Locus 6560

Sequence ID	2R_DroMel_CAF1
Location	20,519,048 – 20,519,196
Length	148
Max. P	0.920842

overview

Window 3

Location	20,519,048 – 20,519,168
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.82
Mean single sequence MFE	-39.42
Consensus MFE	-29.42
Energy contribution	-30.90
Covariance contribution	1.48
Combinations/Pair	1.09
Mean z-score	-1.83
Structure conservation index	0.75
SVM decision value	0.45
SVM RNA-class probability	0.740639
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20519048 120 + 20766785
GCCGUUUUGCCGACCGAGUACUUUUCGAGUUCGAUGGUAAUCGAUGCCUUCCGAUUCCAUUCGGACAUAUCGAUGCAUCGAUAUGUCGUAGUUCACACGACGGCCGCGGCAGCGCUUUCU
(((((...(((.((((((.....)))).))((((((...(((((((...(((((......)))))..))))))).))))))...(((((.(....))))))))).))))).......... ( -43.00)
>DroSec_CAF1 20714 120 + 1
GCCGUUUUGCCGACCGAGUACUUUUCGAGUCCGAUGGUAAUCGAUGCCUUCCGAUUCCGUUCGGACAUAUCGAUGCAUCGAUAUGUUUUAGUACACAAGGCGGCCACGGCAGCGCUUUGA
(((((...((((.((..(((((......(((((((((.(((((........)))))))).))))))(((((((....))))))).....)))))....)))))).))))).......... ( -46.80)
>DroSim_CAF1 20652 120 + 1
GCCGUUUUGCCGACCGAGUACUUUUCGAGUCCGAUGGUAAUCGAUGCCUUCCGAUUCCGUUCGGACAUAUCGAUGCAUCGAUAUGUUUUAGUACACAAGGCGGCCACGGCAGCGCUUUGA
(((((...((((.((..(((((......(((((((((.(((((........)))))))).))))))(((((((....))))))).....)))))....)))))).))))).......... ( -46.80)
>DroEre_CAF1 20891 110 + 1
G--------CCGACCGAGUACUUUUCGAGUUCGAUGGUAAUCGAUGCCUUCCGAUUUCUUCCACA--UAUCGAUGCAUCGAUACGAUUUAGUUCGUCACGCGGCCGCAGCAGCGCUUUGU
(--------(((......((((..(((....))).))))((((((((....((((..........--.))))..))))))))((((......))))....))))(((....)))...... ( -28.30)
>DroYak_CAF1 20914 119 + 1
GUCGUUUAGCCGACCGAGUACUUUUCGAGUUCGAUGGUAAUCGAUGCCUUCCGAUUACCUUCGCAC-UAUCGAUGCAUCGAUUCUAUUUAGUUCAUCACGCGGCCGCAGCAGCGCUUUGU
........((((..((((.....))))(((.(((.((((((((........)))))))).))).))-)...((((.((..(......)..)).))))...))))(((....)))...... ( -32.20)
>consensus
GCCGUUUUGCCGACCGAGUACUUUUCGAGUUCGAUGGUAAUCGAUGCCUUCCGAUUCCGUUCGGACAUAUCGAUGCAUCGAUAUGUUUUAGUUCACAAGGCGGCCGCGGCAGCGCUUUGU
(((((...((((((((((.....)))).)))(((((...(((((((...(((((......)))))..))))))).))))).....................))).))))).......... (-29.42 = -30.90 +   1.48)

alignment

secondary structure

dotplot

Window 4

Location	20,519,048 – 20,519,168
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.82
Mean single sequence MFE	-39.98
Consensus MFE	-28.18
Energy contribution	-27.94
Covariance contribution	-0.24
Combinations/Pair	1.11
Mean z-score	-2.26
Structure conservation index	0.70
SVM decision value	0.82
SVM RNA-class probability	0.858254
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20519048 120 - 20766785
AGAAAGCGCUGCCGCGGCCGUCGUGUGAACUACGACAUAUCGAUGCAUCGAUAUGUCCGAAUGGAAUCGGAAGGCAUCGAUUACCAUCGAACUCGAAAAGUACUCGGUCGGCAAAACGGC
..........((((..(((((((.(((......((((((((((....))))))))))(((.(((((((((......)))))).))))))...........))).))).))))....)))) ( -41.70)
>DroSec_CAF1 20714 120 - 1
UCAAAGCGCUGCCGUGGCCGCCUUGUGUACUAAAACAUAUCGAUGCAUCGAUAUGUCCGAACGGAAUCGGAAGGCAUCGAUUACCAUCGGACUCGAAAAGUACUCGGUCGGCAAAACGGC
..........(((((.((((((....(((((.....(((((((....)))))))((((((..((((((((......)))))).)).))))))......)))))..)).))))...))))) ( -44.90)
>DroSim_CAF1 20652 120 - 1
UCAAAGCGCUGCCGUGGCCGCCUUGUGUACUAAAACAUAUCGAUGCAUCGAUAUGUCCGAACGGAAUCGGAAGGCAUCGAUUACCAUCGGACUCGAAAAGUACUCGGUCGGCAAAACGGC
..........(((((.((((((....(((((.....(((((((....)))))))((((((..((((((((......)))))).)).))))))......)))))..)).))))...))))) ( -44.90)
>DroEre_CAF1 20891 110 - 1
ACAAAGCGCUGCUGCGGCCGCGUGACGAACUAAAUCGUAUCGAUGCAUCGAUA--UGUGGAAGAAAUCGGAAGGCAUCGAUUACCAUCGAACUCGAAAAGUACUCGGUCGG--------C
......(((....)))(((((.(..(((.((....((((((((....))))))--))....))...)))..).))(((((.(((..(((....)))...))).))))).))--------) ( -31.10)
>DroYak_CAF1 20914 119 - 1
ACAAAGCGCUGCUGCGGCCGCGUGAUGAACUAAAUAGAAUCGAUGCAUCGAUA-GUGCGAAGGUAAUCGGAAGGCAUCGAUUACCAUCGAACUCGAAAAGUACUCGGUCGGCUAAACGAC
....(((((....))(((((.(((.............(((((((((.(((((.-.(((....))))))))...)))))))))....(((....)))....))).))))).)))....... ( -37.30)
>consensus
ACAAAGCGCUGCCGCGGCCGCCUUGUGAACUAAAACAUAUCGAUGCAUCGAUAUGUCCGAACGGAAUCGGAAGGCAUCGAUUACCAUCGAACUCGAAAAGUACUCGGUCGGCAAAACGGC
.......(((((((.(..(...................((((((((.(((((...(((....))))))))...)))))))).....(((....)))...)..).))).))))........ (-28.18 = -27.94 +  -0.24)

alignment

secondary structure

dotplot

Window 5

Location	20,519,088 – 20,519,196
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	73.90
Mean single sequence MFE	-33.76
Consensus MFE	-20.90
Energy contribution	-21.58
Covariance contribution	0.68
Combinations/Pair	1.17
Mean z-score	-1.84
Structure conservation index	0.62
SVM decision value	1.14
SVM RNA-class probability	0.920842
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20519088 108 - 20766785
GUG------------UUGACAUAUCGAUGUAUGUGUUUUCAGAAAGCGCUGCCGCGGCCGUCGUGUGAACUACGACAUAUCGAUGCAUCGAUAUGUCCGAAUGGAAUCGGAAGGCAUCGA
(((------------((..(((((((((((((((((((.....)))))).((....)).((((((....).)))))......)))))))))))))(((((......))))).)))))... ( -37.80)
>DroSec_CAF1 20754 102 - 1
GUG----------ACUUCACAAUUCGAUGAG--------CUCAAAGCGCUGCCGUGGCCGCCUUGUGUACUAAAACAUAUCGAUGCAUCGAUAUGUCCGAACGGAAUCGGAAGGCAUCGA
(((----------....)))...((((((.(--------(.(((.(((..((....))))).))).)).((....((((((((....))))))))(((((......))))))).)))))) ( -32.50)
>DroSim_CAF1 20692 102 - 1
GUG----------ACUUCACAAUUCGAUGAG--------CUCAAAGCGCUGCCGUGGCCGCCUUGUGUACUAAAACAUAUCGAUGCAUCGAUAUGUCCGAACGGAAUCGGAAGGCAUCGA
(((----------....)))...((((((.(--------(.(((.(((..((....))))).))).)).((....((((((((....))))))))(((((......))))))).)))))) ( -32.50)
>DroEre_CAF1 20923 110 - 1
UUGGUAAAAUAUGUAUGGAUGUGUCGAUAAG--------CACAAAGCGCUGCUGCGGCCGCGUGACGAACUAAAUCGUAUCGAUGCAUCGAUA--UGUGGAAGAAAUCGGAAGGCAUCGA
.........(((((((.(((((((((((...--------......((((.((....)).)))).((((......))))))))))))))).)))--))))...((..((....))..)).. ( -34.20)
>DroYak_CAF1 20954 109 - 1
UUGG--AUGUGUGUCUUAACAACUCGGUAAG--------CACAAAGCGCUGCUGCGGCCGCGUGAUGAACUAAAUAGAAUCGAUGCAUCGAUA-GUGCGAAGGUAAUCGGAAGGCAUCGA
((((--...((((.((((.(.....).))))--------))))..((((.((....)).))))......))))......(((((((.(((((.-.(((....))))))))...))))))) ( -31.80)
>consensus
GUG__________ACUUCACAAUUCGAUGAG________CACAAAGCGCUGCCGCGGCCGCCUUGUGAACUAAAACAUAUCGAUGCAUCGAUAUGUCCGAACGGAAUCGGAAGGCAUCGA
.......................(((((..................(((....)))(((................((((((((....))))))))(((((......))))).)))))))) (-20.90 = -21.58 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:51 2006