Locus 5989

Sequence ID	X_DroMel_CAF1
Location	15,393,699 – 15,393,913
Length	214
Max. P	0.999595

overview

Window 9

Location	15,393,699 – 15,393,819
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.58
Mean single sequence MFE	-55.80
Consensus MFE	-46.30
Energy contribution	-48.58
Covariance contribution	2.28
Combinations/Pair	1.08
Mean z-score	-4.51
Structure conservation index	0.83
SVM decision value	3.76
SVM RNA-class probability	0.999595
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15393699 120 + 22224390
CAGUAAUUACGGGCCACGCCCCAUUCGCAUACGCCCACAUUGGCAGCUCGCAGGCAAAAGCGAUAGCGCGUGGGCGUGGCGCAGUGGGCGUGGCUGGUAUCGUUUUGAUCAAAAUGAGUU
.......(((.((((((((((.((((((.(((((((((.......(((....)))....(((....))))))))))))))).))))))))))))).)))(((((((....)))))))... ( -60.10)
>DroSec_CAF1 40042 120 + 1
CAGUAAUUACGGGCCACGCCCCUUUCGCAUACGCCCACAUUGACAGCUCGCAGGCAAAAGCGAUAUCGCGUGGGCGUGGCGCAGUGGGCGUGGCUGGUAUCGUUUUGAUCAAAAUGAGUU
.......(((.((((((((((((..(((.(((((((((.......(((....)))....(((....))))))))))))))).)).)))))))))).)))(((((((....)))))))... ( -60.60)
>DroSim_CAF1 34468 120 + 1
CAGUAAUUACGGGCCACGCCCCUUUCGCAUACGCCCACAUUGACAGCUCGCAGGCAAAAGCGAUAUCGCGUGGGCGUGGCGCAGUGGGCGUGGCUGGUAUCGUUUUGAUCAAAAUGAGUU
.......(((.((((((((((((..(((.(((((((((.......(((....)))....(((....))))))))))))))).)).)))))))))).)))(((((((....)))))))... ( -60.60)
>DroEre_CAF1 30921 105 + 1
CAGUAAUUACGAACCAC---------------GCCCACAUGGGCAGCUCGCAGGCAACAGCGAUAUCCUGUGGGCGGGGCGCAGUGGGCGUGGCUGGUAUCGUUUUGAUCAAAAUGAGUU
.......(((.(.((((---------------((((((.((.((.(((((((((............)))))))))...)).)))))))))))).).)))(((((((....)))))))... ( -49.30)
>DroYak_CAF1 22735 120 + 1
CAGUAAUUACGGGACACGCCCCUUUCGCAUACGCCCACAUUGGCAGCUCGCAGGCAAAAGCGAUAUCGUGUGGGCGGGGCGCAGUGGGCGUGGUUGGUAUCGUUUUGAUCAAAAUGAGUU
.......(((.(..(((((((((..(((...(((((((((.((....((((........))))..)))))))))))..))).)).)))))))..).)))(((((((....)))))))... ( -48.40)
>consensus
CAGUAAUUACGGGCCACGCCCCUUUCGCAUACGCCCACAUUGGCAGCUCGCAGGCAAAAGCGAUAUCGCGUGGGCGUGGCGCAGUGGGCGUGGCUGGUAUCGUUUUGAUCAAAAUGAGUU
.......(((.((((((((((....(((.(((((((((.......(((....)))....(((....)))))))))))))))....)))))))))).)))(((((((....)))))))... (-46.30 = -48.58 +   2.28)

alignment

secondary structure

dotplot

Window 0

Location	15,393,699 – 15,393,819
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.58
Mean single sequence MFE	-46.66
Consensus MFE	-39.16
Energy contribution	-40.80
Covariance contribution	1.64
Combinations/Pair	1.07
Mean z-score	-3.36
Structure conservation index	0.84
SVM decision value	3.76
SVM RNA-class probability	0.999594
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15393699 120 - 22224390
AACUCAUUUUGAUCAAAACGAUACCAGCCACGCCCACUGCGCCACGCCCACGCGCUAUCGCUUUUGCCUGCGAGCUGCCAAUGUGGGCGUAUGCGAAUGGGGCGUGGCCCGUAAUUACUG
.....................(((..(((((((((....(((.(((((((((.((..((((........))))...))...)))))))))..)))....)))))))))..)))....... ( -52.50)
>DroSec_CAF1 40042 120 - 1
AACUCAUUUUGAUCAAAACGAUACCAGCCACGCCCACUGCGCCACGCCCACGCGAUAUCGCUUUUGCCUGCGAGCUGUCAAUGUGGGCGUAUGCGAAAGGGGCGUGGCCCGUAAUUACUG
.....................(((..(((((((((....(((.(((((((((.((((((((........))))..))))..)))))))))..)))....)))))))))..)))....... ( -51.60)
>DroSim_CAF1 34468 120 - 1
AACUCAUUUUGAUCAAAACGAUACCAGCCACGCCCACUGCGCCACGCCCACGCGAUAUCGCUUUUGCCUGCGAGCUGUCAAUGUGGGCGUAUGCGAAAGGGGCGUGGCCCGUAAUUACUG
.....................(((..(((((((((....(((.(((((((((.((((((((........))))..))))..)))))))))..)))....)))))))))..)))....... ( -51.60)
>DroEre_CAF1 30921 105 - 1
AACUCAUUUUGAUCAAAACGAUACCAGCCACGCCCACUGCGCCCCGCCCACAGGAUAUCGCUGUUGCCUGCGAGCUGCCCAUGUGGGC---------------GUGGUUCGUAAUUACUG
.....................(((.((((((((((((((.((...((.(.((((.((.......)))))).).)).)).)).))))))---------------)))))).)))....... ( -36.90)
>DroYak_CAF1 22735 120 - 1
AACUCAUUUUGAUCAAAACGAUACCAACCACGCCCACUGCGCCCCGCCCACACGAUAUCGCUUUUGCCUGCGAGCUGCCAAUGUGGGCGUAUGCGAAAGGGGCGUGUCCCGUAAUUACUG
.....................(((....(((((((....(((..((((((((.....((((........))))........))))))))...)))....)))))))....)))....... ( -40.72)
>consensus
AACUCAUUUUGAUCAAAACGAUACCAGCCACGCCCACUGCGCCACGCCCACGCGAUAUCGCUUUUGCCUGCGAGCUGCCAAUGUGGGCGUAUGCGAAAGGGGCGUGGCCCGUAAUUACUG
.....................(((..(((((((((....(((..((((((((.....((((........))))........))))))))...)))....)))))))))..)))....... (-39.16 = -40.80 +   1.64)

alignment

secondary structure

dotplot

Window 1

Location	15,393,819 – 15,393,913
Length	94
Sequences	3
Columns	95
Reading direction	forward
Mean pairwise identity	95.09
Mean single sequence MFE	-14.97
Consensus MFE	-14.97
Energy contribution	-14.97
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	1.00
SVM decision value	0.23
SVM RNA-class probability	0.644423
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15393819 94 + 22224390
AAAUUCCAUUUUCAUUCGCACACACGCAGCUUAGUAUGCAAAUAUGCGAUACAUUCCGUCUCGCUCACC-CUCCAUCGUGCCGUCUCUCUUCGUU
.................((((....(((........)))......((((.((.....)).)))).....-.......)))).............. ( -15.00)
>DroSec_CAF1 40162 95 + 1
AAAUUCCAUUUUCAUUCGCACACACGCAGCUUAGUAUGCACAUAUGCGAUACAUUCCGUCUCGCUCACCGCCCCAUAGUGCCGUCCCUCUCCAUU
.................((((....(((........)))......((((.((.....)).)))).............)))).............. ( -14.90)
>DroSim_CAF1 34588 95 + 1
AAAUUCCAUUUUCAUUCGCACACACGCAGCUUAGUAUGCAAAUAUGCGAUACAUUCCGUCUCGCUCACCGCCCCAUCGUGCCGUCCCUCUCCGUU
.................((((....(((........)))......((((.((.....)).)))).............)))).............. ( -15.00)
>consensus
AAAUUCCAUUUUCAUUCGCACACACGCAGCUUAGUAUGCAAAUAUGCGAUACAUUCCGUCUCGCUCACCGCCCCAUCGUGCCGUCCCUCUCCGUU
.................((((....(((........)))......((((.((.....)).)))).............)))).............. (-14.97 = -14.97 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:34 2006