Locus 544

Sequence ID	3R_DroMel_CAF1
Location	2,034,322 – 2,034,427
Length	105
Max. P	0.809696

overview

Window 6

Location	2,034,322 – 2,034,427
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	90.74
Mean single sequence MFE	-37.84
Consensus MFE	-31.74
Energy contribution	-32.34
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.84
SVM decision value	0.64
SVM RNA-class probability	0.809696
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2034322 105 + 27905053
ACGCCUCCGCACACAAGUGCCCUCGAACUGACGGAAACAAUUUCCGCCGGCGGGCUUCUGUUUGCGGCCUCGUUGGCAGAUCGUGCCUCCGCUGACCGAGGAAAA
........((((....))))(((((..(.(.((((..((...((.(((((((((((.(.....).)))).))))))).))...))..))))).)..))))).... ( -40.30)
>DroSec_CAF1 177465 105 + 1
ACGCCCCCGCACACAAACGCCCUCGAACUGACGGAAACAAUUUCCGCCGGCGGGCUUCUGUUUGCGGCCUCGUUGGCAGAUCGUGCCUCCGCUGACCGAGGAAAA
......(((((.(((...((((.....(((.(((((.....))))).))).))))...))).)))))((((((..((.((.......)).))..).))))).... ( -37.80)
>DroSim_CAF1 182424 102 + 1
---CCCCCGCACACAAACGCCCUCGAACUGACGGAAACAAUUUCCGCCGGCGGGCUUCUGUUUGCGGCCUCGUUGGCAGAUCGUGCCUCCGCUGACCGAGGAAAA
---...(((((.(((...((((.....(((.(((((.....))))).))).))))...))).)))))((((((..((.((.......)).))..).))))).... ( -37.80)
>DroEre_CAF1 177695 93 + 1
------------ACAAGAGCCCUCGAACUGACGGAAACAAUUUCCGCCGGCGGGCUUCUGUUUGCGGCCUCGUUGGCAGAUCGUGCCUCCACUGACCGAGGAAAA
------------........(((((..(....(((..((...((.(((((((((((.(.....).)))).))))))).))...))..)))...)..))))).... ( -32.00)
>DroYak_CAF1 180553 105 + 1
CCCCUACGGCAGACAAGUGCCCUCGAACUGACGGAAACAAUUUCCGCCGGCGGGCUUCUGUUUGCGGCCUCGUUGGCAGAUCGUGCCUACUCUGACCGAGGAAAA
..(((.(((((((..((.((...(((.((...((((.....))))(((((((((((.(.....).)))).))))))))).))).))))..)))).)))))).... ( -41.30)
>consensus
_C_CCCCCGCACACAAGCGCCCUCGAACUGACGGAAACAAUUUCCGCCGGCGGGCUUCUGUUUGCGGCCUCGUUGGCAGAUCGUGCCUCCGCUGACCGAGGAAAA
....................(((((..(...((((..((...((.(((((((((((.(.....).)))).))))))).))...))..))))..)..))))).... (-31.74 = -32.34 +   0.60)

alignment

secondary structure

dotplot

Window 7

Location	2,034,322 – 2,034,427
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	90.74
Mean single sequence MFE	-41.94
Consensus MFE	-35.42
Energy contribution	-36.90
Covariance contribution	1.48
Combinations/Pair	1.03
Mean z-score	-1.41
Structure conservation index	0.84
SVM decision value	0.38
SVM RNA-class probability	0.712678
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2034322 105 - 27905053
UUUUCCUCGGUCAGCGGAGGCACGAUCUGCCAACGAGGCCGCAAACAGAAGCCCGCCGGCGGAAAUUGUUUCCGUCAGUUCGAGGGCACUUGUGUGCGGAGGCGU
....((((((...(((((((((...((((((..((.(((..(.....)..)))))..))))))...)))))))))....))))))((((....))))........ ( -43.30)
>DroSec_CAF1 177465 105 - 1
UUUUCCUCGGUCAGCGGAGGCACGAUCUGCCAACGAGGCCGCAAACAGAAGCCCGCCGGCGGAAAUUGUUUCCGUCAGUUCGAGGGCGUUUGUGUGCGGGGGCGU
...(((((((((..((..((((.....))))..)).))))(((.(((((.((((((.(((((((.....))))))).))....)))).))))).))))))))... ( -45.90)
>DroSim_CAF1 182424 102 - 1
UUUUCCUCGGUCAGCGGAGGCACGAUCUGCCAACGAGGCCGCAAACAGAAGCCCGCCGGCGGAAAUUGUUUCCGUCAGUUCGAGGGCGUUUGUGUGCGGGGG---
....((((((((..((..((((.....))))..)).))))(((.(((((.((((((.(((((((.....))))))).))....)))).))))).))))))).--- ( -45.60)
>DroEre_CAF1 177695 93 - 1
UUUUCCUCGGUCAGUGGAGGCACGAUCUGCCAACGAGGCCGCAAACAGAAGCCCGCCGGCGGAAAUUGUUUCCGUCAGUUCGAGGGCUCUUGU------------
...(((((((...(((((((((...((((((..((.(((..(.....)..)))))..))))))...)))))))).)...))))))).......------------ ( -34.40)
>DroYak_CAF1 180553 105 - 1
UUUUCCUCGGUCAGAGUAGGCACGAUCUGCCAACGAGGCCGCAAACAGAAGCCCGCCGGCGGAAAUUGUUUCCGUCAGUUCGAGGGCACUUGUCUGCCGUAGGGG
....((((((((...((.((((.....)))).))..))))(((.((((..((((((.(((((((.....))))))).))....))))..)))).)))....)))) ( -40.50)
>consensus
UUUUCCUCGGUCAGCGGAGGCACGAUCUGCCAACGAGGCCGCAAACAGAAGCCCGCCGGCGGAAAUUGUUUCCGUCAGUUCGAGGGCACUUGUGUGCGGGGG_G_
....(((((....(((((.......)))))...)))))(((((.((((..((((((.(((((((.....))))))).))....))))..)))).)))))...... (-35.42 = -36.90 +   1.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:40 2006