Locus 10

Sequence ID	2L_DroMel_CAF1
Location	41,324 – 41,460
Length	136
Max. P	0.791148

overview

Window 5

Location	41,324 – 41,426
Length	102
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	81.80
Mean single sequence MFE	-27.93
Consensus MFE	-17.96
Energy contribution	-17.68
Covariance contribution	-0.28
Combinations/Pair	1.21
Mean z-score	-2.30
Structure conservation index	0.64
SVM decision value	0.59
SVM RNA-class probability	0.791148
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 41324 102 + 22407834
UAAG--AUGGCUUGAAAAAGCGGCAUUUCAACAUCGCCUC---------UAAAGCCAUUAAAUUGGUAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUGGCGCAAAUCAUU
...(--(((((((....))))((....))..))))(((((---------(((((((((...((((((....))))))...)))))....)))))).....))).......... ( -27.00)
>DroPse_CAF1 21981 106 + 1
UAAG--UUGGC-----GAGGCGGCAUUUCAACACUGCCUCCGACUUAUUUAAAGCCAUCAAAUUGGCAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUGACGCGAAACAUU
((((--((((.-----.((((((..........))))))))))))))(((((((((((...((((((....))))))...)))))....)))))).................. ( -30.60)
>DroEre_CAF1 18920 102 + 1
UCUU--AUUGCUUGAAAAAGCGGCAUUUCAACACCGCCUC---------UGAAGCUAUAAAAUUGGUAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUGGCGCGAACCAUU
....--.((((((....))))))..........(((((((---------(((((((((...((((((....))))))...)))))....)))))).....)))).)....... ( -24.00)
>DroYak_CAF1 18183 102 + 1
UAAG--AUGGCUGGAAAAGGAGGCAUUUCAACAUCGCCCC---------UGAAGCUAUAAAAUUGGUAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUUGCGCGAACCAUU
....--.(((((.....(((.(((...........)))))---------)...(((((.....((((....)))))))))..))))).......................... ( -21.70)
>DroAna_CAF1 20662 113 + 1
CCAGACUUGGCCAGCCUAGGCGGCAUUUCAACACUGCCUCCGACUUAUUUGAGGCCAUAAAAUUGGCAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUGGCGCGAAACAUU
......(((((((..(((((.((((.........)))).))...........((((((...((((((....))))))...)))))).....))).....)))).)))...... ( -33.70)
>DroPer_CAF1 21741 106 + 1
UAAG--UUGGC-----GAGGCGGCAUUUCAACACUGCCUCCGACUUAUUUAAAGCCAUCAAAUUGGCAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUGACGCGAAACAUU
((((--((((.-----.((((((..........))))))))))))))(((((((((((...((((((....))))))...)))))....)))))).................. ( -30.60)
>consensus
UAAG__AUGGCU_GAAAAGGCGGCAUUUCAACACCGCCUC_________UAAAGCCAUAAAAUUGGCAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUGGCGCGAAACAUU
.........((......((((((..........))))))..............(((((...((((((....))))))...)))))..................))........ (-17.96 = -17.68 +  -0.28)

alignment

secondary structure

dotplot

Window 6

Location	41,324 – 41,426
Length	102
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	81.80
Mean single sequence MFE	-29.80
Consensus MFE	-21.39
Energy contribution	-20.75
Covariance contribution	-0.64
Combinations/Pair	1.23
Mean z-score	-1.40
Structure conservation index	0.72
SVM decision value	0.09
SVM RNA-class probability	0.579530
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 41324 102 - 22407834
AAUGAUUUGCGCCAUUUGUCUAAAUUUGGCCAUGCUAUUGGCGGUUACCAAUUUAAUGGCUUUA---------GAGGCGAUGUUGAAAUGCCGCUUUUUCAAGCCAU--CUUA
..........(((.....(((((....((((((...(((((......)))))...)))))))))---------)))))((((((((((........))))))..)))--)... ( -26.30)
>DroPse_CAF1 21981 106 - 1
AAUGUUUCGCGUCAUUUGUCUAAAUUUGGCCAUGCUAUUGGCGGUUGCCAAUUUGAUGGCUUUAAAUAAGUCGGAGGCAGUGUUGAAAUGCCGCCUC-----GCCAA--CUUA
...(((..((...((((((.(((....((((((...((((((....))))))...))))))))).))))))..(((((.((((....)))).)))))-----)).))--)... ( -29.90)
>DroEre_CAF1 18920 102 - 1
AAUGGUUCGCGCCAUUUGUCUAAAUUUGGCCAUGCUAUUGGCGGUUACCAAUUUUAUAGCUUCA---------GAGGCGGUGUUGAAAUGCCGCUUUUUCAAGCAAU--AAGA
..((((((((((((..(......)..))))((......))))))..)))).((((((.((((.(---------((((((((((....)))))))))))..)))).))--)))) ( -32.40)
>DroYak_CAF1 18183 102 - 1
AAUGGUUCGCGCAAUUUGUCUAAAUUUGGCCAUGCUAUUGGCGGUUACCAAUUUUAUAGCUUCA---------GGGGCGAUGUUGAAAUGCCUCCUUUUCCAGCCAU--CUUA
.((((((.(((((....(((.......)))..))).(((((......)))))......))...(---------((((((.(.....).)))).))).....))))))--.... ( -20.30)
>DroAna_CAF1 20662 113 - 1
AAUGUUUCGCGCCAUUUGUCUAAAUUUGGCCAUGCUAUUGGCGGUUGCCAAUUUUAUGGCCUCAAAUAAGUCGGAGGCAGUGUUGAAAUGCCGCCUAGGCUGGCCAAGUCUGG
...................(((.(((((((((.(((...((((((...((((......(((((..........)))))...))))....))))))..)))))))))))).))) ( -40.00)
>DroPer_CAF1 21741 106 - 1
AAUGUUUCGCGUCAUUUGUCUAAAUUUGGCCAUGCUAUUGGCGGUUGCCAAUUUGAUGGCUUUAAAUAAGUCGGAGGCAGUGUUGAAAUGCCGCCUC-----GCCAA--CUUA
...(((..((...((((((.(((....((((((...((((((....))))))...))))))))).))))))..(((((.((((....)))).)))))-----)).))--)... ( -29.90)
>consensus
AAUGUUUCGCGCCAUUUGUCUAAAUUUGGCCAUGCUAUUGGCGGUUACCAAUUUUAUGGCUUCA_________GAGGCAGUGUUGAAAUGCCGCCUUUUC_AGCCAA__CUUA
........((((((..(......)..)))).........((((((...((((......(((((..........)))))...))))....)))))).......))......... (-21.39 = -20.75 +  -0.64)

alignment

secondary structure

dotplot

Window 7

Location	41,362 – 41,460
Length	98
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	84.19
Mean single sequence MFE	-29.77
Consensus MFE	-18.31
Energy contribution	-18.03
Covariance contribution	-0.28
Combinations/Pair	1.15
Mean z-score	-3.02
Structure conservation index	0.62
SVM decision value	0.18
SVM RNA-class probability	0.620098
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 41362 98 + 22407834
---------UAAAGCCAUUAAAUUGGUAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUGGCGCAAAUCAUUGCACUAAUUGCCACCUCGUUUGG------CAGCGUCAAAU
---------....(((((...((((((....))))))...)))))........(((...(((.((((....)))).))).((((((.......)))------))).))).... ( -27.30)
>DroPse_CAF1 22014 113 + 1
CGACUUAUUUAAAGCCAUCAAAUUGGCAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUGACGCGAAACAUUGCACUAAUUGCCACCUCGUUUGGUGGCAACAUCGUCGAAU
((((...(((((((((((...((((((....))))))...)))))....))))))...(((..((((....)))).....((((((((......))))))))))).))))... ( -36.50)
>DroEre_CAF1 18958 98 + 1
---------UGAAGCUAUAAAAUUGGUAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUGGCGCGAACCAUUGCACUAAUUGCCACCUCGUUCGG------CACCGUCAACC
---------....(((((...((((((....))))))...)))))........(((...(((.((((....)))).)))..((((.........))------))..))).... ( -22.70)
>DroYak_CAF1 18221 98 + 1
---------UGAAGCUAUAAAAUUGGUAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUUGCGCGAACCAUUGCACUAAUUGCCACCUCGUUCGG------CAGCGUCAAAC
---------....(((((...((((((....))))))...)))))........(((...((((.(((((....(((.....)))......))))))------))).))).... ( -23.00)
>DroAna_CAF1 20702 105 + 1
CGACUUAUUUGAGGCCAUAAAAUUGGCAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUGGCGCGAAACAUUGCACUAAUUGCCACCUCGUUUGG------CAGCCGC--AU
............((((((...((((((....))))))...))))))..............(((((((....))))......(((((.......)))------)))))..--.. ( -32.60)
>DroPer_CAF1 21774 113 + 1
CGACUUAUUUAAAGCCAUCAAAUUGGCAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUGACGCGAAACAUUGCACUAAUUGCCACCUCGUUUGGUGGCAACAUCGUCGAAU
((((...(((((((((((...((((((....))))))...)))))....))))))...(((..((((....)))).....((((((((......))))))))))).))))... ( -36.50)
>consensus
_________UAAAGCCAUAAAAUUGGCAACCGCCAAUAGCAUGGCCAAAUUUAGACAAAUGGCGCGAAACAUUGCACUAAUUGCCACCUCGUUUGG______CAGCGUCAAAU
.............(((((...((((((....))))))...)))))........(((.......((((....))))...........((......))..........))).... (-18.31 = -18.03 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:23:11 2006