Locus 2391

Sequence ID	3R_DroMel_CAF1
Location	6,744,853 – 6,745,008
Length	155
Max. P	0.862145

overview

Window 3

Location	6,744,853 – 6,744,968
Length	115
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	91.45
Mean single sequence MFE	-32.04
Consensus MFE	-24.34
Energy contribution	-24.57
Covariance contribution	0.23
Combinations/Pair	1.07
Mean z-score	-2.47
Structure conservation index	0.76
SVM decision value	0.18
SVM RNA-class probability	0.622526
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6744853 115 - 27905053
C-----ACAAGCAUACACACACACACACCCUUUCAAUGUAGUGUGUCUGUGUGCGCAUUUCAAUAAAUCGCUCGCAUCUACAAUAACACGAAAGCAUGCGGCCAAAAGUAGGCAGCCUGC
.-----....(((((((.(((((((((.........))).)))))).)))))))...............((.(((((((.............)).))))))).....(((((...))))) ( -30.32)
>DroSec_CAF1 9574 111 - 1
C-----ACAAGCA----CACACGCACACCCUUUCAAUGUAGUGUGUCUGUGUGCGCAUUUCAAUAAAUCGCUCGCUUCUACAAUAACACGAAAGCAUGCGGCCAAAAGUAGGCAGCCUAC
.-----....(((----((((.((((((............)))))).)))))))((............(((..(((((...........).))))..)))(((.......))).)).... ( -31.70)
>DroYak_CAF1 5226 116 - 1
CCGGACCCGAGCA----CACACGCACACCCUUUCAAUGUAGUGUGUCUGUGUGCGCAUUUCAAUAAAUCGCUCGCUUCUACAAUAACACGAUAGCAUGCGGCCAAAAGUAGGCAGCCUGC
..(((..((((((----((((.((((((............)))))).)))))))((((((....)))).)))))..)))..............(((.((.(((.......))).)).))) ( -34.10)
>consensus
C_____ACAAGCA____CACACGCACACCCUUUCAAUGUAGUGUGUCUGUGUGCGCAUUUCAAUAAAUCGCUCGCUUCUACAAUAACACGAAAGCAUGCGGCCAAAAGUAGGCAGCCUGC
........((((.....((((.((((((............)))))).)))).(((.((((....)))))))..))))................(((.((.(((.......))).)).))) (-24.34 = -24.57 +   0.23)

alignment

secondary structure

dotplot

Window 4

Location	6,744,893 – 6,745,008
Length	115
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	89.14
Mean single sequence MFE	-41.93
Consensus MFE	-32.11
Energy contribution	-31.57
Covariance contribution	-0.55
Combinations/Pair	1.12
Mean z-score	-2.73
Structure conservation index	0.77
SVM decision value	0.66
SVM RNA-class probability	0.815248
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6744893 115 + 27905053
UAGAUGCGAGCGAUUUAUUGAAAUGCGCACACAGACACACUACAUUGAAAGGGUGUGUGUGUGUGUAUGCUUGU-----GUGGUGCUUUUUGAACAACGUUUGGCUGGCUCGUCGCUUGA
......((((((((.(((....(((((((((((.((((.((........)).)))).)))))))))))....))-----)..(.(((..(..(((...)))..)..))).))))))))). ( -40.70)
>DroSec_CAF1 9614 110 + 1
UAGAAGCGAGCGAUUUAUUGAAAUGCGCACACAGACACACUACAUUGAAAGGGUGUGCGUGUG----UGCUUGU-----GUGAGGCCUUUUGAACAACGUUCGGCAGGCUCGUCGCUUG-
...((((((.((((((((...((.((((((((.(.((((((..........))))))))))))----)))))..-----)))))((((.((((((...)))))).))))))))))))).- ( -41.70)
>DroYak_CAF1 5266 115 + 1
UAGAAGCGAGCGAUUUAUUGAAAUGCGCACACAGACACACUACAUUGAAAGGGUGUGCGUGUG----UGCUCGGGUCCGGUGAGGCCUUUUGAACAACGUUUGGCAGGCUCGUCGCUUG-
...((((((.(((((((((((..((.(((((((..((((((..........))))))..))))----))).))..).)))))))((((.(..(((...)))..).))))))))))))).- ( -43.40)
>consensus
UAGAAGCGAGCGAUUUAUUGAAAUGCGCACACAGACACACUACAUUGAAAGGGUGUGCGUGUG____UGCUUGU_____GUGAGGCCUUUUGAACAACGUUUGGCAGGCUCGUCGCUUG_
......((((((((........((((((((((.....((......)).....))))))))))...................((.((((.((((((...)))))).)))))))))))))). (-32.11 = -31.57 +  -0.55)

alignment

secondary structure

dotplot

Window 5

Location	6,744,893 – 6,745,008
Length	115
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	89.14
Mean single sequence MFE	-34.50
Consensus MFE	-24.85
Energy contribution	-25.30
Covariance contribution	0.45
Combinations/Pair	1.04
Mean z-score	-3.37
Structure conservation index	0.72
SVM decision value	0.83
SVM RNA-class probability	0.862145
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6744893 115 - 27905053
UCAAGCGACGAGCCAGCCAAACGUUGUUCAAAAAGCACCAC-----ACAAGCAUACACACACACACACCCUUUCAAUGUAGUGUGUCUGUGUGCGCAUUUCAAUAAAUCGCUCGCAUCUA
....(((((((..((((.....))))...............-----....(((((((.(((((((((.........))).)))))).))))))).............))).))))..... ( -30.20)
>DroSec_CAF1 9614 110 - 1
-CAAGCGACGAGCCUGCCGAACGUUGUUCAAAAGGCCUCAC-----ACAAGCA----CACACGCACACCCUUUCAAUGUAGUGUGUCUGUGUGCGCAUUUCAAUAAAUCGCUCGCUUCUA
-.(((((((((((((...((((...))))...)))).....-----....(((----((((.((((((............)))))).))))))).............))).))))))... ( -38.00)
>DroYak_CAF1 5266 115 - 1
-CAAGCGACGAGCCUGCCAAACGUUGUUCAAAAGGCCUCACCGGACCCGAGCA----CACACGCACACCCUUUCAAUGUAGUGUGUCUGUGUGCGCAUUUCAAUAAAUCGCUCGCUUCUA
-.(((((((((((((....(((...)))....)))).....((....)).(((----((((.((((((............)))))).))))))).............))).))))))... ( -35.30)
>consensus
_CAAGCGACGAGCCUGCCAAACGUUGUUCAAAAGGCCUCAC_____ACAAGCA____CACACGCACACCCUUUCAAUGUAGUGUGUCUGUGUGCGCAUUUCAAUAAAUCGCUCGCUUCUA
....(((((((((((....(((...)))....))))..............(((....((((.((((((............)))))).))))))).............))).))))..... (-24.85 = -25.30 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:18 2006