Locus 5900

Sequence ID	3L_DroMel_CAF1
Location	15,848,668 – 15,848,828
Length	160
Max. P	0.898258

overview

Window 5

Location	15,848,668 – 15,848,788
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.91
Mean single sequence MFE	-27.06
Consensus MFE	-21.06
Energy contribution	-21.54
Covariance contribution	0.48
Combinations/Pair	1.17
Mean z-score	-2.02
Structure conservation index	0.78
SVM decision value	1.00
SVM RNA-class probability	0.898258
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15848668 120 + 23771897
AACUGCUAAGCAAUUUAAUCGGAUAAAAACUAUUUCGAAAUGUAUGCAACAAAGUGAGCAUCGCAUUUCGCGGUAGAGUGUGUGCUUUUAUGUGGCUUCUAUUCGCAUAAAUUUAUUAAU
....((...(((.((((......))))..((((..((((((((((((..........)))).))))))))..))))..)))..)).(((((((((.......)))))))))......... ( -26.20)
>DroSec_CAF1 55889 120 + 1
AACUGCUAAGCAAUUUAAUCGGAUAAAAACUAUUCCGAAAUUUAUGCAACAAAGUGCGCAUCGCAUUUCGCGGUAGAGAGUGUGCUUUUAUGUGGCUUCUAGCCGCAUAAAUUUAUUAAU
.(((((...(((......(((((..........)))))......)))....(((((((...))))))).))))).......(((..((((((((((.....))))))))))..))).... ( -33.70)
>DroSim_CAF1 57115 120 + 1
AACUGCUAAGCAAUUUAAUCGGAUAAAAACUAUUUCGAAAUUUAUGCAACAAAGUGUGCAUCGCAUUUCGCGGUAGAGUGUGUGCUUUUAUGUGGCUUCUAGCCGCAUAAAUUUAUUAAU
....((...(((.((((......))))..((((..((((((..(((((........)))))...))))))..))))..)))..)).((((((((((.....))))))))))......... ( -29.50)
>DroEre_CAF1 55064 115 + 1
AACUACUAAGCAUUAUAAUCGGAUAA-AACUAUUCCAAAAUGUAUGCAACAAA----GUAUCGCAUUUCGCGGUAGAGCACUCGCUUUUAUGCGGCUUCUAUCCACAUCAAUUUAUUAAU
....................(((((.-..((((..(.((((((((((......----)))).)))))).)..))))(((...(((......))))))..)))))................ ( -21.20)
>DroYak_CAF1 97201 119 + 1
AACUACUAAGCAUUAUAAUCGGAUAA-AACUAUUCCAAAAUGUAUGCAACAAAAUGAGCAUCGCAUUUCGCGGUAGAGCACACGCUUUUAUGUGGCUUUUAUCCACAUCAAUUUAUUAAU
....................((((((-(.((((..(.((((((((((..........)))).)))))).)..))))(((.((((......))))))))))))))................ ( -24.70)
>consensus
AACUGCUAAGCAAUUUAAUCGGAUAAAAACUAUUCCGAAAUGUAUGCAACAAAGUGAGCAUCGCAUUUCGCGGUAGAGCGUGUGCUUUUAUGUGGCUUCUAUCCGCAUAAAUUUAUUAAU
..(((((..((.........(((..........)))(((((((((((..........)))).))))))))))))))..........(((((((((.......)))))))))......... (-21.06 = -21.54 +   0.48)

alignment

secondary structure

dotplot

Window 6

Location	15,848,708 – 15,848,828
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.73
Mean single sequence MFE	-28.36
Consensus MFE	-22.20
Energy contribution	-23.24
Covariance contribution	1.04
Combinations/Pair	1.11
Mean z-score	-1.68
Structure conservation index	0.78
SVM decision value	0.45
SVM RNA-class probability	0.740150
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15848708 120 - 23771897
CCCGCGGUGAAUAUUGACUGAAAUACCGGCCAAAACGGCCAUUAAUAAAUUUAUGCGAAUAGAAGCCACAUAAAAGCACACACUCUACCGCGAAAUGCGAUGCUCACUUUGUUGCAUACA
..(((((((..................((((.....)))).........((((((.(.........).))))))...........)))))))..(((((((.........)))))))... ( -27.70)
>DroSec_CAF1 55929 120 - 1
CCCGCGGUGAAUAUUGACUGAAAUACCGGCAAAAACGGCCAUUAAUAAAUUUAUGCGGCUAGAAGCCACAUAAAAGCACACUCUCUACCGCGAAAUGCGAUGCGCACUUUGUUGCAUAAA
..(((((((..................(((.......))).........((((((.(((.....))).))))))...........)))))))..(((((((.........)))))))... ( -31.70)
>DroSim_CAF1 57155 120 - 1
CCCGCGGUGAAUAUUGACUGAAAUACCGGCAAAAACGGCCAUUAAUAAAUUUAUGCGGCUAGAAGCCACAUAAAAGCACACACUCUACCGCGAAAUGCGAUGCACACUUUGUUGCAUAAA
..(((((((..................(((.......))).........((((((.(((.....))).))))))...........)))))))..(((((((.........)))))))... ( -31.70)
>DroEre_CAF1 55103 114 - 1
CCCGAGGUAAA--UUGACUGAAAUACCGACAAAAACUGCCAUUAAUAAAUUGAUGUGGAUAGAAGCCGCAUAAAAGCGAGUGCUCUACCGCGAAAUGCGAUAC----UUUGUUGCAUACA
.....((((..--..........))))..........................(((((.((((.(((((......))).))..)))))))))..(((((((..----...)))))))... ( -23.60)
>DroYak_CAF1 97240 118 - 1
CCCGAGGUAAA--UUGACUGAAAUACCGGCAAAAACUGCCAUUAAUAAAUUGAUGUGGAUAAAAGCCACAUAAAAGCGUGUGCUCUACCGCGAAAUGCGAUGCUCAUUUUGUUGCAUACA
..(((((((..--..........))))((((.....)))).........)))((((((.......))))))......((((((......((((((((.......)))))))).)))))). ( -27.10)
>consensus
CCCGCGGUGAAUAUUGACUGAAAUACCGGCAAAAACGGCCAUUAAUAAAUUUAUGCGGAUAGAAGCCACAUAAAAGCACACACUCUACCGCGAAAUGCGAUGCUCACUUUGUUGCAUACA
..(((((((..................((((.....)))).........((((((.((.......)).))))))...........)))))))..((((((((.......))))))))... (-22.20 = -23.24 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:20 2006