Locus 3110

Sequence ID	2R_DroMel_CAF1
Location	10,633,904 – 10,634,057
Length	153
Max. P	0.651158

overview

Window 3

Location	10,633,904 – 10,634,022
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.52
Mean single sequence MFE	-36.00
Consensus MFE	-23.33
Energy contribution	-23.94
Covariance contribution	0.61
Combinations/Pair	1.19
Mean z-score	-1.40
Structure conservation index	0.65
SVM decision value	0.01
SVM RNA-class probability	0.539223
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10633904 118 - 20766785
UAAACAAAUUCACCCACAUGGCAGCCUCGAUUGGGUGGCGGCAUAUCCCGCCGAUUUUCGGCGUGGGCUGAUUUUUA--GCCGCAUUCGAUUUCGAUUUCGGGUUCAAGACUUGCCAUUC
.........(((((((..(((.....)))..))))))).((((..((((((((.....))))).)((((((...)))--)))(.((((((........)))))).)..))..)))).... ( -37.20)
>DroPse_CAF1 101878 106 - 1
---AUAUGUA----CAUAUG----CAUGCAUUGGGUG---GCACUGGCCGCUGUUCAGUGGCGUGGGCUGAUGUCUGAUGUCCCACCCGAAUUUGAUUUAGGGUUCAAGUCUUGCCAUUC
---..(((((----....))----)))((((((((((---(.((..((((((....))))))..((((....))))...)).))))))))((((((........))))))..)))..... ( -34.50)
>DroSec_CAF1 76017 115 - 1
UAAACAAAUUCACCCACAUGGCAGCCUCGAAUGGGUG---GCAUAGCCCGCCGAUUUUCGGCGUGGGCUGAUUUUUA--GCCGCAUUCGAUUUCGAUUUCGGGUUCAAGACUUGCCGUUC
.................(((((((..((((((((((.---...((((((((((.....))))..)))))).......--))).))))))).((((....))))........))))))).. ( -37.10)
>DroSim_CAF1 77337 107 - 1
UAAACAAAUUCACCCACAU--------CGAAUGGGUG---GCACAGCCCGCUGAUUUUCGGCGUGGGCUGAUUUUUA--GCCGCAUUCGAUUUCGAUUUCGGGUUCAAGACUUGCCAUUC
...........(((((...--------....)))))(---(((((((((((((.....))))..)))))).......--.(((...(((....)))...)))..........)))).... ( -34.60)
>DroEre_CAF1 76592 109 - 1
UAAACAGAAUCACCCACAUGGCAGCCUCGAUUGGGUG---GCACAGCCCGCCGAUUUUCGGCGUGGGCUGAUUUUUA--GCCGCAUUCGA------UUUCGGGUUCAAGACUUGCCAUUC
.................((((((((((.(((((.(((---((.((((((((((.....))))..))))))(....).--)))))...)))------))..))))........)))))).. ( -36.80)
>DroYak_CAF1 83752 109 - 1
UAAACAAAAGCACCCACAUGGCAGCCUCGAUUGGGUG---GCAUAGCCCGCCGAUUUUCGGCGUGGGCUGAUUUUUG--GCCGCAUUCGA------UUUCGGGUUCAAGACUUGCCAUUC
.................((((((((((.(((((.(((---((.((((((((((.....))))..)))))).......--)))))...)))------))..))))........)))))).. ( -35.80)
>consensus
UAAACAAAUUCACCCACAUGGCAGCCUCGAUUGGGUG___GCACAGCCCGCCGAUUUUCGGCGUGGGCUGAUUUUUA__GCCGCAUUCGAUUUCGAUUUCGGGUUCAAGACUUGCCAUUC
..........((((((...............))))))...(((((((((((((.....))))..))))))............(.((((((........)))))).)......)))..... (-23.33 = -23.94 +   0.61)

alignment

secondary structure

dotplot

Window 4

Location	10,633,944 – 10,634,057
Length	113
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	86.83
Mean single sequence MFE	-33.90
Consensus MFE	-22.58
Energy contribution	-22.92
Covariance contribution	0.34
Combinations/Pair	1.11
Mean z-score	-2.14
Structure conservation index	0.67
SVM decision value	0.25
SVM RNA-class probability	0.651158
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10633944 113 + 20766785
CUAAAAAUCAGCCCACGCCGAAAAUCGGCGGGAUAUGCCGCCACCCAAUCGAGGCUGCCAUGUGGGUGAAUUUGUUUAUAAAUACAGUGA-AACUCCGAAAGUAUGAACCGUAC
....((((..((((((((((.....)))).((....(((.............)))..))..))))))..))))(((((((.....((...-..)).(....))))))))..... ( -29.42)
>DroSec_CAF1 76057 110 + 1
CUAAAAAUCAGCCCACGCCGAAAAUCGGCGGGCUAUGC---CACCCAUUCGAGGCUGCCAUGUGGGUGAAUUUGUUUAUAAAUACAGUGA-AACUCCGAGAGUAUGAACUGUCC
....((((..((((((((((.....)))).(((...((---(.(......).))).)))..))))))..))))..........(((((..-.((((...))))....))))).. ( -35.50)
>DroSim_CAF1 77377 101 + 1
CUAAAAAUCAGCCCACGCCGAAAAUCAGCGGGCUGUGC---CACCCAUUCG--------AUGUGGGUGAAUUUGUUUAUAAAUACAGUGA-AACUCCGAAAGUA-GAACUGAUC
........((((((..((.(.....).))))))))...---(((((((...--------..)))))))................((((..-..((.(....).)-).))))... ( -28.30)
>DroEre_CAF1 76626 110 + 1
CUAAAAAUCAGCCCACGCCGAAAAUCGGCGGGCUGUGC---CACCCAAUCGAGGCUGCCAUGUGGGUGAUUCUGUUUAUAAAUACAGUGA-AGCUGCGAGAGCACGAACUUUGC
.....(((((.(((((((((.....)))).(((...((---(.(......).))).)))..))))))))))...............(..(-((.(((....)))....)))..) ( -36.50)
>DroYak_CAF1 83786 111 + 1
CCAAAAAUCAGCCCACGCCGAAAAUCGGCGGGCUAUGC---CACCCAAUCGAGGCUGCCAUGUGGGUGCUUUUGUUUAUAAAUACAGUGAAAACUGCGAGAGCACAAAGUUUGC
(((.....((((((.(((((.....)))))(((...))---)........).))))).....)))(((((((((..........((((....)))))))))))))......... ( -39.80)
>consensus
CUAAAAAUCAGCCCACGCCGAAAAUCGGCGGGCUAUGC___CACCCAAUCGAGGCUGCCAUGUGGGUGAAUUUGUUUAUAAAUACAGUGA_AACUCCGAGAGUACGAACUGUGC
.........(((((..((((.....)))))))))((((...((((((..((.((...)).))))))))...((((........))))..............))))......... (-22.58 = -22.92 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:47 2006