Locus 106

Sequence ID Eco_1
Location 4,173,674 – 4,173,858
Length 184
Max. P 0.998607
window366 window367 window368 window369 window370 window371 window372

overview

Window 6

Location 4,173,674 – 4,173,794
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.22
Mean single sequence MFE -36.53
Consensus MFE -33.89
Energy contribution -33.00
Covariance contribution -0.89
Combinations/Pair 1.07
Mean z-score -1.42
Structure conservation index 0.93
SVM decision value 1.28
SVM RNA-class probability 0.939456
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4173674 120 + 1
UCAGGUAGCCGAGUUCCAGGAUGCGGGCAUCGUAUAAUGGCUAUUACCUCAGCCUUCCAAGCUGAUGAUGCGGGUUCGAUUCCCGCUGCCCGCUCCAAGAUGUGCUGAUAUAGCUCAGUU
...((.(((...))))).(((.(((((((((((.....((......)).((((.......)))))))))(((((.......))))).))))))))).......(((((......))))). ( -39.90)
>Hin_1 1 96 + 1
---------------------UGCGGGCAUCGUAUAAUGGCUAUUACCUUAGCCUUCCAAGCUAAUGAUGCGGGUUCGAUUCCCGCUGCCCGCUCCAGA---CGCUGAUAUAGCUCAGUU
---------------------.(((((((.........(((((......)))))...............(((((.......))))))))))))......---.(((((......))))). ( -34.80)
>Ype_1 1 120 + 1
UCAGGUAGCCGAGUUCUAAGAUGCGGGCAUCGUAUAAUGGCUAUUACCUCAGCCUUCCAAGCUGAUGAUGUGGGUUCGAUUCCCACUGCCCGCUCCAAGAUGUGCUGAUAUAGCUCAGUU
..............(((..((.(((((((((((.....((......)).((((.......)))))))))(((((.......))))).))))))))..)))...(((((......))))). ( -34.90)
>consensus
UCAGGUAGCCGAGUUC_A_GAUGCGGGCAUCGUAUAAUGGCUAUUACCUCAGCCUUCCAAGCUGAUGAUGCGGGUUCGAUUCCCGCUGCCCGCUCCAAGAUGUGCUGAUAUAGCUCAGUU
......................(((((((((((.....((......)).((((.......)))))))))(((((.......))))).))))))..........(((((......))))). (-33.89 = -33.00 +  -0.89)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,173,674 – 4,173,794
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.22
Mean single sequence MFE -42.40
Consensus MFE -38.82
Energy contribution -37.93
Covariance contribution -0.89
Combinations/Pair 1.07
Mean z-score -3.21
Structure conservation index 0.92
SVM decision value 2.80
SVM RNA-class probability 0.997139
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4173674 120 - 1
AACUGAGCUAUAUCAGCACAUCUUGGAGCGGGCAGCGGGAAUCGAACCCGCAUCAUCAGCUUGGAAGGCUGAGGUAAUAGCCAUUAUACGAUGCCCGCAUCCUGGAACUCGGCUACCUGA
..(((((((.....)))...(((.(((((((((.(((((.......)))))(((.((((((.....))))))(((....))).......))))))))).))).)))..))))........ ( -46.80)
>Hin_1 1 96 - 1
AACUGAGCUAUAUCAGCG---UCUGGAGCGGGCAGCGGGAAUCGAACCCGCAUCAUUAGCUUGGAAGGCUAAGGUAAUAGCCAUUAUACGAUGCCCGCA---------------------
..((((......))))..---......((((((.(((((.......)))))(((.((((((.....))))))(((....))).......))))))))).--------------------- ( -36.90)
>Ype_1 1 120 - 1
AACUGAGCUAUAUCAGCACAUCUUGGAGCGGGCAGUGGGAAUCGAACCCACAUCAUCAGCUUGGAAGGCUGAGGUAAUAGCCAUUAUACGAUGCCCGCAUCUUAGAACUCGGCUACCUGA
..(((((((.....)))...(((.(((((((((.(((((.......)))))(((.((((((.....))))))(((....))).......))))))))).))).)))..))))........ ( -43.50)
>consensus
AACUGAGCUAUAUCAGCACAUCUUGGAGCGGGCAGCGGGAAUCGAACCCGCAUCAUCAGCUUGGAAGGCUGAGGUAAUAGCCAUUAUACGAUGCCCGCAUC_U_GAACUCGGCUACCUGA
..((((......))))...........((((((.(((((.......)))))(((.((((((.....))))))(((....))).......)))))))))...................... (-38.82 = -37.93 +  -0.89)

alignment

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secondary structure

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Window 8

Location 4,173,714 – 4,173,834
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.78
Mean single sequence MFE -44.90
Consensus MFE -43.24
Energy contribution -43.47
Covariance contribution 0.22
Combinations/Pair 1.03
Mean z-score -2.67
Structure conservation index 0.96
SVM decision value 2.00
SVM RNA-class probability 0.985339
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4173714 120 - 1
CGAACUGCCGACCUCACCCUUACCAAGGGUGCGCUCUACCAACUGAGCUAUAUCAGCACAUCUUGGAGCGGGCAGCGGGAAUCGAACCCGCAUCAUCAGCUUGGAAGGCUGAGGUAAUAG
....(((...((((((.((((.(((((.((.(((((((....((((......)))).......))))))).)).(((((.......)))))........))))))))).))))))..))) ( -47.80)
>Hin_1 20 117 - 1
UGAACCGCCGACCUCACCCUUACCAAGGGUGCACUCUACCAACUGAGCUAUAUCAGCG---UCUGGAGCGGGCAGCGGGAAUCGAACCCGCAUCAUUAGCUUGGAAGGCUAAGGUAAUAG
...((((((.....((((((.....))))))(.(((((....((((......))))..---..))))).)))).(((((.......)))))....((((((.....)))))))))..... ( -40.60)
>Ype_1 41 120 - 1
CGAACUGCCGACCUCACCCUUACCAAGGGUGCGCUCUACCAACUGAGCUAUAUCAGCACAUCUUGGAGCGGGCAGUGGGAAUCGAACCCACAUCAUCAGCUUGGAAGGCUGAGGUAAUAG
....(((...((((((.((((.(((((.((.(((((((....((((......)))).......))))))).)).(((((.......)))))........))))))))).))))))..))) ( -46.30)
>consensus
CGAACUGCCGACCUCACCCUUACCAAGGGUGCGCUCUACCAACUGAGCUAUAUCAGCACAUCUUGGAGCGGGCAGCGGGAAUCGAACCCGCAUCAUCAGCUUGGAAGGCUGAGGUAAUAG
..........((((((.((((.(((((.((.(((((((....((((......)))).......))))))).)).(((((.......)))))........))))))))).))))))..... (-43.24 = -43.47 +   0.22)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,173,738 – 4,173,858
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.28
Mean single sequence MFE -46.53
Consensus MFE -44.25
Energy contribution -44.03
Covariance contribution -0.22
Combinations/Pair 1.09
Mean z-score -2.36
Structure conservation index 0.95
SVM decision value 1.68
SVM RNA-class probability 0.971937
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4173738 120 + 1
AUGAUGCGGGUUCGAUUCCCGCUGCCCGCUCCAAGAUGUGCUGAUAUAGCUCAGUUGGUAGAGCGCACCCUUGGUAAGGGUGAGGUCGGCAGUUCGAAUCUGCCUAUCAGCACCACUUCU
.((..((((((.((.....))..))))))..))(((.(((((((((..((((........)))).((((((.....)))))).....(((((.......))))))))))))))....))) ( -49.10)
>Hin_1 44 112 + 1
AUGAUGCGGGUUCGAUUCCCGCUGCCCGCUCCAGA---CGCUGAUAUAGCUCAGUUGGUAGAGUGCACCCUUGGUAAGGGUGAGGUCGGCGGUUCAAAUCCGCCUAUCAGCACCA-----
.(((((((((((.((...(((((((((((((....---.(((((......))))).....)))))((((((.....)))))).)).)))))).)).)))))))..))))......----- ( -45.20)
>Ype_1 65 120 + 1
AUGAUGUGGGUUCGAUUCCCACUGCCCGCUCCAAGAUGUGCUGAUAUAGCUCAGUUGGUAGAGCGCACCCUUGGUAAGGGUGAGGUCGGCAGUUCGAAUCUGCCUAUCAGCACCAUUUCU
.((..((((((............))))))..))(((((((((((((..((((........)))).((((((.....)))))).....(((((.......))))))))))))).))))).. ( -45.30)
>consensus
AUGAUGCGGGUUCGAUUCCCGCUGCCCGCUCCAAGAUGUGCUGAUAUAGCUCAGUUGGUAGAGCGCACCCUUGGUAAGGGUGAGGUCGGCAGUUCGAAUCUGCCUAUCAGCACCA_UUCU
.((..((((((............))))))..))....(((((((((..((((........)))).((((((.....)))))).....(((((.......))))))))))))))....... (-44.25 = -44.03 +  -0.22)

alignment

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secondary structure

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Window 0

Location 4,173,738 – 4,173,858
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.28
Mean single sequence MFE -45.77
Consensus MFE -42.45
Energy contribution -42.57
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -2.97
Structure conservation index 0.93
SVM decision value 2.00
SVM RNA-class probability 0.985269
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4173738 120 - 1
AGAAGUGGUGCUGAUAGGCAGAUUCGAACUGCCGACCUCACCCUUACCAAGGGUGCGCUCUACCAACUGAGCUAUAUCAGCACAUCUUGGAGCGGGCAGCGGGAAUCGAACCCGCAUCAU
..(((..((((((((((((((.......))))).....((((((.....)))))).((((........))))..)))))))))..))).(((((((...((.....))..))))).)).. ( -48.60)
>Hin_1 44 112 - 1
-----UGGUGCUGAUAGGCGGAUUUGAACCGCCGACCUCACCCUUACCAAGGGUGCACUCUACCAACUGAGCUAUAUCAGCG---UCUGGAGCGGGCAGCGGGAAUCGAACCCGCAUCAU
-----.(..((((((((((((.......))))).....((((((.....))))))..(((........)))...))))))).---.)((..(((((...((.....))..)))))..)). ( -43.10)
>Ype_1 65 120 - 1
AGAAAUGGUGCUGAUAGGCAGAUUCGAACUGCCGACCUCACCCUUACCAAGGGUGCGCUCUACCAACUGAGCUAUAUCAGCACAUCUUGGAGCGGGCAGUGGGAAUCGAACCCACAUCAU
.((..(((((((....))))(((((..((((((.....((((((.....))))))(((((((....((((......)))).......)))))))))))))..)))))....)))..)).. ( -45.60)
>consensus
AGAA_UGGUGCUGAUAGGCAGAUUCGAACUGCCGACCUCACCCUUACCAAGGGUGCGCUCUACCAACUGAGCUAUAUCAGCACAUCUUGGAGCGGGCAGCGGGAAUCGAACCCGCAUCAU
.......((((((((((((((.......))))).....((((((.....)))))).((((........))))..)))))))))....((..(((((...((.....))..)))))..)). (-42.45 = -42.57 +   0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,173,774 – 4,173,856
Length 82
Sequences 4
Columns 82
Reading direction forward
Mean pairwise identity 93.90
Mean single sequence MFE -34.80
Consensus MFE -35.55
Energy contribution -34.80
Covariance contribution -0.75
Combinations/Pair 1.08
Mean z-score -3.41
Structure conservation index 1.02
SVM decision value 3.16
SVM RNA-class probability 0.998607
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4173774 82 + 1
UGUGCUGAUAUAGCUCAGUUGGUAGAGCGCACCCUUGGUAAGGGUGAGGUCGGCAGUUCGAAUCUGCCUAUCAGCACCACUU
.(((((((((..((((........)))).((((((.....)))))).....(((((.......))))))))))))))..... ( -35.40)
>Sfl_1 1 81 + 1
-GUGCUGAUAUGGCUCAGUUGGUAGAGCGCACCCUUGGUAAGGGUGAGGUCCCCAGUUCGACUCUGGGUAUCAGCACCACUU
-(((((((((..((((........)))).((((((.....)))))).....(((((.......))))))))))))))..... ( -34.60)
>Sty_1 1 82 + 1
UGUGCUGAUAUGGCUCAGUUGGUAGAGCGCACCCUUGGUAAGGGUGAGGUCCCCAGUUCGACUCUGGGUAUCAGCACCACUU
.(((((((((..((((........)))).((((((.....)))))).....(((((.......))))))))))))))..... ( -34.60)
>Ype_1 1 79 + 1
UGUGCUGAUAUGGCUCAGUUGGUAGAGCGCACCCUUGGUAAGGGUGAGGUCCCCAGUUCGACUCUGGGUAUCAGCACCA---
.(((((((((..((((........)))).((((((.....)))))).....(((((.......))))))))))))))..--- ( -34.60)
>consensus
UGUGCUGAUAUGGCUCAGUUGGUAGAGCGCACCCUUGGUAAGGGUGAGGUCCCCAGUUCGACUCUGGGUAUCAGCACCACUU
.(((((((((..((((........)))).((((((.....)))))).....(((((.......))))))))))))))..... (-35.55 = -34.80 +  -0.75)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,173,774 – 4,173,856
Length 82
Sequences 4
Columns 82
Reading direction reverse
Mean pairwise identity 93.90
Mean single sequence MFE -34.90
Consensus MFE -35.65
Energy contribution -34.90
Covariance contribution -0.75
Combinations/Pair 1.08
Mean z-score -4.76
Structure conservation index 1.02
SVM decision value 2.27
SVM RNA-class probability 0.991503
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4173774 82 - 1
AAGUGGUGCUGAUAGGCAGAUUCGAACUGCCGACCUCACCCUUACCAAGGGUGCGCUCUACCAACUGAGCUAUAUCAGCACA
.....((((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))))). ( -36.00)
>Sfl_1 1 81 - 1
AAGUGGUGCUGAUACCCAGAGUCGAACUGGGGACCUCACCCUUACCAAGGGUGCGCUCUACCAACUGAGCCAUAUCAGCAC-
.....((((((((((((((.......))))).....((((((.....)))))).((((........))))..)))))))))- ( -33.40)
>Sty_1 1 82 - 1
AAGUGGUGCUGAUACCCAGAGUCGAACUGGGGACCUCACCCUUACCAAGGGUGCGCUCUACCAACUGAGCCAUAUCAGCACA
.....((((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))))). ( -35.10)
>Ype_1 1 79 - 1
---UGGUGCUGAUACCCAGAGUCGAACUGGGGACCUCACCCUUACCAAGGGUGCGCUCUACCAACUGAGCCAUAUCAGCACA
---..((((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))))). ( -35.10)
>consensus
AAGUGGUGCUGAUACCCAGAGUCGAACUGGGGACCUCACCCUUACCAAGGGUGCGCUCUACCAACUGAGCCAUAUCAGCACA
.....((((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))))). (-35.65 = -34.90 +  -0.75)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:07:24 2006