Locus 3639

Sequence ID	2L_DroMel_CAF1
Location	10,591,985 – 10,592,148
Length	163
Max. P	0.865915

overview

Window 6

Location	10,591,985 – 10,592,088
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.06
Mean single sequence MFE	-17.40
Consensus MFE	-11.72
Energy contribution	-11.58
Covariance contribution	-0.14
Combinations/Pair	1.06
Mean z-score	-1.78
Structure conservation index	0.67
SVM decision value	0.65
SVM RNA-class probability	0.812581
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10591985 103 - 22407834
CAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGACAAGCCA----------CUG----CCUUACCCCACUGCUUCCAUCUACAUCCCUAUGUA---GUACAUA
....((((.((((.....)))))).(((((.....))))).))(((((....))))).----------...----....................((((((....)))))---)...... ( -15.90)
>DroPse_CAF1 81784 104 - 1
AAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUUACAGGCUUAGAAGAGCCC----CAUCUUCUGCCCCCU-CCCCCGGCCACUAUCCUCUCCAU------U-----UCCCCUA
......((.((((.....)))))).(((((.....)))))...(((((((((((....----..)))))))......-.....))))..............------.-----....... ( -16.70)
>DroSec_CAF1 79295 104 - 1
CAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGACAAGCCA----------CUGU---CCUUACCCCACAGCUUCCAUCUACAUCCUUAUGUA---GUACAUA
......((.((((.....))))))...........((..(((.(((((....))))).----------))).---.)).................((((((....)))))---)...... ( -17.50)
>DroSim_CAF1 79876 114 - 1
CAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGACAAGCCACUGCCACCCACUGU---CCUUACCCCACAGCUUCCAUCUACAUCCUUAUGUA---GUACAUA
....((((.((((.....)))))).(((((.....))))).))(((((....)))))...........((((---.........)))).......((((((....)))))---)...... ( -16.90)
>DroEre_CAF1 80291 107 - 1
CCAAUCGAAUUGCAAAUGGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGUCAAGCCA----------CUAUCCGCUUCACCCCACAACUUCCAUCUGCCUCCCUGUGUA---GUACAUA
......(.((((((...((((....(((((.....))))).(((((.((((......)----------)))...))))).................))))......))))---)).)... ( -19.40)
>DroYak_CAF1 82303 110 - 1
CAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGACAAGCCG----------CUGCCCUCUUCACCCCACAACUUCCAUCUACAUCCCUAUGUAGUAGUACAUA
......((.((((.....))))))...........((..(((.(((((....))))).----------)))..))............(((.....((((((....)))))).)))..... ( -18.00)
>consensus
CAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGACAAGCCA__________CUGU___CCUCACCCCACAACUUCCAUCUACAUCCCUAUGUA___GUACAUA
......((.((((.....)))))).(((((.....)))))...(((((....)))))............................................................... (-11.72 = -11.58 +  -0.14)

alignment

secondary structure

dotplot

Window 7

Location	10,592,022 – 10,592,118
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.65
Mean single sequence MFE	-30.82
Consensus MFE	-19.54
Energy contribution	-20.35
Covariance contribution	0.81
Combinations/Pair	1.15
Mean z-score	-2.20
Structure conservation index	0.63
SVM decision value	0.52
SVM RNA-class probability	0.765883
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10592022 96 + 22407834
UAAGG----CAG----------UGGCUUGUCUAAGCCUCUAAACUGAUUAAGUUUUGAUUGCAAUUUGCAAUUCGAUUUGCAAAGAGUCAAAACUUUGCCGUCGG-------GUGU---C
...((----(((----------.(((((....))))).))...(((((.(((((((((((....(((((((......))))))).)))))))))))....)))))-------..))---) ( -30.40)
>DroSec_CAF1 79332 97 + 1
UAAGG---ACAG----------UGGCUUGUCUAAGCCUCUAAACUGAUUAAGUUUUGAUUGCAAUUUGCAAUUCGAUUUGCAAAGAGCCAAAACUUUGCCGUCGG-------CUGU---C
....(---((((----------.(((((....)))))......(((((.((((((((...((..(((((((......)))))))..))))))))))....)))))-------))))---) ( -30.10)
>DroSim_CAF1 79913 107 + 1
UAAGG---ACAGUGGGUGGCAGUGGCUUGUCUAAGCCUCUAAACUGAUUAAGUUUUGAUUGCAAUUUGCAAUUCGAUUUGCAAAGAGCCAAAACUUUGCCGUCGG-------CUGU---C
....(---(((((.(..(((((.(((((....))))).)).........((((((((...((..(((((((......)))))))..)))))))))).)))..).)-------))))---) ( -40.90)
>DroEre_CAF1 80328 107 + 1
UGAAGCGGAUAG----------UGGCUUGACUAAGCCUCUAAACUGAUUAAGUUUUGAUUGCCAUUUGCAAUUCGAUUGGCAAGGAGCCAAAACUUUGCCGUCGGCAAAGUCGUGU---A
....(((.....----------((((((.........((.(((((.....))))).))((((((.(((.....))).)))))).))))))..((((((((...)))))))))))..---. ( -32.20)
>DroYak_CAF1 82343 100 + 1
UGAAGAGGGCAG----------CGGCUUGUCUAAGCCUCUAAACUGAUUAAGUUUUGAUUGCAAUUUGCAAUUCGAUUUGCAAAGAGCCAAAACUUUGCCGUCGG-------GUGU---C
....((.(((((----------.(((((....))))).)).........((((((((...((..(((((((......)))))))..)))))))))).))).))..-------....---. ( -31.20)
>DroAna_CAF1 81883 96 + 1
---AGAGGG-------------GAGACCGACUAAGCCUCUAAACUGAUUAAGUUUUGAUUGCAAUUUGCGAUUCGAUUUCCAGAGAGCCA-AACUUUGCCGCCGG-------AUGGGAGC
---((((((-------------....))......(((((((((((.....))))).((((((.....))))))........)))).))..-..))))((..((..-------..))..)) ( -20.10)
>consensus
UAAAG___ACAG__________UGGCUUGUCUAAGCCUCUAAACUGAUUAAGUUUUGAUUGCAAUUUGCAAUUCGAUUUGCAAAGAGCCAAAACUUUGCCGUCGG_______GUGU___C
.......................(((((....)))))......(((((.((((((((...((..(((((((......)))))))..))))))))))....)))))............... (-19.54 = -20.35 +   0.81)

alignment

secondary structure

dotplot

Window 8

Location	10,592,022 – 10,592,118
Length	96
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.65
Mean single sequence MFE	-27.23
Consensus MFE	-17.00
Energy contribution	-17.28
Covariance contribution	0.28
Combinations/Pair	1.16
Mean z-score	-2.49
Structure conservation index	0.62
SVM decision value	0.70
SVM RNA-class probability	0.827192
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10592022 96 - 22407834
G---ACAC-------CCGACGGCAAAGUUUUGACUCUUUGCAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGACAAGCCA----------CUG----CCUUA
.---....-------.....((((((((((((((..(((((((......)))))))..)...)))))))))............(((((....))))).----------.))----))... ( -25.90)
>DroSec_CAF1 79332 97 - 1
G---ACAG-------CCGACGGCAAAGUUUUGGCUCUUUGCAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGACAAGCCA----------CUGU---CCUUA
(---((((-------.....((..((((((((((..(((((((......)))))))..))...))))))))..))........(((((....))))).----------))))---).... ( -27.70)
>DroSim_CAF1 79913 107 - 1
G---ACAG-------CCGACGGCAAAGUUUUGGCUCUUUGCAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGACAAGCCACUGCCACCCACUGU---CCUUA
(---((((-------..(..((((((((((((((..(((((((......)))))))..))...))))))))............(((((....)))))..))))..)..))))---).... ( -33.10)
>DroEre_CAF1 80328 107 - 1
U---ACACGACUUUGCCGACGGCAAAGUUUUGGCUCCUUGCCAAUCGAAUUGCAAAUGGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGUCAAGCCA----------CUAUCCGCUUCA
.---....(((((((((...)))))))))(((((.....)))))..((.((((.....))))))............(..(((.(((((....))))).----------)))..)...... ( -30.20)
>DroYak_CAF1 82343 100 - 1
G---ACAC-------CCGACGGCAAAGUUUUGGCUCUUUGCAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGACAAGCCG----------CUGCCCUCUUCA
.---....-------..((.((((((((((((((..(((((((......)))))))..))...))))))))............(((((....))))).----------.)))).)).... ( -28.70)
>DroAna_CAF1 81883 96 - 1
GCUCCCAU-------CCGGCGGCAAAGUU-UGGCUCUCUGGAAAUCGAAUCGCAAAUUGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGUCGGUCUC-------------CCCUCU---
(((.((..-------..)).)))......-.........(((.(((((...((.....))..((.(((((.....))))).)).......))))).))-------------).....--- ( -17.80)
>consensus
G___ACAC_______CCGACGGCAAAGUUUUGGCUCUUUGCAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUUAGAGGCUUAGACAAGCCA__________CUGU___CCUUA
................(((..((((((........))))))...)))..((((.....))))((.(((((.....))))).))(((((....)))))....................... (-17.00 = -17.28 +   0.28)

alignment

secondary structure

dotplot

Window 9

Location	10,592,048 – 10,592,148
Length	100
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	79.32
Mean single sequence MFE	-20.85
Consensus MFE	-16.59
Energy contribution	-16.73
Covariance contribution	0.14
Combinations/Pair	1.18
Mean z-score	-1.57
Structure conservation index	0.80
SVM decision value	0.85
SVM RNA-class probability	0.865915
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10592048 100 + 22407834
AAACUGAUUAAGUUUUGAUUGCAAUUUGCAAUUCGAUUUGCAAAGAGUCAAAACUUUGCCGUCGG-------GUGU---CGUCUUUUUACUCGCUGUUCUUUUUUUUUUU
...(((((.(((((((((((....(((((((......))))))).)))))))))))....)))))-------(((.---.((......)).)))................ ( -22.10)
>DroSec_CAF1 79359 100 + 1
AAACUGAUUAAGUUUUGAUUGCAAUUUGCAAUUCGAUUUGCAAAGAGCCAAAACUUUGCCGUCGG-------CUGU---CGUCUUUUCACUUUCUUCUCUUUUUUUUUUU
...(((((.((((((((...((..(((((((......)))))))..))))))))))....)))))-------....---............................... ( -19.60)
>DroSim_CAF1 79950 97 + 1
AAACUGAUUAAGUUUUGAUUGCAAUUUGCAAUUCGAUUUGCAAAGAGCCAAAACUUUGCCGUCGG-------CUGU---CGUCUUUUCACUUUCUGCUCUCUUU---UUU
...(((((.((((((((...((..(((((((......)))))))..))))))))))....)))))-------....---.........................---... ( -19.60)
>DroEre_CAF1 80358 91 + 1
AAACUGAUUAAGUUUUGAUUGCCAUUUGCAAUUCGAUUGGCAAGGAGCCAAAACUUUGCCGUCGGCAAAGUCGUGU---AGACUUUUCACUUU----------------U
(((((.....))))).((((((.....))))))((((.(((((((........)))))))))))(.((((((....---.)))))).).....----------------. ( -24.10)
>DroYak_CAF1 82373 88 + 1
AAACUGAUUAAGUUUUGAUUGCAAUUUGCAAUUCGAUUUGCAAAGAGCCAAAACUUUGCCGUCGG-------GUGU---CGACUUUUCACUUU------------UUUUU
...(((((.((((((((...((..(((((((......)))))))..))))))))))....)))))-------(((.---........)))...------------..... ( -21.10)
>DroAna_CAF1 81907 87 + 1
AAACUGAUUAAGUUUUGAUUGCAAUUUGCGAUUCGAUUUCCAGAGAGCCA-AACUUUGCCGCCGG-------AUGGGAGCGGAUUGCCGCCUU---------------UU
(((((.....)))))............((((((((.((((((..(.((..-.........)))..-------.))))))))))))))......---------------.. ( -18.60)
>consensus
AAACUGAUUAAGUUUUGAUUGCAAUUUGCAAUUCGAUUUGCAAAGAGCCAAAACUUUGCCGUCGG_______GUGU___CGUCUUUUCACUUU______________UUU
...(((((.((((((((...((..(((((((......)))))))..))))))))))....)))))............................................. (-16.59 = -16.73 +   0.14)

alignment

secondary structure

dotplot

Window 0

Location	10,592,048 – 10,592,148
Length	100
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	79.32
Mean single sequence MFE	-20.18
Consensus MFE	-11.27
Energy contribution	-11.68
Covariance contribution	0.42
Combinations/Pair	1.17
Mean z-score	-2.14
Structure conservation index	0.56
SVM decision value	0.66
SVM RNA-class probability	0.815764
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10592048 100 - 22407834
AAAAAAAAAAAGAACAGCGAGUAAAAAGACG---ACAC-------CCGACGGCAAAGUUUUGACUCUUUGCAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUU
................((((((...(((((.---...(-------(....))....))))).))))(((((((......)))))))..)).....(((((.....))))) ( -16.90)
>DroSec_CAF1 79359 100 - 1
AAAAAAAAAAAGAGAAGAAAGUGAAAAGACG---ACAG-------CCGACGGCAAAGUUUUGGCUCUUUGCAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUU
.................(((.(((.......---...(-------((...))).((((((((((..(((((((......)))))))..))...))))))))..))).))) ( -20.50)
>DroSim_CAF1 79950 97 - 1
AAA---AAAGAGAGCAGAAAGUGAAAAGACG---ACAG-------CCGACGGCAAAGUUUUGGCUCUUUGCAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUU
...---...........(((.(((.......---...(-------((...))).((((((((((..(((((((......)))))))..))...))))))))..))).))) ( -20.50)
>DroEre_CAF1 80358 91 - 1
A----------------AAAGUGAAAAGUCU---ACACGACUUUGCCGACGGCAAAGUUUUGGCUCCUUGCCAAUCGAAUUGCAAAUGGCAAUCAAAACUUAAUCAGUUU
.----------------(((.(((((((((.---....))))))((((...((((....(((((.....))))).....))))...)))).............))).))) ( -24.40)
>DroYak_CAF1 82373 88 - 1
AAAAA------------AAAGUGAAAAGUCG---ACAC-------CCGACGGCAAAGUUUUGGCUCUUUGCAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUU
.....------------(((.(((...((((---....-------.))))....((((((((((..(((((((......)))))))..))...))))))))..))).))) ( -22.30)
>DroAna_CAF1 81907 87 - 1
AA---------------AAGGCGGCAAUCCGCUCCCAU-------CCGGCGGCAAAGUU-UGGCUCUCUGGAAAUCGAAUCGCAAAUUGCAAUCAAAACUUAAUCAGUUU
..---------------..(((((....)))))....(-------((((.(((......-..)).).))))).........((.....)).....(((((.....))))) ( -16.50)
>consensus
AAA______________AAAGUGAAAAGACG___ACAC_______CCGACGGCAAAGUUUUGGCUCUUUGCAAAUCGAAUUGCAAAUUGCAAUCAAAACUUAAUCAGUUU
..................((((........................(((..((((((........))))))...))).(((((.....)))))....))))......... (-11.27 = -11.68 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:28 2006