Locus 4434

Sequence ID	3L_DroMel_CAF1
Location	12,942,659 – 12,942,935
Length	276
Max. P	0.996969

overview

Window 5

Location	12,942,659 – 12,942,779
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.25
Mean single sequence MFE	-29.02
Consensus MFE	-26.27
Energy contribution	-26.52
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.57
Structure conservation index	0.91
SVM decision value	0.07
SVM RNA-class probability	0.567986
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12942659 120 + 23771897
GGAUAAACUGACUUAAAUUCAGUUGAAAUUGCCUUUGAAAGUAAAAUUUAUGAAGACAAACAAAAGCAGGAAAACUUGGCAGGACUCGCGGGCGAGUACCCGGCCAAUUGCCAAAGGACU
.....((((((.......)))))).......((((((.............((....)).......((((......(((((.(((((((....))))).))..)))))))))))))))... ( -27.70)
>DroSec_CAF1 59918 120 + 1
GGACAAACUGACUUAAAUUCAGUUGAAAUUGCCUUUGAAAGUAAAAUUUAUGAAGACAAACAAAAGCAGGAAAACUUGGCAGGACUCGCGGGCGAGUACCCGGCCAAUUGCCAAAGGACU
.....((((((.......)))))).......((((((.............((....)).......((((......(((((.(((((((....))))).))..)))))))))))))))... ( -27.70)
>DroEre_CAF1 66164 120 + 1
GAACUAACUGACUUAAAUUCAGUUGAAAUUCCCUUUGAAAGUAGAAUUUAUGAAGACAAACAAAAGCAGGCAAACUUGGCAGGACUCGCGGGCGAGUACCCGGCCAAUUGCCAAAGGACU
....(((((((.......)))))))......(((((..............((....))..........(((((..(((((.(((((((....))))).))..)))))))))))))))... ( -31.80)
>DroYak_CAF1 63719 120 + 1
GAACAAACUGACUUAAAUUCAGUUGAAAUUUCCUUUGAACGUAAAAUUUAUGAAGACAAACAAAAGCAGGAAAACUUGGCAGGACUCGCGGGCGAGAACCCGGCCAAUUGCCAAAGGACU
.....((((((.......))))))......(((((((..((((.....)))).............((((......(((((.((.((((....))))...)).)))))))))))))))).. ( -28.90)
>consensus
GAACAAACUGACUUAAAUUCAGUUGAAAUUGCCUUUGAAAGUAAAAUUUAUGAAGACAAACAAAAGCAGGAAAACUUGGCAGGACUCGCGGGCGAGUACCCGGCCAAUUGCCAAAGGACU
.....((((((.......)))))).......((((((.............((....)).......((((......(((((.(((((((....))))).))..)))))))))))))))... (-26.27 = -26.52 +   0.25)

alignment

secondary structure

dotplot

Window 6

Location	12,942,659 – 12,942,779
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.25
Mean single sequence MFE	-31.43
Consensus MFE	-27.95
Energy contribution	-28.20
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.89
SVM decision value	0.82
SVM RNA-class probability	0.858035
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12942659 120 - 23771897
AGUCCUUUGGCAAUUGGCCGGGUACUCGCCCGCGAGUCCUGCCAAGUUUUCCUGCUUUUGUUUGUCUUCAUAAAUUUUACUUUCAAAGGCAAUUUCAACUGAAUUUAAGUCAGUUUAUCC
.(((....)))..(((((.(((.(((((....))))))))))))).......((((((((...((.............))...)))))))).....((((((.......))))))..... ( -30.22)
>DroSec_CAF1 59918 120 - 1
AGUCCUUUGGCAAUUGGCCGGGUACUCGCCCGCGAGUCCUGCCAAGUUUUCCUGCUUUUGUUUGUCUUCAUAAAUUUUACUUUCAAAGGCAAUUUCAACUGAAUUUAAGUCAGUUUGUCC
........((((.(((((.(((.(((((....))))))))))))).......((((((((...((.............))...)))))))).....((((((.......)))))))))). ( -31.52)
>DroEre_CAF1 66164 120 - 1
AGUCCUUUGGCAAUUGGCCGGGUACUCGCCCGCGAGUCCUGCCAAGUUUGCCUGCUUUUGUUUGUCUUCAUAAAUUCUACUUUCAAAGGGAAUUUCAACUGAAUUUAAGUCAGUUAGUUC
..((((((((((((((((.(((.(((((....)))))))))))))..))))).......((((((....))))))..........)))))).....((((((.......))))))..... ( -34.50)
>DroYak_CAF1 63719 120 - 1
AGUCCUUUGGCAAUUGGCCGGGUUCUCGCCCGCGAGUCCUGCCAAGUUUUCCUGCUUUUGUUUGUCUUCAUAAAUUUUACGUUCAAAGGAAAUUUCAACUGAAUUUAAGUCAGUUUGUUC
..(((((((((..(((((.(((..((((....)))).))))))))..............((((((....)))))).....).))))))))......((((((.......))))))..... ( -29.50)
>consensus
AGUCCUUUGGCAAUUGGCCGGGUACUCGCCCGCGAGUCCUGCCAAGUUUUCCUGCUUUUGUUUGUCUUCAUAAAUUUUACUUUCAAAGGCAAUUUCAACUGAAUUUAAGUCAGUUUGUCC
...(((((((((.(((((.(((.(((((....))))))))))))).......)))....((((((....))))))........)))))).......((((((.......))))))..... (-27.95 = -28.20 +   0.25)

alignment

secondary structure

dotplot

Window 7

Location	12,942,779 – 12,942,895
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.22
Mean single sequence MFE	-30.74
Consensus MFE	-23.50
Energy contribution	-25.34
Covariance contribution	1.84
Combinations/Pair	1.04
Mean z-score	-1.70
Structure conservation index	0.76
SVM decision value	0.30
SVM RNA-class probability	0.678975
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12942779 116 - 23771897
AUUUUUCCUGGCCAAAAUGGCGCUGGCUGCCAAAACUAUUACUCACACUCCUCCGCCAAAC----GAAAGGCGGAAGGAUAAUUCAAAUUGUCCAUUACGCGCAGCUGCCGCUCGAUUUG
............((((.(((((..(((((((....................((((((....----....)))))).(((((((....))))))).....).))))))..))).)).)))) ( -35.70)
>DroSec_CAF1 60038 114 - 1
AAU--UCCUGGCCAAAAUGGCGCUGGCUGCCAAAACUAUUACUCACACUCCUCCGCCAAAC----GAAAGGCGGAAGGAUAAUUCAAAUUGUCCAUUACGCGCAGCUGCCGCUCGAUUUG
...--.......((((.(((((..(((((((....................((((((....----....)))))).(((((((....))))))).....).))))))..))).)).)))) ( -35.70)
>DroSim_CAF1 64381 118 - 1
AAU--UCCUGGCCAAAAUGGCGCUGGCUGCCAAAACUAUUACUCACACUCCUCCGCCCACCACCUGAAAGGCGGAAGGAUAAUUCAAAUUGUCCANNNNNNNNNNNNNNNNNNNNNNNNN
...--....((.(((..(((((.....)))))................(((((((((............))))).)))).........))).)).......................... ( -22.30)
>DroEre_CAF1 66284 114 - 1
AAU--UCGUGGCCAAAAUGGCGCUGGCUGCCAAAACUAUUACUCACACUCCUCCGCCAACG----GAACGACGGACGGAUAAUUCAAAUUGUCCAUUACGCGCAGCUGCCGCUCGAUUUG
...--..((((((.....)))((.(((((((.................(((((((....))----)).....))).(((((((....))))))).....).)))))))))))........ ( -30.80)
>DroYak_CAF1 63839 114 - 1
AAU--UCCUGGCCAAAAUGGCGCUGGCUGCCAAAACUAUUACUCACACUCCUUCGCCAACG----GGAAGACGGACGGAUAAUUCAAAUUGUCCAUUACGCGCAGCUGCCGCUCGAUUUG
...--.......((((.(((((..(((((((.................(((.((.((....----))..)).))).(((((((....))))))).....).))))))..))).)).)))) ( -29.20)
>consensus
AAU__UCCUGGCCAAAAUGGCGCUGGCUGCCAAAACUAUUACUCACACUCCUCCGCCAACC____GAAAGGCGGAAGGAUAAUUCAAAUUGUCCAUUACGCGCAGCUGCCGCUCGAUUUG
..........(((.....)))((.((((((.....................((((((............)))))).(((((((....))))))).......))))))))........... (-23.50 = -25.34 +   1.84)

alignment

secondary structure

dotplot

Window 8

Location	12,942,819 – 12,942,935
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.13
Mean single sequence MFE	-42.76
Consensus MFE	-37.68
Energy contribution	-37.88
Covariance contribution	0.20
Combinations/Pair	1.06
Mean z-score	-1.81
Structure conservation index	0.88
SVM decision value	1.98
SVM RNA-class probability	0.984575
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12942819 116 + 23771897
AUCCUUCCGCCUUUC----GUUUGGCGGAGGAGUGUGAGUAAUAGUUUUGGCAGCCAGCGCCAUUUUGGCCAGGAAAAAUUAUGGAGAUCCAUGAGCCAAGGGCCACUACAUCGACUCCG
.....((((((....----....))))))(((((.((((((.......((((.......))))...(((((.((.....((((((....)))))).))...))))).))).)))))))). ( -44.00)
>DroSec_CAF1 60078 114 + 1
AUCCUUCCGCCUUUC----GUUUGGCGGAGGAGUGUGAGUAAUAGUUUUGGCAGCCAGCGCCAUUUUGGCCAGGA--AUUUAUGGAGAUCCAUGAGCCAAGGGCCACUACAUCGACUCCG
.....((((((....----....))))))(((((.((((((.......((((.......))))...(((((.((.--..((((((....)))))).))...))))).))).)))))))). ( -44.20)
>DroSim_CAF1 64421 118 + 1
AUCCUUCCGCCUUUCAGGUGGUGGGCGGAGGAGUGUGAGUAAUAGUUUUGGCAGCCAGCGCCAUUUUGGCCAGGA--AUUUAUGGAGAUCCAUGAGCCAAGGGCCACUACAUCGACUCCG
.(((.((((((........)))))).)))(((((.((((((.......((((.......))))...(((((.((.--..((((((....)))))).))...))))).))).)))))))). ( -46.10)
>DroEre_CAF1 66324 114 + 1
AUCCGUCCGUCGUUC----CGUUGGCGGAGGAGUGUGAGUAAUAGUUUUGGCAGCCAGCGCCAUUUUGGCCACGA--AUUUAUGGAGAUCCAUGAGCCAAGGGCCACUACAUCGCCUCCG
.....(((((((...----...)))))))((((.(((((((.......((((.......))))...(((((....--.(((((((....))))))).....))))).))).)))))))). ( -43.60)
>DroYak_CAF1 63879 114 + 1
AUCCGUCCGUCUUCC----CGUUGGCGAAGGAGUGUGAGUAAUAGUUUUGGCAGCCAGCGCCAUUUUGGCCAGGA--AUUUAUGGAGAUCCAUGGGCCAAGGGCCACUACAUCGACUCCG
.......((((....----....))))..(((((.((((((.......((((.......))))...(((((.((.--..((((((....)))))).))...))))).))).)))))))). ( -35.90)
>consensus
AUCCUUCCGCCUUUC____GGUUGGCGGAGGAGUGUGAGUAAUAGUUUUGGCAGCCAGCGCCAUUUUGGCCAGGA__AUUUAUGGAGAUCCAUGAGCCAAGGGCCACUACAUCGACUCCG
.....((((((............))))))(((((.((((((.......((((.......))))...(((((.((.....((((((....)))))).))...))))).))).)))))))). (-37.68 = -37.88 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	12,942,819 – 12,942,935
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.13
Mean single sequence MFE	-39.76
Consensus MFE	-35.52
Energy contribution	-35.96
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.05
Structure conservation index	0.89
SVM decision value	2.78
SVM RNA-class probability	0.996969
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12942819 116 - 23771897
CGGAGUCGAUGUAGUGGCCCUUGGCUCAUGGAUCUCCAUAAUUUUUCCUGGCCAAAAUGGCGCUGGCUGCCAAAACUAUUACUCACACUCCUCCGCCAAAC----GAAAGGCGGAAGGAU
.(((((.((.(((((((...(((((..((((....)))).......((.((((.....))).).))..)))))..)))))))))..)))))((((((....----....))))))..... ( -41.50)
>DroSec_CAF1 60078 114 - 1
CGGAGUCGAUGUAGUGGCCCUUGGCUCAUGGAUCUCCAUAAAU--UCCUGGCCAAAAUGGCGCUGGCUGCCAAAACUAUUACUCACACUCCUCCGCCAAAC----GAAAGGCGGAAGGAU
.(((((.((.(((((((...(((((..((((....))))....--.((.((((.....))).).))..)))))..)))))))))..)))))((((((....----....))))))..... ( -41.50)
>DroSim_CAF1 64421 118 - 1
CGGAGUCGAUGUAGUGGCCCUUGGCUCAUGGAUCUCCAUAAAU--UCCUGGCCAAAAUGGCGCUGGCUGCCAAAACUAUUACUCACACUCCUCCGCCCACCACCUGAAAGGCGGAAGGAU
.(((((.((.(((((((...(((((..((((....))))....--.((.((((.....))).).))..)))))..)))))))))..)))))((((((............))))))..... ( -39.90)
>DroEre_CAF1 66324 114 - 1
CGGAGGCGAUGUAGUGGCCCUUGGCUCAUGGAUCUCCAUAAAU--UCGUGGCCAAAAUGGCGCUGGCUGCCAAAACUAUUACUCACACUCCUCCGCCAACG----GAACGACGGACGGAU
.(((((.((.(((((((...(((((.(((((((........))--))))))))))..(((((.....)))))...))))))))).).))))((((((..((----...))..)).)))). ( -40.50)
>DroYak_CAF1 63879 114 - 1
CGGAGUCGAUGUAGUGGCCCUUGGCCCAUGGAUCUCCAUAAAU--UCCUGGCCAAAAUGGCGCUGGCUGCCAAAACUAUUACUCACACUCCUUCGCCAACG----GGAAGACGGACGGAU
.(((((.((.(((((((...((((((...(((...........--))).))))))..(((((.....)))))...)))))))))..)))))((((((..(.----....)..)).)))). ( -35.40)
>consensus
CGGAGUCGAUGUAGUGGCCCUUGGCUCAUGGAUCUCCAUAAAU__UCCUGGCCAAAAUGGCGCUGGCUGCCAAAACUAUUACUCACACUCCUCCGCCAACC____GAAAGGCGGAAGGAU
.(((((....(((((((...(((((..((((....))))..........(((((.........))))))))))..)))))))....)))))((((((............))))))..... (-35.52 = -35.96 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:36 2006