Locus 266

Sequence ID	2R_DroMel_CAF1
Location	1,660,543 – 1,660,683
Length	140
Max. P	0.981982

overview

Window 6

Location	1,660,543 – 1,660,663
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	86.67
Mean single sequence MFE	-41.37
Consensus MFE	-37.10
Energy contribution	-37.10
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.28
Structure conservation index	0.90
SVM decision value	1.31
SVM RNA-class probability	0.940286
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1660543 120 + 20766785
CUAGAUAUGAAAUAUCGAACUGGUUCCAUAGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGUAUUUAUUAUUUUUC
..(((((..((((((((((....)))....(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))))))))))..)))))... ( -43.60)
>DroSec_CAF1 46154 113 + 1
GUA-------AAUAUCAAUCUGGUUUCAUAGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGUGAAUUAUUAUUUUUA
...-------..............(((((.(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))))))))............ ( -39.90)
>DroEre_CAF1 50290 116 + 1
GUAAAUAUAAAAUGUCAUGCAGGUUUCAUAGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGC--UUUUUAUUUU--
......((((((.((((((.......))).(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))))))--.))))))...-- ( -40.60)
>consensus
GUA_AUAU_AAAUAUCAAACUGGUUUCAUAGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGCA_UUAUUAUUUUU_
..............................(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))................. (-37.10 = -37.10 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	1,660,543 – 1,660,663
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	86.67
Mean single sequence MFE	-33.30
Consensus MFE	-30.80
Energy contribution	-30.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.57
Structure conservation index	0.92
SVM decision value	1.90
SVM RNA-class probability	0.981982
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1660543 120 - 20766785
GAAAAAUAAUAAAUACCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUAUGGAACCAGUUCGAUAUUUCAUAUCUAG
((((.............(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))(((.(((....))).)))))))........ ( -35.50)
>DroSec_CAF1 46154 113 - 1
UAAAAAUAAUAAUUCACGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUAUGAAACCAGAUUGAUAUU-------UAC
............((((.(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))..))))..............-------... ( -32.00)
>DroEre_CAF1 50290 116 - 1
--AAAAUAAAAA--GCCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUAUGAAACCUGCAUGACAUUUUAUAUUUAC
--...((((((.--...(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))((((.......))))...))))))...... ( -32.40)
>consensus
_AAAAAUAAUAA_UACCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUAUGAAACCAGAUUGAUAUUU_AUAU_UAC
.................(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))).............................. (-30.80 = -30.80 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	1,660,583 – 1,660,683
Length	100
Sequences	3
Columns	101
Reading direction	forward
Mean pairwise identity	84.56
Mean single sequence MFE	-26.57
Consensus MFE	-25.17
Energy contribution	-25.17
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-0.95
Structure conservation index	0.95
SVM decision value	0.56
SVM RNA-class probability	0.781661
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1660583 100 + 20766785
CGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGUAUUUAUUAUUUUUC-AUGUUCUUUCAUUAUUUAUA
(((..((((...(.(..((((((..((((((....))))))..).)))))..).)))))..)))................-.................... ( -25.40)
>DroSec_CAF1 46187 97 + 1
CGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGUGAAUUAUUAUUUUUAGACGUUCUUU----UUUUAUA
......(((((.((((.(((((....(((((....)))))((((.......))))))))).)))).)))))...................----....... ( -27.00)
>DroEre_CAF1 50330 87 + 1
CGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGC--UUUUUAUUUU--------GUUU----AUAUGUA
.((((.(((..(((....(((((..((((((....))))))..).))))((((......)))).))--)..)))..))--------))..----....... ( -27.30)
>consensus
CGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGCA_UUAUUAUUUUU__A_GUUCUUU____AUUUAUA
(((..((((...(.(..((((((..((((((....))))))..).)))))..).)))))..)))..................................... (-25.17 = -25.17 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	1,660,583 – 1,660,683
Length	100
Sequences	3
Columns	101
Reading direction	reverse
Mean pairwise identity	84.56
Mean single sequence MFE	-18.50
Consensus MFE	-17.57
Energy contribution	-17.57
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.24
Structure conservation index	0.95
SVM decision value	0.94
SVM RNA-class probability	0.885674
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1660583 100 - 20766785
UAUAAAUAAUGAAAGAACAU-GAAAAAUAAUAAAUACCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCG
..........(((((.....-...............(((((....)))))....(......)...)))))(((((...((.....))..)))))....... ( -18.80)
>DroSec_CAF1 46187 97 - 1
UAUAAAA----AAAGAACGUCUAAAAAUAAUAAUUCACGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCG
.......----..........................(((.....(((((.......))))).....((((((.....)))))).)))............. ( -17.70)
>DroEre_CAF1 50330 87 - 1
UACAUAU----AAAC--------AAAAUAAAAA--GCCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCG
.......----....--------.........(--((.((.....(((((.......))))).....((((((.....)))))).)))))........... ( -19.00)
>consensus
UAUAAAU____AAAGAAC_U__AAAAAUAAUAA_UACCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCG
.....................................(((.....(((((.......))))).....((((((.....)))))).)))............. (-17.57 = -17.57 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:05 2006