Locus 1768

Sequence ID	X_DroMel_CAF1
Location	4,883,096 – 4,883,229
Length	133
Max. P	0.989919

overview

Window 1

Location	4,883,096 – 4,883,208
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.28
Mean single sequence MFE	-26.55
Consensus MFE	-17.16
Energy contribution	-18.72
Covariance contribution	1.56
Combinations/Pair	1.04
Mean z-score	-2.09
Structure conservation index	0.65
SVM decision value	0.08
SVM RNA-class probability	0.574936
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4883096 112 - 22224390
UAAUCACAACAAAAAAGAGUCAGUACAGUA-------CUGAGUACUGAGUACUGAGCUCUGUGGGGUUCUUGUUU-UUUUGUUAUCUUAUUCGACUAAUACUUGUUCUUUUUCUACAAAA
.......(((((((((((.(((((((....-------....))))))).)...((((((....))))))...)))-)))))))..................................... ( -22.40)
>DroSim_CAF1 35493 120 - 1
CAAUCACAACAAAAAAGAGCCAGUACAGUACAGUACACUGAGUACUGAGUACUGAGCUCUGUGGGUUUCUUGUUUUUUUUGUUAUCUUAUUCGACUAAUACUUGUUCUUUUUCUACAAAA
.......(((((((((((((((((((....((((((.....)))))).)))))).)))))(..((...))..)..))))))))..................................... ( -26.30)
>DroEre_CAF1 37213 103 - 1
CAAUCACAACAAA-AAGAGCAAGUACAG--------------UACGGAGUACUGAGCUCUGUGGGGUUCUUGUUU--UUUGUUAUCUUAUUCGACUAAUACUUGUUCUUUUUCUACAAAA
..........(((-(((((((((((.((--------------(((((((.((.((((((....))))))..)).)--)))))...........)))..))))))))))))))........ ( -24.80)
>DroYak_CAF1 35077 117 - 1
CAAUCACAACAAA-AAGAGCAAGUACAGUACUGAGUACUCAGUACGGAGUACUGAGCUCUGUGGGGUUCUUGUUU--UUUGUUAUCUUAUUCGACUAAUACUUGUUCUUUUUCUACAAAA
..........(((-(((((((((((..(((((((....)))))))((((.((.((((((....))))))..)).)--)))..................))))))))))))))........ ( -32.70)
>consensus
CAAUCACAACAAA_AAGAGCAAGUACAGUA_______CUGAGUACGGAGUACUGAGCUCUGUGGGGUUCUUGUUU__UUUGUUAUCUUAUUCGACUAAUACUUGUUCUUUUUCUACAAAA
...........((((((((((((((...............(((((...)))))((((((....)))))).............................))))))))))))))........ (-17.16 = -18.72 +   1.56)

alignment

secondary structure

dotplot

Window 2

Location	4,883,136 – 4,883,229
Length	93
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	82.74
Mean single sequence MFE	-28.43
Consensus MFE	-18.33
Energy contribution	-20.20
Covariance contribution	1.87
Combinations/Pair	1.03
Mean z-score	-3.16
Structure conservation index	0.64
SVM decision value	2.19
SVM RNA-class probability	0.989919
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4883136 93 + 22224390
AAAA-AAACAAGAACCCCACAGAGCUCAGUACUCAGUACUCAG-------UACUGUACUGACUCUUUUUUGUUGUGAUUACCAGUUGUUGUUGGGAUUACG
....-.((((((((......((((.(((((((..(((((...)-------)))))))))))))))))))))))((((((.((((......)))))))))). ( -27.40)
>DroSim_CAF1 35533 101 + 1
AAAAAAAACAAGAAACCCACAGAGCUCAGUACUCAGUACUCAGUGUACUGUACUGUACUGGCUCUUUUUUGUUGUGAUUGCCAGUAGUUGUUGCGAUUACG
......((((((((......(((((.((((((.((((((.....))))))....)))))))))))))))))))((((((((...........)))))))). ( -35.40)
>DroEre_CAF1 37253 81 + 1
AAA--AAACAAGAACCCCACAGAGCUCAGUACUCCGUA--------------CUGUACUUGCUCUU-UUUGUUGUGAUUGCCAGUU---GUUGGGAUUACG
...--.(((((((.......(((((..(((((......--------------..))))).))))))-))))))((((((.((((..---.)))))))))). ( -20.71)
>DroYak_CAF1 35117 95 + 1
AAA--AAACAAGAACCCCACAGAGCUCAGUACUCCGUACUGAGUACUCAGUACUGUACUUGCUCUU-UUUGUUGUGAUUGCCAGUA---GUUGGGAUUACG
...--.(((((((.......(((((..(((((...(((((((....))))))).))))).))))))-))))))((((((.((((..---.)))))))))). ( -30.21)
>consensus
AAA__AAACAAGAACCCCACAGAGCUCAGUACUCAGUACUCAG_______UACUGUACUGGCUCUU_UUUGUUGUGAUUGCCAGUA___GUUGGGAUUACG
......((((((((......((((.(((((((...((((..........)))).)))))))))))))))))))((((((.((((......)))))))))). (-18.33 = -20.20 +   1.87)

alignment

secondary structure

dotplot

Window 3

Location	4,883,136 – 4,883,229
Length	93
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	82.74
Mean single sequence MFE	-25.71
Consensus MFE	-15.90
Energy contribution	-17.52
Covariance contribution	1.63
Combinations/Pair	1.04
Mean z-score	-2.30
Structure conservation index	0.62
SVM decision value	0.81
SVM RNA-class probability	0.856633
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4883136 93 - 22224390
CGUAAUCCCAACAACAACUGGUAAUCACAACAAAAAAGAGUCAGUACAGUA-------CUGAGUACUGAGUACUGAGCUCUGUGGGGUUCUUGUUU-UUUU
.(.(((((((........((.......)).......(((((((((((((((-------(...)))))..))))))).)))).))))))))......-.... ( -24.10)
>DroSim_CAF1 35533 101 - 1
CGUAAUCGCAACAACUACUGGCAAUCACAACAAAAAAGAGCCAGUACAGUACAGUACACUGAGUACUGAGUACUGAGCUCUGUGGGUUUCUUGUUUUUUUU
.........(((((..(((.(((..............((((((((((....((((((.....)))))).)))))).))))))).)))...)))))...... ( -26.33)
>DroEre_CAF1 37253 81 - 1
CGUAAUCCCAAC---AACUGGCAAUCACAACAAA-AAGAGCAAGUACAG--------------UACGGAGUACUGAGCUCUGUGGGGUUCUUGUUU--UUU
.......(((..---...)))............(-(((((((((.((..--------------((((((((.....))))))))..)).)))))))--))) ( -22.10)
>DroYak_CAF1 35117 95 - 1
CGUAAUCCCAAC---UACUGGCAAUCACAACAAA-AAGAGCAAGUACAGUACUGAGUACUCAGUACGGAGUACUGAGCUCUGUGGGGUUCUUGUUU--UUU
.(.(((((((..---...((.......)).....-.(((((.(((((.(((((((....)))))))...)))))..))))).))))))))......--... ( -30.30)
>consensus
CGUAAUCCCAAC___AACUGGCAAUCACAACAAA_AAGAGCAAGUACAGUA_______CUGAGUACGGAGUACUGAGCUCUGUGGGGUUCUUGUUU__UUU
.(.(((((((........((.......)).......(((((((((((.((((..........))))...)))))).))))).))))))))........... (-15.90 = -17.52 +   1.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:29 2006