Locus 8503

Sequence ID	3L_DroMel_CAF1
Location	22,295,128 – 22,295,239
Length	111
Max. P	0.811174

overview

Window 7

Location	22,295,128 – 22,295,239
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.00
Mean single sequence MFE	-40.83
Consensus MFE	-29.59
Energy contribution	-30.90
Covariance contribution	1.31
Combinations/Pair	1.04
Mean z-score	-1.95
Structure conservation index	0.72
SVM decision value	0.65
SVM RNA-class probability	0.811174
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22295128 111 + 23771897
UCUUCUUCGGCUGCAUGGGGCGGAUAGAGAGCUACGCCUGGUACAUCAAUUAGUGCCGCACAAAGCCACAGUGGCAUGUGGCAGA----AGACCCCACACCCCAUGCAC-----CCCGAC
......((((.(((((((((.(.............((..(((((........))))))).....((((((......))))))...----........).))))))))).-----.)))). ( -41.50)
>DroSec_CAF1 53665 110 + 1
UUUUCUUCGGCUGCAUGGGGCGGAUAGAGAGCUACGCCUGGUACAUCAAUUAGUGCCGCACAAAGCCACAGUGGCAUGUGGCAGA----AGACCACACACCCCUUGCUC------CCGAC
......((((..(((.((((.(........(((((....(((((........)))))((.....))....))))).((((((...----.).)))))).)))).)))..------)))). ( -40.30)
>DroEre_CAF1 52376 120 + 1
UUUUCUUCGGGUGCAUGGGGUGGAGGGAGAGCAACGCCUGGUACAUCAAUUAGUGCCGCACAAAGCCACAGUGGCAUGUGGCAGACCCCACACCCCACACCCCAUCCCCCUUUGCCCGAC
......(((((((.((((((((..(((........((..(((((........))))))).....((((((......))))))..........)))..)))))))).)......)))))). ( -48.00)
>DroYak_CAF1 18305 105 + 1
UUUUCUUUGGGUGCAUGG-GCGGAUAGAGAG-----CCUGGUACAUCAAUUAGUGCCGCACAAAGCCACAGUGGCAUGUGGCAGG----AGAACCCAAACCCCAUUCCC-----CCCGAC
.....(((((((((..((-((.........)-----)))(((((........))))))).....((((((......))))))...----...)))))))..........-----...... ( -33.50)
>consensus
UUUUCUUCGGCUGCAUGGGGCGGAUAGAGAGCUACGCCUGGUACAUCAAUUAGUGCCGCACAAAGCCACAGUGGCAUGUGGCAGA____AGACCCCACACCCCAUGCCC_____CCCGAC
......(((((.((((((((...................(((((........))))).......((((((......)))))).................)))))))).......))))). (-29.59 = -30.90 +   1.31)

alignment

secondary structure

dotplot

Window 8

Location	22,295,128 – 22,295,239
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.00
Mean single sequence MFE	-44.18
Consensus MFE	-30.70
Energy contribution	-32.89
Covariance contribution	2.19
Combinations/Pair	1.08
Mean z-score	-1.50
Structure conservation index	0.70
SVM decision value	0.03
SVM RNA-class probability	0.550440
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22295128 111 - 23771897
GUCGGG-----GUGCAUGGGGUGUGGGGUCU----UCUGCCACAUGCCACUGUGGCUUUGUGCGGCACUAAUUGAUGUACCAGGCGUAGCUCUCUAUCCGCCCCAUGCAGCCGAAGAAGA
....((-----.((((((((((((((((...----.((((((((......))))((((.(((((.((.....)).))))).))))))))..)))))..))))))))))).))........ ( -46.10)
>DroSec_CAF1 53665 110 - 1
GUCGG------GAGCAAGGGGUGUGUGGUCU----UCUGCCACAUGCCACUGUGGCUUUGUGCGGCACUAAUUGAUGUACCAGGCGUAGCUCUCUAUCCGCCCCAUGCAGCCGAAGAAAA
.((((------..(((.((((((..(((...----.((((((((......))))((((.(((((.((.....)).))))).))))))))....)))..)))))).)))..))))...... ( -42.20)
>DroEre_CAF1 52376 120 - 1
GUCGGGCAAAGGGGGAUGGGGUGUGGGGUGUGGGGUCUGCCACAUGCCACUGUGGCUUUGUGCGGCACUAAUUGAUGUACCAGGCGUUGCUCUCCCUCCACCCCAUGCACCCGAAGAAAA
..........((((.((((((((..(((.(..(.((((((((((......))))))...(((((.((.....)).))))).)))).)..)...)))..)))))))).).)))........ ( -52.90)
>DroYak_CAF1 18305 105 - 1
GUCGGG-----GGGAAUGGGGUUUGGGUUCU----CCUGCCACAUGCCACUGUGGCUUUGUGCGGCACUAAUUGAUGUACCAGG-----CUCUCUAUCCGC-CCAUGCACCCAAAGAAAA
...(((-----.(((..(((((((((..((.----..((((.((((((.....)))...))).))))......))....)))))-----))))...))).)-))................ ( -35.50)
>consensus
GUCGGG_____GGGCAUGGGGUGUGGGGUCU____UCUGCCACAUGCCACUGUGGCUUUGUGCGGCACUAAUUGAUGUACCAGGCGUAGCUCUCUAUCCGCCCCAUGCACCCGAAGAAAA
.(((((.......(((((((((((((((.......(((((((((......))))))...(((((.((.....)).))))).))).......)))))..)))))))))).)))))...... (-30.70 = -32.89 +   2.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:17 2006