Locus 90

Sequence ID	Eco_1
Location	4,034,085 – 4,034,325
Length	240
Max. P	0.998023

overview

Window 2

Location	4,034,085 – 4,034,205
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	88.06
Mean single sequence MFE	-39.67
Consensus MFE	-39.80
Energy contribution	-37.03
Covariance contribution	-2.76
Combinations/Pair	1.25
Mean z-score	-1.12
Structure conservation index	1.00
SVM decision value	0.84
SVM RNA-class probability	0.863446
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4034085 120 + 1
AAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGC
...........(((..((((...((((.....))))(((.....)))))))..)))((((((((.((((((((((...((((.((......)).))))..))))))))))..)))))))) ( -40.90)
>Hin_1 41 120 + 1
AAUACGGAGGGUGCGAGCGUUAAUCGGAAUAACUGGGCGUAAAGGGCACGCAGGCGGUUAUUUAAGUGAGGUGUGAAAGCCCCGGGCUUAACCUGGGAAUUGCAUUUCAGACUGGGUAAC
....(((.((((((((((.(((....(((((((((.((((.......))))...)))))))))...))).))((....))((((((.....))))))..))))))))....)))...... ( -34.70)
>Sty_1 41 120 + 1
AAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUCUGUCAAGUCGGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUUCGAAACUGGCAGGC
...........(((..((((...((((.....))))(((.....)))))))..)))((((((((..(((((((((...((((.((......)).))))..)))))))))...)))))))) ( -43.40)
>consensus
AAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUUUGAAACUGGCAAGC
...........(((..((((...((((.....))))(((.....)))))))..)))((((((((..((((((((......((((((.....))))))....))))))))...)))))))) (-39.80 = -37.03 +  -2.76)

alignment

secondary structure

dotplot

Window 3

Location	4,034,125 – 4,034,245
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	84.72
Mean single sequence MFE	-41.30
Consensus MFE	-40.16
Energy contribution	-38.07
Covariance contribution	-2.10
Combinations/Pair	1.23
Mean z-score	-1.29
Structure conservation index	0.97
SVM decision value	1.35
SVM RNA-class probability	0.945273
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4034125 120 + 1
AAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGG
....((((((((((((((((((((.((((((((((...((((.((......)).))))..))))))))))..)))))))))...)))).......((((......))))..)))).))). ( -43.10)
>Hin_1 81 120 + 1
AAAGGGCACGCAGGCGGUUAUUUAAGUGAGGUGUGAAAGCCCCGGGCUUAACCUGGGAAUUGCAUUUCAGACUGGGUAACUAGAGUACUUUAGGGAGGGGUAGAAUUCCACGUGUAGCGG
........((((.(((((((((((..(((((((..(....((((((.....))))))..)..)))))))...)))))))).............((((........)))).))).).))). ( -35.20)
>Sty_1 81 120 + 1
AAAGCGCACGCAGGCGGUCUGUCAAGUCGGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUUCGAAACUGGCAGGCUUGAGUCUUGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGG
....((((((((((((((((((((..(((((((((...((((.((......)).))))..)))))))))...)))))))))...)))).......((((......))))..)))).))). ( -45.60)
>consensus
AAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUUUGAAACUGGCAAGCUUGAGUCUUGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGG
....((((((((((((((((((((..((((((((......((((((.....))))))....))))))))...)))))))))...))))........(((((...)))))..)))).))). (-40.16 = -38.07 +  -2.10)

alignment

secondary structure

dotplot

Window 4

Location	4,034,205 – 4,034,325
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	88.89
Mean single sequence MFE	-47.03
Consensus MFE	-47.61
Energy contribution	-45.40
Covariance contribution	-2.21
Combinations/Pair	1.20
Mean z-score	-3.55
Structure conservation index	1.01
SVM decision value	2.99
SVM RNA-class probability	0.998023
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4034205 120 + 1
UUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCG
...((((((((..((((.((((...((((((((.(.(((......)))....).))))))))...))))(((.((....)).)))))))..))).)))))...........((....)). ( -51.30)
>Hin_1 161 120 + 1
UAGAGUACUUUAGGGAGGGGUAGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAAUACCGAAGGCGAAGGCAGCCCCUUGGGAAUGUACUGACGCUCAUGUGCGAAAGCG
...((((((((((((.((((((...((((((((.(.(((......)))....).))))))))...))))....((....))..)))))))))...)))))...........((....)). ( -40.30)
>Sty_1 161 120 + 1
UUGAGUCUUGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACAAAGACUGACGCUCAGGUGCGAAAGCG
...((((((((..((((.((((...((((((((.(.(((......)))....).))))))))...))))(((.((....)).)))))))..)).))))))...........((....)). ( -49.50)
>consensus
UUGAGUCUUGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACAAAGACUGACGCUCAGGUGCGAAAGCG
...((((((((...((((((((...((((((((.(.(((......)))....).))))))))...))))(((.((....)).)))))))..))).)))))...........((....)). (-47.61 = -45.40 +  -2.21)

alignment

secondary structure

dotplot

Window 5

Location	4,034,205 – 4,034,325
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	88.89
Mean single sequence MFE	-29.43
Consensus MFE	-29.32
Energy contribution	-27.89
Covariance contribution	-1.44
Combinations/Pair	1.19
Mean z-score	-1.75
Structure conservation index	1.00
SVM decision value	1.56
SVM RNA-class probability	0.963858
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4034205 120 - 1
CGCUUUCGCACCUGAGCGUCAGUCUUCGUCCAGGGGGCCGCCUUCGCCACCGGUAUUCCUCCAGAUCUCUACGCAUUUCACCGCUACACCUGGAAUUCUACCCCCCUCUACGAGACUCAA
(((((........)))))..(((((.(((..(((((((.......)))...((((....(((((........((........)).....)))))....)))).))))..))))))))... ( -32.62)
>Hin_1 161 120 - 1
CGCUUUCGCACAUGAGCGUCAGUACAUUCCCAAGGGGCUGCCUUCGCCUUCGGUAUUCCUCCACAUCUCUACGCAUUUCACCGCUACACGUGGAAUUCUACCCCUCCCUAAAGUACUCUA
(((((........)))))..(((((.......(((((.((((.........))))....(((((........((........)).....)))))......))))).......)))))... ( -24.86)
>Sty_1 161 120 - 1
CGCUUUCGCACCUGAGCGUCAGUCUUUGUCCAGGGGGCCGCCUUCGCCACCGGUAUUCCUCCAGAUCUCUACGCAUUUCACCGCUACACCUGGAAUUCUACCCCCCUCUACAAGACUCAA
(((((........)))))..((((((.((..(((((((.......)))...((((....(((((........((........)).....)))))....)))).))))..))))))))... ( -30.82)
>consensus
CGCUUUCGCACCUGAGCGUCAGUCUUUGUCCAGGGGGCCGCCUUCGCCACCGGUAUUCCUCCAGAUCUCUACGCAUUUCACCGCUACACCUGGAAUUCUACCCCCCUCUACAAGACUCAA
(((((........)))))..(((((.(((..(((((((.......)))...((((....(((((........((........)).....)))))....)))).))))..))))))))... (-29.32 = -27.89 +  -1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:06:25 2006