Locus 5038

Sequence ID	3L_DroMel_CAF1
Location	13,798,533 – 13,798,888
Length	355
Max. P	0.999803

overview

Window 8

Location	13,798,533 – 13,798,653
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.33
Mean single sequence MFE	-34.18
Consensus MFE	-30.00
Energy contribution	-30.00
Covariance contribution	0.00
Combinations/Pair	1.07
Mean z-score	-3.08
Structure conservation index	0.88
SVM decision value	4.12
SVM RNA-class probability	0.999803
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13798533 120 + 23771897
UCUUCCUCCUCCACCUGAUGUCCUUUUUCUAGGACUUUAGCUCUUGCAGAUUCCGCACACGUGCGUGUACCUUUGCUGCCAGGUUAAUGUCCUCAAACGGACAUGUCCUCCUAGGUCCCU
............(((((((((((.(((...(((((.(((((.((.((((.......((((....)))).......)))).))))))).))))).))).)))))).......))))).... ( -33.35)
>DroSec_CAF1 35378 120 + 1
UCUUCUUCCUCCACCUGAUGUCCUUUUUCUAGGACUUUAGCUUUUGCAGAUUCCGCACACGUGCGUGUACCUUUGCUGCCAGGUUAAUGUCCUCAAACGGACAUGUCCACCCAGGUCCCU
............(((((((((((.(((...(((((.(((((((..((((.......((((....)))).......)))).))))))).))))).))).)))))).......))))).... ( -34.15)
>DroSim_CAF1 31560 120 + 1
UCUUCCUCCUCCACCUGAUGUCCUUUUUCUAGGACUUUAGCUUUUGCAGAUUCCGCACACGUGCGUGUACCUUUGCUGCCAGGUUAAUGUCCUCAAACGGACAUGUCCACCCAGGUCCCU
............(((((((((((.(((...(((((.(((((((..((((.......((((....)))).......)))).))))))).))))).))).)))))).......))))).... ( -34.15)
>DroEre_CAF1 36313 120 + 1
UCUUCCUACCCCACAUGAUGUCCUUUUUCUAGGACUUGGGCUCUUGCAGAUUCCGCACACGUGCGUGUACCUUUGCUGCCAGGUUAAUGUCCUCAAACGGACAUGUCCAACUAGGUCCCC
....((((...........(((((......)))))(((((((((.((((.......((((....)))).......)))).)))...((((((......)))))))))))).))))..... ( -34.84)
>DroYak_CAF1 34161 120 + 1
UCUACCUCCUCCACAUGAUGUCCUUUUUCUAGGACCUUAGCUCUUGCAGAUUCCGCACACGUGCGUGUACCUUUGCUGCCAGGUUAAUGUCCUCCAACGGACAUGUCCACCUGGGUCCCC
...............(((.(((((......))))).)))......(((((..(((((....)))).)....)))))..((((((..((((((......))))))....))))))...... ( -34.40)
>consensus
UCUUCCUCCUCCACCUGAUGUCCUUUUUCUAGGACUUUAGCUCUUGCAGAUUCCGCACACGUGCGUGUACCUUUGCUGCCAGGUUAAUGUCCUCAAACGGACAUGUCCACCUAGGUCCCU
............(((((..(((((......)))))....((....(((((..(((((....)))).)....))))).))..((...((((((......))))))..))...))))).... (-30.00 = -30.00 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	13,798,533 – 13,798,653
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.33
Mean single sequence MFE	-38.38
Consensus MFE	-33.86
Energy contribution	-34.26
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.35
Structure conservation index	0.88
SVM decision value	3.21
SVM RNA-class probability	0.998760
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13798533 120 - 23771897
AGGGACCUAGGAGGACAUGUCCGUUUGAGGACAUUAACCUGGCAGCAAAGGUACACGCACGUGUGCGGAAUCUGCAAGAGCUAAAGUCCUAGAAAAAGGACAUCAGGUGGAGGAGGAAGA
.....(((........((((((......))))))..(((((((((.....((((((....)))))).....))))..........(((((......)))))..)))))..)))....... ( -38.00)
>DroSec_CAF1 35378 120 - 1
AGGGACCUGGGUGGACAUGUCCGUUUGAGGACAUUAACCUGGCAGCAAAGGUACACGCACGUGUGCGGAAUCUGCAAAAGCUAAAGUCCUAGAAAAAGGACAUCAGGUGGAGGAAGAAGA
....((((((((....((((((......))))))..)))..((((.....((((((....)))))).....))))..........(((((......)))))..)))))............ ( -38.20)
>DroSim_CAF1 31560 120 - 1
AGGGACCUGGGUGGACAUGUCCGUUUGAGGACAUUAACCUGGCAGCAAAGGUACACGCACGUGUGCGGAAUCUGCAAAAGCUAAAGUCCUAGAAAAAGGACAUCAGGUGGAGGAGGAAGA
....((((((((....((((((......))))))..)))..((((.....((((((....)))))).....))))..........(((((......)))))..)))))............ ( -38.20)
>DroEre_CAF1 36313 120 - 1
GGGGACCUAGUUGGACAUGUCCGUUUGAGGACAUUAACCUGGCAGCAAAGGUACACGCACGUGUGCGGAAUCUGCAAGAGCCCAAGUCCUAGAAAAAGGACAUCAUGUGGGGUAGGAAGA
.....(((........((((((......))))))..((((.(((......((((((....))))))((..((.....))..))..(((((......)))))....))).))))))).... ( -37.60)
>DroYak_CAF1 34161 120 - 1
GGGGACCCAGGUGGACAUGUCCGUUGGAGGACAUUAACCUGGCAGCAAAGGUACACGCACGUGUGCGGAAUCUGCAAGAGCUAAGGUCCUAGAAAAAGGACAUCAUGUGGAGGAGGUAGA
(....)((((((....((((((......))))))..))))))........((((((....))))))....(((((.....(((..(((((......)))))......))).....))))) ( -39.90)
>consensus
AGGGACCUAGGUGGACAUGUCCGUUUGAGGACAUUAACCUGGCAGCAAAGGUACACGCACGUGUGCGGAAUCUGCAAGAGCUAAAGUCCUAGAAAAAGGACAUCAGGUGGAGGAGGAAGA
.....((.........((((((......))))))..(((((((((.....((((((....)))))).....))))..........(((((......)))))..))))))).......... (-33.86 = -34.26 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	13,798,573 – 13,798,692
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.62
Mean single sequence MFE	-34.30
Consensus MFE	-33.30
Energy contribution	-33.58
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-1.57
Structure conservation index	0.97
SVM decision value	2.01
SVM RNA-class probability	0.985558
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13798573 119 + 23771897
CUCUUGCAGAUUCCGCACACGUGCGUGUACCUUUGCUGCCAGGUUAAUGUCCUCAAACGGACAUGUCCUCCUAGGUCCCUGGGGUAGCCAA-ACCAGUUAGCCAGCUGCCUCACAUUCUU
.....((((.....((((((....))))......(((((((((...((((((......))))))..))).((((....))))))))))...-........))...))))........... ( -35.80)
>DroSec_CAF1 35418 119 + 1
CUUUUGCAGAUUCCGCACACGUGCGUGUACCUUUGCUGCCAGGUUAAUGUCCUCAAACGGACAUGUCCACCCAGGUCCCUAGGGUAGCCAA-ACCAGUUAGCCAGCUGCCUCACAUUCUU
.....((((....((((....)))).........((((.(.((((.((((((......))))))....((((((....)).)))).....)-))).).))))...))))........... ( -31.80)
>DroSim_CAF1 31600 119 + 1
CUUUUGCAGAUUCCGCACACGUGCGUGUACCUUUGCUGCCAGGUUAAUGUCCUCAAACGGACAUGUCCACCCAGGUCCCUAGGGUAGCCAA-ACCAGUUAGCCAGCUGCCUCACAUUCUU
.....((((....((((....)))).........((((.(.((((.((((((......))))))....((((((....)).)))).....)-))).).))))...))))........... ( -31.80)
>DroEre_CAF1 36353 120 + 1
CUCUUGCAGAUUCCGCACACGUGCGUGUACCUUUGCUGCCAGGUUAAUGUCCUCAAACGGACAUGUCCAACUAGGUCCCCAGGGUAGCCAGCACCCGUUAGCCAGCUGCCUCACAUUCUU
.....(((((..(((((....)))).)....))))).(((.((((.((((((......))))))....)))).))).....(((((((..((........))..)))))))......... ( -34.60)
>DroYak_CAF1 34201 106 + 1
CUCUUGCAGAUUCCGCACACGUGCGUGUACCUUUGCUGCCAGGUUAAUGUCCUCCAACGGACAUGUCCACCUGGGUCCCCAGGGUAGC--------------CAGCUGCCUCACAUUCUU
.....((((....((((....)))).........((((((.((...((((((......))))))..))..((((....))))))))))--------------...))))........... ( -37.50)
>consensus
CUCUUGCAGAUUCCGCACACGUGCGUGUACCUUUGCUGCCAGGUUAAUGUCCUCAAACGGACAUGUCCACCUAGGUCCCUAGGGUAGCCAA_ACCAGUUAGCCAGCUGCCUCACAUUCUU
.....((((....((((....)))).........((((((.((...((((((......))))))..))..((((....)))))))))).................))))........... (-33.30 = -33.58 +   0.28)

alignment

secondary structure

dotplot

Window 1

Location	13,798,613 – 13,798,728
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.59
Mean single sequence MFE	-37.29
Consensus MFE	-28.23
Energy contribution	-28.15
Covariance contribution	-0.08
Combinations/Pair	1.10
Mean z-score	-2.21
Structure conservation index	0.76
SVM decision value	1.12
SVM RNA-class probability	0.918257
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13798613 115 + 23771897
AGGUUAAUGUCCUCAAACGGACAUGUCCUCCUAGGUCCCUGGGGUAGCCAA-ACCAGUUAGCCAGCUGCCUCACAUUCUUUUUUUUUUUUAAUUGAGAGAGAUAGGAGACGGC----CGA
.((((.((((((......))))))(((.(((((......(((((((((...-............)))))))))..(((((((..((....))..))))))).)))))))))))----).. ( -37.76)
>DroSec_CAF1 35458 111 + 1
AGGUUAAUGUCCUCAAACGGACAUGUCCACCCAGGUCCCUAGGGUAGCCAA-ACCAGUUAGCCAGCUGCCUCACAUUCUUUU----UUUUAAUUGAGAGAGAUAGGAGACGGC----CGG
.(((((((((((......)))).((.(.((((((....)).)))).).)).-....))))))).((((.(((....((((((----((......))))))))...))).))))----... ( -36.50)
>DroSim_CAF1 31640 113 + 1
AGGUUAAUGUCCUCAAACGGACAUGUCCACCCAGGUCCCUAGGGUAGCCAA-ACCAGUUAGCCAGCUGCCUCACAUUCUUUUU--UUUUUAAUUGAGAGAGAUAGGAGACGGC----CGG
.(((((((((((......)))).((.(.((((((....)).)))).).)).-....))))))).((((.(((....(((((((--(........))))))))...))).))))----... ( -36.30)
>DroEre_CAF1 36393 111 + 1
AGGUUAAUGUCCUCAAACGGACAUGUCCAACUAGGUCCCCAGGGUAGCCAGCACCCGUUAGCCAGCUGCCUCACAUUCUUUU----UGUUAAUUGGGAGAGAUAGGAGACGGC----UG-
.((((.((((((......))))))(((...(((..(((((((((((((..((........))..))))))).(((.......----)))....)))).))..)))..))))))----).- ( -35.20)
>DroYak_CAF1 34241 102 + 1
AGGUUAAUGUCCUCCAACGGACAUGUCCACCUGGGUCCCCAGGGUAGC--------------CAGCUGCCUCACAUUCUUUU----UGUUAAUUGAGAGAGAUAGGAGAUAGGAGGCAGG
.(((((((((((......)))))).....(((((....))))).))))--------------)..(((((((....((((((----......((....))...))))))...))))))). ( -40.70)
>consensus
AGGUUAAUGUCCUCAAACGGACAUGUCCACCUAGGUCCCUAGGGUAGCCAA_ACCAGUUAGCCAGCUGCCUCACAUUCUUUU____UUUUAAUUGAGAGAGAUAGGAGACGGC____CGG
.((...((((((......))))))..))......((((((((((((((................)))))))....(((((((............))))))).)))).))).......... (-28.23 = -28.15 +  -0.08)

alignment

secondary structure

dotplot

Window 2

Location	13,798,692 – 13,798,808
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.75
Mean single sequence MFE	-31.70
Consensus MFE	-25.95
Energy contribution	-26.23
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-2.17
Structure conservation index	0.82
SVM decision value	1.83
SVM RNA-class probability	0.979036
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13798692 116 - 23771897
ACAAUUGCAGGAUGCAGUUGUAGGCAGGAUGCUGCAGAUUCGGAAGUGUAAUUAUCCCCAUAUUCCAAUCUGGUGCUCCUUCG----GCCGUCUCCUAUCUCUCUCAAUUAAAAAAAAAA
((((((((.....)))))))).(((((((.((..((((((.(((((((..........))).))))))))))..))))))...----))).............................. ( -30.60)
>DroSec_CAF1 35537 112 - 1
ACAAUUGCAGGAUGCAGUUGUAGGCAGGAUGCUGCAGAUUCGGAAGUGUAAUUAUCCCCAUAUUCCAAUCUGGUGCUCCUCCG----GCCGUCUCCUAUCUCUCUCAAUUAAAA----AA
((((((((.....)))))))).(((.(((.((..((((((.(((((((..........))).))))))))))..))...))).----)))........................----.. ( -30.80)
>DroSim_CAF1 31719 114 - 1
ACAAUUGCAGGAUGCAGUUGUAGGCAGGAUGCUGCAGAUUCGGAAGUGUAAUUAUCCCCAUAUUCCAAUCUGGUGCUCCUCCG----GCCGUCUCCUAUCUCUCUCAAUUAAAAA--AAA
((((((((.....)))))))).(((.(((.((..((((((.(((((((..........))).))))))))))..))...))).----))).........................--... ( -30.80)
>DroEre_CAF1 36473 111 - 1
ACAAUUGCAGGAUGCAGUUGUAGGCAGGAUGCUGCAGAUUCGGAAGUGUAAUUAUCCCCAUAUUCCAAUCUGGUGCUCCC-CA----GCCGUCUCCUAUCUCUCCCAAUUAACA----AA
((((((((.....)))))))).(((.(((.((..((((((.(((((((..........))).))))))))))..))))).-..----)))........................----.. ( -29.50)
>DroYak_CAF1 34307 116 - 1
ACAAUUGCAGGAUGCAGUUGUAGGCAGGAUGCUGCAGAUUCGGAAGUGUAAUUAUCCCUAUAUUCCAAUCUGGUGCGCCUCCUGCCUCCUAUCUCCUAUCUCUCUCAAUUAACA----AA
((((((((.....))))))))(((((((((((..((((((.((((.((((........))))))))))))))..)))..))))))))...........................----.. ( -36.80)
>consensus
ACAAUUGCAGGAUGCAGUUGUAGGCAGGAUGCUGCAGAUUCGGAAGUGUAAUUAUCCCCAUAUUCCAAUCUGGUGCUCCUCCG____GCCGUCUCCUAUCUCUCUCAAUUAAAA____AA
((((((((.....)))))))).(((((((.((..((((((.(((((((..........))).))))))))))..)))))).......))).............................. (-25.95 = -26.23 +   0.28)

alignment

secondary structure

dotplot

Window 3

Location	13,798,728 – 13,798,848
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.00
Mean single sequence MFE	-32.52
Consensus MFE	-30.72
Energy contribution	-30.76
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.89
Structure conservation index	0.94
SVM decision value	1.95
SVM RNA-class probability	0.983668
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13798728 120 - 23771897
UUCUCAAUUAAUUUUAAUUUCAUGUCAACACCUUCGGCCGACAAUUGCAGGAUGCAGUUGUAGGCAGGAUGCUGCAGAUUCGGAAGUGUAAUUAUCCCCAUAUUCCAAUCUGGUGCUCCU
....................................(((.((((((((.....)))))))).)))((((.((..((((((.(((((((..........))).))))))))))..)))))) ( -32.60)
>DroSec_CAF1 35569 120 - 1
UUCUCAAUUAAUUUUAAUUUCAUGUCAACACCUUCGGCCGACAAUUGCAGGAUGCAGUUGUAGGCAGGAUGCUGCAGAUUCGGAAGUGUAAUUAUCCCCAUAUUCCAAUCUGGUGCUCCU
....................................(((.((((((((.....)))))))).)))((((.((..((((((.(((((((..........))).))))))))))..)))))) ( -32.60)
>DroSim_CAF1 31753 120 - 1
UUCUCAAUUAAUUUUAAUUUCAUGUCAACACCUUCGGCCGACAAUUGCAGGAUGCAGUUGUAGGCAGGAUGCUGCAGAUUCGGAAGUGUAAUUAUCCCCAUAUUCCAAUCUGGUGCUCCU
....................................(((.((((((((.....)))))))).)))((((.((..((((((.(((((((..........))).))))))))))..)))))) ( -32.60)
>DroEre_CAF1 36504 120 - 1
UUCUCAAUUAAUUUUAAUUUCAUGUCAACACCUUCGGCCGACAAUUGCAGGAUGCAGUUGUAGGCAGGAUGCUGCAGAUUCGGAAGUGUAAUUAUCCCCAUAUUCCAAUCUGGUGCUCCC
....................................(((.((((((((.....)))))))).))).(((.((..((((((.(((((((..........))).))))))))))..))))). ( -31.70)
>DroYak_CAF1 34343 120 - 1
UUCUCAAUUAAUUUUAAUUUCAUGUCAACACCUUCGGCCGACAAUUGCAGGAUGCAGUUGUAGGCAGGAUGCUGCAGAUUCGGAAGUGUAAUUAUCCCUAUAUUCCAAUCUGGUGCGCCU
....................................(((.((((((((.....)))))))).)))(((.(((..((((((.((((.((((........))))))))))))))..)))))) ( -33.10)
>consensus
UUCUCAAUUAAUUUUAAUUUCAUGUCAACACCUUCGGCCGACAAUUGCAGGAUGCAGUUGUAGGCAGGAUGCUGCAGAUUCGGAAGUGUAAUUAUCCCCAUAUUCCAAUCUGGUGCUCCU
....................................(((.((((((((.....)))))))).))).(((.((..((((((.(((((((..........))).))))))))))..))))). (-30.72 = -30.76 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	13,798,768 – 13,798,888
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.33
Mean single sequence MFE	-31.16
Consensus MFE	-30.40
Energy contribution	-30.60
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.98
SVM decision value	1.45
SVM RNA-class probability	0.955312
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13798768 120 + 23771897
AAUCUGCAGCAUCCUGCCUACAACUGCAUCCUGCAAUUGUCGGCCGAAGGUGUUGACAUGAAAUUAAAAUUAAUUGAGAAUUCCGUGCACAUAGCAACGCAAUCGUGUCGACCAGCAACU
....(((.....((((((.((((.(((.....))).)))).)))...))).(((((((((((((((....)))))........(((((.....)).)))...))))))))))..)))... ( -32.30)
>DroSec_CAF1 35609 120 + 1
AAUCUGCAGCAUCCUGCCUACAACUGCAUCCUGCAAUUGUCGGCCGAAGGUGUUGACAUGAAAUUAAAAUUAAUUGAGAAUUCCGUACACAUAGCAACGCAAUCGUGUCGUCCAGCAACU
....(((((((.((((((.((((.(((.....))).)))).)))...)))))))((((((((((((....)))))..................((...))..))))))).....)))... ( -28.40)
>DroSim_CAF1 31793 120 + 1
AAUCUGCAGCAUCCUGCCUACAACUGCAUCCUGCAAUUGUCGGCCGAAGGUGUUGACAUGAAAUUAAAAUUAAUUGAGAAUUCCGUGCACAUAGCAACGCAAUCGUGUCGUCCAGCAACU
....(((((((.((((((.((((.(((.....))).)))).)))...)))))))((((((((((((....)))))........(((((.....)).)))...))))))).....)))... ( -31.70)
>DroEre_CAF1 36544 120 + 1
AAUCUGCAGCAUCCUGCCUACAACUGCAUCCUGCAAUUGUCGGCCGAAGGUGUUGACAUGAAAUUAAAAUUAAUUGAGAAUUCCGUGCACAUAGCAACGCAAUCGUGUCGUCCAGCAACU
....(((((((.((((((.((((.(((.....))).)))).)))...)))))))((((((((((((....)))))........(((((.....)).)))...))))))).....)))... ( -31.70)
>DroYak_CAF1 34383 120 + 1
AAUCUGCAGCAUCCUGCCUACAACUGCAUCCUGCAAUUGUCGGCCGAAGGUGUUGACAUGAAAUUAAAAUUAAUUGAGAAUUCCGUGCACAUAGCAACGCAAUCGUGUCGUCCAGCAACU
....(((((((.((((((.((((.(((.....))).)))).)))...)))))))((((((((((((....)))))........(((((.....)).)))...))))))).....)))... ( -31.70)
>consensus
AAUCUGCAGCAUCCUGCCUACAACUGCAUCCUGCAAUUGUCGGCCGAAGGUGUUGACAUGAAAUUAAAAUUAAUUGAGAAUUCCGUGCACAUAGCAACGCAAUCGUGUCGUCCAGCAACU
....(((((((.((((((.((((.(((.....))).)))).)))...)))))))((((((((((((....)))))........(((((.....)).)))...))))))).....)))... (-30.40 = -30.60 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:25 2006