Locus 5983

Sequence ID	2R_DroMel_CAF1
Location	18,814,243 – 18,814,342
Length	99
Max. P	0.993172

overview

Window 6

Location	18,814,243 – 18,814,342
Length	99
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	70.75
Mean single sequence MFE	-21.58
Consensus MFE	-10.15
Energy contribution	-11.77
Covariance contribution	1.61
Combinations/Pair	1.17
Mean z-score	-2.48
Structure conservation index	0.47
SVM decision value	2.38
SVM RNA-class probability	0.993172
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18814243 99 + 20766785
UUACGAUCUCCGCCGUCUUCGGAUGCACCUCCUCCUCCCCCU-GCUCCUC----CUACGCCGCUC------CGUAGCAAAAUCCAUUUGCAUAUUUGCAUCCUUAUGCCU
..(((........)))....(((((((...............-.......----.((((......------))))(((((.....))))).....)))))))........ ( -17.30)
>DroVir_CAF1 13490 104 + 1
CUUCGCCCCCCUCGAGCUUCAAC-ACAAU-ACCCCGCGGGUCCCAUUGCA-UG-CUGC--CACACUGUUCGCUUGGCAAAAUGCAUUUGCAUAUUUGUAUCCUUAUGCCU
........(((.((.........-.....-....)).)))......((((-(.-.(((--((..(.....)..)))))..)))))...(((((..........))))).. ( -20.07)
>DroSec_CAF1 6140 90 + 1
UUACGAUCUCCGCCGGCUUCGGAUGCACCUCCUCC----------UCCUC----CUUUGCCGCUC------CGUGGCAAAAUCCAUUUGCAUAUUUGCAUCCUUAUGCCU
..............(((...(((((((........----------.....----.((((((((..------.))))))))...............)))))))....))). ( -23.85)
>DroSim_CAF1 6172 93 + 1
UUACGAUCUCCGCCGGCUUCGGAUGCACCUCCUCCUCC-------UCCUC----CUUUGCCGCUC------CGUGGCAAAAUCCAUUUGCAUAUUUGCAUCCUUAUGCCU
..............(((...(((((((...........-------.....----.((((((((..------.))))))))...(....)......)))))))....))). ( -22.30)
>DroEre_CAF1 4574 87 + 1
UUACGAUCUCCGCCGGCUUCGGAUGCACCGCCUCC---------------C--ACCCCGCCGCUU------CGUGGCAAAAUCCAUUUGCAUAUUUGCAUCCUUAUGCCU
..............(((...(((((((........---------------.--....(((.....------.)))(((((.....))))).....)))))))....))). ( -20.90)
>DroAna_CAF1 728 102 + 1
UUACGA-CUCCUCCAGCUACAGCUACAACUACAGCUCCAGCUUCGUCCCA-GGCCCAGGCCUUGG------CAUGGCAAAAUCCAUUUGCAUAUUUGCAUCCUUAUGCCU
..((((-.......((((..((((........))))..))))))))((.(-(((....)))).))------...((((.........((((....))))......)))). ( -25.07)
>consensus
UUACGAUCUCCGCCGGCUUCGGAUGCACCUCCUCCUCC_______UCCUC____CUACGCCGCUC______CGUGGCAAAAUCCAUUUGCAUAUUUGCAUCCUUAUGCCU
..............(((...(((((((.................................(((.........)))(((((.....))))).....)))))))....))). (-10.15 = -11.77 +   1.61)

alignment

secondary structure

dotplot

Window 7

Location	18,814,243 – 18,814,342
Length	99
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	70.75
Mean single sequence MFE	-28.18
Consensus MFE	-12.76
Energy contribution	-12.60
Covariance contribution	-0.16
Combinations/Pair	1.41
Mean z-score	-1.92
Structure conservation index	0.45
SVM decision value	0.91
SVM RNA-class probability	0.879163
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18814243 99 - 20766785
AGGCAUAAGGAUGCAAAUAUGCAAAUGGAUUUUGCUACG------GAGCGGCGUAG----GAGGAGC-AGGGGGAGGAGGAGGUGCAUCCGAAGACGGCGGAGAUCGUAA
........(((((((..(.(.(...((..((((.(((((------......)))))----.)))).)-)...).).....)..)))))))....((((......)))).. ( -22.60)
>DroVir_CAF1 13490 104 - 1
AGGCAUAAGGAUACAAAUAUGCAAAUGCAUUUUGCCAAGCGAACAGUGUG--GCAG-CA-UGCAAUGGGACCCGCGGGGU-AUUGU-GUUGAAGCUCGAGGGGGGCGAAG
.........(((((((.........(((((.((((((.((.....)).))--))))-.)-)))).....((((...))))-.))))-)))...((((.....)))).... ( -30.60)
>DroSec_CAF1 6140 90 - 1
AGGCAUAAGGAUGCAAAUAUGCAAAUGGAUUUUGCCACG------GAGCGGCAAAG----GAGGA----------GGAGGAGGUGCAUCCGAAGCCGGCGGAGAUCGUAA
.(((....(((((((..(...(.......(((((((...------....)))))))----.....----------.)...)..)))))))...))).(((.....))).. ( -26.72)
>DroSim_CAF1 6172 93 - 1
AGGCAUAAGGAUGCAAAUAUGCAAAUGGAUUUUGCCACG------GAGCGGCAAAG----GAGGA-------GGAGGAGGAGGUGCAUCCGAAGCCGGCGGAGAUCGUAA
.(((....(((((((..(...(.......(((((((...------....)))))))----.....-------....)...)..)))))))...))).(((.....))).. ( -25.99)
>DroEre_CAF1 4574 87 - 1
AGGCAUAAGGAUGCAAAUAUGCAAAUGGAUUUUGCCACG------AAGCGGCGGGGU--G---------------GGAGGCGGUGCAUCCGAAGCCGGCGGAGAUCGUAA
.(((....(((((((....(((......((((((((...------....))))))))--.---------------....))).)))))))...))).(((.....))).. ( -28.70)
>DroAna_CAF1 728 102 - 1
AGGCAUAAGGAUGCAAAUAUGCAAAUGGAUUUUGCCAUG------CCAAGGCCUGGGCC-UGGGACGAAGCUGGAGCUGUAGUUGUAGCUGUAGCUGGAGGAG-UCGUAA
..(((((..........))))).....(((((..((.((------((.((((....)))-).)).)).(((((.(((((......))))).)))))))..)))-)).... ( -34.50)
>consensus
AGGCAUAAGGAUGCAAAUAUGCAAAUGGAUUUUGCCACG______GAGCGGCGAAG____GAGGA_______GGAGGAGGAGGUGCAUCCGAAGCCGGCGGAGAUCGUAA
.(((....(((((((.....(((((.....)))))..((.........)).................................)))))))...))).............. (-12.76 = -12.60 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:38 2006