Locus 5526

Sequence ID	3L_DroMel_CAF1
Location	15,175,811 – 15,175,956
Length	145
Max. P	0.998515

overview

Window 0

Location	15,175,811 – 15,175,922
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	97.48
Mean single sequence MFE	-41.66
Consensus MFE	-40.30
Energy contribution	-40.10
Covariance contribution	-0.20
Combinations/Pair	1.05
Mean z-score	-1.72
Structure conservation index	0.97
SVM decision value	2.22
SVM RNA-class probability	0.990602
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15175811 111 + 23771897
UCUUGAGGCCUAAGAACCGGAGACGUGACGCUCUCCUCAGAACCUCAUCGACGUAAUUGCGGCAGAUGCGGUUCUUUCAUCGCUUUUGGCUGGCGCCUCAGAACGGAGCGA
..((((((((((.(((..(((((((...)).)))))..((((((.((((..(((....)))...)))).)))))))))...((.....))))).))))))).......... ( -37.50)
>DroSec_CAF1 65484 111 + 1
UCUUGAGGCCUAAGAACCGGAGACGUGACGCUCUCCUCAGAACCUCAUCGCCGUAAUUGCGGCAGAUGCGGUUCUUUCAACGCUUUUCGCUGGCGCCUCAGAACGGAGCGA
..((((((((((.(((..(((((((...)).)))))..((((((.(((((((((....))))).)))).))))))..........)))..))).))))))).......... ( -42.70)
>DroSim_CAF1 66835 111 + 1
UCUUGAGGCCUAAGAACCGGAGACGUGACGCUCUCCUCAGAACCUCAUCGCCGUAAUUGCGGCAGAUGCGGUUCUUUCAACGCUUUUCGCUGGCGCCUCAGAACGGAGCGA
..((((((((((.(((..(((((((...)).)))))..((((((.(((((((((....))))).)))).))))))..........)))..))).))))))).......... ( -42.70)
>DroEre_CAF1 66104 111 + 1
UCUUGAGGCCUAAGAACCGGAGACGUGACGCUCUCUGCAGAACCUCAUCGCCGUAAUUGCGGCAGAUGCGGUUCUUUCAUCGCUUUUCGCUGGCGCCUCAGAACGGAGCGA
..((((((((((.(((..(....)((((.((.....))((((((.(((((((((....))))).)))).))))))....))))..)))..))).))))))).......... ( -43.00)
>DroYak_CAF1 68186 111 + 1
UCUUGAGGCCUAAGAACCGGAGACGUGACGCUCUCUUCAGAACCUCAUCGCCGUAAUUGCGGCAGAUGCGGUUCUUUCAUCGCUUUUCGCUGGCGCCUCGGAACGGAGCGA
(((((.....))))).(((....)).).((((((.(((((((((.(((((((((....))))).)))).)))))).....((((.......)))).....))).)))))). ( -42.40)
>consensus
UCUUGAGGCCUAAGAACCGGAGACGUGACGCUCUCCUCAGAACCUCAUCGCCGUAAUUGCGGCAGAUGCGGUUCUUUCAUCGCUUUUCGCUGGCGCCUCAGAACGGAGCGA
(((.((((((((.(((..(((((((...)).)))))..((((((.(((((((((....))))).)))).)))))))))...((.....))))).))))))))......... (-40.30 = -40.10 +  -0.20)

alignment

secondary structure

dotplot

Window 1

Location	15,175,842 – 15,175,956
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	96.84
Mean single sequence MFE	-38.10
Consensus MFE	-36.18
Energy contribution	-36.22
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.04
Structure conservation index	0.95
SVM decision value	3.13
SVM RNA-class probability	0.998515
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15175842 114 + 23771897
UCUCCUCAGAACCUCAUCGACGUAAUUGCGGCAGAUGCGGUUCUUUCAUCGCUUUUGGCUGGCGCCUCAGAACGGAGCGACGUGCUCUUUCUCACCUGGCUUCACCUGGCCCCA
.......((((((.((((..(((....)))...)))).))))))......(((...((.(((.(((..((((.(((((.....))))))))).....))).))))).))).... ( -35.60)
>DroSec_CAF1 65515 114 + 1
UCUCCUCAGAACCUCAUCGCCGUAAUUGCGGCAGAUGCGGUUCUUUCAACGCUUUUCGCUGGCGCCUCAGAACGGAGCGACGUGCUCUUUCUCACCUGGCUUCACCUGGCCCCA
.......((((((.(((((((((....))))).)))).)))))).....((((.......))))....((((.(((((.....))))))))).....((((......))))... ( -37.80)
>DroSim_CAF1 66866 114 + 1
UCUCCUCAGAACCUCAUCGCCGUAAUUGCGGCAGAUGCGGUUCUUUCAACGCUUUUCGCUGGCGCCUCAGAACGGAGCGACGUGCUCUUUCUCACCUGGCUUCACCUGGCCCCA
.......((((((.(((((((((....))))).)))).)))))).....((((.......))))....((((.(((((.....))))))))).....((((......))))... ( -37.80)
>DroEre_CAF1 66135 112 + 1
UCUCUGCAGAACCUCAUCGCCGUAAUUGCGGCAGAUGCGGUUCUUUCAUCGCUUUUCGCUGGCGCCUCAGAACGGAGCGACGUGCUCUUUCUCACCUGGCUUCACCUGGCCC--
.....((((((((.(((((((((....))))).)))).))))).....(((((((...((((....))))...)))))))..)))............((((......)))).-- ( -39.60)
>DroYak_CAF1 68217 114 + 1
UCUCUUCAGAACCUCAUCGCCGUAAUUGCGGCAGAUGCGGUUCUUUCAUCGCUUUUCGCUGGCGCCUCGGAACGGAGCGACGUGCUCUUUCUCACCUGGCUUCACCUGGCCCCA
.......((((((.(((((((((....))))).)))).))))))......((.....)).((.(((..((...(((((.(.(((........))).).))))).)).))).)). ( -39.70)
>consensus
UCUCCUCAGAACCUCAUCGCCGUAAUUGCGGCAGAUGCGGUUCUUUCAUCGCUUUUCGCUGGCGCCUCAGAACGGAGCGACGUGCUCUUUCUCACCUGGCUUCACCUGGCCCCA
.......((((((.(((((((((....))))).)))).)))))).....((((.......))))....((((.(((((.....))))))))).....((((......))))... (-36.18 = -36.22 +   0.04)

alignment

secondary structure

dotplot

Window 2

Location	15,175,842 – 15,175,956
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	96.84
Mean single sequence MFE	-40.74
Consensus MFE	-38.84
Energy contribution	-39.64
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.43
Structure conservation index	0.95
SVM decision value	1.27
SVM RNA-class probability	0.938312
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15175842 114 - 23771897
UGGGGCCAGGUGAAGCCAGGUGAGAAAGAGCACGUCGCUCCGUUCUGAGGCGCCAGCCAAAAGCGAUGAAAGAACCGCAUCUGCCGCAAUUACGUCGAUGAGGUUCUGAGGAGA
(((.(((.((.....))...(.((((.((((.....))))..)))).)))).)))((.....))......((((((.((((.(.((......)).))))).))))))....... ( -35.00)
>DroSec_CAF1 65515 114 - 1
UGGGGCCAGGUGAAGCCAGGUGAGAAAGAGCACGUCGCUCCGUUCUGAGGCGCCAGCGAAAAGCGUUGAAAGAACCGCAUCUGCCGCAAUUACGGCGAUGAGGUUCUGAGGAGA
(((.(((.((.....))...(.((((.((((.....))))..)))).)))).)))((.....))......((((((.((((.((((......)))))))).))))))....... ( -43.30)
>DroSim_CAF1 66866 114 - 1
UGGGGCCAGGUGAAGCCAGGUGAGAAAGAGCACGUCGCUCCGUUCUGAGGCGCCAGCGAAAAGCGUUGAAAGAACCGCAUCUGCCGCAAUUACGGCGAUGAGGUUCUGAGGAGA
(((.(((.((.....))...(.((((.((((.....))))..)))).)))).)))((.....))......((((((.((((.((((......)))))))).))))))....... ( -43.30)
>DroEre_CAF1 66135 112 - 1
--GGGCCAGGUGAAGCCAGGUGAGAAAGAGCACGUCGCUCCGUUCUGAGGCGCCAGCGAAAAGCGAUGAAAGAACCGCAUCUGCCGCAAUUACGGCGAUGAGGUUCUGCAGAGA
--(((((.((.....))...(.((((.((((.....))))..)))).)))).)).((.....))......((((((.((((.((((......)))))))).))))))....... ( -40.40)
>DroYak_CAF1 68217 114 - 1
UGGGGCCAGGUGAAGCCAGGUGAGAAAGAGCACGUCGCUCCGUUCCGAGGCGCCAGCGAAAAGCGAUGAAAGAACCGCAUCUGCCGCAAUUACGGCGAUGAGGUUCUGAAGAGA
(((.(((.((.....))..(.(((...((((.....))))..))))..))).)))((.....))......((((((.((((.((((......)))))))).))))))....... ( -41.70)
>consensus
UGGGGCCAGGUGAAGCCAGGUGAGAAAGAGCACGUCGCUCCGUUCUGAGGCGCCAGCGAAAAGCGAUGAAAGAACCGCAUCUGCCGCAAUUACGGCGAUGAGGUUCUGAGGAGA
(((.(((.((.....))...(.((((.((((.....))))..)))).)))).)))((.....))......((((((.((((.((((......)))))))).))))))....... (-38.84 = -39.64 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:25 2006