Locus 133

Sequence ID	2R_DroMel_CAF1
Location	1,393,216 – 1,393,442
Length	226
Max. P	0.999463

overview

Window 8

Location	1,393,216 – 1,393,336
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.83
Mean single sequence MFE	-27.28
Consensus MFE	-25.84
Energy contribution	-26.52
Covariance contribution	0.68
Combinations/Pair	1.06
Mean z-score	-2.21
Structure conservation index	0.95
SVM decision value	3.17
SVM RNA-class probability	0.998654
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1393216 120 - 20766785
AAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUAUUUUUAUUUAUUCAUGUUCUCACAGCCCCUUGUAGUUCUUUCAUCUGCGUUUUCCGCUGCGUUGCUGUCUUUUAAAAGCC
.....((((((((((.......))))))))))........((((((......((.((...(.((((....(((((.........)))))......)))).)..)))).....)))))).. ( -25.10)
>DroSec_CAF1 19717 120 - 1
AAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUAUUUUUAUUUAUUCAUGUUCUCGCCGCCCCUUGUAGUUCUUUCAUCUGCGUUUUCCGCUGCGUUGCUGUCUUUUAAAAGCC
.....((((((((((.......))))))))))........((((((......((.((...(((.((....(((((.........)))))......)).)))..)))).....)))))).. ( -25.90)
>DroSim_CAF1 24862 120 - 1
AAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUAUUUUUAUUUAUUCAUGUUCUCGCCGCCCCUUGCAGUUCUUUCAUCUGCGUUUUCCGCUGCGUUGCUGUCUUUUAAAAGCC
.....((((((((((.......))))))))))........((((((......((.((...(((.((....(((((.........)))))......)).)))..)))).....)))))).. ( -27.90)
>DroEre_CAF1 18717 120 - 1
AAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUAUUUUUAUUUAUUCAUGCUCUCGCAGCCCCUUGUAGUUCUUUCAUCUGCGUUUUCCGCUGCGUUGCUGUCUUUUAAAAGCC
.....((((((((((.......))))))))))........((((((......((.((...((((((....(((((.........)))))......))))))..)))).....)))))).. ( -32.10)
>DroYak_CAF1 20304 120 - 1
AAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGGUGCACUUAUUUUUAUUUAUUCAUGUUCUCGCAGCCCCUUGUAGUUCUUUCAUCUGCGUUUUCCGCUGCGUUGCCGUCUUUUAAAAGCC
......(((((((((.......))))))))).........((((((.........((...((((((....(((((.........)))))......))))))..)).......)))))).. ( -25.39)
>consensus
AAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUAUUUUUAUUUAUUCAUGUUCUCGCAGCCCCUUGUAGUUCUUUCAUCUGCGUUUUCCGCUGCGUUGCUGUCUUUUAAAAGCC
.....((((((((((.......))))))))))........((((((......((.((...((((((....(((((.........)))))......))))))..)))).....)))))).. (-25.84 = -26.52 +   0.68)

alignment

secondary structure

dotplot

Window 9

Location	1,393,256 – 1,393,376
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.83
Mean single sequence MFE	-25.60
Consensus MFE	-23.50
Energy contribution	-24.14
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-2.74
Structure conservation index	0.92
SVM decision value	3.63
SVM RNA-class probability	0.999463
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1393256 120 + 20766785
AAGAACUACAAGGGGCUGUGAGAACAUGAAUAAAUAAAAAUAAGUGCAGCAUGCCCACUUAAGAGAUGAGCAUGCAAUUUUAAAUAAGAAUUAAGAGCACAAAACUGUUCAACAAGCCAG
.............((((((..((((((......))........((((.((((((.((((....)).)).))))))((((((.....))))))....))))......)))).)).)))).. ( -27.70)
>DroSec_CAF1 19757 120 + 1
AAGAACUACAAGGGGCGGCGAGAACAUGAAUAAAUAAAAAUAAGUGCAGCAUGCCCACUUAAGAGAUGAGCAUGCAAUUUUAAAUAAGAAUUAAGAGCACAAAACUGUUCAACAAGCCAG
.............(((.....((((((......))........((((.((((((.((((....)).)).))))))((((((.....))))))....))))......)))).....))).. ( -25.50)
>DroSim_CAF1 24902 120 + 1
AAGAACUGCAAGGGGCGGCGAGAACAUGAAUAAAUAAAAAUAAGUGCAGCAUGCCCACUUAAGAGAUGAGCAUGCAAUUUUAAAUAAGAAUUAAGAGCACAAAACUGUUCAACAAGCCAG
..(..((....))..)(((..((((((......))........((((.((((((.((((....)).)).))))))((((((.....))))))....))))......)))).....))).. ( -25.70)
>DroEre_CAF1 18757 120 + 1
AAGAACUACAAGGGGCUGCGAGAGCAUGAAUAAAUAAAAAUAAGUGCAGCAUGCCCACUUAAGAGAUGAGCAUGCAAUUUUAAAUAAGAAUUAAGAGCACAAAACUGUUCAACAAGCCAG
.............((((((....)).((((((..((....)).((((.((((((.((((....)).)).))))))((((((.....))))))....)))).....))))))...)))).. ( -29.20)
>DroYak_CAF1 20344 120 + 1
AAGAACUACAAGGGGCUGCGAGAACAUGAAUAAAUAAAAAUAAGUGCACCAUGCCCACUUAAGAGAUGAGCAUGCAAUUUUAAAUAAGAAUUAAGAGCACAAAACUUUUCAACAAGCCAG
.............((((..(((((.((......))........((((..(((((.((((....)).)).))))).((((((.....))))))....)))).....)))))....)))).. ( -19.90)
>consensus
AAGAACUACAAGGGGCUGCGAGAACAUGAAUAAAUAAAAAUAAGUGCAGCAUGCCCACUUAAGAGAUGAGCAUGCAAUUUUAAAUAAGAAUUAAGAGCACAAAACUGUUCAACAAGCCAG
.............((((....((((((......))........((((.((((((.((((....)).)).))))))((((((.....))))))....))))......))))....)))).. (-23.50 = -24.14 +   0.64)

alignment

secondary structure

dotplot

Window 0

Location	1,393,256 – 1,393,376
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.83
Mean single sequence MFE	-25.43
Consensus MFE	-22.93
Energy contribution	-23.93
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.33
Structure conservation index	0.90
SVM decision value	2.75
SVM RNA-class probability	0.996798
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1393256 120 - 20766785
CUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUAAAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUAUUUUUAUUUAUUCAUGUUCUCACAGCCCCUUGUAGUUCUU
..((((((..(((((.....((((..((((.......))))....((((((((((.......)))))))))).)))).................))))).)).))))............. ( -27.65)
>DroSec_CAF1 19757 120 - 1
CUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUAAAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUAUUUUUAUUUAUUCAUGUUCUCGCCGCCCCUUGUAGUUCUU
..(((.....(((((.....((((..((((.......))))....((((((((((.......)))))))))).)))).................))))).....)))............. ( -25.75)
>DroSim_CAF1 24902 120 - 1
CUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUAAAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUAUUUUUAUUUAUUCAUGUUCUCGCCGCCCCUUGCAGUUCUU
..(((.....(((((.....((((..((((.......))))....((((((((((.......)))))))))).)))).................)))))..)))((.....))....... ( -26.05)
>DroEre_CAF1 18757 120 - 1
CUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUAAAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUAUUUUUAUUUAUUCAUGCUCUCGCAGCCCCUUGUAGUUCUU
..(((...............((((..((((.......))))....((((((((((.......)))))))))).)))).................(((....))))))............. ( -25.10)
>DroYak_CAF1 20344 120 - 1
CUGGCUUGUUGAAAAGUUUUGUGCUCUUAAUUCUUAUUUAAAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGGUGCACUUAUUUUUAUUUAUUCAUGUUCUCGCAGCCCCUUGUAGUUCUU
..(((......((((((...((((.(((((.......)))).....(((((((((.......)))))))))).))))..)))))).........(((....))))))............. ( -22.60)
>consensus
CUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUAAAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUAUUUUUAUUUAUUCAUGUUCUCGCAGCCCCUUGUAGUUCUU
..((((....(((((.....((((..((((.......))))....((((((((((.......)))))))))).)))).................)))))....))))............. (-22.93 = -23.93 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	1,393,296 – 1,393,416
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.80
Mean single sequence MFE	-26.42
Consensus MFE	-21.22
Energy contribution	-21.82
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.74
Structure conservation index	0.80
SVM decision value	0.71
SVM RNA-class probability	0.829978
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1393296 120 - 20766785
CUCCCCUCUCUCGUGGACGACCACUUUUGUGUCGUUGCAUCUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUAAAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUA
............(((((((((.((....))))))))((((..((((.(.....)))))..)))).....................((((((((((.......))))))))))..)))... ( -31.20)
>DroSec_CAF1 19797 120 - 1
CUCCCCUCUCUCGUGGACUGCCACUUUUGUGUCGUUGCAUCUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUAAAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUA
............((((....))))....((((....((((..((((.(.....)))))..)))).....................((((((((((.......)))))))))).))))... ( -28.90)
>DroSim_CAF1 24942 107 - 1
CUCCCCUCUCUC-------------UUUGUGUCGUUGCAUCUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUAAAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUA
............-------------...((((....((((..((((.(.....)))))..)))).....................((((((((((.......)))))))))).))))... ( -24.10)
>DroEre_CAF1 18797 120 - 1
CGCCCCUCUCUCGUGGACUCCUACUUUUGUGUCGUUGCAUCUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUAAAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUA
............((((....))))....((((....((((..((((.(.....)))))..)))).....................((((((((((.......)))))))))).))))... ( -26.80)
>DroYak_CAF1 20384 98 - 1
CUCCCCUC----------------------GUCGUUGCAUCUGGCUUGUUGAAAAGUUUUGUGCUCUUAAUUCUUAUUUAAAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGGUGCACUUA
........----------------------.....((((((..((...((((((((..(((......)))..))).)))))....))((((((((.......)))))))))))))).... ( -21.10)
>consensus
CUCCCCUCUCUCGUGGAC__C_ACUUUUGUGUCGUUGCAUCUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUAAAAUUGCAUGCUCAUCUCUUAAGUGGGCAUGCUGCACUUA
............................((((....((((..((((........))))..)))).....................((((((((((.......)))))))))).))))... (-21.22 = -21.82 +   0.60)

alignment

secondary structure

dotplot

Window 2

Location	1,393,336 – 1,393,442
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.53
Mean single sequence MFE	-20.93
Consensus MFE	-15.94
Energy contribution	-16.50
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.60
Structure conservation index	0.76
SVM decision value	0.50
SVM RNA-class probability	0.759427
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1393336 106 - 20766785
--------------GUACCUCAAACGCAAGACUUUUCAUCCUCCCCUCUCUCGUGGACGACCACUUUUGUGUCGUUGCAUCUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUA
--------------..........(((((((((.((((......((......(((((((((.((....)))))))).)))..)).....)))).)))))))))................. ( -22.20)
>DroSec_CAF1 19837 106 - 1
--------------AUACCUCCUACGCAAGACUUUUCAACCUCCCCUCUCUCGUGGACUGCCACUUUUGUGUCGUUGCAUCUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUA
--------------..........(((((((((.((((((.(((.(......).)))..((((....(((......)))..))))..)))))).)))))))))................. ( -24.50)
>DroSim_CAF1 24982 93 - 1
--------------GCACCUCGAACGCAAGACUUUUCAACCUCCCCUCUCUC-------------UUUGUGUCGUUGCAUCUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUA
--------------.......((.(((((((((.((((((....((......-------------..(((......)))...))...)))))).))))))))).)).............. ( -18.80)
>DroEre_CAF1 18837 120 - 1
GUAUGUAGCUGUAUGUAUCUCAAACGCAAGACUUUUCAGCCGCCCCUCUCUCGUGGACUCCUACUUUUGUGUCGUUGCAUCUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUA
(((((((....)))))))......(((((((((.((((((.(((........((((....))))...(((......)))...)))..)))))).)))))))))................. ( -25.10)
>DroYak_CAF1 20424 86 - 1
------------ACAUACCUCAAACGCAAGAAUUUUCAGCCUCCCCUC----------------------GUCGUUGCAUCUGGCUUGUUGAAAAGUUUUGUGCUCUUAAUUCUUAUUUA
------------............(((((((.((((((((....((..----------------------............))...)))))))).)))))))................. ( -14.04)
>consensus
______________GUACCUCAAACGCAAGACUUUUCAACCUCCCCUCUCUCGUGGAC__C_ACUUUUGUGUCGUUGCAUCUGGCUUGUUGAACAGUUUUGUGCUCUUAAUUCUUAUUUA
........................(((((((((.((((((............((((....))))......((((.......))))..)))))).)))))))))................. (-15.94 = -16.50 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:28:49 2006