Locus 2809

Sequence ID	2L_DroMel_CAF1
Location	7,998,741 – 7,998,890
Length	149
Max. P	0.997641

overview

Window 2

Location	7,998,741 – 7,998,854
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	68.21
Mean single sequence MFE	-32.45
Consensus MFE	-13.15
Energy contribution	-12.87
Covariance contribution	-0.28
Combinations/Pair	1.29
Mean z-score	-1.90
Structure conservation index	0.41
SVM decision value	0.69
SVM RNA-class probability	0.823079
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7998741 113 - 22407834
ACUAAAUAUAGCCAUACAAUACGCACAGCGGAGACGCACAC-CAGGGUGCAUGACUGUGCUAGGCAUUGAGCUGUA---ACUCU-AGCUACAUG--CUAUCUGGCAACGCUGGCUUUUAA
.........(((((........((((((((....)((((..-....))))..).))))))..(((((..(((((..---....)-))))..)))--))....(....)..)))))..... ( -34.50)
>DroSec_CAF1 11041 99 - 1
ACUAAAUAUAGCCAUAAAACAGGCACAGCGGAGACGCACAU-CAGGGUAUAUGACUCUGCU--------------A---ACUAU-AGCUACAUG--UAAUCUGGCAACGCUGGGUUUUAA
..............((((((.(((...(((....)))...(-(((..((((((.....(((--------------(---....)-)))..))))--))..))))....)))..)))))). ( -27.50)
>DroSim_CAF1 9391 96 - 1
ACUAAAUAUGGCCAUAA----CGCAUAGCGGAGACACACACCCAGGGUGUGUGACUCUGCU--------------A---ACUAU-AGCUGCAUG--CAAUCUGGCAACGCUGGCUUUCAA
.........(((((...----.((.((((((((.((((((((...)))))))).)))))))--------------)---.....-.((.....)--).....(....))))))))..... ( -34.80)
>DroEre_CAF1 9785 116 - 1
ACUAGUUAUGGCCUGACCAUAUGCUCAGCGGAGACGCACAC-CACGGAGCAGUACUUUGCUAGGCCUUUCGCGGAGCAGGGUGCAAG-CCCACG--CGAUCUGGCAGCGCUGGCUUUCAA
......(((((.....)))))(((((.(((....))).(..-...))))))((((((((((..((.....))..))))))))))(((-((..((--(.........)))..))))).... ( -42.90)
>DroYak_CAF1 9618 98 - 1
ACUAGUUAUAGCCCCACAAUAUGCGCAGCGGAGACGCACAC-CGCGGUGCAUUACCUUGCUACAC--------------------AG-UCCACGCUCGAUCUGGCAACGCUGACAUUUAA
........((((........((((((.((((.(.....).)-))).))))))......))))..(--------------------((-(....(((......)))...))))........ ( -22.54)
>consensus
ACUAAAUAUAGCCAUACAAUACGCACAGCGGAGACGCACAC_CAGGGUGCAUGACUCUGCUA__C__________A___ACUAU_AGCUACAUG__CAAUCUGGCAACGCUGGCUUUUAA
........((((..........((((.(((....))).(......))))).......(((((.......................................)))))..))))........ (-13.15 = -12.87 +  -0.28)

alignment

secondary structure

dotplot

Window 3

Location	7,998,778 – 7,998,890
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	72.07
Mean single sequence MFE	-31.72
Consensus MFE	-14.66
Energy contribution	-15.10
Covariance contribution	0.44
Combinations/Pair	1.22
Mean z-score	-2.46
Structure conservation index	0.46
SVM decision value	2.61
SVM RNA-class probability	0.995719
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7998778 112 + 22407834
U---UACAGCUCAAUGCCUAGCACAGUCAUGCACCCUG-GUGUGCGUCUCCGCUGUGCGUAUUGUAUGGCUAUAUUUAGUACAUUUUCAGUGCCACCACAACAUAUGGCAC----AAUAA
.---..((...((((((...(((((((.((((((....-..))))))....)))))))))))))..))((((....)))).........((((((..........))))))----..... ( -33.30)
>DroSec_CAF1 11078 98 + 1
U---U--------------AGCAGAGUCAUAUACCCUG-AUGUGCGUCUCCGCUGUGCCUGUUUUAUGGCUAUAUUUAGUACAUUUUGAGUGCCACCCCAACAUAUGGCAC----AAUAA
.---.--------------(((.(((.(((((......-)))))...))).)))(((((((((...((((...((((((......))))))))))....))))...)))))----..... ( -24.60)
>DroSim_CAF1 9428 94 + 1
U---U--------------AGCAGAGUCACACACCCUGGGUGUGUGUCUCCGCUAUGCG----UUAUGGCCAUAUUUAGUACAUUUUCAGUGCCACC-CAACAUAUGGCAC----AAUAA
.---(--------------(((.(((.((((((((...)))))))).))).))))....----...(((((((((...((((.......))))....-....))))))).)----).... ( -32.40)
>DroEre_CAF1 9822 118 + 1
CCUGCUCCGCGAAAGGCCUAGCAAAGUACUGCUCCGUG-GUGUGCGUCUCCGCUGAGCAUAUGGUCAGGCCAUAACUAGUACAUUUCCAGUGCCUC-GCAACAUAUGGCAAAUAAAAUAA
..(((...((((..(((((..(...(((.(((((.(((-(.(.....).)))).)))))))).)..))))).......((((.......)))).))-))..(....)))).......... ( -35.60)
>DroYak_CAF1 9652 99 + 1
---------------GUGUAGCAAGGUAAUGCACCGCG-GUGUGCGUCUCCGCUGCGCAUAUUGUGGGGCUAUAACUAGUACAUUUUCAGUGCCUC-GCAACAUAUGGCAU----AAUAA
---------------((((.((.(((((.((..(((((-((((((((.......))))))))))))).((((....)))).......)).))))).-)).)))).......----..... ( -32.70)
>consensus
U___U__________G__UAGCAAAGUCAUGCACCCUG_GUGUGCGUCUCCGCUGUGCAUAUUGUAUGGCUAUAUUUAGUACAUUUUCAGUGCCACCGCAACAUAUGGCAC____AAUAA
....................(((.(((.((((((.......))))))....))).)))..........(((((((...((((.......)))).........)))))))........... (-14.66 = -15.10 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	7,998,778 – 7,998,890
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	72.07
Mean single sequence MFE	-33.94
Consensus MFE	-17.60
Energy contribution	-18.44
Covariance contribution	0.84
Combinations/Pair	1.16
Mean z-score	-2.53
Structure conservation index	0.52
SVM decision value	2.90
SVM RNA-class probability	0.997641
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7998778 112 - 22407834
UUAUU----GUGCCAUAUGUUGUGGUGGCACUGAAAAUGUACUAAAUAUAGCCAUACAAUACGCACAGCGGAGACGCACAC-CAGGGUGCAUGACUGUGCUAGGCAUUGAGCUGUA---A
.....----(((((((........)))))))...............((((((((.....((.((((((((....)((((..-....))))..).)))))))).....)).))))))---. ( -35.70)
>DroSec_CAF1 11078 98 - 1
UUAUU----GUGCCAUAUGUUGGGGUGGCACUCAAAAUGUACUAAAUAUAGCCAUAAAACAGGCACAGCGGAGACGCACAU-CAGGGUAUAUGACUCUGCU--------------A---A
....(----(((((...((((...(((((.....................)))))..))))))))))(((....)))....-((((((.....))))))..--------------.---. ( -31.00)
>DroSim_CAF1 9428 94 - 1
UUAUU----GUGCCAUAUGUUG-GGUGGCACUGAAAAUGUACUAAAUAUGGCCAUAA----CGCAUAGCGGAGACACACACCCAGGGUGUGUGACUCUGCU--------------A---A
....(----(.(((((((.(((-(...(((.(....)))).)))))))))))))...----....((((((((.((((((((...)))))))).)))))))--------------)---. ( -38.40)
>DroEre_CAF1 9822 118 - 1
UUAUUUUAUUUGCCAUAUGUUGC-GAGGCACUGGAAAUGUACUAGUUAUGGCCUGACCAUAUGCUCAGCGGAGACGCACAC-CACGGAGCAGUACUUUGCUAGGCCUUUCGCGGAGCAGG
.........((((......((((-(((((.((((....(((((...(((((.....))))).((((.(((....))).(..-...))))))))))....)))))))..)))))).)))). ( -39.20)
>DroYak_CAF1 9652 99 - 1
UUAUU----AUGCCAUAUGUUGC-GAGGCACUGAAAAUGUACUAGUUAUAGCCCCACAAUAUGCGCAGCGGAGACGCACAC-CGCGGUGCAUUACCUUGCUACAC---------------
.....----........(((.((-((((.......((((((((.((....))..........(((..(((....)))....-))))))))))).)))))).))).--------------- ( -25.40)
>consensus
UUAUU____GUGCCAUAUGUUGCGGUGGCACUGAAAAUGUACUAAAUAUAGCCAUACAAUACGCACAGCGGAGACGCACAC_CAGGGUGCAUGACUCUGCUA__C__________A___A
.........(((((((........))))))).....(((((((.......((..........))...(((....)))........)))))))............................ (-17.60 = -18.44 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:45 2006