Locus 5154

Sequence ID	3L_DroMel_CAF1
Location	14,158,983 – 14,159,219
Length	236
Max. P	0.962328

overview

Window 1

Location	14,158,983 – 14,159,080
Length	97
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	91.94
Mean single sequence MFE	-21.50
Consensus MFE	-17.28
Energy contribution	-17.36
Covariance contribution	0.08
Combinations/Pair	1.10
Mean z-score	-1.51
Structure conservation index	0.80
SVM decision value	0.31
SVM RNA-class probability	0.683964
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14158983 97 - 23771897
GCAUUUGAAUGCAUUUCAAUUUGAGUCGCUCAUUCAGUGAGUCGUUCGAUCAACGAGUUUUUUUUU-------CAGGUUGUUGUUUAAACCAAUUAAAUGUCAA
((((((((.((...........((.(((((.....))))).))(((..(.((((((.((.......-------.)).)))))).)..))))).))))))))... ( -20.40)
>DroSec_CAF1 156671 94 - 1
GCAUUUGAAUGCAUUUCCAUUUGAGUCGCUCAUUCAGUGAGUCGUUCGAUCAACGAGUUU---UUU-------CAGGUUGUUGUUUAAACCAAUUAAAUGUCAA
((((((((.((...........((.(((((.....))))).))(((..(.((((((.((.---...-------.)).)))))).)..))))).))))))))... ( -20.40)
>DroSim_CAF1 159766 94 - 1
GCAUUUGAAUGCAUUUCCAUUUGAGUCGCUCAUUCAGUGAGUCGUUCGAUCAACGAGUUU---UUU-------CAGGUUGUUGUUUAAACCAAUUAAAUGUCAA
((((((((.((...........((.(((((.....))))).))(((..(.((((((.((.---...-------.)).)))))).)..))))).))))))))... ( -20.40)
>DroEre_CAF1 157529 94 - 1
GCAUUUGAAUGCAUUUCCAUUUGAGUCGCUCACUCAGUGGGUCGUUCGAUCAACGAGUUU---UUU-------CAGCUCGUUGUUUAAACCAAUUAAAUGUCAA
((((((((.((....((((((.((((.....))))))))))..(((..(.(((((((((.---...-------.))))))))).)..))))).))))))))... ( -28.00)
>DroYak_CAF1 164209 98 - 1
GCAUUUGAAUGCAUUUCCAUUUGAGUCGCUCAUUCAGUGGGUCGUUCGAUCAACGAGUUU---UUUUUUUGUUCAAC---UUGUUUAAACCAAUUAAAUGUCAA
((((((((.((.........(((((..((((((...))))))..)))))..((((((((.---...........)))---))))).....)).))))))))... ( -18.30)
>consensus
GCAUUUGAAUGCAUUUCCAUUUGAGUCGCUCAUUCAGUGAGUCGUUCGAUCAACGAGUUU___UUU_______CAGGUUGUUGUUUAAACCAAUUAAAUGUCAA
((((((((.((...........((.(((((.....))))).))(((..(.((((((.((...............)).)))))).)..))))).))))))))... (-17.28 = -17.36 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	14,159,015 – 14,159,113
Length	98
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	95.69
Mean single sequence MFE	-21.38
Consensus MFE	-19.14
Energy contribution	-19.10
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.65
Structure conservation index	0.90
SVM decision value	1.54
SVM RNA-class probability	0.962328
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14159015 98 + 23771897
AAAAAAAACUCGUUGAUCGAACGACUCACUGAAUGAGCGACUCAAAUUGAAAUGCAUUCAAAUGCCAUUCCAUCAAACUGGGUCAAAUGCCGCUU---CUU
.........(((((.....)))))((((.....)))).((((((..(((((((((((....))).))))...))))..))))))...........---... ( -17.60)
>DroSec_CAF1 156703 95 + 1
AA---AAACUCGUUGAUCGAACGACUCACUGAAUGAGCGACUCAAAUGGAAAUGCAUUCAAAUGCCAUUCCAUCAAACUGGGUCAAAUGCCGCUU---CUU
..---....(((((.....)))))((((.....)))).((((((.((((((..((((....))))..)))))).....))))))...........---... ( -20.40)
>DroSim_CAF1 159798 95 + 1
AA---AAACUCGUUGAUCGAACGACUCACUGAAUGAGCGACUCAAAUGGAAAUGCAUUCAAAUGCCAUUCCAUCAAACUGGGUCAAAUGCCGCUU---CUU
..---....(((((.....)))))((((.....)))).((((((.((((((..((((....))))..)))))).....))))))...........---... ( -20.40)
>DroEre_CAF1 157561 95 + 1
AA---AAACUCGUUGAUCGAACGACCCACUGAGUGAGCGACUCAAAUGGAAAUGCAUUCAAAUGCCAUUCCAUCAAACUGGGUCAAAUGCCGCUU---CUU
..---....(((.....)))..((((((.(((((.....))))).((((((..((((....))))..)))))).....))))))...........---... ( -24.50)
>DroYak_CAF1 164245 98 + 1
AA---AAACUCGUUGAUCGAACGACCCACUGAAUGAGCGACUCAAAUGGAAAUGCAUUCAAAUGCCAUUCCAUCAAACUGGGUCGAAUGCCGCUUCUUCUU
..---....(((.....))).(((((((.(((.((((...))))..(((((..((((....))))..))))))))...)))))))................ ( -24.00)
>consensus
AA___AAACUCGUUGAUCGAACGACUCACUGAAUGAGCGACUCAAAUGGAAAUGCAUUCAAAUGCCAUUCCAUCAAACUGGGUCAAAUGCCGCUU___CUU
.........(((.....)))..((((((.(((.((((...))))..(((((..((((....))))..))))))))...))))))................. (-19.14 = -19.10 +  -0.04)

alignment

secondary structure

dotplot

Window 3

Location	14,159,015 – 14,159,113
Length	98
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	95.69
Mean single sequence MFE	-26.46
Consensus MFE	-22.24
Energy contribution	-22.20
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.38
Structure conservation index	0.84
SVM decision value	0.08
SVM RNA-class probability	0.575077
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14159015 98 - 23771897
AAG---AAGCGGCAUUUGACCCAGUUUGAUGGAAUGGCAUUUGAAUGCAUUUCAAUUUGAGUCGCUCAUUCAGUGAGUCGUUCGAUCAACGAGUUUUUUUU
(((---((((((........)).(((.(((.(((((((..(((((((...(((.....))).....)))))))...))))))).))))))..))))))).. ( -24.80)
>DroSec_CAF1 156703 95 - 1
AAG---AAGCGGCAUUUGACCCAGUUUGAUGGAAUGGCAUUUGAAUGCAUUUCCAUUUGAGUCGCUCAUUCAGUGAGUCGUUCGAUCAACGAGUUU---UU
.((---((((((........)).(((.(((.(((((((.((..((((......))))..))(((((.....)))))))))))).))))))..))))---)) ( -25.30)
>DroSim_CAF1 159798 95 - 1
AAG---AAGCGGCAUUUGACCCAGUUUGAUGGAAUGGCAUUUGAAUGCAUUUCCAUUUGAGUCGCUCAUUCAGUGAGUCGUUCGAUCAACGAGUUU---UU
.((---((((((........)).(((.(((.(((((((.((..((((......))))..))(((((.....)))))))))))).))))))..))))---)) ( -25.30)
>DroEre_CAF1 157561 95 - 1
AAG---AAGCGGCAUUUGACCCAGUUUGAUGGAAUGGCAUUUGAAUGCAUUUCCAUUUGAGUCGCUCACUCAGUGGGUCGUUCGAUCAACGAGUUU---UU
.((---((((.......((((((....(((((((..((((....))))..)))))))(((((.....))))).))))))..(((.....)))))))---)) ( -28.90)
>DroYak_CAF1 164245 98 - 1
AAGAAGAAGCGGCAUUCGACCCAGUUUGAUGGAAUGGCAUUUGAAUGCAUUUCCAUUUGAGUCGCUCAUUCAGUGGGUCGUUCGAUCAACGAGUUU---UU
....((((((......(((((((....(((((((..((((....))))..)))))))(((((.....))))).))))))).(((.....)))))))---)) ( -28.00)
>consensus
AAG___AAGCGGCAUUUGACCCAGUUUGAUGGAAUGGCAUUUGAAUGCAUUUCCAUUUGAGUCGCUCAUUCAGUGAGUCGUUCGAUCAACGAGUUU___UU
......((((((........)).(((.(((.(((((((.((..((((......))))..))(((((.....)))))))))))).))))))..))))..... (-22.24 = -22.20 +  -0.04)

alignment

secondary structure

dotplot

Window 4

Location	14,159,113 – 14,159,219
Length	106
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	87.69
Mean single sequence MFE	-32.28
Consensus MFE	-19.08
Energy contribution	-19.28
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.91
Structure conservation index	0.59
SVM decision value	-0.05
SVM RNA-class probability	0.508865
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14159113 106 - 23771897
GAGUGUAUACAGAAAAGU-AUGGAGUAAACUUAAUUGAUGGCUUC------UUCUUCAUUUUGGUGCAUUGAACCGGCGGCACAGGUGGAAGAAGAGGAAGCAGAGGAAGUUG
.(.(.(((((......))-))).).).(((((..((....(((((------((((((.(((..((((............))))....))).))))))))))).))..))))). ( -29.20)
>DroSec_CAF1 156798 106 - 1
GCGUGUAUACAGAAAGGU-AUAAAGUGAACUUAAUUGCUGUCUUC------UUCUUCAUUUUGGUGCAUUGAACCGGCGGCACAGGUGGAAGAAGAGGAAGCAGAGGAAGUUG
((...(((((......))-)))..)).(((((..(((((.(((((------((((((......((((............)))).....))))))))))))))))...))))). ( -33.00)
>DroSim_CAF1 159893 106 - 1
GCGUGUAUACAGAAAGGU-AUAAAGUAAACUUUAUUGAUGGCUUC------UUCUUCAUUUUGGUGCAUUGAACCGGUGGCACAGGUGGAAGAAGAGGAAGCAGAGGAAGUUG
((...(((((......))-)))..)).((((((.((....(((((------((((((.(((..((((((((...)))).))))....))).))))))))))).)).)))))). ( -31.20)
>DroEre_CAF1 157656 109 - 1
GAGUGUAAAAC-AGUUGUAGUAAAGGAAACUUAAUUGAUGGCUUCUUC---UUCUUCAUUUCGGUGCAUUGAACCGGCGGCACAGGUAGAAGAAGAGGAAGCAGAGGAAGUUG
..........(-(....((((.(((....))).)))).))((((((((---((((((...(((((.......)))))..((....)).))))))))))))))........... ( -33.20)
>DroYak_CAF1 164343 112 - 1
UAGUGUAUACAAAGUAGU-GUAAAGAAAACUUAAUUGGUGGCUUCUUCUUCUUCUUCAUUUUGGUGCAUUGAACCGGCGGCACAGGUGGAAGAAGAGGAAGCAGAGGAAGUUG
.....(((((......))-))).....(((((..((....(((((((((((((((...((.((.(((.........))).)).))..))))))))))))))).))..))))). ( -34.80)
>consensus
GAGUGUAUACAGAAAAGU_AUAAAGUAAACUUAAUUGAUGGCUUC______UUCUUCAUUUUGGUGCAUUGAACCGGCGGCACAGGUGGAAGAAGAGGAAGCAGAGGAAGUUG
...........................(((((..((....(((((......((((((......((((............)))).....))))))...))))).))..))))). (-19.08 = -19.28 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:10 2006