Locus 7839

Sequence ID	X_DroMel_CAF1
Location	19,532,427 – 19,532,556
Length	129
Max. P	0.872300

overview

Window 1

Location	19,532,427 – 19,532,539
Length	112
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	80.12
Mean single sequence MFE	-34.30
Consensus MFE	-20.53
Energy contribution	-20.62
Covariance contribution	0.09
Combinations/Pair	1.29
Mean z-score	-1.56
Structure conservation index	0.60
SVM decision value	-0.04
SVM RNA-class probability	0.511135
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19532427 112 + 22224390
CGGCCUUGACACAGAAGGGCCUGAAAAAUGUAUUCGACGAGGCCAUCCUGGCCGCCCUCGAGCCACCAGAGCCCACAAAGAAAAGGAAGUGCAAAUUCUUAUAAUUCUGCUU-------
...........((((((((((((......((.(((((.(.((((.....))))..).)))))..))))).)))).........(((((.......)))))....)))))...------- ( -28.60)
>DroVir_CAF1 577 112 + 1
CGGCCCUAACACAGAAGGGCCUGAAAAAUGUCUUCGAUGAGGCCAUAUUGGCCGCCCUGGAGCCGCCAGAGCCAUCCAAGAAGAGGAAAUGCAAAUUCCUCUAAUUAUUUUU-------
.((((((........))))))..(((((((((((.((((.((((.....))))((.((((.....)))).)))))).))))(((((((.......)))))))...)))))))------- ( -43.90)
>DroGri_CAF1 568 112 + 1
CGGCACUAACACAGAAGGGCCUGAAAAACGUUUUCGAUGAGGCCAUUCUGGCCGCACUGGAGCCGCCAGAGCCAUCCAAGAAGAGGAAAUGCAGAUUCCUUUAAUUUUUUUU-------
.(((.............(((((((((.....))))....)))))..((((((.((......)).)))))))))........(((((((.......)))))))..........------- ( -33.00)
>DroWil_CAF1 4883 112 + 1
CGGCUCUGACACAAAAGGGUCUAAAAAAUGUUUUCGAUGAAGCGAUCUUAGCUGCACUCGAGCCGCCAGAGCCAUCCAAGAAAAGGAGAUGCAAGUUCUUAUAAUUUUGCUU-------
.(((((((.......((((((........(((((....))))))))))).((.((......)).))))))))).(((.......)))...(((((..........)))))..------- ( -25.90)
>DroMoj_CAF1 576 112 + 1
CGGCCCUCACGCAGAAGGGACUGAAGAAUGUAUUCGAUGAGGCAAUUCUGGCCGCCUUAGAGCCGCCAGAGCCGACCAAGCGGAGGAAAUGCAGGUUCCUCUAAUUUCUUUU-------
(((((((((....(((...((........)).)))..)))))....((((((.((......)).)))))))))).......(((((((.......)))))))..........------- ( -35.10)
>DroAna_CAF1 546 119 + 1
CGGCUCUGACGCAGAAGGGCCUCAAGAACGUAUUCGACGAGGCCAUUCUUGCCGCAUUGGAGCCCCCAGAGCCGACCAAGAAGAGGAGGUGCAAAUUCUUAUAAUUUUCCUUAUAUUUU
((((((((..((((((.((((((..(((....)))...)))))).))).))).((......))...))))))))........(((((((................)))))))....... ( -39.29)
>consensus
CGGCCCUGACACAGAAGGGCCUGAAAAAUGUAUUCGAUGAGGCCAUUCUGGCCGCACUGGAGCCGCCAGAGCCAACCAAGAAGAGGAAAUGCAAAUUCCUAUAAUUUUUCUU_______
.((((((........))))))...........(((.....(((....(((((.((......)).))))).)))......))).(((((.......)))))................... (-20.53 = -20.62 +   0.09)

alignment

secondary structure

dotplot

Window 2

Location	19,532,427 – 19,532,539
Length	112
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	80.12
Mean single sequence MFE	-36.14
Consensus MFE	-22.49
Energy contribution	-22.80
Covariance contribution	0.31
Combinations/Pair	1.36
Mean z-score	-1.54
Structure conservation index	0.62
SVM decision value	0.09
SVM RNA-class probability	0.580391
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19532427 112 - 22224390
-------AAGCAGAAUUAUAAGAAUUUGCACUUCCUUUUCUUUGUGGGCUCUGGUGGCUCGAGGGCGGCCAGGAUGGCCUCGUCGAAUACAUUUUUCAGGCCCUUCUGUGUCAAGGCCG
-------..(((((.((....)).))))).................(((..((..(.(..((((((((((.....)))).....(((.......)))..))))))..))..))..))). ( -33.50)
>DroVir_CAF1 577 112 - 1
-------AAAAAUAAUUAGAGGAAUUUGCAUUUCCUCUUCUUGGAUGGCUCUGGCGGCUCCAGGGCGGCCAAUAUGGCCUCAUCGAAGACAUUUUUCAGGCCCUUCUGUGUUAGGGCCG
-------((((((....(((((((.......)))))))((((.(((((((((((.....)))))))((((.....)))).)))).)))).))))))..((((((........)))))). ( -48.70)
>DroGri_CAF1 568 112 - 1
-------AAAAAAAAUUAAAGGAAUCUGCAUUUCCUCUUCUUGGAUGGCUCUGGCGGCUCCAGUGCGGCCAGAAUGGCCUCAUCGAAAACGUUUUUCAGGCCCUUCUGUGUUAGUGCCG
-------............(((((.......)))))..........(((.(((((((((.......))))((((.(((((....((((.....))))))))).))))..))))).))). ( -32.40)
>DroWil_CAF1 4883 112 - 1
-------AAGCAAAAUUAUAAGAACUUGCAUCUCCUUUUCUUGGAUGGCUCUGGCGGCUCGAGUGCAGCUAAGAUCGCUUCAUCGAAAACAUUUUUUAGACCCUUUUGUGUCAGAGCCG
-------..((((............))))...(((.......))).(((((((((...((((.((.(((.......))).))))))..(((...............)))))))))))). ( -28.16)
>DroMoj_CAF1 576 112 - 1
-------AAAAGAAAUUAGAGGAACCUGCAUUUCCUCCGCUUGGUCGGCUCUGGCGGCUCUAAGGCGGCCAGAAUUGCCUCAUCGAAUACAUUCUUCAGUCCCUUCUGCGUGAGGGCCG
-------..(((((....((((((.......))))))...(((((.(((((((((.(((....))).))))))...)))..))))).....)))))..(.(((((......))))).). ( -35.80)
>DroAna_CAF1 546 119 - 1
AAAAUAUAAGGAAAAUUAUAAGAAUUUGCACCUCCUCUUCUUGGUCGGCUCUGGGGGCUCCAAUGCGGCAAGAAUGGCCUCGUCGAAUACGUUCUUGAGGCCCUUCUGCGUCAGAGCCG
........(((.(((((.....)))))...)))((.......)).(((((((((..((......)).(((.(((.(((((((..(((....))).))))))).)))))).))))))))) ( -38.30)
>consensus
_______AAAAAAAAUUAUAAGAAUUUGCAUUUCCUCUUCUUGGAUGGCUCUGGCGGCUCCAGGGCGGCCAGAAUGGCCUCAUCGAAUACAUUUUUCAGGCCCUUCUGUGUCAGGGCCG
..............................................((((((((((((......))...(((((.(((((....(((....)))...))))).))))))))))))))). (-22.49 = -22.80 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	19,532,466 – 19,532,556
Length	90
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	80.69
Mean single sequence MFE	-20.79
Consensus MFE	-14.59
Energy contribution	-14.95
Covariance contribution	0.36
Combinations/Pair	1.07
Mean z-score	-1.42
Structure conservation index	0.70
SVM decision value	0.25
SVM RNA-class probability	0.651768
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19532466 90 + 22224390
AGGCCAUCCUGGCCGCCCUCGAGCCACCAGAGCCCACAAAGAAAAGGAAGUGCAAAUUCUUAUAAUUCUGCUU--UCC--UCACACGCGGUAUC
.((((.....))))((((((.........)))............((((((.(((((((.....)))).)))))--)))--).......)))... ( -19.30)
>DroVir_CAF1 616 89 + 1
AGGCCAUAUUGGCCGCCCUGGAGCCGCCAGAGCCAUCCAAGAAGAGGAAAUGCAAAUUCCUCUAAUUAUUUUU--GUUU-C--UUUGUUGUUUU
.((((.....))))((.((((.....)))).)).........(((((((.......)))))))..........--....-.--........... ( -23.60)
>DroPse_CAF1 601 89 + 1
AGGCCAUACUGGCCGCCCUGGAGCCACCAGAACCAACCAAGAAAAGGAAGUGCAAAUUCUUAUAAUUCUUUUUUUUUUC-UUUCUC----UCUC
.((((.....))))...((((.....))))........((((((((((((...................))))))))))-))....----.... ( -18.31)
>DroEre_CAF1 572 90 + 1
AGGCCAUCCUGGCCGCUCUGGAGCCACCAGAGCCCACAAAGAAAAGGAAGUGCAAAUUCUUAUAAUUCUUUUU--UUC--CCACACGCGGUAUC
.((((.....))))(((((((.....)))))))......((((((((((................))))))))--)).--((......)).... ( -24.99)
>DroYak_CAF1 572 92 + 1
AGGCCAUUCUGGCCGCCCUGGAGCCACCAGAGCCCACAAAGAAAAGGAAGUGCAAAUUCUUAUAAUUCUUCUU--UCCCCCCACACGCGGUAUC
.((((.....))))(((((((.....)))).((..........(((((((.................))))))--)..........)))))... ( -20.08)
>DroPer_CAF1 3044 87 + 1
AGGCCAUACUGGCCGCCCUGGAGCCACCAGAACCAACCAAGAAAAGGAAGUGCAAAUUCUUAUAAUU--UUUUUUUUUC-UUUCUC----UCUC
.((((.....))))...((((.....))))........((((((((((((.................--))))))))))-))....----.... ( -18.43)
>consensus
AGGCCAUACUGGCCGCCCUGGAGCCACCAGAGCCAACAAAGAAAAGGAAGUGCAAAUUCUUAUAAUUCUUUUU__UUCC_CCACACGCGGUAUC
.((((.....))))((.((((.....)))).))...........(((((.......)))))................................. (-14.59 = -14.95 +   0.36)

alignment

secondary structure

dotplot

Window 4

Location	19,532,466 – 19,532,556
Length	90
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	80.69
Mean single sequence MFE	-29.12
Consensus MFE	-18.95
Energy contribution	-18.62
Covariance contribution	-0.33
Combinations/Pair	1.19
Mean z-score	-2.25
Structure conservation index	0.65
SVM decision value	0.88
SVM RNA-class probability	0.872300
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19532466 90 - 22224390
GAUACCGCGUGUGA--GGA--AAGCAGAAUUAUAAGAAUUUGCACUUCCUUUUCUUUGUGGGCUCUGGUGGCUCGAGGGCGGCCAGGAUGGCCU
....(((((...((--(((--(.(((((.((....)).)))))..)))))).....)))))(((((.(.....).)))))((((.....)))). ( -31.40)
>DroVir_CAF1 616 89 - 1
AAAACAACAAA--G-AAAC--AAAAAUAAUUAGAGGAAUUUGCAUUUCCUCUUCUUGGAUGGCUCUGGCGGCUCCAGGGCGGCCAAUAUGGCCU
....((.(.((--(-(...--..........(((((((.......))))))))))).).))(((((((.....)))))))((((.....)))). ( -28.11)
>DroPse_CAF1 601 89 - 1
GAGA----GAGAAA-GAAAAAAAAAAGAAUUAUAAGAAUUUGCACUUCCUUUUCUUGGUUGGUUCUGGUGGCUCCAGGGCGGCCAGUAUGGCCU
..((----(((((.-(((........(((((.....)))))....))).)))))))(((((...(((((.(((....))).)))))..))))). ( -24.10)
>DroEre_CAF1 572 90 - 1
GAUACCGCGUGUGG--GAA--AAAAAGAAUUAUAAGAAUUUGCACUUCCUUUUCUUUGUGGGCUCUGGUGGCUCCAGAGCGGCCAGGAUGGCCU
....(((((...((--(((--.....(((((.....)))))....)))))......)))))(((((((.....)))))))((((.....)))). ( -31.90)
>DroYak_CAF1 572 92 - 1
GAUACCGCGUGUGGGGGGA--AAGAAGAAUUAUAAGAAUUUGCACUUCCUUUUCUUUGUGGGCUCUGGUGGCUCCAGGGCGGCCAGAAUGGCCU
....(((((...(((((((--(....(((((.....)))))....))))))))...)))))(((((((.....)))))))((((.....)))). ( -34.30)
>DroPer_CAF1 3044 87 - 1
GAGA----GAGAAA-GAAAAAAAAA--AAUUAUAAGAAUUUGCACUUCCUUUUCUUGGUUGGUUCUGGUGGCUCCAGGGCGGCCAGUAUGGCCU
..((----(((((.-(((......(--((((.....)))))....))).)))))))(((((...(((((.(((....))).)))))..))))). ( -24.90)
>consensus
GAUACCGCGAGUGA_GAAA__AAAAAGAAUUAUAAGAAUUUGCACUUCCUUUUCUUGGUGGGCUCUGGUGGCUCCAGGGCGGCCAGUAUGGCCU
.................................(((((.............))))).....(((((((.....)))))))((((.....)))). (-18.95 = -18.62 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:43 2006