Locus 936

Sequence ID	3R_DroMel_CAF1
Location	3,120,917 – 3,121,141
Length	224
Max. P	0.985034

overview

Window 8

Location	3,120,917 – 3,121,013
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.81
Mean single sequence MFE	-24.78
Consensus MFE	-14.96
Energy contribution	-15.07
Covariance contribution	0.11
Combinations/Pair	1.06
Mean z-score	-2.04
Structure conservation index	0.60
SVM decision value	0.68
SVM RNA-class probability	0.820724
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3120917 96 + 27905053
GAUGCGCGAUGCCAG-----AAAAAUGGAAAUCGAAUAAAAUAAAC-----AUGGUCCGC-------CGCCGGCUG------UGUCAAAAAAUAAAUGCCAGCCGGCUUU-UUUCUAAAC
......((((.(((.-----.....)))..))))............-----..((....)-------)((((((((------.((............))))))))))...-......... ( -24.20)
>DroPse_CAF1 8124 108 + 1
-------GAUGCCUG-----GAAAAUGGAAAUCAAAUAAAAUAAACUCCCAAUGAAACGCCGCAUGCCGCUGGCUGGCUUGCUGUCAAAAAAUAAAUGACAGCCGGCUUUUUUUCUAAAC
-------......((-----(((((.................................(((((.....)).))).((((.(((((((.........))))))).))))..)))))))... ( -24.90)
>DroSec_CAF1 8548 91 + 1
GAUG--CGAUGCCAG-----AAAAAUGGAAAUCGAAUAAAAUAAAC-----AUGGCCCG----------CCGGCUG------GGUCAAAAAAUAAAUGCCAGCCGGCUUU-UUUCUAAAC
....--((((.(((.-----.....)))..))))............-----.......(----------(((((((------(...............)))))))))...-......... ( -25.06)
>DroSim_CAF1 13821 97 + 1
GAUG--CGAUGCCAG-----AAAAAUGGAAAUCGAAUAAAAUAAAC-----AUGGCCCGCCG----CCGCCGGCUG------UGUCAAAAAAUAAAUGCCAGCCGGCUUU-UUUCUAAAC
....--((((.(((.-----.....)))..))))............-----..(((.....)----))((((((((------.((............))))))))))...-......... ( -26.30)
>DroPer_CAF1 8086 108 + 1
-------GAUGCCUG-----GAAAAUGGAAAUCAAAUAAAAUAAACUCCCAAUGAAACGCCGCAUGCCGCUGGCUGGCUUGCUGUCAAAAAAUAAAUGACAGCCGGCUUUUUUUCUAAAC
-------......((-----(((((.................................(((((.....)).))).((((.(((((((.........))))))).))))..)))))))... ( -24.90)
>DroYak_CAF1 12041 99 + 1
GAUG--CGAUGCCAAAACAAAAAAGUGGAAAUCGAAUAAAAUAAAC-----AUGGCCCGC-------CGCCGGCUG------UGUCAAAAAAUAAAUGCCAGCCGGCUUU-UUUCUAAAC
...(--((..((((...........(.(....).)...........-----.)))).)))-------.((((((((------.((............))))))))))...-......... ( -23.30)
>consensus
GAUG__CGAUGCCAG_____AAAAAUGGAAAUCGAAUAAAAUAAAC_____AUGGCCCGC_______CGCCGGCUG______UGUCAAAAAAUAAAUGCCAGCCGGCUUU_UUUCUAAAC
.......(((.((.............))..)))...................................((((((((......(((......))).....))))))))............. (-14.96 = -15.07 +   0.11)

alignment

secondary structure

dotplot

Window 9

Location	3,120,952 – 3,121,044
Length	92
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	92.23
Mean single sequence MFE	-35.06
Consensus MFE	-25.92
Energy contribution	-26.32
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-4.26
Structure conservation index	0.74
SVM decision value	1.99
SVM RNA-class probability	0.985034
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3120952 92 - 27905053
CGGCCCCGCCCGACCUAAGCAUAUGGAAAUAGUUUAGAAAAAAGCCGGCUGGCAUUUAUUUUUUGACACAGCCGGCG---GCGGACCAUGUUUAU
.((..(((((....((((((.(((....)))))))))......((((((((.((.........))...)))))))))---)))).))........ ( -37.50)
>DroSec_CAF1 8581 84 - 1
CGCC-----CCGACCUAAGCAUAUGGAAAUAGUUUAGAAAAAAGCCGGCUGGCAUUUAUUUUUUGACCCAGCCGG------CGGGCCAUGUUUAU
.(((-----(....((((((.(((....)))))))))......(((((((((...(((.....))).))))))))------)))))......... ( -34.00)
>DroSim_CAF1 13854 90 - 1
CGCC-----CCGACCUAAGCAUAUGGAAAUAGUUUAGAAAAAAGCCGGCUGGCAUUUAUUUUUUGACACAGCCGGCGGCGGCGGGCCAUGUUUAU
((((-----((...((((((.(((....)))))))))......((((((((.((.........))...)))))))))).))))............ ( -35.60)
>DroEre_CAF1 8215 85 - 1
CGC-------CGAACUAAGCAUAUGGAAAUAGUUUAGAAAAAAGCCGGCUGGCAUUUAUUUUUUGACACAGCCGGCG---GCGGGCCAUGUUUAU
(((-------(...((((((.(((....)))))))))......((((((((.((.........))...)))))))))---)))............ ( -33.00)
>DroYak_CAF1 12079 86 - 1
CGC------CCGACCUAAGCAUAUGGAAAUAGUUUAGAAAAAAGCCGGCUGGCAUUUAUUUUUUGACACAGCCGGCG---GCGGGCCAUGUUUAU
.((------(((.(((((((.(((....)))))))).......((((((((.((.........))...)))))))))---))))))......... ( -35.20)
>consensus
CGCC_____CCGACCUAAGCAUAUGGAAAUAGUUUAGAAAAAAGCCGGCUGGCAUUUAUUUUUUGACACAGCCGGCG___GCGGGCCAUGUUUAU
.........(((..((((((.(((....)))))))))......((((((((.((.........))...)))))))).....)))........... (-25.92 = -26.32 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	3,121,044 – 3,121,141
Length	97
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.90
Mean single sequence MFE	-25.13
Consensus MFE	-19.93
Energy contribution	-20.02
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-2.23
Structure conservation index	0.79
SVM decision value	1.31
SVM RNA-class probability	0.939996
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3121044 97 + 27905053
GGGAAGCCCC------AAAUGCAACAAGAAAAUAUAAAU------ACAAAUAUUGCAGCGGCGAAA----------CAAAAGCA-AAAUCUAGUCUGGCUUUAGCCAGACACAGUGGGCA
.....(((((------...(((........(((((....------....)))))((....))....----------.....)))-.......(((((((....)))))))...).)))). ( -26.30)
>DroPse_CAF1 8267 120 + 1
GGGGUUUCCCCCCUUAAAAUGCAACAAGAAAAUAUAAAUACGAAUACAAAUAUUGCAGCGGCAACAAUAGGAAGGCCAAAAGCAUAGAGCGAGUCUGGCAGCGACCAGACACAGUCAGCU
((((.....))))......(((((............................)))))(((....)........(((.....((.....))..((((((......))))))...))).)). ( -24.69)
>DroSec_CAF1 8665 97 + 1
GGGAAUCCCC------GAAUGCAACAAGAAUAUAUAAAU------ACAAAUAUUGCAGCGGCGAAA----------CAAAAGCA-AAAUCUAGUCUGGCUUUGGCCAGACACAGUGGGCA
(((....)))------...(((.((..............------.......((((....))))..----------........-.......(((((((....)))))))...))..))) ( -23.90)
>DroSim_CAF1 13944 97 + 1
GGGAAUCCCC------GAAUGCAACAAGAAAAUAUAAAU------ACAAAUAUUGCAGCGGCGAAA----------CAAAAGCA-AAAUCUAGUCUGGCUUUGGCCAGACACAGUGGGCA
(((....)))------...(((.((..............------.......((((....))))..----------........-.......(((((((....)))))))...))..))) ( -23.90)
>DroPer_CAF1 8229 120 + 1
GGGGUUCCCCCCCUUAAAAUGCAACAAGAAAAUAUAAAUACGAAUACAAAUAUUGCAGCGGCAACAAUAGGAAGGCAAAAAGCAUAGAGCGAGUCUGGCAGCGACCAGACACAGUCAGCU
((((.....))))......(((((............................)))))(((....)........(((.....((.....))..((((((......))))))...))).)). ( -25.59)
>DroYak_CAF1 12165 97 + 1
GGGAAGCCCC------GAAUGCAACAAGAAAAUAUAAAU------ACAAAUAUUGCAGCGGCAAAA----------CAAAAGCA-AAAUCUAGUCUGGCUUUGGCCAGACACAGUGGGCA
.....(((((------...(((........(((((....------....)))))((....))....----------.....)))-.......(((((((....)))))))...).)))). ( -26.40)
>consensus
GGGAAUCCCC______AAAUGCAACAAGAAAAUAUAAAU______ACAAAUAUUGCAGCGGCAAAA__________CAAAAGCA_AAAUCUAGUCUGGCUUUGGCCAGACACAGUGGGCA
(((....)))..........((.((...........................((((....))))............................(((((((....)))))))...))..)). (-19.93 = -20.02 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	3,121,044 – 3,121,141
Length	97
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.90
Mean single sequence MFE	-29.65
Consensus MFE	-19.59
Energy contribution	-19.81
Covariance contribution	0.22
Combinations/Pair	1.10
Mean z-score	-2.74
Structure conservation index	0.66
SVM decision value	1.47
SVM RNA-class probability	0.956387
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3121044 97 - 27905053
UGCCCACUGUGUCUGGCUAAAGCCAGACUAGAUUU-UGCUUUUG----------UUUCGCCGCUGCAAUAUUUGU------AUUUAUAUUUUCUUGUUGCAUUU------GGGGCUUCCC
.((((.(((.(((((((....))))))))))....-........----------.........(((((((...((------(....))).....)))))))...------.))))..... ( -28.10)
>DroPse_CAF1 8267 120 - 1
AGCUGACUGUGUCUGGUCGCUGCCAGACUCGCUCUAUGCUUUUGGCCUUCCUAUUGUUGCCGCUGCAAUAUUUGUAUUCGUAUUUAUAUUUUCUUGUUGCAUUUUAAGGGGGGAAACCCC
(((.((.((.(((((((....))))))).)).))...)))...(((............)))..(((((((...((((........)))).....))))))).......((((....)))) ( -34.20)
>DroSec_CAF1 8665 97 - 1
UGCCCACUGUGUCUGGCCAAAGCCAGACUAGAUUU-UGCUUUUG----------UUUCGCCGCUGCAAUAUUUGU------AUUUAUAUAUUCUUGUUGCAUUC------GGGGAUUCCC
......(((.(((((((....))))))))))....-.......(----------..((.(((.(((((((...((------((....))))...)))))))..)------)).))..).. ( -29.40)
>DroSim_CAF1 13944 97 - 1
UGCCCACUGUGUCUGGCCAAAGCCAGACUAGAUUU-UGCUUUUG----------UUUCGCCGCUGCAAUAUUUGU------AUUUAUAUUUUCUUGUUGCAUUC------GGGGAUUCCC
......(((.(((((((....))))))))))....-.......(----------..((.(((.(((((((...((------(....))).....)))))))..)------)).))..).. ( -26.50)
>DroPer_CAF1 8229 120 - 1
AGCUGACUGUGUCUGGUCGCUGCCAGACUCGCUCUAUGCUUUUUGCCUUCCUAUUGUUGCCGCUGCAAUAUUUGUAUUCGUAUUUAUAUUUUCUUGUUGCAUUUUAAGGGGGGGAACCCC
(((.((.((.(((((((....))))))).)).))...)))..((.(((((((.....(((.((...(((((..(((....)))..))))).....)).))).....))))))).)).... ( -31.50)
>DroYak_CAF1 12165 97 - 1
UGCCCACUGUGUCUGGCCAAAGCCAGACUAGAUUU-UGCUUUUG----------UUUUGCCGCUGCAAUAUUUGU------AUUUAUAUUUUCUUGUUGCAUUC------GGGGCUUCCC
.((((.(((.(((((((....))))))))))....-........----------......((.(((((((...((------(....))).....)))))))..)------)))))..... ( -28.20)
>consensus
UGCCCACUGUGUCUGGCCAAAGCCAGACUAGAUUU_UGCUUUUG__________UUUCGCCGCUGCAAUAUUUGU______AUUUAUAUUUUCUUGUUGCAUUC______GGGGAUUCCC
..(((.(((.(((((((....))))))))))................................(((((((........................))))))).........)))....... (-19.59 = -19.81 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:56 2006