Locus 1825

Sequence ID	2R_DroMel_CAF1
Location	6,833,409 – 6,833,528
Length	119
Max. P	0.992459

overview

Window 1

Location	6,833,409 – 6,833,499
Length	90
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	80.31
Mean single sequence MFE	-19.68
Consensus MFE	-14.81
Energy contribution	-15.07
Covariance contribution	0.25
Combinations/Pair	1.25
Mean z-score	-2.07
Structure conservation index	0.75
SVM decision value	1.06
SVM RNA-class probability	0.909071
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6833409 90 - 20766785
AUCCAAAAUCCAAAAGCCAGGUUGCGGUGAA-AAUGCCGCGAUCAAGCUAGAAAACCCCUUU--CCAAGUACUCAAAAUCAAA-CCAUUGUGGA
........((((..(((..(((((((((...-...)))))))))..))).((((.....)))--)..................-......)))) ( -20.90)
>DroPse_CAF1 7856 78 - 1
ACCCCA-----------CAGAUCGAGGCGAAUAAUGCCGCGAUCCAGCUAGGAAACCCCCACAGAGCAGAGACCGUAAUCGAAACGAUU-----
.....(-----------(.(((((.((((.....)))).)))))..(((.((......))....))).......))(((((...)))))----- ( -16.50)
>DroSec_CAF1 6317 90 - 1
AUCCAAAAUCCAAAAGCCAGGUUGCGGUGAA-AAUGCCGCGAUCAAGCUAGAAAAUCCCUUU--CCAAGUACUCCAAAUCAAA-CCAUUGUGGA
........((((..(((..(((((((((...-...)))))))))..))).((((.....)))--)..................-......)))) ( -20.90)
>DroSim_CAF1 4810 90 - 1
AUCCAAAAUCCAAAAGCCAGGUUGCGGUGAA-AAUGCCGCGAUCAAGCUAGAAAACCCCUUU--CCAAGUACUCCAAAUCAAA-CCAUUGUGGA
........((((..(((..(((((((((...-...)))))))))..))).((((.....)))--)..................-......)))) ( -20.90)
>DroEre_CAF1 6975 89 - 1
ACCCA-AAUCCCAAAGCCAGGUUGCGGUGAA-AAUGCCGCGAUCCAGCUAGAAAACCCCUUU--CCAAGUACUCCAAAUCGAA-CCAUUGUGGA
.....-..(((((((((..(((((((((...-...)))))))))..))).((((.....)))--)..................-...))).))) ( -21.50)
>DroYak_CAF1 7169 84 - 1
ACCCA-AAUCCAAAAGCCAGGUUGCGGUGAA-AAUGCCGCGAUCAAGCUAGAAAACCCCUUU--CCAAGUACUCCAAAUCGAA-CA-U----AA
.....-........(((..(((((((((...-...)))))))))..))).((((.....)))--)..................-..-.----.. ( -17.40)
>consensus
ACCCAAAAUCCAAAAGCCAGGUUGCGGUGAA_AAUGCCGCGAUCAAGCUAGAAAACCCCUUU__CCAAGUACUCCAAAUCAAA_CCAUUGUGGA
..............(((..(((((((((.......)))))))))..)))............................................. (-14.81 = -15.07 +   0.25)

alignment

secondary structure

dotplot

Window 2

Location	6,833,438 – 6,833,528
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	94.88
Mean single sequence MFE	-19.08
Consensus MFE	-18.04
Energy contribution	-18.24
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.68
Structure conservation index	0.95
SVM decision value	2.33
SVM RNA-class probability	0.992459
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6833438 90 - 20766785
CUAAACGCUAAACACGCUAUAGUUUCGAUAUCCAAAAUCCAAAAGCCAGGUUGCGGUGAAAAUGCCGCGAUCAAGCUAGAAAACCCCUUU
......((.......)).....(((((((.......)))....(((..(((((((((......)))))))))..))).))))........ ( -18.90)
>DroSec_CAF1 6346 90 - 1
CUAAACGCUAAACACGCAAUAGUUUCGAUAUCCAAAAUCCAAAAGCCAGGUUGCGGUGAAAAUGCCGCGAUCAAGCUAGAAAAUCCCUUU
......((.......)).....(((((((.......)))....(((..(((((((((......)))))))))..))).))))........ ( -19.40)
>DroSim_CAF1 4839 90 - 1
CUAAACGCUAAGCACGCAAUAGUUUCGAUAUCCAAAAUCCAAAAGCCAGGUUGCGGUGAAAAUGCCGCGAUCAAGCUAGAAAACCCCUUU
......((.......)).....(((((((.......)))....(((..(((((((((......)))))))))..))).))))........ ( -19.40)
>DroEre_CAF1 7004 89 - 1
CUAAACGCCAAACACGCAAUAGUUUCCAUACCCA-AAUCCCAAAGCCAGGUUGCGGUGAAAAUGCCGCGAUCCAGCUAGAAAACCCCUUU
......((.......)).................-........(((..(((((((((......)))))))))..)))............. ( -17.80)
>DroYak_CAF1 7193 89 - 1
CUAAACGCUAAGCACGCAACAGUUUCGAUACCCA-AAUCCAAAAGCCAGGUUGCGGUGAAAAUGCCGCGAUCAAGCUAGAAAACCCCUUU
......((.......)).....(((((((.....-.)))....(((..(((((((((......)))))))))..))).))))........ ( -19.90)
>consensus
CUAAACGCUAAACACGCAAUAGUUUCGAUAUCCAAAAUCCAAAAGCCAGGUUGCGGUGAAAAUGCCGCGAUCAAGCUAGAAAACCCCUUU
......((.......)).....(((((((.......)))....(((..(((((((((......)))))))))..))).))))........ (-18.04 = -18.24 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:06 2006