Locus 85

Sequence ID Eco_1
Location 3,942,312 – 3,942,792
Length 480
Max. P 0.973633
window276 window277 window278 window279 window280 window281

overview

Window 6

Location 3,942,312 – 3,942,432
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.81
Mean single sequence MFE -41.15
Consensus MFE -41.45
Energy contribution -41.08
Covariance contribution -0.38
Combinations/Pair 1.03
Mean z-score -2.32
Structure conservation index 1.01
SVM decision value 1.71
SVM RNA-class probability 0.973633
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3942312 120 + 1
ACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGA
..((((((((((((((..((((..((.....))..))))...((....))..((((.....)))).....))))))))))))))..(((.....))).(((((.(((...)))))))).. ( -41.60)
>Sfl_1 599 120 + 1
ACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGA
..((((((((((((((..((((..((.....))..))))...((....))..((((.....)))).....))))))))))))))..(((.....))).(((((.(((...)))))))).. ( -41.60)
>Sty_1 601 120 + 1
ACUUAUAUUCUGUAGCAAGGUUAACCGUAUAGGGGAGCCGGAGGGAAACCGAGUCUUAAUUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGA
..((((((((((((((..((((..((.....))..))))...((....))..((((.....)))).....))))))))))))))..(((.....))).(((((.(((...)))))))).. ( -41.60)
>Ype_1 598 120 + 1
ACUUAUAUUUUGUAGCAAGGUUAACCGAAUAGGGGAGCCGUAGGGAAACCGAGUCUUAACUGGGCGUCUAGUUGCAAGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGA
..((((((((((((((..((((..((.....))..))))...((....))((((((.....)))).))..))))))))))))))..(((.....))).(((((.(((...)))))))).. ( -39.80)
>consensus
ACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGA
..((((((((((((((..((((..((.....))..))))...((....))..((((.....)))).....))))))))))))))..(((.....))).(((((.(((...)))))))).. (-41.45 = -41.08 +  -0.38)

alignment

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secondary structure

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Window 7

Location 3,942,352 – 3,942,472
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.64
Mean single sequence MFE -38.90
Consensus MFE -37.61
Energy contribution -37.67
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -1.57
Structure conservation index 0.97
SVM decision value 0.07
SVM RNA-class probability 0.569339
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3942352 120 + 1
AAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUG
..((....)).((((...((((((.((......)).((((....))))....))))))(((((.(((...))))))))...((((.(((....(.....)....))).)))))))).... ( -39.90)
>Sfl_1 639 120 + 1
AAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUG
..((....)).((((...((((((.((......)).((((....))))....))))))(((((.(((...))))))))...((((.(((....(.....)....))).)))))))).... ( -39.90)
>Sty_1 641 120 + 1
GAGGGAAACCGAGUCUUAAUUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUG
..((....)).((((...((((((.((......)).((((....))))....))))))(((((.(((...))))))))...((((.(((....(.....)....))).)))))))).... ( -37.50)
>Ype_1 638 120 + 1
UAGGGAAACCGAGUCUUAACUGGGCGUCUAGUUGCAAGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUG
..((....)).((((.....(((.(.((((((((....((....((((((...((..((((((.(((...)))))))))..)))))))).))..)))))))).).)))....)))).... ( -38.30)
>consensus
AAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUG
..((....)).((((...((((((.((......)).((((....))))....))))))(((((.(((...))))))))...((((.(((....(.....)....))).)))))))).... (-37.61 = -37.67 +   0.06)

alignment

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secondary structure

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Window 8

Location 3,942,392 – 3,942,512
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 99.58
Mean single sequence MFE -42.67
Consensus MFE -42.84
Energy contribution -42.65
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -3.27
Structure conservation index 1.00
SVM decision value 1.30
SVM RNA-class probability 0.939461
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3942392 120 + 1
AUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGG
......((...((((......(((((((..((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))..)))))))))))....)) ( -42.20)
>Sfl_1 679 120 + 1
AUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGG
......((...((((......(((((((..((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))..)))))))))))....)) ( -42.20)
>Sty_1 681 120 + 1
AUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACCUGUGGCUGGGGGUGAAAGG
......((...((((......(((((((((((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).)))))))))))))))....)) ( -44.10)
>Ype_1 678 120 + 1
AUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGG
......((...((((......(((((((..((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))..)))))))))))....)) ( -42.20)
>consensus
AUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGG
......((...((((......(((((((..((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))..)))))))))))....)) (-42.84 = -42.65 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,942,432 – 3,942,552
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 99.58
Mean single sequence MFE -38.52
Consensus MFE -38.71
Energy contribution -38.52
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -1.91
Structure conservation index 1.00
SVM decision value 0.29
SVM RNA-class probability 0.670074
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3942432 120 + 1
AGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUA
.((((((......))))))(((((((((..(((.(((((........)))))))).....((((..((.((..(((........)))..)).))..)))).))))))))).(....)... ( -38.00)
>Sfl_1 719 120 + 1
AGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUA
.((((((......))))))(((((((((..(((.(((((........)))))))).....((((..((.((..(((........)))..)).))..)))).))))))))).(....)... ( -38.00)
>Sty_1 721 120 + 1
AGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACCUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUA
.((((((......))))))(((((((((..(((.(((((........)))))))).....((((..((.((..(((........)))..)).))..)))).))))))))).(....)... ( -40.10)
>Ype_1 718 120 + 1
AGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUA
.((((((......))))))(((((((((..(((.(((((........)))))))).....((((..((.((..(((........)))..)).))..)))).))))))))).(....)... ( -38.00)
>consensus
AGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUA
.((((((......))))))(((((((((..(((.(((((........)))))))).....((((..((.((..(((........)))..)).))..)))).))))))))).(....)... (-38.71 = -38.52 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,942,552 – 3,942,672
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.25
Mean single sequence MFE -41.58
Consensus MFE -40.62
Energy contribution -40.75
Covariance contribution 0.12
Combinations/Pair 1.03
Mean z-score -1.67
Structure conservation index 0.98
SVM decision value 0.59
SVM RNA-class probability 0.793010
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3942552 120 - 1
UGUCUCCCGUGAUAACAUUCUCCGGUAUUCGCAGUUUGCAUCGGGUUGGUAAGUCGGGAUGACCCCCUUGCCGAAACAGUGCUCUACCCCCGGAGAUGAAUUCACGAGGCGCUACCUAAA
.(((((..((((...(((.((((((.....(.((...((((.(..((((((((..(((....))).))))))))..).)))).)).)..)))))))))...))))))))).......... ( -43.00)
>Sfl_1 839 120 - 1
UGUCUCCCGUGAUAACAUUCUCCGGUAUUCGCAGUUUGCAUCGGGUUGGUAAGUCGGGAUGACCCCCUUGCCGAAACAGUGCUCUACCCCCGGAGAUGAAUUCACGAGGCGCUACCUAAA
.(((((..((((...(((.((((((.....(.((...((((.(..((((((((..(((....))).))))))))..).)))).)).)..)))))))))...))))))))).......... ( -43.00)
>Sty_1 841 120 - 1
UGUCUCCCGUGAUAACAUUCUCCGGUAUUCGCAGUUUGCAUCGGGUUGGUAAGCCGGGAUGGCCCCCUAGCCGAAACAGUGCUCUACCCCCGGAGAUGAAUUCACGAGGCGCUACCUAAA
.(((((..((((...(((.((((((.....(.((...((((.(..(((((.((..(((....))).)).)))))..).)))).)).)..)))))))))...))))))))).......... ( -39.00)
>Ype_1 838 120 - 1
UGUCUCCCGUGAUAACAUUCUUCGGUAUUCGGAGUUUGCAUCGGUUUGGUAAGCCGGGAUGGCCCCCUAGCCGAAACAGUGCUCUACCCCCGAAGAUGAGUUCACGAGGCGCUACCUAAA
.(((((..((((...(((.((((((.....((((((((..((((((.((...(((.....)))..)).))))))..))).)))))....)))))))))...))))))))).......... ( -41.30)
>consensus
UGUCUCCCGUGAUAACAUUCUCCGGUAUUCGCAGUUUGCAUCGGGUUGGUAAGCCGGGAUGACCCCCUAGCCGAAACAGUGCUCUACCCCCGGAGAUGAAUUCACGAGGCGCUACCUAAA
.(((((..((((...(((.((((((.......((...((((.(..((((((((..(((....))).))))))))..).)))).))....)))))))))...))))))))).......... (-40.62 = -40.75 +   0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,942,672 – 3,942,792
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 99.58
Mean single sequence MFE -44.10
Consensus MFE -43.12
Energy contribution -43.12
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.98
SVM decision value -0.00
SVM RNA-class probability 0.533321
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3942672 120 + 1
CACGGCGGGUGCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCU
((((((((..(....)..))))))))....(((......))).((((.........))))((((.(((.(((((..((.(....).)).((((....))))...))))).))).)))).. ( -44.30)
>Sfl_1 959 120 + 1
CACGGCGGGUGCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCU
((((((((..(....)..))))))))....(((......))).((((.........))))((((.(((.(((((..((.(....).)).((((....))))...))))).))).)))).. ( -44.30)
>Sty_1 961 120 + 1
CACGGCGGGUGCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCU
((((((((..(....)..))))))))....(((......))).((((.........))))((((.(((.(((((..((.(....).)).((((....))))...))))).))).)))).. ( -44.30)
>Ype_1 958 120 + 1
CACGGCGGGUGCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCACAGACAGCCAGGAUGUUGGCU
((((((((..(....)..))))))))....(((......))).....((((((.....(((((....(((.(((........))).)))))))).(((.......))).....)))))). ( -43.50)
>consensus
CACGGCGGGUGCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCU
((((((((..(....)..))))))))....(((......))).....((((((.....(((((....(((.(((........))).)))))))).(((.......))).....)))))). (-43.12 = -43.12 +   0.00)

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 11:06:04 2006