Locus 73

Sequence ID	pao_1
Location	4,956,426 – 4,956,655
Length	229
Max. P	0.999997

overview

Window 7

Location	4,956,426 – 4,956,545
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	92.41
Mean single sequence MFE	-44.13
Consensus MFE	-39.29
Energy contribution	-37.85
Covariance contribution	-1.44
Combinations/Pair	1.14
Mean z-score	-1.63
Structure conservation index	0.89
SVM decision value	0.94
SVM RNA-class probability	0.885815
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 4956426 119 + 1
UACCCGAAUCCAACGCGGGCCGCGCCA-AUGGAUUCCUAUUUGGUCUUGCUCCGAGUGGGGUUUACCUAGCCACGCACUGUUGCCAGCCGUGCGGUGCGCUCUUACCGCACCUUUUCACC
.....(((((((..(((.....)))..-.)))))))((((((((.......))))))))((((.....))))..((((.((.....)).))))((((((.......))))))........ ( -40.00)
>pau_1 81 119 + 1
UACCCGAAUCCAACGCGGGCCGCGCCA-AUGGAUUCCUAUUUGGUCUUGCUCCGAGUGGGGUUUACCUAGCCACGCACUGUUGCCAGCCGUGCGGUGCGCUCUUACCGCACCUUUUCACC
.....(((((((..(((.....)))..-.)))))))((((((((.......))))))))((((.....))))..((((.((.....)).))))((((((.......))))))........ ( -40.00)
>pel_1 81 120 + 1
UACCCGGUUCCGACGCGGGCCGCGCCGUAUGGAACCCUAUUUGGUCUUGCUCCGAGUGGGGUUUACCUAGCCACGAACUGUUGCCAGUCGCGCGGUGCGCUCUUACCGCACCUUUUCACC
....((((...((.(((.(((((((......(((((((((((((.......)))))))))))))..........((.(((....)))))))))))).)))))..))))............ ( -48.40)
>pfo_1 81 118 + 1
UACCCGGUCCCAGCGCGGGCCACGCCU--UGGGACCCUAUUUGGUCUUGCUCCAAGUGGGGUUUACCUAGCCACGAACUGUUGCCAGACGUGCGGUGCGCUCUUACCGCACCUUUUCACC
.....((((((((.(((.....))).)--)))))))((((((((.......))))))))((((.....))))..((((((....)))..((((((((......))))))))...)))... ( -46.30)
>pfs_1 81 118 + 1
UACCCGGUCCCAGCGCGGGCCACGCCU--UGGGACCCUAUUUGGUCUUGCUCCAAGUGGGGUUUACCUAGCCACGAACUGUUGCCAGUCGCGCGGUGCGCUCUUACCGCACCUUUUCACC
.((((((((((((.(((.....))).)--))))))).(((((((.......))))))))))).......((..(((.(((....)))))).))((((((.......))))))........ ( -46.40)
>ppk_1 81 120 + 1
UACCCGGUUCCGACGCGGGCCACGCCUGAUGGAACCCUAUUUGGUCUUGCUCCGAGUGGGGUUUACCUAGCCACGAACUGUUGCCAGCCGUGCGGUGCGCUCUUACCGCACCUUUUCACC
.....((((.((((.(((((...)))))...(((((((((((((.......)))))))))))))...............))))..))))((((((((......))))))))......... ( -43.70)
>consensus
UACCCGGUUCCAACGCGGGCCACGCCU_AUGGAACCCUAUUUGGUCUUGCUCCGAGUGGGGUUUACCUAGCCACGAACUGUUGCCAGCCGUGCGGUGCGCUCUUACCGCACCUUUUCACC
.(((((((((((..(((.....)))....))))))).(((((((.......))))))))))).......((.(((..(((....))).)))))((((((.......))))))........ (-39.29 = -37.85 +  -1.44)

alignment

secondary structure

dotplot

Window 8

Location	4,956,426 – 4,956,545
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	92.41
Mean single sequence MFE	-46.77
Consensus MFE	-47.36
Energy contribution	-45.12
Covariance contribution	-2.25
Combinations/Pair	1.22
Mean z-score	-1.40
Structure conservation index	1.01
SVM decision value	2.57
SVM RNA-class probability	0.995389
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 4956426 119 - 1
GGUGAAAAGGUGCGGUAAGAGCGCACCGCACGGCUGGCAACAGUGCGUGGCUAGGUAAACCCCACUCGGAGCAAGACCAAAUAGGAAUCCAU-UGGCGCGGCCCGCGUUGGAUUCGGGUA
(((.....((((((.......)))))).((((((((....)))).))))(((.((....))((....)))))...)))......(((((((.-..(((((...))))))))))))..... ( -44.60)
>pau_1 81 119 - 1
GGUGAAAAGGUGCGGUAAGAGCGCACCGCACGGCUGGCAACAGUGCGUGGCUAGGUAAACCCCACUCGGAGCAAGACCAAAUAGGAAUCCAU-UGGCGCGGCCCGCGUUGGAUUCGGGUA
(((.....((((((.......)))))).((((((((....)))).))))(((.((....))((....)))))...)))......(((((((.-..(((((...))))))))))))..... ( -44.60)
>pel_1 81 120 - 1
GGUGAAAAGGUGCGGUAAGAGCGCACCGCGCGACUGGCAACAGUUCGUGGCUAGGUAAACCCCACUCGGAGCAAGACCAAAUAGGGUUCCAUACGGCGCGGCCCGCGUCGGAACCGGGUA
(((.....((((((.......)))))).((((((((....))).))))).........)))..((((((..(..((((......)))).....(((((((...))))))))..)))))). ( -47.50)
>pfo_1 81 118 - 1
GGUGAAAAGGUGCGGUAAGAGCGCACCGCACGUCUGGCAACAGUUCGUGGCUAGGUAAACCCCACUUGGAGCAAGACCAAAUAGGGUCCCA--AGGCGUGGCCCGCGCUGGGACCGGGUA
(((.....((((((.......)))))).((((.(((....)))..)))))))......((((...((((.......))))....(((((((--..(((((...)))))))))))))))). ( -48.80)
>pfs_1 81 118 - 1
GGUGAAAAGGUGCGGUAAGAGCGCACCGCGCGACUGGCAACAGUUCGUGGCUAGGUAAACCCCACUUGGAGCAAGACCAAAUAGGGUCCCA--AGGCGUGGCCCGCGCUGGGACCGGGUA
(((.....((((((.......)))))).((((((((....))).))))))))......((((...((((.......))))....(((((((--..(((((...)))))))))))))))). ( -50.40)
>ppk_1 81 120 - 1
GGUGAAAAGGUGCGGUAAGAGCGCACCGCACGGCUGGCAACAGUUCGUGGCUAGGUAAACCCCACUCGGAGCAAGACCAAAUAGGGUUCCAUCAGGCGUGGCCCGCGUCGGAACCGGGUA
(((.....((((((.......)))))).((((((((....))).)))))(((.((....))((....)))))...)))......((((((....((((((...))))))))))))..... ( -44.70)
>consensus
GGUGAAAAGGUGCGGUAAGAGCGCACCGCACGGCUGGCAACAGUUCGUGGCUAGGUAAACCCCACUCGGAGCAAGACCAAAUAGGGUUCCAU_AGGCGCGGCCCGCGUUGGAACCGGGUA
(((.....((((((.......)))))).((((((((....)))).))))(((.((....))((....)))))...)))......((((((....((((((...))))))))))))..... (-47.36 = -45.12 +  -2.25)

alignment

secondary structure

dotplot

Window 9

Location	4,956,505 – 4,956,625
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.56
Mean single sequence MFE	-43.85
Consensus MFE	-40.46
Energy contribution	-40.10
Covariance contribution	-0.36
Combinations/Pair	1.08
Mean z-score	-1.98
Structure conservation index	0.92
SVM decision value	2.55
SVM RNA-class probability	0.995166
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 4956505 120 + 1
UUGCCAGCCGUGCGGUGCGCUCUUACCGCACCUUUUCACCCUUACCGGCGCUGUUGCGCUUAGGCGGUUAUUUUCUGUGGCACUUUCCGUAGGCUCGCGCCUCCCAGGCGUUACCUGGCA
.((((.(((((((((((......))))))))......(((((((..(((((....))))))))).)))..........))).........(((...(((((.....)))))..))))))) ( -47.10)
>pst_1 159 120 + 1
UUGCCAGACGUGCGGUGCGCUCUUACCGCACCUUUUCACCCUUACCGGCACCGAAGUGCUUAGGCGGUUAUUUUCUGUGGCACUUUCCGUAGGCUCGCGCCUCCCAGGUGUUACCUGGCA
.((((((..((((((((......))))))))...............((((((((((((((...((((.......))))))))))))..(.((((....)))).)..))))))..)))))) ( -46.40)
>pau_1 160 120 + 1
UUGCCAGCCGUGCGGUGCGCUCUUACCGCACCUUUUCACCCUUACCGGCGCUGUUGCGCUUAGGCGGUUAUUUUCUGUGGCACUUUCCGUAGGCUCGCGCCUCCCAGGCGUUACCUGGCA
.((((.(((((((((((......))))))))......(((((((..(((((....))))))))).)))..........))).........(((...(((((.....)))))..))))))) ( -47.10)
>pel_1 161 120 + 1
UUGCCAGUCGCGCGGUGCGCUCUUACCGCACCUUUUCACCCUUACCGGCGCCGAAGCGCUUAGGCGGUUGUUUUCUGUGGCACUUUCCGUAGGCUCGCGCCUCCCAGGCGUUACCUGGCA
.((((.(((((..((((((.......)))))).....(((((((..(((((....))))))))).)))........))))).........(((...(((((.....)))))..))))))) ( -44.50)
>pf5_1 159 120 + 1
UUACCAGACGUGCGGUGCGCUCUUACCGCACCUUUUCACCCUUACCGGCACCGAAGUGCUUAGGCGGUUAUUUUCUGUGGCACUUUCCGUAGGCUCACGCCCCCCAGGCAUUACCUGGCA
...((((..((((((((......))))))))........(((...(((....((((((((...((((.......))))))))))))))).))).....(((.....))).....)))).. ( -37.90)
>pfs_1 159 120 + 1
UUGCCAGUCGCGCGGUGCGCUCUUACCGCACCUUUUCACCCUUACCGGCACCGAAGUGCUUAGGCGGUUAUUUUCUGUGGCACUUUCCGUAGGCUCACGCCUCCCAGGCAUUACCUGGCA
.((((((..(.((((((((.......))))))........((...(((....((((((((...((((.......))))))))))))))).)))).)..(((.....))).....)))))) ( -40.10)
>consensus
UUGCCAGACGUGCGGUGCGCUCUUACCGCACCUUUUCACCCUUACCGGCACCGAAGCGCUUAGGCGGUUAUUUUCUGUGGCACUUUCCGUAGGCUCGCGCCUCCCAGGCGUUACCUGGCA
.((((((..(.((((((((.......)))))).....(((((((..(((((....))))))))).)))......((((((......)))))))).)(((((.....)))))...)))))) (-40.46 = -40.10 +  -0.36)

alignment

secondary structure

dotplot

Window 0

Location	4,956,505 – 4,956,625
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.56
Mean single sequence MFE	-51.08
Consensus MFE	-51.72
Energy contribution	-50.72
Covariance contribution	-1.00
Combinations/Pair	1.12
Mean z-score	-3.26
Structure conservation index	1.01
SVM decision value	6.19
SVM RNA-class probability	0.999997
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 4956505 120 - 1
UGCCAGGUAACGCCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCGCAACAGCGCCGGUAAGGGUGAAAAGGUGCGGUAAGAGCGCACCGCACGGCUGGCAA
((((((.(..(((((((.((((....))))..((......))...........))(((...((((....)))).)))..))))).....(((((((........)))))))).)))))). ( -49.60)
>pst_1 159 120 - 1
UGCCAGGUAACACCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCACUUCGGUGCCGGUAAGGGUGAAAAGGUGCGGUAAGAGCGCACCGCACGUCUGGCAA
(((((((...(((((((.((((....))))..((......))...........))(((...((((....)))).)))..))))).....(((((((........))))))).))))))). ( -52.10)
>pau_1 160 120 - 1
UGCCAGGUAACGCCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCGCAACAGCGCCGGUAAGGGUGAAAAGGUGCGGUAAGAGCGCACCGCACGGCUGGCAA
((((((.(..(((((((.((((....))))..((......))...........))(((...((((....)))).)))..))))).....(((((((........)))))))).)))))). ( -49.60)
>pel_1 161 120 - 1
UGCCAGGUAACGCCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAGAAAACAACCGCCUAAGCGCUUCGGCGCCGGUAAGGGUGAAAAGGUGCGGUAAGAGCGCACCGCGCGACUGGCAA
((((((....(((((((.((((....))))..((......))...........))(((...((((....)))).)))..))))).....(((((((........)))))))..)))))). ( -52.80)
>pf5_1 159 120 - 1
UGCCAGGUAAUGCCUGGGGGGCGUGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCACUUCGGUGCCGGUAAGGGUGAAAAGGUGCGGUAAGAGCGCACCGCACGUCUGGUAA
..(((((.....))))).((((....)))).((((..((((.............(((((..((((....))))......)))))....((((((.......)))))))))).)))).... ( -50.70)
>pfs_1 159 120 - 1
UGCCAGGUAAUGCCUGGGAGGCGUGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCACUUCGGUGCCGGUAAGGGUGAAAAGGUGCGGUAAGAGCGCACCGCGCGACUGGCAA
((((((.......(((..((((....)))).)))...((((.............(((((..((((....))))......)))))....((((((.......))))))))))..)))))). ( -51.70)
>consensus
UGCCAGGUAACGCCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCACUUCGGCGCCGGUAAGGGUGAAAAGGUGCGGUAAGAGCGCACCGCACGACUGGCAA
((((((.......(((..((((....)))).)))...((((.............(((((..((((....))))......)))))....((((((.......))))))))))..)))))). (-51.72 = -50.72 +  -1.00)

alignment

secondary structure

dotplot

Window 1

Location	4,956,535 – 4,956,655
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	95.28
Mean single sequence MFE	-39.50
Consensus MFE	-39.38
Energy contribution	-39.02
Covariance contribution	-0.36
Combinations/Pair	1.06
Mean z-score	-1.94
Structure conservation index	1.00
SVM decision value	4.08
SVM RNA-class probability	0.999789
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 4956535 120 + 1
CCUUUUCACCCUUACCGGCGCUGUUGCGCUUAGGCGGUUAUUUUCUGUGGCACUUUCCGUAGGCUCGCGCCUCCCAGGCGUUACCUGGCACUCUGCCCUAUGGAGCCCGGACUUUCCUCC
.......(((((((..(((((....))))))))).))).....((((.(((....(((((((....(((((.....))))).....(((.....)))))))))))))))))......... ( -41.20)
>pst_1 189 120 + 1
CCUUUUCACCCUUACCGGCACCGAAGUGCUUAGGCGGUUAUUUUCUGUGGCACUUUCCGUAGGCUCGCGCCUCCCAGGUGUUACCUGGCACUCCGCCCUAUGGAGCCCGGACUUUCCUCC
.......(((((((..(((((....))))))))).))).....((((.(((....((((((((...(((....(((((.....))))).....))))))))))))))))))......... ( -40.50)
>pau_1 190 120 + 1
CCUUUUCACCCUUACCGGCGCUGUUGCGCUUAGGCGGUUAUUUUCUGUGGCACUUUCCGUAGGCUCGCGCCUCCCAGGCGUUACCUGGCACUCUGCCCUAUGGAGCCCGGACUUUCCUCC
.......(((((((..(((((....))))))))).))).....((((.(((....(((((((....(((((.....))))).....(((.....)))))))))))))))))......... ( -41.20)
>pel_1 191 120 + 1
CCUUUUCACCCUUACCGGCGCCGAAGCGCUUAGGCGGUUGUUUUCUGUGGCACUUUCCGUAGGCUCGCGCCUCCCAGGCGUUACCUGGCACUCUGCCCUAUGGAGCCCGGACUUUCCUCC
.......(((((((..(((((....))))))))).))).....((((.(((....(((((((....(((((.....))))).....(((.....)))))))))))))))))......... ( -40.20)
>pf5_1 189 120 + 1
CCUUUUCACCCUUACCGGCACCGAAGUGCUUAGGCGGUUAUUUUCUGUGGCACUUUCCGUAGGCUCACGCCCCCCAGGCAUUACCUGGCACUCCGCCCUAUGGAGCCCGGACUUUCCUCC
.......(((((((..(((((....))))))))).))).....((((.(((....((((((((....((....(((((.....))))).....)).)))))))))))))))......... ( -36.20)
>pfo_1 189 120 + 1
CCUUUUCACCCUUACCGGCGCCGAAGCGCUUAGGCGGUUAUUUUCUGUGGCACUUUCCGUAGGCUCACGCCUCCCAGGCAUUACCUGGCACUUCGCCCUAUGGAGCCCGGACUUUCCUCC
.......(((((((..(((((....))))))))).))).....((((.(((....((((((((....((....(((((.....))))).....)).)))))))))))))))......... ( -37.70)
>consensus
CCUUUUCACCCUUACCGGCGCCGAAGCGCUUAGGCGGUUAUUUUCUGUGGCACUUUCCGUAGGCUCGCGCCUCCCAGGCGUUACCUGGCACUCCGCCCUAUGGAGCCCGGACUUUCCUCC
.......(((((((..(((((....))))))))).))).....((((.(((....((((((((...(((....(((((.....))))).....))))))))))))))))))......... (-39.38 = -39.02 +  -0.36)

alignment

secondary structure

dotplot

Window 2

Location	4,956,535 – 4,956,655
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	95.28
Mean single sequence MFE	-43.62
Consensus MFE	-43.40
Energy contribution	-42.82
Covariance contribution	-0.58
Combinations/Pair	1.07
Mean z-score	-1.62
Structure conservation index	0.99
SVM decision value	3.21
SVM RNA-class probability	0.998756
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 4956535 120 - 1
GGAGGAAAGUCCGGGCUCCAUAGGGCAGAGUGCCAGGUAACGCCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCGCAACAGCGCCGGUAAGGGUGAAAAGG
...((....((((.((((....))))......(((((.....))))).((((....)))).)))).....))............(((((..((((....))))......)))))...... ( -41.00)
>pst_1 189 120 - 1
GGAGGAAAGUCCGGGCUCCAUAGGGCGGAGUGCCAGGUAACACCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCACUUCGGUGCCGGUAAGGGUGAAAAGG
...((....((((.(((((.......))))).(((((.....))))).((((....)))).)))).....))............(((((..((((....))))......)))))...... ( -44.90)
>pau_1 190 120 - 1
GGAGGAAAGUCCGGGCUCCAUAGGGCAGAGUGCCAGGUAACGCCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCGCAACAGCGCCGGUAAGGGUGAAAAGG
...((....((((.((((....))))......(((((.....))))).((((....)))).)))).....))............(((((..((((....))))......)))))...... ( -41.00)
>pel_1 191 120 - 1
GGAGGAAAGUCCGGGCUCCAUAGGGCAGAGUGCCAGGUAACGCCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAGAAAACAACCGCCUAAGCGCUUCGGCGCCGGUAAGGGUGAAAAGG
...((....((((.((((....))))......(((((.....))))).((((....)))).)))).....))............(((((..((((....))))......)))))...... ( -44.30)
>pf5_1 189 120 - 1
GGAGGAAAGUCCGGGCUCCAUAGGGCGGAGUGCCAGGUAAUGCCUGGGGGGCGUGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCACUUCGGUGCCGGUAAGGGUGAAAAGG
...((....((((.(((((.......))))).(((((.....))))).((((....)))).)))).....))............(((((..((((....))))......)))))...... ( -45.70)
>pfo_1 189 120 - 1
GGAGGAAAGUCCGGGCUCCAUAGGGCGAAGUGCCAGGUAAUGCCUGGGAGGCGUGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCGCUUCGGCGCCGGUAAGGGUGAAAAGG
...((....((((.((((....))))......(((((.....))))).((((....)))).)))).....))............(((((..((((....))))......)))))...... ( -44.80)
>consensus
GGAGGAAAGUCCGGGCUCCAUAGGGCAGAGUGCCAGGUAACGCCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCGCUUCGGCGCCGGUAAGGGUGAAAAGG
...((....((((.((((....))))......(((((.....))))).((((....)))).)))).....))............(((((..((((....))))......)))))...... (-43.40 = -42.82 +  -0.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:51:02 2007