Locus 4386

Sequence ID	2L_DroMel_CAF1
Location	12,626,338 – 12,626,462
Length	124
Max. P	0.949853

overview

Window 8

Location	12,626,338 – 12,626,431
Length	93
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	74.33
Mean single sequence MFE	-28.58
Consensus MFE	-16.25
Energy contribution	-16.67
Covariance contribution	0.42
Combinations/Pair	1.20
Mean z-score	-1.43
Structure conservation index	0.57
SVM decision value	0.03
SVM RNA-class probability	0.549362
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12626338 93 + 22407834
UCACCCCAGCAGUUGCACCAUCA--CCACCACCAUCCACUGCAAAUCACGCCGCCCAGCUCGGCGGCCAGUUUGAAAUUGAGU---GGUAUGCUGACG
......((((((.((......))--.)(((((((.......(((((...((((((......))))))..)))))....)).))---))).)))))... ( -27.60)
>DroVir_CAF1 64445 90 + 1
UCGCCGCAGUCGCAGCAG-----GCGUCGCAUCAUCCGCUGCAGAUAACGCCGCCCAAUUCGGCGGCCAGCCUUAAGCUGAGC---GGCAUGCUUACG
..(((((.((((((((.(-----..(......)..).))))).)))...((((((......))))))((((.....)))).))---)))......... ( -38.40)
>DroPse_CAF1 7372 84 + 1
UCCCCGCAGCAGCUCCA--------------CCAUCCGCUCCAGAUCACGCCGCCCAGCUCGGCGGCCAGCAUCAAGAUGAGCGGCGGCAUGCUGACC
......((((((((...--------------....((((((..(((...((((((......))))))....))).....)))))).))).)))))... ( -30.10)
>DroSec_CAF1 7289 93 + 1
UCACCCCAGCAGAUGCACCACCA--CCACCCCCAUCCACUGCAAAUCACGCCGCCCAGCUCAGCGGCCAGUUUGAAAUUGAGC---GGUAUGCUGACG
......(((((((((........--.......)))).(((((.......(((((........)))))((((.....)))).))---))).)))))... ( -23.56)
>DroYak_CAF1 7437 93 + 1
UCACCCCACCAGAUGCACCACCA--CCACCAUCACCCACUGCAGAUCACUCCGCCCAGCUCGGCGGCCAGUCUGAAACUGAGU---GGAAUGCUGACG
.....((((((((((........--....))))........(((((....(((((......)))))...)))))....)).))---)).......... ( -21.70)
>DroPer_CAF1 7614 84 + 1
UCCCCGCAGCAGCUCCA--------------CCAUCCGCUCCAGAUCACGCCGCCCAGCUCGGCGGCCAGCAUCAAGAUGAGCGGCGGCAUGCUGACC
......((((((((...--------------....((((((..(((...((((((......))))))....))).....)))))).))).)))))... ( -30.10)
>consensus
UCACCCCAGCAGCUGCAC_______CCACCACCAUCCACUGCAGAUCACGCCGCCCAGCUCGGCGGCCAGCAUGAAAAUGAGC___GGCAUGCUGACG
......(((((......................................((((((......))))))((((.....))))..........)))))... (-16.25 = -16.67 +   0.42)

alignment

secondary structure

dotplot

Window 9

Location	12,626,363 – 12,626,462
Length	99
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	76.13
Mean single sequence MFE	-33.48
Consensus MFE	-23.66
Energy contribution	-24.63
Covariance contribution	0.98
Combinations/Pair	1.17
Mean z-score	-1.73
Structure conservation index	0.71
SVM decision value	1.40
SVM RNA-class probability	0.949853
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12626363 99 + 22407834
ACCACCAUCCACUGCAAAUCACGCCGCCCAGCUCGGCGGCCAGUUUGAAAUUGAGU---GGUAUGCUGACGCCCAGUACGCCCACCAGUGGCACCCAGAUGA---------
........(((((((((((...((((((......))))))..))))).......((---((..(((((.....)))))..).)))))))))...........--------- ( -33.00)
>DroVir_CAF1 64467 95 + 1
CGCAUCAUCCGCUGCAGAUAACGCCGCCCAAUUCGGCGGCCAGCCUUAAGCUGAGC---GGCAUGCUUACGCCCAGCACGCCCACCAGCGGCACCCAC-------------
........(((((((.......((((((......))))))((((.....)))).))---(((.((((.......)))).)))....))))).......------------- ( -35.30)
>DroPse_CAF1 7389 97 + 1
----CCAUCCGCUCCAGAUCACGCCGCCCAGCUCGGCGGCCAGCAUCAAGAUGAGCGGCGGCAUGCUGACCCCCAGCACCCCCACCAGCGGCACGCAGAUG----------
----.(((((((((..(((...((((((......))))))....))).....)))))(((((.(((((.................))))))).))).))))---------- ( -34.03)
>DroYak_CAF1 7462 99 + 1
ACCAUCACCCACUGCAGAUCACUCCGCCCAGCUCGGCGGCCAGUCUGAAACUGAGU---GGAAUGCUGACGCCCAGCACGCCCACCAGUGGCACCCAGAUGA---------
..((((..(((((((((((....(((((......)))))...))))).......((---((..(((((.....)))))...))))))))))......)))).--------- ( -35.60)
>DroMoj_CAF1 60853 100 + 1
--CAUCAGCCGCUGCAGAUAACGCCGCCUAAUUCGGCAGCCAGCUUGAAGCUGAGC---GGCAUGCUAACGCCCAGCACGCCCACCAGCCACUCGCACACCCAUG------
--.....((.((((........((((((......))).((((((.....)))).))---)))..((....)).))))..((......)).....)).........------ ( -28.90)
>DroAna_CAF1 2079 108 + 1
ACCACCUGCCGCUGCAGAUCACACCCCCCAACUCGGCGGCCAGCUUGAAACUAAGC---GGAAUGCUGACUCCCAGCACACCCACCAGCGGCACCCAGAUGCAGAGCGGCU
.......(((((((((((..............))((..(((.(((((....)))))---((..(((((.....)))))..)).......)))..))...)))..)))))). ( -34.04)
>consensus
ACCACCAUCCGCUGCAGAUCACGCCGCCCAACUCGGCGGCCAGCUUGAAACUGAGC___GGCAUGCUGACGCCCAGCACGCCCACCAGCGGCACCCAGAUG__________
........((((((........((((((......))))))((((.....))))......((..(((((.....)))))..))...)))))).................... (-23.66 = -24.63 +   0.98)

alignment

secondary structure

dotplot

Window 0

Location	12,626,363 – 12,626,462
Length	99
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	76.13
Mean single sequence MFE	-43.30
Consensus MFE	-30.56
Energy contribution	-30.12
Covariance contribution	-0.44
Combinations/Pair	1.35
Mean z-score	-1.05
Structure conservation index	0.71
SVM decision value	0.27
SVM RNA-class probability	0.660318
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12626363 99 - 22407834
---------UCAUCUGGGUGCCACUGGUGGGCGUACUGGGCGUCAGCAUACC---ACUCAAUUUCAAACUGGCCGCCGAGCUGGGCGGCGUGAUUUGCAGUGGAUGGUGGU
---------..........((((((.((.(((((.....))))).))...((---((((((..(((.....((((((......)))))).))).))).)))))..)))))) ( -37.80)
>DroVir_CAF1 64467 95 - 1
-------------GUGGGUGCCGCUGGUGGGCGUGCUGGGCGUAAGCAUGCC---GCUCAGCUUAAGGCUGGCCGCCGAAUUGGGCGGCGUUAUCUGCAGCGGAUGAUGCG
-------------(((....((((((...((((((((.......))))))))---...((((.....))))((((((......))))))........))))))....))). ( -46.10)
>DroPse_CAF1 7389 97 - 1
----------CAUCUGCGUGCCGCUGGUGGGGGUGCUGGGGGUCAGCAUGCCGCCGCUCAUCUUGAUGCUGGCCGCCGAGCUGGGCGGCGUGAUCUGGAGCGGAUGG----
----------(((((((...((.......((.((((((.....)))))).))((((((((.((((..((.....)))))).)))))))).......)).))))))).---- ( -46.70)
>DroYak_CAF1 7462 99 - 1
---------UCAUCUGGGUGCCACUGGUGGGCGUGCUGGGCGUCAGCAUUCC---ACUCAGUUUCAGACUGGCCGCCGAGCUGGGCGGAGUGAUCUGCAGUGGGUGAUGGU
---------(((((......(((((((((((.((((((.....)))))))))---)).......(((((...(((((......)))))...).))))))))))..))))). ( -39.90)
>DroMoj_CAF1 60853 100 - 1
------CAUGGGUGUGCGAGUGGCUGGUGGGCGUGCUGGGCGUUAGCAUGCC---GCUCAGCUUCAAGCUGGCUGCCGAAUUAGGCGGCGUUAUCUGCAGCGGCUGAUG--
------(((.((((((((..((((.(((((.(((((((.....)))))))))---)))((((.....))))((((((......))))))))))..)))).).))).)))-- ( -43.10)
>DroAna_CAF1 2079 108 - 1
AGCCGCUCUGCAUCUGGGUGCCGCUGGUGGGUGUGCUGGGAGUCAGCAUUCC---GCUUAGUUUCAAGCUGGCCGCCGAGUUGGGGGGUGUGAUCUGCAGCGGCAGGUGGU
.((((((((.((.((.(((((((((((((((.((((((.....)))))))))---)))........))).)).)))).)).)).)))))...((((((....))))))))) ( -46.20)
>consensus
__________CAUCUGGGUGCCGCUGGUGGGCGUGCUGGGCGUCAGCAUGCC___GCUCAGCUUCAAGCUGGCCGCCGAGCUGGGCGGCGUGAUCUGCAGCGGAUGAUGGU
....................((((((((.((.((((((.....)))))).))...)).((((.....))))((((((......))))))........))))))........ (-30.56 = -30.12 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:36 2006