Locus 8580

Sequence ID	3R_DroMel_CAF1
Location	22,942,921 – 22,943,117
Length	196
Max. P	0.994888

overview

Window 2

Location	22,942,921 – 22,943,037
Length	116
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	74.56
Mean single sequence MFE	-39.00
Consensus MFE	-26.58
Energy contribution	-26.25
Covariance contribution	-0.33
Combinations/Pair	1.49
Mean z-score	-2.23
Structure conservation index	0.68
SVM decision value	2.14
SVM RNA-class probability	0.988809
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22942921 116 + 27905053
-UAAA--CUUGUUUAGUUUUUUGUGGUUGGCGUGGCUGCCUUGACGACUUCAGUCGUUAGUAUUGCCUAUUGGAUUGGCUUGCCCUUUUGGUGGGCCAAAAGUCAGUUGGUGACCUACU
-.(((--((.....)))))...((((((((((....))))((((((((....))))))))....(((.(((((.((((((..((.....))..))))))...))))).))))))).)). ( -39.30)
>DroVir_CAF1 448 112 + 1
-------UACUUUCAGUUCUUCGUUGUGGGCGUGGCUAUACUGACUACUGCCGUGGUGGGCAUCGCCUAUUGGAUUGGCCUGCCCUUUUGGUGGGCCAAGAGCCAAGUGGCAACAAUAC
-------...............((((((((((((((......).))))((((......))))..)))).((((.((((((..((.....))..))))))...))))...)))))..... ( -42.10)
>DroGri_CAF1 236 112 + 1
-------UACUUUCAGUUUUUCGUAGUGGGUGUUGCUGUUUUGACCACUGUCGUUGUCAGCAUUGCCUAUUGGAUUGGUCUGCCCUUUUGGUGGGCUAAAAGCCAAUUGGCAACGAUUU
-------.............(((((((((((..(((((...((((....))))....)))))..)))))))...((((((..((.....))..))))))..(((....))).))))... ( -37.40)
>DroEre_CAF1 2465 117 + 1
CUAUA--UUUUUUCAGUUUUUUGUGGUUGGCGUGGCUGCCCUGACCACUUCAGUCGUUAGUAUUGCUUACUGGAUUGGCUUGCCCUUUUGGUGGGCCAAGAGUCAGUUGGUGACCUACU
.....--...............((((((((((....))))..))))))..........(((((..((.(((((.((((((..((.....))..))))))...))))).))..)..)))) ( -37.80)
>DroWil_CAF1 129 117 + 1
--GGAUUCUUUUGCAGUUUUUUGUGGUUGGCGUCGCUGCCCUUACCACCGCAGUUGUGAGCAUUGCAUAUUGGAUUGGCUUACCAUUCUGGUGGGCAAAGAGCCAGUUGGCAACUAUAU
--.(((((...((((((.....(((((.((((....))))...)))))(((....)))...))))))....))))).(((((((.....))))))).....(((....)))........ ( -36.10)
>DroAna_CAF1 197 116 + 1
-GUUA--UCAUUUCAGUUUUUUGUGGUGGGAGUGGCUGCCUUGACCACUUCAGUCGUGAGCAUUGCCUACUGGAUUGGACUGCCCUUCUGGUUGGCCAAAAGCCAGCUCAUGACGGUGU
-....--.(((..(((....)))..)))((((((((......).))))))).(((((((((.......((..((..((....))..))..))((((.....)))))))))))))..... ( -41.30)
>consensus
____A__UUUUUUCAGUUUUUUGUGGUGGGCGUGGCUGCCCUGACCACUGCAGUCGUGAGCAUUGCCUAUUGGAUUGGCCUGCCCUUUUGGUGGGCCAAAAGCCAGUUGGCAACCAUAU
.............(((((...(((.....))).)))))..(((((.((....)).)))))..(((((.(((((.((((((((((.....))))))))))...))))).)))))...... (-26.58 = -26.25 +  -0.33)

alignment

secondary structure

dotplot

Window 3

Location	22,942,921 – 22,943,037
Length	116
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	74.56
Mean single sequence MFE	-28.93
Consensus MFE	-13.11
Energy contribution	-14.58
Covariance contribution	1.47
Combinations/Pair	1.50
Mean z-score	-1.86
Structure conservation index	0.45
SVM decision value	0.16
SVM RNA-class probability	0.612865
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22942921 116 - 27905053
AGUAGGUCACCAACUGACUUUUGGCCCACCAAAAGGGCAAGCCAAUCCAAUAGGCAAUACUAACGACUGAAGUCGUCAAGGCAGCCACGCCAACCACAAAAAACUAAACAAG--UUUA-
.((.(((..........(((((((....)))))))(((..(((.......(((......)))(((((....)))))...))).)))..))).))......(((((.....))--))).- ( -28.40)
>DroVir_CAF1 448 112 - 1
GUAUUGUUGCCACUUGGCUCUUGGCCCACCAAAAGGGCAGGCCAAUCCAAUAGGCGAUGCCCACCACGGCAGUAGUCAGUAUAGCCACGCCCACAACGAAGAACUGAAAGUA-------
...((((((...(.(((((.((((((..((.....))..)))))).......(((..((((......))))...))).....))))).)....)))))).............------- ( -31.50)
>DroGri_CAF1 236 112 - 1
AAAUCGUUGCCAAUUGGCUUUUAGCCCACCAAAAGGGCAGACCAAUCCAAUAGGCAAUGCUGACAACGACAGUGGUCAAAACAGCAACACCCACUACGAAAAACUGAAAGUA-------
...((((((((.(((((.((((.((((.......)))).))..)).))))).)))).(((((.....(((....)))....))))).........)))).............------- ( -28.00)
>DroEre_CAF1 2465 117 - 1
AGUAGGUCACCAACUGACUCUUGGCCCACCAAAAGGGCAAGCCAAUCCAGUAAGCAAUACUAACGACUGAAGUGGUCAGGGCAGCCACGCCAACCACAAAAAACUGAAAAAA--UAUAG
.((.(((......(((((((((.((((.......)))).........((((.((.....))....))))))).))))))(((......))).)))))...............--..... ( -26.20)
>DroWil_CAF1 129 117 - 1
AUAUAGUUGCCAACUGGCUCUUUGCCCACCAGAAUGGUAAGCCAAUCCAAUAUGCAAUGCUCACAACUGCGGUGGUAAGGGCAGCGACGCCAACCACAAAAAACUGCAAAAGAAUCC--
...(((((......((((((.((((((((((((.(((....))).))..........(((........))).))))..)))))).)).)))).........)))))...........-- ( -28.56)
>DroAna_CAF1 197 116 - 1
ACACCGUCAUGAGCUGGCUUUUGGCCAACCAGAAGGGCAGUCCAAUCCAGUAGGCAAUGCUCACGACUGAAGUGGUCAAGGCAGCCACUCCCACCACAAAAAACUGAAAUGA--UAAC-
.....((((((((.(((((((((((((..(((..(((((..((.........))...)))))....)))...))))))))..))))))))......((......))..))))--)...- ( -30.90)
>consensus
AGAUCGUCACCAACUGGCUCUUGGCCCACCAAAAGGGCAAGCCAAUCCAAUAGGCAAUGCUCACGACUGAAGUGGUCAAGGCAGCCACGCCAACCACAAAAAACUGAAAAAA__U____
...(((((......(((((....((((.......)))).)))))........((.....))...)))))..(((((...(((......))).)))))...................... (-13.11 = -14.58 +   1.47)

alignment

secondary structure

dotplot

Window 4

Location	22,942,957 – 22,943,077
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.94
Mean single sequence MFE	-43.75
Consensus MFE	-22.98
Energy contribution	-23.68
Covariance contribution	0.70
Combinations/Pair	1.48
Mean z-score	-2.79
Structure conservation index	0.53
SVM decision value	2.52
SVM RNA-class probability	0.994888
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22942957 120 + 27905053
CUUGACGACUUCAGUCGUUAGUAUUGCCUAUUGGAUUGGCUUGCCCUUUUGGUGGGCCAAAAGUCAGUUGGUGACCUACUUCCUCCUCAUUGUGGGCAACUGGCUGCUGCUCAAUGUGGU
.((((((((....))))))))....(((((((((.((((((..((.....))..)))))).((.((((..((..(((((............)))))..))..))))))..)))))).))) ( -47.10)
>DroVir_CAF1 480 120 + 1
ACUGACUACUGCCGUGGUGGGCAUCGCCUAUUGGAUUGGCCUGCCCUUUUGGUGGGCCAAGAGCCAAGUGGCAACAAUACUGCUGCUUAUUGUGGGCAACUGGCUGCUGCUAAACAUUAU
.((.(((((....))))).))....((((((.((.((((((..((.....))..))))))...))(((..(((.......)))..)))...))))))...((((....))))........ ( -46.10)
>DroGri_CAF1 268 120 + 1
UUUGACCACUGUCGUUGUCAGCAUUGCCUAUUGGAUUGGUCUGCCCUUUUGGUGGGCUAAAAGCCAAUUGGCAACGAUUUUAUUGCUCAUCUUUGGCAAUUGGGUGCUGUUGAACAUCAU
...(((....)))(((..((((.(((((.(((((.((((((..((.....))..))))))...))))).)))))..(((..(((((.((....)))))))..)))))))...)))..... ( -40.10)
>DroWil_CAF1 166 120 + 1
CCUUACCACCGCAGUUGUGAGCAUUGCAUAUUGGAUUGGCUUACCAUUCUGGUGGGCAAAGAGCCAGUUGGCAACUAUAUUUUUACUCCUGGUGGGGAACUGGCUGUUGUUAAACGUGAU
.....((((((.(((.((((((..(.(.....).)...)))))).))).))))))((((..(((((((((....)..........((((....)))))))))))).)))).......... ( -40.00)
>DroMoj_CAF1 24 120 + 1
CUUAACCACUGCCGUAGUGUCCAUUGCCUAUUGGAUUGGGCUGCCCUUUUGGUGGGCCAAGAGCCAAGCAGCCACUAUAGUACUGCUCAUCAUAGGCAAUUGGCUGCUGCUGAACAUAAU
.............((((((((.((((((((((((.((((.(..((.....))..).))))...)))(((((..((....)).)))))....))))))))).))).))))).......... ( -42.10)
>DroAna_CAF1 233 120 + 1
CUUGACCACUUCAGUCGUGAGCAUUGCCUACUGGAUUGGACUGCCCUUCUGGUUGGCCAAAAGCCAGCUCAUGACGGUGUUCCUGCUCAUUGUGGGGAACUGGCUACUUCUGAAUGUGGU
....((((((((((((((((((.......((..((..((....))..))..))((((.....))))))))))))((((.((((..(.....)..)))))))).......))))).))))) ( -47.10)
>consensus
CUUGACCACUGCAGUCGUGAGCAUUGCCUAUUGGAUUGGCCUGCCCUUUUGGUGGGCCAAAAGCCAAUUGGCAACGAUAUUACUGCUCAUUGUGGGCAACUGGCUGCUGCUGAACAUGAU
......(((.......)))((((..((((((..((..((....))..))..))))))....((((((.((.(.(((((..........))))).).)).))))))..))))......... (-22.98 = -23.68 +   0.70)

alignment

secondary structure

dotplot

Window 5

Location	22,942,997 – 22,943,117
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.89
Mean single sequence MFE	-39.18
Consensus MFE	-18.98
Energy contribution	-19.54
Covariance contribution	0.56
Combinations/Pair	1.59
Mean z-score	-1.83
Structure conservation index	0.48
SVM decision value	0.29
SVM RNA-class probability	0.670681
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22942997 120 + 27905053
UUGCCCUUUUGGUGGGCCAAAAGUCAGUUGGUGACCUACUUCCUCCUCAUUGUGGGCAACUGGCUGCUGCUCAAUGUGGUUUUCCACUACGUUAUGGCUGUGAUCACGCCGGCUGGUCAU
.((.((..(((((((((((..((.((((..((..(((((............)))))..))..))))))....((((((((.....)))))))).)))))(....).))))))..)).)). ( -39.70)
>DroVir_CAF1 520 120 + 1
CUGCCCUUUUGGUGGGCCAAGAGCCAAGUGGCAACAAUACUGCUGCUUAUUGUGGGCAACUGGCUGCUGCUAAACAUUAUUUUCCAUUAUGUGAUGGCUGUGAUAACGCCCGCUGGACAG
((((((((((((....)))))))..(((..(((.......)))..)))...((((((...((((....))))...(((((...(((((....)))))..)))))...)))))).)).))) ( -40.00)
>DroGri_CAF1 308 120 + 1
CUGCCCUUUUGGUGGGCUAAAAGCCAAUUGGCAACGAUUUUAUUGCUCAUCUUUGGCAAUUGGGUGCUGUUGAACAUCAUCUUCCACUAUGUGAUGGCUGUAAUAACACCACCUGGCCAU
..((((.......)))).....(((((.((((((........)))).))...)))))..(..((((.(((((.((((((((...........))))).)))..))))).))))..).... ( -35.70)
>DroWil_CAF1 206 120 + 1
UUACCAUUCUGGUGGGCAAAGAGCCAGUUGGCAACUAUAUUUUUACUCCUGGUGGGGAACUGGCUGUUGUUAAACGUGAUAUUCCACUAUGUAAUGGCUGUGAUAACGCCGGCCGGUUAU
........(((((.(((....(((((((((....)..........((((....))))))))))))(((((((..(((.((((......)))).)))....)))))))))).))))).... ( -41.20)
>DroMoj_CAF1 64 120 + 1
CUGCCCUUUUGGUGGGCCAAGAGCCAAGCAGCCACUAUAGUACUGCUCAUCAUAGGCAAUUGGCUGCUGCUGAACAUAAUUUUCCACUAUGUAAUGGGUGUGAUUACACCAGCUGGCCAG
..((((.......))))...(.(((((((((((((....))..((((.......))))...)))))))(((..(((((.........)))))....(((((....))))))))))))).. ( -38.00)
>DroAna_CAF1 273 120 + 1
CUGCCCUUCUGGUUGGCCAAAAGCCAGCUCAUGACGGUGUUCCUGCUCAUUGUGGGGAACUGGCUACUUCUGAAUGUGGUCUUCCAUUAUAUUAUGGCCGUGAUUACCCCACCUGGGUAU
..(((.((.((((((((.....)))))).)).)).))).....((((((..((((((....((((((........))))))..((((......)))).........)))))).)))))). ( -40.50)
>consensus
CUGCCCUUUUGGUGGGCCAAAAGCCAAUUGGCAACGAUAUUACUGCUCAUUGUGGGCAACUGGCUGCUGCUGAACAUGAUUUUCCACUAUGUAAUGGCUGUGAUAACGCCAGCUGGCCAU
.((.((..(((((((((((..((((((.((.(.(((((..........))))).).)).))))))........(((((.........)))))..))))).......))))))..)).)). (-18.98 = -19.54 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:14:36 2006