Locus 716

Sequence ID	2R_DroMel_CAF1
Location	3,524,359 – 3,524,473
Length	114
Max. P	0.939953

overview

Window 2

Location	3,524,359 – 3,524,473
Length	114
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	77.47
Mean single sequence MFE	-44.99
Consensus MFE	-30.46
Energy contribution	-31.10
Covariance contribution	0.64
Combinations/Pair	1.25
Mean z-score	-1.91
Structure conservation index	0.68
SVM decision value	1.30
SVM RNA-class probability	0.939953
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3524359 114 + 20766785
CACAGGAUGUCCAGCCCGUUCUUCUUCACCGUGCAGAUGCAGGGCGCGAUCUCGCUCUGCUCCGGACACACUUGAGUCUGCGGUGGACCCUGGCCGAGCACCUGGUCCAU---CACA
..((((.(((((.((.((...........)).)).((.((((((((......)))))))))).)))))..)))).....(.((((((((..((.......)).)))))))---).). ( -41.80)
>DroVir_CAF1 16942 107 + 1
CACAGUAUAUCCAGUCCGUUCUUCUUCACCGUGCAUAUGCAGGGCGAGAUAUCGCCCUGCUCUGGGCACACUUG---UUGCGGUGUGCCUUGGGCGAGUGUCUGGACCA------A-
.........(((((............((((((.((...(((((((((....)))))))))...(((((((((..---....))))))))))).))).))).)))))...------.- ( -46.42)
>DroPse_CAF1 1679 117 + 1
CAGAGUAUGUCCAGGCCGUUCUUCUUCACCGUACAGAUGCAGGGCGAGAUGUCGCCCUGCUCCGGACACACCUGCUGUUGCGGUGUGUUCUGGGACCCCGCCUGGCCCACGCCCACC
..(.(..((.((((((.(((((.............((.(((((((((....))))))))))).(((((((((.((....))))))))))).)))))...))))))..))..).)... ( -52.10)
>DroGri_CAF1 19795 111 + 1
CACAAAACAUCCAAUCCAUUCUUUUUCACCGUACAAAUGCAGGGCGAGAUGUCGCUCUGCUCCGGACACACCUG---UUGCGGUGUUCCCUGGGCCAUCGUCUGACCCAA---CAGU
..........................(((((((((...(((((((((....)))))))))...((.....))))---.))))))).....((((.((.....)).)))).---.... ( -31.50)
>DroAna_CAF1 13642 108 + 1
CACAGGAUGUCCAGGCCGUUCUUCUUCACCGUACAGAUGCAGGGCGAGAUGUCGCUCUGCUCCGGGCACACCUGCAGCGGCGGCGGGCCCUGGGCCAGCACCUGAUG---------G
((((((.(((...((((..................((.(((((((((....))))))))))).((((.(..((((....))))..)))))..)))).))))))).))---------. ( -46.00)
>DroPer_CAF1 1684 117 + 1
CAGAGUAUGUCCAGGCCGUUCUUCUUCACCGUGCAGAUGCAGGGCGAGAUGUCGCCCUGCUCCGGACACACCUGCUGUUGCGGUGUGUUCUGGGACCCCGCCUGGCCCACGCCCACC
..(.(..((.((((((.(((((.............((.(((((((((....))))))))))).(((((((((.((....))))))))))).)))))...))))))..))..).)... ( -52.10)
>consensus
CACAGUAUGUCCAGGCCGUUCUUCUUCACCGUACAGAUGCAGGGCGAGAUGUCGCCCUGCUCCGGACACACCUGC_GUUGCGGUGUGCCCUGGGCCAGCGCCUGGCCCA____CACC
..........((((........................(((((((((....))))))))).(((((((((((.........))))))))).))........))))............ (-30.46 = -31.10 +   0.64)

alignment

secondary structure

dotplot

Window 3

Location	3,524,359 – 3,524,473
Length	114
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	77.47
Mean single sequence MFE	-46.80
Consensus MFE	-27.09
Energy contribution	-27.40
Covariance contribution	0.31
Combinations/Pair	1.28
Mean z-score	-1.66
Structure conservation index	0.58
SVM decision value	0.31
SVM RNA-class probability	0.684182
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3524359 114 - 20766785
UGUG---AUGGACCAGGUGCUCGGCCAGGGUCCACCGCAGACUCAAGUGUGUCCGGAGCAGAGCGAGAUCGCGCCCUGCAUCUGCACGGUGAAGAAGAACGGGCUGGACAUCCUGUG
((((---.((((((.(((.....)))..)))))).))))......((..(((((((.((((((((....)))((...)).))))).(.((........)).).)))))))..))... ( -43.70)
>DroVir_CAF1 16942 107 - 1
-U------UGGUCCAGACACUCGCCCAAGGCACACCGCAA---CAAGUGUGCCCAGAGCAGGGCGAUAUCUCGCCCUGCAUAUGCACGGUGAAGAAGAACGGACUGGAUAUACUGUG
-(------..((((......(((((...(((((((.....---...)))))))....(((((((((....)))))))))........)))))........))))..).......... ( -43.94)
>DroPse_CAF1 1679 117 - 1
GGUGGGCGUGGGCCAGGCGGGGUCCCAGAACACACCGCAACAGCAGGUGUGUCCGGAGCAGGGCGACAUCUCGCCCUGCAUCUGUACGGUGAAGAAGAACGGCCUGGACAUACUCUG
...(((..((..((((((.(..((((...(((((((((....)).))))))).(((((((((((((....))))))))).))))...)).)).......).)))))).))..))).. ( -55.80)
>DroGri_CAF1 19795 111 - 1
ACUG---UUGGGUCAGACGAUGGCCCAGGGAACACCGCAA---CAGGUGUGUCCGGAGCAGAGCGACAUCUCGCCCUGCAUUUGUACGGUGAAAAAGAAUGGAUUGGAUGUUUUGUG
.(((---((((((((.....)))))).((..(((((....---..)))))..))..)))))...(((((((((((.(((....))).)))))..............))))))..... ( -37.93)
>DroAna_CAF1 13642 108 - 1
C---------CAUCAGGUGCUGGCCCAGGGCCCGCCGCCGCUGCAGGUGUGCCCGGAGCAGAGCGACAUCUCGCCCUGCAUCUGUACGGUGAAGAAGAACGGCCUGGACAUCCUGUG
.---------((.((((((((((((..((((.((((((....)).)))).))))(((((((.((((....)))).)))).))).................)))).)).)).)))))) ( -43.80)
>DroPer_CAF1 1684 117 - 1
GGUGGGCGUGGGCCAGGCGGGGUCCCAGAACACACCGCAACAGCAGGUGUGUCCGGAGCAGGGCGACAUCUCGCCCUGCAUCUGCACGGUGAAGAAGAACGGCCUGGACAUACUCUG
...(((..((..((((((.(..((((...(((((((((....)).))))))).(((((((((((((....))))))))).))))...)).)).......).)))))).))..))).. ( -55.60)
>consensus
GGUG____UGGGCCAGGCGCUGGCCCAGGGCACACCGCAAC_GCAGGUGUGUCCGGAGCAGAGCGACAUCUCGCCCUGCAUCUGCACGGUGAAGAAGAACGGCCUGGACAUACUGUG
............((((........((.(((((((((.........))))))))))).((((.(((......))).)))).......(.((........)).).)))).......... (-27.09 = -27.40 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:19 2006