Locus 6844

Sequence ID	3R_DroMel_CAF1
Location	18,110,748 – 18,110,885
Length	137
Max. P	0.882866

overview

Window 6

Location	18,110,748 – 18,110,847
Length	99
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	89.74
Mean single sequence MFE	-33.38
Consensus MFE	-23.70
Energy contribution	-24.20
Covariance contribution	0.50
Combinations/Pair	1.07
Mean z-score	-2.35
Structure conservation index	0.71
SVM decision value	0.54
SVM RNA-class probability	0.773515
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18110748 99 - 27905053
CACGCCCACUCUGGCUGCUGCGGCUGCUGCAGCUGCAAAGGCUGCUGCAGCAACUGAACUUGCAACAGAAGCACUUCAAGUGUAAAAUUCCUGGCUGCA
...(((...((((..(((..(((.(((((((((.((....)).))))))))).))).....))).)))).((((.....)))).........))).... ( -38.90)
>DroSec_CAF1 141592 96 - 1
CACGCCCACUCUGGCUGCUGCGGCUGCUGCAGCUGCAAAGGCUGUUG---CAACUGAACUUGCAACAGAAGCACUUCAAGUGUAAAAUUCCUGGCUGCA
...(((.......((.(((((((...))))))).))..(((((((((---(((......)))))))))..((((.....))))......)))))).... ( -35.00)
>DroSim_CAF1 146318 96 - 1
CACGCCCACUCUGGCUGCUGCGGCUGCUGCAGCUGCAAAGGCUGUUG---CAACUGAACUUGCAACUGAAGCACUUCAAGUGUAAAAUUCCUGGCUGCA
...(((......((((..((((((((...))))))))..))))((((---(((......)))))))....((((.....)))).........))).... ( -32.30)
>DroEre_CAF1 151519 85 - 1
CACGCCCACUUUAGCUGC---------UGCAGCUGCGAAGGCUGUUG---CAACUGAACUUGCAACAGAAGCACUUCAAGUGUGAAAUUCCUGGCUG--
...((((((((((((((.---------..)))))).((((.((((((---(((......))))))))).....)))))))))..........)))..-- ( -27.30)
>consensus
CACGCCCACUCUGGCUGCUGCGGCUGCUGCAGCUGCAAAGGCUGUUG___CAACUGAACUUGCAACAGAAGCACUUCAAGUGUAAAAUUCCUGGCUGCA
...(((...(((((((((.((....)).)))))(((((...(.((((...)))).)...))))).)))).((((.....)))).........))).... (-23.70 = -24.20 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	18,110,785 – 18,110,885
Length	100
Sequences	4
Columns	100
Reading direction	forward
Mean pairwise identity	91.37
Mean single sequence MFE	-44.52
Consensus MFE	-35.54
Energy contribution	-36.23
Covariance contribution	0.69
Combinations/Pair	1.11
Mean z-score	-2.15
Structure conservation index	0.80
SVM decision value	0.85
SVM RNA-class probability	0.866680
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18110785 100 + 27905053
CAAGUUCAGUUGCUGCAGCAGCCUUUGCAGCUGCAGCAGCCGCAGCAGCCAGAGUGGGCGUGGCUGGCCCGCCCGUCUGGCGAGCGUCGCAUGCAUAAGC
........(((((((((((.((....)).))))))))))).(((((.((((((.((((((.((....))))))))))))))(.....))).)))...... ( -53.60)
>DroSec_CAF1 141629 97 + 1
CAAGUUCAGUUG---CAACAGCCUUUGCAGCUGCAGCAGCCGCAGCAGCCAGAGUGGGCGUGGCUGGCCCGCCCGUCUGGCGAGCGUCGCAUGCAUAAGC
......((((((---(((......)))))))))..(((((.((.((.((((((.((((((.((....))))))))))))))..)))).)).)))...... ( -46.90)
>DroSim_CAF1 146355 97 + 1
CAAGUUCAGUUG---CAACAGCCUUUGCAGCUGCAGCAGCCGCAGCAGCCAGAGUGGGCGUGGCUGGCCCGCCCGUCUGGCGAGCGUCGCAUGCAUAAGC
......((((((---(((......)))))))))..(((((.((.((.((((((.((((((.((....))))))))))))))..)))).)).)))...... ( -46.90)
>DroEre_CAF1 151554 88 + 1
CAAGUUCAGUUG---CAACAGCCUUCGCAGCUGCA---------GCAGCUAAAGUGGGCGUGGCUGGGCCGCCCGUCUGGCGAGCGUCGCAUGCAUAAGC
...(((((((((---(..........))))))).)---------)).(((...((((((((.((..(((.....)))..))..))))).))).....))) ( -30.70)
>consensus
CAAGUUCAGUUG___CAACAGCCUUUGCAGCUGCAGCAGCCGCAGCAGCCAGAGUGGGCGUGGCUGGCCCGCCCGUCUGGCGAGCGUCGCAUGCAUAAGC
........((((...)))).((...(((.(((((.......))))).((((((.((((((.((....))))))))))))))..)))..)).......... (-35.54 = -36.23 +   0.69)

alignment

secondary structure

dotplot

Window 8

Location	18,110,785 – 18,110,885
Length	100
Sequences	4
Columns	100
Reading direction	reverse
Mean pairwise identity	91.37
Mean single sequence MFE	-43.82
Consensus MFE	-35.25
Energy contribution	-35.50
Covariance contribution	0.25
Combinations/Pair	1.07
Mean z-score	-2.17
Structure conservation index	0.80
SVM decision value	0.92
SVM RNA-class probability	0.882866
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18110785 100 - 27905053
GCUUAUGCAUGCGACGCUCGCCAGACGGGCGGGCCAGCCACGCCCACUCUGGCUGCUGCGGCUGCUGCAGCUGCAAAGGCUGCUGCAGCAACUGAACUUG
((....)).......((..((((((.(((((((....)).)))))..)))))).))..(((.(((((((((.((....)).))))))))).)))...... ( -50.20)
>DroSec_CAF1 141629 97 - 1
GCUUAUGCAUGCGACGCUCGCCAGACGGGCGGGCCAGCCACGCCCACUCUGGCUGCUGCGGCUGCUGCAGCUGCAAAGGCUGUUG---CAACUGAACUUG
((....)).(((((((((.((((((.(((((((....)).)))))..))))))...((((((((...))))))))..))).))))---)).......... ( -47.00)
>DroSim_CAF1 146355 97 - 1
GCUUAUGCAUGCGACGCUCGCCAGACGGGCGGGCCAGCCACGCCCACUCUGGCUGCUGCGGCUGCUGCAGCUGCAAAGGCUGUUG---CAACUGAACUUG
((....)).(((((((((.((((((.(((((((....)).)))))..))))))...((((((((...))))))))..))).))))---)).......... ( -47.00)
>DroEre_CAF1 151554 88 - 1
GCUUAUGCAUGCGACGCUCGCCAGACGGGCGGCCCAGCCACGCCCACUUUAGCUGC---------UGCAGCUGCGAAGGCUGUUG---CAACUGAACUUG
((....))..(((..(((((.....)))))(((...))).)))....(((((.(((---------.((((((.....)))))).)---)).))))).... ( -31.10)
>consensus
GCUUAUGCAUGCGACGCUCGCCAGACGGGCGGGCCAGCCACGCCCACUCUGGCUGCUGCGGCUGCUGCAGCUGCAAAGGCUGUUG___CAACUGAACUUG
((((.((((.((.......((((((.(((((((....)).)))))..))))))(((.((....)).))))))))).)))).................... (-35.25 = -35.50 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:20 2006