Locus 7264

Sequence ID	3R_DroMel_CAF1
Location	19,192,543 – 19,192,750
Length	207
Max. P	0.957075

overview

Window 4

Location	19,192,543 – 19,192,639
Length	96
Sequences	3
Columns	104
Reading direction	reverse
Mean pairwise identity	80.86
Mean single sequence MFE	-24.70
Consensus MFE	-18.00
Energy contribution	-18.33
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.59
Structure conservation index	0.73
SVM decision value	0.18
SVM RNA-class probability	0.622601
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19192543 96 - 27905053
UUGAGCUGUAAUUGAAUUGCAGUUGCACUCAGGACUCCAUUGGGCCACUAUACGAUGGGUUAGGAGACUACCUUUGUUGGGAAAAUUAGAAA--------AAAA
.((((.((((((((.....))))))))))))((.(((....))))).(((.((((.((((.((....)))))))))))))............--------.... ( -26.10)
>DroEre_CAF1 5828 95 - 1
UUGAGCUGUAAUUGAAUUGCAGUUGCACUCAGGAU---GUU-GGCCACUAUACGAUGGGUUAAGAGUCUACCUUUGUGCGGAAAAUCA----AAUAAUUU-GUA
((((((((((((...))))))))(((((..(((.(---.((-((((.(........))))))).).....)))..))))).....)))----).......-... ( -22.30)
>DroYak_CAF1 8506 95 - 1
UUGAGCUGUAAUUGAAUUGCAGUUGCACUCAGGAU---AUU-GGCCACUAUACGAUGGGUUAAGAGUCCACCUUUGUGCGGAAAAUAA----AAUAGUUU-UCA
.((((.((((((((.....))))))))))))((((---.((-((((.(........)))))))..))))...........((((((..----....))))-)). ( -25.70)
>consensus
UUGAGCUGUAAUUGAAUUGCAGUUGCACUCAGGAU___AUU_GGCCACUAUACGAUGGGUUAAGAGUCUACCUUUGUGCGGAAAAUAA____AAUA_UUU_AAA
(((((.((((((((.....)))))))))))))...............((.(((((.((((.........))))))))).))....................... (-18.00 = -18.33 +   0.33)

alignment

secondary structure

dotplot

Window 5

Location	19,192,572 – 19,192,670
Length	98
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	89.41
Mean single sequence MFE	-32.02
Consensus MFE	-27.80
Energy contribution	-27.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.80
Structure conservation index	0.87
SVM decision value	1.47
SVM RNA-class probability	0.957075
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19192572 98 - 27905053
AUGGCCAUGGCUCUCUGCCGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCAGUUGCACUCAGGACUCC--------AUUGGGCCAC-UAUACGAUGGGUUAGGAGA
(((((..((((.....))))..))))).....(((((((((((...))))))))).))(((..(((.((--------((((......-....)))))))))..))). ( -34.50)
>DroSec_CAF1 4557 107 - 1
AUGGCCAUGGCUCUCUGCCGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCAGUUGCACUCAGGACUCCAAUGCACUAUUGGGCCACUUAUACGAUGGGUUAAAACA
(((((..((((.....))))..))))).....((((.((((((((.....))))))))))))((.(.((((((...)))))))))((((((...))))))....... ( -31.70)
>DroSim_CAF1 4919 107 - 1
AUGGCCAUGGCUCUCUGCCGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCAGUUGCACUCAGGACUCCAAUGCACUAUUGGGCCACUUAUACGAUGGGUUAGGACA
(((((..((((.....))))..)))))....(((((.((((((((.....)))))))))))))...(((...((.((((((...........))))))))..))).. ( -33.50)
>DroEre_CAF1 5860 94 - 1
AUGGCCAUGGCUCUCUGCCGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCAGUUGCACUCAGGAU-----------GUU-GGCCAC-UAUACGAUGGGUUAAGAGU
(((((..((((.....))))..)))))....(((((.((((((((.....)))))))))))))..(-----------.((-((((.(-........))))))).).. ( -30.40)
>DroYak_CAF1 8538 94 - 1
AUGGCCAUGGCUCUCUGCCGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCAGUUGCACUCAGGAU-----------AUU-GGCCAC-UAUACGAUGGGUUAAGAGU
(((((..((((.....))))..)))))....(((((.((((((((.....)))))))))))))...-----------.((-((((.(-........))))))).... ( -30.00)
>consensus
AUGGCCAUGGCUCUCUGCCGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCAGUUGCACUCAGGACUCC________AUUGGGCCAC_UAUACGAUGGGUUAAGAGA
.((((((((((...........)))))....(((((.((((((((.....)))))))))))))..................)))))..................... (-27.80 = -27.80 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	19,192,603 – 19,192,710
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	93.82
Mean single sequence MFE	-36.17
Consensus MFE	-31.03
Energy contribution	-30.76
Covariance contribution	-0.28
Combinations/Pair	1.07
Mean z-score	-1.93
Structure conservation index	0.86
SVM decision value	0.88
SVM RNA-class probability	0.873142
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19192603 107 - 27905053
CGCGGCGGUUCCAUAAACAAAUUGUCGCCGUGCUCUCUAAAUGGCCAUGGCUCUC---------UGCCGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCAGU----UGCACUCAGGACU
((((((((................))))))))........(((((..((((....---------.))))..)))))....(((((.((((((((.....))))----))))))))).... ( -36.29)
>DroSec_CAF1 4597 107 - 1
CGCGGCGGUUCCAUAAACAAAUUGUCGCCGUGCUCUCUAAAUGGCCAUGGCUCUC---------UGCCGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCAGU----UGCACUCAGGACU
((((((((................))))))))........(((((..((((....---------.))))..)))))....(((((.((((((((.....))))----))))))))).... ( -36.29)
>DroSim_CAF1 4959 107 - 1
CGCGGCGGUUCCAUAAACAAAUUGUCGCCGUGCUCUCUAAAUGGCCAUGGCUCUC---------UGCCGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCAGU----UGCACUCAGGACU
((((((((................))))))))........(((((..((((....---------.))))..)))))....(((((.((((((((.....))))----))))))))).... ( -36.29)
>DroEre_CAF1 5888 106 - 1
CGCGGCGGUUCCAUAAACAAAUUGUCGCCGUGCUCUCUAAAUGGCCAUGGCUCUC---------UGCCGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCAGU----UGCACUCAGGAU-
((((((((................))))))))........(((((..((((....---------.))))..)))))....(((((.((((((((.....))))----)))))))))...- ( -36.29)
>DroYak_CAF1 8566 106 - 1
CGCGGCGGUUCCAUAAACAAAUUGUCGCCGUGCUCUCUAAAUGGCCAUGGCUCUC---------UGCCGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCAGU----UGCACUCAGGAU-
((((((((................))))))))........(((((..((((....---------.))))..)))))....(((((.((((((((.....))))----)))))))))...- ( -36.29)
>DroAna_CAF1 10666 119 - 1
CGCGGCGGUUCCAUAAACAAAUUGUCGCCGGGCUCUCUAAAUGGCCAUGGCUCUCAGUGGCUGCUGCUGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCACUGCACUGUACUCAGGAU-
.((((((((..((.........))..))))((((........))))(((((((...(((((.((....)).)))))......)))))))............)))).(((....)))...- ( -35.60)
>consensus
CGCGGCGGUUCCAUAAACAAAUUGUCGCCGUGCUCUCUAAAUGGCCAUGGCUCUC_________UGCCGCUGCCAUGAAAUUGAGCUGUAAUUGAAUUGCAGU____UGCACUCAGGAC_
.(((((((((.........)))))))))...((((.....(((((..((((..............))))..)))))......)))).....((((..((((......)))).)))).... (-31.03 = -30.76 +  -0.28)

alignment

secondary structure

dotplot

Window 7

Location	19,192,639 – 19,192,750
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	95.03
Mean single sequence MFE	-39.02
Consensus MFE	-33.14
Energy contribution	-33.64
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.32
Structure conservation index	0.85
SVM decision value	1.33
SVM RNA-class probability	0.942532
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19192639 111 - 27905053
GCCAAGAGCGAGUGAUUUAUGCACCGCACCAUUUAAAGUCCGCGGCGGUUCCAUAAACAAAUUGUCGCCGUGCUCUCUAAAUGGCCAUGGCUCUC---------UGCCGCUGCCAUGAAA
.......(((.(((.......)))))).(((((((.((..((((((((................))))))))..)).))))))).((((((....---------.......))))))... ( -36.69)
>DroSec_CAF1 4633 111 - 1
GCCAAGAGCGAGUGAUUUAUGCACCGCACCAUUUAAAGUCCGCGGCGGUUCCAUAAACAAAUUGUCGCCGUGCUCUCUAAAUGGCCAUGGCUCUC---------UGCCGCUGCCAUGAAA
.......(((.(((.......)))))).(((((((.((..((((((((................))))))))..)).))))))).((((((....---------.......))))))... ( -36.69)
>DroSim_CAF1 4995 111 - 1
GCCAAGAGCGAGUGAUUUAUGCACCGCACCAUUUAAAGUCCGCGGCGGUUCCAUAAACAAAUUGUCGCCGUGCUCUCUAAAUGGCCAUGGCUCUC---------UGCCGCUGCCAUGAAA
.......(((.(((.......)))))).(((((((.((..((((((((................))))))))..)).))))))).((((((....---------.......))))))... ( -36.69)
>DroEre_CAF1 5923 111 - 1
GCCAGAAGCGAGUGAUUUAUGCACCGCACCAUUUAAAGUCCGCGGCGGUUCCAUAAACAAAUUGUCGCCGUGCUCUCUAAAUGGCCAUGGCUCUC---------UGCCGCUGCCAUGAAA
.......(((.(((.......)))))).(((((((.((..((((((((................))))))))..)).))))))).((((((....---------.......))))))... ( -36.69)
>DroYak_CAF1 8601 111 - 1
GCCAAGAGCGAGUGAUUUAUGCACCGCACCAUUUAAAGUCCGCGGCGGUUCCAUAAACAAAUUGUCGCCGUGCUCUCUAAAUGGCCAUGGCUCUC---------UGCCGCUGCCAUGAAA
.......(((.(((.......)))))).(((((((.((..((((((((................))))))))..)).))))))).((((((....---------.......))))))... ( -36.69)
>DroAna_CAF1 10705 120 - 1
GCCGAGAGCGAGUGAUUUAUGCUCCGGUCCAUUUAAAGUCCGCGGCGGUUCCAUAAACAAAUUGUCGCCGGGCUCUCUAAAUGGCCAUGGCUCUCAGUGGCUGCUGCUGCUGCCAUGAAA
...((((((((((.......)))).((.(((((((.((((((((((((((.........)))))))).))))))...)))))))))...)))))).(((((.((....)).))))).... ( -50.70)
>consensus
GCCAAGAGCGAGUGAUUUAUGCACCGCACCAUUUAAAGUCCGCGGCGGUUCCAUAAACAAAUUGUCGCCGUGCUCUCUAAAUGGCCAUGGCUCUC_________UGCCGCUGCCAUGAAA
.......(((.(((.......)))))).(((((((.((..((((((((................))))))))..)).))))))).((((((....................))))))... (-33.14 = -33.64 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:38 2006