Locus 76

Sequence ID	Eco_1
Location	3,425,441 – 3,425,800
Length	359
Max. P	0.999891

overview

Window 5

Location	3,425,441 – 3,425,561
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.25
Mean single sequence MFE	-38.72
Consensus MFE	-38.90
Energy contribution	-37.18
Covariance contribution	-1.72
Combinations/Pair	1.26
Mean z-score	-1.39
Structure conservation index	1.00
SVM decision value	1.64
SVM RNA-class probability	0.969299
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3425441 120 - 1
ACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGC
........((....(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....)))))...)) ( -39.50)
>Hin_1 201 120 - 1
ACACACGUGCUACAAUGGCGUAUACAGAGGGAAGCGAAGCUGCGAGGUGGAGCGAAUCUCAUAAAGUACGUCUAAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGC
....(((((((....((.......))((((...((...(((....)))...))...))))....))))))).....(((((..(((((((........))))))).....)))))..... ( -34.60)
>Sfl_1 201 120 - 1
ACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGC
........((....(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....)))))...)) ( -39.50)
>Sty_1 201 120 - 1
ACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGC
........((....(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....)))))...)) ( -39.50)
>Ype_1 201 120 - 1
ACACACGUGCUACAAUGGCAGAUACAAAGUGAAGCGAACUCGCGAGAGUCAGCGGACCACAUAAAGUCUGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGC
........((....(((((((((.....(((..((..((((....))))..))....))).....)))))))))..(((((..(((((((........))))))).....)))))...)) ( -40.50)
>consensus
ACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGC
........((....(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....)))))...)) (-38.90 = -37.18 +  -1.72)

alignment

secondary structure

dotplot

Window 6

Location	3,425,481 – 3,425,601
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.25
Mean single sequence MFE	-43.26
Consensus MFE	-43.84
Energy contribution	-42.12
Covariance contribution	-1.72
Combinations/Pair	1.24
Mean z-score	-2.22
Structure conservation index	1.01
SVM decision value	4.41
SVM RNA-class probability	0.999891
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3425481 120 - 1
GGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCG
..((((((.....)))))).(((((((.......)))))))....((..((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))..)) ( -44.20)
>Hin_1 241 120 - 1
GGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCGUAUACAGAGGGAAGCGAAGCUGCGAGGUGGAGCGAAUCUCAUAAAGUACGUCUAAGUCCG
((((((((.....)))))).(((((((.......)))))))...(((((((....((.......))((((...((...(((....)))...))...))))....)))))))......)). ( -37.80)
>Sfl_1 241 120 - 1
GGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCG
..((((((.....)))))).(((((((.......)))))))....((..((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))..)) ( -44.20)
>Sty_1 241 120 - 1
GGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCG
..((((((.....)))))).(((((((.......)))))))....((..((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))..)) ( -44.20)
>Ype_1 241 120 - 1
GGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCAGAUACAAAGUGAAGCGAACUCGCGAGAGUCAGCGGACCACAUAAAGUCUGUCGUAGUCCG
..((((((.....)))))).(((((((.......)))))))....((..((((...(((((((.....(((..((..((((....))))..))....))).....)))))))))))..)) ( -45.90)
>consensus
GGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCG
..((((((.....)))))).(((((((.......)))))))....((..((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))..)) (-43.84 = -42.12 +  -1.72)

alignment

secondary structure

dotplot

Window 7

Location	3,425,521 – 3,425,641
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.67
Mean single sequence MFE	-38.68
Consensus MFE	-37.56
Energy contribution	-37.08
Covariance contribution	-0.48
Combinations/Pair	1.16
Mean z-score	-2.08
Structure conservation index	0.97
SVM decision value	3.84
SVM RNA-class probability	0.999653
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3425521 120 - 1
AACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCU
..(((..((....)).(((((.....)))))......(((..((((((.....)))))).(((((((.......))))))))))..(((((.....))))).......)))......... ( -39.50)
>Hin_1 281 120 - 1
AACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCGUAUACAGAGGGAAGCGAAGC
..(((..((....)).(((((.....)))))......(((..((((((.....)))))).(((((((.......))))))))))..(((.(((......)))))).)))........... ( -36.50)
>Sfl_1 281 120 - 1
AACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCU
..(((..((....)).(((((.....)))))......(((..((((((.....)))))).(((((((.......))))))))))..(((((.....))))).......)))......... ( -39.50)
>Sty_1 281 120 - 1
AACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCU
..(((..((....)).(((((.....)))))......(((..((((((.....)))))).(((((((.......))))))))))..(((((.....))))).......)))......... ( -39.50)
>Ype_1 281 120 - 1
AACUCAAGGGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCAGAUACAAAGUGAAGCGAACU
..(((....))).((((((((.....)))(.((.(..(((..((((((.....)))))).(((((((.......))))))))))...).)).)...)))))................... ( -38.40)
>consensus
AACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCU
..(((..((....)).(((((.....)))))......(((..((((((.....)))))).(((((((.......))))))))))..(((((.....))))).......)))......... (-37.56 = -37.08 +  -0.48)

alignment

secondary structure

dotplot

Window 8

Location	3,425,561 – 3,425,680
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.47
Mean single sequence MFE	-43.82
Consensus MFE	-42.40
Energy contribution	-41.96
Covariance contribution	-0.44
Combinations/Pair	1.09
Mean z-score	-1.45
Structure conservation index	0.97
SVM decision value	1.73
SVM RNA-class probability	0.974219
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3425561 119 - 1
GCGCAACCCUUAUCCUUUGUUGCCAGCG-GUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCU
......(((...(((((((...((..((-(.....)))))....)))))))..((.(((((.....))))).)).....)))((((((.....))))))..((((((.......)))))) ( -43.90)
>Hin_1 321 119 - 1
GCGCAACCCUUAUCCUUUGUUGCCAGCG-ACUUGGUCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCU
......(((...(((((((...((..((-((...))))))....)))))))..((.(((((.....))))).)).....)))((((((.....))))))..((((((.......)))))) ( -43.60)
>Sfl_1 321 119 - 1
GCGCAACCCUUAUCCUUUGUUGCCAGCG-GUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCU
......(((...(((((((...((..((-(.....)))))....)))))))..((.(((((.....))))).)).....)))((((((.....))))))..((((((.......)))))) ( -43.90)
>Sty_1 321 119 - 1
GCGCAACCCUUAUCCUUUGUUGCCAGCG-AUUAGGUCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCU
......(((....((((((((.((.((.-.....)).)).)))....((....)).(((((.....)))))..))))).)))((((((.....))))))..((((((.......)))))) ( -41.70)
>Ype_1 321 120 - 1
GCGCAACCCUUAUCCUUUGUUGCCAGCACGUAAUGGUGGGAACUCAAGGGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCU
......(((....((((((((.(((.((.....)).))).)))....((....)).(((((.....)))))..))))).)))((((((.....))))))..((((((.......)))))) ( -46.00)
>consensus
GCGCAACCCUUAUCCUUUGUUGCCAGCG_GUCAGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCU
......(((....((((((((.((.((.......)).)).)))....((....)).(((((.....)))))..))))).)))((((((.....))))))..((((((.......)))))) (-42.40 = -41.96 +  -0.44)

alignment

secondary structure

dotplot

Window 9

Location	3,425,680 – 3,425,800
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.42
Mean single sequence MFE	-41.06
Consensus MFE	-41.98
Energy contribution	-39.90
Covariance contribution	-2.08
Combinations/Pair	1.32
Mean z-score	-1.34
Structure conservation index	1.02
SVM decision value	1.44
SVM RNA-class probability	0.954037
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3425680 120 - 1
UGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGA
.((.((((((...(((((..(((((((....)))))))...((....))..))))).((((..(((.(((((((((....)))).))))).)))...))))..)))))).))........ ( -42.40)
>Hin_1 440 120 - 1
UACUCUUGACAUCCUAAGAAGAGCUCAGAGAUGAGCUUGUGCCUUCGGGAACUUAGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGA
...(((((......))))).(((((((....)))))))((.....(((((.(((((.((((..(((.(((((((((....)))).))))).)))...))))...))))))))))..)).. ( -40.30)
>Sfl_1 440 120 - 1
UGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGA
.((.((((((...(((((..(((((((....)))))))...((....))..))))).((((..(((.(((((((((....)))).))))).)))...))))..)))))).))........ ( -42.40)
>Sty_1 440 120 - 1
UGGUCUUGACAUCCACAGAACUUUCCAGAGAUGGAUUGGUGCCUUCGGGAACUGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGA
.((.((((((...(((((.(((.((((....))))..))).((....))..))))).((((..(((.(((((((((....)))).))))).)))...))))..)))))).))........ ( -41.60)
>Ype_1 441 120 - 1
UACUCUUGACAUCCACAGAAUUUGGCAGAGAUGCUAAAGUGCCUUCGGGAACUGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGA
....((((((...(((((..(((((((....)))))))...((....))..))))).((((..(((.(((((((((....)))).))))).)))...))))..))))))........... ( -38.60)
>consensus
UGGUCUUGACAUCCACAGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACUGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGA
.((.((((((...(((((..(((((((....)))))))...((....))..))))).((((..(((.(((((((((....)))).))))).)))...))))..)))))).))........ (-41.98 = -39.90 +  -2.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:05:19 2006