Locus 7126

Sequence ID	3L_DroMel_CAF1
Location	19,175,599 – 19,175,798
Length	199
Max. P	0.999737

overview

Window 4

Location	19,175,599 – 19,175,718
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.99
Mean single sequence MFE	-30.98
Consensus MFE	-29.50
Energy contribution	-29.70
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.26
Structure conservation index	0.95
SVM decision value	3.63
SVM RNA-class probability	0.999473
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19175599 119 + 23771897
AUUUCCACACGAUUGAUUUCGCAAAUUCUCGCCGCAACAGAGGCUGCAGGCAAAACAAGCCCCCGAACCUCAAAAACGCC-CCAAAAAGCGGCGAGAAUACAGGUUCUACACUUGUAAUG
.........(((......)))....((((((((((....((((.((..(((.......)))..))..))))......(..-.).....))))))))))(((((((.....)))))))... ( -33.00)
>DroSec_CAF1 4259 120 + 1
AUUUCCACACGAUUGAUUUCGCAAAUUCUCGCCGCAACAGAGGCUGCAGGCAAAACAAGCCCUCGAACCACAAAAACGCCCCCAAAAAGCGGCGAGAAUACAGGUUCUACACUUGUAAUG
.........(((......)))....((((((((((....((((((............)).))))(.....).................))))))))))(((((((.....)))))))... ( -31.00)
>DroSim_CAF1 7162 120 + 1
AUUUCCACACGAUUGAUUUCGCAAAUUCUCGCCGCAACAGAGGCUGCAGGCAAAACAAGCCCUCGAACCACAAAAACGCCCCCAAAAAGCGGCGAGAAUACAGGUUCUACACUUGUAAUG
.........(((......)))....((((((((((....((((((............)).))))(.....).................))))))))))(((((((.....)))))))... ( -31.00)
>DroEre_CAF1 6864 119 + 1
AUUUCCACACGAUUGAUUUCGCAAAUUCUCGCCGCAACAGAGUCUGCAGGCAAAACAAGCCCCCGAACCUCAAAAACGCC-CCAAAAAGCGGCGAGAAUACAGGUUCUACACUUGUAAUG
.........(((......)))....((((((((((..(((...)))..(((.......)))...................-.......))))))))))(((((((.....)))))))... ( -30.10)
>DroYak_CAF1 8847 119 + 1
AUUUCCACACGAUUGAUUUCGCAAAUUCUCGCCGCAACAGAGUCUGCAGGCGAAACAAGCCCCCGAACCUCAAAAACGCC-CCGAAAAGCGGCGAGAAUACUGGUUCUACACUUGUAAUG
....(((..(((......)))...(((((((((((....(((..((..(((.......)))..))...))).....((..-.))....)))))))))))..)))...(((....)))... ( -29.80)
>consensus
AUUUCCACACGAUUGAUUUCGCAAAUUCUCGCCGCAACAGAGGCUGCAGGCAAAACAAGCCCCCGAACCUCAAAAACGCC_CCAAAAAGCGGCGAGAAUACAGGUUCUACACUUGUAAUG
.........(((......)))....((((((((((..(((...)))..(((.......)))...........................))))))))))(((((((.....)))))))... (-29.50 = -29.70 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	19,175,599 – 19,175,718
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.99
Mean single sequence MFE	-39.28
Consensus MFE	-35.94
Energy contribution	-36.18
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.46
Structure conservation index	0.91
SVM decision value	0.97
SVM RNA-class probability	0.892681
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19175599 119 - 23771897
CAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGG-GGCGUUUUUGAGGUUCGGGGGCUUGUUUUGCCUGCAGCCUCUGUUGCGGCGAGAAUUUGCGAAAUCAAUCGUGUGGAAAU
..((((....))))..((...(((((((((((((....)-)))((....((((((.(.((((.......)))).)))))))....)))))))))))..((((......))))..)).... ( -41.20)
>DroSec_CAF1 4259 120 - 1
CAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGGGGGCGUUUUUGUGGUUCGAGGGCUUGUUUUGCCUGCAGCCUCUGUUGCGGCGAGAAUUUGCGAAAUCAAUCGUGUGGAAAU
..((((....))))..((...(((((((((((....(((((((....(((.....)))((((.......))))...)))))))..)))))))))))..((((......))))..)).... ( -40.20)
>DroSim_CAF1 7162 120 - 1
CAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGGGGGCGUUUUUGUGGUUCGAGGGCUUGUUUUGCCUGCAGCCUCUGUUGCGGCGAGAAUUUGCGAAAUCAAUCGUGUGGAAAU
..((((....))))..((...(((((((((((....(((((((....(((.....)))((((.......))))...)))))))..)))))))))))..((((......))))..)).... ( -40.20)
>DroEre_CAF1 6864 119 - 1
CAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGG-GGCGUUUUUGAGGUUCGGGGGCUUGUUUUGCCUGCAGACUCUGUUGCGGCGAGAAUUUGCGAAAUCAAUCGUGUGGAAAU
.....(((((.(.((((((.((....((((.(.....).-))))....))))))))..).)))))(((((((.((((......)))))))))))....((((......))))........ ( -36.90)
>DroYak_CAF1 8847 119 - 1
CAUUACAAGUGUAGAACCAGUAUUCUCGCCGCUUUUCGG-GGCGUUUUUGAGGUUCGGGGGCUUGUUUCGCCUGCAGACUCUGUUGCGGCGAGAAUUUGCGAAAUCAAUCGUGUGGAAAU
..((((....))))..(((..(((((((((((....(((-(((......(.....)(.((((.......)))).).).)))))..)))))))))))..((((......)))).))).... ( -37.90)
>consensus
CAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGG_GGCGUUUUUGAGGUUCGGGGGCUUGUUUUGCCUGCAGCCUCUGUUGCGGCGAGAAUUUGCGAAAUCAAUCGUGUGGAAAU
.....(((((.(.(((((........((((.((....)).)))).......)))))..).)))))(((((((.(((((....))))))))))))....((((......))))........ (-35.94 = -36.18 +   0.24)

alignment

secondary structure

dotplot

Window 6

Location	19,175,639 – 19,175,758
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.32
Mean single sequence MFE	-31.64
Consensus MFE	-28.16
Energy contribution	-28.60
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-3.15
Structure conservation index	0.89
SVM decision value	3.97
SVM RNA-class probability	0.999737
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19175639 119 + 23771897
AGGCUGCAGGCAAAACAAGCCCCCGAACCUCAAAAACGCC-CCAAAAAGCGGCGAGAAUACAGGUUCUACACUUGUAAUGCCUUUUGGCCUCUAGCCAUAAUUACCCAAAAAGCCGAACC
.((((..(((((..(((((.....((((((......((((-.(.....).)))).......))))))....)))))..)))))..((((.....)))).............))))..... ( -34.92)
>DroSec_CAF1 4299 120 + 1
AGGCUGCAGGCAAAACAAGCCCUCGAACCACAAAAACGCCCCCAAAAAGCGGCGAGAAUACAGGUUCUACACUUGUAAUGCCUUUUGGCCUCUAGCCACAAUUACCCAAAAAGCCGAACC
.((((..(((((..(((((.....(((((.......((((.(......).))))........)))))....)))))..)))))..((((.....)))).............))))..... ( -32.96)
>DroSim_CAF1 7202 120 + 1
AGGCUGCAGGCAAAACAAGCCCUCGAACCACAAAAACGCCCCCAAAAAGCGGCGAGAAUACAGGUUCUACACUUGUAAUGCCUUUUGGCCUCUAGCCACAAUUACCCAAAAAGCCGAACC
.((((..(((((..(((((.....(((((.......((((.(......).))))........)))))....)))))..)))))..((((.....)))).............))))..... ( -32.96)
>DroEre_CAF1 6904 119 + 1
AGUCUGCAGGCAAAACAAGCCCCCGAACCUCAAAAACGCC-CCAAAAAGCGGCGAGAAUACAGGUUCUACACUUGUAAUGCCUUUUGGCCUCUAGCCACAAUUACCCAAAAAGCCGAACC
..((.(((((((..(((((.....((((((......((((-.(.....).)))).......))))))....)))))..)))))..((((.....))))..............)).))... ( -31.42)
>DroYak_CAF1 8887 119 + 1
AGUCUGCAGGCGAAACAAGCCCCCGAACCUCAAAAACGCC-CCGAAAAGCGGCGAGAAUACUGGUUCUACACUUGUAAUGCCUUUUGCCCUCUAGCCACAAUUACCCAAAAAGCCGAACC
..((.(((((((..(((((.....(((((.......((((-.(.....).))))........)))))....)))))..)))))...((......))................)).))... ( -25.96)
>consensus
AGGCUGCAGGCAAAACAAGCCCCCGAACCUCAAAAACGCC_CCAAAAAGCGGCGAGAAUACAGGUUCUACACUUGUAAUGCCUUUUGGCCUCUAGCCACAAUUACCCAAAAAGCCGAACC
.((((..(((((..(((((.....(((((.......((((.(......).))))........)))))....)))))..)))))..((((.....)))).............))))..... (-28.16 = -28.60 +   0.44)

alignment

secondary structure

dotplot

Window 7

Location	19,175,639 – 19,175,758
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.32
Mean single sequence MFE	-44.90
Consensus MFE	-39.18
Energy contribution	-39.98
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.87
Structure conservation index	0.87
SVM decision value	3.41
SVM RNA-class probability	0.999171
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19175639 119 - 23771897
GGUUCGGCUUUUUGGGUAAUUAUGGCUAGAGGCCAAAAGGCAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGG-GGCGUUUUUGAGGUUCGGGGGCUUGUUUUGCCUGCAGCCU
((((((((((((.((.((....)).)))))))))...(((((..((((((.(.((((((.((....((((.(.....).-))))....))))))))..).))))))..)))))).)))). ( -47.20)
>DroSec_CAF1 4299 120 - 1
GGUUCGGCUUUUUGGGUAAUUGUGGCUAGAGGCCAAAAGGCAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGGGGGCGUUUUUGUGGUUCGAGGGCUUGUUUUGCCUGCAGCCU
((((((((((((.((.((....)).)))))))))...(((((..((((((.(.(((((........((((.((....)).)))).......)))))..).))))))..)))))).)))). ( -46.46)
>DroSim_CAF1 7202 120 - 1
GGUUCGGCUUUUUGGGUAAUUGUGGCUAGAGGCCAAAAGGCAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGGGGGCGUUUUUGUGGUUCGAGGGCUUGUUUUGCCUGCAGCCU
((((((((((((.((.((....)).)))))))))...(((((..((((((.(.(((((........((((.((....)).)))).......)))))..).))))))..)))))).)))). ( -46.46)
>DroEre_CAF1 6904 119 - 1
GGUUCGGCUUUUUGGGUAAUUGUGGCUAGAGGCCAAAAGGCAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGG-GGCGUUUUUGAGGUUCGGGGGCUUGUUUUGCCUGCAGACU
((((.(((((((.((.((....)).)))))))))...(((((..((((((.(.((((((.((....((((.(.....).-))))....))))))))..).))))))..)))))...)))) ( -44.30)
>DroYak_CAF1 8887 119 - 1
GGUUCGGCUUUUUGGGUAAUUGUGGCUAGAGGGCAAAAGGCAUUACAAGUGUAGAACCAGUAUUCUCGCCGCUUUUCGG-GGCGUUUUUGAGGUUCGGGGGCUUGUUUCGCCUGCAGACU
(((..((((((((((.((....)).)))))))))...((((...((((((.(.(((((........((((.(.....).-)))).......)))))..).))))))...)))).)..))) ( -40.06)
>consensus
GGUUCGGCUUUUUGGGUAAUUGUGGCUAGAGGCCAAAAGGCAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGG_GGCGUUUUUGAGGUUCGGGGGCUUGUUUUGCCUGCAGCCU
((((((((((((.((.((....)).)))))))))...(((((..((((((.(.(((((........((((.((....)).)))).......)))))..).))))))..)))))).)))). (-39.18 = -39.98 +   0.80)

alignment

secondary structure

dotplot

Window 8

Location	19,175,679 – 19,175,798
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.83
Mean single sequence MFE	-36.20
Consensus MFE	-32.88
Energy contribution	-33.28
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.86
Structure conservation index	0.91
SVM decision value	1.83
SVM RNA-class probability	0.979161
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19175679 119 - 23771897
CAAGGGGUGGUUGUGGAAUUUGGGGACUGAAAUUGGAAUUGGUUCGGCUUUUUGGGUAAUUAUGGCUAGAGGCCAAAAGGCAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGG-
(((((((((((...(((((.((((..(((...((((((....))).(((((((((.(.............).)))))))))....)))...)))..)))).))))).))))))))))).- ( -36.72)
>DroSec_CAF1 4339 120 - 1
CAAGGGGUGGUUGUGGAAUUUGGGGACUGAAAUUGGAAUUGGUUCGGCUUUUUGGGUAAUUGUGGCUAGAGGCCAAAAGGCAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGGG
(((((((((((...(((((.((((..(((...((((((....))).(((((((((.(.............).)))))))))....)))...)))..)))).))))).))))))))))).. ( -36.72)
>DroSim_CAF1 7242 120 - 1
CAAGGGGUGGUUGUGGAAUUUGGGGACUGAAAUUGGAAUUGGUUCGGCUUUUUGGGUAAUUGUGGCUAGAGGCCAAAAGGCAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGGG
(((((((((((...(((((.((((..(((...((((((....))).(((((((((.(.............).)))))))))....)))...)))..)))).))))).))))))))))).. ( -36.72)
>DroEre_CAF1 6944 119 - 1
CAAGGGGUGGUUGUGGAAUUUGGGGACUGAAAUUGGAAUUGGUUCGGCUUUUUGGGUAAUUGUGGCUAGAGGCCAAAAGGCAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGG-
(((((((((((...(((((.((((..(((...((((((....))).(((((((((.(.............).)))))))))....)))...)))..)))).))))).))))))))))).- ( -36.72)
>DroYak_CAF1 8927 119 - 1
CAAGGGGUGGUUGUGAAAUUUGGGGACUGAAAUUGGAAUUGGUUCGGCUUUUUGGGUAAUUGUGGCUAGAGGGCAAAAGGCAUUACAAGUGUAGAACCAGUAUUCUCGCCGCUUUUCGG-
(.(((((((((.(.(((....(....)..........((((((((.(((((((((.((....)).))))))))).....((((.....)))).)))))))).))).)))))))))).).- ( -34.10)
>consensus
CAAGGGGUGGUUGUGGAAUUUGGGGACUGAAAUUGGAAUUGGUUCGGCUUUUUGGGUAAUUGUGGCUAGAGGCCAAAAGGCAUUACAAGUGUAGAACCUGUAUUCUCGCCGCUUUUUGG_
(((((((((((..........(....).......(((((.(((((.(((((((((.(.............).)))))))))..(((....))))))))...))))).))))))))))).. (-32.88 = -33.28 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:38 2006