Locus 4044

Sequence ID	2R_DroMel_CAF1
Location	13,345,341 – 13,345,494
Length	153
Max. P	0.795793

overview

Window 5

Location	13,345,341 – 13,345,455
Length	114
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	83.31
Mean single sequence MFE	-31.95
Consensus MFE	-20.20
Energy contribution	-20.87
Covariance contribution	0.67
Combinations/Pair	1.19
Mean z-score	-2.11
Structure conservation index	0.63
SVM decision value	-0.02
SVM RNA-class probability	0.525110
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13345341 114 + 20766785
GAACCCGGGCA-AGGAGCCACCCAUCCUUGGGAUAGUAUAAACGGAUUAGGACCAUGUCUGGCAAAAAUCAACGCAAGACAUGGCAUUUCCUCACAGAUAAGGAUCAACAACUCU
....((((((.-....))).((((....))))..........))).....(.((((((((.((..........)).)))))))))...((((........))))........... ( -31.00)
>DroPse_CAF1 42349 104 + 1
GAACCCAGGCAGAAACGGUGCCCAUCUAUGGGAUAGUAUAAACGGAUUACAGAUGAGUCCUGCGUA---------CAGACAUGGCAUAUCCUUGGAGAUAGAGAUCAAU--CUUU
....(((((..((....((((((((((.(((....((....))...))).))))).(((.((....---------)))))..))))).)))))))((((.(....).))--)).. ( -20.10)
>DroSec_CAF1 44597 114 + 1
GAACCCGGGCA-AGGAGCCACCCAUCCUUGGGAUAGUAUAAACGGAUUAGGACCAUGUCUGGCAAAAAUCAACGCAGGACAUGGCAUUUCCUUACAGAUAAGGAUCAACAACUCU
....((((((.-....))).((((....))))..........))).....(.((((((((.((..........)).)))))))))...((((((....))))))........... ( -33.10)
>DroSim_CAF1 46583 114 + 1
GAACCCGGGCG-AGGAGCCACCCAUCCUUGGGAUAGUAUAAACGGAUUAGGACCAUGUCUGGCAAAAAUCAACGCAAGACAUGGCAUUUCCUCACAGAUAAGGAUCAACAACUCU
....((((((.-....))).((((....))))..........))).....(.((((((((.((..........)).)))))))))...((((........))))........... ( -31.70)
>DroEre_CAF1 45439 110 + 1
GAACCCGGCAG-A-GAGCCACCCAUCCUUGGGAUAGUAUAAACGGAUUAGAACCAUGUCUGGCAAAAAUCAACGCCAGACAUGGCAUUUCCUUAGCGAUAAGGAUCAG---CUCU
....(((((..-.-..))).((((....))))...........))....((.(((((((((((..........)))))))))))....((((((....))))))))..---.... ( -38.60)
>DroYak_CAF1 46232 111 + 1
GAACCCGGCAA-AGGAGCCACCCAUCCUUGGGAUAGUAUAAACGGAUUAGGACCAUGUCUGGCAAAAAUCAACGCCAGACAUGGCAUUUCCUCACAGAUAAGGAUCAU---CACU
((.((.(((..-....))).((((....))))...........(((....(.(((((((((((..........))))))))))))...)))..........)).))..---.... ( -37.20)
>consensus
GAACCCGGGCA_AGGAGCCACCCAUCCUUGGGAUAGUAUAAACGGAUUAGGACCAUGUCUGGCAAAAAUCAACGCAAGACAUGGCAUUUCCUCACAGAUAAGGAUCAAC__CUCU
..............((.((.((((....))))...........(((......((((((((.((..........)).))))))))....)))..........)).))......... (-20.20 = -20.87 +   0.67)

alignment

secondary structure

dotplot

Window 6

Location	13,345,341 – 13,345,455
Length	114
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	83.31
Mean single sequence MFE	-36.57
Consensus MFE	-26.01
Energy contribution	-26.93
Covariance contribution	0.92
Combinations/Pair	1.17
Mean z-score	-2.29
Structure conservation index	0.71
SVM decision value	0.42
SVM RNA-class probability	0.728936
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13345341 114 - 20766785
AGAGUUGUUGAUCCUUAUCUGUGAGGAAAUGCCAUGUCUUGCGUUGAUUUUUGCCAGACAUGGUCCUAAUCCGUUUAUACUAUCCCAAGGAUGGGUGGCUCCU-UGCCCGGGUUC
...........((((((....))))))...(((((((((.(((........))).)))))))))...((((((......((((((...))))))..(((....-.))))))))). ( -38.00)
>DroPse_CAF1 42349 104 - 1
AAAG--AUUGAUCUCUAUCUCCAAGGAUAUGCCAUGUCUG---------UACGCAGGACUCAUCUGUAAUCCGUUUAUACUAUCCCAUAGAUGGGCACCGUUUCUGCCUGGGUUC
..((--((.(....).))))(((.((((((...)))))).---------...(((((((((((((((.....((....))......)))))))))......)))))).))).... ( -19.70)
>DroSec_CAF1 44597 114 - 1
AGAGUUGUUGAUCCUUAUCUGUAAGGAAAUGCCAUGUCCUGCGUUGAUUUUUGCCAGACAUGGUCCUAAUCCGUUUAUACUAUCCCAAGGAUGGGUGGCUCCU-UGCCCGGGUUC
...........((((((....))))))...((((((((..(((........)))..))))))))...((((((......((((((...))))))..(((....-.))))))))). ( -35.70)
>DroSim_CAF1 46583 114 - 1
AGAGUUGUUGAUCCUUAUCUGUGAGGAAAUGCCAUGUCUUGCGUUGAUUUUUGCCAGACAUGGUCCUAAUCCGUUUAUACUAUCCCAAGGAUGGGUGGCUCCU-CGCCCGGGUUC
...........((((((....))))))...(((((((((.(((........))).)))))))))...((((((......((((((...))))))..(((....-.))))))))). ( -37.40)
>DroEre_CAF1 45439 110 - 1
AGAG---CUGAUCCUUAUCGCUAAGGAAAUGCCAUGUCUGGCGUUGAUUUUUGCCAGACAUGGUUCUAAUCCGUUUAUACUAUCCCAAGGAUGGGUGGCUC-U-CUGCCGGGUUC
(((.---....((((((....))))))...(((((((((((((........))))))))))))))))(((((.......((((((...))))))..(((..-.-..)))))))). ( -44.30)
>DroYak_CAF1 46232 111 - 1
AGUG---AUGAUCCUUAUCUGUGAGGAAAUGCCAUGUCUGGCGUUGAUUUUUGCCAGACAUGGUCCUAAUCCGUUUAUACUAUCCCAAGGAUGGGUGGCUCCU-UUGCCGGGUUC
....---....((((((....))))))...(((((((((((((........)))))))))))))...(((((.......((((((...))))))..(((....-..)))))))). ( -44.30)
>consensus
AGAG__GUUGAUCCUUAUCUGUAAGGAAAUGCCAUGUCUGGCGUUGAUUUUUGCCAGACAUGGUCCUAAUCCGUUUAUACUAUCCCAAGGAUGGGUGGCUCCU_UGCCCGGGUUC
...........((((((....))))))...(((((((((.(((........))).)))))))))...(((((.......(((((.....)))))..((.........))))))). (-26.01 = -26.93 +   0.92)

alignment

secondary structure

dotplot

Window 7

Location	13,345,375 – 13,345,494
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.38
Mean single sequence MFE	-30.02
Consensus MFE	-17.31
Energy contribution	-18.07
Covariance contribution	0.75
Combinations/Pair	1.22
Mean z-score	-1.83
Structure conservation index	0.58
SVM decision value	0.30
SVM RNA-class probability	0.678514
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13345375 119 + 20766785
GUAUAAACGGAUUAGGACCAUGUCUGGCAAAAAUCAACGCAAGACAUGGCAUUUCCUCACAGAUAAGGAUCAACAACUCUCGCCC-AGAUCGCUUUCCAGAUCAGGAUAGUGAACGAAAC
........(((....(.((((((((.((..........)).)))))))))...)))((((.(((....)))............((-.((((........)))).))...))))....... ( -28.70)
>DroPse_CAF1 42384 97 + 1
GUAUAAACGGAUUACAGAUGAGUCCUGCGUA---------CAGACAUGGCAUAUCCUUGGAGAUAGAGAUCAAU--CUUUUGGC--UGCUUGUUUUUCGGAUAAAGAGAA----------
((((..(.(((((.(....)))))))..)))---------).((((.((((...((..((((((.(....).))--)))).)).--))))))))((((.......)))).---------- ( -17.40)
>DroSec_CAF1 44631 116 + 1
GUAUAAACGGAUUAGGACCAUGUCUGGCAAAAAUCAACGCAGGACAUGGCAUUUCCUUACAGAUAAGGAUCAACAACUCUCGCCCAAGAUCGCUUUCCAGAUCAGGAUAGUGAACU----
........((.....(.((((((((.((..........)).)))))))))...((((((....))))))..............)).((.(((((.(((......))).))))).))---- ( -30.30)
>DroSim_CAF1 46617 116 + 1
GUAUAAACGGAUUAGGACCAUGUCUGGCAAAAAUCAACGCAAGACAUGGCAUUUCCUCACAGAUAAGGAUCAACAACUCUCGCCCAAGAUCGCUUUCCAGAUCAGGAUAGUGUACG----
((((.....((((.((.((((((((.((..........)).))))))))....((((........))))..............))..))))(((.(((......))).))))))).---- ( -27.40)
>DroEre_CAF1 45472 116 + 1
GUAUAAACGGAUUAGAACCAUGUCUGGCAAAAAUCAACGCCAGACAUGGCAUUUCCUUAGCGAUAAGGAUCAG---CUCUCGCCC-AGAUCGCUUUCCAGAUCAGGAUAGUGAACGAAAC
........((...(((.(((((((((((..........)))))))))))....((((((....))))))....---.)))...))-.(.(((((.(((......))).))))).)..... ( -38.20)
>DroYak_CAF1 46266 116 + 1
GUAUAAACGGAUUAGGACCAUGUCUGGCAAAAAUCAACGCCAGACAUGGCAUUUCCUCACAGAUAAGGAUCAU---CACUCGCCC-AGAUCGAUUUCCAGAUCGGGAUAGUGCACGAAAC
........(((....(.(((((((((((..........))))))))))))...)))((...(((....)))..---((((..(((-.((((........)))))))..))))...))... ( -38.10)
>consensus
GUAUAAACGGAUUAGGACCAUGUCUGGCAAAAAUCAACGCAAGACAUGGCAUUUCCUCACAGAUAAGGAUCAAC__CUCUCGCCC_AGAUCGCUUUCCAGAUCAGGAUAGUGAACG____
........(((......((((((((.((..........)).))))))))....))).....(((....)))...................((((.(((......))).))))........ (-17.31 = -18.07 +   0.75)

alignment

secondary structure

dotplot

Window 8

Location	13,345,375 – 13,345,494
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.38
Mean single sequence MFE	-33.32
Consensus MFE	-20.89
Energy contribution	-22.17
Covariance contribution	1.28
Combinations/Pair	1.23
Mean z-score	-1.81
Structure conservation index	0.63
SVM decision value	0.60
SVM RNA-class probability	0.795793
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13345375 119 - 20766785
GUUUCGUUCACUAUCCUGAUCUGGAAAGCGAUCU-GGGCGAGAGUUGUUGAUCCUUAUCUGUGAGGAAAUGCCAUGUCUUGCGUUGAUUUUUGCCAGACAUGGUCCUAAUCCGUUUAUAC
(((((.(((((..(((......)))(((.((((.-.(((....)))...)))))))....))))))))))(((((((((.(((........))).)))))))))................ ( -35.90)
>DroPse_CAF1 42384 97 - 1
----------UUCUCUUUAUCCGAAAAACAAGCA--GCCAAAAG--AUUGAUCUCUAUCUCCAAGGAUAUGCCAUGUCUG---------UACGCAGGACUCAUCUGUAAUCCGUUUAUAC
----------...............((((..(((--(.((..((--((.(....).))))....((.....)).)).)))---------)..(((((.....))))).....)))).... ( -11.50)
>DroSec_CAF1 44631 116 - 1
----AGUUCACUAUCCUGAUCUGGAAAGCGAUCUUGGGCGAGAGUUGUUGAUCCUUAUCUGUAAGGAAAUGCCAUGUCCUGCGUUGAUUUUUGCCAGACAUGGUCCUAAUCCGUUUAUAC
----((.((.((.(((......))).)).)).))((((((.((........((((((....))))))...((((((((..(((........)))..)))))))).....))))))))... ( -31.50)
>DroSim_CAF1 46617 116 - 1
----CGUACACUAUCCUGAUCUGGAAAGCGAUCUUGGGCGAGAGUUGUUGAUCCUUAUCUGUGAGGAAAUGCCAUGUCUUGCGUUGAUUUUUGCCAGACAUGGUCCUAAUCCGUUUAUAC
----....(((..(((......)))(((.((((...(((....)))...)))))))....))).(((...(((((((((.(((........))).))))))))).....)))........ ( -33.80)
>DroEre_CAF1 45472 116 - 1
GUUUCGUUCACUAUCCUGAUCUGGAAAGCGAUCU-GGGCGAGAG---CUGAUCCUUAUCGCUAAGGAAAUGCCAUGUCUGGCGUUGAUUUUUGCCAGACAUGGUUCUAAUCCGUUUAUAC
.............(((......))).((((((..-((((....)---)....))..))))))..(((...(((((((((((((........))))))))))))).....)))........ ( -42.70)
>DroYak_CAF1 46266 116 - 1
GUUUCGUGCACUAUCCCGAUCUGGAAAUCGAUCU-GGGCGAGUG---AUGAUCCUUAUCUGUGAGGAAAUGCCAUGUCUGGCGUUGAUUUUUGCCAGACAUGGUCCUAAUCCGUUUAUAC
...((((.((((..(((((((........)))).-)))..))))---))))((((((....))))))...(((((((((((((........)))))))))))))................ ( -44.50)
>consensus
____CGUUCACUAUCCUGAUCUGGAAAGCGAUCU_GGGCGAGAG__GUUGAUCCUUAUCUGUAAGGAAAUGCCAUGUCUGGCGUUGAUUUUUGCCAGACAUGGUCCUAAUCCGUUUAUAC
.............(((......)))(((((.....................((((((....))))))...(((((((((.(((........))).))))))))).......))))).... (-20.89 = -22.17 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:22 2006