Locus 401

Sequence ID	2L_DroMel_CAF1
Location	1,218,496 – 1,218,691
Length	195
Max. P	0.922748

overview

Window 4

Location	1,218,496 – 1,218,616
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.64
Mean single sequence MFE	-38.00
Consensus MFE	-26.69
Energy contribution	-26.12
Covariance contribution	-0.56
Combinations/Pair	1.10
Mean z-score	-2.58
Structure conservation index	0.70
SVM decision value	1.15
SVM RNA-class probability	0.922748
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1218496 120 + 22407834
AUUAAGUUUUGAAUCGCAUAUUGAUUAAUGCGACUAUUAUUGCGCAAUAGUAACGACGCCAGAUGGACCGAGCUGCCUUAGCUCGGUAGUAUCGCCCUUUCCAAGGGCAGCGGGUUCAAU
........(((((((........((((.((((.(.......))))).)))).....(((..((((.(((((((((...)))))))))..))))(((((.....))))).)))))))))). ( -42.00)
>DroSim_CAF1 14100 120 + 1
AUUAAGUUUUGAAUCGCAUAUUGAUUAAUGCGACUAUUAUUGCGCAAUAGUAACGACGCCAGGUGGGCCGAGCUGCGUUAGCUUGGUAGUAUCGCCCUUUCCAAGGGCAGCGGGUUCAAU
........(((((((........((((.((((.(.......))))).)))).....(((..((((.(((((((((...)))))))))..))))(((((.....))))).)))))))))). ( -39.60)
>DroEre_CAF1 13912 108 + 1
AUUAAGUUUUGAAUCGCAUAUUGAUUAAUGCGGCUAUGGUUGCGCAAUAGUAACGA---CAAU---------CUGCGUUAGCUUGGCAGUAUCGCCCUUUCCAAGGGCAGCGGGUUCAAU
........(((((((((((((((.(((((((((...(.(((((......))))).)---....---------))))))))).....)))))).(((((.....))))).)).))))))). ( -33.90)
>DroYak_CAF1 15005 111 + 1
AUUCAGUUUUGAAUCGCAUAUUGAUUAAUGCGACUGUUAUUGCGCAAUAAUAACGAUGCCAGG---------UGGCGUUAGCUUCGUAGUAUCGCCCUUUCCAAGGGCAGCGAGUUCAAU
........(((((((((.....(((...(((((..(((((((.....)))))))((((((...---------.))))))....)))))..)))(((((.....))))).)))).))))). ( -36.50)
>consensus
AUUAAGUUUUGAAUCGCAUAUUGAUUAAUGCGACUAUUAUUGCGCAAUAGUAACGACGCCAGG_________CUGCGUUAGCUUGGUAGUAUCGCCCUUUCCAAGGGCAGCGGGUUCAAU
........(((((((((((((((((((.((((.(.......))))).)))).......................((....))....)))))).(((((.....))))).)))).))))). (-26.69 = -26.12 +  -0.56)

alignment

secondary structure

dotplot

Window 5

Location	1,218,496 – 1,218,616
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.64
Mean single sequence MFE	-31.65
Consensus MFE	-22.73
Energy contribution	-22.98
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.07
Structure conservation index	0.72
SVM decision value	0.72
SVM RNA-class probability	0.832334
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1218496 120 - 22407834
AUUGAACCCGCUGCCCUUGGAAAGGGCGAUACUACCGAGCUAAGGCAGCUCGGUCCAUCUGGCGUCGUUACUAUUGCGCAAUAAUAGUCGCAUUAAUCAAUAUGCGAUUCAAAACUUAAU
.(((((..(((((((((.....)))))(((...((((((((.....))))))))..))).))))......((((((.....))))))((((((........)))))))))))........ ( -38.10)
>DroSim_CAF1 14100 120 - 1
AUUGAACCCGCUGCCCUUGGAAAGGGCGAUACUACCAAGCUAACGCAGCUCGGCCCACCUGGCGUCGUUACUAUUGCGCAAUAAUAGUCGCAUUAAUCAAUAUGCGAUUCAAAACUUAAU
.(((((...((((((((.....)))))...........((....))))).((((((....)).))))...((((((.....))))))((((((........)))))))))))........ ( -31.30)
>DroEre_CAF1 13912 108 - 1
AUUGAACCCGCUGCCCUUGGAAAGGGCGAUACUGCCAAGCUAACGCAG---------AUUG---UCGUUACUAUUGCGCAACCAUAGCCGCAUUAAUCAAUAUGCGAUUCAAAACUUAAU
.(((((...((((((((.....))))).....((((((..((((((..---------...)---.)))))...))).))).....)))(((((........))))).)))))........ ( -27.50)
>DroYak_CAF1 15005 111 - 1
AUUGAACUCGCUGCCCUUGGAAAGGGCGAUACUACGAAGCUAACGCCA---------CCUGGCAUCGUUAUUAUUGCGCAAUAACAGUCGCAUUAAUCAAUAUGCGAUUCAAAACUGAAU
.(((((.((((.(((((.....)))))(((...((((.((((......---------..)))).))))...((.(((((.......).)))).))))).....)))))))))........ ( -29.70)
>consensus
AUUGAACCCGCUGCCCUUGGAAAGGGCGAUACUACCAAGCUAACGCAG_________CCUGGCGUCGUUACUAUUGCGCAAUAAUAGUCGCAUUAAUCAAUAUGCGAUUCAAAACUUAAU
.((((...(((((((((.....))))))..........((....)).............................)))........(((((((........)))))))))))........ (-22.73 = -22.98 +   0.25)

alignment

secondary structure

dotplot

Window 6

Location	1,218,536 – 1,218,656
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.71
Mean single sequence MFE	-38.22
Consensus MFE	-26.35
Energy contribution	-26.72
Covariance contribution	0.37
Combinations/Pair	1.06
Mean z-score	-1.84
Structure conservation index	0.69
SVM decision value	0.26
SVM RNA-class probability	0.658422
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1218536 120 + 22407834
UGCGCAAUAGUAACGACGCCAGAUGGACCGAGCUGCCUUAGCUCGGUAGUAUCGCCCUUUCCAAGGGCAGCGGGUUCAAUAACCCAGCCAUGAACCGCCGAACUAUUACAAGUGGGCAAA
(((.((...((((...(((..((((.(((((((((...)))))))))..))))(((((.....))))).)))((((((............)))))).........))))...)).))).. ( -43.90)
>DroSim_CAF1 14140 119 + 1
UGCGCAAUAGUAACGACGCCAGGUGGGCCGAGCUGCGUUAGCUUGGUAGUAUCGCCCUUUCCAAGGGCAGCGGGUUCAAUAACCCAGCCGUGAACCGCCGAACUAUUACAAGUG-GCAAA
(((......))).....(((.((((((((((((((...)))))))))....(((((((.....))))).(((((((....))))).))...)).)))))..(((......))))-))... ( -43.40)
>DroEre_CAF1 13952 107 + 1
UGCGCAAUAGUAACGA---CAAU---------CUGCGUUAGCUUGGCAGUAUCGCCCUUUCCAAGGGCAGCGGGUUCAAUAACCCAGCCGUGAACCGCCGAACUAUUACAAGUG-GCAAA
(((.((...((((((.---(...---------..))))(((.(((((.((.(((((((.....))))).(((((((....))))).))...)))).))))).))).)))...))-))).. ( -31.80)
>DroYak_CAF1 15045 110 + 1
UGCGCAAUAAUAACGAUGCCAGG---------UGGCGUUAGCUUCGUAGUAUCGCCCUUUCCAAGGGCAGCGAGUUCAAUAACCCAGCCAUGAACCGCCGAACUAUUACAAGUG-GCAAA
(((...........((((((...---------.)))))).((((.(((((((((((((.....))))).(((.(((((............)))))))).))..)))))))))).-))).. ( -33.80)
>consensus
UGCGCAAUAGUAACGACGCCAGG_________CUGCGUUAGCUUGGUAGUAUCGCCCUUUCCAAGGGCAGCGGGUUCAAUAACCCAGCCAUGAACCGCCGAACUAUUACAAGUG_GCAAA
(((.((...((((.....................((....))(((((.((.(((((((.....))))).(((((((....))))).))...)))).)))))....))))...)).))).. (-26.35 = -26.72 +   0.37)

alignment

secondary structure

dotplot

Window 7

Location	1,218,536 – 1,218,656
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.71
Mean single sequence MFE	-41.15
Consensus MFE	-32.58
Energy contribution	-32.70
Covariance contribution	0.12
Combinations/Pair	1.06
Mean z-score	-1.84
Structure conservation index	0.79
SVM decision value	0.65
SVM RNA-class probability	0.811532
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1218536 120 - 22407834
UUUGCCCACUUGUAAUAGUUCGGCGGUUCAUGGCUGGGUUAUUGAACCCGCUGCCCUUGGAAAGGGCGAUACUACCGAGCUAAGGCAGCUCGGUCCAUCUGGCGUCGUUACUAUUGCGCA
...........((((((((.(((((.(..((((..(((((....)))))..((((((.....)))))).....((((((((.....))))))))))))..).)))))..))))))))... ( -48.10)
>DroSim_CAF1 14140 119 - 1
UUUGC-CACUUGUAAUAGUUCGGCGGUUCACGGCUGGGUUAUUGAACCCGCUGCCCUUGGAAAGGGCGAUACUACCAAGCUAACGCAGCUCGGCCCACCUGGCGUCGUUACUAUUGCGCA
.....-.....((((((((.(((((.(....(((((((((....)))))((((((((.....)))))...........((....)))))..)))).....).)))))..))))))))... ( -43.30)
>DroEre_CAF1 13952 107 - 1
UUUGC-CACUUGUAAUAGUUCGGCGGUUCACGGCUGGGUUAUUGAACCCGCUGCCCUUGGAAAGGGCGAUACUGCCAAGCUAACGCAG---------AUUG---UCGUUACUAUUGCGCA
.....-.....((((((((.((((((((...(((.(((((....)))))..((((((.....)))))).....)))..((....)).)---------))))---)))..))))))))... ( -40.50)
>DroYak_CAF1 15045 110 - 1
UUUGC-CACUUGUAAUAGUUCGGCGGUUCAUGGCUGGGUUAUUGAACUCGCUGCCCUUGGAAAGGGCGAUACUACGAAGCUAACGCCA---------CCUGGCAUCGUUAUUAUUGCGCA
..(((-..(((.....((..((((((((((((((...)))).))))).)))))..)).....)))((((((..((((.((((......---------..)))).))))...))))))))) ( -32.70)
>consensus
UUUGC_CACUUGUAAUAGUUCGGCGGUUCACGGCUGGGUUAUUGAACCCGCUGCCCUUGGAAAGGGCGAUACUACCAAGCUAACGCAG_________CCUGGCGUCGUUACUAUUGCGCA
...........((((((((.(((((((((..(((.(((((....))))))))(((((.....))))))).))).....((....)).................))))..))))))))... (-32.58 = -32.70 +   0.12)

alignment

secondary structure

dotplot

Window 8

Location	1,218,576 – 1,218,691
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.43
Mean single sequence MFE	-35.12
Consensus MFE	-27.41
Energy contribution	-28.10
Covariance contribution	0.69
Combinations/Pair	1.06
Mean z-score	-1.76
Structure conservation index	0.78
SVM decision value	0.27
SVM RNA-class probability	0.661998
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1218576 115 + 22407834
GCUCGGUAGUAUCGCCCUUUCCAAGGGCAGCGGGUUCAAUAACCCAGCCAUGAACCGCCGAACUAUUACAAGUGGGCAAAU-----CUACUGGCCAAGGUGAGCCACUUCAAAUCACUCA
((((((..((.(((((((.....))))).(((((((....))))).))...))))..))))....((((...(((.((...-----....)).)))..))))))................ ( -34.60)
>DroSim_CAF1 14180 114 + 1
GCUUGGUAGUAUCGCCCUUUCCAAGGGCAGCGGGUUCAAUAACCCAGCCGUGAACCGCCGAACUAUUACAAGUG-GCAAAU-----CUACUGGCCAAGGUGAGUCACUUCAAAUCACUCA
.(((((((((((((((((.....))))).(((((((....))))).))...))...(((..(((......))))-))....-----.)))).))))))((((...........))))... ( -34.00)
>DroEre_CAF1 13980 119 + 1
GCUUGGCAGUAUCGCCCUUUCCAAGGGCAGCGGGUUCAAUAACCCAGCCGUGAACCGCCGAACUAUUACAAGUG-GCAAAUACUUGCUGCUCGCCAAGGUGAGCCACUUCAAAUCACACG
..(((((.((.(((((((.....))))).(((((((....))))).))...)))).)))))........(((((-((((....)))).((((((....)))))))))))........... ( -40.70)
>DroYak_CAF1 15076 119 + 1
GCUUCGUAGUAUCGCCCUUUCCAAGGGCAGCGAGUUCAAUAACCCAGCCAUGAACCGCCGAACUAUUACAAGUG-GCAAAUAGUAGCUACUCUCCAAGGUGAGCCACUUCAAAUCACUCG
.....(((((((((((((.....))))).(((.(((((............)))))))).))..))))))(((((-((.....((....))((.(....).)))))))))........... ( -31.20)
>consensus
GCUUGGUAGUAUCGCCCUUUCCAAGGGCAGCGGGUUCAAUAACCCAGCCAUGAACCGCCGAACUAUUACAAGUG_GCAAAU_____CUACUCGCCAAGGUGAGCCACUUCAAAUCACUCA
.(((((((((((((((((.....))))).(((((((....))))).))...))...((...(((......)))..))..........)))).))))))((((...........))))... (-27.41 = -28.10 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:04 2006