Locus 3705

Sequence ID	2R_DroMel_CAF1
Location	12,289,992 – 12,290,143
Length	151
Max. P	0.860151

overview

Window 0

Location	12,289,992 – 12,290,103
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.37
Mean single sequence MFE	-40.12
Consensus MFE	-21.10
Energy contribution	-22.47
Covariance contribution	1.36
Combinations/Pair	1.21
Mean z-score	-2.01
Structure conservation index	0.53
SVM decision value	0.82
SVM RNA-class probability	0.860151
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12289992 111 - 20766785
CCCAUCACCUCCUGACCCAGCAAACUGGGUUGGAAGAGAGCCUCCGGGCAGCGGAAUCUCUCGCAGCCCAAAACGAUUUUCUGCCCAUCUGGCAGCUCAUAGGUUUCCAC---------C
......((((.(..((((((....))))))..)....((((....((((.((((......)))).))))............((((.....))))))))..))))......---------. ( -40.00)
>DroPse_CAF1 715 111 - 1
CCCAGCAUCUGCAGCCCCAGCAGCUUGGGCUGGAACAGGGCCUCCGGACAGCGGAAGCGCUCGCUUCCGAGCUUAAUCCUCUGGCCGUCGGGCAGCUGGUAGACCUCUUC---------G
.(((((.((((((((((.((...)).))))))...))))((((.(((.(((.(((...(((((....)))))....))).))).)))..)))).)))))...........---------. ( -46.70)
>DroEre_CAF1 2118 111 - 1
CCCAUCACCUCCUGACCCAGCAAACUGGGCUGGAAGAGAGCCUCCGGGCAGCGGAAUCUCUCGCUGCCCAAAACGAUUUUCUGGCCAUCCGGCAGCUCAUAGGUAUCCUC---------C
......((((((.(.(((((....)))))).)))...((((....(((((((((......)))))))))..............(((....))).))))...)))......---------. ( -43.50)
>DroYak_CAF1 895 111 - 1
CCCAUCACCUCCUGACCCAGCAAACUGGGCUGGAAGAGAGCCUCCGGACAGCGGAAUCUCUCGCUGCCCAAAACGAUUUUCUGGCCAUCUGGCAGCUCAUAGGUAUCCUC---------C
......((((((.(.(((((....)))))).))).(((((..((((.....))))..)))))((((((.....((......)).......)))))).....)))......---------. ( -36.70)
>DroMoj_CAF1 2241 120 - 1
CCGGGCACUUCCAGGCCCAGCAUGUUCGGCUUGAACAGUGCCUCCGGGCAGCGGAAGCGCUCGCUGCCAAUGUUGAUGGUUGUGCCAUCAGGCAGCUCGUAGAACUCAUCGAAAUCCGAC
..(((((((..((((((.((....)).))))))...)))))))..((((.((....))))))((((((.....((((((.....))))))))))))............(((.....))). ( -49.50)
>DroAna_CAF1 2134 111 - 1
CCCAUCACCUCCUGACCUAAUAAACUGGGCUGGAACAGUGCCUCCGGACAACGGAAUCUCUCGCUGCCAAGACUGAUCUUCUGGCCAUCUGGCAAUUCGUAGACAUCUUC---------U
.....(((.(((.(.((((......))))).)))...)))..((((.....))))...(((((.(((((.((.((..(....)..)))))))))...)).))).......---------. ( -24.30)
>consensus
CCCAUCACCUCCUGACCCAGCAAACUGGGCUGGAACAGAGCCUCCGGACAGCGGAAUCUCUCGCUGCCCAAAACGAUUUUCUGGCCAUCUGGCAGCUCAUAGAUAUCCUC_________C
.........(((.(.(((((....)))))).)))...((((....((.((((((......))))))))...............(((....))).))))...................... (-21.10 = -22.47 +   1.36)

alignment

secondary structure

dotplot

Window 1

Location	12,290,023 – 12,290,143
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	71.50
Mean single sequence MFE	-46.87
Consensus MFE	-18.50
Energy contribution	-19.20
Covariance contribution	0.70
Combinations/Pair	1.38
Mean z-score	-1.81
Structure conservation index	0.39
SVM decision value	0.06
SVM RNA-class probability	0.565397
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12290023 120 - 20766785
GUCGCAGUUGGUUAUCGAGUGAUGGGUGGCCUCGUGGAUGCCCAUCACCUCCUGACCCAGCAAACUGGGUUGGAAGAGAGCCUCCGGGCAGCGGAAUCUCUCGCAGCCCAAAACGAUUUU
((((..(..((((.(((((((((((((..((....))..)))))))).)))(..((((((....))))))..)..)).))))..)((((.((((......)))).))))....))))... ( -54.50)
>DroVir_CAF1 2256 120 - 1
AUCGCAUUUGAGUAUUGAGUUAAAGACGGCUUCGUGCAGUCCGGGCACCUCCUGGCCCAGCAUGCUGGGCUUAAAGAGCGCCUCCGGGCAACGGAAACGCUCGUUUCCAAUGUUUAUAGU
...(((((...((((.(((((......))))).)))).(((((((..((((..(((((((....)))))))....))).)..)))))))...((((((....)))))))))))....... ( -44.80)
>DroPse_CAF1 746 120 - 1
GUCGCACUGGAGGAUCGACUUGCUGGUGGCCUCGUGCACACCCAGCAUCUGCAGCCCCAGCAGCUUGGGCUGGAACAGGGCCUCCGGACAGCGGAAGCGCUCGCUUCCGAGCUUAAUCCU
...((.(((((((.......((((((((((.....)).)).))))))((((((((((.((...)).))))))...)))).)))))))....(((((((....))))))).))........ ( -51.80)
>DroGri_CAF1 1976 120 - 1
AUCACAUUUGAGUAUCGAAUUGUAGAUGUCCUCAUGGACACCGGGCACCUCCAAGCCGAGCAUGCUGGGCUUGAAGAGUGCCUCCGGACAACGGAAACGUUCGCUGCCCACAUUAAUUGU
........((.(((.((((((((...(((((....)))))((((((((((.((((((.((....)).)))))).)).))))..))))))))((....)))))).))).)).......... ( -45.00)
>DroMoj_CAF1 2281 120 - 1
GUCGCAUUUCUGUAUCGAAUUGUAGACCGCCUCGUGCAGGCCGGGCACUUCCAGGCCCAGCAUGUUCGGCUUGAACAGUGCCUCCGGGCAGCGGAAGCGCUCGCUGCCAAUGUUGAUGGU
((((((.(((......))).))).))).((((((.(((((..(((((((..((((((.((....)).))))))...))))))))).((((((((......))))))))..)))))).))) ( -46.70)
>DroAna_CAF1 2165 119 - 1
GUCGCAGUG-GAGGAGGACUGGUAAGUGGCCUCGUGGAUGCCCAUCACCUCCUGACCUAAUAAACUGGGCUGGAACAGUGCCUCCGGACAACGGAAUCUCUCGCUGCCAAGACUGAUCUU
(((((((((-..(((((((((....(.(((.((...)).))))......(((.(.((((......))))).))).)))).))((((.....)))).)))..))))))...)))....... ( -38.40)
>consensus
GUCGCAUUUGAGUAUCGAAUUGUAGAUGGCCUCGUGCACGCCCAGCACCUCCAGGCCCAGCAUGCUGGGCUGGAACAGUGCCUCCGGACAACGGAAACGCUCGCUGCCAAGAUUGAUCGU
...((......................(((((.((((.......))))...(((((((((....)))))))))...)).)))((((.....)))).......))................ (-18.50 = -19.20 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:20 2006