Locus 3900

Sequence ID	2L_DroMel_CAF1
Location	11,406,290 – 11,406,443
Length	153
Max. P	0.956315

overview

Window 5

Location	11,406,290 – 11,406,405
Length	115
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	84.64
Mean single sequence MFE	-25.07
Consensus MFE	-19.31
Energy contribution	-19.55
Covariance contribution	0.25
Combinations/Pair	1.05
Mean z-score	-1.54
Structure conservation index	0.77
SVM decision value	0.16
SVM RNA-class probability	0.611366
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11406290 115 + 22407834
UGGUAUGAGGUCCCCGGUGGUAAAAAAAAAACAAAAAAAUUAACUAAAAACGGGUGAGGAUGUGUAAUCGAUGUGCUUGCAAGUCGCAAAGUAAUCGAUUGCUGUUGAAAGGACA
.........(((((((.((((.....................))))....))).....((((.(((((((((.(((((((.....)).))))))))))))))))))....)))). ( -26.30)
>DroSec_CAF1 123780 103 + 1
UGGUAUGAGGUCCCCGGUGGUAAAA-----------AAAAUAAGUAAAAACGGGUGAGGAUGUGUAAUCGAUGUGGUUGCAAGUCGCA-GGUAAUCGAUUACUGUUGAAAGGACA
.........(((((((.........-----------..............))).....((((.(((((((((.((.((((.....)))-).)))))))))))))))....)))). ( -23.90)
>DroSim_CAF1 130506 108 + 1
UGGUAUGAGGUCCCCGGUGGUAAAA------UAAAAAAAUGAAGUAAAAACGGGUGAGGAUGUGUAAUCGAUGUGGUUGCAAUUCGCA-GGUAAUCGAUUACUGUUGAAAGGACA
.........(((((((.........------...................))).....((((.(((((((((.((.((((.....)))-).)))))))))))))))....)))). ( -23.69)
>DroEre_CAF1 131373 99 + 1
UGGUACGAGGUCCCCGGCGGUAAA------------AAGCUGAGGAAAAACGGGUG---AUGUGUAAUCGAUUUGGUGGCAAGUCGCA-GGUAAUCGAUUGCUGUUGAAAGAACA
..((.(.(.(((((((.((((...------------..))))........)))).)---)).)((((((((((..((((....)))).-...))))))))))........).)). ( -26.40)
>consensus
UGGUAUGAGGUCCCCGGUGGUAAAA___________AAAUUAAGUAAAAACGGGUGAGGAUGUGUAAUCGAUGUGGUUGCAAGUCGCA_GGUAAUCGAUUACUGUUGAAAGGACA
.........(((((((..................................)))..........(((((((((.....(((.....))).....)))))))))........)))). (-19.31 = -19.55 +   0.25)

alignment

secondary structure

dotplot

Window 6

Location	11,406,290 – 11,406,405
Length	115
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	84.64
Mean single sequence MFE	-17.30
Consensus MFE	-15.37
Energy contribution	-15.93
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-1.87
Structure conservation index	0.89
SVM decision value	1.04
SVM RNA-class probability	0.905871
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11406290 115 - 22407834
UGUCCUUUCAACAGCAAUCGAUUACUUUGCGACUUGCAAGCACAUCGAUUACACAUCCUCACCCGUUUUUAGUUAAUUUUUUUGUUUUUUUUUUACCACCGGGGACCUCAUACCA
.((((........(.(((((((...(((((.....)))))...))))))).)..........(((....(((..((............))..)))....)))))))......... ( -16.20)
>DroSec_CAF1 123780 103 - 1
UGUCCUUUCAACAGUAAUCGAUUACC-UGCGACUUGCAACCACAUCGAUUACACAUCCUCACCCGUUUUUACUUAUUUU-----------UUUUACCACCGGGGACCUCAUACCA
.((((........(((((((((....-(((.....))).....)))))))))..........(((..............-----------.........)))))))......... ( -18.60)
>DroSim_CAF1 130506 108 - 1
UGUCCUUUCAACAGUAAUCGAUUACC-UGCGAAUUGCAACCACAUCGAUUACACAUCCUCACCCGUUUUUACUUCAUUUUUUUA------UUUUACCACCGGGGACCUCAUACCA
.((((........(((((((((....-(((.....))).....)))))))))..........(((...................------.........)))))))......... ( -18.39)
>DroEre_CAF1 131373 99 - 1
UGUUCUUUCAACAGCAAUCGAUUACC-UGCGACUUGCCACCAAAUCGAUUACACAU---CACCCGUUUUUCCUCAGCUU------------UUUACCGCCGGGGACCUCGUACCA
.............(.((((((((...-.((.....)).....)))))))).)....---....((....(((((.((..------------......)).)))))...))..... ( -16.00)
>consensus
UGUCCUUUCAACAGCAAUCGAUUACC_UGCGACUUGCAACCACAUCGAUUACACAUCCUCACCCGUUUUUACUUAAUUU___________UUUUACCACCGGGGACCUCAUACCA
.(((.........(((((((((.....(((.....))).....))))))))).........((((..................................)))))))......... (-15.37 = -15.93 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	11,406,329 – 11,406,443
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	88.44
Mean single sequence MFE	-26.86
Consensus MFE	-20.20
Energy contribution	-20.36
Covariance contribution	0.16
Combinations/Pair	1.05
Mean z-score	-1.68
Structure conservation index	0.75
SVM decision value	0.23
SVM RNA-class probability	0.642798
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11406329 114 + 22407834
UUAACUAAAAACGGGUGAGGAUGUGUAAUCGAUGUGCUUGCAAGUCGCAAAGUAAUCGAUUGCUGUUGAAAGGACACUGCCUCAAGGCGAAAACAGAAACAAUAUUAUUCAACA
............((((((...((((((((((((.(((((((.....)).))))))))))))))((((...((....))(((....)))...))))...)))...)))))).... ( -27.20)
>DroSec_CAF1 123808 113 + 1
AUAAGUAAAAACGGGUGAGGAUGUGUAAUCGAUGUGGUUGCAAGUCGCA-GGUAAUCGAUUACUGUUGAAAGGACAUUGCCUCAAGGCGAAAACAGAAACAAUAUUAUUCAACA
............((((((...((((((((((((.((.((((.....)))-).)))))))))))((((.....))))(((((....)))))........)))...)))))).... ( -27.30)
>DroSim_CAF1 130539 113 + 1
UGAAGUAAAAACGGGUGAGGAUGUGUAAUCGAUGUGGUUGCAAUUCGCA-GGUAAUCGAUUACUGUUGAAAGGACAAUGCCUCAAGGCGAAAACAGAAAAAAUAUUAUUCAACA
...........((..(((((....(((((((((.((.((((.....)))-).)))))))))))((((.....))))...)))))...))......................... ( -24.90)
>DroEre_CAF1 131400 109 + 1
CUGAGGAAAAACGGGUG---AUGUGUAAUCGAUUUGGUGGCAAGUCGCA-GGUAAUCGAUUGCUGUUGAAAGAACAACGCCUCGAGGCGAAAACAGUAGC-AAAUUAUUCAACA
............(((((---((.(((((((((((..((((....)))).-...))))))))(((((((......)..((((....))))..)))))).))-).))))))).... ( -28.90)
>DroYak_CAF1 128013 111 + 1
UUAAAGAAAAACGGGUGAGGAUGUGUAAUCGAUGUGGUUGCAAGUCGCA-GGUGAUCGAUUACUGUUGAAAGGACAAUGCCUCAA-GCGAGAACAGUAAA-AUAUUUUUCAACA
...........((..(((((....(((((((((.((.((((.....)))-).)))))))))))((((.....))))...))))).-.)).(((.((((..-.)))).))).... ( -26.00)
>consensus
UUAAGUAAAAACGGGUGAGGAUGUGUAAUCGAUGUGGUUGCAAGUCGCA_GGUAAUCGAUUACUGUUGAAAGGACAAUGCCUCAAGGCGAAAACAGAAACAAUAUUAUUCAACA
........................(((((((((.....(((.....))).....))))))))).((((((........(((....)))(....).............)))))). (-20.20 = -20.36 +   0.16)

alignment

secondary structure

dotplot

Window 8

Location	11,406,329 – 11,406,443
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	88.44
Mean single sequence MFE	-23.16
Consensus MFE	-18.60
Energy contribution	-19.40
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.14
Structure conservation index	0.80
SVM decision value	1.46
SVM RNA-class probability	0.956315
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11406329 114 - 22407834
UGUUGAAUAAUAUUGUUUCUGUUUUCGCCUUGAGGCAGUGUCCUUUCAACAGCAAUCGAUUACUUUGCGACUUGCAAGCACAUCGAUUACACAUCCUCACCCGUUUUUAGUUAA
(((((((..((((((((((............))))))))))...)))))))(.(((((((...(((((.....)))))...))))))).)........................ ( -25.90)
>DroSec_CAF1 123808 113 - 1
UGUUGAAUAAUAUUGUUUCUGUUUUCGCCUUGAGGCAAUGUCCUUUCAACAGUAAUCGAUUACC-UGCGACUUGCAACCACAUCGAUUACACAUCCUCACCCGUUUUUACUUAU
(((((((..((((((((((............))))))))))...)))))))(((((((((....-(((.....))).....)))))))))........................ ( -28.10)
>DroSim_CAF1 130539 113 - 1
UGUUGAAUAAUAUUUUUUCUGUUUUCGCCUUGAGGCAUUGUCCUUUCAACAGUAAUCGAUUACC-UGCGAAUUGCAACCACAUCGAUUACACAUCCUCACCCGUUUUUACUUCA
(((((((.............(....)(((....)))........)))))))(((((((((....-(((.....))).....)))))))))........................ ( -21.40)
>DroEre_CAF1 131400 109 - 1
UGUUGAAUAAUUU-GCUACUGUUUUCGCCUCGAGGCGUUGUUCUUUCAACAGCAAUCGAUUACC-UGCGACUUGCCACCAAAUCGAUUACACAU---CACCCGUUUUUCCUCAG
((..(((.(((..-(((.........(((....)))((((......)))))))((((((((...-.((.....)).....))))))))......---.....))).)))..)). ( -19.80)
>DroYak_CAF1 128013 111 - 1
UGUUGAAAAAUAU-UUUACUGUUCUCGC-UUGAGGCAUUGUCCUUUCAACAGUAAUCGAUCACC-UGCGACUUGCAACCACAUCGAUUACACAUCCUCACCCGUUUUUCUUUAA
((((((((.....-..((.(((.(((..-..)))))).))...))))))))(((((((((....-(((.....))).....)))))))))........................ ( -20.60)
>consensus
UGUUGAAUAAUAUUGUUUCUGUUUUCGCCUUGAGGCAUUGUCCUUUCAACAGUAAUCGAUUACC_UGCGACUUGCAACCACAUCGAUUACACAUCCUCACCCGUUUUUACUUAA
(((((((.............(....)(((....)))........)))))))(((((((((.....(((.....))).....)))))))))........................ (-18.60 = -19.40 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:16 2006