Locus 2365

Sequence ID	2L_DroMel_CAF1
Location	6,410,257 – 6,410,447
Length	190
Max. P	0.923752

overview

Window 9

Location	6,410,257 – 6,410,367
Length	110
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	93.77
Mean single sequence MFE	-28.36
Consensus MFE	-23.38
Energy contribution	-26.26
Covariance contribution	2.88
Combinations/Pair	1.07
Mean z-score	-1.82
Structure conservation index	0.82
SVM decision value	1.16
SVM RNA-class probability	0.923752
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6410257 110 + 22407834
AUUCCACGGUAUAUUAAUCUUUUCGAUCGGACAAUCAUUGCAGAUUUCUGCACGUUUGUUUACAUAU------AUAGUAGCCGGCUUUUGCACUUCGGUGCACAUUGCCACCACGU
.......(((.((((((((.....))).((((((....(((((....)))))...))))))......------.))))))))(((...(((((....)))))....)))....... ( -29.70)
>DroSec_CAF1 38546 110 + 1
AUUCCAUGGUAUAUUAAUCUUUUCGAUCGGACAAUCAUGGCAGAUUUCUGCGCGUUUGUUUACAUAU------AUAGUAGCCGGCUUUUGCACUUCGGUGUUCAUUACCACCACGU
....((((((...(..(((.....)))..)...))))))((((....))))((((..(.((((....------...)))).)((.....((((....))))......))...)))) ( -22.70)
>DroSim_CAF1 39027 110 + 1
AUUCCACGGUAUAUUAAUCUUUUCGAUCGGACAAUCAUGGCAGAUUUCUGCGCGUUUGUUUACAUAU------AUAGUAGCCGGCUUUUGCACUUCGGUGCACAUUGCCACCACGU
.......(((.((((((((.....))).((((((..(((((((....)))).)))))))))......------.))))))))(((...(((((....)))))....)))....... ( -29.50)
>DroEre_CAF1 37155 115 + 1
AUUCCAUGGCAUAUUAAUCUCUUCGAUCGGACAAUCAUGGCAGAU-UCUGCACGUUUGUUUACAUAUACGUGUAUAGUAGCCGGCUUUCGCACUUCGGUGCACAUUGCCACCACGU
.......(((.(((((((((((..(((......)))..)).))))-..(((((((.((....))...)))))))))))))))(((....((((....)))).....)))....... ( -32.00)
>DroYak_CAF1 42570 110 + 1
AUUCCACGGUAUAUUAAUCUUUUCGAUCGGACAAUCAUGGCAGAUUUCUGCACGUUUGUUUACAUAU------AUAGUAGCCGGCUUUCGCACUUCGGUGCACAUUGCCACCACGU
.......(((.((((((((.....))).((((((..(((((((....)))).)))))))))......------.))))))))(((....((((....)))).....)))....... ( -27.90)
>consensus
AUUCCACGGUAUAUUAAUCUUUUCGAUCGGACAAUCAUGGCAGAUUUCUGCACGUUUGUUUACAUAU______AUAGUAGCCGGCUUUUGCACUUCGGUGCACAUUGCCACCACGU
.......(((.((((((((.....))).((((((.....((((....))))....)))))).............))))))))(((....((((....)))).....)))....... (-23.38 = -26.26 +   2.88)

alignment

secondary structure

dotplot

Window 0

Location	6,410,257 – 6,410,367
Length	110
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	93.77
Mean single sequence MFE	-27.44
Consensus MFE	-25.14
Energy contribution	-25.42
Covariance contribution	0.28
Combinations/Pair	1.11
Mean z-score	-1.18
Structure conservation index	0.92
SVM decision value	0.32
SVM RNA-class probability	0.687225
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6410257 110 - 22407834
ACGUGGUGGCAAUGUGCACCGAAGUGCAAAAGCCGGCUACUAU------AUAUGUAAACAAACGUGCAGAAAUCUGCAAUGAUUGUCCGAUCGAAAAGAUUAAUAUACCGUGGAAU
..((((((((....(((((....)))))...))).)))))...------.(((((..((((.(((((((....)))).))).))))..((((.....)))).)))))......... ( -28.60)
>DroSec_CAF1 38546 110 - 1
ACGUGGUGGUAAUGAACACCGAAGUGCAAAAGCCGGCUACUAU------AUAUGUAAACAAACGCGCAGAAAUCUGCCAUGAUUGUCCGAUCGAAAAGAUUAAUAUACCAUGGAAU
.(((((((.((((......(((.(..(((.....(..(((...------....)))..)....(.((((....)))))....)))..)..))).....))))...))))))).... ( -21.90)
>DroSim_CAF1 39027 110 - 1
ACGUGGUGGCAAUGUGCACCGAAGUGCAAAAGCCGGCUACUAU------AUAUGUAAACAAACGCGCAGAAAUCUGCCAUGAUUGUCCGAUCGAAAAGAUUAAUAUACCGUGGAAU
..((((((((....(((((....)))))...))).)))))...------.............(((((((....))))..(((((....)))))................))).... ( -27.20)
>DroEre_CAF1 37155 115 - 1
ACGUGGUGGCAAUGUGCACCGAAGUGCGAAAGCCGGCUACUAUACACGUAUAUGUAAACAAACGUGCAGA-AUCUGCCAUGAUUGUCCGAUCGAAGAGAUUAAUAUGCCAUGGAAU
.((((((((((.(.(((((....(.((....)))(..(((((((....)))).)))..)....))))).)-...)))).(((((....))))).............)))))).... ( -31.60)
>DroYak_CAF1 42570 110 - 1
ACGUGGUGGCAAUGUGCACCGAAGUGCGAAAGCCGGCUACUAU------AUAUGUAAACAAACGUGCAGAAAUCUGCCAUGAUUGUCCGAUCGAAAAGAUUAAUAUACCGUGGAAU
..((((((((....(((((....)))))...))).)))))...------.(((((..((((.(((((((....))).)))).))))..((((.....)))).)))))......... ( -27.90)
>consensus
ACGUGGUGGCAAUGUGCACCGAAGUGCAAAAGCCGGCUACUAU______AUAUGUAAACAAACGUGCAGAAAUCUGCCAUGAUUGUCCGAUCGAAAAGAUUAAUAUACCGUGGAAU
.(((((((((....(((((....)))))...)))((.(((((((....)))).))).((((.(((((((....)))).))).))))))((((.....)))).....)))))).... (-25.14 = -25.42 +   0.28)

alignment

secondary structure

dotplot

Window 1

Location	6,410,297 – 6,410,407
Length	110
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	92.88
Mean single sequence MFE	-33.28
Consensus MFE	-25.72
Energy contribution	-28.88
Covariance contribution	3.16
Combinations/Pair	1.12
Mean z-score	-2.13
Structure conservation index	0.77
SVM decision value	0.95
SVM RNA-class probability	0.887361
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6410297 110 + 22407834
CAGAUUUCUGCACGUUUGUUUACAUAU------AUAGUAGCCGGCUUUUGCACUUCGGUGCACAUUGCCACCACGUAGACGGCCGUCAGGAAGAUAUAUAAAUAUCUGAGUCAGAC
..((((((((.(((..(((((((....------...(....)(((...(((((....)))))....))).....)))))))..))))))))((((((....))))))..))).... ( -33.30)
>DroSec_CAF1 38586 106 + 1
CAGAUUUCUGCGCGUUUGUUUACAUAU------AUAGUAGCCGGCUUUUGCACUUCGGUGUUCAUUACCACCACGUAGACGGCCGUCAGGAAGAUAUAUAAAUAUCUGA----GAC
.....(((((.(((..(((((((....------..........((....)).....((((........))))..)))))))..))))))))((((((....))))))..----... ( -25.90)
>DroSim_CAF1 39067 110 + 1
CAGAUUUCUGCGCGUUUGUUUACAUAU------AUAGUAGCCGGCUUUUGCACUUCGGUGCACAUUGCCACCACGUAGACGGCCGUCAGGAAGAUAUAUAAAUAUCUGAGUCAGAC
..((((((((.(((..(((((((....------...(....)(((...(((((....)))))....))).....)))))))..))))))))((((((....))))))..))).... ( -32.70)
>DroEre_CAF1 37195 115 + 1
CAGAU-UCUGCACGUUUGUUUACAUAUACGUGUAUAGUAGCCGGCUUUCGCACUUCGGUGCACAUUGCCACCACGUAGACGGCCGGCAGAAAGAUAUAUAAAUAUCUGAGUCAGAC
..(((-(((((((((.((....))...))))))).....(((((((.((((((....))))....(((......))))).)))))))....((((((....))))))))))).... ( -42.80)
>DroYak_CAF1 42610 110 + 1
CAGAUUUCUGCACGUUUGUUUACAUAU------AUAGUAGCCGGCUUUCGCACUUCGGUGCACAUUGCCACCACGUAGACGGCCGUCAGGAGGAUAUAUAAAUAUCUGAGUCAGAC
..((((((((.(((..(((((((....------...(....)(((....((((....)))).....))).....)))))))..))))))))((((((....))))))..))).... ( -31.70)
>consensus
CAGAUUUCUGCACGUUUGUUUACAUAU______AUAGUAGCCGGCUUUUGCACUUCGGUGCACAUUGCCACCACGUAGACGGCCGUCAGGAAGAUAUAUAAAUAUCUGAGUCAGAC
.....(((((.(((..(((((((.((((....))))......(((....((((....)))).....))).....)))))))..))))))))((((((....))))))......... (-25.72 = -28.88 +   3.16)

alignment

secondary structure

dotplot

Window 2

Location	6,410,327 – 6,410,447
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.00
Mean single sequence MFE	-38.16
Consensus MFE	-33.52
Energy contribution	-33.44
Covariance contribution	-0.08
Combinations/Pair	1.15
Mean z-score	-1.46
Structure conservation index	0.88
SVM decision value	0.93
SVM RNA-class probability	0.883468
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6410327 120 + 22407834
GUAGCCGGCUUUUGCACUUCGGUGCACAUUGCCACCACGUAGACGGCCGUCAGGAAGAUAUAUAAAUAUCUGAGUCAGACUGUGCCGCGGGAACUGGAAACGCACAAUUUAAGUUGGAAA
....(((((((.(((((....)))))...(((..((.((....((((((((.((.((((((....))))))...)).))).).))))))))....(....))))......)))))))... ( -36.50)
>DroSec_CAF1 38616 116 + 1
GUAGCCGGCUUUUGCACUUCGGUGUUCAUUACCACCACGUAGACGGCCGUCAGGAAGAUAUAUAAAUAUCUGA----GACUGUGCCGCGGGAGCUGGAAACGCACAAUUUAAGUGGGAAA
((..(((((((((((.....((((........))))........(((...(((..((((((....))))))..----..))).))))))))))))))..)).(((.......)))..... ( -38.70)
>DroSim_CAF1 39097 119 + 1
GUAGCCGGCUUUUGCACUUCGGUGCACAUUGCCACCACGUAGACGGCCGUCAGGAAGAUAUAUAAAUAUCUGAGUCAGACUGUGCCGCGGGAGCUGGA-ACGCACAAUUUAAGUGGGAAA
....(((((((((((.....(((((.....).))))........(((((((.((.((((((....))))))...)).))).).)))))))))))))).-.(.(((.......))).)... ( -39.50)
>DroEre_CAF1 37230 120 + 1
GUAGCCGGCUUUCGCACUUCGGUGCACAUUGCCACCACGUAGACGGCCGGCAGAAAGAUAUAUAAAUAUCUGAGUCAGACUGUGCCGCGGGAGUUGGAAACGCACAAUUUAAGAUGGAAG
...(((((((.((((((....))))....(((......))))).))))))).((.((((((....))))))...))(((.(((((.((....)).(....)))))).))).......... ( -40.50)
>DroYak_CAF1 42640 120 + 1
GUAGCCGGCUUUCGCACUUCGGUGCACAUUGCCACCACGUAGACGGCCGUCAGGAGGAUAUAUAAAUAUCUGAGUCAGACUGUGCCACGGGAGUUGGAAACGCACAAUUUAAAUCGGAAA
((..((((((..(((((....))))...................(((((((.((.((((((....))))))...)).))).).)))..)..))))))..))................... ( -35.60)
>consensus
GUAGCCGGCUUUUGCACUUCGGUGCACAUUGCCACCACGUAGACGGCCGUCAGGAAGAUAUAUAAAUAUCUGAGUCAGACUGUGCCGCGGGAGCUGGAAACGCACAAUUUAAGUGGGAAA
((..(((((((((((.....(((((.....).))))........(((((((.((.((((((....))))))...)).))).).))))))))))))))..))................... (-33.52 = -33.44 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:18 2006