Locus 7458

Sequence ID	3R_DroMel_CAF1
Location	19,904,212 – 19,904,359
Length	147
Max. P	0.790847

overview

Window 8

Location	19,904,212 – 19,904,322
Length	110
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	79.73
Mean single sequence MFE	-37.86
Consensus MFE	-24.57
Energy contribution	-24.90
Covariance contribution	0.33
Combinations/Pair	1.17
Mean z-score	-1.48
Structure conservation index	0.65
SVM decision value	0.22
SVM RNA-class probability	0.639674
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19904212 110 + 27905053
-AUAGCUGACCUCUGCGCU---GCCCCAAACC-CUUU--GCGCUGGCAAAUUUCAGUCCAUCACAUUUUGCAUGCAACCCGCCGAUCGGGGCUAAUGCAAUCAAGUGGGCGUGGUCA
-......((((.(.((((.---..........-....--))))............((((((......((((((....((((.....))))....))))))....))))))).)))). ( -33.46)
>DroSec_CAF1 17637 111 + 1
-AUGGCUGACCUCUGCGC----GCUCCAAAAC-CUUUUGGGGGUGGCAAAUUUCAGCCCAUCGCAUUUUGCAUGCAACCCGUCGAUCGGGGCUAAUGCAAUCAAGUGGGCGUGGUCA
-......((((.((((((----.(((((((..-..))))))))).))).......((((((......((((((....((((.....))))....))))))....))))))).)))). ( -42.70)
>DroSim_CAF1 18515 111 + 1
-AUGGCUGACCUCUGCGC----GCUCCAAACC-CUUUUGGGGGUGGCAAAUUUCAGCCCAUCGCAUUUUGCAUGCAACCCGCCGAUCGGGGCUAAUGCAAUCAAGUGGGCGUGGUCA
-......((((.((((.(----(((((.....-......))))))))).......((((((......((((((....((((.....))))....))))))....))))))).)))). ( -41.70)
>DroEre_CAF1 17965 106 + 1
-AUGGCUGACCUCUGCCCCAU---------GCCCCUU-UGGGGUGGCAAAUUUCAGCCCAUCGCAUUUUGCAUGCAACCAGCCGAUCGGGGCUAAUGCAAUCAAGUGGGCGUGGUCA
-......((((.(((((....---------(((((..-.))))))))).......((((((.((.....)).((((...((((......))))..)))).....))))))).)))). ( -40.40)
>DroYak_CAF1 18389 116 + 1
-AUGGCUGACCUCUGCCCCAAAGCUCCAAAGCUCCAGAGGAGGUGGCAAAUUUCCGUCCAUCGCAUUUUGCAUGCUACCAGCCGAUCGGGGCUAAUGCAAUCAAGUGGGCGUGGUCA
-..((((..((((((......((((....)))).)))))).(((((((.......(.....)((.....)).)))))))))))(((((.(.(((.((....))..))).).))))). ( -37.10)
>DroAna_CAF1 17952 106 + 1
CACAACCCACCUCUCCUA----GCCCCG---CCUAGU-UCGCCUGCCAAC-CUC--UUCACGGGCUUUUGCAUGCAACCCGCCUAUUGGGGCUAAUGCAAUCAAGUGGGCGUGGUCA
..................----(((.((---((((.(-(.(((((.....-...--....)))))..((((((....((((.....))))....))))))..)).)))))).))).. ( -31.80)
>consensus
_AUGGCUGACCUCUGCGC____GCUCCAAACC_CUUU_GGGGGUGGCAAAUUUCAGCCCAUCGCAUUUUGCAUGCAACCCGCCGAUCGGGGCUAAUGCAAUCAAGUGGGCGUGGUCA
.......((((.((((.............................))).......((((((......((((((....((((.....))))....))))))....))))))).)))). (-24.57 = -24.90 +   0.33)

alignment

secondary structure

dotplot

Window 9

Location	19,904,245 – 19,904,359
Length	114
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	77.80
Mean single sequence MFE	-30.48
Consensus MFE	-22.45
Energy contribution	-22.78
Covariance contribution	0.33
Combinations/Pair	1.20
Mean z-score	-1.26
Structure conservation index	0.74
SVM decision value	0.59
SVM RNA-class probability	0.790847
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19904245 114 + 27905053
CGCUGGCAAAUUUCAGUCCAUCACAUUUUGCAUGCAACCCGCCGAUCGGGGCUAAUGCAAUCAAGUGGGCGUGGUCAGCAAAUAGCUGGUAUGAACAAGAAGAAAAAAAUAACA---
.((((((........((((((......((((((....((((.....))))....))))))....))))))...))))))...................................--- ( -30.00)
>DroSec_CAF1 17671 103 + 1
GGGUGGCAAAUUUCAGCCCAUCGCAUUUUGCAUGCAACCCGUCGAUCGGGGCUAAUGCAAUCAAGUGGGCGUGGUCAGCAAAUAGCUGGUAC----------AAA-AAAUAACA---
..(((.......(((((((((......((((((....((((.....))))....))))))....)))))).)))(((((.....))))))))----------...-........--- ( -31.30)
>DroSim_CAF1 18549 104 + 1
GGGUGGCAAAUUUCAGCCCAUCGCAUUUUGCAUGCAACCCGCCGAUCGGGGCUAAUGCAAUCAAGUGGGCGUGGUCAGCAAAUAGCUGGUGC----------AAAAAAAUAACA---
.((((((........).)))))...((((((((...(((((((.((..(.((....))...)..)).)))).)))((((.....))))))))----------))))........--- ( -32.70)
>DroEre_CAF1 17994 114 + 1
GGGUGGCAAAUUUCAGCCCAUCGCAUUUUGCAUGCAACCAGCCGAUCGGGGCUAAUGCAAUCAAGUGGGCGUGGUCAGCAAAUAGCUGGUACGAGCAACAACAAAAAAAUAAAA---
..((.((.....(((((((((.((.....)).((((...((((......))))..)))).....)))))).)))(((((.....))))).....)).))...............--- ( -30.90)
>DroYak_CAF1 18428 101 + 1
AGGUGGCAAAUUUCCGUCCAUCGCAUUUUGCAUGCUACCAGCCGAUCGGGGCUAAUGCAAUCAAGUGGGCGUGGUCAGCAAAUAGCUGCUAUGAAGAACAA----------------
.(((((((.......(.....)((.....)).)))))))((((......))))...........((...(((((.((((.....)))))))))....))..---------------- ( -28.90)
>DroAna_CAF1 17984 96 + 1
GCCUGCCAAC-CUC--UUCACGGGCUUUUGCAUGCAACCCGCCUAUUGGGGCUAAUGCAAUCAAGUGGGCGUGGUCAGCCCA-----G--GC----------AAA-CAACAACAGAG
(((((.....-...--....))))).(((((..((.(((((((((((...((....)).....)))))))).)))..))...-----.--))----------)))-........... ( -29.10)
>consensus
GGGUGGCAAAUUUCAGCCCAUCGCAUUUUGCAUGCAACCCGCCGAUCGGGGCUAAUGCAAUCAAGUGGGCGUGGUCAGCAAAUAGCUGGUAC__________AAA_AAAUAACA___
...............((((((......((((((....((((.....))))....))))))....)))))).....((((.....))))............................. (-22.45 = -22.78 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:34 2006