Locus 3159

Sequence ID	2R_DroMel_CAF1
Location	10,790,503 – 10,790,629
Length	126
Max. P	0.948889

overview

Window 4

Location	10,790,503 – 10,790,605
Length	102
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	75.60
Mean single sequence MFE	-29.87
Consensus MFE	-7.46
Energy contribution	-9.60
Covariance contribution	2.14
Combinations/Pair	1.18
Mean z-score	-2.56
Structure conservation index	0.25
SVM decision value	0.05
SVM RNA-class probability	0.557219
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10790503 102 - 20766785
UUC-GCGAUGGAAAUCUCUUGAGCUGCUCGCAAACAA----AUGGCGA-----ACAGCUGAAAAAA-AGCAU-UGAAAUGGAGCUGUU--UUCAUUGUUAUUCAAG-CAUCCCUGCA-
...-((((((((((((((((.(((((.((((......----...))))-----.))))).))....-..(((-....))))))..)))--)))))))).......(-((....))).- ( -27.10)
>DroPse_CAF1 1029 99 - 1
UUC-AGCCUGGAAGGUACUCGACCUGCCAGCAAACAAUGAAAUGG-GU-----ACACAU-----AAUAGAAUGUGAAUUGGAGG-GCU--UUCAUUAUCCGUUUGGUUGUACCC----
...-.((.(((.((((.....)))).)))))..(((((.((((((-((-----((((((-----......)))))...(((((.-..)--)))).))))))))).)))))....---- ( -29.50)
>DroSec_CAF1 1100 103 - 1
UUC-GCGAUGGAAAUCUCUUGAGCUGUUCGCAAACAA----AUGGCGA-----ACAGCUGAAAAAAUAGCAU-UGAAAUGGAGCCGUU--UUCAUUGUUAUUCAAG-CAUCCCUGCA-
...-(((((....))).((((((((((((((......----...))))-----)))))).....(((((((.-(((((((....)).)--)))).)))))))))))-.......)).- ( -33.40)
>DroEre_CAF1 1100 103 - 1
UUC-GCGAUGGAAAUCUCUUAAGCUGUUCGCAAACAA----AUGGCGA-----ACAGCUGAAAAAAUAGCAU-CGAAAUGGAGCCGUU--UUCAUUGUUAUUCAAG-CAUUCCUCCA-
...-(.((.((((........((((((((((......----...))))-----)))))).....(((((((.-.((((((....))))--))...)))))))....-..))))))).- ( -29.90)
>DroYak_CAF1 1634 105 - 1
UUC-GCGAUGGAAAUCCCUUAAGCUGUUCGCAAACAA----AUGGCGA-----ACAGCUGAAAAAAUAGCAU-CGAAACGGAGCCGUUUUUUCAUUGUUAUUCAAG-CAUCCCUGCA-
...-(((..(((.........((((((((((......----...))))-----))))))(((((((..((..-((...))..))..))))))).............-..))).))).- ( -31.70)
>DroAna_CAF1 1102 108 - 1
UUAGGCGAUGAAAAUCUCUUAAGCUGUCCGCAAACAA----UGGCCGACAAGCACAGCA-AAAAAAUUGAAU-UGAAAUGGAGGCGUU---UCAUUGUUAUUCAAG-UCCCGCUGCAG
(((((.(((....))).)))))((((((.((......----..)).))).))).((((.-......((((((-(((((((....))))---))).....)))))).-....))))... ( -27.60)
>consensus
UUC_GCGAUGGAAAUCUCUUAAGCUGUUCGCAAACAA____AUGGCGA_____ACAGCUGAAAAAAUAGCAU_UGAAAUGGAGCCGUU__UUCAUUGUUAUUCAAG_CAUCCCUGCA_
....((((((((.........((((((((((.............)))).....)))))).................((((....))))..)))))))).................... ( -7.46 =  -9.60 +   2.14)

alignment

secondary structure

dotplot

Window 5

Location	10,790,537 – 10,790,629
Length	92
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.44
Mean single sequence MFE	-21.75
Consensus MFE	-5.84
Energy contribution	-7.92
Covariance contribution	2.08
Combinations/Pair	1.11
Mean z-score	-3.15
Structure conservation index	0.27
SVM decision value	1.39
SVM RNA-class probability	0.948889
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10790537 92 - 20766785
------------ACC---AAAACC-AAAUUACAUUUACAUUUC-GCGAUGGAAAUCUCUUGAGCUGCUCGCAAACAA----AUGGCGA-----ACAGCUGAAAAAA-AGCAU-UGAAAUG
------------...---......-............((((((-(((((....)))..((.(((((.((((......----...))))-----.))))).))....-.))..-.)))))) ( -21.20)
>DroSec_CAF1 1134 92 - 1
------------ACC---AAA-CC-CAAUUACAUUUACAUUUC-GCGAUGGAAAUCUCUUGAGCUGUUCGCAAACAA----AUGGCGA-----ACAGCUGAAAAAAUAGCAU-UGAAAUG
------------...---...-..-............((((((-(((((....)))..((.((((((((((......----...))))-----)))))).))......))..-.)))))) ( -25.40)
>DroEre_CAF1 1134 92 - 1
------------ACC---AAA-CC-AAAUUACAUUUACAUUUC-GCGAUGGAAAUCUCUUAAGCUGUUCGCAAACAA----AUGGCGA-----ACAGCUGAAAAAAUAGCAU-CGAAAUG
------------...---...-..-............((((((-(.(((....))).....((((((((((......----...))))-----)))))).............-))))))) ( -25.00)
>DroYak_CAF1 1670 92 - 1
------------ACC---AAA-CC-AAAUUACAUUUACAUUUC-GCGAUGGAAAUCCCUUAAGCUGUUCGCAAACAA----AUGGCGA-----ACAGCUGAAAAAAUAGCAU-CGAAACG
------------...---...-..-..................-.(((((...........((((((((((......----...))))-----))))))..........)))-))..... ( -21.90)
>DroAna_CAF1 1136 109 - 1
CUUUCAAAGAAAAAC---AAA-CA-AAAUUACAUUUACAUUUAGGCGAUGAAAAUCUCUUAAGCUGUCCGCAAACAA----UGGCCGACAAGCACAGCA-AAAAAAUUGAAU-UGAAAUG
.((((((........---...-..-...............(((((.(((....))).)))))((((((.((......----..)).))).)))......-...........)-))))).. ( -18.70)
>DroPer_CAF1 1060 95 - 1
------------ACAAGAAAA-CCAAAAUUAUAUUCAAAUUUC-AGCCUGGAAGGUACUCGACCUGCCAGCAAACAAUGAAAUGG-GU-----ACACAU-----AAUAGAAUGUGAAUUG
------------.........-.........((((((..((((-(..((((.((((.....)))).)))).......))))))))-))-----)(((((-----......)))))..... ( -18.30)
>consensus
____________ACC___AAA_CC_AAAUUACAUUUACAUUUC_GCGAUGGAAAUCUCUUAAGCUGUUCGCAAACAA____AUGGCGA_____ACAGCUGAAAAAAUAGCAU_UGAAAUG
.....................................((((((...(((....))).....((((((((((.............)))).....))))))...............)))))) ( -5.84 =  -7.92 +   2.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:55 2006