Locus 6521

Sequence ID	3R_DroMel_CAF1
Location	17,199,253 – 17,199,394
Length	141
Max. P	0.987284

overview

Window 7

Location	17,199,253 – 17,199,355
Length	102
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	75.30
Mean single sequence MFE	-31.24
Consensus MFE	-16.03
Energy contribution	-16.12
Covariance contribution	0.09
Combinations/Pair	1.14
Mean z-score	-1.80
Structure conservation index	0.51
SVM decision value	0.38
SVM RNA-class probability	0.713183
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17199253 102 + 27905053
ACAAAUUGGCUUGCAUUUUUUUAAUGAAUUUGCA-CGGCGUUGCCACACAGCCGAAGCACCAGGGCUGCACAUUCAAUUAGGGUUUCCGG----------AAGUGGCAACACC
........(((((((..(((.....)))..))))-.)))((((((((.(((((..........)))))....(((.....((....)).)----------))))))))))... ( -31.80)
>DroSec_CAF1 20769 102 + 1
ACAAAUUGGCUUGCAUUUUUUUUAUGAAUCUGCA-UGGCGUUGCCACAUUACCGAAGGUCCAGGGCUGCACGUUUAAUUAGGGCUUCCGG----------AAGUGGCAACACC
........(((((((..(((.....)))..))))-.)))((((((((.((.(((.((((((.((((.....)))).....)))))).)))----------))))))))))... ( -32.80)
>DroSim_CAF1 21623 101 + 1
ACAAAUUGGCUUGCAUUUU-UUUAUGAAUCUGCA-CGGCGUUGCCACAUUACCGAAGGUCCAGGGGUGCAUAUUCAAUUAGGGUUUCCAG----------GAGUGGCAACACC
........(((((((..((-(....)))..))))-.)))((((((((.....(....)(((..(((.((.((......))..)).))).)----------))))))))))... ( -28.50)
>DroEre_CAF1 22998 101 + 1
ACAAAUUGGCUUGCAUUAU-UUUAUGAUUUUACA-CGGCGUUGCCACCUUGCCGAAGGUCCAGGGCUGCACAUUCAAUUAGGGCUACCGU----------AAGUGGCAACGCC
...................-..............-.(((((((((((.((((.(((.((.((....)).)).))).....((....))))----------))))))))))))) ( -29.80)
>DroYak_CAF1 22783 101 + 1
ACAAAUUUGCCUGCAUUAU-UUUAUGAUUUUGCA-CGGCGUUGCCACUGUACUGAAGAGCCAGGGAUGCACAUGCAAUAAGGGUUGCCGU----------AAGUGGCAACGCC
...........((((..((-(....)))..))))-.((((((((((((.(((.(...((((.....(((....))).....)))).).))----------))))))))))))) ( -36.10)
>DroAna_CAF1 24265 109 + 1
ACAAAUG---CAGCAUAGG-UUUAUCAAUUUUUAGGGGUGUUGCCACCCUAUACAAAACACAGGGUCGUAUUUGCAACCAGGGCUGACAAAAUUCUUGAUAGGUGGCAACACC
.......---.........-................((((((((((((.(((.(((........((((..((((....))))..)))).......)))))))))))))))))) ( -28.46)
>consensus
ACAAAUUGGCUUGCAUUUU_UUUAUGAAUUUGCA_CGGCGUUGCCACAUUACCGAAGGUCCAGGGCUGCACAUUCAAUUAGGGCUUCCGG__________AAGUGGCAACACC
....................................((.((((((((....((.........))................((....))..............)))))))).)) (-16.03 = -16.12 +   0.09)

alignment

secondary structure

dotplot

Window 8

Location	17,199,253 – 17,199,355
Length	102
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	75.30
Mean single sequence MFE	-31.65
Consensus MFE	-21.86
Energy contribution	-22.75
Covariance contribution	0.89
Combinations/Pair	1.39
Mean z-score	-2.26
Structure conservation index	0.69
SVM decision value	2.07
SVM RNA-class probability	0.987284
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17199253 102 - 27905053
GGUGUUGCCACUU----------CCGGAAACCCUAAUUGAAUGUGCAGCCCUGGUGCUUCGGCUGUGUGGCAACGCCG-UGCAAAUUCAUUAAAAAAAUGCAAGCCAAUUUGU
(((((((((((..----------..(....).............((((((..........))))))))))))))))).-.(((((((((((.....))))......))))))) ( -33.00)
>DroSec_CAF1 20769 102 - 1
GGUGUUGCCACUU----------CCGGAAGCCCUAAUUAAACGUGCAGCCCUGGACCUUCGGUAAUGUGGCAACGCCA-UGCAGAUUCAUAAAAAAAAUGCAAGCCAAUUUGU
(((((((((((..----------(((((.(.((...................)).).)))))....))))))))))).-((((...............))))........... ( -30.97)
>DroSim_CAF1 21623 101 - 1
GGUGUUGCCACUC----------CUGGAAACCCUAAUUGAAUAUGCACCCCUGGACCUUCGGUAAUGUGGCAACGCCG-UGCAGAUUCAUAAA-AAAAUGCAAGCCAAUUUGU
(((((((((((..----------..(....)....((((((..(.((....)).)..))))))...))))))))))).-((((..........-....))))........... ( -27.24)
>DroEre_CAF1 22998 101 - 1
GGCGUUGCCACUU----------ACGGUAGCCCUAAUUGAAUGUGCAGCCCUGGACCUUCGGCAAGGUGGCAACGCCG-UGUAAAAUCAUAAA-AUAAUGCAAGCCAAUUUGU
(((((((((((((----------..((....))...(((((.((.((....)).)).)))))..)))))))))))))(-((......)))...-.....(((((....))))) ( -31.50)
>DroYak_CAF1 22783 101 - 1
GGCGUUGCCACUU----------ACGGCAACCCUUAUUGCAUGUGCAUCCCUGGCUCUUCAGUACAGUGGCAACGCCG-UGCAAAAUCAUAAA-AUAAUGCAGGCAAAUUUGU
(((((((((((((----------(((....)((....(((....))).....)).......))).)))))))))))).-(((.....(((...-...)))...)))....... ( -33.00)
>DroAna_CAF1 24265 109 - 1
GGUGUUGCCACCUAUCAAGAAUUUUGUCAGCCCUGGUUGCAAAUACGACCCUGUGUUUUGUAUAGGGUGGCAACACCCCUAAAAAUUGAUAAA-CCUAUGCUG---CAUUUGU
((((((((((((((((((((..((((.((((....))))))))((((....))))))))).))).))))))))))))................-.........---....... ( -34.20)
>consensus
GGUGUUGCCACUU__________CCGGAAACCCUAAUUGAAUGUGCAGCCCUGGACCUUCGGUAAUGUGGCAACGCCG_UGCAAAUUCAUAAA_AAAAUGCAAGCCAAUUUGU
(((((((((((..............((....))..((((((.((.((....)).)).))))))...))))))))))).................................... (-21.86 = -22.75 +   0.89)

alignment

secondary structure

dotplot

Window 9

Location	17,199,286 – 17,199,394
Length	108
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	70.87
Mean single sequence MFE	-33.93
Consensus MFE	-17.83
Energy contribution	-17.97
Covariance contribution	0.14
Combinations/Pair	1.20
Mean z-score	-2.14
Structure conservation index	0.53
SVM decision value	1.87
SVM RNA-class probability	0.980706
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17199286 108 + 27905053
A-CGGCGUUGCCACACAGCCGAAGCACCAGGGCUGCACAUUCAAUUAGGGUUUCCGG----------AAGUGGCAACACCGUCCUCAAUUUCCACAAAAUGGCAACUCCGCAUUAAUUC
.-(((.(((((((..(((((..........)))))............(((.....((----------(.(((....)))..)))......)))......))))))).)))......... ( -33.70)
>DroSec_CAF1 20802 108 + 1
A-UGGCGUUGCCACAUUACCGAAGGUCCAGGGCUGCACGUUUAAUUAGGGCUUCCGG----------AAGUGGCAACACCGCCAUCAAACUGCACGAAAUGGCAACUCUGCAUUUAAUA
.-.((.((((((((.((.(((.((((((.((((.....)))).....)))))).)))----------)))))))))).))(((((.............)))))................ ( -33.92)
>DroSim_CAF1 21655 108 + 1
A-CGGCGUUGCCACAUUACCGAAGGUCCAGGGGUGCAUAUUCAAUUAGGGUUUCCAG----------GAGUGGCAACACCGCCCUCAAACUCCACGAAAUGGCAACUCUGCAUUUAAUA
.-(((.(((((((....(((...)))...(((((.............((....))..----------(((.(((......))))))..)))))......))))))).)))......... ( -29.90)
>DroEre_CAF1 23030 108 + 1
A-CGGCGUUGCCACCUUGCCGAAGGUCCAGGGCUGCACAUUCAAUUAGGGCUACCGU----------AAGUGGCAACGCCGCCCUCAAUCUCCACGAAAUGGCAACUCUACACAUAACG
.-.(((((((((((.((((.(((.((.((....)).)).))).....((....))))----------)))))))))))))(((.....((.....))...)))................ ( -34.40)
>DroYak_CAF1 22815 106 + 1
A-CGGCGUUGCCACUGUACUGAAGAGCCAGGGAUGCACAUGCAAUAAGGGUUGCCGU----------AAGUGGCAACGCCGCCCUCAAUCUCCCGCAAAUGGCAACGCUACAUAUCA--
.-.((((((((((.(((...((.((...((((.(((....)))....(((((((((.----------...))))))).)).))))...))))..)))..))))))))))........-- ( -41.50)
>DroAna_CAF1 24294 114 + 1
AGGGGUGUUGCCACCCUAUACAAAACACAGGGUCGUAUUUGCAACCAGGGCUGACAAAAUUCUUGAUAGGUGGCAACACCACGCGCGAAAACAGAAAAAUA-----UAUACACAGAAUC
...((((((((((((.(((.(((........((((..((((....))))..)))).......)))))))))))))))))).....................-----............. ( -30.16)
>consensus
A_CGGCGUUGCCACAUUACCGAAGGUCCAGGGCUGCACAUUCAAUUAGGGCUUCCGG__________AAGUGGCAACACCGCCCUCAAACUCCACGAAAUGGCAACUCUACAUAUAAUA
..(((.((((((((....((.........))................((....))..............)))))))).)))...................................... (-17.83 = -17.97 +   0.14)

alignment

secondary structure

dotplot

Window 0

Location	17,199,286 – 17,199,394
Length	108
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	70.87
Mean single sequence MFE	-38.49
Consensus MFE	-22.11
Energy contribution	-23.00
Covariance contribution	0.89
Combinations/Pair	1.39
Mean z-score	-1.98
Structure conservation index	0.57
SVM decision value	1.74
SVM RNA-class probability	0.974701
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17199286 108 - 27905053
GAAUUAAUGCGGAGUUGCCAUUUUGUGGAAAUUGAGGACGGUGUUGCCACUU----------CCGGAAACCCUAAUUGAAUGUGCAGCCCUGGUGCUUCGGCUGUGUGGCAACGCCG-U
.((((..((((((((....))))))))..))))....(((((((((((((..----------..(....).............((((((..........))))))))))))))))))-) ( -37.50)
>DroSec_CAF1 20802 108 - 1
UAUUAAAUGCAGAGUUGCCAUUUCGUGCAGUUUGAUGGCGGUGUUGCCACUU----------CCGGAAGCCCUAAUUAAACGUGCAGCCCUGGACCUUCGGUAAUGUGGCAACGCCA-U
((((((((((((((.......))).)))).)))))))..(((((((((((..----------(((((.(.((...................)).).)))))....))))))))))).-. ( -36.81)
>DroSim_CAF1 21655 108 - 1
UAUUAAAUGCAGAGUUGCCAUUUCGUGGAGUUUGAGGGCGGUGUUGCCACUC----------CUGGAAACCCUAAUUGAAUAUGCACCCCUGGACCUUCGGUAAUGUGGCAACGCCG-U
.........((((....((((...))))..))))...(((((((((((((..----------..(....)....((((((..(.((....)).)..))))))...))))))))))))-) ( -31.30)
>DroEre_CAF1 23030 108 - 1
CGUUAUGUGUAGAGUUGCCAUUUCGUGGAGAUUGAGGGCGGCGUUGCCACUU----------ACGGUAGCCCUAAUUGAAUGUGCAGCCCUGGACCUUCGGCAAGGUGGCAACGCCG-U
.............((((((((((.((((((.((.(((((((.((((((....----------..))))))))....((......))))))).)).)))).)).))))))))))....-. ( -41.10)
>DroYak_CAF1 22815 106 - 1
--UGAUAUGUAGCGUUGCCAUUUGCGGGAGAUUGAGGGCGGCGUUGCCACUU----------ACGGCAACCCUUAUUGCAUGUGCAUCCCUGGCUCUUCAGUACAGUGGCAACGCCG-U
--.........((((((((((((((.(((((.(.((((.((.((((((....----------..))))))))....(((....))).)))).).))))).))).)))))))))))..-. ( -47.90)
>DroAna_CAF1 24294 114 - 1
GAUUCUGUGUAUA-----UAUUUUUCUGUUUUCGCGCGUGGUGUUGCCACCUAUCAAGAAUUUUGUCAGCCCUGGUUGCAAAUACGACCCUGUGUUUUGUAUAGGGUGGCAACACCCCU
......((((...-----.((......))....))))(.((((((((((((((((((((..((((.((((....))))))))((((....))))))))).))).)))))))))))).). ( -36.30)
>consensus
GAUUAAAUGCAGAGUUGCCAUUUCGUGGAGAUUGAGGGCGGUGUUGCCACUU__________CCGGAAACCCUAAUUGAAUGUGCAGCCCUGGACCUUCGGUAAUGUGGCAACGCCG_U
.......................................(((((((((((..............((....))..((((((.((.((....)).)).))))))...)))))))))))... (-22.11 = -23.00 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:24 2006