Locus 917

Sequence ID	X_DroMel_CAF1
Location	2,559,861 – 2,560,010
Length	149
Max. P	0.983457

overview

Window 5

Location	2,559,861 – 2,559,979
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.13
Mean single sequence MFE	-48.48
Consensus MFE	-39.74
Energy contribution	-41.10
Covariance contribution	1.36
Combinations/Pair	1.03
Mean z-score	-1.89
Structure conservation index	0.82
SVM decision value	1.20
SVM RNA-class probability	0.930231
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2559861 118 + 22224390
GACGACUCCACUGGACCGGGCGACACGUAAACAACAAUCAGAGCCCGAAGCUUCUGCCAGCGGCGGCU--UUUUAUCGCCGCCUAUGUGGUUGUUGUUGCUGCGCGCCAGGGACGUGGUC
(((.(((((.((((.....(((.((.((((.(((((((((.(.......(((......)))((((((.--.......))))))..).)))))))))))))))))).))))))).)).))) ( -49.30)
>DroSec_CAF1 1881 118 + 1
GACGACUCCACCGGACCGGGCGACACGUAAACAACAAUCAGAGCCCGAAGCUUCUGCCAGCGGCGGCU--UUUUAUCGCCGCCUAUGUGGUUGUUGUUGCUGUGCGCCAGGGACGUAGUC
...((((....((..((.((((.((((..(((((((((((.(.......(((......)))((((((.--.......))))))..).)))))))))))..)))))))).))..)).)))) ( -50.80)
>DroSim_CAF1 3935 118 + 1
GACGACUCCACCGGACCGGGCGACACGUAAACAACAAUCAGAGCCCGAAGCUUCUGCCAGCGGCGGCU--UUUUAUCGCCGCCUAUGUGGUUGUUGUUGCUGUGCGCCAGGGACGUAGUC
...((((....((..((.((((.((((..(((((((((((.(.......(((......)))((((((.--.......))))))..).)))))))))))..)))))))).))..)).)))) ( -50.80)
>DroEre_CAF1 2063 118 + 1
GACGACUCCACCGGACCGGGCGACACGUAAACAACAAUCAGAGCCCGAAGCUUCUGCCAGCGGCGA-UUUUUUUAUCGCCGCCAAUGUGGUUGUUGUUGCUGUG-GCCAUGGGCGUGGCC
.......((((....((((((.(((.((((.(((((((((((((.....))))......(((((((-(......)))))))).....)))))))))))))))).-))).)))..)))).. ( -48.30)
>DroYak_CAF1 3422 119 + 1
GACGACUCCACCGGACCGGUCGACACGUAAACAACAAUCAGAGCCCGAAGCUUCUGCCAGCGGCGACUUUUUUUAUCGCCGCCAAUGUGGUUGUUGUUGCUGUG-GCCAUGGGCGUGGCC
..(((((((...)))...))))(((.((((.(((((((((((((.....))))......(((((((.........))))))).....))))))))))))))))(-(((((....)))))) ( -43.20)
>consensus
GACGACUCCACCGGACCGGGCGACACGUAAACAACAAUCAGAGCCCGAAGCUUCUGCCAGCGGCGGCU__UUUUAUCGCCGCCUAUGUGGUUGUUGUUGCUGUGCGCCAGGGACGUGGUC
.......((((.(..((.((((.((((..(((((((((((((((.....))))......(((((((.........))))))).....)))))))))))..)))))))).))..))))).. (-39.74 = -41.10 +   1.36)

alignment

secondary structure

dotplot

Window 6

Location	2,559,861 – 2,559,979
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.13
Mean single sequence MFE	-49.50
Consensus MFE	-40.20
Energy contribution	-40.76
Covariance contribution	0.56
Combinations/Pair	1.08
Mean z-score	-2.40
Structure conservation index	0.81
SVM decision value	1.94
SVM RNA-class probability	0.983457
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2559861 118 - 22224390
GACCACGUCCCUGGCGCGCAGCAACAACAACCACAUAGGCGGCGAUAAAA--AGCCGCCGCUGGCAGAAGCUUCGGGCUCUGAUUGUUGUUUACGUGUCGCCCGGUCCAGUGGAGUCGUC
..(((((..((.(((((((...(((((((((((....((((((.......--.))))))..)))((((.((.....)))))).))))))))...))).)))).))..).))))....... ( -50.50)
>DroSec_CAF1 1881 118 - 1
GACUACGUCCCUGGCGCACAGCAACAACAACCACAUAGGCGGCGAUAAAA--AGCCGCCGCUGGCAGAAGCUUCGGGCUCUGAUUGUUGUUUACGUGUCGCCCGGUCCGGUGGAGUCGUC
((((.((..((.(((((((...(((((((((((....((((((.......--.))))))..)))((((.((.....)))))).))))))))...))).)))).))..))....))))... ( -52.10)
>DroSim_CAF1 3935 118 - 1
GACUACGUCCCUGGCGCACAGCAACAACAACCACAUAGGCGGCGAUAAAA--AGCCGCCGCUGGCAGAAGCUUCGGGCUCUGAUUGUUGUUUACGUGUCGCCCGGUCCGGUGGAGUCGUC
((((.((..((.(((((((...(((((((((((....((((((.......--.))))))..)))((((.((.....)))))).))))))))...))).)))).))..))....))))... ( -52.10)
>DroEre_CAF1 2063 118 - 1
GGCCACGCCCAUGGC-CACAGCAACAACAACCACAUUGGCGGCGAUAAAAAAA-UCGCCGCUGGCAGAAGCUUCGGGCUCUGAUUGUUGUUUACGUGUCGCCCGGUCCGGUGGAGUCGUC
(((((......))))-).....((((((((.....(..((((((((......)-)))))))..)((((.((.....)))))).)))))))).(((..(((((......)))))...))). ( -45.90)
>DroYak_CAF1 3422 119 - 1
GGCCACGCCCAUGGC-CACAGCAACAACAACCACAUUGGCGGCGAUAAAAAAAGUCGCCGCUGGCAGAAGCUUCGGGCUCUGAUUGUUGUUUACGUGUCGACCGGUCCGGUGGAGUCGUC
(((((......))))-).....((((((((.....(..((((((((.......))))))))..)((((.((.....)))))).)))))))).(((..((.((((...)))).))..))). ( -46.90)
>consensus
GACCACGUCCCUGGCGCACAGCAACAACAACCACAUAGGCGGCGAUAAAA__AGCCGCCGCUGGCAGAAGCUUCGGGCUCUGAUUGUUGUUUACGUGUCGCCCGGUCCGGUGGAGUCGUC
..(((((..((.(((((((...(((((((((((....((((((..........))))))..)))((((.((.....)))))).))))))))...))).)))).))..).))))....... (-40.20 = -40.76 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	2,559,901 – 2,560,010
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.28
Mean single sequence MFE	-39.20
Consensus MFE	-25.08
Energy contribution	-25.00
Covariance contribution	-0.08
Combinations/Pair	1.14
Mean z-score	-2.11
Structure conservation index	0.64
SVM decision value	0.39
SVM RNA-class probability	0.715554
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2559901 109 - 22224390
-------UUCGCAUUUAU-GACCCCCGUUGCAAG-CCCAGGACCACGUCCCUGGCGCGCAGCAACAACAACCACAUAGGCGGCGAUAAAA--AGCCGCCGCUGGCAGAAGCUUCGGGCUC
-------...((......-.......(((((..(-((((((........))))).))...))))).....((.....((((((.......--.))))))(((......)))...)))).. ( -40.80)
>DroSec_CAF1 1921 108 - 1
-------CUUGCGUUUAU-AACCCCCGUUGCCAG-CCCU-GACUACGUCCCUGGCGCACAGCAACAACAACCACAUAGGCGGCGAUAAAA--AGCCGCCGCUGGCAGAAGCUUCGGGCUC
-------...........-....(((((((((((-(...-......((..(((.....)))..))............((((((.......--.))))))))))))))......))))... ( -36.40)
>DroSim_CAF1 3975 108 - 1
-------CUUGCGUUUAU-AACCCCCGUUGCCAG-CCCU-GACUACGUCCCUGGCGCACAGCAACAACAACCACAUAGGCGGCGAUAAAA--AGCCGCCGCUGGCAGAAGCUUCGGGCUC
-------...........-....(((((((((((-(...-......((..(((.....)))..))............((((((.......--.))))))))))))))......))))... ( -36.40)
>DroEre_CAF1 2103 116 - 1
AAGCAGGUUUGCCUUCAU-GGCCCCCGUGCCAAAACCCU-GGCCACGCCCAUGGC-CACAGCAACAACAACCACAUUGGCGGCGAUAAAAAAA-UCGCCGCUGGCAGAAGCUUCGGGCUC
((((...((((((....(-((((..(((((((......)-)).)))).....)))-))...................(((((((((......)-)))))))))))))).))))....... ( -42.50)
>DroYak_CAF1 3462 112 - 1
------GCUUGCGUUCAAGGGUCCCCGCUGCAAGACUCU-GGCCACGCCCAUGGC-CACAGCAACAACAACCACAUUGGCGGCGAUAAAAAAAGUCGCCGCUGGCAGAAGCUUCGGGCUC
------(((((.(((...((....)).((((..(.((.(-(((((......))))-)).)))...............(((((((((.......))))))))).)))).)))..))))).. ( -39.90)
>consensus
_______CUUGCGUUUAU_GACCCCCGUUGCAAG_CCCU_GACCACGUCCCUGGCGCACAGCAACAACAACCACAUAGGCGGCGAUAAAA__AGCCGCCGCUGGCAGAAGCUUCGGGCUC
.......................((((((((.....((..(((...)))...))......)))))............((((((..........))))))(((......)))...)))... (-25.08 = -25.00 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:11 2006