Locus 8060

Sequence ID	3R_DroMel_CAF1
Location	21,641,498 – 21,641,658
Length	160
Max. P	0.822133

overview

Window 5

Location	21,641,498 – 21,641,618
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	88.00
Mean single sequence MFE	-59.28
Consensus MFE	-49.48
Energy contribution	-49.82
Covariance contribution	0.34
Combinations/Pair	1.18
Mean z-score	-1.76
Structure conservation index	0.83
SVM decision value	0.16
SVM RNA-class probability	0.611662
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21641498 120 + 27905053
CAGGAGGCCAAGAAGGCGUCGGACACUCAGGCACCAGCUGCUCUGGCUGCUGCCCGCCAGGUGAAACACCAGCUGGCCGAGAAAGCCAUUGCUGCGGCCAAGGCCGCUGAGGCGGCGCUG
(((..((((.....((((..((...(((.((((.(((((.....))))).)))).(((((.((......)).))))).)))....))..))))..))))...(((((....))))).))) ( -54.00)
>DroSec_CAF1 130844 120 + 1
CAGGAGGCCAAGAAGGCGUCGGACACUCAGGCACCUGCGGCUCUGGCUGCUGCCCGCCAGGUGAAACACCACCUGGCCGAGAAGGCCAUUGCUGCGGCCAAGGCCGCUGAGGCGGCGCUG
(((..((((....(((.(((.(.....).))).)))(((((..(((((....((.((((((((......)))))))).).)..)))))..)))))))))...(((((....))))).))) ( -61.40)
>DroSim_CAF1 127445 120 + 1
CAGGAGGCCAAGAAGGCGUCGGACACUCAGGCACCUGCGGCUCUGGCUGCUGCCCGCCAGGUGAAACACCACCUGGCCGAGAAGGCCAUUGCUGCGGCCAAGGCCGCCGAGGCGGCGCUG
(((..((((....(((.(((.(.....).))).)))(((((..(((((....((.((((((((......)))))))).).)..)))))..)))))))))...(((((....))))).))) ( -62.50)
>DroEre_CAF1 127564 120 + 1
CAGGAGGCCAAGAAGGCGUCGGACACCCAGGCACCUGCGGCCCUGGCUGCCGCCCGCCAGGUGAAACACCAGCUGGCCGAGAAGGCCAUUGCUGCGGCCAAAGCCGCCGAGGCGGCGCUG
(((..((((....(((.(((((....)).))).)))(((((..(((((..(..(.(((((.((......)).))))).).)..)))))..)))))))))...(((((....))))).))) ( -59.60)
>DroYak_CAF1 128095 120 + 1
CAGGAGGCCAAGAAGGCGUCGGACACCCAGGCACCUGCGGCUCUGGCCGCCGCCCGCCAGGUGAAACACCAGCUGGCCGAGAAGGCCAUUGCUGCGGCCAAGGCAGCCGAGGCGGCGCUG
.....((((....(((.(((((....)).))).)))(((((..(((((..(..(.(((((.((......)).))))).).)..)))))..)))))))))..(((.((((...))))))). ( -57.00)
>DroAna_CAF1 110454 120 + 1
AAGGAGGCCAAGCUGGCCUCGGAGUCCCAGCAGCCGGCUGCAUUGGCCGCCGCCUACCAGGUGCGCGUCCAGCUGGCCGACAAGGCUGUCCAAGCGGCCAAGGCCGCAGAGGCAGCUCUG
..(..(((((.(((((((..((....)).((((....))))...)))(((((((.....)))).)))..)))))))))..).((((((((...(((((....)))))...)))))).)). ( -61.20)
>consensus
CAGGAGGCCAAGAAGGCGUCGGACACCCAGGCACCUGCGGCUCUGGCUGCCGCCCGCCAGGUGAAACACCAGCUGGCCGAGAAGGCCAUUGCUGCGGCCAAGGCCGCCGAGGCGGCGCUG
(((..((((....(((.(((((....)).))).)))(((((..(((((.....(.(((((.((......)).))))).)....)))))..)))))))))...(((((....))))).))) (-49.48 = -49.82 +   0.34)

alignment

secondary structure

dotplot

Window 6

Location	21,641,538 – 21,641,658
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.39
Mean single sequence MFE	-54.25
Consensus MFE	-33.60
Energy contribution	-33.30
Covariance contribution	-0.30
Combinations/Pair	1.44
Mean z-score	-1.91
Structure conservation index	0.62
SVM decision value	0.68
SVM RNA-class probability	0.822133
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21641538 120 + 27905053
CUCUGGCUGCUGCCCGCCAGGUGAAACACCAGCUGGCCGAGAAAGCCAUUGCUGCGGCCAAGGCCGCUGAGGCGGCGCUGGCGGGGAAACAACAACUUAUGGAGCAGCUGCAGGACGAGG
.(((.((.((((((((((.((((...))))(((((((((....(((....))).))))))..(((((....)))))))))))))(....).............))))).)).)))..... ( -57.40)
>DroGri_CAF1 108022 120 + 1
CCGCGGAGGUCGCCCGCAUGGUUAAGAAGCAGCUGGCGGAUCGAGCAUAUGCAGCUGCCAAAGCAGCGGAGGCGGCACUCUCUGGCAAGCAACAGAAUGUGGAGCAGCUAGAGCAGGAGA
((((.((((((((((((((((((.....((.....))......))).))))).(((((....))))).).)))))).)))((((((..((..((.....))..)).)))))))).))... ( -44.90)
>DroSim_CAF1 127485 120 + 1
CUCUGGCUGCUGCCCGCCAGGUGAAACACCACCUGGCCGAGAAGGCCAUUGCUGCGGCCAAGGCCGCCGAGGCGGCGCUGGCGGGAAAACAACAGCUUAUGGAGCAGCUGCAGGACGAGG
.(((.((.(((((((((((((((......))))))))......((((........))))...(((((....)))))((((..(......)..))))....)).))))).)).)))..... ( -57.60)
>DroEre_CAF1 127604 120 + 1
CCCUGGCUGCCGCCCGCCAGGUGAAACACCAGCUGGCCGAGAAGGCCAUUGCUGCGGCCAAAGCCGCCGAGGCGGCGCUGGCGGGGAAGCAACAGAUUAUGGAGCAGCUGCAGGACGAGG
.((((((((((.((((((.((((...))))(((((((((....(((....))).))))))..(((((....)))))))))))))).......((.....))).)))))..))))...... ( -59.60)
>DroYak_CAF1 128135 120 + 1
CUCUGGCCGCCGCCCGCCAGGUGAAACACCAGCUGGCCGAGAAGGCCAUUGCUGCGGCCAAGGCAGCCGAGGCGGCGCUGGCGGGGAAACAACAGAUCAUGGAACAGCUGCAGGACGAGG
.((((.((((((((((((.((((...))))((((((((.....)))))..))).((((.......)))).))))).)).)))))(....)..))))........................ ( -50.90)
>DroAna_CAF1 110494 120 + 1
CAUUGGCCGCCGCCUACCAGGUGCGCGUCCAGCUGGCCGACAAGGCUGUCCAAGCGGCCAAGGCCGCAGAGGCAGCUCUGGCCGGGAAGGAGCAGAUAGUCGAACAGCUGCAGGAAGAGG
..((..((((((((.....)))).))...((((((..((((...((((((...(((((....)))))...))))))((((.((.....))..))))..))))..))))))..))..)).. ( -55.10)
>consensus
CUCUGGCUGCCGCCCGCCAGGUGAAACACCAGCUGGCCGAGAAGGCCAUUGCUGCGGCCAAGGCCGCCGAGGCGGCGCUGGCGGGGAAACAACAGAUUAUGGAGCAGCUGCAGGACGAGG
.(((.(((((((((((((((.((......)).)))))................(((((....))))).).))))))...))).))).................................. (-33.60 = -33.30 +  -0.30)

alignment

secondary structure

dotplot

Window 7

Location	21,641,538 – 21,641,658
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.39
Mean single sequence MFE	-51.47
Consensus MFE	-35.09
Energy contribution	-36.82
Covariance contribution	1.73
Combinations/Pair	1.28
Mean z-score	-1.60
Structure conservation index	0.68
SVM decision value	0.60
SVM RNA-class probability	0.794716
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21641538 120 - 27905053
CCUCGUCCUGCAGCUGCUCCAUAAGUUGUUGUUUCCCCGCCAGCGCCGCCUCAGCGGCCUUGGCCGCAGCAAUGGCUUUCUCGGCCAGCUGGUGUUUCACCUGGCGGGCAGCAGCCAGAG
.(((.....((.(((((.((..((((..(((((.(...(((((.(((((....))))).))))).).)))))..)))).....(((((.(((....))).)))))))))))).))..))) ( -52.60)
>DroGri_CAF1 108022 120 - 1
UCUCCUGCUCUAGCUGCUCCACAUUCUGUUGCUUGCCAGAGAGUGCCGCCUCCGCUGCUUUGGCAGCUGCAUAUGCUCGAUCCGCCAGCUGCUUCUUAACCAUGCGGGCGACCUCCGCGG
....(((((((.((.((..((.....))..))..)).)))(((.(.((((..(((((.((.((((((((.....((.......))))))))))....)).)).))))))).)))).)))) ( -35.90)
>DroSim_CAF1 127485 120 - 1
CCUCGUCCUGCAGCUGCUCCAUAAGCUGUUGUUUUCCCGCCAGCGCCGCCUCGGCGGCCUUGGCCGCAGCAAUGGCCUUCUCGGCCAGGUGGUGUUUCACCUGGCGGGCAGCAGCCAGAG
.(((.....((.(((((.((....(((((((((...(.(((((.(((((....))))).))))).).))))))))).......(((((((((....)))))))))))))))).))..))) ( -60.90)
>DroEre_CAF1 127604 120 - 1
CCUCGUCCUGCAGCUGCUCCAUAAUCUGUUGCUUCCCCGCCAGCGCCGCCUCGGCGGCUUUGGCCGCAGCAAUGGCCUUCUCGGCCAGCUGGUGUUUCACCUGGCGGGCGGCAGCCAGGG
......(((((.(((((.((......((((((......(((((.(((((....))))).))))).)))))).(((((.....)))))(((((((...)))).)))))))))).).)))). ( -57.40)
>DroYak_CAF1 128135 120 - 1
CCUCGUCCUGCAGCUGUUCCAUGAUCUGUUGUUUCCCCGCCAGCGCCGCCUCGGCUGCCUUGGCCGCAGCAAUGGCCUUCUCGGCCAGCUGGUGUUUCACCUGGCGGGCGGCGGCCAGAG
.(((.....(((((...((...))...)))))....(((((.((.(((((.(((((.....)))))((((..(((((.....)))))))))...........))))))))))))...))) ( -49.10)
>DroAna_CAF1 110494 120 - 1
CCUCUUCCUGCAGCUGUUCGACUAUCUGCUCCUUCCCGGCCAGAGCUGCCUCUGCGGCCUUGGCCGCUUGGACAGCCUUGUCGGCCAGCUGGACGCGCACCUGGUAGGCGGCGGCCAAUG
((.((.((((((((((..((((...(((.(((....(((((((.(((((....))))).)))))))...))))))....))))..)))))((.......))..))))).)).))...... ( -52.90)
>consensus
CCUCGUCCUGCAGCUGCUCCAUAAUCUGUUGCUUCCCCGCCAGCGCCGCCUCGGCGGCCUUGGCCGCAGCAAUGGCCUUCUCGGCCAGCUGGUGUUUCACCUGGCGGGCGGCAGCCAGAG
.........((.(((((((......((((((((...(.(((((.(((((....))))).))))).).))))))))........(((((.(((....))).)))))))))))).))..... (-35.09 = -36.82 +   1.73)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:01:38 2006