Locus 5626

Sequence ID	2L_DroMel_CAF1
Location	15,962,218 – 15,962,339
Length	121
Max. P	0.993026

overview

Window 8

Location	15,962,218 – 15,962,314
Length	96
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	89.51
Mean single sequence MFE	-27.92
Consensus MFE	-24.41
Energy contribution	-24.97
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-1.50
Structure conservation index	0.87
SVM decision value	0.25
SVM RNA-class probability	0.651594
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15962218 96 - 22407834
GCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCCGAACUCCAUUCCGAGAUCGGAAUAGCCCAGGUCUUCGUUGU
..(((((((.......)))..........(((.((((....))))..)))...((((.(((......))).))))....))))............. ( -29.20)
>DroSec_CAF1 137788 96 - 1
GCGGGAGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCCGAACUCCAUUUCGAGAUCGGAAUAGCCCAGGUCUUCGUCGU
.((((.(((.......)))..........(((.((((....))))..)))..))))..........(((((((((......)).)))).))).... ( -26.00)
>DroSim_CAF1 139935 96 - 1
GCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCCGAACUCCAUUUCGAGAUCGGAAUAGCCCAGGUCUUCGUCGU
..(((((((.......)))..........(((.((((....))))..)))...((((.(((......))).))))....))))............. ( -29.20)
>DroEre_CAF1 124877 96 - 1
GCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCCGAACUCCAUUUCGAGAUCGGAAUAGCCCAGGUCGUCGUCAU
..(((((((.......)))..........(((.((((....))))..)))...((((.(((......))).))))....))))............. ( -29.20)
>DroYak_CAF1 119913 95 - 1
GCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACC-CGAACUCCAUUUCGAGAUCGGAAUAGCCCAGGUCGUCGUCAU
..(((((((.......)))..........(((.((((....))))..)))..(-(((.(((......))).))))....))))............. ( -29.20)
>DroAna_CAF1 73623 82 - 1
ACGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCUAAACUCCAUUUGGUGCUCAGGUUGGCC--------------
..(((((((.......))).........((((.((((....))))((((((........)))))))))))))).((....))-------------- ( -24.70)
>consensus
GCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCCGAACUCCAUUUCGAGAUCGGAAUAGCCCAGGUCUUCGUCGU
..(((((((.......)))..........(((.((((....))))..)))...((((.(((......))).))))....))))............. (-24.41 = -24.97 +   0.56)

alignment

secondary structure

dotplot

Window 9

Location	15,962,243 – 15,962,339
Length	96
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	74.92
Mean single sequence MFE	-25.80
Consensus MFE	-16.21
Energy contribution	-16.13
Covariance contribution	-0.08
Combinations/Pair	1.19
Mean z-score	-1.79
Structure conservation index	0.63
SVM decision value	1.27
SVM RNA-class probability	0.938626
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15962243 96 + 22407834
U--------CUCG-GAAUGGAGUUCGGGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCGCCCGCUU-UCGGCUUCCGAUUUUU-UAUUUAA--------
.--------.(((-((((.(((..(((((.((((.((((....))))))))).........(((.......))).))))..)-)).).)))))).....-.......-------- ( -31.20)
>DroVir_CAF1 95256 85 + 1
C--------CUCGAAAAUGG-------AGUCCAUUGCGGAUAUCCGCACGGCUAUUUUAAUGCAAUUUUUAUGCGCUCGUU--UUGGCUUCCUAUUUUCU-----UA--------
.--------...((((((((-------((.(((..((((....))))(((((.........(((.......))))).))).--.))).)))).)))))).-----..-------- ( -22.10)
>DroPse_CAF1 136042 104 + 1
UGGCACCCACUCU-CUAUGGGGCUCAGGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCGCCCGUUU-UUGGCUUCCGAUUUUU-UAUUUCA--------
.(((.((((....-...)))))))..((((((((.((((....))))))))..........(((.......)))))))....-((((...)))).....-.......-------- ( -26.70)
>DroGri_CAF1 111777 86 + 1
------------GGAAAUGG-------AGUCCAUUGCGGAUAUCCGCACAGCAUUUUUAAUGCAAUUUUUAUGCGCUCGUU--UUGGCUUCCUAUUUUCGUAUUUUA--------
------------((((((((-------((.(((.(((((....)))))..((((.....))))..................--.))).)))).))))))........-------- ( -23.10)
>DroAna_CAF1 73634 105 + 1
G--------CACC-AAAUGGAGUUUAGGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCGCCCGUUUUUUGGCUUCCGAUCUUU-UAUUUCGUUCUCUCA
.--------....-.((((((((..((((((....((((....))))..((..........(((.......)))(((........)))..)))))))).-.))))))))...... ( -25.00)
>DroPer_CAF1 163546 104 + 1
UGGCACCCACUCU-CUAUGGGGCUCAGGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCGCCCGUUU-UUGGCUUCCGAUUUUU-UAUUUCA--------
.(((.((((....-...)))))))..((((((((.((((....))))))))..........(((.......)))))))....-((((...)))).....-.......-------- ( -26.70)
>consensus
U________CUCG_AAAUGG_G_UCAGGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCGCCCGUUU_UUGGCUUCCGAUUUUU_UAUUUCA________
..................(((.....((((.((((((((....)))))..(((.......))).......))).))))(((....))).)))....................... (-16.21 = -16.13 +  -0.08)

alignment

secondary structure

dotplot

Window 0

Location	15,962,243 – 15,962,339
Length	96
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	74.92
Mean single sequence MFE	-25.12
Consensus MFE	-15.94
Energy contribution	-16.13
Covariance contribution	0.19
Combinations/Pair	1.06
Mean z-score	-2.56
Structure conservation index	0.63
SVM decision value	2.37
SVM RNA-class probability	0.993026
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15962243 96 - 22407834
--------UUAAAUA-AAAAAUCGGAAGCCGA-AAGCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCCGAACUCCAUUC-CGAG--------A
--------.......-.....((((((...((-...((((.(((.......)))..........(((.((((....))))..)))..))))...))..)))-))).--------. ( -27.90)
>DroVir_CAF1 95256 85 - 1
--------UA-----AGAAAAUAGGAAGCCAA--AACGAGCGCAUAAAAAUUGCAUUAAAAUAGCCGUGCGGAUAUCCGCAAUGGACU-------CCAUUUUCGAG--------G
--------..-----.((((((.(((..(((.--.(((.(((((.......)))((....)).)))))((((....))))..)))..)-------))))))))...--------. ( -24.50)
>DroPse_CAF1 136042 104 - 1
--------UGAAAUA-AAAAAUCGGAAGCCAA-AAACGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCUGAGCCCCAUAG-AGAGUGGGUGCCA
--------.......-.....((((...(((.-.....((((((.......))).........)))..((((....))))..)))...))))(((((((..-...))))).)).. ( -27.80)
>DroGri_CAF1 111777 86 - 1
--------UAAAAUACGAAAAUAGGAAGCCAA--AACGAGCGCAUAAAAAUUGCAUUAAAAAUGCUGUGCGGAUAUCCGCAAUGGACU-------CCAUUUCC------------
--------...............(((..(((.--.......(((.......))).............(((((....))))).)))..)-------))......------------ ( -19.30)
>DroAna_CAF1 73634 105 - 1
UGAGAGAACGAAAUA-AAAGAUCGGAAGCCAAAAAACGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCUAAACUCCAUUU-GGUG--------C
........(((....-.....)))...(((........)))(((.......))).........((((.((((....))))((((((........)))))))-))).--------. ( -23.40)
>DroPer_CAF1 163546 104 - 1
--------UGAAAUA-AAAAAUCGGAAGCCAA-AAACGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCUGAGCCCCAUAG-AGAGUGGGUGCCA
--------.......-.....((((...(((.-.....((((((.......))).........)))..((((....))))..)))...))))(((((((..-...))))).)).. ( -27.80)
>consensus
________UGAAAUA_AAAAAUCGGAAGCCAA_AAACGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCUGA_C_CCAUUU_CGAG________A
.......................((..(((........)))(((.......)))..........))..((((....)))).((((..........))))................ (-15.94 = -16.13 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:54 2006