Locus 4581

Sequence ID	2L_DroMel_CAF1
Location	13,128,960 – 13,129,250
Length	290
Max. P	0.995831

overview

Window 3

Location	13,128,960 – 13,129,073
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	88.85
Mean single sequence MFE	-43.66
Consensus MFE	-30.90
Energy contribution	-31.14
Covariance contribution	0.24
Combinations/Pair	1.25
Mean z-score	-2.92
Structure conservation index	0.71
SVM decision value	1.21
SVM RNA-class probability	0.930967
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13128960 113 + 22407834
UGUUUGGUAUUUUGUAUUGGGCAUUGGGUGGCUCCAUUCCAAUGGGCACUUUAAUAAAGUGCAGUCCAAAUUGUGGGCCAUCGGGUGGCGGCAGCGCUGCUCUUGCCCGCUUU
..................(((((...((((((.((((.....(((((((((.....))))))...)))....))))))))))(((..(((....)))..))).)))))..... ( -44.30)
>DroSec_CAF1 21893 113 + 1
UGCUUGGUAUUUUGUAUUGGGCAUUGGGUGGCUCCAUUCCAAUGGGCACUUUAAUAAAGUGCAGUCCAAAUUGUGGGCCAUCGGUUGCUAGCAGCGCUGCUUUCGUCGGCUUU
((((..((((...))))..))))...((((((.((((.....(((((((((.....))))))...)))....)))))))))).((((....))))(((((....).))))... ( -39.70)
>DroSim_CAF1 22981 113 + 1
UGCUUGGUAUUUUGUAUUGGGCAUUGGGUGGCUCCAUUCCAAUGGGCACUUUAAUAAAGUGCAGUCCAAAUUGUGGGCCAUCCGUUGGUGGCAGCGCUGCUUUCGUCGGCUUU
((((..((((...))))..))))..(((((((.((((.....(((((((((.....))))))...)))....)))))))))))((((..((.(((...))).))..))))... ( -43.40)
>DroEre_CAF1 23676 113 + 1
UAUUGGGUAUUGGGUAUCGGCCAUUGGGUGGCUCCAUUCCGUUGGGCACUUUAAUAAAGUGCAGUCCAAAUUGUGGGCCGUCGGGUGGCGGCAGCCCUGCUGUUGUCGGCUUU
...........((((..(.((((((.(..(((.((((....((((((((((.....))))))...))))...)))))))..).)))))).)..)))).((((....))))... ( -46.50)
>DroYak_CAF1 22696 113 + 1
UAUUUCGUACUUGGUAUUGGGCAUUGAGUGGCUCCAUUCCAAUGGGCACUUUAAUAAAGUGCAGUCCAAAUUGUGGGCCAUCGGGUGACGGUGGCCCUGCAUUUGCCGGCUUU
..........((((((((((((...(((((....)))))......((((((.....)))))).))))))..((((((((((((.....))))))))).)))..)))))).... ( -44.40)
>consensus
UGUUUGGUAUUUUGUAUUGGGCAUUGGGUGGCUCCAUUCCAAUGGGCACUUUAAUAAAGUGCAGUCCAAAUUGUGGGCCAUCGGGUGGCGGCAGCGCUGCUUUUGUCGGCUUU
((((..((((...))))..))))...((((((.((((.....(((((((((.....))))))...)))....)))))))))).(((((.((((....)))).)))))...... (-30.90 = -31.14 +   0.24)

alignment

secondary structure

dotplot

Window 4

Location	13,128,960 – 13,129,073
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	88.85
Mean single sequence MFE	-31.26
Consensus MFE	-20.86
Energy contribution	-21.10
Covariance contribution	0.24
Combinations/Pair	1.12
Mean z-score	-2.24
Structure conservation index	0.67
SVM decision value	0.05
SVM RNA-class probability	0.556891
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13128960 113 - 22407834
AAAGCGGGCAAGAGCAGCGCUGCCGCCACCCGAUGGCCCACAAUUUGGACUGCACUUUAUUAAAGUGCCCAUUGGAAUGGAGCCACCCAAUGCCCAAUACAAAAUACCAAACA
.....(((((.(.(((....)))).(((.(((((((.(((.....)))...((((((.....)))))))))))))..)))..........))))).................. ( -32.40)
>DroSec_CAF1 21893 113 - 1
AAAGCCGACGAAAGCAGCGCUGCUAGCAACCGAUGGCCCACAAUUUGGACUGCACUUUAUUAAAGUGCCCAUUGGAAUGGAGCCACCCAAUGCCCAAUACAAAAUACCAAGCA
..((((..(....)..).)))(((.....(((((((.(((.....)))...((((((.....)))))))))))))..(((.((........))))).............))). ( -30.50)
>DroSim_CAF1 22981 113 - 1
AAAGCCGACGAAAGCAGCGCUGCCACCAACGGAUGGCCCACAAUUUGGACUGCACUUUAUUAAAGUGCCCAUUGGAAUGGAGCCACCCAAUGCCCAAUACAAAAUACCAAGCA
...((.(.(....)).))(((((((((...)).)))).......((((...((((((.....)))))).((((((..((....)).)))))).))))............))). ( -29.20)
>DroEre_CAF1 23676 113 - 1
AAAGCCGACAACAGCAGGGCUGCCGCCACCCGACGGCCCACAAUUUGGACUGCACUUUAUUAAAGUGCCCAACGGAAUGGAGCCACCCAAUGGCCGAUACCCAAUACCCAAUA
...((........)).((((((.((.....)).)))))).....((((...((((((.....)))))).....((.((.(.((((.....))))).)).))......)))).. ( -31.00)
>DroYak_CAF1 22696 113 - 1
AAAGCCGGCAAAUGCAGGGCCACCGUCACCCGAUGGCCCACAAUUUGGACUGCACUUUAUUAAAGUGCCCAUUGGAAUGGAGCCACUCAAUGCCCAAUACCAAGUACGAAAUA
.....((((....)).((((((.((.....)).))))))...((((((...((((((.....))))))..(((((.((.(((...))).))..))))).)))))).))..... ( -33.20)
>consensus
AAAGCCGACAAAAGCAGCGCUGCCGCCACCCGAUGGCCCACAAUUUGGACUGCACUUUAUUAAAGUGCCCAUUGGAAUGGAGCCACCCAAUGCCCAAUACAAAAUACCAAACA
...((........)).(.(((.(((....(((((((.(((.....)))...((((((.....)))))))))))))..)))))))............................. (-20.86 = -21.10 +   0.24)

alignment

secondary structure

dotplot

Window 5

Location	13,129,000 – 13,129,097
Length	97
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.54
Mean single sequence MFE	-36.15
Consensus MFE	-20.30
Energy contribution	-20.25
Covariance contribution	-0.05
Combinations/Pair	1.42
Mean z-score	-1.90
Structure conservation index	0.56
SVM decision value	0.47
SVM RNA-class probability	0.747326
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13129000 97 + 22407834
AAUG-------GGCACUUUAAUAAAGUGCAGUCCAAAUUGUGGGCCAUCGGGUGGCGGCAGCGCUGCUCUUGCCCGCUUUGUUGUUGCUGU---------CGGUGGU--GCUGAU-----
..((-------(((((((.....))))))...)))......(.(((((((.(..(((((((((..((........))..)))))))))..)---------)))))))--.)....----- ( -37.10)
>DroSec_CAF1 21933 97 + 1
AAUG-------GGCACUUUAAUAAAGUGCAGUCCAAAUUGUGGGCCAUCGGUUGCUAGCAGCGCUGCUUUCGUCGGCUUUGUUGUUGCUGG---------CGAUGGU--GCUGAU-----
....-------.((((((.....)))))).(((((.....)))))(((((.(((((((((((((.(((......)))...).)))))))))---------)))))))--).....----- ( -35.80)
>DroSim_CAF1 23021 97 + 1
AAUG-------GGCACUUUAAUAAAGUGCAGUCCAAAUUGUGGGCCAUCCGUUGGUGGCAGCGCUGCUUUCGUCGGCUUUGUUGUUGCUGU---------CGGUGGU--GCUGAU-----
((((-------(((((((.....)))))).(((((.....)))))...))))).....((((((..(...((.((((.........)))).---------)))..))--))))..----- ( -35.80)
>DroEre_CAF1 23716 97 + 1
GUUG-------GGCACUUUAAUAAAGUGCAGUCCAAAUUGUGGGCCGUCGGGUGGCGGCAGCCCUGCUGUUGUCGGCUUUGUUGUUGCUGU---------CGGUGGU--GCUGAU-----
.(((-------(((((((.....))))))...)))).....(.((((.(.((..((((((((...((((....))))...))))))))..)---------).)))))--.)....----- ( -37.60)
>DroYak_CAF1 22736 102 + 1
AAUG-------GGCACUUUAAUAAAGUGCAGUCCAAAUUGUGGGCCAUCGGGUGACGGUGGCCCUGCAUUUGCCGGCUUUGUUGUUGCUGU---------CAGUGGU--GCUGAUGCGGC
....-------.((((((.....))))))(((((((((.(((((((((((.....))))))))).)))))))..)))).....(((((.((---------(((....--.)))))))))) ( -41.20)
>DroAna_CAF1 28979 107 + 1
GAUGAGCCGAGGGUACUUUAAUAAAGUGCAGUCCAAAUUGAGGUCCACCAG------GCAGCCGGGCUUA--UGGUUUUCGUUGUUGCUGUUAUUUCAAGCGGUGGUAGGCAGAC-----
.....(((((..((((((.....))))))..))...........(((((.(------(((((.((((...--..))))..))))))(((.........))))))))..)))....----- ( -29.40)
>consensus
AAUG_______GGCACUUUAAUAAAGUGCAGUCCAAAUUGUGGGCCAUCGGGUGGCGGCAGCCCUGCUUUUGUCGGCUUUGUUGUUGCUGU_________CGGUGGU__GCUGAU_____
............((((((.....))))))...(((.....)))(((((((....((((((((...((........))......)))))))).........)))))))............. (-20.30 = -20.25 +  -0.05)

alignment

secondary structure

dotplot

Window 6

Location	13,129,073 – 13,129,171
Length	98
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	87.91
Mean single sequence MFE	-47.63
Consensus MFE	-32.93
Energy contribution	-33.82
Covariance contribution	0.89
Combinations/Pair	1.09
Mean z-score	-3.86
Structure conservation index	0.69
SVM decision value	0.42
SVM RNA-class probability	0.731219
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13129073 98 + 22407834
GUUGUUGCUGU---------CGGUGGU--GCUGAU-----------GCGGUGGUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAU
....(((((..---------.((((((--(.((((-----------((.((((((((((....)))).)))))).))))))..)))))))(((.(((.....))).))).)))))..... ( -44.80)
>DroSec_CAF1 22006 98 + 1
GUUGUUGCUGG---------CGAUGGU--GCUGAU-----------GCGGCGGUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAU
....(((((((---------(((((((--..((((-----------((.((((((((((....)))).)))))).)))))))))))))))(((.(((.....))).))).)))))..... ( -53.60)
>DroSim_CAF1 23094 98 + 1
GUUGUUGCUGU---------CGGUGGU--GCUGAU-----------GCGGCGGUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAU
....(((((..---------.((((((--(.((((-----------((.((((((((((....)))).)))))).))))))..)))))))(((.(((.....))).))).)))))..... ( -49.60)
>DroEre_CAF1 23789 98 + 1
GUUGUUGCUGU---------CGGUGGU--GCUGAU-----------GCGGUGGUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAA
....(((((..---------.((((((--(.((((-----------((.((((((((((....)))).)))))).))))))..)))))))(((.(((.....))).))).)))))..... ( -44.80)
>DroYak_CAF1 22809 109 + 1
GUUGUUGCUGU---------CAGUGGU--GCUGAUGCGGCGGUGAUGCGGUGGUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAACAAU
(((((((((((---------(..((((--((....(((((((((((((.((((((((((....)))).)))))).))))))....))))))).)))).))......)))).)).)))))) ( -50.30)
>DroAna_CAF1 29051 109 + 1
GUUGUUGCUGUUAUUUCAAGCGGUGGUAGGCAGAC-----------CUCGGCCUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUAGGAAAAGUGGGGCAGGCAAAUAAU
.((((((((.(..((((.(((((((((((...(((-----------(((((...(((((....)))))..))).)).)))..)))))))))))....))))...).)))).))))..... ( -42.70)
>consensus
GUUGUUGCUGU_________CGGUGGU__GCUGAU___________GCGGUGGUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAU
....(((((............((((((....((((...........((.((((((((((....)))).)))))).))))))...))))))(((.(((.....))).))).)))))..... (-32.93 = -33.82 +   0.89)

alignment

secondary structure

dotplot

Window 7

Location	13,129,097 – 13,129,210
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.45
Mean single sequence MFE	-42.11
Consensus MFE	-39.39
Energy contribution	-39.34
Covariance contribution	-0.05
Combinations/Pair	1.09
Mean z-score	-1.88
Structure conservation index	0.94
SVM decision value	2.62
SVM RNA-class probability	0.995831
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13129097 113 + 22407834
------GCGGUGGUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAUA-AAAACGCGCCCAAACGCAGUCGUCAGGCUCAAAGCACU
------(((..((((((((....)))).))))((((((........))))))....)))..((((((((..((........-.....))))))....(.((((....)))))....)))) ( -41.22)
>DroSec_CAF1 22030 113 + 1
------GCGGCGGUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAUA-AAAACGCGCCCAAACGCAGUCGUCAGGCUCAAAGCACU
------(((((((((((((....)))).))))))(((((..(((((.((((((.(((.....))).))).)))..))))).-.....)))))....)))((((....))))......... ( -42.80)
>DroSim_CAF1 23118 113 + 1
------GCGGCGGUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAUA-AAAACGCGCCCAAACGCAGUCGUCAGGCUCAAAGCACU
------(((((((((((((....)))).))))))(((((..(((((.((((((.(((.....))).))).)))..))))).-.....)))))....)))((((....))))......... ( -42.80)
>DroEre_CAF1 23813 114 + 1
------GCGGUGGUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAAAAAAAACGCGCCCAAACGCAGUCGUCAGGCUCAAAGCACU
------(((..((((((((....)))).))))((((((........))))))....)))..((((((((..((..............))))))....(.((((....)))))....)))) ( -41.14)
>DroYak_CAF1 22838 119 + 1
GGUGAUGCGGUGGUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAACAAUA-AAAACGCGCCCAAACGCAGUCGUCAGGCUCAAAGCACU
..((((((.((((((((((....)))).)))))).))))))......((((((.(((.....))).))).)))........-.....((((......))((((....))))....))... ( -42.50)
>DroAna_CAF1 29086 113 + 1
------CUCGGCCUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUAGGAAAAGUGGGGCAGGCAAAUAAUA-AAAACGCGCCCAAACGCAGCCGUCAGGCUCAAAGCACU
------....(((((((.((.((....((((.((((((........)))))).)).))..)).)).)))))))........-.....((((......))((((....))))....))... ( -42.20)
>consensus
______GCGGUGGUGCUGCAGUUGCAGCCACCGUGGCGUCAAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAUA_AAAACGCGCCCAAACGCAGUCGUCAGGCUCAAAGCACU
......(((..((((((((....)))).))))((((((........))))))....)))..((((((((..((..............))))))....(.((((....)))))....)))) (-39.39 = -39.34 +  -0.05)

alignment

secondary structure

dotplot

Window 8

Location	13,129,131 – 13,129,250
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	95.53
Mean single sequence MFE	-31.62
Consensus MFE	-28.37
Energy contribution	-28.73
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-1.55
Structure conservation index	0.90
SVM decision value	1.05
SVM RNA-class probability	0.906854
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13129131 119 + 22407834
AAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAUA-AAAACGCGCCCAAACGCAGUCGUCAGGCUCAAAGCACUUCAUUGUCAAAUGAGCUUAAACACCACGCCCCUCGGCCCC
.......(((((.....))...(.(((((.((.........-.....(((......))).......(((((((....((......))....))))))).....))..))))).))))... ( -31.10)
>DroSec_CAF1 22064 119 + 1
AAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAUA-AAAACGCGCCCAAACGCAGUCGUCAGGCUCAAAGCACUUCAUUGUCAAAUGAGCUUAAAAACCACGCCCCUCGGCCCC
.......(((((.....))...(.(((((.((.........-.....(((......))).......(((((((....((......))....))))))).....))..))))).))))... ( -31.10)
>DroSim_CAF1 23152 119 + 1
AAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAUA-AAAACGCGCCCAAACGCAGUCGUCAGGCUCAAAGCACUUCAUUGUCAAAUGAGCUUAAACACCACGCCCCUCGGCCCC
.......(((((.....))...(.(((((.((.........-.....(((......))).......(((((((....((......))....))))))).....))..))))).))))... ( -31.10)
>DroEre_CAF1 23847 120 + 1
AAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAAAAAAAACGCGCCCAAACGCAGUCGUCAGGCUCAAAGCACUUCAUUGUCAAAUGAGCUUAAGCACCACGCCCCUCGGCCCC
.......(((((.....))...(.(((((..................(((......)))....((...(((..((((...(((((....))))))))).)))...))))))).))))... ( -32.30)
>DroYak_CAF1 22878 119 + 1
AAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAACAAUA-AAAACGCGCCCAAACGCAGUCGUCAGGCUCAAAGCACUUCAUUGUCAAAUGAGCUUAAACACCACGCCCCUCGGCCCC
.......(((((.....))...(.(((((.((.........-.....(((......))).......(((((((....((......))....))))))).....))..))))).))))... ( -31.10)
>DroAna_CAF1 29120 116 + 1
AAUUAUCGCCGCUGUAGGAAAAGUGGGGCAGGCAAAUAAUA-AAAACGCGCCCAAACGCAGCCGUCAGGCUCAAAGCACUCCAUUGUCAAAUGAGUGCAAAC---ACGCCCCUCGACCCC
.....((.((......))....(.(((((............-.....(((......)))((((....))))....((((((.(((....)))))))))....---..))))).))).... ( -33.00)
>consensus
AAUUAUCGCCGCUGUACGCAAAGUGGGGCAGGCAAAUAAUA_AAAACGCGCCCAAACGCAGUCGUCAGGCUCAAAGCACUUCAUUGUCAAAUGAGCUUAAACACCACGCCCCUCGGCCCC
.......(((((.....))...(.(((((..((..............(((......)))((((....))))....))..((((((....))))))............))))).))))... (-28.37 = -28.73 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:42 2006