Locus 2276

Sequence ID	3L_DroMel_CAF1
Location	6,368,297 – 6,368,388
Length	91
Max. P	0.973195

overview

Window 8

Location	6,368,297 – 6,368,388
Length	91
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	71.64
Mean single sequence MFE	-22.95
Consensus MFE	-14.12
Energy contribution	-14.40
Covariance contribution	0.28
Combinations/Pair	1.42
Mean z-score	-1.89
Structure conservation index	0.62
SVM decision value	1.71
SVM RNA-class probability	0.973195
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6368297 91 + 23771897
AUUUGUUCGGUCUCUGGCAAAUUGCCAGCUAU---AUAAGGCGGAGAAGUCGCUAUGGGAGCACCGAAAGAAAUAAUCUUCAAAUGGGAAAAUA-------------
.(((.(((((((((((((.....)))).((((---(...(((......)))..)))))))).)))))).)))......................------------- ( -23.30)
>DroSec_CAF1 132712 91 + 1
AUUUGUUCGGUCUUUGGCAAAUUGCCAGCCAU---AUAGGGCGGUGAAGUCGCUAUGGGAGCACCGAAAGAAAAAAUCUACAAAUGGGAAAAUA-------------
((((((((((((((((((.....)))))((.(---(((((((......))).))))))))).))))).(((.....))))))))).........------------- ( -23.70)
>DroSim_CAF1 139434 91 + 1
AUUUGUUCGGUCUCUGGCAAAUUGCCAGCCAU---AUAAGGCGGUGAAGUCGCUAUGGGAGCACCGAAAGAAAAAAUCUUCAAAUGGGAAAAUA-------------
.(((.(((((((((((((.....)))).((((---(...(((......)))..)))))))).)))))).)))......................------------- ( -25.60)
>DroEre_CAF1 137147 90 + 1
AUUUGUUCG-UCUCUGGCAAAUUGCCAGCCAU---AUAAGGCGCUGAAGUCGCUGGGGGAGCACAGAAAGAAAA-ACCUUCAAACGG-AAAAUACA-----------
...(((((.-((((((((.....)))))....---....(((((....).))))))).)))))...........-.((.......))-........----------- ( -19.70)
>DroYak_CAF1 145235 100 + 1
AUUUGUUCGCUCUCUGGCAAAUUGCCAGCCAUAAUAUAAGGCGGUGAAGUCGCAAUAGGAGCACAGAAAGAAAA-A-----AAUCAG-GAAAUAUAUAUAGAAUAGA
.(((((((((((((((((.....)))))............((((.....))))....))))).......((...-.-----..))..-............))))))) ( -22.60)
>DroAna_CAF1 135072 75 + 1
AUUUGUUCUGGCUC-GGCAAAUUGCCAGCAGU---CUGCU-UUGUGGAUUUCUAAAGGCGACACAGAGAAAAAA---------UAAG-GU-----------------
((((.((((((((.-(((.....)))))).((---(.(((-((.(((....))))))))))).)))))...)))---------)...-..----------------- ( -22.80)
>consensus
AUUUGUUCGGUCUCUGGCAAAUUGCCAGCCAU___AUAAGGCGGUGAAGUCGCUAUGGGAGCACAGAAAGAAAA_AUCUUCAAAUGG_AAAAUA_____________
.(((.(((((((((((((.....))).(((.........)))...............)))).)))))).)))................................... (-14.12 = -14.40 +   0.28)

alignment

secondary structure

dotplot

Window 9

Location	6,368,297 – 6,368,388
Length	91
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	71.64
Mean single sequence MFE	-19.75
Consensus MFE	-9.95
Energy contribution	-11.62
Covariance contribution	1.67
Combinations/Pair	1.07
Mean z-score	-1.73
Structure conservation index	0.50
SVM decision value	0.60
SVM RNA-class probability	0.794375
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6368297 91 - 23771897
-------------UAUUUUCCCAUUUGAAGAUUAUUUCUUUCGGUGCUCCCAUAGCGACUUCUCCGCCUUAU---AUAGCUGGCAAUUUGCCAGAGACCGAACAAAU
-------------.........(((((((((.....))))(((((.(((.....(((.......))).....---.....((((.....)))))))))))).))))) ( -20.80)
>DroSec_CAF1 132712 91 - 1
-------------UAUUUUCCCAUUUGUAGAUUUUUUCUUUCGGUGCUCCCAUAGCGACUUCACCGCCCUAU---AUGGCUGGCAAUUUGCCAAAGACCGAACAAAU
-------------.........(((((((((.....))).(((((.((.((((((((.......)))....)---)))).((((.....)))).))))))))))))) ( -20.70)
>DroSim_CAF1 139434 91 - 1
-------------UAUUUUCCCAUUUGAAGAUUUUUUCUUUCGGUGCUCCCAUAGCGACUUCACCGCCUUAU---AUGGCUGGCAAUUUGCCAGAGACCGAACAAAU
-------------.........(((((((((.....))))(((((.(((((((((((.......)))....)---)))).((((.....)))))))))))).))))) ( -24.20)
>DroEre_CAF1 137147 90 - 1
-----------UGUAUUUU-CCGUUUGAAGGU-UUUUCUUUCUGUGCUCCCCCAGCGACUUCAGCGCCUUAU---AUGGCUGGCAAUUUGCCAGAGA-CGAACAAAU
-----------........-..(((((((((.-....))))).((.(((.....((.......))(((....---..)))((((.....))))))))-))))).... ( -20.20)
>DroYak_CAF1 145235 100 - 1
UCUAUUCUAUAUAUAUUUC-CUGAUU-----U-UUUUCUUUCUGUGCUCCUAUUGCGACUUCACCGCCUUAUAUUAUGGCUGGCAAUUUGCCAGAGAGCGAACAAAU
...................-......-----.-(((.(((((((.((....((((((....)...(((.........)))..)))))..))))))))).)))..... ( -19.40)
>DroAna_CAF1 135072 75 - 1
-----------------AC-CUUA---------UUUUUUCUCUGUGUCGCCUUUAGAAAUCCACAA-AGCAG---ACUGCUGGCAAUUUGCC-GAGCCAGAACAAAU
-----------------..-....---------.......((((.(((..((((..........))-))..)---)).((((((.....)))-.)))))))...... ( -13.20)
>consensus
_____________UAUUUU_CCAUUUGAAGAU_UUUUCUUUCGGUGCUCCCAUAGCGACUUCACCGCCUUAU___AUGGCUGGCAAUUUGCCAGAGACCGAACAAAU
.......................................((((((.........(((.......)))............(((((.....)))))..))))))..... ( -9.95 = -11.62 +   1.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:28 2006