Locus 5741

Sequence ID	3R_DroMel_CAF1
Location	14,954,969 – 14,955,117
Length	148
Max. P	0.846921

overview

Window 7

Location	14,954,969 – 14,955,067
Length	98
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	80.66
Mean single sequence MFE	-30.61
Consensus MFE	-20.49
Energy contribution	-19.44
Covariance contribution	-1.05
Combinations/Pair	1.29
Mean z-score	-1.49
Structure conservation index	0.67
SVM decision value	0.21
SVM RNA-class probability	0.636001
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14954969 98 + 27905053
AAAGUC---------CGCAUCGACUGCCAACAGCAGGACCAGCACCUUUGAGCGUAUACCCCAAAAGAAAAGCGAGCCGAAGAUGUCGAUCUCCAGCAAACUGGAGA
...(((---------.(((((..((((.....))))..........((((.((......................))))))))))).)))((((((....)))))). ( -23.25)
>DroPse_CAF1 4636 107 + 1
AAAAUCAUUGAAUGUGGCCUCCACGGCCAACAGUCGGACGAGCACCUUUGAGCGCCAGCCGCAGAAGAAGAACGAGCCGAAGAUGGCCAUCUCCAGCAAGCUGGAGA
.............((((...))))(((((....((((.((..(..((((..(((.....))).))))..)..))..))))...))))).(((((((....))))))) ( -36.80)
>DroEre_CAF1 21865 98 + 1
AAAGUC---------CGCAUCGACUGCCAACAGCAGGACGAGCACCUUUGAGCGCAUACCCCAAAAGAAGAGCGAGUCGAAGAUGUCCAUCUCCAGCAAACUGGAGA
......---------.((.(((.((((.....))))..)))))..((((((.(((................)))..)))))).......(((((((....))))))) ( -28.39)
>DroYak_CAF1 5489 98 + 1
AAAGUC---------CGCAUCGGCUGCCAACAGUAGGACCAGCACAUUUGAGCGCGCGCCCCAAAAGAAUAGCGAAGCGAAGAUGUCCAUCUCCAGCAAACUGGAGA
...(((---------(......((((....)))).))))..(.((((((..((...(((............)))..))..)))))).).(((((((....))))))) ( -29.10)
>DroAna_CAF1 5361 98 + 1
CAAGGC---------GGCCUCCACGGCCAAUAGUCGGACCAGCACCUUUGAGCGCCAGCCCCAGAAGAUGAGUGAACCGAAGAUGUCGAUUUCCAGCAAGUUGGAAA
...(((---------((((.....)))).((..((((..((.((.((((..((....))....)))).))..))..))))..)))))..(((((((....))))))) ( -27.90)
>DroPer_CAF1 4640 107 + 1
AAAAUCAUUGAAUGUGGCCUCCACGGCCAACAGUCGGACGAGCACCUUUGAGCGCCAGCCGCAGAAGAAGAGCGAGCCGAAGAUGGCCAUCUCCAGCAAGCUGGAGA
.............((((...))))(((((....((((.((..(..((((..(((.....))).))))..)..))..))))...))))).(((((((....))))))) ( -38.20)
>consensus
AAAGUC_________CGCAUCCACGGCCAACAGUAGGACCAGCACCUUUGAGCGCCAGCCCCAAAAGAAGAGCGAGCCGAAGAUGUCCAUCUCCAGCAAACUGGAGA
................((.....((((.....)))).....))..(((((..(((................)))...))))).......(((((((....))))))) (-20.49 = -19.44 +  -1.05)

alignment

secondary structure

dotplot

Window 8

Location	14,954,969 – 14,955,067
Length	98
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	80.66
Mean single sequence MFE	-37.19
Consensus MFE	-22.33
Energy contribution	-22.00
Covariance contribution	-0.33
Combinations/Pair	1.17
Mean z-score	-2.00
Structure conservation index	0.60
SVM decision value	0.42
SVM RNA-class probability	0.730525
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14954969 98 - 27905053
UCUCCAGUUUGCUGGAGAUCGACAUCUUCGGCUCGCUUUUCUUUUGGGGUAUACGCUCAAAGGUGCUGGUCCUGCUGUUGGCAGUCGAUGCG---------GACUUU
(((((((....)))))))(((.((((...((((.((....(((((((((....).)))))))).)).))))((((.....))))..))))))---------)..... ( -36.00)
>DroPse_CAF1 4636 107 - 1
UCUCCAGCUUGCUGGAGAUGGCCAUCUUCGGCUCGUUCUUCUUCUGCGGCUGGCGCUCAAAGGUGCUCGUCCGACUGUUGGCCGUGGAGGCCACAUUCAAUGAUUUU
(((((((....)))))))(((((.(((.(((((..(..........((((.((((((....)))))).).)))...)..))))).)))))))).............. ( -41.22)
>DroEre_CAF1 21865 98 - 1
UCUCCAGUUUGCUGGAGAUGGACAUCUUCGACUCGCUCUUCUUUUGGGGUAUGCGCUCAAAGGUGCUCGUCCUGCUGUUGGCAGUCGAUGCG---------GACUUU
(((((((....))))))).(..((((((.((..(((.((((....))))...))).)).))))))..)((((.((.((((.....)))))))---------)))... ( -34.30)
>DroYak_CAF1 5489 98 - 1
UCUCCAGUUUGCUGGAGAUGGACAUCUUCGCUUCGCUAUUCUUUUGGGGCGCGCGCUCAAAUGUGCUGGUCCUACUGUUGGCAGCCGAUGCG---------GACUUU
(((((((....))))))).((((.....(((((((.........))))))).((((......))))..))))....(((.(((.....))).---------)))... ( -35.00)
>DroAna_CAF1 5361 98 - 1
UUUCCAACUUGCUGGAAAUCGACAUCUUCGGUUCACUCAUCUUCUGGGGCUGGCGCUCAAAGGUGCUGGUCCGACUAUUGGCCGUGGAGGCC---------GCCUUG
((((((......))))))...........(((..............((((..(((((....)))))..)))).......((((.....))))---------)))... ( -32.90)
>DroPer_CAF1 4640 107 - 1
UCUCCAGCUUGCUGGAGAUGGCCAUCUUCGGCUCGCUCUUCUUCUGCGGCUGGCGCUCAAAGGUGCUCGUCCGACUGUUGGCCGUGGAGGCCACAUUCAAUGAUUUU
(((((((....)))))))(((((.(((.(((((.((..........((((.((((((....)))))).).)))...)).))))).)))))))).............. ( -43.72)
>consensus
UCUCCAGCUUGCUGGAGAUGGACAUCUUCGGCUCGCUCUUCUUCUGGGGCUGGCGCUCAAAGGUGCUCGUCCGACUGUUGGCAGUCGAGGCC_________GACUUU
(((((((....)))))))............................((((..((((......))))..))))........(((.....)))................ (-22.33 = -22.00 +  -0.33)

alignment

secondary structure

dotplot

Window 9

Location	14,955,027 – 14,955,117
Length	90
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	80.03
Mean single sequence MFE	-35.38
Consensus MFE	-23.84
Energy contribution	-23.87
Covariance contribution	0.03
Combinations/Pair	1.35
Mean z-score	-1.89
Structure conservation index	0.67
SVM decision value	0.77
SVM RNA-class probability	0.846921
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14955027 90 - 27905053
ACUGCUGCGCUGGGCAGC---AUCCGCUGCAUCC---AUGGAUCGCUGCUCGAAGAUCUCCAGUUUGCUGGAGAUCGACAUCUUCGGCUCGCUUUU
...((.(.((((((((((---(((((.((....)---)))))).)))))))(..(((((((((....)))))))))..)......))).))).... ( -38.90)
>DroPse_CAF1 4703 93 - 1
GCUGCUGCGCUGGGCCGCCGUGUCCGUGGCAUCG---CUGGAUCGCUGCUCGAAGAUCUCCAGCUUGCUGGAGAUGGCCAUCUUCGGCUCGUUCUU
...((((.....((((((.(((((((((....))---).))).))).))......((((((((....)))))))))))).....))))........ ( -37.30)
>DroGri_CAF1 4725 90 - 1
GCUGCUGCGCUGAGCGCU---GUCCGUGCUGUCG---UGGGCUCGCUGCUCGAAGAUCUCCAGCUUGCUGGAUAUGGACAUCUUUGUCUCAGCUUU
((....))((((((((.(---(((((((..(((.---(((((.....)))))..))).(((((....)))))))))))))....)).))))))... ( -33.70)
>DroEre_CAF1 21923 90 - 1
ACUGCUUCGCUGGGCAGC---AUCCGCUGCAUCC---AUGGAUCGUUGCUCGAAGAUCUCCAGUUUGCUGGAGAUGGACAUCUUCGACUCGCUCUU
........((.(((((((---(((((.((....)---)))))).)))))((((((((((((((....)))))))......))))))))).)).... ( -32.50)
>DroAna_CAF1 5419 93 - 1
GCUGCUCCUUUGGGCAGC---AUCUGUGGCGUCGUUGGUGGAACGCUGCUCGAAGAUUUCCAACUUGCUGGAAAUCGACAUCUUCGGUUCACUCAU
(((((((....)))))))---....((((.(((.((((..(....)..).))).((((((((......)))))))))))..(....).)))).... ( -30.90)
>DroPer_CAF1 4707 93 - 1
GCUGCUGCGCUGGGCCGCCGUGUCCGUGGCAUCG---CUGGAUCGCUGCUCGAAGAUCUCCAGCUUGCUGGAGAUGGCCAUCUUCGGCUCGCUCUU
((.((((.....((((((.(((((((((....))---).))).))).))......((((((((....)))))))))))).....))))..)).... ( -39.00)
>consensus
GCUGCUGCGCUGGGCAGC___AUCCGUGGCAUCG___AUGGAUCGCUGCUCGAAGAUCUCCAGCUUGCUGGAGAUGGACAUCUUCGGCUCGCUCUU
...........(((((((...((((..............)))).)))))))((((((((((((....)))))))......)))))........... (-23.84 = -23.87 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:35 2006