Locus 7409

Sequence ID	X_DroMel_CAF1
Location	18,475,024 – 18,475,141
Length	117
Max. P	0.974815

overview

Window 5

Location	18,475,024 – 18,475,125
Length	101
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	78.14
Mean single sequence MFE	-37.75
Consensus MFE	-24.07
Energy contribution	-24.67
Covariance contribution	0.60
Combinations/Pair	1.30
Mean z-score	-2.54
Structure conservation index	0.64
SVM decision value	1.74
SVM RNA-class probability	0.974815
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18475024 101 + 22224390
UUUUU----U--UCGCUUGCACCUCGGCGCCGUCUCCGAUUCUAGCUCAUCGCUGUGUUUCGGAUGCACAGCUGCCGGAAGUGGAAAUUGGAGUUGGAAUCGGAGUC
.....----.--.((((........))))..(.(((((((((((((((...(((((((.......)))))))..(((....)))......))))))))))))))).) ( -40.20)
>DroSec_CAF1 3708 101 + 1
UUUUU----U--UCGCGUAUACCUCGGCGCCGUCUUCGAUUCCAGCUCACUGCUGUGUUUCGGAUGCACAGCUGCCGGAAGUGGAAAUUGGAGUUGGAAUCGGAGUC
.....----.--..((((........)))).(.(((((((((((((((...(((((((.......)))))))..(((....)))......))))))))))))))).) ( -40.80)
>DroSim_CAF1 2846 101 + 1
UUUUU----U--UCGCGUAUACCUCGGCGACGUCUUCGAUUCCAGCUCACUGCUGUGUUUCGGAUGCACAGCUGCCGGAAGUGGAAAUUGGAGUUGGAAUCGGAGUC
.....----.--((((..........)))).(.(((((((((((((((...(((((((.......)))))))..(((....)))......))))))))))))))).) ( -39.90)
>DroEre_CAF1 4320 98 + 1
UUUCU-------UUGCGUAGACCUCGGCGCCGUCUCCGAUUCCAGUUCACUGCUG--UUUUGGGUGCACAGCUGCCGGAAGCGGUAAUUGGAGUUGGAAUCGGCGUC
..(((-------......)))....(((((((..((((((((((((....(((((--((((.(((((...)).))).)))))))))))))))))))))..))))))) ( -44.90)
>DroYak_CAF1 3753 103 + 1
UUUUUUUUUU--UCGCGUAGACCUCGGCGCCGUCUCCGAUUCCAGUUCACUGCUG--UUUUGGGUGCACAGCUGCCGGAAGUGGAAAUUGGAGUUGGAAUCGGCGUC
..........--.............(((((((..(((((((((((((.....(..--((((.(((((...)).))).))))..).)))))))))))))..))))))) ( -40.30)
>DroPer_CAF1 6865 95 + 1
CUCUCGAUUCAAUUGCG--AGCCUC--CGCUGUGUGUGUGUUCUGCUCUCUGCUC--U-----CUGCACAGUUGCCGGAAAUGGAAAUUAA-AUUGAAAACGAAGAC
.(((((.(((((((...--..((((--(((((((((.(.(....((.....)).)--.-----))))))))....))))...))......)-))))))..)).))). ( -20.40)
>consensus
UUUUU____U__UCGCGUAGACCUCGGCGCCGUCUCCGAUUCCAGCUCACUGCUG__UUUCGGAUGCACAGCUGCCGGAAGUGGAAAUUGGAGUUGGAAUCGGAGUC
..............((((........)))).(.(((((((((((((((...((((.............))))..(((....)))......))))))))))))))).) (-24.07 = -24.67 +   0.60)

alignment

secondary structure

dotplot

Window 6

Location	18,475,048 – 18,475,141
Length	93
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	80.64
Mean single sequence MFE	-33.97
Consensus MFE	-23.20
Energy contribution	-23.18
Covariance contribution	-0.02
Combinations/Pair	1.43
Mean z-score	-3.54
Structure conservation index	0.68
SVM decision value	1.62
SVM RNA-class probability	0.968339
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18475048 93 + 22224390
CGUCUCCGAUUCUAGCU---CAUCGCUGUGUUUCGGAUGCACAGCUGCCGGAAGUGGAAAUUGGAGUUGGAAUCGGAGUCGAAA---UGUAAAUGAAGG----
((.((((((((((((((---(...(((((((.......)))))))..(((....)))......))))))))))))))).))...---............---- ( -40.50)
>DroSec_CAF1 3732 93 + 1
CGUCUUCGAUUCCAGCU---CACUGCUGUGUUUCGGAUGCACAGCUGCCGGAAGUGGAAAUUGGAGUUGGAAUCGGAGUCGAAA---UGUAAAUGGAGA----
((.((((((((((((((---(...(((((((.......)))))))..(((....)))......))))))))))))))).))...---............---- ( -39.60)
>DroSim_CAF1 2870 93 + 1
CGUCUUCGAUUCCAGCU---CACUGCUGUGUUUCGGAUGCACAGCUGCCGGAAGUGGAAAUUGGAGUUGGAAUCGGAGUCGAAA---UGUAAAUAAUGA----
((.((((((((((((((---(...(((((((.......)))))))..(((....)))......))))))))))))))).))...---............---- ( -39.60)
>DroEre_CAF1 4343 91 + 1
CGUCUCCGAUUCCAGUU---CACUGCUG--UUUUGGGUGCACAGCUGCCGGAAGCGGUAAUUGGAGUUGGAAUCGGCGUCGAAA---UGUAAAUGAAGA----
((.(.(((((((((..(---(..(((((--((((.(((((...)).))).)))))))))....))..))))))))).).))...---............---- ( -36.40)
>DroYak_CAF1 3781 91 + 1
CGUCUCCGAUUCCAGUU---CACUGCUG--UUUUGGGUGCACAGCUGCCGGAAGUGGAAAUUGGAGUUGGAAUCGGCGUCGAAA---UGUAAAUGAAGA----
((.(.(((((((((..(---(....(..--((((.(((((...)).))).))))..)......))..))))))))).).))...---............---- ( -31.30)
>DroAna_CAF1 3897 102 + 1
AGUUUUGGAAGCCGGAUUCGUACGACUGU-UUUUGGAAGUACAGCUGCCGGAAAUGGAAAUUGAAAUUGAAACGAAAAACGAAAAAACGAAAAAAAAGAGAUG
.((((..(...((((....((((..((..-....))..)))).....)))).(((....)))....)..)))).............................. ( -16.40)
>consensus
CGUCUCCGAUUCCAGCU___CACUGCUGU_UUUCGGAUGCACAGCUGCCGGAAGUGGAAAUUGGAGUUGGAAUCGGAGUCGAAA___UGUAAAUGAAGA____
((.((((((((((((((.....(((((....(((((..((...))..)))))))))).......)))))))))))))).))...................... (-23.20 = -23.18 +  -0.02)

alignment

secondary structure

dotplot

Window 7

Location	18,475,048 – 18,475,141
Length	93
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	80.64
Mean single sequence MFE	-22.48
Consensus MFE	-15.38
Energy contribution	-16.52
Covariance contribution	1.14
Combinations/Pair	1.28
Mean z-score	-2.10
Structure conservation index	0.68
SVM decision value	0.86
SVM RNA-class probability	0.869754
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18475048 93 - 22224390
----CCUUCAUUUACA---UUUCGACUCCGAUUCCAACUCCAAUUUCCACUUCCGGCAGCUGUGCAUCCGAAACACAGCGAUG---AGCUAGAAUCGGAGACG
----............---...((.(((((((((...(((......((......))..((((((.........))))))...)---))...))))))))).)) ( -25.80)
>DroSec_CAF1 3732 93 - 1
----UCUCCAUUUACA---UUUCGACUCCGAUUCCAACUCCAAUUUCCACUUCCGGCAGCUGUGCAUCCGAAACACAGCAGUG---AGCUGGAAUCGAAGACG
----............---...((.((.((((((((.((((.....((......))..((((((.........)))))).).)---)).)))))))).)).)) ( -25.90)
>DroSim_CAF1 2870 93 - 1
----UCAUUAUUUACA---UUUCGACUCCGAUUCCAACUCCAAUUUCCACUUCCGGCAGCUGUGCAUCCGAAACACAGCAGUG---AGCUGGAAUCGAAGACG
----............---...((.((.((((((((.((((.....((......))..((((((.........)))))).).)---)).)))))))).)).)) ( -25.90)
>DroEre_CAF1 4343 91 - 1
----UCUUCAUUUACA---UUUCGACGCCGAUUCCAACUCCAAUUACCGCUUCCGGCAGCUGUGCACCCAAAA--CAGCAGUG---AACUGGAAUCGGAGACG
----............---...((.(.(((((((((..(((.....(((....)))..(((((.........)--)))).).)---)..))))))))).).)) ( -24.80)
>DroYak_CAF1 3781 91 - 1
----UCUUCAUUUACA---UUUCGACGCCGAUUCCAACUCCAAUUUCCACUUCCGGCAGCUGUGCACCCAAAA--CAGCAGUG---AACUGGAAUCGGAGACG
----............---...((.(.(((((((((..(((.....((......))..(((((.........)--)))).).)---)..))))))))).).)) ( -23.00)
>DroAna_CAF1 3897 102 - 1
CAUCUCUUUUUUUUCGUUUUUUCGUUUUUCGUUUCAAUUUCAAUUUCCAUUUCCGGCAGCUGUACUUCCAAAA-ACAGUCGUACGAAUCCGGCUUCCAAAACU
...............(((((..((.....)).....................((((.(..(((((..(.....-...)..)))))..))))).....))))). (  -9.50)
>consensus
____UCUUCAUUUACA___UUUCGACUCCGAUUCCAACUCCAAUUUCCACUUCCGGCAGCUGUGCAUCCAAAA_ACAGCAGUG___AGCUGGAAUCGAAGACG
.........................(((((((((((..........((......))..(((((...........)))))..........)))))))))))... (-15.38 = -16.52 +   1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:11 2006