Locus 1453

Sequence ID	2R_DroMel_CAF1
Location	5,551,419 – 5,551,568
Length	149
Max. P	0.843705

overview

Window 2

Location	5,551,419 – 5,551,528
Length	109
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	79.76
Mean single sequence MFE	-34.12
Consensus MFE	-22.88
Energy contribution	-23.02
Covariance contribution	0.14
Combinations/Pair	1.26
Mean z-score	-1.83
Structure conservation index	0.67
SVM decision value	0.76
SVM RNA-class probability	0.843705
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5551419 109 + 20766785
UUUCCAAUGUU-GUAAUUACCUUUGGACAAUACGUGGAUCUUGGGUGCGGAUAACGAUGUAACAUAUUGCCGGCAAUCCGGCAAUGUGGAUUGCCUGCUGACCAAAGCAA
..((((.((((-((............))))))..))))..((((..((((....((((....(((((((((((....))))))))))).)))).))))...))))..... ( -33.10)
>DroPse_CAF1 5035 109 + 1
UUCUAUGUGUA-UUCGUUACCUCUGCACAAUGCGCGGAUCUUGGGUGCGUAUGACUAUGUAGCAUAUUGCCGGAAGACCGGCAAUGUGUAUCGCCUGCUGGCCAAAGCAA
...((((((((-((((.....(((((.......)))))...))))))))))))....(((.((((((((((((....))))))))))))...(((....)))....))). ( -37.60)
>DroGri_CAF1 46176 108 + 1
UUCACAAUUUAG--GCUUACCUCUGCACAAUGCGUGGAUCCUGUGUGCGUAUUACAAUGAAACAUAUUGCGGGCAGUCCGGCAAUGUGUAUGGCCUGCUGGCCAAAGCAA
............--((((.....((((((.(((.((((..((((.((((..................)))).))))))))))).))))))(((((....))))))))).. ( -36.37)
>DroWil_CAF1 2146 106 + 1
UUCGAU---UU-UUACUUACCUCUGAACAAUGCGUGGAUCUUGAGUACGGAUGACGAUGUAACAUAUUGCCGGCAAUCCAGCAAUAUGUAUUGCCUGUUGGCCGAAACAA
((((((---(.-.((((((..(((..((.....)))))...))))))..))).........(((((((((.((....)).)))))))))...(((....))))))).... ( -24.10)
>DroMoj_CAF1 56514 99 + 1
UGC-----------ACUUACCUCUGAACAAUACGCGGAUCCUGUGUGCGUAUGACUAUAAAGCAGAUGGCCGGCAGUCCGGCAAUGUGUAUUGCCUGCUGGCCAAAGCAA
(((-----------.......((((....(((((((.((...)).)))))))..........))))(((((((((....((((((....)))))))))))))))..))). ( -35.94)
>DroPer_CAF1 4984 109 + 1
UUCUAUGUGUA-UUCGUUACCUCUGCACAAUGCGCGGAUCUUGGGUGCGUAUGACUAUGUAGCAUAUUGCCGGAAGACCGGCAAUGUGUAUCGCCUGCUGGCCAAAGCAA
...((((((((-((((.....(((((.......)))))...))))))))))))....(((.((((((((((((....))))))))))))...(((....)))....))). ( -37.60)
>consensus
UUCUAU_UGUA_UUACUUACCUCUGCACAAUGCGCGGAUCUUGGGUGCGUAUGACUAUGUAACAUAUUGCCGGCAGUCCGGCAAUGUGUAUUGCCUGCUGGCCAAAGCAA
.............................(((((((.........))))))).........((((((((((((....))))))))))))......((((......)))). (-22.88 = -23.02 +   0.14)

alignment

secondary structure

dotplot

Window 3

Location	5,551,448 – 5,551,568
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.22
Mean single sequence MFE	-35.63
Consensus MFE	-23.14
Energy contribution	-23.50
Covariance contribution	0.36
Combinations/Pair	1.27
Mean z-score	-1.51
Structure conservation index	0.65
SVM decision value	0.19
SVM RNA-class probability	0.627878
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5551448 120 - 20766785
ACACAUUCGCCCUAUCGAUUGGCCUGGCCUUCGGCUACUUUUGCUUUGGUCAGCAGGCAAUCCACAUUGCCGGAUUGCCGGCAAUAUGUUACAUCGUUAUCCGCACCCAAGAUCCACGUA
........((......(((((.(((((((...(((.......)))..))))))..).)))))((.((((((((....)))))))).))..............))................ ( -33.10)
>DroVir_CAF1 68701 120 - 1
ACGCUUUCGCCAUGUCCUUGGGCCUGGCCUUUGGCUACUUUUGCUUUGGCCAGCAGGCCAUACACAUAGCCGGUUUGCCGGCCUUAUGCUAUAUCGUGAUACGCACCCAGGAUCCGCGCA
.......(((...(((((.((((.(((((((((((((.........))))))).))))))....(((((((((....)))))..))))..............)).)).)))))..))).. ( -43.40)
>DroGri_CAF1 46204 120 - 1
ACGUCUUCGCCUUAUCGCUGGGCCUGGCCUUUGGCUACUUUUGCUUUGGCCAGCAGGCCAUACACAUUGCCGGACUGCCCGCAAUAUGUUUCAUUGUAAUACGCACACAGGAUCCACGCA
................(((((((((((((((((((((.........))))))).)))))..(((.(((((.((....)).))))).)))...................))).)))).)). ( -36.70)
>DroWil_CAF1 2172 120 - 1
ACGUGUUUGCCCUAUCACUUGGCCUGACCUUUGGUUACUUUUGUUUCGGCCAACAGGCAAUACAUAUUGCUGGAUUGCCGGCAAUAUGUUACAUCGUCAUCCGUACUCAAGAUCCACGCA
.((((.(((((.......((((((.((((...))))((....))...))))))..))))).((((((((((((....)))))))))))).........................)))).. ( -34.60)
>DroMoj_CAF1 56533 120 - 1
AUGUCUUUGCCCUUUCGCUUGGCCUGGCCUUUGGCUACUUUUGCUUUGGCCAGCAGGCAAUACACAUUGCCGGACUGCCGGCCAUCUGCUUUAUAGUCAUACGCACACAGGAUCCGCGUA
...............(((....((((((...((((((.....((..(((((.(((((((((....))))))....))).)))))...))....))))))...))...))))....))).. ( -38.00)
>DroAna_CAF1 4966 120 - 1
ACACAUUCGCUUUGUCGAUCGGCCUCGCCUUUGGAUACUUUUGUUUCGGUCCCCAGGCCAUUCACAUCGCAGGACUUCCGGCGAUAUGCUACAUUGUUAUUCGAACCCAGGAUCCCCGCA
........((...(..(((((((...)))((((((((.(..(((..(((((....))))......(((((.((....)).)))))..)..)))..).)))))))).....))))..))). ( -28.00)
>consensus
ACGCAUUCGCCCUAUCGCUUGGCCUGGCCUUUGGCUACUUUUGCUUUGGCCAGCAGGCAAUACACAUUGCCGGACUGCCGGCAAUAUGCUACAUCGUCAUACGCACCCAGGAUCCACGCA
........((...(((.....((((((((...(((.......)))..)))...)))))....((.((((((((....)))))))).))......................)))....)). (-23.14 = -23.50 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:16 2006