Locus 619

Sequence ID	3L_DroMel_CAF1
Location	1,803,124 – 1,803,281
Length	157
Max. P	0.997358

overview

Window 2

Location	1,803,124 – 1,803,241
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.45
Mean single sequence MFE	-38.08
Consensus MFE	-33.94
Energy contribution	-34.70
Covariance contribution	0.76
Combinations/Pair	1.03
Mean z-score	-2.26
Structure conservation index	0.89
SVM decision value	2.84
SVM RNA-class probability	0.997358
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1803124 117 + 23771897
GACAGCGUCGAUCGGCGGACAGGUAUUGCUGCAACCGG---CGGCUCAUGCCAAUAUGCAUUGUGCAUAGCAAAUAAGUGCUUGUCAAUGCAAAAUUGUCAAUCAAUUAGCCAAAACGGG
.....((((....))))(((((((((.(((((.....)---))))..)))))....(((((((.(((.((((......))))))))))))))....))))..........((.....)). ( -36.90)
>DroSec_CAF1 18486 117 + 1
GACAGCGCCGAUCGGCGGACAGGUAUUGCUGCAACCGG---CGGCUCAUGCCAAUAUGCAUUGUGCAUAGCAAAUAAGUGCUUGUCAAUGCAAAAUUGUCAAUCAAUUAGCCAAAACGGG
.....((((....))))(((((((((.(((((.....)---))))..)))))....(((((((.(((.((((......))))))))))))))....))))..........((.....)). ( -39.60)
>DroSim_CAF1 18543 117 + 1
GACAGCGCCGAUCGGCGGACAGGUAUUGCUGCAACCGG---CGGCUCACGCCAAUAUGCAUUGUGCAUAGCAAAUAAGUGCUUGUCAAUGCAAAAUUGUCAAUCAAUUAGCCAAAACGGG
(((((((((....))))((((((((((..(((....((---((.....))))..(((((.....))))))))....)))))))))).........)))))..........((.....)). ( -41.10)
>DroEre_CAF1 18720 114 + 1
GACAGCGUCGAUCGGCGGACAGGUAUUGCAGCAACCGG---CGGCUCAUGCCAAUAUGCAUUGUGCAUAGCAAAUAAGAGCU---CAAUGCAAAAUUGUCAAUCAAUUAGCCAAAACGGG
(((((((((....)))).....((((((.(((....((---((.....))))..(((((.....)))))..........)))---))))))....)))))..........((.....)). ( -30.50)
>DroYak_CAF1 18930 120 + 1
GACAGCGCCGAUCGGCGGACAGGUAUUGCUGCAACCGGCGGCGGCUCAUGCCAAUAUGCAUUGUGCAUAGCAAAUAAGUGCUUGUCAAUGCAAAAUUGUCAAUCAAUUAGCCAAAACGGG
(((((((((....))))(((((((((((((((.....))))).(((.((((((((....)))).))))))).....)))))))))).........)))))..........((.....)). ( -42.30)
>consensus
GACAGCGCCGAUCGGCGGACAGGUAUUGCUGCAACCGG___CGGCUCAUGCCAAUAUGCAUUGUGCAUAGCAAAUAAGUGCUUGUCAAUGCAAAAUUGUCAAUCAAUUAGCCAAAACGGG
(((((((((....))))((((((((((..(((..........(((....)))..(((((.....))))))))....)))))))))).........)))))..........((.....)). (-33.94 = -34.70 +   0.76)

alignment

secondary structure

dotplot

Window 3

Location	1,803,162 – 1,803,281
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.48
Mean single sequence MFE	-34.66
Consensus MFE	-29.72
Energy contribution	-30.92
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-2.17
Structure conservation index	0.86
SVM decision value	2.26
SVM RNA-class probability	0.991324
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1803162 119 + 23771897
-CGGCUCAUGCCAAUAUGCAUUGUGCAUAGCAAAUAAGUGCUUGUCAAUGCAAAAUUGUCAAUCAAUUAGCCAAAACGGGGGAUAGUCGAGCCCGCCGACAGCUUAACCGCUGCCUCUUC
-.((((..........(((((((.(((.((((......)))))))))))))).(((((.....)))))))))....((((((.........))).))).((((......))))....... ( -34.40)
>DroSec_CAF1 18524 119 + 1
-CGGCUCAUGCCAAUAUGCAUUGUGCAUAGCAAAUAAGUGCUUGUCAAUGCAAAAUUGUCAAUCAAUUAGCCAAAACGGGGGAUAGUCGAGCCCGCCGACAGCUUAACCGCUGCCUCUUC
-.((((..........(((((((.(((.((((......)))))))))))))).(((((.....)))))))))....((((((.........))).))).((((......))))....... ( -34.40)
>DroSim_CAF1 18581 119 + 1
-CGGCUCACGCCAAUAUGCAUUGUGCAUAGCAAAUAAGUGCUUGUCAAUGCAAAAUUGUCAAUCAAUUAGCCAAAACGGGGGAUAUUCUAUCCCCCCGACAGCUUAACCGCUGCCUCUUC
-.((((..........(((((((.(((.((((......)))))))))))))).(((((.....))))))))).....((((((((...)))))))).(.((((......)))).)..... ( -39.20)
>DroEre_CAF1 18758 116 + 1
-CGGCUCAUGCCAAUAUGCAUUGUGCAUAGCAAAUAAGAGCU---CAAUGCAAAAUUGUCAAUCAAUUAGCCAAAACGGGGCAUAGCCGAGCCCGCCGACAGCUUAACCGCCGCCUCUUC
-.((((.(((((....(((((((.((.............)).---))))))).(((((.....)))))..((.....)))))))))))(((.(.((.(.........).)).).)))... ( -30.62)
>DroYak_CAF1 18970 120 + 1
GCGGCUCAUGCCAAUAUGCAUUGUGCAUAGCAAAUAAGUGCUUGUCAAUGCAAAAUUGUCAAUCAAUUAGCCAAAACGGGGGAUAGCCGAGCCCGCCGACAGCUUAACCGCUGCCUCUUC
(((((((...((....(((((((.(((.((((......)))))))))))))).(((((.....))))).........))((.....))))).)))).(.((((......)))).)..... ( -34.70)
>consensus
_CGGCUCAUGCCAAUAUGCAUUGUGCAUAGCAAAUAAGUGCUUGUCAAUGCAAAAUUGUCAAUCAAUUAGCCAAAACGGGGGAUAGUCGAGCCCGCCGACAGCUUAACCGCUGCCUCUUC
..((((..........(((((((.(((.((((......)))))))))))))).(((((.....)))))))))....((((((.........))).))).((((......))))....... (-29.72 = -30.92 +   1.20)

alignment

secondary structure

dotplot

Window 4

Location	1,803,162 – 1,803,281
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.48
Mean single sequence MFE	-39.62
Consensus MFE	-35.20
Energy contribution	-35.08
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-1.84
Structure conservation index	0.89
SVM decision value	2.01
SVM RNA-class probability	0.985487
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1803162 119 - 23771897
GAAGAGGCAGCGGUUAAGCUGUCGGCGGGCUCGACUAUCCCCCGUUUUGGCUAAUUGAUUGACAAUUUUGCAUUGACAAGCACUUAUUUGCUAUGCACAAUGCAUAUUGGCAUGAGCCG-
.....((((((......))))))((((((...........))))))..((((...((.....((((..(((((((.((((((......)))).))..))))))).)))).))..)))).- ( -37.80)
>DroSec_CAF1 18524 119 - 1
GAAGAGGCAGCGGUUAAGCUGUCGGCGGGCUCGACUAUCCCCCGUUUUGGCUAAUUGAUUGACAAUUUUGCAUUGACAAGCACUUAUUUGCUAUGCACAAUGCAUAUUGGCAUGAGCCG-
.....((((((......))))))((((((...........))))))..((((...((.....((((..(((((((.((((((......)))).))..))))))).)))).))..)))).- ( -37.80)
>DroSim_CAF1 18581 119 - 1
GAAGAGGCAGCGGUUAAGCUGUCGGGGGGAUAGAAUAUCCCCCGUUUUGGCUAAUUGAUUGACAAUUUUGCAUUGACAAGCACUUAUUUGCUAUGCACAAUGCAUAUUGGCGUGAGCCG-
.....((((((......)))))).((((((((...)))))))).....((((...((.....((((..(((((((.((((((......)))).))..))))))).)))).))..)))).- ( -44.60)
>DroEre_CAF1 18758 116 - 1
GAAGAGGCGGCGGUUAAGCUGUCGGCGGGCUCGGCUAUGCCCCGUUUUGGCUAAUUGAUUGACAAUUUUGCAUUG---AGCUCUUAUUUGCUAUGCACAAUGCAUAUUGGCAUGAGCCG-
.....(.((((((.....)))))).).((((((((...(((.......)))...........((((..(((((((---.((.............)).))))))).)))))).)))))).- ( -39.02)
>DroYak_CAF1 18970 120 - 1
GAAGAGGCAGCGGUUAAGCUGUCGGCGGGCUCGGCUAUCCCCCGUUUUGGCUAAUUGAUUGACAAUUUUGCAUUGACAAGCACUUAUUUGCUAUGCACAAUGCAUAUUGGCAUGAGCCGC
.....((((((......)))))).((((.((((((((..........))))).......((.((((..(((((((.((((((......)))).))..))))))).)))).)).))))))) ( -38.90)
>consensus
GAAGAGGCAGCGGUUAAGCUGUCGGCGGGCUCGACUAUCCCCCGUUUUGGCUAAUUGAUUGACAAUUUUGCAUUGACAAGCACUUAUUUGCUAUGCACAAUGCAUAUUGGCAUGAGCCG_
.....((((((......))))))((((((...........))))))..((((...((.....((((..(((((((...(((........))).....))))))).)))).))..)))).. (-35.20 = -35.08 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:56 2006