Locus 79

Sequence ID	pao.561
Location	991,198 – 991,385
Length	187
Max. P	0.976826

overview

Window 8

Location	991,198 – 991,306
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.80
Mean single sequence MFE	-38.73
Consensus MFE	-28.93
Energy contribution	-28.77
Covariance contribution	-0.17
Combinations/Pair	1.08
Mean z-score	-1.53
Structure conservation index	0.75
SVM decision value	0.64
SVM RNA-class probability	0.808216
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.561 991198 108 + 6264404
UUUUUAUCUAAUUUUC-----------CCUUUGCAAACGGGGUAAAGA-UGGGUAUCAUGCGCCCCGUGUUGCGGAGAGGUGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUAC
.............(((-----------((((.(((...((((....((-(....)))..((((((((.....))).....(((((....)))))..))))).))))))).)))))))... ( -40.80)
>pfo.2515 1617232 107 - 6438405
--UUUAUCGAUUUUUA-----------UGUUUGCAAACGGGGAAGAAGGUGGUUAAUAUACGCCCCGUGUUGCGGAGAGCUGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUAC
--..............-----------(.(((((((((((((......((.....)).....)))))).))))))).)(((((((....))))...)))((((((.......)))))).. ( -36.20)
>pf5.2742 1860992 107 - 7074893
--UUUAUCGUUUUUUU-----------UGUUUGCAAACGGGGAGAAAGCUGGUUAAUAUACGCCCCGUGUUGCGGAGAGCUGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUAC
--......((((((.(-----------(.(((((((((((((((....)).((......)).)))))).))))))).))..((((....))))))))))((((((.......)))))).. ( -36.30)
>pel.2216 1731878 118 - 5888780
--UUUUUUGAAGUUUUUUUCAAAAAAAGGGUUGCAAACGAGGAAGGGUGUGUUUAAUAUUCGCCUCGUGUUGCGGUGAGGUGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUAU
--((((((((((....))))))))))..(((..(..((((((..((((((.....)))))).))))))....((((......)))).)..)))......((((((.......)))))).. ( -41.40)
>pau.2472 1877258 106 - 6537648
--UUUAUCUAAUUUUC-----------CCUUUGCAAACGGGGUAAAGA-UGGGUAUCAUGCGCCCCGUGUUGCGGAGAGGUGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUAC
--...........(((-----------((((.(((...((((....((-(....)))..((((((((.....))).....(((((....)))))..))))).))))))).)))))))... ( -40.80)
>ppk.2577 1101921 117 - 6181863
---UUUUUGAAGUUUUUUUCAAAAAAAGGGUUGCAAAGGUGAAAGAGGUUCUUUAAUAUUCGCCUCGUGUUGCGGUGAGGUGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUAU
---(((((((((....)))))))))...(((..(...(((.((((.....))))......(((((((........))))))))))..)..)))......((((((.......)))))).. ( -36.90)
>consensus
__UUUAUCGAAUUUUU___________CGUUUGCAAACGGGGAAAAGG_UGGUUAAUAUACGCCCCGUGUUGCGGAGAGGUGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUAC
.............................(((((((((((((....................)))))).)))))))....(((((....))))).....((((((.......)))))).. (-28.93 = -28.77 +  -0.17)

alignment

secondary structure

dotplot

Window 9

Location	991,198 – 991,306
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.80
Mean single sequence MFE	-35.07
Consensus MFE	-27.91
Energy contribution	-27.88
Covariance contribution	-0.03
Combinations/Pair	1.10
Mean z-score	-3.33
Structure conservation index	0.80
SVM decision value	1.64
SVM RNA-class probability	0.969548
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.561 991198 108 - 6264404
GUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCACCUCUCCGCAACACGGGGCGCAUGAUACCCA-UCUUUACCCCGUUUGCAAAGG-----------GAAAAUUAGAUAAAAA
....((((((.(((((((.(((((...((((....))))......(((.....))))))))..(((....)-))....))))...))).))))-----------)).............. ( -40.90)
>pfo.2515 1617232 107 + 6438405
GUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCAGCUCUCCGCAACACGGGGCGUAUAUUAACCACCUUCUUCCCCGUUUGCAAACA-----------UAAAAAUCGAUAAA--
..............(((((((......((((....)))).)))))))((((.((((((....................)))))))))).....-----------..............-- ( -32.25)
>pf5.2742 1860992 107 + 7074893
GUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCAGCUCUCCGCAACACGGGGCGUAUAUUAACCAGCUUUCUCCCCGUUUGCAAACA-----------AAAAAAACGAUAAA--
..............(((((((......((((....)))).)))))))((((.((((((.(................).)))))))))).....-----------..............-- ( -33.49)
>pel.2216 1731878 118 + 5888780
AUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCACCUCACCGCAACACGAGGCGAAUAUUAAACACACCCUUCCUCGUUUGCAACCCUUUUUUUGAAAAAAACUUCAAAAAA--
...((((((.....)))))).......((((....))))........((((.((((((....................))))))))))......(((((((((......)))))))))-- ( -32.85)
>pau.2472 1877258 106 + 6537648
GUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCACCUCUCCGCAACACGGGGCGCAUGAUACCCA-UCUUUACCCCGUUUGCAAAGG-----------GAAAAUUAGAUAAA--
....((((((.(((((((.(((((...((((....))))......(((.....))))))))..(((....)-))....))))...))).))))-----------))............-- ( -40.90)
>ppk.2577 1101921 117 + 6181863
AUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCACCUCACCGCAACACGAGGCGAAUAUUAAAGAACCUCUUUCACCUUUGCAACCCUUUUUUUGAAAAAAACUUCAAAAA---
...........(((((((..(((((..((((....)))).......((.....)))))))......((((.....))))..))))))).......((((((((......))))))))--- ( -30.00)
>consensus
GUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCACCUCUCCGCAACACGGGGCGAAUAUUAACCA_CCUCUUCCCCGUUUGCAAACA___________AAAAAUUCGAUAAA__
...((((((.....)))))).......((((....))))........((((.((((((....................))))))))))................................ (-27.91 = -27.88 +  -0.03)

alignment

secondary structure

dotplot

Window 0

Location	991,227 – 991,346
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	89.72
Mean single sequence MFE	-49.94
Consensus MFE	-42.59
Energy contribution	-42.03
Covariance contribution	-0.55
Combinations/Pair	1.07
Mean z-score	-2.80
Structure conservation index	0.85
SVM decision value	1.78
SVM RNA-class probability	0.976826
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.561 991227 119 - 6264404
GGAGAGGGGGGGAUUCGAACCCCCGACACCCUUUUGAGGUGUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCACCUCUCCGCAACACGGGGCGCAUGAUACCCA-UCUUUACC
((((((((((((.......)))))...........((((.(..((((((.....))))))..)))))((((....)))).))))))).......(((..........))).-........ ( -53.00)
>pfo.2515 1617259 120 + 6438405
GGAGAACGGGGGAUUCGAACCCCCGACACCCUUUUGAGGUGUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCAGCUCUCCGCAACACGGGGCGUAUAUUAACCACCUUCUUCC
((((((.((((.......(((((((((((((....).))))).........((.(((((((......((((....)))).)))))))))....))))).)).......)).)))))))). ( -49.24)
>pf5.2742 1861019 120 + 7074893
GGAGAACGGGGGAUUCGAACCCCCGACACCCUUUUGAGGUGUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCAGCUCUCCGCAACACGGGGCGUAUAUUAACCAGCUUUCUCC
((((((((((((.......))))))((.((((...((((.(..((((((.....))))))..)))))((((....)))).((.....)).....)))).)).............)))))) ( -51.30)
>pel.2216 1731916 120 + 5888780
GGUGAAGGGGGGAUUCGAACCCCCGAUACCCUUAUGAGGUAUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCACCUCACCGCAACACGAGGCGAAUAUUAAACACACCCUUCC
((((..(((((........)))))((((......((((((...((((((.....)))))).......((((....)))))))))).(((........)))..)))).....))))..... ( -45.50)
>pau.2472 1877285 119 + 6537648
GGAGAGGGGGGGAUUCGAACCCCCGACACCCUUUUGAGGUGUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCACCUCUCCGCAACACGGGGCGCAUGAUACCCA-UCUUUACC
((((((((((((.......)))))...........((((.(..((((((.....))))))..)))))((((....)))).))))))).......(((..........))).-........ ( -53.00)
>ppk.2577 1101958 120 + 6181863
GGUGAAGGGGGGAUUCGAACCCCCGAUACCCUUAUGAGGUAUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCACCUCACCGCAACACGAGGCGAAUAUUAAAGAACCUCUUUC
((((..(((((........)))))..)))).....(((((...((((((.....))))))(((((..((((....)))).......((.....)))))))...........))))).... ( -47.60)
>consensus
GGAGAAGGGGGGAUUCGAACCCCCGACACCCUUUUGAGGUGUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCACCUCUCCGCAACACGGGGCGAAUAUUAACCA_CCUCUUCC
(((((.((((((.......)))))...........((((((..((((((.....)))))))))))).((((....)))).).)))))((........))..................... (-42.59 = -42.03 +  -0.55)

alignment

secondary structure

dotplot

Window 1

Location	991,266 – 991,385
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.42
Mean single sequence MFE	-44.47
Consensus MFE	-38.31
Energy contribution	-37.87
Covariance contribution	-0.44
Combinations/Pair	1.04
Mean z-score	-1.58
Structure conservation index	0.86
SVM decision value	0.35
SVM RNA-class probability	0.699162
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.561 991266 119 + 6264404
UGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUACACCUCAAAAGGGUGUCGGGGGUUCGAAUCCCCCCCUCUCCGCCAUUCAAGUGUUAGAGGUUGAUUCAGGCGGCGA-AAGC
..((((((((((.(((((.((((((.......))))))((((((.....)))))).(((((.......)))))))).)).)))))))........(((.....))).))).((..-..)) ( -49.70)
>pf5.2742 1861059 108 - 7074893
UGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUACACCUCAAAAGGGUGUCGGGGGUUCGAAUCCCCCGUUCUCCGCCAUU------------AUUUGCUUAGUACGUUGUAAUC
.(((..((((((.((..((((((((.......))))))((((((.....)))))).(((((.......)))))))..)).))))))------------....)))............... ( -41.50)
>pst.1101 2014816 107 + 6397126
UGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUACACCUCAAAAGGGUGUCGGGGGUUCGAAUCCCCCGUUCUCCGCCAUU------------AUUUAUGUAGCGCGUCA-GAUU
((((((((((((.((..((((((((.......))))))((((((.....)))))).(((((.......)))))))..)).))))))------------..........)).))))-.... ( -41.70)
>pel.2216 1731956 108 - 5888780
UGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUAUACCUCAUAAGGGUAUCGGGGGUUCGAAUCCCCCCUUCACCGCCAUU------------AUUCGCUCAGGGCGCUUUAAGC
.((((....)))).(((((((((.(((....)))((((((((((.....)))))).(((((........)))))............------------....)))).))))))))).... ( -42.50)
>pau.2472 1877324 119 - 6537648
UGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUACACCUCAAAAGGGUGUCGGGGGUUCGAAUCCCCCCCUCUCCGCCAUUCAAGUGUUAGAGGUUGAUUCAGGCGGCGA-AAGC
..((((((((((.(((((.((((((.......))))))((((((.....)))))).(((((.......)))))))).)).)))))))........(((.....))).))).((..-..)) ( -49.70)
>ppk.2577 1101998 108 - 6181863
UGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUAUACCUCAUAAGGGUAUCGGGGGUUCGAAUCCCCCCUUCACCGCCAUU------------AUUUGCGUAGGGCGCUGUAAAC
.((((....))))(((((.((((((.......))))))((((((.....)))))).((((((....)))))))))))..((((.((------------((....))))))))........ ( -41.70)
>consensus
UGGCCGAGUGGCCGAAGGCGCUCCCCUGCUAAGGGAGUACACCUCAAAAGGGUGUCGGGGGUUCGAAUCCCCCCUUCUCCGCCAUU____________AUUUACUCAGGGCGCUA_AAGC
.((((....))))...(((((((((.......))))))((((((.....)))))).(((((.......))))).......)))..................................... (-38.31 = -37.87 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	991,266 – 991,385
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.42
Mean single sequence MFE	-44.87
Consensus MFE	-40.11
Energy contribution	-39.67
Covariance contribution	-0.44
Combinations/Pair	1.04
Mean z-score	-2.16
Structure conservation index	0.89
SVM decision value	1.27
SVM RNA-class probability	0.938767
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.561 991266 119 - 6264404
GCUU-UCGCCGCCUGAAUCAACCUCUAACACUUGAAUGGCGGAGAGGGGGGGAUUCGAACCCCCGACACCCUUUUGAGGUGUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCA
...(-((.(((((....((((..........))))..))))).)))(((((........)))))...........((((.(..((((((.....))))))..)))))((((....)))). ( -48.10)
>pf5.2742 1861059 108 + 7074893
GAUUACAACGUACUAAGCAAAU------------AAUGGCGGAGAACGGGGGAUUCGAACCCCCGACACCCUUUUGAGGUGUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCA
......................------------...((((.....((((((.......))))))((((((....).))))).((((((.....))))))))))...((((....)))). ( -42.50)
>pst.1101 2014816 107 - 6397126
AAUC-UGACGCGCUACAUAAAU------------AAUGGCGGAGAACGGGGGAUUCGAACCCCCGACACCCUUUUGAGGUGUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCA
....-.................------------...((((.....((((((.......))))))((((((....).))))).((((((.....))))))))))...((((....)))). ( -42.50)
>pel.2216 1731956 108 + 5888780
GCUUAAAGCGCCCUGAGCGAAU------------AAUGGCGGUGAAGGGGGGAUUCGAACCCCCGAUACCCUUAUGAGGUAUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCA
(((.....(((.....)))...------------...)))((((..(((((........))))).((((((....).))))).((((((.....))))))))))...((((....)))). ( -44.70)
>pau.2472 1877324 119 + 6537648
GCUU-UCGCCGCCUGAAUCAACCUCUAACACUUGAAUGGCGGAGAGGGGGGGAUUCGAACCCCCGACACCCUUUUGAGGUGUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCA
...(-((.(((((....((((..........))))..))))).)))(((((........)))))...........((((.(..((((((.....))))))..)))))((((....)))). ( -48.10)
>ppk.2577 1101998 108 + 6181863
GUUUACAGCGCCCUACGCAAAU------------AAUGGCGGUGAAGGGGGGAUUCGAACCCCCGAUACCCUUAUGAGGUAUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCA
.......(((.....)))....------------...((((.....(((((........))))).((((((....).))))).((((((.....))))))))))...((((....)))). ( -43.30)
>consensus
GCUU_UAGCGCCCUAAACAAAU____________AAUGGCGGAGAAGGGGGGAUUCGAACCCCCGACACCCUUUUGAGGUGUACUCCCUUAGCAGGGGAGCGCCUUCGGCCACUCGGCCA
.....................................((((......(((((.......))))).((((((....).))))).((((((.....))))))))))...((((....)))). (-40.11 = -39.67 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:11:21 2007