Locus 4613

Sequence ID	3L_DroMel_CAF1
Location	13,147,201 – 13,147,465
Length	264
Max. P	0.915371

overview

Window 8

Location	13,147,201 – 13,147,308
Length	107
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.93
Mean single sequence MFE	-25.16
Consensus MFE	-18.48
Energy contribution	-18.85
Covariance contribution	0.37
Combinations/Pair	1.07
Mean z-score	-2.34
Structure conservation index	0.73
SVM decision value	1.08
SVM RNA-class probability	0.912262
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13147201 107 + 23771897
----------UAUUUGUU-UGUGACAAAUAACUUUCCAUAGUUCAAG--UACUCGUUAGCCCCAGCCAUUGCUCCCAAAUGGAACAUUUCCAAAUGGAACAUUUUACUUGGGAUGCAAUC
----------((((((.(-((((.............)))))..))))--))................(((((((((((.(((((...((((....))))..))))).)))))).))))). ( -22.92)
>DroSec_CAF1 134855 109 + 1
----------AAUUUGUU-UGUGACAAAUAACUUUCCAUAGUUCAAGCGCACUCGUUUGCCCCAGCCAUUGCUCCCAAAUGGAACAUUUCCAAAUGGAACAUUUUACUUGGGAUGCAAUC
----------.(((((((-...)))))))...........(..((((((....))))))..).....(((((((((((.(((((...((((....))))..))))).)))))).))))). ( -26.00)
>DroSim_CAF1 134728 107 + 1
----------AAUUUAUU-UCUUACAAAGAACUUUCCAUAGUUCAAG--CACUCGUUUGCCCCAGUCAUUGCUUCCAAAUGGAACAUUUCCAAAUGGAACAUUUUACUUGGGAUGCAAUC
----------........-.........(((((......)))))...--.....((...(((.(((...((.(((((..((((.....))))..)))))))....))).)))..)).... ( -23.50)
>DroYak_CAF1 136403 118 + 1
AUGCAAAUAGAAUUUGUUAUAUGACAAGAAACUAUCCACAGUUCAAG--CACUCGUUAGCCCCAGCUAAUGCUCCCAAAUGGAACGUUUCCAAAUGGAACAUUUUACUUGGGAUGCAAUC
.(((........((((((....)))))).((((......))))...)--))...((((((....))))))((((((((.(((((.(((.((....))))).))))).)))))).)).... ( -28.20)
>consensus
__________AAUUUGUU_UGUGACAAAUAACUUUCCAUAGUUCAAG__CACUCGUUAGCCCCAGCCAUUGCUCCCAAAUGGAACAUUUCCAAAUGGAACAUUUUACUUGGGAUGCAAUC
............((((((....)))))).((((......))))........................(((((((((((.(((((...((((....))))..))))).)))))).))))). (-18.48 = -18.85 +   0.37)

alignment

secondary structure

dotplot

Window 9

Location	13,147,201 – 13,147,308
Length	107
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.93
Mean single sequence MFE	-30.05
Consensus MFE	-23.23
Energy contribution	-23.85
Covariance contribution	0.62
Combinations/Pair	1.11
Mean z-score	-2.20
Structure conservation index	0.77
SVM decision value	1.10
SVM RNA-class probability	0.915371
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13147201 107 - 23771897
GAUUGCAUCCCAAGUAAAAUGUUCCAUUUGGAAAUGUUCCAUUUGGGAGCAAUGGCUGGGGCUAACGAGUA--CUUGAACUAUGGAAAGUUAUUUGUCACA-AACAAAUA----------
.(((((.((((((((..((((((((....)).))))))..)))))))))))))(((....))).(((((((--(((..........))).)))))))....-........---------- ( -27.00)
>DroSec_CAF1 134855 109 - 1
GAUUGCAUCCCAAGUAAAAUGUUCCAUUUGGAAAUGUUCCAUUUGGGAGCAAUGGCUGGGGCAAACGAGUGCGCUUGAACUAUGGAAAGUUAUUUGUCACA-AACAAAUU----------
.(((((.((((((((..((((((((....)).))))))..)))))))))))))(..((.((((((((((....))))((((......)))).)))))).))-..).....---------- ( -31.40)
>DroSim_CAF1 134728 107 - 1
GAUUGCAUCCCAAGUAAAAUGUUCCAUUUGGAAAUGUUCCAUUUGGAAGCAAUGACUGGGGCAAACGAGUG--CUUGAACUAUGGAAAGUUCUUUGUAAGA-AAUAAAUU----------
..((((..((((.((....(((((((..((((.....))))..))).))))...)))))))))).....((--(..(((((......)))))...)))...-........---------- ( -27.30)
>DroYak_CAF1 136403 118 - 1
GAUUGCAUCCCAAGUAAAAUGUUCCAUUUGGAAACGUUCCAUUUGGGAGCAUUAGCUGGGGCUAACGAGUG--CUUGAACUGUGGAUAGUUUCUUGUCAUAUAACAAAUUCUAUUUGCAU
...(((.((((((((..((((((((....)).))))))..)))))))))))(((((....)))))..(((.--.....)))(..(((((....((((......))))...)))))..).. ( -34.50)
>consensus
GAUUGCAUCCCAAGUAAAAUGUUCCAUUUGGAAAUGUUCCAUUUGGGAGCAAUGGCUGGGGCAAACGAGUG__CUUGAACUAUGGAAAGUUAUUUGUCACA_AACAAAUU__________
.(((((.((((((((..((((((((....)).))))))..))))))))))))).(((.(......).)))......(((((......)))))(((((......)))))............ (-23.23 = -23.85 +   0.62)

alignment

secondary structure

dotplot

Window 0

Location	13,147,230 – 13,147,348
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.24
Mean single sequence MFE	-27.28
Consensus MFE	-22.69
Energy contribution	-22.38
Covariance contribution	-0.31
Combinations/Pair	1.10
Mean z-score	-1.93
Structure conservation index	0.83
SVM decision value	0.29
SVM RNA-class probability	0.670964
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13147230 118 + 23771897
GUUCAAG--UACUCGUUAGCCCCAGCCAUUGCUCCCAAAUGGAACAUUUCCAAAUGGAACAUUUUACUUGGGAUGCAAUCAAGGCCACCACUUCUCCAACCUGCCUAUUUAGCCACUUGU
...((((--(....(((((........(((((((((((.(((((...((((....))))..))))).)))))).)))))..((((.................))))..))))).))))). ( -26.43)
>DroSec_CAF1 134884 120 + 1
GUUCAAGCGCACUCGUUUGCCCCAGCCAUUGCUCCCAAAUGGAACAUUUCCAAAUGGAACAUUUUACUUGGGAUGCAAUCAAGGCCACCACUUCUCCAACCCGCCUAUUUAGCCACUUGU
(..((((((....))))))..)..((((((((((((((.(((((...((((....))))..))))).)))))).)))))...)))................................... ( -27.10)
>DroSim_CAF1 134757 118 + 1
GUUCAAG--CACUCGUUUGCCCCAGUCAUUGCUUCCAAAUGGAACAUUUCCAAAUGGAACAUUUUACUUGGGAUGCAAUCAAGGCCACCACUUCUCCAACCCGCCUAUUUAGCCACUUGU
...((((--.....(.((((((((((...((.(((((..((((.....))))..)))))))....)).))))..)))).).((((.................)))).........)))). ( -24.53)
>DroYak_CAF1 136443 118 + 1
GUUCAAG--CACUCGUUAGCCCCAGCUAAUGCUCCCAAAUGGAACGUUUCCAAAUGGAACAUUUUACUUGGGAUGCAAUCAAGGCCACCACUUCUCCAACCCGCCUAUUUGGCCACUUGU
...((((--.....((((((....))))))((((((((.(((((.(((.((....))))).))))).)))))).))......(((((......................))))).)))). ( -31.05)
>consensus
GUUCAAG__CACUCGUUAGCCCCAGCCAUUGCUCCCAAAUGGAACAUUUCCAAAUGGAACAUUUUACUUGGGAUGCAAUCAAGGCCACCACUUCUCCAACCCGCCUAUUUAGCCACUUGU
...((((.................((((((((((((((.(((((...((((....))))..))))).)))))).)))))...))).................((.......))..)))). (-22.69 = -22.38 +  -0.31)

alignment

secondary structure

dotplot

Window 1

Location	13,147,230 – 13,147,348
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.24
Mean single sequence MFE	-38.22
Consensus MFE	-33.40
Energy contribution	-34.03
Covariance contribution	0.62
Combinations/Pair	1.05
Mean z-score	-2.19
Structure conservation index	0.87
SVM decision value	0.99
SVM RNA-class probability	0.896828
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13147230 118 - 23771897
ACAAGUGGCUAAAUAGGCAGGUUGGAGAAGUGGUGGCCUUGAUUGCAUCCCAAGUAAAAUGUUCCAUUUGGAAAUGUUCCAUUUGGGAGCAAUGGCUGGGGCUAACGAGUA--CUUGAAC
.(((((((((.....)))............((.(((((((.(((((.((((((((..((((((((....)).))))))..))))))))))))).)...)))))).))..))--))))... ( -36.70)
>DroSec_CAF1 134884 120 - 1
ACAAGUGGCUAAAUAGGCGGGUUGGAGAAGUGGUGGCCUUGAUUGCAUCCCAAGUAAAAUGUUCCAUUUGGAAAUGUUCCAUUUGGGAGCAAUGGCUGGGGCAAACGAGUGCGCUUGAAC
.(((((((((.....)))...........((..((.((((.(((((.((((((((..((((((((....)).))))))..))))))))))))).)..))).)).)).....))))))... ( -37.90)
>DroSim_CAF1 134757 118 - 1
ACAAGUGGCUAAAUAGGCGGGUUGGAGAAGUGGUGGCCUUGAUUGCAUCCCAAGUAAAAUGUUCCAUUUGGAAAUGUUCCAUUUGGAAGCAAUGACUGGGGCAAACGAGUG--CUUGAAC
.(((.(.(((.....))).).))).....((...(((((((.((((..((((.((....(((((((..((((.....))))..))).))))...)))))))))).)))).)--))...)) ( -37.00)
>DroYak_CAF1 136443 118 - 1
ACAAGUGGCCAAAUAGGCGGGUUGGAGAAGUGGUGGCCUUGAUUGCAUCCCAAGUAAAAUGUUCCAUUUGGAAACGUUCCAUUUGGGAGCAUUAGCUGGGGCUAACGAGUG--CUUGAAC
.(((.(.(((.....))).).))).....((...(((((((..(((.((((((((..((((((((....)).))))))..)))))))))))(((((....))))))))).)--))...)) ( -41.30)
>consensus
ACAAGUGGCUAAAUAGGCGGGUUGGAGAAGUGGUGGCCUUGAUUGCAUCCCAAGUAAAAUGUUCCAUUUGGAAAUGUUCCAUUUGGGAGCAAUGGCUGGGGCAAACGAGUG__CUUGAAC
.(((.(.(((.....))).).))).........(((((((.(((((.((((((((..((((((((....)).))))))..)))))))))))))....))))))).((((....))))... (-33.40 = -34.03 +   0.62)

alignment

secondary structure

dotplot

Window 2

Location	13,147,348 – 13,147,465
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.48
Mean single sequence MFE	-39.28
Consensus MFE	-36.35
Energy contribution	-36.85
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.55
Structure conservation index	0.93
SVM decision value	0.09
SVM RNA-class probability	0.578468
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13147348 117 - 23771897
GACGACGAGACGGGGCGUGGUCGGGUCUCAGGAUGCUCGACGCACGCAUUAAAACAAUUUAAAAUUCCCAAAGACCGAAACACUAGGC---AACCCACUACGGUGGGUGGCAUUGCCCAG
...........(((((((((((((((........))))))).))))).(((((....)))))....))).............((.(((---(((((((....)))))).....)))).)) ( -40.60)
>DroSec_CAF1 135004 117 - 1
GACGACGAGACGGGGCGUGGUCGGGUCUCAGGAUGCUCGACGCACGCAUUAAAACAAUUUAAAAUUCCCAAAGACCGAAACACUAGGC---AACCCACAACGGUGGGUGGCAUCGCCCAG
.....(((...(((((((((((((((........))))))).))))).(((((....)))))....))).................((---.((((((....)))))).)).)))..... ( -38.10)
>DroSim_CAF1 134875 117 - 1
GACGACGAGACGGGGCGUGGUCGGGUCUCAGGAUGCUCGACGCACGCAUUAAAACAAUUUAAAAUUCCCAAAGACCGAAACACUAGGC---AACCCACAACGGUGGGUGGCAUCGCCCAG
.....(((...(((((((((((((((........))))))).))))).(((((....)))))....))).................((---.((((((....)))))).)).)))..... ( -38.10)
>DroYak_CAF1 136561 120 - 1
GACGACGAGACGGGGCGUGGUCGGGUCUCAGGAUGCUCGACGCACGCAUUAAAACAAUUUAAAAUUCCCAAAGACCGAAACACUAGACGACGACCCACUACGGUGGGUGGCAUCGCACAG
...(.(((...(((((((((((((((........))))))).))))).(((((....)))))....)))...................(.(.((((((....)))))).)).)))).... ( -40.30)
>consensus
GACGACGAGACGGGGCGUGGUCGGGUCUCAGGAUGCUCGACGCACGCAUUAAAACAAUUUAAAAUUCCCAAAGACCGAAACACUAGGC___AACCCACAACGGUGGGUGGCAUCGCCCAG
...........(((((((((((((((........))))))).))))).(((((....)))))....))).............((.(((....((((((....))))))......))).)) (-36.35 = -36.85 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:32 2006