Locus 5176

Sequence ID	2R_DroMel_CAF1
Location	16,841,577 – 16,841,810
Length	233
Max. P	0.999485

overview

Window 7

Location	16,841,577 – 16,841,692
Length	115
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	88.95
Mean single sequence MFE	-22.26
Consensus MFE	-19.98
Energy contribution	-19.46
Covariance contribution	-0.52
Combinations/Pair	1.14
Mean z-score	-1.48
Structure conservation index	0.90
SVM decision value	0.70
SVM RNA-class probability	0.828099
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16841577 115 + 20766785
UGGCACAGAGAAA-AUCUUCCUUUGGAAAGUAGACUUUCAGACAUAGUUGAGGCGACA-UAACCCACGCCACGAUUGUAUCACUCAAAGUCUAAUAUCUGAAAAAUCUUCGAUCAUA
.....((((....-...((((...))))..((((((((..((.(((((((.((((...-.......)))).))))))).))....))))))))...))))................. ( -25.30)
>DroSec_CAF1 10498 115 + 1
UGGCACAGAGAAA-AUCUUCCUUUGGAAAAUAGACCUUCAGACAUAGUUGAGGCGACA-UAACCUACGCCACGAUUGUAUCACUCAAAGUCUAAUAUCUGAAAAAUCUUCGAUCAUA
.....((((....-...((((...))))..(((((.....((.(((((((.((((...-.......)))).))))))).)).......)))))...))))................. ( -21.50)
>DroSim_CAF1 9700 115 + 1
UGGCACAGAAAAA-AUCUUCCUUUGGAAAAUAGACCUUCAGACAUAGUUGAGGCGAAA-UAACCCACGCCACGAUUGUAUCACUCAAAGUCUAAUAUUUGAAAAAUCUUCGAUCAUA
.....((((....-...((((...))))..(((((.....((.(((((((.((((...-.......)))).))))))).)).......)))))...))))................. ( -18.90)
>DroEre_CAF1 11148 110 + 1
CGGCACAGAAAAAUAUCUUCCUUUGGAAAGUAGACCUUCAGACAUAGUCGAGGUGACC-UAAUCCACGCCACGAUUGUAUCACUCAAAGUCUAAUAUCUGAAUAU------AUUAUA
.....((((........((((...))))..(((((.....((.(((((((.((((...-.......)))).))))))).)).......)))))...)))).....------...... ( -21.60)
>DroYak_CAF1 9646 116 + 1
CGGCACAGAAAAA-AUCUUCCUUUGGAAAGUAAACUUUCAGACAUAGUCGAGGCGACCUUAAUCAACGCCACGAUUGUAUCACUCAAAGUCUAAUAUCUAAAAAAUCACCAUUUAUA
.((....(((...-...)))((((((((((....))))).((.(((((((.((((...........)))).))))))).))...)))))...................))....... ( -24.00)
>consensus
UGGCACAGAAAAA_AUCUUCCUUUGGAAAGUAGACCUUCAGACAUAGUUGAGGCGACA_UAACCCACGCCACGAUUGUAUCACUCAAAGUCUAAUAUCUGAAAAAUCUUCGAUCAUA
.((...(((......))).))((((((...(((((.....((.(((((((.((((...........)))).))))))).)).......)))))...))))))............... (-19.98 = -19.46 +  -0.52)

alignment

secondary structure

dotplot

Window 8

Location	16,841,692 – 16,841,810
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.73
Mean single sequence MFE	-31.92
Consensus MFE	-26.68
Energy contribution	-27.12
Covariance contribution	0.44
Combinations/Pair	1.19
Mean z-score	-3.62
Structure conservation index	0.84
SVM decision value	3.65
SVM RNA-class probability	0.999485
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16841692 118 + 20766785
CUAUUUU-UUU-UACAACGCCAAACUAGUUUUUAUUGCGGCAUCGCUUGCAACUCAUUGAAUUCGUUUUUCUAAUCGAAUAAAAUGAAGUGAGUGUUGCCAAGAGCAAUACACCUUUUCG
.......-...-....................((((((((((.((((..(...(((((..(((((.((....)).)))))..))))).)..)))).))))....)))))).......... ( -26.40)
>DroSec_CAF1 10613 118 + 1
CUGUUCU-UUU-UACAAUGCCAAAUUAGUUUUUAUUGCGGCAUCGCUUGCAACUCAUUGAAUUCGUUUUUCUAAUCGAAUCCAAUGAAGUGAGUGAUGCCAAGAGCAAUACAUCUUUUCG
.((((((-(..-..(((((..(((.....)))))))).(((((((((..(...((((((.(((((.((....)).))))).)))))).)..))))))))))))))))............. ( -36.00)
>DroSim_CAF1 9815 118 + 1
CUGUUCU-UUU-UACAAUGCCAAAUUAGUUUUUAUUGCGGCAUCGCUUGCAACUCAUUGAAUUCGUUUUUCUAAUCGAAUCCAAUGAAGUGAGUGAUGCCAAGAGCAAUACAUCUUUUCG
.((((((-(..-..(((((..(((.....)))))))).(((((((((..(...((((((.(((((.((....)).))))).)))))).)..))))))))))))))))............. ( -36.00)
>DroEre_CAF1 11258 119 + 1
CUAUUUU-UUUUGACAACGUAGAAAUAGUUUUAAUUGCGGCAUCACUUGCAACUUAAUGAAUUCGUAUUUCUAAUCGAAUACAACAAAGUAAGUGUUGCCAAGAGUAAUACACCUCUACG
.......-.........((((((....((.(((.((..((((.(((((((........(....)((((((......))))))......))))))).))))..)).))).))...)))))) ( -26.30)
>DroYak_CAF1 9762 114 + 1
CUAUUUUUUUUUGACAACG-AAAACUAGUUUUUACUGCGGCAACACUUGCAACA--UUGAAUUCGUAAUUGUAAUCGAAUCCAAUGAAGUGAGUGUUGCCAAGAGUAAU---CCUUUUCG
.................((-((((.......(((((..(((((((((..(..((--(((.(((((..........))))).)))))..)..)))))))))...))))).---..)))))) ( -34.90)
>consensus
CUAUUUU_UUU_UACAACGCCAAACUAGUUUUUAUUGCGGCAUCGCUUGCAACUCAUUGAAUUCGUUUUUCUAAUCGAAUCCAAUGAAGUGAGUGUUGCCAAGAGCAAUACACCUUUUCG
.((((((....................((.......))((((((((((((...((((((.(((((..........))))).)))))).)))))))))))).))))))............. (-26.68 = -27.12 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	16,841,692 – 16,841,810
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.73
Mean single sequence MFE	-30.36
Consensus MFE	-20.80
Energy contribution	-21.32
Covariance contribution	0.52
Combinations/Pair	1.23
Mean z-score	-3.00
Structure conservation index	0.69
SVM decision value	1.57
SVM RNA-class probability	0.964350
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16841692 118 - 20766785
CGAAAAGGUGUAUUGCUCUUGGCAACACUCACUUCAUUUUAUUCGAUUAGAAAAACGAAUUCAAUGAGUUGCAAGCGAUGCCGCAAUAAAAACUAGUUUGGCGUUGUA-AAA-AAAAUAG
......(((((..(((.....))))))))((.((((((..(((((.((....)).)))))..)))))).))...(((((((((.(((........)))))))))))).-...-....... ( -25.30)
>DroSec_CAF1 10613 118 - 1
CGAAAAGAUGUAUUGCUCUUGGCAUCACUCACUUCAUUGGAUUCGAUUAGAAAAACGAAUUCAAUGAGUUGCAAGCGAUGCCGCAAUAAAAACUAAUUUGGCAUUGUA-AAA-AGAACAG
......((((((((((....((((((.((((.(((((((((((((.((....)).))))))))))))).))..)).))))))))))).....(......))))))...-...-....... ( -31.60)
>DroSim_CAF1 9815 118 - 1
CGAAAAGAUGUAUUGCUCUUGGCAUCACUCACUUCAUUGGAUUCGAUUAGAAAAACGAAUUCAAUGAGUUGCAAGCGAUGCCGCAAUAAAAACUAAUUUGGCAUUGUA-AAA-AGAACAG
......((((((((((....((((((.((((.(((((((((((((.((....)).))))))))))))).))..)).))))))))))).....(......))))))...-...-....... ( -31.60)
>DroEre_CAF1 11258 119 - 1
CGUAGAGGUGUAUUACUCUUGGCAACACUUACUUUGUUGUAUUCGAUUAGAAAUACGAAUUCAUUAAGUUGCAAGUGAUGCCGCAAUUAAAACUAUUUCUACGUUGUCAAAA-AAAAUAG
(((((((((((.(((.(..(((((.(((((((((...((.(((((..((....))))))).))..))))...))))).)))))..).))).)).))))))))).........-....... ( -29.20)
>DroYak_CAF1 9762 114 - 1
CGAAAAGG---AUUACUCUUGGCAACACUCACUUCAUUGGAUUCGAUUACAAUUACGAAUUCAA--UGUUGCAAGUGUUGCCGCAGUAAAAACUAGUUUU-CGUUGUCAAAAAAAAAUAG
(((((((.---.(((((..((((((((((..(..(((((((((((..........)))))))))--))..)..)))))))))).)))))...))...)))-))................. ( -34.10)
>consensus
CGAAAAGGUGUAUUGCUCUUGGCAACACUCACUUCAUUGGAUUCGAUUAGAAAAACGAAUUCAAUGAGUUGCAAGCGAUGCCGCAAUAAAAACUAAUUUGGCGUUGUA_AAA_AAAAUAG
....((((........))))((((((.((((.(((((((((((((..........))))))))))))).))..)).))))))(((((..(((....)))...)))))............. (-20.80 = -21.32 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:29 2006