Locus 6535

Sequence ID	3R_DroMel_CAF1
Location	17,243,739 – 17,243,873
Length	134
Max. P	0.812687

overview

Window 5

Location	17,243,739 – 17,243,833
Length	94
Sequences	4
Columns	94
Reading direction	forward
Mean pairwise identity	75.68
Mean single sequence MFE	-29.27
Consensus MFE	-17.02
Energy contribution	-18.89
Covariance contribution	1.87
Combinations/Pair	1.13
Mean z-score	-1.83
Structure conservation index	0.58
SVM decision value	0.34
SVM RNA-class probability	0.697029
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17243739 94 + 27905053
AUUUGGGCGCUGAGCGGGUUCAUGCUUGUAUUUUCCCCCUUCUGGCCCAGAUUCACUACCCCUUUCGGUGGUGGAAGGGUCCAUCCACUGCAUC
.(((((((.(.(((.(((...(((....)))...))).)))..))))))))(((((((((......))))))))).(((....)))........ ( -30.50)
>DroSec_CAF1 40206 74 + 1
AUUUGGGCGCUGUG-----------------UUUCCCCCCUCUGGCCCAGAUUCACUACCUCUUUCGGUGGUGGAUGGAUC---CUACUGCAUC
..((((((.(.(.(-----------------........).).)))))))((((((((((......)))))))))).....---.......... ( -21.40)
>DroEre_CAF1 40999 89 + 1
AUUUGGGCGCUGAGCAG-CCCCUGCUUGCCCUCUC-CCCCUCUGGCCCCAAGUCACUACCCCUUUCGGUGGUGGAUGGGUC---CUACUACAUC
....((((...((((((-...))))))))))....-.......((.((((..((((((((......)))))))).)))).)---)......... ( -32.40)
>DroYak_CAF1 62941 89 + 1
AUUUGGGCGCUGAGCAG-CCCAUGCUGGCCCAAUC-CCCCUCUGGACCCGAAUCACUGCCACUUUCGGUGGUGGAUGGGCC---CCACUACAUC
...(((((........)-))))....((((((.((-(......)))......((((..((......))..)))).))))))---.......... ( -32.80)
>consensus
AUUUGGGCGCUGAGCAG_CCCAUGCUUGCCCUUUC_CCCCUCUGGCCCAGAUUCACUACCCCUUUCGGUGGUGGAUGGGUC___CCACUACAUC
....(((....(((((......))))).........)))....(((((..((((((((((......)))))))))))))))............. (-17.02 = -18.89 +   1.87)

alignment

secondary structure

dotplot

Window 6

Location	17,243,765 – 17,243,873
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.03
Mean single sequence MFE	-27.89
Consensus MFE	-11.91
Energy contribution	-11.99
Covariance contribution	0.08
Combinations/Pair	1.21
Mean z-score	-1.83
Structure conservation index	0.43
SVM decision value	0.35
SVM RNA-class probability	0.700705
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17243765 108 + 27905053
----------UGUAUUUUCCCCCUUCUGGCCCAGAUUCA--CUACCCCUUUCGGUGGUGGAAGGGUCCAUCCACUGCAUCAUUUUUAUGUUUGCAUGCUCUUUAAGCCCUCCCGAUCUGG
----------...........((....)).(((((((.(--(((((......))))))((.(((((........((((.(((....)))..))))..........))))).))))))))) ( -28.67)
>DroSec_CAF1 40220 100 + 1
---------------UUUCCCCCCUCUGGCCCAGAUUCA--CUACCUCUUUCGGUGGUGGAUGGAUC---CUACUGCAUCAUUUUUAUGUUUGCAUGCUCUUUAAGCCCUCCCGAUCUGG
---------------...............(((((((((--(((((......)))))))...(((..---....((((.(((....)))..)))).(((.....)))..))).))))))) ( -25.40)
>DroEre_CAF1 41024 104 + 1
----------UGCCCUCUC-CCCCUCUGGCCCCAAGUCA--CUACCCCUUUCGGUGGUGGAUGGGUC---CUACUACAUCAUUUUUAUGUUUGCAUGCUCUUUAAGCCCUCCCGAUCUGG
----------.........-.......((.((((..(((--(((((......)))))))).)))).)---)..(((.(((......(((....)))(((.....)))......))).))) ( -23.50)
>DroYak_CAF1 62966 104 + 1
----------GGCCCAAUC-CCCCUCUGGACCCGAAUCA--CUGCCACUUUCGGUGGUGGAUGGGCC---CCACUACAUCAUUUUUAUGUUUGCAUGCUCUUUAAGCCCUCCCGAUCUGG
----------((((((.((-(......)))......(((--(..((......))..)))).))))))---...(((.(((......(((....)))(((.....)))......))).))) ( -27.70)
>DroAna_CAF1 32022 104 + 1
GACCAGGCAAGGCCC-AUCCCGCCCCUGC-ACCGAUUAGUCCUCCCUCUUGGGAGGCUGGA-GAGU----CCAGUGCAUCAUCUUUAUGUUUGCAUGCCCUUU-AGCUCUCC--------
...((((...(((..-.....))))))).-.......((.((((((....))))))))(((-((((----..((.((((((..........)).)))).))..-.)))))))-------- ( -34.20)
>consensus
__________GGCCCUAUCCCCCCUCUGGCCCCGAUUCA__CUACCCCUUUCGGUGGUGGAUGGGUC___CCACUGCAUCAUUUUUAUGUUUGCAUGCUCUUUAAGCCCUCCCGAUCUGG
.........................................(((((......))))).(((.((((........((((.(((....)))..))))..........)))))))........ (-11.91 = -11.99 +   0.08)

alignment

secondary structure

dotplot

Window 7

Location	17,243,765 – 17,243,873
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.03
Mean single sequence MFE	-32.90
Consensus MFE	-13.26
Energy contribution	-13.06
Covariance contribution	-0.20
Combinations/Pair	1.23
Mean z-score	-1.92
Structure conservation index	0.40
SVM decision value	0.65
SVM RNA-class probability	0.812687
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17243765 108 - 27905053
CCAGAUCGGGAGGGCUUAAAGAGCAUGCAAACAUAAAAAUGAUGCAGUGGAUGGACCCUUCCACCACCGAAAGGGGUAG--UGAAUCUGGGCCAGAAGGGGGAAAAUACA----------
((((((((((((((((......((.((((..(((....))).))))))....)).)))))))(((.((....)))))..--.).)))))).((......)).........---------- ( -35.90)
>DroSec_CAF1 40220 100 - 1
CCAGAUCGGGAGGGCUUAAAGAGCAUGCAAACAUAAAAAUGAUGCAGUAG---GAUCCAUCCACCACCGAAAGAGGUAG--UGAAUCUGGGCCAGAGGGGGGAAA---------------
(((((((((..(((((((....((((.((..........))))))..)))---).)))..))((.(((......))).)--)).)))))).((......))....--------------- ( -24.50)
>DroEre_CAF1 41024 104 - 1
CCAGAUCGGGAGGGCUUAAAGAGCAUGCAAACAUAAAAAUGAUGUAGUAG---GACCCAUCCACCACCGAAAGGGGUAG--UGACUUGGGGCCAGAGGGG-GAGAGGGCA----------
((((.(((((((((((((....((((.((..........))))))..)))---).))).)))(((.((....)))))..--))).)))).(((.......-.....))).---------- ( -29.60)
>DroYak_CAF1 62966 104 - 1
CCAGAUCGGGAGGGCUUAAAGAGCAUGCAAACAUAAAAAUGAUGUAGUGG---GGCCCAUCCACCACCGAAAGUGGCAG--UGAUUCGGGUCCAGAGGGG-GAUUGGGCC----------
((..(((((((((((((.....((.((((..(((....))).)))))).)---))))).))).(((.(....))))...--))))..))((((((.....-..)))))).---------- ( -31.20)
>DroAna_CAF1 32022 104 - 1
--------GGAGAGCU-AAAGGGCAUGCAAACAUAAAGAUGAUGCACUGG----ACUC-UCCAGCCUCCCAAGAGGGAGGACUAAUCGGU-GCAGGGGCGGGAU-GGGCCUUGCCUGGUC
--------((((((((-(....((((.((..........))))))..)))----.)))-)))((((((((....)))))).)).(((((.-((((((.(.....-.).))))))))))). ( -43.30)
>consensus
CCAGAUCGGGAGGGCUUAAAGAGCAUGCAAACAUAAAAAUGAUGCAGUGG___GACCCAUCCACCACCGAAAGAGGUAG__UGAAUCGGGGCCAGAGGGGGGAAAGGGCA__________
........((((((((.....))).((((..(((....))).))))..........)).)))(((.((....)))))..............((....))..................... (-13.26 = -13.06 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:50 2006