Locus 1680

Sequence ID	3R_DroMel_CAF1
Location	4,815,265 – 4,815,446
Length	181
Max. P	0.953130

overview

Window 2

Location	4,815,265 – 4,815,373
Length	108
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	82.47
Mean single sequence MFE	-35.35
Consensus MFE	-29.11
Energy contribution	-29.45
Covariance contribution	0.34
Combinations/Pair	1.23
Mean z-score	-2.33
Structure conservation index	0.82
SVM decision value	1.06
SVM RNA-class probability	0.909392
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4815265 108 + 27905053
GAAACGCGUCGACUGUGGUGCCCAAAAUUAUUGGAAAAACUACUGUGCUUCCGGGAAAACCACUACUACUCCACGCCAAAACAUUAAAACAGAUUGGCGGUAGUAGUG
..............(((((.(((.........((((..((....))..)))))))...)))))(((((((.(.((((((..............))))))).))))))) ( -29.64)
>DroPse_CAF1 6957 108 + 1
GAGGGGGACCCACGAUGGUGCCCAAGAUCAUUGGCAAGACGACAGUGCUGUCGGGCAAGCCACUGCUGCUGCAUGCCAAGGGAAUCAAGCAGCUAGGAGGCGGUAGUG
...(((.(((......))).))).....(((((.(....(((((....))))).....(((.((((((((.....((...)).....)))))).))..)))).))))) ( -38.20)
>DroSec_CAF1 4777 108 + 1
GAAACGCGUCGACUGUGGUGCCCAAAAUUAUUGGAAAAACUACUGUGCUUCCGGGAAAACCACUACUACUGAACGCCAAGACAUUAAAACAGCUUGGCAGCAGUAGUG
..............(((((.(((.........((((..((....))..)))))))...)))))((((((((...((((((.(.........)))))))..)))))))) ( -33.10)
>DroSim_CAF1 6210 108 + 1
GAAACGCGUCGACUGUGGUGCCCAAAAUUAUUGGAAAAACUACUGUGCUUCCGGGAAAACCACUACUACUGCACGCCAAGACAUUAAAACAGCUUGGCAGCAGUAGUG
..............(((((.(((.........((((..((....))..)))))))...)))))(((((((((..((((((.(.........))))))).))))))))) ( -35.50)
>DroYak_CAF1 4610 108 + 1
GAAACACAUCGACUGUGGUACCCAAAAUUAUUGGAAAAACUACUGUGCUUCCGGGAAAACCACUACUACUGCACGCCAAAACAUUAAAACAGCUUGGCGGCAGUAGUG
..............(((((.(((.........((((..((....))..)))))))...)))))(((((((((.((((((..............))))))))))))))) ( -34.24)
>DroPer_CAF1 6921 108 + 1
GAGGGGGACCCACGAUGGUGCCCAAGAUCAUUGGCAAGACGACAGUGCUGUCGGGCAAGCCACUGCUGCUGCAUGCCAAGGCAAUCAAGCAGCUAGGAGGCGGUAGUG
...(((.(((......))).))).....(((((.(....(((((....))))).....(((.((((((((...(((....)))....)))))).))..)))).))))) ( -41.40)
>consensus
GAAACGCAUCGACUGUGGUGCCCAAAAUUAUUGGAAAAACUACUGUGCUUCCGGGAAAACCACUACUACUGCACGCCAAGACAUUAAAACAGCUUGGCGGCAGUAGUG
..............(((((.(((((.....))((((..((....))..)))))))...))))).((((((((.(((((((............))))))))))))))). (-29.11 = -29.45 +   0.34)

alignment

secondary structure

dotplot

Window 3

Location	4,815,265 – 4,815,373
Length	108
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	82.47
Mean single sequence MFE	-34.52
Consensus MFE	-21.42
Energy contribution	-23.70
Covariance contribution	2.28
Combinations/Pair	1.12
Mean z-score	-1.90
Structure conservation index	0.62
SVM decision value	0.01
SVM RNA-class probability	0.536928
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4815265 108 - 27905053
CACUACUACCGCCAAUCUGUUUUAAUGUUUUGGCGUGGAGUAGUAGUGGUUUUCCCGGAAGCACAGUAGUUUUUCCAAUAAUUUUGGGCACCACAGUCGACGCGUUUC
.((((((.(((((((..(((....)))..)))))).).)))))).(((((...((((((((.((....)).)))))((.....))))).))))).............. ( -29.80)
>DroPse_CAF1 6957 108 - 1
CACUACCGCCUCCUAGCUGCUUGAUUCCCUUGGCAUGCAGCAGCAGUGGCUUGCCCGACAGCACUGUCGUCUUGCCAAUGAUCUUGGGCACCAUCGUGGGUCCCCCUC
.....((((......((((((..((.((...)).))..)))))).((((..(((((((((....))))(((........)))...))))))))).))))......... ( -32.40)
>DroSec_CAF1 4777 108 - 1
CACUACUGCUGCCAAGCUGUUUUAAUGUCUUGGCGUUCAGUAGUAGUGGUUUUCCCGGAAGCACAGUAGUUUUUCCAAUAAUUUUGGGCACCACAGUCGACGCGUUUC
.(((((((.((((((((.........).)))))))..))))))).(((((...((((((((.((....)).)))))((.....))))).))))).............. ( -32.40)
>DroSim_CAF1 6210 108 - 1
CACUACUGCUGCCAAGCUGUUUUAAUGUCUUGGCGUGCAGUAGUAGUGGUUUUCCCGGAAGCACAGUAGUUUUUCCAAUAAUUUUGGGCACCACAGUCGACGCGUUUC
.((((((((((((((((.........).))))))).)))))))).(((((...((((((((.((....)).)))))((.....))))).))))).............. ( -37.10)
>DroYak_CAF1 4610 108 - 1
CACUACUGCCGCCAAGCUGUUUUAAUGUUUUGGCGUGCAGUAGUAGUGGUUUUCCCGGAAGCACAGUAGUUUUUCCAAUAAUUUUGGGUACCACAGUCGAUGUGUUUC
.((((((((((((((((.........).))))))).)))))))).(((((...((((((((.((....)).)))))((.....))))).))))).............. ( -38.30)
>DroPer_CAF1 6921 108 - 1
CACUACCGCCUCCUAGCUGCUUGAUUGCCUUGGCAUGCAGCAGCAGUGGCUUGCCCGACAGCACUGUCGUCUUGCCAAUGAUCUUGGGCACCAUCGUGGGUCCCCCUC
.....((((......((((((.(..(((....)))..))))))).((((..(((((((((....))))(((........)))...))))))))).))))......... ( -37.10)
>consensus
CACUACUGCCGCCAAGCUGUUUUAAUGUCUUGGCGUGCAGUAGUAGUGGUUUUCCCGGAAGCACAGUAGUUUUUCCAAUAAUUUUGGGCACCACAGUCGACGCGUUUC
.(((((((((((((((............))))))).)))))))).(((((...((((((((.((....)).)))))((.....))))).))))).............. (-21.42 = -23.70 +   2.28)

alignment

secondary structure

dotplot

Window 4

Location	4,815,293 – 4,815,407
Length	114
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	71.40
Mean single sequence MFE	-32.60
Consensus MFE	-16.84
Energy contribution	-16.81
Covariance contribution	-0.02
Combinations/Pair	1.46
Mean z-score	-1.99
Structure conservation index	0.52
SVM decision value	1.43
SVM RNA-class probability	0.953130
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4815293 114 + 27905053
UAUUGGAAAAACUACUGUGCUUCCGGGAAAACCACUACUACUCCACGCCAAAACAUUAAAACAGAUUGGCGGUAGUAGUGUGCCCACAACCCAGACUACCACAACGACGACAAC
....((((..((....))..))))(((.....(((((((((....((((((..............)))))))))))))))..)))............................. ( -28.74)
>DroVir_CAF1 7358 109 + 1
UAUUGGCAAGACAACUGUUGUGCCCGGCAAACCGCUGCUGCUGCAUGCCAAGACUCUUAAAU---UGGGCGGCAAUACAGGAGUCAGUACACAAACACCCACAGCCACAACG--
...((((..(((..((((..((((.((((..(.((....)).)..))))..(.(((......---.))))))))..))))..))).((......)).......)))).....-- ( -31.00)
>DroPse_CAF1 6985 114 + 1
CAUUGGCAAGACGACAGUGCUGUCGGGCAAGCCACUGCUGCUGCAUGCCAAGGGAAUCAAGCAGCUAGGAGGCGGUAGUGUUGUGACCACUCAACCCACAGCUACAACGACAAC
...((((...((((((.(((((((.((....)).((((((((.....((...)).....)))))).))..))))))).))))))((....))........)))).......... ( -34.90)
>DroEre_CAF1 4655 114 + 1
UAUUGGAAAAACUACUGUGCUUCCUGGAAAACCACUUCUACUGCACGCCAAAACAUUAAAACAGCUUGGCGGCAGUAGUGUGGCCACCACCCAAACCACUACAACGACAACAAC
....((((..((....))..))))(((....((((..(((((((.((((((..............))))))))))))).))))...)))......................... ( -32.44)
>DroAna_CAF1 8049 114 + 1
AAUUGGGAAAACCACAGUGCUCCCGGGAAAACCUCUGCUUUUGAAUGCAAAGACGAUAAAGCAACUGAGCGGCAGCAGUGUGGCCACCACCCAAGUAACCACCGCCACGACCAC
..(((((....(((((.((((.((((.....))...((((.....(((............)))...)))))).)))).)))))......))))).................... ( -30.40)
>DroPer_CAF1 6949 114 + 1
CAUUGGCAAGACGACAGUGCUGUCGGGCAAGCCACUGCUGCUGCAUGCCAAGGCAAUCAAGCAGCUAGGAGGCGGUAGUGUUGUGACCACUCAACCCACAGCUACAACGACAAC
...((((...((((((.(((((((.((....)).((((((((...(((....)))....)))))).))..))))))).))))))((....))........)))).......... ( -38.10)
>consensus
UAUUGGCAAAACGACAGUGCUGCCGGGAAAACCACUGCUGCUGCAUGCCAAGACAAUAAAACAGCUAGGCGGCAGUAGUGUGGCCACCACCCAAACCACCACAACAACGACAAC
....((((..((....))..)))).((....))...((((((((.((((..................))))))))))))((((...............))))............ (-16.84 = -16.81 +  -0.02)

alignment

secondary structure

dotplot

Window 5

Location	4,815,333 – 4,815,446
Length	113
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	80.37
Mean single sequence MFE	-40.85
Consensus MFE	-29.91
Energy contribution	-30.33
Covariance contribution	0.42
Combinations/Pair	1.36
Mean z-score	-2.50
Structure conservation index	0.73
SVM decision value	1.29
SVM RNA-class probability	0.938570
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4815333 113 - 27905053
GCUCCACUGCCGCUUCCCACUGCCGCU-GAUGCAACUGCUGUUGUCGUCGUUGUGGUAGUCUGGGUUGUGGGCACACUACUACCGCCAAUCUGUUUUAAUGUUUUGGCGUGGAG
.((((((((((((..((((((((((((-((((((((....)))).)))))..))))))))..)))..)).))))..........(((((..(((....)))..))))))))))) ( -46.50)
>DroSec_CAF1 4845 104 - 1
GUUCC---------UCCCACUGCCGCU-GAUGCAACUGCUGUUGUCGUCGUUGUGGUGGUCUGGGUAGUGGCCACACUACUGCUGCCAAGCUGUUUUAAUGUCUUGGCGUUCAG
.....---------..((((..(.((.-((((((((....)))).)))))).)..)))).((((((((((....)))))))...(((((((.........).))))))...))) ( -38.50)
>DroSim_CAF1 6278 104 - 1
GUUCC---------UCCCACUGCCGCU-GAUGCAACUGCUGUUGUCGUCGUUGUGGUGGUCUGGGUAGUGGCCACACUACUGCUGCCAAGCUGUUUUAAUGUCUUGGCGUGCAG
...((---------..((((..(.((.-((((((((....)))).)))))).)..))))...))((((((....))))))(((((((((((.........).))))))).))). ( -42.00)
>DroEre_CAF1 4695 104 - 1
GCUCC---------UCCCACUGCCGCU-GAUGCAACUGCUGUUGUUGUCGUUGUAGUGGUUUGGGUGGUGGCCACACUACUGCCGCCAAGCUGUUUUAAUGUUUUGGCGUGCAG
(((((---------.((((..((((((-((((((((.......)))).))))..)))))).)))).)).))).......((((((((((((.........).))))))).)))) ( -41.10)
>DroYak_CAF1 4678 104 - 1
GCUCC---------UCCCACUGCCGCU-GAUGCAACUGCUGUCGUCGUCGUUGUAGUGGUCUGGGUAGUGGCCACACUACUGCCGCCAAGCUGUUUUAAUGUUUUGGCGUGCAG
...((---------..(((((((.((.-(((((.((....)).).)))))).)))))))...))((((((....))))))(((((((((((.........).))))))).))). ( -38.90)
>DroAna_CAF1 8089 91 - 1
-----------------------CGCUAGACGCCGCUGUUGUGGUCGUGGCGGUGGUUACUUGGGUGGUGGCCACACUGCUGCCGCUCAGUUGCUUUAUCGUCUUUGCAUUCAA
-----------------------.((.((((((((((((..(....)..))))))))...((((((((..((......))..))))))))..........))))..))...... ( -38.10)
>consensus
GCUCC_________UCCCACUGCCGCU_GAUGCAACUGCUGUUGUCGUCGUUGUGGUGGUCUGGGUAGUGGCCACACUACUGCCGCCAAGCUGUUUUAAUGUCUUGGCGUGCAG
..................((((((((..((((((((....)))).))))...))))))))(((((((((((.....))))))))((((((.(((....))).))))))...))) (-29.91 = -30.33 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:46 2006