Locus 3380

Sequence ID	X_DroMel_CAF1
Location	9,000,108 – 9,000,301
Length	193
Max. P	0.991213

overview

Window 3

Location	9,000,108 – 9,000,225
Length	117
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	83.87
Mean single sequence MFE	-37.27
Consensus MFE	-33.05
Energy contribution	-33.12
Covariance contribution	0.06
Combinations/Pair	1.05
Mean z-score	-2.54
Structure conservation index	0.89
SVM decision value	2.25
SVM RNA-class probability	0.991213
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9000108 117 - 22224390
UCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGUCCAAACUUUGGCUCCCAGCGAUAUCCAUCCGUGUAUAUCCGUCAAGAGUCCACGACACAGCACAAUCGUAUCCUGGCCAA
....((((((((((((((....)))))).))...((..........(((((...(((((((.((....)).)))).)))...))))).((((..........))))..)).)))))) ( -38.90)
>DroSec_CAF1 799 102 - 1
UCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGUCCAAACUUUGGCUCCCCGCCAUAUUCAUCCGUGUAUAUCCGUCAAGAGU---------------AUCGUAUCCUGGCCAG
.....(((((((((((((....)))))).))..(((.........((((.....)))).......)))..................---------------..........))))). ( -34.89)
>DroEre_CAF1 858 113 - 1
UCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGUCCUAAUUUUGGCUCCCCGCCAUAUCCACCCGUGUAUAUCAGUC-AGAGUCCGC-ACAUUGCC--CACAAAUCCUGGCCAA
....((((((((((((((....)))))).))...(((........((((.....)))).........((((...((....-.))....))-))...)))--..........)))))) ( -38.40)
>DroYak_CAF1 839 109 - 1
UCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGUCCUAACUUUGGCUCCCCGCCACAACCACCCGUGUAUAUCCUCC-AGAGUCCAC-ACA----C--AACAUAUCCUGGCCAA
....((((((((((((((....)))))).))...((.....(((((((........(((........)))........))-)))))))..-...----.--..........)))))) ( -36.89)
>consensus
UCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGUCCAAACUUUGGCUCCCCGCCAUAUCCACCCGUGUAUAUCCGUC_AGAGUCCAC_ACA____C__AACAUAUCCUGGCCAA
....((((((((((((((....)))))).))..(((.........((((.....)))).......)))...........................................)))))) (-33.05 = -33.12 +   0.06)

alignment

secondary structure

dotplot

Window 4

Location	9,000,148 – 9,000,261
Length	113
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	92.48
Mean single sequence MFE	-40.86
Consensus MFE	-36.66
Energy contribution	-37.85
Covariance contribution	1.19
Combinations/Pair	1.14
Mean z-score	-1.98
Structure conservation index	0.90
SVM decision value	1.24
SVM RNA-class probability	0.934578
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9000148 113 + 22224390
GGAUAUACACGGAUGGAUAUCGCUGGGAGCCAAAGUUUGGACCGAUGCACAGCGCCGAAGCGCUGGCGGCCAACUGACGAGGAACUUUGGUUCGUGGUCAUAACGAUAACGAG
.........((.((.(.(((.((((.((((((((((((((.(((.....((((((....)))))).)))))..((....)))))))))))))).)))).))).).))..)).. ( -40.00)
>DroSec_CAF1 824 113 + 1
GGAUAUACACGGAUGAAUAUGGCGGGGAGCCAAAGUUUGGACCGAUGCACAGCGCCGAAGCGCUGGCGGCCAACUGACGAGGAACUUUGGUUCGUCGUCACAACGAUAACGAG
.........((........((((((.((((((((((((((.(((.....((((((....)))))).)))))..((....)))))))))))))).)))))).........)).. ( -43.33)
>DroEre_CAF1 894 113 + 1
UGAUAUACACGGGUGGAUAUGGCGGGGAGCCAAAAUUAGGACCGAUGCACAGCGCCGAAGCGCUGGCGGCCAACUGACGAGGAACUUUGGUUUGGGGUCACAACGAUAACAAG
.........((..((....((((.....)))).......((((..(((.((((((....))))))))).(((((..(.(.....).)..).)))))))).)).))........ ( -32.60)
>DroYak_CAF1 871 113 + 1
GGAUAUACACGGGUGGUUGUGGCGGGGAGCCAAAGUUAGGACCGAUGCACAGCGCCGAAGCGCUGGCGGCCAACUGACAAGGAACUUUGGUUCGUGGUUACAACGAUAACAAG
............((.((((((((.(.(((((((((((.((.(((.....((((((....)))))).)))))..((....)).))))))))))).).)))))))).))...... ( -47.50)
>consensus
GGAUAUACACGGAUGGAUAUGGCGGGGAGCCAAAGUUAGGACCGAUGCACAGCGCCGAAGCGCUGGCGGCCAACUGACGAGGAACUUUGGUUCGUGGUCACAACGAUAACAAG
............((.(.((((((((.(((((((((((.((.(((.....((((((....)))))).)))))..((....)).))))))))))).)))))))).).))...... (-36.66 = -37.85 +   1.19)

alignment

secondary structure

dotplot

Window 5

Location	9,000,148 – 9,000,261
Length	113
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	92.48
Mean single sequence MFE	-34.62
Consensus MFE	-29.74
Energy contribution	-29.43
Covariance contribution	-0.31
Combinations/Pair	1.11
Mean z-score	-1.88
Structure conservation index	0.86
SVM decision value	0.83
SVM RNA-class probability	0.861178
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9000148 113 - 22224390
CUCGUUAUCGUUAUGACCACGAACCAAAGUUCCUCGUCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGUCCAAACUUUGGCUCCCAGCGAUAUCCAUCCGUGUAUAUCC
.....(((((((.((((...((((....))))...))))(..((((((((((((....)))))).))...(((....)))..))))..))))))))................. ( -36.20)
>DroSec_CAF1 824 113 - 1
CUCGUUAUCGUUGUGACGACGAACCAAAGUUCCUCGUCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGUCCAAACUUUGGCUCCCCGCCAUAUUCAUCCGUGUAUAUCC
.............((((((.((((....)))).)))))).((((((((((((((....)))))).))...)).))))....((((.....))))................... ( -38.70)
>DroEre_CAF1 894 113 - 1
CUUGUUAUCGUUGUGACCCCAAACCAAAGUUCCUCGUCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGUCCUAAUUUUGGCUCCCCGCCAUAUCCACCCGUGUAUAUCA
.........((((.((((((((......(.....).....))))..((((((((....)))))).))...)))).))))..((((.....))))................... ( -30.20)
>DroYak_CAF1 871 113 - 1
CUUGUUAUCGUUGUAACCACGAACCAAAGUUCCUUGUCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGUCCUAACUUUGGCUCCCCGCCACAACCACCCGUGUAUAUCC
.........(((((......((.((((((((((..(((....))).((((((((....)))))).))...))....)))))))).))......)))))............... ( -33.40)
>consensus
CUCGUUAUCGUUGUGACCACGAACCAAAGUUCCUCGUCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGUCCAAACUUUGGCUCCCCGCCAUAUCCACCCGUGUAUAUCC
...(((((....)))))...((.((((((((((..(((....))).((((((((....)))))).))...))....)))))))).)).......................... (-29.74 = -29.43 +  -0.31)

alignment

secondary structure

dotplot

Window 6

Location	9,000,188 – 9,000,301
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.27
Mean single sequence MFE	-39.68
Consensus MFE	-24.98
Energy contribution	-22.98
Covariance contribution	-1.99
Combinations/Pair	1.36
Mean z-score	-1.76
Structure conservation index	0.63
SVM decision value	1.18
SVM RNA-class probability	0.926887
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9000188 113 - 22224390
AAAAGCAGGCAGCUGCCUCAAAAAAAUUUCACCUUCAACCCUCGUUAUCGUUAUGACCACGAACCAAAG----UUCCUCG---UCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGU
....(.((((....)))))...........(((.(((((...((....))...((((...((((....)----)))...)---))))))))..((((((((....)))))).))...))) ( -33.70)
>DroPse_CAF1 5813 109 - 1
AGCAGCUAGCAGCUGGCC---AAAGAU------UUCAACCCUCGCUGGGGUUUC--CUCUGGGCCACAGCGGACUCAUCGGCCACAGUUGGCUGCCAGUGCUCCGGCGCUGAGCAUCGCC
.(((((((((.(.(((((---......------...((((((....))))))((--(.(((.....))).)))......)))))).)))))))))((((((....))))))......... ( -47.10)
>DroSec_CAF1 864 113 - 1
AAAAGCAGGCAGCUGCCUCAAAAAAAUUUCACCUUCAACCCUCGUUAUCGUUGUGACGACGAACCAAAG----UUCCUCG---UCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGU
....(.((((....)))))...........(((.(((((...((....))...((((((.((((....)----))).)))---))))))))..((((((((....)))))).))...))) ( -39.30)
>DroEre_CAF1 934 113 - 1
AAAAGCAGGCAGCUGUCUCGACGAAAUUUCACGUUCAACCCUUGUUAUCGUUGUGACCCCAAACCAAAG----UUCCUCG---UCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGU
.......((((((((...(((.(((...(((((...(((....))).....))))).............----))).)))---.))))).)))((((((((....)))))).))...... ( -33.49)
>DroYak_CAF1 911 113 - 1
AAAAGCAGGCAGCUGUCGCGACGAAAUUUCACGUUCAACCCUUGUUAUCGUUGUAACCACGAACCAAAG----UUCCUUG---UCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGU
.......((((((((.(((((((((((................))).)))))))......((((....)----)))...)---.))))).)))((((((((....)))))).))...... ( -37.39)
>DroPer_CAF1 5800 109 - 1
AGCGGCUAGCAGCUGGCC---AAAGAU------UUCAACCCUCGCUGGGGUUUC--CUCUGGGCCACAGCGGACUCAUCGGCCACAGUUGGCUGCCAGUGCUCCGGCGCUGAGCAUCGCC
.(((((((((.(.(((((---......------...((((((....))))))((--(.(((.....))).)))......)))))).))))))(((((((((....)))))).))).))). ( -47.10)
>consensus
AAAAGCAGGCAGCUGCCUC_AAAAAAUUUCAC_UUCAACCCUCGUUAUCGUUGUGACCACGAACCAAAG____UUCCUCG___UCAGUUGGCCGCCAGCGCUUCGGCGCUGUGCAUCGGU
....(((((((((((............................(((((....)))))...(((..........)))........))))).)))..((((((....)))))))))...... (-24.98 = -22.98 +  -1.99)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:59 2006