...)))..))..))..))))))))))..))))..))....))))))))..... ( -29.50)
>DroYak_CAF1 102158 99 + 1
UCCGCCAUGCUAAUACAGAGUCGCUAUGAGUCAGCCAUUGUUGGGCCAUGUUUGCCUUUGAAUGGCUCGUGCUUUUCUUAGUUUUCAUUAGCAUUUUCU
......((((((((((((((..((.((((((((..((.....((((.......)))).))..))))))))))..))))..))....))))))))..... ( -26.60)
>consensus
UCCGCCAUGCUAAUACAGAGUCGCUAUGAGUCAGCCAUUGUUGGGCCAUGUUUGCCUUCGAAUGGCUCGUGCUUUUCUUAGUUUUCAUUAGCAUUUUCU
......((((((((...(((..((((.((((((((((((...((((.......))))...))))))).).))))....)))).)))))))))))..... (-23.20 = -23.80 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	15,853,542 – 15,853,641
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	98.18
Mean single sequence MFE	-24.42
Consensus MFE	-21.36
Energy contribution	-21.56
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.06
Structure conservation index	0.87
SVM decision value	1.65
SVM RNA-class probability	0.969896
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15853542 99 - 23771897
AGAAAAUGCUAAUGAAAACUAAGAAAAGCACGAGCCAUUCGAAGGCAAACAUGGCCCAACAAUGGCUGACUCAUAGCGACUCUGUAUUAGCAUGGCGGA
.(...(((((((((..................(((((((....(((.......)))....)))))))((.((.....)).))..)))))))))..)... ( -22.90)
>DroSec_CAF1 60764 99 - 1
AGAAAAUGCUAAUGAAAACUAAGAAAAGCACGAGCCAUUCGAAGGCAAACAUGGCCCAACAAUGGCUGACUCAUAGCGAGUCUGUAUUAGCAUGGCGGA
.(...(((((((((..................(((((((....(((.......)))....)))))))(((((.....)))))..)))))))))..)... ( -28.90)
>DroSim_CAF1 62332 99 - 1
AGAAAAUGCUAAUGAAAACUAAGAAAAGCACGAGCCAUUCGAAGGCAAACAUGGCCCAACAAUGGCUGACUCAUAGCGACUCUGUAUUAGCAUGGCGGA
.(...(((((((((..................(((((((....(((.......)))....)))))))((.((.....)).))..)))))))))..)... ( -22.90)
>DroEre_CAF1 60576 99 - 1
AGAAAAUGCUAAUGAAAACUAAGAAAAGCACGAGCCAUUCAAAGCCAAACAUGGCCCAACAAUGGCUGACUCAUUGCGACUCUGUAUUAGCAUGGCGGA
.(...(((((((((.......(((...(((..(((((((....((((....)))).....))))))).......)))...))).)))))))))..)... ( -24.50)
>DroYak_CAF1 102158 99 - 1
AGAAAAUGCUAAUGAAAACUAAGAAAAGCACGAGCCAUUCAAAGGCAAACAUGGCCCAACAAUGGCUGACUCAUAGCGACUCUGUAUUAGCAUGGCGGA
.(...(((((((((..................(((((((....(((.......)))....)))))))((.((.....)).))..)))))))))..)... ( -22.90)
>consensus
AGAAAAUGCUAAUGAAAACUAAGAAAAGCACGAGCCAUUCGAAGGCAAACAUGGCCCAACAAUGGCUGACUCAUAGCGACUCUGUAUUAGCAUGGCGGA
.(...(((((((((..................(((((((....(((.......)))....)))))))((.((.....)).))..)))))))))..)... (-21.36 = -21.56 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:22 2006