Locus 9383

Sequence ID	3R_DroMel_CAF1
Location	24,906,922 – 24,907,088
Length	166
Max. P	0.991798

overview

Window 9

Location	24,906,922 – 24,907,030
Length	108
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	92.70
Mean single sequence MFE	-31.82
Consensus MFE	-26.77
Energy contribution	-26.65
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-1.36
Structure conservation index	0.84
SVM decision value	0.27
SVM RNA-class probability	0.662486
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24906922 108 + 27905053
GAGUAGCAAAAUGGGCAGAAUCGUAA-------CUGAAGCACAGACGGAACAAAUUCAUUGUUCAUUGUCGGGCUAAACACGUAUUGGCCAUAAAGCGUACAUGUCGCUGGGCCG
(..((((..(((((((((...(((..-------(((.....))))))(((....))).))))))))).....))))..).......((((....((((.......)))).)))). ( -28.00)
>DroSec_CAF1 18596 108 + 1
GAGUAGCAAAAUGGCCAGAAUCGUAA-------CUGAAGCACAGACGGAACAAAUUCAUUGUUCAUUGUCGGGCUAAACACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCG
(..((((...((((((((...(((..-------....(((...(((.((((((.....))))))...)))..)))....)))..))))))))...(((....))).))))..).. ( -31.20)
>DroSim_CAF1 18235 108 + 1
GAGUGGCAAAAUGGCCAGAAUCGUAA-------CUGAAGCACAGACGGAACAAAUUCAUUGUUCAUUGUCGGGCUAAACACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCG
....(((...((((((((...(((..-------....(((...(((.((((((.....))))))...)))..)))....)))..))))))))..((((.......))))..))). ( -34.90)
>DroEre_CAF1 18684 110 + 1
GAGUAGCGAAAUGGCCAGAAUCGUAACUCGUA-----AGCACAGAUGGAACAAAUUUAUUGUUCAUUGUCGGGCUAAACACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCG
((((.((((...........)))).))))...-----(((...(((.((((((.....))))))...)))..)))...........((((....((((.......)))).)))). ( -31.70)
>DroYak_CAF1 18921 114 + 1
GAGUAGCGAAAUGGCCAGAAUCGUAA-UCGUAACUGAAGCACAGACGGAACAAAUUUAUUGUUCAUUGUCGGGCUAAACACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCG
(..((((((.((((((((...(((..-(((....)))(((...(((.((((((.....))))))...)))..)))....)))..))))))))....((....))))))))..).. ( -33.30)
>consensus
GAGUAGCAAAAUGGCCAGAAUCGUAA_______CUGAAGCACAGACGGAACAAAUUCAUUGUUCAUUGUCGGGCUAAACACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCG
..(((((...((((((((...(((.............(((...(((.((((((.....))))))...)))..)))....)))..))))))))...)).)))..(((....))).. (-26.77 = -26.65 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	24,906,955 – 24,907,053
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	97.76
Mean single sequence MFE	-29.70
Consensus MFE	-29.46
Energy contribution	-29.30
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.71
Structure conservation index	0.99
SVM decision value	2.29
SVM RNA-class probability	0.991798
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24906955 98 + 27905053
ACAGACGGAACAAAUUCAUUGUUCAUUGUCGGGCUAAACACGUAUUGGCCAUAAAGCGUACAUGUCGCUGGGCCGGGCCAAUCUGGCCAAAAGAAUCG
...(((.((((((.....))))))...))).((((((.......))))))....((((.......)))).(((((((....))))))).......... ( -30.10)
>DroSec_CAF1 18629 98 + 1
ACAGACGGAACAAAUUCAUUGUUCAUUGUCGGGCUAAACACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCGGGCCAAAAUGGCCAAAAGAAUCG
...(((.((((((.....))))))...)))...............(((((....((((.......)))).)))))((((.....)))).......... ( -29.60)
>DroSim_CAF1 18268 98 + 1
ACAGACGGAACAAAUUCAUUGUUCAUUGUCGGGCUAAACACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCGGGCCAAUCUGGCCAAAAGAAUCG
...(((.((((((.....))))))...))).((((((.......))))))....((((.......)))).(((((((....))))))).......... ( -30.10)
>DroEre_CAF1 18719 98 + 1
ACAGAUGGAACAAAUUUAUUGUUCAUUGUCGGGCUAAACACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCGGGCCAAUCUGGCCAAAAGAAUCG
...(((.((((((.....))))))...))).((((((.......))))))....((((.......)))).(((((((....))))))).......... ( -28.60)
>DroYak_CAF1 18960 98 + 1
ACAGACGGAACAAAUUUAUUGUUCAUUGUCGGGCUAAACACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCGGGCCAAUCUGGCCAAAAGAAUCG
...(((.((((((.....))))))...))).((((((.......))))))....((((.......)))).(((((((....))))))).......... ( -30.10)
>consensus
ACAGACGGAACAAAUUCAUUGUUCAUUGUCGGGCUAAACACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCGGGCCAAUCUGGCCAAAAGAAUCG
...(((.((((((.....))))))...)))...............(((((....((((.......)))).)))))((((.....)))).......... (-29.46 = -29.30 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	24,906,955 – 24,907,053
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	97.76
Mean single sequence MFE	-27.98
Consensus MFE	-26.86
Energy contribution	-27.26
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.12
Structure conservation index	0.96
SVM decision value	-0.02
SVM RNA-class probability	0.525636
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24906955 98 - 27905053
CGAUUCUUUUGGCCAGAUUGGCCCGGCCCAGCGACAUGUACGCUUUAUGGCCAAUACGUGUUUAGCCCGACAAUGAACAAUGAAUUUGUUCCGUCUGU
..........((((.....)))).(((.....((((((((.(((....)))...))))))))..))).(((...((((((.....)))))).)))... ( -27.00)
>DroSec_CAF1 18629 98 - 1
CGAUUCUUUUGGCCAUUUUGGCCCGGCCCAGCGACGUGUACGCUUUAUGGCCAAUACGUGUUUAGCCCGACAAUGAACAAUGAAUUUGUUCCGUCUGU
..........((((.....)))).(((..(((.((((((..(((....)))..)))))))))..))).(((...((((((.....)))))).)))... ( -28.80)
>DroSim_CAF1 18268 98 - 1
CGAUUCUUUUGGCCAGAUUGGCCCGGCCCAGCGACGUGUACGCUUUAUGGCCAAUACGUGUUUAGCCCGACAAUGAACAAUGAAUUUGUUCCGUCUGU
..........((((.....)))).(((..(((.((((((..(((....)))..)))))))))..))).(((...((((((.....)))))).)))... ( -28.80)
>DroEre_CAF1 18719 98 - 1
CGAUUCUUUUGGCCAGAUUGGCCCGGCCCAGCGACGUGUACGCUUUAUGGCCAAUACGUGUUUAGCCCGACAAUGAACAAUAAAUUUGUUCCAUCUGU
((........((((.....)))).(((..(((.((((((..(((....)))..)))))))))..))))).....((((((.....))))))....... ( -26.50)
>DroYak_CAF1 18960 98 - 1
CGAUUCUUUUGGCCAGAUUGGCCCGGCCCAGCGACGUGUACGCUUUAUGGCCAAUACGUGUUUAGCCCGACAAUGAACAAUAAAUUUGUUCCGUCUGU
..........((((.....)))).(((..(((.((((((..(((....)))..)))))))))..))).(((...((((((.....)))))).)))... ( -28.80)
>consensus
CGAUUCUUUUGGCCAGAUUGGCCCGGCCCAGCGACGUGUACGCUUUAUGGCCAAUACGUGUUUAGCCCGACAAUGAACAAUGAAUUUGUUCCGUCUGU
..........((((.....)))).(((..(((.((((((..(((....)))..)))))))))..))).(((...((((((.....)))))).)))... (-26.86 = -27.26 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	24,906,993 – 24,907,088
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	98.74
Mean single sequence MFE	-23.70
Consensus MFE	-23.70
Energy contribution	-23.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.23
Structure conservation index	1.00
SVM decision value	0.34
SVM RNA-class probability	0.696940
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24906993 95 + 27905053
CACGUAUUGGCCAUAAAGCGUACAUGUCGCUGGGCCGGGCCAAUCUGGCCAAAAGAAUCGGGUAACGAAAUCAAAAUAAAAUUGUCGGUUAAAUU
.......(((((....((((.......)))).)))))((((.....)))).......(((.....)))........................... ( -23.70)
>DroSec_CAF1 18667 95 + 1
CACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCGGGCCAAAAUGGCCAAAAGAAUCGGGUAACGAAAUCAAAAUAAAAUUGUCGGUUAAAUU
.......(((((....((((.......)))).)))))((((.....)))).......(((.....)))........................... ( -23.70)
>DroSim_CAF1 18306 95 + 1
CACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCGGGCCAAUCUGGCCAAAAGAAUCGGGUAACGAAAUCAAAAUAAAAUUGUCGGUUAAAUU
.......(((((....((((.......)))).)))))((((.....)))).......(((.....)))........................... ( -23.70)
>DroEre_CAF1 18757 95 + 1
CACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCGGGCCAAUCUGGCCAAAAGAAUCGGGUAACGAAAUCAAAAUAAAAUUGUCGGUUAAAUU
.......(((((....((((.......)))).)))))((((.....)))).......(((.....)))........................... ( -23.70)
>DroYak_CAF1 18998 95 + 1
CACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCGGGCCAAUCUGGCCAAAAGAAUCGGGUAACGAAAUCAAAAUAAAAUUGUCGGUUAAAUU
.......(((((....((((.......)))).)))))((((.....)))).......(((.....)))........................... ( -23.70)
>consensus
CACGUAUUGGCCAUAAAGCGUACACGUCGCUGGGCCGGGCCAAUCUGGCCAAAAGAAUCGGGUAACGAAAUCAAAAUAAAAUUGUCGGUUAAAUU
.......(((((....((((.......)))).)))))((((.....)))).......(((.....)))........................... (-23.70 = -23.70 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:33:16 2006