Locus 3163

Sequence ID	3L_DroMel_CAF1
Location	9,196,796 – 9,196,909
Length	113
Max. P	0.936083

overview

Window 5

Location	9,196,796 – 9,196,909
Length	113
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	79.68
Mean single sequence MFE	-30.62
Consensus MFE	-18.21
Energy contribution	-19.30
Covariance contribution	1.09
Combinations/Pair	1.19
Mean z-score	-2.26
Structure conservation index	0.59
SVM decision value	0.93
SVM RNA-class probability	0.883609
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9196796 113 + 23771897
UGUCUUGGUUGCGGCAA-GAUUUCUGACAGUUCUGUCAACUAUUUGGGUUGCAACUUGAGCCAGACA--AUUUGCGAAACUAGAACGCCAUCAAAAUACUUGCCACAAUCAAAUAU
....(((((((.(((((-(.....(((((....)))))....(((((.((((((.(((.......))--).))))))..)))))..............)))))).))))))).... ( -32.00)
>DroSec_CAF1 50790 112 + 1
UGUCUUGGUUGCGGCAA-AAU-UCUGACAGUUCUGUCAACUAUUUGGGUUGCAACUUGAGCCAGACA--ACUUGCGAAACUAGAACGCCAUCAAAAUACUUGCCGCAAUCAAAUAU
....(((((((((((((-...-..(((((....)))))....(((((.((((((.(((.......))--).))))))..)))))...............))))))))))))).... ( -34.10)
>DroSim_CAF1 51307 112 + 1
UGUCUUGGUUGCGGCAA-AAU-UCUGACAGUUCUGUCAACUAUCUGGGUUGCAACUGGAGCCAGACA--ACUUGCGAAACUAGAACGCCAUCAAAAUACUUGCCGCAAUCAAAUAU
....(((((((((((((-...-..(((((....)))))....(((((.(((((((((....)))...--..))))))..)))))...............))))))))))))).... ( -37.20)
>DroEre_CAF1 68283 112 + 1
UGUCUUAGUUGCGGCAA-AUU-UCUGACAGUUCUGUCAACUAUUUGGGUUGCAGCUUGAGCCAGACU--ACUUGCGCAACUAGAGCGCCGUCGAAAUACUUGCCACAAUCAAAUAU
.......((((.(((((-(((-((.(((.(((((..(((....)))((((((.((..(((.....))--.)..)))))))))))))...))))))))..))))).))))....... ( -29.80)
>DroYak_CAF1 67373 114 + 1
UGUCUUGGUUGCGGCAA-AUU-UCUGACAGUUCUGUCAACUAUUUGGGUUGCAACUUGAGCCAGACAGCGCUUGCGAAACUAGAGCGCCAUCAAAAUACUUGCCACAAUCAAAUAU
....(((((((.(((((-...-..(((((....)))))..(((((.((((........)))).((..((((((.........))))))..)).))))).))))).))))))).... ( -33.00)
>DroAna_CAF1 52874 91 + 1
GGCUGCCGUUGCGGCAACACU-UCUGACACUUGUGUCACCUAUCUAGGUCUCU------------CUGC-UCUUCGAAUCUGGUU-----------CACUCGGCUCAAUCAACUAU
....((((..((((.......-...((((....))))((((....))))....------------))))-.....((((...)))-----------)...))))............ ( -17.60)
>consensus
UGUCUUGGUUGCGGCAA_AAU_UCUGACAGUUCUGUCAACUAUUUGGGUUGCAACUUGAGCCAGACA__ACUUGCGAAACUAGAACGCCAUCAAAAUACUUGCCACAAUCAAAUAU
....(((((((.(((((.......(((((....)))))....(((((..(((((.................)))))...)))))...............))))).))))))).... (-18.21 = -19.30 +   1.09)

alignment

secondary structure

dotplot

Window 6

Location	9,196,796 – 9,196,909
Length	113
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	79.68
Mean single sequence MFE	-34.15
Consensus MFE	-19.32
Energy contribution	-21.52
Covariance contribution	2.20
Combinations/Pair	1.21
Mean z-score	-2.66
Structure conservation index	0.57
SVM decision value	1.25
SVM RNA-class probability	0.936083
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9196796 113 - 23771897
AUAUUUGAUUGUGGCAAGUAUUUUGAUGGCGUUCUAGUUUCGCAAAU--UGUCUGGCUCAAGUUGCAACCCAAAUAGUUGACAGAACUGUCAGAAAUC-UUGCCGCAACCAAGACA
...((((.((((((((((.(((((..(((((((((.(((..((((.(--((.......))).))))(((.......))))))))))).))))))))))-))))))))).))))... ( -34.10)
>DroSec_CAF1 50790 112 - 1
AUAUUUGAUUGCGGCAAGUAUUUUGAUGGCGUUCUAGUUUCGCAAGU--UGUCUGGCUCAAGUUGCAACCCAAAUAGUUGACAGAACUGUCAGA-AUU-UUGCCGCAACCAAGACA
...((((.((((((((((.((((((((...(((((.(((..((((.(--((.......))).))))(((.......))))))))))).))))))-)))-))))))))).))))... ( -36.80)
>DroSim_CAF1 51307 112 - 1
AUAUUUGAUUGCGGCAAGUAUUUUGAUGGCGUUCUAGUUUCGCAAGU--UGUCUGGCUCCAGUUGCAACCCAGAUAGUUGACAGAACUGUCAGA-AUU-UUGCCGCAACCAAGACA
...((((.((((((((((.((((((((...(((((.(((.(....)(--(((((((.............))))))))..)))))))).))))))-)))-))))))))).))))... ( -38.12)
>DroEre_CAF1 68283 112 - 1
AUAUUUGAUUGUGGCAAGUAUUUCGACGGCGCUCUAGUUGCGCAAGU--AGUCUGGCUCAAGCUGCAACCCAAAUAGUUGACAGAACUGUCAGA-AAU-UUGCCGCAACUAAGACA
...((((.(((((((((((.........((((.......))))....--..((((((.....(((((((.......)))).)))....))))))-.))-))))))))).))))... ( -37.00)
>DroYak_CAF1 67373 114 - 1
AUAUUUGAUUGUGGCAAGUAUUUUGAUGGCGCUCUAGUUUCGCAAGCGCUGUCUGGCUCAAGUUGCAACCCAAAUAGUUGACAGAACUGUCAGA-AAU-UUGCCGCAACCAAGACA
...((((.(((((((((((........((((((...........)))))).((((((.....(((((((.......)))).)))....))))))-.))-))))))))).))))... ( -36.90)
>DroAna_CAF1 52874 91 - 1
AUAGUUGAUUGAGCCGAGUG-----------AACCAGAUUCGAAGA-GCAG------------AGAGACCUAGAUAGGUGACACAAGUGUCAGA-AGUGUUGCCGCAACGGCAGCC
...(((..((((..(..(..-----------..)..)..))))..)-))..------------....((((....))))((((....))))...-...(((((((...))))))). ( -22.00)
>consensus
AUAUUUGAUUGUGGCAAGUAUUUUGAUGGCGUUCUAGUUUCGCAAGU__UGUCUGGCUCAAGUUGCAACCCAAAUAGUUGACAGAACUGUCAGA_AUU_UUGCCGCAACCAAGACA
...((((.(((((((((...........(((.........)))........((((((.....(((((((.......)))).)))....)))))).....))))))))).))))... (-19.32 = -21.52 +   2.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:08 2006