Locus 6938

Sequence ID	2L_DroMel_CAF1
Location	19,307,692 – 19,307,844
Length	152
Max. P	0.996537

overview

Window 7

Location	19,307,692 – 19,307,786
Length	94
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	90.10
Mean single sequence MFE	-31.02
Consensus MFE	-23.70
Energy contribution	-24.38
Covariance contribution	0.68
Combinations/Pair	1.04
Mean z-score	-1.91
Structure conservation index	0.76
SVM decision value	0.67
SVM RNA-class probability	0.818237
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19307692 94 + 22407834
AAAAGAAUGGCAGGCGGAAUUGCAAUGUCAGUGUCUCCGGGGAGGGGGAGCAAGCGGGUGAGAGCUGCACAAUGUUGCCACAUUGCGCCUGA---UG
..........((((((.(((.(((((((..((..((((.....))))..))..((((.(....)))))...)))))))...))).)))))).---.. ( -31.40)
>DroSec_CAF1 361 97 + 1
AAAAGAAUGGCAGGCGGAAUUGCAAUGUCAGUGUCUCCGGGGAGGGGGAGCAACAGGGUGAGAGCUGCACAAUGUUGCCACAUUGCGCCUGAUGAUG
..........(((((......(((((((.....(((((......)))))((((((..(((.......)))..)))))).))))))))))))...... ( -32.50)
>DroSim_CAF1 314 97 + 1
AAAAGAAUGGCAGGCGGAAUUGCAAUGUCAGUGUCUCCGGGGAGGGGGAGCAACAGGGUGAGAGCUGCACAAUGUUGCCACAUUGCGCCUGAUGAUG
..........(((((......(((((((.....(((((......)))))((((((..(((.......)))..)))))).))))))))))))...... ( -32.50)
>DroEre_CAF1 162 97 + 1
AAAAGAAUGGCAGGCGGAAUUGCAAUGUCAGAGUCUCCGGGGAGGGGGAGCAUCAGAGGAGGAGCUGCACCAUGUUGCCACAUUGCGCCUGAUGAGG
..........((((((.(((.((((((((((..(((((...((..(....).))...)))))..))).))...)))))...))).))))))...... ( -31.80)
>DroYak_CAF1 401 97 + 1
AAAAGAAUGGCAAGCGGAAUUGCAAUGUCAGUGUCUCCGGGGAGGGGGAGCAAAAGAAAAAAAACGGCGCAAUGUUGCAAGAUUGCGCCUGAUGAGG
.........((((......))))...((((((..((((.....))))..))..............((((((((........)))))))))))).... ( -26.90)
>consensus
AAAAGAAUGGCAGGCGGAAUUGCAAUGUCAGUGUCUCCGGGGAGGGGGAGCAACAGGGUGAGAGCUGCACAAUGUUGCCACAUUGCGCCUGAUGAUG
..........((((((.(((.(((((((..((((((((.....)))).(((............))))))).)))))))...))).))))))...... (-23.70 = -24.38 +   0.68)

alignment

secondary structure

dotplot

Window 8

Location	19,307,692 – 19,307,786
Length	94
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	90.10
Mean single sequence MFE	-25.20
Consensus MFE	-21.00
Energy contribution	-21.24
Covariance contribution	0.24
Combinations/Pair	1.05
Mean z-score	-2.56
Structure conservation index	0.83
SVM decision value	2.71
SVM RNA-class probability	0.996537
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19307692 94 - 22407834
CA---UCAGGCGCAAUGUGGCAACAUUGUGCAGCUCUCACCCGCUUGCUCCCCCUCCCCGGAGACACUGACAUUGCAAUUCCGCCUGCCAUUCUUUU
..---.((((((((((((....)))))))(((((........)).((((((........)))).)).......)))......))))).......... ( -24.70)
>DroSec_CAF1 361 97 - 1
CAUCAUCAGGCGCAAUGUGGCAACAUUGUGCAGCUCUCACCCUGUUGCUCCCCCUCCCCGGAGACACUGACAUUGCAAUUCCGCCUGCCAUUCUUUU
......(((((((((((((((((((..(((.......)))..)))))))....(((....)))......)))))))......))))).......... ( -27.70)
>DroSim_CAF1 314 97 - 1
CAUCAUCAGGCGCAAUGUGGCAACAUUGUGCAGCUCUCACCCUGUUGCUCCCCCUCCCCGGAGACACUGACAUUGCAAUUCCGCCUGCCAUUCUUUU
......(((((((((((((((((((..(((.......)))..)))))))....(((....)))......)))))))......))))).......... ( -27.70)
>DroEre_CAF1 162 97 - 1
CCUCAUCAGGCGCAAUGUGGCAACAUGGUGCAGCUCCUCCUCUGAUGCUCCCCCUCCCCGGAGACUCUGACAUUGCAAUUCCGCCUGCCAUUCUUUU
......((((((((..(((....)))..))).((......((.((..((((........))))..)).))....))......))))).......... ( -25.20)
>DroYak_CAF1 401 97 - 1
CCUCAUCAGGCGCAAUCUUGCAACAUUGCGCCGUUUUUUUUCUUUUGCUCCCCCUCCCCGGAGACACUGACAUUGCAAUUCCGCUUGCCAUUCUUUU
.....(((((((((((........)))))))).............((((((........)))).)).)))....((((......))))......... ( -20.70)
>consensus
CAUCAUCAGGCGCAAUGUGGCAACAUUGUGCAGCUCUCACCCUGUUGCUCCCCCUCCCCGGAGACACUGACAUUGCAAUUCCGCCUGCCAUUCUUUU
.....(((((((((((((....)))))))))................((((........))))...))))....(((........)))......... (-21.00 = -21.24 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	19,307,751 – 19,307,844
Length	93
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	71.97
Mean single sequence MFE	-16.68
Consensus MFE	-11.48
Energy contribution	-11.72
Covariance contribution	0.24
Combinations/Pair	1.11
Mean z-score	-1.28
Structure conservation index	0.69
SVM decision value	0.53
SVM RNA-class probability	0.771575
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19307751 93 - 22407834
CACUUACUCGCCGAAC-AAAGCUCGUGCCCCACCCCAAGCACCACCCCAACCUCCUGCUCA---UCAGGCGCAAUGUGGCAACAUUGUGCAGCUCUC
.........(((((..-.....))).)).........(((..............(((....---.)))(((((((((....))))))))).)))... ( -20.00)
>DroSec_CAF1 420 95 - 1
CACUUACUCGCCCAAC-AAAGCCCGUGCCCCACC-CAAGCACCACCCCAACCUCCCGCUCAUCAUCAGGCGCAAUGUGGCAACAUUGUGCAGCUCUC
................-..(((..((((......-...))))..........................(((((((((....))))))))).)))... ( -18.40)
>DroSim_CAF1 373 82 - 1
CACUUACUCGCCCAAC-AAAGCCCG--------------CACCACCCCAACCUCCCGCUCAUCAUCAGGCGCAAUGUGGCAACAUUGUGCAGCUCUC
................-..(((..(--------------(................))..........(((((((((....))))))))).)))... ( -14.39)
>DroEre_CAF1 221 77 - 1
CACUUACUCGGCAA-C-AAAACCCGUGCCCCACC-CAA-----------GU------CCCCUCAUCAGGCGCAAUGUGGCAACAUGGUGCAGCUCCU
.........((((.-(-.......))))).....-...-----------..------..........((((((..(((....)))..))).)))... ( -14.40)
>DroYak_CAF1 460 88 - 1
CACUUACGCGCCCAGCAAAAACCCUCGCCCCACC-CAAGCCC--UCUCAGU------CCCCUCAUCAGGCGCAAUCUUGCAACAUUGCGCCGUUUUU
.......((.....))((((((....((......-...))..--.......------..........((((((((........)))))))))))))) ( -16.20)
>consensus
CACUUACUCGCCCAAC_AAAGCCCGUGCCCCACC_CAAGCACCACCCCAACCUCC_GCUCAUCAUCAGGCGCAAUGUGGCAACAUUGUGCAGCUCUC
....................................................................(((((((((....)))))))))....... (-11.48 = -11.72 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:20 2006