Locus 291

Sequence ID	3R_DroMel_CAF1
Location	1,119,320 – 1,119,529
Length	209
Max. P	0.964390

overview

Window 4

Location	1,119,320 – 1,119,435
Length	115
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	83.87
Mean single sequence MFE	-35.02
Consensus MFE	-28.93
Energy contribution	-29.32
Covariance contribution	0.39
Combinations/Pair	1.05
Mean z-score	-1.54
Structure conservation index	0.83
SVM decision value	0.13
SVM RNA-class probability	0.596570
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1119320 115 - 27905053
AACACCGUCCGAAGACUCUGGUGGCUCACCUGUGCCGCCAUUGACUCCGCAUUCGACUCAUUCCGAGGGUCACAUGACCUAUGGGUAAGGACGGAUCUCCGAUCAGCUGUCACCA
....(((((((.((.(..(((((((.(....).)))))))..).)).).............((((.(((((....))))).))))...))))))......(((.....))).... ( -37.50)
>DroVir_CAF1 46912 105 - 1
AACACCGUCCGAAGAAUCUGGUGGGUCGCCAGUGCCGCCAUUGACUCCACACUCGACACAUUCCGAGGGUCACAUGACCUAUGGGUAAGGACGGAUU--GGAUCC--UG------
....((((((........((((((..(....)..))))))...((.(((..((((........))))((((....))))..)))))..))))))...--......--..------ ( -34.10)
>DroGri_CAF1 60554 106 - 1
AACACCGUCCGAAGAAUCUGGUGGGUCGCCAGUGCCGCCAUUAACUCCACAUUCGACACAUUCCGAGGGUCACAUGACCUAUGGGUAAGGACGGAUUU-GGAUGA--UG------
....(((((((..((((.(((..(((.((....)).))).......))).))))..)....((((.(((((....))))).))))...))))))....-......--..------ ( -34.00)
>DroWil_CAF1 56051 105 - 1
AACACCAUCCGAAGACUCUGGUGGCUCACCAGUGCCGCCAUUGACUCCCCAUUCAACACAUUCCGAGGGUCACAUGACCUAUGGGUAAGGCAGUACUU-GUAUAC---------U
....(((((.((....)).)))))...((.(((((.(((.((((........)))).....((((.(((((....))))).))))...))).))))).-))....---------. ( -30.40)
>DroMoj_CAF1 48002 105 - 1
AACACCGUCCGAAGAAUCUGGUGGAUCACCAGUGCCGCCAUUGACACCGCACUCGACACAUUCCGAGGGUCAUAUGACCUAUGGGUAAGGAUGGAUC--GGCAAC--UG------
..(((((...........)))))......(((((((((((((...(((.((((((........))))((((....))))..)))))...)))))..)--))).))--))------ ( -32.90)
>DroAna_CAF1 50713 102 - 1
AACACCGUCCGAGGACUCUGGUGGCUCACCUGUGCCGCCAUUGACUCCGCACUCCACUCAUUCCGAGGGUCACAUGACCUAUGGGUAAGGACGGAUCUA---UC----------C
....(((((((.(((.(((((((((.(....).)))))))..)).))).)...........((((.(((((....))))).))))...)))))).....---..----------. ( -41.20)
>consensus
AACACCGUCCGAAGAAUCUGGUGGCUCACCAGUGCCGCCAUUGACUCCGCACUCGACACAUUCCGAGGGUCACAUGACCUAUGGGUAAGGACGGAUCU_GGAUCC__UG______
....((((((........((((((..........)))))).....................((((.(((((....))))).))))...))))))..................... (-28.93 = -29.32 +   0.39)

alignment

secondary structure

dotplot

Window 5

Location	1,119,395 – 1,119,500
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.04
Mean single sequence MFE	-38.02
Consensus MFE	-29.16
Energy contribution	-28.97
Covariance contribution	-0.19
Combinations/Pair	1.12
Mean z-score	-2.10
Structure conservation index	0.77
SVM decision value	0.96
SVM RNA-class probability	0.890715
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1119395 105 + 27905053
UGGCGGCACAGGUGAGCCACCAGAGUCUUCGGACGGUGUUUUCGAAAAGAGAUUCCCGCCCAGCUCUGAGACCAGAGUAAUGGGCGAGCUAAAUG---------------GUUCGUACAU
(((.(((........))).)))..(((....)))((...((((.....))))...))(((((((((((....))))))..)))))(((((....)---------------))))...... ( -40.50)
>DroVir_CAF1 46977 105 + 1
UGGCGGCACUGGCGACCCACCAGAUUCUUCGGACGGUGUUUUCGAAAACAAGUUGCCGCCCAGCUCUGAUACCAGAGUGAUGGGCGAGCUAAGUA---------------AUUCAUUUAU
(((((((((((.(((..((((....((....)).))))...)))....).)).))))(((((((((((....))))))..)))))..))))....---------------.......... ( -37.00)
>DroPse_CAF1 59612 104 + 1
UGGCGGCACUGGCGAGCCACCAGAGUCUUCGGACGGUGUUUUCGAAAACAGAUUCCCGCCCAGCUCUGAGACCAGAGUAAUGGGCGAGCUAUAGA---------------AUU-UUGUGU
((((((..(((.((((.((((...(((....)))))))..))))....)))...))((((((((((((....))))))..)))))).))))....---------------...-...... ( -38.90)
>DroGri_CAF1 60620 120 + 1
UGGCGGCACUGGCGACCCACCAGAUUCUUCGGACGGUGUUUUCGAAAAUAGAUUGCCGCCCAGCUCUGAGACCAGAGUGAUGGGUGAGCUAAGUAAUUGCAUAUAAACAUUUUUUUUUUU
.((((((((((.(((..((((....((....)).))))...)))....)))..)))))))..((((((....))))))((((.(((.((.((....)))).)))...))))......... ( -35.30)
>DroMoj_CAF1 48067 108 + 1
UGGCGGCACUGGUGAUCCACCAGAUUCUUCGGACGGUGUUUUCGAAAAUAGAUUGCCGCCCAGCUCUGAGACCAGAGUGAUGGGCGAGCUGAUUU---G---------AUUUUGAUUUUU
.((((.(.((((((...))))))..((....)).).)))).((((((.((((((((((((((((((((....))))))..)))))).)).)))))---)---------.))))))..... ( -41.20)
>DroAna_CAF1 50775 92 + 1
UGGCGGCACAGGUGAGCCACCAGAGUCCUCGGACGGUGUUUUCGAAAAUAGAUUCCCGCCCAGCUCUGACACCAGAGUGAUGGGCGAGCUAA----------------------------
(((((((((.((((...))))...(((....))).)))))................((((((((((((....))))))..)))))).)))).---------------------------- ( -35.20)
>consensus
UGGCGGCACUGGCGAGCCACCAGAGUCUUCGGACGGUGUUUUCGAAAAUAGAUUCCCGCCCAGCUCUGAGACCAGAGUGAUGGGCGAGCUAAAUA_______________AUU_AUUUAU
(((((((((((.(((.............)))..)))))))................((((((((((((....))))))..)))))).))))............................. (-29.16 = -28.97 +  -0.19)

alignment

secondary structure

dotplot

Window 6

Location	1,119,395 – 1,119,500
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.04
Mean single sequence MFE	-36.03
Consensus MFE	-28.13
Energy contribution	-27.93
Covariance contribution	-0.19
Combinations/Pair	1.12
Mean z-score	-2.60
Structure conservation index	0.78
SVM decision value	1.29
SVM RNA-class probability	0.940599
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1119395 105 - 27905053
AUGUACGAAC---------------CAUUUAGCUCGCCCAUUACUCUGGUCUCAGAGCUGGGCGGGAAUCUCUUUUCGAAAACACCGUCCGAAGACUCUGGUGGCUCACCUGUGCCGCCA
.....((((.---------------.......((((((((...(((((....))))).))))))))........))))........(((....)))...((((((.(....).)))))). ( -37.29)
>DroVir_CAF1 46977 105 - 1
AUAAAUGAAU---------------UACUUAGCUCGCCCAUCACUCUGGUAUCAGAGCUGGGCGGCAACUUGUUUUCGAAAACACCGUCCGAAGAAUCUGGUGGGUCGCCAGUGCCGCCA
..........---------------....((((((..(((......))).....))))))(((((((.....((((((...........))))))..((((((...))))))))))))). ( -34.10)
>DroPse_CAF1 59612 104 - 1
ACACAA-AAU---------------UCUAUAGCUCGCCCAUUACUCUGGUCUCAGAGCUGGGCGGGAAUCUGUUUUCGAAAACACCGUCCGAAGACUCUGGUGGCUCGCCAGUGCCGCCA
......-...---------------.......((((((((...(((((....))))).)))))))).....(((((((...........)))))))...((((((.(....).)))))). ( -38.70)
>DroGri_CAF1 60620 120 - 1
AAAAAAAAAAAUGUUUAUAUGCAAUUACUUAGCUCACCCAUCACUCUGGUCUCAGAGCUGGGCGGCAAUCUAUUUUCGAAAACACCGUCCGAAGAAUCUGGUGGGUCGCCAGUGCCGCCA
...........(((......)))......((((((..(((......))).....))))))(((((((.....((((((...........))))))..((((((...))))))))))))). ( -33.70)
>DroMoj_CAF1 48067 108 - 1
AAAAAUCAAAAU---------C---AAAUCAGCUCGCCCAUCACUCUGGUCUCAGAGCUGGGCGGCAAUCUAUUUUCGAAAACACCGUCCGAAGAAUCUGGUGGAUCACCAGUGCCGCCA
............---------.---....((((((..(((......))).....))))))(((((((.....((((((...........))))))..((((((...))))))))))))). ( -36.60)
>DroAna_CAF1 50775 92 - 1
----------------------------UUAGCUCGCCCAUCACUCUGGUGUCAGAGCUGGGCGGGAAUCUAUUUUCGAAAACACCGUCCGAGGACUCUGGUGGCUCACCUGUGCCGCCA
----------------------------....((((((((...(((((....))))).))))))))....................(((....)))...((((((.(....).)))))). ( -35.80)
>consensus
AAAAAA_AAA_______________UACUUAGCUCGCCCAUCACUCUGGUCUCAGAGCUGGGCGGCAAUCUAUUUUCGAAAACACCGUCCGAAGAAUCUGGUGGCUCACCAGUGCCGCCA
.............................((((((..(((......))).....))))))(((((.......((((((...........))))))..((((((...))))))..))))). (-28.13 = -27.93 +  -0.19)

alignment

secondary structure

dotplot

Window 7

Location	1,119,435 – 1,119,529
Length	94
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	81.21
Mean single sequence MFE	-28.35
Consensus MFE	-19.20
Energy contribution	-19.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.71
Structure conservation index	0.68
SVM decision value	1.11
SVM RNA-class probability	0.917494
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1119435 94 + 27905053
UUCGAAAAGAGAUUCCCGCCCAGCUCUGAGACCAGAGUAAUGGGCGAGCUAAAUG---GUUCGUACAUGAGUGUGGAAAGUGUAUAUAGGCAAGUUA
............((((((((((((((((....))))))..)))))(((((....)---))))..........).))))..(((......)))..... ( -26.00)
>DroSec_CAF1 53122 94 + 1
UUCGAAAAGAGAUUCCCGCCCAGCUCUGAGACCAGAGUGAUGGGCGAGCUAUAUG---GUUCGUACAUGAGUGUGGAAAGUAUAUAUAGGCAAGAUA
................((((((((((((....))))))..))))))..(((((((---.(((.((((....)))))))....)))))))........ ( -28.00)
>DroSim_CAF1 53663 94 + 1
UUCGAAAAGAGAUUCCCGCCCAGCUCUGAGACCAGAGUGAUGGGCGAGCUAUAUG---GUUCGUACAUGAGUGUGGAAAGUAUAUAUAGGCAAGAUA
................((((((((((((....))))))..))))))..(((((((---.(((.((((....)))))))....)))))))........ ( -28.00)
>DroEre_CAF1 53703 89 + 1
UUCGAAAAUAGAUUCCCGCCCAGCUCUGAGACCAGAGUGAUGGGCGAGCUAUAUG---GU----ACAUAGGUAUGUAAAGUAUAUGUAGGCGGG-UA
..............((((((((((((((....))))))..)))))...(((((((---.(----((((....))))).....)))))))..)))-.. ( -29.90)
>DroYak_CAF1 74191 90 + 1
UUCGAAAAAAGAUUCCCGCCCAGCUCUGAAACCAGAGUAAUGGGCGAGCUAAAUG---GU----ACGUAAGUGUUUUAAGUAUAUGUAGGCGGGAUA
.............(((((((((((((((....))))))..)))))..(((.....---((----((.((((...)))).)))).....))))))).. ( -29.10)
>DroMoj_CAF1 48107 91 + 1
UUCGAAAAUAGAUUGCCGCCCAGCUCUGAGACCAGAGUGAUGGGCGAGCUGAUUUGAUUUUGAUUUUUUUUUAUAGA---GAUAUAUAU---GUAUA
.((((((.((((((((((((((((((((....))))))..)))))).)).)))))).))))))..............---.........---..... ( -29.10)
>consensus
UUCGAAAAGAGAUUCCCGCCCAGCUCUGAGACCAGAGUGAUGGGCGAGCUAAAUG___GUUCGUACAUGAGUGUGGAAAGUAUAUAUAGGCAAGAUA
................((((((((((((....))))))..))))))................................................... (-19.20 = -19.20 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	1,119,435 – 1,119,529
Length	94
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	81.21
Mean single sequence MFE	-23.53
Consensus MFE	-19.48
Energy contribution	-19.65
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-3.15
Structure conservation index	0.83
SVM decision value	1.57
SVM RNA-class probability	0.964390
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1119435 94 - 27905053
UAACUUGCCUAUAUACACUUUCCACACUCAUGUACGAAC---CAUUUAGCUCGCCCAUUACUCUGGUCUCAGAGCUGGGCGGGAAUCUCUUUUCGAA
..................................((((.---.......((((((((...(((((....))))).))))))))........)))).. ( -23.69)
>DroSec_CAF1 53122 94 - 1
UAUCUUGCCUAUAUAUACUUUCCACACUCAUGUACGAAC---CAUAUAGCUCGCCCAUCACUCUGGUCUCAGAGCUGGGCGGGAAUCUCUUUUCGAA
..................................((((.---.......((((((((...(((((....))))).))))))))........)))).. ( -23.69)
>DroSim_CAF1 53663 94 - 1
UAUCUUGCCUAUAUAUACUUUCCACACUCAUGUACGAAC---CAUAUAGCUCGCCCAUCACUCUGGUCUCAGAGCUGGGCGGGAAUCUCUUUUCGAA
..................................((((.---.......((((((((...(((((....))))).))))))))........)))).. ( -23.69)
>DroEre_CAF1 53703 89 - 1
UA-CCCGCCUACAUAUACUUUACAUACCUAUGU----AC---CAUAUAGCUCGCCCAUCACUCUGGUCUCAGAGCUGGGCGGGAAUCUAUUUUCGAA
..-((((((((..((((...(((((....))))----).---..))))((((..(((......))).....)))))))))))).............. ( -25.40)
>DroYak_CAF1 74191 90 - 1
UAUCCCGCCUACAUAUACUUAAAACACUUACGU----AC---CAUUUAGCUCGCCCAUUACUCUGGUUUCAGAGCUGGGCGGGAAUCUUUUUUCGAA
..((((((((.....(((.(((.....))).))----).---.....(((((..(((......))).....)))))))))))))............. ( -24.50)
>DroMoj_CAF1 48107 91 - 1
UAUAC---AUAUAUAUC---UCUAUAAAAAAAAAUCAAAAUCAAAUCAGCUCGCCCAUCACUCUGGUCUCAGAGCUGGGCGGCAAUCUAUUUUCGAA
.....---.........---............................((.((((((...(((((....))))).)))))))).............. ( -20.20)
>consensus
UAUCCUGCCUAUAUAUACUUUCCACACUCAUGUACGAAC___CAUAUAGCUCGCCCAUCACUCUGGUCUCAGAGCUGGGCGGGAAUCUCUUUUCGAA
.................................................((((((((...(((((....))))).)))))))).............. (-19.48 = -19.65 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:40 2006