Locus 71

Sequence ID	Eco_1
Location	3,422,373 – 3,422,585
Length	212
Max. P	0.998469

overview

Window 4

Location	3,422,373 – 3,422,493
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.22
Mean single sequence MFE	-42.92
Consensus MFE	-42.19
Energy contribution	-40.75
Covariance contribution	-1.44
Combinations/Pair	1.15
Mean z-score	-2.60
Structure conservation index	0.98
SVM decision value	2.77
SVM RNA-class probability	0.996926
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3422373 120 - 1
AGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAA
.(((((((.((((....)))).)))).((((((((((..((((....))))..))...(((....)))))))).)))..)))(((((((((.......)))))))))............. ( -46.60)
>Hin_1 361 120 - 1
GUGAGGUUAGUGCAAUGGUAUAAGCAAGCUUAACUGCGAGACAGACAAGUCGAGCAGGUACGAAAGUAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAA
((...(((.((((....)))).)))..))....((((..(((......)))..)))).(((....))).(((....(((..((((((((((.......)))))))))).)))...))).. ( -37.20)
>Sty_1 361 120 - 1
AGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAA
.(((((((.((((....)))).)))).((((((((((..((((....))))..))...(((....)))))))).)))..)))(((((((((.......)))))))))............. ( -46.60)
>Ype_1 361 120 - 1
GUGAGGUUAGUGCAAAGGCAUAAGCUAGCUUGACUGCGAGAGUGACGGCUCGAGCAGGUACGAAAGUAGGUCUUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAA
((..((((.((((....)))).)))).))....((((..((((....))))..)))).(((....))).((((...(((..((((((((((.......)))))))))).)))..)))).. ( -41.30)
>consensus
AGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGAGUGACGGCGCGAGCAGGUACGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAA
....((((.((((....)))).)))).......((((..(((......)))..)))).(((....))).(((....(((..((((((((((.......)))))))))).)))...))).. (-42.19 = -40.75 +  -1.44)

alignment

secondary structure

dotplot

Window 5

Location	3,422,413 – 3,422,533
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.42
Mean single sequence MFE	-42.12
Consensus MFE	-44.39
Energy contribution	-41.20
Covariance contribution	-3.19
Combinations/Pair	1.24
Mean z-score	-2.49
Structure conservation index	1.05
SVM decision value	3.11
SVM RNA-class probability	0.998469
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3422413 120 - 1
ACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAU
.........(((..(((((((((..(((((((.....))))))).....((((....)))).)))))))))((((((..((((....))))..))...(((....)))))))...))).. ( -45.80)
>Hin_1 401 120 - 1
ACGGAGGAGCACGAAGGUUUGCUAAUCACGGUCGGACAUCGUGAGGUUAGUGCAAUGGUAUAAGCAAGCUUAACUGCGAGACAGACAAGUCGAGCAGGUACGAAAGUAGGUCAUAGUGAU
.........(((..(((((((((..(((((((.....))))))).....((((....)))).)))))))))..((((..(((......)))..)))).(((....))).......))).. ( -35.90)
>Sty_1 401 120 - 1
ACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAU
.........(((..(((((((((..(((((((.....))))))).....((((....)))).)))))))))((((((..((((....))))..))...(((....)))))))...))).. ( -45.80)
>Ype_1 401 120 - 1
ACGGAGGAGCACGAAGGUUAGCUAAUCACGGUCGGACAUCGUGAGGUUAGUGCAAAGGCAUAAGCUAGCUUGACUGCGAGAGUGACGGCUCGAGCAGGUACGAAAGUAGGUCUUAGUGAU
((..((((.(....(((((((((..(((((((.....))))))).....((((....)))).)))))))))..((((..((((....))))..)))).(((....)))).)))).))... ( -41.00)
>consensus
ACGGAGGAGCACGAAGGUUGGCUAAUCACGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGAGUGACGGCGCGAGCAGGUACGAAAGCAGGUCAUAGUGAU
.........(((..(((((((((..(((((((.....))))))).....((((....)))).)))))))))..((((..(((......)))..)))).(((....))).......))).. (-44.39 = -41.20 +  -3.19)

alignment

secondary structure

dotplot

Window 6

Location	3,422,453 – 3,422,573
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.17
Mean single sequence MFE	-42.50
Consensus MFE	-43.65
Energy contribution	-41.65
Covariance contribution	-2.00
Combinations/Pair	1.17
Mean z-score	-1.62
Structure conservation index	1.03
SVM decision value	0.99
SVM RNA-class probability	0.896051
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3422453 120 - 1
GGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAG
.(..(...(((((((..(((((..(((((((...........)))))))..))..((....))..)))..))))))).(((((.((((.((((....)))).))))..))))))..)... ( -45.70)
>Hin_1 441 120 - 1
GGUGGGUAGUUUGACUGGGGCGGUCUCCUCCCAAAGCGUAACGGAGGAGCACGAAGGUUUGCUAAUCACGGUCGGACAUCGUGAGGUUAGUGCAAUGGUAUAAGCAAGCUUAACUGCGAG
.....((((((.........((..(((((((...........)))))))..)).(((((((((..(((((((.....))))))).....((((....)))).)))))))))))))))... ( -37.90)
>Sty_1 441 120 - 1
GGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAG
.(..(...(((((((..(((((..(((((((...........)))))))..))..((....))..)))..))))))).(((((.((((.((((....)))).))))..))))))..)... ( -45.70)
>Ype_1 441 120 - 1
GGUGGGUAGUUUGACUGGGGCGGUCUCCUCCCAAAGAGUAACGGAGGAGCACGAAGGUUAGCUAAUCACGGUCGGACAUCGUGAGGUUAGUGCAAAGGCAUAAGCUAGCUUGACUGCGAG
.....((((((.........((..(((((((...........)))))))..)).(((((((((..(((((((.....))))))).....((((....)))).)))))))))))))))... ( -40.70)
>consensus
GGUGGGUAGUUUGACUGGGGCGGUCUCCUCCCAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCACGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAG
.....((((((.........((..(((((((...........)))))))..)).(((((((((..(((((((.....))))))).....((((....)))).)))))))))))))))... (-43.65 = -41.65 +  -2.00)

alignment

secondary structure

dotplot

Window 7

Location	3,422,465 – 3,422,585
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.17
Mean single sequence MFE	-41.52
Consensus MFE	-37.39
Energy contribution	-37.83
Covariance contribution	0.44
Combinations/Pair	1.08
Mean z-score	-1.40
Structure conservation index	0.90
SVM decision value	-0.02
SVM RNA-class probability	0.523606
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3422465 120 - 1
CGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAG
(((((...)))))...(((.(((((((..(((((..(((((((...........)))))))..))..((....))..)))..))))))))))....((((.((((....)))).)))).. ( -43.60)
>Hin_1 453 120 - 1
CGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCCAAAGCGUAACGGAGGAGCACGAAGGUUUGCUAAUCACGGUCGGACAUCGUGAGGUUAGUGCAAUGGUAUAAGCAAG
(..((.((((((((((..((((..((((....((..(((((((...........)))))))..))..)))).))))..)))...))))))).))..)(((.((((....)))).)))... ( -37.90)
>Sty_1 453 120 - 1
CGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAG
(((((...)))))...(((.(((((((..(((((..(((((((...........)))))))..))..((....))..)))..))))))))))....((((.((((....)))).)))).. ( -43.60)
>Ype_1 453 120 - 1
AGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCCAAAGAGUAACGGAGGAGCACGAAGGUUAGCUAAUCACGGUCGGACAUCGUGAGGUUAGUGCAAAGGCAUAAGCUAG
...((.((((((((((..(((((.((((....((..(((((((...........)))))))..))..)))))))))..)))...))))))).))..((((.((((....)))).)))).. ( -41.00)
>consensus
CGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCCAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCACGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAG
(((((...)))))...(((.((((((((((((((..(((((((...........)))))))..))..((....))..)))))))))))))))....((((.((((....)))).)))).. (-37.39 = -37.83 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:05:08 2006