Locus 2941

Sequence ID	X_DroMel_CAF1
Location	7,886,568 – 7,886,665
Length	97
Max. P	0.982535

overview

Window 3

Location	7,886,568 – 7,886,665
Length	97
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	74.81
Mean single sequence MFE	-43.98
Consensus MFE	-31.03
Energy contribution	-31.45
Covariance contribution	0.42
Combinations/Pair	1.42
Mean z-score	-1.80
Structure conservation index	0.71
SVM decision value	1.67
SVM RNA-class probability	0.971219
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7886568 97 + 22224390
----GGU-CUAGUU-------UGGA-AUUACCUUCCGCUCUCCAUGGCGCCUAAUGGCGAGGCGGCCAGAAUGGCCUGAGCGGCCACAGCGGCCGCCACAUGCUGAGCCU
----...-......-------.(((-(.....))))((((..((((.((((....)))).(((((((....(((((.....)))))....))))))).))))..)))).. ( -46.90)
>DroPse_CAF1 406 98 + 1
----GGCAUCAACG-------AGCA-CUUACCUGCCACUCUCCAUAGCCUCCAGGGGCGAGGAGGCCAGGACGGUCUGGGCUGUCAUUGUAGUCGAUACGUUCUGGGCCU
----(((......(-------.(((-......))))..(((((...((((....))))..)))))((((((((...(.(((((......))))).)..))))))))))). ( -37.10)
>DroSec_CAF1 473 104 + 1
----GGU-CCGGUUUUAGGAUUGGG-AUUACCUUCCGCUCUCCAUGGCGCCCAAUGGCGAGGCGGCCAGAAUGGCCUGAGCGGCCACAGCGGCCGCCACAUGCUGAGCCU
----(((-((.......))))).((-(......)))((((..((((.((((....)))).(((((((....(((((.....)))))....))))))).))))..)))).. ( -49.90)
>DroEre_CAF1 525 101 + 1
----GGU-CUUGU---GGGACUGCG-AUUACCUUCCGCUCUCCAUGGCGCCCAAGGGCGAGGCGGCCAGAAUGGCCUGAGCGGCCACAGCGGCCGCCACAUGCUGCGCCU
----(((-.(..(---(((...(((-.........)))..))))..).)))...(((((.(((((((.....))))((.((((((.....))))))))...))).))))) ( -46.50)
>DroYak_CAF1 537 105 + 1
UGGUCGU-CUGGU---GGGAUUGUA-AUUACCUUCCGCUCUCCAUGGCGCCCAAUGGCGAGGCGGCCAAAAUAGCCUGUGCGGCAACAGCGGCCGCCACAUGUUGGGCCU
..(((((-..(((---((((..((.-...)).)))))))....)))))((((((((..(.(((((((......(((.....)))......))))))).).)))))))).. ( -42.60)
>DroAna_CAF1 351 96 + 1
----GGCAAUAG----------GUAACAUACCUUCCGCUUUCCAUGGCGCCCAAAGGCGAGGCUGCCAGUAUGGCUUGGGCAGCCACAGCGGCGGCCACAUGCUGCGCCU
----(((...((----------(((...)))))...((....((((.((((....)))).(((((((.((.(((((.....)))))..))))))))).))))..))))). ( -40.90)
>consensus
____GGU_CUAGU________UGCA_AUUACCUUCCGCUCUCCAUGGCGCCCAAUGGCGAGGCGGCCAGAAUGGCCUGAGCGGCCACAGCGGCCGCCACAUGCUGAGCCU
....................................((((..((((.((((....)))).(((((((....(((((.....)))))....))))))).))))..)))).. (-31.03 = -31.45 +   0.42)

alignment

secondary structure

dotplot

Window 4

Location	7,886,568 – 7,886,665
Length	97
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	74.81
Mean single sequence MFE	-44.07
Consensus MFE	-31.62
Energy contribution	-32.40
Covariance contribution	0.78
Combinations/Pair	1.30
Mean z-score	-1.98
Structure conservation index	0.72
SVM decision value	1.92
SVM RNA-class probability	0.982535
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7886568 97 - 22224390
AGGCUCAGCAUGUGGCGGCCGCUGUGGCCGCUCAGGCCAUUCUGGCCGCCUCGCCAUUAGGCGCCAUGGAGAGCGGAAGGUAAU-UCCA-------AACUAG-ACC----
..((((..((((.((((((((..((((((.....))))))..)))))))).((((....)))).))))..))))((((.....)-))).-------......-...---- ( -50.00)
>DroPse_CAF1 406 98 - 1
AGGCCCAGAACGUAUCGACUACAAUGACAGCCCAGACCGUCCUGGCCUCCUCGCCCCUGGAGGCUAUGGAGAGUGGCAGGUAAG-UGCU-------CGUUGAUGCC----
...........((((((((..((...((.(((...((..(((((((((((........)))))))).)))..)))))..))...-))..-------.)))))))).---- ( -34.20)
>DroSec_CAF1 473 104 - 1
AGGCUCAGCAUGUGGCGGCCGCUGUGGCCGCUCAGGCCAUUCUGGCCGCCUCGCCAUUGGGCGCCAUGGAGAGCGGAAGGUAAU-CCCAAUCCUAAAACCGG-ACC----
..((((..((((.((((((((..((((((.....))))))..)))))))).((((....)))).))))..))))(((......)-))...(((.......))-)..---- ( -49.00)
>DroEre_CAF1 525 101 - 1
AGGCGCAGCAUGUGGCGGCCGCUGUGGCCGCUCAGGCCAUUCUGGCCGCCUCGCCCUUGGGCGCCAUGGAGAGCGGAAGGUAAU-CGCAGUCCC---ACAAG-ACC----
.(((.......(.((((((((..((((((.....))))))..)))))))).)(((....))))))..(((..((((.......)-)))..))).---.....-...---- ( -49.40)
>DroYak_CAF1 537 105 - 1
AGGCCCAACAUGUGGCGGCCGCUGUUGCCGCACAGGCUAUUUUGGCCGCCUCGCCAUUGGGCGCCAUGGAGAGCGGAAGGUAAU-UACAAUCCC---ACCAG-ACGACCA
..((((((..((.((((((((..((.(((.....))).))..)))))))).))...))))))....(((...(.(((..((...-.))..))))---.))).-....... ( -39.80)
>DroAna_CAF1 351 96 - 1
AGGCGCAGCAUGUGGCCGCCGCUGUGGCUGCCCAAGCCAUACUGGCAGCCUCGCCUUUGGGCGCCAUGGAAAGCGGAAGGUAUGUUAC----------CUAUUGCC----
.(((.......(.(((.((((.(((((((.....))))))).)))).))).)(((....)))))).......((((.(((((...)))----------)).)))).---- ( -42.00)
>consensus
AGGCCCAGCAUGUGGCGGCCGCUGUGGCCGCUCAGGCCAUUCUGGCCGCCUCGCCAUUGGGCGCCAUGGAGAGCGGAAGGUAAU_UACA________ACUAG_ACC____
.(((.......(.((((((((..((((((.....))))))..)))))))).)(((....))))))......(.(....).)............................. (-31.62 = -32.40 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:15 2006