Locus 6699

Sequence ID	X_DroMel_CAF1
Location	16,725,850 – 16,725,989
Length	139
Max. P	0.898911

overview

Window 9

Location	16,725,850 – 16,725,952
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.30
Mean single sequence MFE	-24.90
Consensus MFE	-7.70
Energy contribution	-7.98
Covariance contribution	0.28
Combinations/Pair	1.19
Mean z-score	-2.04
Structure conservation index	0.31
SVM decision value	0.42
SVM RNA-class probability	0.730729
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16725850 102 - 22224390
UCUUCAUGCAUGCCUACAAUGCCGUACCGCACUGUAUCCUACAUAUAUGUACAU-------ACAGGCAUUACAGGCAAUCGCAUCGCAUCGAUCUUAAUCGCAUAUGUA-----------
...((((((((((......(((((((..((.((((((..((((....)))).))-------))))))..))).))))...)))).)))).)).................----------- ( -24.70)
>DroSec_CAF1 6719 103 - 1
ACUUCAUGCAUGCCUACAAUGCCGUACCGCACUGUAUCCUA--UAUAUGUAAAGUCUGGUCGCAGUCAUU----GUAAUCGCAUCGCAUCGAUCUCAAUCGCAUAUGGA-----------
...((((((((((.((((((((.((((((.(((.(((....--.....))).))).)))).)).).))))----)))...)))).)))).)).................----------- ( -21.80)
>DroSim_CAF1 6112 103 - 1
ACUUCAUGCAUGCCUACAAUGCCGUACCGCACUGUAUCCUA--UAUAUGUAAAGUCUGGUCGCAGUCAUU----GUAAUCGCAUCGCAUCGAUCUCAAUCGCAUAUGGA-----------
...((((((((((.((((((((.((((((.(((.(((....--.....))).))).)))).)).).))))----)))...)))).)))).)).................----------- ( -21.80)
>DroEre_CAF1 5374 108 - 1
UUUUCAUGCUUACCUACAAUGCCGUAACGCACUGUAUCCCA--UAUA------GUCUAGUCGCAGGCAUU----GUGAUCGCAUCCCAUCGAUCUCAAUCGAACAUGGAUACCGCCAGUU
..((((((......((((((((((..((..(((((((...)--))))------))...))..).))))))----)))...........(((((....))))).))))))........... ( -28.00)
>DroYak_CAF1 5666 97 - 1
GUGUCAUGCAUACCUACAAUCCCGUACCGCACUGUAUCCUA--UAUA------GUGCAGUACCAGGCAUU----GUAAUCGCAUCCCAUCGAUCUCAAUCGCAAAUGGA-----------
.....((((.....((((((((.((((.(((((((((...)--))))------)))).))))..)).)))----)))...)))).((((((((....))))...)))).----------- ( -28.20)
>consensus
ACUUCAUGCAUGCCUACAAUGCCGUACCGCACUGUAUCCUA__UAUAUGUA_AGUCUAGUCGCAGGCAUU____GUAAUCGCAUCGCAUCGAUCUCAAUCGCAUAUGGA___________
.....((((.(((....((((((.........................................))))))....)))...)))).((((((((....))))...))))............ ( -7.70 =  -7.98 +   0.28)

alignment

secondary structure

dotplot

Window 0

Location	16,725,879 – 16,725,989
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	75.66
Mean single sequence MFE	-29.16
Consensus MFE	-18.64
Energy contribution	-18.40
Covariance contribution	-0.24
Combinations/Pair	1.15
Mean z-score	-1.49
Structure conservation index	0.64
SVM decision value	0.08
SVM RNA-class probability	0.572867
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16725879 110 + 22224390
GAUUGCCUGUAAUGCCUGU-------AUGUACAUAUAUGUAGGAUACAGUGCGGUACGGCAUUGUAGGCAUGCAUGAAGAUAUGCUGCCCU--UACUGAGAACUUUU-UUGUUGUGCUAU
....(((((((...(((((-------((((....))))))))).))))).))(((((((((.....((((.(((((....)))))))))((--(...))).......-.))))))))).. ( -33.50)
>DroSec_CAF1 6748 113 + 1
GAUUAC----AAUGACUGCGACCAGACUUUACAUAUA--UAGGAUACAGUGCGGUACGGCAUUGUAGGCAUGCAUGAAGUUAUGCUGCCCUUUUACUAAGAACUUCU-UUGUUGUGCUAU
...(((----((..((((....)))............--(((..((((((((......))))))))((((.(((((....)))))))))......))).........-)..))))).... ( -26.90)
>DroSim_CAF1 6141 113 + 1
GAUUAC----AAUGACUGCGACCAGACUUUACAUAUA--UAGGAUACAGUGCGGUACGGCAUUGUAGGCAUGCAUGAAGUUAUGCUGCCCUUUUACUAAGAACUUCU-UUGUUGUGCUAU
...(((----((..((((....)))............--(((..((((((((......))))))))((((.(((((....)))))))))......))).........-)..))))).... ( -26.90)
>DroEre_CAF1 5414 102 + 1
GAUCAC----AAUGCCUGCGACUAGAC------UAUA--UGGGAUACAGUGCGUUACGGCAUUGUAGGUAAGCAUGAAAAUAUGCCGCCUG--UACUGUGAAGAUUUGUU----UUCUUG
..((((----(.(((..(((.......------....--.....((((((((......)))))))).....(((((....))))))))..)--)).))))).........----...... ( -25.10)
>DroYak_CAF1 5695 101 + 1
GAUUAC----AAUGCCUGGUACUGCAC------UAUA--UAGGAUACAGUGCGGUACGGGAUUGUAGGUAUGCAUGACACUAUGCUGCCAU--AACUAAUAAGAUAU-UU----UUCUAC
...(((----(((.((((.((((((((------(.((--(...))).)))))))))))))))))))((((.(((((....)))))))))..--........(((...-..----.))).. ( -33.40)
>consensus
GAUUAC____AAUGCCUGCGACCAGACU_UACAUAUA__UAGGAUACAGUGCGGUACGGCAUUGUAGGCAUGCAUGAAGAUAUGCUGCCCU__UACUAAGAACUUCU_UUGUUGUGCUAU
.......................................(((..((((((((......))))))))((((.(((((....)))))))))......)))...................... (-18.64 = -18.40 +  -0.24)

alignment

secondary structure

dotplot

Window 1

Location	16,725,879 – 16,725,989
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	75.66
Mean single sequence MFE	-25.80
Consensus MFE	-11.20
Energy contribution	-11.64
Covariance contribution	0.44
Combinations/Pair	1.07
Mean z-score	-2.08
Structure conservation index	0.43
SVM decision value	1.01
SVM RNA-class probability	0.898911
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16725879 110 - 22224390
AUAGCACAACAA-AAAAGUUCUCAGUA--AGGGCAGCAUAUCUUCAUGCAUGCCUACAAUGCCGUACCGCACUGUAUCCUACAUAUAUGUACAU-------ACAGGCAUUACAGGCAAUC
............-..............--.(((((((((......)))).)))))....(((((((..((.((((((..((((....)))).))-------))))))..))).))))... ( -28.60)
>DroSec_CAF1 6748 113 - 1
AUAGCACAACAA-AGAAGUUCUUAGUAAAAGGGCAGCAUAACUUCAUGCAUGCCUACAAUGCCGUACCGCACUGUAUCCUA--UAUAUGUAAAGUCUGGUCGCAGUCAUU----GUAAUC
........((.(-((.....))).))....(((((((((......)))).)))))(((((((.((((((.(((.(((....--.....))).))).)))).)).).))))----)).... ( -24.10)
>DroSim_CAF1 6141 113 - 1
AUAGCACAACAA-AGAAGUUCUUAGUAAAAGGGCAGCAUAACUUCAUGCAUGCCUACAAUGCCGUACCGCACUGUAUCCUA--UAUAUGUAAAGUCUGGUCGCAGUCAUU----GUAAUC
........((.(-((.....))).))....(((((((((......)))).)))))(((((((.((((((.(((.(((....--.....))).))).)))).)).).))))----)).... ( -24.10)
>DroEre_CAF1 5414 102 - 1
CAAGAA----AACAAAUCUUCACAGUA--CAGGCGGCAUAUUUUCAUGCUUACCUACAAUGCCGUAACGCACUGUAUCCCA--UAUA------GUCUAGUCGCAGGCAUU----GUGAUC
...(((----........)))......--.(((.(((((......)))))..)))(((((((((..((..(((((((...)--))))------))...))..).))))))----)).... ( -25.10)
>DroYak_CAF1 5695 101 - 1
GUAGAA----AA-AUAUCUUAUUAGUU--AUGGCAGCAUAGUGUCAUGCAUACCUACAAUCCCGUACCGCACUGUAUCCUA--UAUA------GUGCAGUACCAGGCAUU----GUAAUC
......----..-...........((.--((((((......)))))))).....((((((((.((((.(((((((((...)--))))------)))).))))..)).)))----)))... ( -27.10)
>consensus
AUAGCACAACAA_AAAAGUUCUUAGUA__AGGGCAGCAUAACUUCAUGCAUGCCUACAAUGCCGUACCGCACUGUAUCCUA__UAUAUGUA_AGUCUAGUCGCAGGCAUU____GUAAUC
...............................((((((((......)))).))))((((.(((......))).))))............................................ (-11.20 = -11.64 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:14 2006