Locus 3209

Sequence ID	2R_DroMel_CAF1
Location	10,961,491 – 10,961,586
Length	95
Max. P	0.969368

overview

Window 7

Location	10,961,491 – 10,961,586
Length	95
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	80.95
Mean single sequence MFE	-38.57
Consensus MFE	-26.99
Energy contribution	-27.24
Covariance contribution	0.25
Combinations/Pair	1.08
Mean z-score	-3.93
Structure conservation index	0.70
SVM decision value	1.64
SVM RNA-class probability	0.969368
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10961491 95 + 20766785
------GAGGAGCAUGAGGAAACCUGGUCCUGUGGAGAA-------AAGCCACAGCGGGCGGCACUUUGUCAGCGCAAUAAAAGUUUGCGUGUGAAUUGUGC---UGCCCA
------.((((.((.(.(....)))).))))((((....-------...))))...(((((((((....(((((((((.......)))))).)))...))))---))))). ( -43.20)
>DroSec_CAF1 73847 94 + 1
------GGGGAGCAGGAUGA-AUCUGGUCCUGUGGAGAA-------AAGCCAAAGCGGGCGGCACUUUGUCAGCGCAAUAAAAGUUUGCGUGUGAAUUGUGC---UGCCCA
------.((((.((((....-.)))).)))).(((....-------...)))....(((((((((....(((((((((.......)))))).)))...))))---))))). ( -40.00)
>DroSim_CAF1 76127 100 + 1
AGGGAUGAGGAGCAGGAUGA-AUCUGGUCCUGUGGAGAA-------AAGCCACAGCGGGCGGCACUUUGUCAGCGCAAUAAAAGUUUGCGUGUGAAUUGUGC---UGCCCA
.......((((.((((....-.)))).))))((((....-------...))))...(((((((((....(((((((((.......)))))).)))...))))---))))). ( -43.40)
>DroEre_CAF1 76172 86 + 1
---------------GAGGAAUGCUCGUCCUGUGGAGAG-------AAGCCACAGCGGGCGGCACUUUGUCAGCGCAAUAAAAGUUUGCGUGUGAAUUGUGC---UGCCCA
---------------(((.....)))...((((((....-------...)))))).(((((((((....(((((((((.......)))))).)))...))))---))))). ( -39.30)
>DroYak_CAF1 77297 89 + 1
---------------GAGGAAUCCUCGUCCUGUGGAGAG-------AAGCCACAGCGGGCGGCACUUUGUCAGCGCAAUAAAAGUUUGCGUGUGAAUUGUGCUGCUGCCCA
---------------((((...))))...((((((....-------...)))))).(((((((((....(((((((((.......)))))).))).....).)))))))). ( -37.10)
>DroAna_CAF1 74133 85 + 1
---------------GAGGA--------CAGGGGAAGAGAACGAGUAAGCCUCAGCGGGCGGCACUUUGUCAGUGCAAUAAAAGUUUGCGUGUGAAUUGUGC---UGCCCA
---------------((((.--------....(........).......))))...(((((((((....(((..((((.......))))...)))...))))---))))). ( -28.40)
>consensus
_______________GAGGA_ACCUGGUCCUGUGGAGAA_______AAGCCACAGCGGGCGGCACUUUGUCAGCGCAAUAAAAGUUUGCGUGUGAAUUGUGC___UGCCCA
.............................((((((..............)))))).(((((((((....(((((((((.......)))))).)))...))))...))))). (-26.99 = -27.24 +   0.25)

alignment

secondary structure

dotplot

Window 8

Location	10,961,491 – 10,961,586
Length	95
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	80.95
Mean single sequence MFE	-27.12
Consensus MFE	-20.01
Energy contribution	-20.71
Covariance contribution	0.69
Combinations/Pair	1.05
Mean z-score	-2.38
Structure conservation index	0.74
SVM decision value	1.11
SVM RNA-class probability	0.916692
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10961491 95 - 20766785
UGGGCA---GCACAAUUCACACGCAAACUUUUAUUGCGCUGACAAAGUGCCGCCCGCUGUGGCUU-------UUCUCCACAGGACCAGGUUUCCUCAUGCUCCUC------
.((((.---((((...(((..(((((.......))))).)))....)))).)))).((((((...-------....))))))....(((............))).------ ( -28.30)
>DroSec_CAF1 73847 94 - 1
UGGGCA---GCACAAUUCACACGCAAACUUUUAUUGCGCUGACAAAGUGCCGCCCGCUUUGGCUU-------UUCUCCACAGGACCAGAU-UCAUCCUGCUCCCC------
.((((.---((((...(((..(((((.......))))).)))....)))).))))((....))..-------.........(((.(((..-.....))).)))..------ ( -26.80)
>DroSim_CAF1 76127 100 - 1
UGGGCA---GCACAAUUCACACGCAAACUUUUAUUGCGCUGACAAAGUGCCGCCCGCUGUGGCUU-------UUCUCCACAGGACCAGAU-UCAUCCUGCUCCUCAUCCCU
.((((.---((((...(((..(((((.......))))).)))....)))).))))..(((((...-------....)))))(((.(((..-.....))).)))........ ( -30.80)
>DroEre_CAF1 76172 86 - 1
UGGGCA---GCACAAUUCACACGCAAACUUUUAUUGCGCUGACAAAGUGCCGCCCGCUGUGGCUU-------CUCUCCACAGGACGAGCAUUCCUC---------------
.((((.---((((...(((..(((((.......))))).)))....)))).)))).((((((...-------....))))))..............--------------- ( -28.20)
>DroYak_CAF1 77297 89 - 1
UGGGCAGCAGCACAAUUCACACGCAAACUUUUAUUGCGCUGACAAAGUGCCGCCCGCUGUGGCUU-------CUCUCCACAGGACGAGGAUUCCUC---------------
.((((....((((...(((..(((((.......))))).)))....)))).)))).((((((...-------....))))))...((((...))))--------------- ( -27.70)
>DroAna_CAF1 74133 85 - 1
UGGGCA---GCACAAUUCACACGCAAACUUUUAUUGCACUGACAAAGUGCCGCCCGCUGAGGCUUACUCGUUCUCUUCCCCUG--------UCCUC---------------
.((((.---((((...(((...((((.......))))..)))....)))).))))...(((.....)))..............--------.....--------------- ( -20.90)
>consensus
UGGGCA___GCACAAUUCACACGCAAACUUUUAUUGCGCUGACAAAGUGCCGCCCGCUGUGGCUU_______CUCUCCACAGGACCAGAU_UCCUC_______________
.((((....((((...(((..(((((.......))))).)))....)))).)))).((((((..............))))))............................. (-20.01 = -20.71 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:06 2006