Locus 31

Sequence ID	pao.2789
Location	5,283,959 – 5,284,110
Length	151
Max. P	0.981443

overview

Window 5

Location	5,283,959 – 5,284,076
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.31
Mean single sequence MFE	-37.28
Consensus MFE	-14.22
Energy contribution	-14.00
Covariance contribution	-0.22
Combinations/Pair	1.46
Mean z-score	-2.99
Structure conservation index	0.38
SVM decision value	0.73
SVM RNA-class probability	0.834615
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2789 5283959 117 + 6264404
UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGA-UCAGCCGGUAAGCUGAGA--GACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACG
.((((((((.((((.....)))).)))))))).....((((((....))-))))..(((((.((((((--(.((.((...)).)).))).)))).))))).(((....)))......... ( -33.20)
>pf5.2389 4555422 114 + 7074893
UUGACUUGCAAAUGAUAAUGAUUAUUAUUGCAAGCAACUGGUCGCGAGA-UCAGUCGAUAGCCCAAAG-GACCUUA---GGUCGGA-CCUUUGGAUUAUCUCCUCAUCAGGCUAAUCACG
.((.(((((((.(((((.....))))))))))))))(((((((....))-))))).((((..((((((-(.((...---....)).-)))))))..)))).(((....)))......... ( -38.00)
>pss.1813 3620502 112 + 6093698
UUGACUUGCAAAUGAUAAUGAUUAUUAUUGC-AUCAGCGGGUCGCGAGACUCGCUGGAUAACCCGGAA--GUCUUA---GGUCGG--CUUCCAGAUUAUCUCCUCAUCAGGCUAAUCACG
......(((((.(((((.....)))))))))-)((((((((((....)))))))))).......((((--(((...---....))--))))).(((((...(((....))).)))))... ( -39.20)
>pel.1954 3656602 116 + 5888780
UUGACUGGCAAAUGAUAACGAUUAUUAUUGCACUCAGCAGGUCGCGAGACCCGCUGGAUAACCUGCAACGUCCUCA---GGUCGGA-CGCUCAGAUUAUCUCCUCAUCAGGCUAAUCACG
.(((.((((...((((..................((((.((((....)))).))))(((((.(((...(((((...---....)))-))..))).))))).....)))).)))).))).. ( -38.90)
>ppk.2347 4595202 111 + 6181863
UUGACUGCCAAAUGAUAACGAUUAUUAUUGCACUCAGCUGAUCGCGAGAUCCGCUGGAUAACCUGAAA---GCUUA---GGUCG---CUCUCAGAUUAUCUCCUCAUCAGGCUAAUCACG
.(((..(((..((((...................((((.((((....)))).))))(((((.((((.(---((...---....)---)).)))).)))))...))))..)))...))).. ( -34.00)
>pfo.2147 4145110 113 + 6438405
UUGACUUGCAAAUGAUAAUGAUUAUUAUUGCAAGCAACUGGUCGCGAGA-UCAGUCGAUGGACCAGAG--ACCUUA---GGUCGGU-CUUCUGGACUAUCUCCUCAUCAGGCUAAUCACG
.((.(((((((.(((((.....))))))))))))))(((((((....))-))))).(((((.((((((--(((...---....)))-).))))).))))).(((....)))......... ( -40.40)
>consensus
UUGACUUGCAAAUGAUAAUGAUUAUUAUUGCAAUCAACUGGUCGCGAGA_UCACUCGAUAACCCGAAA__ACCUUA___GGUCGGA_CUUUCAGAUUAUCUCCUCAUCAGGCUAAUCACG
.(((...((...((((.......................((((....)).))....(((((.((((((...((..........))...)))))).))))).....)))).))...))).. (-14.22 = -14.00 +  -0.22)

alignment

secondary structure

dotplot

Window 6

Location	5,283,959 – 5,284,076
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.31
Mean single sequence MFE	-41.27
Consensus MFE	-18.10
Energy contribution	-18.35
Covariance contribution	0.25
Combinations/Pair	1.30
Mean z-score	-3.66
Structure conservation index	0.44
SVM decision value	1.89
SVM RNA-class probability	0.981443
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2789 5283959 117 - 6264404
CGUGAUUAGCCUGAUGAGGAGAUAAUCUGAAGAGUCCGACUGCGUGGGUC--UCUCAGCUUACCGGCUGA-UCUCGCGACCAGUUGAGUGACAUAAUAAUGAUUCUCAUUUCCAUGUCAA
...(((((.(((....)))...))))).........((((((((((((..--..((((((....))))))-.))))))..))))))..((((((...((((.....))))...)))))). ( -35.40)
>pf5.2389 4555422 114 - 7074893
CGUGAUUAGCCUGAUGAGGAGAUAAUCCAAAGG-UCCGACC---UAAGGUC-CUUUGGGCUAUCGACUGA-UCUCGCGACCAGUUGCUUGCAAUAAUAAUCAUUAUCAUUUGCAAGUCAA
(((((.......(((.((..((((..(((((((-.((....---...)).)-))))))..))))..)).)-))))))).......((((((((..(((.....)))...))))))))... ( -38.81)
>pss.1813 3620502 112 - 6093698
CGUGAUUAGCCUGAUGAGGAGAUAAUCUGGAAG--CCGACC---UAAGAC--UUCCGGGUUAUCCAGCGAGUCUCGCGACCCGCUGAU-GCAAUAAUAAUCAUUAUCAUUUGCAAGUCAA
..(((((.((.((((((.(((((((((((((((--.(....---...).)--))))))))))))(((((.(((....))).)))))..-..........)).))))))...)).))))). ( -40.30)
>pel.1954 3656602 116 - 5888780
CGUGAUUAGCCUGAUGAGGAGAUAAUCUGAGCG-UCCGACC---UGAGGACGUUGCAGGUUAUCCAGCGGGUCUCGCGACCUGCUGAGUGCAAUAAUAAUCGUUAUCAUUUGCCAGUCAA
..(((((.((.((((((.(((((((((((((((-(((....---...))))))).)))))))))(((((((((....))))))))).............)).))))))...)).))))). ( -51.50)
>ppk.2347 4595202 111 - 6181863
CGUGAUUAGCCUGAUGAGGAGAUAAUCUGAGAG---CGACC---UAAGC---UUUCAGGUUAUCCAGCGGAUCUCGCGAUCAGCUGAGUGCAAUAAUAAUCGUUAUCAUUUGGCAGUCAA
..(((((.(((((((((.(((((((((((((((---(....---...))---))))))))))))((((.((((....)))).)))).............)).))))))...)))))))). ( -45.80)
>pfo.2147 4145110 113 - 6438405
CGUGAUUAGCCUGAUGAGGAGAUAGUCCAGAAG-ACCGACC---UAAGGU--CUCUGGUCCAUCGACUGA-UCUCGCGACCAGUUGCUUGCAAUAAUAAUCAUUAUCAUUUGCAAGUCAA
(((((.......(((.((..(((.(.(((((.(-(((....---...)))--)))))).).)))..)).)-))))))).......((((((((..(((.....)))...))))))))... ( -35.81)
>consensus
CGUGAUUAGCCUGAUGAGGAGAUAAUCUGAAAG_UCCGACC___UAAGGC__UUUCAGGUUAUCCACCGA_UCUCGCGACCAGCUGAGUGCAAUAAUAAUCAUUAUCAUUUGCAAGUCAA
..(((((.((.((((((.((((((((((((((....(..........)....))))))))))))...........((.....))...............)).))))))...)).))))). (-18.10 = -18.35 +   0.25)

alignment

secondary structure

dotplot

Window 7

Location	5,283,995 – 5,284,110
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.22
Mean single sequence MFE	-44.75
Consensus MFE	-28.99
Energy contribution	-27.72
Covariance contribution	-1.27
Combinations/Pair	1.53
Mean z-score	-4.33
Structure conservation index	0.65
SVM decision value	1.77
SVM RNA-class probability	0.976205
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2789 5283995 115 + 6264404
ACUGGUCGCGAGA-UCAGCCGGUAAGCUGAGA--GACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGC-ACUUUGCCGGGUC-UUUUUUU
.((((((....))-))))(((((((.((((((--(.((.((...)).)).))).)))).))))).(((....)))........)).....((((((((-.....))))))))-....... ( -41.90)
>pf5.2389 4555458 112 + 7074893
ACUGGUCGCGAGA-UCAGUCGAUAGCCCAAAG-GACCUUA---GGUCGGA-CCUUUGGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGC-UUUUUGCCGGGUC-UUUUUUU
(((((((....))-))))).((((..((((((-(.((...---....)).-)))))))..))))........(((((......)))))..((((((((-.....))))))))-....... ( -45.30)
>pst.1877 3549491 112 + 6397126
GCGGUUCGCGAGAACCGCUGGAUAACCUGGAA--GUCUUA---GGUCGG--CUUCCGGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGA-UUUUUUCCGGGUCUUUUUUUU
(((((((....))))))).((((((.((((((--(((...---....))--))))))).)))))).......(((((......)))))..((((((((-.....))))))))........ ( -49.60)
>pel.1954 3656638 114 + 5888780
GCAGGUCGCGAGACCCGCUGGAUAACCUGCAACGUCCUCA---GGUCGGA-CGCUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGC-UUUUUGCCGGGUC-UUUUUUU
((.((((....)))).)).((((((.(((...(((((...---....)))-))..))).)))))).......(((((......)))))..((((((((-.....))))))))-....... ( -43.80)
>ppk.2347 4595238 110 + 6181863
GCUGAUCGCGAGAUCCGCUGGAUAACCUGAAA---GCUUA---GGUCG---CUCUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCUUUUUUGCCGGGUC-UUUUUUU
((.((((....)))).)).((((((.((((.(---((...---....)---)).)))).)))))).......(((((......)))))..((((((((......))))))))-....... ( -40.20)
>pfo.2147 4145146 111 + 6438405
ACUGGUCGCGAGA-UCAGUCGAUGGACCAGAG--ACCUUA---GGUCGGU-CUUCUGGACUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGC-UUUUUGCCGGGUC-UUUUUUU
(((((((....))-))))).(((((.((((((--(((...---....)))-).))))).)))))........(((((......)))))..((((((((-.....))))))))-....... ( -47.70)
>consensus
ACUGGUCGCGAGA_CCACUCGAUAACCUGAAA__ACCUUA___GGUCGGA_CUUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGC_UUUUUGCCGGGUC_UUUUUUU
...((((....)))).....(((((.((((((...((..........))...)))))).)))))........(((((......)))))..((((((((......))))))))........ (-28.99 = -27.72 +  -1.27)

alignment

secondary structure

dotplot

Window 8

Location	5,283,995 – 5,284,110
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.22
Mean single sequence MFE	-47.30
Consensus MFE	-33.38
Energy contribution	-33.08
Covariance contribution	-0.30
Combinations/Pair	1.28
Mean z-score	-5.53
Structure conservation index	0.71
SVM decision value	1.76
SVM RNA-class probability	0.976115
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2789 5283995 115 - 6264404
AAAAAAA-GACCCGGCAAAGU-GCCGGGUCAAAAACCGUGAUUAGCCUGAUGAGGAGAUAAUCUGAAGAGUCCGACUGCGUGGGUC--UCUCAGCUUACCGGCUGA-UCUCGCGACCAGU
.......-((((((((.....-)))))))).....(((.((((((((.(.((((........((((.(((.((.((...)).)).)--))))))))))).))))))-)).)).)...... ( -45.40)
>pf5.2389 4555458 112 - 7074893
AAAAAAA-GACCCGGCAAAAA-GCCGGGUCAAAAACCGUGAUUAGCCUGAUGAGGAGAUAAUCCAAAGG-UCCGACC---UAAGGUC-CUUUGGGCUAUCGACUGA-UCUCGCGACCAGU
.......-((((((((.....-))))))))......(((((.......(((.((..((((..(((((((-.((....---...)).)-))))))..))))..)).)-)))))))...... ( -49.31)
>pst.1877 3549491 112 - 6397126
AAAAAAAAGACCCGGAAAAAA-UCCGGGUCAAAAACCGUGAUUAGCCUGAUGAGGAGAUAAUCCGGAAG--CCGACC---UAAGAC--UUCCAGGUUAUCCAGCGGUUCUCGCGAACCGC
........((((((((.....-))))))))...(((((.(((((.(((....)))...))))))(((((--.(....---...).)--)))).)))).....(((((((....))))))) ( -43.80)
>pel.1954 3656638 114 - 5888780
AAAAAAA-GACCCGGCAAAAA-GCCGGGUCAAAAACCGUGAUUAGCCUGAUGAGGAGAUAAUCUGAGCG-UCCGACC---UGAGGACGUUGCAGGUUAUCCAGCGGGUCUCGCGACCUGC
.......-((((((((.....-))))))))...............(((....))).(((((((((((((-(((....---...))))))).)))))))))..(((((((....))))))) ( -52.80)
>ppk.2347 4595238 110 - 6181863
AAAAAAA-GACCCGGCAAAAAAGCCGGGUCAAAAACCGUGAUUAGCCUGAUGAGGAGAUAAUCUGAGAG---CGACC---UAAGC---UUUCAGGUUAUCCAGCGGAUCUCGCGAUCAGC
.......-((((((((......))))))))........(((((..(((....))).(((((((((((((---(....---...))---))))))))))))..(((.....)))))))).. ( -46.20)
>pfo.2147 4145146 111 - 6438405
AAAAAAA-GACCCGGCAAAAA-GCCGGGUCAAAAACCGUGAUUAGCCUGAUGAGGAGAUAGUCCAGAAG-ACCGACC---UAAGGU--CUCUGGUCCAUCGACUGA-UCUCGCGACCAGU
.......-((((((((.....-))))))))......(((((.......(((.((..(((.(.(((((.(-(((....---...)))--)))))).).)))..)).)-)))))))...... ( -46.31)
>consensus
AAAAAAA_GACCCGGCAAAAA_GCCGGGUCAAAAACCGUGAUUAGCCUGAUGAGGAGAUAAUCCGAAAG_UCCGACC___UAAGGC__UUUCAGGUUAUCCACCGA_UCUCGCGACCAGC
........((((((((......))))))))......(((((....(((....))).((((((((((((....(..........)....)))))))))))).........)))))...... (-33.38 = -33.08 +  -0.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:06:17 2007