Locus 5139

Sequence ID	3R_DroMel_CAF1
Location	13,524,124 – 13,524,424
Length	300
Max. P	0.940296

overview

Window 5

Location	13,524,124 – 13,524,230
Length	106
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	76.45
Mean single sequence MFE	-51.82
Consensus MFE	-33.99
Energy contribution	-35.15
Covariance contribution	1.16
Combinations/Pair	1.22
Mean z-score	-1.42
Structure conservation index	0.66
SVM decision value	0.57
SVM RNA-class probability	0.787013
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13524124 106 + 27905053
CCACUGGCACCCUG---UCCC------UGCGGCUGGCCGCCUUGGAGCAUUUGGGAUUGCGGCGGCGUGCUAGUGGGUGGACCCAUGUUGGUGGGUCCGUGCGGGGGUCCCAUGU
((((((((((.(((---((((------.((((....))))...)).(((........)))))))).))))))))))..((((((((....))))))))....(((...))).... ( -54.10)
>DroSec_CAF1 8723 112 + 1
CCACUGGCACCCUG---UCCCUGACCCUGGGGCUGGCCGCCUUGGAGCAUUUGGGAUUGCGGCGGCGUGCUAGUGGGUGGACCCAUGUUGGUGGGUCCGUGCGGGGGUCCCAUAU
((((((((((...(---((((.......)))))..((((((.....(((........)))))))))))))))))))..((((((((....))))))))....(((...))).... ( -58.00)
>DroEre_CAF1 8707 112 + 1
CCACUGGCGCCCUG---UCCCUGGCCCUGGGGCUGGCCGCCCUGAAGCAUUUGCGAUUGCGGCGGCGUGCUAGUGGGUGGACCCAUGUUGGUGGGUCCGUGCGGGGGUCCCAUGU
((((((((((...(---((((.......)))))..(((((((....((....))....).))))))))))))))))..((((((((....))))))))....(((...))).... ( -59.20)
>DroWil_CAF1 15730 88 + 1
CCGCUGCCUCCCUGGGCUCCC------------------------AGCAU---GGAUUGUGGCGGUGUGCUCGUAGGUGGACCCAUGCUUGUUGGUCCAUGAGGCGGGCCCAUAU
((((..(.(((((((....))------------------------))...---)))..)..))))((.((((((..(((((((.((....)).)))))))...)))))).))... ( -39.70)
>DroYak_CAF1 7996 112 + 1
CCACUGGCGCCCUG---UCCCUGACCCUGGGGCUGGCCGCCCUGGAGCAUUUGCGAUUGUGGCGGCGUGCUAGUGGGUGGACCCAUGUUGGUGGGUCCGUGCGGGGGUCCCAUGU
((((((((((...(---((((.......)))))..(((((((....((....))....).))))))))))))))))..((((((((....))))))))....(((...))).... ( -59.20)
>DroAna_CAF1 21678 109 + 1
CCGCCGGUGGUCUG---CCCUUGUCCCUGCCCCUGA---CCCUGUAGCAUCUGCGACUGAGGCGGCGUGCUGGUAGGUGGGCCCAUACUAGUUGGCCCGUGUGGAGGGCCCAUGU
......((((...(---(((((...((((((.....---......(((((((((.......)))).))))))))))).(((((.((....)).))))).....)))))))))).. ( -40.70)
>consensus
CCACUGGCGCCCUG___UCCCUG_CCCUGGGGCUGGCCGCCCUGGAGCAUUUGCGAUUGCGGCGGCGUGCUAGUGGGUGGACCCAUGUUGGUGGGUCCGUGCGGGGGUCCCAUGU
((((((((((.(((....((........(((((.....)))))...(((........)))))))).))))))))))..((((((((....))))))))(((.((....))))).. (-33.99 = -35.15 +   1.16)

alignment

secondary structure

dotplot

Window 6

Location	13,524,150 – 13,524,270
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.28
Mean single sequence MFE	-39.39
Consensus MFE	-24.27
Energy contribution	-23.88
Covariance contribution	-0.39
Combinations/Pair	1.39
Mean z-score	-1.95
Structure conservation index	0.62
SVM decision value	1.29
SVM RNA-class probability	0.940296
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13524150 120 - 27905053
ACCGGAAUGCAUCCUGGCAUGCCAAUGGGGCCACCCCACCACAUGGGACCCCCGCACGGACCCACCAACAUGGGUCCACCCACUAGCACGCCGCCGCAAUCCCAAAUGCUCCAAGGCGGC
...((..(((....(((....)))..((((....((((.....))))..))))))).(((((((......)))))))..))........(((((((((........))).....)))))) ( -45.30)
>DroVir_CAF1 11617 99 - 1
ACCGGCAUGCAUCCGGCAAUGCCUAUGGGCCCACCACAUCAUAUGGGUCCGCCACAA---------AGUAUGGGGCCACCUACUAGCACGCCGCCUCAGGCU---AUGCUA---------
...(((((((.....)).)))))...(((((((..........)))))))(((.((.---------....)).))).......(((((.(((......))).---.)))))--------- ( -33.10)
>DroPse_CAF1 9016 108 - 1
ACCGGAAUGCACCCUGGCAUGCCAAUGGGUCCGCCCCACCACAUGGGCCCGCCGCACGGGCCAACCAACAUGGGUCCGCCCACGAGCACCCCGCCCCAGUCG---AUGCUC---------
...((.((((......)))).))..(((((..((((.........((((((.....)))))).........))))..))))).((((((..(......)..)---.)))))--------- ( -38.97)
>DroWil_CAF1 15751 107 - 1
ACUGGAAUGCAUCCCGGCAUGCCGAUGGGUCCACCUCAUCAUAUGGGCCCGCCUCAUGGACCAACAAGCAUGGGUCCACCUACGAGCACACCGCCACAAUCC---AUGCU----------
..((((.((.....(((..(((((..(((((((..........)))))))......((((((..........))))))....)).)))..)))...)).)))---)....---------- ( -33.40)
>DroAna_CAF1 21710 117 - 1
ACGGGAAUGCAUCCCGGCAUGCCGAUGGGACCACCUCAUCACAUGGGCCCUCCACACGGGCCAACUAGUAUGGGCCCACCUACCAGCACGCCGCCUCAGUCGCAGAUGCUACAGGG---U
..((((.....))))(((.(((.((((((.....))))))...(((((((.((....))((......))..))))))).......))).)))((((..((.((....)).)).)))---) ( -42.70)
>DroPer_CAF1 8237 108 - 1
ACCGGAAUGCACCCUGGCAUGCCAAUGGGUCCGCCCCACCACAUGGGCCCGCCGCACGGGCCCACCAACAUGGGUCCGCCCACGAGCACCCCGCCCCAGUCG---AUGCUC---------
...((.((((......)))).))..(((((..((((.......((((((((.....)))))))).......))))..))))).((((((..(......)..)---.)))))--------- ( -42.84)
>consensus
ACCGGAAUGCAUCCUGGCAUGCCAAUGGGUCCACCCCACCACAUGGGCCCGCCGCACGGGCCAACCAACAUGGGUCCACCCACGAGCACGCCGCCCCAGUCG___AUGCUC_________
..(((..(((.((((((....)))..(((((((..........))))))).......)))..........((((....))))...)))..)))........................... (-24.27 = -23.88 +  -0.39)

alignment

secondary structure

dotplot

Window 7

Location	13,524,190 – 13,524,305
Length	115
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	77.72
Mean single sequence MFE	-47.40
Consensus MFE	-25.20
Energy contribution	-26.65
Covariance contribution	1.45
Combinations/Pair	1.27
Mean z-score	-2.14
Structure conservation index	0.53
SVM decision value	0.86
SVM RNA-class probability	0.867933
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13524190 115 - 27905053
CGCCGCAGGG---GCCUCAGGGGUACGGCAACGGGCCGACCGGAAUGCAUCCUGGCAUGCCAAUGGGGCCACCCCACCACAUGGGACCCCCGCACGGACCCACCAACAUGGGUCCACC
....((.(((---((((((..(((.((((.....)))))))((.((((......)))).))..)))))))..((((.....))))...)).))..(((((((......)))))))... ( -54.10)
>DroVir_CAF1 11645 103 - 1
GUCCACA------GCCGCAGGGAUAUGGCAAUGGGCCGACCGGCAUGCAUCCGGCAAUGCCUAUGGGCCCACCACAUCAUAUGGGUCCGCCACAA---------AGUAUGGGGCCACC
.......------(((.((......((((..((((((.(..(((((((.....)).)))))..).))))))(((.......)))....))))...---------....)).))).... ( -37.82)
>DroPse_CAF1 9044 118 - 1
CACAGCAGGGCGUGCCGCAAGGCUAUGGCAACGGCCCGACCGGAAUGCACCCUGGCAUGCCAAUGGGUCCGCCCCACCACAUGGGCCCGCCGCACGGGCCAACCAACAUGGGUCCGCC
....((.(((((.(((....)))...(....)((((((...((.((((......)))).))..))))))))))).(((.((((((((((.....))))))......)))))))..)). ( -51.50)
>DroWil_CAF1 15778 112 - 1
CGCCCCA------ACCGCAAGGCUACGGCAAUGGACCGACUGGAAUGCAUCCCGGCAUGCCGAUGGGUCCACCUCAUCAUAUGGGCCCGCCUCAUGGACCAACAAGCAUGGGUCCACC
.(((...------.((....))....)))..((((((..((((........))))(((((....(((((((..........))))))).((....))........))))))))))).. ( -42.50)
>DroYak_CAF1 8068 115 - 1
CGCCUCAGGG---GACUCAAGGCUACGGCAACGGGCCGACCGGUAUGCAUCCUGGUAUGCCAAUGGGGCCACCCCACCACAUGGGACCCCCGCACGGACCCACCAACAUGGGUCCACC
.((....(((---(.((((.((((.((....))))))....(((((((......)))))))..(((((...))))).....)))).)))).))..(((((((......)))))))... ( -51.90)
>DroAna_CAF1 21747 115 - 1
CGCCACAGGG---ACCUCAAGGAUACGGAAACGGUCCGACGGGAAUGCAUCCCGGCAUGCCGAUGGGACCACCUCAUCACAUGGGCCCUCCACACGGGCCAACUAGUAUGGGCCCACC
.......(((---.((....((((.((....))))))..(((((.....))))).(((((.((((((.....)))))).....(((((.......))))).....))))))))))... ( -46.60)
>consensus
CGCCACAGGG___GCCGCAAGGCUACGGCAACGGGCCGACCGGAAUGCAUCCUGGCAUGCCAAUGGGGCCACCCCACCACAUGGGCCCGCCGCACGGACCAACCAACAUGGGUCCACC
..............((....))....(((...(((((.(..((.((((......)))).))..).)))))..((((.....))))...)))....(((((..........)))))... (-25.20 = -26.65 +   1.45)

alignment

secondary structure

dotplot

Window 8

Location	13,524,305 – 13,524,424
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.76
Mean single sequence MFE	-41.27
Consensus MFE	-20.94
Energy contribution	-21.50
Covariance contribution	0.56
Combinations/Pair	1.33
Mean z-score	-1.96
Structure conservation index	0.51
SVM decision value	0.48
SVM RNA-class probability	0.752843
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13524305 119 - 27905053
ACCGCCACCUCCAGUUGUGGGCGGACCACCACCACCGCAGGGCAGUGGAUCACCGCGUCCACUUAACUAUCUGAAGCAGCAUUUACAGCACAAGGGCGGCUAUGGUGGAAGUCCGACUC-
.((((.((.....)).)))).(((((..((((((((((.((((.((((....)))))))).........(((...((..........))...)))))))...))))))..)))))....- ( -42.80)
>DroPse_CAF1 9162 116 - 1
ACCGCCGCCUCCGGUGGUGGG---UCCACCGCCUCCUCAAGGCAGUGGCUCGCCACGCCCACUCAACUAUCUGAAGCAGCAUUUACAGCACAAAGGUGGCUACGGUGGCAGCCCCACGC-
...((.(((.(((((((((((---.((((.((((.....)))).))))))))))))(((.(((((......)))....((.......))......)))))..))).))).)).......- ( -47.20)
>DroGri_CAF1 11860 111 - 1
ACCACCGC---CGGUG------GGGCCACCGCCACCCCAAGGCAGUGGUUCGCCACGCCCACUCAACUAUCUGAAACAGCAUUUACAACACAAAGGUGGAUACGGCGCCAGUCCAGCUGG
.....(((---(((((------....)))).(((((....(((.((((....)))))))...(((......)))....................)))))....))))((((.....)))) ( -37.50)
>DroWil_CAF1 15890 116 - 1
ACCACCAC---CCGUUGGACCAGGCCCACCGCCACCUCAGGGCGGUGGAUCACCACGCCCAUUAAACUAUCUUAAGCAGCAUUUACAGCACAAAGGUGGCUACGGCGGCAGUCCUACAC-
........---..((.((((...((((...(((((((..(((((.(((....))))))))..................((.......))....)))))))....).))).)))).))..- ( -40.20)
>DroMoj_CAF1 12357 110 - 1
ACCACCAC---CAGUU------GGACCACCACCGCCACAGGGCAGUGGCUCUCCGCGUCCUCUUAACUAUCUUAAGCAGCAUUUACAACACAAAGGUGGAUAUGGCGGUAGUCCAGCGG-
.......(---(.(((------((((....(((((((.(((((.((((....))))))))).....(((((((...................)))))))...))))))).)))))))))- ( -37.81)
>DroAna_CAF1 21862 119 - 1
UCCACCGCCACCAGUUGUGGGCGGACCUCCUCCACCGCAAGGAAGCGGCUCGCCACGGCCACUGAACUAUUUGAAGCAGCAUUUACAGCACAAAGGCGGCUACGGAGGUAGUCCAACGC-
(((((.((.....)).))))).((((..(((((.((....))..(..((.((((.(((...)))..............((.......)).....))))))..))))))..)))).....- ( -42.10)
>consensus
ACCACCAC___CAGUUGUGGG_GGACCACCGCCACCGCAAGGCAGUGGCUCGCCACGCCCACUCAACUAUCUGAAGCAGCAUUUACAGCACAAAGGUGGCUACGGCGGCAGUCCAACGC_
......................((((..(((((.......((..((((....))))..))......((((((.....................))))))....)))))..))))...... (-20.94 = -21.50 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:21 2006