Locus 3901

Sequence ID	3R_DroMel_CAF1
Location	10,620,583 – 10,620,697
Length	114
Max. P	0.767515

overview

Window 6

Location	10,620,583 – 10,620,697
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	71.17
Mean single sequence MFE	-37.73
Consensus MFE	-14.06
Energy contribution	-14.21
Covariance contribution	0.14
Combinations/Pair	1.38
Mean z-score	-1.99
Structure conservation index	0.37
SVM decision value	0.52
SVM RNA-class probability	0.767515
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10620583 114 + 27905053
GAGGUGGAUGCCAUCUGGUUUGGUACUCCGCCCAGGGAUAAGAAGGACGAGAAACUGUUUGAGGUGCAUCAUGUGCAGCACAAG------CUGCUGGAUGACAGCAUGCAGUCCUUGAUU
..(((((((((((.......))))).))))))(((((((.................(((((.(.(((((...))))).).))))------)(((((.....)))))....)))))))... ( -41.90)
>DroVir_CAF1 82276 111 + 1
GGCGAGUGCGCCAUUUGGUUUGGCACGCCCCCAAAUGA---------UGCCAAGGCAUUCAAGGUGCAUCAUGUGCAGCAUAAGCCGCAGCUGUUCGAAGAGAGUCUGCAAUCCUUAAUA
((((((((((((....)))((((((((........)).---------)))))).))))))..(.(((((...))))).)....)))((((((.((....)).)).))))........... ( -36.50)
>DroPse_CAF1 101319 105 + 1
GACCCUGAUGGCAUCUGGUUUGGUCCACCACCAAACGA---------UGCCAGGCCCUUCGAGGUACAUCAUGUGCAGCACAAG------AUGCUCGAUGAGAGCCUGCAGUCCCUGGUU
((((..(((((((((..(((((((.....)))))))))---------))))((((.(((((((...((((.((((...)))).)------))))))))..)).))))...)))...)))) ( -39.60)
>DroWil_CAF1 74263 100 + 1
-----UGGUGCAAUUUGGUUUGGCACUCCACCAAAUGA---------UGCCAAACCAUUUGAGGUGCAUCAUGUGCAGCAUAAG------GUAUUCGAUGCAAGUCUUCAAUCCAUGAUA
-----(((.......((((((((((.((........))---------)))))))))).((((((((((((..((((........------))))..))))))...)))))).)))..... ( -32.10)
>DroAna_CAF1 65283 114 + 1
GCUGAGGGAGCUAUUUGGUUCGGCACUCCGCCGAAAGACAAGAAGGAUGCAAAACUUUUCGAGGUGCAUCAUGUGCAGCACAAG------AUGCUGGAUGAGAGCCUGCAGUCCCUGAUU
((((.(((..((.((((.((((((.....))))))...))))...((((((...(((...))).))))))..((.(((((....------.))))).)).))..))).))))........ ( -36.70)
>DroPer_CAF1 89019 105 + 1
GACCCUGAUGGCAUCUGGUUUGGUCCCCCACCAAACGA---------UGCCAGGCCCUUCGAGGUACAUCAUGUGCAGCACAAG------AUGCUCGAUGAGAGCCUGCAGUCCCUGGUU
((((..(((((((((..(((((((.....)))))))))---------))))((((.(((((((...((((.((((...)))).)------))))))))..)).))))...)))...)))) ( -39.60)
>consensus
GACGAGGAUGCCAUCUGGUUUGGCACUCCACCAAACGA_________UGCCAAACCAUUCGAGGUGCAUCAUGUGCAGCACAAG______AUGCUCGAUGAGAGCCUGCAGUCCCUGAUU
......(((((.((((((((((((........................)))))))).....)))))))))...(((((..............((((.....))))))))).......... (-14.06 = -14.21 +   0.14)

alignment

secondary structure

dotplot

Window 7

Location	10,620,583 – 10,620,697
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	71.17
Mean single sequence MFE	-35.48
Consensus MFE	-13.09
Energy contribution	-13.53
Covariance contribution	0.45
Combinations/Pair	1.52
Mean z-score	-1.81
Structure conservation index	0.37
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10620583 114 - 27905053
AAUCAAGGACUGCAUGCUGUCAUCCAGCAG------CUUGUGCUGCACAUGAUGCACCUCAAACAGUUUCUCGUCCUUCUUAUCCCUGGGCGGAGUACCAAACCAGAUGGCAUCCACCUC
....((((((.....(((((((((..((((------(....)))))....))))........))))).....)))))).........(((.(((...(((.......)))..))).))). ( -31.20)
>DroVir_CAF1 82276 111 - 1
UAUUAAGGAUUGCAGACUCUCUUCGAACAGCUGCGGCUUAUGCUGCACAUGAUGCACCUUGAAUGCCUUGGCA---------UCAUUUGGGGGCGUGCCAAACCAAAUGGCGCACUCGCC
..((((((..((((((......))...((..((((((....))))))..)).))))))))))((((....)))---------).....(((((.((((((.......)))))).))).)) ( -36.60)
>DroPse_CAF1 101319 105 - 1
AACCAGGGACUGCAGGCUCUCAUCGAGCAU------CUUGUGCUGCACAUGAUGUACCUCGAAGGGCCUGGCA---------UCGUUUGGUGGUGGACCAAACCAGAUGCCAUCAGGGUC
.(((..((.....(((((((..((((((((------(.((((...)))).))))...))))))))))))((((---------(((((((((.....)))))))..)))))).))..))). ( -44.00)
>DroWil_CAF1 74263 100 - 1
UAUCAUGGAUUGAAGACUUGCAUCGAAUAC------CUUAUGCUGCACAUGAUGCACCUCAAAUGGUUUGGCA---------UCAUUUGGUGGAGUGCCAAACCAAAUUGCACCA-----
.....(((......((..(((((((.....------.............)))))))..))...((((((((((---------(..(.....)..))))))))))).......)))----- ( -25.87)
>DroAna_CAF1 65283 114 - 1
AAUCAGGGACUGCAGGCUCUCAUCCAGCAU------CUUGUGCUGCACAUGAUGCACCUCGAAAAGUUUUGCAUCCUUCUUGUCUUUCGGCGGAGUGCCGAACCAAAUAGCUCCCUCAGC
....(((((..((((((.......((((((------...)))))).....((((((...(.....)...))))))......))))((((((.....)))))).......))))))).... ( -31.20)
>DroPer_CAF1 89019 105 - 1
AACCAGGGACUGCAGGCUCUCAUCGAGCAU------CUUGUGCUGCACAUGAUGUACCUCGAAGGGCCUGGCA---------UCGUUUGGUGGGGGACCAAACCAGAUGCCAUCAGGGUC
.(((..((.....(((((((..((((((((------(.((((...)))).))))...))))))))))))((((---------(((((((((.....)))))))..)))))).))..))). ( -44.00)
>consensus
AAUCAGGGACUGCAGGCUCUCAUCGAGCAU______CUUGUGCUGCACAUGAUGCACCUCGAAGGGCUUGGCA_________UCAUUUGGUGGAGUACCAAACCAAAUGGCACCAGCGUC
..(((((........((((.....)))).........(((.(.((((.....)))).).)))....)))))............((((((((((....)))..)))))))........... (-13.09 = -13.53 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:53 2006