Locus 6581

Sequence ID	2R_DroMel_CAF1
Location	20,584,629 – 20,584,737
Length	108
Max. P	0.750932

overview

Window 6

Location	20,584,629 – 20,584,737
Length	108
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	77.89
Mean single sequence MFE	-36.55
Consensus MFE	-27.87
Energy contribution	-27.87
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.14
Structure conservation index	0.76
SVM decision value	0.48
SVM RNA-class probability	0.750932
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20584629 108 + 20766785
AUAAUAAUGCGGUUCUAUGG-GGACGUAGCUCAGUGGUAGAGCGCUCGCUUCGCAUGUGAGAAGUCCCGGGUUCAAACCCCGGCGUCUCCAUGU-----UCAGG--AGAUAUUGUU---
..((((((((.(.......(-((((....((((...(..((((....))))..)...))))..)))))((((....))))).))((((((....-----...))--))))))))))--- ( -37.70)
>DroVir_CAF1 54753 114 + 1
----CAACCCGUUUUCAUGG-GGACGUAGCUCAGUGGUAGAGCGCUCGCUUCGCAUGUGAGAAGUCCCGGGUUCAAACCCCGGCGUCUCCAUAUUAAAAUCUAGCUAUUGGAUAUUUUU
----............((((-(((((...((((...(..((((....))))..)...)))).....(((((.......))))))))))))))......((((((...))))))...... ( -34.40)
>DroSec_CAF1 36519 102 + 1
AUAAUAGCGGGGUUCCAUGG-GGACGUAGCUCAGUGGUAGAGCGCUCGCUUCGCAUGUGAGAAGUCCCGGGUUCAAACCCCGGCGUCUCCAUUA-----UCGGG--AGGU---------
.......(((((((((...(-((((....((((...(..((((....))))..)...))))..))))).))....)))))))...(((((....-----...))--))).--------- ( -39.70)
>DroYak_CAF1 37980 110 + 1
AUAUUUAUGUGCUUCUAUGG-GGACGUAGCUCAGUGGUAGAGCGCUCGCUUCGCAUGUGAGAAGUCCCGGGUUCAAACCCCGGCGUCUCCAAGA-----UAAGG--AGAAGUUAUUU-U
..........((((((.(((-(((((...((((...(..((((....))))..)...)))).....(((((.......)))))))))))))...-----.....--)))))).....-. ( -35.40)
>DroMoj_CAF1 57681 107 + 1
----CAACUCGUUCUCAUGG-GGACGUAGCUCAGUGGUAGAGCGCUCGCUUCGCAUGUGAGAAGUCCCGGGUUCAAACCCCGGCGUCUCCA-------GUACAACAAUUGGAUAAUUUU
----......(((....(((-(((((...((((...(..((((....))))..)...)))).....(((((.......)))))))))))))-------....))).............. ( -33.80)
>DroAna_CAF1 37711 109 + 1
AAAUGCCCAUUAUCCUAUGGGGGACGUAGCUCAGUGGUAGAGCGCUCGCUUCGCAUGUGAGAAGUCCCGGGUUCAAACCCCGGCGUCUCCAGUC-----U--GG--ACUGGUUAGUU-U
..(((((.............(((((....((((...(..((((....))))..)...))))..)))))((((....)))).)))))..(((((.-----.--..--)))))......-. ( -38.30)
>consensus
AUA_UAACGCGGUUCCAUGG_GGACGUAGCUCAGUGGUAGAGCGCUCGCUUCGCAUGUGAGAAGUCCCGGGUUCAAACCCCGGCGUCUCCAUGA_____UCAGG__AGUGGUUAUUU_U
.................(((.(((((...((((...(..((((....))))..)...)))).....(((((.......)))))))))))))............................ (-27.87 = -27.87 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	20,584,629 – 20,584,737
Length	108
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	77.89
Mean single sequence MFE	-31.82
Consensus MFE	-22.60
Energy contribution	-22.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.01
Structure conservation index	0.71
SVM decision value	0.04
SVM RNA-class probability	0.554067
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20584629 108 - 20766785
---AACAAUAUCU--CCUGA-----ACAUGGAGACGCCGGGGUUUGAACCCGGGACUUCUCACAUGCGAAGCGAGCGCUCUACCACUGAGCUACGUCC-CCAUAGAACCGCAUUAUUAU
---.......(((--((...-----....))))).((.(((((....))))(((((.........((.......))((((.......))))...))))-).......).))........ ( -30.10)
>DroVir_CAF1 54753 114 - 1
AAAAAUAUCCAAUAGCUAGAUUUUAAUAUGGAGACGCCGGGGUUUGAACCCGGGACUUCUCACAUGCGAAGCGAGCGCUCUACCACUGAGCUACGUCC-CCAUGAAAACGGGUUG----
............(((((...((((..(((((.(((((((((.......)))))(.((((.(....).)))))....((((.......))))..)))).-)))))))))..)))))---- ( -31.10)
>DroSec_CAF1 36519 102 - 1
---------ACCU--CCCGA-----UAAUGGAGACGCCGGGGUUUGAACCCGGGACUUCUCACAUGCGAAGCGAGCGCUCUACCACUGAGCUACGUCC-CCAUGGAACCCCGCUAUUAU
---------..((--((...-----....))))..((.(((((((.(....(((((.........((.......))((((.......))))...))))-)..).)))))))))...... ( -33.60)
>DroYak_CAF1 37980 110 - 1
A-AAAUAACUUCU--CCUUA-----UCUUGGAGACGCCGGGGUUUGAACCCGGGACUUCUCACAUGCGAAGCGAGCGCUCUACCACUGAGCUACGUCC-CCAUAGAAGCACAUAAAUAU
.-........(((--((...-----....))))).((..((((....))))(((((.........((.......))((((.......))))...))))-).......)).......... ( -29.60)
>DroMoj_CAF1 57681 107 - 1
AAAAUUAUCCAAUUGUUGUAC-------UGGAGACGCCGGGGUUUGAACCCGGGACUUCUCACAUGCGAAGCGAGCGCUCUACCACUGAGCUACGUCC-CCAUGAGAACGAGUUG----
.........((((((((.(..-------(((.(((((((((.......)))))(.((((.(....).)))))....((((.......))))..)))).-)))..).))).)))))---- ( -31.40)
>DroAna_CAF1 37711 109 - 1
A-AACUAACCAGU--CC--A-----GACUGGAGACGCCGGGGUUUGAACCCGGGACUUCUCACAUGCGAAGCGAGCGCUCUACCACUGAGCUACGUCCCCCAUAGGAUAAUGGGCAUUU
.-......(((((--..--.-----.))))).(((((((((.......)))))(.((((.(....).)))))....((((.......))))..)))).(((((......)))))..... ( -35.10)
>consensus
A_AAAUAACCACU__CCUGA_____AAAUGGAGACGCCGGGGUUUGAACCCGGGACUUCUCACAUGCGAAGCGAGCGCUCUACCACUGAGCUACGUCC_CCAUAGAAACGCGUUA_UAU
................................(((((((((.......)))))(.((((.(....).)))))....((((.......))))..))))...................... (-22.60 = -22.60 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:20 2006