Locus 68

Sequence ID	Eco_1
Location	3,421,403 – 3,421,516
Length	113
Max. P	0.975953

overview

Window 9

Location	3,421,403 – 3,421,516
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.94
Mean single sequence MFE	-36.16
Consensus MFE	-25.69
Energy contribution	-25.75
Covariance contribution	0.06
Combinations/Pair	1.17
Mean z-score	-2.12
Structure conservation index	0.71
SVM decision value	0.80
SVM RNA-class probability	0.854511
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3421403 113 + 1
ACAAAAGGCCCAGUCUUCCGACUGAGCCUU-UUG------UUUUAUUUGAUGUCUGGCAGUUCCCUACUCUCGCAUGGGGAGACCCCACACUACCAUCGGCGCUACGGCGUUUCACUUCU
(((((((((.(((((....))))).)))))-)))------).......((((..(((...(((((((........)))))))...)))......))))(((((....)))))........ ( -40.40)
>Sfl_1 1 119 + 1
ACCAAGGGUGCGCUCUACCAACUGAGCCAUAUCAGCACG-CUAAAUUUGAUGCCUGGCAGUUCCCUACUCUCGCAUGGGGAGACCCCACACUACCAUCGGCGCUACGGCGUUUCACUUCU
....((.((((((((........)))).......)))).-))......((((..(((...(((((((........)))))))...)))......))))(((((....)))))........ ( -32.41)
>Sty_1 1 113 + 1
ACAAAAGGCCCUGUCUUCCGACAGGGCCCU-UCG------UUUUAUUUGAUGCCUGGCAGUUCCCUACUCUCGCAUGGGGAGACCCCACACUACCAUCGGCGCUACGGCGUUUCACUUCU
......(((((((((....)))))))))..-...------........((((..(((...(((((((........)))))))...)))......))))(((((....)))))........ ( -39.60)
>Ype_1 1 120 + 1
ACCAAGGGUGCGCUCUACCAACUGAGCCAUAUCAGCACAACUAAAUUUGAUGCCUGGCAGUGUCCUACUCUCGCAUGGGGAGACCCCACACUACCAUCGGCGCUACGGCGUUUCACUUCU
...(((.((((((((........)))).......)))).........(((.((((((.(((((....(((((.....))))).....))))).)))..)))((....))...)))))).. ( -32.21)
>consensus
ACAAAAGGCCCGCUCUACCAACUGAGCCAU_UCA______CUAAAUUUGAUGCCUGGCAGUUCCCUACUCUCGCAUGGGGAGACCCCACACUACCAUCGGCGCUACGGCGUUUCACUUCU
......(((.(((((....))))).)))....................(((((((((((((.....))).......(((....)))...............)))).))))))........ (-25.69 = -25.75 +   0.06)

alignment

secondary structure

dotplot

Window 0

Location	3,421,403 – 3,421,516
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.94
Mean single sequence MFE	-46.30
Consensus MFE	-33.46
Energy contribution	-35.27
Covariance contribution	1.81
Combinations/Pair	1.09
Mean z-score	-2.96
Structure conservation index	0.72
SVM decision value	1.76
SVM RNA-class probability	0.975953
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3421403 113 - 1
AGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGACAUCAAAUAAAA------CAA-AAGGCUCAGUCGGAAGACUGGGCCUUUUGU
..........(((....)))..((((...((((((((...))))))))..(.((((....)))))...)))).......(------(((-(((((((((((....))))))))))))))) ( -51.60)
>Sfl_1 1 119 - 1
AGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAUCAAAUUUAG-CGUGCUGAUAUGGCUCAGUUGGUAGAGCGCACCCUUGGU
...........((((..((((.((((.(.((((((((...))))))))..(.((((....))))).).))))...((((.-((.(((((......))))))).)))))))).....)))) ( -37.40)
>Sty_1 1 113 - 1
AGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAUCAAAUAAAA------CGA-AGGGCCCUGUCGGAAGACAGGGCCUUUUGU
.....(((...((....))(((..(((((((((((((...))))))((....)).....)))))))))).)))......(------(((-(((((((((((....))))))))))))))) ( -55.90)
>Ype_1 1 120 - 1
AGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGACACUGCCAGGCAUCAAAUUUAGUUGUGCUGAUAUGGCUCAGUUGGUAGAGCGCACCCUUGGU
...........((((..(((((..(((((((((((((...)))).(((....)))..))))))))))))..........(((.(((..((........))..))).))))).....)))) ( -40.30)
>consensus
AGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAUCAAAUAAAA______CGA_AUGGCUCAGUCGGAAGACCGCACCCUUGGU
.....(((...((....))(((..(((((((((((((...))))))((....)).....)))))))))).)))...................(((((((((....)))))))))...... (-33.46 = -35.27 +   1.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:05:01 2006