Locus 1524

Sequence ID	2R_DroMel_CAF1
Location	5,776,623 – 5,776,848
Length	225
Max. P	0.998224

overview

Window 3

Location	5,776,623 – 5,776,741
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.30
Mean single sequence MFE	-29.50
Consensus MFE	-9.66
Energy contribution	-11.74
Covariance contribution	2.08
Combinations/Pair	1.05
Mean z-score	-2.73
Structure conservation index	0.33
SVM decision value	3.04
SVM RNA-class probability	0.998224
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5776623 118 + 20766785
AGUUCUUUAGUCCCAUCUCUUUUAUCCAGAAAUAUGCUCGGUAAAAGAGAAGCCACCGGCGGAUUCUCAGUGAAACUCUCCAAUAAUUAUAGGAGAGUGUAUGUUCUGGCUCUCU--AAC
........(((((..(((((((((((.((.......)).))))))))))).(((...)))))))).((((....(((((((..........))))))).......))))......--... ( -32.10)
>DroSec_CAF1 66909 114 + 1
AGUUCUUUAGUGCCAUCUCUUUUAUCCAGAAAUAUGCUCGGUAAAAGAGAAGCCACCGGUGGUUUCUAGGUAAAACUCUCCAAAAAUUAUAGGAGAGUGUAGG----GGCUCUCU--AAC
(((((((...((((...(((((((((.((.......)).)))))))))(((((((....)))))))..))))..(((((((..........)))))))..)))----))))....--... ( -36.00)
>DroSim_CAF1 68046 114 + 1
AGUUCUUUAGUCCCAUCUCUUUUAUCCAGAAAUAUGCUCGGUAAAAGAGAAGCCACCGGUGGUUUCUCUGUAAAACUCUCCAAAAAUUAUAGGAGAGUGUAGG----GGCUCUCU--AAC
........((((((......((((((.((.......)).))))))((((((((((....)))))))))).....(((((((..........)))))))...))----))))....--... ( -37.10)
>DroEre_CAF1 70027 94 + 1
AGUUGUUUAAUCGCAUCUCUUUUAUCCACAAAAGUGUUCGUUAAAAGAGAAUCCACCGGCUAUUGCUCGGUGAAACACUCCAA--------------------------CUCUCCAAAAC
(((((..........(((((((((..(((....))).....)))))))))...(((((((....)).)))))........)))--------------------------))......... ( -24.00)
>DroYak_CAF1 67519 94 + 1
AGUUGCUUAGUCCCAUCUGUUUUAUGCACUAAUAGGCUCGUUAAAAGAGAAGAAACCGUCGGUUUCUCGGCGAAACUCUCCAA--------------------------CUCUCCAAAAC
(((((.....((((.(((.(((((.((........))....))))).)))(((((((...))))))).)).)).......)))--------------------------))......... ( -18.30)
>consensus
AGUUCUUUAGUCCCAUCUCUUUUAUCCAGAAAUAUGCUCGGUAAAAGAGAAGCCACCGGCGGUUUCUCGGUGAAACUCUCCAA_AAUUAUAGGAGAGUGUA_G____GGCUCUCU__AAC
...............(((((((((((.((.......)).))))))))))).......((.((((((.....))))))..))....................................... ( -9.66 = -11.74 +   2.08)

alignment

secondary structure

dotplot

Window 4

Location	5,776,663 – 5,776,768
Length	105
Sequences	3
Columns	109
Reading direction	reverse
Mean pairwise identity	89.66
Mean single sequence MFE	-28.57
Consensus MFE	-22.13
Energy contribution	-22.03
Covariance contribution	-0.11
Combinations/Pair	1.08
Mean z-score	-2.27
Structure conservation index	0.77
SVM decision value	0.22
SVM RNA-class probability	0.642012
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5776663 105 - 20766785
CUGU----GUGCAUACAGUGUGUGUUUUACAGUUAGAGAGCCAGAACAUACACUCUCCUAUAAUUAUUGGAGAGUUUCACUGAGAAUCCGCCGGUGGCUUCUCUUUUAC
((((----(.((((((...))))))..)))))..((((((((.(((.....(((((((..........))))))))))((((.(......)))))))).)))))..... ( -31.50)
>DroSec_CAF1 66949 101 - 1
CUAU----GUGCAUACAGUGUGUGUUUUACAGUUAGAGAGCC----CCUACACUCUCCUAUAAUUUUUGGAGAGUUUUACCUAGAAACCACCGGUGGCUUCUCUUUUAC
...(----((((((((...))))))...)))...((((((((----((...(((((((..........)))))))........(....)...)).))).)))))..... ( -25.40)
>DroSim_CAF1 68086 105 - 1
CUAUGUAUGUGCAUACAGUGUGUGUUUUACAGUUAGAGAGCC----CCUACACUCUCCUAUAAUUUUUGGAGAGUUUUACAGAGAAACCACCGGUGGCUUCUCUUUUAC
...((((...((((((...))))))..))))...((((((((----((...(((((((..........)))))))......(......)...)).))).)))))..... ( -28.80)
>consensus
CUAU____GUGCAUACAGUGUGUGUUUUACAGUUAGAGAGCC____CCUACACUCUCCUAUAAUUUUUGGAGAGUUUUACAGAGAAACCACCGGUGGCUUCUCUUUUAC
(((.......((((((...))))))........)))...............(((((((..........)))))))......(((((.(((....))).)))))...... (-22.13 = -22.03 +  -0.11)

alignment

secondary structure

dotplot

Window 5

Location	5,776,703 – 5,776,808
Length	105
Sequences	3
Columns	109
Reading direction	forward
Mean pairwise identity	93.10
Mean single sequence MFE	-26.33
Consensus MFE	-24.67
Energy contribution	-24.67
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.20
Structure conservation index	0.94
SVM decision value	1.13
SVM RNA-class probability	0.920417
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5776703 105 + 20766785
CAAUAAUUAUAGGAGAGUGUAUGUUCUGGCUCUCUAACUGUAAAACACACACUGUAUGCAC----ACAGGUGCGUAUCAAUUCCGAUGAUAGCACAUCUUAUCAAUGGA
......((((((((((((..........))))))...))))))..........((((((((----....))))))))....((((.((((((......)))))).)))) ( -25.60)
>DroSec_CAF1 66989 101 + 1
CAAAAAUUAUAGGAGAGUGUAGG----GGCUCUCUAACUGUAAAACACACACUGUAUGCAC----AUAGGUGCGUAUCAAUUCCGAUGAUAGCACAUCUUAUCAAUGGA
......((((((((((((.....----.))))))...))))))..........((((((((----....))))))))....((((.((((((......)))))).)))) ( -26.70)
>DroSim_CAF1 68126 105 + 1
CAAAAAUUAUAGGAGAGUGUAGG----GGCUCUCUAACUGUAAAACACACACUGUAUGCACAUACAUAGGUGCGUAUCAAUUCCGAUGAUAGCACAUCUUAUCAAUGGA
......((((((((((((.....----.))))))...))))))..........((((((((........))))))))....((((.((((((......)))))).)))) ( -26.70)
>consensus
CAAAAAUUAUAGGAGAGUGUAGG____GGCUCUCUAACUGUAAAACACACACUGUAUGCAC____AUAGGUGCGUAUCAAUUCCGAUGAUAGCACAUCUUAUCAAUGGA
......((((((((((((..........))))))...))))))..........((((((((........))))))))....((((.((((((......)))))).)))) (-24.67 = -24.67 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	5,776,741 – 5,776,848
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.74
Mean single sequence MFE	-28.93
Consensus MFE	-21.55
Energy contribution	-22.15
Covariance contribution	0.60
Combinations/Pair	1.13
Mean z-score	-1.85
Structure conservation index	0.74
SVM decision value	0.44
SVM RNA-class probability	0.738144
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5776741 107 + 20766785
UGUAAAACACACACUGUAUGCAC-------------ACAGGUGCGUAUCAAUUCCGAUGAUAGCACAUCUUAUCAAUGGAACCGAGCUGAUAAAAGCGGGAACCCAUCGGACUGGCAAAC
(((............((((((((-------------....))))))))...(((((.((((((......)))))).)))))(((((((......)))((....)).))))....)))... ( -29.90)
>DroSec_CAF1 67023 103 + 1
UGUAAAACACACACUGUAUGCAC-------------AUAGGUGCGUAUCAAUUCCGAUGAUAGCACAUCUUAUCAAUGGAACCGAGCUGAUAAAAGCGGGAACCCAUCGGGCAGGC----
.............((((((((((-------------....)))))).....(((((.((((((......)))))).)))))(((((((......)))((....)).))))))))..---- ( -31.60)
>DroSim_CAF1 68160 107 + 1
UGUAAAACACACACUGUAUGCACAU---------ACAUAGGUGCGUAUCAAUUCCGAUGAUAGCACAUCUUAUCAAUGGAACCGAGCUGAUAAAAGCGGGAACCCAUCGGGCAGGC----
.............((((((((((..---------......)))))).....(((((.((((((......)))))).)))))(((((((......)))((....)).))))))))..---- ( -31.60)
>DroEre_CAF1 70121 115 + 1
UGUAAAACACACAAUGCAUGCACAUGCUGUAUGUACAUAGGUGCGUAUCAAUUCCGAUGAUAGCACAUCUUAUCAAUGGAACCGAGCUGAUAAAAGCGAGAACUCAACG-GCAGGC----
......((.(((..((((((((.....)))))))).....))).)).....(((((.((((((......)))))).)))))(((.(((......)))((....))..))-).....---- ( -26.90)
>DroYak_CAF1 67613 102 + 1
UGUAAAGCACACAAUGCAUGCAC-------------AUAGGUGCGUAUCAAUUCCGAUGAUAGCGCACCUUAUCAAUGGAACCGAGCUGAUAAAACCGGGAACUCAUCG-GCAGGC----
((((..(((.....))).))))(-------------((((((((((((((.......)))).)))))))).....)))...((..((((((..............))))-)).)).---- ( -24.64)
>consensus
UGUAAAACACACACUGUAUGCAC_____________AUAGGUGCGUAUCAAUUCCGAUGAUAGCACAUCUUAUCAAUGGAACCGAGCUGAUAAAAGCGGGAACCCAUCGGGCAGGC____
.............((((((((((.................)))))).....(((((.((((((......)))))).)))))(((((((......)))((....)).))))))))...... (-21.55 = -22.15 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:49 2006