Locus 3026

Sequence ID	3L_DroMel_CAF1
Location	8,691,334 – 8,691,461
Length	127
Max. P	0.867457

overview

Window 9

Location	8,691,334 – 8,691,430
Length	96
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	83.75
Mean single sequence MFE	-26.62
Consensus MFE	-17.49
Energy contribution	-17.85
Covariance contribution	0.36
Combinations/Pair	1.15
Mean z-score	-2.09
Structure conservation index	0.66
SVM decision value	-0.03
SVM RNA-class probability	0.515759
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8691334 96 - 23771897
CCCUAAAAUCCGAUUCUGAUUCGGUGUCAUGUGCAUUGAAGCACGUGCUACACCCGAAAAAAAGGGCAGAGGGCGC-------AAAAAG--------CGUACGAGAAAUGC
........((((.(((((.....(((.(((((((......))))))).))).(((........)))))))).((((-------.....)--------))).)).))..... ( -27.80)
>DroSec_CAF1 79161 95 - 1
CCCAAAAAUCCGACUCUGAUUCGGUGUCAUGUGCAUUGAAGCACGUGCUACACCCGAAA-AAAGGGCAGAAGGCGA-------AAAAAU--------CGUACGAGGAAUGC
........((((.((((..(((((((((((((((......)))))))..))).))))).-..))))).....((((-------.....)--------)))....))).... ( -28.00)
>DroSim_CAF1 79666 96 - 1
CCCAAAAAUCCGACUCUGAUUCGGUGUCAUGUGCAUUGAAGCACGUGCUACACCCGAAAAAAAGGGCAGAAGGCGC-------AAAAAG--------CGUACGAGAAAUGC
........((((.((((..(((((((((((((((......)))))))..))).)))))....))))......((((-------.....)--------))).)).))..... ( -27.10)
>DroEre_CAF1 83544 94 - 1
CGCAAAAAUCUGAUUCUGAUUCGGUGGCAUGUGCAUUGAAGCACGUGCUACACCCGAAA-AAAGAGCAGGAGGCGC-------AAAAAG--------UGUACGA-AAAUGC
.(((....((((.((((..(((((((((((((((......))))))))))...))))).-..))))))))..((((-------.....)--------)))....-...))) ( -32.70)
>DroYak_CAF1 81918 96 - 1
CCCUAAAAUCAGAUUCUGAUUCGGUGUCAUGUGCAUUGGAGCACGUGCUACACCCGAAAAAAAGAGCAGGCGGCGC-------AAAAAG--------UGUUCGAGAAAUGC
......((((((...)))))).((((((((((((......)))))))..)))))...........(((..((((((-------.....)--------)).))).....))) ( -25.00)
>DroAna_CAF1 76002 106 - 1
--CAAAAAUCCGAACCAGAUUUGGUGUCAUGUGCAUUGAAGCACGUGCUACACCCGAAAAGAA---CACAAGACCCCAACAAAAAAAAGUGUAAGAUUGUACGAAAAAUGC
--........((.((..(((((((((((((((((......)))))))..)))))........(---(((...................)))).))))))).))........ ( -19.11)
>consensus
CCCAAAAAUCCGAUUCUGAUUCGGUGUCAUGUGCAUUGAAGCACGUGCUACACCCGAAAAAAAGGGCAGAAGGCGC_______AAAAAG________CGUACGAGAAAUGC
...........(.((((..(((((((((((((((......)))))))..))).)))))....)))))............................................ (-17.49 = -17.85 +   0.36)

alignment

secondary structure

dotplot

Window 0

Location	8,691,359 – 8,691,461
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.68
Mean single sequence MFE	-25.15
Consensus MFE	-15.97
Energy contribution	-16.80
Covariance contribution	0.83
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.63
SVM decision value	0.86
SVM RNA-class probability	0.867457
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8691359 102 - 23771897
------ACUCCU--UCACUUCCUGUCCAGACCCCU-UGAUC--------CCUAAAAUCCGAUUCUGAUUCGGUGUCAUGUGCAUUGAAGCACGUGCUACACCCGAAAAAAAGGGCAGA-G
------......--.......((((((......(.-.((((--------..........))))..).(((((((((((((((......)))))))..))).))))).....)))))).-. ( -27.60)
>DroPse_CAF1 85220 112 - 1
------UCUCUUUAGCACUUCCUGUCAUCCCCCCGCCCAUCUUCCACAUUCAAAAAUCAG-UUGCGAUUCGGUGUCAUGUGCAUUGAAGCACGUGCUACACCCAAAAAAAAGA-CACGCA
------................((((.......(((........................-..)))....((((((((((((......)))))))..))))).........))-)).... ( -20.87)
>DroSim_CAF1 79691 102 - 1
------ACUCCU--UUACUUCCUGUCCAGACCCCU-UGAUC--------CCAAAAAUCCGACUCUGAUUCGGUGUCAUGUGCAUUGAAGCACGUGCUACACCCGAAAAAAAGGGCAGA-A
------......--.......((((((.......(-((...--------.)))..............(((((((((((((((......)))))))..))).))))).....)))))).-. ( -27.20)
>DroEre_CAF1 83568 100 - 1
------ACUCCU--UCACUUCCUGUCUAGACCCC--CGAUC--------GCAAAAAUCUGAUUCUGAUUCGGUGGCAUGUGCAUUGAAGCACGUGCUACACCCGAAA-AAAGAGCAGG-A
------......--.....((((((((.......--.((((--------(........)))))....(((((((((((((((......))))))))))...))))).-..))).))))-) ( -30.20)
>DroYak_CAF1 81943 102 - 1
------ACUUCU--UCACUUCCUGUCUAGACCCCU-CGAUC--------CCUAAAAUCAGAUUCUGAUUCGGUGUCAUGUGCAUUGGAGCACGUGCUACACCCGAAAAAAAGAGCAGG-C
------......--......((((.((.......(-((...--------.....((((((...)))))).((((((((((((......)))))))..)))))))).......))))))-. ( -27.24)
>DroAna_CAF1 76042 97 - 1
AUAAGCCCUCCA--UCACUUCCUGUCCAGACCC-----------------CAAAAAUCCGAACCAGAUUUGGUGUCAUGUGCAUUGAAGCACGUGCUACACCCGAAAAGAA---CACA-A
............--((..(((............-----------------...(((((.......)))))((((((((((((......)))))))..))))).)))..)).---....-. ( -17.80)
>consensus
______ACUCCU__UCACUUCCUGUCCAGACCCCU_CGAUC________CCAAAAAUCCGAUUCUGAUUCGGUGUCAUGUGCAUUGAAGCACGUGCUACACCCGAAAAAAAGAGCAGA_A
.....................((((.............................((((.......)))).((((((((((((......)))))))..)))))...........))))... (-15.97 = -16.80 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:51 2006