Locus 10209

Sequence ID	3R_DroMel_CAF1
Location	27,391,318 – 27,391,410
Length	92
Max. P	0.776867

overview

Window 4

Location	27,391,318 – 27,391,410
Length	92
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	78.28
Mean single sequence MFE	-21.10
Consensus MFE	-15.13
Energy contribution	-15.05
Covariance contribution	-0.08
Combinations/Pair	1.11
Mean z-score	-1.33
Structure conservation index	0.72
SVM decision value	0.55
SVM RNA-class probability	0.776867
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27391318 92 + 27905053
CGAUACAAU--AGAAUGCGCGCUUUUAAAUGCACUGGA-AGACGAG-----------AUUCCAGCAUUUUAAAUCGGCGCAUUGCCAACAAAAGAACGGAAAUUCA
.........--..((((((((.(((.((((((..((((-(......-----------.))))))))))).))).).)))))))....................... ( -20.40)
>DroSec_CAF1 7491 92 + 1
CGAUACGAU--AUAAUGCGCGCUUUUAAAUGCACUGGA-CGACGAG-----------AUUCCAGCAUUUUAAAUCGGCGCAUUGCCAAGAAAAGAACGGAAAUUCA
.........--.(((((((((.(((.((((((..((((-.......-----------..)))))))))).))).).))))))))...................... ( -18.80)
>DroEre_CAF1 8088 91 + 1
UGAU-CAAU--CGAAUGCGCGCUUUUAAAUGCACUGGA-AUGCGCA-----------AUUCCAGCAUUUUAAAUCGGCGCAUUGCCAAGAAAAGAACGGAAAUUUA
....-....--..((((((((.(((.((((((..((((-((.....-----------)))))))))))).))).).)))))))....................... ( -22.10)
>DroYak_CAF1 7436 104 + 1
CGAUACAAU--AGAAUGCGCGCUUUUAAAUGCACUGGAAAUGCACAGGAAAAUGGAGAUUCCAGCAUUUUAAAUCGGCGCAUUGCCAAGAAAAGAACGGAAAUUGA
.....((((--..((((((((.(((.((((((.(((........))).....(((.....))))))))).))).).))))))).((...........))..)))). ( -23.50)
>DroAna_CAF1 8057 97 + 1
CGAUACGAUGAAUAAUGCGCGCUUUUUAAUGCCUUGGA-AAUCCAG--------UGGUUUCCAACAUUUUAAAUCGGCACAUUGCCAAGAAAAAAACGAAAAGUUU
.....(((((.....(((.((.(((..((((..(((((-((((...--------.)))))))))))))..))).)))))))))).........((((.....)))) ( -19.10)
>DroPer_CAF1 46409 92 + 1
UGUCUCUCA--AGAAUGCGCGCUUUUAAAUGCCCUGGA-AAUUGAA----AA----UGUUCCAGCAUUUUGAAUCUGCGCAUUGCCAAUCA---AACGGAAAUUCU
.........--..((((((((..(((((((((..((((-(..(...----.)----..)))))))).))))))..)))))))).((.....---...))....... ( -22.70)
>consensus
CGAUACAAU__AGAAUGCGCGCUUUUAAAUGCACUGGA_AAACGAA___________AUUCCAGCAUUUUAAAUCGGCGCAUUGCCAAGAAAAGAACGGAAAUUCA
.............(((((((...((((((....(((((.....................)))))...))))))...)))))))....................... (-15.13 = -15.05 +  -0.08)

alignment

secondary structure

dotplot

Window 5

Location	27,391,318 – 27,391,410
Length	92
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	78.28
Mean single sequence MFE	-21.50
Consensus MFE	-16.34
Energy contribution	-16.40
Covariance contribution	0.06
Combinations/Pair	1.10
Mean z-score	-1.14
Structure conservation index	0.76
SVM decision value	0.41
SVM RNA-class probability	0.724575
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27391318 92 - 27905053
UGAAUUUCCGUUCUUUUGUUGGCAAUGCGCCGAUUUAAAAUGCUGGAAU-----------CUCGUCU-UCCAGUGCAUUUAAAAGCGCGCAUUCU--AUUGUAUCG
.((((....))))......(((.((((((((..((((((..(((((((.-----------......)-))))))...)))))).).)))))))))--)........ ( -22.30)
>DroSec_CAF1 7491 92 - 1
UGAAUUUCCGUUCUUUUCUUGGCAAUGCGCCGAUUUAAAAUGCUGGAAU-----------CUCGUCG-UCCAGUGCAUUUAAAAGCGCGCAUUAU--AUCGUAUCG
.((((....))))..........((((((((..((((((..((((((..-----------.......-))))))...)))))).).)))))))..--......... ( -19.40)
>DroEre_CAF1 8088 91 - 1
UAAAUUUCCGUUCUUUUCUUGGCAAUGCGCCGAUUUAAAAUGCUGGAAU-----------UGCGCAU-UCCAGUGCAUUUAAAAGCGCGCAUUCG--AUUG-AUCA
.....................(.((((((((..((((((..((((((((-----------.....))-))))))...)))))).).)))))))).--....-.... ( -21.40)
>DroYak_CAF1 7436 104 - 1
UCAAUUUCCGUUCUUUUCUUGGCAAUGCGCCGAUUUAAAAUGCUGGAAUCUCCAUUUUCCUGUGCAUUUCCAGUGCAUUUAAAAGCGCGCAUUCU--AUUGUAUCG
...................(((.((((((((..((((((..(((((((....(((......)))...)))))))...)))))).).)))))))))--)........ ( -23.70)
>DroAna_CAF1 8057 97 - 1
AAACUUUUCGUUUUUUUCUUGGCAAUGUGCCGAUUUAAAAUGUUGGAAACCA--------CUGGAUU-UCCAAGGCAUUAAAAAGCGCGCAUUAUUCAUCGUAUCG
........((((((((..(((((.....))))).....(((((((((((((.--------..)).))-))))..)))))))))))))................... ( -19.50)
>DroPer_CAF1 46409 92 - 1
AGAAUUUCCGUU---UGAUUGGCAAUGCGCAGAUUCAAAAUGCUGGAACA----UU----UUCAAUU-UCCAGGGCAUUUAAAAGCGCGCAUUCU--UGAGAGACA
.........(((---(..(..(.(((((((............((((((..----..----......)-))))).((........))))))))).)--..).)))). ( -22.70)
>consensus
UGAAUUUCCGUUCUUUUCUUGGCAAUGCGCCGAUUUAAAAUGCUGGAAU___________CUCGAAU_UCCAGUGCAUUUAAAAGCGCGCAUUCU__AUUGUAUCG
.......................(((((((...(((.((((((((((.....................))))..)))))).)))..)))))))............. (-16.34 = -16.40 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:51:26 2006