Locus 8560

Sequence ID	3L_DroMel_CAF1
Location	22,335,674 – 22,335,847
Length	173
Max. P	0.973023

overview

Window 9

Location	22,335,674 – 22,335,790
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.75
Mean single sequence MFE	-29.24
Consensus MFE	-16.18
Energy contribution	-15.94
Covariance contribution	-0.24
Combinations/Pair	1.19
Mean z-score	-1.77
Structure conservation index	0.55
SVM decision value	-0.00
SVM RNA-class probability	0.533057
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22335674 116 + 23771897
CCCCAUACCAUCUUGCAAG---CGCGACUCUGUCUCGUAAAAGGCCAGCCACAGAAUUUGUCAUUACGCUUAGUUUUUACAGCUUCUG-AAAACCCAGAAGCAUAAUUUUUAUGGCCCGU
..(((((.......(((((---((.((((((((((.((.....)).))..)))))....)))....))))).)).......(((((((-......)))))))........)))))..... ( -25.70)
>DroPse_CAF1 32776 106 + 1
CCCUAGACUG---UGGAGGGUGGGGGGGAGUGGCU---------CUAGCCACGAAAAA--AAAUUACGCUUAGUUUUUACGGCUUCUGGAGAACCCAGAAGCAUAAUUUUUAUGGUCCAU
(((((..((.---...))..))))).((((((((.---------...)))))....((--((((((......((....)).((((((((.....)))))))).))))))))....))).. ( -37.40)
>DroSim_CAF1 3212 116 + 1
CCCCAUACCAUAUCGCAAG---CGCGACUCUGUCUCGUAAAAGGCCAGCCACAGAAUUUGUCAUUACGCUUAGUUUUUACAGCUUCUG-AAAACCCAGAAGCAUAAUUUUUAUGGCCCGU
.......(((((..(((((---((.((((((((((.((.....)).))..)))))....)))....))))).)).......(((((((-......)))))))........)))))..... ( -26.10)
>DroEre_CAF1 3228 116 + 1
CCCCAUACCAUCUCGCAAG---CGCGACUCUGCCUCAUAAAUGACCAGCCACAGAAUUUGUCAUUACGCUUAGUUUUUACAGCUUCUG-AAAACCCAGAAGCAUAAUUUUUAUGGCCCGU
..(((((.......(((((---((((....)))......((((((.((........)).))))))..)))).)).......(((((((-......)))))))........)))))..... ( -23.60)
>DroPer_CAF1 33170 105 + 1
CCCUAGACUG---UGGAAG---GGGGGGAGUGGCU---------CUAGCCACGAAAUUUGUCAUUACGCUUAGUUUUUACGGCUUCUGGAGAACCCAGAAGCAUAAUUUUUAUGGUCCAU
.....(((((---((((((---(((.(..(((((.---------...)))))((......))....).)))..........((((((((.....))))))))....)))))))))))... ( -33.40)
>consensus
CCCCAUACCAU_UUGCAAG___CGCGACUCUGGCUC_UAAA_G_CCAGCCACAGAAUUUGUCAUUACGCUUAGUUUUUACAGCUUCUG_AAAACCCAGAAGCAUAAUUUUUAUGGCCCGU
...............................................((((.((((..(((.(..((.....))..).)))(((((((.......))))))).....)))).)))).... (-16.18 = -15.94 +  -0.24)

alignment

secondary structure

dotplot

Window 0

Location	22,335,711 – 22,335,813
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.51
Mean single sequence MFE	-28.54
Consensus MFE	-16.83
Energy contribution	-17.39
Covariance contribution	0.56
Combinations/Pair	1.15
Mean z-score	-2.39
Structure conservation index	0.59
SVM decision value	1.70
SVM RNA-class probability	0.973023
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22335711 102 + 23771897
AAGGCCAGCCACAGAAUUUGUCAUUACGCUUAGUUUUUACAGCUUCUG-AAAACCCAGAAGCAUAAUUUUUAUGGCCCGUCUGGGG--------------ACCCU---CGGGCAACCCUU
..(((((.....(((((((((.(..((.....))..).)))(((((((-......)))))))..))))))..))))).(((((((.--------------...))---)))))....... ( -31.60)
>DroPse_CAF1 32808 112 + 1
----CUAGCCACGAAAAA--AAAUUACGCUUAGUUUUUACGGCUUCUGGAGAACCCAGAAGCAUAAUUUUUAUGGUCCAU--GGAAGCCUUUUUUCCCUUACCCUUCGCUGUUAACCCUU
----.((((..((((.((--((((((......((....)).((((((((.....)))))))).))))))))..(((....--(((((.....)))))...))).))))..))))...... ( -26.10)
>DroSim_CAF1 3249 102 + 1
AAGGCCAGCCACAGAAUUUGUCAUUACGCUUAGUUUUUACAGCUUCUG-AAAACCCAGAAGCAUAAUUUUUAUGGCCCGUCUGGGG--------------ACCCU---CGGGCAACCCUU
..(((((.....(((((((((.(..((.....))..).)))(((((((-......)))))))..))))))..))))).(((((((.--------------...))---)))))....... ( -31.60)
>DroEre_CAF1 3265 102 + 1
AUGACCAGCCACAGAAUUUGUCAUUACGCUUAGUUUUUACAGCUUCUG-AAAACCCAGAAGCAUAAUUUUUAUGGCCCGUCUGGGG--------------ACCCU---CGGGCAACCCUU
..(((..((((.((((..(((.(..((.....))..).)))(((((((-......))))))).....)))).))))..))).(((.--------------.((..---..))...))).. ( -29.30)
>DroPer_CAF1 33199 114 + 1
----CUAGCCACGAAAUUUGUCAUUACGCUUAGUUUUUACGGCUUCUGGAGAACCCAGAAGCAUAAUUUUUAUGGUCCAU--GGAAGCCUUUUUCCCCUUACCCUUCGCUGUUAACCCUU
----.((((..((((...(((.(..((.....))..).)))((((((((.....))))))))...........(((....--(((((....)))))....))).))))..))))...... ( -24.10)
>consensus
A_G_CCAGCCACAGAAUUUGUCAUUACGCUUAGUUUUUACAGCUUCUG_AAAACCCAGAAGCAUAAUUUUUAUGGCCCGUCUGGGG______________ACCCU___CGGGCAACCCUU
.......((((.((((..(((.(..((.....))..).)))(((((((.......))))))).....)))).))))......(((................))).....((....))... (-16.83 = -17.39 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	22,335,711 – 22,335,813
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.51
Mean single sequence MFE	-30.52
Consensus MFE	-17.97
Energy contribution	-17.81
Covariance contribution	-0.16
Combinations/Pair	1.11
Mean z-score	-1.66
Structure conservation index	0.59
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22335711 102 - 23771897
AAGGGUUGCCCG---AGGGU--------------CCCCAGACGGGCCAUAAAAAUUAUGCUUCUGGGUUUU-CAGAAGCUGUAAAAACUAAGCGUAAUGACAAAUUCUGUGGCUGGCCUU
..(((..(((..---..)))--------------.)))((.(.(((((((........((((((((....)-)))))))(((....((.....))....))).....))))))).).)). ( -30.50)
>DroPse_CAF1 32808 112 - 1
AAGGGUUAACAGCGAAGGGUAAGGGAAAAAAGGCUUCC--AUGGACCAUAAAAAUUAUGCUUCUGGGUUCUCCAGAAGCCGUAAAAACUAAGCGUAAUUU--UUUUUCGUGGCUAG----
...((((....(((((((((...((((.......))))--....)))..(((((((((((((((((.....)))))))).((....)).....)))))))--))))))))))))..---- ( -28.30)
>DroSim_CAF1 3249 102 - 1
AAGGGUUGCCCG---AGGGU--------------CCCCAGACGGGCCAUAAAAAUUAUGCUUCUGGGUUUU-CAGAAGCUGUAAAAACUAAGCGUAAUGACAAAUUCUGUGGCUGGCCUU
..(((..(((..---..)))--------------.)))((.(.(((((((........((((((((....)-)))))))(((....((.....))....))).....))))))).).)). ( -30.50)
>DroEre_CAF1 3265 102 - 1
AAGGGUUGCCCG---AGGGU--------------CCCCAGACGGGCCAUAAAAAUUAUGCUUCUGGGUUUU-CAGAAGCUGUAAAAACUAAGCGUAAUGACAAAUUCUGUGGCUGGUCAU
..(((..(((..---..)))--------------.))).(((.(((((((........((((((((....)-)))))))(((....((.....))....))).....))))))).))).. ( -35.40)
>DroPer_CAF1 33199 114 - 1
AAGGGUUAACAGCGAAGGGUAAGGGGAAAAAGGCUUCC--AUGGACCAUAAAAAUUAUGCUUCUGGGUUCUCCAGAAGCCGUAAAAACUAAGCGUAAUGACAAAUUUCGUGGCUAG----
...((((....(((...(((....((((......))))--....)))...........((((((((.....)))))))))))...)))).(((...((((......)))).)))..---- ( -27.90)
>consensus
AAGGGUUGCCCG___AGGGU______________CCCCAGACGGGCCAUAAAAAUUAUGCUUCUGGGUUUU_CAGAAGCUGUAAAAACUAAGCGUAAUGACAAAUUCUGUGGCUGG_C_U
..(((..((((.....))))...............)))...(((.((((.....(((((((((((.......))))))).))))..((.....)).............)))))))..... (-17.97 = -17.81 +  -0.16)

alignment

secondary structure

dotplot

Window 2

Location	22,335,751 – 22,335,847
Length	96
Sequences	3
Columns	100
Reading direction	forward
Mean pairwise identity	95.27
Mean single sequence MFE	-30.20
Consensus MFE	-26.40
Energy contribution	-26.73
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	0.87
SVM decision value	0.05
SVM RNA-class probability	0.560139
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22335751 96 + 23771897
AGCUUCUGAAAACCCAGAAGCAUAAUUUUUAUGGCCCGUCUGGGGACCCUCGGGCAACCCUUUGUCCCACCCACCCCCUGCUUGCAGCACUGGU----UG
.(((((((......)))))))...........((((.((((((((((....((....))....)))))...((.....))....))).)).)))----). ( -29.80)
>DroSim_CAF1 3289 100 + 1
AGCUUCUGAAAACCCAGAAGCAUAAUUUUUAUGGCCCGUCUGGGGACCCUCGGGCAACCCUUUGUCCCACCCACCCCCUGCUUGCAGCACUGGUUGGUUG
.(((((((......)))))))............(((((...((....)).)))))............((.(((.((..(((.....)))..)).))).)) ( -33.10)
>DroEre_CAF1 3305 95 + 1
AGCUUCUGAAAACCCAGAAGCAUAAUUUUUAUGGCCCGUCUGGGGACCCUCGGGCAACCCUUUGUGCCACCCACC-CCUGCUUGCAGCACUGCU----UG
.(((((((......)))))))............(((((...((....)).)))))........((((((..((..-..))..))..))))....----.. ( -27.70)
>consensus
AGCUUCUGAAAACCCAGAAGCAUAAUUUUUAUGGCCCGUCUGGGGACCCUCGGGCAACCCUUUGUCCCACCCACCCCCUGCUUGCAGCACUGGU____UG
.(((((((......)))))))............(((((...((....)).)))))...............(((....(((....)))...)))....... (-26.40 = -26.73 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:05 2006